title: CUT&Tag of RNAPS2P  in Late_S cells rep1.

description: Library name: Late_S5_1


title: p145 T cells (7 months) scTCR-seq

status: Public on Sep 10 2025

type: SRA

city: New Haven

first: Meng

last: Wang

state: CT

address: 300 George St

country: USA

institute: Yale University

description:
Library name: p145_T_7m_VDJ
10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger 3.1.0 count subcommand was used to generate the count matrices, barcode assignments, and feature calls for gene expression data.
Cell Ranger 3.1.0 vdj subcommand was used to assemble TCR and BCR sequences.
Seurat v4 was used to filter out low quality cells and Azimuth was used to perform cell type annotations.
Assembly: GCRhg38
Supplementary files format and content: cell ranger count matrix in h5 file format, cell ranger vdj clonotype files, seurat object in RDS format

molecule: polyA RNA

organism: Homo sapiens

source_name: T cells

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated; B cells were positively selected (CD20 beads, Miltenyi). Single-cell suspensions of CD20⁺ B cells and CD4 T cells were prepared at 1,000 cells/µL in 0.04% PBS-BSA, with >90% viability by trypan blue. Samples were transferred to the Yale Center for Genomic Analysis (YCGA) for 10x Chromium processing and sequencing.
10x Genomics Chromium Single Cell 5′ chemistry was used to generate single-cell 5′ gene-expression libraries.

tag: cell type

value: T cells


title: SRKPD004

city: beijing

first: Guangjian

last: Jiang

address: Beijing University of Traditional Chinese Medicine, No. 11 North Third Ring East Road, Beijing City

country: China

institute: Beijing University of Chinese Medicine, Beijing

description: 99,expression matrix.xlsx

library_source: transcriptomic

data_processing:
Screen cDNA fragments of approximately 370~420 bp using AMPure XP beads, amplify by PCR, and purify the PCR product again using AMPure XP beads to obtain the final library. Determine the quality of the library using the Agilent 2100 System (NanoDrop ND-1000) analyzer and accurately quantify it (library effective concentration higher than 2nM) through quantitative real-time polymerase chain reaction before data analysis.
Assembly: Remove ribosome RNA (rRNA) using the Epicentre Ribozero™ rRNA removal kit (Epicentre, USA) before data analysis. Remove linear RNA using RNase R (Epicentre, USA). Finally, merge libraries according to the requirements of effective concentration and data volume, and sequence them using the Illumina NovaSeq 6000.
Supplementary files format and content: The values in the expression matrix are FPKM values for gene expression in subjects

molecule: total RNA

extract_protocol:
The total RNA was extracted from venous blood collected from people with T2DM using Trizol (Invitrogen, USA).  To further control quality, agarose gel electrophoresis was used to test samples' integrity and NanoDrop-1000 was used to quantify them.
To construct each library, 1-2 g of total RNA were selected. Total RNA was first subjected to mRNA enrichment with NEB Next@ Poly A (or rRNA removal using RiboZero Magnetic Gold Kit). In this study, stranded RNA-seq libraries were prepared with KAPA Stranded RNA-Seq Library Prep kit. The KAPA kit uses a dUTP-based method for the construction of chain-specific libraries, which included the following steps: 1) Fragmentation of mRNA enrichment products, 2) reverse transcription of the first strand of cRNA, 3) dUTP synthesis of double-stranded cDNA, 4) Rt-PCR amplification was used to repair double-stranded cDNA ends to create RNA sequencing libraries.

tag: tissue

value: blood

tag: disease state


title: QYD8

description: 99,expression matrix.xlsx


title: SRKPD007

description: 99,expression matrix.xlsx


title: p145 T cells (7 months) scRNA-seq

description:
Library name: p145_T_7m_RNA
10x Genomics


title: CUT&Tag of RFC3  in Late_S cells rep2.

city: hefei

first: sun

last: xuedan

address: daoxiangcun

institute: ustc

description: Library name: Late_S2_2

library_source: genomic

data_processing:
(CUT-tag)The data analysis workflow first involved adapter trimming and removal of low-quality bases from paired-end reads were conducted using Trim Galore software. Clean reads were then aligned to the hg38 reference genome using Bowtie2, followed by the removal of PCR duplicates with Picard. Genome browser tracks in bigWig format were produced from merged replicates using samtools, and peak calling was performed with MACS2 using the parameters -f BAMPE --broad -nomodel. The resulting bigWig data were visualized using the Integrative Genomics Viewer (IGV) software from the Broad Institute, while peak visualizations were prepared using Deeptools.
Assembly: hg38
Supplementary files format and content: bigwig for CUT&Tag
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: liver

extract_protocol:
CUT&Tag experiments, cell capture was achieved using ConA-coated magnetic beads for cell enrichment.
CUT&Tag libraries were prepared according to the protocol established by Steven Henikoff's laboratory.

value: liver

tag: cell line

value: tumor cells

tag: treatment

value: Late_S Phase-Synchronized


title: Spleen, Trp53-/-_mouse_0045, 29_week-old_plate1

city: Hanzhou

first: Guoji

last: Guo

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

description: Updated Microwell-seq_scRNA-seq

data_processing:
The original FASTQ files were converted to BAM format firstly with Drop-seq_tools-1.12, which was used for the subsequent processing except for barcode correction and alignment. The cell barcodes were extracted and tagged with XC in the offered BAM files, and the unique molecular identifiers (UMIs) were tagged with XM. Three 6bp barcodes ware combined to identify a single cell. Reads with the quality of cell barcodes or UMIs less than 10 were tagged with XQ and removed afterwards. Next, the PolyATrimmer was used to trim ployA. Before alignment, the known barcode sequences involved in the library construction were utilized for cell barcode correction, allowing one mismatch in each 6bp barcode.
STAR (version 2.5.2a) was used for reads alignment in single-end mode. The data were aligned to a GRCm38.88 reference genome. Then the aligned BAM files were sorted by query names and were merged with the unaligned BAM files, in order to recover the XC and XM tags that were lost after the alignment. Finally, the top 20,000 cell barcodes ranked by reads number were used to generate the digital expression matrices in each sample or each technical repeat.
Tab-delimited text files of digital expression matrix (DGE) based on raw UMIs counts, with genes as rows and cells as columns.
Assembly: Mus_musculus.GRCm38.88 genome
Supplementary files format and content: Tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

organism: Mus musculus

source_name: Spleen

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq1.1 protocol

treatment_protocol: After anaesthetization with 1% (i.p.) sodium pentobarbital, mice were weighed, shaved, and given transcardial perfusion with 20-30 ml PBS.

value: Spleen

tag: strain

tag: genotype

tag: age

value: 29 weeks

tag: Sex

value: Female


title: Pancreas, Trp53-/-_mouse_0045, 29_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Pancreas

value: Pancreas


title: p145 T cells (week 6) scTCR-seq

description:
Library name: p145_T_6w_VDJ
10x Genomics


title: WSR002

description: 99,expression matrix.xlsx


title: CUT&Tag of RFC3  in Late_S cells rep1.

description: Library name: Late_S2_1


title: p145 T cells (week 6) scRNA-seq

description:
Library name: p145_T_6w_RNA
10x Genomics


title: CUT&Tag of NELFB  in Late_S cells rep1.

description: Library name: Late_NELFB_1


title: YYLXD005

description: 99,expression matrix.xlsx


title: YYLXD004

description: 99,expression matrix.xlsx


title: CUT&Tag of NELFB  in Late_S cells rep2.

description: Library name: Late_NELFB_2


title: CUT&Tag of NELFA  in Late_S cells rep2.

description: Library name: Late_NELFA_2


title: Lung, Trp53-/-_mouse_0045, 29_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Lung

value: Lung


title: Liver, Trp53-/-_mouse_0045, 29_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Liver

value: Liver


title: YYLXD007

description: 99,expression matrix.xlsx


title: YYLXD006

description: 99,expression matrix.xlsx


title: p145 B cells (7 months) scBCR-seq

description:
Library name: p145_B_7m_VDJ
10x Genomics

source_name: B cells

value: B cells


title: Kidney, Trp53-/-_mouse_0045, 29_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Kidney

value: Kidney


title: YYLXD001

description: 99,expression matrix.xlsx


title: CUT&Tag of NELFA  in Late_S cells rep1.

description: Library name: Late_NELFA_1


title: p145 B cells (day 0) scRNA-seq

description:
Library name: p145_B_d0_RNA
10x Genomics


title: p145 B cells (7 months) scRNA-seq

description:
Library name: p145_B_7m_RNA
10x Genomics


title: SRKPD001

description: 99,expression matrix.xlsx


title: Heart, Trp53-/-_mouse_0045, 29_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: Heart

value: Heart


title: CUT&Tag of DHX36  in Late_S cells rep1.

description: Library name: Late_DHX_1


title: BoneMarrow, Trp53-/-_mouse_0045, 29_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: BoneMarrow

value: BoneMarrow


title: p145 B cells (week 6) scBCR-seq

description:
Library name: p145_B_6w_VDJ
10x Genomics


title: YYLXD003

description: 99,expression matrix.xlsx


title: CUT&Tag of BRIP1  in Late_S cells rep2.

description: Library name: Late_BRIP1_2


title: SRKPD010

description: 99,expression matrix.xlsx


title: p145 B cells (week 6) scRNA-seq

description:
Library name: p145_B_6w_RNA
10x Genomics


title: LymphNodes, Trp53-/-_mouse_0045, 29_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: LymphNodes

value: LymphNodes


title: plate2_scRNA_WT0105mouse_Uterus

description: Updated Microwell-seq_scRNA-seq

value: Uterus

value: 13 weeks

tag: plate


title: p145 B cells (day 0) scBCR-seq

description:
Library name: p145_B_d0_VDJ
10x Genomics


title: SRKPD011

description: 99,expression matrix.xlsx

value: blood


title: CUT&Tag of BRIP1  in Late_S cells rep1.

description: Library name: Late_BRIP1_1

value: liver


title: p134 T cells (day 0) scTCR-seq

description:
Library name: p134_T_d0_VDJ
10x Genomics

value: T cells


title: CUT&Tag of G4-DNA  in Late_S cells rep2.

description: Library name: Late_BG4_2

value: tumor cells

value: Late_S Phase-Synchronized


title: p134 T cells (day 0) scRNA-seq

description:
Library name: p134_T_d0_RNA
10x Genomics


title: SRKPD015

description: 99,expression matrix.xlsx


title: plate2_scRNA_WT0105mouse_Thymus

description: Updated Microwell-seq_scRNA-seq

value: Thymus


title: plate2_scRNA_WT0105mouse_Spleen

description: Updated Microwell-seq_scRNA-seq

value: Spleen

value: Female


title: CUT&Tag of G4-DNA  in Late_S cells rep1.

description: Library name: Late_BG4_1


title: SRKPD009

description: 99,expression matrix.xlsx


title: p134 T cells (7 months) scTCR-seq

description:
Library name: p134_T_7m_VDJ
10x Genomics


title: SRKPD008

description: 99,expression matrix.xlsx


title: CUT&Tag of RNAPS5P in G1_S cells rep2.

description: Library name: G1_S_S5_2

value: G1_S Phase-Synchronized


title: plate2_scRNA_WT0105mouse_Pancreas

description: Updated Microwell-seq_scRNA-seq

value: Pancreas


title: p134 T cells (7 months) scRNA-seq

description:
Library name: p134_T_7m_RNA
10x Genomics


title: MammaryGland, Trp53-/-_mouse_0045, 29_week-old_plate1

description: Updated Microwell-seq_scRNA-seq

source_name: MammaryGland

value: MammaryGland

value: 29 weeks


title: SRKPD006

description: 99,expression matrix.xlsx


title: p134 T cells (week 6) scTCR-seq

description:
Library name: p134_T_6w_VDJ
10x Genomics


title: CUT&Tag of RNAPS5P  in G1_S cells rep1.

description: Library name: G1_S_S5_1


title: p134 T cells (week 6) scRNA-seq

description:
Library name: p134_T_6w_RNA
10x Genomics


title: CUT&Tag of RNAPS2P  in G1_S cells rep2.

