title: 520_input_neuroblastoma tumor

city: Ghent

first: Anneleen

last: Decock

address: De Pintelaan 185

country: Belgium

institute: Ghent University

data_processing:
Quality control by FastQC (version 0.9.2)
Paired-end read mapping to the human reference genome using Bowtie2 (version 2.0.0 beta7) and SAMtools (version 0.1.18)
Marking PCR duplicates by Picard (version 1.79)
Mapping quality control by SAMStat (version 1.08) and bamUtil (version 1.0.2)
Peak calling using MACS (version 1.4.0 beta)
Genome_build: hg19
Supplementary_files_format_and_content: .bam: .bam format was used as output file type for read mapping (Bowtie2; duplicates are removed); .bed: location and score of the identified peaks (MACS); .wig.gz: visualization (MACS); .tdf: visualization of the methyl-seq data in IGV.

source_name: primary tumor

extract_protocol:
DNA fragmentation by shearing, followed by MBD capture (MethylCap kit of Diagenode)
PrepX ILM DNA Library Kit (IntegenX) and Multiplexing Sample Preparation Oligonucleotide Kit (Illumina)

tag: age of the patient at diagnosis (months)

tag: inss stage

tag: mycn amplification status

value: non-amplified

tag: overall survival time (days)

tag: overall survival status

value: alive

tag: event-free survival time (days)

tag: event-free survival status

value: no event


title: 511_input_neuroblastoma tumor

status: Public on Dec 15 2015

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens


title: 1537_input_neuroblastoma tumor

value: amplified


title: 1383_input_neuroblastoma tumor


title: H3K4me3_stage9

city: Nijmegen

first: Saartje

last: Hontelez

address: Geert Grooteplein 28

department: Molecular developmental biology

country: Netherlands

institute: Radboud University

description: Three independent biological replicates were pooled.

data_processing:
Reads were mapped to the reference Xenopus tropicalis genome JGI7.1, using the BWA allowing one mismatch
We used MACS2 with standard settings and q-value of 0.05. Fragment size was determined using phantompeakqualtools . Broad settings (--BROAD) were used for H3K4me1, H3K36me3, H3K27me3, H3K9me2, H3K9me3, H4K20me3 and RNAPII. Broad and narrow peaks were merged for H3K4me3. For H3K9ac narrow peaks were used
Peaks that showed at least 75% overlap with 1 kb regions that have <65 input reads, and peaks that have a ChIP-seq RPKM > 95 percentile of random background regions are excluded from further analysis.
Only scaffolds 1-10 were included in the analysis. Relative RPKM  was calculated by dividing the ChIP-seq RPKM of the peaks by the ChIP-seq RPKM of 95 percentile of random background regions.
Relative RPKM  was calculated by dividing the ChIP-seq RPKM of the peaks by the ChIP-seq RPKM of 95 percentile of random background regions.
Genome_build: JGI7.1
Supplementary_files_format_and_content: wig files were generated using bam2bw (https://bitbucket.org/simonvh/bam2bw/src); Scores are scaled with scaling factor 1000000/[total #reads]
Supplementary_files_format_and_content: bed files contain peak locations (scaffold, start, stop)

organism: Xenopus tropicalis

source_name: whole embryo

growth_protocol: Embryos were obtained by in vitro fertilisation and grown at 22 celcius untill the approptate developmental stage.

extract_protocol:
Protein-DNA complexes were isolated with antibody from whole embryo lysates that were fixed, sonicated and yolk depleted.
Libraries were prepared with the Kapa Hyper Prep kit (Kapa Biosystems), and sequencing was done on the Illumina HiSeq2000 platform.

treatment_protocol: Fertilised eggs were injected with 2,3 nl of 2,67 ng/ul α-amanitin and developed until the control embryos reached mid-gastrulation (stage 11)

tag: developmental stage (nf)

tag: treatment

value: not injected

tag: chip antibody

value: anti-H3K4me3 (Abcam ab8580)


title: 1750_input_neuroblastoma tumor


title: 1191_input_neuroblastoma tumor


title: 1013_input_neuroblastoma tumor


title: 750_input_neuroblastoma tumor


title: 1613_input_neuroblastoma tumor


title: 1530_input_neuroblastoma tumor


title: H3K4me3_stage8


title: 821_input_neuroblastoma tumor


title: 1615_input_neuroblastoma tumor


title: H3K4me1_stage30

value: anti-H3K4me1 (Abcam ab8895)


title: 1494_input_neuroblastoma tumor


title: H3K4me1_stage16


title: H3K4me1_stage12


title: H3K4me3_stage11_amanitin

description: Data from one biological replicate.

value: alpha-amanitin injected


title: 1537_MBD_neuroblastoma tumor


title: ChIP_K27ac

city: Beijing

first: Wei

last: Xie

address: zhongguancun beidajie

country: China

institute: Tsinghua University

data_processing:
ChIP-seq reads were aligned to the mm9 genome using bowtie 2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
RNA-seq data sets were aligned to the mouse genome mm9 using TopHat.
The mapped reads were further quantified as fragments per kilobase of transcript per million mapped reads (FPKM) based on the RefSeq database using the Cufflinks program
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited wig files counted by the number of reads falling into 100bp bin in the genome for each ChIP-seq sample
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each RNA-seq Sample

organism: Mus musculus

source_name: C3H10T1/2 cells

growth_protocol: Growth medium: DMEM (high glucose), 10% Fetalclone III serum, PenStrep; Induction medium (d0-d2): DMEM (high glucose), 10% Fetalclone III serum, PenStrep, 5uM DEX, 0.5mM IBMX, 0.12ug/ml Insulin, 1uM Rosi, 1nM T3; Differentiation medium (d2-d7): DMEM (high glucose), 10% Fetalclone III serum, PenStrep, 0.12ug/ml Insulin, 1uM Rosi, 1nM T3. Before differentiation cells were seeded at 70% confluency and growth medium was supplemented with 8.3nM human recombinant BMP7 for 3 days.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at 37◦C; then, crude nuclei were purified. Chromatin was fragmented by sonication with a Bioruptor UCD-300 (Diagenode) to obtain fragments 200–800 bp in length. For each ChIP assay, 2–5 ug of antibodies were added and incubated at 4◦C overnight. ChIP DNA was quantified with a Qubit fluorometer using the Quant-iT dsDNA HS assay kit
ChIP-seq libraries were generated following the procedue described in "TELP, a sensitive and versatile library construction method for next-generation sequencing" by Peng X, Wu J, Brunmeir R, Kim SY, Zhang Q, Ding C, Han W, Xie W, Xu F., published in Nucleic Acids Res. 2015 Mar 31;43(6):e35. doi: 10.1093/nar/gku818. Epub 2014 Sep 15.

tag: strain

tag: cell type

value: mesenchymal stem cell

tag: cell line

tag: chip-antibody


title: 511_MBD_neuroblastoma tumor


title: ChIP_Input


title: H3K4me1_stage10.5


title: 1013_MBD_neuroblastoma tumor


title: 1392_input_neuroblastoma tumor


title: ChIP_K27me3


title: 277_input_neuroblastoma tumor

value: event


title: H3K4me1_stage9


title: 1383_MBD_neuroblastoma tumor


title: 750_MBD_neuroblastoma tumor


title: ChIP_K4me3


title: 1392_MBD_neuroblastoma tumor


title: 821_MBD_neuroblastoma tumor


title: ChIP_K9ac


title: ChIP_PPARgamma


title: 520_MBD_neuroblastoma tumor


title: K4me3_Std_10ng

source_name: 3T3-L1 cells

growth_protocol: Growth medium: DMEM (high glucose), 10% BCS, PenStrep; Induction medium (d0-d2): DMEM (high glucose), 10% FBS, PenStrep, 5uM DEX, 0.5mM IBMX, 0.12ug/ml Insulin; Differentiation medium (d2-d7): DMEM (high glucose), 10% FBS, PenStrep, 0.12ug/ml Insulin. Before differentiation cells were seeded at 70% confluency (d-4).

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at 37◦C; then, crude nuclei were purified. Chromatin was fragmented by sonication with a Bioruptor UCD-300 (Diagenode) to obtain fragments 200–800 bp in length. For each ChIP assay, 2–5 ug of antibodies were added and incubated at 4◦C overnight. ChIP DNA was quantified with a Qubit fluorometer using the Quant-iT dsDNA HS assay kit
ChIP-seq libraries were generated following the the manufactorer's instructions (Illumina ChIP-SEQ. DNA Sample prep. Kit, #1003473, lot#6330828)

value: Swiss albino

value: preadipocyte cell


title: 1750_MBD_neuroblastoma tumor


title: 1494_MBD_neuroblastoma tumor


title: 1615_MBD_neuroblastoma tumor


title: K4me3_TELP_100pg_1


title: 1613_MBD_neuroblastoma tumor


title: 1191_MBD_neuroblastoma tumor


title: 277_MBD_neuroblastoma tumor


title: 1530_MBD_neuroblastoma tumor


title: K4me3_TELP_100pg_2


title: K4me3_TELP_100pg_3


title: K4me3_TELP_1ng


title: Il-4-stimulated keratinocytes (120h) Day 05 sample2

city: Indianapolis

first: Mark

middle: H

last: Kaplan

state: IN

address: 1044 West Walnut St. Room 202

department: Pediatrics, and Microbiology and Immunology

country: USA

institute: Indiana University

description:
Ot6539
Sample 10
processed data file(s): report.ctl.IL.120h.csv

library_source: transcriptomic

data_processing:
The reads (fastq files) were aligned to human reference genome hg19 using tophat v2.1.0 [1], with default parameters and known transcriptome.
Alignment results were filtered by bamutils v0.5.0 [2] to remove reads with multiple mappings.
Statistics data of the resulting alignment files were created using samtools v0.1.18 [3] and bamutils v0.5.0.
The counts of aligned reads mapping to known genes were calculated using bamutils v0.5.0.
EdgeR v2.11 [4] was used for differential expression analysis.
Genome_build: genome hg19
Supplementary_files_format_and_content: comma-delimited text files include RPKM values for each Sample
Supplementary_files_format_and_content: report.ctl.IL.3h.csv (control day 02 versus IL-4 day 02 (3h))
Supplementary_files_format_and_content: report.ctl.IL.24h.csv (control day 02 versus IL-4 day 02 (24h))
Supplementary_files_format_and_content: report.ctl.IL.120h.csv (control day 02 versus control day 05)
Supplementary_files_format_and_content: report.ctls D2xD5_24h.ctl_120h.csv (control day 05 versus IL-4 day 05)
Supplementary_files_format_and_content: edgeR.report st6siRNA.csv (control siRNA plus IL-4 (24h) day 02 versus STAT6siRNA plus IL-4 (24h) day 02)

molecule: total RNA

source_name: Skin

growth_protocol: Human keratinocytes were culured with 2 mM of calcium chloride for 2 or 5 days in Epilife complete media containin 5 ug/ml of keratinocyte frowth supplement.

