title: UWOPS05.217.3 diploid parent

city: Berkeley

first: Rachel

last: Brem

address: 176 Stanley Hall # 3220

institute: University of California, Berkeley

data_processing:
Paired-end read alignment with Bowtie 0.12.7
Read counts per gene determined with custom Python scripts
Counts normalized by library size between lanes and GC content within lanes using EDAseq package in R
Differential expression and p-value significance calculated using DESeq package in R
SGD amended with SNP calls for each respective strain
Supplementary_files_format_and_content: Tab-delimited text files contain the following data: gene name, raw counts per gene for each parental strain (DE_processed_data.txt) or each allele in hybrid strains (ASE_processed_data.txt), the mean normalized gene expression across all strains or alleles, the mean Wine/European expression, the mean Malaysian expression, the fold change of Wine/European : Malaysian expression, the log2 fold change, the p-value significance of the expression difference between Wine/European and Malaysian, the p-value corrected for multiple testing using Benjamini-Hochberg
Genome_build: n/a

source_name: wild-type Malaysian isolate

growth_protocol: Parental and hybrid strains were grown to mid-log phase (0.65-0.72 OD600) in yeast peptone dextrose (YPD) medium (Amberg et al, 2005) at 30° C

extract_protocol:
Total RNA was extracted from cells using the hot phenol method (Ausubel et al, 1995). Poly-A selection was done with magnetic beads, and genomic DNA was removed with Turbo Dnase I
Libraries were prepared as in Mortavazi et al, 2008. After random fragmentation, RNA was reverse-transcribed to double-stranded cDNA. Paired-end adapters were ligated onto cDNA, and size selection occurred through gel electrophoresis. Libraries were sequenced according to Illumina protocols for Genome Analyzer II and HiSeq 2000.

value: UWOPS05.217.3 MATa/@ HO

tag: growth medium

value: YPD


title: RTT5-iPS-34m

status: Public on Oct 25 2013

type: SRA

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

country: Canada

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

description: gene expression in iPSC

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
RNA-seq reads were aligned to hg19 human genome by Tophat.
FPKM value was calculated by Cufflinks
Genome_build: hg19

molecule: total RNA

organism: Homo sapiens

source_name: induced pluripotent stem cell from RTT patient

growth_protocol: ESC and iPSC were cultured in hES medium containing bFGF.

extract_protocol:
Total RNA was isolated using RNeasy kit (QIAGEN) followed by cDNA synthesis usingSuperscript Reverse Transcriptase kit (iScript™ cDNA Synthesis Kit, Bio-rad).
Libraries were prepared according to Illumina’s mRNA Sequencing Sample Preparation Guide for mRNA-Seq 8 Sample Prep Kit (Part# RS-100-0801).

treatment_protocol: iPSCs were incubated in the virus supernatant supplemented with protamine sulfate for 24 hr and then the cells were replaced in fresh ES culturing medium added puromycin at a final concentration of 1 µg/ml. iPSC colonies resistant to puromycin were selected for 2 weeks, and used to confirm the knock-down of MeCP2.

tag: cell type

value: RTT5 fibroblast

tag: passage

tag: mutation

tag: treatment

value: no


title: UWOPS05.227.2 diploid parent

state: CA

country: USA

organism: Saccharomyces cerevisiae

tag: genotype

value: UWOPS05.227.2 MATa/@ HO


title: RTT1-iPS-13w

description: gene expression in iPSC

value: RTT1 fibroblast


title: YHL065 diploid hybrid

source_name: wild-type hybrid

value: UWOPS05.217.3 x BC187 MATa/@ HO


title: UWOPS03.461.4 diploid parent

value: UWOPS03.461.4 MATa/@ HO


title: Ion_H3K4me3_melanoma_tumor_1

city: Cambridge

first: Christine

middle: S

last: Cheng

state: MA

address: 7 Cambridge Center

institute: Broad Institute of MIT and Harvard

library_source: genomic

data_processing:
alignment were performed using BWA aligner
ChIP-seq peak calling was performed using the contiguous segmentation algorithm as part of the Scripture package (http://www.broadinstitute.org/software/scripture/)
Genome_build: mm9, hg19
Supplementary_files_format_and_content: bed files are output from scripture program, which identify ChIP-seq regions that have enriched peaks

molecule: genomic DNA

source_name: Melanoma tumor tissue

growth_protocol: Mouse dendritic cells were isolated from wild type C57BL/6 mice and cultured as previously published. Melanoma tumor derived cell lines were culturedin 10% FCS medium.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were constructed according to Illumina or Ion Torrent protocols.

treatment_protocol: mouse dendritic cells were treated with 0.1ug/ml LPS

tag: antibody concentration (ug/ml)

value: Melanoma tumor tissue


title: PGP9-iPSCs

description: gene expression in iPSC

source_name: induced pluripotent stem cell


title: RTT4-iPS-24w

description: gene expression in iPSC

value: RTT4 fibroblast


title: Detroit551-shMeCP2-iPSCs

description: gene expression in iPSC


title: RTT5-iPS-43bi

description: gene expression in iPSC


title: RM11-1 diploid parent

source_name: wild-type Wine/European isolate

value: RM11-1a x RM11-1b MATa/@ ura3 ho::kanMX


title: 24h_replicate_2_lane_2

city: Indianapolis

first: Lang

last: Li

state: IN

address: 410 West 10th Street HITS 5003 lab

department: Department of Medical and Molecular Genetics, Center for Computational Biology and Bioinformatics

institute: Indiana School of Medicine, Indiana University

description:
Hi-C experiments
100804_s_4

data_processing:
library strategy: Hi-C seq
Conversion of qseq.txt.gz raw files to fastq.gz files using fastqutil module of NGSutils.
Iterative mapping using Mirny's lab library (HiC correction library 0.9).
Fragment filtering using Mirny's lab library (HiC correction library 0.9).
Heatmap processing using Mirny's lab library (HiC correction library 0.9).
Normalization across time points using short-range interaction counts (<10kb).
Removal of translocated and amplified regions.
Genome_build: hg19
Supplementary_files_format_and_content: .csv.gz: interaction count heatmap; .txt: chromosome index

growth_protocol: MCF-7 breast cancer cell line, obtained from the American Type Culture Collection, was maintained in phenol red-free medium.

extract_protocol:
Briefly, cells were fixed with 1% formaldehyde. Chromatin was digested with HindIII (NEB, Ipswich, MA). DNA ends of digested chromatin were marked by biotin-14-dCTP (Invitrogen, Carlsbad, CA) following blunt-end ligation with T4 DNA ligase in diluted condition. Ligated DNA was then de-crosslinked and purified by phenol extraction procedures. Biotin-14-dCTP at non-ligated DNA ends was removed with exonuclease activity of T4 DNA polymerase. Ligated DNA was then applied to paired-end sequencing by using the Illumina sequencing technology platform (Genome Analyzer IIx, Illumina).
Sample preparation for paired-end sequencing was performed following the manufacturer's instructions. Briefly, ligated DNA (5 microg) was sheared to a size of 300-500 basepairs by a nebulizer supplied with the Illumina paired-end sample preparation kit. Fragmented DNA was end-paired using T4 DNA polymerase and Klenow polymerase with T4 polynucleotide kinase to phosphorylate the 5' ends.  A 3' overhang was created using a 3'-5' exonuclease-deficient Klenow fragment, and then subjected to immunoprecipitation by Dynabeads MyOne Streptavin C1 Beads (Invitrogen) in DNA LoBind tubes (Eppendorf, Westbury, NY) with ligation of Illumina paired-end adaptor oligonucleotides.  The ligation mixtures were electrophoresed on E-gel SizeSelect 2% pre-cast agarose gels (Invitrogen) to collect 250-bp fragments. Size-selected DNA fragments were enriched with Illumina paired-end primers by a 15-cycle PCR reaction. DNA samples (20 nM per sample), quantified by an Agilent Bioanalyzer, were loaded onto the paired-end flowcell of Genome Analyzer IIx (GAIIx) in the supplied cluster station according to the manufacturer's protocol. Clusters of PCR colonies were then sequenced on GAIIx with 51-bp per read.

treatment_protocol: After 48 hours of hormone deprivation in 5% charcoal-dextran stripped serum media (no phenol red), cells were stimulated with 70 nM estrogen (E2) for various times: before (0) or after 0.5, 1, 4 and 24 hours of stimulation.

tag: cell line

value: breast cancer cells

tag: time point

value: after 24h of estrogen (E2) stimulation


title: 24h_replicate_1_lane_2

description:
Hi-C experiments
100707_s_8


title: 24h_replicate_2_lane_1

description:
Hi-C experiments
100804_s_3


title: RTT5-iPS-15bi

description: gene expression in iPSC


title: H9

description: gene expression in ESC

source_name: human embryonic stem cell


title: 24h_replicate_1_lane_1

description:
Hi-C experiments
100707_s_7


title: BC187 diploid parent

value: BC187 MATa/@ HO


title: 4h_replicate_2_lane_2

description:
Hi-C experiments
100804_s_2

value: after 4h of estrogen (E2) stimulation


title: RTT1-iPS-10bi

description: gene expression in iPSC


title: RTT5-iPS-31w

description: gene expression in iPSC


title: RTT3-iPS-16m

description: gene expression in iPSC

value: RTT3 fibroblast


title: 4h_replicate_2_lane_1

description:
Hi-C experiments
100804_s_1


title: 4h_replicate_1_lane_1

description:
Hi-C experiments
100707_s_5


title: 1h_replicate_2_lane_2

description:
Hi-C experiments
100729_s_8

value: after 1h of estrogen (E2) stimulation


title: 4h_replicate_1_lane_2

description:
Hi-C experiments
100707_s_6


title: 1h_replicate_2_lane_1

description:
Hi-C experiments
100729_s_7


title: 1h_replicate_1_lane_2

description:
Hi-C experiments
100707_s_4


title: 0.5h_replicate_2_lane_2

description:
Hi-C experiments
100729_s_6

value: after 0.5h of estrogen (E2) stimulation


title: 1h_replicate_1_lane_1

description:
Hi-C experiments
100707_s_3


title: T24

city: New York

first: Christopher

middle: E

last: Mason

address: 1305 York Ave

department: Physiology and Biophysics

institute: Weill Cornell Medical College

data_processing:
Basecalls performed using CASAVA version 1.8
Gene expression: Paired-end RNA sequencing reads were first mapped to the hg19 genome using Tophat and hg19 refseq annotation. Then samtools and bedtools were used to calculate read count expression level.
Genome_build: hg19
Supplementary_files_format_and_content: Gene read count matrix; gene: Refseq gene symbol; chrom: chromosome; start: gene start poition; end: gene end poition; rest column: Sample N22, T22, N23, T23, N24, T24, N25, T25, N26, T26, T25

molecule: polyA RNA

source_name: thyroid tissue

extract_protocol:
RNA were isolated using Rneasy fibrous tissue kit (Qiagen), respectively, according to standard protocols. RNA quality was determined with an Agilent Bioanalyzer.
cDNA libraries for RNA sequencing were prepared using the mRNA-Seq Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s standard protocol. Briefly, poly-A(+) RNA was purified from 2 µg of total RNA for each sample, fragmented by incubation at 94°C for 5 min in fragmentation buffer, and used for double-stranded cDNA synthesis. After ligation of the PE adapter, a fraction of 250–300bp was gel-purified and amplified with 15 cycles of PCR. The resulting libraries were subjected to paired-end sequencing of 76-bp reads on the Genome Analyzer IIx (GAIIx) (Illumina).

