title: 8_12w_ko2_S8

city: Groningen

first: Takuya

last: Oshima

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences of Cells & Systems

country: Netherlands

institute: University Medical Center Groningen

description: Tn5 treated DNA

data_processing:
FASTQ-files were processed with the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline) as previously described (Nott et al., 2019).
FASTQ-files were trimmed with cutadapt (v1.9.1).
Alignment was performed with Bowtie2 (Langmead et al., 2009) to mm10.
SAMtools (H. Li et al., 2009) (v1.2), MarkDuplicates (Picard v1.126), and bedtools (Quinlan, 2014) (v2.26) were used to filter and clean data post alignment.
MACS2 (v2.1.1) was used for peak calling (Y. Zhang et al., 2008).
The pipeline also runs IDR to detect peaks with high reproducibility (Q. Li et al., 2011).
Assembly: mm10

extract_protocol:
Microglia were isolated using a mechanical protocol at 4°C as previously described (Galatro et al., 2017). Microglia were sorted by gating the DAPIneg CD11bhigh CD45int Ly6cneg cells with FACS. Total RNA was isolated using RNeasy Micro Kit (Qiagen, cat# 74004) according to the manufacturer’s instructions.
ATAC-seq library preparation was performed as previously described (Buenrostro et al., 2013) with Nextera DNA Sample Preparation Kit (Illumina, cat# FC-121-1030).
Libraries were sequenced using HiSeq Rapid SBS Kit v2 (50 cycles) using paired end reads on a HiSeq2500 (Illumina).

tag: region

value: whole brain

value: microglia

value: ko

value: 12 week old

tag: strain background

value: C57Bl6J/FVB cross


title: WT1_48

status: Public on Dec 31 2024

type: SRA

city: shanghai

first: Yali

last: Chen

address: 800 Xiangyin Road

country: China

institute: Second Military Medical University

description: Naïve t cells were stimulated with αCD3/CD28 for three days

library_source: transcriptomic

data_processing:
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq platform.
High-quality reads were aligned to the mouse reference genome (GRCm38.p6) using Bowtie2
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM) using RNA-Seq by Expectation Maximization (RSEM).
Assembly: mm10
Supplementary files format and content: Excle file includes raw counts and FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: mouse spleen CD4+ T cells

extract_protocol:
Th0 cells were collected at indicated times for RNA extraction, total RNA was extracted with TRIzol reagent.
cDNA library construction and sequencing were performed by Beijing Genomics Institute using Illumina HiSeq platform.

tag: tissue

value: mouse spleen CD4+ T cells

tag: strain

tag: cell type

value: WT1-Th0 cell

tag: genotype

value: wild type

tag: treatment

value: Stimulated with αCD3/CD28 for three days


title: AG08379 Fib A

city: Saint Louis

first: Kitra

last: Cates

state: MO

address: 4523 Clayton Ave, MCD SCI 361

department: Developmental Biology

country: USA

institute: Washington University in St. Louis

description: Library name: AG08379 Fib A RNAseq

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custompython demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size. Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis. The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights. The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Quantitative CPM expression distances were analyzed by limma and graphically displayed using ComplexHeatmap. Gene function annotation was evaluated using Metascape.
Assembly: Ensembl_R76 h_sapien reference build
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Homo sapiens

source_name: fibroblast

extract_protocol:
Total RNA was extracted using the RNeasy plus micro kit (QIAGEN, USA) as instructed by the manufacturer.
RNA sample integrity was assessed on a 2100 Bioanalyzer (Agilent, USA) before proceeding to library preparation. mRNA was prepared for Illumina sequencing using SMARTer Ultra Low Input RNA Kit (Clontech, USA). cDNA libraries were sequenced on an Illumina NovaSeq 6000.

value: fibroblast

tag: batch

value: biological replicate 1


title: TESC_11

city: Morgantown

first: Pius

last: Joseph

state: WV

address: 1095 Willowdale Road

department: Health Effects Laboratory Division/Toxicology and Molecular Biology Branch

institute: National Institute for Occupational Safety and Health (NIOSh)

data_processing:
Map reads to human genome version 38
normalize libraries usng DESeq2
remove any genes with counts less than 10
convert transcripts to genes using tximeta
identify differentially expressed genes using Deseq2
Supplementary_files_format_and_content: tar folder containing counts and meta data

source_name: blood_dust exposed with silicosis

extract_protocol:
Human blood samples collected were immediately mixed with RNALater (Invitrogen, Carlsbad, CA) and kept frozen until used for RNA isolation. Total RNA was isolated from 2ml blood sample (0.5 ml blood and 1.5 ml RNALater) each using Ribopure Blood Kit (ThermoFisher Scientific, Waltham, MA), including DNA treatment. The RNA extracted was quantified using a Nanodrop ND-1000 (ThermoFisher Scientific) and quality assessed via an Agilent 2100 Bioanalyzer (Agilent Technologies; Santa Clara, CA) using Agilent RNA 6000 Nano Reagents. Only RNA samples with an RNA Integrity Number (RIN) >8.0 were used to construct next generation sequence (NGS) libraries.
Immediately prior to NGS library synthesis, 1.4 mg total RNA per blood sample was used to deplete alpha and beta globin mRNA, using the GLOBINClear kit (ThermoFisher Scientific, Waltham, MA). 0.5mg globin-depleted RNA was then used as input for the Illumina TruSeq Stranded mRNA Kit to synthesize NGS libraries. Library synthesis was carried out using the default protocol in the Low Sample TruSeq Stranded mRNA Sample Preparation Guide with the following two modifications: fragmentation time was reduced to 3 minutes to achieve insert lengths ranging between 125 and 250 bp and the PCR amplification was reduced to 12 cycles. Individual cDNA libraries were quantified using a Qubit 3.0 Fluorometer (Invitrogen by ThermoFisher Scientific) and the dsDNA HS Assay Kit (Invitrogen by ThermoFisher Scientific). The average fragment size for each library was determined using an Agilent 2100 Bioanalyzer with High Sensitivity DNA Reagents.
Libraries were used in 2 x 125 basepair sequencing using the Illumina HiSeq 2500 (Illumina, San Diego, CA) in high output mode with v4 HiSeq Cluster and SBS Kits (Illumina).

tag: radiography

value: silicosis

tag: silica exposure time (years)

value: blood


title: 6_12w_wt2_S6

description: Tn5 treated DNA

library_source: genomic

molecule: genomic DNA

source_name: brain

value: brain

value: wt

tag: age


title: RNA isolated from aged chondrocytes that were exposed to young infrapatellar fat pad conditioned media, replicate 3

city: Boston

first: Gabrielle

last: Gilmer

state: MA

address: 149 13th Street

department: Pathology

institute: University of Pittsburgh

description: male

data_processing:
Partek Flow was used bulk RNA sequencing as described in tutorial
Assembly: mm10
Supplementary files format and content: Gene counts post alignment; contains the chromosome, start, stop, length, strand, gene symbol, biotype, name and source

source_name: cartilage

growth_protocol: cultured in phenol red free low-glucose DMEM with 1% GlutaMAX and 1% PS

extract_protocol:
Qigen Rneasy  Kit
mm10; 40 million reads per sample with a directional library pre

treatment_protocol: see paper for details

value: cartilage

tag: cell line

value: primary

value: chondrocyte

value: young IFP


title: 7_12w_ko1_S7

description: Tn5 treated DNA

value: whole brain

value: microglia

value: ko


title: TESC_10


title: RNA isolated from aged chondrocytes that were exposed to young infrapatellar fat pad conditioned media, replicate 4

description: male


title: 5_12w_wt1_S5

description: Tn5 treated DNA

value: 12 week old

value: C57Bl6J/FVB cross


title: TESC_08


title: 4_6w_ko2_S4

description: Tn5 treated DNA

value: 6 week old


title: RNA isolated from aged chondrocytes that were exposed to young infrapatellar fat pad conditioned media, replicate 1

description: male


title: AG13369 Fib A

description: Library name: AG13369 Fib A RNAseq


title: RNA isolated from aged chondrocytes that were exposed to young infrapatellar fat pad conditioned media, replicate 2

description: male


title: 3_6w_ko1_S3

description: Tn5 treated DNA


title: TESC_06


title: TESC_07


title: Mammary Tumor, IL1α-/-, replicate 2,scRNA seq

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

description:
S04
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files (raw-feature-bc-matrix barcodes.tsv, features.tsv, matrix.mtx).

source_name: Mammary Tumor

growth_protocol: HER2+ H605 mammary tumor cells were grown in DMEM/F12 insulin 10ug/ml, 1%Penn-Step, 10% Fetal Bovine Serum (FBS) and 2x10^6 cells were injected in mammary pad of WT and IL1α-/- mice

extract_protocol:
Two pairs of day-14 HER2+ H605 tumors from transplanted WT and IL1α-/- mice were freshly collected on separate days. Tumors were digested using digestion buffer (DMEM/F12 containing 2mg/ml collagenase IV and 0.2mg/ml hyaluronidase) for 45 minutes at 37°C with agitation at 1000rpm using an Eppendorf shaker/incubator. The digested tissue was then spun down at 500g for 5 minutes and lysed using 1X RBC lysis buffer (Biolegend) according to the manufacturer's protocol. Subsequently, the tube was spun down, and the tissue pellet was resuspended with wash buffer (2% FBS in PBS) and filtered through a 40μm filter to attain a single-cell suspension. This single-cell suspension was counted and enriched for live cells using the Miltenyi Biotec negative selection live enrichment kit according to the manufacturer's protocol. Live cells with 95% viability were used for library preparation.
Library was performed according to the manufacter's instructions(single cell 3' v3.1 protocol, 10x Genomics).

value: Mammary Tumor

value: FVB/NJ

value: 6 - 8 weeks old


title: 2_6w_wt2_S2

description: Tn5 treated DNA


title: Mammary Tumor, WT, replicate 2, scRNA seq

description:
S03
10x Genomics


title: AG13369 miN B

description: Library name: AG13369 miN B RNAseq

source_name: microRNA-induced neuron

value: microRNA-induced neuron

value: biological replicate 2


title: hBVP_9124_A

description: Library name: hBVP_9124_A RNAseq

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custompython demultiplexing program with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected. The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size. Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis. The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights. The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
Quantitative CPM expression distances were analyzed by limma and graphically displayed using ComplexHeatmap. Gene function annotation was evaluated using Metascape. Upstream regulators of DEG and gene expression modules were predicted by Ingenuity Pathway Analysis regulators of DEG and gene expression modules were predicted by Ingenuity Pathway Analysis (Qiagen).
Assembly: Ensembl_R76 h_sapien reference build
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: pericyte

value: pericyte

value: miR-9/9*-124 expression for five days


title: TESC_04

value: silicosis

value: blood


title: Mammary Tumor, IL1α-/-, replicate 1,scRNA seq

description:
S02
10x Genomics


title: 1_6w_wt1_S1

description: Tn5 treated DNA

value: brain

value: wt


title: TESC_03


title: AG13369 miN A

description: Library name: AG13369 miN A RNAseq

value: biological replicate 1


title: hBVP_NS_B

description: Library name: hBVP_NS_B RNAseq

value: miR-NS expression for five days


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

city: South San Francisco

first: Thomas

middle: D

last: Wu

state: CA

address: 1 DNA Way

institute: Genentech, Inc.

