title: IP_CHAT_WT_SALINE Rep4

status: Public on Sep 11 2019

first: Laura

last: Kus

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

description:
polysome bound mRNA
Pooled 4 animals, baseline
1094_Chat_IP_CHAT_WT_SALINE_Rep4_CTTGTA_L003

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UCSC mm10 whole genome using STAR version 2.3.0e_r291, with default settings.
Quantification of aligned reads was done using htseq-count module, part of the ‘HTSeq’ framework, version 0.6.0, using default settings, with ‘union’ mode to handle reads overlapping more than one feature.
Differentially expressed genes were identified by performing a negative binomial test using DESeq2 (R-package version 1.4.5) with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Counts text

source_name: Medial Habenula

growth_protocol: All mice were maintained on a 12h light-dark cycle with ad lib access to food and water. Adult mice were used for all experiments (>8 weeks of age).

extract_protocol:
Brain regions of interest were microdissected, and homogenized immediately for IP using magnetic beads conjugated to anti-GFP. Total RNA was extracted from both the total homogenate (INPUT) and the IP fraction.
Ovation RNA-Seq System V2 kit (Nugen, Cat# 7102) was used with 10ug of RNA for MHb samples or 500pg of RNA for IPN samples for generation of SPIA cDNA. 1ug of SPIA cDNA was fragmented to 250bp before proceeding with library prepartion using the TruSeq DNA Nano LT Sample Prep Kit (Illumina, Cat# 20015964).

treatment_protocol: Animals were sacrificed by live decapitation, brains were rapidly removed and regions of interest dissected on ice. See sample details for specific drug treatments.

tag: background strain

tag: transgene(s)

value: ChAT-TRAP (DW167)

tag: fraction

value: IP


title: IP_CHAT_WT_SALINE Rep2

type: SRA

city: New York

state: NY

country: USA

description:
polysome bound mRNA
Pooled 4 animals, baseline
1092_Chat_IP_WT_SALINE_Rep2_GCCAAT_L001

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus


title: Tumor T_B_005

status: Public on Oct 08 2019

city: Hangzhou

first: Hechen

last: Huang

state: Zhejiang

address: 79 Qingchun Road

department: Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery

country: China

institute: First Affiliated Hospital, School of Medicine, Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg/GRCh38.p12 whole genome using hisat2 v2.1.0.
'featureCounts'' v1.6.4 was used for counting reads to genomic features mapped to GENCODE v30. Reads Per Kilobase of exon model per Million mapped reads (RPKM) were calculated using gfold v1.1.4. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the library.
Genome_build: hg/GRCh38.p12
Supplementary_files_format_and_content: Microsoft Excel files include RPKM and TPM values for each Sample.

organism: Homo sapiens

source_name: liver

extract_protocol:
liver tissues were resected from patients, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: isolate

tag: age

tag: Sex

value: male


title: Tumor T_C_007


title: IP_CHAT_WT_SALINE Rep3

description:
polysome bound mRNA
Pooled 4 animals, baseline
1093_Chat_IP_WT_SALINE_Rep3_GCCAAT_L003


title: Tumor T_W_034


title: IP_CHAT_WT_SALINE Rep1

description:
polysome bound mRNA
Pooled 4 animals, baseline
1091_Chat_IP_WT_SALINE_Rep1_GCCAAT_L006


title: Jurkat cell mRNA-seq

status: Public on Sep 05 2019

city: San Francisco

first: Jesse

last: Zhang

state: CA

department: BTS

institute: UCSF

data_processing:
Basecalling was done with bcl2fastq v2.20
Bead barcode was extracted from position 1-12 of Read 1 and UMI was extracted from position 13-20 of Read 1.
For mRNA reads: Read2 was aligned to a reference human or mouse genome using STAR.
For coordinate reads: Read2 was aligned to a known list of well index sequences using custom Python code.
Digital gene expression matrices were created by, for each bead barcode group, counting the number of unique UMIs for each gene or well index sequence.
To link beads to nanowell position: UMI counts for each bead are scaled based on the number of total UMIs on the bead. Next, the off-target noise of each well index is estimated based on the average expression across all beads and subtracted from scaled UMI counts. The top x, y, and z well index captured on each bead is then extracted. Beads which the top well index is not at least 5 times as abundant as the next most abundant well index for any of the sets of x, y, and z well indexes are removed. The remaining beads are assigned to a nanowell position by matching the most abundant x, y, and z indexes on the bead to a lookup table of the expected x, y, and z positions at each nanowell position. Following position assignment, the bead barcodes of all beads matched at each nanowell position are collected. The columns on the gene expression matrix of all beads matched at the same nanowell position are merged, yielding a revised matrix where the columns represented nanowell positions instead of individual beads.
The gene expression matrix is then annotated by recorded cell fluorescence values obtained during printing.
Genome_build: hg18; mm10
Supplementary_files_format_and_content: Digital gene expression matricies by nanowell position (.csv)
Supplementary_files_format_and_content: Indexed flow cytometry data by nanowell position (.csv)

source_name: Human T lymphocyte cells

growth_protocol: HEK293 and 3T3 cells were grown in DMEM with 10% FBS in a T75 flask. Jurkats were grown in RPMI-1640 with 10% FBS in a suspension culture.

extract_protocol:
Cell-containing drops were merged with lysis buffer drops containing coordinate oligos and barcoded poly dT beads within microwells. Beads were then processed using the Drop-Seq protocol, using the modified CITE-seq/Cell hashing protocol to separate coordinate oligo reads from mRNA reads.
The coordinate library directly had sequencing adapters added with PCR. The mRNA library underwent tagmentation and sequencing adapter addition using the Illumina Nextera XT sample preparation kit. A custom Read 1 primer used in Drop-Seq was used during the sequencing of both libraries.
Drop-Seq; CITE-Seq/Cell hashing

treatment_protocol: Cells were resuspended. HEK293 and 3T3 cells were stained with Calcein Green and Red; Jurkat cells were stained with DRAQ5. Cells were then encapsulated in 80-um droplets.

tag: cell line

value: Jurkat


title: INPUT-MHb-Saccharin-Saline

description:
Pooled 4 animals, 6wk 0.2% saccharin in drinking water, ip saline 3hr before tissue collection
824_Chat_INPUT-MHb-Saccharin-Saline_GCCAAT_L008

value: Input


title: IP_wt_MHb_Saline

description:
polysome bound mRNA
Pooled 3 animals, Osmotic minipump model 2002, 14d saline
852_Chat_IP_wt_MHb_Saline_GCCAAT_L008


title: 1.0 µg/ml WS-CM [38]

status: Public on Sep 25 2019

type: RNA

city: Winston-salem

first: Prasad

last: GL

state: NC

address: 401 N Main St

institute: RAISC

description: gene expression data from isolated PBMC

hyb_protocol: All samples were hybridized to HTA 2.0 Genechip arrays

scan_protocol: All samples were scanned using Affymetrix GeneChip® Scanner 3000.

data_processing: CEL files and CHP files were generated using Affymetrix Expression console. Gene expression values were preprocessed and normalized using Robust Multi-array Average method in R.

label: biotin

source_name: PBMC exposed to 1 µg/ml equi-nicotine of WS-CM for 3 hours and stimulated with agonists for 5 hours

label_protocol: First strand cDNA synthesis, labeling and hybridization were done according to standard protocols provided by Affymetrix.

growth_protocol: Whole blood was collected from healthy non-smoking donors under written consent at a local Clinical Contract Research Organization (Piedmont Medical Group, Winston-Salem, NC) under IRB approval. PBMCs were isolated by standard density gradient centrifµgation by using Isolymph (Arimilli, 2012).  Isolated PBMCs were cryopreserved for further use. Cultured PBMCs were exposed to different concentrations (0, 0.3, 1.0, and 3.0 µg/ml equi-nicotine units) of WSCM or one concentration (100µg/ml equi-nicotine unit) of ST/PB for 3 hours.

extract_protocol: After exposing PBMCs to TPPs for 3h and agonists for 5 h, cells were washed with PBS in RNase-free microtubes.  The cell pellets were dissolved in RLT plus lysis buffer (Qiagen, Valencia, CA) with 2-mercaptoethanol on ice for 30 minutes and stored in an ultra-low temperature freezer and later shipped to Genome Explorations (Memphis, TN) for processing as follows. PBMCs were suspended in 600 µl RLT buffer and 1% β-mercaptoethanol. RNA was extracted from these samples using Qiagen RNeasy Mini Kit following manufacturer’s instructions. RNA concentrations were determined using 1µl of the extracted RNA on the Nano-Drop spectrophotometer. RNA quality assessment was carried out using 1 µl of the extracted RNA on Agilent 2100 Bioanalyzer.

treatment_protocol: WSCM was prepared by passing smoke from four 3R4F reference cigarettes throµgh Roswell Park Memorial Institute (RPMI) 1640 medium without phenol red using the following smoking regimen: 35-60-2, puff volume in mL, puff interval in seconds, and puff duration in seconds, respectively.  Smokeless tobacco extract was prepared by extracting 2S3 smokeless tobacco reference product (North Carolina State University Tobacco Services Analytical Laboratory) in Phosphate buffer (PB) for 2 h followed by filtration. Both preparations of TPPs were aliquoted and stored at –80 °C immediately. Aliquots of frozen WSCM and ST/PB were analyzed to determine the levels of nicotine, tobacco specific nitrosamines, and polycyclic aromatic hydrocarbons.

