title: K22W2P12

description:
polyA RNA
K22W2P12


title: K22W2P11

status: Public on Aug 27 2018

type: SRA

city: BeiJing

first: Yidong

last: Chen

address: Yiheyuan Road

country: China

institute: Peking University

description:
polyA RNA
K22W2P11

library_source: transcriptomic

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw reads were first organized by specific cell barcode information attached in the read 2 of pair-ended reads. Second, unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails. Subsequently, we also removed reads with adapter contaminants and low-quality bases (N>10%).
Third, the cleaned reads were aligned to the hg19 human transcriptome (UCSC) using Tophat (version 2.0.12) (Trapnell et al., 2009). Fourth, uniquely mapped reads were counted using htseq-count of the HTSeq package and grouped by cell-specific barcode (Anders et al., 2014). Based on UMI information, duplicated transcripts of each gene were removed. Finally, within a given cell, distinct UMIs of each gene were counted as the transcript number of that gene.
The expression levels TPM, where TPM (transcript-per-million) was calculated by the number of UMIs of each gene divided by all the number of UMIs of a given cell, then multiplying by 1,000,000.
Genome_build: hg19
Supplementary_files_format_and_content: txt files which include theTPM values of RefSeq genes.

molecule: total RNA

organism: Homo sapiens

source_name: Human Embryonic Kidney Cells

extract_protocol:
A modified Smart-seq2 protocol was applied for single-cell RNA-seq. Briefly,  single cell was picked into the lysis buffer by mouth pippete. The reverse transcription reaction was performed with a 24 oligo (dT) primer, which was  anchored with a 8 bp cell specific barcode and a 8 bp unique molecular identifiers (UMIs).
After the first-strand reaction, the cDNA was amplified by 19 cycles. Then the amplified cDNA of the cells of the same fetal sample were pooled together to proceed the following steps. Biotinylated pre-indexed primer was used to amplify the PCR product by additional 4 cycles to introduce biotin tags to the 3’ end of the amplified cDNA. About 300 ng DNA was sheared to around 300 bp by Covaris S2 and the 3’ ternimal of the DNA was captured by Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher). RNA seq library was constructed using Kapa Hyper Prep Kit (Kapabiosystems) and subjected to 150 bp paired-end sequencing on illumina HiSeq 4000 platform (sequenced by Novogene).

treatment_protocol: With enthic approval, human fetal kidney was first cut into pieces and then tissues were transferred to 1mg/ml collagenase II and collagenase IV mixture in a single tube. The tube was incubated at 37°C with shaken at 950 rpm for 20min. Then the cell suspesion was filtered through a 40 μm nylon straniner. The filtered cell suspesion was  centrifugated at 800g for 5min. We removed the supernate and resuspended the cell pellets using 500 μl DMEM medium. Single cell was picked up by mouth pipette and transfered to 8 strip 0.2 ml PCR tubes.

tag: age

tag: gender

value: female


title: K22W2D32

description:
polyA RNA
K22W2D32


title: H226 shp63, 14 days doxycycline, libB replicate 1

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

country: USA

institute: University of Colorado Anschutz Medical Campus

description:
sgRNA cassette amplicon
DX14B_rep1

library_source: genomic

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the HiSeq 2500 Real-Time Analysis (RTA) software (Illumina)
Conversion to FASTQ format was carried out using bcl2fastq (v1.8.4, Illumina)
Samples were demultiplexed using fastx_barcode_splitter from the fastx_toolkit (v0.0.13.2), allowing 2 mismatches
FASTQC v0.11.2 was used to assess sequence data quality
Sequences were trimmed using fastx_trimmer from the fastx_toolkit (v0.0.13.2), with the following options: -Q33 -f 43 -l 62. This keeps only the section of each read corresponding to the unique sgRNA sequences (positions 43-62 inclusive)
Bases with qual ≥10 were removed with fastx_quality_filter from the fastx_toolkit (v0.0.13.2), with the following options: -Q33 -q 10 -p 94.
Trimmed and filtered sequences were mapped with Bowtie2 v2.2.3 using the following options (--phred33 --end-to-end --very-sensitive)
Genome_build: A reference index was generated for Bowtie2 using only the unique sgRNA sequences from the Human GeCKOv2 library annotation available from https://media.addgene.org/cms/filer_public/7d/87/7d87eaa7-e940-41bf-bf2f-47b43c7ab905/zhang_human_geckov2_grna_sequences.zip (PMID: 24336571; PMID: 25075903)
Supplementary_files_format_and_content: Tab delimited text files containing raw sgRNA counts for each sample

molecule: genomic DNA

source_name: H226 shp63_14 days doxycycline

growth_protocol: H226 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum and were maintained at 37°C in a humidified atmosphere with 5% CO2.

extract_protocol:
CRISPR screen protocol: H226 shp63 cells were transduced with the GeCKOv2 A or B libraries and propogated for 14 days to clear sgRNAs targeting essential genes. The resulting cell populations were treated in triplicate with PBS (vehicle) or doxycycline (to induce p63 knockdown) for 14 days.
Genomic DNA was extracted using a DNeasy Blood and Tissue kit (Qiagen)
Custom

treatment_protocol:
shRNA protocol: Generation of H226 cell lines expressing doxycycline-inducible control and p63-targeting short hairpin RNAs (shRNAs) was described previously (PMID: 2301912). Cells were treated with vehicle (PBS), or 1 µg/mL doxycycline to induce shRNA expression.
Cells were treated with vehicle (PBS), or 1 µg/mL doxycycline to induce shRNA expression.

tag: cell line

tag: cell type

value: lung squamous cell carcinoma

tag: inducible shrna construct

tag: gecko library

value: HGLibB

tag: culture condition

tag: treatment

value: 1 µg/mL doxycycline


title: K22W2D21

description:
polyA RNA
K22W2D21


title: K22W2D12

description:
polyA RNA
K22W2D12


title: K22W2D11

description:
polyA RNA
K22W2D11


title: H226 shp63, 14 days vehicle, libB replicate 1

description:
sgRNA cassette amplicon
NODX14B_rep1

source_name: H226 shp63_14 days vehicle

value: vehicle


title: H226 shp63, 14 days vehicle, libA replicate 2

description:
sgRNA cassette amplicon
NODX14A_rep2

value: HGLibA


title: K22W2C32

description:
polyA RNA
K22W2C32


title: K22W2C31

description:
polyA RNA
K22W2C31


title: K24W1C

description:
polyA RNA
K24W1C

value: male


title: K22W2C11

description:
polyA RNA
K22W2C11


title: K22W2C12

description:
polyA RNA
K22W2C12


title: K22W2C21

description:
polyA RNA
K22W2C21


title: K10W2D2

description:
polyA RNA
K10W2D2


title: K22W2C22

description:
polyA RNA
K22W2C22


title: K22W2D31

description:
polyA RNA
K22W2D31


title: K10W2C1

description:
polyA RNA
K10W2C1


title: K22W2D22

description:
polyA RNA
K22W2D22


title: K7W1P1

description:
polyA RNA
K7W1P1


title: K10W2P1

description:
polyA RNA
K10W2P1


title: K8W1B1

description:
polyA RNA
K8W1B1


title: K10W2D1

description:
polyA RNA
K10W2D1


title: K7W1D1

description:
polyA RNA
K7W1D1


title: K7W1D2

description:
polyA RNA
K7W1D2


title: K7W1C1

description:
polyA RNA
K7W1C1


title: HEK25WP2

description:
polyA RNA
HEK25WP2


title: K7W1C2

description:
polyA RNA
K7W1C2


title: Input HeLa K PWWP2A  siRNA 1

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description: ChIP-seq

data_processing:
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Reads were aligned to a pre-compiled index of the mouse hg19 genome using Bowtie (options: -k 1 -m 1) 0.12.5.
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
The bamCoverage tool of the Deeptools suite was used for extracting coverage vectors (bigwig format).
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq peaks are supplied as BED and coverage vectors as bigwig files

source_name: Human cervical carcinoma cell line

growth_protocol: Cells were grown in DMEM supplemented with 10%FCS and 1% PenStrep.

extract_protocol:
Mononucleosomes from unfixed cells were isolated and histone-DNA complexes were immunoprecipitated.
Libraries were established with the MicroPlex Library Preparation Kit (Diagenode) following the manufacturer’s instructions.

treatment_protocol: Cells were transfected with indicated siRNAs using Oligofectamine according to the manufacturer's protocol. Two days after siRNA transfection, cells were harvested.

value: treated with PWWP2A specific siRNA 1

value: HeLa  Kyoto cells


title: HEK25WD2

description:
polyA RNA
HEK25WD2


title: Input HeLa K PWWP2A  siRNA 2

description: ChIP-seq

value: treated with PWWP2A specific siRNA 2


title: HEK25WP1

description:
polyA RNA
HEK25WP1


title: Input HeLa K Luci siRNA

description: ChIP-seq

value: treated with Luciferase control siRNA


title: K10W2P2

description:
polyA RNA
K10W2P2


title: HEK25WD1

description:
polyA RNA
HEK25WD1


title: K8W1A1

description:
polyA RNA
K8W1A1


title: K8W1B2

description:
polyA RNA
K8W1B2


title: ChIP H2A.Zac HeLa K PWWP2A  siRNA 1

description: ChIP-seq

tag: antibody

value: anti-H2A.Zac (Diagenode, C15410202-050)


title: K7W1P2

description:
polyA RNA
K7W1P2


title: Input HeLa K untreated

description: ChIP-seq

value: untreated


title: K10W2C2

description:
polyA RNA
K10W2C2


title: ChIP H2A.Zac HeLa K Luci siRNA

description: ChIP-seq


title: HEK25WC2

description:
polyA RNA
HEK25WC2


title: ChIP H2A.Zac HeLa K untreated

description: ChIP-seq


title: ChIP H2A.Zac HeLa K PWWP2A  siRNA 2

description: ChIP-seq


title: HEK19W2D2

description:
polyA RNA
HEK19W2D2


title: HEK19W2P1

description:
polyA RNA
HEK19W2P1


title: HEK25WC1

description:
polyA RNA
HEK25WC1


title: HEK19W2D1

description:
polyA RNA
HEK19W2D1


title: ChIP H3K27ac HeLa K PWWP2A  siRNA 2

description: ChIP-seq

value: anti-H3K27ac (Abcam, ab4729)


title: ChIP H3K27ac HeLa K PWWP2A  siRNA 1

description: ChIP-seq


title: ChIP H3K27ac HeLa K Luci siRNA

description: ChIP-seq


title: HEK19W2C1

description:
polyA RNA
HEK19W2C1


title: HEK19W1P1

description:
polyA RNA
HEK19W1P1


title: HEK19W1P2

description:
polyA RNA
HEK19W1P2


title: HEK19W2C2

description:
polyA RNA
HEK19W2C2


title: ChIP H3K27ac HeLa K untreated

description: ChIP-seq


title: HEK19W1D1

description:
polyA RNA
HEK19W1D1


title: HEK13WA

description:
polyA RNA
HEK13WA


title: HEK19W1C1

description:
polyA RNA
HEK19W1C1


title: HEK19W1C2

description:
polyA RNA
HEK19W1C2


title: HEK13WB

description:
polyA RNA
HEK13WB


title: HEK9WP2

description:
polyA RNA
HEK9WP2


title: HEK19W2P2

description:
polyA RNA
HEK19W2P2


title: HEK9WC2

description:
polyA RNA
HEK9WC2


title: HEK9WD2

description:
polyA RNA
HEK9WD2


title: HEK9WP1

description:
polyA RNA
HEK9WP1


title: HEK9WD1

description:
polyA RNA
HEK9WD1


title: HEK7W2P1

description:
polyA RNA
HEK7W2P1


title: HEK7W2D2

description:
polyA RNA
HEK7W2D2


title: HEK7W2C2

description:
polyA RNA
HEK7W2C2


title: HEK7W2P2

description:
polyA RNA
HEK7W2P2


title: HEK9WC1

description:
polyA RNA
HEK9WC1


title: HEK19W1D2

description:
polyA RNA
HEK19W1D2


title: HEK7W2C1

description:
polyA RNA
HEK7W2C1


title: HEK7W2D1

description:
polyA RNA
HEK7W2D1


title: A17-16hpi-repeat3

type: RNA

city: CASTANET TOLOSAN

first: Thomas

middle: R

last: Rey

address: 24 chemin de borde rouge, BP42617

country: France

institute: DE SANGOSSE

description: Gene expression data from pooled roots of germinated seedlings.

hyb_protocol: The labeled and fragmented aRNA was spiked with cDNA hybridization controls (GeneChip® Hybridization Control Kit, Affymetrix), which serve as an internal control for sensitivity and accuracy of the hybridization reaction as well as of the wash and stain procedure. The spiked aRNA samples were hybridized at 45°C for 16 hrs on separate Affymetrix GeneChip® Medicago Genome Arrays. After hybridization, microarrays were stained in two binding cycles using anti-Biotin antibodies and Streptavidin, R-phycoerythrin conjugate.

