title: Day 4, Animal 86

description:
demultiplex
Sample name: 86-4_3_exp_day4

value: Animal 86

tag: cell type

tag: vaccine

tag: vaccine administration

value: intramuscular

tag: time

value: Day 4

tag: serologic response status

value: vaccinated, not protected


title: Scer_SSII_DMS_denatured_genomeWide

status: Public on Sep 16 2016

type: SRA

city: Cambridge

first: Silvi

last: Rouskin

state: MA

address: 455 Main Street

country: USA

institute: Whitehead Institute

library_source: transcriptomic

data_processing:
Illumina bcl2fastq v2.17 was used for base-calling.
Alignments were performed using Tophat v2.1.0 with bowtie2 and the following options for 50bp sequencing run: --no-novel-juncs -N 5 --read-gap-length 7 --read-edit-dist 7 --max-insertion-length 5 --max-deletion-length 5 -g 3
Non-uniquely mapping reads were removed. Additionally, 2nt or 5nt were removed from the 5' end of each read for TGIRT and SSii data, respectively, due non-template addition during reverse transcription.
Mismatch locations were called, and mismatches located within 3nt of an insertions or deletion were masked for future analysis.
In the case of data with a unique molecular index (UMI), sequencing reads were filtered for length >100nt and for unique reads only. For data generated with NexteraXT tagmentation, alignments to both strands were combined.
Genome_build: Saccharomyces cerevisiae assembly R64 (UCSC: sacCer3) or, for human data, the longest RefSeq isoforms from hg19.
Supplementary_files_format_and_content: Tab-delimited files have three columns, representing the name of the aligned sequenced (either chromosome or transcript name), the position within that sequence, and the ratiometric DMS-MaPseq value calculated as the number of mismatches divided by the total sequencing depth at each postion. The position number directly indicates the DMS modified position starting at 1.

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: BY4741 cells

growth_protocol: For the in vivo DMS treatment of S. cerevisiae, DMS was added directly to the growing log phase yeast culture at 5% for 3-4 min. 25% BME, 30% isoamyl alcholol was used to quench the DMS. Cells were lysed with SDS, and RNA was isolated with hot acid phenol. For denatured samples, RNA was first extracted and then heated to 95deg for treatment with DMS.

extract_protocol:
Total RNA was extracted using hot acid phenol. mRNA was randomly fragmented using Ambion fragmentation reagents, followed by PNK, and ligation using T4 K227Q truncated RNA ligase. rRNA was depleted post-ligation using RiboZero (Epicentre), and reverse transcription was done with the TGIRT enzyme. Circ ligase (Epicentre) was used for circularization, and Illumina adapters were introduced by 8-10 cycles of PCR.
Gene specific RT/PCR followed by Nextera XT or LMPCR.
For genome-wide libraries we used 3' ligation, followed by circularixation, and PCR to add the sequencing adapters.

treatment_protocol: Cells  or oocytes were treated with DMS for 5mins, total RNA was extracted with Triazol, rRNA was subtracted with Ribozero (yeast and mammalian cells) or RNaseH with specific oligoes (Drosophila)

tag: strain


title: GM12878 oxaliplatin XR-seq Rep1

city: Jerusalem

first: Sheera

last: Adar

state: Israel

address: Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem

department: Department of Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University of Jerusalem

description: Excised oligomer released in Nucleotide Excision Repair (XR-seq)

library_source: genomic

data_processing:
Library strategy: XR-seq
Base calling using Casava v1.8.2. Demultiplexing performed allowing 1 mismtach in the index
Damage-seq
Reads from undamaged DNA were identified as starting with the sequence 5’-GACTGGTTCCAATTGAAAGTGCTCTTCCGATCT-3’ and filtered with cutadapt (Martin M. 2011)
Paired reads were aligned to the hg19 human reference genome using bowtie (Langmead et al. 2009) with the command options   –q --nomaqround --phred33-quals –S –X 1000 –m 4 –seed 123.
PCR artifacts were filtered by only retaining unique alignments based on both paired reads.
Damage position and nucleotide composition were then determined as the 2 nt  upstream of the first read start using samtools and bedtools
Wiggle base counts files of 25bp fixed step windows were created for the merged biological replicates from the bed files. The count data was normalized for total sequencing depth on each chromosome. Wiggle files were d transferred to bigWig format for viewing on the UCSC browser.
XR-seq
Flanking adapter sequences were removed from the reads using trimmomatic (Bolger et al. 2014).
Reads were aligned to the hg19 human reference genome using bowtie (Langmead et al. 2009) with the command options  -q --nomaqround --phred33-quals -m 4 -n 2 -e 70 -l 20 --best –S
Aligned readsfor each biological replicate were split into “PLUS” and “MINUS” strands, transformed to bed format, and sorted to remove duplicate reads.
Wiggle base counts files of 25bp fixed step windows were created for each of the replicates from the bed files. The count data was normalized for total sequencing depth on each chromosome. Wiggle files were d transferred to bigWig format for viewing on the UCSC browser.
Genome_build: hg19
Supplementary_files_format_and_content: There are bigWig files of normalized 25bp fixedStep count data for both biological replicates, split into plus and minus strands

molecule: genomic DNA

organism: Homo sapiens

source_name: B Lymphocytes

growth_protocol: NHF1 cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 2 mM glutamine at 37 °C in a 5% CO2 humidified chamber. GM12878 cells were cultured in RPMI 1640 medium (without phenol red) supplemented with 15% fetal bovine serum at 37 °C in a 5% CO2 humidified chamber.

extract_protocol:
Cell pellets were resuspended in 900 µL cold lysis buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 250 mM NaCl, 0.5% TritonX-100 and 0.1% SDS) with 10 µL RNaseA (Sigma) and incubated on ice for at least 10 min. Lysates were sonicated by Misonix Sonicator 3000 with microtip on ice water to generate fragments averagely 400 bp in length and then centrifuged at 14,000 rpm for 10 min to pellet debris. The supernatant was incubated with 10 µL Proteinase K (New England Biolabs) at 55°C for 30 min, followed by phenol/chloroform extraction and ethanol precipitation. DNA pellet was dissolved in 100 µL 1xTE buffer, and fragments 200-700 bp in length were selected by 0.5x/0.7x (50/70 µL) HighPrep PCR beads (MagBio) according to manufactory’s guidelines. DNA concentration was determined by NanoDrop 1000 (Thermo).  For naked DNA samples, DNA fragments were prepared from untreated GM12878 cells as described above. For untreated samples, 1 µg size-selected DNA were used to prepare library by NEBNext DNA preparation kit following the manufactory’s instruction (not Damage-seq process). For UV treatment, 5 µg DNA in 50 µL 0.1xTE were irradiated with 20J/m2 UVC as described and subjected to Damage-seq. For cisplatin treatment, 5 µg DNA were incubated with 20 µM cisplatin in a final volume of 50 µL at room temperature for 15 min. Treated DNA were purified through a G50 spin column (GE) immediately and subjected to Damage-seq.
For damage seq:   5 µg size-selected DNA were used for End-repair and dA-tailing by NEBNext DNA preparation kit following manufactory’s instruction. Ad1 ( oligos 5’-phos-GATCGGAAGAGCACACGTCTGAACTCCAGTCA-SpC3 and 5’-NNNNNGACTGGTTCCAATTGAAAGTGCTCTTCCGATC*T, 500 pmol) was ligated to both ends by NEBNext Quik Ligase for more than 12 hr under 16°C, then purified by HighPrep PCR beads and eluted in 126 µL 0.1x TE. Damaged DNA immunoprecipitation was performed as described previously (Hu et al. Genes and Development 2015) with modification. To denature DNA, 42 µL 8M Urea were added (to a final concentration of 2M), followed by boiling for 2 min and immediately putting on ice water for 2 min. Then 50 µg denatured sonicated salmon sperm DNA (Stratagene) and 25 µL 8x IP Buffer (for (6-4)PP and CPD, see below) or 8x PEXB Buffer (for cisplatin and oxaliplatin, see below) were added, followed by incubation with antibody-coated beads which were prepared as described below. For CPD, samples were washed three times with IP Buffer (20 mM Tris-Cl pH 8.0, 2 mM EDTA, 150 mM NaCl, 1% Triton X-100, and 0.5% sodium deoxycholate), then samples were incubated with 5 µL of protein G Dynabeads (10003D, Thermo) slurry and 5 µL of anti-rabbit Dynabeads (11203D, Thermo) slurry with 10 µg carrier DNA, 1 µL of rabbit anti-mouse IgG ((ab46540, Abcam) and 1 µL of anti-CPD (Kamiya Biomedical) antibody in 25 µL of IP Buffer for 3 hrs at 4°C. For (6-4)PP, 10 µL of each Dynabeads, 20 µg denatured sonicated salmon sperm DNA, 2 µL of rabbit anti-mouse IgG and 2 µL of anti-(6-4)PP (Cosmo Bio) antibody were used for one reaction as described above. For cisplatin and oxaliplatin-treated sample, PEXB Buffer (1xPBS, 2 mM EDTA, 0.01% Triton X-100 and 0.025% BSA) was used instead of IP Buffer. Each reaction was incubated with 40 µL of anti-rat Dynabeads (11035, Thermo) slurry and 1.5 µL anti-cisplatin modified DNA antibody (ab103261, Abcam). After incubation, beads were washed by IP Buffer or PEBX Buffer and incubated with denatured DNA overnight at 4°C.   For (6-4)PP or CPD samples, the beads were then washed sequentially with Wash Buffer I (20 mM Tris-Cl pH 8.0, 2 mM EDTA, 1% Triton X-100, and 2M Urea), Wash Buffer II (20 mM Tris-Cl pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% Triton X-100, and 0.1% SDS), Wash Buffer III (10 mM Tris-Cl pH 8.0, 1 mM EDTA, 150 mM LiCl, 1% NP-40, and 1% sodium deoxycholate), Wash Buffer IV (100 mM Tris-Cl pH 8.0, 1 mM EDTA, 500 mM LiCl, 1% NP-40, and 1% sodium deoxycholate) and TE (10 mM Tris-Cl pH 8.0 and 1 mM EDTA) at room temperature. For cisplatin and oxaliplatin samples, the beads were washed sequentially with PEXU Buffer (1xPBS, 2 mM EDTA, 0.01% Triton X-100 and 1.6M Urea), PEX Buffer (1xPBS, 2 mM EDTA, 0.01% Triton X-100), IP Buffer and TE. The fragments containing damage were eluted by incubation with 100 µL of Elution Buffer (50 mM NaHCO3, 1% SDS) at 65°C for 10 min. The eluted DNA was then isolated by phenol/chloroform extraction followed by ethanol precipitation.  NEBNext Q5 Hot Start HiFi PCR Master Mix was used for primer extension in the presence of purified DNA and 30 pmol Bio3 (5’-bio-TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT, without subtractive hybridization) or Bio3U (5’-bio-AGAGTG/dU/GACTGGAGTTCAGACGTGTGCTCTTCCGATCT, with subtractive hybridization) in a thermocycler for 45s at 98°C followed by 5 min at 65°C. Then 2 µL of Exo1 (New England Biolabs) were added to degrade excessive primers at 37°C for 10 min. After HighPrep PCR beads purification, DNA was denatured by boiling for 2 min and immediately putting on ice water for 2 min, then incubated with 5 µL of Dynabeads MyOne Streptavidin C1 (Thermo) in 30 µL of 1x B&W Buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl) at 4°C for 1 hr. For Bio3 primer, biotinylated DNA were eluted by a short incubation (~10s) in 100 µL of nonionic water at 75°C and concentrated by ethanol precipitation.   For Bio3U primer, DNA were released by incubation with 2 µL of USER Enzyme (New England Biolabs) and 1 µL of FastAP (Thermo) in 15 µL of 1x CutSmart Buffer (New England Biolabs) for 20 min at 37°C. The beads were washed with 15 µL of 1x B&W Buffer and both supernatants were combined. For subsequent subtractive hybridization, 30 pmol of oligo SH (5’-bio-NNGACTGGTTCCAATTGAAAGTGCTCTTCCG-SpC3) were added and followed by boiling for 2 min and naturally cooling down to room temperature. Oligo SH was then captured by incubating with 15 µL of Dynabeads MyOne Streptavidin C1 in 50 µL of 1x B&W Buffer. After separating the liquid on magnet, the beads were washed with 60 µL of 1x B&W Buffer and both supernatants were combined. DNA was then isolated by phenol/chloroform extraction followed by ethanol precipitation.  To add the second adaptor to the 3’ end, purified DNA were incubated with 40 pmol of Ad2 (oligos 5’-phos-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT-SpC3 and 5’-ACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNN-SpC3) in 10 µL of 1x Hybridization Buffer for 10 min at 65°C and then for 5 min at 16°C in a thermal cycler. To perform ligation, 4 µL of 5x ligase buffer, 1 µL of T4 DNA ligase HC (Thermo), 1 µL of 50% PEG8000 (New England Biolabs), and 4 µL of H2O were added to each reaction. The reactions were incubated overnight at 16°C.   After HighPrep PCR beads purification, ligated DNA were PCR-amplified by NEBNext Q5 Hot Start HiFi PCR Master Mix for 11-13 cycles with NEBNext Multiplex Oligos for Illumina (New England Biolabs). The PCR products were purified by HighPrep PCR beads and concentration was determined by Pico Green (Thermo).
XR-seq libraries were prepared as described (Hu et al. 2015) with modifications in the damage-specific immunoprecipitation and in vitro reversal steps. GM12878 cells were treated with 200 µM cisplatin or oxaliplatin for 3 hr and collected as described above. Cells were lysed and primary excision products were pulled down by TFIIH co-immunoprecipitation and followed by adaptor ligation on both ends. The damage-specific immunoprecipitation with anti-cisplatin modified DNA antibody was performed as described in Damage-seq with minor difference. For one reaction, 10 µg of denatured sonicated salmon sperm DNA, 25 µL of anti-rat Dynabeads slurry and 1 µL of anti-cisplatin modified DNA antibody were pre-incubated in 100 µL of 1x PEXB buffer at 4°C for 2-4 hours. Pre-incubated beads were then incubated with ligation products and 20 µg of denatured sonicated salmon sperm DNA in 100 µL of 1x PEXB buffer at 4°C overnight. After sequential wash w

