title: N8

city: 天津

first: Yingtang

address: 83 Jintang Road, Hedong District

institute: The Third Central Hospital of Tianjin

description: Library name: Sample24

data_processing:
Raw sequencing data were strictly quality-controlled, filtered for low-quality sequences, validated by Q30 scores, aligned to the GRCh38 reference genome, assembled, quantified, and used to identify novel transcripts and predict lncRNAs.
Assembly: GRCH38
Supplementary files format and content: xls files include FPKM values for each Sample

source_name: serum

extract_protocol:
Total RNA was extracted from EVs, purified, and stored at -80°C.
Constructed long RNA and small RNA libraries, sequenced and analyzed.

value: serum

tag: disease


title: N7

status: Public on Oct 16 2025

type: SRA

last: Gao

country: China

description: Library name: Sample23

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: Cd19-2

city: Madison

first: Owen

middle: James

last: Tamplin

state: WI

address: 1111 Highland Ave

department: Cell and Regenerative Biology

country: USA

institute: University of Wisconsin-Madison

description: Library name: Cd19-2

data_processing:
Bioinformatic analysis of transcriptomic data adhere to recommended ENCODE guidelines and best practices for RNA-Seq (Encode Consortium, 2016). Alignment of adapter-trimmed (Skewer v0.1.123; Jiang et al., 2014) 2x150 (paired-end; PE) bp strand-specific Illumina reads to the Mus musculus GRCm39 genome (assembly accession NCBI: GCA_000001635.9) was achieved with the Spliced Transcripts Alignment to a Reference (STAR 2.7.11b) software (Dobin, et al., 2013), a splice-junction aware aligner, using annotation provided by Ensembl release 110. Expression estimation was performed with RSEM v1.3.1 (RNASeq by Expectation Maximization; Li and Dewey, 2011).
Assembly: GRCm39
Supplementary files format and content: TSV of RSEM normalized RNA expression values for each gene

organism: Mus musculus

source_name: hematopoietic stem and progenitor cells

extract_protocol:
HSPCs were sorted directly into TRIzol LS (Invitrogen) and stored at -80C until ready for RNA extraction. RNA was extracted following TRIzol LS manufacturer's instruction with GenElute-LPA added to facilitate RNA precipitation.
Total RNA libraries were prepared using the Takara SMARTer Stranded RNA v2 Pico kit.

tag: cell type

value: hematopoietic stem and progenitor cells


title: WT_rep5_D

city: Paris

first: Clara

last: Bourbousse

address: 9 quai Saint Bernard

department: UMR 7622 LBD

country: France

institute: Sorbonne Université

data_processing:
Reads were mapped using Salmon (version 1.9.0) (PatroNat Methods 2017) on a merged reference transcriptome composed of the AtRTD3 (ZhangGenome Biol 2022) Arabidopsis transcriptome and the dmel_r6.48 Drosophila transcriptome and using the Arabidopsis (TAIR10) and Drosophila (dmel_r6.48) genome as a decoy sequence.
The read counts were obtained from the median of those inferential replicates via the tximport R package (version 1.30.0, R version 4.3.2) (SonesonF1000Research 2015) with the 'scaledTPM' option. on TAIR10 genes and transposons with htseq-count
Genome_build: TAIR10
Supplementary_files_format_and_content: txt file containing raw read count per locus

organism: Arabidopsis thaliana

source_name: cotyledon

growth_protocol: 5 days of growth on MS 1/2 in darkness or long days

extract_protocol:
Acetone fixation, dissection of cotyledons, grinding and extraction after adding drosohila cells with Qiagen micro RNeasy kit
DNB-seq paired-end stranded

treatment_protocol: Dark-grown seedlings (D) were further exposed to 1h, 6h or 24h of continuous light

tag: time of light

value: D

tag: bio rep

tag: genotype

value: WT


title: WT_rep5_24h


title: Cd19-1

description: Library name: Cd19-1


title: Actr3 KO-2

city: Freiburg

first: Manuel

last: Rogg

state: Baden Wuerttemberg

address: Breisacher Straße 115a

department: Institute of Surgical Pathology

country: Germany

institute: University Medical Center Freiburg

description:
Library name: Sample 4
featureCounts

data_processing:
The Galaxy Europe resource was used for processing and analysis of sequencing data (https://usegalaxy.eu).
Sequenced reads were quality and adapter trimmed using fastp v0.20.1.
Reads were mapped to mm10 whole genome using HISAT2 v2.2.1 with default settings for single-end libraries.
featureCounts v2.0.1 and DESeq2 v2.11.40.7 were applied for differential expression analysis
Assembly: Mouse Dec. 2011 (GRCm38/mm10) (mm10)
Supplementary files format and content: tab-delimited text files include normalized counts for all samples

source_name: Kidney medulla

extract_protocol:
Isolation of total RNA from the medulla of two Actr3 KO and two Actr3 WT animals at p14 was performed using the Qiagen RNAeasy midi Kit (74104, Quiagen) according to the supplier instructions.
Library preparation and Illumina sequencing were performed by Eurofins GATC Biotech.

value: Kidney medulla

tag: strain

value: C57BL/6 mixed

value: Actr3 KO


title: N6

description: Library name: Sample22


title: Huh7 cells hypoxia

city: Shanghai

first: Jun

last: Mi

address: 280 South Chongqing Rd.

department: Biochemistry & Molecular Cell Biology

institute: Shanghai Jiao Tong University

data_processing:
The sequencing data was filtered with SOAPnuke by Removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Assembly: hg38
Supplementary files format and content: tab-delimited includes FPKM for each sample

growth_protocol: Huh7,97H and HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: cell line

value: hepatocellular carcinoma

tag: treatment

value: hypoxia


title: Cmtr1 cKO naive CD4 2

city: Glasgow

first: Alison

last: Galloway

address: Garscube Estate, Switchback Road

country: United Kingdom

institute: Beatson CRUK

data_processing:
Libraries were sequenced on an Illumina Nextseq 500 using a high output 2 X 75bp kit.
Reads were aligned to mm10 with gencode vM12 basic annotation, and read counts for each gene calculated using STAR version 2.5.2b.
Gene expression was compared between controls and Cmtr1 cKO in R using EdgeR (Robinson et al., 2010), using a counts per million (CPM) threshold of 1 in at least three samples.
Assembly: mm10 (GRCm38)
Supplementary files format and content: *ReadsPerGene.out.tab: Each reads per gene file contains a tab-delimited table of reads per gene counted during alignment in STAR. The first column indicates the Ensembl gene id, the second column shows all alignments, the third shows forwards alignments, and the fourth shows reverse alignments (reverse aligned reads are the reads counts to use for this library strategy).

source_name: Naïve CD4 T cells

growth_protocol: Naïve CD4 T cells were FACS sorted (as: TCRb+, CD4+, CD62L+, CD44-, DAPI-) from lymph nodes.

extract_protocol:
RNA was prepared using Trizol.
Libraries were prepared at the Tayside Centre for Genomic Analysis with an Illumina TruSeq kit with Ribozero Gold rRNA depletion.

value: Cmtr1 fl/fl CD4cre +

tag: Sex

value: Male

value: Naive CD4 T cells


title: S2P_Dark_Rep1_IP

library_source: genomic

data_processing:
The Trimmomatic tool is used to trim the reads.
STAR was used to map reads to the TAIR10 genome with --alignIntronMax and  --alignEndsType options to 1 and EndToEnd.
Filters are applied using sambamba view. The flag used is 2572.
Problematic regions of the genome were filtered out from the alignment files using the -L option of sambamba view
The bamCoverage command from deeptools was used to produce bigwig tracks. Specifics about spike-in factor normalization can be found at https://github.com/vidal-adrien/ChIP-Rx-Pipeline-Pub
Assembly: TAIR10
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Cotyledon

growth_protocol: Seeds were surface sterilized and sown on half-strength Murashige and Skoog media (Duchefa Biochemie, The Netherlands) with 1% (w/v) Phytoagar, pH 5.7. After three days of stratification at 4°C in darkness, seeds were exposed to light for 4-6 hours to synchronize germination.

extract_protocol:
For S2P RNA Pol II and H2Bub ChIP-seq, dark and light-grown seedlings were fixed in 1% formaldehyde under safe green light or white ambient light, respectively. 400 cotyledons were dissected, frozen and ground. For S2P RNA Pol II ChIP, a second crosslinking was performed and chromatin was extracted as in (Bourbousse2018). Chromatin was sheared using a Covaris sonicator. Immunoprecipitation and subsequent steps employed the Abcam Ab5095. For H2Bub ChIP, 400 cotyledons were dissected from fixed seedlings and chromatin spike-in and immunoprecipitation was conducted as previously described earlier ({NassrallaheLife2018}) using the Medimabs MM-0029-P antibodies.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645). The sequencing was performed on the DNBSEQ-G400 platform (BGI) in paired-end mode.

treatment_protocol: Plants were either grown under long-day light condition for 5 days (Light) or under three layers of aluminum foil for five days. Dark samples were collected under a green safe light.

value: Cotyledon

value: Col-0 WT

value: Dark


title: het_2F3

city: Memphis

first: Lance

last: Palmer

state: TN - Tennessee

address: 262 Danny Thomas Pl

department: Hematology

institute: St. Jude Children's Research Hospital

data_processing:
Reads were aligned to GRCh38 human genome, genocde vs r31 using that STAR (2.7.9a) alignment program.
Differential expression was performed using voom/limma.  Genes were ranked based on sign of the log2 fold change * FDR.
Gene set enrichment was performed using GSEA.
Assembly: GRCh38, Gencode r31
Supplementary files format and content: A file of gene counts can be found in the tab delimited file counts.txt
Supplementary files format and content: Limma comparison of all mutations vs wild-type is found in the tab-delimited file limmaResults.combined.txt

molecule: polyA RNA

source_name: BJFF.6 iPSCs

growth_protocol: CD43 cell medium

extract_protocol:
RNA was extracted using Zymo Direct-Zol RNA microprep kit (ZymoResearch, cat no. R2063).
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020599).

