title: immune cells, EL4 subcutaneous tumour, Control, rep1

value: CD45 positive cells

value: immune cell

value: CD45 positive cells were sorted from vec-EL3 tumour tissue


title: Infected with IcmD mutant (T4SS mutant) Rep3 [IDK-3]

status: Public on Dec 31 2024

type: SRA

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

country: USA

institute: University of Arkansas for Medical Sciences

library_source: transcriptomic

data_processing:
RNA reads were assessed for quality of sequencing using FastQC.  Adaptors and low-quality bases (%Q30 < 20) were trimmed to a minimum of 36 base pairs using Trimmomatic [50].
Reads that passed quality control were aligned to the reference genomes GRCh38 Ensemble release 99
Differential expression and linear modeling was performed using Limma voom with quality weights [52-54].  Briefly, raw counts were obtained from bam files using Subread’s featuresCount function and transformed to log2 counts per million (CPM) [55].  Low expressed genes were filtered out and libraries normalized by trimmed mean of M-values [56].  Linear modeling and differential expression were performed and sorted by log fold change.  Genes with an FDR p-value < 0.05 and FC > 2 were considered significant.
Assembly: GRCh38 Ensemble release 99
Supplementary files format and content: Raw counts in csv file

molecule: total RNA

organism: Homo sapiens

source_name: THP-1 human monocytes (TIB-202)

growth_protocol: THP-1 human monocytes (TIB-202) were obtained from the American Type Culture Collection (ATCC) and cultured in RPMI1640 containing 10% fetal bovine serum (FBS) at 37°C with 5% CO2.  THP-1 cells were treated with phorbol 12-myristate 13-acetate (PMA; 200 nM) overnight to differentiate monocytes into adherent macrophage-like cells.

extract_protocol:
Cells were cultured in T-25 culture flasks, treated with inhibitors, infected with WT or icmD::Tn C. burnetii, and harvested in TRIzol (Thermofisher).
Illumina Truseq

treatment_protocol: C. burnetii cultivation.  Wild type (Nine Mile II; clone 4; RSA439), icmD::Tn, and mCherry-expressing C. burnetii were cultured for 7 days at 37°C with 5% CO2 and 2.5% O2 in acidified citrate cysteine medium (ACCM).  icmD::Tn mutant cultures contained kanamycin (350 g/mL) and mCherry-expressing bacterial cultures contained chloramphenicol (3 g/mL) for selection.  Cultures were pelleted via centrifugation, washed three times with sucrose phosphate (SP) buffer, and stored in SP buffer at -80°C prior to use.  All infections were performed for 48 h using a multiplicity of infection = 10-25.  Cells were cultured in T-25 culture flasks, treated with inhibitors, infected with WT or icmD::Tn C. burnetii, and harvested in TRIzol (Thermofisher).

tag: cell line

value: THP-1 human monocytes (TIB-202)

tag: cell type

value: Macrophage

tag: treatment

value: Infected with IcmD mutant (T4SS mutant)


title: Lip_rep2

city: Charlottesville

first: Brant

middle: E

last: Isakson

state: Virginia

department: Cardiovascular Research Center

institute: University of Virginia

data_processing:
The paired-end reads were mapped to the hg38 reference genome using STAR (v 2.7.9a). Gene counts were generated with FeatureCounts in the Rsubread (v. 2.8.8) package. DESeq2 (v. 1.34.0) was used to calculate log fold change and adjusted p-values. The adjusted p-values were then adjusted for multiple comparisons between groups by the Benjamini-Hochberg procedure using p.adjust().
Assembly: hg38
Supplementary files format and content: csv file of  raw counts
Supplementary files format and content: csv file of counts normalized with DESeq2
Supplementary files format and content: csv file of differential expression results compared to control group
Supplementary files format and content: csv file of differential expression results compared to lipid treated group

molecule: polyA RNA

source_name: Human Adipose Microvascular Endothelial Cells

extract_protocol:
RNA was isolated using Quick-RNA MiniPrep Kit (Genesee Scientific: 11-328). When necessary, samples were further concentrated and purified with the RNeasy MinElute Cleanup Kit (Qiagen: 74804).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Lip


title: Col-0_t30h_rep1

city: Rostock

first: Andreas

middle: Sven

last: Richter

address: Albert-Einstein-Strasse 3

department: Institute for Biosciences

country: Germany

institute: University of Rostock

description:
WT_30_1
Col0_24hHL+6hNL_fpkm.csv

data_processing:
removing reads containing adapter, reads containing ploy-N and low quality reads
mapping: Hisat2 v2.0.5
calculation of FPKM: featureCounts v1.5.0-p3
Assembly: ensemblplants_arabidopsis_thaliana_tair10_gca_000001735_1
Supplementary files format and content: csv / FPKM

organism: Arabidopsis thaliana

source_name: total leaf

growth_protocol: 4-week old Arabidopsis plants grown in short-day condition (10h light/14h dark) subjected to high light 2h after the onset of light.

extract_protocol:
Citric acid (Oñate-Sánchez and Vicente-Carbajosa, 2008)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP for directional library followed by  end repair, A-tailing, adapter ligation, size selection, enzyme digestion, amplification, and purification

treatment_protocol: 2h normal light (100µmol photons m-2 s-1 ) > 24 h continous high light (500µmol photons m-2 s-1) > 6h normal light

tag: tissue

value: total leaf

tag: genotype

value: Col-0 (WT)

value: 24h high light + 6 h normal light


title: BAT_RB2_rep3

city: La Jolla

first: Ye Ji

last: Shin

address: 9500 Gilman Dr

institute: University of California, San Diego

data_processing:
Adapter sequences and low-quality bases in sequence reads were trimmed and reads with a short sized were removed using Trimmomatic tool. (minlength : 36, window size : 4)
Trimmed reads were then mapped to the Mus Musculus reference genome (mm10) using HISAT2 and Bowtie2 aligners.
The quantification of reads for known transcripts was conducted using StringTie.
Assembly: mm10
Supplementary files format and content: tab delimited text file includes raw counts for each sample

organism: Mus musculus

source_name: Brown adipose tissue

extract_protocol:
RNA was harvested using Rneasy Mini Kit (QIAGEN) and 1.5ug of total RNA wased used for construction of sequencing libraries.
RNA -seq libraries were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols

value: Brown adipose tissue

tag: strain

tag: Sex

value: male

value: wild type


title: Col-0_t16h_rep2

description:
WT_16_2
Col0_16h_fpkm.csv

value: 16h high light


title: Infected with IcmD mutant (T4SS mutant) Rep2 [IDK-2]


title: BAT_RB2_rep2


title: Col-0_t16h_rep1

description:
WT_16_1
Col0_16h_fpkm.csv


title: Infected with IcmD mutant (T4SS mutant) Rep1 [IDK-1]


title: Con_rep3

value: Human Adipose Microvascular Endothelial Cells

value: control


title: Col-0_t8h_rep2

description:
WT_8_2
Col0_8h_fpkm.csv

value: 8h high light


title: BAT_RB2_rep1


title: Infected with IcmD mutant (T4SS mutant) Rep3 [ID-3]


title: Col-0_t8h_rep1

description:
WT_8_1
Col0_8h_fpkm.csv


title: BAT_CON_rep3

value: PBS


title: BAT_CON_rep2


title: Col-0_t4h_rep2

description:
WT_4_2
Col0_4h_fpkm.csv

value: 4h high light


title: Infected with IcmD mutant (T4SS mutant) Rep2 [ID-2]


title: Infected with WT Coxiella burnetii Rep3 [I-3]

value: Infected with WT Coxiella burnetii


title: BAT_CON_rep1


title: malignant tumor 4

city: Jinan

first: Yao

last: Liu

state: Shandong

address: Wenhuaxi Road 107#

country: China

institute: Qilu Hospital of Shandong University

data_processing:
1. Quality control Raw data (raw reads) of fastq format were processed with fastp, an ultra-fast FASTQ preprocessor with  useful quality. Clean data (clean reads) were obtained after quality control, adapter trimming, quality filtering and per-read quality cutting. Then choose a certain range of length from clean reads to do the all the  downstream analyses. 2. Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. The small RNA clean reads were aligned to the reference genome using BWA 0.7.13 to analyze their expression and  distribution on the reference. 3. Known miRNA identification Mapped small RNA tags were aligned to miRBase 22.0 for looking for known miRNA. 4. ncRNA idenfication The mapped small RNA tags were aligned to Rfam13.0 for looking for ncRNA. 5. Novel miRNA identification The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA. The available  software miRDeep2 were used to predict novel miRNA through exploring the secondary structure, the Dicer cleavage  site and the minimum free energy of the small RNA tags unannotated in the former steps.  6. Small RNA summary Summarizing all alignments and annotations obtained before. In the alignment and annotation before, some  small RNA tags may be mapped to more than one category. To make every unique small RNA mapped to only one  annotation, we follow the following priority rule: Known miRNA > rRNA > tRNA > snRNA > snoRNA >gene >  Novel miRNA. The total rRNA proportion was used a marker as sample quality indicator. Usually it should be less  than 60% in plant samples and 40% in animal samples as high quality. 7. miRNA target gene prediction Predicting the target gene of miRNA was performed by miRanda and RNAhybrid . 8. Quantification of miRNA miRNA expression levels were estimated by TPM (transcript per million) through the following criteria:  Normalization formula: Normalized expression = mapped readcount / Total reads * 1000000. 9. Differential expression analysis (For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was  performed using the DESeq R package (1.18.1). 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_x0002_values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes  with |log2(FoldChange)| > 1 and adjusted P-value <0.05 found by DESeq were assigned as differentially expressed. (For EdgeR without biological replicates) Differential expression analysis of two conditions/groups (no replicats) was performed using the EdgeR R  package (1.20.0). An overdispersed Poisson model is used to account for both biological and technical variability.  Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the  reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at  least one phenotype or experimental condition is replicated. The resulting P values were adjusted using the Benjamini  & Hochberg approach for controlling the false discovery rate. Genes with |log2(FoldChange)| > 1 and adjusted P_x0002_value <0.05 found by DESeq were assigned as differentially expressed.
Assembly: hg38
Supplementary files format and content: raw counts of sequencing reads and normalized data

source_name: saliva

extract_protocol:
Total RNA was extracted using Absin's exosomal RNA extraction kit (abs60263).RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoDrop™ One/OneC (Thermo Fisher Scientific, CA, USA). RNA concentration was measured using Qubit® RNA HS Assay Kit in Qubit® 3.0 Flurometer (Life  Technologies CA, USA). RNA integrity was assessed using Agilent 4200 TapeStation (Agilent Technologies, CA, USA).
Library preparation for small RNA sequencing A total amount of 3 µg RNA per sample was used as input material for the small RNA library preparations.  Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina®  (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to  each sample. Briefly, NEB 3' SR Adaptor was directly, and specifically ligated to 3' end of miRNA, siRNA and  piRNA. After the 3' ligation reaction, the SR RT Primer hybridized to the excess of 3' SR Adaptor (that  remained free after the 3' ligation reaction) and transformed the single-stranded DNA adaptor into a double_x0002_stranded DNA molecule. This step is important to prevent adaptor-dimer formation, besides, dsDNAs are not  substrates for ligation mediated by T4 RNA Ligase 1 and therefore do not ligate to the 5´ SR Adaptor in the  subsequent ligation step. 5´ends adapter was ligated to 5´ends of miRNAs, siRNA and piRNA. Then first strand  cDNA was synthesized using M-MuLV Reverse Transcriptase (RNase H–). PCR amplification was performed  using LongAmp Taq 2X Master Mix, SR Primer for illumina and index (X) primer. PCR products were purified  on a 8% polyacrylamide gel (100V, 80 min). DNA fragments corresponding to 140~160 bp (the length of small  noncoding RNA plus the 3' and 5' adaptors) were recovered and dissolved in 8 μL elution buffer. At last, library  quality was assessed on the Agilent 4200 TapeStation. 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 platform.

