title: KP1-sh2_counted_A [ATAC-seq]


title: KP22-empty_2 [RNA-seq]

status: Public on May 10 2016

type: SRA

city: Stanford

first: William

last: Greenleaf

state: CA

address: 279 Campus Drive

country: USA

institute: Stanford University

description:
cell line containing expression vector with no gene
processed data file: refseqmm10.exons_unique_start_end.st.merge.bed, cell_mod.refseqmm10.exons_unique_start_end.st.merge.counts, gene_expression_cqnnorm_deseq.csv

library_source: transcriptomic

data_processing:
Reads were aligned to the genome using TopHat
Exons were found from RefSeq genes, and exons with the same start and end locations were merged.
The number of reads overlapping each merged exon was found using bedtools multicov (-q30). This count was summed for exons all mapping to a particular gene.
Counts were normalized for length and GC bias using cqnnorm (Hansen et al. 2012). The sum of all reads within exons was used for the size factors. The length of all exons per gene was summed to get the length covariate, and the GC covariate was the average GC content within exons annotated per gene.
Differential expressiond was found using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: refseqmm10.exons_unique_start_end.st.merge.bed gives start and end of merged exons per gene (mm10)
Supplementary_files_format_and_content: cell_mod.refseqmm10.exons_unique_start_end.st.merge.counts gives the number of reads intersecting each of the exons given by the bed file above.
Supplementary_files_format_and_content: *deseq_results.csv gives the output from deseq2. Columns appended by '.5' (or '1') assess signficance of abs value of log2fold change being greater than 0.5 (or 1)

molecule: total RNA

organism: Mus musculus

growth_protocol: All murine and human SCLC cell lines used in this study grow as floating spheres and were cultured in RPMI with 10% FBS.

extract_protocol:
Qiagen RNAeasy mini kit
Illumina TruSeq v2 kit

tag: cell line

tag: cell type

value: tumor-derived cell line

tag: genotype/variation

tag: nfib expression level (background)

value: Nfib low

value: expressing empty vector


title: KP22-nfib_1 [RNA-seq]

description:
cell line containing expression vector for Nfib
processed data file: refseqmm10.exons_unique_start_end.st.merge.bed, cell_mod.refseqmm10.exons_unique_start_end.st.merge.counts, gene_expression_cqnnorm_deseq.csv

value: expressing nfib


title: KP1-shLuc_counted_A [ATAC-seq]

description:
processed data file: peak_calls_mm9.nheader.up.bed, cell_mod.deseq_results.csv
cell line with expression vector control

library_source: genomic

data_processing:
library strategy: ATAC-seq
Adapters were trimmed from reads before alignment using bowtie 2 with the -X 2000 flag.  Duplicate fragments for each sample were discarded, as were reads mapping to chrM, reads with mapping quality less than 30
peak calling was done on the merged ex vivo data (samples 1-27) for the mouse data, or on the merged human cell lines (60-67) with MACS2 with the --nomodel, --broad flags
counts per sample were found within peaks, and differential accessibility was called within each group of samples (ex vivo, cell lines, modified cell lines, and human modified cell lines)
Genome_build: mm9 for mus musculus, hg19 for homo sapiens
Supplementary_files_format_and_content: peak_calls_mm9.nheader.up.bed are the peaks used for all mouse data. Four columns indicate chromosome, start, and end of accessible regions, plus a fourth column giving a unique identifier per peak
Supplementary_files_format_and_content: all_merged.H14_H29_H52_H69_H82_H88_peaks.broadPeak are the peaks used for human data. Standard broadpeak output is given.
Supplementary_files_format_and_content: *deseq_results.csv gives the output from deseq2. Columns appended by '.5' (or '1') assess signficance of abs value of log2fold change being greater than 0.5 (or 1)
Supplementary_files_format_and_content: *.bw are bigwig files containing the insertions per base pair, smoothed over 150 bp windows (20bp step size). Sample replicates are merged.

molecule: genomic DNA

source_name: cell line

growth_protocol: All murine and human SCLC cell lines used in this study grow as floating spheres and were cultured in RPMI with 10% FBS. Primary tumors and metastases were dissected and dissociated using collagenase IV, dispase, and trypsin at 37oC for 30 minutes. After dissociation the samples are continually on ice, in contact with ice-cold solutions, and in the presence of 2mM EDTA and 1U/ml DNase to prevent aggregation, and were FACS sorted for purity.

extract_protocol:
Cells were lysed, incubated with  Tn5 transposase, and purified with Qiagen MinElute kit.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit, as per Buenrostro et al. (2013).

treatment_protocol: Stable Nfib knockdown cell lines were generated using lentiviral pLKO/PuroR vectors. Inducible and constitutive Nfib expressing human and mouse cells were generated using lentiviral vectors.

tag: tissue/cell type

value: expressing empty vector (shControl)

tag: induced for

value: 2 weeks


title: KP1-sh2_2 [RNA-seq]

description:
cell line expressing shRNA to Nfib
processed data file: refseqmm10.exons_unique_start_end.st.merge.bed, cell_mod.refseqmm10.exons_unique_start_end.st.merge.counts, gene_expression_cqnnorm_deseq.csv

value: Nfib high

value: expressing shNfib


title: 16T-sh2_1 [RNA-seq]


title: 16T-shLuc_2 [RNA-seq]

description:
cell line with expression vector control
processed data file: refseqmm10.exons_unique_start_end.st.merge.bed, cell_mod.refseqmm10.exons_unique_start_end.st.merge.counts, gene_expression_cqnnorm_deseq.csv

value: expressing shControl


title: KP22_PD1 [ChIP-seq]

description: processed data file: KP22_chip_peaks.bed, KP22_chip_FE.s20.w150.bw, merged_peaks.deseq_results.all.csv

data_processing:
Adapters were trimmed from reads before alignment using bowtie 2 with the -X 2000 flag.  Duplicate fragments for each sample were discarded, as were reads mapping to chrM, reads with mapping quality less than 30
peak calling was done for each cell lines, using the input reads as controls, using MACS2 (callpeak -t 16T_PD1.st.all.rmdup.bam 16T_PD2/16T_PD2.st.all.rmdup.bam -c 16T_input1.st.all.rmdup.bam 16T_input2.st.all.rmdup.bam -B --SPMR -g mm
fold enrichment over input was found using MACS2
differential counts were found using DESeq2
Genome_build: mm9
Supplementary_files_format_and_content: *bed files are the peak calls for each cell line
Supplementary_files_format_and_content: *bw files  are bigwig files containing the fold enrichment of pull down above input per base pair, smoothed over 150 bp windows (20bp step size). Sample replicates are merged.
Supplementary_files_format_and_content: *deseq_results.csv gives the output from deseq2. Columns appended by '.5' (or '1') assess signficance of abs value of log2fold change being greater than 0.5 (or 1)

extract_protocol:
Nuclei were lysed and sonicated, genomic DNA was isolated with antibody and purified with RNAse and Proteinase K before being purified with QIAquick PCR purification kit (Qiagen).
Library was generated following Clontech low input with 1ng of ChIP product. 12 samples were pooled for Illumina Hiseq.

treatment_protocol: Chromatin immunoprecipitation (ChIP) for Nfib was performed as described by the Farnham laboratory (http://farnham.genomecenter.ucdavis.edu/pdf/FarnhamLabChIP%20Protocol.pdf

tag: nfib expression level

tag: sample type

value: Nfib pulldown

tag: chip antibody

value: Nfib antibody (Sigma, #HPA003956)


title: KP1-shLuc_counted_B [ATAC-seq]


title: KP22-nfib_2 [RNA-seq]


title: CD_1

city: Chapel Hill

first: Shehzad

last: Sheikh

state: NC

address: 5023A Genetic Medicine Building

institute: University of North Carolina - Chapel Hill

data_processing:
Reads were filtered such that their identical sequence could appear only up to five times, then were filtered using TagDust (Lassmann et al. 2009). Reads with quality score greater than 20 for 90% of bases were retained. High quality reads were aligned to their respective personalized genomes using the SNP-tolerant GSNAP software (Wu and Nacu 2010).
Peaks were identified for each sample using Fseq (Boyle et al. 2008).
genome build: hg19 (customized)
processed data file format and content: bigWig of raw FAIRE-seq signal

organism: Homo sapiens

source_name: Colonic mucosal biopsy

growth_protocol: CD patients from the adult IBD Center at University of North Carolina were included in this study. A total of 4 samples (2 CD and 2 non-CD controls) were used. Tissue was prepared for FAIRE as previously described (Simon 2012).

extract_protocol:
FAIRE was performed as described previously (Simon 2012).
TruSeq libraries were constructed as per manufacturer's recommendations.

tag: phenotype

value: Crohn's Disease


title: KP1-sh2_1 [RNA-seq]


title: KP22-empty_1 [RNA-seq]


title: KP1-shLuc_1 [RNA-seq]


title: KP1_input2 [ChIP-seq]

description: processed data file: KP1_chip_peaks.bed, KP1_chip_FE.s20.w150.bw, merged_peaks.deseq_results.all.csv

value: input


title: KP1-PD1 [ChIP-seq]


title: 16T_PD1 [ChIP-seq]

description: processed data file: 16T_chip_peaks.bed, 16T_chip_FE.s20.w150.bw, merged_peaks.deseq_results.all.csv


title: 16T_input2 [ChIP-seq]


title: 16T-sh2_2 [RNA-seq]


title: 16T_input1 [ChIP-seq]


title: 16T_PD2 [ChIP-seq]


title: KP22-nfib-2w_B [ATAC-seq]

description:
processed data file: peak_calls_mm9.nheader.up.bed, cell_mod.deseq_results.csv
cell line containing Dox-inducible promoter expressing Nfib. under induction for 2 weeks before ATAC-seq

value: expressing Nfib under Dox-inducible promoter


title: KP1-shLuc_2 [RNA-seq]


title: KP22_input2 [ChIP-seq]


title: KP1_input1 [ChIP-seq]


title: KP22_input1 [ChIP-seq]


title: KP22-nfib-2w_A [ATAC-seq]


title: KP22-nfib-1w_B [ATAC-seq]

description:
processed data file: peak_calls_mm9.nheader.up.bed, cell_mod.deseq_results.csv
cell line containing Dox-inducible promoter expressing Nfib. under induction for 1 week before ATAC-seq

value: 1 week


title: KP1-PD2 [ChIP-seq]


title: KP22-nfib-1w_A [ATAC-seq]


title: 16T-shLuc_1 [RNA-seq]


title: KP22-nfib-2d_B [ATAC-seq]

description:
processed data file: peak_calls_mm9.nheader.up.bed, cell_mod.deseq_results.csv
cell line containing Dox-inducible promoter expressing Nfib. under induction for 2 days before ATAC-seq

value: 2 days


title: KP22_PD2 [ChIP-seq]


title: KP22-nfib-2d_A [ATAC-seq]


title: KP22-nfib-1d_B [ATAC-seq]

description:
processed data file: peak_calls_mm9.nheader.up.bed, cell_mod.deseq_results.csv
cell line containing Dox-inducible promoter expressing Nfib. under induction for 1 day before ATAC-seq

value: 1 day


title: KP22-empty-1w_B [ATAC-seq]

description:
processed data file: peak_calls_mm9.nheader.up.bed, cell_mod.deseq_results.csv
cell line containing Dox-inducible promoter, but no downstream gene. under induction for 1 week before ATAC-seq

value: tumor-derived cell line

value: containing empty vector with Dox-inducible promoter


title: KP22-empty-2w_B [ATAC-seq]

description:
processed data file: peak_calls_mm9.nheader.up.bed, cell_mod.deseq_results.csv
cell line containing Dox-inducible promoter, but no downstream gene. under induction for 2 weeks before ATAC-seq


title: KP22-nfib-1d_A [ATAC-seq]


title: KP22-empty-1w_A [ATAC-seq]


title: KP22-empty-2d_A [ATAC-seq]

description:
processed data file: peak_calls_mm9.nheader.up.bed, cell_mod.deseq_results.csv
cell line containing Dox-inducible promoter, but no downstream gene. under induction for 2days before ATAC-seq


title: KP22-empty-2w_A [ATAC-seq]


title: KP22-empty-1d_B [ATAC-seq]

description:
processed data file: peak_calls_mm9.nheader.up.bed, cell_mod.deseq_results.csv
cell line containing Dox-inducible promoter, but no downstream gene. under induction for 1 day before ATAC-seq


title: KP22-empty-1d_A [ATAC-seq]


title: KP1-shLuc-FACS_A [ATAC-seq]

description:
processed data file: peak_calls_mm9.nheader.up.bed, cell_mod.deseq_results.csv
cell line expressing shRNA to Nfib

value: expressing shRNA to Nfib (shNfib)


title: 16T-sh2-FACS_B [ATAC-seq]


title: 16T_sh2_counted_B [ATAC-seq]


title: 16T-sh2-FACS_A [ATAC-seq]


title: KP1-shLuc-FACS_B [ATAC-seq]


title: 16T-shLuc-FACS_A [ATAC-seq]


title: 16T_sh2_counted_A [ATAC-seq]


title: 16T-shLuc-FACS_B [ATAC-seq]


title: 16T_shLuc_counted_B [ATAC-seq]


title: 16T_shLuc_counted_A [ATAC-seq]

description: cell line with expression vector control


title: KP22-A [ATAC-seq]

description:
processed data file: peak_calls_mm9.nheader.up.bed, cell_lines.deseq_results.csv
cell lines were previously derived from tumors from murine SCLC, grow in culture and undergone ATAC-seq.


