title: RNAPII ChIP-seq Vehicle Rep1

city: Odense M

first: Susanne

last: Mandrup

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: processed data file: RNAPII_Gene_counts.txt

data_processing:
alignment: ChIP-seq reads were mapped to hg19 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21)  specifying --alignIntronMax 1 to avoid potentially aligning across exon-exon junctions.
quantification: RNAPII ChIP-seq coverage within gene bodies were quantified using the iRNA-seq pipeline (Madsen et al, Submitted). The first 500 bp of the gene were omitted to avoid quantifying stalled RNAPII
Genome_build: hg19

source_name: adipocyte_RNAPII ChIP-seq Vehicle

growth_protocol: SGBS cells were grown to confluence in Dulbecco’s Modified Eagle’s Medium/Nutrient Mixture F-12 Ham’s supplemented with 10% fetal bovine serum, 33 µM biotin, 17 µM pantothenate, 100 µg/ml streptomycin, 62.5 µg/ml penicillin, 1ng/µl fibroblast growth factors (FGF) 1, and 90 µg/µl heparin. At two days postconfluency, SGBS cells were stimulated to differentiate with serum-free growth medium supplemented with 10 nM insulin, 200 pM triiodothyronine, 1 µM cortisol, 2 µM BRL 49653, 0.115 mg/ml MIX, 0.25 mmol/L DEX, and 0.01 mg/ml human transferrin. After 3 days, the medium was replaced with the differentiation medium without FGF1 and heparin, and after 6 days Rosiglitazone/BRL49653, MIX, and DEX was removed from the medium.

extract_protocol:
ChIP experiments were performed according to standard protocol as described in (Siersbæk et al. 2012, MCB, 32: 3452-3463)
ChIP-seq libraries were constructed according to the manufacturer's instructions (Illumina) as described in (Nielsen R, Mandrup S, 2014, Methods in Enzymology 2014, Vol. 537, pp. 261-279).

treatment_protocol: Mature SGBS adipocyte D10 were treated with 10ng/ml TNFα or vehicle for 90 min before harvest of total RNA or chromatin.

value: SGBS adipocyte D10

tag: treated with

value: vehicle for 90min

tag: chip antibody

value: RNAPII

tag: chip antibody vendor

value: Diagenode

tag: chip antibody cat. #


title: pGC1::SOC1-GFP/phot1 phot2_rep2

status: Public on Feb 04 2015

type: SRA

city: Nagoya

first: Norihito

last: Nakamichi

state: Aichi

address: Furo-cho, Chikusa

department: Institute of Transformative Bio-Molecules

country: Japan

institute: Nagoya University

library_source: transcriptomic

data_processing:
Base calling and Mapping were done by Torrent Suite (Lifetechnologies).
Bam to Bed conversion was done by GenomicAlignments R package.
Genome_build: Arabidopsis TAIR10 transcripts

molecule: total RNA

organism: Arabidopsis thaliana

source_name: pGC1::SOC1-GFP/phot1 phot2

extract_protocol:
Total RNA was isolated by NucleoSpin RNA Plant kit (Takara).
From total RNA of 4 µg, poly-A containing RNA was enriched by Dynabeads mRNA DIRECT Micro Purification Kit (Lifetechnologies, CA). mRNA was then used to generate an RNA sequencing library using an Ion Total RNA-Seq Kit v2 (Lifetechnologies).Ion 318 Chip v2 was used for sequencing with Ion PGM system.

tag: accession background

tag: genotype/varation

value: pGC1::SOC1-GFP in in phot1 phot2 double mutant

tag: tissue

value: Epidermis including guard cells

tag: age

value: 3 weeks after germination


title: Thio_SREBP1_GW3965_6h

city: Pamplona

first: Daniel

last: Alameda

address: Av. de Pío XII, 55

country: Spain

institute: CIMA

library_source: genomic

data_processing:
Libraries were sequenced 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions. Reads were aligned to the mm9 genome (NCBI build 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. Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped.
Genome_build: mm9
Supplementary_files_format_and_content: UCSC Genome Browser BigWig text files were created by calculating ChIP-Fragment pileups given a fragment size of ~150 bp.

molecule: genomic DNA

organism: Mus musculus

source_name: Primary thioglycollate-elicited peritoneal macrophages

growth_protocol: Primary cells were isolated from 6-8 week-old C57Bl/6 mice. Thioglycollate-elicited macrophages were isolated by peritoneal lavage 3-4 days following peritoneal injection of 2.5 ml thioglycollate. Cells were plated in RPMI medium 1640 and 10% fetal bovine serum, washed after adherence and again fed with fresh medium.

extract_protocol:
20-40 million macrophages were used per immunoprecipitation. Cells were first crosslinked in 2mM disuccinimidyl glutarate (Thermo Fisher Scientific, Rockford, IL, USA) in PBS for 30 minutes, then subsequently in 1% formaldehyde (Sigma-Aldrich, St. Louis, MO, USA) in PBS for 15 minutes all at room temperature. The reactions were quenched by adding glycine (Sigma-Aldrich, St. Louis, MO, USA) to a final concentration of 125 mM, and the cells were centrifuged and washed twice with ice-cold PBS and swollen for 10 min on ice in hypotonic buffer. Nuclei were then pelleted and resuspended in  RIPA lysis buffer (10mM Tris/HCl, 1mM EDTA, 1mM EGTA, 0.1% SDS, 0.5% Na-Deoxycholate, 1% NP-40, 150mM NaCl). Chromatin was sheared to an average DNA size of 100-400 bp by administering 10 pulses of 30 seconds duration at 12 W power output with 1 min pause on wet ice using a Misonix 3000 sonicator. Extracts were clarified by centrifugation at 14,000 rpm for 15 min at 4ºC, pre-cleared with 100 μl of CL4B sepharose beads (Sigma-Aldrich, St. Louis, MO, USA) for 1 hr at 4ºC, then incubated overnight with appropriate specific antibody on rotator. Protein-DNA complexes bound to antibodies were collected by incubation with 40 μl of Protein A beads (GE Healthcare, Pittsburgh, PA, USA) for 2 hr at 4ºC on rotator. Beads were washed 3 times with RIPA lysis buffer, 6 times with LiCl buffer (100mM Tris/HCl, 500mM LiCl, 1% NP-40, 1% Na-Deoxycholate, 1mM EDTA) and twice with TE. Immunoprecipitated chromatin was eluted twice with 100 μl elution buffer (0.1M NaHCO3, 1% SDS) followed by overnight incubation at 65ºC adding NaCl. Samples were treated with RNase A and proteinase K. DNA was isolated using the ChIP DNA Clean & Concentrator kit (Zymo Research, Irvine, CA, USA) according to the manufacturer’s instruction.
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 Genomic adaptors or with NEXTflex DNA barcodes adaptors for 18 cycles and library fragments (ChIP) (insert plus adaptor and PCR primer sequences) were size-selected (150-250bp) from a 2% agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina Genome Analyzer II or Illumina HiSeq 2000 according to the manuactuere’s instructions.

treatment_protocol: Cells were cultured with no treatment overnight. The next day, cells were treated with GW3965 (1uM) for another 6 h.

tag: strain

tag: chip target

tag: genotype

value: wild-type

tag: treatment

tag: cell type

value: macrophages


title: phot1 phot2_rep3

source_name: phot1 phot2

value: phot1 phot2 double mutant


title: phot1 phot2_rep1


title: WT-PPAR-NoTx

data_processing:
Libraries were sequenced for 50 cycles on an Illumina HiSeq 2000 according to the manufacturer’s instructions. Reads were aligned to the mm9 genome (NCBI build 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. Each ChIP-Seq experiment was normalized to a total of 10^7 uniquely mapped tags by adjusting the number of tags at each position in the genome to the correct fractional amount given the total tags mapped.
Genome_build: mm9
Supplementary_files_format_and_content: UCSC Genome Browser BigWig text files were created by calculating ChIP-Fragment pileups given a fragment size of ~150 bp.

treatment_protocol: Cells were maintained in culture for 24 h before processing

value: PPARg


title: WT-RXR-NoTx

value: RXR


title: RNAPII ChIP-seq TNF Rep1

organism: Homo sapiens

source_name: adipocyte_RNAPII ChIP-seq TNF

value: 10ng/ml TNFα for 90min


title: RNA seq of hybrid B

city: Munich

middle: Magnus

last: Bader

address: Feodor-Lynen Str 25

department: Gene Center

country: Germany

institute: Ludwig-Maximilians-University

data_processing:
RNA: read pairs mapped to both reference genomes in parallel using GSNAP 2013-06-27 (Wu et al. 2010 Bioinformatics); BAM files filtered for SAM-flags 83/163 and 99/147 using custom python script; read pair counts per gene generated via htseq-count 0.5.4p5 (Anders et al., 2014 bioRxiv) using filtered alignments and optio  'intersect strict'. DNA: same genotyping protocol as in Wilkening et al. 2013 BMC bioinformatics. We lifted the SNP coordinates from S288c genome version R63 to R64.
Genome_build: S. cerevisiae genome (S288c, sacCer3, version 64.1.1) and SK1 by Nishant et al. 2010 Plos genetics
Supplementary_files_format_and_content: RNA: tab delimeted text file containing read counts per gene, sample and strain. rows: ortholog genes for both strains separated K0001,...,K7272,S0001,...,S7272 (numbers not consecutive). columns: aligned rna-seq data, separated by strain per raw sequencing file. DNA: tab delimeted text files in bed format. rows: SNP marker. columns: chromosome, start, stop, S96 count, SK1 count.

organism: Saccharomyces cerevisiae

source_name: Hybrid B

growth_protocol: See Wilkening et al.(2014 Genetics) for growth protocols. The hybrid is the same and the bulk segregant cells are our spore pool.

