title: P5662

description: Human post-mortem midbrain

value: M

value: Sepulveda


title: M26LA

status: Public on Apr 27 2023

type: SRA

city: Chicago

first: Igor

last: Efimov

state: Illinois

address: 303 E Superior St

country: USA

institute: Northwestern University

library_source: transcriptomic

data_processing:
Adapters and low-quality reads were removed with flexbar.
Mapping with kallisto: Reads were aligned to the GRCh38 human genome assembly with Gencode v37 comprehensive gene annotation with index and quant commands. Estimated isoform-level counts from the kallisto output were summed to genes using tximport R package (v.1.14.2) tximport function.
Assembly: GRCh38, Gencode v37
Supplementary files format and content: Matrix with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: Human donor heart

extract_protocol:
Explanted hearts were arrested with the cardioplegic solution and cooled down to +4 °C for transportation. 0.5 cm3 pieces were collected from the left and right atrial free wall, right and left ventricular base, and inferior and superior sinoatrial node. The tissue was flash frozen or stored in RNAlater (Invitrogen) overnight at +4 °C 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: tissue

value: Human donor heart

tag: cardiac chamber

value: Left atrium

tag: Sex

value: Male

tag: age

tag: health state

value: healthy


title: MCF10A-M2 cells SB 24h treatment replicate-3

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

data_processing:
RNA-Seq files were processed using the opensource BIOWDL RNAseq pipeline v4.1.0 (https://github.com/biowdl/RNA-seq)
This pipeline performs FASTQ preprocessing (including quality control, quality trimming, and adapter clipping), RNA-Seq alignment, read quantification, and optionally transcript assembly.
FastQC was used for checking raw read QC. Adapter clipping was performed using Cutadapt (v2.10) with default settings.
RNA-Seq reads’ alignment was performed using HISAT (v2.2.0) on GRCh38 human reference genome.
The gene read quantification was performed using stringtie (v1.3.6) with the option of fr-secondstrand. The gene annotation used for quantification was NONCODE version 6
Assembly: GRCh38
Supplementary files format and content: Gene TPM count in TSV format

source_name: pre-malignant human breast cell line

growth_protocol: MCF01A-M1 and MCF10A-M2 cells were maintained in DMEM/F12 (GlutaMAX™ Supplement; Thermo Fisher Scientific; Cat. Nr.: 31331028) containing 5% horse serum (Thermo Fisher Scientific; Cat. Nr.: 26050088), 0.1 μg/ml Cholera toxin (Sigma-Aldrich; Cat. Nr.: C8052), 0.02 μg/ml Epidermal Growth Factor (EGF; Sigma-Aldrich; Cat. Nr.: 01-107), 0.5 μg/ml Hydrocortisone (Sigma-Aldrich; Cat. Nr.: H0135), 10 μg/ml Insulin (Sigma-Aldrich; Cat. Nr.: I6634) and 100 U/ml Penicillin/Streptomycin. MDA-MB-231 cells were cultured in Dulbecco’s modified Eagle medium (DMEM; Thermo Fisher Scientific; 41965062) supplemented with 10% fetal bovine serum (FBS; Thermo Fisher Scientific; 16000044) and 100 U/mL penicillin/streptomycin (Thermo Fisher Scientific; 15140163).All the cells were maintained in a 5% CO2, 37 °C, humidified incubator and tested negative for mycoplasma routinely. All the cell lines were checked for authenticity by short tandem repeats (STR) profiling.

extract_protocol:
Total RNA was isolated from the cells by a TRIzol reagent (Thermo Fisher Scientific; 15596026).
Library preparation and sequencing were performed by Beijing Genomics Institute (BGI, Shenzhen, China) using the Illumina platform.

treatment_protocol: Cells were seeded at 80% confluence and cultured in serum-free media overnight. The next day, SB431542 (10 uM) or TGF-beta (5 ng/mL) was added to media. DMSO or ligand buffer was added as vehicle controls, respectively.

tag: cell line

value: MCF10A cells (normal human breast epithelial cell line) tranformed with HA-Ras

tag: treatment

value: Stimulated with SB431542 (10 uM) for 24 h


title: MCF10A-M2 cells TGF-beta 0h treatment replicate-1

value: Non-stimulated (control)


title: P5626

city: Montréal

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

country: Canada

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

description: Human post-mortem midbrain

data_processing:
Library strategy: Single-nuclei RNA-seq and ATAC-seq
Sequence data was preprocessed by CellRanger-arc (v1.0.1)
RNA data was analyzed by Seurat (v4.0.0)
ATAC data was analyzed by Signac (v1.5.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: RNA count matrix, ATAC peak position, and ATAC fragment files are provided by H5, BED, and TSV format, respectively.

molecule: other

source_name: substantia nigra

growth_protocol: We processed the tissue in a dounce homogenizer and then centrifuged it through 1.5 M sucrose to isolate the nuclei

extract_protocol:
10X Genomics Single Cell Multiome ATAC + Gene Expression kit
Libraries were prepared for sequencing using manufacture protocol

treatment_protocol: We stained the nuclei with 7AAD and sorted to purify nuclei from mitochondria

value: Human post-mortem midbrain

tag: group

value: PD

tag: diagnosis

value: Parkinson's disease

tag: pmi (hours)

tag: rin

tag: repository

tag: molecule

value: RNA and DNA


title: T-HEp3-NR2F1si2-AZA+atRA rep2

city: Bronx

first: Julio

middle: A

last: Aguirre-Ghiso

state: NY

address: 1301 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

description: polyA+ RNA

data_processing:
Quality control was performed using FastQC (v0.11.8).
Trim Galore! (version 0.6.5) was used to trim the adapter sequences with a quality threshold of 20. The human genome reference used was GRCh38.p13 and GENCODE release 36.
Alignment was performed using STAR aligner (v2.7.5b).
Gene level read counts were obtained by using Salmon (v1.2.1) for all libraries. All samples passed the quality control requirements with > 60% of reads uniquely mapping (>20M uniquely mapped reads for each library) using STAR.
Differential expression analysis was performed using the gene level read counts and the DESeq2 (v1.28.1) R package.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: xlsx or CSV file of normalized gene counts from all replicates or differential gene expression.
Supplementary_files_format_and_content: T-HEP3_NR2F1_KD_AA_reprog_salmon_gene_counts_normalized.xlsx: Normalized gene counts.
Supplementary_files_format_and_content: T-HEp3_NR2F1_KD_AA_reprog_deseq_comparison_knockdown_effect_all_genes.csv: Differential gene expression.
Supplementary_files_format_and_content: T-HEp3_NR2F1_KD_AA_reprog_deseq_comparison_treatment_effect_all_genes: Differential gene expression.

extract_protocol:
RNA was extracted using RNeasy mini kit and total RNA was selected for polyA+ RNAs.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: T-HEp3 (P1) primary cells derived from chicken CAM model were grown on dish and used to treat with AZA+atRA or DMSO in control and NR2F1 KD (siRNA were used) condition. Cells were seeded on dish, NR2F1 knockdown was performed using specific siRNAs. Cells were treated with 5 nM Azacytidine for two days in charcoal stripped FBS containing medium. AZA containing medium was replaced after 24 hours with fresh AZA+culture medium. On third day, AZA was removed and cells were treated with 1 uM all trans retinoic acid (atRA) in serum free medium for another 48 hours. After the reprogramming cells were used for RNA extraction and sequencing.

tag: cell type

value: head and neck squamous cell carcinoma

value: NR2F1si2 AZA+atRA


title: MCF10A-M2 cells SB 24h treatment replicate-2


title: P5331

description: Human post-mortem midbrain


title: MCF10A-M2 cells SB 24h treatment replicate-1


title: NF-24

city: Madison

first: Vanessa

last: Leone

state: WI

address: 1933 Observatory Dr.

institute: University of Wisconsin-Madison

data_processing:
The raw fastq files generated from the RNA-seq analysis were examined by the fastqc to evaluate the quality
The STAR aligner (version 2.4.2a) was used to map the raw reads to the reference mouse genome
The genetic features from Gencode (version M23) were extracted from the resulting bam file produced by STAR
The raw gene expression count matrix was then generated by featureCounts (version subread-1.4.6-p1)
EdgeR (version 3.22.5) was used to filter low-expressed genes where genes expressed below ten counts-per-million (CPM) in 4 samples were removed
Limma-Voom pipeline (version 3.38.3) was applied to normalize the filtered count matrix and perform differential gene expression analysis for pairwise comparisons
Enrichment analysis on significant DEGs with mouse-specific GO terms and KEGG pathways was conducted through Lynx
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene

organism: Mus musculus

source_name: Liver

extract_protocol:
Livers were removed and a small section was placed directly in Trizol for subsequent RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were fed one of four purified diets for 8 or 24 weeks

tag: strain

value: Liver

value: SPF

tag: 8w or 24w

tag: diet

value: FFHC


title: MCF10A-M2 cells SB 8h treatment replicate-3

value: Stimulated with SB431542 (10 uM) for 8 h


title: NF-23

tag: tissue


title: P5318

description: Human post-mortem midbrain

value: M

value: Sepulveda


title: NF-22

value: LF


title: NF-25


title: P6259

description: Human post-mortem midbrain

value: Maryland


title: P4919

description: Human post-mortem midbrain


title: T-HEp3-NR2F1si2-AZA+atRA rep1

description: polyA+ RNA


title: M26LV

value: Human donor heart

tag: cardiac chamber

value: Left ventricle

value: Male

value: healthy


title: T-HEp3-NR2F1si2-DMSO rep1

description: polyA+ RNA

value: NR2F1si2 DMSO


title: T-HEp3-NR2F1si1-AZA+atRA rep2

description: polyA+ RNA

value: NR2F1si1 AZA+atRA


title: NF-26


title: P4884

description: Human post-mortem midbrain

value: Human post-mortem midbrain

value: PD

value: Parkinson's disease

tag: Sex

value: RNA and DNA


title: T-HEp3-NR2F1si2-DMSO rep2

description: polyA+ RNA

value: head and neck squamous cell carcinoma


title: P4772

description: Human post-mortem midbrain

tag: age


title: NF-21

value: Liver

value: SPF


title: MCF10A-M2 cells SB 8h treatment replicate-1

value: MCF10A cells (normal human breast epithelial cell line) tranformed with HA-Ras

