title: SS32 ATAC-seq

city: Seoul

first: Hyun Mu

last: Shin

address: Biomedical Science Building 202, 103 Daehakro, Jongro-gu

department: Biomedical Sciences

institute: Seoul National University College of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8.2.
ATAC-seq reads were processed using Trimmomatic software.
ATAC-seq reads were aligned to the hg19 genome assembly using bowtie2 v2.3.4.1 with "-k 4 -N 1 -R 5 --end-to-end" options.
The aligned reads were converted into browser extensible data (BED) format using “bedtools bamtobed”, and offset +4 base pair (bp) for positive strand and −5 bp for negative strand.
The aligned reads were used for peak calling process using HOMER suite with “findPeaks” with “-style factor -tbp 3 -region” option.
Genome_build: hg19
Supplementary_files_format_and_content: bigwigs (BWs), genome-wide ATAC-seq signal enrichment.

source_name: Peripheral blood CD8+ T cells

growth_protocol: To obtain CD8+ T cells from thawed PBMCs were stained with appropriate antibodies (Abs), and sorted into CD8+ T cells using a BD FACSAria III™ cell sorter (BD Biosciences, San Jose, CA, USA).

extract_protocol:
Nuclei were isolated from CD8+ T cells and subjected to the transposition reaction with Illumina transposase in 1× Tagment DNA (TD) buffer
Library fragments were amplified with indexing primers from Nextera kit (Illumina, San Diego, CA, USA)

tag: response

value: Stable disease

value: Peripheral blood

value: Primary CD8+ T cells

tag: disease state

value: gastric cancer


title: SS30 ATAC-seq

status: Public on Jan 03 2021

type: SRA

country: South Korea

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: tissue

tag: cell type


title: SS23 ATAC-seq


title: SS24 ATAC-seq


title: SS15 ATAC-seq


title: SS03 ATAC-seq


title: SS31 ATAC-seq

value: Progressive disease


title: WT1

city: Rome

first: Julie

last: Martone

address: P.le Aldo Moro 5

country: Italy

institute: "Sapienza" University

library_source: transcriptomic

data_processing:
Illumina Casava 1.9 software was used for basecalling.
Trimmomatic software was used to remove adapter sequences, setting the simple clip threshold to 8. Reads whose length after trimming was less than 18 nucleotides were discarded.
Bowtie with parameters -v 0 --best --norc -m 1 was then used to align remaining reads to microRNA spike-in sequences. Reads mapping to both exogenous miRNAs were counted using a custom Python script. Since very few reads mapped on cel-miR-2, which was absent from most of the samples, we decided to use only cel-lin-4 for normalization.
We then used Bowtie with --best -v 0 switches to align reads not mapping to spike-in sequences to a sequence database derived from mirBase 21 and composed of canonical human microRNAs and their putative isoforms.
Isomirage software was used to count reads mapping on the template isoforms of each miRNA.
Genome_build: MirBase 21 human miRNAs.
Supplementary_files_format_and_content: Tab-separated raw count table.

molecule: total RNA

source_name: SERUM

extract_protocol:
Circulating microRNAs were extracted from 200µl of serum by miRCURYTM RNA Isolation Kit-Biofluids.
Small RNA libraries were generated from total RNA using TruSeq Small RNA Library Preparation Kit.

tag: disease

value: healthy


title: SS26 ATAC-seq


title: Sham_6h_1

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

country: China

institute: ABLife, Inc.

description: lung tissue of rats collected at 6h after having surgery to marginally rotate their pancreas

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, Qvalue < =0.05
Genome_build: rat_ensembl_v6
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

organism: Rattus norvegicus

source_name: lung tissue

growth_protocol: Sixty healthy male Sprague Dawley (SD) rats (specific pathogen-free, eight weeks old, 180–220 g) with animal license number SYXK (Liao) 2013-0003 were purchased from the Laboratory Animal Center of Dalian Medical University. Another animal license number, SCXK (Liao) 2013-0006 (with qualified number 211003700), was also acquired. The animals were housed in PVC cages. The temperature was controlled at 22 ± 2ºC in a room with 12 h light-dark cycles and free access to standard laboratory food and drinking water for one week prior to the experiments.

extract_protocol:
Total RNA of each lung tissue sample was extracted using TRIzol Reagent (Ambion) according to the manufacturer’s instructions. To eliminate any DNA present, RQ1 DNase (Promega) was added to the extracted total RNA. The absorbance of the purified RNA was measured to determine the quality and concentration with a Smartspec plus (BioRad, Hercules, USA) at 260 nm/280 nm (A260/A280). Agarose gel electrophoresis (1.5%) was conducted to verify the integrity of the RNA
For RNA-seq library preparation, 10 μg of purified total RNA of each sample was purified and concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen). Polyadenylated mRNAs were used for the construction of a directional RNA-seq library. Ion fragmentation of purified mRNAs was conducted at 95ºC following end repair and 5' adaptor ligation. The fragmented mRNAs were reverse-transcribed with RT primer, known 3' adaptors, and random hexamers. Then, purification and amplification of the cDNAs were conducted. The 200–500 bps of amplified cDNAs were collected. The cDNAs for each sample were quantified and stored at -80ºC until sequencing.

treatment_protocol: Animals were randomized into five groups (n = 12 per group); the control group, the sham-operated group, the SAP model group, the SAP-DEX treated group, and the SAP-emodin treated group. Furthermore, each group was sub-divided into 6 h and 24 h subgroups. Briefly, SD rats were denied food for 12 h but had free access to water and were then given 1% pentobarbital sodium anesthesia (intraperitoneal injection, 40 mg/100 g body weight) prior to the surgical operation. The SAP model was induced as previously described  by administering fresh 5.0% sodium taurocholate (0.1 mL/100 g body weight) into the biliopancreatic duct by standard retrograde infusion. This procedure induced SAP and eventually resulted in a SAP-induced ALI, which served as the model. Sterile saline of the same volume was given to the control group of animals. The sham group of animals had surgery to marginally rotate their pancreas. DEX (10 mg/kg body weight) was intravenously administered to the DEX group of animals at 2 h and 12 h post-operation, and an equivalent volume of sterile saline was intravenously administered to the other groups of animals. Emodin (40 mg/ kg body weight) was intragastrically given to the SAP-emodin group at 2 h and 12 h post-operation. An equal volume containing 0.5% carboxymethylcellulose sodium was intragastrically given to the other groups of animals. At 6 h and 24 h post-operation, blood samples were taken via the abdominal aorta for arterial blood gas analysis and serum harvesting, and then stored at -80ºC until used

value: lung


title: SS25 ATAC-seq


title: Sham_24h_1

description: lung tissue of rats collected at 24h  after having surgery to marginally rotate their pancreas


title: Sham_24h_3


title: SAP_24h_2

description: lung tissue of rats collected at 24h after administering fresh 5.0% sodium taurocholate (0.1 mL/100 g body weight) into the biliopancreatic duct


title: SAP_24h_3


title: SS21 ATAC-seq


title: SS22 ATAC-seq


title: SAP_6h_3

description: lung tissue of rats collected at 6h after administering fresh 5.0% sodium taurocholate (0.1 mL/100 g body weight) into the biliopancreatic duct


title: SAP_6h_1


title: SS20 ATAC-seq


title: Emo_6h_3

description: lung tissue of rats collected at 6h after administering fresh 5.0% sodium taurocholate (0.1 mL/100 g body weight) into the biliopancreatic duct and  emodin (10 mg/kg body weight) being  intragastrically given


title: SS19 ATAC-seq


title: Sham_24h_2


title: Emo_6h_2


title: SS16 ATAC-seq


title: SS27 ATAC-seq


title: SS18 ATAC-seq


title: SS17 ATAC-seq


title: Emo_24h_3

description: lung tissue of rats collected at 24h after administering fresh 5.0% sodium taurocholate (0.1 mL/100 g body weight) into the biliopancreatic duct and  emodin (10 mg/kg body weight) being  intragastrically given


title: Emo_6h_1


title: Leukemia cells JOK1 replicate2

type: RNA

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: RhoH expression consequences in JOK1 cells, replicate2

hyb_protocol: Agilent-012391 Whole Human Genome Microarray 44K were scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.9.1.3.1).

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction and LOWESS normalization.

label_protocol: manufacturer's instructions

growth_protocol: Cell lines were grown as described by Galiègue-Zouitina et al (2008) Cancer Res, 68, 4531-4540; Delestré et al (2011) Biochem J, 437, 75-88; Poret et al (2015) Cancer Res, 75, 3902-3911

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: Cell lines were treated as described by Galiègue-Zouitina et al (2008) Cancer Res, 68, 4531-4540; Delestré et al (2011) Biochem J, 437, 75-88; Poret et al (2015) Cancer Res, 75, 3902-3911

tag: treatment

value: empty vector

value: RhoH vector


title: Emo_24h_2


title: SS09 ATAC-seq


title: SS07 ATAC-seq


title: Dex_6h_1

description: lung tissue of rats collected at 6h after administering fresh 5.0% sodium taurocholate (0.1 mL/100 g body weight) into the biliopancreatic duct and  dexamethasone (DEX) (10 mg/kg body weight) being intravenously administered


title: Dex_6h_3


title: SS02 ATAC-seq


title: Dex_24h_2

description: lung tissue of rats collected at 24h after administering fresh 5.0% sodium taurocholate (0.1 mL/100 g body weight) into the biliopancreatic duct and  dexamethasone (DEX) (10 mg/kg body weight) being intravenously administered


title: Dex_6h_2


title: SS28 ATAC-seq

value: Partial response


title: SAP_24h_1


title: SS13 ATAC-seq


title: Dex_24h_3


title: SS29 ATAC-seq


title: SS05 ATAC-seq


title: SAP_6h_2


title: SS14 ATAC-seq


title: SS08 ATAC-seq


title: SS12 ATAC-seq


title: Con_6h_1

description: lung tissue of rats collected at 6h after administering  sterile saline into the biliopancreatic duct


title: Con_6h_2


title: Emo_24h_1


title: SS06 ATAC-seq


title: SS04 ATAC-seq


title: Con_6h_3


title: Con_24h_3

description: lung tissue of rats collected at 24h after administering  sterile saline into the biliopancreatic duct


title: SS11 ATAC-seq

value: Complete response


title: Con_24h_2


title: Con_24h_1


title: Dex_24h_1


title: SS01 ATAC-seq


title: 6_S1P

status: Public on Jan 02 2021

city: Philadelphia

first: David

last: Manning

state: PA

address: 3620 Hamilton Walk

country: USA

institute: University of Pennsylvania

description: processed data file: FINAL_master_list_of_gene_counts_MIN.sense.S1P.txt.gz

data_processing:
RNA-Seq data were aligned to the mouse genome build mm9 (ensemblv67) by STAR-2.5.3a.
Data were normalized at the gene-level, using a resampling strategy PORT (v0.8.4-beta). The code is available at: https://github.com/itmat/Normalization
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: FINAL_master_list_of_gene_counts_MIN.sense.S1P.txt.gz: Tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.

organism: Mus musculus

growth_protocol: C3H10T1/2 cells (ATCC) were plated at 2.6 x 10^4 cells/cm^2 in Minimal Eagle Medium (MEM) plus 10% fetal bovine serum at 37°C at 5% CO2; cells were not used beyond 10 passages from purchase.

extract_protocol:
RNA was extracted with a "Quick RNA Miniprep" kit from Zymo.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: After incubation of plated cells overnight, the medium was changed to Basal Medium Eagle (BME) without fetal bovine serum for 24 hours. The cells were then treated an additional 24 hours with 5 uM sphingosine 1-phosphate (Caymen) or vehicle (0.1% bovine serum albumin, fraction V fatty acid-free). RNA was then prepared.

tag: cell line

value: sphingosine 1-phosphate (S1P)


title: 7_S1P


title: 5_S1P


title: 3_Veh

value: vehicle


title: 4_Veh


title: SS10 ATAC-seq


title: 2_Veh


title: CLS_439_NT_r4

city: Rozzano (MI)

first: Daniele

last: Braga

address: Via Manzoni 56

institute: Humanitas Clinical and Research Center

data_processing:
High-quality paired-end reads aligned to GRCh38 using STAR v.2.5.3a using as reference transcript the gencode (v.28) primary assembly gene transfer file (GTF).
Gene counting performed on files including only uniquely mapped fragments using featurecounts v1.6.2 with custom parameters: --minOverlap 10; only both reads, no multimapping.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited file (.txt) including raw counts for each sample (columns) across 58381 genes (rows)

source_name: cell culture

extract_protocol:
Cells were seeded in 6-well plates (from 3 × 10e5 to 5 × 10e5 cells per well) and treated the day after with MMC 75uM for 1 h at 37C. Total RNA was isolated 15 h after treatment using Directzol (Zymo) according to the manufacturer's instructions, adding a DNase digestion step to eliminate genomic DNA contamination.
TruSeq Stranded mRNA Library Prep

value: bladder cancer cell line CLS-439

value: NT


title: CLS_439_MCC_r3

value: MCC


title: 1_Veh


title: CLS_439_NT_r3


title: CLS_439_MCC_r1


title: CLS_439_NT_r1


title: TCC-SUP_MCC_r4

value: bladder cancer cell line TCC-SUP


title: AT1 cells pH 6.6 adapted #2

city: Halle/S.