description: Library name: G1_S_S2_2


title: SRKPD003

description: 99,expression matrix.xlsx


title: plate2_scRNA_WT0105mouse_MammaryGland

description: Updated Microwell-seq_scRNA-seq


title: plate2_scRNA_WT0105mouse_Ovary

description: Updated Microwell-seq_scRNA-seq

source_name: Ovary, Trp53+/+_mouse_0105, 13_week-old

value: Ovary


title: SRKPD002

description: 99,expression matrix.xlsx


title: p134 B cells (day 0) scBCR-seq

description:
Library name: p134_B_d0_VDJ
10x Genomics

value: B cells


title: CUT&Tag of RNAPS2P  in G1_S cells rep1.

description: Library name: G1_S_S2_1


title: CUT&Tag of DHX36  in Late_S cells rep2.

description: Library name: Late_DHX_2


title: plate2_scRNA_WT0105mouse_LymphNodes

description: Updated Microwell-seq_scRNA-seq

value: LymphNodes


title: CUT&Tag of RFC3  in G1_S cells rep2.

description: Library name: G1_S_RFC3_2


title: p134 B cells (day 0) scRNA-seq

description:
Library name: p134_B_d0_RNA
10x Genomics


title: plate2_scRNA_WT0105mouse_Lung

description: Updated Microwell-seq_scRNA-seq

source_name: Lung, Trp53+/+_mouse_0105, 13_week-old

value: Lung


title: CUT&Tag of RFC3  in G1_S cells rep1.

description: Library name: G1_S_RFC3_1


title: plate2_scRNA_WT0105mouse_SmallIntestine

description: Updated Microwell-seq_scRNA-seq

value: SmallIntestine

value: 13 weeks


title: p134 B cells (7 months) scBCR-seq

description:
Library name: p134_B_7m_VDJ
10x Genomics


title: ZC025

description: 99,expression matrix.xlsx

value: blood

value: Control


title: p134 B cells (7 months) scRNA-seq

description:
Library name: p134_B_7m_RNA
10x Genomics


title: CUT&Tag of NELFB  in G1_S cells rep2.

description: Library name: G1_S_NELFB_2

value: liver

value: tumor cells


title: ZC028

description: 99,expression matrix.xlsx


title: plate2_scRNA_WT0105mouse_Liver

description: Updated Microwell-seq_scRNA-seq

source_name: Liver, Trp53+/+_mouse_0105, 13_week-old

value: Liver


title: plate2_scRNA_WT0105mouse_LargeIntestine

description: Updated Microwell-seq_scRNA-seq

value: LargeIntestine


title: CUT&Tag of NELFB  in G1_S cells rep1.

description: Library name: G1_S_NELFB_1


title: ZC023

description: 99,expression matrix.xlsx


title: p134 B cells (week 6) scBCR-seq

description:
Library name: p134_B_6w_VDJ
10x Genomics


title: CUT&Tag of NELFA  in G1_S cells rep2.

description: Library name: G1_S_NELFA_2


title: ZC024

description: 99,expression matrix.xlsx


title: ZC021

description: 99,expression matrix.xlsx


title: plate2_scRNA_WT0105mouse_Heart

description: Updated Microwell-seq_scRNA-seq

source_name: Heart, Trp53+/+_mouse_0105, 13_week-old

value: Heart

value: Female


title: CUT&Tag of NELFA  in G1_S cells rep1.

description: Library name: G1_S_NELFA_1

value: G1_S Phase-Synchronized


title: plate2_scRNA_WT0105mouse_Kidney

description: Updated Microwell-seq_scRNA-seq

value: Kidney


title: ZC029

description: 99,expression matrix.xlsx


title: p134 B cells (week 6) scRNA-seq

description:
Library name: p134_B_6w_RNA
10x Genomics


title: plate2_scRNA_WT0105mouse_Gallbladder-BileDuct

description: Updated Microwell-seq_scRNA-seq

value: Gallbladder-BileDuct


title: ZC038

description: 99,expression matrix.xlsx


title: CUT&Tag of DHX36  in G1_S cells rep2.

description: Library name: G1_S_DHX_2


title: ZC020

description: 99,expression matrix.xlsx


title: DMSO

city: Ramat Gan

first: Benjamine

last: Dekel

address: Tel Hashomer

country: Israel

institute: heba Medical Center: Tel Hashomer, Tel Aviv, IL

description: Library name: Sample 1

data_processing:
Cell ranger (v3) pipeline was used to perform sample demultiplexing to produce FASTQ files for each sample. Samples were aligned to the GRCh38 reference human genome, and cell barcodes were filtered so that only barcodes connected to unique molecular identifiers and gene IDs were used in a matrix file compatible with Seurat.
Assembly: GRCh38
Supplementary files format and content: Cell ranger (v3) pipeline was used to perform sample demultiplexing to produce FASTQ files for each sample. Samples were aligned to the GRCh38 reference human genome, and cell barcodes were filtered so that only barcodes connected to unique molecular iden
Supplementary files format and content: Cell ranger  ouput containig: barcodes, features and matrix files

source_name: Human Fetal Kidney

extract_protocol:
Culture medium was aspirated and 1 mL of warm 1 mg/mL Dispase (# 07923, Stem Cell Technologies) was added to each well of a 24-well plate containing a BME droplet with hFKOs. The droplets were then gently broken down by pipetting up and down using a treated 1,000-μl pipette tip (obtained by pipetting 1% BSA in PBS up and down five times in standard pipette tips) to prevent hFKOs fragments from sticking to the pipette tip. After a 40-min incubation at 37°C, the BME was dissolved and the hFKOs were transferred to 15-mL tubes containing ice cold DMEM F12, centrifuged, and resuspended in 3 mL 1x TrypLE express (#12605010, Gibco) supplemented with 10 uM ROCKi. The tubes were incubated at 37°C for a 10-min cycles, after which the hFKOs were disturbed by pipetting up and down 15 times and 10 μL of cell suspension was checked under a microscope to determine whether a single-cell suspension had been achieved. This process was then repeated until that was accomplished; two or three cycles are usually enough to break down the hFKOs to single cells without affecting cell viability.
hFKO cells were (harvested, washed and) resuspended in PBS supplemented with 0.5% BSA to achieve an optimal concentration of approximately 1000 cells/μL for loading onto the Next GEM Chip (10x Genomics). Libraries were prepared using the 10x Genomics Chromium Controller in conjunction with the single-cell 3’ v3.1 kit, protocol revision E. cDNA synthesis, barcoding, and library preparation were carried out according to the manufacturer's instructions. Briefly, cDNA amplification was performed for 11 cycles and sample index PCR was performed for 12 cycles using Chromium i7 Sample Indices. The resulting libraries were quantified and analysed with Qubit and TapeStation and were sequenced on the NextSeq 500 platform (Illumina), following the manufacturer's protocol, using a NextSeq 500/550 High Output Kit v2.5 (75 cycles) kit (Illumina).

value: Human Fetal Kidney

value: Primary

value: Human Fetal Kidney Organoids

value: WT

value: DMSO-control


title: hFKO26

description: Library name: Sample 2


title: CUT&Tag of DHX36  in G1_S cells rep1.

description: Library name: G1_S_DHX_1


title: CUT&Tag of BRIP1  in G1_S cells rep2.

description: Library name: G1_S_BRIP1_2


title: ZC039

description: 99,expression matrix.xlsx


title: plate2_scRNA_WT0105mouse_BoneMarrow

description: Updated Microwell-seq_scRNA-seq

value: BoneMarrow

value: 13 weeks


title: ZC030

description: 99,expression matrix.xlsx

value: blood

value: Control


title: CUT&Tag of BRIP1  in G1_S cells rep1.

description: Library name: G1_S_BRIP1_1

value: liver

value: tumor cells


title: Replicate 3, iPSC-derived kidney organoids at day 18 of differentiation protocol

description: Library name: Beno_d18_c

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the GRCh38_p13 genome
Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI
Counting proceeded over genes (1000 bases of the 3’ UTR) using htseq-count
Assembly: GRCh38_p13
Supplementary files format and content: csv file includes read counts for each sample

source_name: Human iPSC-derived kidney organoids

extract_protocol:
Sample were processed with Trizol and Total RNA was prepared using a Direct-zol RNA MiniPrep kit (Zymo Research) according to the manufacturer's instructions.
Bulk MARS-Seq protocol

value: Human iPSC-derived kidney organoids

value: iPSC-derived kidney organoids


title: plate2_scRNA_WT0105mouse_Bladder

description: Updated Microwell-seq_scRNA-seq

value: Bladder

value: Female


title: hFKO18

description: Library name: Sample 1


title: Replicate 2, iPSC-derived kidney organoids at day 18 of differentiation protocol

description: Library name: Beno_d18_b


title: ZC031

description: 99,expression matrix.xlsx


title: DAPT

description: Library name: Sample 2

value: DAPT


title: CUT&Tag of G4-DNA  in G1_S cells rep2.

description: Library name: G1_S_BG4_2

source_name: liver

value: G1_S Phase-Synchronized


title: ZC032

description: 99,expression matrix.xlsx


title: plate2_scRNA_KO0045mouse_Bladder

description: Updated Microwell-seq_scRNA-seq

value: 29 weeks


title: Replicate 1, iPSC-derived kidney organoids at day 18 of differentiation protocol

description: Library name: Beno_d18_a


title: CUT&Tag of RNAPS5P in Early_S cells rep2.

description: Library name: Early_S_S5_2

value: Early S Phase-Synchronized


title: plate1_scRNA_WT0105mouse_Uterus

description: Updated Microwell-seq_scRNA-seq

value: Uterus


title: CUT&Tag of G4-DNA  in G1_S cells rep1.

description: Library name: G1_S_BG4_1


title: plate2_scRNA_WT0105mouse_Brain

description: Updated Microwell-seq_scRNA-seq

source_name: Brain, Trp53+/+_mouse_0105, 13_week-old

value: Brain


title: ZC033

description: 99,expression matrix.xlsx


title: plate1_scRNA_WT0105mouse_Thymus

description: Updated Microwell-seq_scRNA-seq

value: Thymus


title: Replicate 2, iPSC-derived kidney organoids at day 10 of differentiation protocol

description: Library name: Beno_d10_b

value: WT


title: plate1_scRNA_WT0105mouse_Spleen

description: Updated Microwell-seq_scRNA-seq

value: Spleen

value: 13 weeks


title: ZC034

description: 99,expression matrix.xlsx

value: blood

value: Control


title: CUT&Tag of RNAPS5P  in Early_S cells rep1.

description: Library name: Early_S_S5_1

value: liver

value: tumor cells


title: ZC035

description: 99,expression matrix.xlsx


title: Replicate 1, iPSC-derived kidney organoids at day 10 of differentiation protocol

description: Library name: Beno_d10_a

value: Human iPSC-derived kidney organoids

value: iPSC-derived kidney organoids


title: CUT&Tag of RNAPS2P  in Early_S cells rep2.

description: Library name: Early_S_S2_2


title: plate2_scRNA_KO0045mouse_LargeIntestine

description: Updated Microwell-seq_scRNA-seq

value: LargeIntestine

value: Female


title: plate1_scRNA_WT0105mouse_SmallIntestine

description: Updated Microwell-seq_scRNA-seq

value: SmallIntestine


title: CUT&Tag of RNAPS2P  in Early_S cells rep1.

description: Library name: Early_S_S2_1


title: ZC036

description: 99,expression matrix.xlsx


title: plate1_scRNA_WT0105mouse_Pancreas

description: Updated Microwell-seq_scRNA-seq

value: Pancreas


title: CUT&Tag of RFC3  in Early_S cells rep2.

description: Library name: Early_S_RFC3_2

value: Early S Phase-Synchronized


title: ZC005

description: 99,expression matrix.xlsx


title: plate1_scRNA_WT0105mouse_Ovary

description: Updated Microwell-seq_scRNA-seq

value: Ovary


title: Replicate 2, P5 human Fetal kidney organoids cultured for 15 weeks

description: Library name: hFKO_p5_b

value: Human Fetal Kidney

value: primary sample

value: fetal kideny organoid


title: Replicate 1, P6 human Fetal kidney organoids cultured for 18 weeks, 5 months

description: Library name: hFKO_p6_a

value: WT


title: ZC004

description: 99,expression matrix.xlsx


title: CUT&Tag of NELFB  in Early_S cells rep2.

