title: Lun_CT46


title: Lun_CT22

status: Public on Sep 30 2014

type: SRA

city: Philadelphia

first: Nicholas

last: Lahens

state: PA

address: Smilow Center for Translational Research 10-110 3400 Civic Center Blvd, Bldg 421

department: ITMAT

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
Align raw data to mm9 genome using STAR (v2.3.0e) with default parameters. STAR also generated files containing junction data.
Normalize read counts with DESeq2, using default parameters.
Quantify normalized read counts by running HTSeq (v0.5.4p1) in stranded mode, with default parameters. Use Ensembl gene quantifications.
Genome_build: mm9
Supplementary_files_format_and_content: txt files contain normalized, gene-level read counts and are located at series level
Supplementary_files_format_and_content: SJ.out.tab files contain splice  junction data generated by STAR

molecule: total RNA

organism: Mus musculus

source_name: lung

growth_protocol: C57/BL6 mice were entrained to a 12h light : 12h dark schedule for one week. Mice were then transferred to complete darkness prior to collection. Collection began at CT18. Mice were housed in light-tight boxes for the duration of the experiment.

extract_protocol:
Organ samples were homogenized in Trizol reagent (Invitrogen) using a Tissuelyser (Qiagen). RNA was extracted using RNeasy columns (Qiagen) as per manufacturer’s protocol, then pooled from three mice for each organ and time point.
Prepared using Illumina TruSeq Stranded mRNA HT Sample Preparation Kit as per manufacturer’s protocol. Briefly, 1 ug of total RNA was polyA-selected, fragmented by metal-ion hydrolysis, and converted into double-stranded cDNA using Invitrogen Superscript II. The cDNA fragments were subjected to end-repair, adenylation, ligation of Illumina sequencing adapters, and PCR amplification.

tag: mouse strain

tag: tissue

value: lung


title: Liv_CT58

source_name: liver

value: liver


title: Lun_CT28


title: WFat_CT58

source_name: white adipose

value: white adipose


title: WFat_CT52


title: Liv_CT46


title: Liv_CT34


title: Liv_CT40


title: Liv_CT52


title: Liv_CT22


title: Liv_CT28


title: Kid_CT52

source_name: kidney

value: kidney


title: Kid_CT64


title: Kid_CT46


title: Kid_CT40


title: Kid_CT22


title: Hyp_CT46

source_name: hypothalamus

value: hypothalamus


title: Hyp_CT52


title: Kid_CT34


title: Hyp_CT64


title: Hyp_CT58


title: Hyp_CT40


title: Hyp_CT34


title: Hyp_CT28


title: Hyp_CT22


title: Hrt_CT52

source_name: heart

value: heart


title: Hrt_CT58


title: Hrt_CT64


title: Hrt_CT40


title: Hrt_CT46


title: Hrt_CT34


title: Hrt_CT28


title: Hrt_CT22


title: Cer_CT58

source_name: cerebellum

value: cerebellum


title: Cer_CT64


title: Cer_CT40


title: Kid_CT58


title: Cer_CT46


title: Kid_CT28


title: Cer_CT52


title: Cer_CT34


title: Cer_CT28


title: Cer_CT22


title: BFat_CT52

source_name: brown adipose

value: brown adipose


title: BFat_CT46


title: Bstm_CT22

source_name: brainstem

value: brainstem


title: Aor_CT64

source_name: aorta

value: aorta


title: Aor_CT58


title: Aor_CT52


title: Bstm_CT64


title: BFat_CT22


title: BFat_CT34


title: Bstm_CT28


title: BFat_CT28


title: Bstm_CT52


title: Bstm_CT58


title: Bstm_CT40


title: Aor_CT46


title: BFat_CT40


title: BFat_CT58


title: Bstm_CT46


title: BFat_CT64


title: Adr_CT22

source_name: adrenal gland

value: adrenal gland


title: Bstm_CT34


title: Aor_CT40


title: Aor_CT28


title: Aor_CT22


title: Adr_CT28


title: Adr_CT40


title: Adr_CT34


title: Adr_CT64


title: Aor_CT34


title: Adr_CT52


title: Adr_CT58


title: Adr_CT46


title: Hsp90-alpha KO

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

data_processing:
basecalls performed on MiSeq computer
Sequenced reads were trimmed for adaptor sequence and mapped, using seqmap, to known cellular RNAs (rRNA, tRNA, etc), miRNAs (miRBase), transposon consensus sequences (RepBase), and mm9 whole genome.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include sequences and their read counts.

source_name: E16.5 whole testes

growth_protocol: natural mating

extract_protocol:
standard acid-phenol extraction by using Isogen (Toyobo)
TruSeq Small RNA Library Preparation Kit (Illumina)

treatment_protocol: 20 whole testes for each genotype

tag: strain

tag: age

value: embryonic day 16.5

value: testis


title: NarI Mmusculus - bisSeq 2

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description:
Sub representation of the Mouse genome by size selected NarI digest
mouse_NarI_summary.tab

library_source: genomic

data_processing:
150bp long reads were splited in three instances (40-70-40bp). Short reads were used directly.
Bismark/ Bowtie 0.12.7 were used to align bisulfite reads against an in silico converted reference genome (C>T and G>A) and call methylation state for each CG. (mouse-mm9; Ecoli-NC_010473.1)
CGs covered by at least 10 reads were used for analysis. Strain specific SNPs were masked.  Methylation was called per CG and fragment averages were derived using the previously established reference set of regions for the library. Only fragments where >50% of the CG and a minimum of 4 CGs were covered were considered in the analysis.
Genome_build: mm9/NC_010473.1
Supplementary_files_format_and_content: tab delimited fragment report : Fragment level average methylation call

molecule: genomic DNA

source_name: mouse embryonic stem cells

growth_protocol: Wild type embryonic stem cells derived from pure 129S6 background blastocysts, were cultivated on feeder cells or 0.2% gelatine coated dishes. ES cell growth medium consisted of DMEM (Invitrogen) supplemented with 15% foetal calf serum (Invitrogen), 1x non-essential amino acids (Invitrogen), 1mM L-glutamine, LIF and 0.001% beta-mercaptoethanol.

extract_protocol:
Genomic DNA (2μg) of ES cells carrying the libraries was bisulfite converted with the EpiTec Bisulfite Kit (QIAGEN). Libraries were amplified by PCR (AmpliTaq Gold-Invitrogen) using bisulfite compatible primers (5’-AACCTAACTATAATAAACAACC-3’; 5’-GGTATATGTATTTTTTTAGGGT-3’) annealing to the universal priming region flanking the fragments cloning site. PCR product was gel purified and fragmented by sonication (Covaris S220). The sonicated material was used to construct sequencing libraries following Illumina’s recommendations. Samples were sequenced as barcoded pools on Illumina GAII or MiSeq instruments.
http://www.illumina.com/products/chip-seq_dna_sample_prep_kit.ilmn

treatment_protocol: The Recombinase-mediated Cassette Exchange (RMCE) insertion protocol was adapted from Lienert et al to scale the needs of inserting large number of fragments in paralell. Briefly, TC-1 ES cells were selected under hygromycin (250μg/ml, Roche) for 10 days. Next, 12x106 cells were electroporated (Amaxa nucleofection, Amaxa) with 75 μg of L1-library-1L plasmid and 45 μg of pIC-Cre. Negative selection with 3 μM Ganciclovir (Roche) was started 2 d after transfection and continued for 10 days. Pools of selected cells were tested for successful insertion of DNA libraries by PCR using primers recognizing the universal priming region flanking the insertion site.

tag: library type

value: natural genomic fragments

tag: replicate type

value: technical replicate

tag: cell type

value: mouse embryonic stem cells

tag: genetic background

tag: restriction enzyme

value: NarI


title: BstUI Mmusculus - bisSeq 3

description:
Sub representation of the Mouse genome by size selected BstUI digest
mouse_BstU_summary.tab

value: biological replicate

value: BstUI


title: NarI Mmusculus - bisSeq 5


title: MspI E.coli - bisSeq 2

description:
Sub representation of the E.coli genome by size selected MspI digest
e.coli_MspI_summary.tab

organism: Escherichia coli

value: MspI


title: BstUI Mmusculus - bisSeq 1


title: BstUI Mmusculus - bisSeq 2


title: NarI Mmusculus - bisSeq 4


title: extreme E.coli - bisSeq 4

description:
PCR fragments from E.coli genome covering extreme CG denisties
e.coli_extColi_summary.tab


title: extreme E.coli - bisSeq 5


title: extreme E.coli - bisSeq 3


title: extreme E.coli - bisSeq 2


title: Platelets 7th day

city: Rio de Janeiro

first: Daniel

last: Carvalho

state: Rio de Janeiro

address: Caixa Postal 26820

country: Brazil

institute: GenOne Biotetechnologies

data_processing:
cutadapt - Trim 3'
STAR - Aligment
miRbase20 - annotation
htseq count
Genome_build: miRbase20
Supplementary_files_format_and_content: small RNA count

organism: Homo sapiens

extract_protocol:
Trizol
TrueSeq Small RNA

value: platelets


title: Platelets 5th day


title: Platelets 4th day


title: WT


title: NarI Mmusculus - bisSeq 3


title: MspI E.coli - bisSeq 3


title: extreme E.coli - bisSeq 1


title: Platelets 3rd day


title: Platelets 2nd day


title: Platelets first day


title: cultured cells sample 2 (T10-2)

city: Amsterdam

first: Oscar

last: Krijgsman

state: Outside the US or Canada

address: Plesmanlaan 121

department: Molecular Oncology and Immunology

country: Netherlands

institute: Netherlands Cancer Institute

description: shRNA library

library_source: other

data_processing:
Count data was normalized with DESeq in R per pool.
Pools (n=4) were merged after normalisation.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix with normalised count data

source_name: 888mel melanoma cells

growth_protocol: subcutaneous tumors or cells grown in vitro with regular media

extract_protocol:
genomic DNA extracted using DNeasy Blood and Tissue kit (Quiagen). Samples were divided into half-samples and shRNAs were PCR amplified using a common reverse primer (5’-CAAGCAGAAGACGGCATACGAGATTTCTTTCCCCTGCACTGTACCC-3’) and unique forward primers, containing different 5 base-pairs index sequences, to distinguish between samples (5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCTINDEXCTTGTGGAAAGGACGAAACACCGG-3’). After a second round of PCR, all PCR products were pooled and purified (QIAquick PCR Purification Kit - QIAGEN) and submitted to next generation sequencing (Illumina HiSeq2000).
TRC-Hs1.0 kinome and related factors

treatment_protocol: no treatment

tag: biological sample

value: cells cultured in vitro for 10 days


title: Reference sample 1

description: shRNA library

value: reference before set up


title: cultured cells sample 3 (T10-3)

description: shRNA library


title: cultured cells sample 1 (T10)

description: shRNA library


title: tumor 2 (Tu-2)

description: shRNA library

value: tumors grown in NSG mice for 14 days


title: cultured cells sample 4 (T10-4)

description: shRNA library


title: tumor 5 (Tu-5)

description: shRNA library


title: tumor 1 (Tu-1)

description: shRNA library


title: cultured cells sample 6 (T10-6)

description: shRNA library


title: Reference sample 2

description: shRNA library


title: tumor 4 (Tu-4)

description: shRNA library


title: hs52l3_6_PolII+TBBZ+DHT

city: La Jolla

first: Yuliang

last: Tan

state: California

address: Room 345, CMM West, 9500 Gilman Drive, Mail Code 0648

department: School of Medicine

institute: University of California, San Diego

data_processing:
All Raw fastq files are treated with prinseq-lite.pl to remove PCR amplification duplicates.
Then the remaining reads are trimmered 6 bp from the 5' end and keep 40bp for each reads for the mapping.
After that, all reads are mapped to the hg19 genome with bowtie ( -q --offrate 6 -m 1 --best --strata -t -v 3 --sam)
bedGraph files are generated with HOMER using makeUCSCfile, and peaks are determined with the following parameters: -style factor -center -size 200 -minDist 500 -fdr 0.001 -fragLength 150.
Genome_build: hg19

source_name: Pol II ChIP-seq (TBBz)

growth_protocol: F12 medium supplemented with 10% FBS and Glutamine.

extract_protocol:
Sonicated nuclei were precleared with Protein G magnetic beads and antibody chromatin complexes were isolated, and eluted DNA was reverse cross-linked overnight and DNA was purified using Qiagen DNA purification columns using Manufacturer's recommended protocol.
Libraries were prepared using Illumina's recommended protocol

treatment_protocol: The growth medium was changed to Deficient DME High Glucose medium supplemented with 5% Charcoal Dextran Filtered FBS, and treated with 100 nM DHT for 90 min after 3 days.

