title: ControlKD_Rep8_TTseq

status: Public on May 08 2025

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

description: 4sU-labelled RNA

data_processing:
Barcode adapter sequences removed using cutadapt and trimmed using trimmomatic.
Reads mapped to mm10 genome using STAR, with options --outSAMtype SAM, --outFilterMismatchNoverReadLmax 0.02, and --outFilterMultimapNmax 1, and quality filtered using samtools view with options -q 7, -f 2, -bS.
Counts were generated using featureCounts, with options -B -t "exon" -g "gene_name" -F GTF -p -s 2 for Gencode mouse V23 features, with options -B -F SAF -p -s 2 for stranded features, and options -B -F SAF -p -s 0 for unstranded features.
In R/Bioconductor environment, raw count matrices were corrected for batch effects using Combat-seq and differential expression analysis was performed using DEseq2 for all replicates of each condition.
Aligned reads were processed to generate strand specific bigwigs using deeptools bamCoverage with binsize 1 and DEseq2-derived scaling factors.
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: Excel file containing all DEseq2 results for each condition for TTseq.
Supplementary files format and content: Tab-delimited matrix of raw TTseq counts for each sample for all features.
Supplementary files format and content: Tab-delimited matrix of Combatseq corrected raw TTseq counts for each sample for all features.
Supplementary files format and content: Tab-delimited table containing information for Combatseq batch corrected for TT-seq data.
Supplementary files format and content: bed file for all non-coding features in this study.

growth_protocol: ES-E14TG2a (E14) embryonic stem cells from male Mus musculus origin were grown at 37°C and 5% CO2 in DMEM base medium (Sigma) supplemented with 10% FBS (Sigma, 18N103), 1X nonessential amino acids (Corning), 2mM L-glutamine (Corning), β-mercaptoethanol (Acros Organics), and LIF on 10-cm plates precoated with 0.2% gelatin. Cells were passaged every ~48 h using trypsin (Corning) and split at a ratio of ~1:8 with fresh medium. Routine anti-mycoplasma TC hood cleaning was conducted (LookOut DNA Erase spray, Sigma) and cell lines were screened to confirm no mycoplasma presence.

extract_protocol:
RNA was extracted with TRIzol.
Nascent RNA was rRNA depleted using antisense oligos, purified. Nascent RNA-seq libraries were built using the NEBNext Ultra II RNA Library Prep kit according to the manufacturer's modifications, but with modifications to account for higher volume input.

treatment_protocol: After 48 hours of growth to confluency, reverse transfections were performed using 3500-5000 ng of either target or control (GFP) esiRNAs, 25 µL of Lipofectamine 3000 (Invitrogen), and 2 mL of OptiMEM media (Gibco), incubated for 15-30 min at room temperature (RT). During this incubation, ES cells were counted and diluted to 350,000 cells/mL in ES cell media. After incubation, the transfection reaction was added to 4 mL diluted cell suspension and transferred to a pre-gelatinized 10 cm plate. After 16-18 h, the media was replaced with 6 mL fresh ES cell media. Cells were treated with 4sU and harvested 48 h post-transfection.

value: embryonic stem cells

value: wild-type

value: Control KD for 48 hours


title: ControlKD_Rep16_TTseq

type: SRA

country: USA

description: 4sU-labelled RNA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: ControlKD_Rep14_TTseq

description: 4sU-labelled RNA


title: ControlKD_Rep15_TTseq

description: 4sU-labelled RNA


title: ControlKD_Rep12_TTseq

description: 4sU-labelled RNA


title: ControlKD_Rep13_TTseq

description: 4sU-labelled RNA


title: ControlKD_Rep9_TTseq

description: 4sU-labelled RNA


title: ControlKD_Rep11_TTseq

description: 4sU-labelled RNA


title: ControlKD_Rep6_TTseq

description: 4sU-labelled RNA


title: ControlKD_Rep7_TTseq

description: 4sU-labelled RNA


title: ControlKD_Rep5_TTseq

description: 4sU-labelled RNA


title: ControlKD_Rep4_TTseq

description: 4sU-labelled RNA


title: ControlKD_Rep2_TTseq

description: 4sU-labelled RNA


title: Zranb3KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Zranb3 knockdown for 48 hours


title: ControlKD_Rep10_TTseq

description: 4sU-labelled RNA


title: ControlKD_Rep17_TTseq

description: 4sU-labelled RNA


title: ControlKD_Rep1_TTseq

description: 4sU-labelled RNA


title: Ttf2KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Ttf2 knockdown for 48 hours


title: Ttf2KD_Rep1_TTseq

description: 4sU-labelled RNA


title: Slide 2, Xenium In Situ Spatial Gene Expression

status: Public on May 30 2025

type: RNA

city: Hamburg

first: Robin

last: Khatri

address: Falkenried 94

department: Institute of Medical Systems Biology

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: The Xenium samples underwent several rounds of fluorescent probe hybridization, imaging, and probe removal. The Xenium Analyzer captured a Z-stack of images every cycle and in every channel, which needed to be processed and stitched to build a spatial map of the transcripts across the tissue section.

scan_protocol: Xenium In Situ Analyzer

data_processing:
Baysor (v0.6.2) was used to re-segment cells with prior being default segmentations (cell_boundaries.parquet). Scanpy (v1.10.1) workflows were used for normalization to the median the downstream analysis.
The processed anndata object (processed_data.h5ad) contains cells after re-segmentation and integration. .X contains log-normalized counts.

label: Xenium Human Probe Set

organism: Homo sapiens

source_name: 5 µm kidney section

label_protocol: Xenium Human Probe Set

extract_protocol: 5 μm sections were taken for Xenium.

tag: tissue

value: kidney


title: SrcapKD_Rep1_TTseq

description: 4sU-labelled RNA

value: Srcap knockdown for 48 hours


title: Smarcad1KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Smarcad1 knockdown for 48 hours


title: SrcapKD_Rep2_TTseq

description: 4sU-labelled RNA


title: ControlKD_Rep3_TTseq

description: 4sU-labelled RNA


title: Smarcal1KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Smarcal1 knockdown for 48 hours


title: Smarcad1KD_Rep1_TTseq

description: 4sU-labelled RNA


title: Zranb3KD_Rep1_TTseq

description: 4sU-labelled RNA


title: Smarca4KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Smarca4 knockdown for 48 hours


title: Smarcal1KD_Rep1_TTseq

description: 4sU-labelled RNA


title: ShprhKD_Rep1_TTseq

description: 4sU-labelled RNA

value: Shprh knockdown for 48 hours


title: Smarca2KD_Rep1_TTseq

description: 4sU-labelled RNA

value: Smarca2 knockdown for 48 hours


title: Smarca5KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Smarca5 knockdown for 48 hours


title: Smarca5KD_Rep1_TTseq

description: 4sU-labelled RNA


title: Smarca2KD_Rep2_TTseq

description: 4sU-labelled RNA


title: Rad54l2KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Rad54l2 knockdown for 48 hours


title: Smarca4KD_Rep1_TTseq

description: 4sU-labelled RNA


title: ShprhKD_Rep2_TTseq

description: 4sU-labelled RNA


title: Rad54bKD_Rep2_TTseq

description: 4sU-labelled RNA

value: Rad54b knockdown for 48 hours


title: Rad54l2KD_Rep1_TTseq

description: 4sU-labelled RNA


title: Rad54lKD_Rep2_TTseq

description: 4sU-labelled RNA

value: Rad54l knockdown for 48 hours


title: Ino80KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Ino80 knockdown for 48 hours


title: Rad54lKD_Rep1_TTseq

description: 4sU-labelled RNA

value: embryonic stem cells


title: HltfKD_Rep2_TTseq

description: 4sU-labelled RNA

value: wild-type

value: Hltf knockdown for 48 hours


title: Rad54bKD_Rep1_TTseq

description: 4sU-labelled RNA


title: HltfKD_Rep1_TTseq

description: 4sU-labelled RNA


title: HellsKD_Rep2_TTseq

description: 4sU-labelled RNA

value: Hells knockdown for 48 hours


title: Ino80KD_Rep1_TTseq

description: 4sU-labelled RNA


title: Ercc6KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Ercc6 knockdown for 48 hours


title: HellsKD_Rep1_TTseq

description: 4sU-labelled RNA


title: Ercc6lKD_Rep2_TTseq

description: 4sU-labelled RNA

value: Ercc6l knockdown for 48 hours


title: Chd9KD_Rep1_TTseq

description: 4sU-labelled RNA

value: Chd9 knockdown for 48 hours


title: Ep400KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Ep400 knockdown for 48 hours


title: Chd9KD_Rep2_TTseq

description: 4sU-labelled RNA


title: Ep400KD_Rep1_TTseq

description: 4sU-labelled RNA


title: Chd8KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Chd8 knockdown for 48 hours


title: Chd8KD_Rep1_TTseq

description: 4sU-labelled RNA


title: Chd7KD_Rep1_TTseq

description: 4sU-labelled RNA

value: Chd7 knockdown for 48 hours


title: Chd5KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Chd5 knockdown for 48 hours


title: Chd2KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Chd2 knockdown for 48 hours


title: Chd5KD_Rep1_TTseq

description: 4sU-labelled RNA


title: Chd3KD_Rep1_TTseq

description: 4sU-labelled RNA

value: Chd3 knockdown for 48 hours


title: Chd1KD_Rep1_TTseq

description: 4sU-labelled RNA

value: Chd1 knockdown for 48 hours


title: Ercc6lKD_Rep1_TTseq

description: 4sU-labelled RNA


title: Btaf1KD_Rep2_TTseq

description: 4sU-labelled RNA

value: Btaf1 knockdown for 48 hours


title: Chd3KD_Rep2_TTseq

description: 4sU-labelled RNA


title: Chd2KD_Rep1_TTseq

description: 4sU-labelled RNA


title: Ercc6KD_Rep1_TTseq

description: 4sU-labelled RNA


title: AtrxKD_Rep2_TTseq

description: 4sU-labelled RNA

value: Atrx knockdown for 48 hours


title: Chd1lKD_Rep1_TTseq

description: 4sU-labelled RNA

value: Chd1l knockdown for 48 hours


title: Chd1lKD_Rep2_TTseq

description: 4sU-labelled RNA

value: embryonic stem cells


title: Chd1KD_Rep2_TTseq

description: 4sU-labelled RNA

value: wild-type


title: Btaf1KD_Rep1_TTseq

description: 4sU-labelled RNA


title: Chd7KD_Rep2_TTseq

description: 4sU-labelled RNA


title: Chd4KD_Rep1_TTseq

description: 4sU-labelled RNA

value: Chd4 knockdown for 48 hours


title: AtrxKD_Rep1_TTseq

description: 4sU-labelled RNA


title: Patient 10 CSF Low MOCA scRNAseq

status: Public on Apr 23 2025

city: Boston

first: Kris

last: Kahle

address: 55 Fruit Street

institute: MGH

description:
Library name: Sample 19
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)"
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CSF

extract_protocol:
PBMCs were isolated from fresh whole blood using Ficoll-Paque gradient according to manufacturer's protocol. Cells were washed twice in 1× Dulbecco's PBS and resuspended in 1× Dulbecco's PBS with 0.04% bovine serum albumin ranging from 800-1200 cells/ul. Fresh CSF was kept on ice until processing. CSF was centrifuged at 1500 rpm for 10 minutes, and supernatant was aspirated to leave 50 ul for cell counting and loading. PBMC and CSF samples were counted using 4% trypan blue and a hemocytometer. Single-cell suspensions were loaded onto the Chromium Single Cell Controller using 10x Genomics Single Cell 5' v2 kit and protocol. A target cell number of 10000 was used for PBMCs. All CSF cells were loaded.
Library construction was performed by the Yale Center for Genome Analysis according to the manufacturer's (10X Genomics) guidelines. Sequencing was performed on the NovaSeq S4 instrument.

