title: heart, vehicle, Rat_17

description:
Library name: lib652482
Rat_17


title: 147CR_Vehicle 1

status: Public on Jan 23 2025

type: SRA

city: STANFORD

first: James

last: Brooks

address: 300 PASTEUR DR

country: USA

institute: STANFORD UNIVERSITY

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. 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.FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Supplementary files format and content: Tab-delimited excel file

molecule: total RNA

organism: Homo sapiens

source_name: LuCaP 147CR

growth_protocol: Different Prostate cancer PDXs are implanted into the RAG2-/- mice through the intratibial injection  methods, then treated by different componds.The tumors were harvested for the RNAseq.

extract_protocol:
Total RNA was isolated from fresh frozen mouse tibial PDX tumor tissues using an Allprep DNA/RNA mini kit (Qiagen).
After RNA fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

tag: cell line

value: LuCaP 147CR

tag: cell type

value: Tumor Tissue

tag: treatment

value: vehicle

tag: time

value: 30 days


title: rat, MII oocyte, single cell sample 1

city: Stockton

first: Yangqi

last: Su

state: CA

address: 4142 E Morada Ln, Apt 6303

department: Bioinformatics

institute: UNC Charlotte

description: Library name: RU1

library_source: transcriptomic single cell

data_processing:
Raw sequences were trimmed using Trim_galore (Krueger, 2015), with parameters length > 35 and q > 10, and subsequently mapped to the respective reference genome using STAR v2.7.10b (Dobin et al., 2013) with parameters adapted from nf-core/rnaseq workflow settings: --quantMode TranscriptomeSAM --twopassMode Basic --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend --outSAMstrandField intronMotif.
Quantification of read coverage of nascent transcripts was performed using velocyto ( 0.17.17) (La Manno et al., 2018) under the run-smartseq2 option with default parameters.
STAR aligned mappings  were also quantified via HTSeq (Anders et al., 2015) and a custom GTF file of 1kb intergenic regions to obtain intergenic transcription counts.
The resulting mappings were quantified using Salmon (Patro et al., 2017) with default settings to obtain estimated expression levels for transcripts in transcript per million (TPM) units. Transcript TPM values were then aggregated via tximport package to obtain estimated gene counts.
BEDGRAPH files for 3'UTR regions were obtained via processing GTF annotation files for each organism via custom scripts. Estimated alternative polyadenylation was obtained via a modified version of the DaPars2 package.
Assembly: GRCm39 with assembly GCF_000001635.27 for Mice; mRatBN7.2 with assembly GCF_015227675.2 for Rat
Supplementary files format and content: tab delimited files of transcript TPM and  transcript lengths for each sample estimated by Salmon pseudoaligner .
Supplementary files format and content: tab delimited files of nascent and spliced counts for all samples and genes.
Supplementary files format and content: BigWig files of samtools depth output for all samples
Supplementary files format and content: tab delimited files of DaPars2 estimated long, short UTR coverage, PDUI and UTR region information for samples tested for differential alternative polyadenylation.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: MII oocyte

growth_protocol: Mouse and rat oocytes and zygotes were isolated at Horizon Discovery, St. Louis site, operated under approved animal protocols overseen by Horizon Discovery's Institutional Animal Care and Use Committee (IACUC). C57BL/6N mice and Sprague Dawley rats purchased from Taconic Farms were housed in standard cages and maintained on a 12-h light/dark cycle with ad libitum access to food and water.

extract_protocol:
Full-length double-strand cDNA for each oocyte or zygote was prepared using an sc-RNA-seq libraries SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, Mountain View, CA) following the vendor’s instruction, which was based on the Smartseq2 protocol (Picelli et al., 2013).
cDNA-seq libraries were constructed using a Nextera® XT DNA Library Preparation Kit (Illumina, Sandiago, CA, Cat. Nos. FC-131-1024, FC-131-1096) following the vendor’s instruction. The libraries were quantified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara) and sequenced on an Illumina 2500 machine with 150 bp paired end reads.

treatment_protocol: Three- to four-week-old female mice were injected with PMS (5 IU/mouse) 48 hr before hCG (5 IU/mouse) injection, followed by with or without mating to stud males. Fertilized eggs and oocytes were harvested 1 d later, respectively. Four- to five-week-old female rats were injected with 20 units of PMS, which was followed by an injection of 50 units of hCG 48 h later, followed by with or without mating to stud males. Fertilized eggs and oocytes of both species were harvested 1 d later.

value: MII oocyte


title: 35_AXL 1

source_name: LuCaP 35

value: LuCaP 35

value: batiraxcept


title: 01_14_BL6_Emanuel_4-7-21

type: RNA

city: Philadelphia

first: Emanuel

middle: José

last: Novais

state: PA

address: 1025 Walnut St., Suite 511 College Bldg.

department: Department of Orthopaedic Surgery

institute: Thomas Jefferson

description: Gene expression data from young dorsal root ganglion BL/6 mouse Ctr

hyb_protocol: Gene chips (Mouse Clariom S) were hybridized with fragmented and biotin-labeled cDNA. Arrays were washed and stained with GeneChip hybridization wash & stain kit

scan_protocol: scanned on an Affymetrix Gene Chip Scanner 3000 7G, using Command Console Software.

data_processing: Chp files were generated by sst-rma normalization from Affymetrix cel file using Expression Console Software. Experimental group was compared with control group by using Transcriptome array console 4.0 software. The SST-RMA algorithm was used for data normalization.

label: biotin

organism: Mus musculus

source_name: Young DRG BL/6

label_protocol: Fragmented biotin labeled cDNA was synthesized using the GeneChip WT Plus kit according to ABI protocol (Thermo Fisher Scientific).

growth_protocol: DRG and AF tissue were dissected from lumbar discs from BL6 and SM/J mice (n=5-6 per group).

extract_protocol: Pooled tissue from single animal served as an individual sample. Samples were homogenized and total RNA was extracted using RNeasy® Mini kit (Qiagen).

tag: tissue

value: Dorsal root ganglion

tag: strain

tag: age


title: 35_AXL+DOC 1

value: batiraxcept + docetaxel


title: RGC, GFP_5dpi, cell6

city: Hong Kong

first: Kai

last: Liu

address: Clear water bay

department: LIFS

country: China

institute: HKUST

data_processing:
Raw reads were aligned to the GRCm38 (mm10) mouse reference genome using the “Subread” aligner from the Rsubread package, and gene counts were generated using the featureCounts function.
Assembly: mm10
Supplementary files format and content: Comma-separated values (CSV) file includes raw counts for each sample

source_name: retina

extract_protocol:
The RGC-labeled retina was quickly dissected out from mice after cervical dislocation and incubated with 0.5 mg/ml papain at 37 °C for 30 minutes. The retina was then washed with Neurobasal-A medium and triturated into a single-cell suspension by pipetting. After centrifugation at 300g for 6 minutes at 4 °C, the retinal cells were resuspended in Neurobasal-A medium supplemented with 10% B27.Mouth-pipetting was employed to pick single-labeled RGCs manually. A small volume of the RGC suspensions was transferred through a series of 1% BSA-containing PBS drops until a single targeted RGC was isolated. This RGC was then transferred into 4.2 µl lysis buffer, as per the Smart-seq2 protocol, and stored at -80 °C for subsequent processing.The single-cell RGC lysate underwent further processing according to the Smart-seq2 protocol. RNA was reversely transcribed into cDNA using superscript II and TSO primer and followed by amplification with KAPA HiFi HotStart ReadyMix and ISPCR primer for 27 cycles. The amplified product was purified using Ampure XP beads. A fragment analyzer assessed cDNA quality and Qubit dsDNA High Sensitivity (HS) kit measured cDNA concentration. qPCR measured the relative expression level of the Sncg and Rbpms genes. Samples with low cDNA quality or low expression levels of both genes were excluded from downstream library construction.
Library construction utilized the TruePrep DNA Library Prep Kit V2 for Illumina (vazyme) and TruePrep Index Kit V2 for Illumina, following the manufacturer’s instructions. The constructed library was then sent to Novogene company for sequencing with NovaSeq PE150.

value: retina

value: RGC

tag: genotype


title: 05_18_bl6_Emanuel_4-7-21


title: 29_SMJ AF E

description: Gene expression data from 12-month annulus fibrosis SM/J mouse Exp

source_name: 12M AF SM/J

value: Annulus Fibrosus

value: SM/J


title: rat, MII oocyte, single cell sample 15

description: Library name: RU16


title: 35_Vehicle 1


title: RGC, GFP_5dpi, cell7


title: 28_SMJ AF D


title: 27_SMJ AF C


title: 35CR_Vehicle 1

source_name: LuCaP 35CR

value: LuCaP 35CR


title: RGC, GFP_5dpi, cell5


title: RGC, GFP_5dpi, cell3


title: rat, MII oocyte, single cell sample 14

description: Library name: RU15


title: 02_15_BL6_Emanuel_4-7-21


title: rat, MII oocyte, single cell sample 11

description: Library name: RU11


title: rat, MII oocyte, single cell sample 13

description: Library name: RU14


title: RGC, GFP_5dpi, cell4


title: RGC, GFP_5dpi, cell2


title: 26_SMJ AF A


title: RGC, GFP_5dpi, cell1


title: 147CR_Doc 2

value: docetaxel


title: 147CR_Vehicle 4


title: 23_BL6 AF C

description: Gene expression data from 12-month annulus fibrosis C57BL/6 mouse Ctr

source_name: 12M AF BL/6


title: rat, MII oocyte, single cell sample 12

description: Library name: RU12


title: rat, MII oocyte, single cell sample 10

description: Library name: RU10


title: RGC, GFP_5dpi, cell8


title: 24_BL6 AF E


title: rat, zygote, single cell sample 9

description: Library name: RF9

source_name: zygote

value: zygote


title: 147CR_AXL 5


title: rat, zygote, single cell sample 8

description: Library name: RF8


title: RGC, GFP_intact, cell14


title: 147CR_Vehicle 3


title: RGC, GFP_intact, cell15


title: rat, zygote, single cell sample 7

description: Library name: RF7


title: 25_BL6 AF F


title: 22_BL6 AF B


title: Human liver,post-OLT,IR2

city: wuhan

first: Zhongshan

last: Lu

address: 169 Donghu Road, Wuchang District

institute: Zhongnan Hospital of Wuhan University

description:
Library name: IR2
Column name in processed_files.csv: IR13

data_processing:
Genomic and genetic information for Mus musculus was obtained from the National Center for Biotechnology Information database.
Expression levels of all mRNAs were evaluated using StringTie software (v1.3.44d), with the default parameters retained for other  settings.
Supplementary files format and content: csv file includes FPKM values for each Sample

source_name: Hepatic parenchyma

extract_protocol:
total RNA was extracted from tissue samples. Nanodrop2000 was used to detect the concentration and purity of the extracted RNA. Agarose gel electrophoresis was used to detect RNA integrity, and Agilent5300 was used to determine RQN value.
Afteiquantified by Qubit 4.0, the sequencing library was performed on NovaSeq X Plus platform(PE 150) using NovaSeqReagent Kit.

treatment_protocol: Human liver tissues were obtained from donors at the Institute of Hepatobiliary Diseases of Wuhan University Zhongnan Hospital. The donor liver were collected immediately after a period of warm and cold ischemia, and 1 hours after opening the portal vein during liver transplantation, and stored in a fixative or frozen at -80°C.