tag: antibody

value: Anti-Pol II Santa Cruz (N-20)

tag: passages

value: Prostate Carcinoma Cells

tag: cell line

value: LNCaP

tag: treatment

value: 25 μM TBBz for two and a half hour, and 100 nM DHT for last one and a half hour


title: cultured cells sample 5 (T10-5)

description: shRNA library


title: tumor 6 (Tu-6)

description: shRNA library


title: hs46l4_2_CK2a+DHT

source_name: CK2α ChIP-seq

value: Anti- CK2α Abcam (Cat. No. Ab70774)

value: 100 nM DHT for two and a half hour


title: BssH Mmusculus - bisSeq

description:
Sub representation of the Mouse genome by size selected BssHI digest
mouse_BssHII_summary.tab

value: natural genomic fragments

value: BssH


title: tumor 3 (Tu-3)

description: shRNA library


title: MspI E.coli - bisSeq 1

value: mouse embryonic stem cells


title: hs52l3_4_PolII+DHT

value: 25 μM DMSO for two and a half hour, and 100 nM DHT for last one and a half hour


title: NarI Mmusculus - bisSeq 1

value: biological replicate

value: NarI


title: input DNA

city: Portland

first: Gail

last: Mandel

state: OR

address: 3181 SW Sam Jackson Park Rd.

department: Vollum Institute

institute: Oregon Health & Science Universtiy

data_processing:
Illumina software pipeline was used for base-calling.
BWA was used to align sequence reads to mm9 mouse genome assembly and reads with less than 4 individual base mismatches that aligned to a single unique location were filtered for further analysis.
Peak analysis of REST-binding was independently performed using Peak Ranger and MACS analysis software to identify regions of enrichment relative to Input control and overlapping peaks were retained.
Wiggle file were produced using default settings of the PeakRanger wigmodule
Genome_build: mm9

source_name: Embryonic stem cell culture

growth_protocol: Mouse ESC cultures, N6 (WT) and N8 (REST -/-) (Jorgensen et al., 2009), were cultured in DMEM supplemented with 1000 units/ml Leukemia Inhibitory Factor (LIF, ESGRO from Millipore), 15% fetal bovine serum (FBS), 2 mM L-glutamine, 0.1 mM β-mercaptoethanol, 1X non-essential amino acids (NEAA), 1X nucleoside mixture (adenosine, guanosine, uridine, cytidine, and thymidine), and 1X penicillin/streptomycin. ESCs were cultured on feeder layers of irradiated mouse embryonic fibroblasts and passaged three times on plates coated with 0.1% gelatin to eliminate MEFs before harvesting cells for chromatin preparations.

extract_protocol:
Nuclei isolations were lysed and sonicated to shear chromatinbefore immunopurification of crosslined DNA/protein complexes.
ChIP-isolated DNA was pooled (three technical replicates done in parallel from each of two independent biological replicates) and fragments were processed to blunt ends followed by A-tailing to facilitate ligation of Illumina oligo adapters. PCR amplification was run for 12-14 cycles with primers complementary to adapter sequence to amplify the pool of ChIP DNA with addition of the adapter sequence. PCR products in the range of 200-300 bp were isolated by agarose gel electrophoresis followed by gel extraction.

value: embryonic stem cells

tag: chip antibody


title: BB

city: Hangzhou

first: Muhammad Awais

last: Ghani

state: Zhejiang

address: Room# 517, Buliding A, College of agriculture and biotechnology, Zhejiang university

department: Horticulture

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: n/a
Supplementary_files_format_and_content: counts

organism: Brassica nigra

source_name: Leaves

growth_protocol: All of the plants were grown in vermiculite mixed with 30% soil in a growth chamber under growth conditions of 22/18°C (day/night) and 16 h of illumination per day.

extract_protocol:
The total RNA was isolated using the Trizol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions and was sent to Beijing Genomics Institute (BGI) for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Leaves

value: 45 days after seed germination

tag: generation

value: male parent


title: H3K27me3_ChIPSeq_WT

value: anti-H3K27me3 (Cell Signaling 9733 (C36B11) rabbit monoclonal antibody)


title: H3K27me3_ChIPSeq_KO


title: REST_ChIPSeq_WT

value: anti-REST (Rabbit polyclonal antibody raised against a peptide corresponding to the C-terminal portion of REST and described in Nurit Ballas et al. Cell. (2005).)


title: AABB

organism: Brassica rapa x Brassica nigra

tag: ploidy

value: Allotetraploid

value: F2 hybrid


title: AB

value: Allodiploid

value: F1 hybrid


title: OMA1_RIPSeq

status: Public on Sep 29 2014

city: Minneapolis

first: Caroline

last: Spike

state: MN

address: 420 Washington Avenue, SE

department: Genetics, Cell Biology, and Development

institute: University of Minnesota

data_processing:
Illumina basecall (.bcl) files were converted to fastq files and demultiplexed using CASAVA (1.8.2).
Sequences were trimmed for quality and then aligned to the ce10 genome in Galaxy using TopHat (v1.4.1).
We retained all uniquely mapped reads that did not map to rRNA using Filter SAM or BAM (v1.1.0).  Retained reads mapping to: chrI:1-15060287 chrI:15070975 chrII chrIII chrIV chrV:1-11938591 chrV:11938665 chrX chrMtDNA.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated in Galaxy using Cufflinks (v1.3.0).
Genome_build: ce10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values

organism: Caenorhabditis elegans

source_name: Young adult

growth_protocol: Embryos were hatched in the absence of food and raised on peptone-enriched plates seeded with NA22 at 25C. Young adults were collected for lysate preparation approximately 48 hours after being placed on food.

extract_protocol:
Lysates were clarified from sonicated animals. OMA-1-RNA complexes were isolated with antibody and eluted from the immunopurification matrix with AcTEV protease.  RNA was isolated with Trizol Reagent and purified with RNAqueous-Micro columns.
A TruSeq RNA library was prepared with no poly-A mRNA purification, using standard Illumina protocols. 5 microliters purified RNA from an OMA-1 immunopurification was sequenced.

tag: genotype

tag: temperature

tag: rip antibody

value: anti-GFP (Novus Biologicals, NB600-308)


title: P5 rep3

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome with Tophat
Differential analysis was conducted with Cuffdiff v2.02 and RefSeq gene annotation downloaded from Illumina iGenome
Genome_build: mm9
Supplementary_files_format_and_content: tab delimited file, FPKMs and gene differential expression result from Cuffdiff v2.02

source_name: Cortex

growth_protocol: Standard animal husbandry

extract_protocol:
Total RNA was extracted using Qiagen's Rneasy Mini Kit precisely as per the manufacturer's instructions, with the exception that the elution volume used was 40 microlitres.
Libraries were prepared according to Illumina's instructions

treatment_protocol: postnatal day 3 and 5

tag: strain

value: Swiss Webster

tag: tissue

value: Brain

value: upper layer cortical neurons

tag: age

value: postnatal day 5


title: P5 rep2

tag: cell type


title: P3 rep3

value: postnatal day 3


title: P3 rep1


title: P3 rep2


title: P5 rep1


title: Wildtype1_2_8

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

data_processing:
Read quality filtering and barcode extraction: Every read that was considered valid by the Illumina control software was processed and filtered as follows: a) any 3' bases with a quality score of 'B' were removed; b) the well-identifying barcode was extracted from the 5' end of the read; c) if the read ended in a poly(A)-sequence leaving less than 25 transcript-derived bases, the read was discarded; d) the UMI was extracted and if any of the UMI bases had a Phred score less than 17 the read was discarded; e) a maximum of nine template-switching generated Gs were removed from the 5' end of the transcript-derived sequence; f) if the remaining sequence consisted of less than six non-A bases, or a dinucleotide repeat with less than six other bases at either end, the read was discarded.
Alignment:the reads were aligned to the genome using the Bowtie aligner, allowing for up to three mismatches and up to 24 alternative mappings for each read. The genome included an artifical chromosome, containing a concatamer of the ERCC control sequences. Any reads with no alignments were re-aligned against another artifical chromosome, containing all possible splice junctions arising from the exons defined by the known transcript variants. Reads mapping within these splice junctions were translated back to the corresponding actual genomic positions. The UCSC transcript models were used for the expression level calculation. If a locus had several transcript variants, the exons of these were merged to a combined model that represented all expression from the locus. To account for incompete cap site knowledge, the 5' ends of all models were extended by 100 bases, but not beyond the 3' end of any upstream nearby exon of another gene of the same orientation.
Annotation and quantitation: The annotation step was performed barcode-by-barcode. Only reads mapping in sense orientation of an exon were considered as potentially transcript derived. Any such read that had one or more repeat mappings that was outside exons, was assigned randomly as one of these repeats and contributed to the summarized read count of that repeat class. Else, if it had one or more sense mappings to exons, it was assigned at the exon where it was closest to the transcript model 5' end, even if the sequence was repeat-like. If it had no exon mapping, it was assigned randomly at one of the mappings. The expression level of each transcript model was taken as the total number of reads in sense orientation at all its possible mapping positions.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: transcripts per million values summarizing expression from all transcript variants of each gene in each tissue cube. Duplicated genes with the same name and different loci are discriminated by a suffix "_locN".

source_name: medial ganglionic eminence

growth_protocol: GFRa1 mutant embryos were obtained by breeding heterozygous GFRa1 deficient mice

extract_protocol:
E12.5 embryos were immersed in Tissue Tek (Sakura, Japan) and snap frozen in  80  ºC cold isopentane. Serial 50 µm thick coronal sections were made using a cryostat (NX70, Thermo Scientific, USA), collected onto pretreated frame slides (MMI, Switzerland), air dried, shortly immersed in 100 % ethanol and finally transported in 50 ml falcon tubes with desiccant on dry ice to the laser microdissection instrument. A coronal section in the middle portion of the MGE was chosen from each embryo for laser microdissection using a MMI Cellcut Plus instrument (MMI, Switzerland). Cutting parameters used: 14 % cutting velocity, 53.3 % laser focus, 100 % laser power, 3 cutting repeats. Material was collected with a sticky cap strip (MMI, Switzerland) using the “cap down” mode. After isolation, 5 µl cell capture mastermix (1 % Tween 20, 400 nM T30 and 2 µM template switching oligo, 5'-AAGCAGTGGTATCAACGCAGAGTGCAGUGCUxxxxxxrGrGrG-3', where x represents a sample-specific indexing barcode, and rG is ribo-G) was added to each sample and immediately placed on dry ice.
The cell capture plate was thawed, and 5 microlitre reverse transcription mix (4mM DTT, 2mM dNTP, 5U/microlitre SuperscriptII in 100 mM Tris-HCl at pH 8, 375 mM KCl, 0.1% Tween-20, 6 mM MnCl2, 2500 molecules of synthetic control mRNAs) was added to each well. The synthetic mRNA consisted of 92 different ERCC control RNAs. The plate was incubated (10°C for 10 min, 42°C for 45 min) to complete reverse transcription and template switching. To purify the cDNA and remove unreacted primers, 100 microlitre MyOne carboxylatebeads (Invitrogen) was washed twice in 100 microlitre EBT (10 mM Tris-Cl at pH 8.5, 0.02% Tween-20) and then resuspended in 2 mL 14% PEG-6000 in 0.9 M NaCl, and 20 microlitre of this mixture was added to each well. Beads from all wells were pooled, washed in 70% ethanol twice, dried, and eluted in 37 microlitre EBT in a 1.5-mL polyallomer tube (Beckman). The cDNA was amplified in a single tube in 50 microlitre of 200 microM dNTP, 200 nM STRT-PCR primer (5’-biotin-AAGCAGTGGTATCAACGCAGAGT-3’), 1x Advantage2 DNA Polymerase Mix (Clontech) in 1x Advantage2 PCR buffer (Clontech) with 1 min at 95°C followed by 20 cycles of 15 sec at 95°C, 30 sec at 65°C, 4 min at 68°C,with heated lid.A 5 microlitre aliquot was amplified for another five cycles and visualized on a 1.2% agarose E-gel (Invitrogen) to confirm the range of cDNA lengths. The product was immobilized on MyOne C1 Streptavidin beads. Twenty microliters of beads was washed twice in 50 microlitre 2x BWT (10 mM Tris HCl at pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) and added to the remaining 45 microlitre PCR product. After a 10-min incubation at room temperature, the beads were washed three times in 50 microlitre 1x BWT and twice in EBT. Amplified cDNA was fragmented by DNase I in the presence of Mn2+. Beads were resuspended in DNase I buffer supplemented with 10 mM MnCl2 and DNaseI diluted to 0.0003U/microlitre in a total volume of 120 microlitre for exactly 8 min at room temperature. The reaction was stopped by washing the beads five times in 50 microlitre EBT. Beads were resuspended in 25 microlitre EBT, and 25 microlitre NEBNext End Repair reaction mix (New England Biolabs) was added; then the beads were incubated for 30 min at room temperature. The beads were washed twice in EBT, then resuspended in 21 microlitre EBT; 2.5 microlitre NEBNext dA tailing buffer and 1.5 microlitre Klenow exo- (both NEB) were added, and the reaction was incubated for 30 min at 37°C, followed by two washes in 50 microlitre EBT. An adapter containing the Illumina P2 sequence (5’-CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT-3’ and 3’-PHO-GTTCGTCTTCTGCCGTATGCTCGAGAAGGCTAG-PHO-5’) was ligated by resuspending the beads in 25 microlitre EBT and adding 2x ligationmix (2x NEBuffer4, 2 microM adapter,1U/microlitre T4DNAligase,2U/microlitre SalI-HF, and 2mM ATP; all reagents from NEB) and incubating for 30min at 37°C and then washing twice in 25 microlitre EBT. The beads were then used as template in a 100 microlitre PCR reaction (200 microM dNTP, 400 nM each primer of primers 5’-AATGATACGGCGACCACCGAGATCTAAGCAGTGGTATCAACGCAGAGT-3’ and 5’-CAAGCAGAAGACGGCATACGAG-3’, 200 microM dNTP ,0.2U/microlitre Phusion polymerase in PhusionHF buffer ;all from NEB) with 30 sec at 98°C, followed by 12 cycles of [10 sec at 98°C, 30 sec at 65°C, 30 sec at 72°C] followed by 5 min at 72°C. The product was purified by AmPure XP (Beckman Coulter) and resuspended in 20 microlitre EBT. The sample was size-selected on a 2% E-gel with SYBR Safe (Invitrogen), recovering the 200 400 bp range by Qiaquick Gel Extraction (replacing the heating step with 15 min of vigorous agitation). The well indexing barcodes are contained in the reads as bases 1-6.

