title: D25_C

status: Public on Oct 03 2015

city: Jinan

first: Haichao

last: Lin

state: Shandong

address: Sangyuan Road 8.

institute: Institute of animal science and veterinary medicine Shandong academy of agricultural sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1, reads containing sequencing adaptors; 2, reads containing sequencing primer; 3, nucleotide with q quality score lower than 20) were removed.
For each sample, sequenced reads were aligned to to the UCSC (Sscrofa10.2) pig reference genome using Tophat package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. Tophat allows multiple alignments pe read (up to 20 by default) and a maximum of two mismatchs when mapping the reads to the reference. Tophat build a database of potential splice junctions and conforms these by comparing the previously unmapped reads against the database of putative junctions.
The aligned read files were processed by Cufflinks, which uses the normalized RNA-seq fragments counts to measure the relative abundances of the transcripts. The unit of measurement is Fragment Per Kilobase of exon per Million fragments mapped (FPKM).The reference GTF annotation file used in Cufflinks was downloaded from the UCSC database. Cufflink was used to de novo assemble the transcripiome at first; the second, Cuffmerge was used to comerge all transcripts of sample A and B to generate unique transcripts. The downloaded UCSC GTF file was passed to Cuffdiff along with the original alignment (SAM) files produced by Tophat. Cuffdiff re-estimates the abundance of the transcripts listed in the GTF file using alignments from the SAM file and concurrently test for different expression. Only the comparisons with /q value0 less than 0.01 and status marked as "OK" in the Cuffdiff output were regarded as showing differential expression.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Endometrium

extract_protocol:
The endometrium (containing the lamina epithelialis, lamina propria, and tela submucosa, but not the tunica muscularis) were taken from the middle portion of each uterine horn of each sow on day 12. The samples of endometrium (peel off embryo) in attachment site (day 18) and implantation site (day 25) were collected. All tissue samples for isolation of RNA were immediately transferred to RNAlater (Invitrogen), incubated overnight at 4℃, and stored at -80℃ until further use. RNA was harvested using Trizol reagent. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA).And then the paired-end sequencing were performed on an Illumina Hiseq2000 following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Endometrium of pregnancy

tag: Stage

value: Day 25 of pregnancy


title: 764_B1

status: Public on Oct 04 2015

type: SRA

city: Charlotte

first: Kevin

middle: Chad

last: Lambirth

state: NC

address: 9201 University City Blvd

department: Biological Sciences

country: USA

institute: University of North Carolina at Charlotte

library_source: transcriptomic

data_processing:
Sequence reads were trimmed of adapters, mapped to ver. 2.75 G. max reference genome using Tophat 2.0.10 with parameter -I 5000
Mapped reads were quantified using cufflinks 2.2.1 and parameters -u -b

molecule: total RNA

organism: Glycine max

source_name: Ground half-seed

growth_protocol: Soybean parental seeds were geminated in Miracle Grow potting soil mix and transferred to quart and gallon-sized pots during growth.  Light conditions and humidity conditions were kept constant for all plants, and watering was kept as consistant as possible.

extract_protocol:
Seeds were cut in half along the cotyledonary axis.  One half was frozen in liquid nitrogen and ground to a powder, then seed total RNA was extracted using the Qiagen Rneasy plant kit (catalog # 74904) and digested on column with Invitrogen Dnase 1 (catalog # 18068-015).
cDNA libraries were constructed as described in the Illumina TruSeq RNA Sample Prep version 2 protocol utilizing Superscript II Reverse Transcriptase from Invitrogen (catalog # 18064-014). Illumina unique adapters were ligated to each library and quality control was performed on the agilent 2100 bioanalyzer before sequencing.

treatment_protocol: Three of the sample groups, ST77, ST111, and 764, were transformed by Agrobacterium to express the recombinant protein listed above in the samples list.  Each was carried forward multiple generations and sample seeds were chosen from respective generations listed.

tag: transgene

value: non-toxic Staphylococcus enterotoxin B

tag: generation

tag: cultivar

value: Williams 82


title: D18_B

country: China

organism: Sus scrofa

tag: tissue

value: Day 18 of pregnancy


title: D12_A

value: Day 12 of pregnancy


title: IAV-WT_9day_Ifnar1-/-

city: Tarrytown

first: Asiel

middle: Arturo

last: Benitez

state: New York

address: 777 Old Saw Mill River Rd, 92-516A

department: Immunology & Inflammation

institute: Regeneron Pharmaceuticals, Inc

description:
Sample 11
processed data file: BD_BC.txt

data_processing:
Illumina MiSeq Control/RTA used for base-calling.
Illumina MiSeq Reporter for demultiplexing.
Illumina BaseSpace analysis
Bowtie for alignment
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include Ensembl Gene ID, Gene ID, Gene Description, and total raw read count for each gene in each sample

organism: Mus musculus

source_name: WT Influenza A virus (IAV-WT)

extract_protocol:
Trizol method was used according to the manufacturer's instructions
Illumina TruSeq RNA Library Prep Kit v2

tag: strain background

tag: genotype

tag: age

value: 6 weeks

value: lung

tag: days post-infection


title: Mock_9day_Ifnar1-/-

description:
Sample 10
processed data file: BD_BC.txt

source_name: mock infection


title: IAV-NPt_9day_Ifnar1-/-

description:
Sample 12
processed data file: BD_BC.txt

source_name: miRNA-targeted virus (IAV-NPt)


title: 764_B3


title: LALA nuclear fraction replicate #2

city: Edinburgh

first: Stefan

last: Bresson

state: Scotland

address: Max Born Crescent, Swann 5.1

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

description: Genomically integrated PABPN1 with L119A and L136A mutations (LALA), driven by a tetracycline responsive promoter. LALA behaves as a dominant negative and inhibits hyperadenylation.

data_processing:
Samples were sequenced using Illumina HiSeq 2500 (paired-end 100 bp reads).
The reads were mapped, aligned and assembled using TopHat2 and Cufflinks2.2 (Kim et al. 2013; Trapnell et al. 2012).
Differential gene expression was analyzed by Cuffdiff using the iGenomes annotations and EdgeR was employed to determine differential expression of the 13,853 known and novel lncRNAs in the GENCODE annotation (Robinson et al. 2010).
DEGs were identified from the Cuffdiff output by removing those transcripts with an FPKM of <1 in the treatment sample and the remaining transcripts with p-value <0.05 and a false discovery rate (FDR) less than 5% were defined as DEGs. DEGs in the EdgeR data were defined as those with log(counts per million) >3.5 and an FDR <5%.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig for viewing in a genome browser; excel spreadsheet containing RPKM values

organism: Homo sapiens

source_name: LALA nuclear fraction replicate #2

growth_protocol: For PAP knockdown, cells were treated with siRNAs targeting PAPα and PAPγ for three days before harvesting. For LALA expression, doxycycline was removed from the media three days prior to harvesting. One day following siRNA transfection or doxycycline, cells were split to ~25% confluency and allowed to grow for two additional days.

extract_protocol: TruSeq Stranded mRNA preparation kit

tag: cell line


title: LALA nuclear fraction replicate #1

source_name: LALA nuclear fraction replicate #1


title: IAV-WT_2day_Ifnar1-/-

description:
Sample 8
processed data file: BD_BC.txt


title: IAV-NPt_2day_Ifnar1-/-

description:
Sample 9
processed data file: BD_BC.txt


title: siPAP nuclear fraction replicate #2

description: PAPOLA and PAPOLG depleted cells

source_name: siPAP nuclear fraction replicate #2


title: siPAP nuclear fraction replicate #1

description: PAPOLA and PAPOLG depleted cells

source_name: siPAP nuclear fraction replicate #1


title: Mock_2day_Ifnar1-/-

description:
Sample 7
processed data file: BD_BC.txt


title: NL4

city: Waco

first: Tamarah

middle: L

last: Adair

state: Tx

address: One Bear Place 97388

department: Biology

institute: Baylor University

description: treatment: no light during incubation for 2 hours

data_processing:
The Illumina miSeq Next Generation Sequencer software was used.
Illumina files were loaded into GeneSifter (PerkinElmer) for quality analysis.
GeneSifter was used to perform Pairwise analysis on quality reads.
EdgeR statistics including a Benjamini and Hochberg false discovery rate correction were performed using GeneSifter.
The combined results of both independent experiments were analyzed using the Pairwise Analysis tools in GeneSifter®.  In order to identify statistically different expression levels of individual genes we applied the following criteria to the pairwise analysis: (i) Quality must have a minimum number of 10 reads, (ii) the transcript level must change by at least 5-fold, and (iii) the P value for the t test must be 0.05 or less.
Genome_build: NC_002952 was used to align sequnce reads
Supplementary_files_format_and_content: These include the gid, count, rpm, NC accession numbers, gene ID, title, and gene type.

organism: Staphylococcus aureus

source_name: Broth culture

growth_protocol: BUSA2288 was grown overnight in 5mL of Brain Heart Infusion (BHI) broth at 37 °C. Broth cultures were  inoculated from a single colony on a TSA plate. The contents of this overnight culture were added to 45mL BHI broth, resulting in a concentration of 1 x 108 CFU/ml as measured by colony counts. One mL aliquots of this diluted overnight culture were transferred to each well of two BD Falcon™ non-treated 24-well plates.

extract_protocol:
Total RNA was extracted from the NL and BL samples using a modified phenol chloroform extraction method as follows.  The pelleted cells were resuspended in RNAse free water and incubated with an equal volume of 1:1 phenol/chloroform.  Phases were separated after centrifugation, and RNA solution was centrifuged at 12,000 x g for 10 minutes. Two times the volume of isopropanol was added to the aqueous layer. The RNA was pelleted, and the pellet was washed with ethanol on ice and resuspended in Elution Solution (Ambion).  Both samples were treated with DNAse Inactivation Reagent (Ambion).  Enrichment of the RNA was performed using the MICROBExpress Bacterial mRNA Enrichment Kit (Ambion) which involves using a modified capture hybridization involving magnetic beads to remove 16S and 23S ribosomal RNAs.  RNA was analyzed at the University of Oklahoma Science Center’s lab for Molecular Biology and Cytometry Research using Agilent Bioanalyzer 2100 to verify the concentration and purity of the mRNA.
Illumina MiSeq RNA library Building (TruSeq)

treatment_protocol: 1.5 mm Blue (465nm) LED lights were attached to the lid of a 24 well culture dish 0.5 mm above the broth cultures. The lights were operated at a forward current of 20mA for 2 hours resulting in a total light dosage of 250 J/cm2.

tag: strain

tag: source

value: human nasal isolate

tag: antibiotic sensitivity

value: MRSA


title: unc22 (control) RNAi 3fd6 sample 3

city: Portland

first: Bret

middle: J

last: Pearson

state: OR

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

department: Pediatrics

institute: Oregon Health and Science University

data_processing:
Base calls were made using the Illumina pipeline v. 1.6 for Illumina GAIIx and v. OLB 1.9 for HiSeq2000
Untrimmed reads were aligned to the transcriptome associated with BioProject PRJNA205281 using the program Bowtie2 version 2.2.4.  Raw counts were extracted from resulting SAM files and normalized to the number of mapped reads to calculate Counts Per Million reads (CPM).
Pseudocounts of 1 were added to all CPM values.
Genome_build: The transcriptome under NCBI BioProject PRJNA205281, smed20110214.nt
Supplementary_files_format_and_content: Lin_NCBI_processedData.xls  Excel tab delimited.  RPM values for each sample for each transcript are listed as well as baySeq p values.

molecule: polyA RNA

organism: Schmidtea mediterranea

source_name: unc22 (control) RNAi 3fd6

growth_protocol: The clonal strain of Schmidtea mediterranea, CIW4, was grown in a milli-Q-based salt solution on beef liver.  Organisms were starved for 1 week prior to RNAi feeding, fed 3x, then collected 6 days later (3fd6).

extract_protocol:
All 3 tissue samples were RNA extracted in Trizol reagent, and RNA quality was analyzed on a bioanalyzer.  RNA samples were library prepped using Illumina's Truseq Library preps, which included polyA selection.
Illumina TruSeq library prep kit with v4 chemistry.

treatment_protocol: Experiments were performed in biological triplicate for all steps.  RNAi was the only treatment.

