title: 18-24hpi_4SU_rep1

description:
Library name: 18-24hpi_4SU_rep1
slamseq_readcounts.txt


title: OND4, CSF

status: Public on Jan 01 2026

type: SRA

city: San Francisco

first: Joseph

middle: J

last: Sabatino

state: CA

address: 1651 4th St, Room 421A

country: USA

institute: UCSF

description:
Library name: 4_CSF_5pTCR
Column name in Processed_data_allTCR.csv.gz:  89018a

library_source: transcriptomic

data_processing:
CellRanger v3.1.0
ImmCantation v3.1.0
Change-O v0.4.6
Assembly: GRCh38.v94
Supplementary files format and content: csv files
Library strategy: TCR-Seq

molecule: polyA RNA

organism: Homo sapiens

source_name: CSF

extract_protocol:
PBMC and CSF mononuclear cell isolation as described in https://www.biorxiv.org/content/10.1101/2024.09.07.611010v2
5' T cell V(D)J scTCR-seq (10X Genomics)

tag: tissue

value: CSF

tag: cell type

value: T cell

tag: disease state

value: Control


title: 6-12hpi_4SU_rep1

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

country: China

institute: Beijing Institute of Radiation Medicine

description:
Library name: 6-12hpi_4SU_rep1
slamseq_readcounts.txt

data_processing:
Raw paired-end Slam-seq reads were first quality-trimmed using Trim Galore (v0.6.10) with default parameters. The cleaned reads were then aligned to the mm10 mouse reference genome (Mus musculus GRCm38 release 90 from ensembl) using STAR  (v2.7.10a) in end-to-end mapping mode with parameters (--outFilterMismatchNmax 20，--outFilterMultimapNmax 1，--outFilterScoreMinOverLread 0.4 , -- outFilterMatchNminOverLread 0.4), and indexed using Samtools (v1.12). Nascent RNA analysis was conducted using GRAND-SLAM (v2.0.7b) with the parameters(-snpConv 0.3, -trim5p 15, -double), followed by transcript abundance quantification through grandR (v0.2.1) to processing of the output tables.For each gene, we quantified raw read counts, FPKM, and NTR (Nascent-to-Total RNA ratio) in both total RNA and 4sU-labeled (Nascent) RNA.
Paired-end ATAC-seq reads were trimmed using Trim Galore with default parameters. Processed reads were aligned to the mm10 reference genome using Bowtie2 (v2.4.2) in end-to-end mode with parameters (--very-sensitive --no-mixed --no-discordant --phred33 --no-unal -I 10 -X 2000). Then sorted BAM files were created from raw alignment data through Samtools, and PCR duplicates were removed using MarkDuplicates (Picard v2.20.4).The sequencing coverage was normalized using bamCoverage (deeptools v3.5.4) by computing reads per kilobase per million mapped reads (RPKM) in consecutive 50bp genomic windows.
Assembly: mm10
Supplementary files format and content: TSV file for slam-seq readcounts
Supplementary files format and content: bigwig for ATAC-seq

organism: Mus musculus

source_name: embryo

growth_protocol: All mice were housed under specific pathogen-free (SPF) environmental conditions with free access to water and food, a temperature of 20-26°C, 30-70% humidity, and a 12-hour light/12-hour dark cycle at the Animal Core Facility of Nanjing Medical University.

extract_protocol:
For SLAM-seq, the collected embryos were washed six times with 1xPBS and then immediately placed in lysis buffer (Combine 0.2% (vol/vol) Triton X-100 and 2 U µl–1 RNase inhibitor in a volume of 1 µl) and then frozen at -80℃;  For ATAC-seq, the collected embryos were lysed in 5 µl lysis buffer (10 mM Tris-HCl (pH 7.5), 10 mM NaCl, 3 mM MgCl2, and 0.01% digitonin) for 10 min on ice.
For SLAM-seq, samples were taken out from -80℃ freezer, and thawed on ice, 1 µl of alkylation mix was added to the lysis buffer for a final alkylation reaction of 50 mM Tris-HCl (pH 8.4), 10 mM IAA, 45% DMSO. After 15 min at 50 °C, the alkylation reaction was stopped by adding 2 µl of stop solution for a final alkylation reaction of 15 mM DTT, 2 mM dNTP mix (Thermo Fisher Scientific, R0192), 10 µM oligo-dT primer and 2 U µl–1 RNase inhibitor, incubating for 5 min at room temperature. Reverse transcription (RT) and the remaining library preparation were performed according to a modified version of Smart-seq2. The modification step was the removal of DTT from the RT mix. Full length cDNA libraries were fragmented and processed into sequencing libraries by using the TruePrep DNA Library Prep Kit for Illumina (Vazyme, TD503) following the manufacturer's instructions; For ATAC-seq, tagmentation and remaining library preparation were performed by using the Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme, TD711) with minor modification. The tagmentation mix were modified by adding 2.5 µl TTE Mix V50.

treatment_protocol: Embryos in this study were derived from IVF( In Vitro Fertilization). Female mice were superovulated by 5 IU PMSG injection, followed by 5 IU hCG injection 48 h later. COCs were isolated. Embryos at different stages were collected after adding the sperm.About the collection of embryos for SLAM-seq, embryos were obtained by IVF and cultured in KSOM supplemented with 2 mM uridine analog 4-thiouridine (4SU) for 6 hours. IVF assay was modified for the 4SU labeling from 0-6 hpi (hours post insemination). Sperm were isolated and capacitated for 1 hours in HTF with 2 mM 4SU. Then, sperm were added to HTF with 2 mM 4SU containing COCs and co-incubated for 2 hours. Followed by presumptive zygotes were washed and transferred to into KSOM with 2 mM 4SU at once. After 6-hour labeling, the embryos were collected for further lysis.

value: embryo

tag: genotype

value: WT

tag: treatment

value: 4SU labeling


title: MS6, PB

description:
Library name: 6_PB_5pTCR
Column name in Processed_data_allTCR.csv.gz:  87917a

source_name: PBMC

value: PBMC

value: MS


title: 12-18hpi_4SU_rep3

description:
Library name: 12-18hpi_4SU_rep3
slamseq_readcounts.txt


title: MS6, CSF

description:
Library name: 6_CSF_5pTCR
Column name in Processed_data_allTCR.csv.gz:  87917a


title: 6-12hpi_4SU_rep2

description:
Library name: 6-12hpi_4SU_rep2
slamseq_readcounts.txt


title: 0-6hpi_4SU_rep3

description:
Library name: 0-6hpi_4SU_rep3
slamseq_readcounts.txt


title: MS29, PB

description:
Library name: 29_PB_5pTCR
Column name in Processed_data_allTCR.csv.gz:  91518a


title: HC3, PB

description:
Library name: 3_PB_5pTCR
Column name in Processed_data_allTCR.csv.gz:  84917b


title: HC3, CSF

description:
Library name: 3_CSF_5pTCR
Column name in Processed_data_allTCR.csv.gz:  84917b


title: 18-24hpi_4SU_rep3

description:
Library name: 18-24hpi_4SU_rep3
slamseq_readcounts.txt


title: 0-6hpi_4SU_rep1

description:
Library name: 0-6hpi_4SU_rep1
slamseq_readcounts.txt


title: MII_4SU_rep3

description:
Library name: MII_4SU_rep3
slamseq_readcounts.txt

source_name: MII oocyte

value: MII oocyte


title: MS27, PB

description:
Library name: 27_PB_5pTCR
Column name in Processed_data_allTCR.csv.gz:  88818a


title: WT Control_3,Dorsal Root Ganglion,non-treat

first: Zhou

last: Lingxuan

address: No. No.8, Xishiku Street, Xicheng District, Beijing

institute: Peking university first hospital

description: Library name: WT Control_3

data_processing:
featureCounts vl.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10
Supplementary files format and content: fpkm.xlsm

molecule: total RNA

source_name: Dorsal Root Ganglion

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Dorsal Root Ganglion

value: Wild type

value: non-treatment


title: MS29, CSF

description:
Library name: 29_CSF_5pTCR
Column name in Processed_data_allTCR.csv.gz:  91518a


title: WT Control_2,Dorsal Root Ganglion,non-treat

description: Library name: WT Control_2


title: WT Control_1,Dorsal Root Ganglion,non-treat

description: Library name: WT Control_1


title: MS28, CSF

description:
Library name: 28_CSF_5pTCR
Column name in Processed_data_allTCR.csv.gz:  90218a


title: CIS22, PB

description:
Library name: 22_PB_5pTCR
Column name in Processed_data_allTCR.csv.gz:  91618a


title: MS25, CSF

description:
Library name: 25_CSF_5pTCR
Column name in Processed_data_allTCR.csv.gz:  88618a


title: MII_4SU_rep2

description:
Library name: MII_4SU_rep2
slamseq_readcounts.txt


title: MII_4SU_rep1

description:
Library name: MII_4SU_rep1
slamseq_readcounts.txt


title: MS28, PB

description:
Library name: 28_PB_5pTCR
Column name in Processed_data_allTCR.csv.gz:  90218a


title: MS24, CSF

description:
Library name: 24_CSF_5pTCR
Column name in Processed_data_allTCR.csv.gz:  88418b


title: CIS22, CSF

description:
Library name: 22_CSF_5pTCR
Column name in Processed_data_allTCR.csv.gz:  91618a


title: MS25, PB

description:
Library name: 25_PB_5pTCR
Column name in Processed_data_allTCR.csv.gz:  88618a


title: MC903 KO_1,skin,MC903 for 7 days

description: Library name: MC903 KO_1

source_name: skin

value: skin

value: MC903 for 7 days


title: MS27, CSF

description:
Library name: 27_CSF_5pTCR
Column name in Processed_data_allTCR.csv.gz:  88818a


title: MC903 WT_1,skin,MC903 for 7 days

description: Library name: MC903 WT_1


title: MC903 KO_3,skin,MC903 for 7 days

description: Library name: MC903 KO_3


title: MC903 KO_2,skin,MC903 for 7 days

description: Library name: MC903 KO_2


title: MS24, PB

description:
Library name: 24_PB_5pTCR
Column name in Processed_data_allTCR.csv.gz:  88418b


title: MC903 WT_2,skin,MC903 for 7 days

description: Library name: MC903 WT_2


title: OND21, PB

description:
Library name: 21_PB_5pTCR
Column name in Processed_data_allTCR.csv.gz:  77016c


title: HC2, PB

description:
Library name: 2_PB_5pTCR
Column name in Processed_data_allTCR.csv.gz:  85317d


title: MC903 WT_3,skin,MC903 for 7 days

description: Library name: MC903 WT_3


title: HC2, CSF

description:
Library name: 2_CSF_5pTCR
Column name in Processed_data_allTCR.csv.gz:  85317d


title: 0-6hpi_4SU_rep2

description:
Library name: 0-6hpi_4SU_rep2
slamseq_readcounts.txt


title: Control WT_1,skin,non-treat

description: Library name: Control WT_1


title: Control WT_2,skin,non-treat

description: Library name: Control WT_2


title: MS10, PB

description:
Library name: 10_PB_5pTCR
Column name in Processed_data_allTCR.csv.gz:  92418a


