title: INPUT ChIP-seq GH947

source_name: T-47D breast cancer cell line

extract_protocol: Lysates were clarified from sonicated nuclei and GR/DNA, ER/DNA, of FoxA1/DNA complexes were isolated with antibody.

tag: cell type

value: Pleural effusion from a ductal carcinoma of the breast

value: Dexamethasone and 17β-estradiol

tag: concentration

tag: time

value: 30 minutes

tag: replicate

value: replicate 1

tag: antibody

value: FoxA1 ab23738 Abcam

tag: growth proptocol

value: For maintenance cells were cultured in RPMI containing 2mM L-glutamine supplemented 10% calf serum, 1mM sodium pyruvate, 1X non-essential amino acids, and 1% penicillin-streptomycin


title: 100pgTechRepUMI_primer [UMI_primer_sample_0014]

status: Public on Apr 08 2016

type: SRA

city: Haifa

first: Naftalie

last: Senderovich

state: International

address: Technion city, Faculty of biology

department: Biology

country: Israel

institute: Technion - Israel Institute of Technology

description:
100pgTechRepUMI_primer.txt
UMI_primer_sample_0014

library_source: transcriptomic

data_processing:
Libraries were sequenced on the Illumina HiSeq2500 according to standard, paired-end sequencing, protocols. Primary analysis done in RTA 1.17.20,1.13.48
Conversion from BCL to FASTQ and deumltiplexing using CASAVA-1.8 (configureBclToFastq.pl--fastq-cluster-count 1234567890 --mismatches 0 --use-bases-mask Y15n,I6n,Y35n)
Filter and read trimming (barcode minimum quality of 20. trimming of read2 to 35 bases - not required).
CEL-Seq (Hashimshony, et al. 2012) demultiplexing of second mate, using first mate barcode, allowing no mismatches in barcode.
bowtie2, version 2.1.0, against various genomes
Read counting with htseq-count version 0.5.4p3. Reads with the same unique molecular identifiers (UMIs) were colapsed for transcript counting.
Genome_build: GRCm38
Genome_build: mm9 for comparison to Smart-Seq data
Genome_build: WS230
Supplementary_files_format_and_content: Tabular expression matrix includes number of transcript molecules.

molecule: total RNA

organism: Caenorhabditis elegans

source_name: total RNA

growth_protocol:
Mouse ear fibroblasts were derived from 1 month-old CyclinB1-GFP mice. Briefly, a small piece of mouse ear was collected, digested overnight in DMEM containing Collagenase /Dispase. The tissue was then dissociated by gentle pipetting and cells were washed in DMEM/10% FBS/1% Pen-Strep/1% L-Glutamine, pelleted, seeded and cultured for 2-4 days before sorting on a FACS ARIA (Becton Dickinson).
Bone marrow dendritic cells (BMDCs) were collected from 6-8 weeks old female C57BL/6J mice from femora and tibiae and plated. At day 9 post-bone marrow extraction non-adherent cells were collected and stained for CD11c to collect BMDCs.  day 5, floating CD11c+ cells were sorted on the

extract_protocol:
C. elegans total RNA was isolated using TRIzol with addition of ERCC spike-ins and GenElute LPA (Sigma).  BMDCs were lysed by sorting directly into a hypotonic solution before freezing on dry ice. Mouse fibroblasts were lysed in lysis buffer 0.2% NP-40 on C1 IFC. Manually collected fibroblasts were lysed by freezing in liquid nitrogen.
For RNA amplification and library construction see the detailed protocol in "CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq"

tag: strain

tag: tissue

value: embryos

tag: age

value: mixed stages

tag: experimental design

value: 100pg of C. elegans isloted total RNA was used to calibrate the new CEL-Seq2 protocol. Each sample set represent different parameters; old_bc - the original CEL-Seq primer, UMI - unique molecular identifier, short - a shorter version of the original primer with UMI, no_lig - ligation free 3 prime illumina adapter introduction.


title: MNase-seq in Adult Liver High Rep 1.2

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

country: USA

institute: The University of Pennsylvania

library_source: genomic

data_processing:
Bases were called and quality control was performed using the Illumina pipeline (Casava)
Raw MNase-seq data were aligned with bowtie 0.12.5, using -m 1 and --best parameters.
Track views were obtained by reducing all MNase paired-end fragments (pooled across three technical replicates) to the central 140bp region and then binning into contiguous 10bp intervals.
MNase-seq calls were performed independently on low and high Mnase-seq datasets using GeneTrack (46) (sigma or s=40,  exclusion zone or e =200).  Using an exclusion zone of 200 bp prevents MNase-seq calls that are within 100 bp from each other. A 45 bp matching window was used to match MNase-seq calls across low and high MNase-seq datasets.  Subsequently, EdgeR on 145bp window counts (centered around the MNase-seq call midpoints) was used to identify MNase hypersensitive regions that have significantly higher reads in low-MNase-seq datasets with respect to high-MNase-seq datasets.
Genome_build: mm8
Supplementary_files_format_and_content: BED files: *.merge.fragments.bed files show pooled replicate paired-end fragments (start of Watson tag to start of Crick strand), and the Low vs High file contains positions of hypersensitive nucleosomes; bigWig files: contains track views for each biological replicate (pooled across three technical replicates).

molecule: genomic DNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Animal use was approved by an IACUC committee.  Mouse liver from C3H strain was minced with scalpels in SST (150 mM NaCl, 15 mM Na Citrate, 10 mM Tris [pH 7.4]) on ice, and washed with SST in 30 ml Corex tubes three times.  The tissue was resuspended in RSB (10 mM Tris [pH7.4], 10 mM NaCl, 3 mM MgCl2, 10 mM sodium butyrate, 0.5 mg/ml aprotinin, 0.5 mg/ml leupeptin, 1 mg/ml pepstatin) plus 0.5% NP40, and was swollen on ice for 5 min.  The tissue was homogenized with a glass Teflon pestle in a glass homogenizer and a portion was observed under the microscope to confirm nuclear isolation. The nuclear suspension was filtered through a 100 μm cell strainer and pelleted by centrifugation at 1.4K rpm for 7 min at 4°C in 15 ml Corex tubes with a swinging bucket rotor.  The pellet was washed in RSB plus 0.5% NP40 and pelleted by centrifugation at 900 rpm for 10 min at 4°C in 15 ml Corex tubes with a swinging bucket rotor, and this wash step was repeated one more time.  The nuclear pellet was re-suspended in RSB and adjusted to O.D. A260 of 1.  CaCl2 (3 mM final) was added, the nuclear suspension was pre-warmed for 1.5 min at 37°C, and was treated with MNase (Worthington Biochemicals) with 0 U/ml for control, 0.5 or 1 U/ml for low digestion and 20 U/ml for high digestion for 2 min at 37°C.  Quench control (“Q” sample) was without MNase and CaCl2 and not warmed.  The reactions were stopped by adding an equal volume of 2x TNESK (20 mM Tris [pH7.4], 200 mM NaCl, 2 mM EDTA, 2% SDS, 0.2 mg/ml Proteinase K), and incubated overnight at 37 °C.  DNA was purified using phenol-chloroform extraction followed by ethanol precipitation.  The nucleic acid was digested with 10 ng/ml of RNase for 20 min at 37°C and DNA was purified using phenol-chloroform extraction followed by ethanol precipitation.  50 μg samples of low MNase and 10 μg samples of high MNase were run on 6% polyacrylamide gel (TBE).  The mono-nucleosomal DNA was excised from the 140 bp~200 bp size range.  The gel was sliced into small pieces, put in 2 vol of diffusion buffer (500 mM ammonium acetate, 10 mM magnesium acetate, 1 mM EDTA, 0.1% SDS), and rotated overnight. The supernatant was filtered through Whatman GF/C and ethanol precipitated.  DNA was purified using QIA EX II (QIAGEN) or AMPure XP (Beckman) beads. Mono-nucleosomal DNA from low MNase digestion averaged 1.5~2.5% of bulk DNA. Mono-nucleosomal DNA from high MNase digestion averaged 25~30% of bulk DNA.  The percent of mononucleosomal DNA of bulk DNA was estimated based on the amount of mononucleosomal DNA recovered from a preparative PAGE gel, multiplied by 1.25 (PAGE gel extraction recovers about 80% of sample in our hands) compared to the amount of bulk DNA loaded onto to the PAGE gel.
We prepared multiplexing libraries from two biological replicates of 150 ng of low and high MNase digested, purified mono-nucleosomal DNA.  We followed the standard Illumina multiplexing library preparation protocol with the following changes: 1) All QIAGEN purification steps were substituted with AMPure XP beads (Beckman) purifications. 2) For MNase digested mono-nucleosomal DNA, gel purification following adapter ligation was substituted with AMPure XP beads purification in order to remove excess adapters.  3) 10 ng of adapter ligated DNA was used as a template for PCR, wth 10 PCR cycles. 4) Gel purification after PCR was substituted with AMPure XP beads purification in order to remove excess primers.  The DNA libraries were assessed using on an Agilent Technologies 2100 Bioanalyzer.
MNase digested DNA libraries were sequenced as 100-bp paired-end, using Illumina HiSeq2000.

treatment_protocol: Mono-nucleosomal DNA from low MNase digestion is 1.5~2.5 % of bulk DNA. Mono-nucleosomal DNA from high MNase digestion is 25~30 % of bulk DNA.

tag: background strain

value: liver

tag: developmental stage

value: adult

tag: mnase concentration

value: High


title: 100pgTechRepUMI_primer [UMI_primer_sample_0015]

description:
100pgTechRepUMI_primer.txt
UMI_primer_sample_0015


title: E2 rep#1 FoxA1 ChIP-seq GH1072

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

description: hs_RC_E2_FoxA1_T47D_RC_GH1072xGH1462_FDR0.csv

data_processing:
RTA 1.12.42 was used for Basecalling and Casava 1.8.2 ws used for demultiplexing.
Alignment was performed by Bowtie2 software with the hg19 reference genome.
Areas of enrichment were identified using DNase2Hotspots software(http://sorceforge.net/proujects/dnase2hotspots/) software with FDR 0%.
Raw signal density graphs were generated by counting tags at each genomic coordinate after extending the length of sequences to 150bp by strands.
Values for tag densities were normalized to 10 million reads to adjust for differences in the sequencing depth between samples.
Genome_build: hg19
Supplementary_files_format_and_content: comma-delimited (CSV)  text files include genomic locations (Chromosome, start,  end ), z-score, p-value and the maximum density of hotspots. Bedgraph files contain genomic locations and normalized tag density profiles.

organism: Homo sapiens

growth_protocol: see additional columns of the SAMPLES section

treatment_protocol: Cells were plated for experiments in phenol red free growth medium supplemented with 10% charcoal-dextran serum twenty-four hours before hormone treatment.  Cells were left untreated or induced with 100nM dexamethasone or 100nM estradiol for 30 minutes.

