title: SLL-03 H3K27ac

status: Public on Aug 04 2015

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Paired-end sequencing of H3K27ac ChIP and an unenriched chromatin control library was performed on a HiSeq 2500 or NextSeq for all primary lymphoma samples and for 8 cell lines, with read lengths of 36 bp + 25 bp or 42 bp + 42 bp. Single-end sequencing was used for other samples.
Reads were aligned to hg19 using BWA.
The resulting alignment files were then filtered to remove PCR duplicates and reads mapping to >2 sites genome-wide
ChIP-Seq density tracks were generated with ‘igvtools count’ and visualized with IGV.
Genome_build: hg19
Supplementary_files_format_and_content: TDF density files were generated by igvtools

source_name: SLL-03 H3K27ac

growth_protocol: Cell lines were grown in IMDM + 20% FCS (Oci-Ly-7 and Oci-Ly-1) or RPMI + 20% FCS (all others)

extract_protocol:
For histone modification and transcription factor ChIP-Seq in cell lines, 10-20 million cells were crosslinked in growth media + 1% formaldehyde for 10 minutes at 37 C, quenched for 5 minutes with 125 mM glycine, washed twice in cold PBS with protease inhibitors (complete PI, Roche), and stored at -80 C. Pellets were thawed and lysed in cold cytoplasmic lysis buffer (20 mM Tris-HCl ph8.0, 85 mM KCl, 0.5% NP 40 + PI). Nuclei were pelleted  at 3000g , resuspended in cold SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1 + PI) for 10 minutes, sonicated to an average fragment size of 200-400 bp on a Branson sonifier, and cleared of debris by centrifugation. Samples were diluted 1:10 in ChIP dilution buffer (0.01% SDS, 0.25% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl +PI), and rotated at 4 C overnight with 2-5 ug of the appropriate antibody. Antigen-antibody complexes were collected with protein G Dynabeads (Life technologies) for 4 hours at 4 C, and sequentially washed with RIPA buffer (0.1% Na deoxycholate, 0.1% SDS, 1% Triton x-100, 10mM Tris-HCl pH 8.0, 1mM EDTA, 140 Mm NaCl), RIPA/High salt (0.1% Na deoxycholate, 0.1% SDS, 1% Triton x-100, 10mM Tris-HCl pH 8.0, 1mM EDTA, 360 mM NaCl), LiCl Wash Buffer (250mM LiCl, 0.5% NP40, 0.5% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.0), and TE Buffer (10mM Tris-HCl pH 8.0, 1mM EDTA).  Beads were resuspended in Low SDS ChIP elution buffer (10mM Tris-HCl pH 8.0, 0.5M EDTA, 300mM NaCl, 0.1% SDS, 5mM DTT) and incubated for 6 hours at 65 C to elute DNA and reverse crosslinking. Samples were treated with RNAase for 30 minutes and proteinase K for 2 hours at 37 C. ChIP DNA was then purified from supernatants with AMPure beads (Beckman-Coulter). Input DNA was prepared in parallel by adding unenriched, diluted chromatin directly into the elution / reverse crosslinking step. For primary lymphoma samples, tumor cellularity from the frozen block was confirmed by H&E frozen section by a board-certified hematopathologist (RR), and the block was trimmed as needed to remove low tumor cellularity regions. 25 micron sections were then cut to a total of ~50 mg of tissue for each ChIP-Seq chromatin prep. Frozen sections were resuspended and dissociated in PBS + PI + 10 mM Na butyrate, formaldehyde was added to 1%, and crosslinking and quenching were performed as above. Subsequent steps were identical to those performed in cell lines except that 1) the cytoplasmic lysis step was omitted, and 2) following lysis in SDS lysis buffer, the sample was diluted 1:2 to 1:5 with ChIP dilution buffer prior to sonication, and to a final dilution of 1:10 afterwards. Prior to immunoprecipitation, DNA was quantified from sonicated chromatin, and an equivalent of 2-5 million cells was used per ChIP.
ChIP DNA was end-repaired (End-It, Epicentre), A-tailed (Klenow fragment 3'-->5' exo-, New England Biolabs), and ligated to barcoded illumina adaptors (Quick T4 DNA ligase, NEB). Each reaction was followed by clean-up with AMPure beads (Beckman-Coulter). Ligation products were amplified by PCR for 14-18 cycles with illumina primers and PFU Ultra II HS PCR mix (Agilent). Library size selection to 300-600 bp was performed by two-step AMPure bead selection or gel purification (E-Gel SizeSelect 2%, Life technologies).

treatment_protocol: See individual samples

tag: material type

value: Frozen lymphoma biopsy

tag: transgene

value: H3K27ac (39133, Active Motif)


title: SLL-02 Input

type: SRA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: SLL-02 Input

tag: treatment

tag: chip antibody


title: HGB-07 H3K27ac

source_name: HGB-07 H3K27ac


title: HGB-05 Input

source_name: HGB-05 Input


title: SLL-03 Input

source_name: SLL-03 Input


title: HGB-06 Input

source_name: HGB-06 Input


title: HGB-06 H3K27ac

source_name: HGB-06 H3K27ac


title: SLL-01 H3K27ac

source_name: SLL-01 H3K27ac


title: SLL-01 Input

source_name: SLL-01 Input


title: SLL-02 H3K27ac

source_name: SLL-02 H3K27ac


title: HGB-05 H3K27ac

source_name: HGB-05 H3K27ac


title: HGB-07 Input

source_name: HGB-07 Input


title: MCL-04 Input

source_name: MCL-04 Input


title: M23NDcovSplusLP-2

status: Public on Aug 05 2015

city: Notre Dame

first: Yunjuan

last: Bao

state: Indiana

address: 1234 Notre Dame Avenue

country: USA

institute: University of Notre Dame

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8
The reads were aligned to the annotated genome of S. pyogenes M23ND using BWA v0.7. Only uniquely mappable reads were retained.
The expression levels were evaluated by counting the reads uniquely mapping to the encoding regions of the annotated genes in the genome and calculated as RPKM by normalizing to the total uniquely mappable reads and gene lengths.
The gene differential expression was evaluated using DESeq package in R environments. The negative binomial test was used to assess the significance p-value of the differential expression and Benjamini-Hochberg procedure was used for multiple test correction.
Genome_build: CP008695 (Streptococcus pyogenes M23ND)
Supplementary_files_format_and_content: Excel file for the gene expression values and differential expression.

molecule: total RNA

organism: Streptococcus pyogenes

source_name: cell pellets

growth_protocol: covS- mutant strain and the isogenic covS+ derivative were grown in Todd-Hewitt broth supplemented with 0.2% yeast extract (THY; BD-Difco) at 37°C under aerobic conditions. Cells were collected at logarithm phase (OD600=0.6) and stationary phase (OD600=1.0).

extract_protocol:
The cell pellets were harvested by centrifuge at 10,000 rpm for 5 minutes. Total RNA was isolated and purified from the cell pellets using the DNeasy Blood & Tissue Kit (GIAGEN) according to the manufacture’s protocol.
The library was constructed using the Epicentre ScriptSeq v2 Complete Kit (Bacteria) and protocol companion (Illumina, Inc., San Diego, CA). Briefly, the total RNA was treated with rRNA-depletion using the Ribo-Zero rRNA removal solution specifically for gram-positive organisms. The remaining RNA was purified using Agencourt AMPure XP Beads, then heat fragmented at 85°C for 5 minutes. The ends of the fragments were reparied and ligated with adapters. The ligated fragments were PCR amplified and library fragments of ~200 bp band were isolated from the gel. The pair-end 2x79bp sequencing was performed using the Illlumina Miseq platform and Miseq Reagent Kit v3 (Illumina, Inc).

treatment_protocol: The cells were digested with mutanolysin (500u/ml) in 300lm spheroplasting buffer (20mM Tris-HCl pH6.8, 10mM MgCl2, 56% raffinose) and incubated with 100mg/ml chloramphenicol at 37’C for 60 minutes.

tag: strain

tag: genotype

tag: growth

value: Logarithm phase

tag: biological replicate

value: Replicate 2


title: MCL-03 Input

source_name: MCL-03 Input


title: 5hmC_MEF_p5

city: Torino

first: Francesco

last: Neri

state: Italy

address: Via Nizza 52

country: Italy

institute: University of Torino

data_processing:
Library strategy: GLIB-Seq
Basecalls performed using CASAVA version 1.8
Reads for GLIB-Seq were aligned to the mm9 genome assembly using Bowtie v0.12.7 using the following parameters : -q --max /dev/null -v 1  -S --sam-nohead -m 1. Duplicate reads were filtered out using custom script.
genome_build: mm9
supplementary_files_format_and_content: bed files were generated using MACS v1.4.1 with the following setting: --gsize=mm --nolambda --bw=300 -p=1E-8

organism: Mus musculus

source_name: MEF, passage 5

growth_protocol: Mouse embryonic fibroblasts (MEFs) were derived from 13.5d postcoitum C57BL/6 mouse embryos and cultured in DMEM high glucose medium supplemented with 10% fetal calf serum (FCS).

extract_protocol:
Genomic DNA was extracted using DNeasy Blood and Tissue kit (Qiagen).
Genomic DNA was sonicated for 17' pulse 30"ON/30"OFF high  with Bioruptor Twin (Diagenode). GLIB precipitation was performed using Hydroxymethyl Collector (Active Motif). Libraries were generated with ChIP-seq Sample Prep Kit (Illumina) and sequenced on Illumina HiScanSQ Platform.

treatment_protocol: MEFs were harvested after 5 passage

tag: cell type

value: mouse embryonic fibroblasts (MEFs)


title: 227-M2

status: Public on Aug 06 2015

city: Stanford

first: Gokul

last: Ramaswami

state: CA

address: 300 Pasteur Drive Alway M305

institute: Stanford University

data_processing:
Library strategy: mmPCR-seq
Paired-end sequencing reads were combined and mapped onto a combination of the dm3 genome and 100 bp exonic sequencing surrounding known splicing junctions using BWA samse allowing 9 mismatches per read.
Fly RNA editing sites were downloaded from the RADAR database (www.rnaedit.com)
We used samtools mpileup to count the number of 'A' and 'G' reads at each editing site to calculate the editing levels.
Genome_build: dm3
Supplementary_files_format_and_content: The processed data files contain editing level measurements. The columns are formatted: editing site chromosome, editing site position, editing site gene, editing site strand, editing site annotation1, editing site annotation2, sequencing coverage, number of edited reads, editing level.

organism: Drosophila melanogaster

source_name: Male whole body

growth_protocol: Male adult flies were 3-5 days old

extract_protocol:
Total RNA was extracted from fly whole bodies.
Libraries were prepared by pooling all of the PCR products for a particular sample and barcoding them uniquely using a 15 cycle PCR reaction.

tag: replicate

tag: Sex

value: male

tag: tissue

value: whole body


title: M23NDcovS-LP-2


title: MCL-02 Input

source_name: MCL-02 Input


title: 5hmC_MEF_p0

source_name: MEF, passage 0

treatment_protocol: MEFs were harvested after 0 passage


title: MCL-03 H3K27ac

source_name: MCL-03 H3K27ac


title: MCL-02 H3K27ac

source_name: MCL-02 H3K27ac


title: MCL-01 H3K27ac

source_name: MCL-01 H3K27ac


title: MCL-01 Input

source_name: MCL-01 Input


title: HGB-04 Input

source_name: HGB-04 Input


title: HGB-03 Input

source_name: HGB-03 Input


title: HGB-04 H3K27ac

source_name: HGB-04 H3K27ac


title: HGB-03 H3K27ac

source_name: HGB-03 H3K27ac


title: HGB-02 Input

source_name: HGB-02 Input


title: foxo3b MO 48hpf

city: Beijing

first: yadong

last: yang

address: No.1-104 Beichen West Road, Chaoyang

country: China

institute: Beijing Institute of Genomics

description: foxo3b MO 48hpf

data_processing:
TopHat for mapping of Hiseq 2000 RNA-Seq data
Cufflinks for assembling transcripts, estimating their abundances, and testing for differential expression and regulation in RNA-Seq samples
Computation and visualization were achieved using the heatmap plus package in R.
IPA and the Gene Ontology for functional analysis of specific genes
Genome_build: Zv9

organism: Danio rerio

source_name: Gata1+ cells

extract_protocol:
RNA was extracted by TRIzol Regent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time

value: 48 hours post fertilization

value: foxo3b morpholinos

tag: zebrafish strain


title: Control 24hpf

description: Control 24hpf

value: 24 hours post fertilization

value: control


title: wspR2

city: Hong Kong

first: Xin

last: Deng

address: To Yuen Building

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

data_processing:
Bacterial ChIP-seq reads were mapped to the P. auruginosa genome (ASM676v1), using TopHat (version 2.0.0) with two mismatches allowed.
Only the uniquely mapped reads were kept for the subsequent analyses.
The enriched peaks were identified using MACS software (version 2.0.0)
Genome_build: P. aeruginosa PAO1 (ASM676v1)