scan_protocol: Fluorescent signal intensities were detected with the Affymetrix GeneChip® 3000 Scanner and AGCC Scan Control Software v3.2.3.1515 (Affymetrix). Automatic grid was arranged and raw data (*.DAT files) were processed to generate image and intensity files (*:CEL, *.JPG) by the AGCC Scan Control Software.

data_processing: The software tools AGCC Viewer v3.2.0.1515 and Expression Console v1.3.1.187 (both Affymetrix Inc.) were used for quality control and visualization of the performance of microarray analysis. The software tool GeneSpring GX 12.6.1 (Agilent Technologies) was used for visualization and normalization. The RMA algorithm was applied for summarization quantile normalization of the data set.

label: biotin

organism: Medicago truncatula

source_name: A17 seedlings 16hpi

label_protocol: 200 ng total RNA per sample were introduced into an RT-IVT reaction. Prior to RT-IVT, the RNA samples were spiked with polyadenylated transcripts (GeneChip® Poly-A Control Kit, Affymetrix Inc.) which serve as an internal labeling control for linearity, sensitivity and accuracy. The spiked total RNA was reversely transcribed into double-stranded cDNA and then converted into Biotin-labeled aRNA by 16 hrs in-vitro transcription (3´IVT Expression Kit, Affymetrix Inc.). The generated single stranded aRNA was purified and fragmented.

growth_protocol: Growth protocol is described in Rey et al. 2014 (http://www.ncbi.nlm.nih.gov/pubmed/25495186).

extract_protocol: RNA extraction protocol is described in Rey et al. 2014 (http://www.ncbi.nlm.nih.gov/pubmed/25495186).

treatment_protocol: Treatment protocol is described in Rey et al. 2014 (http://www.ncbi.nlm.nih.gov/pubmed/25495186).

tag: line

tag: genotype/variation

value: WT

tag: tissue

value: 10 pooled seedling roots

value: Phytophthora palmivora infection

tag: timepoint


title: WT_CD_3

city: Oviedo

first: Jose

last: Freije

state: Asturias

address: C/ Fernando Bongera s/n

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universidad de Oviedo

description: Gene expression data from liver of WT mice under CD

hyb_protocol: The biotin-labeled cRNA was purified, fragmented, and hybridized to a GeneChip Mouse Gene 1.0 ST Array (Affymetrix).

scan_protocol: Washing and scanning were performed with a Fluidics Station 400 and GeneChip Scanner (Affymetrix).

data_processing: After scanning, raw data were processed with the RMAExpress program (http://RMAExpress.bmbolstad.com), using default settings.

organism: Mus musculus

source_name: liver, WT, control

label_protocol: Double-stranded cDNA was synthesized using the SuperScriptTM cDNA synthesis kit (Invitrogen). In vitro transcription was carried out with the Bioarray high-yield RNA transcript labeling kit (Enzo Diagnostics).

growth_protocol: LmnaG609G/G609G and WT mice in a C57BL/6N background were generated by crossing heterozygous LmnaG609G/+ mice and genotyped in our laboratory as previously described (Osorio et al., 2011). Mice were bred in a specific pathogen free (SPF) area and the experiments were carried out in a conventional area with exclusion barriers. Mice were caged separately by sex and genotype and checked daily for water and food supplies, as well as for good physical condition. All animal experiments were approved by the Committee for Animal Experimentation of the Universidad de Oviedo and performed in accordance with its guidelines, making every effort to minimize the suffering of the mice.

extract_protocol: About 30 mg of frozen liver samples were homogenized in Trizol (Life Technologies) and total RNA was isolated with RNeasy kit (Qiagen).

treatment_protocol: Experiments with modified diets (CD and MR) were initiated at 7 weeks of age. Diets were provided combining solid and crushed pellets in all experimental groups to facilitate the feeding of the mutant mice. Male mice were sacrificed after 6 hours of fasting at 110 days of life and used to obtain liver tissue samples.

tag: diet

value: control

tag: strain

tag: Sex

value: Male

tag: genotype

value: Liver

value: 110 days


title: MB231-Methylstat

city: Singapore

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

country: Singapore

institute: Genome Institute of Singapore

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina GenomeStudio 2010

source_name: Breast cancer cell line

label_protocol: Standard Illumina protocol. In brief, 500 ng total RNA was converted to single-stranded cDNA using a T7 Oligo(dT) primer, and subsequently converted to double-stranded DNA (dsDNA) template for transcription. The dsDNA was then amplified and labeled with biotin to generate biotinylated cRNA.

growth_protocol: All the cells were maitained in DMEM medium (GIBCO) supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with the RNeasy Mini Kit (Qiagen).

treatment_protocol: 2.5μM Methylstat treated for 24hr

value: 2.5μM Methylstat treated for 24hr


title: WCE WT 0.2M HU, 60 min, rep2

type: genomic

city: Montpellier

first: romain

last: forey

address: 142 avenue de la Cardonille

institute: IGH

hyb_protocol: DNA was hybridized to Affymetrix GeneChip S. cerevisiae Tiling 1.0R Array (5-bp resolution) using the GeneChip Hybridization, Wash, and Stain kit (Affymetrix, PN 900720).

scan_protocol: Tiling arrays were scanned with the GeneChip scanner 3000 7G.

data_processing:
Signals were normalized with TAS 1.1.02 (Affymetrix) using quantile normalization. Analysis results were stored in log2 scale for signal intensity and in −10 × log10 scale for P values. Probe signals were analyzed using perfect matches only with a bandwidth of 300 bp. P-value intervals were generated using the following parameters: cutoff, 10−5; maximum gap, 80 bp; min run, 40 bp. Significant intervals were scored as active origins when signal intensity was above a threshold arbitrarily set at 50% of the signal range and when BrdU tracks were larger than 1 kb. Replication profiles (signal log ratio) were displayed with IGB 6.1
Bar files correspond to signal intensities (signal log ratio of BrdU IP relative to WCE) and can be displayed with IGB (Integrated genome Brower).

organism: Saccharomyces cerevisiae

label_protocol: Purified immunoprecipitated DNA was amplified using the WGA2 GenomePlex Complete Whole Genome Amplification kit (Sigma) with the addition of 0.1 mM dUTP in the amplification reaction. Amplified DNA (7 μg) was fragmented and labeled using the GeneChip WT Double-Stranded DNA Terminal Labeling kit (Affymetrix, PN 900812) according to the manufacturer's recommendations.

growth_protocol: Cells were grown in YPD at 25°C

extract_protocol: Standard protocol for BrdU-IP chip. For immunoprecipitation of BrdU-labeled DNA, 1.5 × 10e9 cells were lysed five times for 2 min each time in NIB buffer (17% (v/v) glycerol, 50 mM MOPS buffer, 150 mM potassium acetate, 2 mM magnesium chloride, 500 μM spermidine and 150 μM spermine, pH 7.2) with zirconium beads on a Vibrax shaker (VXR basic, Ika) at 4 °C. DNA was isolated using Qiagen genomic DNA extraction kit and sonicated to yield an average DNA size of 300–600 bp. For each immunoprecipitation, 10 μl of mouse anti-BrdU IgG1 (BD Bioscience, 555627) was prebound to Dynabeads M-280 sheep anti-mouse IgG (Invitrogen, 112.01D) and added to the denatured purified DNA.

treatment_protocol: Samples were released from alpha-factor arrest in the presence of 0.033% or 0.1% MMS and collected respectively at 45 and 60 minutes post G1 release

tag: protocol

value: Input (total genomic DNA)

tag: strain name

value: 0.2M HU, 60 min


title: WCE WT 0.2M HU, 60 min, rep1


title: rad9delta MMS 0.1%, 45 min

description: ratio: JBA46_IPH relative to InputDNA_1 and InputDNA_2

value: BrdU IP


title: HCC70-Methylstat

tag: cell line


title: HCC70-DMSO

value: DMSO


title: api-Mock-repeat3

source_name: api seedlings Mock

value: api mutant

value: mock infection


title: A17-Mock-repeat2

source_name: A17 seedlings Mock


title: A17-16hpi-repeat1


title: api-16hpi-repeat3

source_name: api seedlings 16hpi


title: KI_MR_3

description: Gene expression data from liver of KI mice under MR

source_name: liver, KI, methione restriction

value: methione restriction

value: Lmna G609G/G609G KI

tag: age


title: api-16hpi-repeat2


title: A17-16hpi-repeat2


title: api-16hpi-repeat1


title: MB468-Methylstat


title: MB231-DMSO


title: WT_MR_1

description: Gene expression data from liver of WT mice under MR

source_name: liver, WT, methione restriction


title: MB468-DMSO


title: A17-Mock-repeat3


title: A17-Mock-repeat1


title: api-Mock-repeat2


title: WT_CD_2


title: WT MMS 0.1%, 45 min

description: ratio: JBA46_IPF relative to InputDNA_1 and InputDNA_2


title: WT_MR_2


title: mrc1delta MMS 0.1%, 45 min

description: ratio: JBA46_IPG relative to InputDNA_1 and InputDNA_2


title: Treg_PBS_72h_rep3

city: Miami

last: Malek

state: FL

address: 1600 NW 10th Ave, RMSB, Room 3119

department: Microbiology and Immunology

institute: University of Miami

description: 2017-10-02-Alejandro-Moro-08-T-regs-PBS-8_S7

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then mapped to mm10 whole genome using STAR v2.5.0b with default parameters
Raw read counts were quantified using featureCounts v1.5.0
Genome_build: mm10/GRCm38 with gencode vM13 reference
Supplementary_files_format_and_content: Comma-delimited (.csv) text file includes raw counts for each Sample

source_name: regulatory T cells

extract_protocol:
RNA was isolated from sorted Tregs using TRIzol Reagent (Thermo Fisher) and column purified using miRNeasy Micro Kit (Qiagen). RNA quality was assessed using an Agilent 2100 BioAnalyzer and was quantified using Qubit RNA assay
RNA-seq libraries were prepared from 25 ng of total RNA using the KAPA’s RNA Hyperprep with RiboErase protocol and quantified using Qubit DNA and  Kapa qPCR Library Quantification kit for Illumina (KapaBiosystems).

treatment_protocol: RFP-FoxP3+ BL6 mice were injected with 20 ug of FP or 100 uL of control PBS. 72 hrs post injection splenic Tregs were sorted out.

value: Spleen

tag: cell type

value: regulatory T cells

tag: injected molecule

value: control PBS


title: rad9delta MMS 0.033%, 45 min

description: ratio: JBA20_IPC relative to InputDNA_1 and InputDNA_2


title: WT_MR_3

value: WT


title: Treg_PBS_72h_rep2

description: 2017-10-02-Alejandro-Moro-05-T-regs-PBS-5_S11


title: mrc1delta MMS 0.033%, 45 min

description: ratio: JBA20_IPB relative to InputDNA_1 and InputDNA_2


title: KI_MR_2


title: KI_MR_1


title: WT_CD_1

value: control


title: Treg_PBS_72h_rep1

description: 2017-10-02-Alejandro-Moro-01-T-regs-PBS-1_S2


title: Treg_FP_72h_rep4

description: 2017-10-02-Alejandro-Moro-10-T-regs-FP-10_S16


title: Treg_FP_72h_rep3

description: 2017-10-02-Alejandro-Moro-07-T-regs-FP-7_S5


title: WT MMS 0.033%, 45 min

description: ratio: JBA20_IPA relative to InputDNA_1 and InputDNA_2


title: KI_CD_3

description: Gene expression data from liver of KI mice under CD

source_name: liver, KI, control

value: Male


title: Treg_FP_72h_rep2

description: 2017-10-02-Alejandro-Moro-04-T-regs-FP-4_S8


title: api-Mock-repeat1

description: Gene expression data from pooled roots of germinated seedlings.