title: OND21, CSF

description:
Library name: 21_CSF_5pTCR
Column name in Processed_data_allTCR.csv.gz:  77016c


title: Control KO_2,skin,non-treat

description: Library name: Control KO_2


title: MS1, PB

description:
Library name: 1_PB_5pTCR
Column name in Processed_data_allTCR.csv.gz:  83817b


title: Control KO_3,skin,non-treat

description: Library name: Control KO_3


title: Control KO_1,skin,non-treat

description: Library name: Control KO_1


title: MS10, CSF

description:
Library name: 10_CSF_5pTCR
Column name in Processed_data_allTCR.csv.gz:  92418a


title: MS1, CSF

description:
Library name: 1_CSF_5pTCR
Column name in Processed_data_allTCR.csv.gz:  83817b


title: H4K12la-1-CUT&Tag

description: Library name: E4

library_source: genomic

data_processing:
We utilized CellRanger v6.1.0 and Seurat 4.3.0 software for single-cell RNA sequencing (scRNA-seq) data analysis, with R version 4.1.0, on an Ubuntu 18.04 server. Quality control: After reading the raw data, we initialized a Seurat object using the `CreateSeuratObject` function and employed quality control metrics (QC metrics) to identify and filter out low-quality cells based on their distribution, filtering out cells with UMI counts greater than 1,000 or less than 100,000, as well as cells with a percentage of mitochondrial genes greater than 10% or of red blood cell genes greater than 0.5%. We used the `DoubletFinder` function to identify and remove potential doublets. Normalization: Data normalization is a critical step in scRNA-seq analysis. We employed the `NormalizeData` function in Seurat, which normalizes data to eliminate expression differences between cells, laying the groundwork for subsequent analysis. Feature selection: To identify the most representative genes, we used the `FindVariableFeatures` function. This function helps us recognize genes with the greatest expression variation in the dataset, which are crucial for subsequent clustering and differential expression analysis. Dimension reduction: Dimension reduction is the process of converting high-dimensional data into low-dimensional data for visualization and further analysis. We used the `RunUMAP` function in Seurat, which employs the Uniform Manifold Approximation and Projection (UMAP) algorithm to reduce data dimensions while preserving the original structure of the data as much as possible. Data integration: For datasets from different samples or conditions, we used the `FindIntegrationAnchors` and `IntegrateData` functions for data integration. These functions help us identify shared cell states across datasets and correct technical differences between datasets. Clustering analysis: Clustering is the process of grouping similar cells. We used the `FindClusters` function in Seurat to identify cell populations. This function uses graph-based methods to identify cell populations based on the data after dimension reduction. Differential expression gene analysis: We used the `FindAllMarkers` function to identify differentially expressed genes between different cell populations. The expression patterns of these genes can provide important information about cell functions and states.
Paired-end Cut&Tag reads were aligned to the mm10 genome with the following parameters: --end-to-end --very-sensitive -I 10 -X 2000 --no-mixed --no-discordant by Bowtie2 version 2.4.2. Aligned reads were filtered with a minimum mapping quality of 20 and PCR duplicates were removed. Read coverages over the mm10 genome were estimated by bamCoverage from deepTools v.3.5.1 with parameters --binSize 50 --normalizeUsing RPKM and visualized by UCSC browser. Peaks were called using MACS2 version 2.2.7 with the parameters --nolambda --nomodel. Peaks in all heatmaps were sorted according to peak enrichment in each group. Promoters were defined as ±2.5 kb around the TSS.
Assembly: mm10
Supplementary files format and content: CellRanger output files:mRNA barcodes.tsv.gz, mRNA features.tsv.gz, mRNA matrix.mtx.gz
Supplementary files format and content: CUT&TAG outfile: outfile.bw
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: microglia and macrophage

growth_protocol: Mice were housed 4–5 per cage with a 12-h light/dark cycle and food and water ad libitum. All experimental animal procedures were approved by the institutional animal care and use committee of the Beijing Institute of Basic Medical Sciences.

extract_protocol:
EAE mice at different disease stages, including naïve (day 0), priming (day 13), peak (day18), and chronic stages (day 25, day30, and day 35), were deeply anesthetized with pentobarbital sodium and perfused transcardially with ice-cold saline. The whole spinal cord was immediately removed and washed with prechilled PBS. For scRNA-seq, three spinal cords were pooled as one sample and dissociated into single cell suspensions for sequencing. For in situ sequencing, spinal cords were embedded in Tissue-Tek OCT compound (Sakura) and snap-freezing using dry ice. The OCT-embedded spinal cords were then coronally cryosectioned to a thickness of 10 μm using a cryostat (Leica CM3050S). The lumbar sections were collected and layered onto a spatially barcoded array for the subsequent in situ sequencing.
CUT&Tag was performed with CUT&Tag (Cleavage Under Targets and Tagmentation, Hyperactive pA-Tn5 Transposase for CUT&Tag, S603-01, Vazyme) method. In brief, 100,000 cells were collected and bounded to Concanavalin A–coated beads. Isolated MG/Mac were resuspended in antibody buffer and incubated with primary antibodies against H3K18la (PTM-1427RM, PTM BI) or H4K12la (PTM-1411, PTM BIO) and secondary antibodies in order. The samples were incubated with pA-Tn5 transposase. After transposon activation and tagmentation, DNA was isolated, amplified, and purified to construct library. The library for sequencing was constructed with VAHTS Turbo DNA Library Prep Kit for Illumina (Vazyme Biotech) according to manufacturer’s instructions. AMPure XP beads were used for purification steps. The library was quantified with VAHTS Library Quantification Kit for Illumina (Vazyme Biotech) and sequenced on an Illumina novaseq 150PE.

treatment_protocol: Eight-week-old female mice were used to induce the EAE model as we previously described50. Briefly, each mouse was subcutaneously immunized with 150 μg MOG35–55 peptide (ChinaPeptides Co.,Ltd) emulsified in complete Freund’s adjuvant (#F5881, Sigma-Aldrich) containing 4 mg/ml heat-killed Mycobacterium tuberculosis (#231141, BD Bioscience), followed by intraperitoneal injection of 200 ng pertussis toxin (#180, List Biological) on days 0 and 2, respectively. The bodyweight and clinical score were recorded everyday post immunization. Standard for evaluation of EAE clinical score is based on a five-point scale: 0, no disability; 1, loss of tone in the tail; 2, hind limb paresis; 3, hind limb paralysis; 4, tetraplegia; 5, moribund.

value: microglia and macrophage


title: Rf-KiO-SeoV

city: Daejeon

first: Dongbin

last: Park

address: 55, Expo-ro

country: South Korea

institute: Institute for Basic Science

description:
Library name: F_S4
10x Genomics

library_source: transcriptomic single cell

data_processing:
Cellranger (v5.1.2)
Assembly: Greater horseshoe bat genome (R. ferrumequinum; GCF_004115265.2), Big brown bat (E. fuscus; GCF_027574615.1), MERS-CoV, and SEOV
Supplementary files format and content: matrix files

source_name: Kidney organoid

extract_protocol:
Single cell suspensions were prepared from Rhinolophus ferrumequinum tracheal, Eptesicus serotinus tracheal, R. ferrumequinum bronchoalveolar, or R. ferrumequinum kidney organoids, either infected with MERS-CoV, or SEOV, or left uninfected, using 0.25 % Trypsin EDTA for 12 minutes at 37 °C with 30 times of pipetting in 5-minute intervals. After neutralizing trypsin with 5% FBS, cells were collected by centrifugation and filtered through 40 μm Flowmi cell strainer. Cell viability and single cell dissociation was assessed by LUNA FX7 automated cell counter and the cells were resuspended in phosphate-buffered saline with 0.4% BSA approximately 1000 cells/μL.
10x Genomics Chromium Single Cell 3′ GEM, Library & Gel Bead kit v3.1 (PN-1000121; 10X Genomics)

value: Kidney organoid


title: H3K18la-1-CUT&Tag

description: Library name: E3


title: Rf-KiO-CTRL

description:
Library name: C_S1
10x Genomics


title: H3K18la-2-CUT&Tag

description: Library name: E3_2


title: Rf-BAO-MERS

description:
Library name: E_S3
10x Genomics

source_name: Bronchioalveolar organoid

value: Bronchioalveolar organoid


title: Control WT_3,skin,non-treat

description: Library name: Control WT_3


title: H4K12la-2-CUT&Tag

description: Library name: E4_2


title: RESUB-HD71_R1_001

city: Gainesville

first: Terence

last: Ryan

address: 1864 Stadium Rd

institute: University of Florida

description: Library name: RESUB-HD71_R1_001

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: TPM counts file

source_name: brachialradialis muscle

extract_protocol:
total RNA isolated using Zymo Direct-Zol RNA isolation kit
Illumina library preparation performed by Azenta Life Sciences

value: brachialradialis muscle

tag: time

value: post-operative 6-8 weeks


title: OSK CCC Bulk RNA-seq rep2

city: Guangzhou

first: Hui

last: Zheng

state: Guangdong

address: No.190 Kaiyuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description:
Library name: OSK_CCC2
MEF infected with Oct4, Sox2, Klf4 and Ccne1 for 2 days, and changed into iCD1 medium for reprogammming (Day0). siCcnd1 and siCdkn2a was transfected into cells  on Day0.

data_processing:
Fastq files were generated from illumina BCL raw data using bcl2fastq scripts;
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Mapped read counts were calculated using RSEM(1.2.22) with parameters(-p 8 --estimated-rspd --no-bam-output).
Assembly: mm10
Supplementary files format and content: Comma separated values files include counts for each Sample
Supplementary files format and content: txt

source_name: Mouse embryonic fibroblasts

growth_protocol: Cells were maintained in iCD1 reprogramming medium.

extract_protocol:
Cells were lysised by Trizol and total RNAs were extracted by chloroform-isopropanol method.
Libraries for RNA-seq were prepared using VAHTS mRNA-seq V2 Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: MEF cells were infected with different TF combinations or siRNA combinations.

tag: cell line

value: Mouse embryonic fibroblasts

value: reprgramming cells

value: OSK+Ccne1+siCcnd1+siCdkn2a RNA-seq on total OSK reprogramming cells

tag: batch


title: RESUB-HD72_R1_001

description: Library name: RESUB-HD72_R1_001

value: pre-operative


title: RESUB-HD70_R1_001

description: Library name: RESUB-HD70_R1_001

value: post-operative 4 weeks


title: OSK CCC Bulk RNA-seq rep1

description:
Library name: OSK_CCC1
MEF infected with Oct4, Sox2, Klf4 and Ccne1 for 2 days, and changed into iCD1 medium for reprogammming (Day0). siCcnd1 and siCdkn2a was transfected into cells  on Day0.


title: OSK FN Bulk RNA-seq rep2

description:
Library name: OSK_FN2
MEF infected with Oct4, Sox2, Klf4 and Flag for 2 days, and changed into iCD1 medium for reprogammming (Day0). siNC was transfected into cells  on Day0.

