title: Primed_static

city: Calgary

first: Leili

last: Rohani

state: Alberta

address: 405J, 1919 University Drive, NW

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

data_processing:
The constructed libraries sequenced on an Illumina NextSeq500 generated 75 bp, single-end reads. As this study was exploratory (n =1), no p-values are given and therefore the simple normalized expression (normalization) value comparison was done as Reads per Kilobase per Million (RPKM). To process the samples, the following workflow was used: the quality of raw sequenced reads was checked with FastQC v0.11.5 program. Reads were mapped to the GRCh38 (Latest ENSEMBL human genome assembly) using Tophat2 v2.1.1 mapper. Only the best alignment was preserved and up to 2 mismatches were allowed.
The number of reads in each gene was counted using the featureCounts v1.5.0-p2 program. From the featureCounts results, the normalized RPKM values for each gene were computed using a python script. The RPKM values for each gene within each sample were compared to generate fold change and log2 fold changes values between the samples in a pair-wise comparison (a python script was used to compare RPKM values and to generate the foldchange tables). For the pairwise comparison between static- and bioreactor-cultured naïve hPSCs, the fold change > 1.95 was measured relative to static-cultured naïve hPSCs to derive differentially expressed genes among those samples. For the pairwise comparison between static- and bioreactor-cultured primed hPSCs, the fold change > 1.95 was measured relative to static-cultured primed hPSCs to derive differentially expressed genes among those samples. The differentially expressed genes (fold change > 1.95) among the pair-wise comparisons were used for enriched gene ontology (GO) terms (Molecular Function (MF), Biological Process (BP), and Biological Pathway (rea)) through g:Profiler.
Genome_build: GRCh38 (Latest ENSEMBL human genome assembly)
Supplementary_files_format_and_content: Featurecounts tables containing the number of raw reads in each gene for each sample (rawcount) & the normalized RPKM values for each gene within each sample (rpkms), txt format

source_name: Human embryonic stem cell line_H9

growth_protocol: In static culture, the primed hESC line (H9) were cultured and maintained in standard culture conditions (37°C, 5% CO2) on Corning® Matrigel® hESC qualified Matrix-coated 60-mm tissue culture dishes with mTeSR™1 medium in static culture. Primed hESC cultures were fed every day with fresh mTeSR™1 medium, and the confluent cell cultures (usually 6-7 days) were passaged either as small clumps via Dispase or as single cells via StemPro® Accutase® Cell Dissociation Reagent. The primed hESCs were converted to naïve human pluripotent stem cells using RSeT™ Medium in static culture. Once the primed hESCs reached to 70 – 80% confluency, they were passaged as small clumps (approximately 50 - 200 µm in size) using Dispase, and were transferred onto mitomycin C treated-mitotically inactivated MEFs (iMEFs)-coated plates containing mTeSR™1 medium. The cells were incubated at 37°C for 24 - 36 hours under normoxic conditions (20% O2, 5% CO2) in mTeSR™1 medium. The mTeSR™1 medium was then replaced with RSeT™ medium and a daily full medium change with RSeT™ was done during the reversion to naïve hPSCs. Upon the appearance of domed-shaped and tightly-packed colonies (after 3-4 days in RSeT™ Medium), the colonies were typically ready to be passaged. The naïve hPSC culture was passaged using StemPro® Accutase® Cell Dissociation Reagent, and seeded on new iMEFs containing RSeT™ medium supplemented with Y-27632 to a final concentration of 10 µM. The naïve hPSCs were passaged on iMEFs several times in static culture.  For cell inoculation into stirred suspension bioreactors, naive (P4) and primed hESCs from static culture were inoculated into 100-mL stirred suspension bioreactors at high (50,000cells/mL) cell densities. Confluent primed hESCs from the static culture were enzymatically dissociated into single cells using StemPro® Accutase® Cell Dissociation Reagent and mechanical pipetting. The desired cell concentration was then added to 6-well static suspension culture dishes containing mTeSR™1 medium supplemented with 10 µM Y-27632. Following 1 hr of static suspension, small cell clumps were observed in the culture wells. These clumps were gently pipetted up and down several times and added to the 100-mL bioreactors containing mTeSR™1 medium supplemented with 10 µM Y-27632 and 0.1 nM Rapamycin at an agitation rate of 100 rpm. A similar procedure was used for the bioreactor inoculation of naïve hESCs, though an additional step was required for iMEF removal. Following dissociation into single cells, the naïve hESC and iMEF mixture were seeded onto gelatin coated dishes with complete RSeT™ medium for a period of 45 mins – 1 h. During this time, the iMEFs would adhere to the gelatin coated dishes while the naïve hESCs remained suspended. The naïve hESC suspension was aspirated from the dishes and centrifuged at 200 g for 5 mins. Like the primed hESC culture, naïve hESCs were counted and seeded into suspension wells supplemented with Y-27632 for a period of 1 hr before being added to the bioreactor. Bioreactor naïve hESC culture medium was RSeT™ medium supplemented with 10 µM Y-27632 and 0.1 nM Rapamycin. Naive and primed hESCs were cultured in 100-mL bioreactors for a period of 5 days.

extract_protocol:
Total RNA was extracted using PureLink™ RNA Mini Kit (Thermo Fisher Scientific, 12183018A), according to the manufacturers’ protocol, including DNAse I digestion using DNAse I Amplification Grade (Thermo Fisher Scientific, 18068015). Concentration and quality of the total extracted RNA was checked by using a spectrophotometer (BioPhotometer, Eppendorf) and an RNA 6000 nano chip (Agilent Technologies), respectively. The total RNA was depleted of ribosomal RNA using NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (NEB, E6310L) and 500 ng of the remaining RNA was purified, fragmented, and used for cDNA synthesis and library preparation.
The Illumina sequencing library preparation was done using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB, E7760L) according to manufacturer’s protocol.

value: Inner cell mass (ICM) of blastocyte, human embryo

value: embryonic stem cell

value: Human embryo

value: Female

tag: cell status

value: Primed

tag: culture condition

value: static


title: Naive_bioreactor

status: Public on Aug 31 2020

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: tissue

tag: cell type

tag: age

tag: Sex

value: Naive

value: bioreactor


title: Primed_bioreactor


title: Subject_G_CD27+IgD+_smRNA

city: San Antonio

first: Justin

last: Moroney

state: Texas

address: 7703 Floyd Curl Drive; Medical Building, Rm #5.011V

department: Microbiology, Immunology and Molecular Genetics

country: USA

institute: UT Health San Antonio

description: smRNA_ CD27-IgD+_CD27+IgD+_CD27+IgG+_CD27+IgA+_Transcript_ReadCount.txt

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Hisat2-2.1.0
Abundance measurements were otained using HTSeq-0.11.2
Peak calling was performed using HOMER-4.10
Genome_build: UCSC hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene or miRNA

source_name: Human PBMCs

growth_protocol: Human IgD+ naïve B cells were purified by negative selection from healthy donor PBMCs using the EasySep Human Naïve B Cell Enrichment Kit (19254, STEMCELL Technologies).  Naïve B cells were then cultured in FCS-RPMI and stimulated with trimeric CD154 (10 U ml-1), IL-4 (20 ng ml-1, R&D Systems) and IL-21 (50 ng ml-1, R&D Systems) or CD154 (10 U ml-1), IL-21 (50 ng ml-1) and TGF-β (0.5 ng ml-1) in the presence of nil, butyrate ((1000 M)) for 60 hours.

extract_protocol:
Total RNA was extracted using Direct-zol RNA Miniprep Plus kit (Zymo Research) following manufacturer's instructions.
Libraries were prepared for sequencing using standard Illumina TruSeq protocol

value: CD27+IgD+ B cell


title: Subject_C_CD27+IgA+_smRNA

value: CD27+IgA+ B cell


title: Subject_G_CD27+IgA+_smRNA


title: Subject_G_CD27-IgD+_smRNA

value: CD27-IgD+ B cell


title: Subject_C_CD27+IgG+_smRNA

value: CD27+IgG+ B cell


title: Naive_static


title: Subject_C_CD27-IgD+_smRNA


title: Subject_C_CD27+IgD+_smRNA


title: Subject_B_CD27+IgA+_smRNA


title: Subject_B_CD27+IgG+_smRNA


title: Subject_B_CD27-IgD+_smRNA


title: Subject_G_CD27+IgA+_mRNA_lncRNA

description:
mRNA_ CD27-IgD+_CD27+IgD+_CD27+IgG+_CD27+IgA+_Gene_ReadCount.txt
lncRNA_ CD27-IgD+_CD27+IgD+_CD27+IgG+_CD27+IgA+_Transcript_ReadCount.txt


title: MDA-MB-453 Abemaciclib 7 days (replicate 1)

city: Melbourne

first: Shom

last: Goel

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

molecule: genomic DNA

source_name: Breast carcinoma cell line

growth_protocol: Cells were cultured in sterile dishes in media as described. Cells were plated at densities such that final density at time of ATAC-seq was between 60-70%.

extract_protocol:
Nuclei were isolated following Omni-ATAC-seq protocol (Corces  et al , Nat. Methods, 2017) and ATAC-seq was performed as previously described (Buenrostro  et al.,Curr Protoc Mol Biol ,2015). 50,000 cells / sample were resuspended in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at max speed for 5 min in a pre-chilled (4 C) fixed-angle centrifuge. After centrifugation supernatant was carefully aspirated.  Cell pellets were then resuspended in 50 μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 5 min at max speed in a pre-chilled (4 C) fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50 μl of transposition mix (Corces et al., 2017): 2.5 μl transposase (100 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) by pipetting up and down six times. Transposition reactions were incubated at 37 C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Qiagen columns.
ATAC-seq libraries were amplified as described previously (Buenrostro et al., 2015).

treatment_protocol: Abemaciclib concentration 500 nM or equal volume of DMSO (control) for the indicated times for all cell lines.

value: MDA-MB-453 breast carcinoma cell line

tag: treatment

value: abemaciclib

tag: treatment length

value: 7 days


title: Subject_G_CD27+IgG+_mRNA_lncRNA


title: Subject_G_CD27+IgD+_mRNA_lncRNA


title: Subject_G_CD27-IgD+_mRNA_lncRNA


title: Subject_G_CD27+IgG+_smRNA


title: Subject_B_CD27-IgD+_mRNA_lncRNA


title: Subject_B_CD27+IgA+_mRNA_lncRNA


title: Subject_B_CD27+IgD+_mRNA_lncRNA


title: Subject_C_CD27+IgG+_mRNA_lncRNA


title: Subject_C_CD27+IgA+_mRNA_lncRNA


title: Subject_C_CD27-IgD+_mRNA_lncRNA


title: TSS library annotation run

city: Minneapolis

first: Frank

middle: Wolfgang

last: Albert

state: MN

address: 6-160 Jackson Hall, 321 Church St SE

department: Department of Genetics, Cell Biology, & Development

institute: University of Minnesota

description: DNA amplicon sequencing

data_processing:
library strategy: amplicon sequencing of barcoded library
Paired reads were merged using PEAR (Zhang et al., 2014) using parameters -v 75 -m 250 -j 8 -y 2G -c 40 -b 64
Merged reads were filtered for the presence of sequences expected to separate oligo and barcode based on our cloning strategy
We counted the number of times each barcode/oligo pair was observed
Genome_build: Custom oligo design, based on yeast genome version sacCer3
Supplementary_files_format_and_content: The processed annotation files are tab separated txt files. They list for each barcode (one row per barcode): the barcode sequence, the number of times the barcode was observed in the annotation run, the number of unique oligo sequences the barcode tagged, the distribution of counts of oligos associated with the barcode, the sequence of the oligo most frequently tagged by the barcode, and the fraction of barcode observations in which the barcode tagged the most frequent oligo.