tag: disease state

value: Tumor

tag: tissue

value: thyroid


title: T5


title: T23


title: T25


title: T26


title: 0.5h_replicate_2_lane_1

description:
Hi-C experiments
100729_s_5


title: N26

value: Normal


title: T22


title: 0.5h_replicate_1_lane_1

description:
Hi-C experiments
100707_s_2


title: N25


title: RTT4-iPS-16m

description: gene expression in iPSC

value: no


title: 0.5h_replicate_1_lane_2

description:
Hi-C experiments
100729_s_4


title: N24


title: 0h_replicate_2_lane_2

description:
Hi-C experiments
100729_s_3

value: before (0h) estrogen (E2) stimulation


title: YHL063 diploid hybrid

value: UWOPS03.461.4 x BC187 MATa/@ HO

value: YPD


title: N23


title: 0h_replicate_2_lane_1

description:
Hi-C experiments
100729_s_2


title: Illumina_mDC_polII

organism: Mus musculus

source_name: mouse dendritic cells

tag: chip antibody

value: polII

tag: strain

value: mouse dendritic cells


title: 0h_replicate_1_lane 2

description:
Hi-C experiments
100729_s_1


title: 0h_replicate_1_lane 1

description:
Hi-C experiments
100707_s_1


title: Illumina_mDC_H3K4me3


title: YHL058 diploid hybrid

value: UWOPS03.461.4 x RM11-1b MATa/@ HO


title: Chlamydomonas reinhardtii CC-4348 sta6  minus N 2h SMNBs6N2.TS

status: Public on Oct 24 2013

city: Los Angeles

first: Sabeeha

last: Merchant

state: California

address: 607 Charles E. Young Drive East

department: Department of Chemistry and Biochemistry

institute: University of California Los Angeles

description: Illumina's RNA-Seq whole transcriptome analysis

data_processing:
Illumina's proprietary software was used for basecalling.
The reads were aligned using bowtie  in single-end mode and with a maximum tolerance of 3 mismatches to the Au10.2 transcripts sequences (http://www.phytozome.net/chlamy), corresponding to the version 4.0 assembly of the Chlamydomonas genome.
Expression estimates where obtained for each individual run in units of RPKMs (reads per kilobase of mappable transcript length per million mapped reads) after normalization by the number of aligned reads and transcript mappable length. Final expression estimates and fold changes where obtained from the average of biological replicates when available.
Genome_build: version 4.0 assembly of the Chlamydomonas genome (http://genome.jgi-psf.org/Chlre4/Chlre4.home.html)
Supplementary_files_format_and_content: Processed files correpond to expression estimates per sample, in units of RPKMs.

organism: Chlamydomonas reinhardtii

source_name: Chlamydomonas cultured cells

growth_protocol: Cultures used for the experiments to generate RNA for RNA-sequencing were grown in 1000 ml TAP-medium in 2.8 l flasks in the light (90 µmol photons per m2 per s) under the same conditions until they had reached a cell density of 4x10 6 cells per mL. They were then processed as indicated in the treatment protocol.

extract_protocol: Total RNA was isolated at time-points indicated in the text according to a method described in Boyle et al 2012.  For quantitative transcriptomes, RNAs were sequenced at LANL.

treatment_protocol: Once the cultures had reached 4x10 6 cells per mL they were washed in TAP - ammonium chloride and resuspended in 2.8 l flasks to a final cell density of 2x10 6 cells per ml, final volume of 1 l. Cells for RNA preparation were sampled at the indicated timepoints.

value: minus nitrogen

tag: time


title: Chlamydomonas reinhardtii CC-4348 sta6  minus N 12h SMNBs6N12TS


title: Chlamydomonas reinhardtii CC-4348 sta6  minus N 0.5h SMNBs6N05TS


title: Chlamydomonas reinhardtii CC-4348 sta6  minus N 4h SMNBs6N4.TS


title: Chlamydomonas reinhardtii CC-4348 sta6  minus N 48h SMNBs6N48TS


title: Chlamydomonas reinhardtii CC-4348 sta6  minus N 24h SMNBs6N24TS


title: Chlamydomonas reinhardtii CC-4348 sta6  minus N 0h SMNBs6N0.TS


title: Chlamydomonas reinhardtii CC-4349  minus N 12h SMNBcwN12TS


title: Chlamydomonas reinhardtii CC-4349  minus N 24h SMNBcwN24TS


title: Chlamydomonas reinhardtii CC-4349  minus N 48h SMNBcwN48TS


title: N22


title: Chlamydomonas reinhardtii CC-4349  minus N 2h SMNBcwN2.TS


title: Chlamydomonas reinhardtii CC-4349  minus N 4h SMNBcwN4.TS


title: Chlamydomonas reinhardtii CC-4349  minus N 0h SMNBcwN0.TS


title: Chlamydomonas reinhardtii CC-4349  minus N 0.5h SMNBcwN05.TS


title: Peripheral Axons Rep1

city: Rehovot

first: Avraham

last: Yaron

department: Department of Biological Chemistry

country: Israel

institute: Weizmann Institute of Science

data_processing:
Basecalls performed using GAPipeline-1.4.0
Each of the four samples of RNA-Seq single end 80 bases were mapped with tophat Ver 1.2.0  (Trapnell et al., 2012) against mm9 genome (default parameters).
Cufflinks_UCSC\Refseq_Merged_transcripts - Transcript assembly and quantifications with cufflinks Ver. 0.9.3 was done using either RefSeq (Pruitt et al., 2012)  or UCSC known gene annotations (Hsu et al., 2006). Here, raw data replicates were merged and treated as whole.
merged_igenome_strict_raw_and_norm - Transcripts assembly and quantificationsusing HTSeq (htseq-count -t exon -m intersection-strict).
Counts from HTSeq were normalized using TMM (from edgeR package)
Genome_build: mm9
Supplementary_files_format_and_content: Cufflinks_Refseq_Merged_transcripts - file contains gene ID, genomic locus, FPKM values for DRG and Peipheral axon sample
Supplementary_files_format_and_content: Cufflinks_UCSC_Merged_transcripts - file contains Gene symbol, Refseq annotation, Gene description, UCSC transcript id, genomic locus, transcript length and FPKM values for DRG and Peipheral samples
Supplementary_files_format_and_content: merged_igenome_strict_raw_and_norm.xlsx - xlsx file contains gene ID, Raw counts,TMM per million normalized values and  normalization on total number of counts. This file contain data for each sample individually without merging replicates.

source_name: Dorsal Root Ganglia Peripheral Axons

growth_protocol: DRG or Spinal Cord were dissected from E13 mice embryos, and cultured for 48H on cell culture inserts coated with Fibronectin (40mg/ml). Explants were grown in Neurobasal medium supplemented with B-27, glutamine and pen/strep. In the presence of 50ng/ml of mNGF.

extract_protocol:
Axonal and DRG explant material was collected as described by Zheng J.Q. et al (Zheng et al., 2001).  Briefly, for the isolation of axonal material, the top membrane surface was scraped with a cotton-tipped applicator. Scraping was repeated three times with a fresh applicator altering the direction of scraping 90° each time. Membranes were then cut out and immersed in tri-reagent. For the DRG samples, DRGs were scraped off the top membrane surface using a cell scrapper and collected into tri-reagent. DRGs were homogenized using a 20G syringe. This was followed by a standard tri-reagent RNA extraction protocol. All work was done in a 4°C room.
Samples were prepared using the Illumina mRNA-Seq Sample preparation Kit (RS-100-0801) and according to manufacturers instructions.

value: ICR

tag: age

value: Embryonic day 13

tag: culture

value: 48H in-vitro explant culture

value: Dorsal Root Ganglia Peripheral Axons


title: Peripheral Axons Rep2


title: Dorsal Root Ganglia Rep2

source_name: Dorsal Root Ganglia

value: Dorsal Root Ganglia


title: Dorsal Root Ganglia Rep1


title: MEF_FAIRE

city: Stanford

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

data_processing:
genome build: mm9
Raw reads were uniquely mapped to mouse reference genome (NCBI37/mm9) using bowtie (version 0.12.6) allowing maximum one mismatch (Langmead et al., 2009).
For Chip-Seq, peaks for each sample were called using MACs algorithm (version 1.4.2). For FAIRE-Seq, peaks were called using ZINBA.
Supplementary_files_format_and_content: The processed file is in bed format with called peaks.

source_name: embryonic fibroblasts

growth_protocol: Faire-seq protocol was followed as previously described (Giresi et al., 2007) in order to identify regions in MEFs genome that are nucleosomal-free and could be associated with regulatory activity.

extract_protocol:
The isolated DNA was RNase treated and purified.
For sequencing libraries we followed Illumina’s protocol.

treatment_protocol: Approximately 5-10x106 MEFs were crosslinked with 1% formaldehyde for 7 minutes.

value: embryonic fibroblasts


title: MEF_H3_input

growth_protocol: Embryonic fibroblasts were isolated as previously described from the distal extremities of E14.5 homozygous TauEGFP mice embryos (Vierbuchen et al., 2010). iN cells were generated following the previously described protocol (Vierbuchen et al., 2010).

extract_protocol:
The isolated DNA was RNase treated and purified using Qiagen columns.
For sequencing libraries we followed Illumina’s protocol.

treatment_protocol: ChIP-qPCR and ChIP-seq were carried out following the Farnham protocol (O'Geen et al., 2011) in Ascl1- and BAM-infected MEFs 48 hours after dox, and in Ascl1-infected NPCs 18 hours after induction

tag: antibody

value: none (input)


title: Ascl1_NHDF_input

data_processing:
genome build: hg19
Raw reads were uniquely mapped to mouse reference genome (NCBI37/mm9) using bowtie (version 0.12.6) allowing maximum one mismatch (Langmead et al., 2009).
For Chip-Seq, peaks for each sample were called using MACs algorithm (version 1.4.2). For FAIRE-Seq, peaks were called using ZINBA.
Supplementary_files_format_and_content: The processed file is in bed format with called peaks.

source_name: human dermal fibroblasts

value: human dermal fibroblasts


title: Ascl1_NHDF


title: Ascl1_NHEK

source_name: human epidermal keratinocytes

value: human epidermal keratinocytes


title: MEF_H3

value: Histone mark H3 (ab1791-100)


title: Ascl1_NHEK_input


title: Chlamydomonas reinhardtii CC-4348 sta6  minus N 8h SMNBs6N8.TS


title: Myt1l_BAM_48hrs_input

source_name: embryonic fibroblasts treated with BAM factors


title: Brn2_BAM_48hrs_input

value: embryonic fibroblasts treated with BAM factors


title: Brn2_NPC

source_name: neural progenitor

value: neural progenitor

value: Santa Cruz Biotechnology SC-6029


title: Brn2_BAM_48hrs


title: Chlamydomonas reinhardtii CC-4349  minus N 8h SMNBcwN8.TS


title: Brn2_MEF_48hrs


title: Ascl1_BAM_48hrs_input_R2


title: Ascl1_NPC+Ascl1_input

source_name: neural progenitor treated with Ascl1

value: neural progenitor treated with Ascl1


title: Ascl1_NPC+Ascl1

value: neural progenitor treated with Ascl2


title: Ascl1_BAM_48hrs_R2


title: Ascl1_BAM_48hrs_R1


title: Ascl1_MEF_48hrs_input


title: Ascl1_MEF_48hrs


title: Chlamydomonas reinhardtii CC-4567 STA6  minus N 48h SMIBC6N48TP1


title: MEF_H3K27ac

value: Histone mark H3K27acetyl (ab4729)


title: Chlamydomonas reinhardtii CC-4567 STA6  minus N 0.5h SMIBC6N05.TP1

value: minus nitrogen


title: Chlamydomonas reinhardtii CC-4565 STA6  minus N 48h SMIBC2N48TP1


title: Myt1l_BAM_48hrs


title: Chlamydomonas reinhardtii CC-4566 STA6  minus N 0.5h SMIBC4N05.TP1


title: Chlamydomonas reinhardtii CC-4566 STA6  minus N 4h SMIBC4N4.TP1


title: Brn2_NPC_input


title: NSCs

data_processing:
Paired-end reads were aligned to the mouse reference sequence NCBI Build 37/mm9 with the TopHat (v1.1.3) algorithm.
Expression levels of RefSeq annotated genes were calculated in unit of fragments per kilobase of exon model per million mapped fragments (FPKM).
Genome_build: mm9
Supplementary_files_format_and_content: The processed file is in txt format with expression levels of RefSeq genes calculated in RPKM.

source_name: NPCs

extract_protocol:
Total RNA was purified with Trizol following supplier’s recommended method. Poly-A RNA was isolated from 0.5-3µg total RNA using the MicroPoly(A)Purist Kit (Ambion). Samples were processed according to the manufacturer’s protocol.
libraries were prepared following the dUTP protocol (Levin et al., 2010).