first: Oliver

last: Thews

address: Magdeburger Str. 6

department: Institute of Physiology

country: Germany

institute: University of Halle

description:
OT06AA_1
AT1_cells_long-term_acidosis.csv

data_processing:
Adaptor removal (Cutadapt - v1.8.1)
Alignment (tophat - 2.0.14)
Counting (featureCounts - 2.0.1)
Annotation with ensembl 98
Genome_build: Rnor6
Supplementary_files_format_and_content: .csv files containing raw counts obtained after Counting with featureCounts

source_name: prostate cancer

growth_protocol: For cell culture cells were either incubated at pH 7.4 (HEPES buffered) or pH 6.6 (MES buffered) (-) medium for 24 h. For chronic adaptation cells were kept at pH 7.4 or 6.6 for 11 passages (= 5 weeks)

extract_protocol:
Total RNA was isolated with TriZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNAse (ambion, Life Technologies).
rRNA were removed using RiboMinus (Life Technologies) according to the manufacturer's instructions. RNA was fragmented (w/ Tris-acetate, Potassium acetate and Magnesium acetate) and precipitated (w/ 100% Ethanol, Ammonium acetate and glycogen).
Resulting RNAs were used to generate cDNA libraries using Illumina index adapters.  10nM of pools of up to 10 libraries were used for cluster generation (Illumina cBot). Paired end sequencing (2x100bp) was performed on Illumina HiScanHQ and HiSeq2000.

treatment_protocol: After growing solid tumors tumors were either sham-treated or inspiratory hypoxia (10% O2)+metaiodobenzylguanidine (itensifying glycolytic acidosis=metabolic acidosis)

value: R3327-AT1 carcinoma

tag: organ

value: prostate

value: pH 6.6; 5 weeks


title: TCC-SUP_NT_r4


title: AT1 cells pH 6.6 adapted #4

description:
OT08AA_1
AT1_cells_long-term_acidosis.csv


title: AT1 cells pH 6.6 adapted #3

description:
OT07AA_1
AT1_cells_long-term_acidosis.csv


title: Co-culture-NSC

city: Zhenjiang

first: Wenwen

last: Deng

state: Jiangsu

address: 301 Xuefu Road, Jingkou District

department: School of Pharmacy

institute: Jiangsu University

description: Gene expression data from NSCs co-cultured with EMSCs for 14 days in vitro

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 2.0 in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: embryos at day 13.5 followed neurosphere formation for 10 days and then co-culturing with EMSCs for 14 days in vitro

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

growth_protocol: NSCs were isolated from whole brains of the SD rats at embryo 13.5-day (E13.5). The NSCs were cultured in the medium (containing serum-free DMEM/F12 supplemented with 1% B27 supplement, 1% N2 supplement, 1% NEAA, 25 ng/mL bFGF, 25 ng/mL EGF, 100 U/mL penicillin-streptomycin, and 2 mM L-glutamine) in T25 (cm2) flasks in an atmosphere of 5% CO2 at 37 °C. The culture medium was replaced every 3 days. The GFP-EMSCs were isolated fromtransgenic rats expressing green fluorescence protein (GFP) and cultured in DMEM/F12 (1:1, v/v) medium supplemented with 10% (v/v) FBS and penicillin-streptomycin (100 U/mL) at 5% CO2 and 37 °C.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.

treatment_protocol: GFP-EMSCs at passage 3 were pre-cultured on 6-well plates before seeding the NSCs. When the GFP-EMSCs grown to a conﬂuence of 60-70%, the NSC-containing neurospheres were collected by centrifugation, resuspended in complete culture medium, and seeded on top of the GFP-EMSCs with 60-80 neurospheres per well in 6-well plates. The co-culture system was retained in the complete culture medium  (DMEM/F12 supplemented with 10% FBS and 100 U/mL penicillin-streptomycin), and the medium was changed every 3 days. After 14 days of co-culture,  the NSCs co-cultured with GFP-EMSCs were separated and collected via FACS. The NSCs mono-cultured for 14 days were used as control.

value: brain


title: AT1 cells pH 6.6 adapted #1

description:
OT05AA_1
AT1_cells_long-term_acidosis.csv


title: AT1 cells pH 7.4 adapted #4

description:
OT04AA_1
AT1_cells_long-term_acidosis.csv

value: pH 7.4; 5 weeks


title: 8_S1P


title: AT1 cells pH 7.4 adapted #3

description:
OT03AA_1
AT1_cells_long-term_acidosis.csv


title: CLS_439_MCC_r4


title: TCC-SUP_NT_r3


title: TCC-SUP_MCC_r1


title: AT1 cells pH 7.4 adapted #2

description:
OT02AA_1
AT1_cells_long-term_acidosis.csv


title: AT1 cells pH 7.4 adapted #1

description:
OT01AA_1
AT1_cells_long-term_acidosis.csv


title: Walker-256 tumors metabolic acidosis #4

description:
R24_1
AT1_W256_tumors_short-term_acidosis.csv

source_name: mammary carcinoma

value: Walker-256 carcinoma

value: mammary gland

value: pH tumor acidosis 24h


title: NSC

description: Gene expression data from NSCs mono-cultured for 14 days in vitro

source_name: embryos at day 13.5 followed neurosphere formation for 10 days and then mono-culturing for 14 days in vitro


title: Walker-256 tumors metabolic acidosis #3

description:
R23_1
AT1_W256_tumors_short-term_acidosis.csv


title: 5637_NT_r4

value: bladder cancer cell line 5637


title: 5637_MCC_r3


title: 5637_MCC_r4


title: Walker-256 tumors metabolic acidosis #1

description:
R21_1
AT1_W256_tumors_short-term_acidosis.csv


title: Walker-256 tumors control #4

description:
R18_1
AT1_W256_tumors_short-term_acidosis.csv

value: pH control 24h


title: 5637_NT_r3


title: Walker-256 tumors metabolic acidosis #2

description:
R22_1
AT1_W256_tumors_short-term_acidosis.csv


title: TCC-SUP_MCC_r3


title: Walker-256 tumors control #3

description:
R17_1
AT1_W256_tumors_short-term_acidosis.csv


title: Walker-256 tumors control #2

description:
R15_1
AT1_W256_tumors_short-term_acidosis.csv


title: 5637_MCC_r1


title: Walker-256 tumors control #1

description:
R13_1
AT1_W256_tumors_short-term_acidosis.csv


title: T24_MCC_r4

value: bladder cancer cell line T24


title: 5637_NT_r1


title: T24_MCC_r3


title: AT1 tumors metabolic acidosis #3

description:
R9_1
AT1_W256_tumors_short-term_acidosis.csv


title: AT1 tumors metabolic acidosis #4

description:
R10_1
AT1_W256_tumors_short-term_acidosis.csv


title: AT1 tumors metabolic acidosis #2

description:
R6_1
AT1_W256_tumors_short-term_acidosis.csv


title: TCC-SUP_NT_r1


title: T24_NT_r3


title: T24_NT_r1


title: T24_MCC_r1


title: AT1 tumors control #1

description:
R3_1
AT1_W256_tumors_short-term_acidosis.csv


title: AT1 tumors control #4

description:
R12_1
AT1_W256_tumors_short-term_acidosis.csv


title: AT1 tumors metabolic acidosis #1

description:
R5_1
AT1_W256_tumors_short-term_acidosis.csv


title: AT1 tumors control #3

description:
R11_1
AT1_W256_tumors_short-term_acidosis.csv


title: AT1 tumors control #2

description:
R8_1
AT1_W256_tumors_short-term_acidosis.csv


title: Walker-256 cells pH 6.6 #3

description:
AR_W256_6
AT1_W256_cells_short-term_acidosis.csv


title: Walker-256 cells pH 6.6 #2

description:
AR_W256_5
AT1_W256_cells_short-term_acidosis.csv


title: T24_NT_r4


title: Walker-256 cells pH 7.4 #3

description:
AR_W256_3
AT1_W256_cells_short-term_acidosis.csv


title: Walker-256 cells pH 6.6 #1

description:
AR_W256_4
AT1_W256_cells_short-term_acidosis.csv


title: Chondrocyte_NGF_rep 2

first: Marta

last: Barba

address: L.go F. Vito 1

institute: Università Cattolica del Sacro Cuore

hyb_protocol: Following fragmentation, 5.5 μg of ss-cDNA were hybridized for 16 hr at 45°C on GeneChip Human Transcriptome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Human Transcritpome 2.0 Arrays were scanned on GeneChip® Scanner  7G Plus, using AGCC software (Affymetrix).

data_processing: CEL files were analysed using Expression Console software from Affymetrix. Gene-level calculation was performed by Robust Multichip Average (RMA) to summarize probeset signal and normalization by Quantile Sketch. Unpaired One-way ANOVA was then used to identify differentially expressed gene, using Transcriptome Analysis Console (TAC) from Affymetrix.

label: Biotin

source_name: Chondrocyte cultures_NGF treatment

label_protocol: Biotinylated ss-cDNA were prepared from 200 ng total RNA, according to the manufacting protocol (GeneChip® WT PLUS Reagent Kit, Affymetrix)

growth_protocol: Chondrocyte cultures were obtained from healty cartilage of  the lateral condyle of the knee in 3 subjets (1 male, 2 females). After enzymatic digestion, cells were mainteined in DMEM/F12 medium containing ??? FBS.

extract_protocol: Total RNA was isolated from cultured cells using TRIzol Protocol and further on-column purified using the RNeasy Mini Kit.

treatment_protocol: Chondrocyte  were trypsinized with trypsin-EDTA and subdivided into three group, according to the treamtent protocol: two treatments groups receveing 200 ng/ml Brain-Derived-Neurotrophic Factor (BDNF) or 200 ng/mL Nerve Growth Factor-β (NGF-β), and a untreated, control group. Medium and growth factors were replaced twice weekly. the effects of treatments were evaluated after  14 days.

value: Human Healty Cartilage

tag: agent

value: NGF

tag: Sex

value: female


title: F_2_Spheroid_14

city: Chapel Hill

first: Merrie

last: Mosedale

state: North Carolina

address: 301 Pharmacy Lane, Kerr Hall CB#7569

department: Division of Pharmacotherapy and Experimental Therapeutics

institute: UNC Eshelman School of Pharmacy

description: mouse hepatocyte spheroid RNA

hyb_protocol: Labeled cRNA was fragmented and prepared for hybridization.

scan_protocol: The Affymetrix Gene Titan system was used to perform the hybridization, washing and scanning of the arrays.

data_processing: Affymetrix CEL files were normalized using Robust Multi-array Average method with a log base 2 transformation (Irizarry et al., 2003). Data summarization and QC was performed using the Transcriptome Analysis Console software version 4.0 (ThermoFisher). A filtering step was performed to remove low expression probe sets using Partek Genomics Suite version 7.0 (Partek Inc.).

source_name: mouse, hepatocyte spheroids, female, donor 2, culture day 14

label_protocol: Double-stranded cDNA was synthesized using the GeneChip WT PLUS Reagent Kit (Affymetrix).

growth_protocol: Hepatocytes were isolated from N=12 C57BL/6 mice and cryopreserved in pools of N=3 to create the N=4 (2 male and 2 female) preparations used in this study. Spheroids were generated from each preparation by spontaneous self-aggregation in ultra-low attachment 96-well plates.

extract_protocol: Total cellular RNA was isolated using an RNeasy total RNA isolation kit. The quantity and integrity of the RNA was evaluated spectrophotometrically and with an Agilent 2200 TapeStation.

treatment_protocol: Spheroids were cultured for 1, 7, and 14 days post spheroid formation.