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
B9.4567B.filtered_contig_annotations.csv.gz

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

molecule: polyA RNA

source_name: Blood

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

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

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

value: BALB/c

tag: Sex

value: Female

value: 6-8 weeks

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

value: Blood

value: CD90+ T cells


title: TESC_09


title: TESC_02


title: hBVP_NS_A

description: Library name: hBVP_NS_A RNAseq


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


title: Mammary Tumor, WT, replicate 1, scRNA seq

description:
S01
10x Genomics

value: Mammary Tumor

value: FVB/NJ

value: 6 - 8 weeks old


title: AG13369 Fib B

description: Library name: AG13369 Fib B RNAseq

value: fibroblast

value: biological replicate 2


title: hBVSMC_9124_B

description: Library name: hBVSMC_9124_B RNAseq

source_name: smooth muscle cells

value: smooth muscle cells

value: miR-9/9*-124 expression for five days


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
B9.123B.filtered_contig_annotations.csv.gz


title: IM24h_RiboTag IP_4

city: Bonn

first: Reiner

last: Schneider

address: Venusberg-Campus 1

department: Surgery Department

country: Germany

institute: University Clinics Bonn

data_processing:
Data was analyzed with Partek Flow software and the publicly available Lexogen pipeline (Lexogen12112017)
Assembly: hg38 oder mm10 Ensembl Transcripts release 101
Supplementary files format and content: human_Counts -GSA of gene counts
Supplementary files format and content: human_GSA_results -normalized GSA of transcript counts
Supplementary files format and content: human_Partek_Early_Late_2_Normalization_Normalized_counts -normalized gene counts
Supplementary files format and content: human_Partek_Early_Late_2_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts -gene counts
Supplementary files format and content: Chat-Ribo_ gene counts -GSA of gene counts
Supplementary files format and content: Chat-Ribo_gsa_result -normalized GSA of transcript counts
Supplementary files format and content: Partek_Chat-Ribo-IM3h_Normalization_Normalized_counts -normalized gene counts
Supplementary files format and content: Partek_Chat-Ribo-IM3h_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts -gene counts
Supplementary files format and content: Partek_Chat-Ribo-IM24h_Normalization_Normalized_counts -normalized gene counts
Supplementary files format and content: Partek_Chat-Ribo-IM24h_Quantify_to_annotation_model_(Partek_E_M)_Gene_counts -gene counts

source_name: Small bowel muscularis externa

extract_protocol:
Muscularis externa was prepared from small bowel and subjected to an immunoprecipitation protocol for RiboTag (Leven et al 2021, Application of a RiboTag-based approach to generate and analyze mRNA from enteric neural cells,  https://doi.org/10.1111/nmo.14309). Input samples were generated from total lysate while IP samples underwent the entire precipitation process and were purified afterwards.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Patient samples were collected during surgeryin ice cold krebs-buffer and processed directly after collection. Muscularis externa was prepared from small bowel and subjected to an immunoprecipitation protocol for RiboTag (Leven et al 2021, Application of a RiboTag-based approach to generate and analyze mRNA from enteric neural cells,  https://doi.org/10.1111/nmo.14309).

value: Small bowel muscularis externa

value: B6;129S6-Chattm2(cre)Lowl/J x B6N.129 Rpl22tm1.1Psam/J


title: MECOM_KO, 2, bulk RNA

city: Wenzhou

first: Chenghao

last: Li

state: Zhejiang

address: Wenzhou Medical University, Xueyuan Xi Road

institute: Wenzhou Medical University

data_processing:
Sequence reads were mapped to the hg38 genome and transcriptome by STAR (2.7.10a) and featureCounts (2.0.6).
Assembly: hg38
Supplementary files format and content: Gene expression count matrix from featureCounts

source_name: retina

growth_protocol: Visually healthy and relatively mature hROs were selected beyond day 75. Under a microscope, a sterile V-Lance knife was used to carefully excise the VSX2-tdTomato labeled NR region, ensuring the remainder of the organoid did not contain tdTomato fluorescence. Confocal microscopy was employed for live-cell imaging to dynamically monitor the repair process mediated by CMZ-hNRSCs, tracking the VSX2-tdTomato positive cells. Organoid samples were collected at critical time points during retinal repair for further analysis.To enhance the knockout efficiency of the MECOM in hNRSCs within hROs, a dual-infection strategy was implemented, utilizing CRISPR/Cas9 lentivirus for infecting hROs twice, with a 120-h interval between infections and each infection lasting 8 h.

extract_protocol:
For each sample, total RNA was extracted using TRIzol reagent (Thermo, 15596018CN) and subsequently purified using the RNeasy Mini Kit (Qiagen, 74104), following the manufacturer’s instructions. The quality and quantity of the RNA were assessed using a NanoDrop 2000 spectrophotometer, Agilent 2100 Bioanalyzer, and Agilent RNA 6000 Nano Kit (Agilent, 5067-1511).
To create the sequencing libraries, the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, E7770L) was employed. Library clustering was carried out using the HiSeq PE Cluster Kit v4-cBot-HS (Illumina, PE-401-4001), following the manufacturer’s recommendations. After cluster generation, the libraries were subjected to sequencing on an Illumina platform, generating 150 bp paired-end reads.

treatment_protocol: To enhance the knockout efficiency of the MECOM in hNRSCs within hROs, a dual-infection strategy was implemented, utilizing CRISPR/Cas9 lentivirus for infecting hROs twice, with a 120-h interval between infections and each infection lasting 8 h. The steps are as follows: Initially, hROs that were visually healthy and had matured beyond day 70 were selected. For the initial round of infection, either a MECOM-specific CRISPR/Cas9 sgRNA lentivirus (MECOM-KO) or a Negative Control lentivirus (NControl), designed not to target any mammalian genes, was applied at a dosage of 5 μL (titer of 1×109 infectious viral particles per mL) to every group of 5 hROs in a 5 cm dish. 8 h post-infection, the medium containing the virus was replaced with fresh NR medium to ensure the removal of any residual lentivirus. 120 h after the initial infection, the NR region marked with VSX2-tdTomato was excised under a microscope using a sterile V-Lance knife, with care taken to remove all tdTomato fluorescence from the hROs, marking this as day 0 of retinal repair (R0). Immediately following the excision of the NR region, a second round of infection was conducted using the same lentiviral constructs, adhering to the initial protocol. Samples were collected for qPCR analysis 120 h after the second infection (indicating day 5 of retinal repair, R5) to assess the knockout efficiency. Follow-up observations and imaging were conducted on days 5, 10, 20, and 40 of retinal repair to monitor the progress.

value: retina

value: organoids derived from hPSCs


title: hBVSMC_9124_A

description: Library name: hBVSMC_9124_A RNAseq


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

value: BALB/c


title: MECOM_KO, 1, bulk RNA


title: hBSVSMC_NS_B

description: Library name: hBSVSMC_NS_B RNAseq

value: miR-NS expression for five days


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
B9.4567b.filtered_contig_annotations.csv.gz

value: Female

value: 6-8 weeks


title: IM24h_RiboTag IP_3


title: IM24h_RiboTag IP_2


title: Contrl, 3, bulk RNA

value: control


title: hAst_9124_B

description: Library name: hAst_9124_B RNAseq

source_name: astrocyte

value: astrocyte


title: IM24h_RiboTag IP_1


title: hBVSMC_NS_A

description: Library name: hBVSMC_NS_A RNAseq


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
B9.123b.filtered_contig_annotations.csv.gz

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

value: Blood

value: CD90+ T cells


title: IM24h_RiboTag IP_5


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


title: MECOM_KO, 3, bulk RNA


title: Contrl, 2, bulk RNA


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


title: IM3h_RiboTag IP_3


title: hBVP_9124_B

description: Library name: hBVP_9124_B RNAseq

value: pericyte


title: IM3h_RiboTag IP_4


title: P0263EDR00, EoE distal, rep19

city: Chicago

first: Marie-Pier

last: Tetreault

state: IL

address: 300 East Superior Street

department: Medicine/GI&Hep division

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Assembly: hg38
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: Esophageal mucosal biopsy

extract_protocol:
Esophageal mucosal biopsies were homogenized prior to RNA extraction in RLT lysis buffer (Qiagen). Total RNA was extracted using the RNeasy kit (Qiagen, Germantown, MD) according to the manufacturer’s instructions
Directional mRNA libraries were prepared using NEBNext Kits per the manufacturer’s instructions

value: Esophageal mucosal biopsy

tag: esophagus region

value: Distal

value: Eosinophilic Esophagitis


title: P0259EDR00, EoE distal, rep18


title: hAst_NS_B

description: Library name: hAst_NS_B RNAseq


title: P0207EDR00, EoE distal, rep17


title: hAst_NS_A

description: Library name: hAst_NS_A RNAseq


title: IM3h_RiboTag IP_5

value: Small bowel muscularis externa


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S5.5n.filtered_contig_annotations.csv.gz

source_name: Draining lymph node

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

value: Draining lymph node

value: CD90+CD44+ T cells


title: hDuF_9124_A

description: Library name: hDuF_9124_A RNAseq

source_name: dura fibroblast

value: dura fibroblast

value: miR-9/9*-124 expression for five days


title: Naive_RiboTag IP_5

value: B6;129S6-Chattm2(cre)Lowl/J x B6N.129 Rpl22tm1.1Psam/J

value: naive


title: IM3h_RiboTag IP_2


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S5.2n.filtered_contig_annotations.csv.gz

value: BALB/c

value: Female

value: 6-8 weeks


title: hDuF_9124_B

description: Library name: hDuF_9124_B RNAseq


title: IM3h_RiboTag IP_1


title: hDuF_NS_B

description: Library name: hDuF_NS_B RNAseq

value: miR-NS expression for five days


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S5.3n.filtered_contig_annotations.csv.gz


title: Naive_RiboTag IP_4


title: P0199EDR00, EoE distal, rep15


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S4.6n.filtered_contig_annotations.csv.gz


title: P0205EDR00, EoE distal, rep16


title: hDuF_NS_A

description: Library name: hDuF_NS_A RNAseq


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S5.7n.filtered_contig_annotations.csv.gz


title: hDF_9124_B

description: Library name: hDF_9124_B RNAseq

source_name: dermal fibroblast

value: dermal fibroblast


title: P0137EDR00, EoE distal, rep13


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S4.5n.filtered_contig_annotations.csv.gz