extract_protocol:
RNA was harvested using Trizol reagent and purified using RNA isolation kit with on-column DNase (RNase-free) treatment.
Illumina library preparation and HiSeq2000 sequencing with 20 million paired end 100nt reads per sample

treatment_protocol: Human keratinocytes were differentiated with calcium chloride for 2 days and incubated with media alone or 20ng/ml of recombinant human IL-4 for 3 and 24 hours. Human keratinocytes were differentiated with calcium chloride for 5 days with or wihout recombinant human IL-4 (20ng/ml). Keratinocytes transfected with control or STAT6 siRNA were differentiated with calcium chloride for 2 days and then stimulated with recombinant human IL-4 for 24 hours.

value: n-tert keratinocytes

tag: passage

tag: protocol

value: differentiated with calcium chloride for 5 days with recombinant human IL-4


title: Control siRNA keratinocytes plus IL-4 (24h) Day02 sample2

description:
OtA0155
Sample 12
processed data file(s): edgeR.report st6siRNA.csv

value: transfected with control siRNA, differentiated with calcium chloride for 2 days and then stimulated with recombinant human IL-4 for 24 hours


title: STAT6 siRNA keratinocytes plus IL-4 (24h) Day02 sample1

description:
OtA0153
Sample 13
processed data file(s): edgeR.report st6siRNA.csv

value: transfected with STAT6 siRNA, differentiated with calcium chloride for 2 days and then stimulated with recombinant human IL-4 for 24 hours


title: Il-4-stimulated keratinocytes  (120h) Day 05 sample1

description:
Ot6538
Sample 9
processed data file(s): report.ctl.IL.120h.csv


title: Control keratinocytes (120h) Day 05 sample2

description:
Ot6537
Sample 8
processed data file(s): report.ctl.IL.120h.csv and report.ctls D2xD5_24h.ctl_120h.csv

value: differentiated with calcium chloride for 5 days


title: Control keratinocytes (120h) Day 05 sample1

description:
Ot6536
Sample 7
processed data file(s): report.ctl.IL.120h.csv and report.ctls D2xD5_24h.ctl_120h.csv


title: Il-4-stimulated keratinocytes (24h) Day 02 sample2

description:
Ot6535
Sample 6
processed data file(s): report.ctl.IL.24h.csv

value: differentiated with calcium chloride for 2 days and incubated with recombinant human IL-4 for 24 hours


title: Il-4-stimulated keratinocytes (24h) Day 02 sample1

description:
Ot6534
Sample 5
processed data file(s): report.ctl.IL.24h.csv


title: Il-4-stimulated keratinocytes (3h) Day 02 sample2

description:
Ot6533
Sample 4
processed data file(s): report.ctl.IL.3h.csv

value: differentiated with calcium chloride for 2 days and incubated with recombinant human IL-4 for 3 hours


title: K4me3_TELP_25pg_3


title: K4me3_TELP_25pg_2


title: Il-4-stimulated keratinocytes (3h) Day 02 sample1

description:
Ot6532
Sample 3
processed data file(s): report.ctl.IL.3h.csv


title: Control keratinocytes Day 02 sample2

description:
Ot6531
Sample 2
processed data file(s): report.ctl.IL.3h.csv and report.ctls D2xD5_24h.ctl_120h.csv

value: differentiated with calcium chloride for 2 days


title: RNA_Std_d0

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufactorer's instructions and treated with DnaseI
RNA-seq libraries were generated by BGI following their standard procedure: mRNAs is enriched by using the oligo (dT) magnetic beads. By using the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp), then the first strand cDNA is synthesized by random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and poly (A) addition. Finally, sequencing adapters are ligated to the fragments. The fragments are purified by Agarose gel electrophoresis and enriched by PCR amplification.


title: STAT6 siRNA keratinocytes plus IL-4 (24h) Day02 sample2

description:
OtA0154
Sample 14
processed data file(s): edgeR.report st6siRNA.csv


title: RNA_Std_d7


title: Control keratinocytes Day 02 sample1

description:
Ot6530
Sample 1
processed data file(s): report.ctl.IL.3h.csv and report.ctls D2xD5_24h.ctl_120h.csv


title: RNA_TELP_d0_N9

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufactorer's instructions and treated with DnaseI
RNA-seq libraries were generated following the procedue described in "TELP, a sensitive and versatile library construction method for next-generation sequencing" by Peng X, Wu J, Brunmeir R, Kim SY, Zhang Q, Ding C, Han W, Xie W, Xu F., published in Nucleic Acids Res. 2015 Mar 31;43(6):e35. doi: 10.1093/nar/gku818. Epub 2014 Sep 15.


title: RNA_TELP_d7_N9_ss


title: RNA_TELP_d7_N9


title: RNA_TELP_d7_T18


title: TELP_100pg_PE2


title: BMT-Gan 2 (from MyD88-/-)

city: kanazawa

first: masanobu

last: oshima

address: Kakuma-machi

country: Japan

institute: kanazawa university

data_processing:
HiSeq Control Software (HCS) v2.0.12.0 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome using Tophat version 2.0.13 with parameters -p 4 -g 1.
Geometric mean-normalized FPKMs (fragments per kilobase of exon per million mapped fragments) of each gene in a reference gene annotation (NCBI37/mm9, Ensembl genes) were calculated using Cuffquant and Cuffnorm softwares in Cufflinks v2.2.1.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes geometric mean-normalized FPKM values for each Sample

molecule: polyA RNA

source_name: gastric tumor of adult bone marrow transplanted Gan mice from Myd88-/- mice

extract_protocol:
Total RNA was extracted using ISOGEN (Nippon Gene) and purified using Rneasy Mini Kit (Quiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: stomach

tag: age

value: 40-50 weeks

tag: genotype/variation

value: K19-Wnt1/K19-Ptgs2/K19-Ptges transgenic, bone marrow-transplanted from Myd88-/-


title: BMT-Gan 1 (from MyD88-/-)


title: TELP_1ng_PE2


title: TELP_IgG

value: sigmal Aldrich-i5006


title: Gan 3

source_name: adult Gan mouse gastric tumor

value: K19-Wnt1/K19-Ptgs2/K19-Ptges transgenic


title: Gan 1 (MyD88-/-)

source_name: adult Gan Myd88-/- mouse gastric tumor

value: K19-Wnt1/K19-Ptgs2/K19-Ptges transgenic, Myd88 -/-


title: K4me3_TELP_25pg_1


title: Gan 3 (MyD88-/-)


title: Gan 2 (MyD88-/-)


title: Gan 1


title: Control siRNA keratinocytes plus IL-4 (24h) Day02 sample1

description:
OtA0152
Sample 11
processed data file(s): edgeR.report st6siRNA.csv


title: C2mE 3

source_name: adult C2mE mouse inflamed glandular stomach

value: K19-Ptgs2/K19-Ptges transgenic


title: C2mE 1


title: C2mE 2


title: Gan 2


title: HSB-2 LDB1 I322A

city: Nashville

first: Yan

last: Guo

state: TN

address: 639 Preston Research Bld

institute: Vanderbilt Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control to filter out bad samples and reads
Alignment to human genome (hg19) using Tophat 2
Read count quantification using HTSeq
Genome_build: HG19
Supplementary_files_format_and_content: read count table

source_name: HSB-2  expressing LDB1 I322A

extract_protocol:
Total RNA was isolated with Trizol
libraries were constructed using the Illumina TruSeq Stranded mRNA kit following the manufacturer's supplied protocol.manufacturer's supplied protocol.

value: expressing LDB1 I322A


title: WT 2

source_name: adult normal glandular stomach

value: wild type


title: GAD67-9

city: Milan

first: Vania

last: Broccoli

address: Via Olgettina 58

department: Division of Neuroscience

country: Italy

institute: Ospedale San Raffaele

data_processing:
For data analyses a splice junction library with a length of 120 nucleotides (60+60) per splice junction was created based on known exon-exon junctions according to the Ensembl Genes annotation (v. 67, May 2012)
Alignment of the short reads to the mm10 transcriptome was performed with bwa-0.7.2 [1]
A  table of readcounts per gene was created based on the overlap of the uniquely mapped reads with the Ensembl Genes annotation v. 69 (October 2012) for mm10, using featureCounts (Liao et al., 2013)
Normalization of the raw readcounts based on the library size and testing for differential expression between the different cell types/treatments was performed with the DESeq R package (v.1.10.1) (Anders et al., 2010)
Sample to sample Euclidean distance as well as Pearson's correlation coefficient (r) were computed based on the normalized gene expression level in order to explore correlation between biological replicates and different libraries. For testing for differential expression, the count data were fitted to the negative binomial distribution and the p-values for the statistical significance of the fold change were adjusted for multiple testing with the Benjamini-Hochberg correction for controlling the false discovery rate.
Genome_build: mm10
Supplementary_files_format_and_content: Csv file with counts table from featureCounts

source_name: cortical interneurons

growth_protocol: Primary cells

extract_protocol:
RNA extraction performed by RNeasy Micro Kit - QIAGEN
dUTP method, according to Parkhomchuk et al. (2009) using NEBnext RNA-Seq Ultra chemistries

treatment_protocol: MEFs were tripsynized while iGABA-Ins and Cortical interneurons were trypsinized and sorted for GFP before RNA extraction

value: E18.5 cortical interneurons

tag: passages

value: primary cells


title: WT 1


title: HSB-2 LDB1 LI→AA

source_name: HSB-2  expressing LDB1 LI→AA

value: expressing LDB1 LI>AA


title: WT 3


title: GAD67-8


title: HSB-2 wild type LDB1 replicate 2

source_name: HSB-2  expressing wild type LDB1

value: expressing wild type LDB1


title: HSB-2 LDB1 RLEN→AAAA

source_name: HSB-2  expressing LDB1 RLEN→AAAA

value: expressing LDB1 RLEN>AAAA


title: HSB-2 LDB1ΔLCCD

source_name: HSB-2  expressing LDB1 {delta}LCCD

value: expressing LDB1 {delta}LCCD


title: BMT-Gan 3 (from MyD88-/-)


title: iGABA-5

source_name: iGABA reprogrammed cells

growth_protocol: Maintained 2 DIV in MEF medium and then shifted in neuronal medium

value: iGABA-INs at 14 DIV of reprogramming

value: reprogrammed from P0 MEFs


title: Dicer WT Fibroblasts [ChIP-seq]

city: Cambridge

first: Sara

middle: J

last: Gosline

state: MA

address: 77 Massachusetts Ave

department: Biological Engineering

institute: MIT

data_processing:
Reads for these data and the ChiP-Seq reads from GSE44159 were aligned to the genome using TopHat 1.4
Bed files were input into GEM v1.1 using either the default distribution (H3K36me3) or a distribution derived from reads around Dnase I hypersensitive sites (also determined by GEM v1.1  in murine fibroblasts from ENCODE
WT vs KO were run against one another, with text files for all 3 histone marks included here.
Genome_build: mm9
Supplementary_files_format_and_content: These files are in BED format and contain regions that exhibit significant (q<e-5) histone events in the WT or KO cells according to the background distribution define by the Dnase HS sites.

