title: MacFibrosis_03

data_processing:
Reads were aligned to the mm10 mouse genome using Kallisto and imported into R Studio for analysis via the TxImport package.
Transcripts with low counts were filtered out if they had 1) zero reads in any sample, or 2) less than at least one count per million in at least two samples. Data was then normalized using the trimmed mean of M values normalization method in the EdgeR package.
Mean-variance trend fitting, linear modeling, and Bayesian statistics for differential gene expression analysis were performed using the Voom, LmFit, and eBayes functions, respectively, of the Limma package, yielding differentially expressed genes between control and fibrosis groups.
Assembly: mm10
Supplementary files format and content: abundance.tsv files generated from Kallisto alignment
Supplementary files format and content: csv files of normalized RPKM values

extract_protocol:
Healthy and fibrotic murine liver were perfused with 1X PBS, cut into small pieces and digested in collagenase II (5mg/mL, Worthington Biochemical Corporation) at 37 oC for 2h with shaking. Digested cells were filtered through 40 μm nylon mesh and lysed with ACK lysis buffer (Quality Biological) for 10 min. After spinning, the cells were resuspended into 1X PBS. Hepatocytes were removed by spinning at 50xg for 10 min. The supernatant was further spined at 650xg for 3 min to get the nonparenchymal cells, which was further stained with CD45+ (BV785, Cat#103149, Biolegend) and F4/80+ (BV421, Cat#123132, Biolegend) for 30 min. Cells were further suspended in 1X PBS with 0.1% Draq7 live/dead staining. CD45+/F4/80+ macrophage was further sorted with BD FACSAria Fusion Sorter (BD Biosciences). RNA extracted and amplified (10 ng RNA/sample) using SMART-Seq® HT kit (Takara Bio, #634455) according to the manufacture’s instruction
PolyA-selected RNA was used to generate libraries using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions


title: WT_Con_H3K27ac_HiChIP_SET3_rep1

status: Public on Jul 01 2026

type: SRA

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

description: Library name: WT_Con_H3K27ac_HiChIP_SET3_rep1

library_source: genomic

data_processing:
Paired-end Hi-C sequencing reads were processed using HiC-Pro (v2.11.4).
Chromatin loops from HiChIP data were identified using FitHiChIP (v8.0). Loop calling was performed in peak-to-all mode (IntType=3) using paired ChIP-seq peaks as input. The bin size was set to 5kb (default), with interaction distance range defined as 10kb to 2Mb. Bias correction was enabled using coverage normalization, and peak-to-all background was used for contact probability estimation (UseP2PBackgrnd = 0). Loops were identified at a threshold of Q-value < 0.00001 for H3K27Ac HiChIP data, Q-value < 0.01 for ATF4 HiChIP data.
Assembly: hg19
Supplementary files format and content: hic contaning validpairs
Library strategy: HiChIP

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: The human colorectal cancer cell line HCT116 was cultured in RPMI-1640 medium (Welgene) supplemented with 10% fetal bovine serum (FBS; HyClone) and 1% penicillin–streptomycin (Welgene) at 37 ℃ in a humidified incubator containing 5% CO2. Cells were subcultured every 48–72 h.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature and quenched using 0.125 M glycine for 5 min, followed by washing with cold PBS. After cell lysis, cross-linked chromatin was digested with the DpnII restriction enzyme, with enzyme amounts adjusted in proportion to the number of cells, followed by fill-in with biotin-14-dATP (Jena Bioscience) and proximity ligation. The resulting ligation products were sheared by sonication using a Qsonica sonicator (30 s ON/30 s OFF, 10 cycles) and incubated overnight at 4 ℃ with either an H3K27ac antibody (Abcam, ab4729) or an ATF4 antibody (Cell Signaling Technology, 11815). After sequential washes with standard ChIP wash buffers, chromatin–antibody complexes were reverse cross-linked overnight. De-cross-linked DNA was purified and quantified using Qubit dsDNA HS Assay Kit (Invitrogen, Q32854) and 5 ng of DNA was subjected to biotin pull-down using a streptavidin C-1 magnetic beads.
Tagmentation was directly performed on bead-bound DNA with Tn5 transposase with enzyme amounts adjusted according to the DNA input, followed by washing with appropriate buffers. Tagmented DNA was released from the beads by a simplified PCR procedure and further amplified using Nextera PCR primers. Amplified libraries were size-selected and purified using AMPure XP beads (0.5x–0.75x).

treatment_protocol: Cells were treated with tunicamycin (Sigma-Aldrich) at a final concentration of 0.5 µg ml-1 for 6 h. Cells treated with 0.1% DMSO for the same duration served as vehicle controls.

tag: chip antibody

value: H3K27ac (Abcam #Ab4729)

tag: cell line

tag: cell type

value: Human colorectal cancer

tag: genotype

value: WT

tag: treatment

value: 0.1% DMSO

tag: time


title: MacFibrosis_04

city: Philadelphia

first: Gan

last: Zhao

state: PA Pennsylvania

address: 384E Old Vet Quad 3800 spruce street

country: USA

institute: University of Pennsylvania

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: liver

tag: tissue

value: liver

value: Sorted primary cells

value: liver macrophages

value: BALB/c WT


title: MacFibrosis_02


title: MacControl_04

value: Vehicle control


title: CEBPB_KO_Tm_RNA_SET4_rep3

description: Library name: CEBPB_KO_Tm_RNA_SET4_rep3

data_processing:
Paired-end sequencing reads were trimmed using TrimGalore (v0.6.4)
The trimmed reads were aligned to the human reference genome hg19 using STAR (v2.6.0c)61 with the parameters --chimSegmentMin 20 --twopassMode Basic --quantMode TranscriptomeSAM.
Reads counts at gene-levels are quantified using RSEM (v1.3.1)62 and normalized to transcripts per million (TPM).
Strand specific reads were selected using SAMtools (v1.3.1), and genome-wide coverage tracks were generated using deepTools (v3.4.3).
hg19
Assembly: RSEM output files including raw counts, TPM values
Supplementary files format and content: normalized bigwig

extract_protocol:
Total RNA was extracted from wild-type HCT116 and transcription factor knockout cells using RiboEx (GeneAll Biotechnology)
Sequencing libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, E7760) following the manufacturer’s protocol.

value: 0.5 μg ml tunicamycin


title: CEBPB_KO_Tm_RNA_SET4_rep2

description: Library name: CEBPB_KO_Tm_RNA_SET4_rep2


title: BCIF62

city: Bundoora

first: Quynh Nhu

last: Dinh

state: VIC

address: Kingsbury Drive & Plenty Rd

country: Australia

institute: La Trobe University

data_processing:
High-throughput sequencing was conducted using the HiSeqTM2500 platform
The results were mapped to the Ensembl-released mouse genome sequence and annotation.
Differential expression analysis was conducted using the DESeq R Package V.1.10.1 and P-values were adjusted using the Banjamini and Hochberg’s approach for controlling the false discovery rate
Genes were considered differentially expressed if the adjusted P-value was less than 0.05.
Supplementary files format and content: tab-delimited text files fpkm gene counts

source_name: Cerebral artery

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen).  2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Novogene

treatment_protocol: Mice underwent ad libitum eating or intermittant fasting for 3 months. After 3 months, chronic cerebral hypoperfusion was induced by the bilateral carotid arterys stenosis (BCAS) surgery. Control mice underwent sham surgery. Mice were culled at days 1, 14, 21 and 30 days post-surgery and cerebral arteries were collected.

value: Cerebral artery

tag: strain

tag: Sex

value: Male

tag: disease state

value: Chronic cerebral hypoperfusion


title: MacControl_02


title: MacControl_03


title: SHIF39

value: Control


title: SHIF69


title: CEBPB_KO_Tm_RNA_SET4_rep1

description: Library name: CEBPB_KO_Tm_RNA_SET4_rep1


title: 687g rep2

city: Cambridge

first: Whitney

last: Henry

state: MA

address: 500 Main St

department: Biology

institute: MIT

data_processing:
RNASeq single-end reads from Illumina 1.5 encoding were aligned using STAR (v2.6.1a) to the mouse genome (GRCm38/mm10) with Ensembl annotation (v91) in gtf format: default parameters were used, and an overhang of 39.
featureCounts was used to obtain counts with -s 2 (reversely stranded) and using Ensembl gtf annotation (v91).
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts from featureCounts

source_name: murine mammary carcinoma cell line

growth_protocol: All cell lines were cultured in DMEM/F12 medium containing 5% adult bovine serum with 1X penicillin-streptomycin and 1X non-essential amino acids in a humidified incubator at 37 °C with 5% CO2. All cells were negative for mycoplasma.

extract_protocol:
Total RNA was extracted using the RNeasy mini Kit (Qiagen, Cat.  #74104) according to manufacturer’s instruction.
Libraries were prepared for RNA-Seq using KAPA Biosystems KAPA mRNA HyperPrep Kit, according to manufacturer’s directions

treatment_protocol: Adherent cells grown in monolayer culture

tag: strain background

value: Tumor-derived cell line derived from MMTV-PyMT-Snail-IRES-YFP reporter mouse model


title: BCAL43


title: Epcam hi rep2

value: Epcam hi


title: pB3 rep 2

value: Tumor-derived cell line derived from MMTV-PyMT mouse model


title: SHIF5


title: SHAL34


title: Epcam hi rep1


title: CEBPB_KO_Con_RNA_SET4_rep2

description: Library name: CEBPB_KO_Con_RNA_SET4_rep2


title: pB2 rep2


title: BCIF63


title: CEBPB_KO_Con_RNA_SET4_rep1

description: Library name: CEBPB_KO_Con_RNA_SET4_rep1


title: pB2 rep1


title: ECRT patient tumor, MAP015

city: Paris

first: Franck

last: Bourdeaut

address: 26 rue d'ulm

country: France

institute: Institut Curie

description:
Library name: MAP015
Column name in raw counts and TPM matrixes : MAP015
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt

data_processing:
Raw data were processed using an in-house pipeline developed at the Institut Curie Bioinformatics Core Facility, following standard analysis in the field and available at https://github.com/bioinfo-pf-curie/RNA-seq.
Sequencing adaptors were trimmed using TrimGalore!
read QC were performed using fastqc
read mapping on GRCh39/hg19 reference genome were performed using STAR (version 2.5.3a) and the refFlat gene annotation downloaded from UCSC
duplicated reads were marked with picard and then removed
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: a single tab-delimited text file includes matrix of TPM values with sample in columns and genes on rows

molecule: polyA RNA

source_name: tumor

growth_protocol: I2A cells were maintained in RPMI containing 10% fetal bovine serum (FBS) and supplemented with 50 ng/mL doxycycline, 50 μg/mL hygromycin B and 300 μg/mL geneticin. G401-i cells were maintained in RPMI containing 10% FBS and supplemented with 50 ng/mL doxycycline. For both inducible cell lines, medium was changed every 3-4 days to renew drugs and cells were washed three times in Phosphate Buffer Saline (PBS) to completely remove doxycycline in order to induce SMARCB1 expression.

extract_protocol:
Total RNAs from cell line samples were extracted using the Nucleospin II kit (Macherey-Nagel). Total RNAs from frozen human tumors were extracted using the QIAamp RNAeasy kit (Qiagen)
Barcoded Illumina compatible libraries were generated from 750 ng of total RNA for each sample using TruSeq Stranded mRNA Library Preparation Kit (Illumina, San Diego, California, U.S.,).

treatment_protocol: For low-dose decitabine (DAC) experiments, I2A cells were treated with DAC at 100 nM or DMSO as a control for 21 days.