treatment_protocol: No treatments applied

value: BJFF.6 iPSCs

value: iPSC derived CD43 cells

value: MDM4 c.1361C>T/MDM4 wild type


title: HepG2 cells control

value: control


title: WT_rep5_1h


title: het_2F2


title: WT_rep4_L

value: L


title: N4

description: Library name: Sample20

value: serum


title: N5

description: Library name: Sample21


title: LC9

description: Library name: Sample19

value: liver cirrhosis


title: 97H cells control

value: WT


title: WT_rep4_D

value: D


title: het_2F1


title: Huh7 cells control

value: hepatocellular carcinoma


title: LC8

description: Library name: Sample18


title: WT_rep4_6h


title: 97H cells hypoxia

value: hypoxia


title: LC7

description: Library name: Sample17


title: WT_rep4_24h


title: BMDC,OVApIL12l,24h ,rep3

city: 北京

first: xiangdong

last: zhang

state: 北京市

address: 北京市海淀区清华大学

institute: Tsinghua Univercity

data_processing:
The clean reads were aligned to 10090（Taxonomy ID）genome (version: mm10_Ensembl) using the Hisat2.
Clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to mouse genome (mm10_Ensembl100) using the Hisat2
HTseq was used to get gene counts and RPKM method was used to determine the gene expression.
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample
Supplementary files format and content: Excel file includes FPKM for each sample
Supplementary files format and content: Excel file includes TPM for each sample

source_name: BMDC

growth_protocol: BMDCs  were maintained in RPMI 1640 supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Agilent 2200 and kept at −80°C.
The RNA with RIN (RNA integrity number) > 7.0 is acceptable for cDNA library construction. The cDNA libraries were constructed for each RNA sample using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (vazyme, Inc.) according to the manufacturer’s instructions.

treatment_protocol: BMDC cells in six-well plates were transfected with 1μg of different groups of mRNA

value: BMDC

value: DC maturation


title: BMDC,OVApIL12l,24h ,rep2


title: R445X_3H2

value: MDM4 c.1333C>T/MDM4 wild type


title: BMDC,OVApIL12l,24h ,rep1


title: R445X_3H1


title: LC2

description: Library name: Sample15


title: WT_rep3_L


title: BMDC,OVAoIL12,24h ,rep3


title: R445X_3H3


title: HCC5

description: Library name: Sample14


title: R445X_2D2


title: WT_rep3_D


title: WT_rep3_6h


title: BMDC,OVAoIL12,24h ,rep2


title: HCC4

description: Library name: Sample13


title: LC6

description: Library name: Sample16


title: R445X_2D1


title: HCC3

description: Library name: Sample12


title: WT_rep3_24h


title: het_2C3


title: BMDC,OVA,24h ,rep3


title: WT_rep3_1h


title: het_2C2


title: BMDC,OVA,24h ,rep2


title: WT_rep2_L


title: HCC2

description: Library name: Sample11


title: R445X_2D3


title: HCC1

description: Library name: Sample10


title: BMDC,OVA,24h ,rep1


title: WT_rep4_1h


title: WT_rep2_D


title: L31Tfa_1C3

value: MDM4 c.90_91insA/ MDM4 wild type


title: HA4

description: Library name: Sample9

value: benign liver disease


title: WT_rep2_6h


title: HA3

description: Library name: Sample8


title: L31Tfa_1C2


title: BMDC,OVA-IL12,24h ,rep2


title: BMDC,OVAoIL12,24h ,rep1


title: HA2

description: Library name: Sample7


title: WT_rep2_1h


title: L31Tfa_1C1


title: BMDC,OVA-IL12,24h ,rep1


title: WT_rep2_24h


title: L31Tfs_1B3


title: L31Tfs_1B2


title: het_2C1


title: BMDC,IL12,24h ,rep2


title: WT_rep1_L


title: BMDC,IL12,24h ,rep1


title: BMDC,IL12,24h ,rep3


title: WT_rep1_6h


title: CHB6

description: Library name: Sample5

value: chronic hepatitis B


title: CHB5

description: Library name: Sample4


title: HA1

description: Library name: Sample6


title: L31Tfs_1B1

value: BJFF.6 iPSCs


title: BMDC,OVA-IL12,24h ,rep3


title: BMDC,ctrl,24h ,rep3


title: CHB4

description: Library name: Sample3


title: WT_2

value: iPSC derived CD43 cells

value: wild type


title: WT_3


title: BMDC,ctrl,24h ,rep2


title: WT_rep1_1h


title: CHB1

description: Library name: Sample1


title: WT_rep1_24h


title: BMDC,ctrl,24h ,rep1


title: WT_1


title: F17262_IP

status: Public on Oct 15 2025

city: Los Angeles

first: Yuichiro

last: Itoh

state: California

address: 635 Charles E. Young Drive South

department: Neurology

institute: UCLA

description: microglia RNA isolated from Tmem119-Cre:RiboTag mice

data_processing:
Data quality check was done on Illumina SAV. De-multiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program.
Qualities of raw sequence data were examined using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and Trimmomatic (Bolger et al., 2014) was used for cleaning.
R package “QuasR” (Gaidatzis et al., 2015) was used for the read alignment to the mouse genome (mm10) followed by counting at the gene level.
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts

source_name: hippocampus

extract_protocol:
RNAs were isolated using the Direct-zol™ RNA MiniPrep Plus kit (Zymo Research).
The RNA sequencing library was made using KAPA Stranded RNA-Seq Kit (Kapa Biosystems) which consists of mRNA enrichment, cDNA generation, end repair, A-tailing, adaptor ligation, strand selection, and PCR amplification.

value: hippocampus

value: female

value: microglia

tag: rip antibody

value: Anti-HA Magnetic Beads (Pierce, catalog number 88837)


title: wt_rep1_D

value: WT


title: Lesional UD skin, scratching-induced, TG

city: Houston

first: Yi

last: Zhu

state: TX

address: 1100 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

description:
Library name: ESC252-SI_TT_F4_233355LT3
10x Genomics
ESC252-SI_TT_F4_233355LT3, scratching-induced, rep2

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files were generated from constructed libraries using the Illumina NovaSeq X Plus PE150 platform.
FASTQ files were supplied to the 10x Genomics CellRanger pipeline (CellRanger Count v9.0.1) to count cell barcodes and UMIs to generate CellRanger outputs (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz). Reads were aligned to the mouse reference genome (GRCm39, Mouse 2024-A). Cell types were annotated using the mouse_pca_v1_beta model within CellRanger.
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files containing cell barcodes, genes, and counts per cell

source_name: Lesional UD skin

growth_protocol: Mouse skin tissue was collected and placed in cold [media]. Samples were dissociated and processed within an hour of collection.

extract_protocol:
Tissue was manually and enzymatically dissociated in dispase and then in accutase and collagenase at 37°C. Cell suspensions were filtered with 40 µm cell strainers, washed, and counted prior to capture.
Single cell suspension was captured using the 10x Genomics Chromium GEM-X Single Cell 5' v3 kit. Cell suspensions were loaded into a GEM-X chip along with partitioning oil and gel beads. Library construction was performed according to the manufacturer's specifications (User Guide CG000733) for the 5' v3 chemistry.

treatment_protocol: No additional treatment was applied to tissue after collection.

value: Lesional UD skin

value: Whole-body Has2 overexpression

value: followed by daily tape stripping of the skin (40–50 times per day) to mimic scratching-induced itch for 15 consecutive days


title: E89545_IP


title: Lesional UD skin, scratching-induced, WT

description:
Library name: ESC251-SI_TT_F3_233355LT3
10x Genomics
ESC251-SI_TT_F3_233355LT3, scratching-induced, rep1

value: Wild type


title: Sc_F_WT_12

source_name: spinal cord

value: spinal cord

value: wildtype

value: EAE


title: D61289_INPUT

value: none (input)


title: Sc_F_WT_8


title: E89545_INPUT


title: Sc_F_WT_10


title: D61289_IP


title: Sc_F_WT_11


title: Sc_F_WT_9


title: CHB3

description: Library name: Sample2

value: serum

value: chronic hepatitis B


title: Sc_F_cKO_6

value: Kdm6a cKO


title: Sc_F_WT_7


title: Sc_F_cKO_2


title: Sc_F_cKO_5


title: Sc_F_cKO_1


title: Sc_F_cKO_3


title: B16-OVA,Control,C04

first: Rui

address: Zhennan rode

department: School of Medicine

institute: Tongji University

data_processing:
Quality control 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 and trimming low qulity base with Trimmomatic. 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 mapping to the reference genome  Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level Htseq-count 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.
The differentially expressed genes (DEG) between HMF and Control groups were analyzed by using the DESeq2 (https://pubmed.ncbi.nlm.nih.gov/25516281/).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
RNA was harvasted using Trizol, and using a NanoDrop 2000 and an Agilent 2100/4200 system, the purity and concentration of total RNA were quantified. For RNA sequencing, mRNA was purified using polyT selection.
After the QC procedure, the RNA with poly-A in eukaryotic total RNA was enriched by TIANSeq mRNA Capture Kit (TIANGEN). Then, using the captured RNA as the starting sample, TIANSeq Fast RNA Library Kit (Illumina) was used to construct the transcriptome sequencing libraries.

treatment_protocol: B16-OVA cells were co-incubated with MagRMs at 37℃ for 24 h, then the cells received HMF treatment, the Control  group were untreated cells.

