title: Day 12-control-rep3

city: Los Angeles

first: Greogorio

last: Chazenbalk

state: California

address: 10833 Le Conte Ave

department: Obstetrics and Gynecology

institute: University of California, Los Angeles

description: Pair-match 3-control

data_processing:
Adapters were trimmed with trim_galore with default parameter
Bowtie2 was used fo the mapping of the trimmed reads to the hg19 transcripts set and RSEM v1.3.0 was used for the gene counting
TPM method was used for the gene expression normalization
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file contains normalized counts per million for each sample.

source_name: subcutaneous adipose tissue

growth_protocol: Adipose stem cells were plated in 10 cm dish containing DMEM/10% FCS, 0.05 U/ml penicillin, 0.05 mg/ml streptomycin, 1.25 mg/ml fungizone and cultured at 37°C until confluency and expanded for 2 additional generations. Subsequently, generation 4 ASCs were cultured in adipocyte differentiation medium consisting of DMEM/Ham's F-12 (1:1, v/v), HEPES, pH 7.4, fetal bovine serum, biotin, pantothenate, human insulin, dexamethasone, 3-isobutyl-1-methylxanthine (IBMX), PPARg agonist, penicillin, streptomycin, and amphotericin B (Zen-bio) at 37°C for 3-12 days to allow for differentiation into mature adipocytes.

extract_protocol:
Total cellular RNA was isolated at respective time points using RNeasy mini kit (Qiagen, Carlsbad, CA) according to the manufacturer’s protocol.
RNA quality was checked at the TapeStation using an RNA ScreenTape. 500 ng of total RNA were processed using the KAPA HyperPrep mRNA kit (Roche, Pleasanton, CA) according to the manufacturer's instructions. Briefly, mRNAs were captured with oligo-dT magnetic beads and fragmented for 6 min at 94°C. First strand synthesis was performed on fragmented RNA, followed by second strand synthesis and dA-tailing. Adapter ligation was performed using KAPA single-indexed adapters (KAPA, Pleasanton, CA). The adapter-ligated fragments were amplified with 10 PCR cycles. Final libraries were then pooled and sequenced on a HiSeq4000 single-end 50 nt.

tag: female type

value: control


title: Day 12-PCOS-rep3

status: Public on Aug 12 2020

type: SRA

country: USA

description: Pair-match 3-PCOS

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

value: PCOS


title: Day 12-control-rep2

description: Pair-match 2-control


title: Day 12-PCOS-rep1

description: Pair-match 1-PCOS


title: Day 12-PCOS-rep2

description: Pair-match 2-PCOS


title: subtractedr_rep2

city: Oxford

first: Ilan

last: Davis

address: South Parks Road

department: Biochemistry

country: United Kingdom

institute: University of Oxford

description:
summary_abundance_by_gene_kallisto.csv
summary_abundance_by_gene_htseq.csv

data_processing:
Adaptor removal: For the NEB libraries, the NEB adapter was removed with Cutadapt.
Adaptor removal: For the QuantSeq libraries, poly(A) and Illumina adapters were trimmed from the reads using BBDuk with the parameters "k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20".
Quantification: Reads were quantified with Kallisto against a index containing both processed transcripts and introns plus 30 nt of flanking sequence. For the RNA-seq libraries, the parameters "-l 1 -s 1 --single --rf-stranded" were used and for the QuantSeq libraries, the parameters "-l 1 -s 1 --single --fr-stranded" were used. Gene-level quantification was obtained by summing quantification of individual transcripts.
Differential expression calling: Gene-level differential expression analysis was performed with DESeq2 using the transcript import function.
Genome_build: Drosophila melanogaster, Ensembl release 99, assembly BDGP6.28
Supplementary_files_format_and_content: Abundance measurements by gene and differential expression analysis

organism: Drosophila melanogaster

source_name: wandering third instar larvae

growth_protocol: Drosophila melanogaster wild type strain Oregon-R flies were raised on standard cornmeal-agar medium at 25˚C.

extract_protocol:
Three samples of 40 wandering third instar larvae each were collected, washed, and flash frozen. RNA was extracted with Trizol.
Libraries were constructed using either a random priming approach (NEBNext Ultra II Directional RNA Library Prep, NEB, E7765S) or a poly(A) priming approach (QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina, Lexogen, cat# 015.24).
RNA-seq, QuantSeq

treatment_protocol: Total RNA was either used directly for library construction (input samples) or subjected to rRNA depletion (depleted samples). For rRNA depletion, RNA was mixed with antisense oligonucleotides in hybridization buffer (2X SSC, 0.01% Tween-20). The reaction was heated to 70˚C for 5 min, then added to Streptavidin beads (Dynabeads MyOne Streptavidin C1, ThermoFisher) and incubated for 10 min at 50˚C with mixing. The reaction was transferred to a magnetic rack and the eluate was collected. The beads were washed with wash buffer (0.4X SSC, 0.01% Tween-20) and the eluate collected again. The combined eluate was purified with  bead-based RNA clean-up (Mag-Bind TotalPure NGS , Omega Bio-tek) to yield rRNA-depleted RNA for library construction.

tag: treatment type

value: rRNA-depleted

tag: library type

value: RNA-seq


title: subtractedr_rep3


title: subtractedr_rep1


title: WSNdelNS1-2

city: Hong Kong

first: Honglin

last: Chen

address: Rm 5-19, 5/F, Lab block, 21 Sassoon Road, Pokfulam

department: Department of Microbiology

country: Hong Kong

institute: The University of Hong Kong

data_processing:
Using software from Illumina (bcl2fastq), sequencing reads were assigned into individual samples with adapter trimming and demultiplexing.
Fastq reads were subsequently aligned to the human genome (GENCODE V29 ) with bowtie2 (V2.3.4.3) for ChIP-Seq samples and subsequently sorted and indexed with samtools. STAR (V2.7.2a) was used to align RNA-Seq samples and counts were generated with its in-built htseq-count algorithm.Genes with counts below 10 across all RNA-Seq samples were excluded for differential expression analysis. DESeq2 was used to assess for differential expression.
Peaks were called using MACS2 callpeak function with inputs set as the designated control (-C arguement). (Other MAC2 callpeak parameters: -B --nomodel --extsize 200 -q 0.05 --keep-dup auto -g 2.7e9 --mfold 10 50 --bw 300)
BigWig files for coverage visualization were generated using the bamcompare function from DeepTools. Scores were normalized against signal from input samples.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files were generated with DeepTools. Regions of the human genome that were identified as having routinely anomalous, unstructured, or high signal in NGS experiments were blacklisted. (File is available from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz)
Supplementary_files_format_and_content: Peak files are in BED format with significant peaks enriched over input signal
Supplementary_files_format_and_content: Raw and normalized counts are in csv file format with genes across rows and samples across columns.

source_name: A549 cells

growth_protocol: A549 cells were infected with influenza A/WSN/33 (H1N1) wildtype strain (WSNWT) or one of 2 mutant viruses; WSN3M or WSNdelNS1 at an designated MOI for 8 hours.

extract_protocol:
RNA-Seq: Total RNA was extracted using NucleoSpin® RNA Plus kit (Macherey-nagel) according to the manufacture’s instruction, including an on-column genomic DNA digestion step.  Quality and quantity of RNA was checked with Qubit and Bioanalyzer. Ribosomal RNA (rRNA) depletion was performed using NEBNext® rRNA Depletion Kit (Human/Mouse/Rat). cDNA libraries were prepared by NEBNext® Ultra II Directional RNA Library Prep Kit. Five hundred nanogram of total RNA was used as starting material for ribosomal RNA depletion. Cytoplasmic rRNA and mitrochondrial rRNA were firstly hybridized to ssDNA capture probes and then digested by Ribonuclease H. After that, the residual ssDNA probes were digested by DNase I. The rRNA-depleted RNA was then purified by Agencourt® RNAClean™ XP beads. The purified rRNA-depleted RNA was fragmented to 200 – 500 bp by incubating at 94oC for 10 min in the presence of magnesium ions. The fragmented rRNA-depleted RNA was then applied as template to synthesize the first-strand cDNA by using random hexamer-primer and reverse transcriptase. In the second strand cDNA synthesis, the mRNA template was removed and a replacement strand was generated to form the blunt-end double-stranded (ds) cDNA. The ds cDNA underwent, 3’ adenylation and indexed adaptor ligation, followed by treatment with User Enzyme. The adaptor-ligated libraries were enriched and indexed by 8 cycles of polymerase chain reaction (PCR). The libraries were denatured and diluted to optimal concentration. Illumina NovaSeq 6000 was used for Pair-End 151bp sequencing. ChIP-Seq: Infected cells were fixed with 1.5% formaldehyde for 12 minutes. Cells were subsequently lyzed with lysis buffer (20mM Tris-HCL pH8.0, 85 mM KCL, 0.5% NP-40) on ice for 20 min. Cell nuclei were isolated by centrifuge and resuspended in 1% SDS lysis buffer (50 mM Tris-HCL pH8.0, 5 mM EDTA, 1% SDS). Sonication was then performed (Bioruptor, 8 cycles of 30 sec on and 30 sec off, three times). Samples were then diluted and split into four fractions for each antibody pulldown(1- Millipore, 05-623; 2- Abcam, ab5131; 3- Abcam, ab5095) and plus alpha (4- 10% input) (4 ug antibody per assay). Pulled down experiments used Protein G-beads (Invitrogen, 10004D) followed by washing and elution. Reverse-crosslinked was done overnight (with salt and RNase) and incubated with Proteinase K and finally column-purified for library prep.
Library preparation utilized the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645), following manufacturers intructions. For ChIP-seq, total RNA was Size-selected before PCR (targeting 200 bp) with SPRI beads (Beckman, B23317). PCR consisted of three cycles for inputs and 11-13 cycles for ChIP-ed samples. Library preparation and Illumina sequencing (Pair-End sequencing of 151bp) were done at The University of Hong Kong, LKS Faculty of Medicine, Centre for PanorOmic Sciences (CPOS), Genomics Core.

tag: replicate

tag: viral strain

tag: moi

value: 8 hours


title: WSNdelNS1-3


title: Day 12-control-rep1

description: Pair-match 1-control


title: WSNdelNS1-1


title: T27_LA_Tumor tissue_Luminal A

type: RNA

city: CDMX

first: Alberto

last: Cedro-Tanda

state: CMDX

address: Periferico sur #4809

country: Mexico

institute: INMEGEN

description: SST-RMA expression value derived from Expression Console software

hyb_protocol: Samples were hybridized with GeneChip Human Transcriptome Array 2.0 Arrays (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix). GeneChips were scanned using The Genechip Scanner 3000 7G (Affymetrix , Santa Clara, USA).

data_processing: Array signal intensitive were analyzed with the Affymetrix Expression Console using Signal Space Transformation-Robust Multichip Analysis (SST-RMA) for the background correction.

label: biotin

source_name: Fresh frozen breast cancer tumor

label_protocol: WT Plus Reagent Kit were used to generate the biotinylated cRNA starting from 100ng of total RNA according to the manufacturer (Manual Target preparation for GeneChip Whole transcript (WT) expression arrays, Affymetrix).

