title: Schizont_input

description: Chromatin IP using specific antibody

value: Schizont


title: CO2_1br

status: Public on Sep 23 2015

type: SRA

city: Egham

first: Fabio

last: Manfredini

state: Surrey

address: Bourne Lab Room 4-17

department: Biology

country: United Kingdom

institute: Royal Holloway University of London

description: CO2-treated queens were subjected to 10 min of CO2-narcosis on day 6 and on day 7. The seven caged queens were placed in a zip-lock plastic bag, which was then flushed with compressed CO2 until all queens were completely immobile, and sealed for 10 min. Queens were released in their individual colonies after treatment on both days.

library_source: transcriptomic

data_processing:
Reads were checked with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) for quality control
Reads were also processed with Trimmomatic to remove adapters and low quality bases: reads less than 36 bases long were filtered out
We also dropped reads that matched ribosomal RNA sequences (rRNA) by means of SortMeRna
Surviving reads were aligned with TopHat for Illumina to the latest version of the honey bee genome (Apis mellifera Assembly 4.5) available on BeeBase (http://hymenopteragenome.org/ beebase/?q=download_sequences) by using the Galaxy web-based platform (https://usegalaxy.org/).
Mapped reads were converted into raw read counts with SAMtools idxstats
Raw read counts were analysed with R using the edgeR package from Bioconductor. Read counts were log2 transformed to correct for the skew to zero and large values. Only genes with at least 10 reads per sample were kept in the analysis (12,992 genes).
Normalization was performed with Trimmed Mean of M-values (TMM), a method that is implemented in the edgeR Bioconductor package
We detected differential levels of gene expression using a modified Fisher’s exact test that takes into account both dispersion and multiple samples. Finally, raw P-values for each gene were corrected for multiple comparisons setting a false discovery rate (FDR) of 5%.
Genome_build: Apis mellifera Assembly 4.5
Supplementary_files_format_and_content: Excel spreadsheet file with two sheets: raw read counts and scaled read counts

molecule: total RNA

organism: Apis mellifera

source_name: brain tissue

growth_protocol: We reared 20 sister queens of standard Australian commercial stock using standard beekeeping techniques from a single source colony. The day before the young queens were due to emerge from their pupal cells we transferred them to an incubator at 35 °C and emerged them in individual glass vials. At one day of age we paint-marked the queens and introduced each of them into their own nucleus colony. The entrance of each hive was covered with a queen excluder – a grid that allows workers to exit and enter, but confines the larger queens within the hive.

extract_protocol:
Head capsules were removed and brains were dissected over dry ice. Brains were placed individually in Trizol and macerated to breakdown tissue. After addition of chloroform, samples were briefly vortexed and then centrifuged at 12000g for 15 min at 4 °C to generate an aqueous phase. After addition of isopropyl alcohol, the aqueous phase was again vortexed and centrifuged (10 min) to produce a pellet. The pellet was then washed with 75% ethanol prior to drying and redissolving in ddH2O. The dissolved RNA was treated with DNAse I buffer (Ambion) to remove gDNA contaminations, prior to centrifugation and collection of the aqueous phase. The RNA content of the sample and the purity of the extracts were assessed using a NanoDrop™ 1000 spectrophotometer (Thermo Scientific Inc., Bremen, Germany).
HiSeq Sequencing Kit Trueseq v3 - library construction performed at the Illumina facility following standard protocols

treatment_protocol: When the queens were 6 days old we randomly assigned the twenty queens to one of three treatments (see above). All queens were harvested when they were 8 days old, at the same time of day (15:00 h), directly into liquid nitrogen and then stored at -80 °C.

tag: tissue

value: brain

tag: developmental stage

value: adult

tag: caste

value: queen

tag: strain

value: ligustica

tag: age

tag: treatment

value: double narcosis with carbon dioxide


title: mated_4

description: Mated queens were queens that successfully participated in a mating flight. Early afternoon of the 6th day, we removed the queen excluders, and then monitored the entrances until mating flights with successful mating (as indicated by a mating plug) were observed.

value: naturally mated


title: Native_N6-2_TTAGGC nucleosome core particles (MNase +ExoIII)

city: Bethesda

first: David

middle: Johannes

last: Clark

state: MD

address: 6 Center Drive Bldg 6A Rm 2A02

department: DDB

country: USA

institute: NICHD, NIH

description: Biological replicate 2

library_source: genomic

data_processing:
Nucleosome sequences were aligned to the yeast genome (SacCer2) or the mouse genome (mm10) using Bowtie2 with default settings. Bowtie2 was also used to align the reconstituted nucleosome sequences to the plasmid sequence (supplied here).
This paper describes novel nucleosomal particles distinguished by their lengths. DNA fragment length distributions were calculated from the .sam files for all of the data sets and are supplied for the mouse data as text files.
Nucleosome occupancy maps were created using programs described by Cole et al. (2011) Nucleic Acids Res. 39, 9521-9535. Provided here are bigwig files for the yeast data and text files for the in vitro experiments with pRS-ARG1-B. Occupancy files were not calculated for the mouse nucleosomes, because the coverage is too low (~45m pairs of reads).
This paper describes novel nucleosomal particles distinguished by their lengths. DNA fragment length distributions were calculated from the .sam files for all of the data sets and are supplied for the mouse data as text files.
Genome_build: SacCer2 and mm10 for in vivo data. In vitro reconstitutions: the plasmid sequence (pRS-ARG1-B.fa) is provided here; the S. cerevisiae ARG1 locus (from -1283 to +2936 relative to the start codon) was inserted into pRS414. See paper for more details.
Supplementary_files_format_and_content: Yeast strains (in vivo data): bigwig files showing nucleosome occupancy (all reads included). Reconstituted nucleosomes on plasmid pRS-ARG1B: text files showing nucleosome occupancy at each plasmid coordinate (50-500 bp). Mouse data: length distributions (filenames contain "lengths"): text files with two columns: length (L) in bp, number of molecules of length L.

molecule: genomic DNA

organism: Mus musculus

source_name: female mouse liver nuclei (E13.5)

growth_protocol: Yeast strains were grown to mid-log phase (OD600 about 0.8) at 30 degC in synthetic complete medium.

extract_protocol:
The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.
MNase-seq and MNase-ExoIII-seq

treatment_protocol:
Yeast nuclei were prepared from unfixed cells and then digested with a range of MNase concentrations at two different ExoIII concentrations. Mono-nucleosomal DNA was gel-purified (~150 bp). See paper for details.
In vitro reconstitutions were performed by mixing recombinant yeast histone octamers or native chicken erythrocyte core histones with purified plasmid pRS-ARG1-B DNA followed by salt dialysis. Reconstituted chromatin was digested to mono-nucleosomes using MNase and ExoIII. See paper for details.
Mouse nuclei were prepared from liver (female E13.5) and mildly digested with MNase only. The nuclei were lysed and soluble long chromatin was depleted of histone H1 using a cation exchange resin. Native chromatin and H1-depleted chromatin were digested with MNase and ExoIII. DNA from three digestion points (increasing MNase with fixed ExoIII) was purified. See paper for details.

tag: strain name

value: NIH/S

tag: mnase or exoiii

value: Native chromatin:MNase digest with ExoIII trimming


title: Native_N5-2_CGATGT nucleosome core particles (MNase +ExoIII)

description: Biological replicate 2


title: Trophs_input

city: Pune

first: Krishanpal

last: Karmodiya

state: Maharashtra

address: Dr. Homi Bhabha Road

department: Center of Excellence in Epigenetics

country: India

institute: Indian Institute of Science Education and Research

description: Chromatin IP using specific antibody

data_processing:
Reference genome was converted to color-space using bowtie-build
ChIP-seq data were mapped using the Bowtie allowing two mismatches.
Bed files generated using Samtools
Genome_build: plasFalc1
Supplementary_files_format_and_content: bed

organism: Plasmodium falciparum

source_name: Trophozoite stage of Plasmodium falciparum

growth_protocol: Plasmodium falciparum strain 3D7 was cultured cultured in RPMI1640 medium supplemented with 25 mM HEPES, 0.5% AlbuMAX I, 1.77 mM sodium bicarbonate, 100 μM hypoxanthine and 12.5 μg ml-1 gentamicin sulfate at 37 °C. RBCs were prepared from fresh whole blood obtained from a healthy donor and stored at 4 °C for at least 1 day. Increased yields were obtained by subculturing every 2 days for 6–8 h before invasion. This was done by equally dividing the contents of each flask into two or more flasks and quickly restoring the hematocrit and medium volume in each of the flasks with fresh erythrocytes and fresh medium to keep the hematocrit between 1 and 1.5% in the required volume of culture medium. The culture was synchronized with 5% sorbitol and the parasites were collected at 18, 30 and 40 hpi for chromatin immunoprecipitation.

extract_protocol:
Lysates were clarified from sonicated nuclei and antibody-DNA complexes were isolated with antibody.
ChIP-seq libraries for all the samples were prepared from around 5 ng of DNA using fragment library construction kit from life technolofies for SoLiD sequencing. Briefly ChIPed DNA samples were end repaired and adapters were ligated using T4 DNA ligase. Ligated DNA were subsequently amplified using adapter specific barcoded primers for 15 cycles. DNA purification at every step was performed using Agencourt XP beads. Library profiles were assessed using Agilent bioanalyzer 2100 high sensitivityDNA kit. Equimolar amount of libraries were pooled and 50 bp reads were sequenced in-house using SoLiD 4.0.

treatment_protocol: No treatment

tag: Stage

value: Trophs

tag: antibody


title: Rings_input

description: Chromatin IP using specific antibody

source_name: Ring stage Plasmodium falciparum

value: Rings


title: mated_6


title: 4T1 Vector - sample 7 - input

city: Rockville

first: Ying

last: Hu

email: yhu@mail.nih.gov, hunterk@mail.nih.gov

address: 9609 Medical Center Dr.

department: NCI/CCR

institute: NIH

data_processing:
Trim adaptor sequences and trailing Ns; in-house perl script
Merge to unique reads; in-house perl script
Build sequence database; formatdb
Map to mm9 reference genome; bwa
Genome_build: mm9
Supplementary_files_format_and_content: htseq-count matrix in text tab-delimited file

source_name: 4T1 cell lysate rRNA-depleted transcriptome

growth_protocol: 4T1 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) (Gibco®) supplemented with L-Glutamate (Gibco®), 9% fetal bovine serum (FBS) (Gemini BioProducts), and 1% Penicillin and Streptomycin (P/S) (Gemini BioProducts).

extract_protocol:
4T1 cells expressing 8166-M24-658 control vector or FLAG-CNOT7 constructs were grown to ~85% confluence in ten 15cm culture plates. Cells were then rinsed with 15mL ice cold sterile PBS, scraped off, pelleted (~1mL pellet), and snap frozen in liquid nitrogen. Cells were thawed on ice and lysed in 3.5mL lysis buffer (100mM NaCl, 5mM MgCl2, 10mM HEPES (pH 7.3), 0.5% NP40, 200 units RNasin (Promega), Protease inhibitor cocktail (Roche)). The resulting 4mL of cell lysate was spun down twice at 21,000*g for 20 minutes at 4˚C. 40uL of lysate was saved 1% input to confirm immunoprecipitation. 200uL of lysate was saved for 5% RNA-seq input and was purified by TriPure (Roche) RNA extraction. 25uL beads per 1mL lysate of Protein G Dynabeads® were blocked with 1mL 0.5% BSA in PBS at room temperature for 20 minutes then washed twice with 1mL NT2 wash buffer (50mM Tris-HCl (pH 7.4), 150mM NaCl, 1mM MgCl2, 0.05% NP40). 24ug antibody was added to each sample and incubated at 4˚C overnight then beads were added to each sample and rotated for 30 minutes at room temperature. Beads were washed four times in 1mL NT2 buffer. Eighty five percent of beads were subjected to RNA extraction with TriPure. Protein from the remaining 15% of beads was eluted with Laemli buffer to confirm immunoprecipitation.
Library preparation was performed using the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® with NEBNext® multiplexing oligos using manufacturer’s protocol.  RNA sequencing was conducted on the Illumina® HiSeq 2500.

treatment_protocol: As this was a native RIP protocol, cell were not pretreated prior to the initiation of RIP.

