Kitazawa 2021, ChIP-seq and ATAC-seq in developing sensory neurons.

Description

Mouse embryonic stem cells (ECSs) and developing sensory neurons of the barrelette system at various developmental stages were analyzed with ChIP-seq and ATAC-seq assays. ChIP-seq targets include: Experiments were carried out in different genotypes and under different conditions in order to gain mechanistic insights chromatin state regulation. Sequential ChIP was used to analyze the co-occurrence of H3K27me3 and H3K27ac.

Source

Samples

From M. musculus (July 2007 NCBI37/mm9).

ChIP-seq data:

Filename Description Feature GEO-ID
1 E14_vPrV_H3K27Me3_1.sga E14.5|H3K27me3|vPrV|mix34 H3K27me3 ERS3739687
2 E14_vPrV_H3K27Me3_2.sga E14.5|H3K27me3|vPrV|mix35 H3K27me3 ERS3739688
3 E10_K20TMT_H3K27Ac_1.sga E10.5|H3K27ac|K20TMT|mix19 H3K27ac ERS3739647
4 E10_K20TMT_H3K27Ac_2.sga E10.5|H3K27ac|K20TMT|mix20 H3K27ac ERS3739648
5 E10_K20TMT_H3K27Me3_1.sga E10.5|H3K27me3|K20TMT|mix40 H3K27me3 ERS3739649
6 E10_K20TMT_H3K27Me3_2.sga E10.5|H3K27me3|K20TMT|mix41 H3K27me3 ERS3739650
7 E10_K20TMT_H3K4Me2_1.sga E10.5|H3K4me2|K20TMT|mix28 H3K4me2 ERS3739651
8 E10_K20TMT_H3K4Me2_2.sga E10.5|H3K4me2|K20TMT|mix29 H3K4me2 ERS3739652
9 E12_1day_H3K27me3.sga E12.5 1d|H3K27me3|wt|mix51 H3K27me3 ERS3739653
10 E12_7day_H3K27me3.sga E12.5 7d|H3K27me3|wt|mix52 H3K27me3 ERS3739654
11 E12BS_ctrl_K27Ac.sga E12.5 BS|H3K27ac|wt|mix77 H3K27ac ERS4775388
12 E12BS_ctrl_K27Me3_1.sga E12.5 BS|H3K27me3|wt ctrl|mix79 H3K27me3 ERS4775389
13 E12BS_ctrl_K27Me3_2.sga E12.5 BS|H3K27me3|wt ctrl|mix80 H3K27me3 ERS4775390
14 E12_dCas9-Fos_H3K27Me3_1.sga E12.5|H3K27me3|dCas9-Fos|mix53 H3K27me3 ERS3739655
15 E12_dCas9-Fos_H3K27Me3_2.sga E12.5|H3K27me3|dCas9-Fos|mix54 H3K27me3 ERS3739656
16 E12_dCas9-Fos_H3K27Me3_3.sga E12.5|H3K27me3|dCas9-Fos|mix55 H3K27me3 ERS3739657
17 E12_dCas9Utx-Fos_H3K27Me3_1.sga E12.5|H3K27me3|dCas9Utx-Fos|mix56 H3K27me3 ERS3739658
18 E12_dCas9Utx-Fos_H3K27Me3_2.sga E12.5|H3K27me3|dCas9Utx-Fos|mix57 H3K27me3 ERS3739659
19 E12_dCas9Utx-Fos_H3K27Me3_3.sga E12.5|H3K27me3|dCas9Utx-Fos|mix58 H3K27me3 ERS3739660
20 E12BS_TSA_K27Ac.sga E12.5 BS|H3K27ac|wt +TSA|mix78 H3K27ac ERS4775391
21 E12BS_TSA_K27Me3_1.sga E12.5 BS|H3K27me3|wt +TSA|mix81 H3K27me3 ERS4775392
22 E12BS_TSA_K27Me3_2.sga E12.5 BS|H3K27me3|wt +TSA|mix82 H3K27me3 ERS4775393
23 E14_H3K27Ac-2K.sga E14.5|H3K27ac 2k|wt|mix45 H3K27ac ERS3739663
