title: tumor in boundary of the lesser curvature of cardia, bio rep2

description:
Library name: JM011
Column name in rawCount.csv: JM011


title: tumor in boundary of the greater curvature of cardia, bio rep2

status: Public on Jul 18 2025

type: SRA

city: Fuzhou

first: Shanqiang

last: Zhou

state: Fujian

address: 32 No. 29 Xinquan Road

department: Department of Gastric Surgery

country: China

institute: Fujian Medical University Union Hospital

description:
Library name: JM010
Column name in rawCount.csv: JM010

library_source: transcriptomic

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
We perform a pseudoalignment to a kallisto index created from transcriptomes (Ensembl v96,  Mouse:GRCm38.p6) using kallisto (0.44.0).
We test for differentially expressed genes under various conditions using Sleuth or DESeq2, R packages designed to test differential expression between two experimental groups from RNA-seq counts data.
Assembly: GRCm38.p6
Supplementary files format and content: csv file includes raw counts for each Sample
Supplementary files format and content: csv file includes FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: stomach

extract_protocol:
Total RNA was extracted from the tissue using RNeasy Mini Kit (QIAGEN).
Libraries are sequenced using Illumina NovaSeq 6000 at Columbia Genome Center. We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample.

treatment_protocol: Mice were administered tamoxifen via intraperitoneal injection at a dose of 50 mg/kg (20 mg/mL) for one day.

tag: strain

tag: tissue

value: stomach

tag: age

value: 7-8 weeks old

tag: genotype

value: Pou2f3-CreERT; Rb1fl/fl; Trp53fl/fl; LSL-MycT58A

tag: treatment

value: tamoxifen induction

tag: time

value: 5 weeks


title: normal tissue, bio rep2

description:
Library name: JM008
Column name in rawCount.csv: JM008


title: tumor in boundary of the lesser curvature of cardia, bio rep1

description:
Library name: JM005
Column name in rawCount.csv: JM005


title: HDAC3 knockout-aortic valves 1

city: Worcester

first: Chinmay

last: Trivedi

state: MA

address: 368 Plantation St, AS7-1047

department: Medicine

country: USA

institute: University of Massachusetts Medical School

description: Library name: KO1

data_processing:
Data were aligned to mm10 using STAR, quantified with RSEM, and analyzed for differential expression in DEBrowser.
Assembly: Mouse/mm10
Supplementary files format and content: genes_expression_expected_count.csv

source_name: Aortic valves

extract_protocol:
Aortic valve tissue was dissected from three knockout and three control mice and processed for RNA extraction (RNeasy Mini Kit, Qiagen).
Libraries were prepared and sequenced (NovaSeq 6000 PE150, Novogene).

value: Aortic valves

value: HDAC3 F/F, PostnCre

value: 12 weeks


title: Aortic valves, control 3

description: Library name: Control3

value: HDAC3 F/+


title: HDAC3 knockout-aortic valves 2

description: Library name: KO2


title: Eko male mice, 1707

city: Portland

first: Zheng

last: Xia

state: Oregon

address: 2720 S. Moody Avenue

institute: OREGON HEALTH & SCIENCE UNIVERSITY

description: Library name: EKO 2

data_processing:
Sequence reads were mapped to mm10 using STAR_2.6.1a
Assembly: GRCm38.89
Supplementary files format and content: .txt (raw counts)

molecule: polyA RNA

source_name: Quadriceps

growth_protocol: Mice were maintained on standard chow and in housing conditions with 12-hour light and 12-hour dark cycle.

extract_protocol:
Total RNA was extracted using the RNeasy Fibrous Tissue Mini Kit following the manufacturer's protocol.
The quality of RNA was assessed by 2100 bioanalyzer (Agilent), and RNA with RIN >7.5 was utilized for RNA sequencing using polyA selected RNAs. The cDNA libraries were created following the Illumina TruSeq Stranded mRNA library preparation protocol using 250 ng of total RNA for each sample. The generated libraries were quantified with a NanoDrop spectrophotometer, and their fragment sizes were evaluated using an Agilent Bioanalyzer. The libraries were then pooled and loaded onto a NovaSeq 6000 S4 flow cell, where they were sequenced to a depth of approximately 100 million read pairs per sample. A 150-cycle paired-end run was employed for sequencing on the NovaSeq 6000 system.

treatment_protocol: Muscles from ~20-week-old sedentary WT and Eko male mice were harvested within one hour to account for possible circadian gene expression changes.

value: Quadriceps

value: MEF2D-alpha-2 exon knockout


title: Wild-type (WT) male mice, 1703

description: Library name: WT 1

value: WT


title: tumor in antrum,bio rep3

description:
Library name: JM015
Column name in rawCount.csv: JM015


title: Aortic valves, control 2

description: Library name: Control2


title: Aortic valves, control 1

description: Library name: Control1


title: A3_control_2

city: Columbus

first: Jesse

middle: James

last: Reardon

state: Ohio

address: 420 W 12th Avenue

department: Radiation Oncology

institute: The Ohio State University

description: Library name: A3

data_processing:
Data processing was performed by Novogene.
Assembly: mm39
Supplementary files format and content: gene_fpkm.txt

source_name: Lens

growth_protocol: Mice between the ages of 10-12 days were euthanized, followed immediately by enucleation and lens dissection in room temperature PBS in an RNAse-free environment. PBS was wicked off the lenses using a Kimwipe and lenses were then immediately placed into a microcentrifuge tube and flash frozen on dry ice.

extract_protocol:
RNA extraction was performed by Novogene.
Library construction was performed by Novogene.

value: Lens


title: A1_experimental_1

description: Library name: A1


title: Eko male mice, 1704

description: Library name: EKO 1


title: HetKO 2

city: Frederick

first: Sharan

last: Malagobadan

address: 1050 Boyles Street, Building 560, Room 11-2

institute: National Institutes of Health

description: Library name: HetKO 2

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (mm10) and the annotated transcripts using STAR.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file with TPM for each sample

source_name: teratocarcinoma

extract_protocol:
Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596018).
Library for mRNA-seq was generated using Illumina® Stranded mRNA Prep (Illumina, 20040532) and sequenced on NovaSeq 6000 SP using paired-end sequencing by the NCI CCR Sequencing Facility.

value: teratocarcinoma

tag: cell line

tag: cell type

value: Embryonic carcinoma

value: Dicer (+/-)


title: HetKO 3

description: Library name: HetKO 3


title: Wild-type (WT) male mice, 1706

description: Library name: WT 2


title: A2C_control_1

description: Library name: A2C


title: HDAC3 knockout-aortic valves 3

description: Library name: KO3


title: HetKO 1

description: Library name: HetKO 1


title: normal tissue, bio rep1

description:
Library name: JM002
Column name in rawCount.csv: JM002


title: A4_experimental_2

description: Library name: A4


title: HetKO 5

description: Library name: HetKO 5


title: WD+CCl4 _Dbi+/+

city: PARIS

first: Guido

last: Kroemer

address: 15 rue de L'école de médecine

country: France

institute: Centre de Recherche des Cordeliers

description: Library name: 49342

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequence were aligned to mm10 genome to gene expression count using Loupe Browser 's default settings
Gene expression level of Refseq coding genes were quantified using Loupe Browser's default settings
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: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions.csv : position coordonate (pixel) of samples in fullres image, csv text file
Supplementary files format and content: aligned_tissue_image.jpg : image of tissue
Supplementary files format and content: cytassist_image.tiff : colored image of tissue
Library strategy: Spatial Transcriptomics

source_name: Liver

growth_protocol: Western diet supplemented with high-sugar water (23.1 g/L D-fructose and 18.9 g/L D-glucose) and received weekly i.p. injections of CCl₄

extract_protocol:
Tissue samples were initially screened for RNA quality, selecting only those with DV200 scores above 50% (RNA 6000 Nano Kit, Part No. 5067–1511, Agilent, Santa Clara, CA, USA), following the Visium Tissue Preparation Guide (10x Genomics, Pleasanton, CA, USA). Five-micrometer-thick sections were cut from FFPE blocks and mounted on Superfrost Plus slides (VWR, Radnor, PA, USA). Sections were deparaffinized, imaged, and permeabilized (User Guide, CG000520 Rev B) before probe hybridization. Successfully hybridized probe pairs were ligated, then released within the Visium CytAssist instrument for capture on the FFPE Visium Spatial Gene Expression Slide (10x Genomics, Product No. 1000520; User Guide, CG000495 Rev C).
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium, spatial gene expression slides & reagent kit accoring to manufacturer's construction

treatment_protocol: intraperitoneal (i.p.) injections of tamoxifen at a dose of 75 mg/kg/day for five consecutive days to induce gene deletion; vaccinated intraperitoneally with a mixture of KLH/Montanide or KLH-ACBP/Montanide on days 0 (30 μg), 7 (30 μg), 14 (30 μg), and 21 (10 μg) to induce the generation of anti-ACBP autoantibodies

value: Liver

value: Primary liver cells

value: Primary HCC cells, hepatocytes, other stromal cells

value: Dbi+/+

tag: batch


title: 1k_cells_taps

city: Oxford

first: Jingfei

last: Cheng

state: Oxfordshire

address: Roosevelt Drive

country: United Kingdom

institute: University of Oxford

description: Library name: 1k_cells_taps

library_source: genomic

data_processing:
Raw sequenced reads were demultiplexed using demuxbyname2.sh script from BBMap (version 38.50; https://www.osti.gov/biblio/1241166). Demultiplexed reads were processed with fastp package using default parameters to remove low-quality bases. The trimmed reads were aligned to the reference genome using bwa with default parameters. Reference sequences for mouse genome were downloaded from https://hgdownload.cse.ucsc.edu/goldenpath/mm9/bigZips/; reference sequence for human CD8+ T-cell were downloaded from: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRC h38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_an alysis_set.fna.gz. Uniquely mapped reads were filtered using samtools tools with MAPS>=10. PCR duplicates were called using Picard (2.23.0-Java-11) Mark Duplicates (https://broadinstitute.github.io/picard/). Methylation was called using a custom R script used in our previous project. 10bp at the start or end of reads were excluded for methylation calling. Snakemake pipeline file with detailed steps is provided in the code availability section.
Assembly: MM9 & GRCh38
Supplementary files format and content: bedgraph

molecule: genomic DNA

source_name: mESC

extract_protocol:
E14 mouse embryonic stem cells (mES cells) were cultured on gelatin-coated plates in DMEM supplemented with 15% FBS, 2 mM L-glutamine, 1% non-essential amino acids, 1% penicillin/streptavidin, 0.1 mM β-mercaptoethanol, 1,000 units/ml LIF (leukaemia inhibitory factor), 1 μM PD0325901, and 3 μM CHIR99021. The cells were maintained at 37°C and 5% CO2. Before cell sorting, the cells were harvested by centrifugation and passed through a 40 μm cell strainer (Falcon) to achieve single cell suspension.
Optimized TAPS and CAPS+ reactions: For scTAPS, 96 cells were pooled for DNA purification and subjected to mTET1 oxidation as previously described11. A reaction mixture of 50 μl was prepared, comprising 50 mM HEPES buffer (pH 8.0), 100 μM ammonium iron (II) sulfate, 1 mM α-ketoglutarate, 2 mM L-ascorbic acid, 2.5 mM DTT, 1.2 mM ATP, 100 mM NaCl, and 4 μM mTet1CD. The reaction was conducted at 37°C for 80 minutes. Subsequently, 2.0 U of Proteinase K (New England Biolabs) was introduced to the reaction mixture and incubated at 50°C for 1 hour to stop the oxidation process. The oxidized DNA was purified using 1.8x AMPure XP beads, following the provided guidelines. To ensure complete oxidation, a second round of oxidation was performed. The double-oxidized DNA was purified and then underwent borane reduction under optimized conditions and purification using a Zymo column with Oligo Binding Buffer. For scCAPS+, 96 cells were pooled for DNA purification and subjected to a series of chemical reactions to convert 5hmC into 5fC and then to 5caC as previously described with some modifications12. DNA were incubated with 4-acetamido-2,2,6,6- tetramethylpiperidine-1-oxoammonium tetra-fluoroborate (ACT+ BF4-) in a 25 μl solution comprising sodium phosphate buffer at 25°C for 16 hours. The resultant oxidized DNA was purified using 1.8× AMPure XP Beads. then Pinnick oxidation is conducted in a 30 μl reaction mixture containing sodium acetate buffer, NaClO2, and 2- methyl-2-butene at 25°C for 16 hours. The purified product then underwent borane reduction under optimized conditions and purification using a Zymo column with Oligo Binding Buffer.  scTAPS and scCAP+ library construction and sequencing: Individual cells were isolated into a 96-well plate through FACS, each well containing 4 μL of lysis buffer consisting of 16.67mM TAPS-NaOH buffer (pH 8.5, Alfa Aesar, Cat: J63268), 8.33mM MgCl2(Invitrogen), 0.67x NEB buffer 4 (NEB, B7004S), 0.13%  Triton X-100 (sigma, X100-500ML), and 1 μg Qiagen protease. Following centrifugation at 2,000 rpm for 5 minutes, the plates were either preserved at -80°C or progressed to subsequent procedures. Single cell was lysate by incubating at 50°C for 3 h, followed by incubation at 75°C for 30 min, 80°C for 15 min, and a 4°C hold. Tagmentation was performed at 50°C for 15 minutes in a reaction mix consisting of 1x TAPS buffer (10mM TAPS-NaOH, 5mM MgCl2), 6% PEG (polyethylene glycol) 3,350, 1ul 1x preassembled Tn5, and H2O to a total volume of 10 μ. Tn5 was stripped off by adding 1.11 μL of 1.0% SDS (Sodium Dodecyl Sulfate), followed by incubating at room temperature for 5 minutes. Neutralization was performed by adding 1.24 μL of 5.0% NP40 or Triton X-100, followed by incubating at room temperature for 5 minutes. Subsequently, 12.35 μL of 2x Phusion High-Fidelity PCR Master Mix with HF Buffer (Thermo Scientific, F531L) was added, followed by incubating at 72°C for 5 minutes, and a 4°C hold. The 96 reactions were combined into a 50-mL BD tube and supplemented with 2-kb filler DNA (200 ng) and 0.1% spike in DNAs. Following purification, the TAPS or CAPS+ reaction, was employed as mentioned, and the final sequencing library was amplified utilizing the KAPA HiFi HotStart Uracil+ ReadyMix PCR Kit along with index primers from the Nextera XT Index Kit (Illumina, FC-131- 1001). The amplification protocol involved an initial step at 98°C for 45 seconds, followed by 13 cycles (98°C for 10 seconds, 60°C for 15 seconds, and 72°C for 1 minute), then incubation at 72°C for 3 minutes, 4°C hold. The library was subjected to purification and size selected to 500-700bp by 0.5x-0.25x Ampure XP beads. Custom  sequencing primers are used for custom Nova Sequencing (Read 1 Sequencing Primer: GCGATCGAGGACGGCAGATGTGTATAAGAGACAG; Read 2 Sequencing Primer: CACCGTCTCCGCCTCAGATGTGTATAAGAGACAG; Index 1 Sequencing Primer: CTGTCTCTTATACACATCTGAGGCGGAGACGGTG; Index 2 sequencing primer: CTGTCTCTTATACACATCTGCCGTCCTCGATCGC).