value: mammary gland

tag: cell line

value: 4T1 mammary tumor cell line

tag: cells expressing

value: 8166-M24-658 control vector

tag: rip antibody


title: Native_N4-1_1_ATCACG nucleosome core particles (MNase +ExoIII)

description: Biological replicate 1


title: 4T1 Vector - sample 10 - RIP

source_name: 4T1 RNA immunoprecipitated with M2 FLAG antibody

value: M2 FLAG antibody


title: mated_7


title: Native_N4-2_ATCACG nucleosome core particles (MNase +ExoIII)

description: Biological replicate 2


title: Native_N5-1_9_GATCAG nucleosome core particles (MNase +ExoIII)

description: Biological replicate 1


title: 4T1 M141R - sample 9 - RIP

value: FLAG-Cnot7 (with M141R amino acid substitution)


title: 4T1 M141R - sample 9 - input


title: 4T1 M141R - sample 8 - input


title: H1depl_D5-2_GCCAAT nucleosome core particles (MNase +ExoIII)

description: Biological replicate 2

value: H1-depleted chromatin:MNase digest with ExoIII trimming


title: Native_N3-1_7_CAGATC nucleosome core particles (MNase +ExoIII)

description: Biological replicate 1


title: H1depl_D4-1_12_CTTGTA nucleosome core particles (MNase +ExoIII)

description: Biological replicate 1


title: H1depl_D3-1_11_GGCTAC nucleosome core particles (MNase +ExoIII)

description: Biological replicate 1


title: H1depl_D4-2_ACAGTG nucleosome core particles (MNase +ExoIII)

description: Biological replicate 2


title: H1depl_D3-2_TGACCA nucleosome core particles (MNase +ExoIII)

description: Biological replicate 2


title: 4T1 M141R - sample 6 - RIP


title: 4T1 M141R - sample 7 - RIP


title: 4T1 M141R - sample 10 - input


title: 4T1 M141R - sample 10 - RIP


title: 4T1 M141R - sample 7 - input


title: 4T1 E247A/Y260A - sample 9 - RIP

value: FLAG-Cnot7 (with E247A/Y260A amino acid substitutions)


title: H1depl_D2-1_10_TAGCTT nucleosome core particles (MNase +ExoIII)

description: Biological replicate 1


title: 4T1 M141R - sample 6 - input


title: 4T1 E247A/Y260A - sample 9 - input


title: 4T1 E247A/Y260A - sample 8 - RIP


title: 4T1 E247A/Y260A - sample 8 - input


title: 4T1 M141R - sample 8 - RIP


title: 4T1 Vector - sample 10 - input


title: 4T1 E247A/Y260A - sample 7 - input


title: 4T1 E247A/Y260A - sample 6 - input


title: 4T1 E247A/Y260A - sample 6 - RIP


title: 4T1 E247A/Y260A - sample 10 - RIP


title: 4T1 D40A - sample 9 - RIP

value: FLAG-Cnot7 (with D40A amino acid substitution)


title: 4T1 D40A - sample 9 - input


title: 4T1 D40A - sample 8 - input


title: 4T1 D40A - sample 8 - RIP


title: 4T1 D40A - sample 10 - RIP


title: 4T1 D40A - sample 6 - input


title: 4T1 D40A - sample 6 - RIP


title: 77_MNase-3 nucleosome core particles (MNase)

description: Biological replicate 3

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae

value: JRY4012 (wild type)

tag: genotype

value: MATa can1-100 his3-11,15 leu2-3,112 lys2-delta trp1-1 ura3-1

value: MNase limit digest


title: 381_MNase-Exo_limit-digest-2

description: Biological replicate 2

data_processing:
Nucleosome sequences were aligned to the yeast genome (SacCer2) using Bowtie2 with default settings. Bowtie2 was also used to align the reconstituted nucleosome sequences to the plasmid sequence (supplied here).
Nucleosome occupancy maps were created using programs described by Cole et al. (2011) Nucleic Acids Res. 39, 9521-9535.
The processed data were converted to the bigwig files supplied here (using all sequences).
Genome_build: SacCer2 for in vivo data. In vitro reconstitutions: the plasmid sequence (pRS-ARG1-B.fa) is provided here; the S. cerevisiae ARG1 locus (from -1283 to +2936 relative to the start codon) was inserted into pRS414. See paper for more details.
Supplementary_files_format_and_content: yeast strains (in vivo data): bigwig files showing nucleosome occupancy (all reads included). Reconstituted nucleosomes on plasmid pRS-ARG1B: text files showing nucleosome occupancy at each plasmid coordinate (all lengths).
Supplementary_files_format_and_content: pRS-ARG1-B_688.fa (the plasmid sequence used to align nucleosome reads in the reconstitution experiments).

source_name: nucleosome core particles (MNase +ExoIII)

growth_protocol: Both strains were grown to mid-log phase (OD600 about 0.8) at 30 degC in synthetic complete medium.

extract_protocol:
Nuclei were prepared from unfixed yeast cells and then digested with a range of MNase concentrations at two different ExoIII concentrations. In vitro reconstitutions were performed by mixing recombinant yeast histone octamers with purified plasmid pRS-ARG1-B DNA followed by salt dialysis. In both cases, mono-nucleosomal DNA was gel-purified (~150 bp). See paper for details.
The DNA was repaired using the DNA repair kit from New England Biolabs. The repaired DNA was processed for paired-end sequencing according to the Illumina protocol.

tag: genotype/variation

value: MATa can1-100 his3-11 leu2-3,112 lys2-delta trp1-1 ura3-1 hho1-delta::URA3

value: MNase limit digest with ExoIII trimming


title: 4T1 Cnot7 - sample 9 - input


title: 4T1 Cnot7 - sample 9 - RIP


title: 381_MNase-Exo_less-digested-2

description: Biological replicate 2

value: MNase digest with ExoIII trimming


title: 4T1 E247A/Y260A - sample 7 - RIP


title: LP-3

city: Guangzhou

first: Ji-Long

last: Liu

address: 483 Wushan Rd

country: China

institute: South China Agricultural University

description: mRNA(polyA+)

data_processing:
A computational pipeline was used to process RNA-seq data. Sequence data were mapped to rat reference genome rn5 with Tophat v1.4.0 with default parameters. HTSeq-count was subsequently employed to convert aligned short reads into read counts for each gene model in the ENSEMBL database release 81. Differential expression between was assessed by DEseq using read counts as input. The Benjamini-Hochberg multiple test correction method was enabled. Differentially expressed genes were chosen according to the criteria of fold change > 2 and adjusted p-value < 0.05.
Genome_build: rn5
Supplementary_files_format_and_content: Tab-delimited text files include gene read count values for each sample. The first column is gene ID and the second column is gene name, and the 3rd column is read count value.

organism: Rattus norvegicus

source_name: thyroid collected from rats in late pregnany (LP, day 18), repeat #3

growth_protocol: Adult pregnant Sprague-Dawley rats and their non-pregnant controls were utilized in this study. Pregnant rats were obtained by co-caging two female rats with a male rat overnight. Success of mating was confirmed next morning by the presence of a vaginal plug. The day of the vaginal plug was designated as day 1 of pregnancy. Thyroid tissues were collected from non-pregnant (n = 3) rats and pregnant rats on days 8 (n=3), 12 (n=4) and 18 (n=3) of pregnancy. All collected tissues were then snap-frozen in liquid nitrogen and stored at -80 °C for further analysis.

extract_protocol: Total RNA from thyroid samples was extracted using TRIzol reagent (invitrogen). RNA purity and integrity were assessed by using the ND-1000 Nanodrop and the Agilent 2200 TapeStation, respectively. The following parameters were set for RNA quality control: A260/A280 ratio ≥ 1.8, A260/A230 ratio ≥ 2.0 and RIN value ≥ 7.0. RNA-Seq libraries were prepared using the TruSeq RNA sample preparation kit (Illumina) following the manufacturer’s protocol. Finally, sequencing of the libraries was conducted on an Illumina HiSeq™ 2500 system.

value: thyroid

tag: group

value: in late pregnany (LP, day 18)

value: Sprague-Dawley


title: 381_MNase-Exo_limit-digest-1

description: Biological replicate 1


title: 4T1 E247A/Y260A - sample 10 - input

value: mammary gland


title: LP-2

description: mRNA(polyA+)

source_name: thyroid collected from rats in late pregnany (LP, day 18), repeat #2


title: 381_MNase-Exo_less-digested-1

description: Biological replicate 1


title: 4T1 Cnot7 - sample 8 - RIP

value: 4T1 mammary tumor cell line


title: 4T1 Cnot7 - sample 7 - input


title: NP-3

description: mRNA(polyA+)

source_name: thyroid collected from non-pregnant (NP) rats, repeat #3

value: non-pregnant (NP) rats


title: 4T1 Cnot7 - sample 7 - RIP

value: M2 FLAG antibody


title: 4T1 Cnot7 - sample 8 - input


title: 4T1 Cnot7 - sample 6 - RIP


title: 77_MNase-Exo_less-digested-2

description: Biological replicate 2

value: wild type


title: LP-1

description: mRNA(polyA+)

source_name: thyroid collected from rats in late pregnany (LP, day 18), repeat #1


title: NP-2

description: mRNA(polyA+)

source_name: thyroid collected from non-pregnant (NP) rats, repeat #2


title: 4T1 Cnot7 - sample 6 - input


title: 77_MNase-Exo_limit-digest-1

description: Biological replicate 1


title: 77_MNase-Exo_less-digested-1

description: Biological replicate 1


title: 4T1 D40A - sample 10 - input


title: SLWT_rep2

status: Public on Sep 22 2015

city: Wuhan

first: chaoyang

state: Hubei

address: Huazhong Agricultural University, Wuhan, 430070, China.

department: Huazhong Agricultural University

institute: Key Laboratory of Horticultural Plant Biology (Ministry of Education)

description: replicate 2  for wild type samples

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Solanum lycopersicum whole genome using Top Hat.
Assembles the matched reads to estimates their abundances using HTSeq.
Genome_build: Reference genome sequences and annotations were downloaded from the tomato genome websit (http://solgenomics.net/organism/Solanum_lycopersicum/genome)
Supplementary_files_format_and_content: Excel file includes RPKM values for each Sample

organism: Solanum lycopersicum

source_name: Fruit

extract_protocol:
Total RNA was extracted by Trizol method
20 mg total RNA was prepared to enrich mRNA by using the oligo (dT) magnetic beads. After adding fragmentation buffer, the mRNA was interrupted to short fragments (approximately 200 bp). The first strand cDNA was then synthesized with random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double-strand cDNA was purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors were ligated to the fragments.

tag: variety

value: Ailsa Craig


title: SLWT_rep1

description: replicate 1 for wild type samples


title: 4T1 Cnot7 - sample 10 - input

tag: tissue


title: SLOX_C2_rep2

description: replicate 2 for transgenic samples

value: transgenic expressing citrus gene CsMYBF1


title: 77_MNase-Exo_limit-digest-2

description: Biological replicate 2


title: MethylDNA binding protein-Seq 5

city: Baltimore

first: John

middle: Stephen

last: Dumler

address: 685 W Baltimore St

department: Pathology and Microbiology & Immunology

institute: University of Maryland School of Medicine

data_processing:
Reads were mapped to the human genome hg18 build using Bioscope software.
Regions of methylated DNA enrichment were identified using MACS and SICER.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files generated by MACS or SICER using default reports.

organism: Homo sapiens

source_name: peripheral blood

growth_protocol: A. phagocytophilum was maintained in HL-60 cells until >90-95% infected. Primary peripheral blood neutrophils were isolated from venous blood of healthy adult donors. EDTA-anticoagulated blood was dextran-sedimented and leukocyte-rich plasma centrifuged through a Ficoll-Paque gradient. Mononuclear cells were removed and the remaining erythrocytes were lysed in hypotonic saline.