organism: Pseudomonas aeruginosa

source_name: liquid culture in LB

growth_protocol: LB medium with Amp

extract_protocol:
Wild type P. aeruginosa MAPO1 containing empty pAK1900 or pAK1900-VqsM-VSV was cultured in LB medium supplemented with ampicillin until the mid-log phase (OD=0.6), before was treated with 1% formaldehyde for 10 min at 37 °C. Cross-linking was stopped by addition of 125 mM glycine. Bacterial pellets were washed twice with a Tris buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl), and then re-suspended in 500 µl IP buffer (50 mM Hepes-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, mini-protease inhibitor cocktail (Roche) and sonicated the DNA to sizes of 100-300 bp. Insoluble cellular debris was removed by centrifugation and the supernatant used as input sample in IP experiments. Both control and IP samples were washed by protein A beads (General Electric), and then incubated with 50 ul agarose-conjugated anti-VSV antibodies (Sigma) in IP buffer. Washing, crosslink reversal, and purification of the ChIP DNA were conducted by following previously published protocols.
NEXTflex™ ChIP-Seq Kit (Bioo Scientific)

treatment_protocol: grow until mid-log phase

value: anti-VSV

tag: technology

value: ChIP-seq


title: foxo3b MO 24hpf

description: foxo3b MO 24hpf


title: MCL-04 H3K27ac

source_name: MCL-04 H3K27ac


title: mexT2


title: HGB-01 H3K27ac

source_name: HGB-01 H3K27ac


title: Control 48hpf

description: Control 48hpf


title: HGB-01 Input

source_name: HGB-01 Input


title: wspR1


title: TOLEDO Input

source_name: TOLEDO Input

value: Cell line


title: mexT1


title: exsA2


title: gacA2


title: 2588-2


title: 2588-1


title: gacA1


title: TOLEDO H3K27ac

source_name: TOLEDO H3K27ac


title: SUDHL-4 MEF2B HPA004734

source_name: SUDHL-4 MEF2B HPA004734

value: MEF2B_HPA004734 (Atlas, catalog# HPA004734, lot# R57933)


title: exsA1


title: algR1


title: SUDHL-4 H3K27ac

source_name: SUDHL-4 H3K27ac


title: SUDHL-4 Input

source_name: SUDHL-4 Input


title: HGB-02 H3K27ac

source_name: HGB-02 H3K27ac


title: REC-1 Input

source_name: REC-1 Input


title: algR2


title: vfr1


title: rpoN2


title: PFEIFFER Input

source_name: PFEIFFER Input


title: PFEIFFER H3K27ac

source_name: PFEIFFER H3K27ac


title: OCI-LY-7 PAX5

source_name: OCI-LY-7 PAX5

value: PAX5 (Santa Cruz, catalog# sc-1975x, lot# I1511)


title: OCI-LY-7 PU.1

source_name: OCI-LY-7 PU.1

value: Pu.1 (Santa Cruz, catalog# sc-22805, lot# D0609)


title: SUDHL-4 MEF2B ab33540

source_name: SUDHL-4 MEF2B ab33540

value: MEF2B (Abcam, catalog# ab33540, lot# GR90081-1)


title: rpoN1


title: soxR2


title: soxR1


title: mvfR1


title: mvfR2


title: OCI-LY-7 MEF2B ab33540

source_name: OCI-LY-7 MEF2B ab33540


title: vfr2

source_name: liquid culture in LB


title: OCI-LY-7 EP300

source_name: OCI-LY-7 EP300


title: KARPAS-422 MEF2B ab33540

source_name: KARPAS-422 MEF2B ab33540


title: OCI-LY-7 BACH2

source_name: OCI-LY-7 BACH2

value: Bach2 (ARP39513, AVIVA)


title: KARPAS-422 Input

source_name: KARPAS-422 Input


title: OCI-LY-1 Input

source_name: OCI-LY-1 Input


title: JEKO-1-PI20-MEF2B-HA HA

source_name: JEKO-1-PI20-MEF2B-HA HA

value: Cells were transduced with lentiviral supernatants by spinfection for 90 minutes in the presence of polybrene. After 48 hour recovery, transduced cells were selected by G418 (10+ days). pINDUCER-20 transgene expression was induced with 100 ng/mL doxycycline 48 hours prior to cell harvest.

value: HA (Santa Cruz, catalog# sc-7392x, lot# E0913)


title: JEKO-1-PI20-GFP HA

source_name: JEKO-1-PI20-GFP HA


title: JEKO-1-PI20-MEF2B-HA H3K27ac

source_name: JEKO-1-PI20-MEF2B-HA H3K27ac

value: H3K27ac (39133, Active Motif)


title: JEKO-1 Input

source_name: JEKO-1 Input


title: DOHH2 PAX5

source_name: DOHH2 PAX5


title: DOHH2 PU.1

source_name: DOHH2 PU.1


title: DOHH2 MEF2B ab33540

source_name: DOHH2 MEF2B ab33540


title: DOHH2 Input

source_name: DOHH2 Input


title: MINO Input

source_name: MINO Input


title: OCI-LY-7 Input

source_name: OCI-LY-7 Input


title: DB MEF2B ab33540

source_name: DB MEF2B ab33540


title: DB Input

source_name: DB Input


title: DOHH2 EP300

source_name: DOHH2 EP300


title: DOHH2 BACH2

source_name: DOHH2 BACH2


title: DB MEF2B HPA004734

source_name: DB MEF2B HPA004734


title: Sample 15: N1_12_-

city: Cincinnati

first: Raphael

last: Kopan

state: Ohio

address: 3333 Burnet Avenue

department: Developmental Biology

institute: Cincinnati Children's Hospital

description: Notch1 deletion allele along with Notch1 allele and an allele of Notch1 in which the NICD of Notch1 has been replaced with that of the NICD of Notch2 (Liu et al.  2013).  Endothelial dysfunction is observed in animals with this genotype

data_processing:
Illumina Off-Line Basecaller(OLB) v1.9.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, mapped to mm9 whole genome using tophat v2.0.9 –p 4 –G (UCSC gtf)
Genome_build: mm9

source_name: Endothelial cells

extract_protocol:
Purified endothelial cells were purified using Qiagen mRNAeasy kit following manufacturer's directions
The construction of RNA libraries were generated using Illumina Tagmentation following manufactuer's protocols

treatment_protocol: Endothelial cells from e9.5 were purifed from the whole embryos using flurescently conjugated CD31 antibodies  by FACS.

value: Endothelial cells

value: Whole embryo

tag: developmental stage


title: Sample 14: N1_12_-


title: Sample 16: N1_12_-


title: Sample 11: N1_pl_pl

description: Wild-type Notch1 alleles. Phenotypically Normal endothelial development


title: Sample 7: N1_plus_12

description: Wild-type Notch1 allele and an allele of Notch1 in which the NICD of Notch1 has been replaced with that of the  NICD of Notch2 (Liu et al.  2013). Wild-type Notch1 alleles. Phenotypically Normal endothelial development


title: Sample 13: N1_12_vg

description: Notch1 allele and an allele of Notch1 in which the NICD of Notch1 has been replaced with that of the NICD of Notch2 (Liu et al.  2013).  The other allele contains the Notch1Vg alelle.  The  Notch V1744G allele is the result of an amino acid substituion at position 1744 in which a Glycine has been substituted for Valine  (Huppert et al., 2000), This amino acid substitution from valine to glycine shifts the γ-secretase cleavage site to generate more a more labile (less stable) NICD-L fragrment (Tagami et al., 2008). The subsequent reduction in NICD stability proves detrimental to Notch signaling in vivo. Partial Endothelial dysfunction is seen in animals with this genotype


title: Sample 6: N1_plus_12

description: Wild-type Notch1 allele and an allele of Notch1 in which the NICD of Notch1 has been replaced with that of the  NICD of Notch2 (Liu et al.  2013). Wild-type Notch1 alleles.  Phenotypically Normal endothelial development


title: Sample 8: N1_plus_-

description: Wild-type Notch1 allele and an allele  of Notch1 that has been deleted (Heterozygous animal). Wild-type Notch1 alleles. Phenotypically Normal endothelial development


title: Sample 10: N1_plus_-

description: Wild-type Notch1 allele and an allele  of Notch1 that has been deleted (Heterozygous animal).  Wild-type Notch1 alleles. Phenotypically Normal endothelial development


title: GRANTA-519 Input

source_name: GRANTA-519 Input


title: Sample 9: N1_plus_-


title: Sample 4: N1_plus_plus

description: Wild-type Notch1 alleles  Phenotypically Normal endothelial development


title: JEKO-1-PI20-GFP H3K27ac

source_name: JEKO-1-PI20-GFP H3K27ac


title: Sample 5: N1_plus_12


title: Sample 1: N1_plus_vg

description: Heterozygous animal containing a wild type alelle and the Notch1Vg alelle.  The  Notch V1744G allele is the result of an amino acid substituion at position 1744 in which a Glycine has been substituted for Valine  (Huppert et al., 2000), This amino acid substitution from valine to glycine shifts the γ-secretase cleavage site to generate more a more labile (less stable) NICD-L fragrment (Tagami et al., 2008). The subsequent reduction in NICD stability proves detrimental to Notch signaling in vivo. Wild-type Notch1 alleles.  Phenotypically Normal endothelial development


title: Sample 2: N1_plus_vg


title: Sample 3: N1_plus_vg


title: Human thymocytes-H3K4me3 G5

city: Safed

first: Yaakov

last: Maman

address: Henrietta Szold 8

department: Azrieli Faculty of Medicine

institute: Bar-Ilan University

description:
control: input
G5

data_processing:
mouse and human ChIP-seq reads were aligned to the GRCm38p2/mm10 and  GRCh37/hg19 genome assemblies, respectively.
Alignment done using bowtie version 0.12.7, with the parameters:   --best --all --strata  -n 2 -m1 -l 36
peaks were called using MACS version 1.4.2 with default parameters
Genome_build: GRCm38p2/mm10 for mouse and  GRCh37/hg19 for human
Supplementary_files_format_and_content: wig files were generated using MACS with parameter --space 100, and then normalized to RPM. Scores in the wig files represent the averaged RPM over overlapping 100bp window

source_name: thymocytes

extract_protocol:
cells were crosslinked with 1% HCHO, quenched with 0.125 M glycine, washed and resuspended in RIPA buffer (10 mM Tris pH 7.4, 1 mM EDTA, 1% tritonX-100, 0.1% sodium deoxycholate, 0.1% SDS) containing 0.8 M NaCl and sonicated using a water bath sonicator (Diagenode) to obtain DNA of ≈ 300–500 bp.
libraries were prepared and sequenced following standard Illumina protocols

value: thymocytes

tag: age

value: Mixture:4 months or 1.5 years

value: unknown


title: Human thymocytes-H3K4me3 G3

description:
control: input
G3

value: female


title: Human thymocytes-R1 G4

description:
control: input
G4


title: Human thymocytes-R2 G6

description:
control: input
G6

value: 4 months


title: Human thymocytes-R1 G2

description:
control: input
G2


title: Sample 12: N1_pl_pl


title: Human thymocytes-R1 G1

description:
control: input
G1


title: ATAC_CEBPA_Control

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Library strategy: ATAC-seq
ATAC-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned using Bowtie2 version 2.1.0 with the default parameters.
To create density files, the read density was normalized to ten million mapped reads and converted to BigWig using UCSC BedTools.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files containing the read densities

source_name: Murine MLL-AF9 leukemic cells

growth_protocol: Murine MLL-AF9 leukemic cells were cultured in IMDM plus 15% FBS supplemented with 20 ng/ml murine SCF, 10 ng/ml murine IL-3 and 10 ng/ml murine IL-6.

extract_protocol:
Cell nuclei were fresh prepared from 50,000 cells as previously described (Buenrostro et al. 2013 Nature Methods).
ATAC-seq was performed as previously described (Buenrostro et al. 2013 Nature Methods). For each sample, cell nuclei were prepared from 50,000 cells, and incubated with 2.5 uL transposase (Illumina) in a 50 uL reaction for 30 min at 37°C. Following purification of transposase fragmented DNA, the library was amplified by PCR and subjected to high-throughput sequencing using Illumina HiSeq 2000 platform.

value: MLL-AF9 transformed leukemic cells

value: Cebpa wildtype


title: ATAC_CEBPA_KO

value: Cebpa knock-out


title: 22_c Sox10-infected, +Dox, Venus-negative cells

city: La Jolla

first: Christopher

last: Dravis

address: 10010 North Torrey Pines Road

department: GEL-W

institute: Salk Institute for Biological Studies

data_processing:
We trimmed 10 bases from the 5' end of each read and mapped them to the mouse genome (GRCm38/mm10) using STAR (Dobin et al., 2013). We quantified gene expression as FPKM (Fragments Per Kilobase of gene model per Million reads per sample) using Cufflinks (Trapnell et al., 2010). We used the TM4 software suite (Saeed et al., 2006) for visualization and clustering of Log2-converted, mean-centered, gene-wise normalized FPKM values by Pearson correlation following addition of 1 FPKM to each gene to avoid taking the Log of 0. Fetal MaSC and stromal signature genes derived from expression arrays were retrieved from Spike et al. for comparison (Spike et al., 2012). We identified differentially expressed genes from RNA-Seq data using SAM analysis at FDR<0.01% (Li and Tibshirani, 2013).  For analysis of the Sox10OE cells, FPKM values were compared between Sox10OE cells and uninfected cells. We generated rank order gene lists by ordering expressed genes by their FPKM value in Sox10OE cells and uninfected cells, and comparing the relative ranking of the gene between the two conditions.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: Fetal mammary organoid cells

growth_protocol: Fetal mammary cells were isolated from E17.5 embryos and FACS sorted into the fMaSC and fStroma populations using the markers above and described in the manuscript. To isolate Sox10OE cells, m2rtTA fMaSCs were infected with LV-TRE-hSox10-2A-NLSVenus as described, given dox 72 hours after plating. Organoids were recovered and dissociated to single cells as described above, and FACS sorted for Venus+ and Venus-negative cells. In parallel, we also recovered cells from organoids that were not infected by the virus and organoids that were infected but not given dox.