value: Stimulated with SB431542 (10 uM) for 8 h


title: MCF10A-M2 cells SB 8h treatment replicate-2


title: MCF10A-M2 cells SB 2h treatment replicate-3

value: Stimulated with SB431542 (10 uM) for 2 h


title: NF-20

value: LF


title: P4653

description: Human post-mortem midbrain

value: M

value: Sepulveda


title: NF-19


title: MCF10A-M2 cells SB 2h treatment replicate-2


title: T-HEp3-NR2F1si1-DMSO rep2

description: polyA+ RNA

value: NR2F1si1 DMSO


title: T-HEp3-NR2F1si1-DMSO rep1

description: polyA+ RNA


title: T-HEp3-NR2F1si1-AZA+atRA rep1

description: polyA+ RNA


title: P4560

description: Human post-mortem midbrain

value: F


title: MCF10A-M2 cells SB 2h treatment replicate-1


title: NF-18


title: T-HEp3-scr AZA+atRA rep2

description: polyA+ RNA

value: scr AZA+atRA


title: P4205

description: Human post-mortem midbrain


title: NF-17


title: P02284

description: Human post-mortem midbrain

value: Unknown

value: Harvard


title: MCF10A-M2 cells SB 0h treatment replicate-3

value: Stimulated with SB431542 (10 uM) for 0.5 h


title: T-HEp3-scr-AZA+atRA rep1

description: polyA+ RNA


title: NF-16

value: HF


title: C5410

description: Human post-mortem midbrain

value: Human post-mortem midbrain

value: Aged

value: Unaffected Control

value: RNA and DNA


title: T-HEp3-scr-DMSO control rep2

description: polyA+ RNA

source_name: T-HEp3-scr-DMSO control

value: head and neck squamous cell carcinoma

value: scr DMSO control


title: C4814

description: Human post-mortem midbrain


title: NF-15

value: Liver

value: SPF


title: T-HEp3-scr--DMSO control rep1

description: polyA+ RNA


title: MCF10A-M2 cells SB 0h treatment replicate-1

value: MCF10A cells (normal human breast epithelial cell line) tranformed with HA-Ras


title: NF-14


title: MCF10A-M1 cells TGF-beta 24h treatment replicate-3

source_name: normal human breast cell line

value: MCF10A cells (normal human breast epithelial cell line)

value: Stimulated with TGF-beta (5 ng/mL) for 24 h


title: C4691

description: Human post-mortem midbrain

value: M

value: Sepulveda


title: MCF10A-M1 cells TGF-beta 24h treatment replicate-2


title: NF-13


title: C4660

description: Human post-mortem midbrain

value: F


title: NF-12

value: FFVHC


title: Pre-Transplant LAP+/OC2- Fetal Hepatocyte (biol rep 4)

city: Providence

first: Jennifer

middle: Ann

last: Sanders

state: RI

address: 593 Eddy Street

department: Pediatric Endocrinology

institute: Rhode Island Hospital

data_processing:
The sequencing libraries were clustered on 3 lanes of a flowcell. After clustering, the flowcell was loaded on the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions.
The samples were sequenced using a 2x150bp Paired End (PE) configuration.
Image analysis and base calling were conducted by the HiSeq Control Software (HCS).
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Rattus norvegicus Rnor6.0 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. If a strand-specific library preparation was performed, the reads were strand-specifically counted.
Assembly: Rnor6.0
Supplementary files format and content: Raw hit counts table in text file format.

organism: Rattus norvegicus

source_name: Hepatocyte

extract_protocol:
Isolation of total RNA from adult and immunopurified fetal hepatocytes was accomplished using pellets of approximately 1 million cells and the RNeasy Mini kit (QIAGEN, Hilden, DE). For preparation of total RNA from laser captured tissue samples, tissue on individual LCM caps was digested into extraction buffer and RNA isolated using the PicoPure RNA Isolation Kit (Applied Biosystems).
RNA library preparation and sequencing reactions were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA). Sorted cell RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA). Laser-capture microdissected RNA sequencing libraries were prepared using the SMARTer Stranded Total RNA-seq Kit v2 - Pico Input Mammalian (Takara Bio, Kusatsu, Shiga, JP).

tag: developmental stage

value: Fetal

value: Hepatocyte


title: Pre-Transplant LAP+/OC2- Fetal Hepatocyte (biol rep 5)


title: MCF10A-M1 cells TGF-beta 24h treatment replicate-1

tag: cell line


title: Pre-Transplant LAP+/OC2- Fetal Hepatocyte (biol rep 3)


title: NF-11


title: MCF10A-M1 cells TGF-beta 8h treatment replicate-3

tag: treatment

value: Stimulated with TGF-beta (5 ng/mL) for 8 h


title: C4361

description: Human post-mortem midbrain

value: Human post-mortem midbrain

tag: group

value: Aged


title: MCF10A-M1 cells TGF-beta 8h treatment replicate-2


title: MCF10A-M2 cells SB 0h treatment replicate-2

value: Stimulated with SB431542 (10 uM) for 0.5 h


title: C4322

description: Human post-mortem midbrain

tag: diagnosis

value: Unaffected Control

value: RNA and DNA


title: NF-10

value: Liver


title: Pre-Transplant LAP+/OC2- Fetal Hepatocyte (biol rep 1)


title: MCF10A-M1 cells TGF-beta 8h treatment replicate-1


title: Pre-Transplant LAP+ Fetal Hepatocyte (biol rep 4)


title: Pre-Transplant LAP+ Fetal Hepatocyte (biol rep 3)


title: NF-8

value: SPF

value: FFHC


title: NF-7


title: NF-9


title: C16007

description: Human post-mortem midbrain

tag: pmi (hours)

value: Unknown

value: Miami


title: MCF10A-M1 cells TGF-beta 2h treatment replicate-3

value: MCF10A cells (normal human breast epithelial cell line)

value: Stimulated with TGF-beta (5 ng/mL) for 2 h


title: C4176

description: Human post-mortem midbrain

value: F

tag: rin

value: Sepulveda


title: Pre-Transplant LAP+ Fetal Hepatocyte (biol rep 2)

value: Fetal


title: Pre-Transplant LAP+ Fetal Hepatocyte (biol rep 1)

value: Hepatocyte


title: C4634

description: Human post-mortem midbrain

value: M

tag: repository


title: NF-6


title: Positive control, rep6

city: Ste-Anne-de-Bellevue

first: Yeon-Seon

last: Jeon

state: Quebec

address: 21111 Lakeshore

department: Natural Resource Sciences

institute: McGill University

data_processing:
Processed using the Kallisto module or the Seq2Fun v.2 module on ExpressAnalyst.ca
Assembly: GMGI_Hamer_2.0 Homarus americanus genome assembly (GCA_018991925.1) for Kallisto module; EcoOmicsDB.ca for Seq2Fun v.2 module
Supplementary files format and content: Count table in a tab-delimited text file format with RefSeq IDs for Kallisto-processed data; Count table in a tab-delimited text file format with Seq2Fun IDs for Seq2Fun-processed data

organism: Homarus americanus

source_name: whole larvae

extract_protocol:
RNA was extracted from homogenized whole larvae using Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: whole larvae

value: embryonic day 9

value: 1-methylnaphthalene at 0.3 mg/L


title: MCF10A-M1 cells TGF-beta 2h treatment replicate-1


title: NF-5


title: MCF10A-M1 cells TGF-beta 0h treatment replicate-3

value: Non-stimulated (control)


title: Pre-Transplant LAP+/OC2+ Fetal Hepatocyte (biol rep 4)


title: Negative control, rep6

value: 0.22 µm filtered seawater


title: Negative control, rep5


title: Pre-Transplant LAP+/OC2+ Fetal Hepatocyte (biol rep 3)


title: NF-4

value: Liver

value: LF


title: MCF10A-M1 cells TGF-beta 0h treatment replicate-2


title: MCF10A-M1 cells TGF-beta 0h treatment replicate-1


title: NF-3

value: SPF


title: Positive control, rep5


title: Pre-Transplant LAP+/OC2+ Fetal Hepatocyte (biol rep 1)


title: NF-2


title: MCF10A-M1 cells TGF-beta 2h treatment replicate-2


title: Pre-Transplant Adult Hepatocyte (biol rep 4)

value: Adult


title: NF-1


title: Positive control, rep4


title: MCF10A-M1 cells SB 24h treatment replicate-2

value: Stimulated with SB431542 (10 uM) for 24 h


title: MCF10A-M1 cells SB 24h treatment replicate-3

value: MCF10A cells (normal human breast epithelial cell line)


title: WAF 72%, rep6

value: WAF 72%


title: Pre-Transplant Adult Hepatocyte (biol rep 3)


title: MCF10A-M1 cells SB 24h treatment replicate-1


title: Prmt1-null iGBs replicate 3

first: Claudia

middle: L

last: Kleinman

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

institute: Lady Davis Institute for Medical Research

data_processing:
Raw reads were trimmed using Trimmomatic v0.32. First, adaptors and other Illumina-specific sequences from each read were removed using palindrome mode. Then, a four-nucleotide sliding window removes the bases once the average quality within the window falls below 30. Next, the first four bases at the start of each read were removed. Finally, reads shorter than 30 base pairs were dropped.
Cleaned reads were aligned to the mouse reference genome build mm10 using STAR v2.3.0e with default settings. Reads mapping to more than 10 locations in the genome (MAPQ < 1) were discarded.
Gene expression levels were estimated by quantifying primary alignments mapping to at most 2 locations (MAPQ >= 3) to exonic regions (the maximal genomic locus of each gene and its known isoforms) using featureCounts v1.4.4 and the mm10 ensGene annotation set from Ensembl.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Ensembl.ensGene.exon.raw_counts.tsv: Raw read counts (exonic part of the genes) for all the samples in a tab-separated file.

