title: lumbar spinal cord-14 dpi [sci_14d_L snRNA-seq]

data_processing:
cellranger 6.0.0 software used tor analysis
Assembly: mmul10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
For nuclei extract, the spinal cord was dissociated and homogenized using a glass dounce tissue grinder (D8938; Sigma-Aldrich) in cold Nuclei EZ lysis buffer (EZ PREP NUC-101; Sigma-Aldrich) on ice. The lysate was then diluted with cold sucrose buffer and centrifuged for cell debris removal. Nuclei deposited on the tube wall were collected were suspended in Nuclei Suspension Buffer (NSB; consisting of 1xPBS, 0.01% BSA, and 0.1% RNase inhibitor (Clontech, Cat #2313A)). A final nuclei suspension was filtered through a 40μm cell strainer (Corning, Cat #352235) and used for libraries preparation.
Nuclei were processed using Chromium Single Cell V3 Chemistry Library Kits (10xGenomics) according to the manufacturer's instructions. In brief, nuclei were partitioned into Gel Beads-in-emulsion (GEMs) on the Chromium Controller, followed by full-length cDNA generated, barcoded, and sequenced on an Illumina HiSeq 4000.

value: 7 years old

value: spinal cord

value: 14 days after complete thoracic injury


title: BI_08N arr_3

status: Public on Jul 26 2023

type: SRA

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

library_source: transcriptomic

data_processing:
Raw data files were aligned to the reference genome and the mirbase database using Torrent Suite default parameters.
Assembly: hg19

molecule: total RNA

organism: Homo sapiens

source_name: Plasma

extract_protocol:
Plasma was isolated from EDTA or Lithium Heparin blood samples within 1 hour from collection, with a standard procedure to prevent haemolysis.
Total RNA was extracted with miRNeasy serum/plasma kit (Qiagen) using Exiqon protocol, with the batteriophage MS2RNA carrier (Roche Diagnostics) to promote RNA precipitation and purification on membranes.
For library preparation, smallRNA enriched samples were converted in barcoded cDNA libraries following the Ion Total RNA-Seq kit v2 protocol (Thermo Fisher) with the recommendations for low input RNA quantity. First, RNA samples were enriched for smallRNA fraction using a magnetic bead-based technology. After hybridization and ligation steps, through which 3' and 5' adaptors are directionally and simultaneously attached, reverse transcription was performed to obtain cDNA. cDNA was subsequently purified and size selected and then amplified using barcoded primers (obtained from Ion Xpress™ RNA-Seq Barcode 01-16 Kit, Thermo Fisher or synthesized by Eurofins Genomics as custom oligonucleotides (barcodes 17-24)). Finally, libraries were purified with beads. All the purification steps were performed by means of the Magnetic Bead Cleanup Module included in the kit. Libraries were checked for yield and size distribution by Bioanalyzer and DNA 1000 Kit (Agilent Technologies) and 24 differentially barcoded smallRNA libraries were pooled. Pools were checked by Bioanalyzer and DNA 1000 Kit (Agilent Technologies) to determine the library dilution required for template preparation. Ion Chef™ System (Thermo Fisher) was used for automated templated Ion Sphere Particles preparation and chip loading. Ion 540 chips (Thermo Fisher) were sequenced using Ion GeneStudio S5 System (Thermo Fisher).

tag: tissue

value: Plasma

tag: disease state

value: control


title: BI_22N arr_3


title: Tet2KO ctl rep 2

city: Boston

first: Philipp

last: Rauch

state: MA

address: 450 Brookline Ave

country: USA

institute: DFCI

data_processing:
Reads were mapped to the Mus musculus mm10 reference genome with the CLC Genomics Server program v. 9.0.1. Normalized read counts were obtained from the resulting BAM files using the BiocLite (https://bioconductor.org/biocLite.R) package in R.
Assembly: mm10
Supplementary files format and content: .csv, normalized read counts

molecule: polyA RNA

organism: Mus musculus

source_name: BMDM

growth_protocol: Single cell suspensions from murine whole bone marrow from 10-14 week old mice were differentiated for 6 days in the presence of 10 ng/ml of mM-CSF.

extract_protocol:
Trizol followed by RNeasy Mini columns (Qiagen) followed by DNase (Life Technologies) treatment and Ribo-Zero Kit (Illumina).
Library preparation using poly-A selection, multiplexing, and sequencing were done by Genewiz (South Plainfield, NJ).

treatment_protocol: Day 6 BMDM were allowed to rest for 24h after replating, followed by stimulation with 200 mg/dL of LDL or vehicle control.

tag: cell type

value: BMDM

tag: genotype

tag: treatment

value: ctl


title: lumbar spinal cord-30 dpi [sci_30d_L snRNA-seq]

city: Beijing

first: Xianming

last: Wu

state: Chaoyang District

address: Unit 2, No.1 West Beichen Road

country: China

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

organism: Macaca mulatta

source_name: spinal cord

tag: age

value: 6 years old

tag: developmental stage

value: adult

value: 30 days after complete thoracic injury


title: Injury area of injured spinal cord, LOCS, 6 months

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing and gene counting  were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mmul_10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
For cell preparation, tissues were digested using a papain dissociation system according to the manufacturer’s protocol (LS003126, Worthington). Spinal cords were roughly cut into small pieces and then incubated in papain solution containing DNase I at 37℃ for 1-1.5 h with occasional pipetting. Albumin-ovomucoid inhibitor solution was used to terminate the enzymatic reaction. Subsequently, the cell suspension was further pipetted to generate a single-cell suspension, which was centrifuged at 400 g for 5 min to obtain a cell pellet. Then the cell pellet was resuspended with 20% Percoll (P1644, Sigma) and centrifuged at 400 g for 10 min to remove myelin debris. The cells were resuspended in PBS with 0.04% BSA.  For nuclei extract, the spinal cord was dissociated and homogenized using a glass dounce tissue grinder (D8938, Sigma) in cold Nuclei EZ lysis buffer (NUC101-1KT, Sigma) on ice. The lysate was then diluted with cold sucrose buffer and centrifuged for cell debris removal. Nuclei deposited on the tube wall were suspended in Nuclei Suspension Buffer consisting of 1xPBS and 0.01% BSA and 0.1% RNase inhibitor (2313A, TaKaRa).
Cells and nuclei were processed using Chromium Single Cell V3 Chemistry Library Kits (10xGenomics) according to the manufacturer's instructions. In brief, nuclei were partitioned into Gel Beads-in-emulsion (GEMs) on the Chromium Controller, followed by full-length cDNA generated, barcoded, and sequenced on an Illumina NovaSeq 6000.

value: tissue

tag: Sex

value: female

value: 4-7 years old

value: complete spinal cord injury+LOCS


title: Expt1_bud7_highP_rep2

city: Auckland

first: Zhiwei

last: Luo

state: Auckland

address: 120 Mt Albert Road

country: New Zealand

institute: PLANT AND FOOD RESEARCH

data_processing:
nf-core (https://nf-co.re/rnaseq, version 1.4.2 for experiment 1 and version 3.0 for experiment 3)
Trim Galore (https://github.com/FelixKrueger/TrimGalore)
FastQC
STAR aligner (https://github.com/alexdobin/STAR)
Salmon
Assembly: Petunia axillarisdraft genome sequence v1.6.2

organism: Petunia x hybrida

source_name: axillary buds

growth_protocol: hydroponic

extract_protocol:
sigma spectrum plant RNA kit
mRNA library

value: axillary buds

value: 250 uM phosphate


title: Degenerative area of injured spinal cord, 7 days, rep1

description: 10x Genomics

value: complete spinal cord injury


title: Spared but activated area of injured spinal cord, 30 days, rep1

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting  were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Mmul_10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Library strategy: snRNA-seq

molecule: nuclear RNA


title: Expt1_bud3_highP_rep1


title: Tet2KO LDL rep 1

value: LDL


title: thoracic spinal cord-0 dpi [Mac_T snRNA-seq]

value: 5 years old

value: spinal cord

value: untreat


title: TO_20N_3

value: Plasma

value: control


title: Injury area of injured spinal cord, 6 months

description: 10x Genomics


title: Degenerative area of injured spinal cord, 30 days, rep2

description: 10x Genomics


title: Expt1_bud2_highP_rep1


title: WT LDL rep 1

value: BMDM

value: WT


title: lumbar spinal cord-6 mpi [sci_6m_L snRNA-seq]

value: 6 years old

value: adult

value: 6 months after complete thoracic injury


title: BI_14N_3


title: WT LDL rep 2


title: MCF7_Empty_Vector_replica 5

city: Fribourg

first: Rüegg

last: Curzio

address: Albert-Gockel 1

department: Département de Médecine 3

country: Switzerland

institute: Université de Fribourg

data_processing:
Data processing was performed by the Lausanne Genomic Technologies Facility (University of Lausanne) using the following pipeline: Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 2.5, Martin 2011).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1). Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013).
Reads were aligned against Homo sapiens genome (GRCh38) using STAR (v. 2.5.3a, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Ensembl 102 gene annotation.
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012)
Assembly: Homo sapiens GRCh38
Supplementary files format and content: tab-delimited text file contains RAW counts per sample.

source_name: ER+ breast cancer

growth_protocol: MCF7 cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 1% Penicillin/Streptomycin and maintained at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
RNA was extracted using the Macherey-Nagel™ NucleoSpin™ RNA Plus Kit
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA).

treatment_protocol: Lentivirus Transduction

value: ER+ breast cancer

tag: cell line

value: Carcinoma

value: Lentivirus Transduction with empty vector


title: Injury area of injured spinal cord, 14 days

description: 10x Genomics

value: tissue

value: female

value: 4-7 years old


title: BI_7N_3


title: WT ctl rep 2

value: ctl


title: Dnmt3aKO ctl rep 3


title: WT ctl rep 1


title: BI_26N_2


title: BI_21N_3


title: BI_20N_2


title: 4T1-T_acLDL_High_Rep3

city: Cambridge

first: Kirsty

last: Sawicka

address: Robinson Way

department: University of Cambridge

country: United Kingdom

institute: CRUK Cambridge Insititute

data_processing:
The reads were aligned with STAR (version 2.5.2a), and genes annotated in Gencode VM16 were quantified with featureCounts (v1.4.3-p1).
Normalization and differential expression analysis includin log2 fold change estimation, and FDR p-value calculation were done with DESeq2 (version 1.20.0) with analysis restricted to protein coding genes. Counts generated using featureCounts were used to determine expression differences between acLDL high and low populations. betaPrior was set to TRUE resulting in log2 fold change shrinkage useful for ranking of genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text file with read counts for each sample
Supplementary files format and content: tab-delimited text file with output from DESeq2 DGE analysis

source_name: Breast cancer

growth_protocol: 4T1-T cells were grown in RPMI supplemented with 10% FBS and L-glutamine.

extract_protocol:
Roche High Pure RNA extraction kit (Roche, 11828665001) according to the manufacturer's instructions.
RNA sequencing libraries were prepared using the TruSeq Stranded mRNA Library Preparation Kit (Illumina) in accordance with the manufacturer’s instructions. Briefly, 500 ng of total RNA was used for polyA mRNA purification and fragmentation. Purified mRNA underwent first and second strand cDNA synthesis. cDNA was then adenylated, ligated to illumina sequencing adapters, and amplified by PCR (using 8 cycles). Final libraries were evaluated using fluorescent-based assays and were sequenced on an Illumina HiSeq 2500 (v4 chemistry) using 2 x 50 bp cycles.

treatment_protocol: 4T1-T VM cells were seeded at 40% confluency in 6 well plates. 24 hr later they were swapped to serum starvation medium, consisting of Opti-Mem (Invitrogen) supplemented with 0.3% BSA, and incubated overnight. The next morning Alexa-488 labelled ac-LDL (Thermo Fisher, L23380) was added at a final concentration of 10 ug/mL and cells were incubated for 4 hours. Cells were washed 8 times in PBS (+Ca and Mg), then further incubated in complete growth medium for 1 hour. cells were trypsinized and resuspended in MACS buffer (1x PBS, 0.5% BSA, 2 mM EDTA) and put through a 40 um cell strainer. Cells were then sorted using a Sony SH800 cell sorter using the EGFP gate taking the top 25% as high and bottom 25%.

value: Breast cancer

value: 4T1-T VM sub-clone

value: Cancer cells

value: acLDL High (top 25%)


title: 4T1-T_CellTag_Tumor_Rep2

description: 10x Genomics

data_processing:
Reads were aligned and feature-barcode matrices were generated using Cell Ranger software v3.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38 with addition of celltag vector sequence.
Supplementary files format and content: Tab-separated values files and matrix files

source_name: mammary fat-pad tumor

growth_protocol: 50,000 4T1-T cells labelled with CellTag vector were implanted into the mammary fat-pad of 6-8 week old female BALB/c mice.