extract_protocol:
We generated RNA sequencing libraries from biological replicates of these FACS sorted cell populations using the Illumina TruSeq RNA sample kits, according to the manufacturer's instructions. Libraries were validated using the Agilent Technologies 2100 Bioanalyzer and Quant-iT dsDNA HS Assay (Life Technologies).
100 base paired-end sequencing was carried out on an Illumina HiSeq2000 sequencer in duplicate lanes yielding greater than 25 million reads per sample.

value: Fetal mammary organoid cells

tag: passages

value: Primary organoid

tag: protocol

value: Apparently uninfected


title: 22_d Sox10 infected, no dox

value: No induction of ectopic Sox10


title: 863b_H3K9me3-CHIPSEQ

city: Houston

first: Kadir

middle: Caner

last: Akdemir

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

data_processing:
ChIP-Seq reads were aligned using Bowtie (version 1.0.0) to human genome assembly NCBI Build 37 (UCSC hg19) with the following parameters: -n 1 -m 1 --best –strata (uniquely mapped reads with one mismatch were retained).
Enriched regions were detected by Scripture package with varying window sizes (750,1500), and peaks were defined whose coverage at 0.05 significance. Collapsed repeat regions in the human genome  and "ultra-high signal suspect regions" identified by ENCODE project (https://docs.google.com/spreadsheet/ccc?key=0Am6FxqAtrFDwdE5LYWh2MkVscmtWEdtNUN2eEVEYmc&hl=en#gid=5) were masked during the peak calling procedure. Called regions were merged with BEDTools (20110278).  Intervals longer than 1500 base pair length were excluded from the final list.
Genome_build: hg19
Supplementary_files_format_and_content: wig files generated using MACS version 1.4.1, Scores represents signal strength of H3K9me3 at a particular locus

growth_protocol: LPS cell lines were cultures in DMEM containing 10% fetal bovine serum and maintained in standard tissue culture conditions (5% CO2, 37 degrees Celsius).

extract_protocol:
Cells were treated with 0.25% trypsin, washed with PBS, and cross-linked using 1% paraformaldehyde for 10 min at 37oC.  Reactions were quenched by 0.125M glycine for 5 min.  Cells were then washed with PBS and stored at -80oC.  Cells were thawed on ice the next day and lysed with RIPA buffer (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 140mM NaCl, 1% Triton x-100, 0.2%SDS, 0.1% DOC) for 10 min on ice.  Sonication was performed using the Branson Sonifier 250 to achieve DNA shear length of 200-500bp.  Extracts were then incubated overnight with respective antibody-Dynabead (Life Technologies) mixture (previously incubated together for 1 hr at 4oC [Rabbit IgG (Abcam), H3K9me3 (Abcam)]).  Immune complexes were then washed three times with RIPA buffer, once with RIPA-500 (RIPA with 500mM NaCl) and once with LiCl wash buffer (10mM Tris-HCl pH 8.0, 1mM EDTA pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% DOC).  Elution and de-crosslinking were performed in direct elution buffer (10mM Tris-Cl pH 8.0, 5mM EDTA, 300mM NaCl, 0.5% SDS) by incubating immune complexes at 65oC for 4-16 hr.  Proteinase K (20mg/ml) and RNaseA treatment was performed and DNA cleaned up using AMPure beads (Beckman-Coulter).
Sequencing library preparation was performed using NEB kit (6040) per manufacturer's instructions.

tag: sarcoma type

value: DDLPS

tag: antibody

value: H3K9me3 (Abcam)


title: 445a_input-DNA

value: WDLPS


title: 029b_H3K9me3-CHIPSEQ


title: 246_input-DNA


title: 247b_input-DNA


title: 247b_H3K9me3-CHIPSEQ


title: 029b_input-DNA


title: 30a Uninfected

tag: strain

value: Uninfected


title: 22_a Uninfected


title: 30_d Sox10-infected, +Dox, Venus-neg cells


title: 22_b Sox10-infected, +Dox, Venus+ cells

value: Ectopic Sox10 expressed


title: 4a e17.5 24low/-Lin(-)

source_name: Fetal mammary cells

value: Fetal mammary stroma

value: Primary

tag: sorting markers

value: Isolated CD24low; Lin-neg


title: 30b Sox10-Infected, no Dox


title: 863b_input-DNA


title: 3a e17.5 24low/-Lin-


title: 224b_input-DNA


title: 445a_H3K9me3-CHIPSEQ


title: 246_H3K9me3-CHIPSEQ


title: 30c Sox10-Infected, +Dox, Venus+ cells


title: 224b_H3K9me3-CHIPSEQ


title: 2a e17.5 24+49+Lin(-)

value: Fetal mammary stem cells

value: Isolated CD24+, CD49f+, Lin-neg


title: 1a e17.5 24+49+Lin-


title: 224a_input-DNA


title: 224a_H3K9me3-CHIPSEQ


title: 12a E17.5 Sox10+ Epcam+ lin-

value: Isolated Sox10-Venus+; EpCAM+


title: 13a E17.5 Sox10+ Epcam+


title: Mouse Abelson -R1 N1

description:
control: input  and RAG1-/-
N1

source_name: Abelson

value: Abelson

tag: genotype

value: v-abl

tag: chip antibody


title: Mouse preB-R1(R1ko) K1

description:
control: input  and RAG1-/-
K1

source_name: preB

tag: cell type

value: B cell; CD19+ bone marrow cell

value: 4 weeks

value: pooled male and female


title: Mouse preB-R2(wt) H4

description:
control: input  and RAG2-/-
H4

value: WT

value: male


title: Mouse preB-R2(BD) I4

description:
control: input  and RAG2-/-
I4

value: BD


title: Mouse preB-R1(BD) I3

description:
control: input  and RAG1-/-
I3

value: Db


title: RAG2_mm_RAG1ko_TCRBetaTg_ChIPseq D12

description:
control: input  and RAG2-/-
D12

value: thymocytes

value: 5 weeks


title: Mouse preB-R2(R2ko) J4

description:
control: input  and RAG2-/-
J4


title: RAG2_mm_D708ATg_TCRBetaTg_ChIPseq B12

description:
control: input  and RAG2-/-
B12


title: RAG1ko_thy_mm_TCRBetaTg_RNAseq D23

data_processing:
Libraries were run on Illumina HiSeq Sequencers and Illumina tools were used to generate fastq files from RTA output.
the short reads were then aligned to the mm9 genome with Bowtie (versions 0.12.8 to 1.0.0) (Langmead et al., 2009).
After sorting the resulting alignment files, custom software was used to determine mean density of reads around RefSeq promoters that overlapped a Rag2 peak.
MNase reads were shifted by half a nucleosome size towards the center of the nucleosome.
The resulting data was imported into R (version 3.1) for visualization.
Genome_build: GRCm37/mm9

extract_protocol:
Thymocytes were crosslinked for 15 minutes with 1% formaldehyde, and the crosslinking reaction was quenched with 0.125 M glycine.  Cells were washed twice with ice-cold PBS containing 1 mM PMSF and 1 µg/mL pepstatin A.  Five million crosslinked cells were resuspended in MNase digestion buffer (50 mM Tris-HCl, pH 7.6; 1 mM CaCl2, 0.2% Triton X, 5 mM sodium butyrate, 1 mM PMSF, 1 µg/mL pepstatin A).  Micrococcal nuclease (MNase, 0.2 U) was added to the sample, which was incubated at 25 ºC for 5 minutes.  The nuclease digestion was terminated with 5 mM EDTA.  Crosslinks were reversed using an overnight incubation at 65 ºC in the presence of 0.5% SDS and 200 µg/mL Proteinase K.  DNA was isolated by standard phenol:chloroform extraction and ethanol precipitation.  The sample was then subjected to RNAse digestion (10 µg/mL RNAse A at 37 ºC for 1 hour) and a second proteolysis step to remove the RNAse (200 µg/mL Proteinase K, 0.3% SDS, 65 ºC, 1 hour).  Again, the DNA was isolated by phenol:chloroform extraction and ethanol precipitation and resuspended in water.  The sample was run on a 2% agarose gel, and the ~150 bp mononucleosome band was excised and purified using the Qiagen Gel Extraction kit.
libraries were prepared and sequenced following standard Illumina protocols

value: Rag1:-/-; TCRbeta:+/+/tg


title: RAG1_mm_RAG2ko_TCRBetaTg_ChIPseq C9

description:
control: input  and RAG1-/-
C9

value: female


title: RAG1_mm_RAG1ko_TCRBetaTg_ChIPseq D9

description:
control: input  and RAG1-/-
D9


title: RAG2_mm_RAG1_ChIPseq A12

description:
control: input  and RAG2-/-
A12


title: 14a E17.5 Sox10- Epcam- Lin-

value: Fetal mammary stroma

value: Primary

value: Isolated EpCAM-negative


title: RAG1ko_thy_mm_TCRBetaTg_RNAseq D21


title: RAG2_mm_RAG2ko_TCRBetaTg_ChIPseq C12

description:
control: input  and RAG2-/-
C12

value: 6 weeks


title: RAG2ko_thy_mm_TCRBetaTg_RNAseq C23

value: Rag2:-/-; TCRbeta:+/+/tg


title: RAG2_mm_RAG2dc_ChIPseq F3

description:
control: input  and RAG2-/-
F3


title: RAG1_mm_cRAG1_ChIPseq E2

description:
control: input  and RAG1-/-
E2


title: Mouse preB-H3K4me3(BD) I5

description:
control: input  and RAG2-/-
I5


title: RAG1_mm_RAG2dc_ChIPseq F2

description:
control: input  and RAG1-/-
F2


title: RAG1_mm_RAG1_ChIPseq A9

description:
control: input  and RAG1-/-
A9


title: RAG1_mm_D708ATg_TCRBetaTg_ChIPseq B9

description:
control: input  and RAG1-/-
B9


title: RAG2ko_thy_mm_TCRBetaTg_RNAseq C22


title: RAG2ko_thy_mm_TCRBetaTg_RNAseq C21


title: Mouse preB-R1(R1ko) K2

description:
control: input  and RAG1-/-
K2


title: RAG2ko_thy_mm_TCRBetaTg_RNAseq C17


title: RAG1ko_thy_mm_RAG1_D708ATg_TCRBetaTg_MNaseSeq B23


title: RAG2_mm_cRAG1_ChIPseq E3

description:
control: input  and RAG2-/-
E3


title: RAG1ko_thy_mm_TCRBetaTg_RNAseq D22


title: RAG1_mm_RAG2dc_ChIPseq F1

description:
control: input  and RAG1-/-
F1


title: RAG1ko_thy_mm_TCRBetaTg_RNAseq D17


title: RAG1ko_thy_mm_RAG1_D708ATg_TCRBetaTg_MNaseSeq B17


title: RAG1ko_thy_mm_RAG1_D708ATg_TCRBetaTg_MNaseSeq B21


title: RAG2ko_thy_mm_CD3_RNAseq Q3

data_processing:
The short reads were  aligned to the mm9 genome with GSNAP (version 2012-07-20) (Wu and Nacu, 2010), allowing known splice junctions extracted from RefSeq GTF (June 2013).
After sorting of the alignment files, htseq-count (Htseq version 0.5.4) (Anders et al., 2014) was used to count the number of reads fitting each gene model in the RefSeq GTF (after removing small RNAs).
Counts for each gene were then read into R (version 3.1, http://www.R-project.org) and analyzed with DESeq (version 1.16) (Anders and Huber, 2010).
Genome_build: GRCm37/mm9

extract_protocol:
Total thymocyte RNA was isolated using Trizol (Invitrogen),
RNA-seq libraries were prepared using the Illumina Tru-seq RNA sample prep kit V2 following manufacturer instructions.