source_name: Spleen C57BL6/J

growth_protocol: Cells plated on 40LB cells (Nojima et al., Nat Commun. Doi 2011 10.1038/ncomms1475), IL-4 5 ng/ml, cultured 3.5 days.

extract_protocol:
Total RNA purified using QIAGEN RNeasy Plus Mini kit with On-Column DNase Digestion with the RNase-Free DNase Set step.
KAPA stranded rRNA depletion - RIBOCOP.

treatment_protocol: Activated B cells were purified as described in Nojima et al. by depleting the 40LB cells using biotinylated anti-H2K and antibiotin microbeads (MACS).

tag: genotype

value: Cg1-cre Prmt1f/f

value: Spleen

value: Purified B cells, activated

value: CD40L BAFF IL-4

value: Male


title: Negative control, rep4

value: whole larvae


title: Pre-Transplant Adult Hepatocyte (biol rep 2)

tag: cell type

value: Hepatocyte


title: WAF 72%, rep7

value: embryonic day 9


title: MCF10A-M1 cells SB 8h treatment replicate-3

value: Stimulated with SB431542 (10 uM) for 8 h


title: MCF10A-M1 cells SB 8h treatment replicate-2


title: Pre-Transplant Adult Hepatocyte (biol rep 1)


title: Pre-Transplant LAP+/OC2+ Fetal Hepatocyte (biol rep 2)

value: Fetal


title: Prmt1-null iGBs replicate 1

tag: strain

value: Female


title: Post-Transplant Fetal-Derived Colony (biol rep 249)

value: Liver


title: WAF 72%, rep5


title: Control iGBs replicate 3


title: Control iGBs replicate 2


title: Post-Transplant Adult Host (biol rep 249)


title: MCF10A-M1 cells SB 2h treatment replicate-3

value: Stimulated with SB431542 (10 uM) for 2 h


title: Positive control, rep3

value: 1-methylnaphthalene at 0.3 mg/L


title: Post-Transplant Fetal-Derived Colony (biol rep 248)


title: Control iGBs replicate 1


title: Negative control, rep1

value: 0.22 µm filtered seawater


title: MCF10A-M1 cells SB 2h treatment replicate-1

value: MCF10A cells (normal human breast epithelial cell line)


title: WAF 72%, rep4

value: WAF 72%


title: Post-Transplant Adult Host (biol rep 248)

value: Adult


title: MCF10A-M1 cells SB 2h treatment replicate-2


title: Post-Transplant Fetal-Derived Colony (biol rep 246)


title: WAF 72%, rep3


title: Prmt1-null iGBs replicate 2

value: Cg1-cre Prmt1f/f

value: Spleen


title: MCF10A-M1 cells SB 0h treatment replicate-3

value: Stimulated with SB431542 (10 uM) for 0.5 h


title: Post-Transplant Adult Host (biol rep 246)


title: Negative control, rep3


title: WAF 72%, rep2


title: MCF10A-M1 cells SB 8h treatment replicate-1


title: MCF10A-M1 cells SB 0h treatment replicate-1


title: Post-Transplant Fetal-Derived Colony (biol rep 243)


title: WAF 72%, rep1


title: Positive control, rep2


title: Post-Transplant Adult Host (biol rep 243)


title: Post-Transplant Fetal-Derived Colony (biol rep 242)


title: Negative control, rep2


title: ChickTrunk_2_Visium

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

data_processing:
Visium data was analyzed using Loupe cell browser from 10x Genomics, manually selecting the entire capture area. Data was processed using spaceranger 1.0.0 from 10x Genomics.
Data was aligned to the galGal6 chicken genome from UCSC using annotations from Ensembl 98. Data was aligned with STAR 2.5.1b as part of the spaceranger pipeline.
After spaceranger, data was analyzed in R 3.6.1 using Seurat 3.1.2. Spots were kept with > 10 counts per spot. Sctransform in Seurat was used for normalization.
Assembly: galGal6
Supplementary files format and content: *_barcodes.tsv.gz - output from spaceranger containing the barcodes from the visium experiment
Supplementary files format and content: *_features.tsv.gz - output from spaceranger containing the features (genes) from the visium experiment
Supplementary files format and content: *_matrix.mtx.gz - output from spaceranger containing the gene by spot matrix
Supplementary files format and content: rds file for each of four capture areas on visium slide - serialized R data file containing a Seurat object.
Library strategy: spatial transcriptomics

molecule: polyA RNA

organism: Gallus gallus

source_name: embryonic trunk

extract_protocol:
The Visium Spatial Gene Expression Slide PN-2000233 and associated protocol  (CG000239) from 10X Genomics were used. Fresh frozen HH24 trunk tissues were transversely cryo-sectioned to approximate single cell thickness (10um) and carefully  placed within the fiducial frame on the equilibrated slide within a cryostat set to -20C.  The slide was fixed in methanol at -20C for 30 min and air dried. The slide was then  stained with H&E and imaged using a Zeiss LSM 800 confocal microscope. Tissue was  permeabilized to release mRNA that bound to spatially barcoded capture probes.
Library preparation was done following the Visium Spatial Gene Expression User Guide  using supplied reagents in Visium kit (10X Genomics).
Whole transcriptome libraries  were sequenced and analyzed using Space Ranger (1.0.0) and Loupe browser. 10X  Genomics‘ automated image alignment software had trouble detecting one capture area  and we manually selected it in its Loupe browser based on 10X’s suggestion. Data was  generated for four individual Visium capture areas.

treatment_protocol: none; unlabeled, wild-type tissue

value: embryonic trunk

value: tissue

tag: breed

value: white leghorn

value: wild-type


title: Day4 (HH24) Chick Trunk_puck25_Slide-seq

description: NextSeq 500 Mid Output 44 * 8 * 50

data_processing:
Data processing was performed using the slide-seq tools pipeline from Broad Institute (https://github.com/MacoskoLab/slideseqtools).  Reads were aligned to the galGal6 (Gallus gallus) genome with annotations from  from Ensembl 98, and 91% of reads aligned. Downstream analysis was performed with R  3.6.1 and the Seurat package version 3.1.4.9903 (Stuart et al., 2019; Seurat v4) for  unbiased spatial analysis. In total, we detected a total of 20860 beads with around 8  million UMI counts, averaging about 381.5 umi counts per gene, and 276 mean genes  per bead. The non-tissue covering area was then filtered out based on original  imagings. Slide-seq data was annotated by integrating with 10x single-cell data using  the label transfer function in Seurat software. Prediction scores were generated for each  bead based on its original single-cell cluster annotations. Data was further analyzed and  visualized using in-house generated programs using freeware through Volta and  Scanpy single-cell analysis in Python.
Raw data in the form of bcl files was converted to fastq using bcl2fastq v2.20.0.422.
Fastq files were aligned to the chicken genome galGal6 from UCSC with gene annotations from Ensembl 98 using STAR (2.7.3a) as part of a version of the slide-seq tools pipeline (https://github.com/MacoskoLab/slideseq-tools) modified to run on an interactive server.
Steps of the slide-seq tools pipeline include tagging read sequences with 14 base bead barcode and 8 base UMI sequences, filtering bam based on quality score, trimming start sequence and PolyA tails, alignment using STAR, annotate with GTF, run Cmatcher to get bead barcodes with mismatches <= 1, and generate barcode-gene matrix using filtered barcodes with >10 UMIs.
After slide-seq tools, data was analyzed in R 3.6.1 using Seurat 3.2.3. Area under tissue was manually selected using gatepoints package (0.1.3). After examining the elbow plot, 40 principal components were used for downstream analysis, and a resolution of .2 was used in FindClusters to identify 8 clusters.
Assembly: galGal6
Supplementary files format and content: beadbarcodes.txt.gz - File listing the original barcodes sequenced by Broad institute determined to be on the puck with their locations
Supplementary files format and content: L42443.digital_expression.txt.gz - gzipped tab-delimited text file containing a gene expression matrix with a row for each gene and a column for each slide-seq bead or barcode. Generated by slide-seq tools pipeline.
Supplementary files format and content: ss.rds - serialized R data file containing a Seurat object with low quality or non-tissue beads removed and filtered. Used for downstream analysis.

extract_protocol:
To determine the spatial gene expression within chick trunk tissue at the developmental  stage prior to the dorsal migration of the primary SG and axon extensions from the  spinal-cord based PGNs, we harvested day 4 (HH24) unlabeled chick embryos. Fresh  frozen HH24 trunk tissues were transversely cryo-sectioned to approximate single cell  thickness (10um) and carefully placed on a single sequenced Slide-seq puck containing  ~74,000 uniquely barcoded 10um beads. Tissue was then lysed, and the poly-A mRNA  captured by poly(dT).
Tissue was then lysed, and the poly-A mRNA  captured by poly(dT) for downstream cDNA synthesis, NGS library construction, and  Illumina sequencing on a NextSeq 500 machine using the following paired end length:  44 bp Read1, 8 bp Index and 50 bp Read2.


title: ChickTrunk_1_Visium


title: ChickTrunk_4_Visium


title: ChickTrunk_3_Visium


title: Day4 (HH24) Chick Trunk_SingleCell

data_processing:
Raw data in the form of bcl files was converted to fastq using cellranger mkfastq (3.0.0).
Fastq files were aligned to the chicken genome galGal6 from UCSC with gene annotations from Ensembl 96 using STAR 2.5.1b as part of the cellranger 3.0.0 pipeline
After cellranger, data was analyzed in R 3.6.1 with Seurat 3.1.1. Cells with 500-5000 features were kept, and those which had less than 20% mitochondrial counts. Sctransform was used in Seurat to normalize the data, 43 PCs were chosen for downstream analysis, and a resolution of .5 resulted in 23 clusters.
Assembly: galGal6
Supplementary files format and content: sc_barcodes.tsv.gz - output from cellranger containing the barcodes from the single cell experiment
Supplementary files format and content: sc_features.tsv.gz - output from cellranger containing the features (genes) from the single cell experiment
Supplementary files format and content: sc_matrix.tsv.gz - output from cellranger containing the gene by cell matrix
Supplementary files format and content: sc.rds - serialized R data file containing a Seurat object with data filtered and clustered.