value: 10 pooled seedling roots


title: delta-rocA-2-ME

city: Houston

first: Paul

last: Bernard

state: TX

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

description:
isogenic rocA deletion strain
WT_vs_del_ES.xlsx
del_vs_WT_ME.xlsx

data_processing:
Reads were mapped to the genome of serotype M28 GAS reference strain MGAS6180 and differentional transcript analysis was performed with CLC Genomics Workbench 10.5 (Qiagen) using the default settings.
Supplementary_files_format_and_content: xlsx; contains differential expression analysis and RPKMs for each sample at the corresponding time point

organism: Streptococcus pyogenes

source_name: serotype M28 group A streptococcus strain

growth_protocol: Strains were grown in Todd-Hewitt broth with 0.2% yeast extract until ME (OD600 = 0.5) and ES (OD600 = 1.65) and RNAprotect was added (2:1)

extract_protocol:
Strains were lysed by ballistic disintegration and RNA extracted using Rneasy Mini Kit (Qiagen)
Libraries were prepared using standard Illumina protocols for Gram (+) organisms

value: MGAS28426 delta rocA


title: delta-rocA-2-ES


title: delta-rocA-3-ES


title: Treg_FP_72h_rep1

description: 2017-10-02-Alejandro-Moro-03-T-regs-FP-3_S4


title: delta-rocA-3-ME


title: delta-rocA-1-ES


title: KI_CD_1

value: Liver

value: 110 days


title: MGAS28426-2-ES

description:
wild-type strain
WT_vs_del_ES.xlsx
del_vs_WT_ME.xlsx


title: H460/14 T

city: York

first: John

last: Packer

state: North Yorkshire

address: Wentworth Way

department: Biology

country: United Kingdom

institute: Mr

description: Primary Gleason 9 prostate basal epithelial culture gene expression 2hrs post-3min LTP exposure

hyb_protocol: Labelling, hybridization and scanning were performed by Eurofins according to the Applied Biosystems GeneChip™ WT Pico Reagent Kit on the Clariom D Microarrays - See Manuals at; https://www.thermofisher.com/order/catalog/product/902622

data_processing: Performed by JP on Affymetrix Transcriptome Analysis Console 3

source_name: Prostate biopsy

growth_protocol: See Collins et al. (2005) Prospective identification of tumorigenic prostate cancer stem cells. Cancer Research. 2005 Dec 1;65(23):10946-51.

extract_protocol: Cells were lysed in well using the Qiagen Rneasy animal cell extraction protocol, 2hrs after LTP treatment

treatment_protocol: Cells were treated in a 12 well plate (100,000 cells/well) and exposed to Dielectric Barrier Discharge LTP jet at a distance of 15mm from cell media for 3 minutes.

value: Prostate biopsy

tag: tissue pathology

value: Gleason 9 Cancer

value: treated with LTP


title: H545/15 U

description: Primary Gleason 9 prostate basal epithelial culture gene expression

scan_protocol: Labelling, hybridization and scanning were performed by Eurofins according to the Applied Biosystems GeneChip™ WT Pico Reagent Kit on the Clariom D Microarrays - See Manuals at; https://www.thermofisher.com/order/catalog/product/902622

tag: treatment

value: untreated


title: MGAS28426-1-ES


title: delta-rocA-1-ME


title: MGAS28426-3-ME


title: H545/15 T

label_protocol: Labelling, hybridization and scanning were performed by Eurofins according to the Applied Biosystems GeneChip™ WT Pico Reagent Kit on the Clariom D Microarrays - See Manuals at; https://www.thermofisher.com/order/catalog/product/902622


title: MGAS28426-3-ES


title: KI_CD_2


title: miR202 knock-out Female 20

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

institute: INRA

hyb_protocol: 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array. Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing.

scan_protocol: Microarrays were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3µm and 20bits)

data_processing: Data were then obtained with the Agilent Feature Extraction software (10.7.3.1) according to the appropriate GE protocol (GE1_107_Sep09). Normalization and statistical analysis were performed using GeneSpring software (Agilent).

organism: Oryzias latipes

source_name: miR202 knock-out Female

label_protocol: Labeling and hybridization steps were performed following the “One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling)”Agilent protocol. Briefly, for each sample, 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop.

growth_protocol: Adult medaka (Oryzias latipes) from the CAB strain was used. Wild-types, miR-202 mutants and transgenics Tg(sox9b::EGFP) were raised at 26°C under a growing photoperiod regime before 3 months old (12h light/ 12h dark) or under a reproduction photoperiod regime after 3 months old (14 h light/10 h dark)

extract_protocol: Frozen tissues were lysed with Precellys Evolution Homogenizer (Ozyme, bertin technologies) in TRI Reagent® (TR118, Euromedex) and total RNA was extracted using the “nucleospin RNA” kit (740955, Macherey Nagel).

treatment_protocol: For the CRISPR/Cas9 strategy, the target genomic sequence was identified with the help of the ZiFiT online tool (http://zifit.partners.org/ZiFiT/) and using the medaka genome reference available on the Ensembl genome database (Ensembl gene: ENSORLG00000021212). A short sequence in the mature miR-202-3p was selected as followed: GG-(N)18-NN. Two inverse-complementary primers (Forward 5’-TAGGCATAAGGCATGGGAAAAT-3’ and Reverse 5’-AAACATTTTCCCATGCCTTATG-3’) were annealed and cloned into the pDR274 vector (Addgene plasmid 42250). The modified pDR274 vector was digested with DraI and the miR-202 specific guide RNA (mir202-sgRNA) was transcribed using the T7 RNA polymerase (P207, Promega). For the Cas9-RNA in vitro synthesis, the pCS2-nCas9n vector (Addgene plasmid 47929) was linearized with NotI and capped RNA encoding the Cas9 was transcribed with the mMessage mMachine SP6 Kit (AM1340, Life Technologies) following manufacturer's instructions. Cas9-RNA (100 ng/μL) and mir202-sgRNA (10 ng/μL) were co-injected into one-cell stage embryos. Injected embryos were raised to sexual maturity and 10 fishes were genotyped to identified founder fishes (F0). Fishes harboring the same INDEL mutation (-7+3) were selected and outcrossed with wild-type fishes to obtain F1 heterozygous. Such outcrosses were performed at each generation in order to maintain the line.

value: KO miR202

value: miR202 knock-out

value: ovary


title: YFP+ liver EC, biological replicate 4

city: Mannheim

first: Mahak

last: Singhal

address: Ludolf-Krehl-Straße 13-17

institute: European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University

hyb_protocol: (according to user manual Affymetrix 3’ IVT Pico Reagent Kit) 6,6 ug of fragmented and labeled ds-cDNA were hybridized for 17 hr at 45°C on Affymetrix Mouse Clariom S Arrays.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays

data_processing: All intensity data were quarantile normalized.

label: Biotin

source_name: liver

label_protocol: The Affymetrix 3’ IVT Pico Reagent Kit is used to generate labeled single-stranded cRNA from input amounts of 100pg total RNA. Label: Biotin

growth_protocol: 8 wk old mice were irradiated with 9 Gy (2 x 4.5 Gy). After 2 h resting period, irradiated mice were transplanted with 5000 YFP-labeled LSK cells intravenously.

extract_protocol: Total RNA were isolated using Arcturus PicoPure RNA isolation kit according to the manufacturer described protocol.

treatment_protocol: Mice were euthanized and liver tissue was collected. Briefly, minced liver tissue was incubated in collagenase solution for 30 mins. Next, erythrocytes were lysed with ACK-lysis buffer. Afterward, the single cells were stained with an antibody cocktail (CD45, CD31, CD146) for 20 mins on ice. Liver endothelial cells (EC) were isolated by FACS using CD45- CD31+ CD146+ surface marker profile. Further, liver EC were sorted according to YFP expression into YFP+ EC and YFP- EC.

value: YFP+ (bone marrow-derived endothelial cell)


title: MGAS28426-2-ME


title: YFP+ liver EC, biological replicate 1


title: H434/14 RM T

description: Primary Gleason 7 prostate basal epithelial culture gene expression 2hrs post-3min LTP exposure

value: Gleason 7 Cancer


title: H460/14 U


title: YFP- liver EC, biological replicate 4

value: YFP- (resident liver endothelial cell)


title: YFP+ liver EC, biological replicate 3


title: YFP+ liver EC, biological replicate 2


title: YFP- liver EC, biological replicate 2


title: miR202 knock-out Female 17


title: Wild-type Female 12

source_name: Wild-type Female

value: WT


title: H434/14 LM T

description: Primary prostate basal epithelial culture gene expression 2hrs post-3min LTP exposure

value: Normal


title: MGAS28426-1-ME


title: miR202 knock-out Female 4


title: H329/13 R T


title: YFP- liver EC, biological replicate 3


title: Control subject NPC sample 2

status: Public on Aug 26 2018

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description:
CON5_1
5d_S3_R1_L001

data_processing:
Illumina bcl2fastq2-v2.17.1.14 software used for basecalling.
Sequenced reads were pseudoaligned with Kallisto to an index prepared from the NCBI RefSeq mRNA fasta file.
Variance was estimated by bootstrapping with -b 100 set in Kallisto
Kallisto output files were loaded into the Sleuth package in R and modeled to compare TSC to Control (n-2).  Wald test (1% FDR) and two-fold change (estimated from the beta value by converting the log base) was used to select differentially expressed genes.
TPM (Transcript per million) was output using sleuth_to_matrix function from the sleuth object.
Genome_build: hg38
Supplementary_files_format_and_content: RefSeq NCBI accessions row labels and sample replicate column labels.  The values are TPM

source_name: Control subject NPC sample

growth_protocol: NPC cultures were prepared from iPSC by differentiation with Gibco Neural Induction Supplement and grown in Gibco Neural Expansion Medium

extract_protocol:
Total RNA was isolated using a Zymo Direct-Zol Kit
RNAs were reverse transcribed and converted to libraries using the Illumina TruSeq RNA Sample Preparation Kit v2.

treatment_protocol: No treatment

tag: source subject status

value: unaffected control

value: Control

value: iPSC-derived

tag: enrichment

value: neural progenitor cells (NPCs)


title: miR202 knock-out Female 5


title: H434/14 RM U

description: Primary Gleason 7 prostate basal epithelial culture gene expression


title: Control subject NPC sample 1

description:
CON5_0
05C_S1_R1_L001

tag: genotype/variation


title: TSC subject NPC sample 2

description:
TSC1_1
1d_S4_R1_L001

source_name: TSC subject NPC sample

value: Tuberous Sclerosis Complex (TSC) patient


title: H434/14 LM U

description: Primary prostate basal epithelial culture gene expression

tag: tissue

value: Prostate biopsy


title: TSC subject NPC sample 1

description:
TSC1_0
01C_S2_R1_L001


title: H329/13 R U


title: H3K9ac Un TSA rep2

city: Jerusalem

first: Itamar

last: Simon

state: APO/FPO IRAQ / AFGHANISTAN / MIDDLE EAST

address: Hadassah Ein Kerem

department: Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University medical school

data_processing:
ChIP-Seq reads were aligned to the human genome (hg19) using either BWA or Bowtie. TSA ChIP-seq alignments (PE) were processed by Bowtie2 version 2.2.9, suppressing unpaired and discordant read pairs. RNA Pol II ChIP-seq alignments (SE) were processed by Bowtie version 1.0.0, with parameter m=1, v=2. The rest of the ChIP-seq alignments (PE) were processed by BWA version 0.5.9 with parameters q=5, l=32.
Duplicate alignments were removed with Picard Tools MarkDuplicates.
Peak detection on merged replicates (with WCE dataset as a control) was done using HOMER using default histone style parameters for all histone modifications, and default factor style parameters for PolII and CTCF.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files are ChIP-seq peak files including the coordinates for all peak regions

growth_protocol: HeLa-S3 cells were grown in Spinner flasks in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% Fetal Bovine Serum (FBS), Penicillin-Streptomycin, L-Glutamine, Sodium Pyruvate and 0.1% Pluronic F-68. Cells were incubated at 370C and 5% CO2. Cells were pre-synchronized in G1/S by addition of 2mM thymidine for 16 hrs, washed with PBS, released for 3 hrs in fresh medium and arrested with S-Trityl-L-cysteine (STC) (164739, Sigma) for 12 hrs.

