title: d28Tam_TCR

city: Memphis

first: Mitchell

last: Weiss

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children’s Research Hospital

description: 10X Genomics

data_processing:
Sequencing reads were mapped to the mouse genome (GRCm38) using Cell Ranger v7.0.0 (10x Genomics). GENCODE M23 was used for gene expression analysis and vdj-GRCm38- alts-ensembl-7.0.0 was used for TCR or V(D)J clonotype analysis.
Cells were filtered using the Seurat R package (v4.3.0) based on number of expressed genes (nFeature_RNA) between 200 to 6000 and mitochondrial DNA content (percent.mt) less than 10%.
Assembly: mm10
Supplementary files format and content: R data format
Library strategy: TCR-seq

molecule: other

source_name: Thymus

growth_protocol: All mouse studies were approved by the Institutional Animal Care and Use Committee (IACUC, approval number 612) at St. Jude Children’s Research Hospital and maintained under specific pathogen-free conditions.

extract_protocol:
Thymus from treated mcie were then harvested from treated mice and prepared for FACS sorting of DP and non-DP cells. Sorted cellswere then labled with a TotalSeq (oligonucleotide-conjugated) antibodies (Biolegend) panel for surface protein following the manufacturer’s manual.
A total of 1.4-1.65 x104 cells were loaded separately on the 10x Chromium platform. Gel beads-in-emulsion (GEM) generation, cDNA amplification, and library construction were performed following the protocol of Chromium Next GEM Single Cell 5′ Reagent Kits v2 (Dual Index, 10x Genomics) with target recovery of 8,000–10,000 cells per library or sample. A total of 13 cycles of PCR were then conducted using the Chromium Single Cell 5′ Library and Gel Bead Kit (10x Genomics) according to the manufacturer’s manuals, to amplify the cDNA library for sufficient RNA and TCR V(D)J libraries. Libraries were prepared following the manufacturer’s manual (10x Genomics), followed by quantification using Agilent Tapestation.

treatment_protocol: 10 μg/g body weight of Tamoxifen dissolved in olive oil was administered by intraperitoneal injection. Oil injection served as a control.  30 μg/g body weight of Cyclosporine A (CsA)  or oil was injected intraperitoneally into mice once daily until analysis.

value: Thymus

value: thymocytes


title: AB13861

status: Public on Jul 21 2026

type: SRA

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
Library name: Sample1555
MARS_v2

library_source: transcriptomic

data_processing:
bcl2fastq
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used (most samples) i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Samples467 up to Samples733 Pool-barcode used is 5N (random) + 4N (Pool barcode) On R1 1 humming error was allowed. Well-barcode N7 folowed by UMI N8 in read 2.
Samples 259, 295, 297, 299, 232 and 234 Utilized a 9 Nucleotide cell barcode and compose of 768 cells per sample.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: cells_annotation_for_geo_ver_20250306.xlsx

molecule: polyA RNA

organism: Homo sapiens

source_name: BM

extract_protocol:
BM aspirates were collected from the posterior iliac crest into EDTA-coated tubes (BD Biosciences), diluted 1:1 with ice-cold FACS buffer (PBS supplemented with 2 mM EDTA, pH 8.0, and 0.5% bovine serum albumin), and maintained on ice. Samples were immediately transported to the laboratory for downstream processing and single-cell analysis.
mRNA from cells sorted into barcoded cell capture plates and converted into cDNA, later pooled by using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription, and the resulting RNA is fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina adapters during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration was assessed as described earlier. Overall, barcoding was done in three levels: Cell barcodes allow attribution of each sequence read to its cell of origin, thus enabling pooling; Unique Molecular Identifiers (UMIs) allow tagging each original molecule to avoid amplification bias; and plate barcodes allow elimination of the batch effect.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

tag: tissue

value: BM

tag: gate

value: PC

tag: batch


title: 5dCsA_TCR

department: Department of Hematology

country: USA

description: 10X Genomics

library_source: other

organism: Mus musculus

tag: cell line

tag: genotype


title: AB13859

description:
Library name: Sample1553
MARS_v2


title: 2dCsA_TCR

description: 10X Genomics


title: 1dCsA_TCR

description: 10X Genomics


title: AB13860

description:
Library name: Sample1554
MARS_v2


title: AB13858

description:
Library name: Sample1552
MARS_v2


title: AB14180

description:
Library name: Sample1607
MARS_v2


title: Thymus-12d_TCR

description: 10X Genomics


title: 118 On-Tx Bond 2JJ5_1 | 002 | Full ROI

city: Chapel hill

first: Brent

last: Hanks

state: North Carolina

address: 450 West Dr

department: Medicine

institute: UNC at Chapel Hill

description:
Library name: GE_118On-TxBond2JJ5.1.002
Formalin-fixed paraffin-embedded spatial transcriptome sequencing

data_processing:
A pan-cytokeratin IF marker was used to identify epithelial tumor tissue while CD8 and elastase IF markers were used to assess tumor-infiltrating CD8+ T cell and PMN/neutrophil cell populations
Human Whole Transcriptome Atlas probe was hybridized overnight, slides were washed twice in fresh 2X saline-sodium citrate (SSC, Sigma-Aldrich, S6639-1L) and loaded onto the GeoMx DSP.
UV light was used to cleave oligos that were then collected in a 96-well plate for library preparation and were sequenced on an Illumina NextSeq2000 by the UNC High-Throughput Sequencing Facility (HTSF)
All transcriptional data was analyzed using GeoMx DSP Data Analysis software
dimensionality reduction (PCA) and normalization techniques (Q3 normalization) were used to identify potential outliers
Assembly: GRCh38
Supplementary files format and content: Quantitative counts of genes or proteins  ( .dcc files)
Supplementary files format and content: GE_counts.csv
Supplementary files format and content: Hs_R_NGS_CTA_v1.0.pkc
Library strategy: Spatial Transcriptomics

molecule: total RNA

source_name: Gastric tumor tissue

extract_protocol:
library preparation and were sequenced on an Illumina NextSeq2000
FFPE tissue samples were prepared

value: Gastric tumor tissue

tag: cd8+ count

value: Low

tag: neutrophil count

value: High

tag: clinical response

value: PD

tag: treatment

value: on-Treatment


title: IgG(Mock)_TCR

description: 10X Genomics


title: AB13857

description:
Library name: Sample1551
MARS_v2


title: AB13856

description:
Library name: Sample1550
MARS_v2


title: AB13853

description:
Library name: Sample1547
MARS_v2


title: AB13855

description:
Library name: Sample1549
MARS_v2


title: Thymus-12h_TCR

description: 10X Genomics


title: Thymus-5d_TCR

description: 10X Genomics


title: Thymus-2d_TCR

description: 10X Genomics


title: AB13852

description:
Library name: Sample1546
MARS_v2


title: AB13851

description:
Library name: Sample1545
MARS_v2


title: 2dCsA

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing reads were mapped to the mouse genome (GRCm38) using Cell Ranger v7.0.0 (10x Genomics). GENCODE M23 was used for gene expression analysis and vdj-GRCm38- alts-ensembl-7.0.0 was used for TCR or V(D)J clonotype analysis.
Cells were filtered using the Seurat R package (v4.3.0) based on number of expressed genes (nFeature_RNA) between 200 to 6000 and mitochondrial DNA content (percent.mt) less than 10%.
Assembly: mm10
Supplementary files format and content: R data format


title: AB13848

description:
Library name: Sample1542
MARS_v2


title: AB13850

description:
Library name: Sample1544
MARS_v2


title: AB13849

description:
Library name: Sample1543
MARS_v2


title: IgG(Mock)

description: 10X Genomics


title: AB13847

description:
Library name: Sample1541
MARS_v2


title: Thymus-12d

description: 10X Genomics


title: AB13846

description:
Library name: Sample1540
MARS_v2


title: Thymus-5d

description: 10X Genomics


title: AB13845

description:
Library name: Sample1539
MARS_v2


title: Thymus-12h

description: 10X Genomics


title: AB13842

description:
Library name: Sample1536
MARS_v2


title: AB13843

description:
Library name: Sample1537
MARS_v2


title: AB13844

description:
Library name: Sample1538
MARS_v2


title: Thymus-Oil

description: 10X Genomics


title: liver, normoxia, 4 h, rep3

city: heze

first: guosong

last: zhang

state: shandong

address: No. 1, University Road, Heze City

country: China

institute: Heze University

description: Library name: B3

data_processing:
Raw miRNA sequencing reads were processed by the in-house program ACGT101-miR (v4.2) to remove adapter dimers, junk sequences, low-complexity sequences, and common non-coding RNA sequences (rRNA, tRNA, snRNA, snoRNA) and repeat sequences.
Unique sequences with a length of 18~26 nucleotides were screened, and BLAST search was performed against miRBase 22.1 species precursor database to identify known miRNAs and novel 3p/5p-derived miRNAs, allowing 3’/5’ end length variation and one internal sequence mismatch.
Unmapped unique sequences were aligned with Pelteobagrus vachellii reference genome, and RNAfold software was used to predict hairpin secondary structures of flank 80nt sequences to screen novel miRNA candidates based on standardized secondary structure prediction criteria.
miRNA expression levels were normalized based on deep-sequencing counts, and Student’s t-test was used to screen differentially expressed miRNAs (DEMIs) with the significance threshold set as P < 0.05.
Integrated analysis of differentially expressed miRNAs and liver tissue differentially expressed mRNAs was performed, miRNA target genes were predicted, and miRNA-mRNA negative regulatory network with opposite expression patterns was constructed, followed by KEGG pathway enrichment analysis (P < 0.05).
Assembly: Pelteobagrus vachellii reference genome (GCF_030014155.1) from NCBI datasets
Supplementary files format and content: Processed data (liver miRNA).xlsx: Normalized expression counts of known and novel miRNAs in Norm-EVs and Hypo-EVs samples

organism: Tachysurus vachellii

source_name: liver

growth_protocol: Healthy Pelteobagrus vachellii with uniform specifications (body length 11.5 ± 1.5 cm, body weight 15 ± 0.94 g) were purchased from Sichuan Rongsen Fishery Co., Ltd. All experimental fish were acclimated for two weeks under conventional breeding conditions and fasted for 48 h before hypoxic stress treatment to eliminate the influence of food metabolism on experimental results.

extract_protocol:
Total small RNA was extracted and purified from 6 groups of Norm-EVs and Hypo-EVs samples using the Norgen 58000 kit (Norgen biotech, CA). The RNA concentration was quantified by Qubit (Invitrogen, USA), and RNA integrity was assessed via Agilent 5400 (Agilent, USA) to ensure qualified RNA samples for library construction and sequencing.
1. RNA and 3’ adapter were denatured at 70°C for 2 min, then ligated overnight at 16°C using T4 RNA Ligase 2 (NEB, M0351L, USA), followed by purification. 2. Single-stranded DNA 3’ adapters were neutralized and removed by RTP reagent incubation at 37°C for 30 min. 3. RNA 5’ adapter was ligated with the product using T4 RNA Ligase 1 (NEB, M0204L, USA) at 37°C for 1 h, then purified. 4. Reverse transcription was performed with SuperScript™ II Reverse Transcriptase (Thermo, 18064014, USA) at 50°C for 1 h, followed by 80°C for 10 min termination. 5. Second-strand synthesis and PCR amplification were carried out using Phusion® High-Fidelity DNA Polymerase (NEB, M0530L, USA) with specific indexes. 6. The miRNA library was purified and enriched via PAGE electrophoresis, and finally sequenced on NovaSeq X Plus platform with PE150 strategy, and reads were truncated to single-end 50 bp for subsequent analysis.

treatment_protocol: The dissolved oxygen (DO) of aquaculture water was reduced from 6.8 mg/L to 1.0±0.1 mg/L by sealing the water body and bubbling pure nitrogen to establish a stable hypoxic stress environment. Experimental fish were subjected to continuous hypoxic treatment, and hepatic tissues were collected at different hypoxia and reoxygenation time points. Hepatic tissue-derived extracellular vesicles (EVs) were isolated from normoxic (Norm-EVs) and hypoxic-treated (Hypo-EVs) fish liver tissues for subsequent small RNA sequencing.

