title: sg-Mrpl9_Bl_biorep1


title: rtgill.cat.3.A08

status: Public on Jan 01 2025

type: SRA

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description:
Library name: rtgill.cat.3.A08
Cell lysate
cat.counts.txt
cat.lib8_S1.A08.expression.values

library_source: transcriptomic

data_processing:
RNA-seq Analysis Portal (RAP; Qiagen)
Raw RNA Sequencing fastq files were submitted to QIAGEN’s RNA-seq Analysis Portal (RAP) (QIAGEN). First, raw files were demultiplexed to yield individual reads files for each sample (well) and then mapped to the rainbow trout genome (Omyk_1.0.105) to yield raw counts.
The counts were submitted to ExpressAnalyst for differential expression analysis and benchmark dose response analysis
Assembly: Omyk_1.0.105
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: total RNA

organism: Oncorhynchus mykiss

source_name: RTgill-W1 cat rep 3 conc 8

growth_protocol: Cells were grown in Thermo Scientific™ BioLite™ Cell Culture Treated 100 mm Petri dishes containing 10 ml of complete culture medium (Leibovitz L-15 culture medium supplemented with 10% fetal bovine serum and 1% Penicillin-Streptomycin), at 21°C.

extract_protocol:
OECD Test Guideline 249 for RTgill-W1 cell exposures, and QIAseq UPXome RNA Library Kits (QIAGEN) for library preparation
QIAseq UPXome RNA Library Kits (QIAGEN) protocol  for library preparation

tag: cell line

tag: cell type

value: Rainbow trout gill

tag: treatment


title: Control_1 td -ve

city: Toronto

first: Akram

last: Hamed

department: Molecular Genetics

institute: University of Toronto

description: tumourigenesis.atlas.RData

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were aligned to the mm10 mouse reference using Cell Ranger (v3.1.0). Doublets and multiplets were identified by scDblFinder (v1.4.0), and low-quality cells (percent of mitochondrial > 12%; number of genes detected per cell < 800; number of Unique Molecular Identifier (UMI) per cell < 500) were removed as part of the QC process. Seurat (v4.5) was used to cluster data from all samples together and perform the downstream analyses.
Assembly: mm10
Supplementary files format and content: Seurat RData - tumourigenesis atlas samples
Supplementary files format and content: Seurat RData - malignant cells from the Sox2CEPPT and NestinCPPT mouse models samples (isolated from the tumourigenesis atlas)
Supplementary files format and content: Seurat RData - brain injury samples (Sox2eGFP mice)

organism: Mus musculus

source_name: Brain

extract_protocol:
1) Tumourigenesis atlas samples: fresh brain tissue was harvested from mutant mice at four MRI-defined stages: the “preneoplastic” stage at which the brain imaging shows no signs of neoplastic lesion development; the “early lesion” stage characterized by small abnormalities seen on T2/FLAIR MRI sequences; the “mid-lesion” stage when the lesion has reached a larger size as indicated by T2/FLAIR-bright mass in asymptomatic animals and occupies a significant fraction of the brain hemisphere; and, finally, the “endpoint” stage when mice develop symptoms of raised intracranial pressure or focal neurologic abnormalities, with the tumour extending over a large portion of the brain hemisphere(s), typically with midline shift. Each brain sample was dissociated followed by fluorescent activated cell sorting to separate the mutant (tdTomato+) cells from non-mutant (tdTomato-) cells. Following sorting, both populations were characterized by scRNA-seq using the 10X Genomics platform. 2) Brain injury samples: we removed the cannula on day 5 and collected brain samples at the 5-days post-implantation (5dpi) timepoint as well as 7 days following the removal of the cannula (12dpi timepoint). For each timepoint, we processed the ipsilateral (IP) and contralateral (CR) hemispheres separately so the latter could serve as an internal control. Each sample was dissociated into single cells followed by FACS sorting of the GFP+ and GFP- cells and then each processed for scRNA-seq using the 10X Genomics platform.
We used the 10X Genomics platform according to the manufacturer's protocols.

tag: tissue

value: Brain

tag: genotype

value: Sox2CreER/+; R26td/td


title: sg-Gba_Bl_biorep5

city: Rochester

first: Kirk

last: Wangensteen

state: MN

address: GU1034H, 222 3rd Ave SW

department: Gastroenterology & Hepatology

country: USA

institute: Mayo Clinic

data_processing:
Base call (.bcl) files for each cycle of sequencing were generated by Illumina Real Time Analysis (RTA) software.
2 x 150bp FastQ paired-end reads for 30 samples (n=19.6 Million average reads per sample) were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.
Read mapping was performed via Hisat2 (v2.1.0) using the mouse genome (Mus musculus GRCm39.109) as a reference.
Gene quantification was done via Feature Counts for raw read counts.
Assembly: mm39
Supplementary files format and content: Compressed fastq files contain raw read1 and read2 data
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: liver tumor

extract_protocol:
Total RNA was extracted from approximately 25 mg of liver tumor tissue using the Qiagen RNeasy plus mini kit (Qiagen #74134).
Thirty unique dual-indexed libraries were created using the TruSeq stranded mRNA library preparation kit (Illumina #20020594).

value: liver tumor

value: dCas9+ Black

tag: strain

value: Myc-CRISPRa-sg-Gba


title: rtgill.cat.3.B08

description:
Library name: rtgill.cat.3.B08
Cell lysate
cat.counts.txt
cat.lib8_S1.B08.expression.values

source_name: RTgill-W1 cat rep 3 conc 7


title: Control_1

description: tumourigenesis.atlas.RData


title: sg-Gba_Bl_biorep4


title: BAT, WT, 30C, replicate1

city: Ube

first: Katsuya

last: Tanabe

state: Yamaguchi

address: 1-1-1 Minamikogushi

country: Japan

institute: Yamaguchi University

data_processing:
The bcl2fastq conversion software version 2.19.1.403 was used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Alignment: Raw sequence reads were aligned to the UCSC mm10 reference genome and displayed using UCSC annotated genes using STAR version 2.7.5a with default parameters.
Alingment files were transformed into "Tag Directory" using Homer version 4.11.1  “makeTagDirectory", then differantial gene expression alaysis (DeSeq2) was perfomed using Homer　“getDiffExpression.pl"
TPM files were created using Homer "analyzeRepeats.pl" and specifying "-count exons -tpm" .
Assembly: mm10
Supplementary files format and content: DeSeq2 analysis were performed using HOMER.
Supplementary files format and content: TPM files were generated using HOMER.

source_name: brown adipose tissue

growth_protocol: Txnip-deficient (TxnipKO) and wild-type (WT) mice were acclimated to room temperature (23°C) or thermoneutrality (30°C) for 1week

extract_protocol:
Total RNA was isolated from brown adipose tissue using Direct-zol RNA Miniprep Plus Kit (Zymo Research). Polyadenylated mRNA was purified from 500 ng of total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Sequencing libraries were prepared using NEBNext Ultra II RNA LibraryPrep Kit for Illumina (NEB) according to manufacturer's instructions. Library concentrations were quantified by a Bioanalyzer (Agilent).

value: brown adipose tissue

tag: Sex

value: male

tag: age

value: 10 week old

value: WT

value: 30 C (thermoneutrality)


title: Screen total sequencing repeat 2

city: changsha

first: shen

last: yunfan

state: hunan

address: xiangya road

country: China

institute: central south university

library_source: genomic

data_processing:
The sequencing results were analyzed by the MAGeCK package, which took into consideration the magnitude of enrichment/depletion and the consistency of multiple sgRNAs targeting the same gene, to rank positive/negative regulators.
Assembly: mm10
Supplementary files format and content: Text file displaying sgRNA information was generated by MAGeCK

molecule: genomic DNA

growth_protocol: E14 mESCs were cultured on gelatin-coated dishes in DMEM (High Glucose, with Sodium Pyruvate, with L-Alanyl-L-Glutamine) (Vivacell) supplemented with 15% fetal bovine serum (Vistech), 1× non-essential amino acids (Gibco), 100 μM β-mercaptoethanol (Sigma), and 1000 U/mL of leukemia inhibitory factor (LIF) (Millipore). The cells were incubated at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
Genomic DNA of MERVL-positive and total cells was extracted by phenol/chloroform.
Guide RNA sequences were then amplified using two-round PCR.The PCR products were extracted through agarose gel electrophoresis.

treatment_protocol: The mouse CRISPR-Cas9 library was based on the lentiCRISPRv2 backbone, containing 130209 gRNAs targeting 20611 genes.To construct the ESC library, a total of ~130 million ESCs with the tdTomato reporter were transduced with lentivirus for 24 h in the presence of 4 μg/mL polybrene. The cells were then selected with puromycin (2 μg/mL) for 48 h and then cultured with fresh medium. At day 5, around 0.5 million 2C-positive cells were then sorted through FACS based on tdTomato reporter expression.

value: mouse embryonic stem cell

value: MERVL-tdTomato


title: BAT, TxnipKO, 23C, replicate3

value: Txnip knockout

value: 23 C (room temperature)


title: rtgill.cat.2.G08

description:
Library name: rtgill.cat.2.G08
Cell lysate
cat.counts.txt
cat.lib3_S1.G08.expression.values

source_name: RTgill-W1 cat rep 2 conc 2


title: rtgill.cat.2.H08

description:
Library name: rtgill.cat.2.H08
Cell lysate
cat.counts.txt
cat.lib3_S1.H08.expression.values

source_name: RTgill-W1 cat rep 2 conc 1


title: sg-Vps72_Alb_biorep4

value: dCas9+ albino


title: sg-Vps72_Alb_biorep3


title: BAT, WT, 23C, replicate3


title: sg-Gba_Bl_biorep1


title: rtgill.cat.2.E08

description:
Library name: rtgill.cat.2.E08
Cell lysate
cat.counts.txt
cat.lib3_S1.E08.expression.values

source_name: RTgill-W1 cat rep 2 conc 4


title: Screen total sequencing repeat 1


title: Control_2

description: tumourigenesis.atlas.RData


title: sg-Gba_Bl_biorep2


title: BAT, TxnipKO, 23C, replicate1


title: rtgill.cat.2.F08

description:
Library name: rtgill.cat.2.F08
Cell lysate
cat.counts.txt
cat.lib3_S1.F08.expression.values

source_name: RTgill-W1 cat rep 2 conc 3


title: BAT, WT, 23C, replicate2

value: 23°C (room temperature)


title: Screen MERVL-positive sequencing repeat 1


title: BAT, WT, 23C, replicate1


title: Sipuleucel-T + IL15 4_1

city: St. Louis

first: Kavita

last: Rwat

state: MO

address: St. Louis

department: Oncology

institute: Washington University in St. Louis

data_processing:
CLC Genomics Workbench 24
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
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.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package. GATK (v4.1.1.0) software was used to perform SNP calling. rMATS(4.1.0) software was used to analysis the AS event.
Assembly: hg38
Supplementary files format and content: tab-delimited xls file include raw counts for each sample
Supplementary files format and content: tab- delimited xls file include sample readCount, FKPM and FKPM of each gene group

source_name: skin tumor

growth_protocol: LnCAP cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified cell incubatore at 37C with 5% CO2.

extract_protocol:
Sample RNA was isolated using TRizol  following manufacturer’s recommendation.
The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.
Sample RNA was isolated using TRizol (Invitrogen) following manufacturer’s recommendation. Illumina sequencing libraries were constructed by Novogene Co., Ltd.