value: OVA-expression B16F10 (B16-OVA) melanoma cells

value: Magnetic mechaoregulation


title: B16-OVA,HMF,H01


title: B16-OVA,HMF,H04


title: Sc_F_cKO_4

value: female


title: B16-OVA,HMF,H02


title: B16-OVA,Control,C02


title: B16-OVA,Control,C03


title: F17262_INPUT

value: hippocampus

value: microglia


title: B16-OVA,Control,C01

value: WT


title: BMDCs, Control, C03

data_processing:
Quality control 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 and trimming low qulity base with Trimmomatic. 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 mapping to the reference genome  Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level Htseq-count 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.
The differentially expressed genes (DEG) between LMF and Control groups were analyzed by using the DESeq2 (https://pubmed.ncbi.nlm.nih.gov/25516281/).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: bone marrow derived dendritic cells

growth_protocol: Primary BMDCs (pBMDCs) were derived by a previous standard protocol from C57BL/6 mice. Briefly, BMDCs were isolated from the male WT mice (6 weeks). Then, pBMDCs received the 6-day culture in medium (RPMI containing 10% FBS) at 37℃, which contained 10 ng/mL recombinant mouse IL-4 (Novoprotein, CB15) and 20 ng/mL recombinant mouse GM-CSF (Novoprotein, CB02) at 37℃. The cell culture medium was refreshed every 2 days.

treatment_protocol: After culturing for 6 days, BMDCs were co-incubated with ITRs at 37℃ for 24 h, then the cells received LMF treatment, the Control  group were untreated cells.

value: bone marrow derived dendritic cells

value: Magnetic mechaoactivation


title: BMDCs, Control, C04


title: BMDCs, Control, C02


title: BMDCs, LMF, C14


title: BMDCs, LMF, C13


title: BMDCs, Control, C01


title: uba2a-1_3

city: Warsaw

first: Michal

last: Krzyszton

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics, Polish Academy of Sciences

data_processing:
In our sequencing strategy read R1 contains UMI, barcode and first nucleotide of oligo(dT). We trim read R1 to keep only UMI and barcode. Our oligo(dT) primers has two parts of UMI splited by barcode sequence - we move UMI sequences to be next to each other. For all of this we use single awk command: awk 'NR%2==1 {print $0} NR%2==0 {print substr($1,16,5) substr($1,1,15)}'
Fastq files for read R2 from the pools was demultiplexed into separate fastq files for each replica using BRBseqTools (v 1.6) Demultiplex with parameters -p UB -UMI 14 -n 1. Read R2 of each library was trimmed to remove potential contamination with poly(A) tail using BRBseqTools (v 1.6) Trim and parameters -polyA 10 -minLength 30. Then mapped using STAR (v 2.7.8a) with parameters --sjdbOverhang 99 --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1. Finally, the deduplicated counts for each gene were obtained using BRBseqTools (v 1.6) CreateDGEMatrix with parameters -p UB -UMI 14 -s yes. Counts were used for differential gene expression analysis using DESeq2 R package.
Assembly: TAIR10
Supplementary files format and content: count text files

source_name: dry seeds

growth_protocol: Plants were grown in an air-conditioned greenhouse under a long-day (LD) photoperiod (16 hours of light at 22°C and 8 hours of darkness at 18°C). Seeds were harvested and stored at room temperature.

extract_protocol:
Total RNA from seeds was isolated using a phenol:chloroform extraction protocol. After grinding (30-50 mg dry seeds), samples were resuspended in 500 µl of homogenization buffer (100 mM Tris pH 8.5, 5 mM EDTA, 100 mM NaCl, 0.5% SDS, 1% beta-mercaptoethanol). Samples were centrifuged for 5 min at RT at 8000 g. The supernatant was transferred to the new tubes. Then 250 µl of chloroform was added and samples were shaken for 15 min. Next 250 µl of phenol was added and shakening was repeated, followed by centrifugation for 10 min at 14000 g. The upper phase was transferred to new tubes, and an equal volume of phenol:chloroform:isoamyl alcohol was added, shaken and centrifuged as previously. The upper phase was mixed with 10% of the volume of 3 M sodium acetate (pH 5.2) and an equal volume of isopropanol. After 30 min centrifugation at 20000 g at 4°C the pellet was washed with 70% EtOH and resuspended in water. Subsequently, the Ambion TURBO DNA-free kit (Invitrogen) was used to digest DNA in the samples following the protocol provided by the manufacturer.
500 ng of RNA was used in reverse transcription with 50 mM different barcoded oligo(dT) primers and SuperScript III. 0.25 of each reaction was pooled and pools were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 17 ul of water. 15 ul of recovered cDNA pool was mixed by pipetting with 15 ul of second-strand synthesis mix (2x NEBNext Second Strand Synthesis (dNTP-free) Reaction Buffer (NEB), 1 U RNaseH (NEB), 1 U E. coli DNA ligase I (NEB), 5 U E. coli DNA polymerase (NEB), 30 uM dNTPs) and incubated overnight at 16°C. Reactions were purified with Ampure beads (1.2x beads to sample volumes) and eluted in 4 ul of water. 3 ul of recovered dsDNA sample was used for tagmentation using 3 ul 5x diluted B-loaded Tn5 enzyme (homemade) and 6 ul freshly prepared 2x buffer (20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 50% DMF). Reactions were mixed by pipetting and incubated for 7 min at 55°C followed by 5 min at 80°C. Water was added up to 30 ul, samples were purified with Ampure beads (1.2x beads to sample volumes) and eluted with 11 ul of water. Illumina indexing PCR was performed using 10 ul tagmented DNA in 50 ul reactions with Q5 2× PCR Master Mix (NEB) and 0.5 uM final concentration of primers. Libraries were Illumina Next-seq sequenced to obtain two reads: 21 nt R1 (contain barcode and UMI) and 55 nt R2 (contain mRNA sequence).

value: dry seeds

value: uba2a-1 mutant


title: uba2a-1_2


title: uba2a-3_3

value: uba2a-3 mutant


title: uba2a-3_2


title: uba2a-3_1


title: BMDCs, LMF, C12


title: Col0_4

value: wild type


title: Col0_3


title: uba2a-1_4


title: uba2a-1_1


title: B16-OVA,HMF,H03


title: CTVlo T cells, VAC015, Channel 2, ADT

city: Oxford

first: Sam

middle: Michael

last: Murray

address: Nuffield Department of Medicine, Roosevelt Dr, Headington

institute: University of Oxford

description:
Library name: VAC015_2_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258

library_source: other

data_processing:
FASTQ files were generated from BCL files using Illumina bcl2fastq. FASTQ files for all modalities were mapped to the GRCh38-2020-A reference genome and a custom ADT marker list using the Cell Ranger 7.0.0 multi pipeline for count, ADT and VDJ data. Cell ranger multi TCR readout is provided for each experiment/channel. Data analysis was primarily performed using the Seurat package (v4.3.0) (58) in R (v4.3.0). Quality control was performed as follows: low quality cells were removed (based on low UMI and gene count and high percent mitochondrial reads), doublets were flagged and removed using scDblFinder (59). Immunoglobulin and TCR gene segments, identified from the IMGT database (imgt.org), were removed from the gene expression object, except for the following genes: IGHM, IGHG1, IGHG2, IGHG3, IGHG4, IGHD, IGHE, IGHA1, TRAV1-2, TRAV24, TRDV1, TRDV2, TRDV3. Hashtags for each unique individual within a single experiment were demultiplexed using MULTIseqDemux (60) and then data from each experiment were merged into a single Seurat object. Gene counts were log-normalized (NormalizeData function), variable features were found (n=2000, FindVariableFeatures function) and features were scaled using default Seurat parameters (ScaleData function). The top variable features were used for nearest-neighbor and Louvain clustering (resolution 0.7) and to generate principal components, the top 30 of which were used to generate uniform manifold approximation and projections (UMAP). One individual was identified in the vaccine cohort that had potential previous asymptomatic COVID-19 infection. A sensitivity analysis was performed that indicated that this individual did not differ from other individuals in the vaccine group at either T1 or T2, as previously reported (61), therefore the potentially previously infected donor was retained for further analysis. Following Louvain clustering and expert manual annotation of identified cell clusters, several developmentally distinct cell populations were found to co-cluster based on gene expression and were manually separated as follows: MAIT_2 were separated from the co-clustered VD2 and CD8_Tem populations based on co-expression of SLC4A10 and TRAV1-2; VD1_Eff were separated from the co-clustered CD8_IFNG population based on lack of expression of abTCR chains.  CTV data was similarly processed.
Assembly: GRCh38-2020-A
Supplementary files format and content: GEX and ADT data: Seurat object containing three Assays: Count, ADT and HTO. HTO represents hashtagng ADT data. Seurat object contains the following metadata: ID (demultiplexed based on hashtag antibodies), vaccine type (ChAdOx1 nCoV-19: ChAd; BNT162b2: BNT, COVID-19 infection: COVID), dosing interval (8-12weeks: l; 3-4weeks: s), timepoint (timepoint 1: T1, timepoint 2: T2), and manually annotated custom Louvain clusters
Supplementary files format and content: TCR data: tab-delimited text files with cell-identifying barcodes, immune receptor chain, VDJ genes, cdr3 amino acid sequence, cdr3 nucleotide sequence, raw clonotype id and other alignment statistics/metadata outputted from CellRanger.
Library strategy: CITE-seq

