title: cr_20_27_bap-1

description: Sample name: PJ-14


title: B6rep2

status: Public on Aug 07 2013

type: SRA

city: Cleveland

first: Xiaodong

last: Bai

address: 10900 Euclid Avenue

department: Center for RNA Molecular Biology

country: USA

institute: Case Western Reserve University

description: Isolated whole eye mRNA

library_source: transcriptomic

data_processing:
Base-calling was performed using the Illumina pipeline software ELAND v1.7
Data were processed and aligned with the University of California-Santa Cruz (UCSC) mouse genome assembly and transcript annotation (mm9) using Genomic Short-read Nucleotide Alignment Program (GSNAP),.
Manual extraction of uniquely-mapped reads, HTseq for raw read counts of genes, and manual calculation were done to generate reads per kilobase per million reads (RPKM) statistics by gene.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each eye tissue sample

molecule: total RNA

organism: Mus musculus

source_name: Eye Tissue-B6 1.5 hr-2

extract_protocol:
Mice were euthanized by cervical dislocation. Eyes were enucleated and immediately placed in RNAlater stabilization reagent (Qiagen, Valencia, CA, USA) to preserve RNA content and integrity for whole eye runs.
One mouse eye or two retinas were homogenized at once and passed through a QIAShredder column (Qiagen) as per manufacturer’s directions to further homogenize the eye tissues. Total RNA was then purified by using the RNeasy Mini Kit (Qiagen) with on column DNase treatment (Qiagen) as per manufacturer’s directions. Poly(A) RNA was isolated with the Oligotex kit (Qiagen) as per the manufacturer’s instructions. Pooled total RNA samples of 5 female mice 4 weeks of age were used for each whole eye library preparation.  For first strand cDNA synthesis, instructions from the SuperScript III kit protocol (Invitrogen) were followed. About 400-450 ng of isolated poly(A) RNA was mixed with 50 ng of random primers and 1 mM deoxyribonucleotide triphosphate (dNTP), incubated at 65°C for 5 min and then placed on ice for 5 min. A reaction mixture comprising 5 mM MgCl2, 10 mM DTT, 40 U RNaseOUT, and 200 U SuperScript III reverse transcriptase was added to the initial mix to achieve a total volume of 20 µL. The mixture was incubated at 25°C for 10 min, followed by 50 min at 50°C. The reaction was terminated at 85°C for 5 min and then chilled on ice for 10 min. At this point, 2 U RNase H was added and the mix was incubated at 37°C for 20 min. The first strand cDNA synthesis reaction was immediately used for second strand synthesis. To the first strand product, 300 µM dNTP, E. coli DNA polymerase I buffer, and water was added to obtain a total volume of 95 µL and allowed to incubate on ice for 10 min. Then, 0.05 U E. coli DNA polymerase I (New England Biolabs, Beverly, MA, USA) was added and the mixture was incubated at 16°C for 2.5 h. The resulting double stranded cDNA was purified with the Wizard SV Gel and PCR Clean-up System (Promega, Madison, WI, USA) and eluted in 100 µL nuclease-free water and then fragmented by the Covaris S2 instrument (Woburn, MA, USA) to generate ~200 bp fragments as follows: 10% duty cycle, intensity of 5, 100 cycles per burst, with a bath temperature of 7.7°C and an acoustic power of 24 W.   The Illumina library was prepared according to the manufacturer’s instructions and purified using the Wizard SV Gel and PCR Clean-up System (Promega). Overhangs were converted into blunt ends with T4 DNA polymerase and Klenow DNA polymerase by incubating the mixed sample at 20°C for 30 min. cDNA was purified and eluted in 32 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). The purified sample was then mixed with Klenow fragment (3’ to 5’ exo minus) and incubated at 37°C for 30 min to add an ‘A’ base to the 3’ end of the blunt phosphorylated DNA fragments. The cDNA was then purified and eluted in 23 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). Eluted DNA was mixed with Illumina Adapter Oligo mix and T4 DNA ligase and incubated at room temperature for 15 min to ligate adapters to the ends of the DNA fragments to prepare them for hybridization to the flow cell. cDNA then was purified and eluted in 10 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). cDNAtemplates were purified by running samples on a 1% agarose gel at 120 V for 60 min and excising the region of the gel in the 200 bp range. The 200 bp cDNA enriched fragments were purified and eluted in 30 µL of nuclease free water with the Wizard PlusMinipreps DNA purification system (Promega). cDNA in the library was then amplified by a 15 cycle PCR with two primers that annealed to the ends of the adapters. The amplified cDNA was purified and eluted in 30 µL of nuclease free water with the Wizard Plus Minipreps DNA purification system (Promega). The size, purity and concentration of the final library was checked with the Bio-Rad Experion DNA specific chip prior to sequencing by using the Illumina Genome Analyzer IIx.

tag: strain

tag: tissue

value: Whole Eye

tag: timepoint

value: 1.5 hours after light onset (07:30)


title: T12_Day2

city: Rochester

first: Stephen

last: Welle

state: NY

address: 601 Elmwood Avenue

institute: University of Rochester

description: processed data file: T12_bcel.txt

data_processing:
CASAVA version 1.7 pipeline was used to call bases, demultiplex indexes, align reads to the genome, and count the number of reads aligned with each annotated gene transcript.
RefSeq gene annotations ( hg19 refFlat.txt.gz) were downloaded from UCSC genome broswer and modified to add hg19 loci for constant regions of IGHA2 (chr14:106053890-106054215), IGHG4 (chr14:106090816-106091565), IGHG2 (chr14:106109959-106110289), IGHA1 (chr14:106173508-106173900,106174696-106174994), IGHG1 (chr14:106207813-106208562), IGHG3 (chr14:106235440-106235898), IGHD (chr14:106306703-106307026,106307237-106307563), IGHM (chr14:106320321-106320843) & IGKC (chr2:89156874-89157196).
Base counts per gene (i.e. bases aligned with RefSeq transcripts) were divided by 65 (read length) to obtain reads per gene.
Reads per gene were divided by the total number of RefSeq reads to obtain reads per gene per total reads.
Reads per million RefSeq reads (RPM) were obtained by multilying reads per total reads by one million.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data files contain data from an individual subject (specified in file name), tab delimited text with 12 columns and 21967 rows. The first column contains official gene symbols. The first row indicates study day (0-10). Matrix contains RPM values as defined in description of data processing steps.

molecule: polyA RNA

organism: Homo sapiens

source_name: T12_Day 2 post-vaccine_circulating B cells

extract_protocol:
RNA was extracted with the Qiagen RNeasy micro kit. Concentrations were determined by UV spectrophotometry (Nanodrop) and integrity of ribosomal RNA was confirmed with an Agilent Bioanalyzer.
Polyadenylated RNA was extracted from total RNA, fragmented, ligated to sequencing and indexing adapters, and PCR amplified using Illumina TruSeq RNA kits as recommended by the kit instructions.

treatment_protocol: B cell samples were enriched from heparinized whole blood with RosetteSep Immunodensity separation (Stemcell Technologies, Vancouver, BC, Canada). Negative magnetic immunoaffinity bead separation columns (Miltenyi Biotec, Auburn, CA) were used with anti-CD3 (BD Bioscience, San Diego, CA) and anti-CD235 beads (Miltenyi Biotec, Auburn, CA) to further purify total Bc. Flow cytometric analysis was performed on all isolates, showing >90% purity of the isolates.

tag: subject id

tag: time point

value: Day 2 post-vaccine

tag: cell type

value: circulating B cells


title: cr_27_bap-1

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description: Sample name: PJ-12

data_processing:
bcl files were demultiplexed and converted to fastq files using bcl2fastq in Casava 1.8
fastq seqences were aligned to mm10 using Tophat
number of reads was calculated for each Entrez gene
differential expression analysis was performed using Deseq
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited raw counts with genes in rows and samples in columns

source_name: Hepa-1 cells

growth_protocol: Cells were grown in a-MEM with 5% FBS.  Cells were passaged every 3 days.

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen) according to the manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were grown in the presence of 0.5 mM Cr(VI) or grown normally for 20 or 25 passages.  After Cr(VI) growth treatment cells were treated with 5 mM B[a]P

tag: cell line

tag: treatment

value: Grown for 25 passages with 0.5mM Cr(VI) and then treated for 8 hours with B[a]P

tag: passage


title: T12_Day1

description: processed data file: T12_bcel.txt

source_name: T12_Day 1 post-vaccine_circulating B cells

value: Day 1 post-vaccine


title: B6rep1

description: Isolated whole eye mRNA

source_name: Eye Tissue-B6 1.5 hr-1


title: T12_Day0

description: processed data file: T12_bcel.txt

source_name: T12_Day 0 (pre-vaccine)_circulating B cells

value: Day 0 (pre-vaccine)


title: bap_27-1

description: Sample name: PJ-10

value: Treated with B[a]P for 8 hours


title: Bap+Cr-2

description: Sample name: Pr-125

value: Grown for 20 passages with 0.5mM Cr(VI) and then treated for 8 hours with B[a]P


title: cr_20_27_dmso-1

description: Sample name: PJ-13

value: Grown for 20 passages with 0.5mM Cr(VI) followed by 5 without Cr(VI) and then treated for 8 hours with DMSO


title: dmso_27-1

description: Sample name: PJ-9

value: Treated with DMSO for 8 hours


title: Cr-1

description: Sample name: Pr-120

value: Grown for 20 passages with 0.5mM Cr(VI) and then treated for 8 hours with DMSO