value: Asexual CIW4

value: Whole animal, mascerated

tag: treatment

value: RNAi


title: siPAP total fraction replicate #1

description: PAPOLA and PAPOLG depleted cells

source_name: siPAP total fraction replicate #1


title: unc22 (control) RNAi 3fd6 sample 1


title: IAV-NPt_9day_wildtype

description:
Sample 6
processed data file: ES.txt

value: wildtype


title: siPAP total fraction replicate #2

description: PAPOLA and PAPOLG depleted cells

source_name: siPAP total fraction replicate #2


title: unc22 (control) RNAi 3fd6 sample 2


title: IAV-WT_9day_wildtype

description:
Sample 5
processed data file: ES.txt


title: Mock_9day_wildtype

description:
Sample 4
processed data file: ES.txt


title: yorkie RNAi 3fd6 sample 3

source_name: yorkie RNAi 3fd6


title: IAV-NPt_2day_wildtype

description:
Sample 3
processed data file: ES.txt


title: control total fraction replicate #2

source_name: control total fraction replicate #2


title: IAV-WT_2day_wildtype

description:
Sample 2
processed data file: ES.txt


title: control nuclear fraction replicate #1

source_name: control nuclear fraction replicate #1


title: control total fraction replicate #1

source_name: control total fraction replicate #1


title: yorkie RNAi 3fd6 sample 1


title: BL3

description: treatment: blue light illumination with 2 hour incubation


title: Mock_2day_wildtype

description:
Sample 1
processed data file: ES.txt


title: Live_PLRC [US-1457351-9]

status: Public on Oct 02 2015

city: Seattle

first: Zizhen

last: yao

state: WA

department: MAT

institute: Allen Institute for Brain Science

data_processing:
Raw read data was aligned to GRCh37 (hg19) using the RefSeq annotation gff file downloaded on 4/23/2013. Transcriptome alignment was performed first using RSEM39, unmapped reads were then aligned to hg19 using Bowtie40, and remaining unmapped reads were aligned to the ERCC sequences.
Genome_build: hg19
Supplementary_files_format_and_content: Gene counts and normalized TPM (transcripts per milllion reads) were provided for each single cell sample

source_name: H1 ESCs p40 Live Cells FRSCR

growth_protocol: H1 hESC’s (WiCell, Madison WI) were maintained on Matrigel (Corning) in mTESR1 media (StemCell Technologies, Vancouver BC). Adherent cell cultures were dissociated with StemPro Accutase Cell Dissociation Reagent (Life Technologies, Chicago IL). The cells were centrifuged (220xg, 3 min) and the dissociation solution was removed.

extract_protocol:
Cortical pieces were divided into one half for sectioning and the other half for cell isolation. The half for sectioning was fixed in 4% PFA in PBS overnight at 4oC, then cryoprotected in 30% sucrose in PBS for 48-72 h, rinsed briefly with PBS and embedded and frozen in OCT. The other half (approx. 0.25 - 0.5 mL volume) was minced into small pieces with #5 forceps (Fine Science Tools, Foster City CA) in Ca2+- and Mg2+-free HBSS (14175-095, Life Technologies, Chicago IL, Chicago IL). Minced pieces were treated with 2 mL trypsin solution for 20 min at 37 oC ( Ca2+- and Mg2+-free HBSS, 10 mM HEPES, 0.5 mM EDTA, 0.25 mg/ml bovine pancreatic trypsin (EMD Millipore, Billerica MA), 10 μg/mL DNase I (Roche, Basel, Switzerland), pH 7.6). Digestion was quenched with 6 mL of ice-cold quenching buffer (440 ml Leibovitz L-15 medium, 50 ml water, 5 mL 1M HEPES pH 7.3–7.4, 5 ml 100x Pen-Strep, 20 ml 77.7 mM EDTA pH 8.0 [prepared from Na2H2EDTA], 1g bovine serum albumin [A7030, Sigma, St. Louis MO]) containing 100 μg/mL trypsin inhibitor (T6522, Sigma) and 10 μg/mL DNase I (Roche). Samples were then pelleted (220xg, 4 min, 4°C), resuspended with 1 mL of quenching buffer and triturated on ice with a P1000 pipette set to 1 mL, using 25 gentle cycles up and down without forming bubbles. The cell suspension was then diluted to 30-40 mL in quenching buffer, filtered through a 45 micron cell filter, pelleted (220xg, 10 min, 4°C), resuspended in 5 mL Staining Medium, and counted on a hemocytometer (typically ~30-50 million live cells isolated per cortical piece at ~50% viability).
Library construction was carried out as previously reported by Smart-Seq2 and Nextera XT DNA prep kit.

tag: cell type

value: cultured embryonic stem cells

tag: phenotype

value: DAPI-

tag: sample group

value: Live cells_FRSCR


title: Live_PLRC [US-1457351-8]


title: Live_PLRC [US-1457351-7]


title: ST77_D2

source_name: Ground half-seed

value: human thyroglobulin


title: control nuclear fraction replicate #2

source_name: control nuclear fraction replicate #2


title: Live_RLT [US-1457351-6]

source_name: H1 ESCs p40 Live Cells Triton X Lysis

value: Live cells_Triton X Lysis


title: Live_RLT [US-1457351-2]


title: Live_RLT [US-1457351-3]


title: Live_RLT [US-1457351-4]


title: Live_RLT [US-1457351-5]


title: Fixed_RLT [US-1457351-21]

source_name: H1 ECSs p40 Fixed Cells Triton X Lysis

value: DAPI+

value: Fixed cells_Triton X Lysis


title: Fixed_RLT [US-1457351-22]


title: yorkie RNAi 3fd6 sample 2


title: Fixed_PLRC [US-1457351-15]

source_name: H1 ESCs p40 Fixed Cells FRSCR

value: Fixed cells_FRSCR


title: Fixed_PLRC [US-1457351-16]


title: Fixed_PLRC [US-1457351-17]


title: Live_RLT [US-1457351-1]


title: Fixed_PLRC [US-1457351-18]


title: Fixed_PLRC [US-1457351-14]


title: Fixed_PLRC [US-1457351-19]


title: Live_PLRC [US-1457351-13]


title: Fixed_RLT [US-1457351-20]


title: Live_PLRC [US-1457351-11]


title: Live_PLRC [US-1457351-12]


title: Fixed_RLT [US-1457350-9]


title: Fixed_RLT [US-1457350-7]


title: Fixed_RLT [US-1457350-8]


title: Live_RLT [US-1457350-5]


title: Fixed_RLT [US-1457350-6]


title: Fixed_PLRC [US-1457350-18]


title: Live_RLT [US-1457350-1]


title: Fixed_PLRC [US-1457350-21]


title: Fixed_PLRC [US-1457350-19]


title: Fixed_PLRC [US-1457350-23]


title: Live_RLT [US-1457350-2]


title: Live_PLRC [US-1457350-16]


title: Live_PLRC [US-1457350-17]


title: Live_PLRC [US-1457350-15]


title: Live_PLRC [US-1457351-10]


title: Live_RLT [US-1457350-4]


title: Live_PLRC [US-1457350-14]


title: Live_PLRC [US-1457350-12]


title: MCF10a PTEN KO_t=180_replicate2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description:
Preparation / starvation: Day1: cells were seeded at 320000 cells in 60mm dish in growth medium. Day2: cells are starved in serum-EGF-Insulin for 18h.
Stimulation: Day3: Cells were pre-incubated for 20 min with A66 (2uM) or DMSO (vehicule for A66), then stimulated with EGF (10ng/ml) +/- A66 or DMSO for 15, 40, 90, 180, 300 min or not stimulated (t=0). Except for  A66 no EGF where cells are left in A66 for 300 min without EGF.

data_processing:
Raw FastQ data were trimmed with Trim Galore (v0.3.8, default parameters;  www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and mapped to the human GRCh37 genome assembly using TopHat v2.0.10, with a Bowtie2 index file from Illumina iGenomes. Raw counts for DESeq2 analysis were generated at gene level using HTSeq v0.6.1 (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html). The 1.4.5 version of DESeq2 was used to perform differential expression analysis.
Genome_build: human GRCh37
Supplementary_files_format_and_content: Raw counts RNA-Seq data files are tab delimited and contain the following columns: (1) Gene ID (Ensembl); (2-76) Sample Raw Counts.
Supplementary_files_format_and_content: The RNA-Seq_RPKMs.txt file is tab delimited and includes the gene expression in RPKM units.

source_name: MCF10a Breast Epithelium Cell line

extract_protocol:
Total RNA was extracted from cells using the Qiagen RNeasy kit.
RNA-seq libraries are produced using the Truseq RNA sample prpeparaion kit from Illumina. Amplified libraries were assessed for quality and quantity using High-Sensitivity DNA chips on the Agilent Bioanalyzer, and the KAPA Library Quantification Kit for Illumina (KAPA Biosystems).

value: PTEN KO

tag: condition

value: EGF Stimulation + DMSO

tag: timepoint

value: 180 min


title: MCF10a PTEN KO_t=300_replicate3

value: 300 min


title: MCF10a PTEN KO_t=300_replicate2


title: Live_PLRC [US-1457350-10]


title: Live_RLT [US-1457350-3]


title: Fixed_PLRC [US-1457350-22]


title: Live_PLRC [US-1457350-11]


title: MCF10a PTEN KO_t=90_replicate3

value: 90 min


title: Fixed_PLRC [US-1457350-20]


title: MCF10a PTEN KO_t=90_replicate2


title: MCF10a PTEN KO_t=180_replicate1


title: MCF10a PTEN KO_t=90_replicate1


title: MCF10a PTEN KO_t=15_replicate3

value: 15 min


title: MCF10a PTEN KO_t=40_replicate3

value: 40 min


title: Live_PLRC [US-1457350-13]


title: miRNA seq 12 hours imbibition

city: Wuhan

first: Dongli

last: He

state: HuBei

address: Wuchang

department: plant breeding

institute: Wuhan Botanic Garden

description: sRNA

data_processing:
The raw sequencing data was filtered with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to delete low quality reads, adapters, contamination, and false sequence (such as reads with poly A/T/C/G). After filtering, we collected small RNAs with sizes ranging from 18 to 30 nt and mapped them to the rice genome (MSU Rice Annotation Release 7.0) using Bowtie software, and then the sequences matching known rice rRNA, tRNA, snRNA, and snoRNA in the Rfam11 (https://www.sanger.ac.uk/resources/databases/rfam.html) were discarded.
The unique small RNAs were aligned with the data in miRBase 21 (www.mirbase.org) to search for the conserved miRNAs the unique small RNAs were aligned with the data in miRBase 21 (www.mirbase.org) to search for the conserved miRNAs. De novo prediction of novel miRNA was performed by miRDeep2. Genomic sequences at lengths of 300 bp surrounding the sRNAs (150 nt upstream and 150 nt downstream) were extracted to assess the potential of pre-miRNA secondary structures. The candidates were first ﬁltered with default criteria, and then with stringent criterion of MFEI > 0.85 (MFEI = [(MFE/length of the sRNA sequence) × 100] / (G+C) % )
Supplementary_files_format_and_content: All identified known miRNAs
Supplementary_files_format_and_content: All predicted novel miRNAs

organism: Oryza sativa

source_name: rice seed

growth_protocol: The de-hulled rice (Oryza sativa Nipponbare) seeds were washed three times with distilled water, then placed on plates and imbibed in distilled water at 30oC in a dark biochemical incubator. After 0 h, 12 h, and 24 h imbibition, embryos of rice seeds were dissected manually and collected for each RNA extraction.

extract_protocol:
RNA was extracted with TRIzol Reagent (Invitrogen, US) according to the manufacturer’s instructions.
The small RNA libraries were constructed as described by Lu et al [18]. Briefly, the total RNA was fractionated by 15% polyacrylamide denaturing gel (8 M urea) electrophoresis, and sRNAs in the range of 18-30 nt were excised and purified with a Spin-X cellulose acetate filter (2 ml, 0.45 uM; Fisher, US). After dephosphorylation and sequential ligation of 5’- and 3’- Solexa adaptors, the sRNAs were reverse-transcribed using superscriptTMII reverse transcription kit (Invitrogen, US), and then amplified by PCR with phusion High-Fidelity PCR kit (Finnezymes, US) to produce the sRNA sequencing libraries.

value: embryo

tag: passages

value: 12 hours imbibition

value: Nipponbare


title: miRNA seq 24 hours imbibition

description: sRNA

value: 24 hours imbibition

tag: cultivar


title: MCF10a PTEN KO_t=40_replicate2


title: miRNA seq dry seed

description: sRNA

tag: tissue

value: dry seed


title: MCF10a PTEN KO_t=180_replicate3


title: ST111_I2

tag: transgene

value: myelin-basic protein sigma conjugate

tag: generation

value: Williams 82


title: MCF10a PTEN KO_t=300_replicate1

tag: genotype


title: MCF10a PIK3CA H1047R_t=180_replicate3

value: PIK3CA H1047R


title: MCF10a PTEN KO_t=0_replicate2

value: no EGF + DMSO


title: MCF10a PTEN KO_t=15_replicate2


title: MCF10a PIK3CA H1047R_t=90_replicate3


title: MCF10a PIK3CA H1047R_t=300_replicate2


title: MCF10a PIK3CA H1047R_t=90_replicate2


title: MCF10a PIK3CA H1047R_t=300_replicate1


title: MCF10a PIK3CA H1047R_t=180_replicate2


title: MCF10a PIK3CA H1047R_t=300_replicate3


title: MCF10a PIK3CA H1047R_t=180_replicate1


title: MCF10a PTEN KO_t=0_replicate1


title: MCF10a PIK3CA H1047R_t=90_replicate1


title: MCF10a PTEN KO_t=0_replicate3


title: UVC-10-4aTPA-rep2

city: Wilmington

first: Zhongqiang

last: Chen

state: DE

institute: E.I. du Pont de Nemours and Company

description: Processed file ID: DSTR_D0020

data_processing:
Illumina CASAVA 1.8 was used for base-calling
Sequencing reads were trimmed for adaptor sequences and low quality (Q<20) sequences; reads with length smaller than 24bp were removed.
Sequencing reads were then mapped to consensus CDS (CCDS) sequences (GRCh37.p5, 20110907) using bowtie (v0.12.7) using default parameters; Expression level for each transcript was summarized and normalized by  reads mapping to CCDS per kilobase of transcript per million reads sequenced (RPKM).
Genome_build: GRCh37.p5
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
Raw data files were unavailable at the time of GEO submission. Authors are working to recover raw data and will update the GEO submission if successful.