treatment_protocol: UV irradiation of NHF1 cells was performed as described previously(Gaddameedhi et al. 2010). Briefly, culture medium was removed from ~90% confluent cells in one R150 dish, then cells were irradiated under a GE germicidal lamp emitting primarily 254-nm UV light (1 J/m2/s) connected with a digital timer for 20s (20 J/m2 in total). Following irradiation, the dish was put on ice immediately, and the cells were washed once by ice-cold PBS and harvested with a cell scraper in PBS and collected by centrifugation. GM12878 cells were grown to ~106 cells/ml in colorless medium. 10ml medium (~107 cells) were transferred to one R150 dish and irradiated as described above. Then cells were immediately transferred to a pre-chilled 15 ml tube on ice, collected by centrifugation, washed by ice-cold PBS. Cell pellets were frozen at -80°C.   To treat the cells with cisplatin or oxaliplatin, fresh stocks were made every time before treatment. The drug was dissolved in DMSO to 20 mM and immediately added to medium to a final concentration of 200 µM. Cells were further incubated at 37°C for 1.5 hour. Then both cells were harvested as described above.

tag: cell line

tag: source

value: Coriell Institute

tag: uv exposure

tag: time after irradiation


title: wt_nb.cym19s.direct

city: Budapest

first: <Up loaded by Bioinformatics core  facility>

last: <PI shown in the article>

address: Szigony st 43.

country: Hungary

institute: HUN-REN Institute of Experimental Medicine

description:
Nicotiana benthamiana and Cymbidium ringspot virus
smallRNA-seq

data_processing:
adapter removeal (UEA smallRNA workbanch 3.0)
out filtration of low complexety reads and reads under 14 nt (UEA smallRNA workbanch 3.0)
alignmant to genomes (PatMaN 1.2.2)
normalization, 5' end analysis and visualization programs have been uploaded to: https://github.com/kontral/Burgyan_Lab to ensure reproducibility and transparency.
Genome_build: Niben v1.0.1 and ViralProj15066 (NC_003532.1)
Supplementary_files_format_and_content: Processed data files were uploaded as data matrixes. These matrixes contain a short header followed by the data itself. Header lines alway begin with a '#'.  The first column contains the sequences, second column contains total read counts, the third contains normalized read counts. Columns are TAB delimited.

organism: Nicotiana benthamiana

growth_protocol: plants were grown under constant 21 °C, 16h light - 8h dark

extract_protocol:
Immunoprecipitation RNA was extracted with phenol-chloroform (as described in the material and methods). RNA was fractioned purified by isolating from a 8% denaturing poliacrylamide gel.
Standard Illumina TruSeq Small RNA Library Preparation Kit

treatment_protocol: Young leafs of 5-6 week old plants were inoculated as described. Samples were taken 7 days post inoculation, from upper leafs.

tag: plant genotype

value: wild type

tag: infection with virus

tag: tissue

value: young leaf


title: gurken_tagmentation_UT

organism: Drosophila melanogaster

source_name: Drosophila oocytes

extract_protocol:
Total RNA was extracted using Trizol, and treated with DNase. rRNA was depleted using RNaseH, and tRNA species were depleted using size exclusion columns. A gene-specific primer was used for reverse transcription with the TGIRT enzyme. Gene-specific PCR primers were used to amplify the region of interest, and then dsDNA was fragmented and prepared for sequencing using NexteraXT (Illumina).
Gene specific RT/PCR followed by Nextera XT or LMPCR.
For genome-wide libraries we used 3' ligation, followed by circularixation, and PCR to add the sequencing adapters.

value: OreR

tag: tissue/cell type

value: oocytes


title: Day 5, Animal 86

city: College Station

first: Leslie

middle: Garry

last: Adams

state: TX

address: 402 Raymond Stotzer Blvd.

department: Veterinary Pathobiology

institute: Texas A&M University

description:
demultiplex
Sample name: 86-5_4_exp_day5

data_processing:
Illumina Casava1.7 software used for basecalling.
splitBC was used to split raw barcoded data to create separate fastq files for each sample as listed in sample section
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using trimmomatic.
Reads  mapped to bovine refGenome UMD3.1 whole genome using bowtie2 v2.2.5  with parameters –end-to-end -D 15 -R 2 -N 0 -L 22 -iS,1,1.15
read alignment counts to transcripts by BedTools Multicov with bovine genomic intervals provided by Illumina's Igenome annotation from NCBI
Count table (count to transcript/gene mapping) created by Seralogix's NextGen Sequencing pipeline to form one matrix file genes in rows and samples in column by sample name declared above.
Differential analysis completed by DESeq2
Genome_build: UMD3.1 bovine
Supplementary_files_format_and_content: MP-12vaccinatedCountTableMatrix.txt is a matrix of unnormalized, unfiltered read counts.  First 3 columns are 1) transcript id, 2) gene symbol, 3) gene description.  The remaining columns are sample data corresponding to sample names from above.
Supplementary_files_format_and_content: MP-12normalizedAbundanceTableMatrix.txt generated by DESeq2  is a matrix of normalized and filtered abundance (read counts).  First 5 columns are 1) Unique Identifier, 2) Probe_ID=transcript ID maps to file MP-12vaccinatedCountTableMatrix.txt, 3) Gene Description; 4) Genbank ID, 5) Gene Symbol.  The remaining columns are the normalized data by sample name defined above in Sample descriptions.

organism: Bos taurus

source_name: MP-12 Vaccinated Cattle

growth_protocol: There was no growth protocol, however whole blood was collected from cattle at DAY 0–7, 10, 14 and 21 and immediately mixed at a 3:5 (blood:buffer) ratio with RNALater (Invitrogen). Samples were stored at –20°C until processing.

extract_protocol:
Whole blood was collected at DAY 0–7, 10, 14 and 21 and immediately mixed at a 3:5 (blood:buffer) ratio with RNALater (Invitrogen). Samples were stored at –20°C until processing. To purify RNA, frozen samples were thawed at 37°C, centrifuged at 2000xG, and supernatant discarded. Remaining cell pellets were subjected to two rounds of treatment with Red Blood Cell Lysing Buffer per manufacturer’s instructions (Sigma). RNA from resulting cell pellet was initially extracted by Trizol (Invitrogen) followed by treatment with RNeasy Kit with on-column DNase digestion (Qiagen). Purified RNA was quantified by spectrophotometry on a NanoDrop (Thermo, USA) and by electrophoresis with a BioAnalyzer 2100 (Agilent, USA). Only samples with an RNA Integrity Number (RIN) greater than 8.0 were used for RNASeq analysis.
All RNASeq sequencing was performed at the Texas A&M Genetics and Bioinformatics Center following manufacturer’s instructions. cDNA was generated from RNA samples of sufficient quantity and quality with Ovation RNA-Seq System (NuGen, USA), sheared by focused ultrasound (Covartis, USA) and made into barcoded (multiplexed) libraries with Encore Rapid Library System (NuGen, USA).  Samples were quantified, diluted, pooled re-analyzed with a Bioanalyzer and loaded onto a Genome Analyzer II High-throughput sequencer (Illumina, USA).

treatment_protocol: All cattle were injected subcutaneously or intramuscularly with the Rift Valley fever MP-12 vaccine strain.

tag: individual

value: circulating lymphocytes

value: Rift Valley fever, MP-12 vaccine

value: Day 5


title: wt_nb.mock.agoip_input

description:
Nicotiana benthamiana
smallRNA-seq

value: mock

tag: ip antibody

value: none (input for wt_nb.mock.agoip_ago1ip and wt_nb.mock.agoip_ago2ip)


title: wt_nb.cym19s.agoip_ago2ip.biorep.sRNA

data_processing:
adapter removeal (UEA smallRNA workbanch 3.0)
Filtration of low complexety reads and reads under 14 nt (UEA smallRNA workbanch 3.0)
alignmant to genomes (PatMaN 1.2.2)
reads were normalized to 1 million total reads passing quality control
Genome_build: Niben v1.0.1. and NC_003532.1
Supplementary_files_format_and_content: Processed data files were uploaded as data matrixes. These matrixes contain a short header followd by the data itself. Headder lines alway begin with a '#'.  The first column contains the sequences, second column contains total read counts, the third contains normalised read counts. Column are TAB separsted.
Quality control was done by fastQC 0.10.1
Trim_galore 0.4.1 and FASTX Toolkit 0.0.13 were used to remove adaptor sequences, low quality bases, reads under 20 nt and unpaired reads.
Bowtie2 was used to align reads to the transcriptome
reads were normalized to 1 million total reads passing quality control
Genome_build: Nbv5
Supplementary_files_format_and_content: Processed data were uploaded as a data matrix. The matrix contains a short header followed by the data itself. Header lines always begin with a '#'.  The first column contains the transcriptome IDs, second contains wt uninfected read counts from Baksa et al 2015 doi: 10.1186/s12864-015-2209-6, the third contains  read counts from sample p19syn_nb.cym19s.mRNA, the fourth column contains read counts from sample wt_nb.cym19s.mRNA, the fifth contains read counts from sample p19syn_nb.mock.mRNA. Column are TAB separated.

extract_protocol:
RNA was extracted with phenol-chlorophorm (as described in the material and methods). RNA was fractionated by isolating from a 8% denaturing poliacrylamide gel run.
RNA-seq: RNA was extracted with phenol-chlorophorm (as described in the material and methods). RNA was polyA fractionated prior library prep.
Illumina TruSeq Small RNA Library Preparation Kit and Illumina TruSeq Stranded mRNA library prep

treatment_protocol: Young leafs of 5-6 week old plants were inoculated. Samples were taken 7 days post inoculation, from upper (non inoculated) leafs.

tag: genotype/variation

tag: immunoprecipitation

value: AGO2 IP

value: custom-made NbAGO2 antibody, generated by immunization of rabbits with the synthetic peptide CLEDPEGKDPPRDVF by GenScript


title: ChIP:KOPT-K1_Input_052616 [lab: Look-DFCI]

first: Richard

middle: A

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Aligned using /usr/local/bin/bowtie with configuration -p 4 --best -k 2 -m 2 --sam -l 40
hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

source_name: T-ALL

growth_protocol: Human KOPTK1 cells were purchased from the American Type Culture Collection (ATCC), Manassas, VA. Cells were maintained under typical conditions in RPMI media with 10% Bovine Calf Serum. For location analysis, cells were grown to a density of 1 million per ml and 99% viability prior to cross-linked with formaldehyde for 20 min.

extract_protocol:
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.