title: KP22-B [ATAC-seq]


title: MotL-B   [ATAC-seq]

value: MotL


title: KP1-B [ATAC-seq]


title: MotL-A [ATAC-seq]


title: 2N1-A [ATAC-seq]


title: 2N1-B [ATAC-seq]


title: KP1-A [ATAC-seq]


title: 25L-A [ATAC-seq]


title: KP22-empty-2d_B [ATAC-seq]


title: 16T-B [ATAC-seq]


title: 16T-A [ATAC-seq]


title: KP1-sh2-FACS_A [ATAC-seq]


title: T4-B [ATAC-seq]

description:
processed data file: peak_calls_mm9.nheader.up.bed, primary_tissue.deseq_results.csv, T4.from140625and140115.rmdup.s20.w150sw.bw
6-8 months after tumor intiation, metastasis was dissected from liver and FACS sorted for high purity. ATAC-seq was performed on purified cells.

source_name: primary tumor (lung)

tag: strain background

value: mixed; C57BL/6N, 129S1/SvImJ, 129X1/129Ola, and with some FVB/Ntac

value: lung


title: NCI-H524_nfib_C [ATAC-seq]

description:
processed data file: peak_calls_mm9.nheader.up.bed, human_oe.deseq_results.csv
cell line containing expression vector for Nfib. under induction for 2 weeks before ATAC-seq

value: expressing Nfib

value: 2 weeks


title: NCI-H524_nfib_B [ATAC-seq]


title: T1 [ATAC-seq]

description: processed data file: peak_calls_mm9.nheader.up.bed, primary_tissue.deseq_results.csv, T1.notT1A.from140625and140115.rmdup.s20.w150sw.bw                                                                                !Sample_description = 6-8 months after tumor intiation, metastasis was dissected from liver and FACS sorted for high purity. ATAC-seq was performed on purified cells.


title: T3-B [ATAC-seq]

description: processed data file: peak_calls_mm9.nheader.up.bed, primary_tissue.deseq_results.csv, T3.from140625and140115.rmdup.s20.w150sw.bw                                                                                !Sample_description = 6-8 months after tumor intiation, metastasis was dissected from liver and FACS sorted for high purity. ATAC-seq was performed on purified cells.


title: T3-A [ATAC-seq]


title: T2-A [ATAC-seq]

description: processed data file: peak_calls_mm9.nheader.up.bed, primary_tissue.deseq_results.csv, T2.from140625and140115.rmdup.s20.w150sw.bw                                                                                !Sample_description = 6-8 months after tumor intiation, metastasis was dissected from liver and FACS sorted for high purity. ATAC-seq was performed on purified cells.


title: L4-B [ATAC-seq]

description: processed data file: peak_calls_mm9.nheader.up.bed, primary_tissue.deseq_results.csv, L4.from140625and140115.rmdup.new.s20.w150sw.bw                                                                                !Sample_description = 6-8 months after tumor intiation, metastasis was dissected from liver and FACS sorted for high purity. ATAC-seq was performed on purified cells.

source_name: liver metastasis

value: liver


title: T2-B [ATAC-seq]


title: NCI-H524_nfib_A [ATAC-seq]


title: NCI-H524_empty_C [ATAC-seq]

description:
processed data file: peak_calls_mm9.nheader.up.bed, human_oe.deseq_results.csv
cell line containing expression vector with no gene. under induction for 2 weeks before ATAC-seq

value: empty vector control


title: T4-A [ATAC-seq]


title: L3-A [ATAC-seq]

description: processed data file: peak_calls_mm9.nheader.up.bed, primary_tissue.deseq_results.csv, L3.from140625and140115.rmdup.s20.w150sw.bw                                                                                !Sample_description = 6-8 months after tumor intiation, metastasis was dissected from liver and FACS sorted for high purity. ATAC-seq was performed on purified cells.


title: 25L-B [ATAC-seq]


title: NJH29_nfib_A [ATAC-seq]


title: L2-A [ATAC-seq]

description: processed data file: peak_calls_mm9.nheader.up.bed, primary_tissue.deseq_results.csv, L2.from140625and140115.rmdup.s20.w150sw.bw                                                                                !Sample_description = 6-8 months after tumor intiation, metastasis was dissected from liver and FACS sorted for high purity. ATAC-seq was performed on purified cells.


title: NCI-H524_empty_A [ATAC-seq]


title: L2-B [ATAC-seq]


title: NJH29_empty_A [ATAC-seq]


title: L1-B [ATAC-seq]

description:
processed data file: peak_calls_mm9.nheader.up.bed, primary_tissue.deseq_results.csv, L1.from140625and140115.rmdup.s20.w150sw.bw
6-8 months after tumor intiation, metastasis was dissected from liver and FACS sorted for high purity. ATAC-seq was performed on purified cells.


title: normal ovarian surface epithelial cells (OSE19)

city: Omaha

first: Adam

middle: R.

last: Karpf

state: Nebraska

address: 985950 Nebraska Medical Center

department: Eppley Institute for Research in Cancer

institute: University of Nebraska Medical Center

description: Epithelial layer by mechanical scraping of resected ovaries

data_processing:
Used Cutadapt (version 1.4) in conjuction with Trim Galore (version 0.4) to remove linker sequences from fastq files.
Aligned sequence tags to the human genome (hg19) using Bismark Bisulfite Mapper software (version 0.12.1).
Resulting CpG context file was reduced to only those CpGs that had at least a total of 10 sequences (methylated and/or unmethylated) that was used to represent a final determination of percent methylation. Final CpGs analyzed were only those that were present across all samples (n = 7).
Genome_build: Human hg19 (GRCh37)
Supplementary_files_format_and_content: Processed tab delimited text files contain the following columns and headers. Column 1: chromosome (chr), Column 2: chromosome base location (location). Column 3: CpG percent methylation (percent_meth). Column 4: Number of sequences that were determined to be methylated at that CpG (num_meth_CpG). Column 5: Number of sequences that were determined to be unmethylated at that CpG (num_unmeth_CpG).

source_name: Fresh-frozen normal ovarian surface epithelial cells

extract_protocol:
Isolated genomic DNA using the Puregene Tissue Kit (Qiagen), which includes RNAse treatment
Samples FTE19, OSE19, EOC59 and EOC83 performed Agilent SureSelect Methyl-Seq procedures according to manufacturers recommendation. For FTE11, OSE11, and EOC12 used Zymo Pico Methyl-Seq Library Prep Kit starting with 1000ng of DNA incorporating the Agilent SureSelect human baits to capture the reduced genome representation.

tag: gender

value: Female

tag: patient age


title: Sample siRNA against the MYC gene [2M]

city: Rio de Janeiro

first: Daniel

last: Carvalho

state: Rio de Janeiro

address: Caixa Postal 26820

country: Brazil

institute: GenOne Biotetechnologies

data_processing:
TMAP to map clean reads to gene reference and/or genome reference
Genes expression level are quantified by a software package: Sailfish.
Analysis of DEG between two samples based on the method of the poisson distribution
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample obtained by Sailfish tools and DEG screening results based on poisson distribution.

source_name: Diffuse-type GC

growth_protocol: Three GC cell lines previously established and characterized by our group were used: AGP01 (obtained from ascitic fluid of an intestinal-type GC), ACP02 (diffuse-type GC) and ACP03 (intestinal-type GC). Cell lines were cultured in DMEM medium (Gibco/Invitrogen, Germany) supplemented with 10% fetal bovine serum (Gibco/Invitrogen, Germany), 100 U/ml penicilin, 100 µg/ml streptomycin and 0.25 µg/ml amphotericin B. All cultures were maintained in a 5% CO2 air-humidified atmosphere at 37 °C.

extract_protocol:
Total mRNA was isolated from gastric cancer cell lines 48h after RNAi transfection using the AllPrep DNA/RNA/Protein Kit (Qiagen, Germany) according to the manufacturer's instructions. Then, mRNA was reverse-transcribed using the High-Capacity cDNA Archive kit according to the manufacturer’s protocol (Life Technologies, USA). The mRNA and cDNA concentration and quality was determined using a NanoDrop spectrophotometer (Kisker, Germany) and 1% agarose gels, respectively. Samples were stored at -80 °C until use.
RNA libraries were prepared for sequencing using standard Ion Torrent  protocols

treatment_protocol: An amount of 3x105 cells were seeded into 6cm² plates for each cell line before transfection. Cells were cultured for 24h until cell density was around 50%. A pool or four different double-stranded small interfering RNAs (siRNA) targeting MYC (20 µM, SMARTpool ON-TARGETplus MYC siRNA L-003282-02-0020, Dharmacon, EUA) or scrambled control siRNAs (ON-TARGETplus Non-targeting Pool D-001810-10-05, Dharmacon, GE Lifesciences, EUA) were transfected into AGP01, ACP02 and ACP03 cell lines using Lipofectamine RNAiMAX Transfection Reagent (Life Technologies, EUA). Optimal transfection was reached after 48 h, and total RNA and proteins were extracted with TRIzol reagent. All siRNA experiments were performed three times. In our results, AGP01 scrambled control cells was named 1C, while AGP01 MYC-silenced was called 1M; ACP02 control cells was named 2C, and its MYC-silenced counterpart was represented by 2M; similarly, ACP03 non-targeting control cells was called 3C and the MYC-silenced cells were named 3M.

tag: sirna

value: MYC gene

tag: passages

value: Stomach


title: L4-A [ATAC-seq]


title: L3-B [ATAC-seq]


title: Sample siRNA against the MYC gene [3M]

source_name: Intestinal-type GC


title: Samples treated with control siRNA [3C]

value: control siRNA


title: high grade serous ovarian cancer (EOC83)

description: Female high grade serous ovarian cancer, primary tumor

source_name: Fresh-frozen high grade serous ovarian cancer sample from patient undergoing surgical resection at Roswell Park Cancer Institute

tag: tumor histology

value: Predominantly serous, with focal components of mucinous, clear cell, and endometriod

tag: Stage

value: IIIC

tag: grade


title: fallopian tube epithelial cells (FTE11)

description: Epithelial layer by mechanical scraping of resected fimbriae fallopian tubes

source_name: Fresh-frozen normal fallopian tube epithelial cells


title: Sample siRNA against the MYC gene [1M]

source_name: Ascitic fluid of an intestinal-type GC

tag: cell line


title: Samples treated with control siRNA [1C]


title: yAS418_wt_RNASeq_sorbitol

status: Public on May 09 2016

city: New York

first: Jef

last: Boeke

state: NY

address: 430 East 29th Street

department: Institute of Systems Genetics

institute: NYU Langone Medical Center

description: wild-type +sorbitol

data_processing:
reads were mapped to the reference genome using bowtie2
tag density files were generated by CisGenome
Genome_build: sacCer2, barcodes
Supplementary_files_format_and_content: txt, containing raw counts of gene barcodes and tag densities.

molecule: polyA RNA

organism: Saccharomyces cerevisiae

source_name: Yeast Strain

growth_protocol: The strain was inoculated to a starting OD ~0.1 and grown to mid-log phase before treatment.

extract_protocol:
~5 ODs of cells were used for RNA extraction. The cells were  spun down, flash frozen and stored at –80°C. The cells were thawed on ice, resuspended in 600µl RLT buffer with 6µl of beta-mercaptoethanol and added to 600µl beads. The cells were vortexed for 6 cycles (with 1 minute on, 1 minute off). The QIAGEN RNeasy Mini Kit purification of total RNA from yeast protocol was used to isolate the RNA.
Total RNA quality and quantity were analyzed on an Agilent Bioanalyzer 2100 using a nano chip. RNAseq libraries were prepared using the Illumina TruSeq RNA sample prep v2 kit, starting from 500ng of total RNA, following the manufacturer’s protocol with 13 PCR cycles. The amplified libraries were purified using AMPure beads, quantified by Qubit 2.0 fluorometer, and visualized on the Agilent Tapestation 2200. The libraries were pooled equimolarly, and loaded on the HiSeq 2500.