value: Hepatic parenchyma

value: MIHA

value: Human hepatocyte

value: WT

value: 1 hours after opening the portal vein reperfusion during liver


title: RGC, GFP_intact, cell12


title: rat, zygote, single cell sample 6

description: Library name: RF6


title: 147CR_Vehicle 2

value: LuCaP 147CR

value: Tumor Tissue

value: vehicle

value: 30 days


title: Human liver,post-OLT,IR1

description:
Library name: IR1
Column name in processed_files.csv: IR11


title: 147CR_AXL 4

value: batiraxcept


title: 147CR_AXL 3


title: 21_BL6 AF A


title: RGC, GFP_intact, cell11

value: retina


title: Human liver,post-OLT,IR3

description:
Library name: IR3
Column name in processed_files.csv: IR15


title: rat, zygote, single cell sample 5

description: Library name: RF5


title: rat, zygote, single cell sample 4

description: Library name: RF4


title: Human liver,pre-OLT,control3

description:
Library name: NC3
Column name in processed_files.csv: sham4

value: The tissues from DCD liver transplantation specimens before transplantation were collected as control (pre-OLT)


title: 147CR_Doc 1


title: 147CR_AXL 2


title: RGC, GFP_intact, cell10

value: RGC


title: rat, zygote, single cell sample 3

description: Library name: RF3


title: Human liver,pre-OLT,control2

description:
Library name: NC2
Column name in processed_files.csv: Sham2


title: 147CR_AXL 1


title: RGC, GFP_intact, cell9


title: Human liver,pre-OLT,control1

description:
Library name: NC1
Column name in processed_files.csv: Sham1


title: RGC, GFP_intact, cell13


title: 147_AXL 4

source_name: LuCaP 147

value: LuCaP 147


title: rat, zygote, single cell sample 2

description: Library name: RF2


title: RGC, GFP_intact, cell7


title: GBM_RNA

city: Stanford

first: Julia

last: Belk

state: California

address: 450 Serra Mall

institute: Stanford University

description: SPACE-seq (utilizing the 10X Visium CytAssist v2 workflow)

data_processing:
FASTQ files were trimmed, filtered, and aligned using the spaceranger pipeline from 10X genomics.
Spatial RNA-seq profiles were clustered and visualized using Seurat.
Spatial ATAC-seq fastqs were re-aligned using hisat2, processed into fragment files, and then clustered and visualized using ArchR.
Assembly: mm10 or hg38
Supplementary files format and content: Filtered cell by gene counts matrices (spatial RNA) and fragments files (spatial ATAC) for use in downstream analyses.

source_name: human GBM

extract_protocol:
Tissue sections were isolated from mouse brain or human glioblastoma, imaged, and then used for spatial multi-omics (SPACE-seq).
Spatial multi-ome (paired spatial RNA and spatial ATAC) libraries were constructed using the SPACE-seq protocol and commercially available reagents from 10X Genomics.

value: human GBM

tag: Sex

value: M

value: 40 year old patient

tag: disease state

value: tumor


title: rat, zygote, single cell sample 1

description: Library name: RF1

value: zygote


title: 147_Vehicle 4


title: rat, zygote, single cell sample 16

description: Library name: RF16


title: RGC, GFP_intact, cell6


title: GBM_ATAC

library_source: genomic

molecule: genomic DNA


title: 147_AXL 3


title: 147_AXL 2


title: RGC, GFP_intact, cell5


title: 147_Vehicle 3


title: RGC, GFP_intact, cell4


title: miR-186+0 nM replicate 3, 29 week

city: Louisville

first: Jae Yeon

last: Hwang

state: Kentucky

address: 505 S. Hancock Street

department: Division of Medical Oncology & Hematology

institute: University of Louisville

data_processing:
Sequencing reads were mapped to the hg38.p12 human reference genome with the GRCh38.93 transcriptome (Ensembl GTF release 93) using the STAR aligner (v.2.6.0c). Differentially expressed genes (DEGs) were identified using Cuffdiff (v2.2.1) and filtered with the criteria of p-values <= 0.05.
Assembly: hg38
Supplementary files format and content: tab-delimited text file with FPKM values for each Sample

source_name: HaCaT

growth_protocol: Immortalized but non-malignant human keratinocyte HaCaT cell line was grown. The cells were cultured in MEM alpha modification media supplemented with 10% fetal bovine serum, 100 units/mL penicillin/100 µg/mL streptomycin and 2 mM glutamine. Cultures were maintained at 37 °C in a humidified 5% CO2 atmosphere. Cells were passaged twice a week and 106 cells were plated per 100 mm dish every time. At each passage, the total cells were counted for calculation of population doubling.

extract_protocol:
Total RNA was isolated at two time points (12 and 29 weeks) using mirVanaTM RNA isolation kit as established in our laboratory (Ferragut Cardoso et al., 2022)
The Truseq Stranded mRNA kit was used to prepare mRNA libraries from 1 μg total RNA. Libraries were validated on the Agilent 2100 Bioanalyzer and quantitated using the Illumina Library Quantification Kit. All samples were pooled and run simultaneously, using 2 × 150 paired end sequencing with the 500 High-output v2 (300 cycles) sequencing kit on the Illumina NextSeq500 instrument.

treatment_protocol: Three individual clonal lines each for the empty vector transduced and hsa-miR-186 transduced were maintained for the entire duration of the exposure regimen (0/100 nM iAs), giving rise to four experimental conditions with independent biological triplicates in each

value: HaCaT


title: rat, zygote, single cell sample 14

description: Library name: RF14


title: RGC, GFP_intact, cell3


title: 147_Doc 1

value: docetaxel


title: miR-186+0 nM replicate 2, 29 week


title: RGC, GFP_intact, cell8


title: 147_Vehicle 2


title: RGC, GFP_intact, cell2


title: rat, zygote, single cell sample 11

description: Library name: RF11


title: RGC, GFP_intact, cell1


title: miR-186+0 nM replicate 1, 29 week


title: Targeted scRNA-seq, Fast30h (30h)

city: Bronx

first: Jeffrey

middle: E

last: Pessin

state: NY

address: 1301 Morris Park Avenue

department: Medicine and Molecular Pharmacology

institute: Albert Einstein College of Medicine

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

data_processing:
The raw FASTQ files are mapped to single cells and gene expression levels were reconstructed using Cell Ranger (v6.0.1, 10X Genomics) with a default parameter.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Liver

extract_protocol:
Isolated total hepatocytes were placed into the 10x Genomics Chromium Controller.
The cDNA library from each time point was prepared independently with Chromium Next GEM Single Cell 3' GEM Kit v3 according to the company’s manual, and then went through the targeted gene expression protocol (Target Hybridization Kit, PN-1000248).

value: Liver

value: Male

value: WT

tag: group

value: Fast

tag: diet

value: Normal Chow:lab diet #5053


title: Vector+100 nM replicate 3, 29 week


title: CD4+ T cells, Donor 6, 10nM SUW133

city: Los Angeles

first: Jerome

last: Zack

address: 615 Charles E Young Drive S., Biomedical Sciences Research Building, Rm 173

department: Molecular Biology, Immunology & Molecular Genetics (MIMG)

institute: University of California, Los Angeles

description:
Library name: CD4_6-10nM_SUW133
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_6-10nM_SUW133

data_processing:
Reads were mapped by STAR 2.7.9a
Read counts were normalized by CPM +1.0E-4 in Partek Flow
Assembly: GRCh38.104
Supplementary files format and content: tab-delimited text files includes counts for each sample (Raw-Read-Counts-0338.txt = raw counts, Normalized-Read-Counts-0338.txt = normalized counts)

source_name: Resting CD4+ T cells

growth_protocol: NK and resting CD4+ T cells were maintained in C10 media consisting of RPMI 1640 media supplemented with 10% vol/vol FBS (Omega Scientific), 1% L-glutamine, 1% penicillin/streptomycin (Invitrogen), 500mM 2-mercaptoethanol (Sigma), 1mM sodium pyruvate (Gibco), 0.1mM MEM non-essential amino acids (Gibco), and 10mM HEPES (Gibco) in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using RNeasy mini kit (QIAGEN) according to manufacturer's protocols. 100 - 250 ng of total RNA was used for the construction of sequencing libraries.
Libraries for RNA-Seq were prepared with KAPA mRNA HyperPrep Kit. The workflow consists of depletion of rRNA by hybridization of complementary DNA oligonucleotides, followed by treatment with RNase H and DNase. Next steps include mRNA enrichment and fragmentation, first strand cDNA synthesis using random priming followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporating dUTP into the second cDNA strand. cDNA generation is followed by end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on Illumina NovaSeq6000 for a paired-end 2x50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.

treatment_protocol: NK cells and resting CD4+ T cells were stimulated with C10 media containing PKC agonists (10nM bryostatin-1, 1μM prostratin, or 10nM SUW133) for 24 hours at 37°C and 5% CO2. Unstimulated cells (DMSO only) were cultured in parallel in C10 medium.

value: Resting CD4+ T cells

value: 10nM SUW133


title: Targeted scRNA-seq, Fast24h (24h)


title: CD4+ T cells, Donor 4, 10nM SUW133

description:
Library name: CD4_4-10nM_SUW133
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_4-10nM_SUW133


title: miR-186+100 nM replicate 3, 29 week


title: rat, zygote, single cell sample 15

description: Library name: RF15


title: Vector+0nM replicate 3, 29 week


title: SCAFs 4

city: Illkirch

first: Matej

last: Durik

state: Alsace

address: 1 rue Laurent Fries

department: Development and stem cells

country: France

institute: IGBMC

description: RNA prepared from human IMR90 fibroblasts, in culture

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment: Reads were mapped onto hg38 assembly of mouse genome using STAR 2.5.3a.
Quantification: Gene expression was quantified using HTSeq v0.6.1p1 (union mode) and Ensembl release 98 annotations.
Assembly: hg38
Supplementary files format and content: Tab-separated values file containing raw read counts in each sample.

extract_protocol:
Cells were washed 1x with PBS, lysed in 350 μl of Guanidine thiocyanate- based lysis buffer (LBP lysis buffer, Macherey-Nagel NucleoSpin RNA plus isolation kit, Ref. 740984) and RNA was isolated according to the instructions of the manufacturer of the kit.
RNA-Seq libraries were generated from 250 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: fetal lung fibroblasts

value: SCAFs 300 000 pcs


title: Targeted scRNA-seq, Fast16h (16h)


title: miR-186+100 nM replicate 2, 29 week


title: rat, zygote, single cell sample 13

description: Library name: RF13


title: Targeted scRNA-seq, Fast8h (8h)


title: SCAFs 2


title: SCAFs 3


title: CD4+ T cells, Donor 3, 10nM SUW133

description:
Library name: CD4_3-10nM_SUW133
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_3-10nM_SUW133


title: rat, zygote, single cell sample 12

description: Library name: RF12


title: CD4+ T cells, Donor 2, 10nM SUW133

description:
Library name: CD4_2-10nM_SUW133
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_2-10nM_SUW133


title: SCAFs 1


title: Targeted scRNA-seq, Fed4h (0h)

value: Fed


title: Vector+0nM replicate 2, 29 week


title: miR-186+100 nM replicate 1, 29 week


title: CD4+ T cells, Donor 1, 10nM SUW133

description:
Library name: CD4_1-10nM_SUW133
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_1-10nM_SUW133


title: Vector+100 nM replicate 1, 29 week


title: rat, zygote, single cell sample 10

description: Library name: RF10


title: Beads 4

value: Inert beads 300 000 pcs


title: Standard scRNA-seq, Fast24h (24h)

extract_protocol:
Isolated total hepatocytes were placed into the 10x Genomics Chromium Controller.
The cDNA library from each time point was prepared independently with Chromium Next GEM Single Cell 3' GEM Kit v3 according to the company’s manual. The sequencing was done with sequencing by synthesis (Illumina).


title: 147_AXL 1

value: LuCaP 147

value: Tumor Tissue

value: batiraxcept

value: 30 days


title: CD4+ T cells, Donor 6, 1μM prostratin

description:
Library name: CD4_6-1uM_prostratin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_6-1uM_prostratin

value: 1μM prostratin


title: Vector+0nM replicate 1, 29 week

value: HaCaT


title: miR-186+100 nM replicate 3, 12 week


title: miR-186+0 nM replicate 3, 12 week


title: Beads 3


title: CD4+ T cells, Donor 3, 1μM prostratin

description:
Library name: CD4_3-1uM_prostratin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_3-1uM_prostratin


title: Beads 1


title: Standard scRNA-seq, Fast8h (8h)

value: Liver


title: Beads 2


title: CD4+ T cells, Donor 2, 1μM prostratin

description:
Library name: CD4_2-1uM_prostratin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_2-1uM_prostratin


title: Vector+100 nM replicate 2, 29 week


title: miR-186+100 nM replicate 2, 12 week


title: Standard scRNA-seq, Fed4h (0h)

value: Male


title: Standard scRNA-seq, Fast16h (16h)

value: WT


title: Standard scRNA-seq, Fast4h (4h)

value: Fast


title: total RNA, Male Fast24h WT Digitonin PP, Rep3

data_processing:
Transcript-level counts were estimated by Kallisto v0.46.0
Outputs from Kallisto (v0.46.0) were imported into R using the Bioconductor package tximport (v1.20.0), and the expression levels of each gene were estimated.
Assembly: mm10
Supplementary files format and content: comma-separated text file including gene-level raw counts for each sample

extract_protocol:
Total RNA isolation from isolated hepatocytes and mouse liver was done with RNeasy mini kit (Qiagen, #74106) combined with TRIzol (Invitrogen, #15596026) according to the manufacture’s protocol.
RNA libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina.

