title: NMP-L cells DAY 3 RNA-seq biological replicate 1

city: Dundee

first: Kate

last: Storey

address: Dow Street

department: School of Life Sciences

institute: University of Dundee

description: RNA-seq

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1; Martin M, 2011) with parameters “--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC”.
The RSEM package (version 1.3.0; Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a; Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to hg19 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 7th June 2017. The parameters passed to the “rsem-calculate-expression” command were “--star --star-gzipped-read-file --star-output-genome-bam --forward-prob 0”.
Differential expression analysis was performed with the DESeq2 package (version 1.12.3; Love et al., 2014) within the R programming environment (version 3.3.1).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts and TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.

source_name: neuromesodermal progenitor-like (NMP-L) cells

growth_protocol: Human ES cells (H9, WiCell) were maintained as feeder-free cultures in DEF medium (Cellartis AB) supplemented with bFGF (30 ng/ml, Peprotech) and Noggin (10 ng/ml, Peprotech) on fibronectin- (Millipore, 5 µg cm−2) coated plates, and enzymatically passaged to single cells using TrypLE select (Life Technologies) according to the manufacturer's recommendations.

extract_protocol:
Culture medium was removed and cells were lysed with RLT buffer (Qiagen Rneasy Kit). Samples were collected and stored at -80 until ready to batch process. Samles were DNAse1 digested and RNA extracted as per manufacturer instructions.
The DNA library for sequencing was prepared from Qiagen column purified DNA. Libraries were prepared using the Kapa mRNA HyperPrep kit. DNA quality was confirmed by Agilent TapeStation prior to library preparation using NEB Ultra II DNA. Libraries were sequenced as single-end, 76bp reads on the Illumina High-Seq 4000 platform (Francis Crick Institute).

treatment_protocol: To generate NMP-L cells, Human ES cells were differentiated in N2/B27 containing basal medium + 20ng/ml bFGF + 3µM CHIR99021 for 3 days.

tag: cell line source

value: Human ES cells (H9)

tag: timepoint

value: day 3

value: Neurobasal medium with 20 ng/ml bFgf and 3 µM CHIR99021 for 3 days


title: AF8360

status: Public on Sep 16 2022

type: SRA

city: Madrid

first: Jose Maria

middle: Moreno

last: Navarrete

state: (None)

address: Calle de Monforte de Lemos nº 5

country: Spain

institute: CIBER

library_source: transcriptomic

data_processing:
RNA-seq reads mapped with STAR software v2.5.3a with ENCODE parameters.
Annotated genes quantified with RSEM v1.3.0
Assembly: GRCh38
Supplementary files format and content: Matrix with samples as columns and raw gene counts as rows

molecule: total RNA

organism: Homo sapiens

source_name: Small intestine - Jejunum

extract_protocol:
RNA purification was performed using RNeasy Lipid Tissue Mini Kit (QIAgen, Izasa SA, Barcelona, Spain)
RNA libraries were prepared using TruSeq Stranded total RNA kit (Ribozero)

tag: tissue

value: Small intestine - Jejunum

tag: condition

value: morbidly obese


title: AF8362


title: AF8363


title: AF8364


title: Embryonic stem cells DAY 0 RNA-seq biological replicate 1

middle: G

country: United Kingdom

description: RNA-seq

molecule: polyA RNA

source_name: embryonic stem cells

tag: treatment

value: untreated


title: NMP-L cells DAY 3 RNA-seq biological replicate 2

description: RNA-seq


title: Embryonic stem cells DAY 0 RNA-seq biological replicate 2

description: RNA-seq


title: AF8369


title: Embryonic stem cells DAY 0 RNA-seq biological replicate 3

description: RNA-seq


title: Ascl1-Hnf1a-Myod1-Oct4, 24h biol rep 1

city: Planegg-Martinsried

first: Bob

last: Hersbach

address: Großhaderner Str. 9

department: Institute of Stem Cell Research

country: Germany

institute: Helmholtz Zentrum Munich

description: 10x Genomics v2

library_source: transcriptomic single cell

data_processing:
For the alignment of reads we used the sequences and annotation files for the Mouse genome (GRCm38) from Ensembl (release 97).
The synthetic transcription factors and reporter sequences and a custom generated annotation were appended to the genome sequence and annotation. The Cell Ranger software (version 3.1.0) run with the command ‘cellranger mkref’ created an index of the genome.
The Cell Ranger pipeline run with the command ‘cellranger count’ aligned the reads, generated QC metrics, estimated the number of valid barcodes and created the count matrices.
The command was executed with standard parameters, except that we adjusted the number of expected cells and the chemistry parameter accordingly
AnnData objects of the raw and filtered count matrices were created using the Python package Scanpy (Wolf, Angerer and Theis, 2018), version 1.4.4).
The alignment files (bam) were sorted by barcode using samtools (Li et al., 2009), version 1.10) and Velocyto ((la Manno et al., 2018), version 0.17.17) was run using the ‘velocyto run’ command with the filtered barcodes list from the Cell Ranger run.
Assembly: GRCm38
Supplementary files format and content: Raw and filtered CellRanger output in .h5 file format
Supplementary files format and content: Velocyto ouput containing spliced and unspliced read information in .loom format
Supplementary files format and content: Processed scRNA-seq data in .h5ad format

organism: Mus musculus

source_name: Skin

growth_protocol: DMEM (High Glucose), 10% fetal bovine serum,1x Sodium Pyruvate, 1 mM HEPES, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2/3.1 protocol, 10x Genomics). Briefly, MEFs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Skin

tag: cell type

value: Mouse Embryonic fibroblasts

tag: strain

tag: age

value: Doxycyline


title: Ascl1-Hnf1a-Myod1-Oct4, 48h biol rep 1

description: 10x Genomics v2


title: Ascl1-Hnf1a-Myod1-Oct4, 72h biol rep 1

description: 10x Genomics v2


title: NMP-L cells DAY 3 RNA-seq biological replicate 3

description: RNA-seq


title: RING1B DAY 0 IP ChIP-seq biological replicate 3 [RING1B_IP_ESC_D0_WT_R3]

library_source: genomic

data_processing:
The nf-core/chipseq pipeline (version 1.2.1; Ewels et al., 2020; https://doi.org/10.5281/zenodo.3966161) written in the Nextflow domain specific language (version 19.10.0; Di Tommaso et al., 2017) was used to perform the primary analysis of the samples in conjunction with Singularity (version 2.6.0; Kurtzer et al., 2017).
The command used was "nextflow run nf-core/chipseq --input design.csv --genome hg19 --gtf refseq_genes.gtf --single_end --min_reps_consensus 2 -profile crick -r 1.2.1".
All data was processed relative to the human UCSC hg19 genome (Karolchik et al., 2004) downloaded from AWS iGenomes (https://github.com/ewels/AWS-iGenomes). Gene annotation files in GTF format were originally downloaded from UCSC on June 7th 2017.
For a condensed overview of the pipeline, the bioinformatics tools used in each step and an extensive list of citations please see the pipeline homepage (https://nf-co.re/chipseq).
Genome_build: hg19
Supplementary_files_format_and_content: Normalised genome-wide bigWig coverage files generated from the nf-core/chipseq pipeline command defined above. Normalisation factors were generated by scaling the number of mapped reads to 1 million.
Supplementary_files_format_and_content: MACS2 narrowPeak files generated using from the nf-core/chipseq pipeline command defined above.