value: mESC

tag: experiment type

value: scTAPS


title: HetKO 6

description: Library name: HetKO 6


title: HetKO 4

description: Library name: HetKO 4


title: WD+CCl4_Dbi-/-

description: Library name: 49355

value: hepatocytes, other stromal cells

value: Dbi-/-


title: 10k_cells_caps

description: Library name: 10k_cells_caps

value: scCAPS+


title: 10_cells_caps

description: Library name: 10_cells_caps


title: 100_cells_taps

description: Library name: 100_cells_taps


title: 100_cells_caps

description: Library name: 100_cells_caps


title: WD+CCl4-KLH-DBI

description: Library name: 49330

value: KLH-ACBP


title: WD+CCl4-KLH

description: Library name: 49303

value: KLH


title: HM 1 (RNA-seq)

value: Dicer (HM/-)


title: WT 4 (RNA-seq)

value: Dicer (+/+)


title: WT 3 (RNA-seq)


title: 10k_cells_taps

description: Library name: 10k_cells_taps


title: WT 2 (RNA-seq)


title: 1k_cells_caps

description: Library name: 1k_cells_caps


title: WT 5 (RNA-seq)


title: HM 4 (RNA-seq)


title: HM 5 (RNA-seq)


title: 10_cells_taps

description: Library name: 10_cells_taps


title: Calorie restriction missed meal (ZT18 circadian time) replicate 3

city: Cleveland

first: Roman

last: Kondratov

state: OHIO

address: 2121 euclid ave, bh 411

department: Biological, Geological, and Environmental Sciences (BGES)

institute: Cleveland State University

data_processing:
RNA-seq
Assembly: GRCm38
Supplementary files format and content: text files with matrix of normalized TPMs for every gene and every sample
Supplementary files format and content: text file of the matrix table with expected gene counts for every gene and every sample

extract_protocol:
RNA was isolated from 30 mg of female mouse liver tissue using mini spin column QIAGEN RNeasy Mini Kit.
Non-directional – polyA enrichment library was prepared using NEBNext Ultra™ II RNA Library Prep Kit for Illumina (New England BioLabs), and 50M reads (150bp, paired end) per sample were generated on Illumina NovaSeq 6000 platform.
RNA-seq reads were mapped to the mouse protein coding genes (Ensembl: Mus_musculus; GRCm38) using Bowtie allowing up to 2-mismatches. The gene expected read counts and Transcripts Per Million (TPM) were estimated by RSEM (v1.2.3). The TPMs were further normalized by EBSeq R package to correct potential batch effect.

tag: background

value: 44 months

tag: Sex

value: Female

value: Wild-type


title: HM 3 (RNA-seq)

value: teratocarcinoma

value: Embryonic carcinoma


title: Calorie restriction fed (ZT18 circadian time) replicate 1

value: 39 months

value: Liver


title: HM 6 (RNA-seq)


title: WT 6 (RNA-seq)


title: WT 1 (RNA-seq)


title: Calorie restriction missed meal (ZT18 circadian time) replicate 2

value: 43 months


title: Calorie restriction missed meal (ZT18 circadian time) replicate 1

value: 42 months


title: Calorie restriction fed (ZT18 circadian time) replicate 3

value: 41 months


title: HM 2 (RNA-seq)


title: 22h Fasted replicate 1

value: 36 months


title: Calorie restriction fed (ZT18 circadian time) replicate 2

value: 40 months


title: 22h Calorie restriction replicate 1

value: 32 months


title: 22h Fasted replicate 2

value: 37 months


title: 22h Calorie restriction replicate 4

value: 35 months


title: 22h Calorie restriction replicate 3

value: 34 months


title: 22h Ad libitum replicate 2

value: 30 months


title: 22h Ad libitum replicate 1

value: 29 months


title: 14h Fasted replicate 3

value: 28 months

value: Female


title: 14h Fasted replicate 1

value: 26 months

value: Wild-type


title: 22h Fasted replicate 3

value: 38 months


title: 14h Calorie restriction replicate 3

value: 25 months

value: Liver


title: 14h Ad libitum replicate 2

value: 21 months


title: 14h Calorie restriction replicate 2

value: 24 months


title: 14h Ad libitum replicate 3

value: 22 months


title: 14h Ad libitum replicate 1

value: 20 months


title: 14h Calorie restriction replicate 1

value: 23 months


title: 6h Fasted replicate 3

value: 19 months


title: 6h Fasted replicate 2

value: 18 months


title: 6h Calorie restriction replicate 1

value: 14 months


title: 6h Ad libitum replicate 1

value: 11 months


title: 0h Calorie restriction replicate 2

value: 9 months


title: 6h Calorie restriction replicate 2

value: 15 months


title: 22h Calorie restriction replicate 2

value: 33 months

value: Female


title: 6h Calorie restriction replicate 3

value: 16 months

value: Wild-type


title: 14h Fasted replicate 2

value: 27 months


title: 0h Ad libitum replicate 2

value: 6 months

value: Liver


title: 0h Calorie restriction replicate 1

value: 8 months


title: 22h Ad libitum replicate 3

value: 31 months


title: 0h Ad libitum replicate 3

value: 7 months


title: 0h Ad libitum replicate 1

value: 5 months


title: mouse_neuron_N_pos_3m;N704_i7_9_N502_i5_7

data_processing:
Raw sequenced reads were demultiplexed using demuxbyname2.sh script from BBMap (version 38.50; https://www.osti.gov/biblio/1241166). Demultiplexed reads were processed with fastp package using default parameters to remove low-quality bases. The trimmed reads were aligned to the reference genome using bwa with default parameters. Reference sequences for mouse genome were downloaded from https://hgdownload.cse.ucsc.edu/goldenpath/mm9/bigZips/; reference sequence for human CD8+ T-cell were downloaded from: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRC h38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_an alysis_set.fna.gz. Uniquely mapped reads were filtered using samtools tools with MAPS>=10. PCR duplicates were called using Picard (2.23.0-Java-11) Mark Duplicates (https://broadinstitute.github.io/picard/). Methylation was called using a custom R script used in our previous project. 10bp at the start or end of reads were excluded for methylation calling. Snakemake pipeline file with detailed steps is provided in the code availability section.
Assembly: MM9 & GRCh38
Supplementary files format and content: bedgraph
Library strategy: scCAPS+

source_name: NeuN+

value: NeuN+

value: scCAPS+


title: mouse_neuron_N_pos_3m;N704_i7_9_N502_i5_5


title: mouse_neuron_N_pos_3m;N704_i7_9_N502_i5_8


title: mouse_neuron_N_pos_3m;N704_i7_9_N502_i5_3


title: mouse_neuron_N_pos_3m;N704_i7_9_N502_i5_4


title: mouse_neuron_N_pos_3m;N704_i7_9_N502_i5_6


title: mouse_neuron_N_pos_3m;N704_i7_9_N502_i5_2


title: mouse_neuron_N_pos_3m;N704_i7_9_N502_i5_1


title: mouse_neuron_N_pos_3m;N704_i7_8_N502_i5_7


title: mouse_neuron_N_pos_3m;N704_i7_8_N502_i5_5


title: tumor in boundary of the greater curvature of cardia, bio rep1

description:
Library name: JM004
Column name in rawCount.csv: JM004

value: stomach

value: 7-8 weeks old

value: Pou2f3-CreERT; Rb1fl/fl; Trp53fl/fl; LSL-MycT58A

value: tamoxifen induction

value: 5 weeks


title: 6h Ad libitum replicate 2

value: 12 months

value: Female


title: 6h Fasted replicate 1

value: 17 months

value: Wild-type


title: mouse_neuron_N_pos_3m;N704_i7_8_N502_i5_2


title: mouse_neuron_N_pos_3m;N704_i7_8_N502_i5_4


title: mouse_neuron_N_pos_3m;N704_i7_8_N502_i5_3


title: mouse_neuron_N_pos_3m;N704_i7_7_N502_i5_7


title: mouse_neuron_N_pos_3m;N704_i7_7_N502_i5_8


title: mouse_neuron_N_pos_3m;N704_i7_8_N502_i5_1


title: BACH1-ko1(ChIP-seq)

status: Public on Jul 19 2025

city: Shanghai

first: Jieyu

last: Guo

state: Shanghai

address: 138 Yixueyuan Rd,

institute: fudan university

description: Library name: Sample 3

data_processing:
Basecalls were performed using bcl2fastg v2.17 for Novaseg output
ChlP-seg reads were trimmed from 3' end until the final base had a quality score > 30 using Trimmomatic v0.39
ChlP-seg reads were aligned to the UCSC mm10 genome using Bowtie2 version 2.4.5.
ChlP-seg coverage was created by deepTools and reformatted in the bigWig file format.
Peaks were called uing MACS v2.2.5
Assembly: mm10
Supplementary files format and content: bigWig

source_name: E14Tg2A line

growth_protocol: WT and BACH1-KO mESC maintained in a culture medium for 2 days. The culture mediumconsisting of 90% Dulbecco's modified Eagle's medium (DMEM), 10% fetal bovine serum (FBS) , 1% non-essential amino acids (NEAA), 0.1 mM β-mercaptoethanol , and 200 Units/ml murine leukemia inhibitory factor (mLIF) . Bach1-KO mESCs were generated by using CRISPR/Cas9 genome editing technology. sgRNAs targeting the genomic regions of interest were designed with the CRISPR Design Tool . Annealed sgRNA oligos were cloned into LentiCRISPR V2, transiently transfected into mESCs with Lipofectamine 2000 , and then selected with puromycin ; single-cell clones were sorted 7 days later.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis.chromatin was sonicated using a Q800R2  DNA shearing sonicator (thermocube).
ChlP-seg libraries were prepared using the DNA Library Preparation Kit (nd607-01) complemented with VAHTSTM DNA adapters set2 for Illumina (N802-00) from Vazyme. 25 ng of DNA wasused as starting material for input and ip samples. Libraries were amplified using 13cycles on the thermocycler. Post amplification libraries were size selected at 250-450bpin length using VAHTS DNA clean beads from Beckman Coulter. Libraries were sequenced on Illumina Hiseq X Ten by Basepair Company (Suzhou, China).

