title: Raw 264.7 cells, DMSO LPS 24H_3

data_processing:
Raw sequences were trimmed according to quality using Trimmomatic (version 0.39) using default parameters, except MINLEN, which was set to 36
Trimmed sequences were mapped to Mus musculus, version mm10, reference genome provided by Ensembl, using Hisat2 with default parameters.
Optical duplicates were removed using MarkDuplicates tool from GATK package (version 4.1.2.0) with default parameters except the Optical Duplicate Pixel Distance parameter set to 12000
Mapped reads were associated with transcripts defined in Ensembl database (GRCm38, version 95) using HTSeq-count (version 0.9.1) with default parameters except –stranded set to “reverse”.
Genome_build: mm10
Supplementary_files_format_and_content: COUNTS (Ensembl ID; Gene name; read counts)

growth_protocol: 50000 RAW 264.7 cells were seeded in a presence of 10% Fetal Bovine Serum (FBS) on a 6-well plate a day before the treatment. Next day, cells were pretreated with 500 nM SCH772984 for 1h and then challenged with 10µg/ml LPS for 1h, 4h and 24hrs in 500 nM SCH772984 presence. Cells were collected at indicated time points and pellets were frozen at -80oC.

extract_protocol:
Total RNA was isolated from RAW 264.7 cells and tissues using TRIzol reagents (Sigma; T9424)
TruSeq Stranded Total RNA with RiboZero Gold H/M/R; 100bp PE (library preparation and sequencing at CeGaT GmbH)

treatment_protocol: C57BL/6W (own breeding) mice males, 16-20 wk of age, were maintained under the specific pathogen–free animal facility at Maria Skłodowska-Curie National Research Institute of Oncology according to the institutional guidelines, with the experimental protocols approved by The 2nd Local Ethical Committee for Animal Research in Warsaw, Poland (WAW2/47/2017 granted on 17th May 2017). 2 hours following the cececal ligation and puncture (CLP) procedure mice were injected i.p. with 10 mg/kg SCH772984 or formulation (3% DMSO + 10% Polyethylene Glycol) and every 6hr with another dose of SCH772984 or vehicle. At indicated time points (6h and 12h) anesthesia was induced again with isoflurane and blood collected via cardiac puncture. Sham-operated animals were used as control. The chest was opened and the heart and lungs collected rapidly into cryovials which were immediately snap-frozen in liquid nitrogen. Kidney and liver were collected in a similar fashion immediately thereafter. Lung, kidney, liver and heart tissues collected from four animals in CLP, CLP+ SCH772984 and sham group at 6h and 12h time points post-CLP were subjected to RNA-Seq. Sets of organs are matching same animals in a given group.

tag: drugs


title: DMSO [S2518_Nr36]

status: Public on Sep 24 2021

type: SRA

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

library_source: genomic

data_processing:
Raw sequences were trimmed according to quality using Trimmomatic (version 0.39) using default parameters
Trimmed sequences were mapped to Mus musculus, version mm10, reference genome using bowtie2 (version 2.2.6).
Duplicate reads were marked using Picard (2.24) and reads with MAPQ<30 and in the Encode black list regions were excluded with samtools (version 1.7)
Peaks were called with MACS2 (2.1.1)
Differentially Accessible Regions (DARs) were determined by DiffBind 3.0.12.
Genome_build: mm10
Supplementary_files_format_and_content: xls (MACS2 output)

molecule: genomic DNA

organism: Mus musculus

growth_protocol: 50000 RAW 264.7 cells were seeded in a presence of 10% Fetal Bovine Serum (FBS) on a 6-well plate a day before the treatment

extract_protocol:
Nucleai isolation was performed according to Buenrostro et al. (ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide, Curr Protoc Mol Biol.;109: 21.29.1–21.29.9.)
The ATAC-seq library condstruction was done according to Buenrostro et al. (ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide, Curr Protoc Mol Biol.;109: 21.29.1–21.29.9.). ATAC-seq libraries were sequenced on Illumina NovaSeq 6000 Platform with 75 bps paired-end reads in duplicates at CeGaT GmbH.

treatment_protocol: Cells were pretreated with 500 nM SCH772984 for 1h and then challenged with 10µg/ml LPS  for 1h, 4h and 24hrs in 500 nM SCH772984 presence. Cells were collected and immediately subjected to ATAC-Seq protocol.

tag: strain

value: Raw 264.7 cells

tag: treatment

value: Control

tag: passage

tag: agent

value: vehicle

tag: rin values


title: Adult_CM_DOX6 rep2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

library_source: transcriptomic

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.33 was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nucleotides. Only reads above 30 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package
Reads overlapping multiple genes or aligning to multiple regions were excluded. (GEO) Differentially expressed gene analysis was performed using DESeq2
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Matrix table with normalized counts combined with data from GSE79883

molecule: total RNA

source_name: Adult cardiomyocytes

extract_protocol:
adult cardiomycytes were isolated using langendorff-free method.RNA quality and yield were measured using RNA integrity number (RIN) algorithm, using the Fragment Analyzer (Agilent) preparation. 2 μg of total RNA was used as input VAHTS Stranded mRNA-seq Library preparation.
250-600ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Clontech).

tag: cell type

value: isolated adult mouse cardiomyocytes

tag: genotype

value: Doxycycline 6 days

tag: age

value: 12-16 weeks


title: Raw 264.7 cells, DMSO LPS 4H_3

molecule: polyA RNA

tag: cell line

value: LPS 4h


title: Adult_CM_DOX- rep2

value: no treatment


title: Adult_CM_DOX- rep1


title: SCH-772984 [S2518_Nr37]


title: Raw 264.7 cells, DMSO LPS 1H_3

value: LPS 1h


title: Raw 264.7 cells, SCH-772984 LPS 4h_3


title: Raw 264.7 cells, SCH-772984_3


title: Raw 264.7 cells, SCH-772984 LPS 4h_2


title: Raw 264.7 cells, SCH-7729824 LPS 24h_2

value: LPS 24h


title: Raw 264.7 cells, DMSO LPS 24H_2


title: Raw 264.7 cells, DMSO LPS 4H_2


title: Raw 264.7 cells, SCH-772984 LPS 1h_2


title: Raw 264.7 cells, DMSO_3


title: Raw 264.7 cells, DMSO LPS 1H_2


title: Raw 264.7 cells, DMSO_2


title: DMSO LPS 1H [S2518_Nr38]


title: Raw 264.7 cells, SCH-7729824 LPS 24h_1


title: Raw 264.7 cells, DMSO LPS 24H_1


title: Raw 264.7 cells, SCH-772984_2


title: Raw 264.7 cells, DMSO LPS 4H_1


title: Raw 264.7 cells, SCH-7729824 LPS 24h_3


title: Raw 264.7 cells, SCH-772984 LPS 1h_1


title: Raw 264.7 cells, DMSO LPS 1H_1


title: Raw 264.7 cells, SCH-772984 LPS 1h_3


title: HG_PHY_4

city: Vienna

first: Cátia

last: Pacífico

state: Vienna

address: Veterinaerplatz 1

country: Austria

institute: University of Veterinary Medicine Vienna

data_processing:
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20).
Adapters were trimmed with Skewer (version 0.2.2) (Jiang et al. 2014).
Demultiplexed reads were analyzed using sRNAbench. Reads with an average PHRED score below 20 were discarded.
Genome_build: UMD3_1_mp
Supplementary_files_format_and_content: tab-delimited text file include raw counts of all samples (sRNAbench output)
Supplementary_files_format_and_content: tab-delimited text file include DESeq2-normalized counts of all samples

organism: Bos taurus

source_name: Rumen papillae

extract_protocol:
Total RNA was extracted using NucleoSpin miRNA kit (Macherey-Nagel, Germany).
Library preparation was prepared using the NETflex Small RNA-Seq Kit (Bioo Scientific).

tag: tissue

value: Papillae

tag: diet

value: Grain

value: PHY

tag: breed

value: Holstein


title: Raw 264.7 cells, SCH-772984_1


title: HG_PHY_3


title: Raw 264.7 cells, DMSO_1


title: HG_PHY_2


title: HG_CON_5


title: liver, 79

source_name: liver

value: liver

value: sham-operated


title: liver, 80


title: HG_CON_4


title: liver, 78


title: HG_CON_3


title: liver, 77


title: Raw 264.7 cells, SCH-772984 LPS 4h_1


title: HG_CON_1


title: lung, 76

source_name: lung

value: lung


title: lung, 75


title: lung, 73


title: FD_PHY_3

value: Forage


title: HG_CON_2

value: Control


title: FD_PHY_4


title: FD_PHY_2


title: FD_PHY_1


title: FD_CON_5


title: kidney, 72

source_name: kidney

value: kidney


title: kidney, 71


title: kidney, 69


title: HG_PHY_1


title: FD_CON_4


title: heart, 68

source_name: heart

value: heart


title: UTXKO [RNA-seq]

city: Atlanta

first: Bingzhong

last: Xue

state: Georgia

address: 50 Decatur St SE

department: Biology

country: USA

institute: Georgia State University

description: 170413_I283_FCHHW2KBBXX_L2_FLGRMsP326E6AAAPEI-22

data_processing:
raw reads are filtered into clean reads which will be aligned to the reference sequences.
The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio.
Genes and isoforms expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). FPKM method is used in calculated expression level
Genome_build: mm9
Supplementary_files_format_and_content: FPKM file

source_name: Brown adipose tissue

extract_protocol:
Brown adipose tissues were removed, flash frozen in liquid nitrogen, and RNA was harvested using Tri-reagent.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 or other sequencer when necessary

value: 17 week

value: Chow diet feeding for 5 weeks and high fat diet feeding for 12 weeks

value: Brown adipose tissue


title: heart, 67

value: no treatment


title: heart, 66


title: UTXWT [RNA-seq]

description: 170413_I283_FCHHW2KBBXX_L2_FLGRMsP326D6AAAPEI-21

value: UTXfl/Y


title: FD_CON_1


title: CB74_9_1

city: Aurora

first: Holger

middle: A

last: Russ

state: CO

address: 1775 Aurora Ct

department: Barbara Davis Center for Diabetes

description: scRNA-seq

data_processing:
none provided by the submitter
Supplementary_files_format_and_content: RPKM (Bulk)
Supplementary_files_format_and_content: barcodes (single cells)
Supplementary_files_format_and_content: features (single cells)
Supplementary_files_format_and_content: matrix (single cells)

organism:
Homo sapiens
Mus musculus

source_name: Kidney Graft

growth_protocol: For differentiation, iPSCs were plated on Matrigel at 3.15e5 cells/cm2. Differentiations were initiated 24 hours after plating and were carried out in X-VIVO10 (Lonza 04-743Q). Factors were added at the following concentrations: Activin A, 100ng/ml (d0-4); Wnt3a, 50ng/ml (d0, and d9-13); TTNPB (RAR agonist) 6nM (d4-13); BMP4, 20ng/ml (d5-13); LY364947, 5M (d5-13); FGF8b or FGF8a, 50ng/ml (d9-13); SAG, 100ng/ml (d5-8); SANT-1, 0.25M (d9-13) insulin-transferrin-selenium, 1:5,000 (d0) or 1;2,000 (d1-4). At day 20, cultures where transplated into athymic nude mice under the kidney capsule. Grafts were harvested 14-17 post transplantation and prepared for either bulk or scRNA-seq.