value: CSF


title: Patient 9 PBMC  Low MOCA scRNAseq

description:
Library name: Sample 18
10x Genomics

source_name: PBMC

value: PBMC


title: Patient 10 PBMC  Low MOCA scRNAseq

description:
Library name: Sample 20
10x Genomics


title: Patient 8 CSF Low MOCA scRNAseq

description:
Library name: Sample 15
10x Genomics


title: Chd4KD_Rep2_TTseq

description: 4sU-labelled RNA


title: Patient 9 CSF Low MOCA scRNAseq

description:
Library name: Sample 17
10x Genomics


title: Patient 7 CSF Low MOCA scRNAseq

description:
Library name: Sample 13
10x Genomics


title: Patient 7 PBMC  Low MOCA scRNAseq

description:
Library name: Sample 14
10x Genomics


title: Patient 8 PBMC  Low MOCA scRNAseq

description:
Library name: Sample 16
10x Genomics


title: Patient 6 CSF Unknown MOCA scRNAseq

description:
Library name: Sample 11
10x Genomics


title: Patient 6 PBMC  Unknown MOCA scRNAseq

description:
Library name: Sample 12
10x Genomics


title: Patient 5 PBMC  High MOCA scRNAseq

description:
Library name: Sample 10
10x Genomics


title: Patient 5 CSF High MOCA scRNAseq

description:
Library name: Sample 9
10x Genomics


title: Patient 4 PBMC  High MOCA scRNAseq

description:
Library name: Sample 8
10x Genomics


title: Patient 4 CSF High MOCA scRNAseq

description:
Library name: Sample 7
10x Genomics


title: Patient 1 CSF High MOCA scRNAseq

description:
Library name: Sample 1
10x Genomics


title: Patient 3 CSF High MOCA scRNAseq

description:
Library name: Sample 5
10x Genomics


title: Patient 3 PBMC  High MOCA scRNAseq

description:
Library name: Sample 6
10x Genomics


title: Patient 1 PBMC  High MOCA scRNAseq

description:
Library name: Sample 2
10x Genomics


title: Patient 2 PBMC  High MOCA scRNAseq

description:
Library name: Sample 4
10x Genomics


title: Patient 2 CSF High MOCA scRNAseq

description:
Library name: Sample 3
10x Genomics


title: 7d, biological rep2

status: Public on Apr 22 2025

city: Fujisawa

first: Yoshinao

last: Oki

state: Kanagawa

address: 1866 Kameino

department: Department of Applied Biological Science

country: Japan

institute: Nihon University College of Bioresource Sciences

description: Gene expression data from AC derived from fat tissue

hyb_protocol: Biotin labeled cRNA samples were fragmented and then hybridized to the Affymetrix GeneChip® Porcine Genome Array.

scan_protocol: The data from microarrays was obtained by scanning microarrays using GeneChip® Scanner 3000.

data_processing: The data were analyzed with RMA using R/Bioconductor.

label: biotin

source_name: Liver after 7-day 70% partial hepatectomy in mice.

label_protocol: 5 µg each of high quality total RNA was used in double stranded cDNA synthesis and labeling reactions using the GeneChip® Expression 3’-Amplification IVT Labelling Kit (Affymetrix).

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.

value: liver


title: Bu-KAI-24

status: Public on Apr 02 2025

city: Jacksonville

last: Zhao

state: FL

address: 4500 San Pablo Rd S

department: Neuroscience

institute: Mayo Clinic

description:
Library name: Bu-KAI-24
10X Genomics

data_processing:
The single cell sequence preprocessing was performed using the standard 10x Genomics Cell Ranger Single Cell Software Suite v.3.1.0.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files and matrix files (cellranger output)

source_name: brain cortex

extract_protocol:
Mice were transcardially perfused with PBS and the cortical tissues were quickly dissected and enzymatically digested using the Neural Tissue Dissociation kit (P; Cat# 130-092-628; Miltenyi Biotec) at 37°C in the gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec). The myelin was then removed using magnetic bead separation (Myelin Removal Beads II, Cat# 130-096-733; Miltenyi Biotec) followed by the red blood cell lysis (Cat# 130-094-183; Miltenyi Biotec) and dead cell removal (Cat# 130-090-101; Miltenyi Biotec) according to the manufacturer’s instructions. The final cell pellet was suspended in Ca/Mg-free PBS supplemented with 0.5% FBS for downstream analysis. In all samples, more than 90% of the cells were viable based on trypan blue examination.
scRNA-seq was performed on isolated cortical samples using the chromium platform (10x Genomics) with the 3′ gene expression V3 kit, using a targeted input of ∼6,000–9,000 cells per sample. In brief, gel-beads in emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs using Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly-A-tailing, adaptor ligation, and 10x-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using the TapeStation (Agilent) analysis and then sequenced on a HiSeq 4000 instrument (Illumina) targeting a depth of 25,000–50,000 reads per cell.

value: brain cortex

value: Ctrl

tag: Sex

value: Male


title: 7d, biological rep1


title: 14d, biological rep1

description: Gene expression data from DFAT grew to semiconfluence

source_name: Liver after 14-day 70% partial hepatectomy in mice.


title: Bu-KAI-20

description:
Library name: Bu-KAI-20
10X Genomics

value: Female


title: 4d, biological rep1

source_name: Liver after 4-day 70% partial hepatectomy in mice.


title: 1d, biological rep2

source_name: Liver after 1-day 70% partial hepatectomy in mice.


title: 3d, biological rep1

source_name: Liver after 3-day 70% partial hepatectomy in mice.


title: Bu-KAI-18

description:
Library name: Bu-KAI-18
10X Genomics

value: WT


title: 0d, biological rep3

source_name: Liver after 0-day 70% partial hepatectomy in mice.


title: 14d, biological rep3


title: 14d, biological rep2


title: Bu-KAI-19

description:
Library name: Bu-KAI-19
10X Genomics

value: TAM


title: 2d, biological rep1

source_name: Liver after 2-day 70% partial hepatectomy in mice.


title: 1d, biological rep3


title: 0d, biological rep1


title: 2d, biological rep2


title: Bu-KAI-21

description:
Library name: Bu-KAI-21
10X Genomics


title: 4d, biological rep3


title: Bu-KAI-22

description:
Library name: Bu-KAI-22
10X Genomics


title: 1d, biological rep1


title: 0d, biological rep2


title: Bu-KAI-17

description:
Library name: Bu-KAI-17
10X Genomics


title: 7d, biological rep3


title: 4d, biological rep2


title: 3d, biological rep2


title: 2d, biological rep3


title: 3d, biological rep3


title: Bu-KAI-23

description:
Library name: Bu-KAI-23
10X Genomics


title: Bu-KAI-16

description:
Library name: Bu-KAI-16
10X Genomics


title: Bu-KAI-13

description:
Library name: Bu-KAI-13
10X Genomics


title: Bu-KAI-11

description:
Library name: Bu-KAI-11
10X Genomics


title: Bu-KAI-14

description:
Library name: Bu-KAI-14
10X Genomics


title: Bu-KAI-15

description:
Library name: Bu-KAI-15
10X Genomics


title: Bu-KAI-12

description:
Library name: Bu-KAI-12
10X Genomics


title: Bu-KAI-9

description:
Library name: Bu-KAI-9
10X Genomics


title: Bu-KAI-10

description:
Library name: Bu-KAI-10
10X Genomics


title: Bu-KAI-8

description:
Library name: Bu-KAI-8
10X Genomics


title: Bu-KAI-7

description:
Library name: Bu-KAI-7
10X Genomics


title: Bu-KAI-6

description:
Library name: Bu-KAI-6
10X Genomics


title: Bu-KAI-5

description:
Library name: Bu-KAI-5
10X Genomics


title: Bu-KAI-3

description:
Library name: Bu-KAI-3
10X Genomics


title: MS6_N_NS

status: Public on Mar 17 2025

city: Paris

first: Marc

last: Monot

address: 28 rue du docteur roux

country: France

institute: Institut Pasteur

data_processing:
sequana_rnaseq 0.15.2 from the pipeline Sequana 0.14.1 (Ref. https://joss.theoj.org/papers/10.21105/joss.00352)
Reads were trimmed from adapters using Cutadapt 2.10 then mapped to the human genome (hg38) using STAR 2.7.8 with the following paramaters “--outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 16 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --alignIntronMax 1 --clip3pAdapterSeq TGGAATTCTCGGGTGCCAAGG TGGAATTCTCGGGTGCCAAGG --clip3pAdapterMMp 0.1 0.1”.
FeatureCounts 2.0.1 with the multimapper option was used to produce the count matrix, assigning reads to features using corresponding primary annotation with strand-specificity information.
Differential expression testing was conducted using DESeq2 (PMID: 25516281)
Assembly: human HG38 (GRCh38, NCBI_Assembly:GCA_000001405.15)
Supplementary files format and content: tab-delimited text includes raw counts for each sample

source_name: Blood

extract_protocol:
Total RNA was extracted from thawed QIAzol cell lysates using miRNeasy Mini
Small RNA libraries were prepared from 100 ng of Total RNA using the Netflex Small RNA-Seq Kit v4 with UDIs

treatment_protocol: PBMCs were obtained by Ficoll gradient centrifugation of blood samples and CD4+ T cells were isolated by negative magnetic selection using the CD4+ T cell isolation kit and an autoMACS Pro Separator (Miltenyi Biotec).

value: Blood

tag: disease

value: relapsing-remitting multiple sclerosis

value: CD4+ T cell

value: Naive


title: Bu-KAI-4

description:
Library name: Bu-KAI-4
10X Genomics


title: MS5_N_NS


title: Bu-KAI-1

description:
Library name: Bu-KAI-1
10X Genomics


title: MS1_EM_NS

value: Effector memory


title: MS6_EM_NS


title: MS7_N_NS


title: MS7_EM_NS


title: MS5_EM_NS


title: MS1_N_NS


title: D6_N_NS

value: healthy


title: D6_EM_NS


title: D4_N_NS


title: D4_EM_NS


title: D5_N_NS


title: D5_EM_NS


title: GEX_56R

description: 10X Genomics

data_processing:
SnRNA-Seq data were aligned and quantified using the 10X Genomics Cell Ranger Software Suite (v3.1.0) against a custom "pre-mRNA" human reference (GRCh38-1.2.0.pre-mrna) generated according to the steps detailed by 10x Genomics (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references).
Assembly: GRCh38-1.2.0.pre-mrna
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Brain (temporal cortex)

extract_protocol:
To isolate nuclei, the frozen tissue (50-60 mg) was thawed for 2 minutes in 2 mL of ice-cold Nuclei EZ Lysis Buffer (Sigma, Cat # NUC-101), supplemented with EDTA-free protease inhibitors (Sigma, Cat # 11836170001) and 0.4 U μL−1 recombinant RNase inhibitors (Takara Bio USA, Cat # 2313A) before homogenizing with a glass Dounce tissue grinder (10-15 strokes with pestle A, followed by 10 strokes with pestle B. Sigma, Cat # D8938). An additional 2 mL of lysis buffer supplemented with protease and RNase inhibitor was added to the homogenized tissue and incubated for 5 minutes. The nuclei suspension was then filtered through a 40-μm cell strainer (Corning, Cat # 352340), followed by centrifugation at 300 x g for 5 minutes. The nuclei pellet was resuspended with 900 μL debris removal solution (Miltenyi Biotech, Cat # 130-109-398) containing 0.4 U μL−1 RNase inhibitors and 3.1 mL of Dulbecco's phosphate-buffered saline (DPBS) without calcium and magnesium. Next, 4 mL of DPBS was overlaid carefully onto the top of the nuclei resuspension. The nuclei were then pelleted again by centrifugation for 5 minutes at 3,000 x g. After removing the supernatant, the nuclei were resuspended in 500 µL of 1% BSA in DPBS with 0.4 U μL−1 RNase inhibitors. All procedures for nuclei isolation were carried out on ice or at 4°C. The density of the nuclei suspension was determined using a C-chip-disposable hemocytometer (INCYTO, Cat # DHC-B02-5) with trypan blue staining (Bio-Rad, Cat # 1450013).
The 59 samples were processed in 10 batches. Each batch had 5 to 6 samples from individuals of the same sex randomly selected from each of the AD and APOE genotype groups, i.e., control APOE2 carriers, control APOE3 homozygotes, control APOE4 carriers, AD APOE2 carriers, AD APOE3 homozygotes, and AD APOE4 carriers (6 groups in total). The samples from males and females were processed in alternating batches. A total of 5000 nuclei per sample were loaded to the Chromium microfluidic chip for cDNA library preparation using the Chromium Single Cell 3' Library and Gel Bead kit v3 (10X Genomics, Cat # 1000075) following the manufacturer's instructions.