value: E14Tg2A line

value: mouse embryonic stem cells

tag: chip-antibody

value: BACH1 (#sc-271211, Santa Cruz Biotechnology, Santa Cruz, CA, USA)


title: mouse_neuron_N_pos_3m;N704_i7_7_N502_i5_6


title: mouse_neuron_N_pos_3m;N704_i7_7_N502_i5_5


title: mouse_neuron_N_pos_3m;N704_i7_7_N502_i5_2


title: mouse_neuron_N_pos_3m;N704_i7_7_N502_i5_3


title: mouse_neuron_N_pos_3m;N704_i7_7_N502_i5_4


title: mouse_neuron_N_pos_3m;N704_i7_7_N502_i5_1


title: mouse_neuron_N_pos_3m;N704_i7_6_N502_i5_8


title: mouse_neuron_N_pos_3m;N704_i7_6_N502_i5_6


title: mouse_neuron_N_pos_3m;N704_i7_8_N502_i5_8


title: mouse_neuron_N_pos_3m;N704_i7_6_N502_i5_4


title: mouse_neuron_N_pos_3m;N704_i7_6_N502_i5_5


title: mouse_neuron_N_pos_3m;N704_i7_8_N502_i5_6


title: mouse_neuron_N_pos_3m;N704_i7_6_N502_i5_3


title: mouse_neuron_N_pos_3m;N704_i7_6_N502_i5_7


title: mouse_neuron_N_pos_3m;N704_i7_6_N502_i5_2


title: mouse_neuron_N_pos_3m;N704_i7_6_N502_i5_1


title: mouse_neuron_N_pos_3m;N704_i7_5_N502_i5_7


title: mouse_neuron_N_pos_3m;N704_i7_5_N502_i5_8


title: mouse_neuron_N_pos_3m;N704_i7_5_N502_i5_4


title: mouse_neuron_N_pos_3m;N704_i7_5_N502_i5_5


title: mouse_neuron_N_pos_3m;N704_i7_5_N502_i5_2


title: mouse_neuron_N_pos_3m;N704_i7_5_N502_i5_1


title: mouse_neuron_N_pos_3m;N704_i7_5_N502_i5_3


title: mouse_neuron_N_pos_3m;N704_i7_4_N502_i5_8


title: mouse_neuron_N_pos_3m;N704_i7_4_N502_i5_7


title: mouse_neuron_N_pos_3m;N704_i7_4_N502_i5_3


title: mouse_neuron_N_pos_3m;N704_i7_4_N502_i5_6


title: mouse_neuron_N_pos_3m;N704_i7_4_N502_i5_2


title: mouse_neuron_N_pos_3m;N704_i7_4_N502_i5_1


title: mouse_neuron_N_pos_3m;N704_i7_4_N502_i5_4


title: mouse_neuron_N_pos_3m;N704_i7_3_N502_i5_8


title: mouse_neuron_N_pos_3m;N704_i7_3_N502_i5_6


title: mouse_neuron_N_pos_3m;N704_i7_3_N502_i5_5


title: mouse_neuron_N_pos_3m;N704_i7_3_N502_i5_3


title: mouse_neuron_N_pos_3m;N704_i7_3_N502_i5_1


title: mouse_neuron_N_pos_3m;N704_i7_2_N502_i5_8


title: mouse_neuron_N_pos_3m;N704_i7_2_N502_i5_6


title: mouse_neuron_N_pos_3m;N704_i7_5_N502_i5_6


title: mouse_neuron_N_pos_3m;N704_i7_3_N502_i5_4


title: mouse_neuron_N_pos_3m;N704_i7_3_N502_i5_2


title: mouse_neuron_N_pos_3m;N704_i7_2_N502_i5_7


title: mouse_neuron_N_pos_3m;N704_i7_2_N502_i5_5


title: mouse_neuron_N_pos_3m;N704_i7_2_N502_i5_1


title: mouse_neuron_N_pos_3m;N704_i7_2_N502_i5_2


title: mouse_neuron_N_pos_3m;N704_i7_2_N502_i5_3


title: mouse_neuron_N_pos_3m;N704_i7_1_N502_i5_6


title: mouse_neuron_N_pos_3m;N704_i7_4_N502_i5_5


title: mouse_neuron_N_pos_3m;N704_i7_1_N502_i5_4


title: mouse_neuron_N_pos_3m;N704_i7_1_N502_i5_5


title: mouse_neuron_N_pos_3m;N704_i7_1_N502_i5_2


title: mouse_neuron_N_pos_3m;N704_i7_1_N502_i5_8


title: mouse_neuron_N_pos_3m;N704_i7_1_N502_i5_3


title: mouse_neuron_N_pos_3m;N704_i7_12_N502_i5_8


title: mouse_neuron_N_pos_3m;N704_i7_12_N502_i5_7


title: mouse_neuron_N_pos_3m;N704_i7_12_N502_i5_6


title: mouse_neuron_N_pos_3m;N704_i7_12_N502_i5_5


title: mouse_neuron_N_pos_3m;N704_i7_3_N502_i5_7


title: mouse_neuron_N_pos_3m;N704_i7_1_N502_i5_1


title: mouse_neuron_N_pos_3m;N704_i7_12_N502_i5_4


title: mouse_neuron_N_pos_3m;N704_i7_12_N502_i5_3


title: mouse_neuron_N_pos_3m;N704_i7_12_N502_i5_2


title: mouse_neuron_N_pos_3m;N704_i7_12_N502_i5_1


title: mouse_neuron_N_pos_3m;N704_i7_11_N502_i5_8


title: mouse_neuron_N_pos_3m;N704_i7_11_N502_i5_7


title: mouse_neuron_N_pos_3m;N704_i7_2_N502_i5_4


title: mouse_neuron_N_pos_3m;N704_i7_11_N502_i5_5


title: mouse_neuron_N_pos_3m;N704_i7_11_N502_i5_6


title: mouse_neuron_N_pos_3m;N704_i7_1_N502_i5_7


title: mouse_neuron_N_pos_3m;N704_i7_11_N502_i5_4


title: mouse_neuron_N_pos_3m;N704_i7_10_N502_i5_6


title: mouse_neuron_N_pos_3m;N704_i7_10_N502_i5_5


title: mouse_neuron_N_pos_3m;N704_i7_10_N502_i5_4


title: mouse_neuron_N_pos_3m;N704_i7_11_N502_i5_3


title: mouse_neuron_N_pos_3m;N704_i7_11_N502_i5_2


title: mouse_neuron_N_pos_3m;N704_i7_10_N502_i5_7


title: mouse_neuron_N_pos_3m;N704_i7_10_N502_i5_2


title: mouse_neuron_N_pos_3m;N704_i7_10_N502_i5_3


title: mouse_neuron_N_pos_18m;N706_i7_9_N517_i5_8


title: mouse_neuron_N_pos_3m;N704_i7_10_N502_i5_1


title: mouse_neuron_N_pos_18m;N706_i7_9_N517_i5_6


title: mouse_neuron_N_pos_18m;N706_i7_9_N517_i5_7


title: mouse_neuron_N_pos_18m;N706_i7_9_N517_i5_4


title: mouse_neuron_N_pos_18m;N706_i7_9_N517_i5_5


title: mouse_neuron_N_pos_18m;N706_i7_9_N517_i5_2


title: mouse_neuron_N_pos_18m;N706_i7_9_N517_i5_3


title: mouse_neuron_N_pos_18m;N706_i7_8_N517_i5_8


title: mouse_neuron_N_pos_18m;N706_i7_9_N517_i5_1


title: mouse_neuron_N_pos_18m;N706_i7_8_N517_i5_6


title: mouse_neuron_N_pos_18m;N706_i7_8_N517_i5_7


title: mouse_neuron_N_pos_3m;N704_i7_11_N502_i5_1


title: mouse_neuron_N_pos_3m;N704_i7_10_N502_i5_8


title: mouse_neuron_N_pos_18m;N706_i7_8_N517_i5_2


title: mouse_neuron_N_pos_18m;N706_i7_8_N517_i5_1


title: mouse_neuron_N_pos_18m;N706_i7_8_N517_i5_4


title: mouse_neuron_N_pos_18m;N706_i7_7_N517_i5_8


title: mouse_neuron_N_pos_18m;N706_i7_8_N517_i5_3


title: mouse_neuron_N_pos_18m;N706_i7_7_N517_i5_7


title: mouse_neuron_N_pos_18m;N706_i7_7_N517_i5_5


title: mouse_neuron_N_pos_18m;N706_i7_7_N517_i5_6


title: mouse_neuron_N_pos_18m;N706_i7_7_N517_i5_1


title: mouse_neuron_N_pos_18m;N706_i7_7_N517_i5_4


title: mouse_neuron_N_pos_18m;N706_i7_6_N517_i5_8


title: mouse_neuron_N_pos_18m;N706_i7_7_N517_i5_3


title: mouse_neuron_N_pos_18m;N706_i7_7_N517_i5_2


title: mouse_neuron_N_pos_18m;N706_i7_6_N517_i5_5


title: mouse_neuron_N_pos_18m;N706_i7_6_N517_i5_6


title: mouse_neuron_N_pos_18m;N706_i7_6_N517_i5_4


title: mouse_neuron_N_pos_18m;N706_i7_6_N517_i5_2


title: mouse_neuron_N_pos_18m;N706_i7_6_N517_i5_7


title: mouse_neuron_N_pos_18m;N706_i7_6_N517_i5_1


title: mouse_neuron_N_pos_18m;N706_i7_5_N517_i5_8


title: mouse_neuron_N_pos_18m;N706_i7_5_N517_i5_7


title: mouse_neuron_N_pos_18m;N706_i7_6_N517_i5_3


title: mouse_neuron_N_pos_18m;N706_i7_5_N517_i5_6


title: mouse_neuron_N_pos_18m;N706_i7_5_N517_i5_5


title: mouse_neuron_N_pos_18m;N706_i7_8_N517_i5_5


title: mouse_neuron_N_pos_18m;N706_i7_5_N517_i5_2


title: mouse_neuron_N_pos_18m;N706_i7_5_N517_i5_3


title: mouse_neuron_N_pos_18m;N706_i7_5_N517_i5_1


title: mouse_neuron_N_pos_18m;N706_i7_4_N517_i5_8


title: mouse_neuron_N_pos_18m;N706_i7_4_N517_i5_7


title: mouse_neuron_N_pos_18m;N706_i7_4_N517_i5_6


title: mouse_neuron_N_pos_18m;N706_i7_4_N517_i5_2


title: mouse_neuron_N_pos_18m;N706_i7_4_N517_i5_5


title: mouse_neuron_N_pos_18m;N706_i7_4_N517_i5_4


title: mouse_neuron_N_pos_18m;N706_i7_4_N517_i5_3


title: mouse_neuron_N_pos_18m;N706_i7_4_N517_i5_1


title: mouse_neuron_N_pos_18m;N706_i7_3_N517_i5_7


title: mouse_neuron_N_pos_18m;N706_i7_3_N517_i5_6


title: mouse_neuron_N_pos_18m;N706_i7_3_N517_i5_8


title: mouse_neuron_N_pos_18m;N706_i7_3_N517_i5_4


title: mouse_neuron_N_pos_18m;N706_i7_3_N517_i5_2


title: mouse_neuron_N_pos_18m;N706_i7_3_N517_i5_3


title: abdominal aorta, ITA-NP 3

first: Andrei

last: Maiseyeu

state: OH

address: 2103 Cornell Rd

institute: Case Western Reserve University

description: Library name: Sample7

data_processing:
Nextflow nf-core framework for community-curated bioinformatics pipelines, PMID: 32055031
Assembly: mm10
Supplementary files format and content: Aorta_ITAvsCTRL-logCPM.csv csv file includes FPKM counts for all samples

source_name: abdominal aorta

growth_protocol: Apoe−/− mice fed high-fat diet for 12 weeks

extract_protocol:
RNA was extracted from whole abdominal aortas using TRIzol reagent (Thermo Fisher 15596026) followed by processing and purification with Direct-zol RNA Miniprep (Zymo Research R2051) according to the manufacturer’s instructions. 500 ng of total RNA was used for library prep.
QuantSeq 3’ mRNA-Seq V2 Library Prep Kit

treatment_protocol: 50 mg/kg ITA-LNP or Ctrl-LNP injected i.v. once weekly

value: abdominal aorta

value: aorta


title: abdominal aorta, ITA-NP 1

description: Library name: Sample5


title: mouse_neuron_N_pos_18m;N706_i7_2_N517_i5_8


title: abdominal aorta, control-NP 4

description: Library name: Sample4


title: abdominal aorta, ITA-NP 2

description: Library name: Sample6


title: mouse_neuron_N_pos_18m;N706_i7_5_N517_i5_4


title: mouse_neuron_N_pos_18m;N706_i7_2_N517_i5_6


title: mouse_neuron_N_pos_18m;N706_i7_2_N517_i5_7


title: mouse_neuron_N_pos_18m;N706_i7_2_N517_i5_5


title: abdominal aorta, control-NP 2

description: Library name: Sample2


title: abdominal aorta, control-NP 3

description: Library name: Sample3


title: abdominal aorta, control-NP 1

description: Library name: Sample1


title: mouse_neuron_N_pos_18m;N706_i7_2_N517_i5_4


title: mouse_neuron_N_pos_18m;N706_i7_2_N517_i5_3


title: Neutrophils, ITA-LNP replicate 2

address: 10900 Euclid Ave

description: Library name: ITA_3h_lps_R2

data_processing:
Nextflow nf-core framework for community-curated bioinformatics pipelines, PMID: 32055031
Assembly: mm10
Supplementary files format and content: all_counts.csv csv file includes FPKM counts for all samples

source_name: primary neutrophils

growth_protocol: RPMI without any additives, normal culture conditions at 5M cells/mL

extract_protocol:
RNA was extracted from cultured cells using TRIzol reagent (Thermo Fisher 15596026) followed by processing and purification with Direct-zol RNA Miniprep (Zymo Research R2051) according to the manufacturer’s instructions. 500 ng of total RNA was used for library prep.
QuantSeq 3’ mRNA-Seq V2 Library Prep Kit