value: tumor

value: Rhabdoid tumor

tag: patient id


title: BCAL25

value: WT


title: ATRT patient tumor, RNA161_19_123

description:
Library name: RNA161_19_123
Column name in raw counts and TPM matrixes : RNA161_19_123
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt


title: WT_Tm_RNA_SET4_rep2

description: Library name: WT_Tm_RNA_SET4_rep2

value: Human colorectal cancer


title: ATRT patient tumor, RNA096_18_018

description:
Library name: RNA096_18_018
Column name in raw counts and TPM matrixes : RNA096_18_018
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt


title: ATRT patient tumor, RNA390_23_185

description:
Library name: RNA390_23_185
Column name in raw counts and TPM matrixes : RNA390_23_185
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt


title: BCIF29


title: ATRT patient tumor, RNA386_23_153

description:
Library name: RNA386_23_153
Column name in raw counts and TPM matrixes : RNA386_23_153
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt


title: WT_Tm_RNA_SET4_rep1

description: Library name: WT_Tm_RNA_SET4_rep1


title: WT_Con_RNA_SET4_rep3

description: Library name: WT_Con_RNA_SET4_rep3

value: 0.1% DMSO


title: ATRT patient tumor, RNA385_23_147

description:
Library name: RNA385_23_147
Column name in raw counts and TPM matrixes : RNA385_23_147
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt


title: SHAL67


title: ATRT patient tumor, RNA385_23_146

description:
Library name: RNA385_23_146
Column name in raw counts and TPM matrixes : RNA385_23_146
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt


title: WT_Con_RNA_SET4_rep2

description: Library name: WT_Con_RNA_SET4_rep2


title: ATRT patient tumor, RNA385_23_145

description:
Library name: RNA385_23_145
Column name in raw counts and TPM matrixes : RNA385_23_145
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt


title: SHIF40


title: ATRT patient tumor, RNA373_23_026

description:
Library name: RNA373_23_026
Column name in raw counts and TPM matrixes : RNA373_23_026
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt


title: ATRT patient tumor, RNA373_23_025

description:
Library name: RNA373_23_025
Column name in raw counts and TPM matrixes : RNA373_23_025
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt


title: BCAL60


title: Meningioangiomatosis patient tumor

description:
Library name: RNA371_23_012
Column name in raw counts and TPM matrixes : RNA371_23_012
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt

value: Meningioangiomatosis tumor


title: ATRT patient tumor, RNA371_23_011

description:
Library name: RNA371_23_011
Column name in raw counts and TPM matrixes : RNA371_23_011
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt


title: ATRT patient tumor, RNA371_23_010

description:
Library name: RNA371_23_010
Column name in raw counts and TPM matrixes : RNA371_23_010
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt


title: CHOP_KO_Tm_RNA_SET3_rep2

description: Library name: CHOP_KO_Tm_RNA_SET3_rep2


title: SHAL49


title: ATRT patient tumor, RNA368_22_456

description:
Library name: RNA368_22_456
Column name in raw counts and TPM matrixes : RNA368_22_456
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt


title: CHOP_KO_Tm_RNA_SET3_rep1

description: Library name: CHOP_KO_Tm_RNA_SET3_rep1


title: ATRT patient tumor, RNA365_22_437

description:
Library name: RNA365_22_437
Column name in raw counts and TPM matrixes : RNA365_22_437
raw_counts_RT_MAM_RNAseq.txt
TPM_RT_MAM_RNAseq.txt


title: Tc2_donor_3

city: Solna

first: Chris

middle: Andrew

last: Tibbitt

state: non-US

address: Biomedicum C7,, Tomtebodavägen 16

country: Sweden

institute: KI

description:
Library name: Sample 6
Column name in raw counts all samples.txt: Tc2_donor_3

data_processing:
Sequencing reads were aligned to the human reference genome (GRCh38, Ensembl release 112).
Gene-level read counts were generated using featureCounts v2.0.6.
Assembly: GRCh38 (Ensembl release 112).
Supplementary files format and content: Raw gene-level count matrix generated using featureCounts v2.0.6. Rows correspond to genes and columns correspond to individual samples.

source_name: blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from healthy donor buffy coats by Ficoll density gradient centrifugation. CD14+ and CD19+ cells were depleted by magnetic separation prior to fluorescence-activated cell sorting. Memory CD8+ T cells were cultured in IMDM supplemented with 10% fetal calf serum (FCS), 1% penicillin/streptomycin, plate-bound anti-CD3 (1 μg/mL) and anti-CD28 (3 μg/mL). Cells were polarized for 7 days under Tc1 or Tc2 differentiation conditions with cytokines refreshed on day 4. Tc1 cultures contained IL-12, anti-IL-4, IL-2 and anti-IL-10. Tc2 cultures contained IL-4, anti-IFN-γ, IL-2 and anti-IL-10.

extract_protocol:
Following 7 days of culture, cells were lysed directly in SMART-seq lysis buffer containing 3′ SMART-Seq CDS Primer II A and stored at −80°C until processing. RNA was extracted using the Takara SMART-seq v4 Ultra Low Input RNA Kit according to the manufacturer's protocol.
Full-length cDNA was generated using the Takara SMART-seq v4 Ultra Low Input RNA Kit. Library preparation was performed using the Illumina Nextera DNA Library Preparation Kit with Nextera XT dual indexes. Libraries were quality controlled using an Agilent 2100 Bioanalyzer and sequenced on Illumina NextSeq 500 instrument to generate 40 bp paired-end reads.

treatment_protocol: Cells were cultured under either Tc1- or Tc2-polarizing conditions for seven days. No additional pharmacological treatments were applied to samples used for RNA sequencing.

value: blood

value: CD8+ Tc2 cells

tag: individual


title: CHOP_KO_Con_RNA_SET3_rep3

description: Library name: CHOP_KO_Con_RNA_SET3_rep3


title: Tc1_donor_3

description:
Library name: Sample 5
Column name in raw counts all samples.txt: Tc1_donor_3

value: CD8+ Tc1 cells


title: BCAL10


title: SHIF6


title: Tc2_donor_2

description:
Library name: Sample 4
Column name in raw counts all samples.txt: Tc2_donor_2


title: Tc1_donor_2

description:
Library name: Sample 3
Column name in raw counts all samples.txt: Tc1_donor_2


title: Tc2_donor_1

description:
Library name: Sample 2
Column name in raw counts all samples.txt: Tc2_donor_1


title: GFPpos-4

city: Shanghai

first: Qing

last: Li

state: Shanghai

address: Xuhui Yueyang road 320, ShangHai, China

country: China

institute: Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences

data_processing:
Raw RNA-seq reads were cleaned using fastp (v0.20.0) program, aligned to mm10 using STAR (v2.7.3a)
Only unique mapped reads were kept and counted by featureCounts (v2.0.0)
FPKM and TPM were calculated by stringtie (v2.0)
Genome coverage was counted by bamCoverage (v3.3.1). Differential gene expression was carried out using DESeq2 (v1.30.0), and clusterProfiler (v3.18.1) was used for GO and KEGG analysis in R
Assembly: mm10
Supplementary files format and content: For deep-seq, tale-delimited text file includes number of different reads for each sample. For RNA-seq, tab-delimited text file includes RPKM values for each sample. For WGBS, bed file includes the average methylation sites per 200bp in the genome. For scRNA-seq of E7.5 embryos, cellfocus file includes the representation matrix of different cells.

source_name: Blastocyst

extract_protocol:
For deep-seq, The genomic DNA of various tissues (brain, heart, liver, testis, and tail) from wild-type mice and Gjb235delG/35delG mice derived from diploid compensation, was isolated using the TIANamp Genomic DNA Kit (TIANGEN). This was followed by PCR amplification for Sanger sequencing. Target sites were amplified from the extracted genomic DNA using Phanta® Max Super-Fidelity DNA Polymerase (Vazyme)For RNA-seq, single cells were picked using a Piezo-drill micromanipulator and transferred into a 200 µl tube containing 1.2 µl of lysis buffer. The lysate underwent cDNA amplification with the Single Cell Full Length mRNA Amplification Kit (Vazyme, Cat#N712)
For deep-seq,  the PCR products were then ligated with different barcodes and pooled together. Libraries were generated from adapter-modified PCR products. For RNA-seq, the RNA-seq library was prepared using the TruePrep DNA Library Prep Kit V2 (Vazyme, Cat#TD503) for Illumina sequencing
Libraries of deep-seq and RNA-seq subjected to deep sequencing on Illumina NovaSeq6000 platform following the manufacturer’s instructions (Illumina) to produce 150bp paired-end reads by Genergy Biotechnology Co. Ltd. (Shanghai, China).

value: Blastocyst

tag: genetic modification

value: Actin-GFP transgene


title: 2 Gy Irradiated, organoids, 7 days, mouse 3

city: Groningen

first: Rufina

last: Maturi

address: Antonius Deusinglaan 1

department: Radiotherapy

country: Netherlands

institute: University Medical Center Groningen

description:
Library name: 2 Gy Irradiated, 7 days 3
Smart3SEQ

data_processing:
For the alignment of the fastq files the mouse genome GRCm39 was used. STAR aligner software was used to align the results of the sequencing. Rstudion v4.1.3 was used for downstream analysis and for the generation of CPM files. The R package edgeR was used for normalization and identification of differentially expressed genes.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file including the raw counts from all replicates and conditions is provided.

source_name: Thyroid gland

growth_protocol: Organoids from all animals and conditions were cultured in Matrigel in DMEM/F12, Pen/Strep antibiotics, glutamax 2 mM, EGF 20 ng/ml, FGF2 20 ng/mL, Y27632 10 µM, B27 0.5%. All conditions were kept in culture at 37°C and 5% CO2 until the day of the experiment.

extract_protocol:
For the cDNA library preparation, total RNA was extracted from organoids using Rneasy Mini Kit according to the manufacturer`s instructions and its quality was determined using High Sensitivity RNA ScreenTapes on an Agilent 2100 Bioanalyzer. 100 ng of RNA was used as an input for all samples.
80 ng of highly intact RNA (RIN values > 9) was processed for the cDNA library preparation using the Smart3SEQ protocol, adhering to the manufacturer`s instructions.

treatment_protocol: E

value: Thyroid gland

value: Thyroid gland cells derived from organoids

tag: age

value: 8-12 weeks old

value: Irradiated, 2 Gy


title: 2 Gy Irradiated, organoids, 7 days, mouse 2

description:
Library name: 2 Gy Irradiated, 7 days 2
Smart3SEQ


title: Caco-2 cell lines, Pathological swing group, rep4

city: Chongqing

first: longli

last: peng

address: kaizhou

institute: Chongqing University

description: Library name: Sample 16

data_processing:
Raw data quality control and filtering were performed by fastp v0.23.4.
High-quality data after quality control were evaluated by FastQC v0.12.1.
High-quality data were aligned to the hg38 reference genome using STAR v2.7.11a.
Gene counts were obtained using featureCounts v2.0.6 to generate the gene expression matrix.
Differential expression analysis was performed using DESeq2 v1.42.0.
Assembly: hg38

source_name: Intestinal

extract_protocol:
Total RNA was qualified and quantified as follows: (1) RNA purity and concentration were then examined using NanoDrop 2000; (2) RNA integrity and quantity were measured using the Agilent 2100/4200 system.
RNA library for RNA-seq was prepared as fllows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library

value: Intestinal

value: Human intestinal epithelial cells

value: Pathological swing group


title: Caco-2 cell lines, Pathological swing group, rep3

description: Library name: Sample 15


title: BCAL41

value: Cerebral artery

value: Male

value: Chronic cerebral hypoperfusion


title: WT_Tm_RNA_SET3_rep3

description: Library name: WT_Tm_RNA_SET3_rep3

value: Human colorectal cancer

value: WT

value: 0.5 μg ml tunicamycin


title: BCAL27


title: Caco-2 cell lines, Pathological swing group, rep2

description: Library name: Sample 14


title: WT_Tm_RNA_SET3_rep2

description: Library name: WT_Tm_RNA_SET3_rep2


title: 40B_VH_6NJ_Cue

city: Boston

first: Lisa

last: Goldberg

state: Massachusetts

address: 72 E Concord St, R604

institute: Boston University School of Medicine

description: Library name: 40B_VH

data_processing:
FastQC reports were generated and inspected to check the quality of the dataset
Samples were mapped to the mouse reference genome using Hisat2
Gene-level raw read counts were obtained with featureCounts
Transcript-level read counts were obtained with Kallisto
Normalization and differential expression were done using DESeq2.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file with gene-level raw read counts for each sample
Supplementary files format and content: Tab delimited text file with transcript-level read counts for each sample

source_name: Ventral Hippocampus

extract_protocol:
RNA was extracted using Trizol (Qiagen, Valencia, CA, USA) and RNAeasy extraction kit (Qiagen, Valencia, CA, USA), as previously described(Yazdani, Shen et al. 2016, Goldberg, Zeid et al. 2021). RNA concentration and quality were evaluated using NanoDrop2000 (NanoDrop, Wilmington, DE, USA) and Agilent Bioanalyzer (Agilent, Santa Clara, CA, USA)
Libraries were prepared by the Huck Institutes of the Life Sciences Genomics Core Facility (Penn State University) for 75 bp single-end reads using the Illumina TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA).

