title: PBMC_8789_CD_7

description:
Library name: PBMC_8789_CD_7
RNA-Seq of CHIM PBMC


title: PBMC_8342_CD_7

status: Public on Jul 22 2026

type: SRA

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC - locatie AMC

description:
Library name: PBMC_8342_CD_7
RNA-Seq of CHIM PBMC

library_source: transcriptomic

data_processing:
Paired-end reads that passed Illumina quality filters were further screened to remove sequences aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The remaining reads were aligned to the GRCh38 human reference genome with Gencode v27 annotations using STAR (v2.6.1) [PMID: 23104886]. Read complexity was assessed with PRINSEQ Lite (v0.20.3) [PMID: 21278185], and low-complexity reads (DUST score > 4) were excluded from the BAM files. The alignment results were parsed via the SAMtools [PMID: 19505943] to generate SAM files. Gene-level counts were then obtained using featureCounts (v1.6.5) [PMID: 24227677] using the default option along with a minimum quality cut-off (Phred > 10), and transcripts per million (TPM) reads values were calculated. T cell receptor (TCR) transcripts were aggregated into four groups: TCR-α, TCR-β, TCR-γ, and TCR-δ. B cell receptor (BCR) transcripts were aggregated into light chains (IGK and IGL) and heavy chains (IGH-), with isotype transcripts (IGHG1-4, IGHM, IGHD, IGHE, IGHA1-2) analyzed separately. Transcripts were filtered using EdgeR’s filterByExpr function (v4.2.2) [PMID: 39844453] with “participants + timepoint” as the design. For each participant, baseline TPMs were averaged and raw counts were summed. Differential expression was assessed using the DESeq2 package (v1.44.0) [PMID: 25516281] for NPS and EdgeR for PBMCs in an R (v4.4.0) environment, with gene expression called differential with an FDR<0.05. Gene set enrichment analysis (GSEA) was performed using Metascape [PMID: 30944313] and GSEA (v4.4.0) [PMID: 16199517], both with the Gene Ontology (GO) gene sets [PMID: 36866529].
Assembly: GRCh38
Supplementary files format and content: "PBMC_counts.tsv" contains raw count values per sample and gene of PBMC.
Supplementary files format and content: "PBMC_tpm.tsv" contains TPM values per sample and gene of PBMC.
Supplementary files format and content: "PBMC_tpm_baseline_means_BCR_TCR_aggr.csv" contains TPM values per sample and gene in which TCR and BCR genes were aggregated and baseline PBMC samples per participant were averaged.
Supplementary files format and content: "PBMC_counts_baseline_sums_BCR_TCR_aggr.csv" contains counts per sample and gene in which TCR and BCR genes were aggregated and baseline PBMC samples per participant were summed.
Supplementary files format and content: "NPS_counts.csv" contains raw count values per sample and gene of NPS.
Supplementary files format and content: "NPS_tpm.csv" contains TPM values per sample and gene of NPS.
Supplementary files format and content: "NPS_tpm_baseline_means_TCR_BCR_aggr.csv" contains TPM values per sample and gene in which TCR and BCR genes were aggregated and baseline NPS samples per participant were averaged.
Supplementary files format and content: NPS_counts_baseline_sums_BCR.TCR.aggr.csv" contains counts per sample and gene in which TCR and BCR genes were aggregated and baseline NPS samples per participant were summed.
Supplementary files format and content: "participant_metadata_filtered.csv" contains metadata per participant.

molecule: polyA RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
NPS: RNA was extracted with on-column DNase treatment using the miRNeasy Mini Kit (Qiagen) following the manufacturer's instructions. RNA was quantified by qPCR using the housekeeping gene B2M.
PBMC: 500K cells were stored in 750 μL TRIzol at -80°C. RNA until further processing. RNA was extracted with on-column DNase treatment using the miRNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
NPS: For cDNA synthesis, 10 ng of RNA was reverse-transcribed and pre-amplified (14 cycles) according to the Smart-Seq2 protocol. cDNA was purified with AMPure XP beads (Beckman Coulter), and 0.5 ng was used for Nextera XT sequencing library preparation with 8-bp Unique Dual Index (UDI) barcodes (IDT, Illumina) and the Nextera XT DNA Library Preparation Kit (Illumina). To minimize inter-assay variability, all purification steps were performed using an EpMotion 5075 (Eppendorf), and sequencing libraries were prepared in a 96-well format using a Mantis microfluidics liquid dispenser (Formulamatrix). Quality control included assessment of total RNA quality and quantity, optimization of pre-amplification cycle numbers, and fragment size analysis by capillary electrophoresis (5300 Fragment Analyzer, Agilent). cDNA and final libraries were quantified with the Quant-iT PicoGreen assay (Thermo Fisher Scientific). All samples passed quality thresholds, with >70% of fragments ranging from 300–700 bp and <5% primer dimers. Libraries were quantified by qPCR using the KAPA Library Quantification Kit (Roche), normalized to equimolar concentrations, and loaded onto a NovaSeq X Plus sequencing platform (Illumina) with a 25B flow cell. Paired-end sequencing (150 bp) yielded 4.2 billion total reads, corresponding to an average depth of ~15 million reads per sample.
PBMC: Quantabio Sparq mRNA-Seq kit was used to prepare stranded libraries using 8 ng of high-quality total RNA as input, except in 10 samples where the yield was below 8 ng. Libraries underwent 16-18 PCR amplification cycles and libraries were indexed with xGen 10 nt Unique Dual Indexes (UDIs). Paired-end (50x50) sequencing was performed on a NovaSeq 6000 targeting 40 million reads per library.

tag: tissue

value: Blood

tag: age

tag: cell type

value: PBMC

tag: days post_challenge

tag: Sex

value: female


title: PBMC_8784_CD_7

description:
Library name: PBMC_8784_CD_7
RNA-Seq of CHIM PBMC

value: male


title: Col-2, total RNA, rep1

city: Hong Kong

first: Hon-Ming

last: LAM

address: Room EG02, East Block, Science Centre,The Chinese University of Hong Kong,Shatin, N.T. Hong Kong.

department: School of Life Sciences

country: China

institute: The Chinese University of Hong Kong

description: Total RNA

data_processing:
nf-core/rnaseq bioinformatics pipeline version 3.5 (https://nf-co.re/rnaseq/3.5)
FastQC/MultiQC was used to perform quality checking and reporting of sequencing data
mapped to the Arabidopsis thaliana genome (TAIR10) using STAR mapper
read counts of transcripts were quantified using SALMON
Assembly: Mapped to Arabidopsis thaliana genome (TAIR10)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

molecule: total RNA

organism: Arabidopsis

source_name: 11-days seedlings

extract_protocol:
RNA was isolated and purified with Direct-zol RNA Miniprep Kits (Cat.# R2052, Zymo Research).
Stranded rRNA depleted library construction

value: 11-days seedlings

tag: cell line

tag: genotype

value: WT

tag: treatment

value: Mock


title: WT-1

city: Bunkyo-Ku

first: Ge

last: Peng

state: Tokyo

address: 2-1-1 Hongo

country: Japan

institute: Juntendo University Graduate School of Medicine

description:
Library name: SAMPLE-9
Column name in Mus musculus_tpm_table.csv:cKO-1

data_processing:
The process includes poly(A) mRNA enrichment and fragmentation followed by cDNA synthesis, end repair, adaptor ligations, and PCR amplification.
Assembly: Homo sapiens: GRCh38；Mus musculus: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Mus musculus

source_name: mouse melanoma tissue

extract_protocol:
Total RNA was isolated from cultured keratinocytes using an Rneasy Plus Micro Kit according to the manufacturer's instructions
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit

value: mouse melanoma tissue

value: Campf/f

value: Topical Imiquimod cream


title: Col-2, light polysome, rep3

description: Light polysome


title: PBMC_8783_CD_6

description:
Library name: PBMC_8783_CD_6
RNA-Seq of CHIM PBMC


title: PBMC_8782_CD_7

description:
Library name: PBMC_8782_CD_7
RNA-Seq of CHIM PBMC


title: PBMC_8879_CD_6

description:
Library name: PBMC_8879_CD_6
RNA-Seq of CHIM PBMC


title: cDNA WT 37

type: RNA

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: cDNA labelling for wt 37ºC sample. Replicates 1-3

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them by pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.

scan_protocol: Images were acquired using a Fujifilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for variable times.

data_processing: Raw image quantization with background subtracted and Median Absolute Desviation normalization of each triplicate. The average processed value for each gene was corrected by percentage of guanines (RA data) or uracils (TR data) present in each probe-coding strand as described in García-Martinez et al. 2004.

organism: Saccharomyces cerevisiae

source_name: wild type

label_protocol: Genomic Run On (GRO) protocol For GRO samples: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were frozen in liquid nitrogen. Samples were then permeabilized with 1 mL of 0.5% sarkosyl and cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix. For cDNA samples: cDNA was synthetized by reverse transcription of total mRNA using oligo d(T)15VN as primer and 33P-dCTP for labelling.

growth_protocol: Cells were grown in YPD at 25ºC for at least 15 hours to reach early exponential phase at 0.4-0.5 OD600. Then, an aliquot of these cells was spun-down and collected. Another aliquot was transferred to 37ºC and grown for 4 hours. Each sample was analyzed in biological triplicates.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

tag: strain


title: cko-2

description:
Library name: SAMPLE-8
Column name in Mus musculus_tpm_table.csv:WT-2


title: Col-2, light polysome, rep2

description: Light polysome


title: PBMC_8781_CD_7

description:
Library name: PBMC_8781_CD_7
RNA-Seq of CHIM PBMC


title: PBMC_8780_CD_6_reprep

description:
Library name: PBMC_8780_CD_6_reprep
RNA-Seq of CHIM PBMC

tag: reprep

value: Yes


title: PBMC_8780_CD_6

description:
Library name: PBMC_8780_CD_6
RNA-Seq of CHIM PBMC


title: Col-2, light polysome, rep1

description: Light polysome


title: PBMC_8779_CD_6_reprep

description:
Library name: PBMC_8779_CD_6_reprep
RNA-Seq of CHIM PBMC


city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description:
Library name: Sample 3
Mouse brain microvascular fragment (Replicate 3)

data_processing:
The sequencing reads were first aligned to the Ensembl mouse reference genome GRCm39 with STRA (version 2.7.3a). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw counts values for each sample

source_name: brain

extract_protocol:
Brain tissue from adult mice was mechanically and enzymatically dissociated, and vascular fragments were isolated.
Sequencing libraries were prepared from 400ng total RNA using the TruSeq stranded mRNA library preparation kit (cat# 20020595, Illumina Inc.) including polyA selection. Unique dual indexes (cat# 20022371, Illumina Inc.) were used.The library preparation was performed according to the manufacturers’ protocol (#1000000040498). Paired-end 150bp read length were sequenced.

value: brain

value: tissue


title: Col-2, heavy polysome, rep3

description: Heavy polysome


title: PBMC_8778_CD_7

description:
Library name: PBMC_8778_CD_7
RNA-Seq of CHIM PBMC


description:
Library name: Sample 2
Mouse brain microvascular fragment (Replicate 2)


title: PBMC_8775_CD_8

description:
Library name: PBMC_8775_CD_8
RNA-Seq of CHIM PBMC


title: PBMC_8662_CD_6

description:
Library name: PBMC_8662_CD_6
RNA-Seq of CHIM PBMC


title: Col-2, heavy polysome, rep2

description: Heavy polysome


title: PBMC_8591_CD_5

description:
Library name: PBMC_8591_CD_5
RNA-Seq of CHIM PBMC


title: pro arsenic group 5

city: Tsukuba

first: Takehiro

last: Suzuki

state: Ibaraki

address: 16-2 Onogawa

institute: National Institute for Environmental Studies

description: Library name: A5pro

library_source: genomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (ver. 0.6.5)
Adapter-and quality-trimmed sequencing reads were mapped to the mouse reference genomes (mm10) using the Bismark (ver. 0.22.3)
The methylation level of each CpG was calculated using a methylKit package (ver. 1.22.0)
Assembly: mm10
Supplementary files format and content: txt

molecule: genomic DNA

source_name: testis

extract_protocol:
DNA from prospermatogonia was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instructions and used for the construction of RRBS libraries.
RRBS libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina following manufacturer's protocols.