molecule: genomic DNA

source_name: RING1B DAY 0 IP ChIP-seq

growth_protocol: Human ES cells (H9, WiCell) were maintained as feeder-free cultures in DEF medium (Cellartis AB) supplemented with bFGF (30 ng/ml, Peprotech) and Noggin (10 ng/ml, Peprotech) on fibronectin- (Millipore, 5 µg cm−2) coated plates, and enzymatically passaged to single cells using TrypLE select (Life Technologies) according to the manufacturer's recommendations. To generate NMP-L cells, Human ES cells were differentiated in N2/B27 containing basal medium + 20ng/ml bFGF + 3µM CHIR99021 for 3 days.

extract_protocol:
For each sample approximately 5*10^6 cells were resuspended in ice cold shearing buffer (1% Triton-X 100, 0.15 M NaCl, 1 mM EDTA, 0.5 mM EGTA, 20 mM HEPES (pH 7.6), 0.3% SDS + protease inhibitors) and transferred to three Diagenode TPX tubes. Chromatin was sheared using a Bioruptor plus: 25 cycles of 30s On/30s Off on high setting. Sheared lysates were diluted to 0.15% SDS  prior to immunoprecipitation.
The DNA library for sequencing was prepared from Qiagen column purified DNA. DNA fragmentation of IP and input samples was confirmed by Agilent TapeStation prior to library preparation using NEB Ultra II DNA. Libraries were sequenced as single-end, 76bp reads on the Illumina High-Seq 4000 platform (Francis Crick Institute).

treatment_protocol: Adherent cells were fixed for 45min at room temperature with 2mM Di(N-succinimidyl) glutarate, then fixed for an additional 10min at room temperature with 1% PFA. Fixation was quenched by addition of 2.5M glyceine for 5 minutes.

value: embryonic stem cells

tag: chip antibody

value: Ring1b (MBL D139-3 mouse)


title: RING1B DAY 0 INPUT ChIP-seq biological replicate 1 [INPUT_ESC_D0_WT_R1]

source_name: RING1B DAY 0 INPUT ChIP-seq


title: RING1B DAY 0 IP ChIP-seq biological replicate 2 [RING1B_IP_ESC_D0_WT_R2]


title: RING1B DAY 0 IP ChIP-seq biological replicate 1 [RING1B_IP_ESC_D0_WT_R1]


title: CC-T

type: RNA

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

country: Japan

institute: Toray Industries, Inc.

hyb_protocol: Hybridization solution of the Agilent SurePrint G3 Human Gene Expression v3 8×60K Microarray Kit was added and hybridized for 17 h at 65°C in an Agilent hybridization oven. Hybridization buffer and washing protocol was attached in the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (V 6.5, 2010, Agilent Technology, Inc.).

scan_protocol: Agilent Microarray Scanner D (Agilent Technologies, Inc.) was used for scanning.

data_processing:
Fluorescent value gProcessedSignal is degitalized as the data using Agilent Feature Extraction software v11.0 (Agilent Technologies, Inc.).
Each fluorescent raw value was run in batches from standardization (in the sample direction by Z-score) to principal component analysis.

source_name: Primary hepatobiliary tumor

label_protocol: 200 ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP.

extract_protocol: Mean 28.2 ul of total RNA from tissue samples was extracted and purified using an RNeasy mini kit (Qiagen, Inc.).

tag: histology

value: Cholangiocarcinoma, tumor part

tag: mean age

tag: male/female


title: RING1B DAY 3 IP ChIP-seq biological replicate 2 [RING1B_IP_NMP_D3_WT_R2]

source_name: RING1B DAY 3 IP ChIP-seq

value: neuromesodermal progenitor-like (NMP-L) cells


title: RING1B DAY 0 INPUT ChIP-seq biological replicate 2 [INPUT_ESC_D0_WT_R2]


title: RING1B DAY 3 IP ChIP-seq biological replicate 1 [RING1B_IP_NMP_D3_WT_R1]


title: RING1B DAY 0 INPUT ChIP-seq biological replicate 3 [INPUT_ESC_D0_WT_R3]


title: SNORA59B WT replicate2

city: Guangzhou

first: Jie

last: Lin

address: Shatai Road

country: China

institute: Southern Medical University

data_processing:
Reads with sequence adaptors and reads with more than 10% ‘N’ bases were removed.
Reads with more than 50% bases with QA ≤ 10 were removed.
RNA-seq clean data were mapped to hg38 using HISAT2.
Gene expression files were obtained using StringTie.
Assembly: hg38
Supplementary files format and content: tab-delimited text files (GTF) include RPKM values for each Sample

extract_protocol:
Genome editing using CRISPR-U was used to knockout the lncRNAs' DNA binding domains (DBDs). Before and after the knockout, RNA-sequencing was performed to examine gene expression (performed by Novogene, Beijing, China, http://cn.novogene.com). Ribo-Zero Magnetic Kit is used to remove rRNA before constructing the RNA-seq libraries. By using the fragmentation buffer, the mRNAs and non-coding RNAs are fragmented into short fragments(about 200~500nt), then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates, and dTTP is substituted by dUTP during the synthesis of the second strand. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters, then the second strand is degraded using UNG(Uracil-N-Glycosylase) finally. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: cancer cell

tag: genotype

value: WT


title: SNORA59B KO replicate2

value: KO


title: SNORA59B KO replicate3


title: RP11-426L16.8 WT replicate3

source_name: RKO

value: RKO


title: RP11-426L16.8 WT replicate2


title: SNORA59B KO replicate1


title: SNORA59B WT replicate3


title: RP11-426L16.8 KO replicate1


title: RP11-426L16.8 KO replicate3


title: RP11-426L16.8 KO replicate2


title: RP13-516M14.1 WT replicate3

source_name: Hela

value: Hela


title: RP13-516M14.1 WT replicate1


title: RP13-516M14.1 KO replicate2


title: SNORA59B WT replicate1


title: RP13-516M14.1 KO replicate3


title: RP13-516M14.1 WT replicate2


title: RP11-426L16.8 WT replicate1


title: RING1B DAY 3 INPUT ChIP-seq biological replicate 1 [INPUT_NMP_D3_WT_R1]

source_name: RING1B DAY 3 INPUT ChIP-seq

value: day 3


title: RING1B DAY 3 INPUT ChIP-seq biological replicate 3 [INPUT_NMP_D3_WT_R3]

value: Neurobasal medium with 20 ng/ml bFgf and 3 µM CHIR99021 for 3 days


title: RING1B DAY 3 IP ChIP-seq biological replicate 3 [RING1B_IP_NMP_D3_WT_R3]


title: RING1B DAY 3 INPUT ChIP-seq biological replicate 2 [INPUT_NMP_D3_WT_R2]


title: RP13-516M14.1 KO replicate1


title: M195926_f_band

city: Utica

first: Nathan

last: Tucker

state: NY

address: 2150 Bleecker St

country: USA

institute: Masonic Medical Research Institute

data_processing:
Library strategy: single nuclei RNA-seq
Cellranger 6.0.0 mkfastq to generate FASTQ
CutAdapt v2.8 to trim template switch oligo sequence and its complement, and homopolymers (A30, T30, G30, C30)
CellRanger Count v12 to generate count matrices
CellBender v2.0 to filter ambient RNA byproducts
Scrinvex v13 to filter likely cytoplasmic transcripts
Scrublet to remove doublets
Genome_build: Felis_catus_9.0
Supplementary_files_format_and_content: Normalized and log scale count matrix

organism: Felis catus

source_name: Feline heart left ventricle

extract_protocol:
Nuclei were isolated from flash frozen post-mortem cardiac tissue for microfluidic encapsulation using 10X Genomics' 10X Genomics Chromium Controller v3.1 Next GEM Single Cell 3'. Approximately 100mg of tissue was sectioned to a thickness of 100um then subjected to differential centrifugation and filtering.
10X Genomics Chromium Controller v3.1 Next GEM Single Cell 3'

treatment_protocol: Aortic constriction (banding operation) or sham surgery (normal)

value: Heart

tag: Sex

value: Female

value: Banded


title: M195943_f_band


title: M206230_f_sham

value: Sham operation


title: M206167_f_band


title: M206388_f_sham


title: M195845_m_band

value: Male


title: M206248_f_sham


title: M195748_f_sham


title: M200097_m_band


title: M195756_m_band


title: M202251_m_sham


title: M195853_m_sham


title: M196060_m_sham


title: M209735_m_sham


title: M202307_m_band


title: SVZ_Olig_696 pI [scNOMe-seq]

