title: Mouse aorta, Tcells, gex, control

description: Library name: TCell_Control

data_processing:
Can be found in Methods Amrute et al, 2025
Assembly: GRCh38
Supplementary files format and content: .rds

source_name: mouse aorta

extract_protocol:
In Vivo BiTE Treatment Studies Animal studies were performed in compliance with guidelines set forth by the National Institutes of Health Office of Laboratory Animal Welfare and approved by the Washington University institutional animal care and use committee. Animals were housed in a controlled environment with a 12 h light–dark cycle, with free access to water and a standard chow diet.  All experimental mice were fed a high fat diet containing 21% fat by weight (42% kcal from fat) and 0.2% cholesterol (#TD.88137, Envigo Teklad) for 4, 16, or 20 weeks (For Apoe-/-) starting at 8 or 9 weeks of age. For all studies an isotype BiTE was used for the control group and an anti-FAP BiTE for the treatment group. Animals were injected intraperitoneally and dosed at 400 μg/kg. For the acute model animals were treated with BiTE once a week starting week 1 for a total of 4 injections. For chronic studies mice were treated once a week in the same manner starting at 12 weeks of HFD feeding.  Single cell RNA-seq in murine atherosclerosis The ascending aorta (from beginning of aorta up to aortic arch including first intercostal artery) were isolated and transferred to an enzymatic dissociation cocktail with 250 U ml-1 Collagenase IV (#C5138, Sigma Aldrich), 60 U ml-1 Hyaluronidase (#H3506), and 60 U ml-1 DNase I (#D4527, all purchased from Sigma Aldrich) in Dulbecco’s Modified Eagle Medium (DMEM) and slightly minced. After incubation at 37 °C for 60 min with agitation, the digestion reaction was quenched with 6 mL of HBB buffer (2% Fetal Bovine Serum (FBS) and 0.2% Bovine Serum Albumin (BSA) in Hank’s Balanced Salt Solution (HBSS)), then filtered through 70 μm filters. Samples were pelleted by centrifugation at 4 °C, 1,400 rpm for 5 min and the supernatant was discarded. Cells were resuspended in FACS buffer (2% FBS and 2mM Ethylenediaminetetraacetic acid (EDTA) in calcium/magnesium free PBS) and centrifugation was repeated in above conditions and supernatant aspirated. Cell pellet was resuspended in 100 µL FACS buffer with the addition of 1 µL of DRAQ5 (#564907, Thermo Fisher Scientific) and incubated on ice for 30 min. Solution was washed with FACS buffer three times following same centrifugation as above and then resuspended in 500 µL of FACS buffer and 1 µL DAPI (#564907, BD Biosciences,) and filtered into filter-top FACS tubes. First singlets were gated and subsequent DRAQ5+/DAPI- events were collected in 300 µL cell resuspension buffer (0.04% BSA in PBS) – collected cells were centrifuged as above and resuspended in collection buffer to a target concentration of 1,000 cells µL-1. Cells were counted on a hemocytometer before proceeding with the 10x protocol. Collected cells were processed using the single Cell 3’ Kit v 3.1 (#1000268, 10x Genomics). 10,000 cells were loaded onto ChipG (#1000121) for GEM generation. Reverse transcription, barcoding, and complementary DNA amplification of the RNA was performed as recommended in the 3’ v3.1 chromium protocol. Libraries were sequenced on a NovaSeq 6000.  Isolation of T-cells for scRNA-seq and TCR-seq in murine atherosclerosis The ascending aorta (from beginning of aorta up to aortic arch including first intercostal artery) were isolated and transferred to an enzymatic dissociation cocktail with 2 U ml-1 Liberase (#5401127001, Sigma Aldrich), and 2 U ml-1 Elastase (#LS002279, Worthington) in DMEM and slightly minced. After incubation at 37 °C for 45 min with agitation, the digestion reaction was quenched with 6 mL of HBB buffer, then filtered through 70 μm filters. Samples were pelleted by centrifugation at 4 °C, 1,400 rpm for 5 min and the supernatant was discarded. Cells were resuspended in FACS buffer and centrifugation was repeated in above conditions and supernatant aspirated. Cell pellet was resuspended in 100 µL FACS buffer with the addition of 1 µL of CD45, CD11b, and CD3 and incubated on ice for 30 min. Solution was washed with FACS buffer three times following same centrifugation as above and then resuspended in 500 µL of FACS buffer and filtered into filter-top FACS tubes. First singlets were gated and subsequent CD45+/CD11b-/CD3+ events were collected in 300 µL cell resuspension buffer (0.04% BSA in PBS) – collected cells were centrifuged as above and resuspended in collection buffer to a target concentration of 1,000 cells µL-1. Cells were counted on a hemocytometer before proceeding with the 10x protocol. Collected cells were processed using the single Cell 5’ Kit v 2 (#1000244, 10x Genomics). 10,000 cells were loaded onto ChipK (#2000182) for GEM generation. Reverse transcription, barcoding, and complementary DNA amplification of the RNA were performed as recommended in the 5’ v2 chromium protocol. V(D)J amplification and library construction was performed per protocol (#1000252, 10x Genomics). Libraries were sequenced on a NovaSeq 6000.
For scRNA-seq: Collected cells were processed using the single Cell 3’ Kit v 3.1 (#1000268, 10x Genomics). 10,000 cells were loaded onto ChipG (#1000121) for GEM generation. Reverse transcription, barcoding, and complementary DNA amplification of the RNA was performed as recommended in the 3’ v3.1 chromium protocol. Libraries were sequenced on a NovaSeq 6000.  For TCR: Collected cells were processed using the single Cell 5’ Kit v 2 (#1000244, 10x Genomics). 10,000 cells were loaded onto ChipK (#2000182) for GEM generation. Reverse transcription, barcoding, and complementary DNA amplification of the RNA were performed as recommended in the 5’ v2 chromium protocol. V(D)J amplification and library construction was performed per protocol (#1000252, 10x Genomics). Libraries were sequenced on a NovaSeq 6000.

value: mouse aorta


title: NSCG_BPI

status: Public on Feb 02 2026

type: SRA

city: Leuven

first: Gabriele

last: Bergers

address: Herestraat 49

country: Belgium

institute: KU Leuven

description:
Library name: scrCCB130
10X Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was processed using CellRanger (version 7.0.1) and aligned to the mouse reference genome mm10-2020-A.
Assembly: mm10-2020-A
Supplementary files format and content: Gene expression count matrices in 10X Genomics format: For each sample, three tab-delimited compressed files are provided: (1) *_barcodes.tsv.gz contains cell barcodes (one per line), (2) *_features.tsv.gz contains gene identifiers and symbols (tab-separated: gene_id, gene_symbol, feature_type), and (3) *_matrix.mtx.gz contains the sparse count matrix in Matrix Market format with rows corresponding to genes and columns to cell barcodes.

molecule: polyA RNA

organism: Mus musculus

source_name: Mouse brain tumor

growth_protocol: Mice were maintained in individually ventilated cages in a room with controlled temperature and humidity under a 12-h light/12-h dark cycle with ad libitum access to water and food. 7-10 week old C57BL/6 mice were used for experiments.

extract_protocol:
Tumors were excised, mechanically minced, and incubated with serum-free RPMI containing 3 U/mL Collagenase I (Worthington Biochemical), 133 U/mL Collagenase IV (Worthington Biochemical), and 10 U/mL DNAse I (Worthington Biochemical) and rotated at 37 C for 30 min. Enzymatic digestion was blocked by adding RPMI-1640 containing 2mM EDTA and 2% FBS. The remaining tumor aggregates were dissociated mechanically. The single cell suspension was then passed through a 70mm strainer and red blood cells were lysed by incubation with 3 mL of ACK Lysis Buffer (15 mM NH4Cl, 10 mM KHCO3, 0.1 mM Na2EDTA) for 3 min at RT.
Single cell suspensions were converted to barcoded scRNA-seq libraries using the Chromium Single Cell 3' Library, Gel Bead & Multiplex Kit, and Chip Kit (10x Genomics), aiming for 6,000 cells per library. Samples were processed using kits pertaining to V2 barcoding chemistry of 10x Genomics. Single samples were processed in a single well of a PCR plate, and all samples were processed in parallel in the same thermal cycler.

treatment_protocol: BP treatment: Tumor-bearing mice were treated with 5 mg/kg B20 + 10 mg/kg anti-PD-L1 (BP) or 10mg/kg IgG2b isotype control (IgG) in PBS every three days by intraperitoneal (i.p.) injection beginning 6-7 days after tumor implantation. BPI treatment: Tumor-bearing mice were treated with 5 mg/kg B20 + 10 mg/kg anti-PD-L1 + 10mg/kg IPI-145 (BPI) or 10mg/kg IgG2b isotype control + oral gavage diluent control (IgG). BP were injected i.p. every three days while IPI-145 was given every day via oral gavage. CD40 agonist treatment: Tumor-bearing mice were treated with 100ug/dose of anti-CD40 agonist every five days for in total two doses, with or without DC vaccine therapy.

tag: tissue

value: Mouse brain tumor

tag: cell line

value: NSCG-mCherry (EGFRvIII+ - Arf/Ink4a-/-)

tag: cell type

value: whole tumor

tag: genotype

value: WT

tag: treatment

value: B20 (anti-VEGF) + anti-PD-L1 + IPI-145


title: NSCG_BP_2

description:
Library name: scrCCB129
10X Genomics

value: B20 (anti-VEGF) + anti-PD-L1


title: FMO30-TE14-DMSO-KinA66

city: Brussels

first: Xavier

last: Bisteau

address: Route de Lennik 808

institute: Université Libre de Bruxelles

description: Library name: Sample 30

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality bases using "Trimmomatic v.0.36".
Clean paired sequences were aligned to the human reference genome GRCh38 using “STAR” software v.2.5.3.
The number of reads per gene were obtained using "HTSeq" v.0.9.1.
Raw counts were normalized to obtain counts per 20 millions of reads (CP20M) that were used for differential expression analysis with DESeq2.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file containing matrix of counts normalized to 20 millions of reads for all genes in all samples.

molecule: total RNA

organism: Homo sapiens

source_name: Esophagus

growth_protocol: Cells were cultured in RPMI-1640 medium supplemented with 10% FBS,  sodium pyruvate (1mM) and antibiotics. They were maintained at 37°C in an atmosphere of 5% CO2.

extract_protocol:
Total RNA was isolated using  the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol. RNA quality was checked using a Fragment Analyzer 5200.
cDNA libraries were prepared from 100 ng of total RNA using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New Englands Biolabs) following manufacturer's recommendations.

treatment_protocol: Cells were maintained for 6 days in the presence of 0,1 % DMSO or 1uM of Palbociclib

value: Esophagus

value: eSCC

value: 0,1 % DMSO


title: NSCG_IgG_1

description:
Library name: scrCCB128
10X Genomics

value: control


title: Mouse aorta, stroma, bite

city: St Louis

first: Junedh

last: Amrute

state: MO

address: 660 S Euclid Ave

country: USA

institute: Washington University School of Medicine

description: Library name: FAP_SMC


title: TF_D7_WT_L

city: Grand Forks

first: Kai

last: Guo

state: ND

address: 1301 N Columbia Rd Stop 9037

institute: University of North Dakota

description: Library name: D7_WT

data_processing:
Single-cell RNA-seq data were generated using a combinatorial indexing–based protocol and processed with split-pipe (v1.4.2). Raw sequencing reads were aligned to the Mus musculus GRCm39 reference genome using STAR (v2.7.11b), and gene–cell expression matrices were generated following barcode correction and filtering. Filtered count matrices were imported into R and analyzed using Seurat (v 5.0.2) . Cells with fewer than 200 detected genes and genes detected in fewer than three cells were excluded. Low-quality cells were further removed based on mitochondrial and ribosomal transcript content, library size, and gene complexity, retaining cells with 200-6,000 detected genes and <25% mitochondrial transcripts. Putative doublets were identified and removed on a per-sample basis using DoubletFinder (v 2.22.0) after standard preprocessing.
Assembly: mm10
Supplementary files format and content: barcode, features, matrixs files from split-pipe

source_name: Lung

extract_protocol:
Briefly, lungs were harvested from mock and influenza-infected WT and TFAM+/− mice (n=4 mice per group) and processed into single-cell suspensions. Viable cells were isolated and approximately 25k cells per sample were used for library preparation. Single-cell libraries were generated using Parse Biosciences split-pool combinatorial barcoding chemistry, which enables cell fixation, barcoding, and library construction through successive rounds of molecular indexing. Cell fixation, reverse transcription, barcoding, and library amplification were performed according to the Parse protocol. Barcoded libraries were pooled and sequenced on an Illumina platform to a depth of approximately 56,891 read per cell.
Cells were fixed and processed for sequencing using the Evercode WT single-cell whole-transcriptome kit (Parse Biosciences, Seattle WA) according to the manufacturer’s guidelines. Resulting nucleic acid sublibraries were evaluated for adequacy on an Agilent Bioanalyzer (RNA integrity number >8), pooled, and sequenced on an Illumina Novaseq 6000 sequencer using 100 base pair (bp) paired-end reads (Iowa Institute of Human Genetics, University of Iowa).