source_name: Dicer WT Fibroblasts_H3K27ac ChIP-seq

growth_protocol: Monoclonal immortalized Dicer WT and KO MSCs were cultured in Alpha-MEM supplemented with pen/strep and 10% fetal bovine serum.

extract_protocol:
The cross-linked material was then rinsed with 1× PBS, pelleted, and frozen at -80C for later use. Fixed cells were sonicated to obtain a final DNA fragment size range of 100–500 bp. H3K27ac antibody (ab4729) was first incubated with beads for 6 h and the
For high-throughput sequencing, libraries were prepared according to Illumina’s instructions accompanying the DNA sample kit (0801-0303) and sequenced on an Illumina platform

treatment_protocol: Cells were cross-linked with a 1% formaldehyde solution for 10 min and the cross-linking was quenched by adding glycine to a final concentration of 0.125 M.

value: Dicer WT

value: H3K27ac antibody

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: Dicer WT with Sox9 over-expression [RiboZero-prepped library]

data_processing:
Reads were aligned to the mm9 genome using Bowtie2
BAM-files were filtered for repetitive regions
HT_Seq-Count was used to count reads within exons or introns
DESeq v1.10.1 was used to quantify reads between conditions
Genome_build: mm9
Supplementary_files_format_and_content: DESeq v1.10.1 output is included for all RefSeq transcripts including normalized read counts for the combined replicates, fold change and p-value representing significance of differential expression between WT and KO

source_name: Dicer WT with Sox9 over-expression

extract_protocol:
Total RNA from both untreated fibroblasts as well as transfected fibroblasts was also isolated from subconfluent WT and KO fibroblasts using QIAzol (phenol/chloroform) extraction and RNA was DNase-treated to avoid any gDNA contamination. Illumina TruSeq
The manufacturer’s recommendations were followed to obtain strand-specific libraries which were then then submitted to single-end sequencing on an Illumina HiSeq 2000.

value: Dicer WT with Sox9 over-expression

value: murine mesenchymal stem cells


title: Dicer KO Fibroblasts [ChIP-seq]

source_name: Dicer KO Fibroblasts_H3K27ac ChIP-seq

value: Dicer KO


title: HSB-2 LDB1 RLIT→AAAA

source_name: HSB-2  expressing LDB1 RLIT→AAAA

value: expressing LDB1 RLIT>AAAA


title: iGABA-4


title: Dicer WT with Tead4 over-expression [RiboZero-prepped library]

source_name: Dicer WT with Tead4 over-expression

value: Dicer WT with Tead4 over-expression


title: MEF-3

source_name: mouse embryonic fibroblasts

growth_protocol: Grown in MEF medium and then shifted in neuronal inducing medium

value: E13.5 primary mouse embryonic fibroblasts


title: HSB-2 LDB1ΔLID

source_name: HSB-2  expressing LDB1 {delta}LID

value: expressing LDB1 {delta}LID


title: MEF-2


title: HSB-2 wild type LDB1 replicate 1


title: Dicer WT with Pbx3 over-expression [RiboZero-prepped library]

source_name: Dicer WT with Pbx3 over-expression

value: Dicer WT with Pbx3 over-expression


title: Dicer WT with vector tranfection [RiboZero-prepped library]

description: processed data file: DE_exonCtrlWT_vs_exonPbx3noRN.txt, DE_exonCtrlWT_vs_exonSox9noRN.txt, DE_exonCtrlWT_vs_exonTead4noRN.txt, DE_intronCtrlWT_vs_intronPbx3noRN.txt, DE_intronCtrlWT_vs_intronSox9noRN.txt, DE_intronCtrlWT_vs_intronTead4noRN.txt

source_name: Dicer WT with vector tranfection

value: Dicer WT with vector tranfection


title: HSB-2 empty virus

source_name: HSB-2  expressing empty virus

value: expressing empty virus


title: HSB-2 parental cell line

source_name: HSB-2  parental cell line

value: parental cell line


title: Dicer WT Fibroblasts [RiboZero-prepped library]

description: processed data file: DE_exonWT_vs_exonKOnoRN.txt, DE_intronWT_vs_intronKOnoRN.txt

source_name: Dicer WT Fibroblasts


title: Dicer KO Fibroblasts [RiboZero-prepped library]

source_name: Dicer KO Fibroblasts


title: MEF-1


title: GAD67-7

source_name: cortical interneurons

value: E18.5 cortical interneurons

value: primary cells


title: iGABA-6

growth_protocol: Mainteined 2 DIV in MEF medium and then shifted in neuronal medium

value: iGABA-INs at 14 DIV of reprogramming

value: reprogrammed from P0 MEFs


title: RNA-seq analysis of Blnk-/- preB-cells with an tomoxifen inducible Blnk stimulated for 5 hours_L002

status: Public on Dec 14 2015

city: Hamburg

first: Julia

last: Herglotz

address: Martinistr. 52

country: Germany

institute: Heinrich-Pette-Institut

description:
preB-cells_5h_ATGTCA
murine preB-cells from Blnk-/- KO mice

data_processing:
Reads were mapped to the mouse genome (mm10) using CLC Genomics Workbench v6.5.1 software (Qiagen) using default settings.
For base-calling I have used CASAVA-1.8.2 with following parameters:
-fastq-cluster-count 0
-mismatches 1
No data filtering steps were used.
Genome_build: mm10
Supplementary_files_format_and_content: RPKMs

source_name: preB-cells

extract_protocol:
Blnk-/- preB-cells were infected with an BLNK-ERt2 contruct using retroviral constructs and RNA isolation was performed using the PeqGOLD TriFast method (PeqLab Biotechnology). mRNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation NEB module.
Libraries were generated using the TruSeq: RNA Sample Preparation V2 Low Throughput (LT) Kit (Illumina) or the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (both from New England Biolabs), and sequencing was performed on a HiSeq 2500 system (Illumina).

value: Blnk-/- KO

value: preB-cells

tag: protocol (genetic modification)

value: overexpression of BLNK_ERt2

tag: time

value: 5 hours


title: RNA-seq analysis of Blnk-/- preB-cells with an tomoxifen inducible Blnk stimulated for 5 hours_L003


title: RNA-seq analysis of Blnk-/- preB-cells with an tomoxifen inducible Blnk stimulated for 5 hours_L001


title: RNA-seq analysis of Blnk-/- preB-cells with an tomoxifen inducible Blnk stimulated for 5 hours_L004


title: RNA-seq analysis of Blnk-/- preB-cells with an tomoxifen inducible Blnk stimulated for 1.5 hours_L003

description:
preB-cells_1.5h_AGTCAA
murine preB-cells from Blnk-/- KO mice

value: 1.5 hours


title: RNA-seq analysis of Blnk-/- preB-cells with an tomoxifen inducible Blnk stimulated for 1.5 hours_L004


title: RNA-seq analysis of Blnk-/- preB-cells with an tomoxifen inducible Blnk stimulated for 1.5 hours_L001


title: RNA-seq analysis of Blnk-/- preB-cells with an tomoxifen inducible Blnk stimulated for 0.5 hours_L003

description:
preB-cells_0.5h_TGACCA
murine preB-cells from Blnk-/- KO mice

value: 0.5 hours


title: RNA-seq analysis of Blnk-/- preB-cells with an tomoxifen inducible Blnk stimulated for 0.5 hours_L001


title: RNA-seq analysis of Blnk-/- preB-cells with an tomoxifen inducible Blnk stimulated for 1.5 hours_L002


title: RNA-seq analysis of Blnk-/- preB-cells with an tomoxifen inducible Blnk_L004

description:
preB-cells_control_AGTTCC
murine preB-cells from Blnk-/- KO mice

value: control


title: RNA-seq analysis of proB-cell from Mef2c/d Mb1Cre mice-III

source_name: proB-cells of Mef2cd Mb1cre mice

extract_protocol:
ProB-cell were sorted (Lin-CD19+CD43highB220low) and RNA isolation was performed using the PeqGOLD TriFast method (PeqLab Biotechnology). mRNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation NEB module.
Libraries were generated using the TruSeq: RNA Sample Preparation V2 Low Throughput (LT) Kit (Illumina) or the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (both from New England Biolabs), and sequencing was performed on a HiSeq 2500 system (Illumina).

value: Mef2c/d knockout

value: proB-cells


title: RNA-seq analysis of proB-cell from Mb1Cre mice-III

source_name: proB-cells of Mb1cre mice


title: RNA-seq analysis of Blnk-/- preB-cells with an tomoxifen inducible Blnk_L001


title: RNA-seq analysis of proB-cell from Mef2c/d Mb1Cre mice-II


title: RNA-seq analysis of proB-cell from Mef2c/d Mb1Cre mice-I


title: RNA-seq analysis of proB-cell from Mb1Cre mice-II


title: RNA-seq analysis of Blnk-/- preB-cells with an tomoxifen inducible Blnk_L003


title: RNA-seq analysis of proB-cell from Klf2 Mb1Cre mice_L002

data_processing:
Reads were mapped to the mouse genome (mm10) using CLC Genomics Workbench v6.5.1 software (Qiagen) using default settings.
For base-calling I have used CASAVA-1.8.2 with following parameters:
-fastq-cluster-count 0
-mismatches 1
No data filtering steps were used.
Genome_build: aligned to the mm10 assembly
Supplementary_files_format_and_content: RPKMs

source_name: proB-cells of Klf2 Mb1cre mice

value: Klf2 knockout


title: RNA-seq analysis of Blnk-/- preB-cells with an tomoxifen inducible Blnk_L002


title: RNA-seq analysis of proB-cell from Klf2 Mb1Cre mice_L001


title: RNA-seq analysis of proB-cell from Mb1Cre mice_L002


title: RNA-seq analysis of BMiFLT3 (15-3) cells overexpressing Klf2_L004

source_name: BMiFLT3 (15-3) cells

extract_protocol:
BMiFLT3 cells were infected using retroviral constructs and RNA isolation was performed using the PeqGOLD TriFast method (PeqLab Biotechnology). mRNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation NEB module.
Libraries were generated using the TruSeq: RNA Sample Preparation V2 Low Throughput (LT) Kit (Illumina) or the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (both from New England Biolabs), and sequencing was performed on a HiSeq 2500 system (Illumina).