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

institute: German Cancer Research Center

description: single-cell NOMe-seq

data_processing:
read trimming and adapter removal
Bisulfite-aware read mapping
quantification of CpG and GpC methylation
Assembly: GRCm38 (mm10)
Supplementary files format and content: .csv.gz files: cell x region methylation matrices in gzip-compressed csv (comma-separated values) format. acc: chromatin accessibility (=GpC methylation). meth: DNA (=CpG) methylation. VMR: variably methylated regions identified with the ‘scbs’ software. mfrac: fraction of methylated sites. shrunkResid: shrunken mean of residuals quantified with ‘scbs’.
Supplementary files format and content: .cov.gz files: gzip-compressed tab-separated files produced by Bismark with the following columns: chromosome, start position, end position, methylation percentage, number of methylated cytosines, number of unmethylated cytosines.
Library strategy: Single-cell NOMe-seq

source_name: striatum & ventricular-subventricular zone

extract_protocol:
For the ischemia experiment, the vSVZ and striatum were isolated. For the naïve experiments, vSVZ, striatum, and olfactory bulb were isolated. Depending on the plate, individual or pooled mice were used to sort cells on plate. Tissues were processed and sorted in a BD FACSAria II at the DKFZ Flow Cytometry Facility. Cells were stained with the following antibodies (all conditions and tissues together): O4-APC and O4-APC-Vio770 (Miltenyi; diluted 1:50), Ter119-APC-Cy7 (Biolegend; 1:100), CD45-APC-Cy7 (BD; 1:200), GLAST (ACSA-1)-PE (Miltenyi: 1:20), PSA-NCAM-PE-Vio770 (Miltenyi; 1:75), Prominin1-A488 (eBioscience; 1:75), and Sytox Blue (Life Technologies, 1:1000), CD9-eFluo450 (eBioscience, 1:300).
For profiling the transcriptome and epigenome of single cells we developed and implemented a miniaturized and higher throughput version of the scNMT-seq protocol (Clark et al., 2018). On this new version, the Smart-seq3 (Hagemann-Jensen et al., 2020) method and specific normalization steps were implemented. A detailed version of the protocol is described in Cerrizuela et al., (2022). The samples listed here represent the epigenomic portion of this multi-omic data set, i.e. DNA methylation and chromatin accessibility assessed with single-cell NOMe-seq.

treatment_protocol: Two months old TiCY mice were intraperitoneally injected with tamoxifen. In these mice, tamoxifen-induced Cre recombination takes place in neural stem cells in the vSVZ, which express Tlx (Nr2e1) and will stably activate the production of enhanced YFP, labeling NSCs and their progeny. Two weeks after injection, an injury by bilateral carotid artery occlusion (BCCAO) was performed as described (Llorens-Bobadilla et al., 2015). The animals were sacrificed for single cell sorting either 48 h or 3 weeks after ischemia. WT mice were not subjected to tamoxifen or ischemia.

value: astrocytes and NSC lineage cells

value: TiCY

value: 2 days post ischemia


title: A549_2

city: Nanjing

first: Rong

last: Yin

address: Baiziting 42

department: Thoracic Surgery

institute: Nanjing Medical University Affiliated Jiangsu Cancer Hospital

data_processing:
Data were filtered using the following specifications fastq software，The filtering standards from raw data to clean reads are:：  Check the sample for contamination and, if there is pollution, remove it  If the reads contains a joint sequence, the joint sequence is cut off first  a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window;  Remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed;  if the truncated read length is less than 50 bp, the entire read is removed  Remove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: RGSC6.0/RN6 (UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each Sample

source_name: Lung

growth_protocol: a 6-well Transwell  system, A549 or H1299 cells (1 × 106 ) were plated on the lower chamber, whereas CAFs (1 × 106)  were added to the upper chamber; the pore size was 0.4 μm. All cells were grown in DMEM  supplemented with 10 % fetal bovine serum (FBS), 50 U mL-1 penicillin (Gibco), and 50 μg mL-1  streptomycin (Gibco). All cells were authenticated and tested routinely for their authenticity

extract_protocol:
Total RNA of fibroblasts, LUAD cells, and educated LUAD cells was  extracted with TRIzol. Exosome-packaged RNA extraction was performed using Total Exosome  RNA and Protein Isolation Kit (4478545, Invitrogen).
For RNA sequencing, libraries were prepared  from purified RNA using a NEBNext Ultra Directional RNA Library Prep Kit to ensure the RNA was not fragmented prior to library preparation.

treatment_protocol: Cell proliferation was detected using a Real-time xCELLigence analysis system (RTCA)  according to the manufacturer’s protocol (ACEA Biosciences). Migration assay of LUAD cells was  performed in an 8 μm 24-well Boyden chamber (Millipore). Corning BioCoat Matrigel Invasion  Chambers with 8 μm PET membranes (Corning) were used for invasion assays. LUAD cells (2  × 104) suspended in 100 μL FBS-free DMEM were added to the upper chamber. 1 × 106 CAFs  concentrated in 750 μL of DMEM containing 10% FBS was added to the bottom of a 24-well plate.  LUAD cells were allowed to migrate or invade for 24 h and 48 h, respectively. Quantification was  performed by counting the mean number of cells in three microscopy fields per chamber. For a  specific signaling pathway study, cells were pretreated with the vehicle (DMSO) and 6 μM JSH-23  or 10 μM BMS-345541 for 1 h at 37 °C prior to the experiments.

value: Lung

value: tumor cells


title: sho3_1

value: A549 cells co-cultured with NFs

value: sh LINC01614


title: CAF_2

value: A549 cells co-cultured with CAFs

value: co-cultured


title: sho3_3


title: sho3_2


title: A549_1


title: CAF_1


title: CAF_3


title: A549_3


title: SVZ_Olig_623 pI [scNOMe-seq]

description: single-cell NOMe-seq

value: striatum & ventricular-subventricular zone


title: SVZ_Olig_527 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_552 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_503 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_599 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_504 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Iso-seq_CD8 T cells

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description: The sample used to obtain RNA for sequencing was 91.7% pure CD8 T cells.

