title: Pregnancy total epithelial cell 61


title: Pregnancy total epithelial cell 66

status: Public on Nov 20 2017

type: SRA

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

library_source: transcriptomic

data_processing:
Reads were aligned to the mouse genome using Subread version 1.4.6
Read counts were summarized by Entrez Gene ID using Rsubread's featureCounts function and Rsubread's built-in NCBI annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

molecule: total RNA

organism: Mus musculus

source_name: mammary gland

extract_protocol:
Freshly sorted cells were submitted to a Fluidigm C1 System machine for single cell capture and cDNA synthesis.
Libraries were prepared using the Nextera XT kit and sequencing was carried out on an Illumina Nextseq 500 using standard Illumina protocols.

tag: strain

value: FVB/NJ

tag: animal status

value: Pregnancy

tag: cell source

value: Total epithelium


title: Pregnancy total epithelial cell 56


title: Pregnancy total epithelial cell 57


title: Pregnancy total epithelial cell 60


title: Pregnancy total epithelial cell 54


title: Pregnancy total epithelial cell 52


title: Pregnancy total epithelial cell 53


title: Pregnancy total epithelial cell 74


title: Pregnancy total epithelial cell 49


title: Pregnancy total epithelial cell 75


title: Pregnancy total epithelial cell 51


title: Pregnancy total epithelial cell 50


title: Pregnancy total epithelial cell 48


title: Pregnancy total epithelial cell 47


title: Pregnancy total epithelial cell 41


title: Pregnancy total epithelial cell 46


title: Pregnancy total epithelial cell 58


title: Pregnancy total epithelial cell 38


title: Pregnancy total epithelial cell 43


title: Pregnancy total epithelial cell 40


title: Pregnancy total epithelial cell 55


title: Pregnancy total epithelial cell 44


title: Pregnancy total epithelial cell 39


title: Pregnancy total epithelial cell 34


title: Pregnancy total epithelial cell 36


title: Pregnancy total epithelial cell 32


title: Pregnancy total epithelial cell 35


title: Pregnancy total epithelial cell 33


title: Pregnancy total epithelial cell 45


title: Pregnancy total epithelial cell 30


title: Pregnancy total epithelial cell 28


title: Pregnancy total epithelial cell 37


title: Pregnancy total epithelial cell 29


title: Pregnancy total epithelial cell 27


title: Pregnancy total epithelial cell 26


title: Pregnancy total epithelial cell 25


title: Pregnancy total epithelial cell 24


title: Pregnancy total epithelial cell 31


title: Pregnancy total epithelial cell 22


title: Pregnancy total epithelial cell 23


title: Pregnancy total epithelial cell 42


title: Pregnancy total epithelial cell 59


title: Pregnancy total epithelial cell 21


title: Pregnancy total epithelial cell 20


title: Pregnancy total epithelial cell 18


title: Pregnancy total epithelial cell 15


title: Pregnancy total epithelial cell 16


title: Pregnancy total epithelial cell 13


title: Pregnancy total epithelial cell 17


title: Pregnancy total epithelial cell 19


title: Pregnancy total epithelial cell 14


title: Pregnancy total epithelial cell 11


title: Pregnancy total epithelial cell 12


title: Pregnancy total epithelial cell 9


title: Pregnancy total epithelial cell 7


title: Pregnancy total epithelial cell 8


title: Pregnancy total epithelial cell 10


title: Pregnancy total epithelial cell 5


title: Pregnancy total epithelial cell 6


title: Pregnancy total epithelial cell 2


title: Pregnancy total epithelial cell 3


title: Pregnancy total epithelial cell 1


title: Adult basal cell 112

value: Adult

value: Basal


title: Adult basal cell 110


title: Adult basal cell 108


title: Adult basal cell 111


title: Adult basal cell 109


title: Adult basal cell 107


title: Adult basal cell 106


title: Adult basal cell 105


title: Adult basal cell 104


title: Adult basal cell 101


title: Adult basal cell 103


title: Adult basal cell 102


title: Adult basal cell 97


title: Adult basal cell 98


title: Adult basal cell 99


title: Adult basal cell 95


title: Adult basal cell 94


title: Adult basal cell 93


title: Adult basal cell 91


title: Pregnancy total epithelial cell 4


title: Adult basal cell 96


title: Adult basal cell 89


title: Adult basal cell 92


title: Adult basal cell 88


title: Adult basal cell 86


title: Adult basal cell 85


title: Adult basal cell 84


title: Adult basal cell 87


title: Adult basal cell 82


title: Adult basal cell 81


title: Adult basal cell 80


title: Adult basal cell 79


title: Adult basal cell 78


title: Adult basal cell 77


title: Adult basal cell 100


title: Adult basal cell 75


title: Adult basal cell 76


title: Adult basal cell 73


title: Adult basal cell 70


title: Adult basal cell 74


title: Adult basal cell 72


title: Adult basal cell 69


title: Adult basal cell 71


title: Adult basal cell 90


title: Adult basal cell 68


title: Adult basal cell 67


title: Adult basal cell 66


title: Adult basal cell 64


title: Adult basal cell 62


title: Adult basal cell 65


title: Adult basal cell 63


title: Adult basal cell 83


title: Adult basal cell 60


title: Adult basal cell 61


title: Adult basal cell 58


title: Adult basal cell 57


title: Adult basal cell 56


title: Adult basal cell 59


title: Adult basal cell 54


title: Adult basal cell 55


title: Adult basal cell 52


title: Adult basal cell 51


title: Adult basal cell 50


title: Adult basal cell 49


title: Adult basal cell 47


title: Adult basal cell 48


title: Adult basal cell 44


title: Adult basal cell 46


title: Adult basal cell 42


title: Adult basal cell 40


title: Adult basal cell 41


title: Adult basal cell 39


title: Adult basal cell 38


title: Adult basal cell 37


title: Adult basal cell 36


title: Adult basal cell 35


title: Adult basal cell 34


title: Adult basal cell 33


title: Adult basal cell 31


title: Adult basal cell 29


title: Adult basal cell 53


title: Adult basal cell 30


title: Adult basal cell 28


title: Adult basal cell 27


title: Adult basal cell 26


title: Adult basal cell 25


title: Adult basal cell 24


title: Adult basal cell 23


title: Adult basal cell 22


title: Adult basal cell 45


title: Adult basal cell 43


title: Adult basal cell 19


title: Adult basal cell 20


title: Adult basal cell 18


title: Adult basal cell 17


title: Adult basal cell 16


title: Adult basal cell 14


title: Adult basal cell 15


title: Adult basal cell 32


title: Adult basal cell 9


title: Adult basal cell 10


title: Adult basal cell 12


title: Adult basal cell 11


title: Adult basal cell 13


title: Adult basal cell 8


title: Adult basal cell 2


title: Adult basal cell 7


title: Adult basal cell 6


title: Adult basal cell 5


title: Adult basal cell 4


title: Adult luminal cell 43

value: Luminal


title: Adult luminal cell 42


title: Adult basal cell 3


title: Adult basal cell 21


title: Adult luminal cell 39


title: Adult basal cell 1


title: Adult luminal cell 36


title: Adult luminal cell 41


title: Adult luminal cell 40


title: Adult luminal cell 37


title: Adult luminal cell 35


title: Adult luminal cell 38


title: Adult luminal cell 34


title: Adult luminal cell 26


title: Adult luminal cell 33


title: Adult luminal cell 29


title: Adult luminal cell 31


title: Adult luminal cell 32


title: Adult luminal cell 24


title: Adult luminal cell 28


title: Adult luminal cell 27


title: Adult luminal cell 23


title: Adult luminal cell 19


title: Adult luminal cell 21


title: Adult luminal cell 18


title: Adult luminal cell 17


title: Adult luminal cell 25


title: Adult luminal cell 13


title: Adult luminal cell 20


title: Adult luminal cell 14


title: Adult luminal cell 11


title: Adult luminal cell 15


title: Adult luminal cell 8


title: Adult luminal cell 10


title: Adult luminal cell 16


title: Adult luminal cell 12


title: Adult luminal cell 7


title: Adult luminal cell 6


title: Adult luminal cell 30


title: Adult luminal cell 5


title: Adult luminal cell 2


title: Adult luminal cell 1


title: Adult luminal cell 22


title: P2.5, biological replicate 1, single cells, transcriptome 20

city: Shanghai

first: Xianbin

last: Su

address: Dongchuan Road 800

department: Shanghai Center for Systems Biomedicine

country: China

institute: Shanghai Jiao Tong University

data_processing:
bcl2fastq2 Conversion Software 2.15.0.4 (illumina) was used for de-multiplexing and generation of fastq files for each single cell according the unique barcode combinations of Nextera XT Index kit.
The raw reads in fastq format were mapped to the mouse reference genome GRCm38/mm10 via Tophat 2.1.0.
The transcript levels were quantified as fragments per kilobase of exon model per million mapped reads (FPKM) generated by Cufflinks 2.2.1.
The FPKM of ERCC cells are obtained in the same way with ERCC92 reference sequence.
Genome_build: mm10
Supplementary_files_format_and_content: fpkm_tracking file: tab-delimited text files include FPKM values for each sample

molecule: polyA RNA

source_name: P2.5_biological replicate 1_single cells_transcriptome

extract_protocol:
Single cells were captured on a Fluidigm C1 RNA-Seq IFC (10-17 μm), and all capture sites were visually inspected under microscope to select sites where only one cell is captured. SMARTer Ultra Low RNA kit for Illumina (Clontech Laboratories) were used for on chip cell lysis, reverse transcription and cDNA amplification. ERCC Spike-in Mix (Ambion) were used as technical control.
Sequencing libraries were prepared using Nextera XT Kit and Index Kit (illumina) per the vendor’s protocol.

treatment_protocol: Liver cells were prepared from E11.5, E12.5, E13.5, E14.5, E16.5 and E18.5 embryos and P2.5 neonatal mouse. After adult animal were euthanized by CO2, embryos were removed and sibling fetal livers of one litter were isolated, pooled, minced and digested in 0.05% collagenase IV at 37°C for 30 min. The suspensions were filtered through a 40-μm cell strainer to remove un-digested tissues, and the cells were washed twice with RPMI 1640 medium containing 10% FBS.