description: Library name: Early_S_NELFB_2


title: CUT&Tag of RFC3  in Early_S cells rep1.

description: Library name: Early_S_RFC3_1


title: Replicate 1, P5 human Fetal kidney organoids cultured for 15 weeks

description: Library name: hFKO_p5_a


title: ZC006

description: 99,expression matrix.xlsx


title: plate1_scRNA_WT0105mouse_MammaryGland

description: Updated Microwell-seq_scRNA-seq

value: MammaryGland

value: 13 weeks


title: Replicate 3, Human Fetal kidney organoids cultured for 3 weeks.

description: Library name: hFKO_p0_c


title: plate1_scRNA_WT0105mouse_LymphNodes

description: Updated Microwell-seq_scRNA-seq

value: LymphNodes


title: Replicate 3, iPSC-derived kidney organoids at day 10 of differentiation protocol

description: Library name: Beno_d10_d


title: ZC007

description:
99,expression matrix.xlsx
12.expression matrix.xlsx

value: blood

value: Control


title: CUT&Tag of NELFB  in Early_S cells rep1.

description: Library name: Early_S_NELFB_1

value: liver

value: tumor cells


title: Replicate 2, Human Fetal kidney organoids cultured for 3 weeks.

description: Library name: hFKO_p0_b


title: CUT&Tag of NELFA  in Early_S cells rep2.

description: Library name: Early_S_NELFA_2


title: plate1_scRNA_WT0105mouse_Liver

description: Updated Microwell-seq_scRNA-seq

value: Liver


title: ZC001

description: 99,expression matrix.xlsx


title: plate1_scRNA_WT0105mouse_LargeIntestine

description: Updated Microwell-seq_scRNA-seq

value: LargeIntestine

value: Female


title: Replicate 2, P6 human Fetal kidney organoids cultured for 18 weeks, 5 months

description: Library name: hFKO_p6_b


title: plate1_scRNA_WT0105mouse_Lung

description: Updated Microwell-seq_scRNA-seq

value: Lung


title: ZC009

description: 99,expression matrix.xlsx


title: ZC003

description: 99,expression matrix.xlsx


title: CUT&Tag of DHX36  in Early_S cells rep2.

description: Library name: Early_S_DHX_2

value: Early S Phase-Synchronized


title: Replicate 1, Human Fetal kidney organoids cultured for 3 weeks.

description: Library name: hFKO_0_a


title: CUT&Tag of NELFA  in Early_S cells rep1.

description: Library name: Early_S_NELFA_1


title: ZC008

description: 99,expression matrix.xlsx


title: plate1_scRNA_WT0105mouse_Kidney

description: Updated Microwell-seq_scRNA-seq

value: Kidney


title: CUT&Tag of DHX36  in Early_S cells rep1.

description: Library name: Early_S_DHX_1


title: MM099 treated with siLISR late polysomes fraction rep2

city: Leuven

first: Eleonora

last: Leucci

address: Herestraat 49, bus 818 room 06.423

department: Oncology

country: Belgium

institute: KU Leuven

data_processing:
Quality control of raw reads was performed with FastQC v3
Adapters were filtered with Trimmomatic 1.4
Splice- aware alignment was performed with STAR against the human hg38 human genome assembly. The number of allowed mismatches was 2. Reads that mapped to more than one site to the reference genome were discarded. The minimal score of align- ment quality to be included in count analysis was 10.
Quantification of reads per gene was performed with HT-Seq count v2.2.
Count-based differential expression analysis was done with R-based (The R Foundation for Statistical Computing, Vienna, Austria) Bioconductor package DESeq.
Assembly: human hg38 human genome assembly
Supplementary files format and content: Count files from HT-Seq count v2.2 containing quantification of genes per sample.

growth_protocol: MM099 were grown in F-10 (Gibco, Invitrogen) supplemented with 10% FBS (Gibco, Invitrogen)

extract_protocol:
Cells were treated with 100 µg mL-1 of Cycloheximide (CHX, Sigma-Aldrich) for 12 min at 37 °C and resuspended in lysis buffer.  Lysates were then loaded on a sucrose gradient (the linear sucrose gradient 5-20%). Samples were then centrifugated in an SW41Ti rotor (Beckman Coulter) at 37.000 rpm for 170 min at 4 °C. The fractions were obtained with a BioLogic LP System (Bio-Rad). 14 fractions were collected from each sample, with each fraction having a final volume of 600 µL. From the initial 14 fractions, 4 final samples were obtained (by pulling together some of them): 40S, 60S, 80S and polysomes.
Libraries were prepared with TruSeq Stranded Total RNA kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Cells were trasnfected with siRNAs and incubated for 48h before polysome preparation

tag: fraction

value: late polysomes

value: melanoma

value: siLISR


title: MM099 treated with siLISR late polysomes fraction rep3


title: ZC016

description: 99,expression matrix.xlsx


title: plate1_scRNA_WT0105mouse_Heart

description: Updated Microwell-seq_scRNA-seq

value: Heart


title: plate1_scRNA_WT0105mouse_Gallbladder-BileDuct

description: Updated Microwell-seq_scRNA-seq

value: Gallbladder-BileDuct


title: MM099 treated with siLISR late polysomes fraction rep1


title: CUT&Tag of BRIP1  in Early_S cells rep2.

description: Library name: Early_S_BRIP1_2


title: ZC017

description: 99,expression matrix.xlsx


title: MM099 treated with siControl late polysomes fraction rep3

value: siControl


title: MM099 treated with siControl late polysomes fraction rep2


title: CUT&Tag of G4-DNA  in Early_S cells rep2.

description: Library name: Early_S_BG4_2


title: plate1_scRNA_WT0105mouse_Brain

description: Updated Microwell-seq_scRNA-seq

value: Brain

value: 13 weeks


title: ZC014

description: 99,expression matrix.xlsx

value: blood

value: Control


title: plate1_scRNA_WT0105mouse_BoneMarrow

description: Updated Microwell-seq_scRNA-seq

value: BoneMarrow


title: ZC015

description: 99,expression matrix.xlsx


title: MM099 treated with siControl late polysomes fraction rep1


title: plate1_scRNA_WT0105mouse_Bladder

description: Updated Microwell-seq_scRNA-seq

value: Bladder


title: ZC012

description: 99,expression matrix.xlsx


title: MM099 treated with siLISR early polysomes fraction rep3

value: early polysomes


title: CI92_1130

city: Bethesda

first: Sasisekhar

last: Bennuru

state: MD

address: 10 Center Dr, Bldg 10, Rm 11N208

department: LPD

institute: NIH/NIAID

data_processing:
The basecalled data (Illumina’s run time analysis software RTA 2.4.11), was demultiplexed (Bcl2fastq v2.17) and filtered (cutadapt 1.18) for adaptors and quality and aligned to W. bancrofti genome using STAR 2.7.0f. Picard 2.18.26 and RSEM 1.3.1 were used for statistical analysis and quantification. The data was then filtered conservatively for (i) reads that mapped uniquely to the genome (quality value of 255 in STAR), (ii) reads that did not map to known repetitive regions, (iii) regions that had 5 or more reads in infected samples and less than 5 reads across all control samples.
Assembly: W. bancrofti genome at Washington University School of Medicine, St Louis
Supplementary files format and content: bigwig

source_name: Plasma

extract_protocol:
total RNA extracted from plasma samples of W. bancrofti-infected (n=20) and normal healthy volunteers (n=5) using the Norgen Plasma/Serum RNA Purification kit.
After checking for quality control using Eukaryote total RNA Pico kit on Agilent BioAnalyzer 2100, barcoded Illumina TruSeq stranded total RNA libraries were generated for paired end sequencing using NextSeq’s HiSeq3000/4000 platform with a read length of 76 (2 x 76 cycles).
All samples had 20-28 million pass filter reads with more than 95% of bases above the quality score of Q30.

value: Plasma

tag: biosource

value: Cook Island Samples

tag: group

value: infected plasma

tag: infection

value: Wuchereria bancrofti


title: plate1_scRNA_KO0045mouse_LargeIntestine

description: Updated Microwell-seq_scRNA-seq

value: LargeIntestine

value: 29 weeks

value: Female


title: CI92_1113


title: ZC013

description: 99,expression matrix.xlsx


title: MM099 treated with siLISR early polysomes fraction rep2

value: melanoma

value: siLISR


title: plate1_scRNA_KO0045mouse_Bladder

description: Updated Microwell-seq_scRNA-seq


title: CUT&Tag of BRIP1  in Early_S cells rep1.

description: Library name: Early_S_BRIP1_1

value: liver

value: tumor cells

value: Early S Phase-Synchronized


title: MM099 treated with siLISR early polysomes fraction rep1


title: MM099 treated with siControl early polysomes fraction rep3

value: siControl


title: CI92_1071


title: Uterus, Trp53-/-_mouse_1410, 4.5_month-old

description: Microwell-based ATAC-seq

library_source: genomic single cell

data_processing:
The original FASTQ files were converted to BAM format firstly. Then the cell barcodes were extracted and tagged with CB in the offered BAM files. Three 6bp barcodes and one 10bp Tn5 barcode ware combined to identify a single cell (a single cell barcode consists of four barcode fragments). Reads with the quality of cell barcodes less than 10 were tagged with XQ and removed afterwards. The processing above was based on Drop-seq_tools-2.5.1. Next, the known barcode sequences involved in the library construction were utilized for cell barcode correction, allowing one mismatch in each barcode fragments. Before alignment, the cell barcodes were added to the query names, the BAM files were converted to the FASTQ files and the 28bp barcodes at the 5’ end were trimmed simultaneously.
BWA (version 0.7.15), which is encapsulated in Snaptools, was used for reads alignment in single-end mode. The data were aligned to mm10 reference genome. Snaptools was again used to convert the aligned and shifted BAM files to SNAP files, which was then converted to Fragment files (BED format). The sorted and compressed Fragment files in BED format were required as inputs for subsequent analysis.
Assembly: Mus_musculus.GRCm38.88 genome
Supplementary files format and content: BED files recording coordinates of fragments captured by scATAC-seq

source_name: Uterus

extract_protocol:
Tissues were quickly transferred into cold DPBS, then washed and subjected to manual pulverization via grinded in liquid nitrogen. The pulverized tissues were aliquoted into pre-labelled and pre-chilled 1.5 ml nuclease-free tubes. After that, the powder in each tube was suspended in 1 ml Nuclear Permeabilization Buffer [1 × DPBS, 5% Bovine Serum Albumin, 0.2% IGEPAL CA-630 (Sigma), 1 mM DTT, 1 × Protease inhibitor], and followed by incubation for 3 minutes to isolate the nuclei. The suspension was transferred to a 15 ml centrifuge tubes pre-filled with 5 ml wash buffer, filtered through 40 μm strainers and centrifuged at 600 × g for 5 minutes at 4°C and re-suspended in 1 × DPBS.  For Bone marrow, cells were collected and centrifuged at 300 × g for 5 minutes at 4°C, then suspended in 1 ml Nuclear Permeabilization Buffer and followed by incubation for 6 minutes to isolate the nuclei. The suspension was transferred to 15 ml centrifuge tubes pre-filled with 5 ml wash buffer, centrifuged at 500 × g for 5 minutes at 4°C and re-suspended in 1 × DPBS.
Library preparations were performed with the Microwell ATAC-seq plus protocol

value: Uterus

value: 4.5 months


title: ZC011

description: 99,expression matrix.xlsx

value: blood

value: Control


title: Stomach, Trp53-/-_mouse_1410, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Stomach

value: Stomach


title: ZC019

description: 99,expression matrix.xlsx


title: CI92_1016

value: Plasma

value: Cook Island Samples


title: CUT&Tag of G4-DNA  in Early_S cells rep1.

