title: Nov16Batch, WT, GM_FACS3, iNeuron


title: BTY14 Dasatinib+Paclitaxel treated replicate 4

status: Public on Sep 20 2022

type: SRA

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

country: USA

institute: Koch Institute

description:
BJ02.PD.4
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz

library_source: transcriptomic

data_processing:
NextSeq 500 using v3 chemistry. Software: Control v4.0.0.19, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
3’ DGE FASTQ sequencing reads were collapsed to one representative read per unique molecular identifier using a custom python script.
Gene expression was quantified using salmon version 1.1.0 (Patro et al. 2017) using a transcriptome prepared from the human hg38 primary genome assembly using the ensembl version 98 annotation.  The resulting counts were summarized to the gene level using R version 3.6.2 (R Core Team 2021) running tximport version 1.12.3 (Soneson, Love, and Robinson 2015) and counts per million (cpm) were calculated using utilities implement in edgeR version 3.26.8 (Robinson, McCarthy, and Smyth 2010; McCarthy, Chen, and Smyth 2012). The cpm values with a +1 offset were transformed to log2 space.
Assembly: hg38 with ensembl v98 annotation
Supplementary files format and content: ikohale_intCt.txt.gz is a tab delimited text file of integer count data
Supplementary files format and content: ikohale_l2cpm.txt.gz is a tab delimited text file of log2 counts (with a +1 offset) per million

molecule: total RNA

organism: Homo sapiens

source_name: Patient derived xenograft

growth_protocol: Early passage PDX tumor samples were collected after euthanization of the tumor bearing mice with carbon dioxide. Fresh tumor fragments were implanted subcutaneously in 6 to 8 week-old female NSG (NOD.Cg-Prkdc scid Il2rg tm1Wjl/SzJ) mice for drug treatments.

extract_protocol:
Pulverized frozen tissues were homogenized in TRIzol reagent, and RNA was extracted using Direct-zol-96 RNA kit (Zymo Research) according to manufacturer’s protocol.
High Throughput 3'DGE

treatment_protocol: Once the tumors were palpable and reached approximately 3mm in diameter, mice were randomized into four groups and treated with either vehicle control, paclitaxel (12.5 mg/kg, i.p. twice a week), dasatinib (12.5mg/kg, i.p. 5 days/week), or in combination for three weeks. Tumor growth was monitored by measuring with a caliper twice weekly. Mice were euthanized when met the euthanization criteria. Tumors were resected and flash frozen in liquid nitrogen and stored at -80C.

tag: tissue

value: Patient derived xenograft

tag: cell line

tag: cell type

value: Primary triple negative breast cancer

tag: treatment

value: Dasatinib+Paclitaxel


title: Nov16Batch, WT, GM_FACS1, NSC

city: Boston

first: Serkan

last: Erdin

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

description:
batch Nov16
16p11.2_KCTD13_cellLines_counts.txt.gz

data_processing:
Each bulk RNAseq library of mouse sample was aligned to mouse reference genome GRCm38 version 83 using STAR aligner. Expression counts for each sample was also generated by STAR aligner.
Differential expression analysis was performed by DESeq2 + SVA pipeline, whereas co-expression analysis was performed by WGCNA.
Each bulk RNAseq library of human cell line sample was aligned to human reference genome GRCh37 version 75 using STAR aligner. Expression counts for each sample was also generated by STAR aligner.
For scRNA, raw paired-end reads were aligned by Cellranger (v3.0.2) against human transcriptome GRCh38.92.
For each scRNA sample, its feature list, barcode list and count matrix were then read by Seurat (v4.0.3) into matrix. Cells with top and bottom 2.5% number of RNA molecules were filtered out.
All scRNA samples were then merged into one matrix using "merge" function in Seurat.
Assembly: single cell human reference genome GRCh38 v92; mouse reference genome for bulk RNAseq GRCm38 v83. human reference genome for bulk RNAseq GRCh37 v75.
Supplementary files format and content: "rawCounts_merged_16p_Organoid_GM08330.txt.gz" - gzipped text file for raw counts of scRNA data. Each row represents a gene while each column represents a cell. Outlier cells have been filtered out and not included.
Supplementary files format and content: "16p11.2_KCTD13_cellLines_counts.txt.gz" - gzipped tab delimited text file for raw counts of human cell line bulk RNAseq data including 16p11.2 deletion, 16p11.2 duplication and 16p11.2 wild-type NSCs and iNeurons as well as KCTD13 het del and KCTD13 wild-type iNeurons
Supplementary files format and content: "16p11.2_KCTD13_cellLines_metadata.txt" - metadata of bulk RNAseq data from human cell lines
Supplementary files format and content: "metaData_SCT_merged_16p_Organoid_GM08330.txt" - text file for scRNA meta-data.
Supplementary files format and content: "16p11.2_mouse_counts.txt.gz" - tab delimited text file for raw counts of mouse bulk RNAseq data.

molecule: polyA RNA

growth_protocol: NSCs were maintained in PSC Neural Expansion Medium (ThermoFisher, A1647801) in humidified atmosphere with 5% CO2 at 37C; iNs were maintained in Neural Maintenance Media (Shi et al., 2012) supplemented with BDNF and NT-3 in humidified atmosphere with 5% CO2 at 37C; cerebral organoids were maintained in organoid medium (Lancaster et al., 2014) supplemented with BDNF in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
All RNA samples were extracted with Trizol reagent according to the manufacturer’s instruction (Invitrogen).
Mouse and human cell RNASeq libraries were prepared with customized version of strand specific dUTP method and TruSeq Stranded mRNA Library Kit (Illumina); scRNA-seq libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 (PN-1000075) according to manufacturer’s instructions (CG000183) using a Chromium Single Cell B Chip (PN-1000073) for a targeted cell recovery of 5,000 cells.
RNAseq for mouse tissues and human NSCs and iNs; single-cell RNAseq for cerebral organoids

treatment_protocol: For all CRISPR lines, Passage 7 stage NSCs were dissociated for RNA-seq; iNs were dissociated for RNA-seq on Day 24 of differentiation; For single-cell suspensions of cerebral organoids, organoids at 6 months were prepared using the Worthington Papain Dissociation System (Worthington Biochemical, LK003153).

value: NSC

tag: genotype

value: WT

tag: Sex

value: M


title: BTY14 Dasatinib+Paclitaxel treated replicate 2

description:
BJ02.PD.2
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: Nov16Batch, WT, GM_FACS1, iNeuron

value: Induced neuron


title: SPBC28E12.06c_C2_rep3

city: Mainz

first: Falk

last: Butter

state: Germany

address: Ackermannweg 4

department: Quantitative Proteomics

country: Germany

institute: Institute of Molecular Biology gGmbH

description:
Knock-out strain
3' mRNA-Seq

data_processing:
Sequencing raw files were analyzed using the “NGSpipe2go” RNA-seq pipeline (https://github.com/imbforge/NGSpipe2go). Version of the tools used were: R (3.5.1), FastQC (0.11.8), STAR (2.6.1b), SAMtools (1.5), HTSeq (0.9.0), Subread (1.6.2), BEDTools (2.27.1), Picard (2.17.6), RSeQC (3.0.0), Qualimap (2.2.1), KentUtils (v365), rMATS (4.0.2), FastQScreen (0.12.2), deepTools (3.1.0), BamUtil (1.0.13), and STAR-Fusion (0.8.0). The default RPKM calculation was replaced with CPM (counts per million) as 3’-end sequencing was performed. “ASM294v2.40.gtf” was used as the gene model, and “ASM294v2.dna.toplevel.fa” was used as the genome for S. pombe. “rld” transformation of the data from the “DE_Seq” part of the pipeline was replaced with “vst” transformation due to the high number of samples being processed.
Alignment was done with STAR (2.6.1b).
Read count per gene was done with Subread (1.6.2).
DESeq2 R-package was used for calculating CPM values and statistics of differential regulation.
Genome_build: ASM294v2.dna.toplevel.fa
Supplementary_files_format_and_content: allSamples.CPM.csv: Processed data file is a semicolon-separated text file and includes CPM (counts per million) values for all gene models established in ASM294v2.40.gtf in all conditions.

organism: Schizosaccharomyces pombe

source_name: cell culture

growth_protocol: S. pombe knockout library (Bioneer, version M-3030H) was grown in YES medium (5 g l-1 yeast extract, 30 g l-1 D-glucose, supplemented with 225 mg l-1 adenine, L-histidine, L-leucine, uracil and L-lysine each f.c.) at 32 ºC shaking at 160 rpm for 2 days. A second inoculation was performed with 5 µl of the initial culture in a 96-deepwell plate filled with 2 ml YES media, and grown for another 12-14 hours.

extract_protocol:
Total RNA extraction was performed according to [A rapid and simple method for preparation of RNA from Saccharomyces cerevisiae, Mark E.Schmitt, NAR, 1990] and the RNA pellet was resuspended in 87ul of RNase free water. DNA was digested using 3ul of DNase (Qiagen) and 10ul RDD DNase buffer at 37ºC for 30 minutes. RNA cleanup was performed with the Purelink RNA Mini kit (Thermo Scientific) according to the manufacturer's instructions. RNA integrity was measured on a Bioanalyzer 2100 system (Agilent).
NGS library prep was performed with Lexogen 3´mRNA-Seq Library Prep Kit FWD HT following Lexogens standard protocol (015UG110V0110). Libraries were prepared with a starting amount of 338ng and amplified in 13 PCR cycles. Libraries were profiled using a High Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent) and quantified using the Qubit dsDNA HS Assay Kit in a Qubit 2.0 Fluorometer (Life Technologies). 2x192 libraries were pooled together in equimolar ratio and sequenced in single-end mode on 2 NextSeq 500 High-output flowcells, for 1x75 cycles plus 2x8 cycles for the dual index read.

tag: replicate


title: SPBC2F12.11c_C3_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC24C6.11_C1_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC2F12.12c_C4_rep3

description:
Knock-out strain
3' mRNA-Seq


title: Nov16Batch, 16p_Dup, S7, iNeuron


title: BTY14 Dasatinib+Paclitaxel treated replicate 1

description:
BJ02.PD.1
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY14 Paclitaxel treated replicate 4

description:
BJ02.P.4
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz

value: Paclitaxel


title: Nov16Batch, 16p_Dup, G9, iNeuron


title: SPBC16C6.02c_B9_rep3

description:
Knock-out strain
3' mRNA-Seq


title: BTY14 Paclitaxel treated replicate 3

description:
BJ02.P.3
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: SPBC19G7.10c_B11_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC21B10.03c_B12_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC17A3.06_B10_rep3

description:
Knock-out strain
3' mRNA-Seq


title: Nov16Batch, 16p_Dup, D9, iNeuron


title: Nov16Batch, 16p_Dup, D6, iNeuron


title: BTY14 Paclitaxel treated replicate 2

description:
BJ02.P.2
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: BTY14 Paclitaxel treated replicate 1

description:
BJ02.P.1
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: Nov16Batch, 16p_Dup, D12, iNeuron


title: BTY14 Dasatinib treated replicate 4

description:
BJ02.D.4
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz

value: Dasatinib


title: Nov16Batch, 16p_Dup_A6, iNeuron


title: BTY14 Dasatinib treated replicate 3

description:
BJ02.D.3
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: SPAC23A1.11_A5_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAPB17E12.05_A8_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC3H5.12c_B2_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC22F8.11_A12_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC16A3.17c_B8_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC23A1.07_B1_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC1604.08c_B6_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBP22H7.08_A11_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC637.07_B4_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC25G10.06_A6_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC577.02_A10_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC3G6.02_A7_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC664.15_B5_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC11C11.07_A9_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC1685.01_B7_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC1527.02_A4_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPAC14C4.16_A3_rep3