extract_protocol:
RNA was extracted using Qiagen RNeasy Minikit (Cat No./ID: 74106). RNA was then submitted to the Genomics and Microarray Shared Resource Core at the University of Colorado Anschutz Medical Campus
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hiPSC derived thymic epithelial progenitors


title: CB74_9_4

institute: University of Colorado Anschutz Medical Campus

description: scRNA-seq


title: CB74_9_2

description: scRNA-seq


title: heart, 65


title: NHDF2.2_7_4

description: scRNA-seq


title: CB74_9_3

description: scRNA-seq


title: FD_CON_3

value: Papillae


title: UTXKO2 [ATAC-seq]

description:
Chow diet feeding for 5 weeks and high fat diet feeding for 12 weeks
KO2_CKDL200160504-1a_HCHNNCCX2_L8

data_processing:
ATAC-seq analysis was carried out using Galaxy Server (usegalaxy.org). Adapters were trimmed from paired-end reads using Trim Galore (Galaxy Version 0.6.3), followed by mapping to the mm10 genome (Bowtie2 (Galaxy Version 2.4.2)).
After marking duplicates with Picard Markduplicate (Galaxy Version 2.18.2.2), we filtered to autosomal and high-quality reads using Samtools (Galaxy Version 1.8).
Remove reads that are in any of the regions on an mm10 blacklist (downloaded from https://github.com/Boyle-Lab/Blacklist/blob/master/lists/mm10-blacklist.v2.bed.gz) by using BAM filter (Galaxy Version 0.5.9).
For peak calling, macs2 (Galaxy Version  2.1.1.20160309.6) was used (--nomodel –extension size 200 -). Prior to downstream analysis, the peaks were filtered against an mm10 blacklist.
The final track files were displayed in the bigwig format, which was converted from bam file (generated by BAM filter) by DeepTool: bamCoverage (Galaxy Version 3.3.2.0.0).
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig file

extract_protocol:
Brown adipose tissues were dissected from UTXKO and their respective wild type mice fed high fat diet for 12 weeks and snap-frozen individually in liquid nitrogen. The brown adipose tissue fragment (around 100mg) was further minced. Nuclei from these brown adipose tissues was isolated.
Five thousand nuclei were used in each transposase reaction (Ilumina), followed by barcoding and amplification of sequencing libraries. DNA sequencing was performed on Illumia Hiseq Platform PE150


title: UTXWT3 [ATAC-seq]

description:
Chow diet feeding for 5 weeks and high fat diet feeding for 12 weeks
WT3_CKDL200160502-1a_HCHNNCCX2_L8


title: kidney, 70


title: lung, 74


title: NHDF2.2_7_1

description: scRNA-seq


title: liver, 64


title: NHDF2.2_7_3

description: scRNA-seq


title: UTXKO1 [ATAC-seq]

description:
Chow diet feeding for 5 weeks and high fat diet feeding for 12 weeks
KO1_CKDL200160503-1a_HCHNNCCX2_L8


title: KidGraftCB74_13

description: Bulk RNA seq


title: KidGraftNHDF2.2_7

description: Bulk RNA seq


title: KidGraftNHDF2.2_3

description: Bulk RNA seq


title: FD_CON_2


title: liver, 62


title: liver, 63


title: NHDF2.2_7_2

description: scRNA-seq


title: liver, 61


title: GFP_neg_72h_rep3

first: Karim

last: Abu Nahia

address: Księcia Trojdena 4

institute: IIMCB Warsaw

description: Replicate 3

data_processing:
bcl2fastq v2.16.0.10 has been used for basecalling
RNA-seq reads were aligned to the zebrafish GRCz11 release 95 genome assembly using Salmon version 0.9.1
Low-quality sequences and adapter content were trimmed with cutadapt v. 1.17.
transcripts were quantified using Salmon algorithm v.0.9.1 (Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C: Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods 2017, 14(4):417-419)
Further analysis was performed in R v. 3.5.2 programming language. Differential expression was analyzed using DESeq2 v. 1.29.13 package.
Genome_build: GRCz11
Supplementary_files_format_and_content: raw_counts files were generated with DESeq2

organism: Danio rerio

source_name: Heart

growth_protocol: Zebrafish embryos were maintained according to standard protocol (Westerfield et al., 2000) and staged according to standard morphological criteria (Kimmel et al., 1995).

extract_protocol:
To isolate heart, embryos were anesthetized with Tricaine (0.16 mg/ml in egg water) and large scale extraction was performed according to the previously published protocol with minor adjustments (Lombardo et al. 2015). GFP-expressing hearts were manually separated from remaining tissues under fluorescence stereomicroscope and collected into 0,5 ml of EDM (L-15/10% FBS). Pool of 300-500 hearts was dissociated with Trypsin-EDTA solution (0.05%) as previously described (Winata et al., 2013). FACS Aria II cytometer (BD Biosciences, USA) was used to enrich GFP positive (fluorescent) and GFP negative (nonfluorescent) heart fractions. Gates for cell sorting were calibrated against dissociated hearts extracted from wild type zebrafish embryos at respective developmental stages (48 or 72 hpf).
Cells were sorted directly to 500 µl TRIzol™ LS Reagent (Thermo Fisher Scientific, USA) followed by RNA purification and DNase I treatment by means of Direct-zol™ kit (Zymo Research, USA) according to the manufacturer’s protocol. To obtain sequencing libraries, a two-step approach was applied. First, cDNA carrying full-length transcript information was synthesized with SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (TaKaRa Bio, Japan) followed by Nextera XT DNA Library Preparation Kit (Illumina, USA) according to the manufacturer's guidelines.

value: FACS-enriched EGFP negative cells

tag: developmental stage

value: 72 pf

value: Enhancer trap line sqet31Et


title: lung, 60


title: GFP_neg_72h_rep2

description: Replicate 2


title: GFP_pos_72h_rep3

description: Replicate 3

value: FACS-enriched EGFP positive cells


title: GFP_neg_72h_rep1

description: Replicate 1


title: KidGraftCB74_14

description: Bulk RNA seq


title: GFP_pos_72h_rep1

description: Replicate 1


title: GFP_neg_48h_rep3

description: Replicate 3

value: 48 hpf


title: UTXWT2 [ATAC-seq]

description:
Chow diet feeding for 5 weeks and high fat diet feeding for 12 weeks
WT2_CKDL200160501-1a_HCHNNCCX2_L8


title: CS+LPS+PPG Lung Tissue Replicate 2

type: RNA

city: Beijing

first: Yahong

last: Chen

address: Haidian District, Huanyuan North Road, No49

country: China

institute: Peking University Third Hospital

description:
Gene expression in lung tissue
PPG5

hyb_protocol: 600ng of Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 25x fragmentation buffer and      10x blocking buffer following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x hybridization buffer was added to stop thefragmentaion reaction,and hybridized to Agilent Whole rat Genome Oligo Microarrays for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) to obtain background subtracted and spatially detrended processed signal intensities.

organism: Rattus norvegicus

source_name: Lung

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using  Trizol reagent (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.

treatment_protocol: The COPD rat model was established by cigarette smoking and intratracheal instillation of lipopolysaccharide (LPS).The rats were treated with PPG or NaHS before cigarette smoking ,

value: Lung

tag: gender

value: Male

value: CS+LPS+PPG

tag: disease state

value: rat model of COPD


title: lung, 58

value: lung


title: RNA-seq of TdTomato+ cells from PAH3 mouse

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

country: United Kingdom

institute: UNIVERSITY OF EDINBURGH

description:
b-PAH3
SuHx-834

data_processing:
Quality and adapter read trimming was performed using Trim Galore version 0.5.0.
Gene quantification (read count and normalized expression value as Fragments Per Kilobase Million - FPKM) was obtained using RSEM version 1.3.0 (options: -bowtie2 --p 20 --paired-end), based on GENCODE GRCm38 genome primary assembly with annotation version M16.
The differential expression was assessed using DESeq2 version 1.26.0 by comparing PAH to Control samples.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt file with gene expression (FPKM) and differential gene expression Log fold change and adjusted p-value.

growth_protocol: Cdh5-CreERT2-TdTomato mice were generated by breeding Cdh5-CreERT2 (Tg(Cdh5-cre/ERT2)1Rha) (transgene obtained by inserting the tamoxifen-inducible cre/ERT2 sequence was inserted into a P1 artificial chromosome containing the Cdh5 gene, Ralf H Adams, MGI:3848982) with ROSA-TdTomato(B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze) (JAX stock #007909 from the Jackson laboratory). To achieve induction of Cre gene, female Cdh5-CreERT2-TdTomato mice were gavaged with 400mg/kg of tamoxifen, followed by a two week wash out period.

extract_protocol:
Endothelial mouse lung cells were isolated as previously described (Fehrenbach et al, Am J Physiol Lung Cell Mol Physiol 2009). Cells were then separated using the BD FACSAria II cell sorter based their TdTomato+ status. RNAs isolation were carried out using the Qiagen miRNeasy Micro Kit.
PolyA stranded libraries were prepared by Genewiz using SMARTseq HT Ultra-Low kit (unstranded).

treatment_protocol: Mice were injected once weekly with SU5416 at 20 mg/kg body weight per dose for a total of 3 weeks. Stock Sugen 5416 powder was suspended at 4mg/ml in a solution of 0.5% [w/v] carboxymethylcellulose sodium, 0.9% [w/v] sodium chloride, 0.5% [v/v] polysorbate 80 and 0.9% [v/v] benzyl alcohol in saline, with sonication to aid suspension. During the 3-week period the mice were exposed to chronic hypobaric hypoxia inside a ventilated plexiglass chamber under a controlled atmosphere at 10% oxygen. Ammonia was removed by ventilation and activated charcoal filtration through an air purifier. Control mice were exposed to room air for 3 weeks.

value: EC

tag: condition

value: PAH

tag: replicate


title: CS+LPS+PPG Lung Tissue Replicate 3

description:
Gene expression in lung tissue
PPG35


title: kidney, 56

tag: strain

value: kidney

tag: drugs


title: lung, 57

tag: treatment

tag: passage


title: RNA-seq of TdTomato+ cells from PAH4 mouse

description:
b-PAH4
SuHx-873


title: CS+LPS+PPG Lung Tissue Replicate 1

description:
Gene expression in lung tissue
PPG3


title: GFP_neg_48h_rep1

description: Replicate 1


title: GFP_pos_72h_rep2

description: Replicate 2


title: kidney, 55

tag: rin values


title: GFP_pos_48h_rep3

description: Replicate 3

tag: cell type


title: lung, 59


title: GFP_pos_48h_rep2

description: Replicate 2


title: RNA-seq of TdTomato+ cells from PAH2 mouse

description:
b-PAH2
SuHx-817


title: RNA-seq of TdTomato+ cells from PAH1 mouse

description:
b-PAH1
SuHx-07


title: CS+LPS+NaHS Lung Tissue Replicate 2

description:
Gene expression in lung tissue
N31

value: CS+LPS+NaHS


title: kidney, 54


title: GFP_neg_48h_rep2

description: Replicate 2


title: GFP_pos_48h_rep1

description: Replicate 1


title: heart, 52

value: heart


title: RNA-seq of TdTomato+ cells from Cont5 mouse

description:
b-Cont5
Norm-871

value: Control


title: CS+LPS Lung Tissue Replicate 2

description:
Gene expression in lung tissue
lps19

value: CS+LPS


title: CS+LPS Lung Tissue Replicate 3

description:
Gene expression in lung tissue
lps39


title: RNA-seq of TdTomato+ cells from Cont4 mouse

description:
b-Cont4
Norm-863


title: kidney, 53


title: RNA-seq of TdTomato+ cells from Cont3 mouse

description:
b-Cont3
Norm-851


title: CS+LPS+NaHS Lung Tissue Replicate 1

description:
Gene expression in lung tissue
N16


title: RNA-seq of TdTomato+ cells from Cont2 mouse

description:
b-Cont2
Norm-832


title: heart, 51


title: RNA-seq of TdTomato+ cells from Cont1 mouse

description:
b-Cont1
Norm-08


title: heart, 50


title: heart, 49


title: liver, 48

value: liver

value: vehicle


title: WT testis 18M_2

city: Gwangju

first: Gwidong

last: Han

address: GIST

department: Life Sciences

country: South Korea

institute: Gwangju Institute of Science and Technology

data_processing:
Alignment performed with HISAT2.
Transcript assembly performed with StringTie.
Genome_build: mm10
Supplementary_files_format_and_content: Read count txt file and gtf files

source_name: Testis

extract_protocol:
Total RNA samples were isolated with ribo-zero rRNA removal kit.
Library construction was processed with TruSeq RNA Sample Preparation v2 Guide.