description: Library name: Early_S_BG4_1


title: Thymus, Trp53-/-_mouse_1410, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Thymus

value: Thymus


title: ZC018


title: CI92_1020

value: infected plasma

value: Wuchereria bancrofti


title: MM099 treated with siControl early polysomes fraction rep2

value: early polysomes


title: MM099 treated with siControl early polysomes fraction rep1

value: melanoma


title: ZC051

description: 99,expression matrix.xlsx


title: MM099 treated with siLISR subunit fraction rep3

value: subunits

value: siLISR


title: SmallIntestine, Trp53-/-_mouse_1410, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: SmallIntestine

value: SmallIntestine

value: Female


title: CI92_1011


title: MM099 treated with siLISR subunit fraction rep2


title: Ovary, Trp53-/-_mouse_1410, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Ovary

value: Ovary


title: ZC055

description: 99,expression matrix.xlsx


title: CI92_1037


title: CI92_1012


title: ZC054

description: 99,expression matrix.xlsx


title: ZC010

description: 99,expression matrix.xlsx


title: Pancreas, Trp53-/-_mouse_1410, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Pancreas

value: Pancreas


title: LymphNodes, Trp53-/-_mouse_1410, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: LymphNodes

value: LymphNodes

value: 4.5 months


title: IN84_65

value: India Samples


title: MM099 treated with siControl subunit fraction rep3

value: siControl


title: MM099 treated with siControl subunit fraction rep2


title: ZC041

value: blood

value: Control


title: CI92_1001

value: Plasma

value: Cook Island Samples


title: ZC049

description: 99,expression matrix.xlsx


title: CI92_1013

value: infected plasma

value: Wuchereria bancrofti


title: Spleen, Trp53-/-_mouse_1410, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Spleen

value: Spleen


title: ZC040

description: 99,expression matrix.xlsx


title: Liver, Trp53-/-_mouse_1410, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Liver

value: Liver


title: Lung, Trp53-/-_mouse_1410, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Lung

value: Lung


title: IN84_63


title: MM099 treated with siControl subunit fraction rep1

value: subunits

value: melanoma


title: MM099 treated with siLISR subunit fraction rep1

value: siLISR


title: ZC042

description: 99,expression matrix.xlsx


title: IN84_62


title: MM099 treated with siLISR rep1

value: input


title: MM099 treated with siLISR rep2


title: ZC044

description: 99,expression matrix.xlsx


title: IN84_27


title: Kidney, Trp53-/-_mouse_1410, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Kidney

value: Kidney

value: Female


title: Heart, Trp53-/-_mouse_1410, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Heart

value: Heart

value: 4.5 months


title: MM099 treated with siControl rep3

value: siControl


title: IN84_26

value: India Samples


title: ZC046

description: 99,expression matrix.xlsx

value: blood

value: Control


title: IN84_25

value: Plasma

value: infected plasma


title: MM099 treated with siControl rep2


title: WZC001

description: 99,expression matrix.xlsx


title: IN84_22

value: Wuchereria bancrofti


title: MM099 treated with siControl rep1


title: Brain, Trp53-/-_mouse_1410, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Brain

value: Brain


title: MM099 treated with siLISR rep3


title: ZC043

description: 99,expression matrix.xlsx


title: BoneMarrow, Trp53-/-_mouse_1410, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: BoneMarrow

value: BoneMarrow


title: WZC006


title: IN84_21


title: WZC004


title: LargeIntestine, Trp53-/-_mouse_1410, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: LargeIntestine

value: LargeIntestine


title: E13.5 Hand1 wild type sample NE-4

city: Bloomington

first: Center for Genomics and Bioinformatics

last: IU

state: IN

address: 1001 E Third St

department: Biology

institute: Center for Genomics and Bioinformatics

description: Library name: NE-4

data_processing:
Sequenced reads from the Flex assay  were demultiplexed, aligned to the mouse reference genome (mm10-2020-A) and the count matrices were generated using Cellranger version 8.0.1
The barcode quality control was conducted through subjective assessment of the sample specific metrics: total UMI (Unique Molecular Identifier) count per barcode, number of features per barcode and percent of mitochondrial reads per barcode generated by the package Seurat version 5.1.0 on R version 4.4.1.
PCA (Principal Compoment Analysis) was performed on the integrated sample data for dimensionality reduction and the clusters were visualized using UMAP (Uniform Approximation and Projection).
Results from Seurat analysis were exported to cloupe files using the R package loupeR version 1.1.1.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format

source_name: E13.5 transverse FFPE sections at level of umbilicus

growth_protocol: mouse timed pregancies emrbyo harvest at E13.5

extract_protocol:
Samples were processed following exactly the extraction  protocol provided by 10X genomics.
Libraries were constructed following exactly the library construction protocol provided by 10X genomics.

value: Hand1 wildtype control


title: Bladder, Trp53-/-_mouse_1410, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Bladder

value: Bladder


title: IN84_20

source_name: Plasma


title: IN84_61


title: ZC047


title: E13.5 Hand1 wild type sample REFvB-4

description: Library name: REFvB-4

value: E13.5 transverse FFPE sections at level of umbilicus


title: ZC052

description: 99,expression matrix.xlsx


title: Gallbladder-BileDuct, Trp53-/-_mouse_1410, 4.5_month-old

description: Microwell-based ATAC-seq

source_name: Gallbladder-BileDuct

value: Gallbladder-BileDuct


title: Uterus, 3_month-old_mouse03, rep3

data_processing:
Quality control with Trimmomatic-0.39.
Reads were aligned to the mouse GRCm38 genome assembly using bowtie2 (version 2.3.4.3) with -I 10 -X 700.
Check the duplicate rate and remove duplication using Picard with default configurations.
Filtering on the alignment quality score using samtools. Filter and keep the mapped read pairs by samtools. Convert bam files into bed file, and keep the read pairs that on the same chromosome and fragment length less than 1000bp, then extract the fragment related columns..
Convert bed files to bedgraph format, and use SEACR to call peaks.
Assembly: Mus musculus GRCm38
Supplementary files format and content: Genomic coverage bedgraph file for each sample.
Library strategy: Cut&tag

source_name: Uterus

extract_protocol:
Tissues were quickly transferred into cold DPBS, then washed and subjected to manual pulverization via grinded in liquid nitrogen. The pulverized tissues were aliquoted into pre-labelled and pre-chilled 1.5 ml nuclease-free tubes. After that, the powder in each tube was suspended in 1 ml Nuclear Permeabilization Buffer [1 × DPBS, 5% Bovine Serum Albumin, 0.2% IGEPAL CA-630 (Sigma), 1 mM DTT, 1 × Protease inhibitor], and followed by incubation for 3 minutes to isolate the nuclei. The suspension was transferred to a 15 ml centrifuge tubes pre-filled with 5 ml wash buffer, filtered through 40 μm strainers and centrifuged at 600 × g for 5 minutes at 4°C and re-suspended in 1 × DPBS.  For Bone marrow, cells were collected and centrifuged at 300 × g for 5 minutes at 4°C, then suspended in 1 ml Nuclear Permeabilization Buffer and followed by incubation for 6 minutes to isolate the nuclei. The suspension was transferred to 15 ml centrifuge tubes pre-filled with 5 ml wash buffer, centrifuged at 500 × g for 5 minutes at 4°C and re-suspended in 1 × DPBS.
Library was performed according to the manufacter’s instructions (Hyperactive® Universal CUT&Tag Assay Kit for Illumina, Vazyme). We replaced primers for illumina with primers for MGI, in order to be suitable for the sequencing protocol of DNBSEQ-T7.

value: Uterus

value: 3 months

tag: chip antibody

value: anti-p53 antibody(abcam, #ab246550)

value: Female


title: E13.5 Hand1 wild type sample REFvB-2

description: Library name: REFvB-2


title: ZC053

description: 99,expression matrix.xlsx


title: Uterus, 3_month-old_mouse02, rep2


title: BB010167

value: Blood Bank

value: healthy plasma

value: control


title: Uterus, 3_month-old_mouse01, rep1


title: BB010142

value: Plasma


title: E13.5 Hand1 wild type sample REFvB-1

description: Library name: REFvB-1


title: Thymus, 3_month-old_mouse02, rep2

source_name: Thymus

value: Thymus


title: BB010162


title: BB010165


title: Thymus, 3_month-old_mouse01, rep1


title: ZC056

description: 99,expression matrix.xlsx

value: blood

value: Control


title: E13.5 Hand1 Hand2/Hand2 mutant sample LE-7

description: Library name: LE-7

value: Hand1Hand2/Hand2 mutant


title: MDA-MB-231 cells,5µM MC treated, 9 hours, biol rep3

city: Mumbai

first: Shivani

middle: R.

last: Nandha

address: Trombay

country: India

institute: Bhabha Atomic Research Centre

data_processing:
Demultiplexed FASTQ ﬁles were imported into Strand NGS v4.0 for alignment and analysis.The reads were aligned to the genome and transcriptome of Homo sapiens, using Strand NGS v4.0. The reference transcriptome was obtained from the GRCh38 primary assembly. Gene annotations and locations were derived from NCBI Entrez Gene ﬁles updated on May 05, 2023. Transcript annotations Known RefSeq were obtained from the gﬀ3 ﬁles available on NCBI FTP updated on 21.03.2023. Based on the pre-alignment quality plots, ﬁxed trimming is applied on 5' end: 10 bases and on 3' end: 0 base to remove poor quality 5’ & 3’ ends of the reads.
Assembly: GRCh38 primary assembly
Supplementary files format and content: Tab-delimited text file includes raw files for each Sample
Supplementary files format and content: Tab-delimited text file includes TMM files for each Sample

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB-231 cells were grown in DMEM media supplemented with 10% FBS at 37°C in a humidified atmosphere (5% CO2 and 95% air).

extract_protocol:
RNA was isolated using Trizol method and quantiﬁed using qubit and quality assessed using Tapestation.
The KAPA mRNA Hyper Prep Kit for Illumina sequencing  was used for poly(A) mRNA capture and construction of stranded mRNA-Seq libraries from 50 ng – 1 μg of intact total RNA.

treatment_protocol: MDA-MB-231 cells were subjected to mitocurcumin treatment (5µM) for 9 hours (Treatment group) or DMSO-vehicle treatment for 9 hours (Control group).

value: MDA-MB-231 cells

value: Human Triple Negative Breast Cancer cell line

value: 5µM mitocurcumin treatment for 9 hours


title: Thymus, 3_month-old_mouse02, positive_control_H3K4me3

value: Anti-Histone H3 (tri methyl K4) antibody(abcam, #ab213224)


title: Trp53-/-_mouse_0054, 20.5_week-old, Thymus

description:
scRNA_KO0054mouse_Thymus
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the updated Microwell-seq protocol

value: 20.5 weeks


title: MDA-MB-231 cells,5µM MC treated, 9 hours, biol rep2


title: E13.5 Hand1 Hand2/Hand2 mutant sample LE-6

description: Library name: LE-6

value: E13.5 transverse FFPE sections at level of umbilicus


title: Thymus, 3_month-old_mouse02, negtive_control

description: Replace anti-p53 antibody with Antibody Buffer

value: 3 months


title: BB010173


title: E13.5 Hand1 Hand2/Hand2 mutant sample 24-7

description: Library name: 24-7


title: Thymus, 3_month-old_mouse03, rep3

value: anti-p53 antibody(abcam, #ab246550)


title: E13.5 Hand1 wild type sample REFvB-3

description: Library name: REFvB-3

value: Hand1 wildtype control


title: Trp53-/-_mouse_0054, 20.5_week-old, MammaryGland

description:
scRNA_KO0054mouse_MammaryGland
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.

source_name: MammaryGland

value: MammaryGland

value: Female


title: Trp53-/-_mouse_0054, 20.5_week-old, Ovary

description:
scRNA_KO0054mouse_Ovary
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.

source_name: Ovary

value: Ovary


title: ZC050

description: 99,expression matrix.xlsx


title: MDA-MB-231 cells,5µM MC treated, 9 hours, biol rep1


title: MDA-MB-231 cells,Control, 9 hours, biol rep2

value: DMSO-vehicle treatment for 9 hours


title: Trp53-/-_mouse_0054, 20.5_week-old, LargeIntestine

description:
scRNA_KO0054mouse_LargeIntestine
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.