tag: strain

tag: mouse/donor #

value: F

value: Spheroid

tag: culture day


title: F_2_Spheroid_1

description: mouse hepatocyte spheroid RNA

source_name: mouse, hepatocyte spheroids, female, donor 2, culture day 1


title: F_2_Spheroid_7

description: mouse hepatocyte spheroid RNA

source_name: mouse, hepatocyte spheroids, female, donor 2, culture day 7


title: Walker-256 cells pH 7.4 #1

description:
AR_W256_1
AT1_W256_cells_short-term_acidosis.csv


title: Walker-256 cells pH 7.4 #2

description:
AR_W256_2
AT1_W256_cells_short-term_acidosis.csv


title: Chondrocyte_NGF_rep 3


title: SLA9

value: ALS patient


title: Chondrocyte_BDNF_rep 3

source_name: Chondrocyte cultures_BDNF traetment

value: BDNF


title: Chondrocyte_NGF_rep 1

value: male


title: AT1 cells pH 6.6 #2

description:
AR_AT1_5
AT1_W256_cells_short-term_acidosis.csv

value: R3327-AT1 carcinoma

value: prostate


title: AT1 cells pH 6.6 #3

description:
AR_AT1_6
AT1_W256_cells_short-term_acidosis.csv


title: 3'-seq siRRP40 xPAP rep 1

city: Aarhus C

first: Søren

last: Lykke-Andersen

address: C.F.Møllers Allé 3

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

description: 4sU-labeled RNA

data_processing:
Illumina software used for basecalling (Casava) and demultiplexing
TT-seq/RNA-seq: the fastq files were mapped to the reference genome (GRCh38 + RNA spike-ins) using STAR aligner to generate the BAM alignment files
TT-seq/RNA-seq: the BAM files were filtered to contain only uniquely mapped reads with Samtools
TT-seq/RNA-seq: Size-factors for sequencing depth normalization were obtained using the DESeq2 algorithm from counts on reduced GenCode v21 annotation generated with HTSeq. The reads mapping to spike-ins were used to estimate antisense and contamination bias (contaminating unlabeled RNA in 4sU-labeledRNA).  TT- and RNA-seq data were corrected accordingly. The experiments were done in duplicates in two batches and the data were batch corrected using the limma package.
TT-seq/RNA-seq: TT-seq/RNA-seq: Size-factors for sequencing depth normalization were obtained using the DESeq2 algorithm from counts on reduced GenCode v21 annotation generated with HTSeq. The reads mapping to spike-ins were used to estimate antisense and contamination bias (contaminating unlabeled RNA in 4sU-labeledRNA).  TT- and RNA-seq data were corrected accordingly. The experiments were done in duplicates in two batches and the data were batch corrected using the limma package.
3'-seq: reads were trimmed using the bbduk.sh script from BBMAP and homopolymeric A-stretches removed from reads.
3'-seq: the data was mapped using STAR against a compound index composed of hg38 merged with ERCC spike-ins.
3'-seq: 5' ends of uniquely mapped reads were used for downstream analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig; normalized and bias corrected coverage generated with…

source_name: tissue culture cells

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
TT-seq/RNA-seq: Six in vitro transcribed spike-in RNAs were added to the lysates (TRIzol, Thermo) followed by extraction of RNA according to the manufacturer’s protocol. The RNA was then sonicated and used as input for RNA-seq or for further purification of 4sU-labeled RNA. 4sU-labeled RNA was first biotinylated with EZ-Link HPDP-Biotin (Pierce) and isolated with µMACS Streptavidin Kit (Miltenyi). 4sU-labeld RNA was eluted by cleaving off the biotin with DTT. Both total RNA and 4sU-labeled RNA purified prior to libary preparation using the miRNeasy Micro Kit (Qiagen) including DNse I treatment to remove genomic DNA.
3'-seq:
TT-seq/RNA-seq RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded Total RNA Sample Prep kit).
3'-seq libraries were generated with standard and modified Lexogen 3'-seq protocols. The modified preapration included 3'end polydenylation in vitro using E.coli poly(A) polymerase ('xPAP') preceeding the NGS library preparation with the QuantSeq REV kit according to manufacturer's protocol (Lexogen).
RNA-Seq, paired-end; RNA 3'end seq, single-end

treatment_protocol: Two rounds of transfections were performed. The first transfections were performed using SilentFect (final dilution 1:1000) in RPMI 1640 medium. Two days after the first transfection, the media was changed, and the transfection was repeated using Lipofectamine 2000 (final dilution 1:1000) in RPMI 1640 medium. siRNAs were used at a final concentration of 15 nM of each siRNA. 24 hours after the second round of transfections, cells were labelled for 5 min or 10 min for TT-seq or 3'-seq, respectively, with 500 µM 4-thiouridine minutes and harvested.

value: HeLa Kyoto

value: cervix

value: epithelial

tag: sirna

tag: rna treatment

value: polydenylation with E.coli poly(A) polymerase ('xPAP')


title: Chondrocyte_BDNF_rep 2


title: Chondrocyte_BDNF_rep 1


title: F_1_Spheroid_14

description: mouse hepatocyte spheroid RNA

source_name: mouse, hepatocyte spheroids, female, donor 1, culture day 14


title: F_1_Spheroid_1

description: mouse hepatocyte spheroid RNA

source_name: mouse, hepatocyte spheroids, female, donor 1, culture day 1


title: Chondrocyte_control_rep 3

source_name: Chondrocyte cultures_untreaded


title: F_1_Spheroid_7

description: mouse hepatocyte spheroid RNA

source_name: mouse, hepatocyte spheroids, female, donor 1, culture day 7


title: Chondrocyte_control_rep 2


title: AT1 cells pH 7.4 #3

description:
AR_AT1_3
AT1_W256_cells_short-term_acidosis.csv


title: M_2_Spheroid_7

description: mouse hepatocyte spheroid RNA

source_name: mouse, hepatocyte spheroids, male, donor 2, culture day 7

value: M


title: Trp53 KO & Cdkn2a KO basal cells, biological rep3

city: Stanford

first: Michael

middle: F.

last: Clarke

state: CA

address: 265 Campus Dr

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

hyb_protocol: cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 2.0 ST Array (cartridge).

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Applied Biosystems).

data_processing: Transcriptome Analysis Console Software 4.0 (ThermoFisher Scientific) using all default analysis settings for Expression (Gene) analysis (including RMA Algorithm).

source_name: Mammary epithelial basal cells from an adult female virgin mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Applied biosystems protocol from 10 ug total RNA (GeneChip™ WT Pico Reagent Kit, Manual Target Preparation for GeneChip™ Whole Transcript (WT) Expression Arrays, publication number MAN0017893, 10 July 2018).

growth_protocol: All mice used for this study were maintained at the Stanford Animal Facility in accordance with the guidelines of the animal care use committee.

extract_protocol: Cells were stored in RNAprotect (catalog #76526, Qiagen) according to the manufacturer's instructions and extracted using the RNeasy micro kit (catalog #74004, Qiagen) according to the manufacturer's instructions.

treatment_protocol: Tissue used for transplantation assays was digested in DMEM/F12 (catalog #12634028, Gibco) with collagenase and hyaluronidase (catalog #07912, STEMCELL Technologies Inc.) and DNAse I (Catalog #LS002139, Worthington) for 2 h with gentle pipetting every 30 min. Briefly, lysis of red blood cells in ACK (catalog #BW10548E Lonza) for 5 min was followed by 5 min treatment with prewarmed 0.25% Trypsin-EDTA (catalog #25-510, GenClone), followed by treatment with pre-warmed dispase (catalog #07913, STEMCELL Technologies Inc.) and DNAse I (catalog #LS002139, Worthington) for 2 min. Ultimately, the cells were filtered through a 40 μm mesh and washed and resuspended in HBSS+2%FBS+PSA. For FACS analysis and sorting, mammary single cells were stained with CD45 (clone #30-F11, Biolegend), CD31 (clone #390, Biolegend), TER-119 (clone #TER119, Biolegend), CD49f (clone #GoH3, Biolegend), CD24 (clone #M1/69, Biolegend), CD14 (clone #Sa14-2, Biolegend). To enrich for epithelial cells preceding FACS, most of lineage was depleted on the autoMACS Pro Separator (catalog #130-092-545, Miltenyi Biotec) using microbeads for CD45 (catalog #130052301, Miltenyi Biotec), CD31 (catalog #130097418, Miltenyi Biotec), and TER119 (catalog #130049901, Miltenyi Biotec) according to manufacturer’s instructions. Flow cytometry was performed with a 100 μm nozzle on a BD Flow cytometry Aria II with Flow cytometry Diva software (BD Biosciences). Basal cells were sorted into RNAprotect (catalog #76526, Qiagen).

tag: gender

tag: age

value: adult (8-14 weeks)

value: mammary epithelium

value: basal

tag: genotype


title: M_2_Spheroid_1

description: mouse hepatocyte spheroid RNA

source_name: mouse, hepatocyte spheroids, male, donor 2, culture day 1


title: Trp53 KO & Cdkn2a KO basal cells, biological rep2


title: Trp53 KO & Cdkn2a KO basal cells, biological rep1


title: Chondrocyte_control_rep 1

value: Human Healty Cartilage


title: AT1 cells pH 7.4 #2

description:
AR_AT1_2
AT1_W256_cells_short-term_acidosis.csv

source_name: prostate cancer


title: M_2_Spheroid_14

description: mouse hepatocyte spheroid RNA

source_name: mouse, hepatocyte spheroids, male, donor 2, culture day 14


title: WT basal cells, biological rep3

value: female

value: wild type


title: AT1 cells pH 7.4 #1

description:
AR_AT1_1
AT1_W256_cells_short-term_acidosis.csv


title: AT1 cells pH 6.6 #1

description:
AR_AT1_4
AT1_W256_cells_short-term_acidosis.csv


title: Smutans_2hr_Media_1

status: Public on Jan 01 2021

city: Cambridge

first: Katharina

last: Ribbeck

state: Massachusetts

address: 77 Massachusetts Ave

department: Biological Engineering

institute: Massachusetts Institute of Technology

description: biological replicate 1

data_processing:
Illumina genome analyzer modules Firecrest was used for image analysis, and Bustard was used for base-calling.
Sequence reads were mapped onto the Streptococcus mutans UA159 NCBI reference genome NC_004350.2 using the Burrow Wheeler algorithm on the Galaxy server (usegalaxy.org)
Read counts were quantified in R using Bioconductor tools. Output at this step is provided as processed data. Code is available at https://github.com/cwerlang/Smutans-MUC5B-RNASeq https://github.com/cwerlang/Smutans-MUC5B-RNASeq
Genome_build: Streptococcus mutans UA159 NC_004350.2
Supplementary_files_format_and_content: comma-separated value files with raw read counts

organism: Streptococcus mutans

source_name: shaking batch bacterial cultures in mid-exponential growth phase

growth_protocol: Overnight cultures grown in 50%TH were diluted 1:20 (to approximately 10E7-10E8 CFU/mL) into fresh 25%Todd-Hewitt Broth supplemented with treatments. After 2 hours of growth with rocking at 25rpm at 37°C with 5% CO2, samples were collected (at OD600 of 0.4-0.6) and pelleted at 3000xg at 4°C, supernatant was removed, and the pellets were flash cooled in liquid nitrogen and stored at -80°C for less than one week before extraction.

extract_protocol:
Pellets were thawed on ice and resuspended in RNAase free water, 50 mL of 0.1 mm silica spheres (MP Lysing Matrix B) were added, and samples were bead-beaten for 90 seconds in three intervals at 4°C. Total RNA was then extracted using the MasterPure Complete RNA Purification kit (Lucigen). Genomic DNA was removed using the Turbo DNA-free kit (Ambion). Total RNA was measured with an Agilent 2100 Bioanalyzer (Agilent Technologies). The libraries were prepared using the Ribo-Zero Magnetic Kit (Bacteria; Epicentre) and the KAPA RNA HyperPrep kit (Kapa Biosystems). Library sequencing was performed using the Illumina HiSeq 2000 platform with a single-end protocol and read lengths of 40 nucleotides. Samples were stored at -20°C.
Total RNA (depleted of rRNA) was converted to cDNA and sequenced with Illumina HiSeq 2000 with a single-end protocol and read lengths of 40 nucleotides

treatment_protocol: Samples were treated with 0.1wt% human salivary MUC5B, 0.1wt% human salivary MUC5B glycans, or 0.1wt% porcine MUC5AC glycans.

