title: TNF30min_head

status: Public on Oct 13 2012

city: 4-6-1, Komaba, Meguroku

first: Takahide

last: Kohro

state: Tokyo

country: Japan

institute: LSBM, RCAST

description: 30 min after TNF alpha addition

data_processing:
Library strategy: ChIA-PET
The first 20bases of the fastq files were aligned to hg19 using batman (http://code.google.com/p/batman-aligner/).
Then the aligned files were processed with the ChIA-PET pipeline (Genome Biol. 2010;11(2):R22.).
Data representing intra-chromosomal PETs were used in the analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited files showing paired clusters.

growth_protocol: HUVECs were grown in EGM2MV culture medium, and serum starved on the day before stimulation.  After TNF alpha addition, samples were double crosslinked using EGS and 1%PFA.

extract_protocol: Samples were sonicated for 5 min, and immunoprecipitated using Pd75C9.  DNA was annealed by biotin labeled half linkers and circulated.  After MmeI digestion, PET products and sequencing adopters were annealed for deep sequencing.  Detailed procedure was explained in Curr Protoc Mol Biol. 2010 Jan;Chapter 21:Unit 21.15.1-25. Chromatin immunoprecipitation was done using anti active (3S and 5S of CTD repeat were phosphorylated) RNA polymerase antibody (Pd75C9), which was established and kindly provided by Dr. Kimura, Osaka University.

value: HUVECs

tag: cell passage

value: passage 6

tag: chip-antibody

value: Pd75C9 (p3Sp5S RNA Pol II)

tag: library

value: ChIA-PET


title: TNF00min_tail

type: SRA

description: 0 min after TNF alpha addition

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell type


title: TNF00min_head

description: 0 min after TNF alpha addition


title: H3K27me3-ShRd_ChIPSeq

status: Public on Oct 16 2012

city: Barcelona

first: Luciano

last: Di Croce

address: Dr. Aiguader, 88

country: Spain

institute: Centre for Genomic Regulation

description: Chromatin IP against H3K27me3 in control cell (shRandom)

data_processing:
Basecalls performed using Illumina Pipeline
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the --best option and allowing 2 mismatches in the seed
peaks were called by using MACS version 1.4.1
Genome_build: mm9
Supplementary_files_format_and_content: text file containing peak coordinates

organism: Mus musculus

growth_protocol: Wild-type (E14Tg2A) ES cells were cultured feeder-free in plates coated with 0.1% of gelatin in Glasgow minimum essential medium (Sigma) supplemented with β-mercaptoethanol, sodium pyruvate, essential amino acids, GlutaMAX, 20% fetal bovine serum (Hyclone), and leukemia inhibitory factor (LIF).

extract_protocol:
ESCs were trypsinized and crosslinked in 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with 0.125 M glycine for 5 min. Pelleted cells were lysed in 1 ml ChIP buffer and sonicated for 14 min in a Bioruptor. ChIP-Seq experiments were performed as previously described (Morey et al, Cell Stem Cell. 2012, 10: 47-62). Immunoprecipitated DNA was eluted, reverse crosslinked and purified using Qiagen columns.
It was performed using the NEBNext DNA Sample Prep Reagents Set 1

tag: cell line

value: embryonic stem cells

tag: genotype/variation

value: wild type

tag: antibody

value: H3K27me3 - Millipore, #07449


title: H3K36me2_ChIPSeq

description: Chromatin IP against H3K36me2 (peaks not provided; raw data was used to perform average profiles of H3K36me-reads around TSS or around the center of Phf19-binding sites)

data_processing:
Basecalls performed using Illumina Pipeline
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie version 0.12.7 with the --best option and allowing 2 mismatches in the seed
peaks were called by using MACS version 1.4.1
Genome_build: mm9
Supplementary_files_format_and_content: peaks not provided; raw data was used to perform average profiles of H3K36me-reads around TSS or around the center of Phf19-binding sites


title: PGK_1

status: Public on Oct 15 2012

city: Oxford

first: Stephen

last: Taylor

address: Headington

country: United Kingdom

institute: CBRG

data_processing:
solexa1.3 basecalling
mapping to genome with bowtie -m 1
conversion of sam/bam files to bigwig using bamToGBrowse.pl (http://cpansearch.perl.org/src/LDS/Bio-SamTools-1.14/bin/bamToGBrowse.pl)
Genome_build: mm9

source_name: wild type female embryonic stem cell line paired end 1

growth_protocol: Standard culture conditions including 5% CO2, 37oC, 5% fetal calf serum, penicillin and streptomycin in DMEM culture media.  For ES cell growth cells were maintained with 10% fetal calf serum and supplemented with LIF

extract_protocol: genomic DNA was isolated using a standard protocol after RNase and proteinase K treatment, it was then sonicated to between 200-600 bp, before 20-30 ug was fractionated using a MBD column.  Unmethylated DNA was eluted with 0.715 M NaCl and methylated DNA with 1M NaCl.  Efficient fractionation was confirmed by PCR analysis of fractions for known methylated and unmethylated loci.  Methylated DNA was then pooled, concentrated, desalted in a 30K filter and precipitated.  Samples were resuspended in 20 microlitres of H20 and submitted for sequencing after quality was confirmed using picogreen.  Each sample isolation and MBD-seq was performed.

treatment_protocol: MEF cell lines were untreated.  ES cell differentiation followed the standard embryoid body method.

tag: gender

value: female

value: PGK


title: mock

city: Trieste

first: Miguel

last: Mano

address: Padriciano 99

country: Italy

institute: International Centre for Genetic Engineering and Biotechnology - ICGEB

description: mouse cardiomyocytes mock transfected

library_source: transcriptomic

data_processing:
Illumina Pipeline 1.8.0 was used for data analysis (Casava v1.8)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated according to Mortazavi, A. et al Nature methods 5, 621-628 (2008).
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

source_name: Neonatal cardiomyocytes

growth_protocol: 9.0×105 cardiomyocytes were seeded onto Primaria 60-mm dishes

extract_protocol:
total RNA, including small RNA fraction was isolated from cardiomyocytes using miRNeasy mini kit (Qiagen), according to manufacturer´s instructions.
Samples were processed using TruSeq RNA-seq sample prep kit from Illumina, according to manufacturer´s instructions.

treatment_protocol: Transfection of miRNAs mimics was performed at final concentration of 50nM through a reverse transfection protocol using Lipofectamine RNAimax reagent.

tag: strain

value: CD1 mice

value: cardiomyocytes

tag: age

value: post natal day 1

tag: treatment

value: mock transfected


title: hsa-miR-199a-3p

description: mouse cardiomyocytes transfected with hsa-miR-199a-3p

value: transfected with hsa-miR-199a-3p


title: Lgr5(hi) input DNA

city: Boston

first: Amit

last: Sinha

state: MA

address: 44 Binney St

department: Pediatric Oncology

country: USA

institute: Dana-Farber Cancer Institute

data_processing:
Illumina Casava software used for basecalling.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 2.0.0-beta5 with the following configurations "--end-to-end"
Signal was quantified as total number of reads per million in the region of interest. An empirical background distribution model of reads was constructed to find the significance level of signal in a given region.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using custom software; Scores represent reads per million

source_name: intestinal Lgr5(hi) stem cells

growth_protocol: For Lgr5(hi) stem cells, cells were collected by flow sorting based on the high GFP intensity. Villus epithelium was isolated by EDTA method and collected on top of 70 um filter

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. 18 cycles were used to amplify the DNA

treatment_protocol: Cells were fixed with 1% formaldehyde for 25 minutes at room temperature, washed with cold PBS and resuspended in ChIP lysis buffer. Sonicated and immunoprecipitated procedures were based on Carroll, et al, 2005.

tag: background strain

tag: tissue

value: proximal intestinal epithelium

value: Lgr5(hi) stem cells

tag: chip antibody


title: cel-miR-67

description: mouse cardiomyocytes transfected with cel-miR-67

value: transfected with cel-miR-67


title: TNF30min_tail

description: 30 min after TNF alpha addition

value: HUVECs


title: Lgr5(hi) H3K79me2_ChIPSeq

value: H3K79me2 antibody:Abcam ab3594 (lot number 121826)


title: villus H3K79me2_ChIPSeq

source_name: intestinal villus cells

value: differentiated villus cells


title: viillus input DNA


title: HeLa-siTUTs-1

city: Seoul

first: Hyeshik

last: Chang

state: South Korea

address: Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description: small RNA

data_processing: All small RNA sequences except low-quality reads are provided with the number of reads for each unique sequence. Illumina SRA v1.5 3' adapter sequences are trimmed using half-open Smith-Waterman algorithm (score parameters: 2 for match, -2 for mismatch, -3 for linear gap penalty).

source_name: Cervical cancer cells transfected with siRNAs against TUT7, TUT4, and TUT2 two times over a 4~5 day period (rep 1).

growth_protocol: HeLa cells were grown in DMEM supplemented with 10% FBS.

extract_protocol: To prepare small RNA cDNA libraries, total RNAs were separated on 15% urea-PAGE and 17~30nt RNAs were gel-purified. Size fractionized RNAs were ligated with 3' adapter using T4 RNA ligase2 trucated form (NEB). 3’ adaptor-ligated mixture was hybridized with RT primer (NEB v1.5). After RT primer hybridization, RT primer hybridized mixture was ligated with 5' adapter using T4 RNA ligase1 (NEB). The ligation products were reverse transcribed using superscript II (Invitrogen) and the cDNA was PCR-amplified with Phusion DNA polymerase (NEB).

treatment_protocol: HeLa cells were transfected with 42nM of siLuciferase or 14nM of each siTUT7, 4, and 2 or GFP using Lipofectamine 2000 (Invitrogen). Transfection was performed two times over a 4~5 day period to enhance knockdown efficiency.

tag: transfection

value: siTUTs

value: HeLa


title: hsa-miR-590-3p

description: mouse cardiomyocytes transfected with hsa-miR-590-3p

value: transfected with hsa-miR-590-3p


title: HeLa-siTUTs (RNA-seq)

data_processing:
Reads were mapped, measured and quantifed by cufflinks v2.0.0, tophat v2.0.0 and bowtie v2.0.0-beta5 with --library-type fr-secondstrand and other default options. The gene annotations for cufflinks were retrieved from Illumina iGenome repository as of Sep 11, 2011.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values and log2 fold changes between samples

molecule: polyA RNA

source_name: Cervical cancer cells transfected with siRNA against luciferase two times over a 5 day period.

extract_protocol: To prepare mRNA libraries, mRNAs were purified from total RNAs using Dynabeads mRNA Purification Kit (Invitrogen, 61011). Purified mRNAs were fragmented by RNA Fragmentation Reagents (Ambion, AM8740). After fragmentation, phosphate group at 3′ end was removed by Antarctic phosphatase (NEB, M0289L), and RNAs were 5′ phosphorylated by T4 PNK (NEB). Directional and multiplexed mRNA libraries were generated using TruSeq Small RNA Sample Preparation Kit (Illumina, RS-200–0012). The mRNA libraries were sequenced using Illumina HiSeq 2000.

treatment_protocol: HeLa cells were transfected with 42nM of siLuciferase or 14nM of each siTUT7, 4, and 2 using Lipofectamine 2000 (Invitrogen). Transfection was performed two times over a 4~5 day period to enhance knockdown efficiency.

tag: sirna

value: transfected with 14nM of each siTUT7


title: Input_WSU-DLCL2

status: Public on Oct 12 2012

city: Collegeville

first: Gopinath

last: Ganji

state: PA

address: 1250 South Collegeville Road

institute: GSK

description: Sample 6

data_processing:
Fastq sequence files were aligned to the human reference (build hg19) using Bowtie allowing upto 2 mismatches. Only uniquely mapped reads were used for subsequent analysis.
Peaks of H3K27me3 enrichment were identified using SICER with optimized parameters and taking the corresponding Input sample as control; Fragment size of 250, Window size 750 bp and Gap size 2250 bp was used for calling peaks with SICER (were found to be optimal parameters after running with multiple parameters). Duplicate reads were removed before peak calling by SICER.
Statistically significant peaks (FDR<0.001) enriched in the ChIP sample relative to its corresponding input sample were annotated for genomic location
Genome_build: hg19
Supplementary_files_format_and_content: Bed files generated by SICER

growth_protocol: Cells (5x10^7) were maintained in the appropriate cell culture media for 24 hours prior to fixation.