treatment_protocol: Fresh SC medium with 1M Sorbitol for 45 minutes

tag: strain

tag: genotype/variation

value: lys2delta0  ura3delta0  his3delta1  met15  bar1::pFUS1-GFP-LEU2


title: yAS418_wt_RNASeq_sorbitol_control

description: wild-type no sorbitol control

treatment_protocol: Fresh SC medium for 45 minutes


title: fallopian tube epithelial cells (FTE19)


title: NCI-H524_empty_B [ATAC-seq]

tag: tissue/cell type

value: tumor-derived cell line


title: high grade serous ovarian cancer (EOC12)

value: serous


title: L1-A [ATAC-seq]


title: normal ovarian surface epithelial cells (OSE11)


title: yAS418_wt_RNASeq_alpha_control

description: wild-type no alphaF control


title: yAS418_wt_RNASeq_alpha

description: wild-type +alphaF

treatment_protocol: 10nM alphaF for 45 minutes


title: yAS395_sub1Δ_RNASeq_sorbitol

description: sub1Δ +sorbitol

treatment_protocol: Fresh SC medium with 1M Sorbitol

value: sub1delta::kanMX lys2delta0  ura3delta0  his3delta1  met15  bar1::pFUS1-GFP-LEU2


title: yAS395_sub1Δ_RNASeq_alpha_control

description: sub1Δ no alphaF control


title: yAS395_sub1Δ_RNASeq_alpha

description: sub1Δ +alphaF


title: yAS420_ChIPSeq_alpha_control

description: ChIP-Seq Sub1-3HA tag no alphaF control

extract_protocol:
The ChIP protocol used is described in Kuang, et al. 2014. Briefly, ~50 OD cells were fixed with 1% formaldehyde for 15 minutes at 25°C with shaking at 90 rpm, quenched with 0.125M glycine for 10 minutes at 25°C, washed with water, washed with 1X PBS, pelleted, and stored at –80°C. Briefly, the frozen pellet was resuspended in 0.45ml ChIP lysis buffer and lysed by bead beating with 12 cycles (1 minute on, 1 minute off). The sample was then sonicated for 20 cycles (30 seconds on, 30 seconds off) using a Bioruptor. For the ChIP of Sub1-3HA, the sample was incubated with 5µl of 0.4mg/ml anti-HA 12CA5 (Roche) overnight with rotation.
The KAPA Hyper Prep Kit for Illumina platforms was used for constructing the sequencing library, following the manufacturer’s protocol with 17 cycles for the amplification of the library. The samples for ChIP-Seq were pooled in equimolar amounts and sent for sequencing on the HiSeq 2500.

value: SUB1-3HAtag::kanMX    leu2delta0 lys2delta0  ura3delta0  his3delta1  met15  bar1::pFUS1-GFP-LEU2


title: yAS420_ChIPSeq_sorbitol_control

description: ChIP-Seq Sub1-3HA tag no sorbitol control

treatment_protocol: Fresh SC medium with 1M Sorbitol for 5 minutes


title: yAS420_ChIPSeq_1M_sorbitol

description: ChIP-Seq Sub1-3HA tag +Sorbitol

treatment_protocol: Fresh SC medium for 5 minutes


title: yAS420_ChIPSeq_alpha

description: ChIP-Seq Sub1-3HA tag +alphaF

treatment_protocol: 10nM alphaF for 30 minutes


title: high grade serous ovarian cancer (EOC59)


title: Samples treated with control siRNA [2C]


title: Uninduced_Gfp+_dntag_replicate_3

description: Cells sorted based on fluorescence

data_processing:
Library strategy: Bar-Seq
reads were mapped to the reference genome using bowtie2
tag density files were generated by CisGenome
Genome_build: sacCer2, barcodes
Supplementary_files_format_and_content: txt, containing raw counts of gene barcodes and tag densities.

source_name: YKO Library

growth_protocol: The YKO library was inoculated to a starting OD ~0.1 and grown to mid-log phase before treatment.

extract_protocol:
The sorted cells were grown to saturation in 15ml SC–Leu, spun down, and stored as glycerol stocks at –80°C. ~25 ODs of cells were used for gDNA extraction. The cells were first thawed at room temperature and resuspended in 250µl of reconstitution buffer (1ml of resuspension solution concentrate, 0.18g sorbitol and 1µl beta-mercaptoethanol). 1000 Units of reconstituted lyticase enzyme were added to each tube, and each tube was mixed by inversion a few times. The tubes were incubated at room temperature for 1 hour with gentle mixing by inversion every 15 minutes. To isolate the gDNA, the Norgen Biotek Yeast Genomic DNA Isolation Kit (Product #18600) was used.
The UPTAG and DNTAGS were amplified with primers (sequences available in supplemental methods). Each PCR reaction was performed in a final volume of 100ul, containing 1 Unit of Phusion polymerase, HF phusion buffer diluted to 1X, 250 µM dNTP, 250 nM of each primer and ~100ng genomic DNA. The PCR amplification protocol used was: 30 sec at 98°C; 25 cycles of 10 sec at 98°C, 30 sec at 55°C, 30 sec at 72°C; 7 min at 72°C; ∞ at 4°C.. The PCR reactions were run on a 2% agarose gel, gel extracted using the ZymocleanTM Gel DNA Recovery Kit, pooled in equimolar amounts and sent for single-end, 50-cycle sequencing on an Illumina HiSeq 2500.

value: MATa YKO Library Pool

tag: fluorescence

value: Uninduced Gfp+

tag: barcode (up or dn tag)

value: DNTAG

tag: genotype

value: MATa His+ pool (described in Ooi et al. 2001) transformed with pFUS1-GFP-LEU2 reporter. This haploid pool is 99+% His- but contains a small number of haploids that are His+. Most of the members are BY 4741 derivatives but there are a few 4740 derivatives.


title: Induced_Gfp++_single_experiment_dntag

description: Cells sorted based on fluorescence

treatment_protocol: 10nM alphaF for 2 hours

value: Induced Gfp++


title: Uninduced_Gfp+_dntag_replicate_2

description: Cells sorted based on fluorescence


title: yAS38_ChIPSeq_untagged_veg_control

description: ChIP-Seq No 3HA-tag control

value: leu2delta0 met15delta0 ura3delta0 his3delta1 bar1::pFus1-GFP-LEU2


title: Induced_Gfpbasal_dntag_replicate_3

description: Cells sorted based on fluorescence

value: Induced Gfpbasal


title: Induced_Gfpbasal_dntag_replicate_2

description: Cells sorted based on fluorescence


title: yAS395_sub1Δ_RNASeq_sorbitol_control

description: sub1Δ no sorbitol control

treatment_protocol: Fresh SC medium


title: Induced_Gfp–_dntag_replicate_3

description: Cells sorted based on fluorescence

value: Induced Gfp–


title: Uninduced_Gfp–_dntag_replicate_3

description: Cells sorted based on fluorescence

value: Uninduced Gfp–


title: Induced_presort control_dntag_replicate_2

description: Unsorted control

value: Induced Presort Control


title: Uninduced_Gfp+_uptag_replicate_2

description: Cells sorted based on fluorescence

value: UPTAG


title: Induced_presort control_dntag_replicate_3

description: Unsorted control


title: Uninduced_Gfp+_uptag_replicate_3

description: Cells sorted based on fluorescence


title: Induced_Gfp++_single_experiment_uptag

description: Cells sorted based on fluorescence


title: Uninduced_presort control_dntag_replicate_2

description: Unsorted control

value: Uninduced Presort Control


title: Induced_Gfpbasal_uptag_replicate_3

description: Cells sorted based on fluorescence


title: Induced_Gfp–_uptag_replicate_3

description: Cells sorted based on fluorescence


title: Induced_presort control_uptag_replicate_2

description: Unsorted control


title: Induced_Gfpbasal_uptag_replicate_2

description: Cells sorted based on fluorescence


title: Induced_presort control_uptag_replicate_3

description: Unsorted control


title: Uninduced_Gfp–_uptag_replicate_3

description: Cells sorted based on fluorescence


title: Induced_Gfp–_uptag_replicate_2

description: Cells sorted based on fluorescence


title: Uninduced_Gfp–_uptag_replicate_2

description: Cells sorted based on fluorescence


title: Uninduced_presort control_uptag_replicate_3

description: Unsorted control


title: Uninduced_presort control_uptag_replicate_2

description: Unsorted control


title: Induced_Gfp–_dntag_replicate_2

description: Cells sorted based on fluorescence


title: GDM 5hmC Profiling (hMe-Seal)

city: Atlanta

first: Peng

last: Jin

state: Georgia

address: 615 Michael St., Rm 325

department: Human Genetics

institute: Emory University

data_processing:
Library strategy: 5hmC-seq
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie version 0.12.9 with the standard parameters.
Peaks were called using MACS version 1.4.2 with the following setting: BW (200), GSIZE (hs).
Genome_build: hg19
Supplementary_files_format_and_content: 5hmc peaks in bed file

source_name: umbilical vessels

extract_protocol:
DNA was extracted by phenol/choloroform method.
5hmC enrichment was performed using a previously described procedure with an improved selective chemical labeling method (Song et al, Nature Biotechnology, 2011). DNA libraries were generated following the Illumina protocol for “Preparing Samples for ChIP Sequencing of DNA” (Part# 111257047 Rev. A) using 25-50 ng of input genomic DNA or 5hmC-captured DNA to initiate the protocol. [Song, C.X., Szulwach, K.E., Fu, Y., Dai, Q., Yi, C., Li, X., Li, Y., Chen, C.H., Zhang, W., Jian, X., Wang, J., Zhang, L., Looney, T.J., Zhang, B., Godley, L.A., Hicks, L.M., Lahn, B.T., Jin, P., and He, C. (2011) Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nature Biotechnology, 29(1): 68-72.]

tag: clinical condition

value: gestational diabetes


title: Preeclampsia 5hmC Profiling (hMe-Seal)

value: preeclampsia


title: Control 5hmC Profiling (hMe-Seal)

value: control


title: Control_small RNA-Seq #1

city: Strasbourg

first: Mirjam

middle: B.

last: Zeisel

address: 3, rue Koeberlé

country: France

institute: Inserm

data_processing:
Base calling : Image analysis and base calling were performed using RTA 1.17.20 and CASAVA 1.8.2
sequencing reads were preprocessed using FASTX_Toolkit (http://hannonlab.cshl.edu/fastx_toolkit). Reads of 15 to 40 nt in length were then mapped to the human genome (assembly version hg19 – UCSC repository) using Bowtie v0.12.8, (Langmead et al. Genome Biol 2009). Small RNAs were annotated and quantified using ncPRO-seq software version 1.5.1 (Chen et al. Bioinformatics 2012), which uses the miRBase release 20 . MiRNA measures were normalized  using the DESeq2 software (Love et al. bioRxiv 2014). Only miRNAs present in at least one of the libraries with a minimum of 10 read were kept for further analysis of differential miRNA expression, which was performed using the DESeq2 as well.
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes raw and normalized expression values for each sample

source_name: Huh7.5.1 cells, uninfected

growth_protocol: For proliferation arrest and differentiation, 2.5 x 104  Huh7.5.1 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) containing 1% dimethyl sulfoxide (DMSO) as described (Sainz and Chisari J Virol 2006; Bauhofer et al Gastroenterology 2012; Xiao et al Gut 2015).

extract_protocol:
For total RNA purification, Huh7.5.1 cells were lysed using TRI-reagent (MRC) and RNA purified in combination with the Direct-zol RNA MiniPrep (Zymo Research).
small RNA libraries were prepared using Illumina’s protocol (Truseq small RNA, # 15004197 Rev. F). 1.2ug of total RNA was used to construct small RNA libraries.

treatment_protocol: Fifty-percent confluent Huh7.5.1 cultures were infected with HCVcc Jc1E2FLAG for 7 days. FLAG peptide (100 μg/mL) was used for control experiments.


title: Control_small RNA-Seq #2


title: HCV-infection_small RNA-Seq #3

source_name: Huh7.5.1 cells, infected with HCV strainJc1


title: Control_small RNA-Seq #3


title: Uninduced_Gfp–_dntag_replicate_2

description: Cells sorted based on fluorescence


title: Uninduced_presort control_dntag_replicate_3

description: Unsorted control


title: HCV-infection_small RNA-Seq #2


title: HCV-infection_small RNA-Seq #1


title: H3K27me3 ChIP Seq_anti-Luc shA2B1 #2

city: Aurora

first: Aaron

middle: M

last: Johnson

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

data_processing:
Basecalls performed with casava software
Alignment performed with Bowtie2 using the --local default settings
SICER analysis performed, filtering for a maximum of 5 identifical reads at a given location, window size of 200, gap size of 1000,  E-value of 500, fragment size of 300, effective genome of 0.74
Differential analysis performed using SICER using a FDR of 0.01.
Pileups generated to display  signal per million reads at each basepair position (data filtered to 5 identical reads at a given location, with 300 bp fragment)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain signal per million reads, filtered for a maximum of 5 identical reads at a given location, and reads extended to 300 bp. Wig files contain the ouput of SICER for each sample (replicates merged for analysis). These files provide the reads that fall within H3K27me3 islands identified by the SICER analysis described above, using a window size of 200 bp and gap size of 1000 bp.