value: saliva

tag: rna population

value: exosomal miRNA

tag: patient diagnosis

value: malignant ovarian tumor


title: Col-0_t4h_rep1

description:
WT_4_1
Col0_4h_fpkm.csv


title: malignant tumor 3


title: TFΔPOD mice kidney 3

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

description:
T3
RawCountsAnnotated_21-0008.txt

data_processing:
Before alignment to reference genome each sequence in the raw FASTQ files were trimmed on base call quality and sequencing adapter contamination using fastq-mcf. Reads shorter than 15 bp were removed from FASTQ file. Trimmed reads were aligned to the reference genome using open source short read aligner STAR (https://code.google.com/p/rna-star/)) with settings according to log file.
Feature counts were performed using R packkage Rsubread:FeatureCount with default settings for paired end reads.
Assembly: mm10 or GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Kidney

extract_protocol:
RNA was extracted using RNeasy micro plus kit from Qiagen
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). The RNA sequencing library was generated from 500ng total RNA using Dynabeads® mRNA DIRECT™ Micro Purification Kit (Thermo Fisher) for mRNA purification followed by NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England BioLabs) according to manufacture´s protocols. The libraries were sequenced on Illumina NovaSeq 6000 using NovaSeq 6000 S1 Reagent Kit (100 cycles, paired end run) with an average of 5 x107 reads per RNA sample.

value: Kidney

value: TF{delta}POD


title: Infected with WT Coxiella burnetii Rep2 [I-2]

value: THP-1 human monocytes (TIB-202)

value: Macrophage


title: Col-0_t0_rep1

description:
WT_0_1
Col0_0_fpkm.csv

value: total leaf

value: Col-0 (WT)

value: 2h normal light


title: Lip_rep1

value: Lip


title: Infected with WT Coxiella burnetii Rep1 [I-1]


title: TFΔPOD mice kidney 2

description:
T2
RawCountsAnnotated_21-0008.txt


title: malignant tumor 2


title: malignant tumor 1


title: TFΔPOD mice kidney 1

description:
T1
RawCountsAnnotated_21-0008.txt


title: HCC_141

city: Seongnam

first: Sung Hwan

last: Lee

address: 59 Yatap-ro

department: Department of Surgery

country: South Korea

institute: CHA Bundang Medical Center

data_processing:
QuantSeq 3’ mRNA-Seq reads were aligned using Bowtie2
The read count data were processed based on quantile normalization method using EdgeR within R
Gene classification was based on searches done by DAVID and Medline databases
Assembly: hg19
Supplementary files format and content: raw counts

source_name: Human liver

extract_protocol:
Total RNA was isolated using Trizol reagent.
The construction of library was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit

tag: cell line origin

value: Human Hepatocarcinoma

value: liver cancer tumor tissue


title: ilp1-1_t30h_rep2

description:
ilp_30_2
ilp1_24hHL+6hNL_fpkm.csv

value: 24h high light + 6 h normal light


title: health control 4

value: healthy


title: Con_rep1

value: Human Adipose Microvascular Endothelial Cells

value: control


title: Con_rep2


title: HCC_140


title: ilp1-1_t30h_rep1

description:
ilp_30_1
ilp1_24hHL+6hNL_fpkm.csv


title: TFLoxP mice kidney 3

description:
W3
RawCountsAnnotated_21-0008.txt

value: TFLoxP


title: TFLoxP mice kidney 2

description:
W2
RawCountsAnnotated_21-0008.txt


title: health control 3

value: saliva

value: exosomal miRNA


title: ilp1-1_t16h_rep2

description:
ilp_16_2
ilp1_16h_fpkm.csv

value: 16h high light


title: health control 2


title: Col-0_t0_rep2

description:
WT_0_2
Col0_0_fpkm.csv


title: HCC_138


title: TFLoxP mice kidney 1

description:
W1
RawCountsAnnotated_21-0008.txt

value: Kidney


title: ilp1-1_t16h_rep1

description:
ilp_16_1
ilp1_16h_fpkm.csv


title: HCC_137


title: ilp1-1_t8h_rep2

description:
ilp_8_2
ilp1_8h_fpkm.csv

value: 8h high light


title: benign tumor 4

value: benign ovarian tumor


title: mouse primary podocytes from TFΔPOD mice  3

description:
TF3
RawCountsAnnotated_19-0021.txt

source_name: mouse primary podocytes

value: mouse primary podocytes

value: TF{delta}POD

value: 14 days in vitro differentiation


title: HCC_136


title: benign tumor 3


title: mouse primary podocytes from TFΔPOD mice  1

description:
TF1
RawCountsAnnotated_19-0021.txt


title: ilp1-1_t4h_rep2

description:
ilp_4_2
ilp1_4h_fpkm.csv

value: total leaf

value: 4h high light


title: HCC_134

value: Human Hepatocarcinoma

value: liver cancer tumor tissue


title: benign tumor 2


title: mouse primary podocytes from TFΔPOD mice  2

description:
TF2
RawCountsAnnotated_19-0021.txt


title: benign tumor 1


title: mouse primary podocytes from TFLoxP mice  3

description:
C3
RawCountsAnnotated_19-0021.txt


title: HCC_133


title: HCC_139


title: HCC_135


title: ilp1-1_t8h_rep1

description:
ilp_8_1
ilp1_8h_fpkm.csv


title: mouse primary podocytes from TFLoxP mice  2

description:
C2
RawCountsAnnotated_19-0021.txt


title: ilp1-1_t0_rep1

description:
ilp_0_1
ilp1_0_fpkm.csv

value: 2h normal light


title: Transgels_Hpylori_6dpi, HTO

city: Lausanne

first: Matthias

last: Lutolf

address: Route Cantonale

country: Switzerland

institute: EPFL

description:
6dpi_matrix.mtx.gz
6dpi_barcodes.tsv.gz
6dpi_features.tsv.gz
6dpi_HTO_details_README.csv

data_processing:
The reads were aligned using Cell Ranger v.6.1.2.
Assembly: GRCh38
Supplementary files format and content: Gene expression matrix and barcoad reads

source_name: Antrum

extract_protocol:
Single cell suspensions of samples have been obtained by digesting the collagen hydrogel with 10’000 U/ml Collagenase Type 1 for 12 min at 37°C and by subsequently dissociating the cells with TrypLE Express for 10 min at 37°C. For multiplexing, cells were immunolabelled with TotalSeq-C anti-human Hashtag antibodies at a dilution of 1:500 in staining buffer (PBS+0.1% Bovine Serum Albumin) for 30 min on ice and washed 2 times in 4 ml staining buffer with intermittent centrifugation (300g, 3min). Cells were strained using tubes with 35μm cell strainer caps and counted and assessed for cell viability using an automated cell counter.
10X Chromium Next GEM Single Cell 5’ v2 (Dual Index) chemistry (protocol CG000330 Rev F)

treatment_protocol: Organoid cells were grown on Transgel devices. Different growth conditions, please refer to the publication for details.

value: Antrum

value: in vitro cultured

tag: library type

value: HTO


title: health control 1

value: saliva

value: healthy


title: ilp1-1_t0_rep2

description:
ilp_0_2
ilp1_0_fpkm.csv


title: ilp1-1_t4h_rep1

description:
ilp_4_1
ilp1_4h_fpkm.csv


title: Transgels_Hpylori_2dpi, HTO

description:
2dpi_matrix.mtx.gz
2dpi_barcodes.tsv.gz
2dpi_features.tsv.gz
2dpi_HTO_details_README.csv


title: HCC_131


title: S-28,uIRI45min,28d,scRNA-seq

city: Beijing

first: Weijian

last: YAO

state: Beijing

address: No. 8 Xishiku Street, Xicheng District

department: Renal division

institute: Peking university first hospital

description: 10× genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were analyzed following the standard Chromium’s Cell Ranger pipeline to align the raw sequence reads according to the reference genome (mm10-2.1.0) using STAR. The count matrices from different batches were merged, integrated and processed with the Seurat pipeline
Assembly: mm10-2.1.0
Supplementary files format and content: Tab-separated values files and and matrix files

source_name: Spleen

extract_protocol:
Flow cytometry sorting (FACS)of monocyte or macrophages from kidneys, spleen, and Blood at different time points after uIRI 45 minutes.F4/80+ cells and Cd11b+ cells were sorted separately from kidney samples and mixed at the ratio of 1:1. Cd11b+ cells and Ly6c+ cells were sorted separately from blood samples and collected at a ratio of 1:1. Cd11b+ cells were sorted from spleen samples.
FACS-sorted cells were resuspended to a final cell concentration of 700~1200 cells/μl with more than 85% viability as determined by CountessTM II (Thermo Fisher Scientific). 8,000 to 12,000 cells were captured in droplets (10x Genomics Chromium Single Cell V2,V3,3ʹ Reagent Kits). After the reverse transcription step, fifty nanograms of amplified cDNA was fragmented and end-repaired, and sequenced on an Illumina platform using 150 paired-end reads at a coverage of 40,000 mean reads per cell.

value: Spleen

value: MPC

value: Cd11b+,Ly6c+ cells

tag: gender

value: Male

tag: age

value: Non


title: Transgels_Organoids_comparison, HTO

description:
matrix.mtx.gz
barcodes.tsv.gz
features.tsv.gz
Antrum_HTO_details_README.csv

value: acidic, neutral or air-liquid interface


title: fib1-1 replicate 2

city: Shanghai

first: Chenjiang

last: You

state: Shanghai

address: 2005 Songhu Rd

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and to Arabidopsis genome annotation Araport11 (https://www.araport.org) using bowtie v2 with default parameters
Both ends of read-through reads and 5' ends of longer reads were counted for ScoreMean calculation using an R package "RNAmodR.RiboMethSeq" (https://github.com/FelixErnst/RNAmodR.RiboMethSeq).
To minimize false positives brought by RNA secondary structures, over 3 consecutive nucleotides with ScoreMean over 0.5 were filtered out. Among the remaining sites, those with ScoreMean over 0.8 were retained as positive signals. IGV 2.6.0 was used to visualize the distribution of read ends and ScoreMean
Genome_build: Araport 11
Supplementary_files_format_and_content: WIG file containing the read end coverage

source_name: seedlings

growth_protocol: Seedlings for RiboMeth seq were grown on Murashige and Skoog (MS) plates containing 1% (v/w) sucrose and 0.7% (v/w) agar at 23°C under long day conditions for 14 days.