treatment_protocol: All 12-week-old mice were fed Normal Chow: lab diet #5053

value: periportal hepatocyte

value: Normal Chow:lab diet #5053


title: CD4+ T cells, Donor 1, 1μM prostratin

description:
Library name: CD4_1-1uM_prostratin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_1-1uM_prostratin

value: Resting CD4+ T cells


title: miR-186+100 nM replicate 1, 12 week


title: KELLY_Hmx1 P9225_122

city: Solna

first: Yizhou

last: Hu

state: Stockholm

address: C6 , Biomedicum Karolinska, Solnavägen 9,

country: Sweden

institute: Karolinska Institute

description:
KELLY_Hmx1
Illumina TruSeq Stranded mRNA kit and  Illumina HiSeq 2500 High Output V4, pair-end 125bp

data_processing:
The demultiplexing was processed by bcl2fastq, and the sequence alignment was performed with STAR by using GRCh38.p12 genome assembly.
the quality control was monitored by FastQC
Genome_build: GENCODE: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: Neuroblasotma cell line xenograft bulk tumor

growth_protocol: All cell lines were cultured following the manufacturer’s instruction, and Xenograft tumors were collected after sacrificing the mice.

extract_protocol:
the total RNA was extracted using RNeasy Lipid Tissue Mini Kit (Qiagen).
sample library was prepared in the 96 well plate by using the Illumina TruSeq Stranded mRNA kit,
sample library was prepared in the 96 well plate by using the Illumina TruSeq Stranded mRNA kit, and subsequently sent for pair-end sequencing in Illumina HiSeq 2500 High Output V4 (125bp of each, 2 lanes, The National Genomics Infrastructure, Sweden).

value: Neuroblasotma cell line xenograft

value: KELLY


title: total RNA, Male Fast24h WT Digitonin PP, Rep2


title: KELLY_Hmx1 P9225_123


title: CD4+ T cells, Donor 6, 10nM bryostatin

description:
Library name: CD4_6-nM_bryostatin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_6-nM_bryostatin

value: 10nM bryostatin-1


title: total RNA, Male Fast24h WT Digitonin PP, Rep1

value: periportal hepatocytes


title: miR-186+0 nM replicate 2, 12 week


title: miR-186+0 nM replicate 1, 12 week


title: KELLY_Control P9225_121

description:
KELLY_Control
Illumina TruSeq Stranded mRNA kit and  Illumina HiSeq 2500 High Output V4, pair-end 125bp

value: MYCN-amp


title: CD4+ T cells, Donor 4, 1μM prostratin

description:
Library name: CD4_4-1uM_prostratin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_4-1uM_prostratin


title: CD4+ T cells, Donor 3, 10nM bryostatin

description:
Library name: CD4_3-nM_bryostatin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_3-nM_bryostatin


title: Vector+100 nM replicate 3, 12 week


title: CD4+ T cells, Donor 4, 10nM bryostatin

description:
Library name: CD4_4-nM_bryostatin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_4-nM_bryostatin


title: KELLY_Control P9225_120


title: total RNA, Male Fast24h WT Digitonin PC, Rep3

value: pericentral hepatocytes


title: Vector+0nM replicate 3, 12 week


title: CD4+ T cells, Donor 2, 10nM bryostatin

description:
Library name: CD4_2-nM_bryostatin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_2-nM_bryostatin


title: KELLY_Hmx1 P9225_124


title: total RNA, Male Fast24h WT Digitonin PC, Rep2


title: KELLY_Control P9225_119


title: CD4+ T cells, Donor 1, 10nM bryostatin

description:
Library name: CD4_1-nM_bryostatin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_1-nM_bryostatin


title: total RNA, Male Fast24h WT Digitonin PC, Rep1


title: Vector+0nM replicate 2, 12 week


title: Vector+100 nM replicate 2, 12 week


title: LAN-1_Hmx1 P9225_118

description:
LAN-1_Hmx1
Illumina TruSeq Stranded mRNA kit and  Illumina HiSeq 2500 High Output V4, pair-end 125bp


title: total RNA, Male Fast8h WT Digitonin PP, Rep3


title: CD4+ T cells, Donor 3, DMSO ctrl

description:
Library name: CD4_3-Untreated
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_3-Untreated

value: Untreated (DMSO control)


title: LAN-1_Control P9225_115

description:
LAN-1_Control
Illumina TruSeq Stranded mRNA kit and  Illumina HiSeq 2500 High Output V4, pair-end 125bp


title: CD4+ T cells, Donor 2, DMSO ctrl

description:
Library name: CD4_2-Untreated
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_2-Untreated


title: total RNA, Male Fast8h WT Digitonin PP, Rep1


title: Vector+0nM replicate 1, 12 week


title: total RNA, Male Fast8h WT Digitonin PC, Rep3


title: LAN-1_Control P9225_114


title: mouse, MII oocyte, single cell sample 4

description: Library name: MU4

value: MII oocyte


title: total RNA, Male Fast8h WT Digitonin PC, Rep2


title: CD4+ T cells, Donor 1, DMSO ctrl

description:
Library name: CD4_1-Untreated
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_1-Untreated


title: LAN-1_Control P9225_113


title: NK cells, Donor 17, 10nM SUW133

description:
Library name: NK_17-10nM_SUW133
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_17-10nM_SUW133

source_name: NK cells

value: NK cells

value: 10nM SUW133


title: total RNA, Male Fast8h WT Digitonin PC, Rep1

value: Liver


title: mouse, MII oocyte, single cell sample 34

description: Library name: MU34


title: total RNA, Male Fed4h WT Digitonin PP, Rep3

value: Male

value: Fed


title: CD4+ T cells, Donor 6, DMSO ctrl

description:
Library name: CD4_6-Untreated
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_6-Untreated


title: SKNAS_Hmx1 P9225_112

description:
SKNAS_Hmx1
Illumina TruSeq Stranded mRNA kit and  Illumina HiSeq 2500 High Output V4, pair-end 125bp

value: SKNAS


title: NK cells, Donor 16, 10nM SUW133

description:
Library name: NK_16-10nM_SUW133
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_16-10nM_SUW133


title: mouse, MII oocyte, single cell sample 33

description: Library name: MU33


title: Vector+100 nM replicate 1, 12 week

value: HaCaT


title: NK cells, Donor 15, 10nM SUW133

description:
Library name: NK_15-10nM_SUW133
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_15-10nM_SUW133


title: LAN-1_Hmx1 P9225_117


title: mouse, MII oocyte, single cell sample 32

description: Library name: MU32


title: total RNA, Male Fed4h WT Digitonin PP, Rep2

value: WT

value: periportal hepatocyte

value: Normal Chow:lab diet #5053


title: total RNA, Male Fast8h WT Digitonin PP, Rep2

value: Fast


title: SKNAS_Hmx1 P9225_111

value: Neuroblasotma cell line xenograft


title: LAN-1_Hmx1 P9225_116


title: CD4+ T cells, Donor 4, DMSO ctrl

description:
Library name: CD4_4-Untreated
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: CD4_4-Untreated

value: Resting CD4+ T cells


title: NK cells, Donor 14, 10nM SUW133

description:
Library name: NK_14-10nM_SUW133
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_14-10nM_SUW133


title: SKNAS_Hmx1 P9225_110


title: mouse, MII oocyte, single cell sample 35

description: Library name: MU35


title: total RNA, Male Fed4h WT Digitonin PP, Rep1

value: periportal hepatocytes


title: SKNAS_Control P9225_109

description:
SKNAS_Control
Illumina TruSeq Stranded mRNA kit and  Illumina HiSeq 2500 High Output V4, pair-end 125bp


title: NK cells, Donor 10, 10nM SUW133

description:
Library name: NK_10-10nM_SUW133
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_10-10nM_SUW133


title: mouse, MII oocyte, single cell sample 31

description: Library name: MU31


title: mouse, MII oocyte, single cell sample 30

description: Library name: MU30


title: SKNAS_Control P9225_108


title: NK cells, Donor 17, 1μM prostratin

description:
Library name: NK_17-1uM_prostratin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_17-1uM_prostratin

value: 1μM prostratin


title: total RNA, Male Fed4h WT Digitonin PC, Rep3

value: pericentral hepatocytes


title: total RNA, Male Fed4h WT Digitonin PC, Rep2


title: SKNAS_Control P9225_107


title: mouse, MII oocyte, single cell sample 29

description: Library name: MU29

value: MII oocyte


title: NK cells, Donor 16, 1μM prostratin

description:
Library name: NK_16-1uM_prostratin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_16-1uM_prostratin

value: NK cells


title: mouse, MII oocyte, single cell sample 28

description: Library name: MU28


title: total RNA, Male Fed4h WT Digitonin PC, Rep1


title: NK cells, Donor 15, 1μM prostratin

description:
Library name: NK_15-1uM_prostratin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_15-1uM_prostratin


title: Dorsal SBN from PATSF40 - STI

city: Bloomington

first: Center for Genomics and Bioinformatics

last: IU

state: IN

address: 1001 E Third St

department: Biology

institute: Center for Genomics and Bioinformatics

description:
PATSF40-NT
Tachycineta bicolor (Tree swallow)

data_processing:
Adapters and low quality bases were trimmed using Trimmomatic (version 0.36) with following specific parameters ILLUMINACLIP:<adapters.fa>:2:20:5 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17
Reads were mapped to the transcriptome using Bowtie2 (version 2.3.4.1)
Reads mapped to transcripts were counted using Samtools (version version 1.3.1 ) and custom perl scripts
Assembly: tree swallow transcriptome obtained previously by our laboratory (Bentz et al. 2019)
Supplementary files format and content: txt files with raw RNA-seq read count values for each transcript

organism: Tachycineta bicolor

source_name: Brain (dorsal SBN / diencephalon)

extract_protocol:
We extracted RNA using the phenol-chloroform-based Trizol method (Invitrogen, Carlsbad, CA, USA).
cDNA libraries were constructed using a TruSeq Stranded mRNA kit

treatment_protocol: To measure the brain's response to a social challenge, we exposed 10 wild tree swallows to a 30-minute simulated territorial intrusion, which elicited maternal aggression. These experimental females were compared to 10 unchallenged controls.

value: Brain (dorsal SBN / diencephalon)

value: STI


title: fibro-adipogenic progenitors, BAT, D7, biol rep 3 [sample.bat5_fap]

city: St. Louis

first: Gretchen

last: Meyer

state: MO

address: 507 S Euclid Ave

department: Department of Physical Therapy

institute: Washington University School of Medicine in Saint Louis

data_processing:
RNA-seq reads were then aligned and quantitated to the Ensembl release 101 primary assembly with an Illumina DRAGEN Bio-IT on-premise server running version 3.9.3-8 software.
Assembly: mm10
Supplementary files format and content: tab-seperated text files(tsv) include rawcounts for each sample

source_name: skeletal muscle, supraspinatus

extract_protocol:
RNA was extracted using RNAeasy micro kit (Qiagen).
Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol.