treatment_protocol: To investigate baseline and learning-induced changes in hippocampal transcriptome that may underlie the observed behavioral differences between B6J and B6NJ, dorsal (DH) and ventral hippocampi (VH) were dissected for RNAsequencing (n=6 per group). To determine the impact of learning on hippocampal transcriptome, three groups were utilized: home cage, fear conditioned, and cue alone.

value: Ventral Hippocampus

value: Cue


title: 41A_DH_6NJ_HomeCage

description: Library name: 41A_DH

source_name: Dorsal Hippocapus

value: Dorsal Hippocapus

value: HomeCage


title: Caco-2.batch1.COL.rep2.E10

city: Sainte-Anne-de-Bellevue

first: Niladri

last: Basu

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description: Library name: Caco2_Batch1_COL_2_E10

library_source: other

data_processing:
Reads were aligned using STAR alignment on QIAGEN's CLC workbench software (v25.0.1) and Kallisto alignment on ExpressAnalyst
Raw counts were logCPM normalized and filtered for low abundance (5) and variance (15) using ExpressAnalyst
Normalized counts were analyzed for differential expression using DESeq2
Assembly: CLC workbench used hg38.p14 Ensembl v113 GCA_000001405.29; ExpressAnalyst used hg38.p14 GCA_000001405
Supplementary files format and content: raw files and count files are provided as fastq.gz files and .txt files, respectively.

molecule: other

source_name: cell lysate

growth_protocol: from ms

extract_protocol:
cells were lysed in Qiagen's proprietary lysis buffer and used directly for library preparation
ultraplex 3' transcriptome library preparation following Qiagen's UPXome protocol

treatment_protocol: cells were exposed to various concentrations of 6ppd-quinone for 24 hours after seeding at 35,000 cells per well

value: colon

value: epithelial

value: cell line


title: Caco-2 cell lines, Pathological swing group, rep1

description: Library name: Sample 13


title: BCIF14


title: Caco-2 cell lines, Physiological Swing Group, rep4

description: Library name: Sample 12

value: Physiological Swing


title: WT_Tm_RNA_SET3_rep1

description: Library name: WT_Tm_RNA_SET3_rep1


title: SHIF72

value: Control


title: Caco-2 cell lines, Physiological Swing Group, rep3

description: Library name: Sample 11

value: Intestinal

value: Human intestinal epithelial cells


title: Caco-2 cell lines, Physiological Swing Group, rep2

description: Library name: Sample 10


title: WT_Con_RNA_SET3_rep3

description: Library name: WT_Con_RNA_SET3_rep3

value: 0.1% DMSO


title: Caco-2 cell lines, Physiological Swing Group, rep1

description: Library name: Sample 9


title: SHIF37

value: Cerebral artery

value: Male


title: Caco-2 cell lines, static, rep4

description: Library name: Sample 8

value: Static control


title: Caco-2 cell lines, static, rep2

description: Library name: Sample 6


title: SHIF24

value: WT


title: WT_Con_RNA_SET3_rep2

description: Library name: WT_Con_RNA_SET3_rep2

value: Human colorectal cancer


title: SHIF38


title: Caco-2 cell lines, static, rep3

description: Library name: Sample 7


title: Caco-2.batch1.COL.rep2.A10

description: Library name: Caco2_Batch1_COL_2_A10


title: WT_Con_RNA_SET3_rep1

description: Library name: WT_Con_RNA_SET3_rep1


title: CHOP_KO_Con_RNA_SET3_rep1

description: Library name: CHOP_KO_Con_RNA_SET3_rep1


title: CHOP_KO_Con_RNA_SET3_rep2

description: Library name: CHOP_KO_Con_RNA_SET3_rep2


title: SHAL33


title: Caco-2 cell lines, static, rep1

description: Library name: Sample 5


title: 40A_DH_6NJ_Cue

description: Library name: 40A_DH


title: WT_Tm_NFIL3_rep2

description: Library name: WT_Tm_NFIL3_rep2

data_processing:
Paired-end ChIP-seq reads were trimmed using TrimGalore.
Trimmed reads were aligned to the human hg19 reference genome using BWA (v0.7.17) with default parameters.
Low-quality alingments were filtered using SAMtools with the parameters q 30 –F 1804 –f 2, and duplicate reads were marked using Picard (v2.18.23) with MarkDuplicates function. Uniquely mapped reads were normalized to counts per million (CPM) DNA and duplicate reads were then removed using SAMtools.
Uniquely mapped reads were normalize to generate bigwig file.
Peaks were called for each biological replicate using MACS2 (v2.2.7.1) with the parameters callpeak -f BAMPE --nomodel -g hg19 -q 0.001 --narrow.
Assembly: hg19
Supplementary files format and content: narrowPeak, CPM normalized bigwig

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 min at room temperature and quenched using 0.125 M glycine for 5 min, followed by washing with cold PBS. After cell lysis, chromatin was sheared by sonication using a Qsonica sonicator(30 s ON/30 s OFF, 10 cycles, repeated three times). Lysates were pre-cleared by incubation with protein A/G magnetic beads (Invitrogen) prior to immunoprecipitation. Pre-cleared chromatin was incubated overnight at 4 ℃ with the indicated antibodies.
Tagmentation was then performed directly on bead-bound chromatin using the Nextera DNA Library Prep kit (Illumina) followed by two washes to remove excess transposase. Bead-bound chromatin was incubated overnight  for reverse cross-linking, and the recovered DNA was PCR-amplified using Nextera PCR primers. Amplified libraries were size-selected and purified using AMPure XP beads (0.65x–0.9x)

value: NFIL3 (MBL, #PM097)

value: 0.5 μg ml tunicamycin


title: Caco-2 cell lines, IBDinduction, rep3

description: Library name: Sample 3

value: IBD induction


title: Tc1_donor_1

description:
Library name: Sample 1
Column name in raw counts all samples.txt: Tc1_donor_1

value: blood

value: CD8+ Tc1 cells


title: Caco-2 cell lines, IBDinduction, rep4

description: Library name: Sample 4


title: BCAL75

value: Chronic cerebral hypoperfusion


title: Caco-2 cell lines, IBDinduction, rep2

description: Library name: Sample 2


title: WT_Tm_NFIL3_rep1

description: Library name: WT_Tm_NFIL3_rep1


title: Caco-2 cell lines, IBDinduction, rep1

description: Library name: Sample 1

tag: batch


title: WT_Tm_H3K27ac_HiChIP_SET3_rep2

description: Library name: WT_Tm_H3K27ac_HiChIP_SET3_rep2

value: H3K27ac (Abcam #Ab4729)

value: 0.5 μg/ml tunicamycin


title: SHAL35

value: Control


title: Pat5_rep1_urine_VDJ

city: Berlin

first: Christopher

middle: Mark

last: Skopnik

address: Charitéplatz 1

country: Germany

institute: Charité - Universitätsmedizin Berlin

description:
Library name: Sample24
10X Genomics

library_source: transcriptomic single cell

data_processing:
For gene expression (GEX): Initial FASTQ files were generated from base call files with cellranger mkfastq. From fastq files, GEX reads were mapped against human reference genome as provided by 10X Genomics (GRCh38-2020-A) using cellranger count from Cell Ranger v7.1.0 with default settings but exclusion of intronic reads (--include-introns=false). This generated the files filtered_feature_bc_matrix.h5 and raw_feature_bc_matrix.h5 with respective sample prefixes.
From resulting BAM files, anonymized (bamboozled) versions were generated with the python tool BAMboozle (v.0.5.0) (https://pypi.org/project/BAMboozle/) with default settings. The bamboozled BAM files were converted back to fastq files with cellranger bamtofastq. Bamboozled fastq files were deposited at the Sequencing read archive (SRA).
For T cell receptors (VDJ): TCR reads of VDJ libraries were mapped against GRCh38-alts-ensembl-2.0.0 as provided by 10X Genomics using cellranger vdj with default settings. Here, Cell Ranger v3.0.2 and v5.0.0 were used for Pat2 (replicate one), Pat3, Pat4 and Pat2 (replicate two), Pat5, Pat6, respectively. This generated all_contig_annotations.csv, clonotypes.csv, consensus_annotations.csv, filtered_contig_annotations.csv.
Assembly: GRCh38-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.h5 and raw_feature_bc_matrix.h5 contain unique molecular identifier (UMI) count matrices for GEX. all_contig_annotations.csv, clonotypes.csv, consensus_annotations.csv, filtered_contig_annotations.csv contain TCR chain callings and clonotype annotation for cellular barcodes; all as inferred from VDJ libraries. See 10X Genomics’ documentation for exact file description.

source_name: urine

extract_protocol:
Paired samples of heparinized venous blood and freshly voided non-morning urine (usually 2nd urine of the day; processed less than one-hour post excretion) were collected from patients who were hospitalized at the Charité - Universitätsmedizin Berlin due to acute lupus flares with renal involvement. After dipstick analysis to exclude urinary tract infection urine was diluted 1:2 in Annexin binding buffer (ABB) with 1 % BSA and 2 µg/ml Actinomycin D (ActD). Peripheral blood was treated with 2 µg/ml ActD and both body fluids were incubated for 30 min on ice. ActD should preserve transcriptomes from alteration ex vivo. Urine pellets from centrifugation (300 g, 7 min, 4 °C) and PBMC isolated by density gradient centrifugation (600 g, 20 min, 25 °C) with Ficoll-Paque were subjected to red blood cell lysis with ammonium chloride buffer when necessary. Subsequent to 20 min incubation on ice with AnnexinV-FITC (Biolegend, 640906 or Miltenyi, 130-093-060), FCγR blocking reagent and fluorochrome conjugated mAb against human CD3 (APC-eFluor780, SK7, eBioscience, 47-0036-42), CD4 (PE-Vio770, REA623, Miltenyi, 130-113-227) and CD8 (PE or APC, GN11/134D7, DRFZ in-house) cell pellets were filtered through 30 µm mesh, washed at least 10X volume of ABB, resuspended in 2 ng/ml DAPI -containing ABB and sorted by FACS on machines from BD (FACSAria or FACSAriaII) with 70 µm nozzles for DAPI- AnnexinV- CD3+ and CD4+ or CD8+ events. Cell sorters were maintained by the FCCF at DRFZ in Berlin. Events from urine were sorted into one tube. CD4+ or CD8+ T cell events from blood were sorted separately for and mixed subsequently at the CD4-to-CD8 ratio equivalent to that from paired urine samples. ScRNA-seq was conducted subsequently when absolute sorted event count from urine was 3000 or above.
Library construction was conducted according to protocols Chromium Single Cell 3’ Library and Gel Bead Kit v2 (PN-120267) for Pat0 and Pat1, Chromium Single Cell 5' Library and Gel Bead Kit v1 (PN-1000014) for Pat2 (replicate one) and Pat3 5, Chromium Next GEM Single Cell 5' Library and Gel Bead Kit v1.1 (PN-1000167) for Pat2 (replicate two) and Pat6. Libraries of Pat2 6 were split and separately processed for sequencing of gene expression (GEX) and immune receptors V(D)J, here T cell receptor (TCR). Intermediate and final library quantity and quality was assessed with Qubit and Bioanalyzer2100 (Agilent).

