title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F4_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_G10_AD006_indexed

status: Public on Aug 22 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

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

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

tag: brain region

value: ACA,PL,ILA

tag: Sex

value: male

tag: age

tag: strain


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F4_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F3_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F4_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F4_AD002_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F3_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F3_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F4_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_G10_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F3_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F3_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F2_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F3_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F3_AD002_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F3_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F2_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F1_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F1_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F2_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F2_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F2_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F2_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F2_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F1_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F1_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F1_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F4_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F1_AD002_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F2_AD002_indexed


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title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_H5_AD002_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F11_AD006_indexed


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title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F11_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F10_AD010_indexed


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title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F11_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F11_AD002_indexed


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title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F10_AD008_indexed


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title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E7_AD007_indexed


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title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E5_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E6_AD002_indexed


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title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E5_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_F11_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E4_AD006_indexed


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title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E4_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E3_AD012_indexed


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title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E3_AD002_indexed


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title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E6_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E1_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E1_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E1_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E12_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E12_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E12_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E11_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E1_AD008_indexed


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title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E1_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D9_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E11_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E11_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E11_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E11_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E10_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E10_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E11_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E11_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D9_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E12_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D8_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E10_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E10_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D8_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D9_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E10_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D9_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D9_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D8_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_E11_AD002_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D8_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D8_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D8_AD002_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D6_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D8_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D9_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D6_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D6_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D6_AD002_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D5_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D6_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D6_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D6_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D6_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D8_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D3_AD012_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D5_AD007_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D5_AD004_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D3_AD008_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D5_AD006_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D3_AD010_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_D5_AD001_indexed


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title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_B4_AD002_indexed


title: BL-CAP-C F123 CTCF-AID POLII G5 rep2

city: Farmington

first: Youzhi

last: Cheng

state: Connecticut

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

data_processing:
Library strategy: BL-CAP-C
CAP-C, BL-CAP-C, in-situ Hi-C and PLAC-seq: Each read end sequenced from the proximity ligated libraries was aligned independently to either the mm10, hg19 or dm3 reference genome using BWA-MEM (v 0.7.12). Singletons and chimeric reads were removed. PCR duplicates, unligated reads and reads with a contact distance less than 1Kb were also filtered. PCR duplicates were removed using Picard Tools (v 2.2.2). Unligated reads were defined as both read ends mapping onto the same MboI fragment. A pre-formatted text file was prepared before converting it into a .hic format file with the following resolutions (0.5 Kb, 1 Kb, 2 Kb, 5 Kb, 10 Kb, 25 Kb, 40 Kb, 50 Kb, 100 Kb, 250 Kb, 500 Kb, 1 Mb and 2.5 Mb). Finally, a MAPQ>=1 and MAPQ>=30 .hic file was then generated for each sample. To generate a CAP-C merge file, all G3, G5 and G7 primary and replicated libraries in the pre-formatted text file were concatenated and merged-sorted before using Juicer Tools (v 0.7.0) to convert it into a .hic formatted file.
BL-CAP-C: For DNase I fragmentation-based libraries, we have additional pre-processing steps to be performed prior to the instructions listed in the CAP-C data processing section listed above. We first used SeqPrep to merge overlapping read pairs (2×150 bp). For the resulting merged and unmerged read pairs, cutadapt was used to trim the bridge linker adaptor (ACGCGATATCTTATCTGACT, both forward and reverse-complementary) off the read from the 5’ (-g) and 3’ (-a) direction. Up to 1 adaptor count per read (-n) was used, and a minimum overlap length of 10 threshold (--overlap) between the linker and read was used. Only read pairs where the length of at least one read was too short (<15bp) or merged read pairs that failed to possess a linker were removed (Supplementary Table 2). Because DNase I was used to fragment BL-CAP-C datasets, no restriction cut site annotation files was done to annotate the paired reads.
CAP-C, BL-CAP-C and in-situ Hi-C: Compartments were called using the Eigenvector module of Juicer (v 0.7.0). Peaks/Loops were called using HiCCUPs. Domains were called using Arrowhead. Strength around the ends of the domain boundary or a region of interest was measured by computing the values of the directionality index metric. Aggregate Peak Analysis (APA) was performed on low-resolution contact maps using the APA module of Juicer.
ChIP-seq: ChIP-seq libraries were aligned to the mm10 or hg19 reference genome using BWA-MEM (v 0.7.12). PCR duplicates were removed using Picard Tools (v 2.2.2). Peak calling was performed using MACS2 (Zhang et al.) with both treated and control BAM files, or just the IP sample alone using the following parameters: -q 0.05 –f BAM (–g mm | -g hs). We used bedtools (v 2.27) to create bedGraph files of depth-normalized RPM or FPM values before converting them to bigWig files using UCSC bedGraphToBigWig.
Genome_build: mm10,hg19,dm3
Supplementary_files_format_and_content: Merged primary and replicate samples are labeled with a B0* instead of an S0* or R0*.