extract_protocol:
DNA: see Wilkening et al. 2013 BMC bioinformatics. RNA: see Wilkening et al. 2013 NAR.
RNA: Total RNA was isolated by a standard hot phenol method and treated with RNase-free DNaseI using Turbo DNA-free kit (Ambion). For strand specific total RNA-Seq the libraries were prepared as described in Wilkening et al. 2013 NAR which is a modified protocol of Parkhomchuk et al. 2009 NAR. Briefly, 10 µg of total RNA were fragmented by incubating the samples at 80°C for 5 min in the resence of RNA fragmentation buffer (40 mM Tris-acetate, pH 8.1, 100 mM KOAc and 30 mM MgOAc). The fragmented RNA was purified using 1.5× Ampure XP Beads (Beckman Coulter Genomics). Eluted RNA was reverse transcribed with 3 µl oligo dT18 with a VN anchor (1 µM, Invitrogen), 3 µl random hexamers 30 ng/µl, Invitrogen) and 2 µl 10 mM dNTPs. The samples were incubated at 65°C for 5 min and ransferred to ice. 8 µl 5X First strand buffer (Invitrogen), 4 µl DTT 0.1 M, 0.5 µl Actinomycin D (1.25 mg/ml) and 0.5 µl RNasin plus RNase inhibitor (Promega) were added to each sample and the samples were then incubated at 25°C for 2 min. Following this, 0.5 µl Superscript III reverse transcriptase (200 U/µl, Invitrogen) was added. The retrotranscription was carried out at 25°C for 10 min, at 42°C for 50 min,  and inactivated at 70°C for 15 min. After cleanup, the 2nd strand cDNA synthesis was done with dUTPs  instead of dTTPs. For ligation, 1 µl of forked PE multiplexed adaptors (40 µM) was used. The dUTPs of the second strand were hydrolyzed by incubating the samples at 37°C for 30 min with 5 units of UDG in UDG reaction buffer (NEB). The samples were purified using 1X Ampure XP beads. After 10 cycles of PCR amplification and clean up, samples were submitted to the EMBL core facility for 100bp  paired end sequencing on a HiSeq 2000 (Illumina). DNA: A modified version of the PrepEase Genomic DNA Isolation Kit   (Affymetrix, 78855 1 KT) based on enzymatic cell wall digestion was  used for the DNA isolation from yeast cells. All of the mixing steps  were performed by pipetting using a Biomek FX pipetting robot (Beckman  Coulter) in 96-well plates. Cell pellets from 4 deep-well plates, each  containing 1 ml overnight culture, were combined for the DNA  isolation. The Spheroplast and Enzyme Solution from the   kit was replaced by Qiagen   s Y1 lysis buffer (1 M sorbitol, 100 mM  EDTA, pH 8.0, 14 mM   -mercaptoethanol) freshly supplemented with 2.5  l/ml of Zymolyase (Seikagaku Inc.) and 2.5   l/ml RNase A (10 mg/ml,  Qiagen). 200   l of this buffer was added to each pellet, mixed and  incubated at 37  C for 90 min with gentle shaking every 30 min. 200  l of water was added to each well and the plate was centrifuged at  6000 x g for 4 min (for centrifuges with maximum 3,000 x g,  centrifugation times can be tripled) and the supernatant was decanted.  120   l Homogenization Buffer was added and mixed to resuspend the pellet completely. 100   l of chloroform and 400   l of Protein  Precipitation Buffer were added to the lysate and mixed. Plates were  centrifuged at 6,000    g for 15 min. 450   l of the upper aqueous  phase was transferred with the robot (pipetting height was optimized  in advance) to a 1 ml deep-well plate containing 340   l of  isopropanol per well. The solution was mixed, left for 15 min at room  temperature, and centrifuged at 6,000    g for 15 min. After decanting   the supernatant, 1 ml of cold 70% ethanol was added to the pellet,  mixed and centrifuged at 6,000    g for 10 min. The supernatant was decanted, and the tube was placed upside down on a paper towel and dried for 5 min at 37  C. The DNA pellet was resuspended in 300   l of DNA Resuspension Buffer or Elution Buffer (EB, 10 mM Tris HCl) by shaking plates for 30 min at 37  C and later by mixing. DNA fragmentation was done with a Bandelin and a Covaris sonicator,  except for spore pool B, where only a Covaris fragmentation was applied. Instead of the standard column or bead-based cleanup steps,  we heat-inactivated the enzymes used for end repair, dA-tailing, and  ligation, then added the respective enzyme (+ buffer). DNA  Quantification: For quantification of genomic DNA and pre-PCR  libraries in 96-well plates, we used Quant-iT PicoGreen dsDNA Reagent  (Invitrogen) in optical plates (Greiner). The fluorescence was  measured at 485 nm excitation and 535 nm emission in a Genios  microplate reader (Tecan) according to the manufacturers  instructions. The pooled libraries were quantified before and after PCR with a Qubit spectro-fluorometer (Invitrogen) according to the manufacturers instructions. All pre- and post-PCR libraries were run on a High Sensitivity Bioanalyzer chip (Agilent) to determine  the size distribution. The samples were then diluted to 10 nM and  clustered on the Illumina cBot clustering station for paired-end   sequencing on an Illumina HiSeq 2000.

treatment_protocol: We used only YPD media.

value: S96 x SK1 hybrid cross

tag: growth medium

value: YPD


title: genomic DNA of spore pool B

source_name: Spore pool B

value: spores of S96 x SK1 cross


title: RNA seq of hybrid A

source_name: Hybrid A


title: D11_sh#174_knockdown

city: Ann Arbor

first: Lihong

last: Shi

address: 3608 BSRB, 109 Zina Pitcher Place

country: USA

institute: University of Michigan

data_processing:
The Tophat used is TopHat v2.0.10, and the version for cufflinks is cufflinks v2.1.1.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: RPKM values for each Sample.

source_name: D11-erythroid cells, sh#174 TR4 knockdown

growth_protocol: CD34+ cells, which were mobilized in and isolated from the peripheral blood of healthy donors, were purchased from the Fred Hutchinson Cancer Research Center. The cells were grown and differentiated ex vivo into the erythroid lineage by a two-phase culture method. Briefly, during the first phase (from days 0 to 8), the cells were cultured in IMDM basic medium (Biochrom) supplemented with 40 µg of inositol/ml, 10 µg of folic acid/ml, 160 µM monothioglycerol, 120 µg of iron-saturated human transferrin/ ml, 10 µg of insulin/ml, 900 ng of ferrous sulfate/ml, 90 ng of ferric nitrate/ml, 1 µM hydrocortisone, and 5 ng of interleukin-3 (IL-3)/ml, which were all pur- chased from Sigma-Aldrich, and 200 mM L-glutamine (Invitrogen), 1% deionized bovine serum albumin (Stemcell Technologies), 100 ng of stem cell factor (Prospec)/ml, and 3 IU of erythropoietin/ml, which was purchased from Amgen. During the second phase (day 8 through day 14), the cells were cultured in the same medium without hydrocortisone or IL-3.

extract_protocol:
Total RNA from TR4 knockdown samples purified by ISOGEN (Nippon Gene). RNA integrity and quality were verified using a 2100 Bioanalyzer (Agilent Technologies).
true_seq library preparation protocol from Illumina.

treatment_protocol: The pLKO.1-puro resistant lentiviral shRNAs (short hairpin RNAs) used to knockdown TR4 were purchased from Sigma-Aldrich (TRCN0000245174 and TRCN0000021658).  All of the lentiviruses packages were performed by the University of Michigan vector core facility. For infection, cells were exposed to viruses as well as control on day 4 for 24 hours and then selected by 1 ug/ul puromycin on days 6 until day 14. At day 11, the cells were harvested for examination of TR4 knockdown efficiency and subjected for the library construction and sequencing on an IIlumina HiSeq 2000.

value: erythroid cells

tag: time point

value: day 11 of differentiation

tag: shRNA


title: D11_sh#658_knockdown

source_name: D11-erythroid cells, sh#658 TR4 knockdown


title: RNA seq of spore pool A

source_name: Spore pool A


title: genomic DNA of hybrid A


title: genomic DNA of hybrid B


title: D11_TR4_binding annotation

description: Represents 2 replicates.

data_processing:
ChIP-enriched and input control DNA libraries were sequenced on an Illumina Genome Analyzer II (D8 samples) or an Illumina HiSeq 2000 (D11, D14 samples). DNA sequencing reads that passed FastQC quality control (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) were aligned to the reference genome (hg19, Feb 2009), and peaks were identified using MACS (version 1.4).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text file includes the identified peaks (chr/peaks start/peak end), the closest gene information (official gene symbol/RefSeq ID/distance from middle of peaks to TSS of the closest genes/strand/TSS/TES/peaks position relative to genes).

source_name: D11-erythroid cells, TR4 ChIP

growth_protocol: CD34+ cells, which were mobilized in and isolated from the peripheral blood of healthy donors, were purchased from the Fred Hutchinson Cancer Research Center. The cells were grown and differentiated ex vivo into the erythroid lineage by a two-phase culture method. Briefly, during the first phase (from days 0 to 8), the cells were cultured in IMDM basic medium (Biochrom) supplemented with 40 µg of inositol/ml, 10 µg of folic acid/ml, 160 µM monothioglycerol, 120 µg of iron-saturated human transferrin/ ml, 10 µg of insulin/ml, 900 ng of ferrous sulfate/ml, 90 ng of ferric nitrate/ml, 1 µM hydrocortisone, and 5 ng of interleukin-3 (IL-3)/ml, which were all purchased from Sigma-Aldrich, and 200 mM L-glutamine (Invitrogen), 1% deionized bovine serum albumin (Stemcell Technologies), 100 ng of stem cell factor (Prospec)/ml, and 3 IU of erythropoietin/ml, which was purchased from Amgen. During the second phase (day 8 through day 14), the cells were cultured in the same medium without hydrocortisone or IL-3.

extract_protocol:
1X10^8 cells were harvested on culture days 8, 11 or 14 and cross-linked with 1% formaldehyde. Chromatin in complex with TR4 was then sonicated and incubated with rabbit anti-TR4 antibody (generated in-house) at 4 ºC overnight in IP dilution buffer.
Library construction was performed using the IntegenX ChIP-seq sample preparation kit as per manufacturer's instructions. The libraries were amplified by PCR (15 cycles) and then purified using Agencourt XP beads with a DNA fragment size selection of 500 - 700 bp. ChIP DNA libraries were analyzed on a Bioanalzyer and qPCR assay was used to assess the library quality and pooled in equimolar ratios before sequencing.

tag: developmental stage

value: basophilic ~ polychromatic erythroblast

tag: disease status

value: healthy

value: rabbit anti-TR4 antibody


title: genomic DNA of spore pool A


title: D8_TR4_binding annotation input

description: Represents 2 replicates.

source_name: D8-erythroid cells, input

value: day 8 of differentiation

value: proerythroblast

tag: chip antibody


title: D8_TR4_binding annotation

description: Represents 2 replicates.

source_name: D8-erythroid cells, TR4 ChIP


title: Input DNA (GATA1)

city: Cincinnati

first: Timothy

middle: Michael

last: Chlon

state: OH

address: 3333 Burnet Ave

department: Oncology

institute: Cincinnati Children's

data_processing:
Mappable reads were aligned to mouse genome mm9 using the Illumina pipeline
All mappable reads from 2 biological replicate experiments were combined into single datasets for peak calling.  Peaks were identified with QuEST v2.4 (Valouev et al 2009) set on default parameters for transcription factor analysis (bandwith=30, region size=300).
For identification of GATA1s-deficient GATA1 binding sites, the peak score cut off was relaxed from 30 to 15 on the GATA1s peak call.  A region of 200bp around these peaks was compared base-wise to the GATA1 peak set.  GATA1 peaks without a matching peak in the relaxed GATA1s peak set were identified as GATA1s-deficient binding sites.
Genome_build: mm9
Supplementary_files_format_and_content: bed, wig, peaks

source_name: G1ME cells

growth_protocol: G1ME cells were cultured in 1% TPO supernatant (v/v)

extract_protocol:
Isolated chromatin was sonicated and pre-cleared with isotype-matched mouse non-specific IgG.  Chromatin immunprecipitation was carried out with a HA-tag antibody (Santa Crruz Biotechnology, sc-7392).  The formaldehyde crosslinks were reversed by heating to 65-degrees overnight.  RNA and protein were removed by treatment with RNAse A and Proteinase K, respectively, and the DNA was isolated using the Qiagen PCR Purification Kit.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part#  IP-102-1001).

treatment_protocol: Retroviral supernatant was added to the cells at 1e6 cells per ml, and the culture was centrifuged at 3200rpm for 90min. The cells were incuabted in the virus for an additional 4h, and then the virus was removed.  The cells were crosslinked 48h later.

tag: cell line

value: GATA1-deficient cell line with megakaryocyte and erythrocyte differentiation potential

tag: epitope


title: GATA1s ChIP-Seq

value: anti-HA


title: Gene expression_RNA-Seq  miR-494 BioRep3

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description: processed data file: Gene_expression_miR-494_cuffdiff_fpkm.txt

data_processing:
Illumina CASAVA version 1.8 used for basecalling.
Cutadapt was used to trim adaptors, reads mapping to rRNAs and tRNAs were removed, and the remaining reads were mapped to human genome (hg19) by TopHat 2 software version 2.0.9 with parameters -p 6 --b2-fast --library-type=fr-unstranded --no-novel-juncs --no-novel-indels --transcriptome-index
Cuffdiff was used to combine biological replicates and assign expression values (FPKM) for each RefSeq gene, run with parameters -p 1 -b -u
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values (value 1 and value 2) from cuffdiff combined biological replicates 1-3 for each treatment group and significance estimates comparing miRNA transfection to control siRNA transfection

source_name: HeLa cell

growth_protocol: DMEM supplemented with 10% FBS

extract_protocol:
Lysates from each sample were split into 2 groups.  Group 1: Gene expression samples, total RNA was isolated with TRIzol.  Gene 2: Ago2 immunoprecipitation samples, Ago2 was immunoprecipated with an antibody against Ago2 and the associated RNA was isolated with TRIzol. In more detail, 24 hours post transfection, cells were washed 2X with PBS, 0.5 mL of lysis buffer was added to the plate, followed by incubation at 4°C for 30 minutes. Cell lysates were collected by scraping and debris cleared by centrifugation at 14,000 rpm at 4°C. 50 μl of the lysate was collected as input for total RNA profiling. Lysates were pre-cleared by incubating with 50 μl of protein-G beads (Roche) for 1 hour at 4°C and then collecting supernatants (pre-clearing). Pre-cleared lysates were then incubated with 15 μg of antibody against Argonaute-2 (AGO2)(ab57113, Abcam) at 4°C for 3 hours. AGO2 is a protein component of RISC. Following AGO2 antibody incubation, 50 μl of protein-G beads were added to the lysate and incubated for 1 hour at 4°C. Beads were washed 8 times with lysis buffer and RISC-RNA complexes were extracted by adding 1 mL TRIzol reagent (Invitrogen) directly to the beads. RNA extraction with TRIzol was carried out as per the manufacturers instructions.
rRNAs were removed using the Ribo-Zero rRNA Removal Kit (Epicentre). The remaining RNA was then fragmented with the NEBNext Magnesium RNA Fragmentation Module (New England BioLabs), and size selected using AMPure XP beads (Agencourt) at 1.8X volume. Ends of the fragmented RNAs were then prepared for adaptor ligation using T4 Polynucleotide Kinase (New England BioLabs). Libraries were prepared from the RNA using the NEBNext Small RNA Library Prep Set according to the manufacturers protocol (New England BioLabs). Libraries were cleaned and further size selected using 0.8X volume AMPure XP beads, and additional size selections with 1.0X beads were performed as necessary.