treatment_protocol: stimulated with LPS at 100 ng/mL for 3 h

value: bone marrow

value: neutrophils


title: mouse_neuron_N_pos_18m;N706_i7_2_N517_i5_2

value: NeuN+

value: scCAPS+


title: Neutrophils, Ctrl-LNP replicate 3

description: Library name: C_3h_lps_R3


title: Neutrophils, ITA-LNP replicate 1

description: Library name: ITA_3h_lps_R1


title: Neutrophils, Ctrl-LNP replicate 2

description: Library name: C_3h_lps_R2


title: mouse_neuron_N_pos_18m;N706_i7_2_N517_i5_1


title: mouse_neuron_N_pos_18m;N706_i7_1_N517_i5_8


title: mouse_neuron_N_pos_18m;N706_i7_3_N517_i5_5


title: Neutrophils, Ctrl-LNP replicate 1

description: Library name: C_3h_lps_R1


title: mouse_neuron_N_pos_18m;N706_i7_1_N517_i5_6


title: mouse_neuron_N_pos_18m;N706_i7_3_N517_i5_1


title: mouse_neuron_N_pos_18m;N706_i7_1_N517_i5_5


title: mouse_neuron_N_pos_18m;N706_i7_1_N517_i5_4


title: mouse_neuron_N_pos_18m;N706_i7_1_N517_i5_3


title: mouse_neuron_N_pos_18m;N706_i7_1_N517_i5_2


title: mouse_neuron_N_pos_18m;N706_i7_12_N517_i5_8


title: mouse_neuron_N_pos_18m;N706_i7_1_N517_i5_1


title: cas2

city: changzhou

first: jun

last: huang

state: 江苏

description:
Library name: SAMPLES 2
BD Rhapsody

library_source: transcriptomic single cell

data_processing:
expression matrices were generated using the BD Rhapsody™ sequencing pipelines, converted into Seurat objects, and analyzed. Key steps, including data normalization, identification of highly variable genes, PCA, and clustering analysis, were performed using the Seurat package, with dimensionality reduction via UMAP.
Assembly: hg38
Supplementary files format and content: count matrix

organism: Homo sapiens

source_name: Labial gland

extract_protocol:
Using the BD Rhapsody™ Cartridge Reagent Kit (BD, 633731) and BD Rhapsody™ Cartridge Kit (BD, 633733), we processed a cell suspension containing 300-600 viable cells per microliter, as quantified by Count Star. The cells were loaded onto the BD Rhapsody™ Cartridge to facilitate the generation of single-cell magnetic beads within the microwells, adhering to the manufacturer's guidelines. In brief, we suspended single cells in the provided sample buffer and introduced approximately 6,000 cells into each channel, aiming to recover an estimated 3,000 cells. The captured cells underwent lysis, releasing RNA that was subsequently barcoded during reverse transcription within individual microwells. We conducted reverse transcription using a ThermoMixer® C (Eppendorf) set at 1,200 rpm and 37°C for 45 minutes. This process yielded cDNA, which was amplified and quality-checked using an Agilent 4200, a service provided by CapitalBio Technology, Beijing.
For library preparation, we adhered to the manufacturer's guidelines to construct single-cell RNA-seq libraries using the BD Rhapsody™ WTA Amplification Kit (BD, 633801). CapitalBio Technology, Beijing, sequenced the libraries on an Illumina NovaSeq 6000 platform, achieving a sequencing depth of at least 50,000 reads per cell with a paired-end 150 bp (PE150) strategy.

value: Labial gland

value: cell from human labial gland

value: human labial gland

tag: diagnosis

value: Sjogren's syndrome


title: con2

description:
Library name: SAMPLES 5
BD Rhapsody

value: healthy


title: con3

description:
Library name: SAMPLES 6
BD Rhapsody


title: con1

description:
Library name: SAMPLES 4
BD Rhapsody


title: mouse_neuron_N_pos_18m;N706_i7_12_N517_i5_7


title: mouse_neuron_N_pos_18m;N706_i7_12_N517_i5_6


title: mouse_neuron_N_pos_18m;N706_i7_12_N517_i5_5


title: KOLF2.1J C156R hom3 ApoE4/4 -FBS R1

city: Irvine

first: Ricardo

last: Miramontes

address: 845 Health Sciences Rd

institute: UC Irvine

description:
Library name: KOLF2.1J_C156R_hom3_ApoE4/4_-FBS_R1
Column name in counts.csv: KOLF2.1J_C156R_hom3_ApoE4/4_-FBS_R1

data_processing:
Sequenced reads were trimmed for adaptor sequence or low-quality sequence using Trimmomatic.
Reads were aligned using HISAT2 using an index created from Ensembl GRCh38 release 104.
Gene counts were quantified using featureCounts using the gtf annotation from the same reference as the alignment.
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file including raw count data for all samples.

source_name: KOLF2.1J C156R hom3

extract_protocol:
RNA was extracted using RNeasy Mini Kit (QIAGEN) and 1ug of RNA was used for library preparation.
Library construction was performed using TruSeq RNA stranded kit with rRNA reduction (RiboZero)

value: KOLF2.1J C156R hom3

value: iAstrocytes


title: KOLF2.1J C156R hom3 ApoE4/4 -FBS R3

description:
Library name: KOLF2.1J_C156R_hom3_ApoE4/4_-FBS_R3
Column name in counts.csv: KOLF2.1J_C156R_hom3_ApoE4/4_-FBS_R3


title: KOLF2.1J C156R hom3 ApoE4/4 -FBS R2

description:
Library name: KOLF2.1J_C156R_hom3_ApoE4/4_-FBS_R2
Column name in counts.csv: KOLF2.1J_C156R_hom3_ApoE4/4_-FBS_R2


title: mouse_neuron_N_pos_18m;N706_i7_12_N517_i5_4


title: KOLF2.1J C156R hom3 ApoE4/4 +FBS R3

description:
Library name: KOLF2.1J_C156R_hom3_ApoE4/4_+FBS_R3
Column name in counts.csv: KOLF2.1J_C156R_hom3_ApoE4/4_+FBS_R3


title: mouse_neuron_N_pos_18m;N706_i7_1_N517_i5_7


title: KOLF2.1J C156R hom3 ApoE4/4 +FBS R2

description:
Library name: KOLF2.1J_C156R_hom3_ApoE4/4_+FBS_R2
Column name in counts.csv: KOLF2.1J_C156R_hom3_ApoE4/4_+FBS_R2


title: mouse_neuron_N_pos_18m;N706_i7_12_N517_i5_3


title: mouse_neuron_N_pos_18m;N706_i7_12_N517_i5_1


title: mouse_neuron_N_pos_18m;N706_i7_12_N517_i5_2


title: KOLF2.1J ApoE3/3 -FBS R3

description:
Library name: KOLF2.1J_ApoE3/3_-FBS_R3
Column name in counts.csv: KOLF2.1J_ApoE3/3_-FBS_R3


title: cas3

description:
Library name: SAMPLES 3
BD Rhapsody


title: mouse_neuron_N_pos_18m;N706_i7_11_N517_i5_8


title: KOLF2.1J ApoE3/3 -FBS R2

description:
Library name: KOLF2.1J_ApoE3/3_-FBS_R2
Column name in counts.csv: KOLF2.1J_ApoE3/3_-FBS_R2


title: KOLF2.1J ApoE3/3 -FBS R1

description:
Library name: KOLF2.1J_ApoE3/3_-FBS_R1
Column name in counts.csv: KOLF2.1J_ApoE3/3_-FBS_R1


title: cas1

description:
Library name: SAMPLES 1
BD Rhapsody


title: mouse_neuron_N_pos_18m;N706_i7_11_N517_i5_7


title: mouse_neuron_N_pos_18m;N706_i7_11_N517_i5_6


title: KOLF2.1J ApoE3/3 +FBS R1

description:
Library name: KOLF2.1J_ApoE3/3_+FBS_R1
Column name in counts.csv: KOLF2.1J_ApoE3/3_+FBS_R1


title: Bioni037-A4 ApoE4/4 Replicate 3

description:
Library name: 37-A4 R3
Column name in counts.csv: 37-A4 R3

value: iPSC-derived astrocytes


title: Bioni037-A4 ApoE4/4 Replicate 2

description:
Library name: 37-A4 R2
Column name in counts.csv: 37-A4 R2


title: mouse_neuron_N_pos_18m;N706_i7_11_N517_i5_5


title: Bioni037-A4 ApoE4/4 Replicate 1

description:
Library name: 37-A4 R1
Column name in counts.csv: 37-A4 R1


title: KOLF2.1J ApoE3/3 +FBS R3

description:
Library name: KOLF2.1J_ApoE3/3_+FBS_R3
Column name in counts.csv: KOLF2.1J_ApoE3/3_+FBS_R3


title: mouse_neuron_N_pos_18m;N706_i7_11_N517_i5_2


title: KOLF2.1J ApoE3/3 +FBS R2

description:
Library name: KOLF2.1J_ApoE3/3_+FBS_R2
Column name in counts.csv: KOLF2.1J_ApoE3/3_+FBS_R2


title: Bioni037-A ApoE3/3 Replicate 3

description:
Library name: 37-A R3
Column name in counts.csv: 37-A R3


title: Bioni037-A ApoE3/3 Replicate 2

description:
Library name: 37-A R2
Column name in counts.csv: 37-A R2


title: KOLF2.1J C156R hom3 ApoE4/4 +FBS R1

description:
Library name: KOLF2.1J_C156R_hom3_ApoE4/4_+FBS_R1
Column name in counts.csv: KOLF2.1J_C156R_hom3_ApoE4/4_+FBS_R1


title: mouse_neuron_N_pos_18m;N706_i7_10_N517_i5_6


title: Bioni037-A ApoE3/3 Replicate 1

description:
Library name: 37-A R1
Column name in counts.csv: 37-A R1


title: mouse_neuron_N_pos_18m;N706_i7_11_N517_i5_1


title: mouse_neuron_N_pos_18m;N706_i7_10_N517_i5_7


title: mouse_neuron_N_pos_18m;N706_i7_10_N517_i5_5


title: mouse_neuron_N_pos_18m;N706_i7_10_N517_i5_4


title: mouse_neuron_N_pos_18m;N706_i7_10_N517_i5_3


title: mouse_neuron_N_pos_18m;N706_i7_10_N517_i5_2


title: 237L

city: torrance

first: Omid

last: Khorram

state: CA

address: 1124  w carson st

institute: The lundquist Institute at UCLA medical center

description: Library name: Sample 10

data_processing:
FastQC was used to check quality of reads
(1)Discard the read pair if either one read contains adapter contamination;
(2)Discard the read pair if more than 10% of bases are uncertain in either one read;
(3)Discard the read pair if the proportion of low quality bases is over 50% in either one read.
Hisat2 and featureCounts was used to align and count reads.
DeSeq2 was used for differential expression analysis.
Assembly: hg18
Supplementary files format and content: Processed DATA.xls

source_name: Leiomyoma

extract_protocol:
TRIzol
Performed by Novogene Corporation Inc.
QiaSeq miRNA small RNA

value: Leiomyoma


title: mouse_neuron_N_pos_18m;N706_i7_10_N517_i5_1


title: 383L

description: Library name: Sample 8


title: 355M

description: Library name: Sample 11

source_name: Myometrium

value: Myometrium


title: 237M

description: Library name: Sample 9


title: 383M

description: Library name: Sample 7


title: mouse_neuron_N_pos_18m;N706_i7_11_N517_i5_4


title: mouse_neuron_N_pos_18m;N706_i7_11_N517_i5_3


title: 510L

description: Library name: Sample 6


title: 510M

description: Library name: Sample 5


title: mouse_neuron_N_pos_18m;N706_i7_10_N517_i5_8


title: 469M

description: Library name: Sample 3


title: 469L

description: Library name: Sample 4


title: mouse_neuron_N_neg_3m;N701_i7_9_N502_i5_6

source_name: NeuN-

value: NeuN-


title: mouse_neuron_N_neg_3m;N701_i7_9_N502_i5_5


title: 355L

description: Library name: Sample 12


title: mouse_neuron_N_neg_3m;N701_i7_9_N502_i5_4


title: 346L

description: Library name: Sample 2


title: 346M

description: Library name: Sample 1


title: mouse_neuron_N_neg_3m;N701_i7_9_N502_i5_1


title: mouse_neuron_N_neg_3m;N701_i7_9_N502_i5_2


title: mouse_neuron_N_neg_3m;N701_i7_8_N502_i5_8


title: mouse_neuron_N_neg_3m;N701_i7_9_N502_i5_3


title: GLORI-seq, T24_STM2457_2

city: Heidelberg

first: Jonas

last: Koch

address: Im Neuenheimer Feld 580

department: Epigenetics

country: Germany

institute: German Cancer Research Center

description: Library name: T24_STM2457_2

data_processing:
Adaptor sequences were trimmed using Trim Galore (version 0.6.6).
Reads were aligned to the genome using STAR (version 2.7.10a) and to the transcriptome using bowtie (version 1.3.0)
Pileup was performed using samtools API pysam (version 1.19).
m6A calling was performed using the so-called GLORI-tools pipeline, which is available on github: https://github.com/liucongcas/GLORI-tools.
Assembly: GRCh38
Supplementary files format and content: tab-separated .csv files providing the detected m6A sites in every GLORI-sequenced sample.