extract_protocol:
We harvested HH24 embryonic chick trunk tissue (2 somites in length; same  age/location as used in the Slide-seq and Visium experiments) from 6 embryos and  dissociated cells using a combination of mechanical and enzymatic steps (Morrison et  al., 2017) to generate a single cell suspension. Dissociated cells were loaded onto a  Chromium Single Cell Controller (10X Genomics), based on a live cell concentration of  700-1,200 nuclei/ul.
cDNA libraries were prepared using the Chromium Single Cell 3’  Library and Gel Bead Kit v2 (10X Genomics) according to manufacturer’s directions.  Resulting short fragment libraries were checked for quality and quantity using a  Bioanalyzer 2100 (Agilent Technologies) and Qubit Fluorometer (Invitrogen).

value: dissociated tissue


title: Positive control, rep1

value: whole larvae

value: embryonic day 9


title: HeLa cells, Control, 0h rep3

status: Public on Apr 26 2023

city: Beijing

first: zhu

last: fan

state: State...

address: No.5, Beixiange, Xicheng District, Beijing,

country: China

institute: China Academy of Chinese Medical Sciences Guang'anmen Hospital

data_processing:
SOAPnuke (v1.5.6), Bowtie2 (2.3.4.3),  RSEM (v1.3.1)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAPnuke (parameter--l 15 -q 0.2 -n 0.05)
Bowtie2 was applied to align the clean reads to the gene set, a database built by BGI (Beijing Genomic Institute in ShenZhen)(parameter---q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200)
Expression level of gene was calculated by RSEM (parameter--forward-prob 0)
Supplementary files format and content: hg38
Supplementary files format and content: tab-delimited text files include FPKM values, TPM values and Read counts for each Sample

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Nextera XT DNA Library Preparation Kit following manufacturer's protocols.

treatment_protocol: HeLa cells were treated with 160 μg/mL of FFGL for 48 h

value: HeLa

value: Cervical cancer cell

value: WT

value: untreated


title: HeLa cells, Treat, 48h rep2

value: FFGL 48h


title: HeLa cells, Treat, 48h rep1


title: HeLa cells, Treat, 48h rep3


title: HeLa cells, Control, 0h rep2


title: Post-Transplant Adult Host (biol rep 242)

value: Liver


title: MCF10A-M1 cells SB 0h treatment replicate-2

value: MCF10A cells (normal human breast epithelial cell line)


title: pooled serum from 64 patients with ovarian cancer

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

description: Equal volume of serum were mixed. RNA was extracted from 300 μL of serum using 3D-Gene RNA extraction reagent  miRNA labelling kit (Toray).

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: Serum

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: RNA samples were extracted from serum using miRNesy mini kit (Qiagen).

tag: sample type

value: Serum


title: T16tob, M092, 2

city: Paris

first: André

last: Carvalho

address: 28 Rue du Dr Roux

country: France

institute: Institut Pasteur

description: 0 vs. 16 Tob M092

library_source: genomic

data_processing:
Library strategy: Tn-Seq
Reads were then filtered through transposon mapping to ensure the presence of an informative transposon/genome junction using a previously described mapping algorithm (Pierlé et al., 2014, Negro et al., 2019).
Informative reads were extracted and mapped. Reads were counted when the junction was reported as mapped inside the ORF of a gene plus an additional 50 bp upstream and downstream. Normalization calculations were applied according to van Opijnen et al., 2009
Expansion or decrease of fitness of mutants was calculated in fold changes with normalized insertion numbers. Baggerly’s test on proportions was used to determine statistical significance as well as a Bonferroni correction.
Assembly: NC_002506 and NC_002505
Supplementary files format and content: Matrix table with insertion numbers and insertion reads for every gene and sample

molecule: genomic DNA

organism: Vibrio cholerae O1 biovar El Tor str. N16961

source_name: Bacterial culture

extract_protocol:
Part of the transposon mutant libraries were used for gDNA extraction using Qiagen DNeasy® Blood & Tissue Kit as per manufacturer’s instructions.
Sequencing libraries were prepared using Agilent’s sureselect XT2 Kit with custom RNA baits designed to hybridize the edges of the Mariner transposon. The 100 ng protocol was followed as per manufacturer’s instructions. A total of 12 cycles were used for library amplification. Agilent’s 2100 bioanalzyer was used to verify the size of the pooled libraries and their concentration.

tag: time

value: Bacterial culture

tag: medium

value: MH+Tobramycin 50%MIC


title: T16, M092, 1

description: 0 vs. 16 M092

value: MH


title: T16tob, M092, 1

description: 0 vs. 16 Tob M092


title: T16, M092, 3

description: 0 vs. 16 M092


title: T16, M092, 2

description: 0 vs. 16 M092


title: T16tob, M092, 3

description: 0 vs. 16 Tob M092


title: pooled serum from 41 patients with noncancerous control


title: T16tob, H505, 1

description: 0 vs. 16 TobH505

value: vchM


title: T16tob, H505, 3

description: 0 vs. 16 TobH505


title: T16, H505, 3

description: 0 vs. 16 H505


title: T16, H505, 2

description: 0 vs. 16 H505


title: T16tob, J085, 3

description: 0 vs. 16 tob J085


title: T16, H505, 1

description: 0 vs. 16 H505


title: T16, J085, 1

description: 0 vs. 16 J085


title: T16tob, J085, 1

description: 0 vs. 16 tob J085


title: T16tob, J085, 2

description: 0 vs. 16 tob J085


title: T0, M092, 3

description: 0 vs. 16 M092


title: T16, J085, 3

description: 0 vs. 16 J085


title: T0, M092, 2

description: 0 vs. 16 M092


title: HeLa cells, Control, 0h rep1


title: T16, J085, 2

description: 0 vs. 16 J085


title: T0, H505, 3

description: 0 vs. 16 H505


title: T0, J085, 2

description: 0 vs. 16 J085


title: T0, J085, 3

description: 0 vs. 16 J085


title: T0, J085, 1

description: 0 vs. 16 J085


title: T0, H505, 2

description: 0 vs. 16 H505


title: T0, M092, 1

description: 0 vs. 16 M092


title: T16tob, H505, 2

description: 0 vs. 16 TobH505


title: RNA_Macaque_BA23_M4

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description:
All_Species_UMI_Count_Matrix_snRNAseq.mtx
All_Species_UMI_Count_Matrix_MetaData.txt
All_Species_UMI_Count_Matrix_Genes.txt
All_Species_UMI_Count_Matrix_Barcodes.txt
Seurat_Astrocyte_RNA.RDS
Seurat_Excitatory_RNA.RDS
Seurat_Inhibitory_RNA.RDS
Seurat_Microglia_RNA.RDS
Seurat_OPCOli_RNA.RDS

data_processing:
Barcode correction, alignment are performed using cellranger count (Software: 10x Genomics Cell Ranger 3.1.0)
Chimpanzee, macaque reads were mapped to human (CrossMap)
Reads counted per gene (featureCounts) and gene-cell matrix was constructed (umi-tools)
Ambient RNA contamination removed (CellBender)
Low quality cell barcodes, doublets were removed (Refer to supplementary methods)
Genome_build: Human: GRCh38, Chimpanzee: panTro5 (Pan_tro 3.0), Rhesus Macaque: rheMac10 (Mmul_10)
Supplementary_files_format_and_content: processed expression matrix: mtx files, gene and barcode information are in separate files
Supplementary_files_format_and_content: Cell barcode meta data

organism: Macaca mulatta

source_name: Post-mortem brain, Brodmann Area 23

extract_protocol:
Nuclei for snRNA-seq were isolated from human, chimpanzee, and macaque BA23 brain tissue. Debris was removed with a density gradient centrifugation using the Nuclei PURE 2M Sucrose Cushion Solution and Nuclei PURE Sucrose Cushion Buffer from Nuclei PURE Prep Isolation Kit (#NUC201-1KT, Sigma Aldrich).
Droplet-based single-nuclei RNA-seq libraries were prepared using the Chromium Single Cell 3’ v3.1 (1000121, 10x Genomics) according to the manufacturer’s protocol81. Libraries were sequenced using an Illumina NovaSeq 6000.

tag: tissue

value: brain

tag: brain region

value: Brodmann Area 23

tag: Sex

value: F

tag: molecule subtype

value: nuclear RNA


title: RNA_Macaque_BA23_M3

tag: age


title: RNA_Macaque_BA23_M2

value: M


title: Macaque_BA23_M2

description:
Macaque_Count_Matrix_snATACseq_Barcodes.txt
Macaque_Count_Matrix_snATACseq_Genes.txt
Macaque_Count_Matrix_snATACseq_MetaData.txt
Macaque_Count_Matrix_snATACseq.mtx
Seurat_Astrocyte_ATAC_Macaque.RDS
Seurat_Excitatory_ATAC_Macaque.RDS
Seurat_Inhibitory_ATAC_Macaque.RDS
Seurat_Microglia_ATAC_Macaque.RDS
Seurat_OPCOli_ATAC_Macaque.RDS

data_processing:
Barcode correction, alignment are performed using cellranger count (Software: 10x Genomics Cell Ranger ATAC 1.1.0)
Supplementary_files_format_and_content: Read duplicates were removed (picard MarkDuplicates)
Peak calling (macs2 --nomodel, --keep-dup all, extsize 200, --shift –100 )
Common peak identification across samples and species (Refer to supplementary methods)
Peak-cell matrix generation (custom scripts)
Low quality cell barcodes, doublets were removed (Refer to supplementary methods)
Genome_build: Human: GRCh38, Chimpanzee: panTro5 (Pan_tro 3.0), Rhesus Macaque: rheMac10 (Mmul_10)
Supplementary_files_format_and_content: processed binarized peak-cell matrix: mtx file, peak and barcode information are in separate files
Supplementary_files_format_and_content: Cell barcode meta data

extract_protocol:
Nuclei for snATAC-seq were isolated from human, chimpanzee, and macaque BA23 brain tissue as previously described: https://www.protocols.io/view/isolation-of-nuclei-from-frozen-tissue-for-atac-se-6t8herw
Droplet-based single-nuclei ATAC-seq libraries were prepared using the Chromium Single Cell ATAC Library kit (1000110, 10x Genomics) according to the manufacturer’s protocols. Libraries were sequenced using an Illumina NovaSeq 6000.


