title: ICH25

description:
Library name: sample 25
Hypertension with cerebral hemorrhage group (ICH group),rep25


title: POND-IGF2BP1_50ng_rep1

status: Public on Jun 24 2026

type: SRA

city: Beijing

first: Yangming

last: Wang

address: No.5 Yiheyuan Road, Haidian District

department: Institute of Molecular Medicine, College of Future Technology

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
The 150-bp paired-end sequencing reads were quality-checked by FastQC (v0.11.9) and processed using Trim Galore (v0.6.7) (https://github.com/FelixKrueger/TrimGalore) to eliminate low-quality reads and trim adapter sequences.
Processed reads were then aligned to the human genome (hg38) or mouse genome (mm10) combined with ERCC spike-in sequences (https://assets.thermofisher.cn/TFS-Assets/LSG/manuals/ERCC92.zip) by STAR (v2.7.10a) using the GENCODE (Human v40 or Mouse vM25) transcript annotation as transcriptome guide, with parameters: --outFilterMismatchNoverLmax 0.04.
The raw counts aligned to exonic regions were quantified by Subread featureCounts (v2.0.1).
For RBP POND-seq data, raw counts were normalized to counts per million (CPM) using ERCC spike-ins, and RBP targets were defined as transcripts with CPM >= 50, log2foldchange > 2, and adjusted P-value < 0.05 in RBP-POND versus control (EPN24 or EPN24-GFP) samples by DESeq2 (v1.36.0).
The POND-seq data for mutated RBPs were also quantified using absolute quantification based on ERCC spike-in controls. The total CPM of wild-type RBP-POND were set to 1,000,000, and the CPM of mutated RBPs-POND were calculated relative to that of wild-type RBP. For transcriptome analysis with PABPC1-POND-seq and RNA-seq, raw counts were normalized to transcripts per million (TPM) as gene expression level.
Assembly: GRCh38; mm10
Supplementary files format and content: tab-delimited text files include rawCounts, csv files include DESeq2 results

molecule: cytoplasmic RNA

organism: Homo sapiens

source_name: HEK293T cell line

growth_protocol: HEK293T, Huh-7, and A549 cells were cultured at 37°C under 5% CO2 in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM, Hyclone) supplemented with 10% FBS (PANSera), penicillin (100 U/ml) and streptomycin (100 µg/ml). V6.5 mouse ESCs were grown on gelatin-coated dish at 37°C under 5% CO2, in KnockOutTM DMEM (Gibco) supplemented with 15% FBS (Hyclone), nonessential amino acids, 2-mercaptoethanol, and 1,000 units/ml lymphocyte inhibitory factor. H1 Human ESCs were grown in mTeSRTM (STEMCELL Technologies) on Matrigel-coated dish at 37°C under 5% CO2.

extract_protocol:
Cell supernatant was clariﬁed by centrifugation at 3,000 g for 5 minutes, then filtrated through a cellulose acetate ﬁlter with 0.45 μm pore size (Corning). 200 μl of supernatant was mixed with 800 μl TRIzol reagent (Magen) and 1 μl diluted External RNA Controls Consortium (ERCC) synthetic spike-in RNAs (ThermoFisher). RNA was extracted and dissolved in 15-20 μl nuclease-free water.
For POND-seq, 5 μl RNA was used for library construction with modified VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme). Typically, 5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) for fragmentation at 85℃ for 6 min. For ribosomal depletion, 5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) and 0.7 μl FastSelect reagent (Vazyme) for fragmentation at 85℃ for 6 min. Then 8 μl fragmentated RNA was used for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification (16-18 cycles) according to the manufacture’s instruction manual. The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on Illumina NovaSeq 6000 (Novogene, China) or DNBSEQ-T7 platform (GenePlus, China). For FMR1 mutation screening, library construction was completed with VNL-96P (Vazyme) automated library preparation workstation. Briefly, 4 μl RNA was mixed with 4 μl 2×Prime buffer V2 (Vazyme) and 1 μl FastSelect reagent (Vazyme) for fragmentation at 85°C for 6 min. Then 8 μl fragmentated RNA was adopted for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification (17 cycles) according to VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme). The NGS sequencing was performed on DNBSEQ-T7 platform (GenePlus). For cellular RNA-seq, the total RNA of HEK293T, Huh-7 and A549 were extracted with TRIzol reagent (Magen) and dissolved in nuclease-free water. 500 ng total RNA was used for library construction with VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme). The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on Illumina NovaSeq 6000 (Novogene) or DNBSEQ-T7 platform (GenePlus).

tag: cell line

value: HEK293T cell line

tag: genotype

tag: treatment


title: ICH24

city: shanghai

first: Zuopeng

last: Su

address: 170 Xinsong Road, Xinzhuang Town, Minhang District,

department: Department of Neurosurgery,

institute: Minhang Hospital, Fudan University

description:
Library name: sample 24
Hypertension with cerebral hemorrhage group (ICH group),rep24

data_processing:
The raw reads were preprocessed and filtered using Trimmomatic  with the following steps:Removal of P7 and P5 adapter sequences (sequences provided above),trimming of bases with quality scores <20,discarding reads shorter than 50 bp and singleton reads.
Clean reads after quality control were aligned to the reference genome GRCh38.p13 using HISAT2 to acquire mapping positions.
Alignment outputs from HISAT2 were analyzed using htseq-count (v0.6.0)  to quantify read counts per transcript.
Alternative splice events that occurred in the samples were identified by Multivariate Analysis of Transcript Splicing (MATS, http://rnaseq-mats.sourceforge.net/).
Assembly: GRCh38
Supplementary files format and content: expression.xlsx

molecule: total RNA

source_name: Peripheral Blood

extract_protocol:
RNA was harvested using TIANSeq mRNA Capture Kit (TIANGEN Biotech).
Libraries were constructed using the TIANSeq Fast RNA Library Prep Kit for Illumina (TIANGEN Biotech).

tag: tissue

value: Peripheral Blood

tag: cell type

value: Peripheral Blood Mononuclear Cells

tag: sample group


title: POND-IGF2BP1-WT_rep-1


title: Cnt0hS2

city: Berkeley

first: Sharon

last: Greenblum

state: CA

address: 1 Cyclotron Road

country: USA

institute: DOE Joint Genome Institute

description: Library name: NSWHP

data_processing:
raw data are paired-end interleaved fastq files
BBTools v38.96 bbduk.sh was used to filter raw reads for 1) removal of artifact sequence, RNA spike-in reads, PhiX reads, and reads containing any N, 2) quality trimming with method set at Q6, and 3) removal of reads with <50 bases
Filtered reads from each library were aligned to the A. thaliana TAIR10 reference genome using HISAT2 v2.2.1127
featureCounts was used to generate raw gene counts using Araport 11 gene annotations. Only primary hits assigned to the reverse strand were included (-s 2 -p --primary options)
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: counts.txt: tab-separated matrix containing read counts for each gene (rows) in each library (columns)

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: shoot

growth_protocol: seeds were sterilized, then planted on nylon mesh in agar plates containing 3mM Ca(NO3)2, 1.5mM MgSO4, 1.25mM NH4H2PO4, 1mM KCl, and 1x micronutrients (Murashige and Skoog Micronutrient Salts 100x, MSP18-10LT), in 0.8% agar with pH 5.7. Seeds were sown on plates at a density of 3 rows per plate with ~30 plants per row and plates were placed vertically in a growth chamber under conditions of 16 h light at 22°C, 8 h dark at 19°C

extract_protocol:
mRNA was isolated from an input of 1000 ng of total RNA with oligo dT magnetic beads and fragmented to 300 bp - 400 bp with divalent cations at a high temperature.
Using TruSeq stranded mRNA kit (Illumina), the fragmented mRNA was reverse transcribed to create the first strand of cDNA with random hexamers and SuperScript II Reverse Transcriptase (Thermo Fisher Scientific) followed by second strand synthesis. The double stranded cDNA fragments were treated with A-tailing, ligation with NEXTFLEX UDI Barcodes (PerkinElmer) and enriched using 8.0 cycles of PCR. Sequencing was performed on an Illumina NovaSeq 6000 S4 flow cell, using 2x150 bp paired-end sequencing.

treatment_protocol: On the 5th day, the nylon mesh and plants were transferred using forceps to agar plates containing either 2 μM ABA, 150 μM SA, or the standard growth medium without added hormones as a negative control. Samples were collected at time points of 0, 1, 2, 4, 7, 24, and 48 hours, separating root and shoot tissues with a single razor blade cut at the time of collection.

value: shoot

tag: strain

value: control

tag: timepoint

tag: replicate


title: POND-IGF2BP1-WT_rep-2


title: Cnt0hS4

description: Library name: NSWHT


title: POND-IGF2BP1_72H_rep2


title: POND-GFP_rep-2


title: POND-IGF2BP1_72H_rep1


title: ICH23

description:
Library name: sample 23
Hypertension with cerebral hemorrhage group (ICH group),rep23


title: Cnt0hS3

description: Library name: NSWHS


title: ICH22

description:
Library name: sample 22
Hypertension with cerebral hemorrhage group (ICH group),rep22


title: POND-GFP_rep-1


title: Cnt0hR4

description: Library name: NSWHY

source_name: root

value: root


title: RNA-seq_293T-PABPC1-POND_celllysate_rep-2


title: ICH21

description:
Library name: sample 21
Hypertension with cerebral hemorrhage group (ICH group),rep21


title: POND-IGF2BP1_48H_rep2


title: ICH20

description:
Library name: sample 20
Hypertension with cerebral hemorrhage group (ICH group),rep20


title: POND-IGF2BP1_48H_rep1


title: Cnt0hS1

description: Library name: NSWHO


title: RNA-seq_293T-PABPC1-POND_celllysate_rep-1


title: POND-IGF2BP1_36H_rep2


title: PABPC1-POND-A549_NoDNASE_rep-2

source_name: A549 cell line

value: A549 cell line


title: ICH18

description:
Library name: sample 18
Hypertension with cerebral hemorrhage group (ICH group),rep18


title: POND-IGF2BP1_24H_rep2


title: PABPC1-POND-A549_NoDNASE_rep-1


title: PABPC1-POND-Huh7_NoDNASE_rep-2

source_name: Huh-7 cell line

value: Huh-7 cell line


title: ICH17

description:
Library name: sample 17
Hypertension with cerebral hemorrhage group (ICH group),rep17


title: ABA7hS2

description: Library name: NTGPS

value: ABA


title: POND-IGF2BP1_36H_rep1


title: ICH16

description:
Library name: sample 16
Hypertension with cerebral hemorrhage group (ICH group),rep16


title: POND-IGF2BP1_24H_rep1


title: POND-IGF2BP1_16H_rep2


title: ICH15

description:
Library name: sample 15
Hypertension with cerebral hemorrhage group (ICH group),rep15


title: ABA7hS1

description: Library name: NTGPP


title: PABPC1-POND-293T_NoDNASE_rep-2


title: ABA7hR3

description: Library name: NTGSG


title: ICH14

description:
Library name: sample 14
Hypertension with cerebral hemorrhage group (ICH group),rep14


title: PABPC1-POND-293T_NoDNASE_rep-1


title: ABA7hR2

description: Library name: NTGSC


title: POND-IGF2BP1_8H_rep2


title: ICH13

description:
Library name: sample 13
Hypertension with cerebral hemorrhage group (ICH group),rep13


title: ABA7hR1

description: Library name: NTGSB


title: hBD3-POND-293T_rep-2


title: POND-IGF2BP1_8H_rep1


title: ICH12

description:
Library name: sample 12
Hypertension with cerebral hemorrhage group (ICH group),rep12


title: ABA4hS2

description: Library name: NTGON


title: POND-GFP_48H_rep2


title: ABA4hS3

description: Library name: NTGOO


title: POND-GFP_48H_rep1


title: ICH10

description:
Library name: sample 10
Hypertension with cerebral hemorrhage group (ICH group),rep10


title: ICH9

description:
Library name: sample 9
Hypertension with cerebral hemorrhage group (ICH group),rep9