tag: age

value: Postnatal day 2.5

tag: genotype/variation

value: wild type

tag: tissue

value: Liver


title: P2.5, biological replicate 1, single cells, transcriptome 21


title: P2.5, biological replicate 1, single cells, transcriptome 16


title: P2.5, biological replicate 1, single cells, transcriptome 19


title: P2.5, biological replicate 1, single cells, transcriptome 17


title: P2.5, biological replicate 1, single cells, transcriptome 14


title: P2.5, biological replicate 1, single cells, transcriptome 15


title: Adult luminal cell 9


title: P2.5, biological replicate 1, single cells, transcriptome 13


title: P2.5, biological replicate 1, single cells, transcriptome 11


title: P2.5, biological replicate 1, single cells, transcriptome 5


title: P2.5, biological replicate 1, single cells, transcriptome 9


title: P2.5, biological replicate 1, single cells, transcriptome 7


title: P2.5, biological replicate 1, single cells, transcriptome 6


title: P2.5, biological replicate 1, single cells, transcriptome 8


title: P2.5, biological replicate 1, single cells, transcriptome 10


title: P2.5, biological replicate 1, single cells, transcriptome 12


title: P2.5, biological replicate 1, single cells, transcriptome 2


title: P2.5, biological replicate 1, single cells, transcriptome 3


title: Adult luminal cell 3


title: P2.5, biological replicate 1, single cells, transcriptome 1


title: Adult luminal cell 4


title: P2.5, biological replicate 1, single cells, transcriptome 4


title: Adult epithelial cells

data_processing:
Read alignment and count summarization were performed using CellRanger v1.2.1 using the Illumina BCL files as input.
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx files contain genewise read counts for all cells in a space-efficient matrix market format; genes.tsv files contain Ensembl IDs and gene symbols as tab-delimited text; barcode.tsv files contain the 10X barcodes used to identify cells.

source_name: Mammary gland

extract_protocol:
A 10X Genomics Chromium machine was used for 3,000-5000 single cell capture and cDNA was prepared using the Single Cell 3’ Protocol recommended by the manufacturer.
The 10X Genomics Chromium machine partitions cells into Gel Bead-In-EMulsions (GEMs), where all generated cDNA share a common 10x Genomics barcode but uses a pool of  about 750,000 barcodes to separately index each cell’s transcriptome. The P7 and R2 primers were added during the GEM incubation and the P5, and R1 during library construction via end repair, A-tailing, adaptor ligation and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. The sequencing was carried out on an Illumina Nextseq 500 using parameters recommended by 10X Genomics.

tag: number of cells


title: P2.5, biological replicate 2, single cells, transcriptome 10

source_name: P2.5_biological replicate 2_single cells_transcriptome


title: P2.5, biological replicate 2, single cells, transcriptome 9


title: P2.5, biological replicate 2, single cells, transcriptome 8


title: Adult basal cells

extract_protocol:
A 10X Genomics Chromium machine was used for 3,000-5000 single cell capture and cDNA was prepared using the Single Cell 3’ Protocol recommended by the manufacturer.
The 10X Genomics Chromium machine partitions cells into Gel Bead-In-EMulsions (GEMs), where all generated cDNA share a common 10x Genomics barcode but uses a pool of  about 750,000 barcodes to separately index each cell’s transcriptome. The P7 and R2 primers were added during the GEM incubation and the P5, and R1 during library construction via end repair, A-tailing, adaptor ligation and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. The sequencing was carried out on an Illumina Nextseq 500 with parameters as recommended by 10X Genomics.