extract_protocol: We used AllPrep DNA/RNA Mini Kit

tag: population

value: Mexico hispanic

tag: pam50 molecular subtype

value: Luminal A

tag: tissue

value: RNA from tumor tissue


title: T149_LB_Tumor tissue_Luminal B

value: Luminal B


title: WSNWT-3

value: Wildtype (H1N1)


title: T36_LA_Tumor tissue_Luminal A


title: inputr_rep3

value: input


title: T37_LA_Tumor tissue_Luminal A


title: WSNWT-2


title: Day 7-control-rep2

description: Pair-match 2-control


title: Day 7-control-rep3

description: Pair-match 3-control


title: Day 7-PCOS-rep2

description: Pair-match 2-PCOS


title: Day 7-PCOS-rep3

description: Pair-match 3-PCOS


title: subtractedq_rep3

description:
summary_abundance_by_gene_kallisto.csv
summary_abundance_by_gene_htseq.csv
subtractedq_vs_inputq.diffexp.csv

value: QuantSeq


title: inputr_rep1


title: WSNWT-1


title: Day 7-PCOS-rep1

description: Pair-match 1-PCOS


title: T13_LB_Tumor tissue_Luminal B


title: WSN-3M-3


title: subtractedq_rep2


title: T30_LA_Tumor tissue_Luminal A


title: T189_Ba_Tumor tissue_Basal-like

value: Basal-like


title: T187_LA_Tumor tissue_Luminal A


title: T162_Ba_Tumor tissue_Basal-like


title: T146_He_Tumor tissue_Her2-enriched


title: T158_LB_Tumor tissue_Luminal B


title: T174_Ba_Tumor tissue_Basal-like


title: T183_LA_Tumor tissue_Luminal A


title: WSN-3M-2


title: inputr_rep2


title: T141_LA_Tumor tissue_Luminal A


title: Day 7-control-rep1

description: Pair-match 1-control


title: MOCK-3

value: Uninfected


title: Day 3-PCOS-rep3

description: Pair-match 3-PCOS


title: Day 3-control-rep2

description: Pair-match 2-control


title: inputq_rep3


title: subtractedq_rep1


title: WSN-3M-1


title: Day 3-control-rep3

description: Pair-match 3-control


title: Day 3-PCOS-rep2

description: Pair-match 2-PCOS


title: inputq_rep2


title: inputq_rep1


title: MOCK-2


title: MOCK-1


title: tumor-lung_vdj

city: Boston

first: JAE WON

last: CHO

state: MA

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

description: single-cell VDJ sequencing

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and aggregation of multiple sequencing runs were performed using the Cell Ranger analysis pipeline (v3.1.0)
Background and non-cellular barcodes are removed
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: .tsv: barcodes, genes, .mtx: count matrix, .csv: tcr sequence

organism: Mus musculus

source_name: lung cancer

extract_protocol:
C57BL/6 mice were injected intravenously into the tail vein with 5×10e5 TC1 tumor cells. At 3 weeks post tumor inoculation, tumor-bearing mice were sacrificed. The lungs from tumor-bearing mice and age-matched normal mice were perfused and harvested. Lung tissues were chopped into 1mm3 pieces and digested in RPMI medium supplemented with 10% FBS, 1% P/S, 1% Collagenase IV (Worthington Biochemical corp., Lake wood, NJ, USA), and 0.01% DNase (Sigma Aldrich, St. Louis, MO, USA) for 20 min at 37 °C. The dissociated tissues were filtered through a 40-μm cell strainer. The pulmonary lymphocytes were isolated by conducting a Percoll gradient (Millipore Sigma Corp.) and enriched the CD4+ T cells using a CD4+ T cell isolation kit (Miltenyi Biotec) followed by manufacture’s protocol. The enriched CD4+ T cells were stained with the CD4-fluorescent dye-conjugated antibody and excluded the dead cells by staining the Live/Dead Fixable Near-IR Dead Cell Stain Kit (Invitrogen). The single-cell suspensions were sorted into live CD4+ T cells using fluorescence-activated cell sorting (BD Aria III) for further scRNA- and TCR- sequencing analysis.
To construct libraries and sequencing, we applied the Chronimum 10x Genomics platform with a V(D)J Enrichment kit and 5’ Library & Gel Bead Kit (10x Genomics). To achieve 10,000 targeted cells, the cell suspension was diluted in nuclease-free water and then combined with Single Cell 5′ Gel Beads, a master mix, and Partitioning Oil on Chromium Chip A (GEM). Following to generate the GEMs, RNA transcripts were uniquely barcoded and reverse-transcribed within droplets. 10x Barcoded, full-length cDNA were pooled and enriched via PCR. For V(D)J Enriched Library, the enriched cDNA pool was amplified using primer specific to TCR as in T Cell Mix1 and T Cell Mix2 primer. For 5’ Gene Expression (GEX) Library, the cDNA pool went through an end repair process, A-tailing, adaptor ligation, and sample index PCR to create the 5’ Gene Expression Library. The purified libraries were quantified and qualified using qPCR Quantification Protocol Guide (KAPA) and the Agilent Technologies 4200 TapeStation (Agilent technologies). Afterwards, the libraries were sequenced using HiSeqX platform (Illumina) according to the read length in the user guide.

value: tumor-lung

tag: cell type

value: CD4 T cell


title: normal-lung_vdj

description: single-cell VDJ sequencing

source_name: normal lung

value: normal-lung


title: Pol2_s2p_WSNWT

tag: chip antibody

value: PolII-s2p (Abcam-ab5095)


title: Pol2_s5p_WSNWT

value: PolII-s5p (Abcam-ab5131)


title: Day 3-PCOS-rep1

description: Pair-match 1-PCOS

value: PCOS


title: Day 3-control-rep1

description: Pair-match 1-control

value: control


title: T125_LA_Tumor tissue_Luminal A


title: MM1S cell line - H3K9me3

city: Newcastle upon Tyne

first: Aneta

last: Mikulasova

address: Brewery Lane

department: Biosciences Institute

institute: Newcastle University

library_source: genomic

data_processing:
GRCh38 human assembly was used for alignment.
ChIP-seq chromatin states were determined by ChromHMM (v1.20), the model used in the BLUEPRINT dataset (PMID: 28934481).
The peaks of individual histone marks were detected using MACS2 (v2.2.5) by a pipeline available at BLUEPRINT Data Coordination Center Portal (PMID: 27863955).
Genome_build: GRCh38
Supplementary_files_format_and_content: MACS2 peak files, broad peaks for H3K4me1, H3K9me3, H3K27me3 and H3K36me3, and narrow peaks for H3K4me3 and H3K27Ac
Supplementary_files_format_and_content: bigWig files, generated by bedGraphToBigWig from MACS2 bedGraph
Supplementary_files_format_and_content: bed files, chromatin states segmentation generated by ChromHMM

molecule: genomic DNA

source_name: Cell line

extract_protocol:
1x10^7 cells per mark were fixed in a 1% formaldehyde solution, followed by the addition of glycine to a final concentration of 0.125 M. Cells were washed and resuspended in PBS containing 0.5% lgepal with 1% PMSF, before being pelleted and frozen at -80 ºC.
ChIP-seq for the histone marks H3K4me1, H3K4me3, H3K9me3, H3K27me3, H3K27Ac, and H3K36me3 (Active Motif, Carlsbad, CA, USA) were included in this study.

tag: cell line

value: Plasma cells

tag: antibody, verndor, catalog number

value: Histone H3K9me3 antibody, Active Motif, 39161


title: normal-lung_gex

description: single-cell RNA sequencing


title: T135_LA_Tumor tissue_Luminal A

value: Mexico hispanic

value: Luminal A


title: T108_He_Tumor tissue_Her2-enriched

value: RNA from tumor tissue


title: C81_Adjacent normal tissue

source_name: Fresh frozen adjacent normal tissue

value: RNA from adjacent normal tissue


title: Pol2_WSNWT

value: Wildtype (H1N1)

value: PolII (Millipore-05-623)

value: 8 hours


title: T123_LB_Tumor tissue_Luminal B

value: Luminal B


title: T38_LB_Tumor tissue_Luminal B


title: C6_Adjacent normal tissue


title: C80_Adjacent normal tissue


title: Pol2_s2p_WSNdelNS1


title: tumor-lung_gex

description: single-cell RNA sequencing

value: tumor-lung


title: MM1S cell line - H3K4me1

value: Histone H3K4me1 antibody, Active Motif, 39297


title: HUVEC CONTROL3_TNF

city: Bethesda

first: Manfred

last: Boehm

state: MD

address: 9000 Rockbille Pike

institute: NHLBI

data_processing:
RNA-seq data quality was assessed using FastQC
Reads obtained for each sample were aligned to the hg19 human reference genome using Tophat2
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include total counts values for all samples

source_name: Umbilical Cord

growth_protocol: The cords were shipped overnight from hospitals in PBS supplemented with Penicillin-Streptomycin (No. 15140122, ThermoFisher Scientific). Umbilical veins were washed 3 times with PBS supplemented with Penicillin-Streptomycin and Amphotericin B (No. 400-104, Gemini Bio-Products, West Sacramento, CA) and then filled with collagenase, type II (No.17101-015, ThermoFisher Scientific) at 0.2% in PBS and the ends were closed. The cords were placed in 37C incubator for 20 min. The cells were pelleted from the collagenase suspension, resuspended in endothelial cell culture media (EBM Basal Medium (No.CC-3121, Lonza) supplemented with EGM-2 SingleQuots Kit (No.CC-4176, Lonza)), Penicillin-Streptomycin and Amphotericin B and plated on fibronectin (No. F2006, Sigma) coated T25 flask. The media was changed next day, and cells were routinely cultured on 10 cm fibronectin coated dishes.

extract_protocol:
Total RNA was isolated using TRIzol Reagent (No. 15596026, ThermoFisher Scientific).
One mg of total RNA was used as input for library preparation using the TruSeqRNA Sample Preparation Kit v2 (Illumina) according to manufacturer’s instructions. Sequencing libraries were quantitated by qPCR on a LightCycler 480 Instrument II (Roche) and assessed for size distribution and absence of adapter dimers using a Fragment Analyzer (AATI).  Libraries were pooled for multiplexing and sequencing was performed on the Illumina HiSeq 3000 Sequencing System with run parameters at paired-end 75bp read length for >25 million paired-end reads per sample.

treatment_protocol: For RNA isolation, HUVECs were seeded on 6 well plates at density of 250,000 cells per well. In 48 hours, when cells reached confluence, media was changed to fresh one with or without 50ng/ml TNFα for 8h and total RNA was extracted for RNA-Seq analysis.

tag: isolated cells

value: HUVEC

tag: treatment

value: TNFa 50ng/ml for 8h

tag: genotype/variation


title: Pol2_s5p_WSNdelNS1

value: PolII-s5p (Abcam-ab5131)


title: Pol2_WSNdelNS1


title: C75_Adjacent normal tissue


title: MM1S cell line - H3K27me3

value: Histone H3K27me3 antibody, Active Motif, 39155


title: HUVEC CONTROL2_TNF

value: control


title: HUVEC CONTROL1_TNF


title: HUVEC AD-HIES3_TNF

value: AD-HIES STAT3 mutation


title: MM1S cell line - H3K4me3

value: Plasma cells

value: Histone H3K4me3 antibody, Active Motif, 39159


title: MM1S cell line - H3K27ac

value: Histone H3K27ac antibody, Active Motif, 39133


title: MM1S cell line - H3K36me3

value: Histone H3K36me3 antibody, Active Motif, 61101


title: HUVEC AD-HIES2_TNF


title: KMS11 cell line - H3K9me3

value: Histone H3K9me3 antibody, Active Motif, 39161


title: Pol2_s5p_WSN3M


title: Pol2_s2p_WSN3M

value: PolII-s2p (Abcam-ab5095)


title: HUVEC AD-HIES1_TNF


title: KMS11 cell line - H3K4me3


title: HUVEC CONTROL3_NT

value: no treatment


title: KMS11 cell line - H3K4me1


title: Pol2_s2p_Mock

value: Uninfected

value: 8 hours


title: Pol2_WSN3M

value: PolII (Millipore-05-623)


title: HUVEC CONTROL2_NT


title: KMS11 cell line - H3K36me3


title: Pol2_s5p_Mock


title: Pol2_Mock


title: C71_Adjacent normal tissue

value: Mexico hispanic

value: RNA from adjacent normal tissue


title: HUVEC CONTROL1_NT

value: HUVEC


title: C14_Adjacent normal tissue


title: C74_Adjacent normal tissue


title: C15_Adjacent normal tissue


title: KMS11 cell line - H3K27me3


title: WSNWT_input

description: WSNWT_input (10%)

value: Wildtype (H1N1)


title: HUVEC AD-HIES3_NT


title: C167_Adjacent normal tissue


title: C160_Adjacent normal tissue


title: C106_Adjacent normal tissue


title: C105_Adjacent normal tissue

value: Tissue


title: WSNdelNS1_input

description: WSNdelNS1_input (10%)


title: KMS11 cell line - H3K27ac


title: HUVEC AD-HIES2_NT


title: HUVEC AD-HIES1_NT


title: Mock input

description: Mock input (10%)


title: IP:H3K9me3 AID-METTL3:-METTL14 dd (+IAA) Rep2

status: Public on Aug 11 2020

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

country: France

institute: institut curie

data_processing:
Paired-end reads were trimmed using Trim Galore v0.4.4.
The alignment was performed onto a concatenated genome using the Mouse reference genome (mm10) and the Escherichia coli (str. K-12 substr. MG1655, genbank: NC_000913) with STAR v2.7.0a36 reporting randomly one position, allowing 6% of mismatches (--outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06). PCR duplicates were removed using Picard v2.6.0.
Bigwig files were processed using the bamCoverage function from Deeptools v2.5.3 with the reads aligned to the Mouse reference genome.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files with coverage

source_name: Embryonic Stem Cell

growth_protocol: ES Cells were either cultured in serum-free 'LIF +2i' medium: 50% Neurobasal medium (Gibco), 50% DMEM/F12 (Gibco), 2mM L-glutamine (Gibco), 0.1mM β-mercaptoethanol, Ndiff Neuro-2 medium supplement (Millipore), B-27 medium supplement (Gibco), 1000 U/mL LIF, 3μM Gsk3 inhibitor (CT-99021), 1μM MEK inhibitor (PD0325901).