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S4.3n.filtered_contig_annotations.csv.gz


title: P0128EDR00, EoE distal, rep12


title: Naive_RiboTag IP_3


title: hAst_9124_A

description: Library name: hAst_9124_A RNAseq

value: astrocyte


title: Naive_RiboTag IP_2


title: P0159EDR00, EoE distal, rep14

value: Esophageal mucosal biopsy


title: hDF_9124_A

description: Library name: hDF_9124_A RNAseq


title: Naive_RiboTag IP_1


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S4.2n.filtered_contig_annotations.csv.gz


title: hDF_NS_B

description: Library name: hDF_NS_B RNAseq


title: P0126EDR00, EoE distal, rep11

value: Distal


title: tumor, KO-X757

city: Guang Zhou

first: Yujia

last: Liu

address: 4, Zhongshan Second Road, Yuexiu District, Guangzhou City

institute: sysu

data_processing:
CLC Genomics Workbench v11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RAW COUNT values for each Sample

source_name: EL4 tumor

extract_protocol:
RNA was harvested using TRIzol.1 μg of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protoclos.

value: EL4 tumor

value: HVEM-KO


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.6n.filtered_contig_annotations.csv.gz

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


title: hDF_NS_A

description: Library name: hDF_NS_A RNAseq


title: tumor, KO-X725


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.7n.filtered_contig_annotations.csv.gz

value: Draining lymph node


title: P0116EDR00, EoE distal, rep9

value: Eosinophilic Esophagitis


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.4n.filtered_contig_annotations.csv.gz

value: CD90+CD44+ T cells


title: tumor, KO-X724


title: tumor, KO-X702


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.1n.filtered_contig_annotations.csv.gz


title: P0123EDR00, EoE distal, rep10


title: P0065EDR00, EoE distal, rep7


title: tumor, Vec-X716

value: Vec


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.3n.filtered_contig_annotations.csv.gz


title: P0061EDR00, EoE distal, rep6


title: tumor, Vec-X715


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.2n.filtered_contig_annotations.csv.gz


title: tumor, Vec-X712


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.6n.filtered_contig_annotations.csv.gz

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


title: Contrl, 1, bulk RNA

value: retina

value: organoids derived from hPSCs

value: control


title: Q-input

city: Beijing

first: Tianjiao

last: Sun

address: Balizhuang Street

institute: Peking University Cancer Hospital and Institute

data_processing:
Raw sequencing data generated from Illumina HiSeq was converted into fastq files, which were checked by FastQC (https://github.com/s-andrews/FastQC). Raw single-end 50-bp sequencing reads were mapped to human genome build hg38 using Bowtie2 v.2.2.6 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) with standard settings. Only unique non-duplicate reads were retained. Peaks, areas where there were significantly more enriched reads mapped in the ChIP sample than the input, were determined using MACS with the parameters of P value 0.00001 and false discovery rate 5%. The Bedtools software was used to determine the genes closest to H3K27ac-binding peaks and to calculate the distance between these peaks from TSS of their closest genes
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
ChIP was performed with anti-H3K27ac antibody. Briefly, Huh-7 cells stably expressing MCCC2K269R and MCCC2K269Q were cross-linked with 1% formaldehyde for 15 minutes at room temperature and stop cross-link by glycine.
Chromatin was fragmented to an average size of approximately 300–500 bp by sonication. Then, fragmented chromatin was incubated with 5μg of anti-H3K27ac antibody and nonspecific rabbit IgG at 4°C overnight. After overnight immunoprecipitation, each sample was washed with washing buffers. The precipitated products were then eluted with elution buffer at 65°C and reversed the cross-link with 5 mol/L NaCl at 65°C overnight. The DNA was finally purified by PCR purification kit (Qiagen). The chipped DNA was ligated with adaptors. After purification, PCR reaction was done with adaptor-ligated DNA and index primer for multiplexing sequencing. Library was purified by using magnetic beads to remove all reaction components. Qualities of libraries were checked by High Sensitivity DNA Assay (Agilent Technologies) and sequenced on an Illumina Nova 6,000 sequencer.

value: Hepatocellular carcinoma cells


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.5n.filtered_contig_annotations.csv.gz

value: BALB/c

value: Female

value: 6-8 weeks


title: P0095EDR00, EoE distal, rep8

value: Esophageal mucosal biopsy


title: Q-AC


title: tumor, Vec-X710


title: P0033EDR00, EoE distal, rep3

value: Distal


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.4n.filtered_contig_annotations.csv.gz


title: Q-1

data_processing:
Raw sequence generated from Illumina Nova 6,000 was converted into fastq files and demultiplexed with Trim galore software v.0.6.7 (https://github.com/FelixKrueger/TrimGalore/).After checking quality with the FastQC tool, raw sequencing reads were aligned to human genome build hg38 using STAR v.2.7.10a (https://github.com/alexdobin/STAR/) with standard settings. Mapped reads were converted to BAM format with Samtools v.1.7(https://github.com/samtools/samtools), following quantified by feature Counts v.2.0.1(https://subread.sourceforge.net/) an analyzed for DEGs with the threshold at FDR<0.05, |log2 (fold change) |>1 by DESeq2 v.1.34.0 (https://bioconductor.org/packages/DESeq2/).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: cell line

extract_protocol:
RNA was extracted using the trlzol method
Illumina's Truseq RNA library building method.

value: cell line

value: MCCC2 K269Q


title: R-1

value: MCCC2 K269R


title: R-2


title: Q-2


title: tumor, Vec-X708

value: EL4 tumor


title: P0030EDR00, EoE distal, rep2

value: Eosinophilic Esophagitis


title: R-AC


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

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.3n.filtered_contig_annotations.csv.gz

value: Draining lymph node

value: CD90+CD44+ T cells


title: P0012EDR00, EoE distal, rep1


title: KO.TR.20

city: Verona

first: Marzia

last: Rossato

state: Italy

address: Strada Le Grazie,15

department: Department of Biotechnology

country: Italy

institute: University of Verona

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
Trimmed sequence reads were mapped to GRCm38 with STAR
Read count extraction was performed using RSEM
Differential expression analysis was performed using DESeq2
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: cerebral cortex

extract_protocol:
Cerebral cortices were quickly dissected from the brains of untreated and treated WT and Mecp2 KO animals (P60) and frozen on dry ice. Total RNA was extracted using Purezol (Bio-Rad). RNA integrity was assessed using the RNA 6000 Nano Kit on a Bioanalyzer (Agilent Technologies). RNA samples were quantified using the Qubit RNA BR Assay Kit (Thermo Fisher Scientific). All 24 samples (6 for each experimental group) met the requirement for RNA-sequencing (RIN >7).
Illumina RNA-seq libraries were generated using the TruSeq stranded mRNA ligation kit (Illumina) from 1000 ng of total RNA, according to manufacturer’s instruction.

treatment_protocol: Mice were intranasally administered with rhNGF or PBS (vehicle)

value: cerebral cortex

value: rhNGF

tag: condition

value: Mecp2 KO


title: P0049EDR00, EoE distal, rep5


title: P0048EDR00, EoE distal, rep4


title: Anti-PDL1, replicate 1, lymph node, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.1n.filtered_contig_annotations.csv.gz

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


title: HCE042EDR00, HC distal, rep8

value: Healthy


title: Control, replicate 3, lymph node, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.4n.filtered_contig_annotations.csv.gz

value: BALB/c

value: anti-gp120 mIgG2a, 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week


title: H128-0-Input,ChIP

city: Guangzhou

first: Hong

last: Wang

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

institute: Sun Yat-sen University

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01.bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: Homo sapiens

growth_protocol: SCLC cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
sample 1-6:Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
sample 1-6:ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: H128 cells were treated with HX531 for 48 h.