extract_protocol: Chromatin was extracted from formaldehyde-crosslinked cells and ChIP-ed using anti-H3K27me3 antibody Millipore 07-449 (lot# DAM1662421). ChIP DNA was processed into library by following the Illumina ChIP-Seq library construction protocol.

treatment_protocol: Cells were fixed for 15 minutes at room temperature with freshly prepared formaldehyde solution (final concentrations 1% formaldehyde, 10 mM NaCl, 0.1 mM EDTA pH 8.0, 5 mM HEPES pH 7.9) followed by the addition of glycine to 125mM. Fixed cells were rinsed twice in PBS containing 0.5% Igepal CA-630 (Sigma) and cell pellets were flash frozen.  ChIP assays were performed using a custom assay protocol (ActiveMotif Inc.,San Diego, CA).

value: EZH2 mutant

tag: average gic50

value: Input control


title: Input_KARPAS-422

description: Sample 4


title: H3K27me3_WSU-DLCL2

description: Sample 5

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat. #

tag: chip antibody lot #


title: H3K27me3_KARPAS-422

description: Sample 3


title: Input_Pfeiffer

description: Sample 2

source_name: Pfeiffer

value: Pfeiffer

value: 28 nM


title: H3K36me3_ChIPSeq

description: Chromatin IP against H3K36me3 (peaks not provided; raw data was used to perform average profiles of H3K36me-reads around TSS or around the center of Phf19-binding sites)

tag: cell type

value: embryonic stem cells

value: wild type


title: H3K27me3_Pfeiffer

description: Sample 1

tag: cell line


title: 14-16hr Midline Sample 2

city: Chapel Hill

last: Crews

state: NC

address: 133 N. Medical Dr

department: Biochemistry and Biophysics

institute: UNC Chapel Hill

data_processing:
Alignments to Drosophila melanogaster genome build 5 were performed with Bowtie(v0.12.7) and TopHat(v1.3.1.OSX_x86_64) with the following non-default parameters: -i 20 -I 142000 -g 1 --solexa1.3-quals
Mapped reads were associated with D. melanogaster reference annontation r5.39 using Cufflinks(v1.0.3.OSX_x86_64) with a Mask file to eliminate mapping of reads to rRNA, tRNA, snRNA, snoRNA, snmRNA, and ribosomal protein genes
Genome_build: FlyBase Build 5
Supplementary_files_format_and_content: The genes.fpkm_tracking files were generated from Cufflinks.

organism: Drosophila melanogaster

source_name: Embryonic CNS-midline cells

growth_protocol: Embryos were harvested and aged at 25 degrees C.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Minikit
Poly(A) mRNA was purified using the Poly(A) Purist Mag kit from Ambion and cDNA was generated using Invitrogen's SuperScript III Reverse Transcriptase. cDNA library prep followed the protocol from "Preparing Samples for Sequencing Genomic DNA/Chip-Seq v2.5" provided by the UNC High-Throughput Sequencing Facility.

treatment_protocol: Staged embryos were dissociated into single cells. GFP-positive CNS-midline cells and GFP-negative non-midline cells were FACS sorted on an iCyt/Sony Reflection cell sorter.

value: CNS midline

tag: time-point

value: 14-16 hours After Egg Laying

tag: genotype

value: w1118 ; 3.7sim-GAL4 ; UAS-mCD8.GFP


title: 14-16hr Non-Midline Sample

source_name: Embryonic non-midline cells

value: Non-midline


title: 6-8hr Non-Midline Sample

value: 6-8 hours After Egg Laying


title: HeLa-siLuc-1

description: small RNA

source_name: Cervical cancer cells transfected with siRNA against luciferase two times over a 4~5 day period (rep 1).

value: siLuc


title: HeLa-siTUTs-2

description: small RNA

source_name: Cervical cancer cells transfected with siRNAs against TUT7, TUT4, and TUT2 two times over a 4~5 day period (rep 2).

value: siTUTs


title: Pol II (rpb3) ChIP-seq 1+2

city: Ithaca

first: Leighton

middle: James

last: Core

state: NY

address: 417 Biotechnology Building

department: Moleular Biology and Genetics

institute: Cornell University

description: ChIP

data_processing: Reads were trimmed to 26bp and aligned to Drosophila melanogaster (Dm3 version) genome with MAQ.  Processed data file contains both mapped replicates after pooling the data.  The processed file is in bedgraph format and can be uploaded onto the UCSC genome browser.

source_name: Pol II (rpb3) ChIP-seq

growth_protocol: S2 cells were maintainedat 25oC in M3+BPYE  media supplemented with 10% FBS

extract_protocol: Libraries were constructed as in Nechaev et al (Science, 2010 Vol. 327. no. 5963, pp. 335 - 338). Pol II antibody was made in-house (Adelman Lab) and is the same as mentioned in the citation (Nechaev et al).

treatment_protocol: No treatment (steady-state cell growth)

value: Schneider Line 2 (S2)

tag: antibody

value: anti-Rpb3 (subunit of Pol II)


title: NELF_RNAi GRO-seq 1+2

description: Nuclear Run-on (nascent RNA). Two replicate experiments combined.

data_processing: Reads were trimmed to 26bp and aligned to Drosophila melanogaster (Dm3 version) genome with MAQ.  The number of reads at each position were then normalized for each library by dividing by the number of  reads (in millions) that mapped uniquely to the genome, to a representative  rRNA locus, and to representative  tRNA.  This accounts for the total transcription in cells after treatments that will differentially affect transcription by one or more of the RNA polymerases (I, II, or III).

molecule: nuclear RNA

source_name: NELF_RNAi GRO-seq

extract_protocol: Libraries untr, Mock and NELF RNAi: Nuclei isolation and run-on reactions are performed using standard protocols with the exception that 5-Bromo-UTP is used in place UTP, and the concentration of CTP is adjusted to 1µM.  Samples are treated with Rnase-free RQ1 DNase (promega) and Proteinase K (invitrogen). RNA is then extracted twice with Leder phenol and once with chloroform, then precipitated.  Isolated RNA is then base hydrolyzed to the desired size and RNA fragments are then isolated by binding to anti-deoxy-BrU beads, washed several times, and eluted from the beads.  The RNAs are treated at low pH with tobacco acid pyrophosphatase and then are treated at low pH with T4 polynucleotide kinase (PNK).  The pH is then raised and the RNA is treated again with PNK, except now in the presence of ATP.  A standard Illumina adapter is then added to the 5’-end with T4-RNA ligase and the RNA is bound to anti-deoxy-BrU beads.  This process is then repeated for the addition of the Illumina 3’-adapter.  The affinity-enriched RNAs are then reverse transcribed, amplified, and PAGE purified.  This cDNA was then sequenced on the Illumina Genome Analyzer.  Libraries Plus Sark and Minus Sark: Plus- and minus-Sarkosyl matched GRO-seq libraries were made with three sequential bead enrichment steps as above, but a RNA cloning strategy developed by Ingolia et al. (Science, 2009, Vol. 324. no. 5924, pp. 218 - 223), was used to prepare the samples for sequencing with the following modifications.  PNK treatment to remove 3’-phosphates was performed after the first bead enrichment.  cDNAs were not PAGE purified after circularization because the range of sizes (~150-350bp) of the cDNA prevented efficient separation of the circularized and linearized cDNAs.  Samples were amplified and PAGE purified before sequencing on the Illumina Genome Analyzer.

treatment_protocol: Cells that were RNAi treated received dsRNA targeting the NELF-B and NELF-E subunits or “mock” dsRNA against b-galactosidase for 96 hours prior to harvesting cells.

value: anti-BrdU (Santa Cruz Biotech (sc-32323-AC))


title: C. remanei adult males

status: Public on Oct 11 2012

first: Zhen

last: Shi

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Raw datasets are fastq files generated using Illumina software.
Small RNA sequences were parsed using a custom Python program, then mapped to corresponding nematode reference genomes (Wormbase release WS230) allowing 0 mismatch using Bowtie software.
Genome_build: WS230
Supplementary_files_format_and_content: tab-delimited text files include Sequence and read count

organism: Caenorhabditis remanei

source_name: whole animal

growth_protocol: Animals were grown at 20˚C on E. coli strain OP50.

extract_protocol:
Total RNA was isolated from synchronized animals, and 18-28 nt small RNAs were size selected.
Small RNAs were treated with Tobacco Acid Phosphatase, then ligated to 3’ and 5’ adapters and RT-PCR amplified.

tag: strain

tag: developmental stage

value: young adult

value: whole organism

tag: gender

value: male


title: untreated GRO-seq 1+2

source_name: untreated GRO-seq

tag: treatment


title: C. remanei embryos

value: early embryo

tag: tissue


title: C. briggsae adult males

organism: Caenorhabditis briggsae


title: minus sarkosyl GRO-seq 1+2

source_name: minus sarkosyl GRO-seq

value: minus sarkosyl


title: mock_RNAi GRO-seq 1+2

source_name: mock_RNAi GRO-seq


title: CircLigase_rep1&2

description: Nuclear Run-on

data_processing: GRO-seq libraries were sequenced on the Illumina Genome Analyzer II, using standard protocol at the Cornell bioresources center (http//www.BRC.cornell.edu). Bowtie (Langmead, Trapnell, et al, 2009) was used to map 26mers, with up to two mismatches to the DM3 version on the Drosophila genome.  Reads were also mapped to a representative of repetitive genes transcribed specifically by Pol I (rRNA gene; GenBank accession #: M21017.1), and Pol III (tRNAs; parsed from flybase gene set described below).  The rRNA included the extragenic spacers, and tRNAs, were extended +/- 100 bases to account for nascent transcripts that are processed and not part of the annotated tRNA.

source_name: embryonic

extract_protocol: Libraries untr, Mock and NELF RNAi: Nuclei isolation and run-on reactions are performed using standard protocols with the exception that 5-Bromo-UTP is used in place UTP, and the concentration of CTP is adjusted to 1µM.  Samples are treated with Rnase-free RQ1 DNase (promega) and Proteinase K (invitrogen). RNA is then extracted twice with Leder phenol and once with chloroform, then precipitated.  Isolated RNA is then base hydrolyzed to the desired size and RNA fragments are then isolated by binding to anti-deoxy-BrU beads, washed several times, and eluted from the beads.  The RNAs are treated at low pH with tobacco acid pyrophosphatase and then are treated at low pH with T4 polynucleotide kinase (PNK).  The pH is then raised and the RNA is treated again with PNK, except now in the presence of ATP.  A standard Illumina adapter is then added to the 5’-end with T4-RNA ligase and the RNA is bound to anti-deoxy-BrU beads.  This process is then repeated for the addition of the Illumina 3’-adapter.  The affinity-enriched RNAs are then reverse transcribed, amplified, and PAGE purified.  This cDNA was then sequenced on the Illumina Genome Analyzer.  Libraries Plus Sark and Minus Sark, and the Circ-Ligase replicates were made with three sequential bead enrichment steps as above, but a RNA cloning strategy developed by Ingolia et al. 7, was used to prepare the samples for sequencing with the following modifications.  PNK treatment to remove 3’-phosphates was performed after the first bead enrichment.  cDNAs were not PAGE purified after circularization because the range of sizes (~150-350bp) of the cDNA prevented efficient separation of the circularized and linearized cDNAs.  Samples were amplified and PAGE purified before sequencing on the Illumina Genome Analyzer.

value: Circ-Ligase


title: C. briggsae embryos


title: 14-16hr Midline Sample 1


title: C. briggsae adult hermaphrodites

value: hermaphrodite


title: LNCaP Cells CTCF ChIP-seq

city: Darlinghurst

first: Aaron

last: Statham

state: NSW

address: 384 Victoria St

department: Cancer Department

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
Reads were mapped with bowtie 0.12.7 Only reads mapping uniquely to the genome were kept. Upto 3 mismatches to the reference sequence were allowed. When more than one read mapped to the same genomic position, only one read was kept at that position.
Genome_build: hg18
Supplementary_files_format_and_content: BigWig. Counts across the whole genome in windows 20 bases wide, per 1 million mapped reads.

source_name: LNCaP

growth_protocol: Cells were grown at 37ºC with 5% CO2 in T medium with 10% fetal calf serum.