extract_protocol:
Cells were immobalised to concavalin beads, permeabilised with digitonin and incubated with antibody. After washing, the cells are incubated with A-Mnase protein to digest around the protein-bound DNA. Upon diffussion of DNA-protein complexes out of the cells DNA was collected and size selected with SPRI beads.
We used 10ng DNA input for library preparation using Accel-NGS 2S Plus DNA Library Kit (Swift) according to the manufacturer’s protocol.
Sequencing was performed in 50pb paired-end reads using Novaseq 6000.

tag: age

tag: media

value: IP


title: WSN3M_input

description: WSN3M_input (10%)


title: IP:H3K9me3 AID-METTL3:-METTL14 dd (+IAA) Rep1


title: IP:H3K9me3 AID-METTL3:-METTL14 dd (noIAA) Rep2


title: IP:H3K27ac AID-METTL3:-METTL14 dd (+IAA) Rep2


title: IP:H3K27ac AID-METTL3:-METTL14 dd (+IAA) Rep1


title: IP:H3K27ac AID-METTL3:-METTL14 dd (noIAA) Rep1


title: IP:H3K4me3 AID-METTL3:-METTL14 dd (+IAA) Rep2


title: IP:H3K27ac AID-METTL3:-METTL14 dd (noIAA) Rep2


title: IP:H3K4me3 AID-METTL3:-METTL14 dd (+IAA) Rep1


title: IP:H3K4me3 AID-METTL3:-METTL14 dd (noIAA) Rep2


title: shRNA for linc-PPP1R1B_A

source_name: Treatment

extract_protocol: Trizol method was used to extract the total RNA

value: SKBR3 tumoral cell line

tag: shRNA


title: MDA-MB-231 3D 2 Gy x 4

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: Breast cancer cell line

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: MDA-MB-231 cell line

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

growth_protocol: MDA-MB-231 cells were cultured on Corning Matrigel Basement Membrane Matrix (Corning, USA) for 3D laminin-rich ECM (lrECM) culture.

extract_protocol: Total cellular RNA of MDA-MB-231 cells was isolated using a NucleoSpin RNA kit (MACHEREY-NAGEL, Germany). First-strand cDNA was synthesized from the total RNA with SuperScript reverse transcriptase (Thermo Fisher Scientific, USA).

treatment_protocol: 3D-cultured MDA-MB-231 cells were treated with or without 2 Gy x 4 days radiation treatment.

value: MDA-MB-231 cell line

tag: agent

value: 2 Gy x 4 radiation


title: MDA-MB-231 3D 0 Gy

description: Breast cancer cell line


title: shRNA for linc-PPP1R1B_C


title: Negative Control shRNA_C

source_name: Negative Control

value: Control


title: shRNA for linc-PPP1R1B_B


title: Negative Control shRNA_B


title: Negative Control shRNA_A


title: IP:H3K9me3 AID-METTL3:-METTL14 dd (noIAA) Rep1


title: Primary Tumor 1 (sc)

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

description: Normalized_matrix_single_cell_CJ001_CJ002.txt

data_processing:
Reads were mapped to the mouse mm9 genome, customized to include the EYFP reporter sequence and processed with the CellRanger pipeline v2.0.0 or v3.1.0
Single-cell RNA-seq raw counts were normalized and the variance was stabilized using DESeq2 package (Bioconductor) in R-studio.
EYFP  5’ to 3’  coding sequence: ATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTGGTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCTTCGGCTACGGCGTGCAGTGCTTCGCCCGCTACCCCGACCACATGCGCCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGACAACCACTACCTGAGCTACCAGTCCGCCCTGAGCAAAGACCCCAACGAGAAGCGCGATCACATGGTCCTGCTGGAGTTCGTGACCGCCGCCGGGATCACTCTCGGCATGGACGAGCTGTACAAGTAA
Genome_build: Mouse: UCSC/mm9
Supplementary_files_format_and_content: Tab-delimited text files include DESeq2 normalized values for each sample

source_name: Prostate tumor, AP lobe

extract_protocol:
First, the tissues were minced with scissors and enzymatically digested for 15 minutes at 37C in a mixture containing 1X collagenase/hyaluronidase, 0.5 U/ml dispase II and 0.1mg/ml DNAse 1 in DMEM-F12 media, followed by addition of 0.025% trypsin/EDTA for another 15 minutes (all obtained from Stem Cell Technologies, Cambridge, MA). Cells were resuspended in cold 10% FBS DMEM-F12, filtered through a 40 µm cell strainer and collected by centrifugation at 350 X G in an Eppendorf 5810R tabletop centrifuge for 5 min at 4ºC. After a 5-minute incubation in cold 1X Red Blood Cell Lysis Buffer (ThermoFisher, Bridgewater, NJ) cells were diluted 4-fold in cold PBS, centrifuged as before and resuspended in DMEM-10% FBS for cell counting and viability analysis.
Cells were counted using a Countess II Automated Cell Counter (ThermoFisher) and 10,000 cells with over 70% viability were loaded into a 10x Genomics Chromium Controller for capture and barcoding following the 10x Genomics Single Cell Protocol, using Chromium Single Cell 3ʹ Reagent Kits v2/v3, as described by the manufacturer (10x Genomics, Pleasanton, CA). For cDNA amplification and indexing library amplification, 12 PCR cycles were used for each step, and subsequent RNA sequencing was performed using Illumina NovaSeq6000.

tag: strain

value: Mixed strain, predominantly C57BL/6

value: prostate

value: 6 months

tag: genotype

value: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+; R26R-CAG-LSL-EYFP/+


title: Bone Metastasis 2 (sc)

description: Normalized_matrix_single_cell_CJ003_CJ004.txt

source_name: Bone Metastasis

value: Bone:1 pelvic, 1 femoral and 1 tibial metastases

value: 8 months


title: IP:H3K4me3 AID-METTL3:-METTL14 dd (noIAA) Rep1


title: Bone Metastasis 1 (sc)

value: Bone:2 vertebral and 1 femoral metastases


title: Input AID-METTL3:-METTL14 dd (noIAA)

value: Input


title: Input AID-METTL3:-METTL14 dd (+IAA)


title: Primary Tumor 2 (sc)


title: CT2_3 (Control)

city: Uvalde

first: Vijay

last: Joshi

state: Texas

address: 1619 Garner Field Road

department: Department of Horticultural Sciences

institute: Texas A&M AgriLife Research

description: Control

data_processing:
Illumina Novaseq 6000 used for sequencing
Sequenced reads were trimmed for adaptor sequence by fastp, and masked for low-complexity or low-quality sequence, then mapped to Citrullus_lanatus whole genome using hisat2-2.1.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from mapped read by featureCounts
Differeantial expression analysis with DEseq2
Genome_build: Citrullus_lanatus _WCG_V2
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample, and differential expressed gene for each comparasion

organism: Citrullus lanatus

source_name: Leaf of cultivar Crimson Sweet

growth_protocol: Seedlings of the cv. Crimson Sweet were grown in a non-nutrient sandy/stone soil (Quick Dry Infield Conditioner, Turface Atheletics™, USA) were used for salt stress study. Six-week-old seedlings with three fully expanded leaves were subjected to salinity stress. The seedlings with four replicates for each treatment were carefully lifted out from the media, washed under running water and were incubated in 50mL Conical-Bottom tubes (1) 300 mM NaCl (2) MilliQ water After 7 hours of exposure to salt stress, leaf  tissue samples were collected from seedlings each with 3 replicates for both treatment and flash-frozen by liquid nitrogen before storing at -80℃ for further processing.

extract_protocol:
The flash-frozen leaf samples from three independent plants along with control (well-irrigated) plants were used for RNA-Seq analysis. Total RNA was extracted using a Quick-RNA™ Miniprep Kit (Zymo Research Corporation, Irvine, CA ) as per the manufacturer’s protocol and treated with DNase1 (Zymo Research Corporation, Irvine, CA ).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: protocol

value: 7 hours in water

tag: stress


title: TT2_2 (Drought-stressed)

description: Treatment

value: 7 hours after initiation of salt stress

value: Drought-stressed


title: TT2_3 (Drought-stressed)

description: Treatment


title: CT2_1 (Control)

description: Control


title: CT2_2 (Control)

description: Control


title: TT2_1 (Drought-stressed)

description: Treatment


title: mRNA_72_TNF_b

city: Saint Louis

first: Alison

last: Ross

state: Missouri

address: Couch Biomedical Research Building

institute: Washington University in St. Louis

data_processing:
RNA-seq reads were trimmed with Trimmomatic and Cutadapt
reads were aligned with STAR aligner
reads were counted using featureCounts
Genome_build: mRNA-seq: mm10 from Gencode vM15; miRNA-seq: a custom murine miRNA database based on miRBase v22
Supplementary_files_format_and_content: tab-delimited text files contain non-normalized counts for each sample at each time point and condition

source_name: tissue-engineered cartilage

extract_protocol:
Frozen tissue-engineered cartilage samples were homogenized with a miniature bead beater. Total cellular RNA was isolated using the mirVana miRNA Isolation Kit (Invitrogen) for small RNA sequencing or Total RNA Purification Plus Kit (Norgen) for mRNA sequencing.
miRNA: Illumina TreSeq Small RNA kit; mRNA: Illumina Ribo-Zero Gold kit

value: tissue-engineered cartilage

tag: time point (hr)

value: 20 ng/mL TNF-alpha


title: mRNA_72_IL1_b

tag: tissue

value: 1 ng/mL IL-1beta


title: mRNA_72_0_b

value: control


title: mRNA_72_TNF_a


title: mRNA_72_IL1_a


title: mRNA_72_0_c


title: mRNA_72_TNF_c


title: mRNA_72_IL1_c


title: mRNA_72_0_a


title: mRNA_24_TNF_c


title: mRNA_24_TNF_a


title: mRNA_24_IL1_a


title: mRNA_24_0_c


title: mRNA_24_IL1_c


title: mRNA_24_IL1_b


title: mRNA_24_0_a


title: mRNA_24_0_b


title: mRNA_12_TNF_b


title: mRNA_4_TNF_a


title: mRNA_4_TNF_b


title: mRNA_12_0_c


title: mRNA_12_TNF_a


title: mRNA_12_TNF_c


title: mRNA_12_IL1_c


title: mRNA_12_IL1_a


title: mRNA_4_0_a


title: mRNA_12_0_b


title: mRNA_4_IL1_c


title: mRNA_4_0_c


title: mRNA_4_IL1_b


title: mRNA_0_0_b


title: miRNA_72_TNF_c


title: mRNA_0_0_a


title: mRNA_4_TNF_c


title: miRNA_72_TNF_b


title: mRNA_0_0_c


title: mRNA_12_IL1_b


title: mRNA_4_IL1_a


title: miRNA_72_IL1_c


title: mRNA_12_0_a


title: miRNA_72_IL1_a


title: miRNA_72_IL1_b


title: miRNA_72_TNF_a


title: mRNA_4_0_b


title: miRNA_72_0_c


title: miRNA_72_0_b


title: miRNA_24_TNF_c


title: miRNA_24_TNF_b


title: DZG_1: M. truncatula root without Gongronella sp. w5 inoculation_rep1

city: Hefei

first: Wang

last: Xiaojie

address: No. 111 Road, Kowloon

country: China

institute: Anhui University

data_processing:
FASTQ files are coded with Illumina 1.8+ version
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with the default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Medicago truncatula Genome Database:http://www.medicagogenome.org/
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Medicago truncatula

source_name: M. truncatula root

extract_protocol:
Total RNA of root samples was extracted using the TransZol Plant RNA Kit (Transgen, Beijing, China). Paired-end cDNA sequencing libraries were carried out according to the manufacturer’s protocol of Illumina TruSeq Stranded Total RNA Library Preparation Kit.
Libraries were sequenced with the Illumina HiSeq 2000 platform (Shanghai Personal Biotechnology Co., Ltd)

value: Root

value: untreated


title: miRNA_24_IL1_c


title: CLG_3: M. truncatula root with Gongronella sp. w5 inoculation_rep3

value: Treated with Gongronella sp. w5 for 16 day


title: DZG_2: M. truncatula root without Gongronella sp. w5 inoculation_rep2


title: CLG_1: M. truncatula root with Gongronella sp. w5 inoculation_rep1


title: DZG_3: M. truncatula root without Gongronella sp. w5 inoculation_rep3


title: miRNA_24_TNF_a


title: miRNA_24_IL1_b


title: R8  Met-Hcy+ 12h rep1

city: Irvine

first: Peter

last: Kaiser

state: CA

address: Department of Biological Chemistry, 829 Health Sciences Rd

institute: University of California, Irvine

description:
R8_720_01
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv

data_processing:
Sequenced reads were aligned using HiSAT2 version 2.1.0 to human genome (GRCh38/hg38) modified with ERCC spike-in annotations provided by Thermofisher Scientific.
Read counts were generated using featureCounts in the R package Subread version 1.5.3.
Reads were filtered in the programming language R for any gene with any sample less than 5 reads. Only samples at 0h, 2h, and 12h were used for further processing.
Unwanted variation in sequenced samples was calculated using ERCC spike-in controls and and RUVseq version 1.16.1 (k=2).
In DESeq version 1.22.2, a likelihood ratio test was performed to remove strain specific differences over time. Experimental design parameters (~ W_1 + W_2 + Cell.line + Time + Cell.line:Time) and reduced formula ( W_1 + W_2 + Cell.line + Time). "W_1" and "W_2" are a list of values generated from RUVSeq processing.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: RAW_gene_count_matrix.csv - A table (csv) with raw gene counts for every gene and every sample. Column names correspond to values in "Description" field of the "SAMPLES" section.
Supplementary_files_format_and_content: DESeq2_normalized_filtered_count_matrix.csv - A table (csv) with normalized gene counts generated by DESeq2.
Supplementary_files_format_and_content: DESeq2_results.csv - A table (csv) with DESeq2 results.

