title: A1454_coloncancer

label_protocol: Methylation profiles were generated from 750 ng DNA using the Infinium HumanMethylation450 BeadChip (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions

tag: tissue

value: male

value: moderate

value: Right


title: Predicted ADs Sort Seq Replicate 2 Bin 2

status: Public on Dec 08 2021

type: SRA

city: St. Louis

first: Barak

middle: A

last: Cohen

state: MO

address: 4515 McKinley Ave

department: Genetics

country: USA

institute: Washington University School of Medicine

library_source: genomic

data_processing:
Library strategy: Sort-seq
All raw reads were processed regardless of quality score.
grep -o CTAGC.*.CTCGAG
sort "$i" | uniq -c > "$i"sorted.txt
Barcode sequences that exactly matched the design were used for downstream analysis
Barcode counts were used to create a probability mass function for the abundance of each AD in each bin. Thie PMF and the fluorescence of each bin was used to calculate the activity of the each AD. See paper methods for details
Genome_build: N/A
Supplementary_files_format_and_content: Barcode counts and sequences

molecule: genomic DNA

organism: synthetic construct

growth_protocol: We derived clonal derivatives of K562 cells (ATCC CCL-243) after transfecting out GFP reporter and integrating it at the AAVS1 locus. We integrated libraries of synthetic transcription factors into the LP3 landing pad with G418 selection for 14 days. We enriched for live cells with MACS magnetic separation We then cultured lines in IMDM supplemented with 10% FBS, 1% penicillin-streptomycin, and 1% non-essential amino acids at 37C.

extract_protocol:
We sorted 1e6 cells into each pool. We extracted genomic DNA from these cells with the  Qiamp DNA Mini kit (Qiagen).
 We performed 8 PCRs on each sample. The sequencing libraries were prepared in 2 batches: Batch 1 contained biological replicates 1-3 and Batch 2 contained biological replicate 4 and the 8 bin sort. We did 25 cycles with NEB Q5 polymerase using CP36.P10 and LP_019 primers. We pooled the PCRs, cleaned up the DNA (NEB Monarch), quantified it, digested the entire sample with NheI and EcoRI-HF (NEB) for 90 minutes and then ligated sequencing adaptors with T4 ligase (NEB) for 30 min. These adaptors contained sample barcodes in Read1 and Index1 We used 4 ng of this ligation for a 20 cycle enrichment PCR with Q5 and the EPCR_P1_short and EPCR_PE2_short primers. We sequenced each Batch on a NextSeq 500 1x75 High Output run.

treatment_protocol: We treated cells with ß-estradiol for 48hrs before cell sorting/

tag: cell line

tag: cell type used for experiment

value: Immortalized lymphoblast

tag: genotype

value: AAVS1:UAS GFP (pmvs184) LP3::AD library

tag: treatment

value: Beta-estradiol


title: Predicted ADs Sort Seq Replicate 1 Bin 4


title: Predicted ADs Sort Seq Replicate 2 Bin 1


title: ActA treatment 3

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

country: United Kingdom

institute: University of  Oxford

library_source: transcriptomic

data_processing:
Reads were aligned using STAR aligner to human genome reference (hg19)
Quantitation of gene expressions was performed suing Rsubread package in R
Low expressed features were removed and library size and vsn normalization was performed
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with raw gene counts
Supplementary_files_format_and_content: Tab-delimited text file with normalized gene counts

molecule: polyA RNA

organism: Homo sapiens

source_name: hepatoma cell line

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: HepaRG hepatocyte

tag: cell type

value: bipotent hepatic progenitors actively proliferating

value: ActA treatment


title: Predicted ADs Sort Seq Replicate 1 Bin 2


title: A1444_coloncancer

type: genomic

city: Rotterdam

first: Marcel

last: Smid

address: Dr. Molewaterplein 50

department: Medical Oncology

country: Netherlands

institute: Erasmus MC

hyb_protocol: Methylation profiles were generated from 750 ng DNA using the Infinium HumanMethylation450 BeadChip (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

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

data_processing:
Raw data was processed and normalised using the Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC (ChAMP) package in R [PMID: 24336642; PMID: 28961746]. This package contains functions for filtering low-quality probes, adjustment for Infinium I and Infinium II probe design, batch effect correction, and data normalisation. In short, bad quality probes (detection p value >0.01), probes containing SNPs, probes mapping to multiple locations, and probes mapping to chromosomes X and Y were removed, resulting in 429705 probes for further analysis. Data were normalised by Beta-Mixture Quantile (BMIQ) normalisation to correct for bias between type I and type II probe chemistry and potential batch effects were removed using Combat. The returned Beta values per probe represent the percentage of methylation for that particular CpG dinucleotide.
Processed file includes BMIQ-normalised Beta-values

label: Cy3 and Cy5

source_name: colon cancer, CMS2

extract_protocol: Genomic DNA was isolated from 30 µm frozen tissue sections using the Nucleospin Tissue kit according to the manufacturer’s instructions.

value: colon cancer

tag: cms class

tag: tumor stage

tag: gender

tag: t

tag: n

tag: m

tag: differentiation grade

tag: tumor location

value: Left

tag: adjuvant treatment

value: no


title: Predicted ADs Sort Seq Replicate 1 Bin 1


title: p53 ADs Deep Mutational Scan Sort Seq Replicate 1 Bin 1


title: Predicted ADs Sort Seq Replicate 3 Bin 3


title: 3998755015_H

type: RNA

city: La Jolla

first: Bjoern

last: Peters

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The raw data was quantile normalized and log2 transformed using the Bioconductor package lumi v2.40 in R. The probes accounting for the bottom 50% in each measurement were overlapped, and those probes that fell in the bottom 50% of all measurements (n=20,147) were removed from further analysis, leaving a final set of 27,960 probes of the initial 48,107 probes. Batch effects were removed using the Combat function from the Bioconductor package sva v3.36 in R

label: biotin

molecule: total RNA

source_name: blood

label_protocol: Biotinylated cRNA were prepared with the TotalPrep RNA Amplification Kit (Illumina) according to the manufacturer’s instruction. Quality was assessed using the Agilent bioanalyser.

growth_protocol: No in vitro stimulation

extract_protocol: Total intracellular RNA was extracted from PAXgene® samples using the Blood RNA Kit (Qiagen) according to the manufacturer’s instructions. Bound RNA was treated with DNase I to remove trace amounts of bound DNA and after further washes the RNA was eluted in elution buffer and heat-denatured. The purity and quantity of the isolated total RNA was assessed spectrophotometrically prior to storage at -20oC until required for microarray analysis.

value: blood

tag: cohort

value: Latent TB

tag: timepoint

value: pre-treatment


title: ActA treatment 2


title: A1440_coloncancer

tag: tissue


title: Five acidic AD Sort Seq 8bin sort Bin 8

source_name: Five acidic AD Sort Seq 8bin sort Bin 8

tag: cell line


title: Predicted ADs Sort Seq Replicate 3 Bin 2

tag: cell type used for experiment


title: A1306_coloncancer

value: female


title: ActA treatment 1


title: Predicted ADs Sort Seq Replicate 2 Bin 3

tag: genotype


title: A1450_coloncancer


title: Untreated 2

tag: treatment

value: Untreated


title: A1300_coloncancer


title: Untreated 1

tag: cell type


title: Five acidic AD Sort Seq 8bin sort Bin 5

source_name: Five acidic AD Sort Seq 8bin sort Bin 5


title: Five acidic AD Sort Seq 8bin sort Bin 3

source_name: Five acidic AD Sort Seq 8bin sort Bin 3


title: Predicted ADs Sort Seq Replicate 1 Bin 3


title: Five acidic AD Sort Seq 8bin sort Bin 4

source_name: Five acidic AD Sort Seq 8bin sort Bin 4


title: A1448_coloncancer

tag: cms class

value: male


title: Five acidic AD Sort Seq 8bin sort Bin 1

source_name: Five acidic AD Sort Seq 8bin sort Bin 1


title: C15-3437-1

city: DIJON

first: François

last: Ghiringhelli

address: 1 rue du Professeur Marion

country: France

institute: UMR INSERM 1231

data_processing:
Pseudo alignment and quantification were performed using kallisto 0.45
Genome_build: GRCh37
Supplementary_files_format_and_content: Processed data file is a csv file containing TPM expression values

source_name: biopsy

extract_protocol:
10ng of total RNA or 40ng from FFPE were fragmented and 3’-end of mRNA were captured using an RT primer poly(T) containing a UMI (Unique Molecular Identifier)
Illumina adapters were added during this step by template switching. Fragments were then amplified with two PCR to complete Illumina adapters and add indexing sequences. Libraries were sequenced on NovaSeq 6000 platform

value: lung tumor tissue

tag: disease state

value: squamous

tag: pfs_time (6 months)

tag: pfs_evt (6 months)


title: A1292_coloncancer

tag: tumor stage

tag: gender

tag: t

tag: n

value: moderate


title: Five acidic AD Sort Seq Replicate 4 Bin 4

value: Immortalized lymphoblast

value: AAVS1:UAS GFP (pmvs184) LP3::AD library


title: A1290_coloncancer

tag: m

tag: differentiation grade

tag: tumor location

value: Right

tag: adjuvant treatment


title: Five acidic AD Sort Seq Replicate 4 Bin 3

tag: cell line

value: Beta-estradiol


title: Five acidic AD Sort Seq Replicate 4 Bin 2

tag: cell type used for experiment


title: Five acidic AD Sort Seq 8bin sort Bin 7

source_name: Five acidic AD Sort Seq 8bin sort Bin 7

tag: genotype


title: Five acidic AD Sort Seq Replicate 4 Bin 1

tag: treatment


title: A19-6764

tag: tissue

value: non-squamous


title: A19-5972-1


title: Five acidic AD Sort Seq Replicate 3 Bin 4


title: Five acidic AD Sort Seq 8bin sort Bin 6

source_name: Five acidic AD Sort Seq 8bin sort Bin 6


title: A1276_coloncancer

value: colon cancer

tag: cms class


title: Five acidic AD Sort Seq Replicate 3 Bin 3


title: A19-5795-1

tag: disease state


title: Five acidic AD Sort Seq Replicate 3 Bin 2


title: A1274_coloncancer


title: 3998755016_F

tag: cohort

tag: timepoint

value: post-treatment


title: A19-5242-2

tag: pfs_time (6 months)

tag: pfs_evt (6 months)


title: Five acidic AD Sort Seq Replicate 3 Bin 1


title: A1272_coloncancer

tag: tumor stage

tag: gender

tag: t

value: no


title: Five acidic AD Sort Seq Replicate 2 Bin 4


title: Five acidic AD Sort Seq 8bin sort Bin 2

source_name: Five acidic AD Sort Seq 8bin sort Bin 2


title: A19-718-1


title: C15-2297


title: Five acidic AD Sort Seq Replicate 2 Bin 3


title: Five acidic AD Sort Seq Replicate 2 Bin 2


title: A1270_coloncancer

tag: n

tag: m

tag: differentiation grade

value: Left


title: A19-503-2


title: A1278_coloncancer

tag: tumor location

tag: adjuvant treatment


title: A19-5029-2


title: Five acidic AD Sort Seq Replicate 1 Bin 4

tag: cell line

tag: cell type used for experiment

tag: genotype


title: Five acidic AD Sort Seq Replicate 2 Bin 1

tag: treatment


title: A1266_coloncancer

tag: tissue

tag: cms class


title: Five acidic AD Sort Seq Replicate 1 Bin 2


title: Five acidic AD Sort Seq Replicate 1 Bin 3


title: A19-405

tag: disease state


title: A1262_coloncancer


title: MDA-MB-231_LAP-Smad3_treated

city: Singapore

first: Wee Kiat Jeremy

last: Ng

address: 20 College Road

country: Singapore

institute: Singapore General Hospital

data_processing:
ChIP-seq reads were aligned to the hg38 using bowtie2 and default parameters
Reads were extended to 200 base pairs using bedtools slop
Peak calling was performed using MACS2, using default parameters
Genome_build: hg38
Supplementary_files_format_and_content: peak text files, narrowPeak