source_name: TK6 cell line

growth_protocol: TK6 cells were propagated in RPMI medium (Mediatech, Manassas, VA) supplemented with 10% heat-inactivated fetal bovine serum (Mediatech) and penicillin/streptomycin

extract_protocol:
TK6 cells were removed, washed twice with cold Dulbecco’s phosphate buffered saline (DPBS) and flash frozen in dry ice. RNA was isolated using an RNeasy kit (Qiagen, Valencia, CA) and potential DNA contamination was removed with DNase treatment (TURBO DNA-free(TM) Kit, Life Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: TK6 cells were pretreated with tumor promoters or a solvent control (DMSO, 0.1%) for 72 hours prior to UVC-irradiation;  After UVC-irradiation, the cells were then maintained in media supplemented with the tumor promoting agent or DMSO for the remainder of the experiment.

value: lymphoblast

tag: irradiation

value: UVC

tag: chemical

tag: time

tag: dose


title: UVC-10-4aTPA-rep1

description: Processed file ID: DSTR_D0019

tag: cell line


title: UVC-10-4aTPA-rep3

description: Processed file ID: DSTR_D0021


title: UVC-1-4aTPA-rep2

description: Processed file ID: DSTR_D0017


title: MCF10a PIK3CA H1047R_t=40_replicate3

value: EGF Stimulation + DMSO


title: MCF10a PTEN KO_t=15_replicate1

value: PTEN KO


title: MCF10a PIK3CA H1047R_t=40_replicate2


title: MCF10a PIK3CA H1047R_t=40_replicate1


title: MCF10a PIK3CA H1047R_t=15_replicate3


title: UVC-1-TPA-rep3

description: Processed file ID: DSTR_D0015

value: TPA


title: UVC-1-TPA-rep2

description: Processed file ID: DSTR_D0014


title: UVC-1-TPA-rep1

description: Processed file ID: DSTR_D0013


title: MCF10a PIK3CA H1047R_t=15_replicate2


title: UVC-0.5-TPA-rep3

description: Processed file ID: DSTR_D0012


title: UVC-1-4aTPA-rep3

description: Processed file ID: DSTR_D0018


title: MCF10a PTEN KO_t=40_replicate1


title: MCF10a PIK3CA H1047R_t=0_replicate3


title: MPP_H3K27me3_rep2

city: Baltimore

first: Yixian

last: Zheng

state: MD

address: 3520 San Martin Drive

department: Embryology

institute: Carnegie Institution for Science

library_source: genomic

data_processing:
reads were filtered using the quality of multiplexing indices before mapping to prevent contaminations by erroneous de-multiplexing. Reads with average index quality below 30 were discarded (Kircher et al., 2012). The reads were then mapped to mouse genome (mm9) by Bowtie allowing 2 mismatches per read. Only uniquely mapped reads were retained. The mapped reads were further mapped to carrier genome or biotin-DNA sequences by Bowtie allowing 3 mismatches, and reads mapped to the carrier genome or biotin-DNA were discarded.
H3K4me3 peaks of LT-HSC, ST-HSC, or MPPs are called by MACS with p-value threshold of 10-5 and parameter “llocal=100000” to enable broad peak calling. Then the six sets of peaks (two replicates for LT-HSC, ST-HSC, and MPP each) were merged to obtain a complete peak set, and the numbers of reads were counted for each peak region. We used edgeR (Robinson et al., 2010) to call differentially enriched H3K4me3 peaks between LT-HSC versus ST-HSC and between ST-HSC versus MPP data using standard edgeR  procedure. GO-term was determined by DAVID (Huang da et al., 2009).
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph file for genome browser view

molecule: genomic DNA

source_name: Multipotent progenitors

extract_protocol: mESCs (500 or 1000) or sorted HSC subtypes were mixed with ~5x108 DH5a E.coli and fixed in 1% formaldehyde for 10 min at room temperature. After fixation and washes, the mixtures were sonicated with a 1/16-inch probe for 15 min at 3 watts using a tip sonicator (Misonix sonicator 3000). The lysates were incubated with 2 microliter H3K27me3 antibody (Millipore 07-449) or 1 microliter H3K4me3 antibody (Cell Signaling 9751S) overnight at 4oC. To block any non-specific chromatin absorption, 60 microliter protein G magnetic beads (Life Technologies 10004D) or 10 microliter M-280 streptavidin beads (Life Technologies 11206D) were pre-incubated with ~5x108 fixed and sonicated E.coli lysate or the same E.coli lysate plus 5 ng carrier biotin-DNA, respectively, at 4oC overnight. These treated beads were combined and used to ChIP H3K27me3 or H3K4me3 in the sonicated E.coli+mESC or E.coli+HSC lysates for 4 h at 4oC. The beads were then recovered using a magnetic stand. All washing, de-crosslinking, and library building steps were performed following Illumina True-Seq protocol with 12 PCR amplification cycles. After end repair, A-tailing, and adapter ligation steps, 0.25 micro-M blocker oligo was added during final library amplification.

tag: strain

tag: material source

value: bone marrow from 8-week old C57BL/6J mice

tag: sorting

value: lin-, Sca1+, c-Kit+, Flk2+, CD34+

value: Multipotent progenitors

tag: chip antibody

value: anti-H3K27me3 (Millipore, catalog# 07-449, lot# 2475696)


title: UVC-1-4aTPA-rep1

description: Processed file ID: DSTR_D0016

tag: cell type


title: MPP_H3K4me3_rep2

value: anti-H3K4me3 (Cell Signaling, catalog# 9751S, 11/2014, lot# 8)


title: UVC-0.5-TPA-rep1

description: Processed file ID: DSTR_D0010


title: UVC-0.2-TPA-rep1

description: Processed file ID: DSTR_D0007


title: MCF10a PIK3CA H1047R_t=15_replicate1

tag: condition

tag: timepoint

value: 15 min


title: STHSC_H3K27me3_rep2

source_name: Short-term Hematopoietic stem cells

value: lin-, Sca1+, c-Kit+, Flk2-, CD34+

value: Short-term Hematopoietic stem cells


title: MPP_H3K27me3_rep1


title: MCF10a A66 no EGF_t=300_replicate2

value: WT

value: no EGF + A66

value: 300 min


title: UVC-0.5-TPA-rep2

description: Processed file ID: DSTR_D0011


title: UVC-DMSO-rep3

description: Processed file ID: DSTR_D0006

value: DMSO


title: MCF10a PIK3CA H1047R_t=0_replicate2

value: PIK3CA H1047R

value: no EGF + DMSO


title: MCF10a PIK3CA H1047R_t=0_replicate1


title: MPP_H3K4me3_rep1


title: STHSC_H3K27me3_rep1


title: UVC-0.2-TPA-rep3

description: Processed file ID: DSTR_D0009

value: lymphoblast

value: UVC


title: STHSC_H3K4me3_rep2


title: STHSC_H3K4me3_rep3

value: anti-H3K4me3 (Millipore, catalog# 07-473, lot# 2500603)


title: MCF10a A66 no EGF_t=300_replicate1


title: UVC-DMSO-rep2

description: Processed file ID: DSTR_D0005


title: STHSC_H3K4me3_rep1

value: bone marrow from 8-week old C57BL/6J mice


title: MCF10a A66_t=300_replicate3

value: EGF Stimulation + A66 (20min preincubation)

value: 180 min


title: LTHSC_H3K27me3_rep1

source_name: Long-term Hematopoietic stem cells

value: lin-, Sca1+, c-Kit+, Flk2-, CD34-

value: Long-term Hematopoietic stem cells

value: anti-H3K27me3 (Millipore, catalog# 07-449, lot# 2475696)


title: LTHSC_H3K27me3_rep2


title: UVC-0.2-TPA-rep2

description: Processed file ID: DSTR_D0008

value: TPA


title: UVC-DMSO-rep1

description: Processed file ID: DSTR_D0004


title: LTHSC_H3K4me3_rep2

value: anti-H3K4me3 (Cell Signaling, catalog# 9751S, 11/2014, lot# 8)


title: MCF10a A66_t=300_replicate2

value: WT


title: LTHSC_H3K4me3_rep1


title: ESC_H3K4me3_rep2

source_name: Embryonic stem cells

value: mESC cell line derived from F1 hybrid of 129SvJae/C57BL/6J

value: Embryonic stem cells


title: MOCK-DMSO-rep3

description: Processed file ID: DSTR_D0003

value: MOCK

value: DMSO


title: MOCK-DMSO-rep1

description: Processed file ID: DSTR_D0001


title: MCF10a A66_t=300_replicate1


title: MCF10a A66 no EGF_t=300_replicate3

value: no EGF + A66

value: 300 min


title: MCF10a A66_t=180_replicate2

value: 90 min


title: PABPC1_CLIP-seq_rep2

city: Philadelphia

first: Ian

middle: M

last: Silverman

state: Pennsylvania

address: 433 South University Ave, Room 104

institute: University of Pennsylvania

description: processed data file: PABPC1_Day0_trimmed_NR_merge.tag.mutation.del.CIMS.s30.1nt.001.bed; PABPC1_Day0_trimmed_NR_merge_gencode.tag.2.pk.bed

data_processing:
Trim adapter sequence ' GTGTCAGTCACTTCCAGCGGTCGTATGCCGTCTTCTGCTTG ' with cutadapt 1.4.2 [-e 0.06 -O 6 -m 14]. Align reads with Novoalign V3.02.02 [-t 85-l 15 -s 1 -o Native -r None]. Count reads per gene with htseq-count version 0.6.0 [-s yes -m intersection-nonempty]. CIMS identification as in Moore et al. 2014. Peak calling with Pyicoclip 2.0.7 [--stranded]
Genome_build: mm10
Supplementary_files_format_and_content: PABPC1_Day0_trimmed_NR_merge.tag.mutation.del.CIMS.s30.1nt.001.gencode.transcript.ID.bed: bed file summarizing CIMS analysis; PABPC1_Day0_trimmed_NR_merge_gencode.tag.2.pk.gencode.transcript.ID.bed: bed file summarizing Cluster analysis

growth_protocol: MEL and NIH-3T3 cells were grown under standard conditions in minimal essential medium (MEM) and Dulbecco’s modified Eagle medium (DMEM), respectively, supplemented with 10% (vol/vol) fetal bovine serum (FBS) and 1× antibiotic-antimycotic (Invitrogen).

extract_protocol:
library strategy: CLIP-seq
MEL cells were washed with Hanks’ balanced salt solution (HBSS) and crosslinked with UV (400 mJ/cm2) thrice on ice. CLIP was performed according to previously published protocol (Ule et al. 2005; Chi et al. 2009). Briefly UV cross-linked MEL cells were lysed with 1x PMPG, DNAse I (Promega) treated for 15min followed by RNase One (Promega) for 10 mins.  The lysates were ultra-centrifuged at 90,000g for 20 mins. Immuno-precipitation was performed with protein A Dynabeads coated with PABPC1 antibody (Abcam).
Following the stringent wash steps radiolabeled 3’ adaptor was ligated using T4 RNA ligase (Thermo Scientific) for 16 h at 16oC. The beads were washed and treated with T4 polynucleotide kinase (NEB). The RNP complexes were eluted off of the beads and 90 % of the eluate were used for autoradiography and the rest for immunoblotting.  The RNP complexes were resolved on 4- 12 % NuPage gels (Invitrogen) and transferred to nitrocellulose membrane and then exposed to X-ray film. Using the X-ray film to orient the portion of the nitrocellulose membrane corresponding to PABPC1-RNA complexes was excised and Proteinase K (Roche) treated followed by Phenol extraction, ligation of the 5’ adaptor and RT-PCR to generate sequencing libraries. Samples in biological triplicates with individual bar codes were pooled and sequenced on Illumina HiSeq 2000 sequencing system at the University of Pennsylvania Next Generation Sequencing Core (NGSC).