extract_protocol:
RNAs were extracted using Trizol reagent. NEBNext Small RNA Library Prep Set (Cat#E7330L) was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using protocols described in "High-Throughput Mapping of 2′-O-Me Residues in RNA Using Next-Generation Sequencing, Alexandra Lusser (ed.), RNA Methylation: Methods and Protocols, Methods in Molecular Biology, vol. 1562, DOI 10.1007/978-1-4939-6807-7_12"

tag: developmental stage

value: 14-day-old seedlings

tag: cultivar

value: seedlings


title: HCC_130


title: HCC_132


title: Transgels_Hpylori_6dpi, GEX

value: GEX


title: wild type replicate 2

value: wild type


title: HCC_129

value: Human Hepatocarcinoma

value: liver cancer tumor tissue


title: 6828 Cre+; IkkβL/L EoE, replicate 2, scRNAseq

city: Chicago

first: Marie-Pier

last: Tetreault

state: IL

address: 300 East Superior Street

department: Medicine/GI&Hep division

institute: Northwestern University

description: 10x Genomics

data_processing:
Data was demultiplexed and counted using Cell Range
Cell Ranger output was analyzed using Seurat version 4.3
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: Esophagus

extract_protocol:
Biopsies were briefly washed with DMEM/15%FBS, minced, digested with dispase (5000 caseinolytic Units) followed by trypsin (0.25%). Single cell suspensions were washed in PBS/2% BSA and checked for viability > 85%
10X Genomics NEXT GEM Kit V2, 10X genomics Library Construction kit

value: Esophagus

value: Cre+; IKKBL/L

value: EoE


title: S-5repeat,uIRI45min,5d,scRNA-seq

description: 10× genomics


title: Transgels_Hpylori_2dpi, GEX

value: Antrum

value: in vitro cultured


title: HCC_128


title: mouse primary podocytes from TFLoxP mice 1

description:
C1
RawCountsAnnotated_19-0021.txt

value: mouse primary podocytes

value: TFLoxP

value: 14 days in vitro differentiation


title: Transgels_Organoids_comparison, GEX


title: KM-28,uIRI45min,28d,scRNA-seq

description: 10× genomics

value: Kidney

value: MPC

value: Cd11b+,Ly6c+ cells

value: Male


title: HCC_126


title: 6827 Cre+; IkkβL/L Vehicle, replicate 3, scRNAseq

description: 10x Genomics

value: Vehicle


title: S-7,uIRI45min,7d,scRNA-seq

description: 10× genomics

value: Spleen

value: Non


title: NSCLC-H_B_biol_rep_2 [ADK18B]

city: Verona

first: Marzia

last: Rossato

state: Italy

address: Strada Le Grazie,15

department: Department of Biotechnology

country: Italy

institute: University of Verona

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
Trimmed sequence reads were mapped to GRCh38 with STAR
Read count extraction was performed using RSEM
Differential expression analysis was performed using DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: Non-small cell lung cancer (NSCLC)

extract_protocol:
GenUP Total RNA Kit (Biotechrabbit GmbH, Berlin, Germany)
Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit

value: Non-small cell lung cancer (NSCLC)

value: ICI treatment (hyperprogression)


title: HCC_125

value: Human Hepatocarcinoma

value: liver cancer tumor tissue


title: B-28,uIRI45min,28d,scRNA-seq

description: 10× genomics

source_name: Blood

value: Blood


title: NSCLC-H_A_biol_rep_1 [ADK18A]


title: KM-17,uIRI45min,17d,scRNA-seq

description: 10× genomics


title: HCC_124


title: NSCLC-B_C_biol_rep_3 [ADK17C]

value: prior to ICI initiation (baseline)


title: YFP+_MuSCs_multiplexing

city: Seoul

first: Young-Woo

last: Jo

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

institute: Seoul National University

description: YFP+_MuSCs (Tag06-Middle_aged, Tag07-Geriatric_vehicle, Tag08-Geriatric_DHT_1w, Tag10-Geriatric_DHT_4w)

data_processing:
The count matrix was created from sequenced reads through the BD Rhapsody WTA analysis pipeline (v1.11.1) for Mid and Geri samples.
ASTX-Toolkit's fastx_artifact_filter (hannonlab.cshl.edu/fastx_toolkit/) was used to eliminate sequencing artifacts or PCR duplicates.
The count matrix of Mid and Geri samples are merged by using Scanpy (v1.9.3).
Assembly: GRCm39
Supplementary files format and content: h5ad file of count matrix constructed as n_obj(samples) X n_cells X n_genes

source_name: Limb skeletal muscle

extract_protocol:
Limb Muscles dissected from mice at middle-age(12~14 months old) and geriatric-age(over 28 months old) were dissociated in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% horse serum (Hyclone, Logan, UT, USA), collagenase type II (800 units/mL; Worthington, Lakewood, NJ, USA), and dispase (1.1 units/mL; StemCell Technologies, Vancouver, BC, Canada) at 37 °C for 45 min. Digested suspensions were subsequently triturated and washed with DMEM to harvest mononuclear cells. Mononuclear cells were stained with Sca-1-PacificBlueTM (108120; BioLegend, San Diego, CA, USA), CD31-APC (102510; BioLegend), CD45-APC (103112; BD Biosciences, Franklin Lakes, NJ, USA), and Vcam1-Biotin (553331; BD Biosciences). Streptavindin-PE/Cy7 (BioLegend) was used as a secondary reagent. Lin-/YFP+ Muscle stem cells were isolated using a FACS Aria III cell sorter (BD Biosciences).
BD Rhapsody™ Cartridge Kit (BD bioscience, 633733) and Custom BD Single Cell Multiplexing Set (BD bioscience, 626545) was used for generating library of isolated YFP+ MuSCs according to the manufacturer’s instructions

treatment_protocol: Tamoxifen (20mg/mL in corn oil) (Sigma-Aldrich, St. Louis, MO, USA) was administered orally to Pax7-CreERT2;Rosa-YFP mice for 5 consecutive days(240mg/kg body weight) at 12~14 weeks old age

value: Limb skeletal muscle

value: YFP+ cells (Muscle stem cells)

value: Tamoxifen


title: HCC_122


title: NSCLC-B_B_biol_rep_2 [ADK17B]


title: NSCLC-H_C_biol_rep_3 [ADK18C]


title: HCC_127


title: 6510 Cre+; IkkβL/L EoE, replicate 1, scRNAseq

description: 10x Genomics

value: Esophagus

value: Cre+; IKKBL/L

value: EoE


title: 6266 IkkβL/L, replicate 1, scRNAseq

description: 10x Genomics

value: IkkBetaL/L

value: No treatment


title: KO3

city: Kunming

first: Jiahong

last: Duan

state: Yunnan

address: South Section, East Outer Ring Road, Chenggong District

department: Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences

institute: Yunnan University

data_processing:
The libraries were sequenced on an Illumina NovaSeq platform to generate 150 bp paired-end reads, according to the manufacturer’s instructions.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. Hisat2 tools soft were used to map with reference genome.
The StringTie Reference Annotation Based Transcript (RABT) assembly method was used to construct and identify both known and novel transcripts from Hisat2 alignment results
Gene function was annotated based on the following databases:Nr (NCBI non-redundant protein sequences)； Pfam (Protein family)；KOG/COG (Clusters of Orthologous Groups of proteins)；Swiss-Prot (A manually annotated and reviewed protein sequence database)；KO (KEGG Ortholog database)；GO (Gene Ontology).
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped. The formula is shown as follow: FPKM=cDNAFragmentsMappedFragments(Millions)∗TranscriptLength(kb)
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: colon carcinoma

growth_protocol: CT26 cells were grown in RPMI medium 1640 with 1 % penicillin-streptomycin, and 10% Fetal Bovine Serum (FBS) in a humidified, 5% CO2 at 37 °C

extract_protocol:
The total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA)
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina(Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: colon carcinoma

value: colon carcinoma cells

value: Tead1/4 knockout


title: KO4


title: KO2


title: NSCLC-B_A_biol_rep_1 [ADK17A]

value: Non-small cell lung cancer (NSCLC)


title: 5984 IkkβL/L Vehicle, replicate 1, scRNAseq

description: 10x Genomics

value: Vehicle


title: Geri-age_VCAM1-Neg_rep2

data_processing:
The sequencing reads were preprocessed in five steps. Initially, low-quality reads were trimmed using our in-house software followed by removing adapter sequences using Cutadapt (v3.1).
ASTX-Toolkit's fastx_artifact_filter (hannonlab.cshl.edu/fastx_toolkit/) was used to eliminate sequencing artifacts or PCR duplicates
alignment to the non-coding RNA sequence was performed using Bowtie2 (v2.1.0) to eliminate reads derived from non-coding RNA
in-house software was utilized to merge paired-end reads for subsequent alignment in the analysis. Preprocessed sequencing reads underwent alignment to the mouse genome (GRCm39) utilizing the STAR alignment software (v2.7.5b)
the reads were sorted and indexed, and the quantification of gene expression was performed using the reads per kilobase per million mapped reads (RPKM) metric using Samtools (v0.1.19)
Assembly: GRCm39
Supplementary files format and content: csv file with genes as rows, columns as samples and values in RPKM

extract_protocol:
Limb Muscles dissected from mice at middle-age(12~14 months old) and geriatric-age(over 28 months old) were dissociated in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% horse serum (Hyclone, Logan, UT, USA), collagenase type II (800 units/mL; Worthington, Lakewood, NJ, USA), and dispase (1.1 units/mL; StemCell Technologies, Vancouver, BC, Canada) at 37 °C for 45 min. Digested suspensions were subsequently triturated and washed with DMEM to harvest mononuclear cells. Mononuclear cells were stained with Sca-1-PacificBlueTM (108120; BioLegend, San Diego, CA, USA), CD31-APC (102510; BioLegend), CD45-APC (103112; BD Biosciences, Franklin Lakes, NJ, USA), and Vcam1-Biotin (553331; BD Biosciences). Streptavindin-PE/Cy7 (BioLegend) was used as a secondary reagent. Lin-/YFP+ Muscle stem cells were isolated using a FACS Aria III cell sorter (BD Biosciences). Total RNA was extracted from purified mononucleated cells using TRI Reagent (Invitrogen).
Total RNA libraries were generated using SMART-SeqTM v4 UltraTM Low Input RNA Kit for sequencing (Takara Bio USA, San Diego, CA, USA), according to the manufacturer’s instructions. Libraries were sequenced as paired-ends on an Illumina Hi-Seq 4000 system.


title: Geri-age_VCAM1-Neg_rep3


title: HCC_120

value: Human Hepatocarcinoma


title: KO1


title: KLK8_SDC4 OVE_3

first: Jiankui

last: Du

state: State...

address: 800 Xiangyin Road

department: Department of physiology

institute: Navy medical university

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Clean reads were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.  All the downstream analyses were based on the clean data with high quality.
Paired-end clean reads were aligned to hg38 using Hisat2 (v2.0.5). FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes read counts for each sample

source_name: HGECs

extract_protocol:
The RNA was isolated using Trizol method.
Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols

value: HGECs

value: KLK8 OVE_SDC4 OVE_3


title: KLK8_SDC4 OVE_2

value: KLK8 OVE_SDC4 OVE_2


title: 6957 IkkβL/L, replicate 2, scRNAseq

description: 10x Genomics


title: HCC_119

value: liver cancer tumor tissue


title: B-7,uIRI45min,7d,scRNA-seq

description: 10× genomics

value: Blood

value: MPC

value: Cd11b+,Ly6c+ cells

value: Male

value: Non


title: B-5repeat,uIRI45min,5d,scRNA-seq

description: 10× genomics


title: KLK8_SDC4 OVE_1

value: KLK8 OVE_SDC4 OVE_1


title: Geri-age_VCAM1-Neg_rep1

value: Limb skeletal muscle

value: YFP+ cells (Muscle stem cells)

value: Tamoxifen


title: HCC_123


title: WT4

value: colon carcinoma

value: colon carcinoma cells

value: WT


title: HCC_118

value: Human Hepatocarcinoma


title: WT3


title: KLK8 OVE_3

value: HGECs

value: KLK8 OVE_Lv_vector


title: Geri-age_VCAM1-Low_rep1


title: HCC_117


title: HCC_121


title: Geri-age_VCAM1-High_rep3


title: KLK8 OVE_2


title: HCC_116


title: WT1


title: KLK8 OVE_1


title: Geri-age_VCAM1-High_rep2


title: Geri-age_VCAM1-Low_rep2


title: AGEs3

city: nanchang

first: jiao

last: wang

state: jiangxi

address: 17 Yongwai Street

department: Endocrinology and metabolism

institute: The First Affiliated Hospital of Nanchang University

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < research species > was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as
follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: Mus musculus.GRCm38.v100
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: cell line