value: skeletal muscle, supraspinatus

value: fibro-adipogenic progenitors


title: Ventral SBN from PATSF40 - STI

description:
PATSF40-Hypo
Tachycineta bicolor (Tree swallow)

source_name: Brain (ventral SBN / diencephalon)

value: Brain (ventral SBN / diencephalon)


title: fibro-adipogenic progenitors, BAT, D7, biol rep 2 [sample.bat3_fap_1027]


title: Dorsal SBN from PATSF39 - STI

description:
PATSF39-NT
Tachycineta bicolor (Tree swallow)


title: mouse, MII oocyte, single cell sample 25

description: Library name: MU25

source_name: MII oocyte


title: NK cells, Donor 10, 1μM prostratin

description:
Library name: NK_10-1uM_prostratin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_10-1uM_prostratin


title: mouse, MII oocyte, single cell sample 24

description: Library name: MU24


title: fibro-adipogenic progenitors, BAT, D7, biol rep 1 [sample.bat_1b_fap]


title: Ventral SBN from PATSF39 - STI

description:
PATSF39-Hypo
Tachycineta bicolor (Tree swallow)


title: NK cells, Donor 17, 10nM bryostatin

description:
Library name: NK_17-nM_bryostatin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_17-nM_bryostatin

value: 10nM bryostatin-1


title: Dorsal SBN from PATSF38 - Control

description:
PATSF38-NT
Tachycineta bicolor (Tree swallow)

value: Control


title: Ventral SBN from PATSF38 - Control

description:
PATSF38-Hypo
Tachycineta bicolor (Tree swallow)


title: fibro-adipogenic progenitors, BAT, D7 [sample.bat_1a_fap]

value: WT


title: NK cells, Donor 16, 10nM bryostatin

description:
Library name: NK_16-nM_bryostatin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_16-nM_bryostatin


title: NK cells, Donor 15, 10nM bryostatin

description:
Library name: NK_15-nM_bryostatin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_15-nM_bryostatin


title: mouse, MII oocyte, single cell sample 22

description: Library name: MU22


title: fibro-adipogenic progenitors, BAT, D3, biol rep 3 [sample.bat_3d_3b_p6]


title: mouse, MII oocyte, single cell sample 23

description: Library name: MU23


title: fibro-adipogenic progenitors, BAT, D3, biol rep 2 [sample.bat_3d_3a_p6]


title: fibro-adipogenic progenitors, BAT, D3, biol rep 1 [sample.bat_3d_2b_p6]


title: mouse, MII oocyte, single cell sample 20

description: Library name: MU20


title: NK cells, Donor 14, 10nM bryostatin

description:
Library name: NK_14-nM_bryostatin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_14-nM_bryostatin


title: Ventral SBN from PATSF37 - Control

description:
PATSF37-Hypo
Tachycineta bicolor (Tree swallow)


title: mouse, MII oocyte, single cell sample 27

description: Library name: MU27


title: NK cells, Donor 14, 1μM prostratin

description:
Library name: NK_14-1uM_prostratin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_14-1uM_prostratin


title: mouse, MII oocyte, single cell sample 18

description: Library name: MU18


title: mouse, MII oocyte, single cell sample 21

description: Library name: MU21


title: fibro-adipogenic progenitors, BAT, D3 [sample.bat_d3_p6]


title: Dorsal SBN from PATSF36 - STI

description:
PATSF36-NT
Tachycineta bicolor (Tree swallow)


title: NK cells, Donor 17, DMSO ctrl

description:
Library name: NK_17-Untreated
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_17-Untreated

value: Untreated (DMSO control)


title: mouse, zygote, single cell sample 9

description: Library name: MF9

value: zygote


title: fibro-adipogenic progenitors, CTL, D7, biol rep 3 [sample.ctl5_fap]


title: NK cells, Donor 10, 10nM bryostatin

description:
Library name: NK_10-nM_bryostatin
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_10-nM_bryostatin


title: fibro-adipogenic progenitors, CTL, D7, biol rep 2 [sample.ctl3_fap_1027]


title: Dorsal SBN from PATSF35 - Control

description:
PATSF35-NT
Tachycineta bicolor (Tree swallow)


title: mouse, zygote, single cell sample 8

description: Library name: MF8


title: NK cells, Donor 14, DMSO ctrl

description:
Library name: NK_14-Untreated
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_14-Untreated


title: Ventral SBN from PATSF36 - STI

description:
PATSF36-Hypo
Tachycineta bicolor (Tree swallow)


title: NK cells, Donor 16, DMSO ctrl

description:
Library name: NK_16-Untreated
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_16-Untreated


title: fibro-adipogenic progenitors, CTL, D7, biol rep 1 [sample.ctl_1b_fap]


title: Dorsal SBN from PATSF34 - STI

description:
PATSF34-NT
Tachycineta bicolor (Tree swallow)


title: NK cells, Donor 10, DMSO ctrl

description:
Library name: NK_10-Untreated
Column name in Raw-Read-Counts-0338.txt & Normalized-Read-Counts-0338.txt: NK_10-Untreated


title: mouse, zygote, single cell sample 7

description: Library name: MF7


title: Dorsal SBN from PATSF37 - Control

description:
PATSF37-NT
Tachycineta bicolor (Tree swallow)


title: Ventral SBN from PATSF35 - Control

description:
PATSF35-Hypo
Tachycineta bicolor (Tree swallow)


title: fibro-adipogenic progenitors, CTL, D7 [sample.ctl_1a_fap]


title: mouse, zygote, single cell sample 6

description: Library name: MF6


title: mouse, zygote, single cell sample 5

description: Library name: MF5


title: PT13 blood baseline

city: New York

first: Louis

last: Cohen

address: 1470 Madison Avenue, 8th Fl.

department: Gastroenterology

institute: Icahn School of Medicine at Mount Sinai

description:
Library name: PL9
10x Genomics

data_processing:
FASTQ files underwent processing through the Cellranger Count v6.1.1 pipeline for quality control, alignment, and matrix generation and were then employed in the Seurat wrapper, coreSC for data cleaning and regularization and a Seurat object was created.
Assembly: GRCh38
Supplementary files format and content: tab-separated value files and matrix files

source_name: blood

extract_protocol:
Tissue - Tissue biopsies were taken endoscopically with biopsy forceps and collected in ice cold complete RPMI 1640 supplemented with glutamine, 1x pen/strep, 10mM HEPES and 10% FBS and processed within 1 hour of collection. The biopsy samples were pooled together, 10-20 biopsies per sample. Epithelial cells were dissociated by transfer into dissociation medium (HBSS w/o Ca2+ Mg2+, with HEPES 10mM, EDTA 5mM) and agitated for 30 minutes at 37°C at 100rpm, and then vortexed for 30 seconds and then filtered through 70mm strainer. The biopsies were then washed with complete RMPI 1640 at room temperature and then transferred to digestion media (HBSS with Ca2+ Mg2+, FCS 2%, DNase I 0.5mg/ml,Collagenase IV 0.5mg/ml) and agitated for 40 minutes at 37°C at 100rpm. After digestion the suspension was filtered through a 70mm strainer and washed with complete RPMI, spun down 5 minutes at 2500rpm and resuspended in 1ml red blood cell lysis buffer and incubated for 10 minutes at room temperature, spun again for 5 minutes at 2500 rpm and then resuspended in RPMI and viability and cell count were determined using AO/PI dye and Nexcelcom automated cell counter prior to further processing for downstream analyses. For samples with viability 70% or less, dead cells were depleted using a dead cell removal kit (Miltenyi Biotec) following the protocol from the manufacturer. After dead cell removal, viability was routinely >85%.
Blood - peripheral blood was collected into CPT tubes (BD Vacutainer) and cells were isolated within 2 hours of blood draw. The tubes were centrifuged for 20 min at 1800G at room temperature without break and then the buffy coat layer of PBMCs was collected and then washed with PBS, centrifuged for 15 minutes at 300G. For stem cell graft processing, peripheral mobilized mononuclear cells were obtained from the cellular therapeutic laboratory and were thawed and washed with PBS and centrifuged for 15 min at 300G. CD34+ grafts - Thawed mobilized mononuclear cells were CD34+ selected using an EasySep Human CD34 Selection Kit II (StemCell Technologies) per manufacturers protocol.
Single cell isolations were processed using the 10x Genomics Chromium Single Cell 3’ v3.1 kit per manufacturers protocol and run on the 10x Genomics Chromium iX instrument. Libraries were prepared using 10x Genomics Library Construction Kit and consisted of single cell isolations resuspended in master mix and loaded into chip with partitioning oil and gel beads to generate gel bead-in-emulsion (GEM), the poly-A RNA in each GEM was reverse transcripted to cDNA containing an ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and 10x barcode. The pooled barcoded cDNA was cleaned with Silane DynaBeads, amplified by PCR and appropriate sized fragments were selected with SPRIselect reagent. Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and sample index were added during library construction. Final libraries were sequenced on the Illumina NovaSeq 6000 at the Duke Center for Genomic Computational Biology at Duke University

value: blood

value: PBMC

tag: batch


title: Ventral SBN from PATSF34 - STI

description:
PATSF34-Hypo
Tachycineta bicolor (Tree swallow)


title: fibro-adipogenic progenitors, CTL, D3, biol rep 2 [sample.ctl_3d_3a_p6]


title: fibro-adipogenic progenitors, CTL, D3, biol rep 3 [sample.ctl_3d_3b_p6]


title: Dorsal SBN from PATSF33 - Control

description:
PATSF33-NT
Tachycineta bicolor (Tree swallow)


title: mouse, zygote, single cell sample 4

description: Library name: MF4


title: PT11 blood engraftment

description:
Library name: PL5
10x Genomics


title: fibro-adipogenic progenitors, CTL, D3, biol rep 1 [sample.ctl_3d_2b_p6]


title: mouse, zygote, single cell sample 3

description: Library name: MF3


title: Ventral SBN from PATSF33 - Control

description:
PATSF33-Hypo
Tachycineta bicolor (Tree swallow)


title: PT11 blood stem cell collection

description:
Library name: PL4
10x Genomics


title: fibro-adipogenic progenitors, CTL, D3 [sample.ctl_d3_p6]


title: mouse, zygote, single cell sample 2

description: Library name: MF2


title: Dorsal SBN from PATSF32 - Control

description:
PATSF32-NT
Tachycineta bicolor (Tree swallow)


title: satelite cells, BAT, D7, biol rep 3 [sample.bat5_sc]

value: satelite cells


title: PT12 blood stem cell graft

description:
Library name: PL29
10x Genomics


title: mouse, zygote, single cell sample 1

description: Library name: MF1


title: Ventral SBN from PATSF32 - Control

description:
PATSF32-Hypo
Tachycineta bicolor (Tree swallow)


title: PT19 blood stem cell collection

description:
Library name: PL23
10x Genomics


title: satelite cells, BAT, D7, biol rep 2 [sample.bat3_sc_1027]


title: Dorsal SBN from PATSF31 - Control

description:
PATSF31-NT
Tachycineta bicolor (Tree swallow)


title: mouse, zygote, single cell sample 17

description: Library name: MF17


title: satelite cells, BAT, D7, biol rep 1 [sample.bat_1b_sc]


title: PT11 blood 3 months post-SCT

description:
Library name: PL6
10x Genomics


title: Ventral SBN from PATSF31 - Control

description:
PATSF31-Hypo
Tachycineta bicolor (Tree swallow)


title: satelite cells, BAT, D7 [sample.bat_1a_sc]


title: PT13 blood stem cell graft

description:
Library name: PL22
10x Genomics


title: mouse, zygote, single cell sample 16

description: Library name: MF16


title: PT11 blood 6 months post-SCT

description:
Library name: PL21
10x Genomics


title: mouse, zygote, single cell sample 15

description: Library name: MF15


title: satelite cells, BAT, D3, biol rep 3 [sample.bat_d3_p5]


title: mouse, zygote, single cell sample 14

description: Library name: MF14


title: Dorsal SBN from PATSF30 - STI

description:
PATSF30-NT
Tachycineta bicolor (Tree swallow)


title: Ventral SBN from PATSF30 - STI

description:
PATSF30-Hypo
Tachycineta bicolor (Tree swallow)


title: PT16 blood baseline

description:
Library name: CL5
10x Genomics


title: PT18 blood baseline

description:
Library name: CL9
10x Genomics


title: mouse, zygote, single cell sample 13

description: Library name: MF13


title: mouse, zygote, single cell sample 12

description: Library name: MF12


title: Ventral SBN from PATSF29 - STI

description:
PATSF29-Hypo
Tachycineta bicolor (Tree swallow)


title: satelite cells, BAT, D3, biol rep 2 [sample.bat_3d_3b_p5]


title: mouse, zygote, single cell sample 11

description: Library name: MF11


title: PT12 blood engraftment

description:
Library name: CL4
10x Genomics


title: satelite cells, BAT, D3, biol rep 1 [sample.bat_3d_3a_p5]


title: PT12 blood baseline

description:
Library name: PL16
10x Genomics


title: Dorsal SBN from PATSF29 - STI

description:
PATSF29-NT
Tachycineta bicolor (Tree swallow)


title: Dorsal SBN from PATSF28 - Control

description:
PATSF28-NT
Tachycineta bicolor (Tree swallow)


title: satelite cells, CTL, D7, biol rep 3 [sample.ctl5_sc]


title: Ventral SBN from PATSF28 - Control

description:
PATSF28-Hypo
Tachycineta bicolor (Tree swallow)


title: 293Tcells, RL2 Positive 2

city: Changsha

first: zhang

address: Xiangya road

institute: Xiangya hospital

description: Library name: sample4

data_processing:
The sequencing results were analyzed by the MAGeCK package, which took into consideration the magnitude of enrichment/depletion and the consistency of multiple sgRNAs targeting the same gene, to rank positive/negative regulators.
Assembly: hg38
Supplementary files format and content: Text file displaying sgRNA information was generated by MAGeCK