data_processing:
Sequencing was performed using one SMRTcell 8M per pool of two samples on the Sequel IIe system. Following data generation, multiple, iterative sequences covering a single molecule were collapsed to generate highly accurate circular consensus sequence (CCS) reads. These reads were demultiplexed and then used as input into the Iso-Seq v3 pipeline within SMRTLink v10.1, which filters out amplification artifacts, trims primers and polyA tails to produce de novo full-length non-chimeric (FLNC) transcripts.
The cDNA Cupcake protocol was used for post-processing of Iso-Seq clustered FLNC reads. The alignment files for the FLNC reads were converted to fastq and fasta format. Fasta files were aligned to the Homo sapiens reference genome assembly (hg38.p12) using minimap2 (v2.18-r1015) with the option -secondary=no. The resulting alignment files were collapsed into isoforms based on sequence similarity using the cDNA Cupcake Python script collapse_isoforms_by_sam.py. Isoform abundance was calculated using get_abundance_post_collapse.py, and isoforms were filtered to include those with at least two supporting reads with filter_by_count.py. Isoforms were also filtered to remove possible non-full length reads, indicated by a degraded 5’ prime region (filter_away_subset.py).
To assess short read coverage across the long-read splice junctions, the short reads were realigned using the STAR two-pass method with the reference GTF produced by the cDNA Cupcake analysis.  The resulting SJ.out.tab file was provided as input to SQANTI3 (v4.0) which produced a file with short read coverage across each splice junction in the long reads (junctions.txt). Additional SQANTI3 input included the cDNA Cupcake GTF, Gencode (v39) annotations, the hg38.p12 assembly, long read transcript abundance, a polyA motif list, and a CAGE peak (TSS sites) BED file for human and mouse. A custom script was written to identify isoforms with at least one short read covering all internal splice junctions (not including the first and last junction) using the junction file produced by SQANTI3. Transcripts not meeting the filtering criteria were removed from the GTF resulting in a filtered GTF with high confidence transcripts based on short read coverage. The filtered GTF was then annotated with SQANTI3.
Assembly: hg38
Supplementary files format and content: Annotation file in GTF format for all cells
Supplementary files format and content: Annotation file in GTF format for cell features that has been filtered to include transcripts with short read coverage of at least one read across all internal splice junctions.
Supplementary files format and content: Expression tracks created for the UCSC Genome Browser in bigbed for each cell type (*.bb)
Library strategy: Iso-Seq

source_name: Peripheral Blood CD8 T Cell

growth_protocol: Peripheral blood mononuclear cells (PBMC) were obtained from venous blood of the healthy male donor by density gradient separation using Lymphoprep Density Gradient Media and Sepmate PBMC Isolation Tubes Tubes (StemCell Technologies, 85450). The indicated cell types were then purified using negative magnetic selection via EasySep kits (Stemcell Technologies, CD4 T=17952, CD8 T=19053, NK=19055, Pan B=19554).

extract_protocol:
Two million (B cell) or three million (CD4 T, CD8 T, and NK cell) isolated cells were lysed, and total cellular RNA was extracted and purified using RNeasy Plus Mini Kit (Qiagen, 74134) following the manufacturer’s protocol. High quality RNA (all RIN>8) was used immediately for library construction with no freeze/thaw cycles.
500 ng of high-quality RNA (RIN > 8 ) was used as initial input into oligo-dT primed cDNA synthesis (NEB). Barcoded primers were incorporated onto the cDNA during second strand synthesis. Following double-stranded cDNA amplification, transcripts were equimolar pooled to include two samples per sequencing library preparation. SMRTbells were generated from the pooled cDNA as recommended by the manufacturer. Briefly, the pooled cDNA underwent enzymatic DNA damage and end repair prior to ligation with SMRTbell hairpin adaptors. Final libraries were purified with magnetic beads prior to annealing to sequencing primer (v4) and binding to polymerase (v2.1).

tag: donor sex

tag: donor age

value: 57 years

value: CD8 T cells


title: SVZ_Olig_479 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Iso-seq_CD4 T cells

description: The sample used to obtain RNA for sequencing was 98.2% pure CD4 T cells.

source_name: Peripheral Blood CD4 T Cell

value: CD4 T cells


title: Iso-seq_NK cells

description: The sample used to obtain RNA for sequencing was 97.6% pure NK cells.

source_name: Peripheral Blood NK Cells

value: NK cells


title: Iso-seq_B cells

description: The sample used to obtain RNA for sequencing was 95.8% pure Pan B cells.

source_name: Peripheral Blood Pan B Cells

value: Pan B cells


title: SVZ_Olig_432 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_431 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_528 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_480 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_456 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_729 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_600 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_725 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_727 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_724 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_702 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_692 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_693 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_723 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_711 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_694 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_698 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_679 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_681 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_688 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_682 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_687 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_689 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_703 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_686 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_677 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_691 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_680 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_705 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_690 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_684 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_678 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_712 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_700 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_665 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_676 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_699 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_664 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_662 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_650 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_653 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_646 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_652 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_659 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_637 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_660 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_641 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_642 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_638 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_629 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_657 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_634 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_661 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_639 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_635 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_630 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_658 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_633 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_631 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_628 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_627 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_626 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_632 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_636 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_625 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_722 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_654 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_655 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_622 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_619 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_612 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_617 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_611 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_610 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_609 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_605 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_618 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_594 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_620 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_613 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_593 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_597 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_598 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_595 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_592 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_584 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_574 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_573 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_583 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_570 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_572 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_582 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_591 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_590 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_568 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_585 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_587 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_586 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_589 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_567 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_565 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_571 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Neural progenitor day 6 MEKi biological replicate 1 library 2

data_processing:
Raw reads from each sample were adapter-trimmed using cutadapt (version 1.9.1)  (Martin M, 2011) with parameters “-a CTGTCTCTTATA -A CTGTCTCTTATA --minimum-length=25 –quality-cutoff=20”. If required, the additional parameters “-u <trim_length>” and “-U <trim_length>” were provided to cutadapt in order to trim all reads to 51bp.
BWA (version 0.6.2) (Li et al., 2009) with default parameters was used to perform genome-wide mapping of the adapter-trimmed reads to the human hg19 genome assembly downloaded from the UCSC (Karolchik et al., 2004).
Read group addition, duplicate marking and insert size assessment was performed using the picard tools AddOrReplaceReadGroups, MarkDuplicates and CollectMultipleMetrics, respectively (version 2.1.1) (http://broadinstitute.github.io/picard).
Reads mapped to mitochondrial DNA were removed using the pairToBed command from BEDTools (version 2.26.0) (Quinlan and Hall, 2010).
Additional filtering was performed to only include uniquely mapped, properly-paired reads with insert size <= 2kb, and mismatches <= 1 in both reads. Samtools (version 1.3.1) (Li et al., 2009) was used for bam file sorting and indexing.
The filtered alignments from each library were merged at the replicate-level using the picard MergeSamFiles command. Duplicate marking and removal was reperformed on the merged alignments.
Genome_build: hg19
Supplementary_files_format_and_content: BedGraph coverage tracks representing the accessibility signal per million mapped reads were generated at the replicate-level using BEDTools genomeCoverageBed with the parameters “-bg -pc -scale <SCALE_FACTOR>”. BedGraph files were converted to bigWig using the wigToBigWig binary available from the UCSC with the "-clip" parameter (Kent et al., 2010).