source_name: ATCC

growth_protocol: DMEM with 10% FBS, supplemented with 100U/mL penicillin/ streptomycin and 800μg/mL Geneticin

extract_protocol:
Chromatin Immunoprecipitation (ChIP) was performed with the EZ-Magna ChIP™ A Chromatin Immunoprecipitation Kit (Millipore, Billerica, MA, USA) with anti-GFP antibodies. ChIP DNA was purified with Qiagen PCR purification kit and quantified with the Qubit 3.0 fluorometer with Qubit ds DNA HS assay.
DNA libraries were generated using the TruSeq ChIP sample Prep kit (Illumina) following manufacturers instructions

treatment_protocol: 10ng/mL TGFB1 (Sigma) for 2 hours

value: 10ng/mL TGFB1, 2 hours

tag: chip antibody

value: anti-GFP abcam #ab290


title: Five acidic AD Sort Seq Replicate 1 Bin 1


title: MDA-MB-231_LAP-Smad2_treated


title: A19-2207-1

tag: pfs_time (6 months)

tag: pfs_evt (6 months)


title: MDA-MB-231_LAP-Smad3_untreated

value: untreated


title: A1260_coloncancer

tag: tumor stage

tag: gender

value: female


title: MDA-MB-231_LAP-Smad2_untreated


title: A19-2185-1


title: A1143_coloncancer

tag: t

tag: n


title: A1145_coloncancer

tag: m

tag: differentiation grade


title: A18-7641-2


title: A19-4598


title: A1139_coloncancer

value: male

tag: tumor location

tag: adjuvant treatment


title: A18-7206-1

value: lung tumor tissue


title: A1264_coloncancer


title: A18-6421-1


title: pt1079_p3

city: Minneapolis

first: Sathi

last: Wijeyesinghe

state: MN

institute: University of Minnesota

data_processing:
Quality control of FastQ files - FastQC
Low quality segments and adapters trimmed - Trimmomatic
Aligned to reference genome - HiSat2
Differentially expressed genes were quantified - DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: .csv files with normalized and unnormalized abundance measurements

source_name: GBM tumor

extract_protocol:
RNA was isolated using TRIZOL and further purified using the QIAGEN RNA Cleanup Kit
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Library Prep Kit)

treatment_protocol: Tissues were incubated with viral peptides (10mcg/mL) or in equal volume of DMSO for 9 hours, prior to preservation in RNAlater.

value: glioblastoma multiforme (GBM)

tag: individual

value: Homogenized whole tumor

tag: group

value: Viral peptide (experimental)


title: pt1079_c2

value: DMSO only (control)


title: pt1079_c1


title: pt1079_c3


title: pt969_p1


title: pt1079_p1


title: pt1079_p2


title: pt969_p2


title: A1123_coloncancer

value: moderate


title: pt969_c3


title: A1134_coloncancer

source_name: colon cancer, CMS3


title: A1117_coloncancer


title: pt969_c2


title: A18-6126-2


title: pt969_c1


title: A1113_coloncancer

value: Right


title: pt175_p3


title: pt175_p2


title: A19-1734

value: non-squamous


title: A18-5913


title: A845_coloncancer

value: colon cancer


title: pt175_p1


title: pt969_p3


title: A18-5398-I1


title: pt175_c3


title: A843_coloncancer

value: good


title: pt175_c1


title: A18-5082-I2


title: pt164_p3


title: A18-4271-1


title: A841_coloncancer

value: no


title: A837_coloncancer

value: Left


title: A18-4410-2


title: pt164_p1


title: pt164_c1


title: pt158_p3


title: pt164_c3


title: A18-5943


title: A826_coloncancer


title: pt164_c2


title: A18-4923-2


title: pt164_p2


title: A828_coloncancer


title: pt158_p2


title: A9968_coloncancer


title: A18-4068-2


title: pt158_c3


title: pt158_p1


title: A18-3665


title: pt158_c2


title: A9942_coloncancer


title: pt175_c2


title: A18-3435


title: pt158_c1


title: PDKD-T3

city: Austin

first: Ningling

last: Kang

address: 801 16th Ave NE

department: The Hormel Institute

data_processing:
Illumina Real time Analysis and CASAVA software 1.8.2 were used for basecalling.
Raw reads were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.  Quality control checks on raw sequence data for each sample were performed with FastQC.  Read mapping was performed via Bowtie (v2.2.4.0) using the Human genome (hg19) as reference
Raw reads for each gene generated from the HiSeq2500 sequencer were subjected to statistical analysis using the edgeR package and cuffdiff2 package based on two selection criteria (fold change ≥ 2 & FDR < 0.05, and fold change ≥ 1.5 & FDR < 0.01).  The overlap of these four criteria was used to identify genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for all samples

source_name: Liver hepatic stellate cells

growth_protocol: HSCs obtained from ScienCell were cultured with DMEM supplemented with 10%FBS, streptomycin and penicillin.

extract_protocol:
RNA samples were isolated from HSCs using a RNeasy Plus Mini kit (Qiagen, 74134) and gDNA Eliminator columns were used to eliminate genomic DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were first subjected to serum-starvation for overnight and they were incubated with TGFbeta1 (5 ng/ml) for 24 hours

tag: treatment

value: PD-L1 shRNA + TGFbeta


title: A9941_coloncancer

tag: tissue


title: PDKD-T2


title: A18-2873-1


title: A9940_coloncancer

tag: cms class


title: PDKD-T1


title: PDKD3

value: PD-L1 shRNA


title: PDKD2


title: A18-1848-1

tag: disease state


title: A9386_coloncancer


title: A18-1253


title: NT-T3

value: Control shRNA + TGFbeta


title: PDKD1


title: A18-199-1


title: A9385_coloncancer

value: female


title: A9375_coloncancer

value: male


title: A18-2018-1

value: lung tumor tissue

value: squamous


title: NT1

value: Control shRNA


title: A9388_coloncancer


title: NT2


title: NT3


title: A17-6222


title: NT-T2


title: A17-6220-1


title: S765_islet

city: Campbelltown

first: Mugdha

middle: V.

last: Joglekar

state: NSW

address: Cnr Goldsmith and David Pilgrim Ave

department: School of Medicine

country: Australia

institute: Western Sydney University

data_processing:
Strand Next-generation sequencing (NGS) version 2.5 software was used to analyse the RNA-Seq data
Alignment: Reads from mouse samples were aligned to the mouse mm10 transcriptome and genome using the Ensembl genes and transcript (2013.04.03) model. While for human samples were aligned to the human hg38 transcriptome and genome using the Ensembl genes and transcript (2016.12.01) model. All alignments were processed with novel splices.
Alignment: Raw reads were aligned with a minimum of 90 percent identity, maximum five percent gaps and a minimum match length of 25 base pairs.
Alignment trimming: The read pairs output with more than five valid matches were not reported. Quality trimming was applied to trim 3’ end with an average quality less than 10 and on poorly aligned portion at 3’ end post alignment.
Filtering: Raw reads with an average base quality below 20 and reads which have failed quality control (QC) were removed.
Generation of normalized abundance: Normalized values were calculated using the Deseq algorithm, with the threshold normalized count set at 1 and no baseline transformation.
Genome_build: mm10 (for mouse samples) and hg38 (for human samples)
Supplementary_files_format_and_content: excel (Note: for Hg38_islets and GB-Deseq.xlsx ; the six human islets samples used for analysis are taken from our GSE152111 study and included in this series.)

source_name: Adult human islet

extract_protocol:
RNA was extracted using TRIzol® RNA Isolation (Thermo Fisher Scientific, Waltham, MA) protocol with minor modification  (Joglekar et al. 2012). For mouse RNA samples, poly(A) mRNA extraction was performed for RNA-sequencing on the Ion Torrent (Thermo Fisher Scientific, Waltham, MA)  platform, using the MicroPoly(A)Purist™ Kit (Thermo Fisher Scientific, Waltham, MA) following the manufacturer instructions.
For mouse samples: cDNA libraries were generated using the Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific, Waltham, MA) following manufacturer's protocol. For human samples: libraries were generated through using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) through following manufacturer’s protocol.

value: islet


title: S833_islet


title: A9369_coloncancer


title: A17-5918-2


title: S600_islet


title: S900_islet


title: S295_islet


title: S115_islet


title: A9338_coloncancer


title: A17-5761-1


title: AH_12

description: from a indvidual donor

source_name: Adult human gallbladder

value: Primary gallbladder epithelial cells


title: AH_11

description: from a indvidual donor


title: A17-5-2


title: AH_10

description: from a indvidual donor


title: A17-5217-1


title: A9374_coloncancer

source_name: colon cancer, CMS2


title: A9336_coloncancer

value: moderate


title: AH_09

description: from a indvidual donor


title: A9331_coloncancer


title: AH_08

description: from a indvidual donor


title: A17-3877


title: A9325_coloncancer

value: Right


title: A17-3774-1


title: AMs derived from human CD64- fetal liver cells, biological replicate 3

city: Stockholm

first: Tim

last: Willinger

address: Center for Infectious Medicine (CIM), Alfred Nobels allé 8, level 7

department: Department of Medicine Huddinge

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from fetal-derived AMs

hyb_protocol: Following fragmentation, cRNA were hybridized on human Clariom™ D Array according to standard  Affymetrix protocol.

scan_protocol: GeneChips were scanned using Affymetrix Scanner at the Bioinformatics and Expression Analysis Core Facility.

data_processing: Transcriptome Analysis Console (TAC) software (Thermofisher Scientific) was used for the analysis of the microarray data. Signal values were log2-transformed and normalized using the Signal Space Transformation (SST-RMA) method.

source_name: MISTRG humanized mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol by the Bioinformatics and Expression Analysis Core Facility at Karolinska Institutet.

extract_protocol:
Lungs were perfused with 10 ml ice-cold PBS and digested in RPMI 1640/5% FCS with 0.2 mg/ml of collagenase IV (Sigma) and 0.02 mg/mL of DNAse I (Sigma) for 60 min at 37ºC. Digested cells were then passed sequentially through 18 and 20G needles before density gradient centrifugation using Lymphoprep (Stemcell Technologies). Cells were then sorted into RLT+ buffer (Qiagen)
RNA extraction with RNeasy Micro kit (Qiagen)

treatment_protocol: HSPC-engrafted MISTRG mice were injected intravenously with 2 μg of PE-conjugated anti human CD45 antibody (HI30, BioLegend) before lung harvest to exclude IV CD45-PE+ pulmonary intravascular macrophages from the sorted CD45+CD11b+HLA-DR+CD206+CD169+ subset as described (Evren et al., 2021).