value: LargeIntestine


title: Hand1^Hand2/Hand2 E13.5 transverse sections V52L19-098_B1

description: Library name: 14-6_5B_V52L19-098_B1

data_processing:
Alignment of the sequenced reads from the Visium Spatial assay to the mouse reference genome (mm10-2020-A), tissue detection, barcode counting and feature identification were conducted using the spaceranger count pipeline version 3.0.1.
Specific barcodes that contained ventral body wall and ventral gut structures were captured from 4 Hand1Hand2/Hand2 and 4 Hand1+/+ hearts (4-6 sections per Visium slide).
The identified barcodes were processed using Seurat version 5.1.0 using their recommended workflow in which the data were subjected to SCTransform-based normalization, sample merging, PCA and UMAP visualization to identify clusters.
Eight distinct clusters of spatial barcodes were identified both containing wild-type and mutant cells.
The significantly differentially expressed genes within each cluster were called by applying Wilcox test with FindMarkers function with a cutoff of adjusted pvalue <= 0.05.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: aligned_tissue_image.jpg: aligned tissue image
Supplementary files format and content: cytassist_image.tiff: Visium CytAssist instrument capture images
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: spatial_enrichment.csv: Spatial enrichment file
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics


title: MDA-MB-231 cells,Control, 9 hours, biol rep3


title: Stomach, 3_month-old_mouse02, rep2

source_name: Stomach

value: Stomach


title: E13.5 Hand1 Hand2/Hand2 mutant sample R3-2

description: Library name: R3-2


title: MDA-MB-231 cells,Control, 9 hours, biol rep1


title: Stomach, 3_month-old_mouse01, rep1


title: Hand1^Hand2/Hand2 E13.5 transverse sections V52L18-371_B1

description: Library name: 14-5_6B_V52L18-371_B1


title: Hand1^Hand2/Hand2 E13.5 transverse sections V52L18-371_A1

description: Library name: 14-5_4A_V52L18-371_A1


title: Trp53-/-_mouse_0054, 20.5_week-old, Uterus

description:
scRNA_KO0054mouse_Uterus
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.

value: Uterus


title: Spleen, 3_month-old_mouse04, rep3

source_name: Spleen

value: Spleen


title: C10_CTR_6

city: Madrid

first: Anxo

last: Rio-Vilariño

address: Avenida Reyes Católicos, 2

department: Medical Oncology

country: Spain

institute: Instituto de Investigaciones Sanitarias Fundación Jiménez Díaz (IIS-UAM)

data_processing:
Sample alignment was performed using the Ensembl GRCh38 genome as reference with the STAR program (v.2.7.10b)
Gene Counts were extracted, normalized and used to perform Differentially Gene Expression analysis by u0sing the DESeq2 Algorithm in R.
Assembly: GRCh38
Supplementary files format and content: Matrix file containing raw counts for each sample

growth_protocol: C10 were grown in M6 plates using high-glucose DMEM  (HyClone, UT, USA) supplemented with 10% FBS and 1% penicillin/streptomycin at 60% confluence during 24 hours before being treated with alisertib 350nM or DMSO.

extract_protocol:
RNA was extracted using the NucleoSpin RNA Isolation kit (Macherey-Nagel) and its purity checked using the BioAnalyzer. All samples displayed a RNA Integrity Number of 9 or higher.
RNA libraries for RNA-seq were prepared by Novogene following Novogene's standard protocols.

treatment_protocol: Cells were treated with 350nM

value: CRC Cell Line

value: RAS/RAF wild-type

value: DMSO


title: Trp53-/-_mouse_0054, 20.5_week-old, Stomach

description:
scRNA_KO0054mouse_Stomach
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.


title: Hand1^Hand2/Hand2 E13.5 transverse sections V52L06-338_B1

description: Library name: 14-4_8B_V52L06-338_B1


title: C10_CTR_5


title: Trp53-/-_mouse_0054, 20.5_week-old, Spleen

description:
scRNA_KO0054mouse_Spleen
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.


title: Hand1^Hand2/Hand2 E13.5 transverse sections V52L06-338_A1

description: Library name: 14-4_7A_V52L06-338_A1


title: Hand1^Hand2/Hand2 E13.5 transverse sections V52L19-003_B1

description: Library name: 14-3_7B_V52L19-003_B1


title: Spleen, 3_month-old_mouse01, rep1


title: C10_CTR_4


title: Stomach, 3_month-old_mouse03, rep3


title: C10_CTR_3


title: Trp53-/-_mouse_0054, 20.5_week-old, SmallIntestine

description:
scRNA_KO0054mouse_SmallIntestine
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.

source_name: SmallIntestine

value: SmallIntestine


title: Hand1^Hand2/Hand2 E13.5 transverse sections V52L19-003_A1

description: Library name: 14-3_6A_V52L19-003_A1


title: Trp53-/-_mouse_0054, 20.5_week-old, Pancreas

description:
scRNA_KO0054mouse_Pancreas
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.

source_name: Pancreas

value: Pancreas

value: 20.5 weeks


title: Trp53-/-_mouse_0054, 20.5_week-old, Brain

description:
scRNA_KO0054mouse_Brain
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.

value: Brain


title: C10_CTR_2


title: SmallIntestine, 3_month-old_mouse01, rep1

value: 3 months

value: anti-p53 antibody(abcam, #ab246550)


title: Trp53-/-_mouse_0054, 20.5_week-old, LymphNodes

description:
scRNA_KO0054mouse_LymphNodes
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.

source_name: LymphNodes

value: LymphNodes


title: Hand1 wildtype E13.5 transverse sections V52L19-023_B1

description: Library name: WT-9_9B_V52L19-023_B1

value: E13.5 transverse FFPE sections at level of umbilicus

value: Hand1 wildtype


title: C10_CTR_1


title: SmallIntestine, 3_month-old_mouse03, rep3

value: Female


title: SmallIntestine, 3_month-old_mouse02, positive_control_H3K27me3

value: Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb(Cell signaling,#9733)


title: Trp53-/-_mouse_0054, 20.5_week-old, Lung

description:
scRNA_KO0054mouse_Lung
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.

source_name: Lung

value: Lung


title: C10_ALS_6

value: Alisertib (MLN8237)


title: SmallIntestine, 3_month-old_mouse02, positive_control_H3K4me3

value: Anti-Histone H3 (tri methyl K4) antibody(abcam, #ab213224)


title: Trp53-/-_mouse_0054, 20.5_week-old, Liver

description:
scRNA_KO0054mouse_Liver
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.

source_name: Liver

value: Liver


title: Hand1 wildtype E13.5 transverse sections V52L18-320_B1

description: Library name: WT-8_9B_V52L18-320_B1


title: Spleen, 3_month-old_mouse02, rep2

value: Spleen


title: C10_ALS_5

value: CRC Cell Line

value: RAS/RAF wild-type


title: SmallIntestine, 3_month-old_mouse02, negtive_control

value: SmallIntestine


title: Trp53-/-_mouse_0054, 20.5_week-old, Kidney

description:
scRNA_KO0054mouse_Kidney
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.

source_name: Kidney

value: Kidney

value: 20.5 weeks


title: Hand1 wildtype E13.5 transverse sections V52L18-320_A1

description: Library name: WT-8_8A_V52L18-320_A1

source_name: E13.5 transverse FFPE sections at level of umbilicus


title: C10_ALS_4


title: Hand1 wildtype E13.5 transverse sections V52L18-318_A1

description: Library name: WT-7_8A_V52L18-318_A1


title: Trp53-/-_mouse_0054, 20.5_week-old, Heart

description:
scRNA_KO0054mouse_Heart
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.

source_name: Heart

value: Heart


title: C10_ALS_3


title: Hand1 wildtype E13.5 transverse sections V52L18-318_B1

description: Library name: WT-7_10B_V52L18-318_B1


title: Trp53-/-_mouse_0054, 20.5_week-old, Gallbladder-BileDuct

description:
scRNA_KO0054mouse_Gallbladder-BileDuct
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.

value: Gallbladder-BileDuct


title: C10_ALS_2


title: Pancreas, 3_month-old_mouse06, rep3

value: Pancreas

value: 3 months

value: anti-p53 antibody(abcam, #ab246550)


title: Hand1 wildtype E13.5 transverse sections V52L19-052_B1

description: Library name: WT-10_7B_V52L19-052_B1

value: E13.5 transverse FFPE sections at level of umbilicus

value: Hand1 wildtype


title: Pancreas, 3_month-old_mouse04, rep2

value: Female


title: Trp53-/-_mouse_0054, 20.5_week-old, BoneMarrow

description:
scRNA_KO0054mouse_BoneMarrow
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.

source_name: BoneMarrow

value: BoneMarrow


title: Hand1 wildtype E13.5 transverse sections V52L19-023_A1

description: Library name: WT-9_8A_V52L19-023_A1


title: LIGHT_3

city: La Jolla

first: Michael

last: Croft

state: CA

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

data_processing:
Reads passing Illumina filters were further filtered for those mapping to tRNA, rRNA, adapters, and spike-in controls using Bowtie v1.0.0 (-S --fr)
Filtered reads were against the GRCh38 reference genome and Gencode v27 annotations using STAR v2.6.1 (default options)
Reads mapping to the reference genome are further filtered to remove low-complexity reads with PRINSEQ v0.20.3 (-lc_method "dust" -lc_threshold 4)
Sequencing read coverage per gene was counted using HTSeq-count v0.7.1 (-m union -s yes -t exon -i gene_id) and features with 0 counts across all samples were removed
Assembly: GRCh38.gencode.v27B
Supplementary files format and content: read count matrix with rows as genes and columns as cells

source_name: Human epidermal keratinocyte

growth_protocol: Human epidermal keratinocytes from neonates were purchased from ATCC (NHEK, PS-200-010, ATCC, Manassas, VA) and grown in Dermal Cell Basal Medium (PCS-200-030, ATCC).

extract_protocol:
RNA was isolated from 3 different replicates per group, using a Qiagen kit and subjected to RNA-seq analysis.
Sequencing was performed according to a paired-end strategy using the NovaSeq sequencer (Illumina). Samples that failed quality control standards were eliminated from further analysis21.

treatment_protocol: 3x105 cells/well were cultured in triplicates using a 6-well format plate and stimulated with predetermined optimal concentrations of human rLIGHT (100 ng/ml) for 48 hrs. Controls received PBS.

value: Keratinocyte isolated from human skin

tag: stimulation

value: Recombinant human LIGHT protein

tag: cell subset

value: Primary cells


title: Hand1 wildtype E13.5 transverse sections V52L19-052_A1

description: Library name: WT-10_6A_V52L19-052_A1


title: C10_ALS_1

tag: cell type

value: CRC Cell Line

value: Alisertib (MLN8237)


title: scRNA_KO0042mouse_Uterus

description:
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.

tag: tissue

value: Uterus

value: 21 weeks


title: Bulk RNA-seq Monocytes 2

city: Pamplona

first: Mikel

last: Hernaez

state: Navarra

address: Avda. Pío XII, 55

department: Bioinformatics

institute: CIMA (Centre for Applied Medical Research)

description:
Library name: IndD2_S31
FACS-sorted Monocytes
bulkrna_isolated.tsv

data_processing:
Raw FASTQ files were processed with Cell Ranger (v7.2.0) for single-cell data, aligned to the GRCh38 reference genome.
Count matrices were generated using Cell Ranger count and filtered for high-quality cells.
Bulk RNA-seq reads were aligned using Kallisto v0.46  to GRCh38.
Quality control was performed using Seurat (v4.3.0), filtering cells with >200 genes and <20% mitochondrial content.
Expression data were normalized using log normalization (Seurat) and TPM for bulk data.
Assembly: GRCh38 (GENCODE v39)
Supplementary files format and content: Single-cell: Matrix Market format (MTX), barcodes.tsv, genes.tsv; Bulk: raw matrices in tab-delimited text format.

source_name: PBMC

growth_protocol: Cells were isolated from human peripheral blood mononuclear cells (PBMCs) obtained from healthy donors.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini Kit following the manufacturer’s protocol, including on-column DNase digestion.
Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3’ protocol according to the manufacturer’s instructions.

treatment_protocol: No treatments were applied prior to RNA extraction.