extract_protocol:
DNA was extracted from infected and mock-infected neutrophils at 24h of incubation ex vivo.
2 μg of DNA was sonicated to an average molecular size of ~150–250 bp and end-repaired using the NEBNext SOLiD DNA library preparation kit end-repair module following the manufacturer’s protocol; New England Biolabs, Ipswich, MA, USA. Fragments were purified using a Qiagen PCR purification kit. SOLiD P1 and P2 adapters lacking 5′ phosphate groups (Life Technologies) were ligated to the fragment using the NEBNext adapter ligation module, column-purified, and subjected to isothermal nick-translation by treating with Platinum Taq polymerase to remove the nick.
The resulting library was divided into two fractions, a total input fraction, and an enriched methylated fraction. The enriched methylated fraction was subjected to affinity enrichment of methylated DNA fragments using recombinant C-terminal 6xHis-tagged MBD2-MBD polypeptides immobilized on magnetic beads. The  enriched methylated  and the total input fractions were then subjected to library amplification using the NEBNext amplification module, using 4–6 cycles for the total input, and 10–12 cycles for the enriched methylated fractions. Library fragments between 200–300 bp were selected after agarose gel electrophoresis. The libraries were then subjected to emulsion PCR and bead enrichment following the SOLiD emulsion PCR protocol (Life Technologies). The resulting beads were then deposited on the SOLiD flow cell and subjected to massively parallel 50 bp single-read sequencing on a Life Technologies SOLiD sequencer.

treatment_protocol: Cell-free bacteria were obtained from infected HL-60 cells. Infected cells were centrifuged at 500× g for 5 min and resuspended in 1× PBS. Infected cells were lysed by sonication using an output of four of a Branson Sonifier 250. Lysed cells were then centrifuged at 1000× g for 10 min, and the bacteria enrichedsupernatant was centrifuged at 13,000× g for 30 min. The bacterial pellets were suspended in RMPI  1640 medium. Neutrophils were infected ex vivo in triplicate using MOI of 25:1. An estimate of 10 infectious bacteria per infected HL-60 cell was used.

tag: cell type

value: neutrophils

tag: donor gender

value: female 2

value: Anaplasma phagocytophilum-infected 2

tag: mbd-seq

value: 164 nM MBD2-MBD-His6/1 µg of PentaHis Antibody (Qiagen, Valencia, CA)


title: MethylDNA binding protein-Seq 4

value: female 1

value: Anaplasma phagocytophilum-infected 1

value: 163 nM MBD2-MBD-His6/1 µg of PentaHis Antibody (Qiagen, Valencia, CA)


title: MethylDNA binding protein-Seq 6

value: male 1

value: Anaplasma phagocytophilum-infected 3

value: 165 nM MBD2-MBD-His6/1 µg of PentaHis Antibody (Qiagen, Valencia, CA)


title: MethylDNA binding protein-Seq 1

value: mock-infected 1

value: 160 nM MBD2-MBD-His6/1 µg of PentaHis Antibody (Qiagen, Valencia, CA)


title: atp6ap2_39_ko

city: Barcelona

first: giovanni

last: iacono

state: Spain

address: Baldiri Reixac, 4

department: single cell sequencing

country: Spain

institute: CNAG,Centro Nacional de Análisis Genómico

data_processing:
alignment was done with GSNAP-gmap-2014-12-16
gsnap OPTIONS: -d mm9_gio -A sam -B 5 --max-mismatches=2 -t 15  -s splicesites_gio_mm9_refseq -N 1 -E 100 -w 100000 -n 1
read counting was performed with custom C++ script
DEseq2 was used to call the expression changes
Genome_build: mm9
Supplementary_files_format_and_content: Normalized_counts: excel table including the normalized read counts for all the samples, as well as the DEseq2 pvalues

source_name: brain

extract_protocol:
Total RNA was Trizol extracted from 2 wild-type and 2 mutant samples (frozen hippocampus). RNA was treated with DNase (Qiagen, 79254) and purified on the RNeasy MinElute Cleanup Kit (Qiagen, 74204). 2000 ng of total RNA were treated with the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat; Illumina MRZH11124). Depleted RNA was precipitated 1 h at -80°C in three volumes of ethanol plus 1 µg of glycogen. RNA was then washed and resuspended in 36 µl of RNase free water. RNA fragmentation buffer (NEBNext® Magnesium RNA Fragmentation Module, E6150S) was added to the solution and the RNA was fragmented by incubation at 95°C for 3 minutes. For reverse transcription, cDNA first strand synthesis was performed with random examer primers. cDNA second strand synthesis was performed with dUNTPs, to ensure strand specificity.
The RNA-seq library was synthetized with KAPA Hyper prep kit (KK8504), a treatment with USER enzyme (NEB, M5505L) was added to digest the unspecific strand. The libraries were pooled (4/lane) and sequenced on the illumina HiSeq, which yielded approximately 40 million single-end reads per sample.

value: hippocampus

tag: age

tag: condition

value: conditional het:Atp6ap2Camk2aCre/0

tag: strain


title: MethylDNA binding protein-Seq 2

tag: treatment

value: mock-infected 2

value: 161 nM MBD2-MBD-His6/1 µg of PentaHis Antibody (Qiagen, Valencia, CA)


title: atp6ap2_11_wt

value: wt


title: M7E

city: Taizhou

first: Baoying

last: Qian

state: Zhejiang

address: 1139 Shifu Road, Jiaojiang, Taizhou, Zhejiang 318000, P. R. China

department: School of life science

institute: Taizhou University

data_processing:
Output statistics, such as raw sequence data, and then generate clean reads from raw reads after remove reads with adaptors, remove reads with unknown nucleotides larger than 5% and remove low quality reads which the percentage of low quality bases(base quality≤10) is more than 20%.
The software Htseq was used to calculated the count value,and then calculated the rpkm with RPKM formula.
Alignment with the reference of the large yellow croaker use the software of TopHat.
Unigene GO Classification, Metabolic Pathway Analysis, AS Analysis with the software of ASprofile, gene SSR Analysis and SNP Analysis using Samtools-0.1.19.
GO Classification of Differentially Expressed gene and Pathway Analysis,
Genome_build: ASM74293v1
Supplementary_files_format_and_content: [gene.fasta] We obtained the sequence of the large yellow croaker after alignment with the reference of the large yellow croaker, using the software TopHat (v2.0.12)
Supplementary_files_format_and_content: [M7C.novel_gtf] This data including the chromosome number, source, the prediction of exon region, and so on, which was produced the sample of M7C
Supplementary_files_format_and_content: [M7C.novel_gtf.anno] The annotation of M7C.novel_gtf
Supplementary_files_format_and_content: [M7C.as.fpkm.anno] Alternative splicing of the sample M7C using the soft ware Asprofile.
Supplementary_files_format_and_content: [M7E.novel_gtf] This data including the chromosome number, source, the prediction of exon region, and so on, which was produced the sample of M7E
Supplementary_files_format_and_content: [M7E.novel_gtf.anno] The annotation of M7E.novel_gtf
Supplementary_files_format_and_content: [M7E.as.fpkm.anno] Alternative splicing of the sample M7E using the soft ware Asprofile.
Supplementary_files_format_and_content: [rpkm] The software Htseq was used to calculated the count value,and then calculated the rpkm with RPKM formula.
Supplementary_files_format_and_content: [rpkm.anno] The annotation of the rpkm
Supplementary_files_format_and_content: [M7E_M7C_Up_Down] The compare of M7E-M7C, the results containing the count of up- or down regulation genes and the percent of these genes.
Supplementary_files_format_and_content: [M7E_M7C.anno] The annotation of M7E_M7C_Up_Down
Supplementary_files_format_and_content: [M7C] Integrative Genomics Viewer（IGV）of the sample M7C, including the chromosome number, the location of the reference sequence of a chromosome, and so on.
Supplementary_files_format_and_content: [M7E] Integrative Genomics Viewer（IGV）of the sample M7E, including the chromosome number, the location of the reference sequence of a chromosome, and so on.

organism: Larimichthys crocea

source_name: muscle

extract_protocol:
Muscles were removed, stored in the liquid of RNAstore (CWBIO, China), and RNA was harvested using Trizol reagent. Seqencing libraries were constructed from 1 ug of total RNA using Illumina TruSeq RNA Sample Prep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: muscle

tag: treatment time

value: fasting with 21 days


title: atp6ap2_38_ko


title: atp6ap2_73_wt


title: 4T1 Cnot7 - sample 10 - RIP

value: mammary gland

value: 4T1 mammary tumor cell line

value: M2 FLAG antibody


title: M7C

value: no treatment


title: 243L_ribo

city: Berkeley

first: Michael

last: Harris

state: CA

address: Barker Hall

department: MCB

institute: UC Berkeley

description: old liver ribosome profiling

data_processing:
Basecalling
3' adapter trimming with FastX-toolkit
rRNA alignment with bowtie v1.0.0.0
Transcritptome alignment with TopHat v2.0.10
read quantitation using custom scripts
differential expression analysis with DESeq
differential splicing analysis with MISO
Genome_build: rn4.0 with Ensembl release 3.4.67 annotation
Supplementary_files_format_and_content: *counts.txt- tab-delimited text files with 3 columns: 1. Ensembl transcript ID, 2. transcript length, 3. read counts on CDS

source_name: liver

extract_protocol:
Rnase I footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification
homogenization on ice in TKM0.25

value: liver

value: 24 months

tag: extracted molecule

value: total RNA

tag: library construction

tag: library strategy

value: Ribosome profiling


title: NP-1

description: mRNA(polyA+)

source_name: thyroid collected from non-pregnant (NP) rats, repeat #1

value: thyroid

value: non-pregnant (NP) rats

value: Sprague-Dawley


title: 242L_ribo

description: old liver ribosome profiling

value: Rnase I footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification


title: without_60

city: Jeonju

first: Seunghwan

last: Kim

address: Nongsaengmyeong-ro

department: Genomics Division

country: South Korea

institute: National Academy of Agricultural Science

description: Untreated Xoo for 60 min

data_processing:
CLC Genomics Workbench 4.0 (CLC bio, Aarhus, Denmark) software used for basecalling.
The relative transcript abundance was calculated by counting the number of reads per kilobase per million mapped sequence reads (RPKM)
Genome_build: ASM738v1 [NC_006834.1]
Supplementary_files_format_and_content: RPKM values for each Sample

organism: Xanthomonas oryzae pv. oryzae KACC 10331

source_name: Untreated Xoo for 60 min

growth_protocol: The bacterium was grown in Nutrient broth (Difco, Detroit, MI, USA) , and maintained at 28°C.

extract_protocol:
Total RNA was extracted from each subsample of the harvested Xoo cells separately using the RNeasy Plus Mini Kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The leaves of rice (Oryza sativa L. cv. Milyang 23) were harvested and homogenized in liquid nitrogen with a mortar and pestle. A culture of Xoo was grown to mid-exponential phase (A600 of 0.5), and 1 g of prepared rice leaf extract (RLX) was then added to the culture medium.

value: wild-type

tag: time point

value: 60 min


title: without_5

description: Untreated Xoo for 5 min

source_name: Untreated Xoo for 5 min

tag: genotype

value: 5 min


title: without_45

description: Untreated Xoo for 45 min

source_name: Untreated Xoo for 45 min

value: 45 min


title: without_0

description: Untreated Xoo for 0 min

source_name: Untreated Xoo for 0 min

value: 0 min


title: without_10

description: Untreated Xoo for 10 min

source_name: Untreated Xoo for 10 min

value: 10 min


title: without_30

description: Untreated Xoo for 30 min

source_name: Untreated Xoo for 30 min

value: 30 min


title: without_15

description: Untreated Xoo for 15 min

source_name: Untreated Xoo for 15 min

value: 15 min


title: M23_60

description: Rice-treated Xoo for 60 min

source_name: Rice-treated Xoo for 60 min


title: SLOX_D7_rep1

description: replicate 1 for transgenic samples

value: Ailsa Craig

tag: genotype/variation

value: transgenic expressing citrus gene CsMYBF1


title: 241L_ribo

description: old liver ribosome profiling

value: liver

value: 24 months


title: MethylDNA binding protein-Seq 3

value: neutrophils

value: male 1

value: mock-infected 3

value: 162 nM MBD2-MBD-His6/1 µg of PentaHis Antibody (Qiagen, Valencia, CA)


title: 77_MNase-2

description: Biological replicate 2

source_name: nucleosome core particles (MNase)

tag: strain name

value: wild type

value: MATa can1-100 his3-11,15 leu2-3,112 lys2-delta trp1-1 ura3-1

tag: mnase or exoiii

value: MNase limit digest


title: M23_30

description: Rice-treated Xoo for 30 min

source_name: Rice-treated Xoo for 30 min

value: wild-type


title: 063L_ribo

description: young liver ribosome profiling

tag: tissue

value: 6 months

value: total RNA

value: Rnase I footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification

value: Ribosome profiling


title: M23_45

description: Rice-treated Xoo for 45 min

source_name: Rice-treated Xoo for 45 min

value: 45 min


title: 061L_ribo

description: young liver ribosome profiling


title: M23_10

description: Rice-treated Xoo for 10 min

source_name: Rice-treated Xoo for 10 min

value: 10 min


title: 062L_ribo

description: young liver ribosome profiling


title: M23_15

description: Rice-treated Xoo for 15 min

source_name: Rice-treated Xoo for 15 min

value: 15 min


title: 243B_ribo

description: old brain ribosome profiling

source_name: brain

value: brain


title: 063B_ribo

description: young brain ribosome profiling


title: M23_0

description: Rice-treated Xoo for 0 min

source_name: Rice-treated Xoo for 0 min

value: 0 min


title: 242B_ribo

description: old brain ribosome profiling

value: 24 months


title: M23_5

description: Rice-treated Xoo for 5 min

source_name: Rice-treated Xoo for 5 min

value: 5 min


title: 062B_ribo

description: young brain ribosome profiling


title: 243L_mRNA

description: old liver RNA-Seq

source_name: liver

extract_protocol:
Illumina TruSeq Stranded kit
homogenization on ice in TKM0.25

value: liver

value: Illumina TruSeq Stranded kit

value: RNA-Seq


title: 241B_ribo

description: old brain ribosome profiling


title: 241L_mRNA

description: old liver RNA-Seq


title: 063L_mRNA

description: young liver RNA-Seq


title: VA-13+hTERTmut

first: Qi

last: Zhao

state: Guangdong

address: No. 651, Dongfengdong Road

department: Medical Oncology

institute: Sun Yat-sen University Cancer Center

description: stable cell line

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were filtered those adaptor comtiminated, unpaired, contains N , and  then mapped to hg19 whole genome using tophat 2.0.2 with default parameters
Reads count were calculated by htseq-count(Htseq Frame work v 0.6.0) with parameters  -s no
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell C, Nat. Biotechnol. 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of fragment falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample, each column represents it's expression across all genes while each row shows gene abundence in all samples.

source_name: immortalized fibroblast_hTERTmutant

extract_protocol:
Total RNA was extracted using the Trizol reagent (Takara). A total of 3 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using a NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) according to the manufacturer’s recommendations.

tag: cell line

tag: cell type

value: immortalized fibroblast

tag: overexpression status

value: overexpress hTERTmut


title: U2OS+hTERTmut

description: stable cell line

source_name: osteosarcoma cancer cell_hTERTmutant

value: osteosarcoma cancer cell


title: 242B_mRNA

description: old brain RNA-Seq

tag: age


title: 243B_mRNA

description: old brain RNA-Seq


title: 241B_mRNA

description: old brain RNA-Seq


title: 062L_mRNA

description: young liver RNA-Seq

value: 6 months


title: 242L_mRNA

description: old liver RNA-Seq

value: total RNA


title: 063B_mRNA

description: young brain RNA-Seq


title: U2OS+hTERT

description: stable cell line

source_name: osteosarcoma cancer cell_hTERT

value: overexpress hTERT


title: 061L_mRNA

description: young liver RNA-Seq


title: VA-13+hTERT

description: stable cell line

source_name: immortalized fibroblast_hTERT


title: VA-13+vector

description: stable cell line

source_name: immortalized fibroblast_empty_vector

value: control


title: 062B_mRNA

description: young brain RNA-Seq


title: 061B_mRNA

description: young brain RNA-Seq


title: U2OS+vector

description: stable cell line

source_name: osteosarcoma cancer cell_empty_vector


title: Psm rep3

status: Public on Sep 21 2015

city: Stanford

first: Elizabeth

middle: S.

last: Sattely

address: 443 Via Ortega, Room 271

department: Chemical Engineering

institute: Stanford University

data_processing:
First, the following quality control operations were performed using Trimmomatic  (v. 0.32): Illumina adapter sequences were removed, errors from random hexamer mispriming were excluded by cropping the first 10 bases from each read, low quality bases were removed, and only reads of 40 bases or longer were retained.
Second, reads were aligned to the B. rapa reference genome14 (IVFCAASv1, INSDC Assembly GCA_000309985.1) using TopHat  (v. 2.0.10) with the following modified parameters: minimum intron length was 40, maximum intron length was 5000, allowed up to 3 mismatches per read, and allowed read gaps of up to 3 bases.
Third, transcripts were assembled using the Cufflinks30 package (v. 2.1.1), enabling both multi-read correction and fragment bias correction, and quantified as Fragments Per Kilobase of exon per Million mapped fragments (FPKM).
Genome_build: IVFCAASv1, INSDC Assembly GCA_000309985.1
Supplementary_files_format_and_content: genes.fpkm_tracking.txt: Transcript abundance measurements, averages for each condition
Supplementary_files_format_and_content: genes.read_group_tracking.txt: Transcript abundance measurements of individual replicates

organism: Brassica rapa

source_name: Leaf

growth_protocol: Seeds of Rapid Cycling Brassica rapa (stock #1-33, rapid cycling ideotype) were kindly supplied by the Rapid Cycling Brassica Collection at the University of Wisconsin-Madison. Each seed was germinated in an 8-cm square pot with Pro-Mix HP (Premier Tech), in a 16-h photoperiod growth chamber maintained at 22°C and 50% humidity.

extract_protocol:
Total RNA was isolated from RCBr leaf tissue using TRIzol Reagent. Inspection of total RNA using a BioAnalyzer 2100 indicated that the samples were of adequate RNA integrity (RIN ≥ 6.5).
Library preparation was performed by the Stanford Functional Genomics Facility, using the TruSeq RNA Sample Prep Kit v2 (Illumina). The libraries were sequenced on the Illumina MiSeq platform (2×150 bp paired-end reads).

treatment_protocol: Plants were elicited for phytoalexin production at 15 days old, once 4–5 true leaves had emerged. For elicitation, two young and almost fully expanded leaves per plant (typically true leaves #2 and 3) were infiltrated—using a needleless 1-mL syringe pressed against the abaxial side—with the appropriate elicitor solution (described below) and returned to the growth chamber. At 9 hours post-infiltration (hpi), each elicited leaf was detached at the petiole, placed in a pre-weighed 2-mL Safe-Lock Tube, flash-frozen in liquid nitrogen, and stored at –80°C until RNA extraction.

tag: accession

value: Rapid Cycling Brassica rapa (#1-33)

tag: infiltration solution

value: Psm (OD600 of 0.01, prepared in 10 mM MgCl2)

tag: developmental stage

value: 15 days old; 4-5 true leaves emerged

tag: harvest time

value: 9 hours post-infiltration


title: Psm rep2


title: Mock_P rep3

value: Sterile 10 mM MgCl2


title: Psm rep1


title: 061B_ribo

description: young brain ribosome profiling

value: brain

tag: extracted molecule

value: Rnase I footprinting, ribosome pelleting, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification

value: Ribosome profiling


title: Mock_P rep2


title: Mock_F rep2


title: Mock_F rep3


title: Mock_F rep1


title: Flg22 rep3

value: Flg22 (10 uM, prepared in 10 mM MgCl2)


title: Mock_P rep1


title: Flg22 rep2


title: Flg22 rep1


title: Mxplus_Smc3het_Flt3ITD_ATAC_2

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

institute: Dana-Farber Cancer Institute

description: Cells were purified from whole bone marrow 4-weeks following PIpC injection; mice harbor Mx1-cre, floxed Smc3, and Flt3-ITD alleles

data_processing:
Library strategy: ATAC-seq
Images analysis and base calling was done using the solexa pipeline.
For all samples reads were aligned to their indicated build using bowtie with parameters -n 2 -e 70 -m 2 -k 2 --best -l 40. Seed length (-l) was set to read length for each dataset. Peak-calling was performed using ZINBA with a window size of 300bp and an offset of 75bp
Genome_build: mm9
Supplementary_files_format_and_content: BED files: for all samples, aligned sequences processed through zinba and enriched regions were outputted in BED format

source_name: c-Kit+ cells purified from bone marrow

growth_protocol: Whole bone marrow from individual mice was positively selected for Cd117 (c-Kit) using antibody-conjugated magnetic beads (Cd117 microbeads, Miltenyi Biotec Inc).

extract_protocol: Chromatin accessibility assays utilizing the bacterial Tn5 transposase were performed as described (Buenrostro et al., 2013) with minor modifications. Cells (50,000/sample) were washed twice in cold PBS, and lysed in cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Transposition reactions were set up with the Illumina Nextera DNA Preparation kit (Illumina #FC-121-1030) and incubated at 37 degrees for 60 minutes. Genomic DNA was then purfied, and libraries were PCR-amplified with individual bar-coded PCR primers.

value: bone marrow

value: c-Kit+ cells

value: Smc3 fl/del Flt3-ITD


title: Mxplus_Smc3het_ATAC_2

description: Cells were purified from whole bone marrow 4-weeks following PIpC injection; mice harbor Mx1-cre and Flt3-ITD allele

value: Smc3 del/+


title: Mxplus_Smc3het_Flt3ITD_ATAC_1


title: Mxminus_Smc3fplus_ATAC_2

description: Cells were purified from whole bone marrow 4-weeks following PIpC injection; control mice are negative for Mx1-cre allele

value: Smc3 fl/+


title: Mxplus_Smc3het_ATAC_1


title: Mxplus_Flt3ITD_ATAC_2

description: Cells were purified from whole bone marrow 4-weeks following PIpC injection; mice harbor Mx1-cre and single floxed Smc3 allele


title: Mxplus_Flt3ITD_ATAC_1


title: Active inhibitor 6 day treatment, biological rep1

city: Bronx

first: Britta

last: Will

state: NEW YORK

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

data_processing:
Library strategy: ERRBS
Image capture, analysis and base calling were performed using Illumina’s CASAVA 1.8 .
Read alignment and methylation calls at CpGs were performed using FAR software (Dodt, M, Ahmed R, Dieterich C. FAR – flexible adapter remover. FAR project website 2011, http://sourceforge.net/projects/theflexibleadap/) for adaptor filtering and  bismark was used for whole genome alignment.
CpG Methylation level calls were performed on reads with a phred quality score of greater than thirty three and a 10-fold coverage.
CpG Methlation calls with a minimum of 10 reads were retained, and differential methylation was analyzed using methylkit (http://code.google.com/p/methylkit/) using non-overlapping 1kb-sized differentially methylated regions (DMR) (>10% methylation difference, q<0.001). Differential methylation was assessed between 4 control samples (DMSO and inactive drug) and 2 active drug samples (2 independent replicates per population).
Overlap of DMR between Control and Active drug samples was assessed using 1kb non-overlapping DMR with a minimum coverage of 10 reads per DMC (q<0.001, >25%  methylation difference).
Genome_build: hg19
Supplementary_files_format_and_content: MethylCall files are tab delimited text files that contain the chromosomal locations of cytosines within CpGs covered in the data and their respective methylation levels.  Column headers are as follows: chrBase = cytosine location name ;  chr = chromosome on which the methylated base is located;  base = base location of methylated base on the chromosome; strand = F for forward strand and R for reverse strand; coverage = read coverage for the cytosine;  freqC = % methylated; freqT = % unmethylated

source_name: Primary IDH1 mutant AML cells treated with GSK321

growth_protocol: Serum free media containing recombinant human cytokines 10 ng/mL IL-3, 25 ng/mL IL-6, 50 ng/mL SCF, 100 ng/mL TPO, 50 ng/mL FLT-3L, 1:500 primocin (50 mg/mL; InvivoGen) and 40 mg/mL Low Density Lipoprotein (Sigma) for 12-16 h.

extract_protocol:
DNA was extracted using the Allprep DNA/RNA purification Kit (Qiagen) and analyzed using a Bioanalyzer (Agilent Technologies).
10ng of DNA was digested with the MspI restriction enzyme. End repair and ligation of paired end Illumina sequencing adaptors was followed by size selection for 150-400 bp library fragments by gel extraction (Qiagen gel extraction kit). Bisulfite conversion using the EZ DNA Methylation Kit (Zymo Research) was followed by PCR amplification using Illumina PCR PE1.0 and 2.0 primers. Library products were purified using AMPure XP beads per manufacturer’s recommended protocol (Agencort). Quality control was performed using quantitation on a Qubit 2.0 fluorometer (Invitrogen) and library visualization using a Quant-iT dsDNA HS Assay Kit (Agilent 2100 Bioanalyzer).
Enhanced Reduced Represantation Bisulfite Sequencing (ERRBS): Amplified libraries were sequenced using a 50bp single end read run on a HiSeq2000 per manufacturer’s recommended protocol.