title: Cr-2

description: Sample name: Pr-121


title: Bap-1

description: Sample name: Pr-122


title: Untreated ctrl-2

description: Sample name: Pr-119


title: Untreated ctrl-1

description: Sample name: Pr-118


title: Bap-2

description: Sample name: Pr-123


title: EG008_Smn mutant RNA-seq R2

city: Chapel Hill

first: Eric

middle: L

last: Garcia

state: NC

address: 3344 Genome Science Bldg

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description:
processed data file: ORvSmn_DEUtable.txt
EG004_EG008.a3ss.miso_bf.txt.gz
EG004_EG008.a5ss.miso_bf.txt.gz
EG004_EG008.mxe.miso_bf.txt.gz
EG004_EG008.ri.miso_bf.txt.gz
EG004_EG008.se.miso_bf.txt.gz
EG003_EG008.a3ss.miso_bf.txt.gz
EG003_EG008.a5ss.miso_bf.txt.gz
EG003_EG008.mxe.miso_bf.txt.gz
EG003_EG008.ri.miso_bf.txt.gz
EG003_EG008.se.miso_bf.txt.gz

data_processing:
base-calling: CASAVA v.1.8.2
alignment: TopHat v2.0.8 with Bowtie v2.1.0 and Samtools v0.1.19
analysis of differential expression: Cufflinks v2.0.2
analysis of splicing differences: DEXSeq v1.0.2
analysis of splicing differences: MISO v0.4.8
Genome_build: dm3
Supplementary_files_format_and_content: tracking and diff files, Cuffdiff output; different exon id file, DEXSeq output; pairwise comparison of alternative splicing events file, MISO output; bedGraph files, converted from Tophat output bam files

organism: Drosophila melanogaster

source_name: Smn mutant RNA-seq

growth_protocol: Larvae were cultured on molasses and agar at room temperature (24 ± 1°C)

extract_protocol:
Larvae were collected and washed with water at 74 ± 2 hours post egg laying. Larvae were then crushed in TRIzol and stored at -80°C.
Illumina TruSeq RNA sample preparation kit v2

tag: age

value: 74 ± 2 hours post egg laying

value: whole larvae


title: B6 9hr rep2

description: Isolated whole eye mRNA

source_name: Eye Tissue-B6 9.0 hr-2

value: 9.0 hours after light onset (15:00)


title: EG007_Smn mutant RNA-seq R1

description:
processed data file: ORvSmn_DEUtable.txt
EG003_EG007.a3ss.miso_bf.txt.gz
EG003_EG007.a5ss.miso_bf.txt.gz
EG003_EG007.mxe.miso_bf.txt.gz
EG003_EG007.ri.miso_bf.txt.gz
EG003_EG007.se.miso_bf.txt.gz
EG004_EG007.a3ss.miso_bf.txt.gz
EG004_EG007.a5ss.miso_bf.txt.gz
EG004_EG007.mxe.miso_bf.txt.gz
EG004_EG007.ri.miso_bf.txt.gz
EG004_EG007.se.miso_bf.txt.gz


title: EG003_wild type RNA-seq R1

description:
norm_EG003.bedGraph.gz; Ore-R R1 normalized to EG007.bedGraph median reads
processed data file: ORvSmn_DEUtable.txt
EG003_EG007.a3ss.miso_bf.txt.gz
EG003_EG007.a5ss.miso_bf.txt.gz
EG003_EG007.mxe.miso_bf.txt.gz
EG003_EG007.ri.miso_bf.txt.gz
EG003_EG007.se.miso_bf.txt.gz
EG003_EG008.a3ss.miso_bf.txt.gz
EG003_EG008.a5ss.miso_bf.txt.gz
EG003_EG008.mxe.miso_bf.txt.gz
EG003_EG008.ri.miso_bf.txt.gz
EG003_EG008.se.miso_bf.txt.gz

source_name: wild type RNA-seq

value: Oregon R


title: EG004_wild-type RNA-seq R2

description:
processed data file: ORvSmn_DEUtable.txt
EG004_EG008.a3ss.miso_bf.txt.gz
EG004_EG008.a5ss.miso_bf.txt.gz
EG004_EG008.mxe.miso_bf.txt.gz
EG004_EG008.ri.miso_bf.txt.gz
EG004_EG008.se.miso_bf.txt.gz
EG004_EG007.a3ss.miso_bf.txt.gz
EG004_EG007.a5ss.miso_bf.txt.gz
EG004_EG007.mxe.miso_bf.txt.gz
EG004_EG007.ri.miso_bf.txt.gz
EG004_EG007.se.miso_bf.txt.gz


title: HEART_WCE_TAC

status: Public on Aug 06 2013

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Mouse heart TAC WCE input ChIP

library_source: genomic

data_processing:
Images analysis and base calling was done using the solexa pipeline.
For all samples, reads were aligned to build mm9 using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
Genome_build: MGSCv37
Supplementary_files_format_and_content: WIG files: For all samples aligned sequences processed through MACS 1.4.2 and fragment pileup was outputted in .wig format

molecule: genomic DNA

source_name: mouse heart

growth_protocol: Mice were grown under standard conditions

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: Animals were anesthetized, intubated, then a partial thoracotomy was performed to the second rib under a surgical microscope and the sternum retracted with a chest retractor.  After dissecting away thymus and fat tissue from the aortic arch the transverse aorta was identified and a small piece of 6.0 silk suture is placed between the innominate and left carotid arteries.   Two loose knots are tied around the transverse aorta and a small piece of a 271/2 gauge blunt needle is placed parallel to the aorta.  The first knot is tied against the needle, followed by the second knot and the needle is then removed in order to yield a constriction of approximately 0.4mm diameter.  The chest retractor is removed and the rib cage closed using 6.o prolene interrupted sutures.  The skin is then closed using 6.0 prolene suture with continuous pattern.  The animals were treated with vehicle (DMSO) or JQ1 treatment (50 mg/kg, IP once daily) 12 hours after surgery for 4 days.  Hearts were harvested 4 days after surgery

tag: chip antibody

tag: chip antibody manufacturer

value: None WCE

tag: chip antibody catalog number

value: heart

value: TAC

tag: genetic background


title: Bap+Cr-1

description: Sample name: Pr-124


title: cr_27_dmso-1

description: Sample name: PJ-11

value: Grown for 25 passages with 0.5mM Cr(VI) and then treated for 8 hours with DMSO


title: input_rep2 (EL20-3)

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

data_processing:
For directional libraries, the RNA was phosphatase treated with Shrimp Alkaline Phosphatase (USB corporation), and 5' end labeled with g-[32P]-ATP and T4 polynucleotide kinase (NEB) and run on a 15% denaturing polyacrylamide gel. Bands specific to the IP, ranging from 35 nt to 55 nt, were cut, crushed with a motorized pestle and soaked in 0.3M NaOAc pH 5.2, and extracted RNA was ethanol precipitated with 20 mg glycogen. Samples were digested with RNase H (NEB) using an oligo complimentary to 2S rRNA and then digested with DNase I. Samples were acid:phenol extracted and ethanol precipitated with NH4OAc. 3' adapters (Custom: rAppTTTAACCGCGAATTCCAG/3ddC/) were ligated with T4 RNA ligase (NEB) (ATP was omitted if adenylated linkers were used), and samples were run on a 15% denaturing polyacrylamide gel and purified as before. Samples were precipitated, and 5' end labeled again with g-[32P]-ATP and T4 polynucleotide kinase. 5' adapters (Custom: tccgaaattaaccctcactaaaGrGrGrA) were ligated with T4 RNA ligase, and samples were run on a 12% denaturing polyacrylamide gel and purified and precipitated as before. Samples were reverse transcribed using Superscript III (Invitrogen) using a primer complementary to the 3'adapter (CTGGAATTCGCGGTTAAA) and PCR amplified using Pfu Ultra (Stratagene) using primers corresponding to the 5' and 3' adapters (FW: ATTAACCCTCACTAAAGGGA; REV: CATACGATTTAGGTGACACTATAG). When non-Illumina small RNA adapters were used, libraries were adapted to Illumina compatible ends by PCR amplification (FW: AATGATACGGCGACCACCGACGCTCTTCCGATCTCCGAAATTAACCCTCACTAA; REV: CAAGCAGAAGACGGCATACGACTGGAATTCGCGGTTAAA). Libraries were sequenced on the Illumina Genome Analyzer I or II platforms using commercial or custom sequencing primers (Custom: CGCTCTTCCGATCTCCGAAATTAACCCTCACTAAAGGGA).
For non-directional oligo-dT selected libraries, poly(A)+ RNA was selected using a MicroPoly(A)Purist column (Ambion), and 100 ng was cloned using the standard Illumina mRNA-seq v2.2 cloning protocol.

source_name: 0-24hr-old Oregon-R embryos

extract_protocol: For directional libraries, the RNA was phosphatase treated with Shrimp Alkaline Phosphatase (USB corporation), and 5' end labeled with g-[32P]-ATP and T4 polynucleotide kinase (NEB) and run on a 15% denaturing polyacrylamide gel. Bands specific to the IP, ranging from 35 nt to 55 nt, were cut, crushed with a motorized pestle and soaked in 0.3M NaOAc pH 5.2, and extracted RNA was ethanol precipitated with 20 mg glycogen. Samples were digested with RNase H (NEB) using an oligo complimentary to 2S rRNA and then digested with DNase I. Samples were acid:phenol extracted and ethanol precipitated with NH4OAc.3'dapters were ligated with T4 RNA ligase (NEB) (ATP was omitted if adenylated linkers were used), and samples were run on a 15% denaturing polyacrylamide gel and purified as before. Samples were precipitated, and 5' end labeled again with g-[32P]-ATP and T4 polynucleotide kinase. 5' adapter were ligated with T4 RNA ligase, and samples were run on a 12% denaturing polyacrylamide gel and purified and precipitated as before. Samples were reverse transcribed using Superscript III (Invitrogen) using a primer complementary to the 3'adapteand PCR amplified using Pfu Ultra (Stratagene) using primers corresponding to the 5' and 3' adapters. When non-Illumina small RNA adapters were used, libraries were adapted to Illumina compatible ends by PCR amplification. Libraries were sequenced on the Illumina Genome Analyzer I or II platforms using commercial or custom sequencing primers.  For non-directional oligo-dT selected libraries, poly(A)+ RNA was selected using a MicroPoly(A)Purist column (Ambion), and 100 ng was cloned using the standard Illumina mRNA-seq v2.2 cloning protocol.