value: testis

value: prospermatogonia


title: AtYchF1 overexpressor, total RNA, rep3

description: Total RNA

value: AtYchF1 overexpressor


title: PBMC_8589_CD_6

description:
Library name: PBMC_8589_CD_6
RNA-Seq of CHIM PBMC


title: pro arsenic group 4

description: Library name: A4pro


title: PBMC_8590_CD_7

description:
Library name: PBMC_8590_CD_7
RNA-Seq of CHIM PBMC


title: PBMC_8342_CD_6

description:
Library name: PBMC_8342_CD_6
RNA-Seq of CHIM PBMC


title: AtYchF1 overexpressor, total RNA, rep2

description: Total RNA


title: PBMC_8338_CD_6

description:
Library name: PBMC_8338_CD_6
RNA-Seq of CHIM PBMC


title: pro arsenic group 3

description: Library name: A3pro


title: AtYchF1 overexpressor, total RNA, rep1

description: Total RNA


title: PBMC_8334_CD_7

description:
Library name: PBMC_8334_CD_7
RNA-Seq of CHIM PBMC


title: pro arsenic group 2

description: Library name: A2pro


title: AtYchF1 overexpressor, light polysome, rep3

description: Light polysome


title: PBMC_8325_CD_5

description:
Library name: PBMC_8325_CD_5
RNA-Seq of CHIM PBMC


title: PBMC_8879_CD_5

description:
Library name: PBMC_8879_CD_5
RNA-Seq of CHIM PBMC


title: pro arsenic group 1

description: Library name: A1pro


title: PBMC_8878_CD_6

description:
Library name: PBMC_8878_CD_6
RNA-Seq of CHIM PBMC


title: AtYchF1 overexpressor, light polysome, rep2

description: Light polysome


title: PBMC_8877_CD_5

description:
Library name: PBMC_8877_CD_5
RNA-Seq of CHIM PBMC


title: pro control group 5

description: Library name: C5pro


title: PBMC_8876_CD_6_reprep

description:
Library name: PBMC_8876_CD_6_reprep
RNA-Seq of CHIM PBMC


title: AtYchF1 overexpressor, light polysome, rep1

description: Light polysome


title: PBMC_8876_CD_6

description:
Library name: PBMC_8876_CD_6
RNA-Seq of CHIM PBMC


title: PBMC_8803_CD_6

description:
Library name: PBMC_8803_CD_6
RNA-Seq of CHIM PBMC


title: PBMC_8802_CD_7

description:
Library name: PBMC_8802_CD_7
RNA-Seq of CHIM PBMC


title: pro control group 4

description: Library name: C4pro


title: pro control group 3

description: Library name: C3pro


title: PBMC_8801_CD_7

description:
Library name: PBMC_8801_CD_7
RNA-Seq of CHIM PBMC


title: AtYchF1 overexpressor, heavy polysome, rep2

description: Heavy polysome


title: PBMC_8779_CD_6

description:
Library name: PBMC_8779_CD_6
RNA-Seq of CHIM PBMC


title: PBMC_8799_CD_7

description:
Library name: PBMC_8799_CD_7
RNA-Seq of CHIM PBMC


title: PBMC_8797_CD_6_reprep

description:
Library name: PBMC_8797_CD_6_reprep
RNA-Seq of CHIM PBMC


title: PBMC_8797_CD_6

description:
Library name: PBMC_8797_CD_6
RNA-Seq of CHIM PBMC


title: pro control group 1

description: Library name: C1pro


title: PBMC_8796_CD_8

description:
Library name: PBMC_8796_CD_8
RNA-Seq of CHIM PBMC


title: Col-2, heavy polysome, rep1

description: Heavy polysome


title: PBMC_8590_CD_7_reprep

description:
Library name: PBMC_8590_CD_7_reprep
RNA-Seq of CHIM PBMC


title: lung_control_rep3

city: Poznań

first: Wojciech

last: Langwiński

address: Fredry

country: Poland

institute: Poznan University of Medical Sciences

description: Gene expression in lungs of control rat.

hyb_protocol: For each array, 600 ng of Cy3-labeled cRNA was fragmented according to the Agilent Gene Expression Hybridization protocol. Fragmentation was carried out at elevated temperature in the presence of Agilent fragmentation buffer and blocking agent, followed by immediate cooling on ice. The fragmentation reaction was stopped by adding 2× Hi-RPM hybridization buffer. Hybridization mixtures were carefully loaded onto SurePrint G3 Rat Gene Expression 8×60K Microarrays (Agilent Technologies) and assembled in Agilent hybridization chambers. Arrays were hybridized for 16 hours at 65 °C in a rotating hybridization oven. Following hybridization, slides were disassembled and washed sequentially in Gene Expression Wash Buffer 1 at room temperature and Gene Expression Wash Buffer 2 at 37 °C, supplemented with Triton X-102, and then dried immediately prior to scanning.

scan_protocol: Microarray slides were scanned immediately after washing using the SureScan Dx Microarray Scanner (Agilent Technologies) to minimize signal degradation. Scanning was performed in one-color mode using settings optimized for SurePrint G3 8×60K arrays, with the green (Cy3) channel enabled. The active surface of each slide was oriented according to the manufacturer’s recommendations. Raw image files were generated for subsequent feature extraction and data analysis.

data_processing: Scanned images were processed using Agilent Feature Extraction software with standard one-color gene expression settings and the appropriate grid file for the SurePrint G3 Rat Gene Expression 8×60K platform. Background subtraction and spatial detrending were applied automatically. Features flagged as non-uniform or unreliable by the software were excluded from further analysis. Downstream normalization, quality control, and statistical analyses were performed in GeneSpring GX version 15.5. Differential gene expression was assessed using an unpaired t-test with Benjamini–Hochberg correction for multiple testing. Genes with an adjusted p-value below the accepted threshold and a fold-change of at least 1.5 were considered differentially expressed.

organism: Rattus norvegicus

source_name: lung, control rat 3

label_protocol: Total RNA was isolated from lung and adipose tissue samples and assessed for quality and purity prior to microarray analysis (RIN > 7.0; A260/A280 = 1.8–2.0; A260/A230 > 2.0). RNA concentration was determined using a NanoDrop 2000 spectrophotometer. For each sample, 50 ng of total RNA was used as input for labeling. Cyanine-3 (Cy3)–labeled cRNA was generated using the Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies), following the manufacturer’s instructions. External RNA spike-in controls were added according to the recommended protocol. After in vitro transcription and labeling, amplified cRNA was purified using RNeasy Mini columns (QIAGEN). cRNA yield, dye incorporation, and specific activity were measured spectrophotometrically, and only samples meeting quality criteria were used for downstream hybridization

extract_protocol: Tissues were minced in liquid nitrogen, and RNA was extracted using QIAzol Lysis Reagent according to the manufacturer’s instructions.

treatment_protocol: Brown Norway rats (male, 7-week-old) were sensitized and challenged with house dust mite (HDM). Animals in the study group (n = 5) were subcutaneously injected with 45 µg of HDM in Al(OH)₃ as an adjuvant once per week for three weeks and then intranasally challenged with 120 µg of HDM in saline three times per week for three weeks. Animals in the control group (n = 3) received saline in Al(OH)₃ for subcutaneous sensitization and saline intranasally for challenge.

value: lung

tag: gender


title: PBMC_8793_CD_7

description:
Library name: PBMC_8793_CD_7
RNA-Seq of CHIM PBMC

value: Blood


title: PBMC_8790_CD_6_reprep

description:
Library name: PBMC_8790_CD_6_reprep
RNA-Seq of CHIM PBMC

value: PBMC


title: PBMC_8790_CD_6

description:
Library name: PBMC_8790_CD_6
RNA-Seq of CHIM PBMC

value: female


title: typeA arsenic group 3

description: Library name: A3typeA

extract_protocol:
DNA from type A spermatogonia was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen) according to the manufacturer’s instructions and used for the construction of RRBS libraries.
RRBS libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina following manufacturer's protocols.

value: typeAspermatogonia


title: PBMC_8789_CD_6

description:
Library name: PBMC_8789_CD_6
RNA-Seq of CHIM PBMC

value: male


title: lung_control_rep1

source_name: lung, control rat 1


title: PBMC_8784_CD_6_reprep

description:
Library name: PBMC_8784_CD_6_reprep
RNA-Seq of CHIM PBMC


title: typeA arsenic group 2

description: Library name: A2typeA


title: PBMC_8784_CD_6

description:
Library name: PBMC_8784_CD_6
RNA-Seq of CHIM PBMC


title: PBMC_8783_CD_5

description:
Library name: PBMC_8783_CD_5
RNA-Seq of CHIM PBMC


title: lung_HDM-induced_rep5

description: Gene expression in lungs of HDM-induced rat.

source_name: lung, HDM-induced rat 5


title: lung_HDM-induced_rep4

source_name: lung, HDM-induced rat 4


title: PBMC_8782_CD_6

description:
Library name: PBMC_8782_CD_6
RNA-Seq of CHIM PBMC


title: AtYchF1 overexpressor, heavy polysome, rep3

description: Heavy polysome

value: 11-days seedlings


title: typeA arsenic group 1

description: Library name: A1typeA


title: PBMC_8781_CD_6

description:
Library name: PBMC_8781_CD_6
RNA-Seq of CHIM PBMC


title: typeA control group 4

description: Library name: C4typeA


title: PBMC_8876_CD_7_reprep

description:
Library name: PBMC_8876_CD_7_reprep
RNA-Seq of CHIM PBMC


title: lung_HDM-induced_rep3

source_name: lung, HDM-induced rat 3


title: PBMC_8779_CD_5_reprep

description:
Library name: PBMC_8779_CD_5_reprep
RNA-Seq of CHIM PBMC


title: PBMC_8780_CD_5

description:
Library name: PBMC_8780_CD_5
RNA-Seq of CHIM PBMC


title: typeA control group 3

description: Library name: C3typeA


title: lung_HDM-induced_rep2

source_name: lung, HDM-induced rat 2


title: pro control group 2

description: Library name: C2pro


title: PBMC_8779_CD_5

description:
Library name: PBMC_8779_CD_5
RNA-Seq of CHIM PBMC


title: AtYchF1 overexpressor, heavy polysome, rep1

description: Heavy polysome

value: Mock


title: PBMC_8802_CD_8

description:
Library name: PBMC_8802_CD_8
RNA-Seq of CHIM PBMC


title: typeA control group 2

description: Library name: C2typeA


title: lung_HDM-induced_rep1

source_name: lung, HDM-induced rat 1


title: PBMC_8775_CD_3

description:
Library name: PBMC_8775_CD_3
RNA-Seq of CHIM PBMC


title: PBMC_8662_CD_5

description:
Library name: PBMC_8662_CD_5
RNA-Seq of CHIM PBMC


title: typeA control group 1

description: Library name: C1typeA


title: PBMC_8591_CD_4

description:
Library name: PBMC_8591_CD_4
RNA-Seq of CHIM PBMC


title: adipose_tissue_control_rep3

description: Gene expression in adipose tissue of control rat.

source_name: adipose tissue, control rat 3

value: adipose tissue


title: PBMC_8590_CD_6

description:
Library name: PBMC_8590_CD_6
RNA-Seq of CHIM PBMC


title: lung_control_rep2

description: Gene expression in lungs of control rat.

source_name: lung, control rat 2


title: typeA arsenic group 4

description: Library name: A4typeA


title: RNA-seq of vehicle-injected WT mouse hippocampus replicate 3

city: Gwangju

first: Eunkyung

last: Lee

address: 123 Cheomdan-gwagiro, Buk-gu

country: South Korea

institute: Gwangju Institute of Science and Technology

description: Library name: WT_Veh3

data_processing:
Raw sequencing reads were assessed for quality using FastQC.
Assembly: Mus musculus GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Hippocampus

extract_protocol:
Total RNA was extracted from mouse hippocampal tissue using TRIzol reagent according to the manufacturer's instructions. RNA quality and integrity were assessed prior to library preparation.
RNA-seq libraries were prepared from total RNA using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer's protocol.

value: Hippocampus


title: adipose_tissue_control_rep2

source_name: adipose tissue, control rat 2


title: PBMC_8589_CD_5

description:
Library name: PBMC_8589_CD_5
RNA-Seq of CHIM PBMC

source_name: Blood


title: PBMC_8342_CD_5_reprep

description:
Library name: PBMC_8342_CD_5_reprep
RNA-Seq of CHIM PBMC


title: RNA-seq of vehicle-injected WT mouse hippocampus replicate 2

description: Library name: WT_Veh2


title: PBMC_8342_CD_5

description:
Library name: PBMC_8342_CD_5
RNA-Seq of CHIM PBMC


title: PBMC_8778_CD_6

description:
Library name: PBMC_8778_CD_6
RNA-Seq of CHIM PBMC


title: adipose_tissue_control_rep1

source_name: adipose tissue, control rat 1


title: PBMC_8338_CD_5

description:
Library name: PBMC_8338_CD_5
RNA-Seq of CHIM PBMC


title: RNA-seq of vehicle-injected WT mouse hippocampus replicate 1

description: Library name: WT_Veh1


title: adipose_tissue_HDM-induced_rep5

description: Gene expression in adipose tissue of HDM-induced rat.