value: urine

value: T lymphocyte

tag: replicate

tag: patient sex

value: female

tag: patient age

tag: sort date

tag: 10x library_version

tag: library type

value: T cell receptor (VDJ)


title: WT_Con_NFIL3_rep2

description: Library name: WT_Con_NFIL3_rep2

tag: chip antibody

tag: cell line

tag: cell type

tag: genotype

tag: treatment

value: 0.1% DMSO

tag: time


title: Pat5_rep1_blood_VDJ

description:
Library name: Sample23
10X Genomics

source_name: peripheral blood

tag: tissue

value: peripheral blood


title: BCAL57

value: Cerebral artery

value: WT

tag: strain

tag: Sex

value: Male

tag: disease state


title: Pat4_rep1_urine_VDJ

description:
Library name: Sample22
10X Genomics


title: WT_Con_NFIL3_rep1

description: Library name: WT_Con_NFIL3_rep1

value: NFIL3 (MBL, #PM097)

value: Human colorectal cancer


title: SHIF70


title: Pat3_rep1_urine_VDJ

description:
Library name: Sample20
10X Genomics


title: Pat4_rep1_blood_VDJ

description:
Library name: Sample21
10X Genomics


title: Pat3_rep1_blood_VDJ

description:
Library name: Sample19
10X Genomics


title: SHIF8


title: Pat2_rep1_urine_VDJ

description:
Library name: Sample16
10X Genomics


title: WT_Tm_CEBPB_rep1

description: Library name: WT_Tm_CEBPB_rep1

value: CEBPB (Santa Cruz, #sc7962)

value: 0.5 μg ml tunicamycin


title: Pat2_rep1_blood_VDJ

description:
Library name: Sample15
10X Genomics


title: BCAL44

value: Chronic cerebral hypoperfusion


title: SHAL20


title: WT_HCFC and Chil1-/-_HFHC(WTA)

city: Kunming

first: Bo

last: Chen

address: East Outer Ring South Road

institute: YunnanUniversity

data_processing:
FASTQ files obtained from sequencing were processed using BD Rhapsody WTA analysis pipeline(v1.0.1), and aligned to GRCm38 and GencodeM19 for transcript annotation and quantitation.
Further processing was done with Seurat  (cell and gene filtering, clustering, differential gene expression analysis).
Assembly: GRCm38
Supplementary files format and content: BD Rhapsody WTA analysis output

extract_protocol:
Primary parenchymal cells were isolated from mouse liver tissue, and the cells were captured by BD Rhapsody system according to the manufacturer's instructions.
Using the library preparation scheme provided by BD Biosciences, the cDNA was amplified and the transcriptome library was constructed.

value: liver


title: WT_Tm_CEBPB_rep2

description: Library name: WT_Tm_CEBPB_rep2


title: 39C_DH_6NJ_Shock_Cue

description: Library name: 39C_DH

value: Dorsal Hippocapus


title: MacFibrosis_01

value: Sorted primary cells

value: liver macrophages

value: BALB/c WT


title: Pat5_rep1_urine_GEX

description:
Library name: Sample12
10X Genomics

value: urine

value: T lymphocyte

value: female

value: gene expression (GEX)


title: WT_Con_CEBPB_rep2

description: Library name: WT_Con_CEBPB_rep2

value: 0.1% DMSO


title: MacControl_01

value: Vehicle control


title: SHAL19

value: Cerebral artery

value: WT

value: Male

value: Control


title: Pat4_rep1_urine_GEX

description:
Library name: Sample10
10X Genomics


title: WT_Con_CEBPB_rep1

description: Library name: WT_Con_CEBPB_rep1

value: CEBPB (Santa Cruz, #sc7962)

value: Human colorectal cancer


title: Pat4_rep1_blood_GEX

description:
Library name: Sample9
10X Genomics

value: peripheral blood


title: BCIF61

value: Chronic cerebral hypoperfusion


title: 687g rep1

tag: strain background

value: Tumor-derived cell line derived from MMTV-PyMT-Snail-IRES-YFP reporter mouse model


title: CEBPB_KO_Con_RNA_SET4_rep3

description: Library name: CEBPB_KO_Con_RNA_SET4_rep3


title: Pat3_rep1_urine_GEX

description:
Library name: Sample8
10X Genomics

tag: replicate


title: Pat5_rep1_blood_GEX

description:
Library name: Sample11
10X Genomics

tag: patient sex


title: ATF4_KO_Tm_CHOP_rep2

description: Library name: ATF4_KO_Tm_CHOP_rep2

value: CHOP (Cell signaling technology, #2895)

value: 0.5 μg ml tunicamycin


title: Pat2_rep1_urine_GEX

description:
Library name: Sample4
10X Genomics

value: urine

tag: patient age


title: SHAL3


title: SHIF71


title: BCIF78


title: Pat3_rep1_blood_GEX

description:
Library name: Sample7
10X Genomics

value: T lymphocyte

tag: sort date


title: ATF4_KO_Tm_CHOP_rep1

description: Library name: ATF4_KO_Tm_CHOP_rep1


title: WT_Tm_CHOP_rep2

description: Library name: WT_Tm_CHOP_rep2


title: Pat1_rep1_urine_GEX

description:
Library name: Sample2
10X Genomics

value: female

tag: 10x library_version


title: Pat0_rep1_urine_GEX

description:
Library name: Sample1
10X Genomics

value: male

tag: library type

value: gene expression (GEX)


title: Pat2_rep1_blood_GEX

description:
Library name: Sample3
10X Genomics


title: pB3 rep1

value: Tumor-derived cell line derived from MMTV-PyMT mouse model


title: BCAL58

value: Cerebral artery


title: SEV,FrontotemporalDementia,FTD10

city: Pavia

first: Rosalinda

last: Di Gerlando

address: Via Mondino 2

country: Italy

institute: IRCCS Mondino Foundation

description: Library name: FTD10

data_processing:
FastQ files were generated via Illumina bcl2fastq2 (Version 2.17.1.14 http://support.illumina.com/downloads/bcl2fastq-conversion-software-v217.html).
Quantification of miRNAs was done as described in the literature [13]. The workflow, including quality control filter, trimming of adapters, and reads mapping against miRNA precursors, is implemented in Docker4Seq package
Assembly: HG19
Supplementary files format and content: fastq.gz

source_name: Small Extracellular Vesicles from plasma

growth_protocol: Venus blood from AD patients, FTD patients and CTRL subjects was collected in sodium citrate tubes and then plasma was retrieved. Differential centrifugation method was applied to separate SEVs from LEVs.

extract_protocol:
RNA was extracted from SEVs fractions using miRNeasy Mini kit (Qiagen, Germany) according to manufacturer’s instructions.
Libraries for miRNA sequencing have been prepared using the Small RNA-Seq Library Prep kit (Lexogen) according to the user manual. Sequencing steps have been carried out on the Illumina NextSeq 500.


title: ATF4_KO_Con_CHOP_rep2

description: Library name: ATF4_KO_Con_CHOP_rep2

tag: chip antibody

value: 0.1% DMSO


title: SHIF7

value: WT

value: Male


title: SEV,FrontotemporalDementia,FTD9

description: Library name: FTD9

value: Small Extracellular Vesicles from plasma


title: ATF4_KO_Con_CHOP_rep1

description: Library name: ATF4_KO_Con_CHOP_rep1

tag: cell line

value: Human colorectal cancer


title: SEV,FrontotemporalDementia,FTD8

description: Library name: FTD8


title: SEV,FrontotemporalDementia,FTD6

description: Library name: FTD6


title: BCAL76


title: SEV,FrontotemporalDementia,FTD7

description: Library name: FTD7


title: SEV,FrontotemporalDementia,FTD5

description: Library name: FTD5


title: SEV,FrontotemporalDementia,FTD4

description: Library name: FTD4


title: SHAL66

value: Control


title: SEV,FrontotemporalDementia,FTD2

description: Library name: FTD2


title: NFIL3_KO_Tm_ATF4_rep2

description: Library name: NFIL3_KO_Tm_ATF4_rep2

value: ATF4 (Cell signaling technology, #11815)

tag: cell type


title: SEV,FrontotemporalDementia,FTD1

description: Library name: FTD1


title: NFIL3_KO_Tm_ATF4_rep1

description: Library name: NFIL3_KO_Tm_ATF4_rep1

tag: genotype


title: BCAL26

tag: treatment

value: Chronic cerebral hypoperfusion


title: SEV,HealthyControl,HC20

description: Library name: HC20


title: SEV,HealthyControl,HC21

description: Library name: HC21


title: SEV,HealthyControl,HC19

description: Library name: HC19


title: CEBPB_KO_Tm_ATF4_rep2

description: Library name: CEBPB_KO_Tm_ATF4_rep2

tag: time


title: SEV,HealthyControl,HC18

description: Library name: HC18

tag: tissue


title: BCAL74

tag: strain


title: SEV,HealthyControl,HC17

description: Library name: HC17


title: SEV,HealthyControl,HC16

description: Library name: HC16


title: CEBPB_KO_Tm_ATF4_rep1

description: Library name: CEBPB_KO_Tm_ATF4_rep1


title: SHAL36

tag: Sex


title: SEV,HealthyControl,HC15

description: Library name: HC15


title: CHOP_KO_Tm_ATF4_rep2

description: Library name: CHOP_KO_Tm_ATF4_rep2


title: SHIF56

tag: disease state


title: SEV,HealthyControl,HC13

description: Library name: HC13


title: CHOP_KO_Tm_ATF4_rep1

description: Library name: CHOP_KO_Tm_ATF4_rep1


title: SEV,HealthyControl,HC12

description: Library name: HC12


title: BCIF79


title: XBP1_KO_Tm_ATF4_rep2

description: Library name: XBP1_KO_Tm_ATF4_rep2


title: BCAL59


title: SEV,HealthyControl,HC10

description: Library name: HC10


title: XBP1_KO_Tm_ATF4_rep1

description: Library name: XBP1_KO_Tm_ATF4_rep1


title: SEV,HealthyControl,HC9

description: Library name: HC9


title: SEV,HealthyControl,HC8

description: Library name: HC8


title: BCAL42


title: SEV,HealthyControl,HC7

description: Library name: HC7


title: ATF6_KO_Tm_ATF4_rep2

description: Library name: ATF6_KO_Tm_ATF4_rep2


title: SHAL52


title: SEV,HealthyControl,HC5

description: Library name: HC5


title: SHIF53


title: ATF6_KO_Tm_ATF4_rep1

description: Library name: ATF6_KO_Tm_ATF4_rep1


title: SEV,HealthyControl,HC4

description: Library name: HC4


title: WT_Tm_ATF4_rep2

description: Library name: WT_Tm_ATF4_rep2


title: SEV,HealthyControl,HC2

description: Library name: HC2


title: SEV,HealthyControl,HC3

description: Library name: HC3


title: SHIF21


title: WT_Tm_ATF4_rep1

description: Library name: WT_Tm_ATF4_rep1


title: SEV,Alzheimer'sDisease,AD20

description: Library name: AD20


title: SHAL4


title: NFIL3_KO_Con_ATF4_rep2

description: Library name: NFIL3_KO_Con_ATF4_rep2


title: SEV,Alzheimer'sDisease,AD18

description: Library name: AD18


title: NFIL3_KO_Con_ATF4_rep1

description: Library name: NFIL3_KO_Con_ATF4_rep1


title: SEV,Alzheimer'sDisease,AD17

description: Library name: AD17


title: SEV,Alzheimer'sDisease,AD16

description: Library name: AD16


title: BCIF48


title: SEV,Alzheimer'sDisease,AD15

description: Library name: AD15


title: SEV,Alzheimer'sDisease,AD14

description: Library name: AD14


title: CEBPB_KO_Con_ATF4_rep2

description: Library name: CEBPB_KO_Con_ATF4_rep2


title: SEV,Alzheimer'sDisease,AD13

description: Library name: AD13


title: CEBPB_KO_Con_ATF4_rep1

description: Library name: CEBPB_KO_Con_ATF4_rep1


title: SHAL65


title: SEV,Alzheimer'sDisease,AD11

description: Library name: AD11


title: SEV,Alzheimer'sDisease,AD10

description: Library name: AD10


title: CHOP_KO_Con_ATF4_rep2

description: Library name: CHOP_KO_Con_ATF4_rep2


title: SEV,Alzheimer'sDisease,AD9

description: Library name: AD9


title: SEV,Alzheimer'sDisease,AD8

description: Library name: AD8


title: SEV,Alzheimer'sDisease,AD7

description: Library name: AD7


title: BCIF16


title: XBP1_KO_Con_ATF4_rep2

description: Library name: XBP1_KO_Con_ATF4_rep2


title: BCIF32


title: SEV,Alzheimer'sDisease,AD5

description: Library name: AD5


title: XBP1_KO_Con_ATF4_rep1

description: Library name: XBP1_KO_Con_ATF4_rep1


title: SEV,Alzheimer'sDisease,AD4

description: Library name: AD4


title: SEV,Alzheimer'sDisease,AD6

description: Library name: AD6


title: SHAL1


title: SEV,Alzheimer'sDisease,AD3

description: Library name: AD3


title: BCIF47


title: ATF6_KO_Con_ATF4_rep1

description: Library name: ATF6_KO_Con_ATF4_rep1


title: 8H_REC1_COMBO

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Bioinformatics Core Unit

country: Switzerland

institute: IOR

description:
Library name: 8H_REC1_COMBO
Column name in RawCounts.POL5551.Ibrutinib.Combo.txt and Normalized.LCPM.POL5551.Ibrutinib.Combo.txt: 8H_REC1_pol5551

data_processing:
Illumina Casava1.8 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to HG38 reference genome using bwa mem command, reads that have map quality score less than 30 were removed from downstream analysis.
Alignment files in the bam format were used to quantify the gene expression (gencode v22)
Assembly: hg38
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: tab delimited text file includes mormalized (TMM) log2 CPM for each sample

growth_protocol: Lymphoma cell lines (Supplementary Table S1) were cultured according to the recommended conditions. All media were supplemented with fetal bovine serum (FBS) (10% or 20%) and penicillin-streptomycin-neomycin (≈5,000 units penicillin, 5 mg streptomycin, and 10 mg neomycin/mL; Sigma-Aldrich, Darmstadt, Germany).