extract_protocol:
At day 20 post-implantation tumors were dissociated using Miltenyi tumor dissociation kit (mouse) (#130-096-730) and the gentleMACS Octo Dissociator with heaters from Miltneyi Biotec.Briefly, Tough tumor dissociation protocol was used, program 37_m_TDK_2 followed by program  m_imptumor_01 12,000 cells of the resulting cell suspensions were submitted for single-cell RNA-seq library preparation at the Cancer Research UK Cambridge Institute Genomics Core Facility.
Chromium Single Cell 3′ Library & Gel Bead Kit v3, Chromium Chip B Kit and Chromium Single Cell 3' Reagent Kits v3 User Guide (Manual Part CG000183 Rev A; 10X Genomics). Cell suspensions were loaded on the Chromium instrument with the expectation of collecting gel-beads emulsions containing single cells. RNA from the barcoded cells for each sample was subsequently reverse-transcribed in a C1000 Touch Thermal cycler (Bio-Rad) and all subsequent steps to generate single-cell libraries were performed according to the manufacturer’s protocol with no modifications (12 cycles was used for cDNA amplification). cDNA quality and quantity was measured with Agilent TapeStation 4200 (High Sensitivity 5000 ScreenTape), after which 25% of material was used for gene expression library preparation. Library quality was confirmed with Agilent TapeStation 4200 (High Sensitivity D1000 ScreenTape to evaluate library sizes) and Qubit 4.0 Flourometer (Thermo Fisher Qubit™ dsDNA HS Assay Kit to evaluate dsDNA quantity). Each sample was normalized and pooled in equal molar concentration. To confirm concentration pools were qPCRed using KAPA Library Quantification Kit on QuantStudio 6 Flex before sequencing.

value: mammary fat-pad tumor

value: 4T1-T VM clone labelled with CellTag vector

value: Tumour cells and tumour microenvironment cell types

value: BALB/c mice

value: 6-8 week old female

value: Female


title: Degenerative area of injured spinal cord, 7 days, rep2

description: 10x Genomics

value: spinal cord

value: adult

value: complete spinal cord injury


title: MCF7_MAGI1_KO_SeqB_replica 5

value: ER+ breast cancer

value: Carcinoma

value: Lentivirus Transduction with targeting vector


title: lumbar spinal cord-7 dpi [sci_7d_L snRNA-seq]

value: 7 years old

value: 7 days after complete thoracic injury


title: MCF7_Empty_Vector_replica 2

value: Lentivirus Transduction with empty vector


title: Dnmt3aKO ctl rep 1

value: BMDM

value: ctl


title: MCF7_MAGI1_KO_SeqB_replica 3


title: 4T1-T_acLDL_Low_Rep3

value: Breast cancer

value: 4T1-T VM sub-clone

value: Cancer cells

value: acLDL Low (bottom 25%)


title: BI_18T_2

value: Plasma

value: case


title: BI_14T_2


title: lumbar spinal cord-0 dpi [Mac_L snRNA-seq]

value: 5 years old

value: spinal cord

value: untreat


title: 4T1_CellTag_Tumor_Axit_Rep2

description: 10x Genomics

growth_protocol: 50,000 Parental 4T1 cells labelled with CellTag vector were implanted into the mammary fat-pad of 6-8 week old female BALB/c mice.

extract_protocol:
Tumors were dissociated using Miltenyi tumor dissociation kit (mouse) (#130-096-730) and the gentleMACS Octo Dissociator with heaters from Miltneyi Biotec.Briefly, Tough tumor dissociation protocol was used, program 37_m_TDK_2 followed by program  m_imptumor_01 15,000 cells of the resulting cell suspensions were submitted for single-cell RNA-seq library preparation at the Cancer Research UK Cambridge Institute Genomics Core Facility.
Chromium Single Cell 3′ Library & Gel Bead Kit v3, Chromium Chip B Kit and Chromium Single Cell 3' Reagent Kits v3 User Guide (Manual Part CG000183 Rev A; 10X Genomics). Cell suspensions were loaded on the Chromium instrument with the expectation of collecting gel-beads emulsions containing single cells. RNA from the barcoded cells for each sample was subsequently reverse-transcribed in a C1000 Touch Thermal cycler (Bio-Rad) and all subsequent steps to generate single-cell libraries were performed according to the manufacturer’s protocol with no modifications (12 cycles was used for cDNA amplification). cDNA quality and quantity was measured with Agilent TapeStation 4200 (High Sensitivity 5000 ScreenTape), after which 25% of material was used for gene expression library preparation. Library quality was confirmed with Agilent TapeStation 4200 (High Sensitivity D1000 ScreenTape to evaluate library sizes) and Qubit 4.0 Flourometer (Thermo Fisher Qubit™ dsDNA HS Assay Kit to evaluate dsDNA quantity). Each sample was normalized and pooled in equal molar concentration. To confirm concentration pools were qPCRed using KAPA Library Quantification Kit on QuantStudio 6 Flex before sequencing.

treatment_protocol: After 6 days of tumor growth, animals were treated with vehicle or 50 mg/Kg Axitinib via intraperotoneal injection on a 5 days on 2 days off schedule for 14 days.

value: mammary fat-pad tumor

tag: strain

value: BALB/c

value: 6-8 weeks old

value: Female

value: axitinib


title: Uninjured thoracic spinal cord, 0days

description: 10x Genomics

value: tissue

value: female

value: 4-7 years old

value: adult

value: complete spinal cord injury


title: BI_18N_3

value: control


title: Degenerative area of injured spinal cord, 14 days, rep1

description: 10x Genomics


title: MCF7_MAGI1_KO_SeqB_replica 1

value: ER+ breast cancer

value: Carcinoma

value: Lentivirus Transduction with targeting vector


title: 4T1_CellTag_Tumor_Veh_Rep1

description: 10x Genomics

value: Parental 4T1 cells labelled with CellTag vector

value: vehicle


title: cervical spinal cord-0 dpi [Mac_C snRNA-seq]

value: 5 years old

value: spinal cord

value: untreat


title: WT LDL rep 3

value: BMDM

value: WT

value: LDL


title: Dnmt3aKO ctl rep 2

value: ctl


title: Injury area of injured spinal cord, 30 days

description: 10x Genomics

value: tissue

value: female


title: TO_2T_2

value: Plasma

value: case


title: WT ctl rep 3


title: KO-2 D3_lrg-active

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

data_processing:
Raw reads were trimmed of adapter sequence using cutadapt (https://cutadapt.readthedocs.io/en/stable/
filtered for low quality bases and low quality reads using the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
Remaining reads were mapped to Mus_musculus UCSC mm10
Reads mapping to genes were counted using htseq-count (Anders et al., 2015)
Assembly: mm10
Supplementary files format and content: tab-delimited text file which includes normalized values from each Sample

source_name: Splenic naive follicular B cells from Mavs-/- mice

extract_protocol:
RNA and genomic DNA was extracted using AllPrep DNA/RNA 96 kit as described by the manufacturer (Qiagen, Valencia, CA) including additional on-column Dnase 1 treatment.
RNA libraries for RNA-seq were prepared using TruSeq mRNA with polydT pullout Library Prep Kit following manufacturer's protocols.

treatment_protocol: cells were then stimulated with anti-IgM (10 μg/ml) for 24h

tag: time

value: Day 3

value: MAVS-/-

value: KO

value: anti-B cell receptor


title: TO_14N_2

value: control


title: MCF7_Empty_Vector_replica 4

value: ER+ breast cancer

value: Carcinoma

value: Lentivirus Transduction with empty vector


title: MCF7_Empty_Vector_replica 3


title: Injury area of injured spinal cord, 7 days

description: 10x Genomics

value: spinal cord

value: 4-7 years old

value: adult

value: complete spinal cord injury


title: MCF7_MAGI1_KO_SeqA_replica 2

value: Lentivirus Transduction with targeting vector


title: BI_4T_2


title: CD45+cells from E0771 tumor of FLT3L-treated mice

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

description: 10x Genomics

data_processing:
Raw data bcl files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
Assembly: mm10
Supplementary files format and content: h5 files including raw counts (output CellRanger Count) per sample and text comma-separated metadata files with information per cell

source_name: tumor

extract_protocol:
The extraction protocol can be found in the author's manuscript: The regular tissue processing procedure was followed, with the addition of actinomycin D (Sigma-Aldrich, A1410-5MG) to each buffer. Tumor collection was performed in 30 µM, enzyme incubation and subsequent filtering in 15 µM, and all other steps in 3 µM. 10^6 cells were stained with anti-CD45 APC-Cy7 (1:50, Biolegend), a mouse cell surface protein antibody panel containing 167 oligo-conjugated antibodies for cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) and TruStain FcX™ PLUS Antibody (1:25; Biolegend) in Phosphate buffered saline (PBS) with 0.04% bovine serum albumin (BSA) for 30 minutes on ice. After incubation, cells were incubated with 7AAD (1:100) 5 minutes prior to sorting. 8x10^4 living CD45+ cells were sorted using BD FACSAriaTM II and collected in 500 μl PBS + 0.04% BSA and 3 μM ActD.
The library construction protocol was described in Antunes et al., Nat Neurosci; 2021;24(4):595-610. doi: 10.1038/s41593-020-00789-y.
scRNAseq 10x v3.1

value: tumor


title: BI_3T_2


title: BI_24N_2


title: 4T1-T_acLDL_High_Rep2

value: Breast cancer

value: 4T1-T VM sub-clone

value: Cancer cells

value: acLDL High (top 25%)


title: RNA_seq_BCAS_hippocampus_1

city: Shanghai

first: Zengyu

last: Zhang

state: Shanghai

address: Dong'an Road

department: Neurology

institute: Fudan University

data_processing:
Raw data were first evaluated by FastQC for quality control to determine whether the sequencing data were suitable for subsequent analyses.
Adapter sequences, low-quality reads, and too short reads were removed from raw data with Trim-galore to obtain clean data.
Sequencing reads were aligned to annotated RefSeq genes in the mouse reference genome (UCSC mm10) with HISAT2. And Samtools v1.9 was used to sort and build the alignment file index.
A gene count matrix that contained raw transcript counts for each annotated gene were generated using the featureCounts v1.6.3.
To determine the most appropriate threshold for removing genes with low counts, we relied on the automatic and independent filtering performed by DESeq2 R package (1.16.1). And raw transcript counts were normalized, log2 transformed, and analyzed using the default procedures in DESeq2 to identify genes that were differentially regulated following CCH.
Assembly: mm10
Supplementary files format and content: raw gene counts text files

source_name: right  hippocampus

growth_protocol: The mice were housed at 25°C and fed standard rodent chow and tap water

extract_protocol:
RNA was harvested using the TRIzol Reagent (Life technologies, California, USA). 1 ug of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol:
The control group was exposed to sham operation
The experimental group was exposed to bilateral carotid artery stenosis (BCAS) operation

value: right  hippocampus

value: WT

value: 14 weeks


title: HEK293T input

city: shanghai

first: qian

last: wu

address: siping

department: biology

institute: tongji university

library_source: genomic

data_processing:
150-bp paired-end reads per ChIP-seq were mapped to the human genome using Bowtie2 (Galaxy toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.3+galaxy0) with default parameters.
Peaks were called by model-based analysis of ChIP-seq (MACS2 Galaxy toolshed.g2.bx.psu.edu/repos/iuc/macs2/macs2_callpeak/2.1.1.20160309.6) using GFP input as control and calling p value 1e-6.
Consensus target motif was derived from peak regions by using MEME-ChIP tool (http://meme-suite.org/tools/meme-ChIP).
Heatmap and profile plots then were generated by plotHeatmap or plotProfile (Galaxy toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_heatmap/deeptools_plot_heatmap/3.3.0.0.1, toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_profile/deeptools_plot_profile/3.1.2.0.0) using calculated matrix generated by ComputeMatrix.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

growth_protocol: DMEM High Glucose, 10% fetal bovine serum, 2mM L-glutamine. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. Crosslinked chromatin from 2-4X107 cells fragmented on a Covaris to ~100-300bp was immunoprecipitated with GFP (Invitrogen A-6455), H3K9me3 (Abcam ab8898) antibodies or KAP1 (Abcam ab22553).
library construction using the KAPA Hyper Prep Kit (Roche)

treatment_protocol: ZNF506-GFP and ZNF417-GFP vectors were stably transfected into HEK293T cells respectively, co-transferred with piggyBac transposon vector in the ratio of 1:1. ZNF506 knockout (KO) HEK293T cell lines were generated by CRISPR/Cas9 engineering.