molecule: protein

source_name: peripheral blood mononuclear cell

extract_protocol:
AIM data: PBMCs from each vial were split in R10 across up to 8 wells of a U-bottom 96-well plate at 1e6 PBMCs per well. Pools of overlapping peptides (15mers with 11 amino acid overlap) which covered the entire SARS-CoV-2 spike S1 and S2 protein reons were added to each well at a final concentration of 1 μg/ml and plates were incubated for 24 hours at 37 °C. One well of unstimulated cells per donor was included for use as a gating control for flow cytometric cell sorting. After incubation, plates were centrifuged at 1800 rpm for 2 min, washed in FACS buffer (PBS + 0.05% bovine serum albumin + 1 mM EDTA), and centrifuged again at 1800 rpm for 2 min prior to staining with the following antibodies: FITC-CD19 (HIB19), FITC-CD14 (M5E2), PE-4-1BB (CD137; 4B4-1), PE-OX-40 (CD134; Ber-ACT35), AF700-CD8α (SK1), BV421-CD69 (FN50), BV650-CD4 (OKT4), BV785-CD3 (OKT3), TotalSeq-C0032-CD154 (CD40L; 24-31), TotalSeq-C0155-CD107a (H4A3), TotalSeq-C0088-PD-1 (EH12.2H7), TotalSeq-C0171-ICOS (C398.4A), TotalSeq-C0063-CD45RA (HI100), TotalSeq-C0148-CCR7 (G043H7), TotalSeq-C0080-CD8 (RPA-T8), TotalSeq-C0072-CD4 (RPA-T4) and one of TotalSeq-C anti-human Hashtag antibodies (1-10; LNH-94, 2M2) per donor and timepoint. All antibodies were from BioLegend. TotalSeq antibodies were prepared as per manufacturer instructions and staining was performed in a final volume of 50 μl for 30 min at 4 °C. After staining, cells were washed three times with FACS buffer, resuspended in 100 μl of FACS buffer, and transferred to a 1.5 ml RNase-free Microfuge tube. SYTOX Green was pre-diluted 1:60 in PBS + 0.04% BSA, then diluted 1:100 in each sample. Samples were stored at 4 °C until sorting. Sorting was performed on a BD FACSAria III (BD Biosciences) using an 85-micron nozzle. All AIM+ T cells (CD69+ and OX40+ and/or 4-1BB+ CD3+) from all individual samples were sorted into a single collection tube (RPMI-1640 + 1% NEAA + 1% Na Pyruvate + 2.5% HEPES + 10% FBS), washed twice in collection media and resuspended at 13,700 cells per 38.7 μl of resuspension buffer in preparation for the 10x Genomics Chromium Next GEM Single Cell 5’ v2 (Dual Index) workflow.  CTV data: One vial of cryopreserved PBMCs per vaccinee at the pre-vaccination (baseline; “T0”) timepoint was thawed and washed in R10 (RPMI-1640 + 10% FBS + 1% Penicillin/Streptomycin) + Benzonase (500 U) on the day of use. 5.25 × 106 cells per donor were collected and labeled with CTV, as described (35). Briefly, cells were pelleted and washed twice with sterile PBS. After washing, cells were resuspended in 1 ml of PBS and 0.5 μl of CTV was added (1:2000 dilution). Cells were stained for 10 minutes at room temperature and the reaction was quenched using 4 ml of ice-cold FBS. Media was removed and cells were resuspended in 5 ml of RhuAB10 media (RPMI-1640 + 10% human AB serum + 1% Penicillin/Streptomycin). Cells were allowed to rest for 5 min to allow excess CTV to leach away, counted, and resuspended in fresh RhuAB10 media at 2.5e6 cells per ml. Cells (2.5e5) were added to wells of a 96-well U-bottom plate. Unstimulated control (containing DMSO) and positive control (PHA at 2 μg/ml) wells were included. The remainder of the cells were added in sequential wells so that all cells were used and stimulated with S1 + S2 peptide pools (each at 1 μg/ml) in a final volume of 200 μl. Cells were placed in a 37 °C, 5% CO2 incubator for 7 days. On day 4, the plate was centrifuged (1800 rpm for 3 min) and 100 μl of media was removed and replaced with fresh, pre-warmed RhuAB10 media. On day 7, the plate was centrifuged (1800 rpm for 2 min), and all media was removed. Cells were washed in FACS buffer and wells were merged (3 into 1) to reduce the number of wells to stain. Staining was performed for 30 min at 4 °C using a cocktail of: FITC-CD19 (HIB19), FITC-CD14 (M5E2), AF700-CD8α (SK1), BV650-CD4 (OKT4), BV785-CD3 (OKT3), and one of TotalSeq-C anti-human Hashtag antibodies (1-10; LNH-94, 2M2) per donor. TotalSeq-C antibodies were prepared as described above. After staining, cells were washed three times with FACS buffer, resuspended in 100 μl of FACS buffer, and transferred to a 1.5 ml RNase-free Microfuge tube. SYTOX Green was pre-diluted 1:60 in PBS + 0.04% BSA, then diluted 1:100 in each sample. Samples were stored at 4 °C until sorting. Sorting was performed as per AIM+, but CTVlo CD3+ T cells were sorted out.
The 10X Genomics Chromium Next GEM Single Cell 5' v2 library preparation was performed as per manufacturer instructions for Gene Expression, Feature Barcode and TCR library preparations.

treatment_protocol: For AIM data, PBMC were incubated for 24hours with overlapping peptide pools covering the entire SARS-CoV-2 spike protein. For CTV data, PBMC were incubated for 7days with overlapping peptide pools covering the entire SARS-CoV-2 spike protein.

value: peripheral blood mononuclear cell

value: T cell

value: CTVlo, mixed sample

tag: batch

tag: library type

value: ADT

tag: adt


title: cardiac organoid at day 36

city: Würzburg

first: Anna

middle: Frederike

last: Rockel

address: Koelliker Straße 6

department: Institute of Anatomy and Cell Biology

institute: University of Würzburg

description: Library name: Human cardiac organoid

data_processing:
Cell Ranger
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx

source_name: cardiac organoid

growth_protocol: hiPSCs were cultured in MACS medium and differentitaed in RPMI1640

extract_protocol:
Cardiac organoid samples were dissociated via a cold activated B. Licheniformis protease
Library preparation was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3’ v3.1 protocol CG000390 Rev B, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded, along with partitioning oil and gel beads, into the microfluidic chip to generate a gel beademulsion (GEM). The poly-A RNA from the cell lysate contained within each droplet was reverse transcribed into cDNA, which included an Illumina R1 primer sequence, a Unique Molecular Identifier (UMI), and the 10x Barcode.
The pooled, barcoded cDNA was then purified using Silane DynaBeads, amplified by PCR, and size-selected using SPRIselect reagent to isolate appropriately sized fragments for subsequent library construction. During library construction, the Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences, and a sample index were added.
Library quantification and quality control were performed using a Qubit™ 4.0 Fluorometer (Thermo Fisher) and a 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent). Sequencing was carried out on a NovaSeq 6000 sequencer (Illumina) using an S2 flow cell.

treatment_protocol: For cardiac differentiation small molecules Activin A, BMP4, CHIR99021 and IWP2 were applied

value: cardiac organoid

value: hiPSC cell line

tag: time


title: Col0_2


title: Col0_1


title: CTVlo T cells, VAC014, Channel 4, ADT

description:
Library name: VAC014_4_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258


title: BMDCs, LMF, C11


title: CTVlo T cells, VAC014, Channel 3, ADT

description:
Library name: VAC014_3_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258


title: CTVlo T cells, VAC013, Channel 1, ADT

description:
Library name: VAC013_1_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258


title: CTVlo T cells, VAC015, Channel 1, ADT

description:
Library name: VAC015_1_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258


title: uba2a-3_4


title: CTVlo T cells, VAC015, Channel 1, TCR

description:
Library name: VAC015_1_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: TCR


title: CTVlo T cells, VAC015, Channel 2, TCR

description:
Library name: VAC015_2_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CTVlo T cells, VAC013, Channel 2, ADT

description:
Library name: VAC013_2_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258


title: CTVlo T cells, VAC013, Channel 2, TCR

description:
Library name: VAC013_2_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CTVlo T cells, VAC014, Channel 4, TCR

description:
Library name: VAC014_4_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CTVlo T cells, VAC013, Channel 1, TCR

description:
Library name: VAC013_1_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CTVlo T cells, VAC014, Channel 4, GEX

description:
Library name: VAC014_4_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: GEX


title: CTVlo T cells, VAC014, Channel 3, GEX

description:
Library name: VAC014_3_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CTVlo T cells, VAC015, Channel 1, GEX

description:
Library name: VAC015_1_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CTVlo T cells, VAC013, Channel 1, GEX

description:
Library name: VAC013_1_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CTVlo T cells, VAC015, Channel 2, GEX

description:
Library name: VAC015_2_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CTVlo T cells, VAC013, Channel 2, GEX

description:
Library name: VAC013_2_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC012, Channel 4, ADT

description:
Library name: VAC012_4_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0287

value: AIM+, mixed sample

value: TotalSeq-C0032 anti-human CD154 (CD40L), TotalSeq-C0155 anti-human CD107a, TotalSeq-C0088 anti-human PD-1, TotalSeq-C0171 anti-human ICOS, TotalSeq-C0063 anti-human CD45RA, TotalSeq-C0148 anti-human CCR7, TotalSeq-C0080 anti-human CD8 (RPA-T8), TotalSeq-C0072 anti-human CD4 (RPA-T4), TotalSeq-C0251 (5082,COVID,T1), TotalSeq-C0252 (5082,COVID,T2), TotalSeq-C0253 (112,ChAd-S,T1), TotalSeq-C0254 (112,ChAd-S,T2), TotalSeq-C0255 (6402,ChAd-L,T1), TotalSeq-C0256 (6402,ChAd-L,T2), TotalSeq-C0257 (6451,BNT-S,T1), TotalSeq-C0258 (6451,BNT-S,T2), TotalSeq-C0259 (3871,BNT-L,T1), TotalSeq-C0260 (3871,BNT-L,T2)


title: AIM T cells, VAC012, Channel 2, ADT

description:
Library name: VAC012_2_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0285


title: AIM T cells, VAC011, Channel 4, ADT

description:
Library name: VAC011_4_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0283