tag: tissue

value: peripherial blood mononuclear cells (PBMC)

tag: agent

value: 1.0 microg/ml WS-CM


title: 3.0 µg/ml WS-CM [34]

description: gene expression data from isolated PBMC

source_name: PBMC sxposed to 3 µg/ml equi-nicotine of WS-CM for 3 hours and stimulated with agonists for 5 hours

value: 3.0 microg/ml WS-CM


title: 0.3 µg/ml WS-CM [32]

description: gene expression data from isolated PBMC

source_name: PBMC exposed to 0.3 µg/ml equi-nicotine of WS-CM for 3 hours and stimulated with agonists for 5 hours

value: 0.3 microg/ml WS-CM


title: Media [36]

description: gene expression data from isolated PBMC

source_name: Control (media for 3 hours and PBMC stimulated with agonists for 5 hours)

value: Media


title: Media [31]

description: gene expression data from isolated PBMC


title: 100 µg/ml ST-PO4 [40]

description: gene expression data from isolated PBMC

source_name: PBMC exposed to 100 µg/ml equi-nicotine of STE for 3 hours and stimulated with agonists for 5 hours

value: 100 microg/ml ST-PO4


title: 0.3 µg/ml WS-CM [27]

description: gene expression data from isolated PBMC


title: 100 µg/ml ST-PO4 [35]

description: gene expression data from isolated PBMC


title: coordinate reads for Jurkat cell experiment

organism: synthetic construct

source_name: synthetic DNA


title: 3.0 µg/ml WS-CM [24]

description: gene expression data from isolated PBMC


title: Media [26]

description: gene expression data from isolated PBMC


title: 0.3 µg/ml WS-CM [22]

description: gene expression data from isolated PBMC


title: coordinate reads for 3T3 and HEK293 cell experiment


title: RNA-seq of Homo sapiens: normal P11_N

status: Public on Sep 01 2019

city: Guangzhou

first: Changxi

last: Wang

state: Guangdong

address: No.74, Zhongshan second road

institute: Sun Yat-Sen University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using hisat2.
Read count for each gene was calculated using htseq-count software. Then fragments per kilobase of exon model per million reads mapped (FPKM) were calculated using stringtie.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample.

source_name: Osteosarcoma

extract_protocol:
Sarcoma specimens including tumor, adjacent normal tissues and paired blood samples were obtained from osteosarcoma patients.RNA was extracted using Trizol reagent.
RNA libraries were construncted for sequencing using standard Illumina protocols

value: adjacent normal

tag: gender

value: female

tag: kshv infection

value: negative


title: RNA-seq of Homo sapiens: tumor P11_T

value: tumor

value: positive


title: 1.0 µg/ml WS-CM [33]

description: gene expression data from isolated PBMC


title: 3.0 µg/ml WS-CM [29]

description: gene expression data from isolated PBMC


title: RNA-seq of Homo sapiens: tumor P9_T


title: 100 µg/ml ST-PO4 [30]

description: gene expression data from isolated PBMC


title: Media [21]

description: gene expression data from isolated PBMC


title: 1.0 µg/ml WS-CM [23]

description: gene expression data from isolated PBMC


title: RNA-seq of Homo sapiens: normal P3_N


title: RNA-seq of Homo sapiens: tumor P5_T


title: RNA-seq of Homo sapiens: tumor P3_T


title: RNA-seq of Homo sapiens: normal P1_N


title: RNA-seq of Homo sapiens: normal P9_N


title: RNA-seq of Homo sapiens: tumor P1_T


title: 3T3 and HEK293 cell mRNA-seq

organism:
Homo sapiens
Mus musculus

source_name: Mouse embryo fibroblasts; human embyro kidney cells

value: 3T3 and HEK293 cells


title: RNA-seq of Homo sapiens: normal P5_N


title: WT rep1 [A]

status: Public on Aug 08 2019

city: New Orleans

first: Stryder

last: Meadows

state: LA

address: 6400 Freret

department: Cell and Molecular Biology

institute: Tulane University

data_processing:
Alignment was performed using RNA-Seq aligner (Basespace v1.1.0) using Isis analysis software (v2.6.25.18), STAR aligner (STAR_2.5.0b), Isaac Variant Caller (v2.3.13-31-g3c98c29-dirty), BEDTools (v2.17.0), Cufflinks (v2.2.1) and BLAST (v2.2.26+).
For differential expression, we used Basespace DESeq2 with the following inputs: reference genome- Mus musculus/mm10, strandedness- first strand, aligner- STAR, enabled pairwise differential expression analysis- yes and paired analysis- yes.
Genome_build: Mus Musculus/mm10
Supplementary_files_format_and_content: Comma separated values (.csv) with FPKM values included for all the samples

source_name: wild type_retinal endothelial cells

extract_protocol:
RNA was isolated as previously described (Crist et al., 2019). Briefly, we used the Thermo Fisher GeneJet RNA Purification kit (Thermo #K0732) and quantified RNA via nanodrop (Thermo) and Qubit (Thermo Q33216).  RNA quality was assessed using the Agilent RNA 6000 nanokit (Agilent 5067-1511) before library preparation.
Libraries were constructed using Illumina TruSeq RNA Library Preparation Kit v2 (Illumina RS-122-2001). Quality and quantity of the library were assessed using Agilent DNA 1000 chip (Agilent 5067-1504) and Qubit dsDNA HS Kit (Thermo Q32854), respectively.

tag: strain background

tag: genotype/variation

value: Anxa3 fl/fl

value: postnatal day 7

value: retina

tag: cell type

value: Retinal endothelial cells


title: MUT rep1 [B]

source_name: MUT_retinal endothelial cells

value: Anxa3 fl/fl;Tie2-Cre


title: MUT rep2 [E]


title: WT rep3 [D]


title: Venetoclax day 14 [YUSAABTD14]

status: Public on Apr 30 2019

city: Portland

first: Olga

last: Nikolova

state: OR

address: 2720 SW Moody Ave

department: Computational Biology

institute: OHSU

description:
PCR library sequencing
LIB171004JT_YUSAABTD14_S6_L005

library_source: genomic

data_processing:
Sequences were trimmed using cutadapt version 1.10 called with parameters "cutadapt -n 2 -g {adapter5} -a {adapter3}" where adapter3 = GTTTAAGAGC and adapter5 = ACGAAACACCG
Trimmed reads were aligned using bowtie2 called with parameters "bowtie2 -p 8 --norc -U"
Formatting was done using samtools called as "samtools view -bS"
Filtering was performed using samtools called as "samtools view -bq 10"
MAGeCK( version 0.5.6) count command was executed.
Genome_build: custom reference created from CRISPR library (yusa4bowtie2.fasta) PMID:27760321
Supplementary_files_format_and_content: Raw read counts sgRNA x sample matrix .tsv format

molecule: genomic DNA

source_name: MOLM13 cells infected with library

growth_protocol: MOLM13 cells were grown in RPMI-1640, supplemented with 20% serum, pen/strep, fungizone.

extract_protocol:
10e6 cells were collected for DMSO day 0, 30 miln cells were collected for Venetoclax/DMSO days 7,14. DNA was extracted by desalting method
50 microgramms of DNA were used to PCR amplify library using Herculase II enzyme following published protocols and instructions supplied by authors on Addgene  (Shalem, et al Science 2014. 343(6166): p. 84-87, Tzelepis et al, Cell Rep, 2016. 17(4): p. 1193-1205)
Shalem et al Science 2014. 343(6166): p. 84-87

treatment_protocol: Puromycin was applied at 2mg/ml concentration for 5 days. Venetoclax (1microMolar) or DMSO were applied to 30 million cells in single flask

value: infected with CRISPR/Cas9 library

tag: treatment

value: day 14 post puromycin selection, Venetoclax


title: 0.3 µg/ml WS-CM [37]

description: gene expression data from isolated PBMC

value: peripherial blood mononuclear cells (PBMC)


title: RNA-seq of Homo sapiens: tumor P2_T


title: DMSO day 14 [YUSADMSOD14]

description:
PCR library sequencing
LIB171004JT_YUSADMSOD14_S5_L005

value: day 14 post puromycin selection, DMSO


title: DMSO day 14 replicate [YUSADMSOD14dupl]

description:
PCR library sequencing
LIB171004JT_YUSADMSOD14dupl_S7_L006


title: DMSO day 7 replicate [YUSADMSOD7dupl]

description:
PCR library sequencing
LIB171004JT_YUSADMSOD7dupl_S4_L005

value: day 7 post puromycin selection, DMSO


title: Y.Kosuke Plasmid Library  [YUSAplasmid]

description:
PCR library sequencing
LIB171004JT_YUSAplasmid_S1_L005

source_name: Library plasmid sequencing

tag: sample type

value: Library plasmid sequencing


title: DMSO day 0 [YUSADMSOD0]

description:
PCR library sequencing
LIB171004JT_YUSADMSOD0_S2_L005

value: day 0 post puromycin selection


title: DMSO day 7 [YUSADMSOD7]

description:
PCR library sequencing
LIB171004JT_YUSADMSOD7_S3_L005


title: 36_input_p65_TNF60min

status: Public on Apr 11 2019

city: Tokyo

first: Yoshiki

last: Higashijima

address: 1-5-45 Yushima, Bunkyo

department: Medical Research Institute

country: Japan

institute: Tokyo Medical and Dental University

description: ChIP-seq data of human endothelial cells through TNF-induced inflammatory signaling

data_processing:
Illumina CASAVA1.8.2 software used for basecalling and demultiplexing.
Sequence reads (36-bp single read) from ChIP for histones, KDM7A, UTX, and p65 were mapped to the human reference genome hg19, by using the Illumina alignment program, ELAND. Only sequence reads that mapped uniquely to the reference genome were used for further analysis.
The mapped sequence reads were extended to 500-2000 bp and converted to the continuous signal data in wig format.  Wig files were converted to bigwig files using UCSC wigToBigWig program.
Genome_build: human NCBI genome build 37 (hg19)
Supplementary_files_format_and_content: bigwig

source_name: human umblical vein endothelial cells

growth_protocol: HUVECs were purchased from Lonza Japan Ltd. (Tokyo, Japan) and cultured and passaged every 2 or 3 days in EBM-2 complete medium composed of EBM-2 Basal Medium (Lonza) supplemented with EGM-2 SingleQuot Kit Suppl. & Growth Factors (Lonza) and 3% fetal bovine serum (FBS) (Thermo Fisher Scientific, Waltham, MA). We sub-cultured HUVECs when they reached 80 to 90% confluence to avoid excessive floaters. HUVECs were used within passage 4 to 7 for all experiments in this work. Human monocyte cell line U937 was purchased from JCRB Cell Bank (Osaka, Japan) and grown and passaged every 2 or 3 days in RPMI1640 (Thermo Fisher Scientific) supplemented with 1% penicillin/streptomycin (Wako, Osaka, Japan) and 10% FBS. All cells were cultured at 37 ºC and 5% CO2 in a humidified incubator.