value: Homo sapiens

value: tumor cells


title: KO.UT.8

value: untreated (PBS)


title: H128-10-H3K9me2, ChIP


title: WT.UT.3

value: WT


title: Control, replicate 5, lymph node, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.6n.filtered_contig_annotations.csv.gz

value: Female

value: 6-8 weeks


title: HCE040EDR00, HC distal, rep7

value: Esophageal mucosal biopsy

value: Distal


title: H128-0-H3K9me2, ChIP


title: R-input

value: Hepatocellular carcinoma cells


title: Control, replicate 4, lymph node, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.5n.filtered_contig_annotations.csv.gz

value: Draining lymph node

value: CD90+CD44+ T cells


title: HCE038EDR00, HC distal, rep6


title: WT.TR.15

value: cerebral cortex

value: rhNGF


title: H128-10-H3K4me2, ChIP


title: HCE037EDR00, HC distal, rep5


title: Control, replicate 2, lymph node, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.3n.filtered_contig_annotations.csv.gz


title: WT.TR.14


title: HCE036EDR00, HC distal, rep4


title: WT.UT.2


title: Control, replicate 1, lymph node, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.2n.filtered_contig_annotations.csv.gz


title: H128-0-H3K4me2, ChIP


title: HCE035EDR00, HC distal, rep3


title: WT.TR.18


title: H128-10-Input, ChIP


title: Combo+FTY720, replicate 4, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S5.7t.filtered_contig_annotations.csv.gz

source_name: Tumor

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

value: Tumor

value: CD90+ T cells


title: KO.TR.24

value: Mecp2 KO


title: HCE034EDR00, HC distal, rep2

value: Healthy


title: Combo+FTY720, replicate 3, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S5.5t.filtered_contig_annotations.csv.gz

value: BALB/c


title: 5_PAH_PASMC_M200

city: quebec

first: Sebastien

last: Bonnet

address: 2725 Ch Ste-Foy, Québec, QC G1V 4G5

country: Canada

institute: IUCPQ

data_processing:
FASTQ files from the Novaseq instrument were examined for sequencing quality and adapters contamination using MultiQC. Reads with low quality were removed prior to further analyses and adapters sequences were removed from the reads using Trimmomatic. Alignment of trimmed reads to the human genome (hg38) was performed using the STAR aligner software and the data was converted to gene-level expression using RSEM. Gene counts from the datasets were then used to assess differential expression using DESEQ2
Assembly: hg38
Supplementary files format and content: CSV files containing the counts of each sample

source_name: Pulmonary artery smooth muscle cell (PASMC)

extract_protocol:
RNA was isolated from cells using the Direct-zol RNA MicroPrep Kit (Zymo Research) according to the manufacturer’s instructions
RNA libraries were prepared using the TruSeq® Stranded mRNA Library

tag: disease state

value: PAH


title: HCE032EDR00, HC distal, rep1


title: 5_PAH_PASMC_MR5854_4uM

value: Pulmonary artery smooth muscle cell (PASMC)


title: KO.UT.12

value: untreated (PBS)


title: WT.UT.6

value: WT


title: Combo+FTY720, replicate 1, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S5.2t.filtered_contig_annotations.csv.gz

value: Female

value: 6-8 weeks


title: Combo+FTY720, replicate 2, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S5.3t.filtered_contig_annotations.csv.gz


title: 4_PAH_PASMC_Veh

value: Veh (DMSO)


title: P0263EPR00, EoE proximal, rep19

value: Esophageal mucosal biopsy

value: Proximal

value: Eosinophilic Esophagitis


title: P0259EPR00, EoE proximal, rep18


title: 5_PAH_PASMC_IgG

value: IgG


title: WT.UT.5

value: cerebral cortex


title: KO.TR.23

value: rhNGF


title: Combo, replicate 4, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S4.6t.filtered_contig_annotations.csv.gz

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

value: Tumor

value: CD90+ T cells


title: P0207EPR00, EoE proximal, rep17


title: 5_PAH_PASMC_Veh


title: Combo, replicate 3, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S4.5t.filtered_contig_annotations.csv.gz

value: BALB/c


title: KO.UT.11

value: Mecp2 KO


title: 4_PAH_PASMC_MR5854_4uM

value: Pulmonary artery smooth muscle cell (PASMC)

value: PAH


title: Combo, replicate 2, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S4.3t.filtered_contig_annotations.csv.gz


title: 4_PAH_PASMC_M200


title: KO.TR.22


title: P0205EPR00, EoE proximal, rep16


title: Combo, replicate 1, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S4.2t.filtered_contig_annotations.csv.gz


title: WT.TR.17

value: WT


title: 4_PAH_PASMC_IgG


title: P0159EPR00, EoE proximal, rep14


title: P0199EPR00, EoE proximal, rep15


title: 3_PAH_PASMC_Veh


title: Anti-TIGIT, replicate 6, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.7t.filtered_contig_annotations.csv.gz

value: Female

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


title: KO.UT.9

value: untreated (PBS)


title: 3_PAH_PASMC_MR5854_4uM


title: Anti-TIGIT, replicate 5, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.6t.filtered_contig_annotations.csv.gz

value: 6-8 weeks


title: KO.UT.7


title: 3_PAH_PASMC_M200


title: P0137EPR00, EoE proximal, rep13

value: Esophageal mucosal biopsy

value: Proximal


title: P0128EPR00, EoE proximal, rep12

value: Eosinophilic Esophagitis


title: Anti-TIGIT, replicate 1, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.1t.filtered_contig_annotations.csv.gz


title: Anti-TIGIT, replicate 4, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.4t.filtered_contig_annotations.csv.gz


title: WT.UT.1

value: cerebral cortex


title: P0126EPR00, EoE proximal, rep11


title: 3_PAH_PASMC_IgG

value: IgG


title: P0123EPR00, EoE proximal, rep10


title: WT.TR.13

value: rhNGF


title: KO.TR.19


title: 2_PAH_PASMC_M200


title: Anti-TIGIT, replicate 2, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.2t.filtered_contig_annotations.csv.gz

value: Tumor


title: Anti-TIGIT, replicate 3, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S3.3t.filtered_contig_annotations.csv.gz

value: CD90+ T cells


title: P0095EPR00, EoE proximal, rep8


title: WT.UT.4


title: 2_PAH_PASMC_MR5854_4uM


title: Anti-PDL1, replicate 5, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.6t.filtered_contig_annotations.csv.gz

value: BALB/c

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


title: 2_PAH_PASMC_IgG

value: Pulmonary artery smooth muscle cell (PASMC)


title: KO.UT.10

value: Mecp2 KO


title: WT.TR.16

value: WT


title: Anti-PDL1, replicate 4, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.5t.filtered_contig_annotations.csv.gz

value: Female


title: 1_PAH_PASMC_Veh

value: PAH

value: Veh (DMSO)


title: P0061EPR00, EoE proximal, rep6


title: Anti-PDL1, replicate 3, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.4t.filtered_contig_annotations.csv.gz

value: 6-8 weeks


title: 1_PAH_PASMC_MR5854_4uM


title: KO.TR.21


title: P0048EPR00, EoE proximal, rep4

value: Esophageal mucosal biopsy


title: Anti-PDL1, replicate 1, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.1t.filtered_contig_annotations.csv.gz


title: P0116EPR00, EoE proximal, rep9

value: Proximal


title: 1_PAH_PASMC_M200


title: Anti-PDL1, replicate 2, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S2.3t.filtered_contig_annotations.csv.gz


title: 2_PAH_PASMC_Veh


title: P0033EPR00, EoE proximal, rep3

value: Eosinophilic Esophagitis


title: Littermate TNF negative control mice, synovium_scRNA

city: Rochester

first: Benjamin

last: Korman

state: NY

address: 601 Elmwood Avenue, Box 695

institute: AIR

description: 10x Genomics

data_processing:
Demultiplexing and Counting were made using 10X provided cellranger-7.0.1. Samples were aligned to 10X provided reference refdata-gex-mm10-2020-A
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: synovium

extract_protocol:
Single-cell suspensions were obtained from the lungs and synovium of TNF-Tg and WT mice (n=3-5 per genotype in lung, 5-10 per genotype in synovium) by a combination of mechanical dissociation and enzymatic digestion.  Tissue was pooled by group and dissociated with GentleMACS Octo Dissociator (Miltenyi Biotec) followed by enzymatic digestion with Collagenase A (COLLA-RO, Roche), Elastase (Worthington, ESL LS002292) and Dispase II (Corning 354235) for lung and type II collagenase (Worthington, CLS-2 LS004174) for synovium. 100,000-300,000 cells were collected and submitted for single cell capture.
Single-cell RNA-seq libraries were prepared using Chromium Single-Cell 3′ Library & Gel Bead Kit (version 1.1; 10x Genomics).

value: synovium

value: 4 months


title: Control, replicate 3, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.4t.filtered_contig_annotations.csv.gz

value: anti-gp120 mIgG2a, 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week


title: Littermate TNF negative control mice, lung_scRNA

description: 10x Genomics

source_name: lung

value: lung


title: P0030EPR00, EoE proximal, rep2


title: Control, replicate 5, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.6t.filtered_contig_annotations.csv.gz

value: Tumor

value: CD90+ T cells


title: hTNFtg mice, lung_scRNA

description: 10x Genomics


title: P0012EPR00, EoE proximal, rep1


title: P0065EPR00, EoE proximal, rep7


title: Control, replicate 4, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.5t.filtered_contig_annotations.csv.gz

value: BALB/c


title: HCE042EPR00, HC proximal, rep8

value: Healthy


title: BMDM, Pex5KO, 72H myelin debris, replicate 3

city: Houston

first: Jian

last: Hu

state: TX

address: 1881 East Rd, South Campus Research Building 3

department: Cancer Biology

institute: University of Texas MD Anderson Cancer Center

description: gene_count_matrix column name: KO72M3

data_processing:
Workflow was adopted from StringTie protocol to assess expression of known transcripts from a given reference annotation file.
Sequenced reads were mapped to GrCm38/mm10 using HISAT2 (v2.1.0, options included: --dta).
SAM outputs files were sorted and converted to BAM using Samtools (options included: -sort).
Aligned reads were used to estimate the abundance of known transcripts (read coverage tables) from a reference annotation file (GRCm38.101.gtf) using StringTie (v2.1.1, options included -e, -B, -G).
A matrix of read counts mapped to known genomic features was derived from the read coverage tables generated by StringTie using prepDE.py (options included: -i) Python script. prepDE.py derives hypothetical read counts using the formula: reads_per_transcript = coverage * transcript_len / read_len. Read counts were then fed into DESeq2 in R for differential gene expression analysis.
Assembly: mm10
Supplementary files format and content: comma-seperated values file with raw counts per sample

source_name: Bone marrow derived macrophages

growth_protocol: Bone marrow was harvested from adult (10 wk) Control and Pex5KO male littermates and cultured under BMDM differentiating conditions for 7 days prior to beginning myelin debris challenge. BMDM were cultured in RPMI buffer with 10% fetal bovine serum and 15% L929 cell conditioned medium with penicillin/streptomycin and 1 uM of 4OH-tamoxifen to induce gene knockout. Medium was changed 3 days post harvest and every 2 days therafter.

extract_protocol:
Plated BMDMs were washed with sterile D-PBS twice and directly lysed with RLT lysis buffer (Qiagen, 79216) supplemented with 2-mercaptoethanol (1:100 dilution). Lysate was  homogenized using QIAshredder columns (Qiagen, 79656) per manufacturer’s instructions. Following homogenization, RNA was purified using the Qiagen RNeasy mini columns (Qiagen, 74106) with DNA on-column digestion included using RNase-free DNase I (Qiagen, 79254) per manufacturer’s instructions. Total RNA was eluted in nuclease free water. Total RNA with RIN score > 7.0 were submitted for sequencing
Libraries were generated from total RNA using the NEBNext Ultra II RNA library prep kit (New England Biolabs) per manufacturer's instructions.