value: liver

value: normoxia, 4 h


title: AB13841

description:
Library name: Sample1535
MARS_v2


title: AB13839

description:
Library name: Sample1533
MARS_v2


title: AB13838

description:
Library name: Sample1532
MARS_v2


title: AB13837

description:
Library name: Sample1531
MARS_v2


title: liver, hypoxia, 4 h, rep2

description: Library name: A2

value: hypoxia, 4 h


title: liver, hypoxia, 4 h, rep1

description: Library name: A1


title: AB13836

description:
Library name: Sample1530
MARS_v2


title: AB13835

description:
Library name: Sample1529
MARS_v2


title: AB13833

description:
Library name: Sample1527
MARS_v2


title: Hydra vulgaris (AEP), siAb1, rep3

city: Innsbruck

first: Birgit

last: Lengerer

address: Technikerstr. 25

country: Austria

institute: University of Innsbruck

description: Library name: siAb1_rep3

data_processing:
Sequencing reads were aligned to the Hydra vulgaris AEP (PMID: 36639202) reference genome using the Minimap2 aligner (version 2.28).
The BAM files were aligned using the Hydra AEP Genome Project Portal assembly provided by the NHGRI Hydra portal (https://research.nhgri.nih.gov/HydraAEP/). This corresponds directly to the NCBI assembly accession GCA_024232925.2.
Read counting and differential gene expression analysis was performed with the Rsubread (version 2.22.1) and edgeR (version 4.6.3) packages in R (version 4.5.0).
Assembly: Hydra vulgaris AEP (PMID: 36639202); GCA_024232925.2
Supplementary files format and content: counts.txt: tab delimited count matrix file with gene identifier in first column.
Supplementary files format and content: The sequence identifiers present in our processed data (e.g., HVAEP1.G000001) are the official gene model identifiers derived from the GFF3 annotation provided by the NHGRI group for the Hydra AEP Genome Project. These identifiers are fully traceable and searchable in a public database. They can be queried directly via the official NHGRI Hydra AEP Gene Wiki search engine at:
Supplementary files format and content: https://research.nhgri.nih.gov/HydraAEP/genewiki/

organism: Hydra vulgaris

source_name: Whole animal

growth_protocol: Hydra vulgaris (AEP) grown asexually at 18°C in Hydra medium and fed with Artemia nauplii.

extract_protocol:
RNA was isolated with Monarch® Total Miniprep Kit (New England BioLabs) according to manufacturers protocoll
Library preparation, sequencing and gene expression analysis were performed at the company XPseq Analytics GmbH (Austria) using their ExpressoSeq rapid 3' RNA-Seq service

treatment_protocol: Budless Hydra vulgaris (AEP) were electroporated with a square pulse of 250 V and 25 ms in a Gene Pulser X cellTM (Biorad). Immediately after electroporation precooled recovery medium was added and the polyps were gently transferred to a Petri dish prefilled with cooled recovery medium. After 24 hours the polyps were transferred from recovery medium to Hydra medium. Electroporation was performed on 0, 2, and 4 days past electroporation (dpe).  Animals were fed four times (7, 8, 9 and 14 dpe). Basal discs were amputated at 10dpe and animals allowed to regenerate. RNA was isolated at 15dpe.

value: Whole animal

value: AEP

value: siRNA against Ab1


title: Hydra vulgaris (AEP), siAb1, rep1

description: Library name: siAb1_rep1


title: AB13832

description:
Library name: Sample1526
MARS_v2


title: Hydra vulgaris (AEP), siLb1, rep1

description: Library name: siLb1_rep1

value: siRNA against Lb1


title: AB13831

description:
Library name: Sample1525
MARS_v2


title: AB13830

description:
Library name: Sample1524
MARS_v2


title: Hydra vulgaris (AEP), siGFP, rep3

description: Library name: siGFP_rep3

value: siRNA against GFP


title: Plasma, Major Bleeding, no Stroke, id404

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

institute: TAmiRNA GmbH

data_processing:
fastQC quality assessment
cutadapt adater trimming
bowtie1 genome alignment
miRDeep2 miRNA quantification (mirbase)
bowtie1 RNAcentral mapping
gtRNAdb based tRNA quantification
Assembly: GRCh38.p12
Assembly: RNAcentral version: v19.0
Assembly: mirBase version: v22.1
Supplementary files format and content: csv with tRNA quantifications (raw count)
Supplementary files format and content: csv with miRNA quantifications (raw count)

source_name: Plasma

extract_protocol:
Total RNA was isolated using the miRNeasy kit (Qiagen)
Small RNA libraries were prepared using the RealSeq Somagenics kit

value: Plasma

tag: major bleeding

value: MajorBleeding

tag: stroke


title: Hydra vulgaris (AEP), siGFP, rep1

description: Library name: siGFP_rep1


title: Plasma, Bleeding Control, no Stroke, id405

value: Control


title: Hydra vulgaris (AEP), siGFP, rep2

description: Library name: siGFP_rep2


title: Plasma, Bleeding Control, no Stroke, id391


title: CAMR-ZLD_Spatial

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

description:
Library name: sample2
processed Visium HD spatial transcriptomics output archive

data_processing:
For the single-cell RNA-seq library, raw FASTQ files were aligned to the human GRCh38 reference genome (reference version 6.1.2), and gene expression matrices were quantified with Cell Ranger v4.3.0 using default parameters.
For the Visium HD spatial transcriptomic library, spatial gene expression data were processed with the 10x Genomics Visium HD/Space Ranger workflow using the human GRCh38 reference. Raw spatial counts were read from filtered_feature_bc_matrix.h5, and tissue coordinates were obtained from tissue_positions.parquet.
The Visium HD dataset was analyzed at 8-um binned resolution. A Seurat object was created for quality control; spatial bins were retained if nFeature_Spatial > 50, nCount_Spatial > 50 and mitochondrial transcript fraction < 20%, and genes with zero counts across retained bins were removed.
Spatial cell-type mapping was performed with spacexr/RCTD using the matched single-cell reference. Reference and SpatialRNA objects were constructed from single-cell counts, cell-type labels, spatial counts, spatial coordinates and UMI counts, and RCTD was run in doublet mode.
Spatial ligand-receptor and neighborhood analyses were performed on the processed Visium HD data using spatial coordinates, RCTD-derived annotations and human ligand-receptor resources to evaluate fibroblast-immune interactions and perivascular immune organization.
Assembly: Homo sapiens GRCh38 (10x Genomics Cell Ranger/Visium HD spatial reference)
Supplementary files format and content: CAMR-ZLD_scRNA.tar.gz contains processed single-cell RNA-seq Cell Ranger outputs, including 10x Genomics gene expression matrix files with barcode and feature/gene annotation files and associated Cell Ranger summary or metadata files where available.
Supplementary files format and content: CAMR-ZLD_Spatial.tar.gz contains processed 10x Genomics Visium HD spatial transcriptomic outputs, including spatial gene expression count matrices such as filtered_feature_bc_matrix.h5, tissue coordinate files such as tissue_positions.parquet, spatial metadata and analysis-ready 8-um binned data files where available.
Library strategy: Spatial Transcriptomics

source_name: Renal biopsy tissue

extract_protocol:
For the matched single-cell RNA-seq sample, fresh kidney graft tissue was processed immediately after collection to generate a single-cell suspension. Tissue was minced on ice, enzymatically dissociated according to the 10x Genomics tissue dissociation workflow, mechanically triturated, filtered through 70-um and 40-um strainers, centrifuged and resuspended in PBS containing 0.04% BSA. Cell viability was assessed by trypan blue exclusion. For the matched 10x Genomics Visium HD spatial transcriptomic sample, kidney biopsy tissue was processed for spatial gene expression profiling according to the manufacturer's Visium HD workflow.
For single-cell RNA-seq, the single-cell suspension was loaded onto 10x Genomics Chromium microfluidic chips using 3' v3 chemistry, and cDNA synthesis and gene expression library construction were performed with the Chromium Single Cell 3' v3 reagent kit according to the manufacturer's protocol. For Visium HD spatial transcriptomics, tissue sectioning, spatial barcoding, reverse transcription, indexing and gene expression library construction were performed according to the 10x Genomics Visium HD Spatial Gene Expression workflow. Libraries were sequenced on an Illumina NovaSeq X Plus platform using paired-end sequencing.

value: Renal biopsy tissue

tag: Sex

value: M

tag: age（years）

tag: donor type

value: Living donor

tag: post-transplant time_(years)

tag: maintenance immunosuppressive_regimen

value: Tacrolimus + mycophenolate mofetil + corticosteroids

tag: subject status

value: CAMR

tag: cohort

value: Validation

tag: clinical sample_id

value: CAMR-ZLD


title: Plasma, Major Bleeding, no Stroke, id365

tag: tissue


title: CAMR-ZLD_scRNA

description:
Library name: sample1
processed Cell Ranger single-cell gene expression output archive

data_processing:
For the single-cell RNA-seq library, raw FASTQ files were aligned to the human GRCh38 reference genome (reference version 6.1.2), and gene expression matrices were quantified with Cell Ranger v4.3.0 using default parameters.
For the Visium HD spatial transcriptomic library, spatial gene expression data were processed with the 10x Genomics Visium HD/Space Ranger workflow using the human GRCh38 reference. Raw spatial counts were read from filtered_feature_bc_matrix.h5, and tissue coordinates were obtained from tissue_positions.parquet.
The Visium HD dataset was analyzed at 8-um binned resolution. A Seurat object was created for quality control; spatial bins were retained if nFeature_Spatial > 50, nCount_Spatial > 50 and mitochondrial transcript fraction < 20%, and genes with zero counts across retained bins were removed.
Spatial cell-type mapping was performed with spacexr/RCTD using the matched single-cell reference. Reference and SpatialRNA objects were constructed from single-cell counts, cell-type labels, spatial counts, spatial coordinates and UMI counts, and RCTD was run in doublet mode.
Spatial ligand-receptor and neighborhood analyses were performed on the processed Visium HD data using spatial coordinates, RCTD-derived annotations and human ligand-receptor resources to evaluate fibroblast-immune interactions and perivascular immune organization.
Assembly: Homo sapiens GRCh38 (10x Genomics Cell Ranger/Visium HD spatial reference)
Supplementary files format and content: CAMR-ZLD_scRNA.tar.gz contains processed single-cell RNA-seq Cell Ranger outputs, including 10x Genomics gene expression matrix files with barcode and feature/gene annotation files and associated Cell Ranger summary or metadata files where available.
Supplementary files format and content: CAMR-ZLD_Spatial.tar.gz contains processed 10x Genomics Visium HD spatial transcriptomic outputs, including spatial gene expression count matrices such as filtered_feature_bc_matrix.h5, tissue coordinate files such as tissue_positions.parquet, spatial metadata and analysis-ready 8-um binned data files where available.


title: Plasma, no Bleeding, Stroke, id363

value: Stroke


title: Plasma, no Bleeding, Stroke Control, id357


title: Patient 063,PostNeo, PBMC, RNAseq

city: Los Angeles

first: Lu

last: Sun

state: California

address: 10833 Le Conte Avenue

institute: University of California, LA

description:
Library name: P063-PostNeo
RNA-seq of patients' PBMCs

data_processing:
Paired-end, 2 × 100 base pair (bp) transcriptome reads were mapped to the Genome Reference Consortium Human Build 38 (GRCh38) reference genome using HISAT2 (version 2.0.6)
The gene level counts were generated by the HTSeq-count program (version 0.5.4p5)
We utilized the edgeR (version 3.40.2) R package's cpm() function to compute the normalized gene expression values from the raw gene expression counts. These normalized expression values were log2 transformed after adding a pseudo count of 1.
Assembly: GRCh38
Supplementary files format and content: Gene level raw counts of each sample as computed by htseq-count (tab delimited)

source_name: PBMC

extract_protocol:
RNA and genomic DNA were extracted from resected tumor specimens preserved in AllProtect tissue reagent (Qiagen) at the time of surgery. We divided the tumor tissue in half and employed the Qiagen RNeasy Mini Kit (#74104) for RNA isolation and the Qiagen DNeasy Blood and Tissue Kit (#69504) for DNA isolation. Total RNA from PBMCs was extracted using the Qiagen RNeasy Mini Kit.
TruSeq RNA exome kit is used to construct the RNA sequencing libraries

value: PBMC

value: nivolumab+ipilimumab trial

tag: arm

value: Female

tag: ethnicity

value: Non-Hispanic

tag: age

tag: os


title: Plasma, no Bleeding, Stroke, id271


title: Plasma, no Bleeding, Stroke Control, id252


title: Plasma, Bleeding Control, no Stroke, id228


title: Patient 063,Baseline, PBMC, RNAseq

description:
Library name: P063-Baseline
RNA-seq of patients' PBMCs


title: Patient 062,PostNeo, PBMC, RNAseq

description:
Library name: P062-PostNeo
RNA-seq of patients' PBMCs

value: Male


title: Patient 062,C3D1, PBMC, RNAseq

description:
Library name: P062-C3D1
RNA-seq of patients' PBMCs


title: Plasma, Major Bleeding, no Stroke, id219


title: Plasma, Major Bleeding, no Stroke, id200


title: Plasma, Bleeding Control, no Stroke, id198


title: Patient 062,Baseline, PBMC, RNAseq

description:
Library name: P062-Baseline
RNA-seq of patients' PBMCs


title: Plasma, Bleeding Control, Stroke Control, id180


title: Patient 061,PostNeo, PBMC, RNAseq

description:
Library name: P061-PostNeo
RNA-seq of patients' PBMCs


title: Patient 061,Baseline, PBMC, RNAseq

description:
Library name: P061-Baseline
RNA-seq of patients' PBMCs


title: Plasma, Bleeding Control, Stroke Control, id147


title: Plasma, Major Bleeding, no Stroke, id142


title: Patient 059,PostOp, PBMC, RNAseq

description:
Library name: P059-PostOp
RNA-seq of patients' PBMCs


title: Patient 059,Baseline, PBMC, RNAseq

description:
Library name: P059-Baseline
RNA-seq of patients' PBMCs


title: Plasma, no Bleeding, Stroke, id120


title: Patient 058,C2D1, PBMC, RNAseq

description:
Library name: P058-C2D1
RNA-seq of patients' PBMCs


title: Plasma, no Bleeding, Stroke, id80


title: Patient 057,PostNeo, PBMC, RNAseq

description:
Library name: P057-PostNeo
RNA-seq of patients' PBMCs


title: Plasma, Bleeding Control, no Stroke, id52


title: Patient 059,PostNeo, PBMC, RNAseq

description:
Library name: P059-PostNeo
RNA-seq of patients' PBMCs


title: Patient 057,C3D1, PBMC, RNAseq

description:
Library name: P057-C3D1
RNA-seq of patients' PBMCs


title: Plasma, Major Bleeding, no Stroke, id132


title: Plasma, Major Bleeding, no Stroke, id50


title: Patient 057,C2D1, PBMC, RNAseq

description:
Library name: P057-C2D1
RNA-seq of patients' PBMCs


title: acRIP-seq IP of ac4C mRNA in K562 cell line [WT_IP_2]