title: POND-hLIN28A_hESC_rep-2

source_name: H1 human embryonic stem cells

value: H1 human embryonic stem cells


title: ABA4hR2

description: Library name: NTGOZ


title: ABA4hS1

description: Library name: NTGOH


title: hnrnpa1 KO 2, 30 hpf

city: Munich

first: Bettina

last: Schmid

address: Feodor-Lynen-Str. 17

country: Germany

institute: DZNE

description: Library name: MUC5479

data_processing:
The STAR aligner (v 2.4.2a) (Dobin et al.,2013) with default parameter settings (except one: -twopassMode =Basic) was used for split-read alignment against the zebrafish genome assembly GRCz11 (Ensembl release 91) and Ensembl gene annotation (both downloaded from Ensembl).
To quantify the number of reads mapping to annotated genes we use HTSeq-count (v0.6.0) with default parameter settings (Anders et al., 2015).
FPKM (Fragments Per Kilobase of transcript per Million fragments mapped) values are calculated using custom scripts. The output of HTSeq-count was then used as input for the R Bioconductor package DESeq2 (Love et al., 2014) which was used for differential expression analysis following the standard workflow (https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html).
Assembly: zebrafish genome assembly GRCz11 (Ensembl release 91)
Supplementary files format and content: tab-delimited text files includes raw counts for each sample
Supplementary files format and content: all.fpkms.xlsx

organism: Danio rerio

source_name: whole larvae

growth_protocol: at 28°C in E3 medium

extract_protocol:
RNA was isolated from whole-cell lysates using the AllPrep RNA Kit (Qiagen)
1 ug of RNA was poly(A) selected, fragmented, and reverse transcribed with the Elute, Prime, Fragment Mix (Illumina). End repair, A-tailing, adaptor ligation, and library enrichment were performed as described in the Low Throughput protocol of the TruSeq RNA Sample Prep Guide (Illumina).

treatment_protocol: comparison of hnrnpa1 knockout versus wildtype control

value: whole larvae

tag: developmental stage

value: embryo 30hpf

value: hnrnpa1 knockout


title: ICH7

description:
Library name: sample 7
Hypertension with cerebral hemorrhage group (ICH group),rep7


title: hnrnpa1 KO 1, 30 hpf

description: Library name: MUC5477


title: ABA4hR1

description: Library name: NTGOY


title: wildtype3, 30 hpf

description: Library name: MUC5476

value: WT


title: POND-EPN_forPUM2&YTHDF2_rep-1


title: ABA48hS1

description: Library name: NTPTO


title: wildtype2, 30 hpf

description: Library name: MUC5475


title: POND-PUM2_rep-2


title: ABA48hS3

description: Library name: NTPTS


title: wildtype1, 30 hpf

description: Library name: MUC5473


title: POND-PUM2_rep-1


title: ICH4

description:
Library name: sample 4
Hypertension with cerebral hemorrhage group (ICH group),rep4


title: POND-IGF2BP1_16H_rep1


title: W114_PBMC_G4_HTO

city: La Jolla

first: Patrick

last: Madden

address: 9420 Athena Circle

department: Center for Vaccine Innovation

institute: La Jolla Institute for Immunology

description:
Library name: W114_PBMC_G4_HTO
HTO 5' mRNA library
W114_PBMC_G4_barcodes.tsv.gz
W114_PBMC_G4_features.tsv.gz
W114_PBMC_G4_matrix.mtx.gz

library_source: other

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.2 (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Fasta files, Tab-separated values files and matrix files
Library strategy: CITE-seq

molecule: protein

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
N332-GT5 epitope-specific B cells were isolated from peripheral blood samples collected from rhesus macaques immunized with N332-GT5 and subsequent heterologous boost immunizations. Probes for each boost immunogen were included in flow cytometry staining for each respective Group, allowing determination of the proportion of N332-GT5 epitope-specific cells cross-binding the boost immunogen (N332-GT5++KO– Boost++). Thawed cells were incubated with both N332-GT5 KO and Boost KO probes for twenty minutes at 4°C. Following that, cells were sequentially incubated with the combined Booster WT probes for fifteen minutes at 4°C and then with the combined N332-GT5 WT probes for thirty minutes at 4°C. A master mix of surface staining antibodies was added next, with 2 μg per 5 million cells of anti-human Total-Seq-C hashtag antibodies (Biolegend) following the surface staining, and incubated for thirty minutes at 4°C. Cells were then washed twice and prepared for sorting on BD FACSymphony S6 (BD Biosciences). Epitope-specific B cells were sorted at all time points.Once sorted, epitope-specific PBMC and LN FNA B cells were washed with PBS and loaded onto a Chromium chip and controller following the manufacturers protocol (10X Genomics). Indexed V(D)J, Feature Barcode, and Gene Expression libraries were prepared following the 10X Genomics protocol with the Feature Barcoding Kit (10X Genomics) and sequenced on a NovaSeq 6000 (Illumina).
Libraries were constructed according to the manufacturer's protocol using the Chromium Next GEM Single Cell 5’ Reagent Kit v3.

value: PBMC

value: B cells

value: Protein immunized


title: POND-EPN24_rep2

value: HEK293T cell line


title: ICH3

description:
Library name: sample 3
Hypertension with cerebral hemorrhage group (ICH group),rep3

value: Peripheral Blood


title: POND-EPN_hESC_rep-2


title: ABA48hR2

description: Library name: NTPUB


title: POND-EPN_hESC_rep-1


title: W114_PBMC_G4_GEX

description:
Library name: W114_PBMC_G4_GEX
GEX 5' mRNA library
W114_PBMC_G4_barcodes.tsv.gz
W114_PBMC_G4_features.tsv.gz
W114_PBMC_G4_matrix.mtx.gz

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.2 (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Fasta files, Tab-separated values files and matrix files


title: ICH2

description:
Library name: sample 2
Hypertension with cerebral hemorrhage group (ICH group),rep2

value: Peripheral Blood Mononuclear Cells


title: POND-EPN24_rep1


title: ICH8

description:
Library name: sample 8
Hypertension with cerebral hemorrhage group (ICH group),rep8


city: Frankfurt am Main

first: Josep

last: Biayna Rodriguez

state: Hessen

address: Theodor-Stern-Kai 7

institute: Institute of Cardiovascular Regeneration

description:
Library name: Lib_NUCA_UT
RNA-seq of GM25256 iPSC nuclear fraction untreated Sample A

data_processing:
VAST-TOOLS
Raw RNA-seq reads were processed for alternative splicing and expression analysis using vast-tools, version 2.5.1 (Tapial et al., (2017)), which is available on github (https://github.com/vastgroup/vast-tools).
Assembly: Human (GRCm38)
Supplementary files format and content: iPS_ActD_INCLUSION_LEVELS_FULL-hg38-16 are primary vast-tools output files for human IPS cells samples in tab-delimited format

molecule: nuclear RNA

growth_protocol: hiPSCs WTC-11 (Coriell Institute) were cultured on Vitronectin (Thermo Fisher Scientific) coated plates or 18 mm round glass coverslips (for smRNA FISH and IF) in StemFlex basal medium (Thermo Fisher Scientific) with StemFlex supplement (Thermo Fisher Scientific), RevitaCell supplement with Rock inhibitor (Thermo Fisher Scientific) and 2.5% penicillin-streptomycin

extract_protocol:
hiPSCs were rinsed twice with ice-cold PBS, scraped, and centrifuged at 500 g for 5’. Cell pellets were lysed with 175 μl/106 cells of ice-cold lysis buffer (50 mM Tris-HCl pH 8.0, 140 mM NaCl, 1.5 mM MgCl2, 0.5% NP-40, 1:200 dilution of 20 U/μL SUPERase RNase inhibitor), and incubated on ice for 10’. The lysate was centrifuged at 300 g for 3’ at 4°C to pellet the nuclei and the supernatant was collected as the cytoplasmic fraction. Finally, the nuclear and the cytoplasmic fractions were processed for RNA extraction as described below. The efficiency of RNA fractionation was assessed by quantitative polymerase chain reaction (qPCR) using GAPDH as a marker for the cytoplasm fraction, 45s rRNA for the nuclear fraction
The quantity, quality and integrity of the RNA samples were assessed using Bioanalyzer 5400 (Agilent Technologies, USA). After isolation, RNA was sent to Novogene for sequencing. Briefly, poly(A) RNA was enrichmed with oligo d(T) magnetic beads. Subsequently, RNA was randomly fragmented, and cDNA synthesis proceeds through the use of random hexamers and the reverse transcriptase enzyme. After purification, the resulting products followed end-repair, A-tailing and adapter ligation steps. Fragments of the appropriate size were enriched by PCR, where indexed P5 and P7 primers were introduced, and final products were purified. The library was checked with Qubit 2.0 and real-time PCR for quantification and bioanalyzer Agilent 5400 for size distribution detection. Quantified libraries were pooled and sequenced on Illumina Novaseq 6000/Novaseq X Plus platforms. The qualified libraries were sequenced Next Generation Sequencing (NGS) based on Illumina's Sequencing Technology by Synthesis (SBS)- detection by fluorescence of the nucleotide added during the synthesis of the complementary chain - and in a parallelized and massive way. The Novaseq6000/Novaseq X Plus sequencing systems were used to sequence the libraries. The strategy was paired-end 150bp.

treatment_protocol: Actinomycin D (ActD, Sigma-Aldrich) was used at a final concentration of 5 μg/mL in complete growth media. Cell pellets and coverslips were harvested at 0 h, 0.5 h, 2 h and 4.5 h after adding ActD

tag: biomaterial provider

value: hiPSCs

value: untreated

tag: batch


title: W114_PBMC_G4_VDJ

description:
Library name: W114_PBMC_G4_VDJ
VDJ 5' mRNA library

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.2 (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Fasta files, Tab-separated values files and matrix files
Library strategy: BCR-Seq


title: ABA4hR3

description: Library name: NTGPA

value: root


title: ICH1

description:
Library name: sample 1
Hypertension with cerebral hemorrhage group (ICH group),rep1


title: POND-G3BP1_rep2


title: ABA48hR1

description: Library name: NTPUA


title: W114_PBMC_G3_HTO

description:
Library name: W114_PBMC_G3_HTO
HTO 5' mRNA library
W114_PBMC_G3_barcodes.tsv.gz
W114_PBMC_G3_features.tsv.gz
W114_PBMC_G3_matrix.mtx.gz


description:
Library name: Lib_NUCA_30
RNA-seq of GM25256 iPSC nuclear fraction 30 min Sample A

value: ActD 30 min


title: VisiumHD Spatial transcriptomics SLV18

city: New York

first: Lingting

last: Shi

address: 500 West 120th Street ET351

institute: Columbia University

description:
Library name: SLV18
10X genomics

data_processing:
Raw sequencing data for each sample were processed using the 10x Genomics Cell Ranger or Space Ranger pipeline.
Assembly: GRCh38-2020
Supplementary files format and content: h5ad files for processed RNA Seq data
Supplementary files format and content: csv for processed sc-TCR data
Supplementary files format and content: json for processed sc-TCR data

source_name: gut

extract_protocol:
Gut biopsies were processed to isolate single-cell intraepithelial and lamina propria lymphocytes using sequential buffer treatments and enzymatic digestion. Fresh-frozen GI tissue sections were cryosectioned, stained, and imaged (see Methods section of the manuscript for further details).
CD45⁺ cells were enriched by magnetic selection or sorting. Single-cell RNA and TCR libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 5′ Kit v2, following manufacturer protocols. RNA capture, cDNA synthesis, and library construction were performed on-slide according to the Visium Spatial Gene Expression protocol (VisiumHD, see Methods section of the manuscript for further details).