value: testis

value: post natal month 18


title: liver, 47


title: liver, 46


title: WT testis 12M_3

value: post natal month 12


title: clr6-1-C-H3K9me2

city: San Francisco

first: Bassem

last: Al-Sady

state: CA

address: 513 Parnassus Ave HSW1501

institute: UCSF

data_processing:
Trimming of sequencing adaptors and sliding window quality filtering were performed using Trimmomatic v0.39
Filtered and trimmed Paired-End (PE) reads were aligned to the S. pombe genome with Bowtie2 v2.4.2
Duplicate reads were marked with Picard tools v2.25.2 “MarkDuplicates” command
Filtered bam files were generated with SAMtools v1.12 “view”, "sort", and "index" commands
BigWig files for signal tracks for 25bp bins were generated from the filtered bam files with the bamCompare function from deeptools v3.5.1
Filtered bam files were counted into 300bp and 5kb tiled windows along the genome with the windowCounts() function from the Bioconductor package csaw v1.24.3. Global background was determined from 5kb bin count matrices and interpreted onto the 300bp windows with the csaw filterWindowsGlobal() function. Only 300bp windows where the abundance exceeded a filtering threshold of 1.7 times the global median were retained for further analysis.
Differential Enrichment analysis was performed on these 300bp windows passing the enrichment threshold using the DESeq2 Bioconductor package v1.30.
Genome_build: ASM294v2; pombase.org September 2018 release
Supplementary_files_format_and_content: BigWig files containing signal corresponding to ChIP/Input for 25bp intervals
Supplementary_files_format_and_content: Csv file containing counts per sample in 300bp genomic windows that exceeded the global enrichment threshold
Supplementary_files_format_and_content: Csv file containing counts per sample in 5kb genomic windows.

organism: Schizosaccharomyces pombe

source_name: fission yeast

growth_protocol: Bulk populations of cells for were grown overnight to saturation in YES medium. The following morning, cultures were diluted to OD 0.1 in 60mL YES and grown for 8h at 32°C and 225rpm. Based on OD measurements, 300x10^6 cells were fixed in 1% formaldehyde and flash frozen

extract_protocol:
ChIP DNA was extracted using a bead beater and 0.5mm zirconia beads. Lysates were clarfied following shearing by sonication and then DNA/histone complexes were immunoprecipitated with antibody.
Barcode-indexed sequencing libraries were generated from reverse-crosslinked ChIP-DNA samples using a Kapa Hyper DNA Library Preparation Kit (Kapa Biosystems-Roche, Basel, Switzerland) and NextFlex UDI adapters (PerkinElmer, Waltham, MA). The libraries were amplified with 16 PCR cycles and with SPRI bead protocol according to the instructions of the manufactures. The fragment lengths of the sequencing libraries were verified via micro-capillary gel electrophoresis on a LabChip GX Touch system (PerkinElmer). The libraries were quantified by fluorometry on a Qubit instrument (LifeTechnologies, Carlsbad, CA), and combined in a pool at equimolar ratios. The library pool was size-selected for library molecules in the lengths of 200 to 450 bp using a Pippin-HT instrument (Sage Science, Beverly, Massachusetts). The success of the size-selection was verified on a Bioanalyzer 2100 instrument (Agilent, Santa Clara, CA). The pool was quantified with a Kapa Library Quant kit (Kapa Biosystems-Roche) on a QuantStudio 5 real-time PCR system (Applied Biosystems, Foster City, CA)

tag: chip antibody

tag: genotype


title: clr6-1-B-H3K9me2


title: CS+LPS Lung Tissue Replicate 1

description:
Gene expression in lung tissue
lps1

value: Lung

tag: age


title: liver, 45

tag: tissue


title: clr6-1-A-H3K9me2


title: clrD232N-A-H3K9me2


title: clrD232N--C-H3K9me2


title: clrD232N--B-H3K9me2


title: CS+LPS+NaHS Lung Tissue Replicate 3

description:
Gene expression in lung tissue
N41

value: Male


title: sORF2146ox_14DAS#3

city: Iizuka-shi

first: Tomoyuki

last: Takeda

state: Fukuoka

address: 680-4 Kawazu

department: Bioscience and Bioinformatics

country: Japan

institute: Kyushu Institute of Technology

description: Gene expression in sORF2146ox transgenic plant

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (Cy3CTP incorporation rate >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 uL containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers ｰinstructions. Fragmented Cy3-labelled cRNA was mixed with 55uL of 2xGE Hybridization Byffer HI-RPM and hybridized to Agilent-037209 custom array for 17 hours at 65°C in Agilent Hybridization Oven (G2545A) rotaing 10 rpm. After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Gene Expression Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using AgilentHD_GX_1Color setting for 4x44k array slides (Dye channel: Green, Scan Area: 61x21.6 mm, Scan resolution: 5 um, Tiff file dynamic range: 20 bit, R/G PMT gain: 100% and XDR ratio: NoXDR).

data_processing: The scanned images were analyzed with Feature Extraction Software version 11.5.1.1 (Agilent) using below parameters (protocol GE1_1105_Oct12 and Grid: 037209_D_F_20111030).

organism: Arabidopsis thaliana

source_name: seedling, 14DAS, sORF2146ox transgenic plant, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, then it was purified by Qiagen Rneasy Mini Kit.

growth_protocol: All transgenic plants were grown on solidfied half strength MS medium under long-day condition (Light:14 hour / Dark: 10 hour).

extract_protocol: total RNA was extracted from 14 DAS of seedling using PureLinkTM Plant RNA Reagent (Thermo Fisher Scientific).

value: seedling

value: 14 day

tag: genotype/variation

value: sORF2146ox transgenic


title: Control Lung Tissue Replicate 3

description:
Gene expression in lung tissue
ct33


title: WT testis 18M_3


title: VectorContorol_14DAS#1

description: Gene expression in empty pMDC32 vector transgenic plant

source_name: seedling, 14DAS, empty pMDC32 vector transgenic plant, replicate 1

value: empty pMDC32 vector transgenic


title: VectorContorol_14DAS#3

source_name: seedling, 14DAS, empty pMDC32 vector transgenic plant, replicate 3


title: Control Lung Tissue Replicate 2

description:
Gene expression in lung tissue
ct15


title: VectorContorol_14DAS#2

source_name: seedling, 14DAS, empty pMDC32 vector transgenic plant, replicate 2


title: Control Lung Tissue Replicate 1

description:
Gene expression in lung tissue
ct11


title: sORF2146ox_14DAS#2

source_name: seedling, 14DAS, sORF2146ox transgenic plant, replicate 2


title: lung, 44

value: lung


title: WT testis 12M_2


title: WT testis 18M_1


title: lung, 43


title: prw1-C-H3K9me2


title: prw1-B-H3K9me2


title: WT testis 12M_1


title: lung, 42


title: WT testis 6M_3

value: post natal month 6


title: lung, 41


title: ShNC.mock

city: Hangzhou

first: Lingfang

last: Wang

state: Zhejiang Province

address: 866 Yuhangtang Road

department: Department of Obstetrics and  Gynecology

institute: Zhejiang University

data_processing:
Library strategy: RNA-BisSeq
Quality controlled by Q30
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
Clean reads of input libraries were aligned to reference genome by STAR software
Clean reads of BS-treated libraries were aligned to the reference genome by meRanGh (one component of meRanTK) software.
The methylation status of each C within the genome was extracted by meRanCall (one component of meRankTK) software
Genome_build: hg19
Supplementary_files_format_and_content: excel format: Number of raw junction read

organism: Homo sapiens

source_name: CaSki sh-NC

growth_protocol: CaSki cell line was cultured in 1640 (BI, Israel) containing 10% FBS and maintained at 37°C in 5% CO2.

extract_protocol: The total RNA of cells was extracted with RNAiso Plus (9109, Takara) under the manufacturer’s guiding.

treatment_protocol: We established NSUN2-knockdown stable clones in CaSki cell by lentivirus infection

value: epithelial cell

tag: cell line

value: CaSki

value: wild type


title: kidney, 40

value: kidney


title: ShNC.m5C


title: prw1-A-H3K9me2


title: sORF2146ox_14DAS#1

source_name: seedling, 14DAS, sORF2146ox transgenic plant, replicate 1


title: Sh-3.mock

source_name: CaSki sh-3

value: NSUN2 stable knockdown


title: WT testis 6M_2


title: fkh2-C-H3K9me2


title: Sh-3.m5C


title: kidney, 39

value: vehicle


title: fkh2-B-H3K9me2


title: kidney, 38


title: ShNC

description: Gene Expression Profiling.xlsx

data_processing:
Quality controlled by Q30
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
Clean reads of input libraries were aligned to reference genome by STAR software
Clean reads of BS-treated libraries were aligned to the reference genome by meRanGh (one component of meRanTK) software.
The methylation status of each C within the genome was extracted by meRanCall (one component of meRankTK) software
Genome_build: hg19
Supplementary_files_format_and_content: excel format: Number of raw junction read


title: fkh2-A-H3K9me2


title: WT testis 3M_3

value: testis

value: post natal month 3


title: Sh-3

description: Gene Expression Profiling.xlsx


title: Wildtype-C-H3K9me2

value: WT


title: heart, 36

value: heart


title: Wildtype-B-H3K9me2


title: BTSH replicate 1

city: Salamanca

first: Laura

last: Díaz-Gil

state: SALAMANCA

address: Campus Miguel Unamuno s/n

country: Spain

institute: Instituto de Biología Molecular y Celular del Cáncer

hyb_protocol: Following fragmentation, 3.5 ug of cRNA were hybridized for 16 hr at 45 ºC on Human Gene 2.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A

data_processing:
Data were processed using the RMA algorithm implemented in the Affymetrix Expression Console 1.4. Differentially expressed genes were identified using Transcriptome Analysis Console 4.0 (Affymetrix)
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: tumor cell line

label_protocol: Biotinylated cRNA was prepared according to standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: Cell lines were grown in DMEM medium supplemented with 10% FBS and antibiotics (penicillin 10000 U/ml, streptomycin 100 µg/ml). Cells were cultured at 37 ºC in a humidified atmosphere in the presence of 5% CO2 and 95% air.

extract_protocol: Total RNA was isolated using TRIzol reagent according to manufacturer's instructions.

treatment_protocol: Cells had not received any treatment.

value: breast cancer cell line derived from BT474

tag: cell phenotype

value: hypersensitive to trastuzumab


title: BTSH replicate 2


title: D1KO [RRBS]

description: 160418_I136_FCH7NLNBBXX_L8_WHMUSqylMAAADEAAPEI-62

data_processing:
Clean reads were aligned to genome annotation datasets (University of California Santa Cruz (UCSC) Genome Browser on Mouse (NCBI37/mm9) Assembly).
The software tool Bioconductor, a software repository of R packages, was used to produce such annotations.
The tool kit methylKit v0.9.6. was used to generate methylation report for each sample, and Log2 fold change threshold of 0.5 was used to identify Differentially Methylated Regions (DMRs) between two genotypes.
Genome_build: mm9
Supplementary_files_format_and_content: TDMR file

extract_protocol:
Genomic DNA was isolated from frozen brown adipose tissues
Genomic DNA from brown adipose tissues was isolated by phenol chloroform extraction and a commercial service for DNA methylation sequencing was provided by Beijing Genomics Institute (BGI) (Shenzhen, China). Equal amount of genomic DNAs from 6 animals/group were pooled and used for RRBS analysis. According to the brochure provided by the company, the genomic DNA was digested with the methylation-insensitive restriction enzyme MspI and ligated to methylated sequencing adaptors. The ligated MSPI fragments were size-selected, treated with sodium bisulfite, amplified by PCR and constructed for library, which was sequenced.