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as previously described (Kanki et al., 2011; Kanki et al., 2017). In brief, 10 million HUVECs were cross-linked with 1% formaldehyde (Wako) for 10 min. For p65 and FLAG ChIP analysis, cells were fixed with 2 mM EGS (ethylene glycol bis [succinimidyl succinate]) (Thermo Fisher Scientific) for 1 hr prior to formaldehyde fixation. After neutralization by using 0.2 M glycine, cells were collected, re-suspended in 2 ml SDS lysis buffer composed of 10 mM Tris-HCl; pH8.0 (Thermo Fisher Scientific), 150 mM NaCl (Thermo Fisher Scientific), 1% SDS (Sigma-Aldrich), 1mM EDTA; pH 8.0 (Thermo Fisher Scientific), cOmplete™ EDTA-free Protease Inhibitor Cocktail (Sigma-Aldrich), and fragmented by the Picoruptor (40 cycles for histones and p65, and 20 cycles for FLAG, 30 sec on/30 sec off; Diagenode, Liege Science Park, Belgium). Sonicated solution was diluted by ChIP dilution buffer (20 mM Tris-HCl; pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100 (Sigma-Aldrich)) up to 10.3 ml, which was used for immunoprecipitation (10 ml) and the rest 300 μl as a non-immunoprecipitated chromatin (INPUT). Specific antibody was bound with magnetic Dynabeads M-280 and applied to diluted sonicated solution for immunoprecipitation. Antibodies against H3K4me3, H3K27ac, H3K9me2, H3K27me3 (MAB Institute, Inc. Hokkaido, Japan), p65 (abcam for ChIP-Seq and Santa Cruz Biotechnology Inc for ChIP-PCR), and FLAG (Sigma-Aldrich) were used. Prepared DNA was quantified using NanoDrop 2000 (Thermo Fisher Scientific) and more than 10 ng of DNA was processed for qPCR or sequence.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: 80-90% confluent HUVECs plates were washed with PBS once and then serum starved in EBM-2 Basal Medium containing 0.5% FBS for 16 hrs. HUVECs were stimulated with or without 10 ng/ml TNF-α (Peprotech, Rocky Hill, NJ) for indicated periods thereafter.

tag: antibody

tag: donor

value: pooled from multiple donors

value: HUVECs

tag: passages


title: 100 µg/ml ST-PO4 [25]

description: gene expression data from isolated PBMC

value: 100 microg/ml ST-PO4


title: 35_input_p65_TNF0min


title: 32_H3K4me3_TNF30min


title: 30_input_active_TNF30min


title: 33_H3K27ac_TNF0min


title: WT rep2 [C]


title: 27_H3K27me3_TNF0min_rep2


title: 26_H3K9me3_TNF60min_rep2


title: 28_H3K27me3_TNF60min_rep2


title: 25_H3K9me3_TNF0min_rep2


title: 24_H3K9me2_TNF60min_rep2


title: Venetoclax day 7 [YUSAABTD7]

description:
PCR library sequencing
LIB171004JT_YUSAABTD7_S11_L006

value: day 7 post puromycin selection, venetoclax


title: 1.0 µg/ml WS-CM [28]

description: gene expression data from isolated PBMC

value: 1.0 microg/ml WS-CM


title: 23_H3K9me2_TNF0min_rep2


title: 22_input_repressive_TNF60min_rep2


title: 20_H3K27me3_TNF60min_rep1


title: 34_H3K27ac_TNF30min


title: 18_H3K9me3_TNF60min_rep1


title: 19_H3K27me3_TNF0min_rep1


title: 16_H3K9me2_TNF60min_rep1


title: 29_input_active_TNF0min


title: 15_H3K9me2_TNF0min_rep1


title: 13_input_repressive_TNF0min_rep1


title: 14_input_repressive_TNF60min_rep1


title: 10_UTX_TNF60min_rep1

value: FLAG


title: 9_UTX_TNF0min_rep1


title: 6_KDM7A_TNF60min_rep2


title: 8_input_UTX_TNF60min


title: 7_input_UTX_TNF0min


title: 3_KDM7A_TNF0min_rep1


title: 1_input_KDM7A_TNF0min


title: 4_KDM7A_TNF60min_rep1


title: 2_input_KDM7A_TNF60min


title: 39_p65_TNF60min


title: 17_H3K9me3_TNF0min_rep1


title: 37_p65_TNF0min


title: 38_p65_TNF30min


title: 5_KDM7A_TNF0min_rep2


title: 21_input_repressive_TNF0min_rep2


title: 11_UTX_TNF0min_rep2


title: NTB - Untreated 5 (skin)

status: Public on Nov 28 2018

first: Lisa

last: Coussens

state: Oregon

address: SW Sam Jackson Park Rd

data_processing:
PEAR (v.0.9.6)  is used to combine paired-end sequences
Synthetic template sequences are extracted using custom script
Reads are aligned to TCR sequences and clonotypes are assembled using MiXCR (v2.1.9)
Clonotype counts are normalized using scaling factors based on synthetic templates
repseqio.v1.2:10090 (9a1b61eb20896bbb44a5d38d9359107b)
Supplementary_files_format_and_content: tab-delimited text files containing information on each clonotype: raw counts/frequency, normalized counts/frequency, V, D, J identity, CDR3 sequence, etc.

source_name: primary tumor

growth_protocol: Mice were maintained in standard conditions

extract_protocol:
Dneasy Blood and tissue kit from Qiagen was used to isolate DNA from whole tumor and PBMC lysates
2-step PCR was used to construct libraries for Illumina NextSeq platform

treatment_protocol: PMX-53 was resuspended in water and administered at 1.0 mg/kg/day via subcutaneous implantation via Alzet pump on day 40 when SCCs reached ~50 mm3. Paclitaxel was injected intravenously at 12 mg/kg every 4 days for a total of 3 injections per cycle

value: postnatal 110-140

value: Skin

tag: genotype

value: FvB wild type


title: NTB - Untreated 6 (skin)


title: NTB - Untreated 4 (skin)


title: NTB - Untreated 3 (skin)


title: NTB - Untreated 2 (skin)


title: Sample 4 Media

status: Public on Feb 25 2019

description: gene expression data from isolated PBMC

source_name: peripherial blood mononuclear cells

extract_protocol: After exposing PBMCs to TPPs for 3h, cells were washed with PBS in RNase-free microtubes.  The cell pellets were dissolved in RLT plus lysis buffer (Qiagen, Valencia, CA) with 2-mercaptoethanol on ice for 30 minutes and stored in an ultra-low temperature freezer and later shipped to Genome Explorations (Memphis, TN) for processing as follows. PBMCs were suspended in 600 µl RLT buffer and 1% β-mercaptoethanol. RNA was extracted from these samples using Qiagen RNeasy Mini Kit following manufacturer’s instructions. RNA concentrations were determined using 1µl of the extracted RNA on the Nano-Drop spectrophotometer. RNA quality assessment was carried out using 1 µl of the extracted RNA on Agilent 2100 Bioanalyzer.

value: PBMC

value: Control


title: Sample 4 1.0 ug/ml WS-CM

description: gene expression data from isolated PBMC

value: 1 ug/ml equi-nicotine of WS-CM for 3 hours


title: Sample 3 100 ug/ml ST-PO4

description: gene expression data from isolated PBMC

value: 100 ug/ml equi-nicotine of STE for 3 hours


title: 31_H3K4me3_TNF0min


title: NTB - Untreated 1 (skin)


title: Sample 2 100 ug/ml ST-PO4

description: gene expression data from isolated PBMC


title: Sample 3 3.0 ug/ml WS-CM

description: gene expression data from isolated PBMC

value: PBMC sxposed to 3 ug/ml equi-nicotine of WS-CM for 3 hours


title: Sample 2 3.0 ug/ml WS-CM

description: gene expression data from isolated PBMC


title: Sample 4 0.3 ug/ml WS-CM

description: gene expression data from isolated PBMC

value: 0.3 ug/ml equi-nicotine of WS-CM for 3 hours


title: Sample 2 1.0 ug/ml WS-CM

description: gene expression data from isolated PBMC


title: Sample 4 3.0 ug/ml WS-CM

description: gene expression data from isolated PBMC


title: Sample 1 100 ug/ml ST-PO4

description: gene expression data from isolated PBMC


title: Paclitaxel+PMX53 8 (skin)


title: Sample 1 1.0 ug/ml WS-CM

description: gene expression data from isolated PBMC


title: Sample 2 0.3 ug/ml WS-CM

description: gene expression data from isolated PBMC


title: Sample 3 0.3 ug/ml WS-CM

description: gene expression data from isolated PBMC


title: Paclitaxel+PMX53 4 (skin)


title: Paclitaxel+PMX53 7 (skin)


title: PMX-53 8 (skin)


title: Paclitaxel+PMX53 3 (skin)


title: Sample 1 Media

description: gene expression data from isolated PBMC


title: PMX-53 7 (skin)


title: Paclitaxel+PMX53 5 (skin)


title: Paclitaxel+PMX53 2 (skin)


title: Sample 2 Media

description: gene expression data from isolated PBMC


title: Sample 3 Media

description: gene expression data from isolated PBMC


title: PMX-53 9 (skin)


title: PMX-53 5 (skin)


title: PMX-53 6 (skin)


title: Sample 1 0.3 ug/ml WS-CM

description: gene expression data from isolated PBMC


title: PMX-53 4 (skin)


title: Paclitaxel+PMX53 1 (skin)