value: MEL cells

tag: clip antibody vendor

value: PABPC1 antibody

tag: clip antibody

value: Abcam


title: MOCK-DMSO-rep2

description: Processed file ID: DSTR_D0002

value: lymphoblast


title: ESC_H3K4me3_rep1


title: PABPC1_CLIP-seq_rep1


title: MCF10a A66_t=180_replicate3

value: EGF Stimulation + A66 (20min preincubation)


title: MCF10a A66_t=180_replicate1


title: MEL_RNA-seq_rep2

description: processed data file: MEL_0day_mRNA_gencode_RPKM_name.txt; MEL_0day_mRNA_polyA.bedGraph

data_processing:
Trim adapter sequence 'TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACnnnnnnATCTCGTATGCCGTCTTCTGCTTG' with cutadapt 1.4.2 [-e 0.06 -O 6 -m 14]. Align reads with TopHat v2.0.12 [--library-type fr-secondstrand --read-mismatches 2 --read-edit-dist 2 --max-multihits 10 --b2-very-sensitive  --no-coverage-search] (mRNA-seq). Count reads per gene with htseq-count version 0.6.0 [-s yes -m intersection-nonempty]
Genome_build: mm10
Supplementary_files_format_and_content: MEL_0day_mRNA_gencode_RPKM_name.txt: .txt file summarizing RPKM for gencode vM2 genes; MEL_0day_mRNA_polyA.bedGraph: bedgraph summarizing polyA sites

extract_protocol:
total RNA was purified from MEL cells using miRNeasy kit (Qiagen). PolyA+ RNA was isolated using oligo dT beads (Ambion).  RNA was fragmented for (5 or 7 minutes) using the RNA fragmentation reagents (Ambion).
mRNA-seq libraries were generated using the illumina smRNA-seq kit.


title: MEL_RNA-seq_rep1


title: PABPC1_CLIP-seq_rep3


title: MCF10a A66_t=90_replicate3

value: 40 min


title: MCF10a A66_t=90_replicate2


title: MCF10a A66_t=40_replicate3

value: 15 min


title: UVC_DMSO_24-rep2

description: Processed file ID: DSTR_T0038

value: UVC


title: MCF10a A66_t=40_replicate2


title: UVC_TPA_24-rep2

description: Processed file ID: DSTR_T0041

value: TPA


title: UVC_TPA_24-rep1

description: Processed file ID: DSTR_T0040


title: UVC_DMSO_24-rep3

description: Processed file ID: DSTR_T0039


title: MCF10a A66_t=90_replicate1

value: WT


title: MCF10a A66_t=15_replicate2


title: MOCK_TPA_24-rep1

description: Processed file ID: DSTR_T0034


title: MCF10a A66_t=15_replicate1


title: MOCK_DMSO_24-rep3

description: Processed file ID: DSTR_T0033


title: MOCK_TPA_24-rep3

description: Processed file ID: DSTR_T0036


title: MCF10a A66_t=0_replicate3

value: no EGF + A66 (20min preincubation)


title: MCF10a A66_t=40_replicate1


title: UVC_TPA_8-rep3

description: Processed file ID: DSTR_T0030


title: MOCK_TPA_24-rep2

description: Processed file ID: DSTR_T0035


title: MOCK_DMSO_24-rep2

description: Processed file ID: DSTR_T0032


title: MOCK_DMSO_24-rep1

description: Processed file ID: DSTR_T0031


title: MCF10a A66_t=15_replicate3


title: UVC_TPA_8-rep2

description: Processed file ID: DSTR_T0029


title: MCF10a A66_t=0_replicate1


title: UVC_DMSO_8-rep3

description: Processed file ID: DSTR_T0027


title: MCF10a WT_t=300_replicate2

value: EGF Stimulation + DMSO


title: MCF10a WT_t=180_replicate2

value: 180 min


title: MCF10a WT_t=300_replicate1


title: MCF10a WT_t=180_replicate3


title: MOCK_TPA_8-rep3

description: Processed file ID: DSTR_T0024

value: MOCK


title: UVC_DMSO_8-rep1

description: Processed file ID: DSTR_T0025

value: DMSO


title: MCF10a WT_t=180_replicate1


title: MOCK_TPA_8-rep2

description: Processed file ID: DSTR_T0023


title: UVC_TPA_24-rep3

description: Processed file ID: DSTR_T0042


title: MCF10a A66_t=0_replicate2

value: 300 min


title: MOCK_TPA_8-rep1

description: Processed file ID: DSTR_T0022


title: MCF10a WT_t=90_replicate3

value: 90 min


title: MOCK_DMSO_8-rep3

description: Processed file ID: DSTR_T0021


title: MCF10a WT_t=90_replicate1


title: MOCK_DMSO_8-rep2

description: Processed file ID: DSTR_T0020


title: MCF10a WT_t=40_replicate3


title: MCF10a WT_t=90_replicate2


title: MCF10a WT_t=40_replicate2


title: MOCK_DMSO_8-rep1

description: Processed file ID: DSTR_T0019


title: MCF10a WT_t=300_replicate3


title: UVC_TPA_8-rep1

description: Processed file ID: DSTR_T0028


title: UVC_TPA_4-rep3

description: Processed file ID: DSTR_T0018


title: swr1d_rep2

city: Berkeley

first: Xavier

last: Darzacq

state: CA

address: 475D Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California, Berkeley

description:
Interaction_distance_swr1d.xlsx
GeneCrumple_swr1d.xlsx

data_processing:
Library strategy: Micro-C-seq
OLB 1.9/CASAVA_v1.8.2 were used for base calling
Barcoded libraries were demultiplexed by Novobarcode.
Paired reads were mapped to sacCer3 genome separately by Bowtie2
Parse SAM files and remove duplicate reads.
Mate unique paired mates and generate interaction matrix.
Genome_build: S288C (sacCer3)

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: 100mL yeast culture were grown to midlog phase ~OD 0.55 in YPD media at 30 C.

extract_protocol:
DNA was purified by PCI extraction and ethanol precipitation, treated with RNase A, and ~250-350 bp DNA was gel-purified following 3% agarose gel electrophoresis.
Purified DNA was treated with End-it, subject to A-tailing with Exo- Klenow, and ligated to Illumina adaptors. Adaptor-ligated DNA was then purified with streptavidin beads to isolate ligated Micro-C products away from undigested dinucleosomal DNA. Streptavidin beads were then subject to ~12-15 cycles of PCR using Illumina paired-end primers.
Amplified library was purified and subject to Illumina HiSeq or Nextseq paired end sequencing with 50 bp or 100 bp reads.

treatment_protocol: Yeast cells were fixed with 3% formaldehyde for 15 min, and quenched with 125 mM glycine for 5 min. Cells were pelleted, spheroplasted with Zymolyase, and treated with a level of MNase yielding >95% mononucleosom. After stopping MNase, chromatin supernatant was dephosphorylated using Antarctic phosphatase. Crosslinked chromatin was subject to T4 DNA polymerase / T4 PNK enzyme mix solution to generate blunt ends. Crosslinked chromatin was diluted into 10 mL and treated with T4 DNA ligase. After heat inactivation, chromatin was concentrated to 250uL, and treated with 100U of exonuclease III for 5 min to eliminate biotinylated ends of unligated DNA. Proteinase K was then added and incubated for 65 C overnight.

tag: media

value: YPD


title: MCF10a WT_t=15_replicate3


title: UVC_TPA_4-rep2

description: Processed file ID: DSTR_T0017


title: MCF10a WT_t=15_replicate2


title: swr1d_rep1


title: UVC_DMSO_4-rep3

description: Processed file ID: DSTR_T0015


title: UVC_DMSO_8-rep2

description: Processed file ID: DSTR_T0026


title: UVC_DMSO_4-rep1

description: Processed file ID: DSTR_T0013


title: MCF10a WT_t=15_replicate1


title: UVC_DMSO_4-rep2

description: Processed file ID: DSTR_T0014


title: MCF10a WT_t=0_replicate3

value: no EGF + DMSO


title: MCF10a WT_t=0_replicate2


title: MOCK_TPA_4-rep3

description: Processed file ID: DSTR_T0012


title: MOCK_TPA_4-rep1

description: Processed file ID: DSTR_T0010


title: MCF10a WT_t=0_replicate1


title: MOCK_DMSO_4-rep3

description: Processed file ID: DSTR_T0009


title: MOCK_TPA_0-rep3

description: Processed file ID: DSTR_T0006


title: MOCK_DMSO_4-rep2

description: Processed file ID: DSTR_T0008


title: MOCK_DMSO_0-rep3

description: Processed file ID: DSTR_T0003


title: MOCK_TPA_0-rep1

description: Processed file ID: DSTR_T0004


title: MOCK_DMSO_4-rep1

description: Processed file ID: DSTR_T0007


title: MOCK_TPA_0-rep2

description: Processed file ID: DSTR_T0005


title: MOCK_TPA_4-rep2

description: Processed file ID: DSTR_T0011


title: MCF10a WT_t=40_replicate1


title: MOCK_DMSO_0-rep1

description: Processed file ID: DSTR_T0001


title: High run0141_lane8_read1_index23=5754CO

status: Public on Oct 01 2015

city: Cincinnati

first: Nupur

last: dasgupta

state: OH

address: 3333, Burnet Avenue

department: human Genetics

institute: CCHMC

data_processing:
Alignment is done using the in‐built alignment algorithm COBWeb.
The name loosely comes from the approach taken to
developing the algorithm -‐ a computationally-‐optimized Burrows Wheeler transform (BWT).
Quantification was performed on the filtered reads against the RefSeq annotation. Post filtering the read counts dropped between ~ 65%-70% compared to the alligned reads
Genome_build: MM9

source_name: CO

growth_protocol: Genotype of 4L;C* mice have combined V394L/V394L Gba1 (4L) and saposin C-/- (C*). The strain background of 4L;C* mice was C57BL/6J/129SvEV. The strain- and age-matched WT mice were used as control. All mice were housed under pathogen-free conditions in the barrier animal facility and according to IACUC approved protocol at Cincinnati Children’s Hospital Research Foundation

extract_protocol:
1 µg of total RNA was prepared using the Illumina TruSeq small RNA kit as per the manufacturer’s recommendations except for the library size selection as described from 42-45 days old 4L;C*,  wild-type (WT)  and Isofagamine treated  4L;C* mouse brain.
Briefly, the RNA molecules in the sample were ligated with different adapters at their 5’ and 3’ ends using T4 RNA Ligases 2 and 1 respectively. After reverse transcription from the 3’ adapter, RNAse H treatment and 2nd strand synthesis from the 5’ adapter, the double stranded cDNA molecules were amplified by PCR with primers tailed with Illumina flowcell specific sequences and one of 48 possible 6-base indexes to complete the library construction. After pooling samples with different index in an equimolar fashion, the fraction of the total RNA libraries containing the miRNAs was selected by agarose gel electrophoresis using a SageScience Pippin Prep system which can be programmed to specifically elute the library fragments with inserts of size 18-25 bases. After quantitation and sizing verification on an Agilent Bioanalyzer, the library pool was diluted to 18 nM and separated into individual molecules by hybridization on an Illumina HiSeq flowcell to a density of 850k/mm2, bridge amplified on an Illumina cBot cluster generation instrument and then sequenced on an Illumina HiSeq2000 for 50 cycles in a single direction. After demultiplexing of each library pool according to its barcode sequence, a minimum of 2M reads per sample was available for analysis of miRNA expression levels.

treatment_protocol: The 4L;C* mice were treated with a pharmacological chaperone, isofagamine tartrate (IFG), at 60 mg/kg/d by drinking water as described . The pregnant dames were given drinking water containing IFG staring 3 to 5 days prior to birth and during the weaning period. After weaning, the pups were continued on 60 mg/kg/d IFG in drinking water for entire course .

tag: tissue abbreviation

value: CO

tag: tissue

value: cortex

tag: age


title: High run0141_lane8_read1_index24=5755CO

tag: genotype


title: untreated run0141_lane8_read1_index21=5188CO


title: untreated run0141_lane8_read1_index20=5187CO


title: untreated run0141_lane8_read1_index25=6912CO

description: WT


title: untreated run0141_lane8_read1_index27=6914CO

description: WT


title: NEJmir

city: Montevideo

first: José

middle: Francisco

last: Tort

state: Montevideo

address: Avenida Gral. Flores 2125

department: Department of Genetics

country: Uruguay

institute: Faculty of Medicine, UdelaR

data_processing:
Mask of adaptor sequences and removal of reads smaller than 18 nt.
The clean reads were subjected to quality analysis with Fastx Tools. Reads with 90% of the bases with a Phred score higher than 20 were conserved.
Redundant reads were merged and counted.
High-quality reads were screened against transcriptomic (mRNA) data of platyhelminths available at GenBank, SchistoDB and HelmDB, discarding all reads matching over 85%. Data were further screened with the same stringency criteria (mismatches ≤ 3) against other non-coding RNA databases
The processed reads dataset was used to perform homology searches against the Sanger miRBase release 20 the miRNA sections of Rfam, and miRNA ncRNA.org databases. Reads were also compared to a local database generated with miRNA reported in flatworms.In order to identify novel F .hepatica specific miRNAs, sequences that produced no matches by homology search and with lengths between 20-23 nt were mapped with miRDeep2 on the genomic assembly. Putative predicted miRNAs were considered as novel if they had a miRDeep2 score equal or higher than 10.
Genome_build: In-house genome assembly
Supplementary_files_format_and_content: Comma-separated text files contain sequence, count and ID...