value: Brain (temporal cortex)

tag: pathological diagnosis

value: AD

value: female


title: GEX_58R

description: 10X Genomics

value: Control


title: GEX_55R

description: 10X Genomics


title: GEX_57R

description: 10X Genomics


title: GEX_59R

description: 10X Genomics


title: Bu-KAI-2

description:
Library name: Bu-KAI-2
10X Genomics


title: GEX_49R

description: 10X Genomics

value: male


title: GEX_51R

description: 10X Genomics


title: GEX_52R

description: 10X Genomics


title: GEX_48R

description: 10X Genomics


title: GEX_43R

description: 10X Genomics


title: GEX_44R

description: 10X Genomics


title: GEX_60R

description: 10X Genomics


title: GEX_40R

description: 10X Genomics


title: GEX_46R

description: 10X Genomics


title: GEX_41R

description: 10X Genomics


title: GEX_42R

description: 10X Genomics


title: GEX_38R

description: 10X Genomics


title: GEX_39R

description: 10X Genomics


title: GEX_36R

description: 10X Genomics


title: GEX_45R

description: 10X Genomics


title: GEX_34R

description: 10X Genomics


title: GEX_29R

description: 10X Genomics


title: GEX_31R

description: 10X Genomics


title: GEX_47R

description: 10X Genomics


title: GEX_24R

description: 10X Genomics


title: GEX_32R

description: 10X Genomics


title: GEX_30R

description: 10X Genomics


title: GEX_37R

description: 10X Genomics


title: GEX_50R

description: 10X Genomics


title: GEX_23R

description: 10X Genomics


title: GEX_22R

description: 10X Genomics


title: GEX_26R

description: 10X Genomics


title: GEX_28R

description: 10X Genomics


title: GEX_19R

description: 10X Genomics


title: GEX_35R

description: 10X Genomics


title: GEX_27R

description: 10X Genomics


title: GEX_13R

description: 10X Genomics


title: GEX_14R

description: 10X Genomics


title: GEX_20R

description: 10X Genomics


title: GEX_15R

description: 10X Genomics


title: GEX_17R

description: 10X Genomics


title: GEX_33R

description: 10X Genomics


title: GEX_11R

description: 10X Genomics


title: GEX_21R

description: 10X Genomics


title: GEX_9R

description: 10X Genomics


title: GEX_10R

description: 10X Genomics


title: GEX_7R

description: 10X Genomics


title: GEX_8R

description: 10X Genomics


title: GEX_12R

description: 10X Genomics


title: GEX_18R

description: 10X Genomics


title: GEX_5R

description: 10X Genomics


title: GEX_6R

description: 10X Genomics


title: GEX_4R

description: 10X Genomics


title: GEX_3R

description: 10X Genomics


title: GEX_1R

description: 10X Genomics


title: right atrial appendage, sinus rhythm, patient nr. 1430

status: Public on Mar 08 2025

city: Chicago

first: Igor

last: Efimov

state: Illinois

address: 303 E Superior St

institute: Northwestern University

data_processing:
Sequence reads underwent trimming with Trimmomatic v0.36 to eliminate potential adapter sequences and low-quality nucleotides.
The trimmed reads were then aligned to the Homo sapiens GRCh38 reference genome from ENSEMBL using the STAR aligner v2.5.2b.
Unique gene hit counts were determined using featureCounts from the Subread package v1.5.2, and the results were summarized and reported based on the gene_id feature in the annotation file.
Only unique reads that mapped within exon regions were included in the counts.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: comma-separated text file includes raw counts for each Sample
Supplementary files format and content: comma-separated text file include TPM values for each Sample

source_name: human patient right atrial appendage biopsy

extract_protocol:
Right atrial appendages were obtained from patients undergoing cardiac surgery. Tissues were immediately flash frozen in liquid nitrogennd and stored at -80 °C. Total mRNA was extracted from 40 mg of tissue with RNeasy Fibrous Tissue Mini Kit (Qiagen). RNA purity and yield were quality checked with Agilent Bioanalyzer to satisfy RIN >7 and total RNA amount 3-5 μg.
TruSeq RNA Library Prep Kit (Illumina)

tag: age

tag: diagnosis group

value: sinus rhythm


title: GEX_2R

description: 10X Genomics


title: WT Striatum male mRNA rep4 [Msh2_6mon]

status: Public on Feb 10 2025

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

description:
MRQ121_4STR
mRNA

data_processing:
Libraries for RNA-seq were sequenced using an Illumina Novaseq S4.
The generated reads were mapped to the mouse genome GRCm38 with aligner STAR 2.7.5c with default parameter settings.
Raw counts were obtained with Samtools 1.10 and HTSeq 0.12.3 using refSeq gene model (mm10) as reference. Only uniquely mapped reads were used for the subsequent analyses.
Assembly: Genome version Mouse GRCm38
Supplementary files format and content: Semicolon-delimited csv files include FPKM and Count values for each Sample.

source_name: Corpus Striatum

extract_protocol:
Brain striatal tissues were dissected from all mice at 6 months of age. RNA was extracted using a Qiagen RNeasy kit.
Libraries for RNA-seq were prepared using the Illumina TruSeq stranded library preparation protocol (Illumina Inc).

value: Corpus Striatum

tag: strain/background

value: 6 months

tag: well address

value: Wild type


title: WT Striatum male mRNA rep2 [Msh2_6mon]

description:
MRQ113_3STR
mRNA


title: WT Striatum female mRNA rep4 [Msh2_6mon]

description:
MRQ116_5STR
mRNA


title: WT Striatum female mRNA rep2 [Msh2_6mon]

description:
MRQ108_2STR
mRNA


title: right atrial appendage, sinus rhythm, patient nr. 1426

value: human patient right atrial appendage biopsy


title: WT Striatum male mRNA rep3 [Msh2_6mon]

description:
MRQ117_4STR
mRNA


title: WT Cortex male mRNA rep4 [Msh2_6mon]

description:
MRQ121_4CTX
mRNA

source_name: Cerebral Cortex

value: Cerebral Cortex


title: WT Striatum female mRNA rep1 [Msh2_6mon]

description:
MRQ101_5STR
mRNA


title: WT Cortex male mRNA rep1 [Msh2_6mon]

description:
MRQ100_1CTX
mRNA


title: WT Striatum female mRNA rep3 [Msh2_6mon]

description:
MRQ116_3STR
mRNA


title: WT Cortex female mRNA rep3 [Msh2_6mon]

description:
MRQ116_3CTX
mRNA


title: WT Cortex female mRNA rep4 [Msh2_6mon]

description:
MRQ116_5CTX
mRNA


title: Het (Q140) KI Striatum male mRNA rep4 [Msh2_6mon]

description:
MRQ115_4STR
mRNA

value: Het (Q140) KI


title: WT Cortex female mRNA rep1 [Msh2_6mon]

description:
MRQ101_5CTX
mRNA


title: WT Cortex female mRNA rep2 [Msh2_6mon]

description:
MRQ108_2CTX
mRNA


title: WT Cortex male mRNA rep2 [Msh2_6mon]

description:
MRQ113_3CTX
mRNA


title: Het (Q140) KI Striatum male mRNA rep1 [Msh2_6mon]

description:
MRQ110_4STR
mRNA


title: Het (Q140) KI Striatum male mRNA rep3 [Msh2_6mon]

description:
MRQ113_4STR
mRNA


title: WT Striatum male mRNA rep1 [Msh2_6mon]

description:
MRQ100_1STR
mRNA


title: Het (Q140) KI Striatum female mRNA rep4 [Msh2_6mon]

description:
MRQ112_5STR
mRNA


title: Het (Q140) KI Striatum female mRNA rep2 [Msh2_6mon]

description:
MRQ108_3STR
mRNA


title: Het (Q140) KI Striatum female mRNA rep1 [Msh2_6mon]

description:
MRQ101_1STR
mRNA


title: WT Cortex male mRNA rep3 [Msh2_6mon]

description:
MRQ117_4CTX
mRNA


title: Het (Q140) KI Striatum female mRNA rep3 [Msh2_6mon]

description:
MRQ111_5STR
mRNA


title: Het (Q140) KI Cortex male mRNA rep4 [Msh2_6mon]

description:
MRQ115_4CTX
mRNA


title: Het (Q140) KI Cortex male mRNA rep3 [Msh2_6mon]

description:
MRQ113_4CTX
mRNA


title: Het (Q140) KI Cortex male mRNA rep2 [Msh2_6mon]

description:
MRQ110_5CTX
mRNA


title: Het (Q140) KI Cortex female mRNA rep3 [Msh2_6mon]

description:
MRQ111_5CTX
mRNA


title: Het (Q140) KI Cortex male mRNA rep1 [Msh2_6mon]

description:
MRQ110_4CTX
mRNA


title: Het (Q140) KI Cortex female mRNA rep1 [Msh2_6mon]

description:
MRQ101_1CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Striatum male mRNA rep2 [Msh2_6mon]

description:
MRQ70_4STR
mRNA

value: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl


title: Het (Q140) KI Striatum male mRNA rep2 [Msh2_6mon]

description:
MRQ110_5STR
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Striatum male mRNA rep1 [Msh2_6mon]

description:
MRQ68_1STR
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Striatum female mRNA rep4 [Msh2_6mon]

description:
MRQ106_1STR
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Striatum female mRNA rep2 [Msh2_6mon]

description:
MRQ97_1STR
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Striatum male mRNA rep4 [Msh2_6mon]

description:
MRQ73_2STR
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Striatum female mRNA rep1 [Msh2_6mon]

description:
MRQ77_2STR
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Cortex male mRNA rep3 [Msh2_6mon]

description:
MRQ71_1CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Striatum female mRNA rep3 [Msh2_6mon]

description:
MRQ97_4STR
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Striatum male mRNA rep3 [Msh2_6mon]

description:
MRQ71_1STR
mRNA


title: Het (Q140) KI Cortex female mRNA rep4 [Msh2_6mon]

description:
MRQ112_5CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Cortex female mRNA rep3 [Msh2_6mon]

description:
MRQ97_4CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Cortex female mRNA rep4 [Msh2_6mon]

description:
MRQ106_1CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Cortex male mRNA rep2 [Msh2_6mon]

description:
MRQ70_4CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Cortex female mRNA rep2 [Msh2_6mon]

description:
MRQ97_1CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Cortex female mRNA rep1 [Msh2_6mon]

description:
MRQ77_2CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Striatum male mRNA rep3 [Msh2_6mon]

description:
MRQ133_1STR
mRNA

value: Het (Q140) KI X Rgs9Cre+/-


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Cortex male mRNA rep4 [Msh2_6mon]

description:
MRQ73_2CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Striatum male mRNA rep2 [Msh2_6mon]

description:
MRQ129_2STR
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Striatum female mRNA rep4 [Msh2_6mon]

description:
MRQ127_5STR
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Striatum male mRNA rep1 [Msh2_6mon]

description:
MRQ91_3STR
mRNA


title: Het (Q140) KI Cortex female mRNA rep2 [Msh2_6mon]

description:
MRQ108_3CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Striatum female mRNA rep3 [Msh2_6mon]

description:
MRQ122_3STR
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Cortex male mRNA rep3 [Msh2_6mon]

description:
MRQ133_1CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Striatum female mRNA rep2 [Msh2_6mon]

description:
MRQ116_4STR
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Striatum female mRNA rep1 [Msh2_6mon]

description:
MRQ108_4STR
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Cortex male mRNA rep1 [Msh2_6mon]

description:
MRQ91_3CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Striatum male mRNA rep4 [Msh2_6mon]

description:
MRQ133_3STR
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Cortex male mRNA rep2 [Msh2_6mon]

description:
MRQ129_2CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Cortex female mRNA rep3 [Msh2_6mon]

description:
MRQ122_3CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Cortex male mRNA rep4 [Msh2_6mon]

description:
MRQ133_3CTX
mRNA


title: WT Striatum male mRNA rep5 [Msh2_12mon]

description:
MRQ7_2str
mRNA

value: 12 months


title: WT Striatum male mRNA rep2 [Msh2_12mon]

description:
MRQ23_2str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Cortex male mRNA rep1 [Msh2_6mon]

description:
MRQ68_1CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Cortex female mRNA rep1 [Msh2_6mon]

description:
MRQ108_4CTX
mRNA


title: WT Striatum male mRNA rep3 [Msh2_12mon]

description:
MRQ23_5str
mRNA


title: WT Striatum male mRNA rep1 [Msh2_12mon]

description:
MRQ15_3str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Cortex female mRNA rep4 [Msh2_6mon]

description:
MRQ127_5CTX
mRNA


title: WT Striatum female mRNA rep2 [Msh2_12mon]

description:
MRQ6_1str
mRNA


title: WT Striatum male mRNA rep4 [Msh2_12mon]

description:
MRQ4_1str
mRNA


title: WT Cortex male mRNA rep2 [Msh2_12mon]

description:
MRQ51_1CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Cortex female mRNA rep2 [Msh2_6mon]

description:
MRQ116_4CTX
mRNA


title: WT Cortex male mRNA rep3 [Msh2_12mon]

description:
MRQ7_2CTX
mRNA


title: WT Cortex male mRNA rep1 [Msh2_12mon]

description:
MRQ15_3CTX
mRNA


title: WT Cortex female mRNA rep4 [Msh2_12mon]

description:
MRQ6_1CTX
mRNA


title: WT Cortex female mRNA rep3 [Msh2_12mon]

description:
MRQ4_1CTX
mRNA


title: WT Striatum female mRNA rep1 [Msh2_12mon]

description:
MRQ51_1str
mRNA


title: WT Cortex female mRNA rep1 [Msh2_12mon]

description:
MRQ23_2CTX
mRNA


title: WT Cortex female mRNA rep2 [Msh2_12mon]

description:
MRQ23_5CTX
mRNA


title: Het (Q140) KI Striatum male mRNA rep3 [Msh2_12mon]

description:
MRQ30_2str
mRNA


title: Het (Q140) KI Striatum male mRNA rep4 [Msh2_12mon]

description:
MRQ8_4str
mRNA


title: Het (Q140) KI Striatum female mRNA rep3 [Msh2_12mon]

description:
MRQ51_4str
mRNA


title: Het (Q140) KI Striatum female mRNA rep4 [Msh2_12mon]

description:
MRQ52_2str
mRNA


title: Het (Q140) KI Striatum female mRNA rep1 [Msh2_12mon]

description:
MRQ27_2str
mRNA


title: Het (Q140) KI Striatum female mRNA rep2 [Msh2_12mon]