city: Beijing

first: Yanran

last: Wang

address: No.5, Dongdan Sanjiao, Dongcheng District, Beijing

department: State Key Laboratory of Medical Molecular Biology

institute: Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

data_processing:
library strategy: acRIP-seq
RNA-seq: Adapter were clipped by Cutadapt and low quality reads were trimmed by Trimmomatic. Sequences were filtered for removing mitochondrial, ribosomal RNA and tRNA sequences. Clean reads were mapped to the Homo sapiens genome by STAR. Uniquely mapped reads were retained for further analysis filtered by SAMtools. Reads were counted using featureCounts. Transcript per million (TPM) was calculated using R scripts. DESeq2 was used for differential gene expression analysis.
Assembly: GENCODE Release 36, GRCh38.p13
Supplementary files format and content: raw counts
Supplementary files format and content: bigWig, narrowPeak
Ribo-seq: Adapter were clipped by Cutadapt and low quality reads were trimmed by Trimmomatic.Sequences were filtered for removing mitochondrial, ribosomal RNA and tRNA sequences. Clean reads were mapped to the Homo sapiens genome by STAR. Uniquely mapped reads were retained for further analysis filtered by SAMtools. Reads were counted using featureCounts. Transcript per million (TPM) was calculated using R scripts. DESeq2 was used for differential gene translation efficiency analysis. The TE (Translation Efficiency) value were calculated by taking the ratio of TPM in Ribo-seq over TPM in RNA-seq with R scripts.
acRIP-seq: Sequences were filtered for removing mitochondrial, ribosomal RNA and tRNA sequences. Clean reads were aligned to the Homo sapiens transcripts using bowtie2. ac4C peaks were detected by MACS2, and filtered by log10P < -3. Input samples were used as controls for peak calling. Screening of differential peaks using BEDTools map. ac4C sites that resided in protein coding genes were analyzed for downstream analysis. ChIPseeker was used for annotating the peaks.

growth_protocol: RNA-seq: k562 cells were grown in RPMI-1640 media supplemented with 10% FBS at 37°C in the presence of 5% CO2.

extract_protocol:
RNA-seq: Total RNA was extracted from NAT10 knockout and parental k562 cells using Trizol reagent(Invitrogen).
RNA-seq: RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit following manufacture's protocols.
Ribo-seq: Prepare the suspended cells to a density of 2 x 10^6 cells/mL in 10cm dishes.Incubate cells in growth media with cycloheximide at a final concentration of 100ug/ml for 15 minutes at 37°C with 5 % CO2, harvest, and wash twice with ice-cold PBS containing 100ug/ml cycloheximide.Discard supernatant and resuspend cells in 500 μl MCB lysis buffer(1 M MgCl2,100 % glycerol,1 M HEPES,20 % Triton X-100) combine with 1 M DTT, EDTA free RNase Inhibitor, EDTA free 50×cocktail,10mg/ml cycloheximide and vortex for 5 seconds followed by lysed on ice for 15mins, centrifuge lysates at 15000 rpm for 10 min at 4℃ and transfer supernatant to a new tube, prepare the 20％——50％ sucrose gradients. Remove 500 μl of sucrose gradients from the top and add the same volume of lysates onto each sucrose gradient. Centrifuge at 38000 rpm for 3 hours at 4°C in a Beckman Coulter Optima L-100XP with a SW41 Ti rotor. To collect different gradient ribosome fractions at 0.5ml/fraction, carefully remove tubes from the rotor and place them in the fraction collector. Add 750 μl of Trizol LS(Invitrogen) to each fraction and proceed with the RNA extraction as directed.
Ribo-seq: 12 PCR cycles were used for indexing of libraries and the finial PCR products were purified with RNA Clean & Concentrator-5 kit (Zymo research).
acRIP-seq: Total RNA was rRNA depleted with the NEBNext® rRNA Depletion Kit v2 (Promega) and then subjected to immunoprecipitation. Briefly, RNA was randomly fragmented to ~100 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the ac4C antibody or Normal Rabbit IgG antibody by rotating at room temperature for 2 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. The RNA/antibody complexes are then digested with Proteinase K and the eluted RNA is purified by phenol:chloroform extraction.
acRIP-seq: RNA libraries for IP,IgG and input samples were then constructed with NEBNext® Ultra™ RNA Library Prep Kit by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a Novaseq 6000 platform (Illumina).

tag: cell line

tag: genotype

value: wild type


title: Patient 057,Baseline, PBMC, RNAseq

description:
Library name: P057-Baseline
RNA-seq of patients' PBMCs

tag: treatment


title: acRIP-seq IP of ac4C mRNA in K562 cell line [WT_IP_1]


title: Patient 058,Baseline, PBMC, RNAseq

description:
Library name: P058-Baseline
RNA-seq of patients' PBMCs


title: Patient 056,PostNeo, PBMC, RNAseq

description:
Library name: P056-PostNeo
RNA-seq of patients' PBMCs


title: Plasma, no Bleeding, Stroke Control, id65

value: Plasma

tag: major bleeding

tag: stroke


title: Thymus-Oil_TCR

description: 10X Genomics

value: Thymus

value: thymocytes


title: AB13854

description:
Library name: Sample1548
MARS_v2

value: BM

tag: gate

value: PC

tag: batch


title: d28Tam

description: 10X Genomics


title: acRIP-seq IgG in K562 cell line [WT_IgG_2]

description: acRIP-seq IgG in K562 cell line


title: Patient 056,C3D1, PBMC, RNAseq

description:
Library name: P056-C3D1
RNA-seq of patients' PBMCs

tag: Sex


title: acRIP-seq IgG in K562 cell line [WT_IgG_1]

description: acRIP-seq IgG in K562 cell line


title: 5dCsA

description: 10X Genomics


title: 1dCsA

description: 10X Genomics


title: Patient 056,C2D1, PBMC, RNAseq

description:
Library name: P056-C2D1
RNA-seq of patients' PBMCs


title: acRIP-seq input in K562 cell line [WT_input_2]

description: acRIP-seq input in K562 cell line


title: Thymus-2d

description: 10X Genomics


title: Patient 056,Baseline, PBMC, RNAseq

description:
Library name: P056-Baseline
RNA-seq of patients' PBMCs


title: acRIP-seq input in K562 cell line [WT_input_1]

description: acRIP-seq input in K562 cell line


title: Patient 054,PostNeo, PBMC, RNAseq

description:
Library name: P054-PostNeo
RNA-seq of patients' PBMCs


title: 240min_ABA(+/-) exp2 rep2

city: CHAMPENOUX

first: David

last: Cohen

address: rue d'Amance

department: UMR1434 SILVA

country: France

institute: INRAE

data_processing:
Quality filtering and trimming of paired-end reads were performed using the erne-filter command (Erne v2.1.1, default parameters except --min-size=70; Del Fabbro et al., 2013).
Reads mapping was performed with TopHat2 v2.12 (Trapnell et al., 2009; Kim et al., 2013) on Populus trichocarpa genome sequence v4.1 (Phytozome v13, Goodstein et al. 2012, Tuskan et al. 2006) with the following parameters : -r 83 , --mate-std-dev 21, -g 10, --read-mismatch 15, --read-edit-dist 30, and --read-gap-length 15, and --read-realign-edit-dist 10. A reference annotation-based transcript assembly was constructed on solely mapped reads (RABT; Roberts et al., 2011). Assemblies were performed using Cufflinks v2.2.1 (Trapnell et al., 2010). A merged.gtf file was created from the 48 transcripts.gtf output files using Cuffmerge.
Raw read counts were summarized using the ‘featureCounts’ command (Subread package v1.6.1, Liao et al., 2014) with the following parameters : -O –s2 -p -P -d20 -D55000. The merged.gtf file was supplied as map of genomic features.
read counts normalization, differential expression and significance statistics were computed with Deseq2 package v1.24.0 (Love et al., 2014)
Genome_build: The Populus trichocarpa genome sequence v4.1 (Phytozome v13, Goodstein et al. 2012, Tuskan et al. 2006) was used for read alignment
Supplementary_files_format_and_content: "Normalized_gene_counts_matrix.txt" is tab-delimited text file that includes read counts normalized with DESeq2 package

organism: Populus nigra

source_name: 2cm-long root apices

growth_protocol: Woody cuttings of Populus nigra (genotype 6J29) were surface sterilized with peroxide, and were set for one week in hydroponic opaque tanks containing 18L of nutrient solution (NS : Hoagland solution supplemented with 0.8mM KH2PO4 and adjusted to pH 5.8). To prevent light exposure of roots, the culture system was covered and placed in a dark room (mean air temperature: 23.7°C ± 0.9°C). The solution was bubbled to prevent hypoxia and buds were removed to prevent leaf appearance.

extract_protocol:
2cm-long root apices were collected for all time points and immediately fixed in RNAlater (Sigma-Aldrich, St Quentin Fallavier, France). Total RNA was extracted from a pool of eight root apices collected at the same time-point using a Spectrum Plant Total RNA kit (Sigma-Aldrich, St Quentin Fallavier, France) complemented by a DNAse I treatment. RNA quality was assessed using a Fragment Analyzer 5200 (Agilent Technologies, Santa Clara, CA, USA). mRNA was purified using poly-(T) beads from 4 µg of each total RNA sample.
RNA libraries were prepared at the Genotoul sequencing core facility (Toulouse, France) with TruSeq Stranded mRNA Sample Prep kit (Illumina, California, USA) according to manufacturer instructions

treatment_protocol: After one week, rooted cuttings were randomly assigned to a treatment time-point by carefully transferring 12 rooted cuttings into fresh NS supplemented or not with 2 µM ABA (Sigma-Aldrich, St Quentin Fallavier, France). Abscisic acid-free NS was supplemented with 238 µL 150 mM ethanol to take into account that 2 µM ABA-enriched NS (ABA+) contains the same amount of ethanol. Treatments consisted in ABA-free NS (“CTL”), a time- series of 2 µM ABA treatments (“ABA+” for 2, 5, 15, 30, 60, 180, 480 or 960 min) and in a reverse reciprocal time series in which roots were submitted to ABA+ for 180 min prior being transferred into ABA- (“ABA+/ABA-free NS“ for 60, 180, 240 or 960 min)

value: 2cm-long root apices

value: treated with 2uM ABA for 180min prior being transferred into ABA-free NS for 240min


title: 240min_ABA(+/-) exp2 rep1


title: Patient 054,C2D1, PBMC, RNAseq

description:
Library name: P054-C2D1
RNA-seq of patients' PBMCs


title: AB13840

description:
Library name: Sample1534
MARS_v2


title: liver, normoxia, 4 h, rep2

description: Library name: B2

value: liver

value: normoxia, 4 h


title: 180min_ABA(+/-) exp2 rep2

value: treated with 2uM ABA for 180min prior being transferred into ABA-free NS for 180min