source_name: MDA-MB-231 breast cancer cells

growth_protocol: MDA-MB-231 cells were cultured in RPMI medium with 10% fetal bovine serum and penicillin-streptomycin, in addition to blastidicin and puromycin to maintain selection.

extract_protocol:
Nuclear lysates were prepared from crosslinked cells. Mnase digestion followed by sonication was used to shear chromatin. ChIP was performed with H3K27me3 antibody, and DNA was decrosslinked and proteinase K treated, followed by column purification.
DNA from IP samples was treated with the Epicentre End-Repair Kit. A-base addition was performed with NEB Klenow exo-, and the Illumina TruSeq universal adapter was added by overnight ligation with T4 DNA ligase (NEB). Reaction cleanup and size selection was performed using AMPure XP SPRI beads (Beckman Coulter Genomics). PCR to add indexed primers was performed with 18 cycles using Phusion polymerase. DNA was quantified by Qubit (Invitrogen), and pooled for sequencing with HiSEQ 2000 HT Mode V4 Chemistry (single 50 bp reads).

tag: passage number

value: antisense Luciferase control lncRNA

value: A2/B1 knockdown

tag: antibody

value: Milipore 07-449


title: H3K27me3 ChIP Seq_anti-Luc #2


title: H3K27me3 ChIP Seq_HOTAIR #2

value: HOTAIR lncRNA

value: A2/B1 wild-type


title: H3K27me3 ChIP Seq_anti-Luc #1


title: H3K27me3 ChIP Seq_HOTAIR shA2B1 #1


title: H3K27me3 ChIP Seq_HOTAIR shA2B1 #2


title: H3K27me3 ChIP Seq_anti-Luc shA2B1 #1


title: H3_2ac#5_Ctrl

city: Copenhagen N

first: Marianne

middle: Terndrup

last: Pedersen

address: Ole Maaloes Vej 5

department: University of Copenhagen

country: Denmark

institute: BRIC

data_processing:
Basecalls performed using CASAVA version 1.8.2 for all samples, except K9...clean.fq.gz and K36...clean.fq.gz samples basecalled with BGI in-house tool.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.7 with the following configurations: bowtie -S -m 1 -p 5. For H3K9 and H3K36 samples the following argument was included: -–solexa1.3-qual
bed files are standard BED6 format.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Bed files

source_name: ESCs, Jmjd2ac, Control, H3 ChIP

growth_protocol: Embryonic stem cell (ESC) lines of the specified genotypes were derived from C57Bl/6 mice and cultured on gelatin-coated plates in the presence of leukemia inhibitory factor (LIF) in serum-free N2B27 supplemented with MEK and GSK3 inhibitors (2i medium).

extract_protocol:
Chromatin immunoprecipitation (ChIP) with antibodies specific for Jmjd2a, H3K9me3, H3K36me3, H3K4me3 or H3.
Adaptor-ligated libraries were generated from precipitated DNA using the NEBNext® Ultra DNA library kit for Illumina (New England Biolabs E7370L), subjected to gel-selection and PCR-amplified (15x PCR cycles) using indexed multiplex primers for Illumina sequencing (New England Biolabs E7335), and sequenced on a HiSeq 2000 using 50bp single-end sequencing.

treatment_protocol: ESCs were grown in the absence or presence of 500 nM OHT for up to 12 days to ensure full recombination and cultured for another 6 days before harvesting.

tag: cell type

value: Embryonic stem cell (ESC) line

tag: strain/background

tag: treatment

value: Control

tag: chip antibody

value: anti-H3 (Abcam ab1791)


title: H3_2ac#5_OHT

description:
#5
+OHT

source_name: ESCs, Jmjd2ac, OHT, H3 ChIP

value: OHT


title: H3_2abc#9_Ctrl

source_name: ESCs, Jmjd2abc, Control, H3 ChIP


title: H3K4me3_2abc#9_Ctrl

source_name: ESCs, Jmjd2abc, Control, H3K4me3 ChIP

value: anti-H3K4me3 (C42D8) (Cell Signaling #9751)


title: H3K27me3 ChIP Seq_HOTAIR #1


title: H3_2abc#9_OHT

description:
#9
+OHT

source_name: ESCs, Jmjd2abc, OHT, H3 ChIP


title: H3K36me3_2abc#9_OHT

description:
#9
+OHT

source_name: ESCs, Jmjd2abc, OHT, H3K36me3 ChIP

value: anti-H3K36me3 (D5A7) (Cell Signaling #4909 Lot 1)


title: H3K36me3_2abc#9_Ctrl

source_name: ESCs, Jmjd2abc, Control, H3K36me3 ChIP


title: H3K36me3_2ac#5_Ctrl

source_name: ESCs, Jmjd2ac, Control, H3K36me3 ChIP


title: H3K36me3_2abc#13_Ctrl


title: H3K36me3_2ac#4_OHT

description:
#4
+OHT

source_name: ESCs, Jmjd2ac, OHT, H3K36me3 ChIP


title: H3K36me3_2ac#5_OHT

description:
#5
+OHT


title: H3K4me3_2ac#5_OHT

description:
#5
+OHT

source_name: ESCs, Jmjd2ac, OHT, H3K4me3 ChIP


title: H3K9me3_2abc#9_OHT

description:
#9
+OHT

source_name: ESCs, Jmjd2abc, OHT, H3K9me3 ChIP

value: anti-H3K9me3 (Abcam ab8898 Lot GR102573)


title: H3K9me3_2abc#9_Ctrl

source_name: ESCs, Jmjd2abc, Control, H3K9me3 ChIP


title: H3K9me3_2ac#5_OHT

description:
#5
+OHT

source_name: ESCs, Jmjd2ac, OHT, H3K9me3 ChIP


title: H3K9me3_2ac#5_Ctrl

source_name: ESCs, Jmjd2ac, Control, H3K9me3 ChIP


title: H3K36me3_2abc#13_OHT

description:
#13
+OHT


title: H3K9me3_2abc#13_OHT

description:
#13
+OHT


title: H3K4me3_2abc#9_OHT

description:
#9
+OHT

source_name: ESCs, Jmjd2abc, OHT, H3K4me3 ChIP


title: MCDP02_bclb

city: Seattle

first: David

last: Baker

state: WA

address: Molecular Engineering and Sciences, Box 351655

institute: University of Washington

description: For additional information on experimental protocol, please see Chao et al. Nat Protoc. 2006.

data_processing:
Read alignment (scripts developed in-house)
Counts determined for wild-type sequence and all single mutants (scripts developed in-house)
Enrichment ratios calculated based on counts in naïve library and sorted population
2CDP06 (reference amino acid sequence): ADPKKVLDKAKDEAENRVRELKQKLEELYKEARKLDLTQEMRQELVDKARAASLQASGDIFYAILRALAEAEKLKKAGLVNSQQLDELKRRLEELAEEARRKAEKLGDEFRLKLEY
XCDP07 (reference amino acid sequence): ADPKKVLDKAKDRAENVVRKLKKELEELYKEARKLDLTQEMRDRIRLAAIAARIAAFGDIFHAIMEALEEARKLKKAGLVNSQQLDELKRRLEELDEEAAQRAEKLGKEFELKLEY
WCDP03 (reference amino acid sequence): DPKKVFDEAKDRAENNVRRLKQKLEELYKEARKKDLTQEEREKLKEKYKTAMAAAALAAIGDAFNALLKARKLHKNGQVNEQQLEELARRLQELAKEAFQKAKDYANEFEYKLEY
FCDP01 (reference amino acid sequence): ADPKKVLDKAKDQAENRVRELKQKLEELYKEARKLDLTQEMRKKLQYAAIGAMLAAIGDILNAIMQAKQEADKLKKAGLVNSQQLDELKRRLEELKEEALRKAHDYGSEFYLKLEY
BCDP01 (reference amino acid sequence): ADPKKVLDKAKDQAENRVRELKQELERLYKEARKLDLTQEMRRKLEWRYIAAMLKAIGDILNAIAQAENEADKLKKAGLVNSQQLDELRRRLEELAKEAARKAHDYGREFQLKLEY
MCDP02 (reference amino acid sequence): ADPKKVLDKAKDQAENRVRELKQELEELYKEARKLDLTQEERRKLEESYIAAMLRAIGDIFNAIMQAKNEADKLKKAGLVNSQQLDELRRRLEELRKEASLKAEDYGREFQEKLEY
Supplementary_files_format_and_content: In Excel format, the processed data file contains enrichment ratios calculated at each position for all sorted populations (naïve library counts incorporated as reference value)

source_name: transformed yeast

growth_protocol: Please see our corresponding publication for the yeast protocols for growth and induction of protein expression.

extract_protocol:
Yeast were lysed with 125 U/ml Zymolase at 37 ºC for 5 h, and DNA was harvested (Zymoprep kit from Zymo Research). Genomic DNA was digested with 2 U/µl Exonuclease I and 0.25 U/µl Lambda exonuclease (New England Biolabs) for 90 min at 30 ºC, and plasmid DNA purified with a QIAquick kit (Qiagen).
Gene sequences were diversified by overlapping PCR for site-directed mutagenesis libaries as described in Procko et al. J Mol Bio 2013.

treatment_protocol: Please see our corresponding publication for concentrations of labeled target protein and unlabeled competitors during incubation prior to FACS selection

tag: strain (mating type)

tag: selection markers

value: -Trp, -Leu

tag: construct

tag: facs-sorted population

value: bclb


title: H3K9me3_2abc#13_Ctrl


title: MCDP02_bfl1


title: H3K9me3_2ac#4_Ctrl


title: H3K9me3_2ac#4_OHT

description:
#4
+OHT


title: H3K4me3_2ac#5_Ctrl

source_name: ESCs, Jmjd2ac, Control, H3K4me3 ChIP


title: MCDP02_mcl1


title: MCDP02_bclw

value: bclw


title: Jmjd2a_2a_Ctrl

source_name: ESCs, Jmjd2a, Control, Jmjd2a ChIP

value: anti-Jmjd2a (Cell Signaling Technology, #5328)


title: Jmjd2a_2a_OHT

description: Negative control

source_name: ESCs, Jmjd2a, OHT, Jmjd2a ChIP


title: MCDP02_naive

value: naive


title: D8 NTP1

city: Singapore

first: Chadi

last: El Farran

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
The QC of the generated libraries was performed using FastQC. Reads were mapped to hg19 genome using STAR aligner software. Reads with more than 3 mismatches were filtered out. Reads mapped to more than one region in the human genome were also disregarded. The mapped reads have then undergone Differential Splicing Analysis using MATS.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files that include the exon skipping events detected by MATS.

source_name: BJ Fibroblasts

growth_protocol: BJ fibroblast were cultured in 10% Fetal Bovine Serum (Gibco) for expansion and medium was changed every two days. Human Embryonic Stem Cells (hESCs) and induced Pluripotent Stem Cells (iPSCs) clones were maintained on irradiated murine embryonic fibroblast (MEFs, Global Stem) and cultured in 20% knockout serum replacement (KSR, Life Technologies), 200mM GlutaMAX (Life Technologies), 1 x minimal essential media (MEM) non-essential amino acids solution (Life Technologies), 8 microgram mL-1 bFGF (Life Technologies), 55 micromplar Beta-mercaptoethanol in DMEM/F12 (Life Technogies). ES and iPSCs clones was passagerd every 4-5 days using L7TM hPSC Passaging Solution (Lonza).

extract_protocol:
Total RNA was extracted using the Trizol reagent (Invitrogen, 15596-026). Contaminating DNA was removed by DnaseI (Ambion) treatment, and the RNA was further purified using RNeasy column (Qiagen, 74140)
The RNA samples were subject to mRNA selection, fragmentation, cDNA synthesis, and library preparation using a TruSeq RNA Sample Prep Kit (Illumina, RS-122-2001).

treatment_protocol: BJ Fibroblasts 8 days post induced OSKM viral Expression and treated with non-targeting siRNA.