tag: tissue source

value: Blood

tag: chip antibody

value: none (input)


title: tagmentation_hek293_DMS_fxr2_replicate2

source_name: HEK 293T cells

value: HEK 293T


title: GM12878 cisplatin XR-seq Rep1


title: Scer_tagmentation_rps28B_UT


title: Day 4, Animal 74

description:
demultiplex
Sample name: 74-4_1_exp_day4

value: Animal 74

tag: cell type

tag: vaccine

tag: vaccine administration

value: subcutaneous

tag: time

value: Day 4


title: wt_nb.mock.agoip_ago2ip

description:
Nicotiana benthamiana
smallRNA-seq

value: wild type

value: AGO2 (Genescript a312080523)


title: tHBV2

city: Yokohama

first: Kosuke

last: Hashimoto

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

description: 20 weeks after transduction with AAV-HBV

data_processing:
Basecalls performed using CASAVA version 1.8
FASTQ files were splitted by barcode using FASTX-Toolkit
Ribosomal RNAs were identified and removed using rRNAdust.
Reads were aligned to the human or mouse genomes using BWA v0.7.5a
Unmapped reads were aligned to HBV genome using BWA 0.7.5a
Transcription start sites (CAGE peaks) on HBV genome were identified using Paraclu.
Genome_build: hg19/GRCh37 for human, mm9/NCBI37 for mouse, and GQ358158.1 for HBV
Supplementary_files_format_and_content: Tab-delimited text file in the bed-like format including normalized expression values (tpm) of HBV promoters for 11 samples. This series contains CAGE peaks only for the HBV genome.

organism: Mus musculus

source_name: mouse liver transduced with AAV-HBV

extract_protocol:
Total RNA was prepared using TRIzol reagent (Invitrogen) and TURBO DNase (Ambion).
Total RNA was used to synthesize cDNA with random primers. Full-length cDNAs were biotinylated and captured by streptavidin-coated magnetic beads. The cDNAs were released from cap-trapped RNAs, ligated to 5' linkers including barcode sequences. The detailed protocol is described in Ref [PMID:24927836]

value: liver tissue


title: Day 5, Animal 75

description:
demultiplex
Sample name: 75-5_2_exp_day5

value: Animal 75

tag: serologic response status

value: vaccinated, not protected


title: wt_nb.mock.agoip_ago1ip

description:
Nicotiana benthamiana
smallRNA-seq

value: AGO1 (Eurogentech custom antibody against CHLGKRLPAYDGRKSL)

value: young leaf


title: tHBV1


title: Day 3, Animal 86

description:
demultiplex
Sample name: 86-3_4_exp_day3

value: Animal 86

value: circulating lymphocytes

value: Rift Valley fever, MP-12 vaccine

value: intramuscular

value: Day 3


title: GM12878 untreated Damage-seq Rep1

description:
Genomic DNA extended until polymerase was blocked by damage (Damage-seq)
HLunD_merged_sorted_MINUSNORM_fixedStep_25.bw
HLunD_merged_sorted_PLUSNORM_fixedStep_25.bw

data_processing:
Library strategy: Damage-seq
Base calling using Casava v1.8.2. Demultiplexing performed allowing 1 mismtach in the index
Damage-seq
Reads from undamaged DNA were identified as starting with the sequence 5’-GACTGGTTCCAATTGAAAGTGCTCTTCCGATCT-3’ and filtered with cutadapt (Martin M. 2011)
Paired reads were aligned to the hg19 human reference genome using bowtie (Langmead et al. 2009) with the command options   –q --nomaqround --phred33-quals –S –X 1000 –m 4 –seed 123.
PCR artifacts were filtered by only retaining unique alignments based on both paired reads.
Damage position and nucleotide composition were then determined as the 2 nt  upstream of the first read start using samtools and bedtools
Wiggle base counts files of 25bp fixed step windows were created for the merged biological replicates from the bed files. The count data was normalized for total sequencing depth on each chromosome. Wiggle files were d transferred to bigWig format for viewing on the UCSC browser.
XR-seq
Flanking adapter sequences were removed from the reads using trimmomatic (Bolger et al. 2014).
Reads were aligned to the hg19 human reference genome using bowtie (Langmead et al. 2009) with the command options  -q --nomaqround --phred33-quals -m 4 -n 2 -e 70 -l 20 --best –S
Aligned readsfor each biological replicate were split into “PLUS” and “MINUS” strands, transformed to bed format, and sorted to remove duplicate reads.
Wiggle base counts files of 25bp fixed step windows were created for each of the replicates from the bed files. The count data was normalized for total sequencing depth on each chromosome. Wiggle files were d transferred to bigWig format for viewing on the UCSC browser.
Genome_build: hg19
Supplementary_files_format_and_content: There are bigWig files of normalized 25bp fixedStep count data for both biological replicates, split into plus and minus strands

tag: cell line

tag: source

value: Coriell Institute

tag: uv exposure


title: Day 4, Animal 75

description:
demultiplex
Sample name: 75-4_2_exp_day4


title: Day 3, Animal 88

description:
demultiplex
Sample name: 88-3_3_exp_day3

value: Animal 88


title: GM12878 cisplatin XR-seq Rep2

tag: time after irradiation


title: Day 3, Animal 75

description:
demultiplex
Sample name: 75-3_1_exp_day3


title: wt_nb.cymrsv.agoip_input

tag: plant genotype

tag: infection with virus

value: CymRSV

value: none (input for wt_nb.cymrsv.agoip_ago1ip and wt_nb.cymrsv.agoip_ago2ip)

tag: tissue


title: Input 20 fix

city: Utrecht

first: Jacqueline

last: Deschamps

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Mapping: Bowtie (1.1.0), parameters: -m 1 --best --strata --chunkmbs 512 -S –phred64-quals -q -l 40 -n 1
Read cleanup: Samtools (0.1.19), SAM files were converted to BAM files with and duplicate reads were removed with rmdup
Peak calling: MACS2 (2.1.0), parameters: callpeak -B -p 1e-5 -g mm –SPMR --nomodel --extsize 300 --llocal 100000
Genome_build: mm9

source_name: Wnt3KO EpiSCs

growth_protocol: Pre-streak embryos (E6.0) were isolated in M2 medium; extraembryonic tissue and surrounding primitive endoderm was removed. Explants were put on MEFs and cultured in presence of Wnt inhibitor IWP2 (2 µM, Sigma Aldrich, dissolved in DMSO) in medium containing 20% KOSR, 77% DMEM/F12, 1x penicillin/streptomycin (100 units/mL, Thermo Fisher Scientific), 2 mM L-glutamine, 1x non-essential amino acids, 0.01% β-mercaptoethanol, Fgf-basic (12 ng/mL, ThermoFisher Scientific ), Activin A (20 ng/mL, R&D Systems).  MEF-free culture took place on surface coated by fibronectin (ThermoFisher Scientific) in medium containing 48% DMEM/F12, 48% Neurobasal Medium 1% B27 Supplement, 0.5% N2 Supplement B (all Thermo Fisher Scientific), 1x penicillin/streptomycin, Fgf-basic (12 ng/mL), Activin A (20 ng/mL), IWP2 (2 µM), 0.01% β-mercaptoethanol. Medium was refreshed on daily basis.

extract_protocol:
Crosslink, Lyse, Sonication
Illumina Truseq DNA library protocol

value: Wnt3KO EpiSCs

tag: experiment type

value: ChIP-seq

tag: antibody

tag: wnt stimulation


title: wt_nb.cymrsv.agoip_ago2ip

value: wild type

tag: ip antibody

value: AGO2 (Genescript a312080523)


title: Scer_Tagmentation_HAC1_and_RPS28B

extract_protocol:
Total RNA was extracted using hot acid phenol, and treated with DNase. rRNA was depleted using RNaseH, and tRNA species were depleted using size exclusion columns. A gene-specific primer was used for reverse transcription with the TGIRT enzyme. Gene-specific PCR primers were used to amplify the region of interest, and then dsDNA was fragmented and prepared for sequencing using NexteraXT (Illumina).
Cells or oocytes were treated with DMS for 5mins, total RNA was extracted with Triazol, rRNA was subtracted with Ribozero (yeast and mammalian cells) or RNaseH with specific oligoes (Drosophila)
Gene specific RT/PCR followed by Nextera XT or LMPCR. For genome-wide libraries we used 3' ligation , followed by circularixation, and PCR to add the sequencing adapters.

treatment_protocol: For the in vivo DMS treatment of S. cerevisiae, DMS was added directly to the growing log phase yeast culture at 5% for 3-4 min. 25% BME, 30% isoamyl alcholol was used to quench the DMS. Cells were lysed with SDS, and RNA was isolated with hot acid phenol. For denatured samples, RNA was first extracted and then heated to 95deg for treatment with DMS.

tag: strain

tag: molecule subtype

value: mRNA


title: Input 10 fix


title: Day 3, Animal 74

description:
demultiplex
Sample name: 74-3_2_exp_day3

tag: individual

value: Animal 74

tag: cell type

tag: vaccine

value: subcutaneous

value: vaccinated, not protected


title: GM12878 Cisplatin In Vitro Damage-seq Rep1

description:
Genomic DNA extended until polymerase was blocked by damage (Damage-seq)
HLCisPvitro_merged_sorted_MINUSNORM_fixedStep_25.bw
HLCisPvitro_merged_sorted_PLUSNORM_fixedStep_25.bw

value: 20 µM


title: wt_nb.cymrsv.agoip_ago1ip

value: AGO1 (Eurogentech custom antibody against CHLGKRLPAYDGRKSL)

value: young leaf


title: GM12878 untreated Damage-seq Rep2


title: tHBV3

value: liver tissue


title: Ring1b Wnt3KO Wnt3a5h

extract_protocol:
Crosslink, Lyse, Sonication and Immunoprecipitate
Illumina Truseq DNA library protocol

treatment_protocol: Wnt stimulation was done after at least two passages feeder-free culturing by withdrawal of IWP2 and addition of Wnt3a (Cell Guidance Systems, 125 ng/mL) or Chiron (3 µM).

value: ActiveMotif, 39663

value: 5h Wnt3a 125 ng/ml


title: Day 2, Animal 88

description:
demultiplex
Sample name: 88-2_3_exp_day2

value: Animal 88

value: circulating lymphocytes

value: Rift Valley fever, MP-12 vaccine

tag: vaccine administration

value: intramuscular

tag: time

value: Day 2

tag: serologic response status


title: wt_nb.cym19s.agoip_input

value: wild type

value: none (input for wt_nb.cym19s.agoip_ago1ip and wt_nb.cym19s.agoip_ago2ip)


title: GM12878 oxaliplatin Damage-seq Rep1

description:
Genomic DNA extended until polymerase was blocked by damage (Damage-seq)
HLOxP_merged_sorted_MINUSNORM_fixedStep_25.bw
HLOxP_merged_sorted_PLUSNORM_fixedStep_25.bw

tag: cell line

tag: source

value: Coriell Institute

tag: uv exposure


title: wt_nb.cym19s.agoip_ago2ip

tag: plant genotype

tag: infection with virus

value: AGO2 (Genescript a312080523)


title: Ring1b Wnt3KO Chiron72h

tag: tissue

value: Wnt3KO EpiSCs

tag: experiment type

value: ChIP-seq


title: Day 2, Animal 75

description:
demultiplex
Sample name: 75-2_1_exp_day2

value: Animal 75

value: subcutaneous

value: vaccinated, not protected


title: Day 2, Animal 86

description:
demultiplex
Sample name: 86-2_4_exp_day2

value: Animal 86


title: Ring1b Wnt3KO 0h rep2

tag: antibody

value: ActiveMotif, 39663

tag: wnt stimulation


title: GM12878 Cisplatin Damage-seq Rep2

description:
Genomic DNA extended until polymerase was blocked by damage (Damage-seq)
HLCisP_merged_4nt_sorted_MINUSNORM_fixedStep_25.bw
HLCisP_merged_4nt_sorted_PLUSNORM_fixedStep_25.bw

tag: time after irradiation


title: wt_nb.cym19s.agoip_ago1ip

description:
Nicotiana benthamiana and Cymbidium ringspot virus
smallRNA-seq

tag: ip antibody

value: AGO1 (Eurogentech custom antibody against CHLGKRLPAYDGRKSL)

value: young leaf


title: GM12878 Cisplatin In Vitro Damage-seq Rep2

value: 20 µM


title: NHF1 Cisplatin Damage-seq Rep2

description: Genomic DNA extended until polymerase was blocked by damage (Damage-seq)

source_name: Foreskin fibroblasts

value: W.K. Kaufmann, UNC, Chapel Hill (Heffernan et al. 2002)


title: wt_nb.cymrsv.p19ip-input

value: CymRSV

value: none (input for wt_nb.cymrsv.p19ip-ip)