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA) following the manufacturer's procedure.

value: cell line

value: podocyte

value: AGEs 400µg/mL


title: HCC_112

value: liver cancer tumor tissue


title: Control_2


title: HCC_113


title: AGEs1


title: Mid-age_YFP+_rep2

value: 10 to 14 mo


title: Mid-age_YFP+_rep3


title: DMSO_4h, biol rep 3 [con_4_3]

first: Yi

last: Chen

address: 555 Zuchongzhi Rd.

institute: Shanghai Institute of Materia Medica Chinese Academy of Sciences

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: GRCh38.p13
Supplementary files format and content: gene.TPM.matrix.annot
Supplementary files format and content: gene.count.matrix.annot

growth_protocol: H358 cells were cultured in RPMI 1640 medium supplemented with 10% FBS at 37°C, 5% CO2.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according to the manufacturer’s instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). >1μg high-quality RNA was used to construct sequencing library.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). The XX RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNAwas subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, paired-end RNA-seq sequencing library was sequenced with the NovaSeq Xplus sequencer (2 × 150bp read length).

treatment_protocol: Treated with DMSO or 1 μM TNO155 for indicated times.

value: DMSO

tag: time

value: 4 h


title: Mid-age_YFP+_rep1


title: Control_1


title: HG2

value: HG 50mmol/L


title: AGEs2


title: Control_3


title: HCC_111


title: XBP1_KO_TIL, scRNA-seq

city: New York

first: SUNGMIN

last: HWANG

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
For single-cell RNA-sequencing samples, Cell Ranger (v.3.0.2) analysis pipelines were used to demultiplex raw sequencing data and to perform alignment, filtering, and counting of barcodes and unique molecular identifiers (UMIs). Pipeline coupled with mouse reference version GRCm38 (mm10). Count matrices generated by Cell Ranger imported into R (v.4.2.2) for further analysis using Seurat package (v. 3.0.0). The genes expressed at a proportion >0.1% of the data and cells with >200 genes detected were selected for further analyses. Low-quality cells were removed if they met the following criteria: <800 unique molecular identifiers (UMI), <500 genes, or >5% UMIs derived from the mitochondrial genome. Further, gene expression matrices were normalized by the NormalizeData function, and 2,000 features with high cell-to-cell variation were calculated using the FindVariableFeatures() function. To reduce the dimensionality of the data sets, the RunPCA() function was conducted with default parameters on linear transformation–scaled data generated by the ScaleData() function. In the end, clustering and visualization were performed by running Uniform Manifold Approximation and Projection (UMAP) dimensional reduction of 9 principal components for each cluster resolution of 0.7. Cell types were defined by comparing cluster marker genes with previously published single-cell RNA-sequencing datasets of mouse meninges. Visualization of genes illustrating expression levels was performed using R/Seurat commands (DoHeatmap, FeaturePlot, and DotPlot) package. Differential gene expression analysis was performed in sequencing datasets using Seurat.
Assembly: GRCm38 (mm10)

source_name: Intratumoral T cells (immune cells)

extract_protocol:
The total CD3+ T cells (DAPI-CD45+CD11b-CD19-NK1.1-MHCll-CD3+) of peritoneal lavage were isolated from mice bearing ID8-Defb29/Vegfa ovarian cancer for 23 days and subjected to single-cell RNA sequencing (scRNA-seq). Library preparation, sequencing, and raw data preprocessing were performed at the Genomics Resources Core Facility of Weill Cornell Medicine.
We generated scRNA-seq libraries using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics).

value: Intratumoral T cells (immune cells)

value: ID8-defb29/vegfa OvCa injection


title: Geri-age_VCAM1-High_rep1

value: Limb skeletal muscle

value: YFP+ cells (Muscle stem cells)

value: Tamoxifen


title: HG1

value: WT


title: HCC_114

value: Human Hepatocarcinoma


title: DMSO_4h, biol rep 2 [con_4_2]


title: WT2

value: colon carcinoma

value: colon carcinoma cells


title: DMSO_4h, biol rep 1 [con_4_1]


title: HCC_110


title: XBP1_WT_TIL, scRNA-seq


title: Con3

value: cell line

value: blank


title: SHP2i_4h, biol rep 3 [T5_4_3]


title: KO_OX

city: Blacksburg

first: Liwu

last: Li

state: VA

address: 1015 Life Science Cir

institute: Virginia Tech

data_processing:
Cellranger 3.1.0
All the data were merged using Seurat's integration workflow.
The merged data was then saved in RDS format using the "saveRDS" function.
Assembly: mm10
Supplementary files format and content: RDS file with matrix can be read by Seurat

source_name: monocyte

growth_protocol: Murine bone marrow monocytes were cultured in complete RPMI medium (10% fetal bovine serum, 2 mM L-glutamine, and 1% penicillin/streptomycin) supplemented with 100 ng/ml M-CSF.

extract_protocol:
cDNA libraries were generated from treated cells by using the 10X Genomics Chromium Single Cell 3' Reagent Kits (version 3 Chemistry)
Single-cell suspensions were loaded onto the Chromium Controller to generate 1,000 single-cell gel beads in emulsion per sample. The cDNA of each sample after amplification of 12 cycles was quantified by Qubit and quality-checked by Bioanalyzer to verify the size distribution of cDNA samples and determine indexed PCR amplification of 15 cycles to yield a sufficient and unbiased library for sequencing. After library quality control by Tapestation, indexed library samples were quantified by KAPA library quantification kit (Universal) and pooled with 15 ul of 5 nM for each sample.
Libraries were pooled togegther for sequencing on Illumina Hiseq4000

treatment_protocol: Cultured bone marrow monocytes from WT  mice were treated with PBS, 10 microg/ml oxLDL for a five day period

value: BM derived

tag: agent

value: oxLDL

value: Tram KO


title: HCC_115

value: liver cancer tumor tissue


title: HG3

tag: cell line

value: podocyte


title: HCC_108


title: Con2

tag: cell type


title: HCC_106

tag: treatment


title: Con1

tag: tissue


title: HCC_105


title: WT_OX

tag: genotype


title: SHP2i_4h, biol rep 1 [T5_4_1]

value: 4 h


title: Wild-type rep 4

city: Farmington

first: Justin

middle: S

last: King

state: Connecticut

address: 263 Farmington Ave

institute: UConn Health

description: 100bp paired end; version 1.5 chemistry

data_processing:
After quality control of FASTQ files, reads were mapped to Mus musculus genome (GRCm39) with HISAT/2.1.1 [https://pubmed.ncbi.nlm.nih.gov/31375807/].
Counts were generated against the features with HTSeq-count (htseq/0.13.5)[https://pubmed.ncbi.nlm.nih.gov/25260700/]
Differential expression of genes between conditions was evaluated using DESeq2 R package [http://www.ncbi.nlm.nih.gov/pubmed/25516281].
Normalized counts were used for Gene Set Enrichment Analysis (GSEA) [http://software.broadinstitute.org/gsea/index.jsp].
Assembly: GRCm39
Supplementary files format and content: counts.normalized.xlsx

source_name: Bone marrow stromal cell

growth_protocol: Bone marrow stromal cells cells were maintained in MEM suplemented with 10% fetal bovine surum (FBS) plus antibiotics in humidified atmosphere with 5% CO2 at 37 C

extract_protocol:
RNA was isolated from cell cultures using Trizol (Invitrogen), according to manufacture's protocol.
Illumina Stranded mRNA Ligation Sample Preparation kit following the manufacturer's protocol

treatment_protocol: Osteogenic differentiation media was added for 10 days once cells reached 80-90% confluence (MEM with 10% FBS plus 50 μg/mL ascorbic acid and 4 mM β-glycerophosphate)

tag: strain background

value: Bone marrow stromal cell

value: Osteogenic differentiation


title: HCC_104


title: Wild-type rep 3

description: 100bp paired end; version 1.5 chemistry


title: SHP2i_4h, biol rep 2 [T5_4_2]


title: DMSO_24h, biol rep 2 [con_24_2]

value: DMSO


title: HCC_109


title: KO_PBS

value: PBS


title: DMSO_24h, biol rep 1 [con_24_1]


title: HCC_102


title: HCC_101


title: HCC_103


title: PH72_RNAseq_M560_3mo

city: Geneva

first: Vasilis

last: Dionellis

address: 30, quai Ernest-Ansermet

institute: University of Geneva

data_processing:
RNA sequencing reads were aligned to the mouse reference genome GRCm38/mm10 using the Burrows-Wheeler Aligner mem algorithm, retaining only the reads with the highest quality score
Custom Perl scripts were then developed to process the data for analysis (scripts have been submitted with the manuscript)
Only the canonical  curated transcripts of coding genes found in GRCm38/mm10  RefSeq have been used for the calculation of relative expression (normalized sigma values) of each gene.
Assembly: GRCm38/mm10
Supplementary files format and content: csv with average normalized sigma values of replicates and/or per sample normalized sigma values

source_name: Liver

extract_protocol: none provided

value: Liver

value: hepatocytes


title: PH72_RNAseq_M558_3mo


title: SHP2i_24h, biol rep 3 [T5_24_3]


title: WT_PBS

value: WT


title: Lgr6-null rep 4

description: 100bp paired end; version 1.5 chemistry

value: Lgr6-GFP-ires-CreERT2 homozygote


title: Wild-type rep 1

description: 100bp paired end; version 1.5 chemistry


title: PH72_RNAseq_M559_3mo


title: PH72_RNAseq_M557_3mo


title: SHP2i_24h, biol rep 2 [T5_24_2]


title: Wild-type rep 2

description: 100bp paired end; version 1.5 chemistry


title: HCC_100

value: Human Hepatocarcinoma


title: DMSO_24h, biol rep 3 [con_24_3]


title: PH72_RNAseq_M556_ATRi1x25at24h_3mo


title: Lgr6-null rep 3

description: 100bp paired end; version 1.5 chemistry


title: Lgr6-null rep 2

description: 100bp paired end; version 1.5 chemistry


title: SHP2i_24h, biol rep 1 [T5_24_1]


title: HCC_099


title: DMSO_48h, biol rep 3 [con_48_3]


title: HCC_098


title: PH72_RNAseq_M555_ATRi1x25at24h_3mo


title: Lgr6-null rep 1

description: 100bp paired end; version 1.5 chemistry


title: HCC_096


title: DMSO_48h, biol rep 1 [con_48_1]


title: HCC_095


title: SHP2i_48h, biol rep 3 [T5_48_3]


title: PH72_RNAseq_M554_ATRi1x25at24h_3mo


title: PH72_RNAseq_M552_12mo


title: HCC_093


title: PH72_RNAseq_M551_12mo


title: Young, female, biological replicate 2, technical replicate 2, ST-RNAseq

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description:
Y2FB
10x Genomics Visium