value: WT

tag: cell line

value: BJ


title: H3K36me3_2ac#4_Ctrl

tag: genotype/variation


title: BCDP01_sort2


title: MCDP02_bcl2


title: BCDP01_sort1


title: BCDP01_naive


title: 8D replicate 1

city: Athens

first: Aristidis

last: Charonis

state: Attiki

address: Soranou Efesiou 4

country: Greece

institute: Biomedical Research Foundation of the Academy of Athens

data_processing:
Base calling was performed using software provided with the sequencer.
The FASTQ files containing pair-end sequence reads were mapped to the UCSC mm10 reference genome using tophat2, with the standard parameters for reads obtained from mammalian sequencing with Illumina platforms, proposed by the authors. The --mateinner-dist and --mate-std-dev tophat2 parameters, which are crucial for paired-end reads were estimated for each sample as follows: firstly, the FASTQ files were aligned to the mm10 transcriptome using bowtie2. Then, sequence metrics were collected for the first 10 million properly mapped paired-end reads using Picard Tools. Finally, from the resulting metrics that included average cDNA fragment size and its standard deviation, the aforementioned parameters were estimated by subtracting two times the short read length from the average fragment size, and using the standard deviation as-is respectively.
Differential gene expression analysis was performed with the Bioconductor package metaseqR. Briefly, sequence reads were counted over mm10 exons and after filtering, the final read counts for each gene were calculated as the sums of their exon reads, creating a gene counts table where each row corresponded to an Ensembl gene model and each column corresponded to an RNA-seq sample. The gene counts table was normalized using DESeq after removing genes that had zero counts over all the RNA-seq samples. Prior to the statistical testing procedure, the gene read counts were filtered for possible artifacts that could affect the subsequent statistical testing procedures. Genes presenting any of the following were excluded from further analysis: i) genes with length less than 500, ii) genes whose average reads per 100 bp was less than the 25th quantile of the total normalized distribution of average reads per 100bp, iii) genes with read counts below the median read counts of the total normalized count distribution. The resulting gene counts table was subjected to differential expression analysis for the contrasts SO versus 2D, SO versus 8D and 2D versus 8D, using DESeq.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited files containing DESeq normalized counts for each Ensembl gene.  The file SO_2D_8D_norm_counts.txt.gz, which is available on the series record, contains normalized count data for all samples and includes chromosome. start and stop positions, Ensembl Gene ID and gene name.

growth_protocol: Mice were maintained in grouped cages in a temperature-controlled, pathogen-free facility on a 12-hr light/dark cycle and fed by a standard chow diet (Altromin 1324; 19% protein, 5% fat) and water ad libitum

extract_protocol:
RNA samples were isolated from kidney tissues from all three animal groups using TRI reagent (Life Technologies, Carlsbad, CA). Sample integrity, quality and purity were determined accordingly.
Polyadenylated transcriptome libraries were constructed by EMBL GeneCore (EMBL Genomics Core Facility, Heidelberg, Germany).

treatment_protocol: Mice underwent ligation of the right ureter and were divided into three groups during the surgery: sham operated, 2 days ligated and 8 days ligated. Before surgery the mice were anesthetized via face mask delivering sevoflurane. The right ureter was exposed through a midline abdominal incision and was either completely obstructed 1 cm below the renal pelvis with 5.0 silk ligature (ligated animals) or manipulated similarly but not ligated (sham operated animals).

tag: strain

tag: age

value: 8 to 12-week-old

tag: gender

value: male

tag: tissue

value: kidney


title: 8D replicate 2

tag: genotype


title: 2D replicate 2


title: FCDP01_sort2


title: 2D replicate 3


title: FCDP01_sort1


title: SO replicate 4


title: FCDP01_naive


title: SO replicate 3


title: 2D replicate 1


title: MCDP02_bclxl

value: bclxl


title: 8D replicate 3


title: WCDP03_sort2


title: WCDP03_naive


title: WCDP03_sort1


title: SO replicate 2


title: SO replicate 1


title: XCDP07_sort2


title: ATACSeq KO rep4

city: Bethesda

last: Li

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description: Rre-stimulated 2h with anti-CD3

data_processing:
Library strategy: ATAC-seq
For ChIP-Seq and RNA-Seq, Basecalls performed using CASAVA 1.8
Raw reads were aligned to the mm9 genome assembly using Bowtie 0.12.9 or Tophat 2.0.11
Aligned reads are converted to BAM format using igvtools
For ChIP-Seq, peaks are called using MACS 1.4.2 and visualized using IGV browser. For RNA-Seq, raw counts are calculated using cuffdiff
Genome_build: mm9

source_name: Pre-activated CD8+ T cells

growth_protocol: Cells of indicated phenotype were FACS-sorted from spleens and lymph nodes of WT or Bach2-deficient mice, or from mice reconstituted with WT and Bach2-deficient BM cells. Alternatively, where indicated, cells were harvested at day 5 following stimulation of naïve FACS-sorted cells with plate-bound anti-CD3 and anti-CD28 antibodies in the presence of 100IU IL-2.

extract_protocol:
T cells were chemically crosslinked and sonicated cells to generate fragmented genomic DNA. DNA fragments purified from agarose gels and used for cluster generation and sequencing. Chromatin immunoprecipitation was performed using the following antibodies: BACH2, JunD, p300, H3K4me1, H3K27ac
PCR products were barcoded (indexed) and sequenced on Illumina HiSeq 2000 platform or Genome Analyzer II platform.

treatment_protocol: Where relevant, cells were briefly stimulated ex vivo with plate-bound anti-CD3 and anti-CD28 antibodies for indicated times and harvested for RNA-Seq analysis.

value: Spleen

value: pre-stimulated 2h with anti-CD3


title: XCDP07_sort1


title: 2CDP06_sort1


title: ATACSeq KO rep1

description: Rre-stimulated 2h with anti-CD3


title: ATACSeq KO rep3

description: Rre-stimulated 2h with anti-CD3


title: ATACSeq WT rep4

description: Rre-stimulated 2h with anti-CD3

value: wild type


title: ATACSeq WT rep3

description: Rre-stimulated 2h with anti-CD3


title: ATACSeq KO rep2

description: Rre-stimulated 2h with anti-CD3


title: 2CDP06_naive


title: 2CDP06_sort2


title: ATACSeq WT rep2

description: Rre-stimulated 2h with anti-CD3


title: ATACSeq WT rep1

description: Rre-stimulated 2h with anti-CD3


title: Induced_Gfpbasal_dntag_replicate_1

description: Cells sorted based on fluorescence

source_name: YKO Library

extract_protocol:
The sorted cells were grown to saturation in 15ml SC–Leu, spun down, and stored as glycerol stocks at –80°C. ~25 ODs of cells were used for gDNA extraction. The cells were first thawed at room temperature and resuspended in 250µl of reconstitution buffer (1ml of resuspension solution concentrate, 0.18g sorbitol and 1µl beta-mercaptoethanol). 1000 Units of reconstituted lyticase enzyme were added to each tube, and each tube was mixed by inversion a few times. The tubes were incubated at room temperature for 1 hour with gentle mixing by inversion every 15 minutes. To isolate the gDNA, the Norgen Biotek Yeast Genomic DNA Isolation Kit (Product #18600) was used.
The UPTAG and DNTAGS were amplified with primers (sequences available in supplemental methods). Each PCR reaction was performed in a final volume of 100ul, containing 1 Unit of Phusion polymerase, HF phusion buffer diluted to 1X, 250 µM dNTP, 250 nM of each primer and ~100ng genomic DNA. The PCR amplification protocol used was: 30 sec at 98°C; 25 cycles of 10 sec at 98°C, 30 sec at 55°C, 30 sec at 72°C; 7 min at 72°C; ∞ at 4°C.. The PCR reactions were run on a 2% agarose gel, gel extracted using the ZymocleanTM Gel DNA Recovery Kit, pooled in equimolar amounts and sent for single-end, 50-cycle sequencing on an Illumina HiSeq 2000.

value: MATa YKO Library Pool

tag: fluorescence

value: Induced Gfpbasal

tag: barcode (up or dn tag)

value: DNTAG

value: MATa His+ pool (described in Ooi et al. 2001) transformed with pFUS1-GFP-LEU2 reporter. This haploid pool is 99+% His- but contains a small number of haploids that are His+. Most of the members are BY 4741 derivatives but there are a few 4740 derivatives.


title: Uninduced_Gfp+_dntag_replicate_1

description: Cells sorted based on fluorescence

value: Uninduced Gfp+


title: ChIPSeq WT CD8 T p300

description: ChIP against p300

data_processing:
For ChIP-Seq and RNA-Seq, Basecalls performed using CASAVA 1.8
Raw reads were aligned to the mm9 genome assembly using Bowtie 0.12.9 or Tophat 2.0.11
Aligned reads are converted to BAM format using igvtools
For ChIP-Seq, peaks are called using MACS 1.4.2 and visualized using IGV browser. For RNA-Seq, raw counts are calculated using cuffdiff
Genome_build: mm9

value: p300 (sc-586, Santa Cruz)


title: ChIPSeq KO CD8 T +Stim JunD

description: ChIP against JunD

value: JunD (sc-74, Santa Cruz)


title: Uninduced_Gfp–_dntag_replicate_1

description: Cells sorted based on fluorescence

value: Uninduced Gfp–


title: Induced_presort control_dntag_replicate_1

description: Unsorted control

value: Induced Presort Control


title: ChIPSeq WT CD8 T +Stim JunD

description: ChIP against JunD


title: Induced_Gfp–_dntag_replicate_1

description: Cells sorted based on fluorescence

value: Induced Gfp–


title: Induced_Gfpbasal_uptag_replicate_1

description: Cells sorted based on fluorescence

value: UPTAG


title: RNASeq naive KO+TCR 18h rep1

source_name: naive CD8+ T cells

tag: sample type

value: TCR 18h


title: RNASeq naive KO+TCR 6h rep2

value: TCR 6h


title: RNASeq naive KO+TCR 18h rep2


title: RNASeq naive KO+TCR 6h rep1


title: Uninduced_presort control_dntag_replicate_1

description: Unsorted control

value: Uninduced Presort Control


title: Uninduced_Gfp–_uptag_replicate_1

description: Cells sorted based on fluorescence


title: XCDP07_naive

value: -Trp, -Leu

value: naive


title: Induced_Gfp–_uptag_replicate_1

description: Cells sorted based on fluorescence


title: RNASeq naive KO 0h rep2

value: Spleen

value: control


title: Uninduced_Gfp+_uptag_replicate_1

description: Cells sorted based on fluorescence

value: MATa YKO Library Pool


title: Uninduced_presort control_uptag_replicate_1

description: Unsorted control

treatment_protocol: Vegetative growth


title: Bach2-tdRFP high 3

city: Suita

first: TOMOHIRO

last: KUROSAKI

state: Osaka

address: 3-1 Yamada-oka

country: Japan

institute: Osaka University Immunology Frontier Research Center

data_processing:
Read alignment: TopHat2 v2.0.8 with default settings.
Expression level: Cufflinks v2.1.1 with default settings.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *fpkm.txt: Includes FPKM values.

source_name: IgG1 LZ GC B cells, high Bach2-tdRFP

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
DNA libraries were prepared for sequencing using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: tdRFP low and high IgG1 LZ GC B cells were FACS-sorted from 3 Bach2-tdRFP mice and pooled for each sample.

tag: strain/background

tag: tissue origination

value: spleen

tag: cell type

value: NP-specific IgG1 light zone germinal center B cells

tag: bach2-tdrfp expression

value: high


title: Bach2-tdRFP high 2


title: Bach2-tdRFP low 3

source_name: IgG1 LZ GC B cells, low Bach2-tdRFP

value: low


title: RNASeq naive WT 0h rep2

value: wild type


title: RNASeq naive WT+TCR 18h rep1


title: RNASeq naive KO 0h rep1


title: RNASeq naive WT+TCR 18h rep2


title: RNASeq naive WT+TCR 6h rep2


title: Bach2-tdRFP high 1


title: RNASeq naive WT 0h rep1


title: Bach2-tdRFP low 1


title: Bach2-tdRFP low 2


title: RNASeq d7 DN KO+TCR 6h rep2


title: RNASeq naive WT+TCR 6h rep1


title: RNASeq d7 DN KO+TCR 6h rep1


title: Induced_presort control_uptag_replicate_1

description: Unsorted control

value: MATa His+ pool (described in Ooi et al. 2001) transformed with pFUS1-GFP-LEU2 reporter. This haploid pool is 99+% His- but contains a small number of haploids that are His+. Most of the members are BY 4741 derivatives but there are a few 4740 derivatives.


title: RNASeq d7 DN KO 0h rep1


title: High affinity 2

data_processing:
Read alignment: TopHat2 v2.0.8 with default settings
expression level: Cufflinks v2.1.1 with default settings
Genome_build: mm9
Supplementary_files_format_and_content: genes.fpkm: abundance measurements

source_name: High affinity IgG1 LZ germinal center B cells

extract_protocol:
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
DNA libraries were prepared for sequencing using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB)

treatment_protocol: High and low affinity IgG1 LZ GC B cells were FACS-sorted from 10 mice and pooled for each genotype.