value: OSK+Flag+siNC RNA-seq on total OSK reprogramming cells


title: OSK FN Bulk RNA-seq rep1

description:
Library name: OSK_FN1
MEF infected with Oct4, Sox2, Klf4 and Flag for 2 days, and changed into iCD1 medium for reprogammming (Day0). siNC was transfected into cells  on Day0.


title: Es-TrO-CTRL

description:
Library name: A_S3
10x Genomics

source_name: Trachea organoid

value: Trachea organoid


title: Rf-BAO-CTRL

description:
Library name: B_S4
10x Genomics


title: Naive1-CUT&Tag

description: Library name: C3


title: RESUB-HD69_R1_001

description: Library name: RESUB-HD69_R1_001

value: post-operative 31 weeks


title: RESUB-HD68_R1_001

description: Library name: RESUB-HD68_R1_001


title: Rf-TrO-CTRL

description:
Library name: 1T-Control_S7
10x Genomics


title: Naive2-CUT&Tag

description: Library name: C4


title: RESUB-HD67_R1_001

description: Library name: RESUB-HD67_R1_001


title: RESUB-HD66_R1_001

description: Library name: RESUB-HD66_R1_001


title: CCB ATAC-seq rep2

description:
Library name: CCB2
MEF infected with Oct4, Sox2, Klf4 and Ccne1 for 2 days, and changed into iCD1 medium for reprogammming (Day0). siCcnd1 and siCdkn2a was transfected into cells  on Day0.

data_processing:
Raw ATAC-seq reads were trimmed and ﬁltered for quality control using Trim Galore v0.6.7
Clean paired-end reads were ﬁrst mapped to mouse geneme mm10 using Bowtie2(v2.4.5)  with parameters  '--very-sensitive -X 2000'
PCR duplicates were removed with sambamba(V0.6.8)
Peak calling was performed with MACS2 with parameters ‘––keep-dup all -q 0.05 -f BEDPE ’
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
Cells were collected by trypsin digestion.
Libraries for ATAC-seq were prepared using TruePrepTM DNA Library Prep Kit V2 for Illumina following manufacturer's protocols.

value: reprogramming cells

value: OSK+Ccne1+siCcnd1+siCdkn2a ATAC-seq on total OSK reprogramming cells


title: FNB ATAC-seq rep2

description:
Library name: FNB2
MEF infected with Oct4, Sox2, Klf4 and Flag for 2 days, and changed into iCD1 medium for reprogammming (Day0). siNC was transfected into cells  on Day0.

value: OSK+Flag+siNC ATAC-seq on total OSK reprogramming cells


title: ko2

city: Xiamen

first: Xilin

last: Jiang

address: No. 4221 Xiang'an South Road

institute: Xiamen University

description: Library name: Sample 5

data_processing:
The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Primary microglia and peritoneal macrophages

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.


title: ko3

description: Library name: Sample 6

value: Primary microglia and peritoneal macrophages


title: RESUB-HD65_R1_001

description: Library name: RESUB-HD65_R1_001


title: ko1

description: Library name: Sample 4


title: RESUB-HD64_R1_001

description: Library name: RESUB-HD64_R1_001


title: RESUB-HD62_R1_001

description: Library name: RESUB-HD62_R1_001


title: RESUB-HD61_R1_001

description: Library name: RESUB-HD61_R1_001


title: wt2

description: Library name: Sample 2


title: RESUB-HD63_R1_001

description: Library name: RESUB-HD63_R1_001


title: RESUB-HD57_R1_001

description: Library name: RESUB-HD57_R1_001


title: pulmonary ILCs_Afu_17h_2

city: Vienna

first: Philipp

last: Penninger

address: Dr. Bohr-Gasse 9

country: Austria

institute: Medical University of Vienna

description: Library name: S8

data_processing:
The quality of raw reads were analyzed using FastQC (Andrews, 2010).
TrueSeq (Illumina) adapters were trimmed by using cutadapt v2.8 (https://cutadapt.readthedocs.io/en/stable/; settings: -q 30 -O 1)
Reads were aligned to the Mus musculus reference genome (GRCm38/mm10) using Hisat2 (v 2.0.5). Gene expression was quantified using StringTie (v 1.3.3b) and FeatureCounts (v 1.5.0-p3)
Assembly: Mus musculus reference genome (GRCm38/mm10) using Hisat2 (v 2.0.5)
Supplementary files format and content: tab-delimited text file containing raw counts for each sample and gene annotation

source_name: lung

extract_protocol:
Total RNA was isolated from frozen samples using Quiagen RNAeasy Plus Micro 74035 Kit
The double-strand cDNA was synthesized by LD-PCR amplification (SMART-Seq® v4 Ultra® Low Input RNA Kit), followed by purification with AMPure XP beads and quantification with Qubit. The cDNA samples were then fragmented, end-repaired, A-tailed, and ligated with Illumina adaptors. After size selection and PCR-enrichment, RNA libraries were checked with Qubit and real-time PCR for quantification, and 5400 Bioanalyzer System (Agilent Technologies) for size distribution.

treatment_protocol: intranasal Aspergillus fumigatus (ATCC204305) infection; 3*10^7 spores were diluted in physiological saline solution; cells were isolated at 17h post infection

value: lung

value: Innate Lymphoid Cells

value: wild type

value: intranasal Aspergillus fumigatus infection


title: pulmonary ILCs_control_3

description: Library name: S11

value: intransal saline treatment


title: pulmonary ILCs_control_4

description: Library name: S15


title: RESUB-HD54_R1_001

description: Library name: RESUB-HD54_R1_001

value: brachialradialis muscle


title: RESUB-HD52_R1_001

description: Library name: RESUB-HD52_R1_001

value: post-operative 6-8 weeks


title: wt3

description: Library name: Sample 3


title: RESUB-HD59_R1_001

description: Library name: RESUB-HD59_R1_001


title: lung_tissue_TecILC_transfer_rep3

description: Library name: TF5_21

extract_protocol:
Total RNA was isolated from frozen samples using the TRIZOL method;To remove genomic DNA, RNA samples were treated with DNase I and RiboLock RNAse inhibitor (both Thermo Fisher Scientific) as per the manufacturer's instructions. Total RNA was then purified using the Monarch RNA Cleanup Kit (New England BioLabs, #T2030L).
mRNA was isolated from total RNA using poly-T oligo-attached magnetic beads. Following fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand synthesis. The library preparation included end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Pulmonary ILCs were MAC-enriched and expanded in vitro for 7 days. Expanded ILC subsets were subsequently sorted (viable, CD90+lineage-; BD FACS Melody) and transferred into lymphocyte-deficient Rag2-/-Il2rg-/--recipient mice. Transfer was repeated after 14 days. 3 days after the second transfer, mice were challenged intranasally with Aspergillus fumigatus (ATCC204305; 3*10^7 spores  diluted in physiological saline solution); lung tissue samples were extracted 17 hours post infection and stored in RNA-later (-80°C)

value: whole tissue


title: pulmonary ILCs_control_2

description: Library name: S7


title: RESUB-HD60_R1_001

description: Library name: RESUB-HD60_R1_001


title: lung_tissue_TecILC_transfer_rep1

description: Library name: TF5_7


title: wt1

description: Library name: Sample 1


title: pulmonary ILCs_Afu_17h_3

description: Library name: S12


title: lung_tissue_TecILC_transfer_rep4

description: Library name: TF5_23


title: RESUB-HD50_R1_001

description: Library name: RESUB-HD50_R1_001


title: RESUB-HD53_R1_001

description: Library name: RESUB-HD53_R1_001

value: pre-operative


title: lung_tissue_wtILC_transfer_rep3

description: Library name: TF5_18


title: lung_tissue_TecILC_transfer_rep2

description: Library name: TF5_20


title: pulmonary ILCs_Afu_17h_4

description: Library name: S16


title: RESUB-HD56_R1_001

description: Library name: RESUB-HD56_R1_001


title: RESUB-HD55_R1_001

description: Library name: RESUB-HD55_R1_001


title: RESUB-HD48_R1_001

description: Library name: RESUB-HD48_R1_001


title: RESUB-HD45_R1_001

description: Library name: RESUB-HD45_R1_001


title: pulmonary ILCs_Afu_17h_1

description: Library name: S3


title: RESUB-HD49_R1_001

description: Library name: RESUB-HD49_R1_001


title: RESUB-HD47_R1_001

description: Library name: RESUB-HD47_R1_001


title: RESUB-HD44_R1_001

description: Library name: RESUB-HD44_R1_001


title: RESUB-HD58_R1_001

description: Library name: RESUB-HD58_R1_001


title: RESUB-HD51_R1_001

description: Library name: RESUB-HD51_R1_001


title: lung_tissue_no transfer_ctrl_rep3

description: Library name: TF5_11


title: lung_tissue_no transfer_ctrl_rep1

description: Library name: TF5_5


title: RESUB-HD40_R1_001

description: Library name: RESUB-HD40_R1_001


title: RESUB-HD42_R1_001

description: Library name: RESUB-HD42_R1_001


title: lung_tissue_wtILC_transfer_rep1

description: Library name: TF5_1


title: RESUB-HD43_R1_001

description: Library name: RESUB-HD43_R1_001


title: hippocampus_Mice_Trp2

city: Nanjing

first: Xiaoliang

last: Wang

address: Department of Anesthesiology

institute: Nanjing First Hospital

description:
Library name: hippocampus_Mice_Trp2
HOB2-fpkm

data_processing:
Perform data filtering on Raw Data to remove splice sequences and low-quality reads to obtain high-quality Clean Data.  Sequence comparison between Clean Data and designated reference genomes was performed to obtain Mapped Data.  Based on the Mapped Data, sequencing library quality assessment such as insert fragment length test, randomness test, expression analysis, variable splicing analysis, new gene mining and gene structure optimization are performed.  Based on the expression of genes in different samples or groups of samples, we can perform differential expression analysis, functional annotation of differentially expressed genes, functional enrichment and other advanced analyses.
Assembly: Mouse mm10： BSgenome.Mmusculus.UCSC.mm10 EnsDb.Mmusculus.v79     (1) Use StringTie (stringtie-2.1.3b.Linux_x86_64) software to assemble transcripts according to the bam file, set parameters: -f 0.2 -a 30 -c 5 -j 5 . (2) Use StringTie to fuse the reconstruction results of all samples to get the structure-optimized transcript structure annotation file, set the parameter --merge.
Supplementary files format and content: The raw image data files obtained from high-throughput sequencing (such as Illumina NovaSeq 6000 and other sequencing platforms) are analyzed by Base Calling to be converted into raw sequenced sequences (Sequenced Reads), which we call Raw Data or Raw Reads, and the results are stored in the FASTQ (abbreviated as fq) The results are stored in FASTQ (fq) file format, which contains the sequence information of the sequenced reads and their corresponding sequencing quality information.