data_processing:
The demultiplexing,aligned, extracted barcodes, counted unique molecular identifiers (UMIs), and compiled a feature-barcode matrix for each sample  were made using the Space Ranger software v2.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The feature-barcode matrix from Space Ranger was imported into PartekFlow Genomic Analysis Software (Partek Inc.) for further quality assessments.The barcoded spots were filtered by counts at low.cutoff=1 and high.cutoff=38,855, detected genes at  low.cutoff=1 and high.cutoff=8012, % mitochondrial counts at low.cutoff=0, high.cutoff=35%, % ribosomal counts at low.cutoff=0, high.cutoff=14%. Filtered genes with value ≤ 1.0 in at least 99 % of the cells were excluded.
The data were normalized and scaled to counts per million (CPM, add:1.0, log:2.0). PCA was performed, and the top 100 principal components (PCs) were stored by PartekFlow Genomic Analysis Software (Partek Inc.)
The data were then clustered using graph-based cluster analysis with a clustering resolution set to 0.5. Spots on visium image were classified based on histology and Uniform Manifold Approximation and Projection (UMAP) and annotated to the graph-based clusters by PartekFlow Genomic Analysis Software (Partek Inc.)
ANOVA statistics was applied to each age group comparison for differential analysis with sex as a covariate by PartekFlow Genomic Analysis Software (Partek Inc.)
Assembly: mm10
Supplementary files format and content: H5 File
Library strategy: Spatial transcriptomics

source_name: coronal sections of mouse brain

extract_protocol:
Tissue sections were first stained with Hematoxylin-Eosin (H&E), followed by cDNA synthesis, amplification, barcoding, and library construction (see Methods). Following this demonstrated protocol, we obtained high-quality spatially resolved RNA-seq data from these 24 samples and sequenced them on the NovaSeq™ 6000 platform achieving an average coverage of 171 million read pairs per sample
10 µl (25%) of the total amplified cDNA was used as input to perform enzymatic fragmentation, end repair and A-tailing (10X Genomics, PN1000196). A double-sided size selection was then performed with SPRIselect (Beckman, Coulter B23318). TruSeq read2 primer was added via adaptor ligation (10X Genomics, PN1000196). P5, P7, i7, and i5 sample indices were added via index PCR with the individual dual index TT set A (10X Genomics, 3000431). The cycle number for index PCR was calculated based on the yield of the 25% carry forward cDNA material and 15 cycles were used. A double-sided size selection of the post-index PCR sample was performed with SPRIselect (Beckman, Coulter B23318).

value: coronal sections of mouse brain

tag: strain

value: 11 weeks old

tag: Sex

value: F


title: PH72_RNAseq_M553_ATRi1x25at24h_3mo


title: Young, male, biological replicate 2, technical replicate 2, ST-RNAseq

description:
Y2MB
10x Genomics Visium

value: M


title: DMSO_48h, biol rep 2 [con_48_2]


title: Young, male, biological replicate 2, technical replicate 1, ST-RNAseq

description:
Y2MA
10x Genomics Visium


title: PH72_RNAseq_M550_12mo


title: HCC_092

data_processing:
QuantSeq 3’ mRNA-Seq reads were aligned using Bowtie2
The read count data were processed based on quantile normalization method using EdgeR within R
Gene classification was based on searches done by DAVID and Medline databases
Assembly: hg19
Supplementary files format and content: raw counts

source_name: Human liver

extract_protocol:
Total RNA was isolated using Trizol reagent.
The construction of library was performed using QuantSeq 3’ mRNA-Seq Library Prep Kit


title: SHP2i_48h, biol rep 1 [T5_48_1]


title: Young, female, biological replicate 2, technical replicate 1, ST-RNAseq

description:
Y2FA
10x Genomics Visium


title: HCC_091


title: Young, male, biological replicate 1, technical replicate 2, ST-RNAseq

description:
Y1MB
10x Genomics Visium


title: PH72_RNAseq_M549_12mo


title: HCC_090


title: SK-N-BE(2) shControl_rep2

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Transcripts per Kilobase of exon model per Million mapped reads (TPM) were calculated using a methodology adapted from the StringTie software. In brief, all isoforms of a gene were assembled and merged to generate a composite transcript model. The number of reads mapped to the exonic regions of this composite transcript model was tallied and subsequently normalized. Normalization was achieved by dividing the read count by the length of the composite transcript model (in kilobases) and then scaling the result by the size of the total mapped library (in millions of reads).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include readcount values for each Sample.

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Neuroblastoma cells

value: shControl


title: Young, male, biological replicate 1, technical replicate 1, ST-RNAseq

description:
Y1MA
10x Genomics Visium


title: SK-N-BE(2) shControl_rep1


title: HCC_089

first: Sung Hwan

last: Lee

address: 59 Yatap-ro

institute: CHA Bundang Medical Center

value: liver cancer tumor tissue


title: PH72_RNAseq_M548_ATRi1x25at24h_12mo


title: PH72_RNAseq_M547_ATRi1x25at24h_12mo


title: Young, female, biological replicate 1, technical replicate 2, ST-RNAseq

description:
Y1FB
10x Genomics Visium


title: SHP2i_48h, biol rep 2 [T5_48_2]


title: SK-N-BE(2) shIGF2BP3_rep2


title: PH72_RNAseq_M546_ATRi1x25at24h_12mo


title: HCC_086


title: HCC_087


title: PH72_RNAseq_M545_ATRi1x25at24h_12mo


title: SK-N-BE(2) shControl_rep2_m6A

data_processing:
Raw FASTQ files were trimmed by fastp version 0.23.2
Reads were mapped to human genome version hg38 by HISAT2 version 2.2.0
MACS2 was used to call peaks.
deeptools were used to create bw files.
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Total cellular RNA extracted from cells were fragmented by RNA fragmentation reagents (Thermo, AM8740). Fragmented RNA was incubated with anti-m6A antibody at 4°C for 6 h in 500 μl of NT2 buffer (200 mM NaCl, 50 mM HEPES pH 7.6, 2 mM EDTA, 0.05% NP-40, 0.5 mM DTT, 200 U ml–1 RNase inhibitor).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: antibody

value: m6A antibody


title: PH48_RNAseq_M3_ATRi1x25at24h_12mo


title: SK-N-BE(2) shIGF2BP3_rep1


title: Old, male, biological replicate 2, technical replicate 1, ST-RNAseq

description:
O2MA
10x Genomics Visium

value: 127 weeks old


title: Old, female, biological replicate 2, technical replicate 2, ST-RNAseq

description:
O2FB
10x Genomics Visium

value: 125 weeks old


title: SK-N-BE(2) shControl_rep1_m6A


title: Old, male, biological replicate 2, technical replicate 2, ST-RNAseq

description:
O2MB
10x Genomics Visium


title: SK-N-BE(2) shControl_rep2_Input


title: HCC_084

tag: cell line origin


title: PH48_RNAseq_M2_ATRi1x25at24h_12mo


title: PH48_RNAseq_M1_ATRi1x25at24h_12mo


title: Old, female, biological replicate 2, technical replicate 1, ST-RNAseq

description:
O2FA
10x Genomics Visium


title: SK-N-BE(2) shControl_rep1_Input


title: HCC_083


title: Old, male, biological replicate 1, technical replicate 2, ST-RNAseq

description:
O1MB
10x Genomics Visium


title: PH48_RNAseq_M3_12mo


title: SK-N-BE(2) shIGF2BP3_rep2_m6A


title: HCC_088


title: Old, male, biological replicate 1, technical replicate 1, ST-RNAseq

description:
O1MA
10x Genomics Visium


title: PH48_RNAseq_M2_12mo


title: SK-N-BE(2) shIGF2BP3_rep2_Input


title: HCC_082


title: Young, female, biological replicate 1, technical replicate 1, ST-RNAseq

description:
Y1FA
10x Genomics Visium


title: HCC_085


title: HCC_081


title: Old, female, biological replicate 1, technical replicate 2, ST-RNAseq

description:
O1FB
10x Genomics Visium


title: PH48_RNAseq_M1_12mo


title: HCC_080


title: SK-N-BE(2) shIGF2BP3_rep1_m6A


title: PH48_RNAseq_M3_3mo


title: HCC_78


title: COV-Ex50uM-3

city: Paris Cedex 13

first: Celine

last: Guigon

address: 4 avenue de l'Observatoire

country: France

institute: Université Paris-Cité, CNRS, Inserm, Unité de Biologie Fonctionnelle et Adaptative

description:
hg38_gene_reads.tsv
hg38_gene_tpm.tsv

data_processing:
Quality of raw data was evaluated with FastQC.
Poor quality sequences were trimmed or removed with fastp tool, with default parameters, to retain only good quality paired reads.
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used for mapping on hg38 or mm10 reference genome and quantification with gencode v39 or vM25 annotation gtf file, respectively.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: hg38 or mm10
Supplementary files format and content: tab-delimited text files including expecting counts and TPM
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: COV

growth_protocol: Cells were seeded in 6-well plates at a density of either 1.5x105 (AT29 cells) or 2x105 (COV434 and KGN cells) cells/mL in 10% FBS phenol red-free medium

extract_protocol:
A total of 18 samples for each cell line were lysed in RLT buffer from RNeasy mini kit (#74106, Qiagen) and RNA were extracted following the manufacturer's protocol. The quality and quantity of RNA were estimated by Nanodrop (Thermo Scientific Nanodrop 2000).
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-seq paired

treatment_protocol: Cells were treated with vehicle (DMSO) or EX-527 at 50 μM for 24 hours. The experiment was replicated three times.

tag: source

value: COV

value: granulosa cell tumor

tag: tumor stage

value: primary stage

value: juvenlle


title: HCC_079


title: PH48_RNAseq_M2_3mo

value: Liver

value: hepatocytes


title: SK-N-BE(2) shIGF2BP3_rep1_Input


title: Old, female, biological replicate 1, technical replicate 1, ST-RNAseq

description:
O1FA
10x Genomics Visium

tag: age


title: PH48_RNAseq_M1_3mo


title: Middle, male, biological replicate 2, technical replicate 2, ST-RNAseq

description:
M2MB
10x Genomics Visium

value: 58 weeks old


title: COV-Ex50uM-2

description:
hg38_gene_reads.tsv
hg38_gene_tpm.tsv

tag: developmental stage


title: PH00_RNAseq_Mwt3_3mo


title: Middle, female, biological replicate 2, technical replicate 2, ST-RNAseq

description:
M2FB
10x Genomics Visium

value: coronal sections of mouse brain

value: 57 weeks old


title: HCC_77

value: Human Hepatocarcinoma


title: COV-Ex50uM-1

description:
hg38_gene_reads.tsv
hg38_gene_tpm.tsv


title: HCC_76


title: COV-CTR-3

description:
hg38_gene_reads.tsv
hg38_gene_tpm.tsv

value: COV-CTR

value: control


title: HCC_75


title: PH00_RNAseq_Mwt2_3mo


title: Middle, male, biological replicate 1, technical replicate 2, ST-RNAseq

description:
M1MB
10x Genomics Visium

value: M


title: PH00_RNAseq_Mwt1_3mo


title: HCC_74

value: liver cancer tumor tissue


title: Middle, male, biological replicate 1, technical replicate 1, ST-RNAseq

description:
M1MA
10x Genomics Visium


title: PH00_RNAseq_M558_3mo


title: PH00_RNAseq_M557_3mo


title: COV-CTR-1

description:
hg38_gene_reads.tsv
hg38_gene_tpm.tsv


title: Middle, male, biological replicate 2, technical replicate 1, ST-RNAseq

description:
M2MA
10x Genomics Visium


title: KGN-Ex-50uM-3

description:
hg38_gene_reads.tsv
hg38_gene_tpm.tsv

source_name: KGN

value: KGN

value: metastatic

value: Adult


title: HCC_72


title: KGN-Ex-50uM-2

description:
hg38_gene_reads.tsv
hg38_gene_tpm.tsv


title: HCC_73


title: PH00_RNAseq_M553_3mo


title: Middle, female, biological replicate 1, technical replicate 1, ST-RNAseq

description:
M1FA
10x Genomics Visium

value: F


title: KGN-Ex-50uM-1

description:
hg38_gene_reads.tsv
hg38_gene_tpm.tsv

value: granulosa cell tumor


title: PH00_RNAseq_M554_3mo


title: HCC_71


title: Middle, female, biological replicate 2, technical replicate 1, ST-RNAseq

description:
M2FA
10x Genomics Visium


title: iwat, ko_10week, 3 [H10-KO3_S32]

city: Los Angeles

first: Peter

last: Tontonoz

state: CA

address: 675 Charles E Young Dr.