organism: Escherichia coli

source_name: Synthetic DNA oligo library with barcodes

growth_protocol: Transformed E. coli were grown overnight at 30˚C in LB + carbenicillin medium.

extract_protocol:
Plasmids were isolated using Qiagen Plasmid Plus Purification kits (Qiagen #12963 & #12965)
Sequencing libraries were constructed by PCR targeted at the oligo/barcode pairs.

value: TSS library annotation

tag: strain

value: E. cloni 10G SUPREME Electrocompetent Cells

tag: molecule subtype

value: plasmid DNA


title: UpStream library annotation run

description: DNA amplicon sequencing

value: Upstream library annotation


title: Subject_B_CD27+IgD+_smRNA


title: Opto-KSR-2

city: Baltimore

first: Gabsang

last: Lee

state: MD

address: 733 North Broadway, Suite 747

department: Department of Neurology and Neuroscience

institute: Institute for Cell Engineering, Johns Hopkins University

data_processing:
After sequencing run the Illumina Real Time Analysis (RTA) module was used to perform image analysis, base calling, and the BCL Converter (bcl2fastq v2.17.1.14) were followed to generate FASTQ files which contain the sequence reads.
Read-level Q/C was performed by FastQC (v0.11.5). Pair-end reads of cDNA sequences are aligned back to the human genome (UCSC hg19 from Illumina iGenome) by the spliced read mapper TopHat (v2.0.9) with default option with “--mate-innder-dist 160” and “--library-type fr-firststrand” parameters based on known transcripts of Ensembl Build GRCh37.75.
To achieve gene-level expression profile, the properly paired and mapped reads are achieved by “samtools sort –n” option, and these reads are counted by htseq-count v0.9.1 (with intersection-strict mode and stranded option) according to gene annotation (Ensembl Build GRCh37.75) and RPKM is calculated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: human embryonic stem cell

growth_protocol: hESCs (H9, WiCell) and hiPSCs were cultured using standard protocols. The hESC lines and hiPSC lines were cultured with mouse embryonic fibroblasts (MEFs) (AppliedStemCell) pre-plated at 12,000–15,000 cells/cm2. Medium contained DMEM/F12, 20% knockout serum replacement, 1 mM L-glutamine, 100 μM MEM non-essential amino acids, and 0.1 mM β-mercaptoethanol. 10 ng/mL of FGF-2 was added after sterile filtration, and cells were fed daily, and passaged weekly, using 6 U/mL dispase or mechanically.

extract_protocol:
Trizol Method
RNAseq libraries were constructed using Illumina TruSeq Stranded Total RNA RiboZero Gold sample Prep Kit (RS-122-2303) following the manufacturer’s protocol. The concentration of RNA was measured by Qubit (Life Technologies). Quality of RNAseq library was measured by LabChipGX (Caliper) using HT DNA 1K/12K/HiSens Labchip. The final cDNA libraries were sequenced using HiSeq 3000 for high-throughput DNA sequencing.

tag: growth condition

value: media for ESC without FGF protein

tag: media

value: human ES media contained DMEM/F12, 20% knockout serum replacement, 1 mM L-glutamine, 100   M MEM non-essential amino acids, and 0.1 mM   -mercaptoethanol


title: Opto-KSR-1


title: Opto-KSR-3


title: Opto-hES-2

value: media for human ESC culture

value: human ES media contained DMEM/F12, 20% knockout serum replacement, 1 mM L-glutamine, 100   M MEM non-essential amino acids, and 0.1 mM   -mercaptoethanol + 10 ng/mL of FGF2


title: Opto-hES-3


title: Opto-hES-1


title: Opto-5min-3

value: culture condition with blue light


title: Opto-5min-2


title: Opto-1min-2


title: Opto-1min-3


title: Opto-5min-1


title: Opto-10min-3


title: Opto-1min-1


title: Opto-10min-2


title: Subject_C_CD27+IgD+_mRNA_lncRNA


title: GRO-seq, siRAD21_EtOH (repeat3) MCF7

city: Houston

first: Jiaofang

last: Shao

address: 6431 Fannin St

department: Department of Biochemistry and Molecular Biology

institute: McGovern Medical School, University of Texas Health Science Center

description: GRO-seq, siRAD21_EtOH (repeat3) MCF7

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to h19 whole genome using bowtie2 v2.2.6
The aligned reads were filtered to remove reads with MAPQ<10 by samtools, and converted to bam files. The bam files were then processed by HOMER v4.8.2 to generate bedgraph file.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files

source_name: MCF7 breast cancer cell

growth_protocol: We originally purchased MCF-7 from ATCC, which were maintained in DMEM (Gibco® #10566) media supplemented with 10% FBS (Omega Scientific, CA) in a 5% CO2 humidified incubator at 37°C (MCF-7 without stripping).

extract_protocol: Methods: The transfected MCF7 cells were subjected to GRO-seq experiments. GRO-Seq experiments were performed as previously reported (Li et al., 2013, Nature). Briefly, ~10-20 millions of MCF-7 cells were washed 3 times with cold PBS and then sequentially swelled in swelling buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2) for 5 min on ice, harvested, and lysed in lysis buffer (swelling buffer plus 0.5% NP-40 and 10% glycerol). The resultant nuclei were washed one more time with 10mL lysis buffer and finally re-suspended in 100uL of freezing buffer (50mM Tris-Cl pH8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA). For the run-on assay, re-suspended nuclei were mixed with an equal volume of reaction buffer (10mM Tris-Cl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of SUPERase-IN, 1% sarkosyl, 500uM ATP, GTP, and Br-UTP, 2uM CTP) and incubated for 5 min at 30°C . The resultant nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol LS reagent (Life Technologies) following manufacturer’s instructions. NRO-RNA was fragmented to ~300-500nt by alkaline base hydrolysis on ice and followed by treatment with DNase I and Antarctic phosphatase. These fragmented Br-UTP labeled nascent RNA was then immunoprecipitated with an anti-BrdU argarose beads (Sc32323ac, Santa Cruz Biotechnology) in binding buffer (0.5XSSPE, 1mM EDTA, 0.05% tween) for 3 hrs at 4°C with rotation. Subsequently, T4 PNK was used to repair the end of the immunoprecipitated BrU-NRO-RNA, at 37°C for 1hr. The RNA was extracted and precipitated using acidic phenol-chloroform.    cDNA synthesis was performed as per a published method (54) with few modifications. The RNA fragments were subjected to poly-A tailing reaction by poly-A polymerase (NEB) for 30 min at 37°C. Subsequently, reverse transcription was performed using oNTI223 primer and superscript III RT kit (Life Technologies). The cDNA products were separated on a 10% polyacrylamide TBE-urea gel and only those migrated between ~100-500bp were excised and recovered by gel extraction. After that, the first-strand cDNA was circularized by CircLigase (Epicentre) and re-linearized by APE1 (NEB). Re-linearized single strand cDNA (sscDNA) was separated by a 10% polyacrylamide TBE gel as described above and the product of needed size was excised (~170-400bp) for gel extraction. Finally, sscDNA template was amplified by PCR (usually between 10-14 PCR cycles) using the Phusion High-Fidelity enzyme (NEB) according to the manufacturer’s instructions. The resulted library was subjected to deep sequencing.

treatment_protocol: To induce the estrogen gene transcriptional responses, MCF-7 cells at 60-80% confluency were first hormone-stripped for 3 days in phenol-free DMEM media plus 5% charcoal dextran treated FBS (Omega Scientific, CA), and they were then treated with 100nM 17β-estradiol (E2) (Sigma) for indicated time points (usually for 1 hour). Transfection of small interfering RNAs (siRNAs) into MCF-7 cells was performed using Lipofectamine 2000 (Life technologies) following manufacturer's instructions. For all experiments, two rounds of siRNA transfection (40nM each time) were performed to achieve higher efficiency. The siRNAs used in this study include: Qiagen Negative Control siRNA (Qiagen Cat# 1027310) and/or Sigma Mission siRNA universal control #2 (SIC002); siRAD21 (Sigma SASI_Hs02_00341219 and SASI_Hs01_00195799).

value: MCF7 breast cancer cell

tag: genotype

value: brU sc-32323 AC, Santa Cruz


title: GRO-seq, siCTL_E2 (repeat3) MCF7

description: GRO-seq, siCTL_E2 (repeat3) MCF7


title: siControl virus R4

city: Helsinki

first: Clara

last: Benoit-Pilven

address: Tukholmankatu 8

country: Finland

institute: Helsinki University

data_processing:
After quality control with FastQC, reads were mapped to the human genome (hg38, Gencode v27) and to the A/WSN/33 virus genome (Accession Numbers CY034132 to CY034139) using STAR. The reads mapping to the human genome were isolated from the ones mapping the viral genome for further analysis.
Gene expression and termination readthrough analyses were carried out using HTSeq-count and DESeq2.
Alternative splicing analysis was performed using KisSplice pipeline (Benoit-Pilven et al., Sci Rep, 2018).
Genome_build: hg38 + A/WSN/33 virus
Supplementary_files_format_and_content: Bam file with reads mapping to the human and the viral genome for each sample generated with STAR.
Supplementary_files_format_and_content: Matrix with raw gene counts (from HTSeq-count) for each samples.

molecule: polyA RNA

source_name: A549 cell line

growth_protocol: A549 were grown in complete Dulbecco's modified Eagle's medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin.

extract_protocol:
At 6 hpi, total RNA was extracted and treated with DNase using the RNeasy mini kit (QIAGEN)
Libraries were prepared using TruSeq Stranded Illumina kit.

treatment_protocol: A549 cells plated in 12-well plates (2 x 105 cells per well) were transfected with 25 nM of siRNA (Non-targeting control or anti-RED siRNA, Dharmacon) using the Dharmafect-1 reagent, according to the manufacturer's recommendations. At 48 hours post-transfection, siRNA-treated cells and untreated cells were subjected to infection with the A/WSN/33 virus at a MOI of 5 PFU/cell, or mock-infected.

value: A549 cell line

tag: infection

value: A/WSN/33 virus

tag: transfection

value: tranfected with siControl


title: siRED mock R2

value: mock

value: transfected with siRED


title: siRED virus R2


title: siRED mock R3


title: siControl virus R5


title: siRED virus R4


title: siRED virus R3


title: siControl virus R3


title: siControl mock R5


title: siControl mock R3


title: siControl virus R2


title: siControl mock R4


title: Untreated virus R4

value: not transfected


title: Untreated virus R3


title: GRO-seq, siRAD21_E2 (repeat3) MCF7

description: GRO-seq, siRAD21_E2 (repeat3) MCF7


title: Opto-10min-1


title: Untreated mock R5


title: Untreated virus R2


title: Untreated mock R4


title: Untreated mock R3


title: siRED virus R5


title: Untreated mock R2


title: GRO-seq, siCTL_EtOH (repeat3) MCF7

description: GRO-seq, siCTL_EtOH (repeat3) MCF7


title: siRED mock R5


title: siRED mock R4


title: Subject_B_CD27+IgG+_mRNA_lncRNA

value: CD27+IgG+ B cell


title: Untreated virus R5


title: siControl mock R2


title: ChIP-seq of  H3K4me1_siRAD21_E2_MCF7

extract_protocol:
Cells were cross-linked with 1% formaldehyde at room temperature for 10 min. Or for some cases, cells were double cross-linked with 1mM DSG (ProteoChem) for 1 hr first and then for 10minutes by 1% formaldehyde. In both situations, the crosslinking was quenched by addition of 0.125M glycine for 10 minutes. ChIP chromatin was fragmented using (Diagenode) Bioruptor®300 (20-40 cycles, 30sec on, 30sec off, 4°C). Subsequently, the soluble chromatin was harvested by 16,100g centrifugation, pre-cleared with 10-20ul Dynabeads G (Life Technologies), and was then incubated with 1-5 μg of antibodies at 4°C overnight. The next morning, immuno-precipitated complexes were collected using 30ul Dynabeads protein G (Invitrogen) per reaction. The immune-complexes were subjected to washes with wash buffer I for once, with wash buffer II for twice, and with Tris-EDTA (TE) + 0.1% triton x-100 for once, with TE for once, the beads were incubated at 55°C for 2hrs with proteinase K and de-crosslinked at 65°C for overnight. The final ChIP DNA was extracted and purified using QIAquick spin columns (Qiagen).
The library was processed that the extracted DNA was ligated to specific adaptors for Illumina’s HiSeq system using KAPA Hyper Prep Kit (Kapa Biosystems)

treatment_protocol: To induce the estrogen gene transcriptional responses, MCF-7 cells at 60-80% confluency were first hormone-stripped for 3 days in phenol-free DMEM media plus 5% charcoal dextran treated FBS (Omega Scientific, CA), and they were then treated with 100nM 17β-estradiol (E2) (Sigma) for indicated time points (usually for 1 hour).