value: TotalSeq-C0032 anti-human CD154 (CD40L), TotalSeq-C0155 anti-human CD107a, TotalSeq-C0088 anti-human PD-1, TotalSeq-C0171 anti-human ICOS, TotalSeq-C0063 anti-human CD45RA, TotalSeq-C0148 anti-human CCR7, TotalSeq-C0080 anti-human CD8 (RPA-T8), TotalSeq-C0072 anti-human CD4 (RPA-T4), TotalSeq-C0251 (5418,COVID,T1), TotalSeq-C0252 (5418,COVID,T2), TotalSeq-C0253 (108,ChAd-S,T1), TotalSeq-C0254 (108,ChAd-S,T2), TotalSeq-C0255 (6398,ChAd-L,T1), TotalSeq-C0256 (6398,ChAd-L,T2), TotalSeq-C0257 (6383,BNT-S,T1), TotalSeq-C0258 (6383,BNT-S,T2), TotalSeq-C0259 (6394,BNT-L,T1), TotalSeq-C0260 (6394,BNT-L,T2)


title: AIM T cells, VAC012, Channel 3, ADT

description:
Library name: VAC012_3_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0286


title: AIM T cells, VAC011, Channel 3, ADT

description:
Library name: VAC011_3_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0282


title: AIM T cells, VAC012, Channel 1, ADT

description:
Library name: VAC012_1_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0284


title: AIM T cells, VAC011, Channel 2, ADT

description:
Library name: VAC011_2_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0281


title: AIM T cells, VAC011, Channel 1, ADT

description:
Library name: VAC011_1_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0280


title: AIM T cells, VAC010, Channel 4, ADT

description:
Library name: VAC010_4_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0279

value: TotalSeq-C0032 anti-human CD154 (CD40L), TotalSeq-C0155 anti-human CD107a, TotalSeq-C0088 anti-human PD-1, TotalSeq-C0171 anti-human ICOS, TotalSeq-C0063 anti-human CD45RA, TotalSeq-C0148 anti-human CCR7, TotalSeq-C0080 anti-human CD8 (RPA-T8), TotalSeq-C0072 anti-human CD4 (RPA-T4), TotalSeq-C0251 (5097,COVID,T1), TotalSeq-C0252 (5097,COVID,T2), TotalSeq-C0253 (203,ChAd-S,T1), TotalSeq-C0254 (203,ChAd-S,T2), TotalSeq-C0255 (6388,ChAd-L,T1), TotalSeq-C0256 (6388,ChAd-L,T2), TotalSeq-C0257 (5449,BNT-S,T1), TotalSeq-C0258 (5449,BNT-S,T2), TotalSeq-C0259 (6393,BNT-L,T1), TotalSeq-C0260 (6393,BNT-L,T2)


title: AIM T cells, VAC010, Channel 3, ADT

description:
Library name: VAC010_3_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0278


title: AIM T cells, VAC010, Channel 2, ADT

description:
Library name: VAC010_2_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0277


title: AIM T cells, VAC009, Channel 4, ADT

description:
Library name: VAC009_4_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0275

value: TotalSeq-C0032 anti-human CD154 (CD40L), TotalSeq-C0155 anti-human CD107a, TotalSeq-C0088 anti-human PD-1, TotalSeq-C0171 anti-human ICOS, TotalSeq-C0063 anti-human CD45RA, TotalSeq-C0148 anti-human CCR7, TotalSeq-C0080 anti-human CD8 (RPA-T8), TotalSeq-C0072 anti-human CD4 (RPA-T4), TotalSeq-C0251 (5128,COVID,T1), TotalSeq-C0252 (5128,COVID,T2), TotalSeq-C0253 (95,ChAd-S,T1), TotalSeq-C0254 (95,ChAd-S,T2), TotalSeq-C0255 (5995,ChAd-L,T1), TotalSeq-C0256 (5995,ChAd-L,T2), TotalSeq-C0257 (5083,BNT-S,T1), TotalSeq-C0258 (5083,BNT-S,T2), TotalSeq-C0259 (6400,BNT-L,T1), TotalSeq-C0260 (6400,BNT-L,T2)


title: CTVlo T cells, VAC014, Channel 3, TCR

description:
Library name: VAC014_3_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC009, Channel 1, ADT

description:
Library name: VAC009_1_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0272


title: AIM T cells, VAC009, Channel 2, ADT

description:
Library name: VAC009_2_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0273


title: AIM T cells, VAC010, Channel 1, ADT

description:
Library name: VAC010_1_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0276


title: AIM T cells, VAC008, Channel 8, ADT

description:
Library name: VAC008_8_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0271

value: TotalSeq-C0032 anti-human CD154 (CD40L), TotalSeq-C0155 anti-human CD107a, TotalSeq-C0088 anti-human PD-1, TotalSeq-C0171 anti-human ICOS, TotalSeq-C0063 anti-human CD45RA, TotalSeq-C0148 anti-human CCR7, TotalSeq-C0080 anti-human CD8 (RPA-T8), TotalSeq-C0072 anti-human CD4 (RPA-T4), TotalSeq-C0251 (5146,COVID,T1), TotalSeq-C0252 (5146,COVID,T2), TotalSeq-C0253 (88,ChAd-S,T1), TotalSeq-C0254 (88,ChAd-S,T2), TotalSeq-C0255 (5939,ChAd-L,T1), TotalSeq-C0256 (5939,ChAd-L,T2), TotalSeq-C0257 (2689,BNT-S,T1), TotalSeq-C0258 (2689,BNT-S,T2), TotalSeq-C0259 (6396,BNT-L,T1), TotalSeq-C0260 (6396,BNT-L,T2)


title: AIM T cells, VAC009, Channel 3, ADT

description:
Library name: VAC009_3_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0274


title: AIM T cells, VAC008, Channel 7, ADT

description:
Library name: VAC008_7_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0270


title: AIM T cells, VAC008, Channel 6, ADT

description:
Library name: VAC008_6_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0269


title: AIM T cells, VAC008, Channel 5, ADT

description:
Library name: VAC008_5_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0268


title: AIM T cells, VAC008, Channel 4, ADT

description:
Library name: VAC008_4_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0267


title: AIM T cells, VAC008, Channel 2, ADT

description:
Library name: VAC008_2_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0265


title: AIM T cells, VAC007, Channel 4, ADT

description:
Library name: VAC007_4_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0263

value: TotalSeq-C0032 anti-human CD154 (CD40L), TotalSeq-C0155 anti-human CD107a, TotalSeq-C0088 anti-human PD-1, TotalSeq-C0171 anti-human ICOS, TotalSeq-C0063 anti-human CD45RA, TotalSeq-C0148 anti-human CCR7, TotalSeq-C0080 anti-human CD8 (RPA-T8), TotalSeq-C0072 anti-human CD4 (RPA-T4), TotalSeq-C0251 (5195,COVID,T1), TotalSeq-C0252 (5195,COVID,T2), TotalSeq-C0253 (13,ChAd-S,T1), TotalSeq-C0254 (13,ChAd-S,T2), TotalSeq-C0255 (5918,ChAd-L,T1), TotalSeq-C0256 (5918,ChAd-L,T2), TotalSeq-C0257 (2532,BNT-S,T1), TotalSeq-C0258 (2532,BNT-S,T2), TotalSeq-C0259 (2436,BNT-L,T1), TotalSeq-C0260 (2436,BNT-L,T2)


title: AIM T cells, VAC008, Channel 3, ADT

description:
Library name: VAC008_3_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0266


title: AIM T cells, VAC008, Channel 1, ADT

description:
Library name: VAC008_1_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0264


title: AIM T cells, VAC007, Channel 1, ADT

description:
Library name: VAC007_1_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0260


title: AIM T cells, VAC012, Channel 4, GEX

description:
Library name: VAC012_4_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: mRNA


title: AIM T cells, VAC012, Channel 2, GEX

description:
Library name: VAC012_2_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC007, Channel 2, ADT

description:
Library name: VAC007_2_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0261


title: AIM T cells, VAC011, Channel 4, GEX

description:
Library name: VAC011_4_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC011, Channel 2, GEX

description:
Library name: VAC011_2_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC012, Channel 3, GEX

description:
Library name: VAC012_3_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC011, Channel 3, GEX

description:
Library name: VAC011_3_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC010, Channel 3, GEX

description:
Library name: VAC010_3_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC010, Channel 2, GEX

description:
Library name: VAC010_2_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC010, Channel 4, GEX

description:
Library name: VAC010_4_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC010, Channel 1, GEX

description:
Library name: VAC010_1_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC009, Channel 3, GEX

description:
Library name: VAC009_3_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC008, Channel 8, GEX

description:
Library name: VAC008_8_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC009, Channel 2, GEX

description:
Library name: VAC009_2_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC009, Channel 4, GEX

description:
Library name: VAC009_4_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC008, Channel 7, GEX

description:
Library name: VAC008_7_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC008, Channel 6, GEX

description:
Library name: VAC008_6_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC009, Channel 1, GEX

description:
Library name: VAC009_1_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC008, Channel 5, GEX

description:
Library name: VAC008_5_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC008, Channel 4, GEX

description:
Library name: VAC008_4_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC008, Channel 3, GEX

description:
Library name: VAC008_3_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC007, Channel 3, ADT

description:
Library name: VAC007_3_ADT
Antibody-derived oligonucleotide and Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Antibody/Hashtag Derived Tag reads. Antibodies/tags: TotalSeq-C0032, TotalSeq-C0155, TotalSeq-C0088, TotalSeq-C0171, TotalSeq-C0063, TotalSeq-C0148, TotalSeq-C0080, TotalSeq-C0072, TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253, TotalSeq-C0254, TotalSeq-C0255, TotalSeq-C0256, TotalSeq-C0257, TotalSeq-C0258, TotalSeq-C0259, TotalSeq-C0262


title: AIM T cells, VAC008, Channel 2, GEX

description:
Library name: VAC008_2_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC007, Channel 4, GEX

description:
Library name: VAC007_4_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC012, Channel 1, GEX

description:
Library name: VAC012_1_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC007, Channel 3, GEX

description:
Library name: VAC007_3_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC007, Channel 2, GEX