title: MUT rep3 [F]

value: Anxa3 fl/fl;Tie2-Cre

value: postnatal day 7

value: retina

value: Retinal endothelial cells


title: PMX-53 2 (skin)


title: PMX-53 3 (skin)


title: PMX-53 1 (skin)


title: Paclitaxel 7 (skin)


title: Paclitaxel+PMX53 6 (skin)


title: Paclitaxel 10 (skin)


title: Paclitaxel 5 (skin)


title: Paclitaxel 3 (skin)


title: Paclitaxel 8 (skin)


title: Paclitaxel 1 (skin)


title: Paclitaxel 2 (skin)


title: untreated control 7 (skin)


title: untreated control 8 (skin)


title: untreated control 5 (skin)


title: Paclitaxel 4 (skin)


title: Paclitaxel 6 (skin)


title: untreated control 4 (skin)


title: Paclitaxel 9 (skin)


title: untreated control 6 (skin)


title: Sample 3 1.0 ug/ml WS-CM

description: gene expression data from isolated PBMC


title: Sample 4 100 ug/ml ST-PO4

description: gene expression data from isolated PBMC


title: NTB - Paclitaxel+PMX53 4 (blood)

source_name: peripheral blood mononuclear cells

value: Blood


title: untreated control 3 (skin)


title: untreated control 1 (skin)


title: NTB - Paclitaxel+PMX53 1 (blood)


title: NTB - Paclitaxel+PMX53 5 (blood)


title: NTB - Paclitaxel+PMX53 2 (blood)


title: NTB - Paclitaxel+PMX53 3 (blood)


title: NTB - Untreated 5 (blood)


title: NTB - Untreated 3 (blood)


title: NTB - Untreated 2 (blood)


title: NTB - Untreated 4 (blood)


title: NTB - Untreated 1 (blood)


title: Paclitaxel+PMX53 6 (blood)


title: untreated control 2 (skin)


title: Paclitaxel+PMX53 3 (blood)


title: Paclitaxel+PMX53 1 (blood)


title: Paclitaxel+PMX53 2 (blood)


title: Paclitaxel+PMX53 7 (blood)


title: Paclitaxel+PMX53 8 (blood)


title: Paclitaxel+PMX53 4 (blood)


title: PMX-53 9 (blood)


title: PMX-53 7 (blood)


title: Paclitaxel+PMX53 5 (blood)


title: PMX-53 8 (blood)


title: PMX-53 6 (blood)


title: PMX-53 5 (blood)


title: PMX-53 4 (blood)


title: Paclitaxel 10 (blood)


title: Paclitaxel 4 (blood)


title: Paclitaxel 9 (blood)


title: Paclitaxel 8 (blood)


title: Paclitaxel 6 (blood)


title: Paclitaxel 7 (blood)


title: PMX-53 1 (blood)


title: PMX-53 2 (blood)


title: Paclitaxel 1 (blood)


title: Paclitaxel 2 (blood)


title: Paclitaxel 5 (blood)


title: Paclitaxel 3 (blood)


title: untreated control 3 (blood)


title: untreated control 1 (blood)


title: untreated control 5 (blood)


title: untreated control 4 (blood)


title: untreated control 2 (blood)


title: untreated control 6 (blood)


title: 6hr_release_DMSO

status: Public on Nov 15 2018

city: Stanford

first: Karlene

middle: Anne

last: Cimprich

address: 318 Campus Drive

institute: Stanford University

data_processing:
Alignment to GRCh37 and gencode annotated transcripts (v25) with tophat using --library-type fr-firststrand
Count over gencode transcripts with htseq
Use the DESeq2 bioconductor package to obtain statistics for comparisons between treatment conditions
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab seperated values of raw read counts over Gencode transcripts, as well as DESeq2 called log2 fold changes and adjusted p-values over the same transcripts

growth_protocol: Cells synchronized to early S with 2 mM thymidine for 24 h, washed 3 times with normal growth medium, and relased into normal growth medium

extract_protocol:
Total RNA was extracted using Trizol and the manufacturer's protocol
Libraries were constructed using the KAPA Stranded mRNA-Seq Kit and accompanying protocol

treatment_protocol: 1 hour post-thymidine wash-off, cells were treated with DMSO or ATRi (AZ20, 2 uM) for an additional 3 hours (4hr_release) or an additional 5 hours (6hr_release)

value: Retina

tag: drug

value: DMSO


title: untreated control 7 (blood)

tag: age


title: Cycling: asynchronous control

value: Not treated


title: 6hr_release_ATRi

value: ATRi


title: 4hr_release_ATRi


title: 4hr_release_DMSO


title: G1_S_arrested: un-released control


title: RRBS_Heart_1wk_WT_rep1

status: Public on May 09 2018

city: Philadelphia

first: Klaus

middle: H

last: Kaestner

state: PA

address: University of Pennsylvania, 12-126 Smilow Center for Translational Research, 3400 Civic Center Boulevard

department: Department of Genetics and Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine

institute: University of Pennsylvania

description:
genomic DNA
Big_table_all_samples_RRBS

data_processing:
One-hundred-base pair paired-end sequencing reads from RRBS were trimmed and quality filtered by trim galore software (v0.3.3) using default parameters for RRBS with the following command:
trim_galore–rrbs–paired sample_R1.fastq.gz sample_R2.fastq.gz
BSMAP v2.74 (Xi and Li, 2009) was used for read alignment (genome build mm9) and extraction of single-base resolution methylation levels using the following commands:
bsmap -a sample_R1_val_1.fq.gz -b sample_R2_val_2.fq.gz -d mm9_AllGenome.fa -o bam_file -R -D C-CGG
python methratio.py -i “no-action” -p -g -z -o sample_trim_galore_mm9.fa.meth -d mm9_AllGenome.fa bam_file
Percent methylation was calculated for one-hundred-base pair tiles with a minimum coverage of 10 CpGs.
Genome_build: mm9
Supplementary_files_format_and_content: bed

extract_protocol:
DNA was isolated from mouse hepatocytes or from snap-frozen mouse tissues and incubated in lysis buffer (25 mM Tris-HCl (pH  8), 2 mM EDTA, 0.2% SDS, 200 mM NaCl) supplemented with 300 μg/ml proteinase K (Roche) followed by phenol:chloroform extraction and ethanol precipitation.
RRBS libraries were prepared as described (Boyle et al., 2012) and run on Hiseq 2500 (Illumina).

tag: strain

value: Heart

tag: aav injection time


title: untreated control 8 (blood)

tag: tissue

value: postnatal 110-140

value: FvB wild type


title: Sample 1 3.0 ug/ml WS-CM

description: gene expression data from isolated PBMC

value: PBMC


title: Brx98_1_SC3_072313

status: Public on Feb 19 2018

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description: circulating cells in lysis buffer

data_processing:
Color space reads were aligned using tophat version 2.0.4 and bowtie1 version 0.12.7 with the no-novel-juncs argument set with human genome version hg19 and transcriptome defined by the hg19 knownGene table from genome.ucsc.edu.
Reads that did not align or aligned to multiple locations in the genome were discarded.
The hg19 table knownToLocusLink from genome.ucsc.edu was used to map, if possible, each aligned read to the gene who's exons the read had aligned to. The reads count for each gene was the number of reads that were so mapped to that gene.
The read count was divided by the total number of reads that were mapped to any gene and multiplied by one million to form the reads-per-million (rpm) count.
Genome_build: hg19
Supplementary_files_format_and_content: The readCounts.xls file gives the read counts described above for each sample (columns) and gene (rows). See platform.xls for a description of the IDs in readCounts.xls

source_name: CTCs

extract_protocol:
RNA was extracted as previously described (Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535).
Libraries were constructed as previously described (Tang, F., Barbacioru, C., Nordman, E., Li, B., Xu, N., Bashkirov, V.I., Lao, K., and Surani, M.A. (2010). RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat Protoc 5, 516-535). Briefly, to generate cDNA, samples were treated with reverse transcription master mix (0.05 uL RNase inhibitor, 0.07uL T4 gene 32 protein, and 0.33uL SuperScript III Reverse Transcriptase per 1X volume) and incubated on thermocycler at 50C for 30 minutes and 70C for 15 minutes. To remove free primer, 1.0uL of EXOSAP mix was added to each sample, which was incubated at 37C for 30 minutes and inactivated at 80C for 25 minutes. Next, a 3'-poly-A tail was added to the cDNA in each sample by incubating in master mix (0.6uL 10X PCR Buffer II, 0.36uL 25mM MgCl2, 0.18uL 100mM dATP, 0.3uL Terminal Transferase, 0.3uL RNase H, and 4.26uL H2O per 1X volume) at 37C for 15 minutes and inactivated at 70C for 10 minutes. A second strand cDNA was synthesis by dividing each sample into 4 and incubating in master mix (2.2uL 10X High Fidelity PCR Buffer, 1.76uL 2.5mM each dNTP, 0.066uL UP2 Primer at 100uM, 0.88uL 50mM MgSO4, 0.44uL Platinum Taq DNA Polymerase, and 13.654uL H2O per 1X volume) at 95C for 3 minutes, 50C for 2 minutes, and 72C for 10 minutes. DNA was sheared using a Covaris S2 system and then prepared for ABI 5500XL library construction with end polishing, size selection of 200-500 bp using AMPure XP, ABI barcode adaptor ligation, amplification and purification with AMPure XP, and then pooling of barcoded samples for emulsion PCR wiht template beads preparation.  Samples were then loaded per protocol on the ABI 5500XL.
RNA-Seq using oligo-dT cDNA synthesis and amplification of cDNA libraries using custom universal PCR primers

value: circulating tumor cells

tag: patient

tag: progression

value: Bone (+)