value: Lung


title: AMs derived from human CD64- fetal liver cells, biological replicate 2


title: AMs derived from human CD64- fetal liver cells, biological replicate 1


title: A9281_coloncancer

value: colon cancer


title: NT-T1


title: AMs derived from human CD64+ fetal liver cells, biological replicate 2


title: AH_07

description: A pool of two gallbladder samples coming from two different donors.


title: AMs derived from human CD64+ fetal liver cells, biological replicate 1


title: S990

description: from a individual donor

data_processing:
Strand Next-generation sequencing (NGS) version 2.5 software was used to analyse the RNA-Seq data
Alignment: Reads were aligned to the human hg38 transcriptome and genome with novel splices using the Ensembl genes and transcript (2016.12.01) model.
Alignment: Raw reads were aligned with a minimum of 90 percent identity, maximum five percent gaps and a minimum match length of 25 base pairs.
Alignment trimming: The read pairs output with more than five valid matches were not reported. Quality trimming was applied to trim 3’ end with an average quality less than 10 and on poorly aligned portion at 3’ end post alignment.
Filtering: Raw reads with an average base quality below 20 and reads which have failed quality control (QC) were removed.
Generation of normalized abundance: Normalized values were calculated using the Deseq algorithm, with the threshold normalized count set at 1 and no baseline transformation.
Genome_build: hg38
Supplementary_files_format_and_content: hg38-islets-deseq-all-entities.xlsx

source_name: Human Islets

growth_protocol: Human Islet isolated sample preparations were extracted for RNA. The RNA of each islet sample preparation was used for RNA-seq.

extract_protocol:
RNA was extracted using TRIzol® RNA Isolation (Thermo Fisher Scientific, Waltham, MA) protocol with minor modification (Joglekar et al. 2012)
Sequencing libraries were generated using the rRNA-depleted RNA with the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) through following manufacturer’s protocol.

treatment_protocol: Not applicable (n/a)

tag: cell type

value: Primary islet cells

tag: donor gender (m=male; f=female)

value: M

tag: donor age (yrs)

tag: donor bmi (bmi kg/m2)


title: A9255_coloncancer

tag: tumor stage

tag: gender

value: no


title: A9366_coloncancer

tag: t

tag: n

value: Left


title: A17-2652-2

value: non-squamous

tag: pfs_time (6 months)

tag: pfs_evt (6 months)


title: A17-2572-1


title: S973

description: from a individual donor


title: AMs derived from human CD34+ HSPCs, biological replicate 3

description: Gene expression data from HSPC-derived AMs


title: S971

description: from a individual donor


title: A17-1042-2


title: A9253_coloncancer

tag: m

tag: differentiation grade

tag: tumor location

tag: adjuvant treatment


title: A16-689

tag: tissue


title: S906

description: from a individual donor

value: F


title: S957

description: from a individual donor


title: AMs derived from human CD34+ HSPCs, biological replicate 1


title: A9245_coloncancer

tag: cms class


title: A9244_coloncancer

value: female


title: Fetal monocytes, biological replicate 1

description: Gene expression data from fetal monocytes

data_processing: Transcriptome Analysis Console software (Thermofisher Scientific) was used for the analysis of the microarray data. Signal values were log2-transformed and normalized using the Signal Space Transformation (SST-RMA) method.

source_name: Human fetal liver, second trimester

extract_protocol:
Immunomagnetic selection from buffy coat or fetal liver followed by cell sorting to RLT or RLT plus buffer (Qiagen)
RNA extraction with RNeasy Micro kit or RNeasy Plus Micro kit (Qiagen)

treatment_protocol: No treatment

value: Fetal liver


title: A9239_coloncancer

value: male


title: A16-5521-1

value: lung tumor tissue

tag: disease state


title: A16-5788-II


title: Fetal monocytes, biological replicates 2 and 3 pooled together after RNA extraction


title: S900

description: from a individual donor

tag: cell type


title: AMs derived from human CD34+ HSPCs, biological replicate 2


title: A9250_coloncancer


title: Fetal monocytes, biological replicate 4


title: A9234_coloncancer


title: CD14+CD16- blood monocytes, biological replicate 3

description: Gene expression data from adult CD14+CD16- blood monocytes

source_name: Human adult buffy coat

value: Blood


title: A16-5450


title: A16-6076-1


title: S849

description: from a individual donor

tag: donor gender (m=male; f=female)


title: S848

description: from a individual donor

tag: donor age (yrs)


title: S833

description: from a individual donor

tag: donor bmi (bmi kg/m2)


title: CD14+CD16- blood monocytes, biological replicate 2


title: A16-2894

value: squamous


title: A9207_coloncancer

tag: tumor stage

value: poor


title: A9197_coloncancer

tag: gender

value: moderate


title: CD14+CD16- blood monocytes, biological replicate 1


title: S831

description: from a individual donor


title: A16-6391-1


title: A9243_coloncancer

tag: t


title: A9194_coloncancer

tag: n


title: A16-2286

tag: pfs_time (6 months)


title: A16-212-2

tag: pfs_evt (6 months)


title: S819

description: from a individual donor


title: S789

description: from a individual donor


title: Fetal AM precursors, biological replicate 2

description: Gene expression data from fetal AM precursor-like cells


title: A1268_coloncancer

tag: m

value: Right


title: A16-1658-1


title: A16-1489-1


title: S781

description: from a individual donor


title: Fetal AM precursors, biological replicate 1


title: A1105_coloncancer

tag: differentiation grade

value: good

value: yes


title: A1003_coloncancer

value: colon cancer

value: unknown

tag: tumor location


title: MT_C

city: Nanjing

last: Li

state: Jiangsu

address: No.12, Xuefu Road

country: China

institute: Qingshun Zhao

data_processing:
Illumina Casava1.7 software used for basecalling.
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCz10
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Danio rerio

source_name: Brains of the female atrn-/-

extract_protocol:
Brains were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: age

value: 4 month-post-fertilization

tag: genotype

value: atrn-/-

tag: Sex


title: A15-5889-1

tag: tissue

tag: disease state

value: non-squamous


title: S766

description: from a individual donor

tag: cell type

value: Primary islet cells

tag: donor gender (m=male; f=female)

value: F


title: S767

description: from a individual donor

value: M

tag: donor age (yrs)

tag: donor bmi (bmi kg/m2)


title: A997_coloncancer

tag: cms class

tag: tumor stage

tag: gender

value: male

value: Left

tag: adjuvant treatment


title: WT_C

source_name: Brains of the female wildtype

value: wildtype

value: female


title: A15-5827-

source_name: biopsy

value: lung tumor tissue

tag: pfs_time (6 months)

tag: pfs_evt (6 months)


title: A995_coloncancer

tag: t

tag: n

tag: m

tag: differentiation grade

value: moderate


title: S765

description: from a individual donor


title: A15-5825-1

value: squamous


title: MT_X

source_name: Brains of the male atrn-/-

tag: age

tag: genotype

tag: Sex


title: S750

description: from a individual donor

tag: cell type


title: WT_X

source_name: Brains of the male wildtype

tag: tissue


title: Fetal AM precursors, biological replicate 3

value: Fetal liver


title: A15-5730-1

tag: disease state


title: A993_coloncancer

value: colon cancer

tag: tumor location

value: yes


title: S749

description: from a individual donor

tag: donor gender (m=male; f=female)

tag: donor age (yrs)

tag: donor bmi (bmi kg/m2)


title: A983_coloncancer

tag: cms class

tag: tumor stage

tag: gender

value: Right

tag: adjuvant treatment


title: A991_coloncancer

tag: t

tag: n


title: FACS sorted microglia- Tamoxifen2

city: Bangalore

first: Hiyaa

middle: Singhee

last: Ghosh

state: Karnataka

address: GKVK Campus, Bellary Road

country: India

institute: National Center for Biological Sciences

data_processing:
RNA sequencing analysis was done using open-source platform, usegalaxy.org
After cutting the adapter sequences and quality control check, the reads were aligned to mus musculus genome (mm10) using HISAT2.
Feature counts and Deseq2 packages were used for obtaining raw counts and differential gene expression analysis respectively at default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: FACS sorted microglia- Tamoxifen

extract_protocol:
Microglia were FACS-sorted into RLT plus cell lysis buffer (Qiagen). RNA was extracted using Qiagen Micro plus kit as per manufacturer’s instructions
cDNA libraries were prepared by using NEB stranded mRNA library prep kit as per manufacturer's instructions. PolyA selection method was used to enrich mRNA

treatment_protocol: Pups were treated with Vehicle/Tamoxifen from postnatal day3-5

tag: developmental stage

value: neonate

value: brain

value: microglia

tag: strain

tag: treatment

value: Tamoxifen


title: A15-4305

value: non-squamous

tag: pfs_time (6 months)

tag: pfs_evt (6 months)


title: S715

description: from a individual donor

tag: cell type

value: Primary islet cells

value: M


title: A979_coloncancer

tag: tissue

value: male

tag: m

tag: differentiation grade


title: A977_coloncancer

tag: tumor location


title: A15-3549-1

tag: disease state


title: S710

description: from a individual donor

tag: donor gender (m=male; f=female)

value: F

tag: donor age (yrs)

tag: donor bmi (bmi kg/m2)


title: FACS sorted microglia- Vehicle1

source_name: FACS sorted microglia- Vehicle

value: Vehicle


title: FACS sorted microglia- Tamoxifen1


title: S718

description: from a individual donor


title: A15-2890-2

value: lung tumor tissue


title: A969_coloncancer

tag: cms class

tag: tumor stage

tag: gender

value: good

value: Left

tag: adjuvant treatment


title: A15-4090-1

value: squamous


title: A15-2146-2


title: A851_coloncancer

value: colon cancer

value: female

tag: t

tag: n

value: moderate


title: S673

description: from a individual donor


title: TIFABLSC2

city: Cleveland

first: Chen

last: Zhao

state: OH

address: 2130 Cornell Rd

department: Pathology

institute: Case Western Reserve University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 transcriptome index using kallisto v0.44.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include counts and TPM for each sample

source_name: murine MLL-AF9 leukemia cells

extract_protocol:
Empty vector (Control) or TIFAB transduced MLL-AF9 leukemia cells were sort-purified and total RNA was extracted using standard Qiagen RNease columns
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype

tag: treatment

value: TIFAB transduction


title: A15-2145-II2

tag: tissue

tag: pfs_time (6 months)

tag: pfs_evt (6 months)


title: TIFABLSC1


title: A809_coloncancer

tag: m

tag: differentiation grade

tag: tumor location

value: Right

value: yes


title: S689

description: from a individual donor

tag: cell type

tag: donor gender (m=male; f=female)

tag: donor age (yrs)


title: ConLSC2

value: empty vector


title: S608

description: from a individual donor

tag: donor bmi (bmi kg/m2)


title: A15-1759-1

tag: disease state

value: non-squamous


title: ConLSC1


title: A15-1673-2


title: FACS sorted microglia- Vehicle2

tag: developmental stage

value: neonate

value: brain

value: microglia


title: A14-4829-2


title: S600

description: from a individual donor

value: Primary islet cells

value: M


title: A14-3243-1

value: lung tumor tissue


title: A799_coloncancer

source_name: colon cancer, CMS3

tag: cms class

tag: tumor stage

tag: gender

value: male

tag: t

tag: adjuvant treatment


title: A717_coloncancer

tag: tissue

tag: n

value: good

value: Left


title: A711_coloncancer

value: colon cancer

value: poor


title: GMP-GFP- small RNA 2-4

city: Boston

first: Youmna

last: Kfoury

state: MA

address: 185 Cambridge street

department: Harvard stem cell institute

institute: Harvard University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing reads were aligned to mm10 reference genome using BWA aligner, miRNA expression levels were quantified by miRExpress
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files raw count coverage