extract_protocol: ~ 1 x 106 cells, in a 10cm dish, were fixed by adding formaldehyde at a final concentration of 1% and incubating for 10 minutes at 37°C.  The cells were washed twice with ice cold PBS containing protease inhibitors (1mM phenylmethylsulfonyl fluoride (PMSF), 1mg/ml aprotinin and 1mg/ml pepstatin A), harvested and treated with SDS lysis buffer for 10 min on ice. The resulting lysates were sonicated to shear the DNA to fragment lengths of 200 to 500 basepairs. The complexes were immunoprecipitated with antibody specific for CTCF (Millipore #07-729). 10 ml of antibody was used. No antibody controls were also included, and no precipitation was observed by quantitative Real-Time PCR analysis. The antibody/protein complexes were collected by Protein A/G PLUS agarose beads (Santa Cruz sc-2003) and washed several times. The immune complexes were eluted with 1% SDS and 0.1 M NaHCO3 and samples were treated with proteinase K for 1 hour and DNA was purified by phenol/chloroform extraction, ethanol precipitation and resuspended in 30ml H2O. The ChIP DNA was quantitated using Qubit and 10ng was used for Illumina library preparation using Illumina ChIP-Seq DNA Sample Prep Kit #IP-102-1001.

value: LNCaP

tag: chip antibody

value: CTCF

tag: chip antibody manufacturer

value: Millipore

tag: chip antibody catalog #


title: C. elegans adult males

organism: Caenorhabditis elegans


title: 6-8hr Midline Sample 1

value: CNS midline

value: w1118 ; 3.7sim-GAL4 ; UAS-mCD8.GFP


title: plus sarkosyl GRO-seq 1

description: Nuclear Run-on (nascent RNA)

source_name: plus sarkosyl GRO-seq

value: plus sarkosyl


title: C. elegans embryos


title: tgf and sorafenib H3K9ac

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

country: China

institute: Agricultural Genomes Institute at Shenzhen

description: A549,lung adenocarcinoma cells treated by tgf-beta and sorafenib,H3K9ac

data_processing:
Illumina BclConverter-1.9.0 software was used for basecalling.
Adaptor sequences were removed, and low-quality sequence reads were trimmed. The clean ChIP-seq reads were mapped to hg19 reference with Soap aligner 2.21, parameters used the defaults.
further analisys used unique mapped reads after duplication, differential histone modification regions(DHMR) were found by t-test(p<0.01) and twice difference of signal in enriched region with poission test P<0.001
Genome_build: hg19
Supplementary_files_format_and_content: bed files contained chromsome,reads strart site,reads end sites;wig files include each samples ChIP signal on enriched sites.

source_name: lung adenocarcinoma cells:A549, the histone was h3k9ac,treated by tgf-beta+sorafenib

growth_protocol: Human alveolar epithelial A549 cells were obtained from ATCC (Manassas, VA, USA) and cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (Biochrom, Berlin, Germany) at 37°C with 5% CO2.

extract_protocol: ChIP-seq libraries were prepared using the following the protocol.The cells were cross-linked by a final concentration of 1% formaldehyde following incubation for 10 min at 37°C. Next, the cells were collected by centrifugation, washed twice with ice cold PBS, and dissolved in 500 μl SDS lysis buffer (1% SDS; 10 mM EDTA; protease inhibitors; 50 mM Tris-HCl, pH 8.0) followed by incubation for 30 min on ice. The lysates were sonicated at high power with 8x30 sec pulses in a BioruptorTM200 to generate chromatin fragments between 100 and 500 bp. Cellular debris was removed by centrifugation. Aliquots of 100 μl of the lysate were diluted 1:10 in ChIP dilution buffer (0.01% SDS; 1.1% Triton X-100; 1.2 mM EDTA; 167 mM NaCl; protease inhibitors; 16.7 mM Tris-HCl, pH 8.0). Then, 4ug of each antibody against H3K9ac, H3K4me3, H3K27me3 and H3K9me3 was added to 40ul of protein A/G Dynabeads (equal volume) and incubated for 3 h at 4°C with rotation. The beads were washed with cold PBS to remove free antibodies and added to diluted lysate followed by an overnight incubation at 4°C on a rotating platform. Sequentially, the immunocomplex plus beads were washed with 1 ml of the following buffers: low salt wash buffer (0.1% SDS; 1% Triton X-100; 2 mM EDTA; 150 mM NaCl; 20 mM Tris-HCl, pH 8.0), high salt wash buffer (0.1% SDS; 1% Triton X-100; 2 mM EDTA; 500 mM NaCl; 20 mM Tris-HCl, pH 8.0) and LiCl wash buffer (0.25 M LiCl; 1% Nonidet P-40; 1% sodium deoxycholate; 1 mM EDTA; 10 mM Tris-HCl, pH8.0). Finally, the beads were washed twice with 1 ml TE buffer (1 mM EDTA; 10 mM Tris-HCl, pH 8.0), and the immune complexes were reverse cross-linked directly by adding 200 μl of elution buffer (1% SDS, 100 mM NaHCO3) in the presence of proteinase K to a final concentration of 0.1 mg/ml and incubated for 3 h at 65°C. DNA in the supernatant was extracted with equal volumes of phenol/chloroform, precipitated with ethanol in the presence of glycogen and eluted in 30ul of nuclease-free H2O. The purified DNA was used for cluster generation and standard single-end sequencing with 50 bp reads (E50) using Illumina Hiseq 2000.

treatment_protocol: A549 cells were treated with TGF-β1 (5 ng/mL) and/or sorafenib (5 μM) for 48 h. Cells treated with vehicle only (DMSO) served as controls.

value: TGFbeta and Sorafenib


title: tgf and sorafenib H3K4me3

description: A549,lung adenocarcinoma cells treated by tgf-beta and sorafenib,H3K4me3

source_name: lung adenocarcinoma cells:A549, the histone was h3k4me3,treated by tgf-beta+sorafenib


title: C. elegans adult hermaphrodites


title: tgf beta H3K9ac

description: A549,lung adenocarcinoma cells treated by tgf-beta,H3K9ac

source_name: lung adenocarcinoma cells:A549, the histone was h3k9ac,treated by tgf-beta

value: TGFbeta


title: tgf and sorafenib H3K9me3

description: A549,lung adenocarcinoma cells treated by tgf-beta and sorafenib,H3K9me3

source_name: lung adenocarcinoma cells:A549, the histone was h3k9me3,treated by tgf-beta+sorafenib


title: 6-8hr Midline Sample 2

source_name: Embryonic CNS-midline cells

value: 6-8 hours After Egg Laying


title: tgf and sorafenib H3K27me3

description: A549,lung adenocarcinoma cells treated by tgf-beta and sorafenib,H3K27me3

source_name: lung adenocarcinoma cells:A549, the histone was h3k27me3,treated by tgf-beta+sorafenib


title: HeLa-siLuc-2

description: small RNA

source_name: Cervical cancer cells transfected with siRNA against luciferase two times over a 4~5 day period (rep 2).

tag: transfection

value: siLuc

value: HeLa


title: tgf beta H3K9me3

description: A549,lung adenocarcinoma cells treated by tgf-beta,H3K9me3

source_name: lung adenocarcinoma cells:A549, the histone was h3k9me3,treated by tgf-beta


title: tgf beta H3K4me3

description: A549,lung adenocarcinoma cells treated by tgf-beta,H3K4me3

source_name: lung adenocarcinoma cells:A549, the histone was h3k4me3,treated by tgf-beta


title: tgf beta H3K27me3

description: A549,lung adenocarcinoma cells treated by tgf-beta,H3K27me3

source_name: lung adenocarcinoma cells:A549, the histone was h3k27me3,treated by tgf-beta


title: control H3K9ac

description: A549,lung adenocarcinoma cells,H3K9ac

source_name: lung adenocarcinoma cells:A549, the histone was h3k9ac,without treated


title: C. brenneri adult males

organism: Caenorhabditis brenneri

source_name: whole animal

value: young adult

value: whole organism


title: control H3K9me3

description: A549,lung adenocarcinoma cells,H3K9me3

source_name: lung adenocarcinoma cells:A549, the histone was h3k9me3,without treated


title: C. brenneri embryos

value: early embryo


title: PPARγ_iWAT_ChIPSeq

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Sequence reads from each ChIP-seq library were trimmed to 40 bases, and each library was collapsed using FastX (http://hannonlab.cshl.edu/fastx_toolkit)
Each collapsed library was aligned to the genome (mm9) using Bowtie (Langmead B, et al., Genome Biol. 10:R25) with the following parameters: -m 3 –best –strata, with all other parameters set at default.
Regions enriched for PPARγ binding were identified using HOMER (Heinz S, et al. 2010. Mol. Cell 38:576 –589) with the “-factor” setting and a false-discovery rate (FDR) cutoff of_0.1%. Moreover, only peaks with >4-fold tag count enrichment compared to both input control and local tag density (10-kb region around putative peak) were used for downstream analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Peak files generated using HOMER

source_name: iWAT-derived adipocytes

growth_protocol: Outbred, male (NMRI) mice at the age of 4 to 5 weeks, mice were deprived of food for 2 h and killed between 9 and 11 a.m. by cervical dislocation. BAT was isolated from the interscapular, cervical, and axillary depots and pooled, and WAT was isolated from the epididymal (eWAT) and inguinal/dorsolumbar (iWAT) depots. The pooled adipose tissues were carefully minced and treated with collagenase (typeII, Sigma) to separate the SVF from mature adipocytes. SVFs were cultured under differentiation- inducing conditions in a medium consisting of Dulbecco modified Eagle medium (DMEM) (Sigma), 10% newborn calf serum (NCS) (HyClone), 30 nM insulin, 25 ug/ml sodium ascorbate, 10 mM HEPES pH7.4, at 37°C, 4mML-glutamine (Invitrogen), 100_g/ml streptomycin, 62.5  ug/ml penicillin, and 1 uM rosiglitazone (Novo Nordisk). Cells of SVF were cultured at 37°C and 8% CO2. Medium was changed 1 day after seeding and subsequently every second day.

extract_protocol: eWAT-, iWAT-, and BAT-derived adipocytes were cross-linked using 0.5 M disuccinimidyl glutarate (DSG) (Proteochem, Denver, CO) for 45 min followed by cross-linking using 1% formaldehyde for 10 min. Cross-linking was stopped by the addition of glycine to a final concentration of 0.125 M for 10 min, followed by addition of ChIP lysis buffer (1% Triton X-100, 0.1% SDS, 150 mM NaCl, 1 mM EDTA, and 20 mM Tris, pH 8.0). Samples were sonicated using the Diagenode Bioruptor twin (3 x14 cycles, 30 s on/off, maximum level). Chromatin IP was performed using anti-PPARγ (sc-7196; Santa Cruz). ChIPed DNA was sequenced according to the manufacturer’s instructions (Illumina).

value: anti-PPARγ (sc-7196; Santa Cruz)

value: male

tag: animal model

value: NMRI


title: C. brenneri adult females+males

value: pooled male and female


title: PPARγ_BAT_ChIPSeq

source_name: BAT-derived adipocytes


title: rhesus testis

status: Public on Oct 10 2012

city: Beijing

first: Jia-Yu

last: Chen

address: No.5 Yiheyuan Road Haidian District

department: Institute of Molecular Medicine

institute: Peking University

data_processing:
testis.bam; genome build: rheMac2
testis.bed; genome build: rheMac2
raw reads were aligned by Tophat v1.2.0, detailed parameters can be in header information of *.bam file. *.bam files and *.bed filed were used for the analysis of transcript expression and transcript structure.

organism: Macaca mulatta

source_name: testis

extract_protocol: Total RNA was extracted from five rhesus monkey tissues using the Trizol method and analyzed by an Agilent 2100 bio-analyzer (Agilent Technologies). Poly (A)-positive RNA was purified with the Dynabeads mRNA purification kit (Invitrogen) from 5μg of total RNA with high quality (RNA integrity number >7.5), following the manufacturer's instructions. A strand-specific RNA-Seq library preparation on the basis of the incorporation of deoxy-UTP was performed.