value: Lung


title: Mouse aorta, Tcells, vdj, bite

description: Library name: TCell_FAP-TCR

library_source: other

data_processing:
Can be found in Methods Amrute et al, 2025
Assembly: GRCh38
Supplementary files format and content: .rds
Library strategy: TCR-Seq

molecule: other


title: Mouse aorta, Tcells, vdj, control

description: Library name: TCell_Control-TCR


title: Mouse aorta, stroma, control

description: Library name: Control_SMC


title: FMO24-TE6-6D_PD-KinA66

description: Library name: Sample 24

value: palbociclib 1uM


title: NSCG_IgG_2

description:
Library name: scrCCB137
10X Genomics


title: FMO27-TE10-6D_PD-KinA60

description: Library name: Sample 27


title: Mouse aorta, Tcells, gex, bite

description: Library name: TCell_FAP


title: NSCG_CD40

description:
Library name: scrCCB136
10X Genomics

value: CD40 agonist


title: FMO26-TE10-DMSO-KinA66

description: Library name: Sample 26


title: NFpp10_BP_1

description:
Library name: scrCCB106
10X Genomics

value: NFpp10-GFP (shp53 - shNF1 - shPTEN)


title: FMO25-TE10-DMSO-KinA60

description: Library name: Sample 25


title: FMO21-TE6-DMSO-KinA60

description: Library name: Sample 21


title: NFpp10_CD40

description:
Library name: scrCCB111
10X Genomics


title: NFpp10_UT_1

description:
Library name: scrCCB005
10X Genomics


title: NFpp10_IgG

description:
Library name: scrCCB110
10X Genomics


title: NSCG_UT

description:
Library name: scrCCB001
10X Genomics


title: NFpp10_BP_2

description:
Library name: scrCCB108
10X Genomics


title: Naive_BM

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

description:
Library name: Naive_BM
10X Genomics

data_processing:
The raw reads were produced using the 10X genomics cellranger v3.1 pipeline. Samples were pooled using the cellranger aggr pipeline. The cellranger pipeline outputs containing gene-by-cell expression data were processed using the R package Seurat v5.0. Graphs were generated using plotting functions in the Seurat and scCustomize v3.01 packages. Data quality control measures were implemented using Seurat, and only cells with at least 200 genes and less than 20% of mitochondria gene content were retained for further analysis. Normalization, scaling, dimension reduction, integration, and clustering were carried out using Seurat.
Assembly: mm10
Supplementary files format and content: tab-seprated value and matrix files

source_name: Bone marrow

extract_protocol:
Live cells were enriched using the EasySep Dead Cell Removal kit (Stemcell Technologies). Equal numbers of cells from three individual mice under each condition were mixed and the pooled samples were used for downstream sequencing. Bone marrow cells were stained with anti-CD11b and anti-Ly6C antibodies and sorted for CD11b+Ly6Chi monocytes by Bigfoot Spectral Cell Sorter. The purity of sorted monocytes was greater than 98%.
scRNA-seq libraries were generated using 10X 3’ single cell mRNAseq V3 reagents and sequenced using an Illumina NovaSeq 6000 sequencer.

treatment_protocol: Cyclophosphamide (CTX) was dissolved in PBS and was intraperitoneally injected to mice at 150 mg/kg. Bone marrows were collected from cyclophosphamide-treated mice on day 2 (CTX_D2) and on day 7 (CTX_D7). Bone marrows from untreated mice were used as the control (naïve).

value: Bone marrow

value: BM mononuclear cells

value: Naïve


title: FMO23-TE6-6D_PD-KinA60

description: Library name: Sample 23


title: FMO22-TE6-DMSO-KinA66

description: Library name: Sample 22


title: Naive_BM_sorted

description:
Library name: Naive_BM_sorted
10X Genomics

value: Monocytes


title: NFpp10_UT_2

description:
Library name: scrCCB107
10X Genomics

value: Mouse brain tumor


title: CTX_BM_sorted

description:
Library name: CTX_BM_sorted
10X Genomics

value: Cyclophosphamide


title: NSCG_BP_1

description:
Library name: scrCCB086
10X Genomics

value: NSCG-mCherry (EGFRvIII+ - Arf/Ink4a-/-)

value: whole tumor

value: WT


title: D7_CTX_BM

description:
Library name: D7_CTX_BM
10X Genomics


title: D2_CTX_BM

description:
Library name: D2_CTX_BM
10X Genomics


title: Naive_BM_sorted_3

description: Library name: Naive_BM_sorted_3

library_source: genomic

data_processing:
The ATACseq analysis was performed on Galaxy server. Adaptor and quality trimming were performed using Trim Glore! Modules (Galaxy v0.4.3.1). Trimmed reads were mapped to mouse genome mm10 using Bowtie2 (Galaxy v2.3.4.3) using default settings. Reads mapped to the mitochondria genome were removed using Filter SAM or BAM function under the samtools module (Galaxy v1.8), and PCR duplicates were removed using MarkDuplicates from Picard tool v2.20.2. The mapped reads overlapping with ENCODE blacklist regions (version 2) were filtered before calling peaks.
ATAC-seq peak calling was performed on Galaxy server using MACS2 v2.1.2 with following command “-q 0.05 --nomodel --shift --100 --extsize 200 -B --SPMR --keep-dup all --call -summits”.
Assembly: mm10
Supplementary files format and content: BigWig

molecule: genomic DNA

extract_protocol:
Live cells were enriched using the EasySep Dead Cell Removal kit (Stemcell Technologies). Equal numbers of cells from three individual mice under each condition were mixed and the pooled samples were used for downstream sequencing. Bone marrow cells were stained with anti-CD11b and anti-Ly6C antibodies and sorted for CD11b+Ly6Chi monocytes by Bigfoot Spectral Cell Sorter. The purity of sorted monocytes was greater than 98%.
For each sample, 50,000 nuclei prepared from FACS-sorted CD11b+Ly6Chi were incubated with 2.5 mL Nextera Tn5 transposase (Illumina) in 50mL 1X transposition reaction mixture in a thermocycler at 37 °C for 1hr. The transposition reaction mixtures were purified with a DNA Clean and Concentrator kit (Zymo Research), and amplified for 11-13 cycles using NEBNext High-Fidelity 2X Master Mix (New England Biolabs) and Nextera Index primers (Illumina). The amplified libraries were size-selected by two rounds of AMPure beads purification (0.5X and 1.2X).

treatment_protocol: Cyclophosphamide (CTX) was dissolved in PBS and was intraperitoneally injected to mice at 150 mg/kg. Bone marrows were collected from cyclophosphamide-treated mice on day 7. Bone marrows from untreated mice were used as the control (naïve).


title: FMO19-TE1-6D_PD-KinA60

description: Library name: Sample 19

value: Esophagus


title: Old_Skin_Dox_288

city: Baltimore

first: Andrew

middle: Paul

last: Feinberg

state: Maryland

address: 855 N. Wolfe Street

department: Center for Epigenetics

institute: Johns Hopkins University

data_processing:
base calls and demultiplexing: bcl2fastq v1.8.4
Trim Galore! v0.3.6
Bismark v0.12.3
InformME
Assembly: mm10
Supplementary files format and content: bigWig format.  Tracks include mean methylation level (MML), normalized methylation entropy (NME) and Jensen Shannon Distance (JSD) to measure epigenetic discordance between samples.

source_name: skin

extract_protocol:
Epicentre DNA extraction kit
Illumina TruSeq, NEBNext

treatment_protocol: Both treated and treated mice included in the study carry one copy of an OSKM polycistronic casette and a reverse tetracycline transactivator (4F mice). Treated mice were subjected to a cyclic partial reprogramming protocol. Induction of OSKM was performed by administering doxycilcine (1mg/ml) in drinking water for 2 days followed by 5 days withdrawal per week. Such treatment was performed during 7 months, starting at 15 months until 22 months of age.

value: skin

tag: strain

value: 7 months of cyclic partial reprogramming via doxycicline treatment starting at 15 months until 22 months of age

tag: age at_time_of_sample_collection

value: 22 months


title: Old_Skin_Dox_904


title: Old_Skin_Dox_253


title: Old_Skin_Dox_284


title: Old_Skin_Dox_285


title: FMO18-TE1-DMSO-KinA66

description: Library name: Sample 18

value: eSCC

value: 0,1 % DMSO


title: Naive_BM_sorted_1

description: Library name: Naive_BM_sorted_1


title: Old_Skin_Control_5764

value: untreated


title: FMO20-TE1-6D_PD-KinA66

description: Library name: Sample 20

value: palbociclib 1uM


title: Young_Skin_Control_4

value: 3 months


title: Old_Skin_Control_5762


title: FMO17-TE1-DMSO-KinA60

description: Library name: Sample 17


title: Young_Skin_Control_1


title: CTX_BM_sorted_3

description: Library name: CTX_BM_sorted_3

value: Bone marrow


title: Old_Skin_Control_5760


title: Old_Skin_Control_5761


title: FMO16-COLO680N-6D_PD-KinA77

description: Library name: Sample 16


title: Naive_BM_sorted_2

description: Library name: Naive_BM_sorted_2

value: Naïve


title: Young_Skin_Control_3


title: KO-HDM biol rep 3

city: Thousand Oaks

first: Jonathan

last: Phillips

state: CA

address: 1 Amgen center drive

institute: Amgen

data_processing:
The reads were first mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0 and the gene expression level was estimated using RSEM v1.2.15.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: lung

extract_protocol:
Lungs were snap frozen in liquid nitrogen and homogenized before RNA extraction and rRNA depletion. Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

value: lung

tag: Sex

value: female

value: ALOX15 KO

value: House Dust Mite


title: FMO13-COLO680N-DMSO-KinA76

description: Library name: Sample 13


title: FMO15-COLO680N-6D_PD-KinA76

description: Library name: Sample 15


title: CTX_BM_sorted_1

description: Library name: CTX_BM_sorted_1

value: Monocytes

value: Cyclophosphamide


title: KO-HDM biol rep 4


title: KO-HDM biol rep 5


title: KO-HDM biol rep 2


title: CTX_BM_sorted_2

description: Library name: CTX_BM_sorted_2


title: KO-HDM biol rep 1


title: FMO11-KYSE-510-6D_PD-KinA76

description: Library name: Sample 11

value: Esophagus


title: KO-PBS biol rep 2

value: Saline


title: FMO14-COLO680N-DMSO-KinA77

description: Library name: Sample 14


title: FMO12-KYSE-510-6D_PD-KinA77

description: Library name: Sample 12


title: FMO9-KYSE-510-DMSO-KinA76

description: Library name: Sample 9


title: Mouse neonatal cardiomyocytes, Knockdown of piRNA FERPIR (DQ69304) by antagomir

city: Qingdao

first: Kun

last: Wang

state: Shandong

address: 308 Ningxia Road

country: China

institute: Qingdao University

description: Library name: piRNA

data_processing:
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software.
The trimmed reads were aligned to reference genome with Hisat2 software.
The transcript abundances for each sample was estimated with StringTie (1.3.3).
Raw reads were normalized by calculated FPKM value using Ballgown (2.10.0).
Assembly: GRCm38
Supplementary files format and content: The csv format file contains the FPKM value of gene in every sample

source_name: heart

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE). rRNA were removed using NEBNext® Poly(A) mRNA Magnetic Isolation Module. RNA libraries were constructed using KAPA Stranded RNA-Seq Library Prep Kit and following standard protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample.
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification.