treatment_protocol: Following pre-incubation, viable cells were seeded at 1.5 - 3 x 105 cells per 500 mL media in a 48-well plate and treated with 0.3% DMSO and 3 mM GSK990 or GSK321 inhibitors and were monitored for up to 22 days.

value: primary AML mononuclear cells

value: IDH1 mutant


title: Inactive inhibitor 6 day treatment, biological rep1

source_name: Primary IDH1 mutant AML cells treated with GSK990


title: Active inhibitor 6 day treatment, biological rep2


title: DMSO 6 day treatment, biological rep1

source_name: Primary IDH1 mutant AML cells treated with DMSO


title: PRDM9C-G278A_with_PRDM9A_H3K4me3_Input

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-Seq reads were aligned to the hg19 genome assembly using BWA v.0.5.10
ChIP-Seq reads were filtered to keep only uniquely mapped reads
ChIP-Seq peaks were called using MACS v1.4.2
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

growth_protocol: HEK293 cells were cultured in DMEM (Gibco, Life Technologies) supplemented with 10% FBS (Gibco) at 37 ºC and 5% CO2. 24 hours prior to transfection, cells were seeded at with 10 ml 2.5·105 cell/ml in 10 cm culture treated plates.

extract_protocol:
Nuclei were isolated from cells using hypotonic lysis. Chromatin was fragmented by Mnase digestion. After high speed spin soluble chromatin was removed and used for ChIP
Kapa Hyper Prep Kits (Kapa Biosystems)

treatment_protocol: Cells were transfected using X-tremeGene HP transfection reagent (Roche) following manufacturer’s protocol using a ratio of 3:1 reagent to DNA with 10 µg total plasmid DNA.

tag: cell description

value: embryonic kidney

tag: prdm9 allele

value: PRDM9C-G278A with PRDM9A

tag: ChIP

value: input

tag: antibody manufacturer

tag: antibody catalog number

tag: antibody lot/batch#


title: PRDM9C-G278A_H3K4me3_Input


title: PRDM9C-G278A_H3K4me3_ChIP

value: Millipore/EMD


title: Input Control No Estradiol

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

institute: Newcastle University

description:
Sample name: 0_INPUT
processed data file: MACS_peaks_minus_est.bed
processed data file: SISSRs_peaks_minus_est.bed
processed data file: manual_peaks_minus_est.bed
processed data file: atleast_two_peaks_minus.bed

data_processing:
Reads were mapped to hg18 whole genome using BWA v0.5.8c with parameters: . Alignments were converted to BED format using BEDTools v2.12.0.
Peaks were called using MACS v1.4 using the following parameters: macs14 -t {*_beta.bed} -c {*_input.bed}-n {name} -f BED -g hs --bw=300
Peaks were called using SISSRs using the folllowing parameters: sissrs -i {*_beta.bed} -s 3107677273 -b {*_input.bed} -p {0.001/0.025 minus/plus}
Peaks were called manually by visual inspection in GenomeStudio
Peak overlaps were found using BEDTools: multiIntersectBed -i MACS_peaks_{plus/minus}_est.bed SISSRs_peaks_{plus/minus}_est.bed manual_peaks_{plus/minus}_est.bed | grep ',' > atleast_two_peaks_{plus/minus}.bed
Genome_build: hg18
Supplementary_files_format_and_content: BED format, ChIP-Seq Peaks

source_name: MCF7 Cells

growth_protocol: MCF7 cells were cultured in Minimum Essential Medium Eagle (MEME) (Sigma-Aldrich Inc. M2279) supplemented with 10% (v/v) fetal bovine serum (PAA. A15-151), 1% (v/v) penicillin and streptomycin (PAA. P11-010) and 1% (v/v) glutamine (200mM) (GIBCO. 25030-032), 1% NEAA (Sigma-Aldrich Inc. M7145) in a 37°C incubator with 5% CO2.

extract_protocol:
Cells were fixed with formaldehyde (1% (v/v), Sigma-Aldrich Inc.), neutralised with glycine, washed with 1XPBS and trypsinised (0.05% trypsin in 0.53mM EDTA (Invitrogen Inc. 25300-054). Cells were collected and lysed with cell lysis buffer +PI, collected and resuspended in nuclear lysis buffer +PI. Chromatin was sonicated to between 500-1000bp, 14x15sec cycles, and 5% was removed as “input”. 10.6μg of polyclonal anti-TOP2B antisera was added to protein A magnetic beads (Invitrogen, 100.02D). Chromatin was diluted, incubated with the beads and rotated at 4°C for 4.5hrs. IP’s were washed, Low Salt Buffer, High Salt Buffer, LiCl Buffer and TE Buffer respectively, resuspended in ChIP Elution Buffer+Proteinase K, rotated at 65°C for 2 hours followed by incubation at 95°C for 10 minutes. DNA was then purified using spin columns.
6-21ng/μl of DNA was sent for Illumina ChIP Sequencing.

treatment_protocol: MCF7 cells were grown to ~80% cofluency, treated with 17β-estradiol (10nM, 30 minutes) (Sigma-Aldrich Inc.) or untreated as a control.

tag: agent

value: untreated control

tag: time

value: 0 mins

tag: antibody


title: Inactive inhibitor 6 day treatment, biological rep2

tag: cell type

tag: genotype


title: Topo-2B Antibody 30 mins Estradiol

description:
Sample name: 30_BETA
processed data file: MACS_peaks_plus_est.bed
processed data file: SISSRs_peaks_plus_est.bed
processed data file: manual_peaks_plus_est.bed
processed data file: atleast_two_peaks_plus.bed

tag: cell line

value: Estradiol

value: 30 mins

value: Anti-Top2Beta (3535+30400) [made in-house]


title: Input Control 30 mins Estradiol

description:
Sample name: 30_INPUT
processed data file: MACS_peaks_plus_est.bed
processed data file: SISSRs_peaks_plus_est.bed
processed data file: manual_peaks_plus_est.bed
processed data file: atleast_two_peaks_plus.bed


title: Topo-2B Antibody No Estradiol

description:
Sample name: 0_BETA
processed data file: MACS_peaks_minus_est.bed
processed data file: SISSRs_peaks_minus_est.bed
processed data file: manual_peaks_minus_est.bed
processed data file: atleast_two_peaks_minus.bed


title: PRDM9C-G278A_with_PRDM9A_H3K4me3_ChIP


title: Sus_H3_input

city: New York

first: Eric

last: Nestler

state: NY

address: 1425 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

description: Sample 15

data_processing:
Alignemnt of ChIP-seq: CASAVA 1.8.2 aligned to mm9, and default parameters used.
Segmentation: ChromHMM 1.10, 2 states, window size 200bp, poisson p-value cutoff 1E-6.
Nucleosome events: DANPos 2.1.2, The FDR cutoff was 0.01 for both nucleosome events. For shift events, the cutoff of shifting distance was between 50 and 90 bp. For occupancy events, the FDR of difference between simulation of treatment and control was >0.01.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq wig files were generated by pyicos. The TDF files suffixed with dup2 mean that at most only 2 duplicated reads were kept at the exact same genomic position, generated by rmdup_sorted_bed.pl in diffReps package and igvtools. Segmentation bed files were generated by ChromHMM. Nucleosome events bed were generated by DANPos.

source_name: nucleus accumbens tissue

extract_protocol:
For each ChIP-seq replicate, bilateral 14-gauge NAc punches were pooled from 10 mice.
Tissue was lightly fixed to cross-link DNA with associated proteins, and the material was further sheared (ACF1 and SNF2H) or MNase digested (histone H3) and immunoprecipitated using sheep anti-rabbit magnetic beads (Invitrogen) conjugated to an antibody that specifically recognizes ACF1 (Bethyl), SNF2H, or H3 (Abcam).
Immunoprecipitated DNA and total (input) genomic DNA were prepared for ChIP-seq using an Illumina kit according to the manufacturer’s instructions. Each experimental condition was analyzed with independent biological triplicates. Briefly, each sample underwent end repair followed by addition of an A base to the 3′ end. Proprietary adapters were then ligated to the ends, followed by size selection on a 2% agarose gel. The range of excision was 200–300 bp. After DNA clean up, samples were amplified with 15 (H3) or 19 (ACF1 and SNF2H) cycles of PCR. Amplification and size selection were confirmed with a BioAnalyzer. The resulting libraries were sequenced on an Illumina HiSeq 2500 with 100 bp read length.

treatment_protocol: For the chronic social defeat stress paradigm (CSDS), experimental C57BL/6J mouse was placed into the home cage of a CD1 mouse for 10min during which time it was physically defeated by the CD1 mouse. After the physical interaction, the CD1 and experimental mouse were maintained in sensory contact for 24?hr using a perforated plexiglass partition dividing the resident home cage in two. The experimental mice were exposed to a new CD1 mouse for 10 consecutive days. A social interaction test was performed 24 hr after the last defeat. Mice were placed in an open field which included an interaction zone and two opposing corner zones. A social target (novel CD1 mouse) was placed in a metal meshplastic box in the interaction zone, which allows sensory but not physical interaction. Ethovision XT (Noldus) tracking software was used to measure the time that the test mouse spent in the interaction zone with and without the target CD1 present (2.5 min).

tag: strain

tag: csds and behavior group

value: Susceptible

value: nucleus accumbens cells


title: Con_H3_input

description: Sample 13

value: Control


title: DMSO 6 day treatment, biological rep2


title: Con_H3

description: Sample 10

tag: antibody vendor

value: Abcam

tag: antibody cat. #

tag: antibody lot #


title: Res_H3_input

description: Sample 14

value: Resilient


title: Res_H3

description: Sample 11


title: Sus_H3

description: Sample 12


title: Mxminus_Smc3fplus_ATAC_1

tag: tissue

value: bone marrow

value: c-Kit+ cells

value: Smc3 fl/+


title: Sus_Acf1

description: Sample 9

value: Bethyl Laboratories


title: Con_Acf1

description: Sample 7


title: Res_Acf1

description: Sample 8


title: PRDM9C_H3K4me3_ChIP

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-Seq reads were aligned to the hg19 genome assembly using BWA v.0.5.10
ChIP-Seq reads were filtered to keep only uniquely mapped reads
ChIP-Seq peaks were called using MACS v1.4.2
Genome_build: hg19

tag: cell description

value: embryonic kidney

tag: prdm9 allele


title: Sus1_input

description: Sample 5


title: Sus_SNF2H

description: Sample 6


title: PRDM9A_H3K4me3_Input

tag: ChIP

value: input

tag: antibody manufacturer


title: PRDM9A_H3K4me3_ChIP

value: Millipore/EMD

tag: antibody catalog number

tag: antibody lot/batch#


title: Mxplus_Smc3het_Flt3ITD_RNA_2

description:
Flt3Smc3het_RNA_Seq_1
Cells were purified from whole bone marrow 4-weeks following PIpC injection; mice harbor Mx1-cre, floxed Smc3, and Flt3-ITD alleles

data_processing:
expression levels: Gene-level expression measurements for 23,021 Ensembl mouse genes were reported in fragments per kilobase per million reads (FPKM) by Cufflinks 2.0.0 (http://cufflinks.cbcb.umd.edu/) (Trapnell et al., 2010). Cufflinks assembles transcripts, estimates their abundance, and tests for differential expression and regulation in RNA-Seq samples.  Cufflinks command line-cufflinks --GTF <gtf_file> -q -p 3 -u -b <genome.fa> -o <output directory> <bam_file_from_tophat>
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM files for each sample

molecule: polyA RNA

extract_protocol: Total RNA was isolated using Trizol (Invitrogen), and cDNA was synthesized using the SuperScript First-Strand kit (Invitrogen). Sequencing libraries were constructed using the Nextflex Rapid Directional RNA-seq kit (Bioo Scientific).