treatment_protocol: mature miR-503, miR-103, or miR-494 duplex or control siRNA against GFP duplex, or mock transfection (lipofectamine 2000 alone) was transfected with lipofectamine 2000 at a concentration of 100nM in the well

value: HeLa

tag: transfected construct


title: D11_Control

source_name: D11-erythroid cells, empty vector control


title: D14_TR4_binding annotation input

description: Represents 2 replicates.

source_name: D14-erythroid cells, input

value: day 14 of differentiation

value: polychromatic ~ orthochromatic erythroblast


title: GATA1 ChIP-Seq


title: D11_TR4_binding annotation input

description: Represents 2 replicates.

source_name: D11-erythroid cells, input


title: Gene expression_RNA-Seq  miR-103 BioRep2

description: processed data file: Gene_expression_miR-103_cuffdiff_fpkm.txt


title: D14_TR4_binding annotation

description: Represents 2 replicates.

source_name: D14-erythroid cells, TR4 ChIP


title: Gene expression_RNA-Seq  miR-503 BioRep3

description: processed data file: Gene_expression_miR-503_cuffdiff_fpkm.txt


title: Gene expression_RNA-Seq  mock BioRep3

description: processed data file: Gene_expression_mock_cuffdiff_fpkm.txt

value: none (mock)


title: Gene expression_RNA-Seq  mock BioRep1


title: Ago2 IP mock transfection BioRep3

description:
RNA isolated from Ago2 immunoprecipitation
processed data file: Ago2_immunoprecipitation_mock_cuffdiff_fpkm.txt

tag: antibody

value: Argonaute-2 (AGO2) (ab57113, Abcam)


title: GATA2_ChIP Seq

city: Columbus

first: Qianben

last: Wang

state: Ohio

address: 460 W 12th Avenue

department: Molecular and Cellular Biochemistry and the Comprehensive Cancer Center

institute: Ohio State University

description: genomic DNA

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.0.0 with parameters '-k 2 -v 2' to report up to two valid alignments
Read with multiple valid alignments were removed using a Perl program
Uniquely mapped reads from replicates of the same sample were pooled
Peaks were called using MACS v1.4.2 with parameters '-m 3,30 -g hs -p 1e-8'
Genome_build: hg19
Supplementary_files_format_and_content: wig

source_name: prostate cell line

growth_protocol: LNCaP cells were cultured in 10% FBS RPMI 1640 medium, 1:2.5 split every 2 days. Cells are cultured in 5% charcoal stripped FBS rpmi 1640 medium

extract_protocol:
Lysates were clarified from sonicated nuclei and AR-DNA or FoxA1-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part#15023092 ). Briefly, DNA was end-repaired, phosphorylated ends were treated with Klenow fragment 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, the DNA was size selected from an agarose gel and was PCR amplified with Illumina primers for 15 cycles. Libraries were sequenced on the Hi-seq 2500 following the manufacturer's protocols.

treatment_protocol: LnCaP cells were treated with 40nM siControl or siGATA2 from Dharmacon company for 3 days. For AR ChIP, 1 nM R1881 was added before cell colllection for ChIP assay.

value: androgen-dependent prostate cancer derived cell line LNCaP

tag: passage number

value: androgen dependent

value: GATA2 santa cruz  sc-9008(H116) lot# E0313


title: Gene expression_RNA-Seq  siGFP BioRep2

description: processed data file: Gene_expression_miR-503_cuffdiff_fpkm.txt;Gene_expression_miR-103_cuffdiff_fpkm.txt;Gene_expression_miR-494_cuffdiff_fpkm.txt;Gene_expression_mock_cuffdiff_fpkm.txt

value: siGFP


title: RNA seq of spore pool B

value: spores of S96 x SK1 cross

value: YPD


title: Gene expression_RNA-Seq  siGFP BioRep3


title: Ago2 IP siGFP BioRep2

description:
RNA isolated from Ago2 immunoprecipitation
processed data file: Ago2_immunoprecipitation_miR-503_cuffdiff_fpkm.txt;Ago2_immunoprecipitation_miR-103_cuffdiff_fpkm.txt;Ago2_immunoprecipitation_miR-494_cuffdiff_fpkm.txt;Ago2_immunoprecipitation_mock_cuffdiff_fpkm.txt


title: Gene expression_RNA-Seq  miR-494 BioRep2


title: rpd1_gro

first: Jay

last: Hollick

address: 318 West 12th Avenue

department: Molecular Genetics

institute: The Ohio State University

description:
GRO-Seq
nascent RNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed of adapter sequences, low-complexity and low-quality reads were removed, and remaining high quality reads were mapped to maize rRNAs and tRNAs using bowtie 0.12.7 with parameters: --phred64-quals -t -v 2.
Non-rRNA/tRNA reads were mapped with bowtie to the B73 v2 reference genome using parameters:   --phred64-quals -t -v 2 -m 1
Bowtie-generated SAM alignment files representing non-rRNA/tRNA unique reads were used to generate counts tables for maize FGS gene and transposable element (TE) annotations with the BEDTools intersectBed tool using the parameters -c -wa and either -s or -S (for sense or antisense respectively).
Counts tables were used as inputs for DESeq (Anders et al.) analysis to identify differentially transcribed genes and TEs between wild-type and rpd1 mutant libraries.
Genome_build: B73 RefGen_v2 (ZmB73_RefGen_v2)
Supplementary_files_format_and_content: Text files containing raw counts (wild-type and rpd1 mutant in separate columns) of reads matching maize genes and TEs in either the sense or antisense orientation; text files containing differentially expressed genes and TEs in either the sense or antisense orientiation between the wild-type and rpd1 mutant samples

organism: Zea mays

source_name: Seedling nuclei

growth_protocol: Seeds were planted in vermiculite and sand flats on a lab benchtop, genotyped after cotyledons emerged, and homozygous rpd1 mutants and homozygous wild-type seedlings were harvested on day 8 after planting.

extract_protocol:
Nuclei were prepared as described (Erhard et al. 2009) from whole, above-ground shoot portions of 8 day-old seedlings. Transcription run-on assays were performed as described (Erhard et al. 2009) with the following changes to the protocol:  0.5 mM 5-bromouridine 5’-triphosphate (BrUTP) (Sigma) was substituted for UTP and 2 mM cold cytidine triphosphate (CTP) was added in addition to 10 mL of P32-CTP (Perkin-Elmer).  RNA isolation of in vitro labeled RNA was as described (Erhard et al. 2009).
Libraries were prepared as described (Core et al. 2008) using agarose bead-conjugated a-BrdU antibody (Santa Cruz Biotechnology).

tag: background

value: 8-day post germination

tag: tissue

value: seedling


title: Gene expression_RNA-Seq  miR-494 BioRep1


title: Gene expression_RNA-Seq  siGFP BioRep1


title: Gene expression_RNA-Seq  miR-503 BioRep2


title: Gene expression_RNA-Seq  miR-103 BioRep1


title: Gene expression_RNA-Seq  miR-103 BioRep3


title: Ago2 IP miR-494 BioRep3

description:
RNA isolated from Ago2 immunoprecipitation
processed data file: Ago2_immunoprecipitation_miR-494_cuffdiff_fpkm.txt


title: RNA TNF Rep2

description:
processed data file: RNA_Exon_counts.txt
processed data file: RNA_Intron_counts.txt

data_processing:
alignment: RNA-seq reads were mapped to hg19 with STAR (Dobin, A., et al., Bioinformatics, 2013. 29(1): p. 15-21) using default parameters.
quantification: Total RNA-seq coverage within exons and introns were quantified  using the iRNA-seq pipeline (Madsen et al, Submitted), to asses mature and primary transcript levels, repectively
Genome_build: hg19

source_name: adipocyte_RNA TNF

extract_protocol:
Following Isol extraction and column purification of total RNA, ribosomal RNAs were removed using the Ribo-Zero Human/Mouse/Rat kit (Epicentre).
Library preparation was performed using TruSeq2 RNA Sample Preparation protocol according to the manufacturers (Illumina) instructions.

value: SGBS adipocyte D10

tag: treated with

value: 10ng/ml TNFα for 90min


title: Ago2 IP miR-494 BioRep2


title: Ago2 IP miR-494 BioRep1


title: RNA TNF Rep1


title: Gene expression_RNA-Seq  miR-503 BioRep1


title: Ago2 IP mock transfection BioRep1


title: Gene expression_RNA-Seq  mock BioRep2


title: Ago2 IP siGFP BioRep3


title: wt_gro

description:
GRO-Seq
nascent RNA

tag: genotype

value: wt


title: Ago2 IP mock transfection BioRep2


title: Ago2 IP miR-103 BioRep3

description:
RNA isolated from Ago2 immunoprecipitation
processed data file: Ago2_immunoprecipitation_miR-103_cuffdiff_fpkm.txt


title: RNA Vehicle Rep1

source_name: adipocyte_RNA Vehicle

value: vehicle for 90min


title: RNA Vehicle Rep2


title: Ago2 IP miR-103 BioRep1

value: HeLa


title: Ago2 IP miR-503 BioRep3

description:
RNA isolated from Ago2 immunoprecipitation
processed data file: Ago2_immunoprecipitation_miR-503_cuffdiff_fpkm.txt


title: Ago2 IP miR-103 BioRep2


title: Ago2 IP miR-503 BioRep2


title: Ago2 IP miR-503 BioRep1


title: RNAPII ChIP-seq TNF Rep2

source_name: adipocyte_RNAPII ChIP-seq TNF

value: RNAPII

tag: chip antibody vendor

value: Diagenode

tag: chip antibody cat. #


title: Ago2 IP siGFP BioRep1


title: RNA TNF Rep3

tag: cell type


title: Oct4_rep 2

city: Tainan

first: Yi-Ching

address: No.1, University Road, Tainan 70101, Taiwan, R. O. C.

department: Department of Pharmacology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

description: Sample 4

data_processing:
High-throughput sequencing was performed by SOLiD 5500xl sequencer (Applied Biosystems) and abound 24~29 million raw reads were obtained from samples.
The raw reads were further analyzed using LifeScopeTM Genomic Analysis Software (version 2.5), and mapped to human genome (hg19) released from UCSC database.
To find the significant peak, the mapped profiles were analyzed using the ChIP-seq tool in CLC Genomics Workbench (version 4.9). The peak-finding algorithm included the following four steps: 1) Calculate the null distribution of the background sequencing signal; 2) Scan the mappings to identify candidate peaks with a higher read count than expected from the null distribution; 3) Merge overlapping candidate peaks; 4) Refine the set of candidate peaks based on the count and the spatial distribution of forward and backward reads within the peaks. The estimate for the null distribution of coverage and the calculation of the false discovery rate (FDR) were based on the window size and maximum FDR (%) parameters. In this study, the window size and FDR were set to 200 bp and 5%, respectively.
To determine the high confidence Oct4 binding loci, the ChIP-region was identified by scanning the peaks with significantly higher read count in Oct4 stably-expressing cells compared to those in the vector control cells.
Genome_build: hg19
Supplementary_files_format_and_content: The processed files are BED files which are Oct4 ChIP-seq reads peaks in vector control and stable Oct4 expressing A549 cells.