value: germinal center B cells


title: Low affinity 2

source_name: Low affinity IgG1 LZ germinal center B cells


title: RNASeq d7 DN WT+TCR 6h rep2


title: Low affinity 3


title: High affinity 3


title: Low affinity 1


title: RNASeq d7 DN KO 0h rep2


title: RNASeq d7 DN WT+TCR 6h rep1


title: High affinity 1


title: salt.T60 (KN13_R1)

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

description:
salt.T60
KN13_R1

data_processing:
mapping of reads was done using: bowtie2  -D 20 -R 3 -N 1 -L 20 -i S,1,0.50 --local
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
RPKM values were normalized using the TMM (Trimmed Median Mean) method
Genome_build: Bacillus subtilis subsp. subtilis str. 168 | NC_000964.3 | GI:255767013 | 31-DEC-2013
Supplementary_files_format_and_content: Tab delimited text file reports RPKMs

growth_protocol: Spores of Bacillus subtilis 168 (trpC2; DSM402) were produced in liquid cultures of modified Schaeffer’s Sporulation Medium with glucose (2x SG; as described in Nicholson and Setlow, 1990). The sporulation cultures were incubated at 37 °C for 48 hours in a shaking incubator (200 rpm). Spores were harvested, washed with distilled, sterile water at least seven times, and retrieved by centrifugation. The purity of the spore stocks, as checked by phase-contrast microscopy, was ≥ 99 %.

extract_protocol:
Cell were lysed using glassbead and totRNA was isolated using phenol/chloroform and ethanol precipitation
Standard library preparation kit for IonProton

treatment_protocol: Spores were heat activated at 70 °C for 30 min. Germination and outgrowth experiments were performed in germination media composed of Spizizen Minimal Medium (SMM; as described in Nicholson and Setlow, 1990) with or without 1.2 M NaCl, which additionally contained 50.5 mM D-glucose, 0.5 mM L-tryptophan, and 10 mM of the germination trigger L-alanine.   The experiments were performed in 45 ml germination medium. The medium was inoculated with 1.2 x 1010 heat-activated spores (in total) and 15 ml samples were withdrawn at 30 min, 60 min and 90 min after inoculation. The samples were immediately mixed with ice-cold killing buffer (Nicolas et al., 2012) and washed with ice cold water by centrifugation (1 min at 10,000 x g at 4 °C). The pellet was resuspended in 400 µl  ice-cold LETS buffer (0.1 M LiCl, 0.01 M Na2EDTA, 0.1 M Tris-HCl pH 7.4, 0.2 % SDS), transferred to a pre-cooled Lysing Matrix B tube (MP Biomedicals, Santa Ana, CA, USA) containing 500 µl phenol:chloroform (1:1) and 25 µl 10 % SDS, and used for RNA isolation. For the dormant spore RNA samples, spore suspensions were also heat-treated for consistency. Subsequently they were centrifuged, the pellets were resuspended in LETS buffer, and transferred to Lysing Matrix B tube for RNA isolation.

tag: growth condition

value: Cell culture

tag: stress

value: salt

tag: time

value: 60 min


title: salt.T90 (KN14_R1)

description:
salt.T90
KN14_R1

organism: Bacillus subtilis subsp. subtilis str. 168

value: 90 min


title: RNASeq d5 invitro KO+Stim rep2

value: Rre-stimulated 2h with anti-CD3


title: RNASeq d7 DN WT 0h rep1


title: RNASeq d5 invitro KO+Stim rep3


title: no_salt.T90 (KN11)

description:
no_salt.T90
KN11

value: no salt


title: no_salt.T60 (KN2_R2)

description:
no_salt.T60
KN2_R2


title: no_salt.T60 (KN10)

description:
no_salt.T60
KN10


title: dormant.T0 (KN8)

description:
dormant.T0
KN8

value: dormant

value: 0 min


title: no_salt.T90 (KN3_R2)

description:
no_salt.T90
KN3_R2


title: no_salt.T30 (KN1_R2)

description:
no_salt.T30
KN1_R2

value: 30 min


title: no_salt.T30 (KN9)

description:
no_salt.T30
KN9


title: RNASeq d5 invitro KO-Stim rep2

value: Spleen

value: No re-stimulation


title: RNASeq d5 invitro KO-Stim rep1


title: RNASeq d5 invitro WT+Stim rep2


title: salt.T90 (KN7)

description:
salt.T90
KN7


title: RNASeq d7 DN WT 0h rep2

value: control


title: dormant.T0 (KN4)

description:
dormant.T0
KN4


title: salt.T60 (KN6)

description:
salt.T60
KN6


title: RNASeq d5 invitro WT+Stim rep1


title: salt.T30 (KN5)

description:
salt.T30
KN5


title: salt.T30 (KN12_R1)

description:
salt.T30
KN12_R1


title: RNASeq d5 invitro WT-Stim rep2


title: RNASeq d5 invitro WT-Stim rep1


title: Mutant rep2

status: Public on May 08 2016

city: Vienna

first: Cornelia

last: Vesely

address: Schwarzspanierstrasse 17

department: Anatomy

country: Austria

institute: Medical University of Vienna

data_processing:
The paired-end fragments were trimmed on their 5′ end of the first read by two cycles, adaptors were removed using cutadapt v1.4.241 and reads with a length of less than 18 bp in any read of the pair were discarded.
The trimmed and adaptor-free reads were aligned against rDNA of c. elegans using bowtie v0.12.543.
The rRNA cleaned reads were aligned to the WS220 genome with star-align 2.3.1z4.
The uniquely aligning reads were used for counting per gene with htseq-count v0.6.1p46 with the overlap-resolution mode option set to ‘union’.
Read counts for all samples were normalized using the median-of-ratios method implemented in DESeq2, v1.2.1048 and a theshold of padj<0.05 was applied as significance threshold.
Genome_build: c. elegans WS220
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Caenorhabditis elegans

source_name: mutant_whole body

growth_protocol: 100 young adults for each replicate and each genotype were collected in M9 buffer.

extract_protocol:
Total RNA from whole worm bodies was extracted using peqGOLD TriFast (PEQLAB Biotechnologie GmbH) according to the manufacturers protocol.
Total DNAse treated RNA was cleared from ribosomal RNA using the Ribo Zero Magnetic kit (Epicentre) and subsequently chemically fragmented (by Heat and divalent metal cation), followed by first strand and second strand cDNA synthesis. The cDNA was used for library preparation with the SENSE mRNA-Seq Library Prep Kit (Lexogen) for sequencing on a Genome Analyzer IIx (Illumina). 36 bp single end Sequencing was performed at the CSF NGS Unit (csf.ac.at)

value: mutant

tag: strain info.

value: Young adult

value: Whole body


title: Mutant rep3

tag: genotype/variation


title: RNASeq d5 invitro KO+Stim rep1

tag: strain


title: RNASeq d5 invitro KO-Stim rep3


title: Mutant rep1

tag: age


title: Wild type rep1

source_name: wild type_whole body

value: wild type


title: Sham control 3

city: Melbourne

first: Jenny

last: Ooi

address: 75 Commercial Road

country: Australia

institute: Baker IDI Heart & Diabetes Institute

data_processing:
Sequencing Control Software (SCS) and Consensus Assessment of Sequence and Variation (CASAVA) software programmes from Illumina were used to convert raw image data into intensity scores, base calls, quality scored alignments and additional formats for downstream analysis.
MiRNA-Seq reads were aligned to the mouse reference genome (mm10) using Partek Flow® ; version 3.0 (Partek Inc.) with default settings unless otherwise stated. After removing adaptor sequences, the bases of unaligned reads were trimmed for a minimum Phred quality score of 20 and minimum read length=17. Next, fastq files were aligned to the mm10 reference genome with Bowtie 1 (default parameters used except seed mismatch limit=0, seed length=22, alignments reported per read=10) and Bowtie 2 (default parameters except interval between seeds S,1,1.25, ambiguous characters function L,O.15, default reporting mode=false, max alignments reported per read=10). Read counts were then filtered for reads with minimum mapping quality of 20.
The trimmed, aligned and filtered reads were quantitated to known miRNAs using miRBase mature miRNA version 21.
Reads were normalized to reads per million (RPM) and calculated as follows: (Number of sequenced reads / Total reads) X 1,000,000. MiRNA reads containing less than 5 RPM in all groups were subsequently removed.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include miRNA RPM values for samples

source_name: Ventricle

growth_protocol: FVBN male mice (12 week old) that underwent Transverse Aortic Constriciton (TAC) surgery or Sham controls

extract_protocol:
Ventricles were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent.
NGS library from total RNA were prepared (TruSeqTM Small RNA, Illumina) and samples were multiplexed (24 samples per lane) with adaptor primers and ran on 3 flow cell lanes on Illumina HiSeq2000 sequencing machine. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: FVBN male mice (12 week old) that underwent TAC/Sham surgery were injected subcutaneously a LNA-control or LNA-antimiR-34 for 6 weeks, as previously described (Bernardo PNAS 2012;109(43):17615-20).

value: FVBN

tag: Sex

value: Male

tag: surgery

value: Sham

tag: treatment

value: LNA-control


title: RNASeq d5 invitro WT+Stim rep3

tag: tissue


title: Sham control 4


title: TAC control 3

value: TAC


title: Sham LNA-antimiR 1


title: Sham control 2


title: Sham LNA-antimiR 3


title: TKO ESC [RRBS-seq]

city: Yokohama

first: Takaho

middle: A.

last: Endo

state: Kanagawa

address: 1-7-22 Suehiro, Tsurumi

department: IMS

institute: RIKEN

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
ChIP-seq sequences were aligned on mm9 using bowtie2 (version 2.1.0) with default parameters.
Accumlated reads were mapped on mouse genome and reads per kilobase is recorded in processed files.
Genome_build: mm9
Supplementary_files_format_and_content: wiggle file format of mapped reads per kilobase

source_name: ES cells

growth_protocol: Standard condition for ES cells.

extract_protocol:
Genomic DNA was isolated using QIAGEN All-prep kit
Genomic DNA was digested with MspI, and after ligation of a methylated adapter, was bisulfite converted. Muliplex libraries were prepared for Illumina sequencing.
Libraries were prepared according to NEB's instructions accompanying the NEBNext® ChIP-seq Library Prep Reagent set for Illumina.  Adapter ligated DNA was PCR amplified with Illumina primers for 15 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hi-Seq 1000 following the manufacturer's protocols.

tag: strain background

value: Dnmt Triple KO ESCs


title: DNcDKO ESC [RRBS-seq]

value: Np95 and Dnmt1 (flox/flox) conditional alleles; CreERT2 transgene

tag: time point

value: With 4-OHT (day 6)


title: TAC control 2


title: Sham control 1


title: RNASeq d5 invitro WT-Stim rep3

tag: sample type


title: TAC LNA-antimiR 4


title: Dnmt1 wt ESC [RRBS-seq]

value: Dnmt1 (flox/flox) conditional alleles; CreERT2 transgene

value: Without 4-OHT (day 0)


title: TAC LNA-antimiR 3


title: TAC LNA-antimiR 1


title: Np95 wt ESC, replicate 1 [ChIP-seq]

description: ChIP-seq with native chromatin (Brind'Amour et al., 2015)

data_processing:
Basecalls performed using Illumina offline basecaller (OLB) version 1.9.4
ChIP-seq sequences were aligned on mm9 using bowtie2 (version 2.1.0) with default parameters.
Accumlated reads were mapped on mouse genome and reads per kilobase is recorded in processed files.
Genome_build: mm9
Supplementary_files_format_and_content: Whole genome mapped read counts normalized by the total mapped reads and genome size (mapped reads per kilobase genome per million reads). Mapped reads per kilobase

extract_protocol:
Genomic DNA was isolated using QIAGEN All-prep kit
Libraries were prepared according to NEB's instructions accompanying the NEBNext® ChIP-seq Library Prep Reagent set for Illumina.  Adapter ligated DNA was PCR amplified with Illumina primers for 15 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Hi-Seq 1000 following the manufacturer's protocols.

