title: brain, in vivo, unfixed control

city: Xi'an

first: Jin

last: Ning

state: --- Select One ---

address: Yanta Road 76, Yanta District

institute: Xi'an Jiaotong Univeristy

description:
Library name: IV_UC
SeekOne

data_processing:
Unique molecular identifier (UMI) counts for the SeekOne samples were generated by aligning FASTQ files to the mouse reference genome (mm10) using SeekSoulTools (v1.3.0; SeekGene).
Assembly: Mouse mm10
Supplementary files format and content: Tap-separeted value files and matrix files.

molecule: nuclear RNA

source_name: brain

growth_protocol: 10-week-old C57BL/6 mice were purchased from the Laboratory Animal Center of Xi’an Jiaotong University. Animals were housed under specific pathogen-free (SPF) conditions with standard light/dark cycles and access to food and water ad libitum.

extract_protocol:
Option 1, for unfixed-control samples: Nuclei were extracted using the Boyou Nuclear Isolation Kit (BoHao Biotechnology, Cat. 52201-10). ≤50 mg of tissue was homogenized in 600 μL lysis buffer, incubated on ice for 4 min, filtered, and centrifuged at 500 ×g for 5 min at 4°C. Nuclei were resuspended in 50 μL washing buffer, assessed for integrity using trypan blue and AO/PI staining, and filtered through a 40 μm cell strainer. Samples were kept on ice throughout the process. Option 2, for methanol-fixed samples: Nuclei were extracted using the Boyou Nuclear Isolation Kit (BoHao Biotechnology). Following extraction, pre-chilled 100% methanol was added dropwise to the nuclei suspension to a final concentration of 80%, and samples were incubated at -20°C for 30 minutes. Before library construction, nuclei were processed using the SeekMate Cell/Nucleus Fixation and Preservation Kit (SeekGene, Cat. K02301-0803). The suspension was centrifuged at 1000×g for 5 min at 4°C, resuspended in 400 μL Buffer Q, mixed with 800 μL WB3 buffer, and assessed for integrity.
Single-nucleus suspensions were processed using the SeekOne DD Single-Cell 3' Transcriptome Kit (SeekGene, K00202-0202) according to the manufacturer's instructions. The resulting cDNA was PCR-amplified, and libraries were generated using the SeekOne DD Single Cell RNA Library Prep Kit (SeekGene, K00202-0204).

treatment_protocol: Option 1, for post-mortem samples: Mice were euthanized by cervical dislocation. Brains were immediately harvested, the cerebellum was removed, and the remaining tissues were rinsed twice with ice-cold PBS before being rapidly frozen on dry ice for 10 minutes. Option 2, for in vivo (anesthetized) samples: Mice were deeply anesthetized with isoflurane followed by rapid craniotomy and brain extraction. Brains were immediately harvested, the cerebellum was removed, and the remaining tissues were rinsed twice with ice-cold PBS before being rapidly frozen on dry ice for 10 minutes.

value: brain

value: neuron and glial cell

value: wild type

value: Brain tissue collected via craniotomy under anesthesia (in vivo). Nuclei were isolated and kept fresh (unfixed). Library prepared with SeekOne kit.


title: brain, post-mortem, unfixed control

status: Public on Apr 12 2026

type: SRA

country: China

description:
Library name: PM_UC
SeekOne

library_source: transcriptomic single cell

organism: Mus musculus

tag: tissue

tag: strain

tag: cell type

tag: genotype

tag: treatment

value: Brain tissue collected via cervical dislocation (post-mortem). Nuclei were isolated and kept fresh (unfixed). Library prepared with SeekOne kit.


title: ALS45_deltapurR::Spc_ermBL_ermB_3FLAG_1Ery

city: Chicago

first: Mee-Ngan

middle: F.

last: Yap

state: IL

address: 320 E Superior St

department: Microbiology-Immunology

country: USA

institute: Northwestern University Feinberg School of Medicine

description: Library name: ALS45

library_source: transcriptomic

data_processing:
Quality control and adapter trimming was performed with Trim Galore 16. BBSplit and SortMeRNA were used to remove genome containimants and rRNAs. Salmon and RSEM were used for alignment and quantification. Raw, quantified total counts of each locus are available in the “.tsv” file.
Assembly: GenBank accession CP000255.1
Supplementary files format and content: Text delimited file showing read couts (RPKM) of every locus

molecule: total RNA

organism: Staphylococcus aureus

source_name: whole cell

growth_protocol: S. aureus cells were grown in TSB until early-log phase (OD600~ 0.2) at 37ºC and either treated with and without sublethal 1ug/mL or lethal 400 ug/ml of erythromycin for 120 min.

extract_protocol:
Bacterial cells were disrupted by Lysing Matrix B beads on a MP Biomedical FastPrep 24 instrument for 2 cycles of 40M/s.  Cell lysates were extracted with acidic phenol-chloroform (pH 4.7) at least 2-3 times before subjecting to isopropanol precipitation. Crude RNAs were further cleaned up using the Qiagen RNeasy mini columns. Final total RNA were digested with Turbo DNase I to remove genomic DNA contamination
Ribo-Zero rRNA depletion and cDNA libraries was performed by NUSeq core (Northwestern Univ) using Illumina Unique Dual Indexes.

treatment_protocol: antibiotic (erythromycin) exposure

value: whole cell

tag: cell line

value: delta_purR::Spc ermBL-ermB_3_FLAG

value: 1 ug/mL Erythromycin


title: brain, in vivo, methanol-fixed

description:
Library name: IV_MF
SeekOne

value: Brain tissue collected via craniotomy under anesthesia (in vivo). Nuclei were isolated and fixed with methanol. Library prepared with SeekOne kit.


title: brain, post-mortem, methanol-fixed

description:
Library name: PM_MF
SeekOne

value: Brain tissue collected via cervical dislocation (post-mortem). Nuclei were isolated and fixed with methanol. Library prepared with SeekOne kit.


title: Akk_2

city: chengdu

first: Mingshan

last: Jiang

institute: west china hospital

description:
Library name: Akk_2
splenic CD5+ T cells isolated from DSS-induced colitis mice treated with Akkermansia muciniphila

data_processing:
Raw sequencing reads were quality-controlled and filtered to remove adapters and low-quality reads.
Clean reads were aligned to the Mus musculus reference genome using a standard alignment tool.
Gene-level read counts were generated and normalized expression values (FPKM) were calculated.
Assembly: Mus musculus reference genome (GRCm39)
Supplementary files format and content: Processed data are provided as tab-delimited text files containing gene-level raw counts and FPKM-normalized expression values for all samples.

source_name: spleen

growth_protocol: C57BL/6J mice were maintained under specific pathogen-free (SPF) conditions with free access to food and water.

extract_protocol:
Splenic CD4+ T cells were isolated and total RNA was extracted using standard RNA extraction methods. RNA quality and integrity were assessed prior to sequencing.
RNA sequencing libraries were prepared using poly(A) selection followed by cDNA synthesis and fragmentation according to standard protocols.

treatment_protocol: Colitis was induced by administration of dextran sulfate sodium (DSS) in drinking water. Mice were treated daily with Akkermansia muciniphila or PBS as control.

value: spleen

value: CD4+ T cells

value: Akkermansia muciniphila

tag: batch


title: Ctrl_2

description:
Library name: Ctrl_2
splenic CD5+ T cells isolated from DSS-induced colitis mice treated with PBS

value: PBS


title: Akk_3

description:
Library name: Akk_3
splenic CD6+ T cells isolated from DSS-induced colitis mice treated with Akkermansia muciniphila


title: Ctrl_3

description:
Library name: Ctrl_3
splenic CD6+ T cells isolated from DSS-induced colitis mice treated with PBS


title: ALS41_ermBL_ermB_3FLAG_400Ery

description: Library name: ALS41

value: 400 ug/mL Erythromycin


title: Ctrl_1

description:
Library name: Ctrl_1
splenic CD4+ T cells isolated from DSS-induced colitis mice treated with PBS


title: Akk_1

description:
Library name: Akk_1
splenic CD4+ T cells isolated from DSS-induced colitis mice treated with Akkermansia muciniphila


title: 115_DEN_T_CA_16

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research

description: Library name: Sample 115

data_processing:
Reads were mapped using Salmon-1.4.042 against the GENCODE vM25 mouse transcriptome with GRCm38 mouse genome assembly as a decoy. The Salmon mapping algorithm was used with both random hexamer priming and GC bias correction.
Assembly: Reads were mapped using Salmon-1.4.042 against the GENCODE vM25 mouse transcriptome with GRCm38 mouse genome assembly as a decoy. The Salmon mapping algorithm was used with both random hexamer priming and GC bias correction.
Supplementary files format and content: The R package tximeta-1.8.243 was used to generate raw count matrices from Salmon quant.sf output files.

molecule: polyA RNA

source_name: Liver tumor

extract_protocol:
The mouse liver and liver tumour tissues were snap frozen in liquid nitrogen and stored at −80°C. Total RNA from liver or tumor tissues was extracted using Favor Prep Total RNA Mini Kit (Favorgen, Cat. FABRK 001) with DNase I treatment (Qiagen, Cat. 79256) according to the manufacturer's instructions and stored at −80°C until use.
The RNA-seq libraries were prepared from 100 ng total RNA of liver or tumor tissues using Truseq stranded mRNA library prep kit (Illumina, Cat. 20020595). The libraries were sequenced with signle-end 100bp on NovaSeq 6000 (Illumina) to yield a median of 20 million reads per sample.

value: Liver tumor

value: DEN, CA diet


title: 114_DEN_T_CA_15

description: Library name: Sample 114


title: 113_DEN_nonT_CA_15

description: Library name: Sample 113

source_name: Liver

value: Liver


title: 109_DEN_T_CA_12

description: Library name: Sample 109


title: 111_DEN_T_CA_13

description: Library name: Sample 111


title: 110_DEN_nonT_CA_13

description: Library name: Sample 110


title: 112_DEN_nonT_CA_14

description: Library name: Sample 112


title: 116_DEN_T_CA_17

description: Library name: Sample 116


title: 108_DEN_nonT_CA_12

description: Library name: Sample 108


title: 105_DEN_T_CA_10

description: Library name: Sample 105


title: 106_DEN_nonT_CA_11

description: Library name: Sample 106


title: Sample18-HRS

status: Public on Apr 13 2026

city: New York

first: Isabella

last: Kong

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

description: Library name: Sample 13

data_processing:
Raw data were mapped to the human genome GRCh37 using STAR version 2.3.0e.
Reads that mapped to any of 52,775 genes annotated in Ensembl were counted using HTSeq-counts v.0.6.1 after which genes without a counts per million reads (CPM) in at least 3 samples were excluded from downstream analysis.
Com-bat was used to correct for batch effects.
Count data were normalized using the trimmed mean of M-values (TMM) method and differential gene expression analysis was performed using the limma-voom pipeline.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

organism: Homo sapiens

source_name: Tumour biopsy

growth_protocol: Cell lines were grown in RPMI+10% FBS + 1x gentamicin. Cells were cultured at 37C with 5% CO2.

extract_protocol:
RNA was extracted using the Arcturus PicoPure RNA Isolation kit (KIT0204, Life Technologies, Carlsbad, CA) with RNAse-Free DNase (79254, Qiagen, Venlo, Netherlands) to isolate high quality RNA from viable flow-sorted cells.
We applied the SMARTer Ultra Low Input RNA Kit (Clontech, Mountain View, CA) to 1-4 ng of input total mRNA.  Illumina-compatible libraries were constructed from cDNA using KAPA LTP Library Preparation Kit (KK8221, Woburn, MA).