description:
Knock-out strain
3' mRNA-Seq


title: wt2_A2_rep3

description:
Knock-out strain
3' mRNA-Seq


title: Nov16Batch, 16p_Del, H10,  NSC


title: SPAC57A7.12_B3_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPCC5E4.07_H9_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC22F3.09c_H11_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC3A12.13c_H8_rep2

description:
Knock-out strain
3' mRNA-Seq


title: BTY14 Dasatinib treated replicate 2

description:
BJ02.D.2
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: SPBC530.07c_H10_rep2

description:
Knock-out strain
3' mRNA-Seq


title: wt1_A1_rep3

description:
Knock-out strain
3' mRNA-Seq


title: SPBC660.11_H12_rep2

description:
Knock-out strain
3' mRNA-Seq


title: MCF10A, TGF-beta dosage effect

city: Yokohama

first: Kazuhide

last: Watanabe

state: Kanagawa

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

department: Center for Integrative Medical Sciences

country: Japan

institute: Riken

data_processing:
cellranger ranger2.0.2  used for processing and mapping the raw sequnce reads
Assembly: hg38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, genes.tsv, matrix.mtx)

source_name: Mammary epithelium

extract_protocol:
MCF10A cells were first labelled with Perturb-seq vectors without sgRNA expression using guide barcodes (GBCs) that were originally used to identify sgRNAs. Barcoded MCF10A cells were then treated with different dosages of TGF-β for 14 days and single cells were prepared and mixed at a concentration of approximately 1,000 cell/μL in ice-cold PBS. GBC to Concentration (pM) conversion:
GBC1: 0
GBC2: 12.5
GBC3: 25
GBC4: 50
GBC8: 100
GBC9: 200
GBC12: 400
GBC13: 800
RNA-Seq library was prepared using 10x Chromium Single Cell 3' –end Reagent Kits User Guide (v2 Chemistry)
Libraries were sequenced using paired-end sequencing (26bp Read 1 and 98bp Read 2) with a single sample index (8bp) on the Illumina HiSeq 2500

value: Mammary epithelium


title: BTY14 Dasatinib treated replicate 1

description:
BJ02.D.1
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: Nov16Batch, 16p_Del, D6, iNeuron


title: BTY14 Vehicle treated replicate 2

description:
BJ02.C.2
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz

value: Vehicle


title: BTY14 Vehicle treated replicate 4

description:
BJ02.C.4
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: Nov16Batch, 16p_Del, H10, iNeuron


title: BTY14 Vehicle treated replicate 3

description:
BJ02.C.3
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: Nov16Batch, 16p_Del, D5, iNeuron


title: BTY14 Vehicle treated replicate 1

description:
BJ02.C.1
ikohale_intCt.txt.gz
ikohale_l2cpm.txt.gz


title: Nov16Batch, 16p_Del, C5,  NSC


title: SPBC543.07_G8_rep2

description:
Knock-out strain
3' mRNA-Seq


title: Nov16Batch, 16p_Del, A5, NSC


title: SPBC405.07_G7_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC4G9.16c_H7_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC20G4.07c_G12_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC29B12.04_H6_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC3H7.03c_G9_rep2

description:
Knock-out strain
3' mRNA-Seq


title: Nov16Batch, 16p_Del, C3, NSC


title: SPCC4G3.11_H4_rep2

description:
Knock-out strain
3' mRNA-Seq


title: Nov16Batch, 16p_Del, C5, iNeuron


title: SPBC3E7.05c_G6_rep2

description:
Knock-out strain
3' mRNA-Seq


title: Nov16Batch, 16p_Del, B5, NSC


title: SPCC320.12_H5_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPCC285.09c_G11_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPCC594.05c_H2_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC354.03_G5_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC1105.14_G3_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC16C6.11_G4_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPCC1672.12c_G10_rep2

description:
Knock-out strain
3' mRNA-Seq


title: Nov16Batch, 16p_Del, A3, NSC


title: SPAC18G6.10_F12_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBPB10D8.06c_H3_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC22H12.02_G1_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAPB2B4.04c_G2_rep2

description:
Knock-out strain
3' mRNA-Seq


title: Nov16Batch, 16p_Del, A3, iNeuron


title: SPCC1259.01c_H1_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC887.02_F11_rep2

description:
Knock-out strain
3' mRNA-Seq


title: Nov16Batch, 16p_Del, A5, iNeuron


title: SPBC365.03c_F10_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC29A10.16c_F9_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPCC1393.05_F8_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC25H2.11c_F7_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SW480 sgRELB Hypoxia rep 2

city: New York

first: Ryan

last: Moy

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

data_processing:
Alignment with STAR aligner (v2.6.0a; default settings)
Read counting with STAR's  `--quantMode GeneCounts` parameter
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: SW480 cancer cells

growth_protocol: sgCtrl versus sgITPR3 or sgRELB SW480 cells incubated at normoxia versus hypoxia for 72 hours before RNA isolation and library preparation.

extract_protocol:
Norgen Total RNA extraction kit.
Truseq library preparation kit

treatment_protocol: sgCtrl versus sgITPR3 and sgRELB cells.

tag: crispr guide

tag: condition

value: Hypoxa

value: colorectal cancer


title: SPAC3H5.10_F6_rep2

description:
Knock-out strain
3' mRNA-Seq


title: Nov16Batch, 16p_Del, A12, iNeuron


title: SPBC4F6.10_F5_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPCC576.12c_F3_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC31A2.13c_F4_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SW480 sgITPR3 Hypoxia rep 2


title: Nov16Batch, 16p_Del, A12, NSC


title: BatchOct17, 16p_Dup, 8, NSC

description:
batch Oct17
16p11.2_KCTD13_cellLines_counts.txt.gz


title: SPAC1952.05_F2_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC17A5.02c_F1_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC23E6.01c_E12_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SW480 sgRELB Hypoxia rep 1

value: Hypoxia


title: BatchOct17, 16p_Dup, 7, NSC


title: SW480 sgITPR3 Hypoxia rep 1


title: BatchOct17, 16p_Dup, 6, NSC


title: SW480 sgCTRL Hypoxia rep 2

value: sgCTRL


title: SPBC21C3.12c_E11_rep2

description:
Knock-out strain
3' mRNA-Seq


title: BatchOct17, 16p_Dup, 5, NSC


title: SPAC9E9.09c_E9_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAPB1E7.02c_E10_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SW480 sgCTRL Hypoxia rep 1


title: BatchOct17, 16p_Dup, 4, NSC


title: SW480 sgRELB Normoxia rep 2

value: Normoxia


title: SPBC577.15c_E6_rep2

description:
Knock-out strain
3' mRNA-Seq


title: BatchOct17, 16p_Dup, 3, NSC


title: SPBC3B9.13c_E5_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SW480 sgRELB Normoxia rep 1


title: BatchOct17, 16p_Dup, 2, NSC


title: SPAC4A8.09c_E4_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SW480 sgITPR3 Normoxia rep 2


title: BatchOct17, 16p_Dup, 1, NSC


title: BatchOct17, 16p, control,5,  NSC


title: SW480 sgITPR3 Normoxia rep 1


title: SPBC14C8.17c_E1_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC25H2.15_E2_rep2

description:
Knock-out strain
3' mRNA-Seq


title: BatchOct17, 16p, control,6,  NSC


title: SW480 sgCTRL Normoxia rep 1


title: SPAC8E11.10_D9_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC839.13c_E7_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPCC613.06_D12_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SW480 sgCTRL Normoxia rep 2


title: SPBC3E7.15c_D11_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC28F2.10c_D10_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPCC24B10.14c_E8_rep2

description:
Knock-out strain
3' mRNA-Seq


title: BatchOct17, 16p, control,3,  NSC


title: BatchOct17, 16p, control,4,  NSC


title: SPCC757.09c_E3_rep2

description:
Knock-out strain
3' mRNA-Seq


title: BatchOct17, 16p, control,1,  NSC


title: SPAC29A4.20_D8_rep2

description:
Knock-out strain
3' mRNA-Seq


title: BatchOct17, 16p, control,2,  NSC


title: H3122_LR_scATACseq

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

library_source: genomic

data_processing:
The preprocessing was followed by a pipeline provided by 10X genomics (https://support.10xgenomics.com/single-cell-atac).
The process of converting raw sequencing data (bcl files) into fastqs and aligning to the human reference genome [https://cf.10xgenomics.com/releases/cell-atac/cellranger-atac-1.1.0.tar.gz, v.1.1.0, hg19] were performed using a Cell Ranger atac software (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac).
The Cell Ranger ATAC count module was used to generate the raw peak count matrix and transcription factors.
Genome_build: hg19
Supplementary_files_format_and_content: 10x cell ranger atac count output (raw peak count matrix, raw transcription factor count matrix, cell barcode, peak and transcription factor information table)

molecule: genomic DNA

source_name: H3122 lung cancer cell line

extract_protocol:
Sample extraction was prepared using Chromium Single Cell ATAC Reagent Kits v1 (10X Genomics) according to the manufacturer’s protocols.
Sequencing library was prepared using Chromium Single Cell ATAC Reagent Kits v1 (10X Genomics) according to the manufacturer’s protocols.

value: Certinib


title: Sample_27_HBL1_shSIRT3_2_R3

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Reads were aligned using STAR and annotated to RefSeq annotation using Rsubread
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

growth_protocol: not applicable

extract_protocol: Total RNA was extracted using Trizol (LifeTechnologies) and RNeasy isolation Kit (Qiagen).  Library was prepared as described in manuscript.

tag: cell line/type

value: HBL1 DLBCL cell line

tag: genotype/treatment

value: shSIRT3-2 transfection for 8 days


title: SPAC17A2.13c_D6_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC15D4.10c_D1_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBP35G2.08c_D5_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC17H9.19c_D7_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC3A11.07_D3_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC713.07c_D4_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC947.02_D2_rep2

description:
Knock-out strain
3' mRNA-Seq


title: 5ITU_1

city: Seoul

first: Eun-Ji

last: Kwon

address: 1, Gwanak-ro

institute: Seoul National University

data_processing:
Read quality was assessed using FastQC (v) and poor-quality bases (Phred score < 20) were eliminated using TrimGalore (v0.6.6)
Trimmed reads were aligned to the human reference genome (GRCh38) using the STAR aligner (v2.7.9a) with default parameters
Gene-level expression values such as transcripts per million (TPM) and read counts were calculated using RSEM (v1.3.3.) with human gene annotation (GRCh38.84)
Assembly: GRCh38.84
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: HeLa cells,  5ITU, Day1

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Easy-BLUETM RNA isolation kit (iNtRON Biotechnology) . 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA)
Briefly, the strand-specific protocol included the following steps: (1) strand cDNA synthesis, (2) strand synthesis using dUTPs instead of dTTPs, (3) end repair, A-tailing, and adaptor ligation, and (4) PCR amplification. Each library was then diluted to 8 pM for 76 cycles of paired-read sequencing (2 × 75 bp) on an Illumina NextSeq 500 following the manufacturer’s recommended protocol.