treatment_protocol: After 7 days culture BMDM received myelin debris challenge as follows. BMDM medium was supplemented with 0.5 mg/mL of purified myelin debris (harvested from wildtype C57BL/6 adult mice). BMDM were incubated with myelin debris-supplemented medium for 24 or 72 hours.

value: Bone marrow derived macrophages

value: Pex5 knockout

value: Myelin debris, 0.5 mg/mL

tag: time

value: 72 Hours

value: male


title: P0049EPR00, EoE proximal, rep5


title: BMDM, Pex5KO, 72H myelin debris, replicate 2

description: gene_count_matrix column name: KO72M2


title: hTNFtg mice, synovium_scRNA

description: 10x Genomics


title: HCE040EPR00, HC proximal, rep7


title: hiPSC-CMs; treated with guide RNA to induce Gln3924Glu (Q3924E) mutation in Ryr2; rep 1

city: Charleston

first: Allison

last: Trouten

address: 173 Ashley Ave Room BSB 642

department: Regenerative Medicine and Cell Biology

institute: Medical University of South Carolina

data_processing:
Raw fastq files were aligned using STAR 2.7.6a aligner
Differential expression analysis run using DEseq2 1.44.0
Heatmaps created using pheatmap (1.0.12)
Other plots made via ggplot2 3.5.1
Gene ontology assessment via enrichGO function via clusterprofiler package (4.12.2)
Assembly: hg38
Supplementary files format and content: Tab delimited CSV file includes normalized raw counts for each sample
Supplementary files format and content: Compressed fastq files include raw unaligned sequencing files

source_name: K3 stem cells

growth_protocol: K3 stem cells were obtained and maintained in Stemflex medium

extract_protocol:
Standard Trizol phenol chloroform extraction
Total RNA samples were sent to Novogene for library prep and sequencing (mRNA library preparation poly A enrichment)

treatment_protocol: Cardiogenic differentiation was induced by treating dissociated induced pluripotent stem cells (iPSCs) with CHIR99021 (a GSK3β inhibitor) for 24 h in RPMI/B-27 without insulin. After three days of CHIR99021 treatment, IWR1 (a Wnt signaling inhibitor) was added culture media for 48 h. Cells were then maintained in RPMI/B-27 media without insulin and switched to RPMI/B-27 medium containing insulin (B27(+) medium) when majority of the cells started beating.

value: K3 stem cells

value: Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs)

value: Q3924E mutant

value: cardiogenic differentiation of stem cells to iCMs


title: Control, replicate 1, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.2t.filtered_contig_annotations.csv.gz

value: Female

value: 6-8 weeks


title: 1_PAH_PASMC_IgG

value: Pulmonary artery smooth muscle cell (PASMC)

value: PAH

value: IgG


title: hiPSC-CMs; treated with guide RNA to induce Glu3848Ala (E3848A) mutation in Ryr2, rep 2

value: E3848A mutant


title: HCE038EPR00, HC proximal, rep6

value: Esophageal mucosal biopsy

value: Proximal


title: MTP12, Input

city: Macau

first: Lihua

last: Mo

address: Taipa

institute: University of Macau

data_processing:
The quality of raw data was checked using the FastQC program.
Raw reads were aligned to the mouse reference genome GRCm38.84 using bowtie2 software.
Alignment output from bowtie2 was converted to BAM format using the samtools software suite.
For ChIPseq data visualization, mapped reads were extended to 200 bp in the 5’->3’ direction using the ‘macs2 pileup’ command and scaled to 1 million mapped reads using the ‘macs2 bdgopt’ command from the MACS2 tool.
UCSC Kent utils’ programs ‘bedSort’ and ‘bedGraphToBigWig’ were used to convert the genome coverage files from BedGraph to BigWig format.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Mammary gland

extract_protocol:
The fresh isolated mouse mammary epithelial cells were crosslinked by 1% (v/v) formaldehyde solution for 5 minutes at room temperature. After quenching and cell lysis, chromatin was sonicated using a truChIP Ultra-Low Chromatin Shearing Kit (Covaris, USA, 520154)
The DNA library was prepared with the TruSeq ChIP Sample Prep Kit (illumina, USA, 15034288, 15034289).

value: Mammary gland

value: Mouse mammary epithelial cell


title: WTP12, Input


title: hiPSC-CMs; no guide RNA; rep 2


title: hiPSC-CMs; treated with guide RNA to induce Glu3848Ala (E3848A) mutation in Ryr2, rep 1


title: BMDM, Pex5KO, 24H myelin debris, replicate 3

description: gene_count_matrix column name: KO24M3

value: Bone marrow derived macrophages

value: Pex5 knockout

value: Myelin debris, 0.5 mg/mL

value: 24 Hours


title: hiPSC-CMs; no guide RNA; rep 1

value: K3 stem cells

value: Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs)


title: HCE037EPR00, HC proximal, rep5

value: Healthy


title: HCE036EPR00, HC proximal, rep4


title: BMDM, Pex5KO, 24H myelin debris, replicate 2

description: gene_count_matrix column name: KO24M2

value: male


title: BMDM, Pex5KO, 24H myelin debris, replicate 1

description: gene_count_matrix column name: KO24M1


title: HCE035EPR00, HC proximal, rep3


title: H3K4me3 ChIP-seq in MT sample


title: BMDM, Pex5KO, untreated, replicate 2

description: gene_count_matrix column name: KOB2

value: Empty


title: BMDM, Pex5KO, 72H myelin debris, replicate 1

description: gene_count_matrix column name: KO72M1

value: 72 Hours


title: WT_Line3_2_UT

city: Philadelphia

first: Aaron

last: Haeusler

address: 900 Walnut Street, JHN-Suite 410

department: Neuroscience

institute: Thomas Jefferson University

data_processing:
Data was generated by Novogene and subjected to QC analysis according to their established protocols. Cleaned reads were obtained by removing raw reads with adapters, poly_N, and low quality.
Cleaned reads were aligned to hg38 using STAR(v.2.7.10b)
Read summarization was performed on .bam files to obtain a featurecounts file using the R package Rsubread (v.2.12.3)
Differential Expression analysis was conducted with DESeq2(v.1.36.0)
Assembly: hg38
Supplementary files format and content: LTG_KCL_featurecounts.txt: tab-delimited file includes feature counts from Rsubread(v.2.12.3)
Supplementary files format and content: LTG_TEA_featurecounts.txt: tab-delimited file includes feature counts from Rsubread(v.2.12.3)

extract_protocol:
RNA was isolated using RNeasy Plus Mini Kit (Qiagen), and cDNA was synthesized from 500 ng RNA using a QuantiTect Reverse Transcription Kit (Qiagen)
Library preparation and RNA-sequencing were performed by third-party company, Novogene. RNA libraries for RNA-seq were prepared following Novogene's protocols and sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: UT


title: H3K27Ac ChIP-seq in MT sample


title: hiPSC-CMs; treated with guide RNA to induce Gln3924Glu (Q3924E) mutation in Ryr2; rep 2

value: Q3924E mutant

value: cardiogenic differentiation of stem cells to iCMs


title: Control, replicate 2, tumor, scTCR-seq

description:
VDJ-enriched library: read1 file contains cell barcode and UMI; read2 file contains transcript
S1.3t.filtered_contig_annotations.csv.gz

value: BALB/c

value: Female

value: 6-8 weeks

value: anti-gp120 mIgG2a, 10 mg/kg iv x 1, 10 mg/kg ip x 2, over 1 week

value: Tumor

value: CD90+ T cells


title: HCE034EPR00, HC proximal, rep2

value: Esophageal mucosal biopsy

value: Proximal


title: WT_Line3_1_UT


title: ChIP-seq of ER-alpha in MT sample

value: Mammary gland

value: Mouse mammary epithelial cell


title: H3K27Ac ChIP-seq in WT sample


title: HCE032EPR00, HC proximal, rep1

value: Healthy


title: BMDM, Control, 72H myelin debris, replicate 3

description: gene_count_matrix column name: Cont72M3

value: Bone marrow derived macrophages

value: WT

value: Myelin debris, 0.5 mg/mL

value: male


title: H3K4me3 ChIP-seq in WT sample


title: RA-FLSs cells, sh-NCL3, Day 7

city: Hong Kong

first: chunhao

last: cao

address: Hong Kong

department: School of Chinese Medicine

country: Hong Kong

institute: Hong Kong Baptist University

data_processing:
1. **Quality Control**: Raw sequencing reads were assessed using FastQC to check the quality of the data.
2. **Trimming**: Adapters and low-quality bases were removed using Trimmomatic.
3. **Alignment**: Cleaned reads were aligned to the reference genome (Homo sapiens GRCh38) using HISAT2.
4. **Conversion**: SAM files generated by HISAT2 were converted to BAM files using SAMtools.
5. **Feature Counting**: Gene-level quantification was performed using featureCounts.
Assembly: hg38
Supplementary files format and content: fatqc raw data
Supplementary files format and content: Text files generated by featureCounts containing the read counts per gene for each sample.

source_name: synovial tissue

growth_protocol: RA-FLSs were maintained in DEME supplemented with 20%  fetal bovine serum (FBS) and  1% penicillin-streptomycin. And  cells were maintained at 37°C humid atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using TransZol UP Plus RNA Kit.
RNA quality was assessed using the Agilent 2100 Bioanalyzer. High-quality RNA samples with RIN (RNA Integrity Number) > 7.0 were used for library construction. Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina, following the manufacturer's instructions. Indexed libraries were then sequenced on an Illumina HiSeq 4000 platform to generate 150 bp paired-end reads.

treatment_protocol: Stable NCL knockdown RA-FLSs were generated using lentiviruses expressing human nucleolin shRNA  targeting the nucleolin, cloned in pLKO.1 vector. Transduced cells were selected with puromycin.