source_name: Mouse bone marrow

growth_protocol: Cells were processes directly from the mouse with no in vitro growth

extract_protocol:
Total RNA was extracted using miRNeasy micro kit (Qiagen)
Small RNA libraries were constructed using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to manufacturer's instructions

tag: cell subtype

value: GMP-GFP-

tag: age

value: 10-14 weeks

tag: strain

value: Ocn-GFPTopaz (Bilic-Curcic et al., 2005)

value: Mouse bone marrow granulocyte macrophage progenitors


title: S597

description: from a individual donor

value: F


title: S639

description: from a individual donor


title: S582

description: from a individual donor


title: S562

description: from a individual donor


title: GMP-GFP- small RNA 2-2


title: GMP-GFP- small RNA 2-1


title: A706_coloncancer

tag: m

tag: differentiation grade

tag: tumor location

value: yes


title: S530

description: from a individual donor

tag: cell type

tag: donor gender (m=male; f=female)

tag: donor age (yrs)


title: GMP-GFP- small RNA 1-3


title: A14-118-2

tag: disease state

value: non-squamous

tag: pfs_time (6 months)

tag: pfs_evt (6 months)


title: miRNA_HPV-OSCC_C5

city: binzhou

first: Yue

last: Wang

state: shandong

address: NO.661 Huanghe Er Road, Binzhou City

institute: binzhou medical university

data_processing:
The small RNA tags were mapped to reference sequence by Bowtie (Langmead et al., 2009) without mismatch to analyze their expression and distribution on the reference
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2(Friedlander et al., 2011) and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively
To remove tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA, small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself
Genome_build: homo_sapiens_Ensembl_97
Supplementary_files_format_and_content: custom scripts were used to obtain the identified miRNA counts as well as base bias on the first position with certain length and on each position of all identified miRNA respectively

source_name: OSCC

extract_protocol:
Preparing selected tissue，flash frozen on dry ice，and RNA was harvested using trizol reagent.A total amount of 3 µg total RNA per sample was used as input material for the small RNA library
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq  SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads  were generat

tag: hpv status

value: HPV-

value: OSCC


title: miRNA_HPV-OSCC_C4


title: miRNA_HPV-OSCC_C6


title: GMP-GFP- small RNA 1-2


title: S542

description: from a individual donor

value: Primary islet cells

tag: donor bmi (bmi kg/m2)


title: A701_coloncancer

tag: cms class

tag: tumor stage

tag: gender

tag: t

value: Right

tag: adjuvant treatment


title: S526

description: from a individual donor

value: M


title: A581_coloncancer

tag: tissue

value: male

tag: n

value: moderate


title: GMP-GFP- small RNA 1-1

tag: cell subtype

tag: age

tag: strain


title: GMP-GFP- small RNA 2-3

tag: cell type


title: miRNA_HPV+OSCC_C3

value: HPV+


title: A803_coloncancer

value: colon cancer

value: female

tag: m

tag: differentiation grade

tag: tumor location

value: Left


title: A578_coloncancer


title: GMP-GFP+ small RNA 2-4

value: GMP-GFP+

value: 10-14 weeks


title: miRNA_HPV+OSCC_C2


title: S507

description: from a individual donor

tag: donor gender (m=male; f=female)

tag: donor age (yrs)


title: GMP-GFP+ small RNA 2-3

value: Ocn-GFPTopaz (Bilic-Curcic et al., 2005)

value: Mouse bone marrow granulocyte macrophage progenitors


title: S495

description: from a individual donor

tag: donor bmi (bmi kg/m2)


title: S487

description: from a individual donor

value: F


title: A561_coloncancer

tag: cms class

value: yes


title: S439

description: from a individual donor


title: GMP-GFP+ small RNA 1-2


title: A554_coloncancer

tag: tumor stage


title: S433

description: from a individual donor


title: GMP-GFP+ small RNA 1-3


title: A800_coloncancer

tag: gender


title: mRNA_HPV+OSCC_C3

data_processing:
the lncRNA-seq use PE150 (paired-end 150nt) sequencing for 12G raw data.
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts.
Quantification of the transcripts and genes was performed using StringTie software and Reads Per   Kilobase of transcript per Million mapped reads (RPKM) was obtained
Genome_build: homo_sapiens_Ensembl_97
Supplementary_files_format_and_content: Quantification of the transcripts and genes was performed using StringTie software and Reads Per Kilobase of transcript per Million mapped reads (RPKM) was obtained

extract_protocol:
Preparing selected tissue，flash frozen on dry ice, and RNA was harvested using trizol reagent.RNA library for lncRNA-seq was prepared as rRNA depletion and stranded method.After library construction, the concentration of library was measured by the Qubit® fluorometer and   adjusted to 1ng/uL. Agilent 2100 Bioanalyzer was deployed to examine the insert size of the acquired   library. At last, the accurate concentration of cDNA library was again examined using qPCR. Once   the insert size and concentration of the library was identical, the samples can then be subjected for   sequencing
After library preparation and pooling of different samples, the samples were subjected for Illumina   sequencing. Commonly, the lncRNA-seq use PE150 (paired-end 150nt) sequencing for 12G raw data

tag: hpv status


title: S418

description: S150 and S418 are from the same donor. Although from a different preparation.


title: mRNA_HPV-OSCC_C4

value: HPV-


title: mRNA_HPV-OSCC_C5

value: OSCC


title: mRNA_HPV+OSCC_C2


title: mRNA_HPV+OSCC_C1


title: Extracellular vesicles small RNA sequencing rep3

source_name: Mouse bone marrow Extracellular vesicles

extract_protocol:
Mouse BM extracellular vesicles were isolated from Ocn-GFP Topaz mice using the Exoeasy and miRneasy (Qiagen)
Small RNA libraries were constructed using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to manufacturer's instructions

value: Mouse bone marrow derived extracellular vesicles

value: Ocn-GFPTopaz (Bilic-Curci et al., 2005)


title: mRNA_HPV-OSCC_C6


title: A536_coloncancer

source_name: colon cancer, CMS2

extract_protocol: Genomic DNA was isolated from 30 µm frozen tissue sections using the Nucleospin Tissue kit according to the manufacturer’s instructions.

tag: t

value: Right

tag: adjuvant treatment


title: GMP-GFP+ small RNA 2-1


title: Extracellular vesicles small RNA sequencing rep2


title: S384

description: from a individual donor

value: Primary islet cells


title: Extracellular vesicles small RNA sequencing rep1


title: A564_coloncancer

tag: tissue

value: male

tag: n

value: moderate


title: A541_coloncancer

value: colon cancer

value: poor


title: miRNA_HPV+OSCC_C1

value: HPV+


title: A540_coloncancer


title: A559_coloncancer

value: female

value: Left


title: A529_coloncancer


title: A521_coloncancer


title: A481_coloncancer


title: shPIP4K2AB_uv_rep2

city: Chandigarh

first: Amit

last: Kumar

state: Chandigarh

address: Sector-39 A

institute: CSIR-IMTECH

description: Wild type U2OS cells

data_processing:
STAR is used to generate required genome files for alignment using fasta (GRCh38) and gtf file (Homo_sapiens.GRCh38.103.gtf)
STAR tool is used to align the filtered fastq files with reference genome. The genome files generated from the previous step and the following parameters are used for alignment ; - (STAR --runThreadN {} --genomeDir {} --sjdbGTFfile {}  --sjdbOverhang 100 --readFilesIn R1.fq.gz R2.fq.gz  --readFilesCommand zcat --outSAMtype BAM Unsorted --outFileNamePrefix {} --quantMode TranscriptomeSAM)
Samtools is used to sort and index the BAM files
RSEM (rsem-prepare-reference) is used to prepare reference files for transcript quantification using gtf and reference fasta file (rsem-prepare-reference --gtf $GTF-FILE $FASTA-FILE $NAME)
RSEM (rsem-calculate-expression) is used to calculate FPKM value using the aligned bam file and dependency files generated from the previous step. (rsem-calculate-expression --bam --no-bam-output -p 10 --paired-end $BAM $RSEM-DependencyfilePath $OUTDIRPATH)
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited text files (One file per sample) containing FPKM value for each gene

source_name: shPIP4K2A/2B_UV treated

growth_protocol: PIP4K stable knockdown U2OS cells were grown in DMEM high glucose media (Life techonolgies) supplemented with 10% FBS (Sigma), 1% penicillin-streptomycin (Life technologies) and 1μg puromycin.

extract_protocol:
Cell were washed with 1X PBS, trypsinized and collected. RNA was isolated suing Qiagen RNeasy kit.
1 μg total RNA was subjected to Ribo zero treatment with QIAseq FastSelect – rRNA HMR Kit (Qiagen, #334386) following library preparation. Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®).
Ready to run final libraries were quantified. To identify the insert size of the library, it was queried on Bioanalyser 2100 (Agilent) following manufacturers’ protocol.

treatment_protocol: Cells were UV-C irradiated without culture medium at 30J/m-2  intensity followed by media supplimentation and incubation in CO2 incubator for 6h.

tag: cell line

value: Sarcoma cell line

tag: genotype

tag: treatment

value: UV treated


title: S413

description: from a individual donor

source_name: Human Islets

tag: cell type

value: F


title: S395

description: from a individual donor


title: GMP-GFP+ small RNA 1-1

tag: cell subtype

value: GMP-GFP+

tag: age

value: 10-14 weeks

tag: strain

value: Ocn-GFPTopaz (Bilic-Curcic et al., 2005)

value: Mouse bone marrow granulocyte macrophage progenitors


title: S340

description: from a individual donor

tag: donor gender (m=male; f=female)

tag: donor age (yrs)


title: A534_coloncancer

data_processing:
Raw data was processed and normalised using the Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC (ChAMP) package in R [PMID: 24336642; PMID: 28961746]. This package contains functions for filtering low-quality probes, adjustment for Infinium I and Infinium II probe design, batch effect correction, and data normalisation. In short, bad quality probes (detection p value >0.01), probes containing SNPs, probes mapping to multiple locations, and probes mapping to chromosomes X and Y were removed, resulting in 429705 probes for further analysis. Data were normalised by Beta-Mixture Quantile (BMIQ) normalisation to correct for bias between type I and type II probe chemistry and potential batch effects were removed using Combat. The returned Beta values per probe represent the percentage of methylation for that particular CpG dinucleotide.
Processed file includes BMIQ-normalised Beta-values

tag: cms class

tag: m

tag: differentiation grade

tag: tumor location

value: yes


title: S426

description: from a individual donor

value: M

tag: donor bmi (bmi kg/m2)


title: S378

description: from a individual donor

value: Primary islet cells


title: S369

description: from a individual donor


title: GMP-GFP- rep4

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 reference genome mm10 using STAR
Transcript abundance was calculated using Htseq
Genome_build: mm10
Supplementary_files_format_and_content: count

extract_protocol:
Total RNA was extracted using miRNeasy micro kit (Qiagen)
RNA-Seq libraries were constructed from polyA-selected RNA using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs)

