Barley embryo CAGE, ChIP-seq/Mnase and TSS cluster.

ChiP-seq and CAGE data for three stages of developing barley embryos: 8 days post pollination, 24 days post pollination and 4 days post germination. Most ChIP-seq samples were MNase treated, see below. A promoter list published as supplemental material to the corresponding publication is also included.

• Raw data was downloaded from SRA: SRP427030
• Input file format: FASTQ
• Download date: 14-8-2025

From H. vulgare (Apr 2021 MorexV3).

Genome Annotation:

	Filename	Description	Feature	GEO-ID
1	pavlu23tcs.sga	Barley primary promoter clusters	TSS	-

Transcription Profiling data:

	Filename	Description	Feature	GEO-ID
1	4DAG_CAGE_A.sga	embryo|CAGE|4DAG|A	CAGE	GSM7093279
2	4DAG_CAGE_B.sga	embryo|CAGE|4DAG|B	CAGE	GSM7093280
3	24DAP_CAGE_A.sga	embryo|CAGE|24DAP|A	CAGE	GSM7093281
4	24DAP_CAGE_B.sga	embryo|CAGE|24DAP|B	CAGE	GSM7093282
5	8DAP_CAGE_A.sga	embryo|CAGE|8DAP|A	CAGE	GSM7093283
6	8DAP_CAGE_B.sga	embryo|CAGE|8DAP|B	CAGE	GSM7093284

ChIP-seq data:

	Filename	Description	Feature	GEO-ID
1	all_H3K4me3_merged_c.sga	embryo|H3K4me3|all|merged	H3K4me3	-
2	all_H3K9ac_merged_c.sga	embryo|H3K9ac|all|merged	H3K9ac	-
3	all_H3K27me3_merged_c.sga	embryo|H3K27me3|all|merged	H3K27me3	-
4	all_Input_merged_c.sga	embryo|Input|all|merged	Input	-
5	all_mnase_merged_c.sga	embryo|MNase|all|merged	MNase	-
6	4DAG_H3K4me3_merged_c.sga	embryo|H3K4me3|4DAG|merged	H3K4me3	-
7	4DAG_H3K9ac_merged_c.sga	embryo|H3K9ac|4DAG|merged	H3K9ac	-
8	4DAG_H3K27me3_merged_c.sga	embryo|H3K27me3|4DAG|merged	H3K27me3	-
9	4DAG_Input_merged_c.sga	embryo|Input|4DAG|merged	Input	-
10	24DAP_H3K4me3_merged_c.sga	embryo|H3K4me3|24DAP|merged	H3K4me3	-
11	24DAP_H3K27me3_merged_c.sga	embryo|H3K27me3|24DAP|merged	H3K27me3	-
12	24DAP_Input_merged_c.sga	embryo|Input|24DAP|merged	Input	-
13	8DAP_H3K4me3_merged_c.sga	embryo|H3K4me3|8DAP|merged	H3K4me3	-
14	8DAP_H3K9ac_merged_c.sga	embryo|H3K9ac|8DAP|merged	H3K9ac	-
15	8DAP_H3K27me3_merged_c.sga	embryo|H3K27me3|8DAP|merged	H3K27me3	-
16	8DAP_Input_merged_c.sga	embryo|Input|8DAP|merged	Input	-
17	4DAG_H3K4me3_rep1.sga	embryo|H3K4me3|4DAG|rep1	H3K4me3	GSM7093304
18	4DAG_H3K4me3_rep2.sga	embryo|H3K4me3|4DAG|rep2	H3K4me3	GSM7093305
19	4DAG_H3K9ac_rep1.sga	embryo|H3K9ac|4DAG|rep1	H3K9ac	GSM7093306
20	4DAG_H3K9ac_rep2.sga	embryo|H3K9ac|4DAG|rep2	H3K9ac	GSM7093307
21	4DAG_H3K27me3_rep1.sga	embryo|H3K27me3|4DAG|rep1	H3K27me3	GSM7093308
22	4DAG_H3K27me3_rep2.sga	embryo|H3K27me3|4DAG|rep2	H3K27me3	GSM7093309
23	4DAG_Input_rep1.sga	embryo|Input|4DAG|rep1	Input	GSM7093310
24	4DAG_Input_rep2.sga	embryo|Input|4DAG|rep2	Input	GSM7093311
25	4DAG_Input_K9ac.sga	embryo|Input|4DAG|K9ac	Input	GSM7093312
26	24DAP_H3K4me3_rep1.sga	embryo|H3K4me3|24DAP|rep1	H3K4me3	GSM7093313
27	24DAP_H3K4me3_rep2.sga	embryo|H3K4me3|24DAP|rep2	H3K4me3	GSM7093314
28	24DAP_H3K9ac_rep1A.sga	embryo|H3K9ac|24DAP|rep1A	H3K9ac	GSM7093315
29	24DAP_H3K9ac_rep2A.sga	embryo|H3K9ac|24DAP|rep2A	H3K9ac	GSM7093316
30	24DAP_H3K27me3_rep1.sga	embryo|H3K27me3|24DAP|rep1	H3K27me3	GSM7093317
31	24DAP_H3K27me3_rep2.sga	embryo|H3K27me3|24DAP|rep2	H3K27me3	GSM7093318
32	24DAP_Input_rep1.sga	embryo|Input|24DAP|rep1	Input	GSM7093319
33	24DAP_Input_rep2.sga	embryo|Input|24DAP|rep2	Input	GSM7093320
34	24DAP_Input_rep1A.sga	embryo|Input|24DAP|rep1A	Input	GSM7093321
35	24DAP_Input_rep2A.sga	embryo|Input|24DAP|rep2A	Input	GSM7093322
36	8DAP_H3K4me3_rep1.sga	embryo|H3K4me3|8DAP|rep1	H3K4me3	GSM7093323
37	8DAP_H3K4me3_rep2.sga	embryo|H3K4me3|8DAP|rep2	H3K4me3	GSM7093324
38	8DAP_H3K9ac_rep1.sga	embryo|H3K9ac|8DAP|rep1	H3K9ac	GSM7093325
39	8DAP_H3K9ac_rep2.sga	embryo|H3K9ac|8DAP|rep2	H3K9ac	GSM7093326
40	8DAP_H3K27me3_rep1.sga	embryo|H3K27me3|8DAP|rep1	H3K27me3	GSM7093327
41	8DAP_H3K27me3_rep2.sga	embryo|H3K27me3|8DAP|rep2	H3K27me3	GSM7093328
42	8DAP_Input_rep1.sga	embryo|Input|8DAP|rep1	Input	GSM7093329
43	8DAP_Input_rep2.sga	embryo|Input|8DAP|rep2	Input	GSM7093330
44	8DAP_Input_rep1A.sga	embryo|Input|8DAP|rep1A	Input	GSM7093331