source_name: lung cancer cell line A549

extract_protocol:
Empty vector control and Oct4 stably-expressing A549 cells (1 × 10^7 cells) were cross-linked with 1% formaldehyde, followed by preparation of nuclear lysates using Magna ChIP protein G Kit (Millipore, Billerica, MA, USA) according to the protocols provided by the manufacturer. Nuclear lysates were sonicated for shearing crosslinked DNA to around 200~300 bps using Covaris-S2 machine (Covaris Inc., Woburn, MA, USA). Chromatin was immunoprecipitated with anti-Oct4 antibody (Abcam, #ab19857).
Purified chromatin-immunoprecipitated DNA was subjected to preparation of fragment libraries using 5500 SOLiD Fragment Library Core Kit (Applied Biosystems, Foster City, CA, USA) according to the protocols provided by the manufacturer.

value: lung cancer A549 cells

tag: genotype/variation

value: Oct4 overexpression

value: Oct4 (Abcam, catalog# ab19857)


title: Al_mRNA_rep1

status: Public on Feb 03 2015

city: Lyon

first: François

last: ROUDIER

address: 46 Allée d'Italie

department: Biologie

country: France

institute: Ecole Normale Supérieure de Lyon

data_processing:
Basecalls performed using SHORE v0.7alpha3.
Quality filtering included trimming of low quality nucleotides.
ChIP-seq, MeDIP-seq and RNA-seq reads were mapped against the Arabidopsis lyrata  reference using Bowtie choosing one match in case of multiple ones and allowing one mismatch.
For the ChIP-seq and MeDIP-seq libraries, since average read coverage was highly correlated between the two biological replicates, they were pooled for subsequent analysis. In order to reduce biases introduced by PCR amplification, a maximum of 5 reads mapping at exactly the same positions were taken into account.
Peak detection was done using SICER normalising the ChIP-seq coverage by the INPUT coverage. Window size was adjusted according to the distribution of the mark over the genes: 150 bp for H3K4me3 and 300 bp for H3K27me3. Effective genome size was estimated as 85% of the total genome and FDR set at 10−3 .
mRNA abundance for each gene was estimated as the average number of positions mapped to its transcribed region over the total number of positions covered.
Genome_build: Arabidopsis lyrata
Supplementary_files_format_and_content: bedGraph = scores represent the ChIP-seq and MeDIP-seq coverage ; bed = scores represent number of reads per domain ; covexonsByGene.txt = mRNA abundance per gene

organism: Arabidopsis lyrata

source_name: young leaves

growth_protocol: Plants of Arabidopsis lyrata accession MN47 were grown in soil under long day conditions (16h light/8h dark) at 22.5C.

extract_protocol:
Chromatin and DNA immunoprecipitation was performed essentially as described in Gendrel et al., 2005 and Cortijo et  al., 2014, respectively. Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturers instructions and its quality was validated using RNA 6000 NanoChip (Agilent).
20 ng of immunoprecipitated (IP) and genomic (INPUT) DNA and 1 ug of total RNA were used to prepare libraries with the ChIP-Seq DNA Sample Prep Kit IP-102-1001 and TruSeq RNA Sample Prep Kit v2 RS-122-2002 (Illumina), respectively. Quality of libraries was validated using 2100 Bioanalyzer (Agilent). Libraries were sequenced with Illumina Genome Analyzer IIx according to manufacturers instructions.

tag: strain

value: young leaves


title: Al_MeDIP_rep1

value: 5mC (Diagenode,Mab-006, lot.#DA-0015)


title: RNA Vehicle Rep3


title: Al_H3K27me1_rep2


title: vector_rep 2

description: Sample 2

value: vector control


title: Al_INPUT-MeDIP_rep2


title: Al_INPUT-ChIP_rep1


title: Al_MeDIP_rep2


title: Al_H3K4me3_rep2


title: Al_H3K27me3_rep1


title: Al_H3K4me3_rep1


title: Al_H3K27me3_rep2


title: Al_H3K27me1_rep1


title: RNAPII ChIP-seq Vehicle Rep2

source_name: adipocyte_RNAPII ChIP-seq Vehicle


title: 13_5_MN_VPA_plus

city: Kyoto

first: Megumu

last: Saito

address: 53, Shogoin-Kawahara

institute: Kyoto University

data_processing:
Basecalls performed using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
Data were filtered using Illumina's Quality Filtering and 101th bases in reads were not used.
RNA-seq reads were aligned to the hg19 genome assembly using TopHat version 2.0.8b with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calcurated using RPKMforGenes, downloaded on 19th, October 2012..
Genome_build: hg19
Supplementary_files_format_and_content: Text files which contain RPKM were calcurated using RPKMforGenes, downloaded on 19th, October 2012.

source_name: iPSC derived motor neuron

extract_protocol:
Total RNA was extracted and purified using RNA mini kit (QIAGEN) according to manufacturer’s instruction.
One µg of total RNA was depleted of rRNA using Ribo-Zero gold kit (Epicentre), and then 100 ng of rRNA-depleted RNA fraction was subjected to Illumina’s sequencing library using TruSeq Stranded Total RNA Sample Prep Kit (Illumina). The library was captured on an Illumina flow cell for cluster generation.

treatment_protocol: samples were treated with or without 1 mM VPA for 6 days by changing half of the medium every two days.

tag: treatment

value: VPA

value: iPSC derived motor neuron


title: 201B7_MN_VPA_minus


title: 13_5_MN_VPA_minus


title: FA07_3_KDRCD34_d6

source_name: patient-specific iPSCs

growth_protocol: PSCs were differentiated into hemoangiogenic progenitor cells under serum- and feeder-free monolayer differentiation system.

extract_protocol:
Total RNA was isolated from sorted hemoangiogenic  progenitors using RNAeasy (Qiagen) kit.
We synthesized double-stranded cDNA from single stranded cDNA using PrimeScript Double Strand cDNA Synthesis Kit (TaKaRa). The double-stranded cDNA was then sheared in an AFA microtube using Covaris E210 (Covaris Inc., Woburn, MA, USA) withthe following settings: Intensity 5, Duty Cycle 10%, Cycles/burst 200, Treatment time 120s. Illumina libraries were prepared using 0.43 - 2.62ng of sheared cDNAs by Low Input Library Prep Kit (Clontech Laboratories Inc., Palo Alto, CA, USA) with 8 cycles PCR amplifications.

treatment_protocol: Hemoangiogenic progenitor cells were srtained with CD34 and KDR antibodies, and sorted by Aria-Ⅱ.

value: hemoangiogenic progenitors


title: 201B7_MN_VPA_plus


title: BCKO-2

city: Cleveland

first: Brian

last: Kevany

address: 10900 Euclid Ave.

department: Pharmacology

institute: Case Western Reserve University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Tophat (v2.0.12)
Transcripts were assembled and analyzed sequentially by Cufflinks (v2.2.1), Cuffdiff (v2.2.1) and CummeRbund (v2.6.1)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: n/a
Supplementary_files_format_and_content: RPKM

source_name: Eye

extract_protocol:
Eyes were removed and fixed in RNALater solution and RNA was isolated using the Qiagen Rneasy Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: eye

tag: age

value: Post natal day 21


title: BCKO-1


title: vector_rep 1

description: Sample 1

tag: chip antibody


title: Al_INPUT-MeDIP_rep1


title: B6-3

value: Wild Type


title: cFA07_3_KDRC34_d6


title: B6-2


title: B6-1


title: YY1_d0_Ocf_WT_Oct4_1strep

city: Cold Spring Harbor

first: Cinthya

middle: J

last: Zepeda-Mendoza

state: NY

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description:
PE-4CSeq from ESC line OCF2ΔYY1, viewpoint Oct4 targeting WT allele in chr17, day 0, 1st biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr17_hindiii_fragments.txt
processed data file: YY1_d0_d3_Ocf_WT_Oct4_countmatrix.txt
processed data file: YY1OcfWTOct4_FourCSeqResults.txt

data_processing:
Library strategy: 4C-Seq
Obtained reads were separated using custom perl scripts based on the sample and genotyping SNP on PE1 reads. PE1 reads were trimmed to 30bp to have the highest quality bases for captures mapping. Alignments were performed using bowtie against a reduced database of sequences bordering HindIII restriction sites in the NCBI37/mm9 assembly. Up to 3 mismatches were accepted, and only uniquely mapped reads were taken into account for the 4C data analysis.
Intrachromsomal interaction analysis was performed using the FourCseq bioconductor package (Klein et al., 2014) for the analysis of 4Cseq data between conditions and for identification of significant interactions along the chromosomal profile for viewpoints residing in chr4 and ch17.
Genome_build: mm9
Supplementary_files_format_and_content: Files with the extension .fa contain raw reads processed to select the next 30bp after the HindIII restriction start site. Files with the extension _countmatrix.txt contain the bowtie mapping count data per restriction fragment per chromosome (viewpoints 154.9 reside in chromosome 4; viewpoints that contain the name 'chr11' in name reside in chr11 sequence; viewpoints with the 'WT' classifier in the name reside in chr17). Column 1 specifies the end in bp of the HindIII restriction site as derived from the FourCSeq addFragments command per chromsome, columns 2-5 contain count data of mapped reads per restriction fragment. Files with the extension _hindiii_fragments.txt contain the restriction fragments used to map the bowtie data for the corresponding chromosome. Column 1 is start bp position and 2nd column is end bap position. Files with the extension _FourCSeqResults.txt show the obtained results through contact data analysis by the FourCSeq program. The table shows in the first column the fragments number indexes, whose positions corresponds to the ones from the _hindiii_fragments.txt files. The second column shows the base mean for the given fragment, the third shows the estimated log2 fold change between the two conditions, the fourth the estimated standard error of the log2 fold change, the fifth the Wald test statistic, the sixth the corresponding p-value and the seventh the adjusted p-value.

source_name: Mouse Embryonic Stem Cells

growth_protocol: Routine growth and maintenance of ESCs was carried out as previously described (Eckersley-Maslin et al., 2014), with the exception that Oct4.468/R26-rtTA ESCs were cultured in ESC medium made with Tet System Approved Fetal Bovine Serum (Clontech).