title: GM12878 Cisplatin Damage-seq Rep1


title: H3K4me3 wt Chiron72h

data_processing:
none
Genome_build: mm9

source_name: EpiSCs

value: EpiSCs

value: Abcam, ab8580


title: GM12878 oxaliplatin Damage-seq Rep2

value: Coriell Institute


title: NHF1 Cisplatin Damage-seq Rep1


title: Ring1b Wnt3KO 0h rep1


title: Day 0, Animal 88

description:
demultiplex
Sample name: 88-0_8_cntl_day0

tag: individual

value: Animal 88

value: circulating lymphocytes

value: Rift Valley fever, MP-12 vaccine

value: intramuscular

value: Day 0


title: Day 0, Animal 86

description:
demultiplex
Sample name: 86(-)7_7_cntl_day0

tag: cell type

value: vaccinated, not protected


title: H3K4me3 wt 0h

value: ChIP-seq


title: p19syn_nb.mock.p19ip-ip

description:
Nicotiana benthamiana
smallRNA-seq

value: transgenic p19syn

value: mock

value: p19 (homemade by immunizing with purified protein)


title: Day 0, Animal 76

description:
demultiplex
Sample name: 76-0_1_cntl_day0

value: Animal 76

tag: vaccine

value: subcutaneous

value: unvaccinated


title: Day 0, Animal 75

description:
demultiplex
Sample name: 75-0_4_cntl_day0

value: Animal 75

tag: vaccine administration


title: H3K4me3 Wnt3KO Chiron72h

value: Wnt3KO EpiSCs


title: p19syn_nb.mock.p19ip-input

description:
Nicotiana benthamiana
smallRNA-seq

value: none (input for p19syn_nb.mock.p19ip-ip)

value: young leaf


title: p19syn_nb.cym19s.p19ip-ip


title: H3K4me3 Wnt3KO Chiron12h

value: Abcam, ab8580


title: H3K4me3 Wnt3KO Chiron6h


title: Day 0, Animal 74

description:
demultiplex
Sample name: 74-0_5_cntl_day0

value: Animal 74

value: circulating lymphocytes

tag: time


title: p19syn_nb.cym19s.p19ip-input

value: none (input for p19syn_nb.cym19s.p19ip-ip)


title: Day -7, Animal 75

description:
demultiplex
Sample name: 75(-)7_3_cntl_day0

value: Rift Valley fever, MP-12 vaccine

value: Day -7

tag: serologic response status


title: Scer_Tagmentation_pre-mRNA_RPL14A_and_RPL31B_Rep2

extract_protocol:
Total RNA was extracted using hot acid phenol, and treated with DNase. rRNA was depleted using RiboZero (Epicentre), and tRNA species were depleted using size exclusion columns. A gene-specific primer was used for reverse transcription with the TGIRT enzyme. Gene-specific PCR primers were used to amplify the region of interest, and then dsDNA was fragmented and prepared for sequencing using NexteraXT (Illumina).
Cells or oocytes were treated with DMS for 5mins, total RNA was extracted with Triazol, rRNA was subtracted with Ribozero (yeast and mammalian cells) or RNaseH with specific oligoes (Drosophila)
Gene specific RT/PCR followed by Nextera XT or LMPCR. For genome-wide libraries we used 3' ligation , followed by circularixation, and PCR to add the sequencing adapters.

tag: strain

tag: molecule subtype

value: mRNA


title: Day -7, Animal 76

description:
demultiplex
Sample name: 76(-)7_2_cntl_day0


title: H3K4me3 Wnt3KO 0h

value: ChIP-seq

value: Wnt stimulation:none


title: Scer_Tagmentation_pre-mRNA_RPL14A_and_RPL31B_Rep1


title: H3K27me3 Wnt3KO Chiron72h

value: Millipore, 17-622


title: H3K27me3 Wnt3KO Chiron12h


title: oskar_tagmentation

extract_protocol:
Cells or oocytes were treated with DMS for 5mins, total RNA was extracted with Triazol, rRNA was subtracted with Ribozero (yeast and mammalian cells) or RNaseH with specific oligoes (Drosophila)
Gene specific RT/PCR followed by Nextera XT or LMPCR. For genome-wide libraries we used 3' ligation , followed by circularixation, and PCR to add the sequencing adapters.

value: oocytes


title: wt_nb.cymrsv.p19ip-ip

value: wild type

value: CymRSV

value: p19 (homemade by immunizing with purified protein)


title: Scer_Tagmentation_mature_RPL14A_and_RPL31B_Rep1


title: Scer_Tagmentation_rRNA

extract_protocol:
Total RNA was extracted using hot acid phenol, and treated with DNase. A gene-specific primer was used for reverse transcription with the TGIRT enzyme. Gene-specific PCR primers were used to amplify the region of interest, and then dsDNA was fragmented and prepared for sequencing using NexteraXT (Illumina).
Cells or oocytes were treated with DMS for 5mins, total RNA was extracted with Triazol, rRNA was subtracted with Ribozero (yeast and mammalian cells) or RNaseH with specific oligoes (Drosophila)
Gene specific RT/PCR followed by Nextera XT or LMPCR. For genome-wide libraries we used 3' ligation , followed by circularixation, and PCR to add the sequencing adapters.

value: rRNA


title: H3K27me3 Wnt3KO Chiron6h

value: Wnt3KO EpiSCs


title: H3K27me3 Wnt3KO 0h rep1


title: Scer_SSii/Mn_DMSvivo_Rep2_genomeWide

extract_protocol:
Total RNA was extracted using hot acid phenol. mRNA was randomly fragmented using Ambion fragmentation reagents, followed by PNK, and ligation using T4 K227Q truncated RNA ligase. rRNA was depleted post-ligation using RiboZero (Epicentre), and reverse transcription was done with Superscript II in Mn2+ buffer. Circ ligase (Epicentre) was used for circularization, and Illumina adapters were introduced by 8-10 cycles of PCR.
Cells or oocytes were treated with DMS for 5mins, total RNA was extracted with Triazol, rRNA was subtracted with Ribozero (yeast and mammalian cells) or RNaseH with specific oligoes (Drosophila)
Gene specific RT/PCR followed by Nextera XT or LMPCR. For genome-wide libraries we used 3' ligation , followed by circularixation, and PCR to add the sequencing adapters.


title: H3K27ac wt Chiron24h rep2

value: EpiSCs

value: Abcam, ab4729


title: Scer_TGIRT_DMSdenatured_rRNA

extract_protocol:
Total RNA was extracted using hot acid phenol. mRNA was randomly fragmented using Ambion fragmentation reagents, followed by PNK, and ligation using T4 K227Q truncated RNA ligase. rRNA was depleted post-ligation using RiboZero (Epicentre), and reverse transcription was done with the TGIRT enzyme. Circ ligase (Epicentre) was used for circularization, and Illumina adapters were introduced by 8-10 cycles of PCR.
Cells or oocytes were treated with DMS for 5mins, total RNA was extracted with Triazol, rRNA was subtracted with Ribozero (yeast and mammalian cells) or RNaseH with specific oligoes (Drosophila)
Gene specific RT/PCR followed by Nextera XT or LMPCR. For genome-wide libraries we used 3' ligation , followed by circularixation, and PCR to add the sequencing adapters.


title: H3K27me3 Wnt3KO Wnt3a5h

value: 5h Wnt3a 125 ng/ml


title: Restricted Diet rep2

city: Novato

first: Nuno

middle: Miguel

last: Luis

state: CA

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

description: ribosome bound mRNA

data_processing:
Tophat2 was used for RNA alignment and Cufflink2 was used to calculate differential expression
Genome_build: Ensembl_BDGP5.25
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each group and p-value for each transcript

source_name: intestinal polysome pull down

extract_protocol:
Whole fly homogenates from 100 female flies were immunoprecipitated with anti-FLAG beads against tagged ribosome expressed in the intestine
Illumina TruSeq RNA Library Prep v2

treatment_protocol: Flies were on restricted (0.5% yeast extract) or ad libitum (5% yeast extract) diet for 10 days

value: Intestinal enterocytes

tag: diet

value: restricted diet


title: H3K27me3 Wnt3KO 0h rep2


title: H3K27ac wt 0h


title: Restricted Diet rep4

description: ribosome bound mRNA


title: Scer_SSii/Mn_DMSvivo_Rep1_genomeWide


title: Scer_SSii/Mn_Untreated_genomeWide


title: Restricted Diet rep3

description: ribosome bound mRNA


title: Ad Libitum rep4

description: ribosome bound mRNA

value: ad libitum


title: Scer_TGIRT_DMSvivo_Rep2_genomeWide_additionalSequencing


title: H3K27ac Wnt3KO Chiron6h


title: H3K27ac Wnt3KO Chiron12h


title: Scer_TGIRT_DMSvivo_Rep2_genomeWide


title: Ad Libitum rep2

description: ribosome bound mRNA


title: Ad Libitum rep1

description: ribosome bound mRNA


title: Ad Libitum rep3

description: ribosome bound mRNA


title: H3K27ac Wnt3KO Chiron72h


title: H3K27ac Wnt3KO 0h


title: Scer_TGIRT_Untreated_genomeWide


title: H3K27ac wt Chiron24h rep1


title: Restricted Diet rep1

description: ribosome bound mRNA


title: WRR-D120-B-4

status: Public on Sep 15 2016

city: Nanchang

first: Fengfang

last: Qiu

state: Jiangxi

address: Guanglan Road No.418

department: School of Chemistry, Biology and Material Science

country: China

institute: East China University of Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
For all generated raw reads, adaptor sequences, low quality reads (Sanger bases quality < 20), and contaminant reads were removed.
Clean reads were aligned to chicken reference gene and genome using SOAPaligner/SOAP2.
We used RSEM (RNAseq by Expectation Maximization, v1.2.12) for generating our RPKM data.
Genome_build: Gallus_gallus.Galgal4.73
Supplementary_files_format_and_content: RPKM

organism: Gallus gallus

source_name: Breast muscle

extract_protocol:
Total RNA was extracted from muscle samples with RNAiso reagent (Takara, Otsu, Japan) and treated with DNase I (Takara) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Recessive White Rocks

value: breast muscle

tag: age


title: WRR-D180-B-2

tag: tissue


title: WRR-D180-B-5


title: WC-D180-B-2

value: Wenchang


title: WRR-D120-B-6


title: WC-D120-B-3


title: WC-D120-B-1


title: WC-D180-B-3


title: no DOX-NLRP1 A66V

city: Singapore

first: Franklin

last: ZHONG

state: Singapore

address: 11 Mandalay Road

country: Singapore

institute: NTU LKC School of Medicine

description:
Control group
treatment: Mock treated
RHN162

data_processing:
Illumina HiSeq V3
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CuffLink and CuffDiff.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: N-TERT/1 immortalized keratinocytes. pTRIPZ backbone

growth_protocol: Ksfm media (ThermoFisher); 300mM Ca++

extract_protocol:
Trizol
TruSeq stranded mRNA kit

treatment_protocol: 1ug/ml Doxycycline; 3days

value: N-TERT/1 immortalized keratinocytes

tag: transduction

value: NLRP1 mutant A66V


title: DOX-NLRP1 A66V

description:
Experimental group
treatment: 1ug/ml Doxycycline; 3days
RHN159


title: DOX-mCherry

description:
Control group
treatment: 1ug/ml Doxycycline; 3days
RHN160

value: vector


title: Ripk3Casp8_LPS.6hr_rep2

city: Philadelphia

first: daniel

last: beiting

state: PA

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

data_processing:
fastq files were aligned to version 79 of mouse reference genome GRCm38 using the Subread aligner in the RSubread package.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized using the VOOM function in the Limma package in R
Differentially expressed genes (³1.5-fold and £5% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma package
Genome_build: version 79 of mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2 counts per million (CPM) values for each Sample ...

source_name: Ripk3Casp8, LPS.6hr

growth_protocol: 1x106 BMDMs/well were plated in 6-well tissue culture-treated dishes and placed in a 5% CO2 37 °C incubator for 16 hours

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the TruSeq Stranded Total RNA LT Kit with Ribo-Zero Gold, according to the manufacturer’s instructions.

treatment_protocol: BMDMs were either left unstimulated, or stimulated with LPS (100 ng/mL) for 6 hrs.

tag: genotype/variation

tag: treatment

value: LPS stimulation for 6hr

value: bone marrow-derived macrophages


title: no DOX-NLRP1 A54T

description:
Control group
treatment: Mock treated
RHN161

value: NLRP1 mutant A54T


title: DOX-NLRP1M77T

description:
Experimental group
treatment: 1ug/ml Doxycycline; 3days
RHN158

value: NLRP1 mutant M77T


title: Scer_TGIRT_DMSvivo_Rep1_genomeWide

value: mRNA


title: DOX-NLRP1 A54T

description:
Experimental group
treatment: 1ug/ml Doxycycline; 3days
RHN157


title: Ripk3_LPS.6hr_rep2

source_name: Ripk3, LPS.6hr


title: WT_LPS.6hr_rep1

source_name: WT, LPS.6hr

value: wild-type


title: Ripk3_LPS.6hr_rep1


title: Ripk3Casp8_unstim_rep1

description: Only the R1 paired-end reads have been provided; the R2 paired-end reads are unavailable.