value: testis

tag: library type

value: strand-specific, dUTP protocal


title: control H3K4me3

description: A549,lung adenocarcinoma cells,H3K4me3

source_name: lung adenocarcinoma cells:A549, the histone was h3k4me3,without treated

value: Millipore

tag: chip antibody lot #


title: control H3K27me3

description: A549,lung adenocarcinoma cells,H3K27me3

source_name: lung adenocarcinoma cells:A549, the histone was h3k27me3,without treated


title: rhesus skeletal muscle

data_processing:
muscle.bam; genome build: rheMac2
muscle.bed; genome build: rheMac2
raw reads were aligned by Tophat v1.2.0, detailed parameters can be in header information of *.bam file. *.bam files and *.bed filed were used for the analysis of transcript expression and transcript structure.

source_name: skeletal muscle

value: skeletal muscle


title: rhesus prefrontal cortex

data_processing:
brain.bam; genome build: rheMac2
brain.bed; genome build: rheMac2
raw reads were aligned by Tophat v1.2.0, detailed parameters can be in header information of *.bam file. *.bam files and *.bed filed were used for the analysis of transcript expression and transcript structure.

source_name: prefrontal cortex

value: prefrontal cortex


title: rhesus adipose

data_processing:
adipose.bam; genome build: rheMac2
adipose.bed; genome build: rheMac2
raw reads were aligned by Tophat v1.2.0, detailed parameters can be in header information of *.bam file. *.bam files and *.bed filed were used for the analysis of transcript expression and transcript structure.

source_name: adipose

value: adipose


title: ZGR3 RNA-seq

city: Hangzhou

first: Daoqiong

last: Zheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Institute of Microbiology

institute: College of Life Sciences, Zhejiang University

data_processing:
After removing reads containing sequencing adapters and reads of low quality (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read), the clear reads were aligned to the S. cerevisiae S288c genes (ftp://ftp.ncbi.nih.gov/genomes/Fungi/Saccharomyces_cerevisiae_uid128) and genes using SOAPAligner.Mismatches no more than 2 bases were allowed in the alignment.
Genome_build: sacCer2
Supplementary_files_format_and_content: rpkm

organism: Saccharomyces cerevisiae

source_name: Yeast S. cerevisiae strain

growth_protocol: Yeast cells were cultured in 25mL YPD medium (10g/L yeast extract, 20g/L peptone, and 20g/L glucose) with an initial OD600 of 0.05.

extract_protocol: The total RNA of every sample was extracted using hot phenol method and then treated with RNase-free DNase I (TaKaRa) for 30 min according to the manufacturer’s protocols. The concentration and integrity of total RNA was checked using Agilent Technologies 2100 Bioanalyzer. The poly (A) containing mRNA molecules were then puriﬁed and the cDNA libraries were prepared according to the manufacturer’s instructions (Illumina).

treatment_protocol: mRNA is extrated when yeast cells enter the early-stationary phase.

value: ZGR3, A mutant of ZTW1

tag: application

value: Bioethanol strain

tag: genetic background


title: PPARγ_eWAT_ChIPSeq

source_name: eWAT-derived adipocytes


title: Tup1 YMW97 052410

city: Houston

first: kaifu

last: chen

address: 1 Baylor plaza, suite 450A

institute: Baylor College of Medicine

data_processing:
Reads are mapped to genome using ELAND. Reads that are uniquely mapped and have no more than 2 mismatches are selected for future analysis. DANPOS is used to calculate nucleosome occupancy from raw reads do following analysis.
Genome_build: sacCer1
Supplementary_files_format_and_content: .wig':nucleosome occupancy data. '.bed':uniquely mapped high quality reads.

growth_protocol: cells were grown to a final OD600nm of 0.8 in 200 mL of YEP containing 2% Glucose

extract_protocol: standard Illumina protocol

tag: genotype/variation

value: TUP1 knock out


title: Ssn6 YMW147 052410

value: Ssn6 knockout


title: Ssn6 YMW131 122909


title: ZTW1 RNA-seq

value: ZTW1, a Wild type strain


title: Tup1 YMW97 012210


title: Ssn6 YMW130 052410


title: Wild-type YMW5 012210 1

source_name: Wild-type YMW5 012210 1

value: wild type


title: Wild-type YMW5 092109

source_name: Wild-type YMW5 092109


title: rhesus liver

data_processing:
liver.bam; genome build: rheMac2
liver.bed; genome build: rheMac2
raw reads were aligned by Tophat v1.2.0, detailed parameters can be in header information of *.bam file. *.bam files and *.bed filed were used for the analysis of transcript expression and transcript structure.

source_name: liver

value: liver


title: Tup1 YMW97 092109


title: pro-B, Input EGS

status: Public on Oct 09 2012

city: La Jolla

first: Christopher

last: Benner

state: California

address: 9500 Gilman Dr. MC 0640

department: Medicine

institute: University of California, San Diego (UCSD)

data_processing:
For ChIP-Seq and GRO-Seq samples (single end reads), reads were aligned to the mm9 genome using bowtie (v0.12.7), keeping only reads that mapped best to a single, unique location.  Aligned read files were analyzed with HOMER (http://biowhat.ucsd.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, and perform other analyses in the study.
For Hi-C samples (paired end reads), read ends were aligned separately to the mm9 genome using bowtie (v0.12.7), only keeping read pairs if both ends mapped best to unique locations.  Four additional filtering steps were applied to the mapped reads: 1) Duplicate read pairs aligning to the exact same positions were removed (possible PCR amplification artifacts). 2) Reads aligning within 2x the library size (estimated library insert size = 400) were removed (representing genomic background/religation events).  3) Read pairs where neither read was within 500 bp of a HindIII site were removed. (background ligation events) 4) Read pairs aligning to adjacent restriction enzyme sites representing circularization of a HindIII fragment were removed.  Reads passing these filters are included in the Hi-C summary files.  Read alignment filtering and other Hi-C processing including normalization was performed using HOMER (http://biowhat.ucsd.edu/homer/).  Principle component analysis of normalized Hi-C interaction frequency matrices was performed using HOMER and R (www.r-project.org).  Results for the first principle component are included as BEDGRAPH files.  Positive principle component values correspond to regions that are generally transcriptionally active.
Genome_build: mm9
Supplementary_files_format_and_content: Processed files include BED files (ChIP-Seq peak positions), rpkm text files (GRO-Seq expression data), BEDGRAPH (principle component values along the genome for Hi-C), and Hi-C summary files (raw filtered read pairs from Hi-C data, columns: readName, chr1, 5' position1, strand1, chr2, 5' position2,strand2 [positions are 1-index based]).  All genomic coordinates are relative to mm9 (NCBI 37) mouse assembly.

source_name: progenitor B

growth_protocol: Tcf(E2A)-deficient multipoint progenitors were derived from E2A-deficient fetal liver and grown in the presence of IL7, SCF and FLT3L on sub-confluent S17 stromal cells.  B220 MACS enriched Rag1-deficient bone marrow cells were grown in Opti-MEM 10% FCS/ 2% PSG/ 50 μM β-mercaptoethanol in the presence of IL7 and SCF for 7 days.

extract_protocol:
ChIP-seq: Lysates were clarified from sonicated cells and protein-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (minus exo) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, ChIP DNA was PCR-amplified with Illumina primers with the respective indexes for 18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size- selected from a 8% polyacrylamide gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on a Genome Analyzer II (Illumina) or HiSeq 2000 (Illumina) following the manufacturer's protocols.
GRO-seq: GRO-Seq was performed as described (Core, L.J., Waterfall, J.J., and Lis, J.T., Science 322, 1845-1848 (2008)) with minor modifications. Briefly, nuclei from 10 million cells isolated by hypotonic lysis, and RNA polymerases were run-on for 5 minutes at 30°C in the presence of sarkosyl, BrUTP, ATP, GTP and limiting concentrations of CTP. Total RNA was purified with Trizol/isopropanol precipitiation, DNAse-treated (TURBO-DNase, Ambion), fragmented with fragmentation buffer (Ambion), and re-buffered by size exclusion chromatography. RNA fragments were 3' dephosphorylated with polynucleotide kinase (Enzymatics), and BrUTP-labeled run-on RNA was immunopurified with anti-BrdUTP-coated agarose beads, washed, eluted and EtOH-precipitated. Run-on RNA was then de-capped with tobacco acid pyrophosphatase (Epicentre), 5' phosphorylated with polynucleotide kinase (Enzymatics) and purified with Trizol LS/isopropanol precipitiation. Sequencing libraries were prepared by ligating a single-stranded, 3'-blocked, 5'-adenylated 3’ oligonucleotide with mutant (K227Q) truncated RNA ligase 2 (NEB) to the 3' end of the RNA fragments, followed by annealing a reverse transcription primer complementary to the 3' adapter to suppress adapter dimer formation, and ligating a hybrid 5' DNA-RNA oligonucleotide using RNA ligase I and then reverse-transcribing with SuperScript III reverse transcriptase (Invitrogen). The cDNA was purified with AMPure XL beads and PCR-amplified with primers bearing primer landing sites compatible with Illumina indexed sequencing. The library was size-selected on a PAGE gel to 60-110 bp insert size and sequenced on a HiSeq 2000 (Illumina).
Hi-C: The Hi-C experiment was performed similarly as described (Lieberman-Aiden, E., et al., Science 326, 289-293 (2009)). Libraries were subjected to paired-end sequencing on a HiSeq 2000 (Illumina).

tag: cell type

value: Rag1 deficient pro-B

tag: genotype


title: pro-B, Hi-C FA


title: pro-B, c-Myc ChIP seq

value: c-Myc (sc764x, Santa Cruz), lot# H0107

value: Santa Cruz


title: pre-proB, Hi-C EGS

source_name: multipotent progenitor

value: Tcf3(E2A) deficient pre-pro-B


title: pro-B, GRO seq


title: pro-B, p300 ChIP seq

value: p300 (sc-585x, Santa Cruz), lot# H2610


title: H83M2 Female (HMF3)

city: Columbia

first: Lin

last: Sun

state: MO

address: 311 Tucker Hall

department: Biological Sciences

institute: University of Missouri

description:
H83M2 Female (HMF)
This sample is one of three biological replicates (HMF1, HMF2, HMF3)

data_processing:
We used TopHat to map the RNA-Seq reads of each replicate of each sample to the Drosophila melanogaster genome (dm3) in the UCSC genome browser  in conjunction with the RefSeq genome reference annotation (RefSeq Assembly ID: GCF_000001215.2).
The threshold of mismatch was set to 2. Overall, ~80% of reads of each replicate were mapped to the genome
The reads that were mapped to a unique location on the genome were used to calculate the RNA counts of the genes. We used both our in-house tool (MULTICOM) and a public tool (HTseq)to calculate read counts of the genes in a replicate according to the genome mapping outputs and the RefSeq genome reference annotation.
The counts of the genes in a replicate calculated by MULTICOM or HTseq were normalized by dividing them by the total number of uniquely mapped reads in the replicate
Genome_build: Release 5
Supplementary_files_format_and_content: .txt files with aligned reads and normalized reads for each genes

source_name: adult flies

growth_protocol: The ectopically expressed MSL2 females were obtained using a P-element msl2 construct with a mini-white transformation marker, [(w+) H83M2-6I] (Kelley et al., 1995). The global expression pattern of these females (y w; (w+) H83M2-6I/+; +/+), normal females (y w; +/+; TM3/+) and males (y w; +/+; TM3/+) were obtained by mRNA-sequencing and analyzed by comparing the ratio distributions to each other

extract_protocol:
Total RNA was isolated using TRIZOL Reagent (Invitrogen) and  High-throughput sequencing services were performed at the University of Missouri DNA Core Facility
Libraries were constructed following the manufacturer’s protocol with reagents supplied in Illumina’s TruSeq RNA sample preparation kit (#RS-930-2001).

value: ectopically expressed MSL2 protein

value: female

tag: biological replicate


title: pre-pro-B, Input


title: pre-pro-B, GRO seq


title: pro-B, Input FA


title: pro-B, H3K36me3 ChIP seq

value: Abcam


title: Wild-type YMW5 012210 2

source_name: Wild-type YMW5 012210 2


title: pro-B, Rad21 ChIP seq


title: pro-B, CTCF ChIP seq

value: CTCF (07-729, Millipore), lot# DAM1772428

value: Millipore


title: pre-pro-B, Rad21 ChIP seq


title: Germinating cotyledon

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

description: Williams (ii/ii yellow seed) germinating cotyledon

data_processing: Adapter trimming was performed using the first occurrences of substring TCG as the unique identifier for the beginning of the adapter (TCGTATGCCGTCTTCTGCTTG). The sizes of the small RNAs after adapter trimming ranged from 16 - 35 nt.