value: Human embryonic kidney

tag: chip antibody

value: GFP (Invitrogen A-6455)


title: 4T1-T_acLDL_High_Rep1


title: BI_16T_2

value: Plasma

value: case


title: MCF7_MAGI1_KO_SeqB_replica 4

value: ER+ breast cancer

value: Carcinoma


title: MCF7_Empty_Vector_replica 1

value: Lentivirus Transduction with empty vector


title: TO_3N_1

value: control


title: 4T1-T_CellTag_Tumor_Rep1

description: 10x Genomics

value: mammary fat-pad tumor

value: 4T1-T VM clone labelled with CellTag vector

value: Tumour cells and tumour microenvironment cell types

value: BALB/c mice

value: 6-8 week old female

value: Female


title: 4T1_CellTag_Tumor_Axit_Rep1

description: 10x Genomics

value: Parental 4T1 cells labelled with CellTag vector

value: BALB/c

value: 6-8 weeks old

value: axitinib


title: MCF7_MAGI1_KO_SeqA_replica 5

value: Lentivirus Transduction with targeting vector


title: 4T1-T_acLDL_Low_Rep1

value: Breast cancer

value: 4T1-T VM sub-clone

value: Cancer cells

value: acLDL Low (bottom 25%)


title: 4T1-T_acLDL_Low_Rep2


title: 4T1_CellTag_Tumor_Veh_Rep2

description: 10x Genomics

value: vehicle


title: MCF7_MAGI1_KO_SeqA_replica 4

value: ER+ breast cancer

value: Carcinoma


title: KO-3 D3_lrg-active

value: Day 3

value: Splenic naive follicular B cells from Mavs-/- mice

value: MAVS-/-

value: KO

value: anti-B cell receptor


title: TO_17T_1

value: Plasma

value: case


title: CD45+cells from E0771 tumor of vehicle-treated mice

description: 10x Genomics

value: tumor

value: vehicle-treated


title: RNA_seq_Sham_hippocampus_2

value: right  hippocampus

value: WT

value: Sham operation

value: 14 weeks


title: TO_27N_2

value: control


title: TO_13T_1


title: TO_14T_1


title: ZNF506 OE H3K9me3 ChIP

value: Human embryonic kidney

value: H3K9me3 (Abcam ab8898)


title: BI_1N_2


title: WT-2 Day1_lrg-active

source_name: Splenic naive follicular B cells

value: Day 1

value: Splenic naive follicular B cells


title: RNA_seq_BCAS_hippocampus_3

value: bilateral carotid artery stenosis (BCAS) operation


title: BI_9T_1


title: KO-1 Day1_lrg-active

value: MAVS-/-


title: WT-3 D3_lrg-active

source_name: Splenic naive follicular B cells from B6 mice

value: Day 3


title: MCF7_MAGI1_KO_SeqA_replica 1

value: ER+ breast cancer

value: Carcinoma

value: Lentivirus Transduction with targeting vector


title: KO-2 Day1_lrg-active

value: anti-B cell receptor


title: RNA_seq_BCAS_hippocampus_2


title: BI_7T_1

value: Plasma

value: case


title: WT-2 D3_lrg-active

value: Splenic naive follicular B cells from B6 mice

value: WT


title: BI_2T_2


title: KO-3 D0_small-rest

value: Day 0


title: KO-1 D3_lrg-active

value: Splenic naive follicular B cells from Mavs-/- mice

value: KO


title: ZNF506 KO KAP1 ChIP

value: Human embryonic kidney

value: KAP1 (Abcam ab22553)


title: ZNF417 H3K9me3 ChIP

value: H3K9me3 (Abcam ab8898)


title: TO_12N_1

value: control


title: RNA_seq_Sham_hippocampus_3

value: right  hippocampus

value: Sham operation

value: 14 weeks


title: WT-1 D3_lrg-active

value: Day 3


title: WT-3 D0_small-rest

value: Splenic naive follicular B cells


title: TO_11N_1


title: KO-2 D0_small-rest

value: MAVS-/-

value: anti-B cell receptor


title: TO_10T_1

value: Plasma

value: case


title: 2W_ctrl_ RPE_3

city: Belfast

first: Imre

last: Lengyel

state: Northern Ireland

address: 97 Lisburn Road

department: Wellcome-Wolfson Institute For Experimental Medicine

institute: Queen's University Belfast

data_processing:
bcl2fastq (2.20) was used to demultiplex the samples and convert raw BaseCall files from Illumna sequencing data to FASTQ files.
FASTQ files were processed in Cellranger (3.0.2) Count, aligned against GRCh38 reference package with default parameters
10X-filtered count matrices subject to additional gene- and cell-QC filtering in seurat (3.1), to exclude genes found in <3 cells, and cells with <1000 or >8000 genes, with >20% transcripts aligning to mitochondrial genes, or >40% transcripts. aligning to ribosomal genes
Seurat LogNormalize used to generate normalised expression matrix with default parameters. The top 3000 highly variable genes calculated, and used in iterative pairwise integration with Seurat IntegrateData. The integrated data was scaled using Seurat ScaleData to regress out cellular variation arising from sequencing depth and mitochondrial read percentage. Scaled data was used as input to Principal Component Analysis
Seurat JackStraw was used to determine significant PCs for clustering and UMAP.
Assembly: GRCh38
Supplementary files format and content: count matrix generated by Cellranger Count for each sample

source_name: retinal pigment epithelium

growth_protocol: Primary human fetal RPE cells (ScienCell, Carlsbad, USA) from one donor were purchased and used at passage number three (P3) for the complete study, in duplicates/triplicates with unknown clinical or genetic background. Cells were seeded onto Corning 6-well transwell inserts (10 µm thick polyester inserts with 0.4 µm pore size, 4*106/cm2 pore density, Corning, Wiesbaden, Germany) in 125.000/cm2 in epithelial cell medium (EpiCM, ScienCell, Carlsbad, USA). After one week in culture, cell culture media was replaced with Miller medium with 1% FBS and cells were cultured for two, nine, and nineteen weeks in duplicates.

extract_protocol:
10X Chromium v3.1 GEX 3' recovery
Chromium Single Cell 3ʹ v3

treatment_protocol: Two types of short-term zinc treatment were also conducted, where one-one extra replicates of untreated controls were taken for the two type of zinc treatment experimental setup. Either after one week or after eighteen weeks in culture, cell culture media was replaced with Miller medium with 1% FBS for an additional one week in the absence or presence of 125 µM externally added zinc (as zinc sulphate; Thermo Fisher Scientific, Waltham, USA) apically as well as basally, resulting in ~10 nM bio-available or free zinc. The resulting replicates were the following: duplicates of zinc treated samples, triplicates of untreated controls at the two- and nineteen-week time-point and duplicates of untreated controls at nine-week time-point.

value: 2 weeks

value: primary fetal retinal pigment epithelial cells

value: untreated


title: ZNF506 OE KAP1 ChIP


title: TO_26N_1


title: KO-1 D0_small-rest

value: Day 0


title: KO-3 Day1_lrg-active

value: Day 1


title: ZNF506 KO H3K9me3 ChIP

value: Human embryonic kidney


title: RNA_seq_Sham_hippocampus_1

value: WT


title: WT-3 Day1_lrg-active


title: TO_10N_1

value: control


title: WT-1 D0_small-rest


title: ZNF506 H3K9me3 ChIP

value: H3K9me3 (Abcam ab8898)


title: 19W_ctrl_RPE_3

value: 19 weeks


title: BI_8T_1


title: 19W_zinc_RPE_1

value: Zinc (125 µM) treated


title: BI_16N_1


title: ZNF506 GFP ChIP rep2

value: GFP (Invitrogen A-6455)


title: 2W_ctrl_ RPE_2


title: BI_5T_1


title: 19W_ctrl_RPE_2


title: 96 glial cells_plate4

first: Elijah

middle: D.

last: Lowenstein

address: 3 Blackfan Circle

institute: BIDMC

data_processing:
Dropseq-tools v2.0 pipeline following the cookbook (whitelist of barcodes)
picard-tools v2.18.17
STAR v2.5.3a
Seurat v2 standard pipeline
Assembly: GRCm38.p4
Supplementary files format and content: csv file of raw counts

source_name: Nodose ganglia

extract_protocol:
Vagal ganglia were dissected from 4 Phox2bCre;Ai14 mice at P4 of either sex and placed into ice cold Ringer’s solution (0.125 M sodium chloride, 1.5 mM calcium chloride dihydrate, 5 mM potassium chloride, 0.8 mM sodium phosphate dibasic). Ganglia were transferred to a 1.5 ml Eppendorf tube with 1.5 ml HBSS without calcium, magnesium and phenol red (Thermo Fisher Scientific), 3 µl saturated NaHCO3, 1 mg L-Cysteine and 60 U Papain (Sigma-Aldrich), placed at 37°C and shaken gently for 12 minutes. The 1.5 ml Eppendorf tube was centrifuged at 300 RCF and the solution was discarded, taking care not to disturb the ganglia. A prewarmed (37°C) enzyme solution containing 1 ml HBSS without calcium, magnesium and phenol red (Thermo Fisher Scientific), 4 mg Collagenase NB4 (Serva) and 4.6 mg Dispase II (Gibco) was added to the ganglia, placed at 37°C and shaken gently for 12 minutes. The 1.5 ml Eppendorf tube was centrifuged at 300 RCF and the solution was discarded, taking care not to disturb the ganglia. Prewarmed (37°C) 0.5 ml HBSS without calcium, magnesium and phenol red (Thermo Fisher Scientific) was added to the ganglia, which were triturated with a 1 ml plastic pipette tip until the ganglia began to dissociate, and then with a 200 µl plastic pipette tip until the ganglia were completely dissociated. The dissociated ganglia were passed twice through a 40 µm filter (Falcon) and DAPI (Sigma) was added to a final concentration of 300 nM to label dead cells before sorting.
Single cell RNA-sequencing was done following the CEL-Seq2 protocol (Hashimshony et al., 2016). cDNA Libraries were prepared for 4 96-well plates, pooled together, and sequenced on 1 lane of a HiSeq 1500 (Ilumina) by the next generation sequencing core facility at the Max Delbrück Center for Molecular Medicine.

value: Nodose ganglia

value: Glial cells


title: BI_15N_1


title: Glaucoma treated with Igfbpl1 D23-1168

first: Guangan

last: Hu

address: 500 Main Street

department: Koch Institute

institute: MIT

data_processing:
Raw sequences were demultiplexed, aligned, filtered, barcode counting, unique molecular identifier (UMI) counting with Cell Ranger software v3.1 (10XGenomics) to digitalize the expression of each gene for each cell.
The outlier cells with very low number of gene features (<500), or high number of gene features as doublets (>5000),  or low total UMI (<1000) and high mitochondrial ratio (>10%) from each data set were removed.
Samples were combined based on the  identified anchors for the following integrated analysis.
Assembly: mm10
Supplementary files format and content: CSV files include mRNA molecule count values and single cell barcodes for each Sample

source_name: retina

extract_protocol:
Single-cell suspensions of retinal cells were taken from glaucoma mice and Igfbpl1-treated glaucoma mice . Immune cells were stained by PE anti- mouse CD45 and sorted by flow cytometry. Sorted cells were resuspended and washed in 0.05% RNase-free BSA in PBS for single-cell library preparation.
10x Chromium Next GEM Single Cell 3' Kit.
single cell RNA-Seq by NextSeq500

value: retina

value: microbead-induced glaucoma

value: CD45+ immune cells


title: ZNF506 GFP ChIP rep1


title: TO_13N_1

value: Plasma


title: WT-1 Day1_lrg-active

value: Splenic naive follicular B cells

value: anti-B cell receptor


title: 19W_ctrl_RPE_1

value: primary fetal retinal pigment epithelial cells

value: untreated


title: 96 glial cells_plate2


title: 2W_zinc_ RPE_2

value: 2 weeks


title: 96 glial cells_plate1


title: 2W_zinc_ RPE_1


title: WT-2 D0_small-rest

value: Day 0

value: WT


title: 19W_zinc_RPE_2


title: IDH-mut glioma, Capture Bis-seq, 2

status: Public on Jul 25 2023

first: Gilbert

middle: Joseph

last: Rahme

address: 365 Longwood Ave.