value: Female


title: RAG2ko_thy_mm_CD3_RNAseq Q2


title: RAG1ko_thy_mm_CD3_RNAseq P1


title: RAG1ko_thy_mm_TCRBetaTg_RNAseq D18

value: Male


title: RAG1ko_thy_mm_CD3_RNAseq P2

value: 4 weeks


title: RAG1ko_thy_mm_TCRBetaTg_RNAseq D20


title: RAG1ko_thy_mm_RAG1_D708ATg_TCRBetaTg_RNAseq B19


title: RAG1ko_thy_mm_TCRBetaTg_RNAseq D19


title: D90_GFPneg_rep2

status: Public on Aug 03 2015

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description: flow sorted CRXp-GFP negative cells at 90 days post neural retina induction

data_processing:
Basecalls and quality scores performed using RTA 1.13.48 and Fastq files generated from reads passing chastity filtering.
The reference assembly GRCh37.p13 with transcript annotation Gencode 19 was used for alignment and quantitation. Transcript quantitation was accomplished by streaming read alignment from Bowtie2 (Langmead and Salzberg, 2012) to eXpress (Roberts and Pachter, 2013; Roberts et al., 2013).  Bowtie2 alignment settings were used as previously described (Roberts et al., 2013) and eXpress setting –r-stranded was used for directional transcript analysis.  Bias corrected effective counts were used for downstream normalization and differential expression analysis. Read alignments used for viewing in Integrated Genomics Viewer (IGV) (Thorvaldsdottir et al., 2013) were performed using a 2-step alignment strategy employing TopHat2 (Kim et al., 2013) splice junction mapper keeping the alignment with the best alignment score.  Reads were first aligned to the annotation GTF prior to aligning to the genome reference assembly using the default settings with the exception of the following options: -g 1 –library-type fr-firststrand –G <gtf file>.
Effective counts from eXpress were used to filter and to normalize the data via library size correction using the TMM method within the R package edgeR. Prior to normalization, transcripts showing at least 1 Count Per Million (CPM) in at least half of the samples within each time point were kept for further analysis. Design matrices were created for defining groups (time course) with and without batch definition, however, only the time course factor was used for TMM normalization.  Limma “RemoveBatchEffect” function was executed on log2 transformed CPM data. Batch corrected log2 CPM values were then converted to FPKM values prior to clustering. Affinity Propagation (AP) clustering was used to assess the success of the procedure. Row-wise average of undifferentiated sample values was added as the first column to the processed data after differential expression analysis.
Differential expression was performed using the edgeR likelihood ratio test from on a generalized linear model (glm), with day 37 as the intercept. In the glm, the batch factor was used as a blocking factor. Significance was defined as having a false discovery rate (FDR) less than or equal to 0.05, and 4697 transcripts fit this criterion. Volcano plots of those comparisons were plotted to see the ideal fold change cutoff. The colors of the points those represent the mean expression of the gene between the time points compared. The key observation is that the mean expression of a transcript is getting closer to 0 (blue) as the fold change is getting closer to 0 although all the FDRs in the plot equal 0.05. We decided to restrict our interest to the transcripts having greater than a 2-fold change, therefor, 3241 transcripts were left after this filtering. The boxplot of the remaining transcripts on batch corrected RPKM values was still showing the median expression around 4 RPKM. We applied another filter eliminating the transcripts where their maximum expression values were less than the median of the medians of the remaining transcripts. The final number of the transcripts used for further analysis was 3157.
Genome_build: GRCh37.p13 with Gencode 19
Supplementary_files_format_and_content: GFPneg_eXpress.counts.csv: GFP negative effective counts output from eXpress.
Supplementary_files_format_and_content: GFPpos_eXpress.counts.csv: GFP positive effective counts output from eXpress.
Supplementary_files_format_and_content: Normalized_FPKM.xls: Batch corrected and normalized FPKM values (log2(FPKM+1).
Supplementary_files_format_and_content: DE_transcripts.xls: Differentially expressed transcript list with averaged FPKM values (log2(FPKM+1).

source_name: hES derived neural retina

growth_protocol: H9 hESCs were passaged every 4-5 days at 1:6 ratio by incubating with 2 mg/ml dispase (Invitrogen) at 37°C for 10 min. Colonies were washed, broken into small clumps of cells by pipetting and cultured at 37°C, 5% CO2.

extract_protocol:
The differentiation was performed according previous report with some modification (Nakano, Cell Stem Cell 2012). Human ESCs were dissociated by Accumax™ (Stem cell technologies) containing 10 µM Y-27632. Basal differentiation medium contained GMEM, 20 % (v/v) KSR, 0.1 mM nonessential amino acids, 1mM pyruvate 100 U/ml penicillin and 100 mg/ml streptomycin (Sigma-Aldrich). Cells on day 0 were quickly aggregated in low attachment 96 well-plates with V-bottom shape (NOF corporation) (9,000 cells/well in 100 µl) containing basal differentiation medium plus 3 µM IWR-1-endo (Wnt inhibitor, Calbiochem) and 20 µM Y-27632. Ten microliter of 1.8 µg/µl of Matrigel (growth factor reduced, BD Biosciences) solution was added in day-2 cultures. Aggregates were maintained for further 4 days when half medium was changed with medium containing 3 µM IWR-1-endo and 180 µg/ml and cultured for 6 days. Day-12 aggregates were transferred to low attachment 90 mm Dishes (NOF corporation) containing basal differentiation medium, 10% (v/v) FBS (Atlanta) and 100 nM Smoothened Agonist (SAG) (hedgehog agonist, Enzo Life Sciences) and maintained for 6 days. On day 18 medium was switched to maintenance medium which was DMEM/F12 containing 1% N2 supplement (Invitrogen), 10% (v/v) FBS, 0.5 µM retinoic acid (Sigma-Aldrich), 0.25 mg/ml Fungizone (GIBCO), 100 U/ml penicillin, and 100 mg/ml streptomycin. Human ESC-NR  were grown in maintenance medium in bacterial-grade Dishes from day 18 at 40% O2 and 5% CO2 with medium changed every three day until sample collection.
Total RNA was extracted by RNA purification kit (Norgen Biotek).
Libraries were constructed using a stranded modification of the Illumina TruSeq mRNA (Brooks, et al. Meth Mol Biol 2012). Each library was single-end sequenced in an independent lane of a GAIIx at a length of 76 bases.  Fastq files were generated from reads passing chastity filter.

value: GFP negative neural retina cells

tag: day post induction

value: Day 90


title: D90_GFPneg_rep1


title: RAG1ko_thy_mm_RAG1_D708ATg_TCRBetaTg_RNAseq B18

tag: Sex


title: D67_GFPneg_rep1

description: flow sorted CRXp-GFP negative cells at 67 days post neural retina induction

value: Day 67


title: D67_GFPneg_rep2


title: D47_GFPneg_rep2

description: flow sorted CRXp-GFP negative cells at 47 days post neural retina induction

value: Day 47


title: D37_GFPneg_rep2

description: flow sorted CRXp-GFP negative cells at 37 days post neural retina induction

value: Day 37


title: D47_GFPneg_rep1


title: RAG1ko_thy_mm_RAG1_D708ATg_TCRBetaTg_MNaseSeq B22

value: thymocytes

value: male


title: D90_GFPpos_rep3

description: flow sorted CRXp-GFP positive cells at 90 days post neural retina induction

value: GFP positive neural retina cells


title: D37_GFPneg_rep1


title: D90_GFPpos_rep1


title: D67_GFPpos_rep2

description: flow sorted CRXp-GFP positive cells at 67 days post neural retina induction


title: D67_GFPpos_rep3


title: D67_GFPpos_rep1


title: RAG2ko_thy_mm_CD3_RNAseq Q1


title: D47_GFPpos_rep3

description: flow sorted CRXp-GFP positive cells at 47 days post neural retina induction


title: RAG1ko_thy_mm_CD3_RNAseq P3


title: D47_GFPpos_rep2


title: RAG1ko_thy_mm_RAG1_D708ATg_TCRBetaTg_RNAseq B20

value: 5 weeks


title: D47_GFPpos_rep1


title: D37_GFPpos_rep3

description: flow sorted CRXp-GFP positive cells at 37 days post neural retina induction


title: D37_GFPpos_rep2


title: Undiff_2

description: undifferentiated CRXp-GFP HP hES cells

source_name: CRXp-GFP H9 hES cells

value: hES cells

value: Day 0


title: D37_GFPpos_rep1


title: Undiff_1

description: undifferentiated CRXp-GFP HP hES cells


title: MEF_K4m3_FC_1

city: Vienna, Austria

first: Daniel

last: Andergassen

address: Lazarettgasse 14, AKH BT 25.3

country: Austria

institute: CeMM Research Center for  Molecular Medicine of the  Austrian Academy of Sciences

data_processing:
RNA sequencing data was aligned to the mm10 genome using STAR (version 2.3.1z12). Reads mapping to multiple locations were excluded using specific parameters (STAR:--outFilterMultimapNmax 1). Additional parameters for the STAR alignment were a maximum intron size of 100,000 bp and out-filtering of non-canonical splice junctions.
STAR alignment of ChIPseq data was conducted with different parameters to disable spliced reads, i.e. a maximum intron size of 1, and prevent soft clipping by enforcing end-to-end alignment (--alignEndsType EndToEnd). Reads mapping to multiple locations were excluded using specific parameters (STAR:--outFilterMultimapNmax 1).
The Single Nucleotide Polymorphism (SNP) annotation file was created from a VCF file containing SNP variant data of 18 mouse strains, downloaded from the Sanger institute. SNP information for the strains CAST/EiJ and FVB/NJ were extracted and converted to the required browser extensible data (BED) format using a custom script that is available together with Allelome.PRO. Note that the name field in this file contains SNP information. Only homozygous high quality SNPs were used and SNPs overlapping annotated pseudogenes were removed.
The NCBI RNA reference sequences collection (RefSeq) annotation was downloaded from the UCSC genome browser on July 2nd 2014. Transcripts <100 bp were removed and the remaining transcripts were separated by transcriptional orientation and used for strand specific analysis of RNA-seq by Allelome.PRO. An annotation of +/- 2 kb windows around the transcription start site (TSS) of RefSeq annotations was used to analyse ChIP-seq by Allelome.PRO.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include the Allelome.PRO output for RNA-seq and H3K4me3 Chip-seq (SNP and locus table)

source_name: embryonic fibroblasts (MEFs)

growth_protocol: After reciprocal mating (CASTxFVB and FVBxCAST), mouse embryonic fibroblasts (MEFs) were derived from E12.5 embryos after removing the head, viscera and urogenital system. The remaining carcass was homogenised to a single cell suspension using Trypsin/EDTA (Gibco) and plated on 6 cm dishes.

extract_protocol:
Total RNA and DNA were extracted using TRI-reagent (Sigma-Aldrich T9424) according to the manufacturers protocol. Total RNA was DNaseI treated using the DNA-FreeTM kit (Ambion).
Native ChIP for H3K4me3 (antibody: cat. 07-473, lot 2019729, Millipore) was conducted. ChIP-seq libraries were prepared using the TruSeq ChIP Sample Prep Kit (Illumina). 100 bp paired end sequencing for RNA-seq and 50 bp single end sequencing for ChIP-seq were performed by the Biomedical Sequencing Facility (BSF) in Vienna using the Illumina HiSeq 2000 platform.

value: primary embryonic fibroblasts (MEFs)

value: FVB/NJxCAST/EiJ


title: Undiff_3

description: undifferentiated CRXp-GFP HP hES cells


title: aHe_F

data_processing: RNA sequencing data was aligned to the mm10 genome using STAR (version 2.3.1z12). Reads mapping to multiple locations were excluded using specific parameters (STAR:--outFilterMultimapNmax 1). Additional parameters for the STAR alignment were a maximum intron size of 100,000 bp and out-filtering of non-canonical splice junctions.

source_name: adult heart

extract_protocol:
Total RNA was extracted using TRI-reagent (Sigma-Aldrich T9424) according to the manufacturers protocol. Total RNA was DNaseI treated using the DNA-FreeTM kit (Ambion).
3µg Ribosomal RNA was depleted from total DNaseI-treated RNA using the RiboZero rRNA removal kit (Human/Mouse/Rat) (Epicentre). Strand-specific RNA-seq libraries were prepared employing the TruSeq RNA Sample Prep Kit v2 (Illumina) modified as described for strand-specific sequencing. 100 bp paired end sequencing was performed by the Biomedical Sequencing Facility (BSF) in Vienna using the Illumina HiSeq 2000 platform.

tag: tissue

value: heart

value: FVB/NJ

value: 8 weeks


title: MEF_K4m3_FC_2


title: aHe_C

value: CAST/EiJ


title: MEF_K4m3_CF_2

value: CAST/EiJxFVB/NJ


title: MEF_K4m3_CF_1


title: MEF_FC_2

extract_protocol:
Total RNA and DNA were extracted using TRI-reagent (Sigma-Aldrich T9424) according to the manufacturers protocol. Total RNA was DNaseI treated using the DNA-FreeTM kit (Ambion).
3µg Ribosomal RNA was depleted from total DNaseI-treated RNA using the RiboZero rRNA removal kit (Human/Mouse/Rat) (Epicentre). Strand-specific RNA-seq libraries were prepared employing the TruSeq RNA Sample Prep Kit v2 (Illumina) modified as described for strand-specific sequencing. Native ChIP for H3K4me3 (antibody: cat. 07-473, lot 2019729, Millipore) was conducted. ChIP-seq libraries were prepared using the TruSeq ChIP Sample Prep Kit (Illumina). 100 bp paired end sequencing for RNA-seq and 50 bp single end sequencing for ChIP-seq were performed by the Biomedical Sequencing Facility (BSF) in Vienna using the Illumina HiSeq 2000 platform.