title: Brx97_1_SC5_072313

description: circulating cells in lysis buffer


title: Brx98_1_SC5_072313

description: circulating cells in lysis buffer


title: Brx97_1_SC3_072313

description: circulating cells in lysis buffer


title: 12_UTX_TNF60min_rep2

value: FLAG

value: pooled from multiple donors

value: HUVECs


title: Brx97_1_SC1_072313

description: circulating cells in lysis buffer


title: Brx87_1_SC1_062113

description: circulating cells in lysis buffer


title: Brx97_1_SC4_072313

description: circulating cells in lysis buffer


title: Brx87_1_SC2_062113

description: circulating cells in lysis buffer


title: Brx83_1_SC3_051613

description: circulating cells in lysis buffer


title: Brx73_1_SC1_032013

description: circulating cells in lysis buffer

value: Visceral (+)


title: Brx83_1_SC1_051613

description: circulating cells in lysis buffer


title: Brx83_1_SC2_051613

description: circulating cells in lysis buffer


title: Brx72_1_SC6_031813

description: circulating cells in lysis buffer


title: Brx74_1_SC2_032813

description: circulating cells in lysis buffer


title: Brx78_1_05102013

description: circulating cells in lysis buffer


title: Brx82_1_SC1_051613

description: circulating cells in lysis buffer


title: Brx97_1_SC2_072313

description: circulating cells in lysis buffer


title: Brx73_1_SC2_032013

description: circulating cells in lysis buffer


title: Brx72_1_SC5_031813

description: circulating cells in lysis buffer


title: Brx72_1_SC4_031813

description: circulating cells in lysis buffer


title: Brx72_1_SC3_031813

description: circulating cells in lysis buffer


title: Brx72_1_SC1_031813

description: circulating cells in lysis buffer


title: Brx72_1_SC2_031813

description: circulating cells in lysis buffer


title: Brx71_SC2_031413

description: circulating cells in lysis buffer


title: Brx71_SC1_031413

description: circulating cells in lysis buffer


title: Brx66_2_SC2_012913

description:
circulating cells in lysis buffer
same sample as GSM1253386


title: Brx66_2_SC1_012913

description:
circulating cells in lysis buffer
same sample as GSM1253390


title: Brx83_1_SC4_051613

description: circulating cells in lysis buffer


title: Brx66_2_CL3_012913

description: circulating cells in lysis buffer


title: Brx61_1_SC2_032012

description:
circulating cells in lysis buffer
same sample as GSM1253402


title: Brx66_2_CL1_012913

description: circulating cells in lysis buffer


title: Brx66_2_CL2_012913

description:
circulating cells in lysis buffer
same sample as GSM1253385


title: Brx61_1_SC1_032012

description:
circulating cells in lysis buffer
same sample as GSM1253387


title: Brx61_1_CL6_032012

description: circulating cells in lysis buffer


title: Brx61_1_CL2_032012

description: circulating cells in lysis buffer


title: Brx61_1_CL4_032012

description:
circulating cells in lysis buffer
same sample as GSM1253400


title: Brx53_SC1_010313

description: circulating cells in lysis buffer


title: Brx53_CL1_011513

description: circulating cells in lysis buffer


title: Brx53_CL2_011513

description: circulating cells in lysis buffer


title: Brx61_1_CL1_032012

description: circulating cells in lysis buffer


title: Brx61_1_CL3_032012

description: circulating cells in lysis buffer


title: Brx53_SC_011513

description: circulating cells in lysis buffer


title: Brx52_CL4_020413

description: circulating cells in lysis buffer


title: Brx52_CL3_020413

description: circulating cells in lysis buffer


title: Brx61_1_CL5_032012

description:
circulating cells in lysis buffer
same sample as GSM1253401


title: Brx53_CL2_010313

description:
circulating cells in lysis buffer
same sample as GSM1253375


title: H3118 shCtl, biological rep2

status: Public on Apr 18 2018

city: Gainesville

first: Lizi

last: Wu

state: FL

address: 2033 Mowry Road

institute: University of Florida

description:
W4_shCtl
Gene expression data of control H3118 cells.

hyb_protocol: Following fragmentation, sscDNA were hybridized for 16 hr at 45C on Affymetrix Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner.

data_processing: The data were normalized using SST-RMA normalization approach with Affymetrix Expression Console.

source_name: human mucoepidermoid carcinoma cell line derived from parotid, scrambled shRNA control

label_protocol: Biotinylated sscDNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA.

growth_protocol: Cells were grown in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% inactivated fetal bovine serum at 37°C under 5% CO2.

extract_protocol: RNA was isolated with the Trizol Reagent (Invitrogen) and purified by the Qiagen Column with in column DNase digestion.

treatment_protocol: shCtl: control, and shLINC00473 knock down.

tag: cell line

value: mucoepidermoid carcinoma cell line

tag: shRNA

value: scrambled control


title: Brx66_1_012913

description: circulating cells in lysis buffer


title: Brx52_SC2_020413

description:
circulating cells in lysis buffer
same sample as GSM1253379


title: Brx52_SC1_020413

description:
circulating cells in lysis buffer
same sample as GSM1253392


title: H3118 shLnc473 4A, biological rep2

description:
W6_shLnc473_4A
Gene expression data of LINC00473-depleted H3118 cells.

source_name: human mucoepidermoid carcinoma cell line derived from parotid, LINC00473 knock-down


title: H3118 shLnc473 4A, biological rep1

description:
W3_shLnc473_4A
Gene expression data of LINC00473-depleted H3118 cells.


title: Brx52_CL1_020413

description:
circulating cells in lysis buffer
same sample as GSM1253394


title: Brx50_2_031113

description: circulating cells in lysis buffer


title: Brx52_CL5_020413

description:
circulating cells in lysis buffer
same sample as GSM1253393


title: Brx52_CL2_020413

description:
circulating cells in lysis buffer
same sample as GSM1253395


title: Brx10_1_SC2_041113

description: circulating cells in lysis buffer


title: BrTr12_SC_022813

description: circulating cells in lysis buffer


title: Brx61_1_SC4_032012

description:
circulating cells in lysis buffer
same sample as GSM1253403


title: H3118 shCtl, biological rep1

description:
W1_shCtl
Gene expression data of control H3118 cells.


title: BR29_1_012913

description: circulating cells in lysis buffer


title: BR29_2_012913

description: circulating cells in lysis buffer


title: BrTr08_1_CL1_012913

description: circulating cells in lysis buffer


title: BrTr08_1_CL2_012913

description:
circulating cells in lysis buffer
same sample as GSM1253381


title: BR21_1_SC3_052113

description: circulating cells in lysis buffer


title: BR21_1_SC1_052113

description: circulating cells in lysis buffer


title: BR21_1_SC2_052113

description: circulating cells in lysis buffer


title: Brx10_1_SC3_041113

description: circulating cells in lysis buffer


title: 1772125091_H10

status: Public on Dec 12 2017

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: Processed data file: C1_expression_data.tab.gz

data_processing:
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e., Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA synthesis.
Genome_build: UCSC mm10 (GRCm38)
Supplementary_files_format_and_content: C1_expression_data.tab: Tab-delimited text file of total number of detected mRNA molecules from each gene in each cell.
Supplementary_files_format_and_content: datasetB_cellid_to_sampleid.txt: Tab-delimited text file shows the mapping from the sample IDs used in the referenced publication to the cell IDs in this dataset.

source_name: dentate gyrus, CD-1, postnatal day 16

growth_protocol: Male and female wild type CD-1 mice (Charles River), as well as hGFAP-GFP reporter mice (Zhuo et al., Developmental Biology, 187(1), p36, 1997), between postnatal days 8 and 68 were used.

extract_protocol:
Mice were sacrificed by an overdose of Isoflurane or Ketamin/Xylazine, followed by perfusion through the left ventricle with artificial cerebrospinal fluid, equilibrated in 95%O2/5%CO2 on ice or 4°C. The dentate gyrus was then microdissected from 300 μ m vibratome brain sections. Single-cell suspensions were prepared using the Papain kit (Worthington) with 25-35min enzymatic digestion followed by manual trituration using a BSA-coated p1000 pipette or fire-polished Pasteur pipettes. For hGFAP-GFP mice, GFP-positive cells were sorted on a BD FACSAria II into oxygenated aCSF at 4°C. Cells were loaded at 500-800 cells/μ l at 4° on the C1 Fluidigm medium-sized chip.
Lysis mix, RT mix and PCR mix (described in Islam et al., Nat Methods. 2014 Feb;11(2):163-6) were added to the chip. The plate was placed in the Fluidigm C1 instrument and the 'mRNA Seq: RT + Amp (1772x/1773x)' script was executed, and included lysis, reverse transcription and 21 cycles of PCR. The amplified cDNA was harvested in a total of 13 μL C1 Harvesting Reagent. Amplified cDNA was simultaneously fragmented and barcoded by tagmentation using Tn5 DNA transposase to transfer adaptors to the target DNA as described (Ibid.). 100 µl Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were washed in 2x BWT (10 mM Tris-HCl, pH 7.5, 1 mM EDTA, 2 M NaCl, 0.02% Tween-20) and resuspended in 2 ml 2x BWT. Twenty microliters of beads were added to each well and incubated at room temperature for 15 min. All fractions were pooled, the beads were immobilized and the supernatant removed. The beads were resuspended in 100 μL TNT (20 mM Tris, pH 7.5, 50 mM NaCl, 0.02% Tween), washed in 100 μL Qiagen QIAquick PB, and twice in 100 μL TNT. The beads were resuspended in 100 μL restriction mix (1x NEB CutSmart, 0.4 U/μL PvuI-HF enzyme), designed to cleave 3' fragments carrying a PvuI recognition site. The mix was incubated for 1 h at 37 °C, then washed three times in TNT. Finally, to elute DNA, beads were resuspend in 30 µL ddH2O and incubated 10 minutes at 70°C. Beads were then immediately bound to magnet and the supernatant was collected. To remove short fragments, Ampure beads (Beckman Coulter) were used at 1.8x volume and eluted in 30 µL.