source_name: metastatic breast epithelial cells

growth_protocol: MDA-MB-468 and MDA-MB-468res-R8 cell lines were maintained in DMEM (Sigma-Aldrich, D0422) supplemented with 10 % dialyzed FBS (Omega Scientific), 1.5 μM cyanocobalmin (vitamin B12), 4 mM L- glutamine, 100 μM L-cysteine (Fisher Scientific), and 100 μM L-methionine (Sigma-Aldrich).

extract_protocol:
Total RNA from MDA-MB-468 and MDA-MB-468res-R8 cells was extracted using the RNeasy Plus Mini Kit (Qiagen, Cat No. 74134).
Poly A selected RNA libraries were prepared using TruSeq RNA Library Preparation Kit v2 (Illumina, RS-122-2001 and RS-122-2002) with the ERCC RNA Spike-In mix (ThermoFisher, 4456740) to control for sample preparation variation.

treatment_protocol: Untreated cells collected at time 0h were cultured in methionine containing growth medium (Met+). In the case of methionine-free media, 370 μM DL-homocysteine (Sigma- Aldrich) was added in the absence of methionine (Met-Hcy+). Cells were collected 0.5, 2, and 12 hours post-media switch.

value: Met-Hcy+ 720min (for 12h) - 370uM Homocysteine


title: MB468 Met-Hcy+ 12h rep3

description:
MB468_720_03
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: R8  Met-Hcy+ 12h rep2

description:
R8_720_02
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: R8  Met-Hcy+ 2h rep3

description:
R8_120_03
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv

value: Met-Hcy+ 120min (for 2h) - 370uM Homocysteine


title: MB468 Met-Hcy+ 12h rep1

description:
MB468_720_01
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: R8  Met-Hcy+ 2h rep2

description:
R8_120_02
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: MB468  Met-Hcy+ 2h rep2

description:
MB468_120_02
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: R8  Met-Hcy+ 2h rep1

description:
R8_120_01
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: MB468  Met-Hcy+ 2h rep3

description:
MB468_120_03
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: miRNA_24_IL1_a


title: miRNA_24_0_c


title: miRNA_72_0_a


title: miRNA_24_0_b


title: CLG_2: M. truncatula root with Gongronella sp. w5 inoculation_rep2


title: R8 Met-Hcy+ 0.5h rep3

description:
R8_030_03
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv

value: Met-Hcy+ 30min (for 0.5h) - 370uM Homocysteine


title: R8 Met-Hcy+ 0.5h rep2

description:
R8_030_02
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: R8  Met-Hcy+ 12h rep3

description:
R8_720_03
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: mRNA_24_TNF_b


title: MB468 Met-Hcy+ 12h rep2

description:
MB468_720_02
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: miRNA_24_0_a


title: R8 Met-Hcy+ 0.5h rep1

description:
R8_030_01
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: MB468 Met-Hcy+ 0.5h rep3

description:
MB468_030_03
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: MB468 Met-Hcy+ 0.5h rep2

description:
MB468_030_02
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: miRNA_12_TNF_c


title: R8  Met+ 0h rep2

description:
R8_000_02
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv

value: untreated, Met+ 0h - 100uM Methionine


title: MB468 Met-Hcy+ 0.5h rep1

description:
MB468_030_01
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: R8  Met+ 0h rep3

description:
R8_000_03
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: miRNA_12_TNF_b


title: MB468  Met-Hcy+ 2h rep1

description:
MB468_120_01
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: miRNA_12_TNF_a


title: miRNA_12_IL1_b


title: MB468 Met+ 0h rep1

description:
MB468_000_01
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: miRNA_12_IL1_a


title: MB468 Met+ 0h rep3

description:
MB468_000_03
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: miRNA_12_0_b


title: MB468 Met+ 0h rep2

description:
MB468_000_02
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv


title: NC2-Input

city: Hangzhou

first: Yunhao

address: 79 Qingchun Road

institute: The First Affiliated Hospital, College of Medicine, Zhejiang University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
For meRIP seq, after removal of rRNA and tRNA, sequenced reads were mapped to hg19 using hisat2-align-s (v2.0.5). PCR duplicates were further removed with Picard (v2.16.0) and high quality mapped reads were extracted by samtools view (v0.1.09) “-q 30”. Differenct Regions enriched in the meRIP RNA samples over input RNA samples were identified as m6A peaks using exomePeak(v2.6.0) peak-caller.
Genome_build: hg19
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bed files were generated using exomePeak.

source_name: HCCLM3 cells

growth_protocol: HCCLM3 cells were incubated at 37°C in 5% CO2 incubator with the humidified environment. And they were cultured with Minimum Essential Media (MEM) which were routinely supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was extracted with TRIzol reagent.
mRNA was enriched from total RNA with Poly(A) mRNA Magnetic Isolation Module(NEB#E7490) before fragmented chemically to ~150 nts long size, 10% fragmented mRNA was saved as Input sample while the rest part was subjected to IP using anti-m6A antibodies(Synaptic system#202 003). After stringent washing, bound RNA was eluted by competition with N6-methyladenosine (Sigma-Aldrich#M2780) as IP samples. IP and input library construction was carried out simultaneously with VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (Box2&3, Vazyme#NR603). Qualities of each library were validated using an Agilent 2100 Bioanalyzer, and successful libraries of sample pairs (input and IP) were sequenced on illumina Novaseq sequencer with PE150 strategy.
MeRIP-seq

treatment_protocol: HCCLM3 cells were transfected with lentiviruses expressing Flag-ALKBH5 (OE groups) or empty vector (NC groups) (MOI=30). They were then filtrated using 3-5 μg/ml puromycin for more than one week until the efficiency was examined by qPCR and immunoblot analysis.

value: HCCLM3 cells

tag: cell type

value: hepatocellular carcinoma

value: ALKBH5 -normal

tag: merip antibody


title: miRNA_12_0_a


title: miRNA_12_0_c


title: miRNA_12_IL1_c


title: OE2-IP

tag: cell line

value: anti-m6A antibodies(Synaptic system, #202 003)


title: NC1-IP


title: OE2-Input


title: OE1-IP


title: NC2-IP


title: OE1-Input


title: NC1-Input


title: ED_hiPSC-CM_H3K27ac_HiChIP

city: Stanford

first: Lei

last: Tian

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

data_processing:
ATAC-Seq reads alignment using Bowtie v2.2.6
Sort/remove duplicates using Sambamba v0.6.5
Convert to bam using Samtools v1.2.0
Count feature coverage around features using Deeptools v2.0.0
Count feature coverages using Rsubread v1.26.1
Trim reads/ quality control using Trim Galore v0.4.2
RNA-Seq reads alignment using STAR v2.5.3a
Count feature coverage around transcriptomic features using fetureCounts v1.5.0
Count feature coverages using igvtools v2.3.91
Detect differential regions using DESeq2 v1.16.1
ChIP-seq peaks called using MACS2 version 2.1.1
Genome_build: hg19/panTro4/gorGor3/rheMac3/mm9
Supplementary_files_format_and_content: TDF and BW format, read coverage

source_name: hiPSC-CM (Enhancer Deletion)

growth_protocol: Pluripotent cells were grown on Matrigel-coated plates (1:100 Matrigel in E8 medium) using chemically defined E8 medium. The medium was changed daily and cells were passaged every 3-4 days using EDTA or Accutase. Cardiomyocytes were maintained in RPMI + B27+ with media change every other day.

extract_protocol:
For RNA-seq, RNA was isolated using miRNeasy kit (Qiagen) following the manufacture’s protocol. For ATAC-seq, 100,000 cells were centrifuged 500 g for 5 min at room temperature. The cell pellet was resuspended in 50 ml lysis buffer (10 mM Tris–Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.01% Igepal CA-630) and centrifuged immediately 500 g for 10 min at 4°C. The cell pellet was resuspended in 50 ml transposase mixture (25 ul 2×TD buffer, 22.5 μl dH2O, and 2.5 μl Illumina Tn5 transposase or with final concentration of 100 nM Atto-590-labeled in-house Tn5) and incubated at 37°C for 30 min. After transposition, the mixture was purified with the Qiagen Mini-purification kit and eluted in 10 ul Qiagen EB elution buffer. For transgenic BANCR embryos plasmid vector construction (pRP[Exp]-BetaMHC>hBANCR) and purification, pronuclear plasmid injection of FVB embryos, harvesting and genotyping of E16 embryos were performed by Cyagen Biosciences (Santa Clara, CA,USA). Total RNA was isolated from extracted embryo hearts that were plasmid positive (n=2) or negative (n=2).
Total RNA was submitted to a core facility (Stanford Functional Genomics) for library preparation and Illumina sequencing. For ATAC-seq, sequencing libraries were prepared following the original ATAC-seq protocol (Buenrostro, J. D. et al. Nat Methods 10, 1213-1218 (2013)). The HiChIP protocol was performed as previously described (Mumbach, M. R. et al. Nat Methods 13, 919-922 (2016)).

treatment_protocol: Cardiomyocytes were differentiated from human and NHP pluripotent cells. Briefly, differentiation medium consisted of RPMI-1640 media (11875-085, Life Technologies) supplemented with B27® minus insulin (A1895601, Life Technologies) (RPMI + B27-). To this medium, various small molecules were added over a week-long timetable as previously described. On the first day (D0) of differentiation, 6 µM CHIR 99021 (C-6556, LC Laboratories) was added. On D2, media was aspirated and replaced with RPMI + B27-. On D3, media was aspirated and replaced with 5 µM of IWR-1 (S7086, Selleck Chemicals) in RPMI + B27-. Media was replaced with RPMI + B27- on D5 and RPMI plus B27 supplemented with insulin (17504-044, Life Technologies) (RPMI + B27+) on D7.