value: 36 week

value: Chow diet feeding

value: Brown adipose tissue


title: BTSH replicate 3


title: Wildtype-A-H3K9me2


title: WT testis 6M_1


title: heart, 35

data_processing:
Raw sequences were trimmed according to quality using Trimmomatic (version 0.39) using default parameters, except MINLEN, which was set to 36
Trimmed sequences were mapped to Mus musculus, version mm10, reference genome provided by Ensembl, using Hisat2 with default parameters.
Optical duplicates were removed using MarkDuplicates tool from GATK package (version 4.1.2.0) with default parameters except the Optical Duplicate Pixel Distance parameter set to 12000
Mapped reads were associated with transcripts defined in Ensembl database (GRCm38, version 95) using HTSeq-count (version 0.9.1) with default parameters except –stranded set to “reverse”.
Genome_build: mm10
Supplementary_files_format_and_content: COUNTS (Ensembl ID; Gene name; read counts)


title: D1WT [RRBS]

description: 160418_I136_FCH7T7GBBXX_L5_WHMUSqylMAABDEAAPEI-74


title: clrD232N--C-WCE


title: PBS-1

city: Boston

first: Zhenghui

middle: G

last: Jiang

state: MA

address: 3 Blackfan Cir, CLS605

department: Gastroeneterology

institute: Beth Israel Deaconess Medical Center

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Genome_build: GRCh38
Supplementary_files_format_and_content: counts
Supplementary_files_format_and_content: deseq2

source_name: human PBMC

growth_protocol: Cells were grown in modified RPMI-1640 media containing 2 mM l-glutamine, 1.5 g/L sodium bicarbonate, 4.5 g/L glucose, 10 mM HEPES, and 1 mM sodium pyruvate supplemented with 10% (v/v) fetal bovine serum (FBS) and 1% (v/v) penicillin/streptomycin under standard cell-culture conditions (37°C, 5% CO2, 95% humidified air). Monocytes were treated with 20 ng/ml M-CSF for 7 days piror to ADA2 treatment.

extract_protocol:
Total RNA was extracted and purified from cells using RNeasy Kit (Qiagen). RNA concentration was determined with QubitTM RNA Assay (Thermo Fischer, Waltham, MA) and measured on the TapeStation System.
RNA library preparation was performed using a polyA selection method. RNA sequencing was performed using the Illumina HiSeq system in a 2 × 150-bp configuration with single index per lane).

treatment_protocol: Human monocyte derived macrophages were treated with either ADA2 (100 nM) or PBS for 48 hours

value: monocyte derived macrophages

tag: agent

value: PBS


title: PBS-3


title: WT testis 3M_2


title: clrD232N--B-WCE


title: ADA2-3


title: heart, 33

source_name: heart

extract_protocol:
Total RNA was isolated from RAW 264.7 cells and tissues using TRIzol reagents (Sigma; T9424)
TruSeq Stranded Total RNA with RiboZero Gold H/M/R; 100bp PE (library preparation and sequencing at CeGaT GmbH)


title: heart, 34


title: WT testis 3M_1


title: ADA2-2


title: liver, 32

source_name: liver

value: liver


title: Brain MCAO rep3

city: Tianjin

first: Kai

last: Zheng

address: No.154 Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

data_processing:
The single-cell RNA sequencing data was further analyzed by using the 10x Cell Ranger.Briefly, FASTQ files were generated by demultiplexing the Illumina sequencer's base call files (BCLs), and  then alignment, filtering, barcode and UMI counting were processed. STAR（Spliced Transcripts Alignment to  a Reference）was utilized to perform the read alignments to mouse reference transcriptome (mm10). Cell  Ranger was employed to conduct primary quality control (QC) on the FASTQ files to generate high quality  scRNA-seq data.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Brain

extract_protocol:
The brain was dissected and minced using a scalpel for digestion with papain for 30 minutes at 37°C. After incubation, the mixture was centrifuged at 300g for 5 minutes at room temperature. The cell suspension was then passed through a 40 μm cell strainer and centrifuged at 300 g for 5 minutes. Cell pellets were resuspended in 10 ml of 30% Percoll in PBS and then centrifuged at 700 g for 10 min to remove myelin debris. After the myelin debris fraction floating on the surface was removed, the pelleted cells were immediately resuspended with FACS buffer. Live/dead discrimination reagents for flow cytometry were prepared using Zombie NIR Fixable Viability Kit.
Single Cell 3’ Library was constructed mainly following Chromium Single Cell 3' Reagent Kits User Guide

value: Brain

value: 6-8 weeks


title: clrD232N-A-WCE


title: ADA2-1


title: PBS-2


title: Brain Sham rep2

value: sham


title: Brain Sham rep3


title: clr6-1-B-WCE


title: liver, 30


title: liver, 29


title: prw1-C-WCE


title: Brain Sham rep1


title: liver, 31


title: lung, 27

source_name: lung

value: lung


title: Hippocampus_EE3

city: London

first: Shiva

middle: M

last: Singh

state: ON

address: 1151 Richmond Street

country: Canada

institute: Western University

data_processing:
Base-calling was performed using CASAVA
Paired-end reads for each sample were quantified via pseudoalignment to version 38 of the Ensembl annotation of the mouse transcriptome using kallisto with 100 bootstrap samples taken
Differential analysis of gene expression was determined using sleuth via p-value aggregation
Genome_build: mm10
Supplementary_files_format_and_content: "tpmdata" contains the Sleuth object count matrix using normalized observations in transcripts per million for each transcript detected for sample as a comma separated values file

source_name: Hippocampus

extract_protocol:
Mice were sacrificed via carbon dioxide asphyxiation and cervical spinal dislocation. Hippocampus was dissected, snap-frozen in liquid nitrogen, and stored at -80°C. RNA was isolated using AllPrep DNA/RNA Mini Kit (Qiagen) and stored at -80°C.
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded total RNA Library Preparation protocol with rRNA depletion using RiboZero Gold.

treatment_protocol: C57BL/6 mice were exposed to ethanol via two subcutaneous injections of 2.5 g/kg ethanol in 0.15 M saline two hours apart on postnatal day 6 and 7. Control mice received 0.15 M saline volume-equivalent injections. On P21, each pup was randomly assigned to either the enriched group or standard housing control group. Enriched mice were housed with same-sex littermates in large colony cages of 2-6 individuals supplied with extra bedding, hidden food pellets, additional nest material, running wheels, hoops, ladders, as well as toys and objects of varied shape, color, texture, and size. This protocol generated mice belonging to one of four groups based on ethanol exposure and environmental enrichment: control (no ethanol nor enrichment), enriched (no ethanol), ethanol (no enrichment), and ethanol enriched.

value: postnatal day 70

tag: prenatal treatment

value: ethanol

tag: postnatal treatment

value: enrichment

value: Hippocampus


title: prw1-B-WCE


title: prw1-A-WCE


title: Hippocampus_CE2

value: control


title: Hippocampus_EE1


title: Hippocampus_EE2


title: clr6-1-C-WCE


title: lung, 26


title: M28

city: Gyeonggi-do

first: Jisoo

last: Kim

address: 22, Giheungdanji-ro 24beon-gil, Giheung-gu, Yongin-si

department: New growth team

institute: hy R&BD center

data_processing:
Using the fastp program, Adapter sequences are removed and Error correction was performed for areas where the two reads overlap.
By assembling paired-end sequence created by sequencing both directions of library , the original library and single long reads are obtained. The program used in this process is *FLASH (v.1.2.11)
OTUs of the remained reads are created by cluster cutoff value of 97%. CD-HIT-OTU is a program that is used for this analysis. CD-HIT-OTU is a total package program that is based on cd-hit-est.
QIIME(v1.9 .0) is used for OTU analysis and obtaining taxonomy information. The major sequence of each OTU is referred to Reference DB(NCBI 16S Microbial).

organism: mouse gut metagenome

source_name: Cecal metagenome

extract_protocol:
DNA was extracted using a DNeasy PowerSoil Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. The extracted DNA was quantified using Quant-IT PicoGreen (Invitrogen).
Libraries were prepared for sequencing using standard Illumina 16S metagenomic sequencing library protocols
Sequencing was performed by the Macrogen using Illumina MiSeq platform

value: Cecum


title: M29


title: M30


title: Brain MCAO rep2


title: Brain MCAO rep1


title: fkh2-C-WCE

source_name: fission yeast


title: Hippocampus_CE1


title: clr6-1-A-WCE


title: lung, 28

first: Michal

last: Mikula

address: Roentgena 5

institute: Maria Skłodowska-Curie National Research Institute of Oncology


title: M27


title: Hippocampus_EC3


title: kidney, 24

source_name: kidney

value: kidney


title: Hippocampus_CE3


title: lung, 25


title: Hippocampus_EC2


title: M26


title: fkh2-B-WCE


title: fkh2-A-WCE


title: Wildtype-C-WCE

value: WT


title: M25


title: M24


title: Hippocampus_EC1


title: kidney, 23


title: kidney, 22


title: Hippocampus_CC3


title: kidney, 21


title: M23


title: Liver sinusoidal endothelial cells : 6WR17

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

description: Liver sinusoidal endothelial cells  from six weeks treated rat :6WR17

data_processing:
Raw reads data were converted into FASTQ format and quality control was performed using the FASTQC software (Babraham Bioinformatics).
After trimming for adapters using trim_galore (Babraham Bioinformatics), mapping of the reads were obtained using the STAR program against human genome (Rnor6) and the quantification of genes and transcripts were done with the RSEM program using ENSEMBL v91.
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Genome_build: Rattus norvergicus(Rnor 6.0)
Supplementary_files_format_and_content: RSEM expected counts

source_name: six weeks treated rat_LSECs

growth_protocol: After liver tissue perfusion and digestion, LSECs were isolated by differential centrifugation protocol using iodixanol as density gradient medium.

extract_protocol: Rat LSECs were collected with QIAzol lysis reagent (79306, Qiagen, MA, USA) for RNA extraction using miRNeasy microkit (74004, Qiagen, DE) for subsequent RNA sequencing.