extract_protocol:
4C templates for OCF2ΔOCT4/SOX2 and OCF2ΔYY1 cells were prepared as described in Splinter et al, 2012. Briefly, 1x107 ESC cells were cross-linked for 10 min at RT using 2% formaldehyde (Calbiochem) and 10%FCS in PBS (pH 7.4). 10 ml reactions were transferred to ice and added 1.425ml of 1M glycine, followed by centrifugation for 8 min at 225g at 4°C. Supernatant was subsequently removed and the resulting cell pellet resuspended in 500 μl of ice cold nuclei buffer (10mM Tris pH 7.6, 10mM NaCl, 2mM MgCl2, dH2O) containing protease inhibitors (Roche) for 10 min on ice. An equal volume of nuclei buffer/0.5% NP-40 was added to the tube and incubated for 5 min on ice. Samples were vortexed for 10 s and centrifuged for 1 min at 1,000g and 4°C. Cells were washed once in nuclei buffer/0.5% NP-40 containing protease inhibitors and centrifuged for 1 min at 1,000g and 4°C. Pellets were resuspended in 450µl dH2O and 60µl 10X restriction buffer (buffer 2 supplied with HindIII enzyme, New England BioLabs), incubated 1 hr with 15µl 10% SDS shaking at 900RPM at 37°C, and followed by an additional 1 hr incubation with 75µl 20% Triton X-100. 5 µl aliquots were taken as undigested controls and stored at 4°C. Samples were subsequently digested by adding 800U of HindIII (New England BioLabs) and incubating overnight at 37°C while shaking. 5 µl aliquots were taken as digested controls and de-crosslinked by incubation with 10 μl Proteinase K (10mg/ml, Roche) in 90 μl of 10 mM Tris (pH 7.5) at 65 °C for 1 h. Digestion efficiencies were estimated based on the pattern of smear of the undigested and digested controls by running 20 μl of decrosslinked sample on a 0.6% agarose gel. If digestion was sufficient, HindIII was inactivated by incubating the sample for 20 min at 65°C (shaking gently). The digested nuclei were transferred to a 50 ml falcon tube and mixed with 5.7ml dH2O, 700 μl 10X Ligase Buffer, and 50U T4 Ligase (Roche), and incubated overnight at 16°C. Ligation efficiency was determined by taking 100 μl of ligation reaction and incubating 1 hr at 65°C with 5 μl Proteinase K (10 mg/ml). When run in a 0.6% agarose gel, ligated DNA should appear as a single upper band similar to the undigested control. If ligation occurred, DNA crosslinks were reversed by adding 30 μl of 10 mg/ml Proteinase K and incubation at 65 °C overnight. Subsequently, 15 μl of 20 mg/ml PureLink RNase A (Invitrogen) was added and the reactions incubated for 45 min at 37 °C, followed by phenol extraction and DNA purification as described in Splinter et al, 2012. The DNA pellet was dissolved in 150 μl of 10 mM Tris (pH 7.5), and digested overnight with 50U DpnII (New England BioLabs) at 37°C while shaking. An aliquot of 5 μl was taken from the DpnII reaction and mixed with 95 μl of 10 mM Tris (pH 7.5), and 20 μl loaded into a 0.6% agarose gel to assess digestion efficiency. If sufficient digestion was achieved, DpnII was heat inactivated by incubating 20 minutes at 65°C, and DNA was ligated at low concentrations (12.1ml dH2O, 1.3ml 10X ligation buffer, 100U T4 DNA Ligase) overnight at 16°C. DNA was phenol extracted and ethanol precipitated with glycogen (Roche) as a carrier. The resulting 4C templates were purified using QIAquick PCR purification kit columns (Qiagen), dissolved in 10 mM Tris (pH 7.5), and stored at -20°C.
Inverse 4C amplification primers were designed per viewpoint following standard rules for PCR primer design, and checking alignment uniqueness to the desired fragment as compared to the rest of the genome. Amplification primers for all viewpoints were added the PE1 and PE2 Illumina paired-end primers plus a 1-2 nucleotide barcode in their 5' ends for HiSeq PEx100 sequencing. Each of the 2 viewpoints was amplified from the available OCF2ΔOCT4/SOX2 and OCF2ΔYY1 4C templates in reactions using 3.2µg 4C template, 16µl dNTP (10mM, New England BioLabs), 24µl reading primer PE1 of a 1µg/µl primer stock, 24µl reading primer PE2 of a 1µg/µl primer stock, 11.2 µl Expand Long Template polymerase (Roche), 80µl 10X PCR buffer 1 (supplied with polymerase), and dH2O until completing 800µl total. This volume is then mixed and separated into 16x50µl PCR reactions, and run using the following program: 94 °C for 2 min, followed by 30 cycles of 15 s at 94 °C, 1 min at 55 °C and 3 min at 68 °C, and one final step of 5min at 68 °C. PCR reactions were subsequently collected and pooled together, and purified using AMPure beads (Beckman Coulter) with a 0.9X volume ratio per viewpoints. Equimolar amounts of isolated captured viewpoints were pooled together using the KK4824 kit to correct for insert size lengths (Kapa Biosystems). Pooled libraries were sequenced using two lanes of MiSeq PE300.

tag: passages


title: YY1_d3_154.9_1strep

description:
PE-4CSeq from ESC line OCF2ΔYY1, viewpoint 154.9, day 3, 1st biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr4_hindiii_fragments.txt
processed data file: YY1_d0_d3_154.9_countmatrix.txt
processed data file: YY1154.9_FourCSeqResults.txt


title: YY1_d3_Ocf_Mut_YY1_chr11_2ndrep

description:
PE-4CSeq from ESC line OCF2ΔYY1, viewpoint Oct4 targeting mutated allele in chr11, day 3, 2nd biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr11_hindiii_fragments.txt
processed data file: YY1_d0_d3_Ocf_Mut_YY1_chr11_countmatrix.txt
processed data file: (insertion region, no cis analysis)


title: YY1_d3_154.9_2ndrep

description:
PE-4CSeq from ESC line OCF2ΔYY1, viewpoint 154.9, day 3, 2nd biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr4_hindiii_fragments.txt
processed data file: YY1_d0_d3_154.9_countmatrix.txt
processed data file: YY1154.9_FourCSeqResults.txt


title: YY1_d3_Ocf_WT_Oct4_1strep

description:
PE-4CSeq from ESC line OCF2ΔYY1, viewpoint Oct4 targeting WT allele in chr17, day 3, 1st biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr17_hindiii_fragments.txt
processed data file: YY1_d0_d3_Ocf_WT_Oct4_countmatrix.txt
processed data file: YY1OcfWTOct4_FourCSeqResults.txt


title: YY1_d3_Ocf_WT_Oct4_2ndrep

description:
PE-4CSeq from ESC line OCF2ΔYY1, viewpoint Oct4 targeting WT allele in chr17, day 3, 2nd biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr17_hindiii_fragments.txt
processed data file: YY1_d0_d3_Ocf_WT_Oct4_countmatrix.txt
processed data file: YY1OcfWTOct4_FourCSeqResults.txt


title: YY1_d0_Ocf_Mut_YY1_chr11_1strep

description:
PE-4CSeq from ESC line OCF2ΔYY1, viewpoint Oct4 targeting mutated allele in chr11, day 0, 1st biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr11_hindiii_fragments.txt
processed data file: YY1_d0_d3_Ocf_Mut_YY1_chr11_countmatrix.txt
processed data file: (insertion region, no cis analysis)


title: YY1_d3_Ocf_Mut_YY1_chr11_1strep

description:
PE-4CSeq from ESC line OCF2ΔYY1, viewpoint Oct4 targeting mutated allele in chr11, day 3, 1st biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr11_hindiii_fragments.txt
processed data file: YY1_d0_d3_Ocf_Mut_YY1_chr11_countmatrix.txt
processed data file: (insertion region, no cis analysis)


title: YY1_d0_154.9_2ndrep

description:
PE-4CSeq from ESC line OCF2ΔYY1, viewpoint 154.9, day 0, 2nd biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr4_hindiii_fragments.txt
processed data file: YY1_d0_d3_154.9_countmatrix.txt
processed data file: YY1154.9_FourCSeqResults.txt


title: YY1_d0_154.9_1strep

description:
PE-4CSeq from ESC line OCF2ΔYY1, viewpoint 154.9, day 0, 1st biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr4_hindiii_fragments.txt
processed data file: YY1_d0_d3_154.9_countmatrix.txt
processed data file: YY1154.9_FourCSeqResults.txt


title: YY1_d0_Ocf_WT_Oct4_2ndrep

description:
PE-4CSeq from ESC line OCF2ΔYY1, viewpoint Oct4 targeting WT allele in chr17, day 0, 2nd biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr17_hindiii_fragments.txt
processed data file: YY1_d0_d3_Ocf_WT_Oct4_countmatrix.txt
processed data file: YY1OcfWTOct4_FourCSeqResults.txt


title: OctSox_d3_Ocf_WT_Oct4_2ndrep

description:
PE-4CSeq from ESC line OCF2ΔOCT4/SOX2, viewpoint Oct4 targeting WT allele in chr17, day 3, 2nd biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr17_hindiii_fragments.txt
processed data file: OctSox_d0_d3_Ocf_WT_Oct4_countmatrix.txt
processed data file: OctSoxOcfWTOct4_FourCSeqResults.txt


title: BCKO-3


title: OctSox_d3_Ocf_Mut_OctSox_chr11_2ndrep

description:
PE-4CSeq from ESC line OCF2ΔOCT4/SOX2, viewpoint Oct4 targeting mutated allele in chr11, day 3, 2nd biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr11_hindiii_fragments.txt
processed data file: OctSox_d0_d3_Ocf_Mut_OctSox_chr11_countmatrix.txt
processed data file: (insertion region, no cis analysis)


title: OctSox_d3_Ocf_WT_Oct4_1strep

description:
PE-4CSeq from ESC line OCF2ΔOCT4/SOX2, viewpoint Oct4 targeting WT allele in chr17, day 3, 1st biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr17_hindiii_fragments.txt
processed data file: OctSox_d0_d3_Ocf_WT_Oct4_countmatrix.txt
processed data file: OctSoxOcfWTOct4_FourCSeqResults.txt


title: OctSox_d3_Ocf_Mut_OctSox_chr11_1strep

description:
PE-4CSeq from ESC line OCF2ΔOCT4/SOX2, viewpoint Oct4 targeting mutated allele in chr11, day 3, 1st biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr11_hindiii_fragments.txt
processed data file: OctSox_d0_d3_Ocf_Mut_OctSox_chr11_countmatrix.txt
processed data file: (insertion region, no cis analysis)


title: OctSox_d3_154.9_2ndrep

description:
PE-4CSeq from ESC line OCF2ΔOCT4/SOX2, viewpoint 154.9, day 3, 2nd biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr4_hindiii_fragments.txt
processed data file: OctSox_d0_d3_154.9_countmatrix.txt
processed data file: OctSox154.9_FourCSeqResults.txt


title: OctSox_d3_154.9_1strep

description:
PE-4CSeq from ESC line OCF2ΔOCT4/SOX2, viewpoint 154.9, day 3, 1st biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr4_hindiii_fragments.txt
processed data file: OctSox_d0_d3_154.9_countmatrix.txt
processed data file: OctSox154.9_FourCSeqResults.txt


title: OctSox_d0_Ocf_WT_Oct4_2ndrep

description:
PE-4CSeq from ESC line OCF2ΔOCT4/SOX2, viewpoint Oct4 targeting WT allele in chr17, day 0, 2nd biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr17_hindiii_fragments.txt
processed data file: OctSox_d0_d3_Ocf_WT_Oct4_countmatrix.txt
processed data file: OctSoxOcfWTOct4_FourCSeqResults.txt


title: OctSox_d0_Ocf_Mut_OctSox_chr11_2ndrep

description:
PE-4CSeq from ESC line OCF2ΔOCT4/SOX2, viewpoint Oct4 targeting mutated allele in chr11, day 0, 2nd biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr11_hindiii_fragments.txt
processed data file: OctSox_d0_d3_Ocf_Mut_OctSox_chr11_countmatrix.txt
processed data file: (insertion region, no cis analysis)


title: OctSox_d0_154.9_1strep

description:
PE-4CSeq from ESC line OCF2ΔOCT4/SOX2, viewpoint 154.9, day 0, 1st biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr4_hindiii_fragments.txt
processed data file: OctSox_d0_d3_154.9_countmatrix.txt
processed data file: OctSox154.9_FourCSeqResults.txt


title: OctSox_d0_154.9_2ndrep

description:
PE-4CSeq from ESC line OCF2ΔOCT4/SOX2, viewpoint 154.9, day 0, 2nd biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr4_hindiii_fragments.txt
processed data file: OctSox_d0_d3_154.9_countmatrix.txt
processed data file: OctSox154.9_FourCSeqResults.txt


title: OctSox_d0_Ocf_Mut_OctSox_chr11_1strep

description:
PE-4CSeq from ESC line OCF2ΔOCT4/SOX2, viewpoint Oct4 targeting mutated allele in chr11, day 0, 1st biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr11_hindiii_fragments.txt
processed data file: OctSox_d0_d3_Ocf_Mut_OctSox_chr11_countmatrix.txt
processed data file: (insertion region, no cis analysis)


title: At_INPUT-MeDIP_rep2

data_processing:
Basecalls performed using SHORE v0.7alpha3.
Quality filtering included trimming of low quality nucleotides.
ChIP-seq and MeDIP-seq reads were mapped against the Arabidopsis thaliana reference (TAIR10) using Bowtie choosing one match in case of multiple ones and allowing one mismatch.
For the ChIP-seq and MeDIP-seq libraries, since average read coverage was highly correlated between the two biological replicates, they were pooled for subsequent analysis. In order to reduce biases introduced by PCR amplification, a maximum of 5 reads mapping at exactly the same positions were taken into account.
Peak detection was done using SICER normalising the ChIP-seq coverage by the INPUT coverage. Window size was adjusted according to the distribution of the mark over the genes: 300 bp for H3K27me1 and 150bp for 5mC. Effective genome size was estimated as 85% of the total genome and FDR set at 10−3 .
Genome_build: Arabidopsis thaliana (TAIR10)
Supplementary_files_format_and_content: bedGraph = scores represent the ChIP-seq coverage ; bed = scores represent number of reads per domain

growth_protocol: Plants of Arabidopsis thaliana accession Columbia-0 were grown in soil under short day conditions (8h light/16h dark) at 22.5C.