source_name: hippocampal tissue

extract_protocol:
(1) Nanodrop detects RNA purity (OD260/280), concentration, and whether the nucleic acid absorption peak is normal; (2) Agilent 2100 accurately detects the integrity of RNA, and the detection indexes include: 28S/18S, the presence or absence of uplift of the graph baseline, and 5S peaks.
(1) Enrichment of eukaryotic mRNA with magnetic beads with Oligo (dT); (2) Random interruption of mRNA by adding Fragmentation Buffer; (3) Synthesize the first cDNA strand using mRNA as a template with six-base random primers (random hexamers), then add Buffer, dNTPs, RNase H and DNA polymerase I to synthesize the second cDNA strand and purify the cDNA using AMPure XP beads; (4) The purified double-stranded cDNA was then subjected to end repair, addition of A-tail and ligation of sequencing junctions, followed by fragment size selection using AMPure XP beads; (5) Finally, the cDNA library was obtained by PCR enrichment.  Translated with DeepL.com (free version)

value: hippocampal tissue


title: Ctrl

city: Shanghai

first: Weichen

last: Xu

state: Shanghai

address: No. 301, Middle Yanchang Road, Shanghai, 200072

department: Medical ultrasound

institute: Shanghai Tenth People’s Hospital, School of Medicine, Tongji University

description:
Library name: SAMPLE 1
10x Genomics

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Murine pancreatic cancer

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 5’ Reagent v2 Kits according to the manufacturer’s protocol.

value: Murine pancreatic cancer

value: KPC

value: Tumor cell and other cell


title: hippocampus_Mice_Trp3

description:
Library name: hippocampus_Mice_Trp3
HOB3-fpkm


title: IRE

description:
Library name: SAMPLE 2
10x Genomics

value: IRE


title: lung_tissue_wtILC_transfer_rep2

description: Library name: TF5_17


title: RESUB-HD46_R1_001

description: Library name: RESUB-HD46_R1_001


title: RESUB-HD41_R1_001

description: Library name: RESUB-HD41_R1_001


title: hippocampus_Mice_Trp1

description:
Library name: hippocampus_Mice_Trp1
HOB1-fpkm


title: fatal brains, multiplexed: Ctrl, VPA, VPA + Ro

city: Isehara

first: Takatoshi

last: Iijima

state: Kanagawa

address: 143 Shimokasuya

department: School of Medicine

country: Japan

institute: Tokai University

description:
Library name: fatal_brains_multiplexed
demultiplexed by Sample_Tag01=Ctrl: AAGAGTCGACTGCCATGTCCCCTCCGCGGGTCCGTGCCCCCCAAG, Sample_Tag02=VPA: ACCGATTAGGTGCGAGGCGCTATAGTCGTACGTCGTTGCCGTGCC, Sample_Tag03=VPA+Ro: AGGAGGCCCCGCGTGAGAGTGATCAATCCAGGATACATTCCCGTC

data_processing:
Reads from NovaSeq and MiSeq were merged before processing. Raw sequencing data were processed using cwl-runner with the BD Rhapsody pipeline (rhapsody_wta_2.0b2.cwl).
Samples were demultiplexed based on Sample Tag sequences from BD® Single-Cell Multiplexing Kits.
Reads were aligned and quantified using the BD Rhapsody WTA workflow, generating a gene-cell count matrix based on UMI counts.
Annotation was performed using the GRCm38 reference genome and GENCODE vM19 annotation, both provided by BD Biosciences.
Assembly: mm10
Supplementary files format and content: Demultiplexed comma-separated matrix file

source_name: forebrains

extract_protocol:
Briefly, viable cells were isolated from neural tissue using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec), following the manufacturer’s protocol. The resulting single-cell suspension was sorted using the BD FACS Aria Cell Sorter to enrich for viable single cells.
Library preparation was conducted according to the BD Rhapsody™ WTA Amplification Kit protocol. Initial sequencing was performed using an Illumina NovaSeq, and the Sample Tag sequences were subsequently sequenced on a separate Illumina MiSeq to enhance tag read coverage.

value: forebrains

tag: strain

tag: developmental stage

value: multiplexed sample:control, VPA, VPA + Ro

tag: Sex

value: male


title: RESUB-HD39_R1_001

description: Library name: RESUB-HD39_R1_001


title: RESUB-HD37_R1_001

description: Library name: RESUB-HD37_R1_001


title: hippocampus_Mice_IPA3

description:
Library name: hippocampus_Mice_IPA3
HEB3-fpkm


title: lung_tissue_no transfer_ctrl_rep2

description: Library name: TF5_10

value: lung


title: hippocampus_Mice_HFD3

description:
Library name: hippocampus_Mice_HFD3
WTB3-fpkm

value: High fat diet


title: RESUB-HD34_R1_001

description: Library name: RESUB-HD34_R1_001


title: hippocampus_Mice_HFD1

description:
Library name: hippocampus_Mice_HFD1
WTB1-fpkm


title: hippocampus_Mice_IPA2

description:
Library name: hippocampus_Mice_IPA2
HEB2-fpkm


title: TA_Old_3

city: Saint louis

first: Kentaro

last: Mori

state: Missouri

address: 660 S. Euclid Avenue

institute: Washington University School of Medicine

description: Library name: to3

data_processing:
Illumina’s bcl2fastq2 RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
Assembly: STAR version 2.5.1a
Supplementary files format and content: sf files include TPM values for each Sample

source_name: Skeletal Muscle

extract_protocol:
RNA was isolated from each skeletal muscle sample using the RNeasy Fibrous Tissue Mini kit(74704, Qiagen).
RNA libraries for RNA-seq were prepared using Clontech SMARTer mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Skeletal Muscle

value: WT


title: RESUB-HD28_R1_001

description: Library name: RESUB-HD28_R1_001

value: post-operative 31 weeks


title: RESUB-HD32_R1_001

description: Library name: RESUB-HD32_R1_001

value: brachialradialis muscle


title: hippocampus_Mice_IPA1

description:
Library name: hippocampus_Mice_IPA1
HEB1-fpkm


title: TA_Young_1

description: Library name: ty1


title: RESUB-HD26_R1_001

description: Library name: RESUB-HD26_R1_001


title: RESUB-HD38_R1_001

description: Library name: RESUB-HD38_R1_001


title: hippocampus_Mice_HFD2

description:
Library name: hippocampus_Mice_HFD2
WTB2-fpkm


title: RESUB-HD30_R1_001

description: Library name: RESUB-HD30_R1_001


title: TA_Old_2

description: Library name: to2


title: TA_Old_1

description: Library name: to1


title: Soleus_Young_3

description: Library name: sy3


title: RESUB-HD29_R1_001

description: Library name: RESUB-HD29_R1_001


title: RESUB-HD25_R1_001

description: Library name: RESUB-HD25_R1_001


title: RESUB-HD24_R1_001

description: Library name: RESUB-HD24_R1_001


title: RESUB-HD31_R1_001

description: Library name: RESUB-HD31_R1_001


title: TA_Young_2

description: Library name: ty2


title: Soleus_Young_2

description: Library name: sy2


title: RESUB-HD27_R1_001

description: Library name: RESUB-HD27_R1_001

value: post-operative 6-8 weeks


title: TA_Young_3

description: Library name: ty3


title: RESUB-HD33_R1_001

description: Library name: RESUB-HD33_R1_001


title: RESUB-HD35_R1_001

description: Library name: RESUB-HD35_R1_001


title: RESUB-HD19_R1_001

description: Library name: RESUB-HD19_R1_001


title: Soleus_Young_1

description: Library name: sy1


title: EDL_Young_2

description: Library name: ey2


title: EDL_Young_3

description: Library name: ey3


title: EDL_Old_3

description: Library name: eo3


title: RESUB-HD17_R1_001

description: Library name: RESUB-HD17_R1_001


title: RESUB-HD22_R1_001

description: Library name: RESUB-HD22_R1_001


title: RESUB-HD36_R1_001

description: Library name: RESUB-HD36_R1_001


title: RESUB-HD21_R1_001

description: Library name: RESUB-HD21_R1_001

value: not used


title: RESUB-HD14_R1_001

description: Library name: RESUB-HD14_R1_001


title: db/m treatment 2

city: Yinchuan

first: Xiaojie

last: Ruan

state: Ningxia

address: No.489, Helan West Street, Xixia District, Yinchuan City, Ningxia

institute: Ningxia University

description: Library name: Sample 4

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2.
HTSeq v0.11.2 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Assembly: ITPR3
Supplementary files format and content: File include count and FPKM value for each sample

source_name: MAEC

growth_protocol: Mouse aortic endothelial cells (MAECs) was  brought from Bluefbio Co., LTD in Shanghai.  The cell line was cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The cell line  was grown as usual in 6-well plates. After 48 hours of transfection with exosome, the cells were digested for next studies.

value: MAEC

value: aortic endothelial cell


title: Soleus_Old_3

description: Library name: so3


title: RESUB-HD15_R1_001

description: Library name: RESUB-HD15_R1_001


title: db/db treatment 2

description: Library name: Sample 2


title: RESUB-HD23_R1_001

description: Library name: RESUB-HD23_R1_001

value: pre-operative


title: RESUB-HD13_R1_001

description: Library name: RESUB-HD13_R1_001


title: RESUB-HD20_R1_001

description: Library name: RESUB-HD20_R1_001


title: EDL_Old_1

description: Library name: eo1


title: RESUB-HD18_R1_001

description: Library name: RESUB-HD18_R1_001


title: RESUB-HD16_R1_001

description: Library name: RESUB-HD16_R1_001


title: Soleus_Old_1

description: Library name: so1


title: db/db treatment 1

description: Library name: Sample 1


title: EDL_Old_2

description: Library name: eo2


title: Soleus_Old_2

description: Library name: so2


title: EDL_Young_1

description: Library name: ey1


title: RESUB-HD12_R1_001

description: Library name: RESUB-HD12_R1_001


title: db/m treatment 1

description: Library name: Sample 3


title: tissue cultured primary GPF+ lung tumor cells, eIF2αA/A, rep3

city: Montréal

first: Antonis

last: Koromilas

state: QC

address: 3755 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: Lady Davis Institute - McGill University

description:
Library name: AA_tc_rep3
Column name in raw_counts_ALL_Samples.txt: AA1_CTL_3

data_processing:
FASTQ files of scRNA-seq data generated on the 10X Chromium platform were processed using the standard CellRanger pipeline (version 5.0.0, https://www.10xgenomics.com/support/software/cell-ranger/latest). Reads were aligned to GRCm38/mm10 reference. Also, RNA-seq profiling of tissue cultured primary cells from eIF2αS/S or eIF2αA/A.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tissue cultured primary cells

extract_protocol:
Mice with LUAD tumors were euthanized 35 weeks post-tumor induction. Tumor samples were collected by isolating whole lungs, which were then dissociated using a solution of Dispase II (Gibco, catalog #17105-041; 0.6 U/ml final concentration), Collagenase Type IV (Thermo Fisher Scientific, catalog #17104019; 0.083 U/ml final concentration), and DNase I (Sigma-Aldrich, catalog #69182-3; 10 U/ml final concentration) in RPMI 1640 (Wisent, catalog # 350-700 CL. This mixture was incubated with the lungs at 37°C for 60 minutes. Dissociated cells were filtered through a 100 μm strainer and centrifuged at 300 g for 5 minutes at 4°C. After aspirating the supernatant, red blood cell lysis was performed using ACK Lysing Buffer (Thermo Fisher Scientific, catalog #A1049201). The LUAD cells were then washed with media, pelleted at 300 g for 5 minutes at 4°C, and resuspended in Fluorescence-Activated Cell Sorting (FACS) buffer media (200 mM EDTA with 250 μl heat-inactivated FBS in PBS). Cells in suspension were incubated with appropriate stains for 20 minutes at 4°C, washed twice with ice-cold PBS, and resuspended in FACS buffer. Cells were then strained into FACS tubes using a 70 µm cell strainer before analysis on a BD FACSAria™ Fusion Flow Cytometer.
Single-cell steps were performed using Chromium Next GEM Single Cell 3' Kit v3.1 (10X Genomics). Briefly, sorted cells were manually counted and loaded on the Chromium instrument (10X Genomics). The target cell recovery was 8000 cells for tumor samples. Reverse transcription and library steps were performed; cDNA and library profiles were validated using a 2100 Bioanalyzer (Agilent). Final libraries were sequenced PE100 on a NovaSeq (Illumina). For bulk RNA-seq library construction using total RNA extracted with TRIzol. cDNA from polyA-rich RNA was prepared by Genome Quebec following the Illumina NovaSeq PE100 guidelines.