value: hiPSC-CM

tag: gender

value: male

tag: differentiation days

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: R8  Met+ 0h rep1

description:
R8_000_01
RAW_gene_count_matrix.csv
DESeq2_normalized_filtered_count_matrix.csv
DESeq2_results.csv

tag: treatment


title: miRNA_4_TNF_c

value: tissue-engineered cartilage

value: 20 ng/mL TNF-alpha


title: WT_hiPSC-CM_H3K27ac_HiChIP

description:
H7_HiChIP_H3K27ac_r2_me-GTAGAGGA-GGGCCGGT_S2_L006
processed data file:
WT_hPSC-CM_HiChIP_H3K27ac_combined.hic
WT_hPSC-CM_HiChIP_H3K27ac_combined_FitHiCq7_5kb_WashU.txt

source_name: hiPSC-CM

value: female


title: WT_hESC-CM_H3K27ac_HiChIP

description:
H7_HiChIP_H3K27ac_r1_Mo-AAGAGGCA-GGGCCGGT_S1_L006
processed data file:
WT_hPSC-CM_HiChIP_H3K27ac_combined.hic
WT_hPSC-CM_HiChIP_H3K27ac_combined_FitHiCq7_5kb_WashU.txt

source_name: H7 hESC-CM

value: H7 hESC-CM


title: miRNA_4_TNF_b


title: ED_hiPSC-CM_2_RNA-seq


title: miRNA_4_TNF_a


title: ED_hiPSC-CM_1_RNA-seq


title: WT_hiPSC-CM_2_RNA-seq

source_name: hiPSC-CM (isogenic WT for ED hiPSC-CM)


title: miRNA_4_IL1_c

value: 1 ng/mL IL-1beta


title: miRNA_4_IL1_a


title: WT_hiPSC-CM_ATAC-seq


title: miRNA_4_0_c

value: control


title: miRNA_4_0_a


title: miRNA_4_0_b


title: miRNA_0_0_c


title: WT_hiPSC-CM_1_RNA-seq


title: Tetracycline 2

city: Middletown

first: Joseph

last: Coolon

state: CT

address: 52 Lawn Avenue

department: Biology

institute: Wesleyan University

description:
134486_TACTCCAG-CCTATACC_S8
processed data file: SANCHEZ_et_al_2020_TET_cuffdiff.txt

data_processing:
FASTQC on each of the 12 raw fastq files
Bowtie2 alignment using the S. cerevisae reference genome available at the time of analysis.
Cuffdiff for quantification and differential expression analysis using the S. cerevisae reference genome available at the time of analysis and gene files available at the time of analysis with geometric library normalization
Genome_build: Saccharomyces_cerevisiae.R64-1-1.97.dna.toplevel.fa
Supplementary_files_format_and_content: Tab-delimited Cuffdiff output in text format

organism: Saccharomyces cerevisiae

source_name: Tetracycline_yeast pellet

extract_protocol:
Total RNA was extracted from pelleted cells using Promega SV Total RNA Isolation System
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Yeast was grown in liquid culture (control-YPD) or control media supplemnted with 1.5µg/ml of Dox, Tet or 4EP

value: Tetracycline


title: miRNA_0_0_a


title: Tetracycline 1

description:
134485_TAGGAGCT-GTTAAGGC_S7
processed data file: SANCHEZ_et_al_2020_TET_cuffdiff.txt


title: Control 1

description:
134479_TTACCGAC-CGTATTCG_S1
processed data file: SANCHEZ_et_al_2020_DOX_cuffdiff.txt

source_name: Control_yeast pellet

value: Control


title: Doxycycline 2

description:
134483_AAGACCGT-CAATCGAC_S5
processed data file: SANCHEZ_et_al_2020_DOX_cuffdiff.txt

source_name: Doxycycline_yeast pellet

value: Doxycycline


title: Doxycycline 1

description:
134482_TACGGTCT-GCAATGGA_S4
processed data file: SANCHEZ_et_al_2020_DOX_cuffdiff.txt


title: Tetracycline 3

description:
134487_AGTGACCT-CTCCTAGA_S9
processed data file: SANCHEZ_et_al_2020_TET_cuffdiff.txt


title: 4-Epidoxycycline 2

description:
134489_TCATCTCC-CTAGCAAG_S11
processed data file: SANCHEZ_et_al_2020_4ED_cuffdiff.txt

source_name: 4-Epidoxycycline_yeast pellet


title: Control 2

description:
134480_TCGTCTGA-TCAAGGAC_S2
processed data file: SANCHEZ_et_al_2020_DOX_cuffdiff.txt


title: 4-Epidoxycycline 1

description:
134488_AGCCTATC-GTTACGCA_S10
processed data file: SANCHEZ_et_al_2020_4ED_cuffdiff.txt


title: Doxycycline 3

description:
134484_CAGGTTCA-GGCGTTAT_S6
processed data file: SANCHEZ_et_al_2020_DOX_cuffdiff.txt


title: 4-Epidoxycycline 3

description:
134490_CCAGTATC-ATCTCGCT_S12
processed data file: SANCHEZ_et_al_2020_4ED_cuffdiff.txt


title: miRNA_4_IL1_b


title: rhiPSC-CM

description: abundance data: primates.read.counts.txt

data_processing:
ATAC-Seq reads alignment using Bowtie v2.2.6
Sort/remove duplicates using Sambamba v0.6.5
Convert to bam using Samtools v1.2.0
Count feature coverage around features using Deeptools v2.0.0
Count feature coverages using Rsubread v1.26.1
Trim reads/ quality control using Trim Galore v0.4.2
RNA-Seq reads alignment using STAR v2.5.3a
Count feature coverage around transcriptomic features using fetureCounts v1.5.0
Count feature coverages using igvtools v2.3.91
Detect differential regions using DESeq2 v1.16.1
Genome_build: hg19/panTro4/gorGor3/rheMac3/mm9
Supplementary_files_format_and_content: TDF format, read coverage

organism: Macaca mulatta

source_name: Rhesus macaque iPSC-CM

value: iPSC-CM


title: giPSC

organism: Gorilla gorilla

source_name: Gorilla iPSC

value: iPSC


title: hiPSC-CM_YAP1_ChIP-seq

value: anti-YAP1 antibody (Novus; NB110)


title: rhiPSC

source_name: Rhesus macaque iPSC


title: Control 3

description:
134481_TTCCAGGT-AAGCACTG_S3
processed data file: SANCHEZ_et_al_2020_DOX_cuffdiff.txt


title: rRNA_COLD_CDE1

first: yun

last: wang

state: Anhui

address: 443 HUANGSHAN ROAD

institute: University of Science and Technology of China

description: 26S rRNA and 5.8S rRNA

data_processing:
The Illumina-generated raw reads were first filtered to remove adaptors, low quality tags as well as contaminants to get clean reads at BGI Shenzhen. Clean reads ranging from 17 to 30 nt were mapped to the C. elegans genome and the transcriptome assembly WS243, respectively, using Bowtie2 with default parameters (Langmead and Salzberg Nat Methods 9: 357-359. (2012)). The number of reads targeting each gene was counted by custom Perl scripts and displayed by IGV (Thorvaldsdottir et al. Brief Bioinform 14: 178-192. (2013)). Total mappable reads excluding sense rRNA were used for normalization.
gel purified and then deep sequenced using an Illumina platform, according to the manufacturer′s instructions, by Novogene (Beijing, China). The number of reads with distinct 3′ -end modifications were counted by custom Perl scripts.
Genome_build: WS243
Supplementary_files_format_and_content: .txt files.located in /count content. Basically, the reads were aligned to C. elegans transcriptome WS243 version by Bowtie2 and counted the number of reads targeting each transcript by Perl script.

organism: Caenorhabditis elegans

source_name: L3 stage

growth_protocol: C. elegans strains were cultured on RNAi plates with E. coli HT115 as the food source in a temperature controlled incubator. Worms were maintained at 20°C or 4°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm concentrated HT115 plate (approximately 3000 L2s per plate).

extract_protocol:
total RNA were extracted from L3 larva, digested by DNase I, and then ligated to the following 3′ RNA linkers with T4 RNA ligase (Thermo #EL0021) (1 μg total RNA, 2 μl 3′ RNA linker (10 μM), 1 μl 10× T4 RNA ligation buffer, 2 μl T4 RNA ligase) by incubating at 37 °C for 38 min.
PCR Free
Briefly, total RNA were extracted from L3 larva, digested by DNase I, and then ligated to the following 3′ RNA linkers with T4 RNA ligase (Thermo #EL0021) (1 μg total RNA, 2 μl 3′ RNA linker (10 μM), 1 μl 10× T4 RNA ligation buffer, 2 μl T4 RNA ligase) by incubating at 37 °C for 30 min.  3’ RNA linker-1:   5’-pGATCCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’ (the underlined sequence served as a barcode for sample labeling).  3’ RNA linker-2:   5’-pCGACACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’  3’ RNA linker-3:   5’-pGTACCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’.  The RNAs were reverse transcribed with the following primer:  Universal 3’ linker RT:   5’-GCTGGAATTCGCGGTTAAATCCTTGGTGCCCGAGTGT-3’. The cDNAs were PCR amplified (16 cycles) with the primers 26S rRNA-F: 5’-CAGATCACTCTGGTTCAATGTC-3’ and universal 3’ linker RT primer, or with the primers 5.8S rRNA-F: 5’-GGTTGCATCGAGTATCGATGAA-3’ and universal 3’ linker RT primer, gel purified and then deep sequenced using an Illumina platform, according to the manufacturer′s instructions, by Novogene (Beijing, China). The number of reads with distinct 3’-end modifications were counted by custom Perl scripts. Three biological replicates were conducted in each genotype or treatment.
PCR free

tag: temperature

value: 4 C  n HT115


title: miRNA_0_0_b


title: mouse_1.ST_HSC

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

data_processing:
Illumina HD.3.4.0/RTA 2.7.7 software used for sequencing and basecalling.
10x Genomics Cell Ranger v3.1.0 used for sequencing read alignment and UMI counting.
Genome_build: mm10
Supplementary_files_format_and_content: mtx, tsv: UMI counts of individual genes in single cells

source_name: Bone marrow

extract_protocol:
Single cells were captured using the 10x Chromium system and further processed following the Chromium Single Cell 3’ Reagent Kit (v3) protocol.
cDNA library were fragmented and the sequencing library was generated according to the Single Cell 3’ Reagent Kit (v3) protocol.

tag: mouse

value: mouse #1

value: ST-HSC

value: Tie2-bG-Micm x RosaYFP

tag: age at experiment

value: 14 weeks


title: mouse_2.ST_HSC

value: mouse #2

value: male


title: mouse_2.LT_HSC

value: LT-HSC


title: rRNA_COLD_CDE1_CDE1GFP

description: 26S rRNA and 5.8S rRNA

growth_protocol: C. elegans strains were cultured on RNAi plates with E. coli HT115 as the food source in a temperature controlled incubator. Worms were maintained at 20°C or 4°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm concentrated HT115 plate (approximately 3000 L0s per plate).

extract_protocol:
total RNA were extracted from L3 larva, digested by DNase I, and then ligated to the following 3′ RNA linkers with T4 RNA ligase (Thermo #EL0021) (1 μg total RNA, 2 μl 3′ RNA linker (10 μM), 1 μl 10× T4 RNA ligation buffer, 2 μl T4 RNA ligase) by incubating at 37 °C for 40 min.
PCR Free
Briefly, total RNA were extracted from L3 larva, digested by DNase I, and then ligated to the following 3′ RNA linkers with T4 RNA ligase (Thermo #EL0021) (1 μg total RNA, 2 μl 3′ RNA linker (10 μM), 1 μl 10× T4 RNA ligation buffer, 2 μl T4 RNA ligase) by incubating at 37 °C for 30 min.  3’ RNA linker-1:   5’-pGATCCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’ (the underlined sequence served as a barcode for sample labeling).  3’ RNA linker-2:   5’-pCGACACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’  3’ RNA linker-3:   5’-pGTACCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’.  The RNAs were reverse transcribed with the following primer:  Universal 3’ linker RT:   5’-GCTGGAATTCGCGGTTAAATCCTTGGTGCCCGAGTGT-3’. The cDNAs were PCR amplified (16 cycles) with the primers 26S rRNA-F: 5’-CAGATCACTCTGGTTCAATGTC-3’ and universal 3’ linker RT primer, or with the primers 5.8S rRNA-F: 5’-GGTTGCATCGAGTATCGATGAA-3’ and universal 3’ linker RT primer, gel purified and then deep sequenced using an Illumina platform, according to the manufacturer′s instructions, by Novogene (Beijing, China). The number of reads with distinct 3’-end modifications were counted by custom Perl scripts. Three biological replicates were conducted in each genotype or treatment.
PCR free


title: rRNA_COLD_N2

description: 26S rRNA and 5.8S rRNA

growth_protocol: C. elegans strains were cultured on RNAi plates with E. coli HT115 as the food source in a temperature controlled incubator. Worms were maintained at 20°C or 4°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm concentrated HT115 plate (approximately 3000 L4s per plate).