department: Cancer Biology

institute: Dana-Farber Cancer Institute

data_processing:
HSBS data were aligned to hg19 by methylCtools 0.9.4 (Volker Hovestadt et al. Nature 2014), utilizing BWA mem 0.7.12, removing reads of mapping qualty 0.
PCR duplicates were removed with picard tools 2.9.2
HSBS methylation data were called with methylCtools 0.9.4 (Volker Hovestadt et al. Nature 2014)
Assembly: hg19
Supplementary files format and content: Methylation at CpGs was called by methylCtools 0.9.4. Column 5 represent counts supporting methylated (i.e. not converted) DNA, column 6 represent unmethylated (i.e. converted) DNA at any given loci
Library strategy: capture bisulfite sequencing (hybrid selection bisulfite sequencing)

source_name: Glioma

extract_protocol:
For hybrid-selection bisulfite-sequencing, total genomic DNA was isolated using the DNAeasy Blood & Tissue Kit (Qiagen) and sheared using the Covaris LE220. Ampure XP beads (Agencourt) were then used to size select gDNA fragments within 150-320bp and sheared distribution was verified via BioAnalyzer (Agilient) prior to continuation.
1 microgram of gDNA was then generated into a sequencing library via end repair, 3' A base tailing (KAPA Hyper Prep Kit #KK8502) and sequencing adapter ligation (Roche SeqCap Epi Enrichment System). Post-ligation clean-up was performed using Ampure XP beads. Following bead clean-up, DNA library was then bisulfite converted using the EZ DNA Methylation-Lightning Kit (Zymo Research) and amplified via PCR using KAPA HiFi U+ HotStart ReadyMix (KAPA #KK2800). Equal concentration of each bisulfite-converted library was then combined in sets of either three or four libraries/per pool along with SeqCap Epi universal & indexing oligos and bisulfite capture enhancer (SeqCap Epi Accessory Kit). Each pool was subsequently lyophilized using TOMY Micro-Vac (MV100) and resuspended in hybridization buffer (SeqCap Epi Hybridization and Wash Kit) prior to being hybridized to SeqCap Epi Probe Pool (Roche) for 72 hours at 47C in a thermocycler with a heated lid at 57C. Following the 72-hour incubation, captured bisulfite-converted libraries were recovered (SeqCap Pure Capture Bead Kit) at 47C in a thermocycler for 45 minutes, with intermediate vortexing every 15 minutes. Capture beads were then washed (SeqCap Hybridization and Wash Kit) in a 47C water bath and room temperature, respectively.

value: Glioma


title: IDH-wt GBM, Capture Bis-seq, 1


title: IDH-mut glioma, Capture Bis-seq, 1


title: H3K36me3 ChIP-seq rep2

city: Montpellier

first: Isabelle

last: Jariel-Encontre

state: Montpellier Cedex5

address: 208 Avenue des Apothicaires

country: France

institute: IRCM-U1194- INSERM

data_processing:
Reads were aligned to hg19 genome using Bowtie2 allowing no more than 2 mismatches and no multiple alignment sites.
Aligned reads were processed with R package PASHA (Fenouil et al., 2013; doi: 10.1093/bioinformatics/btw206) to eliminate PCR artefacts, extend reads to an estimated fragment length and generate WIG files.
R Package PASHA was used to normalize the WIG files to calculate the scores per million reads sequenced and Input DNA signal was subtracted from normalized WIG files.
BigWig files from biological replicates were merged.
Assembly: Hg19
Supplementary files format and content: BigWig files

growth_protocol: MDA-MB-231 cells (ATCC, Rockville, MD, USA) were cultured cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal calf serum and penicillin/streptomycin (100µg/ml each) in a humidified 5% CO2 atmosphere at 37°C. Cells freshly amplified and frozen after obtention from the ATCC were used every 3months and were routinely tested for the absence of mycoplasma contamination

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with the anti H3K36me3 antibody from Active Motif (ref 61101)- INPUTs correpond to sonicated chromatin before immuoorecipitation
ChIP-seq libraries were prepared  using the TruSeq ChIP sample reparation kit from Illumina by the MGX sequencing Platform (Montpellier, France)
ChIP-seq - Instrument model :  Illumina HiSeq 2500 (MGX Platform, Montpellier France)

treatment_protocol: experiments were carried out in 2 independent replicates : replicate 1 and replicate 2

value: triple negative breast cancer

tag: antibody

value: anti-H3K36me3 active motf ref 61101


title: H3K36me3 ChIP-seq rep1


title: MB-induced glaucoma D23-1167

value: PBS


title: 2W_ctrl_ RPE_1


title: INPUT ChIP-seq rep1

value: input


title: BI_12T_1

data_processing:
Raw data files were aligned to the reference genome and the mirbase database using Torrent Suite default parameters.
Assembly: hg19

extract_protocol:
Plasma was isolated from EDTA or Lithium Heparin blood samples within 1 hour from collection, with a standard procedure to prevent haemolysis.
Total RNA was extracted with miRNeasy serum/plasma kit (Qiagen) using Exiqon protocol, with the batteriophage MS2RNA carrier (Roche Diagnostics) to promote RNA precipitation and purification on membranes.
For library preparation, smallRNA enriched samples were converted in barcoded cDNA libraries following the Ion Total RNA-Seq kit v2 protocol (Thermo Fisher) with the recommendations for low input RNA quantity. First, RNA samples were enriched for smallRNA fraction using a magnetic bead-based technology. After hybridization and ligation steps, through which 3' and 5' adaptors are directionally and simultaneously attached, reverse transcription was performed to obtain cDNA. cDNA was subsequently purified and size selected and then amplified using barcoded primers (obtained from Ion Xpress™ RNA-Seq Barcode 01-16 Kit, Thermo Fisher or synthesized by Eurofins Genomics as custom oligonucleotides (barcodes 17-24)). Finally, libraries were purified with beads. All the purification steps were performed by means of the Magnetic Bead Cleanup Module included in the kit. Libraries were checked for yield and size distribution by Bioanalyzer and DNA 1000 Kit (Agilent Technologies) and 24 differentially barcoded smallRNA libraries were pooled. Pools were checked by Bioanalyzer and DNA 1000 Kit (Agilent Technologies) to determine the library dilution required for template preparation. Ion Chef™ System (Thermo Fisher) was used for automated templated Ion Sphere Particles preparation and chip loading. Ion 540 chips (Thermo Fisher) were sequenced using Ion GeneStudio S5 System (Thermo Fisher).

value: case


title: 96 glial cells_plate3

value: Nodose ganglia

value: Glial cells


title: BI_10T_1


title: 9W_ctrl_RPE_2

value: 9 weeks


title: BI_1T_1

value: Plasma


title: CtrlUnwoundedGata6-derivedtomatopositive35_batch2

city: London

first: Fiona

middle: Mary

last: Watt

address: Great Maze Road

institute: Kings College London

description:
CtrlUnwoundedGata6-derivedtomatopositive35
WTCHG_946836_70935069

data_processing:
Illumina HiSeq 4000 reads were trimmed and clipped for quality control in Trimmomatic v0.27.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome.
Read quality was checked and alinged to GRCm38 reference genome using STAR version 2.2.
Gene specific counts were calculated using featureCounts from Rsubread 2.7 with mm10 Refseq.
All the downstream analysis was performed using Seurat version 3.2.2 and monocle 2.18.0
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Epidermis

extract_protocol:
Single keratinocytes from mouse epidermis were isolated by flow sorting using appropriate markers. Cells were sorted into individual wells of a 96-well plate containing 2ul lysis buffer (0.8% (volume/volume) Triton X-100 and 2U/ul recombinant RNase inhibitor
Libraries were prepared for sequencing using standard Illumina protocols with SmartSeq2 followed by Nextera XT protocol.

treatment_protocol: For lineage-tracing experiments, mice received a topical dose of 4-hydroxy-tamoxifen (1 mg dissolved in 100 µl acetone) applied to clipped back skin

value: Epidermis

value: Cre (+/-) tdTomato (+/-)


title: CtrlUnwoundedGata6-derivedtomatopositive36_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive36
WTCHG_946836_70945070


title: CtrlUnwoundedGata6-derivedtomatopositive32_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive32
WTCHG_946836_70905066


title: CtrlUnwoundedGata6-derivedtomatopositive33_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive33
WTCHG_946836_70915067


title: IDH-wt GBM, Capture Bis-seq, 4


title: 9W_ctrl_RPE_1

value: primary fetal retinal pigment epithelial cells


title: IDH-mut glioma, Capture Bis-seq


title: CtrlUnwoundedGata6-derivedtomatopositive31_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive31
WTCHG_946836_70895065


title: IDH-wt GBM, Capture Bis-seq, 3


title: CtrlUnwoundednon-Gata6tomatonegative30_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative30
WTCHG_946836_70865062


title: CtrlUnwoundednon-Gata6tomatonegative31_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative31
WTCHG_946836_70875063


title: CtrlUnwoundednon-Gata6tomatonegative29_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative29
WTCHG_946836_70855061


title: IDH-wt GBM, Capture Bis-seq, 2


title: CtrlUnwoundednon-Gata6tomatonegative27_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative27
WTCHG_946836_70835059


title: CtrlUnwoundednon-Gata6tomatonegative28_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative28
WTCHG_946836_70845060


title: INPUT ChIP-seq rep2


title: CtrlUnwoundednon-Gata6tomatonegative32_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative32
WTCHG_946836_70885064


title: CtrlUnwoundedGata6-derivedtomatopositive37_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive37
WTCHG_946836_70955071


title: CtrlUnwoundedGata6-derivedtomatopositive38_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive38
WTCHG_946836_70965072


title: CtrlUnwoundedGata6-derivedtomatopositive26_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive26
WTCHG_946836_70765052


title: CtrlUnwoundedGata6-derivedtomatopositive34_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive34
WTCHG_946836_70925068


title: CtrlUnwoundednon-Gata6tomatonegative21_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative21
WTCHG_946836_70695045


title: CtrlUnwoundednon-Gata6tomatonegative18_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative18
WTCHG_946836_70665042


title: CtrlUnwoundednon-Gata6tomatonegative26_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative26
WTCHG_946836_70825058


title: CtrlUnwoundedGata6-derivedtomatopositive30_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive30
WTCHG_946836_70805056


title: CtrlUnwoundednon-Gata6tomatonegative25_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative25
WTCHG_946836_70815057


title: CtrlUnwoundedGata6-derivedtomatopositive19_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive19
WTCHG_946836_70615037


title: CtrlUnwoundedGata6-derivedtomatopositive20_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive20
WTCHG_946836_70625038


title: CtrlUnwoundedGata6-derivedtomatopositive21_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive21
WTCHG_946836_70635039


title: CtrlUnwoundedGata6-derivedtomatopositive18_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive18
WTCHG_946836_70605036


title: CtrlUnwoundedGata6-derivedtomatopositive29_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive29
WTCHG_946836_70795055


title: CtrlUnwoundedGata6-derivedtomatopositive17_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive17
WTCHG_946836_70595035


title: CtrlUnwoundedGata6-derivedtomatopositive28_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive28
WTCHG_946836_70785054


title: CtrlUnwoundedGata6-derivedtomatopositive15_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive15
WTCHG_946836_70575033


title: CtrlUnwoundednon-Gata6tomatonegative15_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative15
WTCHG_946836_70555031


title: CtrlUnwoundednon-Gata6tomatonegative16_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative16
WTCHG_946836_70565032


title: CtrlUnwoundednon-Gata6tomatonegative14_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative14
WTCHG_946836_70545030


title: CtrlUnwoundedGata6-derivedtomatopositive27_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive27
WTCHG_946836_70775053


title: CtrlUnwoundedGata6-derivedtomatopositive25_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive25
WTCHG_946836_70755051


title: CtrlUnwoundedGata6-derivedtomatopositive24_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive24
WTCHG_946836_70745050


title: CtrlUnwoundedGata6-derivedtomatopositive23_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive23
WTCHG_946836_70735049


title: CtrlUnwoundednon-Gata6tomatonegative10_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative10
WTCHG_946836_70505026


title: CtrlUnwoundednon-Gata6tomatonegative9_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative9
WTCHG_946836_70495025


title: CtrlUnwoundednon-Gata6tomatonegative24_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative24
WTCHG_946836_70725048


title: IDH-mut glioma, Capture Bis-seq, 3


title: CtrlUnwoundedGata6-derivedtomatopositive12_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive12
WTCHG_946836_70465022


title: CtrlUnwoundedGata6-derivedtomatopositive13_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive13
WTCHG_946836_70475023


title: CtrlUnwoundedGata6-derivedtomatopositive11_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive11
WTCHG_946836_70455021


title: CtrlUnwoundedGata6-derivedtomatopositive10_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive10
WTCHG_946836_70445020


title: CtrlUnwoundednon-Gata6tomatonegative23_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative23
WTCHG_946836_70715047


title: CtrlUnwoundedGata6-derivedtomatopositive7_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive7
WTCHG_946836_70415017


title: CtrlUnwoundedGata6-derivedtomatopositive9_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive9
WTCHG_946836_70435019


title: CtrlUnwoundednon-Gata6tomatonegative8_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative8
WTCHG_946836_70405016


title: CtrlUnwoundednon-Gata6tomatonegative20_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative20
WTCHG_946836_70685044


title: CtrlUnwoundednon-Gata6tomatonegative22_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative22
WTCHG_946836_70705046


title: CtrlUnwoundednon-Gata6tomatonegative6_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative6
WTCHG_946836_70385014


title: CtrlUnwoundednon-Gata6tomatonegative7_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative7
WTCHG_946836_70395015


title: CtrlUnwoundednon-Gata6tomatonegative5_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative5
WTCHG_946836_70375013


title: CtrlUnwoundednon-Gata6tomatonegative4_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative4
WTCHG_946836_70365012


title: CtrlUnwoundednon-Gata6tomatonegative3_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative3
WTCHG_946836_70355011