tag: cell line

tag: treatment


title: E2 rep#2 FoxA1 ChIP-seq GH1462

value: replicate 2


title: MNase-seq in Adult Liver High Rep 2.1


title: MNase-seq in Adult Liver High Rep 2.0


title: 100pgTechRepUMI_primer [UMI_primer_sample_0012]

description:
100pgTechRepUMI_primer.txt
UMI_primer_sample_0012


title: MNase-seq in Adult Liver High Rep 2.2


title: 100pgTechRepUMI_primer [UMI_primer_sample_0013]

description:
100pgTechRepUMI_primer.txt
UMI_primer_sample_0013


title: MNase-seq in Adult Liver Low Rep 2.1

value: Low


title: MNase-seq in Adult Liver High Rep 1.0


title: MNase-seq in Adult Liver Low Rep 2.2


title: 100pgTechRepUMI_primer [UMI_primer_sample_0011]

description:
100pgTechRepUMI_primer.txt
UMI_primer_sample_0011


title: untreated rep#2 FoxA1 ChIP-seq GH1460

description: hs_RC_T47D_ER_E2_RC_GH985GH993_FDR0.0.csv

value: untreated


title: 100pgTechRepOld_primer [old_bc_sample_0010]

description:
100pgTechRepOld_primer.txt
old_bc_sample_0010


title: E2 rep#2 ER ChIP-seq GH993

value: ER cocktail:Ab-10 Thermo Scientific Lab Vision, HC-20 sc-543 Santa Cruz


title: Dex rep#1 FoxA1 ChIP-seq GH1071

description: hs_RC_Unt_FoxA1_T47D_RC_GH1070xGH1460_FDR0.csv

value: Dexamethasone


title: MNase-seq in Adult Liver Low Rep 2.0


title: 100pgTechRepOld_primer [old_bc_sample_0009]

description:
100pgTechRepOld_primer.txt
old_bc_sample_0009


title: MNase-seq in Adult Liver High Rep 1.1


title: MNase-seq in Adult Liver Low Rep 1.2


title: MNase-seq in Adult Liver Low Rep 1.1


title: untreated rep#1 FoxA1 ChIP-seq GH1070

value: Pleural effusion from a ductal carcinoma of the breast


title: MNase-seq in Adult Liver Low Rep 1.0


title: H3 ChIP-seq in Adult Liver Rep 2

data_processing:
Bases were called and quality control was performed using the Illumina pipeline (Casava)
H2B/H3 chIP-seq data were aligned with bowtie 0.12.5, using -m 1 and --best parameters; FoxA2 and input chIP-seq data were aligned with ELAND (default parameters).
H2B and H3 tracks were obtained by binning all aligned tags from two pooled biological replicates into contiguous 2bp windows and extending tags 180 bp from the tag start site. Binned tag counts were then normalize to the number of millions of aligned tags. The FoxA2 track was obtained by binning all aligned tags into contiguous 10bp windows, normalizing for total tags, and subtracting a similarly normalized input score.
Genome_build: mm8
Supplementary_files_format_and_content: BED files: contains chromosomal coordinates of aligned sequence tags; bigWig files: contains track views for each replicate

growth_protocol: Wild type mouse strain, no growth protocol

extract_protocol:
Mice were anesthetized in a chamber with isoflurane (Butler Animal Health Supply).  When the mouse was completely under anesthetic, it was transferred to a surgical surface and its head was inserted into a nosecone containing isoflurane.  Mouse livers were perfused with 10 ml of 50 ng/ml heparin in PBS, followed by 5 ml 1% formaldehyde in PBS (Chaya et al, 2001).  Perfused livers sat for 10 min of formaldehyde perfusion time at room temperature.  The mouse was then sacrificed by cervical dislocation.  The livers were removed and placed in 6 ml buffer A (15 mM Hepes [pH 7.6], 60 mM KCl, 15 mM NaCl, 0.2 mM EDTA, 0.5 mM EGTA, 0.34 M sucrose, 0.15 mM 2-mercaptoethanol, 125 mM glycine) on ice, and minced with scalpels.  The liver was homogenized with a Teflon pestle in a glass homogenizer and a portion was observed under a microscope to confirm nuclear isolation.  The nuclear suspension was filtered through a 100 μm cell strainer, layered onto a 1.5 ml cushion of 1:1 of buffer A: buffer B (15 mM Hepes [pH 7.6], 60 mM KCl, 15 mM NaCl, 0.1 mM EDTA, 0.1 mM EGTA, 2.1 M sucrose, 0.15 mM 2-mercaptoethanol) in 15 ml Corex tubes, centrifuged in a fixed angle rotor at 10K rpm for 10 min at 4°C, and the supernatant was removed.  The pellets were suspended in 5 ml solution A and layered again onto 1:1 of buffer A:B, and centrifuged in a fixed angle rotor at 5K rpm for 10 min at 4°C, and the supernatant was removed.  The pellet was suspended into 4 ml sonication buffer (50 mM Tris [pH8], 2 mM EDTA, 0.5 % N-Lauroylsarcosine, complete EDTA-free protease inhibitor cocktail (Roche)) and incubated for 5 min at room temperature, then 5 min on ice.  The nuclear lysate was transferred to two 15 ml polystyrene conical tubes and sonicated for 45 min to 55 min (30 sec ON/ 30 sec OFF setting) with cool down intervals every 5 min using Bioruptor Sonicator UCD-200 equipped with the blue lid adaptor unit.  RNase A was added to 25 ng/ul and incubated at room temperature for 10 min.  Debris was removed by centrifugation at 14K rpm for 10 min at 4°C.  The supernatant was dialyzed in TE (10 mM Tris [pH8], 1 mM EDTA) using 3500 MWCO Slide-A Lyzer Dialysis cassette (Thermo Scientific) at 4°C overnight.  FoxA2 ChIPs were performed as described in (Watts et al., 2011) using FoxA2 antibody (Upstate 07-633).  For H2B and H3 ChIP, 20 ul Dynabeads Protein G (Life technologies) were washed three times with 500 ul blocking solution (0.5 % w/v BSA in PBS).  The beads were resuspended in 20 ul blocking solution and saturated with 5 ug H3 antibody (Abcam, ab1791), H2B antibody (Abcam, ab 1790), or control rabbit IgG (Abcam, 46540-1) by rotating the mixture for 6 hr at 4°C.  The antibody-beads were washed two times with 500 ul blocking solution and two times with 500 ul ChIP buffer (50 mM Hepes-KOH [pH 7.5], 140 mM NaCl, 1 mM EDTA, 0.1 % Triton X-100, 1 mM PMSF, Complete EDTA free protease inhibitor cocktail (Roche)).  ChIP was performed in 100 ul ChIP buffer containing antibody-beads mixture and 30 ug of sonicated chromatin, which was based on O.D. A260 of 1:10 dilution of chromatin with TE, and rotated for 16 hr at 4°C.  The ChIP-beads mixture was washed successively two times with ChIP buffer, one time with ChIP buffer plus 500 mM NaCl, two times with LiCl solution (10 mM Tris-HCl [pH 8], 250 mM LiCl, 1 mM EDTA, 0.5% NP-40), and two times with TE plus 0.1% NP-40.  The chromatin was eluted from the beads in 67 ul TES (50 mM Tris-HCl [pH 8], 10 mM EDTA, 1% SDS) and incubated at 65°C for 15 min.  The supernatant was placed in a fresh tube and the elution was repeated two more times, combining all supernatants.  The eluted chromatin and input chromatin was reverse-crosslinked by adding 200 mM NaCl and incubated at 65°C for 16 hr.  The reverse-crosslinked chromatin was diluted with 200 ml TE and RNase A was added to 0.2 mg/ml and incubated at 37°C for 1 hr.  The chromatin was treated with 0.2 mg/ml Proteinase K and incubated at 37°C for 2 hr.  DNA was purified by phenol-chloroform extraction followed by ethanol precipitation.
We prepared multiplexing libraries from two biological replicates of 150 ng of H3 and H2B purified ChIP DNA.  We used the standard Illumina multiplexing library preparation protocol with the following changes: 1) All QIAGEN purification steps were substituted with AMPure XP beads (Beckman) purifications. 2) For ChIP DNA, gel purification following adapter ligation was substituted with two-step AMPure XP beads purifications in order to remove excess adapters and select 100-300 bp ChIP fragments.  To remove larger fragments of DNA from ChIP products, 0.8 x vol of AMPure XP beads was added to the sample, incubate for 6 min at room temperature and the supernatant was transferred to new tube.   Next, to remove small fragments, 0.6 x vol of AMPure XP beads was added to the supernatant, and processed as for normal AMPure XP beads purification protocol (Beckman). 3) 10 ng of adapter ligated DNA was used as a template for PCR, wth 12 PCR cycles for ChIP DNA. 5) Gel purification after PCR was substituted with AMPure XP beads purification in order to remove excess primers.  The DNA libraries were assessed using on an Agilent Technologies 2100 Bioanalyzer.   For FoxA2 ChIP-seq, we prepared libraries from two biological replicates of FoxA2 ChIP and Input DNA following standard Illumina library preparation protocol, except as follows:  we selected 200 +/- 25 bp and 300 +/- 25 bp DNA from preparative gels after adapter ligation.
H2B and H3 ChIP DNA libraries were sequenced as 50-bp single-end, using Illumina HiSeq2000.  FoxA2 ChIP DNA library were sequenced as 36-bp single-end using Illumina GAIIx.

treatment_protocol: Wild type mouse strain, no treatment protocol

tag: chip antibody

value: anti-H3; Company:Abcam, Catalog#:ab1791, Lot#:GR135165-1


title: H3 ChIP-seq in Adult Liver Rep 1


title: 100pgTechRepOld_primer [old_bc_sample_0008]

description:
100pgTechRepOld_primer.txt
old_bc_sample_0008


title: H2B ChIP-seq in Adult Liver Rep 2

value: anti-H2B; Company:Abcam, Catalog#:ab1790, Lot#:GR47273-1


title: H2B ChIP-seq in Adult Liver Rep 1


title: 100pgTechRepOld_primer [old_bc_sample_0006]

description:
100pgTechRepOld_primer.txt
old_bc_sample_0006


title: FoxA2 ChIP-exo in Adult Liver Rep 2

data_processing:
Bases were called and quality control was performed using the Illumina pipeline (Casava)
Tags were aligned with BWA 0.6.2 to the mm10 assembly. Only uniquely-aligned tags were kept.
ChIP-exo peaks were discovered using GeneTrack in the following way: aligned sequencing tags were merged across biological replicate Foxa2 ChIP-exo experiments. Peak calling was then performed on the 5’ ends of tags using GeneTrack (sigma or s = 5, exclusion zone or e = 10). Peaks were paired if they existed on opposite strands and were offset in the range of -5 to +25 bp (a positive value indicates the offsets were in the 3’ direction). Peak-pairs were filtered to require that the summed 5’ tag counts in 50bp windows centered on the peak-pair midpoints were significantly enriched (p<10-3, Benjamini-Hochberg corrected Binomial test) over the corresponding 5’ tag counts from IgG control experiments. The control experiment normalization factors are estimated via the median read count ratios in 50 kb windows observed between signal and control experiments. FIMO was used to find occurrences of the FoxA2 consensus motif in the 80bp sequences centered on all peak-pair midpoints, with a p-value threshold of 0.001. Only peak-pairs associated with a motif occurrence were retained. Peaks were then lifted over to mm8.
Genome_build: mm8
Supplementary_files_format_and_content: BED file contains ChIP-exo peaks for FoxA2 in two pooled replicates.