source_name: Bladder

growth_protocol: T24 cells were cultured in McCoy medium supplemented with 10% FBS and 1% penicillin/streptomycin. The cells were cultivated as adherent monolayers at 37°C in a humidified incubator with a 5% CO2 atmosphere.

extract_protocol:
Total RNA from T24 cells was isolated with TRIzol. Small RNA fractions were depleted using the MEGAclear Transcription Clean-Up Kit (Thermo Fisher Scientific). Enrichment of mRNA was performed twice using the Dynabeads mRNA Purification Kit (Thermo Fisher Scientific). mRNA was then fragmented by incubation for 3 min at 94 °C using the NEBNext Magnesium RNA Fragmentation Module (New England Biolabs). Fragmented mRNA was then DNase I-treated and purified by the RNA Clean & Concentrator-5 kit (Zymo Research). Fragmented RNA samples were then subjected to the chemical deamination protocol. For RNA protection, 100 – 200 ng of fragmented mRNA supplemented with a synthetic Spike-In RNA oligonucleotide were added into protection buffer (1.32 M Glyoxal solution, 50 % DMSO, prepared in water) and incubated for 30 min at 50 °C in a thermal cycler. The RNA was further stabilized by adding 10 µL of freshly prepared saturated boric acid at RT, followed by incubation for 30 min at 50 °C in a thermal cycler. Protected RNA was then added into 50 µL of freshly prepared deamination buffer (1.5 M NaNO2, 80 mM MES (pH 6.0), 1.76 M Glyoxal solution, prepared in water), and incubated for 8 hours at 16 °C in a thermal cycler. After deamination, RNA was purified by ethanol precipitation ON at – 80 °C. Pelleted RNA was washed twice using 75 % ethanol and air-dried for 5 min at RT. Then, the RNA pellet was resuspended in 50 µL of deprotection buffer (500 mM triethylammonium acetate (pH 8.6), 47.5 % deionized formamide, prepared in water) and incubated for 10 min at 95 °C in a thermal cycler. Deprotected RNA was purified by ethanol precipitation for at least 30 min at – 80 °C. Pelleted RNA was washed twice using 75 % ethanol and air-dried for 5 min at RT. The RNA pellet was then resuspended in 50 µL of water and further purified using the RNA Clean & Concentrator-5 kit (Zymo Research). For sequencing library preparation, a two-step RNA end-repair protocol was pursued. RNA 3’-end dephosphorylation was performed by Antarctic phosphatase (New England Biolabs) treatment in a total reaction volume of 20 µL. The reaction was incubated for 30 min at 37 °C and inactivated for 2 min at 80 °C. Subsequently, RNA 5’-end phosphorylation was performed by T4 Polynucleotide Kinase (New England Biolabs) treatment in a total reaction volume of 50 µL. The reaction was incubated for 30 min at 37 °C, inactivated for 20 min at 65 °C, and purified using the RNA Clean & Concentrator-5 kit (Zymo Research).
The libraries were then prepared using the NEBNext Small RNA Library Prep Set for Illumina in combination with the NEBNext Multiplex Oligos for Illumina (Index Primer Sets 1 and 3) (New England Biolabs). Size selection of the libraries was performed via TBE-PAGE using 8 % TBE polyacrylamide gels (Thermo Fisher Scientific) selecting sequencing competent molecules in a size range of 160 – 250 bp.

treatment_protocol: Upon reaching a confluency of 80 %, T24 cells were treated with DMSO or 50 µM of STM2457 for 48 hours before total RNA isolation.

value: Bladder

value: urinary bladder carcinom

value: Wildtype


title: GLORI-seq, T24_STM2457_3

description: Library name: T24_STM2457_3


title: mouse_neuron_N_neg_3m;N701_i7_9_N502_i5_8


title: mouse_neuron_N_neg_3m;N701_i7_8_N502_i5_7


title: GLORI-seq, T24_STM2457_1

description: Library name: T24_STM2457_1


title: GLORI-seq, T24_DMSO1

description: Library name: T24_DMSO1

value: DMSO


title: mouse_neuron_N_neg_3m;N701_i7_8_N502_i5_4


title: GLORI-seq, T24_DMSO2

description: Library name: T24_DMSO2


title: mouse_neuron_N_neg_3m;N701_i7_8_N502_i5_5


title: GLORI-seq, T24_DMSO3

description: Library name: T24_DMSO3


title: mouse_neuron_N_neg_3m;N701_i7_8_N502_i5_6


title: mouse_neuron_N_neg_3m;N701_i7_9_N502_i5_7


title: DCM_3

city: Bunkyo-ku

first: Manami

last: Katoh

state: Tokyo

address: 7-3-1 Hongo

department: Department of Cardiovascular Medicine

country: Japan

institute: The University of Tokyo

description:
Library name: Sample5
10× Genomics

data_processing:
Raw FASTQ files were processed for each sample using the Cell Ranger software (version 7.2.0 or 6.0.1, 10× Genomics), against the Cell Ranger GRCm38 human reference genome.
Raw mapped counts were used as the input for data processing with the Seurat R package (version 4.1.2, 5.0.1).
To exclude ambient RNA contamination, the data were processed using CellBender.
We removed cells with detected genes <1000, detected counts <2000 and >30000, and mitochondrial gene content > 5%.
Following the filtering step, we normalized the read counts using the ‘NormalizeData’ function (10,000 default scale factor), separately for each dataset.
Assembly: GRCh38 human reference genome
Supplementary files format and content: CellBneder output files: raw_feature_bc_matrix_FPR_0.05_filtered.h5

source_name: Heart

extract_protocol:
5000 nuclei were prepared to a concentration of 1,000 nuclei/µL and loaded into the Chromium Controller (10× Genomics). Single-cell cDNA libraries were generated using a Chromium 3′ v3 Chemistry Kit (PN-1000075, 10× Genomics), except for one sample (CTRL_2), which was processed using a Chromium 3′ v2 Chemistry Kit.
Libraries were sequenced on a NovaSeq 6000 System, using the NovaSeq S4 Reagent Kit (20027466, Illumina).

value: Heart

value: heart failure patients undergoing implantation of left ventricular assist devices due to reduced cardiac function


title: DCM_5

description:
Library name: Sample6
10× Genomics


title: mouse_neuron_N_neg_3m;N701_i7_8_N502_i5_2

value: scCAPS+


title: mouse_neuron_N_neg_3m;N701_i7_8_N502_i5_3


title: DCM_2

description:
Library name: Sample4
10× Genomics


title: DCM_1

description:
Library name: Sample3
10× Genomics


title: mouse_neuron_N_neg_3m;N701_i7_8_N502_i5_1


title: CTRL_2

description:
Library name: Sample2
10× Genomics

value: preserved cardiac function who underwent pathological autopsy


title: mouse_neuron_N_neg_3m;N701_i7_7_N502_i5_8


title: mouse_neuron_N_neg_3m;N701_i7_7_N502_i5_7


title: CTRL_1

description:
Library name: Sample1
10× Genomics


title: mouse_neuron_N_neg_3m;N701_i7_7_N502_i5_6


title: mouse_neuron_N_neg_3m;N701_i7_7_N502_i5_5


title: mouse_neuron_N_neg_3m;N701_i7_7_N502_i5_4


title: A549, WT, IAV_8h, DRIP-seq, rep 2 (Input)

city: hangzhou

first: Ke

last: Jin

address: 866 Yuhangtang Rd

institute: zhejiang university

description: Library name: sample6

data_processing:
Sequencing quality were examined using FastQC software. The 5’, 3’-adaptor bases were trimmed using cutadapt software. The trimmed reads were aligned to human reference genome GRCh38 using bowtie2 software. The aligned reads were used for peak calling of the regions with the StochHMM software. Differentially accessible peaks were analyzed using DiffBind. The peaks that were < 100bp were discarded.The peaks were annotated with the overlapping transcript.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Total nucleic acids were extracted from cells and tissues by SDS/proteinase K treatment followed by phenol_x0002_chloroform extraction and ethanol precipitation, some samples were extracted by DNA Kit. Typically more than 10 µg genomic DNA for each sample was fragmented by ultrasound (Perform 10-15 cycles of 30 s ON/ 30s OFF, spin after 3, 6, 9, and 12 cycles to ensure homogeneous sonication). The fragments length are limited within 500bp as possible.
Followed by second DNA strand synthesis, dsDNA was cleaned up with 1.8 volume of DNA Beads and ligate “A” and adaptor. Add 10 µL ddH2O and 35 uL PEG/NaCl (1:1) to clean up and eluted with 10 µL ddH2O. Add 11 µL KAPA HiFi HotStart ReadyMix (2X) and 1 uL primers to amplify library. Each DNA library was amplified 9 -20 cycles depending on the starting material amount. Library was purified by 0.8 volume of DNA Beads. The library concentration and size distribution were checked by Qubit and 2100

value: IAV 8h


title: A549, RPSA_KO, IAV_8h, DRIP-seq, rep 1 (Input)

description: Library name: sample7


title: A549, RPSA_KO,  IAV_8h, DRIP-seq, rep 2 (Input)

description: Library name: sample8


title: A549, RPSA_KO,  IAV_8h, DRIP-seq, rep 2

description: Library name: sample4


title: A549, WT, IAV_8h, DRIP-seq, rep 1 (Input)

description: Library name: sample5


title: mouse_neuron_N_neg_3m;N701_i7_7_N502_i5_2


title: A549, WT, IAV_8h, DRIP-seq, rep 2

description: Library name: sample2


title: mouse_neuron_N_neg_3m;N701_i7_6_N502_i5_8


title: mouse_neuron_N_neg_3m;N701_i7_6_N502_i5_6


title: A549, RPSA_KO, IAV_8h, DRIP-seq, rep 1

description: Library name: sample3


title: A549, WT, IAV_8h, DRIP-seq, rep 1

description: Library name: sample1


title: mouse_neuron_N_neg_3m;N701_i7_7_N502_i5_1


title: mouse_neuron_N_neg_3m;N701_i7_6_N502_i5_7


title: mouse_neuron_N_neg_3m;N701_i7_6_N502_i5_5


title: mouse_neuron_N_neg_3m;N701_i7_6_N502_i5_4


title: mouse_neuron_N_neg_3m;N701_i7_6_N502_i5_3


title: A549, WT, IAV_12h, CUT&Tag, rep 2

description: Library name: sample2

data_processing:
The QC filtered raw reads were trimmed and aligned to human genome (UCSC HG38) using Bowtie2 software (V2.5.1). The alignment results were filtered with deeptools(V3.5.1) and used for peak calling by MACS2 V2.2.9.1. Statistically significant differential open chromatin regions(DARs) were identified at a default threshold of FoldChange=2 and p-value=0.05. The DARs and peaks were annotated to nearest gene or regulatory elements using UROPA(V4.0.2) and HOMER(V4.11). Known and de novo TF motifs were searched with HOMER among all DARs. Enrichment of ttranscription regulators (with publicly available ChIP-seq profiles) in DARs was analysed with GIGGLE(V0.6.3)
Assembly: hg38
Supplementary files format and content: BigWig
Library strategy: CUT&Tag

extract_protocol:
Cells were harvested, counted and centrifuged for 3 min at 600g at room temperature. Aliquots of cells (60–500,000 cells), were washed twice in 1.5mL Wash Buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5mM Spermidine; 1× Protease inhibitor cocktail) by gentle pipetting. Concanavalin A coated magnetic beads (Bangs Laboratories) were prepared and 10 µL of activated beads were added per sample and incubated at RT for 15min. We observed that binding cells to beads at this step increases binding efficiency. The unbound supernatant was removed.
To amplify libraries, 21 µL DNA was mixed with 2 µL of a universal i5 and i7 primer, using a different barcode for each sample. A volume of 25 µL NEBNext HiFi 2× PCR Master mix was added and mixed. The sample was placed in a Thermocycler with a heated lid using the following cycling conditions: 72°C for 5min (gap filling); 98 °C for 30 s; 14 cycles of 98 °C for 10 s and 63 °C for 30s; final extension at 72°C for 5 min and hold at 4 °C. Post-PCR clean-up was performed by adding 0.9 × volume of Ampure XP beads (Beckman Counter), and libraries were incubated with beads for 15 min at RT, washed twicegently in 80% ethanol, and eluted in 20 µL ddH2O.