value: GMP-GFP-


title: GMP-GFP- rep3


title: shPIP4K2A_uv_rep2

description: Wild type U2OS cells

source_name: shPIP4K2A_UV treated


title: GMP-GFP+ small RNA 2-2


title: shPIP4K2B_uv_rep2

description: Wild type U2OS cells

source_name: shPIP4K2B_UV treated


title: plko_uv_rep2

description: Wild type U2OS cells

source_name: plko.puro_UV treated


title: GMP-GFP- rep2


title: S325

description: from a individual donor


title: shPIP4K2AB_rep2

description: Wild type U2OS cells

value: Control


title: GMP-GFP- rep1


title: S317

description: from a individual donor


title: A473_coloncancer

value: colon cancer

tag: tumor stage

tag: gender

value: male

tag: t

value: Right

tag: adjuvant treatment


title: A967_coloncancer

tag: tissue

value: female

tag: n

value: moderate


title: shPIP4K2B_rep2

description: Wild type U2OS cells

tag: cell line

tag: cell type

value: Sarcoma cell line

tag: genotype

tag: treatment


title: A479_coloncancer

value: Left


title: GMP-GFP+ rep4

tag: cell subtype

tag: age

tag: strain


title: A814_coloncancer

tag: cms class

tag: m


title: S297

description: from a individual donor

tag: donor gender (m=male; f=female)

tag: donor age (yrs)


title: A509_coloncancer

tag: tumor stage

tag: differentiation grade

tag: tumor location


title: GMP-GFP+ rep2


title: shPIP4K2A_rep2

description: Wild type U2OS cells


title: GMP-GFP+ rep3


title: S309

description: from a individual donor

tag: donor bmi (bmi kg/m2)


title: shPIP4K2AB_uv_rep1

description: Wild type U2OS cells

value: UV treated


title: GMP-GFP+ rep1

value: GMP-GFP+


title: shPIP4K2B_uv_rep1

description: Wild type U2OS cells


title: S284

description: from a individual donor

value: F


title: A572_coloncancer

tag: tissue

tag: gender

tag: t

tag: adjuvant treatment


title: shPIP4K2A_uv_rep1

description: Wild type U2OS cells

tag: cell line

tag: cell type

tag: genotype


title: A505_coloncancer

tag: n


title: S279

description: from a individual donor


title: plko_uv_rep1

description: Wild type U2OS cells

tag: treatment


title: WT_NestinCFP_Replicate2

city: Ann Arbor

first: Dogukan

last: Mizrak

state: MI

address: NCRC Building 26, 263S

department: Cardiac Surgery

institute: University of Michigan

data_processing:
Read 1 and read 2 fastq files were generated on basespace.
12-nt cell barcodes (CBs) and 8-nt unique molecular identifiers (UMIs) were extracted from read 1. Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded.
Trimmed reads were aligned to the Mus musculus genome and transcriptome annotation (GRCm38, Gencode annotation vM10) using STAR with parameters --sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted. Only reads with unique, strand-specific alignments to exons were kept for further analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: NestinCFP_all_matrix.txt: Gene expression matrix
Supplementary_files_format_and_content: NestinCFP_all_cell_ID.txt: This file contains ordered cell IDs for each cell in the gene expression matrix
Supplementary_files_format_and_content: NestinCFP_Cell_Barcodes.txt: This file contains ordered cell barcodes for each cell in the gene expression matrix

source_name: Cerebellum

extract_protocol:
mRNA molecules were captured using bead-bound oligo dT(30).
Captured mRNA molecules were reverse transcribed with template switching to obtain cDNA. cDNA was amplified by PCR reactions (14 cycles). Aliquots of amplified cDNA from each sample were pooled, and purified with AMPure XP beads. The purified PCR products were used as input for the Nextera XT reactions to generate the sequencing libraries.

value: Cerebellum

tag: age

tag: strain

value: NestinCFP/+

tag: number of cells analyzed

tag: number of animals


title: A503_coloncancer

tag: cms class

tag: tumor stage

tag: m

value: yes


title: S275

description: from a individual donor

tag: donor gender (m=male; f=female)

tag: donor age (yrs)

tag: donor bmi (bmi kg/m2)


title: A485_coloncancer

tag: tissue

tag: gender

tag: t

tag: differentiation grade

tag: tumor location


title: A469_coloncancer

tag: n

tag: adjuvant treatment


title: WT_NestinCFP_Replicate1

tag: age


title: IR_NestinCFP_Replicate2

tag: strain


title: plko_rep2

description: Wild type U2OS cells

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: S295

description: from a individual donor

value: M


title: A2217_coloncancer

tag: cms class

tag: tumor stage

tag: m

value: no


title: shPIP4K2AB_rep1

description: Wild type U2OS cells


title: A2215_coloncancer


title: shPIP4K2B_rep1

description: Wild type U2OS cells


title: S219

description: from a individual donor

value: Primary islet cells

tag: donor gender (m=male; f=female)

tag: donor age (yrs)

tag: donor bmi (bmi kg/m2)


title: TAT-09: Wild type Male_Chow_Liver

city: Los Angeles

first: Sanda

last: Win

state: CA

address: 2011 Zonal Ave

department: Medicine

institute: Univeristy of Southern California

description: Chow diet fed (up to age 16 week)

data_processing:
The analysis of RNA-seq data was conducted using the RNA-seq workflow in Partek Flow software (v9. Partek Inc., St. Louis, MO, USA)
Raw sequencing reads were first subjected to sequencing quality score based trimming (Phred QC>=20, min read length=25nt)
Trimmed reads were aligned to mm10 using STAR 2.7.3a with default settings
Aligned reads were quantified to Gencode vM24 using Partek E/M
Genes with fewer than 10 aligned reads in any sample among a data set were excluded, remaining genes were normalized using the Upper Quartile method and subjected to differential expression analysis using Partek Gene Specific Analysis method
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file with raw read counts in all samples

source_name: Liver

extract_protocol:
RNA was isolated from snap frozen tissue using the miRNeasy Mini Kit (QIAGEN) according to manufacturer’s instruction with an elution volume of 45 µl. The library preparation was done using TruSeq® stranded total RNA sample preparation kit with rRNA depletion (Illumina inc). Briefly, the starting material (100 ng) of total RNA was rRNA depleted using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads.
The isolated RNA was subsequently fragmented using enzymatic fragmentation. Then first strand synthesis and second strand synthesis were performed and the double stranded cDNA was purified (AMPure XP, Beckman Coulter). The cDNA was end repaired, 3’ adenylated and Illumina sequencing adaptors ligated onto the fragment ends, and the library was purified (AMPure XP). The RNA stranded libraries were pre-amplified with PCR and purified (AMPure XP). The libraries’ size distribution was validated and quality inspected on a 4200 TapeStation (Agilent Technologies). High quality libraries were pooled in equimolar concentrations based on the Bioanalyzer automated electrophoresis system (Agilent Technologies). The library pool(s) were quantified using qPCR and optimal concentration of the library pool used to generate the clusters on the surface of a flow cell before sequencing on a NextSeq500 instrument (2x75 cycles) according to the manufacturer instructions (Illumina Inc.).

treatment_protocol: Chow diet versus HFHC diet

value: C57BL/6N (Envigo)

value: 16 weeks

tag: Sex

value: Male

tag: tissue

value: Liver


title: S181

description: from a individual donor


title: S180

description: from a individual donor


title: A2211_coloncancer

value: colon cancer

tag: gender

value: female

tag: t

tag: differentiation grade

value: poor

tag: tumor location


title: S233

description: from a individual donor


title: TAT-08: Wild type Male_Chow_Liver

description: Chow diet fed (up to age 16 week)

tag: strain

tag: age


title: A2209_coloncancer

value: male

tag: n

value: moderate

value: Right

tag: adjuvant treatment


title: TAT-07: Wild type Male_Chow_Liver

description: Chow diet fed (up to age 16 week)


title: shPIP4K2A_rep1

description: Wild type U2OS cells

tag: cell line

tag: cell type

value: Sarcoma cell line

tag: genotype

tag: treatment

value: Control


title: plko_rep1

description: Wild type U2OS cells


title: S170

description: from a individual donor

tag: donor gender (m=male; f=female)


title: TAT-03: Wild type Male_HFHC_Liver

description: HFHC diet fed (from age 8week to 16 week)


title: DOGMA-LLL_MAESTER

first: Peter

last: van Galen

state: Massachusetts

address: 4 Blackfan Circle

department: Hematology

institute: Brigham and Women's Hospital / Broad Institute of MIT and Harvard

data_processing:
Library strategy: MAESTER
Demultiplexing using Illumina bcl2fastq2 v2.20.0
Alignment using STAR 2.7.2a or CellRanger version 3.1.0 or CellRanger-Arc
Generate single-cell expression matrix using custom scripts or CellRanger version 3.1.0 or CellRanger-Arc
MAESTER: generate single-cell variant call matrix using maegatk version 0.0.2
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression matrices, metadata, maegatk rds output with variant counts

source_name: Peripheral blood mononuclear cells

extract_protocol:
mRNA and mitochondrial mRNA was extracted by hybridization to polyT oligos on Seq-Well or 10x beads. DNA for ATAC-seq was extracted using the 10x multiome protocol with adaptations as described in DOGMA-Seq (Mimitou et al., Nat Biotech 2021).
Seq-Well S3 and 10x 3' v3 single-cell RNA-sequencing library construction methods were utilized for mRNA libraries. MAESTER was used to enrich and sequence mitochondrial mRNA. The 10x Genomics multiome protocol was used for the multiome samples.

tag: technology

value: MAESTER


title: A2207_coloncancer

last: Smid

tag: cms class

tag: tumor stage

tag: m

value: Left


title: DOGMA-LLL_scRNAseq

data_processing:
Demultiplexing using Illumina bcl2fastq2 v2.20.0
Alignment using STAR 2.7.2a or CellRanger version 3.1.0 or CellRanger-Arc
Generate single-cell expression matrix using custom scripts or CellRanger version 3.1.0 or CellRanger-Arc
MAESTER: generate single-cell variant call matrix using maegatk version 0.0.2
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression matrices, metadata, maegatk rds output with variant counts

value: DOGMA-Seq - RNA


title: TAT-02: Wild type Male_HFHC_Liver

tag: Sex

tag: tissue


title: IR_NestinCFP_Replicate1

value: Cerebellum

tag: gender

value: NestinCFP/+

tag: number of cells analyzed

tag: number of animals


title: DOGMA-LLL_scATACseq

value: DOGMA-Seq - ATAC


title: S252

description: from a individual donor

value: Primary islet cells

value: M

tag: donor age (yrs)

tag: donor bmi (bmi kg/m2)


title: A2206_coloncancer

tag: t

tag: n

tag: differentiation grade

tag: tumor location

tag: adjuvant treatment

value: no


title: MGH252-PBMC_SW_MAESTER

source_name: Glioblastoma - PBMCs


title: S135

description: from a individual donor

tag: cell type

tag: donor gender (m=male; f=female)


title: A2203_coloncancer

value: colon cancer

tag: cms class

value: good


title: TAT-01: Wild type Male_HFHC_Liver

tag: strain

value: C57BL/6N (Envigo)