source_name: Ripk3Casp8, unstimulated

value: untreated


title: WT_LPS.6hr_rep2


title: Ripk3Casp8_unstim_rep2


title: Ripk3Casp8_LPS.6hr_rep1


title: Ripk3_unstim_rep1

source_name: Ripk3, unstimulated


title: Ripk3_unstim_rep2


title: WT_unstim_rep1

source_name: WT, unstimulated


title: WT_unstim_rep2


title: IgG_rbr-2_ChIPSeq

city: Copenhagen

first: Anna Elisabetta

last: Salcini

address: Ole Maaloes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

data_processing:
Reads were checked for quality using FastQC and preprocessed to remove adaptors and E. coli sequences.
Reads were mapped to C. elegans genome (WS220) using Bowtie2 (Langmead and Salzberg, 2012; Langmead et al., 2009).The number of reads processed and % aligned were: 40M, 70.3%, N2 H3K4me3; 49M, 75.2%, rbr-2 H3K4me3; 42M, 50.1% N2 IgG; 67M, 63.3%, rbr-2 IgG.
From the alignment files normalized and background (IgG) subtracted bigwig files were created using SES (Dias et al., 2012)  and bamCompare from deepTools (Ramirez et al.,2014).
Please note, that only one bigwig file was created from each sample and corresponding background file.
Genome_build: WS220/ce10
Supplementary_files_format_and_content: Files in bigWig format and background subtracted (IgG)

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: C. elegans strains were cultured using standard growth conditions at 20°C on Escherichia coli OP50 (Brenner, 1974).

extract_protocol:
ChIP was performed with a protocol modified from that of Kolasinska-Zwierz et al., 2009. Lysates were clarified from sonicated chromatin and histone-DNA complexes were isolated with antibody.
Libraries were prepared using the ChIP-seq DNA sample prep kit (Illumina) with a protocol adapted from Meyer and Kircher, 2010.

tag: developmental stage

tag: chip antibody

value: IgG (Sigma-Aldrich I8140)


title: H3K4me3_N2_ChIPSeq

value: wild type Bristol N2

value: H3K4me3 (Abcam ab8580)


title: H3K4me3_rbr-2_ChIPSeq


title: IgG_N2_ChIPSeq


title: morula siKdm5b H3K4me3 rep1

city: Shanghai

first: Shaorong

last: Gao

state: Shanghai

address: 1239 Siping Road, Yangpu District

department: School of life science and technology

institute: Tongji University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using bwa mem command, reads that have map quality score less than 30 were removed from downstream analysis.
Peaks were called using masc2(v 2.0.10.20131216) with the parameters "macs2 callpeak –n Sample -g mm -B -q 0.05 --nomodel --broad --shiftsize=73 --SPMR" relative to input samples.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files are generated using macs2 pileup function and normlized to one million reads per sample using --SPMR option. Scores represent normalized tag counts per million reads.

source_name: mouse embryo

extract_protocol:
500cells were washed three times in 0.5% BSA-PBS solution. Lysates were clarified from micrococcal nuclease treated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to KAPA Hyper Prep Kit for illumina platform (kk8504)

treatment_protocol: For MII oocyte and cleavage-stage embryos, the zona pellucida of embryos was removed by 0.5% pronase E (Sigma). Then the embryo was incubated in Ca2+ free CZB for 5 min. Polar bodies were removed by gentle pipetting using an inner diameter of 120 μm fire polished glass needle. For ICM and TE isolation, the zona pellucida of blastocysts was removed by 0.5% pronase E (Sigma). They were then incubated for 20 min in Ca2+ free CZB，the tight junctions TE cells and ICM cells were separated by gently pipetting in a pipette with a diameter of 40-60 μm.

tag: development stage

value: morula embryo

value: H3K4me3(Cell signaling Technology, #9727)

tag: overexpression


title: morula siKdm5b input


title: morula ctrl input


title: morula siKdm5b H3K4me3 rep2


title: morula ctrl H3K4me3 rep2


title: morula oeKdm5b H3K4me3 rep1


title: morula oeKdm5bl input


title: morula oeKdm5b H3K4me3 rep2


title: morula ctrl H3K4me3 rep1


title: AAF0

city: La Jolla

first: Yifeng

last: Xia

address: 10010 North Torrey Pines Road

department: Laboratory of Genetics

institute: Salk Insitute

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequence reads were mapped to the mm9 mouse genome build using RNA-STAR v2.3.0e.
Raw reads of each individual gene were counted and normalized to fpkm using Cuffdiff v2.1.1.
Genome_build: mm9
Supplementary_files_format_and_content: genes_read_group_tracking file output from Cuffdiff.

source_name: mouse glioblastoma

growth_protocol: Mouse glioblastomas were induced by lentiviral vector expressing HrasG12V and shRNA against p53. Tumor tissues were isolated from mice reached clinical endpoints. Normal brain tissue was trimmed away from GFP+ tumor tissue using a dissecting microscope.

extract_protocol:
RNA was isolated using the Rneasy kit according to manufacturer's protocol with the addition of Dnase (Qiagen).
cDNA libraries were prepared using the TruSeq RNA Sample Prep kit (Illumina).

value: glioblastoma


title: TSC H3K27me3 rep2

source_name: mouse trophoblast stem cells

value: mouse trophoblast stem cells

value: H3K27me3(Diagnode, pAb-069-050)

value: mouse TS cell RO-7


title: TSC H3K4me3 rep3


title: TSC H3K27me3 rep1


title: ESC H3K4me3 rep2

source_name: mouse embryonic stem cells

value: mouse embryonic stem cells

value: mouse ES cell R1


title: TSC input


title: TSC H3K27me3 rep3


title: TSC H3K4me3 rep2


title: TSC H3K4me3 rep1


title: TE H3K27me3 rep2

value: trophoblast


title: TE H3K27me3 rep1


title: TE H3K4me3 rep2


title: ESC H3K4me3 rep1


title: TE H3K4me3 rep1


title: ICM H3K27me3 rep2

value: inner cell mass


title: ICM H3K27me3 rep1


title: TE input


title: ICM H3K4me3 rep2


title: ICM H3K4me3 rep1


title: ICM input


title: morula H3K27me3 rep1


title: morula input


title: morula H3K4me3 rep1


title: 8 cell H3K27me3 rep3

value: 8-cell embryo


title: 8 cell H3K27me3 rep2


title: morula H3K27me3 rep2


title: 8 cell H3K27me3 rep1


title: 8 cell H3K4me3 rep2


title: 8 cell H3K4me3 rep1


title: morula H3K4me3 rep3


title: 8 cell input


title: 4 cell H3K27me3 rep1

value: 4-cell embryo


title: 4 cell H3K27me3 rep2


title: 4 cell H3K27me3 rep3


title: 4 cell H3K4me3 rep3


title: 4 cell input


title: 2 cell H3K27me3 rep2

value: 2-cell embryo


title: 4 cell H3K4me3 rep1


title: 2 cell H3K27me3 rep3


title: 2 cell H3K27me3 rep1


title: 2 cell H3K4me3 rep3


title: 4 cell H3K4me3 rep2


title: 2 cell input


title: 2 cell H3K4me3 rep1


title: 2 cell H3K4me3 rep2


title: MII Oocyte H3K27me3 rep2

source_name: MII oocyte

value: MII Oocyte


title: MII Oocyte H3K27me3 rep1


title: MII Oocyte H3K4me3 rep4


title: morula H3K4me3 rep2


title: MII Oocyte Input


title: MII Oocyte H3K4me3 rep1


title: MII Oocyte H3K4me3 rep3


title: P19_RXRa_24h_ATRA

city: Illkirch; Strasbourg

first: Marco Antonio

last: Mendoza-Parra

address: 1, rue Laurent Fries

country: France

institute: IGBMC

data_processing:
ChIP-seq and related datasets (FAIRE-seq; Input control) were quality certified with NGS-QC Generator tool (www.ngs-qc.org). Specifically, this methodology allows providing enrichment quality descriptors discretized in a scale ranging from “AAA” (Best) to “DDD” (worst).
Relevant binding sites in all ChIP-Seq and FAIRE-Seq datasets were identified with MeDiChISeq, a regression-based approach which after a learning process defines a representative binding pattern from the dataset under analysis (Mendoza-Parra et al; BMC Genomics 2013). Specifically a P-value confidence cutoff of 1x10-2.5 complemented by a peak intensity threshold based on a Poisson distribution background model.
Genome-wide quantile normalization prior multiprofiles comparison has been performed with EPImetheus (Saleem MA; unpublished).
Genome_build: mm9
Supplementary_files_format_and_content: peaks (MeDiChISeq) and quality report (pdf)

source_name: P19 embryonal carcinoma cells

growth_protocol: F9 EC cells were cultures in Dubelcco’s modified Eagle’s medium supplemented with 10% fetal Calf serum. In a similar manner, P19 cell’s medium was supplemented with 5% fetal Calf serum and 5% delipidated Calf serum. In both cases the medium was complemented with 40ug/ml Gentamicin. F9 or P19 EC cells were cultured in monolayer conditions seeded in gelatine-coated tissue culture plates (0.1%).

extract_protocol:
F9 or P19 EC cells were fixed with 1% para-formaldehyde (Electron Microscopy Sciences) for 30 minutes at room temperature. ChIP assays were performed following previously described conditions: chromatin sonication and immunoprecipitation in lysis buffer (50mM Tris–Cl pH=8, 140mM NaCl, 1mM EDTA, 1% Triton, 0.1% Na-deoxycholate) complemented with protease inhibitor cocktail (Roche 11873580001); 2x washes with lysis buffer; 2x washes with lysis buffer containing 360mM NaCl; 2x washes with washing buffer (10mM Tris–Cl pH=8, 250mM LiCl, 0.5% NP-40, 1mM EDTA, 0.5% Na-deoxycholate); 2x washes with 1x TE; elution at 651C; 15 min in elution buffer (50mM Tris–Cl pH=8, 10mM EDTA, 1% SDS). RXRa has been immunoprecipitated with purified polyclonal antibodies generated by immunization of rabbits with the following peptide:mRXRa: PB105 (MDTKHFLPLDFSTQVNSSSLNSPTGRGC). RXRa ChIP assays were performed with 6x106 cells per time point; while histone modification marks were evaluated with 2x106 cells. FAIRE assays were performed as described previously (Giresi et al, 2007; Simon et al, 2012).
qPCR-qualified ChIP assays were quantified (Qubit dsDNA HS assay kit; Invitrogen); then 10 ng of the ChIPed material was used for preparing Illumina sequencing libraries following a multiplexing approach (NEXTflexTM ChIP-seq Bioo Scientific;  ref: 514120). Prepared sequencing libraries were sequenced on the Illumina instrument HiSeq2000 (4 ChIP samples per lane). Regular Illumina pipelines were used for image processing and base calling. Sequence files were then aligned to the mouse genome assembly following by default parameters (mm9; Bowtie).

treatment_protocol: For cell differentiation induction, ATRA was added to plates in a final concentration of 1x10-6 M at different time points. For RAR subtype-specific agonists’ treatment, cells were incubated with BMS961 (RARg specific; final concentration 1x10-7 M), BMS753 (RARa specific; final concentration 1x10-6 M) or BMS641 (RARb specific; final concentration 1x10-7 M).