treatment_protocol: To evaluate the effect of IL-15 treated sip-T on in vivo tumor growth, LNCaP cells (3 × 106) were subcutaneously injected in mice in 200 µl RPMI with 50% matrigel. Once average tumor sizes reached 50-100 mm2, mice received four injections of IL-15 treated, or control sip-T (5x106/100 µl in PBS, intraperitoneally) with one-week intervals. rhIL-15 (1 µg) was also injected subcutaneously at the time of sip-T injection. All control mice were sham dosed with vehicle (PBS). On day 7 post-last-sip-T injection, mice were humanely euthanized by carbon dioxide inhalation followed by cervical dislocation and tissues collected for analysis.

value: skin tumor

value: LnCAP

value: epithelial prostate cancer

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ

value: control sip-T (5x10^6/100 µl in PBS, intraperitoneally) with rhIL-15 (1 µg)


title: Sipuleucel-T + IL15 5_1


title: Screen MERVL-positive sequencing repeat 2


title: rtgill.cat.2.D08

description:
Library name: rtgill.cat.2.D08
Cell lysate
cat.counts.txt
cat.lib3_S1.D08.expression.values

source_name: RTgill-W1 cat rep 2 conc 5

value: Rainbow trout gill


title: BAT, 30C, H3K27ac ChIP, TxnipKO2

data_processing:
The bcl2fastq conversion software version 2.19.1.403 was used for base-calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Alignment: Raw sequence reads were aligned to the UCSC mm10 reference genome and displayed using UCSC annotated genes using bowtie2 version 2.2.6 with default parameters.
Visualization in the Integrative Genomics Viewer (IGV): Alingment files were transformed into "Tag Directory" using Homer version 4.11.1  “makeTagDirectory", then bedgraph files were created using Homer "makeUCSCfile" and specifying "-norm 1e7" for normalization to 10 million reads.
Assembly: mm10
Supplementary files format and content: Bedgraph files were generated using HOMER.

extract_protocol:
The BAT pads were minced in ice-cold PBS and dissociated into single-cell suspensions using the Adipose Tissue Dissociation Kit (Miltenyi Biotec). Collected cell pellets were fixed in 2mM DSG for 30 min and cross-linked with 1% formaldehyde for 10 min. Cross-linking was quenched with addition of 125 mM glycine for 5 min and followed by twice ice-cold 1× PBS washes. Cross-linked cell pellets were re-suspended in ice-cold Shearing Buffer (50 mM Tris pH 8.0, 10 mM EDTA pH 8.0, 1% SDS, and protease inhibitor) and sonicated with a Biorupter (UCD300, Cosmo Bio) to shear chromatin to 200-1000bp fragments. Sonicated chromatin lysates were incubated with the antibody against H3K27ac (CST#8173) at 4 °C overnight and then immunoprecipitated with IgG paramagnetic beads (Invitrogen). Chromatin immune complexes were eluted twice in Bead Elution Buffer (0.1 M NaHCO3 and 1% SDS). The eluted chromatin was de-crosslinked overnight in 0.2M NaCl at 65 °C and the associated proteins were digested with proteinase K. The final DNA was purified with the MinElute PCR Purification Kit (Qiagen).
Sequencing libraries were generated using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer's instructions. Library concentrations were quantified by a Bioanalyzer (Agilent)

value: brown adipose tissue

value: Male

tag: chip antibody


title: BAT, TxnipKO, 23C, replicate2

value: male

value: 10 week old


title: rtgill.cat.2.B08

description:
Library name: rtgill.cat.2.B08
Cell lysate
cat.counts.txt
cat.lib3_S1.B08.expression.values

source_name: RTgill-W1 cat rep 2 conc 7


title: rtgill.cat.2.A08

description:
Library name: rtgill.cat.2.A08
Cell lysate
cat.counts.txt
cat.lib3_S1.A08.expression.values

source_name: RTgill-W1 cat rep 2 conc 8


title: Sipuleucel-T + IL15 3_1


title: sg-Vps72_Alb_biorep2

value: liver tumor


title: rtgill.cat.1.H08

description:
Library name: rtgill.cat.1.H08
Cell lysate
cat.counts.txt
cat.lib12_S1.H08.expression.values

source_name: RTgill-W1 cat rep 1 conc 1


title: BAT, WT, 30C, replicate2

value: WT

value: 30 C (thermoneutrality)


title: sg-Vps72_Alb_biorep1


title: Sipuleucel-T + IL15 2_1


title: BAT, 30C, H3K27ac ChIP, TxnipKO1

value: Txnip knockout


title: sg-Gba_Bl_biorep3

value: dCas9+ Black

value: Myc-CRISPRa-sg-Gba


title: rtgill.cat.2.C08

description:
Library name: rtgill.cat.2.C08
Cell lysate
cat.counts.txt
cat.lib3_S1.C08.expression.values

source_name: RTgill-W1 cat rep 2 conc 6


title: sg-Zbtb7b_Bl_biorep5


title: BAT, 30C, H3K27ac ChIP, WT2


title: sg-Zbtb7b_Bl_biorep4


title: rtgill.cat.1.G08

description:
Library name: rtgill.cat.1.G08
Cell lysate
cat.counts.txt
cat.lib12_S1.G08.expression.values

source_name: RTgill-W1 cat rep 1 conc 2


title: BAT, 30C, H3K27ac ChIP, WT1


title: Sipuleucel-T + IL15 1_1


title: Sipuleucel-T 5_1

value: control sip-T (5x10^6/100 µl in PBS, intraperitoneally)


title: rtgill.cat.1.F08

description:
Library name: rtgill.cat.1.F08
Cell lysate
cat.counts.txt
cat.lib12_S1.F08.expression.values

source_name: RTgill-W1 cat rep 1 conc 3


title: BAT, 30C, Input, TxnipKO2


title: sg-Zbtb7b_Bl_biorep2


title: BAT, 30C, Input, WT2


title: Sipuleucel-T 4_1

value: skin tumor


title: sg-Zbtb7b_Bl_biorep3


title: Sipuleucel-T 2_1

value: LnCAP


title: BAT, 30C, Input, WT1


title: Sipuleucel-T 3_1

value: epithelial prostate cancer


title: sg-Zbtb7b_Bl_biorep1


title: rtgill.cat.1.B08

description:
Library name: rtgill.cat.1.B08
Cell lysate
cat.counts.txt
cat.lib12_S1.B08.expression.values

source_name: RTgill-W1 cat rep 1 conc 7


title: rtgill.cat.1.D08

description:
Library name: rtgill.cat.1.D08
Cell lysate
cat.counts.txt
cat.lib12_S1.D08.expression.values

source_name: RTgill-W1 cat rep 1 conc 5


title: sg-NT_Bl_biorep5

source_name: liver tumor

value: Myc-CRISPRa-sg-NT


title: Sipuleucel-T 1_1

value: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ


title: BAT, 30C, Input, TxnipKO1


title: rtgill.cat.1.A08

description:
Library name: rtgill.cat.1.A08
Cell lysate
cat.counts.txt
cat.lib12_S1.A08.expression.values

source_name: RTgill-W1 cat rep 1 conc 8

value: Rainbow trout gill


title: sg-NT_Bl_biorep4


title: Bone Marrow cells, Female, rep5

city: Cleveland

first: Vladimir

last: Makarov

state: OH

address: 9500 Euclid Ave

department: CITI

institute: CLEVELAND CLINIC LERNER COM-CWRU

data_processing:
FASTQ aligned using STAR, featureCounts program is used to map reads for each gene in GRCm38.p6
Differential Gene expression analysis performed using Deseq
Assembly: mm10
Supplementary files format and content: comma separated file with raw counts
Supplementary files format and content: comma separated file with Deseq normalized counts

source_name: bone marrow

extract_protocol:
Fresh bone marrow was flushed from a single hindlimb from male and female mice. Lineage-depleted populations were separated via magnetic bead separations (Miltenyi Biotec). Separated cell populations were lysed and RNA isolated with the RNA mini plus isolation kit (Qiagen). Samples were sent the same day on dry ice to Azenta for RNA sequencing.
RNAseq libraries were prepared by Azenta life sciences

value: bone marrow

value: primary cells

value: hematopoietic stem and progenitor cell

value: Female


title: LIVER,KO,REP2

city: Milano

first: Diletta

last: Dolfini

state: MI

address: Via Celoria, 26

department: Bioscience

country: Italy

institute: University of Milan

data_processing:
RNA-seq was aligned and transcript quantified with nf-core/RNA-seq pipeline v.3.6. Pipeline set with STAR aligner and RSEM quantifier, indexed on Refseq gtf for mm10 genome.
nextflow run nf-core/rnaseq --aligner 'star_rsem' --rsem_index $RSEM_INDEX --input $LOCAL/documents/metadata_liver.csv --multiqc_title liver-mouse-opa1 --outdir $LOCAL/data/nf_results --fasta $GENOME_FASTA --gtf $GENOME_GTF  --skip_stringtie --max_cpus 16 -profile docker -r 3.6  -bg
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including gene counts and tpm for each Sample
Supplementary files format and content: Tab-delimited text files including transcript counts and tpm for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted from liver using the Monarch total RNA miniprep kit (New England Biolabs) according to manufacturer’s instructions
Quality checked RNA was used for library preparation with Illumina stranded mRNA Prep ligation kit (Illumina, #20040532). Libraries were then Concentrated and fragmentated using the Qubit fluorimeter (Invitrogen) and Tape Station system (Agilent) with developer kits (Qubit dsDNA HS Assay Kit, 500 assay, Thermo fisher, # Q32854) (ScreenTape D1000, #5067-5582, Reagents ScreenTape D1000, #5067-5583, Agilent) according to developers’ instruction

value: liver

value: OPA1 LKO

value: High Fat Diet


title: rtgill.cat.1.C08

description:
Library name: rtgill.cat.1.C08
Cell lysate
cat.counts.txt
cat.lib12_S1.C08.expression.values

source_name: RTgill-W1 cat rep 1 conc 6


title: sg-NT_Bl_biorep6

value: liver tumor


title: LIVER,KO,REP3


title: rtgill.thx.3.H07

description:
Library name: rtgill.thx.3.H07
Cell lysate
thx.counts.txt
thx.lib8_S1.H07.expression.values

source_name: RTgill-W1 thx rep 3 conc 1


title: rtgill.cat.1.E08

description:
Library name: rtgill.cat.1.E08
Cell lysate
cat.counts.txt
cat.lib12_S1.E08.expression.values

source_name: RTgill-W1 cat rep 1 conc 4


title: LIVER,KO,REP1


title: rtgill.thx.3.G07

description:
Library name: rtgill.thx.3.G07
Cell lysate
thx.counts.txt
thx.lib8_S1.G07.expression.values

source_name: RTgill-W1 thx rep 3 conc 2


title: sg-NT_Bl_biorep2

value: dCas9+ Black


title: rtgill.thx.3.F07

description:
Library name: rtgill.thx.3.F07
Cell lysate
thx.counts.txt
thx.lib8_S1.F07.expression.values

source_name: RTgill-W1 thx rep 3 conc 3


title: Bone Marrow cells, Female, rep3


title: Bone Marrow cells, Female, rep4


title: LIVER,WT,REP5

value: CTRL


title: Bone Marrow cells, Female, rep2


title: LIVER,WT,REP4


title: rtgill.thx.3.D07

description:
Library name: rtgill.thx.3.D07
Cell lysate
thx.counts.txt
thx.lib8_S1.D07.expression.values

source_name: RTgill-W1 thx rep 3 conc 5


title: Bone Marrow cells, Male, rep5

value: Male


title: rtgill.thx.3.E07

description:
Library name: rtgill.thx.3.E07
Cell lysate
thx.counts.txt
thx.lib8_S1.E07.expression.values

source_name: RTgill-W1 thx rep 3 conc 4


title: sg-NT_Alb_biorep5

value: dCas9+ albino


title: LIVER,WT,REP3


title: Bone Marrow cells, Female, rep1


title: LIVER,WT,REP2


title: sg-NT_Alb_biorep4


title: rtgill.thx.3.C07

description:
Library name: rtgill.thx.3.C07
Cell lysate
thx.counts.txt
thx.lib8_S1.C07.expression.values

source_name: RTgill-W1 thx rep 3 conc 6


title: rtgill.thx.3.B07

description:
Library name: rtgill.thx.3.B07
Cell lysate
thx.counts.txt
thx.lib8_S1.B07.expression.values

source_name: RTgill-W1 thx rep 3 conc 7


title: Bone Marrow cells, Male, rep4


title: sg-NT_Alb_biorep3


title: sg-NT_Alb_biorep2


title: Endometrium12

city: Guangzhou

first: Xupeng

last: Zang

address: No. 483, Wushan Road, Tianhe District

institute: South China Agricultural University

description: 10X Genomics

data_processing:
The 10X Genomics scRNA-seq data were processed to quantify gene counts using the Cell Ranger pipeline (v.6.1.2) with default parameters.
Assembly: Sscrofa11.1
Supplementary files format and content: Tab-separated values files and matrix files.