value: Tissue cultured primary cells

value: Lung Adenocarcinoma

value: eIF2S1 A/A; Kras G12D; p53 Knockdown


title: RESUB-HD08_R1_001

description: Library name: RESUB-HD08_R1_001


title: tissue cultured primary GPF+ lung tumor cells, eIF2αS/S, rep4

description:
Library name: SS_tc_rep4
Column name in raw_counts_ALL_Samples.txt: SS1_CTL_4

value: eIF2S1 S/S; Kras G12D; p53 Knockdown


title: tissue cultured primary GPF+ lung tumor cells, eIF2αA/A, rep1

description:
Library name: AA_tc_rep1
Column name in raw_counts_ALL_Samples.txt: AA1_CTL_1


title: RESUB-HD10_R1_001

description: Library name: RESUB-HD10_R1_001


title: tissue cultured primary GPF+ lung tumor cells, eIF2αS/S, rep3

description:
Library name: SS_tc_rep3
Column name in raw_counts_ALL_Samples.txt: SS1_CTL_3


title: RESUB-HD11_R1_001

description: Library name: RESUB-HD11_R1_001


title: tissue cultured primary GPF+ lung tumor cells, eIF2αA/A, rep4

description:
Library name: AA_tc_rep4
Column name in raw_counts_ALL_Samples.txt: AA1_CTL_4


title: RESUB-HD05_R1_001

description: Library name: RESUB-HD05_R1_001


title: RESUB-HD06_R1_001

description: Library name: RESUB-HD06_R1_001


title: GPF+ lung tumor cells, eIF2αS/S, ISRIB treated

description:
Library name: SS_ISRIB_tumor_pool
10x Genomics

source_name: Lung tumor

value: Lung tumor

value: Mouse treatment with ISRIB by oral gavage consisting of 0.5% HPMC solution and 0.1% Tween 80


title: RESUB-HD03_R1_001

description: Library name: RESUB-HD03_R1_001


title: RESUB-HD09_R1_001

description: Library name: RESUB-HD09_R1_001


title: RESUB-HD07_R1_001

description: Library name: RESUB-HD07_R1_001


title: GPF+ lung tumor cells, eIF2αS/A, exp2

description:
Library name: SA_tumor_pool_exp2
10x Genomics

value: eIF2S1 S/A; Kras G12D; p53 Knockdown


title: tissue cultured primary GPF+ lung tumor cells, eIF2αA/A, rep2

description:
Library name: AA_tc_rep2
Column name in raw_counts_ALL_Samples.txt: AA1_CTL_2


title: GPF+ lung tumor cells, eIF2αS/S, vehicle treated

description:
Library name: SS_control_tumor_pool
10x Genomics

value: Mouse treatment with vehicle-control by oral gavage consisting of 0.5% HPMC solution and 0.1% Tween 80


title: RESUB-HD02_R1_001

description: Library name: RESUB-HD02_R1_001


title: shNsd2

first: Yuan

last: Qiao

address: Beijing

institute: China-Japan friendship hospital

description: Library name: shNsd2

data_processing:
The raw data (raw reads) generated in high-throughput sequencing are fastq format sequences. In order to obtain high-quality reads that can be used for subsequent analysis, further quality filtering of raw reads is required. First, use the fatsp software to remove adapters, and then filter out low-quality bases and N bases or low-quality reads, and finally obtain high-quality clean reads.
Use Bowtie2 to align the clean reads to the reference genome of the experimental species, and evaluate the sample situation through the genome and gene alignment rate. The parameters used are the default parameters.
To evaluate the IP quality of CUT&Tag experiments, we use strand cross-correlation (SCC) analysis. Theoretically, the reads obtained by sequencing will eventually be distributed approximately equally between the positive and negative strands.
Deeptools software is used to draw a FingerPrint diagram to show the distinction between the CUT&Tag enriched signal and the background signal, and at the same time, the ChIP signal type (narrow peak or broad peak) can be determined.
The sequencing data were compared with the reference genome, and then binding peak detection was performed using SEACR [4] software. Use chipseeker software to annotate the Peaks of each sample on a sample basis, obtain the genes and gene information corresponding to the Peaks, and make statistics on the annotation results.
Assembly: hg19
Supplementary files format and content: peak.annotation
Library strategy: CUT&Tag

source_name: liver

growth_protocol: HepG2 cells were cultured in DMEM medium containing 1% penicillin/streptomycin (Gibco) and 10% fetal bovine serum at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis.
Concanavalin A-coated magnetic beads (ConA beads) were used to bind the cells, and the nonionic detergent digitonin (Digitonin) was used to permeabilize the cell membrane; the cells bound to the magnetic beads were sequentially Incubate with (enter target protein name) primary antibody (enter primary antibody product number and company), secondary antibody and Protein A/Protein G fused with Tn5 transposon (Hyperactive pA/pG-Tn5 Transposon), so that with Protein A/ The Protein G-fused Tn5 transposon precisely targets and cuts the DNA sequence near the target protein; when Tn5 cuts, it will add P5 and P7 adapter sequences to both ends of the cut fragment, and use P5 and P7 primers for PCR amplification. After the purified sequencing library passed the quality inspection of Agilent 2100 Bioanalyzer, the Illumina NovaSeq6000 sequencing platform was used for high-throughput sequencing to generate 150 bp paired-end data for subsequent analysis.

value: liver

tag: chip-antibody

value: H4K20me3 (Cell Signaling Technology, D84D2)


title: GPF+ lung tumor cells, eIF2αA/A, exp1

description:
Library name: AA_tumor_pool_exp1
10x Genomics


title: RESUB-HD01_R1_001

description: Library name: RESUB-HD01_R1_001


title: Batch2_not_perfused_rep1

city: Cambrigde

first: Jose

middle: A

last: Vargas Asencio

state: MA

address: 400 Main st

department: PILM

institute: MIT

description:
Library name: D23-1091
10X' 3'RNA NextGEM

data_processing:
NovaSeq RTA v3.4.4 was used for base calling
Demultiplexing, barcode calling, gene counting and aggregation was performed using  Cellranger v7.0.1
Assembly: GRCh38
Supplementary files format and content: Tab separated values files and matrix files

source_name: iPSC-derived brain organoid

growth_protocol: Cerebral organoid generation protocol as described in "Yoon S-J, Elahi LS, Pașca AM, Marton RM, Gordon A, Revah O, et al. Reliability of human cortical organoid generation. Nat Methods. 2019;16: 75–78"

extract_protocol:
For sequencing, the vascularized cerebral organoids were dissociated using the neural tissue dissociation kit (manufacturer: Miltenyi). The plastic debris from the synthetic vasculature were removed using a bead column before sending the single cells for sequencing.
10X' 3'RNA NextGEM

treatment_protocol: Stem-cell based cerebral organoids were integrated with 3D-printed perfusable synthetic vasculature and grown under active or no perfusion conditions.

value: iPSC-derived brain organoid

value: ~3 week post differentiation brain organoid


title: RESUB-HD04_R1_001

description: Library name: RESUB-HD04_R1_001

value: brachialradialis muscle


title: GPF+ lung tumor cells, eIF2αSS, exp1

description:
Library name: SS_tumor_pool_exp1
10x Genomics


title: Batch2_perfused_rep2

description:
Library name: D23-1089
10X' 3'RNA NextGEM

value: perfused


title: tissue cultured primary GPF+ lung tumor cells, eIF2αS/S, rep2

description:
Library name: SS_tc_rep2
Column name in raw_counts_ALL_Samples.txt: SS1_CTL_2


title: tissue cultured primary GPF+ lung tumor cells, eIF2αS/S, rep1

description:
Library name: SS_tc_rep1
Column name in raw_counts_ALL_Samples.txt: SS1_CTL_1


title: shRNA

description: Library name: Control


title: GPF+ lung tumor cells, eIF2αS/S Atf4 flox/+, exp2

description:
Library name: SS_ATF4KD_tumor_pool_exp2
10x Genomics

value: eIF2S1 S/S; Atf4 flox/+; Kras G12D; p53 Knockdown


city: wu han

first: chentai

last: peng

state: State/Province

address: 湖北省武汉市华中科技大学同济医学院药学院

institute: 华中科技大学

description:
Library name: WT2_3D
WT2_ischemia-reperfusion (I/R) treatment for 3 days

data_processing:
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: GRCm39
Supplementary files format and content: Microsoft Works Spreadsheet

source_name: kidney

extract_protocol:
Wild-type mice and Utxpax2 cre mice were subjected to sham operation or ischemia-reperfusion (I/R) treatment for 3 days and 21 days, respectively. After the designated treatment periods, the mice were euthanized, and kidney tissues were collected. RNA from the kidney tissues was extracted using the Trizol reagent.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: kidney

value: WT


address: 湖北省武汉市华中科技大学同济医学院药学院

description:
Library name: KO2_3D
UtxPax2 Cre KO2_ischemia-reperfusion (I/R) treatment for 3 days

value: UtxPax2 Cre


title: Batch2_not_perfused_rep2

description:
Library name: D23-1092
10X' 3'RNA NextGEM


title: Batch1_perfused_rep1

description:
Library name: D22-5832
10X' 3'RNA NextGEM


title: PRMT2-S12A-Hyp-2

city: Tianjin

first: feng

last: dong

address: Qixiangtai Road 22

institute: Tianjin Medical University

description:
Library name: library name 7
PRMT2-S12A over-expression

data_processing:
Raw data were processed using CASAVA V1.6 package
The quality control of each sample was accomplished using FASTQC V0.11.5
Clean  reads were aligned to human reference genome hg38 by HISAT
Assembly: hg38
Supplementary files format and content: bw

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using NEBNext Ultra RNA library Prep Kit for Illumina.