value: Smc3 fl/del Flt3-ITD


title: Mxplus_Smc3het_Flt3ITD_RNA_1

description:
Flt3Smc3het_RNA_Seq_0
Cells were purified from whole bone marrow 4-weeks following PIpC injection; mice harbor Mx1-cre, floxed Smc3, and Flt3-ITD alleles


title: PRDM9C_H3K4me3_Input


title: Res_SNF2H

description: Sample 4


title: Mxplus_Flt3ITD_2

description:
Flt3_RNA_Seq_1
Cells were purified from whole bone marrow 4-weeks following PIpC injection; mice harbor Mx1-cre and Flt3-ITD allele


title: Mxplus_Flt3ITD_RNA_1

description:
Flt3_RNA_Seq_0
Cells were purified from whole bone marrow 4-weeks following PIpC injection; mice harbor Mx1-cre and Flt3-ITD allele


title: Mxplus_Smc3het_RNA_1

description:
Smc3het_RNA_Seq_0
Cells were purified from whole bone marrow 4-weeks following PIpC injection; mice harbor Mx1-cre and single floxed Smc3 allele

value: Smc3 del/+


title: Con_SNF2H

description: Sample 2


title: Empty_Vector_H3K4me3_ChIP

value: empty vector


title: Mxminus_Smc3fplus_RNA_1

description:
WT_RNA_Seq_0
Cells were purified from whole bone marrow 4-weeks following PIpC injection; control mice are negative for Mx1-cre allele


title: Mxplus_Smc3het_RNA_2

description:
Smc3het_RNA_Seq_1
Cells were purified from whole bone marrow 4-weeks following PIpC injection; mice harbor Mx1-cre and single floxed Smc3 allele


title: Mxminus_Smc3fplus_RNA_2

description:
WT_RNA_Seq_1
Cells were purified from whole bone marrow 4-weeks following PIpC injection; control mice are negative for Mx1-cre allele


title: Res1_input

description: Sample 3


title: Con1_input

description: Sample 1


title: Ring1B I53A/I53A H3K27me3 ChIP rep2

status: Public on Sep 20 2015

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

institute: The University of Edinburgh

description: H3K27me3 ChIP in E14Tg2a-derived Ring1B I53A/I53A mouse ESCs

data_processing:
Base calling was performed using casava (version 1.8.2).
Reads were trimmed with Trim Galore! v0.2.7. The -q 30 option was used to remove reads with a PHRED score lower than 30 using cutadapt v1.2.1.
Trimmed reads were mapped to the mouse genome (mm10) using bowtie2.1.0 with the following arguments:  --local -D 20 -R 3 -N 1 -L 20 -i S,1,0.50.
The obtained SAM files were processed using HOMER v4.3. HOMER tag directories were created using the makeTagDirectory tool with the options -unique and -fragLength 150. These tag directories were used to create bedgraphs for UCSC visualisation (bedGraphs); for identification of enriched regions (Homer peak files); and for quantifications shown in the manuscript. Bedgraphs were created using the makeUCSCfile tool with default options. Enriched regions were identified for ChIP-seq samples using the findPeaks tool with the options -style histone and -minDist 500 with the input sequences as controls.
Sites of robust Ring1b and H3K27me3 enrichment were identified as Homer peaks which were consitently identified in both biological replicate ChIPs (included as supplementary files - Strict peak file)
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraphs were made using HOMER tools and allow the mapped reads to be visualised in a genome browser. Peak files contain the output of the findPeaks tool from HOMER tools. The set of strict peaks (supplementary files) was produced by finding regions of at least 500 bp which are identified as peaks in each replicate of an experiment.

source_name: Ring1B I53A/I53A mESCs

growth_protocol: ES cells were grown in GMEM supplemented with 10 % fetal bovine serum (FBS), 1,000 units/ml LIF, non-essential amino acids, sodium pyruvate, 2-β-mercaptoethanol, L-glutamine and Penicillin/Streptomycin.

extract_protocol:
Trypsinised ESCs (20 million) were washed twice in PBS. Cells were resuspended in 250ml of PBS and fixed by the addition of an equal volume of PBS containing 2% methanol free formaldehyde (Thermo Scientific Pierce PN28906; final concentration of 1%) and incubated at RT for 10 mins. Fixation was stopped by 5 min incubation with 125mM glycine at room temperature. Cells were washed in PBS prior to lysis. All of the buffers were supplemented with the following additives just prior to use: 0.2 mM PMSF, 1 mM DTT, 1x Protease inhibitors (Calbiochem, 539134-1SET). Cell pellets were resuspended in lysis buffer 1 (50mM Tris-HCl pH 8.1, 10mM EDTA and 20% SDS) and incubated for 10 min at 4°C. Lysates were diluted 1:10 in ChIP dilution buffer (0.1% Triton X-100, 2mM EDTA, 150mM NaCl, 20mM and Tris-HCl pH8.1) and sonicated using a chilled Bioruptor (Diagenode; 40x 1 min cycles of 30sec on / 30sec off on ‘high’ setting at 4°C). The sonicated extract was pre-cleared by centrifugation at 16000g for 10 min at 4°C. The supernatant was transferred to a fresh tube and supplemented with BSA and triton X-100 to a final concentration of 25mg/ml and 1% respectively. A sample of the chromatin was retained as an input reference. Antibodies were pre-coupled to a 1:1 mix of protein A and G Dynabeads (Life Technologies; 10001D and 10004D respectively) at a ratio of 1mg antibody per 30ml of dynabeads. 12 million and 6 million cell equivalents of lysate were added to 10ug of Anti-Ring1B (MBL D139-3) or 5ug anti-H3K27me3 (Millipore 07-449) respectively and incubated for 10hrs on a rotating wheel at 4ºC. Bead-associated immune complexes were washed sequentially with wash buffers A, B and C for 10 mins at 4ºC on a rotating wheel followed by 2 washes in TE buffer at RT (wash buffer A - 1% Triton X-100, 2mM EDTA, 150mM NaCl, 20mM and Tris-HCl pH8.1; wash buffer B - 1% Triton X-100, 0.1% Sodium-Deoxycolate, 0.1% SDS, 1mM EDTA, 500mM NaCl, 20mM and Tris-HCl pH8.1; wash buffer C – 1% NP40, 0.1% Sodium-Deoxycolate, 1mM EDTA, 250mM LiCl, 20mM and Tris-HCl pH8.1). Chromatin was released from the beads by incubation with elution buffer (0.1 M NaHCO3 and 1 % SDS) for 15 mins at 37 ºC followed by the addition of RNaseA and Tris pH6.8 (final concentration of 20mg/ml and 100mM respectively) and incubation at 65ºC for 2 hours following by the addition of 50mg of proteinase K and incubation at 65ºC overnight to degrade proteins and reverse the cross-links. Dynabeads were removed using a magnetic rack and the chromatin purified using PCR Purification columns (Qiagen) according to manufacturer’s instructions.
libraries were prepared as previously described (Bowman et al., 2013 - PMID:23837789) with the following modifications. No purification was performed between the A-tailing reaction and the ligation reactions; instead the ligation was supplemented with ligation reagents (400 U of T4 DNA ligase (NEB), 1x buffer 2 (NEB), 7.5% PEG-6000, 1mM ATP and 13.3nM of annealed Illumina adaptors (AU) and incubated at 25°C for 90min. Size selection purifications following the ligation and amplification PCR steps were performed with 1x and 0.8x reaction volumes of Agencourt AMPure XP beads (Beckman Coulter - A63880). Six samples were multiplexed per Hi-seq lane.

tag: gender

value: male

value: Embryonic Stem Cells

value: H3K27me3 (Millipore 07-449)


title: E14Tg2a H3K27me3 ChIP rep1

description: H3K27me3 ChIP in E14Tg2a mouse ESCs

source_name: E14Tg2a mESCs

tag: antibody


title: Ring1B I53A/I53A Ring1B ChIP rep2

description: Ring1B ChIP in E14Tg2a-derived Ring1B I53A/I53A mouse ESCs

tag: cell type

value: Ring1B (MBL D139-3)


title: E14Tg2a Ring1B ChIP rep2

description: Ring1B ChIP in E14Tg2a mouse ESCs


title: E14Tg2a H3K27me3 ChIP rep2

description: H3K27me3 ChIP in E14Tg2a mouse ESCs


title: Ring1B I53A/I53A input rep2

description: Input DNA from E14Tg2a-derived Ring1B I53A/I53A mouse ESCs


title: E14Tg2a Ring1B ChIP rep1

description: Ring1B ChIP in E14Tg2a mouse ESCs


title: Ring1B I53A/I53A H3K27me3 ChIP rep1


title: Ring1B I53A/I53A input rep1


title: Ring1B I53A/I53A Ring1B ChIP rep1


title: E14Tg2a input rep2

description: Input DNA from E14Tg2a mouse ESCs


title: E14Tg2a input rep1

description: Input DNA from E14Tg2a mouse ESCs


title: Control

city: Istanbul

first: Ozgur

last: Cakir

address: Vezneciler

country: Turkey

institute: Istanbul University

data_processing:
Trinity program (release-20130225, http://trinityrnaseq.sourceforge.net/)
Gene Indices Clustering Tools (TGICL, version 2.1)
Phrap (Release 23.0)  (http://www.phrap.org/)
blastx alignment (evalue < 0.00001) in NR, Swiss-Prot, KEGG and COG databases.
SOAP (Release 2.21, http://soap.genomics.org.cn/soapaligner.html), using the parameters “-m 0 -x 500 -s 40 -l 35 -v 5 -r 1”. FPKM (Fragments Per kb per Million reads) method was done.
Supplementary_files_format_and_content: xls file with FPKM values and fold change values

organism: Astragalus chrysochlorus

source_name: callus culture cells

growth_protocol: control callus tissues grown in MS medium supplemented with 0,5 mg/l 2,4-D

extract_protocol:
RNA was extracted by Qiagen total RNA isolation system (RNeasy Plant Mini Kit, 74904, Qiagen) according to the manufacturer's protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Se treated ones also had 5 mg/l Sodium Selenate in medium

value: callus

tag: treatment

value: Control


title: Empty_Vector_H3K4me3_Input


title: Help2

city: Lund

first: Lovisa

last: Heyman-Lindén

address: Klinikgatan 28

country: Sweden

institute: Lund University

description: HpaII test for HELP-tagging

data_processing:
Images generated by the Illumina sequencer were analyzed by Illumina pipeline software (ELAND - 1.7.0).  Initial data processing was performed using the default read length of 100 bp, after which we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).  The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the mm9 freeze of the mouse genome at the UCSC genome browser.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.  To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Illumina Casava was used for basecalling.
After the sequence data was obtained from Illumina HiSeq 2500, we isolated the sequences in which we found adapter-tags on the 3’-end, replaced the tag sequence with a poly(N) sequence of the same length), and re-ran the Illumina ELAND pipeline again  (ver.) on these sequences with the sequence length set at 27 bp (the 2-28 bp subsequence).
The data within the ELAND_extended.txt files were used for counting the number of aligned sequences adjacent to each CCGG (HpaII/MspI) site annotated in the mm9 freeze of the mouse genome at the UCSC genome browser.  We permitted up to two mismatches in each sequence, and allowed a sequence to align to up to a maximum of 10 locations within the genome.  For non-unique alignments, a sequence was assigned a partial count for each aligment location amounting to 1/n, where n represents the total number of aligned positions.
To normalize the data between experiments, the number of sequences associated with each HpaII site was divided by the total number of sequences (including partial counts) aligning to all HpaII sites in the same sample.
Genome_build: mm9
Supplementary_files_format_and_content: Format: wiggle track; content: methylation level for each CpG site

source_name: Mouse liver

extract_protocol:
High molecular weight genomic DNA was extracted from frozen liver tissue using phenol-chloroform extraction.
Two custom adapters were created for HELP-tagging, referred to as AE and AS.  As well as an Illumina adapter sequence, adapter AE contains an EcoP15I recognition site and a T7 promoter sequence.  Adapter AS contains an Illumina sequencing primer sequence.  Five micrograms of genomic DNA were digested with HpaII in 200 μl reactions and purified by phenol/chloroform extraction followed by ethanol precipitation.  The digested genomic DNA was ligated to adapter AE using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 3 μg of HpaII-digested DNA, 0.1 μl of Adapter AE (1 μM), 3 μl of Quick Ligase in a final volume of 50 μl).  After AE ligation, the products were purified using AMpure XP (Agencort), then digested with EcoP15I (NEB).  The restriction fragments were end-repaired to inhibit to dimerization of adapters, and tailed with a single dA, at the 3’ end.  After the dA tailing reaction, adapter AS was ligated to the dA-tailed fragments using an NEB Quick Ligation Kit (25 μl of 2x Quick ligase buffer, 2.5 μl of Adapter AS (10 μM), 2.5 μl of Quick Ligase in a final volume 50 μl).  After ligation, products were purified using the MinElute PCR purification kit (Qiagen) and in vitro-transcribed using MEGAshortscript (Ambion).  Following in vitro transcription, products were purified with an RNeasy clean-up kit (Qiagen) before reverse transcription was performed using the SuperScript III kit (Invitrogen).  The first strand cDNA produced was used as a template for PCR using the following conditions: 96°C for 2 minutes, then 18 cycles of 96°C for 15 seconds and 72°C for 15 seconds followed by 5 minutes at 72°C for the final extension.  After PCR, the library was purified using a QIAQuick PCR clean-up kit (Qiagen).