extract_protocol:
Total RNA was extracted using the All Prep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA concentration and integrity were measured with a NanoDrop ND-1000 spectrophotometer and assessed through the Bioanalyzer 2100 instrument (Agilent Technologies, Santa Clara, CA, USA).
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs Inc.) was employed with the NEBNext Multiplex Oligos for Illumina (New England BioLabs Inc.) and NEBNext Poly(A) mRNA Magnetic Isolation Module for cDNA synthesis with the addition of barcode sequences. The pre-pool sequencing was performed using the NextSeq2000 (Illumina, San Diego, CA, USA) with the P2 reagents kit V3 (100 cycles; Illumina).

treatment_protocol: SPX5551 wes provided by Spexis. Ibrutinib was purchased from Selleckchem (Houston, TX, USA)

value: IBRUTINIB + SPX5551

tag: timepoint

value: 8 hours


title: Dura_OG_IV_scTCR

first: Colin

middle: YC

last: Lee

address: Wellcome Genome Campus, Hinxton

country: United Kingdom

institute: Molecular Immunity Unit

data_processing:
Demultiplexing was performed with Casava (Illumina).
Barcoded processing, gene counting and aggregation were performed using the 10x CellRanger software v7.0 according to the manufacturer's workflow.
Assembly: mm10
Supplementary files format and content: 10x Genomics CellRanger count filtered feature matrices output: Tab-separated values files and matrix files
Supplementary files format and content: 10x Genomics Cellranger vdj output: all_contig annotations (.csv) and alignment (.fasta) files

source_name: Dura

extract_protocol:
Extravascular CD45+ cells were sorted from digested dura or colon tissue for RNA extraction and library preparation.
Gene expression libraries were prepared from FACS-sorted populations of single cells using the 10x Chromium Controller and 10x Chromium Single Cell V(D)J 5’ kit v2 with TCR amplification (10x Genomics, Inc.). Samples were loaded onto the chip following manufacturer’s recommendations.

value: Dura

value: OG Salmonella infection, IV recall


title: 8H_REC1_pol5551

description:
Library name: 8H_REC1_pol5551
Column name in RawCounts.POL5551.Ibrutinib.Combo.txt and Normalized.LCPM.POL5551.Ibrutinib.Combo.txt: 8H_REC1_ibr


title: SEV,FrontotemporalDementia,FTD12

description: Library name: FTD12


title: WT_Tm_CHOP_rep1

description: Library name: WT_Tm_CHOP_rep1

value: CHOP (Cell signaling technology, #2895)

value: 0.5 μg ml tunicamycin


title: SEV,FrontotemporalDementia,FTD11

description: Library name: FTD11


title: WT_Con_CHOP_rep2

description: Library name: WT_Con_CHOP_rep2


title: ATF6_KO_Con_ATF4_rep2

description: Library name: ATF6_KO_Con_ATF4_rep2


title: WT_Con_CHOP_rep1

description: Library name: WT_Con_CHOP_rep1


title: SEV,FrontotemporalDementia,FTD3

description: Library name: FTD3


title: SEV,Alzheimer'sDisease,AD1

description: Library name: AD1


title: SEV,Alzheimer'sDisease,AD2

description: Library name: AD2


title: WT_Con_ATF4_rep2

description: Library name: WT_Con_ATF4_rep2


title: 8H_REC1_Ibrutinib

description:
Library name: 8H_REC1_Ibrutinib
Column name in RawCounts.POL5551.Ibrutinib.Combo.txt and Normalized.LCPM.POL5551.Ibrutinib.Combo.txt: 8H_REC1_dmso

value: IBRUTINIB


title: BAL, MHV1 infection, ZT6 time point, collected post-infection day 2, replicate 3

city: St Louis

first: Jeffery

last: Haspel

state: MO

address: 660 S Euclid Avenue

institute: Washington University, St Louis

description:
Library name: Sample64
all.gene_moderated_log2cpm_BAL.tsv
BAL_5408_RNA

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5
Transcript counts were produced by Sailfish version 0.6.3
Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction known junction saturation, and read distribution over known gene models with RSeQC version 2.3
Gene-level and transcript counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for sample differences in library size.
The TMM size factors and the matrix of counts were imported into R/Bioconductor package Limma, and weighted likelihoods based on the observed mean-variance relationship of every gene/transcript were then calculated for all samples with the Voom function
Assembly: mm10
Supplementary files format and content: tab-delimited text files include log2 counts per million (CPM) values for each Sample.

source_name: BAL

growth_protocol: Mice were maintained and propagated in shoebox-sized cages in a 12-hour light-dark cycle with food available ad lib. To shift the circadian phases of mice, they were acclimated in custom light-tight enclosures (Gorilla Grow Tenet) for two weeks with the light cycle controlled by a programmable timer

extract_protocol:
To obtain BALs, mice were euthanized and their tracheas were cannulated with a 20G flexible catheter, 1-2 mm distal to the larynx.   The lungs were then slowly lavaged in 2 passes with a total of 1 ml sterile phosphate buffered saline (PBS).
Whole lungs were manually excised and immersed in RNAlater solution
Total RNA was isolated from lung homogenates using RNeasy Mini Kits (Qiagen)
RNA from whole lung homogenates or BAL cell pellets were converted to cDNA libraries for sequencing using the the SMARTer kit following manufacturer protocols

treatment_protocol: Mice were anesthetized with 3% isoflurane and then intranasally treated with 30ul of virus diluted in PBS. After viral infection, mice were housed in constant dark conditions until the end of the experiment.

value: BAL

tag: tissue type

value: BAL cell pellet

value: Wild type

value: MHV1 infection, collected post-infection day 2, ZT6


title: SHAL17

value: Cerebral artery

value: WT

value: Male


title: Dura_IV_scTCR

value: IV Salmonella infection


title: SHAL68

value: Control


title: 8H_REC1_DMSO

description:
Library name: 8H_REC1_DMSO
Column name in RawCounts.POL5551.Ibrutinib.Combo.txt and Normalized.LCPM.POL5551.Ibrutinib.Combo.txt: 8H_REC1_Combo

value: DMSO


title: WT_Con_ATF4_rep1

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

institute: Yonsei University College of Medicine

description: Library name: WT_Con_ATF4_rep1

value: ATF4 (Cell signaling technology, #11815)

value: Human colorectal cancer

value: 0.1% DMSO


title: 4H_REC1_COMBO

description:
Library name: 4H_REC1_COMBO
Column name in RawCounts.POL5551.Ibrutinib.Combo.txt and Normalized.LCPM.POL5551.Ibrutinib.Combo.txt: 4H_REC1_pol5551

value: IBRUTINIB + SPX5551

value: 4 hours


title: 4H_REC1_pol5551

description:
Library name: 4H_REC1_pol5551
Column name in RawCounts.POL5551.Ibrutinib.Combo.txt and Normalized.LCPM.POL5551.Ibrutinib.Combo.txt: 4H_REC1_ibr


title: 4H_REC1_DMSO

description:
Library name: 4H_REC1_DMSO
Column name in RawCounts.POL5551.Ibrutinib.Combo.txt and Normalized.LCPM.POL5551.Ibrutinib.Combo.txt: 4H_REC1_Combo


title: Colon_IV_scTCR

source_name: Colon

value: Colon


title: NFIL3_KO_Tm_H3K27ac_SET5_rep2

description: Library name: NFIL3_KO_Tm_H3K27ac_SET5_rep2

value: H3K27ac (Abcam #Ab4729)

value: 0.5 μg ml tunicamycin


title: 4H_REC1_Ibrutinib

description:
Library name: 4H_REC1_Ibrutinib
Column name in RawCounts.POL5551.Ibrutinib.Combo.txt and Normalized.LCPM.POL5551.Ibrutinib.Combo.txt: 4H_REC1_dmso

value: IBRUTINIB


title: NFIL3_KO_Tm_H3K27ac_SET5_rep1

description: Library name: NFIL3_KO_Tm_H3K27ac_SET5_rep1


title: Colon_OG_IV_scTCR

value: OG Salmonella infection, IV recall


title: 12H_REC1_COMBO

description:
Library name: 12H_REC1_COMBO
Column name in RawCounts.POL5551.Ibrutinib.Combo.txt and Normalized.LCPM.POL5551.Ibrutinib.Combo.txt: 12H_REC1_pol5551

value: 12 hours


title: WT_Tm_H3K27ac_SET5_rep2

description: Library name: WT_Tm_H3K27ac_SET5_rep2


title: 12H_REC1_pol5551

description:
Library name: 12H_REC1_pol5551
Column name in RawCounts.POL5551.Ibrutinib.Combo.txt and Normalized.LCPM.POL5551.Ibrutinib.Combo.txt: 12H_REC1_ibr


title: Dura_OG_IV_scRNA

value: Dura


title: SEV,HealthyControl,HC14

description: Library name: HC14

value: Small Extracellular Vesicles from plasma


title: 12H_REC1_Ibrutinib

description:
Library name: 12H_REC1_Ibrutinib
Column name in RawCounts.POL5551.Ibrutinib.Combo.txt and Normalized.LCPM.POL5551.Ibrutinib.Combo.txt: 12H_REC1_dmso


title: SEV,HealthyControl,HC11

description: Library name: HC11


title: 12H_REC1_DMSO

description:
Library name: 12H_REC1_DMSO
Column name in RawCounts.POL5551.Ibrutinib.Combo.txt and Normalized.LCPM.POL5551.Ibrutinib.Combo.txt: 12H_REC1_Combo


title: Dura_IV_scRNA


title: WT_Tm_H3K27ac_SET5_rep1

description: Library name: WT_Tm_H3K27ac_SET5_rep1

value: WT


title: IL1beta-Ribo_3

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg38 (GRCh38) using STAR 2.6.1d  with the parameters "--outFilterMismatchNoverLmax 0.1 --outFilterScoreMinOverLread 0.9 --outFilterMatchNminOverLread 0.9 --outFilterMatchNmin 20 --alignIntronMax 200000" (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
Duplicate reads were removed with Picard 2.21.7 (https://github.com/broadinstitute/picard).
The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
A combined raw count matrix was produced and used for differential expression analysis using DESeq2 version 1.26.0 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data (release 08.03.2018) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: hg38 / GRCh38
Supplementary_files_format_and_content: The tab-delimited matrix shows DESeq normalized counts.