treatment_protocol: Sequential immunopurifications for directional libraries were carried out essentially as described (Lei and Corces 2006) with the following modifications. Nuclear extracts purified from 0-24 h embryos supplemented with 1U/ul Rnasin were preabsorbed to an a-Su(Hw) preimmune sera crosslinked column, then bound to an a-Su(Hw) crosslinked column, washed three times with HBSMT and three times with HBSM (50 mM HEPES, pH 6.7; 150 mM NaCl; 5 mM Kcl; 2.5 mM MgCl2), eluted with 1.25 mL HBSK-100 (50 mM HEPES, pH 6.7; 150 mM NaCl; 100 mM Kcl; 2.5 mM MgCl2) and 1.25 mL HBSK-200 (50 mM HEPES, pH 6.7; 150 mM NaCl; 200 mM Kcl; 2.5 mM MgCl2).  The eluates were combined and added to 2.5 mL of HBSX-BSA (50 mM HEPES, pH 6.7; 150 mM NaCl; 2.5 mM MgCl2; 0.6% TritonX-100; 2 mg/mL BSA) including protease inhibitors and 1 U/ul Rnasin, then bound to an a-CP190 crosslinked column, washed and eluted as described previously (Lei and Corces 2006).  RNA copurified with 250 mM and 1M MgCl2 elutions was acid:phenol extracted, ethanol precipitated with 20 mg glycogen, and digested with Dnase I.

tag: RIP antibody

value: none (input)

tag: replicate

tag: purified length

value: polyA

tag: similar to

value: EL20 (re-sequence)

tag: adapter

value: GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG

tag: directional

value: Non-directional

tag: machine

value: Illumina Genome Analyzer II

tag: original pipeline

tag: fastqs from

value: Pipeline v1.4.0


title: Su(Hw)+CP190_RIP-seq_rep1 (EL22)

molecule: nuclear RNA

value: Su(HW)+CP190 (non-commercial)

value: EL6 (re-sequence)

value: TTTAACCGCGAATTCCAGC

value: directional

value: Illumina HiSeq

value: Pipeline v1.7.0


title: input_rep2 (EL20-2)


title: Su(Hw)+CP190_RIP-seq_rep1 (EL23)


title: Su(Hw)+CP190_RIP-seq_rep2 (EL21)


title: Su(Hw)+CP190_RIP-seq_rep2 (EL21-4)

value: EL21 (re-sequence)

value: Pipeline v1.5.1


title: Su(Hw)+CP190_RIP-seq_rep2 (EL21-2)


title: input_rep2 (EL20)


title: Su(Hw)+CP190_RIP-seq_rep2 (EL18)

value: EL2, but 20-cycle amplification

value: TCGTATGCCGTCTTCTGCTTG


title: Su(Hw)+CP190_RIP-seq_rep2 (EL21-3)


title: Su(Hw)+CP190_RIP-seq_rep2 (EL16)

value: EL4, but 20-cycle amplification


title: unbound_fraction_rep2 (EL17)

value: unbound fraction

value: EL5, but 20-cycle amplification


title: input_rep1 (EL14)

value: none (input)

value: polyA

value: GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG

value: Re-run Pipeline v1.5.1 (intensities) + Ibis (basecalling)


title: T13 [RNA-Seq]

city: Wenzhou

first: Chunming

last: Ding

state: Zhejiang

address: School of Laboratory Medicine and Life Sciences

country: China

institute: Wenzhou Medical University

data_processing:
paired-end/ single-end 36-base pair (bp) reads were filtered based on qseq score
Reads were the subjected to Illumina RNA-seq pipeline (CASAVA 1.7) for RNA-seq analysis, aligned using Hg19 genome as reference, and all default parameters for alignment
From the raw gene counts, normaliation for each gene was done to obtain the number of mapped bases per 1 million aligned bases
Genome_build: hg 19
Supplementary_files_format_and_content: Excel sheet, RNA expression level of selected genes.

source_name: Second trimester Placenta Villi

extract_protocol: Total RNA was extracted using TRIZOL protocol (Life Technologies). Sequencing library was constructed using Illumina mRNA-Seq Sample Preparation protocol.

tag: tissue

value: Fetal placenta tissue

tag: genetic variation

value: Trisomy 21


title: N9 [RNA-Seq]

source_name: First trimester CVS

value: CVS tissue

value: normal


title: T12 [RNA-Seq]

source_name: First trimester Placenta Villi


title: N8 [RNA-Seq]


title: N10 [RNA-Seq]

source_name: Second trimester CVS


title: N7 [RNA-Seq]


title: T3 [RNA-Seq]


title: N5 [RNA-Seq]


title: unbound_fraction_rep2 (EL19)

value: EL3, but 20-cycle amplification

value: directional

value: Illumina Genome Analyzer II

value: Pipeline v1.4.0


title: input_rep2 (EL20-4)

value: EL20 (re-sequence)

value: Non-directional

value: Pipeline v1.5.1


title: N5 [Bisulfite-Seq]

description: Illumina's RRBS for Methylation Analysis

data_processing:
paired-end 36-base pair (bp) reads were filtered based on qseq score
reads were aligned to the bisulfite-converted human genome (UCSC Build hg19, GRCh37, Feb 2009) using Bowtie
Differential DNA methylation between normal and DS samples were analyzed at single CpG level and at genomic region (CGI and promoters) level.
Average methylation for each core promoter for both DS and normal samples were calculated.
List of the genes with differetially methylated promoters was generated if two criteria were met: 1) average methylation difference between DS and normal samples ≥ 10%; 2) wilcoxon rank-sum test p < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Excel sheet, list of genes with differentially methylated promoters between normal and DS samples.

extract_protocol: Genomic DNA was extracted using QIAamp DNA Mini Kit (QIAGEN GmbH, Germany). Library was constructed using modified Illumina RRBS Sample Preparation Protocol.


title: N4 [Bisulfite-Seq]


title: N3 [Bisulfite-Seq]


title: N1 [Bisulfite-Seq]


title: N2 [Bisulfite-Seq]


title: T7 [Bisulfite-Seq]

source_name: Second trimester Placenta villi


title: T6 [Bisulfite-Seq]


title: T11 [Bisulfite-Seq]


title: Su(Hw)+CP190_RIP-seq_rep1 (EL15)

value: Su(HW)+CP190 (non-commercial)


title: T9 [Bisulfite-Seq]


title: T8 [Bisulfite-Seq]


title: T10 [Bisulfite-Seq]


title: T2 [Bisulfite-Seq]


title: T4 [Bisulfite-Seq]

source_name: First trimester Placenta


title: N6 [Bisulfite-Seq]


title: T1 [Bisulfite-Seq]


title: T3 [Bisulfite-Seq]


title: T5 [Bisulfite-Seq]


title: T6 [RNA-Seq]


title: HEART_WCE_TAC_JQ1

description: Mouse heart TAC + JQ1 WCE input ChIP

value: heart

tag: treatment

value: TAC and JQ1


title: HEART_WCE_SHAM

description: Mouse heart sham WCE input ChIP

treatment_protocol: Animals were anesthetized, intubated, undergo thoracotomy as with TAC. In Sham, no suture is placed around the transverse aorta.  Mice hearts were harvested 4 days after surgery.

value: None WCE

value: sham


title: HEART_2_RNA_POL2_TAC_JQ1

description:
Mouse heart TAC + JQ1 RNA Pol II ChIP
Barcode (already removed): TTAGGC

data_processing:
Images analysis and base calling were done using the solexa pipeline.
For all samples, reads were aligned to build mm9 using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset.
Genome_build: MGSCv37
Supplementary_files_format_and_content: WIG files: For all samples, aligned sequences processed through MACS 1.4.2 and fragment pileup were outputted in .wig format.

growth_protocol: Mice were grown under standard conditions.

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: Animals were anesthetized, intubated, then a partial thoracotomy was performed to the second rib under a surgical microscope and the sternum retracted with a chest retractor. After dissecting away thymus and fat tissue from the aortic arch the transverse aorta was identified and a small piece of 6.0 silk suture is placed between the innominate and left carotid arteries. Two loose knots are tied around the transverse aorta and a small piece of a 271/2 gauge blunt needle is placed parallel to the aorta. The first knot is tied against the needle, followed by the second knot and the needle is then removed in order to yield a constriction of approximately 0.4mm diameter. The chest retractor is removed and the rib cage closed using 6.o prolene interrupted sutures. The skin is then closed using 6.0 prolene suture with continuous pattern. The animals were treated with vehicle (DMSO) or JQ1 treatment (50 mg/kg, IP once daily) 12 hours after surgery for 4 days. Hearts were harvested 4 days after surgery

value: RNA Pol II (Rpb1 N-terminus)

value: Santa Cruz


title: HEART_2_WCE_SHAM

description:
Mouse heart sham WCE input ChIP
Barcode (already removed): CAGATC

treatment_protocol: Animals were anesthetized, intubated, undergo thoracotomy as with TAC. In Sham, no suture is placed around the transverse aorta. Mice hearts were harvested 4 days after surgery


title: HEART_2_WCE_TAC

description:
Mouse heart TAC WCE input ChIP
Barcode (already removed): ACTTGA

value: TAC


title: HEART_2_WCE_TAC_JQ1

description:
Mouse heart TAC + JQ1 WCE input ChIP
Barcode (already removed): GATCAG


title: HEART_RNA_POL2_TAC_JQ1

description: Mouse heart TAC + JQ1 RNA Pol II ChIP


title: HEART_2_RNA_POL2_TAC

description:
Mouse heart TAC RNA Pol II ChIP
Barcode (already removed): CGATGT


title: HEART_RNA_POL2_TAC

description: Mouse heart TAC RNA Pol II ChIP


title: HEART_2_RNA_POL2_SHAM

description:
Mouse heart RNA Pol II sham ChIP-Seq
Barcode (already removed): ATCACG


title: HEART_RNA_POL2_SHAM

description: Mouse heart RNA Pol II sham ChIP-Seq

treatment_protocol: Animals were anesthetized, intubated, undergo thoracotomy as with TAC. In Sham, no suture is placed around the transverse aorta.   Mice hearts were harvested 4 days after surgery


title: HEART_BRD4_SHAM

description: Mouse heart sham BRD4 ChIP

treatment_protocol: Animals were anesthetized, intubated, undergo thoracotomy as with TAC. In Sham, no suture is placed around the transverse aorta. Mice hearts were harvested 4 days after surgery.