organism: Sus scrofa

source_name: Endometrium

extract_protocol:
Pig embryos and endometrial samples from days 9 and 12 of pregnancy were rinsed several times with DPBS, minced into small pieces with a scissor, and transferred to the pre-cooled EP tubes. For embryos, the minced tissues were digested in a pre-warmed enzyme cocktail Ⅰ, which contains papain, dispase and DNase Ⅰ, at 37°C for 30 min. While endometrial tissues were digested in an enzyme cocktail II, including type II collagenase, type IV collagenase, dispase and DNase Ⅰ. The dissociated cell suspension was terminated with DMEM medium containing 10% fetal bovine serum (FBS), passed through a 70-μm sterile cell strainer and centrifuged at 500g for 5 min at 4°C. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer and incubated at room temperature for 5 min to exclude remaining red blood cells. Finally, the cell pellets were washed twice and resuspended in DPBS containing 0.04% bovine serum albumin (BSA) for further single-cell RNA sequencing analysis.
Single-cell suspensions were loaded on a Chromium Single Cell Controller (10X Genomics) according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3’ Reagent Kit V3 User Guide). All subsequent steps were performed following a standard manufacturer’s protocols.

value: Endometrium

tag: developmental stage

value: day 12 of pregnancy


title: Bone Marrow cells, Male, rep2


title: rtgill.thx.2.G07

description:
Library name: rtgill.thx.2.G07
Cell lysate
thx.counts.txt
thx.lib3_S1.G07.expression.values

source_name: RTgill-W1 thx rep 2 conc 2


title: sg-NT_Alb_biorep1

value: Myc-CRISPRa-sg-NT


title: rtgill.thx.2.H07

description:
Library name: rtgill.thx.2.H07
Cell lysate
thx.counts.txt
thx.lib3_S1.H07.expression.values

source_name: RTgill-W1 thx rep 2 conc 1


title: sg-NT_Bl_biorep1


title: sg-NT_Bl_biorep3


title: Bone Marrow cells, Male, rep3


title: Endometrium09

description: 10X Genomics

value: day 9 of pregnancy


title: LIVER,WT,REP1


title: Bone Marrow cells, Male, rep1


title: Embryo12

description: 10X Genomics

source_name: Embryo

value: Embryo


title: macrophage, HFD, CKO_3

city: Hangzhou

first: Rifeng

last: Gao

state: Zhejiang

address: No. 88 Jiefang Road

institute: Zhejiang University

data_processing:
RNA quantification and qualification:RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) . RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
Library preparation for Transcriptome sequencing:A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.  Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo attached magnetic beads.  Fragmentation was carried out using divalent cations under elevated temperature  in NEBNext First Strand Synthesis Reaction Buffer(5X).  First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-).  Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities.  After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization.  In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).  Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR.  Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer.  Atlast, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
Clustering and sequencing: The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
Data Analysis: 1. Data quality control Use fastp v 0.19.3 to filter the original data, mainly to remove reads with adapters; when the N content in any sequencing reads exceeds 10% of the base number of the reads, remove the paired reads; when any sequencing reads When the number of low quality (Q<=20) bases contained in reads exceeds 50% of the bases of the reads, this paired reads will be removed. All subsequent analyses are based on clean reads. 2. Reads mapping to the reference genome Download the reference genome and its annotation files from the designated website, use HISAT v2.1.0 to construct the index, and compare clean reads to the reference genome. 3. New transcript prediction Use StringTie v1.3.4d for new gene prediction. StringTie applies network streaming algorithms and optional de novo to splice transcripts. Compared with Cufflinks and other software, StringTie can splice a more complete and accurate transcript, and the splicing speed is faster. 4. Quantification of gene expression levels Use featureCounts v1.6.2 to calculate the gene alignment, and then calculate the FPKM of each gene based on the gene length. FPKM is currently the most commonly used method to estimate gene expression levels. 5. Difference analysis DESeq2 v1.22.1 was used to analyze the differential expression between the two groups, and the P value was corrected using the Benjamini & Hochberg method. The corrected P value and |log2foldchange| are used as the threshold for significant difference expression. 6. Differential gene enrichment analysis The enrichment analysis is performed based on the hypergeometric test. For KEGG, the hypergeometric distribution test is performed with the unit of pathway; for GO, it is performed based on the GO term. 7. Differential AS analysis Use rMATS v3.1.0 to analyze variable splicing events, including five alternative splicing events: SE, RI, MXE, A5SS, and A3SS. 8. SNP analysis Use GATK v4.0.11.0 to analyze the variant sites, and use annovar to annotate the variant sites. 9. Differential gene protein interaction analysis The protein interaction analysis of differentially expressed genes is based on the STRING database of known and predicted protein--protein interactions. For the species existing in the database, we construct the network by extracting the target gene list from the database; otherwise, use blast v2.7.1+ to compare the target gene sequence with the selected reference protein sequence, and then according to the selected reference species Know the interaction to build a network. 10. GSEA Use gsea--3.0.jar for gene set enrichment analysis. 11. WGCNA Use WGCNA v1.69 for weighted gene co--expression network analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: macrophage

growth_protocol: RNA-seq analysis was performed on sorted macrophages from ALKBH5 control (WT, ALKBH5flox/flox, APOE-/-) mice and ALKBH5 macrophage-specific knockout (CKO,  ALKBH5flox/flox, Lyz2-Cre, APOE-/-) mice.

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
Then the libraries were constructed using TruSeq Stranded mRNALTSample Prep Kit(Ilumina,San Diego, CA, USA) .

treatment_protocol: Mice fed a high-fat diet for 4 months

value: macrophage

value: ALKBH5flox/flox, Lyz2-Cre, APOE-/-

value: High-fat diet


title: WGBS-Control mESC, without 4OHT 6-days, rep#2

city: SAN DIEGO

first: Anjana

last: Rao

state: CALIFORNIA

address: 9420 Athena CIRCLE, LA JOLLA

institute: LA JOLLA INSTITUTE

description: Ogt fl/flmESC non treated with 4-OHT for 6 days to generatecontrol mESC samples

data_processing:
Raw data was aligned to mm10 genome + lambda genome, using bsmap aligner for methylation data.
Output files went to duplicate removal using picard and then subject of methylation call using mcall
Assembly: mm10
Supplementary files format and content: Processed methratio files contain CG counts after processed with methratio and aligned with bsmap.

source_name: mESC

growth_protocol: mESC were cultured over mitomycin C-treated mouse embryonic fibroblasts (MEFs) as feeder cells and using knockout DMEM medium  supplemented with LIF, 15% KOSR (KnockOut Serum Replacement), GlutaMAX, 1x MEM nonessential amino acids  and 50 μM β-mercaptoethanol.

extract_protocol:
In order to ensure a high purity of our samples, we isolate specifically the YFP+ population (in the case of 4-OHT-treated Ogt iKO mESC) at the same time that eliminating the presence of mitomycin-C-treated MEFs (used as feeders during our mESC cultures) by FACS (Fluorescence-Activated Cell Sorting) using a FACSAria cell sorter (BD Biosciences). The dissociated mESC were first labeled with the eBioscienceTM Fixable Viability Dye eFluorTM 780 (ThermoFisher, 65- 0865-14) to select viable cells and then stained for surface markers with indicated fluorochrome-conjugated antibodies diluted in FACS buffer (PBS 1X, 0.5% BSA, 0.01% NaN3): CD90.2 (Biolegend, 140319) to positively distinguish the mESC and CD326 (Biolegend, 118227) to negatively exclude MEFs.
Genomic DNA was isolated using a genomic DNA mini kit or FlexiGene DNA Kit (Qiagen, 51206). Unmethylated lambda DNA (Promega, D1521) was spiked into the genomic DNA samples at a ratio of 1:200 to monitor the bisulfite conversion efficiency. The samples were then sheared using Covaris S2, purified with Ampure XP beads (Beckman Coulter) and processed with end repair and dA-Tailing Modules, and ligated to methylated Illumina Adaptors using a quick ligation module. DNA with ligated adaptors was then treated with sodium bisulfite for 4hrs and amplified with index primers using KAPA HiFi HotStart Uracil+ Ready Mix (KAPA Biosystems).

treatment_protocol: To generate Ogt iKO samples, Ogt fl/fl mESCwere cultured during  6 days in presence of 4-OHT; To generate control mESC (Ctrl), Ogt fl/fl were cultured in ES media without 4-OHT.

value: mESC

value: Mouse Embrionic Stem Cells

value: Ogt fl/fl

value: without 4OHT for 6 days


title: macrophage, HFD, CKO_2


title: rtgill.thx.3.A07

description:
Library name: rtgill.thx.3.A07
Cell lysate
thx.counts.txt
thx.lib8_S1.A07.expression.values

source_name: RTgill-W1 thx rep 3 conc 8

value: Rainbow trout gill


title: WGBS-Control mESC, without 4OHT 6-days, rep#1


title: Embryo09

description: 10X Genomics


title: macrophage, HFD, CKO_1


title: macrophage, HFD, WT_3

value: ALKBH5flox/flox, APOE-/-


title: rtgill.thx.2.D07

description:
Library name: rtgill.thx.2.D07
Cell lysate
thx.counts.txt
thx.lib3_S1.D07.expression.values

source_name: RTgill-W1 thx rep 2 conc 5


title: Trigeminal ganglia, pooled, HH1718, biological replicate 3, technical replicate 2

city: Washington

first: Chunling

last: Yi

state: DC

address: 3700 O St NW

institute: Georgetown University

description:
Library name: HH1718_3_02
HH1718.B3.T2

data_processing:
Adapters Trimmed with TrimGalore
Reads Mapped to Genome with HISAT2
Quantifications of Reads-Mappping using Feature Counts
Assembly: bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: Raw Counts Before Filtering and Normalization

organism: Gallus gallus

source_name: trigeminal ganglion

extract_protocol:
Total RNA was isolated from pooled trigeminal ganglia using RNAqueous Total RNA Isolation kit (ThermoFisher).
RNA concentration and integrity were quantified with Nanodrop (ThermoFisher) and Agilent 2100 Bioanalyzer. PolyA-enriched cDNA libraries were prepared using TruSeq sample preparation kit (Illumina), followed by assessment of quality and quantity with the Bioanalyzer.