tag: animal

value: medial ganglionic eminence

value: GFRa1 mutant

tag: genetic background

tag: x-coordinate

tag: y-coordinate


title: Wildtype1_3_2


title: Wildtype1_2_5


title: Wildtype1_3_4


title: Wildtype1_2_7


title: Wildtype1_3_5


title: Wildtype1_3_7


title: Wildtype1_2_4


title: Wildtype1_2_6


title: Wildtype1_3_8


title: Wildtype1_2_2


title: Wildtype1_2_3


title: Wildtype1_3_9


title: Wildtype1_3_10


title: Wildtype1_5_10


title: Wildtype1_4_10


title: Wildtype1_6_10


title: Wildtype1_7_10


title: Wildtype1_8_10


title: Wildtype1_9_10


title: Wildtype1_10_10


title: Wildtype1_11_10


title: Wildtype1_3_3


title: Wildtype1_11_9


title: Wildtype1_3_6


title: Wildtype1_11_8


title: Wildtype1_11_6


title: Wildtype1_11_7


title: Wildtype1_11_2


title: Wildtype1_10_1


title: Wildtype1_11_1


title: Wildtype1_8_1


title: Wildtype1_7_1


title: Wildtype1_4_1


title: Wildtype1_12_1


title: Wildtype1_11_3


title: Wildtype1_6_1


title: Wildtype1_5_1


title: Wildtype1_9_1


title: Wildtype1_12_11


title: Wildtype1_3_1


title: Wildtype1_12_5


title: Wildtype1_12_9


title: Wildtype1_12_7


title: Wildtype1_12_4


title: Wildtype1_11_5


title: Wildtype1_11_11


title: Wildtype1_12_6


title: Wildtype1_12_2


title: Wildtype1_11_4


title: Wildtype1_12_3


title: Wildtype1_12_10


title: Wildtype1_12_8


title: Wildtype1_6_11


title: Wildtype1_7_11


title: Wildtype1_10_11


title: Wildtype1_8_11


title: Wildtype1_9_11


title: Wildtype1_5_11


title: Wildtype1_1_7


title: Wildtype1_1_8


title: Wildtype1_4_11


title: Wildtype1_1_9


title: Wildtype1_2_9


title: Wildtype1_7_2


title: Wildtype1_6_2


title: Wildtype1_5_2


title: Wildtype1_4_2


title: Wildtype1_1_4


title: Wildtype1_1_3


title: Wildtype1_4_8


title: Wildtype1_4_3


title: Wildtype1_10_2


title: Wildtype1_8_2


title: Wildtype1_4_4


title: Wildtype1_1_5


title: Wildtype1_4_6


title: Wildtype1_4_5


title: Wildtype1_9_2


title: Wildtype1_4_7


title: Wildtype1_7_9


title: Wildtype1_10_9


title: Wildtype1_5_9


title: Wildtype1_9_9


title: Wildtype1_4_9


title: Wildtype1_8_9


title: Wildtype1_10_8


title: Wildtype1_10_6


title: Wildtype1_10_7


title: Wildtype1_1_6


title: Wildtype1_10_4


title: Wildtype1_10_3


title: Wildtype1_10_5


title: Wildtype1_5_3


title: Wildtype1_5_5


title: Wildtype1_6_3


title: Wildtype1_5_4


title: Wildtype1_6_9


title: Wildtype1_5_6


title: Wildtype1_7_3


title: Wildtype1_9_3


title: Wildtype1_5_7


title: Wildtype1_5_8


title: Wildtype1_8_3


title: Wildtype1_6_8


title: Wildtype1_7_8


title: Wildtype1_8_8


title: Wildtype1_9_4


title: Wildtype1_9_5


title: Wildtype1_9_8


title: Wildtype1_9_6


title: Wildtype1_7_4


title: Wildtype1_6_4


title: Wildtype1_6_7


title: Wildtype1_6_6


title: Wildtype1_8_7


title: Wildtype1_6_5


title: Wildtype1_8_5


title: Wildtype1_7_5


title: Wildtype1_8_4


title: Wildtype1_9_7


title: Mutant_10_10

value: Mutant


title: Mutant_12_8


title: Mutant_12_9


title: Mutant_12_7


title: Mutant_11_10


title: Mutant_2_9


title: Mutant_1_8


title: Mutant_1_7


title: Mutant_1_6


title: Mutant_2_8


title: Wildtype1_7_7


title: Wildtype1_8_6


title: Mutant_2_7


title: Mutant_2_6


title: Wildtype1_7_6


title: Mutant_2_5


title: Mutant_3_5


title: Mutant_3_6


title: Mutant_3_9


title: Mutant_3_7


title: Mutant_3_8


title: Mutant_3_2


title: Mutant_3_3


title: Mutant_3_4


title: Mutant_1_9


title: Mutant_4_3


title: Mutant_4_5


title: Mutant_4_4


title: Mutant_4_6


title: Mutant_4_7


title: Mutant_4_8


title: Mutant_7_9


title: Mutant_5_9


title: Mutant_4_9


title: Mutant_6_9


title: Mutant_8_9


title: Mutant_10_9


title: Mutant_11_1


title: Mutant_10_1


title: Mutant_2_4


title: Mutant_11_9


title: Mutant_9_1


title: Mutant_5_3


title: Mutant_5_2


title: Mutant_7_1


title: Mutant_4_2


title: Mutant_5_5


title: Mutant_8_1


title: Mutant_5_4


title: Mutant_5_1


title: Mutant_6_1


title: Mutant_5_6


title: Mutant_5_8


title: Mutant_9_9


title: Mutant_8_8


title: Mutant_7_8


title: Mutant_11_8


title: Mutant_11_7


title: Mutant_11_5


title: Mutant_11_3


title: Mutant_11_2


title: Mutant_11_6


title: Mutant_10_8


title: Mutant_11_4


title: Mutant_9_8


title: Mutant_10_2


title: Mutant_8_2


title: Mutant_9_2


title: Mutant_5_7


title: Mutant_6_8


title: Mutant_7_2


title: Mutant_6_5


title: Mutant_6_4


title: Mutant_7_7


title: Mutant_6_7


title: Mutant_6_3


title: Mutant_8_7


title: Mutant_6_6


title: Mutant_10_7


title: Mutant_10_6


title: Mutant_10_4


title: Mutant_10_5


title: Mutant_6_2


title: Mutant_9_3


title: Mutant_9_7


title: Mutant_10_3


title: Mutant_8_3


title: Mutant_7_4


title: Mutant_7_6


title: Mutant_7_5


title: Mutant_7_3


title: Mutant_8_6


title: Mutant_9_5


title: Mutant_9_4


title: Mutant_8_4


title: Mutant_9_6


title: Mutant_8_5


title: Wildtype2_13_4

value: wild type


title: Wildtype2_13_3


title: Wildtype2_13_2


title: Wildtype2_7_9


title: Wildtype2_9_8


title: Wildtype2_5_9


title: Wildtype2_8_9


title: Wildtype2_12_8


title: Wildtype2_6_9


title: Wildtype2_12_7


title: Wildtype2_12_1


title: Wildtype2_11_8


title: Wildtype2_11_7


title: Wildtype2_12_2


title: Wildtype2_11_6


title: Wildtype2_12_5


title: Wildtype2_12_3


title: Wildtype2_12_4


title: Wildtype2_11_5


title: Wildtype2_11_3


title: Wildtype2_11_4


title: Wildtype2_11_1


title: Wildtype2_2_8


title: Wildtype2_3_8


title: Wildtype2_4_8


title: Wildtype2_1_6


title: Wildtype2_10_8


title: Wildtype2_12_6


title: Wildtype2_1_5


title: Wildtype2_2_7


title: Wildtype2_1_4


title: Wildtype2_2_4


title: Wildtype2_2_2


title: Wildtype2_2_3


title: Wildtype2_3_7


title: Wildtype2_3_6


title: Wildtype2_3_5


title: Wildtype2_3_1


title: Wildtype2_4_1


title: Wildtype2_5_8


title: Wildtype2_11_2


title: Wildtype2_4_2


title: Wildtype2_4_3


title: Wildtype2_4_6


title: Wildtype2_5_7


title: Wildtype2_2_6


title: Wildtype2_2_5


title: Day 4 post NGN induction, biological replicate 3

first: Nathan

last: Lewis

state: CA

department: Pediatrics

data_processing:
FASTQ files were compressed to a BAM format using the UCSC_Main_on_Human19__wgEncodeGencodeCompV14_genome.gtf sequence
RNA sequencing reads were aligned to the human genome (Build 37, GRCh37.p10)
FPKM levels were determined for each gene using Cufflinks and the Homo_sapiens.GRCh37.p10.gtf annotation
Differential expression was conducted using CuffDiff2, with the option to combine biological replicates
Genome_build: Build 37, GRCh37.p10
Supplementary_files_format_and_content: txt files have Cufflinks FPKM levels, and BAM files have compressed raw reads

molecule: polyA RNA

source_name: PGP1 iPS cells_Day 4 post NGN induction

growth_protocol: The Personal Genome Project iPS cell line PGP1 (hu43860C) obtainable from Coriell (GM23338, the matching primary fibroblast line is GM23248). PGP1 cells were cultured in mTeSR media (05850, StemCell Technologies). This iPS line was genetically modified by lentiviral gene transfer and genomic integration of the doxycycline inducible Neurogenin vectors. Standard tissue culture plates were coated with Matrigel hESC-qualified Matrix (354277, BD Biosciences) for 1h at room temperature. For passaging, the cells were dissociated using TrypLE™ Express (12604013, Gibco), washed with Phosphate-Buffered Saline (pH 7.4) (10010031, Gibco) and replated using mTeSR supplemented with 3µg/ml InSolution™ Y-27632 Rho Kinase inhibitor (688001, EMD Millipore) and/or frozen using mFreSR media (05854, StemCell Technologies). The doxycycline (D9891-5G, Sigma) concentration for induction was 0.5ug/ml.

extract_protocol:
The RNA extraction was performed using the mirVana™ miRNA Isolation Kit (AM1560, Ambion) following their protocol. The protocol was interrupted after the first column purification step to obtain the total RNA. The isolated RNA was stored at -80C and submitted to the Broad Institute (Cambridge, MA) where the quality control, library preparation (Illumina dUTP RNA-Seq Library (PolyA method)) and RNA sequencing (Illumina HiSeq (Paired End Run 101 Base)) was performed.
Broad Institute (Cambridge, MA) conducted quality control, library preparation (Illumina dUTP RNA-Seq Library (PolyA method)) and RNA sequencing (Illumina HiSeq (Paired End Run 101 Base)) as previously reported.