value: Bethyl


title: MDA-MB-436 cells run at 25M reads

city: Charlottesville

first: Byong

middle: Ha

last: Kang

state: VA

address: 415 Lane Road, MR5-Rm. 2225

department: Department of Biomedical Engineering

institute: University of Virginia

data_processing:
RNA-seq reads were chastity filtered and assessed for overall quality with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequenced reads were mapped using STAR 2.2.0 against the human genome build hg19.
Reads that map to each gene were counted with HTSeq (http://www-huber.embl.de/users/anders/HTSeq/) under the union set, whereby reads that do not completely overlap a gene are still counted. The counts were normalized by the library size (read depth).
RPKM calculations were performed by normalizing to the median transcript length for each gene and the total library size of each sample.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized count in the first column and RPKM value in the second column for each sample

source_name: breast

growth_protocol: HT-29 cells were cultured in McCoy's 5A medium with 10% FBS and 5% CO2. MCF10A cells were cultured in DMEM/F12 medium with 5% horse serum, 20 ng/ml EGF, 500 ng/ml hydrocortisone, 100 ng/ml cholera toxin, and 10 µg/ml insulin.  MDA-MB-436 cells were cultured in L-15 medium with 10% FBS without CO2.

extract_protocol:
Total RNA was isolated with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocols.
Each cDNA library was prepared with the NEBNext first-strand synthesis, second-strand synthesis, end repair, dA tailing, and quick ligation modules (New England Biolabs).  Libraries were indexed with standard Illumina-type adapters and sequenced on an Illumina HiSeq 2000 using version 3 reagents that generate 180–200M reads per lane.  Samples were 50-bp paired-end sequenced in duplicate at 25M and 50M or 100M reads per sample.

treatment_protocol: HT-29 cells were treated with 200 U ml-1 IFN-γ (Roche) for 24 hr.

tag: cell type

value: breast adenocarcinoma

tag: cell line

tag: sample type

value: 25 M reads


title: MDA-MB-436 cells run at 50M reads

value: 50 M reads


title: IFN-g stimulated HT-29 cells run at 25M reads

source_name: colon

value: colon adenocarcinoma

value: IFN-g


title: IFN-g stimulated HT-29 cells run at 50M reads


title: MCF10A cells run at 25M reads

value: mammary epithelial


title: MCF10A cells run at 100M reads


title: Chromatin accessibility assay of Psoas Muscle; DNase.DS20325

city: Seattle

first: Northwest

last: REMC

state: WA

institute: University of Washington

description:
sample_term_id: UBERON_0008450
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20325
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14277
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14034
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1027321_UW.Psoas_Muscle.ChromatinAccessibility.STL001.DNase.DS20325.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20325.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Psoas Muscle Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Psoas Muscle, Donor STL001, Library DNase.DS20325 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17590
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,116,631
FINDPEAKS_SCORE: 0.3858
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.369
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9829
IROC_PERCENTILE: 2
POISSON_SCORE: 0.4339
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM1027321_UW.Psoas_Muscle.ChromatinAccessibility.STL001.DNase.DS20325.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20325.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Psoas Muscle Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Psoas Muscle, Donor STL001, Library DNase.DS20325 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17544
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: PM DNase 01 25
BROWSER_TRACK_DESCRIPTION: UW Psoas Muscle DNase Hypersensitivity Donor STL001 Library DNase.DS20325 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 41,116,631
FINDPEAKS_SCORE: 0.3858
FINDPEAKS_PERCENTILE: 48
HOTSPOT_SCORE: 0.369
HOTSPOT_PERCENTILE: 48
IROC_SCORE: 0.9829
IROC_PERCENTILE: 2
POISSON_SCORE: 0.4339
POISSON_PERCENTILE: 48
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Psoas Muscle tissue; DNase.DS20325

extract_protocol: Library construction protocol: Single read - Illumina

tag: sample alias

tag: sample common name

value: Psoas Muscle

tag: molecule

value: genomic DNA

tag: disease

value: Shin Lin, Stanford University

value: Primary Tissue

value: Autopsy

value: healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)

value: Male

value: Caucasian and African American

value: Chromatin Accessibility

value: Qiagen minElut


title: Chromatin accessibility assay of Gastric Mucosa; DNase.DS20748

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20748
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14249
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.12180
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1027325_UW.Gastric.ChromatinAccessibility.STL003.DNase.DS20748.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20748.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Gastric Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Gastric, Donor STL003, Library DNase.DS20748 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17619
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,160,244
FINDPEAKS_SCORE: 0.2204
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.2221
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9943
IROC_PERCENTILE: 70
POISSON_SCORE: 0.2669
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.99

**********************************************************************

ANALYSIS FILE NAME: GSM1027325_UW.Gastric.ChromatinAccessibility.STL003.DNase.DS20748.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20748.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Gastric Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Gastric, Donor STL003, Library DNase.DS20748 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17573
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Gastric DNase 03 48
BROWSER_TRACK_DESCRIPTION: UW Gastric DNase Hypersensitivity Donor STL003 Library DNase.DS20748 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 44,160,244
FINDPEAKS_SCORE: 0.2204
FINDPEAKS_PERCENTILE: 2
HOTSPOT_SCORE: 0.2221
HOTSPOT_PERCENTILE: 2
IROC_SCORE: 0.9943
IROC_PERCENTILE: 70
POISSON_SCORE: 0.2669
POISSON_PERCENTILE: 2
MAXIMUM_REPLICATE_CORRELATION: 0.99

**********************************************************************

source_name: Gastric tissue; DNase.DS20748

value: Gastric

value: polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)

value: Caucasian


title: Chromatin accessibility assay of Small Bowel Mucosa; DNase.DS20770

description:
sample_term_id: UBERON_0002108
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20770
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14286
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11844
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1027327_UW.Small_Intestine.ChromatinAccessibility.STL003.DNase.DS20770.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20770.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Small Intestine Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Small Intestine, Donor STL003, Library DNase.DS20770 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17611
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 46,049,908
FINDPEAKS_SCORE: 0.4179
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.4312
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9978
IROC_PERCENTILE: 98
POISSON_SCORE: 0.4673
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM1027327_UW.Small_Intestine.ChromatinAccessibility.STL003.DNase.DS20770.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20770.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Small Intestine Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Small Intestine, Donor STL003, Library DNase.DS20770 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17565
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: SI DNase 03 70
BROWSER_TRACK_DESCRIPTION: UW Small Intestine DNase Hypersensitivity Donor STL003 Library DNase.DS20770 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 46,049,908
FINDPEAKS_SCORE: 0.4179
FINDPEAKS_PERCENTILE: 59
HOTSPOT_SCORE: 0.4312
HOTSPOT_PERCENTILE: 63
IROC_SCORE: 0.9978
IROC_PERCENTILE: 98
POISSON_SCORE: 0.4673
POISSON_PERCENTILE: 59
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Small Intestine tissue; DNase.DS20770

value: Small Intestine


title: Chromatin accessibility assay of Pancreas; DNase.DS20753

description:
sample_term_id: UBERON_0001264
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20753
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14271
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11847
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1027326_UW.Pancreas.ChromatinAccessibility.STL003.DNase.DS20753.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20753.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Pancreas Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Pancreas, Donor STL003, Library DNase.DS20753 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17625
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 43,237,714
FINDPEAKS_SCORE: 0.2597
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.272
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9918
IROC_PERCENTILE: 37
POISSON_SCORE: 0.3263
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM1027326_UW.Pancreas.ChromatinAccessibility.STL003.DNase.DS20753.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20753.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreas Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Pancreas, Donor STL003, Library DNase.DS20753 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17579
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Pancreas DNase 03 53
BROWSER_TRACK_DESCRIPTION: UW Pancreas DNase Hypersensitivity Donor STL003 Library DNase.DS20753 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 43,237,714
FINDPEAKS_SCORE: 0.2597
FINDPEAKS_PERCENTILE: 9
HOTSPOT_SCORE: 0.272
HOTSPOT_PERCENTILE: 11
IROC_SCORE: 0.9918
IROC_PERCENTILE: 37
POISSON_SCORE: 0.3263
POISSON_PERCENTILE: 11
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

source_name: Pancreas tissue; DNase.DS20753

value: Pancreas


title: Chromatin accessibility assay of Ovary; DNase.DS20827

description:
sample_term_id: UBERON_0000992
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20827
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14268
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13360
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1027334_UW.Ovary.ChromatinAccessibility.STL002.DNase.DS20827.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20827.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Ovary Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Ovary, Donor STL002, Library DNase.DS20827 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17593
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 52,712,107
FINDPEAKS_SCORE: 0.3075
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.2852
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9839
IROC_PERCENTILE: 4
POISSON_SCORE: 0.3525
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM1027334_UW.Ovary.ChromatinAccessibility.STL002.DNase.DS20827.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20827.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Ovary Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Ovary, Donor STL002, Library DNase.DS20827 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17547
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Ovary DNase 02 27
BROWSER_TRACK_DESCRIPTION: UW Ovary DNase Hypersensitivity Donor STL002 Library DNase.DS20827 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 52,712,107
FINDPEAKS_SCORE: 0.3075
FINDPEAKS_PERCENTILE: 33
HOTSPOT_SCORE: 0.2852
HOTSPOT_PERCENTILE: 17
IROC_SCORE: 0.9839
IROC_PERCENTILE: 4
POISSON_SCORE: 0.3525
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

source_name: Ovary tissue; DNase.DS20827

value: Ovary

value: iron deficiency, bipolar

value: iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)

value: Female


title: Chromatin accessibility assay of Gastric Mucosa; DNase.DS20260

description:
sample_term_id: UBERON_0000945
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20260
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14289
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.13944
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1027320_UW.Gastric.ChromatinAccessibility.STL001.DNase.DS20260.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20260.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Gastric Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Gastric, Donor STL001, Library DNase.DS20260 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17596
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,828,861
FINDPEAKS_SCORE: 0.2662
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.2589
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.9918
IROC_PERCENTILE: 37
POISSON_SCORE: 0.3244
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.99