tag: passages

tag: chip antibody

value: H3K4me1 (abcam, ab8895)


title: genomic DNA from muscle 41

type: genomic

city: Moscow

first: Rinat

middle: I

last: Sultanov

address: Malaya Pirogovskaya, 1a

country: Russia

institute: FRCC of Physical Chemical Medicine of the FMBA of the Russian Federation

description: skeletal muscle

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan

data_processing: RnBeads

label: Cy5 and Cy3

source_name: skeletal muscle 41

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from skeletal muscle samples

tag: gender

value: Male

value: skeletal muscle

tag: disease state

value: normal

tag: type ii fiber type composition

tag: type i fiber type composition


title: genomic DNA from muscle 47

description: skeletal muscle

source_name: skeletal muscle 47

tag: tissue


title: genomic DNA from muscle 24

description: skeletal muscle

source_name: skeletal muscle 24


title: genomic DNA from muscle 23

description: skeletal muscle

source_name: skeletal muscle 23


title: genomic DNA from muscle 34

description: skeletal muscle

source_name: skeletal muscle 34


title: genomic DNA from muscle 25

description: skeletal muscle

source_name: skeletal muscle 25


title: genomic DNA from muscle 40

description: skeletal muscle

source_name: skeletal muscle 40


title: genomic DNA from muscle 31

description: skeletal muscle

source_name: skeletal muscle 31


title: genomic DNA from muscle 21

description: skeletal muscle

source_name: skeletal muscle 21


title: genomic DNA from muscle 46

description: skeletal muscle

source_name: skeletal muscle 46


title: genomic DNA from muscle 22

description: skeletal muscle

source_name: skeletal muscle 22


title: genomic DNA from muscle 33

description: skeletal muscle

source_name: skeletal muscle 33


title: genomic DNA from muscle 38

description: skeletal muscle

source_name: skeletal muscle 38


title: genomic DNA from muscle 45

description: skeletal muscle

source_name: skeletal muscle 45


title: genomic DNA from muscle 28

description: skeletal muscle

source_name: skeletal muscle 28


title: genomic DNA from muscle 27

description: skeletal muscle

source_name: skeletal muscle 27


title: genomic DNA from muscle 19

description: skeletal muscle

source_name: skeletal muscle 19


title: genomic DNA from muscle 18

description: skeletal muscle

source_name: skeletal muscle 18


title: genomic DNA from muscle 37

description: skeletal muscle

source_name: skeletal muscle 37


title: genomic DNA from muscle 29

description: skeletal muscle

source_name: skeletal muscle 29


title: genomic DNA from muscle 42

description: skeletal muscle

source_name: skeletal muscle 42


title: genomic DNA from muscle 36

description: skeletal muscle

source_name: skeletal muscle 36


title: genomic DNA from muscle 44

description: skeletal muscle

source_name: skeletal muscle 44


title: genomic DNA from muscle 30

description: skeletal muscle

source_name: skeletal muscle 30


title: genomic DNA from muscle 26

description: skeletal muscle

source_name: skeletal muscle 26


title: genomic DNA from muscle 32

description: skeletal muscle

source_name: skeletal muscle 32


title: genomic DNA from muscle 43

description: skeletal muscle

source_name: skeletal muscle 43


title: Treg__media_B

type: RNA

city: Gainesville

first: Todd

middle: M

last: Brusko

state: FL

address: 1275 Center Dr BMSB J515

department: Pathology

institute: University of Florida

hyb_protocol: 100ng of total RNA was incubated overnight with the capture and reporter probes from Nanostring GX Human Immunology V1 panel

scan_protocol: Hybridized probes were purified on the nCounter Prep Station and counted on the digital analyzer (Nanostring) following the manufacturers instructions. For each assay, a max density scan was performed.

data_processing: In Partek Genomic Suite (Partek Inc.) counts were normalized to the 10 internal housekeeping genes and the average of the background counts (noise) was subtracted with values lower than background set to one.

label: biotin

source_name: Expanded Treg

growth_protocol: FACS isolated cells were plated at 2.5 × 10e5 Tregs per well in a 24-well plate (Costar, Cambridge, MA) and activated with anti-CD3/anti-CD28–coated microbeads (Invitrogen, Carlsbad, CA) at a 1:1 bead-to-cell ratio. CD4+CD127lo/− cells received rapamycin (100 ng/ml; Wyeth, Madison, NJ) through day 7 of culture (assuming consumption). At day 2, the culture volume was doubled and IL-2 was added (300 units/ml, Proleukin; Chiron Therapeutics, Emeryville, CA). Cells were resuspended and fresh media and IL-2 were added at days 2, 5, 7, 9, and 12 assuming consumption. On day 9, cells were restimulated with fresh anti-CD3/anti-CD28–coated beads at a 1:1 ratio.

extract_protocol: Treg were sorted using a BD FACSAria III into RNALater (Life technologies). RNA was extracted with RNEasy FFPE Kit (Qiagen) with Proteinase K digestion followed by incubation at 80°.

treatment_protocol: IL-12 (1ng/mL) and IL-18 (10 ng/mL) vs Media and IL-2 alone

tag: cell type

value: Expanded Treg

value: control


title: Treg__media_C

tag: treatment


title: Treg__IL12&18_C

source_name: Expanded Treg with IL-12 & IL-18


title: Treg__IL12&18_A


title: genomic DNA from muscle 20

description: skeletal muscle

source_name: skeletal muscle 20


title: genomic DNA from muscle 39

description: skeletal muscle

source_name: skeletal muscle 39


title: Treg__media_A


title: Treg__IL12&18_B


title: leaf_eTK_t=96hr_rep3

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

description: HsfA1a,b,d triple mutant

hyb_protocol: The labeled ss-cDNA samples were hybridized to Arabidopsis Gene 1.1 ST arrays (Affymetrix). The GeneTitan Hybridization Wash, and Stain for Wt Arrays (Affymetrix) was used for the hybridizations according to the protocol of the manufacturer.

scan_protocol: The Arabidopsis Gene 1.1 ST arrays were scanned using the Affymetrix GeneTitan scanner.

data_processing: The data were analyzed with the R statistical programming language (http://cran.r-project.org/) and the bioconductor oligo package. The raw data were normalized using the robust multi-array average (RMA) algorithm (Irizarry et al., 2003; Biostatistics 4: 249-264).

organism: Arabidopsis thaliana

source_name: Leaf material, t=96 hrs

label_protocol: 100 ng total RNA was amplified using the GeneChip WT PLUS Reagent Kit (Affymetrix) generating biotinylated sense-strand DNA targets.

growth_protocol: Plants were grown for 2 weeks at 22C in short day conditions (11 hrs light, 13 hrs dark) on soil-perculite mixture.

extract_protocol: RNA was extracted from ground leaf material using Trizol Reagent (Sigma), which was followed by the RNAeasy mini kit (Qiagen).

treatment_protocol: Plants were shifted to the ambient temperature 28C and RNA was extracted at noon, (t=0), 24 hrs post the shift and 96 hrs post the shift.

tag: genotype/variation

value: eTK


title: leaf_eTK_t=96hr_rep2

description: HsfA1a,b,d triple mutant


title: leaf_eTK_t=24hr_rep3

description: HsfA1a,b,d triple mutant

source_name: Leaf material, t=24 hrs


title: leaf_pad4-1_sumo1-1_amiR-SUM2_t=96hr_rep3 [re-analysis of GSM2574124]

value: pad4-1 sumo1-1 amiR-SUM2


title: leaf_eTK_t=0hr_rep1

description: HsfA1a,b,d triple mutant

source_name: Leaf material, t=0


title: leaf_pad4-1_sumo1-1_amiR-SUM2_t=96hr_rep1 [re-analysis of GSM2574122]


title: leaf_eTK_t=24hr_rep2

description: HsfA1a,b,d triple mutant


title: leaf_eTK_t=24hr_rep1

description: HsfA1a,b,d triple mutant


title: leaf_eTK_t=0hr_rep3

description: HsfA1a,b,d triple mutant


title: leaf_eTK_t=96hr_rep1

description: HsfA1a,b,d triple mutant


title: leaf_eTK_t=0hr_rep2

description: HsfA1a,b,d triple mutant


title: leaf_pad4-1_sumo1-1_amiR-SUM2_t=24hr_rep3 [re-analysis of GSM2574121]


title: leaf_pad4-1_sumo1-1_amiR-SUM2_t=24hr_rep2 [re-analysis of GSM2574120]


title: genomic DNA from muscle 17

description: skeletal muscle

source_name: skeletal muscle 17


title: genomic DNA from muscle 15

description: skeletal muscle

source_name: skeletal muscle 15


title: leaf_pad4-1_sumo1-1_amiR-SUM2_t=0hr_rep2 [re-analysis of GSM2574117]


title: leaf_pad4-1_siz1-2_t=96hr_rep1 [re-analysis of GSM2574113]

value: pad4-1 siz1-2


title: leaf_pad4-1_sumo1-1_amiR-SUM2_t=96hr_rep2 [re-analysis of GSM2574123]


title: genomic DNA from muscle 16

description: skeletal muscle

source_name: skeletal muscle 16


title: leaf_pad4-1_siz1-2_t=96hr_rep2 [re-analysis of GSM2574114]


title: genomic DNA from muscle 35

description: skeletal muscle

source_name: skeletal muscle 35


title: genomic DNA from muscle 9

description: skeletal muscle

source_name: skeletal muscle 9


title: leaf_pad4-1_siz1-2_t=0hr_rep3 [re-analysis of GSM2574109]


title: genomic DNA from muscle 3

description: skeletal muscle

source_name: skeletal muscle 3


title: genomic DNA from muscle 2

description: skeletal muscle

source_name: skeletal muscle 2


title: genomic DNA from muscle 10

description: skeletal muscle

source_name: skeletal muscle 10


title: genomic DNA from muscle 8

description: skeletal muscle

source_name: skeletal muscle 8


title: genomic DNA from muscle 7

description: skeletal muscle

source_name: skeletal muscle 7


title: genomic DNA from muscle 13

description: skeletal muscle

source_name: skeletal muscle 13


title: leaf_pad4-1_siz1-2_t=24hr_rep1 [re-analysis of GSM2574110]