treatment_protocol: After infection, the media was changed to plain mTeSR and the cells were cultured for another day until the doxycycline was added to mTeSR media. Two wells per plate were pooled for one biological replicate. In total, we generated triplicates for each time point. The day 0 samples were not treated with mTeSR plus 0.5ug/ml doxycycline (Sigma). The cells were enzymatically dissociated, washed with Phosphate-Buffered Saline (pH 7.4) (Gibco) and stored at 4º C overnight in RNAlater solution (Ambion). The next day, the samples were frozen at -20C until RNA extraction. The day 1, day 3 and day 4 samples were harvested and treated accordingly.

tag: cell line source

value: Fibroblast derived iPS cells

tag: genotype/variation

value: harboring doxycycline inducible Neurogenin vectors

tag: treated with

value: 0.5ug/ml doxycycline

tag: cell subtype

value: Fibroblast derived iPS cells, differentiated neurons

tag: time point

value: Day 4 post NGN induction


title: Wildtype2_8_7


title: Day 4 post NGN induction, biological replicate 2

value: Personal Genome Project iPS cell line PGP1 (hu43860C)


title: Day 4 post NGN induction, biological replicate 1


title: Day 3 post NGN induction, biological replicate 3

source_name: PGP1 iPS cells_Day 3 post NGN induction

value: Day 3 post NGN induction


title: Wildtype2_10_7


title: Wildtype2_7_7


title: Wildtype2_3_4


title: Wildtype2_10_6


title: Wildtype2_10_5


title: Wildtype2_3_3


title: Day 3 post NGN induction, biological replicate 2


title: Wildtype2_10_2


title: Wildtype2_3_2


title: Wildtype2_10_3


title: Wildtype2_4_4


title: Day 3 post NGN induction, biological replicate 1


title: Wildtype2_4_5


title: Wildtype2_9_7


title: Wildtype2_10_1


title: Wildtype2_4_7


title: Wildtype2_9_1


title: Day 1 post NGN induction, biological replicate 3

source_name: PGP1 iPS cells_Day 1 post NGN induction

value: Day 1 post NGN induction


title: Wildtype2_6_7


title: Day 1 post NGN induction, biological replicate 2


title: Wildtype2_8_1


title: Wildtype2_7_1


title: Wildtype2_6_1


title: Wildtype2_5_1


title: Day 0, biological replicate 3

source_name: PGP1 iPS cells_Day 0

value: none (untreated control)

value: iPS cells

value: Day 0


title: Wildtype2_5_2


title: Day 1 post NGN induction, biological replicate 1


title: Wildtype2_5_3


title: Day 0, biological replicate 1


title: Day 0, biological replicate 2


title: Wildtype2_5_4


title: Wildtype2_5_5


title: Wildtype2_6_6


title: Wildtype2_8_6


title: Wildtype2_5_6


title: Wildtype2_7_6


title: Wildtype2_9_5


title: huESC_KAP1_83

city: Santa Cruz

first: Sofie

last: Salama

address: MS: CBSE, 1156 High St

department: Center for Biomolecular Science and Engineering

institute: Univerity of California, Santa Cruz

description:
fj083
DNA from Chromatin IP

data_processing:
Paired-end samples that were sequenced to 100x100bp were trimmed from the 3' end to 80x80bp. Samples that were sequenced to 50x50bp were not trimmed.
The (possibly trimmed) paired-end reads were mapped with bowtie to the hg19 assembly (human samples) or mm9+hg19chr11 (mouse samples).
For multiply mapped reads, only the best scoring mapping per bowtie2 were kept. Only mappings with both of the paired-end reads mapped were kept.
Potential PCR duplicates were removed with samtools rmdup.
Based on the paired-end mappings, the median length of the fragments was determined for each sample. For input to MACS 1.4 only the read1 mappings were used and the median fragment length was used to determine the "-shiftsize" parameter.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Excel workbook with MACS results.

source_name: embryonic stem cells, KAP1 ChIP

extract_protocol:
O'Geen H, Echipare L, Farnham PJ. Using ChIP-seq technology to generatehigh-resolution profiles of histone modifications. Methods Mol Biol. 2011;791:265-86. doi: 10.1007/978-1-61779-316-5_20. PubMed PMID: 21913086.
TrueSeq DNA library prep, low input protocol.

tag: transchromosomic

value: no

tag: plasmid

value: KAP1 ChIP

tag: chip antibody

value: KAP1 ChIP (abcam ab10483, lot#GR17300)

tag: nickname

value: KAP1 (hESC) r1


title: Wildtype2_9_6

value: medial ganglionic eminence

tag: genotype


title: Wildtype2_9_3

tag: tissue

value: wild type


title: huESC_KAP1_84

description:
fj084
DNA from Chromatin IP

value: KAP1 (hESC) r3


title: humanESC_inpDNA_66

description:
fj066
DNA from input chromatin

source_name: embryonic stem cells, input

value: input DNA

value: inpDNA hESC


title: Wildtype2_9_2


title: Wildtype2_7_2


title: Wildtype2_6_2


title: Wildtype2_9_4


title: humanESC_inpDNA_43

description:
fj043
DNA from input chromatin


title: huESC_KAP4_44

description:
fj044
DNA from Chromatin IP

value: KAP1 (hESC) r2


title: Wildtype2_6_3


title: Wildtype2_8_2


title: Wildtype2_6_5


title: hESC_ZNF486_192

description:
fj192
DNA from Chromatin IP

source_name: embryonic stem cells, ZNF486 ChIP

value: ZNF486 ChIP

value: KZNF (hESC) r2


title: hESC_ZNF486_191

description:
fj191
DNA from Chromatin IP

value: KZNF (hESC) r1


title: Wildtype2_7_5


title: Wildtype2_8_5


title: humanESC_inpDNA_150

description:
fj150
DNA from input chromatin


title: Wildtype2_10_4


title: humanESC_H3K4nz_148

description:
fj148
DNA from Chromatin IP

source_name: embryonic stem cells, H3K4me3 ChIP

value: H3K4me3 ChIP

value: H3K4m3 (hESC) r1


title: muh11ESC_K4z9_215

description:
fj215
DNA from Chromatin IP

data_processing:
Paired-end samples that were sequenced to 100x100bp were trimmed from the 3' end to 80x80bp. Samples that were sequenced to 50x50bp were not trimmed.
The (possibly trimmed) paired-end reads were mapped with bowtie to the hg19 assembly (human samples) or mm9+hg19chr11 (mouse samples).
For multiply mapped reads, only the best scoring mapping per bowtie2 were kept. Only mappings with both of the paired-end reads mapped were kept.
Potential PCR duplicates were removed with samtools rmdup.
Based on the paired-end mappings, the median length of the fragments was determined for each sample. For input to MACS 1.4 only the read1 mappings were used and the median fragment length was used to determine the "-shiftsize" parameter.
Genome_build: mm9 (MGSCv37) + hg19 (GRCh37) chr11
Supplementary_files_format_and_content: Excel workbook with MACS results.

source_name: embryonic stem cells, TC11, ZNF91 plasmid, H3K4me3 ChIP

tag: strain/background


title: Wildtype2_7_3


title: Wildtype2_8_3


title: Wildtype2_7_4


title: muh11ESC_inpDNA_94

description:
fj094
DNA from input chromatin

source_name: embryonic stem cells, TC11, empty vector, input

value: empty vector

value: inpDNA mTC11


title: humanESC_H3K4nz_149

description:
fj149
DNA from Chromatin IP

value: no

value: H3K4m3 (hESC) r2


title: Wildtype2_8_4


title: muh11ESC_K4z9_214

description:
fj214
DNA from Chromatin IP


title: huESC_fj096

data_processing:
Samples were mapped with Tophat2 using Bowtie2 as the underlying alignment tool. Sample dg011 was trimmed to 80x80bp from the 3' end. Others were not trimmed prior to mapping. The target assemblies were hg19 (human samples) and mm9+hg19chr11 (transchromosomic samples). Tophat was supplied with a gene model using the --GTF option. The gene model was UCSC KnownGenes.
For multiply mapped reads, only the best scoring mapping per bowtie2 were kept. Only mappings with both of the paired-end reads mapped were kept.
Potential PCR duplicates were removed with samtool rmdup.
The final set of mappings was converted to coverage using bedTools genomeCoverageBed.
The coverage summed over all exonic positions of a gene was divided by 200 to determine the read per gene for a sample. This was done for all hg19 UCSC KnownGenes.
For input to DESeq all genes with non-zero counts in any sample were considered. Replicates were combined per the DESeq methodology.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Excel workbook with DESeq results.

source_name: embryonic stem cells

growth_protocol: MEF feeders + W8 (fj074, fj095, fj096), feeder-free GMEM+Lif (dg011, fj208-211), MEF feeders + KSR15 (fj078. fj113).

extract_protocol:
Trizol + RNeasy cleanup, followed by ribozero rRNA depletion.
Strand-specific dUTP followed by TruSeq DNA library prep kit.

value: hESC RNA


title: Wildtype2_6_4


title: muh11ESC_K4ev_213

description:
fj213
DNA from Chromatin IP

source_name: embryonic stem cells, TC11, empty vector, H3K4me3 ChIP

value: H3K4m3 (mTC11-EV) r2


title: muh11ESC_K4ev_212

description:
fj212
DNA from Chromatin IP

value: H3K4m3 (mTC11-EV) r1


title: muh11ESC_ev_fj208

data_processing:
Samples were mapped with Tophat2 using Bowtie2 as the underlying alignment tool. Sample dg011 was trimmed to 80x80bp from the 3' end. Others were not trimmed prior to mapping. The target assemblies were hg19 (human samples) and mm9+hg19chr11 (transchromosomic samples). Tophat was supplied with a gene model using the --GTF option. The gene model was UCSC KnownGenes.
For multiply mapped reads, only the best scoring mapping per bowtie2 were kept. Only mappings with both of the paired-end reads mapped were kept.
Potential PCR duplicates were removed with samtool rmdup.
The final set of mappings was converted to coverage using bedTools genomeCoverageBed.
The coverage summed over all exonic positions of a gene was divided by 200 to determine the read per gene for a sample. This was done for all hg19 UCSC KnownGenes.
For input to DESeq all genes with non-zero counts in any sample were considered. Replicates were combined per the DESeq methodology.
Genome_build: mm9 (MGSCv37) + hg19 (GRCh37) chr11
Supplementary_files_format_and_content: Excel workbook with DESeq results.

source_name: embryonic stem cells, TC11, empty vector

value: TC11+EV r1 RNA


title: muh11ESC_z9_fj210

source_name: embryonic stem cells, TC11, ZNF91 plasmid

value: TC11+ZNF91 r1 RNA


title: muh11ESC_z9_fj211

value: TC11+ZNF91 r2 RNA


title: huESC_fj074


title: EC_JQ1_CHEMSEQ_TNF

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: endothelium stimulated with TNF alpha

data_processing:
Library strategy: Chem-Seq
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 1 -m 1 -n 1 --best --concise. Seed length (-l) was set to read length for each dataset.
Genome_build: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

source_name: HUVEC

growth_protocol: M199 + 20% FBS + 0.1% heparin + 50 micrograms/mL endothelial cell growth factors (ECGF).