**********************************************************************

ANALYSIS FILE NAME: GSM1027320_UW.Gastric.ChromatinAccessibility.STL001.DNase.DS20260.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20260.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Gastric Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Gastric, Donor STL001, Library DNase.DS20260 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17550
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Gastric DNase 01 60
BROWSER_TRACK_DESCRIPTION: UW Gastric DNase Hypersensitivity Donor STL001 Library DNase.DS20260 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 48,828,861
FINDPEAKS_SCORE: 0.2662
FINDPEAKS_PERCENTILE: 13
HOTSPOT_SCORE: 0.2589
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.9918
IROC_PERCENTILE: 37
POISSON_SCORE: 0.3244
POISSON_PERCENTILE: 9
MAXIMUM_REPLICATE_CORRELATION: 0.99

**********************************************************************

source_name: Gastric tissue; DNase.DS20260

value: genomic DNA

value: Shin Lin, Stanford University


title: MGC3

status: Public on Aug 05 2013

city: Tallinn

first: Agne

last: Velthut-Meikas

address: Akadeemia tee 15

department: Department of Chemistry and Biotechnology

country: Estonia

institute: Tallinn University of Technology

data_processing:
Base calling and filtering was done using instrument software real time analysis (RTA v1.12.4.2) with default parameters.
Adapter sequences were removed with cutAdapt v0.9.3.
Bowtie v0.12.7 was used to map sequences to human genome 19 (Hg19) allowing no mismatches between the seed and target and reporting only the best aligned match. Aligned sequenced fragments were concatenated into transcripts using the TopHat v1.2.0 algorithm.
The BAM files from TopHat were converted to SAM format by SAMtools v.0.1.18. To get the number of reads per each gene the SAM files and the reference genome were used as input for HTSeq (http://www-huber.embl.de/users/anders/HTSeq), where intersection-nonempty mode was used.
Differential mRNA expression analysis was performed using the R/Bioconductor package EdgeR.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: RNA counts per gene for each sample generated by HTSeq.

source_name: mural granulosa cells

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.
RNA population containing the poly(A) tail was enriched by Sera-Mag Oligo(dT) Magnetic Particles (Thermo Scientific) and library was prepared with mRNA Library Prep Master Mix Set 1 for Illumina (New England Biolabs) according to the manufacturer´s protocols with a few optimized modifications: a) all the purification steps were carried out with Agencourt AMPure XP (Beckman Coulter Inc.) beads, except for purification of fragmented RNA where RNeasy MinElute kit (Qiagen) was used; b) fragmentation incubation time was shortened to 2 minutes to gain longer fragments suitable for long sequencing runs; c) size selection by agarose gel electrophoresis was not performed, the average length of the fragment was 420 bp, including 300 bp of insert and 120 bp of adapter sequences; and d) the template amount for PCR was 15 ng and 10 cycles were carried out.  The library preparation stage included annealing of unique adapters to individual samples for further sample indexing and pooling of all six poly(A) RNA samples. Adapters as well as PCR primers were from NEXTflex DNA Barcodes (Bioo Scientific Corporation). 13 pM of the sample pool was used for template hybridization, clustering and amplification (corresponds to 2.17 pM of individual sample).

value: mural granulosa cells

tag: stimulation protocol

value: GnRH antagonist, rFSH, hCG

tag: etiology of infertility

value: male factor


title: MGC2


title: CGC1

source_name: cumulus granulosa cells

value: cumulus granulosa cells


title: CGC2


title: CGC3


title: Chromatin accessibility assay of Pancreas; DNase.DS20842

description:
sample_term_id: UBERON_0001264
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DNase.DS20842
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.14274
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.14039
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************

data_processing:
**********************************************************************

ANALYSIS FILE NAME: GSM1027335_UW.Pancreas.ChromatinAccessibility.STL002.DNase.DS20842.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20842.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of Pancreas Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Pancreas, Donor STL002, Library DNase.DS20842 were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17620
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 54,151,447
FINDPEAKS_SCORE: 0.259
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.265
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.9922
IROC_PERCENTILE: 43
POISSON_SCORE: 0.3183
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

ANALYSIS FILE NAME: GSM1027335_UW.Pancreas.ChromatinAccessibility.STL002.DNase.DS20842.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNase.DS20842.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of Pancreas Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from  Pancreas, Donor STL002, Library DNase.DS20842 were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.17574
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 9
BROWSER_TRACK_NAME: Pancreas DNase 02 42
BROWSER_TRACK_DESCRIPTION: UW Pancreas DNase Hypersensitivity Donor STL002 Library DNase.DS20842 EA Release 9

QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 54,151,447
FINDPEAKS_SCORE: 0.259
FINDPEAKS_PERCENTILE: 7
HOTSPOT_SCORE: 0.265
HOTSPOT_PERCENTILE: 7
IROC_SCORE: 0.9922
IROC_PERCENTILE: 43
POISSON_SCORE: 0.3183
POISSON_PERCENTILE: 7
MAXIMUM_REPLICATE_CORRELATION: 0.98

**********************************************************************

source_name: Pancreas tissue; DNase.DS20842

value: Primary Tissue

value: Autopsy

value: Chromatin Accessibility


title: OCI-LY1_H3K27Ac_ChIP-seq:siNT

city: New York

first: Katerina

last: Hatzi

address: 413 E 69th Street, BB-1462

department: Hematology/Oncology

institute: WCMC

description: ChIP-seq in OCI-LY1 against H3K27Ac in siNT treated cells

data_processing:
ChIP-seq: Raw images generated went through primary image analysis and basecalling (RTA v1.6) that was followed by Illumina Genome Analyzer Off-Line Basecaller (OLB v1.6) analysis, where reads were aligned to the human genome (UCSC hg18) using ELAND. Only sequences mapped uniquely to the genome with not more than 2 mismatches were used for downstream analysis. Several reads mapping to the same exact location (clonal reads) were considered amplification artifact and were excluded from the analysis.  Table S2 includes information of the total number of mapped reads that where used in our analysis. Read density tracks were visualized using the UCSC browser.   ChIPseeqer peak detection algorithm (http://icb.med.cornell.edu/wiki/index.php/Elementolab/) was used for analyzing ChIP-seq data. Each read was in silico extended to 158bp based on the strand that it aligned to. Each ChIP-seq dataset was normalized to its corresponding input lane.
Genome_build: hg18
Supplementary_files_format_and_content: "Read_density-wig" files are wig tracks  generated using ChIPseeqerMakeReadDensityTrack of the ChIPseqer package. (http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqerMakeReadDensityTrack).They represent the average ChIPseq read density, normalized to the total number of reads. Wgl tracks called "peaks" are the peak locations called for every experiment by our peakcaling algorithm and they were generated using ChIPseeqer (http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_PeaksTrack)

source_name: Human DLBCL cel line

growth_protocol: DLBCL cell lines OCI-Ly1 and OCI-Ly7 were grown in medium containing 90% Iscove’s (Cellgro, Manassas, VA), 10% fetal bovine serum (Gemini, Irvine, CA), and 1% penicillin/streptomycin (Invitrogen, Carlsbad, CA).

extract_protocol:
ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture's instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. A' bases were added to the 3'ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments. After adapter ligation DNA was separated by electrophoresis and size selected by isolating a gel band of 250±25bp. This fragment range corresponds to a ChIP fragment range of about 158±25bp. Size selected fragments were PCR amplified for 15cycles using Illumina genomic DNA primers 1.1 and 1.2 with the following program (30s at 98oC, 15cycles of 10 at 98oC, 30s at 65oC,30s at 72oC and 5min extension at 75oC). Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Q-PCR was repeated to confirm retention of relative enrichment.
RNAseq: Three ug of total RNA was isolated from OCI-Ly1 cells transfected using Nucleofector 96-well Shuttle system (Lonza) with siBCL6 (HSS100968) or siNT (46-2001) (Stealth RNAi, Invitrogen) at 24hrs and 48hrs after nucleofection. RNAeasy Plus Kit (Qiagen) that included a gDNA elimination step was used for RNA isolation. RNA concentration and purity were determined using Nanodrop (Thermo Scientific) and integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Libraries were generated using mRNA-seq sample prep kit by Illumina. Briefly, mRNA was selected by two rounds of purification using magnetic polydT beads and then fragmented. First strand synthesis was performed using random oligos and SupersciptIII (Invitrogen). After second strand synthesis a 200bp paired-end library was prepared following the Illumina paired-end library preparation protocol.