extract_protocol:
Mice were anesthetized in a chamber with isoflurane (Butler Animal Health Supply).  When the mouse was completely under anesthetic, it was transferred to a surgical surface and its head was inserted into a nosecone containing isoflurane.  Mouse livers were perfused with 10 ml of 50 ng/ml heparin in PBS, followed by 5 ml 1% formaldehyde in PBS (Chaya et al, 2001).  Perfused livers sat for 10 min of formaldehyde perfusion time at room temperature.  The mouse was then sacrificed by cervical dislocation.  The livers were removed and placed in 6 ml buffer A (15 mM Hepes [pH 7.6], 60 mM KCl, 15 mM NaCl, 0.2 mM EDTA, 0.5 mM EGTA, 0.34 M sucrose, 0.15 mM 2-mercaptoethanol, 125 mM glycine) on ice, and minced with scalpels.  The liver was homogenized with a Teflon pestle in a glass homogenizer and a portion was observed under a microscope to confirm nuclear isolation.  The nuclear suspension was filtered through a 100 μm cell strainer, layered onto a 1.5 ml cushion of 1:1 of buffer A: buffer B (15 mM Hepes [pH 7.6], 60 mM KCl, 15 mM NaCl, 0.1 mM EDTA, 0.1 mM EGTA, 2.1 M sucrose, 0.15 mM 2-mercaptoethanol) in 15 ml Corex tubes, centrifuged in a fixed angle rotor at 10K rpm for 10 min at 4°C, and the supernatant was removed.  The pellets were suspended in 5 ml solution A and layered again onto 1:1 of buffer A:B, and centrifuged in a fixed angle rotor at 5K rpm for 10 min at 4°C, and the supernatant was removed.  The pellet was suspended into 4 ml sonication buffer (50 mM Tris [pH8], 2 mM EDTA, 0.5 % N-Lauroylsarcosine, complete EDTA-free protease inhibitor cocktail (Roche)) and incubated for 5 min at room temperature, then 5 min on ice.  The nuclear lysate was transferred to two 15 ml polystyrene conical tubes and sonicated for 45 min to 55 min (30 sec ON/ 30 sec OFF setting) with cool down intervals every 5 min using Bioruptor Sonicator UCD-200 equipped with the blue lid adaptor unit.  RNase A was added to 25 ng/ul and incubated at room temperature for 10 min.  Debris was removed by centrifugation at 14K rpm for 10 min at 4°C.  The supernatant was dialyzed in TE (10 mM Tris [pH8], 1 mM EDTA) using 3500 MWCO Slide-A Lyzer Dialysis cassette (Thermo Scientific) at 4°C overnight.
ChIP-exo experiments were carried out essentially as described with minor alterations (Rhee and Pugh, 2012). With prepared sonicated chromatin, chromatin immunoprecipitation (ChIP) was performed on biological duplicates for FoxA2 (Upstate 07-633) and IgG as a control (Upstate 12-370).
See Rhee et al, Cell 2011. Libraries were created for two replicates each of FoxA2 chIP and IgG chIP.  Sequencing was performed using an Illumina HiSeq 2000.

value: Upstate 07-633


title: Dex rep#2 GR ChIP-seq GH988

description: hs_RC_T47D_GR_Dex_RC_GH944GH988_FDR0.0.csv

value: 30 minutes

value: GR E-20X sc-1003 Santa Cruz


title: untreated rep#2 ER ChIP-seq GH991

description: hs_RC_T47D_ER_Unt_RC_GH983GH991_FDR0.0.csv

value: For maintenance cells were cultured in RPMI containing 2mM L-glutamine supplemented 10% calf serum, 1mM sodium pyruvate, 1X non-essential amino acids, and 1% penicillin-streptomycin


title: untreated rep#1 ER ChIP-seq GH983

value: replicate 1


title: 100pgTechRepOld_primer [old_bc_sample_0003]

description:
100pgTechRepOld_primer.txt
old_bc_sample_0003

value: embryos

value: mixed stages

value: 100pg of C. elegans isloted total RNA was used to calibrate the new CEL-Seq2 protocol. Each sample set represent different parameters; old_bc - the original CEL-Seq primer, UMI - unique molecular identifier, short - a shorter version of the original primer with UMI, no_lig - ligation free 3 prime illumina adapter introduction.


title: E2 rep#1 ER ChIP-seq GH985


title: IgG ChIP-exo in Adult Liver Rep 1

value: liver

value: adult

value: Upstate 12-370


title: 100pgTechRepOld_primer [old_bc_sample_0004]

description:
100pgTechRepOld_primer.txt
old_bc_sample_0004


title: 100pgTechRepOld_primer [old_bc_sample_0001]

description:
100pgTechRepOld_primer.txt
old_bc_sample_0001


title: FoxA2 ChIP-exo in Adult Liver Rep 1


title: Dex rep#1 GR ChIP-seq GH944


title: INPUT ChIP-seq GH1003

source_name: ZR-75-1 breast cancer cell line

value: Ascites from a ductal carcinoma of the breast

value: Dexamethasone and 17β-estradiol

value: FoxA1 ab23738 Abcam


title: untreated rep#1 GR ChIP-seq GH943

description: hs_RC_T47D_GR_Unt_RC_GH943GH987_FDR0.0.csv

value: Pleural effusion from a ductal carcinoma of the breast

value: untreated


title: IgG ChIP-exo in Adult Liver Rep 2


title: 100pgTechRepOld_primer [old_bc_sample_0002]

description:
100pgTechRepOld_primer.txt
old_bc_sample_0002


title: 100pgTechRepOld_primer [old_bc_sample_0007]

description:
100pgTechRepOld_primer.txt
old_bc_sample_0007


title: Dex rep#2 FoxA1 ChIP-seq GH1461

value: Dexamethasone

value: replicate 2


title: 100pgTechRepOld_primer [old_bc_sample_0005]

description:
100pgTechRepOld_primer.txt
old_bc_sample_0005


title: Dex rep#2 FoxA1 ChIP-seq GH1067

description: hs_RC_ZR751_FoxA1_Dex_RC_GH1063xGH1067_FDR0.csv

value: 30 minutes


title: UR -1

city: Durham

first: Integrative

last: Bioinformatics

state: NC

address: 111 TW Alexander Drive

department: BCBB

institute: NIEHS

description:
RightColonProcessed.xlsx
76NA

data_processing:
Fastq data files were aligned to the human Hg19 Ensembl genome with Novoalign read aligner version 2.08.02
Novoaligned SAM files were parsed into binary BAM files using SamTransriptomeParser application from USeq software version 8.8.5
Differentially expressed genes were identified using the DefinedRegionDifferentialSeq application from USeq software version 8.8.5
SAMtoUSeq application was used to make normalized read data tracks (FPKM) for visualization in the Integrated Genome Browser from USeq software version 8.8.5
Genome_build: Ensembl Homo sapiens Hg19
Supplementary_files_format_and_content: Excel file with Ensembl IDs, chromosome coordinates, individual sample raw read counts and normalized read counts (FPKM)

source_name: Colon

extract_protocol:
TriZOL
Illumina TruSeq mRNA Sequencing with oligo dT selection

tag: patient cohort

value: Sporadic

value: Uninvolved right colon


title: healthy control 14

city: BUFFALO

first: JAMES

last: JARVIS

state: NY

address: 875 ELLICOTT STREET 8026

department: PEDIATRIC

institute: UNIVERSITY AT BUFFALO

description: healthy control

data_processing:
Sequences were excluded for adapter contamination and low quality bases
Sequences were aligned to hg19 human reference genome using Tophat version 2.0.13
Gene expression abundance was calculated by HTSeq count version 0.6.0
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include gene count values for each sample

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Total RNA was extracted using TRIzol™ reagent according to manufacturer's directions. RNA was further purified using RNeasy MiniElute Cleanup kit including a DNase digest according to the manufacturer's instructions (QIAGEN, Valencia, CA). RNA was quantified spectrophotometrically (Nanodrop, Thermo Scientific, Wilmington, DE) and assessed for quality by capillary gel electrophoresis (Agilent 2100 Bioanalyzer; Agilent Technologies, Inc., Palo Alto, CA)
Samples libraries were prepared using Illumina TruSeq RNA Sample Preparation Kit according to the manufacture's recommended protocols

tag: disease stage

value: healthy control

value: blood

tag: cell type

value: Peripheral Blood Mononuclear Cells


title: Dex rep#1 FoxA1 ChIP-seq GH1063

tag: concentration

tag: time

value: replicate 1

value: For maintenance cells were cultured in RPMI containing 2mM L-glutamine supplemented 10% calf serum, 1mM sodium pyruvate, 1X non-essential amino acids, and 1% penicillin-streptomycin


title: healthy control 12

description: healthy control


title: E2 rep#1 FoxA1 ChIP-seq GH1064

description: hs_RC_ZR751_FoxA1_E2_RC_GH1064xGH1068_FDR0.csv

tag: replicate

tag: antibody


title: healthy control 13

description: healthy control


title: healthy control 16

description: healthy control


title: untreated rep#2 FoxA1 ChIP-seq GH1066

description: hs_RC_ZR751_FoxA1_unt_RC_GH1062xGH1066_FDR0.csv

tag: growth proptocol


title: E2 rep#1 ER ChIP-seq GH1001

description: hs_RC_ZR751_ER_E2_RC_GH1001GH1010_FDR0.0.csv

value: ER cocktail:Ab-10 Thermo Scientific Lab Vision, HC-20 sc-543 Santa Cruz


title: untreated rep#1 FoxA1 ChIP-seq GH1062


title: healthy control 9

description: healthy control

tag: tissue


title: untreated rep#2 ER ChIP-seq GH1008

description: hs_RC_ZR751_ER_Unt_RC_GH999GH1008_FDR0.0.csv


title: E2 rep#2 ER ChIP-seq GH1010


title: JIA patient 85

description: JIA patient

value: JIA patient with clinical remission on medication


title: untreated rep#1 ER ChIP-seq GH999

value: Ascites from a ductal carcinoma of the breast


title: E2 rep#2 FoxA1 ChIP-seq GH1068


title: Dex rep#2 GR ChIP-seq GH1005

description: hs_RC_ZR751_GR_Dex_RC_GH996GH1005_FDR0.0.csv

value: GR E-20X sc-1003 Santa Cruz


title: Dex rep#1 GR ChIP-seq GH996


title: healthy control 15

description: healthy control


title: JIA patient 83

description: JIA patient


title: 100pgTechRepShort_primer [short_sample_0022]

description:
100pgTechRepShort_primer.txt
short_sample_0022

tag: strain

value: embryos

tag: age

value: mixed stages

value: 100pg of C. elegans isloted total RNA was used to calibrate the new CEL-Seq2 protocol. Each sample set represent different parameters; old_bc - the original CEL-Seq primer, UMI - unique molecular identifier, short - a shorter version of the original primer with UMI, no_lig - ligation free 3 prime illumina adapter introduction.


title: healthy control 11

description: healthy control


title: JIA patient 81

description: JIA patient


title: untreated rep#2 GR ChIP-seq GH1004

description: hs_RC_ZR751_GR_Unt_RC_GH995GH1004_FDR0.0.csv

value: untreated


title: JIA patient 80

description: JIA patient


title: untreated rep#1 GR ChIP-seq GH995


title: healthy control 10

description: healthy control


title: E2 rep#2 FoxA1 ChIP-seq GH927

source_name: MCF-7 breast cancer cell line

value: Pleural effusion from an adenocarcinoma of the breast

value: replicate 2

value: FoxA1 ab23738 Abcam

value: For maintenance cells were cultured in DMEM supplemented 10% calf serum, 2mM L-glutamine, 1mM sodium pyruvate, 1X non-essential amino acids, and 1% penicillin-streptomycin