title: Patient 053,PostNeo, PBMC, RNAseq

description:
Library name: P053-PostNeo
RNA-seq of patients' PBMCs


title: Patient 053,C3D1, PBMC, RNAseq

description:
Library name: P053-C3D1
RNA-seq of patients' PBMCs


title: 180min_ABA(+/-) exp2 rep1


title: liver, hypoxia, 4 h, rep3

description: Library name: A3

value: hypoxia, 4 h


title: 480min_ABA(+) exp2 rep3

value: treated with 2uM ABA for 480min


title: 480min_ABA(+) exp2 rep2


title: 480min_ABA(+) exp2 rep1


title: Patient 052,Baseline, PBMC, RNAseq

description:
Library name: P052-Baseline
RNA-seq of patients' PBMCs

value: PBMC

value: nivolumab+ipilimumab trial


title: Patient 052,C2D1, PBMC, RNAseq

description:
Library name: P052-C2D1
RNA-seq of patients' PBMCs

value: Female

value: Non-Hispanic


title: 180min_ABA(+) exp2 rep2

value: treated with 2uM ABA for 180min


title: 180min_ABA(+) exp2 rep3


title: Patient 051,PostNeo, PBMC, RNAseq

description:
Library name: P051-PostNeo
RNA-seq of patients' PBMCs

value: Male


title: Patient 051,Baseline, PBMC, RNAseq

description:
Library name: P051-Baseline
RNA-seq of patients' PBMCs


title: 180min_ABA(+) exp2 rep1


title: Control exp2 rep4

value: untreated


title: Control exp2 rep3


title: Patient 050,C3D1, PBMC, RNAseq

description:
Library name: P050-C3D1
RNA-seq of patients' PBMCs


title: Patient 050,C2D1, PBMC, RNAseq

description:
Library name: P050-C2D1
RNA-seq of patients' PBMCs


title: Control exp2 rep2


title: Patient 050,Baseline, PBMC, RNAseq

description:
Library name: P050-Baseline
RNA-seq of patients' PBMCs


title: Patient 049,PostNeo, PBMC, RNAseq

description:
Library name: P049-PostNeo
RNA-seq of patients' PBMCs


title: Control exp2 rep1


title: 960min_ABA(+/-) exp1 rep1

value: treated with 2uM ABA for 180min prior being transferred into ABA-free NS for 960min


title: 960min_ABA(+/-) exp1 rep2


title: Patient 049,C3D1, PBMC, RNAseq

description:
Library name: P049-C3D1
RNA-seq of patients' PBMCs


title: Patient 049,C2D1, PBMC, RNAseq

description:
Library name: P049-C2D1
RNA-seq of patients' PBMCs


title: 180min_ABA(+/-) exp1 rep2

value: treated with 2uM ABA for 180min prior being transferred into ABA-free NS for 60min


title: Patient 049,Baseline, PBMC, RNAseq

description:
Library name: P049-Baseline
RNA-seq of patients' PBMCs


title: 180min_ABA(+/-) exp1 rep1


title: Patient 048,PostNeo, PBMC, RNAseq

description:
Library name: P048-PostNeo
RNA-seq of patients' PBMCs


title: 960min_ABA(+) exp1 rep2

value: treated with 2uM ABA for 960min


title: 960min_ABA(+) exp1 rep1

value: 2cm-long root apices


title: Patient 048,C2D1, PBMC, RNAseq

description:
Library name: P048-C2D1
RNA-seq of patients' PBMCs


title: Patient 048,Baseline, PBMC, RNAseq

description:
Library name: P048-Baseline
RNA-seq of patients' PBMCs


title: Patient 048,C3D1, PBMC, RNAseq

description:
Library name: P048-C3D1
RNA-seq of patients' PBMCs


title: 180min_ABA(+) exp1 rep3


title: FGR_microglia_H3K9me3_replication_4

city: Shanghai

first: Zhu

last: wei

address: siping road 1239

institute: tongji university

description: Library name: FGR_H3K9me3_4

library_source: genomic

data_processing:
Adapter trimming was done using Trim Galore (v0.6.5)
reads were aligned to the mouse genome (mm10) using Bowtie2 (v2.4.5).
Duplicates were marked with SAMtools (v1.3.1)
callpeak were execute by MACS2 (v2.2.7.1)
Differentially enriched regions analysis was performed using Diffbind (v3.12.0). Annotation of peaks was performed by ChIPpeakAnno(v3.36.1)
Assembly: mm10
Supplementary files format and content: narrowpeaks, bigwig

molecule: genomic DNA

source_name: hippocampus microglia

extract_protocol:
DNA obtained by isopropanol precipitation method
library constructed fellow a protocol of KAPA HyperPrep Kits(Roche, KR0961)

value: hippocampus microglia


title: Patient 047,C3D1, PBMC, RNAseq

description:
Library name: P047-C3D1
RNA-seq of patients' PBMCs


title: 180min_ABA(+) exp1 rep2


title: FGR_microglia_H3K27ac_replication_4

description: Library name: FGR_H3K27ac_4


title: 180min_ABA(+) exp1 rep1


title: Patient 047,Baseline, PBMC, RNAseq

description:
Library name: P047-Baseline
RNA-seq of patients' PBMCs


title: Patient 047,C2D1, PBMC, RNAseq

description:
Library name: P047-C2D1
RNA-seq of patients' PBMCs


title: Patient 046,PostNeo, PBMC, RNAseq

description:
Library name: P046-PostNeo
RNA-seq of patients' PBMCs


title: FGR_microglia_H3K9ac_replication_4

description: Library name: FGR_H3K9ac_4


title: Patient 046,C3D1, PBMC, RNAseq

description:
Library name: P046-C3D1
RNA-seq of patients' PBMCs


title: 60min_ABA(+) exp1 rep4

value: treated with 2uM ABA for 60min


title: Patient 046,C2D1, PBMC, RNAseq

description:
Library name: P046-C2D1
RNA-seq of patients' PBMCs


title: Patient 045,PostNeo, PBMC, RNAseq

description:
Library name: P045-PostNeo
RNA-seq of patients' PBMCs

value: Hispanic or Latino


title: FGR_microglia_H3K4me3_replication_4

description: Library name: FGR_H3K4me3_4


title: Ctrl_microglia_H3K9me3_replication_4

description: Library name: Ctrl_H3K9me3_4


title: Patient 045,C3D1, PBMC, RNAseq

description:
Library name: P045-C3D1
RNA-seq of patients' PBMCs


title: Patient 046,Baseline, PBMC, RNAseq

description:
Library name: P046-Baseline
RNA-seq of patients' PBMCs


title: 60min_ABA(+) exp1 rep2


title: Patient 045,C2D1, PBMC, RNAseq

description:
Library name: P045-C2D1
RNA-seq of patients' PBMCs


title: Ctrl_microglia_H3K27ac_replication_4

description: Library name: Ctrl_H3K27ac_4


title: Patient 050,PostNeo, PBMC, RNAseq

description:
Library name: P050-PostNeo
RNA-seq of patients' PBMCs


title: 60min_ABA(+) exp1 rep1


title: Patient 044,C3D1, PBMC, RNAseq

description:
Library name: P044-C3D1
RNA-seq of patients' PBMCs


title: Patient 045,Baseline, PBMC, RNAseq

description:
Library name: P045-Baseline
RNA-seq of patients' PBMCs


title: 30min_ABA(+) exp1 rep4

value: treated with 2uM ABA for 30min


title: Patient 044,C2D1, PBMC, RNAseq

description:
Library name: P044-C2D1
RNA-seq of patients' PBMCs


title: Ctrl_microglia_H3K4me3_replication_4

description: Library name: Ctrl_H3K4me3_4


title: Patient 044,Baseline, PBMC, RNAseq

description:
Library name: P044-Baseline
RNA-seq of patients' PBMCs


title: ATAC-seq FGR hippocampal microglia p3w replication4

description: Library name: FGR_ATAC_4

data_processing:
Adapter trimming was done using Trim Galore (v0.6.5)
reads were aligned to the mouse genome (mm10) using Bowtie2 (v2.4.5).
Duplicates were marked with SAMtools (v1.3.1)
callpeak were execute by MACS2 (v2.2.7.1).
Differentially accessible regions analysis was performed using Diffbind (v3.12.0). Annotation of peaks was performed by ChIPpeakAnno(v3.36.1)
Assembly: mm10
Supplementary files format and content: narrowPeaks, BigWig

extract_protocol:
The interruption and extraction of DNA follow the protocol of Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711).
Library construction follow the protocol of Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711).


title: Patient 043,PostNeo, PBMC, RNAseq

description:
Library name: P043-PostNeo
RNA-seq of patients' PBMCs


title: Patient 043,Baseline, PBMC, RNAseq

description:
Library name: P043-Baseline
RNA-seq of patients' PBMCs


title: 30min_ABA(+) exp1 rep2


title: Patient 042,PostNeo, PBMC, RNAseq

description:
Library name: P042-PostNeo
RNA-seq of patients' PBMCs


title: ATAC-seq FGR hippocampal microglia p3w replication3

description: Library name: FGR_ATAC_3


title: Patient 042,C3D1, PBMC, RNAseq

description:
Library name: P042-C3D1
RNA-seq of patients' PBMCs


title: Patient 042,C2D1, PBMC, RNAseq

description:
Library name: P042-C2D1
RNA-seq of patients' PBMCs


title: 30min_ABA(+) exp1 rep1


title: Patient 042,Baseline, PBMC, RNAseq

description:
Library name: P042-Baseline
RNA-seq of patients' PBMCs


title: ATAC-seq Ctrl hippocampal microglia p3w replication4

description: Library name: Ctrl_ATAC_4


title: 15min_ABA(+) exp1 rep4

value: treated with 2uM ABA for 15min


title: Patient 041,PostNeo, PBMC, RNAseq

description:
Library name: P041-PostNeo
RNA-seq of patients' PBMCs


title: Patient 041,C3D1, PBMC, RNAseq

description:
Library name: P041-C3D1
RNA-seq of patients' PBMCs


title: ATAC-seq Ctrl hippocampal microglia p3w replication3

description: Library name: Ctrl_ATAC_3


title: 15min_ABA(+) exp1 rep3


title: 60min_ABA(+) exp1 rep3


title: Patient 041,C2D1, PBMC, RNAseq

description:
Library name: P041-C2D1
RNA-seq of patients' PBMCs


title: SPRITE cerebellum, P6, rep1+rep2, batch4

city: Evanston

first: Yue

last: Yang

state: IL

address: 2200 Campus Dr

department: Neurobiology

institute: Northwestern University

description: Library name: SPRITE_pnd22_1+2_4

data_processing:
The DPM sequence was identified from the beginning of read 1 and the odd, even, odd, and terminal odd sequences were identified from read 2 using the Guttman laboratory SPRITE pipeline (https://github.com/GuttmanLab/sprite-pipeline). After trimming the DPM sequence from read 1, the read was aligned to the mm10 reference genome. Mapped reads with MAPQ scores > 30 and a fully identified barcode sequence were kept. Identically mapped reads for a particular barcode sequence were considered PCR duplicates and filtered. After preprocessing, all mapped genomic coordinates with the same barcode sequence were grouped together as a SPRITE cluster. To generate pairwise contact maps, each pairwise interaction was downweighted by 2/n, where n is the total number of reads within a SPRITE cluster. Pairwise contacts < 1Kb were removed. Downweighted contacts were then normalized with KR matrix balancing using Juicer.
Assembly: mm10
Supplementary files format and content: hic files

source_name: cerebellum

extract_protocol:
Cerebella were microdissected and fixed in 1% formaldehyde in PBS. The cell lysis was treated with DNase, followed by sonication. The lysate was then treated with Proteinase K and de-crosslinked. The average DNA fragment size was about 200 bp, and 10 billion molecules of DNA-protein complexes (about 6000 cells) were coupled with 1.7 ml of NHS-Activated Magnetic Beads (Pierce) per experiment.
SPRITE libraries were generated after five rounds of split-pool barcoding reactions using DPM, odd, even, odd, and terminal odd barcodes.

value: cerebellum

tag: cell type

value: cerebellar cells

tag: strain


title: 15min_ABA(+) exp1 rep2


title: Patient 040,PostNeo, PBMC, RNAseq

description:
Library name: P040-PostNeo
RNA-seq of patients' PBMCs

value: PBMC

value: nivolumab+ipilimumab trial


title: Patient 044,PostNeo, PBMC, RNAseq

description:
Library name: P044-PostNeo
RNA-seq of patients' PBMCs

value: Non-Hispanic


title: SPRITE cerebellum, P6, rep1, batch3

description: Library name: SPRITE_pnd22_1_3


title: Patient 040,C3D1, PBMC, RNAseq

description:
Library name: P040-C3D1
RNA-seq of patients' PBMCs

value: Female


title: 15min_ABA(+) exp1 rep1


title: Ctrl_microglia_H3K9ac_replication_4

description: Library name: Ctrl_H3K9ac_4


title: Patient 040,C2D1, PBMC, RNAseq

description:
Library name: P040-C2D1
RNA-seq of patients' PBMCs


title: 30min_ABA(+) exp1 rep3


title: Patient 040,Baseline, PBMC, RNAseq

description:
Library name: P040-Baseline
RNA-seq of patients' PBMCs


title: SPRITE cerebellum, P6, rep1, batch2

description: Library name: SPRITE_pnd22_1_2


title: 5min_ABA(+) exp1 rep4

value: treated with 2uM ABA for 5min


title: Patient 039,PostNeo, PBMC, RNAseq

description:
Library name: P039-PostNeo
RNA-seq of patients' PBMCs

value: Male


title: Patient 039,C3D1, PBMC, RNAseq

description:
Library name: P039-C3D1
RNA-seq of patients' PBMCs


title: SPRITE cerebellum, P6, rep1, batch1

description: Library name: SPRITE_pnd22_1_1


title: 5min_ABA(+) exp1 rep3


title: Patient 041,Baseline, PBMC, RNAseq

description:
Library name: P041-Baseline
RNA-seq of patients' PBMCs


title: Patient 039,C2D1, PBMC, RNAseq

description:
Library name: P039-C2D1
RNA-seq of patients' PBMCs


title: Patient 039,Baseline, PBMC, RNAseq

description:
Library name: P039-Baseline
RNA-seq of patients' PBMCs


title: Patient 038,PostNeo, PBMC, RNAseq

description:
Library name: P038-PostNeo
RNA-seq of patients' PBMCs


title: NMuMG cells transfected with SMAD1-Mnase, added with TGFb1 and BMP4 for 30 min, biol rep 3