treatment_protocol: OCI-Ly1 cells were transfected using Nucleofector 96-well Shuttle system (Lonza) with siBCL6 (HSS100968) or siNT (46-2001) (Stealth RNAi, Invitrogen)

tag: sirna transfection

value: siNT treated

tag: chip antibody


title: OCI-LY1_siNT_24hrs_mRNAseq

description: mRNA sequencing in OCI-Ly1 24hrs after siNT nucleofection

data_processing:
ChIP-seq: Raw images generated went through primary image analysis and basecalling (RTA v1.6) that was followed by Illumina Genome Analyzer Off-Line Basecaller (OLB v1.6) analysis, where reads were aligned to the human genome (UCSC hg18) using ELAND. Only sequences mapped uniquely to the genome with not more than 2 mismatches were used for downstream analysis. Several reads mapping to the same exact location (clonal reads) were considered amplification artifact and were excluded from the analysis.  Table S2 includes information of the total number of mapped reads that where used in our analysis. Read density tracks were visualized using the UCSC browser.
ChIPseeqer peak detection algorithm (http://icb.med.cornell.edu/wiki/index.php/Elementolab/) was used for analyzing ChIP-seq data. Each read was in silico extended to 158bp based on the strand that it aligned to. Each ChIP-seq dataset was normalized to its corresponding input lane.
.
mRNA-seq: Burrows-Wheeler alignment (BWA) algorithm was used to map paired reads using a 3-tiered hierarchal alignment first to a contaminant reference (containing adapter flanks, mitochondrial DNA and ribosomal DNA), then to the reference genome (human hg18), and finally to a junction database (which contains sequence which spans the boundaries between all concurrent exons as indicated by the annotation file). Gene expression values were calculated for each transcript (RPKM, reads per kilobase of exon per million mapped reads) by normalizing the number of bases aligned in a gene by the adjusted gene size (gene size minus any base that overlaps with other genes) and to the bases aligned to exons.

source_name: Human DLBCL cell line

growth_protocol: DLBCL cell lines OCI-Ly1 and OCI-Ly7 were grown in medium containing 90% Iscoveâs (Cellgro, Manassas, VA), 10% fetal bovine serum (Gemini, Irvine, CA), and 1% penicillin/streptomycin (Invitrogen, Carlsbad, CA).

extract_protocol:
ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture's instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. A' bases were added to the 3'ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments. After adapter ligation DNA was separated by electrophoresis and size selected by isolating a gel band of 250±25bp. This fragment range corresponds to a ChIP fragment range of about 158±25bp. Size selected fragments were PCR amplified for 15cycles using Illumina genomic DNA primers 1.1 and 1.2 with the following program (30s at 98oC, 15cycles of 10 at 98oC, 30s at 65oC,30s at 72oC and 5min extension at 75oC). Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Q-PCR was repeated to confirm retention of relative enrichment.

RNAseq: Three ug of total RNA was isolated from OCI-Ly1 cells transfected using Nucleofector 96-well Shuttle system (Lonza) with siBCL6 (HSS100968) or siNT (46-2001) (Stealth RNAi, Invitrogen) at 24hrs and 48hrs after nucleofection. RNAeasy Plus Kit (Qiagen) that included a gDNA elimination step was used for RNA isolation. RNA concentration and purity were determined using Nanodrop (Thermo Scientific) and integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Libraries were generated using mRNA-seq sample prep kit by Illumina. Briefly, mRNA was selected by two rounds of purification using magnetic polydT beads and then fragmented. First strand synthesis was performed using random oligos and SupersciptIII (Invitrogen). After second strand synthesis a 200bp paired-end library was prepared following the Illumina paired-end library preparation protocol.

value: DLBCL cell line OCI-LY1

tag: genotype/variation

value: siNT mediated knockdown

tag: time


title: OCI-LY1_siNT_48hrs_mRNAseq

description: mRNA sequencing in OCI-Ly1 48hrs after siNT nucleofection


title: OCI-LY1_Control_mRNAseq

description: mRNA sequencing in baseline non-nucleofected OCI-Ly1

value: control


title: OCI-LY1_siBCL6_24hrs_mRNAseq

description: mRNA sequencing in OCI-Ly1 24hrs after siBCL6 nucleofection

value: siBCL6 mediated knockdown


title: OCI-LY1_siBCL6_48hrs_mRNAseq

description: mRNA sequencing in OCI-Ly1 48hrs after siBCL6 nucleofection


title: OCI-LY1_H3K27Ac_ChIP-seq:siBCL6

description: ChIP-seq in OCI-LY1 against H3K27Ac in siBCL6 treated cells

value: siBCL6 treated


title: OCI-LY1_48hrs_mRNAseq_3x_siBCL6_R3

description:
mRNA sequencing in baseline non-nucleofected OCI-Ly1
RNAseq_biologicalTriplicates_48h in OCI-Ly1 siBCL6 replicate3

extract_protocol: ChIP-seq libraries were prepared using the Illumina ChIP-seq Library preparation Kit following the manufacture’s instructions with minor modifications. Briefly 10ng of purified ChIP DNA was end repaired by conversion of overhangs to phosphorylated blunt ends. A’ bases were added to the 3’ends of the DNA fragments and Illumina adapters (1:30 dilution) were ligated to the ends of ChIP fragments. After adapter ligation DNA was separated by electrophoresis and size selected by isolating a gel band of 250±25bp. This fragment range corresponds to a ChIP fragment range of about 158±25bp. Size selected fragments were PCR amplified for 15cycles using Illumina genomic DNA primers 1.1 and 1.2 with the following program (30s at 98oC, 15cycles of 10 at 98oC, 30s at 65oC,30s at 72oC and 5min extension at 75oC). Libraries were quantified and validated using Agilent Technologies 2100 Bioanalyser for size, concentration and purity. Q-PCR was repeated to confirm retention of relative enrichment.                               RNAseq: Three ug of total RNA was isolated from OCI-Ly1 cells transfected using Nucleofector 96-well Shuttle system (Lonza) with siBCL6 (HSS100968) or siNT (46-2001) (Stealth RNAi, Invitrogen) at 24hrs and 48hrs after nucleofection. RNAeasy Plus Kit (Qiagen) that included a gDNA elimination step was used for RNA isolation. RNA concentration and purity were determined using Nanodrop (Thermo Scientific) and integrity was verified using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). Libraries were generated using mRNA-seq sample prep kit by Illumina. Briefly, mRNA was selected by two rounds of purification using magnetic polydT beads and then fragmented. First strand synthesis was performed using random oligos and SupersciptIII (Invitrogen). After second strand synthesis a 200bp paired-end library was prepared following the Illumina paired-end library preparation protocol.


title: OCI-LY1_48hrs_mRNAseq_3x_siNT_R2

description:
mRNA sequencing in baseline non-nucleofected OCI-Ly1
RNAseq_biologicalTriplicates_48h in OCI-Ly1 siNT replicate2

value: siNT


title: OCI-LY1_48hrs_mRNAseq_3x_siNT_R1

description:
mRNA sequencing in baseline non-nucleofected OCI-Ly1
RNAseq_biologicalTriplicates_48h in OCI-Ly1 siNT replicate1


title: OCI-LY1_48hrs_mRNAseq_3x_siBCL6_R2

description:
mRNA sequencing in baseline non-nucleofected OCI-Ly1
RNAseq_biologicalTriplicates_48h in OCI-Ly1 siBCL6 replicate2


title: GCB_rep2_INPUT

description: INPUT from Germinal center B cells  (replicate 2)

source_name: Germinal center B cells

value: input

value: Germinal center B cells


title: OCI-LY1_48hrs_mRNAseq_3x_siBCL6_R1

description:
mRNA sequencing in baseline non-nucleofected OCI-Ly1
RNAseq_biologicalTriplicates_48h in OCI-Ly1 siBCL6 replicate1


title: OCI-LY1_48hrs_mRNAseq_3x_siNT_R3

description:
mRNA sequencing in baseline non-nucleofected OCI-Ly1
RNAseq_biologicalTriplicates_48h in OCI-Ly1 siNT replicate3


title: GCB_rep2_BCL6_CHIP

description: ChIP-seq in Germinal center B cells against BCL6 (replicate 2)

value: BCL6 N-3

tag: chip antibody manufacturer

value: Santa Cruz

tag: chip antibody catalog #


title: Input

city: Stanford

first: Kun

last: Qu

state: CA

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

data_processing:
RNA sequencing reads were mapped to NCBI build 36/mm9 using TopHat (Trapnell et al. 2009) with default options.
ChIP sequencing reads were mapped to ucsc build mm9 using Bowtie (Langmead et al. 2009) with default options
RPKM of RefSeq annotated transcripts were obtained by an in-house generated script
ChIP sequencing peak calling was performed using MACS (Zhang et al. 2008)
Genome_build: mm9

source_name: MEFs

growth_protocol: Primary WT MEFs were harvested from littermate 13.5-day-old embryos using standard methods and propagated in DMEM (Invitrogen) plus 10% FBS.  MEFs were passaged a total of four times before all experiments.

extract_protocol: DNA was cross-linked for 10 minutes with 1% formaldehyde and stopped in 0.125 M glycine. Purified chromatin was sonicated to ~250 bp using the Bioruptor (Diagenode, Inc) and incubated with the IgG or Histone H3 (tri methyl K4) as previously described in http://farnham.genomecenter.ucdavis.edu/pdf/FarnhamLabChIP%20Protocol.pdf.