title: CtrlUnwoundednon-Gata6tomatonegative19_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative19
WTCHG_946836_70675043


title: CtrlUnwoundednon-Gata6tomatonegative2_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative2
WTCHG_946836_70345010


title: CtrlUnwoundednon-Gata6tomatonegative17_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative17
WTCHG_946836_70655041


title: CtrlUnwoundedGata6-derivedtomatopositive22_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive22
WTCHG_946836_70645040


title: CtrlUnwoundedGata6-derivedtomatopositive3_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive3
WTCHG_946836_70295005


title: CtrlUnwoundedGata6-derivedtomatopositive4_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive4
WTCHG_946836_70305006


title: CtrlUnwoundedGata6-derivedtomatopositive2_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive2
WTCHG_946836_70285004


title: CtrlUnwoundedGata6-derivedtomatopositive1_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive1
WTCHG_946836_70275003


title: CtrlUnwoundednon-Gata6tomatonegative47_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative47
WTCHG_946836_70235095


title: CtrlUnwoundednon-Gata6tomatonegative45_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative45
WTCHG_946836_70215093


title: CtrlUnwoundednon-Gata6tomatonegative44_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative44
WTCHG_946836_70205092


title: CtrlUnwoundednon-Gata6tomatonegative46_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative46
WTCHG_946836_70225094


title: CtrlUnwoundedGata6-derivedtomatopositive46_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive46
WTCHG_946836_70165088


title: CtrlUnwoundedGata6-derivedtomatopositive44_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive44
WTCHG_946836_70145086


title: CtrlUnwoundedGata6-derivedtomatopositive42_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive42
WTCHG_946836_70125084


title: CtrlUnwoundedGata6-derivedtomatopositive41_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive41
WTCHG_946836_70115083


title: CtrlUnwoundedGata6-derivedtomatopositive16_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive16
WTCHG_946836_70585034


title: CtrlUnwoundednon-Gata6tomatonegative13_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative13
WTCHG_946836_70535029


title: CtrlUnwoundedGata6-derivedtomatopositive14_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive14
WTCHG_946836_70485024


title: CtrlUnwoundednon-Gata6tomatonegative11_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative11
WTCHG_946836_70515027


title: CtrlUnwoundedGata6-derivedtomatopositive40_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive40
WTCHG_946836_70105082


title: CtrlUnwoundedGata6-derivedtomatopositive8_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive8
WTCHG_946836_70425018


title: CtrlUnwoundednon-Gata6tomatonegative36_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative36
WTCHG_946836_70045076


title: CtrlUnwoundednon-Gata6tomatonegative37_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative37
WTCHG_946836_70055077


title: CtrlUnwoundednon-Gata6tomatonegative39_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative39
WTCHG_946836_70075079


title: CtrlUnwoundednon-Gata6tomatonegative33_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative33
WTCHG_946836_70015073


title: CtrlUnwoundednon-Gata6tomatonegative38_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative38
WTCHG_946836_70065078


title: CtrlUnwoundednon-Gata6tomatonegative12_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative12
WTCHG_946836_70525028


title: Day6Gata6-derivedtomatopositive87

description:
Day6Gata6-derivedtomatopositive87
WTCHG_945385_71925168


title: CtrlUnwoundedGata6-derivedtomatopositive6_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive6
WTCHG_946836_70325008


title: CtrlUnwoundednon-Gata6tomatonegative1_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative1
WTCHG_946836_70335009


title: Day6Gata6-derivedtomatopositive81

description:
Day6Gata6-derivedtomatopositive81
WTCHG_945385_71865162


title: Day6Non-Gata6tomatonegative78

description:
Day6Non-Gata6tomatonegative78
WTCHG_945385_71835159


title: Day6Non-Gata6tomatonegative79

description:
Day6Non-Gata6tomatonegative79
WTCHG_945385_71845160


title: CtrlUnwoundednon-Gata6tomatonegative48

description:
CtrlUnwoundednon-Gata6tomatonegative48
WTCHG_946836_70245096


title: CtrlUnwoundednon-Gata6tomatonegative42_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative42
WTCHG_946836_70185090


title: CtrlUnwoundedGata6-derivedtomatopositive43_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive43
WTCHG_946836_70135085


title: CtrlUnwoundedGata6-derivedtomatopositive45_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive45
WTCHG_946836_70155087


title: CtrlUnwoundednon-Gata6tomatonegative43_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative43
WTCHG_946836_70195091


title: CtrlUnwoundednon-Gata6tomatonegative41_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative41
WTCHG_946836_70175089


title: Day6Non-Gata6tomatonegative75

description:
Day6Non-Gata6tomatonegative75
WTCHG_945385_71805156


title: Day6Non-Gata6tomatonegative74

description:
Day6Non-Gata6tomatonegative74
WTCHG_945385_71795155


title: Day6Gata6-derivedtomatopositive86

description:
Day6Gata6-derivedtomatopositive86
WTCHG_945385_71915167


title: Day6Non-Gata6tomatonegative73

description:
Day6Non-Gata6tomatonegative73
WTCHG_945385_71785154


title: Day6Non-Gata6tomatonegative72

description:
Day6Non-Gata6tomatonegative72
WTCHG_945385_71775153


title: Day6Gata6-derivedtomatopositive76

description:
Day6Gata6-derivedtomatopositive76
WTCHG_945385_71735149


title: CtrlUnwoundedGata6-derivedtomatopositive5_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive5
WTCHG_946836_70315007


title: CtrlUnwoundedGata6-derivedtomatopositive39_batch2

description:
CtrlUnwoundedGata6-derivedtomatopositive39
WTCHG_946836_70095081


title: CtrlUnwoundednon-Gata6tomatonegative40_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative40
WTCHG_946836_70085080


title: Day6Gata6-derivedtomatopositive74

description:
Day6Gata6-derivedtomatopositive74
WTCHG_945385_71715147


title: Day6Gata6-derivedtomatopositive73

description:
Day6Gata6-derivedtomatopositive73
WTCHG_945385_71705146


title: Day6Non-Gata6tomatonegative71

description:
Day6Non-Gata6tomatonegative71
WTCHG_945385_71685144


title: Day6Non-Gata6tomatonegative70

description:
Day6Non-Gata6tomatonegative70
WTCHG_945385_71675143


title: Day6Non-Gata6tomatonegative76

description:
Day6Non-Gata6tomatonegative76
WTCHG_945385_71815157


title: Day6Non-Gata6tomatonegative68

description:
Day6Non-Gata6tomatonegative68
WTCHG_945385_71655141


title: CtrlUnwoundednon-Gata6tomatonegative35_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative35
WTCHG_946836_70035075