title: E2 rep#1 FoxA1 ChIP-seq GH919

value: 30 minutes


title: JIA patient 84

description: JIA patient

value: blood


title: JIA patient 78

description: JIA patient

value: Peripheral Blood Mononuclear Cells


title: Dex rep#2 FoxA1 ChIP-seq GH926

description: hs_RC_FoxA1_Dex_RC_GH918GH926_FDR0.0.csv

value: Dexamethasone


title: JIA patient 82

description: JIA patient


title: untreated rep#2 FoxA1 ChIP-seq GH925

description: hs_RC_MCF7_FoxA1_Unt_RC_GH917xGH925_FDR0.csv


title: JIA patient 74

description: JIA patient

value: JIA patient with active disease on treatment


title: JIA patient 75

description: JIA patient


title: JIA patient 72

description: JIA patient


title: JIA patient 73

description: JIA patient


title: JIA patient 77

description: JIA patient


title: JIA patient 76

description: JIA patient


title: Dex rep#1 FoxA1 ChIP-seq GH918

value: replicate 1


title: JIA patient 71

description: JIA patient


title: JIA patient 70

description: JIA patient


title: E2 rep#1 ER ChIP-seq GH622

description: hs_RC_MCF7_ER_E2_RC_GH622xGH630_FDR0.csv

value: ER cocktail:Ab-10 Thermo Scientific Lab Vision, HC-20 sc-543 Santa Cruz


title: E2 rep#2 ER ChIP-seq GH630


title: untreated rep#2 ER ChIP-seq GH628

description: hs_RC_MCF7_ER_unt_RC_GH620xGH628_FDR0.csv


title: JIA patient 79

description: JIA patient

value: JIA patient with clinical remission on medication


title: INPUT ChIP-seq GH929

value: Dexamethasone and 17β-estradiol


title: JIA patient 69

description: JIA patient

value: JIA patient with active, untreated disease


title: Dex rep#2 GR ChIP-seq GH1159

description: hs_RC_MCF7_GR_Dex_RC_GH1158xGH1159_FDR0.csv

value: GR E-20X sc-1003 Santa Cruz


title: untreated rep#1 ER ChIP-seq GH620


title: JIA patient 68

description: JIA patient


title: JIA patient 67

description: JIA patient


title: JIA patient 66

description: JIA patient


title: untreated rep#2 GR ChIP-seq GH921

description: hs_RC_MCF7_GR_unt_RC_GH913xGH921_FDR0.csv


title: Dex rep#1 GR ChIP-seq GH1158


title: untreated rep#1 FoxA1 ChIP-seq GH917


title: JIA patient 64

description: JIA patient


title: JIA patient 65

description: JIA patient


title: JIA patient 63

description: JIA patient


title: JIA patient 60

description: JIA patient


title: HMC_L.T_shKDM3A_input

city: Boston

first: Pin-Ji

last: Lei

state: Massachusetts

address: 100 Blossom Street

department: Department of Radiation Oncology

institute: Massachusetts General Hospital

description:
HMC
breast primary cell with large T and TERT + shKDM3A

data_processing:
For RNA-Seq data quality control was performed by Fastqc. Before downstream analysis, low quality reads and adaptor contamination were deleted. RNA-Seq data mapping was performed by Tophat2 and hg19 as reference genome. Gene assemble and expression quantification was performed by Cufflinks.
Sequence reads for ChIP-Seq is 100bp paired-end and quality control was performed by Fastqc, and then low quality reads and adaptor contamination were deleted. For downstream analysis, data were mapped to hg19 reference genome by bwa aln algorithm and SICER for peaks calling.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each RNA-Seq sample. WIG file for ChIP-Seq mapping results.

source_name: L.T + shKDM3A

extract_protocol:
Total RNA was extracted by using Qiagen RNA extraction kit according to manufacturer’s manual, and then 10ug total RNA was used for downstream library construction. For ChIP asssy, approximately 1×107 cells were fixed with 1% formaldehyde and quenched by glycine. The cells were washed three times with PBS and then harvested in ChIP lysis buffer (50 mM Tris-HCl, pH7.6, 1 mM CaCl2, 0.2% Triton X-100). DNA was digested to 150-300 bp by MNase (SIGMA) before extensive centrifugation. Four volume of ChIP dilution buffer (20 mM Tris-HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS) was added to the supernatant. The resulted lysate was then incubated with protein G beads and antibodies at 4ºC over night. The beads were washed 5 times and DNA was eluted by Chip elution buffer (0.1 M NaHCO3, 1% SDS, 20 µg/ml proteinase K). The elution was incubated at 65ºC over night and DNA was extracted with DNA purification kit (TIANGEN).
RNA-Seq library construction was performed by using Illumina TruSeq kit, briefly, 10ug total RNA as initiation, and then mRNA was purification by oligo-dT magnetic beads. mRNA  was fragmented into 200-400bp and revers transcript into dscDNA for library construction. For ChIP-Seq library construction, cross-linked chromatin was fragmented into 150-300bp, and then fragmented DNA was used for library construction and sequencing by Illumina Hiseq2000.

value: HMC-LT

tag: knockdown

value: ChIP input


title: HMC_L.T.R_siKDM3A_input

description:
HMC
breast primary cell with large T, TERT and HRAS (V12) + siKDM3A

source_name: L.T.R + siKDM3A

value: HMC-LTR


title: HMC_L.T_L.T.R_NC_input

description:
HMC
L.T + L.T.R + NC

source_name: L.T + L.T.R + NC

value: HMC-LT + HMC-LTR

value: negative control


title: JIA patient 59

description: JIA patient


title: JIA patient 62

description: JIA patient


title: HMC_input

description:
HMC
P6 + L + L.T + L.T.R

source_name: P6 + L + L.T + L.T.R

value: HMC-P6 + HMC-L + HMC-LT + HMC-LTR


title: HMC_L.T.R_siKDM3A_H3K9me2


title: HMC_P6_H3K4me3_input

description:
HMC
breast primary cell passage 6


title: JIA patient 58

description: JIA patient


title: HMC_L.T.R_NC_H3K9me2

description:
HMC
breast primary cell with large T, TERT and HRAS (V12) + NC

source_name: L.T.R + NC


title: HMC_L.T_NC_H3K9me2

description:
HMC
breast primary cell with large T and TERT + NC

source_name: L.T + NC


title: HMC_L.T_shKDM3A_H3K9me2


title: HMC_L.T.R_H3K27me3

description:
HMC
breast primary cell with large T, TERT and HRAS (V12)


title: JIA patient 56

description: JIA patient


title: JIA patient 57

description: JIA patient


title: untreated rep#1 GR ChIP-seq GH913

value: Pleural effusion from an adenocarcinoma of the breast

value: untreated

value: 30 minutes

value: For maintenance cells were cultured in DMEM supplemented 10% calf serum, 2mM L-glutamine, 1mM sodium pyruvate, 1X non-essential amino acids, and 1% penicillin-streptomycin


title: JIA patient 52

description: JIA patient

value: blood

value: Peripheral Blood Mononuclear Cells


title: HMC_L.T.R_H3K4me3


title: JIA patient 53

description: JIA patient


title: JIA patient 55

description: JIA patient


title: HMC_L.T.R_H3K9me3


title: JIA patient 54

description: JIA patient


title: JIA patient 61

description: JIA patient


title: HMC_P6_L_L.T_H3K9me2_input

description:
HMC
P6 + L + L.T

source_name: P6 + L + L.T

value: HMC-P6 + HMC-L + HMC-LT


title: JIA patient 50

description: JIA patient

value: JIA patient with clinical remission on medication


title: HMC_L.T_H3K4me3

description:
HMC
breast primary cell with large T and TERT


title: HMC_L.T.R_H3K9me2


title: HMC_L.T_H3K27me3


title: JIA patient 48

description: JIA patient


title: HMC_L.T_H3K9me3


title: JIA patient 47

description: JIA patient


title: JIA patient 46

description: JIA patient


title: HMC_L.T_H3K9me2


title: JIA patient 45

description: JIA patient


title: JIA patient 44

description: JIA patient


title: HMC_L_H3K4me3

description:
HMC
breast primary cell with stable large T expression

source_name: L

value: HMC-L


title: HMC_L_H3K27me3


title: HMC_L_H3K9me2


title: HMC_P6_H3K4me3

description:
HMC
breast primary cell passage 6


title: HMC_L_H3K9me3


title: JIA patient 43

description: JIA patient


title: JIA patient 42

description: JIA patient


title: JIA patient 41

description: JIA patient

value: JIA patient with active disease on treatment


title: JIA patient 40

description: JIA patient


title: JIA patient 39

description: JIA patient


title: manual_CEL-Seq1 [Manual_pos_sample_0101]

description:
CS1_manual.txt
Manual_pos_sample_0101

source_name: Fibloblasts

value: CyclinB1-GFP strain

value: Ear

value: cultered for 2-4 days before sorting

value: 1 month old

tag: experimental design

value: Analysis of manually collected CyclinB1-GFP negative (neg) or positive (pos) single cells by CEL-Seq1 protocol.


title: JIA patient 51

description: JIA patient


title: HMC_P6_H3K27me3

description:
HMC
breast primary cell passage 6


title: HMC_P6_H3K9me2

description:
HMC
breast primary cell passage 6


title: JIA patient 49

description: JIA patient


title: JIA patient 38

description: JIA patient


title: HMC_L.T.R_siKDM3A_RNASeq

value: HMC-LTR


title: JIA patient 36

description: JIA patient


title: HMC_L.T_shKDM3A_RNASeq

value: HMC-LT


title: HMC_L.T.R_RNASeq


title: JIA patient 35

description: JIA patient


title: JIA patient 37

description: JIA patient


title: HMC_L.T_NC_RNASeq

value: negative control


title: JIA patient 32

description: JIA patient


title: JIA patient 34

description: JIA patient


title: JIA patient 33

description: JIA patient


title: HMC_L.T_RNASeq


title: JIA patient 31

description: JIA patient


title: HMC_L_RNASeq


title: JIA patient 30

description: JIA patient


title: HMC_P6_H3K9me3

description:
HMC
breast primary cell passage 6


title: HMC_P6_RNASeq

description:
HMC
breast primary cell passage 6


title: JIA patient 29

description: JIA patient


title: JIA patient 28

description: JIA patient


title: 48h Leflunomide treated A375 cells replicate a

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

description: Gro-seq

data_processing:
For each replicate of DMSO (control), Leflunomide and A771762 treated samples, reads were trimmed at the 3′ends to remove any linker sequence contamination.
Trimmed reads for each sample were aligned to the hg18 version of the human genome using Bowtie 0.12.9 with parameters -k 1 -m 10 -n 2 --best --strata.
RNA repeats were then filtered out from the alignments using bedtools.
Read density at the promoters and within the gene bodies were respectively calculated as the read density within 300 bp of the TSS, and the read density within the TSS +300 bp to the TTS +3 kb. Densities were normalized to the read density at the beta-Actin promoter for each sample  and expressed as a fraction of millions of mapped reads per base pair (rpm/bp). The read densities were calculated on the transcripts which have a TR in the DMSO control condition initially low (TR< 7.5), representing 22442 over 47021 transcripts.
RNA Polymerase II Travelling ratios (TR) were calculated as the ratio of read densities at the promoters over the read densities within the gene bodies for each transcript in each sample. Average TRs were calculated from the TRs calculated in two experimental replicates.
Genome_build: hg18
Supplementary_files_format_and_content: Data table with the Traveling ratio calculated in each DMSO control, Leflunomide treated or A771726 treated conditions and a data table containing the read densities at the promoter and gene bodies.

source_name: A375 cells, 25 μM Leflunomide

growth_protocol: Human A375 malignant melanoma cells (ATCC) are grown on standard tissue culture plates in filter sterilized DMEM (Life Technologies) with 10% heat-inactivated FBS (Atlanta Biologicals), 1X GlutaMAX (Life Technologies) and 1% Penicillin-Streptomycin (Life Technologies).

extract_protocol:
After drug treatment, cells were frozen down, nuclear run-on reaction was performed, and nascent RNA was isolated.
TruSeq small RNA sample prep kit adapters and primers (Illumina) were used to make the samples suitable for multiplexing. The PCR reaction was run for 18 cycles. The indexed libraries were purified on a 6% native polyacrylamide gel, and were cut out between 150 and 300 bp.  The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script.

treatment_protocol: One million A375 cells per condition were treated with DMSO, 25 μM leflunomide, or 25 μM A771726 in duplicate.  Drugs used were leflunomide (Enzo Life Sciences) and A771726 (Enzo Life Sciences). After a 48 hr treatment, cells were washed, swelled, and lysed in lysis buffer with a reduced amount of IGEPAL detergent (composition: 10 mM Tris-Cl pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 10% glycerol, 2 U/mL SUPERasin (Ambion), and 0.25% IGEPAL).