first: Inbal

last: Eizenberg

address: 234 Herzl Street

department: Molecular Genetics

description:
Library name: NMuMG-SMAD1-Mix-3
ChEC-seq in cell culture proteins were inserted using PiggyBack transposon system

data_processing:
Demultiplexing with bcl2fastq
filtering of adapters and adapter-dimers with cutadapt
Mapping of reads with bowtie "-p8 --very-sensitive --trim-to 40 --dovetail -k 1" to the mm10 genome
Indexing with samtools index
Peak calling with the macs3- "--format BAMPE -g mm --nomodel --nolambda --keep-dup all"
Bigwig Generation with deepTools normalizing by the CPM, and removing the Y/M chromosomes and also blacklisted regions
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: ChEC-seq

source_name: Mammary gland

growth_protocol: NMuMG cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1mM sodium pyruvate, 100 unit/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine and 1x MEM non-essential amino acids in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were treated with Proteinase K and DNA was extracted usign an equal volume of Phenol-Chloroform (ChEC-seq: phenol chloroform)
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

treatment_protocol:
Cells were transfected with Smad1-Mnase and selected on Hygromycin. Selected cells were plated at 80% confluency in a 6-well plate with DMEM + 10% FBS, 3 wells for each treatment. 16h after plating, the cells were added with the indicated ligands and cultured for an additional 1 hour. Cells were further handled according to the ChEC-Seq protocol, as described in Zentner et al. 2015.
Treatments: Control- no added ligands; BMP4@48ng/ml; Mix- BMP4@48ng/ml + TGFb1@5.63ng/ml

value: Mammary gland

value: NMuMG

value: Epithel

value: SMAD1-Mnase transfected

value: TGFb1+BMP4, permeabilization followed by 2min Ca2+ Mnase incubation


title: 5min_ABA(+) exp1 rep2

value: 2cm-long root apices


title: 5min_ABA(+) exp1 rep1


title: NMuMG cells transfected with SMAD1-Mnase, added with TGFb1 and BMP4 for 30 min, biol rep 2

description:
Library name: NMuMG-SMAD1-Mix-2
ChEC-seq in cell culture proteins were inserted using PiggyBack transposon system


title: NMuMG cells transfected with SMAD1-Mnase, added with TGFb1 and BMP4 for 30 min, biol rep 1

description:
Library name: NMuMG-SMAD1-Mix-1
ChEC-seq in cell culture proteins were inserted using PiggyBack transposon system


title: Patient 038,C3D1, PBMC, RNAseq

description:
Library name: P038-C3D1
RNA-seq of patients' PBMCs


title: Patient 038,Baseline, PBMC, RNAseq

description:
Library name: P038-Baseline
RNA-seq of patients' PBMCs


title: Patient 038,C2D1, PBMC, RNAseq

description:
Library name: P038-C2D1
RNA-seq of patients' PBMCs


title: 2min_ABA(+) exp1 rep4

value: treated with 2uM ABA for 2min


title: NMuMG cells transfected with SMAD1-Mnase, added with BMP4 for 30 min, biol rep 3

description:
Library name: NMuMG-SMAD1-BMP4-3
ChEC-seq in cell culture proteins were inserted using PiggyBack transposon system

value: BMP4, permeabilization followed by 2min Ca2+ Mnase incubation


title: Patient 037,C3D1, PBMC, RNAseq

description:
Library name: P037-C3D1
RNA-seq of patients' PBMCs


title: Patient 037,PostNeo, PBMC, RNAseq

description:
Library name: P037-PostNeo
RNA-seq of patients' PBMCs


title: 2min_ABA(+) exp1 rep3


title: Patient 037,C2D1, PBMC, RNAseq

description:
Library name: P037-C2D1
RNA-seq of patients' PBMCs


title: NMuMG cells transfected with SMAD1-Mnase, added with BMP4 for 30 min, biol rep 2

description:
Library name: NMuMG-SMAD1-BMP4-2
ChEC-seq in cell culture proteins were inserted using PiggyBack transposon system


title: Patient 037,Baseline, PBMC, RNAseq

description:
Library name: P037-Baseline
RNA-seq of patients' PBMCs


title: 2min_ABA(+) exp1 rep2


title: Patient 053,C2D1, PBMC, RNAseq

description:
Library name: P053-C2D1
RNA-seq of patients' PBMCs


title: Patient 036,PostNeo, PBMC, RNAseq

description:
Library name: P036-PostNeo
RNA-seq of patients' PBMCs


title: NMuMG cells transfected with SMAD1-Mnase, added with BMP4 for 30 min, biol rep 1

description:
Library name: NMuMG-SMAD1-BMP4-1
ChEC-seq in cell culture proteins were inserted using PiggyBack transposon system


title: Patient 036,Baseline, PBMC, RNAseq

description:
Library name: P036-Baseline
RNA-seq of patients' PBMCs


title: 2min_ABA(+) exp1 rep1


title: Patient 035,PostNeo, PBMC, RNAseq

description:
Library name: P035-PostNeo
RNA-seq of patients' PBMCs


title: Patient 053,Baseline, PBMC, RNAseq

description:
Library name: P053-Baseline
RNA-seq of patients' PBMCs


title: NMuMG cells transfected with SMAD1-Mnase, control- no ligands added, biol rep 3

description:
Library name: NMuMG-SMAD1-Ctrl-3
ChEC-seq in cell culture proteins were inserted using PiggyBack transposon system

value: No ligand treatment, permeabilization followed by 2min Ca2+ Mnase incubation


title: Patient 035,C3D1, PBMC, RNAseq

description:
Library name: P035-C3D1
RNA-seq of patients' PBMCs


title: Control exp1 rep4

value: untreated


title: Patient 035,Baseline, PBMC, RNAseq

description:
Library name: P035-Baseline
RNA-seq of patients' PBMCs


title: NMuMG cells transfected with SMAD1-Mnase, control- no ligands added, biol rep 2

description:
Library name: NMuMG-SMAD1-Ctrl-2
ChEC-seq in cell culture proteins were inserted using PiggyBack transposon system


title: Control exp1 rep3


title: Patient 033,Baseline, PBMC, RNAseq

description:
Library name: P033-Baseline
RNA-seq of patients' PBMCs


title: Patient 033,PostNeo, PBMC, RNAseq

description:
Library name: P033-PostNeo
RNA-seq of patients' PBMCs


title: NMuMG cells transfected with SMAD1-Mnase, control- no ligands added, biol rep 1

description:
Library name: NMuMG-SMAD1-Ctrl-1
ChEC-seq in cell culture proteins were inserted using PiggyBack transposon system


title: Patient 032,C3D1, PBMC, RNAseq

description:
Library name: P032-C3D1
RNA-seq of patients' PBMCs


title: Control exp1 rep2


title: Patient 032,C2D1, PBMC, RNAseq

description:
Library name: P032-C2D1
RNA-seq of patients' PBMCs


title: Patient 032,Baseline, PBMC, RNAseq

description:
Library name: P032-Baseline
RNA-seq of patients' PBMCs


title: Control exp1 rep1


title: Patient 031,PostNeo, PBMC, RNAseq

description:
Library name: P031-PostNeo
RNA-seq of patients' PBMCs


title: SPRITE cerebellum, P6, rep1+rep2, batch5

description: Library name: SPRITE_pnd22_1+2_5

value: cerebellum

value: cerebellar cells


title: Patient 031,C3D1, PBMC, RNAseq

description:
Library name: P031-C3D1
RNA-seq of patients' PBMCs

value: PBMC

value: nivolumab+ipilimumab trial


title: AB11356

description: Library name: Sample6

data_processing:
RNA sequencing data were processed starting with the Cell Ranger software (10x Genomics) to perform quality control, read alignment to the human reference genome (GRCh38), and quantification of gene expression levels. Unique Molecular Identifiers (UMIs) were used to count individual mRNA molecules, ensuring accurate expression levels.
The resultant data were then normalized to account for variations in sequencing depth and cell count discrepancies. Differential expression analysis was conducted using the Seurat package in R, which included scaling, principal component analysis, and clustering to identify cell populations and marker genes.
Assembly: refdata-cellranger-GRCh38-1.2.0
Supplementary files format and content: SPID_metadata_annotated.txt

source_name: CSF

extract_protocol:
Human CSF samples were obtained from 14 patients diagnosed with MS, and from 2 CSF inflammatory and 2 peripheral inflammatory donors at Rabin Medical Center hospital, Israel. CSF samples were collected via lumbar puncture by trained medical personnel and were processed within 2-4 hours from collection. CSF samples were diluted with sterile PBS and centrifuged at 350 x g for 5 minutes at 4°C to pellet cells. The supernatant was washed, counted, and used immediately for FACS staining. Sorting gate was immune cells CD45+.
Next Gem single-cell 3′ with Feature Barcode technology for Cell Surface Protein v3.1.

value: CSF

tag: diagnosis

value: Active PPMS

tag: patient

tag: category

value: MS


title: Patient 031,C2D1, PBMC, RNAseq

description:
Library name: P031-C2D1
RNA-seq of patients' PBMCs

tag: tissue

tag: arm

value: Male

value: Non-Hispanic


title: BLAJ dysferlin-deficient gastrocnemius muscle, 3 months, biological replicate 3

city: Moscow

first: Nikita

middle: Sergeevich

last: Gladyshev

address: Tsyurupy 3

country: Russia

institute: Petrovsky National Research Centre of Surgery

description:
Library name: Mutant_3_B172_3_month_S30
Frozen gastrocnemius muscle from a 3-month-old male homozygous B6.A-Dysfprmd/GeneJ mouse B172; independent biological replicate. Column name in counts_matrix_raw.tsv.gz: Mutant_3_B172_3_month_S30.

data_processing:
Raw sequencing reads were assessed using FastQC version 0.12.1, and quality-control reports were aggregated using MultiQC version 1.28. Adapter contamination and substantial deterioration of read quality were not detected; therefore, read trimming was not performed.
Paired-end reads were aligned to the Mus musculus GRCm39 reference genome using STAR version 2.7.11b. The STAR genome index was generated from GRCm39.primary_assembly.fa and the Mus_musculus.GRCm39.109.gtf annotation from Ensembl release 109 using --sjdbOverhang 100.
Gene-level read counts were generated using STAR --quantMode GeneCounts. Column 2 of each ReadsPerGene.out.tab file was used as the non-stranded gene-count output. Individual gene-count tables were combined into a genes-by-samples raw count matrix.
Differential expression analysis was performed in R version 4.5.2 using DESeq2 version 1.50.2. Genes with fewer than 10 total reads across all samples were excluded. The design formula was ~ condition, comparing B6.A-Dysfprmd/GeneJ mice with C57BL/6 controls. Wald tests were used, and P values were adjusted using the Benjamini-Hochberg method.
The complete raw gene-count matrix and differential expression results were exported as tab-delimited files. Sample-specific STAR gene-count files and the MultiQC report were retained as supplementary processed data.
Assembly: GRCm39; Ensembl release 109; Mus_musculus.GRCm39.109.gtf
Supplementary files format and content: The gzip-compressed ReadsPerGene.out.tab files contain sample-specific STAR gene-level counts. Column 2 contains the non-stranded read counts used for downstream analysis. counts_matrix_raw.tsv.gz is a gzip-compressed tab-delimited genes-by-samples matrix containing raw gene-level counts for all six libraries.
Supplementary files format and content: deseq2_results.tsv.gz is a gzip-compressed tab-delimited table containing differential expression statistics for B6.A-Dysfprmd/GeneJ mice compared with C57BL/6 controls. multiqc_report.html contains the aggregated quality-control report generated using MultiQC.

source_name: gastrocnemius muscle

growth_protocol: Male and female B6.A-Dysfprmd/GeneJ mice homozygous for the Dysfprmd mutation and C57BL/6 control mice were studied at 3 months of age. The transcriptomic cohort consisted of three animals per group, with each animal serving as an independent biological replicate. Animals were euthanized by isoflurane overdose followed by cervical dislocation.

extract_protocol:
Total RNA was isolated from frozen gastrocnemius muscle using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. RNA concentration and purity were assessed using a NanoPhotometer, and RNA integrity was evaluated using an Agilent 2100 Bioanalyzer. A total of 800 ng RNA with an RNA integrity number of at least 7.0 was used for library preparation.
Poly(A)-positive RNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module. Directional sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina according to the manufacturer's instructions. Library quality and fragment size were assessed using an Agilent 2100 Bioanalyzer. Libraries were sequenced on an Illumina NovaSeq 6000 in paired-end mode with a read length of 2 x 61 bp, yielding approximately 43.0-53.8 million reads per sample.

treatment_protocol: No experimental treatment was administered. Experimental groups were defined by mouse strain and Dysf genotype.