title: MEF_CF_2


title: MEF_CF_1


title: gemin2 mutant rep 1

city: Buenos Aires

first: Marcelo

last: Yanovsky

state: Ciudad Autonoma de Buenos Aires

address: Av. Patricias Argentinas 435

country: Argentina

institute: Fundación Instituto Leloir. IIBBA- CONICET

data_processing:
Basecalling done with Bustard Illumina Pipelline
Sequence reads were mapped to Arabidopsis thaliana TAIR10 genome using TopHat v2.0.9 with default parameters, except of maximum intron length set in 5000
Count tables for different feature levels were obtained from bam files using custom R v3.0.2 scripts.
Differential gene expression was estimated using edgeR package version 3.4.2 and resulting p-values were adjusted using false discovery rate (fdr) criterion.
The transcriptome was partitioned into subgenic joint features called bins and labeled as exon-bin, intron-bin or alternative-splicing (AS) bins. In addition AS-bins were further classified as exon skipping (ES), 5’ or 3’ alternative (5´alt, 3´alt), intron retention (IR) or multiple. Bins from monoexonic genes and with mean count values lower than 5 reads per condition were discarded.
We used edgeR exactTest for the identification of differential usage of bins corresponding to AS events or introns, and fdr corrected p-values. We also computed read densities in order to have a relationship between the bin and its corresponding gene. A Splicing Index was calculated as bin read density/gene read density, and the Splicing Index Ratio was calculated as Splicing Index in mutants/Splicing Index in WT plants. Only genes with read densities greater than 0.1 in all genotypes, and Splicing Indexes greater than 0.05 in at least one genotype, were used for the analysis. AS events as well as all introns with an absolute Log2 FC (bin read density in the mutant/bin read density in WT) value greater than 0.58, with fdr values lower than 0.15, and an abosolute Log2 Splicing Index Ratio (Splicing Index in the mutant/Splicing Index in WT) greater than 0.58, were deemed as differentially spliced.
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: Comprehensive spreadsheets with the results of the analysis of differential expression and differential splicing detailed above

organism: Arabidopsis thaliana

source_name: pool of tissues_gemin2

growth_protocol: For WT (Col) and gemin2 mutants, seeds were grown on Murashige and Skoog medium containing 0.8% agarose, stratified for 4 d in the dark at 4°C, and then grown at 22°C in continuous light.

extract_protocol:
Total RNA was extracted with RNeasy Plant Mini Kit (QIAGEN) following the manufacturer’s protocols. To estimate the concentration and quality of samples, NanoDrop 2000c (Thermo Scientific) and gel electrophoresis were used, respectively.
Libraries were prepared following the TruSeq RNA Sample Preparation Guide (Illumina). Briefly, 3 μg of total RNA was polyA-purified and fragmented, and first-strand cDNA synthesized by reverse transcriptase (SuperScript II; Invitrogen) and random hexamers. This was followed by RNA degradation and second-strand cDNA synthesis. End repair process and addition of a single A nucleotide to the 3′ ends allowed ligation of multiple indexing adapters. Then, an enrichment step of 12 cycles of PCR was performed. Library validation included size and purity assessment with the NanoDrop 2000c (Thermo Scientific) and the Agilent 2100 Bioanalyzer (Agilent Technologies) with the Agilent RNA 6000 NanoKit, respectively.

treatment_protocol: Whole plants were harvested after 9 d.

tag: ecotype

value: Col

value: gemin2 mutant

value: whole plant

tag: age (days)


title: gemin2 mutant rep 3


title: KO input

city: Ann Arbor

first: Paul

last: Tang

state: MI

address: 2800 Plymouth Road

department: Cardiac surgery

institute: University of Michigan

description: Sample 10

data_processing:
Sequenced reads were aligned to mouse genome using Bowtie with following parameters: -M 1 -q -v 2 -k 1 -X 2000 --best –strata.
Genome_build: mm9
Supplementary_files_format_and_content: wigfile generates from DANPOS contain read occupancy information. wigfiles generate from SICER. Txt files list the coordinates of peaks with readcounts and FDR information.

source_name: Embryonic Stem cells

growth_protocol: mouse ESCs were maintained on MEF feeders using DMEM containing 15% FBS, penicillin/Streptomycin, Glutamax, MEM NEAA, and LIF.

extract_protocol:
ESCs were fixed in 1% Formaldehype 10 minutes at room temperature. Nuclei were isolated and treated with micrococal nuclease followed with brief sonication.
Input DNA was purified, end repaired, dA tailing and ligated to illumina sequencing primers. ChIP DNA was size selected and amplified then sequenced on HiSeq 2000 to generate 50 bp reads.

treatment_protocol: 4 hours after passaging ESCs, apply 1μM 4-OH Tamoxifen (H7904, Sigma) for 36 hour and harvest after 36 hours.

value: BAF250a Knockout

value: none (input)


title: WT H3K4me3 Chip-seq

description: Sample 5

data_processing:
Sequenced reads were aligned to mouse genome using Bowtie with following parameters: -M 1 -q -v 2 -k 1 -X 2000 --best –strata.
Peak detection in H3K4me3 ChIP-seq samples was performed using SICER 1.1 with following parameters: redudancy threshold 1, window size 200, fragment size 150, gap size 200 and FDR 0.05 using input as control.
Genome_build: mm9
Supplementary_files_format_and_content: wigfile generates from DANPOS contain read occupancy information. wigfiles generate from SICER. Txt files list the coordinates of peaks with readcounts and FDR information.

extract_protocol:
ESCs were fixed in 1% Formaldehype 10 minutes at room temperature. Nuclei were isolated and treated with micrococal nuclease followed with brief sonication.  ChIP was performed on the lysate using H3K4me3 antibody.
ChIP DNA was purified, end repaired, dA tailing and ligated to illumina sequencing primers. ChIP DNA was size selected and amplified then sequenced on HiSeq 2000 to generate 50 bp reads.

treatment_protocol: 4 hours after passaging ESCs, apply ethanol for 36 hour and harvest after 36 hours.

value: WT

tag: antibody manufacturer

value: Millipore

tag: antibody catalog number


title: gemin2 mutant rep 2


title: KO MNase-seq rep1

description: Sample 3

data_processing:
Sequenced reads were aligned to mouse genome using Bowtie with following parameters: -M 1 -q -v 2 -k 1 -X 2000 --best –strata.
The fragment counts at each genomic position was calculated using DANPOS with following parameters: -n Q -p 1.
Genome_build: mm9
Supplementary_files_format_and_content: wigfile generates from DANPOS contain read occupancy information. wigfiles generate from SICER. Txt files list the coordinates of peaks with readcounts and FDR information.

extract_protocol:
Cells were harvested and nuclei were isolated with nuclear lysis buffer (5 mM PIPES pH8.0, 85 mM KCl, 0.5% NP-40). Nuclei were treated with micrococcal nuclease.
The DNA fragments was isolated, end-repaired, dA tailing to fragment ends, then ligated with a paired of adaptors. The DNAs were then gel purified and amplified with adaptor primers, then were sequenced on Illumina HiSeq 2000 to generate 50 bp paired-end reads.


title: WT MNase-seq rep2

description: Sample 2


title: KO H2K27me3 Chip-seq

description: Sample 8

data_processing:
Sequenced reads were aligned to mouse genome using Bowtie with following parameters: -M 1 -q -v 2 -k 1 -X 2000 --best –strata.
Peak detection in H3K27me3 ChIP-seq samples was performed using SICER 1.1 with following parameters: redudancy threshold 1, window size 200, fragment size 150, gap size 600 and FDR 0.05 using input as control.
Genome_build: mm9
Supplementary_files_format_and_content: wigfile generates from DANPOS contain read occupancy information. wigfiles generate from SICER. Txt files list the coordinates of peaks with readcounts and FDR information.

extract_protocol:
ESCs were fixed in 1% Formaldehype 10 minutes at room temperature. Nuclei were isolated and treated with micrococal nuclease followed with brief sonication.  ChIP was performed on the lysate using H3K27me3 antibody.
ChIP DNA was purified, end repaired, dA tailing and ligated to illumina sequencing primers. ChIP DNA was size selected and amplified then sequenced on HiSeq 2000 to generate 50 bp reads.


title: KO MNase-seq rep2

description: Sample 4


title: WT H3K27me3 Chip-seq

description: Sample 7


title: KO H3K4me3 Chip-seq

description: Sample 6


title: WT Col rep 2

source_name: pool of tissues_WT

value: Wild type


title: High_rep3

city: Urbana

first: Alison

last: Bell

state: Illinois

address: Justin Smith Morrill Hall, 505 S Goodwin Ave #393

department: Animal Biology

institute: University of Illinois at Urbana Champaign

data_processing:
Illumina Casava1.7 software used for basecalling.
FastQC was used to assess read quality and FastX toolkit was used to filter low quality reads and residual adaptor sequences (hannonlab.cshl.edu/fastx_toolkit/). RNA-seq produced an average of 20 million reads per sample. We aligned reads to Gasterosteus aculeatus reference genome (the repeat masked reference genome, Ensembl release 73), using TopHat (2.0.8) and Bowtie (2.1.0). Reads were assigned to features according to the Ensembl release 73 gene annotation file (ftp://ftp.ensembl.org/pub/release-73/gtf/gasterosteus_aculeatus/). For TopHat alignments, we designated library type “first strand” and otherwise used default parameters.
Identifying differential expression - To estimate differential gene expression we used both Tuxedo [39] and count-based differential expression analysis protocols. Both protocols require each sample’s (Control (6), Low-dose (6), High-dose (6)) reads to align to the reference genome.
In the Tuxedo protocol, cufflinks (2.2.0) reconstructed the transcriptome assembly of each sample by assembling reads into transcripts and estimating their abundance. Later cuffmerge was used to merge together all cufflinks assemblies into a single high quality assembly containing both novel and known isoforms. Finally, cuffdiff [39] was used to call differential gene expression using each treatment group (Control, Low-dose, High-dose) samples alignments and merged transcriptome assembly.
In the count-based protocol, HTSeq was used to calculate reads counts per gene. Later we assessed differential expression between treatments groups (Control, Low-dose, High-dose) using R software package edgeR. This approach uses negative binomial distribution to model counts distribution per gene across sample. Count data were normalized by library size and library composition (using “calcNormFactors” function). A gene was included in the differential expression analysis if the number of counts was greater than or equal to 2 count per million in any sample. We computed a common dispersion estimate followed by tagwise (genewise) dispersion estimation. Finally, to call differential expression between treatment groups, both “exactTest” and “glm” approaches were used.
Genome_build: gasAcu
Supplementary_files_format_and_content: Counts_High_Low_Control.normcounts.txt reports TMM normalized counts

organism: Gasterosteus aculeatus

source_name: Egg Clutch

extract_protocol:
Total RNA was extracted from each pool using Trizol® according to manufacturer instructions and quality analyzed on an Aligent Bioanalyzer (Aligent Technologies, Palo Alto, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: agent

value: maternally derived cortisol

tag: dose

value: high

value: Egg Clutch Pool of 10

tag: age

value: 72 hours post fertilization

value: wild type


title: High_rep6


title: High_rep5


title: WT MNase-seq rep1

description: Sample 1


title: WT Col rep 1


title: High_rep4


title: MEF_FC_1

value: primary embryonic fibroblasts (MEFs)

tag: passages

value: FVB/NJxCAST/EiJ

tag: developmental stage


title: High_rep1


title: WT input

description: Sample 9

tag: strain

tag: antibody


title: High_rep2

tag: genotype


title: Mock_ChIP_Seq

city: Toulouse

first: Yannick

last: Carrier

address: 118, route de narbonne

country: France

institute: CNRS

data_processing:
Basecalls was perfomed by using CASAVA 1.8
ChIP-Seq reads were aligned to the dm3 assembly with Bowtie v0.12.7.
Genome_build: dm3
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)
Supplementary_files_format_and_content: "ChIP_Col-Mock_normalized" file was made with the "bamCompare" module part of deepTools (Ramirez F et al.2014). Normalized read coverage of the "Mock_ChIP_Seq" experiment was substracted from "COL_ChIP_Seq" to obtain a Bedgraph representation.
Supplementary_files_format_and_content: "Chip_Col_Summit" file is a BED file containing Summit coordinates found by the peak calling program "SISSRs". Summits annotation was made by using the PeakAnalyzer software.

source_name: whole embryos

extract_protocol:
Dounced fixed embryos where used to obtain nuclear fraction, then chromatine was sonicated. Cleared nuclear extract were used to perfomed immunoprecipitation. Competitive elution was made with a COL recombinant protein in order to release precipitated Col-DNA complexes.
ChIP-seq 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 analysis DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent). The libraries were loaded in the flowcell at 8pM concentration and clusters were generated using the Cbot and sequenced on the Illumina Genome Analyzer IIx as single-end 54 base reads following Illumina's instructions

value: stage 13-14

tag: chip antibody

value: Non relevant antibody (HA.11 Clone 16B12 Monoclonal Antibody; Covance #MMS-101P lot 14973401)


title: Input_DNA


title: Low_rep6

value: low


title: Low_rep5


title: WT Col rep 3

value: Col


title: Low_rep4


title: Low_rep3


title: Control_rep6

value: control


title: Control_rep4


title: Low_rep1


title: Control_rep5


title: Low_rep2


title: IgG_rep4_ChIPSeq

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

description:
2b-140612_ep_CACCTC_L005_R1_001.fastq.gz
2b-140612_ep_CACCTC_L006_R1_001.fastq.gz

data_processing:
Basecalls performed using CASAVA version v1.8.2
Raw reads were aligned using Bowtie (version 0.12.7)  (Langmead et al., 2009) to build version hg19 of the human genome retaining only uniquely mapped reads.  Redundant reads were removed using SAMtools
The IDR (Irreproducible Discovery Rate) framework was used to assess the reproducibility of replicate experiments and to obtain a single set of peak calls for each TF (Landt et al., 2012)
MACS2 version 2.0.10 (Zhang et al., 2008)  was used to call peaks in individual replicates using IgG ChIP-seq as control sample and an IDR  threshold of 0.01 was applied for all datasets to identify an optimal and robust number of peaks
Genome_build: hg19
Supplementary_files_format_and_content: NarrowPeak files contain the genomic locations of peaks identified using MACS2 and the IDR framework. NarrowPeak format is a BED6+4 format (http://genome.ucsc.edu/FAQ/FAQformat.html#format12)

source_name: MDA-MB-231 breast cancer cells

growth_protocol: MDA MB 231 cells were cultured in DMEM:F12 + 10% FBS.