value: liver

tag: diet

value: High-fat diet + Lingonberries


title: Help3

description: HpaII test for HELP-tagging

tag: strain


title: Se-treated

value: Se-treated


title: Help7

description: HpaII test for HELP-tagging

value: High-fat diet


title: Normal-2

status: Public on Sep 19 2015

city: Shanghai

first: Xianghua

last: Yi

address: NO.389, Xincun Rd, Putuo distrct

department: pathology

institute: Tongji hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
sequencing libraries were then sequenced using the Illumina HiSeq2000 platform. From reads averaging 50 bp in length, we generated 9.0 ± 1.5 million reads per sample. After that, we aligned the reads to the human reference genome (GrCH37, Ensembl build 74) using Tophat version 2.0.12 (ref, 2011), yielding an average mapping rate of 94.8 ± 2.1%.
Gene expression levels, which represented as fragments per kilo-base per million mapped reads (FPKM), were obtained for 63,783 genes/transcripts annotated using Ensemble GrCH37 database release 74.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: lung

extract_protocol:
Total RNA was extracted using Trizol reagent. library construction following standard TruSeq RNA sample preparation v2 protocol (Illumina).
library construction following standard TruSeq RNA sample preparation v2 protocol (Illumina).
The sequencing libraries were sequenced using the Illumina HiSeq2000 platform.

value: nomral lung tissue adjacent to benign pulmonary tumors

tag: age


title: Normal-4


title: Normal-3


title: Normal-1


title: Help8

description: HpaII test for HELP-tagging


title: INSIP-2

value: idiopathic nonspecific interstitial pneumonia

value: female


title: INSIP-3


title: INSIP-1


title: IPF-2

value: idiopathic pulmonary fibrosis


title: Help6

description: HpaII test for HELP-tagging


title: Help5

description: HpaII test for HELP-tagging


title: IPF-1


title: Pt_mRCC_SC_93

status: Public on Sep 18 2015

city: Seoul

first: Kyu-Tae

address: Irwon-Ro 81

department: Samsung Genome Institute

institute: Samsung Medical Center

description: scRNA-seq

data_processing:
For PDX samples, RNA-seq reads only mapped to the mouse genome reference (mm10) were removed. Then, sequencing reads were aligned to the human genome reference (hg19) together with splice junction information of each sample using the 2-pass mode of STAR_2.4.0d (Dobin et al., Bioinformatics 2012). Transcripts Per Million (TPM) was quantified by implementing RSEM v1.2.18 (Li et al., BMC Bioinformatics 2011) in default mode with Genecode v.19 annotation.
Genome_build: hg19
Supplementary_files_format_and_content: Each row of the tab-delimited text file includes ENSEMBL gene ID,ENSEMBL transcript ID, transcript length, effective_length, expected_count, TPM, FPKM for samples.

source_name: patient, metastatic RCC_36

growth_protocol: This study was carried out in accordance with the principles of the Declaration of Helsinki, and approved by The Samsung Medical Center (Seoul, Korea) Institutional Review Board (IRB) (no. 2010-04-004). A participant in this study gave written informed consent for research and publication of the results. Animal experiments were conducted in accordance with the Institute for Laboratory Animal Research Guide for the Care and Use of Laboratory Animals and within the protocols approved by the appropriate IRB at the Samsung Medical Center. After validating the origin of each xenograft by short tandem repeat DNA fingerprinting, sacrified tumor tissues together with prepared patient metastasis tumor samples were dissociated to implement C1™ Single-Cell Auto Prep System.

extract_protocol:
In order to isolate single-cells and amplify initial RNA content enough to transcriptome sequencing, we adopted the C1TM Single-Cell Auto Prep System (Fluidigm, CA, USA) with the SMARTer kit (Clontech, CA, USA). Cells were captured on the C1 chip (17-25 μm) and determined as a live single cell by fluorescence microscopic observation. Quantity and quality of amplified cDNAs from individual single cells were checked by Qubit® 2.0 Fluorometer (Life Technologies, CA, USA) and 2100 Bioanalyzer (Agilent Inc., CA, USA). RNAs from bulk cell samples were also amplified using a SMARTer kit with 10 ng of starting material. For WES, gDNAs were prepared using QIAamp® DNA Mini kit (QIAGEN, CA, USA). Exome sequencing was carried using the SureSelect XT Human All Exon V5 kit (Agilent Inc., CA, USA), according to the manufacturer’s standard protocol.
Libraries were prepared using the Nextera XT DNA Sample Prep Kit (Illumina, CA, USA) following the manufacturer’s instruction, assayed the quantity and quality, pooled, and then sequenced on the HiSeq 2500 (Illumina) using the 100bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina) at the Samsung Genome Institute (Seoul, Korea).  Sequencing of the exome library was carried out on the HiSeq 2500 (Illumina, CA, USA) using the 100bp paired-end mode of the TruSeq Rapid PE Cluster kit and TruSeq Rapid SBS kit (Illumina) at the Samsung Genome Institute (Seoul, Korea).

value: metastatic renal cell carcinoma

tag: cell source

value: patient


title: Pt_mRCC_SC_90

description: scRNA-seq

source_name: patient, metastatic RCC_34


title: Help1

description: HpaII test for HELP-tagging


title: Help4

description: HpaII test for HELP-tagging


title: IPF-3


title: Normal-5


title: IPF-4


title: Pt_mRCC_SC_87

description: scRNA-seq

source_name: patient, metastatic RCC_32


title: Pt_mRCC_SC_85

description: scRNA-seq

source_name: patient, metastatic RCC_30


title: Pt_mRCC_SC_84

description: scRNA-seq

source_name: patient, metastatic RCC_29


title: Pt_mRCC_SC_75

description: scRNA-seq

source_name: patient, metastatic RCC_26


title: Pt_mRCC_SC_81

description: scRNA-seq

source_name: patient, metastatic RCC_28


title: Pt_mRCC_SC_79

description: scRNA-seq

source_name: patient, metastatic RCC_27


title: Pt_mRCC_SC_61

description: scRNA-seq

source_name: patient, metastatic RCC_22


title: Pt_mRCC_SC_69

description: scRNA-seq

source_name: patient, metastatic RCC_24


title: Pt_mRCC_SC_71

description: scRNA-seq

source_name: patient, metastatic RCC_25


title: Pt_mRCC_SC_64

description: scRNA-seq

source_name: patient, metastatic RCC_23


title: Pt_mRCC_SC_59

description: scRNA-seq

source_name: patient, metastatic RCC_21


title: Pt_mRCC_SC_58

description: scRNA-seq

source_name: patient, metastatic RCC_20


title: Pt_mRCC_SC_92

description: scRNA-seq

source_name: patient, metastatic RCC_35


title: Pt_mRCC_SC_86

description: scRNA-seq

source_name: patient, metastatic RCC_31


title: Pt_mRCC_SC_39

description: scRNA-seq

source_name: patient, metastatic RCC_15


title: Pt_mRCC_SC_30

description: scRNA-seq

source_name: patient, metastatic RCC_12


title: Pt_mRCC_SC_33

description: scRNA-seq

source_name: patient, metastatic RCC_13


title: Pt_mRCC_SC_53

description: scRNA-seq

source_name: patient, metastatic RCC_17


title: Pt_mRCC_SC_36

description: scRNA-seq

source_name: patient, metastatic RCC_14


title: Pt_mRCC_SC_56

description: scRNA-seq

source_name: patient, metastatic RCC_18


title: Pt_mRCC_SC_23

description: scRNA-seq

source_name: patient, metastatic RCC_10


title: Pt_mRCC_SC_88

description: scRNA-seq

source_name: patient, metastatic RCC_33


title: Pt_mRCC_SC_21

description: scRNA-seq

source_name: patient, metastatic RCC_9


title: Pt_mRCC_SC_12

description: scRNA-seq

source_name: patient, metastatic RCC_7


title: Pt_mRCC_SC_11

description: scRNA-seq

source_name: patient, metastatic RCC_6


title: Pt_mRCC_SC_17

description: scRNA-seq

source_name: patient, metastatic RCC_8


title: Pt_mRCC_SC_57

description: scRNA-seq

source_name: patient, metastatic RCC_19


title: Pt_mRCC_SC_05

description: scRNA-seq

source_name: patient, metastatic RCC_4


title: Pt_mRCC_SC_01

description: scRNA-seq

source_name: patient, metastatic RCC_2


title: Pt_mRCC_SC_43

description: scRNA-seq

source_name: patient, metastatic RCC_16


title: Pt_mRCC_Pooled

description: bulk RNA-seq

source_name: patient, metastatic RCC_1


title: PDX_pRCC_SC_94

description: scRNA-seq

source_name: PDX, primary RCC_48

value: primary renal cell carcinoma

value: patient-derived xenograft


title: PDX_pRCC_SC_93

description: scRNA-seq

source_name: PDX, primary RCC_47


title: PDX_pRCC_SC_90

description: scRNA-seq

source_name: PDX, primary RCC_45


title: Pt_mRCC_SC_24

description: scRNA-seq

source_name: patient, metastatic RCC_11


title: PDX_pRCC_SC_79

description: scRNA-seq

source_name: PDX, primary RCC_40


title: PDX_pRCC_SC_78

description: scRNA-seq

source_name: PDX, primary RCC_39


title: PDX_pRCC_SC_91

description: scRNA-seq

source_name: PDX, primary RCC_46


title: Pt_mRCC_SC_10

description: scRNA-seq

source_name: patient, metastatic RCC_5


title: PDX_pRCC_SC_75

description: scRNA-seq

source_name: PDX, primary RCC_38


title: CML LT-KLS1

city: Dongjak-Gu

first: Junil

state: Seoul

address: 369 Sangdo-Ro

department: Department of Bioinformatics

institute: SOONGSIL UNIVERSITY

description: CML LT-KLS

data_processing:
Illumina Hiseq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome using DNAnexus
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using DNAnexus.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Bone marrow

extract_protocol:
LT-stem cells, ST-stem cells and KLS- progenitor cells isolated from total normal haematopoietic cells, as well as CML cell subsets, were directly sorted into 200μl Isogene (Nippon Gene) solution. RNA extraction and sequencing were performed by Hokkaido System Science Co. Ltd. (Sapporo, Japan).
Libraries were constructed from total RNA using the SMARTer Ultra Low Input RNA Kit for Illumina Sequencing (Takara Clontech).