title: Macaque_BA23_M4


title: Macaque_BA23_M3


title: T0, H505, 1

description: 0 vs. 16 H505


title: P60, deaf, base, rep2

city: Iowa City

first: Steven

middle: Haym

last: Green

state: Iowa

address: 143 Biology Building

department: Biology

institute: University of Iowa

description:
P60DB2
normalized intensities of technical replicates were averaged to produce one value for each biological replicate

hyb_protocol: Labeled cDNA was hybridized for 20 hours to Roche NimbleGen HD2 rat gene expression arrays. Each biological replicate was analyzed in triplicate (3 technical replicates).

scan_protocol: Arrays were scanned on an Axon GenePix 4200A microarray scanner (Molecular Devices).

data_processing:
Pair files were generated and Lasergene ArrayStar (version 17, DNASTAR) was used for noise subtraction and RMA quantile normalization. Normalized signal intensities were used to calculate fold changes between conditions.
RMA-normalized-data_all-genes.txt is represented in the Data table (represents the normalized signal intensities for all genes present on the microarray).
RMA-normalized-data_expr-only.txt is linked as a supplementary file on the Series record (represents the normalized signal intensities for only the genes we considered to be expressed).

source_name: P60 deaf spiral ganglion, basal half

label_protocol: cDNA was labeled using Cy3-coupled random nonamers (Roche NimbleGen).

growth_protocol: Sprague-Dawley rats from our breeding colony or from pregnant dams purchased from Envigo were used. Rats of both sexes were used. The day of birth was designated as P0.

extract_protocol: The Rneasy mini-kit (Qiagen) was used to extract total RNA from the isolated spiral ganglia. RNA was amplified (3-4X) using an Ambion Message Amp II kit. cDNA was then synthesized using a SuperScript II Reverse Transcriptase Second Strand kit.

treatment_protocol: Male and female Sprague-Dawley rats were injected with kanamycin (400 mg/kg, i.p.) once daily from P8-P16. Cochleae were collected from injected and littermate control (uninjected) rats at P32 or P60. Temporal bones were rapidly removed and placed in ice-cold phosphate-buffered saline, pH 7.4 (PBS) for dissection. The bony capsule and spiral ligament were dissected away from the cochlea. The remaining tissue was divided into apical and basal portions and the organ of Corti was separated from the spiral ganglion. Four to six ganglia were used for each biological replicate.

value: Sprague-Dawley

tag: condition

value: deaf

value: spiral ganglion

tag: cochlear location

value: base


title: P32, deaf, apex, rep3

description:
P32DA3
normalized intensities of technical replicates were averaged to produce one value for each biological replicate

source_name: P32 deaf spiral ganglion, apical half

value: apex


title: P60, deaf, base, rep3

description:
P60DB3
normalized intensities of technical replicates were averaged to produce one value for each biological replicate


title: P60, hearing, base, rep3

description:
P60HB3
normalized intensities of technical replicates were averaged to produce one value for each biological replicate

source_name: P60 hearing spiral ganglion, basal half

value: hearing


title: P60, deaf, apex, rep3

description:
P60DA3
normalized intensities of technical replicates were averaged to produce one value for each biological replicate

source_name: P60 deaf spiral ganglion, apical half


title: P60, hearing, apex, rep3

description:
P60HA3
normalized intensities of technical replicates were averaged to produce one value for each biological replicate

source_name: P60 hearing spiral ganglion, apical half


title: P60, deaf, apex, rep2

description:
P60DA2
normalized intensities of technical replicates were averaged to produce one value for each biological replicate


title: P32, hearing, base, rep2

description:
P32HB2
normalized intensities of technical replicates were averaged to produce one value for each biological replicate

source_name: P32 hearing spiral ganglion, basal half


title: P32, deaf, apex, rep2

description:
P32DA2
normalized intensities of technical replicates were averaged to produce one value for each biological replicate


title: P32, deaf, base, rep3

description:
P32DB3
normalized intensities of technical replicates were averaged to produce one value for each biological replicate

source_name: P32 deaf spiral ganglion, basal half


title: P32, hearing, base, rep3

description:
P32HB3
normalized intensities of technical replicates were averaged to produce one value for each biological replicate


title: P32, hearing, apex, rep3

description:
P32HA3
normalized intensities of technical replicates were averaged to produce one value for each biological replicate

source_name: P32 hearing spiral ganglion, apical half


title: P60, hearing, base, rep2

description:
P60HB2
normalized intensities of technical replicates were averaged to produce one value for each biological replicate


title: P60, hearing, apex, rep2

description:
P60HA2
normalized intensities of technical replicates were averaged to produce one value for each biological replicate


title: 11H_M_2547

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: 11H_M_2552


title: 11H_M_2553


title: 11H_M_2548


title: 11H_M_2555


title: 11H_M_2550


title: 11H_M_2546


title: 11H_M_2551


title: 11H_M_2554


title: P32, deaf, base, rep2

description:
P32DB2
normalized intensities of technical replicates were averaged to produce one value for each biological replicate


title: 11H_M_2549


title: 11H_M_2545


title: 11H_M_2543


title: 11H_M_2544


title: 11H_M_2542


title: P32, hearing, apex, rep2

description:
P32HA2
normalized intensities of technical replicates were averaged to produce one value for each biological replicate