title: P2.5, biological replicate 1, single cells, transcriptome 18


title: P2.5, biological replicate 2, single cells, transcriptome 7


title: P2.5, biological replicate 2, single cells, transcriptome 5


title: P2.5, biological replicate 2, single cells, transcriptome 6


title: P2.5, biological replicate 2, single cells, transcriptome 1


title: E18.5, biological replicate 1, single cells, transcriptome 39

source_name: E18.5_biological replicate 1_single cells_transcriptome

value: Embryonic day 18.5


title: P2.5, biological replicate 2, single cells, transcriptome 2


title: P2.5, biological replicate 2, single cells, transcriptome 3


title: E18.5, biological replicate 1, single cells, transcriptome 38


title: E18.5, biological replicate 1, single cells, transcriptome 33


title: E18.5, biological replicate 1, single cells, transcriptome 36


title: E18.5, biological replicate 1, single cells, transcriptome 34


title: E18.5, biological replicate 1, single cells, transcriptome 32


title: E18.5, biological replicate 1, single cells, transcriptome 35


title: E18.5, biological replicate 1, single cells, transcriptome 37


title: E18.5, biological replicate 1, single cells, transcriptome 29


title: E18.5, biological replicate 1, single cells, transcriptome 27


title: E18.5, biological replicate 1, single cells, transcriptome 28


title: E18.5, biological replicate 1, single cells, transcriptome 25


title: E18.5, biological replicate 1, single cells, transcriptome 24


title: E18.5, biological replicate 1, single cells, transcriptome 23


title: E18.5, biological replicate 1, single cells, transcriptome 20


title: E18.5, biological replicate 1, single cells, transcriptome 22


title: E18.5, biological replicate 1, single cells, transcriptome 18


title: E18.5, biological replicate 1, single cells, transcriptome 19


title: E18.5, biological replicate 1, single cells, transcriptome 21


title: P2.5, biological replicate 2, single cells, transcriptome 4


title: E18.5, biological replicate 1, single cells, transcriptome 16


title: E18.5, biological replicate 1, single cells, transcriptome 15


title: E18.5, biological replicate 1, single cells, transcriptome 13


title: E18.5, biological replicate 1, single cells, transcriptome 10


title: E18.5, biological replicate 1, single cells, transcriptome 11


title: E18.5, biological replicate 1, single cells, transcriptome 12


title: E18.5, biological replicate 1, single cells, transcriptome 30


title: E18.5, biological replicate 1, single cells, transcriptome 31


title: E18.5, biological replicate 1, single cells, transcriptome 26


title: E18.5, biological replicate 1, single cells, transcriptome 9


title: E18.5, biological replicate 1, single cells, transcriptome 7


title: E18.5, biological replicate 1, single cells, transcriptome 3


title: E18.5, biological replicate 1, single cells, transcriptome 6


title: E18.5, biological replicate 1, single cells, transcriptome 4


title: E18.5, biological replicate 2, single cells, transcriptome 18

source_name: E18.5_biological replicate 2_single cells_transcriptome


title: E18.5, biological replicate 2, single cells, transcriptome 19


title: E18.5, biological replicate 1, single cells, transcriptome 1


title: E18.5, biological replicate 1, single cells, transcriptome 8


title: E18.5, biological replicate 1, single cells, transcriptome 17


title: E18.5, biological replicate 1, single cells, transcriptome 2


title: E18.5, biological replicate 2, single cells, transcriptome 14


title: E18.5, biological replicate 2, single cells, transcriptome 16


title: E18.5, biological replicate 2, single cells, transcriptome 15


title: E18.5, biological replicate 2, single cells, transcriptome 17


title: E18.5, biological replicate 2, single cells, transcriptome 11


title: E18.5, biological replicate 2, single cells, transcriptome 12


title: E18.5, biological replicate 2, single cells, transcriptome 13


title: E18.5, biological replicate 1, single cells, transcriptome 14


title: E18.5, biological replicate 2, single cells, transcriptome 9


title: E18.5, biological replicate 2, single cells, transcriptome 10


title: E18.5, biological replicate 2, single cells, transcriptome 6


title: E18.5, biological replicate 2, single cells, transcriptome 5


title: E18.5, biological replicate 2, single cells, transcriptome 8


title: E18.5, biological replicate 2, single cells, transcriptome 3


title: E18.5, biological replicate 2, single cells, transcriptome 4


title: E18.5, biological replicate 2, single cells, transcriptome 7


title: E16.5, biological replicate 1, single cells, transcriptome 56

source_name: E16.5_biological replicate 1_single cells_transcriptome

value: Embryonic day 16.5


title: E16.5, biological replicate 1, single cells, transcriptome 50


title: E16.5, biological replicate 1, single cells, transcriptome 53


title: E16.5, biological replicate 1, single cells, transcriptome 54


title: E16.5, biological replicate 1, single cells, transcriptome 55


title: E16.5, biological replicate 1, single cells, transcriptome 51


title: E16.5, biological replicate 1, single cells, transcriptome 48


title: E18.5, biological replicate 1, single cells, transcriptome 5


title: E16.5, biological replicate 1, single cells, transcriptome 47


title: E18.5, biological replicate 2, single cells, transcriptome 2


title: E16.5, biological replicate 1, single cells, transcriptome 46


title: E16.5, biological replicate 1, single cells, transcriptome 43


title: E16.5, biological replicate 1, single cells, transcriptome 39


title: E16.5, biological replicate 1, single cells, transcriptome 44


title: E16.5, biological replicate 1, single cells, transcriptome 38


title: E16.5, biological replicate 1, single cells, transcriptome 42


title: E16.5, biological replicate 1, single cells, transcriptome 40


title: E16.5, biological replicate 1, single cells, transcriptome 41


title: E16.5, biological replicate 1, single cells, transcriptome 37


title: E16.5, biological replicate 1, single cells, transcriptome 36


title: E16.5, biological replicate 1, single cells, transcriptome 34


title: E16.5, biological replicate 1, single cells, transcriptome 32


title: E16.5, biological replicate 1, single cells, transcriptome 33


title: E18.5, biological replicate 2, single cells, transcriptome 1


title: E16.5, biological replicate 1, single cells, transcriptome 52


title: E16.5, biological replicate 1, single cells, transcriptome 49


title: E16.5, biological replicate 1, single cells, transcriptome 29


title: E16.5, biological replicate 1, single cells, transcriptome 28


title: E16.5, biological replicate 1, single cells, transcriptome 45


title: E16.5, biological replicate 1, single cells, transcriptome 26


title: E16.5, biological replicate 1, single cells, transcriptome 27


title: E16.5, biological replicate 1, single cells, transcriptome 20


title: E16.5, biological replicate 1, single cells, transcriptome 24


title: E16.5, biological replicate 1, single cells, transcriptome 23


title: E16.5, biological replicate 1, single cells, transcriptome 22


title: E16.5, biological replicate 1, single cells, transcriptome 25


title: E16.5, biological replicate 1, single cells, transcriptome 21


title: E16.5, biological replicate 1, single cells, transcriptome 19


title: E16.5, biological replicate 1, single cells, transcriptome 31


title: E16.5, biological replicate 1, single cells, transcriptome 17


title: E16.5, biological replicate 1, single cells, transcriptome 18


title: E16.5, biological replicate 1, single cells, transcriptome 16


title: E16.5, biological replicate 1, single cells, transcriptome 12


title: E16.5, biological replicate 1, single cells, transcriptome 8


title: E16.5, biological replicate 1, single cells, transcriptome 7


title: E16.5, biological replicate 1, single cells, transcriptome 15


title: E16.5, biological replicate 1, single cells, transcriptome 14


title: E16.5, biological replicate 1, single cells, transcriptome 13


title: E16.5, biological replicate 1, single cells, transcriptome 5


title: E16.5, biological replicate 1, single cells, transcriptome 35


title: E16.5, biological replicate 1, single cells, transcriptome 10


title: E16.5, biological replicate 1, single cells, transcriptome 11


title: E16.5, biological replicate 1, single cells, transcriptome 9


title: E16.5, biological replicate 1, single cells, transcriptome 4


title: E16.5, biological replicate 1, single cells, transcriptome 6


title: E16.5, biological replicate 1, single cells, transcriptome 2


title: E16.5, biological replicate 2, single cells, transcriptome 22

source_name: E16.5_biological replicate 2_single cells_transcriptome


title: E16.5, biological replicate 1, single cells, transcriptome 1


title: E16.5, biological replicate 2, single cells, transcriptome 19


title: E16.5, biological replicate 2, single cells, transcriptome 17


title: E16.5, biological replicate 1, single cells, transcriptome 30


title: E16.5, biological replicate 2, single cells, transcriptome 14


title: E16.5, biological replicate 2, single cells, transcriptome 13


title: E16.5, biological replicate 2, single cells, transcriptome 18


title: E16.5, biological replicate 1, single cells, transcriptome 3


title: E16.5, biological replicate 2, single cells, transcriptome 21


title: E16.5, biological replicate 2, single cells, transcriptome 16


title: E16.5, biological replicate 2, single cells, transcriptome 10


title: E16.5, biological replicate 2, single cells, transcriptome 20


title: E16.5, biological replicate 2, single cells, transcriptome 9


title: E16.5, biological replicate 2, single cells, transcriptome 15


title: E16.5, biological replicate 2, single cells, transcriptome 12


title: E16.5, biological replicate 2, single cells, transcriptome 7


title: E16.5, biological replicate 2, single cells, transcriptome 4


title: E16.5, biological replicate 2, single cells, transcriptome 3


title: E16.5, biological replicate 2, single cells, transcriptome 2


title: E16.5, biological replicate 2, single cells, transcriptome 5


title: E16.5, biological replicate 2, single cells, transcriptome 6


title: E16.5, biological replicate 2, single cells, transcriptome 8


title: E16.5, biological replicate 2, single cells, transcriptome 1


title: E14.5, biological replicate 1, single cells, transcriptome 70

source_name: E14.5_biological replicate 1_single cells_transcriptome

value: Embryonic day 14.5


title: E14.5, biological replicate 1, single cells, transcriptome 74


title: E14.5, biological replicate 1, single cells, transcriptome 75


title: E14.5, biological replicate 1, single cells, transcriptome 71


title: E14.5, biological replicate 1, single cells, transcriptome 68


title: E14.5, biological replicate 1, single cells, transcriptome 72


title: E14.5, biological replicate 1, single cells, transcriptome 67


title: E14.5, biological replicate 1, single cells, transcriptome 73


title: E16.5, biological replicate 2, single cells, transcriptome 11


title: E14.5, biological replicate 1, single cells, transcriptome 64


title: E14.5, biological replicate 1, single cells, transcriptome 69


title: E14.5, biological replicate 1, single cells, transcriptome 65


title: E14.5, biological replicate 1, single cells, transcriptome 63


title: E14.5, biological replicate 1, single cells, transcriptome 62


title: E14.5, biological replicate 1, single cells, transcriptome 61


title: E14.5, biological replicate 1, single cells, transcriptome 59


title: E14.5, biological replicate 1, single cells, transcriptome 60


title: E14.5, biological replicate 1, single cells, transcriptome 56


title: E14.5, biological replicate 1, single cells, transcriptome 58


title: E14.5, biological replicate 1, single cells, transcriptome 57


title: E14.5, biological replicate 1, single cells, transcriptome 55


title: E14.5, biological replicate 1, single cells, transcriptome 54


title: E14.5, biological replicate 1, single cells, transcriptome 53


title: E14.5, biological replicate 1, single cells, transcriptome 50


title: E14.5, biological replicate 1, single cells, transcriptome 49


title: E14.5, biological replicate 1, single cells, transcriptome 52


title: E14.5, biological replicate 1, single cells, transcriptome 66


title: E14.5, biological replicate 1, single cells, transcriptome 46


title: E14.5, biological replicate 1, single cells, transcriptome 47


title: E14.5, biological replicate 1, single cells, transcriptome 45


title: E14.5, biological replicate 1, single cells, transcriptome 43


title: E14.5, biological replicate 1, single cells, transcriptome 42


title: E14.5, biological replicate 1, single cells, transcriptome 44


title: E14.5, biological replicate 1, single cells, transcriptome 40


title: E14.5, biological replicate 1, single cells, transcriptome 41


title: E14.5, biological replicate 1, single cells, transcriptome 38


title: E14.5, biological replicate 1, single cells, transcriptome 36


title: E14.5, biological replicate 1, single cells, transcriptome 37


title: E14.5, biological replicate 1, single cells, transcriptome 39


title: E14.5, biological replicate 1, single cells, transcriptome 35


title: E14.5, biological replicate 1, single cells, transcriptome 34


title: E14.5, biological replicate 1, single cells, transcriptome 33


title: E14.5, biological replicate 1, single cells, transcriptome 32


title: E14.5, biological replicate 1, single cells, transcriptome 30


title: E14.5, biological replicate 1, single cells, transcriptome 29


title: E14.5, biological replicate 1, single cells, transcriptome 28


title: E14.5, biological replicate 1, single cells, transcriptome 51


title: E14.5, biological replicate 1, single cells, transcriptome 26


title: E14.5, biological replicate 1, single cells, transcriptome 48


title: E14.5, biological replicate 1, single cells, transcriptome 27


title: E14.5, biological replicate 1, single cells, transcriptome 23


title: E14.5, biological replicate 1, single cells, transcriptome 25


title: E14.5, biological replicate 1, single cells, transcriptome 22


title: E14.5, biological replicate 1, single cells, transcriptome 24


title: E14.5, biological replicate 1, single cells, transcriptome 21


title: E14.5, biological replicate 1, single cells, transcriptome 19


title: E14.5, biological replicate 1, single cells, transcriptome 16


title: E14.5, biological replicate 1, single cells, transcriptome 17


title: E14.5, biological replicate 1, single cells, transcriptome 13


title: E14.5, biological replicate 1, single cells, transcriptome 18


title: E14.5, biological replicate 1, single cells, transcriptome 12


title: E14.5, biological replicate 1, single cells, transcriptome 10


title: E14.5, biological replicate 1, single cells, transcriptome 9