organism: Glycine max

source_name: Germinating cotyledon

growth_protocol: Plants were grown in the greenhouse and tissues harvested from at least four plants of each line. Leaves and stems were harvested from two to four-week-old plants. Stem samples consisted of one centimeter size fragments immediately underneath the base of the unifoliate leaves. The leaf sample was made of first trifoliate sampled over the course of one week. Germinating cotyledons were harvested from two weeks old seedling. The very young whole seeds were collected 12-14 days after flowering.

extract_protocol: Gel purification, cloning and sequencing of small RNAs from the multiple tissue samples was performed at Illumina Inc. (San Diego, CA) using the SBS (sequencing by synthesis) technology.

treatment_protocol: Optimal greenhouse growth conditions

tag: cultivar

value: Williams

value: homozygous for the dominant ii allele that specifies yellow seed coat

tag: tissue and developemental stage

value: 7 day seedling


title: Leaf 1 month plants

source_name: Leaf 1 month plants

value: Leaf 1 month plants


title: pre-pro-B, CTCF ChIP seq


title: pro-B, H3K4me2 ChIP seq


title: pre-pro-B, H3K36me3 ChIP seq


title: BCBL-1 miRNA biological replicate 2

status: Public on Oct 05 2012

city: Gainesville

first: Rolf

last: Renne

address: 2033 Mowry Road

institute: University of Florida

data_processing:
Basecalls performed using CASAVA version 1.4
miRNA library analysis was performed with miRDeep2.0.0.5

source_name: B cell lymphoma

growth_protocol: BCBL-1 and BC-3 cells were grown in RPMI medium (Cellgro) supplemented with 10% FBS to a maximum density of 0.8x10e6 cells/ml

extract_protocol: cells were lysed on ice for 15 min; lysates were cleared by high-speed centrifugation at 4 degree, Ago-miRNA-mRNA complexes extracted by Ago-IP, RNA extracted and libraries for Illumina sequencing were constructed according to Chi et al. Nature 2009 Jul 23;460(7254):479-86

treatment_protocol: KSHV-infected cells were pelleted, resuspended in ice cold cell culture PBS and crosslinked on ice 1x at 400 mJ/cm2 and 1x at 200 mJ/cm2; cells were pelleted again and either stored at -80 degree or lysed for Ago-IP

tag: cell line

tag: infecting virus

value: KSHV

tag: ip antibody

value: anti-Argonaute 2A8


title: pro-B, H3K27me3 ChIP seq

tag: chip antibody

tag: chip antibody manufacturer


title: BC-3 miRNA biological replicate 3

extract_protocol: cell were lysed on ice for 15 min; lysates were cleared by high-speed centrifugation at 4 degree, Ago-miRNA-mRNA complexes extracted by Ago-IP, RNA extracted and libraries for Illumina sequencing were constructed according to Chi et al. Nature 2009 Jul 23;460(7254):479-86


title: BC-3 mRNA

description: This sample included 3 biological replicates.

data_processing:
Basecalls performed using CASAVA version 1.4
mRNA libraries: fastq files were uploaded to CLIPZ database and aligned to hg19 (www.clipz.unibas.ch)
sequence read clusters were called using the CLIPZ super cluster function
Genome_build: hg19
Supplementary_files_format_and_content: bed files (tab-delimited txt) with coordinates of read clusters identified by CLIPZ in 2 of 3 biological replicates (2of3-SCL) or in all 3 biological replicates (3of3-SCL)


title: BCBL-1 miRNA biological replicate 1


title: BC-3 miRNA biological replicate 2


title: BCBL-1 mRNA

description: This sample included 3 biological replicates. One biological replicate has 2 technical replicates


title: normal UUD_UnMet

city: Rotterdam

first: Sjaak

last: Philipsen

address: Dr. Molewaterplein 50

department: Cell Biology

country: Netherlands

institute: ErasmusMC

description: MethylCap

data_processing:
Basecalls performed using bustard 1.4.0 or RTA.
HTS reads were aligned to the Human reference genome (NCBI36.3) using eland_extended
Datafiles are the s_export.txt eland output files
MEDIPS package
For detailed data processing check (Carvalho, RH et al. Epigenetics Chromatin. 2012 Jun 22;5(1):9.)
Genome_build: NCBI36/hg18 (March 2006)
Supplementary_files_format_and_content: bedgraph

source_name: Universal Unmethylated DNA, Chemicon, Millipore

extract_protocol:
DNA was extracted from ressected lung using in house protocol. DNA were sheared and methylated DNA captured using MEDIP, Methylminer (Invitrogen) according to manufactor's protocol
Captured methylated DNA

tag: histology

value: Artificially fully unmethylated

value: normal

tag: sample type


title: pre-pro-B, H3K4me2 ChIP seq

tag: chip antibody catalog #


title: normal UUD_Met

description: MethylCap

value: Artificially fully methylated

value: Universal Unmethylated DNA, Chemicon, Millipore


title: MRC-5 MRC5_UnMet

description: MethylCap

source_name: MRC-5 cell line


title: MRC-5 MRC5

description: The 2257N_02 and 2258T_02 samples were not processed, since their sequence data failed to pass our quality control, therefore their processed files are not available. The MRC5 samples was simply not used for further normalization, and therefore also not processed.

value: cell line


title: MRC-5 MRC5-Met

description: MethylCap


title: adenocarcinoma 2258T_02

source_name: lung ressection

value: nsclc

value: adenocarcinoma

tag: tissue

value: adenocarcinoma tumor


title: normal TB0022he_02

description: MethylCap

value: normal lung


title: normal 2261N_02

description: MethylCap


title: pro-B, Hi-C EGS

value: Rag1 deficient pro-B


title: squamous-cell carcinoma 2262T_02

description: MethylCap

value: squamous-cell carcinoma

value: squamous-cell carcinoma tumor


title: normal 2257N_02


title: normal 2235N_02

description: MethylCap


title: normal 2255N_02

description: MethylCap


title: normal 2213N_02

description: MethylCap


title: squamous-cell carcinoma 2236T_02

description: MethylCap


title: adenocarcinoma 2256T_02

description: MethylCap


title: adenocarcinoma 2246T_02

description: MethylCap


title: squamous-cell carcinoma 2214T_02

description: MethylCap


title: normal 2245N_02

description: MethylCap


title: C. remanei adult females+males

data_processing:
Raw datasets are fastq files generated using Illumina software.
Small RNA sequences were parsed using a custom Python program, then mapped to corresponding nematode reference genomes (Wormbase release WS230) allowing 0 mismatch using Bowtie software.
Genome_build: WS230
Supplementary_files_format_and_content: tab-delimited text files include Sequence and read count

source_name: whole animal

tag: strain

tag: developmental stage

value: young adult

value: whole organism

tag: gender

value: pooled male and female


title: BC-3 miRNA biological replicate 1

value: KSHV


title: normal TB0022he_01

description: MethylCap

tag: cell type


title: large cell carcinoma TB0022tu_01

description: MethylCap

value: large cell carcinoma

value: large cell carcinoma tumor


title: adenocarcinoma 2256T_01

description: MethylCap


title: normal 2257N_01

description: MethylCap

value: normal


title: adenocarcinoma 2258T_01

description: MethylCap


title: normal 2255N_01

description: MethylCap


title: squamous-cell carcinoma 2262T_01

description: MethylCap


title: normal 2261N_01

description: MethylCap


title: normal 2245N_01

description: MethylCap


title: squamous-cell carcinoma 2236T_01

description: MethylCap


title: adenocarcinoma 2246T_01

description: MethylCap


title: normal 2213N_01

description: MethylCap


title: ML-DmBG3-c2 WT Late S-phase Replicate 2 extraction8_seq1 aliquote 1

status: Public on Oct 04 2012

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

data_processing: Illumina_sequencing:DM:1 protocol. Load sample onto flow cell at a (usually 2-8 pM, variable) concentration and run on an Illumina HiSeq 2000 for single-end sequencing for 36 or 76 nt. Image data is then deconvoluted using the most current versions of Firecrest, Bustard, and Gerald (or equivalents).  Processed data are obtained using following parameters: read length is 50 Bowtie alignment:DM:1 protocol. For paired end CNV:Using the default setting, Bowtie2 was used to align paired sequenced reads to the reference genome. Single end HiSeq RepliSeq:Bowtie was used to align sequenced reads to the reference genome, with the following parameters:--phred33-quals -p 6 -n 2 -l 20 -m 1 -k 1 -S -y --best --strata  Processed data are obtained using following parameters: genome version is 5.1 Illumina sequencing WIG Generation RPKM from BAM:DM:1 protocol. For Repliseq experiments, a bin size of 10000 bp stepping every 2500 bp was used.

growth_protocol: The general growth protocol for growing Drosophila cell lines in culture.

extract_protocol:
DNA isolation from Drosophila cell lines. RNAse-treated cellular extract is treated with ethanol in order to precipitate DNA.
Cells are pulse labeled with 50ug/ml BrdU for one hour, and washed with 1x PBS.
FACS Protocol.1. Spin cells down and resuspend in 300µl of PBS. (For large pellets increase this volume and increase the EtOH volume proportionally)2. Fix by adding 5ml of 70% EtOH Dropwise while vortexing gently, incubate at -20ºc for at least 30 minutes.3. Spin, remove EtOH and resuspend in 5ml PBS. Allow cells to rehydrate at 4ºc for at least an hour.4. Spin and resuspend the cells in 4ml of PBS with 10µg/ml RNaseA and 10µg/ml PI. Incubate at RT for at least 30min up to several hours (alternatively incubate for 10min at 37ºc)Cells were sorted into early mid and late S-phase fractions using a FACS Vantage SE (BD Biosciences) equipped with the DiVa acquisition system.
An immunoprecipitation procedure in which anti-BrdU is used to enrich for BrdU labeled DNA.
Generation of a genomic library suitable for Illumina sequencing.Generation of a genomic library suitable for Illumina sequencing. The procedure starts with random shearing of genomic DNA with sonication followed by Illumina-developed sample preparation protocol.

value: CNS-derived cell-line

value: third instar larval stage

tag: genotype

value: y v f mal

tag: Sex

value: Unknown


title: LA1-55n DNMT3B7 54

city: Chicago

first: Kelly

middle: R

last: Ostler

address: 900 E. 57th Street

institute: The University of Chicago

data_processing:
Reads were aligned to the human genome (Human Feb. 2009 (GRCh37/hg19) assembly) using bwa, then reads mapping perfectly to a unique location were retained. Wig files were generated from the retained reads using macs and default settings (--mfold 10).
Genome Build:
LA1-55n_DNMT3B7_54.up_MACS_wiggle.tar: Human Feb. 2009 (GRCh37/hg19) assembly

source_name: Neuroblastoma cell line (LA1-55n)

growth_protocol: Expression of DNMT3B7 or control LA1-55n cells were induced by removing Dox and the cells were allowed to grow for 21 days.  Cells were harvested and counted every 2-3 days and replated (typically 1-1.5 × 106 cells into a T75 flask)

extract_protocol: Total RNAs were isolated using Trizol Reagent (Invitrogen).  RNA integrity was validated by Agilent BioAnalyzer and all samples had an RNA integrity number >9. Libraries were generated following the Illumina protocol for Preparing Samples for Sequencing of mRNA.  Ten µg of total RNA was used to build libraries for single-read sequencing on the Illumina GAII. In brief, mRNA was isolated using polyA selection, fragmented, and randomly primed for reverse transcription followed by second-strand synthesis to create double-stranded cDNA fragments. Ends were repaired with a combination of fill-in reactions and exonuclease activity to produce blunt ends. An 'A'- base was added to the blunt ends followed by ligation to Illumina sequencing adapters. cDNA fragments of 300-500 bp in size were gel purified after the adaptor ligation step. PCR amplified cDNA libraries were quantified on an Agilent 2100 Bioanalyzer and diluted to nine pM for cluster generation and sequencing. Single end sequencing was performed for 36-cycles using Single Read Cluster Generation Kit V4 (Cat# GD-103-4001) and Sequencing Kits (Cat# FC-104-4002). Sequence reads from the RNA-sequencing were aligned to genomic sequence.