extract_protocol:
ChIP was performed either manually on individual samples or automatically using the Bravo liquid handling platform (Agilent model 16050-102, “Bravo”) as described previously (Busby et al. 2016).
Illumina Library construction reactions were performed as we described previously (Garber & Yosef et. al. 2012). SPRI (Solid-phase reversible immobilization; AMPure XP beads (Agencourt)) cleanup steps were done using the Bravo liquid handling platform (Agilent) and a modified version of (Fisher et al., 2011). After the final ChIP step, 120µl SPRI was added to the reverse-crosslinked samples, pipette-mixed 15 times and incubated for 2 minutes. Supernatant was separated from the beads using a 96-well magnet for 4 minutes. Beads were washed on the magnet with 70% ethanol and then air dried for 4 minutes. DNA was eluted in 40µl EB buffer (10 mM Tris-HCl pH 8.0) by pipette mixing (25 times). The remainder of the library construction process (DNA end-repair, A-base addition, adaptor ligation and enrichment) the SPRI cleanup involves addition of PEG buffer (20% PEG and 2.5 M NaCl) to the reaction products. Next, plates were transferred to a magnet plate, incubated for 4 minutes and supernatant removed. Beads are washed on the magnet with 150µl 70% ethanol and air dried for 4 minutes. The DNA is eluted with 40µl of EB buffer (mixing 25 times). Reagent kits are prepared in advance for all enzymatic steps (New England Biolabs). The DNA end-repair was performed by adding 27µl of a master mix (17µl master mix (5µl T4 buffer, 5µl BSA-1mg/ml, 5µl ATP-10mM -2µl dNTPs 10 mM)) plus 5µl T4 PNK enzyme, 5µl T4 polymerase (3 units) to each well. Samples were incubated in a thermal cycler at 12oC for 15 min, 25 oC for 15 min, and finally cooled to 4 oC. The SPRI bead clean up method was used to purify the product (147µl of 20% PEG, 2.5 M NaCl was added to each sample and eluted in 40µl EB). The A-base addition was performed by adding 20µl master mix (17µl A-base add mix, 3µl Klenow to each well and incubated at 37oC for 30 min in a thermal cycler. Product was purified using 132µl PEG buffer and eluted in 19µl EB. Adaptor ligation: was performed by adding 34µl of a master mix (29µl 2x DNA ligase buffer, 5µl DNA ligase) and 5µl indexed oligo adaptors (0.75 uM ) followed by 15min incubation in 25oC in a thermal cycler. Next, ligated products were purified using SPRI bead clean up with size selection (15.5µl of PEG buffer) and eluted in 40µl EB.  The final step of PCR enrichment was was performed by adding 10µl of a master mix (2µl Forward/Reverse Index Primer, 0.5µl dNTP mix, 5µl 10x PfuUltra Buffer, 1µl PfuUltra-II Fusion, 1.5µl Nuclease free water) to each well. Using a thermal cycler, programed to 95C for 2 min, followed by 16 cycles of (95oC for 30 sec, 55oC for 30 sec, 72oC for 60 sec), and a final incubation at 72oC for 10 min. The last SPRI clean up was coupled to size selection (35µl SPRI beads were added to each sample and eluted in 40µl).

treatment_protocol: HDAC blocking was done with 150nM Trichostatin A (TSA, T1952, SIGMA) which was added either to unsynchronized culture or 3 hours after adding the STC for 9 hours.

tag: cell population

value: unsynchronized

tag: tsa treated

value: yes

tag: chip antibody

value: anti H3K9ac (C5B11, Cell Signaling Technologies)


title: H3K9ac Un TSA rep1


title: H3K9ac S TSA rep1

value: synchronized


title: H3K9ac S TSA rep2


title: H3K4me3 Un TSA

value: anti H3K4me3 (C42D8, Cell Signaling Technologies)


title: H3K27ac S rep1

value: no

value: anti H3K27ac (D5E4, Cell Signaling Technologies)


title: H3K27ac S rep2


title: H3K27ac Un rep2


title: H3K27ac Un rep1


title: H3K36me3 Un rep2

value: anti H3K36me3 (D5A7, Cell Signaling Technologies)


title: H3K4me3 S TSA


title: Wild-type Female 7

value: control

value: ovary


title: H3K36me3 S rep2


title: YFP- liver EC, biological replicate 1

tag: strain

value: YFP- (resident liver endothelial cell)


title: Wild-type Female 8

tag: genotype

value: WT


title: Wild-type Female 1


title: H3K9ac Un rep1


title: H3K27me3 Un rep2

value: anti H3K27me3 (C36B11, Cell Signaling Technologies)


title: H3K27me3 S rep2


title: H3K9ac Un rep2


title: CTCF Un rep2

value: anti CTCF G.758.4 (MA5-11187, Invitrogen)


title: H3K4me3 S rep2


title: H3K4me3 Un rep2


title: H3K4me1 S rep2

value: anti H3K4me1 (D1A9, Cell Signaling Technologies)


title: CTCF Un rep1


title: H3K4me1 Un rep2


title: H3K9ac S rep1


title: H3K9ac S rep2


title: H329/13 LB T

value: Gleason 7 Cancer

value: treated with LTP


title: H329/13 LB U

value: Prostate biopsy

value: untreated


title: CTCF S rep2


title: CTCF S rep1


title: WCE Un rep1

value: unsynchronized


title: WCE Un rep2


title: WCE S rep2

value: synchronized


title: WCE S rep1


title: BGC-823 si-YBX1 repeat2

city: nanjing

first: wei

last: de

state: jiangsu

address: longmian da dao

department: Department of Biochemistry and Molecular Biology

institute: Nanjing Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.1.8 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: BGC-823 si-YBX1

growth_protocol: BGC-823 cell lines were cultured in 1640 medium supplemented with 10 % fetal bovine serum (10 % FBS).

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen)
Ion  Proton Sequencing Protocol

treatment_protocol: RNA from BGC-823 cells with HOXC-AS3/YBX1 knockdown and control cells were isolated and quantified.

value: gastric cancer cell line BGC-823

value: YBX1 knockdown


title: BGC-823 HOXC-AS3 ASO repeat3

source_name: BGC-823 HOXC-AS3 ASO

value: HOXC-AS3 ASO

value: HOXC/AS3 knockdown


title: BGC-823 si-YBX1 repeat3


title: BGC-823 si-NC repeat1

source_name: BGC-823 si-NC

value: si-NC

value: control


title: BGC-823 si-YBX1 repeat1


title: BGC-823 si-NC repeat3


title: BGC-823 si-NC repeat2


title: BGC-823 HOXC-AS3 ASO repeat2


title: BGC-823 ASO-NC repeat3

source_name: BGC-823 ASO-NC

value: ASO-NC


title: BGC-823 ASO-NC repeat2


title: BGC-823 HOXC-AS3 ASO repeat1


title: IgG CLIP-seq rep1

city: Beijing

first: Yuanchao

last: Xue

address: Datun Road #15

department: Institute of Biophysics

institute: Chinese Academy of Sciences

description:
rep1 and rep2 were merged for processing
IgG_CLIP-seq.merge.negative.bw
IgG_CLIP-seq.merge.positive.bw

data_processing:
Illumina bcl2fastq-1.8.4 conversion software used for basecalling.
After removing adaptor sequences, the tags longer than 18nt were mapped to the reference mouse genome (mm9) with Bowtie v2.1.0.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using bedtools genomecov v2.17.0 and bedGraphToBigWig v4 software.

source_name: B cells

growth_protocol: The primary B cells were cultured in RPMI1640 medium supplemented with 10% FBS and 100U of Penicillin-Streptomycin in 5% CO2 incubator at 37℃.

extract_protocol:
The spleen was isolated from 8-week-old mice and disrupted in PBS containing 2% fetal bovine serum. Remove aggregates and debris by passing cell suspension through a 70 μm mesh nylon strainer. The untouched and highly purified B cells were isolated from mouse splenocytes by immunomagnetic negative selection following the manufacturer's protocol for EasyStepTM mouse B cell isolate kit (Stem cell, Catalog # 19754).
CLIP-seq was performed as previously described (Xue et al., 2009). Briefly, the 100000000 isolated B cells were irradiated at 400mJ/cm2 with 254nm UV light. The crosslinked cells were lysed and 15ug of ROD1/PTBP3 (Abnova, Catalog # H00009991-M01) or AID (Life Technologies, Catalog # 392500) specific antibody was applied to pull-down protein-RNA complexes. After micrococcal nuclease treatment, 3' RNA linker ligation and 5' end 32P labeling, the immunoprecipitated complexes were fractionated on 10% NuPAGE bis-tris gel and transferred to nitrocellulose membrane. The auto-radiographed ROD1/PTBP3 or AID specific smear bands were cut and treated with Proteinase K to extract respective RNA by phenol and chloroform. The isolated RNA was then added a 5' RNA linker and reverse transcribed by superscript reverse transcriptase III (Life Technologies, catalog# 18080-051). The PCR products were sequenced with Illumina Hiseq 2500 platform. GRO-seq was performed as previously described (Core et al., 2008). Briefly, Splenic B cells from 8-week-old ROD1 WT and KO mice were ex vivo cultured and stimulated by LPS for 3 days. Nuclei was isolated with ice cold swelling buffer (10 mM Tris-HCl, pH 7.5, 2 mM MgCl2, 3 mM CaCl2) and stored in freezing Buffer (40% Glycerol, 5 mM MgCl2, 0.1 mM EDTA, 50 mM Tris-HCl, pH8.3, 2U/ml RNaseOut). 5 x 10^7 nuclei were mixed with an equal volume of reaction buffer (10 mM Tris-Cl pH 8.0, 5 mM MgCl2, 1 mM DTT, 300 mM KCl, 200 U/ml RNaseOut, 1% sarkosyl, 500 uM ATP, GTP, and Br-UTP and 2 µM CTP) and incubated at 30°C for 5 min. The RNA was extracted by Phenol:chloroform and precipitated by ethanol. The pellet resuspended in 20 ul of DEPC-treated water. RNA was then hydrolysed and immunopurified with anti-BrdU beads (Santa Cruz Biotech). The BrdU enriched RNA was polyA-tailed by using a E.coli Poly (A) polymerase and then reverse transcribed, after circulation and relinerization by APE1 (15 U; M0282S, NEB), the cDNA was PCR amplified and gel purified for Illumina HiSeq 2500.

treatment_protocol: Primary B cells were activated by LPS (5ug/ml, Sigma, Catalog #L3024) for 3 days. ROD1/PTBP3 pLKO.1 lentiviral shRNAs (TRCN0000306570, TRCN0000306569 and TRCN0000327080) were purchased from Sigma. shRNA viral particles were used to infect LPS-activated B cells and further selected with puromycin for 3 days to completely deplete ROD1/PTBP3.

value: LPS activated B cells

value: Spleen


title: IgG CLIP-seq rep2


title: GRO-seq WT rep2

description:
GRO-seq_WT_rep2.negative.bw
GRO-seq_WT_rep2.positive.bw


title: GRO-seq ROD1/PTBP3_minus rep2

description:
GRO-seq_ROD1_PTBP3_minus_rep2.negative.bw
GRO-seq_ROD1_PTBP3_minus_rep2.positive.bw

value: B cells depletion of ROD1/PTBP3


title: GRO-seq WT rep1

description:
GRO-seq_WT_rep1.negative.bw
GRO-seq_WT_rep1.positive.bw


title: GRO-seq ROD1/PTBP3_minus rep1

description:
GRO-seq_ROD1_PTBP3_minus_rep1.negative.bw
GRO-seq_ROD1_PTBP3_minus_rep1.positive.bw


title: AID CLIP-seq_ROD1/PTBP3 minus rep1

description:
rep1 and rep2 were merged for processing
AID_CLIP-seq_ROD1_PTBP3_minus.negative.bw
AID_CLIP-seq_ROD1_PTBP3_minus.positive.bw


title: AID CLIP-seq_ROD1/PTBP3 minus rep2


title: ROD1/PTBP3 CLIP_naive rep1

description:
rep1 and rep2 were merged for processing
ROD1_PTBP3_CLIP_naive.negative.bw
ROD1_PTBP3_CLIP_naive.positive.bw

data_processing:
Illumina bcl2fastq-1.8.4 conversion software used for basecalling.
After removing adaptor sequences, the tags longer than 18nt were mapped to the reference mouse genome (mm9) with Bowtie v2.1.0 with the following parameters: -p 10 -L 15 -N 1 -D 50 -R 50 --phred33 --qc-filter --very-sensitive --end-to-end
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using bedtools genomecov v2.17.0 and bedGraphToBigWig v4 software.

extract_protocol:
The spleen was isolated from 8-week-old mice and disrupted in PBS containing 2% fetal bovine serum. Remove aggregates and debris by passing cell suspension through a 70 μm mesh nylon strainer. The untouched and highly purified B cells were isolated from mouse splenocytes by immunomagnetic negative selection following the manufacturer's protocol for EasyStepTM mouse B cell isolate kit (Stem cell, Catalog # 19754).
CLIP-seq was performed as previously described (Xue et al., 2009). Briefly, the 10000000 isolated B cells were irradiated at 400mJ/cm2 with 254nm UV light. The crosslinked cells were lysed and 15ug of ROD1/PTBP3 (Abnova, Catalog # H00009991-M01) or AID (Life Technologies, Catalog # 392500) specific antibody was applied to pull-down protein-RNA complexes. After micrococcal nuclease treatment, 3' RNA linker ligation and 5' end 32P labeling, the immunoprecipitated complexes were fractionated on 10% NuPAGE bis-tris gel and transferred to nitrocellulose membrane. The auto-radiographed ROD1/PTBP3 or AID specific smear bands were cut and treated with Proteinase K to extract respective RNA by phenol and chloroform. The isolated RNA was then added a 5' RNA linker and reverse transcribed by superscript reverse transcriptase III (Life Technologies, catalog# 18080-051). The PCR products were sequenced with Illumina Hiseq 2500 platform.

treatment_protocol: Primary B cells were activated by LPS (5ug/ml, Sigma, Catalog #L3024) for 3 days. ROD1/PTBP3 GIPZ lentiviral shRNAs were purchased from Dharmacon (GE) with catalog # RMM4532-EG230257, which included three different shRNAs and packing mixtures. shRNA viral particles were used to infect LPS-actived B cells for 3 days to completely deplete ROD1/PTBP3.