source_name: Endothelial cells

growth_protocol: Human endothelial cells (passages 2 to 4, 90% confluent) were starved of serum in MCDB131 medium (Gibco/Thermo Fisher Scientific) containing 0.1% bovine serum albumin (BSA) and infected overnight with adenoviruses (20 MOI) carrying the RiboTag. The culture medium was then replaced with MCDB131 medium containing 8% heat inactivated FBS, ECGS/heparin, basic fibroblast growth factor (1 ng/mL) and epidermal growth factor (0.1 ng/mL). Cells were then processed for RiboTag isolation

extract_protocol:
Cells were collected with the aid of cell scrapers in freshly prepared lysis buffer containing: Tris/HCl pH 7.5 (50 mmol/L), NaCl (150 mmol/L), MgCl2 (12 mmol/L), NP-40 (1%), DTT (1 mmol/L), EDTA-free protease inhibitor mix (AppliChem GmbH, Darmstadt, Germany), SUPERase In RNase Inhibitor (200U/mL, Thermo Fisher Scientific), cycloheximide (100 µg/mL) and TURBO DNaseI (25U/mL, Thermo Fisher Scientific), in UltraPure DNase/RNase-free distilled water (Thermo Fisher Scientific). Lysates were passed 5 times through 26G needles on ice and then centrifuged at 16,000 g for 10 minutes at 4°C. Ten % of the total lysate volume was mixed with 9 volumes of QIAZOL and frozen at -80°C. The remaining lysates were incubated with anti-HA antibody-conjugated magnetic beads (50 µl/sample, washed and resuspended in lysis buffer, Biozol, Eching, Germany) before being incubated overnight on end-over-end rocker at 4°C. HA immunoprecipitates were washed three times with a freshly prepared high salt buffer containing: Tris/HCl pH 7.5 (50 mmol/L), NaCl (300 mmol/L), MgCl2 (12 mmol/L), NP-40 (0.5%), DTT (1 mmol/L), SUPERase In RNase Inhibitor (200 U/mL, Thermo Fisher Scientific) and cycloheximide (100 µg/mL). After the final wash, HA immunoprecipitates were resuspended in 700 µL QIAZOL and immediately processed for RNA purification. The total input RNA (from the total lysates) as well as the ribosome-associated RNA (from the RiboTag immunoprecipitates) were purified using the miRNeasy Micro kit (QIAGEN, Hilden, Germany), according to the manufacturer’s instructions.
One hundred ng - 1 µg of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina, Sand Diego, USA) without fragmentation (5 minutes 65°C for RT annealing). Finished libraries were size selected by Pippin device (Sage science, Beverly, USA) for insert sizes < 300nt. Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in 8-62M reads per library (average 25M) with 1x75 nt single-end setup.

treatment_protocol: Solvent (PBS+0.1%BSA) or recombinant human interleukin-1β (20 ng/mL, Peprotech, Hamburg, Germany) for 16 hours.

value: Endothelial cells

tag: protocol

value: RiboTag


title: IL1beta-Ribo_4


title: CEBPB_KO_Tm_H3K27ac_SET4_rep2

city: Seoul

description: Library name: CEBPB_KO_Tm_H3K27ac_SET4_rep2


title: Colon_OG_IV_scRNA


title: IL1beta-Ribo_2


title: Colon_IV_scRNA

value: IV Salmonella infection


title: CEBPB_KO_Tm_H3K27ac_SET4_rep1

description: Library name: CEBPB_KO_Tm_H3K27ac_SET4_rep1


title: IL1beta-Ribo_1


title: IL1beta-Input_4

value: RNA-Seq


title: KO-N2B27D6

city: Guangzhou

first: xiaojuan

last: teng

address: 2 Lujing Road, Yuexiu District, Guangzhou City

institute: Dermatology Hospital, Southern Medical University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using AdapterRemoval
Trimmed sequence reads were mapped to mm10 using STAR.
FPKM values for each Sample were performed using cufflinks.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: The cells (46C-D0) were cultured in normal stem cell medium and the cells were collected and treated. The cells (46C-D4) were cultured in KSR induction medium, and were collected and treated after 4 days of induction. Cells (46C-D6) were cultured in N2B27 induction medium. After 6 days of induction, cells were collected and treated.

extract_protocol:
RNA was extracted from the 8 cell samples using EZBioscience Tissue RNA Purification Kit PLUS kit and extracted according to the manufacturer's instructions.The eight cell samples were sequenced using illumina novaseq 6000 platform at PE150 length.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Mouse embryonic stem cell treatment with N2B27 induced medium toward to neuronal differentiation for 6 days

value: differentiation

value: KO


title: IL1beta-Input_3


title: WT_Tm_H3K27ac_SET4_rep2

description: Library name: WT_Tm_H3K27ac_SET4_rep2

value: Human colorectal cancer


title: IL1beta-Input_2


title: KO-N2B27D0

value: Mouse embryonic stem cell

value: proliferating


title: IL1beta-Input_1


title: Solvent-Ribo_4

value: none (solvent)


title: 46C-N2B27D6


title: Solvent-Ribo_1


title: NFIL3_KO_Con_H3K27ac_SET5_rep1

description: Library name: NFIL3_KO_Con_H3K27ac_SET5_rep1

value: H3K27ac (Abcam #Ab4729)

value: 0.1% DMSO


title: 46C-N2B27D0


title: KO-D4

value: Mouse embryonic stem cell treatment with KSR induced medium toward to neuronal differentiation for 4 days


title: WT_Con_H3K27ac_SET5_rep2

description: Library name: WT_Con_H3K27ac_SET5_rep2


title: Solvent-Input_3


title: Solvent-Input_1


title: Solvent-Input_2


title: WT_Con_H3K27ac_SET5_rep1

description: Library name: WT_Con_H3K27ac_SET5_rep1


title: 46C-D4


title: KO-D0


title: CEBPB_KO_Con_H3K27ac_SET4_rep2

description: Library name: CEBPB_KO_Con_H3K27ac_SET4_rep2


title: CEBPB_KO_Con_H3K27ac_SET4_rep1

description: Library name: CEBPB_KO_Con_H3K27ac_SET4_rep1


title: Dendritic cell, HTO-derived cDNA

city: Chiba

first: Masato

last: Kubo

address: 2669 Yamazaki, Noda-shi

country: Japan

institute: Tokyo University of Science

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
TASseq

data_processing:
Pair-end Fastq files (R1: cell barcode reads, R2: RNA reads) of sample KuboWTA1 were processed as follows. Adapter trimming, quality filtering, and phase-shift base removal of sequencing data was performed by using Cutadapt 4.1. Filtered cell barcode and cDNA reads were annotated and mapped to reference genome (build GRCm39 release-107) by using STARsolo (2.7.10a) and known BD Rhapsody cell barcodes by the following parameters: –outSAMmultNmax 1 –outFilterScoreMinOverLread 0 –outFilterMatchNminOverLread 0 –outFilterMultimapScoreRange 0 –seedSearchStartLmax 30 –soloType CB_UMI_Complex –soloUMIdedup NoDedup –soloMultiMappers Rescue –soloFeatures Gene GeneFull –soloCBmatchWLtype EditDist_2 –soloUMIlen 8 –soloCBposition 0_0_0_8 0_13_0_21 0_26_0_34 –soloUMIposition 0_35_0_42. We do not perform UMI compression because BD Rhapsody UMI length (8-base and directly attatched polyT) is not sufficient to avoid UMI collision (minimum 10-base is required, Perukhov et al Genome Biol 2018). Resulted non-umi count data was converted to genes x cells matrix file and inflection threshold of the barcode rank plot was detected by using DropletUtils package in R version 4.2.1 (2022-06-23). Valid cell barcodes and backgrounds from knee-point threshold to inflection threshold * 1.1 were separated by Dropkick package (Heiser et al Genome Biol 2022). For STAR index build, small RNA annotations were filtered out from gencode.vM30 gtf file. Spliced/unspliced count matrix files for RNA velocity analysis was created by using STARsolo Gene (spliced count data) and GeneFull (spliced+unspliced count data) matrixes. Unspliced count matrix was generated by (GeneFull count matrix) - (Gene count matrix).
Demultiplexing cells by cell hashing: For assignment of each tag to each cell barcode, read counts of each tag in each valid cell barcode, which defined by the cDNA matrix, were extracted from tag/cell barcode expression matrix. Unassigned cell barcodes were labeled as “not-detected” cells. Then, sum of the total read counts of each tags were normalized to 10M reads, and log2 fold-change between first most counted tags and second most counted tags within each cell barcode. Doublet cells (double-positive cells of any pair of Tags (identified by flowDensity package) and log2 fold-change between first and second most counted tags < 0.30906 were identified as doublets. Finally, remained cell barcodes were assigned to the first most counted tags. Each tag expression in each cell barcode were log2(x+1)-transformed, z-scaled by each cell barcode, and visualized by using pheatmap package in R version 4.2.1 (2022-06-23).
Assembly: GRCm39
Supplementary files format and content: rda file (Seurat object file)

source_name: Spleen

extract_protocol:
20,000 live cells were loaded onto the BD Rhapsody cartridge, and cDNA trap and amplification were performed by the TAS-Seq method
Cells were trapped and reverse-transcribed using an BD Rhapsody system (BD) according to the manufacturer’s instructions, followed by the preparation of cDNA libraries and hashtag libraries by TAS-Seq method (Shichino et al. Commun. Biol,, 2022). The library preparation and sequencing analysis were conductd by ImmunoGeneTeqs, Inc (Chiba, Japan) by using Novaseq 6000 sequencer (Illumina, San Diego, CA, USA) and Novaseq S4 200 cycles v1.5 kit (Illumina).

value: Spleen

value: Dendritic cell

value: wild type or Il13ra1flox/flox Cd11c-Cre mice

value: cutaneous allergen sensitization

tag: antibodies/tags

value: Wild type1:TotalSeq-A0309, Wild type2:TotalSeq-A0310, Il13ra1flox/flox Cd11c-Cre mice1:TotalSeq-A0311, Il13ra1flox/flox Cd11c-Cre mice2:TotalSeq-A0312


title: Dendritic cell, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
TASseq


title: WT_Con_H3K27ac_SET4_rep1

description: Library name: WT_Con_H3K27ac_SET4_rep1

value: WT


title: WT_Con_H3K27ac_SET4_rep2

description: Library name: WT_Con_H3K27ac_SET4_rep2


title: Tumor environment 1

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

institute: BMC

data_processing:
Cellranger v4 was used to genenerate fastqs and counts
Seurat v4.0.1 was used to process and anlayse the count data.
Assembly: mm10
Supplementary files format and content: The raw counts are in Counts.mtx, genes and barcodes in genes.tsv and barcodes.tsv respectively. Cell meta data is given in CellMetaData.txt along with UMAP coordinates.

growth_protocol: We transplanted 150 000 primary mouse tumor cells from the LN of a leukemic Cd45.2+/+Ebf1+/-Pax5+/- mouse (LN768) to Wt CD45.1 mice by tail vain injection. The control group received PBS instead of tumor cells.

extract_protocol: Library preparation was conducted according to the Chromium Single Cell 3’ Reagent kit v3 instructions (10x Genomics). Sequencing was performed on a NOVASeq 6000 from Illumina

treatment_protocol: Cells were grown in either control mice or a B-ALL mouse model for 3 weeks and KIT+Lin-CD45.2-CD45.1+ BM cells were sorted for scRNAseq

value: KIT+Lin-CD45.2-CD45.1+ BM cells

value: 3 weeks

value: Growth in a B-ALL environment


title: Tumor environment 2


title: Human skin sample 33

type: RNA

first: Kwang Hoon

address: 50-1, Yonsei-ro, Seodaemun-gu

department: Dermatology

description: Gene expression data of human facial skin metabolites

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16 hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

label: biotin

source_name: Human skin

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

extract_protocol: Total RNA were extracted using QIAGEN Rneasy mini kit following the manufacturer's instructions.

tag: gender

value: Female

tag: age

value: facial skin


title: CordBloodPF3_MPP

city: Indianapolis

first: James

last: Ropa

state: IN

address: 950 W Walnut St

institute: Indiana University

description: Library name: PFCB3_MPP

data_processing:
Reads were psuedo-aligned and assigned abundance per gene using kallisto. Kallisto abundance files were read into DESeq2 where remaining differential expression analyses were performed.
Assembly: GRCh38
Supplementary files format and content: abundance.tsv files generated from kallisto pseudoalignment

source_name: umbilical cord blood

growth_protocol: Cells were not grown. CD34+ cells were harvested from fresh or cryopreserved umbilical cord blood by density gradient centrifugation followed by magnetic bead-antibody based enrichment technology. For Cord blood PF1/2/3, CD34+ cells were then cryopreserved and thawed prior to immunophenotyping. For the remaining units, which were thawed as whole units, CD34+ cells were used immediately for immunophenotyping. Immunophenotyping was performed by staining cell surface with antibodies targeting specific cell surface proteins conjugated to fluorophores. Sorting was performed using flow cytometry and cells were sorted directly into RNA lysis buffer.

extract_protocol:
RNA was harvested using the Qiagen Micro Plus Rneasy kit.
Libraries were prepared using the NEBNext Low Input RNA Library Prep Kit or the Takara SMART-seq v4 Ultra Low Input RNA Kit.