value: trigeminal ganglion

value: wildtype

tag: lane


title: macrophage, HFD, WT_2


title: Trigeminal ganglia, pooled, HH1718, biological replicate 2, technical replicate 2

description:
Library name: HH1718_2_02
HH1718.B2.T2


title: RNAseq-Control mESC, without 4OHT 6-days, rep#2

description: Ogt fl/flmESC without 4-OHT for 6 days to generatecontrol mESC samples

data_processing:
Raw files were aligned using STAR to mm10 genome and then went to duplicates removal using picard
Assembly: mm10
Supplementary files format and content: Processed files contain gene raw counts generated with STAR

molecule: polyA RNA

extract_protocol:
In order to ensure a high purity of our samples, we isolate specifically the YFP+ population (in the case of 4-OHT-treated Ogt iKO mESC) at the same time that eliminating the presence of mitomycin-C-treated MEFs (used as feeders during our mESC cultures) by FACS (Fluorescence-Activated Cell Sorting) using a FACSAria cell sorter (BD Biosciences). The dissociated mESC were first labeled with the eBioscienceTM Fixable Viability Dye eFluorTM 780 (ThermoFisher, 65- 0865-14) to select viable cells and then stained for surface markers with indicated fluorochrome-conjugated antibodies diluted in FACS buffer (PBS 1X, 0.5% BSA, 0.01% NaN3): CD90.2 (Biolegend, 140319) to positively distinguish the mESC and CD326 (Biolegend, 118227) to negatively exclude MEFs.
RNA-sequencing libraries were prepared using Truseq stranded mRNA kit (Illumina) according to the manufacture’s protocol. All libraries were assessed using Qubit™ RNA HS Assay Kit (ThermoFisher, Q32855) and TapeStation High Sensitivity RNA ScreenTape Analysis (Agilent, 5067-5579).


title: rtgill.thx.2.F07

description:
Library name: rtgill.thx.2.F07
Cell lysate
thx.counts.txt
thx.lib3_S1.F07.expression.values

source_name: RTgill-W1 thx rep 2 conc 3


title: rtgill.thx.2.A07

description:
Library name: rtgill.thx.2.A07
Cell lysate
thx.counts.txt
thx.lib3_S1.A07.expression.values

source_name: RTgill-W1 thx rep 2 conc 8


title: Trigeminal ganglia, pooled, HH1718, biological replicate 1, technical replicate 2

description:
Library name: HH1718_1_02
HH1718.B1.T2


title: rtgill.thx.2.B07

description:
Library name: rtgill.thx.2.B07
Cell lysate
thx.counts.txt
thx.lib3_S1.B07.expression.values

source_name: RTgill-W1 thx rep 2 conc 7


title: RNAseq-Ogt_iKO mESC, +4OHT 6-days, rep#2

description: Ogt fl/flmESC treated with 4-OHT for 6 days to generateOgt iKOmESC samples

value: 4OHT for 6 days


title: Trigeminal ganglia, pooled, HH1718, biological replicate 2, technical replicate 1

description:
Library name: HH1718_2_01
HH1718.B2.T1


title: gB-specific B cells

first: Cong

last: Sun

state: Guangdong

address: No.651 Dongfeng East Road

department: Cancer Center

institute: Sun Yat-sen University

description:
NP-gB
10x Genomics VDJ + GEX

data_processing:
Alignment, filtering, barcode counting, UMI counting on the Gene Expression libraries and sequence assembly and paired clonotype calling on the V(D)J libraries was done by cellranger-7.1.0(https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/using/multi#what)
Assembly: mm10
Supplementary files format and content: cellranger-formated gene expresssion matrix files
Supplementary files format and content: comma-delimited value files

source_name: Spleen

extract_protocol:
The immunized mice were euthanized and the spleens were harvested. Then through tissue grinding and red blood cell lysis, the lymphocytes were extracted from the harvested spleens. Then mouse Pan-B cell isolation magnetic beads were used to isolate pan-B cells from collected cells. After cell washing, the B cells were stained with gB-Alexa Fluro467 and gHgL-FITC. Then stained cells were applied to BD FACSmelody sorter to isolate gB- or gHgL-specific B cells. The two antigen-specific B cell samples were further examined for cell viability and quality for single-B cell sequencing for transcriptome and VDJ analysis.
Library construction was performed in following of manufacturer's protocol
10x 5 ' scRNA and VDJ library

value: Spleen

value: Organ-derived live cells

value: gB-specific B cells


title: RNAseq-Control mESC, without 4OHT 6-days, rep#1


title: WGBS-Ogt_iKO mESC, +4OHT 6-days, rep#2


title: gHgL-specific B cells

description:
NP-gHgL
10x Genomics VDJ + GEX

value: gHgL-specific B cells


title: Trigeminal ganglia, pooled, HH1718, biological replicate 3, technical replicate 1

description:
Library name: HH1718_3_01
HH1718.B3.T1


title: rtgill.thx.1.H07

description:
Library name: rtgill.thx.1.H07
Cell lysate
thx.counts.txt
thx.lib12_S1.H07.expression.values

source_name: RTgill-W1 thx rep 1 conc 1


title: RNAseq-Ogt_iKO mESC, +4OHT 6-days, rep#1


title: rtgill.thx.2.E07

description:
Library name: rtgill.thx.2.E07
Cell lysate
thx.counts.txt
thx.lib3_S1.E07.expression.values

source_name: RTgill-W1 thx rep 2 conc 4


title: Trigeminal ganglia, pooled, HH1516, biological replicate 3, technical replicate 2

description:
Library name: HH1516_3_02
HH1516.B3.T2


title: Trigeminal ganglia, pooled, HH1718, biological replicate 1, technical replicate 1

description:
Library name: HH1718_1_01
HH1718.B1.T1


title: Th0 KO1

city: Stockholm

first: Ewoud

last: Ewing

address: CMM L8:05, Karolinska University Hospital

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_249 (TTCAGATCCA-TCCAATGCCA)
P21205_144

data_processing:
Data processed with NF-core RNAseq pipeline
Assembly: Grch38.106
Supplementary files format and content: unnormalised counts in csv
Supplementary files format and content: Normalised counts in csv

source_name: primary splenocytes

extract_protocol:
RNA was prepared using miRNeasy Mini kit (Qiagen) according to the manufacturer instructions. RNA from the in vitro differentiated CD4 T cells was assessed by Bioanalyzer 2100 with the Agilent RNA 6000 Pico Kit (Agilent).
cDNA libraries were made using the TruSeq Stranded mRNA kit (Agilent) and sequenced using Illumina NovaSeq S4-300 flowcell, 2x150 bp paired end, in NGI Stockholm.

treatment_protocol: Sorted naïve CD4+ cells were plated 150000 cells/well on 96-well flat bottom plate coated with mouse anti-CD3 and soluble mouse anti-CD28 in 250 µl complete RPMI (Sigma-Aldrich) and incubated at 37°C with 5% CO2 and 90% humidity for 3 days (Th0 polarizing conditions). For Th1 polarizing conditions, cells were additionally supplemented with IL-12 and anti-IL4. For Treg polarizing conditions, cells were supplemented instead with TGF-b1 and anti-IFN-g.

value: primary splenocytes

value: miR-150 KO

value: in vitro polarization


title: rtgill.thx.1.F07

description:
Library name: rtgill.thx.1.F07
Cell lysate
thx.counts.txt
thx.lib12_S1.F07.expression.values

source_name: RTgill-W1 thx rep 1 conc 3


title: Treg WT5

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_250 (CGGCATATAC-TCCAGCTCAT)
P21205_145

value: Treg

value: miR-150 WT


title: rtgill.thx.1.G07

description:
Library name: rtgill.thx.1.G07
Cell lysate
thx.counts.txt
thx.lib12_S1.G07.expression.values

source_name: RTgill-W1 thx rep 1 conc 2


title: Trigeminal ganglia, pooled, HH1516, biological replicate 3, technical replicate 1

description:
Library name: HH1516_3_01
HH1516.B3.T1


title: Input_CMSIP-Control mESC, without 4OHT 6-days, rep#1

description: Ogt fl/flmESC non treated with 4-OHT for 6 days to generatecontrol mESC samples- Input

data_processing:
Raw data was aligned to mm10 genome + lambda genome, using bismark aligner for methylation data.5hmC enrichment was defined as CMSIP signal over Input
MACS2 was used for callpeaks by comparing CMSIP against Input samples.
MACS2 was used with narrow and broad options, to then merged to identified peaks and compare across conditions (Ogt iKO against control mESC)
Assembly: mm10
Supplementary files format and content: Differential 5hmC peaks

extract_protocol:
In order to ensure a high purity of our samples, we isolate specifically the YFP+ population (in the case of 4-OHT-treated Ogt iKO mESC) at the same time that eliminating the presence of mitomycin-C-treated MEFs (used as feeders during our mESC cultures) by FACS (Fluorescence-Activated Cell Sorting) using a FACSAria cell sorter (BD Biosciences). The dissociated mESC were first labeled with the eBioscienceTM Fixable Viability Dye eFluorTM 780 (ThermoFisher, 65- 0865-14) to select viable cells and then stained for surface markers with indicated fluorochrome-conjugated antibodies diluted in FACS buffer (PBS 1X, 0.5% BSA, 0.01% NaN3): CD90.2 (Biolegend, 140319) to positively distinguish the mESC and CD326 (Biolegend, 118227) to negatively exclude MEFs.
CMS-IP with spike ins

value: mESC

value: Mouse Embrionic Stem Cells


title: WGBS-Ogt_iKO mESC, +4OHT 6-days, rep#1

value: Ogt fl/fl


title: Th1 WT5

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_248 (GAATAGAGTG-AGACGCTGTG)
P21205_143


title: rtgill.thx.2.C07

description:
Library name: rtgill.thx.2.C07
Cell lysate
thx.counts.txt
thx.lib3_S1.C07.expression.values

data_processing:
RNA-seq Analysis Portal (RAP; Qiagen)
Raw RNA Sequencing fastq files were submitted to QIAGEN’s RNA-seq Analysis Portal (RAP) (QIAGEN). First, raw files were demultiplexed to yield individual reads files for each sample (well) and then mapped to the rainbow trout genome (Omyk_1.0.105) to yield raw counts.
The counts were submitted to ExpressAnalyst for differential expression analysis and benchmark dose response analysis
Assembly: Omyk_1.0.105
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: RTgill-W1 thx rep 2 conc 6

extract_protocol:
OECD Test Guideline 249 for RTgill-W1 cell exposures, and QIAseq UPXome RNA Library Kits (QIAGEN) for library preparation
QIAseq UPXome RNA Library Kits (QIAGEN) protocol  for library preparation

value: Rainbow trout gill


title: Trigeminal ganglia, pooled, HH1516, biological replicate 2, technical replicate 2

description:
Library name: HH1516_2_02
HH1516.B2.T2


title: rtgill.thx.1.E07

description:
Library name: rtgill.thx.1.E07
Cell lysate
thx.counts.txt
thx.lib12_S1.E07.expression.values

source_name: RTgill-W1 thx rep 1 conc 4


title: macrophage, HFD, WT_1

value: macrophage

value: ALKBH5flox/flox, APOE-/-

value: High-fat diet


title: Input_CMSIP-Ogt_iKO mESC, +4OHT 6-days, rep#2

description: Ogt fl/flmESC treated with 4-OHT for 6 days to generateOgt iKOmESC samples- Input

value: 4OHT for 6 days


title: Th0 KI4

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_247 (ACTTCCGTTC-CACGGAATTG)
P21205_142

value: miR-150 KI


title: Input_CMSIP-Control mESC, without 4OHT 6-days, rep#2

value: without 4OHT for 6 days


title: rtgill.thx.1.D07

description:
Library name: rtgill.thx.1.D07
Cell lysate
thx.counts.txt
thx.lib12_S1.D07.expression.values

source_name: RTgill-W1 thx rep 1 conc 5


title: Input_CMSIP-Ogt_iKO mESC, +4OHT 6-days, rep#1


title: Trigeminal ganglia, pooled, HH1516, biological replicate 1, technical replicate 1