value: naive B cells


title: AID CLIP-seq rep1

description:
rep1 and rep2 were merged for processing
AID_CLIP-seq.negative.bw
AID_CLIP-seq.positive.bw


title: AID CLIP-seq rep2


title: ROD1/PTBP3 CLIP_naive rep2


title: ROD1/PTBP3 CLIP_activated rep2

description:
rep1 and rep2 were merged for processing
ROD1_PTBP3_CLIP_activated.negative.bw
ROD1_PTBP3_CLIP_activated.positive.bw


title: ROD1/PTBP3 CLIP_activated rep1


title: BGC-823 ASO-NC repeat1


title: H45

city: Shanghai

first: Denghui

last: Liu

state: Shanghai

address: ShengLi Building, 320 Yueyang Road

institute: CAS-MPG Partner Institute for Computational Biology (PICB)

data_processing:
Reads quality was examined by “fastQC”
Filtered reads were aligned to rhesus monkey genome database (AV et al. 2014) by tophat v2.1.0
Only uniquely mapped reads were used to calculate the counts of each gene by HTSeq (Anders et al. 2015).
Reads counts were normalized to library size by DESeq2 , and normalized reads were then used for calculate the FPKM (Fragments Per Kilobase of transcript per Million fragments mapped).
Genome_build: MacaM
Supplementary_files_format_and_content: Contains the expression level of each gene in all samples, measured by FPKM

molecule: polyA RNA

organism: Macaca mulatta

source_name: ICM cell from hatching blastocyst

growth_protocol: Cycling female monkeys were ovarian stimulated by injection of rhFSH (recombinant human follitropin alfa, GONAL-F, Merck Serono) 18 IU twice-daily for 8 days from the onset of menstrual cycle. On day 9, 1000 IU of rhCG (recombinant human chorionic gonadotropin alfa, OVIDREL, Merck Serono) was injected. After 32–35 hr of rhCG administration, mature oocytes were collected by laparoscopic follicular aspiration 63. Oocytes were removed of cumulus cells and those with extrusion of the first polar body (metaphase II stage) were collected for downstream experiments. Successful fertilization was assessed by the presence of two pronuclei. Embryos were then cultured at 37℃, 5% CO2 in 50 μl drops of equilibrated HECM-9 containing 10% FBS (HyClone Laboratories Inc.). Culture medium was changed every other day. Morphologically normal embryos with few fragments were used in the study. 16-cell embryos with good morphology were collected at about E3. Early morulae with compacted blastomeres were collected at about E4. Late morulae with more blastomeres were collected at about E4.5. Early blastocysts having a small cavity were collected at about E5. Middle blastocysts with a cavity occupying around half size of embryos were collected at about E5.5. Late blastocysts with fully expanded cavity were collected at about E6. Hatched blastocysts from the zona pellucida were collected at about E7.

extract_protocol:
To collect single blastomeres, embryos with good quality were transferred into 0.1% Pronase(Merck) in PBS to remove zona pellucida, followed by three washes in 0.05% PVP-PBS. To distinguish the outer and inner cells, embryos were incubated with PKH26 dye (Sigma) which labels the live outer cells with red fluorescence. After labeling, the embryos were washed for three times in PVP-PBS and cut off the blastocele with 1 mL syringe. Then the remaining embryo tissues were rinsed with Ca2+/Mg2+ free PVP-PBS and treated with 0.125% trypsin-EDTA for at least 5 min at 37℃ until the cell surface looks rough. Disaggregating was done by a mouth pipette aided by several finely pulled glass capillaries of different internal diameter. After most cells were separated apart, single cells were individually transferred into small droplets of 0.1% BSA-PBS and the inner/outer cell identity was identified by the fluorescent microscopy. Cells showing no fluorescence were inner cells, whereas those with red fluorescence were outer cells.
Briefly, single cells were washed three times in BSA-PBS and those with a clear round shape were added into cell lysis buffer, followed by First-strand cDNA synthesis and PCR amplification. PCR products were purified by Ampure XP beads and used for libraries construction.
Libraries were deep sequenced on Illumina X-ten platform, using 150-bp paired-end strategy.

tag: Stage

value: hatching blastocyst

tag: position

value: inner cell mass


title: H47


title: H37


title: H35


title: H4


title: H6


title: H8


title: H32


title: H2


title: H39


title: H42


title: H38


title: H5


title: H27


title: H28


title: H24


title: H26


title: H40


title: H22


title: H16


title: H18


title: H1


title: H17


title: L7

source_name: ICM cell from later blastocyst

value: later blastocyst


title: L6


title: L5


title: L9


title: H10


title: H11


title: L8


title: L61


title: L57


title: L56


title: L55


title: L53


title: L52


title: L51


title: L50


title: L4


title: L48


title: L44


title: L49


title: L45


title: L41


title: L47


title: L40


title: H13


title: L59


title: L35


title: L39


title: L36


title: L34


title: L38


title: L28


title: L29


title: L27


title: L25


title: L32


title: L26


title: L33


title: L3


title: L18


title: L21


title: L17


title: L22


title: L16


title: L15


title: L13


title: L14


title: L12


title: HSL79


title: L10


title: HSL23


title: L11


title: HSL2


title: HSL24


title: L31


title: M9

source_name: ICM cell from middle blastocyst

value: middle blastocyst


title: M8


title: M45


title: M5


title: M44


title: M7


title: M4


title: M3


title: M37


title: M36


title: M40


title: M39


title: M55


title: M33


title: M35


title: M32


title: HSL1


title: M41


title: M29


title: M28


title: M6


title: M26


title: M38


title: M22


title: M23


title: M21


title: M20


title: M19


title: M18


title: KW-2450 + Lapatinib for 48hr

city: Sunto-gun

first: Toshio

last: Ota

state: Shizuoka-ken

address: 1188, Shimotogari, Nagaizumi-cho

department: Translational Research Unit

country: Japan

institute: Kyowa Hakko Kirin Co. Ltd.

description: Breast cancer cell line MDA-MB-361 was treated with 100nM KW-2450 + 100nM Lapatinib for 48hr.

hyb_protocol: 1.65 micro grams of labeled cRNA were hybridized onto 4×44 K Human Whole Genome Oligo Microarray Kit G4112F (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instruction, followed by the purification with RNeasy Mini columns (Qiagen, Valencia, CA, USA). Hybridization was carried out at 65C for 17 hours in a hybridization oven rotator. The arrays were washed using GENE expression washing buffers (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instruction.

scan_protocol: Array slides were scanned on a Microarray Scanner Model G2565C (Agilent Technologies, Santa Clara, CA, USA), and Feature Extraction software version 10.7 (Agilent Technologies, Santa Clara, CA, USA) was used for image analysis. The data were analyzed in GeneSpring GX11.02 (Agilent Technologies, Santa Clara, CA, USA).

data_processing: Raw signals were liner-shifted with 65 percentile value of each array as a reference, followed by the baseline transformation by DMSO treatment in each probe.

source_name: breast cancer cell line

label_protocol: Five hundreds nano grams of total RNA was labeled with Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer’s instruction.

growth_protocol: Breast cancer cell line MDA-MB-361 were seeded into 15 cm dishes by 2 x 10^5 cells/mL with assay medium [Leibovit’s L-15 medium supplemented with 10% heat inactivated FBS].

extract_protocol: Total RNA was extracted using TRIzol reagents (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instruction. All RNA samples were quantitated using NanoDrop ND-1000 spectrophotometer (Nanodrop, Wilmington, DE, USA), and RNA quality was analyzed using Bioanalyser 2100 (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Cells were treated with 100 nmol/L KW-2450 and/or 100 nmol/L lapatinib for 48 hours.

value: cancer cell line

tag: cell line

tag: time


title: DMSO for 48hr

description: Breast cancer cell line MDA-MB-361 was treated with DMSO for 48hr.

value: DMSO


title: Vnn Ras (VR) tumor 1

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

institute: CIML

description:
Gene expression data from tumors
ndVR1

hyb_protocol: Following fragmentation and end-labeling, 2 μg of cDNAs were hybridized for 16 hours at 45°C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G at a resolution of 0.7 µm.

data_processing: Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2. The data were RMA normalized in R and Bioconductor, using the oligo package.

source_name: Subcutaneously grown tumor

label_protocol: 3 to 20 ng of total RNA from each sample was used to synthesize biotinylated probes, using the NuGEN Ovation Pico WTA System V2 Kit followed by the NuGEN Encore Biotin Module Kit, according to NuGEN recommendations, with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols

growth_protocol: 2*10^6 tumor cells were subcutaneously grafted on the back of a Nude mouse

extract_protocol: Total RNA was extracted from sorted cell subsets with the Qiagen RNeasy PLUS Micro Kit, according to the manufacturer protocol

treatment_protocol: Tumors were harvested between 2 and 3 weeks depending on their respective growth rate

tag: cell line derived from

value: C57BL/6 mice bearing deficiency for p16 / p19 / Vnn1 genes

value: Vnn Ras (VR) tumor cell line

value: Ras-transformed myofibroblast tumors


title: Vnn Ras (VR) tumor 5

description:
Gene expression data from tumors
ndVR5


title: Vd Ras (VdR)  tumor 4

description:
Gene expression data from tumors
ndVdR4

value: Vd Ras (VdR) tumor cell line


title: Vnn Ras (VR) tumor 2

description:
Gene expression data from tumors
ndVR2


title: Vd Ras (VdR)  tumor 2

description:
Gene expression data from tumors
ndVdR2


title: M24


title: NHP_K_DPI_3

city: Port Saint Lucie

first: Emily

last: Speranza

address: 9801 SW Discovery Wy

department: Florida Research and Innovation Center

institute: Cleveland Clinic Lerner Research Institute

description: Ebola Makona infected Non-Human Primate

data_processing:
Raw files were filtered for read quality and length using the fastx-toolkit
Alignments were generated using Tophat which calls Bowtie2
Counts were generated with HTSeq-count
Genome_build: Rhesus Macaque
Supplementary_files_format_and_content: Count files as a tab delimiated text file

source_name: Whole Blood

growth_protocol: Whole blood samples were collected from NHPs at various days post Ebola Makona infection and treated with Trizol LS at a ratio of 1:3 of blood to Trizol

extract_protocol:
Extration was done following the standard Trizol protocol
Libraries were contstructed using the Illumina Ribo Zero prep kit

treatment_protocol: Samples were inactivated with Trizol LS

tag: dpi


title: NHP_K_DPI_7

description: Ebola Makona infected Non-Human Primate


title: NHP_K_DPI_-13

description: Ebola Makona infected Non-Human Primate


title: NHP_L_DPI_3

description: Ebola Makona infected Non-Human Primate


title: NHP_L_DPI_0

description: Ebola Makona infected Non-Human Primate


title: NHP_K_DPI_5

description: Ebola Makona infected Non-Human Primate


title: NHP_L_DPI_-13

description: Ebola Makona infected Non-Human Primate


title: Ras (R) tumor 5

description:
Gene expression data from tumors
ndR5

value: Ras (R) tumor cell line


title: Ras (R) tumor 4

description:
Gene expression data from tumors
ndR4


title: Lapatinib for 48hr

description: Breast cancer cell line MDA-MB-361 was treated with 100nM Lapatinib for 48hr.

value: Lapatinib


title: Vd Ras (VdR)  tumor 1

description:
Gene expression data from tumors
ndVdR1


title: KW-2450 for 48hr

description: Breast cancer cell line MDA-MB-361 was treated with 100nM KW-2450 for 48hr.