24 E14_H3K27Me3-2K.sga E14.5|H3K27me3 2k|wt|mix46 H3K27me3 ERS3739664
25 E14_H3K27Me3AcDouble_1.sga E14.5|H3K27me3ac 2k|wt|mix47 H3K27me3ac ERS3739665
26 E14_H3K27Me3AcDouble_2.sga E14.5|H3K27me3ac 2k|wt|mix48 H3K27me3ac ERS3739666
27 E14_H3K36Me3.sga E14.5|H3K36me3|wt|mix7 H3K36me3 ERS3739667
28 E14_pCreb.sga E14.5|pCreb|wt|mix6 pCreb ERS3739678
29 E14_Pol2_S2P.sga E14.5|PolII-S2P|wt|mix4 PolII-S2P ERS3739680
30 E14_Pol2_S5P.sga E14.5|PolII-S5P|wt|mix2 PolII-S5P ERS3739681
31 E14_Pol2_S7P.sga E14.5|PolII-S7P|wt|mix3 PolII-S7P ERS3739682
32 E14_PrVPreFix_H3K27Ac.sga E14.5 prefix|H3K27ac|wt|mix21 H3K27ac ERS3739683
33 E14_PrVPreFix_H3K27Me3.sga E14.5 prefix|H3K27me3|wt|mix42 H3K27me3 ERS3739684
34 E14_vPrV_H3K27Ac_1.sga E14.5|H3K27ac|vPrV|mix13 H3K27ac ERS3739685
35 E14_vPrV_H3K27Ac_2.sga E14.5|H3K27ac|vPrV|mix14 H3K27ac ERS3739686
36 E14_vPrV_H3K4Me2_1.sga E14.5|H3K4me2|vPrV|mix26 H3K4me2 ERS3739689
37 E14_vPrV_H3K4Me2_2.sga E14.5|H3K4me2|vPrV|mix27 H3K4me2 ERS3739690
38 E18_pCreb.sga E18.5|pCreb|wt|mix83 pCreb ERS5516335
39 E18_BS_Pol2-S2P.sga E18.5 BS|PolII-S2P|wt|mix62 PolII-S2P ERS4775396
40 E18_BS_Pol2-S7P.sga E18.5 BS|PolII-S7P|wt|mix60 PolII-S7P ERS4775397
41 E18_vPrV_H3K27Ac_1.sga E18.5|H3K27ac|vPrV|mix11 H3K27ac ERS3739691
42 E18_vPrV_H3K27Ac_2.sga E18.5|H3K27ac|vPrV|mix12 H3K27ac ERS3739692
43 E18_vPrV_H3K27Me3_1.sga E18.5|H3K27me3|vPrV|mix32 H3K27me3 ERS3739693
44 E18_vPrV_H3K27Me3_2.sga E18.5|H3K27me3|vPrV|mix33 H3K27me3 ERS3739694
45 E18_vPrV_H3K4Me2_1.sga E18.5|H3K4me2|vPrV|mix24 H3K4me2 ERS3739695
46 E18_vPrV_H3K4Me2_2.sga E18.5|H3K4me2|vPrV|mix25 H3K4me2 ERS3739696
47 ESC-EedKO_S2P.sga ESC|PolII-S2P|EedKO|mix70 PolII-S2P ERS4775398
48 ESC_EedKO_S2P_3.sga ESC|PolII-S2P|EedKO|mix72 PolII-S2P ERS4775403
49 ESC_WT_K27ac.sga ESC|H3K27ac|wt|mix74 H3K27ac ERS4775404
50 ESC_WT_K27ac_2.sga ESC|H3K27ac|wt|mix76 H3K27ac ERS4775405
51 ESC_WT_K27me3_ab3.sga ESC|H3K27me3|wt|mix75 H3K27me3 ERS4775406
52 ESC-WT_S2P.sga ESC|PolII-S2P|wt|mix69 PolII-S2P ERS4775401
53 ESC_WT_S2P_3.sga ESC|PolII-S2P|wt|mix71 PolII-S2P ERS4775407
54 ESC-EedKO_S5P.sga ESC|PolII-S5P|EedKO|mix68 PolII-S5P ERS4775399
55 ESC-WT_K4me2.sga ESC|H3K4me2|wt|mix73 H3K4me2 ERS4775400
56 ESC-WT_S5P.sga ESC|PolII-S5P|wt|mix67 PolII-S5P ERS4775402
57 P4_BS_K36me3_2.sga P4 BS|H3K36me3|wt|mix65 H3K36me3 ERS4775408