treatment_protocol: MEFs were treated for the indicated time with TNF-alpha (20ng/mL)

tag: passages

tag: strain

tag: antibody


title: H3K4me3_ChIPSeq

tag: treatment


title: MGC1

tag: cell type

value: mural granulosa cells

value: GnRH antagonist, rFSH, hCG


title: 0hrs

data_processing:
RNA sequencing reads were mapped to NCBI build 36/mm9 using TopHat (Trapnell et al. 2009) with default options.
ChIP sequencing reads were mapped to ucsc build mm9 using Bowtie (Langmead et al. 2009) with default options
RPKM of RefSeq annotated transcripts were obtained by an in-house generated script
Genome_build: mm9

extract_protocol: Total RNA was isolated from MEFs treated with 20ng/mL TNFa for the indicated times before RNA extraction with Trizol (Invitrogen, 10296-010), followed by RNAeasy kit (Qiagen, 74104) and treated with Turbo DNAse Free Kit (Ambion, AM1907). Poly-A RNA was selected for using the MicroPoly(A) Purist kit (Ambion, AM1919).  200 ng polyA RNA was used for each library.   Paired End Directional library construction was performed for dUTP libraries as described (Levin, Yassour et al. 2010) except libraries were size selected by gel purification after ligation and after PCR amplification.  Libraries were sequenced with an Illumina Genome Analyzer II


title: 6hrs

value: TNF alpha; 6 hours


title: pro-B RNA-seq R2

city: La Jolla

first: Salvatore

last: Loguercio

state: California

address: 10550 North Torrey Pines Rd

department: MB

institute: TSRI

description: B6 RAG-/- pro-B RNA-seq data - replicate II

data_processing:
Raw data were de-multiplexed and aligned to the mouse reference genome (mm9) using TopHat 2.0.7 and Bowtie 2.0.5.
Separate UCSC wig tracks for the forward and reverse strand were generated with IGVtools 2.3.9.
Genome_build: mm9
Supplementary_files_format_and_content: file format: wig; content: tag density, chr12 only

source_name: Rag1 -/- pro-B cells

growth_protocol: Bone marrow cells were isolated from 5- to 8-wk-old Rag1−/− mice and were enriched for CD19+ cells with MACS microbeads.

extract_protocol:
RNA was extracted from C57BL/6 RAG-/- pro-B cells using Trizol® (Life Technologies Corp., Carlsbad CA) and genomic DNA was eliminated using the genomic DNA wipeout buffer in the QuantiTect Reverse transcription kit (QIAGEN). A final purification of the RNA was performed with the RNeasy kit from QIAGEN.
For each  sample, 100 ng of total RNA was used to make RNASeq libraries using the NuGEN Encore Complete DR kits following manufacturer's recommended protocols. Sequencing libraries were gel purified to ensure insert sizes were larger than 100 bp in length and sequenced on an Ilumina HiSeq2000 for 100 bases plus 7 bases for indexing.

tag: tissue

value: pro-B cells

tag: genotype

value: Rag -/-


title: 24hrs

value: TNF alpha; 24 hours


title: 1.5hrs

value: TNF alpha; 1.5 hours


title: pro-B RNA-seq R1

description: B6 RAG-/- pro-B RNA-seq data - replicate I


title: Rad21 input control

description: Rad21 input control

data_processing:
Duplicated reads were removed before mapping.
Experimental and input control fastaq tags were aligned to the mouse reference genome (mm9) using Bowtie 0.12.9. Alignment parameters used: -a -v 2 -m 3 --best --strata
All reads mapping with their best alignment score at more than 3 sites in the genome were discarded.
Tags were extended 300 bp upstream or downstream from the alignment start site, depending on the strand orientation of the mapping.
Final UCSC wig tracks had the input subtracted from the ChIP signal.
For CTCF and Rad21, confident peaks were called using MACS (version 2.0.10), with FDR<= 1% and the default p value (1E-5).
genome build: mm9
file format: UCSC wig; content: tag density (ChIP signal, input subtracted) | file format:bigWig; content: tag density (ChIP signal) | file format: bed; content: confident peaks (as called by MACS)

extract_protocol:
B6 Rag1−/− pro-B cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature. Subsequently, the lysates were sonicated using a Diagenode Biorupter. The chromatin solution was precleared with salmon sperm DNA-protein A agarose beads. The lysate was immunoprecipitated using the following antibodies; CTCF, H3K4me2, H3ac, and H3K27me3 were purchased from EMD Millipore (Billerica, MA), H3K4me3 from Active Motif (Carlsbad, CA), and Rad21 from Abcam (Cambridge, England). Immune complexes were isolated with protein A agarose beads.  Following elution, chromatin-antibody complexes and input DNA were reverse crosslinked by heating at 65°C overnight.  The DNA was purified using the Qiagen DNA purification kit.
The sequencing libraries were prepared using 10 ng of DNA. ChIP DNA sample ends were repaired using the recommended Illumina protocol, including T4 DNA polymerase, Klenow Large Fragment, and T4 polynucleotide kinase. DNA products were purified using the DNA Clean&Concentrator- 5 Kit (Zymo Research). The DNA ends were A-tailed with Klenow Large Fragment (3′→5′ exo-) at 37 °C for 30 min. DNA products were again purified using the DNA Clean&Concentrator- 5 Kit. Next, Illumina Paired End-adapter oligonucleotides (2), at a concentration of 0.33 μM, were ligated to the A-tailed cDNA ends with T4 DNA ligase. DNA products were purified using the DNA Clean&Concentrator-5 Kit. The DNA library products were separated on a 2% (wt/vol) agarose gel, and products corresponding to a size of ∼200–250 bases were removed from the gel and cleaned using the Agencourt SPRI system (Beckman). The DNA material was PCR-amplified with Phusion Polymerase (Finnzymes) with 0.6 μM PCR primers PE 1.0 and PE 2.0 (Illumina) for 15 cycles. The amplified DNA products were further purified on 2% (wt/vol) agarose gel, excised, and isolated again using the ZymocleanGel DNA recovery kit (Zymo Research). The purified DNA library was quantitated using the Qubit quantitation platform (Invitrogen) and sized using the 2100 Bioanalyzer (Agilent). DNA products were then denatured in 0.1 N of NaOH and diluted to a final concentration of 10 pM before being loaded onto the Illumina single read flow cell for 100 base sequencing by synthesis on the Illumina HiSeq2000.

tag: ChIP


title: Rad21 ChIP-seq

description: Rad21 ChIP-seq


title: CTCF ChIP-seq

description: CTCF ChIP-seq

value: CTCF


title: CTCF input control

description: CTCF input control


title: H3K4me3 ChIP-seq

description: H3K4me3 ChIP-seq


title: H3K4me2 H3K4me3 input control

description: H3K4me2 H3K4me3 input control


title: PolII input control

description: PolII input control


title: H3ac H3K27me3 input control

description: H3ac_H3K27me3 input control


title: H3ac ChIP-seq

description: H3ac ChIP-seq


title: H3K4me2 ChIP-seq

description: H3K4me2 ChIP-seq


title: MGC2 (miRNA)

data_processing:
Base calling and filtering was done using instrument software real time analysis (RTA v 1.9.35) with default parameters.
Raw filtered data was submitted to miRDeep2 software (30) that integrates adapter trimming, sequence alignment and miRNA annotation according to miRBase version 18.
Differential miRNA expression analysis was performed using the R/Bioconductor package EdgeR.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: miRNA counts for each sample generated by miRDeep2. Data from technical replicates has been summed.

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. Small RNA fraction (< 200nt) was eluted separately from large RNA fraction.
Small RNA libraries were prepared using Bioo Scientific NEXTflex Small RNA Sequencing Kit and NEXTflex small RNA Barcode Primer Set A (Bioo Scientific Corporation) following the manufacturer’s protocol. Size selection of 140-160 bp fragments corresponding to mature miRNAs and adapters was carried out by gel electrophoresis with 10% Mini-PROTEAN TBE Precast gels (Bio-Rad Laboratories). 0.66 pM of individual indexed samples were pooled for template hybridization and clustering/amplification was performed using TruSeq SR Cluster Kit v2-cBot-GA (Illumina).

value: male factor


title: MGC1 (miRNA)


title: CGC3 (miRNA)

value: cumulus granulosa cells


title: MGC3 (miRNA)


title: H3K27me3 ChIP-seq

description: H3K27me3 ChIP-seq


title: CGC1 (miRNA)


title: CGC2 (miRNA)


title: OCI-LY1_NCOR-p300_INPUT

description: INPUT-seq matching ChIP-seq in OCI-LY1 against NCOR/p300

tag: cell line

value: none (INPUT)


title: OCI-LY1_P300_ChIP-seq

description: ChIP-seq in OCI-LY1 against p300


title: PolII ChIP-seq

description: PolII ChIP-seq

value: PolII


title: Input sample_mitotic K562

status: Public on Aug 04 2013

city: Stockholm

first: Anniina

last: Vihervaara

address: Tomtebodavägen 23A

department: Gene Technology

country: Sweden

institute: KTH Royal Institute of Technology

data_processing:
36nt of each fragment was sequenced with Illumina GAIIx
The sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, and  mapped to human genome (hg19) with Bowtie program
The peaks were called with MACS 1.4 program
Genome_build: hg19
Supplementary_files_format_and_content: fastq files contain the raw reads with quality scores
Supplementary_files_format_and_content: peak files contain coordinates of binding sites and the fold enrichment of each site as analyzed against input
Supplementary_files_format_and_content: wig files contain the sequenced reads in format compatible with genome viewers

source_name: K562 cells

growth_protocol: Human K562 erythroleukemia cells were maintained at 37°C in a humidified 5% CO2 atmosphere and cultured in RPMI medium (Sigma) containing 10% fetal calf serum, 2 mM L glutamate and streptomycin/penicillin.