extract_protocol:
Chromatin and DNA immunoprecipitation was performed essentially as described in Gendrel et al., 2005 and Cortijo et  al., 2014, respectively. Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturers instructions and its quality was validated using RNA 6000 NanoChip (Agilent).
20 ng of immunoprecipitated (IP) and genomic (INPUT) DNA was used to prepare libraries with the ChIP-Seq DNA Sample Prep Kit IP-102-1001. Quality of libraries was validated using 2100 Bioanalyzer (Agilent). Libraries were sequenced with Illumina Genome Analyzer IIx according to manufacturers instructions.


title: At_INPUT-MeDIP_rep1


title: At_MeDIP_rep2


title: YY1_d0_Ocf_Mut_YY1_chr11_2ndrep

description:
PE-4CSeq from ESC line OCF2ΔYY1, viewpoint Oct4 targeting mutated allele in chr11, day 0, 2nd biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr11_hindiii_fragments.txt
processed data file: YY1_d0_d3_Ocf_Mut_YY1_chr11_countmatrix.txt
processed data file: (insertion region, no cis analysis)


title: At_MeDIP_rep1


title: At_H3K27me1_rep1


title: At_H3K27me1_rep2


title: Gata6 ChIP-Seq replicate3

city: Madrid

first: Francesc

last: Madriles

state: Madrid

address: c/ Melchor Fernandez Almagro, 3

department: Cancer Cell Biology

institute: CNIO

data_processing:
Image analysis and per-cycle base-calling was performed with Illumina Real Time Analysis software (RTA1.13). Conversion to FASTQ read format was performed with CASAVA-1.8 (Illumina).
ChIP-seq reads were aligned to the mm9 genome assembly using BWA version 0.5.9-r16 allowing 0-1 mismatches
Unique aligned reads were converted to BED format
Gata6 ChIP-seq replicates were merged into a single file and were normalized randomly to the same number of reads in the Input DNA file.
The reads were directionally extended to 300 bp, and for each base pair in the genome the number of overlapping sequence reads was determined and averaged over a 10 bp window to create a wig file to visualize the data in the University of California Santa Cruz genome browser (http://genome.ucsc.edu)
Peaks were called using macs version 1.4 with the following setting: format (BED), effective genome size (1.87e+09), band width (300), model fold (20,40),  pvalue cutoff (1.00e-05)
Peaks with FDR>1 were discarded
Genome_build: NCBI37/mm9, July 2007
Supplementary_files_format_and_content: peak file (BED) is found on series level and was generated with macs version 1.4 by applying FDR<1. This includes peak coordinates (chromosome, start, end).

source_name: pancreas

extract_protocol:
Pancreata from wild-type mice were removed, minced, crosslinked, and homogenized. The resulting lysate was sonicated and the sheared chromatin was immunoprecipitated with a Gata6-specific antibody. Immunoprecipitated DNA was washed, eluted and used for library preparation. The input DNA library was prepared by pooling equal amounts of DNA from the four input replicates.
DNA was resolved by electrophoresis and fractions of 50-250bp were extracted. Fractions were processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq DNA Sample Preparation Guide" (part # 15005180 Rev. C). Adapter-ligated libraries were completed by limited-cycle PCR with Illumina PE primers (15 cycles). The resulting purified DNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

tag: age (weeks)

value: Pancreas


title: Input DNA pool

value: pool


title: Gata6 ChIP-Seq replicate1


title: Gata6 ChIP-Seq replicate2


title: OctSox_d0_Ocf_WT_Oct4_1strep

description:
PE-4CSeq from ESC line OCF2ΔOCT4/SOX2, viewpoint Oct4 targeting WT allele in chr17, day 0, 1st biological replicate
PCR amplified products of different sizes, sequenced in Illumina's MiSeq
processed data file: chr17_hindiii_fragments.txt
processed data file: OctSox_d0_d3_Ocf_WT_Oct4_countmatrix.txt
processed data file: OctSoxOcfWTOct4_FourCSeqResults.txt


title: Gata6 ChIP-Seq replicate4


title: Oct4_rep 1

description: Sample 3

tag: cell line


title: ASK211

first: Enrique

last: Carrillo de Santa Pau

address: C/ Melchor Fernández Almagro, 3

department: Cancer Cell Biology Programme

institute: Spanish National Cancer Research Centre (CNIO)

data_processing:
Image analysis and per-cycle basecalling was performed with Illumina Real Time Analysis software (RTA1.13). Conversion to FASTQ read format was performed with CASAVA-1.8 (Illumina).
RNA-seq reads were aligned to the mm9 genome assembly using TopHat version 2.0.4 with the following configurations: --bowtie1, --max-multihits 5, --genome-read-mismatches 1, --segment-mismatches 1, --segment-length 19, --splice-mismatches 0
Fragments
 Per
 Kilobase
of
 transcript
 per
 Million
 fragments
mapped (FPKM) were calculated using Cufflinks version 2.0.1 with the following configurations: -N, -u
Genome_build: NCBIm37/mm9, April 2007
Supplementary_files_format_and_content: Tab delimited fpkm_tracking files including FPKM values were generated with Cufflinks version 2.0.1

growth_protocol: mice were maintained under stanrdard conditions

extract_protocol:
pancreas was extracted, flash frozen in liquid nitrogen and homogenized in GTC buffer. RNA was extracted with standard phenol-chloroform protocol
1-2 µg of total RNA samples was used as provided by the user. RNA Integrity Numbers were in the range 7.1 to 8.8 when assayed on an Agilent 2100 Bioanalyzer. PolyA+ RNA fraction was extracted and randomly fragmented, converted to double stranded cDNA and processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq RNA Sample Preparation v2 Protocol" (Part # 15026494 Rev. C). Adapter-ligated library was completed by 8 cycles of PCR with Illumina PE primers. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

value: 6-8 weeks

value: Ptf1a-Cre +/KI

value: mixed

value: pancreas


title: ASK212


title: BKD244P_WT


title: BKD388

value: Ptf1a-Cre +/KI; Gata6 lox/lox


title: BKD176_KO


title: BSH294


title: BKD250N_KO


title: 1118_S536E_Erl_r1

city: San Francisco

first: Saurabh

last: Asthana

state: CA

address: 1450 Third Street, Room HD276

department: Helen Diller Family Comprehensive Cancer Center

institute: UCSF

data_processing:
Reads were aligned against NCBI build 37 (hg19) of the human genome using the NCBI Ensembl transcript annotation (version 75) with RSEM, which also yielded gene-level expression quantification.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: 11-18 cells, infected with constitutively-active RelAS536E & treated with erlotinib

extract_protocol:
RNA from each of the indicated cell lines was extracted by RNeasy kit (Qiagen).
In total, 2 ug of total RNA was used for deep sequencing library preparation using Illumina Truseq sample prep kits (Illumina) according to the manufacturer's protocols. Sequencing libraries with different indices were pooled and sequenced in paired end format to a length of 100bp using the HiSeq2000 platform at Center for Advanced Technology at UCSF.

value: Lung adenocarcinoma


title: ASK210_WT


title: 1118_IKBSR_Veh_r2

source_name: 11-18 cells, infected with vector expressing IkB-alpha super-repressor & treated with DMSO


title: 1118_IKBSR_Erl_r0

source_name: 11-18 cells, infected with vector expressing IkB-alpha super-repressor & treated with erlotinib


title: 1118_IKBSR_Veh_r1

value: infected with vector expressing IkB-alpha super-repressor & treated with DMSO


title: 1118_S536E_Veh_r2

source_name: 11-18 cells, infected with constitutively-active RelAS536E & treated with DMSO


title: 1118_EV_Erl_r2

source_name: 11-18 cells, infected with empty vector & treated with erlotinib


title: 1118_S536E_Erl_r0

value: infected with constitutively-active RelAS536E & treated with erlotinib


title: 1118_IKBSR_Veh_r0


title: 1118_S536E_Veh_r0

value: infected with constitutively-active RelAS536E & treated with DMSO


title: 1118_IKBSR_Erl_r2

value: infected with vector expressing IkB-alpha super-repressor & treated with erlotinib


title: 1118_IKBSR_Erl_r1


title: 1118_EV_Erl_r1

value: infected with empty vector & treated with erlotinib


title: 1118_E_P_r2

source_name: 11-18 cells, treated with erlotinib + PBS-1086

value: treated with erlotinib + PBS-1086


title: 1118_EV_Veh_r2

source_name: 11-18 cells, infected with empty vector & treated with DMSO


title: 1118_EV_Erl_r0


title: 1118_S536E_Erl_r2


title: 1118_EV_Veh_r0

value: infected with empty vector & treated with DMSO


title: 1118_E_P_r1


title: Mock IP pooled reps

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

data_processing:
Bioinformatic analysis of chromatin immunoprecipitation-seq, DNase-seq, and TOMTOM DNA motif enrichment :Purified DNA from ChIP or DNase I digested chromatin were used to prepare libraries for Illumina high-throughput sequencing as described in manufacturer’s protocol (Illumina Sequencing, San Diego, CA, USA). Libraries were sequenced to generate 35 bp single end reads using Illumina GAII sequencer at the Advanced Technology Center, NCI (Frederick, MD). Sequence reads were mapped to the reference genome hg19 by the CASAVA 1.8.2 pipeline.
Hotspot detection for DNase-seq : Regions of local enrichment of sequence tags using a hotspot detection algorithm was identified essentially as previously described [55,77] with a false discovery rate (FDR) of 0.1%.
Hotspot detection and input adjustment for chromatin immunoprecipitation-seq: The hotspot detection algorithm was similarly applied to ChIP-seq data with the following modification. The sequencing data from matching input samples are used for the processing of ChIP data, as a measure of background signal that might be significant. After normalizing the input data to match the number of tags in the ChIP data, the number of input tags is subtracted from the number of ChIP tags in the target window before calculating its z-score.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: CSV (Comma-Separated Values)

source_name: Human colorectal cancer cell line

growth_protocol: Plated to mid-confluency, medium change every 3-5 days. 5 x 175mm3 flasks harvested for each experiment.

extract_protocol:
For chromatin: Mnase treatment followed by mild crosslinking and low salt extraction overnight at 4C. IPs with CENP-A, HJURP or Mock. For DHS fragments: Low DNAse I treatment followed by sucrose gradient purification of DHS fragments. Please see Athwal-Walkiewicz et al Epigenetics and Chromatin 8:3 for full protocol and cited references.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: antibody


title: 1118_E_P_r0


title: 1118_PBS_r2

source_name: 11-18 cells, treated with PBS-1086

value: treated with PBS-1086


title: 1118_S536E_Veh_r1


title: 1118_PBS_r0


title: SW480_HJURP pooled reps

value: HJURP (Bethyl, A302-822A)


title: 1118_PBS_r1


title: HeLa_HJURP pooled reps

source_name: Human cervical cancer cell line

value: HeLa


title: 1118_Erl_r2

source_name: 11-18 cells, treated with erlotinib

value: treated with erlotinib


title: SW480_DHS pooled reps


title: 1118_Erl_r1


title: HeLa_CENP-A pooled reps

value: CENP-A (Santa Cruz, sc-22787 & sc-11277)


title: Epi_Colon_CENP-A pooled reps

source_name: Human normal colon cell line

value: HcoEpiC


title: 1118_Veh_r1

source_name: 11-18 cells, treated with DMSO

value: treated with DMSO


title: 1118_Veh_r0


title: 1118_Erl_r0


title: HeLa _Input pooled reps


title: 1118_EV_Veh_r1


title: SW480_CENP-A pooled reps


title: SW480_Input pooled reps


title: 24_T1_input

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

country: United Kingdom

institute: Cancer Research UK Cambridge Institute

description:
Colon tumor (adenocarcinoma)
SUL_CRC2_24T1_hmC_Inp.689.s_2
hmeDIP-seq
SUL_CRC2_24T1_hmC_Inp.689.s_2

data_processing:
Alignments: Illumina reads were aligned to the Human Reference Genome (assembly hg18, NCBI Build 36.3, March 2008) using BWA
Wap counting: counts of overlapping reads in 300bp windows centered around Inifinium array probes (overlapping windows merged), with overlapping reads in control subtracted
Wide promoter counting: counts of overlapping reads in 3500bp windows, 3000bp upstream of TSSs and 500 bp downstream (overlapping windows merged), with overlapping reads in control subtracted
Narrow promoter counting: counts of overlapping reads in 1500bp windows,1000bp upstream of TSSs and 500 bp downstream (overlapping windows merged), with overlapping reads in control subtracted
Gene counting: counts of overlapping reads in windows from TSS to TES (overlapping windows merged), with overlapping reads in control subtracted
Genome_build: hg18
Supplementary_files_format_and_content: *.counts.bed: bed file with score set to number of reads overlapping a feature (minimum 1)
Supplementary_files_format_and_content: *.rpkm.bed: bed file with score set to RPKM based on reads overlapping a feature (minimum reads 1)

source_name: Colon primary tissue

growth_protocol: not applicable

extract_protocol:
For hmeDIP-seq, Illumina libraries were prepared from sonicated genomic DNA followed by immunoprecipitation with anti-5hmC antibody (Active Motif, 39791) and sequenced.
For TET2 ChIP-seq, formaldehyde cross-linked material was immunoprecipitated with anti-TET2 antibody (SantaCruz sc-136926) followed by Illumina adapter ligation and sequencing.