title: E14.5, biological replicate 1, single cells, transcriptome 31


title: E14.5, biological replicate 1, single cells, transcriptome 7


title: E14.5, biological replicate 1, single cells, transcriptome 6


title: E14.5, biological replicate 1, single cells, transcriptome 8


title: E14.5, biological replicate 1, single cells, transcriptome 5


title: E14.5, biological replicate 1, single cells, transcriptome 14


title: E14.5, biological replicate 1, single cells, transcriptome 1


title: E14.5, biological replicate 1, single cells, transcriptome 4


title: E14.5, biological replicate 1, single cells, transcriptome 3


title: E14.5, biological replicate 2, single cells, transcriptome 23

source_name: E14.5_biological replicate 2_single cells_transcriptome


title: E14.5, biological replicate 1, single cells, transcriptome 20


title: E14.5, biological replicate 1, single cells, transcriptome 2


title: E14.5, biological replicate 2, single cells, transcriptome 24


title: E14.5, biological replicate 2, single cells, transcriptome 21


title: E14.5, biological replicate 2, single cells, transcriptome 22


title: E14.5, biological replicate 2, single cells, transcriptome 20


title: E14.5, biological replicate 1, single cells, transcriptome 15


title: E14.5, biological replicate 2, single cells, transcriptome 19


title: E14.5, biological replicate 2, single cells, transcriptome 16


title: E14.5, biological replicate 2, single cells, transcriptome 13


title: E14.5, biological replicate 2, single cells, transcriptome 17


title: E14.5, biological replicate 2, single cells, transcriptome 18


title: E14.5, biological replicate 2, single cells, transcriptome 14


title: E14.5, biological replicate 2, single cells, transcriptome 11


title: E14.5, biological replicate 1, single cells, transcriptome 11


title: E14.5, biological replicate 2, single cells, transcriptome 12


title: E14.5, biological replicate 2, single cells, transcriptome 15


title: E14.5, biological replicate 2, single cells, transcriptome 10


title: E14.5, biological replicate 2, single cells, transcriptome 9


title: E14.5, biological replicate 2, single cells, transcriptome 7


title: E14.5, biological replicate 2, single cells, transcriptome 6


title: E14.5, biological replicate 2, single cells, transcriptome 8


title: E14.5, biological replicate 2, single cells, transcriptome 2


title: E14.5, biological replicate 2, single cells, transcriptome 3


title: E14.5, biological replicate 2, single cells, transcriptome 4


title: E14.5, biological replicate 2, single cells, transcriptome 1


title: E13.5, biological replicate 1, single cells, transcriptome 71

source_name: E13.5_biological replicate 1_single cells_transcriptome

value: Embryonic day 13.5


title: E13.5, biological replicate 1, single cells, transcriptome 67


title: E13.5, biological replicate 1, single cells, transcriptome 70


title: E13.5, biological replicate 1, single cells, transcriptome 69


title: E13.5, biological replicate 1, single cells, transcriptome 66


title: E13.5, biological replicate 1, single cells, transcriptome 68


title: E13.5, biological replicate 1, single cells, transcriptome 65


title: E13.5, biological replicate 1, single cells, transcriptome 63


title: E13.5, biological replicate 1, single cells, transcriptome 62


title: E13.5, biological replicate 1, single cells, transcriptome 64


title: E13.5, biological replicate 1, single cells, transcriptome 60


title: E13.5, biological replicate 1, single cells, transcriptome 59


title: E13.5, biological replicate 1, single cells, transcriptome 58


title: E13.5, biological replicate 1, single cells, transcriptome 53


title: E13.5, biological replicate 1, single cells, transcriptome 52


title: E13.5, biological replicate 1, single cells, transcriptome 57


title: E13.5, biological replicate 1, single cells, transcriptome 56


title: E13.5, biological replicate 1, single cells, transcriptome 48


title: E13.5, biological replicate 1, single cells, transcriptome 55


title: E13.5, biological replicate 1, single cells, transcriptome 49


title: E13.5, biological replicate 1, single cells, transcriptome 50


title: E13.5, biological replicate 1, single cells, transcriptome 51


title: E14.5, biological replicate 2, single cells, transcriptome 5


title: E13.5, biological replicate 1, single cells, transcriptome 54


title: E13.5, biological replicate 1, single cells, transcriptome 46


title: E13.5, biological replicate 1, single cells, transcriptome 47


title: E13.5, biological replicate 1, single cells, transcriptome 45


title: E13.5, biological replicate 1, single cells, transcriptome 39


title: E13.5, biological replicate 1, single cells, transcriptome 44


title: E13.5, biological replicate 1, single cells, transcriptome 41


title: E13.5, biological replicate 1, single cells, transcriptome 38


title: E13.5, biological replicate 1, single cells, transcriptome 43


title: E13.5, biological replicate 1, single cells, transcriptome 40


title: E13.5, biological replicate 1, single cells, transcriptome 42


title: E13.5, biological replicate 1, single cells, transcriptome 34


title: E13.5, biological replicate 1, single cells, transcriptome 61


title: E13.5, biological replicate 1, single cells, transcriptome 32


title: E13.5, biological replicate 1, single cells, transcriptome 31


title: E13.5, biological replicate 1, single cells, transcriptome 37


title: E13.5, biological replicate 1, single cells, transcriptome 36


title: E13.5, biological replicate 1, single cells, transcriptome 20


title: E13.5, biological replicate 1, single cells, transcriptome 26


title: E13.5, biological replicate 1, single cells, transcriptome 21


title: E13.5, biological replicate 1, single cells, transcriptome 33


title: E13.5, biological replicate 1, single cells, transcriptome 22


title: E13.5, biological replicate 1, single cells, transcriptome 29


title: E13.5, biological replicate 1, single cells, transcriptome 24


title: E13.5, biological replicate 1, single cells, transcriptome 25


title: E13.5, biological replicate 1, single cells, transcriptome 35


title: E13.5, biological replicate 1, single cells, transcriptome 14


title: E13.5, biological replicate 1, single cells, transcriptome 19


title: E13.5, biological replicate 1, single cells, transcriptome 10


title: E13.5, biological replicate 1, single cells, transcriptome 30


title: E13.5, biological replicate 1, single cells, transcriptome 9


title: E13.5, biological replicate 1, single cells, transcriptome 15


title: E13.5, biological replicate 1, single cells, transcriptome 16


title: E13.5, biological replicate 1, single cells, transcriptome 7


title: E13.5, biological replicate 1, single cells, transcriptome 18


title: E13.5, biological replicate 1, single cells, transcriptome 17


title: E13.5, biological replicate 1, single cells, transcriptome 12


title: E13.5, biological replicate 1, single cells, transcriptome 11


title: E13.5, biological replicate 1, single cells, transcriptome 28


title: E13.5, biological replicate 1, single cells, transcriptome 8


title: E13.5, biological replicate 1, single cells, transcriptome 27


title: E13.5, biological replicate 1, single cells, transcriptome 13


title: E13.5, biological replicate 1, single cells, transcriptome 23


title: E13.5, biological replicate 1, single cells, transcriptome 2


title: E13.5, biological replicate 1, single cells, transcriptome 5


title: E13.5, biological replicate 1, single cells, transcriptome 3


title: E12.5, biological replicate 1, single cells, transcriptome 81

source_name: E12.5_biological replicate 1_single cells_transcriptome

value: Embryonic day 12.5


title: E13.5, biological replicate 1, single cells, transcriptome 4


title: E12.5, biological replicate 1, single cells, transcriptome 83


title: E13.5, biological replicate 1, single cells, transcriptome 1


title: E12.5, biological replicate 1, single cells, transcriptome 80


title: E12.5, biological replicate 1, single cells, transcriptome 76


title: E12.5, biological replicate 1, single cells, transcriptome 82


title: E12.5, biological replicate 1, single cells, transcriptome 79


title: E12.5, biological replicate 1, single cells, transcriptome 68


title: E12.5, biological replicate 1, single cells, transcriptome 72


title: E12.5, biological replicate 1, single cells, transcriptome 70


title: E12.5, biological replicate 1, single cells, transcriptome 66


title: E12.5, biological replicate 1, single cells, transcriptome 77


title: E12.5, biological replicate 1, single cells, transcriptome 78


title: E12.5, biological replicate 1, single cells, transcriptome 65


title: E12.5, biological replicate 1, single cells, transcriptome 74


title: E12.5, biological replicate 1, single cells, transcriptome 73


title: E12.5, biological replicate 1, single cells, transcriptome 69


title: E13.5, biological replicate 1, single cells, transcriptome 6


title: E12.5, biological replicate 1, single cells, transcriptome 71


title: E12.5, biological replicate 1, single cells, transcriptome 63


title: E12.5, biological replicate 1, single cells, transcriptome 61


title: E12.5, biological replicate 1, single cells, transcriptome 62


title: E12.5, biological replicate 1, single cells, transcriptome 60


title: E12.5, biological replicate 1, single cells, transcriptome 75


title: E12.5, biological replicate 1, single cells, transcriptome 57


title: E12.5, biological replicate 1, single cells, transcriptome 56


title: E12.5, biological replicate 1, single cells, transcriptome 55


title: E12.5, biological replicate 1, single cells, transcriptome 54


title: E12.5, biological replicate 1, single cells, transcriptome 64


title: E12.5, biological replicate 1, single cells, transcriptome 52


title: E12.5, biological replicate 1, single cells, transcriptome 51


title: E12.5, biological replicate 1, single cells, transcriptome 50


title: E12.5, biological replicate 1, single cells, transcriptome 67


title: E12.5, biological replicate 1, single cells, transcriptome 47


title: E12.5, biological replicate 1, single cells, transcriptome 46


title: E12.5, biological replicate 1, single cells, transcriptome 45


title: E12.5, biological replicate 1, single cells, transcriptome 44


title: E12.5, biological replicate 1, single cells, transcriptome 43


title: E12.5, biological replicate 1, single cells, transcriptome 41


title: E12.5, biological replicate 1, single cells, transcriptome 42


title: E12.5, biological replicate 1, single cells, transcriptome 40


title: E12.5, biological replicate 1, single cells, transcriptome 39


title: E12.5, biological replicate 1, single cells, transcriptome 38


title: E12.5, biological replicate 1, single cells, transcriptome 59


title: E12.5, biological replicate 1, single cells, transcriptome 58


title: E12.5, biological replicate 1, single cells, transcriptome 37


title: E12.5, biological replicate 1, single cells, transcriptome 53


title: E12.5, biological replicate 1, single cells, transcriptome 35


title: E12.5, biological replicate 1, single cells, transcriptome 33


title: E12.5, biological replicate 1, single cells, transcriptome 36


title: E12.5, biological replicate 1, single cells, transcriptome 34


title: E12.5, biological replicate 1, single cells, transcriptome 30


title: E12.5, biological replicate 1, single cells, transcriptome 31


title: E12.5, biological replicate 1, single cells, transcriptome 28


title: E12.5, biological replicate 1, single cells, transcriptome 29


title: E12.5, biological replicate 1, single cells, transcriptome 25


title: E12.5, biological replicate 1, single cells, transcriptome 49


title: E12.5, biological replicate 1, single cells, transcriptome 48


title: E12.5, biological replicate 1, single cells, transcriptome 24


title: E12.5, biological replicate 1, single cells, transcriptome 23


title: E12.5, biological replicate 1, single cells, transcriptome 21


title: E12.5, biological replicate 1, single cells, transcriptome 27


title: E12.5, biological replicate 1, single cells, transcriptome 20


title: E12.5, biological replicate 1, single cells, transcriptome 26


title: E12.5, biological replicate 1, single cells, transcriptome 19


title: E12.5, biological replicate 1, single cells, transcriptome 22


title: E12.5, biological replicate 1, single cells, transcriptome 18


title: E12.5, biological replicate 1, single cells, transcriptome 17


title: E12.5, biological replicate 1, single cells, transcriptome 15


title: E12.5, biological replicate 1, single cells, transcriptome 13


title: E12.5, biological replicate 1, single cells, transcriptome 16


title: E12.5, biological replicate 1, single cells, transcriptome 12


title: E12.5, biological replicate 1, single cells, transcriptome 32


title: E12.5, biological replicate 1, single cells, transcriptome 4


title: E12.5, biological replicate 1, single cells, transcriptome 5


title: E12.5, biological replicate 1, single cells, transcriptome 7


title: E12.5, biological replicate 1, single cells, transcriptome 6


title: E12.5, biological replicate 1, single cells, transcriptome 9


title: E12.5, biological replicate 1, single cells, transcriptome 11


title: E12.5, biological replicate 1, single cells, transcriptome 10


title: E12.5, biological replicate 2, single cells, transcriptome 15

source_name: E12.5_biological replicate 2_single cells_transcriptome


title: E12.5, biological replicate 2, single cells, transcriptome 14


title: E12.5, biological replicate 2, single cells, transcriptome 17


title: E12.5, biological replicate 2, single cells, transcriptome 16


title: E12.5, biological replicate 1, single cells, transcriptome 1


title: E12.5, biological replicate 1, single cells, transcriptome 3


title: E12.5, biological replicate 2, single cells, transcriptome 13


title: E12.5, biological replicate 1, single cells, transcriptome 2


title: E12.5, biological replicate 2, single cells, transcriptome 11


title: E12.5, biological replicate 2, single cells, transcriptome 9


title: E12.5, biological replicate 2, single cells, transcriptome 10


title: E12.5, biological replicate 1, single cells, transcriptome 14


title: E12.5, biological replicate 2, single cells, transcriptome 8


title: E12.5, biological replicate 2, single cells, transcriptome 6


title: E12.5, biological replicate 1, single cells, transcriptome 8


title: Puberty epithelial cells_1

data_processing:
Read alignment and count summarization were performed using CellRanger v2.0 using the Illumina BCL files as input.
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx files contain genewise read counts for all cells in a space-efficient matrix market format; genes.tsv files contain Ensembl IDs and gene symbols as tab-delimited text; barcode.tsv files contain the 10X barcodes used to identify cells.