description:
Library name: HH1516_1_01
HH1516.B1.T1

value: trigeminal ganglion

value: wildtype


title: CMSIP-Control mESC, without 4OHT 6-days, rep#2

description: Ogt fl/flmESC non treated with 4-OHT for 6 days to generatecontrol mESC samples- CMSIP


title: Trigeminal ganglia, pooled, HH1516, biological replicate 2, technical replicate 1

description:
Library name: HH1516_2_01
HH1516.B2.T1


title: rtgill.thx.1.C07

description:
Library name: rtgill.thx.1.C07
Cell lysate
thx.counts.txt
thx.lib12_S1.C07.expression.values

source_name: RTgill-W1 thx rep 1 conc 6


title: rtgill.thx.1.B07

description:
Library name: rtgill.thx.1.B07
Cell lysate
thx.counts.txt
thx.lib12_S1.B07.expression.values

source_name: RTgill-W1 thx rep 1 conc 7


title: rtgill.thx.1.A07

description:
Library name: rtgill.thx.1.A07
Cell lysate
thx.counts.txt
thx.lib12_S1.A07.expression.values

source_name: RTgill-W1 thx rep 1 conc 8


title: CMSIP-Control mESC, without 4OHT 6-days, rep#1

source_name: mESC


title: Treg KO3

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_245 (TCAATACGTG-TATTAGCAGC)
P21205_140

value: primary splenocytes


title: Trigeminal ganglia, pooled, HH1314, biological replicate 3, technical replicate 2

description:
Library name: HH1314_3_02
HH1314.B3.T2

source_name: trigeminal ganglion


title: rtgill.met.3.H06

description:
Library name: rtgill.met.3.H06
Cell lysate
met.counts.txt
met.lib.7_S1.H06.expression.values

source_name: RTgill-W1 met rep 3 conc 1


title: Trigeminal ganglia, pooled, HH1314, biological replicate 3, technical replicate 1

description:
Library name: HH1314_3_01
HH1314.B3.T1


title: CMSIP-Ogt_iKO mESC, +4OHT 6-days, rep#2

description: Ogt fl/flmESC treated with 4-OHT for 6 days to generateOgt iKOmESC samples-CMSIP


title: Th0 WT3

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_243 (ACAGAGGCGT-CCGATATGTC)
P21205_138


title: Treg WT2

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_242 (CATCACCTAA-AATACCACCA)
P21205_137


title: rtgill.met.3.G06

description:
Library name: rtgill.met.3.G06
Cell lysate
met.counts.txt
met.lib.7_S1.G06.expression.values

source_name: RTgill-W1 met rep 3 conc 2


title: CMSIP-Ogt_iKO mESC, +4OHT 6-days, rep#1

description: Ogt fl/flmESC treated with 4-OHT for 6 days to generateOgt iKOmESC samples- CMSIP


title: Th1 KO2

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_241 (CGTGTATGTC-ATAGAGATGC)
P21205_136

value: miR-150 KO


title: Trigeminal ganglia, pooled, HH1314, biological replicate 2, technical replicate 2

description:
Library name: HH1314_2_02
HH1314.B2.T2


title: Trigeminal ganglia, pooled, HH1314, biological replicate 2, technical replicate 1

description:
Library name: HH1314_2_01
HH1314.B2.T1


title: rtgill.met.3.F06

description:
Library name: rtgill.met.3.F06
Cell lysate
met.counts.txt
met.lib.7_S1.F06.expression.values

source_name: RTgill-W1 met rep 3 conc 3


title: Contr_5L

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

data_processing:
Clustering and sequencing (Novogene Experimental Department): The clustering of the index-coded samples was performed on a cBot Cluster Generation System using HiSeq PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500  platform and 125 bp/150 bp paired-end reads were generated
Quality control:  Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20,Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: HTSeq v0.6.1 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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq were assigned as differentially expressed

source_name: Liver

extract_protocol:
RNA quantification and qualification: RNA degradation and contamination was monitored on 1% agarose gels.RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA,USA) .RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer(Life Technologies, CA, USA).RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100system (Agilent Technologies, CA, USA).
Library preparation for Transcriptome sequencing : A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5x). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter)
Beverly, USA).Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: tag

value: Liver

tag: diet

value: corn starch contol


title: Contr_4L


title: Th0 KO5

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_240 (ATAGGCAGTG-CTAAGTTCTG)
P21205_135

value: in vitro polarization


title: Treg KI4

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_246 (TCAATCTAGC-CTTATTCGGA)
P21205_141

value: Treg


title: Trigeminal ganglia, pooled, HH1516, biological replicate 1, technical replicate 2

description:
Library name: HH1516_1_02
HH1516.B1.T2


title: Th1 KI1

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_244 (ACAGCCAGGT-AGTACCATGA)
P21205_139


title: Contr_3L


title: Trigeminal ganglia, pooled, HH1314, biological replicate 1, technical replicate 1

description:
Library name: HH1314_1_01
HH1314.B1.T1


title: Th1 KI3

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_239 (GTACGCATCG-TGAACAACTC)
P21205_134


title: Trigeminal ganglia, pooled, HH1314, biological replicate 1, technical replicate 2

description:
Library name: HH1314_1_02
HH1314.B1.T2


title: Contr_2L


title: rtgill.met.3.B06

description:
Library name: rtgill.met.3.B06
Cell lysate
met.counts.txt
met.lib.7_S1.B06.expression.values

source_name: RTgill-W1 met rep 3 conc 7


title: Dextr_5L

value: dextrose


title: Th1 WT1

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_237 (TCGCATGACA-CATTGGCCAA)
P21205_132

value: miR-150 WT


title: rtgill.met.3.E06

description:
Library name: rtgill.met.3.E06
Cell lysate
met.counts.txt
met.lib.7_S1.E06.expression.values

source_name: RTgill-W1 met rep 3 conc 4

value: Rainbow trout gill


title: rtgill.met.3.D06

description:
Library name: rtgill.met.3.D06
Cell lysate
met.counts.txt
met.lib.7_S1.D06.expression.values

source_name: RTgill-W1 met rep 3 conc 5


title: Th1 KO5

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_236 (GCAACATCAA-AACTAGGTCA)
P21205_131

source_name: primary splenocytes


title: Contr_1L


title: rtgill.met.3.A06

description:
Library name: rtgill.met.3.A06
Cell lysate
met.counts.txt
met.lib.7_S1.A06.expression.values

source_name: RTgill-W1 met rep 3 conc 8


title: KMT2B-HT HPC2

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

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

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

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

organism: Homo sapiens

source_name: KMT2B-HT HPC2

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

extract_protocol: Total RNA was extracted by RNeasy Mini (QIAGEN, Venlo, Netherlands).

value: iPSC-derived hepatic progenitor cells


title: rtgill.met.2.H06

description:
Library name: rtgill.met.2.H06
Cell lysate
met.counts.txt
met.lib.2_S1.H06.expression.values

source_name: RTgill-W1 met rep 2 conc 1


title: Dextr_3L


title: Dextr_4L


title: KMT2B-Int HPC2

source_name: KMT2B-Int HPC2


title: KMT2B-HT HPC1

source_name: KMT2B-HT HPC1


title: Th0 KI3

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_233 (AACCTAGTGC-AGGACCTGTA)
P21205_128


title: rtgill.met.2.G06

description:
Library name: rtgill.met.2.G06
Cell lysate
met.counts.txt
met.lib.2_S1.G06.expression.values

source_name: RTgill-W1 met rep 2 conc 2


title: Th0 WT4

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_234 (GTATCTGAGG-CAAGATACGT)
P21205_129


title: KMT2B-Int HPC1

source_name: KMT2B-Int HPC1


title: rtgill.met.3.C06

description:
Library name: rtgill.met.3.C06
Cell lysate
met.counts.txt
met.lib.7_S1.C06.expression.values

source_name: RTgill-W1 met rep 3 conc 6


title: Dextr_1L


title: rtgill.met.2.E06

description:
Library name: rtgill.met.2.E06
Cell lysate
met.counts.txt
met.lib.2_S1.E06.expression.values

source_name: RTgill-W1 met rep 2 conc 4


title: rtgill.met.2.F06

description:
Library name: rtgill.met.2.F06
Cell lysate
met.counts.txt
met.lib.2_S1.F06.expression.values

source_name: RTgill-W1 met rep 2 conc 3


title: Fruct_5L

value: fructose


title: Treg WT3

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_232 (GATCTGTATG-GCTCTTCGAT)
P21205_127


title: rtgill.met.2.D06

description:
Library name: rtgill.met.2.D06
Cell lysate
met.counts.txt
met.lib.2_S1.D06.expression.values

source_name: RTgill-W1 met rep 2 conc 5


title: Aedes-Olfactory, 12am, Read 1, rep 3

city: PUNE

first: Tanwee

last: Das De

state: MAHARASHTRA

address: Dr. Homi Bhaba Road, Pashan

department: Department of Biology

country: India

institute: Indian Institute of Science Education and Research

data_processing:
The raw reads were demultiplexed and converted to FASTQ format using bcl2fastq software
Sequence reads were trimmed for adaptor sequence and low quality sequence using FastQC tool using default parameter
After quality checking and adaptor trimming the sample specific reads were aligned to the reference genome of An. culicifacies (VectorBase-54-AculicifaciesA-37-Genome) and Ae. aegypti (VectorBase-54-AaegyptiLVP-AGWG-Genome) respectively by using STAR-alignment tool
The transcriptome data of An. culicifacies showed 70-80% alignment rate whereas, Ae. aegypti data showed ~90% alignment
Read counts are calculated by htseq count tool
Assembly: AaegL5.0 &   AculA1.7
Supplementary files format and content: Tab delimited text file includes raw counts of Aedes samples
Supplementary files format and content: Tab delimited text file includes raw counts of Anopheles samples

organism: Aedes aegypti

source_name: Olfactory

growth_protocol: Both Aedes and Anopheles mosquitoes were maintained at 80% relative humidity and 27 ± 2°C temperature under 12hr/12hr LD cycle

extract_protocol:
Total RNA was extracted from the clean olfactory and brain tissues by standard trizol method
cDNA library were prepared using NEBNext® UltraII RNA library preparation kit (Cat No. E7775S) by following the manufacturer protocol.
For multiplexing of the samples NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs) (Cat No. E6440S) were used.

treatment_protocol: To understand the molecular rhythm of the olfactory and the brain system, complete olfactory tissue including antennae, maxillary palp, proboscis and labium, and the brain were dissected from 5-6-day old adult females’ mosquitoes (same cohort) at four different zeitgeber times 6am, 12pm, 6pm and 12am.