extract_protocol:
Cross-linked chromatin was sheared by sonication and immunoprecipitated with YAP, TAZ, TEAD4 and JUN antibodies. DNA was purified by phenol/chloroform extraction and ethanol precipitation.
NuGEN Ovation Ultralow Library Prep System kit

tag: cell line

value: Mouse IgG (SCBT, sc-2025, lot A1813)


title: Control_rep2


title: Control_rep1


title: Control_rep3


title: COL_ChIP_Seq

value: Mix of 3 anti-COL home made monoclonal antibodies


title: JUN_rep1_ChIPSeq

description:
Pooling of IgG_rep3_ChIPSeq and IgG_rep5_ChIPSeq was used as control for Peak calling within the IDR framework
processed data file: MDA-MB-231_JUN_IDR_0.01.narrowPeak
1d-140612_ep_CCTCGG_L003_R1_001.fastq.gz
1d-140612_ep_CCTCGG_L004_R1_001.fastq.gz

value: JUN (BD Bioscience, 610326, lot 3263734)


title: TEAD4_rep2_ChIPSeq

description:
Pooling of IgG_rep3_ChIPSeq and IgG_rep4_ChIPSeq was used as control for Peak calling within the IDR framework
processed data file: MDA-MB-231_TEAD4_IDR_0.01.narrowPeak
2c-140612_ep_GTGGCC_L005_R1_001.fastq.gz
2c-140612_ep_GTGGCC_L006_R1_001.fastq.gz


title: TEAD4_rep1_ChIPSeq

description:
Pooling of IgG_rep3_ChIPSeq and IgG_rep4_ChIPSeq was used as control for Peak calling within the IDR framework
processed data file: MDA-MB-231_TEAD4_IDR_0.01.narrowPeak
1c-140612_ep_TTCAGC_L003_R1_001.fastq.gz
1c-140612_ep_TTCAGC_L004_R1_001.fastq.gz


title: IgG_rep2_ChIPSeq

description:
6-130319_ep_AAGACG_L005_R1_001.fastq.gz
6-130319_ep_AAGACG_L006_R1_001.fastq.gz
6-130319_ep_AAGACG_L007_R1_001.fastq.gz

value: Rabbit IgG (Sigma, I5006)


title: TAZ_rep2_ChIPSeq

description:
Pooling of IgG_rep1_ChIPSeq and IgG_rep2_ChIPSeq was used as control for Peak calling within the IDR framework
processed data file: MDA-MB-231_TAZ_IDR_0.01.narrowPeak
8-130319_ep_CACCTC_L005_R1_001.fastq.gz
8-130319_ep_CACCTC_L006_R1_001.fastq.gz
8-130319_ep_CACCTC_L007_R1_001.fastq.gz

value: WWTR1 (Sigma, HPA007415,lot C78623)


title: YAP_rep2_ChIPSeq

description:
Pooling of IgG_rep1_ChIPSeq and IgG_rep2_ChIPSeq was used as control for Peak calling within the IDR framework
processed data file: MDA-MB-231_YAP_IDR_0.01.narrowPeak
7-130319_ep_GGATGT_L005_R1_001.fastq.gz
7-130319_ep_GGATGT_L006_R1_001.fastq.gz
7-130319_ep_GGATGT_L007_R1_001.fastq.gz


title: YAP_rep1_ChIPSeq

description:
Pooling of IgG_rep1_ChIPSeq and IgG_rep2_ChIPSeq was used as control for Peak calling within the IDR framework
processed data file: MDA-MB-231_YAP_IDR_0.01.narrowPeak
3-130319_ep_GTGTTA_L005_R1_001.fastq.gz
3-130319_ep_GTGTTA_L006_R1_001.fastq.gz
3-130319_ep_GTGTTA_L007_R1_001.fastq.gz


title: IgG_rep1_ChIPSeq

description:
2-130319_ep_TTCGCT_L005_R1_001.fastq.gz
2-130319_ep_TTCGCT_L006_R1_001.fastq.gz
2-130319_ep_TTCGCT_L007_R1_001.fastq.gz


title: D90_GFPpos_rep2

tag: cell type

value: GFP positive neural retina cells

tag: day post induction

value: Day 90


title: TAZ_rep1_ChIPSeq

description:
Pooling of IgG_rep1_ChIPSeq and IgG_rep2_ChIPSeq was used as control for Peak calling within the IDR framework
processed data file: MDA-MB-231_TAZ_IDR_0.01.narrowPeak
4-130319_ep_ACAAAC_L005_R1_001.fastq.gz
4-130319_ep_ACAAAC_L006_R1_001.fastq.gz
4-130319_ep_ACAAAC_L007_R1_001.fastq.gz


title: SI_8025-1-10-dht-polya

first: Marcin

middle: Piotr

last: Cieslik

state: Michigan

address: 500 S State St

department: Pathology

data_processing:
File were aligned using STAR v 3
Reads were counted within Ensembl 75 exon regions that intersect Agilent Whome-Exome Capture V4 probes. FeatureCounts in paired-end mode excluding multi-mapped reads but including duplicate reads was used in stranded mode.
Genome_build: GRCh37
Supplementary_files_format_and_content: featureCounts file format

molecule: polyA RNA

source_name: VcaP_DHT_polyA selection

growth_protocol: Immortalized prostate cancer VCaP cell line was obtained from the American Type Culture Collection (Manassas, VA) and was grown in DMEM (Invitrogen) and supplemented with 10% fetal bovine serum (FBS) with 1% penicillin-streptomycin. Before the treatments cells were grown in androgen-depleted media lacking phenol red and supplemented with 10% charcoal-stripped serum and 1% penicillin-streptomycin.

extract_protocol:
RNA was isolated using the Qiagen AllPrep Kit (cat. no. 80404)
Details of the capture RNA-seq and poly(A) RNA-seq library preparation protocols are provided as Supplementary Data. Briefly, for capture libraries we start with 1-3µg of total RNA, and proceed through first-strand synthesis, second strand synthesis, end repair, A-tailing, adapter ligation, size selection on 3% agarose gel, uridine digestion, hybridization to capture probes, washing, and a final PCR step. For poly(A) libraries the protocol is the same, but the last capture and PCR step is omitted and replaced with oligo dT bead selection on input RNA. The stranded capture and poly(A) libraries were sequenced on an Illumina HiSeq 2500 using V3 chemistry.

treatment_protocol: After 24 hours, cells were treated either with androgen (1nM 5α-dihydrotestosterone, DHT) or anti-androgen (enzalutamide, MDV3100, MDV). Cells were harvested for RNA isolation at 24 hours post-treatment.

tag: cell ;ome

value: VcaP

value: Immortalized prostate cancer cell line

tag: treated with

value: DHT (dihydrotestosterone)

tag: time point

value: 24 hrs post-treatment

tag: library preparation protocol

value: poly(A)+ selection

tag: rin


title: IgG_rep5_ChIPSeq

description: 3a-140930_ep_AAGAGG_L007_R1_001.fastq.gz


title: SI_8026-1-10-dht-polya


title: SI_8029-1-8.2-dht-polya


title: SI_8028-1-9.1-dht-polya


title: SI_8031-2-5.7-dht-polya


title: IgG_rep3_ChIPSeq

description:
1b-140612_ep_GGACCC_L003_R1_001.fastq.gz
1b-140612_ep_GGACCC_L004_R1_001.fastq.gz


title: SI_8033-2-2.5-dht-polya


title: SI_8036-3-10-mdv-polya

source_name: VcaP_MDV_polyA selection

value: MDV3100 (enzalutamide)


title: SI_8034-2-2.4-dht-polya


title: JUN_rep2_ChIPSeq

description:
Pooling of IgG_rep3_ChIPSeq and IgG_rep5_ChIPSeq was used as control for Peak calling within the IDR framework
processed data file: MDA-MB-231_JUN_IDR_0.01.narrowPeak
3b-140930_ep_GGAGAA_L007_R1_001.fastq.gz


title: SI_8039-3-8.3-mdv-polya


title: SI_8037-3-10-mdv-polya


title: SI_8035-3-10-mdv-polya


title: SI_8038-3-9-mdv-polya


title: SI_8027-1-10-dht-polya


title: SI_8032-2-3.5-dht-polya


title: SI_8041-4-5.7-mdv-polya


title: SI_8044-4-3.3-mdv-polya


title: SI_8045-5-10-dht-capture

source_name: VcaP_DHT_exome capture

value: whole-exome capture


title: SI_8040-4-7.3-mdv-polya


title: SI_8046-5-10-dht-capture


title: SI_8047-5-10-dht-capture


title: SI_8048-5-9.1-dht-capture


title: SI_8043-4-3-mdv-polya


title: SI_8030-2-7.3-dht-polya


title: SI_8050-6-7.3-dht-capture


title: SI_8051-6-5.7-dht-capture


title: SI_8049-5-8.2-dht-capture


title: SI_8055-7-10-mdv-capture

source_name: VcaP_MDV_exome capture


title: SI_8052-6-3.5-dht-capture


title: gemin2 mutant 24h rep 1

source_name: pool of tissues

growth_protocol: WT (Col) and gemin2 mutants seeds were grown on Murashige and Skoog medium containing 0.8% agarose, stratified for 4 d in the dark at 4 °C, and then grown for nine days under continuous white light at 22ºC or exposed for 1 or 24 h to 10ºC on the 9th day, before harvesting.

extract_protocol:
Total RNA was extracted with RNeasy Plant Mini Kit (QIAGEN) following the manufacturer’s protocols. To estimate the concentration and quality of samples, NanoDrop 2000c (Thermo Scientific) and gel electrophoresis were used, respectively.
Libraries were prepared following the TruSeq RNA Sample Preparation Guide (Illumina). Briefly, 3 μg of total RNA was polyA-purified and fragmented, and first-strand cDNA synthesized by reverse transcriptase (SuperScript II; Invitrogen) and random hexamers. This was followed by RNA degradation and second-strand cDNA synthesis. End repair process and addition of a single A nucleotide to the 3′ ends allowed ligation of multiple indexing adapters. Then, an enrichment step of 12 cycles of PCR was performed. Library validation included size and purity assessment with the Agilent 2100 Bioanalyzer and the Agilent DNA1000 kit (Agilent Technologies)

tag: ecotype

value: gemin2 mutant

tag: tissue

value: whole plant

tag: age (days)


title: SI_8056-7-10-mdv-capture


title: SI_8054-6-2.4-dht-capture


title: WT Col 24h rep 2

value: Col

value: Wild type


title: WT Col 24h rep 3


title: SI_8042-4-3.6-mdv-polya


title: gemin2 mutant 1h rep 3


title: gemin2 mutant 1h rep 2


title: SI_8059-7-8.3-mdv-capture


title: SI_8057-7-10-mdv-capture


title: WT Col 24h rep 1


title: gemin2 mutant 24h rep 3


title: SI_8058-7-9-mdv-capture


title: SI_8063-8-3-mdv-capture


title: SI_8064-8-3.3-mdv-capture


title: SI_8062-8-3.6-mdv-capture


title: SI_8060-8-7.3-mdv-capture


title: SI_8053-6-2-dht-capture


title: WT Col 1h rep 3


title: gemin2 mutant 1h rep 1


title: gemin2 mutant 24h rep 2


title: Bb_RNA-Seq_with_ND_rep1

city: Zhoushan

first: Jianhua

last: Liu

state: Zhejiang

address: 10 Tiyu Road, Room 502

department: Ocean Research Centre of Zhoushan

institute: Zhejiang University

data_processing:
Low quality reads were filtered with Trimmomatic (trim first 12nts in 5' of reads, trim last 5 nts in 3' of reads if scores were too low; HEADCROP:12 TRAILING:5)
De novo assembly using Trinity with processed reads (--JM 110G --SS_lib_type FR --CPU 60 --min_contig_length 300 --KMER_SIZE 25)
Transcriptome were annotated by running BLASTX to 6 algal genomes (evalue < 1e-7, length of homology to subject/ full length> 40%) (-max_target_seqs 1 -num_threads 60 -outfmt 6 -evalue 1e-7)
Expression levels of annotated EST were determined using Trinity-bundled perl script align_and_estimate_abundance.pl which utilizes RSEM to calculate FPKM values (--est_method RSEM --aln_method bowtie2 --SS_lib_type FR --thread_count 60 --trinity_mode)
Differentially expressed ESTs were identified using Trinity-bundled perl script run_DE_analysis.pl based on the ESTs counts Matrix
Genome_build: B.braunii_non_redundant_transcriptome_assembly_61220.fasta
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Botryococcus braunii

source_name: 779 algae culture cells

growth_protocol: The subisolate was cultivated using BB liquid medium in a 2.5 L low-form flask with shaking at 100 rpm at 25°C under continuous illumination of ~250 mol photon m-2 sec-1. Culture was supplied with 2% CO2 through bubbling.

extract_protocol:
Total RNA was extracted from B. braunii 779 cells prior to and after ND using TRIzol Plus RNA Purification System (Invitrogen-LifeTechnologies Co., Carlsbad, CA, USA) according to manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For analysis of the subisolate in response to ND, the log-phase cells of the subisolate were subjected to medium shift from nitrogen replete-BB medium to nitrogen depleted BB-N medium (i.e., BB medium without sodium nitrate) and cultivation for 3 days for analysis of lipid content and transcriptomic response to ND.