value: heart

value: cardiomyocyte

value: PBS


title: KO-PBS biol rep 4


title: FMO8-KYSE-270-6D_PD-KinA77

description: Library name: Sample 8

value: eSCC


title: WT-HDM biol rep 3

value: Wild Type


title: KO-PBS biol rep 3


title: Mouse neonatal cardiomyocytes, Negative control

description: Library name: Control


title: WT-HDM biol rep 5


title: KO-PBS biol rep 1


title: Heart, Spatial Transcriptomics, TAC 4 weeks

city: Shanghai

first: Hanwen

last: Ni

state: Shanghai

address: 197th, Ruijin 2nd rd.

department: Department of Cardiology

institute: Ruijin Hostpital, School of Medicine, Shanghai Jiao Tong University

description: Library name: TAC4w_ST

data_processing:
Single cell sequencing data processing The raw reads were mapped to the mouse reference genome (refdata-gex-mm10-2020-A) using CellRanger count (v7.0.0) with default  parameters, the digital expression matrix was extracted from the “filtered_feature_bc_matrix” folder outputted by the CellRanger count pipeline.
Spatial transcriptomics data processing In this study, Space Ranger(v1.3.1)was used for data preprocessing, gene expression quantifcation and spot identifcation. The gene spot matrix was generated by using Visium spatial barcodes, and then spot clustering and gene expression analysis were performed.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: barcodes tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene lDs
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.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected tissue image.jpg.gz: 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 list.csv.gz. list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

growth_protocol: Eight-week-old male C57BL/6J mice weighing 25–27 g were used in this study. Animals were maintained under specific pathogen-free (SPF) conditions in a temperature- and humidity-controlled facility, with a 12 h light/dark cycle and free access to standard chow and water. Prior to surgery, mice were anesthetized with isoflurane (2% isoflurane at 0.41 mL/min mixed with air at 4 L/min). The thoracic area was depilated with depilatory cream for 2–3 minutes, and the residual cream was removed using a cotton swab dipped in warm water. The animals were placed on a heating pad in the supine position, and their body temperature was continuously monitored. Limbs were fixed with medical tape to minimize movement. The surgical site was disinfected three times with povidone-iodine solution before thoracic surgery was performed.

extract_protocol:
To isolate single nuclei from adult mouse hearts, tissues were dissected and placed in 2mL Hibernate A®/B27®/GlutaMAX™ (HEB) medium in a 5mL tube on ice.The HEB medium was removed to a 15mL conical and kept on ice. 2mL of chilled lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% Nonidet™ P40 Substitute in Nuclease-Free Water) were added to the tissue, and the tissues were homogenized 10 times through a tissue grinder.After homogenization, the tissue was lysed on ice for 15min, swirling 2–3 times during this incubation period. The reserved chilled HEB media was then returned to the lysed tissue solution, and the tissue was further triturated with 5–7 passes through a 1mL pipette. A 30µm cell strainer (MACS SmartStrainer; Miltenyi Biotech 130-110-915) was washed with 1mL of PBS, and the lysed tissue solution was filtered through the strainer to remove debris and clumps. Filtered nuclei were centrifuged at 500 rcf for 5min at 4°C. The supernatant was removed, and nuclei were washed in 1mL of Nuclei Wash and Resuspension Buffer (1X PBS with 1.0% BSA and 0.2U/µl RNase Inhibitor). Nuclei were manually counted by Trypan blue and AO-PI after each centrifugation (400g, 10 min, 4℃) and resuspended. Single nuclei were processed using Chromium Controller (10X Genomics) according to the manufacturer’s protocol.  The heart tissue samples from the TAC mouse model were collected and embedded in OCT. The samples were then sectioned into 10-20 μm thick slices. RNA was extracted from 10 of these sections using a nucleic acid kit, and the quality of the prepared samples was assessed. Sections that passed the RNA quality inspection were then permeabilized and subjected to a capture labeling experiment.
Library preparation for snRNA-seq: The prepared single nuclei suspension was loaded on the Chromium Controller (10X Genomics). We prepared 3' gene expression libraries using Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer’s protocol. The libraries were sequenced on an Illumina NovaSeq 6000 system.  The libraries were prepared by Visium Spatial Gene Expression Reagent Kits (PN-1000184, 10x Genomics) according to the manufacturer’s protocol. Libraries were loaded at 300 pM and sequenced on a NovaSeq 6000 System (Illumina, San Diego, CA, USA) . Sequencing was performed using the following read protocol (read 1, 28 cycles; i7 index read, 10 cycles; i5 index read, 10 cycles; read 2, 90 cycles) and analyzed at Shanghai Biochip Co., Ltd., Shanghai, China.

treatment_protocol: Mice underwent transverse aortic constriction (TAC) surgery to induce pressure overload. Following anesthesia with isoflurane (2% isoflurane at 0.41 mL/min mixed with air at 4 L/min), the thoracic area was prepared as described above. A midline cervical incision was made, and the sternum was cut to the level of the second rib to expose the aortic arch and carotid artery. A 6-0 silk suture was passed under the aortic arch using a curved needle, and the ligature was tied firmly around a blunted needle or pad placed adjacent to the aorta to achieve a defined constriction. The pad was then gently removed, leaving a reproducible stenosis. The chest wall and skin were closed with 6-0 silk sutures. Sham-operated mice underwent the identical procedure without ligation of the aorta.

value: cardiac tissue sections

value: male

value: wild type

value: transverse aortic constriction (TAC)

tag: batch

value: batch 2


title: KO-PBS biol rep 5

value: lung

value: female


title: FMO7-KYSE-270-6D_PD-KinA76

description: Library name: Sample 7

value: palbociclib 1uM


title: FMO6-KYSE-270-DMSO-KinA77

description: Library name: Sample 6

value: 0,1 % DMSO


title: FMO10-KYSE-510-DMSO-KinA77

description: Library name: Sample 10


title: Heart, Spatial Transcriptomics, Sham

description: Library name: Sham_ST

value: sham surgery

value: batch 1


title: WT-HDM biol rep 4

value: House Dust Mite


title: WT-PBS biol rep 3

value: Saline


title: Heart, Spatial Transcriptomics, TAC 6 weeks

description: Library name: TAC6w_ST

value: heart

value: batch 3


title: WT-HDM biol rep 2


title: FMO5-KYSE-270-DMSO-KinA76

description: Library name: Sample 5

value: Esophagus

value: eSCC


title: Heart, scRNA-seq, Sham

description: Library name: Sham_scRNA

data_processing:
Single cell sequencing data processing The raw reads were mapped to the mouse reference genome (refdata-gex-mm10-2020-A) using CellRanger count (v7.0.0) with default  parameters, the digital expression matrix was extracted from the “filtered_feature_bc_matrix” folder outputted by the CellRanger count pipeline.
Spatial transcriptomics data processing In this study, Space Ranger(v1.3.1)was used for data preprocessing, gene expression quantifcation and spot identifcation. The gene spot matrix was generated by using Visium spatial barcodes, and then spot clustering and gene expression analysis were performed.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: barcodes tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene lDs
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.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected tissue image.jpg.gz: 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 list.csv.gz. list of spatial barcodes and the coordinates specifying spots

value: cardiac cells (mixed cell populations)


title: Heart, scRNA-seq, TAC 6 weeks

description: Library name: TAC6w_scRNA

value: male


title: WT-HDM biol rep 1

value: Wild Type


title: FMO4-KYSE-180-6D_PD-KinA77

description: Library name: Sample 4


title: WT-PBS biol rep 5


title: OVA, aIL4Ra biol rep 3

value: Balb

value: Ovalbumin, Anti-mouse-IL-4Ra Antibody


title: OVA, aIL4Ra biol rep 4

value: lung


title: Heart, Spatial Transcriptomics, TAC 2 weeks

description: Library name: TAC2w_ST

value: cardiac tissue sections

value: wild type

value: transverse aortic constriction (TAC)


title: WT-PBS biol rep 2

value: female


title: WT-PBS biol rep 1


title: WT-PBS biol rep 4


title: OVA, aIL4Ra biol rep 1


title: FMO1-KYSE-180-DMSO-KinA76

description: Library name: Sample 1

value: 0,1 % DMSO


title: MC38_CLK1_inhibitor_1

city: Guangzhou

first: Peisi

last: Li

state: China

address: Yuancunerheng Road

institute: Department of Colorectal Surgery, The Sixth Affiliated Hospital of Sun Yat-sen University

description:
Library name: Sample3
Colume name in gene_fpkm_matrix.csv: CLK1_inhibitor_1

data_processing:
The resulting cDNA library was sequenced using Illumina Novaseq6000(Repugene Technology, Hangzhou, China).
Bioinformatics analysis
reference genome using HISAT2. 2.2.1 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v2.2.1 in a reference-based approach.
RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed genes/transcripts.
Assembly: HISAT2. 2.2.1
Supplementary files format and content: raw courts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: MC38 cells were cultured in high-glucose Dulbecco’s Modified Eagle Medium (DMEM). All media were supplemented with 10% fetal bovine serum (FBS) and 1%penicillin/streptomycin.All cell lines were regularly tested and confirmed to be mycoplasma-free using PCR-based methods.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.

treatment_protocol: MC38 cells were treated with or without CLK1 inhibitor for two days.

value: cancer cell

value: WT

value: with CLK1 inhibitor


title: FMO3-KYSE-180-6D_PD-KinA76

description: Library name: Sample 3

value: palbociclib 1uM


title: Heart, scRNA-seq, TAC 4 weeks

description: Library name: TAC4w_scRNA

value: heart

value: batch 2


title: FMO2-KYSE-180-DMSO-KinA77

description: Library name: Sample 2

value: Esophagus

value: eSCC


title: OVA, aIL4Ra biol rep 2

value: Wild Type


title: MC38_CLK1_inhibitor_2

description:
Library name: Sample4
Colume name in gene_fpkm_matrix.csv: CLK1_inhibitor_2


title: OVA, aIL4Ra biol rep 5

value: Balb


title: Saline, Isotype biol rep 5

value: Saline, Isotype Control Antibody


title: OVA, Isotype biol rep 3

value: lung

value: Ovalbumin, Isotype Control Antibody


title: OVA, Isotype biol rep 2


title: OVA, Isotype biol rep 5


title: OVA, Isotype biol rep 4


title: MC38_Vehicle_1

description:
Library name: Sample1
Colume name in gene_fpkm_matrix.csv: Vehicle_1

value: without CLK1 inhibitor


title: OVA, Isotype biol rep 1


title: ChIP-seq, iPS cells, Input, RETT, s3084, Rep2

city: Tokyo

first: Yutaka

last: Saito

department: Artificial Intelligence Research Center (AIRC)