tag: strain/background

tag: genotype/variation

value: wild type

tag: hgfap-gfp mrna detected (0=no, 1=yes)

tag: Sex

value: Not determined

tag: postnatal day

value: dentate gyrus

tag: cell cluster

value: Granule-immature


title: 1772125091_G09


title: 1772125091_H04


title: 1772125091_H02


title: 1772125091_H01


title: 1772125091_G12


title: 1772125091_H06

value: Neuroblast


title: Brx10_1_SC1_041113

description: circulating cells in lysis buffer

tag: cell type


title: 1772125091_H11


title: 1772125091_H03


title: 1772125091_F10

value: Astrocytes


title: 1772125091_F11


title: 1772125091_G04


title: 1772125091_F06


title: 1772125091_F07


title: 1772125091_E10

value: Granule-mature


title: 1772125091_E08


title: 1772125091_E06


title: 1772125091_E05


title: 1772125091_E01


title: 1772125091_D10


title: 1772125091_D08


title: 1772125091_D06


title: 1772125091_C12


title: 1772125091_D02


title: 1772125091_C04

value: OPC


title: 1772125091_C02


title: 1772125091_B12


title: 1772125091_A11

value: Radial Glia-like


title: 1772125091_B02


title: 1772125091_A04


title: 1772125091_A05


title: 1772125091_A06


title: 1772125091_B11


title: 1772117109_H12

source_name: dentate gyrus, CD-1, postnatal day 12


title: 1772125091_A02


title: 1772125091_B05


title: 1772117109_H07

value: Microglia


title: 1772125091_A08


title: 1772117109_H02


title: 1772117109_G09


title: 1772117109_F11

value: Cajal-Retzius


title: 1772117109_F12


title: 1772117109_H06


title: 1772125091_B10


title: 1772117109_G05


title: 1772117109_H11


title: 1772117109_G11


title: 1772117109_E04

value: Endothelial


title: 1772117109_D11


title: 1772125091_A07


title: 1772117109_H05


title: 1772117109_G08

value: nIPC


title: 1772117109_F07


title: 1772117109_D06


title: 1772117109_C11


title: 1772117109_D04


title: 1772117109_B06


title: 1772117109_C06


title: 1772117109_B05


title: 1772117109_B04


title: 1772117109_C04


title: 1772117109_D12


title: 1772117109_B03


title: 1772117109_E05


title: 1772117109_A08


title: 1772117109_A10


title: 1772117109_C09


title: 1772117109_B02


title: 1772117109_F02


title: 1772117094_H12

value: PVM


title: 1772117109_A06


title: 1772117109_A01


title: 1772117109_D10


title: 1772117094_H08


title: 1772117094_H04


title: 1772117109_C05


title: 1772117109_C10


title: 1772117094_G10


title: 1772117094_G09


title: 1772117109_A11


title: 1772117094_G01


title: 1772117094_G06


title: 1772117094_G07


title: 1772117094_F05


title: 1772117094_G03


title: 1772117094_E12


title: 1772117094_G04

value: OL


title: 1772117094_F02


title: 1772117109_C08


title: 1772117094_D06


title: 1772117094_D03


title: 1772117094_D12


title: 1772117094_E10


title: 1772117094_E07


title: 1772117094_C04


title: 1772117094_E06


title: 1772117094_D05


title: 1772117094_C02


title: 1772117094_C11

value: VLMC


title: 1772117094_C12


title: 1772117094_B09


title: 1772117094_B04


title: 1772117094_A09


title: 1772117094_A11


title: 1772117094_A08


title: 1772117094_B02


title: 1772117094_A07


title: 1772117094_A06


title: 1772117093_H03


title: 1772117093_H11


title: 1772117094_D02


title: 1772117093_G07


title: 1772117093_G05


title: 1772117093_H12


title: 1772117093_F12


title: 1772117093_F11


title: 1772117093_D11


title: 1772117093_E11


title: 1772117093_F05


title: 1772117093_H05


title: 1772117093_H04


title: 1772117093_E06


title: 1772117093_G10


title: 1772117093_F01


title: 1772117093_D10


title: 1772117093_F03


title: 1772117093_B10


title: 1772117093_D01


title: 1772117093_C12


title: 1772117093_B08


title: 1772117094_F03


title: 1772117093_B03


title: 1772117093_C10


title: 1772117093_B01


title: 1772117093_A02


title: 1772117092_H12


title: 1772117093_E04


title: 1772117093_A01


title: 1772117093_D04


title: 1772117092_H04


title: 1772117092_H01


title: 1772117092_H02


title: 1772117092_G06


title: 1772117092_G10


title: 1772117092_G12


title: 1772117092_F07


title: 1772117092_F10


title: 1772117092_F06


title: 1772117093_A07


title: 1772117092_E10


title: 1772117092_E03


title: 1772117092_C12


title: 1772117092_C04


title: 1772117092_C06


title: 1772117092_B12


title: 1772117092_E06


title: 1772117092_A11


title: 1772117092_A06


title: 1772117092_B04


title: 1772117092_C09


title: 1772117092_D06


title: 1772117092_B11


title: 1772117092_H06


title: 1772117092_A03


title: 1772117092_G09


title: 1772117092_H08


title: 1772117092_F03


title: 1772117092_A02


title: 1772117092_A01


title: 1772117091_G01

source_name: dentate gyrus, CD-1, postnatal day 14


title: 1772117091_G10


title: 1772117091_G11


title: 1772117091_G12


title: 1772117091_H04


title: 1772117091_G03


title: 1772117091_F10


title: 1772117091_F06


title: 1772117091_H01


title: 1772117092_C10


title: 1772117091_E12


title: 1772117091_E09


title: 1772117091_E10


title: 1772117091_F01


title: 1772117091_F02


title: 1772117091_E11


title: 1772117091_D06


title: 1772117091_D05


title: 1772117091_D12


title: 1772117091_F03


title: 1772117091_C12


title: 1772117091_E06


title: 1772117091_F05


title: 1772117091_C01


title: 1772117091_C04


title: 1772117091_C06


title: 1772117091_B06


title: 1772117091_B03


title: 1772117091_A04


title: 1772117091_B11


title: 1772117091_A07


title: 1772117090_H12


title: 1772117091_B02


title: 1772117091_B05


title: 1772117091_D08


title: 1772117091_E03


title: 1772117090_H06


title: 1772117090_G05


title: 1772117090_G09


title: 1772117090_G04


title: 1772117090_G01


title: 1772117090_G03


title: 1772117090_G12


title: 1772117090_F04


title: 1772117090_H02


title: 1772117090_H05


title: 1772117090_E04


title: 1772117090_E10


title: 1772117090_E01


title: 1772117090_C03


title: 1772117090_F02


title: 1772117090_D04


title: 1772117090_C05


title: 1772117090_E03


title: 1772117090_A07


title: 1772117090_B06


title: 1772117090_F06


title: 1772117090_A11


title: 1772117090_D10


title: 1772117090_D12


title: 1772117090_H09


title: 1772117090_A03


title: 1772117090_B07


title: 1772117089_H04


title: 1772117089_H12


title: 1772117090_E02


title: 1772117089_H10


title: 1772117090_D07


title: 1772117090_C01


title: 1772117089_H05


title: 1772117089_H08


title: 1772117089_F12


title: 1772117089_G05


title: 1772117089_F09


title: 1772117089_E12


title: 1772117089_E05


title: 1772117089_G11


title: 1772117089_F11


title: 1772117089_E06


title: 1772117089_D10


title: 1772117089_F06


title: 1772117089_C10


title: 1772117089_D02


title: 1772117089_F02


title: 1772117089_C09


title: 1772117089_E04


title: 1772117089_C11


title: 1772117089_E10


title: 1772117089_G10


title: 1772117089_D07


title: 1772117089_C06


title: 1772117089_A11


title: 1772117089_A09


title: 1772117089_B01


title: 1772117089_A08


title: 1772117089_B10


title: 1772117089_A06


title: 1772117088_H12


title: 1772117088_H07


title: 1772117089_B08


title: 1772117088_G12


title: 1772117089_A02


title: 1772117088_H01


title: 1772117088_F02


title: 1772117088_F11


title: 1772117088_G11


title: 1772117088_E07


title: 1772117088_F01


title: 1772117088_D05


title: 1772117088_D06


title: 1772117088_D04


title: 1772117088_G02


title: 1772117088_D03


title: 1772117088_C04


title: 1772117089_C04


title: 1772117088_C11


title: 1772117088_B09


title: 1772117087_H10


title: 1772117088_B10


title: 1772117087_H01


title: 1772117087_G11


title: 1772117087_G12


title: 1772117088_F04


title: 1772117109_A12


title: 1772117087_H06


title: 1772117088_A08


title: 1772117088_C10


title: 1772117087_H11


title: 1772117087_G03


title: 1772117087_G09


title: 1772117087_F12


title: 1772117087_G08


title: 1772117087_G04


title: 1772117087_G05


title: 1772117087_F10


title: 1772117087_F06


title: 1772117087_F04


title: 1772117087_F07


title: 1772117086_H02


title: 1772117087_C08


title: 1772117087_D10


title: 1772117087_C10


title: 1772117087_B12


title: 1772117087_C04


title: 1772117087_D12


title: 1772117087_E01


title: 1772117087_E03


title: 1772117087_E11


title: 1772117087_B06


title: 1772117087_A02


title: 1772117087_E05


title: 1772117087_D04


title: 1772117087_C12


title: 1772117087_C11


title: 1772117087_B10


title: 1772117087_B11


title: 1772117087_F05


title: 1772117087_B04


title: 1772117087_A12


title: 1772117087_A03


title: 1772117087_A08


title: 1772117086_H11


title: 1772117086_G05


title: 1772117086_H09


title: 1772117086_G04


title: 1772117086_F07


title: 1772117086_G07


title: 1772117086_G01


title: 1772117086_G02


title: 1772117086_F11


title: 1772117086_H06


title: 1772117086_F02


title: 1772117086_E03


title: 1772117086_H07


title: 1772117086_G08


title: 1772117086_G11


title: 1772117086_G10


title: 1772117086_G09


title: 1772117086_D09


title: 1772117086_G03


title: 1772117086_E01


title: 1772117086_E10


title: 1772117086_E12


title: 1772117087_D03


title: 1772117087_G02


title: 1772117086_D02


title: 1772117086_C12


title: 1772117086_B03


title: 1772117086_D05


title: 1772117086_B05