source_name: mouse embryonic stem cells

growth_protocol: F123 mouse embryonic stem cells were grown on gamma-irradiated mouse embryonic fibroblast cells under standard conditions (85% High Glucose DMEM, 15% Knockout Serum Replacement, 0.1 mM non-essential amino acids, 0.1 mM β-mercaptoethanol, 1 mM Glutamine, LIF 500U/mL, +P/S). Before harvesting for CAP-C; ChIP-Seq; PLAC-Seq or in-situ Hi-C, F123 mESCs were passaged onto feeder free 0.2% gelatin coated plates for at least 2 passages to rid the culture of feeder cells.

extract_protocol:
For all CAP-C experiment, after dendrimer crosslinking, DNA bound protein was striped away by proteinase K and DNA was extracted by ethanol precopitation.
DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment ( exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 11 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Cells were treated with 1uM flavopiridol for 6-8 hours before harvesting

tag: cell type

value: embyonic stem cells

tag: cell line

tag: chip antibody


title: BL-CAP-C F123 Triptolide

treatment_protocol: Cells were treated with 1 µM triptolide for 6-8 hours before harvesting


title: BL-CAP-C F123 Hexanediol

treatment_protocol: Cells were treated with of 5% (v/v) 1,6-hexanediol at room temperature for 10 minbefore harvesting


title: BL-CAP-C F123 (Native) G7 rep1


title: BL-CAP-C F123 CTCF-AID KO G5 rep1

treatment_protocol: Cells were grown in medium containing 500 uM auxin to deplete CTCF for 48 hours. Medium with auxin was changed every 24 hours.


title: BL-CAP-C F123 (Native) G9 rep1


title: single-cell RNA-seq_sample #2

city: Heidelberg

first: Ana

last: Martin-Villalba

address: Im Neuenheimer Feld 280

department: Molecular Neurobiology

country: Germany

institute: German Cancer Research Center

description: pool of two mice

library_source: transcriptomic

data_processing:
Read pseudoalignment to mm10 genome and mRNA quantification with kallisto|bustools 0.24.4
Filtering, dimensionality reduction and clustering of single cell transcriptomes with Scanpy 1.5.1
Genome_build: mm10
Supplementary_files_format_and_content: matrix with raw expression counts for every gene and every cell

molecule: polyA RNA

source_name: ventricular-subventricular zone, striatum, rostral migratory stream, olfactory bulb

extract_protocol:
After 5 weeks of chase time, the mice were sacrificed and the ventricular-subventricular zone (v-SVZ), striatum, rostral migratory stream and olfactory bulb was isolated. The latter three tissues were pooled as a single tube and were named Rest of the Brain (RoB). From these tissues a single cell suspension was prepared. From the v-SVZ the cells sorted were eYFP+ (O4/CD45/Ter119 negative, eYFP positive) and, from the eYFP negative cells, only Glast+ cells. From the RoB only eYFP+ cells were sorted. 2 TiCY mice were pooled for each sorting day. All the cells were sorted in a volume of 50 μl of Fetal Calf Serum (FSC) 10% in PBS, from which 45 μl were used for loading the Chromium Next GEM Chip G.
One library per each sorting day was prepared by following the manufacturer’s protocol (Chromium Next GEM Single Cell 3’ v3.1) and sequenced on a NovaSeq 6K PE 100 S1.