organism: Fasciola hepatica

source_name: Newly excysted metacercaria

growth_protocol: F. hepatica metacercariae – field strain Shrewsbury – were purchased from Ridgeway Research Ltd. (UK). 5,000 metacercariae were excysted in vitro. Briefly, pure CO2 was bubbled for 30 s in 10 ml cold distilled water. Sodium dithionite to a final concentration of 0.02 M was added to the water, and the tube was closed and incubated at 37°C until a fine cloudy precipitate was produced. Metacercariae were then added to the tube and further incubated at 37°C for 1 h. After incubation, parasites were washed twice by sedimentation with warm distilled water, and 5 ml of Hank's balanced salt solution (Sigma) plus 10% (v/v) rabbit bile and 30 mM HEPES (Sigma) pH 7.4 was added to the dry metacercariae. Parasites were then incubated for 5 h at 37°C. Emerging active parasites were collected with a 20 μl pipette, washed twice with sterile PBS, and stored dry at -80°C until use.

extract_protocol:
Samples were homogenized using the TissuLyser II (QIAgen) and the RNA extraction was performed with the RNeasy Mini Kit (QIAgen) following the manufacturer's instructions. The amount and integrity of total RNA was determined using a 2100 BioAnalyzer (Agilent).
3 μg of total RNA was size-fractionated on a 15% TBE urea polyacrylamide gel and the 15-30 base-pair fraction was excised. The RNA was retrotranscribed into single-stranded cDNA using the Superscript II reverse transcriptase (Invitrogen) and the Illumina’s small RNA RT-Primer following the manufacturer’s instructions. The cDNA was PCR amplified in 15 cycles using Illumina’s small RNA primer set. The PCR products were quantified and subjected to single end Illumina sequencing for 75 cycles.

value: field strain Shrewsbury

tag: developmental stage

value: juvenile


title: untreated run0141_lane8_read1_index2=5187BS

source_name: BS

value: BS

value: Brain Stem


title: untreated run0141_lane8_read1_index9=6914BS

description: WT


title: untreated run0141_lane8_read1_index3=5188BS


title: untreated run0141_lane8_read1_index26=6913CO

description: WT


title: untreated run0141_lane8_read1_index7=6912BS

description: WT


title: High run0141_lane8_read1_index6=5755BS


title: High run0141_lane8_read1_index5=5754BS


title: untreated run0141_lane8_read1_index36=6914MID

description: WT

source_name: MID

value: MID

value: Mid Brain


title: High run0141_lane8_read1_index4=5753BS


title: MOCK_DMSO_0-rep2

description: Processed file ID: DSTR_T0002

value: lymphoblast

tag: irradiation

tag: chemical

tag: time

tag: dose


title: untreated run0141_lane8_read1_index34=6912MID

description: WT

tag: strain

value: WT


title: High run0141_lane8_read1_index22=5753CO


title: High run0141_lane8_read1_index33=5755MID


title: High run0141_lane8_read1_index32=5754MID


title: High run0141_lane8_read1_index31=5753MID


title: untreated run0141_lane8_read1_index30=5188MID


title: untreated run0141_lane8_read1_index35=6913MID

description: WT


title: untreated run0141_lane8_read1_index19=5186CO


title: untreated run0141_lane8_read1_index29=5187MID


title: untreated run0141_lane8_read1_index28=5186MID


title: UVC_DMSO_24-rep1

description: Processed file ID: DSTR_T0037

tag: cell line

value: UVC


title: untreated run0141_lane8_read1_index1=5186BS


title: outlier run0141_lane8_read1_index8=6913BS

description: outlier

source_name: outlier

value: outlier


title: untreated run0141_lane8_read1_index18=6914CB

description: WT

source_name: CB

value: CB

value: cerebellum


title: untreated run0141_lane8_read1_index16=6912CB

description: WT


title: untreated run0141_lane8_read1_index17=6913CB

description: WT


title: High run0141_lane8_read1_index13=5753CB


title: untreated run0141_lane8_read1_index12=5188CB


title: High run0141_lane8_read1_index14=5754CB


title: untreated run0141_lane8_read1_index10=5186CB


title: RS411_Dex1h_PU.1 ChIP

city: Boston

first: Jennifer

middle: Nan-Wah

last: Wu

state: MA

address: 450 Brookline Ave.

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Basecalls performed using CASAVA version 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie version 0.12.8 with default parameters aside from:  seed mismatches = 1 (-n 1); number of alignments <= 1 (-m 1); SAM output format (-S); best stratum reported (--best, --strata)
Peaks were called using MACS version 1.4.1.  Treatments and control/input files were used for each experiment with default parameters in addition to:  effective genome size 2.7e9 (-g hs); generate wig files (-w -S)
Genome_build: hg19
Supplementary_files_format_and_content: .wig.gz files were generated using MACS version 1.4.1 as described above.

growth_protocol: RS4;11 cells were grown in DMEM medium supplemented with 10% fetal calf serum.  Cells were maintained at a density of 1.5-3e6 cells/mL by splitting 1:2 every 2-3 days.

extract_protocol:
Histone modification ChIP and DHS were performed on MNase-digested and DNase-digested native chromatin, respectively.  Transcription factor ChIP was performed on sonicated nuclei isolated from cells treated with EGS and formaldehyde cross-linking agents.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3' to 5' exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 7-9 cycles and library fragments of ~270 bp for histone modification libraries, ~75 bp for DHS libraries, and ~320 bp for transcription factor libraries (insert plus adaptor and PCR primer sequences) were size selected using PippinPrep (Sage Science) 2% agarose gels. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

treatment_protocol: Cells were steroid-starved for 2 days by resuspension in DMEM medium supplemented with 10% charcoal-dextran treated fetal calf serum.  Following starvation, cells were resuspended at a density of 2e6 cells/mL.  Half of cells were treated with 10 nM dexamethasone for 1 hour and half were left unstimulated.

tag: cell type

value: acute lymphoblastic leukemia cell line

tag: treated with

value: 10 nM dexamethasone for 1 hour

tag: chip antibody

value: PU.1 (Pierce, E.388.3; Cell Signaling, 2266; Santa Cruz Biotechnology, SC-352X)


title: RS411_Dex1h_input DNA (sonicated, PU.1 ChIP)

description: input DNA for Dex1h PU.1 ChIP


title: RS411_Dex1h_GR ChIP

value: GR (Novus, NB300-731; Cell Signaling, D8H2; Abcam ab3579)


title: Tumors PBS Control (CisGenome)

city: Heidelberg - Melbourne

last: Thiem

state: Victoria

address: 145 Studley Road

department: Cancer Research

country: Australia

institute: Olivia Newton-John Cancer Research Institute

description:
Control
Chromatin

data_processing:
Base-calling: Base-calling was performed using Illumina software. Reads that have poor sequence quality and/or are made of homopolymers were removed from the datasets.
Read alignment: After filtering of poor quality sequences, ChIP-Seq reads were aligned to the UCSC mm9 genome assembly using NovoAlign software (www.novocraft.com).
File conversion: Conversion of NovoAlign output files to .bed files was performed using Perl.
Peak calling: Peak calling was performed using CisGenome software (Ji et al., 2008 and 2011) with a minimal number of 10 reads within a peak and a standard threshold probability (p-value) of P≤10-5.
Retrieval of relevant peak and associated gene/microRNA information was performed using CisGenome and R programming language for statistical computing (Version 2.12.1).
Genome_build: MGSCv37
Supplementary_files_format_and_content: .bed and .xls files. The three processed data files "Control_Peak_Information_CisGenome_Output.xls", "IL6_Peak_Information_CisGenome_Output.xls" and "IL11_Peak_Information_CisGenome_Output.xls" are the output files of the CisGenome software and contain the following information about significant Stat3-associated peaks: (I) exact peak location (chromosome number and the start and end nucleotide positions), (II) peak width/length (expressed in base pairs), (III) reads/tags per peak (total number of sequence tags counted at each enriched region).

source_name: Pooled gastric tumor tissue from 3 individual PBS-treated gp130F/F mice, Stat3 ChIP

extract_protocol:
Following DNA-Protein cross-linking with formaldehyde and tissue homogenization, chromatin was extracted using "shearing buffer" provided in the SIGMA Imprint ChIP Kit in accordance with the manufacturer's instructions. Chromatin shearing was performed using the Diagenode Bioruptor water bath sonicator. Sheared chromatin was used for immunoprecipitations with a ChIP-validated Stat3 antibody (Santa Cruz SC-482X) and the SIGMA Imprint ChIP Kit according to the manufacturer's instructions.
Libraries were prepared according to Illumina's instructions accompanying the ChIP-Seq DNA Sample Preparation Kit (IP-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow Exo fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters, which have a single 'T' base overhang at the 3' end. Following adapter ligation, DNA was PCR amplified (15 cycles) with Illumina primers, and library fragments of 200-300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: Mice (10-12 weeks, n=3 per treatment cohort) were subjected to a single intraperitoneal injection of PBS (200ul), IL6 or IL11 (5ug diluted in 200ul PBS) 60 min prior to sacrifice. Gastric tumor tissue was resected, snap-frozen on dry ice and stored at -80 degrees Celsius.

tag: genotype/variation

value: gastric tumors

value: 10-12 weeks

tag: treatment

value: PBS


title: Tumors IL11 (CisGenome)

description:
IL11
Chromatin

source_name: Pooled gastric tumor tissue from 3 individual IL11-treated gp130F/F mice, Stat3 ChIP


title: Tumors IL11 (MACS)

description:
IL11
Chromatin

data_processing:
Base-calling: Base-calling was performed using Illumina software. Reads that have poor sequence quality and/or are made of homopolymers were removed from the datasets.
Read alignment: After filtering of poor quality sequences, ChIP-Seq reads were aligned to the UCSC mm9 genome assembly using Bowtie software.
File conversion: Conversion of Bowtie output files to .bed and .wig files was performed using Perl.
Peak calling: Peak calling was performed using MACS software (Zheng et al., 2008) with a fold-enrichment ratio (mfold) of 12 fold and a standard threshold probability (p-value) of P≤10-5.
Retrieval of relevant peak and associated gene/microRNA information was performed using R programming language for statistical computing (Version 2.12.1).
Genome_build: MGSCv37
Supplementary_files_format_and_content: .bed and .xls files. The three processed data files "Control_Peak_Information_MACS_Output.xls", "IL6_Peak_Information_MACS_Output.xls" and "IL11_Peak_Information _MACS_Output.xls" are the original output files of the MACS software and contain the following information about significant Stat3-associated peaks: (I) exact peak location (chromosome number and the start and end nucleotide positions), (II) peak width/length (expressed in base pairs), (III) peak summit (the exact nucleotide position in each peak at which the highest number of tags were counted), (IV) reads/tags per peak (total number of sequence tags counted at each enriched region ), (V) P-value and (VI) fold enrichment of each peak.