department: Pathology & Laboratory Medicine

institute: University of California, Los Angeles

description:
counts.csv
abundances.csv

data_processing:
Fastq files were checked for quality, filtered, trimmed, and corrected for base pair mismatches using fastp (Version 0.23.2)
Salmon was used with full selective alignment to map reads to the mouse transcriptome and quantify transcript counts [mm10 - Ensembl – Release 97]
Transcript counts were summarized to the gene level using tximport package for R.
Assembly: mm10
Supplementary files format and content: .csv files contain Salmon-derived transcript abundances and raw counts from tximport summarized to the gene level

source_name: iWAT

extract_protocol:
Total RNA was extracted using TRIzol and RNeasy Mini Kit with on-column DNase I digestion (Qiagen)
Library preparation and sequencing was performed at the UCLA Technology Center for Genomics & Bioinformatics. Illumina sequencing-compatible cDNA libraries were synthesized from mRNA  enriched by Poly-A capture. 200bp paired-end sequencing cDNA libraries were analyzed with an Agilent TapeStation and sequenced on an Illumina NovaSeq S1 at 200 cycles. Read depth per sample averaged around 130M reads. Raw sequencing reads were demultiplexed using bcl2fastq (Illumina).

value: iWAT

tag: diet

value: Research Diets D12492

value: Male

value: 18-22 weeks


title: PH00_RNAseq_M552_12mo

value: Liver

value: hepatocytes


title: HCC_069

city: Seongnam


title: iwat, ko_10week, 2 [H10-KO2_S31]

description:
counts.csv
abundances.csv


title: HCC_70


title: KGN-CTR-3

description:
hg38_gene_reads.tsv
hg38_gene_tpm.tsv

value: KGN-CTR


title: KGN-CTR-2

description:
hg38_gene_reads.tsv
hg38_gene_tpm.tsv


title: PH00_RNAseq_M551_12mo


title: COV-CTR-2

description:
hg38_gene_reads.tsv
hg38_gene_tpm.tsv

value: COV

value: primary stage

value: juvenlle


title: HCC_068

value: Human Hepatocarcinoma


title: iwat, wt_10week, 4 [H10-WT4_S29]

description:
counts.csv
abundances.csv

value: WT


title: PH00_RNAseq_M550_12mo


title: Middle, female, biological replicate 1, technical replicate 2, ST-RNAseq

description:
M1FB
10x Genomics Visium

value: coronal sections of mouse brain

value: 57 weeks old


title: KGN-CTR-1

description:
hg38_gene_reads.tsv
hg38_gene_tpm.tsv

value: KGN

value: metastatic

value: Adult

value: control


title: HCC_067

value: liver cancer tumor tissue


title: iwat, wt_10week, 3 [H10-WT3_S28]

description:
counts.csv
abundances.csv

value: iWAT

value: Research Diets D12492

value: Male


title: WholeBlood-MDD-F-914

city: Strasbourg

first: Pierre-Eric

last: Lutz

address: 8 allée du général Rouvillois

institute: Institut des Neurosciences Cellulaires et Intégratives, INCI CNRS UPR3212

data_processing:
raw reads were trimmed with bbduk
raw reads were aligned using STAR v2.5.3a and Gencode v29 annotations
gene expression (raw counts) were quantified using HTSeq v0.11.2
Assembly: GRCh38.p12
Supplementary files format and content: csv file includes raw counts for each sample

source_name: Whole blood

growth_protocol: Not applicable

extract_protocol:
Venous blood passed through LeukoLOCK™ filters (Life Technologies, Ambion), followed by total RNA extraction using ethanol precipitation
libraries were prepared from 500 ng of total RNA, using poly-A capture and the QIAseq Stranded mRNA Select kit (Qiagen) in Females (F) OR the TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA) in males (M)

treatment_protocol: Not applicable

value: Whole blood

tag: group

value: MDD

value: Female


title: PH00_RNAseq_M549_12mo

value: Liver

value: hepatocytes


title: HCC_065

value: Human Hepatocarcinoma


title: iwat, wt_10week, 2 [H10-WT2_S27]

description:
counts.csv
abundances.csv

value: WT

value: 18-22 weeks


title: iwat, ko_10week, 4 [H10-KO4_S33]

description:
counts.csv
abundances.csv


title: WholeBlood-MDD-F-912


title: HCC_064


title: iwat, ko_5week, 4 [H5-KO4_S25]

description:
counts.csv
abundances.csv


title: PH00_RNAseq_M548_12mo


title: WholeBlood-MDD-F-911


title: HCC_063


title: iwat, ko_5week, 3 [H5-KO3_S24]

description:
counts.csv
abundances.csv


title: PH00_RNAseq_M547_12mo


title: WholeBlood-MDD-F-910


title: HCC_062


title: PH00_RNAseq_M546_12mo


title: PH00_RNAseq_M545_12mo


title: iwat, ko_5week, 2 [H5-KO2_S23]

description:
counts.csv
abundances.csv


title: WholeBlood-MDD-F-909


title: HCC_061


title: iwat, wt_5week, 4 [H5-WT3_S21]

description:
counts.csv
abundances.csv


title: Pooled mice S4-7, blood day 7, ADT-seq and CITE-seq, sequencing run 2

city: South San Francisco

first: Thomas

middle: D

last: Wu

address: 1 DNA Way

institute: Genentech, Inc.

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
B9.4567B.barcodes.tsv.gz
B9.4567B.features.tsv.gz
B9.4567B.matrix.mtx.gz

library_source: other

data_processing:
Sequencing files from Illumina assays were run through CellRanger version 6.1.1 against a transcriptome derived from ENSEMBL version 2.2.0 for the mouse genome GRCm38.  FASTQ files were generated using "cellranger mkfastq".  Gene expression (RNA-seq), ADT-seq, and CITE-seq libraries were processed using "cellranger count", providing a libraries.csv file (provided as a Supplementary File) to identify ADT-seq and CITE-seq barcodes.  TCR-seq libraries were processed using "cellranger vdj".
Assembly: GRCm38
Supplementary files format and content: For scRNA-seq, ADT-seq, and CITE-seq libraries, CellRanger version 6.1.1 files containing barcodes, features, and count matrices
Supplementary files format and content: For scTCR-seq, CellRanger 6.1.1 files containing filtered contig annotations

molecule: protein

growth_protocol: Mice were inoculated subcutaneously with 0.1 x 10^6 CT26 cells in 100 µL Hank's balanced solution (HBSS) and Matrigel (BD Biosciences, San Jose, CA).  Once tumours achieved a mean volume of 150-200 mm^3, animals were apportioned into treatment groups.

extract_protocol:
After treatment, tumours were dissociated into single-cell suspensions using a gentleMACS dissociator and enzymatically digested in a buffer containing collagenase D (2 mg/ml) and DNAse (40 U/ml).  Single-cell suspensions of draining lymph nodes were obtained by mechanical dissociation through 40 µm cell strainers and performing red blood cell lysis as needed.  Blood was obtained by terminal cardiac puncture and collected in lavender Microtainer Blood Collection Tubes and subjected to red blood cell lysis.  Blood samples were multiplexed using 10 barcodes with a distinct pair used to identify each individual sample before pooling. Tumor and blood samples were sorted by FACS for CD90+ T cells, and draining lymph node samples were sorted for CD90+CD44+ T cells.
5' Chromium Single Cell 5' Library and Gel Bead Kit (10X Genomics).  T cells were allowed to bind to tetramers of gp70 antigen bound to associated ADT barcodes.  CITE-seq was performed using antibodies against 18 selected proteins plus 6 control immunoglobulin proteins.  A total of 14 cycles of PCR amplification were performed.

treatment_protocol: exposed to five different treatment regimens: control anti-gp120, anti-PD-L1, anti-TIGIT, combination, and combination plus FTY720, which blocks egress of T cells from lymphoid tissue.

value: BALB/c

value: 6-8 weeks

value: Pooled treatments from the Control, anti-PDL1, anti-TIGIT, Combo, and Combo+FTY720 groups

value: Blood

value: CD90+ T cells


title: HCC_060

value: liver cancer tumor tissue


title: WholeBlood-MDD-F-908


title: Pooled mice S4-7, blood day 7, ADT-seq and CITE-seq, sequencing run 1


title: WholeBlood-MDD-F-907


title: HCC_059


title: iwat, wt_5week, 2 [H5-WT2_S19]

description:
counts.csv
abundances.csv

value: iWAT


title: Pooled mice S4-7, blood day 7, scRNA-seq, sequencing run 2

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
B9.4567B.barcodes.tsv.gz
B9.4567B.features.tsv.gz
B9.4567B.matrix.mtx.gz


title: HCC_058


title: WholeBlood-MDD-F-906


title: Pooled mice S4-7, blood day 7, scRNA-seq, sequencing run 1


title: HCC_057


title: iwat, ko_1week, 3 [H1-KO3_S16]

description:
counts.csv
abundances.csv

value: Research Diets D12492


title: WholeBlood-MDD-F-905


title: HCC_056


title: Pooled mice S1-3, blood day 7, ADT-seq and CITE-seq, sequencing run 1

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
B9.123B.barcodes.tsv.gz
B9.123B.features.tsv.gz
B9.123B.matrix.mtx.gz


title: WholeBlood-MDD-F-903


title: HCC_055


title: Pooled mice S1-3, blood day 7, scRNA-seq, sequencing run 2

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
B9.123B.barcodes.tsv.gz
B9.123B.features.tsv.gz
B9.123B.matrix.mtx.gz


title: HCC_054


title: WholeBlood-MDD-F-822


title: iwat, wt_1week, 4 [H1-WT4_S13]

description:
counts.csv
abundances.csv

value: Male


title: iwat, wt_1week, 3 [H1-WT3_S12]

description:
counts.csv
abundances.csv


title: iwat, ko_1week, 4 [H1-KO4_S17]

description:
counts.csv
abundances.csv


title: Pooled mice S1-3, blood day 7, scRNA-seq, sequencing run 1


title: iwat, wt_5week, 3 [H5-WT3_S20]

description:
counts.csv
abundances.csv


title: WholeBlood-MDD-F-820

value: Whole blood


title: Pooled mice S4-7, blood day 0, ADT-seq and CITE-seq, sequencing run 2

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
B9.4567b.barcodes.tsv.gz
B9.4567b.features.tsv.gz
B9.4567b.matrix.mtx.gz


title: WholeBlood-MDD-F-817

value: MDD


title: HCC_053


title: iwat, ko_0week, 4 [NCD-KO4_S9]

description:
counts.csv
abundances.csv

value: Standard Chow


title: HCC_052


title: Pooled mice S4-7, blood day 0, ADT-seq and CITE-seq, sequencing run 1

value: Female


title: WholeBlood-MDD-F-811


title: Pooled mice S1-3, blood day 7, ADT-seq and CITE-seq, sequencing run 2


title: HCC_050


title: iwat, ko_1week, 2 [H1-KO2_S15]