tag: age

value: 16 weeks

value: Male

value: Liver


title: MGH252-C_SW_MAESTER

source_name: Glioblastoma - site B

tag: technology


title: ChIP ZT21

city: Houston

first: Chih-Liang

last: Tien

state: TX

address: 1 Baylor Plaza , room 441E

institute: BCM

data_processing:
Non-redundant and uniquely mapped reads were extended to 100bp in both 5' and 3' direction and used for downstream analysis. Read coverage for every 10bp bins were calculated using deepTools bamCoverage (version 3.3.0) function avoiding blacklist regions of the mouse genome (ENCODE project) and genome browser tracks were visualized in Integrative Genome Browser (IGV version 1.5). Peak calling was performed on unique reads with Macs2 (2.1.2) using input as control. Peaks with q > 0.05 and local fold change 4 were used for comparison between ZT9 and ZT21. Common and differential peaks at ZT9 and ZT21 were defined by at least a basepair overlap between peaks using the intersect function of Bedtools v2.26.0
Genome_build: mm10
Supplementary_files_format_and_content: Read coverage for every 10bp bins were calculated using deepTools bamCoverage (version 3.3.0) function avoiding blacklist regions of the mouse genome (ENCODE project) and genome browser tracks were visualized in Integrative Genome Browser (IGV version 1.5). Peak calling was performed on unique reads with Macs2 (2.1.2) using input as control. Peaks with q > 0.05 and local fold change 4 were used for comparison between ZT9 and ZT21. Common and differential peaks at ZT9 and ZT21 were defined by at least a basepair overlap between peaks using the intersect function of Bedtools v2.26.0

source_name: Heart

growth_protocol: All mice were group housed (3-4 mice per cage) in a 12-12 light-dark (7am - 7pm)

extract_protocol:
Nuclei was isolated and purified by PCM-1 antibody, Reverb was pulldown by antibody
ChIP-Seq library prep with 1.0 ng input ChIP-DNA into Rubicon's ThruPlex DNA-Seq library prep kit (protocol p/n QAM-108-002)

tag: antibody

value: Rev-erb


title: S126

description: from a individual donor


title: MGH252-A_SW_MAESTER

source_name: Glioblastoma - site A


title: S122

description: from a individual donor

value: F


title: BPDCN712_10x_GoT_Rxn4.1_ASXL1-1886

source_name: Bone marrow hematopoietic cells

value: Genotyping of Transcriptomes


title: Input ZT 9


title: S115

description: from a individual donor


title: A2202_coloncancer

city: Rotterdam

first: Marcel

address: Dr. Molewaterplein 50

institute: Erasmus MC

tag: tissue

tag: tumor stage

tag: gender

value: female

tag: m

value: moderate

value: Left


title: A2190_coloncancer

value: male


title: A2128_coloncancer

source_name: colon cancer, CMS3

value: poor

value: Right


title: Input ZT21


title: S46

description: from a individual donor

value: Primary islet cells

tag: donor age (yrs)

tag: donor bmi (bmi kg/m2)


title: A2121_coloncancer

tag: t

tag: n

value: no


title: A2126_coloncancer

value: colon cancer

tag: differentiation grade

tag: tumor location


title: N16-77-RNA-116120

last: Ghiringhelli

data_processing:
Pseudo alignment and quantification were performed using kallisto 0.45
Genome_build: GRCh37
Supplementary_files_format_and_content: Processed data file is a csv file containing TPM expression values

source_name: biopsy

extract_protocol:
Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tumor slices (5 × 5 µm) using the Maxwell 16 LEV RNA FFPE Purification kit (Promega) following manufacturer instructions
Libraries were prepared from 12 µl of total RNA with the TruSeq Stranded Total RNA using Ribo-Zero (Illumina) following manufacturer instructions

value: lung tumor tissue

tag: disease state

value: squamous


title: N16-45-RNA-116132


title: BPDCN712_10x_GoT_Rxn3_TET2-3626_ASXL1-1898


title: S150

data_processing:
Strand Next-generation sequencing (NGS) version 2.5 software was used to analyse the RNA-Seq data
Alignment: Reads were aligned to the human hg38 transcriptome and genome with novel splices using the Ensembl genes and transcript (2016.12.01) model.
Alignment: Raw reads were aligned with a minimum of 90 percent identity, maximum five percent gaps and a minimum match length of 25 base pairs.
Alignment trimming: The read pairs output with more than five valid matches were not reported. Quality trimming was applied to trim 3’ end with an average quality less than 10 and on poorly aligned portion at 3’ end post alignment.
Filtering: Raw reads with an average base quality below 20 and reads which have failed quality control (QC) were removed.
Generation of normalized abundance: Normalized values were calculated using the Deseq algorithm, with the threshold normalized count set at 1 and no baseline transformation.
Genome_build: hg38
Supplementary_files_format_and_content: hg38-islets-deseq-all-entities.xlsx

extract_protocol:
RNA was extracted using TRIzol® RNA Isolation (Thermo Fisher Scientific, Waltham, MA) protocol with minor modification (Joglekar et al. 2012)
Sequencing libraries were generated using the rRNA-depleted RNA with the NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) through following manufacturer’s protocol.

tag: cell type

tag: donor gender (m=male; f=female)

value: M


title: BPDCN712_10x_GoT_Rxn4_TET2-4104_ASXL1-1898


title: S21

description: from a individual donor


title: A2115_coloncancer

tag: cms class

tag: adjuvant treatment


title: ChIP ZT9

tag: strain


title: BPDCN712_10x_GoT_Rxn2_TET2-3078_ASXL1-1898

tag: technology


title: Input

first: Parijat

last: Senapati

address: Jakkur

institute: Jawaharlal Nehru Centre for Advanced Scientific Research

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie2 (version 2.3.4) with the --local and -N 1 parameters. RNA-seq reads were aligned to the hg19 genome assembly using HISAT2 2.1.0 using default parameters. Stringtie 1.3.4 was used with default parameters to assemble transcripts and merged using --merge option in Stringtie.
peaks were called using MACS2 version 2.1.1.20160309 with broad peak calling option and q < 0.1 for broad regions and q < 0.05 for narrow regions
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq: Peak files in BED format. RNA-seq: tab-delimited text files include raw counts for each transcript in each sample

source_name: Cervical cancer cells

growth_protocol: HeLa S3 cells and shNPM1-AW13516 cells  were maintained in DMEM and MEM respectivley supplemented with 10% heat-inactivated Fetal Bovine Serum (v/v) and 1X antibiotics containing penicillin and streptomycinat 37°C, 5% CO2 in a humidified chamber.

extract_protocol:
Chromatin lysates were clarified from sonicated cells and histone-DNA complexes were isolated with AcNPM1 antibodies.
ChIP-seq and RNA-se libraries were made using Illumina Tru-Seq library preparation kit and multiplexing barcodes compatible with Illumina HiSeq 2500 technology. RNA-seq libraries were prepared using Kapa Hyper Prep Kit (Kapa Biosystems) and sequenced on Illumina HiSeq 4000 sequencer.

treatment_protocol: Insulin treatment, MDA-MB-231 cells were serum depleted in DMEM high glucose medium containing 0.2% BSA for 24h and stimulated without (untreated) or with 100 nM Insulin for indicated time periods.

tag: cell line

value: HeLa S3

tag: passages

tag: antibody

value: input

tag: treatment


title: N16-309-RNA-121159

first: François

address: 1 rue du Professeur Marion

institute: UMR INSERM 1231

tag: tissue


title: BPDCN712_10x_GoT_Rxn1_TET2-2340_ASXL1-1898


title: AcNPM1 ChIP rep2


title: A2111_coloncancer

source_name: colon cancer, CMS2

tag: tumor stage

tag: gender

tag: m


title: BPDCN712_10x_MAESTER

value: MAESTER


title: AcNPM1 ChIP rep1


title: A2109_coloncancer

tag: t

tag: n

tag: differentiation grade


title: N16-284-RNA-121157

tag: disease state


title: BPDCN712_10x_scRNAseq

value: 10x 3' v3 scRNA-seq


title: HSMM 3

first: Reshma

last: Taneja

address: 2 Medical Drive, MD9

department: Physiology

institute: National University of Singapore

description: processed data file :  HSMM_and_SJ_ARMS_all_readcounts.csv

data_processing:
Raw base call files from HiSeq 4000 were demultiplex with bcl2fastq v2.20 and fastq files were subjected to QC with FastQC.
The paired fastq files were aligned to GRCh38 with STAR-2.7.8a, with -quantMode GeneCounts enabled to quantify read counts from BAM alignments.
The gene read count tab delimited files (TSV) were consolidated with Modern CSV v1.3.23 to produce a combined comma delimited file (CSV), with readcounts for all genes across all conditions.
The CSV readcount file was imported into  iDep0.91, and differential expression analysis was performed with DESeq2 within iDep0.91, comparing the read counts of siEHMT1 versus siSCR to obtain differentially expressed genes (DEGs) beyond a fold change of ±1.2 and p-adj < 0.05.
Functional analysis of DEGs with Gene ontology terms and KEGG terms was performed with ShinyGO v0.61, with a gene set cut-off of p-adj < 0.05.
For HSMM samples, fastq files were aligned to GRCh38 with STAR and read counts were quantified with HTseq.
Raw read counts from HSMM samples were consolidated with read counts from 32 ARMS patient RNA-seq samples and imported into DESeq2 and normalized with DESeq2's estimateSizeFactors() function. Normalized counts from DESeq2 were used to plot  bargraphs  showing EHMT1 gene expression median, upper and lower quantile values.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: comma-separated value files with gene readcounts

source_name: Skeletal Muscle Myoblast

growth_protocol: ARMS cell line, RH41  were cultured in Roswell Park Memorial Institute (RPMI) – 1640 medium with L Glutamine, 10% Fetal Bovine Serum (FBS) and 1% Penicillin-Streptomycin. While, Human skeletal muscle myoblast (HSMM) cells were grown in skeletal muscle cell growth medium (ZenBio, # SKM-M).  All the cells were grown in 2D adherent plate and passaged routinely.