description:
Library name: VAC007_2_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC011, Channel 1, GEX

description:
Library name: VAC011_1_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Unsorted, 28dpi, rep2, GEX

city: Stockholm

first: Margherita

last: Zamboni

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

description: Library name: 28dpi_3_GEX

data_processing:
Raw reads from the Illumina sequencing runs were processed using cellranger-arc standard pipeline (v2.0.2, 10X Genomics), and mapped to the mm10 reference genome, which was supplemented with tdTomato DNA sequence to record expression of the fluorescent reporter in the transgenic line. Raw reads from the MGI sequencing runs were obtained in fastq format, with R2 and the indexes in a single R2 file. For demultiplexing, we first split the R2 file and reverse-complemented the index reads using a custom script, and then demultiplexed by sample using deML (v1.1.4). Subsequently, cellranger-arc count function was used to individually map fastq files of each sample to the reference genome. Following read alignment, we obtained gene expression matrices and fragment files for the transcriptomic and epigenomic modalities, respectively. These sets of data were first pre-processed and filtered separately, prior to integration for multimodal downstream analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated feature matrices

source_name: Spinal cord

extract_protocol:
Fresh spinal cords were microdissected and cleared of the meninges. We obtained 5 mm segments of tissue around the injury epicenter, or at the same rostrocaudal level in uninjured animals. Nuclei from WT mice were isolated with the Chromium Nuclei Isolation Kit (10X Genomics, PN-1000493). These were, subsequently, stained with fluorescently conjugated antibodies against NeuN (1:500) or Sox10 (1:200) for 1h on ice, and with 7AAD (1:50), prior to sorting on BD FACS Influx sorter with a 100 μm nozzle. We used the transgenic line Foxj1-tdTomato to enrich for ependymal cells.We  digested the tissue to obtain single cell suspensions. Briefly, we used papain as digestion enzyme and a GentleMacs Dissociator (Miltenyi) to triturate the samples according to specifications provided in the Miltenyi’s Adult Brain Dissociation protocol. Whole cells were, then, sorted based on expression of the fluorescent reporters and collected in sorting buffer containing 1% BSA for subsequent nuclei isolation (performed according to 10x protocol CG000124 Rev F).
Sequencing-ready libraries were prepared following the Chromium Next GEM Single Cell Multiome protocol (10X Genomics, CG000338 Rev F) and sequenced in an Illumina NextSeq or an MGI machine.

value: Spinal cord

value: WT


title: Unsorted, 28dpi, rep1, GEX

description: Library name: 28dpi_2_GEX


title: AIM T cells, VAC012, Channel 4, TCR

description:
Library name: VAC012_4_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: peripheral blood mononuclear cell

value: T cell


title: Unsorted, 7dpi, rep2, GEX

description: Library name: 7dpi_2_GEX


title: AIM T cells, VAC007, Channel 1, GEX

description:
Library name: VAC007_1_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Unsorted, 7dpi, rep3, GEX

description: Library name: 7dpi_3_GEX


title: AIM T cells, VAC012, Channel 3, TCR

description:
Library name: VAC012_3_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Unsorted, 7dpi, rep1, GEX

description: Library name: 7dpi_1_GEX


title: AIM T cells, VAC012, Channel 2, TCR

description:
Library name: VAC012_2_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Unsorted, 1dpi, rep2, GEX

description: Library name: 1dpi_2_GEX


title: AIM T cells, VAC012, Channel 1, TCR

description:
Library name: VAC012_1_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Unsorted, 1dpi, rep1, GEX

description: Library name: 1dpi_1_GEX


title: Unsorted, 1dpi, rep3, GEX

description: Library name: 1dpi_3_GEX


title: Unsorted, Uninjured, rep3, GEX

description: Library name: U_3_GEX


title: AIM T cells, VAC011, Channel 3, TCR

description:
Library name: VAC011_3_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC011, Channel 4, TCR

description:
Library name: VAC011_4_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC011, Channel 2, TCR

description:
Library name: VAC011_2_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Unsorted, Uninjured, rep2, GEX

description: Library name: U_2_GEX


title: Unsorted, Uninjured, rep1, GEX

description: Library name: U_1_GEX


title: AIM T cells, VAC008, Channel 1, GEX

description:
Library name: VAC008_1_GEX
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Unsorted, 28dpi, rep2, ATAC

description: Library name: 28dpi_3_ATAC

library_source: genomic single cell


title: Unsorted, 7dpi, rep3, ATAC

description: Library name: 7dpi_3_ATAC


title: AIM T cells, VAC010, Channel 2, TCR

description:
Library name: VAC010_2_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC010, Channel 1, TCR

description:
Library name: VAC010_1_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Unsorted, 7dpi, rep2, ATAC

description: Library name: 7dpi_2_ATAC


title: AIM T cells, VAC009, Channel 4, TCR

description:
Library name: VAC009_4_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC009, Channel 3, TCR

description:
Library name: VAC009_3_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Unsorted, 1dpi, rep3, ATAC

description: Library name: 1dpi_3_ATAC


title: AIM T cells, VAC009, Channel 2, TCR

description:
Library name: VAC009_2_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Unsorted, 1dpi, rep2, ATAC

description: Library name: 1dpi_2_ATAC


title: AIM T cells, VAC009, Channel 1, TCR

description:
Library name: VAC009_1_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Unsorted, Uninjured, rep3, ATAC

description: Library name: U_3_ATAC


title: AIM T cells, VAC008, Channel 7, TCR

description:
Library name: VAC008_7_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Unsorted, Uninjured, rep2, ATAC

description: Library name: U_2_ATAC


title: AIM T cells, VAC008, Channel 6, TCR

description:
Library name: VAC008_6_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC008, Channel 8, TCR

description:
Library name: VAC008_8_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC010, Channel 4, TCR

description:
Library name: VAC010_4_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Enhancer library, Uninjured, EYFP, rep1, MPRA

description:
Library name: Enhancer_Uninjured_EYFP_MPRA
enhancer_aav_uninjured_barcodes.tsv.gz
enhancer_aav_uninjured_matrix.mtx
enhancer_aav_uninjured_features.tsv.gz

data_processing:
Raw reads from the MGI sequencing runs were obtained in fastq format, with R2 and the indexes in a single R2 file. For demultiplexing, we first split the R2 file and reverse-complemented the index reads using a custom script, and then demultiplexed by sample using deML (v1.1.4). Subsequently, we mapped fastq files of each sample to the reference genome (mm10) using CellRanger (v8.0.1) with the antibody capture pipeline adapted to detect the custom EYFP enhancer associated barcodes.
Assembly: mm10
Supplementary files format and content: Tab-separated feature matrices

extract_protocol:
Fresh spinal cords were microdissected and cleared of the meninges. We obtained 5 mm segments of tissue around the injury epicenter, or at the same rostrocaudal level in uninjured animals. We  digested the tissue to obtain single cell suspensions. Briefly, we used papain as digestion enzyme and a GentleMacs Dissociator (Miltenyi) to triturate the samples according to specifications provided in the Miltenyi’s Adult Brain Dissociation protocol. Whole cells were, then, sorted based on expression of the fluorescent reporters and processed using Chromium Single Cell 3’ v3.1 (10X Genomics, PN-1000121) according to the manufacurer’s instructions to obtain the gene expression data. We used 25% of the cDNA to further enrich for the barcodes.
Sequencing-ready libraries were prepared following the Chromium Next GEM Single Cell Multiome protocol (10X Genomics, CG000338 Rev F) and sequenced in an Illumina NextSeq or an MGI machine.

treatment_protocol: To test activity of injury-responsive enhancers identified in our analysis, we delivered an enhancer AAV library (2x10^11 vg)  intravenously in mice carrying fluorescently labelled astrocytes (Cx30-Tom). We then subjected the mice to spinal cord injury, and sampled labelled cells at 3 dpi, as well as from uninjured controls.

value: tdTomato+

value: Uninjured, GFP


title: AIM T cells, VAC008, Channel 5, TCR

description:
Library name: VAC008_5_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Unsorted, Uninjured, rep1, ATAC

description: Library name: U_1_ATAC


title: AIM T cells, VAC011, Channel 1, TCR

description:
Library name: VAC011_1_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Enhancer library, Injured, EYFP, rep1, MPRA

description:
Library name: Enhancer_Injured_EYFP_MPRA
enhancer_aav_injured_barcodes.tsv.gz
enhancer_aav_injured_matrix.mtx
enhancer_aav_injured_features.tsv.gz

value: Injured, GFP


title: AIM T cells, VAC008, Channel 3, TCR

description:
Library name: VAC008_3_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: TCR


title: AIM T cells, VAC008, Channel 2, TCR

description:
Library name: VAC008_2_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: Enhancer library, Uninjured, rep1, GEX

description:
Library name: Enhancer_Uninjured_GEX
enhancer_aav_uninjured_barcodes.tsv.gz
enhancer_aav_uninjured_matrix.mtx
enhancer_aav_uninjured_features.tsv.gz

value: Uninjured


title: AIM T cells, VAC010, Channel 3, TCR

description:
Library name: VAC010_3_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: AIM+, mixed sample


title: Unsorted, 28dpi, rep1, ATAC

description: Library name: 28dpi_2_ATAC


title: Unsorted, 7dpi, rep1, ATAC

description: Library name: 7dpi_1_ATAC


title: Enhancer library, Injured, rep1, GEX

description:
Library name: Enhancer_Injured_GEX
enhancer_aav_injured_barcodes.tsv.gz
enhancer_aav_injured_matrix.mtx
enhancer_aav_injured_features.tsv.gz

value: Injured


title: AIM T cells, VAC008, Channel 1, TCR

description:
Library name: VAC008_1_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: GF2_H3K27ac