tag: expressed genes


title: LA1-55n DNMT3B7 16

data_processing:
Reads were aligned to the human genome (Human Feb. 2009 (GRCh37/hg19) assembly) using bwa, then reads mapping perfectly to a unique location were retained. Wig files were generated from the retained reads using macs and default settings (--mfold 10).
Genome Build:
LA1-55n_DNMT3B7_16.up_MACS_wiggle.tar: Human Feb. 2009 (GRCh37/hg19) assembly


title: squamous-cell carcinoma 2214T_01

description: MethylCap

value: nsclc


title: ML-DmBG3-c2 WT LateSphase Replicate 1 extraction4_seq1 aliquote 1


title: ML-DmBG3-c2 WT Mid-Early S-phase_Replicate 2 extraction6_seq1 aliquote 1


title: LA1-55n Vector Control

data_processing:
Reads were aligned to the human genome (Human Feb. 2009 (GRCh37/hg19) assembly) using bwa, then reads mapping perfectly to a unique location were retained. Wig files were generated from the retained reads using macs and default settings (--mfold 10).
Genome Build:
LA1-55n_Vector.up_MACS_wiggle.tar: Human Feb. 2009 (GRCh37/hg19) assembly

value: GFP


title: ML-DmBG3-c2 WT Mid-Early S-phase Replicate 1 extraction2_seq1 aliquote 1


title: large cell carcinoma TB0022tu_02

description: MethylCap


title: ML-DmBG3-c2 WT Early S-phase Replicate 2 extraction5_seq1 aliquote 1


title: S2-DRSC WT Late S-phase Replicate 2 extraction8_seq1 aliquote 1

value: embryo-derived cell-line

value: late embryonic stage

value: Male


title: S2-DRSC WT Mid-Early S-phase Replicate 2 extraction6_seq1 aliquote 1


title: ML-DmBG3-c2 WT Early S-phase Replicate 1 extraction1_seq1 aliquote 1


title: S2-DRSC WT Early S-phase Replicate 2 extraction5_seq1 aliquote 1


title: ML-DmBG3-c2  WT Mid-Late S-phase Replicate 2 extraction7_seq1 aliquote 1


title: S2-DRSC WT Late S-phase Replicate 1 extraction4_seq1 aliquote 1


title: normal 2235N_01

description: MethylCap

value: normal lung


title: KC167 WT Late S-phase Replicate 2 extraction8_seq1 aliquote 1

value: se/e

value: Female


title: KC167 WT Early S-phase Replicate 2 extraction5_seq1 aliquote 1


title: S2-DRSC WT Mid-Early S-phase Replicate 1 extraction2_seq1 aliquote 1


title: KC167 WT Mid-Early S-phase Replicate 2 extraction6_seq1 aliquote 1


title: KC167 WT Mid-Late S-phase Replicate 2 extraction7_seq1 aliquote 1


title: S2-DRSC WT Early S-phase Replicate 1 extraction1_seq1 aliquote 1


title: KC167 WT Late S-phase Replicate 1 extraction4_seq1 aliquote 1


title: ML-DmBG3-c2 WT Mid-Late S-phase Replicate 1 extraction3_seq1 aliquote 1


title: S2-DRSC WT Mid-Late S-phase Replicate 2 extraction7_seq1 aliquote 1


title: KC167 WT Mid-Early S-phase Replicate 1 extraction2_seq1 aliquote 1


title: Cl8 PE CNV Replicate 2 extraction2_seq1 aliquote 1

data_processing: Illumina HS Paired End:DM:1 protocol. Load sample onto flow cell at a (usually ~24 pM, variable) concentration and run on an HiSeq2000 with the paired-end module. Image data is then deconvoluted using the most current versions of Firecrest, Bustard, and Gerald.  Processed data are obtained using following parameters: read length is 50   Bowtie alignment:DM:1 protocol. For paired end CNV:Using the default setting, Bowtie2 was used to align paired sequenced reads to the reference genome. Single end HiSeq RepliSeq:Bowtie was used to align sequenced reads to the reference genome, with the following parameters:--phred33-quals -p 6 -n 2 -l 20 -m 1 -k 1 -S -y --best --strata  Processed data are obtained using following parameters: genome version is 5.1   CNV Paired End Analysis:DM:1 protocol. Read pairs deemed by Bowtie2 to be concordantly aligned, containing those that contain a positive insert length, were used to determine the genomic coverage at each base. The coverage between replicates were summed, and  RPKM was then determined in 1000 bp non-overlapping windows.

extract_protocol:
DNA isolation from Drosophila cell lines. RNAse-treated cellular extract is treated with ethanol in order to precipitate DNA.
Generation of a genomic library suitable for Illumina sequencing.Generation of a genomic library suitable for Illumina sequencing. The procedure starts with random shearing of genomic DNA with sonication followed by Illumina-developed sample preparation protocol.

value: dorsal mesothoracic disc


title: S2-DRSC PE CNV Replicate 2 extraction2_seq1 aliquote 1


title: KC167 WT Early S-phase Replicate 1 extraction1_seq1 aliquote 1


title: S2-DRSC WT Mid-Late S-phase Replicate 1 extraction3_seq1 aliquote 1


title: S2-DRSC PE CNV Replicate 1 extraction1_seq1 aliquote 1


title: KC167 PE CNV Replicate 1 extraction1_seq1 aliquote 1


title: KC167 WT Mid-Late S-phase Replicate 1 extraction3_seq1 aliquote 1


title: Genomic DNA of the cell line K562_IHK016017_SOLiDv2

city: Cologne

first: Axel

last: HILLMER

address: Kerpener Str. 62

department: Institute of Pathology

country: Germany

institute: University of Cologne

description:
genomic structural variations
genomic DNA hydrosheared in 21 kb fragments (std dev: 2709 bp below median; 3681 above median), 2x25bp paired-end (mate pair) sequences, F3 and R3 tag sequence, IHK016

data_processing: Raw data provided. For the project, sequence tags were mapped to the human reference sequence (NCBI Build 36) allowing 2 color code mismatches and paired using SOLiD System Analysis Pipeline Tool, Corona Lite (Applied Biosystems). If sequence tags had multiple mapping locations and one of them was located in the expected distance and orientation to its mate, this location was chosen by a process termed ‘rescue’. Discordant paired-end tags (PETs) were defined and clustered to call structural variations as described by Hillmer et al.: Comprehensive Long Span Paired-End-Tag Mapping Reveals Characteristic Patterns of Structural Variations in Epithelial Cancer Genomes

source_name: Pleural effusion of a 53-year-old woman with chronic myeloid leukemia (CML) in blast crisis

growth_protocol: standard growth conditions for cell lines

extract_protocol: Genomic DNA was hydrosheared, EcoP15I recognition sites were methylated and EcoP15I CAP adaptors were ligated to the ends of DNA fragments. The methylated DNA constructs were separated on agarose gel and 10 Kb sized fragments were selected for ligation resulting in circularized products where 5’ and 3’ ends of 10 Kb fragments were connected by an internal biotinylated adaptor with two flanking non-methylated EcoP15I CAP adaptors. Constructs were digested by methylation sensitive EcoP15I to release 5’ and 3’ paired-end tag (PET) constructs. Sequencing adaptors were ligated to the PET constructs, which were then amplified by PCR and sequenced by the Applied Biosystems SOLiD system.

treatment_protocol: no treatment

tag: tumor type

value: chronic myeloid leukemia

value: myeloid blast cells


title: KC167 PE CNV Replicate 2 extraction2_seq1 aliquote 1

tag: cell line


title: Hi-C library BR

city: Atlanta

first: Chun-hui

last: Hou

address: 1510 Clifton Rd NE

institute: Emory University

description: ligated DNA with biotin labeling

data_processing:
base-calling was carried out by HudsonAlpha Genomic Service Center
Paired reads were aligned to the Drosophila reference genome (Dm3) using Bowtie 0.12.7 (Langmead et al., 2009)  and filtered to remove any pair with one or two ends aligned to multiple locations.
GC content and fragment length effects were normalized as described before (Yaffe and Tanay, 2011)
Genome_build: Dm3
Supplementary_files_format_and_content: txt files for the aligned paired reads from two technical replicates, one biological replicate. 4 columns in each file with the first two columns corresponding to chromosomes and genomic coordinates of the first reads, and the last two columns corresponding to chromosomes and genomic coordicates of the second reads respectively.

source_name: Cultured fruit fly cells

growth_protocol: Fruit fly embryonic Kc167 cells were grown to confluence in CCM3 serum-free insect medium (HyClone SH30065.01) at 25oC and collected for Hi-C experiments.

extract_protocol: Hi-C experiments were carried out as described (Lieberman-Aiden et al., 2009) with some modifications. Cells were lysed then the nuclei were treated with 0.1% SDS at 65 degree for 10mins and the SDS was quenched by adding Triton X-100 to final 1% concentration. Nuclei was digested in 1XNEB (New England Biolaboratory) with 400U of HindIII. Digested DNA was blunted with dATP, dGTP, dTTP and biotin labeled dCTP.  DNA wan then ligated and puried. biotin-labled ligated DNA was purified with streptavidin beads. Illumina paired-end adaptor linkers were ligated to DNA pulled-down and amplified and size selected for sequencing.

treatment_protocol: One hundred million Kc167 cells were suspended in 40ml of CM3 medium, fixed by adding 37% formaldehyde to a final concentration of 1%, and incubated at room temperature for 10 min. The reaction was stopped by adding 1/10 volumes of 1.25 M glycine solution and incubated for 5 min before centrifugation at 3000 rpm for 10 min.

tag: retriction enzyme

value: HindIII

tag: replicate

value: biological 2


title: Cl8 PE CNV Replicate 1 extraction1_seq1 aliquote 1


title: Genomic DNA of the cell line MCF-7_IHM072

description:
genomic structural variations
genomic DNA hydrosheared in 1.3 kb fragments (std dev: 59.2 bp below median; 63.7 above median), 2x25bp paired-end (mate pair) sequences, F3 and R3 tag sequence, IHM072

source_name: Cell line was established from a 69-year-old Caucasian woman (after radio- and hormone therapy)

value: metastatic mammary carcinoma, pleural effusion

value: mammary gland; breast


title: Genomic DNA of the cell line K562_IHK002004_SOLiDv2

description:
genomic structural variations
genomic DNA hydrosheared in 1.1 kb fragments (std dev: 76.3 bp below median; 71.1 above median), 2x36bp paired-end (mate pair) sequences, F3 and R3 tag sequence, IHK004
Processed data file generated from Samples K562_IHK002004_GAII and K562_IHK002004_SOLiDv2:
IHK002004_880_1320.dist.covsmooth.gff [hg18, NCBI build 36; clusters, gff]
Linked as supplementary file on Series record.


title: Hi-C library TR1

description: ligated DNA with biotin labeling

value: biological 1, technical 1


title: liver rep12

city: London

first: Reiner

last: Schulz

address: 8th floor Guy's Tower

department: Medical & Molecular Genetics

institute: King's College London

description:
genomic DNA after MeDIP
pool of three livers

data_processing: Alignments: reads were aligned to mm9 using novoalign except for the sperm samples that were aligned using BWA. Details about aligner version and parameters used are stored in the headers of the BAM files. The stated values for mean insert size and standard deviation are derived from the paired-end alignments using Picard. In the case of the liver samples, which were single-end sequenced, mean and standard deviation of the inserts were estimated from Bioanalyzer measurements after size selection (10 size selections were carried out and pooled).