treatment_protocol: Lentivirus was produced following standard procedures, following transfection of TetO-FUW lentiviral backbones containing the respective cDNAs (available from us via Addgene) together with the 3rd generation packaging plasmids from the Trono laboratory (Dull et al., 1998). Media was changed 16h after transfection and viral supernatant collected after another 24h.

value: NPCs


title: cortical_neurons

source_name: cortical neurons

value: cortical neurons


title: MEFs+BAM_13days_Rep2

tag: transfection

value: infected with Ascl1, Brn2, Myt1l  + dox

value: 13 days

value: MEFs infected with Ascl1, Brn2, Myt1l after 13 days dox


title: Chlamydomonas reinhardtii CC-4565 STA6  minus N 4h SMIBC2N4.TP1


title: MEFs+BAM_13days_Rep1

tag: cell type


title: MEFs+BAM_22days_Rep2

value: 22 days

value: MEFs infected with Ascl1, Brn2, Myt1l after 22 days dox


title: Chlamydomonas reinhardtii CC-4566 STA6  minus N 48h SMIBC4N48TP1


title: MEFs+BAM_48hrs_Rep1

value: MEFs infected with Ascl1, Brn2, Myt1l after 48hrs dox


title: Ascl1_BAM_48hrs_input_R1

value: none (input)


title: Chlamydomonas reinhardtii CC-4348 sta6  minus N 4h SMIBs6N4.TP1


title: Brn2_MEF_48hrs_input

value: embryonic fibroblasts


title: Chlamydomonas reinhardtii CC-4348 sta6  minus N 48h SMIBs6N48TP1


title: MEFs+BAM_48hrs_Rep2


title: MEFs+Brn2_48hrs

value: infected with Brn2 only  + dox

value: MEFs infected with Brn2 only after 48hrs dox


title: Chlamydomonas reinhardtii CC-4567 STA6  minus N 4h SMIBC6N4.TP1


title: MEFs+Myt1l_48hrs

value: infected with Myt1l only  + dox

value: MEFs infected with Myt1l only after 48hrs dox


title: Chlamydomonas reinhardtii CC-4348 sta6  minus N 0.5h SMIBs6N05.TP1


title: MEFs+Ascl1_48hrs_Rep2

value: infected with Ascl1 only  + dox

value: MEFs infected with Ascl1 only after 48hrs dox


title: MEFs+BAM_22days_Rep1


title: Chlamydomonas reinhardtii CC-4349  minus N 4h SMIBcwN4.TP1

value: minus nitrogen


title: MEFs_rtTA_Rep2

value: MEFs


title: Chlamydomonas reinhardtii CC-4349  minus N 0.5h SMIBcwN05.TP1


title: MEFs+Ascl1_48hrs_Rep1


title: Chlamydomonas reinhardtii CC-4349  minus N 48h SMIBcwN48TP1


title: MEFs_rtTA_Rep1


title: Chlamydomonas reinhardtii CC-4565 STA6  minus N 0.5h SMIBC2N05.TP1


title: Bonobo AG05253 iPSC-2 B

status: Public on Oct 23 2013

city: La Jolla

last: Benner

address: 9500 Gilman Dr. MC 0640

institute: University of California, San Diego (UCSD)

description:
polyA+ RNA-Seq (not strand-specific)
Bonobo iPSC CL7B-P12

data_processing:
Paired end reads from all libraries were mapped to both the human (hg19, GRCh37) and chimpanzee (panTro3, CGSC 2.1.3) genomes using STAR (v2.2.0c). Due to the lack of annotation in the chimpanzee genome, human gene models (RefSeq) were used to quantify gene expression. To avoid bias introduced by genome insertions and deletions, only reads mapping to both the human and chimpanzee genomes uniquely were used from each sample when comparing gene expression values (~4% of reads mapped to only one genome per sample).  To calculate gene expression, read counts in the exons of RefSeq transcripts where calculated using HOMER
Genome_build: GRCh37, panTro3
Genome_build: Pan_troglodytes-2.1.3
Supplementary_files_format_and_content: File "rpkm.txt.gz" (linked as a supplementary file to the Series record) is a tab-delimited text file with RPKM values from all experiments and gene annotation information for RefSeq protein-coding genes (hg19 assembly)

organism: Pan paniscus

source_name: induced pluripotent stem cells

growth_protocol: Human iPSC lines WT-33 and ADRC-40 (human IPSC1 and IPSC2 in this work, respectively) and WT-126 were previously described (Marchetto et al., 2010). Fibroblasts from human GM22159 (WT-9), Pan troglodytes (Chimpanzees: PR00818 and PR01209) and from Pan paniscus (Bonobos: AG05253 and PR01086) were acquired from Coriell Cell Repositories (NJ). All fibroblasts were cultured in Minimum Essential Medium (Invitrogen) supplemented with 10% fetal bovine serum (HyClone Laboratories). Retroviral vectors expressing Oct4, c-Myc, Klf4 and Sox2 human cDNAs from Yamanaka's group were obtained from Addgene. Recombinant viruses were produced by transient transfection in 293T cells. Two days after infection, cells were plated on mitotically inactivated mouse embryonic fibroblasts (Chemicon) with hESC medium. After 3 weeks, iPSCs colonies were picked manually and directly transferred to feeder-free conditions on matrigel-coated dishes (BD) using mTeSRTM1 (StemCell Technologies). Established iPSCs colonies were tested for karyotype integrity and expression profile of undifferentiatied markers. Cells were kept in feeder-free conditions indefinitely and passed using mechanical dissociation.

extract_protocol:
Total cellular RNA was extracted from ~5x106 cells using the RNeasy Plus kit (Qiagen, Valencia, CA), according to the manufacturer's instructions.
PolyA+ RNA was fragmented and prepared into sequencing libraries using the Illumina TruSeq RNA sample preparation kit and analyzed on an Illumina HiSeq 2000 sequencer.  (Paired end 2x 100 bp)

value: iPSC


title: Bonobo PR01086 iPSC-1 A

description:
polyA+ RNA-Seq (not strand-specific)
Bonobo iPSC 86 1


title: Bonobo PR01086 iPSC-1 B

description:
polyA+ RNA-Seq (not strand-specific)
Bonobo iPSC 86 2


title: Bonobo AG05253 iPSC-2 A

description:
polyA+ RNA-Seq (not strand-specific)
Bonobo iPSC 53A


title: H3K27Ac ChIP RPMI-8402_ChipSeq

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

description: Chromatin IP against H3K27Ac ChIP RPMI-8402

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -e 70 -k 2 -m 2 -n 2 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg19, mm9
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were processed using Macs -w -S --space=50 --keep-dup=auto to generate WIG files

source_name: T-ALL cell line

growth_protocol: Human RPMI-8402 cells were purchased from the German Collection of Microorganisms and Cell Culture (DSMZ), Leibniz, Germany. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

value: Jurkat T-ALL cell line

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #


title: input nutlin-3 treated

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg18 genome assembly using Burrows-Wheeler Alignment (BWA) Tool with the default configurations
Uniquely mapped reads with mis-match <= 2 were used for peak detection
Peaks were called using QuEST (version 2.4) using the “Transcription factor binding site” setting (bandwidth of 30 bp, region size of 300 bp) and the “stringent peak calling” parameters (corresponding to 50-fold ChIP to input enrichment for seeding the regions, and 3-fold ChIP enrichment for extending the regions).
Peaks with FDR q <= 0.05
Genome_build: hg19

source_name: lymphoblastoid cells

growth_protocol: human lymphoblastoid cells were grown as recommended by Coriell

extract_protocol: Lysates were clarified from sonicated nuclei and p53-DNA complexes were isolated with mouse monoclonal anti-human p53 (BD Pharmingen, cat# 554294).  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: human lymphoblastoid cells were treated at a density of 900,000 cells/ml with 10 μM nutlin-3 (Sigma) or 0.1% (v/v) DMSO as a vehicle control for 18 hours

value: nutlin-3 treated lymphoblastoid cells

tag: coriell id


title: input LCL NT

treatment_protocol: human lymphoblastoid cells were treated at a density of 900,000 cells/ml with 0.5 μM doxorubicin (Sigma) or water as a vehicle control for 18 hours

tag: treatment

value: vehicle treated lymphoblastoid cells


title: input LCL IR treated

treatment_protocol: human lymphoblastoid cells were treated at a density of 975,000 cells/ml with 10-Gy ionizing radiation, and then let them recovered for 4 hours before crosslinking and collecting them

value: IR treated lymphoblastoid cells


title: Ronin ChIP (R3)_ChipSeq

description: Chromatin IP against Ronin ChIP (R3)

source_name: Embryonic stem cells

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates.

tag: strain background

value: V6.5 embryonic stem cells

value: Ronin

tag: chip antibody info

value: Lab Generated (Zwaka) ANTI-RONIN G4275


title: p53 ChIP LCL nutlin-3 treated

value: mouse monoclonal anti-human p53 (BD Pharmingen, cat# 554294)


title: mES_V6.5_polyA_RNA-Seq

description: polyA RNA-Seq

data_processing:
Reads were aligned using TopHat (Trapnell et al., 2009) to the mm9 genome build as a paired-end library with parameters –library-type fr-firststrand –microexon-search –coverage-search.
Reads mapping to exons were removed.  WIG files were created from exon-filtered bam files using bam2wig.
Genome_build: mm9
Supplementary_files_format_and_content: WIG of non-exonic read density

extract_protocol:
Total RNA was purified using mirVana miRNA isolation kit (Life technologies) following the manufacturer instructions.
After DNAse I digestion, polyadenylated RNA and total RNA depleted of ribosomal content was used for preparation of two independent RNA-seq libraries. Polyadenylated and total RNA depleted of rRNA was fragmented with divalent cations under elevated temperature. First strand cDNA synthesis was performed with random hexamers and Superscript III reverse transcriptase. Second strand cDNA synthesis was performed using RNAseH and DNA Polymerase I. In the second-strand synthesis reaction dTTP was replaced with dUTP. Following cDNA synthesis, the double stranded products were end repaired, a single "A" base was added, and Illumina PE adaptors were ligated onto the cDNA products. The ligation products with an average size of 300 bp were purified using agarose gel electrophoresis. Following gel purification, one strand of cDNA was selectively destroyed during incubation of purified double-stranded DNA products with HK-UNG (Epicentre). The adapter ligated single-stranded cDNA was then amplified with 15 cycles of PCR and PCR products were purified using gel electrophoresis.

treatment_protocol: V6.5 murine embryonic stem cells (mESCs) were grown on irradiated murine embryonic fibroblasts (MEFs) unless otherwise stated. Cells were grown under standard mESC conditions as described previously (Boyer et al., 2005).

tag: cell line

value: mouse embryonic stem cell


title: p53 ChIP LCL NT


title: p53 ChIP LCL Doxo

value: Doxo treated lymphoblastoid cells


title: input LCL Doxo


title: MBD3_ChipSeq

description: Chromatin IP against MBD3

value: Santa Cruz


title: Caecum 4C-seq d13

city: Lausanne

first: Marion

last: LELEU

address: EPFL-SV-ISREC-UPDUB- Station 19

department: School of Life Sciences

country: Switzerland

institute: EPFL

data_processing:
Reads were mapped to the mm9 (NCBI m37, July 2007) Mouse genome assembly with bowtie version 0.12.7 (Langmead et al, 2009) with parameters -n 2 --best -strata -m 5. Genome coverage densities were calculated for each strand separately, then averaged and normalized by the total number of mapped reads (times 10^-7).
4C-seq analysis was done using the method applied in Noordermeer et al., Science 2011 and integrated into HTSstation (http://htsstation.epfl.ch).
4C-seq profiles were smoothed by averaging the signal of the previous and next library fragments.
Both the mapping and the 4C-seq analysis were done through HTSstation (http://htsstation.epfl.ch/).
Genome_build: mm9
Supplementary_files_format_and_content: density files (bigWig) and smoothed data (bedGraph), one per viewpoint, per tissue

source_name: Caecum

extract_protocol: 4C PCR was sequenced with Illumina Genome Analyzer IIx. Data was mapped to the mouse genome using HTSstation (http://htsstation.vital-it.ch/).