treatment_protocol: HeLa cells were treated with 500nM LJ4827, 5ITU

value: HeLa

value: Day 1


title: LJ4827_1

source_name: HeLa cells, LJ4827, Day1

value: WT


title: DMSO_2

source_name: HeLa cells, Vehicle (DMSO), Day1


title: SPAC8C9.06c_C12_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC28E12.06c_C2_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC24C6.11_C1_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC19G7.10c_B11_rep2

description:
Knock-out strain
3' mRNA-Seq


title: LJ4827_2


title: 5ITU_2


title: SPAC1783.07c_C11_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPCC24B10.08c_C8_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC776.01_C6_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC2F12.12c_C4_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPCC663.04_C9_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC17A3.06_B10_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC21B10.03c_B12_rep2

description:
Knock-out strain
3' mRNA-Seq


title: DMSO_1


title: SPCC736.08_C10_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC2F12.11c_C3_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC776.17_C7_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC365.10_C5_rep2

description:
Knock-out strain
3' mRNA-Seq


title: Sample_26_HBL1_shSIRT3_2_R2


title: Sample_25_HBL1_shSIRT3_2_R1


title: Sample_24_HBL1_shSIRT3_1_R3

value: shSIRT3-1 transfection for 8 days


title: Sample_23_HBL1_shSIRT3_1_R2


title: Sample_22_HBL1_shSIRT3_1_R1


title: Sample_19_HBL1_shCTRL_R1

value: shCTRL transfection for 8 days


title: Sample_21_HBL1_shCTRL_R3


title: Sample_18_OCILy1_shSIRT3_2_R3

value: OCI-Ly1 DLBCL cell line


title: Sample_20_HBL1_shCTRL_R2


title: SPBC16C6.02c_B9_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC16A3.17c_B8_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAPB17E12.05_A8_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC22F8.11_A12_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC11C11.07_A9_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC1527.02_A4_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC664.15_B5_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC3H5.12c_B2_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC637.07_B4_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC1604.08c_B6_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC57A7.12_B3_rep2

description:
Knock-out strain
3' mRNA-Seq


title: wt2_A2_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC1685.01_B7_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBP22H7.08_A11_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC23A1.11_A5_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC23A1.07_B1_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC577.02_A10_rep2

description:
Knock-out strain
3' mRNA-Seq


title: wt1_A1_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC25G10.06_A6_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC14C4.16_A3_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPAC22F3.09c_H11_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAC3G6.02_A7_rep2

description:
Knock-out strain
3' mRNA-Seq


title: SPBC660.11_H12_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPCC5E4.07_H9_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Sample_15_OCILy1_shSIRT3_1_R3


title: SPBC530.07c_H10_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Sample_16_OCILy1_shSIRT3_2_R1


title: Sample_17_OCILy1_shSIRT3_2_R2


title: Sample_14_OCILy1_shSIRT3_1_R2


title: SPAC3A12.13c_H8_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAC4G9.16c_H7_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAC29B12.04_H6_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPCC320.12_H5_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Sample_13_OCILy1_shSIRT3_1_R1


title: Sample_12_OCILy1_shCTRL_R3


title: Sample_11_OCILy1_shCTRL_R2


title: SPCC4G3.11_H4_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBPB10D8.06c_H3_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Sample_10_OCILy1_shCTRL_R1


title: SPAC20G4.07c_G12_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Sample_9_Karpas422_shSIRT3_2_R3

value: Karpas422 DLBCL cell line


title: SPCC594.05c_H2_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Sample_8_Karpas422_shSIRT3_2_R2


title: SPCC285.09c_G11_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC405.07_G7_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC3H7.03c_G9_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPCC1672.12c_G10_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC543.07_G8_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Sample_6_Karpas422_shSIRT3_1_R3


title: SPBC16C6.11_G4_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC354.03_G5_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC1105.14_G3_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC3E7.05c_G6_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAPB2B4.04c_G2_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Sample_5_Karpas422_shSIRT3_1_R2


title: SPAC22H12.02_G1_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Sample_4_Karpas422_shSIRT3_1_R1


title: SPAC18G6.10_F12_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPCC1259.01c_H1_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC365.03c_F10_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC887.02_F11_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Sample_7_Karpas422_shSIRT3_2_R1


title: Sample_3_Karpas422_shCTRL_R3


title: Sample_2_Karpas422_shCTRL_R2


title: SPBC29A10.16c_F9_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC25H2.11c_F7_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPCC1393.05_F8_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC4F6.10_F5_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAC3H5.10_F6_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAC31A2.13c_F4_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAC17A5.02c_F1_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPCC576.12c_F3_rep1

description:
Knock-out strain
3' mRNA-Seq


title: RPM, Drug rep7

city: Dallas

first: Jane

middle: E

last: Johnson

state: TX

address: 5323 Harry Hines Blvd

department: Neuroscience

institute: UT Southwestern Medical Center

description:
Immunocompetent mouse
INI-43-treated
SW128
GEMM_all_samples_FPKM_matrix.txt

data_processing:
Sequence reads were aligned to the mouse transcriptome using TopHat.
Cufflinks package was used to quantify transcript levels.
DEG analysis was performed using Cuffdiff.
Genome_build: Human (hg38/GRCh38) & mouse (mm10/GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include whole genome FPKM matrices.

organism: Mus musculus

source_name: RPM SCLC GEMM

growth_protocol: Cell lines were cultured in RPMI 1640 Medium supplemented with 10% fetal bovine serum (FBS) and were maintained at 37°C in a humidified incubator with 5% CO2. PDX models JHU-LX44 and JHU-LX22 were established using dissociated cells from resected PDX tumors and were engrafted by subcutaneous injection of 1X10^6 JHU-LX44 cells or 2.4 X10^6 JHU-LX22 cells resuspended 1:1 by volume in Matrigel and HITES media into the flanks of NSG mice. In the RPM model, anesthetized 6-8 week old RPM mice (Rb1fl/fl;p53fl/fl;MycT58ALSL/LSL) (JAX: 029971) were infected intranasally with 1x10^8 plaque-forming units of Ad5-CGRP-Cre.

extract_protocol:
Cells were harvested by centrifugation and resuspended in TRIzolTM Reagent. Total RNA was extracted using a PicoPureTM RNA Isolation Kit. For SCLC tumor samples, tumor tissue was homogenized in TRIzolTM and total RNA was extracted using a Direct-zol RNA Miniprep kit.
Samples were submitted to the UTSW Genomics Sequencing & Microarray Core Facility for mRNAseq-Strand specific library preparation and sequencing of libraries using a NextSeq 500/550 High Output Kit v2.5 (75 Cycles), at 20-30 million reads per sample.

treatment_protocol: In the PDX models, INI-43 drug treatment was initiated at a xenograft volume of ~500 mm3 in JHU-LX44 tumor bearing mice, and ~600 mm3 in JHU-LX22 tumor bearing mice. Mice were intraperitoneally injected every 2 days with Vehicle or 25 mg/kg INI-43 for 2 weeks or 10 days, respectively. In the RPM model, INI-43 drug treatment was initiated at the earliest signs of tumor burden determined by microCT imaging. Mice were treated with Vehicle, or 25 mg/kg INI-43 every 3 days for 9-15 days.

tag: strain

value: RPM

value: RPM lung tumor

tag: age

value: Adult


title: SPAPB1E7.02c_E10_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPCC24B10.14c_E8_rep1

description:
Knock-out strain
3' mRNA-Seq


title: RPM, Drug rep6

description:
Immunocompetent mouse
INI-43-treated
SW114
GEMM_all_samples_FPKM_matrix.txt


title: RPM, Drug rep5

description:
Immunocompetent mouse
INI-43-treated
SW112
GEMM_all_samples_FPKM_matrix.txt


title: H3122_PR_scRNAseq

data_processing:
The preprocessing was followed by a pipeline provided by 10X genomics (https://support.10xgenomics.com/single-cell-gene-expression).
The process of converting raw sequencing data (bcl files) into fastqs and aligning to the human reference genome [http://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-hg19-3.0.0.tar.gz, v.3.0.0, hg19] were performed using a Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
The Cell Ranger count module was used to generate the raw gene expression matrix.
Genome_build: hg19
Supplementary_files_format_and_content: 10x cell ranger count output (raw gene expression matrix, cell barcode and gene information table)

extract_protocol: Sequencing library was prepared using Chromium Single cell 3' Reagent Kits v2 (10X Genomics) according to the manufacturer’s protocols.

treatment_protocol: To create the ceritinib (LDK378)-resistant model, H3122 cells cultured with increasing concentrations of ceritinib, starting with IC30. The dose was increased in a stepwise manner when normal cell proliferation patterns resumed. Fresh drug was added every 72-96 h. Resistant cells (LR) were derived after approximately 6 months of culture in the continuous presence of 1 µM ceritinib.

value: lung cancer


title: H3122_LR_scRNAseq


title: SPBC21C3.12c_E11_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAC9E9.09c_E9_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC839.13c_E7_rep1

description:
Knock-out strain
3' mRNA-Seq


title: RPM, Drug rep4

description:
Immunocompetent mouse
INI-43-treated
801-18
GEMM_all_samples_FPKM_matrix.txt


title: SPBC577.15c_E6_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Sample_1_Karpas422_shCTRL_R1


title: SPAC4A8.09c_E4_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC3B9.13c_E5_rep1

description:
Knock-out strain
3' mRNA-Seq


title: RPM, Drug rep3

description:
Immunocompetent mouse
INI-43-treated
SW129
GEMM_all_samples_FPKM_matrix.txt


title: SPBC23E6.01c_E12_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC25H2.15_E2_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPCC757.09c_E3_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC14C8.17c_E1_rep1

description:
Knock-out strain
3' mRNA-Seq


title: RPM, Drug rep2

description:
Immunocompetent mouse
INI-43-treated
SW122
GEMM_all_samples_FPKM_matrix.txt


title: SPCC613.06_D12_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC28F2.10c_D10_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC3E7.15c_D11_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAC8E11.10_D9_rep1

description:
Knock-out strain
3' mRNA-Seq


title: RPM, Control rep4

description:
Immunocompetent mouse
Untreated tumor
SW132
GEMM_all_samples_FPKM_matrix.txt

value: Untreated


title: SPAC29A4.20_D8_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAC17A2.13c_D6_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBP35G2.08c_D5_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAC17H9.19c_D7_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Diabetic+Pargyline-3 [miRNA]

type: RNA

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: Total RNA was used to label miRNAs. The number in the sample names corresponds to the mouse used.

hyb_protocol: Labelled RNA was hybridized onto microarray slides using a rotational oven at 55° C for 22 h.

scan_protocol: Mycroarrays were scanned in an Agilent microarray scanner (model G2565CA). Agilent Feature Extraction software version 10.5.1.1 was used for image analysis.

data_processing: Raw microarray data were first filtered for the number of miRNAs presenting an expression value above background (0% of undetected values were allowed for each miRNA) and then normalized according to the loess cyclic algorithm.

source_name: Heart-Diabetic treated with Pargyline

label_protocol: 200 ng of total RNA were labelled using miRNA Complete Labeling and Hyb Kit (Agilent Technologies), according to the manufacturer protocol.

growth_protocol: All the animal studies were performed using male C57BL6/J mice (6-7 weeks of age and at least 20 g in weight; Charles River Laboratories, Italy). T1D was induced with streptozotocin (50 mg/kg/day in citrate buffer pH 4.5) administered intraperitoneally for five consecutive days. STZ is a glucosamine-nitrosourea compound toxic to pancreatic β-cells. Mice were then randomized to receive either vehicle or MAO inhibitor pargyline (50 mg/kg/day) for 12 weeks. Blood glucose levels were measured twice a month using glucose meter (OneTouch Ultra 2) and mice with blood glucose levels ≥17 mM were considered diabetic. The following groups were examined: (i) control mice (C), (ii) STZ-treated mice (D), (iii) control mice treated with pargyline (C+P), (iv) STZ mice treated with pargyline (D+P).