source_name: Neural progenitory cells

growth_protocol: To generate neuromesodermal progenitor like cells (NMP-L) cells cultured in neurobasal medium supplemented with N2 and B27 and GlutaMAX™ (final concentration for each 1x) and 20 ng/ml bFgf  and 3 µM CHIR99021 for 3 days. To generate neural progenitor cells (NPs) from these NMP-Ls bFgf and CHIR99021 were removed from the medium and the cells were allowed to differentiate for further 5 days. From day 2 to day 4 the medium was additionally supplemented with BMP and TGFβ inhibitors (Noggin and SB431542).

extract_protocol:
DNA was isolated as previously described (Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218, 2013).
50,000 cells were used for the transposition reaction, that was carried out for 4h at 37°C. Library fragments were amplified using 1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min - this was done for 12 cycles.

treatment_protocol: Treatment with MEK inhibitor (PD184352, 3 µM) or DMSO (equal volume to inhibitor) was administered with the culture medium.

value: day 6

value: MEK inhibitor


title: Neural progenitor day 6 WT biological replicate 1 library 1

value: untreated


title: Neural progenitor day 8  biological replicate 2 library 1

value: day 8


title: Neural progenitor day 8  biological replicate 1 library 1


title: Neural progenitor day 6 WT biological replicate 2 library 1


title: Neural progenitor day 6 MEKi biological replicate 2 library 1


title: Neural progenitor day 8  biological replicate 1 library 2


title: Neural progenitor day 6 WT biological replicate 1 library 2


title: Neural progenitor day 6 MEKi biological replicate 1 library 1


title: SVZ_Glast_563 pI [scNOMe-seq]

description: single-cell NOMe-seq

value: astrocytes and NSC lineage cells

value: TiCY

value: 2 days post ischemia


title: SVZ_Glast_564 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_562 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_557 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_556 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_561 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_555 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_549 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_548 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Neural progenitor day 5 WT biological replicate 1 library 2

value: day 5


title: Neural progenitor day 5 WT biological replicate 2 library 1


title: Neural progenitor day 6 DMSO biological replicate 2 library 1

value: DMSO


title: Neural progenitor day 6 DMSO biological replicate 1 library 2


title: Neural progenitor day 5 MEKi biological replicate 2 library 2


title: Neural progenitor day 5 WT biological replicate 2 library 2


title: SVZ_Glast_547 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Neural progenitor day 5 MEKi biological replicate 2 library 1


title: SVZ_Glast_545 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Neural progenitor day 5 MEKi biological replicate 1 library 2


title: Neural progenitor day 5 MEKi biological replicate 1 library 1


title: Neural progenitor day 6 DMSO biological replicate 1 library 1


title: SVZ_Glast_560 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Neural progenitor day 5 WT biological replicate 1 library 1


title: SVZ_Glast_542 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_543 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_550 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_539 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NMP biological replicate 2 library 1

source_name: Neuromesodermal progenitory like cells

value: day 3


title: Neural progenitor day 5 DMSO biological replicate 1 library 1


title: Neural progenitor day 5 DMSO biological replicate 2 library 2


title: NMP biological replicate 1 library 2


title: NMP biological replicate 2 library 3


title: NMP biological replicate 2 library 2


title: SVZ_Glast_538 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Neural progenitor day 5 DMSO biological replicate 1 library 2


title: NMP biological replicate 1 library 1


title: SVZ_Glast_533 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_532 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_534 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_525 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Neural progenitor day 5 DMSO biological replicate 2 library 1


title: SVZ_Glast_541 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_536 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_526 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO7 pC [scNOMe-seq]

description: single-cell NOMe-seq

source_name: ventricular-subventricular zone

value: ventricular-subventricular zone

value: oligodendrocyte

value: WT

value: naive


title: OLIGO8 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO4 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO6 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_540 pI [scNOMe-seq]

description: single-cell NOMe-seq

value: striatum & ventricular-subventricular zone


title: SVZ_Glast_521 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_523 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_519 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_524 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO5 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO32 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO29 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_518 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO28 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO26 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_517 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO31 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO30 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO25 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO27 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_515 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_514 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_511 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_512 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO23 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO22 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO19 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_510 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_508 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO21 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_502 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_513 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_509 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO17 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO16 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_501 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_516 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_500 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO15 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO24 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_499 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO12 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO14 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO10 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO11 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_497 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_492 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_493 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_495 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_494 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC32 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_488 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_487 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC3 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_486 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC28 pC [scNOMe-seq]

description: single-cell NOMe-seq

value: aNSC


title: NSC25 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC24 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_484 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_477 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_478 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_475 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC23 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_472 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC8 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_471 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC17 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_470 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_463 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC31 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_469 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC15 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC27 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC14 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC11 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_461 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB9 pC [scNOMe-seq]

description: single-cell NOMe-seq

value: neuroblast


title: NSC10 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NB8 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_452 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_453 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB7 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_446 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB6 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC16 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_438 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_439 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC20 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_429 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_457 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC12 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NB31 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NB32 pC [scNOMe-seq]

description: single-cell NOMe-seq

value: TAP


title: SVZ_Glast_427 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_428 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_454 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB30 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_423 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB29 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NB28 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_405 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_406 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_404 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB27 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NB26 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NB4 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NB25 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NB24 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NB23 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_403 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_90 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_89 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_86 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_84 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB20 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NB22 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NB21 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_81 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_82 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB18 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_79 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_80 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB19 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NB16 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NB17 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_99 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_7 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_78 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_70 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB14 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_72 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB12 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NB11 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_68 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_66 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO9 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO6 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: NB13 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_61 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB10 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_65 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO5 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO8 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_59 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_58 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO4 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_62 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO30 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_60 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_64 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO3 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_57 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO32 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_56 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO28 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_50 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO26 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO27 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_5 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_51 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO25 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_49 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO24 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_46 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO7 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO23 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_42 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_44 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO17 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO22 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_41 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO18 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO16 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO12 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_40 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO15 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO11 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_45 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_39 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_34 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO13 pC [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_332 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO7 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_33 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO4 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO6 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO22 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_334 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_333 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO23 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_32 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO20 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_310 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO19 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_30 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_309 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC5 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: OLIGO10 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_298 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC4 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_292 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_290 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_295 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC22 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC23 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC3 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_312 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC2 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_278 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_286 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC1 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC19 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_28 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB7 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_273 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_27 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_268 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB8 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: NSC21 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_267 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_265 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB6 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_335 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB4 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_258 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_263 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_251 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB21 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: NB20 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_25 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB22 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_248 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB2 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: NB19 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_249 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_247 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB17 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_246 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_245 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_237 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_238 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_241 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB5 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: NB16 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: NB15 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: NB11 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_252 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_234 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB10 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_232 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB18 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: NB1 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: NB14 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_242 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: NB12 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_228 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_229 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_224 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO22 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_22 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO20 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO4 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_219 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_218 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO17 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_222 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO19 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_217 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO16 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_216 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO11 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_215 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO14 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: ASTRO9 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_212 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_696 pI

description: single-cell RNA-seq

data_processing:
mapping with STAR via zUMIs
transcript quantification with featureCounts via zUMIs
Assembly: GRCm38 (mm10)
Supplementary files format and content: Single-cell RNA-seq count matrix in gzip-compressed csv (comma-separated values) format. Values are not normalized, decimals are due to distribution of multimapping reads.