title: genomic DNA from muscle 6

description: skeletal muscle

source_name: skeletal muscle 6


title: genomic DNA from muscle 14

description: skeletal muscle

source_name: skeletal muscle 14


title: Nrf2KO iodide 807

city: Lausanne

first: Dionysios

last: Chartoumpekis

address: Ave de la Sallaz 8

department: Service of Endocrinology Diabetes and Metabolism

country: Switzerland

institute: Lausanne University Hospital CHUV

data_processing:
Tuxedo software package
TopHat and Bowtie2 for mapping and aligning the sequence reads
Cufflinks takes the alignment results from Tophat to assemble the aligned sequences into transcripts
When comparing groups, Cuffdiff is used to calculate the FPKM (number of fragments per kilobase per million mapped fragments) and test for differential expression and regulation among the assembled transcripts across the submitted samples using the Cufflinks output.
Genome_build: GRCm38

organism: Mus musculus

source_name: thyroid

extract_protocol:
Modified protocol with Trizol reagent PMID: 27613051
samples were submitted to Exiqon (Aarchus, Denmark) for RNA quality assessment, library preparation, RNA-Seq and initial bioinformatic analysis. Standard Illumina protocols were followed. TruSeq Stranded mRNA Sample Prep Kit was used for library construction

tag: strain

value: thyroid

tag: age

value: 3-4 months old

value: Nrf2 knockout

value: 0.05% NaI in drinking water for seven days


title: Nrf2KO iodide 804


title: genomic DNA from muscle 11

description: skeletal muscle

source_name: skeletal muscle 11


title: genomic DNA from muscle 5

description: skeletal muscle

source_name: skeletal muscle 5


title: Nrf2KO iodide 803


title: Nrf2KO iodide 801


title: genomic DNA from muscle 12

description: skeletal muscle

source_name: skeletal muscle 12


title: genomic DNA from muscle 1

description: skeletal muscle

source_name: skeletal muscle 1


title: Nrf2KO iodide 806


title: Nrf2KO Control 810

value: regular drinking water


title: Nrf2KO Control 812


title: Nrf2KO Control 811


title: Nrf2KO Control 815


title: leaf_pad4-1_siz1-2_t=24hr_rep2 [re-analysis of GSM2574111]


title: leaf_pad4-1_sumo1-1_amiR-SUM2_t=24hr_rep1 [re-analysis of GSM2574119]


title: leaf_pad4-1_t=96hr_rep2 [re-analysis of GSM2574105]


title: leaf_pad4-1_t=96hr_rep3 [re-analysis of GSM2574106]


title: leaf_pad4-1_t=96hr_rep1 [re-analysis of GSM2574104]


title: leaf_pad4-1_t=0hr_rep2 [re-analysis of GSM2574099]


title: leaf_pad4-1_siz1-2_t=96hr_rep3 [re-analysis of GSM2574115]


title: leaf_pad4-1_t=0hr_rep3 [re-analysis of GSM2574100]


title: leaf_pad4-1_siz1-2_t=24hr_rep3 [re-analysis of GSM2574112]


title: leaf_pad4-1_t=0hr_rep1 [re-analysis of GSM2574098]


title: WT iodide 825

value: Wild-type


title: leaf_pad4-1_t=24hr_rep3 [re-analysis of GSM2574103]


title: leaf_pad4-1_t=24hr_rep1 [re-analysis of GSM2574101]


title: leaf_pad4-1_sumo1-1_amiR-SUM2_t=0hr_rep3 [re-analysis of GSM2574118]


title: genomic DNA from muscle 4

description: skeletal muscle

source_name: skeletal muscle 4


title: WT iodide 831


title: WT control 834


title: WT control 838


title: WT iodide 827


title: leaf_pad4-1_siz1-2_t=0hr_rep2 [re-analysis of GSM2574108]


title: leaf_pad4-1_sumo1-1_amiR-SUM2_t=0hr_rep1 [re-analysis of GSM2574116]


title: WT iodide 829


title: 11-1-ctrl-Q_S1

city: Los Angeles

first: Quan

last: Wen

state: Ca

address: 2250 Alcazar St. CSA 123

institute: University of Southern California

data_processing:
raw reads were aligned using Bowtie2 with the mm10 genome
MACS2 was used for detecting genomic enrichment regions
Runx2 binding motifs were analyzed using HOMER
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of number of motif counts

source_name: lower 1st molar

extract_protocol:
The apical halves of lower first molars was collected for ATAC-seq
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage


title: WT control 836


title: FLAG-RBM7_rep2

city: Suita

first: Daisuke

last: Motooka

address: Yamadaoka

country: Japan

institute: Osaka University

description: immunoprecipitated RNA

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 100-base paired-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (hg38) using TopHat v2.1.1 in combination with Bowtie2 ver. 2.2.9.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: hg38

source_name: HEK293 cells

extract_protocol:
RNA eluted from RIP samples (n = 2 biological replicates) and total RNA from WT and Rbm7−/− HEK293 cells treated with or without 50 µM etoposide (Tokyokasei) (4 µg/sample) were depleted of ribosomal RNA using a Ribo-Zero Gold rRNA removal kit (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

tag: antibody

value: FLAG


title: RBM7-KO_etoposide-treated

tag: genotype


title: FLAG-empty_rep1

description: immunoprecipitated RNA


title: FLAG-RBM7_rep1

description: immunoprecipitated RNA


title: FLAG-empty_rep2

description: immunoprecipitated RNA


title: RBM7-KO


title: kidney_w5.3

city: London

first: JONATHAN

last: CARON

state: Greater London

address: New Hunt's House, Newcomen St

department: Cancer Studies

country: United Kingdom

institute: KING'S COLLEGE LONDON

hyb_protocol: Finally, the samples were denatured at 99°C and hybridized on the chip (Affymetrix, Santa Clara, California, USA) for 17 h at 45°C.

scan_protocol: At the end of the hybridization, the chips were washed and placed in a high resolution scanner in order to obtain the expression values corresponding to each probe.

data_processing: The fluorescence values  obtained for each of the probes were normalized using the RMA algorithm (Robust Microarray Analysis)

organism: Rattus norvegicus

source_name: Kidney, W5

label_protocol: The RNAs of interest were diluted to a concentration of 100 ng/μL before starting the synthesis of the first strands of cDNA. The cDNAs were synthesized using a NuGEN kit (San Carlos, California, USA), the 2nd cDNA strands from the previous ones; the double-stranded cDNA thus obtained was purified by magnetic method. Linear amplification (SPIA technology) of these double-stranded DNAs was then performed to obtain a sufficient amount of hybridization material on the chips while maintaining the respective proportions of each RNA of the original sample. After purification, the amplified cDNAs were enzymatically fragmented and associated with a fluorescent label.

growth_protocol: All animals were kept in an air-conditioned room with food and tap water ad libitum. All these studies were authorized by an Ethics Committee (#12215). All animal procedures were in accordance with the European Union Guidelines for the Care and Use of Laboratory Animals.

extract_protocol: One quarter of each animal's kidney was thawed and ground, and the RNA was extracted using Trizol (Invitrogen, Camarillo, California, USA). The quantity, purity and quality of the RNAs was verified using Nanodrop (Thermo Fisher Scientific, Waltham, Mass., USA) and a Bioanalyzer (Agilent Technologies, Santa Clara, California, USA).

treatment_protocol: NO synthesis was inhibited by administrating NG-nitro-L-arginine methyl ester (L-NAME, 15 mg/kg per day) to male Sprague–Dawley rats (250 g, Harlan) as previously described (2). L-NAME is a competitive inhibitor of NO synthases (NOS), and therefore induces high blood pressure, loss of peritubular microvessels, hypoxia, and renal fibrosis (3). We added NaCl (6 g/L) in the drinking water to accelerate the model and worsen the severity of renal injury as previously detailed (10). All procedures were in accordance with European Union Guidelines for the Care and the use of laboratory animals and were approved the local ethic committee (Comité National de Reflexion Ethique sur l’expérimentation Animale #05).

value: kidney

tag: time

value: week 5

value: Sprague Dawley

value: male


title: kidney_w5.2


title: kidney_w1.1

source_name: Kidney, W1

value: week 1


title: WT_etoposide-treated


title: kidney_ctl3

source_name: Kidney, CTL

value: control


title: kidney_w0.2

source_name: Kidney, W0

value: week 0


title: kidney_w1.3


title: WT


title: kidney_w5.1


title: leaf_pad4-1_siz1-2_t=0hr_rep1 [re-analysis of GSM2574107]


title: kidney_w0.1


title: kidney_w1.2


title: kidney_ctl2


title: kidney_ctl1


title: kidney_w0.3


title: 2115 L2 CD

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.10.1.1).

data_processing: Bioconductor package MANOR was used for loess normalisation and quality filtering of data followed by copy number calling using the R packages CGHcall and CGHregions.

source_name: liver tumor

label_protocol: 250 ng of genomic DNA were labelled with Cy3 (test) or Cy5 (reference) using the Enzo Oligo Array CGH Labelling Kit

extract_protocol: genomic DNA was extracted from FFPE sections using the Qiagen Dneasy FFPE kit

treatment_protocol: C57BL/6 mice fed with CD-HFD for 12 months alone or fed with CD-HFD for 12 months followed by 8 weeks of treatment with anti-PD-1. A subgroup of animals developed liver tumors.

value: liver tumor

source_name: pool of liver tails

value: pool of liver tails


title: 2064 L2 CD


title: 822 CD


title: WT baseline

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
The Cell Ranger Single Cell Software Suite 2.0 was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger v2.0 possorted_genome.bam BAM files and corresponding filtered gene barcodes matrices.

source_name: Interneurons

growth_protocol: PND 18 full brains were dissected and processd mechanically and enzymatically to dissociate cells and isolate neurons.

extract_protocol: Single-cell suspensions were converted to barcoded scRNA-seq libraries by using the Chromium Single Cell 3’ Library, Gel Bead & Multiplex Kit and Chip Kit (10x Genomics), aiming for an estimated 2.000 cells per library and following the manufacturer’s instructions. Samples were processed using kits pertaining to V2 barcoding chemistry of 10X Genomics. Libraries were sequenced on an Illumina NextSeq500, and mapped to the mouse genome (build mm10) using CellRanger (10X Genomics). Gene positions were annotated as per Ensembl build 84.

treatment_protocol: Neurons were processed with the aiFACS technique and sorted cells were distinguished in baseline cells (not stimulated) and AMPA-stimulated cells.

value: Neuronal cells

tag: developmental stage

value: Post Natal Day (PND) 18

value: No stimulation


title: 2094 L2 PD-1


title: Fmr1-KO AMPA

growth_protocol: PND 18 full brains were dissected and processed mechanically and enzymatically to dissociate cells and isolate neurons.

value: AMPA stimulation


title: 608 L3 PD-1


title: 1109 PD-1


title: leaf_pad4-1_t=24hr_rep2 [re-analysis of GSM2574102]


title: 2064 L1 CD


title: 612 L5 PD-1


title: 2116 L1 PD1


title: shear stress-stimulated rat collateral tissue replicate 5

city: Bad Nauheim

first: Kerstin

last: Troidl

address: Ludwigstr. 43

institute: Max-Planck-Institute for Heart and Lung Research

description:
Sample name: Psk 32 sk
Biological replicate 5 of 5. Collateral tissue Psk 32 sk (AF665) and collateral tissue Psk 27 kk (AF546)

hyb_protocol: Two differentially labelled reactions were combined into one tube and loaded onto the array

scan_protocol: Arrays were scanned using a GenePix 400B microarray scanner (Molecular Devices)

data_processing:
The annotated data were normalized using a Latin Squares algorithm by the NCode™ Profiler data analysis software
The pairwise median fold-change, P-value, tissue rank, and test statistics for the miRNAs are listed in the Analyzed Data File.  The values for each individual miRNA probe sequence printed in triplicate on the array are listed as separate rows in the analysis file. The miRNAs with p-values <0.05 for two out of the three spots on the array are considered statistically significant. A list of the statistically significant miRNAs for follow-up studies is provided on the second sheet in the Analyzed Data workbook. The replicate values for median fold-change, P-value, tissue rank, and test statistics for each of the miRNAs collapsed into one value are listed in the Collapsed Data File.
Data analysis used only the miRNA_IDs annotated in NCode Multi-Species miRNA Microarray V2.