value: proB cells from a murine BCP-ALL

value: Klf2 overexpression


title: RNA-seq analysis of proB-cell from Mb1Cre mice_L001


title: RNA-seq analysis of proB-cell from Mb1Cre mice-I


title: RNA-seq analysis of BMiFLT3 (15-3) cells overexpressing BFP_L002

value: BFP overexpression


title: RNA-seq analysis of BMiFLT3 (15-3) cells overexpressing BFP_L003


title: RNA-seq analysis of BMiFLT3 (15-3) cells overexpressing Klf2_L001


title: RNA-seq analysis of BMiFLT3 (15-3) cells overexpressing Klf2_L002


title: RNA-seq analysis of BMiFLT3 (15-3) cells overexpressing BFP_L001


title: RNA-seq analysis of BMiFLT3 (15-3) cells overexpressing BFP_L004


title: H3K4me3_BMDC_UBC9KO_18hrLPS

city: Paris

first: Adrien

last: Decque

address: 28 rue du Docteur Roux

country: France

institute: Institut Pasteur

description:
H3K4me3-DNA complexes immunoprecipitated from UBC9 KO LPS-stimulated (18h) BMDC chromatin.
Sample name: KO_18h

data_processing:
sequencing on Illumina Hiseq-2500.
Reads were aligned on genome build mm9 using bowtie2.
Aligned reads were converted to bam files using samtools 1.0.
Visualization files for IGV were generated from bam files in IGVtools (in IGV 2.0) using count.
Genome_build: mm9
Supplementary_files_format_and_content: TDF files for visualization in IGV.

source_name: Bone marrow derived dendritic cells

extract_protocol:
Lysates were clarified from sonicated nuclei and H3K4me3-DNA complexes were isolated with anti-H3K4me3 antibody.
Libraries were prepared using ChIP-Seq Sample Prep Kit (#IP-102-1001, Illumina) following the manufacturer's protocol with some modifications. Briefly, 10 ng of ChIP enriched DNA or control DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single A nucleotide was added to the 3 ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR (30 sec at 98°C; [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] x 14 cycles; 5 min at 72°C) and then purified using Agencourt AMPure XP beads (#A63881, Beckman). DNA library size selection was performed by excising the 250-350 bp fragments from a 2% agarose gel followed by purification using a QIAquick Gel Extraction Kit (#28906, Qiagen). Prior to analyses DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent).

tag: genotype

value: UBC9 KO

value: BMDC

value: H3K4me3 (17-614 Millipore)

tag: stimulation

value: LPS 10ng/ml 18 hours


title: RNA-seq analysis of Blnk-/- preB-cells with an tomoxifen inducible Blnk stimulated for 0.5 hours_L002

value: Blnk-/- KO


title: RNA-seq analysis of Blnk-/- preB-cells with an tomoxifen inducible Blnk stimulated for 0.5 hours_L004

value: preB-cells


title: H3K4me3_BMDC_UBC9KO_4hrLPS

description:
H3K4me3-DNA complexes immunoprecipitated from UBC9 KO LPS-stimulated (4h) BMDC chromatin.
Sample name: KO_4h

tag: chip antibody

value: LPS 10ng/ml 4 hours


title: H3K4me3_BMDC_UBC9KO_noLPS

description:
H3K4me3-DNA complexes immunoprecipitated from UBC9 KO unstimulated BMDC chromatin.
Sample name: KO_0


title: H3K4me3_BMDC_UBC9WT_18hrLPS

description:
H3K4me3-DNA complexes immunoprecipitated from UBC9 WT LPS-stimulated (18h) BMDC chromatin.
Sample name: WT_18h

value: UBC9 WT


title: H3K4me3_BMDC_UBC9WT_4hrLPS

description:
H3K4me3-DNA complexes immunoprecipitated from UBC9 WT LPS-stimulated (4h) BMDC chromatin.
Sample name: WT_4h


title: H3K4me3_BMDC_UBC9WT_unstim

description:
H3K4me3-DNA complexes immunoprecipitated from UBC9 WT unstimulated BMDC chromatin.
Sample name: WT_0


title: RNA-seq analysis of BMiFLT3 (15-3) cells overexpressing Klf2_L003


title: Mef2c_ChIPseq_I

data_processing:
Illumina Casava 1.8.2 software was used for base calling.
Sequence tags were aligned with Bowtie (v. 0.12.8) reporting only top scoring unique mapping tags.
The MACS algorithm was used to identify bound regions by comparing the enrichment of the Mef2c-IP sample against a control IgG-IP for background correction. MACS version 1.4.01 was run with all parameters at their default settings, except m-fold, which was set at 8,30, to identify Mef2c-bound regions.
Genome_build: aligned to the mm9 assembly (NCBI Build 37)
Supplementary_files_format_and_content: bed files

growth_protocol: Cells were routinely grown in α-MEM with 10% FCS, glutamine and sodium pyruvate.

extract_protocol:
ChIP experiments using anti-Mef2c (Santa Cruz; sc-13266X; Lot#C2309) or anti-IgG (Santa Cruz; sc-2028; Lot#J2114) antibodies were performed using the EZ-ChIP Kit (Upstate/Millipore) according to the manufacturer’s protocol.
Purified DNA from chromatin immunoprecipitations (10-50 ng) was adapter-ligated using the Illumina-compatible NEXTflexTM ChIP Seq-Kit (Bioo Scientific) for DNA inserts ≥70 bps.DNA fragments between 350-550 bp were isolated using PippinPrep (Sage Science) and quantified and sized on a microfluidics-based Bioanalyzer 2100 using a High Sensitivity DNA Kit (Agilent).

value: anti-Mef2c (Santa Cruz; catalog# sc-13266X; lot# C2309)


title: IgG_ChIPseq_II

value: anti-IgG (Santa Cruz; catalog# sc-2028; lot# J2114)


title: SUMO1_BMDC_1hLPS

description:
Sample name: SUMO1_1h
SUMO1-DNA complex immunoprecipitated from LPS-stimulated UBC9 WT BMDC chromatin (1hr)

data_processing:
sequencing on Illumina Hiseq-2000.
Reads were aligned on genome build mm9 using bowtie2.
Aligned reads were converted to bam files using samtools 1.0.
Visualization files for IGV were generated from bam files in IGVtools (in IGV 2.0) using count.
Genome_build: mm9
Supplementary_files_format_and_content: processed data files format is .tdf, for visualization of ChIPseq signal in IGV.

extract_protocol:
Lysates were clarified from sonicated nuclei and SUMO1-, SUMO2-, or RNAPolII-DNA complexes were isolated with antibody, as described in Blecher-Gonen et al., Nature Protocols 2013.
Libraries were prepared according to Blecher-Gonen et al., Nature Protocols 2013.

tag: antibody

value: SUMO1 (Y299 monoclonal antibody)

value: LPS 10ng/ml 1 hours


title: Mef2c_ChIPseq_II

tag: cell type


title: IgG_ChIPseq_I

tag: cell line


title: SUMO2_BMDC_1hLPS

description:
Sample name: SUMO2_1h
SUMO2-DNA complex immunoprecipitated from LPS-stimulated UBC9 WT BMDC chromatin (1hr)


title: Pol2_BMDC_UBC9KO_unstim

description:
BMDC_UBC9KO_noLPS
Sample name: KO_Pol2_noLPS
Pol2-DNA complexes immunoprecipitated from UBC9 KO unstimulated BMDC chromatin

value: RNAPolII (8WG16 monoclonal antibody)


title: C7_input

city: Amherst

first: Lawrence

middle: M

last: Schwartz

address: 211 Morrill Science Center, 611 North Pleasant Street

department: Department of Biology

institute: University of Massachusetts

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie (version 1.0.0) allowing 1 mismatch.
Mapped reads were used for the input of the MACS algorithm (version 1.4.0rc2) to identify regions in the genome that are enriched in H3K4me3. The detected H3K4me3 peaks with false discovery rate (FDR) ≤ 0.01 were analyzed in the downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: BED files were generated using MACS; the scores (the 5th column) represent {-10 * log10} P-values.

source_name: rostral prefrontal cortex

extract_protocol:
Neuronal nuclei from prefrontal cortex BA9 were NeuN+ labeled and fluorescence activated sorted (FACS) for subsequent H3K4me3 ChIP-seq. Briefly, approximately 300mg to 500mg of -80oC frozen grey matter dissected from BA9 was homogenized in 5ml lysis buffer and ultracentrifuged over sucrose solution at 24,400 rpm for two hours at 4oC. The resulting pellet was suspended in 550ul PBS, and immunolabeled with NeuN for 60 minutes while rotated in darkness. NeuN+ and NeuN- fractions were separated and collected by FACS.
ChIP sequencing was performed for the NeuN+ fraction. Briefly, genomic regions with H3K4me3 modification were extracted by chromatin immunoprecipitation using anti-H3K4me3 antibody and further prepared into ChIP-seq library for sequencing. For each brain sample, 1 ug of DNA was used to construct sequencing libraries using Illumina’s TruSeq Sample Prep Kit, according to the manufacturer’s protocol (Illumina, San Diego, CA), and sequenced using 36nt single-end reads on Illumina’s GA II.