tag: cell type

tag: agent

value: ATRA

tag: time point

value: 24 hours


title: P19_RXRa_48_ATRA

value: 48 hours


title: F9_INPUT_control

source_name: F9 embryonal carcinoma cells

value: EtOH


title: P19_INPUT_control


title: P19_RXRa_6h_ATRA

value: 6 hours


title: P19_RXRa_2h_ATRA

value: 2 hours


title: P19_RXRa_48_EtOH


title: MII Oocyte H3K27me3 rep3


title: P19_H3K27me3_24h_ATRA

value: Millipore 07-449


title: P19_RNAPol2_48_ATRA

value: Santa Cruz sc-9001


title: P19_RNAPol2_48_EtOH


title: P19_H3K27me3_2h_ATRA


title: P19_H3K27me3_6h_ATRA


title: P19_H3K4me3_48_ATRA

value: Abcam ab8580


title: P19_RNAPol2_6h_ATRA


title: P19_H3K4me3_24h_ATRA


title: P19_FAIRE-seq_48h_ATRA


title: P19_H3K4me3_48h_EtOH


title: MII Oocyte H3K4me3 rep2

value: H3K4me3(Cell signaling Technology, #9727)


title: P19_FAIRE-seq_6h_ATRA


title: P19_FAIRE-seq_24h_ATRA


title: P19_FAIRE-seq_48h_EtOH


title: P19_RNAPol2_2h_ATRA


title: P19_RNAPol2_24h_ATRA


title: F9_RXRa_48_ATRA


title: P19_H3K27me3_48_ATRA


title: F9_RXRa_2h_ATRA


title: P19_FAIRE-seq_2h_ATRA


title: F9_RNAPol2_24h_ATRA


title: F9_RXRa_48_EtOH


title: P19_H3K4me3_2h_ATRA


title: F9_RXRa_6h_ATRA


title: P19_H3K4me3_6h_ATRA


title: P19_H3K27me3_48_EtOH


title: F9_RNAPol2_6h_ATRA


title: F9_RNAPol2_48_ATRA


title: F9_RNAPol2_2h_ATRA


title: F9_RNAPol2_48_EtOH


title: F9_H3K27me3_24h_ATRA


title: ChIP-Seq sperm K4Me3 rep1

city: Beijing

first: Bingjie

last: Zhang

state: Beijing

address: 30 Shuangqing Rd

institute: Tsinghua University

description: processed data files: sperm_K4me3_broadpeak.bed.gz

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
RNA-Seq reads were aligned to the mm9 genome assembly using Tophat version 2.0.11, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: The bed files include RPKM values in 100bp bins for each ChIP-seq sample. Bed files labeled maternal or paternal contain RPKM values for two parental alleles, allelic reads were normalized to total reads number. Tab-delimited text files include FPKM values RNA-seq sample.

source_name: Sperm

extract_protocol:
Pure sperm were treated with DTT and NEM
ChIP-Seq libraries were prepared using TELP developed by PengXu et al. with slightly modification

treatment_protocol: Dissect the caudal epididymi from adult males. Make small cuts in each epididymis. Add 3 ml of Donners medium and incubate the tube at 37 °C for 1 h. Collect the upper 2.5 ml of the liquid from each tube. Spin the mixture at 2,500g for 6 min at 4 °C and discard the supernatant

value: PWK

value: Sperm

value: custom-made H3K4Me3 antibody (Abmart)


title: ChIP-Seq Paternal pronucleus of PN3 zygote K4Me3

source_name: Preimplantation embryo

extract_protocol:
Female pronuclei were collected using a piezo-drill micromanipulator and the residuals that contain male pronuclei were then treated by pronase to remove the zona pellucida. After that, these samples were incubated in lysis buffer for ChIP-seq.
ChIP-Seq libraries were prepared using TELP developed by PengXu et al. with slightly modification

treatment_protocol: Zygotes at PN3-4 stage were collected from superovulated C57BL/6N female that mated to BDA/2N males. Female pronuclei were collected using a piezo-drill micromanipulator and the residuals that contain male pronuclei were then treated by pronase to remove the zona pellucida. After that, these samples were incubated in lysis buffer for ChIP-seq.

value: Preimplantation embryo


title: F9_H3K27me3_6h_ATRA


title: ChIP-Seq sperm K4Me3 rep2

value: sperm

value: custom-made H3K4Me3 antibody

tag: chip antibody vendor

value: Abmart


title: F9_H3K27me3_2h_ATRA

value: ATRA


title: ChIP-Seq Maternal pronucleus of PN3 zygote K4Me3

tag: strain


title: PN3_2cell_early_amanitin_RNA_rep1

description: processed data file: early_2cell_alpha_amanitin_FPKM.txt.gz

molecule: polyA RNA

extract_protocol:
After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
RNA-Seq libraries were prepared using Smart-Seq2 protocol with slightly modification

treatment_protocol: To inhibit transcription, zygotes at PN2-3 stage were cultured to early 2-cell stage in CZB supplemented with alpha-Amanitin.

value: C57BL/6N x PWK

tag: tissue/cell type


title: PN3_2cell_early_amanitin_RNA_rep2


title: F9_RXRa_24h_ATRA

value: 24 hours


title: F9_H3K27me3_48_EtOH

value: EtOH

value: 48 hours


title: F9_H3K4me3_48_ATRA


title: F9_H3K4me3_24h_ATRA


title: conventional ChIP-Seq mESC K27Me3

source_name: Embryonic stem cell

extract_protocol:
mES cells were washed with PBS and incubated in lysis buffer.
ChIP-Seq libraries were prepared as described by RenBing' lab

treatment_protocol: Mouse ES cells were cultured without irradiated mouse embryonic fibroblasts (MEFs) in DMEM containing 15% FBS, leukemia inhibiting factor (LIF), penicillin/streptomycin, L-glutamine, β-mercaptoethanol, and non-essential amino acids. After digestion with 0.05% trypsin, counted cells were lysed for STAR ChIP-seq or Smart-seq2.

value: Embryonic stem cell

value: Diagenode

tag: chip antibody cat. #


title: ChIP-Seq 2-cell late K27Me3 with ActiveMotif antibody

extract_protocol:
After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
ChIP-Seq libraries were prepared using TELP developed by PengXu et al. with slightly modification (Peng, Xu, et al. "TELP, a sensitive and versatile library construction method for next-generation sequencing." Nucleic acids research (2014): gku827.)

value: ActiveMotif


title: ChIP-Seq E13.5 female PGC K27Me3

source_name: primordial germ cell

extract_protocol:
PGCs were washed with PBS and incubated in lysis buffer.
ChIP-Seq libraries were prepared using TELP developed by PengXu et al. (PMID: 25223787) with slightly modification.

value: primordial germ cell


title: ChIP-Seq cortex K27Me3

source_name: Somatic cortex

extract_protocol:
Tissue cells were washed with PBS and incubated in lysis buffer.
ChIP-Seq libraries were prepared using TELP developed by PengXu et al. (PMID: 25223787) with slightly modification.

value: Somatic cortex


title: F9_H3K4me3_2h_ATRA

value: 2 hours

value: Abcam ab8580


title: F9_H3K27me3_48_ATRA

value: Millipore 07-449


title: F9_FAIRE-seq_48h_ATRA


title: F9_H3K4me3_48h_EtOH


title: ChIP-Seq 500-cell-number mESC K27Me3

description: ChIP-seq of exact 1000 mES cells

extract_protocol:
mES cells were washed with PBS and incubated in lysis buffer.
ChIP-Seq libraries were prepared using TELP developed by PengXu et al. (PMID: 25223787) with slightly modification.


title: ChIP-Seq 1000-cell-number mESC K27Me3

description: ChIP-seq of exact 500 mES cells.


title: ChIP-Seq epiblast E6.5 K27Me3 rep2

description:
processed data file: E6.5_epiblast_k27me3.bed.gz; E6.5_epiblast_K27me3_maternal.bed.gz
E6.5_epiblast_k27me3_broadpeak.bed.gz, E6.5_epiblast_k27me3_maternal_broadpeak.bed.gz, E6.5_epiblast_k27me3_paternal_broadpeak.bed.gz

source_name: E6.5 epiblast

extract_protocol:
embryonic cells were washed with PBS and incubated in lysis buffer.
ChIP-Seq libraries were prepared using TELP developed by PengXu et al. (PMID: 25223787) with slightly modification.

treatment_protocol: To isolate E5.5 or E6.5 epiblast and extraembryonic ectoderm, naturally mated female mice were sacrificed and embryos were dissected from uterus, decidua and Reichert’s membrane in a dish containing DMEM plus 10% FBS. Carefully cut off ectoplacental cone using syringe needle and subject embryos to pancreatic and trypsin enzyme digestion for 2~3 minutes. Embryos were recovered 5 minutes in DMEM medium plus 10% FBS. Gently suck and blow the embryo into a capillary pipet to remove the visceral endoderm and then cut off epiblast and extraembryonic ectoderm along the boundary of embryonic and extraembryonic region using syringe needle.

value: E6.5 epiblast


title: ChIP-Seq 2cell alpha-amanitin K27Me3

extract_protocol:
After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
ChIP-Seq libraries were prepared using TELP developed by PengXu et al. (PMID: 25223787) with slightly modification.

treatment_protocol: Late zygotes (PN5) and early 2-cell embryos were cultured in CZB supplemented with alpha-Amanitin for about 14h.

value: Preimplantation embryo


title: F9_FAIRE-seq_24h_ATRA


title: F9_FAIRE-seq_6h_ATRA

value: 6 hours


title: F9_FAIRE-seq_48h_EtOH


title: ChIP-Seq ICM K27Me3 rep2

description:
processed data file: ICM_k27me3.bed.gz; ICM_k27me3.bed.gz; ICM_K27me3_maternal.bed.gz
ICM_k27me3_broadpeak.bed.gz, ICM_k27me3_maternal_broadpeak.bed.gz, ICM_k27me3_paternal_broadpeak.bed.gz

source_name: Inner cell mass

treatment_protocol: Embryos were collected from C57BL/6N mice induced to superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours apart and mated to PWK males. Each set of embryos at a particular stage was flushed from the reproductive tract at defined time periods after hCG administration: 20h (MII oocyte), 27-28h (PN5 zygote), 30h (early 2-cell), 43h (late 2-cell), 54-56 h (4-cell), 68-70 h (8-cell) and 92-94 h (blastocysts) in Hepes-buffered CZB medium. The zona pellucida of embryos selected by cell number or morphology was gently removed by treatment of 10 IU/ml pronase (Sigma P8811) for several minutes. The embryos were then manually picked and treated with the lysis buffer for STAR ChIP-seq or Smart-seq2.

value: Inner cell mass


title: ChIP-Seq ICM K27Me3 rep1

description:
processed data file: ICM_k27me3.bed.gz; ICM_K27me3_maternal.bed.gz
ICM_k27me3_broadpeak.bed.gz, ICM_k27me3_maternal_broadpeak.bed.gz, ICM_k27me3_paternal_broadpeak.bed.gz


title: ChIP-Seq 2-cell K27Me3 rep2

description:
processed data file: 2cell_k27me3.bed.gz; 2cell_K27me3_maternal.bed.gz
2cell_k27me3_broadpeak.bed.gz, 2cell_k27me3_maternal_broadpeak.bed.gz, 2cell_k27me3_paternal_broadpeak.bed.gz


title: ChIP-Seq 8-cell K27Me3


title: ChIP-Seq 2-cell early K27Me3


title: ChIP-Seq PN5 zygote K27Me3 rep2

description:
processed data file: PN5_zygote_k27me3.bed.gz; PN5_zygote_K27me3_paternal.bed.gz; PN5_zygote_K27me3_maternal.bed.gz
PN5_zygote_k27me3_broadpeak.bed.gz, PN5_zygote_k27me3_maternal_broadpeak.bed.gz, PN5_zygote_k27me3_paternal_broadpeak.bed.gz


title: ChIP-Seq 2-cell K27Me3 rep1


title: ChIP-Seq PN5 zygote K27Me3 rep1


title: ChIP-Seq GV 8weeks  K27Me3

source_name: GV oocyte

treatment_protocol: Collection of 8w GV oocytes from 5IU PMSG injected C57BL/6N mice was performed 44-48h after hCG injection, followed by hyaluronidase treatment to remove cumulus cells.

value: GV oocyte


title: ChIP-Seq growing oocyte 14days K27Me3

source_name: Growing oocyte

treatment_protocol: Follicles were isolated from 14-day old C57BL/6 mice by mechanical dissection using a 26 gauge needle, followed by the digestion with 4 mg/ml of collagenase I and 0.02 mg/ml of DNase I in L15 medium for 30 min at 37°C. To remove the granulosa cells, the dissociated oocyte-granulosa cells complexes were transferred into PBS (Ca2+, Mg2+-free) containing 1 mg/ml of collagenase I and were digested for 20 min. Oocytes were then incubated in lysis buffer after removing the zona pellucida by pronase treatment.

value: Growing oocyte


title: ChIP-Seq MII oocyte K27Me3 rep2

description:
processed data file: MII_oocyte_k27me3.bed.gz
MII_oocyte_k27me3_broadpeak.bed.gz

treatment_protocol: Collection of MII oocytes from superovulated C57BL/6N mice was performed 20h after hCG injection.

value: MII oocyte


title: ChIP-Seq liver K27me3

source_name: Somatic liver

value: Somatic liver


title: ChIP-Seq growing oocyte 7days K27Me3

treatment_protocol: Follicles were isolated from 10-day old C57BL/6 mice by mechanical dissection using a 26 gauge needle, followed by the digestion with 4 mg/ml of collagenase I and 0.02 mg/ml of DNase I in L15 medium for 30 min at 37°C. To remove the granulosa cells, the dissociated oocyte-granulosa cells complexes were transferred into PBS (Ca2+, Mg2+-free) containing 1 mg/ml of collagenase I and were digested for 20 min. Oocytes were then incubated in lysis buffer after removing the zona pellucida by pronase treatment.