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 precipitated using streptavidin conjugated beads. Purified precipitated 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.

treatment_protocol: Treated cells were stimulated with human TNFalpha (25 ng/mL, hr)

value: Streptavidin

tag: antibody catalog number

tag: cell type

value: endothelium

tag: agent

value: TNF alpha

tag: duration

value: 1 hour


title: muh11ESC_nt_dg011

source_name: embryonic stem cells, TC11

value: TC11 RNA


title: muh11ESC_ev_fj209

value: TC11+EV r2 RNA


title: Control_MCF10A_for_5metC_ChIPSeq

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

description: control sample without antibody

data_processing: Supplementary_files_format_and_content: Bedgraph files were generated from peak files built from reads mapping uniquely to the genome with at most 0,1,2 mismatches, using Pyicos (Althammer et al., 2011). Significant ChIP-Seq signal was calculated from the coverage of reads comparing each samples with its specific control sample. The significant peaks per sample in bedgraph format are the following: MCF10-HP1-CTRL.MA.pvalue.bedgraph, MCF7HP1-CTRL.MA.pvalue.bedgraph, 4B8-MCF10-CTRL.MA.pvalue.bedgraph, 4B8-MCF7-CTRL.MA.pvalue.bedgraph, MCF10-5metC-CTRL.MA.pvalue.bedgraph, MCF7-5metC-CTRL.MA.pvalue.bedgraph, MCF10-RNAPII-CTRL.MA.pvalue.bedgraph). AGO1 MCF7 Millipore significant peaks were calculated using Pyicos (Althammer et al., 2011).

source_name: Human breast cells

growth_protocol: MCF7 and mCF10 human breast cells were plate and incubated during 72 hours in complete medium (DMEM high glucose GutaMAX life Technologies), then the medium was changed by cross-linking medium containing 1% folmaldehyde.

extract_protocol: Performed with Illumina protocol. 10Ng of inmunoprecipitated DNA was end-repaired, and Illumina double stranded adapters for single read sequencing were ligated to the DNA. After purification of the sample with a MinElute spin column, we size-selected libraries on a 2% agarose gel and fragments corresponding to an insert size range of around 130bp were recovered. The libraries were finally amplified with an 18-cycle PCR reaction, and library quality was confirmed on the Agilent 2100 Bioanalyzer. The samples were loaded at concentrations of 8-11 pm onto Illumina single read flowcells and sequenced on the Illumina Genome Analyzer  IIx using a 40 cycles recipe.


title: Control_MCF7_for_5metC_ChIPSeq

description: control sample without antibody


title: Control_MCF7_for_HP1_sample_ChIPSeq

description: control sample without antibody


title: rhESC_fj113

description:
fj113
Rhesus macaque

data_processing:
Samples were mapped with Tophat2 using Bowtie2 as the underlying alignment tool. Sample dg011 was trimmed to 80x80bp from the 3' end. Others were not trimmed prior to mapping. The target assemblies were hg19 (human samples) and mm9+hg19chr11 (transchromosomic samples). Tophat was supplied with a gene model using the --GTF option. The gene model was UCSC KnownGenes.
For multiply mapped reads, only the best scoring mapping per bowtie2 were kept. Only mappings with both of the paired-end reads mapped were kept.
Potential PCR duplicates were removed with samtool rmdup.
The final set of mappings was converted to coverage using bedTools genomeCoverageBed.
The coverage summed over all exonic positions of a gene was divided by 200 to determine the read per gene for a sample. This was done for all hg19 UCSC KnownGenes.
For input to DESeq all genes with non-zero counts in any sample were considered. Replicates were combined per the DESeq methodology.
Genome_build: rheMac2
Supplementary_files_format_and_content: Excel workbook with DESeq results.

organism: Macaca mulatta

value: rhESC RNA


title: rhESC_fj078

description:
fj078
Rhesus macaque


title: EC_JQ1_CHEMSEQ_CON

description: resting unstimulated endothelium


title: Control_MCF7_ChIPSeq

description: control sample without antibody


title: Control_MCF10A_ChIPSeq

description: control sample without antibody


title: PolIIS2ph ChIP in untreated cells

city: Oxford

first: Kinga

last: Kamieniarz-Gdula

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description: cIPminus_macs0.05shift100_peaks.narrowPeak

data_processing:
The raw data were processed using the Solexa Pipeline and mapped to the reference genome (NCBI Build 36, hg19) using Eland (Illumina)
Peak calling has been performed using MACS2 2.0.10.2013-05-22 with the parameters: -q 0.05 --nomodel --shiftsize 100
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 generated peak coordinates in narrowPeak format for the ChIP samples versus their corresponding input

source_name: PolIIS2ph ChIP in untreated cells

growth_protocol: HeLa cells were grown in DMEM with addition of 10% FCS

extract_protocol:
Cross-linking with 1% FA, chromatin shearing with bioruptor, IP with PolIIS2ph antibody (abcam ab5095) for ChIP samples, de-crosslinking and purification over Qiagen columns
NEBNext ChIP-Seq Library Prep Reagent Set for Illumina according to manufacturer's instructions

treatment_protocol: Cells described as treated exposed to 10 μΜ of BIX-01294 inhibitor for 72h and tranfected with GFP-RNase H1 plasmid for 32h.

tag: cell line

value: HeLa

tag: antibody

tag: antibody vendor/catalog

value: Abcam ab5095


title: huESC_fj095

value: no

value: hESC RNA r1


title: siAGO1_MCF7_rep1

growth_protocol: Cells were growth in  DMEM-Glutamax (10%  SFB).

treatment_protocol: We transfect 20 nM of either siLuc (control) or siAGO1 (specific knockdown) by triplicates in a 6 well plate using Lipofectamine 2000 (Invitrogen). We mantain the cells without changing the medium (OptiMEM) for 72 hs.

tag: transfection


title: siAGO1_MCF7_rep2


title: EC_JQ1_CHEMSEQ_WCE_CON

description: resting unstimulated endothelium


title: input from BIX treated RNaseH1 overexpressing cells

description: cIPplus_macs0.05shift100_peaks.narrowPeak


title: Control_MCF7_ChIPSeq_for_AGO1-4B8_MCF7

description: control sample without antibody


title: RNAPII_MCF10A_ChIPSeq

value: RNAPII

tag: antibody vendor

value: Abcam

tag: antibody catalog#


title: AGO1-4B8_MCF10A_ChIPSeq

value: Monoclonal anti-AGO1


title: siLuc_MCF7_rep1

description: For each lane the txt files of the gene read counts and RPKM. For each lane Fastq files of the reads mapped to exon-exon junctions. Additional excel file with the differential expression results, geneid information, log fold change and p-values.

value: siLuc


title: Control_MCF10A_ChIPSeq_for_AGO1-4B8_MCF10A

description: control sample without antibody


title: 5metC_MCF10A_ChIPSeq

value: Diagenode


title: HP1_alpha_MCF10A_ChIPSeq


title: H3K27me3_MCF10A_ChIPSeq

value: Millipore

value: Upstate 07-449


title: siLuc_MCF7_rep2


title: EC_WCE_TNF_JQ1_2

description: endothelium stimulated with TNF alpha and JQ1

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: hg18
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences were extended 150bp upstream and 0bp downstream (with respect to read strand) and allocated into 25bp bins. Counts were normalized to reads per million, and bins with at least 1 read per million are shown.

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.

treatment_protocol: Cells were stimulated with human TNFalpha (25 ng/mL, hr) in the presence or absence of JQ1 (500 nM, 1 hour pretreatment)

value: endothelium

value: TNF alpha and JQ1

value: 1 hour pretreatment with JQ1 followed by 1 hour TNF alpha treatment


title: EC_WCE_TNF_2

description: resting unstimulated endothelium


title: EC_WCE_TNF


title: H3K36me3_MCF10A_ChIPSeq


title: H3K9me2_MCF10A_ChIPSeq

value: Upstate 07-441


title: EC_WCE_CON_2

description: endothelium stimulated with TNF alpha

value: TNF alpha

value: 1 hour TNF alpha treatment


title: AGO1_Milli_MCF10A_ChIPSeq


title: EC_WCE_CON

description: resting unstimulated endothelium


title: EC_RNA_POL2_TNF_JQ1

value: RNA Polymerase II


title: input from untreated cells

source_name: input from untreated cells

value: HeLa


title: EC_RNA_POL2_TNF

description: endothelium stimulated with TNF alpha


title: H3_MCF10A_ChIPSeq


title: EC_P65_TNF_JQ1


title: EC_P65_TNF

description: endothelium stimulated with TNF alpha


title: HP1_alpha_MCF7_ChIPSeq


title: H3K27me3_MCF7_ChIPSeq


title: EC_P65_CON

description: resting unstimulated endothelium


title: EC_H3K4ME3_TNF_JQ1


title: EC_H3K4ME3_CON

description: resting unstimulated endothelium


title: H3K36me3_MCF7_ChIPSeq


title: EC_H3K27AC_TNF_JQ1


title: EC_H3K27AC_CON

description: resting unstimulated endothelium


title: H3K9me2_MCF7_ChIPSeq


title: EC_BRD4_CON

description: resting unstimulated endothelium


title: EC_BRD4_TNF

description: endothelium stimulated with TNF alpha


title: EC_BRD4_TNF_JQ1


title: AGO1-4B8_MCF7_ChIPSeq


title: 5metC_MCF7_ChIPSeq


title: CBP_null1_EtOH

city: Memphis

first: Suzanne

middle: J

last: Baker

state: TN

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St Jude Children's Research Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome assembly using BWA version 0.5.9 with default setting
Duplicate reads as well as reads with map quality score of less than 1 were removed
Peaks were called using MACS (version 1.4.2) with p-value cutoff of 1E-5
Genome_build: mm9
Supplementary_files_format_and_content: bigWig file were generated based on read coverage

source_name: primary CBP null MEF (e14.5)

growth_protocol: 6 15 cm dishes of each p5 wild type and CBP conditional (flox//flox) MEF were plated at 4x10^6 cells/dish in 25ml DMEM+10%FBS containing Cre recombinase expressing adenovirus at an MOI of 100 and grown in a 3% O2 5%CO2 incubator.  Medium was changed 16hrs later for 25ml DMEM + 10%FBS and MEFs were grown for 48hrs in 3% O2 5%CO2 incubator.  MEFs were transferred to a normoxia 5% CO2 incubator and grown for 24hrs.

extract_protocol:
Cell lysates were sonicated (5x 10sec @ 15micron amplitude, MSE Soniprep 150) and immunoprecipitated using CBP antibody (MEFs lacking CBP provide control for antibody specificity)
library prepared according to Illumina protocol "Preparing Samples for ChIP Sequencing of DNA" (2007).   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.

treatment_protocol: 25ul of 100mM 2',2'-dipyridyl or ethanol vehicle was added to each plate and plates were returned to normoxia 5% CO2 incubator for 2hrs.  Medium was then removed from the plates and 15ml 3% paraformaldehyde in PBS was added and cells were allowed to fix for 20min at room temperature.  Fixed adherent cells were washed 2x with PBS and scraped from plates into PBS to harvest.  Cells were lysed in buffer containing 1% SDS.

tag: strain

tag: treatment

value: 2hrs ethanol vehicle

tag: passage

value: CBP (CREBBP) Brindle 8690


title: EC_RNA_POL2_CON

description: resting unstimulated endothelium

tag: chip antibody


title: CBP_null2_EtOH


title: WT2_EtOH

source_name: primary wild type MEF (e14.5)


title: WT1_EtOH


title: CBP_null2_DP

value: 2hrs 100uM dipyridyl


title: CBP_null1_DP


title: WT2_DP


title: H3_MCF7_ChIPSeq

value: Abcam


title: WT1_DP


title: Individual_7

city: Belfast

first: David

middle: Arthur

last: Simpson

state: N. Ireland

address: QUB Institue of clinical Science, Block A, RVH

department: Centre for Experimental Medicine

institute: Queen's University Belfast

data_processing:
Basecalls performed using Illumina Real Time Analysis (RTA 1.17.22)
Sequenced reads were trimmed to remove adaptor sequences and collapsed to generate unique reads using Genomics Workbanch v5.5.1 (CLCbio, Aarhus, Denmark)

source_name: Plasma

extract_protocol:
Blood samples were collected in EDTA-treated tubes and plasma separated immediately by centrifugation for 10 minutes at 1,000g for 10 min and subsequently at 10,000g for 10 min prior to RNA extraction using a miRNeasy kit (Qiagen, Crawley, UK).
Small RNA libraries were prepared using an Illumina Truseq small RNA sample prep kit

value: plasma


title: EC_H3K27AC_TNF

description: endothelium stimulated with TNF alpha


title: Individual_9


title: PPARα KO ChIP-seq_GW7647

status: Public on Sep 27 2014

city: Houston

last: Moore

state: Texas

address: One Baylor Plaza

institute: Baylor College of Medicine

description: GW7647 treatment (twice, oral gavage, 12:00 am and 12:00 pm)

data_processing:
Sequenced reads were aligned to the mouse reference genome (mm9) using Bowtie v0.12.8 (Langmead et al., 2009) with parameters ‘-n 1 -l 30  -m 1’. Only one uniquely aligning read per genomic position was kept for further analysis.
Peakcalling and wiggle file generation was performed with MACS14 using default settings. Then normalized to the total number of reads for each sample (reads/per million reads)
Genome_build: mm9

source_name: Liver

growth_protocol: All mice maintained in ad libitum normal chow diet and drinking water

extract_protocol:
Liver harvested from anesthetized mouse was snap-frozen in liquid nitrogen. Lysates were clarified from sonicated nuclei and PPARα-genomic DNA complexes were isolated with PPARα antibody.
10 ng of the pooled DNA was then amplified according to ChIP Sequencing Sample Preparation Guide provided by Illumina, using adaptor oligo and primers from Illumina, enzymes from New England Biolabs and PCR Purification Kit and MinElute Kit from Qiagen.