value: glioblastoma cell line

value: Hypoxia


title: Batch1_not_perfused_rep1

description:
Library name: D22-5835
10X' 3'RNA NextGEM


title: GPF+ lung tumor cells, eIF2αS/S, exp2

description:
Library name: SS_tumor_pool_exp2
10x Genomics

value: Lung Adenocarcinoma

value: eIF2S1 S/S; Kras G12D; p53 Knockdown


title: UtxPax2 Cre KO2

address: 湖北省武汉市华中科技大学同济医学院药学院

description:
Library name: KO2
UtxPax2 Cre KO2

value: UtxPax2 Cre KO2


title: Batch1_not_perfused_rep2

description:
Library name: D22-5836
10X' 3'RNA NextGEM


address: 湖北省武汉市华中科技大学同济医学院药学院

description:
Library name: KO1_3D
UtxPax2 Cre KO1_ischemia-reperfusion (I/R) treatment for 3 days


address: 湖北省武汉市华中科技大学同济医学院药学院

description:
Library name: WT1_3D
WT1_ischemia-reperfusion (I/R) treatment for 3 days


title: Tregdiff_T2_WT3

city: Paris

first: Fiorella

last: Grandi

address: 105 Bld d'Hopital

department: Centre de Recherche de Myologie

country: France

institute: Sorbonne Universite

description:
Library name: Tregdiff_T2_WT3
TrefDiff_WT_T2_n9

data_processing:
aligned to mm10
nf-core/rnaseq pipeline
Deseq2 for differential expression
Assembly: mm10
Supplementary files format and content: Whole_Thymus_counts.tsv; tab-separeted file containing counts
Supplementary files format and content: SortedCells_Thymus_d30_d120.tsv, tab-separated file containing counts
Supplementary files format and content: iLN_Tregdiff_counts.tsv; tab-separeted file contianing counts

extract_protocol:
digestion of thymus + staining and facs sorting for each cell population; whole thymus samples were processed for RNA without sorting
SMARTseq v4 (Takara) low input kit

value: Treg

tag: timepoint


title: Batch2_perfused_rep1

description:
Library name: D23-1088
10X' 3'RNA NextGEM


title: UtxPax2 Cre KO1

address: 湖北省武汉市华中科技大学同济医学院药学院

description:
Library name: KO1
UtxPax2 Cre KO1

value: UtxPax2 Cre KO1


title: Batch1_perfused_rep2

description:
Library name: D22-5833
10X' 3'RNA NextGEM


title: PRMT2-WT-Hyp-2

description:
Library name: library name 5
PRMT2-WT over-expression


title: Tregdiff_T2_WT2

description:
Library name: Tregdiff_T2_WT2
TrefDiff_WT_T2_n21


title: TG02-Hyp-2

description:
Library name: library name 3
TG20 treatment


title: WT1

address: 湖北省武汉市华中科技大学同济医学院药学院

description:
Library name: WT1
WT1


title: Tregdiff_T2_Sod3

description:
Library name: Tregdiff_T2_Sod3
TrefDiff_SOD_T2_n24


title: Tregdiff_T2_Sod1

description:
Library name: Tregdiff_T2_Sod1
TrefDiff_SOD_T2_n12


title: Control, replicate 2

city: Davos Wolfgang

first: Cezmi

middle: A.

last: Akdis

state: Grisons

address: Herman-Burchard-Strasse 9

department: SIAF

country: Switzerland

institute: University of Zurich

description: Library name: SAMPLE 8

data_processing:
Raw sequencing reads were first subjected to quality control checks and trimming using BBDuk, which removes adapter sequences and low-quality bases. The high-quality, trimmed reads were then aligned to the human reference genome (GRCh38.p14) using the Subread aligner, ensuring accurate mapping of reads. Gene-level expression was quantified using featureCounts, part of the Rsubread package. This method counts reads mapping to known gene features annotated in Gencode release 46, providing robust expression metrics.
Assembly: GRCh38.p14
Supplementary files format and content: tsv file includes raw counts

growth_protocol: Caco-2 Cell culture: Caco-2 cells were purchased from Sigma Aldrich (#86010202) and were used between passages 20 and 45 in all experiments. Cells were cultured as a monolayer in Eagle's minimal essential medium (ATCC) supplemented with 10% FBS (Sigma-Aldrich), 1% penicillin/streptomycin (Sigma-Aldrich), 1% nonessential amino acids (Sigma-Aldrich), and 1% sodium pyruvate (Sigma-Aldrich) in a 150-cm2 T-flask in a humidified incubator at 37°C in 5% CO2. Gut-on-a-chip system: A gut-on-a-chip system was used to assess the effect of aspartame on colon epithelial cells12,13. Gut-on-a-chip cultures were established with OrganoPlate® 3-lane 64 plates  (Mimetas BV, Leiden, The Netherlands) following the manufacturer's protocols. The extracellular matrix gel is prepared by combining 1 M HEPES, 37 g/L NaHCO₃, and 5 mg/mL collagen-I in a ratio of 1:1:8. The gel mixture is added to the gel channel as 2 µl and incubated in a 37 °C humidified incubator with 5% CO2 for 15 minutes. After incubation 30 µl PBS was added to the gel channel. After 24 hours Caco-2 cell were seeded in the right channel as 20,000 cells/channel from right perfusion inlet in Eagle's minimal essential medium (EMEM, ATCC) supplemented with 10% FBS (Sigma-Aldrich), 1% penicillin/streptomycin (Sigma-Aldrich), 1% nonessential amino acids (Sigma-Aldrich), and 1% sodium pyruvate (Sigma-Aldrich). To allow the cells to settle on the extracellular matrix gel, the OrganoPlate® was incubated on its side for 4 hours in a 37 °C humidified incubator with 5% CO2. After incubation, all perfusion inlets were filled with 50 µl of previously described cell culture media.

extract_protocol:
Total RNAs were extracted and purified with the RNeasy Plus Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific) and 2200 Tape Station Automated Electrophoresis System (Agilent Technologies, Santa Clara, Calif) were used to determine the quantity and quality of the isolated RNA.
The samples with RNA integrity numbers 9.4 or more were chosen for sequencing. RNA sequencing (RNAseq) was performed on Illumina NovaSeq 6000 with the TruSeq RNA Stranded Sample Prep Kit (Illumina, San Diego, Calif).

treatment_protocol: On day 8 of gut-on-a-chip culture, the chips were exposed to 10mg/ml, 2.5mg/ml and 0.63mg/ml aspartame dissolved in culture media for 24 hours.

value: Colon enterocystes

value: Untreated


title: WT2

address: 湖北省武汉市华中科技大学同济医学院药学院

description:
Library name: WT2
WT2


title: DMSO-Hyp-2

description:
Library name: library name 1
DMSO treatment


title: Tregdiff_T20_WT3

description:
Library name: Tregdiff_T20_WT3
TrefDiff_WT_T20_n10


title: Tregdiff_T2_WT1

description:
Library name: Tregdiff_T2_WT1
TrefDiff_WT_T2_n15


title: Tregdiff_T20_WT2

description:
Library name: Tregdiff_T20_WT2
TrefDiff_WT_T20_n22


title: Tregdiff_T20_Sod3

description:
Library name: Tregdiff_T20_Sod3
TrefDiff_SOD_T20_n25


title: Control, replicate 3

description: Library name: SAMPLE 9


title: Aspartame 2.5 mg/ml, replicate 3

description: Library name: SAMPLE 6

value: Aspartame 2.5 mg/ml


title: Tregdiff_T20_Sod1

description:
Library name: Tregdiff_T20_Sod1
TrefDiff_SOD_T20_n13


title: Tregdiff_T20_WT1

description:
Library name: Tregdiff_T20_WT1
TrefDiff_WT_T20_n16


title: Tregdiff_T20_Sod2

description:
Library name: Tregdiff_T20_Sod2
TrefDiff_SOD_T20_n19


title: Aspartame 2.5 mg/ml, replicate 1

description: Library name: SAMPLE 4


title: Tregdiff_T2_Sod2

description:
Library name: Tregdiff_T2_Sod2
TrefDiff_SOD_T2_n18


title: Aspartame 10 mg/ml, replicate 1

description: Library name: SAMPLE 1

value: Aspartame 10 mg/ml


title: Aspartame 2.5 mg/ml, replicate 2

description: Library name: SAMPLE 5


title: Control, replicate 1

description: Library name: SAMPLE 7


title: Tregdiff_T0_WT1

description:
Library name: Tregdiff_T0_WT1
TrefDiff_WT_T0_n14


title: Tregdiff_T0_WT2

description:
Library name: Tregdiff_T0_WT2
TrefDiff_WT_T0_n20


title: Tregdiff_T0_Sod2

description:
Library name: Tregdiff_T0_Sod2
TrefDiff_SOD_T0_n17


title: Tregdiff_T0_Sod1

description:
Library name: Tregdiff_T0_Sod1
TrefDiff_SOD_T0_n11


title: Aspartame 10 mg/ml, replicate 3

description: Library name: SAMPLE 3


title: Tregdiff_T0_WT3

description:
Library name: Tregdiff_T0_WT3
TrefDiff_WT_T0_n8


title: Aspartame 10 mg/ml, replicate 2

description: Library name: SAMPLE 2


title: control-Nor-2

description: Library name: library name 3

data_processing:
The quality control of each sample was accomplished using FASTQC V0.11.5.
For Cut&tag data, clean reads were aligned to human reference genome (hg38) using Hisat2 version 2.1.0.
Peak calling and annotation were performed using R package exomePeak and ChIPseeker respectively.
SAMtools52 was used to remove PCR duplicate and unmapped reads.
Bigwig files were generated by deepTools V2.4.0
Assembly: hg38
Supplementary files format and content: bw
Library strategy: Cut&tag

extract_protocol:
All cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) and maintained at 37 °C with 5% CO2, but hypoxia experiments were performed inhypoxic incubator with 5% CO2 and 1% O2.
Libraries were prepared according to Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD903-01; vazyme, China).