extract_protocol:
total RNA were extracted from L3 larva, digested by DNase I, and then ligated to the following 3′ RNA linkers with T4 RNA ligase (Thermo #EL0021) (1 μg total RNA, 2 μl 3′ RNA linker (10 μM), 1 μl 10× T4 RNA ligation buffer, 2 μl T4 RNA ligase) by incubating at 37 °C for 36 min.
PCR Free
Briefly, total RNA were extracted from L3 larva, digested by DNase I, and then ligated to the following 3′ RNA linkers with T4 RNA ligase (Thermo #EL0021) (1 μg total RNA, 2 μl 3′ RNA linker (10 μM), 1 μl 10× T4 RNA ligation buffer, 2 μl T4 RNA ligase) by incubating at 37 °C for 30 min.  3’ RNA linker-1:   5’-pGATCCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’ (the underlined sequence served as a barcode for sample labeling).  3’ RNA linker-2:   5’-pCGACACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’  3’ RNA linker-3:   5’-pGTACCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’.  The RNAs were reverse transcribed with the following primer:  Universal 3’ linker RT:   5’-GCTGGAATTCGCGGTTAAATCCTTGGTGCCCGAGTGT-3’. The cDNAs were PCR amplified (16 cycles) with the primers 26S rRNA-F: 5’-CAGATCACTCTGGTTCAATGTC-3’ and universal 3’ linker RT primer, or with the primers 5.8S rRNA-F: 5’-GGTTGCATCGAGTATCGATGAA-3’ and universal 3’ linker RT primer, gel purified and then deep sequenced using an Illumina platform, according to the manufacturer′s instructions, by Novogene (Beijing, China). The number of reads with distinct 3’-end modifications were counted by custom Perl scripts. Three biological replicates were conducted in each genotype or treatment.
PCR free


title: mouse_1.LT_HSC


title: Exp4.GMP2

source_name: GMP

tag: strain background

value: PolyloxExpress mice

tag: age

value: between 7 and 20 weeks after birth

value: Bone marrow

tag: experiment

value: exp 4

value: Granulocyte-monocyte progenitors

tag: replicate

value: sample 2


title: FaDucell_60Gy_rep1

city: Chongqing

first: Liu

last: Chuan

address: No 1, Yixueyuan Road

department: Otorhinolaryngology

institute: Chongqing Medical University

description: Gene expression in 60Gy-irradiated FaDu cells

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: FaDu cell,60Gy

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: The cells were cultured in standard DMEM media (Hyclone, Logan City, Ulah, USA) supplemented with 10% fetal bovine serum (PBS), 100 units/ml penicillin, and 100 μg/ml streptomycin at 37°C and 5% CO2.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Radiation-resistant cell was derived from parental FaDu cell after repeated exposure to ionizing radiation with a dose of 10 Gy each time (16 MV X-rays) using a linear accelerator (UNIQUE; Varian, Palo Alto, CA, USA) at a dose rate of approximately 3 Gy/min. An interval of 3 to 4 weeks between each radiation allowed the surviving cells to regenerate. Stable passage cells after treating with doese of 20 Gy, 40 Gy, 60 Gy radiation were collected respectively.

value: FaDu

value: x-ray radiation

tag: dose


title: rRNA_CDE1_CDE1GFP

description: 26S rRNA and 5.8S rRNA

growth_protocol: C. elegans strains were cultured on RNAi plates with E. coli HT115 as the food source in a temperature controlled incubator. Worms were maintained at 20°C or 4°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm concentrated HT115 plate (approximately 3000 L10s per plate).

extract_protocol:
total RNA were extracted from L3 larva, digested by DNase I, and then ligated to the following 3′ RNA linkers with T4 RNA ligase (Thermo #EL0021) (1 μg total RNA, 2 μl 3′ RNA linker (10 μM), 1 μl 10× T4 RNA ligation buffer, 2 μl T4 RNA ligase) by incubating at 37 °C for 30 min.
PCR Free
Briefly, total RNA were extracted from L3 larva, digested by DNase I, and then ligated to the following 3′ RNA linkers with T4 RNA ligase (Thermo #EL0021) (1 μg total RNA, 2 μl 3′ RNA linker (10 μM), 1 μl 10× T4 RNA ligation buffer, 2 μl T4 RNA ligase) by incubating at 37 °C for 30 min.  3’ RNA linker-1:   5’-pGATCCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’ (the underlined sequence served as a barcode for sample labeling).  3’ RNA linker-2:   5’-pCGACACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’  3’ RNA linker-3:   5’-pGTACCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’.  The RNAs were reverse transcribed with the following primer:  Universal 3’ linker RT:   5’-GCTGGAATTCGCGGTTAAATCCTTGGTGCCCGAGTGT-3’. The cDNAs were PCR amplified (16 cycles) with the primers 26S rRNA-F: 5’-CAGATCACTCTGGTTCAATGTC-3’ and universal 3’ linker RT primer, or with the primers 5.8S rRNA-F: 5’-GGTTGCATCGAGTATCGATGAA-3’ and universal 3’ linker RT primer, gel purified and then deep sequenced using an Illumina platform, according to the manufacturer′s instructions, by Novogene (Beijing, China). The number of reads with distinct 3’-end modifications were counted by custom Perl scripts. Three biological replicates were conducted in each genotype or treatment.
PCR free

tag: genotype


title: rRNA_CDE1_SUSI1

description: 26S rRNA and 5.8S rRNA

growth_protocol: C. elegans strains were cultured on RNAi plates with E. coli HT115 as the food source in a temperature controlled incubator. Worms were maintained at 20°C or 4°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm concentrated HT115 plate (approximately 3000 L6s per plate).

extract_protocol:
total RNA were extracted from L3 larva, digested by DNase I, and then ligated to the following 3′ RNA linkers with T4 RNA ligase (Thermo #EL0021) (1 μg total RNA, 2 μl 3′ RNA linker (10 μM), 1 μl 10× T4 RNA ligation buffer, 2 μl T4 RNA ligase) by incubating at 37 °C for 34 min.
PCR Free
Briefly, total RNA were extracted from L3 larva, digested by DNase I, and then ligated to the following 3′ RNA linkers with T4 RNA ligase (Thermo #EL0021) (1 μg total RNA, 2 μl 3′ RNA linker (10 μM), 1 μl 10× T4 RNA ligation buffer, 2 μl T4 RNA ligase) by incubating at 37 °C for 30 min.  3’ RNA linker-1:   5’-pGATCCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’ (the underlined sequence served as a barcode for sample labeling).  3’ RNA linker-2:   5’-pCGACACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’  3’ RNA linker-3:   5’-pGTACCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’.  The RNAs were reverse transcribed with the following primer:  Universal 3’ linker RT:   5’-GCTGGAATTCGCGGTTAAATCCTTGGTGCCCGAGTGT-3’. The cDNAs were PCR amplified (16 cycles) with the primers 26S rRNA-F: 5’-CAGATCACTCTGGTTCAATGTC-3’ and universal 3’ linker RT primer, or with the primers 5.8S rRNA-F: 5’-GGTTGCATCGAGTATCGATGAA-3’ and universal 3’ linker RT primer, gel purified and then deep sequenced using an Illumina platform, according to the manufacturer′s instructions, by Novogene (Beijing, China). The number of reads with distinct 3’-end modifications were counted by custom Perl scripts. Three biological replicates were conducted in each genotype or treatment.
PCR free

value: cde-1(tm936) dsRNA susi-1


title: rRNA_SUSI1

description: 26S rRNA and 5.8S rRNA

growth_protocol: C. elegans strains were cultured on RNAi plates with E. coli HT115 as the food source in a temperature controlled incubator. Worms were maintained at 20°C or 4°C prior to the experiment. Worms were synchronized by using the standard egg-prep protocol. L1s were released onto 10 cm concentrated HT115 plate (approximately 3000 L8s per plate).

extract_protocol:
total RNA were extracted from L3 larva, digested by DNase I, and then ligated to the following 3′ RNA linkers with T4 RNA ligase (Thermo #EL0021) (1 μg total RNA, 2 μl 3′ RNA linker (10 μM), 1 μl 10× T4 RNA ligation buffer, 2 μl T4 RNA ligase) by incubating at 37 °C for 32 min.
PCR Free
Briefly, total RNA were extracted from L3 larva, digested by DNase I, and then ligated to the following 3′ RNA linkers with T4 RNA ligase (Thermo #EL0021) (1 μg total RNA, 2 μl 3′ RNA linker (10 μM), 1 μl 10× T4 RNA ligation buffer, 2 μl T4 RNA ligase) by incubating at 37 °C for 30 min.  3’ RNA linker-1:   5’-pGATCCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’ (the underlined sequence served as a barcode for sample labeling).  3’ RNA linker-2:   5’-pCGACACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’  3’ RNA linker-3:   5’-pGTACCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’.  The RNAs were reverse transcribed with the following primer:  Universal 3’ linker RT:   5’-GCTGGAATTCGCGGTTAAATCCTTGGTGCCCGAGTGT-3’. The cDNAs were PCR amplified (16 cycles) with the primers 26S rRNA-F: 5’-CAGATCACTCTGGTTCAATGTC-3’ and universal 3’ linker RT primer, or with the primers 5.8S rRNA-F: 5’-GGTTGCATCGAGTATCGATGAA-3’ and universal 3’ linker RT primer, gel purified and then deep sequenced using an Illumina platform, according to the manufacturer′s instructions, by Novogene (Beijing, China). The number of reads with distinct 3’-end modifications were counted by custom Perl scripts. Three biological replicates were conducted in each genotype or treatment.
PCR free


title: giPSC-CM

source_name: Gorilla iPSC-CM

tag: tissue

value: iPSC-CM


title: FaDucell_0Gy_rep1

description: Gene expression in 0Gy-irradiated FaDu cells

source_name: FaDu cell,0Gy

value: control


title: FaDucell_20Gy_rep1

description: Gene expression in 20Gy-irradiated FaDu cells

source_name: FaDu cell,20Gy


title: FaDucell_40Gy_rep1

description: Gene expression in 40Gy-irradiated FaDu cells

source_name: FaDu cell,40Gy


title: Exp4.GMP1

tag: strain

tag: cell type

value: sample 1


title: Exp4.MEP

source_name: MEP

value: Megakaryocyte-erythrocyte progenitors


title: rRNA_CDE1

description: 26S rRNA and 5.8S rRNA

extract_protocol:
total RNA were extracted from L3 larva, digested by DNase I, and then ligated to the following 3′ RNA linkers with T4 RNA ligase (Thermo #EL0021) (1 μg total RNA, 2 μl 3′ RNA linker (10 μM), 1 μl 10× T4 RNA ligation buffer, 2 μl T4 RNA ligase) by incubating at 37 °C for 28 min.
PCR Free
Briefly, total RNA were extracted from L3 larva, digested by DNase I, and then ligated to the following 3′ RNA linkers with T4 RNA ligase (Thermo #EL0021) (1 μg total RNA, 2 μl 3′ RNA linker (10 μM), 1 μl 10× T4 RNA ligation buffer, 2 μl T4 RNA ligase) by incubating at 37 °C for 30 min.  3’ RNA linker-1:   5’-pGATCCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’ (the underlined sequence served as a barcode for sample labeling).  3’ RNA linker-2:   5’-pCGACACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’  3’ RNA linker-3:   5’-pGTACCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’.  The RNAs were reverse transcribed with the following primer:  Universal 3’ linker RT:   5’-GCTGGAATTCGCGGTTAAATCCTTGGTGCCCGAGTGT-3’. The cDNAs were PCR amplified (16 cycles) with the primers 26S rRNA-F: 5’-CAGATCACTCTGGTTCAATGTC-3’ and universal 3’ linker RT primer, or with the primers 5.8S rRNA-F: 5’-GGTTGCATCGAGTATCGATGAA-3’ and universal 3’ linker RT primer, gel purified and then deep sequenced using an Illumina platform, according to the manufacturer′s instructions, by Novogene (Beijing, China). The number of reads with distinct 3’-end modifications were counted by custom Perl scripts. Three biological replicates were conducted in each genotype or treatment.
PCR free


title: Exp4.CMP

source_name: CMP

value: Common myeloid progenitors


title: Exp4.HSC

source_name: HSC

value: Hematopoietic stem cells


title: Exp4.MPP

source_name: MPP

value: Multipotent progenitors


title: Exp3.HSC1

value: exp 3


title: Exp2.MEP2

value: PolyloxExpress mice

value: exp 2


title: Exp2.MEP1

value: between 7 and 20 weeks after birth

value: Bone marrow


title: Exp2.GMP2

value: Granulocyte-monocyte progenitors


title: Exp2.CMP2

value: sample 2


title: Exp2.GMP1


title: Exp3.proB

source_name: proB

value: Pro B cells


title: Exp2.MPP1


title: Exp2.MPP2


title: Parkinson, 2-way_cell_D22_rep2_batch1_uni (Barcode NGS)

city: Pokfulam, Hong Kong

first: Alan

last: Wong

address: 21 Sassoon Road

department: School of Biomedical Sciences

institute: The University of Hong Kong

description:
SK-N-MC with no treatment.
Two-way Parkinson's Disease gRNA screen_count per million reads.xlsx

data_processing:
(Barcode NGS) fastq files preprocessed and analyzed using customized codes (https://github.com/AWHKU/CombiPIPE)
(RNA-seq) Trimmed pair-end adaptors by Trimmomatic 0.39
(RNA-seq) Aligned sequence reads by STAR aligner version 2.7
(RNA-seq) Extracted raw counts by Rsubread
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: excel files with NGS CPM barcode reads
csv files with RNA-seq raw counts

source_name: Neuroblastoma cells

growth_protocol: SK-N-MC-Cas9 cells were cultured in DMEM supplemented with 10% FBS and 1 X antibiotic-antimycotic (Life Technologies) at 37°C with 5% CO2. OVCAR8-ADR cells and OVCAR8-ADR-Cas9 cells were cultured in RPMI 1640 supplemented with 10% FBS and 1 X antibiotic-antimycotic at 37°C with 5% CO2.