value: gastrocnemius muscle

value: Dysfprmd/Dysfprmd

value: no treatment

tag: isolate

tag: age

value: 3 months

tag: developmental stage

value: adult

value: male

tag: disease

value: dysferlinopathy

tag: phenotype

value: dysferlin-deficient muscular dystrophy phenotype


title: Patient 030,PostNeo, PBMC, RNAseq

description:
Library name: P030-PostNeo
RNA-seq of patients' PBMCs

tag: treatment

tag: ethnicity

tag: os


title: Patient 030,Baseline, PBMC, RNAseq

description:
Library name: P030-Baseline
RNA-seq of patients' PBMCs


title: AB11355

description: Library name: Sample5

tag: batch


title: Patient 029,PostNeo, PBMC, RNAseq

description:
Library name: P029-PostNeo
RNA-seq of patients' PBMCs

tag: Sex


title: BLAJ dysferlin-deficient gastrocnemius muscle, 3 months, biological replicate 2

description:
Library name: Mutant_2_D461_3_month_S29
Frozen gastrocnemius muscle from a 3-month-old female homozygous B6.A-Dysfprmd/GeneJ mouse D461; independent biological replicate. Column name in counts_matrix_raw.tsv.gz: Mutant_2_D461_3_month_S29.

tag: genotype

value: female


title: 960min_ABA(+) exp1 rep3

value: 2cm-long root apices

value: treated with 2uM ABA for 960min


title: Patient 029,C3D1, PBMC, RNAseq

description:
Library name: P029-C3D1
RNA-seq of patients' PBMCs

value: PBMC

value: nivolumab+ipilimumab trial


title: AB11354

description: Library name: Sample4

value: CSF

value: Active PPMS


title: Patient 029,C2D1, PBMC, RNAseq

description:
Library name: P029-C2D1
RNA-seq of patients' PBMCs

value: Male


title: BLAJ dysferlin-deficient gastrocnemius muscle, 3 months, biological replicate 1

description:
Library name: Mutant_1_D467_3_month_S28
Frozen gastrocnemius muscle from a 3-month-old female homozygous B6.A-Dysfprmd/GeneJ mouse D467; independent biological replicate. Column name in counts_matrix_raw.tsv.gz: Mutant_1_D467_3_month_S28.

tag: strain


title: AB11353

description: Library name: Sample3

tag: diagnosis

value: MS


title: Patient 047,PostNeo, PBMC, RNAseq

description:
Library name: P047-PostNeo
RNA-seq of patients' PBMCs

value: Female

value: Non-Hispanic


title: SPRITE cerebellum, P6, rep1+rep2, batch6

description: Library name: SPRITE_pnd22_1+2_6

value: cerebellum

tag: cell type

value: cerebellar cells


title: Patient 029,Baseline, PBMC, RNAseq

description:
Library name: P029-Baseline
RNA-seq of patients' PBMCs


title: C57BL/6 control gastrocnemius muscle, 3 months, biological replicate 3

description:
Library name: Contrl_3_black_2_3_month_S27
Frozen gastrocnemius muscle from a 3-month-old male C57BL/6 control mouse black_2; independent biological replicate. Column name in counts_matrix_raw.tsv.gz: Contrl_3_black_2_3_month_S27.

value: gastrocnemius muscle

value: wild type

value: no treatment

value: 3 months

value: adult

value: not applicable

value: wild-type phenotype


title: Patient 028,PostNeo, PBMC, RNAseq

description:
Library name: P028-PostNeo
RNA-seq of patients' PBMCs

value: PBMC


title: AB10362

description: Library name: Sample2

tag: patient

tag: category


title: Patient 028,C2D1, PBMC, RNAseq

description:
Library name: P028-C2D1
RNA-seq of patients' PBMCs

tag: tissue

value: nivolumab+ipilimumab trial

tag: arm


title: C57BL/6 control gastrocnemius muscle, 3 months, biological replicate 2

description:
Library name: Contrl_2_black_1_3_month_S26
Frozen gastrocnemius muscle from a 3-month-old male C57BL/6 control mouse black_1; independent biological replicate. Column name in counts_matrix_raw.tsv.gz: Contrl_2_black_1_3_month_S26.

tag: isolate

tag: age

value: male


title: Patient 027,PostNeo, PBMC, RNAseq

description:
Library name: P027-PostNeo
RNA-seq of patients' PBMCs


title: AB10361

description: Library name: Sample1

value: CSF

value: Active PPMS


title: Patient 027,C2D1, PBMC, RNAseq

description:
Library name: P027-C2D1
RNA-seq of patients' PBMCs


title: C57BL/6 control gastrocnemius muscle, 3 months, biological replicate 1

description:
Library name: Contrl_1_x235_3_month_S25
Frozen gastrocnemius muscle from a 3-month-old male C57BL/6 control mouse x235; independent biological replicate. Column name in counts_matrix_raw.tsv.gz: Contrl_1_x235_3_month_S25.

tag: developmental stage

tag: disease


title: Patient 027,Baseline, PBMC, RNAseq

description:
Library name: P027-Baseline
RNA-seq of patients' PBMCs

tag: treatment


title: Patient 026,PostNeo, PBMC, RNAseq

description:
Library name: P026-PostNeo
RNA-seq of patients' PBMCs

value: Male

tag: ethnicity


title: AB18840

description:
Library name: Sample1909
MARS_v2

data_processing:
bcl2fastq
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used (most samples) i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Samples467 up to Samples733 Pool-barcode used is 5N (random) + 4N (Pool barcode) On R1 1 humming error was allowed. Well-barcode N7 folowed by UMI N8 in read 2.
Samples 259, 295, 297, 299, 232 and 234 Utilized a 9 Nucleotide cell barcode and compose of 768 cells per sample.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: cells_annotation_for_geo_ver_20250306.xlsx

value: BM

tag: gate

value: PC


title: DRG culture, ISR.cKO, siCONTROL, t=42h, rep4

city: San Francisco

first: Trent

middle: A.

last: Watkins

state: CA

address: 675 Nelson Rising Lane, Rm 214A

institute: University of California at San Francisco

description: Library name: ISR-cKO_siCTL_4

data_processing:
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: A single comma-separated value (.csv) file contains counts for all samples.

source_name: primary adult dorsal root ganglia cell culture

growth_protocol: Dissociated cells cultured in Neurobasal-A medium with B27 supplement.

extract_protocol:
RNA was extracted using the Qiagen RNeasy micro kit (#74004).
RNA libraries were prepared according to Novogene procedures by polyA capture (or rRNA removal) and reverse transcription of cDNA.

treatment_protocol: Dharnafect 2-mediated transfection of Dharnacon ON-TARGETplus siRNA pools.

value: siCONTROL


title: Patient 026,C3D1, PBMC, RNAseq

description:
Library name: P026-C3D1
RNA-seq of patients' PBMCs

value: Non-Hispanic

tag: os


title: AB18839

description:
Library name: Sample1908
MARS_v2

tag: batch


title: Patient 026,C2D1, PBMC, RNAseq

description:
Library name: P026-C2D1
RNA-seq of patients' PBMCs

tag: Sex


title: DRG culture, ISR.cKO, siCONTROL, t=42h, rep3

description: Library name: ISR-cKO_siCTL_3

value: primary adult dorsal root ganglia cell culture

tag: genotype


title: Patient 026,Baseline, PBMC, RNAseq

description:
Library name: P026-Baseline
RNA-seq of patients' PBMCs


title: AB18838

description:
Library name: Sample1907
MARS_v2


title: Patient 024,PostNeo, PBMC, RNAseq

description:
Library name: P024-PostNeo
RNA-seq of patients' PBMCs


title: DRG culture, ISR.cKO, siCONTROL, t=42h, rep2

description: Library name: ISR-cKO_siCTL_2


title: Patient 024,Baseline, PBMC, RNAseq

description:
Library name: P024-Baseline
RNA-seq of patients' PBMCs


title: AB18837

description:
Library name: Sample1906
MARS_v2


title: DRG culture, ISR.cKO, siCONTROL, t=42h, rep1

description: Library name: ISR-cKO_siCTL_1


title: Patient 023,PostNeo, PBMC, RNAseq

description:
Library name: P023-PostNeo
RNA-seq of patients' PBMCs

value: Female


title: Patient 023,C3D1, PBMC, RNAseq

description:
Library name: P023-C3D1
RNA-seq of patients' PBMCs


title: AB18836

description:
Library name: Sample1905
MARS_v2


title: Patient 023,Baseline, PBMC, RNAseq

description:
Library name: P023-Baseline
RNA-seq of patients' PBMCs


title: Patient 022,Baseline, PBMC, RNAseq

description:
Library name: P022-Baseline
RNA-seq of patients' PBMCs


title: AB18835

description:
Library name: Sample1904
MARS_v2


title: DRG culture, Atf4.cKO, siCebpg, t=42h, rep4

description: Library name: Atf4-cKO_siCebpg_4

value: Atf4-fl/fl; Avil-wt/Cre

value: siCebpg


title: DRG culture, Atf4.cKO, siCebpg, t=42h, rep3

description: Library name: Atf4-cKO_siCebpg_3


title: Patient 021,PostNeo, PBMC, RNAseq

description:
Library name: P021-PostNeo
RNA-seq of patients' PBMCs

value: Hispanic or Latino


title: Patient 021,C3D1, PBMC, RNAseq

description:
Library name: P021-C3D1
RNA-seq of patients' PBMCs


title: AB18834

description:
Library name: Sample1903
MARS_v2


title: AB17975

description:
Library name: Sample1902
MARS_v2


title: Patient 021,Baseline, PBMC, RNAseq

description:
Library name: P021-Baseline
RNA-seq of patients' PBMCs


title: Patient 020,PostNeo, PBMC, RNAseq

description:
Library name: P020-PostNeo
RNA-seq of patients' PBMCs


title: DRG culture, Atf4.cKO, siCebpg, t=42h, rep1

description: Library name: Atf4-cKO_siCebpg_1


title: AB17974

description:
Library name: Sample1901
MARS_v2


title: DRG culture, Atf4.cKO, siCONTROL, t=42h, rep4

description: Library name: Atf4-cKO_siCTL_4


title: Patient 020,C3D1, PBMC, RNAseq

description:
Library name: P020-C3D1
RNA-seq of patients' PBMCs


title: MLN_CCR8+_4

city: Wuhan

first: Hao

last: Panax

address: 1277# Jie-Fang Avenue

institute: Huazhong University of Science and Technology

description:
Library name: SAMPLE16
Ln_p4

data_processing:
After library preparation, 125 bp/150 bp paired-end reads were produced using the Illumina NovaSeq 6000 platform for sequencing.
To obtain clean reads for RNA-sequencing data analysis, raw data in the FASTQ format were first processed internally using a script. Low-quality reads containing adapters or poly-N were eliminated. Following the acquisition of clean reads, the GC, Q20, and Q30 contents were computed.
The analyses were all predicated on clean and high-quality data. The reference genome index was created by aligning the reads to the mm10 mouse gene annotation from the UCSC Transcript database using Hisat2 v2.0.5.
The number of reads mapped to each gene was counted using FeatureCounts v1.5.0-p3.
The number of fragments per kilobase of transcript per million mapped fragments was calculated based on the length and read count of each gene.
Assembly: Mus musculus GRCm38 reference genome
Supplementary files format and content: tab-delimited text files include count values for each sample

source_name: mediastinal lymph nodes

growth_protocol: Cells FACS sorted from murine tissue. Kept in FACS flow buffer on ice prior to RNA isolation.

extract_protocol:
total RNA
To build libraries and add index codes, NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was utilized. The library fragments were purified using AMPure XP technology (Beckman Coulter, Beverly, MA, USA) to select 250–300 bp cDNA fragments.