source_name: collateral blood vessel tissue shunt (fluid shear stress-stimulated)

label_protocol: The samples were directly labeled using Ncode Rapid labeling System (#MIRLSRPD-20) and arrayed on the multi-species miRNA Microarray V2 (#MIRA2-05)

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Single femoral artery ligation and arteriovenous shunt to maximize fluid shear stress in collateral arteries. Contralateral leg was sham-operated and served as control

value: Spraque-Dawley

value: collateral blood vessel tissue shunt (fluid shear stress- stimulated)

source_name: collateral blood vessel tissue control

value: collateral blood vessel tissue control


title: shear stress-stimulated rat collateral tissue replicate 4

description:
Sample name: Psk 31 sk
Biological replicate 4 of 5. Collateral tissue Psk 31 sk (AF665) and collateral tissue Psk 32 sk (AF546)


title: genomic DNA from YCC10

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

source_name: Gastric cancer cell line

extract_protocol: genomic DNA was extracted and purified from cells

value: Gastric cancer cell line

tag: cell line


title: shear stress-stimulated rat collateral tissue replicate 3

description:
Sample name: Psk 30 sk
Biological replicate 3 of 5. Collateral tissue Psk 30 sk (AF665) and collateral tissue Psk 31 sk (AF546)


title: 2085 L1 CD


title: genomic DNA from SNU484


title: genomic DNA from SNU719


title: shear stress-stimulated rat collateral tissue replicate 2

description:
Sample name: Psk 28 sk
Biological replicate 2 of 5. Collateral tissue Psk 28 sk (AF665) and collateral tissue Psk 30 sk (AF546)


title: 2094 L3 PD-1


title: 2088 L1 CD


title: 2067 L2 CD


title: 2094 L1 PD-1


title: genomic DNA from SNU16


title: 2097 L2 PD-1


title: shear stress-stimulated rat collateral tissue replicate 1

description:
Sample name: Psk 27 sk
Biological replicate 1 of 5. Collateral tissue Psk 27 sk (AF665) and collateral tissue Psk 28 sk (AF546)


title: LOV-3

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

country: China

institute: Qingdao Agricultural University

description: The group information is prefixed with LOV-3 in the column of processed data file

data_processing:
ChIPseeqer, a computational framework for the identification of high methylated regions, identified as peaks, across the genome, was used for genome-wide detection of methylation peaks according to the following threshold: t 2 -fold_t 1 -readlen 101 -fraglen 250. ChIPseeqer modules were used to annotate methylated regions according to the reference genome CHIR_v1.0 annotation, and explore methylation distribution in genomic regions (promoters, 3′ UTR, exon, intron, intergenic and distal regions). The analysis of the distribution of methylation peaks per chromosome was performed by dividing the number of peaks by the length of each chromosome. The ratio obtained was further normalized dividing it by the total number of reads per organ. Methylation densities in different genome regions were normalized according to their representation within the genome. The CpG islands were scanned by CpG cluster a distance-based algorithm for CpG-island detection. CGIs were defined according to three criteria: length > 200 bp, ≥50% GC content, ≥ 0.6 of CpG observed/expected. Bedtools v2.25.0 intersect was used to calculate the overlap (of at least 90% length/length) between CGIs and methylation peaks.
Genome_build: ARS1
Supplementary_files_format_and_content: chrBase chr     base    strand  coverage        freqC   freqT

organism: Capra hircus

extract_protocol:
Ovarian samples were isolated for DNA. Then DNA samples were sequenced.
DNA was used for the library.DNA mehtylation-Seqencing

tag: breed

value: Ji'Ning Grey Goat

value: Ovaries

tag: group

value: low fertility


title: 1770 L1 CD


title: genomic DNA from SNU1967


title: 1770 L4 CD


title: genomic DNA from NUGC3


title: control rat collateral tissue replicate 5

description:
Sample name: Psk 32 kk
Biological replicate 5 of 5. Collateral tissue Psk 32 kk (AF665) and collateral tissue Psk 27 sk (AF546)

tag: gender

value: male


title: control rat collateral tissue replicate 4

description:
Sample name: Psk 31 kk
Biological replicate 4 of 5. Collateral tissue Psk 31 kk (AF665) and collateral tissue Psk 32 kk (AF546)


title: 612 L2 PD-1


title: LOV-2

description: The group information is prefixed with LOV-2 in the column of processed data file


title: genomic DNA from OCUM1


title: control rat collateral tissue replicate 3

description:
Sample name: Psk 30 kk
Biological replicate 3 of 5. Collateral tissue Psk 30 kk (AF665) and collateral tissue Psk 31 kk (AF546)


title: HOV-3

description: The group information is prefixed with HOV-3 in the column of processed data file

value: high fertility


title: 608 L6 PD-1


title: 608 L1 PD-1


title: HOV-2

description: The group information is prefixed with HOV-2 in the column of processed data file


title: 604 L1 PD-1


title: genomic DNA from SNU1750


title: genomic DNA from HFE145


title: genomic DNA from NCC24


title: HOV-1

description: The group information is prefixed with HOV-1 in the column of processed data file


title: genomic DNA from NCC19


title: genomic DNA from MKN1


title: Experiment 4

city: Kahoku

first: Eri

last: Kubo

state: Ishikawa

address: 1-1 Daigaku, Uchinada

department: Ophthalmology

institute: Kanazawa Medical University

description: Gene expression of pterygium tissue

hyb_protocol: Labeled cDNA was hybridized to SurePrint G3 Human 8x60K microarray kit v2 (Agilent) using the Agilent® Gene Expression Hybridization Kit according to the manufacturer's protocol.

scan_protocol: Air-dried slides were scanned with an Agilent Microarray Scanner.

data_processing:
Scanned images were analyzed with Feature Extraction Software (v. 10.7.3.1) (Agilent)
Per chip normalization was done by dividing each gene's measurement by the specific control measurements or by the average intensity in the single array. Normalized data were exported for the subsequent analysis. Genes with a normalized ratio >2.0-fold or <0.5-fold between three samples were selected as significant genes for the progression of pterygium.

source_name: Pterygium tissue

label_protocol: The Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA) was used for RNA labeling. Briefly, for each labeling, 100 ng of total RNA was reverse-transcribed in the presence of CDS primer mix and MMLV reverse transcriptase. Cyanine 3-CTP (CTP) was coupled to the first-strand cDNA.

growth_protocol: Pterygium specimens were collected from 3 pterygium patients and as controls conjunctival tissues from conjunctivochalasis were obtained from one patient

extract_protocol: Total RNA from each sample was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA) by following the manufacturer's protocol.

treatment_protocol: Excised pterygium and conjunctiva tissues were divided into apical portion including head (apical part present in cornea) and neck (limbal part) (PA) and basal portions (PB). PA  tissues were further divided laterally into two identical and symmetric pieces

value: Pterygium

tag: Sex

value: female


title: genomic DNA from IM95


title: genomic DNA from NCC59


title: Experiment 2

description: Gene expression of pterygium tissue


title: Experiment 3

description: Gene expression of pterygium tissue


title: msm pMV_MTS1338_rep2

first: Artem

last: Grigorov

address: Ulitsa Miklukho-Maklaya, 16/10

department: Genomics and Postgenomic Technologies

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

data_processing:
Sequenced reads were mapped to M.Smegmatis genome using bowtie2 v2.3.4.3 with parameters -p 4 --local --dovetail
Fragments counting was performed using FeatureCounts (Annotation of the genome was retrieved from Mycobrowser). For every annotated gene, the number of fragments overlapping the gene at least by one nucleotide was calculated. Only unambiguously mapped, non-chimeric fragments were used. The files "Counts_XXX_repX.txt" represent these counts (File "Counts_all.csv" contains values for all samples).
Search for differentially expressed genes was done with DESeq2 package (using only CDS transcripts). The results are represented in file "DifferentialExpression.csv"
Genome_build: NC_008596.1
Supplementary_files_format_and_content: Counts - the numbers of overlapping reads for every annotated gene in each sample; DifferentialExpression.csv - the results of search for differentially expressed genes using DESeq2 package.

organism: Mycolicibacterium smegmatis

source_name: in vitro infected THP-1 macrophages

growth_protocol: Mycobacterium smegmatis mc 2 155 was taken from frozen stocks (bacterial collection of Bach  Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of  Sciences, Moscow, Russia), pre-cultured for 24 h at 37°C on an orbital shaker (200 rpm) in 40  mL of the rich medium Nutrient Broth (Himedia, India) supplemented with 0.05% of Tween-80  and used as an inoculum.

extract_protocol:
Infected macrophage cells were collected, and total RNA was isolated by bacterial cell  disruption and phenol-chloroform extraction. M. smegmatis 1338 and pMV cultures (10  mL) were centrifuged at 4,000 × g for 15 min, and bacterial pellets washed twice with fresh  medium, rapidly cooled on ice, and centrifuged again. Total RNA was isolated by phenol-  chloroform extraction and cell disruption by with Bead Beater (BioSpec Products, USA) as  described (Rustad et al., 2009) and treated with Turbo DNase (Life Technologies, USA) to  remove traces of genomic DNA.
RNA samples were depleted of 16S and  23S rRNA using RiboMinus Transcriptome Isolation Kit, bacteria (Invitrogen,USA). Sequencing  libraries were generated using the resulting ribosomal transcript-depleted RNA and NEBNext  Ultra II Directional RNA Library Prep Kit (NEB, USA) according to the manufacturers’  protocol.

treatment_protocol: For macrophage infection experiments M. smegmatis-pMV (empty plasmid control) and 1338  (MTS1338 expressing) cells were inoculated in the same medium and grown up to early log  phase (OD 600 =0,6-0,8).

tag: phase

value: logarithmic

tag: vector


title: msm pMV_MTS1338_rep3


title: Experiment 1

description: Gene expression of cinjunctiva tissue

source_name: Conjunctiva tissue

tag: tissue

value: Conjunctiva


title: msm pMV_Empty rep3


title: control rat collateral tissue replicate 2

description:
Sample name: Psk 28 kk
Biological replicate 2 of 5. Collateral tissue Psk 28 kk (AF665) and collateral tissue Psk 30 kk (AF546)


title: msm pMV_Empty rep2


title: IC8-L1597H-4h-MAML1

city: Boston

first: Li

last: Pan

state: MA

address: 77 Ave Louis Pasteur

institute: Brigham and Women's Hospital

data_processing:
Reads were trimmed with Trim Galore (v.0.3.7 using cutadapt v.1.8), assessed for quality with FastQC (v.0.11.3), and aligned to GRCh38/hg38 with bowtie (v.2.0.0).
Peaks were identified using MACS2 (v.2.1.1) and annotated using Homer (v3.12, 6-8-2012).
Genome_build: hg38
Supplementary_files_format_and_content: bw files

source_name: Squamous cell carcinoma (SCC) cells

growth_protocol: Cells were grown in keratinocyte medium with 1 μM GSI (compound E).

extract_protocol:
Chromatin was prepared and immunoprecipitated with antibodies against MAML1 or RBPJ and Dynabeads bearing sheep anti-rabbit Ig (Thermo Fisher Scientific).
NEBNext Ultra II DNA Library Prep Kit (New England BioLabs)

treatment_protocol: GSI washout was performed for 4 hours.