description:
MRQ45_2str
mRNA


title: Het (Q140) KI Striatum male mRNA rep1 [Msh2_12mon]

description:
MRQ20_1str
mRNA


title: Het (Q140) KI Cortex male mRNA rep4 [Msh2_12mon]

description:
MRQ51_4CTX
mRNA


title: Het (Q140) KI Cortex male mRNA rep3 [Msh2_12mon]

description:
MRQ30_2CTX
mRNA


title: Het (Q140) KI Cortex female mRNA rep4 [Msh2_12mon]

description:
MRQ8_4CTX
mRNA


title: Het (Q140) KI Cortex male mRNA rep1 [Msh2_12mon]

description:
MRQ20_1CTX
mRNA


title: Het (Q140) KI Cortex male mRNA rep2 [Msh2_12mon]

description:
MRQ24_4CTX
mRNA


title: Het (Q140) KI Cortex female mRNA rep1 [Msh2_12mon]

description:
MRQ27_2CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Striatum male mRNA rep4 [Msh2_12mon]

description:
MRQ46_1str
mRNA


title: Het (Q140) KI Cortex female mRNA rep2 [Msh2_12mon]

description:
MRQ45_2CTX
mRNA


title: Het (Q140) KI Cortex female mRNA rep3 [Msh2_12mon]

description:
MRQ52_2CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Striatum male mRNA rep1 [Msh2_12mon]

description:
MRQ12_5str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Striatum male mRNA rep3 [Msh2_12mon]

description:
MRQ42_3str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Striatum female mRNA rep3 [Msh2_12mon]

description:
MRQ49_3str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Cortex male mRNA rep4 [Msh2_12mon]

description:
MRQ9_3CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Striatum female mRNA rep1 [Msh2_12mon]

description:
MRQ31_1str
mRNA


title: Het (Q140) KI Striatum male mRNA rep2 [Msh2_12mon]

description:
MRQ24_4str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Striatum female mRNA rep4 [Msh2_12mon]

description:
MRQ9_3str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Cortex male mRNA rep3 [Msh2_12mon]

description:
MRQ46_1CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Cortex female mRNA rep4 [Msh2_12mon]

description:
MRQ49_3CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Striatum male mRNA rep2 [Msh2_12mon]

description:
MRQ16_3str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Cortex male mRNA rep1 [Msh2_12mon]

description:
MRQ12_5CTX
mRNA


title: Rgs9Cre+/- X Msh2fl/fl Striatum male mRNA rep3 [Msh2_12mon]

description:
MRQ59_2str
mRNA

value: Rgs9Cre+/- X Msh2fl/fl


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Cortex female mRNA rep1 [Msh2_12mon]

description:
MRQ16_3CTX
mRNA


title: Rgs9Cre+/- X Msh2fl/fl Striatum female mRNA rep1 [Msh2_12mon]

description:
MRQ42_4str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Cortex female mRNA rep2 [Msh2_12mon]

description:
MRQ31_1CTX
mRNA


title: Rgs9Cre+/- X Msh2fl/fl Striatum female mRNA rep3 [Msh2_12mon]

description:
MRQ8_5str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Striatum female mRNA rep2 [Msh2_12mon]

description:
MRQ39_3str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Cortex male mRNA rep2 [Msh2_12mon]

description:
MRQ42_3CTX
mRNA


title: Rgs9Cre+/- X Msh2fl/fl Striatum male mRNA rep1 [Msh2_12mon]

description:
MRQ24_1str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2fl/fl Cortex female mRNA rep3 [Msh2_12mon]

description:
MRQ39_3CTX
mRNA


title: Rgs9Cre+/- X Msh2fl/fl Striatum male mRNA rep2 [Msh2_12mon]

description:
MRQ3_3str
mRNA


title: Rgs9Cre+/- X Msh2fl/fl Striatum female mRNA rep2 [Msh2_12mon]

description:
MRQ44_1str
mRNA


title: Rgs9Cre+/- X Msh2fl/fl Cortex male mRNA rep3 [Msh2_12mon]

description:
MRQ42_4CTX
mRNA


title: Rgs9Cre+/- X Msh2fl/fl Cortex female mRNA rep2 [Msh2_12mon]

description:
MRQ8_5CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2+/fl Striatum male mRNA rep1 [Msh2_12mon]

description:
MRQ25_2str
mRNA

value: Het (Q140) KI X Rgs9Cre+/- X Msh2+/fl


title: Rgs9Cre+/- X Msh2fl/fl Cortex male mRNA rep1 [Msh2_12mon]

description:
MRQ24_1CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2+/fl Striatum male mRNA rep2 [Msh2_12mon]

description:
MRQ3_2str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2+/fl Striatum male mRNA rep4 [Msh2_12mon]

description:
MRQ5_3str
mRNA


title: Rgs9Cre+/- X Msh2fl/fl Cortex female mRNA rep1 [Msh2_12mon]

description:
MRQ59_2CTX
mRNA


title: Rgs9Cre+/- X Msh2fl/fl Cortex male mRNA rep4 [Msh2_12mon]

description:
MRQ44_1CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2+/fl Striatum female mRNA rep3 [Msh2_12mon]

description:
MRQ29_3str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2+/fl Striatum female mRNA rep4 [Msh2_12mon]

description:
MRQ33_4str
mRNA


title: Rgs9Cre+/- X Msh2fl/fl Cortex male mRNA rep2 [Msh2_12mon]

description:
MRQ3_3CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2+/fl Cortex male mRNA rep3 [Msh2_12mon]

description:
MRQ30_4CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2+/fl Cortex male mRNA rep4 [Msh2_12mon]

description:
MRQ5_3CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2+/fl Striatum male mRNA rep3 [Msh2_12mon]

description:
MRQ30_4str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2+/fl Striatum female mRNA rep2 [Msh2_12mon]

description:
MRQ25_3str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2+/fl Striatum female mRNA rep1 [Msh2_12mon]

description:
MRQ24_2str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2+/fl Cortex male mRNA rep2 [Msh2_12mon]

description:
MRQ3_2CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2+/fl Cortex male mRNA rep1 [Msh2_12mon]

description:
MRQ24_2CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2+/fl Cortex female mRNA rep2 [Msh2_12mon]

description:
MRQ25_3CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Striatum female mRNA rep5 [Msh2_12mon]

description:
MRQ8_2str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2+/fl Cortex female mRNA rep3 [Msh2_12mon]

description:
MRQ29_3CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Striatum female mRNA rep3 [Msh2_12mon]

description:
MRQ33_5str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Striatum female mRNA rep1 [Msh2_12mon]

description:
MRQ12_2str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Striatum male mRNA rep3 [Msh2_12mon]

description:
MRQ48_3str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Striatum female mRNA rep4 [Msh2_12mon]

description:
MRQ39_1str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Cortex male mRNA rep4 [Msh2_12mon]

description:
MRQ48_3CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Cortex female mRNA rep2 [Msh2_12mon]

description:
MRQ39_1CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Striatum female mRNA rep2 [Msh2_12mon]

description:
MRQ12_4str
mRNA


title: Rgs9Cre+/- Striatum male mRNA rep4 [Msh2_12mon]

description:
MRQ8_3str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Striatum male mRNA rep1 [Msh2_12mon]

description:
MRQ26_2str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2+/fl Cortex female mRNA rep4 [Msh2_12mon]

description:
MRQ33_4CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- X Msh2+/fl Cortex female mRNA rep1 [Msh2_12mon]

description:
MRQ25_2CTX
mRNA


title: Rgs9Cre+/- Striatum male mRNA rep1 [Msh2_12mon]

description:
MRQ4_3str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Cortex male mRNA rep3 [Msh2_12mon]

description:
MRQ26_2CTX
mRNA


title: Rgs9Cre+/- Striatum female mRNA rep4 [Msh2_12mon]

description:
MRQ7_3str
mRNA


title: Rgs9Cre+/- Striatum female mRNA rep2 [Msh2_12mon]

description:
MRQ23_4str
mRNA


title: Rgs9Cre+/- Striatum female mRNA rep3 [Msh2_12mon]

description:
MRQ35_1str
mRNA


title: Rgs9Cre+/- Striatum male mRNA rep3 [Msh2_12mon]

description:
MRQ5_4str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Cortex female mRNA rep4 [Msh2_12mon]

description:
MRQ8_2CTX
mRNA


title: Rgs9Cre+/- Striatum male mRNA rep2 [Msh2_12mon]

description:
MRQ5_2str
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Cortex male mRNA rep2 [Msh2_12mon]

description:
MRQ12_4CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Cortex female mRNA rep1 [Msh2_12mon]

description:
MRQ33_5CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Cortex male mRNA rep1 [Msh2_12mon]

description:
MRQ12_2CTX
mRNA


title: Rgs9Cre+/- Striatum female mRNA rep1 [Msh2_12mon]

description:
M2R22_1str
mRNA


title: Rgs9Cre+/- Cortex male mRNA rep4 [Msh2_12mon]

description:
MRQ7_3CTX
mRNA


title: Rgs9Cre+/- Cortex male mRNA rep2 [Msh2_12mon]

description:
MRQ5_2CTX
mRNA


title: Rgs9Cre+/- Cortex male mRNA rep3 [Msh2_12mon]

description:
MRQ5_4CTX
mRNA


title: Rgs9Cre+/- Cortex male mRNA rep1 [Msh2_12mon]

description:
M2R22_1CTX
mRNA


title: Rgs9Cre+/- Cortex female mRNA rep4 [Msh2_12mon]

description:
MRQ8_3CTX
mRNA


title: Rgs9Cre+/- Cortex female mRNA rep2 [Msh2_12mon]

description:
MRQ35_1CTX
mRNA


title: Rgs9Cre+/- Cortex female mRNA rep3 [Msh2_12mon]

description:
MRQ4_3CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Striatum male mRNA rep2 [Msh2_12mon]

description:
MRQ4_2str
mRNA


title: Het (Q140) KI X Msh2fl/fl Striatum male mRNA rep2 [Msh2_12mon]

description:
MRQ33_3str
mRNA

value: Het (Q140) KI X Msh2fl/fl


title: Het (Q140) KI X Msh2fl/fl Striatum male mRNA rep3 [Msh2_12mon]

description:
MRQ46_2str
mRNA


title: Het (Q140) KI X Msh2fl/fl Striatum female mRNA rep4 [Msh2_12mon]

description:
MRQ34_2str
mRNA


title: Het (Q140) KI X Msh2fl/fl Cortex male mRNA rep2 [Msh2_12mon]

description:
MRQ34_2CTX
mRNA


title: Msh2fl/fl Striatum female mRNA rep3 [Msh2_12mon]

description:
MRQ55_4str
mRNA


title: Rgs9Cre+/- Cortex female mRNA rep1 [Msh2_12mon]

description:
MRQ23_4CTX
mRNA


title: Het (Q140) KI X Msh2fl/fl Striatum female mRNA rep5 [Msh2_12mon]

description:
MRQ40_5str
mRNA


title: Het (Q140) KI X Msh2fl/fl Cortex male mRNA rep3 [Msh2_12mon]

description:
MRQ40_5CTX
mRNA


title: Het (Q140) KI X Msh2fl/fl Striatum female mRNA rep1 [Msh2_12mon]

description:
MRQ26_1str
mRNA


title: Msh2fl/fl Striatum male mRNA rep4 [Msh2_12mon]

description:
MRQ49_1str
mRNA


title: Msh2fl/fl Striatum male mRNA rep3 [Msh2_12mon]

description:
MRQ39_4str
mRNA


title: Het (Q140) KI X Msh2fl/fl Cortex female mRNA rep4 [Msh2_12mon]

description:
MRQ33_3CTX
mRNA


title: Het (Q140) KI X Msh2fl/fl Cortex male mRNA rep4 [Msh2_12mon]

description:
MRQ46_2CTX
mRNA


title: Het (Q140) KI X Msh2fl/fl Cortex female mRNA rep2 [Msh2_12mon]

description:
MRQ33_1CTX
mRNA


title: Msh2fl/fl Striatum male mRNA rep2 [Msh2_12mon]

description:
MRQ36_2str
mRNA


title: Msh2fl/fl Striatum male mRNA rep5 [Msh2_12mon]

description:
MRQ55_1str
mRNA


title: Het (Q140) KI X Msh2fl/fl Cortex female mRNA rep3 [Msh2_12mon]

description:
MRQ33_2CTX
mRNA


title: Het (Q140) KI X Msh2fl/fl Striatum female mRNA rep3 [Msh2_12mon]

description:
MRQ33_2str
mRNA


title: Msh2fl/fl Striatum male mRNA rep1 [Msh2_12mon]

description:
MRQ24_5str
mRNA


title: Het (Q140) KI X Msh2fl/fl Cortex male mRNA rep1 [Msh2_12mon]

description:
MRQ26_1CTX
mRNA


title: Het (Q140) KI X Msh2fl/fl Striatum female mRNA rep2 [Msh2_12mon]