tag: strain background

value: Wistar Han

tag: treatment/group

value: six weeks treated rat

value: liver sinusoidal endothelial cells (LSECs)


title: Hippocampus_CC2

tag: strain


title: heart, 20

city: Warsaw

value: heart

tag: treatment

tag: drugs


title: Wildtype-B-WCE


title: M21


title: M22


title: Wildtype-A-WCE


title: heart, 19

tag: passage

tag: rin values


title: Hippocampus_CC1


title: Liver sinusoidal endothelial cells : 6WR16

description: Liver sinusoidal endothelial cells  from six weeks treated rat :6WR16

tag: cell type


title: PMs, Lyz2Cre-BHLHE40-Fl-LPS-3

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to mouse genome mm10 using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: genematrix.tsv

source_name: peritoneal macrophages (PMs)

extract_protocol:
Total RNA was isolated from indicated samples using the High Pure RNA Isolation Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PMs

value: Postnatal week 10

tag: genotype

value: LPS


title: heart, 18


title: PMs, Lyz2Cre-BHLHE40-Fl-LPS-2

tag: age


title: M20

tag: tissue


title: Liver sinusoidal endothelial cells : 6WR15

description: Liver sinusoidal endothelial cells  from six weeks treated rat :6WR15


title: PMs, Lyz2Cre-BHLHE40-Fl-LPS-1


title: Liver sinusoidal endothelial cells : 6WR13

description: Liver sinusoidal endothelial cells  from six weeks treated rat :6WR13


title: M18


title: liver, 16

value: liver

value: vehicle


title: M19


title: Liver sinusoidal endothelial cells : 6WR12

description: Liver sinusoidal endothelial cells  from six weeks treated rat :6WR12


title: PMs, Lyz2Cre-BHLHE40-Fl-Control-3


title: Liver sinusoidal endothelial cells : 2WR8

description: Liver sinusoidal endothelial cells  from two weeks treated rat :2WR8

source_name: two weeks treated rat_LSECs

value: two weeks treated rat


title: liver, 14


title: liver, 13


title: M15


title: M17


title: M16


title: liver, 15


title: PMs, Lyz2Cre-BHLHE40-Fl-Control-1


title: Liver sinusoidal endothelial cells : 2WR4

description: Liver sinusoidal endothelial cells  from two weeks treated rat :2WR4


title: Liver sinusoidal endothelial cells : 2WR2

description: Liver sinusoidal endothelial cells  from two weeks treated rat :2WR2


title: M14


title: lung, 11

value: lung


title: PMs, Lyz2Cre-LPS-2


title: heart, 17


title: M13


title: lung, 10


title: PMs, Lyz2Cre-BHLHE40-Fl-Control-2


title: PMs, Lyz2Cre-LPS-1


title: M12


title: lung, 9


title: M11


title: Liver sinusoidal endothelial cells : T15

description: Liver sinusoidal endothelial cells  from TAA control rat :T14

source_name: TAA control rat_LSECs

value: TAA control rat


title: Liver sinusoidal endothelial cells : 2WR1

description: Liver sinusoidal endothelial cells  from two weeks treated rat :2WR1


title: PMs, Lyz2Cre-Control-2


title: kidney, 8


title: PMs, Lyz2Cre-Control-3


title: PMs, Lyz2Cre-LPS-3


title: Liver sinusoidal endothelial cells : T14

description: Liver sinusoidal endothelial cells  from TAA control rat :T13


title: Liver sinusoidal endothelial cells : 2WR3

description: Liver sinusoidal endothelial cells  from two weeks treated rat :2WR3


title: M10


title: M9


title: lung, 12


title: Liver sinusoidal endothelial cells : T12

description: Liver sinusoidal endothelial cells  from TAA control rat :T11


title: PMs, Lyz2Cre-Control-1


title: kidney, 7


title: P0 Six2 TGC Tsc1

city: Cincinnati

first: Alison

last: Jarmas

state: Ohio

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Raw scRNA-Seq data was processed using cellranger (v2.0.0 10xGenomics) (https://github.com/10XGenomics/cellranger). Reads were aligned to mouse genome [mm10] to produce counts of genes across barcodes. Barcodes with less than ~5k UMI counts were not included in downstream analysis. QC, Filtering, Normalization and Clustering was carried out using Seurat [v2.3.4]
Genome_build: mm10
Supplementary_files_format_and_content: Processed .RDS file is provided with seurat clusters, celltypes and umap/tsne coordinates

source_name: Kidney cortex

extract_protocol:
Isolated kidneys were digested with 10mg/ml Bacillus licheniformis proetase at 10 degrees celsius for 5-10 minutes, from which single-cell suspensions were generated.
Libraries were prepared using Chromium Single Cell Library kit V2 (10x Genomics) and sequenced on an Illumina HiSeq 2500 using 75bp paired-end sequencing.

value: mixed

value: Six2 TGC Tsc1

value: Kidney cortex


title: Liver sinusoidal endothelial cells : T13

description: Liver sinusoidal endothelial cells  from TAA control rat :T12


title: kidney, 6

value: kidney


title: P0 Six2TGC

value: Six2 TGC


title: M8

value: Cecum


title: Liver sinusoidal endothelial cells : T10

description: Liver sinusoidal endothelial cells  from TAA control rat :T10

value: Wistar Han


title: M7


title: kidney, 5


title: P0 Six2KI

value: Six2 KI


title: Liver sinusoidal endothelial cells : T5

description: Liver sinusoidal endothelial cells  from control rat :T5

value: control

value: liver sinusoidal endothelial cells (LSECs)


title: heart, 4

value: heart


title: Liver sinusoidal endothelial cells : T4

description: Liver sinusoidal endothelial cells  from control rat :T4


title: E14 Six2 TGC Tsc1


title: Liver sinusoidal endothelial cells : T3

description: Liver sinusoidal endothelial cells  from control rat :T3


title: M5


title: heart, 3


title: E14 Six2TGC


title: heart, 2


title: M4


title: Liver sinusoidal endothelial cells : T2

description: Liver sinusoidal endothelial cells  from control rat :T2


title: E14 Six2KI


title: P0 Tsc1 rep4

data_processing:
Raw reads in fastq format were mapped mm10 mouse genome assembly using kalisto.
Genome_build: mm10
Supplementary_files_format_and_content: Transcripts per million per gene across samples

source_name: Nephron progenitor cells

extract_protocol:
E14 or P0 kidneys weredigested with 0.25%Trypsin/0.2% Collagenase at 20˚C in a Thermomixer R. After 10-15 minutes, the kidneys were removed, and the single-cell suspension was rinsed twice NPCs were labeled using cell-surface primary antibodies (Itga8+, Pdgfra- cells were sorted from the GFP-positive population) on the Sony SH800S instrument.
Clontech SMARTer library kit V2 was used for cDNA library construction. Libraries were sequenced on an Illumina HiSeq 2500 using 75bp paired-end sequencing.

value: Nephron progenitor cells


title: M3


title: Liver sinusoidal endothelial cells : T1

description: Liver sinusoidal endothelial cells  from control rat :T1


title: heart, 1


title: M2


title: Liver sinusoidal endothelial cells : CT6

description: Liver sinusoidal endothelial cells  from Untreated rat :CT6

source_name: Untreated rat_LSECs

value: Untreated rat


title: M1


title: P0 Tsc1 rep3


title: P0 Tsc1 rep2


title: Liver sinusoidal endothelial cells : CT4

description: Liver sinusoidal endothelial cells  from Untreated rat :CT4


title: Liver sinusoidal endothelial cells : CT5

description: Liver sinusoidal endothelial cells  from Untreated rat :CT5


title: MUT_NCD_rep2 [S30]

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

data_processing:
Sequenced reads were trimmed via TrimGalore v0.4.1 using cutadapt v1.18 and FastQC v0.11.8 in paired-end mode.
Technical replicates were pooled and reads were aligned against to mouse genome (GRCm38.p6 primary assembly, masked for nuclear mitochondrial sequences) with STAR v2.7.0f and the GENCODE vM23 gene annotation with a customised mitochondrial annotation.
Full fragment length mitochondrial coverage profiles were generated with samtools v1.10 and bedtools v2.26.0, and normalised to total reads mapped to the mouse genome.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: wig files of normalised mitochondrial coverage, by strand

source_name: Pancreatic islet cells

growth_protocol: The mice were housed in standard cages (45 cm Å~ 29 cm Å~ 12 cm) under a 12-h light/dark schedule (lights on 7 a.m. to 7 p.m.) in controlled environmental conditions of 22 + 2 °C and 50 + 10% relative humidity.

extract_protocol:
RNA was isolated from pancreatic islets of Langherans using the miRNeasy Mini kit (Qiagen) incorporating an on-column RNase-free DNase digestion to remove all DNA.
Sequencing libraries were prepared according to the Illumina Tru-Seq protocol.

treatment_protocol: Normal chow diet and water were provided ad libitum. High fat diet feed was provided ad libitum for 14 weeks. The feed was provided by Rat & Mouse Chow, Specialty Feeds, Glen Forrest, Western Australia.


title: MUT_NCD_rep1 [S29]


title: WT_NCD_rep3 [S28]


title: MUT_NCD_rep3 [S31]


title: P0 Tsc1 rep1


title: M6


title: aCMs2

city: Catanzaro

first: Daniele

last: Torella

state: Catanzaro

address: Viale Europa, loc. Germaneto

department: Experimental and clinical medicine

country: Italy

institute: University "Magna Graecia"

description:
Sample8_total_aCMs
processed data file: Total_RPKM_raw_counts.xlsx

data_processing:
total RNA: All libraries were sequenced on the Illumina HiSeq 1000 generating 100 bp paired end reads.
small RNA: All libraries were sequenced on the Illumina HiSeq 2500 generating 50 bp single end reads.
total RNA: RNA-seq has been performed by using StrandNGS with its default parameters
small RNA: small RNA-seq has been performed by using iSMART with its default parameters
Raw data sequences have been pre-processed and then related to mus musculus genome. Alignment parameters have been set as it follows: minimum percentage identity = 90 %; maximum percentage gaps = 5 %; maximum number of novel splices = 1; minimum match length = 25.
Reads with less than 5 valid matches have been filtered out, finally obtaining expression values for reads (quantification phase). To detect novel genes and exons we set the parameters, in term of percentile, as it follows: minimum exon length equals to 10.0; minimum intron length equals to 10.0; maximum intron length equals to 90.0; minimum gene length equals to 10.0; minimum exon RPKM equals to 50.0.
mRNA Analysis: Differential expressions were performed using DESeq algorithm. We performed fold change (FC) analysis on filtered expression values using normalized signal values in log-scale. We considered a fold change cut off equals to 2.5 to identify up and down regulated genes.
microRNA analysis: The raw counts were normalized using DESeq2 (version 1.28.1) on R (version 4.0.2) and the differentially expressed miRNA were filtered with a p-adjust < 0.05 and a Fold Change of |1.5| (Log2 FC |0.6|).
Gene Ontology has been used to functional enrichment of the data. TargetScan, MicroRNa.org, MiRDB have been used to identify mirna Targets. miRNA/mRNA networks have been built in Cytoscape.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: Cardiomyocytes

growth_protocol:
CSCs and aCMs isolation protocol: Heart were digested with Collagenese and aCMs were obtained through gradient separation. CSCs were enriched through immunomagnetic negative sorting for CD45 e CD31 and positive sorting for c-kit.
CSCs were plated in gelatin-coated dishes in CSC growth medium supplemented with 10% ESQ-FBS. Cells were maintained at 37C in ambient O2 (21%) and 5% CO2.

extract_protocol:
RNA was extracted using TRIzol Reagent. The extracted RNA integrity was measured with an Agilent 2100 Bioanalyzer, and a sample with an RNA Integrity Number greater than or equal to 8 was considered acceptable
The libraries were generated using depleted RNA obtained from 1ug total RNA by TruSeq Sample Preparation RNA Kit according to the manufacturer's without further modifications. The first step involves the removal of ribosomal RNA rRNA using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads that depletes samples of both cytoplasmic and mitochondrial rRNA. Following purification, the RNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter (Multiple indexing adapters were ligate to the ends of the ds cDNA). The products are purified and enriched with PCR to create the final cDNA library.