title: 11H_M_2541


title: 11H_M_2540


title: 11H_M_2537


title: 11H_M_2536


title: 11H_M_2539


title: 11H_M_2530


title: 11H_M_2533


title: 11H_M_2528


title: 11H_M_2532


title: 11H_M_2529


title: 11H_M_2534


title: 11H_M_2531


title: 11H_M_2522


title: 11H_M_2518


title: 11H_M_2524


title: 11H_M_2526


title: 11H_M_2527


title: 11H_M_2517


title: 11H_M_2525


title: 11H_M_2521


title: 11H_M_2514


title: 11H_M_2515


title: 11H_M_2516


title: 11H_M_2513


title: 11H_M_2538


title: 11H_M_2535


title: 11H_M_2511


title: 11H_M_2512


title: 11H_M_2509


title: 11H_M_2510


title: 11H_M_2520


title: 11H_M_2508


title: 11H_M_2519


title: 11H_M_2507


title: 11H_M_2506


title: 11H_M_2504


title: 11H_M_2505


title: 11H_M_2499


title: 11H_M_2523


title: 11H_M_2500


title: 11H_M_2493


title: 11H_M_2492


title: 11H_M_2498


title: 11H_M_2501


title: 11H_M_2497


title: 11H_M_2495


title: 11H_M_2496


title: 11H_M_2491


title: 11H_M_2490


title: 11H_M_2494


title: 11H_M_2488


title: 11H_M_2487


title: 11H_M_2485


title: 11H_M_2486


title: 11H_M_2502


title: 11H_M_2482


title: 11H_M_2503


title: 11H_M_2481


title: 11H_M_2478


title: 11H_M_2477


title: 11H_M_2479


title: 11H_M_2480


title: 11H_M_2473


title: 11H_M_2474


title: 11H_M_2472


title: 11H_M_2471


title: 11H_M_2470


title: 11H_M_2468


title: 11H_M_2469


title: 11H_M_2466


title: 11H_M_2465


title: 11H_M_2476


title: 11H_M_2467


title: 11H_M_2463


title: 11H_M_2484


title: 11H_M_2483


title: 11H_M_2464


title: 11H_M_2461


title: 11H_M_2460


title: 11H_M_2462


title: 11H_M_2489


title: 11H_M_2458


title: 11H_M_2475


title: 11H_M_2457


title: 11H_M_2455


title: 11H_M_2454


title: 11H_M_2453


title: 11H_M_2456


title: 11H_M_2452


title: 11H_M_2451


title: 11H_M_2450


title: 11H_M_2447


title: 11H_M_2444


title: 11H_M_2445


title: 11H_M_2443


title: 11H_M_2440


title: 11H_M_2439


title: 11H_M_2441


title: 11H_M_2438


title: 11H_M_2437


title: 11H_M_2459


title: 11H_M_2436


title: 11H_M_2435


title: 11H_M_2434


title: 11H_M_2432


title: 11H_M_2431


title: 11H_M_2433


title: 11H_M_2430


title: 11H_M_2428


title: 11H_M_2429


title: 11H_M_2427


title: 11H_M_2426


title: 11H_M_2422


title: 11H_M_2423


title: 11H_M_2425


title: 11H_M_2424


title: 11H_M_2448


title: 11H_M_2449


title: 11H_M_2446


title: 11H_M_2421


title: 11H_M_2442


title: 11H_M_2420


title: 11H_M_2417


title: 11H_M_2418


title: 11H_M_2416


title: 11H_M_2419


title: 11H_M_2415


title: 11H_M_2412


title: 11H_M_2414


title: 11H_M_2411


title: 11H_M_2408


title: 11H_M_2410


title: 11H_M_2409


title: 11H_M_2407


title: 11H_M_2405


title: 11H_M_2404


title: 11H_M_2406


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title: 11H_M_815


title: 11H_M_807


title: 11H_M_806


title: 11H_M_816


title: 11H_M_810


title: 11H_M_808


title: 11H_M_814


title: 11H_M_804


title: 11H_M_1025


title: 11H_M_809


title: 11H_M_803


title: 11H_M_805


title: 11H_M_801


title: 11H_M_800


title: 11H_M_802


title: 11H_M_798


title: 11H_M_797


title: 11H_M_821


title: 11H_M_820


title: 11H_M_791


title: 11H_M_793


title: 11H_M_789


title: 11H_M_792


title: 11H_M_790


title: 11H_M_782


title: 11H_M_788


title: 11H_M_787


title: 11H_M_786


title: 11H_M_794


title: 11H_M_785


title: 11H_M_799


title: 11H_M_776


title: 11H_M_781


title: 11H_M_777


title: 11H_M_779


title: 11H_M_774


title: 11H_M_778


title: 11H_M_796


title: 11H_M_773


title: 11H_M_772


title: 11H_M_770


title: 11H_M_768


title: 11H_M_780


title: 11H_M_769


title: 11H_M_784


title: 11H_M_766


title: 11H_M_763


title: 11H_M_764


title: 11H_M_765


title: 11H_M_762


title: 11H_M_795


title: 11H_M_775


title: 11H_M_759


title: 11H_M_758


title: 11H_M_760


title: 11H_M_755


title: 11H_M_752


title: 11H_M_761


title: 11H_M_756


title: 11H_M_754


title: 11H_M_783


title: 11H_M_757


title: 11H_M_753


title: 11H_M_750


title: 11H_M_746


title: 11H_M_744


title: 11H_M_751


title: 11H_M_771


title: 11H_M_748


title: 11H_M_749


title: 11H_M_747


title: 11H_M_745


title: 11H_M_740


title: 11H_M_739


title: 11H_M_767


title: 11H_M_741


title: 11H_M_743


title: 11H_M_738


title: 11H_M_742


title: 11H_M_736


title: 11H_M_737


title: 11H_M_734


title: 11H_M_732


title: 11H_M_728


title: 11H_M_729


title: 11H_M_731


title: 11H_M_730


title: 11H_M_735


title: 11H_M_733


title: 11H_M_727


title: 11H_M_725


title: 11H_M_726


title: 11H_M_723


title: 11H_M_721


title: 11H_M_720


title: 11H_M_722


title: 11H_M_719


title: 11H_M_718


title: 11H_M_709


title: 11H_M_713


title: 11H_M_717


title: 11H_M_715


title: 11H_M_712


title: 11H_M_710


title: 11H_M_714


title: 11H_M_711


title: 11H_M_707


title: 11H_M_708


title: 11H_M_510


title: 11H_M_704


title: 11H_M_508


title: 11H_M_507


title: 11H_M_705


title: 11H_M_511


title: 11H_M_504


title: 11H_M_506


title: 11H_M_724


title: 11H_M_502


title: 11H_M_716


title: 11H_M_497


title: 11H_M_499


title: 11H_M_498


title: 11H_M_494


title: 11H_M_495


title: 11H_M_493


title: 11H_M_490


title: 11H_M_492


title: 11H_M_496


title: 11H_M_489


title: 11H_M_706


title: 11H_M_509


title: 11H_M_485


title: 11H_M_503


title: 11H_M_488


title: 11H_M_482


title: 11H_M_484


title: 11H_M_505


title: 11H_M_501


title: 11H_M_491


title: 11H_M_476


title: 11H_M_477


title: 11H_M_480


title: 11H_M_478


title: 11H_M_479


title: 11H_M_475


title: 11H_M_481


title: 11H_M_474


title: 11H_M_483


title: 11H_M_473


title: 11H_M_472


title: 11H_M_470


title: 11H_M_469


title: 11H_M_466


title: 11H_M_468


title: 11H_M_487


title: 11H_M_500


title: 11H_M_465


title: 11H_M_464


title: 11H_M_486


title: 11H_M_461


title: 11H_M_459


title: 11H_M_460


title: 11H_M_462


title: 11H_M_457


title: 11H_M_453


title: 11H_M_454


title: 11H_M_456


title: 11H_M_455


title: 11H_M_467


title: 11H_M_471


title: 11H_M_383


title: 11H_M_382


title: 11H_M_451


title: 11H_M_374


title: 11H_M_378


title: 11H_M_452


title: 11H_M_372


title: 11H_M_376


title: 11H_M_379


title: 11H_M_377


title: 11H_M_380


title: 11H_M_381


title: 11H_M_448


title: 11H_M_375


title: 11H_M_449


title: 11H_M_371


title: 11H_M_370


title: 11H_M_369


title: 11H_M_373


title: 11H_M_368


title: 11H_M_458


title: 11H_M_367


title: 11H_M_365


title: 11H_M_463


title: 11H_M_366


title: 11H_M_363


title: 11H_M_364


title: 11H_M_450


title: 11H_M_361


title: 11H_M_362


title: 11H_M_360


title: 11H_M_359


title: 11H_M_358


title: 11H_M_352


title: 11H_M_354


title: 11H_M_357


title: 11H_M_351


title: 11H_M_353


title: 11H_M_348


title: 11H_M_345


title: 11H_M_347


title: 11H_M_346


title: 11H_M_344


title: 11H_M_341


title: 11H_M_342


title: 11H_M_350


title: 11H_M_349


title: 11H_M_340


title: 11H_M_339


title: 11H_M_337


title: 11H_M_336


title: 11H_M_335


title: 11H_M_334


title: 11H_M_333


title: 11H_M_355


title: 11H_M_332


title: 11H_M_331


title: 11H_M_356


title: 11H_M_330


title: 11H_M_328


title: 11H_M_329


title: 11H_M_326


title: 11H_M_324


title: 11H_M_343


title: 11H_M_321


title: 11H_M_320


title: 11H_M_322


title: 11H_M_318


title: 11H_M_319


title: 11H_M_323


title: 11H_M_317


title: 11H_M_316


title: 11H_M_325


title: 11H_M_311


title: 11H_M_312


title: 11H_M_313


title: 11H_M_314


title: 11H_M_315


title: 11H_M_338


title: 11H_M_309


title: 11H_M_308


title: 11H_M_306


title: 11H_M_305


title: 11H_M_304


title: 11H_M_303


title: 11H_M_302


title: 11H_M_327


title: 11H_M_298


title: 11H_M_299


title: 11H_M_296


title: 11H_M_301


title: 11H_M_295


title: 11H_M_300


title: 11H_M_297


title: 11H_M_307


title: 11H_M_289


title: 11H_M_292


title: 11H_M_290


title: 11H_M_288


title: 11H_M_310


title: 11H_M_285


title: 11H_M_286


title: 11H_M_287


title: 11H_M_284


title: 11H_M_281


title: 11H_M_283


title: 11H_M_282


title: 11H_M_280


title: 11H_M_279


title: 11H_M_277


title: 11H_M_278


title: 11H_M_291


title: 11H_M_275


title: 11H_M_276


title: 11H_M_274


title: 11H_M_294


title: 11H_M_293


title: 11H_M_272


title: 11H_M_269


title: 11H_M_267


title: 11H_M_271


title: 11H_M_270


title: 11H_M_268


title: 11H_M_273


title: 11H_M_262


title: 11H_M_266


title: 11H_M_265


title: 11H_M_263


title: 11H_M_264


title: 11H_M_261


title: 11H_M_259


title: 11H_M_256


title: 11H_M_191


title: 11H_M_258


title: 11H_M_257


title: 11H_M_190


title: 11H_M_260


title: 11H_M_189


title: 11H_M_188


title: 11H_M_186


title: 11H_M_187


title: 11H_M_184


title: 11H_M_185


title: 11H_M_183


title: 11H_M_182


title: 11H_M_181


title: 11H_M_180


title: 11H_M_176


title: 11H_M_178


title: 11H_M_179


title: 11H_M_177


title: 11H_M_173


title: 11H_M_174


title: 11H_M_171


title: 11H_M_169


title: 11H_M_170


title: 11H_M_166


title: 11H_M_167


title: 11H_M_163


title: 11H_M_168


title: 11H_M_165


title: 11H_M_172


title: 11H_M_161


title: 11H_M_162


title: 11H_M_160


title: 11H_M_158


title: 11H_M_157


title: 11H_M_156


title: 11H_M_155


title: 11H_M_154


title: 11H_M_152


title: 11H_M_153


title: 11H_M_151


title: 11H_M_175


title: 11H_M_148


title: 11H_M_150


title: 11H_M_147


title: 11H_M_146


title: 11H_M_145


title: 11H_M_142


title: 11H_M_164


title: 11H_M_144


title: 11H_M_141


title: 11H_M_143


title: 11H_M_140


title: 11H_M_139


title: 11H_M_136


title: 11H_M_138


title: 11H_M_159


title: 11H_M_135


title: 11H_M_134


title: 11H_M_132


title: 11H_M_129


title: 11H_M_63


title: 11H_M_62


title: 11H_M_61


title: 11H_M_131


title: 11H_M_60


title: 11H_M_57


title: 11H_M_130


title: 11H_M_56


title: 11H_M_58


title: 11H_M_55


title: 11H_M_59


title: 11H_M_149


title: 11H_M_49


title: 11H_M_137


title: 11H_M_48


title: 11H_M_52


title: 11H_M_47


title: 11H_M_50


title: 11H_M_46


title: 11H_M_53


title: 11H_M_133


title: 11H_M_128


title: 11H_M_44


title: 11H_M_43


title: 11H_M_41


title: 11H_M_40


title: 11H_M_42


title: 11H_M_39


title: 11H_M_36


title: 11H_M_37


title: 11H_M_35


title: 11H_M_31


title: 11H_M_32


title: 11H_M_34


title: 11H_M_54


title: 11H_M_30


title: 11H_M_33


title: 11H_M_29


title: 11H_M_51


title: 11H_M_28


title: 11H_M_27


title: 11H_M_24


title: 11H_M_26


title: 11H_M_25


title: 11H_M_22


title: 11H_M_19


title: 11H_M_21


title: 11H_M_18


title: 11H_M_23


title: 11H_M_17


title: 11H_M_38


title: 11H_M_15


title: 11H_M_12


title: 11H_M_14


title: 11H_M_16


title: 11H_M_13


title: 11H_M_11


title: 11H_M_10


title: 11H_M_9


title: 11H_M_5


title: 11H_M_6


title: 11H_M_7


title: 11H_M_2


title: 11H_M_8


title: 11H_M_3


title: 11H_M_4


title: 11H_M_20


title: 11H_M_1


title: 11H_M_0


title: 73_ko

city: St. Louis

first: Eric

last: Tycksen

state: Missouri

address: 4444 Forest Park Avenue

department: McDonnell Genome Institute

institute: Washington University in St. Louis School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.76
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: isolated astrocytes

growth_protocol: All mice were maintained on a C57BL\6 background and housed under 12-h light/12-h dark conditions. All mice (Cre- and Cre+) were given tamoxifen (Sigma, dissolved in corn oil, 2 mg/mouse/day for 5 days) by oral gavage at 2 months of age to induce Bmal1 astrocyte-specific deletion. All mice were group housed with food and water available ad libitum.