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: Library name: iPS ChIPseq Input s3084 biol rep 2

data_processing:
Raw ChIP-seq reads were aligned to Hg38 reference genome, or GRCh38 (GRCh38 Genome Reference Consortium Human Reference 38) from UCSC (without alternative contigs) using Bowtie2.
CTCF and H3K27ac peaks were called using MACS (version 3.0.0a7) using the following parameters: callpeak -g hs -f BAMPE. Input samples were used as the background.
Differential peak analysis was performed using DiffBind R package to identify differentially changed peaks (log2(fold change)>1 or <-1 and FDR < 0.05).
Assembly: hg38
Supplementary files format and content: the narrowpeak formatted file contains peaks obtained from MACS

source_name: iPS

growth_protocol: Healthy individuals hiPSCs (HPS0076, WT) and Rett syndrome disease-specific hiPSCs (HPS3042, HPS3049, HPS3084) were obtained from the RIKEN BRC through the National BioResource Project of the MEXT, Japan, and cultured under feeder-free conditions using mTeSR™ Plus medium (VERITAS, #ST-100-0276) on tissue culture-treated plates coated with hESC-qualified Matrigel® (Corning, #354277), according to the manufacturer's instructions. Cells were maintained at 37°C in a humidified incubator with 5% CO₂ and passaged every 5–7 days using Versene Solution (Gibco, # 15040066). The medium was changed daily. For ChIP-seq, those iPS cells cultured in 10 cm dishes coated with Matrigel were used.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed according to a protocol published by Agilent technologies (Santa Clara, CA, http://www.agilent.com). Briefly, iPS cells were fixed by 1% formaldehyde solution for 10 min. After harvesting the fixed cells, the cells were lysed in lysis buffer, and sonicated using Misonix XL2020 sonicator (MISONIX Inc., NY, http://misonix.com) until the DNA fragments were 200–600 base pairs in length. 3.0% of the total volume was stored as input at −20°C, until use. Immunoprecipitation was performed at 4°C, overnight with antibodies described bellow. DNA/beads was washed with a low salt buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 2 mM EDTA, 0.1% sodium dodecyl sulfate (SDS), 1% Triton X-100) once, and then further washed with a high-salt buffer (20 mM Tris-HCl pH 7.4, 400 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) once before washing with a RIPA buffer. Immune complexes were disrupted with direct elution buffer (50 mM Tris-HCl pH8.0, 10 mM EDTA, 1% SDS) and the covalent links between immunoprecipitates and input chromatin were disrupted by incubation at 65°C for overnight. DNA was further incubated with RNaseA and proteinase K (Nacalai Tesque), purified by phenol extraction, and ethanol precipitated. DNA pellets were dissolved in Tris-EDTA (TE) buffer (10 mM Tris-HCl, 1 mM EDTA pH8.0). The antibodies were used anti-CTCF(3418S, Cell Signaling Technology) and Acetyl-Histone H3 (Lys27) (H3K27ac, 8173S, Cell Signaling Technology)
A sequencing library was prepared using the NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB) according to the manufacturer's instructions.

tag: disease state

value: RETT

value: iPS

value: human induced pluripotent stem (iPS) cells

tag: chip antibody


title: Saline, Isotype biol rep 3

value: female


title: Heart, scRNA-seq, TAC 2 weeks

description: Library name: TAC2w_scRNA

value: cardiac cells (mixed cell populations)

value: male

value: wild type

value: transverse aortic constriction (TAC)

value: batch 1


title: Saline, Isotype biol rep 2


title: MC38_Vehicle_2

description:
Library name: Sample2
Colume name in gene_fpkm_matrix.csv: Vehicle_2

value: cancer cell

value: WT


title: MeHg_2

city: Ottawa

first: Jing

state: Ontario

address: 501 smyth road

country: Canada

institute: University of Ottawa

description: Library name: MeHg_2

data_processing:
DESeq2 was used for differential gene expression analysis (Love et al. 2014). Differentially expressed genes (DEGs) generated via the NovoMagic platform were then filtered and analyzed using the R programming language in RStudio (v.4.3.0).
Assembly: mm39
Supplementary files format and content: gene_count.txt
Supplementary files format and content: gene_fpkm_group.txt

source_name: Cerebellum

extract_protocol:
Frozen brain tissue samples were each suspended in 1 mL of TRIzol (cat#15596026, Thermo Fisher) reagent and were added directly to a microcentrifuge tube. The tissue was homogenized using a tissue homogenizer and incubated for 5 minutes at room temperature. 200 μL of chloroform (cat#C2432-1L, Sigma-Aldrich) was added to the mixture, which was then vortexed for 15 seconds to ensure thorough mixing. The samples were incubated at room temperature for 2-3 minutes and then centrifuged at 12,000 x g for 15 minutes at 4°C. The aqueous phase was carefully transferred to a new RNAse-free tube, and an equal volume of 70% ethanol was added. Washes were performed using the PureLink RNA Mini Kit (cat# 12183020, Thermo Fisher). The extracted RNA was stored at -80°C for long-term preservation. The quantity and purity of the extracted RNA were assessed using a spectrophotometer.
RNA samples from biological triplicates (both female and male mice) were isolated as previously described and sent to Sacramento, California, for RNA-Seq analysis at Novogene Bioinformation Technology Co., Ltd. (Sacramento, USA). Sequencing was performed using the Illumina NovaSeq platform with paired-end 150 base pair reads (PE150) and reference genome mm39.

treatment_protocol: Pregnant C57BL/6 mice were dosed with 0 ppm or 0.2 ppm MeHg via drinking water starting from the first day of their pregnancy (E0) until birth (P0). The 0.2 ppm MeHg solution was prepared by a 1:5000 dilution of a stock solution of 4mM MeHg(II)Cl (cat#33553, Alfa Aesar) in drinking water. At sacrifice, the brains were dissected, and the cerebellum was isolated and immediately frozen with liquid nitrogen and stored at -80°C for analysis.

tag: biological replicate

value: biol rep 2

value: Cerebellum

value: Male

tag: developmental stage

value: 0.2ppm MeHg


title: Saline, Isotype biol rep 1

value: lung

value: Balb

value: Wild Type

value: Saline, Isotype Control Antibody


title: ChIP-seq, iPS cells, Input, RETT, s3049, Rep1

description: Library name: iPS ChIPseq Input s3049 biol rep 1

value: RETT

value: iPS

value: human induced pluripotent stem (iPS) cells


title: ChIP-seq, iPS cells, Input, RETT, s3084, Rep1

description: Library name: iPS ChIPseq Input s3084 biol rep 1


title: ChIP-seq, iPS cells, Input, RETT, s3042, Rep2

description: Library name: iPS ChIPseq Input s3042 biol rep 2


title: MeHg_3

description: Library name: MeHg_3

value: biol rep 3

value: Female


title: LBD brain 5 with APOE3/3 and SNCA triplication

city: Rochester

first: Alexander

middle: Quinn

last: Wixom

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

description:
Library name: LBD3
FFPE Spatial transcriptomics

data_processing:
Raw sequencing data were processed using the 10x Genomics Space  Range pipeline to generate FASTQ files.
Sequences were aligned to hg38 genome to quantify gene expression counts using Space Rangers default settings
Gene expression level of refseq coding genes were quantified using Space Ranger's default settings
Assembly: hg38
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 expression 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: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Postmortem temporal cortex

extract_protocol:
FFPE-embedded tissues were sectioned at 5um for H&E staining and library construction.
Spatial transcriptomic sequencing libraries were prepared with 10xGenomics Visium Spatail Gene Expression Slides & Reagent kit according to manufacturer's construction.

value: Postmortem temporal cortex

tag: sample group

value: LBD brain with APOE3/3 and SNCA triplication


title: Saline, Isotype biol rep 4

value: female


title: ChIP-seq, iPS cells, Input, RETT, s3049, Rep2

description: Library name: iPS ChIPseq Input s3049 biol rep 2


title: LBD brain 6 with APOE3/4 and SNCA triplication

description:
Library name: LBD4
FFPE Spatial transcriptomics

value: LBD brain with APOE3/4 and SNCA triplication


title: Control_3

description: Library name: Control_3

value: Control


title: MeHg_1

description: Library name: MeHg_1

value: biol rep 1

value: Cerebellum


title: LBD brain 4 with APOE3/4

description:
Library name: LBD12
FFPE Spatial transcriptomics

value: LBD brain with APOE3/4


title: ChIP-seq, iPS cells, Input, Healthy, Rep2

description: Library name: iPS ChIPseq Input WT biol rep 2

value: Healthy


title: ChIP-seq, iPS cells, Input, RETT, s3042, Rep1

description: Library name: iPS ChIPseq Input s3042 biol rep 1


title: LBD brain 2 with APOE3/3

description:
Library name: LBD8
FFPE Spatial transcriptomics

value: LBD brain with APOE3/3


title: LBD brain 3 with APOE3/4

description:
Library name: LBD11
FFPE Spatial transcriptomics


title: Control_2

description: Library name: Control_2

value: biol rep 2


title: LBD brain 1 with APOE3/3

description:
Library name: LBD6
FFPE Spatial transcriptomics


title: Control_1

description: Library name: Control_1


title: Control brain 2 with APOE3/3

description:
Library name: LBD7
FFPE Spatial transcriptomics

value: Control brain with APOE3/3


title: Control brain 4 with APOE3/4

description:
Library name: LBD9
FFPE Spatial transcriptomics

value: Control brain with APOE3/4


title: ChIP-seq, iPS cells, CTCF, RETT, s3084, Rep2

description: Library name: iPS ChIPseq CTCF s3084 biol rep 2

value: RETT

value: iPS

value: CTCF


title: HepG2-NTCP-A3-Vector-S10, HA, ChIP

city: Lethbridge

first: Trushar

last: Patel

state: Alberta

address: Science Commons

department: chemistry and Biochemistry

institute: university of lethbridge

data_processing:
Base calls were performed using  bcl2fastq 2.17 software
Paired-end reads were checked for quality using FastQC V0.11.9
Reads with quality <30 Phred score were removed using Trimmomatic 0.39
The reads were aligned with Hepatitis B virus genome (GenBank V01460.1) and human genome hg19 using Bowtie2 with no-discordant mode
The coverage plots were made using bedtools and visualized in Integrative Genomics Viewer (IGV) by shifting HBV genome for 500 nt.
Assembly: hg19 and Hepatitis B virus
Supplementary files format and content: bw

growth_protocol: Prior to infection with HBV: HepG2-NTCP-A3 cells containing either vector only, S1-HA, or S10-HA were cultured in DMEM supplemented with 10% FBS, 1mM Glutamax, 1mM pyruvate, 100IU/mL penicillin, 400µg/mL streptomycin, 2µg/mL puromycin, and 20µg/mL blasticidin at 37 degrees at 5% CO2. Following infection, 2.5% DMSO was added to the media described.

extract_protocol:
Cells were fixed with 0.6% formaldehyde, and quenched with 125mM glycine. Sonication was performed using the Bioruptor Plus (Diagenode) at high intensity 30s on and 90s off for 60 mins at 4 degrees.
Library preparation and sequencing was perfomed by Genewiz Inc/Azenta (Agilent Technologies, Palo Alto, CA, USA). Library preparation was performed using the NEB NextUltra DNA library preparation kit with 100ng of each immunoprecipitation. Briefly, the ChIP DNA was end-repaired and adapters were ligated after adenylation of the 3’ ends. Adapter-ligated DNA was size selected, followed by clean up, and limited cycle PCR enrichment. The ChIP library was validated using Agilent TapeStation and quantified using Qbit 2.0 Fluorometer and real-time PCR (Applied Biosystems, Carlsbad, CA, USA). The sequencing libraries were multiplexed and clustered on a flowcell. After clustering the flowcell was loaded on the Illumina HiSeq 4000 and sequencing was performed with 2 x 150 Paired End (PE) reads. Image analysis and base calling were conducted by the Control Software. Raw sequence data (.bcl files) generated from Illumina instrument was converted into fastq files and de-multiplexes using Illumina’s bcl2fastq 2.17 software.

treatment_protocol: HepG2-NTCP-A3 cells containing either vector only, S1-HA, or S10-HA were infected with HBV derived from HepAD38 cells at an MOI 500. The cells were incubated with the media described above with the addition of DMSO and 4% PEG-8000 for 18hrs. The cells were then washed 3 times with dPBS and maintained with the maintenence media containing 2.5% DMSO for 14 days post infection.

value: Human Hepatoma

value: NTCP-A3 clone

value: HepG2-NTCP-A3 cells were transduced with lentiviruses produced in HEK293T cells transfected with pWPI-blasti contianing S10-HA sequence, pSPAX, and PMDG.2


title: HFD3

city: Nanjing

first: Xinwei

state: -- None selected --

institute: China Pharmaceutical university

description: Library name: sample6

data_processing:
The raw read data was processed using fastp (v0.23.0, https://github.com/OpenGene/fastp) to remove low-quality reads and retain reads with lengths between 18-36 base pairs (--length_required 18-36bp). The reference genome and gene model annotation files (Mus musculus, Ensembl GRCm38) were then downloaded directly from the genome website. Clean data was mapped to the reference genome using hisat2 (v2.2.1, http://daehwankimlab.github.io/hisat2/). Annotation was performed using species-specific miRNA databases. miRNA expression was quantified using custom scripts, and RPM values were calculated.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: csv files include RPM values for each sample

source_name: islet

extract_protocol:
Total RNA from exosomes were extracted using the miRNeasy Mini Kit (Qiagen, 217004).  miRNA library construction was used Small RNA Library Prep Kit according to manufacturer's instruction.
The library was sequenced using the Illumina NovaSeq 6000 platform.