value: gut


title: POND-G3BP1_rep1


title: ABA2hS1

description: Library name: NSWTS

value: shoot

value: ABA


title: POND-GFP_+ribodel_rep2


title: VisiumHD Spatial transcriptomics SLV17

description:
Library name: SLV17
10X genomics


title: ABA2hS3

description: Library name: NSWTU


title: VisiumHD Spatial transcriptomics SLV16

description:
Library name: SLV16
10X genomics


title: POND-GFP_+ribodel_rep1


title: ABA2hS2

description: Library name: NSWTT


title: W114_PBMC_G2_HTO

description:
Library name: W114_PBMC_G2_HTO
HTO 5' mRNA library
W114_PBMC_G2_barcodes.tsv.gz
W114_PBMC_G2_features.tsv.gz
W114_PBMC_G2_matrix.mtx.gz


title: VisiumHD Spatial transcriptomics SLV15

description:
Library name: SLV15
10X genomics


title: W114_PBMC_G2_GEX

description:
Library name: W114_PBMC_G2_GEX
GEX 5' mRNA library
W114_PBMC_G2_barcodes.tsv.gz
W114_PBMC_G2_features.tsv.gz
W114_PBMC_G2_matrix.mtx.gz


title: VisiumHD Spatial transcriptomics SLV14

description:
Library name: SLV14
10X genomics


title: ABA2hR2

description: Library name: NTGNW


title: W114_PBMC_G2_VDJ

description:
Library name: W114_PBMC_G2_VDJ
VDJ 5' mRNA library


title: POND-GFP_-ribodel_rep2


title: W95_PBMC_G4_HTO

description:
Library name: W95_PBMC_G4_HTO
HTO 5' mRNA library
W95_PBMC_G4_barcodes.tsv.gz
W95_PBMC_G4_features.tsv.gz
W95_PBMC_G4_matrix.mtx.gz


title: VisiumHD Spatial transcriptomics SLV12

description:
Library name: SLV12
10X genomics


title: ABA24hS3

description: Library name: NTGWA


title: preLSC, WT, rep4

city: Edinburgh

first: Yuka

last: Kabayama

address: Max Born Crescent

country: United Kingdom

institute: University of Edinburgh

description: Library name: Control_4

data_processing:
Adapter was removed using cutadapt (1.17),
Trimmed reads were mapped to GRCm38 genome_tran (release 84) with HISAT2 (2.1.0).
Mapped reads per gene were counted with htseq-count (HTSeq 0.11.1).
Differentially expressed genes were analysed using DESeq2.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file which contains ensemble gene ID and raw read count.

organism: Mus musculus

source_name: preleukemic cells

growth_protocol: Meis1/Hoxa9 preleukemic cells were cultured at 200,000 cells/mL in IMDM supplemented with 10% FBS, Stem Cell Factor (40 ng/mL), IL-6 (20 ng/mL), IL-3 (20 ng/mL), Penicillin and Streptomycin, 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted using QIAzol and teated with DNase I following QIAGEN RNA mini extraction kit's instructions.
Libraries were prepared from 1 ug of total RNA using the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB, cat. no. E7760) with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB, cat. no. E6310) following the manufacture’s protocol. Eight cycles of PCR was performed to amplify libraries and the pooled library was sequenced on Illumina NextSeq 550 with 85 bp single-end.

value: preleukemic cells

value: Control


title: VisiumHD Spatial transcriptomics SLV11

description:
Library name: SLV11
10X genomics


title: ABA48hR3

description: Library name: NTPUC


title: ABA24hS2

description: Library name: NTGUZ


title: W114_PBMC_G3_GEX

description:
Library name: W114_PBMC_G3_GEX
GEX 5' mRNA library
W114_PBMC_G3_barcodes.tsv.gz
W114_PBMC_G3_features.tsv.gz
W114_PBMC_G3_matrix.mtx.gz


title: W95_PBMC_G4_VDJ

description:
Library name: W95_PBMC_G4_VDJ
VDJ 5' mRNA library


title: W114_PBMC_G3_VDJ

description:
Library name: W114_PBMC_G3_VDJ
VDJ 5' mRNA library


title: POND-IGF2BP1_-ribodel_rep2


title: UA41 TCR-seq

description:
Library name: UA41_TCR
10X genomics

data_processing:
Raw sequencing data for each sample were processed using the 10x Genomics Cell Ranger or Space Ranger pipeline.
Assembly: GRCh38-2020
Supplementary files format and content: h5ad files for processed RNA Seq data
Supplementary files format and content: csv for processed sc-TCR data
Supplementary files format and content: json for processed sc-TCR data
Library strategy: TCR-Seq

molecule: other


title: POND-IGF2BP1_-ribodel_rep1


title: POND-IGF2BP1_+ribodel_rep2


title: ABA2hR3

description: Library name: NTGNX


title: ABA24hS1

description: Library name: NTGUY


title: POND-IGF2BP1_+ribodel_rep1


title: W95_PBMC_G3_HTO

description:
Library name: W95_PBMC_G3_HTO
HTO 5' mRNA library
W95_PBMC_G3_barcodes.tsv.gz
W95_PBMC_G3_features.tsv.gz
W95_PBMC_G3_matrix.mtx.gz


title: UA41 RNA-seq

description:
Library name: UA41_GEX
10X genomics


title: POND-GFP_500ng_rep2


title: ABA24hR2

description: Library name: NTGWS


title: W95_PBMC_G3_GEX

description:
Library name: W95_PBMC_G3_GEX
GEX 5' mRNA library
W95_PBMC_G3_barcodes.tsv.gz
W95_PBMC_G3_features.tsv.gz
W95_PBMC_G3_matrix.mtx.gz


title: UA40 TCR-seq

description:
Library name: UA40_TCR
10X genomics


title: POND-GFP_500ng_rep1


title: VisiumHD Spatial transcriptomics SLV13

description:
Library name: SLV13
10X genomics


title: ABA24hR3

description: Library name: NTGWT


title: ABA2hR1

description: Library name: NTGNU


title: UA40 RNA-seq

description:
Library name: UA40_GEX
10X genomics


title: W95_PBMC_G3_VDJ

description:
Library name: W95_PBMC_G3_VDJ
VDJ 5' mRNA library


title: POND-IGF2BP1_500ng_rep2


title: ABA24hR1

description: Library name: NTGWP


title: W95_PBMC_G2_HTO

description:
Library name: W95_PBMC_G2_HTO
HTO 5' mRNA library
W95_PBMC_G2_barcodes.tsv.gz
W95_PBMC_G2_features.tsv.gz
W95_PBMC_G2_matrix.mtx.gz


title: UA39 TCR-seq

description:
Library name: UA39_TCR
10X genomics


title: POND-IGF2BP1_500ng_rep1


title: ABA1hS2

description: Library name: NSWNG


title: W95_PBMC_G2_GEX

description:
Library name: W95_PBMC_G2_GEX
GEX 5' mRNA library
W95_PBMC_G2_barcodes.tsv.gz
W95_PBMC_G2_features.tsv.gz
W95_PBMC_G2_matrix.mtx.gz


title: POND-SLBP_rep2


title: UA39 RNA-seq

description:
Library name: UA39_GEX
10X genomics


title: ABA1hS1

description: Library name: NSWNC


title: POND-GFP_-ribodel_rep1


title: W95_PBMC_G2_VDJ

description:
Library name: W95_PBMC_G2_VDJ
VDJ 5' mRNA library


title: UA38 TCR-seq

description:
Library name: UA38_TCR
10X genomics


title: POND-SLBP_rep1


title: ABA1hS3

description: Library name: NSWNH


title: UA38 RNA-seq

description:
Library name: UA38_GEX
10X genomics


title: W83_FNA_G4_HTO

description:
Library name: W83_FNA_G4_HTO
HTO 5' mRNA library

source_name: LN FNA

extract_protocol:
N332-GT5 epitope-specific B cells were isolated from peripheral blood samples collected from rhesus macaques immunized with N332-GT5 and subsequent heterologous boost immunizations. Probes for each boost immunogen were included in flow cytometry staining for each respective Group, allowing determination of the proportion of N332-GT5 epitope-specific cells cross-binding the boost immunogen (N332-GT5++KO– Boost++). Thawed cells were incubated with both N332-GT5 KO and Boost KO probes for twenty minutes at 4°C. Following that, cells were sequentially incubated with the combined Booster WT probes for fifteen minutes at 4°C and then with the combined N332-GT5 WT probes for thirty minutes at 4°C. A master mix of surface staining antibodies was added next, with 2 μg per 5 million cells of anti-human Total-Seq-C hashtag antibodies (Biolegend) following the surface staining, and incubated for thirty minutes at 4°C. Cells were then washed twice and prepared for sorting on BD FACSymphony S6 (BD Biosciences). Epitope-specific B cells were sorted at all time points.Once sorted, epitope-specific PBMC and LN FNA B cells were washed with PBS and loaded onto a Chromium chip and controller following the manufacturers protocol (10X Genomics).  Indexed V(D)J, Feature Barcode, and Gene Expression libraries were prepared following the 10X Genomics protocol with the Feature Barcoding Kit (10X Genomics) and sequenced on a NovaSeq 6000 (Illumina).
Libraries were constructed according to the manufacturer's protocol using the Chromium Next GEM Single Cell 5’ Reagent Kit v3.

value: LN FNA


title: ABA1hR3

description: Library name: NSWTB


title: RBPJ_ChIP_RBPJKO_Input

city: Philadelphia

first: Tobias

last: Friedrich

state: Pennsylvania

address: 421 Curie Boulevard

institute: University of Pennsylvania

description: Library name: RBPJ_ChIP_RBPJKO_Input

library_source: genomic

data_processing:
The fastq files were against hg19 aligned using Hisat2 v.2.2.1
Duplicated reads were removed using Picard tools.
bigWig files were generated using bamCoverage.
MACS2 was used for peak calling.
Assembly: hg19
Supplementary files format and content: Normalized coverage as bigwig files and RBPJ peaks called with MACS2.

molecule: genomic DNA

growth_protocol: Human H1299 cells were grown at 37°C with 5% CO2 in RPMI-1640 medium (Gibco 61870) supplemented with 10% FCS and penicillin/streptomycin.

extract_protocol:
ChIP was done essentially as previously described (Giaimo et al. Jove 2017, doi:  10.3791/55907).
Lybrary-prep kit for ChIP-Seq: Diagenode MicropPlex Library Preparation kit v2 (C05010012).

treatment_protocol: Human H1299 cells were treated for 12  hours with 20 uM or with DMSO as control. Human H1299 cells depleted of RBPJ were generated using the CRISPR/Ca9 technology.

value: Carcinoma; Non-small cell lung cancer     Large cell carcinoma subtype

value: sgRNA RBPJ


title: W83_FNA_G4_GEX

description:
Library name: W83_FNA_G4_GEX
GEX 5' mRNA library

value: B cells


title: UA37 TCR-seq

description:
Library name: UA37_TCR
10X genomics


title: RBPJ_ChIP_RBPJKO_2

description: Library name: RBPJ_ChIP_RBPJKO_2


title: ABA1hR2

description: Library name: NSWTA


title: UA37 RNA-seq

description:
Library name: UA37_GEX
10X genomics


title: W83_FNA_G4_VDJ

description:
Library name: W83_FNA_G4_VDJ
VDJ 5' mRNA library

value: Protein immunized


title: ABA1hR1

description: Library name: NSWSZ


title: RBPJ_ChIP_RBPJKO_1

description: Library name: RBPJ_ChIP_RBPJKO_1


title: W83_FNA_G3_HTO

description:
Library name: W83_FNA_G3_HTO
HTO 5' mRNA library


title: UA36 TCR-seq

description:
Library name: UA36_TCR
10X genomics


title: RBPJ_ChIP_ev_Input

description: Library name: RBPJ_ChIP_ev_Input

value: sgRNA control


title: 10X_replicate2

city: Ghent

first: Bert

last: De Rybel

address: Technologiepark 71

department: Center for Plant Systems Biology

country: Belgium

institute: VIB

description:
Library name: 10X_replicate2
10X Genomics 3' v3.1

data_processing:
Read alignment + counting; STARsolo v2.7.11a
Assembly: TAIR10
Supplementary files format and content: zip file of raw count matrix
Supplementary files format and content: zip file of filtered count matrix
Supplementary files format and content: Merged Seurat file in .rds format

growth_protocol: Arabidopsis thaliana ecotypes Columbia-0 (Col-0) and Landsberg erecta-0 (Ler-0) were used for protoplast isolation and single cell transcriptomics. Seeds were surface-sterilized and germinated on ½MS (Murashige and Skoog, Duchefa) medium after 2 d stratification at 4 °C. Seedlings were grown at 22 °C in continuous light conditions.