source_name: Mammary gland, 5wk

value: Puberty

tag: cell type

value: mammary gland epithelium cell

tag: number of cells (combined for both puberty samples)


title: Puberty epithelial cells_2


title: Adult estrus epithelial cells

source_name: Mammary gland, P7E

value: Adult in estrus phase


title: Adult diestrus epithelial cells

source_name: Mammary gland, P7D

value: FVB/NJ

value: Adult in diestrus phase


title: 50,000 primary erythroid cells processed with LI Capture-C protocol replicate 2

city: Oxford

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
3C library preparation followed by double oligonucleotide capture
Low-input Capture-C products

library_source: genomic

data_processing:
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (custom scripts)
Alignment to the genome (Bowtie -m 2) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads and mapping to restriction enzyme fragments (custom scripts)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Genome_build: mm9
Supplementary_files_format_and_content: small_cell_nr_full_prot_alpha_gfc.txt Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)

molecule: genomic DNA

source_name: Primary erythroid cells

growth_protocol: Ter-119+ erythroid cells were obtained from the spleens of female C57BL/6 mice treated with phenylhydrazine (three doses of 40 mg/g body weight given 12 hours apart; mice were sacrificed after five days).

extract_protocol:
Spleens were gently dissociated into a single cell suspension and cells were passed through a 70 μm strainer to remove clumps. For ter-119+ cell selection, cells were stained with phycoerythrin conjugated anti-ter-119 antibodies and positively selected using anti-phycoerythrin MACS beads before fixation with formaldehyde.
The Capture-C technologies combine 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. Detailed description follows. The protocol used for the generation of the 3C libraries was similar to other 3C-based methods. Briefly, cells were crosslinked with 2% formaldehyde (this was varied for the reduced crosslinking experiments), quenched with cold glycine, washed in phosphate buffered saline, resuspended in cold lysis buffer and snap frozen to -80. Cells were thawed on ice, washed in Milli-Q dH2O and Dounce homogenized on ice. Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37 °C for 1h at 1400 rpm on a Thermomixer, followed by a further incubation of 1h after the addition of Triton X-100 (final concentration 1.67%). An overnight digestion was performed using DpnII (final concentration 500U/ml; 37 °C / 1400 rpm). The digested chromatin was ligated overnight using T4 DNA HC ligase (final concentration 10U/ml; 16 °C / 1400 rpm). The samples were de-crosslinked overnight with Proteinase K at 65 °C, followed by a 30 min incubation at 37 °C with RNAse. A Phenol/Chloroform extraction was performed, followed by an ethanol precipitation and wash. Digestion efficiencies were assessed by gel electrophoresis and RT-PCR, which showed digestion efficiencies higher than 80%. The DNA contents of the DpnII 3C libraries were quantitated using a Qubit fluorometer. Different strategies were used for the sequencing library preparation. For the low-input experiments, the LI Capture-C or Tag-Capture-C protocol was used, for which 50-200 ng of DNA was adapter ligated using a strategy based on sonication combined with the NEBNext Ultra DNA Library Prep kit, or the Illumina Nextera DNA Library Prep kit, respectively. For the reduced cross-linking experiments, the NG Capture-C protocol was used, for which 5 ug of DNA was adapter ligated using a strategy based on sonication combined with the NEBNext DNA Library Prep kit. The quality of the libraries was assessed using the Agilent ScreenTape system. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. 700 ng-2 ug of the adapter ligated libraries was hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resulting captured library was assessed using the Agilent ScreenTape system. The libraries were sequenced using the Illumina MiSeq (150bp paired end reads) platform.

value: Ter-119+ cells isolated from phenylhydrazine treated spleen

tag: genes analysed


title: 20,000 primary erythroid cells processed with LI Capture-C protocol replicate 3

treatment_protocol: Ter-119+ erythroid cells were obtained from the spleens of female C57BL/6 mice treated with phenylhydrazine (three doses of 40 mg/g body weight given 12 hours apart; mice were sacrificed after five days).


title: 20,000 primary erythroid cells processed with LI Capture-C protocol replicate 2


title: 10,000 primary erythroid cells processed with LI Capture-C protocol replicate 2


title: 10,000 primary erythroid cells processed with LI Capture-C protocol replicate 3


title: 50,000 primary erythroid cells processed with LI Capture-C protocol replicate 3


title: 20,000 primary erythroid cells processed with LI Capture-C protocol replicate 1


title: 100,000 primary erythroid cells processed with LI Capture-C protocol replicate 2


title: 100,000 primary erythroid cells processed with LI Capture-C protocol replicate 3


title: E12.5, biological replicate 2, single cells, transcriptome 12


title: 100,000 primary erythroid cells processed with LI Capture-C protocol replicate 1


title: 10,000 primary erythroid cells processed with LI Capture-C protocol replicate 1


title: E12.5, biological replicate 2, single cells, transcriptome 7


title: P3.25, EpCAM+ single cells, transcriptome 50

source_name: Liver

treatment_protocol: Liver cells were prepared from P3.25 neonatal mouse. Sibling fetal livers of one litter were isolated, pooled, minced and digested in 0.05% collagenase IV at 37°C for 30 min. The suspensions were filtered through a 40-μm cell strainer to remove un-digested tissues, and the cells were washed twice with RPMI 1640 medium containing 10% FBS. The fetal liver cells were then incubated with PE-labeled anti-mouse CD326 (Ep-CAM) antibodies (BioLegend, PN 118205) per the vendor’s suggestions, and EpCAM+ cells were sorted for downstream experiment.

value: Postnatal day 3.25

tag: genotype


title: P3.25, EpCAM+ single cells, transcriptome 51


title: P3.25, EpCAM+ single cells, transcriptome 52


title: P3.25, EpCAM+ single cells, transcriptome 48


title: P3.25, EpCAM+ single cells, transcriptome 46


title: P3.25, EpCAM+ single cells, transcriptome 49


title: P3.25, EpCAM+ single cells, transcriptome 47


title: P3.25, EpCAM+ single cells, transcriptome 45


title: P3.25, EpCAM+ single cells, transcriptome 44


title: P3.25, EpCAM+ single cells, transcriptome 42


title: P3.25, EpCAM+ single cells, transcriptome 43


title: 50,000 primary erythroid cells processed with LI Capture-C protocol replicate 1


title: P3.25, EpCAM+ single cells, transcriptome 41


title: P3.25, EpCAM+ single cells, transcriptome 39


title: P3.25, EpCAM+ single cells, transcriptome 38


title: P3.25, EpCAM+ single cells, transcriptome 37


title: P3.25, EpCAM+ single cells, transcriptome 35


title: P3.25, EpCAM+ single cells, transcriptome 36


title: P3.25, EpCAM+ single cells, transcriptome 33


title: P3.25, EpCAM+ single cells, transcriptome 34


title: P3.25, EpCAM+ single cells, transcriptome 40


title: P3.25, EpCAM+ single cells, transcriptome 28


title: P3.25, EpCAM+ single cells, transcriptome 27


title: P3.25, EpCAM+ single cells, transcriptome 31


title: P3.25, EpCAM+ single cells, transcriptome 30


title: P3.25, EpCAM+ single cells, transcriptome 32


title: P3.25, EpCAM+ single cells, transcriptome 24


title: P3.25, EpCAM+ single cells, transcriptome 21


title: P3.25, EpCAM+ single cells, transcriptome 19


title: P3.25, EpCAM+ single cells, transcriptome 13


title: P3.25, EpCAM+ single cells, transcriptome 14


title: P3.25, EpCAM+ single cells, transcriptome 16


title: P3.25, EpCAM+ single cells, transcriptome 15


title: P3.25, EpCAM+ single cells, transcriptome 26


title: P3.25, EpCAM+ single cells, transcriptome 12


title: P3.25, EpCAM+ single cells, transcriptome 23


title: P3.25, EpCAM+ single cells, transcriptome 25


title: P3.25, EpCAM+ single cells, transcriptome 22


title: P3.25, EpCAM+ single cells, transcriptome 18


title: P3.25, EpCAM+ single cells, transcriptome 17


title: P3.25, EpCAM+ single cells, transcriptome 29


title: P3.25, EpCAM+ single cells, transcriptome 11


title: P3.25, EpCAM+ single cells, transcriptome 9


title: P3.25, EpCAM+ single cells, transcriptome 6


title: P3.25, EpCAM+ single cells, transcriptome 10


title: P3.25, EpCAM+ single cells, transcriptome 7


title: P3.25, EpCAM+ single cells, transcriptome 5


title: P3.25, EpCAM+ single cells, transcriptome 8


title: Pregnancy basal cell 74

data_processing:
Reads were aligned to the mouse genome by Subread version 1.5.0
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rusbread's in-built NCBI annotation.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