value: PBMC

value: Monocytes

value: WT

tag: batch


title: Pancreas, 3_month-old_mouse05, rep1

value: Pancreas


title: Bulk RNA-seq B cells 2

description:
Library name: IndC2_S29
FACS-sorted Neutrophils
bulkrna_isolated.tsv

value: B cells


title: scRNA_KO0042mouse_Thymus

value: Thymus


title: SmallIntestine, 3_month-old_mouse02, rep2

value: SmallIntestine

value: 3 months

value: anti-p53 antibody(abcam, #ab246550)


title: LIGHT_1


title: Ovary, 3_month-old_mouse03, rep3

value: Ovary

value: Female


title: Bulk RNA-seq B cells 1

description:
Library name: IndC1_S28
FACS-sorted Neutrophils
bulkrna_isolated.tsv


title: LIGHT_2

value: Keratinocyte isolated from human skin

value: Recombinant human LIGHT protein


title: Ovary, 3_month-old_mouse02, rep2


title: MammaryGland, 3_month-old_mouse03, rep3

value: MammaryGland


title: scRNA_KO0042mouse_Ovary


title: Ovary, 3_month-old_mouse01, rep1


title: scRNA_KO0042mouse_Spleen

value: Spleen


title: PBS stimulation_3

value: PBS stimulation

value: Primary cells


title: PBS stimulation_2


title: Trp53-/-_mouse_0054, 20.5_week-old, Bladder

description:
scRNA_KO0054mouse_Bladder
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.

source_name: Bladder

value: Bladder

value: 20.5 weeks


title: scRNA_KO0042mouse_MammaryGland

value: 21 weeks


title: PBS stimulation_1


title: LymphNodes, 3_month-old_mouse02, rep2

value: LymphNodes


title: Bulk RNA-seq T cells 2

description:
Library name: IndB2_S27
FACS-sorted B cells
bulkrna_isolated.tsv

value: PBMC

value: T cells

value: WT


title: Bulk RNA-seq T cells 1

description:
Library name: IndB1_S26
FACS-sorted B cells
bulkrna_isolated.tsv


title: MammaryGland, 3_month-old_mouse02, rep2

value: 3 months


title: IEFE (SiO₂@NFAu, 1 min) replicate 2

first: zhidi

last: chen

state: 广东省

address: 深圳市南山区创新科技中心T4 1405

institute: 深圳大学

description: Library name: SAMPLES-R2

data_processing:
Adapter sequences were removed from the reads using fastp, which also trimmed bases at the 5′ ends that were not A, G, C, or T. Low-quality bases at the ends of reads (quality score < Q20) were trimmed, reads containing ≥10% ambiguous bases (N) were discarded, and reads shorter than 25 bp after adapter removal and quality trimming were removed. These steps yielded high-quality clean data. Clean reads from each sample were then aligned to the reference genome provided by the client using Bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Transcript abundance was estimated with RSEM, and expression levels were calculated in TPM units.
Assembly: GCF_016864475.1
Supplementary files format and content: Processed data are provided as normalized gene expression matrices in tab-delimited text format.

organism: Escherichia coli

source_name: Transcriptome profiling of E. coli after treatment with SiO₂@NF_Au under IEFE conditions for 1 min. Replicate 2.

growth_protocol: E. coli cultures were grown in LB medium at 37 °C with shaking at 200 rpm until reaching mid-log phase.

extract_protocol:
Bacterial were collected by centrifugation at 4000×g at 4 °C for 12 min. Total RNA was extracted using TRIzol reagent (Thermo Fisher, USA) according to the manufacturer’s instructions.
RNA integrity was assessed using agarose gel electrophoresis and an Agilent 2100 system. mRNA was isolated by removing rRNA, fragmented to ~200 bp, and used for first-strand cDNA synthesis with random primers. Second-strand cDNA synthesis was performed with dUTP substitution for dTTP. Libraries were prepared using a TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA), and the second strand was digested with UNG before PCR amplification.

treatment_protocol: Bacterial suspensions were treated with SiO₂@NF_Au under IEFE conditions for 1 min. Control samples were left untreated.

value: Bacterial cultures


title: Bulk RNA-seq Monocytes 1

description:
Library name: IndD1_S30
FACS-sorted Monocytes
bulkrna_isolated.tsv

value: Monocytes


title: scRNA_KO0042mouse_Lung

value: Lung

value: Female


title: Bulk RNA-seq Neutrophils 1

description:
Library name: IndA1_S24
FACS-sorted T cells
bulkrna_isolated.tsv

value: Neutrophils


title: Bulk RNA-seq Neutrophils 2

description:
Library name: IndA2_S25
FACS-sorted T cells
bulkrna_isolated.tsv


title: scRNA_KO0042mouse_LymphNodes


title: IEFE (SiO₂@NFAu, 1 min) replicate 3

address: 深圳市南山区创新科技中心T4 1405

description: Library name: SAMPLES-R3

source_name: Transcriptome profiling of E. coli after treatment with SiO₂@NF_Au under IEFE conditions for 1 min. Replicate 3.


title: LymphNodes, 3_month-old_mouse01, rep1

value: anti-p53 antibody(abcam, #ab246550)


title: MammaryGland, 3_month-old_mouse01, rep1

source_name: MammaryGland

value: MammaryGland


title: scRNA_KO0042mouse_Liver

value: Liver


title: IEFE (SiO₂@NFAu, 1 min) replicate 1

address: 深圳市南山区创新科技中心T4 1405

description: Library name: SAMPLES-R1

source_name: Transcriptome profiling of E. coli after treatment with SiO₂@NF_Au under IEFE conditions for 1 min. Replicate 1.


title: Bulk RNA-seq mixture Mix7.1

description:
Library name: Mix71_S44
Bulk mixture with proportions: 50% T, 50% Neutrophils
bulkrna_labmixed.tsv

value: Mix (T/B/N/M)


title: scRNA_KO0042mouse_Heart

value: Heart


title: Bulk RNA-seq mixture Mix7.2

description:
Library name: Mix72_S45
Bulk mixture with proportions: 50% T, 50% Neutrophils
bulkrna_labmixed.tsv


title: Bulk RNA-seq mixture Mix6.2

description:
Library name: Mix62_S43
Bulk mixture with proportions: 25% T, 25% B, 0% Neutrophils, 50% Monocytes
bulkrna_labmixed.tsv


title: Control (PBS) replicate 2

address: 深圳市南山区创新科技中心T4 1405

description: Library name: CONTROL-R2

source_name: Transcriptome profiling of E. coli without treatment (control). Replicate 2.

value: untreated


title: scRNA_KO0042mouse_Kidney

value: Kidney

value: 21 weeks


title: Control (PBS) replicate 1

address: 深圳市南山区创新科技中心T4 1405

description: Library name: CONTROL-R1

source_name: Transcriptome profiling of E. coli without treatment (control). Replicate 1.


title: scRNA_KO0042mouse_BoneMarrow

value: BoneMarrow


title: Lung, 3_month-old_mouse02, rep2


title: Lung, 3_month-old_mouse01, rep1


title: Lung, 3_month-old_mouse03, rep3


title: Bulk RNA-seq mixture Mix6.1

description:
Library name: Mix61_S42
Bulk mixture with proportions: 25% T, 25% B, 0% Neutrophils, 50% Monocytes
bulkrna_labmixed.tsv

value: PBMC


title: scRNA_KO0042mouse_Brain

value: Brain


title: Bulk RNA-seq mixture Mix5.1

description:
Library name: Mix51_S40
Bulk mixture with proportions: 49% T, 49% Neutrophils, 1% B, 1% Monocytes
bulkrna_labmixed.tsv

value: WT


title: NC_2

city: Xi'an

first: Muqi

state: Shaanxi

address: No.157 West Fifth Road, Xincheng District

institute: The Second Affiliated Hospital of Xi'an Jiaotong University

description: Library name: Sample8

data_processing:
Cleaned reads were aligned to a reference genome using STAR or HISAT2, requiring ≥85% alignment rate. Gene-level counts were generated with featureCounts or HTSeq, and normalized to transcripts per million (TPM) or fragments per kilobase per million (FPKM).
Assembly: Use the STAR software to perform sequence alignment between the preprocessed sequence and the reference genome sequence of the sequenced species. Based on the results of the Reads alignment to the reference genome, using the StringTie software, the transcripts in the sample were assembled based on the position information file of the known transcripts on the genome. Transcripts with an expression level of 0 were filtered out. Then, the StringTie-assembled transcripts from all samples were re-assembled separately. For the assembled transcripts from StringTie, the comparison results between gffcompare and the known gene reference genome position information can be used to classify the assembled transcripts.
Supplementary files format and content: gene counts of every sample with symbol

organism: Enterovirus A71

extract_protocol:
Total RNA was extracted using TRIzol, on-column DNase digestion to eliminate genomic DNA contamination. The extracted RNA samples were sent to Jingneng Biotechnology (Shanghai, China) for subsequent transcriptome sequencing.
RNA extraction and preparation: Total RNA is extracted from the sample, and mRNA is enriched (typically through polyA tail selection), followed by fragmentation. cDNA synthesis and library construction: The fragmented mRNA is reverse transcribed into double-stranded cDNA, sequencing adapter linkers are ligated to both ends, and fragment screening and library quality control are performed. The final product is a cDNA library suitable for high-throughput sequencing.

tag: cell line

value: Immune cells

value: Control group


title: Bulk RNA-seq mixture Mix5.2

description:
Library name: Mix52_S41
Bulk mixture with proportions: 49% T, 49% Neutrophils, 1% B, 1% Monocytes
bulkrna_labmixed.tsv


title: scRNA_KO0042mouse_Bladder

value: Bladder


title: Liver, 3_month-old_mouse03, rep3

value: 3 months

value: Female


title: Liver, 3_month-old_mouse02, rep2

value: anti-p53 antibody(abcam, #ab246550)


title: NC_3

description: Library name: Sample9

tag: treatment


title: scRNA_KO0014mouse_Thymus

data_processing:
The original FASTQ files were converted to BAM format firstly with Drop-seq_tools-1.12, which was used for the subsequent processing except for barcode correction and alignment. The cell barcodes were extracted and tagged with XC in the offered BAM files, and the unique molecular identifiers (UMIs) were tagged with XM. Three 6bp barcodes ware combined to identify a single cell. Reads with the quality of cell barcodes or UMIs less than 10 were tagged with XQ and removed afterwards. Next, the PolyATrimmer was used to trim polyA. Before alignment, the known barcode sequences involved in the library construction were utilized for cell barcode correction, allowing one mismatch in each 6bp barcode.
STAR (version 2.5.2a) was used for reads alignment in single-end mode. The data were aligned to a GRCm38.88 reference genome. Then the aligned BAM files were sorted by query names and were merged with the unaligned BAM files, in order to recover the XC and XM tags that were lost after the alignment. Finally, the top 20,000 cell barcodes ranked by reads number were used to generate the digital expression matrices in each sample or each technical repeat.
Tab-delimited text files of digital expression matrix (DGE) based on raw UMIs counts, with genes as rows and cells as columns.
Assembly: Mus_musculus.GRCm38.88 genome
Supplementary files format and content: Tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

value: Thymus

tag: strain

value: 23.5 weeks


title: NC_1

description: Library name: Sample7

tag: genotype


title: Liver, 3_month-old_mouse01, rep1

value: Liver

tag: age


title: Bulk RNA-seq mixture Mix4.2

description:
Library name: Mix42_S39
Bulk mixture with proportions: 47% T, 47% Neutrophils, 6% B
bulkrna_labmixed.tsv

value: Mix (T/B/N/M)


title: LymphNodes, 3_month-old_mouse03, rep3

value: LymphNodes

value: anti-p53 antibody(abcam, ab246550)

tag: Sex


title: LargeIntestine, 3_month-old_mouse03, rep3

source_name: LargeIntestine

value: LargeIntestine


title: Control (PBS) replicate 3

address: 深圳市南山区创新科技中心T4 1405

description: Library name: CONTROL-R3

source_name: Transcriptome profiling of E. coli without treatment (control). Replicate 3.

value: Bacterial cultures

value: untreated


title: scRNA_KO0014mouse_Spleen

description:
Illumina HiSeq X Ten & DNBSEQ-T7
Updated Microwell-seq_scRNA-seq; The files named ".bam" are generated by Illumina sequencing, while the files named "_additional_1.bam" or "_additional_2.bam" are generated by DNBSEQ-T7 sequencing.