treatment_protocol: Cardiospheres derived from CSCs were manteined in StemPro Medium with specific growth factors: BMP-4, Activin A, beta-FGF, Wnt11, Wnt5A and DKK1

value: Heart

value: Cardiomyocytes


title: P0 rep3


title: WT_NCD_rep2 [S27]


title: Liver sinusoidal endothelial cells : CT2

description: Liver sinusoidal endothelial cells  from Untreated rat :CT2


title: aCMs1

description:
Sample7_total_aCMs
processed data file: Total_RPKM_raw_counts.xlsx


title: P0 rep1


title: WT_NCD_rep1 [S26]


title: MUT_HFD_rep3 [S25]


title: Liver sinusoidal endothelial cells : CT1

description: Liver sinusoidal endothelial cells  from Untreated rat :CT1


title: Liver sinusoidal endothelial cells : CH6

description: Liver sinusoidal endothelial cells  from CCL4 treated rat :CH6

source_name: CCL4 treated rat_LSECs

value: CCL4 treated rat


title: iCMs1

description:
Sample4_total_iCMs
processed data file: Total_RPKM_raw_counts.xlsx

source_name: CSC-derived CMs

value: CSC-derived CMs


title: E14 rep3

value: mixed


title: MUT_HFD_rep2 [S24]


title: Liver sinusoidal endothelial cells : CH5

description: Liver sinusoidal endothelial cells  from CCL4 treated rat :CH5


title: E14 rep2


title: MUT_HFD_rep1 [S23]


title: Liver sinusoidal endothelial cells : CT3

description: Liver sinusoidal endothelial cells  from Untreated rat :CT3


title: CSCs3

description:
Sample3_total_CSCs
processed data file: Total_RPKM_raw_counts.xlsx

source_name: Cardiac Stem Cells

value: Cardiac Stem Cells


title: E14 rep1


title: Liver sinusoidal endothelial cells : CH4

description: Liver sinusoidal endothelial cells  from CCL4 treated rat :CH4


title: P0 rep2


title: H89CH28

description: Liver sinusoidal endothelial cells from H89CH28

data_processing:
Raw reads data were converted into FASTQ format and quality control was performed using the FASTQC software (Babraham Bioinformatics).
After trimming for adapters using trim_galore (Babraham Bioinformatics), mapping of the reads were obtained using the STAR program against human genome (hg38) and the quantification of genes and transcripts were done with the RSEM program using GENCODE v26..
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Genome_build: Human genome (hg38)
Supplementary_files_format_and_content: RSEM expected counts

source_name: Liver sinusoidal endothelial cells

growth_protocol: After liver tissue perfusion and digestion, human LSECs were labeled by incubation with human CD32 primary antibody (1:1000; Fitzgerald, MA, USA) and isolated by immunomagnetism with Dynabeads® CELLection Pan Mouse IgG Kit (11531D, ThermoFisher Scientific, USA) according to the manufacturer’s instructions.

extract_protocol: Human LSECs were collected with QIAzol lysis reagent (79306, Qiagen, MA, USA) for RNA extraction using miRNeasy microkit (74004, Qiagen, DE) for subsequent RNA sequencing.

value: Cirrhosis


title: CSCs2

description:
Sample2_total_CSCs
processed data file: Total_RPKM_raw_counts.xlsx


title: WT_HFD_rep3 [S22]


title: iCMs3

description:
Sample6_total_iCMs
processed data file: Total_RPKM_raw_counts.xlsx


title: CSCs1

description:
Sample1_total_CSCs
processed data file: Total_RPKM_raw_counts.xlsx


title: WT_HFD_rep2 [S21]


title: aCMs1 [miRNA]

description:
Sample7_small_aCMs
processed data file: Small_CPM_raw_counts.xlsx

tag: molecule subtype

value: small RNA


title: Liver sinusoidal endothelial cells : CH2

description: Liver sinusoidal endothelial cells  from CCL4 treated rat :CH2


title: WT_HFD_rep1 [S20]


title: H81CH25

description: Liver sinusoidal endothelial cells from H81CH25


title: iCMs2

description:
Sample5_total_iCMs
processed data file: Total_RPKM_raw_counts.xlsx


title: iCMs3 [miRNA]

description:
Sample6_small_iCMs
processed data file: Small_CPM_raw_counts.xlsx


title: H79CH23

description: Liver sinusoidal endothelial cells from H79CH23


title: MUT_HFD_rep3

data_processing:
Sequenced reads were trimmed via TrimGalore [1] v0.6.5 using cutadapt [2] 0.18 and FastQC [3] v0.11.8 in paired-end mode with a minimum length of 18 nt.
Technical replicated were pooled and paired reads were merged using NGmerge v0.3 [9]. Merged reads were aligned to the GRCm38.p6 [4] genome sequence using STAR [5] and the GENCODE vM21 gene annotation [6] (with customised mitochondrial annotations).
Mitochondrial tRNA counts produced by STAR were normalised to total mapped reads and tRNA position 9 mismatch rates were calculated by extracting nucleotide frequencies from genomic BAM files with pysamstats [10] (--type variation_strand).
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-delimited txt files containing nucleotide frequencies of mitochondrially mapped reads across the mitochondrial genome

extract_protocol:
RNA was isolated from pancreatic islets of Langherans using the miRNeasy Mini kit (Qiagen) incorporating an on-column RNase-free DNase digestion to remove all DNA.
Sequencing libraries were prepared according to the Illumina Tru-Seq Small RNA protocol.

treatment_protocol: High fat diet feed was provided ad libitum for 14 weeks. The feed was provided by Rat & Mouse Chow, Specialty Feeds, Glen Forrest, Western Australia.


title: MUT_HFD_rep2


title: Liver sinusoidal endothelial cells : CH3

description: Liver sinusoidal endothelial cells  from CCL4 treated rat :CH3


title: aCMs2 [miRNA]

description:
Sample8_small_aCMs
processed data file: Small_CPM_raw_counts.xlsx


title: MUT_HFD_rep1


title: H49RC

description: Liver sinusoidal endothelial cells from H49RC

value: Healthy


title: TK212s2: GVHD donor2

city: Vienna

first: Georg

last: Stary

address: Spitalgasse 23

department: Dermatology

institute: Medical University of Vienna

description:
10x Genomics single cell RNA-seq
*** Submitter Comment: Due to security issue we are not submitting the raw data ***

data_processing:
Cell Ranger (v3.0.2) mkfastq method demultiplexed raw base call (BCL) files generated by Illumina sequencers into FASTQ files.
Cell Ranger (v3.0.2) count method took FASTQ files from cellranger mkfastq and performs alignment to the Homo sapiens genome (GRCh38.92 assembly), filtering, barcode counting, and UMI counting.
Cell Ranger (v3.0.2) aggr method was used to aggregate the outputs from three runs of cellranger count.
Downstream analysis were perfored using R package Seurat v3.02 and 10x Genomics Loupe Browser.
processed data files format and content: 10x single cell Transcriptome processed files were generated by cellranger count method
Genome_build: hg38

source_name: CD45+ cells

growth_protocol: freshly isolated PBMC from human blood

extract_protocol:
PBMCs were isolated on Ficoll gradient
SMART-seq2/10X Genomics

treatment_protocol: freshly isolated PBMCs were immideately frozen, then thawed and stained for FACS-sorting and subsequent library preparation

value: BLOOD

value: CD45+ cells

tag: sorting criteria

value: live CD45+


title: H76CH22

description: Liver sinusoidal endothelial cells from H76CH22


title: WT_HFD_rep3


title: TK281s1: GVHD donor1


title: TK212s1: GVHD donor2


title: H43RC

description: Liver sinusoidal endothelial cells from H43RC


title: CSCs3 [miRNA]

description:
Sample3_small_CSCs
processed data file: Small_CPM_raw_counts.xlsx


title: cTRM_Donor2: Circulating tissue resident memory T cells donor 2

description:
Bulk RNA-seq
*** Submitter Comment: Due to security issue we are not submitting the raw data ***

data_processing:
Single-end reads were trimmed for low quality bases and removal of low-quality reads using ReadTools
Trimmed reads were mapped to the Homo sapiens genome (GRCh38.92 assembly) using STAR (v2.5.3a) mapper
The reads mapped in multiple genomic locations were eliminated by using Samtools (v1.4)
Read counts for features (exons) were generated using the featureCounts function from the Subread package (v 1.22.1)
processed data files format and content: Raw gene count matrix was generated using featureCounts function from the Subread package (v 1.22.1) with Ensembl Known Gene models (version GRCh38.92) as reference annotations
Genome_build: hg38

source_name: Bulk RNA PBMCs

value: T cells

value: live CD45+ CD3+ CD4+ CLA+ CD103+


title: H51CL

description: Liver sinusoidal endothelial cells from H51CL


title: CSCs2 [miRNA]

description:
Sample2_small_CSCs
processed data file: Small_CPM_raw_counts.xlsx


title: WT_HFD_rep2


title: cTRM_Donor3: Circulating tissue resident memory T cells donor 3


title: H85CL

description: Liver sinusoidal endothelial cells from H85CL


title: cTRM_Donor1: Circulating tissue resident memory T cells donor 1


title: CSCs1 [miRNA]

description:
Sample1_small_CSCs
processed data file: Small_CPM_raw_counts.xlsx


title: Liver sinusoidal endothelial cells : CH1

description: Liver sinusoidal endothelial cells  from CCL4 treated rat :CH1

value: Wistar Han

value: liver sinusoidal endothelial cells (LSECs)


title: H83CL

description: Liver sinusoidal endothelial cells from H83CL


title: iCMs2 [miRNA]

description:
Sample5_small_iCMs
processed data file: Small_CPM_raw_counts.xlsx


title: Tconv_Donor3: Conventational T cells donor 3

value: live CD45+ CD3+ CD4+ CD103-


title: WT_HFD_rep1


title: Db/db Saline rep5

first: Xin

last: Huang

state: Zhejiang

address: 88 Jiefang Road

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.
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.
Genome_build: Mus_musculus_Ensemble_94.fa
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample

source_name: Heart

growth_protocol: Db/db mice and BKS mice were all male and 16 weeks old at the time of sacrifice and heart resection.

extract_protocol:
Heart were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 1 µg RNA per sample was used as input material for the RNA  sample preparations.
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.

treatment_protocol: Mice were housed under standard conditions with food and water provided without limitation and maintained on a 12 hour light/12 hour dark cycle.

value: Heart


title: iCMs1 [miRNA]

description:
Sample4_small_iCMs
processed data file: Small_CPM_raw_counts.xlsx


title: Db/db Saline rep4


title: Tconv_Donor2: Conventational T cells donor 2


title: Db/db Saline rep3


title: Db/db Saline rep2


title: Tconv_Donor1: Conventational T cells donor 1


title: Thy_7.2_3

city: Aurora

first: Holger

last: Russ

address: 1775 Aurora Ct

description: scRNA-seq

data_processing:
none provided by the submitter
Supplementary_files_format_and_content: RPKM (Bulk)
Supplementary_files_format_and_content: barcodes (single cells)
Supplementary_files_format_and_content: features (single cells)
Supplementary_files_format_and_content: matrix (single cells)

source_name: Human neonatal thymus

extract_protocol:
RNA was extracted using Qiagen RNeasy Minikit (Cat No./ID: 74106). RNA was then submitted to the Genomics and Microarray Shared Resource Core at the University of Colorado Anschutz Medical Campus
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Primary thymic epithelial cells/Thymocytes


title: Db/db Saline rep1


title: Thy_7.2_2

institute: University of Colorado Anschutz Medical Campus

description: scRNA-seq


title: Thy_7.2_1

description: scRNA-seq


title: Thy_7.2_4

description: scRNA-seq


title: Thy_7.1_4

description: scRNA-seq


title: Bks Saline rep3


title: Bks Saline rep5


title: Bks Saline rep1


title: Thy_7.1_1

description: scRNA-seq


title: Thy_7.1_3

description: scRNA-seq


title: Bks Saline rep2


title: scRNA-seq of TdTomato+ cells from PAH1 mouse

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

institute: UNIVERSITY OF EDINBURGH

data_processing:
fastq files obtained from Edinburgh Genomics
Read mapping and generation of the expression matrix was done using CellRanger version 3.1.0 on a custom annotation based on mm10 and including the TdTomato transcript.
Genome_build: mm10 + TdTomato transcript
Supplementary_files_format_and_content: h5 file from CellRanger output

source_name: lung

extract_protocol:
Endothelial mouse lung cells were isolated as previously described (Fehrenbach et al, Am J Physiol Lung Cell Mol Physiol 2009). Cells were then separated using the BD FACSAria II cell sorter based their TdTomato+ status.
Single cell RNA-sequencing libraries were prepared using the Single Cell 3′ Reagent Kit User Guide v2 (10x Genomics)

treatment_protocol: To induce PAH for experiment 2, mice were injected once weekly with SU5416 at 20 mg/kg body weight per dose for a total of 3 weeks. Stock Sugen 5416 powder was suspended at 4mg/ml in a solution of 0.5% [w/v] carboxymethylcellulose sodium, 0.9% [w/v] sodium chloride, 0.5% [v/v] polysorbate 80 and 0.9% [v/v] benzyl alcohol in saline, with sonication to aid suspension. During the 3-week period the mice were exposed to chronic hypobaric hypoxia inside a ventilated plexiglass chamber under a controlled atmosphere at 10% oxygen. Ammonia was removed by ventilation and activated charcoal filtration through an air purifier. Control mice were exposed to room air for 3 weeks.