value: islet

value: exosomes

value: WT

value: HFD


title: Control brain 3 with APOE3/4

description:
Library name: LBD5
FFPE Spatial transcriptomics

value: Postmortem temporal cortex


title: Control brain 1 with APOE3/3

description:
Library name: LBD1
FFPE Spatial transcriptomics


title: HepG2-NTCP-A3-S1, HA, ChIP

value: HepG2-NTCP-A3 cells were transduced with lentiviruses produced in HEK293T cells transfected with pWPI-blasti contianing S1-HA sequence, pSPAX, and PMDG.2


title: ChIP-seq, iPS cells, Input, Healthy, Rep1

description: Library name: iPS ChIPseq Input WT biol rep 1

value: Healthy

value: human induced pluripotent stem (iPS) cells


title: HepG2-NTCP-A3-Vector-Control, Sp1, ChIP

value: HepG2-NTCP-A3 cells were transduced with lentiviruses produced in HEK293T cells transfected with pWPI-blasti, pSPAX, and PMDG.2


title: HepG2-NTCP-A3-Vector-Control, H3K27Ac ChIP


title: HFD1

description: Library name: sample4


title: HFD2

description: Library name: sample5


title: NCD3

description: Library name: sample3

value: NCD


title: HepG2-NTCP-A3-Vector-Control, HBcAg, ChIP


title: 60 mgt zebrafish larvae, Biol rep 3, plod3 KO

city: Nashville

first: Ela

last: Knapik

state: TN

address: 2215 Garland Ave.

department: Medicine

institute: Vanderbilt University Medical Center

description:
Library name: 6931 DC 10
Column name in RPKM_MGT_AB_whole_emb_no_outliers.csv: X6931.DC.10_read_counts_new.txt

data_processing:
Raw sequence files were first checked using FASTQC to assess base call accuracy (Phred>30), missing base calls, and to identify overrepresented sequences.
Adaptor sequences were trimmed using CutAdapt v5.2. Option used was to trim from both 5' and 3' ends of reads using default CutAdapt filters.
Trimmed sequence files were aligned to the zebrafish reference genome (GRCz11) using STAR alignment. Read counts were generated using HT-seq.
Assembly: GRCz11 Ensembl
Supplementary files format and content: csv file containing RPKM values for each sample.

organism: Danio rerio

source_name: Whole Larvae

growth_protocol: Zebrafish were raised and maintained under standard laboratory conditions in concordance the Institutional Animal Care and Use Committee (IACUC) at Vanderbilt University Medical Center.

extract_protocol:
Total RNA was extracted from 4 days post fertilization zebrafish larvae using TRIzol/chloroform and isolated through a series of isopropanol and ethanol washes. 60 larvae were used per RNA sample.
Total RNA samples were submitted to the VANTAGE (Vanderbilt Technologies for Advanced Genomics) core for RNA quality assessment and library construction using either the NEBNext rRNA depletion or Illumina Ribo-Zero Plus rRNA depletion kit.

treatment_protocol: Samples are bulk RNA from zebrafish larvae of either AB (WT) or mgt (plod3 KO) genetic background.

value: Whole Larvae

value: plod3 KO


title: ChIP-seq, iPS cells, CTCF, RETT, s3049, Rep2

description: Library name: iPS ChIPseq CTCF s3049 biol rep 2

value: RETT

value: iPS


title: HepG2-NTCP-A3-Vector-Control, HA, ChIP

value: Human Hepatoma


title: ChIP-seq, iPS cells, CTCF, RETT, s3049, Rep1

description: Library name: iPS ChIPseq CTCF s3049 biol rep 1

value: CTCF


title: 60 mgt zebrafish larvae, Biol rep 1, plod3 KO

description:
Library name: 6931 DC 6
Column name in RPKM_MGT_AB_whole_emb_no_outliers.csv: X6931.DC.6_read_counts_new.txt


title: NCD2

description: Library name: sample2


title: ChIP-seq, iPS cells, CTCF, RETT, s3084, Rep1

description: Library name: iPS ChIPseq CTCF s3084 biol rep 1


title: ChIP-seq, iPS cells, CTCF, RETT, s3042, Rep2

description: Library name: iPS ChIPseq CTCF s3042 biol rep 2


title: 60 AB zebrafish larvae, Biol rep 3, WT

description:
Library name: 7050 DC 3
Column name in RPKM_MGT_AB_whole_emb_no_outliers.csv: X7050.DC.4_read_counts_new.txt

value: AB WT


title: ChIP-seq, iPS cells, CTCF, Healthy, Rep2

description: Library name: iPS ChIPseq CTCF WT biol rep 2


title: ChIP-seq, iPS cells, H3K27ac, RETT, s3084, Rep2

description: Library name: iPS ChIPseq H3K27ac s3084 biol rep 2


title: PA-1 knockout replicate 2, RNA-Seq

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

description:
Library name: KO2
Replicate 2

data_processing:
Paired-end reads of 100 nts were aligned to the human genome (GRCh38.p13) using HISAT2 (version 2.1.0) with options: --no-discordant --no-mixed --no-unal.
Transcript counts for each sample were created with featureCounts (Rsubread version 2.2.6), using reverse counts and excluding reads that aligned to the genome multiple times.
Normalisation and statistical analysis was carried out with DESeq2 (version 1.32.0), using apeglm for fold change shrinkage .
Assembly: GRCh38.p13
Supplementary files format and content: csv file of gene feature count data (raw)

growth_protocol: PA-1 cell lines were cultured in DMEM + Glutamax supplemented with 20% FBS, 1x non-essential amino acids and 1x penicillin/streptomycin.

extract_protocol:
Total RNA from  DGCR8 knockout PA-1 cells was extracted from a 60% confluent T75 cell flask  with the miRNeasy Mini Kit (Qiagen), following the protocol for Purification of Total RNA, Including Small RNAs, from Animal Cells was followed, including the additional on-column DNAse digestion.
For total RNA-seq, after extraction, ≥ 200 ng of total RNA was used for rRNA removal stranded library sequencing with DNBseq PE100 by BGI Genomics.

value: DGCR8 KO


title: ChIP-seq, iPS cells, CTCF, Healthy, Rep1

description: Library name: iPS ChIPseq CTCF WT biol rep 1


title: 60 mgt zebrafish larvae, Biol rep 2, plod3 KO

description:
Library name: 6931 DC 9
Column name in RPKM_MGT_AB_whole_emb_no_outliers.csv: X6931.DC.9_read_counts_new.txt


title: 60 AB zebrafish larvae, Biol rep 2, WT

description:
Library name: 7050 DC 2
Column name in RPKM_MGT_AB_whole_emb_no_outliers.csv: X7050.DC.2_read_counts_new.txt


title: PA-1 knockout replicate 4, RNA-Seq

description:
Library name: KO4
Replicate 4


title: ChIP-seq, iPS cells, H3K27ac, RETT, s3049, Rep1

description: Library name: iPS ChIPseq H3K27ac s3049 biol rep 1


title: Glomeruli, MN, day5, rep4

city: Hamburg

first: Ming

last: Huang

address: Martinistrasse 52

department: III. Department of Medicine

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: Library name: d5MN_5436

data_processing:
The quality of the raw reads was assessed using FastQC (v0.11.9).
Sequencing reads were trimmed using trimmomatic (0.39) PE mode.
After quality assessment and trimming, paired-end clean reads were aligned to the mouse reference genome (GRCm39, Ensembl release 104) and quantified with Kallisto (0.46.2, parameter boostrap-samples=100).
Assembly: GRCm39
Supplementary files format and content: Transcripts Per Million (TPM) for each sample

source_name: kidney glomeruli

extract_protocol:
RNA was extracted from mouse glomeruli using RNeasy Mini Kit (QIAGEN, 74104) following manufacturer's instructions.
500 ng of RNA was used for library preparation using Novogene NGS RNA Library Prep Set (PT042), following the manufacturer's protocols.

treatment_protocol: Wildtype Balb/c mice were injected intraperitoneally with 2.0 mg of either control rabbit preimmune IgG or anti-THSD7A IgG. Mice used for bulk RNA sequencing were euthanized after 1 and 5 days, and mice injected with control IgG at both time points were combined into a single control group for analysis.

value: kidney glomeruli

value: anti-THSD7A IgG induced membranous nephropathy model, day5


title: Glomeruli, MN, day5, rep2

description: Library name: d5MN_5430


title: 60 AB zebrafish larvae, Biol rep 1, WT

description:
Library name: 7050 DC 1
Column name in RPKM_MGT_AB_whole_emb_no_outliers.csv: X7050.DC.1_read_counts_new.txt


title: ChIP-seq, iPS cells, H3K27ac, RETT, s3084, Rep1

description: Library name: iPS ChIPseq H3K27ac s3084 biol rep 1


title: PA-1 knockout replicate 1

description:
Library name: KO1
S29

data_processing:
For each sample, identical small RNA-seq reads were collapsed and only reads that were present more than once were included in further analysis. Mature miRNAs were identified and counted using miRDeep2, using the quantification function with human hairpin and mature miRNA sequences files from miRbase (version 22.1) and allowing no mismatches. Raw miRNA counts were normalized per sample by the total tRNAs detected with blastn (version 2.6.0+) using the commands -num_threads 20 -max_target_seqs 1 -max_hsps 1 1 -outfmt '6 std qseq sseq' -task blastn -word_size 6 -dust no, relative to WT sample 1.
Assembly: GRCh38.p13
Supplementary files format and content: tsv file of miRDeep gene feature count data (raw)

source_name: PA-1 cells

extract_protocol:
Total RNA from DGCR8 knockout PA-1 cells was extracted from a 60% confluent T75 cell flask  with the miRNeasy Mini Kit (Qiagen), following the protocol for Purification of Total RNA, Including Small RNAs, from Animal Cells was followed, including the additional on-column DNAse digestion. After extraction, ≥ 200 ng of total RNA was used for library sequencing with DNBseq SE50 by BGI Genomics.
For small RNA-seq,  200 ng of total RNA was used for library sequencing with DNBseq SE50 by BGI Genomics.

value: PA-1 cells

value: knockout


title: ChIP-seq, iPS cells, CTCF, RETT, s3042, Rep1

description: Library name: iPS ChIPseq CTCF s3042 biol rep 1


title: PA-1 knockout replicate 1, RNA-Seq

description:
Library name: KO1
Replicate 1


title: PA-1 knockout replicate 3

description:
Library name: KO3
S31


title: NCD1

description: Library name: sample1

value: islet

value: exosomes

value: WT


title: PA-1 knockout replicate 3, RNA-Seq

description:
Library name: KO3
Replicate 3


title: PA-1 knockout replicate 4

description:
Library name: KO4
S32


title: Glomeruli, MN, day5, rep3

description: Library name: d5MN_5431


title: Glomeruli, MN, day1, rep3

description: Library name: d1MN_5424

value: anti-THSD7A IgG induced membranous nephropathy model, day1


title: PA-1 knockout replicate 2

description:
Library name: KO2
S30


title: Glomeruli, MN, day1, rep2

description: Library name: d1MN_5423


title: Glomeruli, MN, day5, rep1

description: Library name: d5MN_5429


title: ChIP-seq, iPS cells, H3K27ac, RETT, s3042, Rep2

description: Library name: iPS ChIPseq H3K27ac s3042 biol rep 2

value: human induced pluripotent stem (iPS) cells


title: Glomeruli, ctrl, rep5

description: Library name: ctrl_5432

value: Control group, treated by control rabbit IgG


title: Glomeruli, MN, day1, rep1

description: Library name: d1MN_5422


title: Glomeruli, MN, day1, rep4

description: Library name: d1MN_5425


title: ChIP-seq, iPS cells, H3K27ac, RETT, s3049, Rep2

description: Library name: iPS ChIPseq H3K27ac s3049 biol rep 2


title: Ch3-S3-70E-C9

type: RNA

city: Albuquerque

first: Rajanikanth

last: Vadigepalli

state: PA

address: 1 University of New Mexico

institute: University of New Mexico

description:
Single Neurosphere
Neurospheres cultured from neuro-epithelial stem cells of the fetal mouse dorsal telencephalon microdissected at gestational day (GD12.5)

data_processing: Target gene signals normalized to median expression of each sample across all genes followed by centering the delta CT values across all samples within a gene.