title: Day6Non-Gata6tomatonegative67

description:
Day6Non-Gata6tomatonegative67
WTCHG_945385_71645140


title: Day6Non-Gata6tomatonegative65

description:
Day6Non-Gata6tomatonegative65
WTCHG_945385_71625138


title: CtrlUnwoundednon-Gata6tomatonegative34_batch2

description:
CtrlUnwoundednon-Gata6tomatonegative34
WTCHG_946836_70025074


title: Day6Gata6-derivedtomatopositive85

description:
Day6Gata6-derivedtomatopositive85
WTCHG_945385_71905166


title: Day6Gata6-derivedtomatopositive69

description:
Day6Gata6-derivedtomatopositive69
WTCHG_945385_71585134


title: Day6Gata6-derivedtomatopositive75

description:
Day6Gata6-derivedtomatopositive75
WTCHG_945385_71725148


title: Day6Gata6-derivedtomatopositive67

description:
Day6Gata6-derivedtomatopositive67
WTCHG_945385_71565132


title: Day6Gata6-derivedtomatopositive66

description:
Day6Gata6-derivedtomatopositive66
WTCHG_945385_71555131


title: Day6Gata6-derivedtomatopositive84

description:
Day6Gata6-derivedtomatopositive84
WTCHG_945385_71895165


title: Day6Non-Gata6tomatonegative62

description:
Day6Non-Gata6tomatonegative62
WTCHG_945385_71515127


title: Day6Non-Gata6tomatonegative58

description:
Day6Non-Gata6tomatonegative58
WTCHG_945385_71475123


title: Day6Gata6-derivedtomatopositive83

description:
Day6Gata6-derivedtomatopositive83
WTCHG_945385_71885164


title: Day6Non-Gata6tomatonegative57

description:
Day6Non-Gata6tomatonegative57
WTCHG_945385_71465122


title: Day6Non-Gata6tomatonegative56

description:
Day6Non-Gata6tomatonegative56
WTCHG_945385_71455121


title: Day6Gata6-derivedtomatopositive63

description:
Day6Gata6-derivedtomatopositive63
WTCHG_945385_71445120


title: Day6Gata6-derivedtomatopositive82

description:
Day6Gata6-derivedtomatopositive82
WTCHG_945385_71875163


title: Day6Gata6-derivedtomatopositive58

description:
Day6Gata6-derivedtomatopositive58
WTCHG_945385_71395115


title: Day6Gata6-derivedtomatopositive57

description:
Day6Gata6-derivedtomatopositive57
WTCHG_945385_71385114


title: Day6Non-Gata6tomatonegative77

description:
Day6Non-Gata6tomatonegative77
WTCHG_945385_71825158


title: Day6Gata6-derivedtomatopositive79

description:
Day6Gata6-derivedtomatopositive79
WTCHG_945385_71765152


title: Day6Gata6-derivedtomatopositive77

description:
Day6Gata6-derivedtomatopositive77
WTCHG_945385_71745150


title: Day6Gata6-derivedtomatopositive78

description:
Day6Gata6-derivedtomatopositive78
WTCHG_945385_71755151


title: Day6Gata6-derivedtomatopositive60

description:
Day6Gata6-derivedtomatopositive60
WTCHG_945385_71415117


title: Day6Gata6-derivedtomatopositive56

description:
Day6Gata6-derivedtomatopositive56
WTCHG_945385_71375113


title: Day6Gata6-derivedtomatopositive80

description:
Day6Gata6-derivedtomatopositive80
WTCHG_945385_71855161


title: Day6Non-Gata6tomatonegative69

description:
Day6Non-Gata6tomatonegative69
WTCHG_945385_71665142


title: Day6Gata6-derivedtomatopositive72

description:
Day6Gata6-derivedtomatopositive72
WTCHG_945385_71695145


title: Day6Non-Gata6tomatonegative50

description:
Day6Non-Gata6tomatonegative50
WTCHG_945385_71315107


title: Day6Non-Gata6tomatonegative48

description:
Day6Non-Gata6tomatonegative48
WTCHG_945385_71295105


title: Day6Non-Gata6tomatonegative66

description:
Day6Non-Gata6tomatonegative66
WTCHG_945385_71635139


title: Day6Non-Gata6tomatonegative64

description:
Day6Non-Gata6tomatonegative64
WTCHG_945385_71615137


title: Day6Gata6-derivedtomatopositive70

description:
Day6Gata6-derivedtomatopositive70
WTCHG_945385_71595135


title: Day6Gata6-derivedtomatopositive71

description:
Day6Gata6-derivedtomatopositive71
WTCHG_945385_71605136


title: Day6Gata6-derivedtomatopositive49

description:
Day6Gata6-derivedtomatopositive49
WTCHG_945385_71225098


title: Day6Gata6-derivedtomatopositive50

description:
Day6Gata6-derivedtomatopositive50
WTCHG_945385_71235099


title: Day6Gata6-derivedtomatopositive54

description:
Day6Gata6-derivedtomatopositive54
WTCHG_945385_71275103


title: Day6Gata6-derivedtomatopositive68

description:
Day6Gata6-derivedtomatopositive68
WTCHG_945385_71575133


title: Day6Non-Gata6tomatonegative91

description:
Day6Non-Gata6tomatonegative91
WTCHG_945385_71165188


title: Day6Gata6-derivedtomatopositive64

description:
Day6Gata6-derivedtomatopositive64
WTCHG_945385_71535129


title: Day6Gata6-derivedtomatopositive65

description:
Day6Gata6-derivedtomatopositive65
WTCHG_945385_71545130


title: Day6Non-Gata6tomatonegative93

description:
Day6Non-Gata6tomatonegative93
WTCHG_945385_71185190


title: Day6Non-Gata6tomatonegative94

description:
Day6Non-Gata6tomatonegative94
WTCHG_945385_71195191


title: Day6Non-Gata6tomatonegative63

description:
Day6Non-Gata6tomatonegative63
WTCHG_945385_71525128


title: Day6Non-Gata6tomatonegative61

description:
Day6Non-Gata6tomatonegative61
WTCHG_945385_71505126


title: Day6Non-Gata6tomatonegative60

description:
Day6Non-Gata6tomatonegative60
WTCHG_945385_71495125


title: Day6Non-Gata6tomatonegative59

description:
Day6Non-Gata6tomatonegative59
WTCHG_945385_71485124


title: Day6Gata6-derivedtomatopositive88

description:
Day6Gata6-derivedtomatopositive88
WTCHG_945385_71055177


title: Day6Non-Gata6tomatonegative87

description:
Day6Non-Gata6tomatonegative87
WTCHG_945385_71045176


title: Day6Gata6-derivedtomatopositive61

description:
Day6Gata6-derivedtomatopositive61
WTCHG_945385_71425118


title: Day6Gata6-derivedtomatopositive59

description:
Day6Gata6-derivedtomatopositive59
WTCHG_945385_71405116


title: Day6Non-Gata6tomatonegative84

description:
Day6Non-Gata6tomatonegative84
WTCHG_945385_71015173


title: Day6Non-Gata6tomatonegative55

description:
Day6Non-Gata6tomatonegative55
WTCHG_945385_71365112


title: Day6Gata6-derivedtomatopositive62

description:
Day6Gata6-derivedtomatopositive62
WTCHG_945385_71435119


title: Day6Non-Gata6tomatonegative53

description:
Day6Non-Gata6tomatonegative53
WTCHG_945385_71345110


title: Day6Non-Gata6tomatonegative52

description:
Day6Non-Gata6tomatonegative52
WTCHG_945385_71335109


title: Day6Non-Gata6tomatonegative81

description:
Day6Non-Gata6tomatonegative81
WTCHG_945385_70985170


title: Day6Non-Gata6tomatonegative51

description:
Day6Non-Gata6tomatonegative51
WTCHG_945385_71325108


title: Day6Gata6-derivedtomatopositive36

description:
Day6Gata6-derivedtomatopositive36
WTCHG_945385_70925068


title: Day6Gata6-derivedtomatopositive55

description:
Day6Gata6-derivedtomatopositive55
WTCHG_945385_71285104


title: Day6Gata6-derivedtomatopositive38

description:
Day6Gata6-derivedtomatopositive38
WTCHG_945385_70945070


title: Day6Gata6-derivedtomatopositive34

description:
Day6Gata6-derivedtomatopositive34
WTCHG_945385_70905066


title: Day6Gata6-derivedtomatopositive52

description:
Day6Gata6-derivedtomatopositive52
WTCHG_945385_71255101


title: Day6Gata6-derivedtomatopositive53

description:
Day6Gata6-derivedtomatopositive53
WTCHG_945385_71265102


title: Day6Non-Gata6tomatonegative54

description:
Day6Non-Gata6tomatonegative54
WTCHG_945385_71355111


title: Day6Non-Gata6tomatonegative49

description:
Day6Non-Gata6tomatonegative49
WTCHG_945385_71305106


title: Day6Gata6-derivedtomatopositive51

description:
Day6Gata6-derivedtomatopositive51
WTCHG_945385_71245100


title: Day6Gata6-derivedtomatopositive48

description:
Day6Gata6-derivedtomatopositive48
WTCHG_945385_71215097


title: Day6Non-Gata6tomatonegative92

description:
Day6Non-Gata6tomatonegative92
WTCHG_945385_71175189


title: Day6Non-Gata6tomatonegative89

description:
Day6Non-Gata6tomatonegative89
WTCHG_945385_71145186


title: Day6Non-Gata6tomatonegative88

description:
Day6Non-Gata6tomatonegative88
WTCHG_945385_71135185


title: Day6Gata6-derivedtomatopositive94

description:
Day6Gata6-derivedtomatopositive94
WTCHG_945385_71115183


title: Day6Gata6-derivedtomatopositive93

description:
Day6Gata6-derivedtomatopositive93
WTCHG_945385_71105182


title: Day6Gata6-derivedtomatopositive92

description:
Day6Gata6-derivedtomatopositive92
WTCHG_945385_71095181


title: Day6Non-Gata6tomatonegative90

description:
Day6Non-Gata6tomatonegative90
WTCHG_945385_71155187


title: Day6Gata6-derivedtomatopositive91

description:
Day6Gata6-derivedtomatopositive91
WTCHG_945385_71085180


title: Day6Gata6-derivedtomatopositive90

description:
Day6Gata6-derivedtomatopositive90
WTCHG_945385_71075179


title: Day6Gata6-derivedtomatopositive89

description:
Day6Gata6-derivedtomatopositive89
WTCHG_945385_71065178


title: Day6Non-Gata6tomatonegative85

description:
Day6Non-Gata6tomatonegative85
WTCHG_945385_71025174


title: Day6Non-Gata6tomatonegative86

description:
Day6Non-Gata6tomatonegative86
WTCHG_945385_71035175


title: Day6Non-Gata6tomatonegative82

description:
Day6Non-Gata6tomatonegative82
WTCHG_945385_70995171


title: Day6Non-Gata6tomatonegative80

description:
Day6Non-Gata6tomatonegative80
WTCHG_945385_70975169


title: Day6Gata6-derivedtomatopositive27

description:
Day6Gata6-derivedtomatopositive27
WTCHG_945385_70755051


title: Day6Gata6-derivedtomatopositive30

description:
Day6Gata6-derivedtomatopositive30
WTCHG_945385_70785054


title: Day6Gata6-derivedtomatopositive39

description:
Day6Gata6-derivedtomatopositive39
WTCHG_945385_70955071


title: Day6Non-Gata6tomatonegative83

description:
Day6Non-Gata6tomatonegative83
WTCHG_945385_71005172


title: Day6Gata6-derivedtomatopositive40

description:
Day6Gata6-derivedtomatopositive40
WTCHG_945385_70965072


title: Day6Gata6-derivedtomatopositive37

description:
Day6Gata6-derivedtomatopositive37
WTCHG_945385_70935069


title: Day6Gata6-derivedtomatopositive25

description:
Day6Gata6-derivedtomatopositive25
WTCHG_945385_70735049


title: Day6Non-Gata6tomatonegative23

description:
Day6Non-Gata6tomatonegative23
WTCHG_945385_70715047


title: Day6Non-Gata6tomatonegative24

description:
Day6Non-Gata6tomatonegative24
WTCHG_945385_70725048


title: Day6Gata6-derivedtomatopositive33

description:
Day6Gata6-derivedtomatopositive33
WTCHG_945385_70895065


title: Day6Non-Gata6tomatonegative30

description:
Day6Non-Gata6tomatonegative30
WTCHG_945385_70865062


title: Day6Non-Gata6tomatonegative29

description:
Day6Non-Gata6tomatonegative29
WTCHG_945385_70855061


title: Day6Non-Gata6tomatonegative31

description:
Day6Non-Gata6tomatonegative31
WTCHG_945385_70875063


title: Day6Gata6-derivedtomatopositive35

description:
Day6Gata6-derivedtomatopositive35
WTCHG_945385_70915067


title: Day6Non-Gata6tomatonegative28

description:
Day6Non-Gata6tomatonegative28
WTCHG_945385_70845060


title: Day6Non-Gata6tomatonegative19

description:
Day6Non-Gata6tomatonegative19
WTCHG_945385_70675043


title: Day6Gata6-derivedtomatopositive24

description:
Day6Gata6-derivedtomatopositive24
WTCHG_945385_70645040


title: Day6Non-Gata6tomatonegative17

description:
Day6Non-Gata6tomatonegative17
WTCHG_945385_70655041


title: Day6Non-Gata6tomatonegative32

description:
Day6Non-Gata6tomatonegative32
WTCHG_945385_70885064


title: Day6Gata6-derivedtomatopositive21

description:
Day6Gata6-derivedtomatopositive21
WTCHG_945385_70615037


title: Day6Gata6-derivedtomatopositive19

description:
Day6Gata6-derivedtomatopositive19
WTCHG_945385_70595035


title: Day6Gata6-derivedtomatopositive17

description:
Day6Gata6-derivedtomatopositive17
WTCHG_945385_70575033


title: Day6Non-Gata6tomatonegative25

description:
Day6Non-Gata6tomatonegative25
WTCHG_945385_70815057


title: Day6Gata6-derivedtomatopositive31

description:
Day6Gata6-derivedtomatopositive31
WTCHG_945385_70795055


title: Day6Non-Gata6tomatonegative27

description:
Day6Non-Gata6tomatonegative27
WTCHG_945385_70835059


title: Day6Non-Gata6tomatonegative16

description:
Day6Non-Gata6tomatonegative16
WTCHG_945385_70565032


title: Day6Gata6-derivedtomatopositive28

description:
Day6Gata6-derivedtomatopositive28
WTCHG_945385_70765052


title: Day6Gata6-derivedtomatopositive29

description:
Day6Gata6-derivedtomatopositive29
WTCHG_945385_70775053


title: Day6Non-Gata6tomatonegative12

description:
Day6Non-Gata6tomatonegative12
WTCHG_945385_70525028


title: Day6Non-Gata6tomatonegative11

description:
Day6Non-Gata6tomatonegative11
WTCHG_945385_70515027


title: Day6Non-Gata6tomatonegative10

description:
Day6Non-Gata6tomatonegative10
WTCHG_945385_70505026


title: Day6Gata6-derivedtomatopositive15

description:
Day6Gata6-derivedtomatopositive15
WTCHG_945385_70475023


title: Day6Non-Gata6tomatonegative9

description:
Day6Non-Gata6tomatonegative9
WTCHG_945385_70495025


title: Day6Gata6-derivedtomatopositive14

description:
Day6Gata6-derivedtomatopositive14
WTCHG_945385_70465022


title: Day6Gata6-derivedtomatopositive22

description:
Day6Gata6-derivedtomatopositive22
WTCHG_945385_70625038


title: Day6Gata6-derivedtomatopositive26

description:
Day6Gata6-derivedtomatopositive26
WTCHG_945385_70745050


title: Day6Non-Gata6tomatonegative22

description:
Day6Non-Gata6tomatonegative22
WTCHG_945385_70705046


title: Day6Gata6-derivedtomatopositive13

description:
Day6Gata6-derivedtomatopositive13
WTCHG_945385_70455021


title: Day6Non-Gata6tomatonegative21

description:
Day6Non-Gata6tomatonegative21
WTCHG_945385_70695045


title: Day6Non-Gata6tomatonegative18

description:
Day6Non-Gata6tomatonegative18
WTCHG_945385_70665042


title: Day6Gata6-derivedtomatopositive23

description:
Day6Gata6-derivedtomatopositive23
WTCHG_945385_70635039


title: Day6Gata6-derivedtomatopositive11

description:
Day6Gata6-derivedtomatopositive11
WTCHG_945385_70435019