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

value: human embryonic kidney cell

value: positive


title: PT19 blood stem cell graft

description:
Library name: CL3
10x Genomics


title: satelite cells, CTL, D7, biol rep 2 [sample.ctl3_sc_1027]


title: PT14 blood baseline

description:
Library name: CL30
10x Genomics


title: mouse, zygote, single cell sample 10

description: Library name: MF10


title: satelite cells, BAT, D3 [sample.bat_3d_2b_p5]


title: PT13 blood 6 months post-SCT

description:
Library name: CL24
10x Genomics


title: Dorsal SBN from PATSF27 - Control

description:
PATSF27-NT
Tachycineta bicolor (Tree swallow)


title: Dorsal SBN from PATSF26 - STI

description:
PATSF26-NT
Tachycineta bicolor (Tree swallow)


title: PT18 blood engraftment

description:
Library name: CL23
10x Genomics


title: PT12 blood 6 months post-SCT

description:
Library name: CL25
10x Genomics


title: satelite cells, CTL, D7, biol rep 1 [sample.ctl_1b_sc]


title: 293Tcells, RL2 Control 1

description: Library name: sample1

value: control


title: PT11 blood 12 months post-SCT

description:
Library name: CL22
10x Genomics


title: Ventral SBN from PATSF27 - Control

description:
PATSF27-Hypo
Tachycineta bicolor (Tree swallow)


title: Ing4-/- MPP

city: Columbia

first: Katie

middle: L

last: Kathrein

state: SC

address: 715 Sumter St CLS 304

institute: University of South Carolina

description: Library name: Sample 6

data_processing:
Data processing was performed by Azenta using their propriety pipeline.  Counts were generated by Azenta and used for downstream analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: bone maroow

growth_protocol: Hematopoietic stem and progenitor cells were harvested, lineage depleted, and stained with a profiling panel for FACS sorting.  Cells were sorted directly into QIAGEN RLT buffter.  After sorting, RNA was extracted using the QIAGEN Rneasy micro kit.

extract_protocol:
RNA was extreacted using the RNeasy micro kit.
Library was prepared by Azenta.

value: bone maroow

value: Hematopoietic progenitor cell


title: satelite cells, CTL, D7 [sample.ctl_1a_sc]


title: Dorsal SBN from PATSF25 - STI

description:
PATSF25-NT
Tachycineta bicolor (Tree swallow)

value: Brain (dorsal SBN / diencephalon)

value: STI


title: Ventral SBN from PATSF26 - STI

description:
PATSF26-Hypo
Tachycineta bicolor (Tree swallow)


title: satelite cells, CTL, D3, biol rep 2 [sample.ctl_3d_3b_p5]

value: skeletal muscle, supraspinatus


title: WT MPP

description: Library name: Sample 5


title: PT18 blood stem cell graft CD34+ selected

description:
Library name: CL21
10x Genomics


title: satelite cells, CTL, D3, biol rep 1 [sample.ctl_3d_3a_p5]


title: WT ST-HSC

description: Library name: Sample 3

value: Hematopoietic stem cell


title: Dorsal SBN from PATSF24 - Control

description:
PATSF24-NT
Tachycineta bicolor (Tree swallow)


title: 293Tcells, RL2 Control 2

description: Library name: sample2


title: PT18 blood stem cell graft

description:
Library name: CL20
10x Genomics


title: PT18 blood stem cell collection

description:
Library name: CL19
10x Genomics


title: Ventral SBN from PATSF24 - Control

description:
PATSF24-Hypo
Tachycineta bicolor (Tree swallow)

value: Brain (ventral SBN / diencephalon)


title: satelite cells, CTL, D3, biol rep 3 [sample.ctl_d3_p5]


title: 293Tcells, RL2 Positive 1

description: Library name: sample3


title: Rhapsody-SampleTag

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

description: BD Rhapsody

library_source: other

data_processing:
10X Genomics: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Hashtags 10X Genomics: Processing of the HTO samples was performed using CITEseq-Count,
Bulk RNAseq: Basecalling performed using Illumina bcl2fastq v2.20 Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence Reads were processed for mapping and quantification using nf-core rnaseq pipeline v3.0.0 (https://nf-co.re/rnaseq/3.0/usage ) and using Gene set from Ensembl.org release 102.
BD Rhapsody : Data were processed using rhapsody_wta_2.0b2 pipeline ( https://bitbucket.org/CRSwDev/cwl/src/master/v2.0b2/ ) from BD Genomics.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: other

source_name: mesenteric LN

extract_protocol:
scRNA-seq: spleen or mesLN tissue were harvested and cells were dissociated  using PBS, scissors and syringe plunger on a 40um cell strainer. After washing, cells were counted and CD8+ T cells were enriched using negative selection Mojo Sort magnetic beads (Biolegend). mesLN cells were further stained to detect CD124+ and CD124- CD8+ T cells (anti-CD124-BV421, anti-CD8-FITC, anti-CD44-PECy7, anti-TCRb-BV711, DAPI),  cells and sorted using a FACS Aria uIII (BD Biosciences). Then cells were tagged using mouse multiplexing HashTags 1 to 6 (TotalSeq, Biolegend) or using Mouse multiplexing Sample Tag 1 and 2 (BD Biosciences) before pooled were made. Cell capture was performed using 10X Genomics Chromium controller (spleen samples) or using the BD Rhapsody scanner and express (mesLN).
RNA-seq and TCR-seq: spleens  were harvested and cells were dissociated using PBS, scissors and syringe plunger on a 40um cell strainer. After washing, cells were counted and CD8+ T cells were enriched using negative selection Mojo Sort magnetic beads (Biolegend). Enriched CD8+ T cells were further stained using (anti-CXCR3-BV421, anti-CD8-FITC, anti-CD44-PECy7, anti-TCRb-BV711, anti-CD49d-BV650, anti-CD22-PE, DAPI) and subpopulations sorted using a FACS Aria uIII (BD Biosciences) for each individual mouse (200,000 cells per mouse). Then, total RNA was extracted using the RNeasy micro kit (Qiagen) and eluted in 14 uL of distilled RNAse-free water before stored at -80°C for less then 2 weeks. RNA integrity was analysed using a 2100 Bioanalyzer (Agilent).
scRNA-seq: Chromium Single Cell 3’ v3 chemistry (10X Genomics) or BD Rhapsody Whole Transcriptome Analysis cDNA synthesis (BD Biosciences)
RNA-seq: SMART-seq HT cDNA synthesis kit (Takara)
TCR-seq: template-switch anchored RT-PCR using oligodT during the cDNA generation and the following mouse-specific Cα and Cβ primers for the PCR amplification: TRAC ‘5-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGTCCTGAGACCGAGGATCTTT and TRBC ‘5-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGGGTAGCCTTTTGTTTGTTTG (adapters in italic)

treatment_protocol: IL-4c treatment consisted in the administration of combined recombinant mouse IL-4 (5ug, Biolegend) with monoclonal anti-IL-4 antibody (11B11 clone, 25ug, Biolegend) at day -4 and at day -2 intrapertioneally in 100 uL sterile PBS. H. polygyrus infection consisted in the administration by oral gavage of 200 uL distilled water containing 200 infectious L3 larvae.

value: mesenteric LN

value: CD8+ T cells

value: E8i-Cre Il4ra-lox/lox BALB/c

value: day 15 after H. polygyrus infection


title: PT13 blood engraftment

description:
Library name: CL2
10x Genomics

value: blood


title: Rhapsody-WTA

description: BD Rhapsody


title: Dorsal SBN from PATSF23 - STI

description:
PATSF23-NT
Tachycineta bicolor (Tree swallow)


title: PT15 blood baseline

description:
Library name: CL14
10x Genomics

value: PBMC


title: Ing4-/- LT-HSC

description: Library name: Smaple 2


title: Ventral SBN from PATSF23 - STI

description:
PATSF23-Hypo
Tachycineta bicolor (Tree swallow)


title: satelite cells, CTL, D3 [sample.ctl_3d_2b_p5]

value: satelite cells

value: WT


title: PBSnaive4

description:
PBSnaive_4_R1
Table_RawCounts.csv

source_name: spleen

value: spleen

value: PBS naive T cells

value: BALB/cJ

value: PBS control


title: BETA-mouse-P-vm-6B

description: TRB chain

data_processing:
10X Genomics: The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Hashtags 10X Genomics: Processing of the HTO samples was performed using CITEseq-Count,
Bulk RNAseq: Basecalling performed using Illumina bcl2fastq v2.20 Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence Reads were processed for mapping and quantification using nf-core rnaseq pipeline v3.0.0 (https://nf-co.re/rnaseq/3.0/usage ) and using Gene set from Ensembl.org release 102.
BD Rhapsody : Data were processed using rhapsody_wta_2.0b2 pipeline ( https://bitbucket.org/CRSwDev/cwl/src/master/v2.0b2/ ) from BD Genomics.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: TCR-seq

value: PBS Tvm


title: WT LT-HSC

description: Library name: Sample 1

value: bone maroow


title: PBSnaive3

description:
PBSnaive_3_R1
Table_RawCounts.csv


title: Ventral SBN from PATSF25 - STI

description:
PATSF25-Hypo
Tachycineta bicolor (Tree swallow)

value: STI


title: PT13 blood 3 months post-SCT

description:
Library name: CL12
10x Genomics


title: Dorsal SBN from PATSF22 - Control

description:
PATSF22-NT
Tachycineta bicolor (Tree swallow)

value: Brain (dorsal SBN / diencephalon)

value: Control


title: BETA-mouse-P-vm-5B

description: TRB chain


title: PT17 blood baseline

description:
Library name: CL1
10x Genomics


title: Ing4-/- ST-HSC

description: Library name: Sample 4

value: Hematopoietic stem cell


title: Ventral SBN from PATSF22 - Control

description:
PATSF22-Hypo
Tachycineta bicolor (Tree swallow)

value: Brain (ventral SBN / diencephalon)


title: PT13 ileum baseline

description:
Library name: PL8
10x Genomics

source_name: ileum

value: ileum

value: lamina propria

value: tissue


title: PBSnaive1

description:
PBSnaive_1_R1
Table_RawCounts.csv


title: PBSnaive2

description:
PBSnaive_2_R1
Table_RawCounts.csv


title: BETA-mouse-P-vm-4B

description: TRB chain


title: BETA-mouse-P-vm-3B

description: TRB chain


title: Dorsal SBN from PATSF21 - STI

description:
PATSF21-NT
Tachycineta bicolor (Tree swallow)


title: PBSCD22neg4

description:
PBSCD22neg_4_R1
Table_RawCounts.csv


title: PT11 ileum 6 months post-SCT

description:
Library name: PL19
10x Genomics


title: BETA-mouse-P-vm-2B

description: TRB chain


title: PBSCD22neg3

description:
PBSCD22neg_3_R1
Table_RawCounts.csv


title: Ventral SBN from PATSF21 - STI - EXCLUDED

description:
PATSF21-Hypo
Tachycineta bicolor (Tree swallow)


title: high glucose, rep3

first: Yao Wei

address: 2011 Zonal Ave

department: Department of Medicine

institute: University of Southern California

data_processing:
Sequencing data were processed using Trimmomatic software. Low-quality reads were removed to retain only high-quality sequences for analysis. These clean reads were then aligned to the mouse reference genome GRCm38 (mm10) using the HISAT2 alignment tool. StringTie was used to for transcriptome assembly. The edgeR package in R was used to quantify gene expression.
Assembly: GRCm38/mm10
Supplementary files format and content: gene_count_matrix.csv

source_name: skin

growth_protocol: Primary mouse ECs were obtained from mouse skin and cultured according to previously established protocols with some modifications. Briefly, to isolate ECs from the skin, 4-6 mice aged 2-3 months were used. The mice were anesthetized with isoflurane and humanely euthanized by cervical dislocation. The skin was excised from the mice using surgical scissors or a scalpel, then diced into small fragments on ice and subjected to enzymatic digestion with collagenase Type IV (2 mg/mL; Gibco Laboratories) in a 37°C water bath with agitation (10 rpm) for a duration of 60-90 minutes. Digestion was stopped by adding an equal volume of ice-cold FBS. The resulting digested tissue was filtered through a 40 µm cell strainer (BD) to separate the cells from debris. The resulting cell suspension was then centrifuged at 400 g for 5 minutes at 4°C. 10 μL anti-mouse CD31 MicroBeads (Miltenyi Biotec) were added into about 107 isolated cells in 90 μL of buffer (PBS, pH 7.2, 0.5% BSA, and 2 mM EDTA). The cell mixture was then incubated for 15 minutes at 4 °C. These isolated cells were utilized for downstream experiments.