label: EvaGreen

label_protocol: qPCR was performed using 96.96 BioMark™ Dynamic Arrays (Fluidigm®, South San Francisco, CA) enabling quantitative measurement of multiple mRNAs and samples under identical reaction conditions (Spurgeon et al. 2008). DNA intercalating dye based approach (EvaGreen ) was used for quantitative detection of qPCR products. Each qPCR experiment consisted of 30 amplification cycles (15s at 95°C, 5s at 70°C, 60s at 60°C). Ct values were calculated by the Real-Time PCR Analysis Software (Fluidigm).

growth_protocol: Fetal dorsal telencephalic ventricular neuroepithelium corresponding to the precursor projection neurons of the developing cerebral cortical plate were obtained by sterile microsurgical dissection from gestational day (GD) 12.5 C57/Bl6 mouse fetuses. This period corresponds to the late 1st trimester-equivalent period for cortical development in human pregnancy. Neuroepithelial cells collected from two entire litters at a time, were dispersed in a defined culture medium DMEM F12 (Invitrogen, #11039-047), 20 ng/ml Basic Fibroblast Growth Factor (bFGF, BD Biosciences, #354060), 20 ng/ml human recombinant Epidermal Growth factor (EGF, Invitrogen #47743-568), 0.15 ng/ml recombinant human Leukemia Inhibitory Factor (LIF, Alomone, #L-200), ITS (Insulin, Transferrin, Selenium) supplement (Invitrogen, #51500-056), 0.85 units/ml Heparin (Sigma-Aldrich, #H-4784), 20 nM progesterone (Sigma-Aldrich, #P7556) and cultured as non-adherent neurosphere aggregates. Independent replicates for the reported experiments were from neurospheres established from a total of six sets of neuroepithelium isolations, from 12 different pregnancies.

extract_protocol: Each neurosphere was imaged, prior to collection in 6ul of Cells Direct Lysis Buffer (Invitogen #117753-100) and stored at -80oC, prior to being processed for RT-qPCR using the Biomark HD system (protocol ADP 42), for mRNA expression across 96 genes. Single neurospheres were processed directly to reverse transcription and pre-amplification reaction (Fluidigm protocol ADP 42), without RNA extraction to minimize RNA loss.

treatment_protocol: Neurosphere cultures were randomly assigned to control and ethanol-exposed (120 mg/dl (26 mM), 320 mg/dl (70 mM) and 450mg/dl (100mM)) groups. The final ethanol concentration in the culture media was determined by gas chromatography (TRACE™ 1310, Thermo Fisher Scientific), from samples of the media collected at the beginning of the treatment at day 0, at day 3 for re-feeding and at day 5 before collection.

value: C57/Bl6 mouse

value: dorsal telencephalon

tag: culture group

value: Set-B

tag: ethanol (etoh) treatment

tag: neurosphere diameter (um)

tag: neurosphere size group

value: M


title: Ch3-S3-70E-C1

source_name: fetal mouse dorsal telencephalon microdissected at gestational day (GD12.5)

tag: tissue

value: S


title: Ch3-S3-70E-C2


title: Ch3-S3-70E-C8


title: Ch3-S3-70E-B8


title: Glomeruli, ctrl, rep3

description: Library name: ctrl_5426


title: Ch3-S3-70E-B7

value: L


title: Ch3-S3-70E-B5


title: Ch3-S3-70E-C7


title: Ch3-S3-70E-C6


title: Ch3-S3-70E-C5


title: ChIP-seq, iPS cells, H3K27ac, RETT, s3042, Rep1

description: Library name: iPS ChIPseq H3K27ac s3042 biol rep 1

value: RETT

tag: cell line

value: iPS

tag: cell type


title: Ch3-S3-70E-B4


title: Ch3-S3-70E-C4


title: Glomeruli, ctrl, rep1

description: Library name: ctrl_5418

value: kidney glomeruli

tag: treatment


title: HHUA sh51

city: Sapporo

first: Hiroyuki

last: Kurosu

state: Hokkaido

address: Kita 15, Nishi 7, Kita-ku

department: Faculty of Medicine and Graduate School of Medicine

institute: Hokkaido University

description:
Library name: Sample3
HHUA_sh51

data_processing:
Sequencing reads were mapped to the human reference genome (hg38) using proprietary pipelines provided by Rhelixa Inc.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample and FPKM values for each sample
Supplementary files format and content: The bw files are position data of reads mapped onto the genome.

source_name: endometrial cancer tissue

extract_protocol:
Total RNA was extracted from using RNAiso Plus (Takara Bio Inc., Japan) .
Strand-specific libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (Cat No. E7760, New England Biolabs).

value: endometrial cancer tissue

value: HHUA

value: cancer

tag: genotype

value: L1CAM knockdown


title: Ch3-S3-70E-C3

tag: strain


title: IGRP-CD8 T cells from HEL tolerized graft [HEL_graftt_TCR]

city: Aurora

first: James

middle: E

last: DiLisio

state: CO

address: 1775 Aurora Ct

department: Immunology and Microbiology

institute: University of Colorado

description:
Library name: HEL_graftt_TCR_S11
10X genomics

data_processing:
Following sequencing, standard quality control, filtering, and normalization were applied using default CellRanger pipelines. TCR sequences were annotated using the scRepertoire package.
Indidivudal animals were deconvulated in each sample using the CSP hashtags liked in the feature_README.txt
Assembly: Mouse mm10
Supplementary files format and content: tab seperated value files and matrix files

source_name: islet graft

extract_protocol:
Single cell suspension were made from islet graft by digesting for 15 minutes in 2U/ml dispase II in HBSS. IGRPCD8 T cells were sorted by FACS from day 8 islet grafts (lymphocytes, live, CD45+, lineage-(CD11c, CD11b, CD19, Ly6G, CD4), IGRP tetramer+). After sorting, cells from individual animals were barcoded with hashtag antibodies biolegend type C (information on hastags in "feature_README.txt") to deconvolute after sequencing. Three animals were hashed in the 2.5HIP sample and 4 animals hashed in the HEL sample. Cells were resuspended in .1% FBS in PBS for capture.
Single cell gene expression profile, cell surface proteomics profile, and T cell receptor profile were obtained using the Chromium Single-Cell 5’ NextGEM Library and Gel Bead Kit from 10X Genomics. Sorted and hashed cells were partitioned on the 10X Genomics Chromium X instrument for single cell capture, followed by amplification of cDNA and library preparation to recover 10,000 - 12,000 cells per sample. Individual libraries corresponding to gene expression (GEX), cell surface protein (CSP), and T cell receptor (TCR) were quantified, pooled, and sequenced on the Illumina NovaSeq 6000 sequencer at a depth of 50,000 reads/cell for gene expression, 5,000 reads/cell for cell surface protein, and 5,000 reads/cell for T cell receptor, respectively.

treatment_protocol: NOD mice were treated with 2.5mg of 2.5HIP- or HEL- conjugated nanoparticles day -7,+, and +7 relative to a islet transplant from NODscid mice.

value: islet graft

value: HEL nanoparticles

value: IGRP CD8 T cells

tag: mouse strain

value: NOD

tag: number of_hashed_animals


title: ChIP-seq, iPS cells, H3K27ac, Healthy, Rep2

description: Library name: iPS ChIPseq H3K27ac WT biol rep 2

tag: disease state

value: Healthy

value: human induced pluripotent stem (iPS) cells


title: Ch3-S3-70E-B11

value: C57/Bl6 mouse

value: dorsal telencephalon

value: Set-B


title: Ch3-S3-70E-B2

value: S


title: ChIP-seq, iPS cells, H3K27ac, Healthy, Rep1

description: Library name: iPS ChIPseq H3K27ac WT biol rep 1

tag: chip antibody


title: IGRP-CD8 T cells from HEL tolerized graft [HEL_graftt_GEX]

description:
Library name: HEL_graftt_GEX_S7
10X genomics


title: Glomeruli, ctrl, rep4

description: Library name: ctrl_5427

value: Control group, treated by control rabbit IgG


title: Ch3-S3-70E-B9

value: L


title: Ch3-S3-70E-B1

value: M


title: pooled library of all cell lines, cortical + subpallial organoids, day 150

city: Vestec

first: Zuzana

last: Matusova

address: Prumyslova 595

department: Laboratory of Glial Biology and Omics Technologies

country: Czech Republic

institute: Institute of Biotechnology of the Czech Academy of Sciences

description:
Library name: pool2
seurat_object_hCO.rds
seurat_object_hSO.rds
supplementary_file.xlsx
multiplexed library containing 8 samples from day 150 organoids, details in supplementary_file.xlsx and README_barcode_sequences.txt

data_processing:
The data were pre-processed with CTG singleCellWorkflows – Nextflow pipeline (release 1.6.2 – containing CellRanger v7.1.0, FastQC v0.11.9, and MultiQC v1.16). Count matrices from CellRanger were filtered with EmptyDrops (DropletUtils R package v1.16.0), with FDR <= 0.01, to remove empty droplets, yielding approx. 5.7k – 7.6k cells per sample and ~17.6k genes per sample. The data were further processed using R programming language (v4.2.2) and the Seurat package (v4.3.0).
The data were split to two subsets – hCOs and hSOs – and integrated within each subset sample-wise. From now on, the two subsets were analysed separately, following standard Seurat processing pipeline (LogNormalize, ScaleData, and SCTransform). Quality control (QC) and filtering included identification of doublets with DoubletFinder (v2.0.4, estimated doublet rate set to 5% according to 10x recommendation) and removal of cells with mitochondrial transcript abundance over 15% (keeping percent.mt < 15%) and less than 2000 genes (keeping nFeature > 2000). After these QC steps, the datasets contained 43,339 cells and 18,485 genes (hCOs), and 39,234 cells and 18,472 genes (hSOs). For clustering, integrated assay was used in hCOs dataset (to overlay one outlier sample better), and SCT assay was used in hSOs dataset. A small cluster of excitatory neurons, which was unique to a single sample (GD-iso at day 150), as well as several scattered clusters of low-quality cells, were excluded from the hSO dataset.
Assembly: GRCh38 2020 A
Supplementary files format and content: Data pre-processed in CellRanger, which entered the analysis in R, are provided as barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz for each sample within each pool. These data went though the Seurat analysis pipeline, including their quality control and filtering, separating cortical and subpallial dataset. The resulting Seurat objects (per organoid type), are provided as processed data (seurat_object_hCO.rds and seurat_object_hSO.rds) and should contain gene counts, normalized gene counts, SCT assay, integrated assay, clustering, and metadata information per cell.

source_name: cortical + subpallial organoids

extract_protocol:
Cell suspension was prepared from several pooled organoids that were chopped to smaller pieces, using papain dissociation followed by trituration in Low Ovo solution. The suspensions were fixed according to the Chromium Fixed RNA Profilling Sample Preparation kit (10X Genomics) instructions.
Sequencing of the samples was performed by the Center for Translational Genomics (CTG) at Lund University, using the 10X Next GEM protocol and probe set version 1. Sequencing was done in two batches (D75 batch 1 and D150 batch 2), samples were multiplexed, labeled with barcodes, and split to multiple lanes.