value: embryonic stem cells (ESCs)

value: Np95 (flox/flox) conditional alleles; CreERT2 transgene

tag: treated with

tag: chip antibody

value: Anti-H3K9me3 mAb (Active Motif, 39161)

tag: molecule subtype

value: Native chromatin


title: Wild type rep2

value: Young adult


title: Np95cKO ESC, replicate 1 [ChIP-seq]

tag: cell type

value: With 4-OHT (day 4)


title: Np95cKO ESC, Input [ChIP-seq]

description: Input DNA

value: input DNA


title: TAC control 1

value: FVBN


title: TAC LNA-antimiR 2

value: Male


title: Np95cKO ESC [RRBS-seq]

value: Np95  (flox/flox) conditional alleles; CreERT2 transgene


title: Np95cKO ESC [ChIP-seq]

description: ESCs were corsslinked with 1% formaldehyde and after nuclear lysis, chromatin was sheared by sonication (30s on/off, 15 cycles) and immunoprecipitated with an anti-H3K9me3 antibody (MBL, MABI0318) using Protein A + G magnetic beads (Millipore)

value: Anti-H3K9me3 mAb (MBL, MABI0318)

value: Crosslinked chromatin


title: KO Macrophage 2HR Rep2

city: Stanford

first: Howard

last: Chang

address: 269 Campus Dr. Stanford, CA

institute: Stanford University

data_processing:
library strategy: ATAC-seq
ATAC-seq paired-end reads were trimmed for Illumina adapter sequences and transposase sequences using an in-house script and mapped to mm9 using Bowtie2 v2.1.0 with parameters –very sensitive. Duplicate reads were removed with Picard . Peak calling was performed by MACS2 narrow peak mode with parameters –q 0.01 –nomodel –shift 0.
Genome_build: mm9
Supplementary_files_format_and_content: Peak files are ENCODE narrowPeak format. 1  chrom, 2 chromStart, 3 chromEnd, 4 name, 5 score, 6 strand, 7 signalValue, 8 pvalue, 9 qvalue

source_name: LincRNA-EPS KO mouse bone marrow-derived macrophage

growth_protocol: Bone marrow cells from WT or lincRNA-EPS KO mice were grown in L929 macrophage growth supplement (20%) for 9 days.

extract_protocol:
50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit and sequenced using an Illumina NextSeq.

treatment_protocol: Cells were stimulated with 100ng/ml LPS for 0, 2, or 6 hours and subjected to ATAC-Seq

value: LincRNA-EPS KO

tag: gender

value: female

value: macrophage

value: 100ng/ml LPS for 2h


title: KO Macrophage 2HR Rep1


title: KO Macrophage 6HR Rep2

value: 100ng/ml LPS for 6h


title: KO Macrophage 0HR Rep1

value: 100ng/ml LPS for 0h


title: KO Macrophage 0HR Rep2


title: WT Macrophage 6HR Rep1

source_name: WT mouse bone marrow-derived macrophage

value: wild type


title: WT Macrophage 2HR Rep2


title: WT Macrophage 6HR Rep2


title: DN+Myc-Np95 wt ESC [ChIP-seq]

description: ESCs were corsslinked with 1% formaldehyde and after nuclear lysis, chromatin was sheared by sonication (30s on/off, 15 cycles) and immunoprecipitated with an anti-Myc tag antibody (CST, 9B11) using Protein A + G magnetic beads (Millipore)

value: embryonic stem cells (ESCs)

value: Dnmt1 and Np95 double (flox/flox) conditional alleles; exogenous Myc-tagged Np95 expressed; CreERT2 transgene

value: Without 4-OHT (day 0)

value: anti Myc-tag antibody (CST, 9B11, mouse mAb)


title: Dnmt1cKO ESC [RRBS-seq]

value: Dnmt1 (flox/flox) conditional alleles; CreERT2 transgene

value: With 4-OHT (day 6)


title: Np95 wt ESC, Input [ChIP-seq]

description: Input DNA

value: Np95 (flox/flox) conditional alleles; CreERT2 transgene

value: input DNA

value: Native chromatin


title: Np95 wt ESC [ChIP-seq]

value: Anti-H3K9me3 mAb (MBL, MABI0318)

value: Crosslinked chromatin


title: WT Macrophage 2HR Rep1

value: female


title: Myc-Dnmt1 wt ESC [ChIP-seq]

value: Exogenous Myc-tagged Dnmt1 expressed


title: KO Macrophage 6HR Rep1

value: LincRNA-EPS KO

value: macrophage


title: WT Macrophage 0HR Rep1

value: 100ng/ml LPS for 0h


title: DN+Myc-Np95 cDKO ESC [ChIP-seq]

value: With 4-OHT (day 4)


title: cell 1

status: Public on May 07 2016

city: Tarrytown

first: Ruoyu

last: Zhang

address: 777 Old Saw Mill River Road

institute: Regeneron

data_processing:
Library strategy: DNA-Seq
Raw sequencing reads were trimmed by Trimmomatic
Cleaned reads were then mapped to hg19 human reference sequence with rCRS mitochondrial reference genome by bowtie2
PCR duplicates were removed with Picard
mtDNA heteroplasmies were called by customer scripts
Genome_build: hg19,rCRS

source_name: cell standard process method

extract_protocol:
In standard method, DNA was extracted by DNeasy Blood and Tissue Kit (No. 69504; Qiagen); in optimized method, DNA was extracted by QIAamp DSP DNA Blood Mini Kit (No. 61104; Qiagen). White blood cell DNA was extracted by DNeasy Blood and Tissue Kit (No. 69504; Qiagen).
In standard method, libraries were prepared by standard library preparation protocol. In optimized method, libraries were prepared by KAPA Hyper Prep Kits (No. KK8502; Kapa). Cell DNA libraries were prepared by by Nextera XT DNA library preparation kit (Illumina, FC-131-1024).

value: white blood cell


title: cell 17


title: cell 2


title: cell 42


title: optimized and size selection 69

description: plasma DNA

library_source: other

molecule: other

source_name: optimized and size selection process method

value: plasma


title: optimized and size selection 93

description: plasma DNA


title: optimized and size selection 17

description: plasma DNA


title: optimized and size selection 42

description: plasma DNA


title: optimized and size selection 2

description: plasma DNA


title: optimized and size selection 1

description: plasma DNA


title: WT Macrophage 0HR Rep2

value: wild type


title: optimized and size selection 78

description: plasma DNA


title: optimized 42

description: plasma DNA

source_name: optimized process method


title: optimized 69

description: plasma DNA


title: standard 17

description: plasma DNA

source_name: standard process method


title: Sham LNA-antimiR 2

value: FVBN

value: Male

value: Sham


title: standard 2

description: plasma DNA


title: optimized 93

description: plasma DNA


title: optimized 2

description: plasma DNA


title: optimized 78

description: plasma DNA


title: standard 93

description: plasma DNA


title: optimized 17

description: plasma DNA


title: optimized 1

description: plasma DNA


title: standard 78

description: plasma DNA


title: standard 69

description: plasma DNA


title: standard 42

description: plasma DNA


title: human3_PS_input_for_ChIP

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

data_processing:
Image analysis and base calling was done using the standard Illumina pipeline for HiSeq2500.
Data was quality-filtered using fastq_quality_filter from the FASTX toolkit with the following parameters: -q 20 -p 80. For libraries with >50% adapter reads (one library total: human_PS_K4me3_ChIP), reads containing only adapter sequence were discarded using fastx_clipper.
For ChIP-seq, alignment was done using Bowtie 1.1.1 with the following parameters: -k 1 -m 1 -n 1 -l 40.  For RNA-seq, alignment was done using TopHat 2.0 with default settings, with Ensembl transcripts as a reference (-G parameter).
For ChIP-seq, peaks were called using MACS 1.4 at p < 10^-5 (-p 1e-5), with default parameters.
For ChIP-seq, raw counts in the +/- 2kb intervals surrounding the transcription start sites were calculated using htseq-count with the following settings: -m intersection-nonempty -s no.
genome build: hg19
processed data files format and content: All files are tab-delimited text (.txt).  For RNA-seq, FPKM is reported for each Ensembl (build 75) transcript and gene.  For ChIP-seq, raw counts normalized to (aligned, non-duplicated) library size are reported for the +/- 2kb region surrounding each Ensembl (build 75) transcript.

source_name: adult testis

growth_protocol: Human testis samples were obtained from patients undergoing vasectomy reversals at the Infertility Clinic of St. Louis.

extract_protocol:
Pachytene spermatocyte and round spermatid fractions were collected by StaPut (Bellve et al 1993).  Purity was assessed under phase optics and was consistently >95% for each desired cell type.  Cells were washed once in PBS and then split into two aliquots.  One aliquot (for ChIP) was fixed in 1% formaldehyde then quenched with 2.5M glycine, while the second (for RNA) was left unfixed.  Both fixed and unfixed aliquots were snap frozen in liquid nitrogen, then stored at -80C.  ChIP was performed as previously described (Lesch et al 2013).
ChIP-seq libraries were prepared using a TruSeq ChIP sample prep kit (Illumina) according to the manufacturer’s instructions, except that size selection was performed after instead of before PCR amplification.

value: testis

value: pachytene spermatocytes


title: human2_RS_input_for_ChIP

value: round spermatids


title: human3_RS_RNA

data_processing:
Image analysis and base calling was done using the standard Illumina pipeline for HiSeq2500.
Data was quality-filtered using fastq_quality_filter from the FASTX toolkit with the following parameters: -q 20 -p 80. For libraries with >50% adapter reads (one library total: human_PS_K4me3_ChIP), reads containing only adapter sequence were discarded using fastx_clipper.
For RNA-seq, FPKM values were generated using Cufflinks 2.2 with default parameters, except that a transcript gtf was supplied (-G option), and average fragment length of the library was supplied under the -m flag.
genome build: hg19
processed data files format and content: All files are tab-delimited text (.txt).  For RNA-seq, FPKM is reported for each Ensembl (build 75) transcript and gene.  For ChIP-seq, raw counts normalized to (aligned, non-duplicated) library size are reported for the +/- 2kb region surrounding each Ensembl (build 75) gene.

extract_protocol:
Pachytene spermatocyte and round spermatid fractions were collected by StaPut (Bellve et al 1993).  Purity was assessed under phase optics and was consistently >95% for each desired cell type.  Cells were washed once in PBS and then split into two aliquots.  One aliquot (for ChIP) was fixed in 1% formaldehyde then quenched with 2.5M glycine, while the second (for RNA) was left unfixed.  Both fixed and unfixed aliquots were snap frozen in liquid nitrogen, then stored at -80C.  ChIP was performed as previously described (Lesch et al 2013).  Genomic DNA was removed using gDNA eliminator columns supplied with the kit.
RNA-seq libraries were prepared using a SMARTer stranded RNA prep kit (Clontech) according to the manufacturer’s instructions.


title: human2_RS_RNA

extract_protocol:
Pachytene spermatocyte and round spermatid fractions were collected by StaPut (Bellve et al 1993).  Purity was assessed under phase optics and was consistently >95% for each desired cell type.  Cells were washed once in PBS and then split into two aliquots.  One aliquot (for ChIP) was fixed in 1% formaldehyde then quenched with 2.5M glycine, while the second (for RNA) was left unfixed.  Both fixed and unfixed aliquots were snap frozen in liquid nitrogen, then stored at -80C.  Unfixed aliquots of sorted cells were thawed on ice, and RNA isolation was performed using the RNEasy Mini kit according to the manufacturer’s instructions.  Genomic DNA was removed using gDNA eliminator columns supplied with the kit.
RNA-seq libraries were prepared using a SMARTer stranded RNA prep kit (Clontech) according to the manufacturer’s instructions.


title: human3_PS_K4me3_ChIP

value: H3K4me3 (abcam, #ab8580)


title: human3_PS_K27me3_ChIP


title: human3_RS_K27me3_ChIP


title: human3_RS_K4me3_ChIP


title: human2_RS_K27me3_ChIP


title: human2_PS_RNA


title: human2_RS_K4me3_ChIP


title: human2_PS_K27me3_ChIP


title: standard 1

description: plasma DNA


title: human1_RS_input_for_ChIP


title: human1_RS_RNA


title: human2_PS_input_for_ChIP


title: human1_RS_K27me3_ChIP


title: human1_RS_K4me3_ChIP


title: mouse1_RS_RNA

data_processing:
Image analysis and base calling was done using the standard Illumina pipeline for HiSeq2500.
Data was quality-filtered using fastq_quality_filter from the FASTX toolkit with the following parameters: -q 20 -p 80. For libraries with >50% adapter reads (one library total: human_PS_K4me3_ChIP), reads containing only adapter sequence were discarded using fastx_clipper.
For RNA-seq, FPKM values were generated using Cufflinks 2.2 with default parameters, except that a transcript gtf was supplied (-G option), and average fragment length of the library was supplied under the -m flag.
genome build: mm10
processed data files format and content: All files are tab-delimited text (.txt).  For RNA-seq, FPKM is reported for each Ensembl (build 75) transcript and gene.  For ChIP-seq, raw counts normalized to (aligned, non-duplicated) library size are reported for the +/- 2kb region surrounding each Ensembl (build 75) gene.

growth_protocol: Testes were obtained from adult CD1 wild type male mice (Charles River Laboratories).