title: 1772117086_A06


title: 1772117020_H10

source_name: dentate gyrus, CD-1, postnatal day 18


title: 1772117086_D06


title: 1772117020_H11


title: 1772117086_B02


title: 1772117086_C10


title: 1772117086_A09


title: 1772117086_B10


title: 1772117020_H12


title: 1772117020_G11


title: 1772117020_H09


title: 1772117020_H02


title: 1772117020_H06


title: 1772117086_C06


title: 1772117086_C03


title: 1772117020_G10


title: 1772117020_E09


title: 1772117020_E11


title: 1772117086_B04


title: 1772117020_E06


title: 1772117086_A03


title: 1772117020_G04


title: 1772117020_D12


title: 1772117086_C02


title: 1772117020_D06


title: 1772117020_D05


title: 1772117020_D07


title: 1772117020_A03


title: 1772117020_G05


title: 1772117020_B12


title: 1772117020_B09


title: 1772117020_A11


title: 1772117019_H10


title: 1772117019_H04


title: 1772117020_F08


title: 1772117019_H02


title: 1772117019_F11


title: 1772117019_E12


title: 1772117020_E01


title: 1772117020_D09


title: 1772117019_C10


title: 1772117019_G04


title: 1772117020_B11


title: 1772117019_B12


title: 1772117019_A12


title: 1772117019_A08


title: 1772117019_E04


title: 1772117019_F08


title: 1772117019_E02


title: 1772117019_H11


title: 1772117019_D07


title: 1772117019_D09


title: 1772117019_D06


title: 1772117017_H10


title: 1772117017_H04


title: 1772117017_F12


title: 1772117017_G04


title: 1772117020_B04


title: 1772117019_D02


title: 1772117019_C06


title: 1772117019_B11


title: 1772117017_E10


title: 1772117017_H12


title: 1772117017_D04


title: 1772117017_E04


title: 1772117017_H11


title: 1772117017_C09


title: 1772117017_C01


title: 1772117017_G03


title: 1772117019_A05


title: 1772117017_H05


title: 1772117017_G12


title: 1772117017_F07


title: 1772117086_D08


title: 1772117017_G01


title: 1772117017_F10


title: 1772117017_A12


title: 1772117017_A11


title: 1772117017_F06


title: 1772117017_E11


title: 1772117019_G05


title: 1772117017_A03


title: 1772117017_C02


title: 1772117016_E03


title: 1772117017_B10


title: 1772117017_B09


title: 1772117017_B05


title: 1772117017_B07


title: 1772117020_A10


title: 1772117017_B04


title: 1772117017_C10


title: 1772117016_D01


title: 1772117017_A02


title: 1772117016_A11


title: 1772117017_A06


title: 1772117019_E08


title: 1772117017_A04


title: 1772099307_G10

source_name: dentate gyrus, CD-1, postnatal day 8


title: 1772117016_G09


title: 1772117016_E02


title: 1772117016_C12


title: 1772117016_D04


title: 1772117016_B07


title: 1772117016_B06


title: 1772117016_B04


title: 1772099307_E12


title: 1772117016_A12


title: 1772117017_A05


title: 1772099307_E08


title: 1772099307_G01


title: 1772099307_E03


title: 1772099307_H06


title: 1772099307_F07


title: 1772099307_F08


title: 1772099307_E05


title: 1772099307_F11


title: 1772099307_F01


title: 1772099307_H03


title: 1772099307_B08


title: 1772099307_G03


title: 1772099307_D06


title: 1772099307_D09


title: 1772099307_E07


title: 1772099307_D03


title: 1772099307_H12


title: 1772099307_B11


title: 1772099307_D02


title: 1772099307_B04


title: 1772099307_B02


title: 1772099307_F10


title: 1772099278_H05

source_name: dentate gyrus, CD-1, postnatal day 10

value: Female


title: 1772099307_A02

value: wild type


title: 1772099307_A05

value: Not determined


title: 1772099307_A10

value: dentate gyrus


title: 1772099278_H09

value: Granule-immature


title: 1772099278_G10


title: 1772099307_A07


title: 1772099278_G06


title: 1772099278_G04


title: 1772099307_C03


title: 1772099278_G05


title: 1772099307_B03


title: 1772099278_F04


title: 1772099278_F09


title: 1772099278_F06


title: 1772099278_E08


title: 1772099278_E02


title: 1772099278_E11


title: 1772099278_E10


title: 1772099278_F01


title: 1772099278_D11


title: 1772099278_D10


title: 1772099278_D08


title: 1772099278_D09


title: 1772099278_D06


title: 1772099278_C09


title: 1772099278_C02


title: 1772099278_C06


title: 1772099278_C03


title: 1772099278_B10


title: 1772099278_B11


title: 1772099278_B08

value: Neuroblast


title: 1772099278_C01

value: Astrocytes


title: 1772099278_B05


title: 1772099278_B01


title: 1772099278_F02

value: Granule-mature


title: 1772099278_A05


title: 1772099277_H02


title: 1772099277_G12


title: 1772099278_A07


title: 1772099278_A06


title: 1772099277_G11


title: 1772099277_H12


title: 1772099277_H05


title: 1772099277_G08


title: 1772099277_G01


title: 1772099277_G03


title: 1772099277_F08


title: 1772099277_F06


title: 1772099277_F11


title: 1772099277_F05


title: 1772099277_F04


title: 1772099277_G10


title: 1772099277_F02


title: 1772099277_E12


title: 1772099277_E06


title: 1772099277_F01


title: 1772099277_D06


title: 1772099277_D09


title: 1772099277_H10


title: 1772099277_D04


title: 1772099277_C11


title: 1772099277_D02


title: 1772099277_C06


title: 1772099277_C10


title: 1772099277_C05


title: 1772099277_C03


title: 1772099277_B10


title: 1772099277_B05


title: 1772099277_B09


title: 1772099275_H04


title: 1772099277_B04


title: 1772099277_A11


title: 1772099275_H07


title: 1772099275_H02


title: 1772099275_G04


title: 1772099277_F03


title: 1772099277_D10


title: 1772099275_G12


title: 1772099275_G10


title: 1772099275_H03


title: 1772099277_A10


title: 1772099275_G02


title: 1772099275_G01


title: 1772099275_F11


title: 1772099275_F07


title: 1772099275_F10


title: 1772099275_D12


title: 1772099275_E08


title: 1772099275_D06


title: 1772099275_E09


title: 1772099275_B02


title: 1772099275_A12


title: 1772099275_A09


title: 1772099275_E05


title: 1772099275_A08


title: 1772099275_A05


title: 1772099274_H11


title: 1772099274_H12


title: 1772099275_E12


title: 1772099274_F11


title: 1772099274_F09


title: 1772099274_H04


title: 1772099274_G06


title: 1772099274_G12


title: 1772099274_H06


title: 1772099274_G05


title: 1772099274_G03


title: 1772099274_F05


title: 1772099274_G04


title: 1772099274_F12


title: 1772099274_H05


title: 1772099275_B03


title: 1772099275_A10


title: 1772099274_E12


title: 1772099274_F01


title: 1772099274_F04


title: 1772099274_E03


title: 1772099274_E04


title: 1772099274_E11


title: 1772099274_E09


title: 1772099274_E02


title: 1772099274_D04


title: 1772099274_D02


title: 1772099274_D05


title: 1772099274_D12


title: 1772099274_C11


title: 1772099274_D11


title: 1772099274_C12


title: 1772099274_C07


title: 1772099274_C01


title: 1772099274_A12


title: 1772099274_C04


title: 1772099274_A05


title: 1772099274_B10


title: 1772099274_E07


title: 1772099274_A08


title: 1772099274_B11


title: 1772099274_A07


title: 1772099274_B04


title: 1772099274_B03


title: 1772099274_B09


title: 1772099257_H12


title: 1772099257_H05


title: 1772099257_H03


title: 1772099257_H06


title: 1772099257_G11


title: 1772099257_G09


title: 1772099257_G08


title: 1772099257_G03


title: 1772099257_F02


title: 1772099257_F11


title: 1772099257_E12


title: 1772099257_F09


title: 1772099257_E06


title: 1772099257_F01


title: 1772099257_E05


title: 1772099257_D06


title: 1772099257_D05


title: 1772099257_D10


title: 1772099257_C06


title: 1772099257_D01


title: 1772099257_C08


title: 1772099257_D02


title: 1772099257_C03


title: 1772099257_B08


title: 1772099257_C01


title: 1772099257_A07


title: 1772099257_D04


title: 1772099257_B12


title: 1772099257_C11


title: 1772099257_A03


title: 1772099256_H10


title: 1772099257_C05


title: 1772099257_E01


title: 1772099257_A08


title: 1772099257_C02


title: 1772099257_G04


title: 1772099257_A05


title: 1772099256_H07


title: 1772099256_H05


title: 1772099256_H04


title: 1772099256_G04


title: 1772099256_G05

value: OPC


title: 1772099256_G10


title: 1772099256_F08


title: 1772099256_F07


title: 1772099256_H12


title: 1772099256_F03

value: Radial Glia-like


title: 1772099256_F02


title: 1772099256_F04


title: 1772099256_E06


title: 1772099256_E12


title: 1772099256_E10


title: 1772099256_E09


title: 1772099256_E07


title: 1772099256_D11


title: 1772099256_C08


title: 1772099256_C07


title: 1772099256_D08


title: 1772099256_D02


title: 1772099256_C03


title: 1772099256_G12


title: 1772099256_D07


title: 1772099256_C05


title: 1772099256_D03


title: 1772099256_B09


title: 1772099256_C12


title: 1772099256_C06


title: 1772099256_B08


title: 1772099256_B03


title: 1772099256_A09


title: 1772099256_A08


title: 1772099256_A02


title: 1772099256_A03


title: 1772099256_A01


title: 1772099255_G04


title: 1772099255_G05


title: 1772099255_H06


title: 1772099256_B12


title: 1772099255_F03


title: 1772099256_A11


title: 1772099255_C06


title: 1772099255_D01


title: 1772099255_C10


title: 1772099255_D04


title: 1772099255_B12


title: 1772099255_E03


title: 1772099255_A09


title: 1772099255_C04


title: 1772099255_B07


title: 1772099255_A06


title: 1772099255_D03


title: 1772099218_H12

description:
hGFAP-GFP: human glial fibrillary acidic protein promoter-green fluorescent protein
Processed data file: C1_expression_data.tab.gz

