Information about how to download and map on mm9 each sequencing experiment used in the SeqCode standalone manual can be found here:

• ChIPseq of H3K4me3 (mESCs).
• ChIPseq of H3K36me3 (mESCs).
• ChIPseq of Input (mESCs).
• RNAseq (mESC).

Basic information:

• Reference:
  Erk1/2 Activity Promotes Chromatin Features and RNAPII Phosphorylation at Developmental Promoters in Mouse ESCs.
  Tee WW, Shen SS, Oksuz O, Narendra V, Reinberg D. Cell 156: 678-690 (2014).
  
  
• PUBMED ID link:
  24529373
  
  
• Experiment in GEO/SRA:
  WT_H3K4me3 [SRX367147]
  SRR1015741.sra

Converting SRA format into FASTQ format:

> fastq-dump -v -O raw_data raw_data/SRR1015741.sra

Read 37610875 spots for raw_data/SRR1015741.sra

Mapping the ChIPseq sample into a SAM file:

> bowtie -p 4 -t -m 1 -S -q mm9/genome raw_data/SRR1015741.fastq map_files/SRR1015741.sam

# reads processed: 37610875
# reads with at least one reported alignment: 27855696 (74.06%)
# reads that failed to align: 1886532 (5.02%)
# reads with alignments suppressed due to -m: 7868647 (20.92%)
Reported 27855696 alignments to 1 output stream(s)

Filtering unaligned reads and converting into BAM format:

> samtools view -b -F 0x4 -o map_files/SRR1015741.bam map_files/SRR1015741.sam

Basic information:

• Reference:
  Phf19 links methylated Lys36 of histone H3 to regulation of Polycomb activity.
  Ballare C, Lange M, Lapinaite A, Martin GM et al. Nature Structural and Molecular Biology 19:1257-1265 (2012).
  
  
• PUBMED ID link:
  23104054
  
  
• Experiment in GEO/SRA:
  H3K36me3_ChIPSeq [GSM1019769]
  SRR592584.sra

Converting SRA format into FASTQ format:

> fastq-dump -v -O raw_data raw_data/SRR592584.sra

Read 32646084 spots for raw_data/SRR592584.sra

Mapping the ChIPseq sample into a SAM file:

> bowtie -p 4 -t -m 1 -S -q mm9/genome raw_data/SRR592584.fastq map_files/SRR592584.sam

# reads processed: 32646084
# reads with at least one reported alignment: 18755923 (57.45%)
# reads that failed to align: 6819793 (20.89%)
# reads with alignments suppressed due to -m: 7070368 (21.66%)
Reported 18755923 alignments to 1 output stream(s)

Filtering unaligned reads and converting into BAM format:

> samtools view -b -F 0x4 -o map_files/SRR592584.bam map_files/SRR592584.sam

Basic information:

• Reference:
  Erk1/2 Activity Promotes Chromatin Features and RNAPII Phosphorylation at Developmental Promoters in Mouse ESCs.
  Tee WW, Shen SS, Oksuz O, Narendra V, Reinberg D. Cell 156: 678-690 (2014).
  
  
• PUBMED ID link:
  24529373
  
  
• Experiment in GEO/SRA:
  WT Input [SRX336236]
  SRR953585.sra

Converting SRA format into FASTQ format:

> fastq-dump -v -O raw_data raw_data/SRR953585.sra

Read 24803923 spots for raw_data/SRR953585.sra

Mapping the ChIPseq sample into a SAM file:

> bowtie -p 4 -t -m 1 -S -q mm9/genome raw_data/SRR953585.fastq map_files/SRR953585.sam

# reads processed: 24803923
# reads with at least one reported alignment: 16779501 (67.65%)
# reads that failed to align: 1444555 (5.82%)
# reads with alignments suppressed due to -m: 6579867 (26.53%)
Reported 16779501 alignments to 1 output stream(s)

Filtering unaligned reads and converting into BAM format:

> samtools view -b -F 0x4 -o map_files/SRR953585.bam map_files/SRR953585.sam

Basic information:

• Reference:
  The nucleoporin Nup153 regulates embryonic stem cell pluripotency through gene silencing.
  Jacinto FV, Benner C, Hetzer MW. Genes and Development 29:1224-1238 (2015).
  
  
• PUBMED ID link:
  26080816
  
  
• Experiment in GEO/SRA:
  ES-RNAseq-shCtrl [GSM1562339]
  SRR1699465.sra

Converting SRA format into FASTQ format:

> fastq-dump -v -O raw_data raw_data/SRR1699465.sra

Read 35331381 spots for raw_data/SRR1699465.sra

Mapping the RNAseq sample into a SAM file:

> tophat -p 4 -g 1 -o map_files/SRR1699465 --library-type=fr-firststrand mm9/genome raw_data/SRR1699465.fastq

Reads:
          Input     :  35331381
           Mapped   :  27910472 (79.0% of input)
79.0% overall read mapping rate.

Filtering unaligned reads and converting into BAM format:

> samtools view map_files/SRR1699465/accepted_hits.bam | grep "XS:A:+" > map_files/SRR1699465/accepted_hits_plus0.sam
> samtools view map_files/SRR1699465/accepted_hits.bam | grep "XS:A:-" > map_files/SRR1699465/accepted_hits_minus0.sam

> samtools view -H map_files/SRR1699465/accepted_hits.bam > map_files/SRR1699465/header.sam
> cat map_files/SRR1699465/header.sam map_files/SRR1699465/accepted_hits_plus0.sam > map_files/SRR1699465/accepted_hits_plus.sam
> cat map_files/SRR1699465/header.sam map_files/SRR1699465/accepted_hits_minus0.sam > map_files/SRR1699465/accepted_hits_minus.sam

> samtools view -b -o map_files/SRR1699465/accepted_hits_plus.bam map_files/SRR1699465/accepted_hits_plus.sam
> samtools view -b -o map_files/SRR1699465/accepted_hits_minus.bam map_files/SRR1699465/accepted_hits_minus.sam