description:
MRQ29_5str
mRNA


title: Het (Q140) KI X Msh2fl/fl Cortex female mRNA rep1 [Msh2_12mon]

description:
MRQ29_5CTX
mRNA


title: Msh2fl/fl Striatum female mRNA rep1 [Msh2_12mon]

description:
MRQ16_4str
mRNA


title: Msh2fl/fl Cortex male mRNA rep2 [Msh2_12mon]

description:
MRQ53_2CTX
mRNA


title: Het (Q140) KI X Rgs9Cre+/- Cortex female mRNA rep3 [Msh2_12mon]

description:
MRQ4_2CTX
mRNA


title: Msh2fl/fl Cortex male mRNA rep4 [Msh2_12mon]

description:
MRQ55_4CTX
mRNA


title: Msh2fl/fl Cortex male mRNA rep3 [Msh2_12mon]

description:
MRQ55_1CTX
mRNA


title: Het (Q140) KI X Msh2fl/fl Striatum male mRNA rep1 [Msh2_12mon]

description:
MRQ33_1str
mRNA


title: Msh2fl/fl Striatum female mRNA rep2 [Msh2_12mon]

description:
MRQ53_2str
mRNA


title: Msh2fl/fl Cortex male mRNA rep1 [Msh2_12mon]

description:
MRQ24_5CTX
mRNA


title: Msh2fl/fl Cortex female mRNA rep4 [Msh2_12mon]

description:
MRQ49_1CTX
mRNA


title: Msh2fl/fl Cortex female mRNA rep3 [Msh2_12mon]

description:
MRQ39_4CTX
mRNA


title: Msh2fl/fl Cortex female mRNA rep2 [Msh2_12mon]

description:
MRQ36_2CTX
mRNA


title: Msh2fl/fl Cortex female mRNA rep1 [Msh2_12mon]

description:
MRQ16_4CTX
mRNA


title: Brain, Mecp2 KO/+, exp4

status: Public on Jan 31 2025

city: St. Louis

first: Mati

middle: Tesfaye

last: Nemera

state: Missouri

address: 660 S Euclid Ave

institute: Washington University in St. Louis School of Medicine

description: Vizgen MERSCOPE Instrument

hyb_protocol: Hybridization of the tissue to gene probes for MERFISH was performed according to instructions provided by Vizgen. Briefly, after aspiration of the 70% ethanol, the 10 μm-thick tissue section mounted onto the MERSCOPE slide was washed with Sample Prep Wash Buffer (Vizgen, PN 20300001) and Formamide Wash Buffer (Vizgen, PN 20300002) while placed in the petri dish, and incubated at 37°C for 30 min in a benchtop incubator (INCU-Line, VWR). The Formamide Wash Buffer was then aspirated, and 50 μL of a custom-designed MERSCOPE gene panel mix was delivered onto the tissue section. A 2 × 2 cm piece of Parafilm M (Fisher Scientific) was carefully placed onto the tissue so that the gene panel mix was evenly spread across the tissue and no bubbles were introduced between the tissue and the film. The petri dish was closed with a lid and sealed with Parafilm M, sterilized with 70% ethanol, and placed in a humidified benchtop incubator (INCU-Line, VWR) set at 37°C for 36–48 h.

data_processing:
Cells were segmented using the Watershed algorithm, using DAPI as the Seed Stain and PolyT as the Watershed Stain.
Single-cell expression matrices were produced from quantifying the number of RNA transcripts in segmented cells.
Cell-by-gene matrix csv files provide the RNA counts of each gene in each cell. Metadata csv files provide information about each cell such as cell volume and location.

extract_protocol: Brains were placed in O.C.T-containing molds and flash frozen in liquid nitrogen. 10 μm-thick coronal tissue sections were prepared from the O.C.T. compound-embedded brain using a cryostat. Tissue sections were mounted onto specialized MERSCOPE slides (Vizgen, PN 20400001), and maintained in 70% ethanol in a sealed petri dish until gene probe hybridization according to Vizgen's protocol.

value: Brain

tag: strain

value: Mecp2 KO/+

tag: gender

value: Female


title: Brain, Mecp2 KO/+, exp2

description: Vizgen MERSCOPE Instrument


title: T4A_52x_1rep

status: Public on Jan 16 2025

city: Austin

first: Qian

last: Zhang

state: TX

address: 2515 Speedway

institute: The Unibersity of Texas at Austin

description: Library name: T4A_52x_1rep

data_processing:
Clean single-end data were trimmed with cutadapt v.4.6, using sequence ‘AGATCGGAAGAGCACACGTCT’ as 3’-adapter (-a) and sequence ‘GTTCAGAGTTCTACAGTCCGACGATC’ as 5’-adapter (-g). Only reads with minimal length of 17 bp were retained after trimming.
Next, trimmed reads were mapped onto pre-indexed human reference genome (hg38) using bowtie2 v.2.3.5.1 with the following parameters -N 0 -k 5 --ignore-quals.
Quantification was performed using featureCounts v.1.5.0 with parameters  ‘-t exon -O -s 1 -M - T 4’ and pre-filtered gencode hg38 .gtf file containing genomic coordinates of small RNAs: miRNAs, snoRNAs, snRNAs, and miscRNAs.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts for each Sample

growth_protocol: Human embryonic kidney cells (HEK293T) were routinely cultured in Dulbecco’s-modified Eagle’s media (DMEM, Sigma-Aldrich, St. Louis, MO) supplemented with 10% Opti-Gold fetal bovine serum, FBS (GenDEPOT, Katy, TX) and 1% HyClone penicillin and streptomycin (P/S) mix (Cytiva, Marlborough, MA) at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated from HEK293T cells (at least ~106 cells per sample) using TRI reagent (Sigma-Aldrich) and DirectZol RNA Miniprep kit (Zymo Research, Irvine, CA, #R2050/#R2070).
Small RNA-Seq (single-end strategy 50bp) libraries were prepared at Novogene Co. according to the manufacturer’s instructions for the Illumina platform (Illumina, San Diego, CA).

treatment_protocol: To generate 52X T4A and 52X WT CTD HEK293T cells, transient transfection of 1.5 μg of either plasmid (per 1 well of 6-well plate) was performed using PEI (polyethylenimine) reagent (6.6 μl per 1 well). Next day after transfection, cells were selected with α-amanitin (2.5 μg/ml, Sigma-Aldrich, #A2263) for 72 hours with daily drug replenishment based on preliminary time-course experiment that had shown that untransfected cells are eliminated by this time-point.

value: Human embryonic kidney

value: a-amanitin

tag: time


title: Brain, Mecp2 KO/+, exp1

description: Vizgen MERSCOPE Instrument


title: Brain, WT

description: Vizgen MERSCOPE Instrument

value: WT


title: T4A_52x_2rep

description: Library name: T4A_52x_2rep


title: APC_male_wt_4

status: Public on Jan 08 2025

city: Fayetteville

first: Ana

middle: Regina

last: Cabrera

state: AR

address: 155 Stadium Dr

institute: University of Arkansas

data_processing:
Raw counts were obtained using Salmon 1.10.2 and imported into R 4.4.1 using the tximport package, with GRCm39 annotation from AH116909.
The RNA-seq count data was stored in a DGEList object from the edgeR package, which was then transformed using the voom function from the limma package.
CPM and calcNormFactors were used to normalize the data.
Assembly: mm39
Supplementary files format and content: Matrix table with raw gene counts.

source_name: Tibialis anterior

extract_protocol:
TA were snap frozen in liquid nitrogen. RNA was extracted using trizol and a commercial kit (Thermo Fisher, PureLink RNA Mini Kit, Cat. No. 12183025).
The RNA sequencing was rered to Novogene for a mRNA library preparation (poly A enrichment)

value: Tibialis anterior

value: male

tag: timepoint

value: wild type


title: APC_male_wt_7


title: APC_male_wt_6


title: APC_male_apc_1

value: APC+/Min


title: APC_male_wt_2


title: APC_male_wt_8


title: APC_male_apc_2


title: APC_male_apc_4


title: APC_male_apc_5


title: APC_male_apc_6


title: APC_male_wt_5


title: APC_female_apc_6

value: female


title: APC_male_apc_3


title: APC_female_apc_5


title: APC_male_wt_1


title: APC_female_apc_4


title: Brain, Mecp2 KO/+, exp3

description: Vizgen MERSCOPE Instrument


title: WT_52x_2rep

description: Library name: WT_52x_2rep


title: APC_male_wt_3


title: WT_52x_1rep

description: Library name: WT_52x_1rep


title: APC_female_apc_2


title: APC_female_apc_3


title: APC_female_wt_8


title: APC_female_wt_7


title: APC_female_wt_3


title: APC_female_wt_5


title: APC_female_wt_6


title: APC_female_wt_4


title: APC_female_wt_1


title: C26_male_25days_5

value: 25 days


title: C26_male_25days_2


title: APC_female_apc_1


title: C26_male_20days_4

value: 20 days


title: C26_male_20days_3


title: C26_male_20days_7


title: C26_male_20days_6


title: C26_male_25days_8


title: C26_male_25days_4


title: APC_female_wt_2


title: C26_male_25days_7


title: C26_male_25days_3


title: C26_male_20days_5


title: C26_male_25days_6


title: C26_male_10days_8

value: 10 days


title: C26_male_20days_2


title: C26_male_10days_5


title: C26_male_10days_4


title: C26_male_10days_2


title: C26_male_10days_1


title: C26_male_25days_1


title: C26_male_10days_6


title: C26_male_pbs_7

value: control

value: pbs


title: C26_male_pbs_6


title: C26_male_10days_7


title: C26_male_pbs_8


title: C26_male_10days_3


title: C26_male_pbs_2


title: C26_male_pbs_1


title: C26_male_20days_1


title: C26_female_25days_6


title: C26_male_pbs_5


title: C26_male_pbs_3


title: C26_male_pbs_4


title: C26_female_25days_3


title: C26_female_20days_4


title: C26_female_25days_4


title: C26_female_20days_7


title: C26_female_20days_2


title: C26_female_25days_5


title: C26_female_20days_1


title: C26_female_25days_1


title: C26_female_25days_2


title: C26_female_20days_8


title: C26_female_20days_6


title: C26_female_10days_6


title: C26_female_10days_8


title: C26_female_20days_3


title: C26_female_10days_4


title: C26_female_10days_5


title: C26_female_10days_7


title: C26_female_10days_3


title: C26_female_20days_5


title: C26_female_10days_2


title: C26_female_pbs_5


title: C26_female_10days_1


title: C26_female_pbs_3


title: C26_female_pbs_7


title: C26_female_pbs_4


title: HCF09, EF-1

status: Public on Nov 13 2024

city: Leuven

first: Hywel

middle: Llewelyn

last: Roderick

address: Gasthuisberg

department: Cardiovascular Sciences

country: Belgium

institute: KULeuven

data_processing:
Gene expression was quantified at the transcript level using Salmon, with the validatMappings and -gcBias parameters switched on, to the human transcriptome. Transcript level counts were aggregated to gene level count using the import in the tximport package, setting countsFromAbundance to ‘lengthScaledTPM’ in the R.
DESeq2 was used for differential gene expression between different conditions. The batch variability of different sequencing runs was accounted for by defining “batch” as a covariate in the linear model to analyze differential gene expression.
Differential gene expression heat maps were generated by using the pheatmap, and volcano plots by EnhancedVolcano.
The overlapping genes between different conditions were obtained by VennDiagram.
Functional enrichment of the differentially expressed genes was determined using a hypergeometric test against the Gene Ontology database by using the ClueGO module of Cytoscape with Benjamini–Hochberg adjusted (FDR) P < 0.05.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw count for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

molecule: polyA RNA

source_name: heart atrium

growth_protocol: Human atrial cardiac fibroblasts (HCF) were cultured in a fibroblast medium supplemented with fetal bovine serum (FBS), fibroblast growth supplement (FGS), and penicillin/streptomycin solution.

extract_protocol:
Total RNA was isolated using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
RNA-seq library were prepared with TruSeq RNA Sample Preparation Kit following manufacturer's manual

treatment_protocol: HCFs were seeded at a density of 150000 cells/well in an antibiotic-free medium in 12-well plates.

value: heart atrium

value: HCF

value: atrial cardiac fibroblasts


title: HCF08, EF-1


title: C26_female_pbs_6


title: HCF07, EF-1


title: HCF03, Control

value: PBS


title: HCF05, NRG1


title: iAM12, EF-1

description: Immortalized atrial cardiomyocytes - iAM12

data_processing:
Gene expression was quantified at the transcript level using Salmon, with the validatMappings and -gcBias parameters switched on, to the Rnor transcriptome. Transcript level counts were aggregated to gene level count using the import in the tximport package, setting countsFromAbundance to ‘lengthScaledTPM’ in the R.
DESeq2 was used for differential gene expression between different conditions. The batch variability of different sequencing runs was accounted for by defining “batch” as a covariate in the linear model to analyze differential gene expression.
Differential gene expression heat maps were generated by using the pheatmap, and volcano plots by EnhancedVolcano.
The overlapping genes between different conditions were obtained by VennDiagram.
Functional enrichment of the differentially expressed genes was determined using a hypergeometric test against the Gene Ontology database by using the ClueGO module of Cytoscape with Benjamini–Hochberg adjusted (FDR) P < 0.05.
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text file includes raw count for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

organism: Rattus norvegicus

source_name: iAM

growth_protocol: Immortalized rat atrial cardiomyocytes (iAM) were cultured in Advanced DMEM F-12 supplemented with 2% heat-inactivated FBS, 1% penicillin/streptomycin, 1X GlutaMAX, and 100 ng/mL doxycycline for proliferation. To induce differentiation, iAM were transferred to medium without doxycycline.