extract_protocol: Total RNA from macrophages was isolated with TRIzol reagent (ThermoFisher) according to manufacturer protocol. RNA quantification was performed using the NanoDrop 1000 spectrophotometer (Nanodrop, Wilmington, DE, USA). Total RNA integrity and content of miRNAs in each sample were assessed by capillary electrophoresis using the Agilent Bioanalyzer 2100 with the RNA 6000 Nano and the Small RNA Nano LabChips, respectively (Agilent Technologies, Palo Alto, CA, USA). Only total RNA samples with an RNA integrity number > 7 and small RNAs concentration < 30% were used for miRNA or mRNA gene expression analysis.

treatment_protocol: After the induction of dyabetes with streptozotocin mice were randomly treated for the inhibitio of MAO with pargyline. See the growth protocol for more specific data.

tag: gender

value: Male

value: Heart muscle

value: 5 months

value: Diabetic treated with Pargyline


title: Diabetic+Pargyline-2 [miRNA]


title: Diabetic+Pargyline-1 [miRNA]


title: RPM, Control rep3

description:
Immunocompetent mouse
Vehicle-treated control
SW134
GEMM_all_samples_FPKM_matrix.txt

value: Vehicle


title: SPBC947.02_D2_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAC3A11.07_D3_rep1

description:
Knock-out strain
3' mRNA-Seq


city: Guangzhou

first: Haixia

last: Wei

address: #1, Xinzao Road

department: Department of Pathogen Biology and Immunology

country: China

institute: Guangzhou Medical University

description: Gene expression data from CD4+PD-1+ T cells from the spleen of Plasmodium yoelii infected C57BL/6 mice

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: NOT PROVIDED; REQUESTED

label: biotin

label_protocol: standard Affymetrix protocol

extract_protocol: NOT PROVIDED; REQUESTED

value: female

value: 8 weeks

value: spleen

value: CD4+PD-1+ T cells


title: SPBC15D4.10c_D1_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAC8C9.06c_C12_rep1

description:
Knock-out strain
3' mRNA-Seq


title: RPM, Control rep1

description:
Immunocompetent mouse
Vehicle-treated control
SW131
GEMM_all_samples_FPKM_matrix.txt


title: Diabetic-3 [miRNA]

source_name: Heart-Diabetic

value: Diabetic


title: SPAC1783.07c_C11_rep1

description:
Knock-out strain
3' mRNA-Seq


description: Gene expression data from CD4+PD-1- T cells from the spleen of Plasmodium yoelii infected C57BL/6 mice

value: CD4+PD-1- T cells


title: Diabetic-2 [miRNA]


title: SPCC663.04_C9_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Diabetic-1 [miRNA]


title: SPBC713.07c_D4_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC776.17_C7_rep1

description:
Knock-out strain
3' mRNA-Seq


title: RPM, Control rep2

description:
Immunocompetent mouse
Vehicle-treated control
SW133
GEMM_all_samples_FPKM_matrix.txt


title: Control+Pargyline-3 [miRNA]

source_name: Heart-Treated with Pargyline

value: Treated with Pargyline


title: SPCC24B10.08c_C8_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC365.10_C5_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Control+Pargyline-2 [miRNA]


title: SPAC1952.05_F2_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC2F12.11c_C3_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Diabetic+Pargyline-3

description:
Total RNA was used to label mRNA and lncRNAs using low imput labelling kit
Diabetic+pargyline-24

hyb_protocol: Labeled sample was dispensed onto the microarray to perform hybridization at 65°C for 17 h with 10 rpm rotation.

scan_protocol: Microarray slides were scanned using G2505C scanner (Agilent Technologies) at 3 µm resolution.

data_processing: Raw microarray gene expression data corresponding only to coding genes were quantile normalized and probe expression values that did not pass filter (positive and significant) were set as NA (not available). Probes with more than 50% of NA per condition were excluded from the analysis. To identify differentially expressed genes multiple t-tests were performed using adjusted Bonferroni correction and 0.05 as p-value cut off.

label_protocol: 200 ng of total RNA were labelled using mRNA low imput labelling and Hyb Kit (Agilent Technologies), according to the manufacturer protocol.

extract_protocol: Total RNA from heart samples was isolated with TRIzol reagent (ThermoFisher) according to manufacturer protocol. RNA quantification was performed using the NanoDrop 1000 spectrophotometer (Nanodrop, Wilmington, DE, USA). Total RNA integrity and content of miRNAs in each sample were assessed by capillary electrophoresis using the Agilent Bioanalyzer 2100 with the RNA 6000 Nano and the Small RNA Nano LabChips, respectively (Agilent Technologies, Palo Alto, CA, USA). Only total RNA samples with an RNA integrity number > 7 and small RNAs concentration < 30% were used for miRNA or mRNA gene expression analysis.

tag: group/treatment


title: SPBC28E12.06c_C2_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Diabetic+Pargyline-2

description:
Total RNA was used to label mRNA and lncRNAs using low imput labelling kit
Diabetic+pargyline-22


title: Control+Pargyline-1 [miRNA]


title: Control-3 [miRNA]

source_name: Heart-Control

value: Control


title: SPBC24C6.11_C1_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Diabetic+Pargyline-1

description:
Total RNA was used to label mRNA and lncRNAs using low imput labelling kit
Diabetic+pargyline-19


title: SPBC21B10.03c_B12_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC19G7.10c_B11_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Diabetic-3

description:
Total RNA was used to label mRNA and lncRNAs using low imput labelling kit
Diabetic-18


title: SPBC17A3.06_B10_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Control-2 [miRNA]


title: SPBC2F12.12c_C4_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC776.01_C6_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC16C6.02c_B9_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC16A3.17c_B8_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Control-1 [miRNA]


title: SPBC1604.08c_B6_rep1

description:
Knock-out strain
3' mRNA-Seq


title: Control+Pargyline-3

description:
Total RNA was used to label mRNA and lncRNAs using low imput labelling kit
Control+pargyline-10


title: Diabetic-2

description:
Total RNA was used to label mRNA and lncRNAs using low imput labelling kit
Diabetic-12


title: Diabetic-1

description:
Total RNA was used to label mRNA and lncRNAs using low imput labelling kit
Diabetic-11


title: SPAC664.15_B5_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAC637.07_B4_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAC57A7.12_B3_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAC3H5.12c_B2_rep1

description:
Knock-out strain
3' mRNA-Seq


title: JHU-LX22, Drug rep3

description:
INI-43-treated
LX22_PDX_Drug_number8
FPKM_matrix_whole_genome_LX22_veh_drug_samples.txt

source_name: JHU-LX22 PDX

value: JHU-LX22 PDX

value: Human SCLC-N tumor cells grown in NSG mouse

value: PDX from lung tumor


title: SPAC23A1.07_B1_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAC22F8.11_A12_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC1685.01_B7_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBP22H7.08_A11_rep1

description:
Knock-out strain
3' mRNA-Seq


title: JHU-LX22, Drug rep2

description:
INI-43-treated
LX22Drug-7-690p3ng-per-uL
FPKM_matrix_whole_genome_LX22_veh_drug_samples.txt


title: JHU-LX22, Drug rep1

description:
INI-43-treated
LX22Drug-10-647ng-per-uL
FPKM_matrix_whole_genome_LX22_veh_drug_samples.txt


title: SPAPB17E12.05_A8_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC577.02_A10_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPBC11C11.07_A9_rep1

description:
Knock-out strain
3' mRNA-Seq


title: DET2-XY-R2

city: Hangzhou

first: Yao

last: Wang

address: 866 Yu Hang tang Road

institute: Zhejiang University

data_processing:
The Raw Reads obtained by sequencing may contain unqualified Reads with low overall quality, sequencing primers, low end quality, etc., and the unqualified Reads are filtered to obtain clean Reads that can be used for data analysis.
Use Hisat2 (version: 2.0.4) split mapping algorithm to perform Genome mapping on the preprocessed reads. This algorithm allows the splitting of reads that cannot be fully matched for mapping.
Estimate the level of gene expression by mapping to the number of reads in the gene region.
In order to make the gene expression levels of different genes and different samples comparable, the reads are converted into FPKM to standardize the gene expression levels.
Use Stringtie (version: 1.3.0) to count the number of fragments of each gene after Hisat2 comparison, then use TMM (trimmed mean of M values) method to normalize, and finally use perl script to calculate the FPKM of each gene value.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Populus alba x Populus glandulosa

source_name: xylem

growth_protocol: The greenhouse environment is 23-26℃, long day light (16h light/8h dark), two months of cultivation.

extract_protocol:
The fresh material was ground in liquid nitrogen,RNA Sample Prep Kit (Cat.No.74104) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard protocols

tag: cultivar

value: untreated

value: DET2 overexpression

value: two-month-old

value: xylem


title: DET2-XY-R3


title: SPAC3G6.02_A7_rep1

description:
Knock-out strain
3' mRNA-Seq


title: DET2-XY-R1


title: RPM, Control rep5

description:
Immunocompetent mouse
Untreated tumor
SW135
GEMM_all_samples_FPKM_matrix.txt

value: RPM

value: RPM lung tumor

value: Adult

value: Untreated


title: DET2-CZ-R3

source_name: cambium

value: cambium


title: SPCC736.08_C10_rep1

description:
Knock-out strain
3' mRNA-Seq


title: DET2-CZ-R2


title: DET2-CZ-R1


title: DET2-SAM-R3

source_name: shoot apical meristem

value: shoot apical meristem


title: MTYC_FLC_R2

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

description: rpn4∆/∆ clone y (MTYC) with 3µg/ml fluconazole replicate 2

data_processing:
Processing is automated using the Tail-Tools pipeline, version 1.8 (https://github.com/Monash-RNA-Systems-Biology-Laboratory/tail-tools), and proceeds as follows: Reads are stripped of trailing poly(A) sequences. Reads are aligned using the STAR aligner. (Multi-mapping reads are assigned to one location at random.) Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 500 bases down-strand of a gene but not proceeding into another gene on the same strand are counted towards that gene.
Genome_build: Candida albicans SC5314 assembly 21, supplemented with AF167163.
Supplementary_files_format_and_content: CSV file containing read counts associated with each gene.

organism: Candida albicans

source_name: rpn4-delta/delta clone y (MTYC) with 3ug/ml fluconazole

growth_protocol: Overnight cultures of C. albicans wild type and two independent clones of rpn4∆/∆ (rpn4∆/∆ x and rpn4∆/∆ y) were grown in YPD medium overnight, shaking at 200 rpm at 30˚C.

extract_protocol:
Total RNA was extracted from snap frozen cell pellets using the hot phenol extraction method. RNA was then submitted for library preparation.
Library construction was by the Quant-seq method (Lexogen) according to the manufacturers specifications.
HiSeq3000 using 150bp forward read. Pooled libraries were purified using AMPureXp beads and QC’d by Qubit, Bioanalyzer and qPCR.  c-bot clustering using 200pM of library pool. Illumina Protocol 15006165 v02 Jan 2016.

treatment_protocol: On the next day, overnight cultures were adjusted to a cell density of OD600nm = 0.2 and grown in YPD medium with shaking at 200 rpm at 37˚C. Once log phase growth was achieved, cells were treated with either DMSO or 3 µg/ml fluconazole for 30 min with shaking at 200 rpm at 37˚C. Cultures were harvested by centrifugation and cell pellets were snap frozen in dry ice and stored at -80˚C until RNA was extracted.