value: Tumour biopsy

tag: patient

value: Primary tumour

value: Sorted HRS cells


title: 101_DEN_T_CA_8

description: Library name: Sample 101


title: 107_DEN_T_CA_11

description: Library name: Sample 107


title: 96_DEN_T_CA_5

description: Library name: Sample 96


title: 103_DEN_T_CA_9

description: Library name: Sample 103


title: 100_DEN_T_CA_7

description: Library name: Sample 100


title: 99_DEN_nonT_CA_7

description: Library name: Sample 99


title: 97_DEN_nonT_CA_6

description: Library name: Sample 97


title: 98_DEN_T_CA_6

description: Library name: Sample 98


title: 102_DEN_nonT_CA_9

description: Library name: Sample 102


title: 104_DEN_nonT_CA_10

description: Library name: Sample 104


title: 90_DEN_T_CA_2

description: Library name: Sample 90


title: 91_DEN_nonT_CA_3

description: Library name: Sample 91


title: 95_DEN_nonT_CA_5

description: Library name: Sample 95


title: 93_DEN_nonT_CA_4

description: Library name: Sample 93


title: 94_DEN_T_CA_4

description: Library name: Sample 94


title: 88_DEN_T_CA_1

description: Library name: Sample 88


title: 89_DEN_nonT_CA_2

description: Library name: Sample 89


title: 92_DEN_T_CA_3

description: Library name: Sample 92


title: 86_DEN_nonT_ChR_15

description: Library name: Sample 86

value: DEN, ChR diet


title: 87_DEN_nonT_CA_1

description: Library name: Sample 87


title: 82_DEN_nonT_ChR_13

description: Library name: Sample 82


title: 85_DEN_T_ChR_14

description: Library name: Sample 85


title: 83_DEN_T_ChR_13

description: Library name: Sample 83


title: 79_DEN_T_ChR_11

description: Library name: Sample 79


title: 81_DEN_T_ChR_12

description: Library name: Sample 81


title: 78_DEN_nonT_ChR_11

description: Library name: Sample 78


title: 76_DEN_T_ChR_9

description: Library name: Sample 76


title: 80_DEN_nonT_ChR_12

description: Library name: Sample 80


title: 84_DEN_nonT_ChR_14

description: Library name: Sample 84


title: 73_DEN_nonT_ChR_8

description: Library name: Sample 73


title: 75_DEN_nonT_ChR_9

description: Library name: Sample 75


title: 69_DEN_nonT_ChR_6

description: Library name: Sample 69


title: 72_DEN_T_ChR_7

description: Library name: Sample 72


title: 74_DEN_T_ChR_8

description: Library name: Sample 74


title: 67_DEN_nonT_ChR_5

description: Library name: Sample 67


title: 66_DEN_T_ChR_4

description: Library name: Sample 66


title: 65_DEN_nonT_ChR_4

description: Library name: Sample 65


title: 68_DEN_T_ChR_5

description: Library name: Sample 68


title: 77_DEN_nonT_ChR_10

description: Library name: Sample 77


title: 57_DEN_T_HS_16

description: Library name: Sample 57

value: DEN, HS diet


title: 60_DEN_T_HS_18

description: Library name: Sample 60


title: 61_DEN_nonT_ChR_1

description: Library name: Sample 61


title: 55_DEN_nonT_HS_15

description: Library name: Sample 55


title: 71_DEN_nonT_ChR_7

description: Library name: Sample 71


title: 53_DEN_nonT_HS_14

description: Library name: Sample 53


title: 62_DEN_nonT_ChR_2

description: Library name: Sample 62


title: 64_DEN_T_ChR_3

description: Library name: Sample 64


title: 52_DEN_T_HS_13

description: Library name: Sample 52


title: 63_DEN_nonT_ChR_3

description: Library name: Sample 63


title: 70_DEN_T_ChR_6

description: Library name: Sample 70


title: 54_DEN_T_HS_14

description: Library name: Sample 54


title: 51_DEN_nonT_HS_13

description: Library name: Sample 51


title: 56_DEN_nonT_HS_16

description: Library name: Sample 56


title: 46_DEN_nonT_HS_10

description: Library name: Sample 46


title: 59_DEN_T_HS_17

description: Library name: Sample 59


title: 49_DEN_T_HS_11

description: Library name: Sample 49


title: 50_DEN_nonT_HS_12

description: Library name: Sample 50


title: 45_DEN_T_HS_9

description: Library name: Sample 45


title: 58_DEN_nonT_HS_17

description: Library name: Sample 58


title: 48_DEN_nonT_HS_11

description: Library name: Sample 48


title: 40_DEN_nonT_HS_7

description: Library name: Sample 40


title: 47_DEN_T_HS_10

description: Library name: Sample 47


title: 44_DEN_nonT_HS_9

description: Library name: Sample 44


title: 43_DEN_T_HS_8

description: Library name: Sample 43


title: 42_DEN_nonT_HS_8

description: Library name: Sample 42


title: 32_DEN_nonT_HS_2

description: Library name: Sample 32


title: 37_DEN_nonT_HS_5

description: Library name: Sample 37


title: 41_DEN_T_HS_7

description: Library name: Sample 41


title: 39_DEN_T_HS_6

description: Library name: Sample 39


title: 34_DEN_nonT_HS_3

description: Library name: Sample 34


title: 35_DEN_nonT_HS_4

description: Library name: Sample 35


title: 33_DEN_T_HS_2

description: Library name: Sample 33


title: 38_DEN_nonT_HS_6

description: Library name: Sample 38


title: 31_DEN_T_HS_1

description: Library name: Sample 31


title: 29_DEN_T_NC_19

description: Library name: Sample 29

value: DEN, NC diet


title: 28_DEN_nonT_NC_19

description: Library name: Sample 28


title: 30_DEN_nonT_HS_1

description: Library name: Sample 30


title: 26_DEN_T_NC_17

description: Library name: Sample 26


title: 36_DEN_T_HS_4

description: Library name: Sample 36


title: 23_DEN_nonT_NC_16

description: Library name: Sample 23


title: 20_DEN_T_NC_14

description: Library name: Sample 20


title: 24_DEN_T_NC_16

description: Library name: Sample 24


title: 22_DEN_T_NC_15

description: Library name: Sample 22


title: 16_DEN_T_NC_12

description: Library name: Sample 16


title: 18_DEN_T_NC_13

description: Library name: Sample 18


title: 21_DEN_nonT_NC_15

description: Library name: Sample 21


title: 17_DEN_nonT_NC_13

description: Library name: Sample 17


title: 15_DEN_nonT_NC_12

description: Library name: Sample 15


title: 25_DEN_nonT_NC_17

description: Library name: Sample 25


title: 19_DEN_nonT_NC_14

description: Library name: Sample 19


title: 27_DEN_T_NC_18

description: Library name: Sample 27


title: 13_DEN_nonT_NC_11

description: Library name: Sample 13


title: 8_DEN_nonT_NC_7

description: Library name: Sample 8


title: 10_DEN_nonT_NC_9

description: Library name: Sample 10


title: 5_DEN_T_NC_4

description: Library name: Sample 5


title: 11_DEN_T_NC_9

description: Library name: Sample 11


title: 9_DEN_nonT_NC_8

description: Library name: Sample 9


title: 6_DEN_nonT_NC_5

description: Library name: Sample 6


title: 14_DEN_T_NC_11

description: Library name: Sample 14


title: 3_DEN_nonT_NC_3

description: Library name: Sample 3


title: 4_DEN_nonT_NC_4

description: Library name: Sample 4


title: 1_DEN_nonT_NC_1

description: Library name: Sample 1


title: 2_DEN_nonT_NC_2

description: Library name: Sample 2


title: ATAC-Seq - Atg5fl/fl_FLOX4_4

city: Guangzhou

first: Junyu

last: He

address: School of Basic Medicine, Southern Medical University, Guangzhou

institute: School of Basic Medical Sciences, Southern Medical University

description: Library name: Sample7

library_source: genomic

data_processing:
Omicsmart
Assembly: Ensembl_release112
Supplementary files format and content: CSV

molecule: genomic DNA

source_name: intestines

extract_protocol:
Cell samples were obtained and nuclei were extracted. Tn5 transposase was added to the nuclear suspension to perform the transposition reaction.
After the reaction was completed, DNA fragments were purified; subsequently, PCR amplification was carried out, and the fragments were purified using AMPure XP beads (Beckman Coulter, Brea, CA, USA).Sequencing libraries were constructed. Upon completion of library construction, the libraries were subjected to quality inspection using an Agilent 2100 (Agilent, Santa Clara, CA).Libraries that passed the quality inspection were used for on-machine sequencing (NovaSeq X Plus) to obtain sequence information of the open chromatin region fragments to be tested.

value: intestines

value: DN ILC3


title: Xeno_T_4

description: Library name: Sample 4

extract_protocol:
The mouse tumour tissues were snap frozen in liquid nitrogen and stored at −80°C. Total RNA from liver or tumor tissues was extracted using Favor Prep Total RNA Mini Kit (Favorgen, Cat. FABRK 001) with DNase I treatment (Qiagen, Cat. 79256) according to the manufacturer's instructions and stored at −80°C until use.
The RNA-seq libraries were prepared from 100 ng total RNA of liver or tumor tissues using Truseq stranded mRNA library prep kit (Illumina, Cat. 20020595). The libraries were sequenced with signle-end 100bp on NovaSeq 6000 (Illumina) to yield a median of 20 million reads per sample.

value: Tumor xenograft


title: Xeno_T_3

description: Library name: Sample 3


title: 7_DEN_nonT_NC_6

description: Library name: Sample 7


title: ATAC-Seq - Atg5fl/fl_FLOX3_3

description: Library name: Sample6


title: Xeno_T_1

description: Library name: Sample 1


title: 12_DEN_nonT_NC_10

description: Library name: Sample 12


title: Xeno_T_2

description: Library name: Sample 2


title: ATAC-Seq - RorccreAtg5fl/fl_CKO3_3

description: Library name: Sample3


title: ATAC-Seq - RorccreAtg5fl/fl_CKO2_2

description: Library name: Sample2


title: ATAC-Seq - Atg5fl/fl_FLOX1_1

description: Library name: Sample4


title: Xeno_T_5

description: Library name: Sample 5


title: ATAC-Seq - RorccreAtg5fl/fl_CKO1_1

description: Library name: Sample1


title: L141_34_hippocampus_left

city: Hangzhou

first: Li

last: Li

state: Zhejiang

address: Shilongshan ST #18, Xihu District

institute: Westlake University

description:
Library name: L141_34_hippocampus_left
CRISPR array amplicon (Col1a1) from genomic DNA

data_processing:
In the Spatio-DARLIN amplicon library, Read 1 (85 bp) contains the spatial barcode (SB) and UMI (UB), whereas Read 2 (350 bp) captures the 5′ flanking sequence, the lineage barcode, and the 3′ flanking sequence. The three target arrays (CA, TA, and RA) are distinguished by array-specific flanking sequences.
We used cutadapt (v5.0) to extract lineage barcodes (LB) from Read 2. Reads that lack identifiable flanking sequences were discarded at this step. We associated LBs with spots by extracting SB and UB from the paired Read 1 using BSTMatrix (v2.4.f.1). The sequencing errors in SB and UB were also corrected at this step.
Subsequently, a customized computational pipeline was applied to this data to address three major classes of errors: PCR/sequencing errors, amplification artifacts, and capture-oligo carryover artifacts.
After QC, physical coordinates were assigned to SR (corrected spatial barcode), and a spot-level UMI count matrix (SRs × LRs, corrected lineage barcodes) was constructed using BSTMatrix. Finally, cell-level UMI count matrices (cells × LRs) were generated by aggregating spots within the same cell segmentation mask. All downstream analyses were performed exclusively at the cell level. The processing pipeline is under https://github.com/JarningGau/spatio_DARLIN/
Assembly: >CA CGCCGGACTGCACGACAGTCGACGATGGAGTCGACACGACTCGCGCATACGATGGAGTCGACTACAGTCGCTACGACGATGGAGTCGCGAGCGCTATGAGCGACTATGGAGTCGATACGATACGCGCACGCTATGGAGTCGAGAGCGCGCTCGTCGACTATGGAGTCGCGACTGTACGCACACGCGATGGAGTCGATAGTATGCGTACACGCGATGGAGTCGAGTCGAGACGCTGACGATATGGAGTCGATACGTAGCACGCAGACGATGGGAGCT >TA TCGCCGGAGTCGAGACGCTGACGATATGGAGTCGACACGACTCGCGCATACGATGGAGTCGCGAGCGCTATGAGCGACTATGGAGTCGATAGTATGCGTACACGCGATGGAGTCGACTACAGTCGCTACGACGATGGAGTCGATACGATACGCGCACGCTATGGAGTCGCGACTGTACGCACACGCGATGGAGTCGACTGCACGACAGTCGACGATGGAGTCGATACGTAGCACGCAGACGATGGGAGCGAGAGCGCGCTCGTCGACTATGGA >RA GCGCCGGCGAGCGCTATGAGCGACTATGGAGTCGACACGACTCGCGCATACGATGGAGTCGACTACAGTCGCTACGACGATGGAGTCGATACGATACGCGCACGCTATGGAGTCGACTGCACGACAGTCGACGATGGAGTCGATACGTAGCACGCAGACGATGGGAGCGAGTCGAGACGCTGACGATATGGAGTCGATAGTATGCGTACACGCGATGGAGTCGCGACTGTACGCACACGCGATGGAGTCGAGAGCGCGCTCGTCGACTATGGA
Supplementary files format and content: barcodes.tsv.gz: list of segmented cell IDs
Supplementary files format and content: barcodes_pos.tsv.gz: list of spatial coordinates of segmented cell IDs
Supplementary files format and content: features.tsv.gz: list of clone barcodes
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: features_allele.tsv.gz: list of clone barcodes and mutation details