treatment_protocol: iAM were seeded at a density of 6x106 cells/mL in a differentiation medium in T75-flasks and incubated for 9 days. Then, cells were treated with either compound EF-1 (32 µM), PBS, or NRG1 (0.1 µM), and cells were incubated for 16 h at 37 °C.

tag: genetic modification

value: Freshly isolated neonatal rat atrial cardiomyocytes (AMs) were transduced with a lentiviral vector conferring doxycycline (dox)-controlled expression of simian virus 40 large T antigen and stable cell lines generated through selection using puromycin

value: iAM

value: atrial myocytes


title: HCF06, NRG1

tag: cell line

value: WT


title: iAM07, NRG1

description: Immortalized atrial cardiomyocytes - iAM07

tag: cell type


title: iAM08, NRG1

description: Immortalized atrial cardiomyocytes - iAM08

tag: genotype


title: HCF01, Control

tag: treatment


title: iAM11, EF-1

description: Immortalized atrial cardiomyocytes - iAM11


title: C26_female_pbs_2

tag: tissue

value: Tibialis anterior


title: iAM09, EF-1

description: Immortalized atrial cardiomyocytes - iAM09


title: iAM05, NRG1

description: Immortalized atrial cardiomyocytes - iAM05


title: C26_female_pbs_1

tag: Sex


title: iAM02, Control

description: Immortalized atrial cardiomyocytes - iAM02


title: iAM04, Control

description: Immortalized atrial cardiomyocytes - iAM04


title: MCF7 tumor,Glucose, UCP1l 1

status: Public on Oct 17 2024

city: San Francisco

first: Nadav

last: Ahituv

state: CA

address: 1550 4th St., Rock Hall, room RH584C

department: Bioengineering and Therapeutic Sciences & Institute for Human Genetics

institute: UCSF

data_processing:
RNA-seq analysis was performed using Partek Flow
Sequences were trimmed for adapter sequence
Trimmed sequences were aligned to hg38 using STAR method
DEG were annonated using DE2Seq
Assembly: hg38
Supplementary files format and content: tab-demilited files include raw count for each sample
Supplementary files format and content: tab-demilited files include KRPM count for each sample

source_name: Xenograft from breast cancer cells

extract_protocol:
Total RNA was isolated using RNEasy Plus Kit
Libraries were constructed using TruSeq Stranded Total RNA Library Prep Kit (Illumina)

value: Xenograft from breast cancer cells

value: Breast cancer

value: ER+, PR+, HER2+

value: 15% Glucose water


title: HCF02, Control


title: iAM03, Control

description: Immortalized atrial cardiomyocytes - iAM03


title: MCF7 tumor,Glucose, control 2


title: MCF7 tumor, HFD, UCP1 3

value: High-fat diet


title: iAM01, Control

description: Immortalized atrial cardiomyocytes - iAM01


title: MCF7 tumor, HFD, UCP1 2


title: MCF7 tumor,Glucose, control 3


title: MCF7 tumor,Glucose, control 1


title: HCF04, NRG1


title: MCF7 tumor, HFD, UCP1 1


title: iAM10, EF-1

description: Immortalized atrial cardiomyocytes - iAM10


title: iAM06, NRG1

description: Immortalized atrial cardiomyocytes - iAM06


title: MCF7 tumor, HFD, control 3


title: MCF7 tumor, HFD, control 1


title: MCF7 tumor, HFD, control 2


title: MCF7 tumor,Glucose, UCP1l 2


title: MCF7 tumor, chow, UCP1 2

value: Chow diet


title: MCF7 tumor, chow, control 1


title: R299_alpha

status: Public on Oct 15 2024

city: bethesda

first: Efsun

last: Arda

state: Maryland

address: 41 medlars drive

institute: National Institutes of Health

description:
HiCh_46
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_alphaCell_5kbfilt_UCSC18_log2PET.bb
EPtree_alpha_ucsc_log2PET.bb

library_source: genomic

data_processing:
Raw reads Mapping: HiC pro
Loop calling: hichipper and FitHiChIP
Assembly: hg38
Supplementary files format and content: tab-delimited text file include consensus loops with pair-ended tags (PETs) for each cell type
Library strategy: HiChIP

molecule: genomic DNA

source_name: alpha

extract_protocol:
Sorted cells are fixed with 1% formaldehyde for 10 minutes at room temperature, after quenching, cell lysis, in situ chromatin digestion and proximity ligation, the ligated chromatin was extracted from nuclei following the protocol described in Mumbach et al (PMID: 27643841)
custom DNA libraries were prepared following the protocol described in Mumbach et al (PMID: 27643841)

value: alpha

tag: sample origin

value: Pancreas

tag: disease status

value: normal

value: Female

tag: bmi


title: R299_beta.

description:
HiCh_47
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_betaCell_5kbfilt_UCSC18_log2PET_2.bb
EPtree_beta_ucsc_log2PET.bb

source_name: beta

value: beta


title: R300_duct

description:
HiCh_45
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_ductCell_5kbfilt_UCSC18_log2PET.bb
EPtree_duct_ucsc_log2PET.bb

source_name: duct

value: duct


title: SAMN10977276_alpha

description:
HiCh_40
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_alphaCell_5kbfilt_UCSC18_log2PET.bb
EPtree_alpha_ucsc_log2PET.bb

value: Male


title: SAMN10977276_beta

description:
HiCh_41
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_betaCell_5kbfilt_UCSC18_log2PET_2.bb
EPtree_beta_ucsc_log2PET.bb


title: SAMN10977276_delta

description:
HiCh_42
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_deltaCell_5kbfilt_UCSC18_log2PET.bb
EPtree_delta_ucsc_log2PET.bb

source_name: delta

value: delta


title: SAMN10913630_delta

description:
HiCh_38
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_deltaCell_5kbfilt_UCSC18_log2PET.bb
EPtree_delta_ucsc_log2PET.bb


title: R303_delta

description:
HiCh_34
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_deltaCell_5kbfilt_UCSC18_log2PET.bb
EPtree_delta_ucsc_log2PET.bb


title: MCF7 tumor, chow, UCP1 3


title: SAMN10913630_beta

description:
HiCh_37
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_betaCell_5kbfilt_UCSC18_log2PET_2.bb
EPtree_beta_ucsc_log2PET.bb


title: R303_beta

description:
HiCh_33
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_betaCell_5kbfilt_UCSC18_log2PET_2.bb
EPtree_beta_ucsc_log2PET.bb


title: SAMN10913630_alpha

description:
HiCh_36
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_alphaCell_5kbfilt_UCSC18_log2PET.bb
EPtree_alpha_ucsc_log2PET.bb


title: SAMN10391370_alpha.

description:
HiCh_25
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_alphaCell_5kbfilt_UCSC18_log2PET.bb
EPtree_alpha_ucsc_log2PET.bb


title: MCF7 tumor, chow, control 2


title: MCF7 tumor, chow, UCP1 1


title: SAMN10737781_beta

description:
HiCh_30
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_betaCell_5kbfilt_UCSC18_log2PET_2.bb
EPtree_beta_ucsc_log2PET.bb


title: R303_alpha

description:
HiCh_32
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_alphaCell_5kbfilt_UCSC18_log2PET.bb
EPtree_alpha_ucsc_log2PET.bb


title: SAMN10737781_delta

description:
HiCh_29
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_deltaCell_5kbfilt_UCSC18_log2PET.bb
EPtree_delta_ucsc_log2PET.bb


title: SAMN10391370_beta.

description:
HiCh_24
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_betaCell_5kbfilt_UCSC18_log2PET_2.bb
EPtree_beta_ucsc_log2PET.bb


title: R290_duct.

description:
HiCh_21
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_ductCell_5kbfilt_UCSC18_log2PET.bb
EPtree_duct_ucsc_log2PET.bb


title: R290_acinar.

description:
HiCh_22
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_acinarCell_5kbfilt_UCSC18_log2PET.bb
EPtree_acinar_ucsc_log2PET.bb

source_name: acinar

value: acinar


title: SAMN10391370_delta.

description:
HiCh_27
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_deltaCell_5kbfilt_UCSC18_log2PET.bb
EPtree_delta_ucsc_log2PET.bb


title: MCF7 tumor, chow, control 3


title: SAMN10391370_delta

description:
ATAC_07
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_delta_merged_sort.bw

data_processing:
Raw reads were processed using PEPATAC package (PMID: 34859208)
Homer Suite was used to generate counts table
Assembly: hg38
Supplementary files format and content: tab-delimited file containing consensus peaks with normalized counts in each donor and cell type

extract_protocol:
sorted cells were transposed following steps described in Corces et al (PMID: 28846090), then transcposed DNA fragments were purified using a Zymo DNA Clean and Concentrator-5 Kit
custom DNA libraries were prepared following the protocol described in Corces et al (PMID: 28846090).

tag: dsease status


title: R325_alpha

description:
HiCh_59
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_alphaCell_5kbfilt_UCSC18_log2PET.bb
EPtree_alpha_ucsc_log2PET.bb


title: SAMN10737781_alpha

description:
HiCh_31
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_alphaCell_5kbfilt_UCSC18_log2PET.bb
EPtree_alpha_ucsc_log2PET.bb


title: SAMN10391370_beta

description:
ATAC_05
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_beta_merged_sort.bw


title: SAMN10391370_alpha

description:
ATAC_06
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_alpha_merged_sort.bw


title: R290_duct

description:
ATAC_01
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_duct_merged_sort.bw


title: R299_beta

description:
ATAC_23
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_beta_merged_sort.bw


title: SAMN12572087_duct

description:
HiCh_64
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_ductCell_5kbfilt_UCSC18_log2PET.bb
EPtree_duct_ucsc_log2PET.bb


title: SAMN11773852_acinar

description:
HiCh_55
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_acinarCell_5kbfilt_UCSC18_log2PET.bb
EPtree_acinar_ucsc_log2PET.bb


title: SAMN11773852_duct

description:
HiCh_56
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_ductCell_5kbfilt_UCSC18_log2PET.bb
EPtree_duct_ucsc_log2PET.bb


title: SAMN13283508_acinar.

description:
HiCh_67
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_acinarCell_5kbfilt_UCSC18_log2PET.bb
EPtree_acinar_ucsc_log2PET.bb


title: SAMN14124567_acinar

description:
ATAC_98
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_acinar_merged_sort.bw

value: male


title: SAMN11788169_duct

description:
HiCh_58
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_ductCell_5kbfilt_UCSC18_log2PET.bb
EPtree_duct_ucsc_log2PET.bb


title: R341_duct

description:
HiCh_68
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_ductCell_5kbfilt_UCSC18_log2PET.bb
EPtree_duct_ucsc_log2PET.bb


title: R325_beta

description:
HiCh_60
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_betaCell_5kbfilt_UCSC18_log2PET_2.bb
EPtree_beta_ucsc_log2PET.bb


title: R357_delta

description:
ATAC_84
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_delta_merged_sort.bw


title: R360_beta

description:
ATAC_90
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_beta_merged_sort.bw

value: female


title: R357_beta

description:
ATAC_82
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_beta_merged_sort.bw


title: SAMN11788169_acinar

description:
HiCh_57
CONSENSUS.LOOPs_EDGEs_combined_refloops_edge_level_zscore.txt
sorted_Complete_cons.loop_acinarCell_5kbfilt_UCSC18_log2PET.bb
EPtree_acinar_ucsc_log2PET.bb


title: SAMN14132340_alpha

description:
ATAC_99
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_alpha_merged_sort.bw


title: R356_delta

description:
ATAC_79
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_delta_merged_sort.bw


title: R361_delta

description:
ATAC_96
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_delta_merged_sort.bw


title: R356_alpha

description:
ATAC_78
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_alpha_merged_sort.bw


title: R360_delta

description:
ATAC_91
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_delta_merged_sort.bw


title: R360_alpha

description:
ATAC_89
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_alpha_merged_sort.bw


title: R361_alpha

description:
ATAC_94
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_alpha_merged_sort.bw


title: R356_beta

description:
ATAC_77
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_beta_merged_sort.bw


title: HP20010_duct

description:
ATAC_73
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_duct_merged_sort.bw


title: SAMN14124567_duct

description:
ATAC_97
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_duct_merged_sort.bw


title: HP20010_acinar

description:
ATAC_74
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_acinar_merged_sort.bw


title: HP19244_duct

description:
ATAC_126
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_duct_merged_sort.bw