treatment_protocol: Three months old TiCY mice were stereotactically injected into the lateral ventricle with 10^9 vg of the AAV1_P5_Cre capsid.

value: 4 months

tag: tissue

value: brain


title: BL-CAP-C F123 (Native) G5 rep1


title: BL-CAP-C F123 CTCF-AID KO-POLII G5 rep2

treatment_protocol: Cells were grown in medium containing 500 uM auxin to deplete CTCF for 48 hours. Medium with auxin was changed every 24 hours. 6-8 hours before havesting, cells were treated with 1uM flavopiridol for 6-8 hours.


title: BL-CAP-C F123 CTCF-AID KO G5 rep2


title: single-cell RNA-seq_sample #1

description: pool of two mice

value: ventricular-subventricular zone, striatum, rostral migratory stream, olfactory bulb


title: BL-CAP-C F123 CTCF-AID POLII G5 rep1


title: DNaseHiC F123 rep2


title: DNaseHiC F123 rep1


title: BL-CAP-C F123 CTCF-AID KO-POLII G5 rep1


title: BL-CAP-C F123 CTCF-AID WT G5 rep2


title: BL-CAP-C F123 CTCF-AID WT G5 rep1


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_B4_AD006_indexed


title: BL-CAP-C F123 G7 rep2


title: BL-CAP-C F123 G7 rep1


title: BL-CAP-C F123 G3 rep1


title: BL-CAP-C F123 G5 rep1


title: BL-CAP-C F123 G5 rep2


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_F2_AD006_indexed

city: Bethesda

first: GEO

last: admin

state: MD

address: 9000 Rockville Pike

institute: NCBI/NLM/NIH

value: AON


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_E5_AD001_indexed


title: 180309_CEMBA_mm_P56_P63_4A_CEMBA180205_4A_1_CEMBA180205_4A_2_B6_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_1_CEMBA180208_1C_2_B3_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_1_CEMBA180208_1C_2_E2_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H9_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H9_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H9_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H9_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H8_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H9_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H9_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H9_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H8_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H8_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_1_CEMBA180208_1C_2_A10_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H8_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H8_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H7_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H7_AD008_indexed


title: BL-CAP-C F123 G3 rep2


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H8_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_F2_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H8_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H7_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H7_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_1_CEMBA180208_1C_2_A5_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H7_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H7_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H7_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H6_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H9_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H6_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H6_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H5_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H5_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H7_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H6_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H5_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H6_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H5_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H5_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H5_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H6_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H4_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H4_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H4_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H4_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H5_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H4_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H3_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H4_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H4_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H3_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H3_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H3_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H4_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H3_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H2_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H2_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H2_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H3_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H2_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H2_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H3_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H2_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H12_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H1_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H1_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H2_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H1_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H1_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H1_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H1_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H3_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H2_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H1_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H11_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H10_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H10_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H12_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H11_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H11_AD006_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H11_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H11_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H11_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H6_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H10_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H10_AD008_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H10_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H11_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H11_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H10_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_G9_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_G9_AD004_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H12_AD010_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_G9_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H10_AD001_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_G9_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_G8_AD002_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_H10_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_G8_AD007_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_G8_AD012_indexed


title: 180320_CEMBA_mm_P56_P63_1C_CEMBA180208_1C_3_CEMBA180208_1C_4_G8_AD010_indexed


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