treatment_protocol: Chromosome conformation capture on chip (4C) technique was performed as described (Hagège et al., 2007; Simonis et al., 2006). Caeca and brain were dissected from E13.5 embryos, dissociated with collagenase (Sigma Aldrich/Fluka) and filtered through a 35 micron mesh to isolate single cells. Cells were fixed in formaldehyde 2% for 10 min at room temperature and reaction was quenched on ice with glycine. Cells were further lysated with 10 mM Tris pH 7.5, 10 mM NaCl, 5 mM MgCl2, 0.1 mM EGTA, PIC 1x to isolate nuclei. Nuclei from pools of one hundred caecum or two brains were digested with NlaIII (New England Biolabs) and ligated with T4 DNA ligase HC (Promega) in diluted conditions to promote intramolecular ligation. Sequences ligated to fragments of interest were digested again with DpnII (New England Biolabs), ligated with T4 DNA ligase HC (Promega) in diluted conditions and amplified using AmpliTaq DNA polymerase (Applied Biosystems) and inversed PCR primers flanked with adaptors allowing multiplexing. Hoxd13, Hoxd11, Hoxd9 and Hoxd4 PCR primers were described before (Noordermeer et al., 2011).

value: Caecum

tag: genotype

value: wild type


title: Caecum 4C-seq lncRNA Tss

tag: tissue


title: Caecum 4C-seq d11


title: Caecum SOAP splice

data_processing:
Reads were mapped to the mm9 (NCBI m37, July 2007) Mouse genome assembly with bowtie version 0.12.7 (Langmead et al, 2009) with parameters -n 2 --best -strata -m 5. Genome coverage densities were calculated for each strand separately, then averaged and normalized by the total number of mapped reads (times 10^-7).
data was analyzed with SOAPsplice (http://soap.genomics.org.cn/ soapsplice.html) to uncover splicing junctions. The number of threads was set to 10, the insert length of paired-end reads to 190 and the minimum distance between paired-end reads to 80. Splicing junctions were verified using RLM-RACE (see supplemental experimental procedures).
Genome_build: mm9
Supplementary_files_format_and_content: bed file with a list of found junctions.

extract_protocol:
Caeca were dissected from E13.5 embryos and and stored in RNAlater reagent (QIAGEN) until further processing. After disruption with PT1200E Polytron (Kinematica), RNA was isolated using the RNeasy minikit (QIAGEN).
Libraries and clusters were prepared using standard Illumina protocols and sequenced with Illumina Genome Analyzer IIx and paired-end sequencing of 80 bp.

treatment_protocol: Total RNA was depleted of rRNA using Ribo-Zero rRNA Removal Kit (Epicentre).


title: Brain 4C-seq lncRNA Tss

source_name: Brain

value: Brain


title: Caecum 4C-seq d4


title: Caecum 4C-seq d9


title: Brain 4C-seq d11


title: Brain 4C-seq d13


title: Brain 4C-seq d9


title: Human smRNA iPSC2

description:
small RNA
small RNA-Seq (strand specific)

data_processing:
Adapter sequences were trimmed from all single-end reads and mapped to the human (hg19, GRCh37) genome using bowtie2 (v2.1.0).  To calculate miRNA expression, reads with 5' ends mapping to miRBase transcripts where found using HOMER
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file with normalized read count totals for miRNAs found in miRBase (hg19 assembly)

extract_protocol:
Total cellular RNA was extracted from ~5x106 cells using the RNeasy Plus kit (Qiagen, Valencia, CA), according to the manufacturer's instructions.
Small RNA (15-40 nt) libraries were prepared using the Illumina TruSeq Small RNA sample preparation kit and sequenced on an Illumina HiSeq 2000 sequencer (Single end 50 bp)


title: Human smRNA iPSC1


title: Brain 4C-seq d4


title: Human WT-126 iPSC

description:
polyA+ RNA-Seq (not strand-specific)
Human iPSC WT126


title: Human GM22159 (WT-9) iPSC

description:
polyA+ RNA-Seq (not strand-specific)
Human iPSC WT9


title: p53 ChIP LCL IR treated

tag: chip antibody


title: ChIP-Seq for CBP

description: Chromatin IP against CBP

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for one passage off of MEFs, on gelatinized tissue-culture plates.

value: CBP


title: Human WT-33 iPSC-1 B

description:
polyA+ RNA-Seq (not strand-specific)
Human iPSC WT33 1

value: iPSC


title: Human ESC HUES-6

description:
polyA+ RNA-Seq (not strand-specific)
Human ESC HUES-6

source_name: embryonic stem cells

value: ESC


title: Human ESC H1

description:
polyA+ RNA-Seq (not strand-specific)
Human ESC H1


title: MEF_H3K36me3

city: Bethesda

first: Wenfei

last: Jin

state: MD

address: 9000 Rockville Pike

department: Systems Biology Center

institute: NHLBI,NIH

description: ChIP-seq

data_processing:
Basecalls performed using GAPipeline 1.3.2 or CASAVA 1.0
ChIP-Seq reads were mapped to the mouse genome (mm9, or NCBI 37) using Bowtie, only allowing ‘one read per position’ matching. Redundant reads were removed from each ChIP-Seq library.
We identified ChIP-Seq tag enriched peaks using SICER. For calling of H3.3 peaks, we set the window size =200bp and gap size =600bp. Peaks with a false discovery rate (FDR) of higher than 0.01 were excluded from the analysis, compared with the input control libraries.
The total number of H3.3 peaks was identified by peak-calling at the 72h time point when both early-appearing and late-appearing peaks were readily detected.  The number of reads in each peak region was recorded and normalized over the total mapped reads in the library. We obtained the H3.3/molecules relative enrichment of each peak by normalizing over input.
Genome_build: mm9
Supplementary_files_format_and_content: Bed: plan text file. Each line is one read. The six columns are chrom, start position, end position, length, alignment score and strand.

source_name: NIH/3T3 Tet-On® 3G cells

growth_protocol: cDNA of human H3.3B or mouse H3.1 (Hist1h3h) was subcloned in-frame with a HA and FLAG tag at the C-terminus and cloned into the lentiviral plvx-Tight-Puro Vector (Clontech).  Lentiviral particles were packaged in 293T cells with the psPAX2 packaging plasmid. Subsequently, we transduced NIH/3T3 Tet-On® 3G cells (Clontech) and drug-selected with puromycin for stable integration. NIH/3T3 MEFs were cultured in standard conditions with medium containing tetracycline-compatible FBS.

extract_protocol:
Cells were crosslinked with formaldehyde treatment and chromatin fragmented to 200 to 300 bp by sonication. Chromatin from 2 × 107 cells was used for each ChIP experiment, which yielded approximately 200 ng of DNA. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. The ChIP DNA ends were repaired using PNK and Klenow enzyme, followed by treatment with Taq polymerase to generate a protruding 3′ A base used for adaptor ligation. Following ligation of a pair of Solexa adaptors to the repaired ends, the ChIP DNA was amplified using the adaptor primers for 17 cycles and the fragments around 220 bp (mononucleosome + adaptors) isolated from agarose gel. Libraries were sequenced on the Hi-seq following the manufacturer's protocols. As described in Barski et al., 2007 (A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837).

treatment_protocol: MEFs were grown to 100% confluence and treated with 1ug/ml aphidicolin for 18 hours. Adding 3ug/ml doxycycline hyclate before crosslinking with formaldehyde at various time points induced HA/FLAG-H3.3 expression.

value: NIH/3T3 fibroblast cell line

value: aphidicolin

tag: h3.3 induction (hour)


title: Human WT-33 iPSC-1 A

description:
polyA+ RNA-Seq (not strand-specific)
Human iPSC WT33 2


title: MEF_H2AZ

description: ChIP-seq


title: MEF_H3K9ac

description: ChIP-seq


title: MEF_H3K27ac

description: ChIP-seq


title: MEF_H3K9me2

description: ChIP-seq


title: MEF_H3.1

description: ChIP-seq

value: HA


title: MEF_H3K27me3

description: ChIP-seq


title: MEF_H3K4me1

description: ChIP-seq


title: MEF_RNAseq

description: RNA-seq


title: MEF_H3.3_72h_Input


title: Human ADRC-40 iPSC-2 A

description:
polyA+ RNA-Seq (not strand-specific)
Human iPSC ADRC 2


title: MEF_H3K4me3

description: ChIP-seq


title: MEF_H3.3_18h_Input


title: MEF_H3.3_24h_Input


title: MEF_H3.3_12h_Input


title: MEF_H3.3_5h_Input


title: MEF_H3.3_4h_Input


title: MEF_H3.3_6h_Input


title: MEF_H3.3_3h_Input


title: MEF_H3.3_48h_Input


title: MEF_H3.3_0h_Input


title: MEF_H3.3_2h_Input


title: MEF_H3.3_48h_r2

description: ChIP-seq


title: MEF_H3.3_24h_r2

description: ChIP-seq


title: Human ADRC-40 iPSC-2 B

description:
polyA+ RNA-Seq (not strand-specific)
Human iPSC ADRC 1


title: MEF_H3.3_18h_r2

description: ChIP-seq


title: MEF_H3.3_12h_r2

description: ChIP-seq


title: MEF_H3.3_6h_r2

description: ChIP-seq


title: MEF_H3.3_5h_r2

description: ChIP-seq


title: MEF_H3.3_3h_r2

description: ChIP-seq


title: MEF_H3.3_0h_r2

description: ChIP-seq


title: MEF_H3.3_1h_r2

description: ChIP-seq


title: MEF_H3.3_4h_r2

description: ChIP-seq


title: MEF_H3.3_72h_r1

description: ChIP-seq


title: MEF_H3.3_2h_r2

description: ChIP-seq


title: MEF_H3.3_24h_r1

description: ChIP-seq


title: MEF_H3.3_6h_r1

description: ChIP-seq


title: MEF_H3.3_12h_r1

description: ChIP-seq


title: MEF_H3.3_18h_r1

description: ChIP-seq


title: MEF_H3.3_4h_r1

description: ChIP-seq


title: Mouse Caecum

data_processing:
Reads were mapped to the mm9 (NCBI m37, July 2007) Mouse genome assembly with bowtie version 0.12.7 (Langmead et al, 2009) with parameters -n 2 --best -strata -m 5. Genome coverage densities were calculated for each strand separately, then averaged and normalized by the total number of mapped reads (times 10^-7).
Reads Per Kilobase per Million reads (RPKM) for each gene were calculated from the number of reads for all the exons and normalized by the total length of the exons and by then total number of reads mapped.
Differential expression analysis was done using the R package DEseq (Anders et al. 2010)
Both the mapping and the differential expression analysis were done through HTSstation (http://htsstation.epfl.ch/).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file include raw counts, RPKM values, fold change and p-values.

extract_protocol:
For transcriptome profiling along the mouse gut (E13.5), in addition to stomach, caecum and colon samples, the small intestine was separated into three isometric portions considered as the presumptive duodenum, jejunum and ileum. Tissues were stored in RNAlater reagent (QIAGEN) until further processing. After disruption of single samples with PT1200E Polytron (Kinematica), RNA was isolated using either the RNeasy micro- or minikit (QIAGEN).
Libraries and clusters were prepared and sequenced with Illumina Genome Analyzer IIx and paired-end sequencing of 100 bp.

treatment_protocol: Polyadenylated RNA was prepared using TruSeq RNA Sample Preparation (Illumina).