value: cortical + subpallial organoids

value: GD, GD-iso, HC-KO, HC

tag: timepoint

value: day 150

tag: probe set


title: Ch3-S3-70E-B6

tag: developmental stage


title: Glomeruli, ctrl, rep2

description: Library name: ctrl_5419

value: kidney glomeruli


title: HHUA sh24

description:
Library name: Sample2
HHUA_sh24

value: endometrial cancer tissue

value: HHUA

value: cancer

value: L1CAM knockdown


title: Ch3-S3-25E-C7

tag: culture group


title: Ch3-S3-70E-B12

tag: ethanol (etoh) treatment


title: DUX4_patient 19

city: Paris

first: Hélène

last: CAVE

state: France

address: 48 Bd sérurier

department: Genetics

country: France

institute: APHP Hôpital Robert Debré

description: Library name: 15247

data_processing:
Alignment is performed by STAR (https://github.com/alexdobin/STAR). The duplicate reads (e.g., paired-end reads in which the insert DNA molecules have identical start and end locations in the Human genome) are removed (sambamba tools).
Counting of reads per gene are performed by STAR with --quantMode GeneCounts option. Next, RawCount is normalized by the Transcripts Per Kilobase Million (TPM) method.
Assembly: hg38
Supplementary files format and content: txt file including TPM values for all samples
Supplementary files format and content: txt file including FPKM values for all samples

growth_protocol: mononucleated cells were obtained by Ficoll from fresh EDTA or Heparin Lithium tumoral bone marrow at ALL diagnosis

extract_protocol:
Qiagen miRNeasy kit
RNA were quantified and qualified using Fragment Analyzer®, Agilent®. A cDNA library was generated by reverse transcription of mRNA after poly(A) capture (NEBNext® Poly(A) mRNA Magnetic Isolation Modules, NEBNext® Ultra II RNA First Strand Synthesis Module & Directional RNA Second Strand Module, New England Biolabs®). Size selection and subsequent purification steps were carried out on magnetic beads (Sera-Mag magnetic beads®, GE Healthcare®). The library was prepared (NEBNext® Ultra II End repair/A-tailing module & Ligation module, New England Biolabs®) and amplified by PCR (KAPA Hifi HotStart ReadyMix, Roche®). The final library was qualified by capillary migration (Fragment Analyzer®, Agilent®) and quantified by qPCR (NEBNext® Custom 2X Library Quant Kit Master Mix, New England Biolabs®; QuantStudio 6 Flex Real-Time PCR System®, Life Technologies®). The libraries were sequenced in 'pair-end' (2 times 100 cycles) using SBS technology (Flow Cell S2, NovaSeq 6000®, Illumina®). Image analysis and base calling is performed using Illumina Real Time Analysis with default parameters.

value: Bone marrow

value: Mononucleated cells

tag: batch

tag: gender


title: IGRP-CD8 T cells from 2.5HIP tolerized graft [2_5_graftt_GEX]

description:
Library name: 2_5_graftt_GEX_S8
10X genomics

tag: tissue

value: islet graft

value: 2.5HIP nanoparticles

value: IGRP CD8 T cells

value: NOD


title: HHUA scramble

description:
Library name: Sample1
HHUA_scramble

tag: cell line

value: L1CAM scramble


title: Ch3-S3-25E-C6

value: C57/Bl6 mouse

value: dorsal telencephalon

value: Set-B

tag: neurosphere diameter (um)

tag: neurosphere size group


title: Ch3-S3-70E-B3

value: M


title: pooled library of all cell lines, cortical + subpallial organoids, day 75

description:
Library name: pool1
seurat_object_hCO.rds
seurat_object_hSO.rds
supplementary_file.xlsx
multiplexed library containing 8 samples from day 75 organoids, details in supplementary_file.xlsx and README_barcode_sequences.txt

value: cortical + subpallial organoids

value: GD, GD-iso, HC-KO, HC

value: day 75


title: Ch3-S3-25E-C5


title: Ch3-S3-70E-B10


title: Ch3-S3-25E-C9


title: DUX4_patient 16

description: Library name: 25892

treatment_protocol: mononucleated cells were obtained by Ficoll from fresh EDTA or Heparin Lithium tumoral bone marrow at ALL diagnosis

tag: cell type

tag: genotype

value: F


title: Dnmt3L_K412R_3

city: Seoul

first: DONG-MYUNG

last: SHIN

address: Pungnap-2 dong, Songpa-gu

department: Department of Biomedical Sciences

country: South Korea

institute: University of Ulsan College of Medicine

description:
Library name: sample_4_3
Dnmt3L-K412R over-expressing R1-derived teratoma

data_processing:
Illumina GATK software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastp), then mapped to GRCm39 whole genome using STAR
Calculation mapped reads using salmon
CPM + TMM calculation using conorm
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: Teratoma

growth_protocol: Murine R1 ESCs were grown in FBS-LIF medium which was based on DMEM-high glucose medium (HyClone, Pittsburgh, PA, USA) supplemented with 2 mM L-glutamine, 20 mM HEPES, MEM nonessential amino acid solution, penicillin/streptomycin solution (Gibco, Waltham, Waltham, USA), 0.1 mM β-mercaptoethanol (Sigma-Aldrich, St Louis, MO, USA), 15% heat-inactivated FBS (HyClone), and 100 IU/ml ESGRO/LIF (Millipore, Billerica, MA, USA) on a 0.1% gelatin (Sigma-Aldrich) coated tissue culture.

extract_protocol:
RNA was extracted using a QIAGEN RNeasy Mini Kit
RNA libraries were prepared for sequencing using the CORALL RNA-seq V2 Library Prep Kit standard protocols.

treatment_protocol: All animal experiments were approved and performed in accordance with the guidelines and regulations of the Institutional Animal Care and Use Committee of the University of Ulsan College of Medicine (IACUC 2021-12-271). We subcutaneously injected eight-week-old male NOD-PrkdcEM1 mice (JA BIO, Suwon-si,Gyeonggi-do, Korea) with 5x106 cells of each ESC cultured with FBS-LIF medium. The mice and site of injection were monitored for 46 days. Teratomas were recovered by dissection to measure tumor size and for histological examination or for transcriptome analysis at day 21 post-injection. Total RNA was extracted from teratomas collected after euthanasia of immunodeficient mice following cell injection.

value: Teratoma

value: Embryonic stem cell

value: Dnmt3L overexpression via pEZ-LV235 CAG vector

tag: treatment


title: Ch3-S3-25E-C8

tag: strain

value: L


title: IGRP-CD8 T cells from 2.5HIP tolerized graft [2_5_graftt_TCR]

description:
Library name: 2_5_graftt_TCR_S12
10X genomics

value: islet graft

tag: mouse strain

tag: number of_hashed_animals


title: IGRP-CD8 T cells from HEL tolerized graft [HEL_graftt_CSP]

description:
Library name: HEL_graftt_CSP_S9
10X genomics

value: HEL nanoparticles


title: DUX4_patient 20

description: Library name: 15811

value: Bone marrow

value: Mononucleated cells


title: Dnmt3L_K412R_2

description:
Library name: sample_4_2
Dnmt3L-K412R over-expressing R1-derived teratoma


title: DUX4_patient 1

description: Library name: 13176


title: IGRP-CD8 T cells from 2.5HIP tolerized graft [2_5_graftt_CSP]

description:
Library name: 2_5_graftt_CSP_S10
10X genomics

value: 2.5HIP nanoparticles

value: IGRP CD8 T cells

value: NOD


title: Ch3-S3-25E-B8

value: C57/Bl6 mouse

value: dorsal telencephalon

value: Set-B


title: Ch3-S3-70E-A12

value: M


title: DUX4_patient 25

description: Library name: 12751


title: Dnmt3L_K412R_1

description:
Library name: sample_4_1
Dnmt3L-K412R over-expressing R1-derived teratoma


title: Ch3-S3-25E-C4


title: DUX4_patient 3

description: Library name: 24455


title: DUX4_patient 4

description: Library name: 18828


title: Ch3-S3-25E-B5

value: S


title: Ch3-S3-25E-C3


title: Ch3-S3-25E-C2


title: Ch3-S3-25E-B3


title: DUX4_patient 23

description: Library name: 19073

value: F


title: Ch3-S3-25E-C1


title: Ch3-S3-25E-B9


title: Ch3-S3-25E-B7


title: Ch3-S3-25E-B11


title: Ch3-S3-25E-B10


title: Dnmt3L_K238R_3

description:
Library name: sample_3_3
Dnmt3L-K238R over-expressing R1-derived teratoma

value: Teratoma


title: Ch3-S3-100E-C9


title: Ch3-S3-25E-B6


title: Ch3-S3-25E-B4


title: DUX4_patient 14

description: Library name: 9399


title: Ch3-S3-100E-C8


title: Ch3-S3-100E-C6


title: Dnmt3L_WT_1

description:
Library name: sample_2_1
Dnmt3L-WT over-expressing R1-derived teratoma

value: Embryonic stem cell

value: WT


title: DUX4_patient 10

description: Library name: 20997


title: Ch3-S3-100E-C7

description:
Single Neurosphere
Neurospheres cultured from neuro-epithelial stem cells of the fetal mouse dorsal telencephalon microdissected at gestational day (GD12.5)


title: DUX4_patient 18

description: Library name: 18458


title: ET_3

description:
Library name: sample_1_3
The teratoma sample was derived from R1 mESCs (ET).

value: Overexpression via pEZ-LV235 CAG vector

value: ET


title: DUX4_patient 21

description: Library name: 22511


title: Dnmt3L_K238R_2

description:
Library name: sample_3_2
Dnmt3L-K238R over-expressing R1-derived teratoma

value: Dnmt3L overexpression via pEZ-LV235 CAG vector


title: DUX4_patient 9

description: Library name: 18445

value: Bone marrow


title: Ch3-S3-100E-C2


title: Ch3-S3-25E-B12


title: DUX4_patient 11

description: Library name: 12358

value: Mononucleated cells


title: ET_2

description:
Library name: sample_1_2
The teratoma sample was derived from R1 mESCs (ET).


title: Dnmt3L_K238R_1

description:
Library name: sample_3_1
Dnmt3L-K238R over-expressing R1-derived teratoma


title: Ch3-S3-100E-C1


title: Dnmt3L_WT_3

description:
Library name: sample_2_3
Dnmt3L-WT over-expressing R1-derived teratoma


title: Ch3-S3-100E-B9


title: DUX4_patient 12

description: Library name: 15606


title: DUX4_patient 24

description: Library name: 26023


title: Fkbp5-KO, LPS_7d_5

city: Taipei City

first: Yu-Ling

last: Gan

address: No. 155, Sec. 2, Linong St. Beitou Dist.

department: Department and Institute of Physiology

country: Taiwan

institute: National Yang Ming Chiao Tung University

description:
Library name: FKOL7d_5
Column name in Original_read_count.txt: FKOL7d_5

data_processing:
Raw reads were processed using Trimmomatic (v0.38) to remove low-quality reads and adaptor sequences (parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30). Quality control of raw reads was performed using FastQC and MultiQC.
Read counts for individual genes were extracted using FeatureCounts (v1.6.0)
Assembly: mm10
Supplementary files format and content: Original_read_count.txt

source_name: Hippocampus

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following the manufacturer’s protocols.

treatment_protocol: Twelve-week-old male wild-type and Fkbp5 knockout mice received a single intraperitoneal injection of either saline or 3 mg/kg lipopolysaccharide (LPS), and hippocampal tissues were collected 7 days later for RNA-seq analysis.

value: Hippocampus

tag: Sex

value: male

value: LPS

tag: time

value: Day 7


title: Ch3-S3-100E-B6

value: C57/Bl6 mouse

value: dorsal telencephalon

tag: developmental stage


title: Fkbp5-KO, LPS_7d_4

description:
Library name: FKOL7d_4
Column name in Original_read_count.txt: FKOL7d_4


title: Dnmt3L_WT_2

description:
Library name: sample_2_2
Dnmt3L-WT over-expressing R1-derived teratoma


title: Ch3-S3-25E-B1

tag: culture group

value: Set-B


title: Ch3-S3-25E-B2

tag: ethanol (etoh) treatment

value: S


title: Ch3-S3-100E-B4


title: Ch3-S3-100E-B5


title: DUX4_patient 13

description: Library name: 19405

source_name: Bone marrow

tag: batch

value: F


title: Ch3-S3-100E-C4


title: Ch3-S3-100E-C5


title: ET_1

description:
Library name: sample_1_1
The teratoma sample was derived from R1 cells (ET).