value: IAV 12h


title: A549, RPSA_KO, IAV_12h, CUT&Tag, rep 1

description: Library name: sample3


title: A549, WT, IAV_12h, CUT&Tag, rep 1

description: Library name: sample1


title: mouse_neuron_N_neg_3m;N701_i7_6_N502_i5_2


title: mouse_neuron_N_neg_3m;N701_i7_5_N502_i5_8


title: Y-83K-7d-Virus

city: Chapel Hill

first: Hong

last: Dang

state: North Carolina

address: 125 Mason Farm Rd, Cb#7248

department: Marsico Lung Institute

institute: University of North Carolina at Chapel Hill

description: Library name: Y-83K-7d-Virus

data_processing:
Illumina bcl2fastq v2.19 used for basecalling.
Sequence reads in FASTQ files were mapped to GRCh38 reference genome appended with SARS-CoV-2 RefSeq genome (NC045512) with GENCODE 37 gene annotation and SARS-CoV-2 gene annotation from ENSEMBL COVID-19 by STAR, and gene expression estimates were derived from StringTie using default parameters.
Viral TPM values were estimated with StringTie with combined human and viral gene annotations
Human gene expression (hG) estimates were extracted with StringTie using GENCODE 37 gene annotation only, which exclude viral specific transcripts.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include estimated count values as integers for each sample
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: Primary bronchial airway epithelial cells

growth_protocol: Human bronchial epithelial (HBE) cells were obtained from freshly isolated large airway epithelium of non-smoker lung transplant donors with lungs unsuitable for transplant. Isolated HBE cells were expanded using a modified conditional reprogramming cell culture. The cells were seeded onto 12mm Transwell inserts at 0.25 millon cells per insert.The cells were cultured under submerged condition until confluence. Then they were cultured under air-liquid interface (ALI) culture until full-differention confirmed by ciliation under light microscopic examination.

extract_protocol:
Cell culture membranes were kept in TRI Reagent and the RNA extracted according to the manufacturer’s instructions. RNA concentrations were determined using a NanoDrop-8000 spectrophotometer.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The HBE cells were inoculated with SARS-CoV-2 (D614G strain) at MOI=0.5 for two hours. The cells were maintained under ALI culture until 1-, 3- 7- and 14-day post inoculation.RNAs were extracted from the cell lysates.

value: Primary cells

value: Epithelial cells

tag: donor code

tag: age group

value: Y

value: M

value: Virus

tag: titer

tag: titer duplicate


title: Y-83K-3d-Virus

description: Library name: Y-83K-3d-Virus

tag: tissue

value: Primary bronchial airway epithelial cells


title: Y-83K-3d-Mock

description: Library name: Y-83K-3d-Mock

value: Mock


title: mouse_neuron_N_neg_3m;N701_i7_5_N502_i5_7

value: NeuN-


title: mouse_neuron_N_neg_3m;N701_i7_7_N502_i5_3


title: mouse_neuron_N_neg_3m;N701_i7_5_N502_i5_6


title: Y-83K-1d-Virus

description: Library name: Y-83K-1d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_5_N502_i5_5


title: A549, RPSA_KO, IAV_12h, CUT&Tag, rep 2

description: Library name: sample4


title: Y-83K-14d-Virus

description: Library name: Y-83K-14d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_5_N502_i5_4


title: mouse_neuron_N_neg_3m;N701_i7_5_N502_i5_3


title: Y-46M-7d-Virus

description: Library name: Y-46M-7d-Virus

value: F


title: mouse_neuron_N_neg_3m;N701_i7_5_N502_i5_2


title: mouse_neuron_N_neg_3m;N701_i7_5_N502_i5_1


title: Y-46M-7d-Mock

description: Library name: Y-46M-7d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_4_N502_i5_8


title: Y-46M-3d-Virus

description: Library name: Y-46M-3d-Virus


title: Y-46M-3d-Mock

description: Library name: Y-46M-3d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_4_N502_i5_7


title: mouse_neuron_N_neg_3m;N701_i7_6_N502_i5_1


title: mouse_neuron_N_neg_3m;N701_i7_4_N502_i5_6


title: mouse_neuron_N_neg_3m;N701_i7_4_N502_i5_5


title: Y-83K-7d-Mock

description: Library name: Y-83K-7d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_4_N502_i5_4


title: Y-46M-14d-Virus

description: Library name: Y-46M-14d-Virus


title: Y-46M-1d-Virus

description: Library name: Y-46M-1d-Virus


title: Y-18I-7d-Virus

description: Library name: Y-18I-7d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_4_N502_i5_2


title: Y-46M-14d-Mock

description: Library name: Y-46M-14d-Mock


title: Y-18I-7d-Mock

description: Library name: Y-18I-7d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_4_N502_i5_3


title: Y-83K-1d-Mock

description: Library name: Y-83K-1d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_4_N502_i5_1


title: mouse_neuron_N_neg_3m;N701_i7_3_N502_i5_8


title: Y-83K-14d-Mock

description: Library name: Y-83K-14d-Mock


title: Y-18I-3d-Virus

description: Library name: Y-18I-3d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_3_N502_i5_7


title: Y-18I-3d-Mock

description: Library name: Y-18I-3d-Mock


title: Y-18I-1d-Virus

description: Library name: Y-18I-1d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_3_N502_i5_6


title: Y-18I-14d-Virus

description: Library name: Y-18I-14d-Virus


title: Y-18I-1d-Mock

description: Library name: Y-18I-1d-Mock


title: Y-18I-14d-Mock

description: Library name: Y-18I-14d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_3_N502_i5_3


title: Y-46M-1d-Mock

description: Library name: Y-46M-1d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_3_N502_i5_4


title: M-51K-7d-Virus

description: Library name: M-51K-7d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_3_N502_i5_2


title: mouse_neuron_N_neg_3m;N701_i7_3_N502_i5_1


title: mouse_neuron_N_neg_3m;N701_i7_2_N502_i5_8


title: mouse_neuron_N_neg_3m;N701_i7_2_N502_i5_6


title: M-51K-7d-Mock

description: Library name: M-51K-7d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_2_N502_i5_7


title: M-51K-3d-Virus

description: Library name: M-51K-3d-Virus


title: M-51K-1d-Virus

description: Library name: M-51K-1d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_2_N502_i5_5


title: M-51K-1d-Mock

description: Library name: M-51K-1d-Mock


title: M-51K-14d-Virus

description: Library name: M-51K-14d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_2_N502_i5_4


title: mouse_neuron_N_neg_3m;N701_i7_2_N502_i5_3


title: M-51K-14d-Mock

description: Library name: M-51K-14d-Mock


title: M-35P-7d-Virus

description: Library name: M-35P-7d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_3_N502_i5_5


title: M-35P-7d-Mock

description: Library name: M-35P-7d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_2_N502_i5_1


title: M-35P-3d-Virus

description: Library name: M-35P-3d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_1_N502_i5_8


title: mouse_neuron_N_neg_3m;N701_i7_1_N502_i5_7


title: M-35P-3d-Mock

description: Library name: M-35P-3d-Mock


title: M-35P-1d-Mock

description: Library name: M-35P-1d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_1_N502_i5_6


title: M-51K-3d-Mock

description: Library name: M-51K-3d-Mock


title: M-35P-1d-Virus

description: Library name: M-35P-1d-Virus


title: M-35P-14d-Virus

description: Library name: M-35P-14d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_1_N502_i5_4


title: mouse_neuron_N_neg_3m;N701_i7_1_N502_i5_5


title: M-35P-14d-Mock

description: Library name: M-35P-14d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_1_N502_i5_2


title: M-21M-7d-Virus

description: Library name: M-21M-7d-Virus


title: M-21M-7d-Mock

description: Library name: M-21M-7d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_12_N502_i5_8


title: mouse_neuron_N_neg_3m;N701_i7_1_N502_i5_1


title: mouse_neuron_N_neg_3m;N701_i7_2_N502_i5_2


title: M-21M-3d-Mock

description: Library name: M-21M-3d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_12_N502_i5_7


title: M-21M-1d-Virus

description: Library name: M-21M-1d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_12_N502_i5_6


title: mouse_neuron_N_neg_3m;N701_i7_12_N502_i5_5


title: M-21M-1d-Mock

description: Library name: M-21M-1d-Mock


title: M-21M-14d-Virus

description: Library name: M-21M-14d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_12_N502_i5_4


title: mouse_neuron_N_neg_3m;N701_i7_12_N502_i5_3


title: M-21M-14d-Mock

description: Library name: M-21M-14d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_12_N502_i5_2


title: mouse_neuron_N_neg_3m;N701_i7_12_N502_i5_1


title: mouse_neuron_N_neg_3m;N701_i7_1_N502_i5_3


title: E-41T-3d-Mock

description: Library name: E-41T-3d-Mock

value: E


title: E-41T-3d-Virus

description: Library name: E-41T-3d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_11_N502_i5_6


title: mouse_neuron_N_neg_3m;N701_i7_11_N502_i5_8


title: mouse_neuron_N_neg_3m;N701_i7_11_N502_i5_7


title: mouse_neuron_N_neg_3m;N701_i7_11_N502_i5_5


title: E-41T-7d-Mock

description: Library name: E-41T-7d-Mock


title: M-21M-3d-Virus

description: Library name: M-21M-3d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_11_N502_i5_3


title: E-41T-14d-Mock

description: Library name: E-41T-14d-Mock


title: E-41T-1d-Mock

description: Library name: E-41T-1d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_11_N502_i5_4


title: E-30T-7d-Virus

description: Library name: E-30T-7d-Virus


title: E-41T-14d-Virus

description: Library name: E-41T-14d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_11_N502_i5_1


title: E-30T-7d-Mock

description: Library name: E-30T-7d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_11_N502_i5_2


title: E-41T-7d-Virus

description: Library name: E-41T-7d-Virus


title: E-30T-3d-Virus

description: Library name: E-30T-3d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_10_N502_i5_8


title: E-30T-3d-Mock

description: Library name: E-30T-3d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_10_N502_i5_6


title: E-30T-1d-Virus

description: Library name: E-30T-1d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_10_N502_i5_5


title: mouse_neuron_N_neg_3m;N701_i7_10_N502_i5_7


title: E-30T-14d-Virus

description: Library name: E-30T-14d-Virus


title: mouse_neuron_N_neg_3m;N701_i7_10_N502_i5_3


title: E-41T-1d-Virus

description: Library name: E-41T-1d-Virus


title: E-30T-14d-Mock

description: Library name: E-30T-14d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_10_N502_i5_2


title: E-11G-3d-Virus

description: Library name: E-11G-3d-Virus


title: mouse_neuron_N_neg_18m;N702_i7_9_N504_i5_8


title: E-11G-7d-Mock

description: Library name: E-11G-7d-Mock


title: mouse_neuron_N_neg_3m;N701_i7_10_N502_i5_1


title: mouse_neuron_N_neg_18m;N702_i7_9_N504_i5_7


title: mouse_neuron_N_neg_18m;N702_i7_9_N504_i5_6


title: E-11G-1d-Mock

description: Library name: E-11G-1d-Mock


title: E-11G-1d-Virus

description: Library name: E-11G-1d-Virus


title: mouse_neuron_N_neg_18m;N702_i7_9_N504_i5_4


title: E-11G-14d-Virus

description: Library name: E-11G-14d-Virus


title: E-11G-7d-Virus

description: Library name: E-11G-7d-Virus


title: mouse_neuron_N_neg_18m;N702_i7_9_N504_i5_3


title: E-11G-14d-Mock

description: Library name: E-11G-14d-Mock


title: mouse_neuron_N_neg_18m;N702_i7_9_N504_i5_5


title: mouse_neuron_N_neg_18m;N702_i7_9_N504_i5_1


title: mouse_neuron_N_neg_3m;N701_i7_10_N502_i5_4


title: Multiome,colorectal organoid,tumor_organoid_P009,ATAC

city: Utrecht

first: Hendrik

middle: G

last: Stunnenberg

state: Utrecht

address: Heidelberglaan 25

department: Research Department

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

description:
Library name: TO009_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TO009.h5
TO009_atac_fragments.tsv.gz

library_source: genomic single cell

data_processing:
The Cell Ranger ARC 2.0.2 pipelines (from 10x Genomics) were used to process the multiomics sequencing data. The pipelines first demultiplexed the BCL files into FASTQ files, which were then converted into BAM files and feature-barcode matrixes. The pipeline performed alignment to the UCSC hg38 transcriptome, barcode counting, UMI counting/peak calling and ultimately produced feature-barcode matrixes as output.
A multiplexing strategy was used in this project, where samples from two individual patients were pooled prior to library preparation within a 10x Genomics Multiome kit reaction. This strategy leverages natural genetic variation, allowing computational tools to demultiplex samples based on those variations, such as single nucleotide polymorphisms (SNP). Specifically, the software tools cellsnp-lite and vireo were used for the SNP-based demultiplexing, assigning 10x barcodes to different patients. SNP files were generated independently by cellsnp-lite for the snRNA-seq and snATAC-seq libraries. These SNP files were then concatenated into a matrix, and vireo was used to separate the samples by patients. In addition to SNP variation information, gender information also utilized during the demultiplexing process to further distinguish between the two pooled patients.
Assembly: hg38
Supplementary files format and content: CellRanger-ARC output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz

source_name: colorectal organoid

extract_protocol:
Cryopreserved primary samples and organoid samples were thawed in a 37°C water bath following standard thawing protocols. Next, the cell pellet was resuspended in NP40 Lysis Buffer and transferred to a 70 µm MACS SmartStrainer (Miltenyi Biotec) tissue grinder. To isolated nuclei from the tissue, the sample was processed with five strokes using a loose pestle, followed by ten strokes with a tight pestle. Then, the nuclei suspension went through 70 µm and 40 µm Flowmi cell strainer (Bel-Art), followed by 7-AAD staining (1:1000, Invitrogen 15239004) before sorting. Fluorescence-activated nucleus sorting (FANS) was used to purify and collect intact nuclei, with at least 200,000 nuclei collected from each sample. For the nuclei permeabilization step, 0.1x Lysis Buffer was used, and the nuclei were suspended in Diluted Nuclei Buffer to achieve a final concentration of around 5000 nuclei/µl. All buffers used in the protocol were freshly prepared.
snRNA and snATAC libraries were prepared according to the protocol provided by the vender using the 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (CG000338 RevE). In brief, transposition was performed on nuclei, followed by the formation of functional Gel Beads in Emulsion (GEMs), which were also barcoded. This process was followed by post-GEM incubation cleanup, pre-amplification PCR, ATAC library construction, cDNA amplification and gene expression library construction. As a result, fragments from the same single nucleus carry the same barcode, enabling sequencing reads to be mapped back to the same original nucleus. Every snRNA and snATAC library were quality-checked using the Agilent Bioanalyzer High Sensitivity DNA chip on a 2100 Bioanalyzer before sequencing.