description:
counts.csv
abundances.csv


title: Pooled mice S4-7, blood day 0, scRNA-seq, sequencing run 2

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
B9.4567b.barcodes.tsv.gz
B9.4567b.features.tsv.gz
B9.4567b.matrix.mtx.gz


title: WholeBlood-MDD-F-904


title: iwat, ko_0week, 2 [NCD-KO2_S7]

description:
counts.csv
abundances.csv


title: HCC_049


title: WholeBlood-MDD-F-806


title: Pooled mice S4-7, blood day 0, scRNA-seq, sequencing run 1


title: HCC_048


title: HCC_047


title: iwat, wt_0week, 3 [NCD-WT3_S4]

description:
counts.csv
abundances.csv


title: WholeBlood-MDD-F-804


title: Pooled mice S1-3, blood day 0, ADT-seq and CITE-seq, sequencing run 2

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
B9.123b.barcodes.tsv.gz
B9.123b.features.tsv.gz
B9.123b.matrix.mtx.gz


title: iwat, wt_1week, 2 [H1-WT2_S11]

description:
counts.csv
abundances.csv


title: iwat, wt_0week, 2 [NCD-WT2_S3]

description:
counts.csv
abundances.csv


title: iwat, wt_0week, 4 [NCD-WT4_S5]

description:
counts.csv
abundances.csv


title: Pooled mice S1-3, blood day 0, scRNA-seq, sequencing run 2

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
B9.123b.barcodes.tsv.gz
B9.123b.features.tsv.gz
B9.123b.matrix.mtx.gz


title: WholeBlood-MDD-F-801


title: HCC_045


title: HCC_046


title: shMOF_LPS3_Rep3

city: Freiburg

first: Asifa

last: Akhtar

address: Stuebeweg 51

department: Chromatin Regulation

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
The data processing, quality control, trimming and mapping were performed using snakePipes mRNA-seq pipeline (Bhardwaj et al., 2019)
Differential expression analysis was performed using DESeq2 with a FDR cut-off of 0.05
Assembly: mm10
Supplementary files format and content: Tab deliminated file of DESEQ2 followed with paired compairsion analysis

source_name: bone-marrow derived macrophage isolated ex-vivo

extract_protocol:
RNA extractions were performed simultaneously for all samples using Direct-zol RNA Miniprep Plus Kits (Zymo)
Paired-end (100 bp length) libraries were prepared using the Illumina TruSeq Stranded mRNA Prep, Ligation (Illumina, 20040534)

value: MOF depletion (shMOF Knockdown)

value: 100ng/ml LPS stimulated, 3hours


title: Pooled mice S1-3, blood day 0, ADT-seq and CITE-seq, sequencing run 1


title: WholeBlood-MDD-F-639


title: iwat, ko_0week, 3 [NCD-KO3_S8]

description:
counts.csv
abundances.csv


title: Pooled mice S1-3, blood day 0, scRNA-seq, sequencing run 1


title: WholeBlood-MDD-F-802


title: HCC_044

value: Human Hepatocarcinoma


title: Combo+FTY720, replicate 4, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S5.7n.barcodes.tsv.gz
S5.7n.features.tsv.gz
S5.7n.matrix.mtx.gz

source_name: Draining lymph node

value: anti-PDL1 mIgG2a LALAPG (clone 6E11), 10 mg/kg iv x 1, 5 mg/kg ip x 2, plus anti-TIGIT mIgG2a (clone 10A7), 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week

value: Draining lymph node

value: CD90+CD44+ T cells


title: shMOF_LPS3_Rep2

value: bone-marrow derived macrophage isolated ex-vivo


title: WholeBlood-MDD-F-807


title: shMOF_LPS3_Rep1


title: HCC_043


title: WholeBlood-MDD-F-632


title: HCC_042


title: Combo+FTY720, replicate 4, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S5.7n.barcodes.tsv.gz
S5.7n.features.tsv.gz
S5.7n.matrix.mtx.gz

value: BALB/c

value: 6-8 weeks


title: Combo+FTY720, replicate 3, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S5.5n.barcodes.tsv.gz
S5.5n.features.tsv.gz
S5.5n.matrix.mtx.gz


title: shCTRL_LPS3_Rep3

value: WT (shRNA control)


title: WholeBlood-MDD-F-629


title: Combo+FTY720, replicate 3, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S5.5n.barcodes.tsv.gz
S5.5n.features.tsv.gz
S5.5n.matrix.mtx.gz


title: HCC_040

value: liver cancer tumor tissue


title: WholeBlood-MDD-F-625


title: shCTRL_LPS3_Rep2


title: Combo+FTY720, replicate 2, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S5.3n.barcodes.tsv.gz
S5.3n.features.tsv.gz
S5.3n.matrix.mtx.gz


title: shCTRL_LPS3_Rep1


title: HCC_039


title: Combo+FTY720, replicate 2, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S5.3n.barcodes.tsv.gz
S5.3n.features.tsv.gz
S5.3n.matrix.mtx.gz


title: WholeBlood-MDD-F-620


title: WholeBlood-MDD-F-636


title: shMOF_LPS0_Rep2

value: unstimulated


title: Combo+FTY720, replicate 1, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S5.2n.barcodes.tsv.gz
S5.2n.features.tsv.gz
S5.2n.matrix.mtx.gz


title: HCC_037


title: WholeBlood-MDD-F-618


title: WholeBlood-MDD-F-615


title: HCC_036


title: Combo+FTY720, replicate 1, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S5.2n.barcodes.tsv.gz
S5.2n.features.tsv.gz
S5.2n.matrix.mtx.gz


title: shMOF_LPS0_Rep1


title: Combo, replicate 4, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S4.6n.barcodes.tsv.gz
S4.6n.features.tsv.gz
S4.6n.matrix.mtx.gz


title: WholeBlood-MDD-F-612


title: HCC_035


title: shCTRL_LPS0_Rep2


title: HCC_041


title: WholeBlood-MDD-F-611


title: HCC_034


title: WholeBlood-MDD-F-623


title: Combo, replicate 3, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S4.5n.barcodes.tsv.gz
S4.5n.features.tsv.gz
S4.5n.matrix.mtx.gz


title: WholeBlood-MDD-F-604


title: shMOF_LPS0_Rep3


title: Combo, replicate 3, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S4.5n.barcodes.tsv.gz
S4.5n.features.tsv.gz
S4.5n.matrix.mtx.gz


title: HCC_038


title: Zfp362-/-, snRNA-seq

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

institute: HCI - Helmholtz Centre for Infection Research

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using CellRanger software (cellranger-arc-2.0.1, 10x Genomics).
Assembly: mm10, refdata-cellranger-arc-mm10-2020-A-2.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: colon, small intestine

extract_protocol:
For the preparation of single-cell suspensions from colon, colons were opened longitudinally and washed with predigestion medium (phosphate-buffered saline, PBS, containing 0.2 % bovine serum albumin, BSA (Merck) and 5 mM EDTA (Sigma-Aldrich)) to remove feces. Subsequently, colons were incubated with predigestion medium at 37°C three times for 15 min. After washing with Hank's Balanced Salt Solution (HBSS with Mg2+ and Ca2+; Gibco), predigested colons were cut into 1-2 mm pieces and digested in HBSS containing 1 mg ml-1 Collagenase D (Roche), 100 μg ml-1 DNaseI (Roche), and 25 mM HEPES (Gibco) at 37°C for 1 h. Subsequently, cells were subjected to 30%/ 70% Percoll (GEHealthcare) gradient centrifugation (780 g, room temperature, 20 min, acceleration and brake off). Cells in the interphase layer were harvested, washed and resuspended in PBS containing 0.2 % BSA. For the preparation of single-cell suspensions from small intestine (SI), the mouse lamina propria dissociation kit (Miltenyi Biotec) using the gentleMACS™ Octo dissociator (Miltenyi Biotec) with heaters was applied according to the manufacturer’s protocol. Cells from colon and small intestine were stained with antibodies aginst Cd8a, CD11c, CD45R, F4/80, CD4, CD62L and CD44. Nuclei were prepared from pooled colon and SI CD8a-CD11c-CD45R-F4/80-CD4+CD44+CD62L- effector T cells isolated by Fluorescence-activated cell sorting (FACS) and subjected to a droplet-based library preparation technique (10x Genomics).
For droplet-based snRNA-seq, libraries were prepared using Single Cell Multiome ATAC + Gene Expression kit according to manufacturer’s instructions. (10x Genomics), targeting 5,000 nuclei per sample after counting with a Countess II Automated Cell Counter (Thermo Fisher). Seven cycles were applied to generate cDNA followed by 15 cycles for final library generation. Generated snRNA-seq libraries were sequenced on a NovaSeq 6000 (100 cycles, paired-end).
snRNA-seq

value: colon, small intestine

value: CD4+ effector T cells

tag: sort marker

value: 26-33 weeks old


title: WholeBlood-MDD-F-603

value: Whole blood

value: MDD


title: Combo, replicate 2, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S4.3n.barcodes.tsv.gz
S4.3n.features.tsv.gz
S4.3n.matrix.mtx.gz

value: Female

tag: cell line


title: shCTRL_LPS0_Rep3

tag: cell type


title: HCC_031

tag: treatment


title: Combo, replicate 2, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S4.3n.barcodes.tsv.gz
S4.3n.features.tsv.gz
S4.3n.matrix.mtx.gz

tag: tissue


title: WholeBlood-MDD-F-601


title: Zfp362+/+, snRNA-seq

description: 10X Genomics

tag: genotype


title: HCC_032


title: WholeBlood-MDD-F-511


title: Ercc_mic_12w_ko_3

city: Groningen

first: Takuya

last: Oshima

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences of Cells & Systems

country: Netherlands

institute: University Medical Center Groningen

data_processing:
Quality control was performed using third-party (FastQC v0.11.9) and in-house (FastQA v3.1.25) QC tools.
Sequence reads were trimmed to remove possible adapter sequences using cutadapt v2.10.
The trimmed reads were mapped to the mouse GRCm39 (Mus_musculus.GRCm39.dna.primary_assembly.fa) provided in the References directory. The reads were mapped to the reference sequence using a short read aligner based on Burrows-Wheeler Transform (Tophat v2-2.1) with default settings.
The alignment files were sorted and indexed with the samtools v1.10 package
After alignment duplicate reads were marked and removed with MarkDuplicates of the Picard v2.13.2 package.
Based on the mapped locations in the alignment file the frequency of how often a read was mapped on a transcript was determined with HTSeq v0.11.0.
Assembly: mouse GRCm39 (Mus_musculus.GRCm39.dna.primary_assembly.fa)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: brain

extract_protocol:
Microglia were isolated using a mechanical protocol at 4°C as previously described (Galatro et al., 2017). Microglia were sorted by gating the DAPIneg CD11bhigh CD45int Ly6cneg cells with FACS. Total RNA was isolated using RNeasy Micro Kit (Qiagen, cat# 74004) according to the manufacturer’s instructions.
Sequencing libraries were generated using the NEBNext Low Input RNA Library Prep Kit for Illumina (New England Biolabs, cat# E6420S/L).
DNA sequencing was performed using a NovaSeq6000 according to the manufacturer's protocols. NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

value: brain

value: female

tag: region

value: whole brain

value: microglia

value: ko

value: 12 week old

tag: strain background

value: C57Bl6J/FVB cross


title: Combo, replicate 1, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S4.2n.barcodes.tsv.gz
S4.2n.features.tsv.gz
S4.2n.matrix.mtx.gz