extract_protocol:
For the ischemia experiment, the vSVZ and striatum were isolated. For the naïve experiments, vSVZ, striatum, and olfactory bulb were isolated. Depending on the plate, individual or pooled mice were used to sort cells on plate. Tissues were processed and sorted in a BD FACSAria II at the DKFZ Flow Cytometry Facility. Cells were stained with the following antibodies (all conditions and tissues together): O4-APC and O4-APC-Vio770 (Miltenyi; diluted 1:50), Ter119-APC-Cy7 (Biolegend; 1:100), CD45-APC-Cy7 (BD; 1:200), GLAST (ACSA-1)-PE (Miltenyi: 1:20), PSA-NCAM-PE-Vio770 (Miltenyi; 1:75), Prominin1-A488 (eBioscience; 1:75), and Sytox Blue (Life Technologies, 1:1000), CD9-eFluo450 (eBioscience, 1:300).
For profiling the transcriptome and epigenome of single cells we developed and implemented a miniaturized and higher throughput version of the scNMT-seq protocol (Clark et al., 2018). On this new version, the Smart-seq3 (Hagemann-Jensen et al., 2020) method and specific normalization steps were implemented. A detailed version of the protocol is described in Cerrizuela et al., (2022). The samples listed here represent the transcriptomic portion of this multi-omic data set.
Single-cell RNA-seq (Smart-seq3)


title: Str_Glast_211 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_210 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_623 pI

description: single-cell RNA-seq


title: SVZ_Olig_599 pI

description: single-cell RNA-seq


title: Str_Glast_209 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_214 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_207 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_528 pI

description: single-cell RNA-seq


title: ASTRO1 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_206 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_200 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_202 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_527 pI

description: single-cell RNA-seq


title: SVZ_Olig_503 pI

description: single-cell RNA-seq


title: Str_Glast_201 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_2 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_479 pI

description: single-cell RNA-seq


title: Str_Glast_198 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_199 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_600 pI

description: single-cell RNA-seq


title: SVZ_Olig_456 pI

description: single-cell RNA-seq


title: Str_Glast_196 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_729 pI

description: single-cell RNA-seq


title: SVZ_Olig_431 pI

description: single-cell RNA-seq


title: Str_Glast_192 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_504 pI

description: single-cell RNA-seq


title: ASTRO6 pA [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_191 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_480 pI

description: single-cell RNA-seq


title: Str_Glast_19 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_725 pI

description: single-cell RNA-seq


title: SVZ_Glast_724 pI

description: single-cell RNA-seq


title: SVZ_Glast_727 pI

description: single-cell RNA-seq


title: SVZ_Olig_432 pI

description: single-cell RNA-seq


title: Str_Glast_189 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_552 pI

description: single-cell RNA-seq


title: SVZ_Glast_723 pI

description: single-cell RNA-seq


title: Str_Glast_184 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_186 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_194 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_722 pI

description: single-cell RNA-seq


title: SVZ_Glast_703 pI

description: single-cell RNA-seq


title: SVZ_Glast_702 pI

description: single-cell RNA-seq


title: Str_Glast_176 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_183 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_179 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_187 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_705 pI

description: single-cell RNA-seq


title: SVZ_Glast_711 pI

description: single-cell RNA-seq


title: SVZ_Glast_700 pI

description: single-cell RNA-seq


title: Str_Glast_168 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_699 pI

description: single-cell RNA-seq


title: SVZ_Glast_694 pI

description: single-cell RNA-seq


title: SVZ_Glast_698 pI

description: single-cell RNA-seq


title: Str_Glast_166 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_693 pI

description: single-cell RNA-seq


title: SVZ_Glast_712 pI

description: single-cell RNA-seq


title: Str_Glast_169 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_180 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_691 pI

description: single-cell RNA-seq


title: SVZ_Glast_692 pI

description: single-cell RNA-seq


title: Str_Glast_162 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_165 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_16 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_690 pI

description: single-cell RNA-seq


title: Str_Glast_159 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_681 pI

description: single-cell RNA-seq


title: Str_Glast_150 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_148 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_684 pI

description: single-cell RNA-seq


title: SVZ_Glast_689 pI

description: single-cell RNA-seq


title: SVZ_Glast_687 pI

description: single-cell RNA-seq


title: Str_Glast_140 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_688 pI

description: single-cell RNA-seq


title: Str_Glast_146 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_143 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_680 pI

description: single-cell RNA-seq


title: Str_Glast_137 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_141 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_677 pI

description: single-cell RNA-seq


title: Str_Glast_132 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_679 pI

description: single-cell RNA-seq


title: Str_Glast_135 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_131 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_126 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_665 pI

description: single-cell RNA-seq


title: Str_Glast_127 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_133 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_676 pI

description: single-cell RNA-seq


title: SVZ_Glast_686 pI

description: single-cell RNA-seq


title: SVZ_Glast_664 pI

description: single-cell RNA-seq


title: Str_Glast_123 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_138 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_682 pI

description: single-cell RNA-seq


title: Str_Glast_120 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_661 pI

description: single-cell RNA-seq


title: SVZ_Glast_660 pI

description: single-cell RNA-seq


title: Str_Glast_115 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_658 pI

description: single-cell RNA-seq


title: Str_Glast_116 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_657 pI

description: single-cell RNA-seq


title: Str_Glast_112 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_655 pI

description: single-cell RNA-seq


title: SVZ_Glast_654 pI

description: single-cell RNA-seq


title: Str_Glast_108 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_653 pI

description: single-cell RNA-seq


title: SVZ_Glast_652 pI

description: single-cell RNA-seq


title: Str_Glast_109 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_107 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_662 pI

description: single-cell RNA-seq


title: Str_Glast_105 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_650 pI

description: single-cell RNA-seq


title: Str_Glast_106 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_642 pI

description: single-cell RNA-seq


title: SVZ_Olig_9 pH [scNOMe-seq]

description: single-cell NOMe-seq

value: 21 days post ischemia


title: Str_Glast_103 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_646 pI

description: single-cell RNA-seq


title: SVZ_Olig_6 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_5 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_641 pI

description: single-cell RNA-seq


title: Str_Glast_118 pI [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_659 pI

description: single-cell RNA-seq


title: SVZ_Glast_639 pI

description: single-cell RNA-seq


title: SVZ_Glast_678 pI

description: single-cell RNA-seq


title: SVZ_Glast_637 pI

description: single-cell RNA-seq


title: SVZ_Glast_634 pI

description: single-cell RNA-seq


title: SVZ_Glast_635 pI

description: single-cell RNA-seq


title: SVZ_Glast_632 pI

description: single-cell RNA-seq


title: SVZ_Glast_633 pI

description: single-cell RNA-seq


title: SVZ_Glast_638 pI

description: single-cell RNA-seq


title: SVZ_Olig_14 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_3 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_15 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_16 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_4 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_636 pI

description: single-cell RNA-seq


title: SVZ_Olig_13 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Olig_11 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_625 pI

description: single-cell RNA-seq


title: SVZ_Glast_626 pI

description: single-cell RNA-seq


title: SVZ_Glast_627 pI

description: single-cell RNA-seq


title: SVZ_Glast_629 pI

description: single-cell RNA-seq


title: SVZ_Glast_622 pI

description: single-cell RNA-seq


title: SVZ_Glast_630 pI

description: single-cell RNA-seq


title: SVZ_Glast_617 pI

description: single-cell RNA-seq


title: SVZ_Glast_612 pI

description: single-cell RNA-seq


title: SVZ_Glast_628 pI

description: single-cell RNA-seq


title: SVZ_Glast_619 pI

description: single-cell RNA-seq


title: SVZ_Glast_613 pI

description: single-cell RNA-seq


title: SVZ_Glast_631 pI

description: single-cell RNA-seq


title: SVZ_Glast_620 pI

description: single-cell RNA-seq


title: SVZ_Glast_618 pI

description: single-cell RNA-seq


title: SVZ_Olig_10 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_99 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_611 pI