value: colorectal organoid

value: epithelial cells


title: Multiome,colorectal organoid,tumor_organoid_P008,ATAC

description:
Library name: TO008_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TO008.h5
TO008_atac_fragments.tsv.gz


title: mouse_neuron_N_neg_18m;N702_i7_9_N504_i5_2


title: Multiome,colorectal organoid,tumor_organoid_P007,ATAC

description:
Library name: TO007_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TO007.h5
TO007_atac_fragments.tsv.gz


title: E-30T-1d-Mock

description: Library name: E-30T-1d-Mock


title: mouse_neuron_N_neg_18m;N702_i7_8_N504_i5_6


title: mouse_neuron_N_neg_18m;N702_i7_8_N504_i5_8


title: Multiome,colorectal organoid,tumor_organoid_P006,ATAC

description:
Library name: TO006_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TO006.h5
TO006_atac_fragments.tsv.gz


title: Multiome,colorectal organoid,tumor_organoid_P005,ATAC

description:
Library name: TO005_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TO005.h5
TO005_atac_fragments.tsv.gz


title: mouse_neuron_N_neg_18m;N702_i7_8_N504_i5_5


title: mouse_neuron_N_neg_18m;N702_i7_8_N504_i5_7


title: Multiome,colorectal organoid,tumor_organoid_P004,ATAC

description:
Library name: TO004_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TO004.h5
TO004_atac_fragments.tsv.gz


title: E-11G-3d-Mock

description: Library name: E-11G-3d-Mock


title: Multiome,colorectal organoid,tumor_organoid_P003,ATAC

description:
Library name: TO003_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TO003.h5
TO003_atac_fragments.tsv.gz


title: mouse_neuron_N_neg_18m;N702_i7_8_N504_i5_4


title: Multiome,colorectal organoid,tumor_organoid_P002,ATAC

description:
Library name: TO002_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TO002.h5
TO002_atac_fragments.tsv.gz


title: mouse_neuron_N_neg_18m;N702_i7_8_N504_i5_3


title: mouse_neuron_N_neg_18m;N702_i7_8_N504_i5_2


title: Multiome,colorectal organoid,tumor_organoid_P001,ATAC

description:
Library name: TO001_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TO001.h5
TO001_atac_fragments.tsv.gz


title: Multiome,colorectal organoid,tumor_organoid_P009,GEX

description:
Library name: TO009_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TO009.h5


title: Multiome,colorectal organoid,tumor_organoid_P006,GEX

description:
Library name: TO006_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TO006.h5


title: Multiome,colorectal organoid,tumor_organoid_P007,GEX

description:
Library name: TO007_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TO007.h5


title: mouse_neuron_N_neg_18m;N702_i7_7_N504_i5_8


title: mouse_neuron_N_neg_18m;N702_i7_7_N504_i5_7


title: mouse_neuron_N_neg_18m;N702_i7_7_N504_i5_6


title: mouse_neuron_N_neg_18m;N702_i7_8_N504_i5_1


title: mouse_neuron_N_neg_18m;N702_i7_7_N504_i5_5


title: Multiome,colorectal organoid,tumor_organoid_P005,GEX

description:
Library name: TO005_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TO005.h5


title: Multiome,colorectal organoid,tumor_organoid_P004,GEX

description:
Library name: TO004_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TO004.h5


title: mouse_neuron_N_neg_18m;N702_i7_7_N504_i5_4


title: Multiome,colorectal organoid,tumor_organoid_P002,GEX

description:
Library name: TO002_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TO002.h5


title: Multiome,colorectal organoid,tumor_organoid_P001,GEX

description:
Library name: TO001_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TO001.h5


title: mouse_neuron_N_neg_18m;N702_i7_7_N504_i5_3


title: mouse_neuron_N_neg_18m;N702_i7_6_N504_i5_8


title: Multiome,colorectal organoid,tumor_organoid_P003,GEX

description:
Library name: TO003_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TO003.h5


title: Multiome,colorectal organoid,normal_organoid_P009,ATAC

description:
Library name: NO009_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NO009.h5
NO009_atac_fragments.tsv.gz


title: mouse_neuron_N_neg_18m;N702_i7_7_N504_i5_1


title: mouse_neuron_N_neg_18m;N702_i7_7_N504_i5_2


title: Multiome,colorectal organoid,normal_organoid_P008,ATAC

description:
Library name: NO008_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NO008.h5
NO008_atac_fragments.tsv.gz


title: Multiome,colorectal organoid,normal_organoid_P005,ATAC

description:
Library name: NO005_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NO005.h5
NO005_atac_fragments.tsv.gz


title: mouse_neuron_N_neg_18m;N702_i7_6_N504_i5_7


title: mouse_neuron_N_neg_18m;N702_i7_6_N504_i5_6


title: mouse_neuron_N_neg_18m;N702_i7_6_N504_i5_4


title: Multiome,colorectal organoid,tumor_organoid_P008,GEX

description:
Library name: TO008_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TO008.h5


title: mouse_neuron_N_neg_18m;N702_i7_6_N504_i5_3


title: Multiome,colorectal organoid,normal_organoid_P007,ATAC

description:
Library name: NO007_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NO007.h5
NO007_atac_fragments.tsv.gz


title: Multiome,colorectal organoid,normal_organoid_P002,ATAC

description:
Library name: NO002_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NO002.h5
NO002_atac_fragments.tsv.gz


title: Multiome,colorectal organoid,normal_organoid_P004,ATAC

description:
Library name: NO004_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NO004.h5
NO004_atac_fragments.tsv.gz


title: mouse_neuron_N_neg_18m;N702_i7_6_N504_i5_2


title: Multiome,colorectal organoid,normal_organoid_P001,ATAC

description:
Library name: NO001_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NO001.h5
NO001_atac_fragments.tsv.gz


title: Multiome,colorectal organoid,normal_organoid_P003,ATAC

description:
Library name: NO003_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NO003.h5
NO003_atac_fragments.tsv.gz


title: mouse_neuron_N_neg_18m;N702_i7_5_N504_i5_8


title: mouse_neuron_N_neg_18m;N702_i7_6_N504_i5_1


title: mouse_neuron_N_neg_18m;N702_i7_5_N504_i5_7


title: Multiome,colorectal organoid,normal_organoid_P008,GEX

description:
Library name: NO008_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NO008.h5


title: Multiome,colorectal organoid,normal_organoid_P009,GEX

description:
Library name: NO009_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NO009.h5


title: mouse_neuron_N_neg_18m;N702_i7_5_N504_i5_5


title: Multiome,colorectal organoid,normal_organoid_P007,GEX

description:
Library name: NO007_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NO007.h5


title: Multiome,colorectal organoid,normal_organoid_P006,GEX

description:
Library name: NO006_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NO006.h5


title: mouse_neuron_N_neg_18m;N702_i7_5_N504_i5_4


title: Multiome,colorectal organoid,normal_organoid_P005,GEX

description:
Library name: NO005_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NO005.h5


title: mouse_neuron_N_neg_18m;N702_i7_5_N504_i5_3


title: Multiome,colorectal organoid,normal_organoid_P006,ATAC

description:
Library name: NO006_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NO006.h5
NO006_atac_fragments.tsv.gz


title: Multiome,colorectal organoid,normal_organoid_P004,GEX

description:
Library name: NO004_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NO004.h5


title: mouse_neuron_N_neg_18m;N702_i7_6_N504_i5_5


title: mouse_neuron_N_neg_18m;N702_i7_5_N504_i5_1


title: mouse_neuron_N_neg_18m;N702_i7_5_N504_i5_2


title: Multiome,colorectal organoid,normal_organoid_P003,GEX

description:
Library name: NO003_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NO003.h5


title: Multiome,colorectal organoid,normal_organoid_P002,GEX

description:
Library name: NO002_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NO002.h5


title: Multiome,colorectal organoid,normal_organoid_P001,GEX

description:
Library name: NO001_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NO001.h5


title: mouse_neuron_N_neg_18m;N702_i7_4_N504_i5_6


title: Multiome,colorectal tissue,tumor_primary_P009,ATAC

description:
Library name: TP009_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TP009.h5
TP009_atac_fragments.tsv.gz

source_name: colorectal

value: colorectal

value: primary colorectal tumor tissue


title: mouse_neuron_N_neg_18m;N702_i7_4_N504_i5_5

value: scCAPS+


title: Multiome,colorectal tissue,tumor_primary_P005,ATAC

description:
Library name: TP005_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TP005.h5
TP005_atac_fragments.tsv.gz


title: Multiome,colorectal tissue,tumor_primary_P006,ATAC

description:
Library name: TP006_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TP006.h5
TP006_atac_fragments.tsv.gz


title: Multiome,colorectal tissue,tumor_primary_P008,ATAC

description:
Library name: TP008_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TP008.h5
TP008_atac_fragments.tsv.gz


title: Multiome,colorectal tissue,tumor_primary_P007,ATAC

description:
Library name: TP007_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TP007.h5
TP007_atac_fragments.tsv.gz


title: mouse_neuron_N_neg_18m;N702_i7_5_N504_i5_6


title: mouse_neuron_N_neg_18m;N702_i7_4_N504_i5_2


title: mouse_neuron_N_neg_18m;N702_i7_4_N504_i5_1


title: mouse_neuron_N_neg_18m;N702_i7_4_N504_i5_4


title: Multiome,colorectal tissue,tumor_primary_P003,ATAC

description:
Library name: TP003_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TP003.h5
TP003_atac_fragments.tsv.gz


title: Multiome,colorectal tissue,tumor_primary_P004,ATAC

description:
Library name: TP004_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TP004.h5
TP004_atac_fragments.tsv.gz


title: Multiome,colorectal tissue,tumor_primary_P002,ATAC

description:
Library name: TP002_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TP002.h5
TP002_atac_fragments.tsv.gz


title: mouse_neuron_N_neg_18m;N702_i7_3_N504_i5_6


title: mouse_neuron_N_neg_18m;N702_i7_3_N504_i5_7


title: Multiome,colorectal tissue,tumor_primary_P001,ATAC

description:
Library name: TP001_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TP001.h5
TP001_atac_fragments.tsv.gz


title: mouse_neuron_N_neg_18m;N702_i7_3_N504_i5_8


title: Multiome,colorectal tissue,tumor_primary_P009,GEX

description:
Library name: TP009_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TP009.h5


title: mouse_neuron_N_neg_18m;N702_i7_3_N504_i5_5


title: Multiome,colorectal tissue,tumor_primary_P008,GEX

description:
Library name: TP008_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TP008.h5


title: mouse_neuron_N_neg_18m;N702_i7_3_N504_i5_4


title: mouse_neuron_N_neg_18m;N702_i7_4_N504_i5_8


title: mouse_neuron_N_neg_18m;N702_i7_4_N504_i5_7


title: mouse_neuron_N_neg_18m;N702_i7_3_N504_i5_3


title: Multiome,colorectal tissue,tumor_primary_P007,GEX

description:
Library name: TP007_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TP007.h5


title: mouse_neuron_N_neg_18m;N702_i7_3_N504_i5_1


title: Multiome,colorectal tissue,tumor_primary_P005,GEX

description:
Library name: TP005_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TP005.h5


title: Multiome,colorectal tissue,tumor_primary_P006,GEX

description:
Library name: TP006_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TP006.h5


title: mouse_neuron_N_neg_18m;N702_i7_2_N504_i5_8


title: Multiome,colorectal tissue,tumor_primary_P004,GEX

description:
Library name: TP004_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TP004.h5


title: mouse_neuron_N_neg_18m;N702_i7_4_N504_i5_3


title: Multiome,colorectal tissue,tumor_primary_P002,GEX

description:
Library name: TP002_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TP002.h5


title: mouse_neuron_N_neg_18m;N702_i7_2_N504_i5_5


title: mouse_neuron_N_neg_18m;N702_i7_2_N504_i5_7


title: mouse_neuron_N_neg_18m;N702_i7_2_N504_i5_4


title: Multiome,colorectal tissue,normal_primary_P009,ATAC

description:
Library name: NP009_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NP009.h5
NP009_atac_fragments.tsv.gz