treatment_protocol: For bulk RNA-sequencing analyses, approximately 100 CCR8+ Tregs and CCR8- Tregs were double-sorted by magnetic-activated cell sorting and FACS as mentioned above into special cell lysates

value: mediastinal lymph nodes

value: Tregs


title: AB17973

description:
Library name: Sample1900
MARS_v2

extract_protocol:
BM aspirates were collected from the posterior iliac crest into EDTA-coated tubes (BD Biosciences), diluted 1:1 with ice-cold FACS buffer (PBS supplemented with 2 mM EDTA, pH 8.0, and 0.5% bovine serum albumin), and maintained on ice. Samples were immediately transported to the laboratory for downstream processing and single-cell analysis.
mRNA from cells sorted into barcoded cell capture plates and converted into cDNA, later pooled by using an automated pipeline. The pooled sample is then linearly amplified by T7 in vitro transcription, and the resulting RNA is fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina adapters during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration was assessed as described earlier. Overall, barcoding was done in three levels: Cell barcodes allow attribution of each sequence read to its cell of origin, thus enabling pooling; Unique Molecular Identifiers (UMIs) allow tagging each original molecule to avoid amplification bias; and plate barcodes allow elimination of the batch effect.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)


title: Patient 020,Baseline, PBMC, RNAseq

description:
Library name: P020-Baseline
RNA-seq of patients' PBMCs

value: PBMC


title: MLN_CCR8+_3

description:
Library name: SAMPLE15
Ln_p3


title: AB17972

description:
Library name: Sample1899
MARS_v2


title: DRG culture, Atf4.cKO, siCONTROL, t=42h, rep2

description: Library name: Atf4-cKO_siCTL_2


title: MLN_CCR8+_2

description:
Library name: SAMPLE14
Ln_p2


title: AB17971

description:
Library name: Sample1898
MARS_v2


title: Patient 019,C3D1, PBMC, RNAseq

description:
Library name: P019-C3D1
RNA-seq of patients' PBMCs

value: nivolumab+ipilimumab trial


title: Patient 019,PostNeo, PBMC, RNAseq

description:
Library name: P019-PostNeo
RNA-seq of patients' PBMCs


title: DRG culture, Atf4.cKO, siCONTROL, t=42h, rep1

description: Library name: Atf4-cKO_siCTL_1


title: MLN_CCR8+_1

description:
Library name: SAMPLE13
Ln_p1


title: DRG culture, wildtype, siPerk, t=42h, rep4

description: Library name: WT_siPerk_4

value: wildtype

value: siPerk


title: Patient 019,C2D1, PBMC, RNAseq

description:
Library name: P019-C2D1
RNA-seq of patients' PBMCs


title: AB17969

description:
Library name: Sample1896
MARS_v2


title: Patient 019,Baseline, PBMC, RNAseq

description:
Library name: P019-Baseline
RNA-seq of patients' PBMCs


title: MLN_CCR8-_3

description:
Library name: SAMPLE11
Ln_n3


title: DRG culture, wildtype, siPerk, t=42h, rep3

description: Library name: WT_siPerk_3


title: AB17968

description:
Library name: Sample1895
MARS_v2


title: Patient 018,PostNeo, PBMC, RNAseq

description:
Library name: P018-PostNeo
RNA-seq of patients' PBMCs


title: DRG culture, wildtype, siPerk, t=42h, rep2

description: Library name: WT_siPerk_2


title: AB17967

description:
Library name: Sample1894
MARS_v2


title: MLN_CCR8-_2

description:
Library name: SAMPLE10
Ln_n2


title: DRG culture, wildtype, siPerk, t=42h, rep1

description: Library name: WT_siPerk_1


title: Patient 018,C2D1, PBMC, RNAseq

description:
Library name: P018-C2D1
RNA-seq of patients' PBMCs


title: MLN_CCR8-_1

description:
Library name: SAMPLE9
Ln_n1


title: AB17966

description:
Library name: Sample1893
MARS_v2


title: Patient 018,C3D1, PBMC, RNAseq

description:
Library name: P018-C3D1
RNA-seq of patients' PBMCs


title: DRG culture, wildtype, siCebpg, t=42h, rep4

description: Library name: WT_siCebpg_4


title: heart_CCR8+_4

description:
Library name: SAMPLE8
H_p4

source_name: heart

value: heart


title: AB17965

description:
Library name: Sample1892
MARS_v2


title: Patient 017,PostNeo, PBMC, RNAseq

description:
Library name: P017-PostNeo
RNA-seq of patients' PBMCs


title: DRG culture, wildtype, siCebpg, t=42h, rep3

description: Library name: WT_siCebpg_3


title: AB17964

description:
Library name: Sample1891
MARS_v2


title: Patient 021,C2D1, PBMC, RNAseq

description:
Library name: P021-C2D1
RNA-seq of patients' PBMCs

value: Male


title: DRG culture, Atf4.cKO, siCebpg, t=42h, rep2

description: Library name: Atf4-cKO_siCebpg_2


title: heart_CCR8+_3

description:
Library name: SAMPLE7
H_p3


title: Patient 017,C3D1, PBMC, RNAseq

description:
Library name: P017-C3D1
RNA-seq of patients' PBMCs


title: DRG culture, wildtype, siCebpg, t=42h, rep2

description: Library name: WT_siCebpg_2


title: Patient 020,C2D1, PBMC, RNAseq

description:
Library name: P020-C2D1
RNA-seq of patients' PBMCs


title: heart_CCR8+_2

description:
Library name: SAMPLE6
H_p2


title: Patient 017,C2D1, PBMC, RNAseq

description:
Library name: P017-C2D1
RNA-seq of patients' PBMCs


title: DRG culture, wildtype, siCebpg, t=42h, rep1

description: Library name: WT_siCebpg_1


title: AB17963

description:
Library name: Sample1890
MARS_v2

value: BM


title: heart_CCR8+_1

description:
Library name: SAMPLE5
H_p1


title: AB17962

description:
Library name: Sample1889
MARS_v2

value: PC


title: Patient 016,PostNeo, PBMC, RNAseq

description:
Library name: P016-PostNeo
RNA-seq of patients' PBMCs


title: DRG culture, wildtype, siAtf4, t=42h, rep4

description: Library name: WT_siAtf4_4


title: heart_CCR8-_4

description:
Library name: SAMPLE4
H_n4


title: DRG culture, Atf4.cKO, siCONTROL, t=42h, rep3

description: Library name: Atf4-cKO_siCTL_3

value: siCONTROL


title: AB17961

description:
Library name: Sample1888
MARS_v2


title: Patient 014,PostNeo, PBMC, RNAseq

description:
Library name: P014-PostNeo
RNA-seq of patients' PBMCs


title: DRG culture, wildtype, siAtf4, t=42h, rep3

description: Library name: WT_siAtf4_3


title: AB17970

description:
Library name: Sample1897
MARS_v2


title: heart_CCR8-_3

description:
Library name: SAMPLE3
H_n3


title: AB17960

description:
Library name: Sample1887
MARS_v2


title: Patient 014,C3D1, PBMC, RNAseq

description:
Library name: P014-C3D1
RNA-seq of patients' PBMCs


title: DRG culture, wildtype, siAtf4, t=42h, rep2

description: Library name: WT_siAtf4_2


title: heart_CCR8-_2

description:
Library name: SAMPLE2
H_n2


title: AB17959

description:
Library name: Sample1886
MARS_v2


title: Patient 014,C2D1, PBMC, RNAseq

description:
Library name: P014-C2D1
RNA-seq of patients' PBMCs


title: DRG culture, wildtype, siAtf4, t=42h, rep1

description: Library name: WT_siAtf4_1


title: heart_CCR8-_1

description:
Library name: SAMPLE1
H_n1


title: AB17958

description:
Library name: Sample1885
MARS_v2


title: MLN_CCR8-_4

description:
Library name: SAMPLE12
Ln_n4


title: Patient 014,Baseline, PBMC, RNAseq

description:
Library name: P014-Baseline
RNA-seq of patients' PBMCs


title: Exp. C, Day 4 of culture_NTHi_rep3

city: Homburg

first: Felix

last: Ritzmann

address: Kirrberger Street

country: Germany

institute: Saarland University

description: Library name: C8

data_processing:
Raw data were processed with STAR Alignment and DESeq2 pipeline
Assembly: GRCm39
Supplementary files format and content: Pooled count matrices

source_name: Primary cells

extract_protocol:
Macherey Nagel RNA Isolation Kit
Performed at sequencer's facility

value: lung

value: Airway epithelial cells

value: C57BL/6 wild type

value: NTHI treated

value: Experiment C


title: AB17957

description:
Library name: Sample1884
MARS_v2

source_name: BM


title: DRG culture, wildtype, siCONTROL, t=42h, rep3

description: Library name: WT_siCTL_3

value: primary adult dorsal root ganglia cell culture


title: DRG culture, wildtype, siCONTROL, t=42h, rep4

description: Library name: WT_siCTL_4


title: Exp. C, Day 4 of culture_NTHi_rep2

description: Library name: C7


title: Patient 013,PostNeo, PBMC, RNAseq

description:
Library name: P013-PostNeo
RNA-seq of patients' PBMCs

value: Non-Hispanic


title: DRG culture, wildtype, siCONTROL, t=42h, rep2

description: Library name: WT_siCTL_2


title: Patient 013,C3D1, PBMC, RNAseq

description:
Library name: P013-C3D1
RNA-seq of patients' PBMCs


title: AB17955

description:
Library name: Sample1882
MARS_v2


title: Exp. C, Day 4 of culture_NTHi_rep1

description: Library name: C6


title: AB17956

description:
Library name: Sample1883
MARS_v2


title: Patient 013,C2D1, PBMC, RNAseq

description:
Library name: P013-C2D1
RNA-seq of patients' PBMCs


title: DRG culture, wildtype, siCONTROL, t=42h, rep1

description: Library name: WT_siCTL_1


title: Exp. C, Day 4 of culture_control_rep3

description: Library name: C5

value: untreated control


title: Patient 013,Baseline, PBMC, RNAseq

description:
Library name: P013-Baseline
RNA-seq of patients' PBMCs

value: PBMC


title: AB17954

description:
Library name: Sample1881
MARS_v2


title: set2-NLRP3A whole tumor 3

description: Library name: BN14-NLRP3A- crispr

data_processing:
Illumina NovaSeq 6000 system
Each sample yielded twenty million reads at PE150 depth.
Assembly: Mouse mm10
Supplementary files format and content: Tab delimited text file includes raw counts for each sample

source_name: Melanoma tumor

extract_protocol:
Total RNA was isolated with the RNeasy Plus Mini Kit (Qiagen, 74134)
The library was prepared with the NEBNext Ultra II RNA Library Prep Kit following manufacturer's protocol