tag: cell type

value: SCC IC8 cells

tag: chip antibody

value: clone D3K7B (Cell signaling Technology)

tag: treatment

value: GSI washout for 4h


title: msm pMV_Empty rep1

tag: strain


title: IC8-L1597H-4h-RBPJ

value: clone D10A11 (Cell Signaling Technology)


title: IC8-L1597H-0h-RBPJ

value: GSI (Compound E 1 microM)


title: msm pMV_MTS1338_rep1


title: D_ileum, Tcrbd-/-, DAOG181R/G181R

city: Tokyo

first: Masataka

last: Suzuki

address: 35, Shinanomachi, Shinjuku-ku

department: Pharmacology

institute: KEIO University, School of Medicine

description: Gene expression in intestinal epithelial tissue

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (Cy3-CTP incorporation > 6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent Fragmentation Buffer and 2x Agilent Blocking Agent according to the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x GE Hybridization Buffer HI-RPM (Agilent) was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE Microarray 8x60k Ver2.0 (G4852B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash Buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan (G4900DA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green, Green PMT is set to 100% and TIFF file dynamic range is 20bit).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: ileum, Tcrbd-/-DAOG181R/G181R

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: mice: 9 weeks of age

extract_protocol: Jejunal or ileal epithlia was mechanically scraped and homogenized in Qiazol and tota RNA was purified and treated with Dnase using Rneasy microarray Kit (Qiagen) according to manufacture's protocol. The quality of total RNA was analyzed using Agilent 2200 Tapestation (Agilent Technologies) and NanoDrop ND-2000 (ThermoFisher Scientific). RNA integlity numbers of each sample were over 9.

treatment_protocol: jejunum or ileum of Tcrbd-/-, DAOwt/wt or  Tcrbd-/-, DAOG181R/G181R mice

tag: strain background

tag: genotype/variation

value: Tcrbd-/-, DAOG181R/G181R

tag: age

value: 9 weeks

value: ileal epithelium


title: B_jejunum, Tcrbd-/-, DAOG181R/G181R

source_name: jejunum, Tcrbd-/-DAOG181R/G181R

value: jejunual epithelium


title: C_ileum, Tcrbd-/-, DAOwt/wt

source_name: ileum, Tcrbd-/-DAOwt/wt

value: Tcrbd-/-, DAOwt/wt


title: A_jejunum, Tcrbd-/-, DAOwt/wt

source_name: jejunum, Tcrbd-/-DAOwt/wt


title: WT AMPA

value: Neuronal cells

value: Post Natal Day (PND) 18

value: AMPA stimulation


title: TAM111_GrainFilling_Dry_rep1 (tamu17)

status: Public on Aug 29 2020

city: Amarillo

first: Shuyu

last: Liu

address: 6500 Amarillo Blvd West

department: Texas A&M AgriLife Research

institute: Texas A&M University System

data_processing:
Illumina BCL2fastq v1.7 was used for basecalling.
Raw reads were filtered by removing adapters and trimming low quality bases (Phred score < 20) at the end of reads using Trimmomatic v0.38 (Bolger et al. 2014). The wheat genome RefSeq v1.0 assembly and gene model annotation files were downloaded from the International Wheat Genome Sequencing Consortium (IWGSC) website (https://urgi.versailles.inra.fr/download/iwgsc/IWGSC_RefSeq_Assemblies/v1.0/) (IWGSC 2014).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
The filtered reads were then aligned to the reference genome using tool TopHat2 (Kim et al. 2013). Transcript assembles were generated using the computer package Cufflinks (Trapnell et al. 2012), and all assembled transcripts were further merged through the tool Cuffmerge using the wheat reference gene annotation as a guide. The tool Cuffdiff that was included in the Cufflinks package was then used to calculate gene expression level and normalize transcripts abundance to FPKM value (Fragment per kilobase of transcript per million reads mapped) and then make calls of differentially expressed genes (DEGs). The significance (P-values) of DEGs were adjusted using the Benjamini and Hochberg multiple test correction approach (Benjamini and Hochberg 1995) to control the false discovery rate (FDR), and only the genes with an adjusted P-value < 0.05 (FDR < 0.05) and had a fold change value greater than two (the absolute value of Log2 [expression level under dry/wet] is no less than one) were considered to have significant expression difference.
Genome_build: GCA_900519105.1

organism: Triticum aestivum

source_name: Flag Leaf

extract_protocol:
Flag leaf tissues from primary tillers of four individual plants in each replicate were collected and pooled as one sample at each stage of heading (HD) (79 days after transplanting) and grain filling (GF) (100 days after transplanting). Leaf samples were immediately put into liquid nitrogen after their harvest and then stored at -80 ˚C for processing. RNA was extracted using a Qiagen-RNeasy Mini kit according to instruction provided by the manufacturer.
For preparing sequencing libraries, the TruSeq RNA Sample Preparation kit v2 was used following the manufacturer’s instructions.

value: GrainFilling

value: Dry

tag: cultivar

value: Flag Leaf


title: TAM112_GrainFilling_Dry_rep2 (tamu24)

tag: developmental stage


title: TAM111_Heading_Wet_rep1 (tamu3)

value: Heading

value: Wet


title: TAM111_Heading_Dry_rep2 (tamu6)


title: TAM112_Heading_Dry_rep2 (tamu11)


title: TAM111_GrainFilling_Wet_rep2 (tamu15)


title: TAM112_Heading_Dry_rep1 (tamu10)


title: TAM112_Heading_Wet_rep2 (tamu8)


title: TAM111_Heading_Dry_rep1 (tamu5)


title: TAM112_Heading_Wet_rep1 (tamu7)


title: TAM112_GrainFilling_Dry_rep1 (tamu23)


title: TAM112_GrainFilling_Wet_rep2 (tamu21)


title: TAM111_GrainFilling_Wet_rep1 (tamu14)


title: TAM111_GrainFilling_Dry_rep2 (tamu18)


status: Public on Aug 28 2020

city: Cleveland

first: Zhenghe

last: Wang

state: OH

address: 2103 Cornell Rd, WRB 3204

institute: Case Western Reserve Univeristy

description: Gene expression data of HCT116 PIK3CA WT -Gln, biological replicate 2

hyb_protocol: Hybridization, washing, staining and data collection were carried out in the Affymetrix Gene Titan MC [multi channel] instrument in the Gene Expression & Genotyping Facility Core facility

data_processing: Affymetrix GeneChip Command Console software (AGCC*) was used to normalize the data and produced the values.

label: Biotin

source_name: Tissue culture cells

label_protocol: Affymetrix WT [whole transcript] labeling protocol was performed by the Gene Expression & Genotyping Facility Core facility at Case Western Reserve University

growth_protocol: Cells were grown in DMEM medium with or without glutamine in 10% dialyzed fetal bovine serum.

extract_protocol: Qiagen RNA purification kit

value: colon cancer

tag: cell line

tag: genotype

value: WT

value: without Gln


description: Gene expression data of HCT116 PIK3CA Mut -Gln, biological replicate 2

scan_protocol: Hybridization, washing, staining and data collection were carried out in the Affymetrix Gene Titan MC [multi channel] instrument

value: PIK3CA Mut


description: Gene expression data of HCT116 PIK3CA Mut -Gln, biological replicate 1


description: Gene expression data of HCT116 PIK3CA WT +Gln, biological replicate 2

value: with Gln


title: SX014F U87 DRIP-seq Setx KD rep2

status: Public on Aug 24 2020

city: Davis

first: Frederic

last: Chedin

state: CA

address: 1 Shields Avenue

department: MCB

institute: UC Davis

data_processing:
Library strategy: DRIP-seq
Raw fastq reads were trimmed with fastq-mcf v2.4.4 and mappved with bowtie2 v2.2.6 (sDRIP-seq).
DRIP-seq peaks were called using HMM (Sanz et. al, 2016). For both, HTseq-count v0.6.0 was then used to count the total number of reads of each peak.
Gencode v19 APPRIS gene annotation was used for our analysis, prioritizing highest principal isoform. Differentially expressed regions were called using one-way ANOVA.
Genome_build: hg19
Supplementary_files_format_and_content: DRIP-seq signals were generated using bedtools genomecov and converted into bigWig using wigToBigWig; DRIP-seq bed files were generated using HMM and converted into bigBed using bedToBigBed;

source_name: human primary glioblastoma cell

extract_protocol:
DRIP-seq: Genomic DNA was gently extracted using salt/ethanol percipitation,  fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI, and immunoprecipitated with S9.6 antibody.
Standard Illumina library construction protocol

value: Setx KD


description: Gene expression data of DLD1 PIK3CA WT -Gln, biological replicate 1


description: Gene expression data of DLD1 PIK3CA Mut -Gln, biological replicate 2


title: SX014E U87DRIP-seq Setx KD rep1


title: SX014D U87 DRIP-seq WT rep2


description: Gene expression data of HCT116 PIK3CA WT -Gln, biological replicate 1


title: SX014C U87 DRIP-seq WT rep1


title: LOV-1

description: The group information is prefixed with LOV-1 in the column of processed data file

tag: breed

value: Ji'Ning Grey Goat

value: Ovaries

tag: group

value: low fertility


description: Gene expression data of HCT116 PIK3CA Mut +Gln, biological replicate 2


description: Gene expression data of HCT116 PIK3CA WT +Gln, biological replicate 1


description: Gene expression data of HCT116 PIK3CA Mut +Gln, biological replicate 1


description: Gene expression data of DLD1 PIK3CA WT -Gln, biological replicate 2


title: TAM112_GrainFilling_Wet_rep1 (tamu19)


description: Gene expression data of DLD1 PIK3CA Mut -Gln, biological replicate 1


title: Female6-Brd4-rep7

status: Public on Aug 23 2020

city: St. Louis

first: Zongtai

last: Qi

state: Missouri

address: 4515 Mckinley Ave

department: Genetics

institute: Washington University in St Louis

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB-Brd4 fusion rep7
F6_Brd4_pBC.ccf

data_processing:
Library strategy: Calling-Card
Raw reads from transposon calling cards were aligned to the murine genome build mm10 using Bowtie2 (version 2.3.4.3)
Significant Calling Cards peaks or Brd4 enriched enhancer sites were identified by a modified version of the previously described algorithm, which also has similarities to the MACS2 ChIP-Seq peak caller (42). Briefly, transposon insertions were grouped into peaks using a hierarchical clustering algorithm with a maximum distance of 5 Kb between insertions. Significant peaks were identified using Poisson distribution to test for enrichment over the background (unfused transposase) Calling Card data with an adjusted p-value threshold less than 0.05. The expected number of transposon insertions per TTAA was estimated by considering the total number of insertions observed in a large region of 100 Kb distance centered at the Calling Card cluster/insertion. We computed a p-value based on the expected number of insertions and identified Brd4 enriched enhancer sites using Poisson distribution.
Genome_build: mm10
Supplementary_files_format_and_content: F6_Brd4_mBC.ccf:  Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB-Brd4 fusion rep1-5
F6_Brd4_pBC.ccf:  Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB-Brd4 fusion rep6-10
F6_WT_pBC.ccf:  Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB alone rep 1-10
M6_Brd4_mBC.ccf:  Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB-Brd4 fusion rep1-5
M6_Brd4_pBC.ccf:  Calling Card file (ccf) for insertion sites  in male astroctye tranfected with PB-Brd4 fusion rep6-10
M6_WT_mBC.ccf:  Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB alone rep1-5
M6_WT_pBC.ccf:  Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB alone rep6-10
fpeak_h20_gene.txt:  Genes close to Calling Card Brd4 enriched peak sites in female astrocyte
fpeak_p005_h20.txt:  Calling Card Brd4 enriched peak sites in female astrocyte
mfpeak_share.txt:  Calling Card Brd4 enriched peak sites in male and female astrocyte
mpeak_h20.gene.txt:  Genes close to Calling Card Brd4 enriched peak sites in male astrocyte
mpeak_p005_h20.txt:  Calling Card Brd4 enriched peak sites in male astrocyte

source_name: Astrocytes

growth_protocol: Cells were grown in DMEM/F12 media supplemented with 10% FBS and 1% penicillin-streptomycin. These astrocytes serve as a model of GBM and we refer to them as male and female GBM astrocytes.