value: Teratoma


title: Ch3-S3-100E-B8


title: Ch3-S3-100E-B3


title: DUX4_patient 8

description: Library name: 16904

tag: gender


title: Ch3-S3-100E-C3

tag: tissue


title: Ch3-S3-100E-B2


title: Fkbp5-KO, LPS_7d_2

description:
Library name: FKOL7d_2
Column name in Original_read_count.txt: FKOL7d_2


title: Fkbp5-KO, LPS_7d_1

description:
Library name: FKOL7d_1
Column name in Original_read_count.txt: FKOL7d_1


title: Ch3-S3-100E-B7


title: Ch3-S3-100E-B12


title: Fkbp5-KO, LPS_7d_3

description:
Library name: FKOL7d_3
Column name in Original_read_count.txt: FKOL7d_3


title: DUX4_patient 17

description: Library name: 12552


title: DUX4_patient 6

description: Library name: 13922

value: M


title: Ch3-S3-100E-B1


title: DUX4_patient 22

description: Library name: 22547


title: DUX4_patient 2

description: Library name: 23146


title: Ch3-S3-100E-B11


title: Fkbp5-KO, saline_7d_5

description:
Library name: FKOS7d_5
Column name in Original_read_count.txt: FKOS7d_5

value: saline


title: Ch3-S3-100E-A12


title: Ch3-S3-100E-B10


title: Fkbp5-KO, saline_7d_4

description:
Library name: FKOS7d_4
Column name in Original_read_count.txt: FKOS7d_4


title: non DUX4 hyperdiploidy, control 21

description: Library name: 30499

value: Hyperdip


title: Ch3-S3-0E-C9


title: Ch3-S3-0E-C8


title: non DUX4 hyperdiploidy, control 19

description: Library name: 29660


title: non DUX4 hyperdiploidy, control 20

description: Library name: 30469


title: Ch3-S3-0E-C7


title: Ch3-S3-0E-C5


title: non DUX4 hyperdiploidy, control 18

description: Library name: 29332


title: non DUX4 hyperdiploidy, control 17

description: Library name: 29313


title: Ch3-S3-0E-C3


title: Fkbp5-KO, saline_7d_3

description:
Library name: FKOS7d_3
Column name in Original_read_count.txt: FKOS7d_3


title: non DUX4 hyperdiploidy, control 16

description: Library name: 28372


title: Fkbp5-KO, saline_7d_2

description:
Library name: FKOS7d_2
Column name in Original_read_count.txt: FKOS7d_2


title: Ch3-S3-0E-C6

description:
Single Neurosphere
Neurospheres cultured from neuro-epithelial stem cells of the fetal mouse dorsal telencephalon microdissected at gestational day (GD12.5)


title: WT, LPS_7d_4

description:
Library name: WTL7d_4
Column name in Original_read_count.txt: WTL7d_4

value: WT


title: Ch3-S3-0E-C1


title: Fkbp5-KO, saline_7d_1

description:
Library name: FKOS7d_1
Column name in Original_read_count.txt: FKOS7d_1


title: Ch3-S3-0E-B8


title: WT, LPS_7d_3

description:
Library name: WTL7d_3
Column name in Original_read_count.txt: WTL7d_3


title: Ch3-S3-0E-C4


title: Ch3-S3-0E-B5


title: Ch3-S3-0E-C10


title: Ch3-S3-0E-C2


title: WT, LPS_7d_5

description:
Library name: WTL7d_5
Column name in Original_read_count.txt: WTL7d_5


title: Ch3-S3-0E-B6


title: non DUX4 hyperdiploidy, control 15

description: Library name: 28224


title: WT, LPS_7d_2

description:
Library name: WTL7d_2
Column name in Original_read_count.txt: WTL7d_2


title: non DUX4 hyperdiploidy, control 14

description: Library name: 27669


title: Ch3-S3-0E-B4


title: Ch3-S3-0E-B9


title: Ch3-S3-0E-B7


title: WT, LPS_7d_1

description:
Library name: WTL7d_1
Column name in Original_read_count.txt: WTL7d_1


title: WT, saline_7d_5

description:
Library name: WTS7d_5
Column name in Original_read_count.txt: WTS7d_5


title: non DUX4 hyperdiploidy, control 12

description: Library name: 27034


title: Ch3-S3-0E-B3


title: non DUX4 hyperdiploidy, control 11

description: Library name: 26603


title: Ch3-S3-0E-B2

value: L


title: WT, saline_7d_4

description:
Library name: WTS7d_4
Column name in Original_read_count.txt: WTS7d_4


title: non DUX4 hyperdiploidy, control 10

description: Library name: 25782

value: Bone marrow


title: non DUX4 hyperdiploidy, control 13

description: Library name: 27124

value: Mononucleated cells


title: Ch3-S3-0E-B12


title: Ch3-S3-0E-B11


title: non DUX4 hyperdiploidy, control 8

description: Library name: 25740


title: non DUX4 hyperdiploidy, control 7

description: Library name: 25439


title: WT, saline_7d_2

description:
Library name: WTS7d_2
Column name in Original_read_count.txt: WTS7d_2

value: Hippocampus


title: Ch3-S3-0E-B1


title: non DUX4 hyperdiploidy, control 5

description: Library name: 25049


title: Microglia LPS Serpine2 knockout 2

city: Los Angeles

first: Ye

last: Zhang

address: 635 Charles E Young Dr S

institute: UCLA

data_processing:
STAR alignment, v2.6.0c (astrocytes) & v2.7.8a (microglia)
HTSeq quantification
Assembly: GRCm38 (astrocytes) & GRCm39 (microglia)
Supplementary files format and content: tab-delimited text files of gene counts, labelled with Ensembl gene IDs

source_name: whole brain

extract_protocol:
Mice were perfused for 10 minutes with phosphate buffered saline solution before dissection of the cerebral cortex (astrocytes) or whole brain (microglia).  For astrocytes, cortical tissue was roughly chopped then placed in a papain solution (12 units/mL) for enzymatic digestion at 34.5C for 45 minutes. Digested tissue was washed with ovomucoid inhibitor and mechanically digested via trituration.  Cells were spun down and resuspended in PBS with 0.02% bovine serum albumin, then passed through a mesh filter to generate a single cell suspension. Tissue for microglia was dounced, spun down through a Percoll solution, and then resuspended to get a single cell suspension. The final cell suspensions were incubated on various petri dishes (10-20 min/dish) that were coated with antibodies targeting a desired cell population.  Cells bound to each dish were rinsed with PBS, and RNA was harvested immediately with 700 uL of TRIzol before flash freezing in liquid nitrogen. RNA was purified for sequencing using the miRNeasy kit (Qiagen).
RNA libraries were constructed with the Ovation V2 system (Tecan) and the NEBNext Ultra RNA Library Prep Kit (New England Biolabs)

value: whole brain

value: microglia

value: Serpine2 knockout

value: male


title: Ch2-S2-70E-C3

value: C57/Bl6 mouse

value: dorsal telencephalon

value: Set-A


title: Ch3-S3-0E-B10

value: Set-B

value: S


title: Ch2-S2-70E-C6


title: Ch2-S2-70E-C5


title: Ch3-S3-0E-A12

value: M


title: WT, saline_7d_3

description:
Library name: WTS7d_3
Column name in Original_read_count.txt: WTS7d_3

value: saline

value: Day 7


title: Ch2-S2-70E-C9


title: non DUX4 hyperdiploidy, control 9

description: Library name: 25771

value: Hyperdip


title: huSTING cells cGAMP treated 1

city: Beaverton

first: Victor

middle: Robert

last: DeFilippis

state: Oregon

address: 505 NW 185th Ave.

department: Vaccine and Gene Therapy Institute

institute: Oregon Health and Science University

hyb_protocol: Samples were hybridized with Clariom S arrays (Affymetrix) and scanned at the Oregon Health and Science University Integrated Genomics Core facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing:
Raw data were processed with the Transcriptome Analysis Console (Affymetrix) for background correction and RMA normalization as well as fold change calculation and statistical significance (FDR < 0.01).
RMA expression value derived from Transcriptome Analysis Console

label: biotin

source_name: Healthy male

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Cells were grown in 12 well dishes in RPMI + 10% FCS.

extract_protocol: RNA was isolated from collected cell pellets using Zymo DNA free RNA isolation kits per the manufacturer's instructions.

treatment_protocol: Cells were treated for 6 h with DMSO (mock), 50 nM diABZI, 10µg/mL cGAMP, or 100 ng/mL LPS as indicated.

value: Bone Marrow Derived Dendritic Cells

value: huSTING mice

value: cGAMP treated


title: WT, saline_7d_1

description:
Library name: WTS7d_1
Column name in Original_read_count.txt: WTS7d_1

value: Hippocampus

value: WT


title: Ch2-S2-70E-C8


title: Microglia LPS Serpine2 knockout 3

value: whole brain

value: microglia

value: female


title: non DUX4 hyperdiploidy, control 4

description: Library name: 24881

value: Bone marrow

value: Mononucleated cells

value: F


title: Microglia LPS Serpine2 control 3

value: control


title: non DUX4 hyperdiploidy, control 3

description: Library name: 23616


title: huSTING cells LPS treated 1

description: RMA expression value derived from Transcriptome Analysis Console

value: male

value: LPS treated


title: huSTING cells LPS treated 2


title: Ch2-S2-70E-C1

value: C57/Bl6 mouse

value: dorsal telencephalon

value: Set-A

value: S


title: Ch2-S2-70E-C7

value: M


title: Ch2-S2-70E-C4


title: non DUX4 hyperdiploidy, control 6

description: Library name: 25195

value: Hyperdip


title: Ch2-S2-70E-B8


title: Ch2-S2-70E-B9


title: Microglia LPS Serpine2 knockout 1

value: Serpine2 knockout


title: huSTING cells mock treated 2

value: Bone Marrow Derived Dendritic Cells

value: huSTING mice

value: mock treated


title: Microglia saline Serpine2 knockout 2

value: whole brain

value: microglia

value: female


title: Ch2-S2-70E-C2


title: huSTING cells cGAMP treated 2

value: cGAMP treated


title: Microglia saline Serpine2 knockout 3


title: Microglia LPS Serpine2 control 2

value: control


title: huSTING cells diABZI treated 2

value: male

value: diABZI treated


title: Ch2-S2-70E-B5

value: C57/Bl6 mouse


title: non DUX4 hyperdiploidy, control 2

description: Library name: 18543

value: Bone marrow

value: Mononucleated cells

value: F


title: non DUX4 ETV6-RUNX1, control 14

description: Library name: 33378

value: M


title: non DUX4 hyperdiploidy, control 1

description: Library name: 14390

value: Hyperdip


title: Microglia saline Serpine2 control 3


title: C57Bl/6 cells LPS treated 1

value: C57Bl/6 mice

value: LPS treated


title: Microglia LPS Serpine2 control 1


title: huSTING cells diABZI treated 1

value: Bone Marrow Derived Dendritic Cells

value: huSTING mice


title: Microglia saline Serpine2 control 2

value: whole brain


title: Ch2-S2-70E-B3

value: dorsal telencephalon

value: Set-A


title: Microglia saline Serpine2 control 1

value: microglia


title: C57Bl/6 cells cGAMP treated 1

value: cGAMP treated


title: Ch2-S2-70E-B6


title: non DUX4 ETV6-RUNX1, control 9

description: Library name: 27633


title: huSTING cells mock treated 1

value: male

value: mock treated


title: Microglia saline Serpine2 knockout 1

value: Serpine2 knockout


title: non DUX4 ETV6-RUNX1, control 13

description: Library name: 31027

value: Bone marrow


title: non DUX4 ETV6-RUNX1, control 12

description: Library name: 29776

value: Mononucleated cells


title: Astrocyte LPS Serpine2 knockout 3

source_name: cerebral cortex

value: cerebral cortex

value: astrocyte

value: female


title: non DUX4 ETV6-RUNX1, control 11

description: Library name: 29056

value: F


title: non DUX4 ETV6-RUNX1, control 10

description: Library name: 28366


title: Ch2-S2-70E-B7

value: C57/Bl6 mouse

value: L


title: C57Bl/6 cells cGAMP treated 2

value: Bone Marrow Derived Dendritic Cells

value: C57Bl/6 mice


title: Astrocyte LPS Serpine2 knockout 1


title: Ch2-S2-70E-B4

value: dorsal telencephalon

value: M


title: C57Bl/6 cells LPS treated 2

value: LPS treated


title: C57Bl/6 cells mock treated 2