value: Spleen


title: Inactivated_EV71_3

description: Library name: Sample6

value: WT

value: Infected with inactivated EV-A71


title: Bulk RNA-seq mixture Mix4.1

description:
Library name: Mix41_S38
Bulk mixture with proportions: 47% T, 47% Neutrophils, 6% B
bulkrna_labmixed.tsv

value: PBMC


title: Inactivated_EV71_2

description: Library name: Sample5

value: Immune cells


title: Bulk RNA-seq mixture Mix3.1

description:
Library name: Mix31_S36
Bulk mixture with proportions: 50% T, 50% Neutrophils
bulkrna_labmixed.tsv


title: scRNA_KO0014mouse_Stomach

value: Stomach


title: LargeIntestine, 3_month-old_mouse02, rep2

value: 3 months

value: Female


title: LargeIntestine, 3_month-old_mouse01, rep1

value: anti-p53 antibody(abcam, #ab246550)


title: scRNA_KO0014mouse_SmallIntestine

value: SmallIntestine

value: 23.5 weeks


title: scRNA_KO0014mouse_Uterus

value: Uterus


title: Inactivated_EV71_1

description: Library name: Sample4


title: Bulk RNA-seq mixture Mix2.2

description:
Library name: Mix22_S35
Bulk mixture with proportions: 30% T, 30% Neutrophils, 10% B, 30% Monocytes
bulkrna_labmixed.tsv

value: Mix (T/B/N/M)


title: EV71_2

description: Library name: Sample2

value: Infected with EV-A71


title: Kidney, 3_month-old_mouse02, rep2

value: Kidney


title: EV71_1

description: Library name: Sample1


title: Kidney, 3_month-old_mouse01, rep1


title: scRNA_KO0014mouse_LymphNodes

value: LymphNodes


title: Bulk RNA-seq mixture Mix1.1

description:
Library name: Mix11_S32
Bulk mixture with proportions: 25% T, 25% B, 25% Neutrophils, 25% Monocytes
bulkrna_labmixed.tsv


title: scRNA_KO0014mouse_Ovary

value: Ovary


title: scRNA_KO0014mouse_Liver

value: Liver


title: Kidney, 3_month-old_mouse03, rep3


title: NPM::ALK plasmacytoma 6_1

type: genomic

city: Ulm

first: Selina

last: Glaser

address: Albert-Einstein-Allee 11

country: Germany

institute: Ulm University and Ulm University Medical Center

description: Plasmacytoma from NPM::ALK transgenic mice

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina MouseMethylation Beadchip using standard Illumina protocol.

scan_protocol: The arrays were scanned using a iScan device.

data_processing: Raw idat files were analysed using GenomeStudio software. Normalization was performed against the intrinsic controls and without background correction.

label: biotin

source_name: around the gut

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified according to commercially available kits from Qiagen according to standard instructions

value: around the gut


title: scRNA_KO0014mouse_MammaryGland

value: MammaryGland


title: scRNA_KO0014mouse_LargeIntestine

value: LargeIntestine


title: Bulk RNA-seq mixture Mix1.2

description:
Library name: Mix12_S33
Bulk mixture with proportions: 25% T, 25% B, 25% Neutrophils, 25% Monocytes
bulkrna_labmixed.tsv

value: PBMC

value: WT


title: NPM::ALK plasmacytoma 6_2


title: Heart, 3_month-old_mouse02, rep2

value: Heart

value: 3 months


title: Bulk RNA-seq mixture Mix3.2

description:
Library name: Mix32_S37
Bulk mixture with proportions: 50% T, 50% Neutrophils
bulkrna_labmixed.tsv


title: Heart, 3_month-old_mouse03, rep3

value: anti-p53 antibody(abcam, #ab246550)

value: Female


title: scRNA-seq of Mix1 sample

description:
Library name: sc_Mix1
Single-cell RNA-seq from Mix1, a 25%-each mixture of T, B, Neutrophils, Monocytes


title: Bulk RNA-seq mixture Mix2.1

description:
Library name: Mix21_S34
Bulk mixture with proportions: 30% T, 30% Neutrophils, 10% B, 30% Monocytes
bulkrna_labmixed.tsv


title: NPM::ALK plasmacytoma 5_2


title: scRNA_KO0014mouse_Heart

value: 23.5 weeks


title: Heart, 3_month-old_mouse01, rep1


title: Lag3-/-; 5xFAD+, 9 month, female, rep3

city: Research Triangle Park

first: Elizabeta

last: Gjoneska

state: North Carolina

address: 111 TW Alexander Dr., David P Rall Building A030

department: Neurobiology Laboratory

institute: National Institute of Environmental Health Sciences (NIEHS/NIH)

description: Library name: Q171

data_processing:
STAR Alignment to Mm10 genome
Subread featureCounts to summarize read counts across genes. Genes without read counts in all samples were excluded. The edgeR package was used for analysis.
Assembly: Mm10
Supplementary files format and content: Counts.Raw.txt
Supplementary files format and content: RPKM.values.txt

source_name: hippocampus

growth_protocol: Animals were maintained on a 12-hour light/ 12-hour dark cycle with ad libitum access to water and standard chow.

extract_protocol:
Total RNA from FACS purified CD11b+; CD45low hippocampal microglia was isolated using RNeasy Plus Mini Kit (Qiagen) and stored at -80°C. cDNA was generated using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara).
The cDNA libraries were prepared using the Nextera XT DNA Library Prep Kit and Nextera XT index Kit (Illumina) and sequenced by the NIEHS Epigenomics and DNA Sequencing Core Facility using a NextSeq 500 NGS system (Illumina).

value: hippocampus

value: microglia

value: 9 month

value: female


title: scRNA_KO0014mouse_Kidney

value: Kidney


title: Lag3-/-; 5xFAD+, 9 month, female, rep1

description: Library name: Q140


title: NPM::ALK plasmacytoma 4_2


title: EV71_3

description: Library name: Sample3

value: Immune cells

value: Infected with EV-A71


title: GallbladderBileDuct, 3_month-old_mouse02, rep2

source_name: GallbladderBileDuct

value: GallbladderBileDuct


title: Lag3-/-, 9 month, female, rep3

description: Library name: Q261


title: NPM::ALK plasmacytoma 4_1

value: around the gut


title: NPM::ALK plasmacytoma 5_1


title: GallbladderBileDuct, 3_month-old_mouse03, rep3


title: scRNA_KO0014mouse_BoneMarrow

value: BoneMarrow


title: Brain, 3_month-old_mouse04, rep3

source_name: Brain

value: Brain


title: Lag3-/-, 9 month, female, rep2

description: Library name: Q200


title: Lag3-/-, 9 month, female, rep1

description: Library name: Q199


title: scRNA_KO0014mouse_Bladder

value: Bladder


title: NPM::ALK plasmacytoma 3_2


title: 5xFAD+, 9 month, female, rep3

description: Library name: A129


title: Brain, 3_month-old_mouse05, rep2


title: NPM::ALK plasmacytoma 2_2


title: scRNA_KO0058mouse_Uterus

description: Updated Microwell-seq_scRNA-seq

data_processing:
The original FASTQ files were converted to BAM format firstly with Drop-seq_tools-1.12, which was used for the subsequent processing except for barcode correction and alignment. The cell barcodes were extracted and tagged with XC in the offered BAM files, and the unique molecular identifiers (UMIs) were tagged with XM. Three 6bp barcodes ware combined to identify a single cell. Reads with the quality of cell barcodes or UMIs less than 10 were tagged with XQ and removed afterwards. Next, the PolyATrimmer was used to trim ployA. Before alignment, the known barcode sequences involved in the library construction were utilized for cell barcode correction, allowing one mismatch in each 6bp barcode.
STAR (version 2.5.2a) was used for reads alignment in single-end mode. The data were aligned to a GRCm38.88 reference genome. Then the aligned BAM files were sorted by query names and were merged with the unaligned BAM files, in order to recover the XC and XM tags that were lost after the alignment. Finally, the top 20,000 cell barcodes ranked by reads number were used to generate the digital expression matrices in each sample or each technical repeat.
Tab-delimited text files of digital expression matrix (DGE) based on raw UMIs counts, with genes as rows and cells as columns.
Assembly: Mus_musculus.GRCm38.88 genome
Supplementary files format and content: Tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq1.1 protocol

value: Uterus

value: 15 weeks


title: NPM::ALK plasmacytoma 3_1


title: Lag3-/-; 5xFAD+, 9 month, female, rep2

description: Library name: Q166


title: Brain, 3_month-old_mouse01, rep1

value: 3 months

value: anti-p53 antibody(abcam, #ab246550)


title: 5xFAD+, 9 month, female, rep2

description: Library name: A128


title: scRNA_KO0058mouse_Thymus

description: Updated Microwell-seq_scRNA-seq

value: Thymus

value: Female


title: scRNA_KO0014mouse_Gallbladder-BileDuct

value: Gallbladder-BileDuct

value: 23.5 weeks


title: scRNA_KO0058mouse_Spleen

description: Updated Microwell-seq_scRNA-seq

value: Spleen


title: 5xFAD+, 9 month, female, rep1

description: Library name: A126

value: hippocampus

value: microglia

value: 9 month

value: female


title: BoneMarrow, 3_month-old_mouse01, rep1


title: NPM::ALK plasmacytoma 2_1

value: around the gut


title: BoneMarrow, 3_month-old_mouse03, rep3

value: BoneMarrow

value: anti-p53 antibody(abcam, ab246550)


title: scRNA_KO0058mouse_SmallIntestine

description: Updated Microwell-seq_scRNA-seq

value: SmallIntestine


title: BoneMarrow, 3_month-old_mouse02, rep2


title: scRNA_KO0058mouse_Stomach

description: Updated Microwell-seq_scRNA-seq

value: Stomach


title: NPM::ALK plasmacytoma 1_2


title: GallbladderBileDuct, 3_month-old_mouse01, rep1

value: GallbladderBileDuct


title: Bladder, 3_month-old_mouse04, rep4

value: Bladder

value: 3 months


title: WT, 9 month, female, rep3

description: Library name: A168


title: WT, 9 month, female, rep1

description: Library name: A159


title: NPM::ALK plasmacytoma 1_1


title: Lag3-/-; 5xFAD+, 6 month, female, rep3

description: Library name: Q562

value: 6 month


title: gcBC1

description: normal B cells, germinal center phenotype

source_name: Spleen


title: WT, 9 month, female, rep2

description: Library name: A160


title: gcBC3


title: Bladder, 3_month-old_mouse02, rep2

value: anti-p53 antibody(abcam, #ab246550)

value: Female


title: scRNA_KO0058mouse_MammaryGland

description: Updated Microwell-seq_scRNA-seq

value: MammaryGland

value: 15 weeks


title: scRNA_KO0058mouse_Pancreas

description: Updated Microwell-seq_scRNA-seq

value: Pancreas


title: gcBC2

value: Spleen


title: Bladder, 3_month-old_mouse03, rep3


title: scRNA_KO0058mouse_Ovary

description: Updated Microwell-seq_scRNA-seq

value: Ovary


title: Lag3-/-; 5xFAD+, 6 month, female, rep2

description: Library name: Q560

value: hippocampus

value: microglia

value: female


title: N8_2_CTRL_S25

city: Baltimore

first: Lena

last: Smirnova

address: 615 N. Wolfe St

department: Environmental Health & Engineering

institute: Johns Hopkins University

description:
Library name: S25
Column name in counts.csv: N8_2_CTRL_S25

data_processing:
Samples were processed with the nf-core/rnaseq pipeline v3.14.0 run with Nextflow 23.10.1
Raw sequence reads were trimmed for adaptors and low-quality bases using Trim Galore v0.6.7 with Cutadapt v5.0 (quality cutoff Q=20, auto-detecting adapters).
Trimmed reads were aligned to the GRCh38 reference genome using STAR v2.7.10a (default alignment settings, splice-aware).
Transcript-level quantification was performed using Salmon v1.10.1 in alignment-based mode (--libType auto, kmer size 31).
Gene-level counts were generated using featureCounts from Subread v2.0.1
Assembly: GRCh38
Supplementary files format and content: Comma-delimited text file includes the raw counts for each sample