extract_protocol: 200 ng of genomic DNA was sonicated to an average size of 150bp. The  sample was then purified using a Zymo DNA Clean and Concentrator-5 kit  (according to the supplier’s instructions), and finally eluted in 20    μl of water (pre-heated to 50°C). The DNA was then end repaired: the    following reaction (total vol = 25 μl) was prepared in 0.2 ml PCR    tubes:    • 200 ng of sonicated DNA (+ water if reqd so that the total vol = 18    μl)    • 2.5 μl 10 X T4 DNA ligase buffer with 10mM ATP (NEB)    • 1 μl of 10 µM dNTP mix    • 1.25 μl of T4 DNA polymerase (from 3U/μl stock, NEB)    • 1.25 μl of 1/5 dilution (in water) of Klenow DNA polymerase (from    5U/μl stock, NEB)    • 1.25 μl of T4 Polynucleotide Kinase (from 10U/μl stock, NEB)    Samples were gently mixed and incubate in a PCR machine for 30 minutes    at 20°C, and then purified using a Zymo DNA Clean and Concentrator-5    kit (using 100 μl of binding buffer), and eluted in 13.5 μl of    Elution buffer. The fragments were then A-tailed: the following    reaction (total vol = 20 μl) was prepared in 0.2 ml PCR tubes:    • DNA sample (13 μl)    • 2 μl NEB Buffer 2 (from 10X stock)    • 4 μl dATP (from 1 mM stock)    • 1 μl Klenow exo (3’ to 5’ exo-) (from 5U/μl stock)    The reaction was incubated for 30 minutes at 37°C in a PCR machine,    and then purified a using Zymo DNA Clean and Concentrator-5 kit (using    100 μl of binding buffer), eluting in 14.5 μl of elution buffer.    Illumina paired-end sequencing adaptors were ligated: the following    reaction (total vol = 20 μl) was performed in 1.5 ml eppendorf tubes:    • DNA sample (14 μl)    • 4 μl of 5 X DNA ligase buffer (NEB, USA)    • 1 μl of 1/10 dilution (in 1 X DNA ligase buffer) of standard    Illumina PE adapter oligo mix    • 1 μl NEB Quick ligase (NEB, USA)    The reaction was incubated for 15 minutes at room temperature, and    then purified using a Zymo DNA Clean and Concentrator-5 kit (using 100    μl of binding buffer), eluting in 25 μl of elution buffer (pre-heated    to 50°C). 1 μl of this was kept aside as input, and another 1 μl    analyzed on an Agilent Bioanalyzer to ensure ligation had occurred,    with no significant left over adaptor contamination. 100ng of this    ligated sample was transferred to a 1.5ml eppendorf tube and made up    to 24 µl with water. This was denatured at 100°C for 10 minutes and    immediately cooled on ice for 5 minutes. Then, 25 µl of chilled 2 X IP    buffer (20 mM Na-Phosphate pH 7.0, 280 mM NaCl, 0.1 % Triton X-100)    and 1 µl of 1/5 dilution (in 1 X IP buffer) of 5mC mAb was added, and    the sample incubated overnight at 4°C with slow rotation. The next    morning 1 µl of Dynabeads (Invitrogen,USA) were washed in 200 µl of 1    X IP buffer by capturing the beads with a magnetic rack (2 minutes).    The buffer was then removed and discarded, the MeDIP sample was added    to the Dynabeads, and then incubated for 6 hours at 4°C with slow    rotation. Then, 150 µl of 1 X IP was added to the sample, the beads    captured with a magnetic rack (for 2 minutes), supernatant discarded,    and the beads washed with 200 µl 1 X IP buffer 3 more times (each time    capturing the beads for 2 minutes). The beads were finally re-   suspended in 50 µl Proteinase K digestion buffer (50 mM Tris pH 8.0,    10 mM EDTA, 0.5 % SDS) containing 0.5 µl of Proteinase K (10 mg/ml    stock), and incubated for 1 hour at 55°C with rotation. The samples    were briefly spun down, and the beads captured with a magnetic rack (2    minutes), and the supernatant transferred to 700 µl of binding buffer    from the Zymo DNA Clean and Concentrator-5 kit and purified following    the manufacturer’s instructions, finally eluting in 35 μl of water    (pre-heated to 50°C). Then, the MeDIP and input samples were amplified    as described below:    • MeDIP sample (35 μl) or [1 μl input DNA + 34 μl water]    • 5 μl of 10X Platinum Pfx polymerase buffer (Invitrogen, USA).    • 2 μl of MgSO4 (from Platinum Pfx kit, Invitrogen, USA).    • 2 μl of 10 mM dNTP mix    • 0.8 μl of Platinum Pfx polymerase (Invitrogen, USA).    • 2.5 μl of Illumina PCR primer 1.1 (from 10 μM stock)    • 2.5 μl of Illumina PCR primer 2.1 (from 10 μM stock)    Cycling conditions:    a. 2 min/94°C s    b. 12 cycles of: 15 s/94°C, 30 s/65°C, 30 s/68°C    c. 5 min/68°C    d. Hold/10°C    PCR products were purified using the Qiagen PCR purification kit    (using 650 μl buffer PB), and finally eluted in 30 μl EB buffer.    MeDIP enrichment was checked by qPCR using the primers listed in    Rakyan et al., 2008. Finally, approximately half of the PCR sample was    run on a thin 3% Nusieve agarose gel, a band corresponding to 250 –    275 bp was excised and then purified using a Qiagen gel extraction kit    as per the manufacturer’s instructions except that the gel was    dissolved gel at room temp. for 10 minutes with vortexing. The sample  was finally eluted in 30 μl of buffer EB and checked on an Agilent  Bioanalyzer.

value: wild type

tag: age

value: mixed

value: liver

tag: mean insert/fragment size

tag: stddev insert/fragment size

value: genomic DNA after MeDIP


title: liver rep10

tag: sample type


title: Hi-C library TR2

description: ligated DNA with biotin labeling

value: biological 1, technical 2


title: mmuES_input_gDNA

first: Elizaveta

middle: V

last: Benevolenskaya

address: 900 S. Ashland Ave.

department: Biochemistry and Molecular Genetics

institute: University of Illinois at Chicago

description: input DNA

data_processing:
Alignment: Sequence reads were obtained using the Illumina Genome Analyzer Pipeline and reads were  mapped to the mouse (July, 2007) genomes (NCBI37/mm9) using BOWTIE aligner program (http://bowtie-bio.sourceforge.net/index.shtml) (Ref: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.) All reads mapping uniquely with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: Kdm5a f/f ES cells

growth_protocol: Wild-type (Kdm5a f/f) and Kdm5a-/- (Kdm5a KO) ES cells were maintained on irradiated mouse embryonic fibroblast (IEF) feeders in standard ES medium (DMEM, Dulbecco's Modified Eagle Medium, supplemented with 15% heat-inactivated fetal calf serum, 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acid, 1% of nucleoside mix (100X stock, Sigma), 1000U/ml recombinant leukemia inhibitory factor (LIF; Chemicon) and antibiotics). For ChIP assyas, the cells were seeded on gelatin-coated plates.

extract_protocol: ChIP and genomic library preparation was performed as described (Beshiri, M.L, A. Islam A, D.C. DeWaal, W.F. Richter, Love J, N. Lopez-Bigas, and E.V. Benevolenskaya. 2010. Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets. JoVE. 41. http://www.jove.com/index/details.stp?id=2101, doi: 10.3791/2101).  After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of ~320 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: embryonic stem cells

tag: genotype/variation

value: Wild-type (Kdm5a f/f)

tag: chip antibody


title: liver rep11

source_name: liver

tag: strain

tag: tissue


title: liver rep5


title: liver rep6


title: liver rep9


title: liver rep7


title: liver rep4


title: KDM5A_ChIPSeq_3

description: Chromatin IP against RBP2, negative control

source_name: Kdm5a KO ES cells

growth_protocol: Wild-type (Kdm5a f/f) and Kdm5a-/- (Kdm5a KO) ES cells were maintained on irradiated mouse embryonic fibroblast (IEF) feeders in standard ES medium (DMEM, Dulbecco's Modified Eagle's Medium, supplemented with 15% heat-inactivated fetal calf serum, 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acid, 1% of nucleoside mix (100X stock, Sigma), 1000U/ml recombinant leukemia inhibitory factor (LIF; Chemicon) and antibiotics). For ChIP assyas, the cells were seeded on gelatin-coated plates.

value: Kdm5a-/- (Kdm5a KO)

value: 1416 (Benevolenskaya et al.,Mol Cell 18, 623-635)


title: KDM5A_ChIPSeq_2

description: Chromatin IP against RBP2

growth_protocol: Wild-type (Kdm5a f/f) and Kdm5a-/- (Kdm5a KO) ES cells were maintained on irradiated mouse embryonic fibroblast (IEF) feeders in standard ES medium (DMEM, Dulbecco's Modified Eagle's Medium, supplemented with 15% heat-inactivated fetal calf serum, 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM non-essential amino acid, 1% of nucleoside mix (100X stock, Sigma), 1000U/ml recombinant leukemia inhibitory factor (LIF; Chemicon) and antibiotics. For ChIP assays, the cells were seeded on gelatin-coated plates.


title: KDM5A_ChIPSeq_1

description: Chromatin IP against KDM5A


title: liver rep3


title: Genomic DNA of the cell line HCT116_IHH021

description:
genomic structural variations
genomic DNA hydrosheared in 1.4 kb fragments (std dev: 230 bp below median; 304 above median), 2x25bp paired-end (mate pair) sequences, F3 and R3 tag sequence, library IHH021

source_name: Cell line was established from the primary colon carcinoma of an adult man

value: primary carcinoma

value: colon


title: liver rep8


title: liver rep2


title: sperm rep3

description: genomic DNA after MeDIP

source_name: sperm

value: 3 months

value: male

value: sperm


title: liver rep1


title: sperm rep2

description: genomic DNA after MeDIP


title: sperm rep1

description: genomic DNA after MeDIP


title: embryo dnmt3l-  rep1

description:
genomic DNA after MeDIP
pool of embryos

source_name: whole embryo

value: embryo


title: embryo dnmt3l-  rep2

description:
genomic DNA after MeDIP
pool of embryos


title: embryo wt  rep1

description:
genomic DNA after MeDIP
pool of embryos


title: embryo wt  rep2

description:
genomic DNA after MeDIP
pool of embryos


title: Parkinson's Disease PD 16

city: New York

first: Herve

last: RHINN

state: New York

institute: Columbia University

description: Sample 32

data_processing:
Illumina reads were converted to FASTQ Sanger format using FASTQ Groomer (Galaxy)
The first 27 bp at their 5’ends of the reads were trimmed using FASTQ Trimmer to remove the polyA and adapters sequences
The reads were mapped to human hg19 genome using Burrows-Wheeler Alignment tools  with Galaxy’s default settings allowing 4% of missing alignments.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files contain the quantification for each sample of the 5 3'UTR isoforms detected for alpha-synuclein

source_name: Brain cortex

extract_protocol: RNA was extracted from frozen brain tissue using miRNeasy kits (Qiagen) and quantified using a Nanodrop (Thermo). First-strand cDNA was synthesized from 1 μg of RNA per biological sample using SuperScript III (Invitrogen) following manufacturer’s instructions and using the pdT-FS oligonucleotide to prime the reverse transcription. Barcoded first-strand samples from different samples were then pooled and treated with RNase H (Invitrogen)  at 37°C for 20 minutes followed by 15 minutes at 75°C to degrade RNA template. First-stand cDNA was then purified using QIAquick PCR Purification kit (Qiagen) in a total volume of 30uL. Second-strand cDNA was synthesized from 25uL of first-strand cDNA template by adding 10 μl 10x buffer 2 (NEB), 5 μl 10 mM dNTPs, 20 U Klenow Fragment (3’ → 5’exo-; NEB), 10 μl of 100 μM tagged 2nd strand primer (R-SS oligonucleotide: 5’-TCCGATCTGANNNNNNN-3’  with N=A,C,T,G mix) and 46 μl water. The reaction mix was incubated at 37°C for 30 minutes, followed by 10 minutes at 75°C then cooled down at 4°C. Double-stranded cDNA was purified using PureLink PCR micro columns (Invitrogen) in a 30uL volume. Illumina-compatible libraries were then generated by PCR from 25uL of double-stranded cDNA template using Accuprime Pfx polymerase (Invitrogen) following manufacturer’s instruction with NNSR forward (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTCT-3’) and NNSR reverse (5’-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCTGA-3’) primers. Thermo-cycling conditions were 2 min at 94 °C followed by 2 cycles of 94 °C for 10 s, 40 °C for 2 min, 68 °C for 1 min; 8 cycles of 94 °C for 10 s, 60 °C for 30 s, 68 °C for 1 min; 15 cycles of 94 °C for 15 s, 60 °C for 30 s, 68 °C for 1 min with an additional 10 s added at each cycle; and 68 °C for 5 min before cooling to 4 °C. Amplified libraries were purified using PureLink PCR micro columns (Invitrogen) and directly used to generate clusters for sequencing-by-synthesis using the Illumina HiSeq 2000 platform. 100bp single-end reads were obtained by sequencing to generate more than 300 million reads for the 34 samples.