source_name: adipose tissue, HDM-induced rat 5


title: PBMC_8336_CD_6

description:
Library name: PBMC_8336_CD_6
RNA-Seq of CHIM PBMC


title: PBMC_8334_CD_6

description:
Library name: PBMC_8334_CD_6
RNA-Seq of CHIM PBMC


title: RNA-seq of vehicle-injected 5xFAD mouse hippocampus replicate 3

description: Library name: 5xFAD_Veh_3


title: adipose_tissue_HDM-induced_rep4

source_name: adipose tissue, HDM-induced rat 4


title: PBMC_8325_CD_9

description:
Library name: PBMC_8325_CD_9
RNA-Seq of CHIM PBMC


title: PBMC_8878_CD_5

description:
Library name: PBMC_8878_CD_5
RNA-Seq of CHIM PBMC


title: adipose_tissue_HDM-induced_rep3

source_name: adipose tissue, HDM-induced rat 3


title: PBMC_8879_CD_4

description:
Library name: PBMC_8879_CD_4
RNA-Seq of CHIM PBMC


title: RNA-seq of vehicle-injected 5xFAD mouse hippocampus replicate 2

description: Library name: 5xFAD_Veh_2


title: PBMC_8877_CD_4

description:
Library name: PBMC_8877_CD_4
RNA-Seq of CHIM PBMC


title: RNA-seq of vehicle-injected 5xFAD mouse hippocampus replicate 1

description: Library name: 5xFAD_Veh_1


title: adipose_tissue_HDM-induced_rep2

source_name: adipose tissue, HDM-induced rat 2


title: PBMC_8876_CD_5

description:
Library name: PBMC_8876_CD_5
RNA-Seq of CHIM PBMC


title: adipose_tissue_HDM-induced_rep1

source_name: adipose tissue, HDM-induced rat 1


title: RNA-seq of QA-injected 5xFAD mouse hippocampus replicate 2

description: Library name: 5xFAD_QA_2


title: cko-1

description:
Library name: SAMPLE-7
Column name in Mus musculus_tpm_table.csv:WT-1

source_name: mouse melanoma tissue

value: mouse melanoma tissue

value: Topical Imiquimod cream


title: PBMC_8803_CD_5

description:
Library name: PBMC_8803_CD_5
RNA-Seq of CHIM PBMC


title: PBMC_8802_CD_6

description:
Library name: PBMC_8802_CD_6
RNA-Seq of CHIM PBMC


title: RNA-seq of QA-injected 5xFAD mouse hippocampus replicate 3

description: Library name: 5xFAD_QA_3


title: RNA-seq of QA-injected 5xFAD mouse hippocampus replicate 1

description: Library name: 5xFAD_QA_1


title: 1910_lib_19152AAE

city: Valencia

first: Jordi

last: Planells

address: Doctor Moliner, 50 street

department: Biologia celular, biologia funcional y antropologia fisica

institute: Universitat de València

description: Library name: WT input replicate 2

data_processing:
Initial read quality assessment with FastQC (v 0.11.5)
Truseq adapter was trimmed. Low quality (q > 20) and short reads (length < 40bp) were discarded. fastp (v.0.23.1)
Read mapping to reference genome (see below) with Hisat2 (v2.2.1)
Samtools (v1.13) was used to process raw alignments. Duplicate reads were eliminated (samtools rmdup) and processed files were sorted and indexed (samtools sort, index)
Metagenes were obtained with ngs.plot (v.2.61), representing the sequencing depth normalized log2 (IP/Input) signal.
Assembly: R64-1-1, Assembly GCA_000146045.2
Supplementary files format and content: Signal tracks for inputs and IPs in .bedgraph format. Gzip compressed

growth_protocol: Yeast cell cultures were grown at 25°C in YPD and transferred to 37°C for 4 hours. For the cross-linking reaction, formaldehyde was added (1% final concentration) to a volume of 45 mL of culture for 15 min at room temperature with occasional inversion.

extract_protocol:
ChIP was performed as previously described in Li et al., 2016. DNA was purified using the GeneJET PCR Purification Kit (Thermo Fisher Scientific, #K0702)
NEBNext Ultra II DNA Library Prep kit for Illumina

value: MATa ura3delta0 leu2delta0 his3delta1 met15delta0

tag: batch


title: PBMC_8796_CD_7

description:
Library name: PBMC_8796_CD_7
RNA-Seq of CHIM PBMC


title: 1909_lib_19151AAE

description: Library name: WT input replicate 1


title: PBMC_8797_CD_5_reprep

description:
Library name: PBMC_8797_CD_5_reprep
RNA-Seq of CHIM PBMC

value: Yes


title: PBMC_8801_CD_6

description:
Library name: PBMC_8801_CD_6
RNA-Seq of CHIM PBMC


title: PBMC_8797_CD_5

description:
Library name: PBMC_8797_CD_5
RNA-Seq of CHIM PBMC


title: PBMC_8799_CD_6

description:
Library name: PBMC_8799_CD_6
RNA-Seq of CHIM PBMC


title: PBMC_8790_CD_5

description:
Library name: PBMC_8790_CD_5
RNA-Seq of CHIM PBMC


title: 1906_lib_19149AAE

description: Library name: WT eIF5 ChIP replicate 1


title: PBMC_8789_CD_5_reprep

description:
Library name: PBMC_8789_CD_5_reprep
RNA-Seq of CHIM PBMC


title: PBMC_8784_CD_5

description:
Library name: PBMC_8784_CD_5
RNA-Seq of CHIM PBMC


title: Patient14, Grade 4, IDH1 wt, Primary

city: Taipei

first: Wen-Bin

last: Yang

address: 250 Wu-Hsing Street

country: Taiwan

institute: Taipei Medical University

description:
Library name: Patient14_Primary
Column name in counts_All_Samples.txt: Patient14_Primary

data_processing:
The sequence was directly determined using Illumina's sequencing-by-synthesis (SBS) technology. Sequencing data (FASTQ files) were generated by Welgene's pipeline based on Illumina's basecalling program bcl2fastq v2.2.0.
BaseCall Conversion Illumina official tool, bcl2fastq2 conversion Software v2.20 can be used to convert BCL files from all Illumina sequencing systems.
Adaptor Clipping In addition to removing lower base quality data, one would also remove adapters, PCR primers and other artifacts. In practice one would combine the adapter clipping with quality trimming approaches.
Sequence Quality Trimming In order to cope with lower quality data, quality trimming is required to remove low quality reads/bases. Typically, one would remove lower quality bases from the the 3' end using a sliding-window approach as the per base quality gradually drops toward the 3' end of reads. Trimmomatic is a tool for trimming Illumina FASTQ data and removing adapters using a sliding-window apporach. Both adaptor clipping and sequence quality trimming were accomplished by Trimmomatic Ver 0.36.
Alignment Tool: HISAT2 HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads to genomes. The new indexing scheme of HISAT2 is based on hierarchical graph FM index (GFM index). HISAT2 using global GFM index and a large set of small GFM indexes that collectively cover the whole genome for rapid and accurate alignment. Furthermore, small GFM index sets come with a great performance for splicing junction alignment, so HISAT2 could be an effective tools for transcriptome alignment.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: Brain tumor

extract_protocol:
Total RNA was extracted using Trizol® Reagent (Invitrogen, USA) according to the instruction manual. Purified RNA was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology,USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 LabChip kit (Agilent Technologies, USA).
All RNA Sample preparation procedures were carried out according to the official Illumina protocol. Agilent's SureSelect Strand-Specific RNA Library Preparation Kit were used for library construction followed by AMPure XP Beads size selection.

value: Brain tumor

tag: subject id

tag: grade

value: Grade 4

value: IDH1 wt

tag: tissue type

value: Primary


title: PBMC_8783_CD_4

description:
Library name: PBMC_8783_CD_4
RNA-Seq of CHIM PBMC

value: Blood


title: Control 2

city: Atlanta

first: Valentina

last: Daponte

state: Georgia

address: 21 Ortho Ln

country: USA

institute: Emory University

description: Library name: Sample 2

data_processing:
Raw data were exported in FASTQ (fq) format and FastQC (v0.11.8) was applied to check error rate and GC content distribution
Trimmomatic (v0.38) was used to cut adaptors and trim low-quality bases with default settings
Trimmed reads  were aligned to the Mus musculus GRCm38 reference genome using DNASTAR SeqMan Ngen
Unique gene hit counts were calculated using HTseq-count (version 0.11.2).
Assembly: GRCm38
Supplementary files format and content: Microsoft Excel Comma Separated Values File (.csv) includes raw counts for each Sample

source_name: bone

growth_protocol: Femurs and tibias were collected, distal and proximal epiphyses were cut away with a scalpel, and bone marrow was removed. The periosteum was aseptically removed using a scalpel, and bones were bisected lengthwise to expose the endosteum. The long bones from each mouse were combined and incubated with 4 mL of collagenase solution (3 mg/mL Collagenase Type II in PBS, Gibco) at 37 °C for 15 min under continuous agitation. The first digestion was discarded, and bones were digested in two additional 4 mL collagenase solutions for 30 min each. Cells recovered with each digestion were mixed with an equal volume of α-MEM (Gibco) supplemented with 10% FBS (Gibco), 1x antibiotic-antimycotic (Gibco). Cells were pelleted at 2000 x g for 5 min and used for RNA isolation.

extract_protocol:
RNA was isolated using the RNeasy Kit (Qiagen) following manufacturer’s instructions. The purification included a DNase treatment using the RNase free DNase Set (Qiagen). Libraries were prepared from a minimum of 35 ng of RNA.
Library preparation and ultra-low input sequencing were performed at Admera Health. Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit (New England Biosciences) using PolyA Selection.

value: bone


title: LysM-Cre;Wnt5aF/F 3

description: Library name: Sample 6


title: PBMC_8790_CD_5_reprep

description:
Library name: PBMC_8790_CD_5_reprep
RNA-Seq of CHIM PBMC

value: PBMC

value: female


title: LysM-Cre;Wnt5aF/F 2

description: Library name: Sample 5


description:
Library name: Sample 1
Mouse brain microvascular fragment (Replicate 1)

source_name: brain

value: brain

value: tissue


title: 1907_lib_19150AAE

description: Library name: WT eIF5 ChIP replicate 2


title: PBMC_8793_CD_6

description:
Library name: PBMC_8793_CD_6
RNA-Seq of CHIM PBMC


title: Patient14, Grade 4, IDH1 wt, Recurrent

description:
Library name: Patient14_Recurrent
Column name in counts_All_Samples.txt: Patient14_Recurrent

value: Recurrent


title: PBMC_8336_CD_7

description:
Library name: PBMC_8336_CD_7
RNA-Seq of CHIM PBMC


title: Control 3

description: Library name: Sample 3


title: LysM-Cre;Wnt5aF/F 1

description: Library name: Sample 4


title: PBMC_8789_CD_5

description:
Library name: PBMC_8789_CD_5
RNA-Seq of CHIM PBMC

value: male


title: PBMC_8784_CD_5_reprep

description:
Library name: PBMC_8784_CD_5_reprep
RNA-Seq of CHIM PBMC


title: PBMC_8782_CD_5

description:
Library name: PBMC_8782_CD_5
RNA-Seq of CHIM PBMC


title: Patient13, Grade 4, IDH1 wt, Recurrent

description:
Library name: Patient13_Recurrent
Column name in counts_All_Samples.txt: Patient13_Recurrent


title: GM71001

city: 北京市

first: Zhaochen

last: Wang

address: 2 Yuanmingyuan West Road, Haidian District, Beijing

institute: China Agricultural University

description: Library name: M71001

data_processing:
Clean paired-end RNA-seq reads were aligned to the Bos taurus reference genome (ARS-UCD1.2) using HISAT2 (v2.2.1) with default settings except that only uniquely mapping reads were retained.
Gene-level read quantification was performed with featureCounts (Subread) using parameters -t exon -g gene_id against the corresponding GTF annotation.
Assembly: ARS-UCD1.2
Supplementary files format and content: counts_hisat2_all.txt

organism: Bos taurus

source_name: ovary

extract_protocol:
For single oocytes and cumulus cells (CCs), cells were lysed directly using the Single Cell Full-Length mRNA Amplification Kit (Vazyme). For mural granulosa cells (MGCs), total RNA was extracted using standard protocols.
For oocytes and CCs, cDNA was amplified using the SMART-seq2 protocol and libraries were constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme). For MGCs, standard bulk RNA-seq libraries were constructed. All libraries were sequenced on an Illumina NovaSeq 6000 platform.