extract_protocol:
Isolated astrocytes and flowthrough samples were lysed with Trizol reagent. After chloroform separation, RNA was prepared using a PureLink RNA Mini Kit (Life Technologies). RNA was stored at −80 °C
Takara Clontech SMARTer v1

treatment_protocol: At 20 months of age, brains were collected. After collagenase digestion and debris removal, astrocytes were isolated from the rest of the brain cells (termed "flowthrough") using Miltenyi MACS Anti-ACSA-2 magnetic beads.

value: Bmal fl/fl; ALDH1L1-CreERT2

value: 20 months

value: Cre+ knockout


title: 64_wt_flow

source_name: brain cell flowthrough

value: Cre- wildtype


title: 78_wt


title: 60_ko


title: 62_ko


title: 56_wt


title: 132_ko_flow


title: 132_ko


title: 56_wt_flow


title: 265_wt

treatment_protocol: At 7 months of age, brains were collected. After collagenase digestion and debris removal, astrocytes were isolated from the rest of the brain cells (termed "flowthrough") using Miltenyi MACS Anti-ACSA-2 magnetic beads.

value: 7 months


title: 221_ko


title: 208_ko


title: 205_ko


title: 205_ko_flow_b


title: 203_ko


title: 203_ko_flow_b


title: 202_wt_flow_b


title: 202_wt


title: 201_wt_flow_b


title: 64_wt


title: Sham

city: Shanghai

first: Wenyong

last: Lin

address: No. 528, zhangheng Rd

department: Cardiovascular Research Institute of Traditional Chinese Medicine

institute: Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files and histology images were processed by sample with the Space Ranger software v.1.3.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: heart

extract_protocol:
Heart tissues of C57BL/6 mice was gently washed with cold PBS and cut into 4-6 mm3 pieces,tissue placed cut side into a plastic mold.  The OCT-filled mold was then snap frozen in chilled isopentane.Cryosections were cut at 10-µm thickness (Leica,cm1950).Brightfield histology images were taken using a 20x objective on Pannoramic MIDI scanner (3D HISTECH). Raw images were stitched together using pannoramic MIDI and  exported as .tiff files with low- and high-resolution settings. For tissue optimization experiments, fluorescent  images were taken with a TRITC filter using a 20x objective.
Libraries were prepared according to the Visium Spatial Gene Expression User Guide (CG000239:https://assets.ctfassets.net/an68im79xiti/3pyXucRaiKWcscXy3cmRHL/a1ba41c77cbf60366202805ead8f64d7/CG0  00239_VisiumSpatialGeneExpression_UserGuide_Rev_A.pdf). They were loaded and sequenced on a  NovaSeq 6000 System (Illumina).The sequencing and bioinformatics analysis were performed by Majorbio Co., Ltd (Shanghai, China).
scSpatial-seq

value: heart

tag: treatment

value: Gavage with vehicle for 7 days before operation, needles only, no ligation.


title: 60_ko_flow

value: brain


title: 57_wt


title: cGAS_20

city: New York

first: Li

last: Gan

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

description: mRNA expression in mouse hippocampus

data_processing:
Gene counts were obtained by aligning reads to the mm10 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 3 cells, cells with unique gene counts over 9,000 or less than 300, and cells with high fraction of mitochondrial reads (> 5%).
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
Seurat v3.0 (Butler et al., 2018) R package used for analysis.
Assembly: mm10 genome
Supplementary files format and content: mtx

source_name: single nuclei from mouse hippocampus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2022
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: cGAS_25

description: mRNA expression in mouse hippocampus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2024
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: cGAS_18

description: mRNA expression in mouse hippocampus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2021
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: 222_ko


title: single nuclei from mouse hippocampus Joe_D22

description: mRNA expression in mouse hippocampus

data_processing:
Gene counts were obtained by aligning reads to the mm10 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 3 cells, cells with unique gene counts over 9,000 or less than 300, and cells with high fraction of mitochondrial reads (> 5%).
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
Seurat v3.0 (Butler et al., 2018) R package used for analysis.
Assembly: mm10 genome

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)

value: P301S tau:+

value: TDI

value: Male


title: single nuclei from mouse hippocampus Joe_D50

description: mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus Joe_C96

description: mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus Joe_C94

description: mRNA expression in mouse hippocampus

value: Ctrl


title: single nuclei from mouse hippocampus Joe_D13

description: mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus Joe_D28

description: mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus Joe_D49

description: mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus Joe_D46

description: mRNA expression in mouse hippocampus

value: P301S tau:-


title: single nuclei from mouse hippocampus Joe_D27

description: mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus Joe_C90

description: mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus Joe_C92

description: mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus Joe_D45

description: mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus Joe_D18

description: mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus Joe_D17

description: mRNA expression in mouse hippocampus


title: 201_wt


title: single nuclei from mouse hippocampus IFNARKO_5

description:
IFNARKO_5
mRNA expression in mouse hippocampus

value: DMXAA


title: single nuclei from mouse hippocampus IFNARKO_3

description:
IFNARKO_3
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus IFNARKO_10

description:
IFNARKO_10
mRNA expression in mouse hippocampus

value: vehicle


title: single nuclei from mouse hippocampus IFNARKO_1

description:
IFNARKO_1
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus IFNARKO_2

description:
IFNARKO_2
mRNA expression in mouse hippocampus


title: IR

description: 10x Genomics

value: Gavage with vehicle for 7 days before operation, LAD ligation for 30 minutes, followed by recanalization for 24 hours.


title: single nuclei from mouse hippocampus IFNARKO_9

description:
IFNARKO_9
mRNA expression in mouse hippocampus


title: MUSKARDIA

description: 10x Genomics

value: Gavage with MUSKARDIA solution for 7 days before operation, LAD ligation for 30 minutes, followed by recanalization for 24 hours.


title: single nuclei from mouse hippocampus IFNARKO_8

description:
IFNARKO_8
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus IFNARKO_7

description:
IFNARKO_7
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus DMXAA_10

description:
DMXAA_10
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus DMXAA_9

description:
DMXAA_9
mRNA expression in mouse hippocampus


title: cGAS_23

description: mRNA expression in mouse hippocampus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2023
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

value: M


title: single nuclei from mouse hippocampus DMXAA_20

description:
DMXAA_20
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_77

description:
cGAS_77
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus Joe_D15

description: mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus DMXAA_12

description:
DMXAA_12
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus DMXAA_13

description:
DMXAA_13
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_66

description:
cGAS_66
mRNA expression in mouse hippocampus

value: F


title: single nuclei from mouse hippocampus DMXAA_3

description:
DMXAA_3
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus DMXAA_11

description:
DMXAA_11
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_57

description:
cGAS_57
mRNA expression in mouse hippocampus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: single nuclei from mouse hippocampus cGAS_27

description:
cGAS_27
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_46

description:
cGAS_46
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus DMXAA_1

description:
DMXAA_1
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_74

description:
cGAS_74
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus Joe_C95

description: mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_65

description:
cGAS_65
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_33

description:
cGAS_33
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_43

description:
cGAS_43
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_42

description:
cGAS_42
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_59

description:
cGAS_59
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_63

description:
cGAS_63
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_36

description:
cGAS_36
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_30

description:
cGAS_30
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_29

description:
cGAS_29
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_21

description:
cGAS_21
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_22

description:
cGAS_22
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_19

description:
cGAS_19
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_62

description:
cGAS_62
mRNA expression in mouse hippocampus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2020
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)


title: single nuclei from mouse hippocampus cGAS_45

description:
cGAS_45
mRNA expression in mouse hippocampus


title: single nuclei from mouse hippocampus cGAS_61

description:
cGAS_61
mRNA expression in mouse hippocampus


title: cGAS KO mouse primary microglia treated with tau fibrils KO_tau3

data_processing:
RNA-seq reads were mapped using the BlueBee genomics platform and the GENCODE GRCm38 mouse genome (Lexogen QuantSeq 2.2.3) as reference genome.
Counts were normalized with the trimmed mean normalization method.
Differential gene expression was calculated with R package edgeR and limma.
Assembly: GRCm38

extract_protocol:
total RNA was extracted using Quick-RNA miniprep (R1055, Zymo Research).
cDNA library generation was done using the QuantSeq 3′ mRNA-Seq Library Prep Kit (FWD) for Illumina (K01596, Lexogen) following manufacturer’s instructions.