value: Olfactory

value: WT

value: Circadian Cycle


title: Treg KI2

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_238 (TCGTGACGAC-AGTTAGTCAC)
P21205_133

value: miR-150 KI


title: Th0 WT1

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_231 (CTTAGTACGC-TCGTTGTAGC)
P21205_126


title: Treg KO4

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_235 (AAGAGCTCGC-GATCTATTGG)
P21205_130


title: Aedes-Olfactory, 6pm, Read 1, rep 3


title: Th0 KI1

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_230 (TTCGCGGACT-ACCACTCTCT)
P21205_125


title: Fruct_4L

source_name: Liver


title: Fruct_3L


title: rtgill.met.2.B06

first: Niladri

last: Basu

institute: McGill University

description:
Library name: rtgill.met.2.B06
Cell lysate
met.counts.txt
met.lib.2_S1.B06.expression.values

source_name: RTgill-W1 met rep 2 conc 7


title: Aedes-Olfactory, 12pm, Read 1, rep 3


title: Dextr_2L


title: Th1 KI4

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_229 (GAATCGCCTG-GCCGTCAATG)
P21205_124


title: KMT2B-WT HPC1

source_name: KMT2B-WT HPC1


title: Fruct_2L


title: Aedes-Olfactory, 12am, Read 1, rep 2


title: Aedes-Olfactory, 6am, Read 1, rep 3


title: rtgill.met.2.A06

description:
Library name: rtgill.met.2.A06
Cell lysate
met.counts.txt
met.lib.2_S1.A06.expression.values

source_name: RTgill-W1 met rep 2 conc 8


title: Th0 KO4

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_227 (ACAACACACA-AGTGCCGATG)
P21205_122

source_name: primary splenocytes


title: Fruct_1L


title: Contr_5G

source_name: Gut,duodenum

value: Gut,duodenum


title: rtgill.met.1.H06

description:
Library name: rtgill.met.1.H06
Cell lysate
met.counts.txt
met.lib.11_S1.H06.expression.values

source_name: RTgill-W1 met rep 1 conc 1


title: Th1 KO3

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_226 (GCGACTCGTA-ACATGGCCTG)
P21205_121


title: Aedes-Olfactory, 12pm, Read 1, rep 2


title: Treg KI3

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_225 (TAGAAGATCG-ACACTGGTCG)
P21205_120


title: rtgill.met.1.G06

description:
Library name: rtgill.met.1.G06
Cell lysate
met.counts.txt
met.lib.11_S1.G06.expression.values

source_name: RTgill-W1 met rep 1 conc 2


title: KMT2B-WT HPC2

source_name: KMT2B-WT HPC2


title: Aedes-Olfactory, 12am, Read 1, rep 1


title: Aedes-Olfactory, 6am, Read 1, rep 2


title: rtgill.met.2.C06

description:
Library name: rtgill.met.2.C06
Cell lysate
met.counts.txt
met.lib.2_S1.C06.expression.values

source_name: RTgill-W1 met rep 2 conc 6


title: Aedes-Olfactory, 6pm, Read 1, rep 2


title: Contr_4G


title: Contr_2G


title: Th1 WT2

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_224 (CCGACAACCT-ACAGGTAGAA)
P21205_119


title: rtgill.met.1.F06

description:
Library name: rtgill.met.1.F06
Cell lysate
met.counts.txt
met.lib.11_S1.F06.expression.values

source_name: RTgill-W1 met rep 1 conc 3


title: Treg KO2

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_228 (CCTGGAATTA-TTCGATGACG)
P21205_123


title: Contr_3G


title: Th0 KO2

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_223 (AGTACAACTG-GAACTCAATG)
P21205_118


title: Contr_1G


title: rtgill.met.1.D06

description:
Library name: rtgill.met.1.D06
Cell lysate
met.counts.txt
met.lib.11_S1.D06.expression.values

source_name: RTgill-W1 met rep 1 conc 5


title: Aedes-Olfactory, 12pm, Read 1, rep 1


title: Th1 KO1

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_222 (AACGCGACTG-CTCGTAGGTC)
P21205_117


title: Dextr_5G


title: Aedes-Olfactory, 6am, Read 1, rep 1


title: Treg KI1

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_220 (TTACACCAAC-CCTAACTCAT)
P21205_115


title: rtgill.met.1.C06

description:
Library name: rtgill.met.1.C06
Cell lysate
met.counts.txt
met.lib.11_S1.C06.expression.values

source_name: RTgill-W1 met rep 1 conc 6


title: Dextr_3G


title: Th1 KI5

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_221 (TGCAACACTA-TACCAGAACG)
P21205_116


title: Dextr_4G


title: Aedes-brain, 6pm, rep 3

source_name: Bain

value: Bain


title: Aedes-brain, 12am, rep 3


title: rtgill.met.1.E06

description:
Library name: rtgill.met.1.E06
Cell lysate
met.counts.txt
met.lib.11_S1.E06.expression.values

source_name: RTgill-W1 met rep 1 conc 4


title: rtgill.imi.3.H05

description:
Library name: rtgill.imi.3.H05
Cell lysate
imz.counts.txt
imi.lib.7_S1.H05.expression.values

source_name: RTgill-W1 imi rep 3 conc 1


title: Dextr_2G


title: Aedes-brain, 12pm, rep 3


title: Treg WT4

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_218 (AGGCAGCCAT-CTAGACACTC)
P21205_113

value: primary splenocytes


title: Th0 WT5

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_217 (GTACGCTCAA-CGCCATCAAT)
P21205_112


title: rtgill.imi.3.G05

description:
Library name: rtgill.imi.3.G05
Cell lysate
imz.counts.txt
imi.lib.7_S1.G05.expression.values

source_name: RTgill-W1 imi rep 3 conc 2


title: Treg K05

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_216 (CTTACTCTCT-CCTTAAGCAG)
P21205_111

value: miR-150 KO


title: rtgill.met.1.A06

description:
Library name: rtgill.met.1.A06
Cell lysate
met.counts.txt
met.lib.11_S1.A06.expression.values

source_name: RTgill-W1 met rep 1 conc 8


title: Fruct_5G


title: rtgill.imi.3.F05

description:
Library name: rtgill.imi.3.F05
Cell lysate
imz.counts.txt
imi.lib.7_S1.F05.expression.values

source_name: RTgill-W1 imi rep 3 conc 3


title: Th1 KI2

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_215 (AGTCAGATGC-AGTGTGTGAG)
P21205_110


title: rtgill.met.1.B06

description:
Library name: rtgill.met.1.B06
Cell lysate
met.counts.txt
met.lib.11_S1.B06.expression.values

source_name: RTgill-W1 met rep 1 conc 7


title: Dextr_1G


title: rtgill.imi.3.E05

description:
Library name: rtgill.imi.3.E05
Cell lysate
imz.counts.txt
imi.lib.7_S1.E05.expression.values

source_name: RTgill-W1 imi rep 3 conc 4


title: Aedes-brain, 6am, rep 3


title: Fruct_3G


title: Fruct_4G


title: Aedes-Olfactory, 6pm, Read 1, rep 1

source_name: Olfactory


title: Aedes-brain, 12pm, rep 2


title: Th0 KI5

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_214 (GAAGCAAGCG-TAGTCGGTGA)
P21205_109

source_name: primary splenocytes


title: Aedes-brain, 6am, rep 2


title: Aedes-brain, 6pm, rep 2


title: rtgill.imi.3.D05

description:
Library name: rtgill.imi.3.D05
Cell lysate
imz.counts.txt
imi.lib.7_S1.D05.expression.values

source_name: RTgill-W1 imi rep 3 conc 5


title: Aedes-brain, 12am, rep 1


title: rtgill.imi.3.A05

description:
Library name: rtgill.imi.3.A05
Cell lysate
imz.counts.txt
imi.lib.7_S1.A05.expression.values

source_name: RTgill-W1 imi rep 3 conc 8


title: Aedes-brain, 6pm, rep 1


title: Th0 KO3

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_213 (AGGCAATCGC-ACAGACTCAT)
P21205_108


title: rtgill.imi.3.C05

description:
Library name: rtgill.imi.3.C05
Cell lysate
imz.counts.txt
imi.lib.7_S1.C05.expression.values

source_name: RTgill-W1 imi rep 3 conc 6


title: Treg WT1

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_212 (TGACATAGGT-ATCTCTGGTA)
P21205_107


title: Th1 KO4

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_211 (CGAGATTAGA-CCGCGATTAG)
P21205_106


title: rtgill.imi.3.B05

description:
Library name: rtgill.imi.3.B05
Cell lysate
imz.counts.txt
imi.lib.7_S1.B05.expression.values

source_name: RTgill-W1 imi rep 3 conc 7


title: Th1 WT4

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_209 (GAGTCGCTTC-AATCTTCGCT)
P21205_104


title: Aedes-brain, 12pm, rep 1


title: Fruct_1G

source_name: Gut,duodenum


title: rtgill.imi.2.F05

description:
Library name: rtgill.imi.2.F05
Cell lysate
imz.counts.txt
imi.lib.2_S1.F05.expression.values

source_name: RTgill-W1 imi rep 2 conc 3


title: Treg KI5

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_210 (AGTCCAGCGT-CAATACGACA)
P21205_105


title: rtgill.imi.2.H05

description:
Library name: rtgill.imi.2.H05
Cell lysate
imz.counts.txt
imi.lib.2_S1.H05.expression.values

source_name: RTgill-W1 imi rep 2 conc 1


title: Orthochromatic, Luciferase-shRNA_rep3, RNA-seq

city: zhengzhou

first: Hengchao

last: Zhang

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zzu

data_processing:
Reads with quality less than 30 and length less than 20 bp were trimmed using Trim Galore version 0.6.6.
Trimmed reads were then mapped to the hg19 genome using TopHat version 2.0.13 (http://ccb.jhu.edu/software/tophat/).
Gene expression was analyzed using the Cufflinks version 2.1.1 (http://cole-trapnell-lab.github.io/cufflinks/) package.
Differentially expressed genes (DEGs) were defined by FPKM > 10, q < 0.05, and fold change > 2 using Cufflinks computational cuffdiff function.
Assembly: hg19
Supplementary files format and content: normalized gene expression (FPKM) values for each sample

source_name: human umbilical cord blood

growth_protocol: Primary human CD34+ cells from cord blood were isolated by positive selection using a CD34+ magnetic selective bead system. The purity of isolated CD34+ cells was 95% to 98%. The CD34+ cells were differentiated towards the erythroid lineage using a three-phase culture system. Composition of the base culture medium was Iscove’s Modified Dulbecco’s Medium, 2% human peripheral blood plasma, 3% human AB serum, 200 mg/mL human Holo-transferrin, 3 IU/mL heparin, and 10 mg/mL insulin. In the first phase (day 0 to day 7), CD34+ cells at a concentration of 105 /mL were cultured in the presence of 10 ng/mL stem cell factor, 1 ng/mL IL-3, and 3 IU/mL erythropoietin. In the second phase (day 7 to day 11), IL-3 does not need to be added into the culture medium. In the third phase that lasted until day 21, the cell concentration was adjusted to 106 /mL on day 11 and to 5×106/mL on day 15, respectively, the medium for this phase was the base medium plus 3 IU/mL erythropoietin, and the concentration of transferrin was adjusted to 1 mg/mL. The cells were cultured at 37°C in the presence of 5% CO2.

extract_protocol:
RNA was extracted from FACS-sorted orthochromatic erythroblasts following luciferase control and DNMT1 knockdown. Cells (1 × 106) were collected and washed twice with PBS. RNA was extracted from cell cultures using RNA extract kits (cat.no.74104, Qiagen) according to the manufacturer’s instructions.
RNA was extracted and used as the cDNA input, the cDNA library was prepared using a Truseq DNA library kit (Illumina), and the library was sequenced on a sequencing platform (HiSeq X Ten, Illumina).