extract_protocol:
Root tips (0.5 cm) from 6-day-old Arabidopsis seedlings were used for protoplast isolation, adapted from Wendrich et al. (2020). Briefly, root tips were incubated in digestion buffer (0.4 M mannitol, 20 mM KCl, 20 mM MES, 10 mM CaCl2, 1.5% Cellulase YC, 0.1% Pectolyase, pH 5.6) for 60 minutes at room temperature with gentle agitation (30 rpm). The resulting digestion mixture was filtered (70 μm cell strainer), and protoplasts were collected by centrifugation (250 g, 6 minutes, room temperature). Protoplasts were then resuspended in 350 μL wash buffer (0.4 M mannitol, 20 mM KCl, 20 mM MES, 10 mM CaCl2, pH 5.6). For single-cell RNA sequencing (scRNA-seq), cell viability was assessed by adding propidium iodide (PI, 14 μM) and calcein AM (15 μM, Thermo Fisher Scientific). Protoplasts were isolated separately for each Arabidopsis ecotype (Col-0 and Ler-0). Viable cells from each ecotype were enriched using magnetic levitation (LeviCell, Levitas Bio; 255 μL cell suspension, 45 μL levitation buffer, 5-minute settling time, split line: 15). The enriched cell suspensions (approximately 60 μL per ecotype) were counted, and a master sample containing 40,000 cells (50:50 Col-0:Ler-0 mix) was prepared.
Protoplasts were divided and processed using two scRNA-seq platforms: 10X Chromium (Single Cell 3′ GEM, Library & Gel Bead Kit v3.1) and BD Rhapsody (HT cartridge, enhanced cartridge reagents v2, cDNA and WTA amplification kit), following the manufacturers’ protocols for reverse transcription, cDNA amplification, and library construction.

tag: accession

value: Col-0 and Ler-0

value: WT


title: W95_PBMC_G4_GEX

description:
Library name: W95_PBMC_G4_GEX
GEX 5' mRNA library
W95_PBMC_G4_barcodes.tsv.gz
W95_PBMC_G4_features.tsv.gz
W95_PBMC_G4_matrix.mtx.gz

value: PBMC


title: W83_FNA_G3_GEX

description:
Library name: W83_FNA_G3_GEX
GEX 5' mRNA library


title: RBPJ_ChIP_ev_2

description: Library name: RBPJ_ChIP_ev_2


title: BD_replicate2

description:
Library name: BD_replicate2
BD Rhapsody


title: UA36 RNA-seq

description:
Library name: UA36_GEX
10X genomics


title: W83_FNA_G3_VDJ

description:
Library name: W83_FNA_G3_VDJ
VDJ 5' mRNA library


title: UA35 TCR-seq

description:
Library name: UA35_TCR
10X genomics


title: RBPJ_ChIP_ev_1

description: Library name: RBPJ_ChIP_ev_1


title: W83_FNA_G2_HTO

description:
Library name: W83_FNA_G2_HTO
HTO 5' mRNA library


title: UA35 RNA-seq

description:
Library name: UA35_GEX
10X genomics


title: 10X_replicate1

description:
Library name: 10X_replicate1
10X Genomics 3' v3.1


title: Mods_12h_ISX9_Input

description: Library name: Mods_12h_ISX9_Input

value: 12h ISX9


title: BD_replicate1

description:
Library name: BD_replicate1
BD Rhapsody

value: root


title: W83_FNA_G2_GEX

description:
Library name: W83_FNA_G2_GEX
GEX 5' mRNA library


title: UA34 TCR-seq

description:
Library name: UA34_TCR
10X genomics


title: Mods_12h_DMSO_Input

description: Library name: Mods_12h_DMSO_Input

value: 12h DMSO


title: SUM159PT, ATAC-seq, rep2

city: Toronto

first: Mathieu

last: Lupien

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

description: Library name: SUM159PT_rep2

data_processing:
Reads were aligned to the hg38 genome build using bowtie2/2.05 using default parameters
Duplicated reads, mitochondrial reads, chrY reads, unmapped reads, poor quality reads (Q<30), and the reads overlapping with the ENCODE blacklisted regions (http://hgdownload.cse.ucsc.edu/goldenPath/hg38/encodeDCC/wgEncodeMapability/) were removed using samtools/0.1.18. After the alignment of the filtered reads, accessible chromatin regions were called using MACS2 with these parameters: “--keep-dup all -B --shift -75 --extsize 150 --nomodel --SPMR -q 0.01”
Assembly: hg38
Supplementary files format and content: NARROWPEAK

growth_protocol: Cells were grown to 95% confluence in RPMI 1640 medium supplemented with 10% foetal bovine serum

extract_protocol:
Lysates were extracted from 50k sorted nuclei using a nuclei lysis buffer (according to ATAC-seq protocol from Buenrostro et al 2013). Transposase reaction was carried out following the protocol of the Nextera DNA library preparation kit (illumina).
Libraries were prepared using the NeBNext buffer and appropriate ATAC-seq libraries adaptors (Illumina, Buenrostro et al, 2013). The library was size-selected using the DNA on a ChIP technology. ATAC-seq library and ATAC-seq adaptors (Buenrostro et al, 2013)

value: TNBC


title: UA34 RNA-seq

description:
Library name: UA34_GEX
10X genomics

value: gut


title: K4me3_ChIP_12h_ISX9_2

description: Library name: K4me3_ChIP_12h_ISX9_2


title: W83_FNA_G1_HTO

description:
Library name: W83_FNA_G1_HTO
HTO 5' mRNA library


title: SUM159PT, ATAC-seq, rep1

description: Library name: SUM159PT_rep1


title: W83_FNA_G2_VDJ

description:
Library name: W83_FNA_G2_VDJ
VDJ 5' mRNA library


title: K4me3_ChIP_12h_ISX9_1

description: Library name: K4me3_ChIP_12h_ISX9_1


title: UA33 TCR-seq

description:
Library name: UA33_TCR
10X genomics


title: SUM149PT, ATAC-seq, rep2

description: Library name: SUM149PT_rep2


title: W83_FNA_G1_GEX

description:
Library name: W83_FNA_G1_GEX
GEX 5' mRNA library


title: UA33 RNA-seq

description:
Library name: UA33_GEX
10X genomics


title: HCCC9810 cells, control2, 24 hours

city: Hangzhou

first: Wangyang

last: Chen

address: 261 Huansha Road, Hangzhou, Zhejiang, 310006, China

institute: Zhejiang University

description:
Library name: Sample_2
HCCC9810 control (vehicle) for 24 h

data_processing:
Raw reads were processed to remove adaptor sequences and low-quality reads. High-quality reads were mapped to the human reference genome. Gene abundance was quantified and normalized. Differentially expressed genes were identified using DESeq2 (q-value < 0.05, fold change > 2).
Assembly: GRCh38
Supplementary files format and content: Comma-separated values (CSV) text file containing raw read counts for all samples. Rows represent gene symbols and columns represent samples.
Supplementary files format and content: Comma-separated values (CSV) text file containing normalized gene expression levels (FPKM) for all samples. Rows represent gene symbols and columns represent samples.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen). RNA integrity was verified using an Agilent 2100 Bioanalyzer.
RNA libraries for RNA-seq were prepared using standard Illumina mRNA-seq library prep kits following manufacturer's protocols.

value: cholangiocarcinoma cells

value: wild type

value: vehicle (DMSO) for 24 h


title: SUM149PT, ATAC-seq, rep1

description: Library name: SUM149PT_rep1


title: K4me3_ChIP_12h_DMSO_2

description: Library name: K4me3_ChIP_12h_DMSO_2


title: W83_FNA_G1_VDJ

description:
Library name: W83_FNA_G1_VDJ
VDJ 5' mRNA library

value: LN FNA


title: UA32 TCR-seq

description:
Library name: UA32_TCR
10X genomics


title: K4me3_ChIP_12h_DMSO_1

description: Library name: K4me3_ChIP_12h_DMSO_1

value: Carcinoma; Non-small cell lung cancer     Large cell carcinoma subtype


title: MX1, ATAC-seq, rep2

description: Library name: MX1_rep2


title: W73_FNA_G4_HTO

description:
Library name: W73_FNA_G4_HTO
HTO 5' mRNA library


title: UA32 RNA-seq

description:
Library name: UA32_GEX
10X genomics


title: MX1, ATAC-seq, rep1

description: Library name: MX1_rep1


title: W73_FNA_G4_GEX

description:
Library name: W73_FNA_G4_GEX
GEX 5' mRNA library


title: K4me1_ChIP_12h_ISX9_2

description: Library name: K4me1_ChIP_12h_ISX9_2


title: UA31 TCR-seq

description:
Library name: UA31_TCR
10X genomics


title: K4me1_ChIP_12h_ISX9_1

description: Library name: K4me1_ChIP_12h_ISX9_1


title: MDA-MB-468, ATAC-seq, rep2

description: Library name: MDA-MB-468_rep2


title: W73_FNA_G4_VDJ

description:
Library name: W73_FNA_G4_VDJ
VDJ 5' mRNA library


title: K4me1_ChIP_12h_DMSO_2

description: Library name: K4me1_ChIP_12h_DMSO_2


title: UA31 RNA-seq

description:
Library name: UA31_GEX
10X genomics


title: MDA-MB-468, ATAC-seq, rep1

description: Library name: MDA-MB-468_rep1


title: W73_FNA_G3_HTO

description:
Library name: W73_FNA_G3_HTO
HTO 5' mRNA library


title: UA30 TCR-seq

description:
Library name: UA30_TCR
10X genomics


title: MDA-MB-436, ATAC-seq, rep2

description: Library name: MDA-MB-436_rep2


title: K4me1_ChIP_12h_DMSO_1

description: Library name: K4me1_ChIP_12h_DMSO_1


title: UA30 RNA-seq

description:
Library name: UA30_GEX
10X genomics


title: W73_FNA_G3_GEX

description:
Library name: W73_FNA_G3_GEX
GEX 5' mRNA library


title: K27ac_ChIP_12h_ISX9_2

description: Library name: K27ac_ChIP_12h_ISX9_2


title: MDA-MB-436, ATAC-seq, rep1

description: Library name: MDA-MB-436_rep1


title: W73_FNA_G3_VDJ

description:
Library name: W73_FNA_G3_VDJ
VDJ 5' mRNA library


title: UA26 TCR-seq

description:
Library name: UA26_TCR
10X genomics


title: EO771_co3

city: Cold Spring Harbor

first: Yue

last: Wu

state: NY

address: One Bungtown Rd, Demerec RM 120

department: Cancer and Neuroscience

institute: Cold Spring Harbor Laboratory

description: Library name: Sample9

data_processing:
JupyterHub platform
Quality control: FastQC, Trimming: cutadapt wrapper; Alignment: STAR; featureCounts;
Quantification: Differential expression: DESeq2 and visulization in JupyterHub with R kernel
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: EO771 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was harvested using Trizol. 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NextSeq2000 P1 PE150 mRNA-Seq Library Prep Kit following manufacturer’s protocols.