treatment_protocol: not applicable

tag: sample id

tag: fraction

value: Input

value: Colon tumor (adenocarcinoma)


title: 35_T1_input

description:
Colon tumor (adenocarcinoma)
SUL_CRC2_35T1_hmC_Inp.689.s_2
hmeDIP-seq
SUL_CRC2_35T1_hmC_Inp.689.s_2

tag: tissue


title: 42_T1_input

description:
Colon tumor (adenocarcinoma)
SUL_CRC2_42T1_hmC_Inp.689.s_6
hmeDIP-seq
SUL_CRC2_42T1_hmC_Inp.689.s_6


title: 44_T1_input

description:
Colon tumor (adenocarcinoma)
SUL_CRC2_44T1_hmC_Inp.689.s_5
hmeDIP-seq
SUL_CRC2_44T1_hmC_Inp.689.s_5


title: HeLa_DHS pooled reps


title: 42_T1_bound

description:
Colon tumor (adenocarcinoma)
SUL_CRC2_42T1_hmC_bnd.689.s_5
hmeDIP-seq
SUL_CRC2_42T1_hmC_bnd.689.s_5

value: hmC_bound fraction

value: anti 5-hmC rabbit polyclonal (Active Motif, catalog# 39791, lot# 02511003)


title: 24_T1_bound

description:
Colon tumor (adenocarcinoma)
SUL_CRC2_24T1_hmC_bnd.689.s_1
hmeDIP-seq
SUL_CRC2_24T1_hmC_bnd.689.s_1


title: 35_T1_bound

description:
Colon tumor (adenocarcinoma)
SUL_CRC2_35T1_hmC_bnd.689.s_1
hmeDIP-seq
SUL_CRC2_35T1_hmC_bnd.689.s_1


title: 24_NC_Input

description:
Normal Colon Close to tumor
SLX-3718.607.s_7
hmeDIP-seq
SLX-3718.607.s_7

value: Normal Colon Close to tumor


title: Ep300_ChIP-seq

city: La Jolla

first: MICHAEL

middle: G

last: ROSENFELD

address: 9500 Gilman Drive

institute: HHMI/UCSD

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The sequencing reads were aligned to mm8  by using Bowtie or Bowtie2.
The bedgraph files were generated by using HOMER (http://homer.salk.edu/homer/).
The peak finding was carried by using HOMER (http://homer.salk.edu/homer/).
The motif enrichment analysis was carried by using HOMER (http://homer.salk.edu/homer/).
Genome_build: mm8

source_name: AtT20 cells

growth_protocol: AtT-20 cells were obtained from ATCC, maintained in UltraCULTURE medium (Lonza) supplemented with 5% FBS and 1X GlutaMAX (Invitrogen) without antibiotics at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
Cells were cross-linked with 1% formaldehyde in PBS at room temperature for 10 minutes. Chromatin was fragmented to 300-500 bp using a tip sonicator and centrifuged at 16,000 g for 10 min. The supernatant was pre-cleared with 20μl magnetic beads. The pre-cleared chromatin was incubated with 2-5 μg antibodies at 4°C overnight. Antibody-protein-DNA complexes were pulled down by incubating with 20μl Protein G Dynabeads (Life Technologies) and washed. The eluted complex was de-crosslinked overnight at 65°C. BLRP-tagged ChIP was performed using Nanolink Streptavidin Magnetic beads (Solulink) to directly pull down BLRP-tagged protein–DNA complex. Additional brief washes with 1% SDS in TE and TE buffer were introduced after normal washes. The washed streptavidin beads were then subjected to TEV protease (Life Technologies) digestion to release tagged protein and DNA complex before de-crosslinking at 65°C overnight.
Extracted DNA was ligated to specific adaptors followed by deep sequencing on the Illumina GAII system according to the manufacturer’s instructions.

treatment_protocol: To make cell lines expressing tagged-ASCL1 or LDB1, we modified in vivo biotin-tagging system . AtT20 cell lines expressing high level of the bacterial biotin ligase (BirA) were selected and tested for biotin ligation efficiency. Two lines were chosen as parental lines to make BLRP-tagged expression cell lines. Expression vectors for Tagged-ASCL1 and LDB1 were engineered from a modified pCAGGS vector, which was inserted a double-stranded oligonucleotides encoding the peptide of MAGGLNDIFEAQKIEWHEDTGGSWRAPGGGGGSGGGGSGENLYFQSSDYKDHDGDYKDHDIDYKDDDDK. The BLRP (amino acids 3-20), in which the lysine residue (underlined) can be biotinylated by BirA, was followed by a glycine-rich region, a specific recognition site for TEV protease (ENLYFQS) and a 3XFLAG sequence. The glycine-rich region serves as a spacer between BLRP and TEV site. To further increase the specificity, the TEV site is included for cleaving the tagged protein from the BLRP tag (Life Technologies). Specific antibodies used in this study are as following: anti-P300 (sc585), anti-H3K4me1 (07-436) from Millipore; anti-H3K27Ac (ab4729) from Abcam; anti-TBX19 (HPA005800) from Sigma-Aldrich.


title: Ascl1 ChIP-seq


title: 35_NC_bound

description:
Normal Colon Close to tumor
SLX-3737.607.s_2
hmeDIP-seq
SLX-3737.607.s_2


title: H3K4me1_ChIP-seq

value: anti-H3K4me1 (07-436, Millipore)


title: Tbx19_ChIP-seq

value: anti-TBX19 (HPA005800, Sigma-Aldrich)


title: H3K27ac_ChIP-seq

value: anti-H3K27ac (b4729, Abcam)


title: Ldb1_ChIP-seq


title: 44_NC_bound

description:
Normal Colon Close to tumor
SLX-3733.607.s_3
hmeDIP-seq
SLX-3733.607.s_3


title: 24_NC_bound

description:
Normal Colon Close to tumor
SLX-3717.607.s_6
hmeDIP-seq
SLX-3717.607.s_6


title: Aa_INPUT-MeDIP_rep1

data_processing:
Basecalls performed using SHORE v0.7alpha3.
Quality filtering included trimming of low quality nucleotides.
ChIP-seq, MeDIP-seq and RNA-seq reads were mapped against the Arabis alpina reference using Bowtie choosing one match in case of multiple ones and allowing one mismatch.
For the ChIP-seq and MeDIP-seq libraries, since average read coverage was highly correlated between the two biological replicates, they were pooled for subsequent analysis. In order to reduce biases introduced by PCR amplification, a maximum of 5 reads mapping at exactly the same positions were taken into account.
Peak detection was done using SICER normalising the ChIP-seq coverage by the INPUT coverage. Window size was adjusted according to the distribution of the mark over the genes: 150 bp for H3K4me3 and 5mC; 300 bp for H3K27me3 and H3K27me1. Effective genome size was estimated as 75% of the total genome and FDR set at 10−3 .
mRNA abundance for each gene was estimated as the average number of positions mapped to its transcribed region over the total number of positions covered.
Genome_build: Arabis alpina
Supplementary_files_format_and_content: bedGraph = scores represent the ChIP-seq and MeDIP-seq coverage ; bed = scores represent number of reads per domain ; covexonsByGene.txt = mRNA abundance per gene

organism: Arabis alpina

source_name: young leaves

growth_protocol: Plants of Arabis alpina accession Pajares were grown in soil under long day conditions (16h light/8h dark) at 22.5C.

value: Pajares

value: young leaves


title: Aa_INPUT-MeDIP_rep2


title: 24_NA_bound

description:
Normal Colon Away from tumor (20cm)
SLX-3705.607.s_5
hmeDIP-seq
SLX-3705.607.s_5

value: Normal Colon Away from tumor (20cm)


title: input DNA

data_processing:
Image analysis and per-cycle basecalling was performed with Illumina Real Time Analysis software (RTA1.13). Conversion to FASTQ read format was performed with CASAVA-1.8 (Illumina).
ChIP-seq reads were aligned to the hg19 genome assembly using BWA version 0.5.9-r16 allowing 0-1 mismatches
Unique aligned reads were converted to BED format
GATA6 ChIP-seq & Input DNA aligment files were normalized to the same number of reads randomly.
The reads were directionally extended to 300 bp, and for each base pair in the genome the number of overlapping sequence reads was determined and averaged over a 10 bp window to create a wig file to visualize the data in the University of California Santa Cruz genome browser (http://genome.ucsc.edu)
Peaks were called using macs version 1.4 with the following setting: format (BED), effective genome size (2.70e+09), band width (300), model fold (20,40),  pvalue cutoff (1.00e-05)
Peaks with FDR>1 were discarded
Genome_build: GRCh37/hg19, February 2009
Supplementary_files_format_and_content: peak file was generated with macs version 1.4

growth_protocol: PaTu8988S cells were grown in DMEM plus 10% FBS. When cells were at 70-80% confluence, proteins were cross-linked to DNA with formaldehyde 1% 15 minutes.

extract_protocol:
Cells were lysed in 0.5% SDS, lysates were sonicated and clarified. Chromatin was diluted 5 fold and incubated with beads for pre-clearing. After pre-clearing, chromatin was incubated o/n with anti-GATA6 antibody.
DNA samples were provided by the user. Input sample corresponds to a balanced blend of the inputs from the three individual samples. Both 20ng of input pool and 6ng of individual sample DNA, as quantitated by fluorometry, were resolved by electrophoresis and fractions of 50-250bp were taken. 1-3 ng of DNA fraction per sample was processed through subsequent enzymatic treatments of end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq DNA Sample Preparation Guide" (part # 15005180 Rev. C). Adapter-ligated libraries were completed by limited-cycle PCR with Illumina PE primers (13 cycles). The resulting purified DNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer's protocols.

value: pancreatic ductal adenocarcinoma

value: anti hGATA6 R&D AF1700

tag: chip antibody catalog #

tag: chip antibody manufacturer

value: R&D


title: Aa_MeDIP_rep2

value: 5mC (Diagenode,Mab-006, lot.#DA-0015)


title: GATA6 ChIP-seq


title: 42_NC_bound

description:
Normal Colon Close to tumor
SLX-3713.607.s_1
hmeDIP-seq
SLX-3713.607.s_1


title: Aa_MeDIP_rep1


title: Aa_mRNA_rep1


title: Aa_H3K27me3_rep2


title: Aa_H3K27me1_rep2


title: Aa_INPUT-ChIP_rep1


title: Aa_H3K4me3_rep2


title: Aa_H3K27me3_rep1


title: Aa_H3K4me3_rep1


title: 37_NC_bound

description:
Normal Colon Close to tumor
SLX-3721.607.s_8
hmeDIP-seq
SLX-3721.607.s_8


title: wild-type S phase (75 min)

city: Norwich

first: Conrad

middle: A

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

data_processing:
Sequence reads were mapped to the S. pombe reference genome using stampy.
Sequence reads mapping to a single genomic location were summed in 1 kb bins. Windows where fewer than 250 reads were mapped in either sample were excluded.
Normalised copy numbers were generated by dividing the sequence read counts from the replicating sample by counts from the non-replicating 45 min post-elutriation.
The resulting absolute ratios reflect the read numbers; therefore data were normalized for read number and the fraction of bulk genome replication (determined by flow cytometry).  This resulted in >95% of the data points lying between 1 and 2 (a biologically imposed restraint).
Genome_build: ASM294v2
Supplementary_files_format_and_content: Wig & bedgraph files containing analysed datasets.