extract_protocol:
RNA was isolated with TRIzol using manufacture protocol
Illumina library was made in house and sequencing was process by BGI using DNBSeq platform

treatment_protocol: Cells were treated with normal glucose (5 mmol/L) or high glucose (20 mmol/L) medium for 48 hours

value: skin

value: endothelial cell

value: 20 mmol/L glucose


title: PBSCD22neg2

description:
PBSCD22neg_2_R1
Table_RawCounts.csv

value: spleen


title: PT19 ileum baseline

description:
Library name: PL14
10x Genomics


title: PT16 ileum baseline

description:
Library name: CL7
10x Genomics


title: PT14 ileum baseline

description:
Library name: CL31
10x Genomics


title: PBSCD22neg1

description:
PBSCD22neg_1_R1
Table_RawCounts.csv


title: high glucose, rep2


title: PT12 ileum 6 months post-SCT

description:
Library name: CL29
10x Genomics


title: BETA-mouse-P-n-5B

description: TRB chain

value: PBS naive T cells


title: high glucose, rep1


title: IL4cnaive8

description:
IL4cnaive_8_R1
Table_RawCounts.csv

value: IL4c treated naive T cells

value: BALB/cJ

value: IL-4 complex treatment


title: IL4cnaive7

description:
IL4cnaive_7_R1
Table_RawCounts.csv


title: normal glucose, rep3

value: 5 mmol/L glucose


title: BETA-mouse-P-n-4B

description: TRB chain

value: PBS control


title: PT12 jejunum 6 months post-SCT

description:
Library name: CL28
10x Genomics

source_name: jejunum

value: jejunum


title: normal glucose, rep2


title: BETA-mouse-P-n-3B

description: TRB chain


title: PT13 ileum 6 months post-SCT

description:
Library name: CL26
10x Genomics


title: IL4cnaive6

description:
IL4cnaive_6_R1
Table_RawCounts.csv


title: normal glucose, rep1


title: PT15 jejunum baseline

description:
Library name: CL18
10x Genomics


title: RGC, ONC3D, rep2-2

data_processing:
Raw reads were aligned to the GRCm38 (mm10) mouse reference genome using the “Subread” aligner from the Rsubread package, and gene counts were generated using the featureCounts function.
Assembly: mm10
Supplementary files format and content: Comma-separated values (CSV) file includes raw counts for each sample

source_name: retina

extract_protocol:
The RGC-labeled retina was quickly dissected out from mice after cervical dislocation and incubated with 0.5 mg/ml papain at 37 °C for 30 minutes. The retina was then washed with Neurobasal-A medium and triturated into a single-cell suspension by pipetting. After centrifugation at 300g for 6 minutes at 4 °C, the retinal cells were resuspended in Neurobasal-A medium supplemented with 10% B27.Fluorescence-activated cell sorting (FACS) was used to isolate labeled RGCs. AAV-DIO-GFP was injected into the vitreous body of vGlut2-cre mice eye to label RGCs one month before any injury was applied to the animals. FACS gating was performed to isolate the desired population by sequentially excluding dead cells (DAPI-negative), selecting singlet cells, and then gating on GFP-positive cells to enrich the GFP-expressing population. 200 cells from one eye were collected into one tube containing smart-seq2 lysis buffer as a biological replicate. The RGC lysate underwent further processing according to the Smart-seq2 protocol. RNA was reversely transcribed into cDNA using superscript II and TSO primer and followed by amplification with KAPA HiFi HotStart ReadyMix and ISPCR primer for 19 cycles. The amplified product was purified using Ampure XP beads. A fragment analyzer assessed cDNA quality and Qubit dsDNA High Sensitivity (HS) kit measured cDNA concentration. qPCR measured the relative expression level of the Sncg and Rbpms genes.
Then the RGC cDNA was sent to BioCRF in HKUST for full Next Generation Sequencing (NGS) service.

value: retina

tag: isolation day

value: RGC

value: Vglut2-ires-cre knock-in (C57BL/6J), homozygote


title: BETA-mouse-P-n-2B

description: TRB chain


title: IL4cnaive1

description:
IL4cnaive_1_R1
Table_RawCounts.csv


title: BETA-mouse-P-vm-1B

description: TRB chain

value: PBS Tvm


title: BETA-mouse-P-n-6B

description: TRB chain


title: PT15 ileum baseline

description:
Library name: CL17
10x Genomics

value: ileum

value: lamina propria


title: BETA-mouse-P-n-1B

description: TRB chain


title: IL4cCD22neg8

description:
IL4cCD22neg_8_R1
Table_RawCounts.csv

value: IL4c treated CD22- Tvm


title: IL4cCD22neg7

description:
IL4cCD22neg_7_R1
Table_RawCounts.csv


title: RGC, OTI1D, rep2-2


title: BETA-mouse-IL4-vm-5B

description: TRB chain


title: RGC, ONC1D, rep2-2


title: PT18 ileum baseline

description:
Library name: CL10
10x Genomics

value: tissue


title: IL4cCD22neg6

description:
IL4cCD22neg_6_R1
Table_RawCounts.csv


title: BETA-mouse-IL4-vm-6B

description: TRB chain


title: RGC, ONC1D, rep1-2


title: H1299 cells, shWDR4 exosomes, rep1

city: Taipei

first: Nai Yang

last: Yeat

address: 128, Academia Road Sec. 2, Nankang

country: Taiwan

institute: Academia Sinica

data_processing:
Initial assessment of raw sequencing reads is performed using FastQC and miRTrace to evaluate data quality.
Adapter sequences are removed from the reads using TrimGalore to enhance alignment accuracy. Reads are aligned against the mature miRNA sequences from miRBase using Bowtie1.
Separately, reads are aligned to the miRbase hairpin sequences and unaligned reads are processed. For Post-Alignment Processing, SAMtools is utilized for additional processing of the aligned reads, generating basic statistics and ensuring alignment accuracy.
The counts of mature miRNA are analyzed using edgeR, with TMM normalization applied to account for library size differences. The counts of mature are analyzed using DEGseq. Differential expression analysis filters miRNAs with q-value < 0.001 and |logFC| > 2 as significantly differentially expressed miRNAs for subsequent analysis.
Target mRNAs corresponding to the significantly differentially expressed miRNAs are predicted using PITA, TargetScan, and miRanda. The intersection of the predicted target mRNAs from these tools is taken for further analysis. The target mRNAs are subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis using the clusterProfiler R package to identify relevant biological pathways and functions.
Assembly: miRBase using Bowtie1
Supplementary files format and content: Excel file for each independent sample

growth_protocol: H1299 cells were maintained in M10 medium (DMEM High Glucose:DMEM Low Glucose = 1:1) supplemented with 10% fetal bovine serum (FBS) and antibiotics (Penicillin/Streptomycin) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
miRNA was harvested with High Pure miRNA Isolation Kit (Roche).
Sequencing libraries were generated using QIAseq® miRNA Library Kit (QIAGEN, Germany) following the manufacturer’s recommendations. Briefly, 3’ and 5’ adaptors were directly and specifically ligated to 3’ and 5’ end of small RNA, respectively. Then first-strand cDNA was synthesized using QIAseq miRNA NGS RT Enzyme and RT primer. After PCR amplification, the library was size-selected with 170 - 200 bp by QIAseq beads. The quality and quantity of purified libraries were assessed on the Qsep400 system (Bioptic Inc., Taiwan) and Qubit 2.0 Fluorometer (Thermo Scientific, Waltham, MA, USA).

treatment_protocol: H1299 cells were cultured in 15cm petridish with 20ml exosome-free M10 medium for 48 hours.

value: Non-small cell lung cancer cells

value: Wild type


title: IL4cCD228

description:
IL4cCD22_8_R1
Table_RawCounts.csv

value: spleen

value: IL4c treated CD22+ Tvm


title: IL4cCD22neg1

description:
IL4cCD22neg_1_R1
Table_RawCounts.csv

value: BALB/cJ


title: BETA-mouse-IL4-vm-3B

description: TRB chain

value: IL-4 complex treatment


title: RGC, ONC3D, rep1-2


title: BETA-mouse-IL4-vm-2B

description: TRB chain


title: H1299 cells, Control exosomes, rep2


title: IL4cCD227

description:
IL4cCD22_7_R1
Table_RawCounts.csv


title: RGC, OTI7D, rep3-2


title: BETA-mouse-IL4-vm-1B

description: TRB chain


title: H1299 cells, Control exosomes, rep1


title: IL4cCD226

description:
IL4cCD22_6_R1
Table_RawCounts.csv


title: RGC, Intact, rep1-2

value: Intact


title: BETA-mouse-IL4-n-6B

description: TRB chain

value: IL4c treated naive T cells


title: H1299 cells, shWDR4 exosomes, rep2


title: RGC, ONC1D, rep3-2


title: H1299 cells, shWDR4 exosomes, rep3


title: RGC, OTI1D, rep1-2


title: BETA-mouse-IL4-vm-4B

description: TRB chain


title: BETA-mouse-IL4-n-5B

description: TRB chain


title: HTO-WT-Naive

description:
10X Genomics
Hashtags

value: CD8+ T cells

value: Il4ra-lox/lox BALB/c

value: PBS control


title: IL4cCD221

description:
IL4cCD22_1_R1
Table_RawCounts.csv


title: RGC, OTI3D, rep3-2

value: retina

value: RGC

value: Vglut2-ires-cre knock-in (C57BL/6J), homozygote


title: GBM094

first: Christina

last: Jackson

address: 3400 Civic Center Boulevard

department: Neurosurgery

institute: University of Pennsylvania

description:
10X Genomics
MyeloidSeurat.RDS
TumorSeurat.RDS

data_processing:
Lymphoid, myeloid, and tumor data sets were processed separately. After combining raw counts from the filtered output of CellRanger, we further filtered cells based on both minimum number of genes and counts. Selection of each was performed using histograms of each parameter by cell (Figure S1A). In each case, a minimum threshold of 500 genes and 750 UMI counts was sufficient to exclude populations of low-quality cells visible as the lower portion of the bimodal/multimodal distributions visualized in the histogram. Genes expressed in fewer than .1% of the cells were also removed. Finally, counts were normalized to the total UMI count by cell and log-scaled using Seurat.
Seurat’s CellCycleScoring was used to identify cells with high G2M or S phase contributions. While this was not used for regression of gene expression values during scaling of all cells, it was used to identify clusters of cells undergoing mitosis. These clusters were isolated and then scaling was performed on these cells alone with regression of cell cycle scores. Finally, principal component analysis and clustering was performed on the regressed, scaled values to attempt to identify types of cells present in the cycling clusters.
Scaling of both corrected and uncorrected normalized gene expression values was calculated, although the uncorrected values were used only for visualization of differential gene expression with heatmaps. In both cases, values were scaled to a mean of zero and a standard deviation of 4 one by gene. The scaled, corrected values were used for principal component analysis, after which 60 principal components were selected based on elbow plot for all data sets. The 60 principal components were used for dimensional reduction by uniform manifold approximation projection (UMAP) as well as generation of a shared-nearest neighbor network followed by Louvain clustering. Clusters with very similar gene expression profiles were combined and in some cases, clusters were isolated for further clustering.
Data integration was performed using Seurat v3 using reciprocal principal component analysis to project cells into a shared space followed by identification of anchors for mutual nearest neighbor integration. One female and one male patient were selected as references for integration.
Assembly: GRCh38 10X Genomics Ref
Supplementary files format and content: h5 files are filtered outputs from 10X genomics pipeline directly. Seurat objects are RDS files with complete analysis and metadata included.