extract_protocol:
The cells were cross-linked with a final concentration of 1% formaldehyde followed by quenching with a final concentration of 125 mm glycine. Chromatin was fragmented by sonication (Bioruptor, Diagenode) to 100 - 500 bp. Immunoprecipitation was performed after preclearing with 50% slurry of protein G-coated Sepharose beads containing bovine serum albumin (100 μg/ml, Amersham Biosciences) at 4 °C overnight. Washing of immunocomplexes was performed three times in wash buffer 1 (0.1% SDS, 1% Triton X-100, 2 mm EDTA, pH 8.0, 150 mm NaCl, 20 mm Tris-HCl, pH 8.0), twice in wash buffer 2 (0.1% SDS, 1% Triton X-100, 2 mm EDTA, pH 8.0, 500 mm NaCl, 20 mm Tris-HCl, pH 8.0), and three times in wash buffer 3 (20 mm Tris-HCl, pH 8.0, 1 mm EDTA, pH 8.0, 10% glycerol). Cross-links were reversed by incubating the samples overnight at 65 °C. DNA was purified with phenol:chloroform, and EtOH precipitated. Ten PCR-verified ChIP-replicates per each sample were pooled and purified with Qiaquick columns.
Sequencing libraries were generated using New England BioLabs NEBNext sample preparation kits according to the manufacturer´s protocols. Used adapters, PCR and Index primers were from Bioo Scientific AIR DNA Barcodes kit. Template amplification and cluster generation were performed using cBot and Truseq SR Cluster kit for cBot v.

value: K562 cells

tag: cell cycle phase

value: arrested to mitosis

value: 30 min at 42C


title: HSF2_heat-treated mitotic K562


title: OCI-LY1_Ser2-P_PolII_CHIP

description: ChIP-seq in OCI-LY1 against Ser2-P RNA pol II

value: Ser2-P RNA pol II


title: HSF1_heat-treated mitotic K562


title: IgG_heat-treated mitotic K562

value: IgG (sc-2027, Santa Cruz, Lot#A2412)


title: OCI-LY1_Ser2/Ser5-P_PolII_INPUT

description: INPUT-seq matching OCI-LY1 Ser2/Ser5-P RNA PolII ChIP


title: Input sample_cycling K562

value: freely cycling


title: OCI-LY1_BCL6_N-3_rep2_INPUT

description: INPUT-seq matching OCI-LY1 ChIP against BCL6 (N3-antibody) REPLICATE 2


title: OCI-LY1_BCL6_D-8_INPUT

description:
INPUT-seq matching ChIP-seq in OCI-LY1 against BCL6 (D8-antibody)
qseq files unavailable, as this study took several years: OCI-Ly1_BCL6_D8_INPUT_qseq.tar


title: OCI-LY1_SMRT_INPUT

description: INPUT-seq matching ChIP-seq in OCI-LY1 against SMRT


title: OCI-LY1_BCOR_INPUT

description:
INPUT-seq matching OCI-LY1 BCOR ChIP
qseq files unavailable, as this study took several years: OCI-LY1_BCOR_INPUT_qseq.tar


title: OCI-LY1_BCL6_N-3_rep2_CHIP

description: ChIP-seq in OCI-LY1 against BCL6 (N3-antibody) REPLICATE 2

value: BCL6 (N3-antibody)


title: OCI-LY1_Ser5-P_PolII_CHIP

description: ChIP-seq in OCI-LY1 against Ser5-P RNA pol II

value: Ser5-P RNA pol II


title: IgG_non-treated mitotic K562

value: no treatment


title: HSF1_heat-treated cycling K562


title: HSF2_heat-treated cycling K562


title: IgG_heat-treated cycling K562


title: OCI-LY1_SMRT_CHIP

description: ChIP-seq in OCI-LY1 against SMRT

value: SMRT


title: OCI-LY1_BCL6_D-8_CHIP

description:
ChIP-seq in OCI-LY1 against BCL6 (D8-antibody)
qseq files unavailable, as this study took several years: OCI-Ly1_BCL6_D8_CHIP_qseq.tar

value: BCL6 (D8-antibody)


title: OCI-LY1_BCOR_CHIP

description:
ChIP-seq in OCI-LY1 against BCOR
qseq files unavailable, as this study took several years: OCI-LY1_BCOR_CHIP_lane1_qseq.tar
qseq files unavailable, as this study took several years: OCI-LY1_BCOR_CHIP_lane2_qseq.tar
INPUT-seq matching OCI-LY1 ChIP against RNA polymerase II is same sample as INPUT-seq matching OCI-LY1 BCOR ChIP

value: BCOR


title: OCI-LY1_NCOR_ChIP-seq

description: ChIP-seq in OCI-LY1 against NCOR

value: NCOR


title: HSF2_non-treated cycling K562


title: Top3b

city: Baltimore

first: Minoru

last: Ko

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

data_processing:
Library strategy: HITS-CLIP
Sequence tags (41 bp long) were aligned to human genome (hg18, NCBI/NIH ) using ELAND software (Illumina) (Bentley 2006) using maximum 2 mismatches and <=5 matches in the genome. Among tags with multiple matches, we only selected those with the minimum number of mismatches. We used the predicted coordinate of the center of sequenced DNA fragments, assuming their length of 200 bp.  Genome coordinates of genes, exons, and ORF were retrieved from UCSC (http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/refGene.txt.gz).
We used a PERL script to estimate the location of sequenced DNA fragments within each transcript, distance to exon junction, ORF start and ORF end.
Genome_build: hg18
Supplementary_files_format_and_content: HG18 tag density: Top3b_tags_hg18.txt.gz
Supplementary_files_format_and_content: HG18 tags: align_s8_human.txt.gz
Supplementary_files_format_and_content: Human Refseq tags: align_s8_refseq.txt.gz

source_name: Top3b High 9pM

growth_protocol: HeLa and HEK293 cells were cultured in DMEM supplemented with 10% fetal calf serum at 37 oC, 5% CO2.

extract_protocol:
The RNA topoisomerase assay followed a previously published protocol. Briefly, the P-labled purified RNA circle substrate (1 nM) was incubated with the indicated topoisomerase in 10 μl of reaction buffer containing 20 mm Tris-HCll  (pH 7.5), 5 mm MgCl2, 2 mm DTT, 0.1 mg/ml BSA, 5% glycerol and 10% PEG400 at 37 °C for 90 min. Reactions were terr minated by adding 10 μl stop buffer (0.5% SDS, 20 mm EDTA and 0.2 mg/ml proteinase K) and incubated at 50 °C for    30 min. After phenol/chloroform extraction and ethanol precipitation, the mixtures were fractionated on 15% TBE-Urea gels and analyzed by autoradiography or PhosphoImager.
To study whether Top3β binds mRNAs in vivo and also to identify its genome-wide RNA targets, we performed HITS-CLII P (high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation). In this method, proteins are covalently crosslinked with bound RNAs in vivo, thus allowing specific mapping of the sites of interaction of the protein with the RNA. The level of RNA obtained by Flag-Top3β IP from HeLa cells expressing HFTop3β was significantt ly higher than the background signal from a mock IP using cells that do not express the tagged protein, indicating that Top3β binds RNA in vivo. The majority of 2.4 million sequencing readhad a sense orientation, and the density   of tags within exons was 58-fold higher than within introns, suggesting that Top3β binds mRNA.

treatment_protocol: Transfections of plasmids and siRNAs were carried out with Lipofectamine 2000 and Lipofectamine RNAiMAX (Invitrogen), respectively, according to manufacturer's protocols. Top3β and TDRD3 expression vectors were made by linking their amino termminus in-frame with a double-tag containing 6xHistidine and a Flag51; the products obtained were then subcloned into pIRESpuro3 vector (Clonetech).  The expression vectors for wildtype and mutant FMRP, which are all double-tagged with Flag and EGFP, were kindly provided by Dr. S. Ceman16. TDRD3 Smart-Pool siRNA oligos were purchased from Dharmacon. FMR1 siRNA oligos were purchased from Santa Cruz Biotech. Top3β-/- MEF cells were derived and cultured as preeviously described.

value: HeLa cell


title: HSF1_non-treated cycling K562


title: IgG_non-treated cycling K562


title: G20_LS4D

status: Public on Aug 03 2013

city: Berkeley

first: Morgan

middle: N

last: Price

address: 1 Cyclotron Road Mailstop 955-512L

department: Physical Biosciences Division

institute: Lawrence Berkeley National Lab

description: Mid-log phase G20 in LS4D

data_processing:
The reads were mapped to the genome NC_007519 using RTA 1.8 and Eland by the sequencing center.
The Eland output was converted to wig format by a custom perl script.
genome build: ASM1266v1

organism: Oleidesulfovibrio alaskensis G20

source_name: G20 grown in defined lactate/sulfate media

growth_protocol: Experiments were conducted within a Coy anaerobic chamber with an atmosphere of about 2% H2 and 5% CO2

extract_protocol:
We used Terminator 5'-Phosphate-Dependent Exonuclease (Epicentre) to try to remove 5'-monophosphate (degraded) transcripts and then converted 5'-triphosphate ends to 5'-monophosphate ends with RNA 5' Polyphosphatase (Epicentre).  Between each enzymatic reaction of this library, RNA was purified using Agencourt RNAClean XP beads. Molecules smaller than 100 nucleotides and unligated adaptors were mostly lost in these clean-up reactions.  We then added a sequencing adaptor onto the 5' end with Ambion T4 RNA ligase.
We used random hexamer primers with a sequencing adaptor on their 5' end to obtain first-strand cDNA. We size-selected products of 150-500 bases from an agarose gel. We PCR amplified the library to enrich for products that contained both adaptors and to complete the 5' adaptor.  We purified the PCR products and removed unincorporated nucleotides, primers, and adaptor-only products with AMPure XP Beads (Agencourt).

treatment_protocol: Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes.  Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment.  RNA quality was confirmed with an Agilent Bioanalyzer.  Ribosomal RNA was depleted with the MICROBExpress kit (Ambion), which uses magnetic beads coated with oligonucleotides that hybridize to ribosomal RNA.

tag: media