58 P4_BS_K36me3_3.sga P4 BS|H3K36me3|wt|mix66 H3K36me3 ERS4775409
59 P4_H3K36Me3.sga P4|H3K36me3|wt|mix8 H3K36me3 ERS3739697
60 P4_pCreb.sga P4|pCreb|wt|mix5 pCreb ERS3739698
61 P4_BS_Pol2-S2P.sga P4 BS|PolII-S2P|wt|mix61 PolII-S2P ERS4775410
62 P4_BS_Pol2-S7P.sga P4 BS|PolII-S7P|wt|mix59 PolII-S7P ERS4775411
63 P4_vPrV_H3K27Ac_1.sga P4|H3K27ac|vPrV|mix9 H3K27ac ERS3739699
64 P4_vPrV_H3K27Ac_2.sga P4|H3K27ac|vPrV|mix10 H3K27ac ERS3739700
65 P4_vPrV_H3K27Me3_1.sga P4|H3K27me3|vPrV|mix30 H3K27me3 ERS3739701
66 P4_vPrV_H3K27Me3_2.sga P4|H3K27me3|vPrV|mix31 H3K27me3 ERS3739702
67 P4_vPrV_H3K4Me2_1.sga P4|H3K4me2|vPrV|mix22 H3K4me2 ERS3739703
68 P4_vPrV_H3K4Me2_2.sga P4|H3K4me2|vPrV|mix23 H3K4me2 ERS3739704
69 E14_a2CreEzh2homo_H3K36me3.sga E14.5|H3K36me3|a2Ezh2KO|mix50 H3K36me3 ERS3739661
70 E14_a2CreEzh2wt_H3K36me3.sga E14.5|H3K36me3|a2Ezh2wt|mix49 H3K36me3 ERS3739662
71 E14_BS_Cdk9.sga E14.5 BS|Cdk9|wt|mix63 Cdk9 ERS4775394
72 E14_BS_Ring1b.sga E14.5 BS|Ring1b|wt|mix64 Ring1b ERS4775395
73 E14_K20Ezh2KO_H3K27Ac_1.sga E14.5|H3K27ac|K20Ezh2KO|mix17 H3K27ac ERS3739668
74 E14_K20Ezh2KO_H3K27Ac_2.sga E14.5|H3K27ac|K20Ezh2KO|mix18 H3K27ac ERS3739669
75 E14_K20Ezh2KO_H3K27Me3_1.sga E14.5|H3K27me3|K20Ezh2KO|mix38 H3K27me3 ERS3739670
76 E14_K20Ezh2KO_H3K27Me3_2.sga E14.5|H3K27me3|K20Ezh2KO|mix39 H3K27me3 ERS3739671
77 E14_K20TMT_H3.3_1.sga E14.5|H3.3|K20TMT|mix43 H3.3 ERS3739672
78 E14_K20TMT_H3.3_2.sga E14.5|H3.3|K20TMT|mix44 H3.3 ERS3739673
79 E14_K20TMT_H3K27Ac_1.sga E14.5|H3K27ac|K20TMT|mix15 H3K27ac ERS3739674
80 E14_K20TMT_H3K27Ac_2.sga E14.5|H3K27ac|K20TMT|mix16 H3K27ac ERS3739675
81 E14_K20TMT_H3K27Me3_1.sga E14.5|H3K27me3|K20TMT|mix36 H3K27me3 ERS3739676
82 E14_K20TMT_H3K27Me3_2.sga E14.5|H3K27me3|K20TMT|mix37 H3K27me3 ERS3739677
83 E14_Pol2_8WG16.sga E14.5|PolII-8WG16|wt|mix1 PolII-8WG16 ERS3739679
84 E18_Jmjd3KO_K27Me3_1.sga E18.5|H3K27me3|Jmjd3KO|mix86 H3K27me3 ERS5516331
85 E18_Jmjd3KO_K27Me3_2.sga E18.5|H3K27me3|Jmjd3KO|mix87 H3K27me3 ERS5516332
86 E18_Jmjd3wt_K27Me3_1.sga E18.5|H3K27me3|Jmjd3wt|mix84 H3K27me3 ERS5516333
87 E18_Jmjd3wt_K27Me3_2.sga E18.5|H3K27me3|Jmjd3wt|mix85 H3K27me3 ERS5516334
88 ESC_EedKO_NELFB_1.sga ESC|Nelfb|EedKO|mix89 Nelfb ERS5516336
89 ESC_EedKO_NELFB_2.sga ESC|Nelfb|EedKO|mix91 Nelfb ERS5516337
90 ESC_WT_NELFB_1.sga ESC|Nelfb|wt|mix88 Nelfb ERS5516338
91 ESC_WT_NELFB_2.sga ESC|Nelfb|wt|mix90 Nelfb ERS5516339