value: Melanoma tumor

tag: cell line

value: Gemm6 mouse melanoma cell line

value: Melanoma tumor cells

value: NLRP3A CRISPR


title: Exp. C, Day 4 of culture_control_rep2

description: Library name: C4

tag: cell type


title: AB17953

description:
Library name: Sample1880
MARS_v2


title: Patient 012,C2D1, PBMC, RNAseq

description:
Library name: P012-C2D1
RNA-seq of patients' PBMCs

value: nivolumab+ipilimumab trial

value: Female


title: set2-NLRP3A whole tumor 2

description: Library name: BN13-NLRP3A-crispr


title: Exp. C, Day 4 of culture_control_rep1

description: Library name: C3


title: AB17952

description:
Library name: Sample1879
MARS_v2

value: BM

value: PC


title: Patient 012,Baseline, PBMC, RNAseq

description:
Library name: P012-Baseline
RNA-seq of patients' PBMCs


title: set2-NLRP3A whole tumor 1

description: Library name: BN12-NLRP3A crispr


title: Exp. C, Day of airlift_rep2

description: Library name: C2

value: lung


title: AB17951

description:
Library name: Sample1878
MARS_v2


title: Patient 011,PostNeo, PBMC, RNAseq

description:
Library name: P011-PostNeo
RNA-seq of patients' PBMCs

value: Male


title: AB17950

description:
Library name: Sample1877
MARS_v2


title: set-2-control whole tumor 3

description: Library name: BN11-Control-crispr

value: Control CRISPR


title: Patient 010,PostNeo, PBMC, RNAseq

description:
Library name: P010-PostNeo
RNA-seq of patients' PBMCs


title: Exp. C, Day of airlift_rep1

description: Library name: C1

value: Airway epithelial cells

value: C57BL/6 wild type


title: set-2-control whole tumor 2

description: Library name: BN10-Control-crispr


title: Exp. C, Day of isolation

description: Library name: C0

value: Experiment C


title: AB17949

description:
Library name: Sample1876
MARS_v2


title: Patient 010,C3D1, PBMC, RNAseq

description:
Library name: P010-C3D1
RNA-seq of patients' PBMCs

value: Non-Hispanic


title: Exp. B, Day 4 of culture_NTHi_rep2

description: Library name: B6

value: NTHI treated

value: Experiment B


title: set-2-control whole tumor 1

description: Library name: BN9-Control-cripr

value: Melanoma tumor


title: AB17948

description:
Library name: Sample1875
MARS_v2


title: Patient 010,C2D1, PBMC, RNAseq

description:
Library name: P010-C2D1
RNA-seq of patients' PBMCs

value: PBMC


title: KO whole tumoe 3

description: Library name: TS23-1-NLRP3KO

value: Gemm6 mouse melanoma cell line

value: Melanoma tumor cells

value: BRAF V600E PTEN-/- NLRP3-/- -KO3


title: Exp. B, Day 4 of culture_NTHi_rep1

description: Library name: B5


title: AB17947

description:
Library name: Sample1874
MARS_v2


title: Patient 010,Baseline, PBMC, RNAseq

description:
Library name: P010-Baseline
RNA-seq of patients' PBMCs

value: nivolumab+ipilimumab trial


title: Exp. B, Day 4 of culture_control_rep2

description: Library name: B4

value: untreated control


title: AB17946

description:
Library name: Sample1873
MARS_v2

value: BM

value: PC


title: Patient 009,PostNeo, PBMC, RNAseq

description:
Library name: P009-PostNeo
RNA-seq of patients' PBMCs

value: Female

value: Hispanic or Latino


title: KO whole tumor 2

description: Library name: TS10-2-NLRP3KO

value: BRAF V600E PTEN-/- NLRP3-/- -KO2


title: KO whole tumor 1

description: Library name: TS9-3-NLRP3KO

value: BRAF V600E PTEN-/- NLRP3-/- -KO1


title: Exp. B, Day 4 of culture_control_rep1

description: Library name: B3

value: lung

value: Airway epithelial cells

value: C57BL/6 wild type


title: AB17945

description:
Library name: Sample1872
MARS_v2


title: WT whole tumor 2

description: Library name: TS12-1-WT

value: BRAF V600E PTEN-/- -WT2


title: Patient 009,C2D1, PBMC, RNAseq

description:
Library name: P009-C2D1
RNA-seq of patients' PBMCs


title: Exp. B, Day of airlift_rep2

description: Library name: B2

value: Experiment B


title: AB17944

description:
Library name: Sample1871
MARS_v2


title: Patient 009,Baseline, PBMC, RNAseq

description:
Library name: P009-Baseline
RNA-seq of patients' PBMCs

value: PBMC


title: Exp. B, Day of airlift_rep1

description: Library name: B1


title: WT whole tumor 1

description: Library name: TS9-2 - WT

value: Melanoma tumor

value: Gemm6 mouse melanoma cell line

value: BRAF V600E PTEN-/- -WT1


title: AB17943

description:
Library name: Sample1870
MARS_v2


title: Patient 008,PostNeo, PBMC, RNAseq

description:
Library name: P008-PostNeo
RNA-seq of patients' PBMCs

value: nivolumab+ipilimumab trial

value: Non-Hispanic


title: NLRP3A CRISPR sorted cells 2

description: Library name: BX-19-4-NLRP3A

value: Melanoma tumor cells

value: NLRP3A CRISPR sorted tumor cell


title: AB17942

description:
Library name: Sample1869
MARS_v2

value: BM


title: Patient 008,C3D1, PBMC, RNAseq

description:
Library name: P008-C3D1
RNA-seq of patients' PBMCs

value: Female


title: Control CRISPR sorted cells 1

description: Library name: BX-19-2-Control

value: Control CRISPR sorted tumor cell


title: Exp. A, Day 4 of culture_NTHi_rep2

description: Library name: A6

value: NTHI treated

value: Experiment A


title: AB17941

description:
Library name: Sample1868
MARS_v2


title: Patient 008,Baseline, PBMC, RNAseq

description:
Library name: P008-Baseline
RNA-seq of patients' PBMCs


title: NLRP3A CRISPR whole tumor 2

description: Library name: BX-18-10-NLRP3A

value: NLRP3A CRISPR


title: Exp. A, Day 4 of culture_NTHi_rep1

description: Library name: A5

value: lung

value: Airway epithelial cells

value: C57BL/6 wild type


title: Exp. B, Day of isolation

description: Library name: B0

value: untreated control

value: Experiment B


title: AB17940

description:
Library name: Sample1867
MARS_v2

value: PC


title: Patient 007,PostNeo, PBMC, RNAseq

description:
Library name: P007-PostNeo
RNA-seq of patients' PBMCs

value: PBMC

value: Male


title: NLRP3A CRISPR whole tumor 1

description: Library name: BX-18-9-NLRP3A

value: Melanoma tumor

value: Gemm6 mouse melanoma cell line


title: Exp. A, Day 4 of culture_control_rep2

description: Library name: A4


title: AB17939

description:
Library name: Sample1866
MARS_v2


title: Patient 007,C2D1, PBMC, RNAseq

description:
Library name: P007-C2D1
RNA-seq of patients' PBMCs

value: nivolumab+ipilimumab trial

value: Non-Hispanic


title: Control CRISPR whole tumor 2

description: Library name: BX-18-4 -Control

value: Melanoma tumor cells

value: Control CRISPR


title: AB17938

description:
Library name: Sample1865
MARS_v2

value: BM


title: Exp. A, Day 4 of culture_control_rep1

description: Library name: A3

value: Experiment A


title: Patient 007,Baseline, PBMC, RNAseq

description:
Library name: P007-Baseline
RNA-seq of patients' PBMCs


title: Control CRISPR whole tumor 1

description: Library name: BX-18-3 -Control


title: Exp. A, Day of airlift_rep2

description: Library name: A2


title: AB17937

description:
Library name: Sample1864
MARS_v2


title: Patient 006,PostNeo, PBMC, RNAseq

description:
Library name: P006-PostNeo
RNA-seq of patients' PBMCs


title: AB13090

description: Library name: Sample 137

data_processing:
RNA sequencing data were processed starting with the Cell Ranger software (10x Genomics) to perform quality control, read alignment to the mouse reference genome (GRCm38), and quantification of gene expression levels. Unique Molecular Identifiers (UMIs) were used to count individual mRNA molecules, ensuring accurate expression levels.
The resultant data were then normalized to account for variations in sequencing depth and cell count discrepancies.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: tab delimited cell metadata

source_name: spinal cord

extract_protocol:
Mice were transcardially perfused with sterile PBS, and brain, spinal cord, spleen, lung and CSF were extracted 10 days post CAR T administration.
Next Gem single-cell 3′ with Feature Barcode technology for Cell Surface Protein v3.1.

treatment_protocol: For each mouse, 4 days after EAE induction, 3x10^⁶ cells in 100ul were injected retro-orbitally under isoflurane anesthesia, or 100ul of PBS for the control EAE untreated group. Tissues were harvested for scRNA-seq on day 14.

value: spinal cord

tag: mouse

tag: score

value: Untreated (PBS)

tag: eae model

value: peptide MOG


title: Exp. A, Day of airlift_rep1

description: Library name: A1

tag: tissue

value: lung

value: Airway epithelial cells

value: C57BL/6 wild type


title: Patient 006,C2D1, PBMC, RNAseq

description:
Library name: P006-C2D1
RNA-seq of patients' PBMCs

tag: arm


title: AB17788

description:
Library name: Sample1863
MARS_v2


title: AB13089

description: Library name: Sample 136


title: Exp. A, Day of isolation

description: Library name: A0

value: untreated control


title: AB17787

description:
Library name: Sample1862
MARS_v2


title: Patient 006,Baseline, PBMC, RNAseq

description:
Library name: P006-Baseline
RNA-seq of patients' PBMCs

value: PBMC

tag: age


title: AB13088

description: Library name: Sample 135


title: Mouse lung tumor, Kras-H3K36M-Setd2KO, Xenium

type: RNA

city: Philadelphia

first: Carson

last: Poltorack

state: PA

address: 421 Curie Blvd, Rm 445

department: Pathology

institute: University of Pennsylvania Perelman School of Medicine

description: Xenium run 29059

hyb_protocol: A 5006-gene mouse Xenium panel was used. Probe hybridization, ligation, rolling circle amplification, and decoding were performed on the Xenium Analyzer per manufacturer's protocol.

scan_protocol: Image acquisition, decoding, quality score generation, and DAPI-based cell segmentation were performed automatically by the Xenium Analyzer system.

data_processing: Xenium Onboard Analysis (instrument software). Downstream processing in Python (scanpy 1.10): QC (min_genes=55); cell-area normalization → log1p; HVG; PCA (n=100); neighbors (k=10, n_pcs=35); UMAP; Leiden (resolution=0.5, random_state=1); manual cell-type annotation; cellular neighborhoods via scimap KNN (k=30, k=30); tumor segmentation; T-cell scoring; macrophage M1/M2 characterization; hotspot module discovery; gseapy/Enrichr GSEA. Code at https://github.com/cdpolt/Gladstein-et-al-Xenium

label: Xenium probe set

source_name: lung

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: Tumor-laden lung tissue was dissected into 10% neutral-buffered formalin overnight at room temperature before paraffin embedding. Embedded tissue was sectioned at a thickness of 5um.

treatment_protocol: Mice of different genotypes were infected with AAV Cre and lentiCRISPRv2 targeting Setd2 to initiate lung tumors

tag: tissue preservation method

value: FFPE

value: Kras (LSL-G12D) + H3K36M + Setd2 KO


title: AB17786

first: Ido

last: Amit

address: 234 Herzl st.

description:
Library name: Sample1861
MARS_v2

value: PC


title: Patient 005,PostNeo, PBMC, RNAseq

description:
Library name: P005-PostNeo
RNA-seq of patients' PBMCs

value: nivolumab+ipilimumab trial

value: Male


title: AB13087

description: Library name: Sample 134


title: Mouse lung tumor, Kras-Setd2KO, Xenium

description: Xenium run 29072

value: Kras (LSL-G12D) + Setd2 KO


title: AB17785

description:
Library name: Sample1860
MARS_v2


title: Patient 005,C3D1, PBMC, RNAseq

description:
Library name: P005-C3D1
RNA-seq of patients' PBMCs

value: Non-Hispanic


title: AB13086

description: Library name: Sample 133


title: Mouse lung tumor, Kras-H3K36M, Xenium

description: Xenium run 29964

value: Kras (LSL-G12D) + H3K36M


title: AB17784

description:
Library name: Sample1859
MARS_v2

value: BM


title: Patient 005,C2D1, PBMC, RNAseq

description:
Library name: P005-C2D1
RNA-seq of patients' PBMCs


title: AB13085

description: Library name: Sample 132

value: spinal cord


title: Mouse lung tumor, Kras-Ctrl, Xenium

description: Xenium run 30373

value: Kras (LSL-G12D) control


title: AB17783

description:
Library name: Sample1858
MARS_v2


title: Patient 005,Baseline, PBMC, RNAseq

description:
Library name: P005-Baseline
RNA-seq of patients' PBMCs


title: AB13084

description: Library name: Sample 131

value: Untreated (PBS)

value: peptide MOG


title: DRG culture, untransfected, t=0, rep4

description: Library name: t_0_4

data_processing:
Kallisto paired-end quantification
Assembly: Mus_musculus.GRCm39.108
Supplementary files format and content: A comma-separated values (.csv) file contains kallisto estimated counts for siRNA samples.
Supplementary files format and content: A comma-separated values (.csv) file contains kallisto estimated counts for mRNA samples.

extract_protocol:
RNA was extracted using the Qiagen RNeasy micro kit (#74004).
Illumina Stranded mRNA Prep

treatment_protocol: Dharnafect 2-mediated transfection of Dharnacon ON-TARGETplus siRNA pools or custom mRNA generated by GenScript.

value: primary adult dorsal root ganglia cell culture

value: wildtype


title: AB17782

description:
Library name: Sample1857
MARS_v2


title: Patient 004,PostNeo, PBMC, RNAseq

description:
Library name: P004-PostNeo
RNA-seq of patients' PBMCs

data_processing:
Paired-end, 2 × 100 base pair (bp) transcriptome reads were mapped to the Genome Reference Consortium Human Build 38 (GRCh38) reference genome using HISAT2 (version 2.0.6)
The gene level counts were generated by the HTSeq-count program (version 0.5.4p5)
We utilized the edgeR (version 3.40.2) R package's cpm() function to compute the normalized gene expression values from the raw gene expression counts. These normalized expression values were log2 transformed after adding a pseudo count of 1.
Assembly: GRCh38
Supplementary files format and content: Gene level raw counts of each sample as computed by htseq-count (tab delimited)

extract_protocol:
RNA and genomic DNA were extracted from resected tumor specimens preserved in AllProtect tissue reagent (Qiagen) at the time of surgery. We divided the tumor tissue in half and employed the Qiagen RNeasy Mini Kit (#74104) for RNA isolation and the Qiagen DNeasy Blood and Tissue Kit (#69504) for DNA isolation. Total RNA from PBMCs was extracted using the Qiagen RNeasy Mini Kit.
TruSeq RNA exome kit is used to construct the RNA sequencing libraries

value: Female


title: AB13083

description: Library name: Sample 130


title: DRG culture, untransfected, t=0, rep3

description: Library name: t_0_3


title: AB17781

description:
Library name: Sample1856
MARS_v2


title: Patient 004,C3D1, PBMC, RNAseq

description:
Library name: P004-C3D1
RNA-seq of patients' PBMCs

value: PBMC


title: DRG culture, untransfected, t=0, rep2

description: Library name: t_0_2


title: AB13082

description: Library name: Sample 129


title: AB17780

description:
Library name: Sample1855
MARS_v2


title: Patient 004,C2D1, PBMC, RNAseq

description:
Library name: P004-C2D1
RNA-seq of patients' PBMCs


title: AB13081

description: Library name: Sample 128


title: Patient 004,Baseline, PBMC, RNAseq

description:
Library name: P004-Baseline
RNA-seq of patients' PBMCs


title: AB17779

description:
Library name: Sample1854
MARS_v2


title: AB13080

description: Library name: Sample 127


title: DRG culture, untransfected, t=0, rep1

description: Library name: t_0_1


title: DRG culture, Atf4 mRNA+Cebpg mRNA, t=42h, rep4

description: Library name: ATF4_CEBPG_4


title: AB17778

description:
Library name: Sample1853
MARS_v2


title: AB13079

description: Library name: Sample 126


title: DRG culture, Atf4 mRNA+Cebpg mRNA, t=42h, rep3

description: Library name: ATF4_CEBPG_3