value: malignant melanoma

tag: assayed molecule

value: nascent RNA


title: 48h Leflunomide treated A375 cells replicate b

description: Gro-seq

tag: cell line


title: HMC_L.T.R_NC_RNASeq


title: JIA patient 26

description: JIA patient


title: 48h A771726 treated A375 cells replicate b

description: Gro-seq


title: JIA patient 27

description: JIA patient


title: JIA patient 24

description: JIA patient


title: healthy control 8

description: healthy control

value: healthy control


title: JIA patient 25

description: JIA patient

value: blood


title: 48h DMSO treated A375 cells replicate b

description: Gro-seq

source_name: A375 cells, DMSO


title: 48h DMSO treated A375 cells replicate a

description: Gro-seq


title: healthy control 6

description: healthy control

value: Peripheral Blood Mononuclear Cells


title: healthy control 3

description: healthy control


title: healthy control 7

description: healthy control


title: healthy control 5

description: healthy control


title: healthy control 4

description: healthy control


title: healthy control 2

description: healthy control


title: 48h A771726 treated A375 cells replicate a

description: Gro-seq


title: JIA patient 22

description: JIA patient


title: JIA patient 18

description: JIA patient


title: JIA patient 19

description: JIA patient


title: JIA patient 20

description: JIA patient


title: JIA patient 21

description: JIA patient


title: healthy control 1

description: healthy control


title: JIA patient 17

description: JIA patient


title: JIA patient 16

description: JIA patient


title: JIA patient 11

description: JIA patient


title: JIA patient 10

description: JIA patient


title: JIA patient 14

description: JIA patient


title: JIA patient 8

description: JIA patient


title: JIA patient 7

description: JIA patient

value: JIA patient with active, untreated disease


title: JIA patient 5

description: JIA patient


title: JIA patient 3

description: JIA patient


title: JIA patient 13

description: JIA patient


title: JIA patient 6

description: JIA patient


title: JIA patient 15

description: JIA patient


title: JIA patient 9

description: JIA patient


title: JIA patient 23

description: JIA patient

value: JIA patient with clinical remission on medication


title: JIA patient 1

description: JIA patient


title: JIA patient 2

description: JIA patient


title: HEXIM1 ChIP on A771726-treated cells

data_processing:
ChIP-Seq aligned to hg19 with Bowtie with max mismatch 2bp
peaks were called using MACS 2.0 with the following setting: q-value 0.05
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph pileup from MACS 2.0 output

source_name: A375 melanoma cell line

extract_protocol:
DNA was sonicated and chromatin immunoprecipitation was performed with either HEXIM1 (Abcam) or CDK9 (Santa Cruz) antibodies. DNA was then de-cross-linked from pulled down protein and purified by phenol:chloroform:isoamyl alcohol extraction.
The NEBNext multiplex oligos for Illumina Kit (NEB) was used to make the samples suitable for multiplexing. The PCR reaction was run for 18 cycles. The indexed libraries were purified on a 2% agarose gel, and were cut out between 150 and 350 bp.  The concentration of the isolated libraries was estimated with a high-sensitivity DNA chip from Agilent according to manufacturer’s protocol and libraries were mixed in equal quantities and sequenced on Illumina Hi-Seq2000. Index sequences from multiplexed primers were used to identify treatment group and reads were demultiplexed using a perl script.

treatment_protocol: One hundred million A375 cells per condition were treated with DMSO, 25 μM leflunomide or 25 μM A771726.  Drugs used were leflunomide (Enzo Life Sciences) and A771726 (Enzo Life Sciences). After a 48 hr treatment, cells were washed, proteins and DNA were cross-linked with 11% formaldehyde and cell pellets were frozen down at -80C.

value: HEXIM1 (Abcam)


title: PA1 4sU 4 hr ribo-RNA replicate 1

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

description:
RNA labeled with 4sU 4 hr ribo-RNA
processed data file: PA1_4sU_4hr.bw

data_processing:
Basecalling using Illumina Casava1.8.4 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh37/hg19 human reference genome with the UCSC Genes annotation (hg19 knownGene.txt updated at 2013/6/30) using TopHat2 (Kim et al., 2013) 2.0.9 (parameters: -g 1 -a 6 --microexon-search -m 2).
Bam to Bedgraph using genomeCoverageBed
Bedgraph to bigwig using UCSC bedGraphToBigWig
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: bigwig file (UCSC bigwig in an indexed binary format. http://genome.ucsc.edu/goldenPath/help/bigWig.html)

source_name: PA1 4sU 4 hr ribo-RNA

growth_protocol: Human embryonal carcinoma (EC) line PA1 were cultured with MEMα medium supplemented with L-Glutamine and 10% FBS. H9 hESCs were cultured on plates coated with growth-factor-depleted Matrigel in fibroblast-conditional medium (CM) supplemented with 4ng/mL human Basic Fibroblast Growth Factor (bFGF). hESCs-derived forebrain neuron progenitor cells (FB D26) were cultured on laminin-coated substrate with NDM medium.

extract_protocol:
100-140 μg total RNA was used for biotinylation and purification of 4sU labeled nascent RNA. 4sU labeled RNA was biotinylated in biotinylation buffer (10 mM Tris pH 7.4, 1 mM EDTA) with 0.2 mg/ml EZ-link biotin-HPDP (Pierce, 21341), which was dissolved in dimethylformamide (DMF, Sigma, D4551) at a concentration of 1 mg/ml, and incubated at room temperature for 1.5 h with rotation. Unbound biotin-HPDP was removed by equal volume chloroform extraction twice, and RNA was precipitated at 1,3000 rpm for 15min at 4℃ with 1:10 volume of 5 M NaCl and an equal volume of isopropanol. The RNA pellet was washed twice with 75% ethanol and resuspended in 150 μl DEPC•H2O. RNA quality was checked by electrophoretical analysis to exclude RNA degradation. 4sU labeled and unlabeled RNA was separated by using Streptavidin-coated magnetic beads (Invitrogen). Biotinylated RNA was incubated with 150 μl Streptavidin beads at room temperature for 20 min. Beads were washed four times with 0.9 ml of 65 ℃ washing buffer (100 mM Tris pH 7.4, 10 mM EDTA, 1 M NaCl, 0.1% Tween 20), followed by four times with 0.9 ml of room temperature washing buffer. Nascent RNA was eluted with 100 μl 0.1 M dithiotheitol (DTT) twice, and RNA was precipitated with 40 μl of 4 M LiCl, 2 μl glycogen and 600 μl ice-cold ethanol. Before preparation of nascent RNA-seq library, ribosomal RNA was depleted from 4sU labeled RNAs with RiboMinusTM Human/Mouse Transcriptome Isolation Kit (Invitrogen, K1550-01) according to the manufacturer’s protocol.
4sUDRB and ribo-RNA-seq libraries were prepared with Illumina TruSeq Total RNA LT Sample Prep Kit without oligo(dT) enrichment. Deep sequencing was performed on Illumina Hiseq 2500 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: PA1, H9 and FB cells were incubated with 100 μM DRB (Sigma, D1916) for 3 h to block Pol II transcription. Transcription was recovered after DRB release and newly transcribed RNA was labeled with 300 μM 4sU (Sigma, T4509). TRizol (Invitrogen) was added to stop transcription and total RNA was extracted at each indicated transcription elongation time point.

tag: treatment

value: 3 h DRB 4 hr 4sU-labeling

value: ribo-RNA


title: PA1 4sU 16 hr ribo-RNA replicate 1

description:
RNA labeled with 4sU 16 hr ribo-RNA
processed data file: PA1_4sU_16hr.bw

source_name: PA1 4sU 16 hr ribo-RNA

value: 3 h DRB 16 hr 4sU-labeling


title: PA1 4sU 16 hr ribo-RNA replicate 2


title: HEXIM1 ChIP on DMSO-treated cells

tag: chip antibody


title: PA1 4sU 4 hr ribo-RNA replicate 2


title: ZF_Uninjured_Fin_2

city: Madison

first: Junsu

last: Kang

state: WI

address: 1111 Highland Avenue, Room 4451, WIMR II, Kang lab, CRB

department: Department of Cell and Regenerative Biology

institute: University of Wisconsin - Madison

data_processing:
Base calling with Casava
Alignment with TopHat
Counts summarized with R using TopHat output
Analysis performed with EdgeR package of Bioconductor
Genome_build: Zv9
Supplementary_files_format_and_content: "Regenerate_fin_counts.txt" and "Uninjured_fin_Control_counts.txt" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.

organism: Danio rerio

source_name: Uninjured fins

extract_protocol:
Either uninjured fins or fins at 4 days post amputation were collected.  10 fins were dissected, rinsed in PBS, placed in Trizol and homogenized.  RNA was then extracted.
Illumina RNA-Seq, 50 bp Single end libraries

treatment_protocol: Fins were amputated to 50% of their original length using razor blades

value: EK

tag: line

value: Wild type


title: Input ChIP on DMSO-treated cells


title: Input ChIP on A771726-treated cells


title: ZF_Uninjured_Fin_1


title: CDK9 ChIP on DMSO-treated cells

value: CDK9 (Santa Cruz)


title: CDK9 ChIP on A771726-treated cells


title: ZF_4dpa_Fin_2

source_name: Fins 4d post amputation

value: Fin Amputation


title: JIA patient 12

description: JIA patient

source_name: Peripheral Blood Mononuclear Cells

tag: disease stage

value: JIA patient with active disease on treatment


title: ZF_4dpa_Fin_1


title: Wildtype head X1 single cell 24

city: Portland

first: Bret

middle: J

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

data_processing:
Base calls and demultiplexing was performed with Illumina bcl2fastq version 1.8.3
Trimmed reads (3' 15 bp) were aligned to the transcriptome associated with BioProject 215411 using the program Bowtie2 version 2.2.4.  Raw counts were extracted from resulting SAM files and normalized using DESeq2.
The 1000 most highly variable transcripts across the single cell data were extracted based on mean and coefficient of variation values. The expression values for these transcripts in each cell were log transformed with a small pseudo-counts (+ 0.001) and used for heirarchical clustering and t-distributed stocastic neighbor embedding. Cell groups were defined by producing a dendrogram of the heirarchical clustering results and cutting the tree into 10 groups.
Genome_build: NCBI BioProject PRJNA215411  SmedASXL_transcripts_20130210.nt
Supplementary_files_format_and_content: [Molinaro_NCBI_rawcounts.txt] Raw counts values for each sample for each transcript are listed.  Only transcripts that were detected in at least one sample are listed. [Molinaro_NCBI_normalizedcounts.txt] single cell DESeq2-normalized counts.

molecule: polyA RNA

organism: Schmidtea mediterranea

source_name: Wildtype animal heads

growth_protocol: The clonal strain of Schmidtea mediterranea, CIW4, was grown in a milli-Q-based salt solution on beef liver.  Organisms were starved for 1 week prior to tissue collection.

extract_protocol:
All samples were prepared using the Smartseq2 protocol and the Nextera XT DNA library preparation kit from Illumina.
Illumina V4 chemistry and reagents

treatment_protocol: Cells from the heads of 30 animals were FACS sorted to obtain 96 single X1s and 72 single X2s and cDNA was prepared from poly-A+ mRNA for each cell using Smartseq2 and deep sequenced to a depth of 5M reads, as illustrated in Figure 1A of the manuscript. cDNA from two X1 and 1 X2 bulk tube controls of 200 cells each was prepared using the same protocol and sequenced to a depth of 10-20M reads each.

value: Asexual CIW4

tag: facs gate

value: Amputation fragment

value: heads

tag: sample type

value: single cell


title: Wildtype head X1 single cell 23


title: ZF_Uninjured_Hearts_2 (PG-2)

first: Ravi

last: Karra

address: 464 Nanaline Duke, 307 Research Drive

department: Cell Biology

institute: Duke

data_processing:
Base calling with Casava
Alignment with TopHat
Counts summarized with R using TopHat output
Analysis performed with EdgeR package of Bioconductor
Genome_build: Zv9
Supplementary_files_format_and_content: "Reads_cpms.txt" is tab delimited text file.  CPMs were calculated using edgeR.
Supplementary_files_format_and_content: "Raw_read_counts.txt" is a tab delimited text file containing summarized counts for each transcript.  This was the dataset entered into edgeR.