tag: strain background

value: Candida albicans SN152

tag: strain reference

value: obtained from Oliver R. Homann (https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000783)

value: leu2{delta}/leu2{delta}::RPN4::C.d.ARG4, rpn4{delta}::RPN4::p-A.g.TEF1- C.a.NAT1- t-A.g.TEF1::C.d.HIS1/ rpn4{delta}::C.m.LEU2, his1{delta}/his1{delta}, arg4{delta}/ arg4{delta}, ura3{delta}/URA3, iro1{delta}/IRO1

tag: clone

value: rpn4-delta/delta clone y

value: 3ug/ml fluconazole


title: MTYC_FLC_R3

description: rpn4∆/∆ clone y (MTYC) with 3µg/ml fluconazole replicate 3


title: MTYC_DMSO_R3

description: rpn4∆/∆ clone y (MTYC) with DMSO replicate 3

source_name: rpn4-delta/delta clone y (MTYC) with DMSO

value: DMSO


title: MTYC_FLC_R1

description: rpn4∆/∆ clone y (MTYC) with 3µg/ml fluconazole replicate 1


title: DET2-SAM-R2

tag: tissue


title: DET2-SAM-R1

tag: treatment


title: 84K-1-XY-R3

tag: genotype

value: WT


title: JHU-LX44, Drug rep3

description:
INI-43-treated
LX44Drug_number3_4_6_20
FPKM_matrix_whole_genome_LX44_veh_drug.txt

source_name: JHU-LX44 PDX

tag: cell line

value: JHU-LX44 PDX

tag: cell type

value: Human SCLC-A tumor cells grown in NSG mouse

value: PDX from lung tumor


title: JHU-LX22, Vehicle rep2

description:
Vehicle-treated control
LX22Vehicle-3-from10-11-19
FPKM_matrix_whole_genome_LX22_veh_drug_samples.txt

value: JHU-LX22 PDX

value: Human SCLC-N tumor cells grown in NSG mouse

value: Vehicle


title: JHU-LX22, Vehicle rep1

description:
Vehicle-treated control
LX22Vehicle-231p3ng-per-uL
FPKM_matrix_whole_genome_LX22_veh_drug_samples.txt


title: JHU-LX22, Vehicle rep3

description:
Vehicle-treated control
PDX_LX22_ref
FPKM_matrix_whole_genome_LX22_veh_drug_samples.txt


title: MTYC_DMSO_R1

description: rpn4∆/∆ clone y (MTYC) with DMSO replicate 1


title: MTXC_DMSO_R3

description: rpn4∆/∆ clone x (MTXC) with DMSO replicate 3

source_name: rpn4-delta/delta clone x (MTXC) with DMSO

value: rpn4-delta/delta clone x


title: MTXC_FLC_R3

description: rpn4∆/∆ clone x (MTXC) with 3 µg/ul fluconazole replicate 3

source_name: rpn4-delta/delta clone x (MTXC) with 3 ug/ul fluconazole

value: fluconazole


title: MTYC_DMSO_R2

description: rpn4∆/∆ clone y (MTYC) with DMSO replicate 2


title: MTXC_FLC_R2

description: rpn4∆/∆ clone x (MTXC) with 3 µg/ul fluconazole replicate 2


title: MTXC_FLC_R1

description: rpn4∆/∆ clone x (MTXC) with 3 µg/ul fluconazole replicate 1


title: RPM, Control rep6

description:
Immunocompetent mouse
Untreated tumor
SW138
GEMM_all_samples_FPKM_matrix.txt

value: RPM

value: RPM lung tumor

value: Adult

value: Untreated


title: SPAC23A1.11_A5_rep1

description:
Knock-out strain
3' mRNA-Seq

source_name: cell culture

tag: replicate


title: SPAC25G10.06_A6_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAC1527.02_A4_rep1

description:
Knock-out strain
3' mRNA-Seq


title: SPAC14C4.16_A3_rep1

description:
Knock-out strain
3' mRNA-Seq


title: RPM, Drug rep1

description:
Immunocompetent mouse
INI-43-treated
SW096
GEMM_all_samples_FPKM_matrix.txt


title: MTXC_DMSO_R2

description: rpn4∆/∆ clone x (MTXC) with DMSO replicate 2

value: Candida albicans SN152

value: obtained from Oliver R. Homann (https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1000783)

value: leu2{delta}/leu2{delta}::RPN4::C.d.ARG4, rpn4{delta}::RPN4::p-A.g.TEF1- C.a.NAT1- t-A.g.TEF1::C.d.HIS1/ rpn4{delta}::C.m.LEU2, his1{delta}/his1{delta}, arg4{delta}/ arg4{delta}, ura3{delta}/URA3, iro1{delta}/IRO1


title: wt_A2_rep2

description:
Wild-type reference
3' mRNA-Seq

value: wt


title: 84K-1-XY-R2

value: untreated

value: WT

value: two-month-old

value: xylem


title: WT_FLC_R3

description: Wild type treated with 3 µg/ml fluconazole replicate 3

source_name: Wild type treated with 3 ug/ml fluconazole

value: Candida albicans SN425

value: obtained from Susan Noble (https://pubmed.ncbi.nlm.nih.gov/20543849/)

value: leu2{delta}::C.d.HIS1/leu2{delta}::C.m.LEU2, arg4{delta}/arg4{delta}::C.d.ARG4, his1{delta}/his1{delta}, ura3{delta}/URA3, iro1{delta}/IRO1

value: Wild type clone


title: MTXC_DMSO_R1

description: rpn4∆/∆ clone x (MTXC) with DMSO replicate 1

value: rpn4-delta/delta clone x

value: DMSO


title: WT_FLC_R1

description: Wild type treated with 3 µg/ml fluconazole replicate 1

value: fluconazole


title: 84K-1-CZ-R3

value: cambium


title: 84K-1-XY-R1


title: WT_DMSO_R3

description: Wild type treated with DMSO replicate 3

source_name: Wild type treated with DMSO


title: WT_DMSO_R1

description: Wild type treated with DMSO replicate 1


title: 84K-1-CZ-R2


title: 84K-1-CZ-R1


title: WT_DMSO_R2

description: Wild type treated with DMSO replicate 2


title: NCI-H2107 Empty Vector rep2

description:
Empty Vector Control for CRISPRi ASCL1 experiment
Empty_1
dCas9_ASCL1_H2107_fpkm_matrix_whole_genome.txt

source_name: NCI-H2107 cell line

value: SCLC-A subtype cell line

value: Lung tumor

value: Control

value: Empty Vector


title: 84K-1-SAM-R2

value: shoot apical meristem


title: NCI-H2107 Empty Vector rep1

description:
Empty Vector Control for CRISPRi ASCL1 experiment
Empty_2
dCas9_ASCL1_H2107_fpkm_matrix_whole_genome.txt


title: WT_FLC_R2

description: Wild type treated with 3 µg/ml fluconazole replicate 2


title: 84K-1-SAM-R3

value: untreated


title: 84K-1-SAM-R1

value: WT


title: NCI-H2107 CRISPRi ASCL1 rep1

description:
ASCL1 KD
dCas_6d_1
dCas9_ASCL1_H2107_fpkm_matrix_whole_genome.txt

value: ASCL1 KD

value: CRISPRi ASCL1


title: NCI-H2107 CRISPRi ASCL1 rep2

description:
ASCL1 KD
dCas_6d_2
dCas9_ASCL1_H2107_fpkm_matrix_whole_genome.txt


title: NCI-H2107 Empty Vector tech rep2

description:
Empty Vector Control for CRISPRi KPNB1 experiment
H2107_emp2
FPKM_matrix_whole_genome_H2107_ASCL1_high_dCas9_KPNB1.txt


title: NCI-H2107 Empty Vector tech rep1

description:
Empty Vector Control for CRISPRi KPNB1 experiment
H2107_emp1
FPKM_matrix_whole_genome_H2107_ASCL1_high_dCas9_KPNB1.txt


title: wt_A1_rep1

description:
Wild-type reference
3' mRNA-Seq

value: wt


title: Uninfected_RK_2

city: Baltimore

first: Venu

last: Raman

state: Maryland

address: 720 Rutland Ave, Traylor 338

department: Radiology

institute: Johns Hopkins University

data_processing:
Raw sequencing data was QC'ed by SOAPnuke v 1.5.2 and filtered clean reads were aligned to the reference genome using HISAT2 v 2.0.4  the results of which were also QC'ed. This was analysed for gene expression.
Assembly: hg38.p12
Supplementary files format and content: tab-delimited text file with FPKM, TPM, and Read Count values for genes in each sample.

growth_protocol: Calu-3 cells (8 x 105) were plated in 12-well plates 24 h prior to drug treatment.

extract_protocol:
Total RNA was extracted from virus containing cell lysates using Trizol LS (Invitrogen, Carlsbad, CA) and purified using a column purification method (Qiagen, Germany) in accordance with manufacturer’s recommendations that were modified to isolate both small and large RNA species. RNA concentration and preliminary quality control was estimated on a NanoDrop spectrophotometer (ThermoFisher Scientific) while RNA-Seq was performed commercially (BGI Americas, San Jose, CA).
Libraries were constructed by BGI. Briefly, RNA was QC'ed and mRNA enriched by oligo(dT) beads, followed by fragmentation and ds cDNA synthesis. Ds cDNA was end repaired, added an A, and adapter ligated followed by UDG degradation of dUTP-marked strand and PCR. This was followed by single strand separation and digestion of uncircularized DNA to obtain the final library which was QC estimated. Sequencing: Single-stranded cyclized DNA molecules were replicated via rolling cycle amplification, and a DNA nanoball (DNB) containing multiple copies of DNA was generated. DNBs were loaded into patterned nanoarrays and sequenced through combinatorial Probe-Anchor Synthesis (cPAS) on the DNBSEQ platform.

treatment_protocol: Cells were then incubated with RK-33 at 5µM concentration for 24 h followed by infection with SARS CoV-2 variant as indicated, at MOI 0.1. One hour post infection infectant was removed, cells were washed one time with PBS and fresh complete medium supplemented with RK-33 at 5µM concentration was added. Cells infected with SARS CoV-2 as well as virus containing supernatants were collected 48 h post infection.


title: Uninfected_RK_4


title: Uninfected_RK_3


title: JHU-LX44, Vehicle rep1

description:
Vehicle-treated control
LX44Veh_number10
FPKM_matrix_whole_genome_LX44_veh_drug.txt

value: JHU-LX44 PDX

value: Human SCLC-A tumor cells grown in NSG mouse

value: PDX from lung tumor

value: Vehicle


title: JHU-LX44, Drug rep1

description:
INI-43-treated
LX44Drug_number1_4_8_20
FPKM_matrix_whole_genome_LX44_veh_drug.txt


title: JHU-LX44, Drug rep2

description:
INI-43-treated
LX44Drug_number2
FPKM_matrix_whole_genome_LX44_veh_drug.txt


title: NCI-H2107 CRISPRi KPNB1 rep2

description:
KPNB1 KD
H2107_dKP2
FPKM_matrix_whole_genome_H2107_ASCL1_high_dCas9_KPNB1.txt

value: KPNB1 KD

value: CRISPRi KPNB1


title: JHU-LX44, Vehicle rep2

description:
Vehicle-treated control
LX44Veh_number6_4_8_20
FPKM_matrix_whole_genome_LX44_veh_drug.txt


title: NCI-H2107 CRISPRi KPNB1 rep1

description:
KPNB1 KD
H2107_dKP1
FPKM_matrix_whole_genome_H2107_ASCL1_high_dCas9_KPNB1.txt


title: iPSC, A10 rep 1

city: Worcester

first: JAE-HYUCK

last: SHIM

state: Massachusetts

address: 364 Plantation street

institute: University of Massachusetts Medical School

data_processing:
mapped to the human reference genome (GCF_000001405.38_GRCh38.p12) with STAR aligner (v.2.6.1b)
read counts were generated by using HTSeq-count (v.0.11.3)
The read counts were used for a differential expression analysis between control and A9 group, and control and A10 group using DESeq2 (v.1.28.1) with the ashr shrinkage estimator (v.2.2.47)
Assembly: GCF_000001405.38_GRCh38.p12
Supplementary files format and content: txt file has the count of total RNA-seq (first column has the gene name and second column has the count)

source_name: bone

growth_protocol: Cells were cultured in DMEM with 20% FBS, glycerol-2-phosphate, 4 μM dexamethasone, 0.1 mM 2-mercaptoethanol, and 50 μg/ml L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate.