title: RS411_Dex1h_input DNA (sonicated, GR ChIP)

description: input DNA for Dex1h GR ChIP


title: Tumors IL6 (CisGenome)

description:
IL6
Chromatin

source_name: Pooled gastric tumor tissue from 3 individual IL6-treated gp130F/F mice, Stat3 ChIP


title: Tumors PBS Control (MACS)

description:
Control
Chromatin


title: RS411_Dex1h_H3K4me2 ChIP

value: H3K4me2 (Millipore, 07-030)


title: RS411_Dex1h_H3K4me3 ChIP

value: H3K4me3 (Abcam, ab8580)


title: RS411_Dex1h_DHS


title: RS411_Dex1h_input DNA (MNase digested)

description: input DNA for Dex1h histone modification ChIP


title: High run0141_lane8_read1_index15=5755CB


title: RS411_NoStim_input DNA (sonicated, PU.1 ChIP)

description: input DNA for NoStim PU.1 ChIP

source_name: RS4;11_no stimulation

value: none (no stimulation control)


title: RS411_Dex1h_H3K27Ac ChIP

value: H3K27Ac (Abcam, ab4729)


title: RS411_NoStim_input DNA (sonicated, GR ChIP)

description: input DNA for NoStim GR ChIP


title: untreated run0141_lane8_read1_index11=5187CB


title: RS411_NoStim_DNase-digested genomic DNA

description: input DNA for DHS


title: RS411_NoStim_GR ChIP


title: RS411_NoStim_DHS


title: RS411_NoStim_H3K4me2 ChIP


title: RS411_NoStim_H3K4me3 ChIP


title: RS411_NoStim_H3K27Ac ChIP


title: RS411_NoStim_input DNA (MNase digested)

description: input DNA for NoStim histone modification ChIP


title: Tumors IL6 (MACS)

description:
IL6
Chromatin


title: RS411_NoStim_H3K4me1 ChIP

value: H3K4me1 (Abcam, ab8895)


title: N35a

city: Shenzhen

first: Desheng

last: Gong

address: No.7 PengFei road

institute: Agricultural Genomes Institute at Shenzhen

data_processing:
Genomic DNA from sperms was extracted, and sequenced by BS technology using Illumina HiSeq2000 sequencer.
Raw sequencing data was processed by the Illumina base-calling pipeline. Low-quality reads that contained more than 10% ’N’s or over 50% of the sequence with low quality value (quality value <20) per read were omitted from the data analysis.
The clean reads were aligned to the reference genome using BSMAP software.
The uniquely aligned reads were used for methylation analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Cout files include chromosome ID,C sites' coordinate, the number of methylated reads and non-methylated reads

source_name: normozoospermia_high motile sperm

extract_protocol:
DNA was isolated using AllPrep DNA/RNA Mini Kit (Qiagen, Germantown, MD, USA) following the manufacturer's protocols.
1ug of genomic DNA was fragmented into approximately 200-300 bp using a Covarias sonication system (Covarias, Woburn, MA, USA). After purification, the fragmented fractions were treated with a mixture of T4 DNA polymerase, Klenow Fragment and T4 polynucleotide kinase to repair blunt and phosphorylate ends. The blunt DNA fragments were subsequently 3' adenylated using Klenow Fragment (3'-5' exo-) and then ligated by T4 DNA Ligase to adapters that were synthesized with 5'-methylcytosine instead of 5'-cytosine and contain index sequences inside. After each step, the reaction products were purified using QIAquick PCR purification kit (Qiagen, Germantown, MD, USA). Following quantification by a Qubit fluorometer with Quant-iT dsDNA HS Assay Kit (Invitrogen, Carlsbad, CA, USA), the constructed libraries were hybrided to promoter targeted probes, designed and synthesized by Roche Nimblegen Incorporation (Roche NimbleGen, Madison, WI, USA). Following liquid hybridization capture procedure, bisulfite conversion was performed using ZYMO EZ DNA Methylation-Gold Kit (ZYMO, Irvine, CA, USA). Finally, the purified libraries were quantified by the Bioanalyzer analysis system (Agilent, Santa Clara, CA, USA) and real-time PCR assay and then analyzed using Illumina Hiseq2000 (Illumina, San Diego, CA, USA).

tag: age (yrs)

tag: phenotype

value: normozoospermia

value: sperm

tag: motility

value: high motile sperm


title: RS411_NoStim_PU.1 ChIP


title: N35c

source_name: normozoospermia_low motile sperm

tag: tissue

value: low motile sperm


title: N34c


title: RS411_Dex1h_H3K4me1 ChIP


title: N34a


title: N29c


title: N29a


title: N28a


title: N26c


title: N26a


title: N28c


title: N24a


title: A53a

source_name: asthenozoospermia_high motile sperm

value: asthenozoospermia


title: A53c

source_name: asthenozoospermia_low motile sperm


title: N25c


title: N25a


title: N23c


title: N23a


title: A44a


title: A40a


title: A40c


title: A38c


title: N24c


title: A38a


title: A44c


title: A50c


title: A36a


title: A36c


title: A50a


title: A34a


title: A34c


title: HuCCT1 CDK9 siRNA Control

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

data_processing:
Reads have been aligned against Human reference genome hg19 using Bowtie2 aligner with default parameters. Aligned reads have been used either for coverage evaluation (normalized by library size) stored in bigWig format or for peak-calling procedures using MACS software (version 1.3.7.1) with a lower enrichment cutoff of 5 (mfold=5) and a pvalue cutoff of 10e-08
in order to find regions for significant coverage enrichment. IgG signal has been used to model the background noise for all datasets analyzed with MACS..
Genome_build: hg19
Supplementary_files_format_and_content: bed file containing the genomic positions of the significant peaks output by MACS. BigWig file containing normalized coverage data

source_name: HuCCT1 human cell line

extract_protocol:
Cells were cross-linked in 1% formaldehyde for 10 minutes at room temperature after which the reaction was stopped by addition of 0.125M glycine. Cells were lysed and harvested in ChIP buffer (100 mM Tris at pH 8.6, 0.3% SDS, 1.7% Triton X-100 and 5 mM EDTA) and the chromatin disrupted by sonication using a Diagenode Bioruptor sonicator UCD-200 to obtain fragments of 200-500 bp in size. Suitable amounts of chromatin were incubated with specific antibodies overnight. Antibodies used are: H3K4Me3 (Millipore – Cat. # 07-473), H3K27Ac (Abcam – Cat. # ab4729), H3K4Me1 (Abcam – Cat. # ab8895), MED1 (Bethyl – Cat. # A300-793A), SMC1 (Bethyl – Cat. # A300-005A), Pol2 (Santa Cruz – Cat. # sc-899), Phospho-Rpb1 CTD (Ser2) (Cell Signaling – Cat. # 13499), Phospho-Rpb1 CTD (Ser5) (Cell Signaling – Cat. # 13523), CDK9 (Santa Cruz – Cat. # sc-484)
Libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina and barcoded using NEBNext Multiplex Oligos for Illumina according to manufacturer recommendation.

tag: sirna

value: Control

value: CDK9 (Santa Cruz, catalog# sc-484, lot# I0414)


title: HuCCT1 CDK9 siRNA YAP/TAZ

value: YAP/TAZ


title: HuCCT1 unrelated IgG

value: IgG


title: HuCCT1 SMC1 siRNA YAP/TAZ

value: SMC1 (Bethyl, catalog# A300-005A, lot# A300-055A-3)


title: HuCCT1 Pol2 siRNA Control

value: Pol2 (Santa Cruz, catalog# sc-899, lot# L0412)


title: HuCCT1 Ps2 Pol2 siRNA Control

value: Phospho-Rpb1 CTD (Ser2) (Cell Signaling, catalog# 13499, lot# 1)


title: HuCCT1 Ps2 Pol2 siRNA YAP/TAZ


title: HuCCT1 H3K4Me1 siRNA YAP/TAZ

value: H3K4Me1 (Abcam, catalog# ab8895, lot# GR61306-1)


title: HuCCT1 SMC1 siRNA Control


title: HuCCT1 H3K4Me1 siRNA Control


title: HuCCT1 H3K27Ac siRNA Control

value: H3K27Ac (Abcam, catalog# ab4729, lot# GR144577-1)


title: HuCCT1 MED1 siRNA Control

value: MED1 (Bethyl, catalog# A300-793A, lot# A300-793A)


title: HuCCT1 MED1 siRNA YAP/TAZ


title: HuCCT1 H3K4Me3

value: H3K4Me3 (Millipore, catalog# 07-473, lot# 2384705)


title: HuCCT1 H3K27Ac siRNA YAP/TAZ


title: HuCCT1 TAZ (WWTr1)

data_processing:
Reads have been aligned against Human reference genome hg19 using Bowtie2 aligner with default parameters. Aligned reads have been used for peak-calling procedures using MACS software (version 1.3.7.1). A lower enrichment cutoff of 5 (mfold=5) and a pvalue cutoff of 10e-08 have been set.
in order to find regions for significant coverage enrichment. IgG signal has been used to model the background noise for YAP, TEAD1, TEAD2 and TAZ datasets; GFP signal has been used to model the background noise for HAYAP5SA dataset.
Genome_build: hg19
Supplementary_files_format_and_content: bed file containing the genomic positions of the significant peaks output by MACS

extract_protocol:
Cells were cross-linked in 1% formaldehyde for 10 minutes at room temperature after which the reaction was stopped by addition of 0.125M glycine. Cells were lysed and harvested in ChIP buffer (100 mM Tris at pH 8.6, 0.3% SDS, 1.7% Triton X-100 and 5 mM EDTA) and the chromatin disrupted by sonication using a Diagenode Bioruptor sonicator UCD-200 to obtain fragments of 200-500 bp in size. Suitable amounts of chromatin were incubated with specific antibodies overnight. Antibodies used are: YAP (Cell Signaling – Cat. # 14074), TEAD1 (BD – Cat. # 610922), TEAD4 (Abcam – Cat. # ab58310), TAZ (Cell signaling Cat. # 4883), HA (Covance – Cat. # MMS-101P)
Libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina and barcoded using NEBNext Multiplex Oligos for Illumina according to manufacturer recommendation.


title: HuCCT1 IgG


title: HuCCT1 Input

value: Input


title: HuCCT1 YAP

value: YAP


title: HuCCT1 GFP

value: GFP


title: HuCCT1 HAYAP5SA


title: HuCCT1 TEAD1


title: MSTO H3K27ac

data_processing:
Reads have been aligned against Human reference genome hg19 using Bowtie2 aligner with default parameters. Aligned reads have been used for peak-calling procedures using MACS software (version 1.3.7.1). A lower enrichment cutoff of 5 (mfold=5) and a pvalue cutoff of 10e-08 have been set.
in order to find regions for significant coverage enrichment. IgG signal has been used to model the background noise for all datasets.
Genome_build: hg19
Supplementary_files_format_and_content: bed file containing the genomic positions of the significant peaks output by MACS

source_name: MSTO human cell line

extract_protocol:
Cells were cross-linked in 1% formaldehyde for 10 minutes at room temperature after which the reaction was stopped by addition of 0.125M glycine. Cells were lysed and harvested in ChIP buffer (100 mM Tris at pH 8.6, 0.3% SDS, 1.7% Triton X-100 and 5 mM EDTA) and the chromatin disrupted by sonication using a Diagenode Bioruptor sonicator UCD-200 to obtain fragments of 200-500 bp in size. Suitable amounts of chromatin were incubated with specific antibodies overnight. Antibodies used are: YAP (Cell Signaling – Cat. # 14074), TEAD1 (BD – Cat. # 610922), H3K27ac (Abcam – Cat. # ab4729)
Libraries were generated using NEBNext Ultra DNA Library Prep Kit for Illumina and barcoded using NEBNext Multiplex Oligos for Illumina according to manufacturer recommendation.

value: MSTO

tag: antibody


title: HuCCT1 ps5 Pol2 siRNA Control

value: Phospho-Rpb1 CTD (Ser5) (Cell Signaling, catalog# 13523, lot# 1)


title: HuCCT1 Pol2 siRNA YAP/TAZ


title: HuCCT1 ps5 Pol2 siRNA YAP/TAZ


title: MSTO YAP


title: MSTO IgG


title: MSTO TEAD1


title: H3K27me3 ChIPseq: Control cycle 6

city: Singapore

first: Jeremie

last: Poschmann

state: Singapore

address: 60 Biopolis street

country: Singapore

institute: Genome Institute Singapore

description:
CHU014
H3K27me3 ChIPseq: MSC-44 cycle 6

data_processing:
mapping with BWA
Peak calling with MACS following user guidelines for each antibody
GC normalization following user guidelines from Homer ChIP-seq suite
log2 conversion
Genome_build: hg19
Supplementary_files_format_and_content: tagcount files contain the union of peaks for each antibody, with the normalized read counts in log2 for each library

source_name: umbilical cord derived mesenchymal stem cells (UC-MSC)

growth_protocol: Primary mesenchymal stem cell (MSC) lines were isolated from fresh umbilical cord and propagated in standard DMEM growth medium, supplemented with Fiboblast Growth Factor (FGF)

extract_protocol:
Approximately 5 million cells from each cell line were cross-linked with 1% formaldehyde for 15 min and excess formaldehyde quenched by addition of glycine (0.625 M). Nuclei were prepared and collected for sonication in 1% SDS-buffer
DNA was enrepaired, followed by "A" attachment, adapter ligation and 15 cycles of PCR with multiplex primers. Size selection was performed with 1.5% low melting agarose gels.

treatment_protocol: MSC differentiation into mature adipocytes followed standard procedures including the addition of a specific induction cocktail for three days followed by one day in insulin medium. These cycles were repeated 6 times until the cells fully differentiated into adipocytes.