description: single-cell RNA-seq


title: SVZ_Glast_610 pI

description: single-cell RNA-seq


title: SVZ_Glast_87 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_89 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_85 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_91 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_98 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_94 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_84 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_86 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_82 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_93 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_97 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_9 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_81 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_88 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_90 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_77 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_78 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_79 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_609 pI

description: single-cell RNA-seq


title: SVZ_Glast_584 pI

description: single-cell RNA-seq


title: SVZ_Glast_597 pI

description: single-cell RNA-seq


title: SVZ_Glast_594 pI

description: single-cell RNA-seq


title: SVZ_Glast_598 pI

description: single-cell RNA-seq


title: SVZ_Glast_587 pI

description: single-cell RNA-seq


title: SVZ_Glast_592 pI

description: single-cell RNA-seq


title: SVZ_Glast_589 pI

description: single-cell RNA-seq


title: SVZ_Glast_605 pI

description: single-cell RNA-seq


title: SVZ_Glast_595 pI

description: single-cell RNA-seq


title: SVZ_Glast_593 pI

description: single-cell RNA-seq


title: SVZ_Glast_585 pI

description: single-cell RNA-seq


title: SVZ_Glast_586 pI

description: single-cell RNA-seq


title: SVZ_Glast_590 pI

description: single-cell RNA-seq


title: SVZ_Glast_591 pI

description: single-cell RNA-seq


title: SVZ_Glast_7 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_68 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_73 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_64 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_72 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_65 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_76 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_66 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_74 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_75 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_71 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_583 pI

description: single-cell RNA-seq


title: SVZ_Glast_69 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_63 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_582 pI

description: single-cell RNA-seq


title: SVZ_Glast_61 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_62 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_573 pI

description: single-cell RNA-seq


title: SVZ_Glast_574 pI

description: single-cell RNA-seq


title: SVZ_Glast_59 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_60 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_6 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_572 pI

description: single-cell RNA-seq


title: SVZ_Glast_55 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_563 pI

description: single-cell RNA-seq


title: SVZ_Glast_564 pI

description: single-cell RNA-seq


title: SVZ_Glast_557 pI

description: single-cell RNA-seq


title: SVZ_Glast_567 pI

description: single-cell RNA-seq


title: SVZ_Glast_570 pI

description: single-cell RNA-seq


title: SVZ_Glast_56 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_565 pI

description: single-cell RNA-seq


title: SVZ_Glast_51 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_50 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_5 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_54 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_561 pI

description: single-cell RNA-seq


title: SVZ_Glast_58 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_53 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_562 pI

description: single-cell RNA-seq


title: SVZ_Glast_560 pI

description: single-cell RNA-seq


title: SVZ_Glast_571 pI

description: single-cell RNA-seq


title: SVZ_Glast_49 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_568 pI

description: single-cell RNA-seq


title: SVZ_Glast_556 pI

description: single-cell RNA-seq


title: SVZ_Glast_549 pI

description: single-cell RNA-seq


title: SVZ_Glast_548 pI

description: single-cell RNA-seq


title: SVZ_Glast_555 pI

description: single-cell RNA-seq


title: SVZ_Glast_550 pI

description: single-cell RNA-seq


title: SVZ_Glast_543 pI

description: single-cell RNA-seq


title: SVZ_Glast_541 pI

description: single-cell RNA-seq


title: SVZ_Glast_547 pI

description: single-cell RNA-seq


title: SVZ_Glast_542 pI

description: single-cell RNA-seq


title: SVZ_Glast_545 pI

description: single-cell RNA-seq


title: SVZ_Glast_3 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_29 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_31 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_41 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_28 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_30 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_32 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_43 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_42 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_45 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_40 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_48 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_44 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_36 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_35 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_38 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_39 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_37 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_533 pI

description: single-cell RNA-seq


title: SVZ_Glast_534 pI

description: single-cell RNA-seq


title: SVZ_Glast_538 pI

description: single-cell RNA-seq


title: SVZ_Glast_536 pI

description: single-cell RNA-seq


title: SVZ_Glast_540 pI

description: single-cell RNA-seq


title: SVZ_Glast_532 pI

description: single-cell RNA-seq


title: SVZ_Glast_539 pI

description: single-cell RNA-seq


title: SVZ_Glast_524 pI

description: single-cell RNA-seq


title: SVZ_Glast_526 pI

description: single-cell RNA-seq


title: SVZ_Glast_523 pI

description: single-cell RNA-seq


title: SVZ_Glast_525 pI

description: single-cell RNA-seq


title: SVZ_Glast_514 pI

description: single-cell RNA-seq


title: SVZ_Glast_20 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_2 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_25 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_22 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_512 pI

description: single-cell RNA-seq


title: SVZ_Glast_190 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_27 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_186 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_187 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_189 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_191 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_516 pI

description: single-cell RNA-seq


title: SVZ_Glast_515 pI

description: single-cell RNA-seq


title: SVZ_Glast_517 pI

description: single-cell RNA-seq


title: SVZ_Glast_21 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_518 pI

description: single-cell RNA-seq


title: SVZ_Glast_521 pI

description: single-cell RNA-seq


title: SVZ_Glast_23 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_19 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_188 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_509 pI

description: single-cell RNA-seq


title: SVZ_Glast_511 pI

description: single-cell RNA-seq


title: SVZ_Glast_184 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_510 pI

description: single-cell RNA-seq


title: SVZ_Glast_513 pI

description: single-cell RNA-seq


title: SVZ_Glast_185 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_519 pI

description: single-cell RNA-seq


title: SVZ_Glast_183 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_501 pI

description: single-cell RNA-seq


title: SVZ_Glast_502 pI

description: single-cell RNA-seq


title: SVZ_Glast_182 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_500 pI

description: single-cell RNA-seq


title: SVZ_Glast_177 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_179 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_181 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_176 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_178 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_180 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_172 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_170 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_508 pI

description: single-cell RNA-seq


title: SVZ_Glast_17 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_494 pI

description: single-cell RNA-seq


title: SVZ_Glast_487 pI

description: single-cell RNA-seq


title: SVZ_Glast_499 pI

description: single-cell RNA-seq


title: SVZ_Glast_497 pI

description: single-cell RNA-seq


title: SVZ_Glast_495 pI

description: single-cell RNA-seq


title: SVZ_Glast_484 pI

description: single-cell RNA-seq


title: SVZ_Glast_486 pI

description: single-cell RNA-seq


title: SVZ_Glast_169 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_168 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_493 pI

description: single-cell RNA-seq


title: SVZ_Glast_492 pI

description: single-cell RNA-seq


title: SVZ_Glast_478 pI

description: single-cell RNA-seq


title: SVZ_Glast_167 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_477 pI

description: single-cell RNA-seq


title: SVZ_Glast_166 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_164 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_488 pI

description: single-cell RNA-seq


title: SVZ_Glast_175 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_162 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_470 pI

description: single-cell RNA-seq


title: SVZ_Glast_471 pI

description: single-cell RNA-seq


title: SVZ_Glast_472 pI

description: single-cell RNA-seq


title: SVZ_Glast_475 pI

description: single-cell RNA-seq


title: SVZ_Glast_163 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_463 pI