source_name: hippocampus

extract_protocol:
Firstly, we did perfusion on the mice with approximately 20 mL of precooled phosphate buffered saline (PBS) to remove blood, then excised the small intestine and rinsed the intestinal lumen with precooled PBS to remove its contents. Small intestine tissues were carefully cleaned from adipose tissue and divided into three segments equal in length named PSI (Proximal small intestine), MSI (Middle small intestine) and DSI (Distal small intestine). Each segment was cut longitudinally, starting from the most distal portion with the luminal side facing upward, the small intestine was rolled resulting in a Swiss-roll with the distal SI in the center and the proximal SI in the outer portion of the roll. The fresh tissue was then embedded in Optimal Cutting Temperature compound (OCT, Sakura Tissue-TEK) on dry ice and stored at -80 °C.
The BMKMANU S3000 RNA-seq was performed with the BMKMANU S3000 Gene Expression kit (BMKMANU, ST03010). In brief, OCT blocks were cut with a pre-cooled cryostat at 10 μm thickness, and sections were transferred to fit the 6.8*6.8 mm2 oligo-barcoded capture areas on the BMK S3000 slide. The experimental slide with small intestine tissue was fixed and stained with hematoxylin and eosin (H&E) and imaged. Sequence libraries were then processed according to manufacturer’s instructions. After cDNA amplification, cDNA quality inspection was performed using Agilent 2100. Before performing the complete protocol, Tissue Optimization (BMKMANU, ST03003) was performed according to manufacturer’s instructions, and the fluorescent footprint was imaged using a fluorescence microscope. About thirty minutes was selected as optimal permeabilization time. In parallel, we used unfragmented cDNA as starting material and a nested PCR approach to perform targeted amplification with KAPA HiFi HotStart ReadyMix (Roche Applied Science, 07958935001). We amplified each of the three target arrays individually by performing three separate PCR reactions for each sample. We first amplified the CA-, TA-, and RA-array libraries for 9 cycles using a 1/5th of the purified cDNA, the P5_PR1 primer, and either the NGS_CA_R1, NGS_TA_R1, or NGS_RA_R1 primer. The three PCR products were purified, and each was subject to a second PCR with 9 cycles, again using the P5_PR1 primer and either the NGS_CA_R2, NGS_TA_R2, or NGS_RA_R2 primer. Each of the resulting PCR products was further purified and used to perform an indexing PCR for 9 cycles using the primers included in this kit (New England Biosciences, E6609S). We used 0.8X SPRI SELECT REAGENT beads (Beckman Coulter, B23318) to purify the PCR product from each step once except the final indexing PCR product (0.8X, twice purification). The final indexing libraries were pooled and quantified with VAHTS Library Quantification Kit for Illumina (Vazyme, NQ101), and sequenced on an Illumina NovaSeq 6000 using NovaSeq 6000 SP kits (Read 1: 85 cycles; i7 Index: 8 cycles; Read 2: 350 cycles; Illumina, MS-102-2003) with 10% PhiX sequencing control v3 (Illumina, FC-110-3001).

treatment_protocol: To label adult mice, doxycycline (ABCONE, D48978) was administered via drinking water for one week (2 mg/mL, supplemented with 10 mg/mL sucrose) and three intraperitoneal injections (50 μg/g) every other day during the same week. To label embryonic-stage mice, pregnant dams were anesthetized and injected a single dose of doxycycline (50 μg/g) through the retro-orbital route.

value: hippocampus

tag: age

value: 5 weeks

tag: locus

value: Dox induction for 12h at E10

tag: time after_dox_induction

value: 6 weeks


title: L141_34_cortex_dorsal_right

description:
Library name: L141_34_cortex_dorsal_right
CRISPR array amplicon (Col1a1) from genomic DNA

source_name: dorsal cortex

value: dorsal cortex


title: L141_34_thalamus_left

description:
Library name: L141_34_thalamus_left
CRISPR array amplicon (Col1a1) from genomic DNA

source_name: thalamus

value: thalamus


title: ATAC-Seq - Atg5fl/fl_FLOX2_2

description: Library name: Sample5


title: L141_12_thalamus_right

description:
Library name: L141_12_thalamus_right
CRISPR array amplicon (Col1a1) from genomic DNA


title: L141_34_cortex_ventral_left

description:
Library name: L141_34_cortex_ventral_left
CRISPR array amplicon (Col1a1) from genomic DNA

source_name: ventral cortex

value: ventral cortex


title: L141_34_cortex_ventral_right

description:
Library name: L141_34_cortex_ventral_right
CRISPR array amplicon (Col1a1) from genomic DNA


title: L141_34_dura

description:
Library name: L141_34_dura
CRISPR array amplicon (Col1a1) from genomic DNA

source_name: dura mater

value: dura mater


title: L141_34_cortex_dorsal_left

description:
Library name: L141_34_cortex_dorsal_left
CRISPR array amplicon (Col1a1) from genomic DNA


title: L141_12_thalamus_left

description:
Library name: L141_12_thalamus_left
CRISPR array amplicon (Col1a1) from genomic DNA


title: L141_12_hippocampus_right

description:
Library name: L141_12_hippocampus_right
CRISPR array amplicon (Col1a1) from genomic DNA


title: L141_12_hypothalamus

description:
Library name: L141_12_hypothalamus
CRISPR array amplicon (Col1a1) from genomic DNA

source_name: hypothalamus

value: hypothalamus


title: L141_12_hippocampus_left

description:
Library name: L141_12_hippocampus_left
CRISPR array amplicon (Col1a1) from genomic DNA


title: CNS LK/CLP 4

city: Edinburgh

first: Alasdair

last: Duguid

address: 5 Little France Drive

department: Institute for Regeneration and Repair

country: United Kingdom

institute: University of Edinburgh

data_processing:
The Cogent NGS Analysis Pipeline v2.0 (TaKaRa) in the command line was used for data preprocessing.
SummarizedExperiment objects containing count matrices were created using the GenomicAlignments package and the aligned BAM files.
SummarizedExperiment objects were transformed into DESeqDataSet objects, prefiltered, normalised and a results table created using the DESeq2 package.
Assembly: GRCm39
Supplementary files format and content: Normalised count matrix

source_name: CNS

extract_protocol:
RNA was extracted from freshly sorted leukaemia propagating cells harvesed from the bone marrow and central nervous system of  using the Quick-RNA Microprep Kit (Zymo, R1050).
cDNA library preparation was performed using SMARTer Stranded Total RNA-Seq Kit v3 – Pico Input Mammalian (TaKaRa, 634487).

value: CNS

tag: disease state

value: Pro B-ALL

value: LK

value: miR-128a overexpressing Kmt2a-AFF1+


title: CNS LSK 4


title: BM LK/CLP 4

source_name: BM

value: BM


title: L141_34_hypothalamus

description:
Library name: L141_34_hypothalamus
CRISPR array amplicon (Col1a1) from genomic DNA


title: BM LSK 4


title: L141_34_thalamus_right

description:
Library name: L141_34_thalamus_right
CRISPR array amplicon (Col1a1) from genomic DNA


title: L141_12_cortex_ventral_left

description:
Library name: L141_12_cortex_ventral_left
CRISPR array amplicon (Col1a1) from genomic DNA


title: CNS LK/CLP 3


title: BM LK/CLP 3


title: L141_12_dura

description:
Library name: L141_12_dura
CRISPR array amplicon (Col1a1) from genomic DNA


title: L141_12_cortex_ventral_right

description:
Library name: L141_12_cortex_ventral_right
CRISPR array amplicon (Col1a1) from genomic DNA


title: CNS LSK 3


title: L141_12_cortex_dorsal_left

description:
Library name: L141_12_cortex_dorsal_left
CRISPR array amplicon (Col1a1) from genomic DNA


title: L141_34_hippocampus_right

description:
Library name: L141_34_hippocampus_right
CRISPR array amplicon (Col1a1) from genomic DNA


title: ALS39_ermBL_ermB_3FLAG_0Ery

description: Library name: ALS39

value: whole cell

value: ethanol mock


title: BM LK/CLP 2


title: L126_Brain_s3_CA

description:
Library name: L126_Brain_s3_CA
CRISPR array amplicon (Col1a1) from Fresh frozen Spatial transcriptome sequencing

library_source: other

data_processing:
In the Spatio-DARLIN amplicon library, Read 1 (85 bp) contains the spatial barcode (SB) and UMI (UB), whereas Read 2 (350 bp) captures the 5′ flanking sequence, the lineage barcode, and the 3′ flanking sequence. The three target arrays (CA, TA, and RA) are distinguished by array-specific flanking sequences.
We used cutadapt (v5.0) to extract lineage barcodes (LB) from Read 2. Reads that lack identifiable flanking sequences were discarded at this step. We associated LBs with spots by extracting SB and UB from the paired Read 1 using BSTMatrix (v2.4.f.1). The sequencing errors in SB and UB were also corrected at this step.
Subsequently, a customized computational pipeline was applied to this data to address three major classes of errors: PCR/sequencing errors, amplification artifacts, and capture-oligo carryover artifacts.
After QC, physical coordinates were assigned to SR (corrected spatial barcode), and a spot-level UMI count matrix (SRs × LRs, corrected lineage barcodes) was constructed using BSTMatrix. Finally, cell-level UMI count matrices (cells × LRs) were generated by aggregating spots within the same cell segmentation mask. All downstream analyses were performed exclusively at the cell level. The processing pipeline is under https://github.com/JarningGau/spatio_DARLIN/
Assembly: >CA CGCCGGACTGCACGACAGTCGACGATGGAGTCGACACGACTCGCGCATACGATGGAGTCGACTACAGTCGCTACGACGATGGAGTCGCGAGCGCTATGAGCGACTATGGAGTCGATACGATACGCGCACGCTATGGAGTCGAGAGCGCGCTCGTCGACTATGGAGTCGCGACTGTACGCACACGCGATGGAGTCGATAGTATGCGTACACGCGATGGAGTCGAGTCGAGACGCTGACGATATGGAGTCGATACGTAGCACGCAGACGATGGGAGCT >TA TCGCCGGAGTCGAGACGCTGACGATATGGAGTCGACACGACTCGCGCATACGATGGAGTCGCGAGCGCTATGAGCGACTATGGAGTCGATAGTATGCGTACACGCGATGGAGTCGACTACAGTCGCTACGACGATGGAGTCGATACGATACGCGCACGCTATGGAGTCGCGACTGTACGCACACGCGATGGAGTCGACTGCACGACAGTCGACGATGGAGTCGATACGTAGCACGCAGACGATGGGAGCGAGAGCGCGCTCGTCGACTATGGA >RA GCGCCGGCGAGCGCTATGAGCGACTATGGAGTCGACACGACTCGCGCATACGATGGAGTCGACTACAGTCGCTACGACGATGGAGTCGATACGATACGCGCACGCTATGGAGTCGACTGCACGACAGTCGACGATGGAGTCGATACGTAGCACGCAGACGATGGGAGCGAGTCGAGACGCTGACGATATGGAGTCGATAGTATGCGTACACGCGATGGAGTCGCGACTGTACGCACACGCGATGGAGTCGAGAGCGCGCTCGTCGACTATGGA
Supplementary files format and content: barcodes.tsv.gz: list of segmented cell IDs
Supplementary files format and content: barcodes_pos.tsv.gz: list of spatial coordinates of segmented cell IDs
Supplementary files format and content: features.tsv.gz: list of clone barcodes
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: features_allele.tsv.gz: list of clone barcodes and mutation details
Library strategy: Spatial Transcriptomics

molecule: other

source_name: Brain

value: Brain

value: 7 weeks

value: 8 weeks


title: BM LSK 2


title: L126_Brain_s3_RA

description:
Library name: L126_Brain_s3_RA
CRISPR array amplicon (Rosa26) from Fresh frozen Spatial transcriptome sequencing