source_name: Whole uninjured hearts

extract_protocol:
Hearts were collected 7 days after treatment.  10 ventricles were dissected, rinsed in heparin, placed in Trizol and homogenized.  RNA was then extracted.
Illumina RNA-Seq, 50 bp Single end libraries

treatment_protocol: Animals were treated with Tamoxifen of propylene glycol

value: EK/AB

value: Propylene glycol


title: ZF_Uninjured_Hearts_1 (PG-1)


title: Wildtype head X1 single cell 21


title: ZF_Ablated_Hearts_2 (TAM-2)

source_name: Whole hearts 7d post ablation

value: Tamoxifen


title: Wildtype head X1 single cell 19


title: ZF_Ablated_Hearts_1 (TAM-1)


title: JIA patient 4

description: JIA patient

value: JIA patient with active, untreated disease

value: blood

tag: cell type

value: Peripheral Blood Mononuclear Cells


title: Wildtype head X1 single cell 18


title: Rag2 48h replicate 2

city: Kansas City

first: Ning

last: Zhang

state: MO

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

data_processing:
Reads with low quality (average Phred score < 26) were removed.
Filtered reads were mapped to the reference genome using TopHat (v1.4.1) with default parameters. Reads mapped to multiple genomic locations were excluded from further analysis.
Read counts were calculated using htseq-count (Version 0.5.3) with option -m union -s no.
Differential expression was done using edgeR package in R using the read counts as input.
Another strategy of differential expression analysis was done using Cuffdiff (v1.3.0) with default parameters. A gene was considered significantly regulated between two conditions when its relative fold change was higher than 2 or below 0.5, and its false discovery rate (FDR) was below 0.05 with both pipelines.
Genome_build: Schmutz J, et al. Nature 2010
Supplementary_files_format_and_content: aphid_read_counts.txt: tab delimited file including the read counts for each sample. edger_*h.txt: tab delimited files from edgeR output including the fold change (log2(Rag2/rag2)), p-value, adjusted p-value (FDR), etc. Cuffdiff_*h.gene_exp.diff: tab delimited files from Cuffdiff output including gene info, fold change, p-value, q-value, etc. sample_1 = rag2 and sample_2 = Rag2; The log fold change is calculated as log2(Rag2/rag2).

organism: Glycine max

source_name: Soybean leaf resistant to aphid

extract_protocol:
Total RNA were extracted using Trizol reagent according to manufacturer's instruction
Complementary DNA libraries were built according to the manusfacturer’s instruction (mRNA sequencing, Sample preparation guide; Illumina, San Diego, CA) using 10 µg of RNA. Each library was labeled with a 4 nucleotide specific barcode ACGT, CGTT, GTAT and sequenced using a HiSeq 2000 (Illumina, San Diego, CA)

tag: genotype

value: Leaf

tag: trait

value: resistant

tag: treatment stage

value: 48 h after aphid infestation


title: Rag2 8h replicate 2

tag: tissue

value: 8 h after aphid infestation


title: Wildtype head X1 single cell 16

tag: strain


title: Rag2 48h replicate 1


title: Rag2 4h replicate 2

value: 4 h after aphid infestation


title: Wildtype head X1 single cell 15


title: Wildtype head X1 single cell 17


title: Rag2 0h replicate 2

value: No aphids


title: Wildtype head X1 single cell 13


title: Wildtype head X1 single cell 14


title: Wildtype head X1 single cell 12


title: Rag2 8h replicate 1


title: Rag2 24h replicate 1

value: 24 h after aphid infestation


title: Rag2 4h replicate 1


title: Wildtype head X1 single cell 11

value: Asexual CIW4


title: rag2 48h replicate 2

source_name: Soybean leaf susceptible to aphid

value: susceptible


title: Wildtype head X1 single cell 10

value: Amputation fragment

value: heads


title: Wildtype head X1 single cell 22

value: single cell


title: Wildtype head X1 single cell 9


title: Rag2 0h replicate 1


title: Wildtype head X1 single cell 8


title: Wildtype head X1 single cell 20


title: rag2 4h replicate 2


title: Wildtype head X1 single cell 7


title: rag2 8h replicate 2


title: rag2 24h replicate 2


title: Wildtype head X1 single cell 6


title: Wildtype head X1 single cell 4


title: Wildtype head X1 single cell 5


title: Rag2 24h replicate 2


title: rag2 4h replicate 1


title: rag2 8h replicate 1


title: rag2 48h replicate 1


title: Wildtype head X1 single cell 1


title: rag2 0h replicate 1


title: rag2 24h replicate 1


title: Wildtype head X1 single cell 2


title: Wildtype head 200 X1s 1

value: bulk (200 cells)


title: coIP CJ NCTC11168 WT

status: Public on Apr 07 2016

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

data_processing:
Demultiplexing
Fastq quality trimming using FastX and a cut-off value of 20
Fastq to fasta conversion using FastX
Size filtering: discarding reads shorter than 12 nt (READemption)
Read mapping using segemehl version 0.1.7 (READemption)
Coverage calculation and normalization (READemption)
Genome_build: C. jejuni NCTC11168: ASM908v1 (NC_002163.1); C. jejuni 81-176: ASM1552v1 (NC_008770.1, NC_008787.1, NC_008790.1)
Supplementary_files_format_and_content: wiggle

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

source_name: Campylobacter jejuni NCTC11168 cells

growth_protocol: C. jejuni wildtype and csrA-3XFLAG strains were grown to mid-exponential phase (~0.6 OD600) in Brucella Broth. Cells corresponding to 60 OD600 were harvested to perform the coIP.

extract_protocol:
Phenol/Chloroform/Isoamyl alcohol RNA extraction (Rieder et. al., RNA Biology 2012)
The libraries were generated by Vertis Biotechnologie AG (Munich, Germany). The samples were poly(A)-tailed by using poly(A) polymerase. The 5'-PPP were removed using tobacco acid pyrophosphatase (TAP) followed by the ligation of the RNA adapter to the 5'-monophosphate of the RNA. First-strand cDNA synthesis was performed with an oligo(dT)-adapter primer and the M-MLV reverse transcriptase. The resulting cDNA was PCR-amplified to reach a concentration of 20-30 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis. The primers used for PCR amplification were designed for TruSeq sequencing according to the instructions of Illumina.

treatment_protocol: Cells were lysed and anti-FLAG antibody/sepharose beads were used to co-immunoprecipitate CsrA-3xFLAG and bound RNA.

tag: genotype/variation

value: WT

tag: rip antibody

value: Antibody-Monoclonal ANTI-FLAG M2 (Sigma, catalog# F1804, Batch no.(lot)# SLBD6976)


title: coIP CJ NCTC11168 csrA-3xFLAG


title: ENCLB612WYL

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Library strategy: eCLIP-seq
Takes output from raw files.  Run to trim off both 5’ and 3’ adapters on both reads. Command: quality-cutoff 6  -m 18  -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT  AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1. Run to trim off the 3’ adapters on read 2, to control for double ligation events. Command: cutadapt -f fastq --match-read-wildcards  --times 1  -e 0.1  -O 5  --quality-cutoff 6  -m 18  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2.  Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir /path/to/RepBase_human_database_file --genomeLoad LoadAndRemove  --readFilesIn /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz --outSAMunmapped Within  --outFilterMultimapNmax 30  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam --outSAMattributes All  --readFilesCommand zcat  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam
Takes output from STAR rmRep.  Maps unique reads to the human genome.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir  /path/to/STAR_database_file --genomeLoad LoadAndRemove  --readFilesIn  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate1  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate2  --outSAMunmapped Within  --outFilterMultimapNmax 1  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --outSAMattributes All  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam
takes output from STAR genome mapping.  Custom random-mer-aware script for PCR duplicate removal. Command: barcode_collapse_pe.py  --bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --out_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  --metrics_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.metrics
Takes output from barcode collapse PE.  Sorts resulting bam file for use downstream.  Command: java  -Xmx2048m  -XX:+UseParallelOldGC  -XX:ParallelGCThreads=4  -XX:GCTimeLimit=50  -XX:GCHeapFreeLimit=10  -Djava.io.tmpdir=/full/path/to/files/.queue/tmp  -cp /path/to/gatk/dist/Queue.jar  net.sf.picard.sam.SortSam  INPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  TMP_DIR=/full/path/to/files/.queue/tmp  OUTPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  VALIDATION_STRINGENCY=SILENT  SO=coordinate  CREATE_INDEX=true
Takes output from sortSam, makes bam index for use downstream.  Command: samtools index  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam.bai
Takes inputs from multiple final bam files.  Merges the two technical replicates for further downstream analysis.  Command: samtools  merge  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam /full/path/to/files/file_R1.D08.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam
Takes output from sortSam, makes bam index for use downstream.  Command: samtools  index  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/CombinedID.merged.bam.bai
Takes output from sortSam.  Only outputs the second read in each pair for use with single stranded peak caller.  This is the final bam file to perform analysis on.  Command: samtools view -hb -f 128  /full/path/to/files/CombinedID.merged.bam  >  /full/path/to/files/CombinedID.merged.r2.bam
Takes results from samtools view.  Calls peaks on those files.  Command: clipper  -b /full/path/to/files/CombinedID.merged.r2.bam  -s hg19  -o /full/path/to/files/CombinedID.merged.r2.peaks.bed  --bonferroni  --superlocal  --threshold-method binomial  --save-pickle
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, bigBed, bed (col1: chrom, col2: chromStart, col3: chromEnd, col4: -log10 pvalue, col5: log2 fold enrichment above input, col6: strand) format, contains clusters of predicted RBP binding

growth_protocol: HepG2 cells were grown under standard conditions (DMEM + 10% FBS + Pen/Strep (100U / mL)). K562 cells were grown in suspension in standard media (RPMI + 10% FBS + Pen/Strep (100U / mL)).

extract_protocol:
Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest (Protein G sheep anti-rabbit Dynabeads), and stringent washes.
After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB) (at this step, multiple replicates of the same RBP, or potentially RBPs of similar size and bound RNA amount, can be uniquely barcoded and pooled after ligation to simplify downstream steps - see Supplementary Fig. 2A). Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to > 90%. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

treatment_protocol: While plated, HepG2 cells were crosslinked with UV (254 nm, 400 mJ/cm2). HepG2 cells were then isolated with cell scrapers, pelleted at 200g, and snap frozen. K562 suspension cells were pelleted at 200g and resuspended in 1X PBS to 20 million cells per mL. 60 million cells in 3 mL were UV crosslinked (254 nm, 400 mJ/cm2) per 10 cm dish, pelleted, and snap frozen.

tag: antibody

tag: antibody manufacturer

value: Bethyl

tag: antibody catalog #

tag: antibody lot#

tag: rnase i fragmentation condition


title: ENCLB679DRC

tag: cell line


title: ENCSR496UBM

value: none (input)


title: ENCSR445LJH


title: ENCLB203AIU

value: Abcam


title: Wildtype head X1 single cell 3

tag: treatment


title: ENCLB238HOU

value: PPIG


title: ENCLB354LPS


title: ENCLB483UDN


title: ENCSR775UPS


title: ENCLB019FNY


title: ENCLB371PGL


title: ENCSR090VXV


title: ENCLB436IZW


title: ENCLB933GRD


title: ENCLB195YGJ

value: Genetex


title: ENCSR129SCO


title: ENCSR736LKF


title: ENCSR828NSY


title: ENCSR687HHB


title: ENCLB874IKE


title: untreated rep#2 GR ChIP-seq GH987

description: hs_RC_T47D_GR_Unt_RC_GH943GH987_FDR0.0.csv

source_name: T-47D breast cancer cell line

extract_protocol: Lysates were clarified from sonicated nuclei and GR/DNA, ER/DNA, of FoxA1/DNA complexes were isolated with antibody.