extract_protocol:
The puromycin resistant cells were harvested and processed by transposon calling card protocol as described 'Self-Reporting Transposons Enable Simultaneous Readout of Gene Expression and Transcription Factor Binding in Single Cells'.
The Calling Card library was prepared by assigning each well a unique Illumina P7 index, so that each well of a sample could be demultiplexed as a set of unique barcoded insertions. All 4 sets of libraries, Male6-WT (Male_PB_helper), Male6-Brd4 (Male_PB_Brd4_fusion), Female6-WT (Female_PB_helper), and Female6-Brd4 (Female_PB_Brd4_fusion), were then pooled and sequenced on an Illumina HiSeq 300.

treatment_protocol: Briefly, each well received 3 µg of plasmid DNA containing a piggyBac transposon (carrying a puromycin selection marker) with or without 3 µg of a transposase plasmid encoding Brd4 fused to the N-terminus of hyperactive piggyBac (HyPBase). Plasmids were delivered using Lipofectamine LTX/Plus Reagent (Invitrogen). Before transfection, cells were incubated in DMEM without FBS or antibiotics for 30 minutes, and then replaced with fresh media containing DMEM/F12 with 10% FBS and 1% penicillin-streptomycin. Transfection complexes were applied to cells for 12-18 hours at 37 °C and 5% CO2. Cells were allowed to recover in fresh medium for another 24-48 hours. Each well was then separately expanded onto 10 cm dishes and placed in medium containing puromycin at a concentration of 2.5 µg/ml for 3 days. After 3 days, cells that received transposon DNA alone showed no growth, while those that also received transposase DNA showed robust growth.

value: Female GBM astrocytes

value: null for Nf1 and p53

tag: transfection experiment


description: Gene expression data of DLD1 PIK3CA WT +Gln, biological replicate 2


title: Female6-Brd4-rep6

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB-Brd4 fusion rep6
F6_Brd4_pBC.ccf


title: Female6-Brd4-rep9

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB-Brd4 fusion rep9
F6_Brd4_pBC.ccf


title: Female6-Brd4-rep8

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB-Brd4 fusion rep8
F6_Brd4_pBC.ccf


description: Gene expression data of DLD1 PIK3CA WT +Gln, biological replicate 1


title: Female6-Brd4-rep5

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB-Brd4 fusion rep5
F6_Brd4_mBC.ccf


description: Gene expression data of DLD1 PIK3CA Mut +Gln, biological replicate 2


title: Female6-Brd4-rep4

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB-Brd4 fusion rep4
F6_Brd4_mBC.ccf


description: Gene expression data of DLD1 PIK3CA Mut +Gln, biological replicate 1


title: Female6-Brd4-rep10

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB-Brd4 fusion rep10
F6_Brd4_pBC.ccf


title: Female6-Brd4-rep3

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB-Brd4 fusion rep3
F6_Brd4_mBC.ccf


title: Female6-Brd4-rep1

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB-Brd4 fusion rep1
F6_Brd4_mBC.ccf


title: Male6-Brd4-rep9

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB-Brd4 fusion rep9
M6_Brd4_pBC.ccf

value: Male GBM astrocytes


title: Female6-Brd4-rep2

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB-Brd4 fusion rep2
F6_Brd4_mBC.ccf


title: Male6-Brd4-rep10

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB-Brd4 fusion rep10
M6_Brd4_pBC.ccf


title: Male6-Brd4-rep6

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB-Brd4 fusion rep6
M6_Brd4_pBC.ccf


title: Male6-Brd4-rep3

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB-Brd4 fusion rep3
M6_Brd4_mBC.ccf


title: Male6-Brd4-rep8

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB-Brd4 fusion rep8
M6_Brd4_pBC.ccf


title: Male6-Brd4-rep2

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB-Brd4 fusion rep2
M6_Brd4_mBC.ccf


title: Male6-Brd4-rep1

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB-Brd4 fusion rep1
M6_Brd4_mBC.ccf


title: Male6-Brd4-rep7

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB-Brd4 fusion rep7
M6_Brd4_pBC.ccf


title: Male6-Brd4-rep5

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB-Brd4 fusion rep5
M6_Brd4_mBC.ccf


title: Male6-Brd4-rep4

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB-Brd4 fusion rep4
M6_Brd4_mBC.ccf


title: Female6-WT-rep10

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB alone rep10
F6_WT_pBC.ccf


title: Female6-WT-rep9

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB alone rep9
F6_WT_pBC.ccf


title: Female6-WT-rep8

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB alone rep8
F6_WT_pBC.ccf


title: Female6-WT-rep7

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB alone rep7
F6_WT_pBC.ccf


title: Female6-WT-rep4

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB alone rep4
F6_WT_pBC.ccf


title: Female6-WT-rep5

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB alone rep5
F6_WT_pBC.ccf


title: Female6-WT-rep3

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB alone rep3
F6_WT_pBC.ccf


title: Male6-WT-rep6

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB alone rep6
M6_WT_pBC.ccf


title: Female6-WT-rep6

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB alone rep6
F6_WT_pBC.ccf


title: Female6-WT-rep1

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB alone rep1
F6_WT_pBC.ccf


title: Female6-WT-rep2

description:
Calling Card file (ccf) for insertion sites in female astroctye tranfected with PB alone rep2
F6_WT_pBC.ccf


title: Male6-WT-rep9

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB alone rep9
M6_WT_pBC.ccf


title: Male6-WT-rep10

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB alone rep10
M6_WT_pBC.ccf


title: Male6-WT-rep7

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB alone rep7
M6_WT_pBC.ccf


title: Male6-WT-rep4

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB alone rep4
M6_WT_mBC.ccf


title: Male6-WT-rep2

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB alone rep2
M6_WT_mBC.ccf


title: Male6-WT-rep3

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB alone rep3
M6_WT_mBC.ccf


title: Male6-WT-rep1

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB alone rep1
M6_WT_mBC.ccf


title: Male6-WT-rep5

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB alone rep5
M6_WT_mBC.ccf


title: Male6-WT-rep8

description:
Calling Card file (ccf) for insertion sites in male astroctye tranfected with PB alone rep8
M6_WT_pBC.ccf


title: Small Wound Hic1:tdTomato+ve 8 DPI

status: Public on Aug 04 2020

city: Calgary

first: Jeff

last: Biernaskie

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

institute: University of Calgary

data_processing:
All raw FASTQs reads were aligned to the mouse GRCm38.p5 (primary assembly) reference genome using the STAR algorithm and quantified through the 10X Genomics cellranger v2.0.1 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat (v2.1.0 ) R toolkit for quality control and all downstream analysis. All functions were run with default or recommended parameters, unless specified otherwise. Low quality cells (<400 genes/cell and <20 cells/gene) were excluded from the overall experiment. Gene expression was log normalized to a scale factor of 10,000. To begin unsupervised clustering of cells, a selection of highly variable genes (1195 genes) was obtained and used to calculate up to 75 principle components. Significance of principle components was determined using JackStraw analysis and by creating a PCElbowPlot. PCs 1 to 20 were used to run and plot a tSNE plot for all cells. Expression of selected marker genes across cell clusters identified by graph based clustering (run in Seurat at: res = 0.2) was used to select only fibroblasts for all subsequent analysis. Differential and marker gene analysis of cells defined by FACS sorting sample or graph-clustering was also run in Seurat using the negative binomial test for genes expressed by at least 25% of cells in the defined cell group being compared.
Genome_build: mm10 (GRCm38.p5)
Supplementary_files_format_and_content: Filtered gene - barcode matrix output from CellRanger

source_name: 8 days post injury skin wound

extract_protocol:
Large and small wounds from adult mice (n = 2 per sample) were dissected and enzymatically dissociated with dispase (StemCell Technologies) for 20 mins at 37 oC to remove the epidermis. Remaining dermis was dissociated using 0.2% collagenase for 2 hours at 37 oC. Cell suspensions were diluted with cold Hank’s Buffered Salt Solution (HBSS; Life Technologies), strained through 40 µm cell filters (Falcon) and centrifuged at 280 X g. Liberated single cells were re-suspended in 0.5% bovine serum album in HBSS before FACS purification. For FACS purification, a stringent initial forward and side scatter gates were used to exclude debris, and cell doublets. Wildtype cells were used as negative control to determine gates for detection of tdTomato-fluorescence, then cells from Hic1CreERT2:tdTomato mice were purified.
Libraries were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v2 Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 0.1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed first using Illumina MiSeq SR50 to approximate the number of recovered cells in each sample. We recovered 4061, 3776, 2604, and 3293 cells for Samples 1-4, respectively, with an estimated doublet rate of ≈3%. Based on this, we determined lane distributions for sequencing using Illumina HiSeq 4000 PE (75 bp paired-end reads) with a targeted sequencing depth of ~115,000 reads/cell.

treatment_protocol: Cre-recombination was initiated with two intraperitoneal injections of 4-hydroxy-tamoxifen (4-OHT; 1mg/20g in sterile sunflower oil, Sigma-Aldrich) at postnatal day (P) 3 and 4.

tag: transgenic strain

tag: background

tag: facs strategy

value: tdTomato+positive

tag: library preparation

value: 10X Genomics Single Cell RNAseq v2


title: bulk Primed Input

status: Public on Aug 22 2020

city: Tainjin

first: Weiyu

last: Zhang

address: No.38 Tongyan Road, Jinnan District

institute: Nankai University

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Cutadapt, then sequence reads were mapped to mm10 genome using Bowtie2.
Bigwig file was generated by bamCompare from Deeptools
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files, ChIP-seq normalized signal

source_name: Embryonic stem cell

growth_protocol: Naive cells were cultured in serum+LIF condition on feeders, primed cells were cultured in bFGF+Activin A condition on feeders.

extract_protocol:
The ULI-NChIP procedure was performed as previously described(Brind'Amour et al., 2015; Wang et al., 2018).
Sequencing libraries were generated using AT seq library following manufacturer's recommendations and index codes were added. The library quality was assessed on the Qubit 2.0 Fluorometer (Thermo Scientific) and Agilent Bioanalyzer 2100 system. At last, the library was sequenced on an Illumina HiSeq x platform and 150 bp paired-end reads were generated
Ultra-low-input micrococcal nuclease-based native ChIP (ULI-NChIP)

treatment_protocol: For ULI-NChIP-seq, about 50000 naïve or primed cells were used per reaction. For bulk ChIP-seq, about 5000000 naïve or primed cells were used per reaction.