value: ovary

value: mural granulosa cells

value: MGCs from medium follicle (7.1mm)


title: Brain single cell 187

description: Library name: Sample 187

data_processing:
The sequencing reads were first aligned to the Ensembl mouse reference genome GRCm39 with STRA (version 2.7.3a). The duplicated reads were removed using samtools software (version 1.16.1). The raw read counts for each gene were then calculated using featureCounts function from the Subread package (version 1.4.6-p5)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw counts values for each sample

extract_protocol:
Brain tissue from adult mice was mechanically and enzymatically dissociated, and vascular fragments were isolated, followed by further digestion to obtain a single-cell suspension.
Libraries for RNA-seq were prepared by using SMART-seq2 methodology

value: microglia


title: GL62802

description: Library name: M62802

value: MGCs from large follicle (10.2mm)


title: PBMC_8780_CD_4

description:
Library name: PBMC_8780_CD_4
RNA-Seq of CHIM PBMC


title: PBMC_8779_CD_4_reprep

description:
Library name: PBMC_8779_CD_4_reprep
RNA-Seq of CHIM PBMC

value: Yes


title: GM70502

description: Library name: M70502

value: MGCs from medium follicle (6.4mm)


title: Brain single cell 174

description: Library name: Sample 174


title: DEN-initiated SOR- and CAF-treated mouse replicate 5

city: Botucatu

first: Guilherme

middle: Ribeiro

last: Romualdo

state: SP

address: Rua Dr José Barbosa de Barros, 1486

country: Brazil

institute: UNESP

description:
Library name: CAF_SOR5
Column name in CAF_SOR_FPKM.csv: CAF_SOR5

data_processing:
Raw reads of fastq format were first 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 (Bolger et al., 2014). All the downstream analyses were based on clean data with high quality. Reference genome (GRCm39/mm39) and gene model annotation files were downloaded from the genome website directly. The index of the reference genome was built, and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. The abundance of each transcript was quantified using feature Counts v1.5.0-p3.
Assembly: GRCm39/mm39
Supplementary files format and content: csv. files contain fpkm data for each sample

source_name: Liver

extract_protocol:
Total RNA was isolated using QIAzol lysis reagent and RNeasy column-based system (Qiagen, UK) according to the manufacturer's instructions.
SMARTer Prep Kit according to the manufacturer's instructions

treatment_protocol: Five-week-old male mice of HCC-susceptible C3H/HeJ mice (n=30 animals) were obtained from the University of São Paulo and kept in the animal facility of the Experimental Research Unit (UNIPEX) at São Paulo State University (Botucatu). After acclimatization, the animals were subjected to a chemically induced model of hepatocarcinogenesis, undergoing 5 cycles of intraperitoneal (i.p.) applications of the diethylnitrosamine (DEN) carcinogen: twice a week, at a dose of 25 mg/kg of body weight (b.w.) for 3 weeks, followed by a one-week rest period. Negative controls received 0.9% saline solution with the same frequency and route of administration. After the five DEN cycles (4 months), the animals had a one-month rest period and were then allocated into 5 experimental groups (Figure 1A) (n=6 animals/group): some were treated with CAF (50 mg/kg b.w., 3×/week) via intragastric (i.g.) administration (Romualdo et al., 2020); SOR (30 mg/kg b.w., i.g., 2×/week, vehicle: corn oil + 2% DMSO) alone (Liu et al., 2006); CAF + SOR (same regimen) or vehicles for 3 weeks (Figure 1A). CAF was administered on Mondays, Wednesdays, and Fridays, while SOR was given on Tuesdays and Thursdays, all in the morning (8-9 h). The remaining animals received the drug vehicles at the respective frequencies and routes of administration: SOR was dissolved in 100% DMSO and diluted in saline corn oil to the desired concentration with a final DMSO concentration of 2% (v/v). CAF was directly diluted in tap water.

value: Liver


title: PBMC_8781_CD_5

description:
Library name: PBMC_8781_CD_5
RNA-Seq of CHIM PBMC


title: Brain single cell 191

description: Library name: Sample 191


title: PBMC_8778_CD_5

description:
Library name: PBMC_8778_CD_5
RNA-Seq of CHIM PBMC


title: PBMC_8779_CD_4

description:
Library name: PBMC_8779_CD_4
RNA-Seq of CHIM PBMC


title: PBMC_8780_CD_4_reprep

description:
Library name: PBMC_8780_CD_4_reprep
RNA-Seq of CHIM PBMC


title: DEN-initiated SOR- and CAF-treated mouse replicate 4

description:
Library name: CAF_SOR4
Column name in CAF_SOR_FPKM.csv: CAF_SOR4


title: Patient12, Grade 4, IDH1 mutant, Primary

description:
Library name: Patient12_Primary
Column name in counts_All_Samples.txt: Patient12_Primary

value: Brain tumor

value: Grade 4

value: IDH1 mutant

value: Primary


title: Patient13, Grade 4, IDH1 wt, Primary

description:
Library name: Patient13_Primary
Column name in counts_All_Samples.txt: Patient13_Primary

value: IDH1 wt


title: PBMC_8662_CD_4

description:
Library name: PBMC_8662_CD_4
RNA-Seq of CHIM PBMC

value: Blood

value: PBMC


title: Control 1

description: Library name: Sample 1

value: bone


title: Patient12, Grade 4, IDH1 mutant, Recurrent

description:
Library name: Patient12_Recurrent
Column name in counts_All_Samples.txt: Patient12_Recurrent

value: Recurrent


title: DEN-initiated SOR- and CAF-treated mouse replicate 3

description:
Library name: CAF_SOR3
Column name in CAF_SOR_FPKM.csv: CAF_SOR3


title: PBMC_8590_CD_5

description:
Library name: PBMC_8590_CD_5
RNA-Seq of CHIM PBMC

value: male


title: Patient11, Grade 4, IDH1 wt, Recurrent

description:
Library name: Patient11_Recurrent
Column name in counts_All_Samples.txt: Patient11_Recurrent


title: PBMC_8589_CD_4_reprep

description:
Library name: PBMC_8589_CD_4_reprep
RNA-Seq of CHIM PBMC

value: female


title: PBMC_8589_CD_4

description:
Library name: PBMC_8589_CD_4
RNA-Seq of CHIM PBMC


title: DEN-initiated SOR- and CAF-treated mouse replicate 2

description:
Library name: CAF_SOR2
Column name in CAF_SOR_FPKM.csv: CAF_SOR2


title: Patient11, Grade 4, IDH1 wt, Primary

description:
Library name: Patient11_Primary
Column name in counts_All_Samples.txt: Patient11_Primary


title: DEN-initiated SOR- and CAF-treated mouse replicate 1

description:
Library name: CAF_SOR1
Column name in CAF_SOR_FPKM.csv: CAF_SOR1


title: PBMC_8342_CD_4

description:
Library name: PBMC_8342_CD_4
RNA-Seq of CHIM PBMC


title: PBMC_8338_CD_4

description:
Library name: PBMC_8338_CD_4
RNA-Seq of CHIM PBMC


title: PBMC_8336_CD_5

description:
Library name: PBMC_8336_CD_5
RNA-Seq of CHIM PBMC


title: Patient10, Grade 4, IDH1 wt, Recurrent

description:
Library name: Patient10_Recurrent
Column name in counts_All_Samples.txt: Patient10_Recurrent


title: PBMC_8334_CD_5

description:
Library name: PBMC_8334_CD_5
RNA-Seq of CHIM PBMC


title: DEN-initiated SOR-treated mouse replicate 4

description:
Library name: SOR4
Column name in SOR_FPKM.csv: SOR4


title: Patient10, Grade 4, IDH1 wt, Primary

description:
Library name: Patient10_Primary
Column name in counts_All_Samples.txt: Patient10_Primary


title: PBMC_8325_CD_4

description:
Library name: PBMC_8325_CD_4
RNA-Seq of CHIM PBMC


title: PBMC_8879_CD_3_reprep

description:
Library name: PBMC_8879_CD_3_reprep
RNA-Seq of CHIM PBMC


title: DEN-initiated SOR-treated mouse replicate 3

description:
Library name: SOR3
Column name in SOR_FPKM.csv: SOR3


title: ATAC-seq, Bonobo LCL, Nutlin, 1 hour, rep 2

city: Boulder

first: Robin

middle: D.

last: Dowell

state: CO

address: 596 UCB

department: Molecular, Cellular and Developmental Biology

institute: University of Colorado Boulder

data_processing:
Read quality was assessed using FastQC (v0.11.5).
Read quality and adapter trimming was done using BBMap (v38.05) bbduk with options ktrim=r qtrim=10, k=23, mink=11, hdist=1, maq=10, minlen=25, tpe, tbo, literal=AAAAAAAAAAAAAAAAAAAAAAA, ref= The FASTA file containing common adapters found in https://github.com/Dowell-Lab/Nascent-Flow/blob/master/bin/adapters.fa.
Mapping was done using HISAT2 (v2.1.0) with options --new-summary --very-sensitive --no-spliced-alignment to each species' reference genomes.
Converted mapped SAM to BAM files using Samtools (v1.8) view -F 4 to remove unmapped reads.
Read duplicates were removed using Sambamba (v0.6.6) markdup with options --remove-duplicates, --overflow-list-size=300000.
Bedgraph files were obtained using deepTools (v3.0.1) bamCoverage with options --binSize 1, --normalizeUsing CPM.
Assembly: Human (Homo sapiens) datasets were mapped to hg38,  and Bonobo (Pan paniscus) datasets were mapped to panPan3.
Supplementary files format and content: The *.bigwig are bigwig visualization files normalized for coverage using deepTools using --normalizeUsing RPKM.

organism: Pan paniscus

growth_protocol: The human, chimp, bonobo, gorilla, orangutan, gibbon, rhesus, baboon, squirrel monkey, owl monkey, and cow LCLs were cultured in RPMI-1640 media (Gibco Ref. 72400-047), 15% FBS (R&D Systems Ref. S11150), and 100 U/mL Penicillin-Streptomycin (Gibco Ref. 15140-122). The chicken LCLs were cultured in RPMI-1640 media (Gibco Ref. 72400-047), 10% FBS (R&D Systems Ref. S11150), 5% Chicken serum (Sigma Ref. C5405-100ML), 10% Tryptose phosphate broth (Sigma Ref. T8154), 0.05 mM β-mercaptoethanol (MP Ref. 194834), and 100 U/mL Penicillin-Streptomycin (Gibco Ref. 15140-122). All LCLs were cultured using vent-cap T-25 flasks (Corning 430639), and kept at a confluency between 400,000 cells/mL and 800,000 cells/mL during cell culture at 37°C with 5% CO2, except for the chicken LCLs which were kept between 1,000,000 cells/mL and 2,500,000 cells/mL.

extract_protocol: The ATAC-seq libraries were made following the [Corces2017] (https://doi.org/10.1038/nmeth.4396) protocol. Briefly, after the 1 hour treatments, the 100,000 cells were transferred from their 12-well plate wells to 1.8 mL eppendorf tubes, and centrifuged at 500 x g for 7 minutes at 4°C. The supernatant was carefully removed and replaced with 50 μL of ice-cold lysis buffer (water with 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL, 0.1% Tween-20, 0.01% Digitonin), the cells resuspended 4 times pipetting up and down, and incubated on ice for 5 minutes. Then, added 1 mL of wash buffer (water with 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) and the tubes inverted 4 times to mix. The tubes were centrifuged at 500 x g for 10 minutes at 4°C and the supernatant was carefully removed without disturbing the small cell pellet. The pellets were then carefully resuspended by pipetting 6 times with 50 μL of the transposition mix (25 μL Tagment DNA Buffer Illumina Ref. 15027866, 2.5 μL Tagment DNA Enzyme 1 Illumina Ref. 15027865, 0.5 μL Digitonin diluted 1:1 with water, 0.5 μL 10% Tween-20, 5 μL water, 16.5 μL PBS), and were incubated for 30 minutes in a heat block at 37°C, flicking the tube often. Afterwards, the samples were cleaned using the DNA Clean and Concentrator-5 Kit (Zymo Research Ref. D4014) following the manufacturer's instructions, and eluted in 21 μL elution buffer. Then, a PCR pre-amplification was done using NEBNext Ultra II Q5 Master Mix (NEB Ref. M0544S) using 5 cycles. Then, a qPCR was done using NEBNext Ultra II Q5 Master Mix, SYBR Gold (Life Tech Ref. S11494), and 5 μL of the pre-amplified sample, and the results used to determine the additional number of extra PCR cycles using Nextera DNA CD Indices (Illumina Ref. 20015882), which was just 1 additional cycle. The post-amplified ATAC-libraries were cleaned-up with the DNA Clean and Concentrator-5 Kit (Zymo Research Ref. D4014). The libraries were size-selected to remove DNA fragments greater than 1000 bp with a Sage Science BluePippin. The ATAC-seq libraries were quantified with Qubit HS DNA assay and their fragment size-distributions determined with Agilent HS D5000 ScreenTape. All samples were processed in parallel. After the samples were pooled and size-selected, they were cleaned-up using AMPure XP beads (Beckman Coulter Ref. A63881) at 1.5x volume and eluted into 20 μL of EB buffer (Qiagen Ref. 19086).