value: Dox induction for 12h at E10


title: CNS LK/CLP 2


title: CNS LSK 2


title: L126_Brain_s3_TA

description:
Library name: L126_Brain_s3_TA
CRISPR array amplicon (Tigre) from Fresh frozen Spatial transcriptome sequencing

value: Tigre


title: L126_Brain_s2_RA

description:
Library name: L126_Brain_s2_RA
CRISPR array amplicon (Rosa26) from Fresh frozen Spatial transcriptome sequencing


title: L141_12_cortex_dorsal_right

description:
Library name: L141_12_cortex_dorsal_right
CRISPR array amplicon (Col1a1) from genomic DNA

value: dorsal cortex

value: 5 weeks

value: 6 weeks


title: L126_Brain_s2_CA

description:
Library name: L126_Brain_s2_CA
CRISPR array amplicon (Col1a1) from Fresh frozen Spatial transcriptome sequencing


title: CNS LSK 1


title: BM LSK 1


title: L126_Brain_s2_TA

description:
Library name: L126_Brain_s2_TA
CRISPR array amplicon (Tigre) from Fresh frozen Spatial transcriptome sequencing


title: L126_Brain_s1_CA

description:
Library name: L126_Brain_s1_CA
CRISPR array amplicon (Col1a1) from Fresh frozen Spatial transcriptome sequencing


title: RNA-seq of HeLa cells arrested in metaphase by proTAME (replicate 2)

city: Tel Aviv

first: Daniel

last: Benhalevy

address: Chaim Levanon St 55

country: Israel

institute: Tel Aviv University

description:
Library name: RNAseq_proTAME_rep2
proTAME_RNAseq_merged_counts_Inputs.txt

data_processing:
Adapter trimming using cutadapt. Demultiplexing: bcl2fastq. Alignment: STAR aligner (to GRCh38)
Differential expression and binding using DESeq2, and PARalyzer
Assembly: GRCh38
Supplementary files format and content: proTAME_RNAseq_merged_counts_Inputs.txt, proTAME_RNAseq_merged_counts_Inputs_protein_coding.txt (generated for both replicates, linked to the rep1 records)
Supplementary files format and content: groups.csv

source_name: HeLa S3

growth_protocol: HeLa and HeLa S3 cultured in DMEM + 10% FBS at 37°C.

extract_protocol:
Cell extract was sampled for RNA-seq and loaded over a density gradinet. Endogenous hnRNPC was immunoprecipitated for low- and highdensity fractions, and beads were treated with RNaseI, followed by dephosphorylation of the RNA fragment (CIP), 3' ligation using using T4 Rnl2(1–249)K227Q, and phosphorylation (T4 PNK). Flluorescent RNA-protein complex was separated by SDS-PAGE and excised. After proteinase K treatment, RNA was extracted and 5' end labelled with T4 RNA ligase. Following small RNA cDNA library preparation was performed. See Anastasakis et al., PMID:33503264.
For fCLIP: Ligation products were reverse transcribed and amplified by PCR. For RNA-seq: RiboEX extraction; Ribo-Zero Gold depletion; TruSeq Stranded Total RNA Library Prep Gold.

treatment_protocol: Treatment: proTAME 12 µM; 254nm UV crosslinking.

value: HeLa S3

value: proTAME metaphase arrest, 254nm UV


title: L126_Brain_s1_TA

description:
Library name: L126_Brain_s1_TA
CRISPR array amplicon (Tigre) from Fresh frozen Spatial transcriptome sequencing


title: BM LK/CLP 1


title: CNS LK/CLP 1

value: CNS


title: L126_Brain_s1_RA

description:
Library name: L126_Brain_s1_RA
CRISPR array amplicon (Rosa26) from Fresh frozen Spatial transcriptome sequencing


title: Healthy Control6

city: Indiana University

first: Reza

last: Shahbazi

address: 980 W Walnut st

institute: Indiana University

description: Library name: HMN822875

data_processing:
All raw input data were distributed across 10 wells, meaning each well contained a portion of the sequencing data for all samples. The Cell Ranger pipeline (version 7.2.0) from 10x Genomics was used to process the raw sequencing data, including quality filtering, alignment to the human reference genome (GRCh38), cell barcode assignment, and generation of unique molecular identifier (UMI) counts to produce the gene expression matrix. Data from all wells were then aggregated to generate a unified H5 gene expression file and corresponding TCR data for each individual sample.
Antibody-derived tags (ADTs) were included using 137 predesigned sequences from TotalSeq™-C antibodies. The cellranger multi pipeline from the 10x Genomics 5′ gene expression workflow was utilized to simultaneously process gene expression, antibody-derived, and hashtag oligo data.
For T cell receptor (TCR) clonotype analysis, the V(D)J reference dataset refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0 was used to distinguish γδTCR and αβTCR lineages. Background correction for all antibodies was performed using the isotyping method to subtract non-specific signal.
Partek® Flow® software version 11.0.23.1204, Bowtie2 v2.2.5
Partek® Flow® software version 11.0.23.1204, STAR v2.7.8a
Assembly: hg38
Supplementary files format and content: h5 files includes gene expression and anti-body
Supplementary files format and content: csv files includes VDJ data
Supplementary files format and content: tab-delimited text file includes raw counts of miRNAs for each sample
Supplementary files format and content: tab-delimited text file includes raw counts of RNAs for each sample

source_name: Exosomes were isolated from bone marrow aspirates

growth_protocol: Triple-Negative Breast Cancer Panel 3 cell lines (TCP-1003) were obtained from the American Type Culture Collection (ATCC) and cultured in RPMI-1640 media supplemented with 10% exosome-depleted fetal bovine serum (Gibco) and 1% penstrep. Cells were passaged using TrypLE express enzyme (Gibco™) upon reaching 70-80% confluency. The conditioned media was collected for exosome isolation.

extract_protocol:
Human CD3⁺ T cells were isolated from peripheral blood and cultured for 72 hours in the presence of ImmunoCult™ Human CD3/CD28 T Cell Activator, followed by treatment with tumor-derived exosomes from 17 TNBC cell lines for 48 hours. After incubation, cells were harvested, washed, and stained with the TotalSeq™-C Human Universal Cocktail, v2.0 (BioLegend), which includes a panel of oligo-conjugated antibodies targeting key T cell surface markers. To enable multiplexing of biological replicates and experimental conditions, cells were also stained with TotalSeq™-C anti-human Hashtag antibodies (BioLegend), following the manufacturer’s recommended titration and staining protocol. Non-coding RNAs were isolated from exosomes derived from 17 TNBC cell lines as well as from plasma samples of 28 TNBC patients and 7 healthy donors, using the MagMAX™ mirVana™ Total RNA Isolation Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol. The isolated RNA, enriched for small and non-coding RNAs, was quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific), and RNA quality was assessed with an Agilent Bioanalyzer 2100 (Agilent Technologies).
For single cell RNA-seq, following staining, cells were counted and loaded onto the Chromium X system (10x Genomics) using the Chromium Single Cell 5′ High Throughput (HT) Immune Profiling Kit. Single-cell Gel Bead-In-Emulsions (GEMs) were generated, and barcoded cDNA libraries, including gene expression and antibody-derived tag (ADT) libraries, were constructed according to the manufacturer’s instructions. The resulting libraries were sequenced on an Illumina NovaSeq 6000 platform using an S4 flow cell to a targeted depth of ~50,000 reads per cell. For noncoding RNAs, library preparation was performed using the NEXTFLEX® Small RNA-Seq Kit v4 with Unique Dual Indices (UDIs) (Revvity), which includes 3′ and 5′ adapter ligation, reverse transcription, PCR amplification, and size selection steps optimized for non-coding RNA capture. Prepared libraries were quantified using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and validated for size distribution using the Agilent Bioanalyzer. Sequencing was conducted on an Illumina platform following standard procedures for small RNA libraries.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from healthy donor leukopaks by Lymphoprep (STEMCELL Technologies) density gradient centrifugation. CD3⁺ T cells were then purified using the EasySep™ Human T Cell Negative Isolation Kit (STEMCELL Technologies) according to the manufacturer’s instructions. Cells were resuspended in RPMI 1640 supplemented with 10% FBS and 10 ng/mL recombinant human IL-2 (STEMCELL Technologies). T cell activation was performed using ImmunoCult™ Human CD3/CD28 T Cell Activator (STEMCELL Technologies) at the recommended concentration for 72 hours. Following activation, T cells were washed and treated with tumor-derived exosomes isolated from 17 distinct TNBC cell lines. Exosome exposure was carried out for 48 hours before cells were harvested for downstream analyses.


title: Healthy Control7

description: Library name: NormalHuman

value: Exosomes were isolated from bone marrow aspirates


title: B16F10_T4_3_p110_PBS_1

city: Shanghai

first: Zhichao

last: Ai

state: Shanghai

address: 371 Lishizhen Road

department: Oncology

institute: China Innovation Center of Roche (CICoR)

description:
Library name: B16F10_T4_3_p110_PBS_1
panKO_p110_PBS

data_processing:
Reads were mapped to the mm10 genome using STAR with the options: “—runMode alignReads –outFilterMismatchNmax 2.” Uniquely mapped read pairs were counted over annotated genes using feature Counts with the options: “-T 18 -s 2 -Q 255.” Differential expression was then analysed with DESeq2
Assembly: GRCh38/GRCm38
Supplementary files format and content: Matrix files

growth_protocol: All cell lines were passed and cultured at 37°C with 5% CO2 in appropriate media. The cells in their exponential growth phase were harvested and used for cellular and in vivo assays.

extract_protocol:
After RNA isolation, oly-A selected mRNA libraries were sequenced on Illumina HiSeq4000 yielding 20-30x106 150 b.p. paired end reads per sample. Total RNAs were extracted using RNeasy mini kit (Qiagen) according to the manufacturer’s instruction.
Libraries were generated using the QIAseq 1-Step Amplicon Library Kit. mRNA was enriched via poly-A selection, followed by cDNA synthesis, adapter ligation, and PCR amplification.

value: cancer cells

value: PBS


title: B16F10_T4_3_p150_PBS_2

description:
Library name: B16F10_T4_3_p150_PBS_2
panKO_p150_PBS


title: Healthy Control4

description: Library name: HMN822873


title: B16F10_T4_3_p110_IFNb_2

description:
Library name: B16F10_T4_3_p110_IFNb_2
panKO_p110_IFNb

value: IFNb


title: Healthy Control5

description: Library name: HMN822874


title: B16F10_T4_3_p150_IFNb_2

description:
Library name: B16F10_T4_3_p150_IFNb_2
panKO_p150_IFNb


title: B16F10_T4_3_p110_IFNb_1

description:
Library name: B16F10_T4_3_p110_IFNb_1
panKO_p110_IFNb


title: B16F10_T4_3_p150_PBS_1

description:
Library name: B16F10_T4_3_p150_PBS_1
panKO_p150_PBS


title: Healthy Control2

description: Library name: HMN822871


title: Healthy Control1

description: Library name: HMN822870


title: Breast Cancer Patient27

description: Library name: UHB1810-07

source_name: Exosomes were isolated from Plasma

value: Exosomes were isolated from Plasma


title: B16F10_T4_3_p150_IFNb_1

description:
Library name: B16F10_T4_3_p150_IFNb_1
panKO_p150_IFNb


title: B16F10_T4_3_p110_PBS_2

description:
Library name: B16F10_T4_3_p110_PBS_2
panKO_p110_PBS


title: Breast Cancer Patient28

description: Library name: UHTN-04


title: RNA-seq of HeLa cells arrested in metaphase by proTAME (replicate 1)

description:
Library name: RNAseq_proTAME_rep1
proTAME_RNAseq_merged_counts_Inputs.txt


title: Breast Cancer Patient25

description: Library name: UH1803-02


title: Healthy Control3

description: Library name: HMN822872


title: B16F10_T4_3_175_195_197_PBS_1

description:
Library name: B16F10_T4_3_175_195_197_PBS_1
panKO_ZaMUTp150_PBS


title: B16F10_T4_3_IFNb_1

description:
Library name: B16F10_T4_3_IFNb_1
panKO_IFNb

value: panKO


title: Breast Cancer Patient23

description: Library name: UH1709-24


title: BM LSK 3

value: BM

value: Pro B-ALL

value: miR-128a overexpressing Kmt2a-AFF1+


title: B16F10_T4_3_175_195_197_PBS_2

description:
Library name: B16F10_T4_3_175_195_197_PBS_2
panKO_ZaMUTp150_PBS


title: Breast Cancer Patient26

description: Library name: UH1901-02


title: Breast Cancer Patient22

description: Library name: UH1609-20


title: Breast Cancer Patient24

description: Library name: UH1801-20


title: Breast Cancer Patient20

description: Library name: UH1407-34


title: B16F10_T4_3_IFNb_2

description:
Library name: B16F10_T4_3_IFNb_2
panKO_IFNb


title: Breast Cancer Patient21

description: Library name: UH1508-10


title: B16F10_T4_3_175_195_197_IFNb_1

description:
Library name: B16F10_T4_3_175_195_197_IFNb_1
panKO_ZaMUTp150_IFNb


title: B16F10_PBS_2

description:
Library name: B16F10_PBS_2
WT_PBS

value: WT


title: B16F10_PBS_1

description:
Library name: B16F10_PBS_1
WT_PBS


title: Breast Cancer Patient17

description: Library name: UH-1306-16


title: B16F10_T4_3_175_195_197_IFNb_2

description:
Library name: B16F10_T4_3_175_195_197_IFNb_2
panKO_ZaMUTp150_IFNb


title: Breast Cancer Patient18

description: Library name: UH1309-35


title: B16F10_IFNb_1

description:
Library name: B16F10_IFNb_1
WT_IFNb


title: B16F10_IFNb_2

description:
Library name: B16F10_IFNb_2
WT_IFNb


title: Lyz+antiPD1_2

description:
Library name: AG23654
10x Genomics Single Cell 3’ Library Kit V2.