title: ChIP-Seq epiblast E6.5 K27Me3 rep1

value: C57BL/6N x PWK


title: F9_FAIRE-seq_2h_ATRA

value: ATRA


title: RNA-Seq 2cell alpha-amanitin

description: processed data file: FPKM_inhibition.txt.gz


title: RNA-Seq 2cell aphidicolin rep2

treatment_protocol: Late zygotes (PN5) and early 2-cell embryos were cultured in CZB medium supplemented with Aphidicolin for about 14h.


title: RNA-Seq PN5 zygote alpha-amanitin


title: RNA-Seq ICM rep1

description: processed data file: FPKM_stage.txt.gz

treatment_protocol: Embryos were collected from C57BL/6N mice induced to superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin(Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours apart and mated to PWK males. Blastocysts from E3.5-4.0 were incubated in a 1:3 dilution of anti-mouse rabbit serum in DMEM for 20 min, washed in PBS and further incubated for 20 min in a 1:5 dilution of rat serum in DMEM for the complement reaction. The ICM was subsequently cleaned from lysed trophectoderm with a narrow glass pipette.


title: RNA-Seq 8cell_rep2

description: processed data file: FPKM_stage.txt.gz


title: RNA-Seq 8cell_rep1

description: processed data file: FPKM_stage.txt.gz


title: RNA -seq ICM rep2

description: processed data file: FPKM_stage.txt.gz


title: ChIP-Seq E5.5 epiblast K27Me3

source_name: E5.5 epiblast

value: E5.5 epiblast

value: Diagenode


title: RNA-Seq 4cell_rep2

description: processed data file: FPKM_stage.txt.gz


title: RNA-Seq 4cell_rep1

description: processed data file: FPKM_stage.txt.gz


title: RNA-Seq 2cell_late_rep2

description: processed data file: FPKM_stage.txt.gz


title: RNA-Seq 2cell_late_rep1

description: processed data file: FPKM_stage.txt.gz


title: RNA-Seq 2cell_early_rep2

description: processed data file: FPKM_stage.txt.gz


title: RNA-Seq zygote_PN5_rep2

description: processed data file: FPKM_stage.txt.gz


title: ChIP-Seq MII oocyte K27Me3 rep1


title: RNA-Seq 2cell_early_rep1

description: processed data file: FPKM_stage.txt.gz


title: RNA-Seq zygote_PN5_rep1

description: processed data file: FPKM_stage.txt.gz


title: RNA-Seq MII_oocyte_rep1

description: processed data file: FPKM_stage.txt.gz


title: RNA-Seq MII_oocyte_rep2

description: processed data file: FPKM_stage.txt.gz


title: RNA-Seq Growing_oocyte_14days

description: processed data file: FPKM_stage.txt.gz


title: RNA-Seq Growing_oocyte_10days

description: processed data file: FPKM_stage.txt.gz


title: ChIP-Seq PWK sperm K27Me3

source_name: Mature sperm

extract_protocol:
Pure sperm were treated with DTT and NEM
ChIP-Seq libraries were prepared using TELP developed by PengXu et al. (PMID: 25223787) with slightly modification.

value: PWK

value: Mature sperm


title: RNA-Seq 2cell aphidicolin rep1


title: ChIP-Seq 500 mESC K27Ac

growth_protocol: mESCs were cultured routinely in LIF and serum medium.

extract_protocol:
After washing with PBS, mESCs were incubated in lysis buffer
ChIP-Seq libraries were prepared using TELP developed by PengXu et al. with slightly modification

value: Embryonic stem cell

value: custom-made H3K4Me3 antibody (Abmart)


title: ChIP-Seq 1000 mESC K27Me3


title: ChIP-Seq 500 mESC commercial antibody K4Me3


title: ChIP-Seq 200 mESC K4Me3 rep1


title: ChIP-Seq 500 mESC K4Me3 rep1


title: Vehicle5

city: East Lansing

first: Uros

last: Midic

state: MI

address: 474 S. Shaw Lane

department: Animal Sciences

institute: Michigan State University

data_processing:
Illumina Real Time Analysis (RTA) v1.18.6
TopHat 2.1.1 alignment to combined MacaM v7 (Macaca mulatta) + NCBI GRCm38 (Mus musculus) assemblies
Trimming 6 bases from 5' end of unaligned reads (from first alignment); alignment of trimmed reads
Trimming 6 bases from 5' end of unaligned reads (from second alignment); alignment of trimmed reads
Merging accepted_hits.bam from three alignment step (samtools merge)
Filtering of .bam files, using proprietary Python code, to remove alignment records for reads originating from mouse feeder cells (best alignment is to mouse genome)
Cuffdiff 2.2.1 comparisons of 5 Vehicle libraries and each group of 4 or 5 toxicant treated libraries
Genome_build: MacaM_Assembly_v7 (Macaca mulatta) + GRCm38.p5 (Mus musculus)
Supplementary_files_format_and_content: gene_exp.diff files (one for each toxicant) are produced by Cuffdiff; FPKMs.fpkm file contains FPKM values extracted from genes.read_group_tracking files produced by Cuffdiff

organism: Macaca mulatta

source_name: Vehicle control-treated ESCs

growth_protocol: Oregon Rhesus Macaque Embryonic Stem (ORMES)-6 line cells were maintained on feeder layers of mouse embryonic fibroblast (mEF) cells that had been mitotically inactivated. Cell were maintained in Dulbecco’s modified Eagle/F-12 medium (DMEM/F12, 11320-033; Invitrogen, Carlsbad, CA) supplemented with 15% fetal bovine serum (Hyclone, Logan, UT), 1% minimum essential medium (MEM) nonessential amino acids, 1 mM L-glutamine, 0.1 mM β-mercaptoethanol, and 0.1% gentamycin in 60-mm cell culture dishes (Mitalipov et al., 2006). Cultures were incubated at 37°C in 5% CO2 and 5% O2. Components for cell culture medium were purchased from Sigma (St. Louis, MO) unless otherwise noted.

extract_protocol:
The cells were harvested and lysed approximately 24 hrs after the last media change.  At harvest, all colonies in each well were cut and lifted, and divided into two microcentrifuge tubes, and centrifuged at 3,000 x g for three min and supernatant removed. Cells were resuspended in 1 mL DPBS with 10% BSA and 25 mM EDTA and centrifuged as above. Supernatant was removed and the remaining cell pellet was lysed in 100 ul PicoPureTM extraction buffer (Thermo Fisher Scientific, Life Technologies, Grand Island, NY). RNA was isolated following the PicoPureTM RNA Extraction kit manufacturer protocol, with DNAse digestion to remove any contaminating DNA.
100 ng of each RNA sample were processed first using the Ovation RNA-Seq System v2 using  Ribo-SPIATM Technology (Nugen, San Carlos, CA). This was followed by fragmentation to an average of 300 bp using a Covaris-2 sonicator and a brief S1 nuclease digestion.  After purification, the cDNA was processed through the Ovation Ultralow DR Multiplex Systems 1-8 and 9-16 (NuGen) for end repair, barcoding and final library production. Barcoded libraries were pooled, loaded on flowcells and sequenced with Illumina HISeq 2500 in rapid run mode to generate 50 nt single end reads. The samples were loaded at 65% of optimal loading concentration, along with PhiX Control library (Illumina) added at 10% of loading concentration to increase read sequence complexity.
50bp single-end RNAseq

treatment_protocol:
ESC colonies were cultured in 6-well plates (Falcon 353046), 1 plate for each treatment group. Approximately 40 random colonies per dish were transferred to fresh feeder layers each time ESC colonies were passaged, which occurred every 3 to 4 days. Colonies for passage were taken from a pre-marked, wedge-shaped section of each dish to assure a random sample. Media changes were performed daily (2 mL) and experimental treatments continued for a total of four weeks.
Chemicals for testing were made as 1000x stocks in methanol and were added to aliquots of ESC maintenance medium up to 48 hours before use and stored at 4°C until use. Chemicals were obtained from Sigma (DEHP: Bis(2-ethylhexyl) phthalate – 47994; PFOA: Perfluorooctanoic acid – 171468; ATR: Atrazine – 45330; TBT: Tributyltin chloride – 442869; BPA: Bisphenol A – 133027).  Treatment groups included a vehicle control (methanol) and each of five EDCs at environmentally relevant doses [10 nM BPA (36 nM fetal serum), 5 uM DEHP (7.7uM pubertal serum), 30 uM ATR (up to 7 uM drinking water reported), 100 nM PFOA (average 94 nM >12 year old serum), and 25 nM TBT (0.17 – 534 adult nM serum).

value: Methanol (vehicle control)

tag: passages

value: Embryonic stem cells


title: Vehicle2


title: Vehicle3


title: ChIP-Seq 5000 mESC K4Me3


title: ChIP-Seq 2000 mESC K4Me3


title: Vehicle1


title: TBT5

source_name: Tributyltin chloride-treated ESCs

value: Tributyltin chloride


title: Vehicle4


title: TBT3


title: TBT4


title: RNA-Seq GV_8weeks

description: processed data file: FPKM_stage.txt.gz


title: ChIP-Seq MII oocyte commercial antibody K4Me3

source_name: MII oocyte

extract_protocol:
After removing the zona pellucida, embryonic cells were washed with PBS and incubated in lysis buffer.
ChIP-Seq libraries were prepared using TELP developed by PengXu et al. with slightly modification


title: ChIP-Seq PN5 zygote histone H3

value: Preimplantation embryo


title: ChIP-Seq 2cell aphidicolin K4Me3

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq peaks were called using MACS2 with the parameters --broad --nomodel --nolambda and noisy peaks with very weak signals (summed RPKM < 30) were removed.
RNA-Seq reads were aligned to the mm9 genome assembly using Tophat version 2.0.11, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: The bed files counted by the number of reads falling into 100bp bin in the genome. Tab-delimited bed files include RPKM values for each sample. The peak files included regions of all peaks called in each sample.


title: TBT1


title: ChIP-Seq 2cell alpha-amanitin K4Me3


title: ChIP-Seq epiblast E6.5 K4Me3

treatment_protocol: To isolate the E6.5 epiblast from post-implantation embryos, extraembryonic ectoderm was removed firstly with a wide, mouth-controlled pipette. Through a narrow glass pipette, the visceral endoderm was then mechanically separated.

value: E6.5 epiblast


title: PFOA4

source_name: Perfluorooctanoic acid-treated ESCs

value: Perfluorooctanoic acid


title: ChIP-Seq ICM K4Me3 rep2

description: processed data files: ICM_K4me3_broadpeak.bed.gz, ICM_maternal_broadpeak.bed.gz, ICM_paternal_broadpeak.bed.gz

value: Inner cell mass


title: ChIP-Seq cortex K4Me3

source_name: Cortex

treatment_protocol: The cortex tissue was isolated from 8-week old male C57BL/6 mice following a protocol that was previously described by ENCODE: http://genome.ucsc.edu/ENCODE/protocols/cell/mouse/Cortex_Ren_protocol.pdf.

value: Cortex


title: PFOA2


title: PFOA5


title: PFOA3


title: ChIP-Seq ICM K4Me3 rep1


title: PFOA1


title: DEHP4

value: Bis(2-ethylhexyl) phthalate


title: ChIP-Seq 8-cell K4Me3 rep2

description: processed data files: 8cell_K4me3_broadpeak.bed.gz, 8cell_maternal_broadpeak.bed.gz, 8cell_paternal_broadpeak.bed.gz

value: C57BL/6N x PWK


title: ChIP-Seq 8-cell K4Me3 rep1


title: ChIP-Seq 4-cell K4Me3 rep2

description: processed data files: 4cell_K4me3_broadpeak.bed.gz, 4cell_maternal_broadpeak.bed.gz, 4cell_paternal_broadpeak.bed.gz


title: DEHP3


title: BPA5

source_name: Bisphenol A-treated ESCs

value: Bisphenol A


title: ChIP-Seq 4-cell K4Me3 rep1

source_name: Preimplantation embryo


title: DEHP1


title: ChIP-Seq 2-cell early K4Me3 rep2

description: processed data files: 2cell_early_K4me3_broadpeak.bed.gz, 2cell_early_maternal_broadpeak.bed.gz, 2cell_early_paternal_broadpeak.bed.gz


title: TBT2


title: DEHP2


title: BPA4


title: BPA3


title: ChIP-Seq PN5 zygote K4Me3 rep2

description: processed data files: PN5_zygote_K4me3_broadpeak.bed.gz, PN5_zygote_maternal_broadpeak.bed.gz, PN5_zygote_paternal_broadpeak.bed.gz


title: ChIP-Seq PN5 zygote K4Me3 rep1


title: BPA1


title: ATR5

source_name: Atrazine-treated ESCs

value: Atrazine


title: ChIP-Seq 2-cell late K4Me3 rep1

description: processed data files: 2cell_late_K4me3_broadpeak.bed.gz, 2cell_late_maternal_broadpeak.bed.gz, 2cell_late_paternal_broadpeak.bed.gz


title: ATR4


title: ChIP-Seq MII oocyte K4Me3 rep1

description: processed data files: MII_oocyte_K4me3_broadpeak.bed.gz

value: MII oocyte


title: ChIP-Seq 2-cell late K4Me3 rep2


title: ChIP-Seq GV 8weeks  K4Me3

value: GV oocyte


title: ChIP-Seq growing oocyte 14days K4Me3

value: Growing oocyte


title: ChIP-Seq 2-cell early K4Me3 rep1


title: V448_sRNAs

city: Murcia

first: Livia

last: Donaire

state: Murcia

address: Campus de Espinardo

department: Plant Pathology

country: Spain

institute: Centro de Edafología y Biología Aplicada del Segura

data_processing:
Library strategy: smallRNA-Seq
Illumina Casava1.7 software used for basecalling.
sequence reads were trimmed for adapter sequences using AdapterRemoval
Reads were filtered by length in 18 to 30 nts and unique reads were count using our own Perl scripts
Supplementary_files_format_and_content: unique sequences and their abundance

organism: Botrytis cinerea

source_name: Mycellium

growth_protocol: Stock cultures were stored in 20% glycerol at -80ºC and in potato dextrose agar (PDA) plates at 4ºC.