title: control-TG02-Hyp-2

description: Library name: library name 5


title: control-Hyp-2

description: Library name: library name 1


title: iLymphNode_D120_Wt1_Rep1

description:
Library name: iLymphNode_D120_Wt1_Rep1
iLN_WT_n4

source_name: inguinal lymph node

value: inguinal lymph node

value: whole


title: iLymphNode_D120_Sod1_Rep2

description:
Library name: iLymphNode_D120_Sod1_Rep2
iLN_SOD1_n3


title: Tregdiff_T0_Sod3

description:
Library name: Tregdiff_T0_Sod3
TrefDiff_SOD_T0_n23


title: H3R8me2a-PRMT2-S12A-Hyp-2

description: Library name: library name 7


title: iLymphNode_D120_Wt1_Rep3

description:
Library name: iLymphNode_D120_Wt1_Rep3
iLN_WT_n7


title: iLymphNode_D120_Wt1_Rep2

description:
Library name: iLymphNode_D120_Wt1_Rep2
iLN_WT_n5


title: iLymphNode_D120_Sod1_Rep3

description:
Library name: iLymphNode_D120_Sod1_Rep3
iLN_SOD_n6


title: WT_Thymus_Treg_Day120_Rep3

description:
Library name: WT_Thymus_Treg_Day120_Rep3
WT_d120_TReg_6

source_name: thymus

value: thymus


title: iLymphNode_D120_Sod1_Rep1

description:
Library name: iLymphNode_D120_Sod1_Rep1
iLN_SOD1_n2


title: WT_Thymus_cTEC_Day120_Rep2

description:
Library name: WT_Thymus_cTEC_Day120_Rep2
WT_d120_cTEC_5

value: cTEC


title: WT_Thymus_mTEC_Day120_Rep2

description:
Library name: WT_Thymus_mTEC_Day120_Rep2
WT_d120_mTEC_5

value: mTEC

value: WT


title: p-Wnt1-kl2

first: Liangxiang

last: Xiao

address: No. 201-209, Hubin South Road

institute: Zhongshan Hospital of Xiamen University

description:
Library name: sample8
p-Wnt1-kl2_fpkm

data_processing:
Reads were further filtered by fastp (version 0.18.0). The parameters were as follows:  1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides (N);  3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: hg38
Supplementary files format and content: FPKM values and counts for each Sample

source_name: Kidney

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB#7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000.

value: Kidney

value: Overexpression of Wnt1 gene in HKC-8 cell line

value: treated with the Wnt1 plasmid and KP6


title: WT_Thymus_CD4_Day120_Rep3

description:
Library name: WT_Thymus_CD4_Day120_Rep3
WT_d120_CD4_6


title: H3R8me2a-PRMT2-WT-Hyp-2

description: Library name: library name 9

value: glioblastoma cell line


title: WT_Thymus_CD4_Day120_Rep1

description:
Library name: WT_Thymus_CD4_Day120_Rep1
WT_d120_CD4_3


title: WT_Thymus_CD4_Day120_Rep2

description:
Library name: WT_Thymus_CD4_Day120_Rep2
WT_d120_CD4_5


title: WT_Thymus_mTEC_Day120_Rep3

description:
Library name: WT_Thymus_mTEC_Day120_Rep3
WT_d120_mTEC_6


title: WT_Thymus_Treg_Day120_Rep2

description:
Library name: WT_Thymus_Treg_Day120_Rep2
WT_d120_TReg_5


title: p-Wnt1-kl3

description:
Library name: sample9
p-Wnt1-kl3_fpkm


title: WT_Thymus_cTEC_Day120_Rep3

description:
Library name: WT_Thymus_cTEC_Day120_Rep3
WT_d120_cTEC_6


title: WT_Thymus_Treg_Day120_Rep1

description:
Library name: WT_Thymus_Treg_Day120_Rep1
WT_d120_TReg_3


title: p-Wnt1-3

description:
Library name: sample6
p-Wnt1-3_fpkm

value: treated with the Wnt1 plasmid


title: p-Wnt1-kl1

description:
Library name: sample7
p-Wnt1-kl1_fpkm


title: p-Wnt1-1

description:
Library name: sample4
p-Wnt1-1_fpkm


title: p-Wnt1-2

description:
Library name: sample5
p-Wnt1-2_fpkm


title: WT_Thymus_mTEC_Day120_Rep1

description:
Library name: WT_Thymus_mTEC_Day120_Rep1
WT_d120_mTEC_3


title: control2

description:
Library name: sample2
control2_fpkm

value: control

value: treated with the empty vector (pcDNA3)


title: control3

description:
Library name: sample3
control3_fpkm


title: WT_Thymus_cTEC_Day120_Rep1

description:
Library name: WT_Thymus_cTEC_Day120_Rep1
WT_d120_cTEC_3


title: SOD1mut_Thymus_CD4_Day120_Rep3

description:
Library name: SOD1mut_Thymus_CD4_Day120_Rep3
SOD1_d120_CD4_4


title: control1

description:
Library name: sample1
control1_fpkm


title: SOD1mut_Thymus_Treg_Day120_Rep3

description:
Library name: SOD1mut_Thymus_Treg_Day120_Rep3
SOD1_d120_TReg_4

value: Treg


title: SOD1mut_Thymus_mTEC_Day120_Rep3

description:
Library name: SOD1mut_Thymus_mTEC_Day120_Rep3
SOD1_d120_mTEC_4


title: cell-free DNA, Preeclampsia pregnancy DNA124845

city: Ghent

first: Bram

last: Van Gaever

address: C. Heymanlsaan 10

country: Belgium

institute: Ghent University

description:
Library name: DNA124845
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

data_processing:
Demultiplexing was performed using bcl-convert on standard settings
fastq files were processed with the bismark workflow of the nf-core/methylseq pipeline https://github.com/nf-core/methylseq/
the --rrbs flag was enabled for processing.
further data processing code can be found in the following git repo:https://github.com/bravgaev/ExPECT-analysis
Assembly: hg38
Supplementary files format and content: bismark coverage file

source_name: Blood plasma

extract_protocol:
Cell-free DNA (cfDNA) was extracted using the Maxwell RSC LV ccfDNA kit (Promega) according to the manufacturer’s instructions
The cfRRBS protocol was followed as described by De Koker et al.  and adapted by Van Paemel et al. https://doi.org/10.1080/15592294.2020.1790950 the EZ DNA Lightning kit (ZymoResearch) was used.

value: Blood plasma

value: Preeclampsia

tag: blood tube_type

value: EDTA

tag: patient id

tag: gestational age_(weeks)

tag: sequencing batch


title: cell-free DNA, Preeclampsia pregnancy DNA124367

description:
Library name: DNA124367
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

tag: tissue

value: PAXgene DNA


title: SOD1mut_Thymus_CD4_Day120_Rep2

description:
Library name: SOD1mut_Thymus_CD4_Day120_Rep2
SOD1_d120_CD4_2

tag: cell type


title: cell-free DNA, Preeclampsia pregnancy DNA124361

description:
Library name: DNA124361
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

tag: disease state


title: SOD1mut_Thymus_cTEC_Day120_Rep3

description:
Library name: SOD1mut_Thymus_cTEC_Day120_Rep3
SOD1_d120_cTEC_4

tag: genotype


title: SOD1mut_Thymus_Treg_Day120_Rep2

description:
Library name: SOD1mut_Thymus_Treg_Day120_Rep2
SOD1_d120_TReg_2


title: cell-free DNA, Preeclampsia pregnancy DNA124365

description:
Library name: DNA124365
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: SOD1mut_Thymus_cTEC_Day120_Rep2

description:
Library name: SOD1mut_Thymus_cTEC_Day120_Rep2
SOD1_d120_cTEC_2


title: SOD1mut_Thymus_mTEC_Day120_Rep2

description:
Library name: SOD1mut_Thymus_mTEC_Day120_Rep2
SOD1_d120_mTEC_2


title: cell-free DNA, Preeclampsia pregnancy DNA124359

description:
Library name: DNA124359
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA124358

description:
Library name: DNA124358
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: SOD1mut_Thymus_CD4_Day120_Rep1

description:
Library name: SOD1mut_Thymus_CD4_Day120_Rep1
SOD1_d120_CD4_1


title: cell-free DNA, Preeclampsia pregnancy DNA124353

description:
Library name: DNA124353
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA124354

description:
Library name: DNA124354
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: SOD1mut_Thymus_Treg_Day120_Rep1

description:
Library name: SOD1mut_Thymus_Treg_Day120_Rep1
SOD1_d120_TReg_1


title: cell-free DNA, Preeclampsia pregnancy DNA124349

description:
Library name: DNA124349
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: SOD1mut_Thymus_mTEC_Day120_Rep1

description:
Library name: SOD1mut_Thymus_mTEC_Day120_Rep1
SOD1_d120_mTEC_1


title: cell-free DNA, Preeclampsia pregnancy DNA124348

description:
Library name: DNA124348
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA124346

description:
Library name: DNA124346
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: SOD1mut_Thymus_cTEC_Day120_Rep1

description:
Library name: SOD1mut_Thymus_cTEC_Day120_Rep1
SOD1_d120_cTEC_1


title: cell-free DNA, Preeclampsia pregnancy DNA124341

description:
Library name: DNA124341
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WholeThymus_D120_WT2

description:
Library name: WholeThymus_D120_WT2
WT2

value: wholethymus


title: WholeThymus_D120_WT3

description:
Library name: WholeThymus_D120_WT3
WT3

value: thymus


title: WholeThymus_D120_WT1

description:
Library name: WholeThymus_D120_WT1
WT1


title: cell-free DNA, Preeclampsia pregnancy DNA124337

description:
Library name: DNA124337
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WholeThymus_D120_Sod3

description:
Library name: WholeThymus_D120_Sod3
Sod3


title: cell-free DNA, Preeclampsia pregnancy DNA124329

description:
Library name: DNA124329
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA124330

description:
Library name: DNA124330
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WholeThymus_D120_Sod2

description:
Library name: WholeThymus_D120_Sod2
Sod2


title: cell-free DNA, Preeclampsia pregnancy DNA124328

description:
Library name: DNA124328
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA124338

description:
Library name: DNA124338
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA124326

description:
Library name: DNA124326
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WT_Thymus_Treg_Day30_Rep3

description:
Library name: WT_Thymus_Treg_Day30_Rep3
SOD1_d30_Treg_JL11


title: WT_Thymus_mTEC_Day30_Rep3

description:
Library name: WT_Thymus_mTEC_Day30_Rep3
SOD1_d30_mTEC_JL10


title: cell-free DNA, Preeclampsia pregnancy DNA124327

description:
Library name: DNA124327
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WholeThymus_D120_Sod1

description:
Library name: WholeThymus_D120_Sod1
Sod1


title: WT_Thymus_cTEC_Day30_Rep3

description:
Library name: WT_Thymus_cTEC_Day30_Rep3
SOD1_d30_cTEC_JL21

value: cTEC


title: cell-free DNA, Preeclampsia pregnancy DNA124325

description:
Library name: DNA124325
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: SOD1mut_Thymus_CD4_Day30_Rep3

description:
Library name: SOD1mut_Thymus_CD4_Day30_Rep3
SOD1_d30_CD4_JL20


title: WT_Thymus_CD4_Day30_Rep3

description:
Library name: WT_Thymus_CD4_Day30_Rep3
SOD1_d30_CD4_JL12


title: SOD1mut_Thymus_Treg_Day30_Rep3

description:
Library name: SOD1mut_Thymus_Treg_Day30_Rep3
SOD1_d30_Treg_JL19


title: cell-free DNA, Preeclampsia pregnancy DNA124323

description:
Library name: DNA124323
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Preeclampsia pregnancy DNA124322

description:
Library name: DNA124322
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: SOD1mut_Thymus_mTEC_Day30_Rep3

description:
Library name: SOD1mut_Thymus_mTEC_Day30_Rep3
SOD1_d30_mTEC_JL18

value: mTEC


title: cell-free DNA, Preeclampsia pregnancy DNA124320

description:
Library name: DNA124320
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124188

description:
Library name: DNA124188
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Healthy