tag: gender

value: Female

value: Normal

tag: fat differentiation cycle

value: cycle 6

value: 3ug H3K27me3; Millipore (cat:07-449, lot DAM1588246)


title: H3K27me3 ChIPseq: SGA cycle 0

description:
CHU009
H3K27me3 ChIPseq: MSC-01 cycle 0

value: Small-for-Gestational-Age (SGA)

value: cycle 0


title: H3K27me3 ChIPseq: Control cycle 0

description:
CHU012
H3K27me3 ChIPseq: MSC-44 cycle 0


title: H3K27me3 ChIPseq: SGA cycle 6

description:
CHU011
H3K27me3 ChIPseq: MSC-01 cycle 6


title: H3K27ac ChIPseq: Control cycle 6

description:
CHU008
H3K27ac ChIPseq: MSC-44 cycle 6

value: 3ug H3K27ac Actif motif (cat 39133,lot19208002)


title: H3K27me3 ChIPseq: Control cycle 3

description:
CHU013
H3K27me3 ChIPseq: MSC-44 cycle 3

value: cycle 3


title: H3K27ac ChIPseq: Control cycle 3

description:
CHU007
H3K27ac ChIPseq: MSC-44 cycle 3


title: HuCCT1 TEAD4


title: H3K27ac ChIPseq: SGA cycle 3

description:
CHU004
H3K27ac ChIPseq: MSC-01 cycle 3


title: H3K27ac ChIPseq: Control cycle 0

description:
CHU006
H3K27ac ChIPseq: MSC-44 cycle 0


title: Input: Control

description:
CHU002
Input: MSC-44

value: pooled


title: H3K27ac ChIPseq: SGA cycle 0

description:
CHU003
H3K27ac ChIPseq: MSC-01 cycle 0


title: Input: SGA

description:
CHU001
Input: MSC-01


title: CWR22PC_Input_DNA

city: New York

first: Yu

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

description: input DNA

data_processing:
Alignment: ChIP-seq reads were obtained and mapped to the human genome (hg18, build 36) using either the AB SOLiD pipeline (LNCaP-AR and VCaP) or the Illumina CASAVA pipeline (v1.8.0; CWR22PC). Unique reads mapped to a single genomic location (allowing two mismatches) were kept for peak identification and data analysis.
Peak detection was performed with the software MACS (Version 1.4.0) with input as controls.
Genome_build: hg18
Supplementary_files_format_and_content: The processed data are peaks in the standard bed format.

source_name: Prostate cancer cells

growth_protocol: LNCaP-AR cells were grown in RPMI containing 10% FBS, VCaP cells were grown in DMEM containing 10% FBS, CWR22PC cells were grown in RPMI containing 10% FBS plus 0.1nM DHT

extract_protocol: ChIP library was prepared for sequencing by the SOLiD (LNCaP-AR and VCaP) or HiSeq2000 (CWR22PC) instruments according to manufacturer recommended procedures.

treatment_protocol: LNCaP-AR cells were grown in charcoal-stripped serum containing phenol-red free media for 72hrs and then treated with vehicle or 1nM R1881 or 1nM R1881 plus 10µM Bicalutamide or 1nM R1881 plus 10µM MDV3100 for 1hr. VCaP and CWR22PC cells were grown in regular media and treated with vehicle or 1nM DHT or 1nM DHT plus 10µM Bicalutamide or 1nM DHT plus 10µM MDV3100 for 1hr.

value: Prostate cancer

value: none (input)


title: CWR22PC_DHT+MDV3100_AR_ChIP-seq

description: Chromatin IP against AR

value: AR (Millipore, 06-680)


title: CWR22PC_DHT+Bicalutamide_AR_ChIP-seq

description: Chromatin IP against AR


title: CWR22PC_Vehicle_AR_ChIP-seq

description: Chromatin IP against AR


title: T29_MethylC-seq_rep1

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

data_processing:
Basecalls performed using CASAVA version 1.8
The low quality reads and adapter sequences were firstly removed from the raw reads by Trim Galore. The quality of resulted clean reads was checked by FastQC
The reads from MethylC-seq or MeDIP-seq were aligned to the hg18 genome assembly using SOAP2.21 with 2 mismatches allowed in the seed (30 bp) and 5 mismatches in the whole read
RRBS-analyser was used to process the alignment results of MethylC-seq to identify the methylcytosines where at least three reads were covered
Genome_build: UCSC hg18
Supplementary_files_format_and_content: Tab-delimited text files of MethylC-seq include methylation information of each chromosone for each Sample.Scores represent chromosone,position,strand,Cpattern,Csequence,copy number,methylC reads number,unmethylC reads number,binomial expection
Supplementary_files_format_and_content: Tab-delimited text files of MeDIP-seq include read information for antibody enrichment.Scores represent chromosone,start_position,end_position,0,0,strand

source_name: ovarian epithelial cell line

extract_protocol:
Genomic DNA were extracted from T29 cell lines by Qiagen DNeasy Blood & Tissue Kit (Qiagen, Germany) and 20 mg/mL RNase (Qiagen, Germany) was used to degrade contaminated RNA in DNA samples. DNA integrity was verified by agarose gel electrophoresis. Quantity of DNA was measured using Quant-iT PicoGreen dsDNA Kits on Qubit 2.0 (Invitrogen, USA)
Final libraries were quantified by Quant-iT PicoGreen dsDNA Kits (Invitrogen, USA) and Library Quantification Kit-Illumina/Universal (Kapa Biosystems, Inc. Woburn, MA) and sequenced on Illumina HiSeq 2000

value: an immortalized but non-transformed ovarian epithelial cell line

tag: passages

value: ovarian epithelial


title: T29_MB-seq_rep4

description: MB-seq

data_processing:
Basecalls performed using CASAVA version 1.8
The low quality reads and adapter sequences were firstly removed from the raw reads by Trim Galore. The quality of resulted clean reads was checked by FastQC
MB-seq reads were aligned to the hg18 genome assembly using SOAP2.21 with 2 mismatches allowed in the seed (30 bp) and 5 mismatches in the whole read
RRBS-analyser was used to process the alignment results to identify the methylcytosines where at least three reads were covered
Genome_build: UCSC hg18
Supplementary_files_format_and_content: Tab-delimited text files include methylation information of each chromosone for each Sample.Scores represent chromosone,position,strand,Cpattern,Csequence,copy number,methylC reads number,unmethylC reads number,binomial expection

extract_protocol:
Genomic DNA were extracted from T29 and T29H cell lines by Qiagen DNeasy Blood & Tissue Kit (Qiagen, Germany) and 20 mg/mL RNase (Qiagen, Germany) was used to degrade contaminated RNA in DNA samples. DNA integrity was verified by agarose gel electrophoresis. Quantity of DNA was measured using Quant-iT PicoGreen dsDNA Kits on Qubit 2.0 (Invitrogen, USA)
Genomic DNA from T29 cell line with the input amount of 1 μg, 500 ng, 200 ng, 50 ng, respectively, was fragmented to ~100-500 bp using Covaris E210 sonicator (Covaris Inc. USA). Fragmented DNA was end-repaired, A-tailed, and ligated to C-hydroxylmethylated Illumina Multiplexing adapters following the standard Illumina protocol.MB-seq library construction for genomic DNA from T29H exactly followed the protocol mentioned above.


title: T29_MethylC-seq_rep2


title: H3K27me3 ChIPseq: SGA cycle 3

description:
CHU010
H3K27me3 ChIPseq: MSC-01 cycle 3


title: T29_MB-seq_rep2

description: MB-seq


title: T29H_MB-seq_rep1

description: MB-seq

value: a RasV12-transformed human ovarian epithelial cell line


title: T29_MeDIP-seq


title: T29_MethylC-seq_rep4


title: T29_MethylC-seq_rep3


title: T29_MB-seq_rep1

description: MB-seq


title: T29H_RNA-seq

data_processing:
Basecalls performed using CASAVA version 1.8
The low quality reads and adapter sequences were firstly removed from the raw reads by Trim Galore. The quality of resulted clean reads was checked by FastQC
To estimate gene expression level and identify differentially expressed genes between T29 and T29H sample, sequencing library derived from poly(A)-enriched cellular RNA were sequenced on Illumina high throughput sequencing platform in paired-end mode. After using script Trim Galore to trim off sequencing adaptors, low quality sequencing reads and then estimate sequencing data qualities, software TopHat2 was used to map reads to genome by following  criterion  allowing up to 2 mismatches and Phered-scaled mapping quality >= 4. Detailed sequencing information was summarized in supplemental Table S8.
We used bioconductor package edgeR to identify differentially expressed genes between two samples T29 and T29H based on number of mapped paired-end reads counted by python package HTSeq (http://www.htseq.org/) for each gene. The edgeR could work under few or even no replicate situations like ours (one data to one sample), so we take strategies suggested by edgeR manuals for no replicates testing to set one argument BCV to 0.1. Differentially expression protein-coding genes and lncRNA genes were listed in two supplementary files, respectively.
Genome_build: UCSC hg18
Supplementary_files_format_and_content: Tab-delimited text files include reads counts values for each sample.

extract_protocol:
Total RNAs were extracted from T29 and T29H with RNeasy Mini Kit (QIAGEN, Germany).
Total RNAs were extracted from T29 and T29H with RNeasy Mini Kit (QIAGEN, Germany). RNA quality was quality-controlled by Bioanalyser 2100 (RNA nano kits, Agilent). mRNA-Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA), and then subjected to transcriptome sequencing on the Illumina Hiseq 2000


title: H3K27ac ChIPseq: SGA cycle 6

description:
CHU005
H3K27ac ChIPseq: MSC-01 cycle 6


title: CClp1 TEAD

data_processing:
Reads have been aligned against Human reference genome hg19 using Bowtie2 aligner with default parameters. Aligned reads for YAP, YAP  second run, YAP Santa Cruz, TEAD1 and Flag-Bio-YAP5SA have been used for peak-calling procedures using MACS software (version 1.3.7.1). A lower enrichment cutoff of 5 (mfold=5) has been set.
in order to find regions for significant coverage enrichment. IgG signal has been used to model the background noise for YAP, YAP Santa Cruz and TEAD1. Input signal has been used as background for YAP second run. BirA has been used as background for Flag-Bio-YAP5SA
Genome_build: hg19
Supplementary_files_format_and_content: bed file containing the genomic positions of the significant peaks output by MACS

source_name: CClp1 human cell line

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 min and cross-linking was quenched by addition of 0.125 M glycine. Cells were then harvested in ChIP buffer and sonicated with a Bioruptor UCD-300 to obtain fragments around 250 bp in size. Precipitated DNA was recovered by purification with a QIAquick PCR purification kit (Qiagen)
Libraries for sequencing were obtained using a ChIP-Seq DNA sample prep kit (Illumina) according to the manufacturer's reccomendations

value: TEAD


title: CClp1 Flag-Bio-YAP5SA

data_processing:
Reads have been aligned against Human reference genome hg19 using Bowtie2 aligner with default parameters. Aligned reads for YAP, YAP second run, YAP Santa Cruz, TEAD1 and Flag-Bio-YAP5SA have been used for peak-calling procedures using MACS software (version 1.3.7.1). A lower enrichment cutoff of 5 (mfold=5) has been set.
in order to find regions for significant coverage enrichment. IgG signal has been used to model the background noise for YAP, YAP Santa Cruz and TEAD1. Input signal has been used as background for YAP Avruch second run. BirA has been used as background for Flag-Bio-YAP5SA
Genome_build: hg19
Supplementary_files_format_and_content: bed file containing the genomic positions of the significant peaks output by MACS


title: T29_RNA-seq


title: CClp1 IgG

value: IgG


title: G_RISK309

first: Rebekah

last: Karns

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Ileal biopsy from a cCD naïve treatment A1b Male with cCD, Male

data_processing:
Illumina Hi-Seq 2000 for sequencing
Reads were aligned using TopHat, using Hg19 as the reference genome and mapping reads per kilobase per million mapped reads (RPKM) as output.
RPKM were normalized using the DESeq algorithm using Avaids NGS software, where normalized counts were log2-transformed and base-lined to the median expression of control samples.
Normalized expression values were baselined to the median of all samples
We removed all transcripts that did not have at least 5 RPKM in at least 5 different samples.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited files contain normalized and baselined RPKM values for each sample.

growth_protocol: Ileal biopsies were stored in RNAlater at -80C.