title: M17


title: NHP_J_DPI_7

description: Ebola Makona infected Non-Human Primate


title: NHP_K_DPI_0

description: Ebola Makona infected Non-Human Primate


title: Vd Ras (VdR)  tumor 5

description:
Gene expression data from tumors
ndVdR5


title: M16


title: Ras (R) tumor 2

description:
Gene expression data from tumors
ndR2


title: Ras (R) tumor 1

description:
Gene expression data from tumors
ndR1


title: NHP_J_DPI_5

description: Ebola Makona infected Non-Human Primate


title: Vnn Ras (VR) tumor 4

description:
Gene expression data from tumors
ndVR4


title: M15


title: NHP_J_DPI_0

description: Ebola Makona infected Non-Human Primate


title: NHP_J_DPI_-13

description: Ebola Makona infected Non-Human Primate


title: NHP_J_DPI_3

description: Ebola Makona infected Non-Human Primate


title: NHP_I_DPI_5

description: Ebola Makona infected Non-Human Primate


title: M14


title: M11


title: NHP_H_DPI_3

description: Ebola Makona infected Non-Human Primate


title: NHP_I_DPI_3

description: Ebola Makona infected Non-Human Primate


title: HSM2


title: NHP_I_DPI_0

description: Ebola Makona infected Non-Human Primate


title: NHP_I_DPI_-13

description: Ebola Makona infected Non-Human Primate


title: NHP_H_DPI_NEC

description: Ebola Makona infected Non-Human Primate

value: NEC


title: M13


title: NHP_H_DPI_-13

description: Ebola Makona infected Non-Human Primate


title: M10


title: NHP_G_DPI_7

description: Ebola Makona infected Non-Human Primate


title: NHP_H_DPI_5

description: Ebola Makona infected Non-Human Primate


title: NHP_G_DPI_3

description: Ebola Makona infected Non-Human Primate


title: E9

source_name: ICM cell from early blastocyst

value: early blastocyst


title: NHP_F_DPI_7

description: Ebola Makona infected Non-Human Primate


title: NHP_G_DPI_0

description: Ebola Makona infected Non-Human Primate


title: NHP_I_DPI_7

description: Ebola Makona infected Non-Human Primate


title: NHP_F_DPI_5

description: Ebola Makona infected Non-Human Primate


title: E7


title: NHP_F_DPI_-13

description: Ebola Makona infected Non-Human Primate


title: NHP_F_DPI_3

description: Ebola Makona infected Non-Human Primate


title: M12


title: HSM1


title: NHP_G_DPI_5

description: Ebola Makona infected Non-Human Primate


title: NHP_H_DPI_0

description: Ebola Makona infected Non-Human Primate


title: NHP_F_DPI_0

description: Ebola Makona infected Non-Human Primate


title: E8


title: NHP_G_DPI_-13

description: Ebola Makona infected Non-Human Primate


title: NHP_E_DPI_-13

description: Ebola Makona infected Non-Human Primate


title: NHP_E_DPI_NEC1

description: Ebola Makona infected Non-Human Primate


title: NHP_E_DPI_5

description: Ebola Makona infected Non-Human Primate


title: E5


title: E6


title: E48


title: NHP_F_DPI_NEC

description: Ebola Makona infected Non-Human Primate


title: E4


title: NHP_E_DPI_3

description: Ebola Makona infected Non-Human Primate


title: NHP_D_DPI_NEC

description: Ebola Makona infected Non-Human Primate


title: MDA231-LM2_Spheres, biological replicate 2

city: Heidelberg

first: Jacob

last: Insua-Rodríguez

state: Baden-Württemberg

address: Im Neuenheimer Feld 280

department: Division of Stem Cells and Cancer

institute: German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ)

description: Gene expression of MDA231-LM2 cells cultured as oncospheres

hyb_protocol: 11 ug of fragmented and labeled cRNA were hybridized for 17 hours at 45°C on Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays, according to user manual GeneChip® 3' IVT PLUS Reagent Kit, P/N 703210.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays  (P/N 702731)

data_processing: The raw data was processed using R and bioconductor package affy; normalization method is quantile normalization.

source_name: MDA231-LM2 breast cancer cells, cultured as oncospheres

label_protocol: The Affymetrix Gene Chip 3´IVT PLUS Reagent Kit was used to generate labeled single-stranded cRNA from input amounts of 100ng total RNA. The label used was biotin.

growth_protocol: Layer cultures of MDA231-LM2 cells were grown in DMEM GlutaMAX supplemented with 10% vol/vol fetal bovine serum (FBS), 100 IU/ml penicillin, 100 μg/ml streptomycin and 1 μg/ml amphotericin B. Sphere cultures of MDA231-LM2 cells were grown in HuMEC medium supplemented with 5 μg/ml human insulin, 20 ng/ml epidermal growth factor (EGF), 10 ng/ml basic fibroblast growth factor (bFGF) and 2% vol/vol B27 supplement.

extract_protocol: RNA extraction was performed using the RNEasy Kit (Qiagen) according to manufacturer's instructions

treatment_protocol: For Layer treatment, MDA231-LM2 cells were seeded at a density of approximately 28.000 cells/cm2 and let to attach to the culture dish overnight. Then cell medium was renewed and cells were cultured in regular conditions for 48h. For Spheres treatment, MDA231-LM2 cells were seeded in ultra-low adhesive plates at a density of 25.000 cells/ml and cultivated for 4 days.

tag: tissue type

value: breast cancer

tag: cell morphology

value: Spheres


title: E47


title: NHP_D_DPI_9

description: Ebola Makona infected Non-Human Primate


title: MDA231-LM2_Spheres, biological replicate 1


title: NHP_D_DPI_7

description: Ebola Makona infected Non-Human Primate


title: NHP_D_DPI_5

description: Ebola Makona infected Non-Human Primate


title: NHP_E_DPI_NEC2

description: Ebola Makona infected Non-Human Primate


title: NHP_D_DPI_3

description: Ebola Makona infected Non-Human Primate


title: NHP_E_DPI_0

description: Ebola Makona infected Non-Human Primate


title: E45


title: MDA231-LM2_Layer, biological replicate 1

description: Gene expression of MDA231-LM2 cells cultured as a monolayer

source_name: MDA231-LM2 breast cancer cells, cultured as a monolayer

value: Layer


title: NHP_C_DPI_5

description: Ebola Makona infected Non-Human Primate


title: NHP_C_DPI_0

description: Ebola Makona infected Non-Human Primate


title: NHP_D_DPI_0

description: Ebola Makona infected Non-Human Primate


title: NHP_C_DPI_7

description: Ebola Makona infected Non-Human Primate


title: NHP_B_DPI_7

description: Ebola Makona infected Non-Human Primate


title: E42


title: E43


title: NHP_B_DPI_3

description: Ebola Makona infected Non-Human Primate


title: NHP_B_DPI_0

description: Ebola Makona infected Non-Human Primate


title: E46


title: MDA231-LM2_Layer, biological replicate 3


title: E44


title: NHP_A_DPI_7

description: Ebola Makona infected Non-Human Primate


title: NHP_B_DPI_NEC

description: Ebola Makona infected Non-Human Primate


title: E40


title: MDA231-LM2_Layer, biological replicate 2


title: MDA231-LM2_Paclitaxel, biological rep3

source_name: MDA231-LM2 breast cancer cells, treated with paclitaxel 5nM, 48h

growth_protocol: MDA231-LM2 cells were grown in DMEM GlutaMAX supplemented with 10% vol/vol fetal bovine serum (FBS), 100 IU/ml penicillin, 100 μg/ml streptomycin and 1 μg/ml amphotericin B.

treatment_protocol: MDA231-LM2 cells were seeded at a density of approximately 28.000 cells/cm2 and let to attach to the culture dish overnight. Then cells were treated with either a vehicle control (DMSO) or 5nM paclitaxel for 48h prior to lysis for RNA extraction.

tag: treatment


title: NHP_A_DPI_5

description: Ebola Makona infected Non-Human Primate


title: MDA231-LM2_Paclitaxel, biological rep1


title: MDA231-LM2_Paclitaxel, biological rep2


title: MDA231-LM2_DMSO_Vehicle, biological rep3

source_name: MDA231-LM2 breast cancer cells, treated with DMSO vehicle, 48h


title: NHP_A_DPI_NEC

description: Ebola Makona infected Non-Human Primate


title: MDA231-LM2_DMSO_Vehicle, biological rep2


title: NHP_B_DPI_5

description: Ebola Makona infected Non-Human Primate


title: E3


title: MDA231-LM2_DMSO_Vehicle, biological rep1


title: NHP_A_DPI_-13

description: Ebola Makona infected Non-Human Primate


title: NHP_A_DPI_3

description: Ebola Makona infected Non-Human Primate


title: MDA231-LM2_JNKi, biological replicate 3

description: Gene expression of MDA231-LM2 cells treated with the JNK inhibitor CC-401 (4µM)

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays  (P/N 702731).

source_name: MDA231-LM2 breast cancer cells, treated with JNK inhibitor CC-401 4 µM, 48h

extract_protocol: RNA extraction was performed using the RNEasy Kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: MDA231-LM2 cells were seeded at a density of approximately 28.000 cells/cm2 and let to attach to the culture dish overnight. For active JNK overexpression, cells transduced with an empty vector (Control), MKK7-JNK or MKK7-JNK(mut) were cultured in regular conditions for 48h prior to RNA extraction. For JNK inhibition, cells were treated with the JNK inhibitor CC-401 (4 µM) or a DMSO vehicle control (Vehicle) for 48h.


title: E41


title: E38


title: E37


title: E36


title: MDA231-LM2_Spheres, biological replicate 3


title: +TIR +auxin, no treatment 2hr fp

city: Berkeley

first: Gloria

last: Brar

address: 626 Barker Hall

department: MCB

institute: UC Berkeley

description:
processed data file: April2017_auxin_QEXP.txt
J FP

data_processing:
Basecalls performed with CASAVA bcl2fastq_v2.17
reads were trimmed
trimmed reads were aligned using bowtie2 and excluding multiple alignments
ribosome footprint reads were assigned to one genomic position based on a-site analysis of fragment length distribution
Genome_build: sk1_revised_100331 (published in Brar et. al, Science, 2012)
Supplementary_files_format_and_content: txt matrix files of RPKM measurements using standard SGD genome annotations

source_name: +TIR +auxin_no treatment

growth_protocol: Strains were grown in YEPD(2%) at 30C, with shaking. Plate-based growth assays were carried out on YEPD(4%) plates at 30C.

extract_protocol:
For ribosome profiling, cells were flash frozen and mixermilled at -80 together with ribosome profiling lysis buffer, extract was clarified with a low and high speed spin, all as described in Ingolia et. al, Science, 2009. For mRNA, cells were flash frozen and lysed using hot acid phenol and SDS as described in Ingolia et al., Science, 2009
As described in Ingolia et al, Science 2009

treatment_protocol:
For the hac1 delete experiment: After approximately 2 doublings, cultures were split into 3 subcultures. Per strain, a first subculture received no treatment, a second was treated with 5mM DTT, and a third was treated with 2μg/mL Tm (Calbiochem).
For the auxin experiment: After approximately 2 doublings, cultures were split into 2 subcultures. Per strain, one subculture was treated with 500μM auxin (Sigma) and 4μM IP6 (Sigma) and the other with equivalent volumes of DMSO and water. After 15 min, the subcultures treated with auxin and IP6 were further split into 2 subcultures. Per strain, 1 auxin-pre-treated culture was not treated further (+auxin), and 1 was treated with 5mM DTT (+auxin +DTT). For each strain, the DMSO pre-treated subculture was treated with 5mM DTT (+DTT +vehicle).

tag: strain background

value: +TIR

tag: treated with

value: +auxin, no treatment

tag: molecule subtype

value: ribosome footprints


title: +TIR +DMSO, +DTT 2hr fp

description:
processed data file: April2017_auxin_QEXP.txt
K FP

source_name: +TIR +DMSO_+DTT

tag: genotype/variation

value: +DMSO, +DTT


title: +TIR +auxin, no treatment 1hr fp

description:
processed data file: April2017_auxin_QEXP.txt
G FP


title: +TIR +DMSO, +DTT 1hr fp

description:
processed data file: April2017_auxin_QEXP.txt
H FP


title: NHP_A_DPI_0

description: Ebola Makona infected Non-Human Primate


title: +TIR +auxin +DTT 1hr fp

description:
processed data file: April2017_auxin_QEXP.txt
I FP

source_name: +TIR +auxin +DTT

value: +auxin +DTT


title: E35

value: inner cell mass


title: E34


title: no TIR +DMSO, +DTT 2hr fp

description:
processed data file: April2017_auxin_QEXP.txt
E FP

source_name: no TIR +DMSO_+DTT

value: no TIR


title: no TIR +auxin +DTT 1hr fp

description:
processed data file: April2017_auxin_QEXP.txt
C FP

source_name: no TIR +auxin +DTT


title: no TIR +DMSO, +DTT 1hr fp

description:
processed data file: April2017_auxin_QEXP.txt
B FP


title: +TIR +DMSO, +DTT 2hr mRNA

description:
processed data file: April2017_auxin_QEXP.txt
K mRNA

value: mRNA


title: +TIR +auxin +DTT 2hr mRNA

description:
processed data file: April2017_auxin_QEXP.txt
L mRNA


title: E32


title: E33


title: no TIR +auxin +DTT 2hr fp

description:
processed data file: April2017_auxin_QEXP.txt
F FP


title: no TIR +auxin, no treatment 1hr fp

description:
processed data file: April2017_auxin_QEXP.txt
A FP

source_name: no TIR +auxin_no treatment


title: E31


title: MDA231-LM2_JNKi, biological replicate 2


title: MDA231-LM2_JNKi, biological replicate 1


title: MDA231-LM2_DMSO_Vehicle, biological replicate 2

description: Gene expression of MDA231-LM2 cells treated with a DMSO vehicle control