value: rostral prefrontal cortex

tag: condition

value: control (input DNA)

tag: gender

value: female

tag: onset age

tag: age at death

tag: cag repeat

tag: post-mortem interval

value: input


title: H_0001

source_name: prefrontal cortex (BA9)

tag: tissue

value: brain prefrontal cortex (Brodmann Area 9)

value: HD

value: male


title: H_0601

value: unknown


title: H_0008


title: H_0009


title: Pol2_BMDC_UBC9WT_unstim

description:
BMDC_UBC9WT_noLPS
Sample name: WT_Pol2_noLPS
Pol2-DNA complexes immunoprecipitated from UBC9 WT unstimulated BMDC chromatin

value: BMDC


title: Pol2_BMDC_UBC9WT_2hrLPS

description:
BMDC_UBC9WT_2hLPS
Sample name: WT_Pol2_2hLPS
Pol2-DNA complexes immunoprecipitated from UBC9 WT LPS-stimulated BMDC chromatin

value: LPS 10ng/ml 2 hours


title: C2

value: control


title: C5


title: C4


title: SUMO2_BMDC_UBC9WT_2hrLPS

description:
SUMO2_BMDC_2hLPS
Sample name: SUMO2_2h
SUMO2-DNA complex immunoprecipitated from LPS-stimulated UBC9 WT BMDC chromatin


title: C6


title: C1


title: SUMO2_BMDC_UBC9WT_unstim

description:
SUMO2_BMDC_unstim
Sample name: SUMO2_0h
SUMO2-DNA complex immunoprecipitated from unstimulated UBC9 WT BMDC chromatin


title: SUMO1_BMDC_UBC9WT_2hrLPS

description:
SUMO1_BMDC_2hLPS
Sample name: SUMO1_2h
SUMO1-DNA complex immunoprecipitated from LPS-stimulated UBC9 WT BMDC chromatin


title: T47D_sgRNA_enh588 _rep1

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

description: 16_c_t_ER_ACCTCCAA_L004_R1_001_se.intersect.bed

data_processing:
Sequences were generated by the Illumina Hiseq 2000 genome analyser (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Human Reference Genome (hg19) using BWA version 0.7.5.
Peaks were called using DFilter version 1.0 (Kumar V et al. Nat Biotechnol 2013;31(7):615-22) and MACS peak caller version 1.4 (Zhang Y et al. Genome Biol 2008;9(9):R137). Only peaks called by both algorithms were used for the analysis. MACS was run with the default parameters, except p=10-7, DFilter was run with bs=50, ks=30, refine, nonzero.
Genome_build: hg19
Supplementary_files_format_and_content: intersect.bed files contain peaks called by both peak calling algorithms

source_name: Human breast cancer cell line

growth_protocol: MCF-7 and T47D cells were cultured in DMEM medium (Gibco), supplemented with 10% FCS (Hyclone), and 1% penicillin/streptomycin (Gibco).

extract_protocol:
Chromatin Immunoprecipitation was performed as described (Zwart W et al. EMBO J. 2011, 30:4764-76) : 10ug of antibody was used, with 100ml of Protein A magnetic beads. Antibody used was raised to detect Estrogen Receptor alpha (HC-20, SC-543; Santa Cruz). DNA was amplified as described (Ross-Innes CS et al. Nature 2012;481(7381):389-93).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: Cell lines were infected with lentivirus supernatants supplemented with 8μg/ml polybrene (Sigma). At 24h post-infection, medium was replaced and cells were selected with 2μg/ml puromycin (Gibco). Antibiotic selection was stopped as soon as no surviving cells remained in the no-transduction control plate. As a control cells were transduced with a non-targeting sgRNA pool.

tag: procedure

value: ChIP-seq

value: anti-ERa (SC-543; Santa Cruz)


title: T47D_sgRNA_enh588 _rep2


title: H_0681


title: Pol2_BMDC_UBC9KO_2hrLPS

description:
BMDC_UBC9KO_2hLPS
Sample name: KO_Pol2_2hLPS
Pol2-DNA complexes immunoprecipitated from UBC9 KO LPS-stimulated BMDC chromatin


title: T47D_cntrl


title: MCF-7_sgRNA_enh588 _rep2

description: 13_c_m_ER_GATGAATC_L004_R1_001_se.intersect.bed


title: MCF-7_sgRNA_enh588 _rep1


title: H_0003


title: MCF-7_cntrl


title: SUMO1_BMDC_UBC9WT_unstim

description:
SUMO1_BMDC_unstim
Sample name: SUMO1_0h
SUMO1-DNA complex immunoprecipitated from unstimulated UBC9 WT BMDC chromatin


title: C3


title: 1302 MLL-AF9 (MSCVneo-MLL-AF9+MSCVpuro) polyA RNA-Seq

city: Atlanta

first: Keith

middle: E

last: Szulwach

state: GA

address: 615 Michael Street, Whitehead Suite 301

institute: Emory University

data_processing:
Illumina Basecalling, CASAVA 1.8.2
FASTQ sequences were aligned to NCBIv1/mm9 with Bowtie v0.17.2 retaining unique non-duplicate matches to the genome, with no more than 3 mismatches in the first 30 bases
Enriched regions derived from MACS v1.4, --bw=200 -g 1.87e9, using genotype matched input controls
RNA-Seq reads were aligned using tophat-1.4.1 and RPKM expression values were extracted using cufflinks-1.3.0 using RefSeq gene models.
Genome_build: mm9
Supplementary_files_format_and_content: BED format, containing regions of enrichment and RPKM expression values

source_name: Mouse bone marrow mononuclear cells

extract_protocol:
25 ng of 5hmC-enriched DNA, or non-enriched sonicated input genomic DNA was end-repaired, adenylated, and ligated to Illumina Genomic DNA Adapters (Genomic DNA adapter oligo mix) according to standard Illumina protocols for ChIP-Seq library construction, maintaining the proper molar ratios of adapter to insert. Adapter-ligated fragments of ~200-350 bp were gel-purified by 2% agarose gel electrophoresis and PCR-amplified for 18 PCR cycles. Libraries were checked for quality and quantified using an Agilent 2100 Bioanalyzer DNA 1000 Chip.
RNA-Seq expression libraries were generated from duplicate samples per genotype using the Illumina TruSeq RNA Sample Preparation Kit v2. Libraries were sequenced using the Illumina HiScan platform. Cluster generation was performed with Illumina TruSeq cluster kit v2-cBot-HS. Single-read 51-bp sequencing was completed with Illumina TruSeq SBS kit v3-HS. Single-read 51-bp sequencing was completed with Illumina TruSeq SBS kit v3-HS.

tag: strain

value: bone marrow mononuclear cells

tag: treatment

value: MLL-AF9 (MSCVneo-MLL-AF9+MSCVpuro)


title: 2385 Control (MSCVneo +MSCVpuro) polyA RNA-Seq

value: Control (MSCVneo +MSCVpuro)


title: 2387 Control (MSCVneo +MSCVpuro) polyA RNA-Seq


title: 1216 Control (MSCVneo +MSCVpuro) polyA RNA-Seq


title: 2390 MLL-AF9 (MSCVneo-MLL-AF9+MSCVpuro) polyA RNA-Seq


title: 5hmC enriched DNA from MLL-AF9 (MSCVneo-MLL-AF9+MSCVpuro) treated cells


title: 5hmC enriched DNA from Control (MSCVneo +MSCVpuro) treated cells


title: 1303 MLL-AF9 (MSCVneo-MLL-AF9+MSCVpuro) polyA RNA-Seq


title: Total DNA control - PcrA

status: Public on Dec 13 2015

city: Seattle

first: Christopher

last: Merrikh

state: WA

address: 1705 NE Pacific St.

department: Microbiology Department

institute: University of Washington

description: Total DNA (PcrA depleted)

data_processing:
Paired-end mapping was conducted using Bowtie2
Samtools mpileup function was used to produce wiggle files from .sam/.bam files
Wiggle files were normalized to by total signal (i.e. The signal at each nt position was divided by the total signal times a multiplier.)
Data were cleaned to remove artificial peaks (i.e. shoulderless peaks less than 15 nt in width - these were validated as artificial peaks by qPCR)
Differential signal was calculated by subtracting the signal at each nt position in the total sample from the corresponding position in the ChIP sample.
The resulting ChIP-total wiggle files were further compared for the + IPTG and -IPTG conditions by subtracting the signal at each nt position in the - IPTG from the + IPTG condition.
Genome_build: Genbank CP007800.1
Supplementary_files_format_and_content: wiggle file format (.wig)

organism: Bacillus subtilis subsp. subtilis str. JH642

source_name: Strain HM448

growth_protocol: Cells were grown to mid-log then diluted back to OD 0.1 in LB medium at 30 degrees. At ~ OD 0.20 the culture was split in half and cells were either left untreated, or IPTG was added to 1mM to induce the adaptor protein SspB.

extract_protocol:
Cells were lysed in solution A + 1 mg/ml lysozyme, then sonicated and spun to clear the extract.
Libraries were prepped by the University of Washington High Throughput Sequencing Facility

treatment_protocol: Plus or minus IPTG, crosslinked with 1% formaldehyde for 20 minutes at room temperature, then quenched with glycine.

value: pcrA::pcrA-ssrA  thrC::Pspank(hy)-sspB


title: Input DNA from Control (MSCVneo +MSCVpuro) treated cells


title: Myc Control ChIP in WT

description: Myc control ChIP in a strain lacking the Myc epitope

source_name: Strain HM1

growth_protocol: Cells were grown to mid-log then diluted back to OD 0.1 in LB medium supplemented with IPTG at 30 degrees

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 20 minutes at room temperature

value: Untagged


title: DnaC ChIP + PcrA

description: DnaC localization in the presence of PcrA


title: Myc Control Total DNA

description: Total DNA from WT cells


title: MycPcrA Total DNA

description: Total DNA from Myc-PcrA cells

source_name: Strain HM224

value: c-Myc


title: MycPcrA ChIP

description: PcrA localization


title: DnaC ChIP - PcrA

description: DnaC localization in the absence of PcrA


title: pre-iPS_rep.RNA-Seq

city: Shanghai

first: Xiaobai

last: Zhang

address: 1239 Siping Road

institute: Tongji University

data_processing:
ChIP-Seq reads were aligned to the mouse mm9 reference genome using Bowtie (version 1.0.1). Only uniquely aligned reads with no more than two mismatches were used for the subsequent analysis.
Nucleosome locations, including histone modified nucleosomes, were predicted by GeneTrack.
Tophat (version 2.0.4) was used to map the RNA-seq reads to the mouse mm9 reference genome. Only the uniquely mapped reads were used for subsequent analysis.
Cufflinks (version 2.0.2) was employed to calculate the expression abundances and identify the differentially expressed genes (FDR<0.05).
Genome_build: mm9
Supplementary_files_format_and_content: For H3, H3K4me3, H3K27me3 and H3K9me3 ChIP-Seq data, processed data files are tab-delimited files with enriched peaks predicted by GeneTrack. For CTCF ChIP-Seq data, processed data files are tab-delimited text files with enriched peaks predicted by MACS. For RNA-Seq data, processed data files are tab-delimited files showing gene expresssion levels with FPKM.

source_name: intermediate stage of somatic cell reprogramming

growth_protocol: MEFs were derived from day13.5 embryos (e13.5) hemizygous of Oct4-GFP transgenic allele and Rosa26 allele and were maintained in fibroblast medium: DMEM supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine, and 1% non-essential amino acid (NEAA). iPSCs were routinely expanded on MEF feeder layers (MEFs inactivated with mitomycin C) in FBS-containing medium (mES). mES medium consisted of DMEM supplemented with 15% FBS, 1% L-glutamine, 1% NEAA, 1% sodium pyruvate, 1% penicillin/ streptomycin, 1 mM β-mercaptoethanol, and 1000 units/ml leukemia inhibitory factor (LIF).