extract_protocol:
For gRNA-library-transduced cell pool, genomic DNA was extracted from cells with DNeasy Blood and Tissue kit (Qiagen). For drug-treated OVCAR8-ADR cells, total RNAs were isolated by MiniBEST universal RNA extraction kit (Takara).
Barcode libraries from NGS and RNA libraries were prepared for sequencing using standard Illumina protocols.
Barcode NGS and RNA-seq

treatment_protocol: For the barcode libraries, SK-N-MC-Cas9 cells and OVCAR8-ADR-Cas9 cells were transduced by the lentiviruses with respective combinatorial gRNA libraries at a multiplicity of infection (MOI) of ~0.3-0.5. For the RNA-seq libraries, OVCAR8-ADR cells were treated with Azacitidine, Fludarabine, Erlotinib, Azacitidine+Fludarabine, Azacitidine+Erlotinib, Fludarabine+Erlotinib, and Azacitidine+Fludarabine+ Erlotinib.

tag: cell line

value: SK-N-MC

value: Untreated


title: Parkinson, 2-way_cell_D22_rep2_batch1_mpp (Barcode NGS)

description:
SK-N-MC treated with 1-methyl-4-phenylpyridinium replicate 2.
Two-way Parkinson's Disease gRNA screen_count per million reads.xlsx

value: 1-methyl-4-phenylpyridinium (600uM)


title: Parkinson, 2-way_cell_D22_rep2_batch2_uni (Barcode NGS)


title: Parkinson, 2-way_cell_D22_rep2_batch3_uni (Barcode NGS)


title: Parkinson, 2-way_cell_D22_rep2_batch2_mpp (Barcode NGS)


title: Parkinson, 2-way_cell_D22_rep2_batch3_mpp (Barcode NGS)


title: Exp3.HSC2


title: Parkinson, 2-way_cell_D22_rep1_batch2_ro (Barcode NGS)

description:
SK-N-MC treated with Rotenone replicate 1.
Two-way Parkinson's Disease gRNA screen_count per million reads.xlsx


title: Parkinson, 2-way_cell_D22_rep1_batch3_ro (Barcode NGS)


title: Exp1.proB

value: exp 1


title: Exp1.CMP

value: sample 1


title: Exp2.CMP1


title: Exp1.CLP

source_name: CLP

value: Common lymphoid progenitors


title: Parkinson, 2-way_cell_D22_rep2_batch3_ro (Barcode NGS)

description:
SK-N-MC treated with Rotenone replicate 2.
Two-way Parkinson's Disease gRNA screen_count per million reads.xlsx


title: Exp1.MPP2


title: Exp3.CLP2


title: Exp3.preT

source_name: preT

value: Thymus

value: Pre T cells


title: Parkinson, 2-way_cell_D22_rep1_batch1_ro (Barcode NGS)


title: Parkinson, 2-way_cell_D22_rep2_batch2_ro (Barcode NGS)


title: Exp1.HSC2

value: Hematopoietic stem cells


title: Exp1.MPP1

value: Multipotent progenitors


title: Bone Metastasis 5

data_processing:
The resulting average sequencing depth was more than 80x, and reads were mapped to the mouse mm10 genome build using bwa
Substitutions and indels were called using SAVI; only variants with a mutant allele frequency of 5% or greater were included for further analysis
Copy number variations were analyzed and called using CNVkit
Genome_build: Mouse: UCSC/mm10

source_name: Bone Metastasis 5 (Mouse 2262)

extract_protocol:
Genomic DNA was isolated from snap-frozen tissues using the DNeasy Blood & Tissue Kit (Qiagen) and DNA quality confirmed by gel electrophoresis and visual observation of a clear, non-degraded main band of DNA.
Sequencing was done by BGI Americas Corporation using the HiSeq4000 platform and Agilent Sure Select Mouse Exon kit (50Mb) for exome capture to produce paired-end sequenced data of up to 150bp read length.

value: Mixed strain, predominantly C57BL/6

value: 9 months

value: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+; R26R-CAG-LSL-EYFP/+


title: Exp2.HSC2

value: PolyloxExpress mice

value: between 7 and 20 weeks after birth

value: Bone marrow

value: exp 2


title: Exp1.HSC1


title: Parkinson, 2-way_cell_D22_rep1_batch3_mpp (Barcode NGS)

description:
SK-N-MC treated with 1-methyl-4-phenylpyridinium replicate 1.
Two-way Parkinson's Disease gRNA screen_count per million reads.xlsx

value: SK-N-MC


title: Lung Metastasis 5

source_name: Lung Metastasis 5 (Mouse 2262)

value: Lung


title: Primary Tumor 5

source_name: Prostate tumor 5, AP lobe (Mouse 2262)

value: Prostate


title: Bone Metastasis 4

source_name: Bone Metastasis 4 (Mouse 9788)

value: 5 months


title: Parkinson, 2-way_cell_D22_rep1_batch2_mpp (Barcode NGS)

value: 1-methyl-4-phenylpyridinium (600uM)


title: Tail 5

source_name: Tail 5 (Mouse 2262)

value: Normal DNA from Tail


title: Parkinson, 2-way_cell_D22_rep1_batch1_mpp (Barcode NGS)


title: Primary Tumor 4

source_name: Prostate tumor 4, DLP lobe (Mouse 9788)


title: Lung Metastasis 4

source_name: Lung Metastasis 4 (Mouse 9788)


title: rRNA_N2

description: 26S rRNA and 5.8S rRNA

source_name: L3 stage

extract_protocol:
total RNA were extracted from L3 larva, digested by DNase I, and then ligated to the following 3′ RNA linkers with T4 RNA ligase (Thermo #EL0021) (1 μg total RNA, 2 μl 3′ RNA linker (10 μM), 1 μl 10× T4 RNA ligation buffer, 2 μl T4 RNA ligase) by incubating at 37 °C for 26 min.
PCR Free
Briefly, total RNA were extracted from L3 larva, digested by DNase I, and then ligated to the following 3′ RNA linkers with T4 RNA ligase (Thermo #EL0021) (1 μg total RNA, 2 μl 3′ RNA linker (10 μM), 1 μl 10× T4 RNA ligation buffer, 2 μl T4 RNA ligase) by incubating at 37 °C for 30 min.  3’ RNA linker-1:   5’-pGATCCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’ (the underlined sequence served as a barcode for sample labeling).  3’ RNA linker-2:   5’-pCGACACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’  3’ RNA linker-3:   5’-pGTACCACACTCGGGCACCAAGGATTTAACCGCGAATTCCAGC-NH2-3’.  The RNAs were reverse transcribed with the following primer:  Universal 3’ linker RT:   5’-GCTGGAATTCGCGGTTAAATCCTTGGTGCCCGAGTGT-3’. The cDNAs were PCR amplified (16 cycles) with the primers 26S rRNA-F: 5’-CAGATCACTCTGGTTCAATGTC-3’ and universal 3’ linker RT primer, or with the primers 5.8S rRNA-F: 5’-GGTTGCATCGAGTATCGATGAA-3’ and universal 3’ linker RT primer, gel purified and then deep sequenced using an Illumina platform, according to the manufacturer′s instructions, by Novogene (Beijing, China). The number of reads with distinct 3’-end modifications were counted by custom Perl scripts. Three biological replicates were conducted in each genotype or treatment.
PCR free


title: Tail 4

source_name: Tail 4 (Mouse 9788)


title: Parkinson, 2-way_cell_D22_rep1_batch2_uni (Barcode NGS)

value: Untreated


title: Bone Metastasis 3

source_name: Bone Metastasis 3 (Mouse 7770)

value: 7 months


title: Exp3.CLP1

value: exp 3

value: Common lymphoid progenitors

value: sample 1


title: Parkinson, 2-way_cell_D22_rep1_batch1_uni (Barcode NGS)


title: Primary Tumor 3

source_name: Prostate tumor 3, DLP lobe (Mouse 7770)

value: Mixed strain, predominantly C57BL/6


title: Lung Metastasis 3

source_name: Lung Metastasis 3 (Mouse 7770)

value: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+; R26R-CAG-LSL-EYFP/+


title: Exp3.MPP

source_name: MPP

value: PolyloxExpress mice

value: Multipotent progenitors


title: Parkinson, 2-way_cell_D10 (Barcode NGS)


title: Tail 3

source_name: Tail 3 (Mouse 7770)


title: Bone Metastasis 2

source_name: Bone Metastasis 2 (Mouse 6100)

value: 6 months


title: Bone Metastasis 1B

source_name: Bone Metastasis 1B (Mouse 1173)


title: Ovarian cancer, 3-way_cell_D26_rep2_batch2 (Barcode NGS)

description: Three-way ovarian cancer gRNA screen_count per million reads.xlsx

source_name: Ovarian cancer cells

value: Lentiviral gRNA library transduction


title: Ovarian cancer, 3-way_cell_D26_rep2_batch3 (Barcode NGS)


title: Tail 2

source_name: Tail (2 Mouse 6100)


title: Ovarian cancer, 3-way_cell_D26_rep2_batch1 (Barcode NGS)


title: Bone Metastasis 1A

source_name: Bone Metastasis 1A (Mouse 1173)


title: Lung Metastasis 1

source_name: Lung Metastasis 1 (Mouse 1173)


title: Tail 1

source_name: Tail 1 (Mouse 1173)


title: Parkinson, 2-way_cell_D22_rep1_batch3_uni (Barcode NGS)

source_name: Neuroblastoma cells

value: SK-N-MC


title: Primary Tumor 1

source_name: Prostate tumor 1, AP lobe (Mouse 1173)


title: Ovarian cancer, 3-way_cell_D26_rep1_batch2 (Barcode NGS)


title: Normal Liver 2

data_processing:
RNA-seq pipeline description: Columbia Genome Center standard pipeline
Libraries were sequenced using Illumina HiSeq2500/4000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp reads for each sample, as a fraction of 280-400 million reads for the whole lane.
We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming. We map the reads to a reference genome (Mouse: UCSC/mm9) using Tophat (version 2.1.0) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation. We test for differentially expressed genes under various conditions using DESeq2. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Genome_build: Mouse: UCSC/mm9
Supplementary_files_format_and_content: Tab-delimited text files include DESeq2 normalized values for each sample

source_name: Liver

extract_protocol:
RNA was prepared from snap-frozen tissues the using MagMAX-96 total RNA isolation kit and only RNA samples having between >200 ng and 1 ug and with an RNA integrity number (RIN) > 8 were used.
Libraries were prepared by the Columbia Genome Center. Poly-A pull-down was used to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required). Libraries were prepared using TruSeq RNA library prep kit v2 or TruSeq Stranded mRNA library prep kit.