value: Pregnancy

value: Basal


title: P3.25, EpCAM+ single cells, transcriptome 2


title: P3.25, EpCAM+ single cells, transcriptome 1


title: P3.25, EpCAM+ single cells, transcriptome 4


title: P3.25, EpCAM+ single cells, transcriptome 20


title: P3.25, EpCAM+ single cells, transcriptome 3


title: Pregnancy basal cell 72


title: Pregnancy basal cell 70


title: Pregnancy basal cell 67


title: Pregnancy basal cell 71


title: Pregnancy basal cell 68


title: Pregnancy basal cell 66


title: Pregnancy basal cell 64


title: Pregnancy basal cell 63


title: Pregnancy basal cell 65


title: Pregnancy basal cell 62


title: Pregnancy basal cell 60


title: Pregnancy basal cell 69


title: Pregnancy basal cell 59


title: Pregnancy basal cell 61


title: Pregnancy basal cell 58


title: Pregnancy basal cell 56


title: Pregnancy basal cell 54


title: Pregnancy basal cell 57


title: Pregnancy basal cell 53


title: Pregnancy basal cell 55


title: Pregnancy basal cell 73


title: Pregnancy basal cell 50


title: Pregnancy basal cell 51


title: Pregnancy basal cell 49


title: Pregnancy basal cell 47


title: Pregnancy basal cell 46


title: Pregnancy basal cell 45


title: Pregnancy basal cell 43


title: Pregnancy basal cell 42


title: Pregnancy basal cell 40


title: Pregnancy basal cell 38


title: Pregnancy basal cell 37


title: Pregnancy basal cell 36


title: Pregnancy basal cell 34


title: Pregnancy basal cell 44


title: Pregnancy basal cell 39


title: Pregnancy basal cell 33


title: Pregnancy basal cell 31


title: Pregnancy basal cell 52


title: Pregnancy basal cell 32


title: Pregnancy basal cell 29


title: Pregnancy basal cell 35


title: Pregnancy basal cell 27


title: Pregnancy basal cell 30


title: Pregnancy basal cell 26


title: Pregnancy basal cell 25


title: Pregnancy basal cell 23


title: Pregnancy basal cell 24


title: Pregnancy basal cell 21


title: Pregnancy basal cell 19


title: Pregnancy basal cell 22


title: Pregnancy basal cell 20


title: Pregnancy basal cell 18


title: Pregnancy basal cell 17


title: Pregnancy basal cell 15


title: Pregnancy basal cell 41


title: Pregnancy basal cell 16


title: Pregnancy basal cell 11


title: Pregnancy basal cell 12


title: Pregnancy basal cell 14


title: Pregnancy basal cell 10


title: Pregnancy basal cell 9


title: Pregnancy basal cell 28


title: Pregnancy basal cell 75


title: Pregnancy basal cell 5


title: Pregnancy basal cell 7


title: Pregnancy basal cell 8


title: Pregnancy basal cell 3


title: Pregnancy basal cell 6


title: Pregnancy basal cell 1


title: Pregnancy basal cell 4


title: Adult basal cell 237

value: Adult


title: Pregnancy basal cell 2


title: Adult basal cell 236


title: Adult basal cell 233


title: Adult basal cell 234


title: Adult basal cell 231


title: Pregnancy basal cell 13


title: Adult basal cell 232


title: Adult basal cell 235


title: Adult basal cell 230


title: Pregnancy basal cell 48


title: Adult basal cell 226


title: Adult basal cell 225


title: Adult basal cell 227


title: Adult basal cell 223


title: Adult basal cell 222


title: Adult basal cell 221


title: Adult basal cell 220


title: Adult basal cell 228


title: Adult basal cell 215


title: Adult basal cell 217


title: Adult basal cell 213


title: Adult basal cell 218


title: Adult basal cell 211


title: Adult basal cell 210


title: Adult basal cell 209


title: Adult basal cell 224


title: Adult basal cell 214


title: E12.5, biological replicate 2, single cells, transcriptome 4

value: wild type


title: Adult basal cell 216


title: E12.5, biological replicate 2, single cells, transcriptome 2

value: Liver


title: Adult basal cell 219


title: E11.5, biological replicate 1, single cells, transcriptome 69

source_name: E11.5_biological replicate 1_single cells_transcriptome

value: Embryonic day 11.5


title: E12.5, biological replicate 2, single cells, transcriptome 1


title: E12.5, biological replicate 2, single cells, transcriptome 3


title: E11.5, biological replicate 1, single cells, transcriptome 70


title: Adult basal cell 229

source_name: Mammary gland


title: E11.5, biological replicate 1, single cells, transcriptome 68


title: Adult basal cell 212


title: E11.5, biological replicate 1, single cells, transcriptome 65


title: E11.5, biological replicate 1, single cells, transcriptome 67


title: E11.5, biological replicate 1, single cells, transcriptome 66


title: E11.5, biological replicate 1, single cells, transcriptome 64


title: E11.5, biological replicate 1, single cells, transcriptome 61


title: E11.5, biological replicate 1, single cells, transcriptome 62


title: E11.5, biological replicate 1, single cells, transcriptome 59


title: E11.5, biological replicate 1, single cells, transcriptome 60


title: E12.5, biological replicate 2, single cells, transcriptome 5


title: E11.5, biological replicate 1, single cells, transcriptome 58


title: E11.5, biological replicate 1, single cells, transcriptome 57


title: E11.5, biological replicate 1, single cells, transcriptome 55


title: E11.5, biological replicate 1, single cells, transcriptome 53


title: E11.5, biological replicate 1, single cells, transcriptome 49


title: E11.5, biological replicate 1, single cells, transcriptome 50


title: E11.5, biological replicate 1, single cells, transcriptome 48


title: E11.5, biological replicate 1, single cells, transcriptome 44


title: E11.5, biological replicate 1, single cells, transcriptome 46


title: E11.5, biological replicate 1, single cells, transcriptome 43


title: E11.5, biological replicate 1, single cells, transcriptome 47


title: E11.5, biological replicate 1, single cells, transcriptome 41


title: E11.5, biological replicate 1, single cells, transcriptome 63


title: E11.5, biological replicate 1, single cells, transcriptome 40


title: E11.5, biological replicate 1, single cells, transcriptome 42


title: E11.5, biological replicate 1, single cells, transcriptome 39


title: E11.5, biological replicate 1, single cells, transcriptome 38


title: E11.5, biological replicate 1, single cells, transcriptome 37


title: E11.5, biological replicate 1, single cells, transcriptome 56


title: E11.5, biological replicate 1, single cells, transcriptome 36


title: E11.5, biological replicate 1, single cells, transcriptome 35


title: E11.5, biological replicate 1, single cells, transcriptome 34


title: E11.5, biological replicate 1, single cells, transcriptome 54


title: E11.5, biological replicate 1, single cells, transcriptome 51


title: E11.5, biological replicate 1, single cells, transcriptome 33


title: E11.5, biological replicate 1, single cells, transcriptome 29


title: E11.5, biological replicate 1, single cells, transcriptome 52


title: E11.5, biological replicate 1, single cells, transcriptome 30


title: E11.5, biological replicate 1, single cells, transcriptome 32


title: E11.5, biological replicate 1, single cells, transcriptome 45


title: E11.5, biological replicate 1, single cells, transcriptome 31


title: E11.5, biological replicate 1, single cells, transcriptome 28


title: E11.5, biological replicate 1, single cells, transcriptome 27


title: E11.5, biological replicate 1, single cells, transcriptome 21


title: E11.5, biological replicate 1, single cells, transcriptome 25


title: E11.5, biological replicate 1, single cells, transcriptome 24


title: E11.5, biological replicate 1, single cells, transcriptome 23


title: E11.5, biological replicate 1, single cells, transcriptome 22


title: E11.5, biological replicate 1, single cells, transcriptome 20


title: E11.5, biological replicate 1, single cells, transcriptome 19


title: E11.5, biological replicate 1, single cells, transcriptome 18


title: E11.5, biological replicate 1, single cells, transcriptome 15


title: E11.5, biological replicate 1, single cells, transcriptome 13


title: E11.5, biological replicate 1, single cells, transcriptome 16


title: E11.5, biological replicate 1, single cells, transcriptome 9


title: E11.5, biological replicate 1, single cells, transcriptome 12


title: E11.5, biological replicate 1, single cells, transcriptome 8


title: E11.5, biological replicate 1, single cells, transcriptome 7


title: E11.5, biological replicate 1, single cells, transcriptome 10


title: E11.5, biological replicate 1, single cells, transcriptome 4


title: E11.5, biological replicate 1, single cells, transcriptome 2


title: E11.5, biological replicate 1, single cells, transcriptome 1


title: L5-20

city: La Jolla

first: Carsten

last: Pfeffer

state: CA

address: 9500 Gilman Drive

country: USA

institute: UCSD

description:
CP-B_88
ERCC_tpm5.txt
ERCC_UMI_5reads.txt

data_processing:
Illumina Casava 1.8 for basecalling
Reads were demultiplexed, trimmed, and filtered (prinseq, parameters: -lc_method dust –lc_threshold 15 –trim_left 7) before mapping (bowtie2, standard parameters; (Langmead and
Salzberg, 2012)) the reads to the mouse transcriptome (ENSEMBLE cDNA sequences or ab initio predicted genes), the ERCC transcriptome and mapped reads counted (htseq-count;
(Anders et al., 2014)) following the Cel-seq general pipeline.
Genome_build: Ensemble cDNA sequences or ab initio predicted genes; mouse ensemble release v76; GRCm38.p2
Supplementary_files_format_and_content: tab-delimited text files include tpm values for each Sample

source_name: cortex

extract_protocol:
Mice aged P35 or older were anaesthetized with ketamine and xylazine (100mg*kg-1 and 10mg*kg-1, respectively), perfused transcardially with cold sucrose solution (in mM: NaCl, 83;
KCl, 2.5; MgSO4, 3.3; NaH2PO4, 1; NaHCO3, 26.2; D-glucose, 22; sucrose, 72; and CaCl2, 0.5, bubbled with 95% O2 and 5% CO2) and decapitated, and the visual cortex was cut into
300µm coronal or tangential sections in cold sucrose solution. Slices were incubated in sucrose solution in a submerged chamber at 34°C for 30min and then at room temperature (21°C) until
used for RNA harvest from patch-clamped cells.
RNA was harvested as described previously (Pfeffer et al., 2013). In brief, slices were mounted under a 40x 0.8 NA water lens and superfused with sucrose solution (same as in slice
preparation). Cells were identified using GFP or tdTomato  fluorescence and visualized with IR-DIC. Cells were then patched with regular RNAse free patch pipettes (2-4 MOhm resistance) in
whole-cell mode using the voltage-clamp configuration. After seal establishment and break-in the cell was held at -70mV and the cell content including cell nucleus was harvested using
negative pressure and expelled in an Eppendorf tube and frozen at -70C. Intracellular solution was RNAse free: in mM: CsMeSO4, 115; NaCl, 4; HEPES, 10; Na3GTP, 0.3; MgATP, 4; EGTA,
0.3; BAPTA(4Cs), 10; adjusted to pH 7.4 with CsOH; mOsm 295. The procedures lasted approximately 2-3 minutes per cell (from targeting to tube freezing).
Single cell RNA-seq was carried out following the Cel-seq protocol (Hashimshony et al., 2016; Hashimshony et al., 2012). RT and second strand synthesis were performed using Superscript
III (Invitrogen) and second strand synthesis kit (Invitrogen), respectively, before IVT amplification (Maxiscript T7, Ambion). 96 samples (up to 94 cells and 2-8 control samples) were
handled in parallel to construct one sequencing library. After library fragmentation (Mg-Acetat + heat) and 3’ adaptor attachment, 11-15 cycles of PCR were used for library amplification (final
concentration > 1ng/microL, library peak fragment size ~350 nt). Libraries were sequenced using Illumina HiSeq 2500 and HiSeq 4000 at the UCSD genomics core (1st read 13 cycles for
the barcode, 2nd read 50 cycles for the 3’ end of the transcript).