treatment_protocol: The human and bonobo LCLs were used for obtaining ATAC-seq libraries. They were treated for 1 hour with either 20 μM Nutlin-3a (Sigma Ref. SML0580), treated for 1 hour with either 100 U/mL of human IFN-α2 (Proteintech Ref. HZ-1066), or treated with 0.001% DMSO as a negative control. The treatments were done in 12-well plate wells so that each well had 100,000 cells in 2 mL volume. Each condition was prepared in duplicates, and all samples were processed in parallel.

value: Female

value: Lymphoblastoid cell line

value: WT

value: Nutlin

tag: time

value: 1 hour


title: Patient09, Grade 4, IDH1 mutant, Recurrent

description:
Library name: Patient09_Recurrent
Column name in counts_All_Samples.txt: Patient09_Recurrent


title: ATAC-seq, Bonobo LCL, Nutlin, 1 hour, rep 1


title: DEN-initiated SOR-treated mouse replicate 2

description:
Library name: SOR2
Column name in SOR_FPKM.csv: SOR2

value: Liver


title: Patient09, Grade 4, IDH1 mutant, Primary

description:
Library name: Patient09_Primary
Column name in counts_All_Samples.txt: Patient09_Primary

value: Brain tumor


title: PBMC_8879_CD_3

description:
Library name: PBMC_8879_CD_3
RNA-Seq of CHIM PBMC


title: Patient08, Grade 4, IDH1 wt, Recurrent

description:
Library name: Patient08_Recurrent
Column name in counts_All_Samples.txt: Patient08_Recurrent

value: Grade 4


title: DEN-initiated CAF-treated mouse replicate 5

description:
Library name: CAF5
Column name in CAF_FPKM.csv: CAF5


title: ATAC-seq, Bonobo LCL, hsIFNa2, 1 hour, rep 2


title: Patient08, Grade 4, IDH1 wt, Primary

description:
Library name: Patient08_Primary
Column name in counts_All_Samples.txt: Patient08_Primary


title: ATAC-seq, Bonobo LCL, DMSO, 1 hour, rep 1

value: DMSO


title: Brain single cell 168

description: Library name: Sample 168

value: brain

value: microglia


title: PBMC_8803_CD_4

description:
Library name: PBMC_8803_CD_4
RNA-Seq of CHIM PBMC

value: Blood


title: GS62004

description: Library name: M62004

value: ovary

value: mural granulosa cells

value: MGCs from small follicle (3.6mm)


title: PBMC_8876_CD_4

description:
Library name: PBMC_8876_CD_4
RNA-Seq of CHIM PBMC

value: PBMC


title: Patient06, Grade 4, IDH1 wt, Recurrent

description:
Library name: Patient06_Recurrent
Column name in counts_All_Samples.txt: Patient06_Recurrent

value: IDH1 wt

value: Recurrent


title: DEN-initiated CAF-treated mouse replicate 2

description:
Library name: CAF2
Column name in CAF_FPKM.csv: CAF2


title: Patient07, Grade 4, IDH1 wt, Primary

description:
Library name: Patient07_Primary
Column name in counts_All_Samples.txt: Patient07_Primary

value: Primary


title: Rat cortex, TBI + ELV biological rep 2, snRNA

city: New Orleans

first: Surjyadipta

last: Bhattacharjee

state: Louisiana

address: 2020 Gravier Street, Suite D, 8th floor

department: Neuroscience Center of Excellence

institute: LSU Health, New Orleans

description:
Library name: ELV_2_RNA
10x Genomics Multiome

library_source: transcriptomic single cell

data_processing:
Cell Ranger ARC 2.0.2 was used to annotate, process, and aggregate the mRNA and ATAC sequencing data using the mRATBN7.2 genome assembly.
Assembly: mRatBN7.2
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz for each sample from filtered_feature_bc_matrix folder
Supplementary files format and content: CellRanger output files: fragments.tsv.gz for each sample

molecule: nuclear RNA

source_name: Brain, cortex

extract_protocol:
Lesional cortex from Sham, Veh, and ELV rats was dissected and snap-frozen at –80°C. More information about the tissue dissection can be found in Supplementary Fig. 8C. The tissue was thoroughly homogenized, and single-nuclei were isolated using the 10x Genomics protocol (Pleasanton, CA, CG000505). The protocol involved lysis and dissociation of the tissue, followed by filtration on the Nuclei Isolation Column using centrifugation. Nuclei were resuspended in 50 µL of resuspension buffer with debris removal buffer to ensure purity. Nuclei concentration was determined with a Luna-FL cell counter (Logos Biosystems, Annandale, VA).
Using the 10x Genomics Chromium Controller, RNA and ATAC libraries were generated on a cell-by-cell basis using microfluidic partitioning to capture single cells and prepare barcoded, next-generation sequencing (NGS) libraries. All samples were processed in the same batch. The pooled mRNA and ATAC libraries from all 6 samples were sequenced separately with a NextSeq 2000 system using two flow cells (one for ATAC and one for mRNA) (Illumina, San Diego, CA), targeting a minimum of 20,000 read pairs per cell for the mRNA library and 25,000 read pairs per cell for the ATAC library.

treatment_protocol: Controlled cortical impact (CCI) as TBI model: Sprague-Dawley (SD) male young rats (3-4 months old, weight 300-500 g) were used for all experiments. Traumatic brain injury was induced using controlled cortical impact (CCI) on the right hemisphere. Rats were anesthetized with 3% isoflurane, 70% nitrous oxide, and a balance of oxygen, intubated, and catheters were inserted into the femoral artery and vein for blood pressure monitoring, IV infusion, and blood sampling for arterial gases, pH, hematocrit, and plasma glucose. Cranial and rectal temperature was monitored during the surgical procedure. The animals then underwent impact using a magnetic-guided stereotactic apparatus pre-programmed to a depth and speed of impact (velocity: 5 m/s, dwell time: 0.2 sec, depth: 2.5 mm). The craniotomy window was not sealed and was loosely covered by sewing over the underlying fascia as well as the scalp. ELV-N34 (Cayman Chemical, Ann Arbor, MI, USA) was dissolved in saline + 10% ethanol to be delivered intranasally (IN) according to the study protocol. Rats in the Veh and Sham group received an intranasal delivery of saline + 10% ethanol at 1h and 24h after TBI. Rats in the ELV group received ELV-N34:6 (20 µg/dose) dissolved in saline + 10% ethanol at 1h and 24h after TBI. Rats were lightly anesthetized with isoflurane to minimize variability in the delivery. 10 µl of solution was delivered to each nostril, with a rest of 30 seconds between nostrils, for a total volume of 20 µl delivered per treatment. IN delivery was given after behavioral scoring at 1h and 24h.

value: Brain, cortex

value: male

value: 3-4 months

value: CCI + ELV

tag: library type

value: mRNA


title: Patient06, Grade 4, IDH1 wt, Primary

description:
Library name: Patient06_Primary
Column name in counts_All_Samples.txt: Patient06_Primary

tag: tissue

value: Brain tumor

value: Grade 4


title: DEN-initiated mouse replicate 6

description:
Library name: DEN6
Column name in DEN_FPKM.csv: DEN6

value: Liver


title: Patient05, Grade 4, IDH1 wt, Recurrent

description:
Library name: Patient05_Recurrent
Column name in counts_All_Samples.txt: Patient05_Recurrent


title: DEN-initiated mouse replicate 5

description:
Library name: DEN5
Column name in DEN_FPKM.csv: DEN5


title: Rat cortex, TBI + ELV biological rep 1, snRNA

description:
Library name: ELV_1_RNA
10x Genomics Multiome

tag: age


title: Patient04, Grade 4, IDH1 wt, Recurrent

description:
Library name: Patient04_Recurrent
Column name in counts_All_Samples.txt: Patient04_Recurrent


title: DEN-initiated mouse replicate 3

description:
Library name: DEN3
Column name in DEN_FPKM.csv: DEN3


title: PBMC_8793_CD_5

description:
Library name: PBMC_8793_CD_5
RNA-Seq of CHIM PBMC

extract_protocol:
NPS: RNA was extracted with on-column DNase treatment using the miRNeasy Mini Kit (Qiagen) following the manufacturer's instructions. RNA was quantified by qPCR using the housekeeping gene B2M.
PBMC: 500K cells were stored in 750 μL TRIzol at -80°C. RNA until further processing. RNA was extracted with on-column DNase treatment using the miRNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
NPS: For cDNA synthesis, 10 ng of RNA was reverse-transcribed and pre-amplified (14 cycles) according to the Smart-Seq2 protocol. cDNA was purified with AMPure XP beads (Beckman Coulter), and 0.5 ng was used for Nextera XT sequencing library preparation with 8-bp Unique Dual Index (UDI) barcodes (IDT, Illumina) and the Nextera XT DNA Library Preparation Kit (Illumina). To minimize inter-assay variability, all purification steps were performed using an EpMotion 5075 (Eppendorf), and sequencing libraries were prepared in a 96-well format using a Mantis microfluidics liquid dispenser (Formulamatrix). Quality control included assessment of total RNA quality and quantity, optimization of pre-amplification cycle numbers, and fragment size analysis by capillary electrophoresis (5300 Fragment Analyzer, Agilent). cDNA and final libraries were quantified with the Quant-iT PicoGreen assay (Thermo Fisher Scientific). All samples passed quality thresholds, with >70% of fragments ranging from 300–700 bp and <5% primer dimers. Libraries were quantified by qPCR using the KAPA Library Quantification Kit (Roche), normalized to equimolar concentrations, and loaded onto a NovaSeq X Plus sequencing platform (Illumina) with a 25B flow cell. Paired-end sequencing (150 bp) yielded 4.2 billion total reads, corresponding to an average depth of ~15 million reads per sample.
PBMC: Quantabio Sparq mRNA-Seq kit was used to prepare stranded libraries using 8 ng of high-quality total RNA as input, except in 10 samples where the yield was below 8 ng. Libraries underwent 16-18 PCR amplification cycles and libraries were indexed with xGen 10 nt Unique Dual Indexes (UDIs). Paired-end (50x50) sequencing was performed on a NovaSeq 6000 targeting 40 million reads per library.