value: C57 x CBA

tag: cell type

value: mESCs

tag: condition

value: Primed

tag: passages

tag: chip antibody


title: micro Primed Input

tag: strain


title: MCF-7 C2

status: Public on Aug 20 2020

city: Heifei

first: Mingming

last: Wu

state: Anhui

address: inZhai Road Baohe District

institute: University of Science and Technology of China

data_processing:
SOAPnuke v1.5.2 software for reads filtration, Remove low-quality reads that containing joints, with unknown base N content greater than 5%,
The clean reads were mapped reference genome using HISAT2 v2.0.4
Bowtie2 v2.2.5 was used  to align Clean reads to the reference gene sequence
RSEM v1.2.8 was used to calculate the gene expression level of each sample
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include expression and FPKM values for each Sample

source_name: Breast cancer cells

growth_protocol: The MCF-7 cell were cultured in 6-well palte for 48 hours

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard protocols

treatment_protocol: The cells were cultured with CM derived from parental MCF-7 cell or BCSCs derived from mammospheres culture

tag: treatment

value: Cultured with control CM

tag: tissue

value: Breast cancer cells


title: MCF-7 M1

value: Cultured with BCSC CM


title: bulk Primed Input replicate

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Cutadapt, then sequence reads were mapped to mm10 genome using Bowtie2.
The aligment files of bulk  ChIP-seq and micro ChIP-seq were merge together, and Bigwig file was generated by bamCompare from Deeptools
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files, ChIP-seq normalized signal

value: Embryonic stem cell

value: primed

tag: passage

tag: chip anitbody


title: Large Wound Center Hic1:tdTomato+ve 14DPI

source_name: 14 days post injury skin wound

value: large wound center


title: MCF-7 C3

tag: cell line


title: MCF-7 M2


title: RNA-Seq_MSIPS-2

status: Public on Jul 23 2020

city: Stanford

first: Fabian

last: Grubert

address: 300 Pasteur Drive

institute: Stanford University

data_processing:
FASTQ files were downsampled to 60 million reads
Transcript abundances were  quantified using kallisto (version 0.43.0; non-default parameters: --bias). Transcript sequences (i.e., target sequences) were obtained from Gencode (Release 25; lifted to GRCh37 coordinates).
To visualize RNA-seq data as signal tracks, down-sampled FASTQ files were aligned to the hg19 genome using HiSat2 (version 2.0.5; non-default parameters: -X 1000 --fr --no-mixed --no-discordant)7, after which genome-wide coverage tracks were produced using bedtools (bedtools genomecov -bga -split -ibam). Coverage values were scaled by a constant factor (109/total # of reads) to account for differences in sequencing depth.
Genome_build: hg19

source_name: iPS Line

growth_protocol: All cell lines were cultured following the manufacturer’s recommendations

extract_protocol:
RNA samples were extracted using the Qiagen All-Prep kit per manufacturer instructions.
Libraries were prepared from total RNA using the TruSeq Stranded Total RNA Library Prep Kit per manufacturer instructions. All libraries were sequenced on the Illumina Hiseq 4000

tag: disease

value: normal

tag: germ layer

value: Primitive


title: RNA-Seq_NCI-H1437-2

source_name: lung; metastatic site to pleural effusion

value: adenocarcinoma; non-small cell lung cancer

value: Endoderm


title: RNA-Seq_NCI-H1437-1


title: RNA-Seq_MSIPS-1


title: MCF-7 C1


title: RNA-Seq_MCF7 2

source_name: mammary gland; metastatic to pleural effusion

value: adenocarcinoma

value: Ectoderm


title: bulk Naive Input replicate

value: Naïve


title: RNA-Seq_MSLCL-1

source_name: B cell; lymphoblastoid

value: Immortalized with EBV

value: Mesoderm


title: RNA-Seq_MSFIB-2

source_name: skin; fibroblast


title: MCF-7 M3


title: RNA-Seq_LX-2

source_name: Liver cell


title: RNA-Seq_LX-1


title: RNA-Seq_LNCaP 2

source_name: prostate; metastatic site to lymph node

value: carcinoma


title: bulk Naive Input

value: C57 x CBA

value: mESCs


title: micro Naive Input


title: RNA-Seq_LNCaP 1


title: RNA-Seq_MSFIB-1


title: RNA-Seq_MSLCL-2


title: RNA-Seq_K562-2

source_name: bone marrow

value: chronic myelogenous leukemia


title: RNA-Seq_KU19-1

source_name: urinary bladder transitional cell


title: RNA-Seq_KU19-2


title: RNA-Seq_K1-2

source_name: Thryoid

value: papillary thyroid carcinoma


title: RNA-Seq_K562-1


title: RNA-Seq_K1-1


title: RNA-Seq_hTERT-HME1-1

source_name: mammary gland

value: Immortalized with hTERT


title: RNA-Seq_HT-1376-1

source_name: urinary bladder


title: RNA-Seq_H9-hESC-2

source_name: Embryonic Stem Cell


title: RNA-Seq_Jurkat-1

source_name: T lymphocyte

value: acute T cell leukemia


title: RNA-Seq_HepG2-2

source_name: liver

value: hepatocellular carcinoma


title: RNA-Seq_MCF7 1


title: RNA-Seq_HT1197-2


title: RNA-Seq_H9-hESC-1

value: normal


title: RNA-Seq_HepG2-1


title: RNA-Seq_HT1197-1


title: RNA-Seq_HT-1376-2


title: RNA-Seq_H1-hESC-2

value: Primitive


title: RNA-Seq_H1-hESC-1


title: SV18148_491 CAMP Subject

status: Public on Jul 08 2020

first: Jiang

last: Li

state: Massachusetts

address: 181 Longwood Avenue

department: Medicine

description:
CAMP_RAW_COUNT.txt
CAMP_NORMALIZED_COUNT.txt

data_processing:
ExceRpt (http://genboree.org/theCommons/projects/exrna-tools-may2014/wiki/Small_RNA-seq_Pipeline) was employed to assess the read quality and annotate miRNAs.
The read count was log transformed and normalized by quantile normalization (R package: preprocessCore).
Raw read counts less than five were filtered out and miRNAs with coverage less than 80% of all subjects were removed.
Coverage refers to the number of subjects in which a specific miRNA was detected at >=5 counts.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files of miRNA count for each sample

source_name: Blood Serum

extract_protocol:
Total RNA was isolated from serum samples by the Qiagen miRNeasy Serum/Plasma extraction kit and QIAcube automation. All samples were quantified using the Nanodrop spectrophotometer prior to plating.
Norgen Biotek Small RNA Library Prep Kit

tag: treatment group

value: Placebo

tag: Sex

value: Male

tag: age

tag: prebronchodilator fev1% predicted baseline

tag: prebronchodilator fev1% predicted year4


title: SV18148_488 CAMP Subject

value: Budesonide

value: high


title: SV18148_489 CAMP Subject

value: Female


title: SV18148_487 CAMP Subject


title: SV18148_490 CAMP Subject

value: median


title: RNA-Seq_Jurkat-2

value: Mesoderm


title: RNA-Seq_hTERT-HME1-2

value: Ectoderm


title: SV18148_486 CAMP Subject


title: SV18148_485 CAMP Subject


title: SV18148_484 CAMP Subject


title: SV18148_471 CAMP Subject


title: SV18148_464 CAMP Subject


title: SV18148_481 CAMP Subject


title: SV18148_465 CAMP Subject


title: SV18148_468 CAMP Subject


title: SV18148_458 CAMP Subject


title: SV18148_466 CAMP Subject


title: SV18148_476 CAMP Subject


title: SV18148_459 CAMP Subject


title: SV18148_475 CAMP Subject

value: low


title: SV18148_477 CAMP Subject


title: SV18148_473 CAMP Subject


title: SV18148_492 CAMP Subject


title: SV18148_470 CAMP Subject


title: SV18148_478 CAMP Subject


title: SV18148_474 CAMP Subject


title: SV18148_455 CAMP Subject


title: SV18148_452 CAMP Subject


title: SV18148_483 CAMP Subject


title: SV18148_472 CAMP Subject


title: SV18148_451 CAMP Subject


title: SV18148_448 CAMP Subject


title: SV18148_454 CAMP Subject


title: SV18148_447 CAMP Subject


title: SV18148_446 CAMP Subject


title: SV18148_445 CAMP Subject


title: SV18148_442 CAMP Subject


title: SV18148_444 CAMP Subject


title: SV18148_439 CAMP Subject


title: SV18148_440 CAMP Subject


title: SV18148_433 CAMP Subject


title: SV18148_429 CAMP Subject


title: SV18148_435 CAMP Subject


title: SV18148_412 CAMP Subject


title: SV18148_413 CAMP Subject


title: SV18148_420 CAMP Subject


title: SV18148_409 CAMP Subject


title: SV18148_426 CAMP Subject


title: SV18148_438 CAMP Subject


title: SV18148_410 CAMP Subject


title: SV18148_425 CAMP Subject


title: SV18148_418 CAMP Subject


title: SV18148_432 CAMP Subject


title: SV18148_414 CAMP Subject


title: SV18148_441 CAMP Subject


title: SV18148_415 CAMP Subject


title: SV18148_403 CAMP Subject


title: SV18148_404 CAMP Subject


title: SV18148_407 CAMP Subject


title: SV18148_401 CAMP Subject


title: SV18148_400 CAMP Subject


title: SV18148_431 CAMP Subject


title: SV18148_423 CAMP Subject


title: SV18148_421 CAMP Subject


title: SV18148_411 CAMP Subject


title: SV18148_395 CAMP Subject


title: SV18148_394 CAMP Subject


title: SV18148_406 CAMP Subject


title: SV18148_405 CAMP Subject


title: SV18148_396 CAMP Subject


title: SV18148_393 CAMP Subject


title: SV18148_389 CAMP Subject


title: SV18148_390 CAMP Subject


title: SV18148_385 CAMP Subject


title: SV18148_392 CAMP Subject


title: SV18148_387 CAMP Subject


title: SV18148_388 CAMP Subject


title: SV18148_383 CAMP Subject


title: SV18148_391 CAMP Subject


title: SV18148_381 CAMP Subject


title: SV18148_386 CAMP Subject


title: SV18148_384 CAMP Subject


title: SV18148_379 CAMP Subject


title: SV18148_378 CAMP Subject


title: SV18148_377 CAMP Subject


title: SV18148_376 CAMP Subject


title: SV18148_375 CAMP Subject


title: SV18148_380 CAMP Subject


title: SV18148_399 CAMP Subject


title: SV18148_373 CAMP Subject


title: SV18148_374 CAMP Subject


title: SV18148_372 CAMP Subject


title: SV18148_371 CAMP Subject


title: SV18148_370 CAMP Subject


title: SV18148_369 CAMP Subject


title: SV18148_368 CAMP Subject


title: SV18148_366 CAMP Subject


title: SV18148_382 CAMP Subject


title: SV18148_363 CAMP Subject


title: SV18148_360 CAMP Subject


title: SV18148_358 CAMP Subject


title: SV18148_364 CAMP Subject


title: SV18148_357 CAMP Subject


title: SV18148_362 CAMP Subject


title: SV18148_359 CAMP Subject


title: SV18148_353 CAMP Subject


title: SV18148_354 CAMP Subject


title: SV18148_355 CAMP Subject


title: SV18148_356 CAMP Subject


title: SV18148_352 CAMP Subject


title: SV18148_349 CAMP Subject


title: SV18148_348 CAMP Subject


title: SV18148_351 CAMP Subject


title: SV18148_367 CAMP Subject


title: SV18148_350 CAMP Subject


title: SV18148_347 CAMP Subject


title: SV18148_346 CAMP Subject


title: SV18148_365 CAMP Subject


title: SV18148_361 CAMP Subject


title: SV18148_345 CAMP Subject


title: SV18148_344 CAMP Subject


title: SV18148_342 CAMP Subject


title: SV18148_343 CAMP Subject


title: SV18148_341 CAMP Subject


title: SV18148_340 CAMP Subject


title: SV18148_335 CAMP Subject


title: SV18148_334 CAMP Subject


title: SV18148_336 CAMP Subject


title: SV18148_338 CAMP Subject


title: SV18148_337 CAMP Subject


title: SV18148_330 CAMP Subject


title: SV18148_333 CAMP Subject


title: SV18148_327 CAMP Subject


title: SV18148_326 CAMP Subject


title: SV18148_328 CAMP Subject


title: SV18148_331 CAMP Subject


title: SV18148_325 CAMP Subject


title: SV18148_322 CAMP Subject


title: SV18148_329 CAMP Subject


title: SV18148_324 CAMP Subject


title: SV18148_323 CAMP Subject


title: SV18148_320 CAMP Subject