value: synovial tissue

value: RA-FLSs

value: fibroblast-like synoviocytes cells

value: NCL knockdown


title: BMDM, Control, 72H myelin debris, replicate 2

description: gene_count_matrix column name: Cont72M2

value: 72 Hours


title: WT_Line3_1_TEA

value: TEA


title: RA-FLSs cells, sh-NCL1, Day 7


title: ChIP-seq of ER-alpha in WT sample


title: BMDM, Control, 72H myelin debris, replicate 1

description: gene_count_matrix column name: Cont72M1


title: RA-FLSs cells, sh-NCL2, Day 7


title: WT_Line2_2_UT

value: UT


title: WT_Line3_2_TTX

value: TTX


title: BMDM, Control, 24H myelin debris, replicate 3

description: gene_count_matrix column name: Cont24M3

value: 24 Hours


title: WT_Line2_2_TTX


title: CD11b+ MG-WT-rep2

city: College Station

first: Jianrong

address: VBEC Receiving, VICI Bldg Rm127, 4458 TAMUS

department: Department of Veterinary Integrative Biosciences

institute: Texas A&M University

data_processing:
Illumina HiSeq 2500 used for basecalling.
A total of 286 million reads were mapped against GRCm38/mm10 assembly using TopHat version 2.0.13 with default settings, out of which a total of 274 million reads (approximately 95%) were aligned to the reference genome.
Differential expression analysis of all the samples was done using DESeq2. Between 8 million and 32 million reads were generated per sample.
Genome_build: mm10
Supplementary_files_format_and_content: normalized expression data

source_name: sorted CD11b+ from P8 forebrain

extract_protocol:
At P6, toe clips were obtained to determine genotypes. At P8, the mice were anesthetized with ketamine and xylazine, and transcardially perfused with 10 ml PBS.  The brains of pups with the same genotype were pooled and digested in 5 ml Stempro Accutase (A11105-01; Life Technologies, Carlsbad, CA) at 37°C for 30 min. Every 5 min during the incubation, the tube was inversed several times. After the 30-min incubation, the enzyme activity of Accutase was blocked by addition of 2 ml FBS. The digested tissue was then filtered through a 70-μm cell strainer to make a single cell suspension. Cells were centrifuged and resuspended in 5 ml 35% Percoll (P4937; Sigma-Aldrich) in PBS. 3 ml of 70% Percoll was slowly added to the bottom using a Pasteur pipette. The tubes were then centrifuged at 2,000 × g for 20 min at 18°C with the brake set to 0. The top lipid/myelin layer was quickly removed using a pipette. Cells in the interphase between the 35% and 70% Percoll layers were harvested with a Pasteur pipette, washed by centrifugation and resuspended in ice-cold PBS. The cells were stained with α-ms CD11b APC (#17-0112; eBioscience), washed, and resuspended in PBS containing propidium iodide and 1 mM EDTA. CD11b+PI- cells were FACS-sorted and resuspended in 500 µl Tri Reagent, flash frozen, and stored at -80°C until use. RNA was extracted with the Directzol RNA isolating kit (Zymed).  Samples with high RNA integrity number (>8) were used for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols. Each sample (200 ng) was poly-A selected, fragmented, and library prepared using the TruSeqRNASample Prep Kit (Illumina).

value: CD11b+ forebrain

value: postnatal 8

value: untreated


title: RA-FLSs cells, sh-NC3, Day 7


title: BMDM, Control, 24H myelin debris, replicate 2

description: gene_count_matrix column name: Cont24M2


title: RA-FLSs cells, sh-NC2, Day 7


title: WT_Line3_2_TEA

value: Healthy


title: CD11b+ MG-WT-rep1


title: BMDM, Control, 24H myelin debris, replicate 1

description: gene_count_matrix column name: Cont24M1

value: Bone marrow derived macrophages


title: WT_Line2_1_UT


title: RA-FLSs cells, sh-NC1, Day 7

value: WT


title: WT_Line2_1_TTX


title: BMDM, Control, untreated, replicate 2

description: gene_count_matrix column name: ContB2

value: Empty


title: WT_Line3_1_TTX


title: CD11b+ MG-KO-rep3


title: ChIP-seq of Flag tagged BRCA1 in WT sample

value: Mammary gland

value: Mouse mammary epithelial cell


title: WT_Line2_1_TEA


title: CD11b+ MG-KO-rep1


title: WholeBlood-MDD-M-913

city: Strasbourg

first: Pierre-Eric

last: Lutz

address: 8 allée du général Rouvillois

country: France

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

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

source_name: Whole blood

growth_protocol: Not applicable

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

treatment_protocol: Not applicable

value: Whole blood

tag: group

value: MDD

value: Male


title: WholeBlood-MDD-M-901


title: BMDM, Control, untreated, replicate 1

description: gene_count_matrix column name: ContB1

value: male


title: WT_Line1_2_UT


title: WholeBlood-MDD-M-823


title: BMDM, Pex5KO, untreated, replicate 1

description: gene_count_matrix column name: KOB1

value: Pex5 knockout


title: WT_Line2_2_TEA

value: TEA


title: WT_Line1_2_TEA


title: Lung tissues in strategy2, CasRx + sgRNA5, 6 wpi, rep 3

city: Bengbu

first: Xiaojing

state: China

address: No 287, Changhuai Road

institute: The first affiliated hospital of Bengbu Medical college

description:
gene_exp_strategy2_6 wpi.xls
ensembl_blast_potential_off-target_genes.xls

data_processing:
Trimmomatictools  v 0.36
The clean reads were obtained after removal of reads containing adapter, ploy-N and at low quality from raw data Trimmomatic (base quality less than Q20) and filtered by length (less than 52).
Paired-end reads were aligned to the mouse reference genome mm10/hg19/rn6 with HISAT2
HTSeq v0.12.4 was used to count the reads numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: Excel files include raw counts and TPM values for each sample
Supplementary files format and content: Excel file includes potential off-target genes  for all of the samples

source_name: Lung

extract_protocol:
Total RNA was isolated from lung tissues of mice using TRIZOL reagent,and the quantity and integrity of RNA yield was assessed by using the K5500(BeijingKaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately.
The mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA), and then fragmented to approximately 200bp. Subsequently, the RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycleaccording to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina. The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit (Thermo Fisher Scientific, USA).

treatment_protocol:
In the above SAMPLES section, sample 1 ~ sample 9 were from mice administrated with AAV-Luci-Cre to induce the tumorigenesis and simultaneously co-injected with the respective AAV therapeutic vectors for two weeks.
In the above SAMPLES section, sample 10 ~ sample 18 were from mice administrated with AAV-Luci-Cre to induce the tumorigenesis and simultaneously co-injected with the respective AAV therapeutic vectors for twelve weeks.
In the above SAMPLES section, sample 19 ~ sample 28 were from tumors developed over a six-week period and subsequently treated with the respective AAV therapeutic vectors for an additional  six weeks.

value: Lung

value: KrasLSL-G12D; Tp53fl/fl (KP)

tag: administration strategy

value: strategy 2:tumor formation and then treatment

value: AAV-CasRx + sgRNA5

tag: time of_therapeutic_duration

value: 6 weeks


title: WholeBlood-MDD-M-813

tag: tissue


title: Empty Vector, ZFP-ChIP biological replicate 2

city: Freiburg

first: Patrick

middle: Piero

last: Bovio

address: Albertstr. 19

department: Department of Molecular Embryology

institute: Albert-Ludwigs University Freiburg, Institute of Anatomy and Cell Biology

description:
F_Ctrl_ChIP_r2
processed data file:
Ctrl R2 ChIP vs Input log2 SES norm.bigwig

data_processing:
HiSeq Ctrl Software version 2.2.58
TrimGalore: adaptor removal
trim_galore  --phred33   --quality 15  --stringency 3  -e 0.1  --length 20
Bowtie2: Mapping on UCSC-main RefSeq GRCm38/mm10
MarkDuplicates: duplicate removal
bamCompare: log2 (ratio of the number of reads) of ChIP to input, pseudocount of 1 and a bin size of 25 bp, signal extraction scaling (SES) for data normalization.
Genome_build: UCSC-main RefSeq GRCm38/mm10
Supplementary_files_format_and_content: bigwig

source_name: Empty Vector_ZFP-ChIP

growth_protocol: V6.5 mESC were grown on a monolayer of mytomicin-c-inactivated mouse embryonic fibroblasts (MEFs) in complete mESC medium (DMEM, 15 % FBS, 1 x non-essential amino acids, 1 x glutamax, 1 x penicillin/streptomycin, 5 μl per 500 ml ß-mercaptoethanol, 10^3 U ml^-1 leukemia inhibitor factor (LIF)). Before harvesting mESC were transferred to gelatin-coated plates after at least three passages until MEFs were not visible.

extract_protocol:
MYC-Tag (9B11) antibody (#2276, Cell Signaling) was used with the NEXSON (Arrigoni L, Richter AS, Betancourt E, et al. Standardizing chromatin research: a simple and universal method for ChIP-seq. Nucleic Acids Res. 2016;44(7):e67. doi:10.1093/nar/gkv1495) ChIP protocol to pull down ZFP982-MYC and empty vector.
Diagenode, Belgium

treatment_protocol: For overexpression (OE) of Zfp982 in mESC the pEXP-Zfp982 plasmid (NovoPro, Catalog Number: 767203-1) containing the Zfp982 cDNA was used. The pEXP-empty vector was also used as a control. pEXP-Zfp982 (ZFP982-MYC tagged expression vector) and pEXP-empty vectors were transfected using Lipofectamine 2000 (Invitrogen) according to the manufacturer's instructions. Briefly, mESC were trypsinized, pelleted by centrifugation, and resuspended into a single‐cell suspension. Subsequently, a total of 1×10^6 mESC were combined with freshly prepared transfection complexes and plated down in 6 cm diameter dishes. Cells were treated with 700 µg/ml G418 (Invitrogen; Thermo Fisher Scientific, Inc.) for one week to select transfected cells expressing pEXP-Zfp982 and pEXP-empty vector. RT-qPCR analyses and immunoblots were performed using the G418-resistant clones to confirm overexpression and knock-down of Zfp982 expression. The morphology of cells was also evaluated after one week.