tag: strain


title: MEF_H3.3_1h_Input


title: MEF_H3.3_2h_r1

description: ChIP-seq


title: MEF_H3.3_3h_r1

description: ChIP-seq


title: Mouse Colon

source_name: Colon

value: Colon

tag: age


title: MEF_H3.3_1h_r1

description: ChIP-seq


title: MEF_H3.3_0h_r1

description: ChIP-seq


title: MEF_H3.3_48h_r1

description: ChIP-seq


title: Chimp PR01209 iPSC-1 A

description:
polyA+ RNA-Seq (not strand-specific)
Chimpanzee iPSC 029 1

organism: Pan troglodytes


title: Hedgehog Colon

data_processing:
Reads were mapped to a chimeric genome consisting of E.europaeus (Ensembl v.68) Scaffold and GeneScaffolds, together with the genomic sequence of the HoxD, Hotdog and Twin of Hotdog loci. The mapping were done using Bowtie version 0.12.7 (Langmead et al, 2009) with parameters -n 2 --best -strata -m 5. Genome coverage densities were calculated for each strand separately, then averaged and normalized by the total number of mapped reads (times 10^-7).
Reads mapping within hedgehog-specific repeats (RepeatMaker) were removed along with 50 bp of adjacent DNA to remove unspecific transcription signals.
Genome coverage densities were calculated for each strand separately, then averaged and normalized by the total number of mapped reads (times 10^-7).
Coordinates of the resulting density profiles have been transposed to mm9 for visualisation purpose (based on chr2:74507174 for the HoxD cluster, and on chr2:74881531 for the lncRNA)
Genome_build: hedgehog (ensembl v68) + HoxD_lncRNA scaffold
Supplementary_files_format_and_content: One bedGraph file per tissue containing normalised density profiles (in mm9).

organism: Atelerix albiventris

extract_protocol:
For transcription profiling along the hedgehog gut (E23), in addition to the stomach, the full-length intestine was separated into four isometric portions considered as the presumptive duodenum, jejunum, ileum and colon. Tissues were stored in RNAlater reagent (QIAGEN) until further processing. After disruption of single samples with PT1200E Polytron (Kinematica), RNA was isolated using either the RNeasy micro- or minikit (QIAGEN).
Libraries and clusters were prepared and sequenced with Illumina Genome Analyzer IIx and paired-end sequencing of 100 bp.


title: Chimp PR01209 iPSC-1 B

description:
polyA+ RNA-Seq (not strand-specific)
Chimpanzee iPSC 029 2


title: Chimp PR00818 iPSC-2 B

description:
polyA+ RNA-Seq (not strand-specific)
Chimpanzee iPSC 08018B


title: Mouse Ileum

source_name: Ileum

value: Ileum


title: Chimp PR00818 iPSC-2 A

description:
polyA+ RNA-Seq (not strand-specific)
Chimpanzee iPSC CL5-P12


title: virulent strain [V3]

city: Pullman

first: Audrey

middle: Oi-ting

last: Lau

state: Washington State University

department: Veterinary Microbiology & Pathology

institute: Washington State University

description:
mRNA profiling
L17_V3

data_processing:
Following the sequencing process, image analysis and base calling were performed with Illumina RTA v1.13.
Reads were aligned to B. bovis T2Bo genome (www.piroplasmaDB.org) using Tophat v.2.0.4 and Bowtie v.0.12.8.
Counts were generated using htseq-count v.0.5.3p9 with the default “union” overlapping mode.
Certain genes were removed from consideration if count< 1 per 2 samples.
Differentially expressed genes pairing the samples by their biological source were identified using edgeR v.2.6.12.
Genes were considered significantly and differentially regulated if |log fold change (FC)|≥1 & false detection rate (FDR)< 5%.
Genome_build: B. bovis T2Bo genome (Piroplasmadb.org v.2.0)
Supplementary_files_format_and_content: Tab-delimited counts.txt reports counts for all samples.

organism: Babesia bovis

source_name: infected bovine_virulent Bb strain

growth_protocol: Parasites were propagted in vivo and infected red blood cells were subsequently collected and propagated in vitro for <30 days.

extract_protocol:
Total RNA was extracted using TriZOL and total RNA was purified using Qiagen quick cleanup protocol
Libraries were prepared according to Illumina's instructions using Illumina Truseqv.2 kit).
All six samples were multiplexed in a single lane with 50 cycles pair-end runs.  The estimated reads per library were 25 million.

tag: pathogenicity

value: virulent to mammalian host

tag: host

value: bovine


title: attenuated strain [A1]

description:
mRNA profiling
L17_A1

source_name: infected bovine_attenuated Bb strain

value: vaccine strain


title: attenuated strain [A2]

description:
mRNA profiling
L17_A2


title: prp4-1

status: Public on Oct 22 2013

city: Santa Cruz

first: Lily

last: Shiue

address: 1156 High Street

department: MCD Biology

institute: UCSC

description: spliceosomal mutant (prp4-1)

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads (100bp read1, 58bp read2) were mapped to sacCer3 using tophat, allowing for a maximum intron size of 1200bp, with an estimated mean distance between the read pairs of 85bp (std dev 100bp).
A gtf file of previously known splice sites was supplied to tophat. Tophat's coverage search and segment search intron-finding algorithms were also enabled. In the case of multiply-mapped reads, the single best hit as scored by bowtie was kept.
Expression values (i.e., reads per exon or per gene) are calculated by summing the coverage at each position and dividing by read length.
Genome_build: sacCer3
Supplementary_files_format_and_content: spreadsheet containing summarized gene expression, intron and exon2 read counts, as well as calculated Intron Accumulation Indexes

source_name: Yeast cells

extract_protocol:
total RNA was extracted according to Rio et al., Cold Spring Harb Protoc, 2010 "Method 1"
strand-specific libraries (dUTP/USER) were made from polyA selected mRNA; adaptors, end repair through enrichment steps using Illumina DNA Sample Prep kit V2

value: prp4-1 (MATalpha prp4-1 ade2- leu2-3,112 ura3-52 his3-delta-200)

tag: growth conditions

value: 26ºC YPD OD=0.5


title: prp4-1_pGAL-IFH

description: ~50% down-regulation of IFH1 transcription factor (specific for ribosomal protein genes)

value: k-HIS3:pGAL1-IFH1, prp4-1


title: BY-Rapa60'-Rep1

description: treated with 200ng/mL rapamycin for 60 min

value: 30ºC YPD OD=0.5

value: 200ng/mL rapamycin for 60 min


title: virulent strain [V1]

description:
mRNA profiling
L17_V1


title: MEF_H3.3_5h_r1

description: ChIP-seq


title: attenuated strain [A3]

description:
mRNA profiling
L17_A3


title: BY-noRapa-Rep2


title: BY-Rapa10'-Rep2

description: treated with 200ng/mL rapamycin for 10 min

value: 200ng/mL rapamycin for 10 min


title: BY-Rapa60'-Rep2


title: BY-noRapa-Rep1

value: BY4741 (MATa his3-delta-0 leu2-delta-0 met15-delta-0 ura3-delta-0)


title: Hedgehog Ileum

value: wild type


title: Lung Xenograft RVH6849

city: Toronto

first: Shirley

last: Tam

state: Ontario

address: 661 University Avenue, Suite 510, MaRS Building, West Tower

department: Genome Technologies

institute: Ontario Institute for Cancer Research

data_processing:
Base-calling was performed using CASAVA v1.8.2.  Short read sequences were output in FASTQ format with corresponding base quality scores.  Quality control of the raw sequences from each sequenced library was investigated using FastQC v0.9.1 to check for homopolymers, adapters, and distribution of base quality.  The raw data was initially filtered for reads containing ambiguous base calls, which did not meet the Illumina chastity filter based on quality measures.
The remaining reads were trimmed for adapters and mapped to the miRBase v16 mature miRNA reference using Novocraft's Novoalign v2.07.14.
The summarized count data was loaded into the R statistical environment (v2.14.0) and normalized by linear regression using the median count value of each miRNA across the samples as reference.
Genome_build: miRBase version 16.0
Supplementary_files_format_and_content: Tab-delimited text file contains linear-normalized counts for each aligned microRNA.

source_name: Total RNA from RVH6849 xenograft

growth_protocol: Cells were cultured in RPMI-1640, supplemented with 10% FBS and 1X Penicillin/Streptomycin.  Xenografts were grown by subcutaneous injection of two million trypsin-dissociated tumor cells into non-obese diabetic/severe combinted immunodeficient mice.

extract_protocol:
Total RNA was isolated from confluent cell lines or fresh-frozen xenograft tissues using Trizol reagent (Life Technologies, Carlsbad, CA, USA) according to the manufacturer's instructions, followed by Dnase I treatment (Life Technologies) and purification using the Qiagen RNeasey kit (Qiagen, Venlo, Netherlands).  RNA quantity and quality was assessed using the Qubit Fluorometer (Life Technologies), NanoDrop 1000 (Nanodrop Technologies, Wilmington, DE, USA), and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).  Five micrograms of total RNA was fractionated using the flashPAGETM fractionator system (Life Technologies) and small RNAs (~<40nt) were recovered by ethanol precipitation.  Small RNA enrichment was confirmed using the small RNA Lab-on-a-Chip kit and the Bioanalyzer 2100 (Agilent).
Libraries were prepared from fractionated small RNA samples as per Illumina TruSeq Small RNA protocol (version D) (Illumina, San Diego, CA, USA).

treatment_protocol: Not Applicable


title: Lung Xenograft H1264

source_name: Total RNA from H1264 xenograft


title: Lung Cancer Cell Line H1264

source_name: Total RNA from H1264 cells


title: SHP -/-  replicate 1

city: Durham

first: Integrative

last: Bioinformatics

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

description: Sample 4

data_processing:
36 cycle paired end reads (fastq files) were aligned to mouse July 2007 (NCBI37/mm9) genome with novoalign version 2.05.33 software
Novoaligned sam files were parsed into binary point data files with Useq version 6.2 software.
Differential gene expression was determined using Useq MultipleReplicaDefinedRegionScanSeqs (MRDRSS) application to count reads intersecting exons of each annotated gene.
Sequencing reads for each sample were normalized using reads per kilobase gene length per million reads (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: Single text file containing raw read counts for each sample, average normalized read counts for each mouse genotype, log2 ratio, negative binomial p-value and false discovery rate of SHP -/- to wild type comparison.

extract_protocol:
Total RNA extracted with TriZOL, then 5' capped RNA selected with high affinity EIF4E variant (Choi and Hagedorn, 2003, PNAS 100:7033-7038)
Standard Illumina library protocol for barcoding samples. Three barcoded samples were sequenced per lane. 36 cycle paired end reads were generated for each sample.

tag: genotype/varation

value: SHP -/- knockout

tag: gender

value: male

value: 2 months

value: liver

tag: molecule subtype

value: 5' capped RNA


title: SHP -/-  replicate 3

description: Sample 6


title: Wild type replicate 3

description: Sample 3


title: Wild type replicate 2

description: Sample 2


title: Lung Xenograft H520

source_name: Total RNA from H520 xenograft


title: Lung Cancer Cell Line H520

source_name: Total RNA from H520 cells


title: Wild type replicate 1

description: Sample 1


title: virulent strain [V2]

description:
mRNA profiling
L17_V2


title: Lung Xenograft H460

source_name: Total RNA from H460 xenograft


title: Lung Xenograft A549

source_name: Total RNA from A549 xenograft


title: BY-Rapa10'-Rep1


title: Lung Cancer Cell Line A549

source_name: Total RNA from A549 cells


title: S. cerevisiae x S. paradoxus rep2

status: Public on Oct 21 2013

city: San Francisco

first: Yulia

last: Mostovoy

address: 555 Mission Bay Blvd South

institute: University of California, San Francisco

data_processing:
Basecalling with Illumina CASAVA version 1.7
For each pairwise comparison between species, reads from both parents and hybrids were mapped simultaneously to both species’ genomes from http://www.saccharomycessensustricto.org/ using Bowtie version 0.12.7 with default settings and flags -m1 -X1000.
Filtering: To ensure that poly-A tails did not originate from stretches of As or Ts encoded endogenously in the genome, we discarded reads whose stretch of As or Ts contained more than 50% matches to the reference genome. In order to filter for potential oligo-dT mispriming during cDNA synthesis, we also discarded reads that contained 10 or more As in the 20 nucleotides upstream of their transcription termination site.
GC correction: For each lane of sequencing, we grouped sets of overlapping reads and normalized abundance according to GC content of the overlapping region using full-quantile normalization as implemented in the package EDASeq. Normalized abundance was divided by raw abundance to generate a weight that was assigned to every read in the group. These weights were used in place of raw read counts in all downstream analyses.
Genome_build: Assemblies from http://www.saccharomycessensustricto.org
Supplementary_files_format_and_content: Abundance measurements were calculated as follows: for each gene, we searched for reads that had mapped to either its sense or antisense region, and obtained GC-normalized read counts for each such feature by summing the weighted abundance of the reads.