value: Breast cancer cell

value: coculture with DRG


title: K27ac_ChIP_12h_ISX9_1

description: Library name: K27ac_ChIP_12h_ISX9_1


title: MDA-MB-231, ATAC-seq, rep2

description: Library name: MDA-MB-231_rep2


title: W73_FNA_G2_HTO

description:
Library name: W73_FNA_G2_HTO
HTO 5' mRNA library

value: B cells

value: Protein immunized


title: hBD3-POND-293T_rep-1

value: HEK293T cell line


title: K27ac_ChIP_12h_DMSO_2

description: Library name: K27ac_ChIP_12h_DMSO_2


title: MDA-MB-231, ATAC-seq, rep1

description: Library name: MDA-MB-231_rep1

value: WT


title: UA26 RNA-seq

description:
Library name: UA26_GEX
10X genomics


title: W73_FNA_G2_GEX

description:
Library name: W73_FNA_G2_GEX
GEX 5' mRNA library


title: UA24 TCR-seq

description:
Library name: UA24_TCR
10X genomics


title: K27ac_ChIP_12h_DMSO_1

description: Library name: K27ac_ChIP_12h_DMSO_1


title: UA24 RNA-seq

description:
Library name: UA24_GEX
10X genomics


title: MB157, ATAC-seq, rep2

description: Library name: MB157_rep2


title: W73_FNA_G2_VDJ

description:
Library name: W73_FNA_G2_VDJ
VDJ 5' mRNA library


title: ATAC_12h_ISX9_2

description: Library name: ATAC_12h_ISX9_2

extract_protocol:
ATAC-Seq was performed using a kit (Active Motif 53150).
Lybrary-prep kit for ATAC-Seq: ATAC-Seq kit (Active Motif 53150).


title: W73_FNA_G1_HTO

description:
Library name: W73_FNA_G1_HTO
HTO 5' mRNA library


title: UA23 TCR-seq

description:
Library name: UA23_TCR
10X genomics


title: ATAC_12h_ISX9_1

description: Library name: ATAC_12h_ISX9_1


title: HS578, ATAC-seq, rep2

description: Library name: HS578_rep2


title: W73_FNA_G1_GEX

description:
Library name: W73_FNA_G1_GEX
GEX 5' mRNA library


title: UA23 RNA-seq

description:
Library name: UA23_GEX
10X genomics


title: ATAC_12h_DMSO_2

description: Library name: ATAC_12h_DMSO_2


title: W73_FNA_G1_VDJ

description:
Library name: W73_FNA_G1_VDJ
VDJ 5' mRNA library


title: HS578, ATAC-seq, rep1

description: Library name: HS578_rep1


title: HCC70, ATAC-seq, rep2

description: Library name: HCC70_rep2


title: ATAC_12h_DMSO_1

description: Library name: ATAC_12h_DMSO_1


title: UA22 TCR-seq

description:
Library name: UA22_TCR
10X genomics


title: UA22 RNA-seq

description:
Library name: UA22_GEX
10X genomics


title: W57_FNA_G4_HTO

description:
Library name: W57_FNA_G4_HTO
HTO 5' mRNA library


title: MB157, ATAC-seq, rep1

description: Library name: MB157_rep1


title: RNA_RBPJKO_2

description: Library name: RNA_RBPJKO_2

data_processing:
The fastq files were against hg19 aligned using Hisat2 v.2.2.1
Count tables were generated from BAM files using the summarizeOverlaps function.
Assembly: hg19
Supplementary files format and content: Count tables of raw read counts per gene in xls format.

extract_protocol:
RNeasy Mini Kit (Qiagen #74104) using the QIAshredder (Qiagen #79654) and  RNase-free DNase (Qiagen #79254).
Libraries were prepared at Novogene UK.

treatment_protocol: Human H1299 cells were treated for 12 or 24 hours with 20 uM or with DMSO as control. Human H1299 cells depleted of RBPJ were generated using the CRISPR/Ca9 technology.

value: sgRNA RBPJ


title: HCC70, ATAC-seq, rep1

description: Library name: HCC70_rep1


title: Patient BM060207: Proteomic and transcriptomic profiling identifies TIPRL as a potential target in MM with 1q gain

city: Phoenix

first: Esteban

last: Braggio

state: AZ

address: 6161 E Mayo Blvd

department: Hematology

institute: Mayo Clinic

description: Library name: BM060207

data_processing:
An internally developed RNA-seq analysis workflow (MAPRSeq v2.0.0) was used to perform read alignment, quality control, and expression quantification. Paired-end reads were aligned by BWA against the hg19 (GRCh37/b37) genome with decoy contigs, quality control across genes was performed with RSeQC (v2.3.2; ref. 22), gene counts were generated with featureCounts from Subread package (http://subread.sourceforge.net/, v1.4.4). For each sample, gene counts were normalized using Conditional Quantile Normalization method (CQN) and generate gene and exon expression levels scaled against gene lengths and sample read depths (RPKM, reads per kilo base-pair per million mapped reads). Differentially expressed genes will be submitted to ingenuity pathway analysis (IPA, http://www.ingenuity.com/) for pathway enrichment analysis.
Assembly: hg19
Supplementary files format and content: RPKM RNA matrix (.csv), clinical metadata (.xlsx), bam index files (.bai)

source_name: Bone marrow

extract_protocol:
Bone marrow samples were collected after approval from the Institutional Review Board at Mayo Clinic, Rochester. CD138+ plasma cells were enriched from bone marrow aspirates and processed using AllPrep DNA/RNA/Protein extraction kit (Qiagen) using manufacturer’s protocol for DNA and RNA extraction. The flow-through from the RNA extraction step was precipitated with advanced protein precipitation buffer (Qiagen) to obtain the protein fraction and the protein pellets were stored at -80˚C until further processing.
RNA libraries were prepared using the TruSeq RNA sample prep kit v2 (Illumina, San Diego, CA) according to the manufacturer’s instructions.

value: Bone marrow

value: Plasma cells

value: Untreated


title: POND-FMR1-N34S_rep1

data_processing:
The 150-bp paired-end sequencing reads were quality-checked by FastQC (v0.11.9) and processed using Trim Galore (v0.6.7) (https://github.com/FelixKrueger/TrimGalore) to eliminate low-quality reads and trim adapter sequences.
Processed reads were then aligned to the human genome (hg38) or mouse genome (mm10) combined with ERCC spike-in sequences (https://assets.thermofisher.cn/TFS-Assets/LSG/manuals/ERCC92.zip) by STAR (v2.7.10a) using the GENCODE (Human v40 or Mouse vM25) transcript annotation as transcriptome guide, with parameters: --outFilterMismatchNoverLmax 0.04.
The raw counts aligned to exonic regions were quantified by Subread featureCounts (v2.0.1).
For RBP POND-seq data, raw counts were normalized to counts per million (CPM) using ERCC spike-ins, and RBP targets were defined as transcripts with CPM >= 50, log2foldchange > 2, and adjusted P-value < 0.05 in RBP-POND versus control (EPN24 or EPN24-GFP) samples by DESeq2 (v1.36.0).
The POND-seq data for mutated RBPs were also quantified using absolute quantification based on ERCC spike-in controls. The total CPM of wild-type RBP-POND were set to 1,000,000, and the CPM of mutated RBPs-POND were calculated relative to that of wild-type RBP. For transcriptome analysis with PABPC1-POND-seq and RNA-seq, raw counts were normalized to transcripts per million (TPM) as gene expression level.
Assembly: GRCh38; mm10
Supplementary files format and content: tab-delimited text files include rawCounts, csv files include DESeq2 results

extract_protocol:
Cell supernatant was clariﬁed by centrifugation at 3,000 g for 5 minutes, then filtrated through a cellulose acetate ﬁlter with 0.45 μm pore size (Corning). 200 μl of supernatant was mixed with 800 μl TRIzol reagent (Magen) and 1 μl diluted External RNA Controls Consortium (ERCC) synthetic spike-in RNAs (ThermoFisher). RNA was extracted and dissolved in 15-20 μl nuclease-free water.
For POND-seq, 5 μl RNA was used for library construction with modified VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme). Typically, 5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) for fragmentation at 85℃ for 6 min. For ribosomal depletion, 5 μl RNA was mixed with 5 μl 2×Prime buffer (Vazyme) and 0.7 μl FastSelect reagent (Vazyme) for fragmentation at 85℃ for 6 min. Then 8 μl fragmentated RNA was used for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification (16-18 cycles) according to the manufacture’s instruction manual. The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on Illumina NovaSeq 6000 (Novogene, China) or DNBSEQ-T7 platform (GenePlus, China). For FMR1 mutation screening, library construction was completed with VNL-96P (Vazyme) automated library preparation workstation. Briefly, 4 μl RNA was mixed with 4 μl 2×Prime buffer V2 (Vazyme) and 1 μl FastSelect reagent (Vazyme) for fragmentation at 85°C for 6 min. Then 8 μl fragmentated RNA was adopted for first and secondary strand cDNA synthesis, followed by adapter ligation and PCR amplification (17 cycles) according to VAHTS Universal V10 RNA-seq Library Prep Kit for Illumina (Vazyme). The NGS sequencing was performed on DNBSEQ-T7 platform (GenePlus). For cellular RNA-seq, the total RNA of HEK293T, Huh-7 and A549 were extracted with TRIzol reagent (Magen) and dissolved in nuclease-free water. 500 ng total RNA was used for library construction with VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme). The DNA library was purified with VAHTS DNA Clean Beads (Vazyme) and dissolved in 20 μl nuclease-free water. The 150-nt paired-end sequencing was performed on Illumina NovaSeq 6000 (Novogene) or DNBSEQ-T7 platform (GenePlus).