value: primary colorectal normal tissue


title: mouse_neuron_N_neg_18m;N702_i7_2_N504_i5_6


title: mouse_neuron_N_neg_18m;N702_i7_2_N504_i5_3


title: Multiome,colorectal tissue,normal_primary_P007,ATAC

description:
Library name: NP007_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NP007.h5
NP007_atac_fragments.tsv.gz


title: mouse_neuron_N_neg_18m;N702_i7_2_N504_i5_2


title: Multiome,colorectal tissue,normal_primary_P006,ATAC

description:
Library name: NP006_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NP006.h5
NP006_atac_fragments.tsv.gz


title: Multiome,colorectal tissue,normal_primary_P005,ATAC

description:
Library name: NP005_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NP005.h5
NP005_atac_fragments.tsv.gz


title: Multiome,colorectal tissue,normal_primary_P004,ATAC

description:
Library name: NP004_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NP004.h5
NP004_atac_fragments.tsv.gz


title: mouse_neuron_N_neg_18m;N702_i7_2_N504_i5_1


title: mouse_neuron_N_neg_18m;N702_i7_1_N504_i5_7


title: Multiome,colorectal tissue,normal_primary_P003,ATAC

description:
Library name: NP003_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NP003.h5
NP003_atac_fragments.tsv.gz


title: mouse_neuron_N_neg_18m;N702_i7_1_N504_i5_5


title: Multiome,colorectal tissue,normal_primary_P002,ATAC

description:
Library name: NP002_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NP002.h5
NP002_atac_fragments.tsv.gz


title: Multiome,colorectal tissue,normal_primary_P001,ATAC

description:
Library name: NP001_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NP001.h5
NP001_atac_fragments.tsv.gz


title: Multiome,colorectal tissue,normal_primary_P009,GEX

description:
Library name: NP009_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NP009.h5


title: mouse_neuron_N_neg_18m;N702_i7_1_N504_i5_4


title: mouse_neuron_N_neg_18m;N702_i7_1_N504_i5_3


title: Multiome,colorectal tissue,tumor_primary_P001,GEX

description:
Library name: TP001_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TP001.h5


title: mouse_neuron_N_neg_18m;N702_i7_1_N504_i5_2


title: Multiome,colorectal tissue,tumor_primary_P003,GEX

description:
Library name: TP003_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
TP003.h5


title: Multiome,colorectal tissue,normal_primary_P008,GEX

description:
Library name: NP008_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NP008.h5


title: mouse_neuron_N_neg_18m;N702_i7_12_N504_i5_8


title: mouse_neuron_N_neg_18m;N702_i7_12_N504_i5_7


title: Multiome,colorectal tissue,normal_primary_P007,GEX

description:
Library name: NP007_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NP007.h5


title: Multiome,colorectal tissue,normal_primary_P005,GEX

description:
Library name: NP005_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NP005.h5


title: mouse_neuron_N_neg_18m;N702_i7_1_N504_i5_1


title: Multiome,colorectal tissue,normal_primary_P003,GEX

description:
Library name: NP003_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NP003.h5


title: mouse_neuron_N_neg_18m;N702_i7_12_N504_i5_6


title: Multiome,colorectal tissue,normal_primary_P004,GEX

description:
Library name: NP004_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NP004.h5


title: Multiome,colorectal tissue,normal_primary_P008,ATAC

description:
Library name: NP008_snATAC
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NP008.h5
NP008_atac_fragments.tsv.gz


title: mouse_neuron_N_neg_18m;N702_i7_12_N504_i5_5


title: mouse_neuron_N_neg_18m;N702_i7_1_N504_i5_6


title: mouse_neuron_N_neg_18m;N702_i7_1_N504_i5_8


title: Multiome,colorectal tissue,normal_primary_P002,GEX

description:
Library name: NP002_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NP002.h5


title: mouse_neuron_N_neg_18m;N702_i7_12_N504_i5_4


title: mouse_neuron_N_neg_18m;N702_i7_3_N504_i5_2


title: mouse_neuron_N_neg_18m;N702_i7_12_N504_i5_3


title: UMUC3_KO3

description:
Library name: UMUC3_KO3
APA_sites_UMUC3_KO.txt

data_processing:
Adaptor sequences were trimmed using Trim Galore (version 0.6.6).
Reads were aligned using HISAT2 (version 2.2.1).
Mapped reads were quantified using featureCounts (version 2.0.6).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including alternative polyadenylation events in patient and cell line samples.

growth_protocol: T24 cells were cultured in McCoy’s 5A (modified) medium supplemented with 10% FBS and 1% penicillin/streptomycin. UM-UC-3 cells were cultured in DMEM high glucose medium supplemented with 10% FBS and 1% penicillin/streptomycin. Both cell lines were cultivated as adherent monolayers at 37°C in a humidified incubator with a 5% CO2 atmosphere.

extract_protocol:
Total RNA from tissue samples and cell lines were isolated using TRIzol. To remove residual gDNA contaminants, total RNA samples were DNase I-digested and further purified using the RNA Clean & Concentrator-5 kit (Zymo Research).
Libraries for RNA sequencing were prepared by the Genomics and Proteomics Core Facility of the German Cancer Research Center using the Illumina TruSeq Stranded RNA kit.

treatment_protocol: T24 and UM-UC-3 cells were cultured until reaching a confluency of approximately 80%. The cells were then treated for 48h with DMSO or 50 µM of the METTL3 inhibitor STM2457.

value: Bladder

value: Urothelial carcinoma cell

value: METTL3 knockout


title: UMUC3_Ctrl2

description:
Library name: UMUC3_Ctrl2
APA_sites_UMUC3_KO.txt

value: Control


title: mouse_neuron_N_neg_18m;N702_i7_11_N504_i5_8


title: UMUC3_Ctrl3

description:
Library name: UMUC3_Ctrl3
APA_sites_UMUC3_KO.txt


title: Multiome,colorectal tissue,normal_primary_P001,GEX

description:
Library name: NP001_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NP001.h5


title: mouse_neuron_N_neg_18m;N702_i7_11_N504_i5_5


title: 2016_05_11_17_13_03_144

city: Singapore

first: Wenjing

last: Wang

address: Tahir Foundation Building, MD1 12 Science Drive 2; #13-05; Singapore 117549

country: Singapore

institute: National University of Singapore

description: Library name: RHP3447

data_processing:
Raw sequencing data were processed through a standard RNA-seq analysis pipeline. First, fastp was used for quality control and adapter trimming of raw reads. Quality of sequencing data was assessed using MultiQC. The filtered reads were then aligned to the human reference genome hg38 using STAR aligner. Finally, gene expression quantification was performed using featureCounts to obtain read counts for each gene.
Assembly: hg38
Supplementary files format and content: The file contains raw gene or exon counts generated by featureCounts. Each row represents a gene or exon, and each column (starting from the second column) represents a sample.

extract_protocol:
Total RNA was isolated from the snap frozen samples of skeletal muscle biopsies from the subject’s vastus lateralis using NucleoSpin kit. RNA-seq was done on these extracted RNA using HiSeq4000 (Illumina), sequencing up to 80 million bidirectional reads of up to 151 base pairs.
For library construction, replicate sequencing runs from the same sample were prepared in a single library to ensure technical consistency. This means multiple sequencing runs were performed on the same library preparation rather than creating independent libraries for technical replicates.

value: Skeletal muscle


title: 2016_05_11_17_44_41_567

description: Library name: RHP3448


title: UMUC3_Ctrl1

description:
Library name: UMUC3_Ctrl1
APA_sites_UMUC3_KO.txt


title: Multiome,colorectal tissue,normal_primary_P006,GEX

description:
Library name: NP006_snRNA
10x Genomics Chromium Next GEM Single Cell Multiome ATAC+Gene Expression (CG000338 Rev E)
NP006.h5


title: mouse_neuron_N_neg_18m;N702_i7_12_N504_i5_2


title: 2016_04_28_15_28_03_529

description: Library name: RHU092


title: T24_KO2

description:
Library name: T24_KO2
APA_sites_T24_KO.txt


title: mouse_neuron_N_neg_18m;N702_i7_11_N504_i5_7


title: UMUC3_KO1

description:
Library name: UMUC3_KO1
APA_sites_UMUC3_KO.txt


title: 2016_05_16_22_59_25_661

description: Library name: RHP3554


title: T24_KO1

description:
Library name: T24_KO1
APA_sites_T24_KO.txt


title: 2016_05_16_22_38_30_248

description: Library name: RHP3553


title: mouse_neuron_N_neg_18m;N702_i7_11_N504_i5_6


title: mouse_neuron_N_neg_18m;N702_i7_11_N504_i5_3


title: UMUC3_KO2

description:
Library name: UMUC3_KO2
APA_sites_UMUC3_KO.txt


title: mouse_neuron_N_neg_18m;N702_i7_12_N504_i5_1


title: mouse_neuron_N_neg_18m;N702_i7_11_N504_i5_1


title: mouse_neuron_N_neg_18m;N702_i7_11_N504_i5_2


title: mouse_neuron_N_neg_18m;N702_i7_11_N504_i5_4


title: T24_KO3

description:
Library name: T24_KO3
APA_sites_T24_KO.txt


title: 2016_05_16_14_42_52_112

description: Library name: RHP3460


title: T24_Ctrl3

description:
Library name: T24_Ctrl3
APA_sites_T24_KO.txt


title: 2016_05_11_18_58_22_611

description: Library name: RHP3459


title: T24_Ctrl2

description:
Library name: T24_Ctrl2
APA_sites_T24_KO.txt


title: 2016_04_28_15_33_18_189

description: Library name: RHU093


title: 2016_05_11_19_06_06_63/2016_05_16_15_10_17_312

description: Library name: RHP3458


title: mouse_neuron_N_neg_18m;N702_i7_10_N504_i5_8


title: mouse_neuron_N_neg_18m;N702_i7_10_N504_i5_7


title: 2016_05_16_14_30_39_597

description: Library name: RHP3457


title: 2016_04_28_17_09_38_128

description: Library name: RHU101


title: T24_Ctrl1

description:
Library name: T24_Ctrl1
APA_sites_T24_KO.txt


title: mouse_neuron_N_neg_18m;N702_i7_10_N504_i5_6


title: 2016_05_16_20_31_57_294

description: Library name: RHP3534


title: UMUC3_STM2457_3

description:
Library name: UMUC3_STM2457_3
APA_sites_UMUC3_inh.txt

value: Wildtype


title: 2016_05_16_20_19_12_887

description: Library name: RHP3533


title: 2016_05_18_13_48_18_324

description: Library name: RHP3476


title: UMUC3_STM2457_2

description:
Library name: UMUC3_STM2457_2
APA_sites_UMUC3_inh.txt


title: 2016_05_16_17_27_01_390

description: Library name: RHP3475


title: mouse_neuron_N_neg_18m;N702_i7_10_N504_i5_4


title: 2016_05_16_18_30_55_533

description: Library name: RHP3489


title: 2016_05_16_20_13_49_910

description: Library name: RHP3532


title: mouse_neuron_N_neg_18m;N702_i7_10_N504_i5_3


title: UMUC3_DMSO3

description:
Library name: UMUC3_DMSO3
APA_sites_UMUC3_inh.txt

value: DMSO


title: UMUC3_STM2457_1

description:
Library name: UMUC3_STM2457_1
APA_sites_UMUC3_inh.txt


title: mouse_neuron_N_neg_18m;N702_i7_10_N504_i5_2


title: 2016_05_16_20_10_57_451

description: Library name: RHP3531


title: 2016_05_16_16_22_56_461

description: Library name: RHP3468


title: 2016_05_16_18_44_07_999

description: Library name: RHP3490


title: UMUC3_DMSO2

description:
Library name: UMUC3_DMSO2
APA_sites_UMUC3_inh.txt


title: 2016_04_28_16_37_23_39

description: Library name: RHU100


title: 2016_05_16_16_04_45_787

description: Library name: RHP3467


title: 2016_05_16_20_03_57_457

description: Library name: RHP3502


title: 2016_05_16_20_39_12_196

description: Library name: RHP3536


title: cd8_tcells

description: Library name: cd8_tcells

data_processing:
Raw sequenced reads were demultiplexed using demuxbyname2.sh script from BBMap (version 38.50; https://www.osti.gov/biblio/1241166). Demultiplexed reads were processed with fastp package using default parameters to remove low-quality bases. The trimmed reads were aligned to the reference genome using bwa with default parameters. Reference sequences for mouse genome were downloaded from https://hgdownload.cse.ucsc.edu/goldenpath/mm9/bigZips/; reference sequence for human CD8+ T-cell were downloaded from: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRC h38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_an alysis_set.fna.gz. Uniquely mapped reads were filtered using samtools tools with MAPS>=10. PCR duplicates were called using Picard (2.23.0-Java-11) Mark Duplicates (https://broadinstitute.github.io/picard/). Methylation was called using a custom R script used in our previous project. 10bp at the start or end of reads were excluded for methylation calling. Snakemake pipeline file with detailed steps is provided in the code availability section.
Assembly: MM9 & GRCh38
Supplementary files format and content: bedgraph

source_name: CD8+ T cell

value: CD8+ T cell

value: TAPS