tag: growth medium

value: 25% Todd-Hewitt broth

tag: growth time

value: 2 h


title: Smutans_2hr_MUC5Bmucins_2

description: biological replicate 2

value: 0.1wt% human salivary MUC5B mucin


title: Smutans_2hr_MUC5Bglycans_1

description: biological replicate 1

value: 0.1wt% human salivary MUC5B glycans


title: Smutans_2hr_MUC5ACglycans_1

description: biological replicate 1

value: 0.1wt% porcine gastric MUC5AC glycans


title: M_1_Spheroid_7

description: mouse hepatocyte spheroid RNA

source_name: mouse, hepatocyte spheroids, male, donor 1, culture day 7

tag: cell type

value: Spheroid


title: Smutans_2hr_MUC5Bmucins_1

description: biological replicate 1


title: Smutans_2hr_Media_2

description: biological replicate 2


title: M_1_Spheroid_14

description: mouse hepatocyte spheroid RNA

source_name: mouse, hepatocyte spheroids, male, donor 1, culture day 14


title: Smutans_2hr_MUC5Bglycans_2

description: biological replicate 2


title: WT basal cells, biological rep1

tag: tissue


title: 02A6-5 rep1

city: Hangzhou

first: Jianping

last: Lu

state: Zhejiang

address: 866 Yuhantang Road

department: College of Life Sciences

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Magnaporthe oryzae 70-15 (MG8) whole genome using tophat 2.0.8b with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks 2.1.1
Genome_build: MG8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

organism: Pyricularia oryzae

source_name: Mycelium

growth_protocol: The strains were cultured in liquid CM medium at 25˚C with shaking at 180 rpm for 2 d

extract_protocol:
Total RNA was extracted from ground mycelia in liquid nitrogen with RNeasy Plant mini kit (QIAGEN)
RNA libraries were prepared for sequencing using NEBNext RNA sample preparation kit (NEB) with standard Illumina protocols

treatment_protocol: The mycelia were collected and incubated in H2O at 25˚C for 4 h

tag: developmental stage

value: Mycelia under starvation


title: 02A6-5 rep2


title: 02A6-5 rep3


title: Smutans_2hr_MUC5ACglycans_2

description: biological replicate 2

tag: treatment


title: reproductive sample 2

city: Jishou

first: Gui-Sheng

last: Li

address: 120 Renmin South Street

institute: Jishou University

data_processing:
Trimmomatic v0.36 to purify reads
HISAT2, v2.1.0 to align reads to genome sequences
Genome_build: de novo transcript assembly

organism: Selaginella nipponica

source_name: erect shoots including sporangia

growth_protocol: growing in wild field

extract_protocol:
Total RNA was isolated with CTAB method
purified mRNA by virtue of oligo (dT) was fragmented into 100 – 400 bp long with divalent cations. Random hexamer primers were used to synthesize the first-strand cDNA, and Illumina paired-end adapters were then ligated onto the both ends of the double-strand cDNA, which would produce 200 ± 25 bp molecules that immediately underwent gel purification. Sequencing was conducted on the Illumina HiSeq2000 or 4000 platform in Beijing Genomics Institute (BGI) - Shenzhen (Shenzhen, China, http://www,genomics.cn/index.php). Both forward and reverse strands were analyzed using a sequencing-by-synthesis method.

treatment_protocol: no treatments

tag: sample type

value: reproductive


title: vegetative sample 1

source_name: prostrate shoots including emergents roots

value: vegetative


title: vegetative sample 3


title: reproductive sample 3


title: vegetative sample 2


title: reproductive sample 1


title: YAMATseq, S.italica seedling

city: Tianjin

first: Xuan

last: Ma

address: Binshui West Road

institute: Tianjin Normal University

description: pretreated RNA

data_processing:
Library strategy: YAMAT-seq
tRNA-seq data were first processed to remove the 5’ and 3’ adaptor sequences using cutadapt with the parameters “-m 17 --trim-n -f fastq -a AGATCGGAAGAGCAC -A GATCGTCGGACTGTA -g TACAGTCCGACGATC -G GTGCTCTTCCGATCT -n 2”. Then, the trimmed data were analyzed by a self-designed pipeline for quantifications of tRFs and tRNAs.
YAMAT-seq data were first processed to trim the 5’ and 3’ adaptor sequences using Cutadapt, and the 5’ nucleotide complementary to the discriminator base was also trimmed. Then, the adaptor-free sequences that have perfect match to annotated mature tRNAs were counted and normalized against total tRNA reads to measure mature tRNA expression levels.
Genome_build: TAIR10, Phytozome
Supplementary_files_format_and_content: The file tRNAseq_tRNA.xlsx summarizes tRNA expressions in various plants. The YAMATseq files are tRNA count data.

organism: Setaria italica

source_name: S.italica seedling

growth_protocol: Arabidopsis thaliana, Glycine max, Hordeum vulgare, Setaria italica, Sorghum bicolor, Triticum aestivum, Zea mays plants were germinated in the soil and grown at 23 ºC under the standard long-day condition (16 hours of light followed by 8 hours of darkness). The 10-day old seedlings were collected for tRNA-seq or YAMAT-seq analysis.

extract_protocol:
RNA extraction was conducted using TRIzol reagent (Invitrogen). Ethanol precipitation was performed overnight at -20ºC to maximize sRNA yield.
RNA pretreatment was conducted using rtStar tRF&tiRNA pretreatment kit (Arraystar). Pretreated RNAs were purified by Phenol:Chloroform extraction and ethanol precipitation. tRNA-seq library was constructed using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme). Purification of PCR amplified cDNAs were conducted using VAHTS DNA Clean Beads (Vazyme). YAMAT-seq was performed as previously described (Shigematsu et al Nucleic Acids Res. 2017) with some modifications. The design of Y-shaped adapters followed previous study. 2 µl of 3’ adaptor (10 µM) and 2 µl of 5’ adaptor mix (10 µM) were incubated at 70ºC for 2 min and cooled at room temperature to allow 5’ and 3’ adaptors to fully anneal. Then, the Y-shaped adaptor was mixed with 2 µg pretreated RNA, 4 unit T4 Rnl2 (New England Biolabs) and 2 µl ligation buffer with total reaction of 20 µl, and incubated at 37 ºC for 2 h. Next, 1 µl RNA RT Primer (RTP, Illumina) was added to the reaction and incubated at 70 ºC for 3 min, and then immediately chilled on ice. Subsequently, reverse transcription and cDNA amplification reactions were performed using VAHTS Small RNA Library Prep Kit for Illumina (Vazyme). A Universal Primer and RNA PCR Index Primers (Illumina) were used for amplifying cDNAs with 12 PCR cycles. The PCR products were purified using VAHTS DNA Clean Beads (Vazyme).

value: seedling


title: WT basal cells, biological rep2


title: M_1_Spheroid_1

description: mouse hepatocyte spheroid RNA

source_name: mouse, hepatocyte spheroids, male, donor 1, culture day 1

value: M


title: HD_Sroot_2

city: Ningbo

first: Xie

last: Xiaoting

address: 1 Qianhu South Road

department: Biotechnology and chemical Engineering

institute: NingboTech University

description: Roots of dwarf seedlings

data_processing:
Illumina Casava1.8 software used for basecalling.
Firstly, Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases;
Then denovo assembly of the transcriptome was performed with Trinity , and salmon was used to perform expression level for unigenes by calculating TPM;
All assembled unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/),Gene ontology (GO) (http://www.geneontology.org), SwissProt (http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.jp/kegg/), Protein family (Pfam) (http://pfam.xfam.org/) and eggnog (http://eggnogdb.embl.de/) databases using DIAMOND with a threshold of E value < 0.00001.
Supplementary_files_format_and_content: tab-delimited text file include TPM values and fasta file include all trinity gene sequences

molecule: polyA RNA

organism: Picea schrenkiana

source_name: Roots of dwarf seedlings treated with high concentration DHAP_2

growth_protocol: Under the condition of 23 ° C day / 18 ° C night and 6000 lux light, the seeds of Tianshan-spruce were sowed in soil mixed with vermiculite and perlite for 2 weeks.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA was purified from total RNA using poly-T oligo-attached magnetic beads by two rounds of purification. Then the left RNA was fragmented into small pieces using divalent cations under elevated temperature.The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina, San Diego, USA).

treatment_protocol: The seedlings were irrigated with 1mM high concentration DHAP (3, 4-dihydroxyacetophenone) for 10 days, and the seedlings were treated with water irrigation as control.After 10 days high concentration DHAP irrigation, short seedlings, high seedlings, seedlings with growth termination (inhibition) and control seedlings with water irrigation,their roots were pruned to extract total RNA.

value: roots

tag: condition

value: dwarf

value: DHAP


title: W_root_1

description: Water treated roots

source_name: Water treated roots_1

value: control

value: water


title: W_root_2

description: Water treated roots

source_name: Water treated roots_2


title: HD_Sroot_3

description: Roots of dwarf seedlings

source_name: Roots of dwarf seedlings treated with high concentration DHAP_3


title: HD_Iroot_3

description: Suppressed seedling roots

source_name: Suppressed seedling roots were grown with high concentrations of DHAP_3

value: suppressed


title: HD_Iroot_2

description: Suppressed seedling roots

source_name: Suppressed seedling roots were grown with high concentrations of DHAP_2


title: HD_Iroot_1

description: Suppressed seedling roots

source_name: Suppressed seedling roots were grown with high concentrations of DHAP_1


title: HD_Sroot_1

description: Roots of dwarf seedlings

source_name: Roots of dwarf seedlings treated with high concentration DHAP_1


title: W_root_3

description: Water treated roots

source_name: Water treated roots_3


title: HD_Hroot_3

description: Roots of high seedlings

source_name: Roots of high seedlings treated with high concentrations of DHAP_3

value: high


title: CLO2

city: Toyama

first: Tetsushi

last: Hirano

state: Toyama

address: 2630 sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

hyb_protocol: The biotinylated cRNA was hybridized to arrays at 45°C for 16 hours.

scan_protocol: The arrays were washed and stained using wash and stain kit on the Affymetrix Fluidics Station 450 (Affymetrix).

data_processing: The data were normalized with the RMA algorism using a GeneSpring GX software (Agilent Technologies, Inc.).

source_name: exposure group

label_protocol: The total RNA (250 ng) was used to synthesize cRNA with a GeneChip WT Amplification Kit. The cDNA was fragmentated and labeled with a GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: On postnatal day 21 of age of the litter, left ovaries were collected.

extract_protocol: RNA was extracted from cells using a NucleoSpin® XS RNA isolation kit (MACHEREY-NAGEL, GmbH) along with on-column DNase I treatment. RNA quality was analyzed using a Bioanalyzer 2100 (Agilent Technologies, Inc.). The RNA samples with RIN (RNA integrity number) values >9.0 were considered acceptable.

treatment_protocol: Pregnant mice were administrated 65 mg/kg/day of CLO or vehicle (1%DMSO) from gestational day 1.5 to postnatal day 21 of age of the litter.

tag: Sex

value: female

value: 3 weeks; postnatal day 21

value: 65 mg/kg/day of CLO

value: ovary


title: WT keratinocytes_IL-4(+)

city: Meguro-ku

first: Hideyuki

last: Yanai

state: Tokyo

address: Komaba 4-6-1

institute: University of Tokyo

description: RMA expression value derived from Expression Console software; core-exon analysis.

hyb_protocol: Following fragmentation, 2 μg of Single-Stranded cDNA was hybridized for 16 hr at 45 ̊C on Clariom S Array, Mouse. Arrays were washed and stained in the GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: Clariom S array was scanned using GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Expression Console Software 1.4 offered SST-RMA for gene level analysis using Thermo Fisher Scientific default analysis settings.

source_name: WT keratinocytes

label_protocol: Biotinylated cDNA was prepared from 100 ng total RNA using GeneChip WT PLUS Reagent Kit(Thermo Fisher Scientific) following the manufacturer's instructions.

growth_protocol: Primary keratinocytes were cultured and maintained in EpiLife (Thermo Fisher Scientific) medium in humid 5% CO2 atmosphere at 37ºC.

extract_protocol: Total RNA was extracted from keratinocytes by using ReliaPrep RNA Cell Miniprep System (Promega).

treatment_protocol: Primary Keratinocytes were cultured with or without rIL-4 (100ng/ml) for 12 hours in EpiLife medium.