extract_protocol:
The total RNA was purified from cells and tissues using QIAzol (QIAGEN).
Isolate polyA RNA using dynabeads mRNA purification kit (Life Technologies).
Fragmentation/The first cDNA systhesis (SuperScript II reverse transcription kit)/The second-strand synthesis (Rnase H (Life Techonologies)/DNA polymerase (Enzymatics)/ Short double-stranded cDNA fragments purification: QIA quick PCR purification kit and Agencourt AMPure beads/end-repair with klenow polymerase (T4 DNA polymerase and T4 polynucleotide kinase)/ A single 3' A adding to the double-stranded cDNA (Kelnow (Enzymatics) and dATP (GE Healthcare)/The illumina PE Adapter oligo mix ligation/library amplification/denaturation of library with sodium hydroxide and diluted to 2.5 pM in hybridization buffer for loading into a HiSeq flowell.

treatment_protocol: 5 x 10^10 GCs of AAV carrying  control, A9 (RH6) or A10 (RH7) were transduced to human FOP (fibrodysplasia ossificans progressiva) patients-derived iPSCs (inducible pluripotent stem cells).

tag: disease state

value: Fibrodysplasia ossificans progressiva (FOP)

value: bone

value: FOP patients-derived iPSCs

value: osteoblast

value: ACVR1-R206H mutant

value: A10 (RH7)-AAV


title: iPSC, Ctrl1

value: Control-AAV


title: iPSC, A9, rep 1

value: A9 (RH6)-AAV


title: iPSC, A9, rep 2


title: iPSC, A10 rep 2


title: iPSC, Ctrl2


title: Uninfected_DMSO_4

value: WT

value: DMSO


title: Uninfected_DMSO_1


title: Uninfected_DMSO_3


title: Uninfected_DMSO_2


title: Uninfected_RK_1


title: Infected_RK_4

value: RK-33 + SARS-CoV-2


title: Infected_RK_2


title: Infected_RK_3


title: Infected_DMSO_1

value: DMSO + SARS-CoV-2


title: Infected_DMSO_3


title: Infected_RK_1


title: Infected_DMSO_4


title: Infected_DMSO_2


title: A549 flag-hnRNPM TGFβ Rep3

city: chengdu

first: PAN

last: YiTong

address: Wangjiang Street

institute: Sichuan University

data_processing:
The data were compared to the reference genome GRCh37 using HISAT2 software.
Bam files are first sorted using SamTools sort and then quantified using StringTie.
bigWig files were generated using DeepTools' bamCoverage function.
Assembly: GRCh37
Supplementary files format and content: bigWig, csv

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
cells were harvested and lysed in RIP lysis buffer (20mM Tris-HCl, pH7.4, 10mM MgCl2, and 0.1M NaCl, 10% glycerol, 0.5% NP-40, 0.5% Triton X-100, phosphatase inhibitors, protease inhibitors cocktail and RNase inhibitor) on ice for 5 min, followed by homogenizing for additional 20 min to release the nuclear components.
Equivalent amount of RNA was mixed with spike-in (Invitrogen #4456740) to generate RIP-hnRNP M libraries using VAHTS Universal V6 RNA-seq Library Prep Kit (Vazyme #NRM604-01), according to the manufacture instruction.

value: Human lung carcinoma

tag: chip antibody

value: ANTI-FLAG® M2 Affinity Gel (Sigma #A2220)


title: HDM201_5

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

description: Gene expression from OCI-AML3_treated with HDM201

hyb_protocol: Labeled fragments were hybridized to Affymetrix Clariom S Human arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CEL files were analysed using the oligo R package. RMA method, log2 transformed were used to normalized the probe intensities.

label: Biotin

source_name: OCI-AML3_treated with HDM201_biological replicate 5

label_protocol: We used the Affymetrix WT Pico kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

growth_protocol: OCI-AML3 cells were cultured in RPMI-medium supplemented with 10% Fetal Calf Serum at 37°C and maintained at a desity of 0.1-1.0x10^6 cells/ml.

extract_protocol: After harvesting RNA of OCI-AML3 cells was extracted using miRNAeasy Mini kit and Dnase as described by the manufacturer.

treatment_protocol: OCI-AML3 cells were treated with DMSO, RG7112 (2 µM) or HDM201 (500 nM) for 24 hours.

value: OCI-AML3 cells

tag: agent

value: wildtype


title: RG7112_6

description: Gene expression from OCI-AML3_treated with RG7112

source_name: OCI-AML3_treated with RG7112_biological replicate 6


title: Con_10

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

data_processing:
Library strategy: 16S rDNA
Illumina HiSeq software used for basecalling.
The qualified genomic DNA samples were amplified by PCR, and the library was constructed. The range and concentration of fragments in the library were detected by Agilent 2100 Bioanalyzer, and the hiseq platform was selected for sequencing.
Through the overlap relationship between the reads, the reads are spliced into tags.
Tags were clustered into OTUs and compared with database, and species were annotated.
Species complexity analysis, species diversity analysis, association analysis and model prediction were carried out.
Genome_build: susScr11
Supplementary_files_format_and_content: percentage of bacterium

organism: Sus scrofa

source_name: fecal

extract_protocol:
30 ng of qualified genomic DNA samples and corresponding fusion primers were used to prepare PCR reaction system, and PCR reaction parameters were set for PCR amplification.
16S rDNA libraries were prepared for sequencing using standard IlluminaHiSeq protocols

tag: strain

value: Duroc

value: fecal

value: 42 months

value: control


title: RG7112_2

source_name: OCI-AML3_treated with RG7112_biological replicate 2


title: HDM201_1

source_name: OCI-AML3_treated with HDM201_biological replicate 1


title: Control-1

description:
Total RNA was used to label mRNA and lncRNAs using low imput labelling kit
Control-13

source_name: Heart-Control

tag: Sex

value: Male

tag: age

value: 5 months

value: Control

value: Heart muscle


title: Control+Pargyline-2

description:
Total RNA was used to label mRNA and lncRNAs using low imput labelling kit
Control+pargyline-8

source_name: Heart-Treated with Pargyline

tag: group/treatment

value: Treated with Pargyline


title: Control-3

description:
Total RNA was used to label mRNA and lncRNAs using low imput labelling kit
Control-5


title: HDM201_6

source_name: OCI-AML3_treated with HDM201_biological replicate 6


title: RG7112_4

source_name: OCI-AML3_treated with RG7112_biological replicate 4


title: HDM201_2

source_name: OCI-AML3_treated with HDM201_biological replicate 2


title: RG7112_3

source_name: OCI-AML3_treated with RG7112_biological replicate 3


title: atgox3

city: Granada

first: Laura

middle: Carmen

last: Terron Camero

state: Granada

address: Avda. del Conocimiento 17. P. T. Ciencias de la Salud

department: Bioinformática

country: Spain

institute: IPBLN

description: Control condition

hyb_protocol: Hybridization was performed by the Functional Genomics Lab (Univ. Verona, IT) using NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by the Functional Genomics Lab (Univ. Verona, IT) using NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Differential expression analysis has been performed with LIMMA (Linear Models Microarray Analysis; G. K. Smyth, 2005) R package and custom functions. Data preprocessing:background correction: normexp, quantile normalization,  internal replicate summarization: median. Statistical analysis:linear models approach for the assessment of differential expression, P values were adjusted for multiplicity with BH method (Benjamini and Hochberg, 1995).

organism: Arabidopsis thaliana

source_name: atgox Control condition

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Seedlings were grown for two weeks on solid MS medium, three independent biological replicates, each composed of at least five different seedlings, were used per experimental condition

extract_protocol: Total RNA was isolated from seedlings by the acid guanidine thiocyanate–phenol–chloroform method using the Trizol reagent kit according to the manufacturer's instructions.

treatment_protocol: Seedlings were incubated with 100uM cadmium for 30 minutes or 24 hours. Controls were incubated in a cadmium-free solution.

tag: ecotype

value: leaves

tag: expt condition

value: atgox Control condition


title: atgox1

description: Control condition


title: Con_9

value: 41 months


title: Control+Pargyline-1

description:
Total RNA was used to label mRNA and lncRNAs using low imput labelling kit
Control+pargyline-6


title: A549 flag-hnRNPM TGFβ Rep1


title: HDM201_3

source_name: OCI-AML3_treated with HDM201_biological replicate 3


title: A549 flag-hnRNPM TGFβ Rep2


title: DMSO_6

description: Gene expression from OCI-AML3_treated with DMSO

source_name: OCI-AML3_treated with DMSO_biological replicate 6

value: DMSO


title: RG7112_1

source_name: OCI-AML3_treated with RG7112_biological replicate 1


title: Con_8

value: 40 months


title: RG7112_5

source_name: OCI-AML3_treated with RG7112_biological replicate 5


title: HDM201_4

source_name: OCI-AML3_treated with HDM201_biological replicate 4


title: A549 flag-hnRNPM CTRL Rep3

value: Human lung carcinoma

value: ANTI-FLAG® M2 Affinity Gel (Sigma #A2220)


title: Con_7

value: 39 months


title: A549 flag-hnRNPM CTRL Rep2


title: Con_5

value: Duroc

value: 38 months


title: s35s_24h2

description: Cd 100uM 24h

source_name: s35s Cd 100uM 24h

value: s35s Cd 100uM 24h


title: Con_4

value: fecal

value: 37 months

value: control


title: A549 flag-hnRNPM CTRL Rep1


title: Con_3

value: 36 months


title: s35s_24h3

description: Cd 100uM 24h


title: atgox2

description: Control condition


title: Con_2

value: 35 months


title: Con_1

value: 34 months


title: mature rudiment 1, scRNAseq

city: Napoli

first: Maria Ina

last: Arnone

address: Villa Comunale 1

department: Biology and Evolution of Marine Organisms

institute: Stazione Zoologica Anton Dohrn

description:
pl_mature_rudiment_integrated.rds
pl_mr_photoreceptors2.rds
pl_mr_photoreceptors3.rds

data_processing:
Fastq reads were aligned onto P. lividus genome to obtain output feature, barcode and matrix files using Cell Ranger 3.0.2 (10x Genomics).
Cell Ranger output files were loaded Seurat v4.0.5 R package.
Genes transcribed in less than three cells and cells with less than  200 transcribed genes were excluded.
Data was normalized and variable genes were found using vst method with 2000 variable features maximum.
Data was integrated using anchors between the two different R Seurat objects.
Data was scaled and principal component (PCA) analysis was performed. Sharing Nearest Neighbor (SNN) was computed with 32 dimensions (resolution 1.0). UMAP clustering dimensionality reduction was performed.
Sub-clustering analysis was performed for photoreceptor 2 and photoreceptor 3 cells. For photoreceptor 2 and photoreceptor 3  SNN graphs were computed with 8 and 6 dimensions respectively (resolution 1.0).
Assembly: P.lividus genome v1
Supplementary files format and content: tab separated values, Matrix Market Exchange matrices, R Seurat objects

organism: Paracentrotus lividus

source_name: dissected mature rudiment

growth_protocol: Adult Paracentrotus individuals were kept in circulating seawater aquaria at Stazione Zoologica Anton Dohrn in Naples. Spawning was induced by vigorous shaking of gravid animals. Embryos and larvae were raised at 18°C in filtered Mediterranean Sea water (FSW) at 12/12h light/dark cycle with 37 ppt salinity in 2L beakers. Larval concentration less than 5 larvae/mL. Half of the water was exchanged 2 times per week. After the 2 days post fertilization (dpf)  larvae were fed 3 times per week 1000 cells/mL Dunaliella sp. Once at juvenile stage, animals were fed with Ulva lactuca.