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: Library name: GF2_H3K27ac

data_processing:
Illumina sequencing reads were de-multiplexed, trimmed to remove adapter sequences, and checked for quality using fastqc ad multiqc.
Reads were aligned to the mouse reference genome (assembly GRCm38/mm10) using Bowtie/2-2.4.2.
Aligned reads were filtered to retain alignments with a minimum mapping quality of 2 using samtools/1.9. Reads mapping to Encyclopedia of DNA Elements (ENCODE) blacklist regions were removed using intersect function in bedtools/2.30.0.
RPKM normalized bigWig files were generated using the bamCoverage function in deepTools/3.5.0.
Broad peaks were called using MACS/2.2.7.1. Differential peak analysis was performed using DiffBind/3.2.6. ROSE (Rank Ordering of Super-Enhancers) algorithm was used to classify enhancers.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig coverage files
Library strategy: CUT&Run

source_name: muscle

extract_protocol:
CUT&RUN was performed to profile enhancer histone modifications H3K4me1 and H3K27ac from young, old and geriatric MuSCs following guidelines in the CUTANA CUT&RUN Protocol (EpiCypher). Briefly, MuSCs were pelleted, and resuspended in wash buffer. ~10,000 cells per sample were bound to activated Concanavalin A beads (Bangs Laboratories). The bead-bound cells were incubated with antibody in wash buffer supplemented with 2 mM EDTA and 0.01% digitonin overnight at 4ºC, digitonin was added to permeabilize cells for antibody binding in situ. After washing with 0.01% digitonin in wash buffer, CUTANA® pAG-MNase (1:20) was added to each sample and incubated at RT for 10 mins to allow binding to antibody-labeled chromatin. Samples were then equilibrated on ice water for 5 mins. 2 mM CaCl2 was added to each sample to activate MNase and cleave antibody-bound chromatin. After 2 h of incubation with CaCl2 at 4ºC, reactions were stopped by adding 33 µL stop buffer to degrade RNA and release DNA fragments. DNA was purified using the Monarch DNA Cleanup Kit (NEB) following manufacturer's instructions and the concentration of CUT&RUN-enriched DNA was determined using the Qubit fluorometer with a DNA high sensitivity kit.
~2 ng of purified DNA was used to prepare libraries using NEBNext Ultra II library preparation kit with unique dual index PCR primers (NEB). The library concentrations were determined using Qubit fluorometer with a DNA high sensitivity kit. Library quality and quantity were confirmed on a BioAnalyzer (Agilent) high sensitivity DNA chip. Equimolar amounts of each library were combined, and the pooled library was further quantified using a NEBNext Library Quant Kit (NEB). The CUT&RUN libraries were subjected to paired-end sequencing with on the NextSeq 2000 platform using a P2 100 cycle kit (Illumina).

value: muscle

value: FISC/MuSC


title: GF1_H3K27ac

description: Library name: GF1_H3K27ac


title: AIM T cells, VAC007, Channel 3, TCR

description:
Library name: VAC007_3_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: AIM T cells, VAC007, Channel 2, TCR

description:
Library name: VAC007_2_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: GM3_H3K27ac

description: Library name: GM3_H3K27ac


title: AIM T cells, VAC007, Channel 4, TCR

description:
Library name: VAC007_4_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: GM2_H3K27ac

description: Library name: GM2_H3K27ac


title: Unsorted, 1dpi, rep1, ATAC

description: Library name: 1dpi_1_ATAC


title: GM1_H3K27ac

description: Library name: GM1_H3K27ac


title: OF3_H3K27ac

description: Library name: OF3_H3K27ac


title: ECEV_72h_2

city: Chicago

first: Heidi

last: Yuan

address: 801 S Paulina St

institute: University of Illinois Chicago

description: Library name: Sample 5

data_processing:
Clean data was obtained by using in-house perl scripts (Novogene America) to remove reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Hisat2 (v2.0.5) was used to index and map reads to the human reference genome. The reference genome and gene model annotation files were downloaded from the genome website directly.
The mapped reads were assembled with StringTie (v1.3.3b).
Read numbers mapped to each gene were then counted in R with FeatureCounts (v1.5.0-p3) and an FPKM of each gene was calculated.
Assembly: hg38
Supplementary files format and content: CSV file includes gene counts for each sample
Supplementary files format and content: Additional supplementary file is DESeq2 output from Novogene. Only genes with p-adjusted value < 0.05 are included.

source_name: Skin

growth_protocol: Cells were grown to maximum confluency prior to treatment.

extract_protocol:
RNA was harvested using Trizol and purified with an RNA Clean & Concentrator-25 kit (Zymo, Tustin, CA, USA). RNA samples were submitted to Novogene (Novogene Corporation Ince., Sacramento, CA, USA) for quality control, library preparation, sequencing, and quantitation as per the in-house standard for gene expression analysis.
The library preparation, genome mapping, and raw gene counts for mRNA-sequencing analysis were performed by Novogene (Novogene America). The following methods were those provided by Novogene. Libraries generated for mRNA-sequencing were checked with Qubit and real-time (RT) PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina sequencing platforms (Illumina, Omaha, NE, USA) and clean data was obtained by using in-house Perl scripts from Novogene (Novogene America, Sacramento, CA, USA). Hisat2 (v2.0.5) was used to index and map reads to the human reference genome (GRCh38/hg38), and the mapped reads were assembled by StringTie (v1.3.3b) [22]. Read numbers mapped to each gene were counted in R using the FeatureCounts package (v1.5.0-p3) and an FPKM of each gene was calculated [23].

treatment_protocol: Cells were treated with either control media or endothelial cell-derived extracellular vesicles (ECEVs) in control media for 72h prior to RNA extraction.

value: Skin

value: primary

value: Dermal fibroblasts

value: ECEVs in exosome-depleted media


title: ECEV_72h_1

description: Library name: Sample 4


title: OF1_H3K27ac

description: Library name: OF1_H3K27ac


title: ECEV_72h_3

description: Library name: Sample 6


title: CTRL_72h_1

description: Library name: Sample 1

value: Exosome-depleted media


title: OM4_H3K27ac

description: Library name: OM4_H3K27ac


title: CTRL_72h_2

description: Library name: Sample 2


title: AIM T cells, VAC008, Channel 4, TCR

description:
Library name: VAC008_4_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript


title: CTRL_72h_3

description: Library name: Sample 3


title: OM2_H3K27ac

description: Library name: OM2_H3K27ac


title: OM3_H3K27ac

description: Library name: OM3_H3K27ac


title: PBMC, post heart transplantation [Library6]

city: La Jolla

first: Yuko

last: Tada

state: CA

address: 9500 Gilman Dr

institute: UC San Diego

description:
Library name: Library6
BD Rhapsody
Ab_raw.csv
Genes_raw.csv
Metadata.csv
Vdj_combined.csv

data_processing:
FASTQ files obtained from the sequencing were processed in the Seven Bridges Genomics pipeline (BD Biosciences).  R1 reads were annotated for cell labels and unique molecular identifiers (UMI). R2 reads were aligned to the reference panel sequences and annotated for mRNA, AbSeq and Sample tags. Reads with the same cell label, same UMI sequence, and same bioproduct were collapsed into a single raw molecule. After errors within the UMI were corrected and putative cells were identified, expression matrices of mRNA and antibody-derived tag (ADT) were obtained. Multiplets and undetermined cells were removed by the sample tag expression data. Low quality cells were removed by using the following thresholds: low numbers of genes per cell (<30), low numbers of UMIs per cell (<50), and the low complexity of RNA score (Log10 Genes per UMI < 0.60). Doublets were additionally removed using Doublet Finder (v2.0.3)
Assembly: 1900mRNAref_file_Immune_response_panel_and_100sup_genes.fasta | BDAbSeq_Ref_ImmuneDiscoveryPanel_and_additonal_antibodies.fasta
Supplementary files format and content: Genes_raw.csv, Ab_raw.csv, Metadata.csv, Vdj_combined.csv
Library strategy: CITE-seq

source_name: Blood

extract_protocol:
Peripheral blood samples were collected in Cell Preparation Tubes (BD Biosciences) and mononuclear cells were isolated by density gradient centrifugation. PBMCs were cryopreserved in the freezing media (5-10 million cells per tube; CryoStor CS10, STEMCELL technologies) and stored in liquid nitrogen until assay.  PBMCs were thawed in a 37°C water bath and contaminating red blood cells were lysed with red blood cell lysis buffer (eBioscience). After being washed, cells were suspended in Stain Buffer (BD Biosciences). After cells from each patient were tagged with the Single-Cell Multiplexing Kit (BD Biosciences), cells from different samples were combined for hash-tagging. Samples were adjusted to contain up to 1 million cells and, after Fc blocking, incubated with Abseq Ab-Oligos according to the manufacturer’s protocol. Abseq Ab-Oligos master mix was created by mixing the reconstituted AbSeq Immune discovery panel containing 30 antibodies (BD Biosciences) with 26 individual Abseq antibodies. After washing, single cells were loaded on the Rhapsody Cartridge (30,000 cells per cartridge). Cells were lysed and mRNA, Ab-Oligos, and Sample Tags were hybridized with the barcoded oligos on the cell beads.
Libraries of mRNA, Sample Tag, Abseq, and VDJ regions were prepared according to BD’s library preparation protocol (23-22204-00). Cell capture beads underwent template switching, Klenow extension, and exonuclease I treatment. Two-step nested amplification was performed and followed by an index PCR. PCR1 products were separated by double-sided AMPure bead purification into the shorter AbSeq and Sample Tag PCR products, and the longer targeted mRNA and VDJ PCR products. The AbSeq PCR1 product proceeded with index PCR. Targeted mRNA, VDJ, and Sample Tag PCR products underwent PCR2 amplification followed by index PCR. Quality of the final libraries were quantified using the Qubit dsDNA HS Kit and Agilent TapeStation high sensitivity D1000 screentape. mRNA, AbSeq, and SMK libraries were pooled together and sequenced by NovaSeq 6000 - S4 sequencer with 75 bp x 75 bp paired read. VDJ libraries were sequenced with the SP sequencer with 75 bp x 225 bp paired read. 400pM of the library was loaded, and 20-30% PhiX was included. Sequencing read depth was calculated by 1000 reads/Ab/cell for Abseq, 10000 reads per cell for mRNA, 1000-1200 reads per cell for sample tag, and 3000 reads per cell for VDJ.