value: WT

value: Male

value: Keratinocytes


title: HD_Hroot_2

description: Roots of high seedlings

source_name: Roots of high seedlings treated with high concentrations of DHAP_2


title: Ctrl1

source_name: control group

tag: strain

value: vehicle (1%DMSO)


title: tRNAseq, S.italica seedling

description:
pretreated RNA
tRNAseq_tRNA.xlsx

data_processing:
tRNA-seq data were first processed to remove the 5’ and 3’ adaptor sequences using cutadapt with the parameters “-m 17 --trim-n -f fastq -a AGATCGGAAGAGCAC -A GATCGTCGGACTGTA -g TACAGTCCGACGATC -G GTGCTCTTCCGATCT -n 2”. Then, the trimmed data were analyzed by a self-designed pipeline for quantifications of tRFs and tRNAs.
YAMAT-seq data were first processed to trim the 5’ and 3’ adaptor sequences using Cutadapt, and the 5’ nucleotide complementary to the discriminator base was also trimmed. Then, the adaptor-free sequences that have perfect match to annotated mature tRNAs were counted and normalized against total tRNA reads to measure mature tRNA expression levels.
Genome_build: TAIR10, Phytozome
Supplementary_files_format_and_content: The file tRNAseq_tRNA.xlsx summarizes tRNA expressions in various plants. The YAMATseq files are tRNA count data.

value: seedling


title: CLO1


title: tRNAseq, G.max seedling

description:
pretreated RNA
tRNAseq_tRNA.xlsx

organism: Glycine max

source_name: G.max seedling


title: Ctrl2


title: KO keratinocytes_IL-4(+)

source_name: KO keratinocytes

value: HMGB1 KO


title: HD_Hroot_1

description: Roots of high seedlings

source_name: Roots of high seedlings treated with high concentrations of DHAP_1

value: roots


title: WT keratinocytes_IL-4(-)


title: KO keratinocytes_IL-4(-)


title: J774M-ctrl-1

city: Augusta

first: Kebin

last: Liu

state: GA

address: 1410 Laney Walker Blvd

department: Biochemistry and Molecular Biology

institute: Medical College of Georgia

hyb_protocol: The labeled cDNAs were hybridized onto the arrays using Affymetrix GeneChip fluidics station 450 systems.

scan_protocol: Arrays were scanned on GeneChip 3000 G7

data_processing: The expression data were imported into Partek GS version 6.6 using a standard import tool with GeneChip robust multiarray analysis normalization. The differential expressions were calculated using ANOVA of Partek package.

label: biotin using GeneChip WT PLUS Reagent kit

source_name: cell line J774M

label_protocol: Total RNA samples were processed using the Ambion WT expression kit (Life Technologies, Calsbad, CA) and a GeneChip WT terminal labeling kit (Affymetrix). The synthesized sense strand cDNAs were fragmented and biotin-labeled using a GeneChip WT terminal labeling kit.

growth_protocol: Cells were cultured in RPMI medium with 10% FBS

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

treatment_protocol: Add NC06 to 10 uM and cultured for 24h

tag: cell line

value: Myeloid-derived suppressor cells (MDSCs)


title: J774M-nC06-2


title: J774M-ctrl-2


title: Ad-shRegnase-1 infected primary mouse articular chondrocytes, exp 1

city: Gwangju

first: Jeong-In

last: Yang

address: 123 Cheomdangwagiro

institute: Gwangju Institute of Science and Technology

description: Gene expression data from Ad-Zip8 infected primary mouse articular chondrocytes

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)
Probe signals in the raw data were normalized by the RMA (Robust Multi-array Average)

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Cultured were maintained at 37 °C in an humidified atmosphere containing 5% CO2 as a monolayer in Dulbecco’s modified Eagle’s medium (DMEM; Gibco) supplemented with 10% fetal bovine serum and antibiotics (penicillin G and streptomycin). 37 °C, 5% CO2

extract_protocol: Total RNA was extracted from mouse articular chondrocytes using a Purelink RNA mini kit (Ambion). The concentration, purity, and integrity of the extracted RNA were determined by spectrophotometry.

treatment_protocol: Primary mouse articular chondrocytes were infected with null (Ad-C) or Ad-Regnase-1 or Ad-shRegnase-1. The cells were harvested for total RNA extraction at 36 h post infection.

value: Ad-shRegnase-1 infected


title: Ad-shRegnase-1 infected primary mouse articular chondrocytes, exp 2


title: Ad-Regnase-1 infected primary mouse articular chondrocytes, exp 3

value: Ad-Regnase-1 infected


title: Ad-Regnase-1 infected primary mouse articular chondrocytes, exp 1

description: Gene expression data from Ad-null control infected primary mouse articular chondrocytes


title: Ad-null infected primary mouse articular chondrocytes, exp 3

value: Ad-null infected


title: J774M-nC06-1


title: Ad-Regnase-1 infected primary mouse articular chondrocytes, exp 2


title: Ad-shRegnase-1 infected primary mouse articular chondrocytes, exp 3


title: Ad-null infected primary mouse articular chondrocytes, exp 1


title: DMSO MM.1S cells 2

city: Houston

first: Qiang

last: Wang

state: Texas

address: 6550 FANNIN STREET

institute: HOUSTON METHODIST RESEARCH INSTITUTE

hyb_protocol: Fragmented and labeled ss-cDNA was hybridyzed for 16 hr at 45°C on GeneChip Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: All GeneChips were scanned on an Affymetrix GeneChip Scanner 3000.

data_processing: Normalization was performed using the Robust Multiarray Average and differentially expressed genes between two groups were identified by R/Bioconductor using limma package.

source_name: Human MM cell line MM.1S

label_protocol: Total RNA was labeled using the GeneChip WT PLUS Reagent Kit.

growth_protocol: MM.1S MM cells were cultured in RPMI1640 medium containing 10% fetal bovine serum and 100 U penicillin / 0.1 mg/ml streptomycin.

extract_protocol: Total RNA were extracted using Rneasy mini kit (Qiagen).

treatment_protocol: MM.1S MM cell line was pulsed with Cfz for 1 h and then cultured with DMSO or 10µM ATRA for 12 h.

value: Human MM

value: DMSO-treated MM.1S cells after Cfz treatment


title: GFB1

city: Goyang-si

first: Junghyun

last: Jung

state: Gyeonggi-do

address: Dongguk University Biomedi Campus 32, Dongguk-ro, Ilsandong-gu

institute: Dongguk Uvi.

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Mouse 2.0 ST Array at 45°C for 16hour

data_processing: Raw data were preprocessed and normalized using the robust multi-array average (RMA) method in the oligo R package

source_name: high fat diet + GFB

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: Five-week-old C57BL/6 mice (Envigo, Indianapolis, IN, USA) were housed in a temperature- (22 ± 2°C) and humidity-controlled (50 ± 5%) room with a 12/12 h light/dark cycle and free access to food and water.

extract_protocol: Liver tissue was dissected from the mice after an overnight fast, snap-frozen in liquid nitrogen, then stored at -75°C until analysis. Total RNA was extracted from liver tissue of the RD, HFD, and GFB groups using an RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Mice were randomly divided into three groups as follows: 1) a RD-fed group, 2) a HFD-fed group, 3) a HFD plus GFB 500 mg/kg

tag: diet

value: high fat diet + GFB

value: liver


title: ATRA MM.1S cells 1

value: ATRA-treated MM.1S cells after Cfz treatment


title: HFD1

source_name: high fat diet

value: high fat diet


title: RD2

source_name: regular diet

value: regular diet


title: GFB3


title: DMSO MM.1S cells 1


title: HFD2


title: GFB2


title: BE(2)-C DDX21 shRNA-2 DOX

city: Kensington

first: Pei

address: C25 Lowy Cancer Research Centre

country: Australia

institute: CCIA

description: We used Affymetrix GeneChip Command Console (AGCC) software to generate the CEL files from the image files, DAT files

hyb_protocol: 3.5 ug of fragmented, labeled cDNA was prepared for hybridisation. Samples were hybridised to arrays for 17 hours at 45°C rotating at 60 rpm in the Affymetrix Hybridisation Oven. Arrays were washed on the Affymetrix Fluidics 4500 Station as per manufacturer’s protocol using program FS450_0002.

scan_protocol: Arrays were scanned in the GCS 3000 7G scanner as per manufacturer’s protocol.

data_processing: Results from the microarray experiment were analyzed in R (http://www.r-project.org/) with bioconductor package (http://www.bioconductor.org/), and normalized with RMA normalization method (https://www.ncbi.nlm.nih.gov/pubmed/12925520).

source_name: BE(2)-C DDX21 shRNA-2 DOX

label_protocol: We used the Affymerix GeneChip WT Plus Reagent Kit: Manual Target Preparation for GeneChip Whole Transcript Expression Arrays (Affymetrix_WT_Plus_User_Guide). 100 ng of total RNA was used for input.

growth_protocol: Control shRNA, DDX21 shRNA-1 and DDX21 shRNA-2 BE(2)-C neuroblastoma cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal calf serum.

extract_protocol: Total RNA was extracted using Rneasy Plus kit (Qiagen, Hamburg, Germany) according to the manufacturer's instructions.

treatment_protocol: Control shRNA, DDX21 shRNA-1 and DDX21 shRNA-2 BE(2)-C neuroblastoma cells were treated with DMSO vehicle control or DOX for 32 hours.

value: neuroblastoma


title: BE(2)-C DDX21 shRNA-2 DMSO

source_name: BE(2)-C DDX21 shRNA-2 DMSO


title: KO1_Hippocampus

city: Heidelberg

first: Tang

last: Yiheng

address: Im Neuenheimer Feld 224

department: Department of Neuropathology

institute: Heidelberg University Hospital

data_processing:
Raw reads obtained from the Illumina libraries were processed with Trim Galore (version 0.6.4) and Cutadapt (version 2.10), and then mapped to the mouse genome (GRCm38.p6) using STAR (version 2.7.3a) in the two pass mode with default parameters.
Gene quantification was performed on uniquely mapped reads from the output of STAR with the software featureCounts (version 2.0.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited file with raw read counts of each gene from each sample

source_name: hippocampus

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, 15596-026) according to the manufacturer's instructions, and RNA was subjected to DNaseI (Invitrogen, AM2222) treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: hippocampus

value: CARIP-/-


title: KO2_Hippocampus


title: WT2_Hippocampus

value: wild type


title: WT3_Hippocampus


title: ATRA MM.1S cells 3


title: ATRA MM.1S cells 2


title: WT3_Cerebrum

source_name: cerebral cortex

value: cerebral cortex


title: WT2_Cerebrum


title: DMSO MM.1S cells 3


title: RD1


title: BE(2)-C Control shRNA DOX

source_name: BE(2)-C Control shRNA DOX


title: KO3_Cerebellum

source_name: cerebellum

value: cerebellum


title: KO1_Cerebrum


title: BE(2)-C Control shRNA DMSO

source_name: BE(2)-C Control shRNA DMSO


title: WT3_Cerebellum


title: T25

city: Cold Spring Harbor

first: Semir

last: Beyaz

state: NY

address: 1 Bungtown road

institute: Cold Spring Harbor Laboratory

data_processing:
FastQC for sequencing quality control
Map reads to mm10 genome using STAR  and RSEM for quantification
GTF file for gene annotation
DESeq2 for differential gene expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each Sample ...

source_name: liver cell ΔN90-β-catenin induced

extract_protocol:
total RNA extraction from frozen liver tumors
RNA libraries were prepared for sequencing using strand specific library protocol

treatment_protocol: hydrodynamic injection to model cancer in liver

value: liver cells

tag: variation

value: [delta]N90-[beta]-catenin induced


title: BE(2)-C DDX21 shRNA-1 DMSO

source_name: BE(2)-C DDX21 shRNA-1 DMSO


title: WT2_Cerebellum


title: HFD3


title: Ad-null infected primary mouse articular chondrocytes, exp 2


title: T23


title: BE(2)-C DDX21 shRNA-1 DOX

source_name: BE(2)-C DDX21 shRNA-1 DOX


title: KO2_Cerebellum


title: KO1_Cerebellum


title: WT1_Cerebellum


title: KO2_Cerebrum


title: C3

source_name: liver cell sgActin and YAPS127A

value: sgActin and YAPS127A


title: T22


title: C2


title: RD3


title: T21

source_name: liver cell β-catenin skip 2 isoform induced

value: [beta]-catenin skip 1 isoform induced


title: T24


title: T9

source_name: liver cell subtype B

value: subtype B


title: T11


title: T17

source_name: liver cell β-catenin skip 1 isoform induced


title: T8


title: T12


title: T15


title: T10


title: T16


title: C1


title: T19


title: T3

source_name: liver cell subtype A

value: subtype A


title: T18


title: T2


title: T6


title: C8

source_name: liver cell β-catenin skip 1 isoform alone

value: [beta]-catenin skip 1 isoform alone


title: T13


title: T1


title: C9

source_name: liver cell β-catenin skip 2 isoform alone


title: C7


title: T4


title: T5


title: C10


title: C6


title: C5

source_name: liver cell wild type


title: T20


title: WT_rep3

first: Seonghyeon

last: Hong

address: 123 Cheomdangwagi-ro, Buk-gu, Gwangju, 61005, Korea

department: School of Life Science

institute: GIST

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10_refseq.gtf using HiSAT2
FPKM calculation using Cufflink
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Testis