title: MDA231-LM2_DMSO_Vehicle, biological replicate 3


title: MDA231-LM2_pLVX-Puro-MKK7-JNK(mut), biological replicate 3

description: Gene expression of MDA231-LM2 cells overexpressing an inactive form of Jnk1a1

source_name: MDA231-LM2 breast cancer cells, transduced with pLVX-Puro-Flag-MKK7B2Jnk1a1(APF)

value: Untreated


title: MDA231-LM2_DMSO_Vehicle, biological replicate 1


title: MDA231-LM2_pLVX-Puro-MKK7-JNK(mut), biological replicate 2


title: MDA231-LM2_pLVX-Puro-MKK7-JNK, biological replicate 3

description: Gene expression of MDA231-LM2 cells overexpressing a constitutively active form of Jnk1a1

source_name: MDA231-LM2 breast cancer cells, transduced with pLVX-Puro-Flag-MKK7B2Jnk1a1


title: +TIR +auxin +DTT 2hr fp

description:
processed data file: April2017_auxin_QEXP.txt
L FP


title: +TIR +auxin, no treatment 2hr mRNA

description:
processed data file: April2017_auxin_QEXP.txt
J mRNA


title: MDA231-LM2_pLVX-Puro-MKK7-JNK(mut), biological replicate 1


title: +TIR +DMSO, +DTT 1hr mRNA

description:
processed data file: April2017_auxin_QEXP.txt
H mRNA


title: no TIR +auxin +DTT 2hr mRNA

description:
processed data file: April2017_auxin_QEXP.txt
F mRNA


title: +TIR +auxin, no treatment 1hr mRNA

description:
processed data file: April2017_auxin_QEXP.txt
G mRNA


title: +TIR +auxin +DTT 1hr mRNA

description:
processed data file: April2017_auxin_QEXP.txt
I mRNA


title: E30


title: no TIR +auxin, no treatment 1hr mRNA

description:
processed data file: April2017_auxin_QEXP.txt
A mRNA


title: E2


title: E29


title: no TIR +DMSO, +DTT 1hr mRNA

description:
processed data file: April2017_auxin_QEXP.txt
B mRNA


title: 4431 Tm fp

description:
processed data file: Dec2016_qexpr_rpkm_MERGE.txt
4431 Tm fp merge rpkm

source_name: vegetative exponential hac1 delete cells treated with Tm

value: hac1 deleted

value: 2μg/mL Tm


title: no TIR +auxin +DTT 1hr mRNA

description:
processed data file: April2017_auxin_QEXP.txt
C mRNA


title: E28


title: E27


title: 4431 DTT fp

description:
processed data file: Dec2016_qexpr_rpkm_MERGE.txt
4431 DTT fp merge rpkm

source_name: vegetative exponential hac1 delete cells treated with DTT

value: 5mM DTT


title: H3K36me3 Un rep1

tag: cell population

value: unsynchronized

tag: tsa treated

value: no

value: anti H3K36me3 (D5A7, Cell Signaling Technologies)


title: E26

value: early blastocyst


title: H3K36me3 S rep1

value: synchronized

tag: chip antibody


title: MDA231-LM2_pLVX-Puro-MKK7-JNK, biological replicate 2

value: breast cancer


title: MDA231-LM2_pLVX-Puro-MKK7-JNK, biological replicate 1


title: 4431 fp

description:
processed data file: Dec2016_qexpr_rpkm_MERGE.txt
4431 fp merge rpkm

source_name: vegetative exponential hac1 delete cells untreated

value: none (untreated)


title: 1362 dtt fp

description:
processed data file: Dec2016_qexpr_rpkm_MERGE.txt
1362 dtt fp merge rpkm

source_name: vegetative exponential WT cells treated with DTT

value: WT


title: MDA231-LM2_pLVX-Puro-Empty, biological replicate 3

description: Gene expression of MDA231-LM2 cells bearing a control pLVX-Puro-Empty lentiviral plasmid

source_name: MDA231-LM2 breast cancer cells, transduced with pLVX-Puro-Empty


title: 1362 fp

description:
processed data file: Dec2016_qexpr_rpkm_MERGE.txt
1362 fp merge rpkm

source_name: vegetative exponential WT cells untreated


title: MDA231-LM2_pLVX-Puro-Empty, biological replicate 2


title: H3K27me3 Un rep1

value: anti H3K27me3 (C36B11, Cell Signaling Technologies)


title: 1362 Tm fp

description:
processed data file: Dec2016_qexpr_rpkm_MERGE.txt
1362 Tm fp merge rpkm

source_name: vegetative exponential WT cells treated with Tm


title: MDA231-LM2_pLVX-Puro-Empty, biological replicate 1


title: E25

source_name: ICM cell from early blastocyst


title: no TIR +DMSO, +DTT 2hr mRNA

description:
processed data file: April2017_auxin_QEXP.txt
E mRNA

value: +DMSO, +DTT


title: 4431 mRNA Tm

description:
processed data file: Dec2016_qexpr_rpkm_MERGE.txt
4431 mRNA Tm merge rpkm

value: ribosome footprints


title: H3K27me3 S rep1


title: 4431 mrna

description:
processed data file: Dec2016_qexpr_rpkm_MERGE.txt
4431 mrna merge rpkm


title: 4431 DTT mrna

description:
processed data file: Dec2016_qexpr_rpkm_MERGE.txt
4431 DTT mrna merge rpkm


title: 1362 Tm mrna

description:
processed data file: Dec2016_qexpr_rpkm_MERGE.txt
1362 Tm mrna merge rpkm


title: H3K4me3 Un rep1

value: anti H3K4me3 (C42D8, Cell Signaling Technologies)


title: 1362 DTT mrna

description:
processed data file: Dec2016_qexpr_rpkm_MERGE.txt
1362 DTT mrna merge rpkm


title: E21

value: inner cell mass


title: H3K4me3 S rep1


title: E20


title: E1


title: X2

description: Total RNA from whole blood from Ebola Makona infected Ferrets

data_processing:
Raw sequencing files were filtered for short or poor quality reads using the fastx-toolkit
Reads were aligned using tophat which calls bowtie2
Count files were generated using HT-Seq count
Genome_build: Ferret Genome
Supplementary_files_format_and_content: Counts as tab delimated files

organism: Mustela putorius furo

source_name: Whole Blood

extract_protocol:
RNA was extracted following the standard Trizol protocol
NEBNext Ultra II

treatment_protocol: Whole blood was collected from ferrets following Ebola Makona infection were inactivated with Trizol


title: E19


title: X1


title: H3K4me1 Un rep1

value: anti H3K4me1 (D1A9, Cell Signaling Technologies)


title: H3K4me1 S rep1


title: E23


title: X3


title: X10


title: RNA pol II Un rep1

value: anti RNA polymerase II 8WG16 (ab817, Abcam)


title: RNA pol II Un rep2


title: E18


title: E17


title: E16


title: X4


title: X9


title: X11


title: E15


title: RNA pol II S rep2


title: RNA pol II S rep1


title: X12


title: E14


title: X13


title: 1362 mrna

description:
processed data file: Dec2016_qexpr_rpkm_MERGE.txt
1362 mrna merge rpkm


title: RNA pol II Un WCE rep2


title: E13


title: RNA pol II Un WCE rep1


title: X14


title: E12


title: X15


title: HEKn_diff_siZNF185rep2

city: Rome

first: Artem

last: Smirnov

address: Via Montpellier, 1

department: Dept. of Exp. Medicine and Surgery

country: Italy

institute: University of Rome "Tor Vergata"

description: Gene expression after silencing with siZNF185 siRNA

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human 8x60k Microarrays (G4858A) 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 DNA Microarray Scanner (G2505B) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.3.7.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 039494_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Normal human epidermal keratinocytes differentiated

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng RNA using the Low Input Quick Amp LabellingKit One colour (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Normal human epidermal keratinocytes were purchased from Invitrogen. Cells were cultured in EpiLife medium with Human Keratinocyte Growth Supplements added (Life Technologies) at 37°C in 5% CO2.  Experiments were carried out at passage 2.

extract_protocol: Cells were lysed with RLT lysis buffer and total RNA was extracted with RNeasy mini kit (Qiagen, cat. no. 74104) including DNA digestion with DNase I (Qiagen, cat. no. 79254). RNA was quantified using a NanoDrop-1000 spectrophotometer. The quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 2.5 million of HEKn were transfected with either siCTRL siRNA (Qiagen, cat. no. SI03650318, 80 pmol) or siZNF185 siRNA (Qiagen, cat. no. SI04156320, 80 pmol) using Lipofectamine RNAiMAX transfection reagent (Invitrogen). After 48 h cells were induced for differentiation by adding of 1.2 mM calcium chloride for 3 days.

tag: cell type

value: Normal human epidermal keratinocytes


title: HEKn_diff_siZNF185rep3


title: HEKn_diff_siZNF185rep4

treatment_protocol: 2.5*105Cells were transfected with either siCTRL siRNA (Qiagen, cat. no. SI03650318, 80 pmol) or siZNF185 siRNA (Qiagen, cat. no. SI04156320, 80 pmol) using Lipofectamine RNAiMAX transfection reagent (Invitrogen). After 48 h cells were induced for differentiation by adding of 1.2 mM CaCl2 for 3 days


title: HEKn_diff_siCTRLrep3

description: Gene expression after silencing with control siRNA

treatment_protocol: 2.5 millions of HEKn were transfected with either siCTRL siRNA (Qiagen, cat. no. SI03650318, 80 pmol) or siZNF185 siRNA (Qiagen, cat. no. SI04156320, 80 pmol) using Lipofectamine RNAiMAX transfection reagent (Invitrogen). After 48 h cells were induced for differentiation by adding of 1.2 mM calcium chloride for 3 days.


title: HEKn_diff_siCTRLrep4


title: X16


title: HEKn_diff_siZNF185rep1


title: RNA pol II S WCE rep1


title: E10

tag: Stage


title: HEKn_diff_siCTRLrep1


title: HEKn_diff_siCTRLrep2


title: RNA pol II S WCE rep2


title: vIRF1 (1) GF200 002

status: Public on Aug 25 2018

city: NANJING

first: WAN

last: LI

state: JIANGSU

address: 101Longmian Avenue

description: Product=miRCURY LNA microRNA Array, 7th generation - hsa, mmu & rno;Supplier=Exiqon A/S;ProductNumber=208500,208501,208502,208510

hyb_protocol: hyb protocol See  manufacturer's website

scan_protocol: Slides were scanned by Axon GenePix 4000B microarray scanner  (GF200_001 and GF200_002 ) or Agilent Microarray Scanner(GF200_003,GF200_004,GF200_005 and GF200_006 )

data_processing:
The scanned images were analyzed with GenePix pro V6.0(GF200_001 and GF200_002 ) or Agilent GeneSpring GX v12.1(GF200_003,GF200_004,GF200_005 and GF200_006 )
Processed data files include normalized signal intensity.

source_name: HUVECs were transduced with lentiviral vIRF1

label_protocol: miRNA labeling Kits : miRCURYTM Array Power Labeling kit (Cat #208032-A, Exiqon)(GF200_001 and GF200_002 ) or Agilent miRNA Commplete Labeling and Hyb Kit(GF200_003,GF200_004,GF200_005 and GF200_006 )

growth_protocol: HUVECs were cultured in complete EBM-2 culture media  (LONZA, Allendale, NJ, USA)

extract_protocol: Pellet cells by centrifugation. Lyse cells in TRIzol Reagent by repetitive pipetting. Use 1 ml of the reagent per 5-10 × 10^6 of  cells. Washing cells before addition of TRIzol Reagent should be avoided as this increases the possibility of mRNA degradation. Disruption of some yeast and bacterial cells may require the use of a homogenizer.

treatment_protocol: HUVECs were transduced with vIRF1 or control lentivirus (pHAGE), respectively.

value: HUVEC

tag: transduced with

value: lentiviral vIRF1


title: pHAGE of vIRF1(1) GF200 001

source_name: HUVECs were transduced with control lentivirus (pHAGE)

value: control lentivirus (pHAGE)


title: SW-948_EXO_wt

first: Jan

last: Provaznik

state: Baden-Wuerttemberg

address: Meyerhofstr. 1

department: Genomics Core Facility

institute: EMBL Heidelberg

description: miRNA

hyb_protocol: Hybridization was done as described in miRNA Microarray System protocol v 1.7 from Agilent Technologies

scan_protocol: Scanning was done on Agilent Microarray Scanner G2565BA, Agilent Scan Control Software,

data_processing:
IPA was used for miRNA analysis and for correlating miRNA with protein expression after predicted targets were selected by miRNA databases (http://www.microrna.org, http://www.targetscan.org). For pathway analysis PANTHER (http://pantherdb.org), KEGG (http://www.kegg.jp), Reactome (https://reactome.org), and STRING (http://string-db.org) databases were used
after normalization, data were compared between identical non-transfected versus transfected cells and exosomes, respectively. In most instances, 2-fold differences were considered significant. In exosome preparations, 1.5-fold differences were occassionally included. For processed data, the program suggestions were followed.