value: 129S2/SvPasCrl, CD-1 mix

value: postnatal day >p35

value: SepW1-Cre, WT

tag: position

value: primary visual cortex layer 5


title: E11.5, biological replicate 1, single cells, transcriptome 26


title: L5-17

description:
CP-B_47
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: L5-18

description:
CP-B_48
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: L5-14

description:
CP-B_44
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: E11.5, biological replicate 1, single cells, transcriptome 14


title: E11.5, biological replicate 1, single cells, transcriptome 3


title: L5-13

description:
CP-B_43
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: L5-10

description:
CP-B_40
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: L5-15

description:
CP-B_45
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: L5-12

description:
CP-B_42
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: L5-11

description:
CP-B_41
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: L5-9

description:
CP-B_39
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: L5-8

description:
CP-B_38
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: L5-4

description:
CP-B_34
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: L5-7

description:
CP-B_37
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: E11.5, biological replicate 1, single cells, transcriptome 5


title: L5-5

description:
CP-B_35
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: L5-6

description:
CP-B_36
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: E11.5, biological replicate 1, single cells, transcriptome 6


title: E11.5, biological replicate 1, single cells, transcriptome 11


title: L5-3

description:
CP-B_33
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: L5-2

description:
CP-B_32
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: L5-16

description:
CP-B_46
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: L5-1

description:
CP-B_31
ERCC_tpm5.txt
ERCC_UMI_5reads.txt


title: HS-39

description:
CP-M_88
HS-LS_tpm5.txt

value: primary visual cortex layer 2

tag: sensory response properties

value: highspeed moving gratings


title: LS-21

description:
CP-M_90
HS-LS_tpm5.txt

value: lowspeed moving gratings


title: HS-40

description:
CP-M_9
HS-LS_tpm5.txt


title: HS-36

description:
CP-M_81
HS-LS_tpm5.txt


title: LS-19

description:
CP-M_78
HS-LS_tpm5.txt


title: LS-20

description:
CP-M_89
HS-LS_tpm5.txt


title: LS-18

description:
CP-M_77
HS-LS_tpm5.txt


title: HS-34

description:
CP-M_76
HS-LS_tpm5.txt


title: HS-38

description:
CP-M_84
HS-LS_tpm5.txt


title: HS-32

description:
CP-M_73
HS-LS_tpm5.txt


title: HS-35

description:
CP-M_80
HS-LS_tpm5.txt


title: HS-33

description:
CP-M_75
HS-LS_tpm5.txt


title: HS-30

description:
CP-M_71
HS-LS_tpm5.txt


title: HS-27

description:
CP-M_67
HS-LS_tpm5.txt


title: HS-28

description:
CP-M_69
HS-LS_tpm5.txt


title: LS-15

description:
CP-M_61
HS-LS_tpm5.txt


title: HS-24

description:
CP-M_63
HS-LS_tpm5.txt


title: HS-26

description:
CP-M_66
HS-LS_tpm5.txt


title: LS-16

description:
CP-M_62
HS-LS_tpm5.txt


title: HS-25

description:
CP-M_64
HS-LS_tpm5.txt


title: HS-37

description:
CP-M_82
HS-LS_tpm5.txt


title: LS-17

description:
CP-M_68
HS-LS_tpm5.txt


title: HS-21

description:
CP-M_58
HS-LS_tpm5.txt


title: HS-29

description:
CP-M_70
HS-LS_tpm5.txt


title: HS-23

description:
CP-M_6
HS-LS_tpm5.txt


title: HS-31

description:
CP-M_72
HS-LS_tpm5.txt


title: HS-22

description:
CP-M_59
HS-LS_tpm5.txt


title: LS-14

description:
CP-M_56
HS-LS_tpm5.txt


title: HS-17

description:
CP-M_51
HS-LS_tpm5.txt


title: HS-16

description:
CP-M_50
HS-LS_tpm5.txt


title: HS-19

description:
CP-M_53
HS-LS_tpm5.txt


title: HS-12

description:
CP-M_41
HS-LS_tpm5.txt


title: HS-18

description:
CP-M_52
HS-LS_tpm5.txt


title: HS-11

description:
CP-M_4
HS-LS_tpm5.txt


title: HS-20

description:
CP-M_55
HS-LS_tpm5.txt


title: LS-11

description:
CP-M_42
HS-LS_tpm5.txt


title: HS-14

description:
CP-M_49
HS-LS_tpm5.txt


title: LS-12

description:
CP-M_43
HS-LS_tpm5.txt


title: HS-15

description:
CP-M_5
HS-LS_tpm5.txt


title: LS-9

description:
CP-M_34
HS-LS_tpm5.txt


title: LS-10

description:
CP-M_35
HS-LS_tpm5.txt


title: LS-8

description:
CP-M_33
HS-LS_tpm5.txt


title: HS-6

description:
CP-M_25
HS-LS_tpm5.txt


title: HS-5

description:
CP-M_24
HS-LS_tpm5.txt


title: HS-8

description:
CP-M_30
HS-LS_tpm5.txt


title: LS-13

description:
CP-M_44
HS-LS_tpm5.txt


title: HS-7

description:
CP-M_3
HS-LS_tpm5.txt


title: HS-9

description:
CP-M_32
HS-LS_tpm5.txt


title: LS-7

description:
CP-M_29
HS-LS_tpm5.txt


title: LS-6

description:
CP-M_28
HS-LS_tpm5.txt


title: HS-3

description:
CP-M_2
HS-LS_tpm5.txt


title: HS-4

description:
CP-M_21
HS-LS_tpm5.txt


title: LS-5

description:
CP-M_23
HS-LS_tpm5.txt


title: LS-4

description:
CP-M_19
HS-LS_tpm5.txt


title: LS-3

description:
CP-M_16
HS-LS_tpm5.txt


title: LS-2

description:
CP-M_15
HS-LS_tpm5.txt


title: HS-10

description:
CP-M_37
HS-LS_tpm5.txt


title: HS-2

description:
CP-M_12
HS-LS_tpm5.txt


title: HS-13

description:
CP-M_46
HS-LS_tpm5.txt


title: LS-1

description:
CP-M_13
HS-LS_tpm5.txt


title: AL-73

description:
CP-L_89
L2PM-L2AL_tpm5.txt

value: visual cortex anterior lateral layer 2


title: AL-67

description:
CP-L_83
L2PM-L2AL_tpm5.txt


title: AL-61

description:
CP-L_77
L2PM-L2AL_tpm5.txt


title: AL-71

description:
CP-L_87
L2PM-L2AL_tpm5.txt


title: AL-69

description:
CP-L_85
L2PM-L2AL_tpm5.txt


title: AL-76

description:
CP-L_92
L2PM-L2AL_tpm5.txt


title: AL-64

description:
CP-L_80
L2PM-L2AL_tpm5.txt


title: AL-77

description:
CP-L_93
L2PM-L2AL_tpm5.txt


title: AL-62

description:
CP-L_78
L2PM-L2AL_tpm5.txt


title: AL-75

description:
CP-L_91
L2PM-L2AL_tpm5.txt


title: AL-72

description:
CP-L_88
L2PM-L2AL_tpm5.txt


title: AL-74

description:
CP-L_90
L2PM-L2AL_tpm5.txt


title: AL-78

description:
CP-L_94
L2PM-L2AL_tpm5.txt


title: AL-68

description:
CP-L_84
L2PM-L2AL_tpm5.txt


title: AL-63

description:
CP-L_79
L2PM-L2AL_tpm5.txt


title: AL-70

description:
CP-L_86
L2PM-L2AL_tpm5.txt


title: AL-60

description:
CP-L_76
L2PM-L2AL_tpm5.txt


title: AL-59

description:
CP-L_75
L2PM-L2AL_tpm5.txt


title: PM-85

description:
CP-L_73
L2PM-L2AL_tpm5.txt

value: visual cortex posterior medial layer 2


title: PM-84

description:
CP-L_72
L2PM-L2AL_tpm5.txt


title: PM-83

description:
CP-L_71
L2PM-L2AL_tpm5.txt


title: PM-82

description:
CP-L_69
L2PM-L2AL_tpm5.txt


title: PM-80

description:
CP-L_67
L2PM-L2AL_tpm5.txt


title: HS-1

description:
CP-M_11
HS-LS_tpm5.txt


title: PM-79

description:
CP-L_66
L2PM-L2AL_tpm5.txt


title: AL-65

description:
CP-L_81
L2PM-L2AL_tpm5.txt


title: PM-78

description:
CP-L_65
L2PM-L2AL_tpm5.txt