description: single-cell RNA-seq


title: SVZ_Glast_165 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_161 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_160 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_461 pI

description: single-cell RNA-seq


title: SVZ_Glast_159 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_158 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_157 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_457 pI

description: single-cell RNA-seq


title: SVZ_Glast_156 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_454 pI

description: single-cell RNA-seq


title: SVZ_Glast_453 pI

description: single-cell RNA-seq


title: SVZ_Glast_155 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_469 pI

description: single-cell RNA-seq


title: SVZ_Glast_154 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_446 pI

description: single-cell RNA-seq


title: SVZ_Glast_439 pI

description: single-cell RNA-seq


title: SVZ_Glast_438 pI

description: single-cell RNA-seq


title: SVZ_Glast_452 pI

description: single-cell RNA-seq


title: SVZ_Glast_153 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_15 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_428 pI

description: single-cell RNA-seq


title: SVZ_Glast_423 pI

description: single-cell RNA-seq


title: SVZ_Glast_152 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_147 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_406 pI

description: single-cell RNA-seq


title: SVZ_Glast_427 pI

description: single-cell RNA-seq


title: SVZ_Glast_146 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_405 pI

description: single-cell RNA-seq


title: SVZ_Glast_144 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_140 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_141 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_143 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_142 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_404 pI

description: single-cell RNA-seq


title: Str_Glast_99 pI

description: single-cell RNA-seq


title: SVZ_Glast_429 pI

description: single-cell RNA-seq


title: SVZ_Glast_14 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_89 pI

description: single-cell RNA-seq


title: SVZ_Glast_403 pI

description: single-cell RNA-seq


title: Str_Glast_84 pI

description: single-cell RNA-seq


title: Str_Glast_90 pI

description: single-cell RNA-seq


title: Str_Glast_82 pI

description: single-cell RNA-seq


title: Str_Glast_86 pI

description: single-cell RNA-seq


title: Str_Glast_81 pI

description: single-cell RNA-seq


title: SVZ_Glast_149 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_136 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_138 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_148 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_135 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_80 pI

description: single-cell RNA-seq


title: Str_Glast_79 pI

description: single-cell RNA-seq


title: SVZ_Glast_133 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_134 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_78 pI

description: single-cell RNA-seq


title: SVZ_Glast_131 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_132 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_137 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_70 pI

description: single-cell RNA-seq


title: Str_Glast_7 pI

description: single-cell RNA-seq


title: SVZ_Glast_129 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_13 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_68 pI

description: single-cell RNA-seq


title: SVZ_Glast_128 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_125 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_122 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_123 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_119 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_62 pI

description: single-cell RNA-seq


title: Str_Glast_66 pI

description: single-cell RNA-seq


title: Str_Glast_59 pI

description: single-cell RNA-seq


title: Str_Glast_61 pI

description: single-cell RNA-seq


title: Str_Glast_65 pI

description: single-cell RNA-seq


title: Str_Glast_60 pI

description: single-cell RNA-seq


title: Str_Glast_64 pI

description: single-cell RNA-seq


title: SVZ_Glast_120 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_12 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_118 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_58 pI

description: single-cell RNA-seq


title: SVZ_Glast_121 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_72 pI

description: single-cell RNA-seq


title: Str_Glast_57 pI

description: single-cell RNA-seq


title: Str_Glast_56 pI

description: single-cell RNA-seq


title: SVZ_Glast_116 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_115 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_50 pI

description: single-cell RNA-seq


title: SVZ_Glast_114 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_46 pI

description: single-cell RNA-seq


title: SVZ_Glast_112 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_45 pI

description: single-cell RNA-seq


title: SVZ_Glast_111 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_117 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_44 pI

description: single-cell RNA-seq


title: Str_Glast_41 pI

description: single-cell RNA-seq


title: Str_Glast_40 pI

description: single-cell RNA-seq


title: SVZ_Glast_109 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_11 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_34 pI

description: single-cell RNA-seq


title: Str_Glast_51 pI

description: single-cell RNA-seq


title: Str_Glast_335 pI

description: single-cell RNA-seq


title: Str_Glast_39 pI

description: single-cell RNA-seq


title: SVZ_Glast_100 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_5 pI

description: single-cell RNA-seq


title: SVZ_Glast_108 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_10 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_332 pI

description: single-cell RNA-seq


title: Str_Glast_49 pI

description: single-cell RNA-seq


title: Str_Glast_97 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_333 pI

description: single-cell RNA-seq


title: Str_Glast_95 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: SVZ_Glast_113 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_33 pI

description: single-cell RNA-seq


title: SVZ_Glast_105 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_42 pI

description: single-cell RNA-seq


title: SVZ_Glast_103 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_312 pI

description: single-cell RNA-seq


title: SVZ_Glast_101 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_93 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_32 pI

description: single-cell RNA-seq


title: Str_Glast_334 pI

description: single-cell RNA-seq


title: Str_Glast_309 pI

description: single-cell RNA-seq


title: SVZ_Glast_102 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_310 pI

description: single-cell RNA-seq


title: Str_Glast_91 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_90 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_89 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_30 pI

description: single-cell RNA-seq


title: Str_Glast_298 pI

description: single-cell RNA-seq


title: Str_Glast_292 pI

description: single-cell RNA-seq


title: Str_Glast_295 pI

description: single-cell RNA-seq


title: Str_Glast_290 pI

description: single-cell RNA-seq


title: Str_Glast_94 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_28 pI

description: single-cell RNA-seq


title: Str_Glast_278 pI

description: single-cell RNA-seq


title: Str_Glast_27 pI

description: single-cell RNA-seq


title: Str_Glast_268 pI

description: single-cell RNA-seq


title: Str_Glast_267 pI

description: single-cell RNA-seq


title: Str_Glast_286 pI

description: single-cell RNA-seq


title: Str_Glast_265 pI

description: single-cell RNA-seq


title: Str_Glast_273 pI

description: single-cell RNA-seq


title: Str_Glast_258 pI

description: single-cell RNA-seq


title: Str_Glast_263 pI

description: single-cell RNA-seq


title: Str_Glast_252 pI

description: single-cell RNA-seq


title: Str_Glast_251 pI

description: single-cell RNA-seq


title: Str_Glast_25 pI

description: single-cell RNA-seq


title: Str_Glast_248 pI

description: single-cell RNA-seq


title: Str_Glast_249 pI

description: single-cell RNA-seq


title: Str_Glast_246 pI

description: single-cell RNA-seq


title: Str_Glast_245 pI

description: single-cell RNA-seq


title: Str_Glast_242 pI

description: single-cell RNA-seq


title: Str_Glast_247 pI

description: single-cell RNA-seq


title: Str_Glast_60 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_62 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_72 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_83 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_80 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_61 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_87 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_88 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_71 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_66 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_86 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_6 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_82 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_76 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_85 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_64 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_7 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_84 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_81 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_70 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_73 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_58 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_56 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_57 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_241 pI

description: single-cell RNA-seq


title: Str_Glast_234 pI

description: single-cell RNA-seq


title: Str_Glast_237 pI

description: single-cell RNA-seq


title: Str_Glast_232 pI

description: single-cell RNA-seq


title: Str_Glast_238 pI

description: single-cell RNA-seq


title: Str_Glast_45 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_35 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_37 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_40 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_52 pH [scNOMe-seq]

description: single-cell NOMe-seq


title: Str_Glast_47 pH [scNOMe-seq]

description: single-cell NOMe-seq