tag: cell type

value: mESC

tag: genotype/variation

value: pEXP-empty vector

tag: chip antibody


title: Lung tissues in strategy2, CasRx + sgRNA5, 6 wpi, rep 1

tag: genotype

tag: treatment


title: ZFP over expression, Input biological replicate 2

description:
G_OE_Input_r2
processed data file:
OE R2 ChIP vs Input log2 SES norm.bigwig

source_name: ZFP over expression_Input

value: pEXP-Zfp982 (ZFP982-MYC tagged expression vector)


title: Empty Vector, Input biological replicate 2

description:
H_Ctrl_Input_r2
processed data file:
Ctrl R2 ChIP vs Input log2 SES norm.bigwig

source_name: Empty Vector_Input


title: CD11b+ MG-KO-rep2

value: CD11b+ forebrain

value: postnatal 8

value: untreated


title: Lung tissues in strategy2, CasRx + sgRNA5, 6 wpi, rep 2


title: WT_Line1_2_TTX

value: Healthy

value: TTX


title: WholeBlood-MDD-M-633

value: Whole blood

value: MDD

value: Male


title: WT_Line1_1_UT

value: UT


title: ZFP over expression, ZFP-ChIP biological replicate 2

description:
E_OE_ChIP_r2
processed data file:
OE R2 ChIP vs Input log2 SES norm.bigwig

source_name: ZFP over expression_ZFP-ChIP

value: MYC-Tag (9B11) antibody (#2276, Cell Signaling)


title: WT_Line1_1_TTX


title: WholeBlood-MDD-M-631


title: Lung tissues in strategy2, CasRx + sgNC, 6 wpi, rep 6

value: Lung

value: KrasLSL-G12D; Tp53fl/fl (KP)

value: AAV-CasRx + sgNC


title: Empty Vector, Input biological replicate 1

description:
D_Ctrl_Input_r1
processed data file:
Ctrl R1 ChIP vs Input log2 SES norm.bigwig


title: Lung tissues in strategy2, CasRx + sgNC, 6 wpi, rep 5

value: strategy 2:tumor formation and then treatment

value: 6 weeks


title: WholeBlood-MDD-M-621


title: WT_Line1_1_TEA

value: TEA


title: ZFP over expression, Input biological replicate 1

description:
C_OE_Input_r1
processed data file:
OE R1 ChIP vs Input log2 SES norm.bigwig

value: mESC

value: pEXP-Zfp982 (ZFP982-MYC tagged expression vector)


title: C9_Line3_2_UT


title: WholeBlood-MDD-M-619


title: Lung tissues in strategy2, CasRx + sgNC, 6 wpi, rep 4


title: C9_Line3_2_TTX


title: Lung tissues in strategy2, CasRx + sgNC, 6 wpi, rep 3


title: WholeBlood-MDD-M-608


title: ZFP over expression, ZFP-ChIP biological replicate 1

description:
A_OE_ChIP_r1
processed data file:
OE R1 ChIP vs Input log2 SES norm.bigwig


title: CCR6highCCR2pos CD4 T cells D2

city: Bethesda

first: Farhat

last: Parween

state: MD

address: 10 Center Drive

department: NIAID

institute: NIH

description: Library name: Sample 24

data_processing:
Each library was down sampled to equivalent sequencing depth and libraries were merged with cellranger aggr v2.0.2 pipeline (10X Genomics). Data were imported into R Studio (R 3.6.2), and the Seurat package (Seurat 3.1.4, https://github.com/satijalab/seurat) was used to process and analyze the gene expression data.
Assembly: GRCh38
Supplementary files format and content: raw_feature_bc_matrix.h5

source_name: Human Blood

growth_protocol: After FACS sorting, cells were maintained in RPMI medium supplemented with 10% FBS in a 37 degree CO2 incubator

extract_protocol:
Human memory as well as CCR6highCCR2pos CD4+ T cells were isolated from the elutriated lymphocytes to approximately 90% purity by negative selection using RosetteSep human CD4+ T cell enrichment cocktail using Ficoll/Hypaque density centrifugation. After staining with the antibodies, cells were sorted by FACS.
Cells were loaded onto the Chromium Single Cell Library & Gel Bead Kit v3.1 (10x Genomics), to generate libraries for scRNA-seq .

treatment_protocol: After FACS prification, Memory  as well as CCR6highCCR2pos CD4+ T cells were stimulated with PMA for 3 hours.

value: Human Blood

value: Primary cells

value: CD4 T cells


title: WholeBlood-MDD-M-515


title: WholeBlood-MDD-M-514


title: Memory D2

description: Library name: Sample 23


title: Lung tissues in strategy2, CasRx + sgNC, 6 wpi, rep 2


title: C9_Line3_1_UT


title: Lung tissues in strategy1, CasRx + sgRNA5, 12 wpi, rep 3

description:
gene_exp_strategy1_12 wpi.xls
ensembl_blast_potential_off-target_genes.xls

value: Strategy 1:simultaneous tumor induction and treatment

value: AAV-CasRx + sgRNA5

value: 12 weeks


title: C9_Line3_1_TTX

value: TTX


title: Lung tissues in strategy1, CasRx + sgRNA5, 12 wpi, rep 2


title: CCR6highCCR2pos CD4 T cells D1

description: Library name: Sample 22


title: WholeBlood-MDD-M-509

value: Whole blood

value: MDD

value: Male


title: C9_Line3_1_TEA


title: Lung tissues in strategy1, CasRx + sgRNA5, 12 wpi, rep 1

value: Lung

value: KrasLSL-G12D; Tp53fl/fl (KP)


title: Memory D1

description: Library name: Sample 21


title: WholeBlood-MDD-M-504


title: Empty Vector, ZFP-ChIP biological replicate 1

description:
B_Ctrl_ChIP_r1
processed data file:
Ctrl R1 ChIP vs Input log2 SES norm.bigwig

value: pEXP-empty vector

value: MYC-Tag (9B11) antibody (#2276, Cell Signaling)


title: C9_Line3_2_TEA

value: TEA


title: Lung tissues in strategy1, CasRx + sgRNA2, 12 wpi, rep 2

value: AAV-CasRx + sgRNA2


title: Lung tissues in strategy2, CasRx + sgNC, 6 wpi, rep 1

value: strategy 2:tumor formation and then treatment

value: AAV-CasRx + sgNC

value: 6 weeks


title: C9_Line2_2_UT

value: UT


title: WholeBlood-MDD-M-513


title: C9_Line2_2_TTX


title: WholeBlood-MDD-M-501


title: WholeBlood-MDD-M-502


title: C9_Line2_2_TEA


title: WholeBlood-MDD-M-322


title: C9_Line2_1_UT


title: Lung tissues in strategy1, CasRx + sgRNA2, 12 wpi, rep 1

value: Strategy 1:simultaneous tumor induction and treatment


title: 5_S5_L002_R1_001

city: Baltimore

first: Kenneth

middle: W

last: Witwer

state: Maryland

address: 733 N. Broadway

department: Molecular and Comparative Pathobiology

institute: Johns Hopkins University

description: Library name: EXR-KWITW1LPPFRAC18-BS

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

source_name: Plasma

extract_protocol:
RNA Isolation method was Trizol-LS. RNA Isolation kit was Trizol + spin column.
Library construction kit was BioLiqX small RNA Library Kit. Samples were multiplexed. Type of Starting Material was total RNA.

value: Plasma

value: Healthy Control

tag: anatomical location

value: Entire body system

tag: rna source

tag: rna isolation kit

value: Trizol + spin column


title: 5_S5_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACQ20-BS


title: 6_S6_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACD2-BS


title: 6_S6_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACD4-BS


title: C9_Line2_1_TTX

tag: cell line

value: TTX


title: 7_S7_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACD6-BS


title: Lung tissues in strategy1, CasRx + sgNC, 12 wpi, rep 2

value: 12 weeks


title: WholeBlood-MDD-M-317

value: Whole blood

value: MDD

tag: Sex

value: Male


title: Lung tissues in strategy1, CasRx + sgRNA2, 12 wpi, rep 3

value: Lung

value: KrasLSL-G12D; Tp53fl/fl (KP)


title: C9_Line2_1_TEA

value: TEA


title: WholeBlood-MDD-M-316


title: Lung tissues in strategy1, CasRx + sgNC, 12 wpi, rep 1


title: 1_S1_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACQ3-BS

tag: condition

value: protein-lipid-RNA complex


title: C9_Line1_2_UT


title: Lung tissues in strategy1, CasRx + sgRNA5, 2 wpi, rep 3

description:
gene_exp_strategy1_2 wpi.xls
ensembl_blast_potential_off-target_genes.xls

value: AAV-CasRx + sgRNA5

value: 2 weeks


title: WholeBlood-MDD-M-401


title: WholeBlood-MDD-M-315


title: C9_Line1_2_TTX


title: Lung tissues in strategy1, CasRx + sgNC, 12 wpi, rep 3

value: AAV-CasRx + sgNC


title: 2_S2_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACQ5-BS


title: C9_Line1_2_TEA


title: WholeBlood-MDD-M-313


title: Lung tissues in strategy1, CasRx + sgRNA5, 2 wpi, rep 2

value: Strategy 1:simultaneous tumor induction and treatment


title: 2_S2_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACQ7-BS

value: Plasma


title: WholeBlood-MDD-M-311


title: Lung tissues in strategy1, CasRx + sgRNA5, 2 wpi, rep 1


title: 11_S11_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACQ3R2-BS

value: Healthy Control


title: Lung tissues in strategy1, CasRx + sgRNA2, 2 wpi, rep 3

value: AAV-CasRx + sgRNA2


title: C9_Line1_1_UT

value: UT


title: WholeBlood-MDD-M-303


title: 12_S12_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACQ5R2-BS

value: Entire body system

value: Trizol + spin column


title: Lung tissues in strategy1, CasRx + sgRNA2, 2 wpi, rep 2


title: C9_Line1_1_TEA


title: 12_S12_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACQ6R2-BS


title: 3_S3_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACQ11-BS


title: WholeBlood-Control-M-1100

value: Whole blood

value: Control


title: Lung tissues in strategy1, CasRx + sgRNA2, 2 wpi, rep 1


title: WT_Line3_3_6

value: Healthy

value: KCL


title: 5_S5_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACQ19-BS


title: Lung tissues in strategy1, CasRx + sgNC, 2 wpi, rep 3

value: Lung

value: KrasLSL-G12D; Tp53fl/fl (KP)