organism: Saccharomyces cerevisiae x Saccharomyces paradoxus

source_name: S. cerevisiae x S. paradoxus yeast cells

growth_protocol: Cultures were grown at 25°C in YPD medium to log phase (between 0.65-0.75 OD at 600 nm).

extract_protocol: Total RNA was isolated by the hot acid phenol method and treated with Turbo DNA-free (Ambion) according to the manufacturer's instructions.  Libraries for 3’end RNA-seq were generated according to the published protocol (Yoon and Brem, RNA 2010) with the following modifications: 1) AmpureXP beads (Beckman) were used to clean up enzymatic reactions; 2) the gel purification and size-selection step was removed; 3) the oligo-dT primer used for cDNA synthesis was phosphorothioated at position ten (TTTTTTTTTT*TTTTTTTTTTVN, V=A,C,G, N=A,C,G,T, *=phosphorothioate linkage, Integrated DNA Technologies); and 4) 12 PCR cycles were performed.

tag: parents


title: S. cerevisiae x S. bayanus rep2

organism: Saccharomyces cerevisiae x Saccharomyces bayanus

source_name: S. cerevisiae x S. bayanus yeast cells


title: TBP_input_2.5min_MNase_WT_Mot1_(20130705_1_5)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: TATA-binding protein (TBP) input, 2.5' MNase, WT Mot1, 45 minute 35 degrees C heat shock

data_processing: 1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. If a read was mapped to multiple locations, one location was picked at random. 2. We extracted properly paired reads (Supplementary file .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig) .

source_name: TBP input

extract_protocol: Nuclear isolation, chromatin preparation, and immunoprecipitation were performed as described (PMID 23468649). Sequencing libraries were prepared as described (PMID 22025700), except that TruSeq adapters were used for multiplexing and the ratio of sample to Ampure beads was changed from 5:9 to 1:1 in the two cleanup steps to compensate for the longer length of the TruSeq adapters.

tag: cell

value: nuclei

tag: mutant

value: WT

value: mot1::TRP1 pAV20 (EE-MOT1+LEU2+CEN ARS) TBP-13MYC-HIS3MX6


title: TBP_input_10min_MNase_WT_Mot1_(20130705_1_6)

description: TATA binding protein (TBP) input, 10' MNase, WT Mot1, 45 minute 35 degrees C heat shock

data_processing: 1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. If a read was mapped to multiple locations, one location was picked at random. 2. We extracted properly paired reads (Supplementary file .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .wig)


title: TBP_input_10min_MNase_mot1-42_(20130705_1_8)

description: TATA-binding protein (TBP) input, 10' MNase, mot1-42, 45 minute 35 degrees C heat shock

value: mot1::TRP1 pMot221 (mot1-42 LEU2+CEN ARS) TBP-13MYC-HIS3MX6


title: TBP_IP_2.5min_MNase_mot1-42_(20130705_1_3)

description: TATA-binding protein (TBP) IP, 2.5' MNase, mot1-42, 45 minute 35 degrees C heat shock

source_name: TBP IP

tag: antibody

value: anti-Myc (Santa Cruz sc-40x)


title: TBP_IP_2.5min_MNase_WT_Mot1_(20130705_1_1)

description: TATA-binding protein (TBP) IP, 2.5' MNase, WT Mot1, 45 minute 35 degrees C heat shock


title: SHP -/-  replicate 2

description: Sample 5

tag: strain background


title: TBP_IP_10min_MNase_mot1-42_(20130705_1_4)

description: TATA binding protein (TBP) IP, 10' MNase, mot1-42, 45 minute 35 degrees C heat shock

tag: genotype


title: Mot1_input_10min_MNase_60min_rapamycin_(20130705_2_8)

description: Mot1 input, 10' MNase, 60 minute 1 mcg/ml rapamycin treatment

source_name: Mot1 input

value: tor1-1 fpr1::natMX RPL13A-2xFKBP12::TRP1 TBP-FRB-kanMX6 MOT1-3FLAG-hphMX4


title: Mot1_input_2.5min_MNase_60min_rapamycin_(20130705_2_6)

description: Mot1 input, 2.5' MNase, 60 minute 1 mcg/ml rapamycin treatment


title: TBP_IP_10min_MNase_WT_Mot1_(20130705_1_2)

description: TATA-binding protein (TBP) IP, 10' MNase, WT Mot1, 45 minute 35 degrees C heat shock

source_name: Mot1 TBP IP


title: Mot1_input_10min_MNase_no_rapamycin_(20130705_2_7)

description: Mot1 input, 10' MNase, no rapamycin treatment

data_processing: 1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. We also mapped the reads to release 5.30 of D.melanogaster (Sep 2010) obtained from FlyBase. If a read was mapped to multiple locations, one location was picked at random.  2. We extracted properly paired reads that were only mapped to one organism (Supplementary files .bed). 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary files .wig)

organism:
Saccharomyces cerevisiae
Drosophila melanogaster


title: Mot1_IP_2.5min_MNase_no_rapamycin_(20130705_2_1)

description: Mot1 IP, 2.5' MNase, no rapamycin treatment

source_name: Mot1 IP

value: anti-FLAG beads (Sigma #8823)


title: Mot1_IP_10min_MNase_no_rapamycin_(20130705_2_3)

description: Mot1 IP, 10' MNase, no rapamycin treatment


title: S. cerevisiae x S. mikatae rep2

organism: Saccharomyces cerevisiae x Saccharomyces mikatae

source_name: S. cerevisiae x S. mikatae yeast cells


title: Mot1_input_2.5min_MNase_no_rapamycin_(20130705_2_5)

description: Mot1 input, 2.5' MNase, no rapamycin treatment


title: S. bayanus rep2

description: Sample 12

data_processing:
Basecalling with Illumina CASAVA version 1.7
Reads were mapped to the corresponding species’ genome from http://www.saccharomycessensustricto.org/ using Bowtie version 0.12.7 with default settings and flags -m1 -X1000.
Filtering: To ensure that poly-A tails did not originate from stretches of As or Ts encoded endogenously in the genome, we discarded reads whose stretch of As or Ts contained more than 50% matches to the reference genome. In order to filter for potential oligo-dT mispriming during cDNA synthesis, we also discarded reads that contained 10 or more As in the 20 nucleotides upstream of their transcription termination site.
GC correction: For each lane of sequencing, we grouped sets of overlapping reads and normalized abundance according to GC content of the overlapping region using full-quantile normalization as implemented in the package EDASeq. Normalized abundance was divided by raw abundance to generate a weight that was assigned to every read in the group. These weights were used in place of raw read counts in all downstream analyses.
Genome_build: Assemblies from http://www.saccharomycessensustricto.org
Supplementary_files_format_and_content: Abundance measurements were calculated as follows: for each gene, we searched for reads that had mapped to either its sense or antisense region, and obtained GC-normalized read counts for each such feature by summing the weighted abundance of the reads.

organism: Saccharomyces bayanus

source_name: S. bayanus_yeast cells

extract_protocol: Total RNA was isolated by the hot acid phenol method' and treated with Turbo DNA-free (Ambion) according to the manufacturer's instructions.  Libraries for 3’end RNA-seq were generated according to the published protocol (Yoon and Brem, RNA 2010) with the following modifications: 1) AmpureXP beads (Beckman) were used to clean up enzymatic reactions; 2) the gel purification and size-selection step was removed; 3) the oligo-dT primer used for cDNA synthesis was phosphorothioated at position ten (TTTTTTTTTT*TTTTTTTTTTVN, V=A,C,G, N=A,C,G,T, *=phosphorothioate linkage, Integrated DNA Technologies); and 4) 12 PCR cycles were performed.

tag: genotype/variation


title: S. bayanus rep1

description: Sample 11


title: S. cerevisiae x S. mikatae rep1


title: Lung Cancer Cell Line H460

source_name: Total RNA from H460 cells

tag: cell line


title: TBP_input_2.5min_MNase_mot1-42_(20130705_1_7)

description: TATA-binding protein (TBP) input, 2.5' MNase, mot1-42, 45 minute 35 degrees C heat shock


title: normal esophagus

city: Bronx

first: Yiting

last: Yu

state: NY

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

description: Sample name: NE

data_processing:
Initial processing of data was done by the Illumina Sequence Control Software (SCS) and Pipeline 1.n software packages. These software components perform the functions of image analysis (Firecrest), base-calling (Bustard) and alignment of sequence tags to the Appropriate reference genome (ELAND), sorting samples by the index sequences (up to 4 per lane). Differential expression analysis between samples was performed by edgeR, a bioconductor package specifically for the analysis of replicated count-based expression data  (Robinson MD et al., 2010).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: The tab-delimited .txt files include normalized gene expression (abundance of all genes that were detected, including lncRNAs) for each Sample.

source_name: snap frozen tissue of matched normal esophagus

extract_protocol:
Total RNA was isolated from snap frozen tissues using a Qiagen RNeasy Plus Mini Kit (Qiagen, Valencia, CA).
An adaptor ligated cDNA library was prepared from the sample RNAs using Illumina® TruSeq® RNA Sample Preparation Kit v2 (Illumina Inc., San Diego, CA). The resulting libraries were sequenced using Illumina HiSeq 2500 sequencer (single-end reads).

tag: disease state

value: esophageal adenocarcinogenesis

tag: tissue

value: snap frozen tissue of normal esophagus


title: S. cerevisiae x S. paradoxus rep1

tag: strain


title: Barrett’s esophagus

description: Sample name: BE

source_name: snap frozen tissue of matched Barrett’s esophagus

value: snap frozen tissue of Barrett’s esophagus


title: esophageal adenocarcinoma

description: Sample name: EAC

source_name: snap frozen tissue of matched esophageal adenocarcinoma cells

value: snap frozen tissue of esophageal adenocarcinoma cells


title: S. cerevisiae rep5

description: Sample 9

source_name: S. cerevisiae _yeast cells

value: wild type


title: S. cerevisiae rep6

description: Sample 10


title: Sample_WT2

first: Craig

middle: B

last: Thompson

address: 1275 York Ave

department: Cancer Biology and Genetics

institute: Memorial Sloan-Kettering Cancer Center

description:
ERRBS
replicate 2

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were filtered from the adapter sequences using FAR software and aligned to genome using the bismark alignment software, retaining uniquely aligning reads with maximum of 2 directional mismatches
methylCall files were generated using methylKit
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited

source_name: isogenic cell line

extract_protocol: Genomic DNA was extracted using Qiagen Puregene kit protocol; Libraries were prepared as described previously (Akalin et al. PLoS Genet. 2012): 1000 ng of high quality genomic DNA were digested with 200 U of MspI (New England Biolabs, NEB) in a 100 ul reaction for up to 16 hours at 37 C. DNA was isolated using standard phenol chloroform extraction and ethanol precipitation and resuspended into 30 ul of 10 mM TrIs pH 8.0. End repair of digested DNA was performed in a 100 ul reaction using 15 U of T4 DNA polymerase (NEB M0203L), 5 U of Klenow DNA polymerase (NEB M0210L), 50 U of T4 Polynucleotide Kinase (NEB M0201L), 4 ul of premixed nucleotide triphosphates each at 10 mM (NEB N0447L) using T4 DNA ligase buffer with 10 mM dATP (NEB B0202S). The reaction was incubated at 20 C for 30 minutes and products were isolated using QIAquick PCR purification columns per manufacturer's recommended protocol (Qiagen) into 32 ul of EB buffer. Adenylation was performed in a 50 ul reaction using 15 U Klenow fragment (3 to 5 exo minus, NEB M0212L), 10 ul of dATP at 1 mM concentration using Klenow buffer (NEB). The reaction was incubated at 37 C for 30 minutes and products were isolated using MinElute PCR purification columns per manufacturer's recommended protocol (Qiagen) into 10 ul EB buffer. Adenylated DNA fragments were ligated with pre-annealed 5-methylcytosine-containing Illumina adapters in a 20 or 50 ul reaction for 5 ng or 50 ng or higher starting materials respectively using 2000 U T4 DNA ligase (NEB M0202T) and 1.2 M final concentration of methylated adapters at 16 C for a minimum of 16 hours. Products were isolated using MinElute columns per manufacturer's recommended protocol (Qiagen) into 10 ul EB buffer. Library fragments of 150 250 and 250-400 bp were gel isolated from a 1.5% agarose gel (using low range ultra agarose from Biorad) using the Qiaquick Gel Extraction kit per manufacturer's recommended protocol (Qiagen) into 40 ul EB buffer. Bisulfite treatment was performed using the EZ DNA Methylation Kit (Zymo Research) per manufacturer's recommended protocol with the following modifications: 1) incubation after the addition of CT conversion reagent was conducted in a thermocycler (Mastercycler ep gradient, Eppendorf) with the following conditions: 30 seconds at 95 C followed by 15 minutes at 50 C for 55 cycles and, 2) products were eluted into 40 ul nuclease free water. PCR amplification for each library was performed in a 200 ul reaction containing 2 ul FastStart Hifidelity DNA Polymerase (Roche), 0.5 M each of Illumina PCR primers PE1.0 and 2.0, 0.25 mM each nucleotide triphosphate using buffer 2 per manufacturer's recommendation and divided into four 50 ul reactions. The thermocycler conditions were: 5 minutes at 94 C, 18 cycles of 20 seconds at 94 C, 30 seconds at 65 C, 1 minutes at 72, followed by 3 minutes at 72 C. PCR products were isolated using AMPure XP beads per manufacturer's recommended protocol (Agencort) into 50 ul of EB buffer. All amplified libraries underwent quality control steps including using Qubit 1.0 fluorometer and a Quant-iT dsDNA HS Assay Kit for quantitation (Invitrogen) and bioanalyzer visualization (Agilent 2100 Bioanalyzer).

tag: cell type

value: 10T isogenic cell line with IDH2 wild type


title: Sample_WT1

description:
ERRBS
replicate 1


title: Sample 19

description: ERRBS

source_name: human chondrosarcoma

value: primary tumor

tag: sample type

value: tumor with IDH wild type


title: Sample 18

description: ERRBS


title: Mot1_IP_2.5min_MNase_60min_rapamycin_(20130705_2_2)

description: Mot1 IP, 2.5' MNase, 60 minute 1 mcg/ml rapamycin treatment


title: Sample 20

description: ERRBS


title: Sample_MUT1

description:
ERRBS
replicate 1

value: 10T isogenic cell line with IDH2 mutation


title: Sample_Vec2

description:
ERRBS
replicate 2

value: 10T isogenic cell line with vector wild type


title: Sample_Vec1

description:
ERRBS
replicate 1


title: S. cerevisiae rep3

description: Sample 5


title: S. cerevisiae rep4

description: Sample 6


title: Sample 17

description: ERRBS


title: Sample 15

description: ERRBS


title: Sample 14

description: ERRBS


title: Sample 16

description: ERRBS


title: S. cerevisiae rep1

description: Sample 1

source_name: S. cerevisiae_yeast cells


title: Sample_MUT2

description:
ERRBS
replicate 2


title: Sample 12

description: ERRBS


title: S. cerevisiae rep2

description: Sample 2


title: Sample 11

description: ERRBS


title: Sample 13

description: ERRBS


title: Sample 9

description: ERRBS

value: tumor with IDH2 mutation


title: Sample 8

description: ERRBS


title: Sample 10

description: ERRBS


title: S. mikatae rep2

description: Sample 8

organism: Saccharomyces mikatae

source_name: S. mikatae_yeast cells


title: Sample 5

description: ERRBS

value: tumor with IDH1 mutation


title: Sample 4

description: ERRBS


title: Mot1_IP_10min_MNase_60min_rapamycin_(20130705_2_4)

description: Mot1 IP, 10' MNase, 60 minute 1 mcg/ml rapamycin treatment

value: nuclei

value: WT


title: S. paradoxus rep2

description: Sample 4

organism: Saccharomyces paradoxus

source_name: S. paradoxus_yeast cells

value: CBS 432


title: Sample 2

description: ERRBS


title: S. paradoxus rep1

description: Sample 3


title: Nitrate-2 M. tuberculosis

first: Genomics-core-facility

last: WCM

address: 1300 York Ave.

institute: Weill Cornell Medicine

description: cDNA (rRNA extracted)

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Sequenced reads were trimmed for low-quality sequences by using fastq_quality_trimmer in the FASTX toolkit with parameters -t 20 -l 45; then mapped to the NCBI Mycobacterium tuberculosis H37Rv complete genome using bwa v0.6.1 with default parameters.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) and genes with statistically significant changes in expression was selected by using Cufflinks v2.0.2 package, following a protocol from "Trapnell C. et al., Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nature Protocol, 2012 Mar 1;7(3):562-78.". Reads that aligned to rRNAs were masked by "--mask-file" option.
Genome_build: ASM19595v2
Supplementary_files_format_and_content: excel file including gene name, ENTREZ_GENE_ID, locus, RPKM values of both conditions, for each gene

organism: Mycobacterium tuberculosis H37Rv

source_name: Nitrate treated  M. tuberculosis

growth_protocol: In 3 independent experiments axenic cultures of wild type H37Rv Mtb was cultuvated in 7H9/ADNaCl and treated with or without 5 mM nitrate for 3 days at 1% oxygen to allow for the generation of endogenous nitrite and then transferred the cultures to 21% oxygen overnight.

extract_protocol:
Mtb was cultured as above, RNA harvested using Trizol reagent followed by Qiagen column isolation , rRNA was extracted and the illumina TruSeq RNA Sample Prep Kit was used to generate the sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: 5 mM nitrate

tag: medium

value: standard 7H9/ADNaCl


title: Gata6 morphant, 6-somites, rep 2

first: Todd

last: Evans

state: New York

address: 1300 York Avenue  Box 282

institute: Weill Medical College of Cornell University

data_processing:
All data processing steps were performed in GobyWeb (Dorff, K. C. et al 2013 GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. Quantitative Methods (q-bio.QM); Genomics (q-bio.GN). (in press) arXiv:1211.6666).
Alignments performed against Zv9.61 assembly.
Genome_build: Zv9
Supplementary_files_format_and_content: tab-separated files include RPKM values for each Sample

organism: Danio rerio

source_name: Whole embryo

extract_protocol:
40 embryos were collected per sample in Trizol (Invitrogen), and polyA mRNA was prepared for sequencing using the Illumina mRNA-seq Sample Preparation Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Gata6 morphant

value: whole embryo


title: Gata5/6 morphant, 6-somites, rep 1

value: Gata5/6 morphant


title: Nitrate-0 M. tuberculosis

description: cDNA (rRNA extracted)


title: Nitrate-1 M. tuberculosis

description: cDNA (rRNA extracted)


title: Gata5 morphant, 6-somites, rep 2

value: Gata5 morphant


title: Untreated-2 M. tuberculosis

description: cDNA (rRNA extracted)

source_name: Untreated M. tuberculosis


title: Gata5 morphant, 6-somites, rep 1


title: Untreated-1 M. tuberculosis

description: cDNA (rRNA extracted)


title: WT, 6-somites, rep 2


title: Sample 21

description: ERRBS

organism: Homo sapiens


title: WT, 6-somites, rep 1


title: Sample 3

description: ERRBS


title: Untreated-0 M. tuberculosis

description: cDNA (rRNA extracted)


title: S. cerevisiae x S. bayanus rep1

source_name: S. cerevisiae x S. bayanus yeast cells


title: Gata6 morphant, 6-somites, rep 1


title: Sample 7

description: ERRBS


title: Gata5/6 morphant, bud, rep 2

value: bud


title: Gata5/6 morphant, 6-somites, rep 2


title: Gata5/6 morphant, bud, rep 1


title: Sample 6

description: ERRBS


title: S. mikatae rep1

description: Sample 7

value: wild type


title: Phytophthora infestans mycelium small RNA rep1

city: Saint Louis

first: James

middle: C

last: Carrington

state: MO

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

description: Small RNA isolated from total RNA extracted from Phytophthora infestans mycelium

data_processing:
Sequencing reads from small RNA libraries were computationally processed to remove 3’ adaptor sequences, and sequences were consolidated to generate read counts per unique small RNA.
Unique small RNAs were aligned to the Phytophthora infestans genome using Bowtie v0.12.8 with settings allowing for perfect matches only (bowtie –f –v 0 –a –S –p 10).
Genome_build: Phytophthora infestans T30-4, version 1; http://www.ncbi.nlm.nih.gov/assembly/GCA_000142945.1/
Supplementary_files_format_and_content: GFF (version 3) files are provided that contain small RNA mapping data and read abundances (non-normalized) used in our study. GFF formats are specified in the header of each file.

organism: Phytophthora infestans

source_name: mycelium_small RNA

growth_protocol: Mycelium was grown from Phytophthora infestans T30-4 maintained on cleared 10% V8 agar medium (100 mL V8 juice; 1 g CaCO3; 30 mg/L β-sitosterol; 15 g agar; 900 mL deionized water) in a 20°C incubator in the dark. Mycelia were grown in V8 broth (V8 agar medium without agar) on a rotating shaker in flasks and collected after 4 days.

extract_protocol:
Mycelium samples were frozen in liquid nitrogen, ground into a fine powder and homogenized in Trizol (1g:10mL, Life Technologies). After adding 2 mL chloroform per 10 mL Trizol, samples were mixed, incubated at room temperature for 5 minutes and centrifuged at 8400 x g for 10 minutes. Two additional chloroform extractions were done before RNA was precipitated in 0.7 volumes isopropanol for 20 minutes at room temperature and spun for 30 minutes at 8400 x g. Minimally dried pellets were resuspended in 200 μL 0.1X TE, extracted 2 times with phenol:chloroform:isoamyl alcohol (50:49:1), and once with chloroform. Total RNA was precipitated with 5M ammonium acetate and ethanol at -80°C overnight, spun at 12000 x g for 30 minutes at 4°C, resuspended in 100 microliters 0.1X TE and quantitated by Nanodrop (Thermo Scientific).
Small RNA was extracted from total RNA (100 μg) by size fractionation and converted to DNA amplicons by serial adaptor ligation followed by RT-PCR as in (Fahlgren et al., RNA 2009). The 3' adaptor sequence was 5'- CTGTAGGCACCATCAATC-3'.

value: mycelium

tag: molecule subtype

value: small RNA


title: Phytophthora infestans mycelium small RNA rep2


title: Sample 1

description: ERRBS

value: primary tumor


title: Gata5 morphant, bud, rep 2


title: Gata6 morphant, bud, rep 2


title: Gata5 morphant, bud, rep 1


title: WT, bud, rep 2


title: WT, bud, rep 1


title: Mot1_IP_10min_MNase_(20121214_7_5)

description: Mot1 IP, 10' MNase

data_processing: 1. We used Novoalign (2.08.01 - Mar 14 2012) to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC. If a read was mapped to multiple locations, one location was picked at random 2. We extracted properly paired reads (Supplementary file .bed) 3. For each base pair in the genome, we counted the number of paired-end fragments aligned over it. 4. We normalized base pair counts by dividing by the total number of counts for all base pairs and then multiplying by the total number of base pairs in the genome (Supplementary file .bedGraph) 4. We broke down aligned paired-end fragments into sub-groups by insert size length and repeated steps 3. and 4. for the paired-end fragments in each sub-group.