organism: Schizosaccharomyces pombe

source_name: Genomic DNA from cells 125 minutes post-elutriation

extract_protocol:
Library preparation and sequencing was carried out according to Illumina instructions.
DNA was prepared using the QIAGEN 100/G Genomic-tip"

tag: relevant genotype

tag: growth protocol

value: Cells were synchronised in G2 by elutriation, concentrated into a volume of 200 mls, grown in fresh media at 27 °C and a sample taken after 125 min.

tag: treatment protocol

value: None.


title: wild-type S phase (15 min)

source_name: Genomic DNA from cells 65 minutes post-elutriation

value: Cells were synchronised in G2 by elutriation, concentrated into a volume of 200 mls, grown in fresh media at 27 °C and a sample taken after 65 min.


title: wild-type S phase (35 min)

source_name: Genomic DNA from cells 85 minutes post-elutriation

value: Cells were synchronised in G2 by elutriation, concentrated into a volume of 200 mls, grown in fresh media at 27 °C and a sample taken after 85 min.


title: wild-type S phase (30 min)

source_name: Genomic DNA from cells 80 minutes post-elutriation

value: Cells were synchronised in G2 by elutriation, concentrated into a volume of 200 mls, grown in fresh media at 27 °C and a sample taken after 80 min.


title: wild-type S phase (25 min)

source_name: Genomic DNA from cells 75 minutes post-elutriation

value: Cells were synchronised in G2 by elutriation, concentrated into a volume of 200 mls, grown in fresh media at 27 °C and a sample taken after 75 min.


title: wild-type S phase (45 min)

source_name: Genomic DNA from cells 95 minutes post-elutriation

value: Cells were synchronised in G2 by elutriation, concentrated into a volume of 200 mls, grown in fresh media at 27 °C and a sample taken after 95 min.


title: The ribonucletide incorpration due to DNA synthesis by Pol-delta

description:
PU-seq_leftward_moving_fork.wig
PU-seq_terminaton-events.wig
origin-effici.bedgraph
PU-seq_Trep.wig

data_processing:
Sequence pair-end reads were mapped to the S. pombe reference genome using bowtie2 with 50bp-triming of 3'-side of R1 and R2 reads.
Pairs of seqeunce reads which were properly aligned were selected based on 0x2 bit of the flag paramer of each pair.
Pairs of seqeunce read mapping to a single genomic location were summed in 300 bins in the strand-specifc manner.
Normalised numbers were generated by dividing the sequence pair counts at each bin by the total number of reads.
The resulting numbers reflect the numbers of incorporated ribonucletides at each location in one strand (Watson or Crick strand) either in pol?-L519G or pol?-M630F mutants; the dataset of the count in bin is the list of these numbers.
The subsequent informatics analysis generated the following datasets; the ratios of Pol-Usage (separately in Watson, Crick and both strands, smoothed & unsmoothed versions),  fork direction rates,  replication timing, probabilities of termination events and the list of replication initiation sites.
Genome_build: ASM294v2
Supplementary_files_format_and_content: Wig & bedgraph files containing analysed datasets.

source_name: Genomic DNA from exponential phase cells

extract_protocol:
Genomic DNA was alkaline treated and fragments of 300-500 bp of the ssDNA were isolated from agarose gel. ssDNA was converted to dsDNA using the BioPrime DNA Labelling system (invitrogen) with dTTP substituted by dUTP. dsDNA was used for Illumina library preparation using NEBNext® Ultra™ DNA Library Prep Kit with the following modified protocol: end-cleaning of DNA fragments and adaptor-ligation was performed without USER treatment followed by size selection of insert (250 - 600 bp) using AMpure XP beads. Purified DNA was treated with USER enzyme and subsequent PCR (13 cycle) using multiplexing index-primers generated Illumina libraries.
DNA was prepared using the QIAGEN 100/G Genomic-tip"

value: h+ rnh201::KanMX cdc6-L591G::lox Ura4-D18 leu1-32 ade6-704

value: Cells were harvested from early-log phase cultures grown in rich medium.


title: The ribonucletide incorpration due to DNA synthesis by Pol-epsilon

value: h+ rnh201::KanMX cdc20-M603F::lox Ura4-D18 leu1-32 ade6-704


title: 44_T1_bound

description:
Colon tumor (adenocarcinoma)
SUL_CRC2_44T1_hmC_bnd.689.s_7
hmeDIP-seq
SUL_CRC2_44T1_hmC_bnd.689.s_7

value: hmC_bound fraction

value: anti 5-hmC rabbit polyclonal (Active Motif, catalog# 39791, lot# 02511003)

value: Colon tumor (adenocarcinoma)


title: GROseq_siCTL_hs10l3_1

description:
GROseq_siCTL
GRO-seq

data_processing:
The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline.
The sequencing reads were aligned to mm8 or mm9  by using Bowtie, Bowtie2 or BFAST.
Tho bedgraph files were generated by using HOMER (http://homer.salk.edu/homer/)
For siCTL, siAscl1, siLdb1, and siTbx19 GRO-seq analysis, we have used the same number of randomly extracted reads (7 millions) in order to define the differentially expressed genes, excluding a 400bp promoter-proximal region. The sequencing reads were counted over the genes by using BEDTools (http://bedtools.readthedocs.org) or HOMER (http://homer.salk.edu/homer/).  edgeR was used for statistical significance analysis of the  differential expression  (FDR< 0.01, FC > 1.2).
Genome_build: mm8

growth_protocol: AtT20 cells were obtained from ATCC, maintained in UltraCULTURE medium (Lonza) supplemented with 5% FBS and 1X GlutaMAX (Invitrogen) without antibiotics at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
GRO-seq experiments were performed as previously reported. Briefly, 20 millions of AtT20 cells, treated with siRNAs for 2 days, were washed 3 times with cold PBS, and then incubated in swelling buffer (10mM Tris-HCl pH7.5, 2mM MgCl2, 3mM CaCl2) on ice for 5 min. Cells were lysed in 1ml of lysis buffer (swelling buffer plus 0.5% NP-40, 10% glycerol and 20 units of SUPERase-In) with 15 sec vortex at 800 rpm. The nuclei pellets were washed twice with 10ml lysis buffer and 1 ml of freezing buffer (50mM Tris-HCl pH8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA). The isolated nuclei were suspended in 100μl of freezing buffer. For the run-on assay, an equal volume of reaction buffer (10mM Tris-HCl pH 8.0, 5mM MgCl2, 300mM KCl, 1% sarkosyl, 500μM ATP, GTP, and Br-UTP, 2μM CTP,  1mM DTT, 20 units of SUPERase-In) was added to the isolated nuclei, and incubated for 5 minute at 30°C. The nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol LS reagent (Life Technologies). NRO-RNA was hydrolyzed to ~300-500 nucleotides by alkaline base on ice for 30 min and followed by treatment with DNase I and antarctic phosphatase. The fragmented NRO-RNA was pulled down with anti-BrdU argarose beads (Santa Cruz Biotechnology) in binding buffer (0.5XSSPE, 1mM EDTA, 0.05% tween) for 1-3 hours at 4°C with rotation. Subsequently, T4 PNK was used to repair the ends of the precipitated Br-UTP labeled RNA at 37°C for 1hour. The RNA was extracted and precipitated using acidic phenol-chloroform. The RNA fragments were subjected to poly-A tailing reaction by poly-A polymerase (NEB) for 30 minute at 37°C, and reverse transcribed using oNTI223 primer and superscript III RT kit (Life Technologies). The 100-500 bp cDNA products were isolated using 10% polyacrylamide TBE-urea gels. Next, the purified first-strand cDNA was circularized by CircLigase (Epicentre) and re-linearized by APE1 (NEB). ~120-320bp of re-linearized single strand cDNA (sscDNA) was isolated with a 10% polyacrylamide TBE gel. Finally, the purified sscDNA template was amplified by PCR using the Phusion High-Fidelity enzyme (NEB).
The oligonucleotide primers oNTI200 and oNTI201 were used to generate DNA for deep sequencing. DNA was ligated to specific adaptors followed by deep sequencing on the Illumina GAII system according to the manufacturer’s instructions.

treatment_protocol: To efficiently knockdown endogenous proteins, Neon Transfection System (Invitrogen) was employed to electroporate gene-specifics siRNAs to AtT20 cells at 1,400 V for 30 ms, following manufacturer’s instructions. 10 ul of 50 uM total siRNA was used for 1X106 cells in a 100 ul of tip.

tag: cell type

value: AtT20 cells

tag: transfected with

value: siCTL


title: GROseq_siMash1_hs10l3_2

description:
GROseq_siMash1(Ascl1)
GRO-seq

value: siMash1 (Ascl1)


title: GROseq_siLdb1_hs10l3_3

description:
GROseq_siLdb1
GRO-seq


title: MB_TI_ChIPSeq

status: Public on Feb 02 2015

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL

data_processing:
Raw reads were mapped to the human genome (mm9) using Bowtie 2.2.1 in sensitive mode
Peaks were called using MACS
Genome_build: mm9
Supplementary_files_format_and_content: bedfiles contain the results of the peakcalled using MACS

source_name: C2C12 myoblasts

growth_protocol: C2C12 myoblasts were routinely grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum (FCS) and penicillin/streptomycin.

extract_protocol:
C2C12 cells at various stages were washed 2x (in PBS + Protease inhibitor), counted to normalize by cell number, cross-linked (ten minutes rotation in 1% formaldehyde), quenched with glycine (at 125mM on ice), washed 3x (PBS+PI) and pelleted at 10e7 cells per eppendorf. Pellets were lysed, resuspended in 1ml sonication buffer on ice (10mM Tris pH 8, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% NaDOC, 0.25% NLS and protease inhibitors), transferred to glass 12x12mm tubes (Covaris: 520081) and sonicated (Covaris settings: 5% duty cycle, PIP 140, 200cyles/ burst, 25 minutes). Sonication was then assessed by reverse cross-linking overnight in the presence of proteinase K and RNase, followed by DNA extraction and quantification on a Bioanalyzer (Agilent 2100 machine). Libraries were prepared according to Illumina's instructions.
Libraries were prepared according to Illumina's instructions

treatment_protocol: For differentiation, cells were placed in media containing Dulbecco's Modified Eagle Medium (DMEM) supplemented with 2% horse serum, penicillin/streptomycin and insulin-Transferrin-selenium-A.

tag: strain

tag: developmental stage

value: proliferating myoblasts

tag: chip antibody (epitope/name)


title: GROseq_siTbx19_hs10l3_4

description:
GROseq_siTbx19
GRO-seq


title: Aa_H3K27me1_rep1

extract_protocol:
Chromatin and DNA immunoprecipitation was performed essentially as described in Gendrel et al., 2005 and Cortijo et  al., 2014, respectively. Total RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturers instructions and its quality was validated using RNA 6000 NanoChip (Agilent).
20 ng of immunoprecipitated (IP) and genomic (INPUT) DNA and 1 ug of total RNA were used to prepare libraries with the ChIP-Seq DNA Sample Prep Kit IP-102-1001 and TruSeq RNA Sample Prep Kit v2 RS-122-2002 (Illumina), respectively. Quality of libraries was validated using 2100 Bioanalyzer (Agilent). Libraries were sequenced with Illumina Genome Analyzer IIx according to manufacturers instructions.

value: Pajares

tag: chip antibody

value: young leaves


title: HCT116

description:
HCT116 human colorectal cancer cell line
HCT116
HCT116

data_processing:
Alignments: For HCT116 TET2 ChIP-seq, Illumina reads were aligned to the Human Reference Genome (assembly hg18, NCBI Build 36.3, March 2008) using BWA version 0.5.9.
Peak calling: For HCT116 TET2 ChIP-seq, enriched regions (peaks) were identified using MACS version 1.4 (Zhang et al, 2008) with the default parameters and a p-value cut-off < 10-10. Peaks were then filtered to avoid significant overlaps (< 80%) with repetitive regions using the UCSC repeat marker tracks.
Genome_build: hg18
Supplementary_files_format_and_content: MACS peaks in .bed file format

source_name: human colorectal cancer cell line

value: anti TET2 (SantaCruz, catalog# sc-136926, lot# H2412)

value: HCT116 colorectal cancer cell line