tag: condition

value: pulmonary arterial hypertension (PAH)

tag: replicate

tag: experiment

value: experiment 2


title: scRNA-seq of TdTomato+ cells from PAH3 mouse


title: NHDF2.2 TEPs

description: Bulk RNA seq

source_name: thymic epithelial progenitors

value: hiPSC derived thymic epithelial progenitors


title: scRNA-seq of TdTomato+ cells from Cont1 mouse

value: Cont


title: CB74 TEPs

description: Bulk RNA seq


title: Thy007w

description: Bulk RNA seq


title: Thy009

description: Bulk RNA seq


title: scRNA-seq of TdTomato+ cells from ContB mouse

value: B

value: experiment 1


title: scRNA-seq of TdTomato+ cells from ContA mouse

value: A


title: Bks Saline rep4


title: Fed_GAA 3

status: Public on Sep 23 2021

city: Minneapolis

first: Douglas

middle: Gene

last: Mashek

state: Minnesota

address: Suite 6-155, 321 Church St. SE

department: Biochemistry, Molecular Biology and Biophysics

institute: University of Minnesota

data_processing:
Raw sequence that passed CASAV 1.8P/F filter were assessed by fastqc (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Read mapping was performed via hisat2 (2.1.0) using the mouse genome (mm10) as a reference.
Counts were quantified via Feature counts (Subread Package).
Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood City, CA) using raw read counts.
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: transfected with shGAA lentivirus

growth_protocol: C2C12 cells were grown in 10% FBS media containing 4.5 g/l glucose, glutamine, penstrep

extract_protocol:
RNA was extracted using a QIAGEN Rneasy minikit (Cat # 74004) and 1 ug of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with shscrambled or shGAA lentivirus, differentiated into myotubes, and then harvested for RNA sequencing

tag: cell line

tag: differentiation protocol

value: Differentiated in 2% horse serum media, 4.5 g/l gucose, glutamine

tag: differentiation status

value: myotubes


title: Fed_SC 1

source_name: transfected with shscrambled


title: Fed_SC 3


title: Fed_GAA 2


title: Fed_SC 2


title: Fed_GAA 1


title: Thy_7.1_2

description: scRNA-seq


title: DBA4

first: Deena

last: Iskander

address: Du Cane Road

institute: Imperial College

data_processing:
Sequencing data was demultiplexed and 100 bp reads aligned to the GRCh38 3.0.0 using “STAR 2.5.3a”
Post-alignment QC was performed using Picard and Sequence Alignment/Map (SAM) tools
Raw counts at the gene level were obtained using the “Rsubread” Bioconductor package
Data normalization and differential expression analysis across different groups were performed using the “DESeq2” Bioconductor package
Genome_build: CRCh38 3.0.0
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: Bone marrow

extract_protocol:
Bone marrow mononuclear cells were thawed then 1000 to 80 000 CD71+GYPA+ EB were FACS-isolated from each sample. Total RNA was extracted and mRNA isolated by the NEBNext Poly (A) mRNA Magnetic Isolation Module, followed by first and second strand cDNA synthesis (NEBNext Directional RNA First and Second Strand Synthesis Modules), per the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: EB purified from thawed bone marrow

tag: diagnosis

value: DBA

tag: treatment for anemia

value: None; pre-treatment

tag: Sex

value: F


title: DBA5

value: Steroids


title: DBA3

value: Transfusions


title: scRNA-seq of TdTomato+ cells from PAH2 mouse


title: Con3

value: Healthy donor

value: Control


title: Con2

value: M


title: Con1


title: DBA2


title: S-N

city: Nagoya

first: Joyce

last: Cartagena

address: Furo-cho, Chikusa-ku

institute: Nagoya University

data_processing:
Adaptor sequences and low-quality reads/nucleotides were removed using trimmomatic (ver. 0.32).
Cleaned reads were used for mapping on reference sequence using bowtie (ver. 2-2.2.2) and tophat (ver. 2.0.11).
Assembly of transcripts and the calculation of the expression level were done using cufflinks (ver. 2.2.1).
Transcripts of all the samples obtained using cufflinks were assembled using cuffmerge (ver. 2.2.1).
Using cuffdiff (ver. 2.2.1), the expression level was compared among samples using the transcripts information obtained from the cuffmerge analysis.
Genome_build: IRGSP-1.0_genome.fa
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
Supplementary_files_format_and_content: COUNT_TRACKING File
Supplementary_files_format_and_content: FPKM_TRACKING File
Supplementary_files_format_and_content: diff

organism: Oryza sativa

source_name: nodal roots

growth_protocol: Growth condition: at 30°C/25°C, humidity of 70%/75% (day12h/night12h)

extract_protocol:
Total RNA was extracted from root tissues using RNeasy Plant Mini Kit (QIAGEN).
strand-specific mRNA-seq library (insert size 200 bp)

treatment_protocol: Control and salt treatment (50 mM NaCl) for 7 days

tag: treatment

value: Salt


title: S-L

source_name: L-type lateral roots


title: S-S

source_name: S-type lateral roots


title: C-N


title: C-S


title: C-L


title: DBA1


title: S-N1

data_processing:
Adaptor sequences and low-quality reads/nucleotides were removed using trimmomatic (ver. 0.32).
Cleaned reads were used for mapping on reference sequence using bowtie (ver. 2-2.2.2) and tophat (ver. 2.0.11).
Assembly of transcripts and the calculation of the expression level were done using cufflinks (ver. 2.2.1).
Transcripts of all the samples obtained using cufflinks were assembled using cuffmerge (ver. 2.2.1).
Using cuffdiff (ver. 2.2.1), the expression level was compared among samples using the transcripts information obtained from the cuffmerge analysis.
Genome_build: IRGSP-1.0_genome.fa
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: COUNT_TRACKING File
Supplementary_files_format_and_content: FPKM_TRACKING File

value: Mulai


title: C-N1


title: S-L1


title: C-L1


title: S-S1


title: C-S1


title: LEC treated biological replicate 2_10GY

city: Parkville

first: Matthew

last: Ritchie

state: Victoria

address: 1G Royal Parade

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
Sequenced reads were mapped to the hg19  human reference genome using the R/Bioconductor Rsubread package (version 1.10.5).
Gene-level counts were summarised using the featureCounts function of Rsubread.
Gene counts were normalised using the trimmed mean of M-values (TMM) methods in edgeR (version 3.8.1).
Sample and gene reweighting was performed using the voom function in the limma package (version 3.32.4).
Differential expression analysis was conducted using limma (version 3.32.4)
Genome_build: hg19
Supplementary_files_format_and_content: Summarised gene counts, columns are Entrez gene identifier, gene length (number of bases overlapping exons), and normalised read count.

source_name: LEC RNAseq radiotherapy timecourse

growth_protocol: Standardized numbers of each proliferating cell line were plated in cell culture flasks and irradiated once 80-90% confluence was achieved.

extract_protocol:
RNA extraction was undertaken at 4 hours using the QIAGEN® RNEasy Plus Universal Kit as per manufacturer's instructions.
Illumina Hiseq

treatment_protocol: Each proliferating cell line was subjected to a single dose of radiotherapy (10Gy) or no radiotherapy (0Gy - control).  For the ADSC and LEC cells, there was also a fractionated dose (5 x 2Gy over a 48 hour period).

tag: sequencing lane

value: LEC


title: PERI treated biological replicate 1_10GY

source_name: PERI RNAseq radiotherapy timecourse

value: PERI


title: NHEK treated biological replicate 1_10GY

source_name: NHEK RNAseq radiotherapy timecourse

value: NHEK


title: PERI untreated biological replicate 1_0GY


title: NHDF treated biological replicate 1_10GY

source_name: NHDF RNAseq radiotherapy timecourse

value: NHDF


title: LEC treated biological replicate 1_2GYx5


title: NHDF untreated biological replicate 2_0GY


title: PERI treated biological replicate 2_10GY


title: NHDF treated biological replicate 2_10GY


title: PERI untreated biological replicate 2_0GY


title: NHEK untreated biological replicate 1_0GY


title: LEC untreated biological replicate 2_0GY


title: LEC treated biological replicate 2_2GYx5


title: NHEK untreated biological replicate 2_0GY


title: NHDF untreated biological replicate 1_0GY


title: NHEK treated biological replicate 2_10GY


title: HMEC treated biological replicate 2_10GY

source_name: HMEC RNAseq radiotherapy timecourse

value: HMEC


title: LEC treated biological replicate 1_10GY


title: HMEC untreated biological replicate 2_0GY


title: HMEC untreated biological replicate 1_0GY


title: HMEC treated biological replicate 1_10GY


title: ADSC treated biological replicate 2_10GY

source_name: ADSC RNAseq radiotherapy timecourse

value: ADSC


title: ADSC untreated biological replicate 1_0GY


title: ADSC untreated biological replicate 2_0GY


title: ADSC treated biological replicate 2_2GYx5


title: ADSC treated biological replicate 1_2GYx5


title: U2OS_HNF4A8_BMAL1_ChIPseq_2

city: Los Angeles

first: Meng

last: Qu

state: California

address: 1002 West Childs Way

department: Keck Medical School

institute: University of Southern California

data_processing:
Illumina HiSeq 150 bp reads produced by ChIP-Seqs were mapped to the mm10 or hg38 genome using Bowtie2.
Peak calling was performed with MACS2.
Genome_build: mm10, hg38
Supplementary_files_format_and_content: bigWig files were merged replicates and generated using DeepTools with RPGC normalization. Peak files were generated by MACS2.

extract_protocol:
~ 50 mg of blood perfused liver tissue were dissected and snap frozen in liquid nitrogen. Frozen liver tissues were minced with razor blades and homogenized by pushing through 18G needle followed by 21G needle to release nuclei. Nuclei were immediately crosslinked with 1% formaldehyde for 10 min at room temperature and then quenched with glycine. After two washes, the nuclei were lysed in nuclear lysis buffer (50 mM Tris-HCl pH 8.0, 1% SDS, 10 mM EDTA) containing 1x EDTA-free protease inhibitor cocktail (Roche) and kept on ice for 5 min. Immediately, the lysates were sonicated 17 times for 30 sec by using Bioruptor (Diagenode). After centrifugation at 17,000 rpm for 15 minutes at 4°C, fragmented chromatin was diluted 10-fold with IP dilution buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% Triton X-100, 1 mM EDTA) supplemented with 1x EDTA-free protease inhibitor cocktail, and incubated with antibody overnight at 4°C. Dynabeads Protein G (Invitrogen cat. #10004D) was added to the chromatin and incubated for another 3 h. Afterwards, the beads were washed once with low salt wash buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA) and once with high salt wash buffer (20 mM Tris-HCl pH 8.0, 500 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA). IP elution buffer (1% SDS, 100 mM NaHCO3) was applied to the bead pellet and incubated at 30°C for 15 min. The eluate was added with NaCl to final conc. of 200 mM and reverse-crosslinked at 65°C overnight. To remove RNA and protein, RNase A and proteinase K were subsequently applied by incubating at 45°C for 1 h. Finally, DNA was purified with QIAquick PCR Purification columns.  ChIP-seq experiments with human cell lines were similar. The differences are the cells were crosslinked in culture dishes with 1% formaldehyde, and then scraped off for cell lysis and chromatin fragmentation.
2 ng of each sample was prepared using the NEB Ultra DNA Library Prep Kit for Illumina following manufacturer’s instructions. Each library was dual size selected with 0.55X and 0.14X Ampure beads followed by PCR amplification with Kappa HiFi 2x PCR mix (15 cycles). PCR product was then quantitated using the Qubit (Thermo Fisher) and BioAnalyzer (Agilent BioAnalyzer 2100) to determine library quantity. Libraries were then gel purified on a 2% agarose gel to remove secondary PCR amplification artifacts, quantitated on the Qubit and loaded onto HiSeq to generate more than 20M reads per sample.