value: primary microglia

value: Tau

value: Cgas KO


title: cGAS KO mouse primary microglia treated with HT-DNA KO_DNA2

value: DNA


title: cGAS KO mouse primary microglia treated with HT-DNA KO_DNA1


title: cGAS KO mouse primary microglia treated with tau fibrils KO_tau2


title: cGAS KO mouse primary microglia treated with HT-DNA KO_DNA3


title: single nuclei from mouse hippocampus cGAS_41

description:
cGAS_41
mRNA expression in mouse hippocampus


title: cGAS KO mouse primary microglia treated with tau fibrils KO_tau1


title: single nuclei from mouse hippocampus cGAS_55

description:
cGAS_55
mRNA expression in mouse hippocampus


title: cGAS KO mouse primary microglia treated with vehicle KO_NT2

value: Vehicle


title: cGAS KO mouse primary microglia treated with vehicle KO_NT1

value: brain


title: wildtype mouse primary microglia treated with tau fibrils WT_Tau2

value: WT


title: wildtype mouse primary microglia treated with HT-DNA WT_DNA3


title: wildtype mouse primary microglia treated with HT-DNA WT_DNA2


title: wildtype mouse primary microglia treated with tau fibrils WT_Tau1


title: bulk hippocampal tissue from P301S mice cGAS_77

source_name: bulk hippocampal tissue from P301S mice

tag: age (m)


title: wildtype mouse primary microglia treated with vehicle WT_Ctrl1


title: wildtype mouse primary microglia treated with HT-DNA WT_DNA1


title: wildtype mouse primary microglia treated with vehicle WT_Ctrl2


title: wildtype mouse primary microglia treated with vehicle WT_Ctrl3


title: bulk hippocampal tissue from P301S mice cGAS_65


title: bulk hippocampal tissue from P301S mice cGAS_63


title: bulk hippocampal tissue from P301S mice cGAS_43


title: bulk hippocampal tissue from P301S mice cGAS_36


title: bulk hippocampal tissue from P301S mice cGAS_29


title: bulk hippocampal tissue from non-transgenic mice cGAS_71


title: bulk hippocampal tissue from non-transgenic mice cGAS_68


title: bulk hippocampal tissue from non-transgenic mice cGAS_61


title: bulk hippocampal tissue from non-transgenic mice cGAS_62


title: cGAS KO mouse primary microglia treated with vehicle KO_NT3


title: bulk hippocampal tissue from non-transgenic mice cGAS_55


title: bulk hippocampal tissue from non-transgenic mice cGAS_35


title: INPUT_WT_Ncor2_PD3_rep1

city: Vienna

first: Andreas

last: Lackner

address: Schwarzspanierstrasse 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

data_processing:
read trimming: CUTADAPT (2.8)
alignment: bowtie 2 (2.3.5.1)
alignment processing: samtools (1.10)
peak calling: MACS2 (2.2.7.1)
idr_filtering: ChIPpeakAnno (3.26.4)
Assembly: mm10
Supplementary files format and content: bigwig, bed/peaksets

source_name: mouse trophoblast stem cells (mTSCs)

growth_protocol: Mouse TS cells were grown in a standard TS medium (RPMI 1640 supplemented with 20% fetal calf serum, 2mM L-Glutamine, 2mM sodium pyruvate and 100mM 2-mercaptoethanol) containing 70% mouse embryonic fibroblast -conditioned medium and 100 ng ml-1 Fgf2 and 1 µg ml-1 heparin. Cells were split every third day using trypsin.

extract_protocol: ChIPseq: cells were fixed in 1% FA for 10min and fixation was quenched by 0.125 M glycine at RT. Cells were scraped in PBS, centrifuged at 500g for 5min and pellet was resuspended in an ice-cold IP-buffer, a 2:1 mixture of SDS-buffer (100mM NaCl, 50mM Tris-Cl pH 8.0, 5mM EDTA pH 8.0, 0.5% SDS) and Triton-X-buffer (100mM NaCl, 100mM Tris-Cl pH 8.6, 5mM EDTA pH 8.0, 5% Triton X), containing complete Protease inhibitor tabs (11873580001, Sigma). After 30min incubation on ice chromatin was sonicated 15s on (pulsed, with 90% actual sonication time) /30s off for 20 cycles using the UW2070 sonicator (Bandelin) at ~40% power. 30µg and 10µg chromatin (DNA equivalent) were precipitated using the listed antibodies.

treatment_protocol: For differentiation, TSCs were exposed to 3 µM PD0325901 (Tocris) in full TSC media for 24h

tag: differentiation state

value: 3h differentiation with PD (PD3)

tag: modification

tag: parental cell line

value: TSGFP


title: INPUT_WT_Ncor2_PD3_rep2


title: INPUT_WT_Ncor1_PD3_rep2


title: wildtype mouse primary microglia treated with tau fibrils WT_Tau3

tag: cell type

tag: genotype


title: Ncor2_WT_PD3_rep2

tag: chip antibody

value: anti-Ncor2 (Abcam/ ab5802)


title: INPUT_WT_Ncor1_PD3_rep1


title: Ncor2_WT_PD3_rep1


title: Ncor1_WT_PD3_rep1

value: anti-Ncor1 (Abcam/ab3482)


title: 3_D6_Tbl1x_R

data_processing:
read trimming: bbduk (38.86)
alignment: STAR (2.7.3a)
alignment processing: samtools (1.10)
read counting: htseq-count (0.11.2)
Assembly: mm10
Supplementary files format and content: txt/counts

extract_protocol:
RNAseq. RNA was extracted using RNeasy mini kit (Qiagen) and treated with DNaseI (Qiagen).
Quantseq libraries were prepared with 250 ng RNA using QuantSEQ 3’ mRNA-Seq Library Prep Kit FWD for Illumina (015.96, Lexogen) according to manufacturer’s recommendations. The libraries were pooled and sequenced with a 50-base-pair single-end protocol on an Illumina HiSeq 2500 sequencer. ChIPseq libraries were generated with 5-10ng DNA using the NEBNext Ultra II DNA library preparation master mix (New England Biolabs, E7645) according to the manufacturer’s instructions.

value: trophoblast stem cells (mTSCs)


title: 3_D6_Tbl1x_KO


title: 3_D6_ERF_R


title: 3_D6_Erf_KO

value: ErfKO


title: Dopaminergic neuron nuclei, female

city: Chicago

first: Zachary

last: Gaertner

address: 320 E Superior, Searle 7-450

department: Neurology

institute: Northwestern University, Feinberg School of Medicine

description: 10x Genomics snRNA-Seq experiment

data_processing:
Data was demultiplexed and counted using Cell Ranger version 6.0.0
Downstream analysis was performed in Seurat v4.0.2.
Assembly: mm10-2020-A
Supplementary files format and content: 10x Cell Ranger output files corresponding to barcodes, features, and matrix of counts.
Supplementary files format and content: 10x Cell Ranger output files corresponding to barcodes, features, and matrix of counts.

molecule: nuclear RNA

source_name: Midbrain

extract_protocol:
A 2-3mm thick block of ventral midbrain tissue was dissected out and collected for subsequent isolation. Tissue was dounce homogenized in a nuclear extraction buffer (10mM Tris, 146mM NaCl, 1mM CaCl2, 21mM MgCl2, 0.1% NP-40, 40u/mL Protector RNAse inhibitor (Roche 3335399001). Dounce homogenizer was washed with 4mL of a washing buffer (10mM Tris, 146mM NaCl, 1mM CaCl2, 21mM MgCl2, 0.01% BSA, 40U/mL Protector RNAse inhibitor) and filtered through a 30uM cell strainer. After three rounds of washing by centrifugation (500g for 5 minutes) and resuspension in a nuclei resuspension buffer (10mM Tris, 146mM NaCl, 1mM CaCl2, 21mM MgCl2, 2% 104 BSA, 0.02% Tween-20), nuclei suspension was stained with DAPI and filtered through a 20uM strainer. This nuclei suspension was then sorted via FACS with a 100uM nozzle at a frequency of 30.0K and pressure of 20 PSI, with gates set for isolation of GFP+ singlet nuclei.
The cDNA and library were generated using the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (10X Genomics, PN-1000286) and Dual Index Kit TT Set A (10X Genomics, PN-1000215) according to the manufacturer’s manual with following modification: PCR cycle used for cDNA generation was 16 and the resulting PCR products was size-selected using 0.8X SPRI beads instead of 0.6X SPRI beads as stated in protocol.

value: Midbrain

tag: strain

value: Dat-IRES-Cre, CAG-Sun1/sfGFP

value: Dopaminergic neurons

tag: developmental stage

value: adult

value: female


title: Dopaminergic neuron nuclei, male

description: 10x Genomics snRNA-Seq experiment

tag: tissue

value: male


title: 3_D6_V5


title: 3_D6_GFP


title: 3_D4_ERF_R


title: 3_D4_Erf_KO


title: 3_D4_GFP


title: 3_D4_V5


title: 3_D2_Tbl1x_R


title: 3_D4_Tbl1x_KO


title: 3_D4_Tbl1x_R


title: 3_D2_ERF_R


title: 3_D2_Erf_KO


title: bulk hippocampal tissue from non-transgenic mice cGAS_46

value: F


title: 3_D2_GFP


title: 3_D2_V5


title: 3_D0_Tbl1x_KO


title: 3_D0_Erf_KO


title: 3_D0_ERF_R


title: 3_D0_GFP


title: Ncor1_WT_PD3_rep2


title: 2_D6_Tbl1x_R


title: 3_D0_V5


title: 2_D6_Tbl1x_KO


title: 2_D6_Erf_KO


title: 2_D4_Tbl1x_R


title: 2_D6_V5


title: 2_D6_GFP


title: 2_D4_Tbl1x_KO


title: 2_D4_ERF_R


title: 2_D4_V5


title: 2_D4_GFP


title: 2_D2_Tbl1x_R


title: 2_D2_ERF_R


title: 2_D2_Tbl1x_KO


title: 3_D2_Tbl1x_KO


title: 2_D2_Erf_KO


title: 2_D2_GFP


title: 2_D2_V5


title: 2_D0_Tbl1x_R


title: 2_D0_Tbl1x_KO


title: 2_D0_ERF_R


title: 2_D0_Erf_KO


title: 3_D0_Tbl1x_R


title: 1_D6_Tbl1x_KO


title: 2_D0_V5


title: 2_D0_GFP


title: 1_D6_Erf_KO


title: 1_D6_Tbl1x_R


title: 1_D6_GFP


title: 1_D6_V5


title: 1_D6_ERF_R


title: 2_D6_ERF_R


title: 1_D4_Tbl1x_R


title: 1_D4_ERF_R


title: 1_D4_Tbl1x_KO


title: 1_D4_Erf_KO


title: 2_D4_Erf_KO


title: 1_D4_V5


title: 1_D4_GFP


title: 1_D2_Tbl1x_KO


title: 1_D2_Tbl1x_R


title: 1_D2_ERF_R


title: 1_D2_Erf_KO


title: 1_D2_GFP


title: 1_D0_Tbl1x_R


title: 1_D2_V5


title: 1_D0_Erf_KO


title: 1_D0_GFP


title: 1_D0_Tbl1x_KO


title: 1_D0_ERF_R


title: 1_D0_V5