value: Blood

value: post heart transplantation

value: PBMC

value: 4 patients


title: PBMC, post heart transplantation [Library5]

description:
Library name: Library5
BD Rhapsody
Ab_raw.csv
Genes_raw.csv
Metadata.csv
Vdj_combined.csv


title: OM1_H3K27ac

description: Library name: OM1_H3K27ac


title: PBMC, post heart transplantation [Library4]

description:
Library name: Library4
BD Rhapsody
Ab_raw.csv
Genes_raw.csv
Metadata.csv
Vdj_combined.csv


title: YF2_H3K27ac

description: Library name: YF2_H3K27ac


title: YF1_H3K27ac

description: Library name: YF1_H3K27ac


title: YM3_H3K27ac

description: Library name: YM3_H3K27ac


title: AIM T cells, VAC007, Channel 1, TCR

description:
Library name: VAC007_1_TCR
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

value: peripheral blood mononuclear cell

value: T cell


title: PBMC, post heart transplantation [Library2]

description:
Library name: Library2
BD Rhapsody
Ab_raw.csv
Genes_raw.csv
Metadata.csv
Vdj_combined.csv


title: OF2_H3K27ac

description: Library name: OF2_H3K27ac


title: YM1_H3K27ac

description: Library name: YM1_H3K27ac


title: GF1_H3K4me1

description: Library name: GF1_H3K4me1


title: GM1_H3K4me1

description: Library name: GM1_H3K4me1


title: Endometrial cells, P+5, 887

city: Hangzhou

first: Jiucheng

last: Chen

state: Zhejiang

address: No.866 Yuhangtang Road

institute: Zhejiang University

description: Library name: ERA0286

data_processing:
Use the fastp tool for quality control of sequencing data. Remove sequences with the following low-quality criteria: Sequences with unknown bases numbering 5 or more. Sequences with a length less than 75bp. Sequences with an average base quality value less than 15. The resulting data after this step is termed Clean Data.
Use the sortmerna tool to align the Clean Data against a ribosomal database. Exclude sequences that align to the ribosomal database. The data obtained after this step is termed de-rRNA Clean Data.
Use the STAR tool to align the de-rRNA Clean Data to the reference genome.
Use the RSeQC tool to assess the quality of the alignment results from STAR.
Use the featureCounts tool to quantify gene expression from the alignment results. Use the edgeR tool for differential gene expression analysis.
Assembly: hg19
Supplementary files format and content: tab-delimited rawcount files for each samples
Supplementary files format and content: tab-delimited FPKM files for each samples

source_name: endometrium tissue

growth_protocol: All endometrial biopsy samples were obtained with disposable uterine-cavity tissue-suction tubes (Runting), and all the collected samples were stored in All protect Tissue Reagent (QIAGEN). The samples were transported to our laboratory on ice packs and stored at -80°C before processing.

extract_protocol:
RNA was extracted from endometrial tissue using RNAprep Pure Tissue Kit (DP341; Tiangen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using a KAPA Stranded RNA-Seq Library Preparation Kit (KR0934, KAPA Biosystems), following the manufacturer’s instructions.

treatment_protocol: The estradiol administration of all patients was started from the second day of menstruation with 4 mg estradiol valerate (Progynova; Bayer, Leverkusen, Germany) per day. When endometrial thickness was at least 7 mm and endogenous progesterone level was less than 1.5 ng/ml, 90 mg progesterone sustained-release vaginal gel (Crinone; Merck-Serono, Darmstadt, Germany) was applied transvaginally per day. The initial day of progesterone administration was recognized as “P+0” and endometrial biopsies were respectively taken on days P+3, P+5, and P+7 for each patient by a dedicated physician.

value: endometrium tissue


title: Endometrial cells, P+7, 890

description: Library name: ERA0278


title: Oocytes isolated from encapsulated follicles cultured in 10 kPa dextran - replicate 3

city: Singapore

first: Chii Jou

last: Chan

address: 5A Engineering Drive 1

department: Mechanobiology Institute

country: Singapore

institute: National University of Singapore

description:
Library name: OO_Dex_3
Column name in salmon.merged.gene_counts_OO.txt: OO_Dex_3

data_processing:
Raw FASTQ files were processed using the nf-core/rnaseq pipeline, a standardized and reproducible bioinformatics workflow built using Nextflow.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Ovarian follicle

growth_protocol: Isolated ovarian follicles were encapsulated in alginate and grown for three days in MEM-αGlutamax + 10% fetal bovine serum (FBS) +1% PenStrep, supplemented with 1X Insulin-Transferrin-Selenium (ITS) and 50 mIU/ml Follicle Stimulating Hormone (FSH) under different treatments

extract_protocol:
We identified encapsulated follicles in the different culture conditions that grew beyond 180 µm and removed the alginate from them. Immediately after retrieval, the follicles were mechanically separated into oocytes and granulosa cells (GCs) within 5–10 minutes. While 1-2 oocytes were pooled together, a few hundred GCs were pooled into one sample set respectively. This was repeated individually for the different conditions to maintain similar levels of harvested RNA in each case. Each set of samples was promptly transferred into lysis buffer from the RNeasy Plus Micro Kit (Qiagen) and stored at –80 °C until RNA isolation. To minimize technical variability, RNA extraction was performed simultaneously for all biological replicates after the completion of all experiments.  Total RNA was extracted using the RNeasy Plus Micro Kit (Qiagen), following the manufacturer's instructions, and eluted in RNase-free water before being stored at –80 °C.
Sequence-ready libraries were prepared following the manufacturer’s instructions. Each sample utilized 8 µL of total RNA for cDNA synthesis, with cDNA amplification performed over 15 PCR cycles. Libraries were indexed using the NEBNext Multiplex Oligos for Illumina (NEB, E6440L)

treatment_protocol: The three treatments are control, Blebbistatin added to the medium (Blebb, 20 µM), and dextran added to the medium (Dex, 10 kPa)

value: Ovarian follicle

value: primary cells

value: Oocyte

value: WT

value: 10 kPa

value: Day 3


title: Endometrial cells, P+7, 887

description: Library name: ERA2101178


title: OF4_H3K4me1

description: Library name: OF4_H3K4me1

value: muscle

value: FISC/MuSC


title: OF3_H3K4me1

description: Library name: OF3_H3K4me1


title: Oocytes isolated from encapsulated follicles cultured in 10 kPa dextran - replicate 2

description:
Library name: OO_Dex_2
Column name in salmon.merged.gene_counts_OO.txt: OO_Dex_2


title: Oocytes isolated from encapsulated follicles cultured in 10 kPa dextran - replicate 1

description:
Library name: OO_Dex_1
Column name in salmon.merged.gene_counts_OO.txt: OO_Dex_1


title: OF1_H3K4me1

description: Library name: OF1_H3K4me1


title: OM5_H3K4me1

description: Library name: OM5_H3K4me1


title: Endometrial cells, P+3, 889

description: Library name: ERA2101184


title: Endometrial cells, P+5, 890

description: Library name: ERA2101186


title: PBMC, post heart transplantation [Library3]

description:
Library name: Library3
BD Rhapsody
Ab_raw.csv
Genes_raw.csv
Metadata.csv
Vdj_combined.csv


title: OF2_H3K4me1

description: Library name: OF2_H3K4me1


title: OM4_H3K4me1

description: Library name: OM4_H3K4me1


title: Oocytes isolated from encapsulated follicles cultured in control - replicate 4

description:
Library name: OO_Ctrl_4
Column name in salmon.merged.gene_counts_OO.txt: OO_Ctrl_4

value: Control


title: PBMC, post heart transplantation [Library1]

description:
Library name: Library1
BD Rhapsody
Ab_raw.csv
Genes_raw.csv
Metadata.csv
Vdj_combined.csv


title: YM2_H3K27ac

description: Library name: YM2_H3K27ac


title: Endometrial cells, P+7, 888

description: Library name: ERA2101081


title: OM2_H3K4me1

description: Library name: OM2_H3K4me1


title: GM2_H3K4me1

description: Library name: GM2_H3K4me1


title: Oocytes isolated from encapsulated follicles cultured in control - replicate 3

description:
Library name: OO_Ctrl_3
Column name in salmon.merged.gene_counts_OO.txt: OO_Ctrl_3


title: OM1_H3K4me1

description: Library name: OM1_H3K4me1


title: Endometrial cells, P+5, 886

description: Library name: ERA210419


title: Endometrial cells, P+3, 887

description: Library name: ERA0222


title: Oocytes isolated from encapsulated follicles cultured in 10 kPa dextran - replicate 4

description:
Library name: OO_Dex_4
Column name in salmon.merged.gene_counts_OO.txt: OO_Dex_4


title: Oocytes isolated from encapsulated follicles cultured in control - replicate 2

description:
Library name: OO_Ctrl_2
Column name in salmon.merged.gene_counts_OO.txt: OO_Ctrl_2


title: YF3_H3K4me1

description: Library name: YF3_H3K4me1


title: YF2_H3K4me1

description: Library name: YF2_H3K4me1


title: YF1_H3K4me1

description: Library name: YF1_H3K4me1


title: YM3_H3K4me1

description: Library name: YM3_H3K4me1


title: Endometrial cells, P+5, 884

description: Library name: ERA2101270


title: Oocytes isolated from encapsulated follicles cultured in control - replicate 1

description:
Library name: OO_Ctrl_1
Column name in salmon.merged.gene_counts_OO.txt: OO_Ctrl_1


title: Endometrial cells, P+7, 885

description: Library name: ERA2101316