tag: strain

value: BALB/c

tag: Sex

value: 6-8 weeks

value: anti-PDL1 mIgG2a LALAPG (clone 6E11), 10 mg/kg iv x 1, 5 mg/kg ip x 2, plus anti-TIGIT mIgG2a (clone 10A7), 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week

value: Draining lymph node

value: CD90+CD44+ T cells


title: WholeBlood-MDD-F-516


title: Ercc_mic_12w_ko_4

value: male


title: HCC_029

tag: cell line origin

value: Human Hepatocarcinoma

value: liver cancer tumor tissue


title: HCC_030


title: Combo, replicate 4, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S4.6n.barcodes.tsv.gz
S4.6n.features.tsv.gz
S4.6n.matrix.mtx.gz


title: WholeBlood-MDD-F-510

value: Whole blood

value: MDD


title: Combo, replicate 1, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S4.2n.barcodes.tsv.gz
S4.2n.features.tsv.gz
S4.2n.matrix.mtx.gz

value: Female


title: shCTRL_LPS0_Rep1

value: bone-marrow derived macrophage isolated ex-vivo

value: WT (shRNA control)

value: unstimulated


title: HCC_028


title: HCC_033


title: HCC_027


title: WholeBlood-MDD-F-503


title: Anti-TIGIT, replicate 6, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S3.7n.barcodes.tsv.gz
S3.7n.features.tsv.gz
S3.7n.matrix.mtx.gz

value: anti-TIGIT mIgG2a (clone 10A7), 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week


title: Ercc_mic_12w_wt_8

value: brain

value: whole brain

value: microglia

value: wt

value: 12 week old


title: Anti-TIGIT, replicate 6, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.7n.barcodes.tsv.gz
S3.7n.features.tsv.gz
S3.7n.matrix.mtx.gz

value: BALB/c

value: 6-8 weeks

value: Draining lymph node


title: WholeBlood-MDD-F-408


title: HCC_026

value: Human Hepatocarcinoma


title: Ercc_mic_12w_wt_5_6

value: male

value: C57Bl6J/FVB cross


title: Anti-TIGIT, replicate 5, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S3.6n.barcodes.tsv.gz
S3.6n.features.tsv.gz
S3.6n.matrix.mtx.gz

value: CD90+CD44+ T cells


title: WholeBlood-MDD-F-404

value: Whole blood

value: MDD

value: Female


title: HCC_025

value: liver cancer tumor tissue


title: Anti-TIGIT, replicate 5, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.6n.barcodes.tsv.gz
S3.6n.features.tsv.gz
S3.6n.matrix.mtx.gz

value: anti-TIGIT mIgG2a (clone 10A7), 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week


title: WholeBlood-MDD-F-323


title: Ercc_mic_12w_wt_4

value: brain


title: WholeBlood-MDD-F-314


title: Ercc_mic_12w_wt_3

value: female

value: whole brain


title: HCC_023


title: Ercc_mic_6w_ko_4

value: microglia

value: ko

value: 6 week old


title: Anti-TIGIT, replicate 4, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S3.4n.barcodes.tsv.gz
S3.4n.features.tsv.gz
S3.4n.matrix.mtx.gz

value: BALB/c

value: 6-8 weeks


title: WholeBlood-MDD-F-309


title: Ercc_mic_12w_ko_2

value: 12 week old


title: HCC_022

value: Human Hepatocarcinoma


title: Ercc_mic_12w_ko_1

value: male

value: C57Bl6J/FVB cross


title: Anti-TIGIT, replicate 4, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.4n.barcodes.tsv.gz
S3.4n.features.tsv.gz
S3.4n.matrix.mtx.gz

value: Draining lymph node

value: CD90+CD44+ T cells


title: Ercc_mic_6w_ko_3


title: WholeBlood-MDD-F-307

value: Whole blood

value: MDD

value: Female


title: Anti-TIGIT, replicate 1, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S3.1n.barcodes.tsv.gz
S3.1n.features.tsv.gz
S3.1n.matrix.mtx.gz

value: anti-TIGIT mIgG2a (clone 10A7), 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week


title: WholeBlood-MDD-F-222


title: Ercc_mic_6w_ko_2

value: brain

value: female


title: HCC_020

value: liver cancer tumor tissue


title: Anti-TIGIT, replicate 1, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.1n.barcodes.tsv.gz
S3.1n.features.tsv.gz
S3.1n.matrix.mtx.gz


title: Ercc_mic_6w_ko_1

value: whole brain

value: microglia

value: ko


title: Anti-TIGIT, replicate 3, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S3.3n.barcodes.tsv.gz
S3.3n.features.tsv.gz
S3.3n.matrix.mtx.gz

value: BALB/c

value: 6-8 weeks


title: WholeBlood-MDD-F-218


title: WholeBlood-MDD-F-216


title: Ercc_mic_6w_wt_4

value: wt

value: 6 week old


title: HCC_018

value: Human Hepatocarcinoma


title: Ercc_mic_6w_wt_3

value: C57Bl6J/FVB cross


title: Anti-TIGIT, replicate 3, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.3n.barcodes.tsv.gz
S3.3n.features.tsv.gz
S3.3n.matrix.mtx.gz

value: Draining lymph node

value: CD90+CD44+ T cells


title: WholeBlood-MDD-F-211

value: Whole blood

value: MDD


title: Anti-TIGIT, replicate 2, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S3.2n.barcodes.tsv.gz
S3.2n.features.tsv.gz
S3.2n.matrix.mtx.gz

value: Female

value: anti-TIGIT mIgG2a (clone 10A7), 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week


title: HCC_024


title: HCC_017


title: WholeBlood-MDD-F-210


title: Ercc_mic_6w_wt_1

value: brain

value: male


title: Anti-TIGIT, replicate 2, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.2n.barcodes.tsv.gz
S3.2n.features.tsv.gz
S3.2n.matrix.mtx.gz


title: HCC_021

value: liver cancer tumor tissue


title: Anti-PDL1, replicate 5, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S2.6n.barcodes.tsv.gz
S2.6n.features.tsv.gz
S2.6n.matrix.mtx.gz

value: anti-PDL1 mIgG2a LALAPG (clone 6E11), 10 mg/kg iv x 1, 5 mg/kg ip x 2, over 1 week


title: HCC_015


title: HCC_016


title: WholeBlood-MDD-F-205


title: Ercc_mic_6w_wt_2

value: female

value: whole brain

value: microglia


title: Anti-PDL1, replicate 5, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.6n.barcodes.tsv.gz
S2.6n.features.tsv.gz
S2.6n.matrix.mtx.gz

value: BALB/c

value: 6-8 weeks


title: WholeBlood-Control-F-199

value: Control


title: Th17_MSCV_ADAR2_E396A rep2

city: San Diego

first: Wendy

last: Huang

address: 9500 Gilman Drive #0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

description: RNA-seq

data_processing:
Paired-end reads were aligned to the mouse mm10 genome with the STAR aligner version 2.6.1a using the parameters: "--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000".
Uniquely mapped reads overlapping with exons were counted using featureCounts for each gene in the GENCODE.vM21 annotation
Differential expression analysis was performed using DESeq2 (v1.18.1 package) , including a covariate in the design matrix to account for differences in harvest batch
Assembly: mm10
Supplementary files format and content: Txt files include normalized Deseq count for each gene per sample

source_name: Th17 72h cells

growth_protocol: All mice were raised in Specific Pathogen Free (SPF) facility on normal diet. 8-12 week old animals were used for experiments.

extract_protocol:
RNA were isolated using Qiagen Rneasy mini kit (74106)
Ribosome-depleted RNAs were used to generate the cDNA libraries using the KAPA Hyper Prep Kit (KR0961) according to the manufacturer's instructions. Briefly, DNA was end-repaired and A-tailed to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Post-ligation clean was used to remove the extra adapters. Then the adapter-ligated DNA was PCR amplified with Illumina primers for 8 cycles, followed with post-amplification clean with KAPA pure beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina NovaSeq S4 following the manufacturer's protocols.

treatment_protocol: Naïve CD4+ T cells  were activated and polarized toward Th17 in hamster IgG pre-coated plate with  0.25 μg/mL anti-CD3ε (eBioscience) and 1 μg/mL anti-CD28 (eBioscience), 0.1 ng/mL TGF-β (R&D Systems) and 20 ng/mL IL-6 (R&D Systems). 24hrs post activation, activated T cells were transduced with MSCV retroviruses and then polarized toward Th17 in the presence of 0.3 ng/mL TGF-β (R&D Systems) and 20 ng/mL IL-6 (R&D Systems) for another 48hrs.

value: Th17 72h cells


title: HCC_014

value: Human Hepatocarcinoma


title: Anti-PDL1, replicate 4, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S2.5n.barcodes.tsv.gz
S2.5n.features.tsv.gz
S2.5n.matrix.mtx.gz

value: Draining lymph node

value: CD90+CD44+ T cells


title: WholeBlood-Control-F-198

value: Whole blood


title: Th17_MSCV_ADAR2_WT rep2

description: RNA-seq


title: HCC_019


title: HCC_013


title: Th17_MSCV_empty control rep2

description: RNA-seq

value: MSCV_empty control


title: Anti-PDL1, replicate 4, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.5n.barcodes.tsv.gz
S2.5n.features.tsv.gz
S2.5n.matrix.mtx.gz

value: Female


title: WholeBlood-Control-F-196


title: HCC_012


title: Th17_MSCV_ADAR2_E396A rep1

description: RNA-seq


title: WholeBlood-Control-F-194


title: HCC_011


title: Anti-PDL1, replicate 3, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S2.4n.barcodes.tsv.gz
S2.4n.features.tsv.gz
S2.4n.matrix.mtx.gz


title: Th17_MSCV_ADAR2_WT rep1

description: RNA-seq


title: WholeBlood-Control-F-193


title: Anti-PDL1, replicate 3, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.4n.barcodes.tsv.gz
S2.4n.features.tsv.gz
S2.4n.matrix.mtx.gz


title: HCC_010


title: Th17_MSCV_empty control rep1

description: RNA-seq


title: Anti-PDL1, replicate 2, lymph node, ADT-seq and CITE-seq

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
S2.3n.barcodes.tsv.gz
S2.3n.features.tsv.gz
S2.3n.matrix.mtx.gz


title: HCC_009


title: Th17_PSIN_sgAdarb1 rep2

description: RNA-seq

data_processing:
Paired-end reads were aligned to the mouse mm10 genome with the STAR aligner version 2.6.1a using the parameters: "--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000".
Uniquely mapped reads overlapping with exons were counted using featureCounts for each gene in the GENCODE.vM21 annotation with parameters "-p -B --ignoreDup"
Differential expression analysis was performed using DESeq2 (v1.18.1 package) , including a covariate in the design matrix to account for differences in harvest batch
Assembly: mm10
Supplementary files format and content: Txt files include normalized Deseq count for each gene per sample

treatment_protocol: Naïve CD4+ T cells  were activated in hamster IgG pre-coated plate with  0.25 μg/mL anti-CD3ε (eBioscience) and 1 μg/mL anti-CD28 (eBioscience). 24hrs post activation, activated T cells were transduced with retroviruses and then polarized toward Th17 in the presence of 0.3 ng/mL TGF-β (R&D Systems) and 20 ng/mL IL-6 (R&D Systems) for 72hrs.

value: Cas9 transgene


title: Anti-PDL1, replicate 2, lymph node, scRNA-seq

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.3n.barcodes.tsv.gz
S2.3n.features.tsv.gz
S2.3n.matrix.mtx.gz


title: WholeBlood-Control-F-191