tag: cell type

value: female


title: DEN-initiated mouse replicate 2

description:
Library name: DEN2
Column name in DEN_FPKM.csv: DEN2


title: PBMC_8801_CD_5

description:
Library name: PBMC_8801_CD_5
RNA-Seq of CHIM PBMC

value: Blood

tag: days post_challenge


title: Brain single cell 160

description: Library name: Sample 160

value: brain

value: microglia


title: PBMC_8790_CD_4_reprep

description:
Library name: PBMC_8790_CD_4_reprep
RNA-Seq of CHIM PBMC

value: Yes

tag: Sex


title: DEN-initiated CAF-treated mouse replicate 4

description:
Library name: CAF4
Column name in CAF_FPKM.csv: CAF4


title: ATAC-seq, Bonobo LCL, hsIFNa2, 1 hour, rep 1

value: Female

tag: cell line

value: Lymphoblastoid cell line

value: WT

value: 1 hour


title: GS50506

description: Library name: W-6M

value: ovary

value: mural granulosa cells

value: MGCs from small follicle (3.3mm)


title: Patient03, Grade 4, IDH1 wt, Primary

description:
Library name: Patient03_Primary
Column name in counts_All_Samples.txt: Patient03_Primary

tag: genotype

value: IDH1 wt

value: Primary


title: PBMC_8796_CD_6

description:
Library name: PBMC_8796_CD_6
RNA-Seq of CHIM PBMC

value: PBMC


title: DEN-initiated mouse replicate 4

description:
Library name: DEN4
Column name in DEN_FPKM.csv: DEN4


title: Patient05, Grade 4, IDH1 wt, Primary

description:
Library name: Patient05_Primary
Column name in counts_All_Samples.txt: Patient05_Primary

value: Brain tumor

value: Grade 4


title: Rat cortex, TBI + Saline biological rep 2, snATAC

description:
Library name: Veh_2_ATAC
10x Genomics Multiome

library_source: other

molecule: other

value: Brain, cortex

value: male

value: 3-4 months

tag: treatment

value: CCI + Saline

value: ATAC


title: PBMC_8790_CD_4

description:
Library name: PBMC_8790_CD_4
RNA-Seq of CHIM PBMC

value: Blood

value: female


title: PBMC_8797_CD_4

description:
Library name: PBMC_8797_CD_4
RNA-Seq of CHIM PBMC


title: Patient04, Grade 4, IDH1 wt, Primary

description:
Library name: Patient04_Primary
Column name in counts_All_Samples.txt: Patient04_Primary


title: Patient03, Grade 4, IDH1 wt, Recurrent

description:
Library name: Patient03_Recurrent
Column name in counts_All_Samples.txt: Patient03_Recurrent

value: Recurrent


title: Rat cortex, TBI + ELV biological rep 2, snATAC

description:
Library name: ELV_2_ATAC
10x Genomics Multiome

value: CCI + ELV


title: Brain single cell 153

description: Library name: Sample 153

value: brain

value: microglia


title: Rat cortex, sham biological rep 2, snATAC

description:
Library name: Sham_2_ATAC
10x Genomics Multiome

value: Saline


title: DEN-initiated SOR-treated mouse replicate 1

description:
Library name: SOR1
Column name in SOR_FPKM.csv: SOR1

value: Liver


title: Brain single cell 170

description: Library name: Sample 170


title: PBMC_8789_CD_4

description:
Library name: PBMC_8789_CD_4
RNA-Seq of CHIM PBMC


title: PBMC_8878_CD_4

description:
Library name: PBMC_8878_CD_4
RNA-Seq of CHIM PBMC


title: PBMC_8799_CD_5

description:
Library name: PBMC_8799_CD_5
RNA-Seq of CHIM PBMC


title: PBMC_8877_CD_3

description:
Library name: PBMC_8877_CD_3
RNA-Seq of CHIM PBMC


title: Untreated mouse replicate 4

description:
Library name: Control4
Column name in Control_FPKM.csv: Control4


title: Rat cortex, sham biological rep 2, snRNA

description:
Library name: Sham_2_RNA
10x Genomics Multiome

value: mRNA


title: Patient02, Grade 3, IDH1 mutant, Primary

description:
Library name: Patient02_Primary
Column name in counts_All_Samples.txt: Patient02_Primary

value: Grade 3

value: IDH1 mutant

value: Primary


title: PBMC_8784_CD_4_reprep

description:
Library name: PBMC_8784_CD_4_reprep
RNA-Seq of CHIM PBMC

value: PBMC

value: Yes


title: DEN-initiated mouse replicate 1

description:
Library name: DEN1
Column name in DEN_FPKM.csv: DEN1


title: PBMC_8802_CD_5

description:
Library name: PBMC_8802_CD_5
RNA-Seq of CHIM PBMC

value: male


title: Rat cortex, sham biological rep 1, snATAC

description:
Library name: Sham_1_ATAC
10x Genomics Multiome

value: Brain, cortex

value: 3-4 months


title: Patient07, Grade 4, IDH1 wt, Recurrent

description:
Library name: Patient07_Recurrent
Column name in counts_All_Samples.txt: Patient07_Recurrent

value: Brain tumor

value: Grade 4

value: IDH1 wt


title: PBMC_8784_CD_4

description:
Library name: PBMC_8784_CD_4
RNA-Seq of CHIM PBMC

value: Blood


title: Patient01, Grade 3, IDH1 wt, Primary

description:
Library name: Patient01_Primary
Column name in counts_All_Samples.txt: Patient01_Primary


title: PBMC_8783_CD_3

description:
Library name: PBMC_8783_CD_3
RNA-Seq of CHIM PBMC


title: CeA_snRNAseq_Yoked_M36

city: Austin

first: Elizabeth

last: Osterndorff-Kahanek

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description: Library name: M36

data_processing:
Fastq files were processed using the CellRanger (v7.0.0) pipeline. CellRanger outputs were imported to Seurat (v4.3.0) for further processing.
Assembly: mRatBN7
Supplementary files format and content: Tab-separated values files, comma-separated values files, matrix files

source_name: central amygdala (CeA)

extract_protocol:
Rats were immediately sacrificed after last footshock session, and brains were fresh frozen and then stored at −80°C until further processing. We sectioned the brains at a cryostat (Leica CM3050s) and collected 300 µm slices from approximately bregma -1.6mm to -2.8mm based on the rat brain in stereotaxic coordinates. Then CeA tissue was harvested bilaterally from the brain slices using a 1.5 mm diameter biopsy punch and tissue blocks were stored at −80°C. Nuclei were isolated using the Chromium Nuclei Isolation Kit with RNase inhibitor (10X Genomics) following the manufacturer's instructions with a lysis time of 6.5 minutes and a single wash following debris removal. The nuclei were resuspended in a final volume of 50–100 µL at a target concentration of 500–1,200 nuclei/µL.
Single-nucleus RNA-seq libraries were generated using the Chromium Next GEM Single Cell 3′ Kit v3.1 (10x Genomics), targeting 10,000 nuclei per sample. Libraries were sequenced on an  Illumina NovaSeq 6000 system using an S1 flow cell, producing approximately 500 million reads per sample.

value: central amygdala (CeA)

tag: strain

value: Wistar

tag: phenotpe

value: Yoked


title: FFPE, LateProgressive,nr105

city: Bergen

first: Tony

last: Chen

address: Haukelandsveien 22

country: Norway

institute: Haukeland University Hospital

description:
Library name: LP_105
Novogene

data_processing:
Alignment using Hisat2 v2.0.5
Adapter contamination, uncertain nucleotides constitute more than 10% of reads and low base quality  were filtered for clean reads.
Assembly: Homo_sapiens_Ensemble_94
Supplementary files format and content: raw_gene_count.csv

source_name: Formalin Fixed Paraffin embedded kidney tissue

extract_protocol:
For RNA bulk sequencing, the RNA was extracted using miRNeasy extraction kit. 10 ng/ul was used for library construction.
For bulk RNA sequencing, RNA libraries was prepared according to the Truseq Exome library prep kit following manufacturers protocol.


title: FFPE, LateProgressive,nr102

description:
Library name: LP_102
Novogene

value: Formalin Fixed Paraffin embedded kidney tissue


title: PBMC_8781_CD_4

city: Amsterdam

first: Lisa

last: Willemsen

address: Meibergdreef 9

institute: Amsterdam UMC - locatie AMC

description:
Library name: PBMC_8781_CD_4
RNA-Seq of CHIM PBMC

data_processing:
Paired-end reads that passed Illumina quality filters were further screened to remove sequences aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The remaining reads were aligned to the GRCh38 human reference genome with Gencode v27 annotations using STAR (v2.6.1) [PMID: 23104886]. Read complexity was assessed with PRINSEQ Lite (v0.20.3) [PMID: 21278185], and low-complexity reads (DUST score > 4) were excluded from the BAM files. The alignment results were parsed via the SAMtools [PMID: 19505943] to generate SAM files. Gene-level counts were then obtained using featureCounts (v1.6.5) [PMID: 24227677] using the default option along with a minimum quality cut-off (Phred > 10), and transcripts per million (TPM) reads values were calculated. T cell receptor (TCR) transcripts were aggregated into four groups: TCR-α, TCR-β, TCR-γ, and TCR-δ. B cell receptor (BCR) transcripts were aggregated into light chains (IGK and IGL) and heavy chains (IGH-), with isotype transcripts (IGHG1-4, IGHM, IGHD, IGHE, IGHA1-2) analyzed separately. Transcripts were filtered using EdgeR’s filterByExpr function (v4.2.2) [PMID: 39844453] with “participants + timepoint” as the design. For each participant, baseline TPMs were averaged and raw counts were summed. Differential expression was assessed using the DESeq2 package (v1.44.0) [PMID: 25516281] for NPS and EdgeR for PBMCs in an R (v4.4.0) environment, with gene expression called differential with an FDR<0.05. Gene set enrichment analysis (GSEA) was performed using Metascape [PMID: 30944313] and GSEA (v4.4.0) [PMID: 16199517], both with the Gene Ontology (GO) gene sets [PMID: 36866529].
Assembly: GRCh38
Supplementary files format and content: "PBMC_counts.tsv" contains raw count values per sample and gene of PBMC.
Supplementary files format and content: "PBMC_tpm.tsv" contains TPM values per sample and gene of PBMC.
Supplementary files format and content: "PBMC_tpm_baseline_means_BCR_TCR_aggr.csv" contains TPM values per sample and gene in which TCR and BCR genes were aggregated and baseline PBMC samples per participant were averaged.
Supplementary files format and content: "PBMC_counts_baseline_sums_BCR_TCR_aggr.csv" contains counts per sample and gene in which TCR and BCR genes were aggregated and baseline PBMC samples per participant were summed.
Supplementary files format and content: "NPS_counts.csv" contains raw count values per sample and gene of NPS.
Supplementary files format and content: "NPS_tpm.csv" contains TPM values per sample and gene of NPS.
Supplementary files format and content: "NPS_tpm_baseline_means_TCR_BCR_aggr.csv" contains TPM values per sample and gene in which TCR and BCR genes were aggregated and baseline NPS samples per participant were averaged.
Supplementary files format and content: NPS_counts_baseline_sums_BCR.TCR.aggr.csv" contains counts per sample and gene in which TCR and BCR genes were aggregated and baseline NPS samples per participant were summed.
Supplementary files format and content: "participant_metadata_filtered.csv" contains metadata per participant.


title: Rat cortex, TBI + Saline biological rep 1, snRNA

description:
Library name: Veh_1_RNA
10x Genomics Multiome

value: CCI + Saline

value: mRNA


title: Rat cortex, TBI + ELV biological rep 1, snATAC

description:
Library name: ELV_1_ATAC
10x Genomics Multiome

value: CCI + ELV

value: ATAC


title: DEN-initiated CAF-treated mouse replicate 1

description:
Library name: CAF1
Column name in CAF_FPKM.csv: CAF1

value: Liver


title: CeA_snRNAseq_Yoked_M34

description: Library name: M34


title: Rat cortex, TBI + Saline biological rep 2, snRNA

description:
Library name: Veh_2_RNA
10x Genomics Multiome


title: FFPE, LateProgressive,nr92

description:
Library name: LP_92
Novogene


title: Patient02, Grade 3, IDH1 mutant, Recurrent

description:
Library name: Patient02_Recurrent
Column name in counts_All_Samples.txt: Patient02_Recurrent

value: Grade 3

value: IDH1 mutant

value: Recurrent


title: PBMC_8780_CD_3

description:
Library name: PBMC_8780_CD_3
RNA-Seq of CHIM PBMC

value: PBMC

value: female


title: Untreated mouse replicate 3

description:
Library name: Control3
Column name in Control_FPKM.csv: Control3


title: CeA_snRNAseq_Yoked_M33

description: Library name: M33

value: male


title: 20433X2 miR155 Vehicle C1498-OVA AML

city: Salt Lake City

first: Ryan

last: O'Connell

state: UT

address: Emma Eccles Jones, Medical Research Building, 15 North Medical Drive East

department: Pathology, Microbiology & Immunology

institute: University of Utah

description: Library name: 2

data_processing:
The Fastq files were aligned to the refdata-gex-mm10-2020-A mouse reference dataset from 10x Genomics.
Cellranger count 7.0.1 was used to create quality control metrics, Loupe Browser files and filtered gene barcode matrices.
Assembly: mm10
Supplementary files format and content: Filtered feature barcode matrices in MEX format

source_name: Bone Marrow

growth_protocol: miR-155 TCKO mice were generated by crossing C57/BlL6 mir155-flox/flox lines expressing miR155 normally to C57/BlL6 mir155-flox/flox animals heterozygous for CD4-Cre. The resulting offspring were programmed to conditionally delete miR155 only in CD4+ and CD8+ T-cells, while their mir155-flox/flox littermates with no Cre driver served as miR155-replete WT controls. Mice wer 6-12 weeks old at the onset of treatment, and were age and sex matched for each experiment.