title: RNA_ev_2

description: Library name: RNA_ev_2

value: sgRNA control


title: HCC38, ATAC-seq, rep1

description: Library name: HCC38_rep1

value: TNBC


title: W57_FNA_G4_GEX

description:
Library name: W57_FNA_G4_GEX
GEX 5' mRNA library


title: UA21 TCR-seq

description:
Library name: UA21_TCR
10X genomics

value: gut


title: W57_FNA_G3_HTO

description:
Library name: W57_FNA_G3_HTO
HTO 5' mRNA library


title: RNA_RBPJKO_1

description: Library name: RNA_RBPJKO_1


title: HCC38, ATAC-seq, rep2

description: Library name: HCC38_rep2


title: W57_FNA_G4_VDJ

description:
Library name: W57_FNA_G4_VDJ
VDJ 5' mRNA library


title: UA21 RNA-seq

description:
Library name: UA21_GEX
10X genomics


title: UA20 TCR-seq

description:
Library name: UA20_TCR
10X genomics


title: RNA_ev_1

description: Library name: RNA_ev_1


title: HCC3153, ATAC-seq, rep2

description: Library name: HCC3153_rep2


title: UA20 RNA-seq

description:
Library name: UA20_GEX
10X genomics


title: W57_FNA_G3_GEX

description:
Library name: W57_FNA_G3_GEX
GEX 5' mRNA library


title: RNA_ISX9_24h_2

description: Library name: RNA_ISX9_24h_2

value: 24h ISX9


title: UA19 TCR-seq

description:
Library name: UA19_TCR
10X genomics


title: RNA_ISX9_24h_1

description: Library name: RNA_ISX9_24h_1


title: W57_FNA_G2_HTO

description:
Library name: W57_FNA_G2_HTO
HTO 5' mRNA library


title: W57_FNA_G2_GEX

description:
Library name: W57_FNA_G2_GEX
GEX 5' mRNA library


title: UA19 RNA-seq

description:
Library name: UA19_GEX
10X genomics


title: HCC1937, ATAC-seq, rep1

description: Library name: HCC1937_rep1


title: W57_FNA_G3_VDJ

description:
Library name: W57_FNA_G3_VDJ
VDJ 5' mRNA library


title: RNA_ISX9_12h_2

description: Library name: RNA_ISX9_12h_2

value: 12h ISX9


title: HCC3153, ATAC-seq, rep1

description: Library name: HCC3153_rep1


title: UA15 TCR-seq

description:
Library name: UA15_TCR
10X genomics


title: HCC1806, ATAC-seq, rep2

description: Library name: HCC1806_rep2


title: RNA_ISX9_12h_1

description: Library name: RNA_ISX9_12h_1


title: W57_FNA_G2_VDJ

description:
Library name: W57_FNA_G2_VDJ
VDJ 5' mRNA library

value: LN FNA


title: UA15 RNA-seq

description:
Library name: UA15_GEX
10X genomics


title: HCC1806, ATAC-seq, rep1

description: Library name: HCC1806_rep1


title: RNA_DMSO_24h_2

description: Library name: RNA_DMSO_24h_2

value: Carcinoma; Non-small cell lung cancer     Large cell carcinoma subtype

value: 24h DMSO


title: UA14 RNA-seq

description:
Library name: UA14_GEX
10X genomics


title: RNA_DMSO_24h_1

description: Library name: RNA_DMSO_24h_1


title: W57_FNA_G1_GEX

description:
Library name: W57_FNA_G1_GEX
GEX 5' mRNA library


title: RNA_DMSO_12h_2

description: Library name: RNA_DMSO_12h_2

value: 12h DMSO


title: HCC1937, ATAC-seq, rep2

description: Library name: HCC1937_rep2


title: UA14 TCR-seq

description:
Library name: UA14_TCR
10X genomics


title: W57_FNA_G1_HTO

description:
Library name: W57_FNA_G1_HTO
HTO 5' mRNA library

value: B cells


title: HCC1395, ATAC-seq, rep1

description: Library name: HCC1395_rep1


title: W57_FNA_G1_VDJ

description:
Library name: W57_FNA_G1_VDJ
VDJ 5' mRNA library

value: Protein immunized


title: RNA_DMSO_12h_1

description: Library name: RNA_DMSO_12h_1


title: UA13 TCR-seq

description:
Library name: UA13_TCR
10X genomics


title: HCC1143, ATAC-seq, rep2

description: Library name: HCC1143_rep2


title: W47_FNA_G4_HTO

description:
Library name: W47_FNA_G4_HTO
HTO 5' mRNA library


title: HCC1143, ATAC-seq, rep1

description: Library name: HCC1143_rep1


title: UA13 RNA-seq

description:
Library name: UA13_GEX
10X genomics


title: P5217 scRNA-seq library

city: St Louis

first: Thomas

middle: F

last: Barrett

state: MO

address: 660 Euclid Ave

department: Otolaryngology

institute: Washington University

description:
Library name: P5217_scrna
Freshly dissociated single cell transcriptomic sequencing

data_processing:
Raw sequencing data were processed using the 10X Genomics Cellranger pipeline to generate fastq files
After sequencing, the resulting FASTQ files were aligned to a custom genome, combining the human genome (grch38) with genomes of the main high-risk HPV genotypes—HPV16, 18, 31, 33 and 35.
Assembly: grch38 with genomes of high-risk HPV genotypes - HPV16, 18, 31, 33, and 35.
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: barcodes.tsv.gz: list of cell barcodes

source_name: Head and neck mucosal squamous cell carcinoma

extract_protocol:
Samples were were dissociated using the Miltenyi Human Tumor Dissociation Kit, cleaned with ACK RBC lysis, and sorted with CD45+ beads. Cells were loaded onto the 10X chip with a ratio of 70% CD45- and 30% CD45+ cells
cDNA libraries were prepared according to the 10X Chromium Next GEM Single Cell 3' Reagent Kits v3.1 protocol.

tag: hpv-related

value: No


title: HCC1395, ATAC-seq, rep2

description: Library name: HCC1395_rep2

value: WT


title: W47_FNA_G4_GEX

description:
Library name: W47_FNA_G4_GEX
GEX 5' mRNA library


title: UA12 TCR-seq

description:
Library name: UA12_TCR
10X genomics


title: P5219 scRNA-seq library

description:
Library name: P5219_scrna
Freshly dissociated single cell transcriptomic sequencing

value: Head and neck mucosal squamous cell carcinoma


title: CAL85-1, ATAC-seq, rep2

description: Library name: CAL85-1_rep2


title: W47_FNA_G4_VDJ

description:
Library name: W47_FNA_G4_VDJ
VDJ 5' mRNA library


title: UA12 RNA-seq

description:
Library name: UA12_GEX
10X genomics


title: P5469 scRNA-seq library

description:
Library name: P5469_scrna
Freshly dissociated single cell transcriptomic sequencing


title: CAL85-1, ATAC-seq, rep1

description: Library name: CAL85-1_rep1


title: W47_FNA_G3_HTO

description:
Library name: W47_FNA_G3_HTO
HTO 5' mRNA library


title: UA11 TCR-seq

description:
Library name: UA11_TCR
10X genomics


title: CAL120, ATAC-seq, rep2

description: Library name: CAL120_rep2


title: P5448 scRNA-seq library

description:
Library name: P5448_scrna
Freshly dissociated single cell transcriptomic sequencing


title: W47_FNA_G3_GEX

description:
Library name: W47_FNA_G3_GEX
GEX 5' mRNA library


title: UA11 RNA-seq

description:
Library name: UA11_GEX
10X genomics


title: CAL120, ATAC-seq, rep1

description: Library name: CAL120_rep1


title: P5418 scRNA-seq library

description:
Library name: P5418_scrna
Freshly dissociated single cell transcriptomic sequencing


title: UA10 TCR-seq

description:
Library name: UA10_TCR
10X genomics


title: W47_FNA_G3_VDJ

description:
Library name: W47_FNA_G3_VDJ
VDJ 5' mRNA library


title: BT549, ATAC-seq, rep2

description: Library name: BT549_rep2


title: W47_FNA_G2_HTO

description:
Library name: W47_FNA_G2_HTO
HTO 5' mRNA library


title: UA10 RNA-seq

description:
Library name: UA10_GEX
10X genomics


title: P5751 scRNA-seq library

description:
Library name: P5751_scrna
Freshly dissociated single cell transcriptomic sequencing


title: P5736 scRNA-seq library

description:
Library name: P5736_scrna
Freshly dissociated single cell transcriptomic sequencing


title: BT549, ATAC-seq, rep1

description: Library name: BT549_rep1


title: W47_FNA_G2_GEX

description:
Library name: W47_FNA_G2_GEX
GEX 5' mRNA library


title: UA09 TCR-seq

description:
Library name: UA09_TCR
10X genomics


title: P5735 scRNA-seq library

description:
Library name: P5735_scrna
Freshly dissociated single cell transcriptomic sequencing

value: Yes


title: BT20, ATAC-seq, rep2

description: Library name: BT20_rep2


title: W47_FNA_G2_VDJ

description:
Library name: W47_FNA_G2_VDJ
VDJ 5' mRNA library


title: UA09 RNA-seq

description:
Library name: UA09_GEX
10X genomics


title: BT20, ATAC-seq, rep1

description: Library name: BT20_rep1


title: P5710 scRNA-seq library

description:
Library name: P5710_scrna
Freshly dissociated single cell transcriptomic sequencing


title: T47D, ATAC-seq

description: Library name: T47D

value: Luminal A


title: W47_FNA_G1_GEX

description:
Library name: W47_FNA_G1_GEX
GEX 5' mRNA library


title: UA08 TCR-seq

description:
Library name: UA08_TCR
10X genomics


title: W47_FNA_G1_HTO

description:
Library name: W47_FNA_G1_HTO
HTO 5' mRNA library


title: P5684 scRNA-seq library

description:
Library name: P5684_scrna
Freshly dissociated single cell transcriptomic sequencing


title: UA08 RNA-seq

description:
Library name: UA08_GEX
10X genomics


title: MCF7, ATAC-seq

description: Library name: MCF7


title: W47_FNA_G1_VDJ

description:
Library name: W47_FNA_G1_VDJ
VDJ 5' mRNA library


title: P5666 scRNA-seq library

description:
Library name: P5666_scrna
Freshly dissociated single cell transcriptomic sequencing


title: UA07 TCR-seq

description:
Library name: UA07_TCR
10X genomics


title: P5457_1, spatial transcriptomics

description: Fresh frozen spatial transcriptomic sequencing

data_processing:
Raw sequencing data were processed using the 10X Genomics Space Ranger pipeline to generate fastq files
After sequencing, the resulting FASTQ files were aligned to a custom genome, combining the human genome (grch38) with genomes of the main high-risk HPV genotypes—HPV16, 18, 31, 33 and 35.
Assembly: grch38 with genomes of high-risk HPV genotypes - HPV16, 18, 31, 33, and 35.
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange format
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Library strategy: Spatial transcriptomics

extract_protocol:
Fresh tissue were simultaneously embedded and frozen in OCT and 10 μm sections were cut using a cryostat
Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expression Slides and Reagent Kit according to manufacturer's instructions


title: SUM149, ATAC-seq

description: Library name: SUM149


title: W18_FNA_G4_2_HTO

description:
Library name: W18_FNA_G4_2_HTO
HTO 5' mRNA library

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.2 (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Fasta files, Tab-separated values files and matrix files
Library strategy: CITE-seq


title: UA07 RNA-seq

description:
Library name: UA07_GEX
10X genomics


title: P5217, spatial transcriptomics


title: MDA468, ATAC-seq

description: Library name: MDA468


title: W18_FNA_G4_2_VDJ

description:
Library name: W18_FNA_G4_2_VDJ
VDJ 5' mRNA library


title: UA06 TCR-seq

description:
Library name: UA06_TCR
10X genomics


title: W18_FNA_G4_2_GEX

description:
Library name: W18_FNA_G4_2_GEX
GEX 5' mRNA library

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.2 (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Fasta files, Tab-separated values files and matrix files


title: UA06 RNA-seq

description:
Library name: UA06_GEX
10X genomics


title: P5219, spatial transcriptomics


title: HS-578-T, ATAC-seq

description: Library name: HS-578-T


title: HDQP-1, ATAC-seq

description: Library name: HDQP-1


title: UA05 TCR-seq

description:
Library name: UA05_TCR
10X genomics


title: W18_FNA_G4_1_HTO

description:
Library name: W18_FNA_G4_1_HTO
HTO 5' mRNA library


title: P5418, spatial transcriptomics


title: P5448, spatial transcriptomics


title: HCC3153, ATAC-seq

description: Library name: HCC3153


title: W18_FNA_G4_1_GEX

description:
Library name: W18_FNA_G4_1_GEX
GEX 5' mRNA library


title: UA05 gut scRNA-seq

description:
Library name: UA05_GEX
10X genomics


title: HCC1806, ATAC-seq

description: Library name: HCC1806


title: UA04 TCR-seq

description:
Library name: UA04_TCR
10X genomics


title: W18_FNA_G4_1_VDJ

description:
Library name: W18_FNA_G4_1_VDJ
VDJ 5' mRNA library


title: HCC1187, ATAC-seq

description: Library name: HCC1187


title: P5456, replicate 1, spatial transcriptomics


title: W18_FNA_G3_HTO

description:
Library name: W18_FNA_G3_HTO
HTO 5' mRNA library


title: UA04 gut scRNA-seq

description:
Library name: UA04_GEX
10X genomics


title: P5612, spatial transcriptomics


title: W18_FNA_G3_GEX

description:
Library name: W18_FNA_G3_GEX
GEX 5' mRNA library


title: HBL100, ATAC-seq

description: Library name: HBL100


title: P5624, spatial transcriptomics


title: UA03 TCR-seq

description:
Library name: UA03_TCR
10X genomics


title: AM3

city: SHANGHAI

first: Shufang

address: 2800 Gong Wei Road

institute: Shanghai Pudong Hospital

description: Library name: AM3

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: GRCh38
Supplementary files format and content: excel,expression profiles

source_name: lung

growth_protocol: A549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS)and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

treatment_protocol: After lentiviral transduction of cells, collect the culture medium and isolate exosomes by ultracentrifugation method

value: lung

value: NSCLC cell

value: A549 + pLVX-Puro-empty


title: W18_FNA_G3_VDJ

description:
Library name: W18_FNA_G3_VDJ
VDJ 5' mRNA library

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were performed using Cell Ranger v7.2 (10X Genomics). VDJ reads were assembled de novo in Cell Ranger, and GEX sequencing libraries were aligned to the Macaca mulatta reference genome.
Assembly: Mmul10
Supplementary files format and content: Fasta files, Tab-separated values files and matrix files
Library strategy: BCR-Seq


title: UA03 gut scRNA-seq

description:
Library name: UA03_GEX
10X genomics

data_processing:
Raw sequencing data for each sample were processed using the 10x Genomics Cell Ranger or Space Ranger pipeline.
Assembly: GRCh38-2020
Supplementary files format and content: h5ad files for processed RNA Seq data
Supplementary files format and content: csv for processed sc-TCR data
Supplementary files format and content: json for processed sc-TCR data