Notes on samples nomenclature:

All ChIP-seq samples inlcuding inputs were MNase treated except the following:

      4DAG_Input_K9ac.sga     embryo|Input|4DAG|K9ac
      24DAP_H3K9ac_rep1A.sga  embryo|H3K9ac|24DAP|rep1A
      24DAP_H3K9ac_rep2A.sga  embryo|H3K9ac|24DAP|rep2A
      24DAP_Input_rep1A.sga   embryo|Input|24DAP|rep1A
      24DAP_Input_rep2A.sga   embryo|Input|24DAP|rep2A
      8DAP_Input_rep1A.sga    embryo|Input|8DAP|rep1A

Those were cross-linked and sonicated.

Merged samples:

Merged samples were merged from all corresponding MNase-treated ChIP-seq samples (sonicated samples excluded).

The promoter/TCs list (file pavlu23tcs.sga) is based on Supplementary Data file S1 from Pavlu et al. 2023. All TCs were included, which were annotated as "Promoter" (table field 8) and type "primary" (field 14). The summit (field 7) was transferred to the position field of the SGA file.

CAGE and ChIP-seq data processing: FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit v2.10.8) and mapped to the genome using Bowtie2 v1.2.2. SAM output was then processed to SGA files with customezed perl scripts.

• Pavlu S, Nikumbh S, Kovacik M, An T, Lenhard B, Simkova H, Navratilova P.
  Core promoterome of barley embryo. Comput Struct Biotechnol J. 2023 Dec 5;23:264-277. doi: 10.1016/j.csbj.2023.12.003. 38173877
• GEO series GSE227219 Core promoterome of barley embryo

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