tag: treatment

value: with nitrogen deprivation (ND)


title: gemin2 mutant control rep 2


title: gemin2 mutant control rep 3


title: Bb_RNA-Seq_with_ND_rep2


title: gemin2 mutant control rep 1


title: SI_8061-8-5.7-mdv-capture


title: Bb_RNA-Seq_without_ND_rep1

value: without nitrogen deprivation (ND)


title: Bb_RNA-Seq_without_ND_rep2


title: Time21-replicate 2

status: Public on Aug 01 2015

city: East Lansing

first: Eric

middle: Robert

last: Poliner

address: 612 Wilson Road

institute: Michigan State University

description: Time21-replicate 2

data_processing:
Reads of each of samples were mapped using Tophat with default parameters except for intron length (min 13, max 8712) and max-multi-hits (1). Gene models on non-chromosomal fragments were not considered.
FPKM (Fragments Per Kilobase of transcript per Million mapped reads) per gene was calculated using Cufflinks (Trapnell et al. 2010) with parameter –I 8712.
Genome_build: N. oceanica CCMP1779 V1 (Vieler et al., 2012b)
Supplementary_files_format_and_content: fpkm data are available in the text files associated with each sample record. The genome and assembly files (fasta and GFF) are available on the series record.

organism: Nannochloropsis oceanica

source_name: N. oceanica 9 hours into dark period

growth_protocol: For all experiments N. oceanica CCMP1779 cells were grown in flasks containing f/2 media under 12 h light:12 h dark cycles at 22 C under agitation (100 rpm).  Light intensity during light periods was 40 micromol s-1 m-2. ZT0-9 and ZT12-21 sets of samples were grown in two identical incubators set to reversed light/dark cycles. The ZT0 samples were collected in the dark and ZT12 samples in the light.

extract_protocol:
RNA was extracted from ground frozen pellets using the Omega eZNA Plant RNA kit (Omega Biotek).
Library preparation was by the Illumina Tru-Seq Stranded kit


title: Input DNA

status: Public on Aug 02 2015

city: Jerusalem

first: Eran

last: Meshorer

address: Givat Ram

institute: The Hebrew University of Jerusalem

data_processing:
HPβ1 ChIP-Seq reads were aligned to the mouse genome (mm9) using Bowtie (Longmead et al., Genome Biol 2009), taking only uniquely aligned reads with no more than 1 mismatch.
Peaks were extracted using MACS 1.4 (Zhang et al., Genome Biol 2008), setting a minimal P-value cutoff 10-3 and a fold change range for a model building between 8-30.
HPβ1 was associated with a gene if it had a peak within the gene body or within 5 kb upstream from the TSS.
Genome_build: MGSCv37 (mm9)
Supplementary_files_format_and_content: BED file includes peaks.

source_name: Mouse ESCs, input

growth_protocol: mESC were maintained in PowerStem EsPro1 supplemented with LIF on gelatine.

extract_protocol:
For each sample, 1 x 10^6 cells were cross-linked with 1% PFA and cell nuclei were prepared using a swelling buffer (25 mM Hepes, pH 7.8, 1 mM MgCl2, 10 mM KCl, 0.1% NP-40, 1 mM DTT). Chromatin was sheared to dinucleosomal fragments.
Libraries were prepared according to Illumina standard protocols with external barcodes.

tag: strain/background

value: embryonic stem cells (ESCs)


title: WT Col 1h rep 1


title: Time18-replicate 2

description: Time18-replicate 2

source_name: N. oceanica 6 hours into dark period

tag: strain


title: Time21-replicate 1

description: Time21-replicate 1


title: Time15-replicate 2

description: Time15-replicate 2

source_name: N. oceanica 3 hours into dark period


title: Time18-replicate 1

description: Time18-replicate 1


title: WT Col 1h rep 2


title: Time15-replicate 1

description: Time15-replicate 1


title: HP1β ChIP-Seq

description: ChIP DNA

source_name: Mouse ESCs, HP1β ChIP

value: HP1β (Euromedex 1MOD-1A9-AS, lot# 091809)


title: Time9-replicate 1

description: Time9-replicate 1

source_name: N. oceanica 9 hours into light period


title: Time9-replicate 2

description: Time9-replicate 2


title: Time12-replicate 2

description: Time12-replicate 2

source_name: N. oceanica 12 hours into light period


title: Time6-replicate 2

description: Time6-replicate 2

source_name: N. oceanica 6 hours into light period


title: Time12-replicate 1

description: Time12-replicate 1


title: Time6-replicate 1

description: Time6-replicate 1


title: Time3-replicate 2

description: Time3-replicate 2

source_name: N. oceanica 3 hours into light period


title: Time0-replicate 1

description: Time0-replicate 1

source_name: N. oceanica just prior to lights on


title: Time3-replicate 1

description: Time3-replicate 1


title: RPL_yeast_ligase_rep2

city: San Francisco

first: Vijay

last: Ramani

state: California

department: Biochemistry & Biophysics

institute: UCSF

data_processing:
Adapter trimming and read fusion of mate-pairs by SeqPrep
Alignment via STAR/2.4.0 (following parameters:
Processing of STAR intron calls using custom bash/python scripts provided with manuscript
Genome_build: hg19 / SacCer3
Supplementary_files_format_and_content: "Pairs" files that document coordinates of ligation junctions between/within molecular species

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae strain FY

growth_protocol: GM12878 were grown at 37 in RPMI-1640 containing 15% FBS, 1X Anti-Anti, and 1X Plasmocin; FY were struck out on YPD plates and grown at 30

extract_protocol:
RNA was extracted using TRIZol and Zymo DirectZOL columns
Illumina TruSeq

treatment_protocol: Cells were treated in situ using the RPL protocol as described in the associated manuscript

value: FY


title: Time0-replicate 2

description: Time0-replicate 2


title: WT Col control rep 3


title: WT Col control rep 2


title: control

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

data_processing:
Reads were mapped to the human genome (hg19) with Bowtie2.
Aligned files were converted to bam and sorted using Samtools.
Peaks detection was carried with case-control strategy (detected peaks are given in bed files)
HSF target sites were annotated to genomic regions using HOMER software (annotated binding sites are given in text file)
Genome_build: hg19
Supplementary_files_format_and_content: fastq - raw data from Illumina sequencer; bed - detected peaks, can be open in text editors/Excel; txt - annotated binding sites, can be opened in text editors/Excel.

source_name: HSF1 ChIP DNA from untreated cells cultured at 37°C

growth_protocol: Experiments were performed using the human U-2 OS osteosarcoma cell line (cells were purchased from ATCC; ref. no. HTB-96); cells were grown in McCoy’s medium supplemented with 10% heat-inactivated fetal bovine serum at 37°C and 5% CO2.

extract_protocol:
Cells were fixed by adding of formaldehyde to a final concentration of 1% and incubated at room temperature for 10 minutes. Next 2.5 M glycine was added (1/20 volume) for 5 minutes. Cells were washed with ice-cold PBS and lysed following the manufacturer’s protocol. For analyses of HSF1 binding, the ChIP assay was carried out according to protocol for ChIP kit of Invitrogen (Dynabeads Protein A). For 40 µg of chromatin, sonicated to 100-500 bp fragments and 4 µg of rabbit anti-HSF1 (cat. no SPA-901, Enzo) polyclonal antibodies were used.
Sequencing libraries were generated using ChIP-Seq Sample Prep Kit (Illumina). Template amplification and cluster generation were performed using the cBot and TruSeq SR Cluster Kit v2 cBot-GA for cBot, and 80 nucleotides were sequenced with Illumina Genome Analyzer IIx using TruSeq SBS Kit v5 sequencing kits.

treatment_protocol:
untreated
Described separately for particular samples.

value: U-2 OS

tag: antibody

tag: Sex

value: female

tag: tissue/cells

value: bone/osteosarcoma

tag: age

value: 15 years


title: HS_20

source_name: HSF1 ChIP DNA from cells heat shocked at 43°C for 20 minutes

treatment_protocol:
A growth medium from experimental dish was replaced with an equal volume of CO2 saturated, pre-heated to 43°C medium. Dish was then placed in a growth incubator at 43°C and cultured for 20 minutes.
Described separately for particular samples.

tag: cell line


title: WT Col control rep 1

tag: genotype


title: HS_10

source_name: HSF1 ChIP DNA from cells heat shocked at 43°C for 10 minutes

treatment_protocol:
A growth medium from experimental dish was replaced with an equal volume of CO2 saturated, pre-heated to 43°C medium. Dish was then placed in a growth incubator at 43°C and cultured for 10 minutes.
Described separately for particular samples.


title: C57BL/6J Parent Liver

city: Salt Lake City

last: Gregg

state: Utah

address: 323 Wintrobe Bldg 530, 20 North 1900 East

department: Neurobiology & Anatomy

institute: University of Utah

description: Used for SNP validation

data_processing: Supplementary_files_format_and_content: Allele expression counts are derived by summing reads from SNPs in the same gene and presented as Cast (CastEiJ) and C57 (C57BL/6J) allele read counts for each replicate. Column titles indicate the cross direction (F1i: Cast mother X C57 father; F1r: C57 mother X Cast father), the allele (Cast or C57) and the replicate (1-9)

source_name: Adult Male and Female Parental Liver pooled

extract_protocol:
RNA was extracted using Trizol reagent and Dnase Treated and purified using Qiagen Rneasy Kit
Libraries were prepared according to the Illumina TrueSeq sample prep kit manual
Illumina TrueSeq mRNA Sample Prep with poly(A) selection


title: Cast Parent Liver

description: Used for SNP validation

value: CastEiJ


title: Cast Parent DRN

description: Used for SNP validation

source_name: Adult Male and Female Parental DRN pooled


title: C57BL/6J Parent DRN

description: Used for SNP validation


title: WT Adult pancreas reg VP2_4C

city: Madrid

first: Ana

last: Losada

state: Madrid

address: C/ Melchor Fernández Almagro, 3.

department: Molecular Oncology Programme

country: Spain

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

description:
4cutter 4C sequencing
processed data file: AC_4C_1214_WT_VP1_raw.txt.gz

data_processing:
Library strategy: 4C-seq
Read files were quality-checked with FastQC.
Convert BAM files to FASTQ using bedtools v2.20.1 where needed
Transform to Illumina FASTQ using NGSQCToolkit v2.3
Convert and process (map, calculate cis interactions) FASTQ files using 4cseqpipe
Genome_build: GRCm37/mm9
Supplementary_files_format_and_content: Processed data files are 4cseqpipe mapped files for each original FASTQ/BAM file. They allow to generate figures for interactions around the viewpoints with 4cseqpipe

source_name: pancreas

extract_protocol:
Preparation of 4C samples was performed as described (van de Werken, 2012) with some modifications. Freshly collected tissues were incubated with collagenase (0.0065% collagenase I in 10% FBS/PBS for cortex, and 1.33 mg/ml collagenase P in HBSS for pancreas) for 40 min at 37ºC in a shaker. The resulting cell suspension was filtered through a 40-μm cell strainer in order to get a single cell preparation. Cells were centrifuged at 1,100 rpm for 5 min at RT and the cell pellet was resuspended in 10 ml of fixing solution containing 2% formaldehyde in 10% FBS/PBS. After 10 min, 0.125 M glycine was added to stop fixation and the mixture was incubated for 5 min at RT. Cells were pelleted and nuclei isolated upon incubation in cold lysis buffer in the following conditions: For the brain, 10 min in 50 mM Tris pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% TX-100 + protease inhibitors cocktail; for the pancreas, 40 min in 50 mM Tris pH 7.5, 50 mM NaCl, 5 mM EDTA, 1% NP40, 2% TX-100 + protease inhibitors cocktail. Proper lysis was determined by methyl green-pyronin staining.
4C-seq libraries were amplified using long primers with 18-21 bp homology to the bait sequence and Illumina paired-end adapter flanks. HindIII and CvIQ (NEB) were used as as first and second cutters, respectively for preparation of the 6-cutter libraries. DpnII and CvIQ (NEB) were used as first and second cutters, respectively for preparation of the 4-cutter libraries.  Pairs of samples were sequenced together thus the raw and processed data files are shared among samples. The 4cseqpipe software identifies the viewpoints and the possible cut points out of the raw data files and flags them in the processed files.