data_processing:
Raw sequencing reads (FASTQ files) are processed using Cell Ranger (10x Genomics) or similar tools (e.g., STARsolo, Alevin) for alignment (to GRCh38/GRCm38), barcode/UMI correction, and gene counting. Low-quality cells are filtered (mitochondrial reads <20%, gene counts 200–6,000/cell, UMI >500). Data normalization (e.g., SCTransform, LogNormalize) and integration (Harmony, Seurat) are applied to correct batch effects. Dimensionality reduction (PCA, UMAP) and clustering (Louvain, Leiden) identify cell populations, followed by differential gene expression analysis (Wilcoxon, MAST). Cell types are annotated using reference databases (SingleR, Azimuth with manual correction). Results are visualized and exported for downstream analysis.
Assembly: GRCh38/GRCm38
Supplementary files format and content: Tab and matrix files

source_name: Tumor

growth_protocol: 5e106 MC38 transplanted to the back of C57

extract_protocol:
Fresh tumor tissue is minced and enzymatically dissociated (e.g., Collagenase IV/DNase I, 37°C, 15–45 min), followed by mechanical disruption and filtration (70 µm → 40 µm). After RBC lysis (if needed), cells are washed, debris/dead cells are removed (e.g., FACS or density gradient), and viability (>85%) is confirmed. Cells are resuspended in scRNA-seq buffer (700–1,200 cells/µL) and immediately processed for library prep (e.g., 10x Chromium) or stabilized in RNA preservation buffer. Maintain cold conditions and minimize processing time to preserve RNA integrity.
Isolated tumor cells (700–1,200 cells/µL in PBS + 0.04% BSA) are loaded onto a microfluidic platform (e.g., 10x Genomics Chromium) for single-cell encapsulation and barcoding. Reverse transcription is performed using template-switching oligos (TSO) to generate cDNA, followed by amplification and fragmentation. Indexed libraries are prepared via end-repair, A-tailing, and adapter ligation, then pooled and quantified (e.g., Bioanalyzer/Qubit). Sequencing is performed on an Illumina platform (e.g., NovaSeq) with recommended read lengths (e.g., 28 bp Read 1, 91 bp Read 2, 8 bp index). Quality control (QC) includes assessing cDNA yield, library size distribution, and doublet rates. Store libraries at –80°C until sequencing.

value: Tumor

value: Za-mutant


title: B16F10_T4_3_PBS_1

description:
Library name: B16F10_T4_3_PBS_1
panKO_PBS


title: Breast Cancer Patient19

description: Library name: UH1403-44


title: Lyz+antiPD1_1

description:
Library name: AG23651
10x Genomics Single Cell 3’ Library Kit V2.


title: WT+antiPD1_2

description:
Library name: AG23649
10x Genomics Single Cell 3’ Library Kit V2.

value: wild-type


title: Breast Cancer Patient12

description: Library name: 678-635


title: Breast Cancer Patient14

description: Library name: M-HBT286


title: Breast Cancer Patient11

description: Library name: 678-579


title: Breast Cancer Patient13

description: Library name: 678-9


title: eIF2αA/A cells, siChchd10, rep3

city: Montréal

first: Antonis

last: Koromilas

state: QC

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

country: Canada

institute: Lady Davis Institute - McGill University

description:
Library name: AA_siChchd10_set3
Column name in Counts_siCTL_sic10.csv: AA siChchd10 set 3

data_processing:
FASTQ files were processed using the standard DESeq2 pipeline (version 1.24.0). Reads were aligned to the mm10 reference mouse genome. Count matrices were generated using DESeq2. Data were filtered to only include genes with 10 or more counts in 2 or more samples.
Assembly: mm10
Supplementary files format and content: comma-separated values includes raw counts for each sample

source_name: Tissue cultured primary cells

extract_protocol:
For Bulk RNA-seq, total RNA of cells was isolated with Trizol (Thermo Fisher Scientific).
RNA-Seq libraries were prepared following the Illumina TruSeq Stranded Total RNA protocol according to the manufacturer’s instructions. The final PCR product, confirmed for size and quantity, was sequenced on an Illumina NovaSeq 6000 System.

value: Tissue cultured primary cells

value: Lung Adenocarcinoma

value: Chchd10 knockdown


title: eIF2αA/A cells, siChchd10, rep1

description:
Library name: AA_siChchd10_set1
Column name in Counts_siCTL_sic10.csv: AA siChchd10 set 1


title: WT+antiPD1_1

description:
Library name: AG23646
10x Genomics Single Cell 3’ Library Kit V2.


title: Breast Cancer Patient15

description: Library name: UH1209-02


title: Breast Cancer Patient16

description: Library name: UH-1305-48


title: eIF2αA/A cells, siChchd10, rep4

description:
Library name: AA_siChchd10_set4
Column name in Counts_siCTL_sic10.csv: AA siChchd10 set 4


title: eIF2αA/A cells, siChchd10, rep2

description:
Library name: AA_siChchd10_set2
Column name in Counts_siCTL_sic10.csv: AA siChchd10 set 2


title: eIF2αA/A cells, siControl, rep4

description:
Library name: AA_siCtrl_set4
Column name in Counts_siCTL_sic10.csv: AA siCtrl set 4

value: siControl


title: Breast Cancer Patient8

description: Library name: 678-35


title: Breast Cancer Patient7

description: Library name: 678-341


title: eIF2αA/A cells, siControl, rep3

description:
Library name: AA_siCtrl_set3
Column name in Counts_siCTL_sic10.csv: AA siCtrl set 3


title: eIF2αA/A cells, siControl, rep2

description:
Library name: AA_siCtrl_set2
Column name in Counts_siCTL_sic10.csv: AA siCtrl set 2


title: eIF2αA/A cells, siControl, rep1

description:
Library name: AA_siCtrl_set1
Column name in Counts_siCTL_sic10.csv: AA siCtrl set 1


title: Breast Cancer Patient5

description: Library name: 678-21


title: Breast Cancer Patient4

description: Library name: 678-19


title: Breast Cancer Patient6

description: Library name: 678-243


title: Breast Cancer Patient10

description: Library name: 678-449


title: Breast Cancer Patient9

description: Library name: 678-4


title: eIF2αS/S cells, siChchd10, rep3

description:
Library name: SS_siChchd10_set3
Column name in Counts_siCTL_sic10.csv: SS siChchd10 set 3


title: Breast Cancer Patient3

description: Library name: 678-17


title: eIF2αS/S cells, siChchd10, rep4

description:
Library name: SS_siChchd10_set4
Column name in Counts_siCTL_sic10.csv: SS siChchd10 set 4


title: Breast Cancer Patient2

description: Library name: 678-14


title: eIF2αS/S cells, siChchd10, rep2

description:
Library name: SS_siChchd10_set2
Column name in Counts_siCTL_sic10.csv: SS siChchd10 set 2


title: exosomes extracted from Primary Breast

description: Library name: P.Breast

source_name: Exosomes were isolated from cell-line

value: Exosomes were isolated from cell-line


title: eIF2αS/S cells, siControl, rep3

description:
Library name: SS_siCtrl_set3
Column name in Counts_siCTL_sic10.csv: SS siCtrl set 3


title: eIF2αS/S cells, siControl, rep1

description:
Library name: SS_siCtrl_set1
Column name in Counts_siCTL_sic10.csv: SS siCtrl set 1


title: Breast Cancer Patient1

description: Library name: 0534-339


title: eIF2αS/S cells, siChchd10, rep1

description:
Library name: SS_siChchd10_set1
Column name in Counts_siCTL_sic10.csv: SS siChchd10 set 1


title: exosomes extracted from MDA-MB-453

description: Library name: MDA-MB-453


title: exosomes extracted from MDA-MB-468

description: Library name: MDA-MB-468


title: eIF2αS/S cells, siControl, rep2

description:
Library name: SS_siCtrl_set2
Column name in Counts_siCTL_sic10.csv: SS siCtrl set 2


title: exosomes extracted from MDA-MB-231

description: Library name: MDA-MB-231


title: eIF2αS/S cells, shAtf4, rep1

description:
Library name: shATF4_1_CTL_rep1
Column name in Counts_pLKO_shATF4.csv: shATF4_1_CTL_rep1

value: Atf4 knockdown

value: Atf4 shRNA


title: eIF2αS/S cells, shAtf4, rep3

description:
Library name: shATF4_1_CTL_rep3
Column name in Counts_pLKO_shATF4.csv: shATF4_1_CTL_rep3


title: exosomes extracted from Hs578T

description: Library name: Hs578T


title: exosomes extracted from HCC70

description: Library name: HCC70


title: exosomes extracted from MDA-MB-436

description: Library name: MDA-MB-436


title: eIF2αS/S cells, shControl, rep4

description:
Library name: pLKO_CTL_rep4
Column name in Counts_pLKO_shATF4.csv: plko_CTL_rep4

value: scramble shRNA


title: exosomes extracted from MDA-MB-157

description: Library name: MDA-MB-157


title: eIF2αS/S cells, siControl, rep4

description:
Library name: SS_siCtrl_set4
Column name in Counts_siCTL_sic10.csv: SS siCtrl set 4


title: exosomes extracted from HCC1806

description: Library name: HCC1806


title: exosomes extracted from HCC38

description: Library name: HCC38


title: eIF2αS/S cells, shControl, rep3

description:
Library name: pLKO_CTL_rep3
Column name in Counts_pLKO_shATF4.csv: plko_CTL_rep3


title: exosomes extracted from HCC1937

description: Library name: HCC1937


title: eIF2αS/S cells, shControl, rep2

description:
Library name: pLKO_CTL_rep2
Column name in Counts_pLKO_shATF4.csv: plko_CTL_rep2


title: eIF2αS/S cells, shAtf4, rep4

description:
Library name: shATF4_1_CTL_rep4
Column name in Counts_pLKO_shATF4.csv: shATF4_1_CTL_rep4


title: exosomes extracted from HCC1599

description: Library name: HCC1599


title: exosomes extracted from HCC1395

description: Library name: HCC1395


title: eIF2αS/S cells, shAtf4, rep2

description:
Library name: shATF4_1_CTL_rep2
Column name in Counts_pLKO_shATF4.csv: shATF4_1_CTL_rep2


title: si PAK4, rep 4

city: Jeonju

first: Chang Yeob

last: Han

address: 20, Geonji-ro, Deokjin-gu

department: School of Pharmacy

country: South Korea

institute: Jeonbuk National University

description: Library name: HSC_siPAK4_4

data_processing:
bcl2fastq2-v2.20.0 package was used for basecalling.
Quality check of basecalling was done using FastQC v0.11.7 by calculating phred quality score.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic0.38, then mapped to mm10 whole genome using HISAT2 v2.1.0 and Bowtie2 v2.3.4.1
Transcript assembly and calculation of normalized Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were done using StringTie v2.1.3b.
Assembly: mm10
Supplementary files format and content: Expression_Profile.mm10.gene.txt
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: primary hepatic stellate cells

extract_protocol:
Total RNA from hepatic stellate cells was extracted using Trizol.
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA LT Sample Prep Kit (#RS-122-2001)

treatment_protocol: Primary hepatic stellate cells from mice were transfected with siRNA targeting PAK4.