value: gut


title: AM2

description: Library name: AM2

value: After lentiviral transduction of cells, collect the culture medium and isolate exosomes by ultracentrifugation method


title: P5636, spatial transcriptomics


title: P5659, spatial transcriptomics


title: P5469, spatial transcriptomics


title: UA02 TCR-seq

description:
Library name: UA02_TCR
10X genomics


title: AM1

description: Library name: AM1


title: W18_FNA_G2_HTO

description:
Library name: W18_FNA_G2_HTO
HTO 5' mRNA library


title: W18_FNA_G2_GEX

description:
Library name: W18_FNA_G2_GEX
GEX 5' mRNA library


title: UA02 gut scRNA-seq

description:
Library name: UA02_GEX
10X genomics


title: AF3

description: Library name: AF3

value: A549 + pLVX-Puro-FXR


title: P5666, spatial transcriptomics


title: UA01 TCR-seq

description:
Library name: UA01_TCR
10X genomics


title: W18_FNA_G2_VDJ

description:
Library name: W18_FNA_G2_VDJ
VDJ 5' mRNA library

value: LN FNA


title: P5684, spatial transcriptomics


title: AF2

description: Library name: AF2


title: UA01 gut scRNA-seq

description:
Library name: UA01_GEX
10X genomics


title: W18_FNA_G1_HTO

description:
Library name: W18_FNA_G1_HTO
HTO 5' mRNA library


title: AF1

description: Library name: AF1


title: RH_09 gut scRNA-seq

description:
Library name: RH_09_GEX
10X genomics


title: W18_FNA_G1_GEX

description:
Library name: W18_FNA_G1_GEX
GEX 5' mRNA library


title: P5692, spatial transcriptomics


title: P5707, spatial transcriptomics


title: W18_FNA_G1_VDJ

description:
Library name: W18_FNA_G1_VDJ
VDJ 5' mRNA library


title: INPUT

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

description: Library name: Sample 8

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Assembly: mm10
Supplementary files format and content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

growth_protocol: C2C12 myoblast cells were purchased from ATCC (ATCC® CRL-1772™). Cells were cultured in Dulbecco’s modified Eagle’s medium containing 10% Foetal Bovine Serum (Fisher scientific, 11531831) and 1% Penicilin-Streptomycin (Sigma, P4333) at 37 °C in an incubator with 5% CO2. Between 60 and 80% of confluency, myoblasts were differentiated in myotubes with differentiation medium (identical medium, with 0.1% Fetal Bovine Serum). Culture medium was changed every day and transfections were performed between 5-15 passages.

extract_protocol:
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen).
ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7  cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

treatment_protocol: C2C12 were cultured in 6-well plates until 60% of confluency. Cells were transfected with siRNA in differentiation medium using Lipofectamine RNA iMAX (Fischer scientific sas, 13778150) according to the manufacturer’s instructions. siRNA against FUS, Mef2a, ETV1, ETV, ETV5 and negative control siRNA were provided by Dharmacon. Cells were harvested 48h after transfection.


title: FUS 293- 4

description: Library name: Sample 7


title: RH14 TCR-seq

description:
Library name: RH14_TCR
10X genomics

data_processing:
Raw sequencing data for each sample were processed using the 10x Genomics Cell Ranger or Space Ranger pipeline.
Assembly: GRCh38-2020
Supplementary files format and content: h5ad files for processed RNA Seq data
Supplementary files format and content: csv for processed sc-TCR data
Supplementary files format and content: json for processed sc-TCR data
Library strategy: TCR-Seq


title: P5709, spatial transcriptomics


title: W13_FNA_G4_HTO

description:
Library name: W13_FNA_G4_HTO
HTO 5' mRNA library


title: RH14 gut scRNA-seq

description:
Library name: RH14_GEX
10X genomics


title: P5710, spatial transcriptomics

description: Fresh frozen spatial transcriptomic sequencing


title: FUS293 - 3

description: Library name: Sample 6


title: W13_FNA_G4_GEX

description:
Library name: W13_FNA_G4_GEX
GEX 5' mRNA library


title: RH13 TCR-seq

description:
Library name: RH13_TCR
10X genomics


title: FUS293 - 2

description: Library name: Sample 5


title: RH13 gut scRNA-seq

description:
Library name: RH13_GEX
10X genomics


title: W13_FNA_G4_VDJ

description:
Library name: W13_FNA_G4_VDJ
VDJ 5' mRNA library


title: RNApol2 S5

description: Library name: Sample 4


title: P5735, spatial transcriptomics


title: W13_FNA_G3_2_HTO

description:
Library name: W13_FNA_G3_2_HTO
HTO 5' mRNA library


title: P5736, spatial transcriptomics


title: RH12 TCR-seq

description:
Library name: RH12_TCR
10X genomics


title: RNApol2 S2

description: Library name: Sample 3


title: P5751, spatial transcriptomics


title: W13_FNA_G3_2_GEX

description:
Library name: W13_FNA_G3_2_GEX
GEX 5' mRNA library


title: RH12 gut scRNA-seq

description:
Library name: RH12_GEX
10X genomics


title: RNApol2

description: Library name: Sample 2


title: P5756, spatial transcriptomics


title: W13_FNA_G3_2_VDJ

description:
Library name: W13_FNA_G3_2_VDJ
VDJ 5' mRNA library


title: RH11 TCR-seq

description:
Library name: RH11_TCR
10X genomics


title: W13_FNA_G3_1_HTO

description:
Library name: W13_FNA_G3_1_HTO
HTO 5' mRNA library


title: WAB

description: Library name: Sample 1


title: RH11 gut scRNA-seq

description:
Library name: RH11_GEX
10X genomics


title: P5764, spatial transcriptomics


title: P5766, spatial transcriptomics


title: 66_2_Mx1T3_2

city: BERKELEY

first: DANICA

last: CHEN

address: 119 Morgan Hall

department: NST

institute: UC BERKELEY

description: Library name: 66_2_Mx1T3_2

data_processing:
16bp sequence containing a constant 4 bp space followed by 12 bp random priming sequence was removed by HEADCROP with Trimmomatic (v0.38). TruSeq adaptor and low-quality tails were removed by BBMap (v38.96). Trimmed reads were aligned to the UCSC mm10 genome using HISAT2 (v2.2.1) and counted with featureCounts (v2.0.1). Differential gene expression analysis was performed using DeSeq2. GSEA were performed with the GSEAPY Python package (v.0.10.3). Transcription factor binding prediction analysis of differentially expressed genes with p<0.05 was performed using TRRUST software.
Assembly: mm10
Supplementary files format and content: .xlsx File include geneID and raw read counts.

source_name: HSC

extract_protocol:
Total RNA of 40,000 sorted HSCs was isolated with RNeasy Plus Micro kit (Qiagen) following the manufacturer’s instructions.
RNA-sequencing libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen), and sequencing was performed on HiSeq 4000 at UC Davis Genome Center

value: HSC


title: 72_1_Mx1T3_3

description: Library name: 72_1_Mx1T3_3


title: W13_FNA_G3_1_GEX

description:
Library name: W13_FNA_G3_1_GEX
GEX 5' mRNA library


title: P5767, spatial transcriptomics


title: RH10 TCR-seq

description:
Library name: RH10_TCR
10X genomics

extract_protocol:
Gut biopsies were processed to isolate single-cell intraepithelial and lamina propria lymphocytes using sequential buffer treatments and enzymatic digestion. Fresh-frozen GI tissue sections were cryosectioned, stained, and imaged (see Methods section of the manuscript for further details).
CD45⁺ cells were enriched by magnetic selection or sorting. Single-cell RNA and TCR libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 5′ Kit v2, following manufacturer protocols. RNA capture, cDNA synthesis, and library construction were performed on-slide according to the Visium Spatial Gene Expression protocol (VisiumHD, see Methods section of the manuscript for further details).


title: W13_FNA_G3_1_VDJ

description:
Library name: W13_FNA_G3_1_VDJ
VDJ 5' mRNA library


title: RH10 gut scRNA-seq

description:
Library name: RH10_GEX
10X genomics


title: 62_7_Mx1Cre_2

description: Library name: 62_7_Mx1Cre_2


title: P5903, spatial transcriptomics


title: W13_FNA_G2_3_HTO

description:
Library name: W13_FNA_G2_3_HTO
HTO 5' mRNA library


title: RH09 TCR-seq

description:
Library name: RH09_TCR
10X genomics


title: W13_FNA_G2_3_GEX

description:
Library name: W13_FNA_G2_3_GEX
GEX 5' mRNA library


title: P5909, spatial transcriptomics


title: RH08 TCR-seq

description:
Library name: RH08_TCR
10X genomics


title: 62_3_Mx1Cre_1

description: Library name: 62_3_Mx1Cre_1


title: Transplanted human cells and chicken neighboring cells, day17_rep2

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Trimmomatic was employed to trim reads ends where average base calling qualities (in 5 bp windows) were below Q20. Only reads with minimum length of 30 bp were kept for further analyses.
To separate reads that originated from human and chicken cells, we concatenated Ensembl human genome version hg38 (GRCh38) and Ensembl chicken genome version galgal5 (5.0.90), created an index file for this “chimeric reference genome”, and aligned all trimmed and filtered reads into it by using STAR version 2.7.1a.
Uniquely mapped reads were counted using featureCounts in Subread toolkit 1.6.473. By this approach, each read was only aligned and counted for the reference genome that had higher similarity to, and the reads with equal similarity to both genomes were excluded.
Counts normalization and differential expression analysis were performed using the R/Bioconductor package DESeq2. Genes having absolute log2 fold-change higher than 1 and Benjamini-Hochberg adjusted P-value less than 0.05 were considered as significant differentially expressed genes (DEGs).
The shrinkage of log fold changes was performed using “ashr” shrinkage estimator. Visualization of the results was done by ggplot2, pheatmap and EnhancedVolcano packages. Overrepresentation analysis was performed in DAVID Bioinformatics Resources76. Gene set enrichment analysis was performed using Broad Institute GSEA software.
Assembly: hg38 (GRCh38) / galgal5 (5.0.90)
Supplementary files format and content: Txt file of raw counts

organism:
Gallus gallus
Homo sapiens

source_name: Transplanted NECs and surrounding chicken tissue

extract_protocol:
miRNeasy micro kit (Qiagen)
Libraries for cell and tissue samples were generated by SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takar Bio).

tag: time


title: Transplanted human cells and chicken neighboring cells, day17_rep1

value: Transplanted NECs and surrounding chicken tissue


title: SL4 cell with overexpression of SEMA6A_3

city: Beijing

first: Fang

last: Zhang

address: No. 2 Nanwei Road

institute: Chinese Academy of Medical Sciences

description:
Library name: 6A3
SemA_3

data_processing:
Fastp software was used to process raw reads in fastq format. Clean reads were obtained after low-quality reads were removed for subsequent data analysis. We use Bowtie2 to map clean reads to reference gene and use HISAT to reference genome. RSEM was used for gene qualification and FPKM values.
Assembly: mm39
Supplementary files format and content: csv file includes FPKM values for each sample

extract_protocol:
Total RNA was extracted from CRC cells using the RNeasy kit (Beyotime, Shanghai, China, R0027) and subjected to reverse transcription using the SuperScript II reverse transcriptase. (TaKaRa, Japan, RR047) according to the manufacturer´s instructions.
The concentration and purity of the extracted RNA were detected by Nanodrop2000, the integrity of RNA was detected by agarose gel electrophoresis, and the RIN value was determined by Agilent2100. The total amount of RNA required for a single library construction is ≥ 1ug, the concentration is ≥ 35ng/μL, OD260/280 is ≥ 1.8, and OD260/230 is ≥ 1.0.