source_name: neural organoid

growth_protocol: hiPSCs (passage 7-15) were maintained in mTESR plus medium on Vitronectin (ThermoFisher Scientific, Catalog# A14700) coated plates (ThermoFisher Scientific, Catalog #08-772-49), then plated at low density on Matrigel (Corning, Catalog# 354277) coated plates (ThermoFisher Scientific, Catalog #140675) and differentiated to NPCs using Gibco neural induction medium (ThermoFisher Scientific, Catalog #A1647801) for 7 days, following manufacturer’s instructions. NPCs were then cultured in Neural Expansion Medium, comprised of Neurobasal/ADVANCED DMEM/F12 media and induction supplement (ThermoFisher Scientific, Catalog # A1647801), and advanced DMEM/F-12 (ThermoFisher Scientific, Catalog #12634028), for at least five passages with stable and homogenous morphology prior to all experiments. Microglial differentiation was performed in three phases. First, hiPSCs (passage 13-17) were differentiated to hematopoietic progenitor cells (HPCs) utilizing the STEMdiffTM Hematopoietic Kit (STEMCELL TechnologiesTM, Catalog #05310), according to the manufacturer’s recommendations. Subsequently, HPCs were differentiated into premature microglia (PMs, STEMdiffTM Microglia Differentiation kit (STEMCELL TechnologiesTM, Catalog #100-0019), with terminal maturation, using the STEMdiffTM Microglia Maturation Kits (STEMCELL TechnologiesTM, Catalog #100-0020). This protocol uses a single medium to differentiate HPCs into immature microglia (PMs) over 24 days. PMs and NPCs were seeded in a 50:50 ratio with 1000 PMs and 1000 NPCs per well to form µbMPS96-6. NPCs only controls containing 2,000 NPCs/well were used for comparison (bMPS96-6). After 3 days in 96-well plates in Neural Expansion Medium, all 96 µbMPS96-6 or bMPS96-6 were transferred to a single well of a non-coated 6-well plate, medium was exchanged to bMPS Differentiation Medium (Neurobasal® Plus Medium (ThermoFisher Scientific, Catalog # A3653401) supplemented with 1x B-27 plus (ThermoFisher Scientific, Catalog # A3582801), 1% glutamax (ThermoFisher Scientific, Catalog #35050061), 0.02 μg/mL human recombinant GDNF (GeminiBio, Catalog# 300-121P-010), 0.02 μg/mL human recombinant BDNF (GeminiBio catalog #300-104P-1MG)) and 0.5 mg/mL pen/strep/glutamine (ThermoFisher Scientific, Catalog#10378016)  and cultures were maintained under gyratory shaking (88 rpm, 19 mm orbit) for 9 weeks.

extract_protocol:
bMPS were washed with ice-cold PBS twice, all supernatant removed, then snap frozen in liquid nitrogen. Samples were stored at -80°C before RNA extraction (Quick-RNA miniprep Kit, Zymo Research, Catalog # R1054). RNA quantity and purity were determined using a NanoDrop 2000c (ThermoFisher Scientific, Catalog # ND-2000C).
Samples were processed by the Johns Hopkins Genomics Core for library preparation and Illumina sequencing. mRNA libraries were constructed by the core facility according to the manufacturer’s recommended protocol with the NEBNext® RNA Library Prep Kit for Illumina Sequencing. Samples were then multiplexed and run on a NovaSeq 6000 instrument at Johns Hopkins Genomics Core Facility to generate 50 million, 150-base pair, paired-end reads per sample.

treatment_protocol: No treatment was done

value: neural organoid

tag: organoid model

value: Brain Microphysiological Systems

value: Control


title: Bladder, 3_month-old_mouse01, rep1


title: Lag3-/-; 5xFAD+, 6 month, female, rep1

description: Library name: Q557


title: scRNA_KO0058mouse_LymphNodes

description: Updated Microwell-seq_scRNA-seq

value: LymphNodes


title: N8_1_CTRL_S24

description:
Library name: S24
Column name in counts.csv: N8_1_CTRL_S24


title: R01006RF_STREP

city: Hospitalet de Llobregat

first: Jordi

last: Llorens

state: Catalunya

address: Feixa Llarga s/n

department: Ciències Fisiològiques

institute: Universitat de Barcelona

description: Library name: AN0802

data_processing:
RNAseq reads were mapped to the rat reference genome (Rnor6.0) with STAR/2.5.3a with ENCODE parameters
Genes were quantified with RSEM/1.3.0 with default parameters
The gene annotation file was ensembl92
Assembly: Rnor6.0
Supplementary files format and content: text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: Vestibular epithelium

extract_protocol:
Vestibular epithelia were quickly dissected in ice-cold PBS. Two utricles and six crista from each animal were pooled and stored at -80C. Total RNA was extracted using the Qiagen RNeasy mini kit and protocol.
RNA sequencing libraries were prepared following the SMARTseq2 protocol (Picelli et al., 2014) with some modifications. Briefly, reverse transcription of the total RNA input material of 1.8 µl (6-11 ng, in function of the sample availability) was performed using SuperScript II (Invitrogen) in the presence of oligo-dT30VN (1µM; 5′-AAG CAG TGG TAT CAA CGC AGA GTA CT30VN-3′), template-switching oligonucleotides (1 µM) and betaine (1M). The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (2x) (Roche) and 100 nM IS PCR primer (5′-AAG CAG TGG TAT CAA CGC AGA GT-3′) with 8 cycles of PCR amplification. Following purification with Agencourt Ampure XP beads (1:1 ratio; Beckmann Coulter), the product size distribution and the quantity were assessed with a Bioanalyzer High Sensitivity DNA Kit (Agilent). The amplified cDNA (200 ng) was fragmented for 10 min at 55 ºC using Nextera XT (Illumina) and amplified for 12 cycles with indexed Nextera PCR primers. The library was purified twice with Agencourt Ampure XP beads (0.8:1 ratio) and quantified on a Bioanalyzer using a High Sensitivity DNA Kit.

treatment_protocol: Subchronic ototoxicity rats were given 500 mg/kg of streptomycin (free base, as streptomycin sulphate, Sigma-Aldrich S6501) s.c. in PBS, once a day for 6 weeks starting at post-natal day 21; control rats received PBS.

value: Vestibular epithelium

value: Long-Evans

value: Subchronic ototoxicity


title: Lag3-/-, 6 month, female, rep3

description: Library name: Q630

value: 6 month


title: scRNA_KO0058mouse_Lung

description: Updated Microwell-seq_scRNA-seq

value: Lung

value: Female


title: Lag3-/-, 6 month, female, rep2

description: Library name: Q626


title: R01004RF_STREP

description: Library name: AN0800

value: male


title: PPDO, Treated, rep4

city: Oberschleissheim

first: Christos

last: Karampelias

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum Munich

description: Library name: Bulk RNA sequencing_PPDO_Treated_4

data_processing:
For the bulk RNA-Seq: The nf-core pipeline (v3.14) was used for read alignment to a modified Sus Scrofa genome and quantificatoin of transcripts using the salmon tool. Raw counts were aggregated as described in the manuscirpt. For the scRNA-seq: The CelRanger software v7.1.0 was used to process sequencing data that were aligned to the Sus Scrofa custom genome annotation or the GRCh38 human genome release. All scRNA-Seq procesing data downstream of CellRanger can be found in teh methods of the corresponding manuscript.
Assembly: Grch38 and the improved Sus Scrofa genome assaembly: sus_scrofa_Sscrofa11.1_custom_release101_egfp
Supplementary files format and content: Bulk_PPDO_RNASEQ_salmon_raw_gene_counts.tsv tab-delimited file containing the raw unaggregated counts of the bulk RNA-Seq experiment
Supplementary files format and content: *barcodes.tsv, *features.tsv and *matrix.mtx files are the output of the CellRanger pipeline for each of the scRNA-Seq samples
Supplementary files format and content: *.h5ad are anndata object files containing the processed scRNA-seq datasets following normalization and cluster annotation. Counts layer of the anndata object contains the raw counts for each file.

organism: Sus scrofa

source_name: Pancreas

extract_protocol:
For the bulk RNA-Seq experiments: PPDO were treated with control and differentiation media followed by 2 washes with PBS 1X. The Arcturus PicoPure RNA kit was used to extract RNA and quality assessed using a Bioanalyzer instrument (all samples had RIN>9). For the scRNA-Seq experiments: porcine pancreas was dispersed into single cell suspension using collagenase V and TrypLE digestion and single alive cells were sorted using a FACSAria III instrument. HPDO and PPDO cells were dissociated using TrypLE express into single cell suspnsions and 10000 alive cells were sorted using the FACSAria III instrument for library preparation.
For the bulk RNA-Seq: The Illumina mRNA prep ligation (poly-A selection) was used for library preparation according to manufacturer's guidelines. For the scRNA-seq: the Chromium Single Cell 3' reagent kit v3.1 was used for library construction according to manufacturer's instructions.

value: Pancreas

value: Primary pancreatic ductal organoids

value: PPDO treated with endocrine induction media


title: PPDO, Treated, rep3

description: Library name: Bulk RNA sequencing_PPDO_Treated_3


title: scRNA_KO0058mouse_Liver

description: Updated Microwell-seq_scRNA-seq

value: Liver

value: 15 weeks


title: R01009RF_Control

description: Library name: AN0799

value: female


title: scRNA_KO0058mouse_Kidney

description: Updated Microwell-seq_scRNA-seq

value: Kidney


title: scRNA_KO0058mouse_LargeIntestine

description: Updated Microwell-seq_scRNA-seq

value: LargeIntestine


title: PPDO, Treated, rep2

description: Library name: Bulk RNA sequencing _PPDO_Treated_2


title: R01007RF_Control

description: Library name: AN0798

value: Control


title: 5xFAD+, 6 month, female, rep2

description: Library name: A166

value: hippocampus

value: microglia


title: Lag3-/-, 6 month, female, rep1

description: Library name: Q621


title: scRNA_KO0058mouse_Heart

description: Updated Microwell-seq_scRNA-seq

value: Heart


title: R01003RF_Control

description: Library name: AN0797

value: Vestibular epithelium

value: Long-Evans


title: 5xFAD+, 6 month, female, rep1

description: Library name: A154

value: 6 month


title: PPDO, Control, rep4

description: Library name: Bulk RNA sequencing_PPDO_Control_4


title: N8_3_CTRL_S15

description:
Library name: S15
Column name in counts.csv: N8_3_CTRL_S15

value: neural organoid

value: Brain Microphysiological Systems


title: R01004LF_STREP

description: Library name: AN0801

value: male

value: Subchronic ototoxicity


title: Vestibular epithelium, R00966NM_IDPN4w

description: Library name: AN0796

treatment_protocol: Subchronic ototoxicity rats were given 20 mM of 3,3'-iminodipropionitrile (CAS# 111-94-4; >98%) in the drinking water for 4 weeks; control rats received plain drinking water.


title: WT, 6 month, female, rep3

description: Library name: A771


title: scRNA_KO0058mouse_Brain

description: Updated Microwell-seq_scRNA-seq

value: Brain

value: Female


title: PPDO, Control, rep3

description: Library name: Bulk RNA sequencing_PPDO_Control_3

value: Pancreas

value: Primary pancreatic ductal organoids

value: PPDO treated with endocrine induction media


title: scRNA_KO0058mouse_BoneMarrow

description: Updated Microwell-seq_scRNA-seq

value: BoneMarrow

value: 15 weeks


title: WT, 6 month, female, rep2

description: Library name: A769

value: hippocampus

value: female


title: PPDO, Control, rep2

description: Library name: Bulk RNA sequencing_PPDO_Control_2


title: Vestibular epithelium, R00966RF_IDPN4w

description: Library name: AN0794


title: PPDO, Control, rep1

description: Library name: Bulk RNA sequencing_PPDO_Control_1


title: Vestibular epithelium, R00966LF_IDPN4w

description: Library name: AN0795


title: Vestibular epithelium, R00968RF_Control

description: Library name: AN0793

value: Control


title: scRNA_KO0058mouse_Bladder

description: Updated Microwell-seq_scRNA-seq

value: Bladder


title: PPDO, Treated, rep1

description: Library name: Bulk RNA sequencing_PPDO_Treated_1


title: 5xFAD+, 6 month, female, rep3

description: Library name: A805

value: microglia


title: Lag3-/-; 5xFAD+, 3 month, female, rep3

description: Library name: Q185

value: 3 month


title: Vestibular epithelium, R00965NM_Control

description: Library name: AN0792

value: Vestibular epithelium

value: Long-Evans