extract_protocol:
Mononucleosomes were prepared according to Cell Signaling SimpleChIP® Enzymatic Chromatin IP protocols. For MNase-ChIP, 18 μg nucleosomes were incubated with 10 μg antibodies for each immunoprecipitation overnight at 4°C. 30 μl protein G dynabeads were then added for 2 hr at 4°C with rotation. Immune complexes were washed with low salt wash buffer three times and high salt wash buffer once. Mononucleosomes were eluted twice from the protein G magnetic beads and reversecrosslinked with addition of 12 μl 5 M NaCl and 4 μl 20 mg/ml protease kinase (PK) and overnight incubation at 65°C. Then the ChIPed DNA was purified with MinElute PCR purification Kits (Qiagen) and quantitated by Quant-iTTM Picogreen® dsDNA reagent (Invitrogen). Regular ChIP-seq for H3, H3K4me3, H3K27e3, H3K9me3 and CTCF was performed as described in a previous study (Huang et al., 2013). For RNA-Seq, cultured cells were harvested and dissolved in Trizol for total RNA extraction and treated with DNase I (Ambion) to remove any potential contaminated DNA fraction.
We generated ChIP-seq libraries by using the ChIP-seq kit from Illlumina. For nucleosome preparation, we excised the band between 220-370 bp. For the libraries from CTCF, we excised the bands between 300-500 bp. For RNA-Seq, the library generation and sequencing were conducted by Beijing Genome Institutes (BGI) in Shenzhen.

treatment_protocol: Retrovirus production and generation of pre-iPSCs and iPSCs were described previously (Chen et al., 2013). Embryo-derived mouse embryonic fibroblasts were maintained and cultured for no more than three passages before preparing for RNA sequencing (RNA-seq). Pre-iPSCs and iPSCs were cultured for 6 passages, respectively, before RNA-seq.


title: iPS_rep.H3K4me3.ChIP-Seq

source_name: induced pluripotent stem cells

value: induced pluripotent stem cells

value: anti-Histone H3K4me3 antibody (ab8580, ChIP grade)


title: MEF_rep.RNA-Seq

source_name: mouse embryo fibroblasts

value: Embryo-derived mouse embryonic fibroblasts


title: iPS_rep.H3.MNase-ChIP-Seq

value: Mnase-ChIP with anti-Histone H3 antibody (ab1791, ChIP grade)


title: iPS_rep.H3K27me3.ChIP-Seq

value: anti-Histone H3K27me3 antibody (ab6002, ChIP grade)


title: pre-iPS_rep.H3K4me3.ChIP-Seq

value: intermediate stage of somatic cell reprogramming


title: pre-iPS_rep.H3K27me3.ChIP-Seq


title: MEF_rep.H3.MNase-ChIP-Seq


title: MEF_rep.H3K27me3.ChIP-Seq


title: MEF_rep.H3K4me3.ChIP-Seq


title: Total DNA control + PcrA

description: Total DNA (PcrA present)


title: iPS.H3K27me3.ChIP-Seq

data_processing:
ChIP-Seq reads were aligned to the mouse mm9 reference genome using Bowtie. Only uniquely aligned reads with no more than two mismatches were used for the subsequent analysis.
Nucleosome locations, including histone modified nucleosomes, were predicted by GeneTrack.
Enriched intervals of CTCF were identified by MACS using a P-value cutoff of 10−4.
Tophat (version 2.0.4) was used to map the RNA-seq reads to the mouse mm9 reference genome. Only the uniquely mapped reads were used for subsequent analysis.
Cufflinks (version 2.0.2) was employed to calculate the expression abundances and identify the differentially expressed genes (FDR<0.05).
Genome_build: mm9
Supplementary_files_format_and_content: For H3, H3K4me3, H3K27me3 and H3K9me3 ChIP-Seq data, processed data files are tab-delimited files with enriched peaks predicted by GeneTrack. For CTCF ChIP-Seq data, processed data files are tab-delimited text files with enriched peaks predicted by MACS. For RNA-Seq data, processed data files are tab-delimited files showing gene expresssion levels with FPKM.

extract_protocol:
Mononucleosomes were prepared according to Cell Signaling SimpleChIP® Enzymatic Chromatin IP protocols. For MNase-ChIP, 18 μg nucleosomes were incubated with 10 μg antibodies for each immunoprecipitation overnight at 4°C. 30 μl protein G dynabeads were then added for 2 hr at 4°C with rotation. Immune complexes were washed with low salt wash buffer three times and high salt wash buffer once. Mononucleosomes were eluted twice from the protein G magnetic beads and reversecrosslinked with addition of 12 μl 5 M NaCl and 4 μl 20 mg/ml protease kinase (PK) and overnight incubation at 65°C. Then the ChIPed DNA was purified with MinElute PCR purification Kits (Qiagen) and quantitated by Quant-iTTM Picogreen® dsDNA reagent (Invitrogen). Regular ChIP-seq for H3, H3K4me3, H3K27e3, H3K9me3 and CTCF was performed as described in a previous study (Huang et al., 2013). For RNA-Seq, cultured cells were harvested and dissolved in Trizol for total RNA extraction and treated with DNase I (Ambion) to remove any potential contaminated DNA fraction.
We generated ChIP-seq libraries by using the ChIP-seq kit from Illlumina. For nucleosome preparation, we excised the band between 220-370 bp. For the libraries from CTCF, we excised the bands between 300-500 bp. For RNA-Seq, the library generation and sequencing were conducted by Beijing Genome Institutes (BGI) in Shenzhen.
ChIP-Seq for Samples 1-15, and RNA-Seq for Samples 16-18

tag: genetic background

value: CBA/CaJ  and C57BL/6J


title: iPS.H3K9me3.ChIP-Seq

value: anti-Histone H3K9me3 antibody (ab8898, ChIP grade)


title: iPS.RNA-Seq


title: iPS.H3.MNase-ChIP-Seq


title: pre-iPS.H3K9me3.ChIP-Seq


title: iPS.H3K4me3.ChIP-Seq


title: pre-iPS.RNA-Seq


title: MEF.RNA-Seq


title: iPS_rep.RNA-Seq


title: pre-iPS.H3.MNase-ChIP-Seq


title: MEF.H3.MNase-ChIP-Seq


title: pre-iPS.H3K4me3.ChIP-Seq


title: MEF.H3K4me3.ChIP-Seq


title: MEF.H3K27me3.ChIP-Seq


title: MEF.H3K9me3.ChIP-Seq


title: pre-iPS.H3K27me3.ChIP-Seq


title: pre-iPS_rep.H3.MNase-ChIP-Seq


title: MCF7_E2_Input

status: Public on Dec 12 2015

city: Huddinge

first: Karin

last: Dahlman-Wright

address: Blickagången 16

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

description: DNA from MCF7 cells treated with E2

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.9 with the default configurations
peaks were called using MACS Peak Calling with default setting
PeakAnalyzer_1.4 was used to annotate peaks
Genome_build: hg19
Supplementary_files_format_and_content: ERa_Input_peaks.bed: During Peak calling ERa_E2 was treated as Chip and Input as control.

source_name: MCF breast cancer cells

growth_protocol: The human breast cancer cell line MCF7 was maintained in DMEM medium  supplemented with 10% fetal bovine serum (FBS) (Invitrogen) at 37°C, under a humidified atmosphere of 5% carbon dioxide.

extract_protocol:
Standard Illumina DNA library construction
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were fixed with 1% formaldehyde for 10 minutes, then glycine-quenched and harvested

value: ERalpha-positive breast cancer cells


title: MCF7_ERa_E2_ChIP

description: ERalpha antibody used in MCF7 cells treated with E2

value: ERalpha (H-20, Santa Cruz)


title: LN3 [Exome-seq]

city: Doha

first: Najeeb

last: Halabi

address: Education City

country: Qatar

institute: Weill Cornell Medicine in Qatar

description: Processed data file: P3_LN.txt

data_processing:
Library strategy: Exome-Seq
Base calling: Illumina OLB (version 1.9.3).
Alignment: BWA,version 0.7.9a, bwa mem -t 4
Deduplication: Picard mark duplicates, version 1.110
Realignment: GenomeAnalysisTK-3.1-1, $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T RealignerTargetCreator -o ${LETTER}.intervals --known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero    $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T IndelRealigner -targetIntervals ${LETTER}.intervals -o ${LETTER}_sorted_rg_realigned.bam -known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 9
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.

source_name: Lymph node tumor

extract_protocol:
QIAGEN AllPrep DNA and RNA extraction kit.
SureSelect Human All Exon (Part No. G3362B, Agilent Technologies, Santa Clara, CA).

value: lymph node metastasis

tag: tumor site

value: lymph node

tag: patient identifier


title: PE2 [Exome-seq]

description: Processed data file: P2_PE.txt

data_processing:
Library strategy: Exome-Seq
Base calling: Illumina OLB (version 1.9.3).
Alignment: BWA,version 0.7.9a, bwa mem -t 4
Deduplication: Picard mark duplicates, version 1.110
Realignment: GenomeAnalysisTK-3.1-1, $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T RealignerTargetCreator -o ${LETTER}.intervals --known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero    $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T IndelRealigner -targetIntervals ${LETTER}.intervals -o ${LETTER}_sorted_rg_realigned.bam -known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 23
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.

source_name: Peritoneum tumor

value: peritoneum metastasis

value: peritoneum


title: OV3 [Exome-seq]

description: Processed data file: P3_OV.txt

data_processing:
Library strategy: Exome-Seq
Base calling: Illumina OLB (version 1.9.3).
Alignment: BWA,version 0.7.9a, bwa mem -t 4
Deduplication: Picard mark duplicates, version 1.110
Realignment: GenomeAnalysisTK-3.1-1, $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T RealignerTargetCreator -o ${LETTER}.intervals --known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero    $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T IndelRealigner -targetIntervals ${LETTER}.intervals -o ${LETTER}_sorted_rg_realigned.bam -known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 17
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.

source_name: Ovarian tumor

value: primary epithelial ovarian tumor

value: ovary


title: LN2 [Exome-seq]

description: Processed data file: P2_LN.txt

data_processing:
Library strategy: Exome-Seq
Base calling: Illumina OLB (version 1.9.3).
Alignment: BWA,version 0.7.9a, bwa mem -t 4
Deduplication: Picard mark duplicates, version 1.110
Realignment: GenomeAnalysisTK-3.1-1, $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T RealignerTargetCreator -o ${LETTER}.intervals --known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero    $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T IndelRealigner -targetIntervals ${LETTER}.intervals -o ${LETTER}_sorted_rg_realigned.bam -known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 7
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.