value: Pleural effusion from a ductal carcinoma of the breast

value: untreated

tag: time

value: 30 minutes

tag: replicate

value: replicate 2

value: GR E-20X sc-1003 Santa Cruz

tag: growth proptocol

value: For maintenance cells were cultured in RPMI containing 2mM L-glutamine supplemented 10% calf serum, 1mM sodium pyruvate, 1X non-essential amino acids, and 1% penicillin-streptomycin


title: ENCLB778RFV

value: DROSHA


title: ENCLB893EAL


title: ENCSR130TOJ


title: ENCLB472AWB


title: ENCLB238JYQ

value: QKI


title: ENCLB278TOU


title: ENCSR257OYO


title: ENCLB004PMM


title: ENCSR615AAW


title: ENCLB235NQC

value: MBL International


title: ENCSR575DKE


title: ENCLB263TUG


title: ENCLB419TPX


title: ENCLB423YJJ


title: ENCLB550OFF

value: FTO


title: ENCLB152QMP


title: ENCSR595PFU


title: ENCSR393STP


title: ENCLB022FVI


title: ENCSR461LGW


title: ENCLB541BNB


title: ENCLB436FYS


title: ENCLB850EER

value: GPKOW


title: ENCLB288CKF


title: ENCLB123NMA


title: ENCLB650JTP


title: ENCLB959KMS


title: ENCSR585TQT


title: ENCLB689GWR


title: ENCSR439GXW


title: ENCSR067UKU


title: ENCLB156RWL


title: ENCLB676CIS


title: ENCSR188OHK


title: ENCLB155HIP


title: ENCLB175BHT


title: ENCLB909IOJ


title: ENCLB026DPK


title: ENCSR298SAD


title: ENCSR044NGV


title: ENCLB097KHV


title: ENCLB134VGD


title: IMP1_CLIP_biosample1

description: CLIP-RNA

data_processing:
Library strategy: eCLIP-Seq
Takes output from raw files.  Run to trim off both 5’ and 3’ adapters on both reads. Command: quality-cutoff 6  -m 18  -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT  AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1. Run to trim off the 3’ adapters on read 2, to control for double ligation events. Command: cutadapt -f fastq --match-read-wildcards  --times 1  -e 0.1  -O 5  --quality-cutoff 6  -m 18  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2.  Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir /path/to/RepBase_human_database_file --genomeLoad LoadAndRemove  --readFilesIn /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz --outSAMunmapped Within  --outFilterMultimapNmax 30  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam --outSAMattributes All  --readFilesCommand zcat  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam
Takes output from STAR rmRep.  Maps unique reads to the human genome.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir  /path/to/STAR_database_file --genomeLoad LoadAndRemove  --readFilesIn  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate1  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate2  --outSAMunmapped Within  --outFilterMultimapNmax 1  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --outSAMattributes All  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam
takes output from STAR genome mapping.  Custom random-mer-aware script for PCR duplicate removal. Command: barcode_collapse_pe.py  --bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --out_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  --metrics_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.metrics
Takes output from barcode collapse PE.  Sorts resulting bam file for use downstream.  Command: java  -Xmx2048m  -XX:+UseParallelOldGC  -XX:ParallelGCThreads=4  -XX:GCTimeLimit=50  -XX:GCHeapFreeLimit=10  -Djava.io.tmpdir=/full/path/to/files/.queue/tmp  -cp /path/to/gatk/dist/Queue.jar  net.sf.picard.sam.SortSam  INPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  TMP_DIR=/full/path/to/files/.queue/tmp  OUTPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  VALIDATION_STRINGENCY=SILENT  SO=coordinate  CREATE_INDEX=true
Takes output from sortSam, makes bam index for use downstream.  Command: samtools index  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam.bai
Takes inputs from multiple final bam files.  Merges the two technical replicates for further downstream analysis.  Command: samtools  merge  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam /full/path/to/files/file_R1.D08.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam
Takes output from sortSam, makes bam index for use downstream.  Command: samtools  index  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/CombinedID.merged.bam.bai
Takes output from sortSam.  Only outputs the second read in each pair for use with single stranded peak caller.  This is the final bam file to perform analysis on.  Command: samtools view -hb -f 128  /full/path/to/files/CombinedID.merged.bam  >  /full/path/to/files/CombinedID.merged.r2.bam
Takes results from samtools view.  Calls peaks on those files.  Command: clipper  -b /full/path/to/files/CombinedID.merged.r2.bam  -s hg19  -o /full/path/to/files/CombinedID.merged.r2.peaks.bed  --bonferroni  --superlocal  --threshold-method binomial  --save-pickle
Genome_build: hg19
Supplementary_files_format_and_content: bed format, contains clusters of predicted RBP binding, txt format contains counts of reads for both IP and Input for each gene in subtranscriptomic region, bigWigs are read densities for positive and negative strand genome wide

source_name: H9 embryonic stem cell line

growth_protocol: H9 or H1 human embryonic stem cell lines were grown on Matrigel (BD biosciences) using mTeSR1 medium (Stem Cell Technologies). Cells were routinely passaged using Dispase (2mg/ml) and scraping the colonies with a glass pipet.

extract_protocol:
Ten million UV-crosslinked (400mJ/cm2 constant energy) H9 or H1 ES cells were lysed in standard iCLIP lysis buffer and sonicated (BioRuptor).
After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB) (at this step, multiple replicates of the same RBP, or potentially RBPs of similar size and bound RNA amount, can be uniquely barcoded and pooled after ligation to simplify downstream steps - see Supplementary Fig. 2A). Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to > 90%. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

tag: target protein

value: antibody manufacturer:MBL

tag: antibody lot #


title: Size-matched_Input_biosample1

description: CLIP-RNA


title: IgG_CLIP_biosample2

description: CLIP-RNA

value: antibody:IgG isotype control

value: antibody manufacturer:Thermo Fisher

value: antibody catalog#:02-6102


title: IMP2_CLIP_biosample1

description: CLIP-RNA


title: RBFOX2_size-matched_input

description: CLIP-RNA

source_name: H1 embryonic stem cell line


title: Size-matched_Input_biosample2

description: CLIP-RNA


title: IMP1_CLIP_biosample2

description: CLIP-RNA


title: IMP2_CLIP_biosample2

description: CLIP-RNA


title: RBFOX2_CLIP

description: CLIP-RNA

value: antibody manufacturer:Bethyl

value: antibody catalog#:A300-864A


title: ENCLB080PWY

value: Genetex


title: KO_nascent_RNA_rep2

first: Yang

last: Shi

address: NO. 138, Yi-Xue-Yuan Road

institute: Fudan university

description: nascent RNA

data_processing:
base_calling: CASAVA package (Illumina v1.7)
alignment: bowtie (version 1.0.0)
strand_separation: samtools (version 0.3.3)
Genome_build: hg19

source_name: ZR-75-30 cell

growth_protocol: ZR-75-30 were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Hyclone) supplemented with 10% fetal bovine serum (FBS, Gibco).

extract_protocol:
Nascent RNA capture was carried as manual (C-10365, Iife technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: RACK7 knockout


title: H9 ES IMP1 KD 3

data_processing:
RNA-seq libraries were first trimmed of polyA tails, adapters, and low quality ends using cutadapt with parameters --match-read-wildcards --times 2 -e 0 -O 5 --quality-cutoff' 6 -m 18 -b TCGTATGCCGTCTTCTGCTTG -b ATCTCGTATGCCGTCTTCTGCTTG -b CGACAGGTTCAGAGTTCTACAGTCCGACGATC -b TGGAATTCTCGGGTGCCAAGG -b AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT.
Reads were then mapped against a database of repetitive elements derived from RepBase18.05. Bowtie version 1.0.0 with parameters -S -q -p 16 -e 100 -l 20 was used to align reads against an index generated from Repbase sequences (Langmead et al., 2009).
Reads not mapped to Repbase sequences were aligned to the hg19 human genome (UCSC assembly) using STAR (Dobin et al., 2013) version 2.3.0e with parameters --outSAMunmapped Within –outFilterMultimapNmax 1 –outFilterMultimapScoreRange 1.
counts of reads for each gene annotated in gencode v17 were calculated from featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: csv count file, containts counts of reads for each sample

growth_protocol: H9 and HUES6 human embryonic stem cell lines were grown on Matrigel (BD biosciences) using mTeSR1 medium (Stem Cell Technologies). Cells were routinely passaged using Dispase (2mg/ml) and scraping the colonies with a glass pipet.

extract_protocol:
Total RNA was extracted from cells using TRIzol (Invitrogen) according to manufacturer’s instructions. 1 ug of total RNA was DNase treated and subjected to Ribo-Zero treatment
TruSeq Stranded Total RNA Sample Preparation Kit

treatment_protocol: Lentivirus containing shRNA hairpins were generated by transfecting 293T cells with indicated shRNA plasmids. Following titering, a dilution series was performed on hESCs to determine maximum shRNA efficiency with minimal cell death; equal amounts of virus were used for all experiments. Cells were single-cell dissociated to 200k cells/sample and incubated with concentrated virus for 1 hour at 37 degrees, 5% CO2 before plating out into 1 well of a 6 well plate supplemented with 10μM Rock Inhibitor Y-26732 (Calbiochem). Medium was refreshed the following day and selection with 1μg/ml Puromycin (Sigma) began 48hours following transduction and continued for 5 days when the cells were collected for experiments.

tag: shRNA

tag: knockdown

value: IMP1 knockdown


title: IMP3_CLIP_biosample2

description: CLIP-RNA


title: KO_mRNA_rep3

data_processing:
base_calling: CASAVA package (Illumina v1.7)
alignment: tophat (version 2.0.12)
FPKM_calculating: cufflinks (version 2.2.1)
Genome_build: hg19

extract_protocol:
mRNA purification was carried as manual (61011, Iife technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: parental_mRNA_rep3

value: parental


title: KO_mRNA_rep2


title: parental_mRNA_rep2


title: H9 ES Control 2

value: control


title: H9 ES IMP1 KD 1


title: KO_KDM5C_ChIP_rep2

data_processing:
base_calling: CASAVA package (Illumina v1.7)
alignment: bowtie (version 1.0.0)
peak_calling: macs14 (version 1.4)
Genome_build: hg19

extract_protocol:
Chromatin samples were incubated with specific antibodies in ChIP Lysis buffer (50mM HEPES pH7.5, 500mM NaCl, 1mM EDTA, 1%Triton, 0.1%Na-deoxylcholate, 0.1% SDS) overnight at 4℃. The protein-DNA complexes were immobilized on protein A/G beads (10μl per reaction). The bound fractions were washed 3 times with Lysis buffer, and 3 times with RIPA buffer (50mM Hepes, 300mM LiCl, 1mM EDTA, 0.5%NP-40, 0.7%Nadeoxylcholate), and once with TE. Elution and Reverse crosslinking were carried out in Elution buffer (50mM Tris, PH8.0, 1mM EDTA, 1% SDS) 65℃ for 6 hours. After RNase A and protease K digestion, DNA fraction was purified using PCR extraction kit (QIAGEN).
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

value: Bethyl, A301-034A


title: rag2 0h replicate 2

tag: tissue

value: Leaf

tag: trait

value: susceptible

tag: treatment stage

value: No aphids


title: parental_nascent_RNA_rep2

description: nascent RNA

tag: antibody


title: KO_H3K27Ac_ChIP_rep2

value: Millipore, 07-360


title: H9 ES Control 1


title: KO_H3K4me3_ChIP_rep2

value: Cell Signaling, 9751S


title: H9 ES IMP1 KD 2


title: MCF7.shPHF20_E2-_rep2

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
RNA-seq reads were aligned to hg19 genome using tophat v2.0.10
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq reads count were calculated using HTSeq 0.6.1p1

source_name: MCF7 cells_shPHF20_E2-

growth_protocol: Human MCF-7 (ATCC) were cultured in DMEM (Cellgro) supplemented with 10% fetal bovine serum (Sigma).

extract_protocol:
mRNA was prepared using the RNeasy Plus kit (Qiagen) and reverse-transcribed using the First Strand Synthesis kit  (Invitrogen).
Libraries were prepared using the Illumina TruSeq RNA  Library Prep kit following the manufactory manual.

