Tsankov 2015, TF binding dynamics during human ES cell differentiation.

Description

This serie is part of the RoadMap consortium. It contains data for the HUES64 cell line (an embryonic stem cell) as it go through differentiation in mesoendoderm, mesoderm, endoderm and ectoderm. Several transcription factors and histone marks were analyzed at each stage of differentiation.

Source

• Raw data was downloaded from: NCBI SRA database
• Input file format: SRA

Samples

From H. sapiens (Feb 2009 GRCh37/hg19).

ChIP-seq data:

Notes on samples nomenclature

Cell lines used:

• dMS: HUES64 cell line grown in medium to differentiate towards mesendoderm
• dEN: HUES64 cell line grown in medium to differentiate towards endoderm
• dME: HUES64 cell line grown in medium to differentiate towards mesoderm
• dEC: HUES64 cell line grown in medium to differentiate towards ectoderm

Merge samples

None.

Technical Notes

FASTQ files were extracted from SRA files using fastq-dump (SRA toolkit) with --split-3 option for paired-end reads and mapped to the genome using Bowtie. SAM files were then converted into bam using samtools and to bed using bamToBed (bedtools). SGA conversion was carried out using bed2sga (ChIP-seq).
Inportant note: according to the publication, all the samples should have been paired-end but fastq-dump did not always output the 2 files expected (one with the 5' end reads and the other with the 3' end) for all samples. Instead in some cases it only output one file and in others 3. In the first case the samples were treated as single-end, whereas in the second the samples were splitted in single-end and paired-end.

References

• Tsankov AM, Gu H, Akopian V, Ziller MJ, Donaghey J, Amit I, Gnirke A, Meissner A
  Transcription factor binding dynamics during human ES cell differentiation. Nature. 2015 Feb 19;518(7539):344-9. doi: 10.1038/nature14233. 25693565

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