DNase FAIRE data:

Filename Description Feature GEO-ID
1 E10_K20TMT_ATAC_1.sga E10.5|ATAC-seq|K20TMT|mix7 ATACseq ERS3739546
2 E10_K20TMT_ATAC_2.sga E10.5|ATAC-seq|K20TMT|mix8 ATACseq ERS3739547
3 E12Drg11_KCl0h_ATAC_1.sga E12.5|ATAC-seq|Drg11 KCl0h|mix15 ATACseq ERS5516323
4 E12Drg11_KCl1h_ATAC_1.sga E12.5|ATAC-seq|Drg11 KCl1h|mix16 ATACseq ERS5516324
5 E14_a2CreEzh2hetero_ATAC_1.sga E14.5|ATAC-seq|a2CreEzh2het|mix9 ATACseq ERS5516325
6 E14_a2CreEzh2hetero_ATAC_2.sga E14.5|ATAC-seq|a2CreEzh2het|mix10 ATACseq ERS5516326
7 E14_a2CreEzh2hetero_ATAC_3.sga E14.5|ATAC-seq|a2CreEzh2het|mix11 ATACseq ERS5516327
8 E14_a2CreEzh2hetero_ATAC_4.sga E14.5|ATAC-seq|a2CreEzh2het|mix12 ATACseq ERS5516328
9 E14_a2CreEzh2homo_ATAC_1.sga E14.5|ATAC-seq|a2CreEzh2hom|mix13 ATACseq ERS5516329
10 E14_a2CreEzh2homo_ATAC_2.sga E14.5|ATAC-seq|a2CreEzh2hom|mix14 ATACseq ERS5516330
11 E14_vPrV_ATAC_1.sga E14.5|ATAC-seq|vPrV|mix5 ATACseq ERS3739548
12 E14_vPrV_ATAC_2.sga E14.5|ATAC-seq|vPrV|mix6 ATACseq ERS3739549
13 E18_vPrV_ATAC_1.sga E18.5|ATAC-seq|vPrV|mix3 ATACseq ERS3739550
14 E18_vPrV_ATAC_2.sga E18.5|ATAC-seq|vPrV|mix4 ATACseq ERS3739551
15 P4_vPrV_ATAC_1.sga P4|ATAC-seq|vPrV|mix1 ATACseq ERS3739552
16 P4_vPrV_ATAC_2.sga P4|ATAC-seq|vPrV|mix2 ATACseq ERS3739553

Notes on samples nomenclature: 
    Cell type, developmental stages, preparation:

      E10.5        mitotic progenitors
      E12.5        short-term cultured hindbrain neurons
      E12.5        day1 culterd hindbrain neurons at day 1
      E12.5        day7 culterd hindbrain neurons at day 7
      E14.5        early postmitotic
      E18.5        perinatal
      P4           neonate, consolidated barrelette stage
      prefix       prefixed tissue

    Genotypes and conditions:

      vPrV         Drg11::Cre;Rosa::ZsGreen;r2::mCherry
      K20TMT       Krox20::Cre;ROSA::tdTomato
      EedKO        EedKO
      a2Ezh2KO     Hoxa2::Cre;Ezh2fl/fl;Rosa::RFP
      a2Ezh2wt     Hoxa2::Cre;Rosa::tdTomato
      K20Ezh2KO    Krox20::Cre;Ezh2fl/fl;Rosa::RFP
      Jmjd3KO      Jmjd3KO
      Jmjd3wt      Jmjd3wt
      Drg11        Drg11::Cre;Rosa::tdTomato
      a2CreEzh2het Hoxa2::Cre;Ezh2fl/+;Rosa::RFP
      a2CreEzh2hom Hoxa2::Cre;Ezh2fl/fl;Rosa::RFP
      dCas9-Fos    overespression of control dCas9 targeted to Fos 
      dCas9Utx-Fos overespression of dCas9-UTX target to Fos 
                   for selective demethylation of H3K27me3
      +TSA         overnight trichostatin A (TSA) treatment 

    Replicates:
 
      mix1-mix89   Mix numbers copied from ArrayExpress metadata serve to
                   distinguish otherwise identical experiments.

Technical Notes

FASTQ files were downloaded from ENA (see above Paragraph Source) and mapped to the genome using Bowtie v1.2.2. SAM files were then converted to BAM using samtools v1.9 and to BED using bamToBed v2.27.0 (bedtools). BED to SGA conversion was carried out using bed2sga (ChIP-Seq v. 1.5.5).

Note that ChIP-seq and ATAC-seq data are provided as single-end or paired-end reads, respectively, and were mapped to the genome with bowtie accordingly.

References

Last update: 22 Dec 2021
Page made by: Philipp Bucher