title: PE3 [Exome-seq]

description: Processed data file: P3_PE.txt

data_processing:
Library strategy: Exome-Seq
Base calling: Illumina OLB (version 1.9.3).
Alignment: BWA,version 0.7.9a, bwa mem -t 4
Deduplication: Picard mark duplicates, version 1.110
Realignment: GenomeAnalysisTK-3.1-1, $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T RealignerTargetCreator -o ${LETTER}.intervals --known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero    $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T IndelRealigner -targetIntervals ${LETTER}.intervals -o ${LETTER}_sorted_rg_realigned.bam -known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 25
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.


title: PE1 [Exome-seq]

description: Processed data file: P1_PE.txt

data_processing:
Library strategy: Exome-Seq
Base calling: Illumina OLB (version 1.9.3).
Alignment: BWA,version 0.7.9a, bwa mem -t 4
Deduplication: Picard mark duplicates, version 1.110
Realignment: GenomeAnalysisTK-3.1-1, $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T RealignerTargetCreator -o ${LETTER}.intervals --known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero    $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T IndelRealigner -targetIntervals ${LETTER}.intervals -o ${LETTER}_sorted_rg_realigned.bam -known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 21
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.


title: OV1 [Exome-seq]

description: Processed data file: P1_OV.txt

data_processing:
Library strategy: Exome-Seq
Base calling: Illumina OLB (version 1.9.3).
Alignment: BWA,version 0.7.9a, bwa mem -t 4
Deduplication: Picard mark duplicates, version 1.110
Realignment: GenomeAnalysisTK-3.1-1, $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T RealignerTargetCreator -o ${LETTER}.intervals --known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero    $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T IndelRealigner -targetIntervals ${LETTER}.intervals -o ${LETTER}_sorted_rg_realigned.bam -known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 13
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.


title: LN1 [Exome-seq]

description: Processed data file: P1_LN.txt

data_processing:
Library strategy: Exome-Seq
Base calling: Illumina OLB (version 1.9.3).
Alignment: BWA,version 0.7.9a, bwa mem -t 4
Deduplication: Picard mark duplicates, version 1.110
Realignment: GenomeAnalysisTK-3.1-1, $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T RealignerTargetCreator -o ${LETTER}.intervals --known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero    $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T IndelRealigner -targetIntervals ${LETTER}.intervals -o ${LETTER}_sorted_rg_realigned.bam -known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 5
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.


title: OV2 [Exome-seq]

description: Processed data file: P2_OV.txt

data_processing:
Library strategy: Exome-Seq
Base calling: Illumina OLB (version 1.9.3).
Alignment: BWA,version 0.7.9a, bwa mem -t 4
Deduplication: Picard mark duplicates, version 1.110
Realignment: GenomeAnalysisTK-3.1-1, $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T RealignerTargetCreator -o ${LETTER}.intervals --known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero    $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T IndelRealigner -targetIntervals ${LETTER}.intervals -o ${LETTER}_sorted_rg_realigned.bam -known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 15
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.


title: LN3 [RNA-seq]

description: Processed data file: P3_LN.txt

data_processing:
Base calling: Illumina RTA (version 1.12.4.2).
Alignment: RNA STAR, 2.4.1b, $PATH_STAR/STAR --readFilesIn $DATAPATH/${READ1n}_R1.fastq $DATAPATH/${READ1n}_R2.fastq --runThreadN 4 --genomeDir $PATH_GENOME --outFileNamePrefix $RESULTPATH/${RESULTNAME}2pass --genomeLoad NoSharedMemory --sjdbGTFfile $PATH_ANNO --outSAMtype BAM SortedByCoordinate --twopassMode Basic
Deduplication: Picard mark duplicates, version 1.110
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 10
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.

extract_protocol:
QIAGEN AllPrep DNA and RNA extraction kit.
Ovation RNA-Seq System V2 (Part No. 7102, Nugen Technologies, San Carlos, CA).


title: PE3 [RNA-seq]

description: Processed data file: P3_PE.txt

data_processing:
Base calling: Illumina RTA (version 1.12.4.2).
Alignment: RNA STAR, 2.4.1b, $PATH_STAR/STAR --readFilesIn $DATAPATH/${READ1n}_R1.fastq $DATAPATH/${READ1n}_R2.fastq --runThreadN 4 --genomeDir $PATH_GENOME --outFileNamePrefix $RESULTPATH/${RESULTNAME}2pass --genomeLoad NoSharedMemory --sjdbGTFfile $PATH_ANNO --outSAMtype BAM SortedByCoordinate --twopassMode Basic
Deduplication: Picard mark duplicates, version 1.110
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 26
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.


title: OV3 [RNA-seq]

description: Processed data file: P3_OV.txt

data_processing:
Base calling: Illumina RTA (version 1.12.4.2).
Alignment: RNA STAR, 2.4.1b, $PATH_STAR/STAR --readFilesIn $DATAPATH/${READ1n}_R1.fastq $DATAPATH/${READ1n}_R2.fastq --runThreadN 4 --genomeDir $PATH_GENOME --outFileNamePrefix $RESULTPATH/${RESULTNAME}2pass --genomeLoad NoSharedMemory --sjdbGTFfile $PATH_ANNO --outSAMtype BAM SortedByCoordinate --twopassMode Basic
Deduplication: Picard mark duplicates, version 1.110
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 18
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.


title: PE2 [RNA-seq]

description: Processed data file: P2_PE.txt

data_processing:
Base calling: Illumina RTA (version 1.12.4.2).
Alignment: RNA STAR, 2.4.1b, $PATH_STAR/STAR --readFilesIn $DATAPATH/${READ1n}_R1.fastq $DATAPATH/${READ1n}_R2.fastq --runThreadN 4 --genomeDir $PATH_GENOME --outFileNamePrefix $RESULTPATH/${RESULTNAME}2pass --genomeLoad NoSharedMemory --sjdbGTFfile $PATH_ANNO --outSAMtype BAM SortedByCoordinate --twopassMode Basic
Deduplication: Picard mark duplicates, version 1.110
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 24
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.


title: OE [RNA-seq]

description: Processed data file: OE.txt

data_processing:
Base calling: Illumina RTA (version 1.17.20).
Alignment: RNA STAR, 2.4.1b, $PATH_STAR/STAR --readFilesIn $DATAPATH/${READ1n}_R1.fastq $DATAPATH/${READ1n}_R2.fastq --runThreadN 4 --genomeDir $PATH_GENOME --outFileNamePrefix $RESULTPATH/${RESULTNAME}2pass --genomeLoad NoSharedMemory --sjdbGTFfile $PATH_ANNO --outSAMtype BAM SortedByCoordinate --twopassMode Basic
Deduplication: Picard mark duplicates, version 1.110
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 12
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.

source_name: Ovarian epithelial cells

extract_protocol:
QIAGEN AllPrep DNA and RNA extraction kit.
Ovation Single Cell RNA-Seq System (Part No. 0342, Nugen Technologies, Inc., San Carlos, CA).

value: OE

value: normal ovarian epithelial cell line


title: PE1 [RNA-seq]

description: Processed data file: P1_PE.txt

data_processing:
Base calling: Illumina RTA (version 1.12.4.2).
Alignment: RNA STAR, 2.4.1b, $PATH_STAR/STAR --readFilesIn $DATAPATH/${READ1n}_R1.fastq $DATAPATH/${READ1n}_R2.fastq --runThreadN 4 --genomeDir $PATH_GENOME --outFileNamePrefix $RESULTPATH/${RESULTNAME}2pass --genomeLoad NoSharedMemory --sjdbGTFfile $PATH_ANNO --outSAMtype BAM SortedByCoordinate --twopassMode Basic
Deduplication: Picard mark duplicates, version 1.110
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 22
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.


title: OV2 [RNA-seq]

description: Processed data file: P2_OV.txt

data_processing:
Base calling: Illumina RTA (version 1.12.4.2).
Alignment: RNA STAR, 2.4.1b, $PATH_STAR/STAR --readFilesIn $DATAPATH/${READ1n}_R1.fastq $DATAPATH/${READ1n}_R2.fastq --runThreadN 4 --genomeDir $PATH_GENOME --outFileNamePrefix $RESULTPATH/${RESULTNAME}2pass --genomeLoad NoSharedMemory --sjdbGTFfile $PATH_ANNO --outSAMtype BAM SortedByCoordinate --twopassMode Basic
Deduplication: Picard mark duplicates, version 1.110
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 16
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.


title: LN1 [RNA-seq]

description: Processed data file: P1_LN.txt

data_processing:
Base calling: Illumina RTA (version 1.12.4.2).
Alignment: RNA STAR, 2.4.1b, $PATH_STAR/STAR --readFilesIn $DATAPATH/${READ1n}_R1.fastq $DATAPATH/${READ1n}_R2.fastq --runThreadN 4 --genomeDir $PATH_GENOME --outFileNamePrefix $RESULTPATH/${RESULTNAME}2pass --genomeLoad NoSharedMemory --sjdbGTFfile $PATH_ANNO --outSAMtype BAM SortedByCoordinate --twopassMode Basic
Deduplication: Picard mark duplicates, version 1.110
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 6
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.


title: LN2 [RNA-seq]

description: Processed data file: P2_LN.txt

data_processing:
Base calling: Illumina RTA (version 1.12.4.2).
Alignment: RNA STAR, 2.4.1b, $PATH_STAR/STAR --readFilesIn $DATAPATH/${READ1n}_R1.fastq $DATAPATH/${READ1n}_R2.fastq --runThreadN 4 --genomeDir $PATH_GENOME --outFileNamePrefix $RESULTPATH/${RESULTNAME}2pass --genomeLoad NoSharedMemory --sjdbGTFfile $PATH_ANNO --outSAMtype BAM SortedByCoordinate --twopassMode Basic
Deduplication: Picard mark duplicates, version 1.110
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 8
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.


title: OV1 [RNA-seq]

description: Processed data file: P1_OV.txt

data_processing:
Base calling: Illumina RTA (version 1.12.4.2).
Alignment: RNA STAR, 2.4.1b, $PATH_STAR/STAR --readFilesIn $DATAPATH/${READ1n}_R1.fastq $DATAPATH/${READ1n}_R2.fastq --runThreadN 4 --genomeDir $PATH_GENOME --outFileNamePrefix $RESULTPATH/${RESULTNAME}2pass --genomeLoad NoSharedMemory --sjdbGTFfile $PATH_ANNO --outSAMtype BAM SortedByCoordinate --twopassMode Basic
Deduplication: Picard mark duplicates, version 1.110
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 14
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.