title: Day6Non-Gata6tomatonegative8

description:
Day6Non-Gata6tomatonegative8
WTCHG_945385_70405016


title: Day6Non-Gata6tomatonegative7

description:
Day6Non-Gata6tomatonegative7
WTCHG_945385_70395015


title: Day6Non-Gata6tomatonegative4

description:
Day6Non-Gata6tomatonegative4
WTCHG_945385_70365012


title: Day6Gata6-derivedtomatopositive18

description:
Day6Gata6-derivedtomatopositive18
WTCHG_945385_70585034


title: Day6Non-Gata6tomatonegative15

description:
Day6Non-Gata6tomatonegative15
WTCHG_945385_70555031


title: Day6Non-Gata6tomatonegative14

description:
Day6Non-Gata6tomatonegative14
WTCHG_945385_70545030


title: Day6Non-Gata6tomatonegative13

description:
Day6Non-Gata6tomatonegative13
WTCHG_945385_70535029


title: Day6Gata6-derivedtomatopositive3

description:
Day6Gata6-derivedtomatopositive3
WTCHG_945385_70275003


title: Day6Gata6-derivedtomatopositive6

description:
Day6Gata6-derivedtomatopositive6
WTCHG_945385_70305006


title: Day6Non-Gata6tomatonegative1

description:
Day6Non-Gata6tomatonegative1
WTCHG_945385_70335009


title: Day6Gata6-derivedtomatopositive20

description:
Day6Gata6-derivedtomatopositive20
WTCHG_945385_70605036


title: Day6Gata6-derivedtomatopositive12

description:
Day6Gata6-derivedtomatopositive12
WTCHG_945385_70445020


title: Day6Non-Gata6tomatonegative42

description:
Day6Non-Gata6tomatonegative42
WTCHG_945385_70185090


title: Day6Gata6-derivedtomatopositive10

description:
Day6Gata6-derivedtomatopositive10
WTCHG_945385_70425018


title: Day6Gata6-derivedtomatopositive4

description:
Day6Gata6-derivedtomatopositive4
WTCHG_945385_70285004


title: Day6Non-Gata6tomatonegative5

description:
Day6Non-Gata6tomatonegative5
WTCHG_945385_70375013


title: Day6Non-Gata6tomatonegative6

description:
Day6Non-Gata6tomatonegative6
WTCHG_945385_70385014


title: Day6Non-Gata6tomatonegative3

description:
Day6Non-Gata6tomatonegative3
WTCHG_945385_70355011


title: Day6Gata6-derivedtomatopositive45

description:
Day6Gata6-derivedtomatopositive45
WTCHG_945385_70135085


title: Day6Gata6-derivedtomatopositive46

description:
Day6Gata6-derivedtomatopositive46
WTCHG_945385_70145086


title: Day6Gata6-derivedtomatopositive16

description:
Day6Gata6-derivedtomatopositive16
WTCHG_945385_70485024


title: Day6Non-Gata6tomatonegative2

description:
Day6Non-Gata6tomatonegative2
WTCHG_945385_70345010


title: Day6Gata6-derivedtomatopositive7

description:
Day6Gata6-derivedtomatopositive7
WTCHG_945385_70315007


title: Day6Gata6-derivedtomatopositive8

description:
Day6Gata6-derivedtomatopositive8
WTCHG_945385_70325008


title: Day6Non-Gata6tomatonegative41

description:
Day6Non-Gata6tomatonegative41
WTCHG_945385_70175089


title: Day6Non-Gata6tomatonegative40

description:
Day6Non-Gata6tomatonegative40
WTCHG_945385_70085080


title: Day6Non-Gata6tomatonegative39

description:
Day6Non-Gata6tomatonegative39
WTCHG_945385_70075079


title: Day6Non-Gata6tomatonegative47

description:
Day6Non-Gata6tomatonegative47
WTCHG_945385_70235095


title: Day6Non-Gata6tomatonegative44

description:
Day6Non-Gata6tomatonegative44
WTCHG_945385_70205092


title: Day6Non-Gata6tomatonegative45

description:
Day6Non-Gata6tomatonegative45
WTCHG_945385_70215093


title: Day6Gata6-derivedtomatopositive9

description:
Day6Gata6-derivedtomatopositive9
WTCHG_945385_70415017


title: Day6Gata6-derivedtomatopositive1

description:
Day6Gata6-derivedtomatopositive1
WTCHG_945385_70255001


title: Day6Non-Gata6tomatonegative43

description:
Day6Non-Gata6tomatonegative43
WTCHG_945385_70195091


title: Day6Non-Gata6tomatonegative46

description:
Day6Non-Gata6tomatonegative46
WTCHG_945385_70225094


title: Day6Gata6-derivedtomatopositive5

description:
Day6Gata6-derivedtomatopositive5
WTCHG_945385_70295005


title: Day6Non-Gata6tomatonegative34

description:
Day6Non-Gata6tomatonegative34
WTCHG_945385_70025074


title: Day6Gata6-derivedtomatopositive2

description:
Day6Gata6-derivedtomatopositive2
WTCHG_945385_70265002


title: Day6Gata6-derivedtomatopositive47

description:
Day6Gata6-derivedtomatopositive47
WTCHG_945385_70155087


title: Day6Gata6-derivedtomatopositive43

description:
Day6Gata6-derivedtomatopositive43
WTCHG_945385_70115083


title: Day6Gata6-derivedtomatopositive41

description:
Day6Gata6-derivedtomatopositive41
WTCHG_945385_70095081


title: Day6Gata6-derivedtomatopositive44

description:
Day6Gata6-derivedtomatopositive44
WTCHG_945385_70125084


title: Day6Non-Gata6tomatonegative38

description:
Day6Non-Gata6tomatonegative38
WTCHG_945385_70065078


title: Day6Non-Gata6tomatonegative37

description:
Day6Non-Gata6tomatonegative37
WTCHG_945385_70055077


title: Day6Non-Gata6tomatonegative35

description:
Day6Non-Gata6tomatonegative35
WTCHG_945385_70035075


title: Day9-2Gata6-derivedtomatopositive33

description:
Day9-2Gata6-derivedtomatopositive33
WTCHG_945384_72825258


title: microglia, female, LPS, 24month, rep3

first: Bo

last: Peng

address: 138 Yixueyuan Road

department: Institute for Translational Brain Research

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by removing reads containing sequencing adapter;
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%;
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by RSEM (v1.2.12)
Sva(3.35.2) was used to correct batch effect.
Assembly: mm10
Supplementary files format and content: comma-separated values files include counts values for each Sample

source_name: brain

extract_protocol:
Total RNA extractionTotal RNA was extracted from the tissues using RNeasy Micro kit (QIAGEN, GER) according to the manual instruction.Appropriate tissues were ground into powder by liquid nitrogen, then, transferred into a new tube with appropriate volume of Buffer RL and 1 volume of 70% ethanol.Mixture was transferred into an RNeasy MinElute spin column, centrifuged for 15 s at ≥ 8000 xg.After discarding the flow-through, Buffer RW1, DNase I, Buffer RPE, and 80% ethanol were added in turns then centrifuged in turns. The RNeasy MinElute spin column which contained RNA was placed in a new 2 mL collection tube, centrifuged with lid opened at full speed for 5 min to dry the membrane, followed by transferred to a new 1.5mL tube with 14 uL RNase-free water.Finally, tubes were centrifuged for 1 min at full speed to elute the RNA. Total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA). High quality RNA was used for mRNA library construction.
Limited RNA (more than 200pg, high-quality) was amplified with oligo-dT and dNTPs, incubated at 72°C and immediately put back on ice, then reverse transcribed to cDNA based on polyA tail. The template was switched to the 5' end of the RNA and the full-length cDNA was generated by PCR. Agilent 2100 bioanalyzer instrument (Thermo Fisher Scientific, MA, USA) was used to determine the average molecule length of PCR product. Purified cDNA from previous steps was fragmented into small pieces with fragment buffer by PCR, and the product was purified and selected by the Agencourt AMPure XP-Medium kit (Thermo Fisher Scientific, USA). cDNA was quantified by Agilent Technologies 2100 bioanalyzer. The double stranded PCR product undergo QC step was heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was quantitated in two ways in order to ensure the high quality of the sequencing data: Determined the average molecule length used the Agilent 2100 bioanalyzer instrument, quantified library used real-time quantitative PCR (qPCR).The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGISEQ500 platform(BGI-Shenzhen, China)

value: brain

value: microglia

value: LPS

value: 24 month

value: female


title: Day9-2Gata6-derivedtomatopositive32

description:
Day9-2Gata6-derivedtomatopositive32
WTCHG_945384_72815257


title: Day9-2Non-Gata6tomatonegative31

description:
Day9-2Non-Gata6tomatonegative31
WTCHG_945384_72795255


title: Day9-2Non-Gata6tomatonegative32

description:
Day9-2Non-Gata6tomatonegative32
WTCHG_945384_72805256


title: Day6Non-Gata6tomatonegative33

description:
Day6Non-Gata6tomatonegative33
WTCHG_945385_70015073


title: Day9-2Gata6-derivedtomatopositive37

description:
Day9-2Gata6-derivedtomatopositive37
WTCHG_945384_72865262


title: Day9-2Gata6-derivedtomatopositive38

description:
Day9-2Gata6-derivedtomatopositive38
WTCHG_945384_72875263


title: Day9-2Non-Gata6tomatonegative30

description:
Day9-2Non-Gata6tomatonegative30
WTCHG_945384_72785254


title: Day9-2Non-Gata6tomatonegative29

description:
Day9-2Non-Gata6tomatonegative29
WTCHG_945384_72775253


title: microglia, female, LPS, 24month, rep1

value: WT


title: Day6Non-Gata6tomatonegative36

description:
Day6Non-Gata6tomatonegative36
WTCHG_945385_70045076


title: Day9-2Gata6-derivedtomatopositive39

description:
Day9-2Gata6-derivedtomatopositive39
WTCHG_945384_72885264


title: Day9-2Gata6-derivedtomatopositive36

description:
Day9-2Gata6-derivedtomatopositive36
WTCHG_945384_72855261


title: microglia, female, LPS, 14month, rep4

value: 14 month


title: microglia, female, LPS, 24month, rep2


title: Day6Non-Gata6tomatonegative26

description:
Day6Non-Gata6tomatonegative26
WTCHG_945385_70825058


title: Day6Gata6-derivedtomatopositive42

description:
Day6Gata6-derivedtomatopositive42
WTCHG_945385_70105082


title: Day9-2Non-Gata6tomatonegative28

description:
Day9-2Non-Gata6tomatonegative28
WTCHG_945384_72765252


title: microglia, female, LPS, 14month, rep3


title: microglia, female, LPS, 14month, rep5


title: Day9-2Non-Gata6tomatonegative27

description:
Day9-2Non-Gata6tomatonegative27
WTCHG_945384_72755251


title: microglia, female, LPS, 14month, rep1


title: Day9-2Non-Gata6tomatonegative26

description:
Day9-2Non-Gata6tomatonegative26
WTCHG_945384_72745250


title: Day9-2Non-Gata6tomatonegative25

description:
Day9-2Non-Gata6tomatonegative25
WTCHG_945384_72735249


title: microglia, female, LPS, 3month, rep2

value: 3 month


title: microglia, female, LPS, 3month, rep3


title: microglia, female, LPS, 3month, rep1


title: Day9-2Gata6-derivedtomatopositive30

description:
Day9-2Gata6-derivedtomatopositive30
WTCHG_945384_72715247


title: Day9-2Gata6-derivedtomatopositive28

description:
Day9-2Gata6-derivedtomatopositive28
WTCHG_945384_72695245


title: Day9-2Gata6-derivedtomatopositive29

description:
Day9-2Gata6-derivedtomatopositive29
WTCHG_945384_72705246


title: Day9-2Gata6-derivedtomatopositive31

description:
Day9-2Gata6-derivedtomatopositive31
WTCHG_945384_72725248


title: Day9-2Gata6-derivedtomatopositive27

description:
Day9-2Gata6-derivedtomatopositive27
WTCHG_945384_72685244


title: microglia, male, PBS, 24month, rep2

value: PBS

value: male


title: microglia, male, PBS, 24month, rep4


title: Day9-2Gata6-derivedtomatopositive26

description:
Day9-2Gata6-derivedtomatopositive26
WTCHG_945384_72675243


title: microglia, male, PBS, 24month, rep3


title: microglia, male, PBS, 19month, rep5

value: 19 month


title: microglia, male, PBS, 24month, rep1


title: Day9-2Non-Gata6tomatonegative24

description:
Day9-2Non-Gata6tomatonegative24
WTCHG_945384_72645240


title: Day9-2Gata6-derivedtomatopositive25

description:
Day9-2Gata6-derivedtomatopositive25
WTCHG_945384_72665242


title: microglia, male, PBS, 19month, rep4


title: Day9-2Non-Gata6tomatonegative22

description:
Day9-2Non-Gata6tomatonegative22
WTCHG_945384_72625238


title: Day9-2Gata6-derivedtomatopositive24

description:
Day9-2Gata6-derivedtomatopositive24
WTCHG_945384_72655241


title: microglia, male, PBS, 19month, rep3


title: microglia, male, PBS, 19month, rep2


title: Day9-2Non-Gata6tomatonegative23

description:
Day9-2Non-Gata6tomatonegative23
WTCHG_945384_72635239


title: microglia, male, PBS, 19month, rep1


title: microglia, female, LPS, 14month, rep2


title: Day9-2Non-Gata6tomatonegative19

description:
Day9-2Non-Gata6tomatonegative19
WTCHG_945384_72595235


title: Day9-2Non-Gata6tomatonegative18

description:
Day9-2Non-Gata6tomatonegative18
WTCHG_945384_72585234


title: Day9-2Non-Gata6tomatonegative21

description:
Day9-2Non-Gata6tomatonegative21
WTCHG_945384_72615237


title: microglia, male, PBS, 16month, rep4

value: 16 month


title: microglia, male, PBS, 16month, rep2


title: microglia, male, PBS, 16month, rep3


title: Day9-2Non-Gata6tomatonegative17

description:
Day9-2Non-Gata6tomatonegative17
WTCHG_945384_72575233


title: Day9-2Gata6-derivedtomatopositive23

description:
Day9-2Gata6-derivedtomatopositive23
WTCHG_945384_72565232


title: microglia, male, PBS, 16month, rep1


title: microglia, male, PBS, 12month, rep2

value: 12 month


title: Day9-2Gata6-derivedtomatopositive19

description:
Day9-2Gata6-derivedtomatopositive19
WTCHG_945384_72525228


title: Day9-2Gata6-derivedtomatopositive22

description:
Day9-2Gata6-derivedtomatopositive22
WTCHG_945384_72555231


title: Day9-2Gata6-derivedtomatopositive18

description:
Day9-2Gata6-derivedtomatopositive18
WTCHG_945384_72515227


title: microglia, male, PBS, 9month, rep3

value: 9 month


title: microglia, male, PBS, 12month, rep1


title: Day9-2Gata6-derivedtomatopositive21

description:
Day9-2Gata6-derivedtomatopositive21
WTCHG_945384_72545230

value: Epidermis


title: microglia, male, PBS, 9month, rep1


title: microglia, male, PBS, 9month, rep4


title: microglia, male, PBS, 9month, rep2


title: microglia, male, PBS, 6month, rep3

value: 6 month


title: Day9-2Gata6-derivedtomatopositive20

description:
Day9-2Gata6-derivedtomatopositive20
WTCHG_945384_72535229

value: Cre (+/-) tdTomato (+/-)