extract_protocol:
WT and miR-155 TCKO littermate mice each received mRNA-OVA LNP or vehicle control after challenge with an OVA-expressing C1498 AML cell line, in two doses at Day 1 and Day 7 of the experimental procedure. For each dose, 2.5 µg of mRNA vaccine was mixed with 10 µl RNAiMAX Transfection Reagent (Thermo Fisher), assembled at room temperature for 15 min after delicate mixing, and diluted to working concentration using 85 µl of PBS under sterile conditions. Each dose was then injected as 100 µl total mRNA-OVA-LNP solution, or the same solution without RNA as the vehicle control. At Day 21, all mice were injected with 2.5 million cells per mouse of the C1498-OVA AML line via tail vein.
10x Genomics Chromium Next GEM Single Cell  5' v2 Gene Expression Library Preparation

value: Bone Marrow

value: C1498-OVA AML

value: CD45+ Cd3+ T-cells

value: Vehicle


title: FFPE, LateProgressive,nr73

description:
Library name: LP_73
Novogene


title: 20433X1 WT Vehicle C1498-OVA AML

description: Library name: 1

treatment_protocol: WT and miR-155 TCKO littermate mice each received mRNA-OVA LNP or vehicle control after challenge with an OVA-expressing C1498 AML cell line, in two doses at Day 1 and Day 7 of the experimental procedure. For each dose, 2.5 µg of mRNA vaccine was mixed with 10 µl RNAiMAX Transfection Reagent (Thermo Fisher), assembled at room temperature for 15 min after delicate mixing, and diluted to working concentration using 85 µl of PBS under sterile conditions. Each dose was then injected as 100 µl total mRNA-OVA-LNP solution, or the same solution without RNA as the vehicle control. At Day 21, all mice were injected with 2.5 million cells per mouse of the C1498-OVA AML line via tail vein.

value: C57Bl/6 WT (mir155-flox/flox)


title: 20433X4 miR155 OVA mRNA Vaccine C1498-OVA AML

description: Library name: 4

value: OVA mRNA / LNP


title: Patient01, Grade 3, IDH1 wt, Recurrent

description:
Library name: Patient01_Recurrent
Column name in counts_All_Samples.txt: Patient01_Recurrent

value: Brain tumor

value: IDH1 wt


title: PBMC_8779_CD_3

description:
Library name: PBMC_8779_CD_3
RNA-Seq of CHIM PBMC

source_name: Blood

value: Blood


title: SREBP2_KO8

city: Miami

first: Thomas

middle: R

last: Malek

state: FL

address: 1600 NW 10th Avenue

department: Microbiology/Immunology

institute: University of Miami

description: Library name: Sample 6

data_processing:
Cell Ranger
HISAT2 (ver.2.2.1) for alignment
Raw counts were generated with UCSC annotations
Assembly: mm10
Supplementary files format and content: tab-deliminated text files with the raw counts for each Sample

source_name: Spleen and lymph nodes

extract_protocol:
RNA was extracted using Qiagen Rneasy kit
Library preparation was completed with the KAPA RNA Hyperprep kit with RiboErase (HMR)

value: Spleen and lymph nodes

value: Srebp2cKO Tregs


title: PBMC_8780_CD_3_reprep

description:
Library name: PBMC_8780_CD_3_reprep
RNA-Seq of CHIM PBMC

tag: reprep

value: Yes


title: CeA_snRNAseq_Yoked_M31

description: Library name: M31

value: central amygdala (CeA)

value: Wistar

value: Yoked


title: Untreated mouse replicate 1

description:
Library name: Control1
Column name in Control_FPKM.csv: Control1

value: Liver


title: FFPE, LateProgressive,nr68

description:
Library name: LP_68
Novogene

value: Formalin Fixed Paraffin embedded kidney tissue


title: CeA_snRNAseq_Yoked_M35

description: Library name: M35

value: male


title: Untreated mouse replicate 2

description:
Library name: Control2
Column name in Control_FPKM.csv: Control2


title: PBMC_8779_CD_3_reprep

description:
Library name: PBMC_8779_CD_3_reprep
RNA-Seq of CHIM PBMC

value: PBMC

value: female


title: CeA_snRNAseq_Yoked_M32

description: Library name: M32


title: SREBP2_KO6

description: Library name: Sample 4


title: PBMC_8775_CD_7

description:
Library name: PBMC_8775_CD_7
RNA-Seq of CHIM PBMC


title: FFPE, LateProgressive,nr70

description:
Library name: LP_70
Novogene


title: Rat cortex, sham biological rep 1, snRNA

description:
Library name: Sham_1_RNA
10x Genomics Multiome

value: Brain, cortex

value: 3-4 months

value: Saline

value: mRNA


title: SREBP2_WT5

description: Library name: Sample 3

value: Srebp2WT Tregs


title: CeA_snRNAseq_Yoked_M28

description: Library name: M28


title: FFPE, LateStable,nr112

description:
Library name: LS_112
Novogene


title: FFPE, LateStable,nr109

description:
Library name: LS_109
Novogene


title: 20433X3 WT OVA mRNA Vaccine C1498-OVA AML

description: Library name: 3

value: Bone Marrow

value: C1498-OVA AML

value: CD45+ Cd3+ T-cells

value: C57Bl/6 WT (mir155-flox/flox)

value: OVA mRNA / LNP


title: SREBP2_WT1

description: Library name: Sample 1

value: Spleen and lymph nodes


title: FFPE, LateProgressive,nr72

description:
Library name: LP_72
Novogene


title: FFPE, LateStable,nr108

description:
Library name: LS_108
Novogene


title: PBMC_8778_CD_4

description:
Library name: PBMC_8778_CD_4
RNA-Seq of CHIM PBMC

value: Blood


title: FFPE, LateProgressive,nr67

description:
Library name: LP_67
Novogene


title: CeA_snRNAseq_Yoked_M29

description: Library name: M29

value: central amygdala (CeA)

value: Wistar

value: Yoked


title: PBMC_8342_CD_3

description:
Library name: PBMC_8342_CD_3
RNA-Seq of CHIM PBMC

value: PBMC


title: PBMC_8591_CD_3

description:
Library name: PBMC_8591_CD_3
RNA-Seq of CHIM PBMC

value: female


title: SREBP2_KO7

description: Library name: Sample 5

value: Srebp2cKO Tregs


title: FFPE, LateStable,nr107

description:
Library name: LS_107
Novogene

value: Formalin Fixed Paraffin embedded kidney tissue


title: PBMC_8338_CD_3

description:
Library name: PBMC_8338_CD_3
RNA-Seq of CHIM PBMC


title: CeA_snRNAseq_Yoked_M30

description: Library name: M30

value: male


title: DEN-initiated CAF-treated mouse replicate 3

description:
Library name: CAF3
Column name in CAF_FPKM.csv: CAF3

value: Liver


title: FFPE, LateStable,nr91

description:
Library name: LS_91
Novogene


title: PBMC_8590_CD_4

description:
Library name: PBMC_8590_CD_4
RNA-Seq of CHIM PBMC


title: FFPE, LateStable,nr85

description:
Library name: LS_85
Novogene


title: CeA_snRNAseq_Yoked_M26

description: Library name: M26


title: BulkCA1_F3_022, WT female, ZT6

first: Laura

middle: K

last: Fonken

address: 107 W Dean Keeton St

department: Pharmacy

institute: The University of Texas at Austin

description:
Library name: BulkCA1_F3_022
Column name in bulkCA1_counts.csv: F3-022

data_processing:
Samples were sequenced on a NovaSeq S1, SR100.
FASTQ files from multiple sequencing lanes were combined, if needed, and PCR-duplicate sequences were collapsed (deduplicated). The 5' inline barcode Tag, adapter, and polyA tail were removed.
Reads were mapped to the mm39 genome using STAR with default settings and quantMode to produce transcript quantifications.
Library quality and mapping performance was assessed on each sample using the STAR Log.final.out file and by viewing the read alignments using Interactive Genome Viewer. Microglia samples were excluded from analysis if any of the following criteria were met: input reads<1000000, uniquely mapped reads < 900000, uniquely mapped percentage < 85%, mismatch rate per base > 0.85, or if mapping coverage was judged to be poor by a blinded observer in Interactive Genome Viewer.
The counts matrix was created using column 3 (first read strand aligned with RNA) from the ReadsPerGene.out.tab file. Genes with >10 counts in at least 80% (CA1) or 20% (microglia) of samples were considered for analysis.
A PCA was performed on the filtered data to check for outliers. None were detected or excluded here.
Differential gene expression was modelled using limma-voom with TMM normalization. False discovery rate was determined by Benjamini-Hochberg multiplicity correction  (microglia) or permutation analysis (CA1).
Assembly: mm39
Supplementary files format and content: csv file contains raw counts for each sample

source_name: hippocampus, area CA1

extract_protocol:
Mice were intracardially perfused with PBS on postnatal day 28 at zeitgeber time 6. Brains were removed, flash-frozen whole on dry ice and stored at -80C. The hippocampus was sectioned into 100um-thick coronal slices on a cryostat at 20C, and tissue from area CA1 was collected via micropunch and stored at -80C until RNA extraction. RNA extractions were performed using the RNeasy kit (Qiagen) with on-column DNase digestion according to the manufacturer’s instructions.  300ng total RNA was used for library construction.
Mice were intracardially perfused with PBS on postnatal day 28 at zeitgeber time 6 or 18. Brains were removed and hippocampi were incubated for 15min at 37C in digestion mix containing HBSS, 5% FBS, 10uM HEPES, 2mg/mL collagenase A, and 28U/mL DNase I. Tissue was dissociated using a series of fire-polished glass pipettes, and myelin was removed using Miltenyi Biotec's Debris Removal Kit. Cells were incubated with Miltenyi CD11b microbeads, and microglia were isolated using Mintenyi MACS Separation Columns with MACS MultiStand magnet. Microglia were stored in PBS at -80C until RNA extractions. RNA was extracted using TRizol/chloroform, according to manufacturer's instructions. 150ng total RNA was used for library construction.
Total RNA was fragmented with Mg+ buffer via hydrolysis. cDNA was synthesized with a poly-dT oligo, PCR-amplified, and purified with DNA-binding magnetic beads. Among-sample concentrations were normalized and sample-specific barcodes were added via PCR. Samples were pooled to select a small range of fragment sizes via automated gel extraction (400-500bp). Postextraction products were quantified by Qubit and normalized among pools.

treatment_protocol: Microglia-specific Bmal1 conditional knockout mice (Tmem119wt/CreER2::Bmal1fl/fl, KO ) and wildtype (Tmem119wt/wt::Bmal1fl/fl , WT) littermates were administered 50ug tamoxifen i.p. on postnatal days 3-5.

value: hippocampus, area CA1

value: wt

value: F

tag: zeitgeber time


title: CeA_snRNAseq_Resistant_M22

description: Library name: M22

value: Resistant


title: CeA_snRNAseq_Yoked_M27

description: Library name: M27


title: BulkCA1_A4_025, WT female, ZT6

description:
Library name: BulkCA1_A4_025
Column name in bulkCA1_counts.csv: A4-025


title: CeA_snRNAseq_Resistant_M21

description: Library name: M21


title: PBMC_8325_CD_8

description:
Library name: PBMC_8325_CD_8
RNA-Seq of CHIM PBMC


title: FFPE, EarlyProgressive,nr122

description:
Library name: EP_122
Novogene


title: BulkCA1_E3_021, WT male, ZT6

description:
Library name: BulkCA1_E3_021
Column name in bulkCA1_counts.csv: E3-021

value: M


title: PBMC_8879_CD_2

description:
Library name: PBMC_8879_CD_2
RNA-Seq of CHIM PBMC


title: BulkCA1_D3_020, KO female, ZT6

description:
Library name: BulkCA1_D3_020
Column name in bulkCA1_counts.csv: D3-020

value: ko


title: SREBP2_WT3

description: Library name: Sample 2

value: Spleen and lymph nodes

value: Srebp2WT Tregs


title: BulkCA1_G3_023, KO female, ZT6

description:
Library name: BulkCA1_G3_023
Column name in bulkCA1_counts.csv: G3-023


title: CeA_snRNAseq_Resistant_M24

description: Library name: M24

value: central amygdala (CeA)


title: CeA_snRNAseq_Yoked_M25

description: Library name: M25

value: Wistar


title: PBMC_8589_CD_3

description:
Library name: PBMC_8589_CD_3
RNA-Seq of CHIM PBMC

value: Blood


title: CeA_snRNAseq_Resistant_M20

description: Library name: M20


title: BulkCA1_H3_024, KO female, ZT6

description:
Library name: BulkCA1_H3_024
Column name in bulkCA1_counts.csv: H3-024


title: CeA_snRNAseq_Resistant_M23

description: Library name: M23


title: PBMC_8334_CD_4

description:
Library name: PBMC_8334_CD_4
RNA-Seq of CHIM PBMC

value: PBMC


title: PBMC_8878_CD_3_reprep

description:
Library name: PBMC_8878_CD_3_reprep
RNA-Seq of CHIM PBMC

value: Yes


title: BulkCA1_C3_019, KO female, ZT6

description:
Library name: BulkCA1_C3_019
Column name in bulkCA1_counts.csv: C3-019