value: Human brain cortex (BA9)

tag: disease state

value: Parkinson's Disease PD

tag: gender

value: M

tag: age at death (y)


title: Parkinson's Disease PD 17

description: Sample 33

value: F


title: Parkinson's Disease PD 13

description: Sample 29


title: Parkinson's Disease PD 7

description: Sample 23


title: Parkinson's Disease PD 8

description: Sample 24


title: Parkinson's Disease PD 15

description: Sample 31


title: Parkinson's Disease PD 9

description: Sample 25


title: Parkinson's Disease PD 11

description: Sample 27


title: Parkinson's Disease PD 10

description: Sample 26


title: Parkinson's Disease PD 5

description: Sample 21


title: Parkinson's Disease PD 12

description: Sample 28


title: Parkinson's Disease PD 6

description: Sample 22


title: Parkinson's Disease PD 3

description: Sample 19


title: Parkinson's Disease PD 2

description: Sample 18


title: Parkinson's Disease PD 4

description: Sample 20


title: Tbx21-KO H3K27me3 ChIP-seq

city: Bethesda

first: Andrew

middle: J

last: Oler

state: MD

address: 31 Center Drive, Room 3B62E

department: Bioinformatics and Computational Biosciences Branch (BCBB)

institute: NIAID/NIH

description: C57BL/6 Tbx21-/- T-bet-ZsGreen

data_processing:
Basecalls performed using CASAVA version 1.7
Samples were demultiplexed using fastx_barcode_splitter.pl from the FASTX-toolkit.  Barcodes (6bp) were trimmed off the 5' end of the reads with fastx_trimmer (option -f 7).
For ChIP-seq, read were mapped to the mouse genome (mm9) by Bowtie 0.12.7 with options -a --best --strata -m 1 to repress reads mapped to multiple positions (Langmead et al., 2009).
ChIP-seq peaks were called with MACS 1.4.1 (Zhang et al., 2008), allowing only one read per genomic position to minimize the impact from PCR amplification bias (--keep-dup=1). Static Tbet peaks were determined using Tbet ChIP-seq reads as treatment and Th1 input reads (SRR332376 and SRR332372) as control.  Peaks of differential histone methylation (i.e., H3K4me1, H3K27me3) were identified by using Tbx21-/- ChIP-seq reads as treatment and the corresponding WT ChIP-seq reads as control (e.g., Tbx21-/- H3K4me1 ChIP-seq compared to WT H3K4me1 ChIP-seq).  They were subsequently filtered for a –log10(p-value) score of ≥130 to retain highly significant peaks.  All peaks of differential methylation above the default p-value—both positive and negative peaks— were retained for analysis. Peaks were associated with the closest gene using FindNeighboringGenes (part of the USeq package (Nix et al., 2010), http://useq.sourceforge.net/) (settings -o and -c to only report the closest gene) against the mm9 refFlat table downloaded from the UCSC Table Browser (http://genome.ucsc.edu/) (Karolchik et al., 2004).  We used custom Perl scripts to join tables of peaks to tables of genes.
For RNA-seq, reads were mapped to the mm9 genome with TopHat 1.3.3 with settings --bowtie-n --phred64-quals –segment-length 22 and using refFlat file for -G option.
We measured differential gene expression using OverdispersedRegionScanSeqs (USeq), using a flattened refFlat table for annotation (merged transcripts using MergeUCSCGeneTable [USeq]).  This application calculates a Negative Binomial P-value using DESeq (Anders and Huber, 2010), followed by a Benjamin and Hochberg false discovery rate (FDR).  Differentially expressed genes were those with an FDR ≤10%, log2 ratio above 1, and an expression level of ≥5 Fragments per kilobase of exon model per million mapped reads (FPKM) in either WT or Tbx21-/-.
Genome_build: mm9
Supplementary_files_format_and_content: .xls file contains output of RNA-seq and ChIP-seq samples

growth_protocol: Naïve CD62LhiCD44loCD25negZsGnegCD4+ T cells were sorted by FACSAria (BD Biosciences).  T cell-depleted splenocytes were prepared by incubation with anti-Thy1.2 mAb supernatant and rabbit complement (Cedarlane Laboratories Limited) at 37oC for 45 min followed by irradiation at 30 Gy (3,000 rad). Naïve CD4+ T cells were cultured with irradiated T cell-depleted splenocytes at a ratio of 1:5 in the presence of 1 μg/ml of anti-CD3 (145-2C11) and 3 μg/ml of anti-CD28 (37.51) for 3-4 days with various combinations of antibodies and cytokines: For Th1 conditions, 10 IU/ml of hIL-2, 10 ng/ml of IL-12 and 10 μg/ml anti-IL-4 (11B11).  The activated cells were then cultured in RPMI-1640 medium with 10% FBS that contains IL-2 (50 U/ml).  T-bet-ZsGreen positive cells were then sorted and further expanded under Th1 conditions for another three days.

extract_protocol:
Total RNAs were isolated using a combination of TRIzol (Invitrogen) and RNeasy Kit (QIAGEN). RNA-seq libaries were prepared using the standard Illumina mRNA-Seq protocol.
ChIP-Seq experiments were performed as previously described (Barski et al., 2007). Briefly, chromatin was prepared from the cells cross-linked with 1% formaldehyde for 10min by fragmentation and immunoprecipitated with antibody. The ChIP DNA was blunt-ended, ligated to the Solexa adaptors, amplified and sequenced using an Illumina HiSeq system.

tag: cell type

tag: dna fragmentation method

value: MNase to generate approximately 80% mononucleosomes and 20% dinucleosomes

value: Tbx21 KO


title: Tbx21-KO H3K4me1 ChIP-seq

description: C57BL/6 Tbx21-/- T-bet-ZsGreen

value: H3K4me1 (ab8895, Abcam)


title: WT H3K27me3 ChIP-seq

description: C57BL/6 T-bet-ZsGreen

value: WT


title: Control Und. 16

description: Sample 16

value: Control


title: WT H3K4me1 ChIP-seq

description: C57BL/6 T-bet-ZsGreen


title: Control Und. 14

description: Sample 14


title: Control Und. 15

description: Sample 15


title: Tbx21-KO RNA-seq rep2

description: C57BL/6 Tbx21-/- T-bet-ZsGreen


title: Parkinson's Disease PD 14

description: Sample 30


title: Tbx21-KO RNA-seq rep1

description: C57BL/6 Tbx21-/- T-bet-ZsGreen


title: Control Und. 12

description: Sample 12


title: Control Und. 10

description: Sample 10


title: Control Und. 11

description: Sample 11


title: Control Und. 8

description: Sample 8


title: WT RNA-seq rep2

description: C57BL/6 T-bet-ZsGreen


title: Control Und. 5

description: Sample 5


title: Control Und. 6

description: Sample 6


title: Control Und. 9

description: Sample 9


title: WT RNA-seq rep1

description: C57BL/6 T-bet-ZsGreen


title: RAD21-A

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
Sequencing reads were aligned to human genome assembly hg18 (NCBI version 36) using Helisphere software. Only the reads that were uniquely aligned to reference genome with read alignment score higher than 4.5 were retained for further analysis.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
Genome_build: hg18
Supplementary_files_format_and_content: Mapped read bed file, wig file, and peak bed file

source_name: Human primary adult proerythroblasts (ProEs)

growth_protocol: Primary maturing fetal or adult erythroblasts were generated ex vivo using a serum-free two-phase liquid culture system.

extract_protocol: For ChIP-seq analysis using the HeliScope™ Single Molecule Sequencer, ChIP DNA was processed for 3’ polyA tailing followed by 3’ ddATP-blocking. Processing samples by ligation, amplification and size selection are not required by Helicos sequencing. Briefly, 6-9 ng of ChIP DNA or input DNA was used in the 3’ polyA tailing reaction in 14.8 ul containing 2 ul of 2.5 mM CoCl2, 2 ul of 10 x terminal transferase buffer and nuclease-free water. The reaction mixture was denatured in 95C for 5 min, followed by rapid cooling in ice water slurry. Then 1 U of terminal transferase, 4 ul of 50 uM dATP and 0.2 ul of NEB BSA were added to the mixture. Samples were incubated in a thermocycler at 37C for 1 h, 70C 10 min, followed by denaturing at 95C for 5 min and rapid cooling in ice water slurry. For 3’ ddATP-blocking, 0.5 ul of 200 uM ddATP, 1 ul of 10 x terminal transferase, 1 ul of 2.5 mM CoCl2, 1 U of terminal transferase, and 6.5 ul of nuclear-free water were added to the above reaction. Samples were incubated in a thermocycler at 37C for 1 h and 70C for 20 min. Then 2 picomoles of carrier oligonucleotide were added to the reaction, and samples were hybridized to the Helicos flow cells.

value: CD34+ HSPC-derived proerythroblasts

tag: developmental stage

value: adult bone marrow

tag: vendor

value: Abcam

tag: catalog#


title: Input-F

source_name: Human primary fetal proerythroblasts (ProEs)

value: 2-trimester fetal liver


title: Parkinson's Disease PD 1

description: Sample 17


title: Input-A


title: PolII-F

value: PolII

value: Santa Cruz Biotechnology


title: Control Und. 4

description: Sample 4


title: PolII-A


title: Control Und. 3

description: Sample 3


title: CTCF-A

value: CTCF

value: Millipore


title: Control Und. 7

description: Sample 7

value: Human brain cortex (BA9)


title: RAD21-F


title: Control Und. 2

description: Sample 2


title: CTCF-F


title: NFE2-A


title: Control Und. 1

description: Sample 1


title: Input-F2

data_processing:
Sequencing reads were aligned to human genome assembly hg18 (NCBI version 36) using Illumina software pipeline.  Only ChIP-seq reads that aligned to exactly one location in the reference human genome (UCSC, hg18) were retained for downstream data analysis.
Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/).
Genome_build: hg18
Supplementary_files_format_and_content: Mapped read bed file, wig file, and peak bed file

extract_protocol: For ChIP-seq analysis using the Illumin HiSeq2000, 10-20 ng of ChIP DNA was processed for library generation using the ChIP-seq Sample Preparation Kit (Illumina) following the manufacturer’s protocol. Raw ChIP-seq data were processed using the Illumina software pipeline. Only ChIP-seq reads that aligned to exactly one location in the reference human genome (UCSC, hg18) were retained for downstream data analysis.


title: Control Und. 13

description: Sample 13


title: Input-A2


title: TAL1-A


title: NFE2-F


title: PolII-A (HiSeq 2000)


title: PolII-F (HiSeq 2000)


title: H3K27ac-F


title: GATA1-F


title: H3K9ac-A


title: H3K36me2-A


title: H3K36me3-F


title: TAL1-F


title: H3K36me2-F


title: H3K36me3-A


title: Genomic DNA of the cell line K562_IHK002004_GAII

description:
genomic structural variations
genomic DNA hydrosheared in 1.1 kb fragments (std dev: 76.3bp below median; 71.1 above median), 2x25bp paired-end (mate pair) sequences, tag 1 and tag 2 sequence, IHK002
Deviation from 'library construction protocol' for the K562_GenomeAnalyzerII-samples: Illumina sequencing adaptors were ligated to the PET constructs, which were then amplified by PCR and sequenced by an Illumina Genome Analyzer II. For the above menioned study, 36 bp tags were trimmed to 27 bp tags for further analysis.
Processed data file generated from Samples K562_IHK002004_GAII and K562_IHK002004_SOLiDv2:
IHK002004_880_1320.dist.covsmooth.gff [hg18, NCBI build 36; clusters, gff]
Linked as supplementary file on Series record.

tag: cell line

tag: tumor type

value: chronic myeloid leukemia

value: myeloid blast cells


title: H3K9ac-F


title: H3K27me3-F


title: H3K27me3-A


title: H3K4me3-F


title: H3K9me3-F


title: H3K4me2-F


title: H3K4me2-A


title: H3K4me3-A


title: H3K9me3-A


title: WT T-bet ChIP-seq

description:
C57BL/6 T-bet-ZsGreen
Control: Th1 input reads (SRR332376 and SRR332372).

value: sonication

value: anti-T-bet antibody (sc-21749, Santa Cruz)


title: H3K4me1-A