extract_protocol:
Cells were lysed with Trizol reagent followed by RNA extraction and cleanup. RNA purity and integrity were assessed with Nanodrop and Agilent 2100 respectively. mRNA is purified from total RNA using poly-T oligo-attached magnetic beads.The mRNA is first fragmented randomly by addition of fragmentation buffer.
RNA libraries were prepared for sequencing using NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol: RH41 cells (0.28 x 10^6) were transfected with non-target siRNA  (siControl) and EHMT1 specific siRNA (siEHMT1) using lipofectamine RNAiMAX for 48 hours. While, HSSMM did not undergo any treatment procedures

value: HSMM primary cell line

tag: genotype

value: no treatment


title: A2092_coloncancer

tag: cms class

value: good

tag: tumor location


title: HSMM 2


title: HSMM 1


title: K562-BT142_10x_scRNAseq

source_name: K562 and BT142 cell line mix


title: N16-274-RNA-251251


title: N16-292-RNA-121158


title: N16-274-RNA-116116


title: K562-BT142_10x_MAESTER


title: K562-BT142_SW_MAESTER


title: RH41 siControl 3

description: processed data file :  RH41_siEHMT1_vs_siControl_readcounts.csv

source_name: Alveolar Rhabdomyosarcoma

value: patient-derived RD cell line

value: siControl


title: A2086_coloncancer

value: male

value: moderate

value: Left

tag: adjuvant treatment


title: A2088_coloncancer

value: no


title: N16-159-RNA-116131


title: Healthy_8_Healthy_9_PBMC_GEX

city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

description: gene expression feature barcode matrix

data_processing:
Demultiplexing raw reads with bcl2fastq2 (Illumina, v2.20.0)
Cellranger count (10X Genomics, v3.1.0) to generate feature barcode matrices
CITEseqCount (v1.4.3) to identify TotalSeq-C associated UMI counts for sample demultiplexing
Creation of unified feature barcode expression matrix with Seurat (v3.1.2) in R (v.3.6.0)
Genome_build: GRCh38 + SARS-COV-2 (NC_045512.2)
Supplementary_files_format_and_content: Feature barcode expression matrices create with bcl2fastq and CellRanger Count
Supplementary_files_format_and_content: CITEseq feature barcode matrix
Supplementary_files_format_and_content: gene expression feature barcode matrix

extract_protocol:
Peripheral blood mononuclear cells were isolated from whole blood by density grandient centrifugation, then washed with Hank's Buffered Saline Solution followed red blood cell lysis using BD Pharm Lyse. Cell were then counted using a Nexcelom Cellometer with acridine orange/propidium iodide for live/dead discrimination. Endotracheal aspirates were extensively diluted with Hank's Buffered Saline Solution, followed by pipetting repeatedly to break up sputum and create single-cell suspensions. Red blood cells were lysed using BD Pharm Lyse.
Single cell suspensions of peripheral blood mononuclear cells or endotracheal aspirates were resuspended in 0.04% PBS/BSA and loaded on a 10X Genomics Chip A for use with the 5prime V1 chemsitry kit. In some instances samples were labeled with TotalSeq-C cell hashiing antibodies, and two samples were pooled prior to loading cells for droplet generation. Gene expression and cell hashing libraries were generated following the manufacturer's protocols.

tag: time point

tag: disease

value: Healthy donor

value: Peripheral blood mononuclear cells


title: RH41 siControl 2

tag: cell line


title: A2104_coloncancer

value: colon cancer


title: N16-135-RNA-116123

city: DIJON

value: lung tumor tissue

value: non-squamous


title: N15-504-RNA-116126


title: A2080_coloncancer

value: female


title: RH41 siControl 1

city: Singapore


title: Healthy_7_ARDS_3_day_1_PBMC_GEX

description: gene expression feature barcode matrix

value: NA, day 1


title: Healthy_5_Healthy_6_PBMC_GEX

description: gene expression feature barcode matrix


title: RH41 siEHMT3


title: N16-276-RNA-121155


title: Healthy_3_Healthy_4_PBMC_GEX

description: gene expression feature barcode matrix


title: RH41 siEHMT2


title: N15-479-RNA-116127

value: squamous


title: Healthy_10_ARDS_5_day_1_PBMC_GEX

description: gene expression feature barcode matrix

value: Healthy donor, Acute respiratory distress syndrome


title: N15-443-RNA-116119


title: A1838_coloncancer

value: Right


title: N15-243-RNA-116125


title: A1848_coloncancer

value: good


title: Dox rep2 RNA

source_name: Oral cancer cells

extract_protocol:
Chromatin lysates were clarified from sonicated cells and histone-DNA complexes were isolated with AcNPM1 antibodies.
ChIP-seq and RNA-seq libraries were made using Illumina Tru-Seq library preparation kit and multiplexing barcodes compatible with Illumina HiSeq 2500 technology. RNA-seq libraries were prepared using Kapa Hyper Prep Kit (Kapa Biosystems) and sequenced on Illumina HiSeq 4000 sequencer.

tag: passages

value: Doxycycline treatment for 48 hrs


title: A1836_coloncancer


title: RH41 siEHMT1

value: patient-derived RD cell line


title: N15-220-RNA-116118


title: A1834_coloncancer


title: COVID_8_day_5_PBMC_GEX

description: gene expression feature barcode matrix

value: day 5


title: A1828_coloncancer

value: moderate


title: UT rep2 RNA

tag: treatment


title: COVID_8_day_1_COVID_9_day_1_PBMC_GEX

description: gene expression feature barcode matrix

value: day 1

tag: tissue


title: A1824_coloncancer

tag: tumor stage

value: Left

value: no


title: N15-198-RNA-116128


title: UT rep1 RNA


title: N15-178-RNA-116122


title: A1595_coloncancer

tag: gender


title: bHLH60-IP

city: Shanghai

first: Chuanwei

last: Yang

address: 2005 Songhu Road, Yangpu District

department: school of life sciences

institute: Fudan university

data_processing:
Raw sequence reads were initially processed by FastQC for quality control, and then adapter sequences and poor quality reads were removed by using Trimmomatic.
Quality filtered reads were then mapped to Tair10 reference genome using BWA (0.7.10), and only uniquely mapped reads were kept.
Sam files were converted to Bam format using Samtools and used for peak calling. MACS2 (2.1.1) was used to call peaks and an initial threshold q-value of 0.05 as cutoff.
Visualization of read count data was performed by converting raw bam files to bigwig files using IGV tools.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files

organism: Arabidopsis thaliana

source_name: 8-day-old white light-grown with 1hr shade treatment seedlings

growth_protocol: 8-day-old white light-grown 35S::PIF7-Flash and 35S::bHLH60-Flag seedlings treated with 1 hr shade.

extract_protocol:
Sample extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NovaSeq  following the manufacturer's protocols.

treatment_protocol: With 1 hr shade (R/FR=0.4) treatment.

tag: genotype/variation

value: whole seedlings

tag: age

value: 8 days

value: 1 hr shade

tag: chip antibody

value: anti-FLAG


title: COVID_7_day_10_PBMC_ETA_GEX

description: gene expression feature barcode matrix

source_name: Peripheral blood mononuclear cells, endotracheal aspirate

value: day 10


title: Healthy_1_Healthy_2_PBMC_GEX

description: gene expression feature barcode matrix

value: Healthy donor

value: Peripheral blood mononuclear cells


title: A1593_coloncancer

value: colon cancer

value: female

tag: t

tag: n

tag: m

tag: differentiation grade


title: COVID_6_day_10_COVID_18_day_1_PBMC_GEX

description: gene expression feature barcode matrix

value: day 1, day 10


title: COVID_7_day_1_day_5_PBMC_GEX

description: gene expression feature barcode matrix

value: day 1, day 5


title: A2082_coloncancer

tag: cms class

value: male

tag: tumor location

value: Right


title: Dox rep1 RNA

value: Doxycycline treatment for 48 hrs


title: N15-158-RNA-116124

value: lung tumor tissue

tag: disease state

value: squamous


title: COVID_5_day_1_day_5_PBMC_GEX

description: gene expression feature barcode matrix

tag: time point

tag: disease


title: COVID_6_day_1_day_5_PBMC_GEX

description: gene expression feature barcode matrix


title: PIF7-IP

value: anti-Myc


title: PIF7-Input

value: whole seedlings


title: N15-154-RNA-116130


title: A1591_coloncancer

value: moderate

value: Left

tag: adjuvant treatment

value: no


title: 16008668


title: N15-205-RNA-116129

value: non-squamous


title: bHLH60-Input

value: 8 days

tag: treatment

value: 1 hr shade


title: 16008059

tag: tissue


title: COVID_4_day_10_PBMC_GEX

description: gene expression feature barcode matrix

value: day 10

value: Peripheral blood mononuclear cells


title: A1578_coloncancer

value: colon cancer

tag: tumor stage


title: A1585_coloncancer

tag: gender

value: female


title: CT2_RNAseq_rep2

city: Beijing

first: Huayang

address: Haidian strict, Xiang Mountain South Road, Xiang Mountain South Village 20#

department: Institute of Botany

institute: University of Chinese Academy of Sciences

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 grape whole genome using TopHat v2.1.1 with parameters -r 200 --library-type fr-unstranded -i 45 -I 5000 --min-segment-intron 45 --max-segment-intron 5000
FragmentsPer Kilobase per Million (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: grape

organism: Vitis amurensis

source_name: in vitro plants

growth_protocol: In vitro plants of V. amurensis were subcultured monthly in half strength B5 medium (PhytoTech Lab, USA)supplemented with 0.2 mg/L IBA under 16/8 (light/dark) condition

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: in vitro plants with uniform growth status were transferred to a prechilled incubator set to 4°C and constant light (approximately 100 μmol m-2 s-1). Samples were collected at 2 h after cold treatment (CT2). Untreated plants cultured at 26°C under the same light condition were sampled as the control (WT0).

value: leaf

tag: genotype

value: Wild-type

value: one-month-old

value: cold stress


title: CT2_RNAseq_rep3

tag: age


title: 16007916

value: lung tumor tissue


title: A1583_coloncancer

value: Right


title: CT2_RNAseq_rep1


title: 16007195

value: squamous


title: A1462_coloncancer

value: male

value: moderate


title: A1442_coloncancer

value: no


title: WT0_RNAseq_rep3

value: control


title: 16000827

value: non-squamous


title: N15-173-RNA-116117


title: A1125_coloncancer


title: COVID_3_day_1_COVID_4_day_1_PBMC_GEX

description: gene expression feature barcode matrix

source_name: Peripheral blood mononuclear cells

value: day 1


title: COVID_22_day_5_PBMC_GEX

description: gene expression feature barcode matrix

value: day 5


title: COVID_24_day_1_PBMC_ETA_GEX

description: gene expression feature barcode matrix

value: Peripheral blood mononuclear cells, endotracheal aspirate


title: 15005773A


title: COVID_4_day_5_COVID_10_day_1_PBMC_GEX

description: gene expression feature barcode matrix

value: day 1, day 5

value: Peripheral blood mononuclear cells


title: WT0_RNAseq_rep1

value: leaf


title: 15012306


title: COVID_22_day_10_PBMC_GEX

description: gene expression feature barcode matrix

value: day 10


title: vom3

first: Qing

last: Cui

state: Shanghai

address: Dongfang Lu No.1678

institute: Shanghai Children′s Medical Center Affiliated to Shanghai Jiaotong University School of Medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b)  (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the  DESeq2 R package (1.20.0).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was  implemented by the clusterProfiler R package, in which gene length bias  wascorrected.We used clusterProfiler R package to test the  statistical enrichment of differential expression genes in KEGG pathways.
GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were  filtered with GATK standard filter method and other parameters (cluster:3;  WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10 and SnpEff software was used to  annotation for the Variablesite).
Genome_build: GCA_000001895.4
Supplementary_files_format_and_content: FPKM

organism: Rattus norvegicus

source_name: RV free wall myocardium

extract_protocol:
Myocardium of RV free wall was rapidly removed from executed rat and flash frozen in -80? refrigerator , RNA was harvested using Trizol reagent.
A total amount of 1 ?g RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: strain

value: SD

value: myocardium

tag: treatment method

value: volume overload(AVF)