extract_protocol:
Fresh mycelia were dried by pressing with sterile filter paper and total RNA was purified from 1 g of dry mycelia using TRIZOL reagent (Invitrogen) as described (Rodríguez-García et al. 2014)
5-10 ug of total RNA was used for library preparation as described (Al Rwahnih et al. 2011) and subjected to deep-sequencing using the Illumina platform (HiSeq2000, 2 x 100 bp length, IGA Technology Services, Udine, Italy, http://www.igatechnology.com) (Donaire et al. 2016)

tag: origin

value: Grapevine


title: ATR1


title: ChIP-Seq oocyte K4Me3 zebrafish

organism: Danio rerio

source_name: Zebrafish oocyte

extract_protocol:
In order to deyolk oocytes (where yolk mass were highly abundant), dechorionated oocytes were transferred into a 1.5ml tube and washed with PBS for several times, then disrupted with 200ul tips. The cells of oocytes were spun down at 5000rpm for 5 min at 4°C. The remaining cells were incubated in lysis buffer
ChIP-Seq libraries were prepared using TELP developed by PengXu et al. with slightly modification

treatment_protocol: The wild-type zebrafish lines Tübingen (Tu) and AB were utilized in this study. Unfertilized oocytes were obtained by squeezing the females gently on the ventral side. Next, the oocytes were activated by adding 3ml fresh holfreter (0.05g/L KCl, 0.1g/L CaCl2, 0.025g/L NaHCO3, 3.5g/L NaCl, pH 7.0) in 35mm dishes, and then followed by standard pronase dechorionation treatment

value: AB

value: Zebrafish oocyte


title: ChIP-Seq growing oocyte 10days K4Me3

value: custom-made H3K4Me3 antibody (Abmart)


title: BPA2

value: Embryonic stem cells


title: Pi285.8_sRNAs

value: Pepper


title: V446_sRNAs

organism: Botrytis paeoniae


title: ChIP-Seq growing oocyte 7days K4Me3

treatment_protocol: Follicles were isolated from 7-day old C57BL/6 mice by mechanical dissection using a 26 gauge needle, followed by the digestion with 4 mg/ml of collagenase I and 0.02 mg/ml of DNase I in L15 medium for 30 min at 37°C. To remove the granulosa cells, the dissociated oocyte-granulosa cells complexes were transferred into PBS (Ca2+, Mg2+-free) containing 1 mg/ml of collagenase I and were digested for 20 min. Oocytes were then incubated in lysis buffer after removing the zona pellucida by pronase treatment.


title: AB-C1

status: Public on Sep 14 2016

city: Ithaca

first: John

last: Schimenti

state: New York

address: Veterinary Research Tower T9 007

department: Molecular Biology and Genetics

institute: Cornell University

description: High Arid1a

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.5 (-m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0.13 (--no-novel-juncs --library-type fr-firststrand) was used to map reads to the Mouse mm10 reference genome (UCSC).
cuffquant (--no-novel-juncs --library-type fr-firststrand) was used to quantify transcripts based on the Mouse mm10 reference transcriptome (UCSC).
cuffdiff v2.2.1 (--library-type fr-firststrand) was used to call differentially expressed genes based on the Mouse mm10 reference transcriptome (UCSC).
Genome_build: Mouse mm10 (UCSC)
Supplementary_files_format_and_content: Tab delimited text files including counts, FPKM values, and p-values generated from Cuffdiff2 when corrected for multiple hypothesis testing

source_name: High Arid1a_mammary tumor cells

extract_protocol:
Cancer cells were lysed on culture dishes and RNA was extracted using TOTLA RNA I etraction kit (Omega-Biotek). Total RNA was treated with DNAse (ThermoFisher RapidOut) prior to library preparation.
Directional RNA-seq libraries were prepared from 500ng total RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: AB-C1 and AB-C2 cells were transduced with a lentivirus expression vector for over-expression of Arid1a gene.

tag: arid1a expression

value: High Arid1a

value: mammary tumor cells


title: UT-R2

description: Low Arid1a

source_name: Low Arid1a_mammary tumor cells

value: Low Arid1a


title: AB-C2

description: High Arid1a


title: UT-R1

description: Low Arid1a


title: ATR3


title: ChIP-Seq MII oocyte K4Me3 rep2


title: caki1.si.ctl

city: Ann Arbor

first: Chinnaiyan

middle: M

last: Arul

state: Michigan

address: 5309 Comprehensive Cancer Center, 1400 E. Medical Center Drive

department: Michigan Center for Translational Pathology

institute: University of Michigan

description:
Non Target siRNA
SI_13579
RIN=10

data_processing:
Following sequencing and base-calling, RNA-seq data was aligned using STAR (2.4.0g1) to the GRCh38.p1 reference genome, using the “basic” version of gencode 22 to construct the splice junction database. Expression of protein-coding genes was quantified by counting the reads overlapping exons of annotated protein coding genes in strand-specific mode.
Genome_build: GRCh38.p1
Supplementary_files_format_and_content: text (tab delimited) file that contains serial number, HUGO gene symbol, followed by FPKM values in each experimental condition.

source_name: Kidney

growth_protocol: Caki-1, HK2 and A704 cells were purchased from ATCC and grown in McCoy, Keratinocyte and RPMI media supplemented with 10% FBS, penicillin, and streptomycin.

extract_protocol:
Total RNA was isolated using miRNA easy kit (Qiagen) following manufacturer's protocol.
RNA-Seq libraries were generated using KAPA Stranded RNA-Seq Library Preparation Kit (Kappa Biosystems) following the manufacturer's instruction

treatment_protocol: siRNAs were obtained from Ambion and transfected (25nM) using Lipofectamine RNAimax (Invitrogen).  For transfection 0.4 million cells were plated in a 6-well plate before transfection. 48 hrs after transfection cells were trypsinized, counted and replated for proliferation assay. Remaining cells were used for total RNA isolation.

tag: cell line

tag: disease state

value: Cancer

value: Epithelial

tag: si target

value: non-targeting


title: ATR2


title: hk2.si.ptpn.2

description:
PTPN14 siRNA -1
SI_13585
RIN=10

value: Normal


title: caki1.si.lats

description:
LATS siRNA
SI_13582
RIN=10

value: LATS


title: hk2.si.lats

description:
LATS siRNA
SI_13586
RIN=10


title: hk2.si.ctl

description:
Non Target siRNA
SI_13583
RIN=10


title: caki1.si.ptpn.1

description:
PTPN14-siRNA-2
SI_13580
RIN=10


title: caki1.si.ptpn.2

description:
PTPN14 siRNA -1
SI_13581
RIN=10


title: a704.si.ctl

description:
Non Target siRNA
SI_13587
RIN=9.6


title: a704.si.ptpn.1

description:
PTPN14-siRNA-2
SI_13588
RIN=10


title: hk2.si.ptpn.1

description:
PTPN14-siRNA-2
SI_13584
RIN=10


title: a704.si.ptpn.2

description:
PTPN14 siRNA -1
SI_13589
RIN=10


title: NT Poly b

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

institute: Weizmann Institute of Science

data_processing:
Reads were demultiplexed the reads into the different samples
Reads were aligned to the hg19 genome built using Tophat (v1.3.3)
Expression at the gene level was quantified by applying Partek Genomics Suite, and using the RefSeq in gtf format as annotation.
Differential expression was calculated utilizing the DESeq2 software (version 1.2.8).
For analysis of translational changes, a two-factor model including the RNA type (total or polysomal) and the genotype (NT or DAP5 KD) and the interaction between them was built using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file including DESeq2 normalized counts, the translation efficiency: fold change of the ratio:  (poly DAP5/Total DAP5)/(poly NT/Total NT), p-value and FDR for each gene.

source_name: shNT H9 cells

growth_protocol: hESC were grown on iMEF and passaged using colagenase IV. One passage before experiment, the cells were plated on Matrigel coated plates and grown with conditioned media contianing bFGF.

extract_protocol:
100ug/ml cyclohexamide was add to the meduim for 10min. Plates were wash and harvest in LBA (20mM Tris ph7.5, 45mM KCl, 10mM MgCl2, 0.1mg/ml CHX, 1mM DTT, 2.5ul/ml RNasin, Protease inhibitor cocktail) with 1% NP-40. 12 O.D of the cleared lysate were loaded on 10-50% sucrose gradients in LBA and centrifuge for 100min at 39,000 rpm in SW-41 rotor (Beckman Optima LE-80k Ultracentrifuge). The gradients were collected with Teledyne ISCO (UA-6), 0.5ml fractions were collected. 30l of 10% SDS and 1ml of 100% Ethanol was added to each fraction. The fractions were incubated at -20ºC overnight, and centrifuged for 15min at 20,000g. The pellet was resuspended in Tri-reagent and RNA was purified according to the protocol. For total RNA, the same procedure was done directly on lysate samples.
Total RNA (0.5 μg) was processed using the TruSeq RNA Sample Preparation Kit protocol (Illumina) according to the manufacture instructuctions . Libraries were evaluated by Qubit and Bioanalyzer. Sequencing libraries were constructed with barcodes to allow multiplexing of eight samples on one lane. The sequencing was run on an Illumina HiSeq 2000 instrument.

tag: state

value: Pluripotent

tag: passage

tag: molecule

value: Heavy polysomal RNA

tag: expression

value: shNT


title: DAP5 Tot b

source_name: shDAP5 H9 cells

value: Total Poly A+RNA


title: DAP5 Poly b


title: NT Tot b

value: Total PolyA+ RNA


title: NT Poly a


title: DAP5 Poly a


title: DAP5 Tot a

value: Total Poly A+ RNA


title: NT Tot a


title: MDA_MB_231_Ctrl

city: Lyon

first: Robert

last: Dante

address: 28, rue Laennec

department: Department of Tumoral Escape

institute: Cancer Research Center – Lyon

data_processing:
Reads were aligned on the UCSC Homo sapiens hg19 genome using TopHat2.
Differential expression analysis was performed using Cuffdiff from Galaxy web site
Only genes with at least 1 read per million (FPKM) in at least 2 of the samples were kept for subsequent analyses.
Genome_build: hg19
Supplementary_files_format_and_content: Cuffdiff  txt files contain, FPKM,  log2 of the fold change, and Pvalue, and qvalue for each studied of conditions.

source_name: cell line

growth_protocol: HMLER cell lines were kindly provided by Anne-Pierre Morel (CRCL, Lyon, France). They were cultivated as previously described (Morel et al. PLoS One 2008). MDA-MB-231 cell lines were human breast cancer cell  line.

extract_protocol:
Total RNA was extracted with the NucleoSpin RNA kit (Macherey-Nagel, Hoerdt, France) following the manufacturer's instructions. RNA purity and integrity were examined on agarose gel, and quantified with a NanoDrop 1000 (Thermo Scientific, Wilmington, DE).
Illumina TruSeq RNA sample preparation Kit.

treatment_protocol: Cells were seeded at 1.105 per well in six-well plates. The day after plating, cells were  treated every day with 10 µM of 5-aza-2'-deoxycytidine (Sigma-Aldrich). Cells were collected 72 h after the start of the treatments.

tag: treatment