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

value: Testis

value: 8 weeks


title: C4


title: T7


title: WT_rep1


title: KO_rep2

value: Wild type


title: WT_rep2


title: KO_rep1


title: GDF15 Sup 1

city: Ann Arbor

first: Martin

middle: G

last: Myers Jr

state: MI

address: 1000 Wall St

institute: University of Michigan

data_processing:
FASTQ was filtered for phred > 20 with fastq_quality_filter from fastq_toolkit 0.0.14
read alignment and feature counting with STAR_2.5.3a_modified
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: CSV file of counts from STAR for all samples

source_name: Area postrema

growth_protocol: Mice were maintained on standard chow diet

extract_protocol:
The brain was subsequently removed from the skull the AP/NTS dissected from the brainstem and homogenized in lysis buffer. Between 15-20 mice were used for TRAP experiments. GFP-tagged ribosomes were immunoprecipitated and RNA isolated
RNA was subject to ribodepletion and the resultant mRNA was fragmented and copied into first strand cDNA. The products were purified and enriched by PCR to create the final cDNA library. Samples were sequenced on a 50-cycle single end run on a HiSeq 2500 (Illumina) according to manufacturer's protocols.

treatment_protocol: Mice (GfralCreROSA26eGFP-L10a) were treated with vehicle or 400 ug/kg GDF15 and euthanized six hours post-injection with isolfuorane and decapitated.

tag: batch

tag: cells

value: Sup


title: GDF15 Sup 2


title: Vehicle Sup 2

value: Vehicle


title: KO_rep3

tag: age


title: Vehicle Bead 1

value: Bead


title: Vehicle Bead 2


title: GDF15 Bead 3


title: GDF15 Bead 2


title: Vehicle Sup 1


title: GDF15 Sup 3


title: GDF15 Bead 1


title: Sup 1


title: Murine pancreatic tumor 3 Vehicle

city: Allen

first: Wei

last: Lin

state: TX

address: 1525 Evanvale Dr.

institute: Translational Genomics Research Institute

description: Processed RNA-Seq on MNL treated mice

data_processing:
ChIP-seq reads were aligned to a reference genome (version hg19) using Bowtie2 with default parameters
H3K27Ac peak finding was performed using MACS (v1.4.2) and Homer with default settings.
Peak finding for each sample was performed separately with their matched input genomic DNA as a background control.
ROSE (Young lab) was then used to call and rank Super-enhancers and their associated genes
For RNAseq raw paired-end reads were trimmed using fastx-trimmer tools prior to mapping
TopHat (version 2.0.14) was used to map reads to a reference genome with parameters ‘–library-type fr-firststrand’ (for a strand-specific library) ‘—mate-std-dev #stdev’ and ‘-r #insert-distance’. The #stdev and #insert-distance were estimated from sub-sampling of samples individually
After mapping, bam files were further analyzed using Arraystudio (Omicsoft) software with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: beg files for ChIPseq data were generated using MACS (v1.4.2)
Supplementary_files_format_and_content: tab-delimited text file that include FPKM values or htseqcounts for  RNAseq samples

source_name: Murine pancreas

growth_protocol: Tumor growth was monitored using ultrasound imaging. Tumor was harvested when its size reached ~200 mm3 in size

extract_protocol:
Total RNA was isolated using RNeasy® Midi Kit (Qiagen)
Sequencing libraries were prepared according to Illumina's instructions.

treatment_protocol: Mice treated with vehicle control (saline)

value: Untreated


title: Murine pancreatic tumor 2 Minnelide treated

description: Processed RNA-Seq on MNL treated mice

growth_protocol: Tumor growth was monitored using ultrasound imaging. Mice was treated with Minnelide when tumor size reached 100-200 mm4

treatment_protocol: Mice treated with Minnelide when tumor reached 100-200 mm3 in size

value: Minnelide (0.42mg/kg, QDx7) treated


title: Murine pancreatic tumor 3 Minnelide treated

description: Processed RNA-Seq on MNL treated mice

growth_protocol: Tumor growth was monitored using ultrasound imaging. Mice was treated with Minnelide when tumor size reached 100-200 mm5


title: Murine pancreatic tumor 1 Vehical

description: Processed RNA-Seq on MNL treated mice


title: Bead 1


title: Matrigel/rhBMP2+IgG

city: Philadelphia

first: Maurizio

last: Pacifici

address: 3600 civic center blvd

department: Orthopaedic

institute: Children Hospital of Philadelphia

data_processing:
Cell Ranger (version 3.0.2) was used to de-multiplex reads, followed by extraction of cell barcode and unique molecular identifiers (UMIs).
The cDNA insert was aligned to reference mouse genome (mm10)
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv
Supplementary_files_format_and_content: features.tsv
Supplementary_files_format_and_content: matrix.mtx

source_name: Ectopic mass cells

extract_protocol:
Ectopic tissue masses were harvested on day 5 from initial implantation, minced and dissociated into single cell suspension
cDNA libraries of cells from each group were generated by Chromium controller (10X Genomics Inc.), barcoded and purified as described by the manufacturer, and sequenced using a 2x150 pair-end configuration on an Illumina HiSeq platform
10X Single Cell 3' v3


title: Matrigel/rhBMP2+nAct Ab

value: matrigel/rhBMP2+nAct Ab


title: Matrigel only

value: matrigel alone


title: MouseE17ChatNos

first: Michael

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

institute: University of Pennsylvania

data_processing:
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent kit v2 per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium i7 Sample Index Kit, pooled, and sequenced on an Illumina HiSeq/NovaSeq sequencer in a paired-end, single indexing run. Sequencing for each library  targeted 25,000 mean reads per cell. Data was then processed using the Cellranger pipeline (10x genomics, v.3.0.2) for demultiplexing and alignment of sequencing reads to a pre-mRNA transcriptome references of human (GRCh38) and mouse (mm10). These custom references were created using the protocol at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references for creation of feature-barcode matrices. For mouse distal colon and human colon, both intronic and exonic reads were included. Individual single cell RNAseq libraries were aggregated using the cellranger aggr pipeline. Libraries were normalized for sequencing depth across all libraries during aggregation. Secondary analysis on the aggregated feature barcode matrix was performed using the Seurat package (v.2.3.4 for mouse distal colon and human colon and v.3.1.2 for E17.5 small intestine) within the R computing environment. For mouse distal colon and human colon, cells expressing less than 200 or more than 5000 genes were excluded from further analysis. Additionally, cells expressing >10% mitochonrial genes were excluded. For E17.5 mouse bowel, cells expressing less than 1000 or more than 9000 genes were excluded from further analysis. Additionally, cells expressing >5% mitochondrial genes were excluded.
Genome_build: Mouse distal colon and E17.5 mouse: pre-mRNA mm10, Human colon: pre-mRNA GRCh38

source_name: ChAT and nNOS-expressing cells from E17.5 whole bowel

extract_protocol:
Mouse distal colon: Colon was removed, flushed with phosphate buffered saline, cut along the mesentery, pinned mucosal side down. Muscularis was carefully peeled from the mucosa and placed in cold O.C.T. compound in a biopsy specimen cryomold frozen in methylbutane on dry ice, and stored at -80°C. Human colon: Colons were maximally stretched and pinned. Tissue was incubated 10 minutes in 9 parts carboxygenated Krebs-Ringer solution and 1 part 4-(4-(Dimethylamino)styryl) -N-Methylpyridinium Iodide (4-Di-2-Asp) at room temperature. Tissue was transferred to ice-cold carboxygenated Krebs-Ringers solution under a fluorescence dissecting scope and fluorescent ENS was carefully dissected from muscularis by peeling away longitudinal muscle strips with forceps, placed in cold O.C.T. compound, frozen in methylbutane on dry ice, and stored at -80°C. Mouse distal colon and human colon: These pieces were sectioned at 100 microns. To isolate nuclei, frozen  sections in ice-cold lysis buffer were chopped rapidly with iridectomy scissors, transferred to a pre-cooled Dounce homogenizer on ice, homogenized, filtered through MACS SmartStrainer, centrifuged, resuspended in staining buffer with 2.5µg/mL Hoechst 33342 Trihydrochloride Trihydrate, filtered and flow sorted into 5µL staining buffer (1x phosphate-buffered saline (PBS), 1% w/v Ultrapure BSA, 0.2U/mL Protector RNase inhibitor) using a 70µm nozzle to isolate Hoechst+/mCherry+ nuclei (mouse) or Hoechst+ nuclei (human). E17.5 Mouse: E17.5 Nos1-CreERT2;ChAT-L10A-EGFP;R26R-TdTomato dams, tamoxifen treated (200 mg/kg) at E15.5 was euthanized, and pups were rapidly dissected on ice (2 TdTomato+, 3 GFP+). Full-length small intestines and colon dissociated together were used for RNA-seq. Tissue in carboxygenated 1x Hanks’ Balanced Salt Solution (HBSS) was cut into small pieces with insulin needles, and dissociated with Liberase plus DNase I, MgCl2, and CaCl2 in HBSS (37oC, 40 minutes) with repeated trituration (P1000). Dissociated cells were, passed 2-3x through 35 µm filters, pelleted in 10% fetal bovine serum (FBS)/Iscove's DMEM, resuspended in FACS buffer (0.04% w/v BSA  in HBSS, filtered again, and sorted (100µm nozzle) into 300μL FACS buffer for sequencing.
Mouse distal colon: Dataset consists of a total of 3 single-nucleus datasets generated using the 10x Genomics Chromium platform. Prior to GEM generation, sample concentration was estimated using nuclei numbers reported from FACS and a hemocytometer. Human colon: Dataset consists of a total of 16 single-nucleus datasets generated using the 10x Genomics Chromium platform.  Prior to GEM generation, sample concentration was estimated using nuclei numbers reported from FACS and a hemocytometer. Mouse E17.5 bowel: Dataset consists of one single-cell dataset, sequenced twice to improve read depth. Prior to GEM generation, the sample’s concentration (cells/ul) and viability (%) were determined by staining the cells with trypan blue and by manually counting using an inverted microscope. All: Next-generation sequencing libraries were prepared following the 10X Single Cell v2 protocol without modification. Sample quality was evaluated using Agilent’s Bioanalyzer High Sensitivity reagent kit following cDNA amplification and library construction. The completed libraries were quantified using the Kapa Library Quantification Kit and the Life Technologies Viia7 Real-time PCR instrument. Libraries were sequenced in a paired-end, single-indexed format on the Illumina HiSeq2500 or NovaSeq 6000.

tag: genotype

value: whole cell

value: Mouse E17.5 Whole Bowel


title: Mouse_Adult_Distal_Colon_3

source_name: Enteric neuron and glial nuclei from adult mouse distal colon

value: Pooled:47-52 day old

value: nuclei

value: Mouse distal colon


title: Mouse_Adult_Distal_Colon_1


title: Mouse_Adult_Distal_Colon_2


title: Murine pancreatic tumor 2 Vehicle

description: Processed RNA-Seq on MNL treated mice


title: Murine pancreatic tumor 1 Minnelide treated

description: Processed RNA-Seq on MNL treated mice

growth_protocol: Tumor growth was monitored using ultrasound imaging. Mice was treated with Minnelide when tumor size reached 100-200 mm3


title: Ago2_HITSCLIP_Flox_rep3

city: San Francisco

first: Eric

middle: Joseph

last: Wigton

address: 500 Parnassus Ave.

department: Immunology

institute: UCSF

description: ready for alignment to genome

data_processing:
Raw Fastqs were binned based on barcode using python bst  and perl fastx_barcode_splitter.pl
barcodes and adapters were trimmed using parallel -j3 'cutadapt -e 0.2 -a GTGTCTTTACACAGCTACGGCGTCG -m 19 --cut 11
The fastq files were then aligned to the mm9 genome and combined into single BAM using bowtie2 and samtools
BAM files were intersected to exclude miRNA reads using miRBASE bam filed and samtools BAM files converted to SAM files using samtools for downstream use on dCLIP
For RNAseq fastq files were aligned using STAR and compared using DESeq2 to give All_genes text files
Genome_build: mm9
Supplementary_files_format_and_content: read count and DESeq analysis for RNA-seq data. dCLIP analysis produces dCLIP_output.txt and dCLIP_summary.bed files containing the results (WT file 1 input KO file 2 input) IGV tool TDF files for peak viewing of individual library samples.