title: 8_S8_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACD11-BS

value: protein-lipid-RNA complex


title: WT_Line3_3_0


title: WholeBlood-MDD-M-208

value: MDD

value: Male


title: Lung tissues in strategy1, CasRx + sgNC, 2 wpi, rep 2

value: AAV-CasRx + sgNC

value: 2 weeks


title: WT_Line3_3_2


title: WholeBlood-MDD-M-302


title: 9_S9_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACD13-BS

value: Plasma


title: Lung tissues in strategy1, CasRx + sgNC, 2 wpi, rep 1

value: Strategy 1:simultaneous tumor induction and treatment


title: C9_Line1_1_TTX

value: TTX


title: WholeBlood-MDD-M-215


title: WholeBlood-MDD-M-207


title: 4_S4_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACQ16-BS

value: Healthy Control


title: WT_Line3_2_6


title: B cells, KO3

city: Taiyuan City

first: Yukai

last: Jing

state: Shanxi

address: 99 Longcheng Street

department: Department of Clinical Laboratory

institute: Third Hospital of Shanxi Medical University

data_processing:
The image data measured by the high-throughput sequencer are converted into  sequence data (reads) by CASAVA base recognition.
Raw data (raw reads) of fastq  format were firstly processed through fastp software. In this step, clean data (clean reads)  were obtained by removing reads containing adapter, reads containing N base and low  quality reads from raw data.
At the same time, Q20, Q30 and GC content the clean data  were calculated. All the downstream analyses were based on the clean data with high  quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice  junctions based on the gene model annotation file and thus a better mapping result than  other non-splice mapping tools.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: spleen

extract_protocol:
Total RNA was used as input material for the RNA sample preparations. Briefly,  mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads.  Fragmentation was carried out using divalent cations under elevated temperature in  First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using  random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to  degrade the RNA. Second strand cDNA synthesis was subsequently performed using  DNA Polymerase I and dNTP.
Remaining overhangs were converted into blunt ends  via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments,  Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order  to select cDNA fragments of preferentially 370~420 bp in length, the library fragments  were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR  amplification, the PCR product was purified by AMPure XP beads, and the library was  finally obtained.

value: spleen

value: lymphocyte

tag: cell subset

value: CD19+B cell


title: WT_Line3_2_2


title: WholeBlood-MDD-M-202

value: Whole blood


title: 6_S6_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACD3-BS

value: Entire body system

value: Trizol + spin column


title: B cells, KO2


title: WholeBlood-Control-M-197

value: Control


title: 8_S8_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACD10-BS


title: WT_Line3_2_0

value: Healthy

value: KCL


title: B cells, KO1


title: WholeBlood-Control-M-195


title: 11_S11_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACD21-BS


title: WT_Line3_1_6


title: B cells, WT3

value: WT


title: WholeBlood-Control-M-190

value: Male


title: WT_Line3_1_2


title: WholeBlood-Control-M-189


title: WT_Line3_1_0


title: B cells, WT2


title: 1_S1_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACQ2-BS

value: protein-lipid-RNA complex


title: 1_S1_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACQ4-BS


title: WT_Line2_2_6


title: WholeBlood-Control-M-188


title: WholeBlood-Control-M-186


title: 8_S8_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACD9-BS


title: AT29-Ex50uM-3

city: Paris Cedex 13

first: Celine

last: Guigon

address: 4 avenue de l'Observatoire

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

description:
mm10_gene_reads.tsv
mm10_gene_tpm.tsv

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

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

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

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

tag: source

value: granulosa cell tumor

tag: tumor stage

value: primary stage

tag: developmental stage

value: Not defined


title: WT_Line2_2_2


title: WholeBlood-Control-M-183

tag: group


title: WT_Line2_2_0


title: 10_S10_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACD20-BS

tag: tissue

value: Plasma


title: WholeBlood-Control-M-181


title: WT_Line2_1_6


title: AT29-Ex50uM-1

description:
mm10_gene_reads.tsv
mm10_gene_tpm.tsv

tag: cell type


title: 11_S11_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACQ2R2-BS

value: Healthy Control


title: AT29-CTR-3

description:
mm10_gene_reads.tsv
mm10_gene_tpm.tsv

value: control


title: WT_Line2_1_2


title: WholeBlood-Control-M-179


title: AT29-CTR-2

description:
mm10_gene_reads.tsv
mm10_gene_tpm.tsv


title: 12_S12_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACQ4R2-BS


title: WholeBlood-MDD-M-219

value: MDD


title: WholeBlood-Control-M-177


title: WT_Line2_1_0


title: 11_S11_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACQ1R2-BS


title: B cells, WT1

value: spleen

value: lymphocyte

value: CD19+B cell


title: WholeBlood-Control-M-175

value: Whole blood


title: AT29-CTR-1

description:
mm10_gene_reads.tsv
mm10_gene_tpm.tsv


title: WT_Line1_2_6


title: 10_S10_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACD18-BS

value: Entire body system

value: Trizol + spin column


title: 4_S4_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACQ13-BS


title: AT29-Ex50uM-2

description:
mm10_gene_reads.tsv
mm10_gene_tpm.tsv


title: E14.5dKO, scRNA-seq

first: Chao

last: Song

state: Pennsylvania

address: 4141 Spruce St., Room 308

institute: Children's Hospital of Philadelphia

description: 10X Genomics

data_processing:
Cell Ranger was used for demultiplexing, extraction of cell barcode and quantification of unique molecular identifiers (UMIs) (10x Genomics). Downstream analyses were performed with Seurat v3
Assembly: mm10
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: Interzone

extract_protocol:
Cartilage anlagen were isolated from the hindlimbs of E13.5 or E14.5 embryos, and cleaned of soft tissues by rolling on Kimwipe paper. Presumptive knee joint regions were excised under a dissecting microscope (Leica) and digested in 4 mg/ml collagenase D (Sigma-Aldrich, Cat# 11088858001) on an orbital shaker at 120 rpm, 37℃ for 20 mins.
Libraries were constructed with the Single Cell 3’ Reagent Kits v3.1 (10x Genomics), and sequenced with a NovaSeq sequencer at the Center for Applied Genomics of The Children’s Hospital of Philadelphia.
Libraries were constructed with the Single Cell 3’ Reagent Kits v3.1 (10x Genomics), and sequenced with a NovaSeq sequencer at the Center for Applied Genomics of The Children’s Hospital of Philadelphia.

value: Interzone

value: Interzone cells

value: No


title: WholeBlood-Control-M-170

value: Control

value: Male


title: E14.5G1KO, scRNA-seq

description: 10X Genomics


title: WholeBlood-Control-M-171


title: 4_S4_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACQ15-BS


title: WT_Line1_2_2

value: Healthy

value: KCL


title: WT_Line1_2_0


title: 5_S5_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACQ17-BS

value: Plasma


title: Lung tissues in strategy2, CasRx + sgRNA5, 6 wpi, rep 4

value: Lung

value: KrasLSL-G12D; Tp53fl/fl (KP)

tag: administration strategy

value: strategy 2:tumor formation and then treatment

value: AAV-CasRx + sgRNA5

tag: time of_therapeutic_duration

value: 6 weeks


title: WholeBlood-Control-M-166


title: E13.5WT, scRNA-seq

description: 10X Genomics

tag: genotype

value: No cre


title: WT_Line1_1_6

tag: treatment


title: 1_S1_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACQ1-BS

value: Healthy Control

tag: anatomical location

value: protein-lipid-RNA complex


title: 7_S7_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACD8-BS

value: Entire body system

tag: rna source

value: Trizol + spin column


title: WholeBlood-Control-M-162

value: Whole blood


title: Syngap1+/-: CSP  (R3)

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

data_processing:
BCL to FASTq files were obtained using CASAVA Pipeline
NFCORE-RNASEq pipeline was used to process the FASTQ to obtain Read Count Files
Read Count data was TPM normalized for further downstream analysis
Assembly: Hg19
Supplementary files format and content: TPM Normalized data of expressed transcripts in .xlsx format

source_name: Hippocampus

extract_protocol:
Trizol method. Briefly, Mice were sacrificed by cervical dislocation; the dorsal hippocampus was dissected out and chopped finely with a razor blade. All reagents and instruments used for RNA isolation were DEPC treated. Samples were homogenized in TRIzol reagent (Invitrogen). RNA was isolated by the traditional phenol: chloroform method. After phenol-chloroform treatment, the aqueous phase was collected, and ethanol precipitated using absolute ethanol. The pellets were washed twice with 70% ethanol and air-dried. RNA pellets were resuspended in RNase-free water.  DNase treatment was done for 30 min at 37 ºC. RNA samples were further purified by chloroform/phenol extraction and ethanol precipitated. Pellets were washed twice with 70% ethanol and resuspended in RNase-free water at 65 ºC for 10 mins. RNA concentration was determined by Nano-drop
As per Illumina recommended Protocol

treatment_protocol: Mice were treated with 3 dose (20mg/Kg) of CSP/CSP-TTK21 (1 dose/ week). After 1 week, MWM training was performed for 4 days and mice were sacrificed after 2 hours.

value: Hippocampus

value: CSP


title: WholeBlood-Control-M-154

value: Control

value: Male


title: WT_Line1_1_2

value: Healthy

value: KCL


title: WT_Line1_1_0


title: 9_S9_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACD15-BS

value: Plasma

tag: rna isolation kit


title: WT: CSP (R3)

tag: cell line

value: WT


title: C9_Line3_3_6


title: C9_Line3_3_2


title: WholeBlood-Control-M-152

tag: Sex


title: Syngap1+/-: CSP (R2)


title: 10_S10_L003_R1_001

description: Library name: EXR-KWITW1LPPFRACD19-BS

tag: condition


title: WholeBlood-Control-M-147


title: C9_Line3_3_0


title: E14.5WT, scRNA-seq

description: 10X Genomics

value: Interzone

value: Interzone cells

value: No


title: 10_S10_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACD17-BS


title: WholeBlood-Control-M-146


title: Syngap1+/-: Saline (R3)

value: Saline


title: C9_Line3_2_6


title: WholeBlood-Control-M-149


title: WT: CSP (R2)


title: WT: CSP (R1)


title: WholeBlood-Control-M-144