tag: treatment  age

value: postnatal day 1

tag: test age

value: postnatal day 7


title: A1121_coloncancer

value: colon cancer

value: female

tag: t

tag: n

tag: m

tag: differentiation grade

value: Left


title: 15000683

value: lung tumor tissue

tag: disease state

value: squamous


title: COVID_22_day_1_PBMC_GEX

description: gene expression feature barcode matrix

tag: time point

value: day 1

tag: disease


title: vom2


title: COVID_4_day_10_ETA_GEX

description: gene expression feature barcode matrix


title: 15001489

value: non-squamous


title: vom1


title: COVID_21_day_10_PBMC_GEX

description: gene expression feature barcode matrix


title: A9389_coloncancer

tag: cms class

value: male

value: moderate

tag: tumor location

tag: adjuvant treatment

value: no


title: A9395_coloncancer

tag: tissue

tag: tumor stage

tag: gender

value: good

value: Right


title: A9372_coloncancer


title: A2071_coloncancer


title: 14014368


title: COVID_21_day_1_PBMC_ETA_GEX

description: gene expression feature barcode matrix

value: Peripheral blood mononuclear cells, endotracheal aspirate


title: sham3

tag: strain

value: SD

value: myocardium

value: operated-sham


title: WT0_RNAseq_rep2

last: Li

value: leaf

tag: genotype

value: Wild-type

tag: age

value: one-month-old

tag: treatment

value: control


title: A9360_coloncancer

value: colon cancer

tag: t

value: Left


title: COVID_23_day_1_COVID_20_day_1_PBMC_GEX

description: gene expression feature barcode matrix

value: day 1

value: Peripheral blood mononuclear cells


title: 14008707

value: lung tumor tissue

value: non-squamous


title: sham2

tag: treatment method

tag: treatment  age

value: postnatal day 1

tag: test age

value: postnatal day 7


title: A9319_coloncancer

value: male

tag: n

tag: m

tag: differentiation grade

value: moderate

value: no


title: 14000702

tag: disease state

value: squamous


title: COVID_2_day_10_ARDS_2_day_1_PBMC_GEX

description: gene expression feature barcode matrix

tag: time point

value: day 1, day 10

tag: disease

value: Acute respiratory distress syndrome, COVID-19


title: COVID_2_day_1_day_5_PBMC_GEX

description: gene expression feature barcode matrix

value: day 1, day 5

tag: tissue


title: 13013321


title: T24_TCP3

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Pseudo alignment and quantification were performed using kallisto 0.45
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed data file is a csv file containing TPM expression values

source_name: LLC1 cells

extract_protocol: RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: cell line

value: LLC1 cells

value: Cisplatin-Pemetrexed + Trametinib

tag: time

value: 24 hours


title: MGH252-PBMC_SW_scRNAseq

source_name: Glioblastoma - PBMCs

tag: technology

value: Seq-Well S3


title: A9210_coloncancer

extract_protocol: Genomic DNA was isolated from 30 µm frozen tissue sections using the Nucleospin Tissue kit according to the manufacturer’s instructions.

value: colon cancer

tag: cms class

tag: tumor stage

tag: gender

value: female

tag: tumor location

value: Left

tag: adjuvant treatment


title: MGH252-C_SW_scRNAseq

description:
MGH252_A_C_Expression.txt
MGH252_A_C_PBMC_MetaData.txt

source_name: Glioblastoma - site B


title: sham1

tag: strain

value: SD

value: myocardium

tag: treatment method

value: operated-sham

tag: treatment  age


title: T24_TCP2

tag: treatment


title: COVID_20_day_5_COVID_19_day_5_PBMC_GEX

description: gene expression feature barcode matrix

value: day 5

value: Peripheral blood mononuclear cells


title: T24_T3

value: Trametinib


title: K562_bulk_ATAC

value: ATAC-Seq


title: T24_T2


title: COVID_19_day_10_PBMC_GEX

description: gene expression feature barcode matrix

value: day 10


title: COVID_18_day_5_PBMC_ETA_GEX

description: gene expression feature barcode matrix

value: Peripheral blood mononuclear cells, endotracheal aspirate


title: MGH252-A_SW_scRNAseq

source_name: Glioblastoma - site A


title: COVID_19_day_1_PBMC_GEX

description: gene expression feature barcode matrix

value: day 1


title: T24_T1

value: LLC1 cells


title: COVID_18_day_10_PBMC_ETA_GEX

description: gene expression feature barcode matrix


title: K562-BT142_SW_scRNAseq


title: T24_CP3

value: Cisplatin-Pemetrexed


title: A00830102

city: Sherbrooke

first: Laurence

last: Faucher-Giguère

state: Québec

address: 3201 rue jean Mignault

department: Microbiology and Infectiology

country: Canada

institute: Université de Sherbrooke

description: cDNA library generated with TGIRT

data_processing:
Fastq files were checked for quality using FastQC v0.11.15 and trimmed using Cutadapt v1.18 and Trimmomatic v0.36with TRAILING:30 to remove Illumina sequencing adapters and portions of reads of low quality, respectively. Reads were aligned using STAR v 2.6.1a with the following options:  --outFilterScoreMinOverLread 0.3, --outFilterMatchNminOverLread 0.3, --outFilterMultimapNmax 100, --winAnchorMultimapNmax 100, --alignEndsProtrude 5 ConcordantPair. Only primary alignments were kept using samtools view -F 256 (v1.5).
The alignments (BAM) of samples LGr RT157 and LGr RT353 from individual lanes were merge together using samtools merge (v1.5).
The gene quantification was done using CoCo correct_count module (v.0.2.0) with the option -s 1 and -p.
DESeq2 was used for differential expression analysis using raw counts obtained by CoCo.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix tables with raw gene counts and CPM  for every gene and every sample

source_name: Ovary

extract_protocol:
HGSC and SBT tissues were obtained from the FRQS tissue bank (Université de Sherbrooke), the Ontario Tumor Bank (OTB) and the Alberta Research Tumor Bank (ARTB). Each 30 mg tissue sample was homogenized in 1 mL of TRIzol Reagent (Ambion) using a Polytron tissue homogenizer. RNA was isopropanol precipitated and resuspended in water and stored at −80°C. RNA integrity and concentration was assessed using the 2100 Bioanalyzer (Agilent).
The prepared libraries were ribodepleted using the Illumina Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat). The ribodepleted RNA was purified with Zymo RNA Clean & Concentrator using a modified form of the protocol to conserve small RNAs (8X sample volume of 95-100% ethanol instead of 3X). Nonfragmented, ribodepleted RNA was then used as input for TGIRT template-switching reactions with 1 µM TGIRT-III RT (InGex, LLC) for 15 min at 60°C, as previously described (Qin et al. 2016). During the template-switching reaction, a starting molecule composed of a DNA oligonucleotide encoding the reverse complement of an Illumina Read 2 sequencing primer binding site annealed to an RNA oligonucleotide such that there is a single nucleotide 3’ DNA overhang. This overhang (an equimolar mix of A, T, G, C) anneals to the 3’ end of a target RNA molecule, which upon addition of dNTPs, causes TGIRT to initiate cDNA synthesis, resulting in seamless addition of the adapter sequence to the 5’ end of the cDNA. After cDNA cleanup with QIAGEN MinElute Enzyme Reaction Cleanup kit, purified cDNAs are then ligated at their 3’ ends to a 5’-adenylated DNA oligonucleotide encoding the reverse complement of an Illumina Read 1 sequencing primer binding site. Finally, index and capture sequences required for Illumina sequencing are added by PCR (12 cycles). Libraries were size-selected with AMPure XP beads (Beckman Coulter) and library quality was evaluated using an Agilent 2100 Bioanalyzer. TGIRT-seq libraries were sequenced on an Illumina HiSeq 4000 or 2500 instrument (PE 2x150 and PE 2x125, respectively) at the Genome Sequencing and Analysis Facility (GSAF) at the University of Texas at Austin.
TGIRT-Seq

value: High grade serous carcinoma tissue


title: COVID_17_day_10_PBMC_GEX

description: gene expression feature barcode matrix


title: HGr OVC563 OG

description: cDNA library generated with TGIRT


title: T24_TCP1

value: Cisplatin-Pemetrexed + Trametinib

value: 24 hours


title: COVID_17_day_1_day_5_PBMC_GEX

description: gene expression feature barcode matrix

value: day 1, day 5


title: T24_CP2


title: stimulated PBMCs of HC, biological rep1

city: Xindu district, Chengdu city

first: Mao

last: Lu

state: Sichuan

address: Baoguang Road middle segment

department: Department of Dermatovenereology,

institute: The First Affiliated Hospital, Chengdu Medical College, Chengdu, China

description: gene expression in stimulated  PBMCs with M. globosa of healthy control 1

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human PrimeView Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000.

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) was used to analyze array images to get raw data. Next, Genespring software (version 13.1; Agilent Technologies) was employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the RMA algorithm.

source_name: stimulated PBMCs of healthy control patient 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: PBMCs were extracted from 5 ml venous blood of each participant at room temperature (RT) by density gradient centrifugation.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The PBMCs suspension in each well of 6-well plate was equally divided into two wells. One was added with 0.6 ml M. globosa suspension and the other was added with an equal volume of culture solution. After cultured at 37 ˚C in 5% CO2 and saturated humidity for 48 h, the cell suspension was centrifuged at 1000 rpm for 10 min. Finally, the cell precipitation was added with 1 ml Trizol lysate preserving at -80 ˚C.

value: PBMCs

value: Male

tag: age

value: 8 years old

tag: agent

value: M. globosa


title: T24_CP1


title: stimulated PBMCs of HC, biological rep3

description: gene expression in stimulated  PBMCs with M. globosa of healthy control 3

source_name: stimulated PBMCs of healthy control patient 3

value: 13 years old


title: stimulated PBMCs of AD, biological rep3

description: gene expression in stimulated  PBMCs with M. globosa of AD patient 3

source_name: stimulated PBMCs of AD patient 3

value: 12years old


title: stimulated PBMCs of AD, biological rep1

description: gene expression in stimulated  PBMCs with M. globosa of AD patient 1

source_name: stimulated PBMCs of AD patient 1


title: stimulated PBMCs of HC, biological rep2

description: gene expression in stimulated  PBMCs with M. globosa of healthy control 2

source_name: stimulated PBMCs of healthy control patient 2

value: 9 years old


title: stimulated PBMCs of AD, biological rep2

description: gene expression in stimulated  PBMCs with M. globosa of AD patient 2

source_name: stimulated PBMCs of AD patient 2

value: 10 years old


title: non-stimulated PBMCs of HC, biological rep3

description: gene expression in non-stimulated PBMCs of healthy control 3

source_name: non-stimulated PBMCs of healthy control patient 3


title: COVID_16_day_5_day_10_PBMC_GEX

description: gene expression feature barcode matrix

tag: time point

value: day 5, day 10

value: Peripheral blood mononuclear cells


title: LGr RT353

description: cDNA library generated with TGIRT

value: Serous borderline tumor tissue


title: Hgr B00091102

description: cDNA library generated with TGIRT


title: COVID_15_day_10_COVID_16_day_1_PBMC_GEX

description: gene expression feature barcode matrix

value: day 1, day 10

tag: disease


title: T24_NT2

value: LLC1 cells

value: No treatment


title: LGr RT157

description: cDNA library generated with TGIRT

tag: tissue


title: T24_NT3

tag: cell line


title: COVID_15_day_1_day_5_PBMC_GEX

description: gene expression feature barcode matrix


title: COVID_14_day_5_day_10_PBMC_GEX

description: gene expression feature barcode matrix


title: T24_NT1

tag: time


title: LGr RT9

description: cDNA library generated with TGIRT


title: T6_TCP3

value: Cisplatin-Pemetrexed + Trametinib

value: 6 hours


title: COVID_13_day_10_COVID_14_day_1_PBMC_GEX

description: gene expression feature barcode matrix


title: COVID_13_day_1_day_5_PBMC_GEX

description: gene expression feature barcode matrix

value: day 1, day 5