source_name: activated splenic B cells

growth_protocol: Cells were grown in 96 well plates sitmulated with aCD40 (500ng/ml) IL4 (25ng/ml) and IL21 (10ng/ml) for 4 days

extract_protocol:
RNA was extracted by Trizol for RNAseq or by Ago2 immunoprecipitation for Ago2-HITS-CLIP
RNAseq library multiplexed for HISEQ4000.  Ago2-HITS-CLIP custom library design for HISEQ2500 (see Gagnon JD, et al 2019 and Loeb, et al 2012)

value: spleen

value: B cell

tag: rna fraction

value: Ago2-bound RNA


title: AP2

city: Ceske Budejovice

first: Lenka

last: Gahurova

address: Branisovska 1760

department: Department of molecular biology and genetics

country: Czech Republic

institute: University of South Bohemia

data_processing:
Read trimming (adapters and low quality bases) - Trim Galore! v0.4.1
Quality control - FastQC v0.11.5
Mapping - Hisat2 v2.0.5
Genome_build: GRCm38
Supplementary_files_format_and_content: delLlano_FPKM_values.txt - a text values with quantified FPKM values for individual genes for individual replicates and for samples (averages of values of corresponding replicates)

source_name: polysomal fractions

growth_protocol: GV oocytes were obtained from 58 weeks old CD1 mice 46 h after injection by 5 IU pregnant mare serum gonadotropin. Oocytes were isolated in germinal vesicle stage by puncturing ovarian follicles in M2 medium supplemented with 100 µM 3-isobutyl-1-methylxanthine (IBMX) to prevent nuclear envelope breakdown. Selected fully grown oocytes were denuded and cultured in M16 (IBMX free) medium at 37 ᵒC, 5% CO2 for next 180 minutes.

extract_protocol:
Supernatants were loaded onto 10–50% linear sucrose gradients prepared in SW55 Ti tubes and centrifugated at 35,000× g for 65 min at 4 °C. Polysome profiles were recorded using ISCO UA-5 UV absorbance reader. Ten equal fractions were recovered from each sample and subjected to RNA isolation by Trizol reagent. Fractions corresponding to polysomal and non-polysomal part, respectively, were pulled together. These sub-samples were concentrated to 16 µL of Clean & Concentrator-5 (R1014, Zymo Research).
Ribosomal RNA was removed by Ribozero-Gold (MRZG12324, Illumina). Afterwards, RNA was reverse transcribed with a mixture of random and oligodT primers and amplified using the REPLI-g WTA Single Cell Kit (150063, Qiagen), followed by library preparation using the Nextera DNA Library Prep Kit (FC-121-1030, Illumina).

treatment_protocol: Cycloheximide at final concentration 0.1 mg/ml was added to medium and oocytes were cultured for next 10 minutes. 200 NEBD-stage oocytes  were washed three times in PBS/PVA supplemented with cycloheximide and frozen at –80 °C in low-binding tube. To disrupt the zona pellucida and lysate the oocytes, 250 µL of zirconia-silica beads were added to the tube with frozen oocytes together with 350 µL of lysis buffer and Ribolock. Oocytes were disrupted in the mixer mill apparatus MM301. Lysates were clarified by centrifugation at 8000× g for 5 min at 4 °C.

tag: replicate

value: NEBD oocytes


title: AP1


title: CLP

city: los angeles

first: Du

last: Jiang

state: ca

address: 1425 san pablo st bcc 305

department: stem cell

institute: university of southern california

data_processing:
raw fastq files were generated by Illumina bcl2fastq software with default parameters
fastq files of each sample were processed separately using cellranger software (v2.1.0) "cellranger count" with default settings
data from all these samples were aggregated using cellranger software (v2.1.0) "cellranger aggr" with default settings
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 file containing UMI matrix of each gene in each cell

source_name: CLP (common lymphoid progenitor)

growth_protocol: Mouse bone marrow cells were expanded in SCF/2i medium for 3 passages (10 days).

extract_protocol: Chromium Single Cell 3’ Library (10X Genomics, V2)

value: bone marrow

tag: expanded days


title: ANP2

source_name: non-polysomal fractions

tag: tissue


title: Ago2_HTISLCIP_KO_rep4

description: ready for alignment to genome

tag: cell type


title: Ago2_HTISLCIP_KO_rep3

description: ready for alignment to genome


title: ANP3


title: AP3


title: Ago2_HITSCLIP_Flox_rep4

description: ready for alignment to genome


title: CMP

source_name: CMP (common myeloid progenitor)


title: MEP


title: Ago2_HTISLCIP_KO_rep1

description: ready for alignment to genome


title: Ago2_HITSCLIP_Flox_rep1

description: ready for alignment to genome


title: GMP

source_name: GMP (granulocyte-monocyte progenitor)


title: HSC

source_name: HSC (hematopoietic stem cell)


title: IkBaKO-8h-08h-RNA-Rep2

city: Los Angeles

first: Quen

last: Cheng

address: 611 Charles E Young Dr E

institute: UCLA

description:
CtrlvKO_RNA_counts.txt
4KO.8h.b2

data_processing:
Samples were sequenced and base calls performed on Illumina HiSeq 2500
Reads were trimmed of adapter sequences and low-quality reads (q<30), then mapped to mm10 genome with bowtie2 (ChIP, ATAC) or STAR (RNA)
Aligned reads were filtered based on mapping score (MAPQ ≥ 30) by Samtools. For ChIP and ATAC-seq, duplicated reads were removed using Picard MarkDuplicates.
For ChIP-seq, MACS2 version 2.1.0 was used in broad mode to identify peaks for each sample using pooled input samples as control, FDR < 0.01, and extension size of average fragment length. These peaks were merged to generate a single reference peak file, and the number of reads that fell into each peak was counted using deeptools multiBamSummary with extension size of average fragment length
For ATAC-seq, BAM files were analyzed with the R package csaw, using windows 200-nt wide, with 100-nt spacing. Windows with zero or background signal were removed.
Genome_build: mm10
Supplementary_files_format_and_content: Raw count tables are provided (unnormalized). For ChIP and ATAC data, genomic regions of interest were defined by peak-calling (ChIP) or sliding windows in csaw (ATAC). For RNA data, the featureCounts function in the Subread package was used.

source_name: bone marrow-derived macrophage

growth_protocol: BMDMs were generated by isolating bone marrow from the femurs and tibias of sex-matched mice between the ages of six and 12 weeks. Bone marrow cells were incubated in L929-conditioned media (RPMI + 30% L929 media, 10% FBS, 100 IU/ml penicillin, 100 ug/ml streptomycin, 2 mM L-glutamine) at 370C for seven days.

extract_protocol:
H3K4me1 ChIP was performed on lysed and sonicated chromatin using rabbit anti-H3K4me1 (Abcam ab8895). ATAC-seq samples were prepared as described in Buenrostro et al, 2013 using Tn5 transposase from Illumina. Total RNA was extracted by Trizol according to manufacturer's instructions.
Libraries were prepared according to manufacturer's instructions: ChIP-seq with NEBNext Ultra II DNA Library Prep Kit (New England Biolabs E7645), ATAC-seq with Nextera DNA Library Preparation Kit (Illumina, FC-121), RNA-seq with KAPA Stranded mRNA-seq Library Preparation kit (KAPA Biosystems)

treatment_protocol: Cells were stimulated with TNFa (10 ng/ml, R&D Systems 410-MT), Pam3CSK4 (100 ng/ml, Invivogen tlrl-pms), CpG (1 uM, Invivogen tlrl-1668), LPS (100 ng/ml, Sigma-Aldrich L2880), or Poly(I:C) (50 ug/ml, Invivogen tlrl-picw).

value: Tnf-/-Rel-/-Nfkbie-/-Nfkbia-/-

tag: agent

value: TNFa (10 ng/ml)

tag: time point


title: IkBaKO-8h-08h-RNA-Rep1

description:
CtrlvKO_RNA_counts.txt
4KO.8h.b1


title: IkBaKO-8h-03h-RNA-Rep2

description:
CtrlvKO_RNA_counts.txt
4KO.3h.b2


title: Ago2_HITSCLIP_Flox_rep2

description: ready for alignment to genome


title: IkBaKO-8h-01h-RNA-Rep2

description:
CtrlvKO_RNA_counts.txt
4KO.1h.b2


title: IkBaKO-8h-01h-RNA-Rep1

description:
CtrlvKO_RNA_counts.txt
4KO.1h.b1

value: Tnf-/-Rel-/-Nfkbie-/-


title: Ago2_HTISLCIP_KO_rep2

description: ready for alignment to genome


title: IkBaKO-8h-00h-RNA-Rep2

description:
CtrlvKO_RNA_counts.txt
4KO.wash.b2

value: 0h (wash)


title: ANP1


title: SCF/2i expanded bone marrow cell

source_name: SCF/2i expanded bone marrow cell


title: IkBaKO-0h-RNA-Rep2

description:
CtrlvKO_RNA_counts.txt
4KO.NT.b2

value: basal


title: IkBaKO-0h-RNA-Rep1

description:
CtrlvKO_RNA_counts.txt
4KO.NT.b1


title: Ctrl-8h-08h-RNA-Rep1

description:
CtrlvKO_RNA_counts.txt
3KO.8h.b1


title: IkBaKO-8h-03h-RNA-Rep1

description:
CtrlvKO_RNA_counts.txt
4KO.3h.b1


title: Ctrl-8h-01h-RNA-Rep1

description:
CtrlvKO_RNA_counts.txt
3KO.1h.b1


title: Ctrl-8h-03h-RNA-Rep1

description:
CtrlvKO_RNA_counts.txt
3KO.3h.b1


title: Ctrl-8h-08h-RNA-Rep2

description:
CtrlvKO_RNA_counts.txt
3KO.8h.b2


title: WT-ATAC-08-Rep2

description:
WTvkBmut_ATAC_counts.txt
WT.R2.8h

value: NfkbiakB/kB


title: Ctrl-8h-00h-RNA-Rep2

description:
CtrlvKO_RNA_counts.txt
3KO.wash.b2


title: Ctrl-0h-RNA-Rep2

description:
CtrlvKO_RNA_counts.txt
3KO.NT.b2


title: WT-ATAC-04-Rep2

description:
WTvkBmut_ATAC_counts.txt
WT.R2.4h


title: WT-ATAC-04-Rep1

description:
WTvkBmut_ATAC_counts.txt
WT.R1.4h


title: WT-ATAC-02-Rep1

description:
WTvkBmut_ATAC_counts.txt
WT.R1.2h

value: WT


title: WT-ATAC-08-Rep1

description:
WTvkBmut_ATAC_counts.txt
WT.R1.8h


title: IkBakB-ATAC-08-Rep2

description:
WTvkBmut_ATAC_counts.txt
MM.R2.8h


title: WT-ATAC-00-Rep2

description:
WTvkBmut_ATAC_counts.txt
WT.R2.0h


title: IkBakB-ATAC-04-Rep2

description:
WTvkBmut_ATAC_counts.txt
MM.R2.4h


title: IkBakB-ATAC-08-Rep1

description:
WTvkBmut_ATAC_counts.txt
MM.R1.8h


title: WT-ATAC-02-Rep2

description:
WTvkBmut_ATAC_counts.txt
WT.R2.2h


title: WT-ATAC-00-Rep1

description:
WTvkBmut_ATAC_counts.txt
WT.R1.0h


title: IkBaKO-8h-00h-RNA-Rep1

description:
CtrlvKO_RNA_counts.txt
4KO.wash.b1


title: IkBakB-ATAC-02-Rep1

description:
WTvkBmut_ATAC_counts.txt
MM.R1.2h


title: IkBakB-ATAC-04-Rep1

description:
WTvkBmut_ATAC_counts.txt
MM.R1.4h


title: IkBakB-ATAC-02-Rep2

description:
WTvkBmut_ATAC_counts.txt
MM.R2.2h


title: IkBaKO-ChIP-input-Rep4

description:
WTvkBmut_ATAC_counts.txt
(not in count table)

tag: antibody


title: IkBakB-ATAC-00-Rep1

description:
WTvkBmut_ATAC_counts.txt
MM.R1.0h


title: IkBakB-ATAC-00-Rep2

description:
WTvkBmut_ATAC_counts.txt
MM.R2.0h


title: Ctrl-8h-03h-RNA-Rep2

description:
CtrlvKO_RNA_counts.txt
3KO.3h.b2


title: IkBaKO-ChIP-input-Rep2

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
(not in count table)