extract_protocol:
Per biological replicate, three rudiments were collected through dissection using tungsten needles under a stereoscope. Each rudiment was dissected out of the larva, while larval tissues were discarded. Dissected rudiments were dissociated t 37°C for 40 min with a pipette in Ca2+Mg2+ free Artificial Sea Water (CaMg-free ASW) with 1% Protease XIV and 0.05% Liberase. Larval debri were removed with 0.22 µm mesh, the dissociated cells were spun down at 700 g for 5 min and washed several times with CaMg-free ASW. Cell viability was assessed using Propidium Iodide (1µg/mL) and Calcein AM (2 µg/mL). Single cells were counted using a hemocytometer and diluted following 10x Genomix guidelines.
Single cell cDNA libraries were prepared using the Chromium Single Cell 3’ Reagent Kit, Chemistry v3.
Libraries were indexed, multiplexed and sequenced on Illumina NextSeq 500 to generate paired end reads.

value: mature rudiment cells


title: mature rudiment 2, scRNAseq


title: AOS10_10

source_name: fecal

value: 33 months


title: A549 flag TGFβ Rep1


title: A549 flag TGFβ Rep3


title: A549 flag TGFβ Rep2


title: A549 flag CTRL Rep2


title: A549 flag CTRL Rep3


title: Patient nCounter 115

city: Bordeaux

first: ELodie

last: Darbo

address: 229 cours de l'Argonne

department: INSERM

country: France

institute: University of Bordeaux

description: Total RNA samples runs were performed on the nCounter FLEX Analysis System based on the NanoString PanCancer Immuno-Oncology panel (IO360), made of 770 genes and a custom panel of 30 genes, in which we included genes from Hendrickx et al.’s Immunologic Constant of Rejection (ICR) signature.

hyb_protocol: According to Nanostring protocol

scan_protocol: Sample runs were performed on the nCounter FLEX Analysis System (automated nCounter® Prep station and the nCounter® Digital Analyzer optical scanner, NanoString Technologies, Seattle, WA, USA) according to the manufacturer’s protocol.

data_processing: We refined the 20-housekeeping gene list defined in NanoString IO360 panel using three independent datasets grouping triple negative breast cancer patients retrieved from xenaBrowser [TCGA BRCA primary tumors with 123 patients, Chin et al. 2006 : 41 patients and Hess et al. 2006  : 27 patients]. We computed gene expression variability as the inter-quantile (5%-95%) ratio in each dataset and selected 6 of the 20 genes showing ratios under 1.5 in all datasets: ERCC3, POLR2A, SF3A1, TBC1D10B, TMUB2, UBB.  We normalized the expression values using NanoStringNorm R package v1.2.1.1 with options CodeCount ='geo.mean', Background ='mean.2sd', SampleContent ='housekeeping.geo.mean', round.values = TRUE, take.log = TRUE.

source_name: Residual Triple Negative Breast Cancer

label_protocol: According to Nanostring protocol

extract_protocol: Total tumor RNA was extracted from four to six 10-micron tumor sections after identification of the residual tumor by a pathologist on a corresponding H&E section. RNA was extracted using the High Pure FFPET RNA Isolation Kit (Roche®), following the manufacturer’s instructions. RNA quantity and quality were assessed by Nanodrop 1000 spectrophotometer (ThermoFisher, Waltham, MA, USA) and 2100 Bioanalyser with Agilent RNA 6000 Nano kit (Agilent, Santa Clara, CA, USA). 200ng of total RNA was used from each sample for gene expression profiling (acceptation criteria 260/280 ratio: 1.8 -2.3, 230/280 ratio: 1.7-2.3).

tag: lve

tag: tils

tag: metastasis


title: AOS10_9

tag: tissue

value: 32 months

tag: treatment


title: AOS10_8

value: 31 months


title: A549 flag CTRL Rep1

tag: cell line


title: AOS10_7

value: 30 months


title: s35s_24h1

description: Cd 100uM 24h

value: leaves


title: SKMEL113, M216+Tram, 24h, Rep3

city: Charlottesville

first: Mohammad

last: Fallahi-Sichani

state: VA

address: 415 Lane Rd

institute: University of Virginia

data_processing:
All processing steps were performed on Galaxy server. Reads were mapped to the human genome (hg38) using HISAT2.
Transcripts were assembled and quantified using StringTie.
Assembly: hg38
Supplementary files format and content: csv files include FPKM/TPM values for each sample

extract_protocol:
Samples were washed once with PBS and then lysed with Rneasy Buffer RLT (Qiagen). RNA was extracted using QIAshredder (Qiagen) and Rneasy Mini Kit (Qiagen). RNA was Dnase treated (Qiagen) and then eluted. RNA quality was assessed by Bioanalyzer. All samples had RINs of 9.0 or higher
Prior to poly-A enrichment, 500 ng of each RNA sample was supplemented with 1 μL (1:100 dilution) of ERCC spike-in control. Poly-A RNA enrichment was performed using NEBNext Poly(A) kit. Fragments were end-modified with adaptors using NEBNext Multiplex Oligos for Illumina Set 2, following library amplification (PCR, 11 cycles). Resulting libraries were prepared using NEBNext Ultra II Directional RNA Kit.

tag: cell type

value: melanoma cells

tag: genotype

value: NF1 loss-of-function

value: MTX-216 (1 µM) + Trametinib (0.1 µM)

tag: time

value: 24 hours


title: Patient nCounter 113


title: SKMEL113, M216+Tram, 24h, Rep2


title: Patient nCounter 114


title: s35s_30m2

description: Cd 100uM 0.5h


title: AOS10_6

value: Duroc

value: 29 months


title: Patient nCounter 112


title: Patient nCounter 110


title: Patient nCounter 111


title: AOS10_5

value: fecal

value: 28 months


title: AOS10_4

value: 27 months


title: Patient nCounter 108


title: Patient nCounter 109


title: AOS10_3

value: 26 months


title: DMSO_5

source_name: OCI-AML3_treated with DMSO_biological replicate 5

value: OCI-AML3 cells

value: DMSO

value: wildtype


title: s35s30m3

description: Cd 100uM 0.5h


title: atgox2_24h1

description: Cd 100uM 24h

source_name: atgox2 Cd 100uM 24h

value: atgox2 Cd 100uM 24h


title: SKMEL113, Tram, 24h, Rep2

value: Trametinib (0.1 µM)


title: SKMEL113, M216+Tram, 24h, Rep1


title: SKMEL113, Tram, 24h, Rep3


title: SKMEL113, Tram, 24h, Rep1


title: AOS10_2

value: 25 months


title: AOS10_1

value: 24 months


title: SKMEL113, M216, 24h, Rep3

value: melanoma cells


title: SKMEL113, M216, 24h, Rep2

value: NF1 loss-of-function


title: atgox2_24h2

description: Cd 100uM 24h

value: leaves


title: wt30m3

description: Cd 100uM 0.5h

source_name: wt30m Cd 100uM 0.5h

value: wt30m Cd 100uM 0.5h


title: Patient nCounter 107


title: SKMEL113, M216, 24h, Rep1

value: 24 hours


title: DMSO_1

source_name: OCI-AML3_treated with DMSO_biological replicate 1


title: DMSO_2

source_name: OCI-AML3_treated with DMSO_biological replicate 2


title: ChIPseq.MIN6.WT.H3K27ac

city: Boston

first: Cigall

last: Kadoch

address: 450 Brookline Avenue

institute: Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber Cancer Institute

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
For the ChIPseq data, output BAM files were converted into BigWig track files using MACS2 and UCSC utilities in order to display coverage throughout the genome (in RPM).
For the ChIPseq data, peaks were called with MACS2 using a q-value cutoff of 0.001.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: MIN6 cells were cultured in DMEM with 15% heat inactivated FBS, 1% L-Glutamine, 1% Pen/Strep, and 0.0005% β-mercaptoethanol.

extract_protocol:
Cells were trypsonized, washed with room temperature PBS twice to remove trypsin, and divided into 40 million-cell aliquots.  Cells were fixed using 1% formaldehyde (Sigma Aldrich) for 10 min at 37 °C with constant stirring to keep cells in solution, and finally quenched with 125 mM glycine for 5 min at 37 °C. Quenched cells were washed with cold PBS, and stored in 10-million aliquots at −80 °C until they were used. 10 millions cells were used per epitope in subsequent chromatin immunoprecipitations. Following nuclei extraction, chromatin was sonicated using a Covaris E220 Focused-Ultrasonicator system. Sonicated chromatin was cleared by centrifugation for 10 min at 10,000 r.p.m. (15,000 g). Soluble fractions were incubated with the indicated antibodies (see antibody list) overnight at 4°C, and captured using Protein G Dynabeads (Thermo Fisher). Antibody-chromatin complexes were captured with Protein G Dynabeads (Thermo Fisher), washed extensivley, eluted, and treated with RNAse A (Roche) for 30 min at 37 °C and Proteinase K (Life Technologies) for 3 h at 65 °C. ChIP DNA samples were extracted using SPRI beads (Beckman Coulter Agencourt AMP Xpure), washed with 80% Ethanol, and eluted using 0.1X TE. ChIP DNA samples were stored at -20C before library prep were initiated. All ChIP seq libraries were processed with Illumina’s NEBNext Ultra II DNA library Prep Kit (Followed standard protocols). All ChIP seq libraries were sequenced on the Illumina Next-seq 500 with 75 bp read single-end sequencing.
ChIP-sequencing libraries were prepared with Illumina’s NEBNext Ultra II DNA library Prep Kit using standard protocols.

treatment_protocol: Mouse Arid1a sgRNA (GCTGCTGCTGATACGAAGGTTGG) was cloned into the LentiGuide-puro plasmid (Addgene #52963). Lentivirus was packaged in 293T cells in 10 cm dishes. The day after seeding cells, each dish was transfected with pVSV-G, pLenti-gag pol, LentiCas9-puro-sgArid1a, or LentiCas9-Blast plasmid (Addgene #52962) in Lipofectamine 3000 (Life Technologies #L3000015). The media containing virus was collected 60h after transfection. To create stable Cas9 expressing cell lines, cells were infected with Cas9 lentivirus and subjected to blasticidin selection at 2 ug/mL for 4 days. Then Cas9 expressing cells were infected with the Arid1a sgRNA lentivirus. Three days after the infection, we selected cells for 3 days with 2 ug/mL puromycin. 50 to 200 cells were plated in 15 cm dishes for single clone selection. Clones were picked and verified with PCR genotyping and Western blotting for ARID1A to determine WT, ARID1A heterozygous KO, and ARID1A homozygous KO clones.