title: SOD1mut_Thymus_cTEC_Day30_Rep3

description:
Library name: SOD1mut_Thymus_cTEC_Day30_Rep3
SOD1_d30_cTEC_JL17


title: cell-free DNA, Healthy pregnancy DNA124249

description:
Library name: DNA124249
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124186

description:
Library name: DNA124186
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WT_Thymus_Treg_Day30_Rep2

description:
Library name: WT_Thymus_Treg_Day30_Rep2
SOD1_d30_Treg_JL07

value: WT


title: WT_Thymus_mTEC_Day30_Rep2

description:
Library name: WT_Thymus_mTEC_Day30_Rep2
SOD1_d30_mTEC_JL06


title: WT_Thymus_CD4_Day30_Rep2

description:
Library name: WT_Thymus_CD4_Day30_Rep2
SOD1_d30_CD4_JL08


title: WT_Thymus_cTEC_Day30_Rep2

description:
Library name: WT_Thymus_cTEC_Day30_Rep2
SOD1_d30_cTEC_JL09


title: cell-free DNA, Healthy pregnancy DNA124185

description:
Library name: DNA124185
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: SOD1mut_Thymus_Treg_Day30_Rep2

description:
Library name: SOD1mut_Thymus_Treg_Day30_Rep2
SOD1_d30_Treg_JL15


title: SOD1mut_Thymus_CD4_Day30_Rep2

description:
Library name: SOD1mut_Thymus_CD4_Day30_Rep2
SOD1_d30_CD4_JL16


title: cell-free DNA, Healthy pregnancy DNA124187

description:
Library name: DNA124187
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124184

description:
Library name: DNA124184
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124183

description:
Library name: DNA124183
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: SOD1mut_Thymus_cTEC_Day30_Rep2

description:
Library name: SOD1mut_Thymus_cTEC_Day30_Rep2
SOD1_d30_cTEC_JL13


title: WT_Thymus_Treg_Day30_Rep1

description:
Library name: WT_Thymus_Treg_Day30_Rep1
SOD1_d30_Treg_JL23


title: cell-free DNA, Healthy pregnancy DNA124182

description:
Library name: DNA124182
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: WT_Thymus_mTEC_Day30_Rep1

description:
Library name: WT_Thymus_mTEC_Day30_Rep1
SOD1_d30_mTEC_JL22


title: SOD1mut_Thymus_CD4_Day30_Rep1

description:
Library name: SOD1mut_Thymus_CD4_Day30_Rep1
SOD1_d30_CD4_JL04


title: SOD1mut_Thymus_mTEC_Day30_Rep2

description:
Library name: SOD1mut_Thymus_mTEC_Day30_Rep2
SOD1_d30_mTEC_JL14


title: SOD1mut_Thymus_Treg_Day30_Rep1

description:
Library name: SOD1mut_Thymus_Treg_Day30_Rep1
SOD1_d30_Treg_JL03


title: SOD1mut_Thymus_mTEC_Day30_Rep1

description:
Library name: SOD1mut_Thymus_mTEC_Day30_Rep1
SOD1_d30_mTEC_JL02


title: cell-free DNA, Healthy pregnancy DNA124181

description:
Library name: DNA124181
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124180

description:
Library name: DNA124180
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124175

description:
Library name: DNA124175
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: SOD1mut_Thymus_cTEC_Day30_Rep1

description:
Library name: SOD1mut_Thymus_cTEC_Day30_Rep1
SOD1_d30_cTEC_JL01


title: cell-free DNA, Healthy pregnancy DNA124177

description:
Library name: DNA124177
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124176

description:
Library name: DNA124176
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124179

description:
Library name: DNA124179
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124178

description:
Library name: DNA124178
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124170

description:
Library name: DNA124170
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, Control for Carmofur, rep11

city: CAMBRIDGE

first: Qiming

last: Zhang

address: 88 Ames Street

institute: Koch institute

description: Library name: nAKP.Control.201141.intCt

data_processing:
The reads were used to quantify transcripts from the mm10 mouse assembly with the Ensembl version 101 annotation using Salmon version 1.3.0 and gene level summaries were prepared using tximport version 1.16.1
Assembly: mm10
Supplementary files format and content: Tab-delimited csv file includes raw counts for each sample

source_name: Colon

extract_protocol:
RNA was extracted from organoids using TRIzol and Ambion PureLink RNA Mini Kit (Thermo Fisher Scientific, 12-183-018 A) according to the manufacturer’s instructions
NEBNext Ultra II Directional RNA preparation with poly(A) selection is used to selectively capture mRNA from total RNA and barcoded libraries were generated

value: Colon

value: tumor

value: AKP

tag: treatment

value: Control


title: cell-free DNA, Healthy pregnancy DNA124171

description:
Library name: DNA124171
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124173

description:
Library name: DNA124173
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, Carmofur, rep14

description: Library name: nAKP.Carm.201138.intCt

value: Carmofur


title: Colon tumor, Carmofur, rep13

description: Library name: nAKP.Carm.201137.intCt


title: Colon tumor, Control for Carmofur, rep10

description: Library name: nAKP.Control.201140.intCt


title: Colon tumor, Control for Carmofur, rep9

description: Library name: nAKP.Control.201133.intCt


title: Colon tumor, Control for Carmofur, rep12

description: Library name: nAKP.Control.201142.intCt


title: cell-free DNA, Healthy pregnancy DNA124166

description:
Library name: DNA124166
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124164

description:
Library name: DNA124164
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, Control for Carmofur, rep8

description: Library name: nAKP.Control.201132.intCt


title: cell-free DNA, Healthy pregnancy DNA124169

description:
Library name: DNA124169
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124167

description:
Library name: DNA124167
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124165

description:
Library name: DNA124165
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, Carmofur, rep15

description: Library name: nAKP.Carm.201139.intCt


title: Colon tumor, Control for Carmofur, rep7

description: Library name: nAKP.Control.201131.intCt


title: Colon tumor, Carmofur, rep12

description: Library name: nAKP.Carm.201130.intCt


title: cell-free DNA, Healthy pregnancy DNA124161

description:
Library name: DNA124161
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, Carmofur, rep11

description: Library name: nAKP.Carm.201129.intCt


title: Colon tumor, Carmofur, rep10

description: Library name: nAKP.Carm.201128.intCt


title: cell-free DNA, Healthy pregnancy DNA124163

description:
Library name: DNA124163
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124159

description:
Library name: DNA124159
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, Carmofur, rep9

description: Library name: nAKP.Carm.201127.intCt


title: cell-free DNA, Healthy pregnancy DNA124160

description:
Library name: DNA124160
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124162

description:
Library name: DNA124162
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124157

description:
Library name: DNA124157
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, Carmofur, rep8

description: Library name: nAKP.Carm.201126.intCt


title: PBMC sorted cell TEMRA, Mini, sublibrary 6

city: Los Angeles

first: Alejandro

last: Espinoza

address: 610 Charles E Young Dr S. 5000C

institute: University of California, Los Angeles

description: Library name: Parse_TEMRA_S6.fastq.gz

data_processing:
The demultiplexing, barcoded process were done using Cell Ranger (v7). Parse sample demultiplexing, read mapping and gene expression quantification were done using split-pipe (v1.1.2) with the following parameters: --mode all --chemistry v2.
Assembly: Human hg38
Supplementary files format and content: Raw counts matrices saved as a seurat object are provided for PBMC and TEMRA samples, separately.

source_name: PBMC

extract_protocol:
cell suspensions were filtered through a 40 µm flowmi cell strainer (SP BEL-ART) and the cell count, and viability were determined using 0.4% trypan blue dye (Gibco). Live PBMCs (viability > 95%) were then resuspended with 1 mL 1X PBS containing 1% UltraPure bovine serum albumin (Thermo Fisher Scientific).
The cells were loaded onto the Chip G and Chromium Controller instrument (10x Genomics) to generate gel bead-in-emulsions (GEM) and indexed sequencing libraries according to the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 user guide.

value: PBMC

value: TEMRA


title: PBMC sorted cell TEMRA, Mini, sublibrary 7

description: Library name: Parse_TEMRA_S7.fastq.gz


title: PBMC sorted cell TEMRA, Mini, sublibrary 3

description: Library name: Parse_TEMRA_S3.fastq.gz


title: PBMC, human, Donor 1

description: Library name: 10X_PBMC_D1


title: PBMC, Parse WT, sublibrary 1

description: Library name: Parse_PBMC_S2.fastq.gz


title: cell-free DNA, Healthy pregnancy DNA124155

description:
Library name: DNA124155
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated

value: Blood plasma


title: PBMC, human, Donor 3

description: Library name: 10X_PBMC_D3


title: PBMC sorted cell TEMRA, 10X

description: Library name: 10X_TEMRA


title: PBMC sorted cell TEMRA, Mini, sublibrary 1

description: Library name: Parse_TEMRA_S1.fastq.gz


title: PBMC, Parse WT, sublibrary 2

description: Library name: Parse_PBMC_S1.fastq.gz


title: PBMC, human, Donor 2

description: Library name: 10X_PBMC_D2


title: PBMC sorted cell TEMRA, Mini, sublibrary 4

description: Library name: Parse_TEMRA_S4.fastq.gz


title: PBMC sorted cell TEMRA, Mini, sublibrary 5

description: Library name: Parse_TEMRA_S5.fastq.gz


title: PBMC sorted cell TEMRA, Mini, sublibrary 8

description: Library name: Parse_TEMRA_S8.fastq.gz


title: PBMC sorted cell TEMRA, Mini, sublibrary 2

description: Library name: Parse_TEMRA_S2.fastq.gz


title: Colon tumor, Control for Carmofur, rep6

description: Library name: nAKP.Control.201121.intCt


title: cell-free DNA, Healthy pregnancy DNA124154

description:
Library name: DNA124154
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, Control for Carmofur, rep5

description: Library name: nAKP.Control.201120.intCt


title: cell-free DNA, Healthy pregnancy DNA124152

description:
Library name: DNA124152
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124151

description:
Library name: DNA124151
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, Carmofur, rep5

description: Library name: nAKP.Carm.201117.intCt


title: Colon tumor, Control for Carmofur, rep4

description: Library name: nAKP.Control.201119.intCt


title: cell-free DNA, Healthy pregnancy DNA124148

description:
Library name: DNA124148
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124145

description:
Library name: DNA124145
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: cell-free DNA, Healthy pregnancy DNA124139

description:
Library name: DNA124139
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, Carmofur, rep1

description: Library name: nAKP.Carm.201113.intCt


title: Colon tumor, Carmofur, rep2

description: Library name: nAKP.Carm.201114.intCt


title: cell-free DNA, Healthy pregnancy DNA124140

description:
Library name: DNA124140
bismark .cov.gz files columns: Chromosome, Start position, End position, Methylation percentage, Count methylated, Count unmethylated


title: Colon tumor, PA batch2, rep1

description: Library name: PA_1_2

value: Palmitic acid


title: Colon tumor, Carmofur, rep4

description: Library name: nAKP.Carm.201116.intCt


title: Colon tumor, PA batch2, rep2

description: Library name: PA_2_2