treatment_protocol: Vehicle (4:1 mixture of PEG-400 and Tween80), GW7647 (5 mg/kg body weight), twice, oral gavage at 12:00 am and 12:00 pm

tag: age and sex

tag: age sex

value: male

tag: nutrient state

value: ad libitum fed


title: Benzoate culture

status: Public on Sep 28 2014

city: Berkeley

first: Hiroshi

last: Otani

address: 1 Cyclotron Road

department: DOE Joint Genome Institute

institute: Lawerence Berkeley National Laboratory

data_processing:
Torrent Suite™ Software v3.4.1. was used for basecall
Sequenced reads were trimmed for adaptor sequence.
Sequences below a minimum of Phred quality value 20 scanning from the 3’ end to 5’ of the single-ended sequencing reads were trimmed using the FASTQ Quality Trimmer tool of the FASTX-toolkit v0.0.13. If the read fell below 35 bases after trimming, it was removed from further analysis.
Trimmed reads were aligned to the RHA1 genome using Bowtie 2 v2.1.0 in end-to-end mode with parameters -q --very-sensitive. Mapped read counts per gene were obtained using the htseq-count script of the HTSeq package v0.5.4.
Genome_build: ASM1456v1
Supplementary_files_format_and_content: Tab-delimited text files include the mapped read counts per gene

organism: Rhodococcus jostii

source_name: Rhodococcus jostii RHA1 cells

growth_protocol: R. jostii RHA1 cells were cultivated in M9 supplemented with Goodies, and ferulate or benzoate. Mid-log phase cultures were collected.

extract_protocol:
Total RNA was extracted using TRIzol® Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacture’s instructions. The RNA was treated with TURBOTM DNase (Invitrogen, Carlsbad, CA, USA) and then TURBOTM DNase was removed by phenol-chloroform extraction. Ten µg of total RNA was enriched in mRNA by using Ribominus™ Transcriptome Isolation Kit (Invitrogen, Carlsbad, CA, USA).
Libraries for RNA-seq analysis were prepared from 500 ng of rRNA-depleted RNA samples using Ion Total RNA-Seq Kit v2 (Life TechnologiesTM, Carlsbad, CA, USA) according to the manufacture’s procedures

tag: carbon source

value: benzoate

tag: molecule subtype

value: rRNA-depleted RNA


title: WT PPARα ChIP-seq_Vehicle

description: Vehicle treatment (twice, oral gavage, 12:00 am and 12:00 pm)


title: Ferulate culture

value: ferulate


title: PPARα KO ChIP-seq_Vehicle


title: Blueprint_S00NN3H1_H3K4me1

status: Public on Sep 26 2014

city: Nijmegen

first: Hindrik

last: Kerstens

address: Geert Grooteplein Zuid 26

department: Molecular Biology

institute: Radboud University

description:
chromatin IP
raw file: H0LRGAGXX_1_5642.sorted.bam

data_processing:
Cluster generation and sequencing were performed using the Illumina HiSeq2000 genome analyzer. The image files were processed to extract DNA sequence data using CASAVA-1.8.2. The 42 bp sequence tags were mapped to the reference human genome hg19 (NCBI build37), using the BWA allowing one mismatch. Only uniquely mapped-reads were used for data analysis and visualization. The output data were converted to bam files for downstream analysis. Details about aligner version and parameters used are stored in the headers of the BAM files. PCR duplicates were removed, therefore the final BAM files only contain uniquely mapped reads. Wig files were generated by counting the number of sequence reads (directionally extended to a final 300 bp) per 10-bp genomic window and can be used for viewing the data in the UCSC Genome Browser.
DNAseI bam files were merged per source-treatment (Monocytes RPMI, Macrophages RPMI, Macrophages LPS, Macrophage BG), and DNaseI hotspots were called on the merged bam using the published “Hotspots” pipeline (Neph et al 2012).
Peak calling was performed using MACS2-2.0.10.09132012 using Blueprint C000S5H2 Input Monocytes as a reference input.
For archiving RNA-seq 42-bp reads were aligned to hg19 using GSNAP release 2012-07-20 using parameters -N 1 -n 1  -m 1 -Q.
Gene expression quantification was performed by first aligning RNA-Seq tags to the Ensembl GRCh37 version 68 transcriptome using bowtie with parameters "-a --best --strata -S -m 100 --chunkmbs 256". Name sorted bamfiles were converted using bam2hits and gene expression was quantitated using mmseq (doi: 10.1186/gb-2011-12-2-r13). Results are given in log (base e) RPKM.
Genome_build: hg19
Supplementary_files_format_and_content: Bed.gz files are the peak regions called by MACS2, wig.gz files visualizes the mapped data in the UCSC genome browser. RNA-Seq results are reported as log (base e) RPKM.

extract_protocol: Chromatin was fixed in 1% formaldehyde for 10 minutes, sheared to 200-700bp using a Bioruptor (Diagenode), immunoprecipitated using the indicated antisera, purified and sequenced using HiSeq 2000 as recommended by the manufacturer. DNaseI treatment was done on isolated nuclei for 3 minutes and reaction was stopped with stop buffer ( 50mM Tris-HCl, pH 8, 100mM NaCl, 0.10% SDS, 100mM EDTA, pH 8.0, 1mM Spermidine, 0.3mM Spermine), sample was further fractionated on 9% Sucrose gradient for  24hrs/25000rpm at 16ºC . Further sequenced using HiSeq as recommended by the manufacturer.

treatment_protocol: Monocytes were pre-incubated either with cell culture medium (RPMI), β-glucan (5µg/mL) or with LPS (100ng/mL), for 24 hours in a total volume of 10 mL. After a wash-out, cells were cultured in RPMI supplemented with 10% human pool serum. Monocytes were collected at different time points (0 h and 6 d after treatment) and counted before further treatment for chromatin immunoprecipitation or DNaseI treatment.

tag: cell type


title: Blueprint_S00NM5H1_H3K27ac

description:
chromatin IP
raw file: H0LRGAGXX_1_5638.sorted.bam

growth_protocol: Monocytes were pre-incubated either with cell culture medium (RPMI), β-glucan (5µg/mL) or with LPS (100ng/mL), for 24 hours in a total volume of 10 mL. After a wash-out, cells were cultured in RPMI supplemented with 10% human pool serum.


title: Blueprint_S00NM5H1_H3K4me3

description:
chromatin IP
raw file: H0LRGAGXX_1_5637.sorted.bam


title: Blueprint_S00NN3H1_H3K27ac

description:
chromatin IP
raw file: H0LRGAGXX_1_5641.sorted.bam


title: WT PPARα ChIP-seq_GW7647


title: Blueprint_S00NN3H1_H3K4me3

description:
chromatin IP
raw file: H0LRGAGXX_1_5640.sorted.bam


title: Blueprint_S00NM5H1_H3K4me1

description:
chromatin IP
raw file: H0LRGAGXX_1_5639.sorted.bam


title: Individual_8

tag: tissue


title: Blueprint_S00NK9H1_H3K27ac

description:
chromatin IP
raw file: H0LRGAGXX_1_5635.sorted.bam


title: Blueprint_S00NK9H1_H3K4me3

description:
chromatin IP
raw file: H0LRGAGXX_1_5634.sorted.bam


title: WT heart2

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

country: Spain

institute: CNIC

data_processing:
Samples were sequenced in an Illumina GAIIx sequencer
Base calls produced by Illumina pipeline version 1.13.48
Base calls were extracted using illumina2bam tool release 0.03 from Wellcome Trust Sanger Institute. Standard Phred Scale
Reads were pre-processed with Cutadapt 1.2.1, to remove TruSeq adaptor sequences.
Resulting reads were mapped on the mouse transcriptome (Ensembl gene-build GRCm38.v70) And quantified using RSEM v1.17
Only genes with at least 2 counts per million in at least 1 sample were considered for statistical analysis.
Data were normalized and differential expression tested using the Bioconductor package EdgeR. We considered as differentially expressed those genes with a Benjamini-Hochberg adjusted p-value <0.05.
Genome_build: GRCm38.v70
Supplementary_files_format_and_content: normalized_data_matrix.txt file contains ENSEMBL gene Ids, MGI gene names and normalized counts per million obtained using edgeR

source_name: Adult heart ventricles

growth_protocol: Adult mice were fed tamoxifen diet for 4 weeks at weaning and sacrified 2 weeks after

extract_protocol:
Whole hearts were dissected and tissue was lysated using TissueLyser. For RNA extraction, we used the miRNAeasy kit from Qiagen,
Libraries were made using the standard TruSeq RNA Sample Preparation v2 Kit from Illumina

treatment_protocol: 0.5 mg/Kg Teklad tamoxifen Diet for 4 weeks

tag: genotype/variation

value: iMOS t1-Myc; WT

value: Adult heart ventricles

tag: Stage

value: 8 weeks


title: WT heart1


title: Blueprint_S00NJBH1_H3K27ac

description:
chromatin IP
raw file: H0LRGAGXX_1_5632.sorted.bam

source_name: Primary Monocytes(BC17)

value: Primary Monocytes(BC17)


title: HEK293_microRNAs

city: Indianapolis

first: Scot

last: Matkovich

state: IN

address: Lilly Corporate Center

institute: Eli Lilly and Company

description: small RNA (<70 nt)

data_processing:
Illumina Casava1.8 software was used for basecalling; all 50 nt reads use phred33 quality scores.
Sequence reads were mapped to the human or rat genome, followed by microRNA assignment and quantitation using sRNAbench
Processed data are supplied as read counts as well as reads per million.
Genome_build: Human GRCh38; rat Rn5
Supplementary_files_format_and_content: tab-delimited text files include read count and reads per million values for each microRNA

source_name: Human HEK293 cells

extract_protocol:
Culture medium was aspirated from 35 mm diameter dishes and cells were lysed immediately in Trizol (Invitrogen) for total RNA extraction.
Small RNA sequencing libraries were prepared using Illumina TruSeq Small RNA Sequencing kits (version C); following adapter ligation to total RNA, small RNAs were PCR-amplified and size-selected on 6% TBE PAGE.

tag: cell line


title: H3K4me3 Rep1

city: Lund

first: Carl

last: Sanden

address: BMC B13, Klinikgatan 26

department: Department of Hematology

institute: Lund University

data_processing:
The Illumina OLB v1.9 was used for base conversion.
The Bowtie 2 software was used for the alignment of reads to the hg19 reference genome.
Peak calling was performed using MACS v1.4.1. Parameters: -g 2.70e+9 -bw 300 -p 1.00e+5 -mfold 10.30
Genome_build: hg19
Supplementary_files_format_and_content: peaks, bed

source_name: U937 cell line

growth_protocol: U937 cells were grown in RPMI 1640 medium supplemented with 10% FBS (Life Technologies).

extract_protocol:
Chromatin immunoprecipitation was performed on U937 cells using the Magna-ChIP A/G Chromatin Immunoprecipitation Kit (Merck Millipore) after crosslinking with 1% formaldehyde for 15 min. Chromatin shearing was achieved by sonication in a Bioruptor UCD-200 (Diagenode).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: H3K4me3 (Abcam, ab-8580)


title: H3K4me3 Rep2


title: PolIIS2ph ChIP in BIX treated RNaseH1 overexpressing cells

tag: antibody

tag: antibody vendor/catalog

value: Abcam ab5095


title: Myc heart2

value: iMOS t1-Myc; merCreMer mhy6-Cre


title: Blueprint_S00NK9H1_H3K4me1

description:
chromatin IP
raw file: H0LRGAGXX_1_5636.sorted.bam


title: EC_WCE_TNF_JQ1

description: endothelium stimulated with TNF alpha

tag: antibody catalog number

value: endothelium

tag: agent

value: TNF alpha

tag: duration

value: 1 hour TNF alpha treatment


title: Myc heart 1


title: pbs2 (SALT)

city: Buffalo

first: Paul

last: Cullen

state: NY

address: 341 Cooke Hall

department: Biology

institute: SUNY-Buffalo

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.17 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's CASAVA v1.8.2 software (http://www.illumina.com/software.ilmn).
For analysis of the RNA seq data, reads of low quality were filtered out prior to alignment to the reference genome (S. cerevisiae assembly R64-1-1, Ensembl release 75) using TopHat v2.0.9
Genes with low counts across all samples were removed, prior to identification of differentially expressed genes using the Bioconductor package edgeR v3.4.2.
A false discovery rate (FDR) method was employed to correct for multiple testing.
Differential expression was defined as log2 (ratio) greater than or equal to 0.585 (plus or minus 1.5-fold) with the FDR set to 5 percent.
Genome_build: S. cerevisiae assembly R64-1-1, Ensembl release 75 using TopHat v2.0.9
Supplementary_files_format_and_content: For each RNA sequence comparison, the following data was included: logFC, represents  log2 fold change,  logCPM, (log2 counts per million), Pvalue defined as significant if the value  less than 0.0001, FDR, false discovery rate, sig , a gene was designated  sig (significant) if logFC greater than or equal to .585 and FDR less than .05. Sig genes will have a value of 1 in the sig column, otherwise 0, and normalized gene counts for the three independent  trials, raw gene counts, and GO annotations are also indicated.