extract_protocol:
Populations of pachytene spermatocytes and round spermatids were recovered using a StaPut gradient as previously described (Bellve et al, 1993).  All isolated fractions were at least 95% pure.  Cells were washed once in PBS and then split into two aliquots.  One aliquot (for ChIP) was fixed in 1% formaldehyde then quenched with 2.5M glycine, while the second (for RNA) was left unfixed.  Both fixed and unfixed aliquots were snap frozen in liquid nitrogen, then stored at -80C.  Unfixed aliquots of sorted cells were thawed on ice, and RNA isolation was performed using the RNEasy Mini kit according to the manufacturer’s instructions.
RNA-seq libraries were prepared using the IlluminaTruSeq RNA-seq sample prep kit, according to the manufacturer's instructions.


title: human1_PS_RNA


title: human2_PS_K4me3_ChIP


title: human1_PS_K4me3_ChIP


title: human3_PS_RNA


title: human total sperm RNA-Seq rep2

city: reno

first: Wei

last: Yan

state: NV

address: 1664 N. Virginia Street

department: Physiology

institute: University of Nevada

data_processing:
Torrent suite
RNA-Seq: Sequenced reads were mapped to (mm10, mouse; rn5, rat; oryCun2, rabbit; hg19, human) whole genome using TOPHAT; sncRNA-Seq: Sequenced reads were matched to sncRNA sequences via Sequery and then mapped to (mm10, mouse; rn5, rat; oryCun2, rabbit; hg19, human) via Bowtie.
RNA-Seq: Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated and isoforms were assembled by using a protocol from Cufflinks; sncRNA-Seq: reads per 100,000 aligned reads (RPK) were calculated
Genome_build: mm10, mouse; hg19, human; oryCun2, rabbit; rn5, rat
Supplementary_files_format_and_content: Averaged, normalized expression values are provided for the RNA-Seq (RPKM) and sncRNA-Seq (RPK) samples. The processed data table is organized by gene name ("Gene"), species of origin ("Species"), sample type, i.e., total sperm or sperm head ("Sample"), class of RNA ("Class"), normalized average expression ("Expression")

source_name: human total sperm RNA-Seq

extract_protocol:
Total RNA was extracted from sperm samples using the mirVana total RNA extraction protocol. Human and rabbit sperm samples were pipeted up and down during lysis; mouse sperm samples were homogenized for one minute during lysis; rat samples were homogenized for 90 seconds and subsequently incubated at 65C for five minutes during lysis.
RNA libraries were prepared for sequencing using standard Ion Torrent protocols

value: adult

tag: genotype

value: total sperm


title: human total sperm RNA-Seq rep1


title: mouse1_RS_input_for_ChIP

data_processing:
Image analysis and base calling was done using the standard Illumina pipeline for HiSeq2500.
Data was quality-filtered using fastq_quality_filter from the FASTX toolkit with the following parameters: -q 20 -p 80. For libraries with >50% adapter reads (one library total: human_PS_K4me3_ChIP), reads containing only adapter sequence were discarded using fastx_clipper.
For ChIP-seq, alignment was done using Bowtie 1.1.1 with the following parameters: -k 1 -m 1 -n 1 -l 40.  For RNA-seq, alignment was done using TopHat 2.0 with default settings, with Ensembl transcripts as a reference (-G parameter).
For ChIP-seq, peaks were called using MACS 1.4 at p < 10^-5 (-p 1e-5), with default parameters.
For ChIP-seq, raw counts in the +/- 2kb intervals surrounding the transcription start sites were calculated using htseq-count with the following settings: -m intersection-nonempty -s no.
genome build: mm10
processed data files format and content: All files are tab-delimited text (.txt).  For RNA-seq, FPKM is reported for each Ensembl (build 75) transcript and gene.  For ChIP-seq, raw counts normalized to (aligned, non-duplicated) library size are reported for the +/- 2kb region surrounding each Ensembl (build 75) transcript.

extract_protocol:
Populations of pachytene spermatocytes and round spermatids were recovered using a StaPut gradient as previously described (Bellve et al, 1993).  All isolated fractions were at least 95% pure.  Cells were washed once in PBS and then split into two aliquots.  One aliquot (for ChIP) was fixed in 1% formaldehyde then quenched with 2.5M glycine, while the second (for RNA) was left unfixed.  Both fixed and unfixed aliquots were snap frozen in liquid nitrogen, then stored at -80C.  ChIP was performed as previously described (Lee et al 2006).
ChIP-seq libraries were prepared using an Illumina ChIP-seq sample prep kit (#1003473), according to the manufacturer's instructions


title: mouse1_RS_K27me3_ChIP

value: H3K27me3 (Millipore, #07449)


title: mouse1_PS_K27me3_ChIP


title: mouse1_RS_K4me3_ChIP


title: mouse1_PS_RNA


title: mouse1_PS_input_for_ChIP


title: mouse1_PS_K4me3_ChIP


title: SS_cDNA_KD2

city: Leuven

first: Zeynep

last: Kalender Atak

address: Herestraat 49

country: Belgium

institute: KULeuven

description: cDNA

data_processing:
Library strategy: STARR-Seq
Files were cleaned and trimmed where needed.
Reads were mapped to the hg19 genome using STAR.
The sensitive-local setting for Bowtie2 was used to correct for a high percentage of mismatches at the start of a read, resulting in the removal of the first five base pairs for each read.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *counts.txt: Counts are normalized and were generated using HTseq counts.

source_name: MCF7, p53 knockdown, non-stimulated

growth_protocol: Cells were grown at 37°C to 85% confluency before harvest. Medium used was Ham's F-10 nutrient mix supplemented with FBS and l-alanyl-glutamine.

extract_protocol:
DNA was extracted with a plasmid extraction protocol from Qiagen; RNA was extracted using the RNeasy protocol from Qiagen.
Custom library prep.

treatment_protocol: p53 stimulation with Nutlin-3a or stable knockdown of p53.

tag: cell line

value: stable knockdown of p53

tag: capturing system

value: MYbaits custom capturing system


title: SS_cDNA_KD1

description: cDNA

tag: genotype/variation


title: p53_KD1

description: Biological replicate 1 of 2.

data_processing:
Basecalls performed using CASAVA version 1.8.
Sequenced reads were trimmed for adaptor sequence and for the first basepair.
The reads were then mapped to hg19 whole genome using TopHat2 v2.0.9 and Bowtie2 v2.2.0 with --read-realign-edit-dist 0 and sensitive-local setting.
Read counts per gene were obtained from the aligned reads using htseq-count package (HTSeq 0.5.4p5).
Genome_build: hg19 (GRCh37, GENCODE v18)
Supplementary_files_format_and_content: *counts.txt: Tab-delimited text files include gene-based read counts per sample.

extract_protocol:
RNA was extracted using the RNeasy protocol from Qiagen.
Illumina TruSeq library prep.

treatment_protocol: Stable knockdown of p53.


title: ChIP_H3K27acetyl_nutlin

data_processing:
Reads were mapped to the hg19 genome using Bowtie2 2.1.0.
The sensitive-local setting for Bowtie2 was used to correct for a high percentage of mismatches at the start of a read, resulting in the removal of the first five base pair for each read.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files were generated from bam files using BEDTools 2.17.0 and the scores represent the coverage.

source_name: MCF7, WT, nutlin-3a stimulated

extract_protocol:
Chromatin was extracted using the MagnaChIP-seq kit (Millipore). Sonication was performed for 12 cycles, 30 sec pulses using the Biorupter.
Illumina TruSeq.

treatment_protocol: Cells were treated with Nutlin-3a.

value: WT

value: anti-H3K27ac (Abcam ab4729, lot GR125454-2)


title: human1_PS_input_for_ChIP


title: SS_cDNA_N2

description: cDNA


title: SS_cDNA_N1

description: cDNA


title: human total sperm RNA-Seq rep3

tag: age


title: SS_plasmid_WT2

description: Extracted plasmid DNA.

source_name: MCF7, WT, non-stimulated


title: SS_plasmid_N2

description: Extracted plasmid DNA.


title: SS_plasmid_KD2

description: Extracted plasmid DNA.


title: SS_plasmid_WT1

description: Extracted plasmid DNA.


title: SS_plasmid_N1

description: Extracted plasmid DNA.


title: human1_PS_K27me3_ChIP


title: PacBio_enhancer-Barcodes

description:
Plasmid DNA library input.
PacBio long-read sequencing of the plasmid library (i.e., the 2-3kb length fragment spanning the cloned enhancer, the reporter and the barcode in the plasmid).

data_processing:
Library strategy: CHEQ-Seq
Files were cleaned and trimmed where needed.
Reads were mapped to the hg19 genome using STAR.
The sensitive-local setting for Bowtie2 was used to correct for a high percentage of mismatches at the start of a read, resulting in the removal of the first five base pairs for each read.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *counts.txt: Counts are raw and were generated using HTseq counts.

source_name: MCF7, input


title: CS_cDNA_N2

description: cDNA


title: CS_plasmid_KD2

description: Extracted plasmid DNA.


title: CS_cDNA_N1

description: cDNA


title: ChIP_H3K27acetyl_NS


title: CS_plasmid_WT2

description: Extracted plasmid DNA.


title: p53_KD2

description: Biological replicate 2 of 2.


title: CS_plasmid_WT1

description: Extracted plasmid DNA.


title: CS_plasmid_KD1

description: Extracted plasmid DNA.


title: CS_plasmid_N2

description: Extracted plasmid DNA.


title: opossum2_RS_K27me3_ChIP

description: Testes from Monodelphis domestica were obtained from animals culled from a colony maintained at the Texas Biomedical Research Institute.

data_processing:
Image analysis and base calling was done using the standard Illumina pipeline for HiSeq2500.
Data was quality-filtered using fastq_quality_filter from the FASTX toolkit with the following parameters: -q 20 -p 80.
For ChIP-seq, alignment was done using Bowtie 1.1.1 with the following parameters: -k 1 -m 1 -n 1 -l 40.  For RNA-seq, alignment was done using TopHat 2.0 with default settings, with Ensembl transcripts as a reference (-G parameter).
For ChIP-seq, peaks were called using MACS 1.4 at p < 10^-5 (-p 1e-5), with default parameters.
For ChIP-seq, raw counts in the +/- 2kb intervals surrounding the transcription start sites for each transcript were calculated using htseq-count with the following settings: -m intersection-nonempty -s no.
genome build: monDom5
processed data files format and content: All files are tab-delimited text (.txt).   For ChIP-seq, raw counts normalized to (aligned, non-duplicated) library size are reported for the +/- 2kb region surrounding each Ensembl (build 75) gene.

organism: Monodelphis domestica

extract_protocol:
Populations of pachytene spermatocytes and round spermatids (purity 89-90%) were recovered using a StaPut gradient as previously described (Bellve et al, 1993).  Cells were washed once in PBS and then split into two aliquots.  One aliquot (for ChIP) was fixed in 1% formaldehyde then quenched with 2.5M glycine, while the second (for RNA) was left unfixed.  Both fixed and unfixed aliquots were snap frozen in liquid nitrogen, then stored at -80C. ChIP was performed as previously described (Lesch et al 2013).
ChIP-seq libraries were prepared using a TruSeq ChIP sample prep kit (Illumina) according to the manufacturerÕs instructions, except that size selection was performed after instead of before PCR amplification.


title: CS_plasmid_N1

description: Extracted plasmid DNA.


title: opossum2_PS_RNA

data_processing:
Image analysis and base calling was done using the standard Illumina pipeline for HiSeq2500.
Data was quality-filtered using fastq_quality_filter from the FASTX toolkit with the following parameters: -q 20 -p 80.
For RNA-seq, FPKM values were generated using Cufflinks 2.2 with default parameters, except that a transcript gtf was supplied (-G option), and average fragment length of the library was supplied under the -m flag.
genome build: monDom5
processed data files format and content: All files are tab-delimited text (.txt). For RNA-seq, FPKM is reported for each Ensembl (build 75) transcript and gene.

extract_protocol:
Populations of pachytene spermatocytes and round spermatids (purity 89-90%) were recovered using a StaPut gradient as previously described (Bellve et al, 1993).  Cells were washed once in PBS and then split into two aliquots.  One aliquot (for ChIP) was fixed in 1% formaldehyde then quenched with 2.5M glycine, while the second (for RNA) was left unfixed.  Both fixed and unfixed aliquots were snap frozen in liquid nitrogen, then stored at -80C. ChIP was performed as previously described (Lesch et al 2013).
RNA-seq libraries were prepared using an Apollo 324 library prep instrument with supplied reagents (Integenx).


title: opossum2_RS_RNA


title: opossum2_PS_K4me3_ChIP


title: opossum2_RS_K4me3_ChIP


title: SS_plasmid_KD1

description: Extracted plasmid DNA.


title: opossum2_PS_input_for_ChIP