source_name: dentate gyrus, hGFAP-GFP, postnatal day 63

value: hGFAP-GFP

value: Male


title: 1772099255_A02


title: 1772099255_B01


title: 1772099255_H10


title: 1772099255_H07


title: 1772099255_F08


title: 1772099218_G08


title: 1772099218_F12


title: 1772099255_G11


title: 1772099255_E05


title: 1772099218_F06


title: 1772099218_F08


title: 1772099218_F01


title: 1772099218_E03


title: 1772099218_E01


title: 1772099218_D09


title: 1772099218_D07


title: 1772099218_D06


title: 1772099218_H03


title: 1772099218_B03


title: 1772099218_A12


title: 1772099218_D04


title: 1772099218_C08


title: 1772099217_H11


title: 1772099218_B11


title: 1772099217_H03


title: 1772099218_A05


title: 1772099218_A02


title: 1772099217_G04


title: 1772099218_A11

value: Endothelial


title: 1772099217_E10


title: 1772099218_G01


title: 1772099217_D05

value: nIPC


title: 1772099217_D08


title: 1772099215_H10


title: 1772099217_A11


title: 1772099215_G10


title: 1772099215_H04


title: 1772099218_C11


title: 1772099215_G07


title: 1772099215_G03


title: 1772099215_G06


title: 1772099218_A06


title: 1772099215_F05


title: 1772099215_F11


title: 1772099215_F02


title: 1772099215_E02


title: 1772099215_E04


title: 1772099215_C10


title: 1772099215_D11


title: 1772099215_C05


title: 1772099215_C01

value: PVM


title: 1772099215_A11

value: OL


title: 1772099215_B12


title: 1772099215_B06


title: 1772099215_A10


title: 1772099215_A08


title: 1772099215_C07


title: 1772099215_D09


title: 1772099215_H07


title: 1772099215_A07


title: 1772099215_A03


title: 1772099215_A05


title: 1772099215_A04


title: 1772099214_H04


title: 1772099215_B02


title: 1772099214_H02


title: 1772099214_H01


title: 1772099214_F07


title: 1772099214_G03


title: 1772099214_F02


title: 1772099214_E10


title: 1772099214_E12


title: 1772099214_E05


title: 1772099214_E03


title: 1772099214_D12


title: 1772099214_D10


title: 1772099214_D01


title: 1772099214_E01


title: 1772099215_D08


title: 1772099214_C07


title: 1772099214_D11


title: 1772099214_C05


title: 1772099214_B10


title: 1772099214_C11


title: 1772099256_B04


title: 1772099214_B11


title: 1772099214_E09


title: 1772099214_E08


title: 1772099202_H11

source_name: dentate gyrus, CD-1, postnatal day 68


title: 1772099214_B08


title: 1772099214_A12


title: 1772099214_A10


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title: 1772099202_B01


title: 1772099202_A05


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title: 1772099201_E07


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title: 1772099201_E11


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title: 1772099200_C06


title: 1772099200_D01


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value: Microglia


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value: Female


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value: wild type


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title: 1772099199_B01


title: 1772099199_A07


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source_name: dentate gyrus, CD-1, postnatal day 67


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title: 1772099194_B03


title: 1772099146_E11

source_name: dentate gyrus, hGFAP-GFP, postnatal day 50


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title: 1772099099_B10


title: 1772099099_A11


title: 1772096123_H05

source_name: dentate gyrus, CD-1, postnatal day 25


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title: 1772096123_H03


title: 1772099099_A01


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value: VLMC


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value: dentate gyrus


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title: 1772096122_A11


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title: 1772094162_H07

source_name: dentate gyrus, CD-1, postnatal day 20


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title: 1772096120_A12


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value: Cajal-Retzius


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title: 1772096120_A03


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value: Neuroblast


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value: Astrocytes


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value: Granule-mature


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title: 1772094154_G04


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title: 1772094154_F04


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title: 1772094154_D06


title: 1772094154_E11


title: 1772094154_E09

value: OPC


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title: 1772094154_C04


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title: 1772094154_D09


title: 1772094142_E03

source_name: dentate gyrus, CD-1, postnatal day 21


title: 1772094142_G03


title: 1772094142_E04


title: 1772094154_B07


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title: 1772094142_E08


title: 1772094142_D05


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title: 1772094154_A01


title: 1772094141_D12


title: 1772094142_B01


title: 1772094142_B03


title: 1772094142_A12

value: Radial Glia-like


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title: 1772094141_D03


title: 1772094141_H06


title: 1772094142_A07


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title: 1772094142_A01


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title: 1772094141_D11


title: 1772094141_A01


title: 1772094141_A05


title: 1772094141_C02


title: 1772094140_H06

source_name: dentate gyrus, CD-1, postnatal day 28


title: 1772094141_C03


title: 1772094141_B11


title: 1772094141_A12


title: 1772094140_H05


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title: 1772094137_H06


title: 1772094137_H05


title: 1772094138_E09


title: 1772094137_A04


title: 1772094134_H12

source_name: dentate gyrus, CD-1, postnatal day 24


title: 1772094138_D07


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title: 1772094134_G11


title: 1772094134_H03


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title: 1772094132_E07


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title: 1772094132_E02


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title: 1772094132_B02


title: 1772094132_B01


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title: 1772094131_E05


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title: 1772094131_B05


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title: 1772094125_H10

source_name: dentate gyrus, CD-1, postnatal day 22


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title: 1772094125_A06


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title: 1772094125_A04


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title: 1772094125_A09


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title: 1772094124_H04


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title: 1772094124_E11


title: 1772094124_E06


title: 1772094125_C06


title: 1772094124_E07


title: 1772094124_E04


title: 1772094124_E02


title: 1772094124_D07


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title: 1772094124_D04


title: 1772094124_H08


title: 1772094124_D01


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title: 1772094124_C12


title: 1772094124_C06


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title: 1772094124_C01


title: 1772094124_C03


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title: 1772094124_E05


title: 1772094124_E10


title: 1772094124_A03


title: 1772094124_A01


title: 1772094124_A04


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title: 1772094122_G04


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title: 1772094122_G03


title: 1772094122_F03


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title: 1772094124_A05


title: 1772094122_F01


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title: 1772094122_F02


title: 1772094122_E11


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title: 1772094122_E05


title: 1772094122_E04


title: 1772094122_E02


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title: 1772094121_A12


title: 1772094121_B04


title: 1772094121_A08


title: 1772094121_B07


title: 1772094121_A06


title: 1772094121_F08


title: 1772094118_G12

value: Not determined


title: 1772094118_F04


title: 1772094118_E10


title: 1772094118_D06


title: 1772094118_E01


title: 1772094118_B05


title: 1772094118_C05


title: 1772094121_E02


title: 1772094118_B04


title: 1772094116_H07


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title: 1772094116_E01


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title: 1772094116_B11


title: 1772094116_B04


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title: 1772094116_A12


title: 1772094116_A10


title: 1772094116_A07


title: 1772094116_A11


title: 1772094116_A03


title: 1772094116_A02


title: 1772094114_H11


title: 1772094114_H12


title: 1772094114_G09


title: 1772094114_H01


title: 1772094114_H04


title: 1772094114_F05


title: 1772094114_E07


title: 1772094114_H02


title: 1772094114_G10


title: 1772094114_G07


title: 1772094114_H05


title: 1772094114_E02


title: 1772094114_E04


title: 1772094114_E11


title: 1772094114_D12


title: 1772094114_D08


title: 1772094114_D11


title: 1772094114_D02


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title: 1772094114_C07


title: 1772094114_C06


title: 1772094114_E12


title: 1772094114_B10


title: 1772094114_C01


title: 1772094114_B11


title: 1772094114_G05


title: 1772094114_F09


title: 1772094114_B08


title: 1772094114_E05


title: 1772094114_A07


title: 1772094114_A08


title: 1772094114_B07


title: 1772094111_H08

value: Male


title: 1772094114_B05


title: 1772094111_H05


title: 1772094124_G02


title: 1772094111_F12


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title: 1772094111_H04


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title: 1772094111_A09


title: 1772094111_A10


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title: 1772094111_F07


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title: 1772094110_G05


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title: 1772094111_E03


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title: 1772094110_F06


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title: 1772094110_E10


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title: 1772094110_G09


title: 1772094110_C03


title: 1772094110_C01


title: 1772094110_B11


title: 1772094110_B05

value: Endothelial


title: 1772094110_B08


title: 1772094110_B12


title: 1772094110_A07


title: 1772094110_A10


title: 1772094110_B04


title: 1772094110_A09


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title: 1772094108_A03


title: 1772094110_A01


title: 1772094108_A11


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title: 1772094108_A01


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title: 1772092319_A06


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title: 1772092314_F04


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title: 1772092314_D04

value: nIPC


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title: 1772092314_A06


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title: 1772092313_G06


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title: 1772092314_C11


title: 1772092313_A11


title: 1772092314_A08


title: 1772092313_H08


title: 1772092307_H12

source_name: dentate gyrus, CD-1, postnatal day 23


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title: 1772092305_A11


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title: 1772092293_D04


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title: 1772092293_D02


title: 1772092293_C01

value: PVM


title: 1772092293_B09


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