source_name: Brain

extract_protocol:
Patient tumors or non-malignant brain tissue were mechanically cut into about 1mm3 tissue in DMEM medium (Gibco). They were then enzymatically digested with MACS tumor dissociation kit (Miltenyi Biotec) on the gentleMACS Dissociator (Miltenyi Biotec) per manufacture instructions. Dissociated cells were filtered by a 70-mm strainer and centrifuged at 300g for 7 min. After removing the supernatant, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) for 2 min to remove red blood cells. Tumor samples with significant extent of myelin underwent myelin removal process using magnetic Myelin Removal Beads (Miltenyi Biotec) on the autoMACS (Miltenyi Biotec). The cells were then washed with sorting buffer (PBS supplemented with 2% FBS) and accessed for viability using trypan blue exclusion.
scRNA-sequencing of myeloid and tumor cells were performed using the 10X Single Cell 3’ Gene Expression Kit v3 and scRNA-seq and scTCR-seq of T cells were performed using the 10X Single Cell 5’ Immune Profiling Kit v1.1 (10X Genomics, Pleasanton, CA, USA). Cells were captured in droplets at a targeted cell recovery of 5000-10,000 cells per lane. scRNA library generation was performed per protocol. Following cell barcoding in droplets and reverse 3 transcription, emulsions were broken and cDNA purified using Dynabeads. cDNA was amplified by 11 PCR cycles for 3’ gene expression and 13 PCR cycles for 5’ immune profiling. Amplified cDNA was then used for 3’ gene expression library construction or 5’ gene expression library construction and TCR enrichment.

value: Brain

value: F

tag: 2021 classification

value: Normal

tag: grade


title: BETA-mouse-IL4-n-3B

description: TRB chain


title: RGC, OTI1D, rep3-2

first: Kai

address: Clear water bay

institute: HKUST


title: BETA-mouse-IL4-n-4B

description: TRB chain


title: GBM086


title: GBM089

value: M


title: H1299 cells, Control exosomes, rep3

value: Non-small cell lung cancer cells

value: Wild type


title: HTO-WT-Hp

description:
10X Genomics
Hashtags

value: spleen

value: day 15 after H. polygyrus infection


title: BETA-mouse-IL4-n-2B

description: TRB chain

value: BALB/cJ

value: IL-4 complex treatment


title: GBM082

value: Glioblastoma, IDH-WT

value: IV

value: High

value: wild type

value: not amplified

value: no loss

value: not mutated


title: RGC, OTI7D, rep3-1

value: retina

value: RGC

value: Vglut2-ires-cre knock-in (C57BL/6J), homozygote


title: GBM081

value: Brain

value: F

value: Oligo, IDH-mutant & 1p/19q codel.

value: II

value: Low

value: mutant


title: GBM090

value: M

value: Normal


title: BETA-mouse-IL4-n-1B

description: TRB chain

value: spleen

value: IL4c treated naive T cells

value: BALB/cJ

value: IL-4 complex treatment


title: HTO-KO-IL4C

description:
10X Genomics
Hashtags

value: CD8+ T cells

value: E8i-Cre Il4ra-lox/lox BALB/c


title: BETA-mouse-IL4-cd22-6B

description: TRB chain

value: IL4c treated CD22+ Tvm


title: HTO-KO-Hp

description:
10X Genomics
Hashtags

value: day 15 after H. polygyrus infection


title: RGC, ONC3D, rep3-2

value: retina

value: RGC

value: Vglut2-ires-cre knock-in (C57BL/6J), homozygote


title: HTO-WT-IL4C

description:
10X Genomics
Hashtags

value: Il4ra-lox/lox BALB/c


title: cDNA-WT-Naive

description:
10X Genomics
GEX

value: PBS control


title: GBM077

value: Brain


title: RGC, OTI3D, rep1-2


title: GBM076


title: cDNA-WT-IL4C

description:
10X Genomics
GEX


title: RGC, Intact, rep2-2

value: Intact


title: BETA-mouse-IL4-cd22-5B

description: TRB chain


title: RGC, ONC7D, rep2-2


title: BETA-mouse-IL4-cd22-4B

description: TRB chain


title: BETA-mouse-IL4-cd22-2B

description: TRB chain


title: RGC, OTI7D, rep1-2


title: BETA-mouse-IL4-cd22-3B

description: TRB chain


title: RGC, ONC7D, rep3-2


title: cDNA-WT-Hp

description:
10X Genomics
GEX


title: GBM073

value: M

value: Astrocytoma, IDH-mutant

value: IV

value: High

value: unmethylated

value: mutant

value: not amplified

value: no loss

value: mutated

value: not mutated


title: cDNA-KO-Naive

description:
10X Genomics
GEX

value: spleen

value: CD8+ T cells

value: E8i-Cre Il4ra-lox/lox BALB/c


title: RGC, OTI3D, rep2-2

value: retina

value: RGC

value: Vglut2-ires-cre knock-in (C57BL/6J), homozygote


title: HTO-KO-Naive

description:
10X Genomics
Hashtags

value: PBS control


title: BETA-mouse-IL4-cd22-1B

description: TRB chain

value: IL4c treated CD22+ Tvm

value: BALB/cJ

value: IL-4 complex treatment


title: cDNA-KO-IL4C

description:
10X Genomics
GEX


title: GBM070

value: Brain

value: F

value: Astrocytoma, IDH-mutant

value: II

value: Low


title: RGC, ONC7D, rep1-2


title: GBM069

value: Oligo, IDH-mutant & 1p/19q codel.

value: mutant

value: not amplified

value: no loss


title: ALPHA-mouse-P-vm-6A

description: TRA chain

value: spleen

value: PBS Tvm


title: RGC, ONC3D, rep2-1

value: retina

value: RGC


title: cDNA-KO-Hp

description:
10X Genomics
GEX

value: CD8+ T cells

value: E8i-Cre Il4ra-lox/lox BALB/c

value: day 15 after H. polygyrus infection


title: ALPHA-mouse-P-vm-5A

description: TRA chain

value: BALB/cJ

value: PBS control


title: GBM074

value: Brain

value: F

value: not mutated


title: Conchiformibius steedae in BSTSY+FBS stationary, replicate3

city: Vienna

first: Silvia

last: Bulgheresi

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

data_processing:
Reads adapter-trimmed and filtered using trimmomativ v0.39 (ILLUMINACLIP:adapters.fa:2:30:10 LEADING:3 TRAILING:3 MINLEN:80 SLIDINGWINDOW:4:15) and prinseq-lite v0.20.4 (-min_qual_mean 30 -min_len 25). PhiX contaminant sequences were removed using bbduk.sh of bbmap v38.90 (k=31 hdist=1), as well as further contaminants (human, animal, plant, fungi) removed against repeat-masked references (minid=0.95 maxindel=3 bwr=0.16 bw=12 quickmatch fast minhits=2 qtrim=rl trimq=10 untrim). Reads mapping to rRNA were removed using sortmerna v4.1.0 against the pre-built sortmerna rRNA databases and the organism-specific rRNA sequences. Reads were mapped against the reference genomes (XXX upload Csteedae) using bowtie2 v2.4.4, and Q>30 filtered and index-sorted using samtools v1.9. Reads were counted using featureCounts of the subread-package v2.0.0 in paired-end mode (-s 2 -p -B -C) against the ”gene” features of the reference genomes’ gff-file (see supplementary file).
Assembly: CP097501.1
Supplementary files format and content: raw counts

organism: Conchiformibius steedae DSM 2580

source_name: bacteria

growth_protocol: Cells grown in BSTSY+FBS 37°C 350 rpm

extract_protocol:
500 µl liquid culture were fixed with 1 ml RNAprotect Bacteria Reagent (Qiagen), and cells grown on solid medium scraped off and resuspended in 1 ml thereof, and stored at -70°C until the next day. Total RNA was extracted using the RNeasy® Mini Kit (Qiagen) for low cell numbers, including the on-column DNA digestion. Eluted RNA (30 ul) was treated with 2 U of DNase for 30 min using the TURBO DNA-free kit (Invitrogen). RNA was cleaned up using the RNA Clean & Concentrator-25 kit (Zymo) including the on-column DNA digestion. Absence of DNA was checked via PCR (35 cycles) against a ~200 bp fragment of gyrB.
RNA was quality checked (all samples had a RIN > 9), rRNA depleted using an in-facility developed protocol, and reverse-stranded sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs).

value: bacteria


title: ALPHA-mouse-P-vm-4A

description: TRA chain


title: RGC, OTI1D, rep2-1

value: Vglut2-ires-cre knock-in (C57BL/6J), homozygote


title: GBM068

city: Philadelphia

value: Oligo, IDH-mutant & 1p/19q codel.

value: II

value: Low

value: unmethylated

value: mutant


title: GBM075

value: Astrocytoma, IDH-mutant

value: III

value: High

value: not amplified

value: no loss

value: mutated


title: RGC, ONC1D, rep2-1

city: Hong Kong

value: retina

value: RGC


title: ALPHA-mouse-P-vm-3A

description: TRA chain

value: spleen

value: PBS Tvm

value: BALB/cJ

value: PBS control


title: Conchiformibius steedae in BSTSY+FBS stationary, replicate2

value: bacteria


title: GBM066

value: Brain

value: M

value: Glioblastoma, IDH-WT

value: IV

value: wild type

value: amplified

value: not mutated


title: GBM060

value: F

value: Astrocytoma, IDH-mutant

value: III

value: High

value: unmethylated

value: mutant

value: not amplified


title: RGC, OTI1D, rep1-1

value: retina

value: RGC

value: Vglut2-ires-cre knock-in (C57BL/6J), homozygote


title: Conchiformibius steedae on BSTSY+FBS plate 24h, replicate1

value: bacteria


title: ALPHA-mouse-P-vm-2A

description: TRA chain

value: spleen

value: PBS Tvm

value: BALB/cJ

value: PBS control


title: ALPHA-mouse-P-n-6A

description: TRA chain

value: PBS naive T cells


title: RGC, Intact, rep1-1

value: Intact


title: Conchiformibius steedae on BSTSY+FBS plate 24h, replicate2


title: ALPHA-mouse-P-vm-1A

description: TRA chain


title: Conchiformibius steedae in BSTSY+FBS stationary, replicate1


title: RGC, ONC3D, rep1-1


title: GBM065

value: Brain

value: M

value: Glioblastoma, IDH-WT

value: IV

value: methylated

value: wild type

value: amplified

value: no loss

value: not mutated

value: mutated


title: Conchiformibius steedae in BSTSY+FBS exponential, replicate2

value: bacteria


title: GBM056

value: F

value: High

value: not amplified


title: ALPHA-mouse-P-n-5A

description: TRA chain

value: spleen

value: BALB/cJ

value: PBS control


title: GBM064

value: Brain

value: Astrocytoma, IDH-mutant

value: unmethylated

value: mutant


title: GBM055

value: III

value: methylated


title: Conchiformibius steedae in BSTSY+FBS exponential, replicate3


title: RGC, ONC1D, rep1-1

value: retina

value: RGC

value: Vglut2-ires-cre knock-in (C57BL/6J), homozygote


title: RGC, OTI3D, rep3-1


title: Conchiformibius steedae in BSTSY+FBS exponential, replicate1


title: DOPAC, replicate 2, Chip_seq

city: Jinan

first: Jing

last: Shen

address: Wenhua West Road 44

institute: Shandong University

description: Library name: DOPAC_2

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseg output.
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Cells were fixed with 1% formaledehyde for 10 minutes. After quenching and cell lysis, chromatin was fragmented using Micrococcal Nuclease (Beyotime).
ChIP-seq libraries were prepared using theVAHTS Universal DNA Library Prep Kit for Illumina V4 complemented with VAHTS Multiplex Oligos Set 4/5 for Illumina. 10 ng of DNA wasused as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450 bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated usino the Agilent High Sensitivity DNA Kit.