value: 8-10 week old


title: C57BL/6J Parent ARN

description: Used for SNP validation

source_name: Adult Male and Female Parental ARN pooled


title: Wild Mouse Daughter Trio #3

source_name: Adult female hypothalamus

value: Idaho derived wild mouse

tag: gender

value: hypothalamus


title: Wild Mouse Father Trio #3

source_name: Adult male hypothalamus

value: male


title: Wild Mouse Mother Trio #2


title: Cast Parent Muscle

description: Used for SNP validation

source_name: Adult Male and Female Parental Muscle pooled


title: Cast Parent ARN

description: Used for SNP validation


title: Wild Mouse Mother Trio #1


title: RPL_yeast_ligase


title: Wild Mouse Daughter Trio #1


title: Wild Mouse Daughter Trio #2


title: Wild Mouse Father Trio #2


title: F1i Muscle Rep#5

description:
Muscle/F1r_rep6_muscle/F1r_rep6_muscle_ALL.txt.gz, Index 10 TAGCTT, GATCGGAAGAGCACACGTCTGAACTCCAGTCACTAGCTT ,ATCTCGTATGCCGTCTTCTGCTTG
Muscle_AlleleCountData.txt

source_name: Adult female muscle

value: F1i Hybrid (CastEiJ mother X C57BL/6J father)

value: 8 weeks

value: muscle


title: Wild Mouse Father Trio #1


title: F1i Muscle Rep#3

description:
Muscle/F1r_rep3_muscle/F1r_rep3_muscle_ALL.txt.gz, Index 5 ACAGTG, GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTG ,ATCTCGTATGCCGTCTTCTGCTTG
Muscle_AlleleCountData.txt


title: Wild Mouse Mother Trio #3


title: F1i Muscle Rep#4

description:
Muscle/F1r_rep4_muscle/F1r_rep4_muscle_ALL.txt.gz, Index 8 ACTTGA, GATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGA ,ATCTCGTATGCCGTCTTCTGCTTG
Muscle_AlleleCountData.txt


title: F1i Muscle Rep#2

description:
Muscle/F1r_rep2_muscle/F1r_rep2_muscle_ALL.txt.gz, Index 4 TGACCA, GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCA ,ATCTCGTATGCCGTCTTCTGCTTG
Muscle_AlleleCountData.txt


title: SA1 +/-  Adult pancreas reg VP2_4C

description:
4cutter 4C sequencing
processed data file: AC_4C_1214_HT_VP1_raw.txt.gz


title: F1i Muscle Rep#8

description:
Muscle/F1r_rep9_muscle/F1r_rep9_muscle_ALL.txt.gz, Index 16 CCGTCC, GATCGGAAGAGCACACGTCTGAACTCCAGTCACCCGTCC ,ATCTCGTATGCCGTCTTCTGCTTG
Muscle_AlleleCountData.txt


title: F1i Muscle Rep#1

description:
Muscle/F1r_rep1_muscle/F1r_rep1_muscle_ALL.txt.gz, Index 2 CGATGT, GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGT ,ATCTCGTATGCCGTCTTCTGCTTG
Muscle_AlleleCountData.txt


title: F1r Muscle Rep#7

description:
Muscle/F1i_rep8_muscle/F1i_rep8_muscle_ALL.txt.gz, Index 12 CTTGTA, GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTA ,ATCTCGTATGCCGTCTTCTGCTTG
Muscle_AlleleCountData.txt

value: F1R Hybrid (CastEiJ father X C57BL/6J mother)


title: F1r Muscle Rep#8

description:
Muscle/F1i_rep9_muscle/F1i_rep9_muscle_ALL.txt.gz, Index 14 AGTTCC, GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTCC ,ATCTCGTATGCCGTCTTCTGCTTG
Muscle_AlleleCountData.txt


title: F1r Muscle Rep#4

description:
Muscle/F1i_rep5_muscle/F1i_rep5_muscle_ALL.txt.gz, Index 7 CAGATC, GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATC ,ATCTCGTATGCCGTCTTCTGCTTG
Muscle_AlleleCountData.txt


title: F1r Muscle Rep#1

description:
Muscle/F1i_rep1_muscle/F1i_rep1_muscle_ALL.txt.gz, Index 1 ATCACG, GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACG ,ATCTCGTATGCCGTCTTCTGCTTG
Muscle_AlleleCountData.txt


title: F1i Liver Rep#8

description:
Liver/Flowcell_13_s2/111004_SN343_0221_AC07DYACXX,IlluminaIndex6,GCCAAT,GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAAT,ATCTCGTATGCCGTCTTCTGCTTG
Liver_AlleleCountData.txt

source_name: Adult female liver

value: liver


title: F1r Muscle Rep#2

description:
Muscle/F1i_rep3_muscle/F1i_rep3_muscle_ALL.txt.gz, Index 3 TTAGGC, GATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGC ,ATCTCGTATGCCGTCTTCTGCTTG
Muscle_AlleleCountData.txt


title: F1r Muscle Rep#6

description:
Muscle/F1i_rep7_muscle/F1i_rep7_muscle_ALL.txt.gz, Index 11 GGCTAC, GATCGGAAGAGCACACGTCTGAACTCCAGTCACGGCTAC ,ATCTCGTATGCCGTCTTCTGCTTG
Muscle_AlleleCountData.txt


title: F1r Muscle Rep#5

description:
Muscle/F1i_rep6_muscle/F1i_rep6_muscle_ALL.txt.gz, Index 9 GATCAG, GATCGGAAGAGCACACGTCTGAACTCCAGTCACGATCAG ,ATCTCGTATGCCGTCTTCTGCTTG
Muscle_AlleleCountData.txt


title: F1i Liver Rep#7

description:
Liver/Flowcell_13_s1/111004_SN343_0221_AC07DYACXX,59,IlluminaIndex4,TGACCA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCA,ATCTCGTATGCCGTCTTCTGCTTG
Liver_AlleleCountData.txt


title: F1i Liver Rep#4

description:
Liver/Flowcell_12_s1/111001_SN343_0220_BD0C63ACXX/Project_Chris,59,IlluminaIndex4,TGACCA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCA,ATCTCGTATGCCGTCTTCTGCTTG
Liver_AlleleCountData.txt


title: F1i Muscle Rep#6

description:
Muscle/F1r_rep7_muscle/F1r_rep7_muscle_ALL.txt.gz, Index 13 AGTCAA, GATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTCAA ,ATCTCGTATGCCGTCTTCTGCTTG
Muscle_AlleleCountData.txt


title: F1i Liver Rep#5

description:
*Liver/Flowcell_12_s6/111001_SN343_0220_BD0C63ACXX/Project_Chris,59,IlluminaIndex4,TGACCA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCA,ATCTCGTATGCCGTCTTCTGCTTG
Liver_AlleleCountData.txt


title: F1i Liver Rep#6

description:
Liver/Flowcell_12_s3/111001_SN343_0220_BD0C63ACXX/Project_Chris,59,IlluminaIndex2,CGATGT,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGT,ATCTCGTATGCCGTCTTCTGCTTG
Liver_AlleleCountData.txt


title: F1i Liver Rep#2

description:
Liver/Flowcell_11_s2/111109_SN343_0251_BC062MACXX,IlluminaIndex6,GCCAAT,GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAAT,ATCTCGTATGCCGTCTTCTGCTTG
Liver_AlleleCountData.txt


title: F1r Liver Rep#8

description:
Liver/Flowcell_13_s7/111004_SN343_0221_AC07DYACXX,59,IlluminaIndex12,CTTGTA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTA,ATCTCGTATGCCGTCTTCTGCTTG
Liver_AlleleCountData.txt


title: F1i Liver Rep#3

description:
Liver/Flowcell_11_s3/111109_SN343_0251_BC062MACXX,59,IlluminaIndex2,CGATGT,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGT,ATCTCGTATGCCGTCTTCTGCTTG,CGATGT
Liver_AlleleCountData.txt


title: F1i Muscle Rep#7

description:
Muscle/F1r_rep8_muscle/F1r_rep8_muscle_ALL.txt.gz, Index 15 ATGTCA, GATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCA ,ATCTCGTATGCCGTCTTCTGCTTG
Muscle_AlleleCountData.txt


title: F1r Liver Rep#7

description:
Liver/Flowcell_13_s6/111004_SN343_0221_AC07DYACXX,59,IlluminaIndex4,TGACCA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCA,ATCTCGTATGCCGTCTTCTGCTTG
Liver_AlleleCountData.txt


title: F1r Liver Rep#6

description:
Liver/Flowcell_13_s5/111004_SN343_0221_AC07DYACXX,IlluminaIndex2,CGATGT,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGT,ATCTCGTATGCCGTCTTCTGCTTG
Liver_AlleleCountData.txt


title: F1i Liver Rep#1

description:
Liver/Flowcell_11_s1/111109_SN343_0251_BC062MACXX,59,IlluminaIndex4,TGACCA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCA,ATCTCGTATGCCGTCTTCTGCTTG
Liver_AlleleCountData.txt


title: F1r Liver Rep#3

description:
Liver/Flowcell_12_s5/111001_SN343_0220_BD0C63ACXX/Project_Chris,IlluminaIndex2,CGATGT,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGT,ATCTCGTATGCCGTCTTCTGCTTG
Liver_AlleleCountData.txt


title: F1r Liver Rep#2

description:
Liver/Flowcell_11_s7/111109_SN343_0251_BC062MACXX,IlluminaIndex12,CTTGTA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTA,ATCTCGTATGCCGTCTTCTGCTTG
Liver_AlleleCountData.txt


title: F1i DRN Rep#5

description:
Dorsal Raphe/Flowcell5_s2/110722_SN343_0177_BC001DABXX,IlluminaIndex4,TGACCA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCA,ATCTCGTATGCCGTCTTCTGCTTG
DRN_AlleleCountData.txt

source_name: Adult female dorsal raphe nucleus

value: dorsal raphe nucleus


title: F1i DRN Rep#9

description:
Dorsal Raphe/Flowcell6_s3/110726_SN343_0181_BB09D6ABXX,59,IlluminaIndex5,ACAGTG,GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTG,ATCTCGTATGCCGTCTTCTGCTTG
DRN_AlleleCountData.txt


title: F1i DRN Rep#6

description:
Dorsal Raphe/Flowcell5_s3/110722_SN343_0177_BC001DABXX,59,IlluminaIndex5,ACAGTG,GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTG,ATCTCGTATGCCGTCTTCTGCTTG
DRN_AlleleCountData.txt


title: F1i DRN Rep#4

description:
Dorsal Raphe/Flowcell5_s1/110722_SN343_0177_BC001DABXX,59,IlluminaIndex2,CGATGT,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGT,ATCTCGTATGCCGTCTTCTGCTTG,CGATGT
DRN_AlleleCountData.txt


title: F1r Liver Rep#1

description:
Liver/Flowcell_11_s6/111109_SN343_0251_BC062MACXX,59,IlluminaIndex4,TGACCA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCA,ATCTCGTATGCCGTCTTCTGCTTG
Liver_AlleleCountData.txt


title: F1i DRN Rep#7

description:
Dorsal Raphe/Flowcell6_s1/110726_SN343_0181_BB09D6ABXX,59,IlluminaIndex2,CGATGT,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATGT,ATCTCGTATGCCGTCTTCTGCTTG,CGATGT
DRN_AlleleCountData.txt


title: F1r Muscle Rep#3

description:
Muscle/F1i_rep4_muscle/F1i_rep4_muscle_ALL.txt.gz, Index 6 GCCAAT, GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAAT ,ATCTCGTATGCCGTCTTCTGCTTG
Muscle_AlleleCountData.txt


title: F1i DRN Rep#8

description:
Dorsal Raphe/Flowcell6_s2/110726_SN343_0181_BB09D6ABXX,IlluminaIndex4,TGACCA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCA,ATCTCGTATGCCGTCTTCTGCTTG
DRN_AlleleCountData.txt


title: F1i DRN Rep#3

description:
Dorsal Raphe/Flowcell4_s3/110719_SN343_0176_BB0AVFABXX,59,IlluminaIndex5,ACAGTG,GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTG,ATCTCGTATGCCGTCTTCTGCTTG
DRN_AlleleCountData.txt


title: F1i DRN Rep#2

description:
Dorsal Raphe/Flowcell4_s2/110719_SN343_0176_BB0AVFABXX,IlluminaIndex4,TGACCA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACTGACCA,ATCTCGTATGCCGTCTTCTGCTTG
DRN_AlleleCountData.txt


title: F1r DRN Rep#9

description:
Dorsal Raphe/Flowcell6_s7/110726_SN343_0181_BB09D6ABXX,IlluminaIndex12,CTTGTA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTA,ATCTCGTATGCCGTCTTCTGCTTG
DRN_AlleleCountData.txt


title: F1r DRN Rep#8

description:
Dorsal Raphe/Flowcell6_s6/110726_SN343_0181_BB09D6ABXX,59,IlluminaIndex7,CAGATC,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAGATC,ATCTCGTATGCCGTCTTCTGCTTG
DRN_AlleleCountData.txt


title: F1r DRN Rep#7

description:
Dorsal Raphe/Flowcell6_s5/110726_SN343_0181_BB09D6ABXX,IlluminaIndex6,GCCAAT,GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAAT,ATCTCGTATGCCGTCTTCTGCTTG
DRN_AlleleCountData.txt


title: F1r DRN Rep#6

description:
Dorsal Raphe/Flowcell5_s7/110722_SN343_0177_BC001DABXX,59,IlluminaIndex12,CTTGTA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTA,ATCTCGTATGCCGTCTTCTGCTTG
DRN_AlleleCountData.txt


title: F1r Liver Rep#4

description:
Liver/Flowcell_12_s2/111001_SN343_0220_BD0C63ACXX/Project_Chris,IlluminaIndex6,GCCAAT,GATCGGAAGAGCACACGTCTGAACTCCAGTCACGCCAAT,ATCTCGTATGCCGTCTTCTGCTTG
Liver_AlleleCountData.txt


title: F1r Liver Rep#5

description:
Liver/Flowcell_12_s7/111001_SN343_0220_BD0C63ACXX/Project_Chris,IlluminaIndex12,CTTGTA,GATCGGAAGAGCACACGTCTGAACTCCAGTCACCTTGTA,ATCTCGTATGCCGTCTTCTGCTTG
Liver_AlleleCountData.txt