value: primary hepatic stellate cells

tag: Sex

value: male

value: si PAK4 transfection

value: Batch 1


title: si PAK4, rep 3

description: Library name: HSC_siPAK4_3


title: exosomes extracted from HCC1187

description: Library name: HCC1187


title: si PAK4, rep 2

description: Library name: HSC_siPAK4_2


title: exosomes extracted from DU4475

description: Library name: DU4475


title: eIF2αS/S cells, shControl, rep1

description:
Library name: pLKO_CTL_rep1
Column name in Counts_pLKO_shATF4.csv: plko_CTL_rep1


title: exosomes extracted from HCC1143

description: Library name: HCC1143


title: si PAK4, rep 1

description: Library name: HSC_siPAK4_1


title: exosomes extracted from BT-549

description: Library name: BT-549


title: si Control, rep 3

description: Library name: HSC_sicon3

value: si Control transfection


title: exosomes extracted from BT-20

description: Library name: BT-20


title: si Control, rep 2

description: Library name: HSC_sicon2


title: TCRγδ samples from TNBC exosome-treated T cells and one untreated control, Well 10

description:
Library name: Well 10_γδ
Gene expression profiling and TCRγδ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 10

source_name: Exosomes and TCRγδ extracted from 17 T cells samples treated via different TNBC cell-lines and one untreated T cells sample

value: Expression profile which provided as H5 files and TCRγδ were isolated from T cell


title: si Control, rep 1

description: Library name: HSC_sicon1


title: TCRγδ samples from TNBC exosome-treated T cells and one untreated control, Well 9

description:
Library name: Well 9_γδ
Gene expression profiling and TCRγδ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 9


title: L0927_Brain_RA

description:
Library name: L0927_Brain_RA
CRISPR array amplicon (Rosa26) from Fresh frozen Spatial transcriptome sequencing

data_processing:
In the spatio-DARLIN amplicon library, Read 1 (85 bp) contains the spatial barcode, while Read 2 (350 bp) captures the 5′ primer, array sequence, and 3′ primer of three target arrays (CA, TA, RA). To extract the array sequences, Cutadapt was used to sequentially trim Read 2: first removing the 3′ primer from the end of the read (right trimming), and then trimming the 5′ primer from the start (left trimming). Reads that did not contain identifiable primer sequences were discarded.
Then the paired Read 1 was processed with BSTMatrix (v2.4.f.1) to extract spatial barcodes and assign spot coordinates.
Subsequent spot-level quality control included: (i) filtering spots with fewer than 10 reads, (ii) denoising array sequences by correcting single-base errors within a Hamming distance of 1, and (iii) removing ambiguous spots (spots do not have a dominant lineage barcode) using the calculate_read_fraction_per_clone_cell function from the MosaicLineage Python package (https://github.com/ShouWenWang-Lab/MosaicLineage), with parameters read_fraction_per_clone_cell_cutoff = 0.2 and mode = "max".
Finally, UMI counts for each array were aggregated across spots belonging to the same cell mask, based on the cell segmentation results from the spatial transcriptomics preprocessing step.
Supplementary files format and content: barcodes.tsv.gz: list of segmented cell IDs
Supplementary files format and content: barcodes_pos.tsv.gz: list of spatial coordinates of segmented cell IDs
Supplementary files format and content: features.tsv.gz: list of clone barcodes
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: features_allele.tsv.gz: list of clone barcodes and mutation details
Assembly: >CA
Assembly: CGCCGGACTGCACGACAGTCGACGATGGAGTCGACACGACTCGCGCATACGATGGAGTCGACTACAGTCGCTACGACGATGGAGTCGCGAGCGCTATGAGCGACTATGGAGTCGATACGATACGCGCACGCTATGGAGTCGAGAGCGCGCTCGTCGACTATGGAGTCGCGACTGTACGCACACGCGATGGAGTCGATAGTATGCGTACACGCGATGGAGTCGAGTCGAGACGCTGACGATATGGAGTCGATACGTAGCACGCAGACGATGGGAGCT
Assembly: >TA
Assembly: TCGCCGGAGTCGAGACGCTGACGATATGGAGTCGACACGACTCGCGCATACGATGGAGTCGCGAGCGCTATGAGCGACTATGGAGTCGATAGTATGCGTACACGCGATGGAGTCGACTACAGTCGCTACGACGATGGAGTCGATACGATACGCGCACGCTATGGAGTCGCGACTGTACGCACACGCGATGGAGTCGACTGCACGACAGTCGACGATGGAGTCGATACGTAGCACGCAGACGATGGGAGCGAGAGCGCGCTCGTCGACTATGGA
Assembly: >RA
Assembly: GCGCCGGCGAGCGCTATGAGCGACTATGGAGTCGACACGACTCGCGCATACGATGGAGTCGACTACAGTCGCTACGACGATGGAGTCGATACGATACGCGCACGCTATGGAGTCGACTGCACGACAGTCGACGATGGAGTCGATACGTAGCACGCAGACGATGGGAGCGAGTCGAGACGCTGACGATATGGAGTCGATAGTATGCGTACACGCGATGGAGTCGCGACTGTACGCACACGCGATGGAGTCGAGAGCGCGCTCGTCGACTATGGA
Library strategy: Spatial Transcriptomics

value: Brain

value: 7 weeks

value: Dox induction for 12h at E10

value: 8 weeks


title: si Control, rep 4

description: Library name: HSC_sicon4

value: wild-type


title: L0927_Brain_TA

description:
Library name: L0927_Brain_TA
CRISPR array amplicon (Tigre) from Fresh frozen Spatial transcriptome sequencing

value: Tigre


title: TCRγδ samples from TNBC exosome-treated T cells and one untreated control, Well 5

description:
Library name: Well 5_γδ
Gene expression profiling and TCRγδ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 5


title: NEC

description: Library name: Sample2

data_processing:
The raw sequencing data were converted and preprocessed by Gene Denovo Biotechnology Co., Ltd. (Guangzhou, China) using 10× Genomics Cell Ranger software V3.1.0 with the default parameters.
Omicsmart
Assembly: GRCm39
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: intestines

extract_protocol: Gel beads containing barcode information are combined with a mixture of cells and enzymes, then enter a reservoir where they are separated by oil to form GEMs (Gel Beads-In-Emulsions). Subsequently, the gel beads dissolve to release capture sequences containing barcode sequences, reverse transcribe cDNA fragments, and label the sample. The gel beads are broken and the oil droplets are disrupted, and PCR amplification is performed using the cDNA as a template. The products from all GEMs are mixed to construct a standard sequencing library.

value: intestines

value: ILC

tag: group

value: NEC


title: TCRγδ samples from TNBC exosome-treated T cells and one untreated control, Well 4

description:
Library name: Well 4_γδ
Gene expression profiling and TCRγδ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 4


title: TCRγδ samples from TNBC exosome-treated T cells and one untreated control, Well 6

description:
Library name: Well 6_γδ
Gene expression profiling and TCRγδ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 6


title: TCRγδ samples from TNBC exosome-treated T cells and one untreated control, Well 7

description:
Library name: Well 7_γδ
Gene expression profiling and TCRγδ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 7


title: TCRγδ samples from TNBC exosome-treated T cells and one untreated control, Well 8

description:
Library name: Well 8_γδ
Gene expression profiling and TCRγδ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 8


title: TCRγδ samples from TNBC exosome-treated T cells and one untreated control, Well 3

description:
Library name: Well 3_γδ
Gene expression profiling and TCRγδ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 3


title: Atg5fl/fl_FLOX2_2

description:
Library name: Sample5
FLOX2

data_processing:
Omicsmart
Assembly: Ensembl_release112
Supplementary files format and content: CSV file represents tpm and count

extract_protocol:
Cells were extracted for RNA by Trizol reagent and subsequently sequenced using the Illumina platform
RNA libraries were prepared for sequencing using standard Illumina platform protocols


title: Atg5fl/fl_FLOX4_4

description:
Library name: Sample7
FLOX7


title: Atg5fl/fl_FLOX3_3

description:
Library name: Sample6
FLOX6


title: TCRγδ samples from TNBC exosome-treated T cells and one untreated control, Well 1

description:
Library name: Well 1_γδ
Gene expression profiling and TCRγδ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 1


title: RorccreAtg5fl/fl_CKO3_3

description:
Library name: Sample3
CKO3


title: Atg5fl/fl_FLOX1_1

description:
Library name: Sample4
FLOX1


title: TCRγδ samples from TNBC exosome-treated T cells and one untreated control, Well 2

description:
Library name: Well 2_γδ
Gene expression profiling and TCRγδ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 2


title: TCRαβ samples from TNBC exosome-treated T cells and one untreated control, Well 10

description:
Library name: Well 10_αβ
Gene expression profiling and TCRαβ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 10

source_name: Exosomes and TCRαβ extracted from 17 T cells samples treated via different TNBC cell-lines and one untreated T cells sample

value: Expression profile which provided as H5 files and TCRαβ were isolated from T cell


title: RorccreAtg5fl/fl_CKO2_2

description:
Library name: Sample2
CKO2


title: RorccreAtg5fl/fl_CKO1_1

description:
Library name: Sample1
CKO1


title: TCRαβ samples from TNBC exosome-treated T cells and one untreated control, Well 8

description:
Library name: Well 8_αβ
Gene expression profiling and TCRαβ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 8


title: WT

description: Library name: Sample1

value: WT


title: TCRαβ samples from TNBC exosome-treated T cells and one untreated control, Well 7

description:
Library name: Well 7_αβ
Gene expression profiling and TCRαβ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 7


title: TCRαβ samples from TNBC exosome-treated T cells and one untreated control, Well 9

description:
Library name: Well 9_αβ
Gene expression profiling and TCRαβ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 9


title: TCRαβ samples from TNBC exosome-treated T cells and one untreated control, Well 5

description:
Library name: Well 5_αβ
Gene expression profiling and TCRαβ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 5


title: TAg

city: Suita

first: Shotaro

last: Tatekawa

state: Osaka

address: 2-2(D10), Yamadaoka, Suita-city

department: Departments of Radiation Oncology,

country: Japan

institute: The University of Osaka Graduate School of Medicine

description:
Library name: EL1
10x Genomics

data_processing:
The generated raw reads were analyzed using Cell Ranger (10x Genomics). scRNA-seq data analysis was conducted using R v4.1 and Seurat v4.0.5 packages.
To conduct batch correction across multiple datasets, we implemented data integration utilizing canonical correlation analysis (CCA) following the established protocols outlined in the developer's documentation (https://satijalab.org/seurat/articles/integration_introduction.html). In brief, individual datasets underwent normalization via SCTransform 46, a method that simultaneously executes variance stabilization and normalization while maintaining biological heterogeneity. Highly variable genes were subsequently identified through the Seurat function "SelectIntegrationFeatures" applied to the SCTransform-normalized datasets. Integration anchors were then determined using the Seurat function "FindIntegrationAnchors" with parameters set to 30 principal components and CCA designated as the dimensionality reduction approach. Post-integration, the data underwent scaling, principal component analysis, and visualization through UMAP.
Assembly: Mouse mm10
Supplementary files format and content: filtered_feature_bc_matrix.Wtg_CD45plus.h5, filtered_feature_bc_matrix.EL_CD45plus.h5