organism: Saccharomyces cerevisiae

source_name: Sigma 1278b background

growth_protocol: Wild type and mutant cells were grown to mid-log phase in YEPD (4.5 hours), YEP-GAL (5.5 hours), YEPD + 0.4 M KC (10 minutes)l, or YEPD + 2.5 ug tunicamycin (3 hours).

extract_protocol:
Total RNA was extracted from cells by the hot acid phenol method. Isolated RNA was purified over a RNAeasy column (Qiagen). RNA concentration was measured using the NanoDrop2000 spectrophotometer (Thermo Scientific, Wilmington, DE) and purity was established by the A260/A280 ratio. RNA was detected by running samples on an 8M Urea 6%polyacylamide gel, stained by ethidium bromide. Three independent inductions were evaluated for RNA-seq analysis. Total RNA integrity was checked using an Agilent 2200 TapeStation (Agilent Technologies, Inc., Santa Clara, CA) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences, Hopkinton, MA).
RNA-seq libraries were prepared from total RNA using the TruSeq RNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA). Library size distributions were validated using an Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA). Additional library QC, blending of pooled indexed libraries, and cluster optimization was performed using Life Technologies’ Invitrogen Qubit 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA, USA).  RNA-seq libraries were pooled (24-plex) and clustered onto a flow cell lane using an Illumina cBot. Sequencing was performed using an Illumina HiSeq 2500 in Rapid Mode employing a paired-end, 50 base read length (PE50) sequencing strategy.

treatment_protocol: Three independent experiments were performed for the 8 conditions.

tag: genetic background

value: Sigma 1278b background

tag: genotype

tag: treatment

value: salt


title: DEK Rep1

tag: chip antibody

value: DEK (Abcam, ab-74975)


title: Input Rep2


title: ste12 (GALACTOSE, GAL)

value: galactose


title: Human ESCs PolII Vehicle- treated 6h 09

city: New york

first: RAFFAELLA

last: Di MICCO

state: New York

address: 550 1st avenue,  Smilow 305

department: Pathology

institute: NYU School of Medicine

description: ChIP-Seq analysis PolII from human ESCs (H9 line) FGF cultured  Vehicle- treated 6h

data_processing:
Basecalls performed using CASAVA
Bowtie (Langmead et al., 2009) version 0.12.7 was used for alignment of sequenced reads. RNA-seq data analysis was performed using the Cufflinks protocol (Trapnell et al., 2012) version 1.3. MACS (Zhang et al., 2008) version 1.4.2 was used for ChIP-seq peak discovery. GenomicTools (Tsirigos et al., 2012) version 2.7.0 was used for performing genomic interval mathematical operations, genomic interval annotation and Pol II occupancy profile construction.
RNA-seq data analysis was performed using the Cufflinks protocol (Trapnell et al., 2012) version 1.3.  For ChIP-seq peak discovery was performed with MACS version 2.0.10.20131216 using a broad peak caller and the following parameters: (a) –nomodel, (b) --shiftsize=200, (c) --keep-dup=2, (d) --to-large, (e) –broad, and (f) --broad-cutoff=0.01.
Genome_build: hg19

source_name: human H9 cell lines

growth_protocol: For RNA-seq H9 cell lines were grown on matrigel in the presence of FGF (10ng/ml), vehicle (DMSO) or MS436 (10uM). For ChIP-seq experiments chromatin was isolated from FGF-maintained hESCs, vehicle or MS417-treated (at 250nM concentration for 6h).

extract_protocol:
RNeasy kit (Qiagen) for RNA-seq; 1% formaldheyde crosslinked chromatin for ChIP-seq
Poly-A+ selection (magnetic oligodT-containing beads)  was used for RNA-seq library preparation. cDNA preparation and library construction was performed as described by the manufacturer (Illumina, CA, USA) . RNA libraries were sequenced using Genome Analyzer IIx System 50bp single-read method. Llibraries for ChIP-sequencing were generated as described in (Ntziachristos et al., 2012), including end-repair, A-tailing, adapter (Illumina Truseq system) ligation and PCR amplification of the libraries. We performed cluster amplification and 50-nucleotide single-read sequencing using the Illumina HiSeq 2000, following manufacturer’s protocols.
Library construction was performed as described by the manufacturer (Illumina, CA, USA)

value: Pol II Santa cruz (N20)


title: Human ESCs PolII MS417- treated 6h 10

description: ChIP-Seq analysis PolII from human ESCs (H9 line) FGF cultured MS417- treated 6h


title: Wild type (SALT)

value: wild type


title: Wild type  (TUNICAMYCIN, TUN)

value: tunicamycin


title: Human ESCs BRD3 Vehicle- treated 6h 09

description: ChIP-Seq analysis BRD3 from human ESCs (H9 line) FGF cultured  Vehicle- treated 6h

value: BRD3 Bethyl  (A302-368A)


title: pbs2 (GALACTOSE, GAL)


title: Wild type


title: Human ESCs BRD2 MS417- treated 6h 08

description: ChIP-Seq analysis BRD2 from human ESCs (H9 line) FGF cultured MS417- treated 6h

value: BRD2 Bethyl (A302-583A)


title: Wild type (GALACTOSE, GAL)


title: Blueprint_S00NJBH1_H3K4me1

description:
chromatin IP
raw file: H0LRGAGXX_1_5633.sorted.bam


title: DEK Rep2


title: Human ESCs BRD2 Vehicle- treated 6h 07

description: ChIP-Seq analysis BRD2 from human ESCs (H9 line) FGF cultured  Vehicle- treated 6h


title: Human ESCs BRD3 MS417- treated 6h 10

description: ChIP-Seq analysis BRD3 from human ESCs (H9 line) FGF cultured MS417- treated 6h


title: Input Rep1


title: Human ESCs BRD4 MS417- treated 6h (rep1+rep2)

description: ChIP-Seq analysis BRD4 from human ESCs (H9 line) FGF cultured MS417- treated 6h

value: BRD4 Bethyl (A301-985A)


title: Human ESCs IgG MS417- treated 6h 02

description: ChIP-Seq analysis IgG from human ESCs (H9 line) FGF cultured MS417- treated 6h

value: IgG Santa Cruz (2027)


title: Human ESCs IgG Vehicle- treated 6h 01

description: ChIP-Seq analysis IgG from human ESCs (H9 line) FGF cultured Vehicle- treated 6h


title: Monocytes_Day6_BG_CD3depleted_Buffy12_80U

description:
DNAseI-seq
raw file: C3JYVACXX_7_5402.sorted.bam
BAM file for this sample used to derive:
BGall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed


title: Human ESCs BRD4 Vehicle- treated 6h (rep1+rep2)

description: ChIP-Seq analysis BRD4 from human ESCs (H9 line) FGF cultured Vehicle- treated 6h


title: pbs2  (TUNICAMYCIN, TUN)


title: Monocytes_Day0_CD3depleted_Buffy12_80U_RUN2

description:
DNAseI-seq
raw file: C3TCNACXX_8_5399.sorted.bam
BAM file for this sample used to derive:
Buffy101112Day0merge.hg19.hotspot.twopass.fdr0.01.bed

source_name: Primary Monocytes(BC12)

value: Primary Monocytes(BC12)


title: Monocytes_Day6_RPMI_CD3depleted_Buffy12_80U

description:
DNAseI-seq
raw file: C3JYVACXX_7_5400.sorted.bam
BAM file for this sample used to derive:
RPMIall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed


title: Monocytes_Day0_CD3depleted_Buffy12_80U_RUN1

description:
DNAseI-seq
raw file: C3JYVACXX_8_5399.sorted.bam
BAM file for this sample used to derive:
Buffy101112Day0merge.hg19.hotspot.twopass.fdr0.01.bed


title: Monocytes_Day6_BG_CD3depleted_Buffy11_80U

description:
DNAseI-seq
raw file: C3JYVACXX_7_5398.sorted.bam
BAM file for this sample used to derive:
BGall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed


title: Monocytes_Day6_LPS_CD3depleted_Buffy11_80U

description:
DNAseI-seq
raw file: C3JYVACXX_8_5397.sorted.bam
BAM file for this sample used to derive:
LPSall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed


title: AGO1_Milli_MCF7_ChIPSeq

tag: antibody vendor

value: Millipore

tag: antibody catalog#


title: DNaseI_Monocytes_Day6_LPS_CD3depleted_buffycoat_9_RUN2

description:
DNAseI-seq
raw file: C2NTEACXX_8_4754.sorted.bam
BAM file for this sample used to derive:
LPSall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed


title: DNaseI_Monocytes_Day6_bglu_CD3depleted_buffycoat_9

description:
DNAseI-seq
raw file: C2NE2ACXX_8_4755.sorted.bam
BAM file for this sample used to derive:
BGall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed


title: DNaseI_Monocytes_Day6_RPMI_CD3depleted_buffycoat_9_RUN1

description:
DNAseI-seq
raw file: C2NE2ACXX_8_4753.sorted.bam
BAM file for this sample used to derive:
RPMIall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed


title: DNaseI_Monocytes_Day6_RPMI_CD3depleted_buffycoat_9_RUN2

description:
DNAseI-seq
raw file: C2NTEACXX_8_4753.sorted.bam
BAM file for this sample used to derive:
RPMIall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed


title: Monocytes_Day6_LPS_CD3depleted_Buffy8_80U_RUN1

description:
DNAseI-seq
raw file: C2MVTACXX_8_4644.sorted.bam
BAM file for this sample used to derive:
LPSall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed


title: EC_H3K4ME3_TNF

description: endothelium stimulated with TNF alpha

source_name: HUVEC


title: Monocytes_Day6_RPMI_CD3depleted_Buffy8_80U_RUN1

description:
DNAseI-seq
raw file: C2MVTACXX_8_4643.sorted.bam
BAM file for this sample used to derive:
RPMIall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed


title: Monocytes_Day6_LPS_CD3depleted_Buffy8_80U_RUN2

description:
DNAseI-seq
raw file: C2N9FACXX_8_4644.sorted.bam
BAM file for this sample used to derive:
LPSall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed


title: Monocytes_Day6_LPS_CD3depleted_Buffy12_80U

description:
DNAseI-seq
raw file: C3JYVACXX_7_5401.sorted.bam
BAM file for this sample used to derive:
LPSall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed


title: Monocytes_Day0_CD3depleted_Buffy10_80U_RUN1

description:
DNAseI-seq
raw file: C3JYVACXX_8_5391.sorted.bam
BAM file for this sample used to derive:
Buffy101112Day0merge.hg19.hotspot.twopass.fdr0.01.bed

source_name: Primary Monocytes(BC10)

value: Primary Monocytes(BC10)


title: Blueprint_Primary_PBMC_A_Pop4_RNAseq

description:
RNA-seq
raw file: C3TCNACXX_6_5451.sorted.bam

source_name: Primary Monocytes(rest cell population after CD14+ selection)(BC13)


title: Blueprint_Primary_PBMC_B_Pop4_RNAseq

description:
RNA-seq
raw file: C3TCNACXX_6_5455.sorted.bam

source_name: Primary Monocytes(rest cell population after CD14+ selection)(BC14)


title: Monocytes_Day6_RPMI_CD3depleted_Buffy8_80U_RUN2

description:
DNAseI-seq
raw file: C2N9FACXX_8_4643.sorted.bam
BAM file for this sample used to derive:
RPMIall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed


title: RNASeq_Monocytes_Day6_LPS_CD3depleted_buffycoat_12

description:
RNA-seq
raw file: C3JYVACXX_6_5389.sorted.bam


title: Blueprint_Primary_PBMC_A_Pop3_RNAseq

description:
RNA-seq
raw file: C3TCNACXX_5_5450.sorted.bam

source_name: Primary MonocytesCD14+(BC13)

value: Primary MonocytesCD14+(BC13)


title: RNASeq_Monocytes_Day6_bglu_CD3depleted_buffycoa_12

description:
RNA-seq
raw file: C3JYVACXX_6_5390.sorted.bam


title: RNASeq_Monocytes_Day6_RPMI_CD3depleted_buffycoa_11

description:
RNA-seq
raw file: C3JYVACXX_6_5384.sorted.bam


title: RNASeq_Monocytes_Day6_bglu_CD3depleted_buffycoa_11

description:
RNA-seq
raw file: C3JYVACXX_6_5386.sorted.bam


title: RNASeq_Monocytes_Day6_RPMI_CD3depleted_buffycoa_12

description:
RNA-seq
raw file: C3JYVACXX_6_5388.sorted.bam


title: RNASeq_Monocytes_Day6_bglu_CD3depleted_buffyc_9_re

description:
RNA-seq
raw file: C2NTEACXX_7_4820.sorted.bam


title: RNASeq_Monocytes_Day6_LPS_CD3depleted_buffycoat_11

description:
RNA-seq
raw file: C3JYVACXX_6_5385.sorted.bam


title: DNaseI_Monocytes_Day6_LPS_CD3depleted_buffycoat_9_RUN1

description:
DNAseI-seq
raw file: C2NE2ACXX_8_4754.sorted.bam
BAM file for this sample used to derive:
LPSall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed


title: RNASeq_Monocytes_Day6_LPS_CD3depleted_buffyc_9_rep

description:
RNA-seq
raw file: C2NTEACXX_7_4819.sorted.bam


title: Monocytes_Day0_CD3depleted_Buffy10_80U_RUN2

description:
DNAseI-seq
raw file: C3TCNACXX_8_5391.sorted.bam
BAM file for this sample used to derive:
Buffy101112Day0merge.hg19.hotspot.twopass.fdr0.01.bed


title: RNASeq_Monocytes_Day0_CD3depleted_buffycoat_11

description:
RNA-seq
raw file: C3JYVACXX_6_5383.sorted.bam

source_name: Primary Monocytes(BC11)

value: Primary Monocytes(BC11)


title: Monocytes_Day6_BG_CD3depleted_Buffy8_80U

description:
DNAseI-seq
raw file: C2MVTACXX_8_4645.sorted.bam
BAM file for this sample used to derive:
BGall4Buffy891112merge.hg19.hotspot.twopass.fdr0.01.bed


title: RNASeq_Monocytes_Day6_RPMI_CD3depleted_buffyc_9_re

description:
RNA-seq
raw file: C2NTEACXX_7_4818.sorted.bam


title: RNASeq_Monocytes_Day0_CD3depleted_buffyc_9_rep

description:
RNA-seq
raw file: C2NTEACXX_7_4817.sorted.bam

source_name: Primary Monocytes(BC9)

value: Primary Monocytes(BC9)


title: RNASeq_Monocytes_Day0_RPMI_CD3depleted_dup

description:
RNA-seq
raw file: C2MVTACXX_7_4639.sorted.bam

source_name: Primary Monocytes(BC8)

value: Primary Monocytes(BC8)


title: RNASeq_Monocytes_Day0_CD3depleted_buffycoat_12

description:
RNA-seq
raw file: C3JYVACXX_6_5387.sorted.bam


title: RNASeq_Monocytes_Day6_bglu_CD3depleted_dup

description:
RNA-seq
raw file: C2MVTACXX_7_4642.sorted.bam


title: RNASeq_Monocytes_Day6_RPMI_CD3depleted_dup

description:
RNA-seq
raw file: C2MVTACXX_7_4640.sorted.bam


title: Blueprint_S00COJH1_H3K4me3

description:
chromatin IP
raw file: C2N9FACXX_1_4718.sorted.bam


title: Blueprint_Primary_PBMC_B_Pop3_RNAseq

description:
RNA-seq
raw file: C3TCNACXX_5_5454.sorted.bam

source_name: Primary MonocytesCD14+(BC14)

value: Primary MonocytesCD14+(BC14)


title: Blueprint_S00BYTH1_H3K4me3

description:
chromatin IP
raw file: C2N9FACXX_1_4715.sorted.bam


title: Blueprint_S00COJH1_H3K4me1

description:
chromatin IP
raw file: C2N9FACXX_5_4719.sorted.bam


title: Blueprint_S00COJH1_H3K27ac

description:
chromatin IP
raw file: C2N9FACXX_1_4720.sorted.bam


title: Blueprint_S00BXVH1_H3K4me3

description:
chromatin IP
raw file: C2N9FACXX_1_4712.sorted.bam


title: RNASeq_Monocytes_Day6_LPS_CD3depleted_dup

description:
RNA-seq
raw file: C2MVTACXX_7_4641.sorted.bam


title: Blueprint_S00BXVH1_H3K27ac

description:
chromatin IP
raw file: C2N9FACXX_3_4714.sorted.bam


title: Blueprint_S00BXVH1_H3K4me1

description:
chromatin IP
raw file: C2N9FACXX_2_4713.sorted.bam


title: Blueprint_S00BYTH1_H3K27ac

description:
chromatin IP
raw file: C2N9FACXX_3_4717.sorted.bam


title: Blueprint_S00BWXH1_H3K4me1

description:
chromatin IP
raw file: C2N9FACXX_2_4722.sorted.bam


title: Blueprint_S00BWXH1_H3K27ac

description:
chromatin IP
raw file: C2N9FACXX_4_4723.sorted.bam


title: Blueprint_S00NJBH1_H3K4me3

description:
chromatin IP
raw file: H0LRGAGXX_1_5631.sorted.bam

value: Primary Monocytes(BC17)


title: Blueprint_S00BWXH1_H3K4me3

description:
chromatin IP
raw file: C2N9FACXX_4_4721.sorted.bam


title: H9c2_microRNAs

description: small RNA (<70 nt)

organism: Rattus norvegicus

source_name: Rat H9c2 cells


title: KH22_20

first: Shih-Chin

last: Cheng

address: Geert Grooteplein Zuid 10

department: Department of Internal Medicine

institute: Radboudumc

data_processing:
STAR aligment version 2.3.0
Htseq quantification version 0.5.4p3
Genome_build: mm10
Supplementary_files_format_and_content: a matrix of raw counts, rows are genes, column are 12 samples

source_name: Splenocytes

extract_protocol:
Splenocytes were isolated and the total RNA was harvested with Trizol reagent
RNAseq libraries were prepared from 1 ug RNA of each cell population using Illumina’s TruSeq RNA kit (San Diego, CA, USA) according to the manufacturer’s instructions

value: HIF-KO

value: splenocyte

value: PBS


title: KH22_16


title: KH22_14

value: littermate (BL6)


title: KH22_7

value: B-glucan


title: KH22_9


title: KH22_11


title: KH22_15


title: KH22_6


title: KH22_4


title: KH22_1


title: KH22_3


title: Human ESCs MS46 day5

description: RNA-Seq analysis from human ESCs (H9 line) MS436 treated day5


title: Human ESCs FGF day5

description: RNA-Seq analysis from human ESCs (H9 line) FGF treated day5


title: Human ESCs FGF day1

description: RNA-Seq analysis from human ESCs (H9 line) FGF treated day1


title: Human ESCs MS46 day1

description: RNA-Seq analysis from human ESCs (H9 line) MS436 treated day1


title: H3K27me3 normoxia

city: Amsterdam

first: Michiel

middle: Emanuel

last: Adriaens

address: Meibergdreef 15

department: Experimental Cardiology

institute: AMC

data_processing:
Image processing and base calling was performed using Illumina software tools provided by the manufacturer.
Subsequent paired-end genome alignment was performed using Novoalign with Human Genome 18 (HG18) used as a reference genome.  Only uniquely aligned reads were used for further analysis.
To remove PCR artifacts all data were collapsed prior to peak calling.
To identify H3K27me3 marked regions the peak caller Findpeaks (version 4.0) was used using standard settings.
Genome_build: HG18
Supplementary_files_format_and_content: WIG files containing H3K27me3 marked regions

source_name: H3K27me3 normoxia

growth_protocol: MCF7 (human mammary adenocarcinoma) were cultured at 37°C, 5% CO2, 100% humidity in Dulbecco's Modified Eagle Medium:Nutrient Mixture F-12 (DMEM/F12 1:1; MCF7) and DMEM McCoy’s 5A medium (DU145). The culture medium was supplemented with 10% fetal calf serum (FCS), 200 mM L-glutamine and antibiotics.

extract_protocol:
MCF7 cells were transferred to hypoxic culturing conditions for the indicated durations and immediately fixed to avoid reoxygenation. Cells were disrupted by sonication, yielding genomic DNA fragments ranging from 200-1000 bp, with a bulk size of 200-500bp. For each immunoprecipitation 10-20 million cells were used. ChIPs were performed and analyzed using standard protocols (antibody: H3K27me3 (07-449; Upstate)).
ChIP-seq libraries were prepared for sequencing using standard 36 bp paired-end protocol for the Illumina Genome Analyser IIx (GAIIx). Two lanes were used per sample for sufficient coverage.

treatment_protocol: For hypoxic exposure, cells were transferred to a MACS VA500 microaerophilic workstation (Don Whitley Scientific, Shipley, UK) for the indicated duration. The atmosphere in the chamber consisted of <0.02% O2, 5% H2, 5% CO2, and 74% N2.

tag: oxygen state

value: normoxia

tag: timepoint

value: 0 hours

tag: oxygen concentration


title: KH22_17

tag: cell type


title: H3K27me3 hypoxia 8 hours

source_name: H3K27me3 hypoxia 8 hours

value: hypoxia

value: 8 hours


title: H2347_INPUT

status: Public on Sep 25 2014

city: Dallas

first: Ralf

last: Kittler

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Image scanning and basecalls were performed using BioScope (v. 1.2.1)
ChIP-seq reads were aligned to hg19 geneome assembly using BioScope (v. 1.2.1)
Mapped reads were filtered to remove low quality, ambiguous and redundant reads
Peaks were called using the MACS (v. 1.4.2)
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files contains SOX2 peak coordinates in BED format

source_name: NCI-H2347 cell line

growth_protocol: We generated PPARG-LAP BAC transgenic NCI-H2347 and NCI-H1993 cell lines using the BAC-transgenesis approach, cells were cultured in RPMI-1640 with 5% FBS.

extract_protocol:
Cells at 80% confluency (~1-1.5x107) were cross-linked with 1% formaldehyde for 10 minutes at 37°C, and quenched with 125 mM glycine at room temperature for 5 minutes. The fixed cells were washed twice with cold PBS, scraped, and transferred into 1 ml PBS containing protease inhibitors (Roche). After centrifugation at 700 g for 4 minutes at 4°C, the cell pellets were resuspended in 100 μl ChIP lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl [pH 8.1] with protease inhibitors) and sonicated at 4°C with a Bioruptor (Diagenode) (30 seconds ON and 30 seconds OFF at highest power for 12 minutes). The sheared chromatin with a fragment length of ~200 – 600 bp) was centrifuged at 10,000 g for 10 minutes at 4°C). 100 μl of the supernatant was used for ChIP or as input. A 1:10 dilution of the solubilized chromatin in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 167 mM NaCl 16.7 mM Tris-HCl [pH 8.1]) was incubated at 4°C overnight with 6 μg/ml of a goat anti-GFP (raised against His-tagged full-length eGFP and affinity-purified with GST-tagged full-length eGFP). Immunoprecipitations were carried out by incubating with 40 μl pre-cleared Protein G Sepharose beads (Amersham Bioscience) for 1 hour at 4°C, followed by five washes for 10 minutes with 1ml of the following buffers: Buffer I: 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.1], 150 mM NaCl; Buffer II: 0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl [pH 8.1], 500 mM NaCl; Buffer III: 0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl [pH 8.1]; twice with TE buffer [pH 8.0]. Elution from the beads was performed twice with 100 μl ChIP elution buffer (1% SDS, 0.1 M NaHCO3) at room temperature (RT) for 15 minutes. Protein-DNA complexes were de-crosslinked by heating at 65°C in 192 mM NaCl for 16 hours. DNA fragments were purified using QiaQuick PCR Purification kit (Qiagen) and eluted into 30 μl H2O according to the manufacturer’s protocol after treatment with RNase A and Proteinase K.
Libraries were prepared according to SOLiD 5500 instructions accompanying the ChIP-seq kit with barcoding beta protocol. AMPure® XP beads were used in this protocol. Briefly, DNA was end-repaired using a combination of 5X reaction buffer, dNTP mix (10mM), end polishing enzyme 1 and 2, and nuclease free water included in the kit. Binding and washing of end-paired DNA was performed using AMPure® XP beads and 70% ethanol respectively. Then, the end-paired DNA was eluted with elution buffer included in the kit. Then,  the 5500 barcoded adaptors were liagted to the DNA and purified using 70% ethanol. Purified adaptor ligated DNA was PCR amplified for 10-15cycles. Amplified DNA was purified and ~1μL of purified amplified product was run on a 2% E-Gel® EX Gel to confirm the removal of any primer dimers.This product was quantified using qPCR. Following qPCR quantitation, the SOLiD™ ChIP-Seq fragment library was subjected to templated bead preparation.

treatment_protocol: Not applicable


title: H3K27me3 hypoxia 24 hours

source_name: H3K27me3 hypoxia 24 hours

value: 24 hours