value: human umbilical cord blood

value: Cultured CD34+ cells

value: Orthochromatic

value: Luciferase-shRNA


title: Orthochromatic, Luciferase-shRNA_rep2, RNA-seq

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: Aedes-brain, 12am, rep 2

source_name: Bain


title: rtgill.imi.2.E05

city: Sainte-Anne-de-Bellevue

description:
Library name: rtgill.imi.2.E05
Cell lysate
imz.counts.txt
imi.lib.2_S1.E05.expression.values

source_name: RTgill-W1 imi rep 2 conc 4


title: rtgill.imi.2.G05

description:
Library name: rtgill.imi.2.G05
Cell lysate
imz.counts.txt
imi.lib.2_S1.G05.expression.values

source_name: RTgill-W1 imi rep 2 conc 2


title: Orthochromatic, Luciferase-shRNA_rep1, RNA-seq

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: Treg KO1

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_208 (GCCTAGAGTC-AGAGAACCAT)
P21205_103

value: Treg

value: in vitro polarization


title: Orthochromatic, DNMT1-shRNA_rep2, RNA-seq

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: Aedes-brain, 6am, rep 1


title: Orthochromatic, DNMT1-shRNA_rep3, RNA-seq

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: rtgill.imi.2.D05

description:
Library name: rtgill.imi.2.D05
Cell lysate
imz.counts.txt
imi.lib.2_S1.D05.expression.values

source_name: RTgill-W1 imi rep 2 conc 5

value: Rainbow trout gill


title: Skimmed milk powder EV miRNA 2A

city: St Genès-Champanelle

first: Christine

last: LEROUX

address: Route de Theix

country: France

institute: INRAE

data_processing:
After ttrimming of adaptor sequences and removal of reads containing ambiguous base calls (FASTX-Toolkit, http://hannonlab.cshl.edu/fastx_toolkit/index.html), reads were filtered according to their size (15–40 nt). Reads quantification and annotation were performed using the ncPRO-seq pipeline (Chen et al., 2012).
Assembly: The sequence reads were aligned against the Bos taurus btau 5.0.1 genome and with miRBase_v22.1. Precursors and mature miRNAs were identified using the miRDeep2 core module, miRDeep2.pl (Friedländer et al., 2012).
Supplementary files format and content: tab-delimited text file

organism: Capra hircus

source_name: Milk powder EV

extract_protocol:
RNA extraction performed using a mirVana Total Isolation kit (life Technologies)
Small RNA-Seq libraries were generated using Library prep for small RNA-seq kit (Illumina, San Diego, CA). Acrylamide gel purifications of 140-160 nt amplified cDNA (corresponding to cDNA obtained from small RNA + 120 nt from the adapters) were performed. The final cDNA libraries were checked for quality and quantified using capillary electrophoresis. Libraries were loaded in the flow cell and sequenced as single-end 50 base reads

treatment_protocol: Mil samples were reconstituted from powedrs in warm water, then extracellular vesicles were isolated using SEC

value: Milk powder EV


title: rtgill.imi.2.C05

description:
Library name: rtgill.imi.2.C05
Cell lysate
imz.counts.txt
imi.lib.2_S1.C05.expression.values

source_name: RTgill-W1 imi rep 2 conc 6


title: IL-8 + SCH

city: Shanghai

first: Xiaojie

last: Shi

state: Shanghai

address: No. 393 Huaxia Road

department: SIAIS

institute: ShanghaiTech University

description: the processed data file is a matrix containing multiple samples, in which the columns for this sample are Sch-IL8-1, Sch-IL8-2 and Sch-IL8-3

data_processing:
CLC Genomics Workbench
mapped to human reference genome sequence (GRCh38) in the GenBank followed by further gene profiling analyses. Reads number of each gene was normalized to sample volume, and evaluated as transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: comma-separated values file containing a matrix includes total counts, RPKM, TPM and CPM for all samples

source_name: isolated from PBMC

growth_protocol: Neutrophil cells were maintained in RPMI 1640 in humidified atmosphere with 5% CO2 at 37 ℃

extract_protocol:
TRIrizol reagent was used to purify the total RNA of isolated circulating neutrophils according to the manufacturer’s instruction.
After qualifying the RNA samples, mRNA is enriched using magnetic beads with Oligo(dT). Then, the mRNA is broken into short fragments by adding fragmentation buffer. Use the mRNA as a template to synthesize first-strand cDNA using random hexamers. Next, add buffer, dNTPs, DNA polymerase I, and RNase H to synthesize second-strand cDNA. Double-stranded cDNA is then purified by AMPure XP beads. Repair the ends of the purified double-stranded cDNA, and ligate sequencing adapter by adding A-tails. Perform size selection of the cDNA fragments using AMPure XP beads. Finally, perform PCR amplification, purify the PCR products using AMPure XP beads, and obtain the final library. The constructed library is quantitated using Qubit 2.0. Agilent 2100 is used to detect the size of the inserted fragments then. Once the inserted fragments meet the expected size, qPCR is finally employed to accurately quantify the effective concentration of the library to ensure its quality.

treatment_protocol: Neutrophils were subjected to the treatment of 10 nM IL-8 alone, 10 nM Gro-α alone, 10 nM abN48-2-IgG1 alone, 10 nM IL-8 followed by 10 nM abN48-2-IgG1, or  10 nM IL-8 followed by Sch527123 for 2 hours in RPMI 1640 growth media, along with a negative control group (NC) of neutrophils incubated in the media without treatment for 2 hours.

value: isolated from PBMC

value: primary

value: neutrophils

value: incubated with IL-8, then SCH527123 (Navarixin)


title: IL-8 + Ab

description: the processed data file is a matrix containing multiple samples, in which the columns for this sample are H8-2-IL8-1, H8-2-IL8-2 and H8-2-IL8-3

value: WT

value: incubated with IL-8, then AbN48-2-IgG1


title: Th0 WT2

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_206 (AGGAGACCAC-CTACGTGGTA)
P21205_101

value: miR-150 WT


title: Skimmed milk powder EV miRNA 2C


title: Skimmed milk powder EV miRNA 2B


title: Fruct_2G

value: Gut,duodenum

value: fructose


title: Th1 WT3

description:
Illumina TruSeq Stranded mRNA (polyA)
Index: IDT_10nt_UD_207 (TTAGTTGCTG-AATCCGCCAT)
P21205_102

value: primary splenocytes


title: Whole milk powder EV miRNAs 1C


title: rtgill.imi.2.B05

address: 21,1111 Lakeshore Blvd, Apt #2

description:
Library name: rtgill.imi.2.B05
Cell lysate
imz.counts.txt
imi.lib.2_S1.B05.expression.values

source_name: RTgill-W1 imi rep 2 conc 7


title: rtgill.imi.2.A05

description:
Library name: rtgill.imi.2.A05
Cell lysate
imz.counts.txt
imi.lib.2_S1.A05.expression.values

source_name: RTgill-W1 imi rep 2 conc 8


title: Ab

description: the processed data file is a matrix containing multiple samples, in which the columns for this sample are H8-2-1, H8-2-2 and H8-2-3

value: incubated with 10 nM of the antibody AbN48-2-IgG1


title: RAW miR-125b NC 2

city: nanjing

first: Rui

last: Li

address: 138 Xianlin Avenue

institute: Nanjing University of Traditional Chinese Medicine

data_processing:
Use Qubit2.0 for preliminary quantification
Use fastp  to strictly control the quality of data
Use HISAT2  to sequence compare Clean Reads with the reference genome to obtain the location information on the reference genome or gene and the sequence characteristic information unique to the sequenced sample
Use DESeq2  to analyze the differential expression between sample groups,
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: RAW264.7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cell transfection

value: Mouse monocyte macrophage leukemia cells

value: miR-125b WT

value: transfection


title: RAW miR-125b NC 3


title: RAW miR-125b mimic 2

value: miR-125b overexpression


title: RAW miR-125b mimic 3


title: APAP,12h,exp2

city: Kunming

first: Xue

middle: Ruo

last: Yang

address: Wujiaying Street, Chenggong District, Kunming, Yunnan

institute: Yunnan university

description:
fpkm_APAP122
gene_expression6h_12h.xls

data_processing:
Raw data (raw reads) in fastq format were processed using in-house Perl scripts. Clean data (clean reads) were obtained by removing reads containing adapters, reads containing poly-N, and low-quality reads from the raw data. Quality metrics such as Q20, Q30, GC-content, and sequence duplication levels were calculated for the clean data. All downstream analyses were based on high-quality clean data. Reads were mapped against the reference genome and transcript annotation (GRCm38) using Hisat2 software
Assembly: GRCm38(Mus musculus)
Supplementary files format and content: tab-delimited text file includes raw count for each Sample

source_name: liver

extract_protocol:
Wild-type C57BL/6J mice were anesthetized using a CO2 chamber. To avoid contamination of the peritoneal cavity with fur, the skin and peritoneum were opened separately. The inferior vena cava was clamped with forceps, and a catheter was inserted into the superior vena cava via the right atrium. The portal vein was then cut once the buffer started to perfuse into the liver. The liver was perfused with 1x Hank's Balanced Salt Solution (HBSS) containing 53.6 mM KCl, 4.4 mM KH2PO4, 1367.5 mM NaCl, 3.36 mM NaHPO4, 55.5 mM D-Glucose, and 100 mL 1 M HEPES (pH 7.2-7.4) for 3-5 minutes until it appeared clear. Subsequently, the buffer was switched to a collagenase digestion solution (1xHBSS with 1.25 mM MgSO4, 4 mM CaCl2, Collagenase Type I, and 50 μg/mL DNase) for 15-20 minutes of digestion. Post-digestion, the liver was dissected and placed in chilled 1xHBSS in a Petri dish to keep it cool until further processing. The gallbladder was removed, and the liver was chopped into 2-3 mm pieces and incubated in 10-20 mL digestion buffer at 37°C for 15 minutes. The liver tissue was then mashed using a 70 μm cell strainer placed over a 50 mL tube and rinsed with 1xHBSS to a final volume of 50 mL. The suspension was centrifuged at 50xg for 5 minutes (acceleration/brake = 0) to remove hepatocytes, with the resulting supernatant containing nonparenchymal cells (NPCs). The supernatant was further centrifuged at 450xg for 5 minutes (acceleration/brake ≥ 5), and the pellet, containing hepatic NPCs, was resuspended in 4 mL of 20% OptiPrep solution diluted with 1xHBSS. This suspension was carefully layered with 5 mL of 1xHBSS buffer in a 15 mL tube and centrifuged at 3000 rpm for 17 minutes (acceleration/brake = 0). The cell fraction between the 20% OptiPrep and 1xHBSS layers, containing Kupffer cells (KCs) and liver endothelial sinusoidal cells (LESCs), was collected and washed with 1xHBSS.To isolate KCs, the cell fraction was incubated in a cell culture dish at 37°C for 10 minutes. KCs adhered to the plate, while LESCs remained in suspension. The adhered KCs were then collected for subsequent experiments. The purity and viability of isolated KCs reached 90% and 80%, respectively, which was confirmed by staining with anti-Timd4 antibodies or trypan blue.
Mice were treated according to different experimental protocols. Kupffer cells (KCs) were isolated and lysed in 1 mL RNAiso Plus reagent (TaKaRa, Cat #9109). RNA concentration and purity were measured using a NanoDrop 2000 (Thermo Fisher Scientific), and RNA integrity was assessed using the RNA Nano 6000 Assay Kit on the Agilent Bioanalyzer 2100 system (Agilent Technologies). A total of 1 μg RNA per sample was used for RNA sample preparation. Sequencing libraries were generated using the NEB Next Ultra™ RNA Library Prep Kit for Illumina (NEB) following the manufacturer’s recommendations. Index codes were added to attribute sequences to each sample. Clustering of the index-coded samples was performed on a cBot Cluster Generation System using the TruSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions

value: liver

value: Kupffer cell

value: macrophage

value: acetaminophen treated


title: RAW miR-125b mimic 1


title: RAW miR-125b NC 1


title: rtgill.imi.1.F05

description:
Library name: rtgill.imi.1.F05
Cell lysate
imz.counts.txt
imi.lib.11_S1.F05.expression.values

source_name: RTgill-W1 imi rep 1 conc 3

value: Rainbow trout gill


title: Whole milk powder EV miRNAs 1B

value: Milk powder EV


title: rtgill.imi.1.G05

description:
Library name: rtgill.imi.1.G05
Cell lysate
imz.counts.txt
imi.lib.11_S1.G05.expression.values

source_name: RTgill-W1 imi rep 1 conc 2


title: Whole milk powder EV miRNAs 1A


title: rtgill.imi.1.H05

description:
Library name: rtgill.imi.1.H05
Cell lysate
imz.counts.txt
imi.lib.11_S1.H05.expression.values