title: PBMC_8336_CD_4

description:
Library name: PBMC_8336_CD_4
RNA-Seq of CHIM PBMC

value: female


title: FFPE, EarlyProgressive,nr98

description:
Library name: EP_98
Novogene

value: Formalin Fixed Paraffin embedded kidney tissue


title: PBMC_8878_CD_3

description:
Library name: PBMC_8878_CD_3
RNA-Seq of CHIM PBMC

value: male


title: BulkCA1_A3_017, KO male, ZT6

description:
Library name: BulkCA1_A3_017
Column name in bulkCA1_counts.csv: A3-017


title: FFPE, EarlyProgressive,nr94

description:
Library name: EP_94
Novogene


title: FFPE, LateStable,nr84

description:
Library name: LS_84
Novogene


title: CeA_snRNAseq_Resistant_M19

description: Library name: M19


title: PBMC_8877_CD_2

description:
Library name: PBMC_8877_CD_2
RNA-Seq of CHIM PBMC


title: PBMC_8803_CD_3

description:
Library name: PBMC_8803_CD_3
RNA-Seq of CHIM PBMC


title: FFPE, EarlyProgressive,nr111

description:
Library name: EP_111
Novogene


title: CeA_snRNAseq_Resistant_M18

description: Library name: M18


title: BulkCA1_H2_016, KO male, ZT6

description:
Library name: BulkCA1_H2_016
Column name in bulkCA1_counts.csv: H2-016


title: BulkCA1_B3_018, KO female, ZT6

description:
Library name: BulkCA1_B3_018
Column name in bulkCA1_counts.csv: B3-018


title: CeA_snRNAseq_Resistant_M15

description: Library name: M15


title: CeA_snRNAseq_Resistant_M16

description: Library name: M16


title: FFPE, EarlyProgressive,nr81

description:
Library name: EP_81
Novogene


title: PBMC_8876_CD_3

description:
Library name: PBMC_8876_CD_3
RNA-Seq of CHIM PBMC


title: BulkCA1_F2_014, KO male, ZT6

description:
Library name: BulkCA1_F2_014
Column name in bulkCA1_counts.csv: F2-014


title: PBMC_8802_CD_4

description:
Library name: PBMC_8802_CD_4
RNA-Seq of CHIM PBMC


title: FFPE, EarlyProgressive,nr75

description:
Library name: EP_75
Novogene


title: BulkCA1_G2_015, KO male, ZT6

description:
Library name: BulkCA1_G2_015
Column name in bulkCA1_counts.csv: G2-015


title: FFPE, EarlyProgressive,nr69

description:
Library name: EP_69
Novogene


title: BulkCA1_E2_013, WT female, ZT6

description:
Library name: BulkCA1_E2_013
Column name in bulkCA1_counts.csv: E2-013


title: PBMC_8799_CD_4

description:
Library name: PBMC_8799_CD_4
RNA-Seq of CHIM PBMC


title: FFPE, EarlyProgressive,nr45

description:
Library name: EP_45
Novogene


title: BulkCA1_C2_011, WT male, ZT6

description:
Library name: BulkCA1_C2_011
Column name in bulkCA1_counts.csv: C2-011


title: CeA_snRNAseq_Sensitive_M12

description: Library name: M12

value: Sensitive


title: BulkCA1_D2_012, KO female, ZT6

description:
Library name: BulkCA1_D2_012
Column name in bulkCA1_counts.csv: D2-012

value: hippocampus, area CA1


title: PBMC_8796_CD_5

description:
Library name: PBMC_8796_CD_5
RNA-Seq of CHIM PBMC


title: PBMC_8797_CD_9_reprep

description:
Library name: PBMC_8797_CD_9_reprep
RNA-Seq of CHIM PBMC


title: CeA_snRNAseq_Sensitive_M9

description: Library name: M9


title: FFPE, EarlyStable,nr79

description:
Library name: ES_79
Novogene


title: CeA_snRNAseq_Sensitive_M10

description: Library name: M10


title: BulkCA1_A2_009, WT male, ZT6

description:
Library name: BulkCA1_A2_009
Column name in bulkCA1_counts.csv: A2-009

value: wt


title: PBMC_8797_CD_9

description:
Library name: PBMC_8797_CD_9
RNA-Seq of CHIM PBMC


title: FFPE, EarlyStable,nr76

description:
Library name: ES_76
Novogene


title: CeA_snRNAseq_Sensitive_M11

description: Library name: M11


title: CeA_snRNAseq_Sensitive_M8

description: Library name: M8


title: FFPE, EarlyStable,nr39

description:
Library name: ES_39
Novogene


title: BulkCA1_G1_007, WT male, ZT6

description:
Library name: BulkCA1_G1_007
Column name in bulkCA1_counts.csv: G1-007


title: PBMC_8790_CD_3_reprep

description:
Library name: PBMC_8790_CD_3_reprep
RNA-Seq of CHIM PBMC


title: PBMC_8790_CD_3

description:
Library name: PBMC_8790_CD_3
RNA-Seq of CHIM PBMC


title: BulkCA1_F1_006, KO female, ZT6

description:
Library name: BulkCA1_F1_006
Column name in bulkCA1_counts.csv: F1-006

value: F


title: FFPE, EarlyStable,nr33

description:
Library name: ES_33
Novogene


title: FFPE, EarlyStable,nr32

description:
Library name: ES_32
Novogene


title: CeA_snRNAseq_Sensitive_M6

description: Library name: M6


title: FFPE, EarlyStable,nr31

description:
Library name: ES_31
Novogene


title: BulkCA1_E1_005, WT female, ZT6

description:
Library name: BulkCA1_E1_005
Column name in bulkCA1_counts.csv: E1-005


title: PBMC_8789_CD_3

description:
Library name: PBMC_8789_CD_3
RNA-Seq of CHIM PBMC


title: CeA_snRNAseq_Sensitive_M5

description: Library name: M5


title: BulkCA1_D1_004, WT female, ZT6

description:
Library name: BulkCA1_D1_004
Column name in bulkCA1_counts.csv: D1-004


title: PBMC_8784_CD_3_reprep

description:
Library name: PBMC_8784_CD_3_reprep
RNA-Seq of CHIM PBMC


title: CeA_snRNAseq_Sensitive_M4

description: Library name: M4


title: FFPE, EarlyStable,nr24

description:
Library name: ES_24
Novogene


title: PBMC_8784_CD_3

description:
Library name: PBMC_8784_CD_3
RNA-Seq of CHIM PBMC


title: CeA_snRNAseq_Sensitive_M3

description: Library name: M3


title: FFPE, EarlyStable,nr22

description:
Library name: ES_22
Novogene


title: PBMC_8783_CD_8

description:
Library name: PBMC_8783_CD_8
RNA-Seq of CHIM PBMC


title: FFPE, EarlyStable,nr20

description:
Library name: ES_20
Novogene


title: BulkCA1_C1_003, KO male, ZT6

description:
Library name: BulkCA1_C1_003
Column name in bulkCA1_counts.csv: C1-003


title: BulkCA1_B1_002, KO male, ZT6

description:
Library name: BulkCA1_B1_002
Column name in bulkCA1_counts.csv: B1-002


title: BulkCA1_A1_001, WT male, ZT6

description:
Library name: BulkCA1_A1_001
Column name in bulkCA1_counts.csv: A1_001


title: CeA_snRNAseq_Sensitive_M1

description: Library name: M1


title: OEKZ24243-01

city: 贵阳

first: 鹏

last: 陈

state: 贵州

address: 贵州省贵阳市花溪区大学城栋青南路

institute: 贵州中医药大学

description:
Library name: Sham51_77_5
Fresh frozen Spatial transcriptome sequencing

data_processing:
Evaluation of the quality of raw data
Space Ranger gene quantitative quality control
Quantitative quality control
Genetic expression normalization processing
Assembly: GRCh38，mm10
Supplementary files format and content: Tab-delimited text file including the ratio at which each gene appears cells in each sample cell
Supplementary files format and content: Tab-delimited text file including the cell count of the cluster in each sample
Library strategy: Spatial Transcriptomics

source_name: spinal cord

extract_protocol:
Collect fresh tissue, freeze it, slice it, and perform HE staining for imaging. Optimize to determine whether the slices cover the targeted area.
Using the 10xGenomics Visium kit, the sequencing libraries were constructed according to the manufacturer's procedures.

value: spinal cord

value: Murine spinal cord tissue lineage

value: Stromal cells

value: Sham


title: PBMC_8780_CD_9_reprep

description:
Library name: PBMC_8780_CD_9_reprep
RNA-Seq of CHIM PBMC


title: Microglia_A7_049, KO female, ZT18

description:
Library name: Microglia_A7_049
Column name in microglia_counts.csv: A7-049

value: brain

value: microglia

value: ko


title: Microglia_B7_050, KO female, ZT18

description:
Library name: Microglia_B7_050
Column name in microglia_counts.csv: B7-050


title: PBMC_8780_CD_9

description:
Library name: PBMC_8780_CD_9
RNA-Seq of CHIM PBMC

value: Blood


title: FFPE, EarlyProgressive,nr94, nr 95, nr 122

description:
Library name: EP_spatial
10X Genomics

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files and bam files.
Sequences were aligned to GRCh38 genome to gene expression count using Space Ranger deafult settings.
Assembly: GRCh38
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of tissue image
Supplementary files format and content: aligned_tissue_image.jpg: image of tissue and spots.
Supplementary files format and content: cytassist_image.tiff: image of image in Cytassist
Supplementary files format and content: tissue_hires_image.jpg: high res image of tissue
Supplementary files format and content: tissue_lowres_image.jpg: low res image of tissue
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_positions.csv: spatial barcodes and the coordinates specifying spots
Supplementary files format and content: barcodes.tsv: list of spatial barcodes
Supplementary files format and content: features.tsv list of gene Ids
Supplementary files format and content: matrix.mtx gene expression count data in Matrix Market Exchange Format
Library strategy: Spatial Transcriptomics

extract_protocol:
Spatial transcriptomics, ffpe tissue with the 5 um sections was mounted onto glass slides for cytassist imaging and library construction.
Spatial transcriptome sequencing  libraries were prepared with 10X genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction.


title: Microglia_H6_048, KO female, ZT18

description:
Library name: Microglia_H6_048
Column name in microglia_counts.csv: H6-048


title: Rat cortex, TBI + Saline biological rep 1, snATAC

description:
Library name: Veh_1_ATAC
10x Genomics Multiome

value: Brain, cortex

value: 3-4 months

value: CCI + Saline

value: ATAC


title: OEKZ24242-01

address: 贵州省贵阳市花溪区大学城栋青南路

description:
Library name: CCI2_23_22
Fresh frozen Spatial transcriptome sequencing


title: PBMC_8779_CD_8_reprep

description:
Library name: PBMC_8779_CD_8_reprep
RNA-Seq of CHIM PBMC

value: PBMC

value: Yes

value: female


title: Microglia_G6_047, WT male, ZT18

description:
Library name: Microglia_G6_047
Column name in microglia_counts.csv: G6-047

value: wt

value: M


title: FFPE, EarlyStable,nr63,nr64,nr80

description:
Library name: ES_spatial
10X Genomics

value: Formalin Fixed Paraffin embedded kidney tissue


title: sham7

address: 贵州省贵阳市花溪区大学城栋青南路

description: Library name: Sample 3

data_processing:
Cell Ranger gene quantification quality control.
Post-quantification quality control: Filtering out low-quality cells, filtering out low-abundance genes (depending on the specific circumstances of the project), etc.
Standardization processing of gene expression.
Cell heterogeneity analysis: dimensionality reduction clustering, marker gene identification, cell type identification, cell subpopulation and other downstream personalized analyses.
Gene expression analysis: differential gene analysis, differential gene enrichment analysis, and other downstream personalized analyses.
Assembly: GRCh38，mm10
Supplementary files format and content: Tab-delimited text file including the ratio at which each gene appears cells in each sample cell
Supplementary files format and content: Tab-delimited text file including the cell count of the cluster in each sample

extract_protocol:
The 10x Genomics platform utilizes microfluidic technology to encapsulate beads with Cell Barcodes and cells in droplets. The droplets containing cells are collected, and then the cells are lysed within the droplets, allowing the mRNA within the cells to connect with the Cell Barcodes on the beads, forming Single Cell GEMs. Reverse transcription reactions are carried out within the droplets.
Based on 10×genomics technology to establish  library,follow the standard process of 10×genomics,we get the great result

value: spinal cord