extract_protocol:
Single-cell isolation and sequencing procedures followed previously established protocols (Tatekawa, S. et al. N(6)-methyladenosine methylation-regulated polo-like kinase 1 cell cycle homeostasis as a potential target of radiotherapy in pancreatic adenocarcinoma. Scientific reports 12 (2022)). In brief, for single-cell isolation from solid tissue specimens, tissues were rinsed with phosphate-buffered saline (PBS), sectioned into small fragments, and treated in culture medium supplemented with 10% fetal bovine serum (FBS), 2 mg/mL collagenase D (Roche, Basel, Switzerland), and 15 μg/mL DNase I (Roche). Following digestion, tissues were filtered through a 40 μm cell strainer. The resulting cell suspension was washed in culture medium, treated with 3 mL ACK buffer for 3 minutes to eliminate red blood cells, and subsequently washed again in medium. Cells were resuspended in PBS supplemented with 2% FBS. The cell suspension was labeled with surface antibodies for 30 minutes at 4°C, followed by 7-AAD staining (BD Biosciences, Franklin Lakes, NJ). Flow cytometric analysis and cell sorting were conducted using a FACSAria II system (BD Biosciences) to evaluate cell viability. Data analysis was performed using FlowJo software (Tree Star, San Carlos, CA).
For single-cell RNA sequencing (scRNA-seq), single-cell suspensions were prepared using the 10x Genomics Chromium Controller following the protocol outlined in the Chromium Single Cell 3' Reagent Kits User Guide, utilizing the Chromium Next GEM Single Cell 3' Kit v3.1 (Cat# PN-1000269), Chromium Next GEM Chip G Single Cell Kit (Cat# PN-1000127), and Dual Index Kit TT Set A (Cat# PN-1000215). Approximately 16,500 viable cells per sample were introduced into the Chromium controller to produce 10,000 single-cell gel bead emulsions for library construction and sequencing. Oil droplets encapsulating individual cells and barcoded beads (GEMs) underwent reverse transcription on a Veriti Thermal Cycler (Thermo Fisher Scientific) to generate cDNA labeled with cell barcodes and unique molecular identifiers (UMIs). The cDNA was subsequently amplified, and single-cell libraries were constructed following the manufacturer's instructions. Library quantification was conducted using the Agilent Bioanalyzer High-Sensitivity DNA assay (Agilent, High-Sensitivity DNA Kit, Cat# 5067-4626). The amplified cDNA underwent enzymatic fragmentation, end-repair, and polyA-tagging. Size selection and purification were executed using SPRIselect magnetic beads (Beckman-Coulter, SPRIselect, Cat# B23317). Illumina sequencing adapters were attached to the size-selected fragments, followed by an additional purification step using SPRIselect magnetic beads. Sample indexes were chosen, amplified, and double-sided size selection was performed using SPRIselect magnetic beads. Final library quality control was assessed using the Agilent Bioanalyzer High-Sensitivity DNA assay. Samples were subsequently sequenced in paired-end format on a NovaSeq 6000 (Illumina) or DNBSEQ-G400RS (MGI) platform.

value: Tumor

value: TAg


title: TCRαβ samples from TNBC exosome-treated T cells and one untreated control, Well 4

description:
Library name: Well 4_αβ
Gene expression profiling and TCRαβ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 4


title: TCRαβ samples from TNBC exosome-treated T cells and one untreated control, Well 3

description:
Library name: Well 3_αβ
Gene expression profiling and TCRαβ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 3


title: TAg/Mettl3

description:
Library name: WTg
10x Genomics


title: S. Typhimurium infected and Laurocapram-treated cells, replicate 3

city: changchun

first: rundong

last: shu

address: xinzhu road

institute: jilin university

description: Library name: D3

data_processing:
Data quality control was performed using fastp software. Adapters, reads containing poly-N, and low-quality reads were removed to obtain clean reads. Q20, Q30, and GC content were calculated for the clean data.
An index of the reference genome was built and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
Read counts mapped to each gene were quantified using featureCounts (v1.5.0-p3). Subsequently, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values were calculated for each gene based on its length and read count.
Differential expression analysis was performed using the DESeq2 R package (v1.20.0).
Assembly: GRCm38
Supplementary files format and content: The processed data file (gene_fpkm.xls) is a table where rows represent genes and columns represent samples. The values indicate FPKM (Fragments Per Kilobase of transcript per Million mapped reads) for each gene in each sample.

source_name: RAW264.7 cells

growth_protocol: RAW264.7 cells were cultured in RPMI 1640 medium supplemented with 10% Fetal Bovine Serum (FBS) in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Thermo Fisher Scientific) according to the manufacturer's instructions.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Cells were seeded in 6-well plates at a density of 1 × 10⁶ cells per well and incubated in a 37°C, 5% CO₂ incubator until reaching approximately 80% confluence. For the infection group, cells were infected with Salmonella Typhimurium at a multiplicity of infection (MOI) of 20 for 1 hour, followed by a gentamicin protection assay (100 μg/mL gentamicin treatment for 1 hour) to selectively eliminate extracellular bacteria. For the drug treatment group, Laurocapram was added to the culture medium at a final concentration of 16 μg/mL. All specific treatment conditions for each experimental group were maintained for a total of 6 hours before termination of the experiment.

value: RAW264.7 cells

value: S. Typhimurium infected and Laurocapram


title: S. Typhimurium infected and Laurocapram-treated cells, replicate 1

description: Library name: D1


title: S. Typhimurium-infected RAW264.7 cells, replicate 3

description: Library name: X3

value: S. Typhimurium


title: S. Typhimurium infected and Laurocapram-treated cells, replicate 2

description: Library name: D2


title: TCRαβ samples from TNBC exosome-treated T cells and one untreated control, Well 2

description:
Library name: Well 2_αβ
Gene expression profiling and TCRαβ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 2


title: TCRαβ samples from TNBC exosome-treated T cells and one untreated control, Well 6

description:
Library name: Well 6_αβ
Gene expression profiling and TCRαβ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 6


title: Laurocapram-treated RAW264.7 cells, replicate 3

description: Library name: Y3

value: Laurocapram


title: S. Typhimurium-infected RAW264.7 cells, replicate 1

description: Library name: X1


title: S. Typhimurium-infected RAW264.7 cells, replicate 2

description: Library name: X2


title: Laurocapram-treated RAW264.7 cells, replicate 2

description: Library name: Y2


title: Rat kidney cortex, DEFND, 82 weeks, rat V22, RNA

city: Philadelphia

first: Hanzhi

last: Wang

address: 422 Curie Blvd

institute: University of Pennsylvania

description:
Library name: RAGE24-V22-KYC-LN-01-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.

data_processing:
Basecalls and sample demultiplexing were performed withh bcl-convert v4.3.6 (for Oracle 8) to generate Fastq files.
ATAC libraries were aligned to rat reference genome with cellranger-atac-2.1.0 to generate fragment maps. Gene expression libraries were mapped to the same rat reference genome and counted with cellranger-8.0.1, and then aggregated without normalization using cellranger-8.0.1. The result aggregated gene expression object was processed with Seurat v4.
Assembly: Rat reference genome GRCr8 supplemented with mitochonrial genome from mRatBN7.2 Assembly.
Supplementary files format and content: Cell Ranger ATAC outputs: [library_id]_filtered_peak_bc_matrix.h5, fragments.tsv.gz, fragments.tsv.gz.tbi
Supplementary files format and content: Cell Ranger individual library outputs: [library_id]_filtered_feature_bc_matrix.h5
Supplementary files format and content: Cell Ranger aggr output filtered feature-barcode matrices HDF5 file of scRNA libraries: RAGE24_single_cell_gex_aggr_filtered_feature_bc_matrix.h5
Supplementary files format and content: RAGE24_single_cell_gex_aggr_annotated_seurat_obj.rds (doublet-filtered, SC-Transformed and annotated Seurat object of aggregated RNA libraries. The file can be loaded into R)
Supplementary files format and content: feature_reference.csv (Cell Ranger aggr feature reference csv file)
Supplementary files format and content: aggregation.csv (cellranger aggr)
Supplementary files format and content: RAGE24_single_cell_gex_aggr_cell_annotation.csv (cell-type-annotated cell barcode information of aggregated gene expression libraries. This was exported from the Seurat object.)

organism: Rattus norvegicus

source_name: kidney cortex flash frozen

extract_protocol:
Rat kidneys were dissected immediately following euthanasia and flash-frozen in liquid nitrogen. For each preparation, approximately ~35 mg of frozen tissue was processed. Tissues were mechanically dissociated using a gentleMACS™ Tissue Dissociator and nuclei were released by lysis under standard nuclei isolation conditions. Isolated nuclei were either processed using the standard 10x Genomics Chromium Multiome workflow (RNA + ATAC) or subjected to lithium diiodosalicylate pretreatment following the DEFND-seq protocol (Olsen et al. Nature Methods, 2025) to achieve nucleosome depletion.
Final nuclei suspensions were loaded onto the 10x Genomics Chromium platform for droplet-based single-cell library preparation according to the manufacturer’s protocol (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression User Guide-Rev F). Libraries were generated following standard 10x Multiome (scRNA + scATAC) chemistry and sequenced on Illumina platforms.

value: kidney cortex flash frozen

tag: library type

value: RNA

value: 82 weeks

value: male

tag: library construction

value: DEFND


title: Rat kidney cortex, DEFND, 82 weeks, rat V22, ATAC

description:
Library name: RAGE24-V22-KYC-LN-01-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA.

library_source: genomic single cell

value: ATAC


title: Rat kidney cortex, DEFND, 82 weeks, rat W23, RNA

description:
Library name: RAGE24-W23-KYC-LN-01-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.


title: Rat kidney cortex, Multiome, 82 weeks, rat U21, RNA

description:
Library name: RAGE24-U21-KYC-LN-01-Multiome-RNA
Gene expression (3'mRNA) part of 10X Genomics single cell multiome.

value: Multiome


title: Laurocapram-treated RAW264.7 cells, replicate 1

description: Library name: Y1


title: TCRαβ samples from TNBC exosome-treated T cells and one untreated control, Well 1

description:
Library name: Well 1_αβ
Gene expression profiling and TCRαβ sequencing were performed on T cells treated with exosomes derived from 17 distinct TNBC cell lines, as well as on one untreated T cell sample from Well 1


title: Untreated RAW264.7 cells, replicate 3

description: Library name: B3


title: Untreated RAW264.7 cells, replicate 2

description: Library name: B2


title: Rat kidney cortex, DEFND, 82 weeks, rat W23, ATAC

description:
Library name: RAGE24-W23-KYC-LN-01-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA.


title: Rat kidney cortex, Multiome, 82 weeks, rat U21, ATAC

description:
Library name: RAGE24-U21-KYC-LN-01-Multiome-ATAC
ATAC part of 10X Genomics single cell multiome.


title: Rat kidney cortex, DEFND, 82 weeks, rat U21, RNA

description:
Library name: RAGE24-U21-KYC-LN-01-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.


title: Untreated RAW264.7 cells, replicate 1

description: Library name: B1


title: Rat kidney cortex, DEFND, 82 weeks, rat U21, ATAC

description:
Library name: RAGE24-U21-KYC-LN-01-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA. We performed DEFND-seq on rat T20 with second aliquot from the sample tissue.


title: Y195_MSI_s3_TA

description:
Library name: Y195_MSI_s3_TA
CRISPR array amplicon (Tigre) from Fresh frozen Spatial transcriptome sequencing

data_processing:
In the spatio-DARLIN amplicon library, Read 1 (85 bp) contains the spatial barcode, while Read 2 (350 bp) captures the 5′ primer, array sequence, and 3′ primer of three target arrays (CA, TA, RA). To extract the array sequences, Cutadapt was used to sequentially trim Read 2: first removing the 3′ primer from the end of the read (right trimming), and then trimming the 5′ primer from the start (left trimming). Reads that did not contain identifiable primer sequences were discarded.
Then the paired Read 1 was processed with BSTMatrix (v2.4.f.1) to extract spatial barcodes and assign spot coordinates.
Subsequent spot-level quality control included: (i) filtering spots with fewer than 10 reads, (ii) denoising array sequences by correcting single-base errors within a Hamming distance of 1, and (iii) removing ambiguous spots (spots do not have a dominant lineage barcode) using the calculate_read_fraction_per_clone_cell function from the MosaicLineage Python package (https://github.com/ShouWenWang-Lab/MosaicLineage), with parameters read_fraction_per_clone_cell_cutoff = 0.2 and mode = "max".
Finally, UMI counts for each array were aggregated across spots belonging to the same cell mask, based on the cell segmentation results from the spatial transcriptomics preprocessing step.
Assembly: >CA
Assembly: CGCCGGACTGCACGACAGTCGACGATGGAGTCGACACGACTCGCGCATACGATGGAGTCGACTACAGTCGCTACGACGATGGAGTCGCGAGCGCTATGAGCGACTATGGAGTCGATACGATACGCGCACGCTATGGAGTCGAGAGCGCGCTCGTCGACTATGGAGTCGCGACTGTACGCACACGCGATGGAGTCGATAGTATGCGTACACGCGATGGAGTCGAGTCGAGACGCTGACGATATGGAGTCGATACGTAGCACGCAGACGATGGGAGCT
Assembly: >TA
Assembly: TCGCCGGAGTCGAGACGCTGACGATATGGAGTCGACACGACTCGCGCATACGATGGAGTCGCGAGCGCTATGAGCGACTATGGAGTCGATAGTATGCGTACACGCGATGGAGTCGACTACAGTCGCTACGACGATGGAGTCGATACGATACGCGCACGCTATGGAGTCGCGACTGTACGCACACGCGATGGAGTCGACTGCACGACAGTCGACGATGGAGTCGATACGTAGCACGCAGACGATGGGAGCGAGAGCGCGCTCGTCGACTATGGA
Assembly: >RA
Assembly: GCGCCGGCGAGCGCTATGAGCGACTATGGAGTCGACACGACTCGCGCATACGATGGAGTCGACTACAGTCGCTACGACGATGGAGTCGATACGATACGCGCACGCTATGGAGTCGACTGCACGACAGTCGACGATGGAGTCGATACGTAGCACGCAGACGATGGGAGCGAGTCGAGACGCTGACGATATGGAGTCGATAGTATGCGTACACGCGATGGAGTCGCGACTGTACGCACACGCGATGGAGTCGAGAGCGCGCTCGTCGACTATGGA
Supplementary files format and content: barcodes.tsv.gz: list of segmented cell IDs
Supplementary files format and content: barcodes_pos.tsv.gz: list of spatial coordinates of segmented cell IDs
Supplementary files format and content: features.tsv.gz: list of clone barcodes
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: features_allele.tsv.gz: list of clone barcodes and mutation details
Library strategy: Spatial Transcriptomics

source_name: Intestine (middle)

treatment_protocol: To label adult mice, doxycycline (ABCONE, D48978) was administered via drinking water for one week (2 mg/mL, supplemented with 10 mg/mL sucrose) and three intraperitoneal injections (50 μg/g) every other day during the same week.