title: FB [RNA-seq]

description: Processed data file: FB.txt

data_processing:
Base calling: Illumina RTA (version 1.17.20).
Alignment: RNA STAR, 2.4.1b, $PATH_STAR/STAR --readFilesIn $DATAPATH/${READ1n}_R1.fastq $DATAPATH/${READ1n}_R2.fastq --runThreadN 4 --genomeDir $PATH_GENOME --outFileNamePrefix $RESULTPATH/${RESULTNAME}2pass --genomeLoad NoSharedMemory --sjdbGTFfile $PATH_ANNO --outSAMtype BAM SortedByCoordinate --twopassMode Basic
Deduplication: Picard mark duplicates, version 1.110
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 2
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.

source_name: Fibroblasts

value: FB

value: normal fibroblast cell line


title: GC [RNA-seq]

description: Processed data file: GC.txt

data_processing:
Base calling: Illumina RTA (version 1.17.20).
Alignment: RNA STAR, 2.4.1b, $PATH_STAR/STAR --readFilesIn $DATAPATH/${READ1n}_R1.fastq $DATAPATH/${READ1n}_R2.fastq --runThreadN 4 --genomeDir $PATH_GENOME --outFileNamePrefix $RESULTPATH/${RESULTNAME}2pass --genomeLoad NoSharedMemory --sjdbGTFfile $PATH_ANNO --outSAMtype BAM SortedByCoordinate --twopassMode Basic
Deduplication: Picard mark duplicates, version 1.110
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 4
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.

value: ovarian tumor cell line


title: OE [Exome-seq]

description: Processed data file: OE.txt

data_processing:
Library strategy: Exome-Seq
Base calling: Illumina RTA (version 1.17.20).
Alignment: BWA,version 0.7.9a, bwa mem -t 4
Deduplication: Picard mark duplicates, version 1.110
Realignment: GenomeAnalysisTK-3.1-1, $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T RealignerTargetCreator -o ${LETTER}.intervals --known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero    $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T IndelRealigner -targetIntervals ${LETTER}.intervals -o ${LETTER}_sorted_rg_realigned.bam -known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 11
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.

extract_protocol:
QIAGEN AllPrep DNA and RNA extraction kit.
SureSelectXT2 Human All Exon V5 (Part No. 5190-6217, Agilent Technologies, Santa Clara, CA).


title: SK [RNA-seq]

description: Processed data file: SK.txt

data_processing:
Base calling: Illumina RTA (version 1.17.20).
Alignment: RNA STAR, 2.4.1b, $PATH_STAR/STAR --readFilesIn $DATAPATH/${READ1n}_R1.fastq $DATAPATH/${READ1n}_R2.fastq --runThreadN 4 --genomeDir $PATH_GENOME --outFileNamePrefix $RESULTPATH/${RESULTNAME}2pass --genomeLoad NoSharedMemory --sjdbGTFfile $PATH_ANNO --outSAMtype BAM SortedByCoordinate --twopassMode Basic
Deduplication: Picard mark duplicates, version 1.110
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 28
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.


title: FB [Exome-seq]

description: Processed data file: FB.txt

data_processing:
Library strategy: Exome-Seq
Base calling: Illumina RTA (version 1.17.20).
Alignment: BWA,version 0.7.9a, bwa mem -t 4
Deduplication: Picard mark duplicates, version 1.110
Realignment: GenomeAnalysisTK-3.1-1, $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T RealignerTargetCreator -o ${LETTER}.intervals --known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero    $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T IndelRealigner -targetIntervals ${LETTER}.intervals -o ${LETTER}_sorted_rg_realigned.bam -known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 1
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.


title: GC [Exome-seq]

description: Processed data file: GC.txt

data_processing:
Library strategy: Exome-Seq
Base calling: Illumina RTA (version 1.17.20).
Alignment: BWA,version 0.7.9a, bwa mem -t 4
Deduplication: Picard mark duplicates, version 1.110
Realignment: GenomeAnalysisTK-3.1-1, $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T RealignerTargetCreator -o ${LETTER}.intervals --known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero    $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T IndelRealigner -targetIntervals ${LETTER}.intervals -o ${LETTER}_sorted_rg_realigned.bam -known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 3
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.


title: P2 [Exome-seq]

description: This Sample provided information to prepare the processed data for the other patient samples (basically to determine what variation is somatic and what is germline).

data_processing:
Library strategy: Exome-Seq
Base calling: Illumina RTA (version 1.17.20).
Alignment: BWA,version 0.7.9a, bwa mem -t 4
Deduplication: Picard mark duplicates, version 1.110
Realignment: GenomeAnalysisTK-3.1-1, $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T RealignerTargetCreator -o ${LETTER}.intervals --known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero    $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T IndelRealigner -targetIntervals ${LETTER}.intervals -o ${LETTER}_sorted_rg_realigned.bam -known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 20
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.

source_name: Normal ovary

value: normal ovary


title: P1 [Exome-seq]

data_processing:
Library strategy: Exome-Seq
Base calling: Illumina RTA (version 1.17.20).
Alignment: BWA,version 0.7.9a, bwa mem -t 4
Deduplication: Picard mark duplicates, version 1.110
Realignment: GenomeAnalysisTK-3.1-1, $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T RealignerTargetCreator -o ${LETTER}.intervals --known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero    $PATH_JAVA/java -Xmx4g -Djava.io.tmpdir=$PATH_SCRATCH -jar $PATH_GATK/GenomeAnalysisTK.jar -I ${LETTER}_sorted_rg2.bam -R $PATH_GATKBUNDLE/ucsc.hg19.fasta -T IndelRealigner -targetIntervals ${LETTER}.intervals -o ${LETTER}_sorted_rg_realigned.bam -known $PATH_GATKBUNDLE/Mills_and_1000G_gold_standard.indels.hg19.vcf --read_filter MappingQualityZero
Filter map quality: samtools view -b -q 20 ${name} > ${shortname}_m20.bam
Variant calls: VarScan.v2.3.7.jar mpileup2snp --min-coverage 5 --min-reads2 0 --min-avg-qual 20 --min-var-freq 0 --output-vcf 19
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files containing reference allele fraction differences for every variant where exome and RNA data exists. In addition to the differences, the chromosomal location, rsid, impact, gene, exome and rna read counts, allele fractions and p-values are given.


title: Mouse 9 month astro

status: Public on Dec 11 2015

first: Steven

last: Sloan

address: 615 Michael Street, Whitehead Building Room 375

data_processing:
The FASTQ files were first groomed using the FASTQ groomer and then mapped using TopHat2, which invokes Bowtie as an internal read mapper (Trapnell et al., 2009). The paired end option was selected and human genome version 19 (hg19) was used as the reference genome. We then ran Cufflinks to assemble transcripts and estimate expression level as fragments per kilobase of transcript sequence per million mapped fragments (FPKM) (Trapnell et al., 2010).
Genome_build: Hg19 or mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Mouse cortex

extract_protocol:
Tissue was dissociated in papain (30units / ml) for 1.5 hours before trituration. Cells were immunopanned on a sequence of plates in the following order: CD45 --> GalC --> GalC --> Thy1 --> HepaCAM. Cells bound to HepaCAM plate were then scraped in Qiazol to harvest RNA
Nugen Ovation V2 kit (7102-32), followed by sonication in the Covaris machine, followed by indexing with NEB Next Ultra kit (E7530L)

tag: age

value: post natal day 270

tag: cell subtype

value: HepaCAM positive cells

value: Astrocyte


title: Mouse 1 month astro

value: post natal day 30

tag: cell type


title: HeLa E2F7_normoxia

city: Utrecht

first: Michal

last: Mokry

address: Lundlaan 6

institute: Wilhelmina Children's Hospital, University Medical Center Utrecht

description: ChIP DNA

data_processing:
Sequencing reads were mapped against the reference genome (hg19 assembly, NCBI build 37) using BWA package
Multiple reads mapping to same location and strand have been collapsed to single read and only uniquely placed reads were used for peak-calling. Cisgenome was used for peak-calling from the ChIP-seq data.
Genome_build: hg19
Supplementary_files_format_and_content: peak coordinates file : number_chromosome_start_end_length_fold-enrichment

growth_protocol: The cervical cancer (HeLa) cell line was cultured in DMEM (Invitrogen, 41966-052) supplemented with 10% FBS (Lonza, DE14-802F) and 1% Penicillin/Streptomycin (Lonza, DE17-602E).

extract_protocol:
ChIP was performed according the EZ ChIP protocol (Upstate, 17-371) with the following specifications: HeLa cells were seeded at day 1 at a concentration of 7x10^6 cells per 145mm plate. Next day, cells were cultured overnight in hypoxia, or continued to grow under normoxia, and harvested on day 3. For single and double ChIP, 5 145mm plates were used per condition. In vitro crosslinking was performed on a shaker at room temperature (RT) for 10 minutes, using 1% freshly made paraformaldehyde. Crosslinking was quenched for 5 minutes incubation at RT on a shaker. Next, cells were washed twice on ice with PBS (40C, supplemented with protease inhibitors (11873580001, Roche)), and harvested, pelleted and resuspended in 2ml lysis buffer (0.3% SDS, 10mM EDTA, 50mM Tris and protease inhibitors). Sonication (10 cycles of 10 seconds followed by 1 minute incubation on ice) was performed in a FACS tubes using a Soniprep 150 sonicator (MSE). 10µl of sonicated sample was analyzed on gel to check for sonication efficiency. Sonicated lysates were centrifugated (10 minutes, 40C) to remove insoluble components and large DNA fragments. 200µL lysate was used per ChIP sample. The DNA concentration in the sonicated lysate was measure using a Nanodrop to normalize the amount of input DNA between normoxic and hypoxic ChIP samples. Protein G agarose beads (16-266, Milipore) were coated overnight in 0,1% BSA (Sigma, A3294), and 60 µL was used for pre-clear (2h, 40C) and final precipitation of immune complexes (1h, 40C). For single ChIP 5µg and for double ChIP 10g was used. immunorecipitation were performed overnight at 40C on a rotating platform. In case of double ChIP, eluates were diluted in dilution buffer and incubated with another 10ug of antibody overnight. The following antibodies were used: ChIP grade HIF1α (ab2185, Abcam) E2F7 (sc-66870), E2F1 (sc-193), IgG (2729S; cell signaling). De-crosslinked DNA was purified over a column (Qiagen, 28106) and eluted in 65 µl H2O
immunoprecipitated chromatin was sheared, end-repaired, sequencing adaptors were ligated and the library was amplified by ligation mediated PCR (LMPCR). After LMPCR, the library was purified and checked for the proper size range and for the absence of adaptor dimers on a 2% agarose gel, barcoded and sequenced on SOLiD/AB sequencer in multiplexed way to produce 50-bp long reads.

tag: cell line

value: HeLa

tag: antibody

value: E2F7 (sc-66870, Santa Cruz Biotechnology)