source_name: RTgill-W1 imi rep 1 conc 1


title: Gro-α

description: the processed data file is a matrix containing multiple samples, in which the columns for this sample are Ga-1, Ga-2 and Ga-3

value: isolated from PBMC

value: primary

value: neutrophils

value: WT

value: incubated with 10 nM Gro-a (CXCL1)


title: NC

description: the processed data file is a matrix containing multiple samples, in which the columns for this sample are NC-1, NC-2 and NC-3

value: PBS


title: Orthochromatic, DNMT1-shRNA_rep1, RNA-seq

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

value: human umbilical cord blood

value: Cultured CD34+ cells

value: Orthochromatic


title: IL-8

description: the processed data file is a matrix containing multiple samples, in which the columns for this sample are IL8-1, IL8-2 and IL8-3

value: incubated with 10 nM IL-8 (CXCL8)


title: rtgill.imi.1.D05

description:
Library name: rtgill.imi.1.D05
Cell lysate
imz.counts.txt
imi.lib.11_S1.D05.expression.values

source_name: RTgill-W1 imi rep 1 conc 5


title: APAP,6h,exp2

description:
fpkm_APAP62
gene_expression6h_12h.xls


title: APAP,12h,exp1

description:
fpkm_APAP121
gene_expression6h_12h.xls


title: TCR d22 KO #4

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

institute: Genentech

description: TCR

data_processing:
10X immune profiling single-cell RNA sequencing data were processed with our in-house pipeline. Briefly, the expression library, the feature barcode library, and the TCR library were first demultiplexed followed by alignment to the mouse reference genome (GRCm38) using Cell Ranger (version 6.0.1). A gene by cell barcode matrix was generated for the gene expression library and a similar matrix was generated for each TotalSeq™-C antibodies (Cd44, Cd39, and Klrg1) and each dCODE™ Dextramer® (for peptides NP396, GP33, Human CMV, and GP276).
Seurat (version 4.0.4) was used for all downstream analysis. Cells with detected genes between 200 and 3000, and with less than 5% mitochondrial mapped reads were kept for downstream analysis. Wildtype, day 15, replicate #3 was removed from further analysis as it showed strong batch effects. Initial clustering showed contamination of B and/or myeloid cells. To address this issue, we used an iterative process where we first performed clustering, identified and removed B/myeloid cells, followed by another round of clustering until majority of contaminating cells were removed. After filtering, we detected  56,550 cells across the whole dataset. We next performed Seurat’s Canonical Correlation Analysis (CCA) to integrate the dataset across day 15 and day 22. During the scaling step, we also regressed out the difference between G2M and S phase scores to maintain the difference between cycling and non-cycling cells. After normalizing the integrated data, we performed linear dimensionality reduction using PCA. We ranked the principal components (PCs) by the amount of variance explained by each and found that after the first 15 PCs the explained variance plateaus. To visualize the data in two-dimensional space, Uniform Manifold Approximation and Projection (UMAP) was performed using the first 15 PCs. We then used the UMAP dimensions to determine the nearest neighbor of each cell and perform clustering by setting the resolution parameter to 0.6. Marker genes for each cluster were determined using FindAllMarkers function (only.pos = T and logfc.threshold = 0.25). We first identified the naïve CD8 T cell clusters using marker genes per cluster. Automatic annotation of other non-naïve clusters was performed using SingleR and using virus specific CD8+ T cells from an LCMV infection model as a reference dataset. Gene set enrichment analysis was performed using fgsea. Briefly, for each cluster, the genes were ranked using a Wilcoxon rank sum test and genes enriched in the Stk40 knockout samples were searched against MSigDB categories: hallmark gene sets (H), curated gene sets (C2), motif gene sets (C3:TFT Legacy), GO gene sets (C5), and immunologic gene sets (C7).
Genome_build: mm10

source_name: Spleen

extract_protocol:
For chronic LCMV infections, mice were infected with 2 x 106 PFU of LCMV clone 13 intravenously and depleted of CD4 T cells in two doses of anti-CD4 (clone GK1.5): 500ug i.v. 4 days prior to infection and 250ug i.p. 3 days post infection. CD8+ T cells were magnetically purified from spleens of CD4CreER; Stk40loxp/loxp (Stk40 ko) and CD4+/+; Stk40loxp/loxp (WT) LCMV-cl13 infected mice at d15 and d22 after infection. LCMV-specific cells were enriched using Dextramer labeling followed by Miltenyi magnetic purification with anti-PE microbeads. Dextramer labeling was carried out in accordance with Immudex protocol.
Cell capture and scRNAseq-, feature-, and TCRseq- library constructions were carried out using the 10X Chromium Controller and the Chromium Next GEM Single Cell 5’ Reagent Kits v2 (Dual Index) in accordance with the manufacture’s protocol (CG000330 Rev A). Prior to loading into the chromium controller, cells were washed once with PBS and resuspended in PBS at 700-1200 cells/ul for a target cell recovery of 7000 cells.

tag: background

value: 7-9 weeks

value: Stk40 knock out


title: MDSmonoNucle_SHI_R2

city: Beijing

first: Hsiang-Ying

last: Lee

address: No.5 Yiheyuan Road

institute: Peking University

data_processing:
After checking data quality using FastQC (version 0.11.7), the paired-end reads were mapped to the hg19 human reference genome by Hisat2 (version 2.1.0).
Read counts were estimated with HTSeq (version 0.12.4).
The reads counts were normalized to TPM (transcription per million).
The DESeq2 package was used to identify differentially expressed genes.
Motif enrichment was performed using Homer software54 with “-start -400 -end 100” parameters.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

source_name: bone marrow

growth_protocol: The cells were maintained in two staged culture medium in humidified atmosphere with 5%CO2 at 37C

extract_protocol:
RNA was  harvested using TRIzol. For RNA-seq, the quality was evaluated using an Agilent 2100 Bioanalyzer. 1 μg of total RNA was used to prepare RNA-seq libraries.
RNA libraries for RNA-seq were prepared using Illumina mRNA-seq Library Prep Kit following manufacturer’s protocols

treatment_protocol: The cell culture system was divided two stages: amplification stage (0-4 days): The cells were cultured in SFEM II medium containing CC100 cytokine and 2% Penicillin streptomycin at a concentration of 105 cells/mL for 4 days. Differentiation stage (5-14 days): Cells were cultured in IMDM-based red differentiation medium containing 5 ng/mL rIL-, 3,100 ng/mL rhSCF and 6 U/mL rhEpo.

value: bone marrow

value: mono nucler cells

value: MED16 knockdown

tag: time

value: MDS


title: TCR d22 KO #1

description: TCR


title: SHI

data_processing:
The scRNA-seq library preparation, sequencing and expression matrix generation (hg38) were performed using a BD Rhapsody System following a standard protocol by Sinotech Genomics.
The downstream pipeline was constructed using R (version 4.0.2) with the Seurat package (version 4.1.0).
Low-quality cells were removed and the samples were normalized by sequencing depth.
The samples were integrated using the IntegrateData function and the merged object was scaled.
12 clusters were found using the first 30 components and first 30 neighbors. We then used the FindAllMarkers function to find markers and defined 8 clusters.
Cell cycle regression was performed using the CellCycleScoring function due to the presence of similar cell markers among the 3 erythroid cell populations.
Assembly: hg38
Supplementary files format and content: csv

source_name: cord blood

extract_protocol:
Single cell samples were obtained from cultured shSCR and shMED16 erythroblasts on day 4.
The scRNA-seq library preparation were performed using a BD Rhapsody System following a standard protocol by Sinotech Genomics.

value: cord blood

value: erythroblast

value: erythroid differentiation


title: APAP,12h,exp3

description:
fpkm_APAP123
gene_expression6h_12h.xls

value: liver

value: Kupffer cell

value: macrophage

value: acetaminophen treated


title: rtgill.imi.1.E05

description:
Library name: rtgill.imi.1.E05
Cell lysate
imz.counts.txt
imi.lib.11_S1.E05.expression.values

source_name: RTgill-W1 imi rep 1 conc 4

value: Rainbow trout gill


title: rtgill.imi.1.B05

description:
Library name: rtgill.imi.1.B05
Cell lysate
imz.counts.txt
imi.lib.11_S1.B05.expression.values

source_name: RTgill-W1 imi rep 1 conc 7


title: TCR d22 KO #2

description: TCR


title: rtgill.imi.1.A05

description:
Library name: rtgill.imi.1.A05
Cell lysate
imz.counts.txt
imi.lib.11_S1.A05.expression.values

source_name: RTgill-W1 imi rep 1 conc 8


title: MDSmonoNucle_SCR_R2

value: WT


title: APAP,6h,exp3

description:
fpkm_APAP63
gene_expression6h_12h.xls


title: rtgill.imi.1.C05

description:
Library name: rtgill.imi.1.C05
Cell lysate
imz.counts.txt
imi.lib.11_S1.C05.expression.values

source_name: RTgill-W1 imi rep 1 conc 6


title: SCR


title: TCR d22 WT #4

description: TCR

value: wild type


title: rtgill.imz.3.H04

description:
Library name: rtgill.imz.3.H04
Cell lysate
imz.counts.txt
imz.lib.7_S1.H04.expression.values

source_name: RTgill-W1 imz rep 3 conc 1


title: APAP,6h,exp1

description:
fpkm_APAP61
gene_expression6h_12h.xls


title: APAP,3h,exp3

description:
fpkm_WT_AP3
gene_expression0h_3h.xls


title: MDSmonoNucle_SCR_R1


title: MDSmonoNucle_SHI_R1


title: TCR d22 WT #3

description: TCR


title: APAP,3h,exp2

description:
fpkm_WT_AP2
gene_expression0h_3h.xls


title: TCR d22 WT #1

description: TCR


title: TCR d22 KO #3

description: TCR


title: OE-2_Day12

value: erythroid cell

value: MED16 over expression

value: Day 12


title: APAP,0h,exp3

description:
fpkm_WT_PBS3
gene_expression0h_3h.xls


title: rtgill.imz.3.F04

description:
Library name: rtgill.imz.3.F04
Cell lysate
imz.counts.txt
imz.lib.7_S1.F04.expression.values

source_name: RTgill-W1 imz rep 3 conc 3


title: OE-1_Day12


title: TCR d22 WT #2

description: TCR

value: 7-9 weeks


title: TCR d15 KO #4

description: TCR

value: Stk40 knock out


title: APAP,3h,exp1

description:
fpkm_WT_AP1
gene_expression0h_3h.xls


title: rtgill.imz.3.G04

description:
Library name: rtgill.imz.3.G04
Cell lysate
imz.counts.txt
imz.lib.7_S1.G04.expression.values

source_name: RTgill-W1 imz rep 3 conc 2


title: VO-2_Day12


title: TCR d15 KO #3

description: TCR


title: APAP,0h,exp1

description:
fpkm_WT_PBS1
gene_expression0h_3h.xls


title: APAP,0h,exp2

description:
fpkm_WT_PBS2
gene_expression0h_3h.xls


title: rtgill.imz.3.D04

description:
Library name: rtgill.imz.3.D04
Cell lysate
imz.counts.txt
imz.lib.7_S1.D04.expression.values

source_name: RTgill-W1 imz rep 3 conc 5


title: TCR d15 KO #2

description: TCR


title: VO-1_Day12


title: TCR d15 KO #1

description: TCR


title: SH-2_Day4

value: Erythroblasts

value: MED16 knockdown

value: Day 4


title: rtgill.imz.3.B04

description:
Library name: rtgill.imz.3.B04
Cell lysate
imz.counts.txt
imz.lib.7_S1.B04.expression.values

source_name: RTgill-W1 imz rep 3 conc 7