tag: chip antibody

value: Wildtype


title: ChIPseq.MIN6.Homozygous.ARID1A.KO.H3K27ac

value: Homozygous ARID1A KO


title: s35s30m1

description: Cd 100uM 0.5h


title: SKMEL113, DMSO, 24h, Rep3


title: ChIPseq.MIN6.Heterozygous.ARID1A.KO.H3K27ac

value: Heterozygous ARID1A KO


title: H3122_LR_2_450K

type: genomic

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

institute: Korea Research Institute of Bioscience and Biotechnology

hyb_protocol: Samples were randomly assigned to one of nine Illumina 450K plates and hybridized according to protocol.

scan_protocol: Not provided

data_processing:
Data was analyzed in R (v.3.4.2) using minfi (v.1.30.0). Poorly performing probes (detection p-value < 0.05) and sex chromosome probes were removed from the analysis.
SWAN normalization were performed using the minfi package according author guidelines.
Normalized average beta values included in processed data.

label: Cy3, Cy5

source_name: H3122 lung cancer cell line

label_protocol: Not provided

extract_protocol: DNA was extracted using QIAamp Blood DNA mini kit (QIAGEN). 1 ug of extracted DNA per sample was treated with bisulfite and used in the assay.

value: lung cancer

value: Certinib


title: SKMEL113, DMSO, 24h, Rep2


title: Patient nCounter 103


title: Patient nCounter 102


title: H3K27Ac Clino 24h

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

institute: Chiba University

data_processing:
Reads were aligned to the mm9 mouse genome using STAR.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bedGraph files were generated using Homer.

source_name: C2C12 myotube

growth_protocol: C2C12 myoblasts (ATCC CRL-1772) were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin. Myogenic differentiation was induced in DMEM supplemented with 5% horse serum and 1% penicillin-streptomycin at 37C under 5% CO2.

extract_protocol:
Ten million C2C12 cells were used. Briefly, the cells were crosslinked in 1% formaldehyde, after which they were collected and resuspended for 5 min in swelling buffer (10 mM HEPES/KOH pH 7.9, 85 mM KCl, 1 mM EDTA, 0.5% IGEPAL CA-630) containing protease inhibitors. The cells were then spun down and resuspended in 500 µl of lysis buffer (50 mM Tris/HCL pH7.4, 1 % SDS, 0.5 % Empigen BB, 10 mM DETA) containing protease inhibitors, and chromatin was sheared by sonication. The lysate was diluted with 750 µl of dilution buffer (20 mM Tris/HCl, 100 mM NaCl, 0.5% TritonX-100, 2 mM EDTA), after which 1% was taken as input DNA, immunoprecipitation was carried out overnight using Dynabeads protein G (Thermo Fisher) coated with H3K27Ac antibody (Abcam, Ab4729). Thereafter, the beads were washed two times each with wash buffer I (20 mM Tris/HCl, 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 2 mM EDTA), wash buffer II (10 mM Tris/HCl, 250 mM LiCl, 1% IGEPAL CA-630, 0.7% Na-deoxycholate, 1 mM EDTA), TE plus 0.2% Triton X-100, and TE plus 50 mM NaCl and then eluted with elution buffer containing 1% SDS. DNA was reverse crosslinked and purified using a QIAquick PCR purification Kit (Qiagen) according to the manufacturer's instructions.
ChIP-seq libraries were prepared using a NEBNext UltraII RNA Library Prep kit for Illumina (NEB) according to the manufacturer’s protocol.

treatment_protocol: Microgravity conditions were produced using a 3D-Clinorotation apparatus (Gravite®, Space Bio-Laboratories Co., Ltd.). This device produces an environment similar to that of outer space (0.001 G) by rotating a sample around two axes, integrating a gravity vector with a temporal axis. This is accomplished by rotation of a chamber at the center of the device, which results in uniform dispersion of the gravity vector within a spherical volume, with a constant angular velocity. Within 8 min, these conditions produced a simulated environment of 10-3 G, measured with a gravity acceleration sensor, which was defined as simulated microgravity. Differentiated C2C12 myotubes were cultured in a cell culture flask (T-75, Corning) filled with differentiation media for 8, 24, and 48 hours under simulated microgravity at 37C. As a control, C2C12 myotubes cultured in the same cell culture flask under the ground condition were used.

value: Myotube

value: Clinorotation 24h


title: H3K27Ac Clino 0h

value: Control 0h


title: Patient nCounter 104


title: Patient nCounter 100


title: Patient nCounter 101


title: Patient nCounter 106


title: Patient nCounter 105


title: Patient nCounter 99


title: wt24h2

description: Cd 100uM 24h

source_name: wt Cd 100uM 24h

value: wt Cd 100uM 24h


title: Patient nCounter 98


title: wt1

description: Control condition

source_name: wt Control condition

value: wt Control condition


title: Control-2

description:
Total RNA was used to label mRNA and lncRNAs using low imput labelling kit
Control-4

source_name: Heart-Control

value: Male

value: 5 months

value: Control

value: Heart muscle


title: s35Sc3

description: Control condition

source_name: s35Sc Control condition

value: leaves

value: s35Sc Control condition


title: Atgox2_30m2

description: Cd 100uM 0.5h

source_name: Atgox2 Cd 100uM 0.5h

value: Atgox2 Cd 100uM 0.5h


title: RNA-pol2 HiChIP of Mus musculus: NPC-KLF4-KO-Rep1

city: Tianjin

first: Niannian

last: Li

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

institute: Nankai University

data_processing:
Clean reads of RNA-seq were mapped to mm10 using HISAT2(2.1.0)
Expression levels of all genes were counted and expression profile matrix was constructed with featureCounts(2.0.3)
Differential expression analysis was calculated in R using DESeq2(1.18.1), with p value < 0.05 and fold change > 2 or < 1/2
Clean reads of ChIP-seq were mapped to mm10 using bowtie2(version 2.4.4)
Peak calling using MACS2(2.2.7.1)
Clean reads of HiChIP-seq were mapped to mm10 using HiC-Pro(2.11.1)
Loop calling using hichipper(0.7.7)
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample;Bigwig file with ChIP signal for every sample; Bedpe file with HiChIP loops for every sample
Library strategy: HiChIP

source_name: Embryonic stem cell

growth_protocol: Mouse ESCs (E14) were grown in culture dishes coated with 0.1% gelatin in DMEM supplemented with 15% FBS, 100 nM NEAA, 200 mM L-Glutamate, 1% Penicillin-streptomycin, 50 μM β-mercaptoethanol, 10 ng/mL LIF, 1 μM PD0325901 and 3 μM CHIR99021. The medium was replaced every 1 - 2 days. All cells are maintained at 37 °C in a 5% CO2 incubator.

extract_protocol:
For RNA-seq: cells were lysed with Trizol reagent (Life Technologies) and RNA was extracted according to the manufacturer's instructions. For Chip-seq, 10 M cells cells were crosslinked with 1% formaldehyde (methanol free) in DMEM at a volume of 1 mL of formaldehyde for every one million cells. Cells were cross-linked 10 min at room temperature with rotation. Glycine was added into a final concentration of 125 mM to quench the formaldehyde. Samples were incubated 15 min on ice and then spun down at 2500 g for 5 min. The supernatant was discarded, and pelleted nuclei were washed once with 500 μL pre-chilled cell Lysis Buffer (10mM Tris-HCl pH 8.0, 10mM NaCl, 0.2% NP-40, 1×protease inhibitors) and then rotated at 4°C for 30 min. Samples were then spun down at 2500 g for 5 min and the supernatant discarded, while pelleted nuclei were washed twice with 500 μL of ice-cold ChIP Lysis Buffer. The volume of pelleted material was brought up to 1mL in Nuclear Lysis Buffer (50mM Tris-HCl pH 7.5, 10 mM EDTA, 1% SDS, 1×protease inhibitors) and incubated 5 min at room temperature. Samples were then divided equally into 3 parts, sheared for 30 cycles (30 s “ON” and 30 s of “OFF”), and then spun down at 16100 g for 15 min. Supernatant were collected into new low-adsorption 1.5mL EP tubes. Then, 60 μL of Protein A beads for every 107 cells were washed in ChIP Dilution Buffer and resuspended in 50 μL Dilution Buffer per tube (100 μL per ChIP). Protein A beads were added to samples, which were rotated 1 h at 4 °C for precleaning. Sample supernatants were then separated using a magnet and transferred into new tubes, and then 7.5 μg antibodies per 107 cells were incubated at 4 °C overnight with rotation. The next day, 60 μL Protein A beads were washed and added to samples and then rotated 2 h at 4 °C. Beads were washed three times each with Low Salt Wash Buffer, High Salt Wash Buffer, and LiCl Wash Buffer. Chip-DNA was de-crosslinking with Proteinase K and purification using AmpureXP beads.For HiChIP:Briefly, 1.5×107 cells were crosslinked with 1% formaldehyde and lysed and then chromatin was digested using 400U MboI (NEB). Then 37.5μL biotin14-d-ATP was added and restriction-cut ends were ligated using 4000U T4 ligase (NEB). Pelleted nuclei were dissolved in nuclear lysis buffer (50 mM Tris-HCl, pH 7.5, 10 mM EDTA, 1% SDS, and protease inhibitors), sonicated and diluted in ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 7.5, and 167 mM NaCl). Immunoprecipitation was performed overnight at 4 °C by incubating RNA polⅡ antibodies (Biolegend) precoated on protein A-coated magnetic beads (Thermo Fisher Scientific). Immunocomplexes were washed three times each with low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 7.5, and 150 mM NaCl), high-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 7.5, and 500 mM NaCl), and LiCl buffer (10 mM Tris-HCl, pH 7.5, 250 mM LiCl, 1% NP−40, 1% Na-Doc, and 1 mM EDTA), and beads were resuspended in DNA elution buffer (50 mM NaHCO3 and 1% SDS). After elution, ChIP samples were incubated with 10 mg/mL proteinase K 4 h at 55 °C, and then DNA was purified using AMPure XP Beads (Beckman).
For RNA-seq: Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system. Then 3 µl USER Enzyme (NEB, USA) was used with size selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq 6000 platform and 150 bp paired-end reads were generated.For ChIP-Seq:Chip-seq library preparation was performed using eluted ChIP DNA with NEBNext Ultra DNA Library Prep Kit, according to manufacturer's protocol.For HiChIP:Streptavidin C1 beads were used to capture biotinylated DNA. QIAseq FX DNA Library Kits were used to generate the sequencing library. HiChIP libraries were size-selected to 300–700 bp using AMPure XP beads (Beckman) and subjected to 2 × 150-bp paired-end sequencing on HiSeq XTen (Illumina). Two biological replicates were analyzed for each experimental condition.

treatment_protocol: RNA-seq was performed using neuro induction (12 d) WT and KLF4-KO NPCs, ChIP-Seq was performed using undifferentiated mESCs and KLF4-KO mESCs.

value: embryo, blastocyst embryo, blastocyst

value: NPC


title: RNA-pol2 HiChIP of Mus musculus: NPC-KLF4-KO-Rep2


title: MeWo, Tram, 24h, Rep1

source_name: MeWo

value: MeWo

value: melanoma cells

value: NF1 loss-of-function

value: Trametinib (0.1 µM)

value: 24 hours


title: SKMEL113, DMSO, 24h, Rep1

value: DMSO


title: MeWo, Tram, 24h, Rep2


title: MeWo, Tram, 24h, Rep3