extract_protocol:
RNA was isolated using the Qiagen AllPrep RNA/DNA Mini Kit, RNA quality and concentration was measured by Agilent Bioanalyzer 2100 using the RNA 6000 Nano Assay.
RNA sequencing (RNA-seq) libraries were prepared using the Illumina TruSeq RNA preparation kit and sequenced on the Illumina Hi-Seq 2000 with single-end 50-bp reads (Illumina, San Diego, CA)

value: ileum

tag: sample type

value: Ileal biopsy

tag: diagnosis

value: cCD

tag: age at diagnosis

value: Male

tag: paris age at diagnosis


title: G_RISK310

source_name: Ileal biopsy from a cCD naïve treatment A1b Male


title: CWR22PC_DHT_AR_ChIP-seq

description: Chromatin IP against AR

tag: cell line

tag: cell type


title: G_RISK308


title: T29_MB-seq_rep3

description: MB-seq


title: G_RISK305


title: G_RISK304


title: G_RISK303

description: Ileal biopsy from a cCD naïve treatment A1b Female with cCD, Female

value: Female


title: G_RISK302

source_name: Ileal biopsy from a cCD naïve treatment A1b Female


title: G_RISK301


title: G_RISK298


title: CClp1 Input

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 min and cross-linking was quenched by addition of 0.125 M glycine. Cells were then harvested in ChIP buffer and sonicated with a Bioruptor UCD-300 to obtain fragments around 250 bp in size.  Precipitated DNA was recovered by purification with a QIAquick PCR purification kit (Qiagen)
Libraries for sequencing were obtained using a ChIP-Seq DNA sample prep kit (Illumina) according to the manufacturer's reccomendations

tag: chip antibody

value: Input


title: G_RISK300


title: G_RISK296


title: G_RISK297


title: G_RISK299


title: CClp1 BirA

value: BirA


title: G_RISK293


title: G_RISK292


title: CClp1 YAP

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 min and cross-linking was quenched by addition of 0.125 M glycine. Cells were then harvested in ChIP buffer and sonicated with a Bioruptor UCD-300 to obtain fragments around 250 bp in size. Precipitated DNA was recovered by purification with a QIAquick PCR purification kit (Qiagen)
Libraries for sequencing were obtained using a ChIP-Seq DNA sample prep kit (Illumina) according to the manufacturer's recommendations

value: YAP


title: G_RISK295


title: G_RISK294


title: G_RISK290


title: G_RISK291


title: G_RISK289


title: G_RISK287


title: G_RISK307


title: G_RISK288


title: G_RISK286


title: G_RISK285


title: G_RISK283


title: G_RISK284


title: G_RISK281


title: G_RISK277


title: G_RISK278


title: G_RISK279


title: G_RISK276


title: G_RISK275


title: G_RISK269

description: Ileal biopsy from a cCD naïve treatment A1a Female with cCD, Female


title: G_RISK266

source_name: Ileal biopsy from a cCD naïve treatment A1a Female


title: G_RISK274


title: G_RISK262


title: G_RISK268


title: G_RISK272


title: G_RISK264


title: G_RISK273


title: G_RISK270


title: G_RISK263


title: G_RISK265


title: G_RISK271


title: G_RISK260

description: Ileal biopsy from a cCD naïve treatment A1a Male with cCD, Male


title: G_RISK253

description: Ileal biopsy from a iCD naïve treatment A1b Male with iCD, Male

value: iCD


title: G_RISK259

description: Ileal biopsy from a iCD naïve treatment A1b Female with iCD, Female


title: G_RISK261

source_name: Ileal biopsy from a cCD naïve treatment A1a Male


title: G_RISK267


title: G_RISK249

source_name: Ileal biopsy from a iCD naïve treatment A1b Male


title: G_RISK251

source_name: Ileal biopsy from a iCD naïve treatment A1b Female


title: G_RISK252


title: G_RISK282


title: G_RISK244


title: G_RISK280


title: G_RISK236


title: G_RISK234


title: G_RISK233


title: G_RISK222


title: G_RISK206


title: G_RISK203


title: G_RISK219


title: G_RISK212


title: G_RISK218


title: G_RISK258


title: G_RISK198


title: G_RISK170


title: G_RISK174


title: G_RISK201


title: G_RISK182


title: G_RISK175


title: G_RISK183


title: G_RISK157


title: G_RISK172


title: G_RISK152


title: G_RISK190


title: G_RISK186


title: G_RISK158


title: G_RISK164


title: G_RISK230


title: G_RISK143


title: G_RISK204


title: G_RISK214


title: G_RISK145


title: G_RISK169


title: G_RISK135


title: G_RISK138


title: G_RISK139


title: G_RISK132


title: G_RISK137


title: G_RISK131


title: G_RISK123


title: G_RISK142


title: G_RISK119


title: G_RISK112


title: G_RISK111


title: G_RISK109


title: G_RISK89

description: Ileal biopsy from a iCD naïve treatment A1a Male with iCD, Male


title: G_RISK257


title: G_RISK84

description: Ileal biopsy from a iCD naïve treatment A1a Female with iCD, Female


title: G_RISK87

source_name: Ileal biopsy from a iCD naïve treatment A1a Male


title: G_RISK68


title: G_RISK255


title: G_RISK54

source_name: Ileal biopsy from a iCD naïve treatment A1a Female


title: G_RISK256


title: G_RISK110


title: G_RISK254


title: G_RISK248


title: G_RISK247


title: G_RISK246


title: G_RISK245


title: G_RISK242


title: G_RISK241


title: G_RISK122


title: G_RISK240


title: G_RISK239


title: G_RISK243


title: G_RISK237


title: G_RISK238


title: G_RISK232


title: G_RISK235


title: G_RISK231


title: G_RISK229


title: G_RISK250


title: G_RISK306


title: G_RISK226


title: G_RISK223


title: G_RISK221


title: G_RISK216


title: G_RISK225


title: G_RISK215


title: G_RISK224


title: G_RISK211


title: G_RISK217


title: G_RISK227


title: G_RISK228


title: G_RISK220


title: G_RISK210


title: G_RISK163


title: G_RISK202


title: G_RISK200


title: G_RISK208


title: G_RISK205


title: G_RISK207


title: G_RISK196


title: G_RISK197


title: G_RISK213


title: G_RISK193


title: G_RISK195


title: G_RISK189


title: G_RISK192


title: G_RISK199


title: G_RISK191


title: G_RISK194


title: G_RISK185


title: G_RISK187


title: G_RISK180


title: G_RISK209


title: G_RISK178


title: G_RISK171


title: G_RISK176


title: G_RISK179


title: G_RISK177


title: G_RISK173


title: G_RISK167


title: G_RISK165


title: G_RISK166


title: G_RISK162


title: G_RISK161


title: G_RISK160


title: G_RISK154


title: G_RISK156


title: G_RISK155


title: G_RISK159


title: G_RISK181


title: G_RISK188


title: G_RISK184


title: G_RISK150


title: G_RISK153


title: G_RISK149


title: G_RISK151


title: G_RISK148


title: G_RISK147


title: G_RISK136


title: G_RISK168


title: G_RISK134


title: G_RISK141


title: G_RISK144


title: G_RISK146


title: G_RISK140


title: G_RISK128


title: G_RISK133


title: G_RISK130


title: G_RISK129


title: G_RISK127


title: G_RISK126


title: G_RISK120


title: G_RISK121


title: G_RISK118


title: G_RISK117


title: G_RISK116


title: G_RISK115


title: G_RISK114


title: G_RISK113


title: G_RISK108


title: G_RISK106


title: G_RISK104


title: G_RISK105


title: G_RISK99


title: G_RISK100


title: G_RISK98


title: G_RISK101


title: G_RISK103


title: G_RISK96


title: G_RISK97


title: G_RISK95


title: G_RISK91


title: G_RISK125


title: G_RISK94


title: G_RISK92


title: G_RISK124


title: G_RISK88


title: G_RISK85


title: G_RISK86


title: G_RISK107


title: G_RISK82


title: G_RISK83


title: G_RISK102


title: G_RISK77


title: G_RISK80


title: G_RISK73


title: G_RISK75


title: G_RISK81


title: G_RISK70


title: G_RISK71


title: G_RISK93


title: G_RISK76


title: G_RISK74


title: G_RISK79


title: G_RISK72


title: G_RISK69


title: G_RISK90


title: G_RISK78


title: G_RISK64


title: G_RISK65


title: G_RISK63


title: G_RISK66


title: G_RISK62


title: G_RISK61


title: G_RISK67


title: G_RISK58


title: G_RISK57


title: G_RISK60


title: G_RISK55


title: G_RISK52


title: G_RISK53


title: G_RISK56


title: G_RISK51

description: Ileal biopsy from a Not IBD naïve treatment Male, Not IBD, Male

value: Not IBD


title: G_RISK45

description: Ileal biopsy from a Not IBD naïve treatment Female, Not IBD, Female


title: G_RISK48

source_name: Ileal biopsy from a Not IBD naïve treatment Female


title: G_RISK46

source_name: Ileal biopsy from a Not IBD naïve treatment Male


title: G_RISK47


title: G_RISK49


title: G_RISK50


title: G_RISK59


title: G_RISK44


title: G_RISK42


title: G_RISK38


title: G_RISK39


title: G_RISK41


title: G_RISK40


title: G_RISK34


title: G_RISK36


title: G_RISK31


title: G_RISK33


title: G_RISK37


title: G_RISK30


title: G_RISK29


title: G_RISK35


title: G_RISK27


title: G_RISK25


title: G_RISK26


title: G_RISK24


title: G_RISK23


title: G_RISK22


title: G_RISK43


title: G_RISK21


title: G_RISK18


title: G_RISK32


title: G_RISK11


title: G_RISK17


title: G_RISK7


title: G_RISK19


title: G_RISK16


title: G_RISK13


title: G_RISK28


title: G_RISK5


title: G_RISK15


title: G_RISK12


title: G_RISK2


title: G_RISK14


title: G_RISK10


title: G_RISK8


title: G_RISK4


title: G_RISK1


title: Cytosol mRNA-seq 4 h Tg 2

city: Durham

first: David

last: Reid

state: NC

address: 436 Nanaline Duke Bldg., Box 3709 DUMC

department: Biochemistry

institute: Duke University

data_processing:
Map reads to transcriptome with Bowtie (no mismatches)
Quantify translation as RPKM
Genome_build: hg19 (longest transcript isoform)
Supplementary_files_format_and_content: Excel spreadsheet indicating RPKM values

source_name: Mouse embryonic fibroblasts, GADD34-/-

growth_protocol: Cultured in DMEM + 10% FBS, 37C, 5% CO2

extract_protocol:
Pre-treatment with 180 uM cycloheximide for 30s. PBS wash. Release cytosol with digitonin. Extract remaining sample with dodecyl maltoside.
Ribosome profiling: Digest with Mnase (30 min 10 ug/ml, 37C), pellet ribosomes, extract RNA, PNK treat, gel isolation, library generation with NEB Directional Small RNA kit
mRNA-seq: RiboMinus, library prepataion using TruSeq RNA Sample Preparation Kit (Illumina)

treatment_protocol: Treatment with 1uM thapsigargin

value: embryonic fibroblast

tag: treatment

value: 4 h Tg

tag: compartment

value: Cytosol

tag: analysis

value: mRNA-seq

tag: replicate


title: HET_CD4_2

city: San Francisco

first: Jason

last: Cyster

address: 513 Parnassus Avenue, HSE-1001A

department: Microbiology and Immunology

institute: University of California, San Francisco

data_processing:
Base calling performed using RTA (Real-time Analysis), demultiplexed FASTQ files generated using CASAVA
RNA-seq paired end reads were aligned using Tophat (ver. 2.0.8b, Linux) to output read alignments that map once to the genome; other parameters were set as default
Aligned reads were then analyzed for differential expression using cufflinks (ver. 2.1.1).
Cufflinks output was transferred to excel file and then formatted.
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet containing gene expression matrix reported as FPKM values

source_name: CD4 dendritic cells from PBS treated control mouse

extract_protocol:
Mice were euthanized and CD4 dendritic cells (CD11c+I-Ab+CD4+CD8-) were sorted from spleens on a FACSAriaIII (purity >99%). Equal number of DCs (5.0x105) in SRBC or PBS immunized group were then snap-frozen immediately for RNA isolation.
Barcoded sequencing libraries were generated using 100ng of RNA with the Ovation RNA-seq System V2 and Encore Rapid Library System.
RNA-seq for Illumina HiSeq 2500

treatment_protocol: Mice were immunized with PBS (100uL) or sheep red blood cells (1x10^9 cells, from Colorado Serum Co.) for 1 hour.

tag: strain / genotype

value: C57BL/6 GPR183 Heterozygote

value: CD4 dendritic cells


title: IMM_CD4_1

source_name: CD4 dendritic cells from SRBC treated mouse


title: IMM_CD4_2


title: Cytosol mRNA-seq 2 h Tg 2

value: 2 h Tg


title: G_RISK20

tag: tissue

value: ileum


title: Cytosol mRNA-seq 0.5 h Tg 2

value: 0.5 h Tg


title: Cytosol mRNA-seq Untreated 2

value: Untreated


title: G_RISK6

value: Ileal biopsy

value: Male


title: G_RISK9


title: Cytosol mRNA-seq 4 h Tg 1


title: G_RISK3


title: Cytosol mRNA-seq 1 h Tg 2

value: 1 h Tg


title: Cytosol mRNA-seq 2 h Tg 1


title: ER mRNA-seq 0.5 h Tg 2

value: ER


title: ER mRNA-seq 1 h Tg 2


title: Cytosol mRNA-seq 0.5 h Tg 1


title: ER mRNA-seq 1 h Tg 1


title: ER mRNA-seq 4 h Tg 1


title: Cytosol Ribosome profiling 4 h Tg 2

value: Ribosome profiling


title: ER mRNA-seq Untreated 2


title: Cytosol mRNA-seq Untreated 1


title: ER mRNA-seq 2 h Tg 1


title: HET_CD4_1


title: ER mRNA-seq 0.5 h Tg 1


title: ER mRNA-seq Untreated 1


title: Cytosol Ribosome profiling 1 h Tg 2


title: Cytosol Ribosome profiling 2 h Tg 1


title: Cytosol Ribosome profiling Untreated 2


title: Cytosol Ribosome profiling 1 h Tg 1


title: Cytosol Ribosome profiling 2 h Tg 2


title: Cytosol Ribosome profiling 0.5 h Tg 2


title: Cytosol mRNA-seq 1 h Tg 1