source_name: exosome

label_protocol: Labeling was done as described in miRNA Microarray System protocol v 1.7 from Agilent Technologies

growth_protocol:
The human pancreatic adenocarcinoma lines A818.4 and Capan-1 are maintained in RPMI1640/10%FCS/pyruvate/L-glutamine/antibiotics. Confluent cells are trypsinized and split.
A818.4-Tspan8kd, A818.4-CD151kd, A818.4-CD44v6kd, Capan-1-CD44v6kd  cells were derived from transfection with shRNA (Qiagen, Hilden, Germany) and maintained in RPMI1640/10%FCS/pyruvate/L-glutamine/antibiotics containing 0.5µg/ml G418. Single cell kd clones were derived by 2 rounds of single cell cloning.
The human colorectal cancer lines HT29 and SW948 are maintained in RPMI1640/10%FCS/L-glutamine/antibiotics. Confluent cells are trypsinized and split.
Ht29-cld7 kd, SW948-cld7 kd and SW948-CD44v6 kd lines were derived from transfection with shRNA (Qiagen, Hilden, Germany) and maintained in RPMI1640/10%FCS/pyruvate/L-glutamine/antibiotics containing 0.5µg/ml G418. Single cell kd clones were derived by 2 rounds of single cell cloning.

extract_protocol: Cell and exosome mRNA/microRNA was extracted using the miRNeasyMinikit following the supplier's suggestion (Qiagen, Hildesheim, Germany). Exosomes were pretreated with RNAse to avoid contamination by attached free mRNA.

treatment_protocol: Cells have not undergone any special treatment. All exosome preparation were derived from culture supernatant after cells have been cultured in serum-free medium for 48h-72h. Culture supernatant was collected and cleared (2x10min, 500g, 1x20min, 2000g, 1x30min, 10000g), filter sterizied (0.2µm) and were centrifuged (120min, 100000g). The pellet was washed (PBS, 120min, 100000g), resuspended in 40% sucrose overlaid by a discontinuous sucrose gradient (30%-5%) and centrifuged (16h, 100000g). Exosomes were collected from the 10%-5% sucrose interface (light density fractions, d: 1.15-1.56g/ml).

tag: cell line

value: colorectal cancer

tag: cell compartment

value: exosome

tag: condition

value: wt


title: INPUT_22Rv1_delSite1_Clone11/12-D8_rep2

city: Los Angeles

first: Yu

middle: (Phoebe)

last: Guo

state: California

address: 1450 Biggy Street, NRT 6514

institute: Univ. of Southern California

data_processing:
Sequencing results were aligned to hg19 using bwa
Peaks were called using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: BED files containing ChIP-seq peaks

source_name: 22Rv1 cells

growth_protocol: 22Rv1 cells were grown according to ATCC protocol

extract_protocol:
Chromatins were prepared using the protocol previously published (PMID: 29429977). Briefly, cells were crosslinked by 1%formedelhyde for 10 mins and lysised into nuclei. Nuclei were sonicated using BioRuptor to break into chromatin fragments.
Libraries were prepared using KAPA Hyper Prep Kit (Kapa #KK8505) according to provided protocol

value: prostate carcinoma cell line 22Rv1

tag: genotype

value: Site 1 complete deletion (chr1:154850252-154851859 in hg19)

tag: grna used

tag: clone number


title: H3K27Ac_22Rv1_delSite1_Clone11/12-D8_rep2

value: Histone H3 acetyl Lys27 rabbit pAb (Active Motif, catalog# 39133, lot# 31814008)


title: H3K27Ac_22Rv1_delSite1_Clone11/12-F6_rep2


title: H3K27Ac_22Rv1_delSite1_Clone11/12-F6_rep1


title: H3K27Ac_22Rv1_delSite4_Clone22/23-F8_rep1

value: Site 4 complete deletion (chr12:53272450-53275325 in hg19)


title: A818.4_EXO_Tspan8 Kd

description: miRNA

value: pancreatic adenocarcinoma

value: Tspan8 Kd


title: Capan-1_EXO_CD44v6 Kd_2

description: miRNA

value: CD44v6 Kd


title: SW-948_EXO_Cld7 Kd

description: miRNA

value: Cld7 Kd


title: INPUT_22Rv1_delSite4_Clone22/23-F8_rep1


title: INPUT_22Rv1_delSite1_Clone11/12-F6_rep2


title: A818.4 EXO_wt

description:
miRNA
HCX_07

scan_protocol: Scanning was done on Agilent Microarray Scanner G2565C

data_processing:
IPA was used for miRNA analysis and for correlating miRNA with protein expression after predicted targets were selected by miRNA databases (http://www.microrna.org, http://www.targetscan.org). For pathway analysis PANTHER (http://pantherdb.org), KEGG (http://www.kegg.jp), Reactome (https://reactome.org), and STRING (http://string-db.org) databases were used
after normalization, data were compared between identical non-transfected versus transfected cells and exosomes, respectively. In most instances, 2-fold differences were considered significant. In exosome preparations, 1.5-fold differences were occassionally included. For processed data, the programm suggestions were followed.

growth_protocol:
The human pancreatic adenocarcinoma lines  lines A818.4 and Capan-1 are maintained in RPMI1640/10%FCS/pyruvate/L-glutamine/antibiotics. Confluent cells are trypsinized and split.
A818.4-Tspan8kd, A818.4-CD151kd, A818.4-CD44v6kd, Capan-1-CD44v6kd  cells were derived from transfection with shRNA (Qiagen, Hilden, Germany) and maintained in RPMI1640/10%FCS/pyruvate/L-glutamine/antibiotics containing 0.5µg/ml G418. Single cell kd clones were derived by 2 rounds of single cell cloning.
The human colorectal cancer lines HT29 and SW948 are maintained in RPMI1640/10%FCS/L-glutamine/antibiotics. Confluent cells are trypsinized and split.
Ht29-cld7 kd, SW948-cld7 kd and SW948-CD44v6 kd lines were derived from transfection with shRNA (Qiagen, Hilden, Germany) and maintained in RPMI1640/10%FCS/pyruvate/L-glutamine/antibiotics containing 0.5µg/ml G418. Single cell kd clones were derived by 2 rounds of single cell cloning.


title: 22Rv1_wildType_clone-G6

data_processing:
RNA-seq results were aligned to Gencode v19 and reads were counted using STAR
Read count table is generated using STAR as well
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count for each gene

extract_protocol:
Total RNA were extracted following the trizol protocol
Libraries were prepared using Kapa Stranded mRNA kit with beads (Kapa #KK8421) according to provided protocol

value: Wild type clone


title: HT-29_EXO_Cld7 Kd

description: miRNA


title: H3K27Ac_22Rv1_delSite1_Clone11/12-D8_rep1


title: Capan-1 EXO_wt

description:
miRNA
HCX_08

value: Capan-1 EXO


title: SW-948_wt_2

description:
miRNA
HCX_05

source_name: whole cell

value: whole cell


title: HT-29_EXO_wt

description: miRNA


title: A818.4_EXO_CD44v6 Kd

description: miRNA


title: SW-948_Cld7 Kd

description:
miRNA
HCX_06


title: SW-948_CD44v6 Kd

description:
miRNA
HCX_04


title: A818.4_EXO_CD151 Kd

description: miRNA

value: CD151 Kd


title: 22Rv1_wildType_clone-C6


title: 22Rv1_wildType_clone-A4


title: 22Rv1_delSite4_Clone22/23-F8_rep3


title: A818.4_CD44v6 Kd

description:
miRNA
HCX_01


title: 22Rv1_delSite4_Clone22/23-F8_rep2


title: 22Rv1_delSite4_Clone22/23-F8_rep1


title: Capan-1_CD44v6 Kd

description:
miRNA
HCX_02


title: SW-948_wt_1

description:
miRNA
HCX_03


title: 22Rv1_delSite4_Clone22/23-A5_rep3


title: 22Rv1_delSite4_Clone22/23-A5_rep2


title: 22Rv1_delSite1_Clone11/12_F6_rep3


title: 22Rv1_delSite1_Clone11/12_F6_rep1


title: 22Rv1_delSite1_Clone11/12-D8_rep2


title: 22Rv1_delSite1_Clone11/12-D8_rep3


title: 22Rv1_delSite3_Clone5/6-F3

value: Site 3 complete deletion (chr1:154531542-154532455 in hg19)


title: 22Rv1_delSite1_Clone11/12_F6_rep2


title: 22Rv1_delSite3_Clone5/6-H3


title: SS2_16_295_P12_R1 Control

city: Stockholm

first: David

last: van Bruggen

state: Stockholm

address: Scheeles väg 2

department: MBB

country: Sweden

institute: Karolinska Institutet

description:
Complete Freund’s adjuvant
SS2_16_295_counts-ercc.tab
SS2_16_295_counts.tab
SS2_16_295_rpkms-ercc.tab
SS2_16_295_rpkms.tab

data_processing:
SmartSeq2 raw data was processed according to procedures described in S. Picelli et al. 1096-1098 (2013)
Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods 10
Genome_build: mm10

extract_protocol:
Cells were isolated from the spinal cord of P90 Pdgfra-H2B-GFP and Pdgfra-Cre-LoxP-GFP mice. Tissue was then dissociated into a single cell suspension, as previously described in Marques et al 2016, with some modifications. Mice were perfused with oxygenated cutting solution (87 mM, NaCl, 2.5 mM KCl, 1.25 mM NaH2PO4, 26 mM NaHCO3, 75 mM sucrose, 20 mM glucose, 1 mMCaCl2, and 2 mM MgSO4) and the brain was quickly dissected and dissociated using the Adult brain dissociation kit from Miltenyi (130-107-677) following the manufacturer’s instructions (red blood cells removal step was not included). After debris removal, cell suspension was filtered with 30μm filter (Partec) and processed by FACS sorting. Spinal cord single GFP+ cells were selected in a BD Influx sorter and collected into a 384 plate for SmartSeq2, according to procedures described in.
SmartSeq2 raw data was processed according to procedures described in S. Picelli et al., Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods 10, 1096-1098 (2013)

treatment_protocol: For the induction of chronic EAE, animals were injected subcutaneously with an emulsion in MOG35-55 in complete Freud’s adjuvant (CFA) (EK-2110 kit from Hooke Laboratories) followed by the administration of pertussis toxin in PBS (0,2μg per animal), for two consecutive days (all according to manufacture’s instructions). Spinal cords and cerebellum were collected at the chronic stage of the disease with clinical score=3 representing limp tail and complete paralysis of hind legs. Animals that did not reach this clinical score were not analysed in this study. Additional animals were injected subcutaneously with a CFA emulsion (CK-2110 kit from Hooke Laboratories) and used as controls.

tag: strain

tag: tissue

value: Spinal Cord

tag: celltype

value: GFPpositive FACS sorted cells from spinal cord


title: SS2_16_295_P15_R1 Control


title: SS2_16_295_P23_R1 Control


title: SS2_16_295_P17_R1 Control


title: SS2_16_295_P20_R1 Control


title: SS2_16_295_P10_R1 Control


title: SS2_16_295_P19_R1 Control


title: SS2_16_295_P18_R1 Control


title: SS2_16_295_P14_R1 Control


title: SS2_16_295_P13_R1 Control


title: SS2_16_295_P24_R1 Control


title: SS2_16_295_P22_R1 Control


title: SS2_16_295_P21_R1 Control


title: SS2_16_295_P7_R1 Control


title: SS2_16_295_P8_R1 Control


title: SS2_16_295_P9_R1 Control


title: SS2_16_295_P11_R1 Control


title: SS2_16_295_P6_R1 Control


title: SS2_16_295_P5_R1 Control


title: 22Rv1_delSite4_Clone22/23-A5_rep1


title: 22Rv1_delSite1_Clone11/12-D8_rep1


title: SS2_16_295_P4_R1 Control


title: SS2_16_295_P3_R1 Control


title: SS2_16_295_P2_R1 Control


title: SS2_16_295_P1_R1 Control


title: SS2_16_295_O24_R1 Control


title: SS2_16_295_O23_R1 Control


title: SS2_16_295_O22_R1 Control


title: SS2_16_295_O20_R1 Control


title: SS2_16_295_O21_R1 Control


title: SS2_16_295_O18_R1 Control


title: SS2_16_295_O5_R1 Control


title: SS2_16_295_O6_R1 Control


title: SS2_16_295_O9_R1 Control


title: SS2_16_295_O10_R1 Control


title: SS2_16_295_O15_R1 Control


title: SS2_16_295_O8_R1 Control


title: SS2_16_295_O3_R1 Control


title: SS2_16_295_N24_R1 Control


title: SS2_16_295_O12_R1 Control


title: SS2_16_295_O11_R1 Control