tag: diagnosis

value: chronic myeloid leukemia

value: long-term stem cells


title: PDX_pRCC_SC_89

description: scRNA-seq

source_name: PDX, primary RCC_44


title: PDX_pRCC_SC_70

description: scRNA-seq

source_name: PDX, primary RCC_35


title: PDX_pRCC_SC_73

description: scRNA-seq

source_name: PDX, primary RCC_37


title: Pt_mRCC_SC_03

description: scRNA-seq

source_name: patient, metastatic RCC_3


title: CML LT-KLS2

description: CML LT-KLS


title: PDX_pRCC_SC_72

description: scRNA-seq

source_name: PDX, primary RCC_36


title: Normal KLS- 2 months old

description: Normal KLS- 2 months old

value: healthy

value: KLS-progenitor cells


title: PDX_pRCC_SC_68

description: scRNA-seq

source_name: PDX, primary RCC_34


title: Normal ST-KLS 2 months old

description: Normal ST-KLS 2 months old

value: short-term stem cells


title: PDX_pRCC_SC_67

description: scRNA-seq

source_name: PDX, primary RCC_33


title: Normal LT-KLS 6 months old

description: Normal LT-KLS 6 months old


title: PDX_pRCC_SC_66

description: scRNA-seq

source_name: PDX, primary RCC_32


title: Normal LT-KLS 2 months old

description: Normal LT-KLS 2 months old


title: PDX_pRCC_SC_88

description: scRNA-seq

source_name: PDX, primary RCC_43


title: PDX_pRCC_SC_84

description: scRNA-seq

source_name: PDX, primary RCC_41


title: PDX_pRCC_SC_65

description: scRNA-seq

source_name: PDX, primary RCC_31


title: PDX_pRCC_SC_58

description: scRNA-seq

source_name: PDX, primary RCC_26


title: PDX_pRCC_SC_59

description: scRNA-seq

source_name: PDX, primary RCC_27


title: PDX_pRCC_SC_62

description: scRNA-seq

source_name: PDX, primary RCC_30


title: PDX_pRCC_SC_60

description: scRNA-seq

source_name: PDX, primary RCC_28


title: PDX_pRCC_SC_57

description: scRNA-seq

source_name: PDX, primary RCC_25


title: PDX_pRCC_SC_56

description: scRNA-seq

source_name: PDX, primary RCC_24


title: PDX_pRCC_SC_55

description: scRNA-seq

source_name: PDX, primary RCC_23


title: PDX_pRCC_SC_61

description: scRNA-seq

source_name: PDX, primary RCC_29


title: CML KLS-

description: CML KLS-

source_name: Bone marrow


title: CML ST-KLS

description: CML ST-KLS


title: PDX_pRCC_SC_52

description: scRNA-seq

source_name: PDX, primary RCC_21


title: PDX_pRCC_SC_53

description: scRNA-seq

source_name: PDX, primary RCC_22


title: PDX_pRCC_SC_50

description: scRNA-seq

source_name: PDX, primary RCC_19


title: PDX_pRCC_SC_51

description: scRNA-seq

source_name: PDX, primary RCC_20


title: PDX_pRCC_SC_29

description: scRNA-seq

source_name: PDX, primary RCC_12


title: PDX_pRCC_SC_35

description: scRNA-seq

source_name: PDX, primary RCC_14


title: PDX_pRCC_SC_34

description: scRNA-seq

source_name: PDX, primary RCC_13


title: PDX_pRCC_SC_46

description: scRNA-seq

source_name: PDX, primary RCC_17


title: PDX_pRCC_SC_37

description: scRNA-seq

source_name: PDX, primary RCC_16


title: PDX_pRCC_SC_27

description: scRNA-seq

source_name: PDX, primary RCC_10


title: PDX_pRCC_SC_49

description: scRNA-seq

source_name: PDX, primary RCC_18


title: PDX_pRCC_SC_28

description: scRNA-seq

source_name: PDX, primary RCC_11


title: PDX_pRCC_SC_10

description: scRNA-seq

source_name: PDX, primary RCC_5


title: PDX_pRCC_SC_13

description: scRNA-seq

source_name: PDX, primary RCC_6


title: PDX_pRCC_SC_03

description: scRNA-seq

source_name: PDX, primary RCC_2


title: PDX_pRCC_SC_06

description: scRNA-seq

source_name: PDX, primary RCC_4


title: PDX_pRCC_SC_05

description: scRNA-seq

source_name: PDX, primary RCC_3


title: PDX_pRCC_SC_14

description: scRNA-seq

source_name: PDX, primary RCC_7


title: PDX_pRCC_SC_16

description: scRNA-seq

source_name: PDX, primary RCC_8


title: PDX_pRCC_Pooled

description: bulk RNA-seq

source_name: PDX, primary RCC_1


title: PDX_mRCC_SC_95

description: scRNA-seq

source_name: PDX, metastatic RCC_37


title: PDX_mRCC_SC_94

description: scRNA-seq

source_name: PDX, metastatic RCC_36


title: PDX_mRCC_SC_93

description: scRNA-seq

source_name: PDX, metastatic RCC_35


title: PDX_mRCC_SC_92

description: scRNA-seq

source_name: PDX, metastatic RCC_34


title: PDX_mRCC_SC_90

description: scRNA-seq

source_name: PDX, metastatic RCC_33


title: PDX_mRCC_SC_89

description: scRNA-seq

source_name: PDX, metastatic RCC_32


title: PDX_mRCC_SC_88

description: scRNA-seq

source_name: PDX, metastatic RCC_31


title: PDX_pRCC_SC_36

description: scRNA-seq

source_name: PDX, primary RCC_15


title: PDX_mRCC_SC_87

description: scRNA-seq

source_name: PDX, metastatic RCC_30


title: PDX_pRCC_SC_24

description: scRNA-seq

source_name: PDX, primary RCC_9


title: PDX_pRCC_SC_87

description: scRNA-seq

source_name: PDX, primary RCC_42


title: PDX_mRCC_SC_80

description: scRNA-seq

source_name: PDX, metastatic RCC_27


title: PDX_mRCC_SC_70

description: scRNA-seq

source_name: PDX, metastatic RCC_24


title: PDX_mRCC_SC_79

description: scRNA-seq

source_name: PDX, metastatic RCC_26


title: PDX_mRCC_SC_86

description: scRNA-seq

source_name: PDX, metastatic RCC_29


title: PDX_mRCC_SC_81

description: scRNA-seq

source_name: PDX, metastatic RCC_28


title: PDX_mRCC_SC_64

description: scRNA-seq

source_name: PDX, metastatic RCC_21


title: PDX_mRCC_SC_68

description: scRNA-seq

source_name: PDX, metastatic RCC_22


title: PDX_mRCC_SC_69

description: scRNA-seq

source_name: PDX, metastatic RCC_23


title: PDX_mRCC_SC_63

description: scRNA-seq

source_name: PDX, metastatic RCC_20


title: PDX_mRCC_SC_60

description: scRNA-seq

source_name: PDX, metastatic RCC_18


title: PDX_mRCC_SC_56

description: scRNA-seq

source_name: PDX, metastatic RCC_17


title: PDX_mRCC_SC_61

description: scRNA-seq

source_name: PDX, metastatic RCC_19


title: PDX_mRCC_SC_52

description: scRNA-seq

source_name: PDX, metastatic RCC_16


title: PDX_mRCC_SC_44

description: scRNA-seq

source_name: PDX, metastatic RCC_15


title: PDX_mRCC_SC_20

description: scRNA-seq

source_name: PDX, metastatic RCC_11


title: PDX_mRCC_SC_34

description: scRNA-seq

source_name: PDX, metastatic RCC_13


title: PDX_mRCC_SC_14

description: scRNA-seq

source_name: PDX, metastatic RCC_9


title: PDX_mRCC_SC_41

description: scRNA-seq

source_name: PDX, metastatic RCC_14


title: PDX_mRCC_SC_21

description: scRNA-seq

source_name: PDX, metastatic RCC_12


title: PDX_mRCC_SC_12

description: scRNA-seq

source_name: PDX, metastatic RCC_8


title: PDX_mRCC_SC_06

description: scRNA-seq

source_name: PDX, metastatic RCC_6


title: PDX_mRCC_SC_77

description: scRNA-seq

source_name: PDX, metastatic RCC_25


title: PDX_mRCC_SC_03

description: scRNA-seq

source_name: PDX, metastatic RCC_3


title: PDX_mRCC_SC_04

description: scRNA-seq

source_name: PDX, metastatic RCC_4


title: PDX_mRCC_SC_05

description: scRNA-seq

source_name: PDX, metastatic RCC_5


title: PDX_mRCC_SC_01

description: scRNA-seq

source_name: PDX, metastatic RCC_2


title: PDX_mRCC_Pooled

description: bulk RNA-seq

source_name: PDX, metastatic RCC_1


title: p65_Compound A

first: Xun

last: Lan

address: 318 Campus Dr. Room S240

department: Genetics

data_processing:
ChIP-exo Alignment: Sequence reads were obtained and mapped to the human (hg19) genomes using the Bowtie. All reads mapping with two or fewer mismatches were retained. Only reads with unique mapping location is used for downstream analysis.
RNA-Seq: Read alignment was conducted using TopHat 2.0.13, and relative transcript abundances and differentially expressed genes were determined using Partek Genomics Suite (v6.6) with default settings.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files are in bigwig format. Each file is the reads counts of all 5 bp bins in the human genome for that sample.

source_name: p65_Compound A

growth_protocol: The TNBC cell line MDA-MB-231 were obtained from the American Type Culture Collection, and cultured in DMEM 10% FBS.

extract_protocol:
After treatment with 100 nM Dex, 10 uM CpdA or vehicle for 1 h, MDA-MB-231 cells were crosslinked with 1% formaldehyde for 10 min. Sonicated chromatin was enriched by immunoprecipatation with an anti-GR antibody. MDA-MB-231 cells were treated with 100 nM Dex, or 10 M CpdA for 2h and 4h, respectively. RNA was extracted using the RNeasy Mini Kit.
For ChIP-exo, T4 DNA polymerase, T4 PNK, and Klenow DNA Polymerase were used together for end polishing. The ligation step was performed with less reducing agent. Protein A Dynal magnetic beads were washed using modified RIPA buffer (50mM Tris-HCL pH 7.8, 1mM EDTA, 0.25% Na Deoxycholate, 1% NP-40, 0.5M LiCl). The library was amplified with only 10 or 12 PCR cycles, and prepared without gel-based size selection. For RNA-seq, libraries were constructed using the Illumina Truseq RNA Sample Prep Kit according to the manufacturer’s protocol.

treatment_protocol: For hormone responsive experiments, MDA-MB-231 cells were maintained in phenol red-free RPMI medium with 5% charcoal-stripped FBS for 3 days, and then treated with vehicle and different ligands.

tag: cell line

tag: cancer

value: Breast adenocarcinoma

tag: type

value: TNBC

tag: chip antibody

value: NFκB p65 Antibody (C-20) from Santa Cruz Biotechnology


title: p65_Dexamethasone


title: PDX_mRCC_SC_15

description: scRNA-seq

source_name: PDX, metastatic RCC_10


title: RNA_Compound A 4h_2

description: RNA-seq replicate 2

source_name: RNA_Compound A 4h_2


title: AP1_Dexamethasone

value: c-Jun Antibody (H-79) from Santa Cruz Biotechnology


title: RNA_Dexamethasone 4h_2

description: RNA-seq replicate 2

source_name: RNA_Dexamethasone 4h_2


title: PDX_mRCC_SC_08

description: scRNA-seq

source_name: PDX, metastatic RCC_7


title: RNA_Compound A 4h_1

description: RNA-seq replicate 1

source_name: RNA_Compound A 4h_1


title: RNA_Compound A 2h_1

description: RNA-seq replicate 1

source_name: RNA_Compound A 2h_1


title: GR_Compound_A_1

description:
TNBC
ChIP-exo replicate 1

data_processing:
ChIP-exo Alignment: Sequence reads were obtained and mapped to the human (hg19) genomes using the Bowtie. All reads mapping with two or fewer mismatches were retained. Only reads with unique mapping location is used for downstream analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Processed files are in bigwig format. Each file is the reads counts of all 5 bp bins in the human genome for that sample.

source_name: MDA-MB-231 cells

extract_protocol:
After treatment with 100 nM Dex, 10 uM CpdA or vehicle for 1 h, MDA-MB-231 cells were crosslinked with 1% formaldehyde for 10 min. Sonicated chromatin was enriched by immunoprecipatation with an anti-GR antibody.
For ChIP-exo, T4 DNA polymerase, T4 PNK, and Klenow DNA Polymerase were used together for end polishing. The ligation step was performed with less reducing agent. Protein A Dynal magnetic beads were washed using modified RIPA buffer (50mM Tris-HCL pH 7.8, 1mM EDTA, 0.25% Na Deoxycholate, 1% NP-40, 0.5M LiCl). The library was amplified with only 10 or 12 PCR cycles, and prepared without gel-based size selection.

value: Glucocorticoid Receptor (D8H2) XP® Rabbit mAb #3660 from CST


title: GR_Dexamethasone_1

description:
TNBC
ChIP-exo replicate 1


title: GR_Dexamethasone_2

description:
TNBC
ChIP-exo replicate 2


title: RNA_Dexamethasone 2h_1

description: RNA-seq replicate 1

source_name: RNA_Dexamethasone 2h_1


title: p65_Vehicle


title: AP1_Compound A

source_name: AP1_Compound A


title: RNA_Vehicle_1

description: RNA-seq replicate 1


title: GR_Vehicle_1

description:
TNBC
ChIP-exo replicate 1


title: RNA_Vehicle_2

description: RNA-seq replicate 2