title: Ctrl-8h-00h-RNA-Rep1

description:
CtrlvKO_RNA_counts.txt
3KO.wash.b1


title: IkBaKO-ChIP-24h-Rep4

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
4KO.R4.24h


title: Ctrl-0h-RNA-Rep1

description:
CtrlvKO_RNA_counts.txt
3KO.NT.b1


title: IkBaKO-ChIP-02h-Rep2

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
4KO.R2.2h


title: IkBaKO-ChIP-00h-Rep4

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
4KO.R4.0h


title: IkBaKO-ChIP-08h-Rep4

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
4KO.R4.8h


title: IkBaKO-ChIP-00h-Rep2

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
4KO.R2.0h


title: IkBaKO-ChIP-24h-Rep2

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
4KO.R2.24h


title: Ctrl-ChIP-input-Rep4


title: IkBaKO-ChIP-08h-Rep2

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
4KO.R2.8h


title: IkBaKO-ChIP-02h-Rep4

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
4KO.R4.2h


title: Ctrl-ChIP-08h-Rep4

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
3KO.R4.8h


title: Ctrl-ChIP-08h-Rep2

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
3KO.R2.8h


title: Ctrl-ChIP-24h-Rep2

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
3KO.R2.24h


title: Ctrl-ChIP-24h-Rep4

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
3KO.R4.24h


title: Ctrl-ChIP-02h-Rep2

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
3KO.R2.2h


title: IkBaKO-ATAC-24h-Rep1

description:
CtrlvKO_ATAC_counts.txt
KO.TNF_24.rep1


title: Ctrl-ChIP-00h-Rep4

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
3KO.R4.0h


title: Ctrl-ChIP-00h-Rep2

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
3KO.R2.0h


title: IkBaKO-ATAC-08h-Rep3

description:
CtrlvKO_ATAC_counts.txt
KO.TNF_08.rep3


title: IkBaKO-ATAC-02h-Rep1

description:
CtrlvKO_ATAC_counts.txt
KO.TNF_02.rep1


title: IkBaKO-ATAC-02h-Rep3

description:
CtrlvKO_ATAC_counts.txt
KO.TNF_02.rep3


title: IkBaKO-ATAC-04h-Rep1

description:
CtrlvKO_ATAC_counts.txt
KO.TNF_04.rep1


title: IkBaKO-ATAC-04h-Rep3

description:
CtrlvKO_ATAC_counts.txt
KO.TNF_04.rep3


title: IkBaKO-ATAC-00h-Rep3

description:
CtrlvKO_ATAC_counts.txt
KO.NT.rep3


title: Ctrl-ATAC-24h-Rep3

description:
CtrlvKO_ATAC_counts.txt
Ctrl.TNF_24.rep3


title: IkBaKO-ATAC-00h-Rep1

description:
CtrlvKO_ATAC_counts.txt
KO.NT.rep1


title: Ctrl-ATAC-24h-Rep1

description:
CtrlvKO_ATAC_counts.txt
Ctrl.TNF_24.rep1


title: IkBaKO-ATAC-08h-Rep1

description:
CtrlvKO_ATAC_counts.txt
KO.TNF_08.rep1


title: Ctrl-ChIP-input-Rep2

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
(not in count table)


title: Ctrl-ATAC-04h-Rep3

description:
CtrlvKO_ATAC_counts.txt
Ctrl.TNF_04.rep3


title: Ctrl-ATAC-08h-Rep3

description:
CtrlvKO_ATAC_counts.txt
Ctrl.TNF_08.rep3


title: Ctrl-ATAC-08h-Rep1

description:
CtrlvKO_ATAC_counts.txt
Ctrl.TNF_08.rep1


title: IkBaKO-ATAC-24h-Rep3

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
KO.TNF_24.rep3


title: Ctrl-ATAC-04h-Rep1

description:
CtrlvKO_ATAC_counts.txt
Ctrl.TNF_04.rep1


title: dKO-ChIP-unstim

description:
Irf3Ifnar_H3K4me1-CHIP_counts.txt
None


title: Ctrl-ATAC-00h-Rep3

description:
CtrlvKO_ATAC_counts.txt
Ctrl.NT.rep3


title: Ctrl-ATAC-02h-Rep1

description:
CtrlvKO_ATAC_counts.txt
Ctrl.TNF_02.rep1


title: Ctrl-ChIP-02h-Rep4

description:
CtrlvKO_H3K4me1-ChIP_counts.txt
3KO.R4.2h


title: dKO-ChIP-TNF

description:
Irf3Ifnar_H3K4me1-CHIP_counts.txt
TNF


title: dKO-ChIP-input

description:
Irf3Ifnar_H3K4me1-CHIP_counts.txt
(not in count table)


title: dKO-ChIP-Pam3

description:
Irf3Ifnar_H3K4me1-CHIP_counts.txt
Pam3CSK

value: Pam3CSK (100 ng/ml)


title: dKO-ChIP-LPS

description:
Irf3Ifnar_H3K4me1-CHIP_counts.txt
LPS

value: LPS (100 ng/ml)


title: WT-ChIP-TNF-Rep2

description:
WT_H3K4me1-CHIP_counts.txt
TNF_2


title: Ctrl-ATAC-02h-Rep3

description:
CtrlvKO_ATAC_counts.txt
Ctrl.TNF_02.rep3


title: WT-ChIP-TNF-Rep1

description:
WT_H3K4me1-CHIP_counts.txt
TNF_1


title: dKO-ChIP-CpG

description:
Irf3Ifnar_H3K4me1-CHIP_counts.txt
CpG

value: CpG (10 uM)


title: WT-ChIP-pIC-Rep1

description:
WT_H3K4me1-CHIP_counts.txt
pIC_1

value: Poly(I:C) (50 uM)


title: WT-ChIP-Pam3CSK-Rep1

description:
WT_H3K4me1-CHIP_counts.txt
Pam3CSK_1


title: WT-ChIP-pIC-Rep2

description:
WT_H3K4me1-CHIP_counts.txt
pIC_2


title: WT-ChIP-CpG-Rep2

description:
WT_H3K4me1-CHIP_counts.txt
CpG_2


title: WT-ChIP-LPS-Rep1

description:
WT_H3K4me1-CHIP_counts.txt
LPS_1


title: WT-ChIP-LPS-Rep2

description:
WT_H3K4me1-CHIP_counts.txt
LPS_2


title: WT-ChIP-none-Rep1

description:
WT_H3K4me1-CHIP_counts.txt
None_1


title: Ctrl-ATAC-00h-Rep1

description:
CtrlvKO_ATAC_counts.txt
Ctrl.NT.rep1


title: WT-ChIP-input-Rep1

description:
WT_H3K4me1-CHIP_counts.txt
(not in count table)


title: WT-ChIP-Pam3CSK-Rep2

description:
WT_H3K4me1-CHIP_counts.txt
Pam3CSK_2


title: WT-ChIP-input-Rep2


title: 13w_replicate3

city: Epalinges

first: Grégory

last: Verdeil

address: Ch. des Boveresses 155

department: Department of Oncology

country: Switzerland

institute: University of Lausanne

data_processing:
RNAseq quantification was performed with kallisto 0.44.0 with sequence-based bias correction using transcript sequences obtained from ENSEMBLE (GRCm38.p6). All other parameters were set to default when running kallisto.
Kallisto's transcript-level estimates were further summarized at the gene-level using tximport 1.8.0 from Bioconductor.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: CSV table of raw estimated counts as obtained from tximport. Rows represent genes and columns represent samples.

source_name: Bladder tumor cells

growth_protocol: Tumors were induced by the injection of an adenoviral vector that expresses the Cre-recombinase directly in the bladder of P53 Fl/F lPTEN Fl/Fl mice. At 5/9/13 weeks tumors were harvested and tumor cells were isolated using percoll gradient.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit (#74034, Qiagen) according to manufacturer’s recommendations
Truseq Stranded RNA, using 500ng of total RNA per sample

value: Bladder tumor cells

tag: Sex

value: female

tag: cell passage number

tag: time

value: 13 weeks

tag: genotype/variation

value: P53 Fl/F lPTEN Fl/Fl mice


title: 13w_replicate1

value: male


title: dKO-ChIP-pIC

description:
Irf3Ifnar_H3K4me1-CHIP_counts.txt
pIC

tag: strain


title: 5w_replicate3

tag: batch

value: 5 weeks


title: 5w_replicate2


title: 5w_replicate1


title: 9w_replicate1

value: 9 weeks


title: 9w_replicate3


title: EYFP294 [RNA-seq]

city: New York City

first: Dan

last: Li

department: HOPP

institute: Memorial Sloan-Kettering Cancer Center

description:
TMPRSS2-EYFP294_IGO_05957_G_3_S12_L001
processed data file:
rlog_normalized_counts_RNAseq_02252019_nodup.csv

data_processing:
ATAC-seq and primary data processing: ATAC-seq was performed as previously described (Buenrostro et al., 2013). Primary data processing and peak calling was performed using ENCODE ATAC-seq pipeline (https://github.com/kundajelab/atac_dnase_pipelines). Briefly, paired-end reads were trimmed, filtered and aligned against mm9 using Bowtie2 (Langmead et al., 2009). PCR duplicates and reads mapped to mitochondrial chromosome or repeated regions were removed. Mapped reads were shifted +4/-5 to correct for the Tn5 transposase insertion. Peak calling was performed using MACS2(Zhang et al., 2008), with p value < 0.01 as cutoff. Reproducible peaks from two biological replicates were defined as peaks overlapped by more than 50%. On average 25 million uniquely mapped pairs of reads were remained after filtering. The distribution of inserted fragment length shows typical nucleosome banding pattern, and the TSS enrichment score (reads that are enriched around TSS against background) ranges between 28 and 33, suggesting the libraries have high quality and were able to capture the majority of regions of interests.
Differential peak accessibility: Reads aligned to peak regions were counted using R package GenomicAlignments_v1.12.2 (Lawrence et al., 2013). Read count normalization and differential accessible peaks were called with DESeq2_v1.16.1 in R 3.4.1 (Love et al., 2014). Differential peaks were defined as peaks with adjusted p value < 0.01 and |log2(FC)| > 1.  For visualization, coverage bigwig files were generated using bamCoverage command from deepTools2, normalizing using the size factor generated by DESeq2. The differential ATAC-seq peak density plot was generated with deepTools2 (Ramírez et al., 2018), using regions that were significantly more or less accessible in ETV4AAA samples relative to EYFP samples.
Motif analysis: Enriched motif and de novo motif analysis using Homer (findMotifsGenme.pl) (Heinz et al., 2010) with ‘size -given -mask’ was applied to differentially accessible regions in ETV4AAA relative to EYFP, with the non-differentially accessible peaks as background.
RNA-seq analysis: The extracted RNA was processed for RNA-sequencing by the Integrated Genomics Core Facility at MSKCC.  The libraries were sequenced on an Illumina HiSeq-2500 platform with 51 bp paired-end reads to obtain a minimum yield of 40 million reads per sample. The sequenced data were aligned using STAR v2.3 (Dobin et al., 2013) with GRCm38.p6 as annotation. DESeq2_v1.16.1 (Love et al., 2014) was subsequently applied on read counts for normalization and the identification of differentially expressed genes between ETV4AAA and EYFP groups, with adjusted p value < 0.05 as threshold. Genes were ranked by sign(log2(FC)) * (-log(p value)) as input for GSEA analysis using ‘Run GSEA Pre-ranked’ with 1000 permutations (Subramanian et al., 2005).
Genome_build: mm9
Supplementary_files_format_and_content: csv files include log2_normalized_counts of all samples

source_name: primary prostate cells_EYFP

extract_protocol:
Intraperitoneal injection of tamoxifen was administered in 8-week-old mouse. 1 week after tamoxifen treatment, mouse prostate was digested 1 hour with Collagenase/Hyaluronidase (STEMCELL, #07912) and then 30 minutes with TrypLETM Express Enzyme (Thermo Fischer, # 12605028) at 37°C to isolate single prostate cells. The prostate cells were stained with PE/Cy7 conjugated anti-mouse CD326 (EpCAM) antibody (BioLegend, 118216) and then, CD326 and EYFP double positive cells were sorted out by flow cytometry. The mRNA or genomic DNA were extracted from these double positive cells and then were used for ATAC-sequencing and RNA-sequencing analysis.
DNA and RNA libraries were prepared for sequencing using standard Illumina protocols

value: 2 months old

value: EYFP

tag: tissue/cell type

value: Isolated primary mouse prostate cells

tag: cell population

value: CD326 and EYFP double positive cells


title: EYFP293 [RNA-seq]

description:
TMPRSS2-EYFP293_IGO_05957_G_2_S11_L001
processed data file:
rlog_normalized_counts_RNAseq_02252019_nodup.csv

tag: age