value: umbilical cord blood

value: Multipotent progenitor

tag: engraftment capacity

value: n/a not used in transplant


title: CordBloodPF3_MLP

description: Library name: PFCB3_MLP

value: Multilymphoid progenitor


title: PBS control 2

value: Growth in control mice


title: Human skin sample 32


title: CordBloodPF3_MEP

description: Library name: PFCB3_MEP

value: Megakaryocyte erythrocyte progenitor


title: Human skin sample 31


title: CordBloodPF3_HSC

description: Library name: PFCB3_HSC

value: Hematopoietic stem cell


title: Human skin sample 27

value: Male


title: Human skin sample 29


title: Cis7d_3: Cis7d Group rep3 scRNA-seq

city: Nanjing

first: Bingquan

last: Deng

state: Jiangsu

address: Nanjing Medical University, No.109 Longmian Avenue, Jiangning District

institute: Nanjing Medical University

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software（version2.20）
Sample demultiplexing, barcode processing and single-cell 3’gene counting by using the Cell Ranger pipeline(version 3.1.0) and scRNA-seq data were aligned to GRCm38 reference genome
The Cell Ranger output was loaded into Seurat(version 3.1.1) be used to Dimensional reduction, clustering, and analysis of scRNA-seq data
Cells were captured from 8 samples and screened by control threshold of gene expressed >200 and mitochondrial-DNA <70%
Markers genes that expressed in more than 10% of the cells in a cluster (the average log(Fold Change) ≥0.26, P value ≤0.01) were selected
Genome_build: GRCm38
Supplementary_files_format_and_content: tsv and mtx include barcodes, genes and matrix for each Sample

source_name: Kidney

extract_protocol:
Single-cell suspensions were loaded to 10x Chromium to capture more than 5000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3)
The cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp) at a minimum depth of 90,000 reads per cell

treatment_protocol: 3/7 days after intraperitoneal injection of 20mg/kg (body weight) cisplatin, Sham group injected with the same volume of normal saline

value: kidney

value: 7 days after intraperitoneal injection of cisplatin


title: Human skin sample 28


title: CordBloodPF3_GMP

description: Library name: PFCB3_GMP

value: Granulocyte macrophage progenitor


title: Human skin sample 26


title: CordBloodPF3_CMP

description: Library name: PFCB3_CMP

value: Common myeloid progenitor


title: Cis7d_2: Cis7d Group rep2 scRNA-seq


title: Cis7d_1: Cis7d Group rep1 scRNA-seq


title: Cis3d_2: Cis3d Group rep2 scRNA-seq

value: 3 days after intraperitoneal injection of cisplatin


title: Human skin sample 21


title: Human skin sample 22


title: CordBloodPF2_MPP

description: Library name: PFCB2_MPP


title: Human skin sample 19


title: Cis3d_1: Cis3d Group rep1 scRNA-seq


title: CordBloodPF2_MLP

description: Library name: PFCB2_MLP


title: Human skin sample 18


title: Human skin sample 25


title: Human skin sample 23


title: Human skin sample 24


title: NS_3: Sham Group rep3 scRNA-seq

value: Intraperitoneal injection of saline


title: CordBloodPF3_CD34

description: Library name: PFCB3_CD34

value: CD34positive cell


title: Human skin sample 17


title: Human skin sample 16


title: CordBloodPF2_MEP

description: Library name: PFCB2_MEP


title: Human skin sample 15

value: Female


title: NS_2: Sham Group rep2 scRNA-seq


title: CordBloodPF2_HSC

description: Library name: PFCB2_HSC


title: Human skin sample 14

value: facial skin


title: NS_1: Sham Group rep1 scRNA-seq


title: Human skin sample 20


title: Human skin sample 13


title: CordBloodPF2_GMP

description: Library name: PFCB2_GMP

value: umbilical cord blood


title: Human skin sample 12


title: Human skin sample 11


title: CT26 cells, Oxaliplatin pool_L4

city: Hangzhou

first: Sheng

last: Biao

address: jiefang road

institute: Zhejiang University

description: Library name: CT26_Oxaliplatin_Pool, L4

data_processing:
Raw sequencing reads (fastq files) were first subjected to quality control using FastQC (v0.11.9). Adapter sequences and low-quality bases were trimmed using Trimmomatic (v0.39) with parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36. The trimmed reads were then aligned to the mouse reference genome (mm10/GRCm38) using Bowtie2 (v2.4.2) with default parameters. For sgRNA quantification, reads aligning to the sgRNA library sequences were counted using MAGeCK (v0.5.9.4) ‘count’ function. Only perfectly matched reads were retained for downstream analysis.
Assembly: The mouse reference genome assembly GRCm39 (mm39) was used for off-target assessment. sgRNA abundance counting was performed against the provided library sequence file.
Supplementary files format and content: The processed data file oxa_resistance_screen_counts_matrix.txt is a tab-delimited text file. The first column (sgRNA) contains the sgRNA identifier. The second column (Gene) contains the target gene symbol. Subsequent columns contain raw read counts for each sample: blank_1 (vehicle-treated pool) and oxa_1 (oxaliplatin-treated pool). Rows correspond to individual sgRNAs.
Library strategy: CRISPR Screen

extract_protocol:
Genomic DNA was extracted from approximately 1x10^7 cells using the DNeasy Blood & Tissue Kit (Tiangen, cat no. DP304) according to the manufacturer's instructions. DNA concentration and purity were measured by NanoDrop.
The sgRNA cassette was amplified from 5 µg of genomic DNA using Herculase II Fusion DNA Polymerase (Agilent) with specific primers containing Illumina adapter sequences. PCR products were purified using AMPure XP beads. The final library was quantified by Qubit and its size distribution was checked on a Bioanalyzer.

value: CRISPR knockout library pool

value: Oxaliplatin


title: CT26 cells, Oxaliplatin pool_L3

description: Library name: CT26_Oxaliplatin_Pool, L3


title: CordBloodPF2_CMP

description: Library name: PFCB2_CMP

value: n/a not used in transplant


title: Human skin sample 10


title: Human skin sample 9


title: CordBloodPF2_CD34

description: Library name: PFCB2_CD34


title: Human skin sample 8


title: NFIL3_KO_Con_H3K27ac_SET5_rep2

description: Library name: NFIL3_KO_Con_H3K27ac_SET5_rep2

tag: chip antibody

value: H3K27ac (Abcam #Ab4729)

value: Human colorectal cancer

value: 0.1% DMSO


title: Solvent-Ribo_3

value: Endothelial cells

value: none (solvent)

value: RiboTag


title: WT_Tm_H3K27ac_SET4_rep1

description: Library name: WT_Tm_H3K27ac_SET4_rep1

tag: cell line

value: WT

value: 0.5 μg ml tunicamycin


title: Human skin sample 7

value: Male


title: Solvent-Ribo_2

tag: cell type


title: CT26 cells, Vehicle control pool, L4

description: Library name: CT26_Control_Pool, L4

tag: genotype

value: Vehicle control


title: CordBloodPF1_MPP

description: Library name: PFCB1_MPP

value: Multipotent progenitor


title: Solvent-Input_4

tag: treatment

value: RNA-Seq


title: Human skin sample 6

value: facial skin


title: Human skin sample 5


title: Human skin sample 4

value: Female


title: CT26 cells, Vehicle control pool, L2

description: Library name: CT26_Control_Pool, L2

value: CRISPR knockout library pool


title: CT26 cells, Vehicle control pool, L3

description: Library name: CT26_Control_Pool, L3


title: CordBloodPF1_MLP

description: Library name: PFCB1_MLP

value: umbilical cord blood

value: Multilymphoid progenitor


title: CordBloodPF1_MEP

description: Library name: PFCB1_MEP

value: Megakaryocyte erythrocyte progenitor

value: n/a not used in transplant


title: Human skin sample 3


title: mouse PP,cd45+ immune cells,sfb(+),rep2

city: Bethesda

first: Byunghyun

last: Kang

state: Maryland

address: 9000 Rockville Pike

institute: NIAID

description: Library name: sfb_pos_2

data_processing:
Read alignment to the mouse genome (mm10) and generation of gene count matrices from raw sequence FASTQ files were performed using the CellRanger pipeline, version 5.0.1 (10x Genomics) in computational resources of the NIH High Performing Computation Biowulf cluster (http://hpc.nih.gov).
Assembly: mm10
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: cells

extract_protocol:
Peyer’s patches (PPs) were dissected from the small intestine under a microscope and washed twice with buffer A (HBSS containing 25 mM HEPES and 5% FBS) to remove debris. Tissues were then incubated in HBSS supplemented with 5 mM EDTA, 1 mM DTT, 15 mM HEPES, and 10% FBS at 37°C for 10 minutes in a shaking thermomixer (1000 rpm), followed by two washes with buffer A and one with buffer B (HBSS + 25 mM HEPES) to eliminate epithelial cells. PPs were minced and digested in complete Iscove’s media containing 0.5 mg/ml Liberase TL and 30 µg/ml DNase I for 30 minutes at 37°C (1000 rpm), then passed through a 100 µm strainer. CD45⁺ cells from SFB(-) and SFB(+) Taconic WT mice were FACS-sorted.
Single-cell libraries were prepared using the Chromium Single Cell 3′ v3.1 Library Kit (10x Genomics) according to the manufacturer’s instructions. Approximately 6,000 sorted cells were loaded per GEM chip, aiming to recover ~4,000 single cells per sample. RNA from lysed cells was reverse transcribed into cDNA within GEMs. cDNA quality was assessed using the Bioanalyzer 2100 with a DNA High Sensitivity chip (Agilent Technologies), followed by amplification, fragmentation, adapter ligation, and size selection to generate 3′ gene expression and feature barcode libraries. Libraries were sequenced on the Illumina HiSeq X platform (Psomagen, Inc.).

value: cells

value: immune cells

value: wild-type

value: sfb(+)

value: female


title: Human skin sample 2


title: CordBloodPF1_HSC

description: Library name: PFCB1_HSC

value: Hematopoietic stem cell


title: 46C-D0

value: Mouse embryonic stem cell

value: proliferating

value: WT


title: Human skin sample 1


title: KO-ARS, biological replicate 2

city: London

first: Sean

middle: Patrick

last: Cregan

state: Ontario

address: 1151 Richmond St N

department: Physiology & Pharmacology

institute: University of Western Ontario

description: Gene expression data from cortex

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on Mouse Gene 2.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Probe level data was generated using Affymetrix Command Console v3.2.4. Probe data were summarized to gene level data in Partek Genomics Suite v6.6 (Partek, St. Louis, MO) using the RMA algorithm

source_name: Cortical neurons treated with arsenite

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA as per the Affymetrix GeneChip WT PLUS Reagent Kit Assay (http://media.affymetrix.com/support/downloads/manuals/wtplus_reagentkit_assay_manual.pdf, Affymetrix, Santa Clara, CA).

growth_protocol: Cortical neurons were dissected from embryonic mice (E14.5-15.5), dissociated into a single cell suspension, resuspended and plated in Neurobasal/B27 plus media supplemented with Glutamax and antibiotics

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cortical neurons were treated at 7 days in vitro with sodium arsenite (5uM) or vehicle for 12 hours and RNA extracted.