value: CD8+ T

value: lymphocyte

value: WT

value: DOPAC


title: RGC, OTI3D, rep1-1

last: Liu


title: ALPHA-mouse-P-n-2A

description: TRA chain

value: PBS naive T cells


title: ALPHA-mouse-P-n-3A

description: TRA chain

value: spleen


title: ALPHA-mouse-P-n-4A

description: TRA chain

value: BALB/cJ


title: RGC, ONC1D, rep3-1


title: Conchiformibius steedae on BSTSY+FBS plate 24h, replicate3

value: bacteria


title: GBM059

value: Brain

value: F

value: Oligo, IDH-mutant & 1p/19q codel.

value: II

value: Low

value: not amplified

value: no loss

value: not mutated


title: RGC, OTI7D, rep2-2

value: retina

value: RGC

value: Vglut2-ires-cre knock-in (C57BL/6J), homozygote


title: GBM057

value: Glioblastoma, IDH-WT

value: IV

value: High

value: methylated

value: wild type

value: amplified


title: GBM052

value: Brain

value: M

value: mutated


title: ALPHA-mouse-P-n-1A

description: TRA chain

value: spleen

value: PBS naive T cells

value: BALB/cJ

value: PBS control


title: GBM054

value: F

value: unmethylated

value: not amplified

value: no loss

value: not mutated


title: RGC, OTI1D, rep3-1

value: retina

value: RGC

value: Vglut2-ires-cre knock-in (C57BL/6J), homozygote


title: DOOAC, replicate 1, Chip_seq

description: Library name: DOPAC_1

value: CD8+ T

value: lymphocyte

value: WT

value: DOPAC


title: ALPHA-mouse-IL4-vm-6A

description: TRA chain

value: IL4c treated CD22- Tvm

value: IL-4 complex treatment


title: Control, replicate 2, Chip_seq

description: Library name: Control_2

value: spleen

value: Control


title: ALPHA-mouse-IL4-vm-5A

description: TRA chain

value: BALB/cJ


title: RGC, ONC7D, rep3-1


title: GBM050

value: Brain

value: F

value: Glioblastoma, IDH-WT

value: IV

value: High

value: wild type


title: RGC, OTI7D, rep2-1

value: retina

value: RGC


title: IgG, Chip_seq

description: Library name: IgG

value: CD8+ T


title: GBM046

value: M

value: III

value: methylated

value: not amplified

value: no loss

value: not mutated

value: mutated


title: GBM048

value: amplified


title: ALPHA-mouse-IL4-vm-4A

description: TRA chain

value: spleen

value: IL4c treated CD22- Tvm

value: BALB/cJ

value: IL-4 complex treatment


title: GBM049

value: Brain

value: Glioblastoma, IDH-WT

value: IV

value: High


title: RGC, ONC3D, rep3-1

value: retina

value: RGC

value: Vglut2-ires-cre knock-in (C57BL/6J), homozygote


title: ALPHA-mouse-IL4-vm-2A

description: TRA chain


title: RGC, OTI7D, rep1-1


title: Mutant_S7, 14DPI, rep2

city: Fargo

first: Lili

last: Qi

state: ND

address: 1616 Albrecht Blvd. North

institute: USDA-ARS

data_processing:
Adapters were trimmed and low-quality reads were discarded using Trimmomatic version 0.38
Mapping of apadter trimmed RNA-Seq reads to the sunflower XRQr2.1 reference genome assembly was performed using HISAT2
Transcript assembly and quantification was performed using StringTie (Pertea et al., 2016) and count data was extracted using the Python script prepDE.py3 (http://ccb.jhu.edu/software/stringtie/dl/prepDE.py3).
Differentially expressed genes for comparisons across timepoints and between HA-R9 and mutant lines were subsequently identified using DESeq2
Assembly: XRQr2.1
Supplementary files format and content: File R11_gene_count_matrix.txt is a tab-delimited text file containing read count data for all 27 RNA-seq samples

organism: Helianthus annuus

source_name: Leaf

extract_protocol:
RNA was extracted using RNeasy Plant Mini Kit (Qiagen)
RNA libraries for RNA-seq were prepared by The Genewiz corporation, NJ, USA following their protocols.

value: Leaf

value: Rust inoculation

value: Day 14


title: ALPHA-mouse-IL4-vm-1A

description: TRA chain


title: RGC, Intact, rep2-1

value: Intact


title: Mutant_S7, 14DPI, rep3


title: RGC, ONC7D, rep2-1


title: GBM045

value: F

value: Oligo, IDH-mutant & 1p/19q codel.

value: II

value: Low

value: mutant

value: not mutated


title: ALPHA-mouse-IL4-n-6A

description: TRA chain

value: spleen

value: IL4c treated naive T cells

value: BALB/cJ

value: IL-4 complex treatment


title: Mutant_S7, 14DPI, rep1


title: GBM051

value: Brain

value: M

value: Glioblastoma, IDH-WT

value: IV

value: High

value: unmethylated

value: wild type

value: amplified

value: no loss

value: not amplified


title: Control, replicate 1, Chip_seq

description: Library name: Control_1

value: CD8+ T

value: lymphocyte

value: WT

value: Control


title: RGC, OTI3D, rep2-1

value: retina

value: RGC

value: Vglut2-ires-cre knock-in (C57BL/6J), homozygote


title: GBM043

value: Brain

value: mutated

value: not mutated


title: Mutant_S7, 7DPI, rep3

value: Leaf

value: Rust inoculation

value: Day 7


title: Mutant_S7, 7DPI, rep2


title: RGC, ONC7D, rep1-1


title: ALPHA-mouse-IL4-vm-3A

description: TRA chain

value: spleen

value: IL4c treated CD22- Tvm

value: BALB/cJ

value: IL-4 complex treatment


title: GBM037

value: M

value: Glioblastoma, IDH-WT

value: IV

value: High

value: unmethylated

value: wild type

value: amplified

value: no loss

value: not amplified


title: ALPHA-mouse-IL4-n-3A

description: TRA chain

value: IL4c treated naive T cells


title: GBM035

value: Brain

value: F

value: not mutated


title: Mutant_S7, 0DPI, rep3

value: Leaf

value: Rust inoculation

value: Day 0


title: Control, replicate 1, scRNA_seq

description: Library name: Control_library1

data_processing:
Sequencing data filtered and gene expression matrix was obtained using DNBelab C Series scRNA analysis-software (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software).
Assembly: GRCm38
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: tumor

extract_protocol:
The colon tissues were enzymatically digested into single-cell suspensions using Multi Tissue Dissociation Kits (Miltenyi Biotec)
The single-cell suspensions were converted to barcoded scRNA-seq libraries through steps including droplet encapsulation, emulsion breakage, mRNA captured bead collection, reverse transcription, cDNA amplification, and purification.

value: tumor

value: CD45+ cells

value: lymphocyte

value: WT

value: Control


title: GBM036

value: Glioblastoma, IDH-WT

value: IV

value: High

value: methylated

value: homozygous loss

value: mutated


title: Mutant_S7, 7DPI, rep1

value: Day 7


title: ALPHA-mouse-IL4-n-1A

description: TRA chain

value: spleen

value: IL4c treated naive T cells

value: BALB/cJ

value: IL-4 complex treatment


title: shEhbp1 MASH liver 4

first: Bishuang

last: Cai

address: 675 Charles E. Young Dr South, Rm 1220

department: Medicine

description:
Library name: BC41
shEhbp1.gene.exp.txt

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality. Reads were pre-processed by Trim Galore (v.0.6.3) and Cutadapt programs.
Reads were aligned to the mouse genome mm10 using STAR (v2.7.6a) with the default settings.
Transcript assembly and differential expression analysis were performed using Cufflinks (v2.2.1). Assembling of novel transcripts was not allowed (-G), other parameters of Cufflinks followed the default setting.
A tab-delimited matrix file containing FPKM values for RefSeq genes in each sample generated using Cufflinks.
Assembly: mm10
Supplementary files format and content: tab-delimited text file

source_name: liver

extract_protocol:
Total liver RNA from mice was extracted using the RNeasy kit (Qiagen) according to the manufacturer’s instructions
RNA-seq library construction was performed at BGI with a standard polyA-enrichment protocol.

value: liver

value: Male

value: 18 weeks

value: MASH diet with shEhbp1 virus


title: shEhbp1 MASH liver 3

description:
Library name: BC40
shEhbp1.gene.exp.txt


title: GBM029

value: Brain

value: F

value: unmethylated

value: wild type

value: not amplified

value: no loss

value: not mutated


title: Mutant_S7, 0DPI, rep2

value: Leaf

value: Rust inoculation

value: Day 0


title: DOPAC, replicate 1, scRNA_seq

description: Library name: DOPAC_library1

value: tumor

value: CD45+ cells

value: lymphocyte

value: WT

value: DOPAC


title: Mutant_S7, 0DPI, rep1


title: GBM010

value: M

value: Glioblastoma, IDH-WT

value: IV

value: High

value: methylated

value: amplified

value: mutated


title: ALPHA-mouse-IL4-cd22-6A

description: TRA chain

value: spleen

value: IL4c treated CD22+ Tvm

value: BALB/cJ

value: IL-4 complex treatment


title: shEhbp1 MASH liver 2

description:
Library name: BC38
shEhbp1.gene.exp.txt

value: liver

value: Male

value: 18 weeks

value: MASH diet with shEhbp1 virus


title: GBM030

value: Brain

value: F

value: unmethylated

value: wild type

value: not amplified

value: homozygous loss

value: not mutated


title: Mutant_S6, 14DPI, rep3

value: Leaf

value: Rust inoculation

value: Day 14


title: ALPHA-mouse-IL4-n-5A

description: TRA chain

value: spleen

value: IL4c treated naive T cells


title: ALPHA-mouse-IL4-cd22-5A

description: TRA chain

value: IL4c treated CD22+ Tvm

value: BALB/cJ

value: IL-4 complex treatment


title: Mutant_S6, 14DPI, rep2


title: ALPHA-mouse-IL4-n-4A

description: TRA chain


title: shEhbp1 MASH liver 1

description:
Library name: BC37
shEhbp1.gene.exp.txt

value: liver

value: Male

value: 18 weeks


title: Mutant_S6, 14DPI, rep1


title: GBM009

value: Brain

value: M

value: Glioblastoma, IDH-WT

value: IV

value: High

value: methylated

value: amplified

value: mutated


title: shCon MASH liver 4

description:
Library name: BC35
shEhbp1.gene.exp.txt

value: MASH diet with shCon virus


title: GBM006

value: F

value: unmethylated

value: wild type

value: no loss

value: not amplified

value: not mutated


title: ALPHA-mouse-IL4-cd22-3A

description: TRA chain

value: spleen

value: IL4c treated CD22+ Tvm

value: BALB/cJ

value: IL-4 complex treatment


title: ALPHA-mouse-IL4-n-2A

description: TRA chain

value: IL4c treated naive T cells


title: shCon MASH liver 2

description:
Library name: BC31
shEhbp1.gene.exp.txt

value: liver

value: Male

value: 18 weeks


title: shCon MASH liver 1

description:
Library name: BC30
shEhbp1.gene.exp.txt


title: ALPHA-mouse-IL4-cd22-1A

description: TRA chain


title: Mutant_S6, 7DPI, rep3

value: Leaf

value: Rust inoculation

value: Day 7


title: shCon MASH liver 3

description:
Library name: BC34
shEhbp1.gene.exp.txt

value: MASH diet with shCon virus


title: Mutant_S6, 0DPI, rep3

value: Day 0


title: Mutant_S6, 7DPI, rep2


title: ALPHA-mouse-IL4-cd22-2A

description: TRA chain