value: Liver

value: Intact, un-induced mouse


title: Normal Liver 1

value: 5 months


title: Ovarian cancer, 3-way_cell_D26_rep1_batch1 (Barcode NGS)


title: Liver Metastasis 5

source_name: Liver Metastasis

value: 9 months

value: Intact, mouse without bone metastasis


title: Liver Metastasis 4

value: 8 months

value: Intact, mouse with bone metastasis


title: Ovarian cancer, 3-way_cell_D15_rep2_batch3 (Barcode NGS)


title: Lung Metastasis 2

source_name: Lung Metastasis 2 (Mouse 6100)

value: Lung


title: Liver Metastasis 3


title: Ovarian cancer, 3-way_cell_D15_rep2_batch2 (Barcode NGS)


title: Liver Metastasis 2

value: 7 months


title: Liver Metastasis 1


title: Primary Tumor 2

source_name: Prostate tumor 2, DLP lobe (Mouse 6100)

value: Prostate


title: Bone Metastasis 12

source_name: Bone Metastasis

value: Mixed strain, predominantly C57BL/6

value: Castrated


title: Bone Metastasis 11

value: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+; R26R-CAG-LSL-EYFP/+


title: Parkinson, 2-way_cell_D22_rep2_batch1_ro (Barcode NGS)


title: Ovarian cancer, 3-way_cell_D15_rep1_batch3 (Barcode NGS)


title: Ovarian cancer, 3-way_cell_D15_rep2_batch1 (Barcode NGS)


title: Ovarian cancer, 3-way_cell_D26_rep1_batch3 (Barcode NGS)


title: Lung Metastasis 10

source_name: Lung Metastasis

value: lung

value: Castrated, mouse with bone metastasis


title: Ovarian cancer, 3-way_cell_D15_rep1_batch2 (Barcode NGS)

value: Lentiviral gRNA library transduction


title: Primary Tumor 19

source_name: Prostate tumor, AP lobe

value: prostate

value: Castrated, mouse without bone metastasis


title: Exp3.CMP

source_name: CMP

value: PolyloxExpress mice

value: between 7 and 20 weeks after birth

value: Bone marrow

value: exp 3

value: Common myeloid progenitors

value: sample 1


title: Primary Tumor 18

source_name: Prostate tumor, DLP lobe

value: 10 months


title: Primary Tumor 16


title: Primary Tumor 17

value: 9 months


title: Exp2.HSC1

source_name: HSC

value: exp 2

value: Hematopoietic stem cells


title: Ovarian cancer, 3-way_cell_D15_rep1_batch1 (Barcode NGS)

source_name: Ovarian cancer cells


title: Ovarian cancer, 3-way_cell_D9 (Barcode NGS)


title: Primary Tumor 15

value: Mixed strain, predominantly C57BL/6

value: 6 months


title: Primary Tumor 14

value: 7 months

value: Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+; R26R-CAG-LSL-EYFP/+


title: Ovarian cancer, 2-way_cell_D21_rep2 (Barcode NGS)

description: Two-way ovarian cancer gRNA screen_count per million reads.xlsx

value: Lentiviral gRNA library transduction


title: Ovarian cancer, 2-way_cell_D21_rep1 (Barcode NGS)


title: negative control shRNA2

city: Shanghai

first: Shan

last: Huang

address: 1111 Xianxia Road

department: Department of Endocrinology

institute: Tongren Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Adapters and reads with lower mapping quility were trimed by trim_galore.
Reads were aligned to the mouse mm10 reference genomes using the Hisat2.
Raw counts were quantified against Ensemble transcript annotations by featureCount.
Differentially expressing genes were detected by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw count for each sample.

source_name: MMC_negative control shRNA

growth_protocol: Cultured in Dulbecco modified Eagle medium (DMEM) (Gibco, USA) with 10% fetal bovine serum (FBS) (Gibco, USA) in a humidified incubator with 5% CO2 at 37°C;

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA), then RNA concentration, purity and integrity were assessed. Subsequently, mRNA was captured by Dynabeads Oligo (dT)25 (Thermo Fisher Scientific, USA), then first and second strands of the cDNA were synthesized and library fragments were purified using AMPure XP system (Beckman Coulter, USA).
PCR assay and measurement of libraries quality were conducted using Bioanalyzer 2100 system (Agilent Technologies, USA), then clustering of index-coded samples was performed using HiSeq PE Cluster Kit v4 cBot (Illumina, USA), and the libraries were sequenced on Illumina Hiseq X10 platform (Illumina, USA) followed by that 150 bp paired-end reads were produced after cluster generation for mRNA.

treatment_protocol: Then 30 mmol/L glucose were added to treat SV40 MES13 cells for 96h to construct the DN cellular model.

value: SV40 MES 13

value: mouse mesangial cells (MMC)

tag: genotype/variation

value: negative control shRNA


title: negative control shRNA3


title: Ovarian cancer, 2-way_cell_D15_rep2 (Barcode NGS)


title: negative control shRNA1


title: Ovarian cancer, 2-way_cell_D15_rep1 (Barcode NGS)


title: LncRNA Dlx6os1 ShRNA3

source_name: MMC_LncRNA Dlx6os1 shRNA

value: LncRNA Dlx6os1 ShRNA


title: LncRNA Dlx6os1 shRNA1


title: LncRNA Dlx6os1 shRNA2


title: Lung Metastasis 11

value: lung

value: Castrated, mouse with bone metastasis


title: Gravity

city: Cochin

first: Ravi

last: Gupta

state: Kerala

address: Plot no: 43A,SDF, 3rd floor, A Block,CSEZ, Kakkanad

department: Bioinformatics

country: India

institute: SciGenom Labs Pvt. Ltd.

data_processing:
Illumina bcl2fastq Conversion Software v1.8.4 used for basecalling.
Alignment performed using STAR (2.4.2a) program to the Ensembl Release 81 Gallus gallus reference genome and genemodel
cuffllinks (version 2.2.1) used for gene and isoform expression estimation
cuffdiff program of cufflinks (version 2.2.1) used for differential expression  analysis
Genome_build: Hg19 Human Genome
Supplementary_files_format_and_content: Gene expressionof the samples in excel format

source_name: HUVECs

growth_protocol: cells were grown in cell culture plates were subjected to microgravity condition for 2h at 37 c. Follwed by this, isolation of RNA were done for Gravity, and microgravity samples.

extract_protocol:
Total RNA was isolated using Trizol reagent, Invitrogen Life Technologies. The total RNA samples was checked for quality using Nanodrop and 1% agarose gel. RNA  samples, free of DNA and protein contamination was resuspended in in nuclease free water. 1ug of RNA sample for each stage was given for Next Generation Sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Three-dimensional clinostat was used to simulate microgravity. Cells grown in culture plates were subjected to microgravity for 2 h at 37°  C.   cycles of rotation were electronically  controlled at an outer frame rotation of 20 rpm and an inner frame rotation of 13 rpm to achieve microgravity condition. Then, RNA isolation were done using standard protocol.

tag: sample type

value: static


title: Microgravity

value: clinostat


title: Bone Metastasis 10

value: Intact


title: 1_2

city: Tsukuba

first: Xiao

last: Deng

state: Ibaraki

address: 1-1 Namiki

institute: National Institute for Materials Science

data_processing:
NovaSeq 6000 System Sequencing Control Software 1000000019358 v02 was used for basecalling.
Trimmomatic program was used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 were trimmed. Afterwards, reads with length shorter than 36bp were dropped to produce trimmed data.
Trimmed reads were mapped to reference genome (AP017378.1) with Bowtie.
Read count per gene was extracted from known gene annotations with HTSeq program.
Expression profiles are represented as read count and normalization value which is based on transcript length and depth of coverage. The RPKM (Reads Per Kilobase of transcript per Million mapped reads) is used as a normalization value.
Genome_build: AP017378.1
Supplementary_files_format_and_content: A xlsx file include RPKM values for D. ferrophilus IS5 cells incubated on electrodes poised at two different potentials, −0.4 and −0.5 V (vs. SHE).

organism: Desulfovibrio ferrophilus

source_name: Bacterial cells incubated on electrodes

growth_protocol: Desulfovibrio ferrophilus IS5 cells were incubated in H-type reactors for 10 ten days with electrodes (poised at −0.4 and −0.5 V vs. SHE) and sulfate served as the sole electron donor and acceptor, respectively. 1 mM acetate was added in the artificial seawater electrolyte as a carbon source. No organic electron donors or amino acids were contained in the electrolyte.

extract_protocol:
TAKARA Nucleobond RNA kit was used to extract total RNA from cells following the manufacturer’s instructions.
rRNA was removed from total RNA using a Ribo-Zero magnetic kit (Gram-negative bacteria), and a complementary DNA (cDNA) library was prepared for sequencing using the TruSeq Stranded mRNA Library Prep Kit (Illumina) following the manufacturer’s guidelines.

treatment_protocol: After incubation, cells attached on the electrodes were homogenized by thoroughly pipetting with Tris-EDTA (TE) buffer (pH 8) containing 2 mg/mL lysozyme on the electrode surface. Subsequently, the cells were transferred to a sterile microtube and proceeded to RNA extraction.

value: Bacterial cells incubated on electrodes

tag: electrode potential

value: −0.4 V versus standard hydrogen electrode

tag: incubation reactor

value: H-type three-electrode reactor

tag: incubation time

value: 10 days


title: 3_4

value: −0.5 V versus standard hydrogen electrode


title: Ribosome profiling from radicicol cells, rep 2

city: Berkeley

first: Timothy

middle: J

last: Eisen

state: CALIFORNIA

address: Stanley Hall

institute: UC Berkeley

data_processing:
Library strategy: Ribosome profiling
Adapter trimming, cutadapt v1.18, cutadapt -j 10 -u 8 -m 10 -a TCGTATGCCGTCTTCTGCTTG
Alignment, STAR v2.7.1a, --alignIntronMax 1 --outSAMtype BAM SortedByCoordinate --genomeDir $star_index --runThreadN 30 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSJfilterReads Unique --readFilesIn $directory/${filename}_trimmed_fastq.txt --outFileNamePrefix $directory/${filename}_ > $directory/${filename}_stdOut_logFile.txt
Indexing, samtools v1.9, samtools index
Counting reads, featureCounts, featureCounts -T 10 -s 1 -f -a $gtf_file -o $directory/${filename}_featureCounts.txt $directory/${filename}_Aligned.sortedByCoord.out.bam
Genome_build: SacCer3
Supplementary_files_format_and_content: Tab-delimited tables of reads per gene model

molecule: polyA RNA

source_name: yeast lysate from o/n culture

growth_protocol: Three individual yeast colonies were picked and grown o/n in liquid culture. Each colony culture was dilituded to mediawithand without  10uM radicicol and grown o/n. Cultures were further diluted to 0.001 OD600 in 100ml media and grown for 24 hours and collected for ribosome profiling or RNA-seq

extract_protocol:
Samples were rapidly collected using filtration and ground to a fine powder using a Freezer/Mill (SPEX SamplePrep) and stored at -80 °C.
To prepare RNA-seq libraries with fragment sizes that matched the ribosome profiling libraries, 25 µg of total RNA was poly(A)-selected, digested into 27–33 nt fragments, and used to prepare libraries in parallel with the ribosome-protected fragments. For ribosome profiling libraries, aliquots of lysate were digested with 1 U/μL RNase I (Ambion) for 30 min at room temperature and then run on a 10–50% sucrose gradient to purify monosomes (Subtelny et al., 2014). RNAs from both RNA-seq and ribosome profiling were then size-selected, ligated to adapters, reverse-transcribed, and amplified (Subtelny et al., 2014).

treatment_protocol: 10uM radicicol treatment o/n prior to further diliution to 0.001 OD600 and an additional o/n growth

tag: treatment

value: 10 µM radicicol pre-treatment

tag: sequenced molecule

value: ribosome-protected RNA fragments


title: RNA-seq from radicicol cells, rep 3

data_processing:
Adapter trimming, cutadapt v1.18, cutadapt -j 10 -u 8 -m 10 -a TCGTATGCCGTCTTCTGCTTG
Alignment, STAR v2.7.1a, --alignIntronMax 1 --outSAMtype BAM SortedByCoordinate --genomeDir $star_index --runThreadN 30 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSJfilterReads Unique --readFilesIn $directory/${filename}_trimmed_fastq.txt --outFileNamePrefix $directory/${filename}_ > $directory/${filename}_stdOut_logFile.txt
Indexing, samtools v1.9, samtools index
Counting reads, featureCounts, featureCounts -T 10 -s 1 -f -a $gtf_file -o $directory/${filename}_featureCounts.txt $directory/${filename}_Aligned.sortedByCoord.out.bam
Genome_build: SacCer3
Supplementary_files_format_and_content: Tab-delimited tables of reads per gene model

value: poly(A)-selected, fragmented RNA


title: RNA-seq from radicicol-treated cells, rep 1


title: Ribosome profiling from untreated cells, rep 2

value: untreated


title: Ribosome profiling from radicicol cells, rep 1


title: Ribosome profiling from radicicol cells, rep 3


title: Ribosome profiling from untreated cells, rep 3


title: RNA-seq from untreated cells, rep 3


title: RNA-seq from untreated cells, rep 2


title: Ovarian cancer, 2-way_cell_D9 (Barcode NGS)

value: Lentiviral gRNA library transduction


title: Parkinson, 2-way_plasmid (Barcode NGS)

description: Two-way Parkinson's Disease gRNA screen_count per million reads.xlsx

molecule: other

organism: synthetic construct

value: Plasmid gRNA library control


title: Ovarian cancer, 3-way_plasmid (Barcode NGS)


title: Ribosome profiling from untreated cells, rep 1


title: Ovarian cancer, 2-way_plasmid (Barcode NGS)