value: Brain, cortex

value: ATF4 deficient


title: mouse PP,cd45+ immune cells,sfb(+),rep1

description: Library name: sfb_pos_1


title: CordBloodPF1_GMP

description: Library name: PFCB1_GMP

value: Granulocyte macrophage progenitor


title: KO-ARS, biological replicate 1

description: Gene expression data from cortex


title: KO-Ctrl, biological replicate 2

description: Gene expression data from cortex

source_name: Cortical neuron control


title: mouse PP,cd45+ immune cells,sfb(-),rep2

description: Library name: sfb_neg_2

value: sfb(-)


title: KO-Ctrl, biological replicate 1

description: Gene expression data from cortex


title: WT-ARS, biological replicate 4

description: Gene expression data from cortex

value: wildtye


title: CordBloodPF1_CMP

description: Library name: PFCB1_CMP

value: umbilical cord blood

value: Common myeloid progenitor


title: WT-ARS, biologoical replicate 3

description: Gene expression data from cortex


title: mouse PP,cd45+ immune cells,sfb(-),rep1

description: Library name: sfb_neg_1


title: WT-ARS, biological replicate 2

description: Gene expression data from cortex


title: immune profiling,sfbpos, class-switched pp b cells, BCR, rep2

description: Library name: pp_p_2_bcr

data_processing:
Single-cell immune profiling raw data of sorted IgA⁺, IgG1⁺, and IgG2b⁺ CSB cells, generated using the 5′ Chromium 10X kit, were initially processed using the Cell Ranger Multi pipeline (v7.0.0) with the Cell Ranger V(D)J reference (vdj-GRCm38-alts-ensembl-7.0.0). This initial processing step produced three datasets: gene expression (GEX), antibody-derived tags (ADT), and B-cell receptor (BCR) sequences. A Seurat object was constructed from the 5′ GEX and ADT data using the Seurat package.
The BCR sequencing results generated using cellranger multi were further processed with Dandelion. BCR contigs from 'all_contigs.fasta' and 'all_contig_annotations.csv' were re-annotated using an Immcantation-inspired preprocessing pipeline included in the Dandelion Singularity container (v0.3.0).
Assembly: mm10
Supplementary files format and content: cellranger multi output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: dandelion_singularity out files: AIRR formatted

source_name: peyer's patches

extract_protocol:
For PP B cell immune profiling, IgA⁺, IgG1⁺, or IgG2b⁺ class-switched B (CSB) cells (CD45⁺CD19⁺TCRβ⁻Isotype⁺) from SFB-negative and SFB-positive Taconic WT mice (five mice pooled per group) were individually FACS-sorted.
The three isotype-positive CSB populations were then mixed to reflect their natural ratio in PPs from SFB-negative and SFB-positive mice. The sorted and pooled cells were subsequently stained with the following TotalSeqTM C antibodies (BioLegend): IgD (Cat# 405747), IgM (Cat# 406541), CD62L (Cat# 104455), and CD38 (Cat# 102735), and processed using the Chromium Next GEM Single Cell 5′ Library & Gel Bead Kit v2 (10x Genomics) along with the 5′ Feature Barcode Library Kit and Mouse B Cell V(D)J Enrichment Kit, according to the manufacturer’s instructions.

value: peyer's patches

value: B cells

value: wild type

tag: library type

value: BCR


title: CordBloodPF1_CD34

description: Library name: PFCB1_CD34

tag: tissue

value: CD34positive cell

value: n/a not used in transplant


title: CordBlood609_HSC_highengraftment

description: Library name: CB609_HSC

value: Hematopoietic stem cell

value: high


title: WT-Ctrl, biological replicate 2

description: Gene expression data from cortex


title: immune profiling,sfbpos, class-switched pp b cells, ADT, rep2

description:
Library name: pp_p_2_adt
GEX processed data include ADT

molecule: protein

value: sfb(+)

value: ADT


title: Dura_TCR_9

city: Cambridge

description:
Takara Bio SMARTER TCRa/b profiling
M1-meningesM9aR8-bR8F6

data_processing:
Raw MiSeq reads were filtered for base quality using QUASR.
Data was processed (alignment and clonotype assembly) using MIXCR (v3.0.13), following the 'analyze amplicon' workflow with default settings. Further downstream analysis was performed in vdjtools v1.2.1.
Supplementary files format and content: MIXCR alignment output (.vdjca), tab delimited file
Supplementary files format and content: MIXCR contig/clonotype assembly output (.clns), tab delimited file

extract_protocol:
Tissues were digested and RNA was extracted using the RNA pure link mini kit (Thermo Fisher) as per the manufacturer's instructions.
Libraries were prepared using the Takara Bio mouse TCRa/b profiling kit as per the manufacturer's instructions.

value: Dura

value: DSS


title: WT-Ctrl, biological replicate 1

description: Gene expression data from cortex

value: Brain, cortex


title: Human skin sample 30

value: Male

value: facial skin


title: WT-ARS, biological replicate 1

description: Gene expression data from cortex

value: wildtye


title: Dura_TCR_8

description:
Takara Bio SMARTER TCRa/b profiling
L8-meningesM8aR8-bR8F5


title: CordBlood415_HSC_lowengraftment

description: Library name: CB415_HSC

value: umbilical cord blood

value: low


title: PBS control 1

value: KIT+Lin-CD45.2-CD45.1+ BM cells

tag: time

value: 3 weeks

value: Growth in control mice


title: Dura_TCR_7

description:
Takara Bio SMARTER TCRa/b profiling
L7-meningesM7aR8-bR8F4


title: immune profiling,sfbpos, class-switched pp b cells, GEX, rep2

description:
Library name: pp_p_2_mRNA
GEX(5' mRNA) library

value: peyer's patches

value: B cells

value: wild type

value: mRNA


title: Dura_TCR_6

description:
Takara Bio SMARTER TCRa/b profiling
L6-meningesM6aR8-bR8F3


title: immune profiling,sfbpos, class-switched pp b cells, BCR, rep1

description: Library name: pp_p_1_bcr

value: sfb(+)

value: BCR


title: CordBlood410_HSC_lowengraftment

description: Library name: CB410_HSC

value: Hematopoietic stem cell


title: Dura_TCR_5

description:
Takara Bio SMARTER TCRa/b profiling
L5-meningesM5aR8-bR8F2

value: Dura

value: DSS


title: CordBlood397_HSC_lowengraftment

description: Library name: CB397_HSC


title: immune profiling,sfbpos, class-switched pp b cells, ADT, rep1

description:
Library name: pp_p_1_adt
GEX processed data include ADT

value: ADT


title: Dura_TCR_4

description:
Takara Bio SMARTER TCRa/b profiling
L4-meningesM4aR8-bR8F1


title: Dura_TCR_2

description:
Takara Bio SMARTER TCRa/b profiling
L2-meningesM2aR7-bR7F11


title: Dura_TCR_3

description:
Takara Bio SMARTER TCRa/b profiling
L3-meningesM3aR7-bR7F12


title: CordBlood320_HSC_highengraftment

description: Library name: CB320_HSC

value: high


title: immune profiling,sfbpos, class-switched pp b cells, GEX, rep1

description:
Library name: pp_p_1_mRNA
GEX(5' mRNA) library


title: Dura_TCR_1

description:
Takara Bio SMARTER TCRa/b profiling
L1-meningesM1aR7-bR7F10


title: CordBlood239_HSC_lowengraftment

description: Library name: CB239_HSC


title: Distal_colon_TCR_9

description:
Takara Bio SMARTER TCRa/b profiling
K2-c-distalM9aR7-bR7F9

source_name: Distal colon

value: Distal colon


title: immune profiling,sfbneg, class-switched pp b cells, BCR, rep2

description: Library name: pp_n_2_bcr

value: sfb(-)


title: CD34cells_CBU2_HTO

description:
Library name: CB189_hto
Hashtag-derived oligonucleotide
HTO library
Processed files contain combined GEX+HTO matrices for CBU2
CB189.barcodes.tsv.gz
CB189.features.tsv.gz
CB189.matrix.mtx.gz

data_processing:
Files were aligned, quality control filtered, and combined into GEX+HTO matrices using PIPseeker version 3.2 software.
Sensitivity matrix level 3 generated by PIPseeker software was used for further downstream analysis.
Seurat was used for demultiplexing and downstream analysis.
Assembly: GRCh38
Supplementary files format and content: Combined GEX+HTO matrices: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq

growth_protocol: CD34+ cells derived from human umbilical cord blood were isolated using magnetic separation technology. Purified CD34+ cells were cultured in serum free media in the presence of growth factors in variable oxygen conditions using controlled oxygen incubators.

extract_protocol:
Cells originating from the same cord blood unit were pooled into the same unit. Cells were captured using PIPseq fluidics free emulsification technology.
Single cell libraries were prepared using the PIPseq T20 kit.

treatment_protocol: Cells were grown in 1%, 3%, 5%, 14%, and 21% oxygen and were harvested two days or seven days following seeding or were isolated fresh as input control. Prior to single cell RNA-seq library prep, cells were stained with TotalSeq-A cell hashing antibodies based on their treatment condition to allow for multiplexing. Cells were washed twice and counted prior to pooling. This procedure was performed in a hypoxia chamber set to 3% oxygen for 1%, 3%, and 5% oxygen conditions or was performed in ambient air for 14% and 21% conditions.

value: umbilical cord blood

value: CD34 Cells

value: mixed sample (1% oxygen, 3% oxygen, 5% oxygen, 14% oxygen, 21% oxygen)

tag: days in_culture

value: HTO

tag: hto

value: TotalSeq-A0251 anti human Hashtag 1 (1% oxygen); TotalSeq-A0252 anti human Hashtag 2 (3% oxygen); TotalSeq-A0253 anti human Hashtag 3 (5% oxygen); TotalSeq-A0254 anti human Hashtag 4 (14% oxygen); TotalSeq-A0255 anti human Hashtag 5 (21% oxygen)


title: Distal_colon_TCR_7

description:
Takara Bio SMARTER TCRa/b profiling
J8-c-distalM7aR7-bR7F7


title: Distal_colon_TCR_8

description:
Takara Bio SMARTER TCRa/b profiling
K1-c-distalM8aR7-bR7F8


title: immune profiling,sfbneg, class-switched pp b cells, ADT, rep2

description:
Library name: pp_n_2_adt
GEX processed data include ADT

value: peyer's patches

value: B cells


title: Distal_colon_TCR_6

description:
Takara Bio SMARTER TCRa/b profiling
J7-c-distalM6aR7-bR7F6


title: CD34cells_CBU2_GEX

description:
Library name: CB189_mrna
polyA RNA
GEX library
Processed files contain combined GEX+HTO matrices for CBU2

value: mRNA


title: Distal_colon_TCR_5

description:
Takara Bio SMARTER TCRa/b profiling
J6-c-distalM5aR7-bR7F5


title: SHAL18

city: Bundoora

first: Quynh Nhu

last: Dinh

address: Kingsbury Drive & Plenty Rd

institute: La Trobe University

data_processing:
High-throughput sequencing was conducted using the HiSeqTM2500 platform
The results were mapped to the Ensembl-released mouse genome sequence and annotation.
Differential expression analysis was conducted using the DESeq R Package V.1.10.1 and P-values were adjusted using the Banjamini and Hochberg’s approach for controlling the false discovery rate
Genes were considered differentially expressed if the adjusted P-value was less than 0.05.
Supplementary files format and content: tab-delimited text files fpkm gene counts

source_name: Cerebral artery

extract_protocol:
RNA was extracted using RNeasy mini kit (Qiagen).  2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by Novogene

value: Cerebral artery

value: WT

tag: strain

tag: Sex

value: Male

tag: disease state

value: Control


title: immune profiling,sfbneg, class-switched pp b cells, GEX, rep2

description:
Library name: pp_n_2_mRNA
GEX(5' mRNA) library

value: wild type


title: Distal_colon_TCR_4

description:
Takara Bio SMARTER TCRa/b profiling
J5-c-distalM4aR7-bR7F4


title: CD34cells_CBU1_HTO

description:
Library name: CB176_hto
Hashtag-derived oligonucleotide
HTO library
Processed files contain combined GEX+HTO matrices for CBU1
CB176.barcodes.tsv.gz
CB176.features.tsv.gz
CB176.matrix.mtx.gz


title: Distal_colon_TCR_3

description:
Takara Bio SMARTER TCRa/b profiling
J4-c-distalM3aR7-bR7F3


title: immune profiling,sfbneg, class-switched pp b cells, BCR, rep1

description: Library name: pp_n_1_bcr

value: BCR


title: CD34cells_CBU1_GEX

description:
Library name: CB176_mrna
polyA RNA
GEX library
Processed files contain combined GEX+HTO matrices for CBU1


title: Distal_colon_TCR_1

description:
Takara Bio SMARTER TCRa/b profiling
J2-c-distalM1aR7-bR7F1


title: Distal_colon_TCR_2

description:
Takara Bio SMARTER TCRa/b profiling
J3-c-distalM2aR7-bR7F2


title: immune profiling,sfbneg, class-switched pp b cells, ADT, rep1

description:
Library name: pp_n_1_adt
GEX processed data include ADT

value: ADT


title: Proximal_colon_TCR_9

description:
Takara Bio SMARTER TCRa/b profiling
J1-c-proximalM9aR6-bR6F12

source_name: Proximal colon

value: Proximal colon

value: DSS


title: Proximal_colon_TCR_8

description:
Takara Bio SMARTER TCRa/b profiling
I8-c-proximalM8aR6-bR6F11