title: microglia, male, PBS, 6month, rep4

value: brain


title: Day9-2Gata6-derivedtomatopositive16

description:
Day9-2Gata6-derivedtomatopositive16
WTCHG_945384_72495225


title: Day9-2Gata6-derivedtomatopositive17

description:
Day9-2Gata6-derivedtomatopositive17
WTCHG_945384_72505226


title: Day9-2Non-Gata6tomatonegative16

description:
Day9-2Non-Gata6tomatonegative16
WTCHG_945384_72485224


title: microglia, male, PBS, 6month, rep2

value: microglia


title: microglia, male, PBS, 6month, rep1


title: Day9-2Non-Gata6tomatonegative13

description:
Day9-2Non-Gata6tomatonegative13
WTCHG_945384_72455221


title: microglia, male, PBS, 3month, rep3


title: microglia, male, PBS, 3month, rep4


title: Day9-2Non-Gata6tomatonegative15

description:
Day9-2Non-Gata6tomatonegative15
WTCHG_945384_72475223


title: microglia, male, PBS, 3month, rep2


title: Day9-2Non-Gata6tomatonegative12

description:
Day9-2Non-Gata6tomatonegative12
WTCHG_945384_72445220


title: Day9-2Non-Gata6tomatonegative10

description:
Day9-2Non-Gata6tomatonegative10
WTCHG_945384_72425218


title: Day9-2Non-Gata6tomatonegative11

description:
Day9-2Non-Gata6tomatonegative11
WTCHG_945384_72435219


title: microglia, male, PBS, 3month, rep1


title: microglia, female, PBS, 24month, rep1


title: Day9-2Non-Gata6tomatonegative14

description:
Day9-2Non-Gata6tomatonegative14
WTCHG_945384_72465222


title: microglia, female, PBS, 24month, rep2


title: Day9-2Non-Gata6tomatonegative9

description:
Day9-2Non-Gata6tomatonegative9
WTCHG_945384_72415217


title: microglia, female, PBS, 24month, rep3


title: Day9-2Gata6-derivedtomatopositive15

description:
Day9-2Gata6-derivedtomatopositive15
WTCHG_945384_72405216


title: microglia, female, PBS, 16month, rep3


title: microglia, female, PBS, 16month, rep5


title: Day9-2Gata6-derivedtomatopositive14

description:
Day9-2Gata6-derivedtomatopositive14
WTCHG_945384_72395215


title: microglia, female, PBS, 16month, rep2


title: Day9-2Gata6-derivedtomatopositive11

description:
Day9-2Gata6-derivedtomatopositive11
WTCHG_945384_72365212


title: Day9-2Gata6-derivedtomatopositive13

description:
Day9-2Gata6-derivedtomatopositive13
WTCHG_945384_72385214


title: microglia, female, PBS, 16month, rep4


title: microglia, female, PBS, 16month, rep1


title: Day9-2Gata6-derivedtomatopositive10

description:
Day9-2Gata6-derivedtomatopositive10
WTCHG_945384_72355211


title: microglia, female, PBS, 14month, rep4


title: Day9-2Gata6-derivedtomatopositive9

description:
Day9-2Gata6-derivedtomatopositive9
WTCHG_945384_72345210


title: microglia, female, PBS, 14month, rep5


title: Day9-2Gata6-derivedtomatopositive8

description:
Day9-2Gata6-derivedtomatopositive8
WTCHG_945384_72335209


title: microglia, female, PBS, 14month, rep3


title: Day9-2Non-Gata6tomatonegative7

description:
Day9-2Non-Gata6tomatonegative7
WTCHG_945384_72315207


title: microglia, female, PBS, 14month, rep1


title: microglia, female, PBS, 14month, rep2


title: Day9-2Non-Gata6tomatonegative8

description:
Day9-2Non-Gata6tomatonegative8
WTCHG_945384_72325208


title: Day9-2Non-Gata6tomatonegative5

description:
Day9-2Non-Gata6tomatonegative5
WTCHG_945384_72295205


title: Day9-2Non-Gata6tomatonegative6

description:
Day9-2Non-Gata6tomatonegative6
WTCHG_945384_72305206


title: Day9-2Gata6-derivedtomatopositive12

description:
Day9-2Gata6-derivedtomatopositive12
WTCHG_945384_72375213


title: microglia, female, PBS, 12month, rep4


title: microglia, female, PBS, 12month, rep3


title: Day9-2Non-Gata6tomatonegative4

description:
Day9-2Non-Gata6tomatonegative4
WTCHG_945384_72285204


title: Day9-2Non-Gata6tomatonegative2

description:
Day9-2Non-Gata6tomatonegative2
WTCHG_945384_72265202


title: microglia, female, PBS, 12month, rep2


title: microglia, female, PBS, 9month, rep3


title: microglia, female, PBS, 9month, rep2


title: microglia, female, PBS, 9month, rep1


title: Day9-2Gata6-derivedtomatopositive4

description:
Day9-2Gata6-derivedtomatopositive4
WTCHG_945384_72215197


title: Day9-2Gata6-derivedtomatopositive3

description:
Day9-2Gata6-derivedtomatopositive3
WTCHG_945384_72205196


title: microglia, female, PBS, 3month, rep4


title: Day9-2Non-Gata6tomatonegative1

description:
Day9-2Non-Gata6tomatonegative1
WTCHG_945384_72255201


title: Day9-2Gata6-derivedtomatopositive1

description:
Day9-2Gata6-derivedtomatopositive1
WTCHG_945384_72185194


title: Day9-2Non-Gata6tomatonegative47

description:
Day9-2Non-Gata6tomatonegative47
WTCHG_945384_72155287


title: microglia, female, PBS, 3month, rep2


title: microglia, female, PBS, 6month, rep2


title: Day9-2Gata6-derivedtomatopositive5

description:
Day9-2Gata6-derivedtomatopositive5
WTCHG_945384_72225198


title: microglia, female, PBS, 6month, rep1


title: Day9-2Gata6-derivedtomatopositive2

description:
Day9-2Gata6-derivedtomatopositive2
WTCHG_945384_72195195


title: microglia, female, PBS, 3month, rep1


title: Day9-2Non-Gata6tomatonegative3

description:
Day9-2Non-Gata6tomatonegative3
WTCHG_945384_72275203


title: Day9-2Non-Gata6tomatonegative45

description:
Day9-2Non-Gata6tomatonegative45
WTCHG_945384_72135285


title: Day9-2Gata6-derivedtomatopositive6

description:
Day9-2Gata6-derivedtomatopositive6
WTCHG_945384_72235199


title: ATAC-seq_microglia,24month,PBS.rep1

data_processing:
The paired-end adapter reads were trimmed using Cutadapt (version 2.8) with parameter “cutadapt -j 0 -m 20 -q 20”. Reads were then aligned to reference mouse genome mm10 using Bowtie2 (version 2.4.1) with parameter “bowtie2 -p 8 -X 1000 --dovetail --very-sensitive”. The duplicate reads were excluded using samtools markdup command, reads aligning to mitochondria genome and reads aligning to ENCOD blacklisted regions were filtered out using Genrich with default parameters, peaks also were called by Genrich.
Heatmaps of coverage at transcriptional start site (TSS) were generated using computeMatrix with parameters “computeMatrix reference-point --referencePoint TSS -b 1000 -a 1000 -R” and plotHeatmap functions in deepTools (version 3.5.1). Interested peaks were visualized using make_tracks_file and pygenometracks, the corresponding chromatin location information was obtained by IGV
ATAC-seq peak count matrix was generated using package Rsubread (version 2.0.1) following protocols provided in https://rockefelleruniversity.github.io/RU_ATAC_Workshop.html. Differentially accessible regions in young versus old microglia, or PBS versus LPS treated microglia were identified using DESeq2, and the results were reviewed in IGV (version 2.8.0)
The differentially accessible regions were then used for further annotation analysis. For the annotation of differential ATAC-seq regions, the differential accessible regions were annotated by annotatePeak function with parameter “TxDb = TxDb.Mmusculus.UCSC.mm10.knownGene, annoDb = "org.Mm.eg.db"” in ChIPseeker (version 1.22.1), results were visualized using plotAnnoBar function
For transcription factor motifs finding, we used the sets of genes from AAMs and DEGs identified between samples as input for HOMER findMotifsGenome.pl command with default parameters (http://homer.ucsd.edu/homer/introduction/programs.html)
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
The brain without cerebellum were cut into pieces and then dissociated in 8U/mL papain lysis buffer containing 125 U/mL DNaseI) for 20 minutes at 37 ℃ with mild shaking. This process was then terminated by adding a 10% ovomucoid in L15 culture medium (2 mg/mL). After digestion, cell clusters were removed by filtering through 70 um nylon cell strainers (Faclon). Myelin and cell debris were removed from the mixed cell through the density gradient centrifugation in 37% Percol (SolarBio). Then whole brain single cells were thorough rinsed by EDTA-free FACS buffer (0.5% BSA in DPBS) and used for single cell sequencing.
Grinding the frozen tissues to release the nuclei, mitochondria and chloroplasts，and to obtain the nuclei the mitochondria and chloroplasts should be removed. Nuclei were counted after addition of trypan blue, which stains all nuclei due to membrane permeabilization from freezing. 50,000 counted nuclei were then transferred to a tube containing 1 ml of ATAC-seq RSB with 0.1% Tween-20. Nuclei were pelleted by centrifugation at 500r.c.f. for 10 min in a pre-chilled (4 °C) fixed-angle centrifuge. Supernatant was removed using the two pipetting steps described above. Because the nuclei were already permeabilized, no lysis step was performed, and the transposition mix (25μl 2× TD buffer, 2.5μl transposase (100nM final), 16.5μl PBS, 0.5μl 1% digitonin, 0.5μl 10% Tween-20, 5μl water) was added directly to the nuclear pellet and mixed by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000r.p.m. Polymerase chain reaction amplification and size selection (150-500 bp) were performed using Agincourt AMPure XP (Beckman Coulter) and Bioanalyzer 2100 (Agilent). Libraries were pooled at equimolar ratios with barcodes and sequenced on the BGISEQ-500 platform ( BGI-Shenzhen, China).


title: Day9-2Non-Gata6tomatonegative43

description:
Day9-2Non-Gata6tomatonegative43
WTCHG_945384_72115283


title: Day9-2Gata6-derivedtomatopositive7

description:
Day9-2Gata6-derivedtomatopositive7
WTCHG_945384_72245200


title: ATAC-seq_microglia,24month,LPS.rep1

value: LPS


title: ATAC-seq_microglia,14month,PBS.rep2


title: ATAC-seq_microglia,24month,PBS.rep2


title: microglia, female, PBS, 12month, rep1


title: Day9-2Non-Gata6tomatonegative46

description:
Day9-2Non-Gata6tomatonegative46
WTCHG_945384_72145286


title: Day9-2Non-Gata6tomatonegative44

description:
Day9-2Non-Gata6tomatonegative44
WTCHG_945384_72125284


title: Day9-2Non-Gata6tomatonegative42

description:
Day9-2Non-Gata6tomatonegative42
WTCHG_945384_72105282


title: ATAC-seq_microglia,24month,LPS.rep2


title: ATAC-seq_microglia,14month,PBS.rep1


title: ATAC-seq_microglia,14month,LPS.rep2


title: Day6Gata6-derivedtomatopositive32

description:
Day6Gata6-derivedtomatopositive32
WTCHG_945385_70805056


title: Day9-2Gata6-derivedtomatopositive46

description:
Day9-2Gata6-derivedtomatopositive46
WTCHG_945384_72075279


title: microglia, female, PBS, 3month, rep3


title: Day9-2Gata6-derivedtomatopositive43

description:
Day9-2Gata6-derivedtomatopositive43
WTCHG_945384_72045276


title: Day9-2Gata6-derivedtomatopositive47

description:
Day9-2Gata6-derivedtomatopositive47
WTCHG_945384_72085280


title: ATAC-seq_microglia,14month,LPS.rep1


title: Day9-2Gata6-derivedtomatopositive44

description:
Day9-2Gata6-derivedtomatopositive44
WTCHG_945384_72055277


title: Day9-2Gata6-derivedtomatopositive42

description:
Day9-2Gata6-derivedtomatopositive42
WTCHG_945384_72035275


title: ATAC-seq_microglia,3month,PBS.rep2


title: ATAC-seq_microglia,3month,PBS.rep1


title: ATAC-seq_microglia,3month,LPS.rep2


title: ATAC-seq_microglia,3month,LPS.rep1


title: Day9-2Non-Gata6tomatonegative38

description:
Day9-2Non-Gata6tomatonegative38
WTCHG_945384_71985270