title: SAMN12736601_duct

description:
ATAC_124
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_duct_merged_sort.bw


title: R357_alpha

description:
ATAC_83
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_alpha_merged_sort.bw


title: SAMN14327036_alpha

description:
ATAC_134
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_alpha_merged_sort.bw


title: R364_delta

description:
ATAC_133
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_delta_merged_sort.bw


title: SAMN12736601_acinar

description:
ATAC_125
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_acinar_merged_sort.bw


title: SAMN13283508_acinar

description:
ATAC_109
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_acinar_merged_sort.bw


title: SAMN13898077_acinar

description:
ATAC_103
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_acinar_merged_sort.bw


title: R364_beta

description:
ATAC_132
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_beta_merged_sort.bw


title: SAMN13283508_duct

description:
ATAC_108
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_duct_merged_sort.bw


title: SAMN13898077_duct

description:
ATAC_102
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_duct_merged_sort.bw


title: SAMN13086797_acinar

description:
ATAC_113
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_acinar_merged_sort.bw


title: SAMN13047843_duct

description:
ATAC_114
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_duct_merged_sort.bw


title: Replicate 1, 5 Days

status: Public on Oct 09 2024

data_processing:
The RNA‐seq analysis was performed with the Sequana framework (Cokelaer et al, 2017 doi:10.21105/joss.00352)
Version used: RNA‐seq pipeline (v0.13.0)
FeatureCounts 2.0.1 with the multimapper option was used to produce the count matrix, assigning reads to features using corresponding primary annotation with strand-specificity information.
Differential expression testing was conducted using DESeq2 (PMID: 25516281)
Assembly: Leptospira interrogans serovar manilae, NZ_CP011931.1
Supplementary files format and content: Files in CSV that contains Gene_ID, log2FoldChange, pvalue

organism: Leptospira interrogans serovar Manilae

source_name: serovar Manilae strain L495

extract_protocol:
Total RNA was extracted from biofilm or planktonic cells. Cells were collected by centrifugation for 15 min at 3000xg at 4°C and resuspended in 1mL TRIzol
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus prep kit following manufacturer's protocol

value: planktonic culture


title: Replicate 1, 3 Weeks

value: biofilm


title: Replicate 3, 3 Weeks


title: SAMN14132340_beta

description:
ATAC_100
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_beta_merged_sort.bw


title: Replicate 2, 5 Days


title: Replicate 4, 3 Weeks


title: Replicate 3, 5 Days


title: Replicate 4, 5 Days


title: R362_delta

description:
ATAC_130
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_delta_merged_sort.bw


title: R362_alpha

description:
ATAC_128
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_alpha_merged_sort.bw


title: Replicate 2, 3 Weeks


title: Prostate cancer - DACTPL rep1

status: Public on Oct 01 2024

city: Baltimore

first: Jianyong

last: Liu

address: 1550 Orleans St

department: Oncology

institute: Johns Hopkins University

data_processing:
rsem-1.2.09 was used for running the alignments to hg19 as well as generating transcript expression levels  for each gene, measured in expected counts and transcripts per million (TPM)
DESeq2 was used for differential expression analysis between treatment groups; TPM was used as an input
R version 4.0.4 was used to convert TPM to z-scores
Genome_build: hg19
Supplementary_files_format_and_content: Matrix of z-score, expected counts, and TPM for each gene and sample. Table of fold changes and statistical results comparing treatment groups for each gene.

source_name: Prostate cancer

growth_protocol: All cells were incubated at 37°C & 5% CO2 in ATCC-recommended medium and grown to 80-90% confluence before addition of treatment.

extract_protocol:
Following the 20-day treatment period, total RNA was extracted and purified for using Qiagen Allprep method.
250-500ng of total RNA was subjected to library synthesis using the Illumina TruSeq Stranded Total RNA Sample Preparation kit. Quantification of the libraries is performed by qPCR with the NEBNext Library Quant Kit or by the Agilent Bioanalyzer, and equimolar concentrations of each library were pooled together. Cluster generation was performed on the cBot with Illumina’s TruSeq PE Cluster Kit v3, and sequencing performed on an Illumina HS2500 platform for a 100bp x 100bp, paired end sequencing with both the TruSeq Rapid PE Cluster Kit and TruSeq Rapid SBS Kit v3 (200 cycles).

treatment_protocol: DU145 cells were exposed to either 2 nM triptolide alone, 33 nM decitabine alone, or both 2 nM triptolide and 3 nM decitabine once daily for 3 days, followed by 17 more days of treatment-free growth.

value: 2 nM triptolide + 33 nM decitabine (20 days)

tag: disease state

value: prostate cancer, CNS metastasis


title: Prostate cancer - DAC rep2

value: 33 nM decitabine (20 days)


title: Prostate cancer - DACTPL rep3


title: Prostate cancer - TPL rep3

value: 2 nM triptolide (20 days)


title: Prostate cancer - TPL rep2


title: Prostate cancer - DAC rep1


title: Prostate cancer - DAC rep3


title: Prostate cancer - Ctrl rep3

value: Vehicle (DMSO; 20 days)


title: Prostate cancer - TPL rep1


title: Prostate cancer - DACTPL rep2


title: SAMN14327036_delta

description:
ATAC_136
normalized_counts_ATACHiChIPset5_DESEQ.txt
ATAC_delta_merged_sort.bw

value: Pancreas


title: Prostate cancer - Ctrl rep1


title: Prostate cancer - Ctrl rep2


title: SNCA Tri organoid 12

status: Public on Sep 18 2024

description: 10x Genomics v3

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were performed using cellranger v6.1.1
Assembly: GRCh38-2020-A
Supplementary files format and content: compressed tab-separated and matrix values

source_name: Human induced pluripotent stem cells (hIPSCs)

extract_protocol:
Protocol of Neural Tissue Dissociation Kits (Miltenyi Biotec) according to manufacturer’s instructions
Chromium platform (10x Genomics)

tag: subclone id

value: SNCA trip

tag: flow cell

value: C

tag: lane

tag: collection date


title: SNCA Tri organoid 11

description: 10x Genomics v3

value: Human induced pluripotent stem cells (hIPSCs)


title: SNCA Tri organoid 8

description: 10x Genomics v3


title: SNCA Tri organoid 10

description: 10x Genomics v3


title: Ctrl organoids 12

description: 10x Genomics v3

value: Ctrl


title: Ctrl organoids 10

description: 10x Genomics v3

value: Male

value: B


title: SNCA Tri organoid 5

description: 10x Genomics v3


title: SNCA Tri organoid 6

description: 10x Genomics v3


title: Ctrl organoids 11

description: 10x Genomics v3


title: SNCA Tri organoid 4

description: 10x Genomics v3


title: SNCA Tri organoid 9

description: 10x Genomics v3


title: Ctrl organoids 9

description: 10x Genomics v3

value: Female


title: Ctrl organoids 8

description: 10x Genomics v3


title: Ctrl organoids 7

description: 10x Genomics v3


title: SNCA Tri organoid 3

description: 10x Genomics v3


title: SNCA Tri organoid 2

description: 10x Genomics v3

value: A


title: SNCA Tri organoid 1

description: 10x Genomics v3


title: Ctrl organoids 5

description: 10x Genomics v3


title: Ctrl organoids 6

description: 10x Genomics v3


title: Ctrl organoids 4

description: 10x Genomics v3


title: Ctrl organoids 3

description: 10x Genomics v3


title: Ctrl organoids 2

description: 10x Genomics v3


title: SNCA Tri organoid 7

description: 10x Genomics v3


title: Prostate cancer - TPL_5d_rep2

type: genomic

hyb_protocol: Genomic DNA was bisulfite converted using the Zymo Research EZ DNA methylation approach according to the manufacturer’s instructions, amplified, and hybridized to Illumina Infinium Human Methylation Beadchip using the standard Illumina protocol

scan_protocol: Array were imaged using the Illumina BeadArray Reader using the recommended Illumina iScan settings

data_processing: R version 4.0.4 was used to generate raw and normalized beta values. Normalization included preprocessing for Illumina methylation microarrays as used in Genome Studio followed by subset-quantile within array normalization (SWAN).

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol for Cy5 and Cy3 labelling

extract_protocol: Genomic DNA was extracted with DNeasy kit according manufacturer’s protocol.

treatment_protocol: DU145 cells were exposed to either 2 nM triptolide alone, 33 nM decitabine alone, or both 2 nM triptolide and 3 nM decitabine once daily for 3 days, followed by  2 more days (5 days total) or 17 more days (20 days total) of treatment-free growth.

value: 33 nM decitabine

tag: time

value: 5 days


title: LBD brain (SNCA Dup)

description: 10x Genomics v3

data_processing:
The demultiplexing, barcode processing, gene counting, and aggregation were performed using cellranger v7.0.1
Assembly: GRCh38-2020-A
Supplementary files format and content: compressed tab-separated and matrix values

source_name: Postmortem brain

extract_protocol:
Nuclei were isolated from the frozen superior temporal cortices as described previously with some modifications (Jakel, S. et al., Nature, 2019). Briefly, the frozen tissue samples were briefly exposed to 2 mL of Nuclei EZ Lysis Buffer (Sigma), supplemented with EDTA-free protease inhibitors (Sigma) and recombinant RNase inhibitors (Takara Bio USA) at 4°C. The tissue was then homogenized using a glass Dounce tissue grinder through 10-15 strokes with pestle A, followed by 10 strokes with pestle B. Then, an additional 2 mL of lysis buffer containing protease and RNase inhibitors was added to the homogenized tissue, followed by 5-minute incubation. Subsequently, the nuclei suspension was filtered using a 40-μm cell strainer and pelleted by centrifugation at 300 x g for 5 minutes. The nuclei pellets were resuspended in 900 μL of debris removal solution (Miltenyi Biotech) containing 0.4 U μL−1 RNase inhibitors and 3.1 mL of calcium and magnesium-free Dulbecco's phosphate-buffered saline (DPBS). Next, 4 mL of DPBS was carefully overlayed onto the nuclei resuspension was performed, followed by another centrifugation at 3,000 x g for 5 minutes. Post-centrifugation, the supernatant was discarded, and the nuclei were resuspended in the solution consisting of 1% BSA in DPBS, supplemented with 0.4 U μL−1 RNase inhibitors. Throughout the process, the nuclei were kept on ice or at 4°C. Lastly, the density of the nuclei suspension was calculated using a C-chip-disposable hemocytometer (INCYTO) with trypan blue staining (Bio-Rad).
Chromium platform (10x Genomics)

value: Postmortem brain

tag: npid

tag: type

value: LBD

tag: pathdx

value: M

tag: age

tag: apoe

tag: rin

tag: batch

tag: seqsat


title: Ctrl organoids 1

description: 10x Genomics v3

tag: tissue

tag: cell line

tag: genotype

tag: Sex


title: Prostate cancer - DACTPL_20d_rep2

tag: treatment

value: 2 nM triptolide+ 33 nM decitabine

value: 20 days

tag: disease state

value: prostate cancer, CNS metastasis


title: Ctrl brain 3

description: 10x Genomics v3

value: Normal


title: LBD brain 2

description: 10x Genomics v3

value: DLBD


title: LBD brain 1

description: 10x Genomics v3

value: TLBD


title: Ctrl brain 2

description: 10x Genomics v3


title: LBD brain 3

description: 10x Genomics v3


title: Ctrl brain 1

description: 10x Genomics v3


title: shACSL6_2

status: Public on Aug 02 2024

city: Guangzhou

first: Ziyang

last: Wang

state: --- Select One ---

address: 58 Zhongshan 2nd Road

country: China

institute: Ziyang Wang, Doctor, The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCh38 using Hisat2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . RSEM was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: MHCC97H cells were grown in DMEM supplemented with 10% FBS, at 37 °C in a humidified atmosphere with 5% CO2

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MHCC97H cells were infected with shNT or ACSL6 knockdown lentiviruses for 48 h, and then screened by puromycin for 3 days.

tag: cell type

value: Human liver cancer cells

value: ACSL6 knockdown

value: infected with shACSL6


title: shACSL6_1


title: HEK293T, WT, rep2

status: Public on Jul 31 2024

data_processing:
Sequence reads were trimmed using Trimmomatic v.0.38  to omit adaptor sequences
trimmed sequences were mapped to hg38 using HISAT2 v.2.2.1 (parameter: -unstranded)
read count extraction was conducted using featurecounts v.2.0.1
Assembly: hg38
Supplementary files format and content: text file including raw counts for each sample

growth_protocol: HEK293T cells were maintained in DMEM supplemented in 10% FBS and antibiotics in a humidified chamber with 5% CO2 at 37°C

extract_protocol:
RNA was isolated from HEK293T cells (at least ~106 cells per sample) using DirectZol RNA Miniprep kit (Zymo Research).
Libraries were prepared at Novogene Co. according to manufacturer’s instructions for the NEBNext Ultra RNA Library kit for Illumina.