title: RH08 gut scRNA-seq

description:
Library name: RH08_GEX
10X genomics


title: W13_FNA_G2_3_VDJ

description:
Library name: W13_FNA_G2_3_VDJ
VDJ 5' mRNA library

extract_protocol:
N332-GT5 epitope-specific B cells were isolated from peripheral blood samples collected from rhesus macaques immunized with N332-GT5 and subsequent heterologous boost immunizations. Probes for each boost immunogen were included in flow cytometry staining for each respective Group, allowing determination of the proportion of N332-GT5 epitope-specific cells cross-binding the boost immunogen (N332-GT5++KO– Boost++). Thawed cells were incubated with both N332-GT5 KO and Boost KO probes for twenty minutes at 4°C. Following that, cells were sequentially incubated with the combined Booster WT probes for fifteen minutes at 4°C and then with the combined N332-GT5 WT probes for thirty minutes at 4°C. A master mix of surface staining antibodies was added next, with 2 μg per 5 million cells of anti-human Total-Seq-C hashtag antibodies (Biolegend) following the surface staining, and incubated for thirty minutes at 4°C. Cells were then washed twice and prepared for sorting on BD FACSymphony S6 (BD Biosciences). Epitope-specific B cells were sorted at all time points.Once sorted, epitope-specific PBMC and LN FNA B cells were washed with PBS and loaded onto a Chromium chip and controller following the manufacturers protocol (10X Genomics).  Indexed V(D)J, Feature Barcode, and Gene Expression libraries were prepared following the 10X Genomics protocol with the Feature Barcoding Kit (10X Genomics) and sequenced on a NovaSeq 6000 (Illumina).
Libraries were constructed according to the manufacturer's protocol using the Chromium Next GEM Single Cell 5’ Reagent Kit v3.


title: SL4 cell with overexpression of SEMA6A_2

description:
Library name: 6A2
SemA_2


title: W13_FNA_G2_2_HTO

description:
Library name: W13_FNA_G2_2_HTO
HTO 5' mRNA library


title: RH07 TCR-seq

description:
Library name: RH07_TCR
10X genomics


title: Transplanted human cells and chicken neighboring cells, day15_rep2


title: SL4 cell with overexpression of SEMA6A_1

description:
Library name: 6A1
SemA_1


title: W13_FNA_G2_2_GEX

description:
Library name: W13_FNA_G2_2_GEX
GEX 5' mRNA library


title: RH07 gut scRNA-seq

description:
Library name: RH07_GEX
10X genomics


title: Transplanted human cells and chicken neighboring cells, day15_rep1


title: W13_FNA_G2_2_VDJ

description:
Library name: W13_FNA_G2_2_VDJ
VDJ 5' mRNA library


title: SL4 cell without overexpression of SEMA6A_3

description:
Library name: C3
NC6A_3


title: RH06 TCR-seq

description:
Library name: RH06_TCR
10X genomics


title: Transplanted human cells and chicken neighboring cells, day12_rep2


title: W13_FNA_G2_1_HTO

description:
Library name: W13_FNA_G2_1_HTO
HTO 5' mRNA library


title: RH06 gut scRNA-seq

description:
Library name: RH06_GEX
10X genomics


title: Transplanted human cells and chicken neighboring cells, day12_rep1


title: SL4 cell without overexpression of SEMA6A_2

description:
Library name: C2
NC6A_2


title: SL4 cell without overexpression of SEMA6A_1

description:
Library name: C1
NC6A_1


title: W13_FNA_G2_1_GEX

description:
Library name: W13_FNA_G2_1_GEX
GEX 5' mRNA library


title: RH05 TCR-seq

description:
Library name: RH05_TCR
10X genomics


title: Transplanted human cells and chicken neighboring cells, day9_rep2


title: W13_FNA_G2_1_VDJ

description:
Library name: W13_FNA_G2_1_VDJ
VDJ 5' mRNA library


title: C42b cells, N5, NT-PGC1a

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

description:
Library name: N5
sample name in rlog_gene_expression: N5

data_processing:
Raw fastq fies are aligned to GRCh38_110 and quantification is carried by Salmon v1.10.2.
Illumina universal adapters were trimmed using Cutadapt v4.1.
Gene level aggreagted transcript counts were generated using Deseq2
Assembly: GRCh38 v110
Supplementary files format and content: Raw files are submitted as .fastq.gz and the raw count metrices are submitted as rlog_gene_expression_allsamples.tsv
Supplementary files format and content: tsv files inlcude aggregated TPM counts for each sample.

source_name: Prostate

growth_protocol: C42b cells were maintained in RPMI1640 complete media supplemented with 10% foetal bovine serum and 1% antibiotics in a humidified atmosphere with 5% CO2 at 37 degrees Celsius.

extract_protocol:
RNA was extracted using the RNeasy Qiagen mini kit and cleaned with the Zymo RNA Clean and Concentrator kits.
RNAseq libraries were made from 200ng Total RNA using the Watchmaker Genomics Ltd mRNA Library Prep and RNA Library Prep Kits according to manufacturer’s instructions.Libraries were dual indexed using IDT xGen™ Stubby Adapter-UDI Primers.

treatment_protocol: The cells were treated with empty nanoparticles and mRNA loaded-nanoparticles for a period of 72 hours.

value: Prostate

value: prostate epithelial cells

value: NT-PGC1a mRNA-loaded nanoparticles

value: Same


title: RH05 gut scRNA-seq

description:
Library name: RH05_GEX
10X genomics


title: C42b cells, N4, NT-PGC1a

description:
Library name: N4
sample name in rlog_gene_expression: N4

value: WT


title: RH04 TCR-seq

description:
Library name: RH04_TCR
10X genomics


title: W13_FNA_G1_HTO

city: La Jolla

first: Patrick

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

description:
Library name: W13_FNA_G1_HTO
HTO 5' mRNA library

value: B cells

value: Protein immunized


title: Transplanted human cells and chicken neighboring cells, day9_rep1


title: Transplanted human cells and chicken neighboring cells, day6_rep2


title: W13_FNA_G1_GEX

description:
Library name: W13_FNA_G1_GEX
GEX 5' mRNA library


title: C42b cells, N3, NT-PGC1a

description:
Library name: N3
sample name in rlog_gene_expression: N3


title: RH04 gut scRNA-seq

description:
Library name: RH04_GEX
10X genomics


title: Transplanted human cells and chicken neighboring cells, day6_rep1


title: W13_FNA_G1_VDJ

description:
Library name: W13_FNA_G1_VDJ
VDJ 5' mRNA library


title: RH03 TCR-seq

description:
Library name: RH03_TCR
10X genomics


title: Transplanted human cells and chicken neighboring cells, day3_rep2


title: C42b cells, N2, NT-PGC1a

description:
Library name: N2
sample name in rlog_gene_expression: N2


title: C42b cells, N1,NT-PGC1a

description:
Library name: N1
sample name in rlog_gene_expression: N1


title: RH03 gut scRNA-seq

description:
Library name: RH03_GEX
10X genomics


title: W82_PBMC_G4_HTO

description:
Library name: W82_PBMC_G4_HTO
HTO 5' mRNA library

value: PBMC


title: W82_PBMC_G4_GEX

description:
Library name: W82_PBMC_G4_GEX
GEX 5' mRNA library


title: Transplanted human cells and chicken neighboring cells, day3_rep1


title: C42b cells, E5, empty

description:
Library name: E5
sample name in rlog_gene_expression: E5

value: Empty nanoparticles


title: RH02 TCR-seq

description:
Library name: RH02_TCR
10X genomics


title: BxPC3,FOXA3 ko, Replicate4, RNA-seq

city: NEW YORK

first: Xinhe

last: Xue

state: New York

address: 101 Avenue of the Americas

institute: New York Genome Center/New York University

description: Library name: BxPC3_FOXA3 ko_Rep4

data_processing:
For fastq files, adaptors were trimmed with Cutadapt (Martin et al., 2011) v4.4 with options -q 20 -m 20 --trim -n.
Reads from were aligned to GRCh38 (gencode.v36.annotation) with HISAT2 aligner (version 2.2.1) (Kim et al., 2019).
Assembly: hg38
Supplementary files format and content: feature count

growth_protocol: BxPC-3 cells were cultured in RPMI-1640 (Thermo Fisher Scientific) supplemented with 10% Serum Plus-II (Thermo Fisher)

extract_protocol:
Total RNA was isolated using the Direct-zol RNA Purification Kit (Zymo R2062) with DNaseI treatment (n = 4 biological replicates).
For the library preparation, 500ng total RNA was used for the RNA library preparation with Stranded mRNA Prep kit (Illumina 20040534) and RNA UD Indexes Set A Ligation kit (Illumina 20040553). Samples were sequenced on Illumina NovaSeq X sequencing platform to generate 50 million read pairs or more per sample.

treatment_protocol: In BxPC-3 cells, FOXA3 was perturbed using pCC_01 (Addgene 139086) encoding FOXA3- targeting gRNA or non-targeting gRNA. Cells were selected with 2 ug/mL puromycin for 5 days. Following selection, cells were treated with 100 IU/mL IFNγ for 48 hours.

value: PDAC

value: IFNγ treatment


title: C42b cells, E4, empty

description:
Library name: E4
sample name in rlog_gene_expression: E4


title: RH02 gut scRNA-seq

city: New York

first: Lingting

address: 500 West 120th Street ET351

institute: Columbia University

description:
Library name: RH02_GEX
10X genomics

value: gut


title: BxPC3,FOXA3 ko, Replicate3, RNA-seq

description: Library name: BxPC3_FOXA3 ko_Rep3


title: W82_PBMC_G4_VDJ

last: Madden

description:
Library name: W82_PBMC_G4_VDJ
VDJ 5' mRNA library


title: C42b cells, E3, empty

description:
Library name: E3
sample name in rlog_gene_expression: E3


title: W82_PBMC_G3_HTO

description:
Library name: W82_PBMC_G3_HTO
HTO 5' mRNA library


title: RH01 TCR-seq

description:
Library name: RH01_TCR
10X genomics


title: BxPC3,FOXA3 ko, Replicate2, RNA-seq

description: Library name: BxPC3_FOXA3 ko_Rep2


title: W82_PBMC_G3_GEX

description:
Library name: W82_PBMC_G3_GEX
GEX 5' mRNA library


title: RH01 gut scRNA-seq

description:
Library name: RH01_GEX
10X genomics


title: C42b cells,E2, empty

description:
Library name: E2
sample name in rlog_gene_expression: E2


title: W82_PBMC_G3_VDJ

description:
Library name: W82_PBMC_G3_VDJ
VDJ 5' mRNA library


title: BxPC3,FOXA3 ko, Replicate1, RNA-seq

description: Library name: BxPC3_FOXA3 ko_Rep1


title: C42b cells, E1, empty

description:
Library name: E1
sample name in rlog_gene_expression: E1


title: old6

first: Bowen

state: Zhejiang

address: NO.79 Qinchun Road

institute: The First Affiliated Hospital, Zhejiang University School of  Medicine

description: Library name: Sample12

data_processing:
RNA-seq
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used Ensembl (ftp://ftp.ensembl.org/pub/release-107/fasta/homo_sapiens/dna/) to map reads to the reference genome of homo sapiens Ensembl_v107. The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: homo_sapiens Ensembl_v107
Supplementary files format and content: FPKM values for each sample

source_name: Blood

extract_protocol:
Total RNA from the cells was collected using RNA-Quick Purification Kit (YiShan Biotech, China) following the manufacturer's procedure.  The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).  The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.   Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.  e6150, USA) under 94℃ 5-7min.   Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.   1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.  m0209, USA), RNase H (NEB, cat.  m0297, USA) and dUTP Solution (Thermo Fisher, cat.  R0133, USA）.   An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters.   Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA.   Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.   After the heat-labile UDG enzyme (NEB, cat.  m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min;   8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec;   and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 400±50 bp.   At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ X Plus (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Blood

value: macrophage

value: old

value: induced with MSCF (20 ng/ml) for five days, and LPS (100 ng/ml) for two days


title: BxPC3, no ko, Replicate4, RNA-seq

description: Library name: BxPC3_NT_Rep4


title: W82_PBMC_G2_HTO

description:
Library name: W82_PBMC_G2_HTO
HTO 5' mRNA library