value: HNF4A8 overexpressed

tag: chip antibody


title: LEC untreated biological replicate 1_0GY


title: U2OS_GFP(HNF4A8_control)_BMAL1_ChIPseq_1

tag: genotype

value: GFP overexpressed


title: U2OS_GFP(HNF4A8_control)_BMAL1_ChIPseq_2


title: ADSC treated biological replicate 1_10GY


title: Bcell_82-V7

city: Chicago

first: Slim

last: Fourati

state: Illinois

address: 300 E Superior St

department: Medicine

institute: Northwestern University

data_processing:
Raw reads were trimmed for low quality reads and miscalled nucleotides using Trimmomatic v. 0.33.
Reads that passed the trimming step were aligned to human genome (Ensembl GRCh38 release 80) using the STAR aligner (version 2.4.2a).
Aligned reads were counted using HTSeq (version 0.6.1).
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample.

source_name: Blood B cells

extract_protocol:
RNA was extracted from sorted cells from PBMC of HVTN 505 vaccinees using RNAzolRT (MRC Inc.) as per recommendations from the manufacturer.
Polyadenylated transcripts were purified on oligo-dT magnetic beads, fragmented, reverse transcribed using random hexamers and incorporated into barcoded cDNA libraries based on the Illumina TruSeq platform. Next, libraries were validated by electrophoresis, quantified, pooled and clustered on Illumina TruSeq v2 flow cells. Clustered flow cells were sequenced on an Illumina HiSeq (2000/4000) using 2 x 75 base paired-end runs.

tag: cell type

value: Blood B cells

tag: participant id

tag: visit id

tag: timepoint

value: month 7

value: Vaccine

tag: hiv-1 acquisition

value: No


title: Bcell_81-V2

value: pre-vaccination

value: Yes


title: Bcell_81-V9

value: month 12


title: Bcell_69-V9


title: Bcell_82-V9


title: Bcell_74-V7


title: Bcell_75-V2


title: Bcell_80-V9


title: Bcell_71-V2


title: Bcell_71-V7


title: Bcell_75-V7


title: Bcell_79-V7


title: Bcell_74-V2


title: Bcell_82-V2


title: Bcell_81-V7


title: Bcell_79-V9


title: Bcell_80-V7


title: Bcell_79-V2


title: Bcell_80-V2


title: Bcell_69-V7


title: Bcell_70-V2


title: Bcell_70-V7


title: Bcell_69-V2


title: Bcell_74-V9


title: U2OS_HNF4A8_BMAL1_ChIPseq_1


title: Bcell_68-V7


title: Bcell_68-V9


title: Bcell_64-V7


title: Bcell_62-V7


title: Bcell_63-V2


title: Bcell_57-V7


title: Bcell_63-V7


title: Bcell_55-V9


title: Bcell_57-V9


title: Bcell_61-V2


title: infected primary brain cell 14d - 1

city: Lille

first: Mathieu

last: Gissot

address: 1, rue du Pr. calmette

country: France

institute: CNRS

data_processing:
Clusters were generated on a flow cell within a cBot using the Cluster Generation Kit (Illumina), and libraries were sequenced as 50-bp reads on a HiSeq 2000 using a Sequence By Synthesis (SBS) technique (Illumina).
Image analysis and base calling were performed using the HiSeq Control Software and Real-Time Analysis component. Demultiplexing was performed using Illumina’s conversion software (bcl2fastq 2.17). The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software Sequence Analysis Viewer (SAV). Potential contaminants were investigated with the FastQ Screen software from the Babraham Institute.
Datasets were aligned with HiSAT2 v2.1.0  against the T. gondii ME49 genome from (ToxoDB-39)  and to the rat genome (Rattus norvegicus Rn6 (UCSC)). Final read alignments having more than three mismatches were discarded. Gene counting was performed using HTSeq-count 0.6.1p1 (union mode). Because the data come from a strand-specific assay, the read must be mapped to the opposite strand of the gene. Before statistical analysis, genes with less than 15 reads (combining all the analyzed samples) were filtered out. Differentially expressed genes were identified using the Bioconductor package edgeR 3.6.7. The data were normalized using the Relative Log Expression (RLE) normalization factors. Genes with adjusted p-values less than 5% (according to the FDR method from Benjamini-Hochberg) were declared differentially expressed.

organism:
Toxoplasma gondii
Rattus norvegicus

source_name: Brain cell primary culture infected with T. gondii 76K

growth_protocol: Intracellular parasite were grown for 1, 2, 4, 7 and 14 days

extract_protocol:
Total RNA was extrated using TRIzol reagent according to manufacturer’s protocol.
Library preparation was performed using the TruSeq Stranded mRNA Sample Preparation kit (Illumina) according to the manufacturer’s instructions. Libraries were validated using a Fragment Analyzer and quantified by qPCR (ROCHE LightCycler 480).

tag: tissue

value: Brain cell primary culture


title: Bcell_62-V2


title: Bcell_55-V2


title: Bcell_54-V9


title: Bcell_68-V2


title: infected primary brain cell 14d - 3


title: infected primary brain cell 14d - 2


title: Bcell_51-V7


title: Bcell_61-V7


title: Bcell_48-V7


title: Bcell_54-V7


title: Bcell_48-V9


title: infected primary brain cell 7d - 3


title: Bcell_64-V9


title: Bcell_62-V9


title: Bcell_55-V7


title: infected primary brain cell 7d - 2


title: MC

city: Xi'an

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

data_processing:
Useful Perl script was used to filter the original raw data, to trim Smart_seq2 public primer sequence from the reads , remove the contaminated reads for adapters, remove the low quality reads and remove the reads whose N base more than 5% for total bases . scRNA-seq data was processed using stander CellRanger pipeline.
Bowtie2 v2.2.3 was used for building the genome index, and clean data was mapped to the reference genome using TopHat v2.0.12. scRNA-seq data was processed using stander CellRanger pipeline.
Transcript assemble, difference expression anlysis was  finished by Cufflinks 2.2.1. scRNA-seq data was processed using stander CellRanger and Seurat pipeline.
Genome_build: Anas_platyrhynchos.BGI_duck
Supplementary_files_format_and_content: The BAM (Binary Alignment/Map) file format is a generic and highly compressed format for storing alignments.txt file could use as BAMs in Cuffquant to quantifies gene and transcript expression levels. Matrix file containing the transcription profiles of all single cells could be loaded to Seurat for further analysis.

organism: Anas platyrhynchos

source_name: PWBC scRNA-seq

growth_protocol: Seperated cells were maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, 100 μg/ml streptomycin and 2 mM L_glutamine. Cell cultures were incubated at 37°C/5% CO2.

extract_protocol:
Seperated single_cell samples were treated by Smart_Seq2 protocol to get amplified cDNA.
RNA libraries were prepared for sequencing using standard Illumina scRNA-seq and 10 × Chromium platform protocols

treatment_protocol: Peripheral blood samples from 45-week-old male specific pathogen-free (SPF) ducks and removed erythrocytes from blood samples using erythrocyte lysis solution. Then, cells were first separated by density gradient centrifugation using a duck lymphocyte isolation kit.The peripheral blood mononuclear cells (PBMCs), which were located in the middle layer, were further separated by differential adhesion in culture dishes preloaded with sterilized glass coverslips according to the different adherent properties of PBMCs.

value: peripheral white blood cells


title: Bcell_54-V2


title: Bcell_51-V2


title: infected primary brain cell 7d - 1


title: Bcell_46-V9


title: infected primary brain cell 4d - 3


title: infected primary brain cell 2d - 3


title: Bcell_46-V7


title: infected primary brain cell 4d - 2


title: infected primary brain cell 2d - 2


title: infected primary brain cell 2d - 1


title: infected primary brain cell 1d - 3


title: Bcell_43-V7


title: Bcell_43-V2


title: infected primary brain cell 1d - 2


title: Bcell_44-V2


title: Bcell_44-V7


title: Bcell_42-V9


title: Bcell_42-V7


title: Bcell_43-V9


title: infected primary brain cell 4d - 1


title: Bcell_40-V7


title: Bcell_48-V2


title: A375-BRAFV600E/NRASQ61K_1

city: Tucson

middle: Thomas

last: Wondrak

state: Arizona

address: UA Cancer Center, 1515 N Campbell Ave, Room 3971

department: Pharm/Tox

institute: University of Arizona

description: Total RNA analyzed for gene expression of 770 transcripts by nCounter PanCancer Progression panel

hyb_protocol: All samples were run targeting 100 ng of total RNA (19 h at 65°C) prior to being processed on the nCouner FLEX Analysis System.

scan_protocol: Samples were run on the nCounter Prep Station with high sensitivity settings followed by imaging on the Digital Analyzer with FOV (Field of View) data resolution set to 555.

data_processing:
Raw data files were uploaded (RCC files) to the NanoString nSolver Analysis 4.0 software. According to nSolver Advanced Analysis Module (version 2.0.115) specifications, the geNorm algorithm (pairwise variation statistics) was used to choose an ideal set of housekeeping genes (from a total set of 30) with minimal pairwise variation for normalization. Based on NanoString cancer pathway score analysis [indicating expression changes relevant to EMT (epithelial to mesenchymal transition)], a select number of genes (23 in total) displaying statistically significant expression changes was included in our manuscript, substantiating the specific role of NRAS-driven EMT changes in malignant melanoma.
The nCounterTM Advanced Analysis software (version 2.0.115) within a NanoString nSolver analysis 4.0 software was used for p-value adjustment (Benjamini-Yekutieli false discovery rate). Data with p-values lower than 0.05 were deemed statistically significant. Genes relevant to melanoma EMT were included in the tabular summary of expression changes as displayed in our manuscript.

label: reporter probe: fluorescent barcode; capture probe: biotin

label_protocol: NanoString nCounter gene expression assay protocol was followed (https://www.nanostring.com/wp-content/uploads/2021/03/MAN-10056-05-Gene-Expression-Hybridization-Protocol.pdf).

growth_protocol: Both isogenic malignant melanoma cell lines were grown in DMEM media supplemented with 10% FBS at 37°C, 5%CO2 (analysis occurred no later than 5 population doublings after thawing).

extract_protocol: Total RNA was extracted from cell lysates using Qiagen RNeasy Mini kit according to manufacturer instructions.

treatment_protocol: No special treatment was performed; two isogenic malignant melanoma cell lines differing in NRAS status [NRAS wildtype and NRAS mutant (NRAS Q61K)] were compared.

value: ATCC  CRL-1619IG-2-LUC2

value: malignant melanoma cell line


title: Bcell_59-V7


title: Bcell_39-V2


title: Bcell_28-V2


title: Bcell_34-V7


title: A375-BRAFV600E/NRASQ61_1

value: ATCC  CRL-1619-LUC2


title: A375-BRAFV600E/NRASQ61_2


title: Bcell_27-V7


title: Bcell_27-V9


title: A375-BRAFV600E/NRASQ61_3


title: infected primary brain cell 1d - 1


title: Bcell_63-V9


title: Bcell_42-V2