treatment_protocol: Cells were transfected with an alpha amanitin-resistant RPB1 construct with a wild-type or T4A sequence. After 1 day the cells were supplemented with 2.5μg/ml of alpha amanitin for 48 hours

value: human embryonic kidney cells

value: transfected with RPB1 construct containing the wild-type CTD sequence


title: shNT_1

value: Control

value: infected with shNT


title: HEK293T,WT, rep1


title: LBD brain (SNCA Tri)

description: 10x Genomics v3


title: HEK293T, T4A, rep2

value: transfected with RPB1 construct containing the T4A mutation


title: Prostate cancer - TPL_20d_rep2

value: 33 nM decitabine


title: Covid_male_42409_3_B044_ATAC

status: Public on May 30 2024

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

data_processing:
Binary Base Call (BCL) files were demultiplexed into FASTQ files was performed using 10x cellranger/cellranger-atac mkfastq (10x Genomics v.1.1.0).
10x cellranger/cellranger-atac count was used to process sequencing reads by performing adapter trimming and sequence alignment to the GRCh38 (hg38) reference genome (refdata-cellranger-atacGRCh38-1.1.0). The output files for rna: atac: fragments.tsv.gz and singlecell.csv were utilized for downstream processing and quality control analysis.
HDF5 files (filtered) were then uploaded into R statistical programming language using the Seurat package (version 4.0) where normalization, scaling, integration and reference based label transfer was performed.
Genome_build: Ensembl GRCh38-3.0.0
Supplementary_files_format_and_content: Fragment TSVs (Tab separated), Single cell CSVs (Commas separated), and HDF5 file (Hierarchical Data Format).

source_name: peripheral blood mononuclear cells

extract_protocol:
PBMCs were removed from liquid nitrogen storage and immediately thawed in a 37C water bath. Cells were diluted dropwise with 37°C AIM V media up to a final volume of 10 mL. A single wash was performed in 10 mL of PBS+BSA. PBMCs were resuspended 2 mL in PBS+BSA, counted on a ViCell or Cellometer Spectrum, as above, and 1x106 cells were incubated sequentially or together with Human Trustain FcX (BioLegend #422302) and Fixable Viability Stain 510 (BD #564406), on ice according to manufacturer’s instructions. Cell were washed with PBS+BSA and stained with a master mix cocktail of antibodies (STAR*Methods/Antibodies) on ice for 25-30 minutes
Single-cell RNA-seq libraries were generated using the 10X Genomics Chromium 3’ Single Cell Gene Expression assay (#100075 or #1000121) and Chromium Controller Instrument according to the manufacturer’s published protocol. 16,000 cells from each PBMC sample was loaded into a separate Chromium Single Cell Chip B (10X Genomics #1000073) well targeting a recovery of 10,000 cells. Gel Beads-in-emulsion (GEMs) were then generated using the 10X Chromium Controller.

tag: disease

value: male

tag: visit

value: Visit 3


title: Covid_male_32209_4_B044_ATAC

value: Visit 4


title: Covid_male_42409_4_B044_ATAC


title: Covid_male_32416_4_B044_ATAC


title: Covid_male_32131_4_B044_ATAC


title: Prostate cancer - Ctl_5d_rep1

value: Vehicle (DMSO)

tag: time

value: 5 days


title: Covid_male_32415_3_B044_ATAC


title: Covid_female_32054_4_B044_ATAC

value: female


title: Covid_female_32245_4_B044_ATAC


title: Prostate cancer - Ctl_20d_rep2

value: 20 days

value: prostate cancer, CNS metastasis


title: Covid_female_31945_4_B044_ATAC


title: Prostate cancer - DAC_5d_rep1

value: 2 nM triptolide


title: Prostate cancer - TPL_5d_rep1


title: Covid_female_32140_4_B044_ATAC


title: Healthy_male_11872_1_B044_ATAC

value: Healthy

value: Visit 1


title: Prostate cancer - DACTPL_20d_rep1

value: 2 nM triptolide+ 33 nM decitabine


title: Healthy_female_11096_1_B044_ATAC


title: Covid_male_32416_3_B044_ATAC


title: Prostate cancer - Ctl_20d_rep1


title: HEK293T, T4A, rep1

value: human embryonic kidney cells


title: Healthy_male_11160_1_B038_ATAC


title: Covid_female_32255_4_B044_ATAC


title: Prostate cancer - DACTPL_5d_rep2


title: Prostate cancer - DAC_5d_rep2


title: Covid_male_32416_1_B038_ATAC


title: Covid_male_32415_4_B044_ATAC


title: Prostate cancer - Ctl_5d_rep2


title: Covid_female_32196_1_B038_ATAC


title: Prostate cancer - DAC_20d_rep2


title: Prostate cancer - TPL_20d_rep1


title: Covid_male_32251_4_B038_ATAC


title: Covid_male_42409_2_B038_ATAC

value: Visit 2


title: Covid_female_32140_3_B038_ATAC


title: Covid_male_32415_2_B038_ATAC


title: Prostate cancer - DACTPL_5d_rep1


title: Covid_female_32124_3_B038_ATAC


title: shNT_2

value: Human liver cancer cells

value: Control

value: infected with shNT


title: Covid_male_32416_2_B038_ATAC

value: male


title: Prostate cancer - DAC_20d_rep1


title: Covid_female_32196_3_B038_ATAC

value: Visit 3


title: Covid_male_42409_1_B038_ATAC


title: Healthy_female_11085_1_B038_ATAC


title: Covid_female_32196_2_B038_ATAC


title: Covid_female_32220_4_B038_ATAC

value: Visit 4


title: Covid_female_32245_3_B037_ATAC


title: Covid_male_32415_1_B038_ATAC


title: Healthy_female_11534_1_B037_ATAC


title: Covid_male_32209_2_B037_ATAC


title: Covid_male_32209_1_B037_ATAC


title: Covid_male_32209_3_B037_ATAC


title: Covid_female_32245_2_B037_ATAC


title: Covid_female_32255_2_B037_ATAC


title: Covid_female_32255_1_B037_ATAC


title: Covid_female_32038_5_B037_ATAC

value: Visit 5


title: Covid_female_31945_3_B033_ATAC


title: Covid_male_32131_2_B037_ATAC


title: Covid_female_31945_2_B033_ATAC


title: Healthy_male_11090_1_B037_ATAC


title: Covid_male_31874_4_B037_ATAC


title: Covid_female_32220_3_B033_ATAC


title: Covid_female_32255_3_B037_ATAC


title: Covid_male_32131_3_B037_ATAC


title: Covid_male_32131_1_B037_ATAC


title: Healthy_female_11224_1_B033_ATAC


title: Covid_female_31945_1_B033_ATAC


title: Healthy_female_11032_1_B033_ATAC


title: Covid_female_32038_4_B033_ATAC


title: Covid_male_32251_3_B033_ATAC


title: Covid_female_32054_3_B027_ATAC


title: Healthy_female_11776_1_B033_ATAC


title: Covid_female_32140_2_B027_ATAC


title: Covid_female_32124_2_B027_ATAC


title: Covid_female_32054_2_B027_ATAC


title: Covid_female_32054_1_B027_ATAC


title: Covid_male_32251_1_B027_ATAC


title: Covid_male_32251_2_B027_ATAC


title: Covid_female_32124_1_B027_ATAC


title: Covid_female_32220_1_B027_ATAC


title: Healthy_female_11404_1_B025_ATAC


title: Healthy_male_11820_1_B025_ATAC


title: Healthy_female_11161_1_B025_ATAC


title: Covid_male_31874_2_B025_ATAC


title: Covid_female_32038_2_B025_ATAC


title: Covid_female_31924_1_B025_ATAC


title: Covid_female_32140_1_B027_ATAC


title: Covid_female_32038_1_B025_ATAC


title: Covid_male_31874_1_B025_ATAC


title: Covid_female_31924_2_B025_ATAC


title: Covid_male_31874_3_B025_ATAC


title: Covid_female_32038_3_B025_ATAC


title: Covid_female_31924_3_B025_ATAC


title: Covid_female_32220_2_B027_ATAC


title: Healthy_male_11075_1_B024_ATAC


title: Covid_male_31207_1_B024_ATAC


title: Healthy_female_11058_1_B021_ATAC


title: Healthy_female_11004_1_B021_ATAC


title: Covid_male_31207_2_B024_ATAC


title: Healthy_male_11261_1_B024_ATAC


title: Covid_male_31207_4_B024_ATAC


title: Healthy_male_11012_1_B011_ATAC


title: Healthy_male_11222_1_B011_ATAC


title: Healthy_male_11196_1_B011_ATAC


title: Healthy_male_11558_1_B025_ATAC


title: Healthy_male_11219_1_B011_ATAC


title: Healthy_male_11423_1_B011_ATAC


title: Vector_Day_6_clone 4_biol rep 4

status: Public on May 19 2024

city: Madrid

first: Vicente

middle: Pérez

last: García

state: Madrid

address: C/ Nicolás Cabrera 1

department: Tissue and organ homeostasis

country: Spain

institute: Centro de Biologia Molecular Severo Ochoa

data_processing:
Reads were mapped to Mus musculus GRCm38 genome  assembly using HISAT2 v2.1.0.
Read counts and normalization were performed with SeqMonk software.
Assembly: GRCm38
Supplementary files format and content: Matrix with raw counts for each sample per column

extract_protocol:
Total RNA was extracted with Trizol followed by Dnase treatment using TURBO DNA-free kit (Life Technologies AM1907).
RNA-seq libraries were generated from 500ng using TruSeq Stranded mRNA library prop (Illumina, 20020594).

value: Trophoblast stem cells

value: Vector

tag: time point


title: Vector_Day_6_clone 2_biol rep 2


title: Covid_female_32245_1_B037_ATAC

data_processing:
Binary Base Call (BCL) files were demultiplexed into FASTQ files was performed using 10x cellranger/cellranger-atac mkfastq (10x Genomics v.1.1.0).
10x cellranger/cellranger-atac count was used to process sequencing reads by performing adapter trimming and sequence alignment to the GRCh38 (hg38) reference genome (refdata-cellranger-atacGRCh38-1.1.0). The output files for rna: atac: fragments.tsv.gz and singlecell.csv were utilized for downstream processing and quality control analysis.
HDF5 files (filtered) were then uploaded into R statistical programming language using the Seurat package (version 4.0) where normalization, scaling, integration and reference based label transfer was performed.
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: Fragment TSVs (Tab separated), Single cell CSVs (Commas separated), and HDF5 file (Hierarchical Data Format).

value: female


title: Vector_Day_6_clone 5_biol rep 5


title: Vector_Day_3_clone 5_biol rep 5


title: Covid_male_31207_3_B024_ATAC


title: Vector_Day_3_ clone1_biol rep 1


title: Vector_Day_0_clone 2_biol rep 2


title: Vector_Day_3_clone 4_biol rep 4


title: Vector_Day_0_clone 4_biol rep 4


title: Pigl_KO_Day_6_clone 5_biol rep 5


title: Pigl_KO_Day_6_clone 4_biol rep 4


title: Vector_Day_3_clone 3_biol rep 3


title: Vector_Day_6_ clone1_biol rep 1


title: Vector_Day_3_clone 2_biol rep 2


title: Pigl_KO_Day_6_clone 3_biol rep 3


title: Vector_Day_0_clone 3_biol rep 3


title: Vector_Day_0_clone 5_biol rep 5


title: Pigl_KO_Day_6_clone 2_biol rep 2


title: Pigl_KO_Day_6_ clone1_biol rep 1


title: Pigl_KO_Day_3_ clone1_biol rep 1


title: Pigl_KO_Day_3_clone 4_biol rep 4


title: Pigl_KO_Day_0_clone 5_biol rep 5


title: Pigl_KO_Day_3_clone 2_biol rep 2


title: Vector_Day_6_clone 3_biol rep 3


title: Pigl_KO_Day_3_clone 3_biol rep 3


title: Pigl_KO_Day_0_clone 4_biol rep 4


title: Pigf_KO_Day_6_clone 5_biol rep 5


title: Pigl_KO_Day_0_clone 2_biol rep 2


title: Pigl_KO_Day_0_clone 3_biol rep 3


title: Pigf_KO_Day_6_clone 2_biol rep 2


title: Pigf_KO_Day_6_clone 3_biol rep 3


title: Pigl_KO_Day_0_ clone1_biol rep 1


title: Pigf_KO_Day_3_clone 4_biol rep 4


title: Pigl_KO_Day_3_clone 5_biol rep 5


title: Pigf_KO_Day_3_clone 5_biol rep 5


title: Pigf_KO_Day_3_clone 3_biol rep 3


title: Pigf_KO_Day_3_ clone1_biol rep 1


title: Pigf_KO_Day_6_clone 4_biol rep 4


title: Pigf_KO_Day_0_clone 5_biol rep 5


title: Pigf_KO_Day_3_clone 2_biol rep 2


title: Pigf_KO_Day_6_ clone1_biol rep 1


title: Pigf_KO_Day_0_clone 3_biol rep 3


title: Pigf_KO_Day_0_clone 1_biol rep 1