value: Intestine (middle)

value: 8 weeks

value: Tigre

value: Dox induction for 1 week

value: 1 week


title: Rat kidney cortex, DEFND, 82 weeks, rat T20, ATAC, sample aliquot 2

description:
Library name: RAGE24-T20-KYC-LN-02-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA. We performed DEFND-seq on rat T20 with second aliquot from the sample tissue.


title: Rat kidney cortex, DEFND, 82 weeks, rat T20, RNA, sample aliquot 2

description:
Library name: RAGE24-T20-KYC-LN-02-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.


title: Rat kidney cortex, Multiome, 82 weeks, rat T20, RNA

description:
Library name: RAGE24-T20-KYC-LN-01-Multiome-RNA
Gene expression (3'mRNA) part of 10X Genomics single cell multiome.


title: Y195_MSI_s3_CA

description:
Library name: Y195_MSI_s3_CA
CRISPR array amplicon (Col1a1) from Fresh frozen Spatial transcriptome sequencing


title: Y195_MSI_s2_RA

description:
Library name: Y195_MSI_s2_RA
CRISPR array amplicon (Rosa26) from Fresh frozen Spatial transcriptome sequencing


title: Y195_MSI_s2_TA

description:
Library name: Y195_MSI_s2_TA
CRISPR array amplicon (Tigre) from Fresh frozen Spatial transcriptome sequencing


title: Rat kidney cortex, Multiome, 56 weeks, rat Q17, RNA

description:
Library name: RAGE24-Q17-KYC-LN-01-Multiome-RNA
Gene expression (3'mRNA) part of 10X Genomics single cell multiome.

value: 56 weeks


title: Rat kidney cortex, Multiome, 56 weeks, rat Q17, ATAC

description:
Library name: RAGE24-Q17-KYC-LN-01-Multiome-ATAC
ATAC part of 10X Genomics single cell multiome.


title: Y195_MSI_s1_CA

description:
Library name: Y195_MSI_s1_CA
CRISPR array amplicon (Col1a1) from Fresh frozen Spatial transcriptome sequencing


title: Y195_MSI_s1_RA

description:
Library name: Y195_MSI_s1_RA
CRISPR array amplicon (Rosa26) from Fresh frozen Spatial transcriptome sequencing


title: Y195_MSI_s3_RA

description:
Library name: Y195_MSI_s3_RA
CRISPR array amplicon (Rosa26) from Fresh frozen Spatial transcriptome sequencing


title: Rat kidney cortex, DEFND, 82 weeks, rat T20, ATAC, sample aliquot 1

description:
Library name: RAGE24-T20-KYC-LN-01-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA.


title: Rat kidney cortex, DEFND, 56 weeks, rat Q17, RNA

description:
Library name: RAGE24-Q17-KYC-LN-01-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.


title: Y195_DSI_RA

description:
Library name: Y195_DSI_RA
CRISPR array amplicon (Rosa26) from Fresh frozen Spatial transcriptome sequencing

source_name: Intestine (distal)

value: Intestine (distal)


title: Rat kidney cortex, DEFND, 56 weeks, rat Q17, ATAC

description:
Library name: RAGE24-Q17-KYC-LN-01-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA.


title: Rat kidney cortex, DEFND, 56 weeks, rat P16, RNA

description:
Library name: RAGE24-P16-KYC-LN-01-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.


title: Rat kidney cortex, Multiome, 82 weeks, rat T20, ATAC

description:
Library name: RAGE24-T20-KYC-LN-01-Multiome-ATAC
ATAC part of 10X Genomics single cell multiome.


title: Y195_PSI_RA

description:
Library name: Y195_PSI_RA
CRISPR array amplicon (Rosa26) from Fresh frozen Spatial transcriptome sequencing

source_name: Intestine (proximal)

value: Intestine (proximal)


title: Rat kidney cortex, DEFND, 82 weeks, rat T20, RNA, sample aliquot 1

description:
Library name: RAGE24-T20-KYC-LN-01-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.


title: Rat kidney cortex, DEFND, 56 weeks, rat P16, ATAC

description:
Library name: RAGE24-P16-KYC-LN-01-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA.


title: Rat kidney cortex, DEFND, 56 weeks, rat O15, RNA, sample aliquot 2

description:
Library name: RAGE24-O15-KYC-LN-02-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform. We performed DEFND-seq on rat O15 with second aliquot from the sample tissue.


title: Y195_MSI_s1_TA

description:
Library name: Y195_MSI_s1_TA
CRISPR array amplicon (Tigre) from Fresh frozen Spatial transcriptome sequencing


title: Y195_DSI_CA

description:
Library name: Y195_DSI_CA
CRISPR array amplicon (Col1a1) from Fresh frozen Spatial transcriptome sequencing


title: Rat kidney cortex, Multiome, 56 weeks, rat O15, RNA

description:
Library name: RAGE24-O15-KYC-LN-01-Multiome-RNA
Gene expression (3'mRNA) part of 10X Genomics single cell multiome.


title: Y195_PSI_TA

description:
Library name: Y195_PSI_TA
CRISPR array amplicon (Tigre) from Fresh frozen Spatial transcriptome sequencing


title: Y003_PSI_RA

description:
Library name: Y003_PSI_RA
CRISPR array amplicon (Rosa26) from Fresh frozen Spatial transcriptome sequencing

value: 4 weeks

value: 3 weeks


title: Rat kidney cortex, DEFND, 56 weeks, rat O15, ATAC, sample aliquot 2

description:
Library name: RAGE24-O15-KYC-LN-02-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA. We performed DEFND-seq on rat O15 with second aliquot from the sample tissue.

value: kidney cortex flash frozen


title: Y195_PSI_CA

description:
Library name: Y195_PSI_CA
CRISPR array amplicon (Col1a1) from Fresh frozen Spatial transcriptome sequencing


title: Y003_PSI_TA

description:
Library name: Y003_PSI_TA
CRISPR array amplicon (Tigre) from Fresh frozen Spatial transcriptome sequencing


title: Rat kidney cortex, Multiome, 56 weeks, rat O15, ATAC

description:
Library name: RAGE24-O15-KYC-LN-01-Multiome-ATAC
ATAC part of 10X Genomics single cell multiome.


title: B16F10_T4_3_PBS_2

description:
Library name: B16F10_T4_3_PBS_2
panKO_PBS

value: cancer cells

value: panKO

value: PBS


title: Y003_PSI_CA

description:
Library name: Y003_PSI_CA
CRISPR array amplicon (Col1a1) from Fresh frozen Spatial transcriptome sequencing


title: Rat kidney cortex, DEFND, 56 weeks, rat O15, RNA, sample aliquot 1

description:
Library name: RAGE24-O15-KYC-LN-01-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.

value: RNA

value: male

value: DEFND


title: Rat kidney cortex, DEFND, 56 weeks, rat N14, ATAC

description:
Library name: RAGE24-N14-KYC-LN-01-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA.

value: ATAC


title: Y004_PSI_RA

description:
Library name: Y004_PSI_RA
CRISPR array amplicon (Rosa26) from Fresh frozen Spatial transcriptome sequencing

value: 2 weeks


title: Rat kidney cortex, DEFND, 56 weeks, rat N14, RNA

description:
Library name: RAGE24-N14-KYC-LN-01-DEFND-RNA
Gene expression (3'mRNA) part of DEFND-seq based on 10X Genomics single cell multiome platform.


title: Y004_PSI_TA

description:
Library name: Y004_PSI_TA
CRISPR array amplicon (Tigre) from Fresh frozen Spatial transcriptome sequencing

value: Tigre


title: Y195_MSI_s2_CA

description:
Library name: Y195_MSI_s2_CA
CRISPR array amplicon (Col1a1) from Fresh frozen Spatial transcriptome sequencing

value: Intestine (middle)

value: 8 weeks

value: Dox induction for 1 week


title: Rat kidney cortex, Multiome, 30 weeks, rat L12, RNA

description:
Library name: RAGE24-L12-KYC-LN-01-Multiome-RNA
Gene expression (3'mRNA) part of 10X Genomics single cell multiome.

value: 30 weeks

value: Multiome


title: Y004_PSI_CA

description:
Library name: Y004_PSI_CA
CRISPR array amplicon (Col1a1) from Fresh frozen Spatial transcriptome sequencing

value: Intestine (proximal)

value: 4 weeks


title: Y007_PSI_TA

description:
Library name: Y007_PSI_TA
CRISPR array amplicon (Tigre) from Fresh frozen Spatial transcriptome sequencing

value: 1 week


title: HSD17B13

city: Beijing

first: Jinchen

last: Xu

address: Tiantan xili

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

description: Library name: Sample 4

data_processing:
Paired-end reads were harvested from sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome with Tophat2 software. Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization, then differentially expressed mRNAs were identified by p-value and fold change. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs
Assembly: NC_002645.1
Supplementary files format and content: Gene Expression Profiling  Column A: gene_id, the id of the gene. Column B ~ E: count, the count of mapped reads. Column F ~ I: logCPM by edgeR. Column J ~ Q: annotation of the genes.

organism: Human coronavirus 229E

extract_protocol:
Total RNA was extracted using Trizol reagent
Ribosome profiling was performed by CloudSeq Inc. (Shanghai, China) following the GenSeq Ribo Profile Kit manual (GenSeq, Inc.). Briefly, cycloheximide-treated Huh7 cells were lysed with lysis buffer and digested with nuclease. Ribosome footprints were purified by size-exclusion chromatography, and ribosome-protected fragments were size-selected by polyacrylamide gel electrophoresis (PAGE), followed by rRNA depletion. Purified RNA fragments were end-repaired, ligated with 3' adapters and reverse-transcribed to cDNA. The cDNA products were purified by PAGE, circularized, and amplified by PCR. The resulting libraries were purified and sequenced on a NovaSeq platform (Illumina).


title: hnRNPC2

description: Library name: Sample 3


title: Rat kidney cortex, Multiome, 30 weeks, rat L12, ATAC

description:
Library name: RAGE24-L12-KYC-LN-01-Multiome-ATAC
ATAC part of 10X Genomics single cell multiome.

value: kidney cortex flash frozen


title: Y007_PSI_RA

description:
Library name: Y007_PSI_RA
CRISPR array amplicon (Rosa26) from Fresh frozen Spatial transcriptome sequencing


title: Rat kidney cortex, DEFND, 30 weeks, rat L12, ATAC

description:
Library name: RAGE24-L12-KYC-LN-01-DEFND-ATAC
Genomic DNA part of DEFND-seq based on 10X Genomics single cell multiome platform. After nucleosome depletion, this mainly contains genomic DNA.