treatment_protocol: For shRNA knockdown, 293T cells were co-transfected with pMD2.G and pPAX2 (Addgene) together with pLKO-shRNA constructs or a non-targeting pLKO-shRNA (pLKO-shCtrl). Viral supernatants were harvested after 48 hrs. For infections, MCF-7 or T-47D cells were incubated with viral supernatants in the presence of 8 µg/ml polybrene. After 48 hrs, puromycin (2 µg/ml) was added to the DMEM. Cells were grown, with selection for 5-7 days to select for stable knockdown cells before estrogen treatment. For estrogen treatment, cells were starved in phenol red-free DMEM supplemented with 10% charcoal-stripped FBS (Sigma) for 3-4 days, and 10 nM 17β-estradiol (Sigma) or ethanol (vehicle) were added to the medium  (3 or 6 hrs) before the cells were harvested.

value: PHF20 knock down without E2 treatment


title: MCF7.shPHF20_E2+_rep2

source_name: MCF7 cells_shPHF20_E2+

value: PHF20 knock down with E2 treatment


title: MCF7.shPHF20_E2+_rep1


title: MCF7.shNT_E2-

source_name: MCF7 cells_shNT_E2-

value: Control without E2 treatment


title: MCF7.shNT_E2-_rep2


title: MCF7.shNT_E2+_rep2

source_name: MCF7 cells_shNT_E2+

value: Control with E2 treatment


title: MCF7.shNT_E2+_rep1


title: Rack7_ChIP_rep2

value: Bethyl, A302-090A


title: parental_H3K4me3_ChIP_rep2


title: parental_H3K4me2_ChIP_rep2

value: Millipore, 07-030


title: parental_H3K27Ac_ChIP_rep2


title: parental_H3K4me1_ChIP_rep2

value: ActiveMotif, 39297


title: ZR-75-30_Parental_P300_ChIP_rep2

data_processing:
base_calling: CASAVA package (Illumina v1.7)
alignment: bowtie (version 1.0.0)
peak_calling: macs14 (version 1.4)
Genome_build: mES_Rack7_ChIP: mm9, others: hg19

growth_protocol: ZR-75-30 and MCF-7were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Hyclone) supplemented with 10% fetal bovine serum (FBS, Gibco). mES cells were grown on 0.1% gelatinized (Sigma, G1890) tissue culture plates in ESC media. ESC media: DMEM supplemented with 10% fetal bovine serum, 1000 U/mL LIF, 100 µM nonessential amino acids (Invitrogen, 11140-050), 2 mM L-glutamine (Invitrogen, 25030-081), 100 U/mL penicillin, 100 µg/mL streptomycin (Invitrogen, 15140-122), and 1 μL/mL of 2-mercaptoethanol (Sigma, M7522).

value: Santa Cruz, SC-584


title: MCF7.shNT_E2-_rep1


title: ZR-75-30_Parental_P300_ChIP_rep1


title: MCF7.shG9a_E2-

source_name: MCF7 cells_shG9a_E2-

value: G9a knock down without E2 treatment


title: parental_KDM5C_ChIP_rep2

value: parental


title: MCF7.shNT_E2+


title: KO_H3K4me2_ChIP_rep2

value: RACK7 knockout


title: MCF7_Parental_H3K4me3_ChIP

source_name: MCF-7 cell


title: MCF7.shPHF20_E2-_rep1


title: MCF7_Parental_H3K4me1_ChIP


title: KO_H3K4me1_ChIP_rep2


title: MCF7_RACK7_KO_H3K4me1_ChIP


title: MCF7_RACK7_KO_H3K4me3_ChIP


title: Th17 48h rep3

city: Espoo

first: Sini

last: Rautio

address: Konemiehentie 2

country: Finland

institute: Aalto University

description: Th17 polarization was initiated with IL-6 (20 ng/ml, Roche), IL1β (10 ng/ml, R&D Systems) and TGFβ (10 ng/ml, R&D Systems)

data_processing:
Illumina Casava1.8 software used for basecalling.
Samples Prof3_1, Prof3_2,Prof3_3, Prof3_4,Prof3_5 were truncated to 50nt and only R1 fastq files were used
Sequence reads were mapped using Tophat (version 1.3.2) with default parameters to the GRCh37 release 63 human reference genome and NCBIM37 release 63 mouse reference genome.
Expression levels were estimated for Ensembl genes using Python script rpkmforgenes with parameters -readcount -no3utr -rmnameoverlap -bamu (Ramsköld et al.,2009). 3' untranslated regions were ignored and regions where several transcripts with different gene identifiers overlap were removed. Genes with RPKM values <3 in at least two replicates at all time points were filtered out from the downstream analysis.
Human lncRNAs were obtained from Gencode (http://www.gencodegenes.org) database and mouse lncRNAs from NONCODE (http://noncode.org). Expression values of lncRNAs were calculated using Python package HTSeq (http://www-huber.embl.de/users/anders/HTSeq), where overlapping reads with protein-coding genes were excluded. Lncrnas with RPKM values <0.5 in at least two replicates at all time points were filtered out from the downstream analysis.
Genome_build: human: hg19
Genome_build: mouse: mm9
Supplementary_files_format_and_content: rc_human_samples.txt: Read count measurements of Ensembl genes
Supplementary_files_format_and_content: rc_mouse_samples.txt: Read count measurements of Ensembl genes
Supplementary_files_format_and_content: rc_human_lncrna.txt: Read count measurements of lncrnas
Supplementary_files_format_and_content: rc_mouse_lncrna.txt: Read count measurements of lncrnas

source_name: Cord blood CD4+ cells 48h after activation and polarization towards Th17

growth_protocol:
human samples: Human CD4+ T cells were purified from umbilical cord blood of healthy neonates (Turku University Central Hospital, Finland). Mononuclear cells were isolated (Ficoll-Paque, Amersham Biosciences) after which CD4+ cells were collected (Dynal CD4 Positive Isolation Kit, Invitrogen). Cells were activated with plate-bound αCD3 (750 ng/24w culture plate well, Immunotech, France) and soluble αCD28 (1 µg/ml, Immunotech) in density of 0.5x106 cells/ml of X-vivo 20 serum free medium (Lonza) supplemented with 2 mM L-Glutamine (#G7513, Sigma), 50 U/ml Penicillin and 50 μg/ml Streptomycin (#P0781, Sigma) and neutralizing αIFNg (1 µg/ml) and αIL4 (1 µg/ml), and cultured at 37°C in 5 % CO2.
mouse samples: Naïve CD4 T cells (CD4+CD25-CD44lo) were isolated from C57BL/6 mice and the cells were sort-purified and cultured in IMDM (Sigma-Aldrich) supplemented with 5% FCS, 2x10-3 M L-glutamine, 100 U/ml penicillin, 100 µg/ml streptomycin and 5x10-5 M β-mercaptoethanol (all Sigma) in the presence of plate-bound α-CD3 (0.5 µg/ml; 2C11) and plate-bound α-CD28 (5 µg/ml; 37.51; both from Large Scale Facility, Medical Research Council National Institute for Medical Research).

extract_protocol:
RNA from human and mouse samples was extracted with RNeasy mini kit (Qiagen) according to manufacturer's instructions. In-column DNase (RNase-Free DNase Set, Qiagen) treatment was performed for 15 minutes. RNA was eluted in dH2O.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: source

value: Cord blood

tag: cell type

tag: human biological replicate


title: Th17 72h rep3

source_name: Cord blood CD4+ cells 72h after activation and polarization towards Th17


title: Th17 24h rep3

source_name: Cord blood CD4+ cells 24h after activation and polarization towards Th17


title: Th17 12h rep3

source_name: Cord blood CD4+ cells 12h after activation and polarization towards Th17


title: Th17 6h rep3

source_name: Cord blood CD4+ cells 6h after activation and polarization towards Th17


title: Th17 2h rep3

source_name: Cord blood CD4+ cells 2h after activation and polarization towards Th17


title: Th17 0.5h rep3

source_name: Cord blood CD4+ cells 0.5h after activation and polarization towards Th17


title: MCF7.shG9a_E2+

source_name: MCF7 cells_shG9a_E2+

tag: cell line

value: G9a knock down with E2 treatment


title: Th0 72h rep3

source_name: Cord blood CD4+ cells 72h after activation


title: Th17 4h rep3

source_name: Cord blood CD4+ cells 4h after activation and polarization towards Th17


title: KO_mRNA_rep1

source_name: ZR-75-30 cell


title: MCF7_Parental_H3K27ac_ChIP


title: KO_input_rep1


title: KO_H3K27me3_ChIP_rep1

value: Cell Signaling, 9733S


title: parental_input_rep1


title: MCF7_RACK7_ChIP


title: C57BL/6 Th17 72h rep3

description: Th17 polarization was initiated with IL-6 (20 ng/ml, R&D Systems), IL1β (10 ng/ml, R&D Systems) and TGFβ (1 ng/ml, R&D Systems)

source_name: Mouse CD4+ cells 72h after activation and polarization towards Th17

tag: mouse biological replicate


title: Th0 12h rep3

source_name: Cord blood CD4+ cells 12h after activation


title: Th0 48h rep3

source_name: Cord blood CD4+ cells 48h after activation


title: KO_nascent_RNA_rep1

description: nascent RNA


title: parental_mRNA_rep1


title: Th0 24h rep3

source_name: Cord blood CD4+ cells 24h after activation


title: Th17 1h rep3

source_name: Cord blood CD4+ cells 1h after activation and polarization towards Th17


title: C57BL/6 Th17 48h rep3

source_name: Mouse CD4+ cells 48h after activation and polarization towards Th17


title: C57BL/6 Th17 24h rep3

source_name: Mouse CD4+ cells 24h after activation and polarization towards Th17


title: C57BL/6 Th17 12h rep3

source_name: Mouse CD4+ cells 12h after activation and polarization towards Th17


title: C57BL/6 Th17 6h rep3

source_name: Mouse CD4+ cells 6h after activation and polarization towards Th17


title: C57BL/6 Th17 4h rep3

source_name: Mouse CD4+ cells 4h after activation and polarization towards Th17


title: parental_nascent_RNA_rep1

description: nascent RNA


title: C57BL/6 Th17 2h rep3

source_name: Mouse CD4+ cells 2h after activation and polarization towards Th17


title: Th0 6h rep3

source_name: Cord blood CD4+ cells 6h after activation


title: C57BL/6 Th17 0.5h rep3

source_name: Mouse CD4+ cells 0.5h after activation and polarization towards Th17


title: KO_H3K27Ac_ChIP_rep1


title: Th0 0.5h rep3

source_name: Cord blood CD4+ cells 0.5h after activation


title: parental_H3K4me3_ChIP_rep1


title: Th0 4h rep3

source_name: Cord blood CD4+ cells 4h after activation


title: parental_H3K27me3_ChIP_rep1


title: parental_H3K27Ac_ChIP_rep1


title: Thp rep3

source_name: Cord blood CD4+ cells without any treatments


title: KO_H3K4me3_ChIP_rep1

source_name: ZR-75-30 cell


title: C57BL/6 Th17 1h rep3

source_name: Mouse CD4+ cells 1h after activation and polarization towards Th17


title: KO_H3K4me2_ChIP_rep1


title: parental_H3K4me2_ChIP_rep1


title: C57BL/6 Th17 72h rep2

source_name: Mouse CD4+ cells 72h after activation and polarization towards Th17


title: Th0 1h rep3

source_name: Cord blood CD4+ cells 1h after activation


title: KO_KDM5C_ChIP_rep1

value: Bethyl, A301-034A


title: Th17 24h rep2

source_name: Cord blood CD4+ cells 24h after activation and polarization towards Th17


title: C57BL/6 Th17 48h rep2


title: C57BL/6 Th17 6h rep2