organism: Saccharomyces cerevisiae

source_name: Mot1 IP

value: anti-FLAG beads (Sigma #8823)


title: Mot1_input_10min_MNase_(20121214_7_6)

description: Mot1 input, 10' MNase

source_name: Mot1 input


title: Mot1_input_2.5min_MNase_(20121214_7_4)

description: Mot1 input, 2.5' MNase


title: Lung Cancer Cell Line RVH6849

source_name: Total RNA from RVH6849 cells


title: Single Cell C1 Microfluidics 86

status: Public on Oct 20 2013

first: Angela

middle: Ruohao

last: Wu

address: 318 Campus Drive, Clark Center E300

department: Bioengineering

institute: Stanford University

data_processing:
remove adapter sequences using cutadapt-1.2.1
trim base quality and remove low complexity reads using prinseq-lite-0.20.3
alignment using bowtie-0.12.9 if single end, using bowtie2-2.1.0 if paired end, and tophat-2.0.8 against hg19
FPKM values computed using cufflinks-2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: R dataframe format; one combined file for all samples. Contains tophat/cufflinks generated FPKM values.
Supplementary_files_format_and_content: pcr_cts.txt: tab-delimited text file that includes the qPCR data.

growth_protocol: standard cell culture protocol according to instructions from ATCC

extract_protocol:
standard cell lysis to extract RNA, followed by either kit specific mRNA priming or polyT bead extraction of mRNA. Microfluidic preparation sample cells were lysed within the microfluidic device.
Most were prepared using Illumina Nextera kit per illumina's protocols; some prepared using NEBNext kit per protocol instructions. Samples prepared using each are identified above in "overall design", in the sample descriptions, and in the associated manuscript

tag: cdna synthesis method

value: Clontech SMARTer

tag: library construction method

value: Nextera (transposon)


title: Single Cell C1 Microfluidics 87


title: Single Cell C1 Microfluidics 90


title: Single Cell C1 Microfluidics 89


title: Single Cell C1 Microfluidics 93


title: Single Cell C1 Microfluidics 88


title: Single Cell C1 Microfluidics 91


title: Single Cell C1 Microfluidics 95


title: Single Cell C1 Microfluidics 82


title: Single Cell C1 Microfluidics 81


title: Single Cell C1 Microfluidics 94


title: Single Cell C1 Microfluidics 85


title: Single Cell C1 Microfluidics 96


title: Gata6 morphant, bud, rep 1


title: Single Cell C1 Microfluidics 80


title: Single Cell C1 Microfluidics 79


title: Single Cell C1 Microfluidics 92


title: Mot1_IP_2.5min_MNase_(20121214_7_2)

description: Mot1 IP, 2.5' MNase

tag: cell

value: nuclei

tag: mutant


title: Single Cell C1 Microfluidics 77


title: Single Cell C1 Microfluidics 83


title: Single Cell C1 Microfluidics 76


title: Single Cell C1 Microfluidics 75


title: Single Cell C1 Microfluidics 74


title: Single Cell C1 Microfluidics 78


title: Single Cell C1 Microfluidics 71


title: Single Cell C1 Microfluidics 84


title: Single Cell C1 Microfluidics 70


title: Single Cell C1 Microfluidics 73


title: Single Cell C1 Microfluidics 69


title: Single Cell C1 Microfluidics 63


title: Single Cell C1 Microfluidics 61


title: Single Cell C1 Microfluidics 68


title: Single Cell C1 Microfluidics 66


title: Single Cell C1 Microfluidics 65


title: Single Cell C1 Microfluidics 62


title: Single Cell C1 Microfluidics 54


title: Single Cell C1 Microfluidics 64


title: Single Cell C1 Microfluidics 57


title: Single Cell C1 Microfluidics 59


title: Single Cell C1 Microfluidics 52


title: Single Cell C1 Microfluidics 58


title: Single Cell C1 Microfluidics 53


title: Single Cell C1 Microfluidics 56


title: Single Cell C1 Microfluidics 72


title: Single Cell C1 Microfluidics 49


title: Single Cell C1 Microfluidics 51


title: Single Cell C1 Microfluidics 60


title: Single Cell C1 Microfluidics 50


title: Single Cell C1 Microfluidics 46


title: Single Cell C1 Microfluidics 45


title: Single Cell C1 Microfluidics 67


title: Single Cell C1 Microfluidics 48


title: Single Cell C1 Microfluidics 44


title: Single Cell C1 Microfluidics 42


title: Single Cell C1 Microfluidics 43


title: Single Cell C1 Microfluidics 41


title: Single Cell C1 Microfluidics 40


title: Single Cell C1 Microfluidics 55


title: Single Cell C1 Microfluidics 39


title: Single Cell C1 Microfluidics 36


title: Single Cell C1 Microfluidics 38


title: Single Cell C1 Microfluidics 37


title: Single Cell C1 Microfluidics 47


title: Single Cell C1 Microfluidics 28


title: Single Cell C1 Microfluidics 30


title: Single Cell C1 Microfluidics 26


title: Single Cell C1 Microfluidics 19


title: Single Cell C1 Microfluidics 25


title: Single Cell C1 Microfluidics 20


title: Single Cell C1 Microfluidics 24


title: Single Cell C1 Microfluidics 32


title: Single Cell C1 Microfluidics 23


title: Single Cell C1 Microfluidics 22


title: Single Cell C1 Microfluidics 33


title: Single Cell C1 Microfluidics 14


title: Single Cell C1 Microfluidics 16


title: Single Cell C1 Microfluidics 13


title: Single Cell C1 Microfluidics 21


title: Single Cell C1 Microfluidics 27


title: Single Cell C1 Microfluidics 11


title: Single Cell C1 Microfluidics 12


title: Single Cell C1 Microfluidics 31


title: Single Cell C1 Microfluidics 9


title: Single Cell C1 Microfluidics 8


title: Single Cell C1 Microfluidics 15


title: Single Cell C1 Microfluidics 29


title: Single Cell C1 Microfluidics 7


title: Single Cell C1 Microfluidics 34


title: Single Cell C1 Microfluidics 18


title: Single Cell C1 Microfluidics 17


title: Single Cell C1 Microfluidics 35


title: Single Cell C1 Microfluidics 6


title: Single Cell C1 Microfluidics 5


title: Single Cell C1 Microfluidics 3


title: Single Cell Ovation-NEB 2

value: NuGEN Ovation

value: NEBNext (ligation)


title: Single Cell Ovation-NEB 1


title: Single Cell C1 Microfluidics 1


title: Single Cell C1 Microfluidics 10


title: Single Cell C1 Microfluidics 4


title: Single Cell Ovation-Nextera 4


title: Single Cell Ovation-Nextera 3


title: Single Cell Ovation-Nextera 1


title: Single Cell TransPlex 1

value: Sigma WTA TransPlex


title: Single Cell SMARTer 3


title: Single Cell Ovation-Nextera 2


title: Single Cell TransPlex 3


title: Single Cell TransPlex 2


title: Single Cell SMARTer 2


title: Bulk RNA SMARTer 2


title: Bulk RNA Superscript 2

value: Superscript RT


title: Bulk RNA SMARTer 1


title: Single Cell SMARTer 1


title: ChIP-Seq H3K27ac HUVEC

city: Cleveland

first: Fulai

state: OH - OHIO

address: 10900 Euclid Avenue

institute: Case Western Reserve University

data_processing:
The paired-end Hi-C reads were mapped to human genome hg18 using BOWTIE. Only first 36 bases were used for mapping when reads is longer. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed.
For GRO-seq, the first round of mapping used the first 36 bases; the unmapped reads were then mapped in two additional iterations using first 30 or 25 bases.
For ChIP-Seq, first 36 bases of each read were used for mapping.
RNA-seq data were analyzed using TOPHAT and CUFFLINK packages.
Genome_build: hg18
Supplementary_files_format_and_content: Mapped non-redundant reads for RNA-seq, GRO-seq and ChIP-seq are in BED format. Mapped non-redundant read pairs for Hi-C are in txt format.

source_name: primary HUVEC cells

growth_protocol: IMR90 cells were grown as described in (Hawkins, R.D. et al. Cell Stem Cell 6, 479-91). MCF7 cells (ATCC), LNCaP cells (ATCC), and Human primary HUVEC cells (Lonza) were cultured following manufacturer’s instructions.

extract_protocol:
Hi-C experiments were conducted in biological replicates using HindIII according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).).  ChIP-seq protocol can be found from http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf. GRO-seq experiments were performed according to previous publication (Wang, D. et al. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474, 390-4 (2011).).
Libraries were prepared according to Illumina's instruction or cited literatures.

treatment_protocol: TNF-a (R&D Systems, 10 ng/mL, 1 hr) treatment were performed in IMR90 or HUVEC cells.  Flavopiridol (Sigma, 1 μM for 1 hr) and IFN-γ (R&D, 50ng/mL for 2hrs) were performed in IMR90 cells. To find out primary TNF-α responsive genes, IMR90 cells were pre-treated with 5µg/mL of cycloheximide (sigma) for 30mins before TNF-α was added. Starvation and treatment of MCF7 cells with β-estradiol (Sigma, 100nM for 160min) were performed as described in previous literature (Hah, N. et al. Cell 145, 622-634, 2011); and LNCaP cells were starved and treated with 5α-dihydrotestosterone (DHT, 100nM, 4hr) as previously described(Wang, D. et al. Nature 474, 390-394, 2011)

value: no treat

tag: experiment

value: ChIP-seq

tag: antibody

value: H3K27ac (Abcam, ab4729)

tag: restriction enzyme

value: no


title: ChIP-Seq H3K27a HUVEC+TNF-α

value: TNF-α (10ng/mL) 1hr


title: ChIP-Seq p65 HUVEC+TNF-α

value: NF-κB p65 (Santa Cruz sc-372)


title: ChIP-Seq input IMR90+IFN-γ

source_name: fetal lung fibroblast

value: IFN-γ (50ng/mL) 2hr


title: ChIP-Seq input HUVEC+TNF-α


title: Single Cell Ovation-NEB 3

tag: cell line


title: Single Cell C1 Microfluidics 2


title: ChIP-Seq input HUVEC


title: RNA-Seq MCF7 + E2

source_name: breast cancer MCF7 cells

value: β-estradiol (100nM) 160min

value: RNA-Seq


title: RNA-Seq MCF7


title: RNA-Seq LNCaP

source_name: prostate cancer LNCaP cells


title: RNA-Seq LNCaP + DHT

value: 5α-dihydrotestosterone (100nM) 4hr


title: RNA-Seq IMR90+IFN-γ 0hr


title: RNA-Seq IMR90+IFN-γ 2hr


title: Bulk RNA Superscript 1


title: RNA-Seq HUVEC+TNF-α


title: RNA-Seq IMR90+TNF-α with CHX

value: TNF-α (10ng/mL) 1hr; cycloheximide (5µg/mL) pretreat 30min


title: RNA-Seq IMR90 with CHX

value: cycloheximide (5µg/mL) pretreat 30min


title: RNA-Seq HUVEC


title: ChIP-Seq H3K27a IMR90+IFN-γ


title: Hi-C IMR90+TNF-α replicate 5

value: Hi-C

value: HindIII


title: Hi-C IMR90+TNF-α replicate 3


title: Hi-C IMR90+TNF-α replicate 4


title: RNA-Seq IMR90


title: ChIP-Seq PolII IMR90+flavopiridol

data_processing:
The paired-end Hi-C reads were mapped to human genome hg18 using BOWTIE. Only first 36 bases were used for mapping when reads is longer. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed.
For GRO-seq, the first round of mapping used the first 36 bases; the unmapped reads were then mapped in two additional iterations using first 30 or 25 bases.
For ChIP-Seq, first 36 bases of each read were used for mapping.
Genome_build: NCBI36
Supplementary_files_format_and_content: Mapped non-redundant reads for GRO-seq and ChIP-seq are in BED format. Mapped non-redundant read pairs for Hi-C are in txt format.

growth_protocol: IMR90 cells were grown as described in: Hawkins, R.D. et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6, 479-91

treatment_protocol: Untreated or IMR90 cells treated with TNF-α (R&D Systems, 10 ng/mL, 1 hr) or flavopiridol (Sigma, 1 μM for 1 hr for ChIP-seq experiments, and 1 μM for 2 hr for Hi-C experiments) were used.

value: flavopiridol (1μM, 1hr)

value: PolII (Santa Cruz sc-899)


title: ChIP-Seq PolII IMR90+TNF-α