title: PM-77

description:
CP-L_63
L2PM-L2AL_tpm5.txt


title: PM-71

description:
CP-L_56
L2PM-L2AL_tpm5.txt


title: PM-69

description:
CP-H_9
L2PM-L2AL_tpm5.txt


title: PM-76

description:
CP-L_62
L2PM-L2AL_tpm5.txt


title: PM-75

description:
CP-L_61
L2PM-L2AL_tpm5.txt


title: PM-74

description:
CP-L_60
L2PM-L2AL_tpm5.txt


title: AL-55

description:
CP-H_50
L2PM-L2AL_tpm5.txt


title: AL-57

description:
CP-H_52
L2PM-L2AL_tpm5.txt


title: PM-73

description:
CP-L_58
L2PM-L2AL_tpm5.txt


title: PM-72

description:
CP-L_57
L2PM-L2AL_tpm5.txt


title: AL-66

description:
CP-L_82
L2PM-L2AL_tpm5.txt


title: PM-70

description:
CP-L_55
L2PM-L2AL_tpm5.txt


title: AL-50

description:
CP-H_45
L2PM-L2AL_tpm5.txt


title: PM-68

description:
CP-H_8
L2PM-L2AL_tpm5.txt


title: PM-66

description:
CP-H_6
L2PM-L2AL_tpm5.txt


title: PM-81

description:
CP-L_68
L2PM-L2AL_tpm5.txt


title: AL-56

description:
CP-H_51
L2PM-L2AL_tpm5.txt


title: PM-65

description:
CP-H_5
L2PM-L2AL_tpm5.txt


title: AL-58

description:
CP-H_53
L2PM-L2AL_tpm5.txt


title: AL-52

description:
CP-H_47
L2PM-L2AL_tpm5.txt


title: AL-47

description:
CP-H_42
L2PM-L2AL_tpm5.txt


title: AL-54

description:
CP-H_49
L2PM-L2AL_tpm5.txt


title: AL-51

description:
CP-H_46
L2PM-L2AL_tpm5.txt


title: AL-49

description:
CP-H_44
L2PM-L2AL_tpm5.txt


title: AL-48

description:
CP-H_43
L2PM-L2AL_tpm5.txt


title: AL-46

description:
CP-H_41
L2PM-L2AL_tpm5.txt


title: PM-64

description:
CP-H_4
L2PM-L2AL_tpm5.txt


title: PM-63

description:
CP-H_38
L2PM-L2AL_tpm5.txt


title: PM-61

description:
CP-H_36
L2PM-L2AL_tpm5.txt


title: PM-60

description:
CP-H_35
L2PM-L2AL_tpm5.txt


title: PM-62

description:
CP-H_37
L2PM-L2AL_tpm5.txt


title: PM-58

description:
CP-H_33
L2PM-L2AL_tpm5.txt


title: AL-53

description:
CP-H_48
L2PM-L2AL_tpm5.txt


title: PM-67

description:
CP-H_7
L2PM-L2AL_tpm5.txt


title: PM-57

description:
CP-H_32
L2PM-L2AL_tpm5.txt


title: PM-55

description:
CP-H_3
L2PM-L2AL_tpm5.txt


title: PM-53

description:
CP-H_28
L2PM-L2AL_tpm5.txt


title: PM-59

description:
CP-H_34
L2PM-L2AL_tpm5.txt


title: PM-52

description:
CP-H_27
L2PM-L2AL_tpm5.txt


title: PM-54

description:
CP-H_29
L2PM-L2AL_tpm5.txt


title: PM-51

description:
CP-H_26
L2PM-L2AL_tpm5.txt


title: PM-56

description:
CP-H_31
L2PM-L2AL_tpm5.txt


title: PM-47

description:
CP-H_21
L2PM-L2AL_tpm5.txt


title: PM-45

description:
CP-H_2
L2PM-L2AL_tpm5.txt


title: PM-44

description:
CP-H_19
L2PM-L2AL_tpm5.txt


title: PM-48

description:
CP-H_22
L2PM-L2AL_tpm5.txt


title: PM-46

description:
CP-H_20
L2PM-L2AL_tpm5.txt


title: PM-50

description:
CP-H_25
L2PM-L2AL_tpm5.txt


title: PM-49

description:
CP-H_24
L2PM-L2AL_tpm5.txt


title: PM-41

description:
CP-H_16
L2PM-L2AL_tpm5.txt


title: PM-42

description:
CP-H_17
L2PM-L2AL_tpm5.txt


title: PM-37

description:
CP-H_12
L2PM-L2AL_tpm5.txt


title: PM-36

description:
CP-H_11
L2PM-L2AL_tpm5.txt


title: PM-38

description:
CP-H_13
L2PM-L2AL_tpm5.txt


title: PM-43

description:
CP-H_18
L2PM-L2AL_tpm5.txt


title: PM-39

description:
CP-H_14
L2PM-L2AL_tpm5.txt


title: PM-33

description:
CP-G_93
L2PM-L2AL_tpm5.txt


title: PM-32

description:
CP-G_92
L2PM-L2AL_tpm5.txt


title: PM-40

description:
CP-H_15
L2PM-L2AL_tpm5.txt


title: AL-43

description:
CP-G_89
L2PM-L2AL_tpm5.txt


title: AL-45

description:
CP-G_91
L2PM-L2AL_tpm5.txt


title: AL-44

description:
CP-G_90
L2PM-L2AL_tpm5.txt


title: AL-42

description:
CP-G_88
L2PM-L2AL_tpm5.txt


title: AL-41

description:
CP-G_87
L2PM-L2AL_tpm5.txt


title: E11.5, biological replicate 1, single cells, transcriptome 17


title: AL-40

description:
CP-G_86
L2PM-L2AL_tpm5.txt


title: AL-38

description:
CP-G_84
L2PM-L2AL_tpm5.txt


title: AL-39

description:
CP-G_85
L2PM-L2AL_tpm5.txt


title: AL-37

description:
CP-G_83
L2PM-L2AL_tpm5.txt


title: PM-30

description:
CP-G_81
L2PM-L2AL_tpm5.txt


title: AL-36

description:
CP-G_77
L2PM-L2AL_tpm5.txt


title: PM-31

description:
CP-G_82
L2PM-L2AL_tpm5.txt


title: PM-29

description:
CP-G_80
L2PM-L2AL_tpm5.txt


title: PM-27

description:
CP-G_78
L2PM-L2AL_tpm5.txt


title: PM-28

description:
CP-G_79
L2PM-L2AL_tpm5.txt


title: AL-35

description:
CP-G_75
L2PM-L2AL_tpm5.txt


title: PM-35

description:
CP-H_10
L2PM-L2AL_tpm5.txt


title: PM-34

description:
CP-H_1
L2PM-L2AL_tpm5.txt


title: AL-34

description:
CP-G_74
L2PM-L2AL_tpm5.txt


title: PM-25

description:
CP-G_70
L2PM-L2AL_tpm5.txt


title: AL-32

description:
CP-G_72
L2PM-L2AL_tpm5.txt


title: PM-26

description:
CP-G_71
L2PM-L2AL_tpm5.txt


title: AL-33

description:
CP-G_73
L2PM-L2AL_tpm5.txt


title: AL-30

description:
CP-G_64
L2PM-L2AL_tpm5.txt


title: AL-29

description:
CP-G_63
L2PM-L2AL_tpm5.txt


title: AL-26

description:
CP-G_60
L2PM-L2AL_tpm5.txt


title: AL-28

description:
CP-G_62
L2PM-L2AL_tpm5.txt


title: AL-31

description:
CP-G_65
L2PM-L2AL_tpm5.txt


title: PM-23

description:
CP-G_67
L2PM-L2AL_tpm5.txt


title: AL-22

description:
CP-G_56
L2PM-L2AL_tpm5.txt


title: AL-27

description:
CP-G_61
L2PM-L2AL_tpm5.txt


title: AL-21

description:
CP-G_55
L2PM-L2AL_tpm5.txt


title: AL-20

description:
CP-G_54
L2PM-L2AL_tpm5.txt


title: AL-24

description:
CP-G_58
L2PM-L2AL_tpm5.txt


title: AL-25

description:
CP-G_59
L2PM-L2AL_tpm5.txt


title: AL-23

description:
CP-G_57
L2PM-L2AL_tpm5.txt


title: AL-17

description:
CP-E_76
L2PM-L2AL_tpm5.txt


title: AL-14

description:
CP-E_72
L2PM-L2AL_tpm5.txt


title: AL-15

description:
CP-E_73
L2PM-L2AL_tpm5.txt


title: AL-16

description:
CP-E_74
L2PM-L2AL_tpm5.txt


title: AL-18

description:
CP-E_77
L2PM-L2AL_tpm5.txt


title: AL-13

description:
CP-E_70
L2PM-L2AL_tpm5.txt


title: AL-11

description:
CP-E_66
L2PM-L2AL_tpm5.txt


title: AL-10

description:
CP-E_65
L2PM-L2AL_tpm5.txt


title: AL-9

description:
CP-E_64
L2PM-L2AL_tpm5.txt


title: PM-22

description:
CP-E_63
L2PM-L2AL_tpm5.txt


title: PM-21

description:
CP-E_62
L2PM-L2AL_tpm5.txt


title: PM-15

description:
CP-E_55
L2PM-L2AL_tpm5.txt


title: AL-19

description:
CP-E_78
L2PM-L2AL_tpm5.txt


title: PM-16

description:
CP-E_56
L2PM-L2AL_tpm5.txt


title: PM-17

description:
CP-E_57
L2PM-L2AL_tpm5.txt


title: PM-20

description:
CP-E_61
L2PM-L2AL_tpm5.txt


title: PM-18

description:
CP-E_58
L2PM-L2AL_tpm5.txt


title: AL-5

description:
CP-E_34
L2PM-L2AL_tpm5.txt


title: AL-8

description:
CP-E_38
L2PM-L2AL_tpm5.txt


title: AL-4

description:
CP-E_33
L2PM-L2AL_tpm5.txt


title: AL-3

description:
CP-E_32
L2PM-L2AL_tpm5.txt


title: AL-6

description:
CP-E_36
L2PM-L2AL_tpm5.txt


title: AL-7

description:
CP-E_37
L2PM-L2AL_tpm5.txt


title: AL-2

description:
CP-E_31
L2PM-L2AL_tpm5.txt


title: PM-14

description:
CP-E_29
L2PM-L2AL_tpm5.txt


title: PM-13

description:
CP-E_28
L2PM-L2AL_tpm5.txt


title: AL-1

description:
CP-E_30
L2PM-L2AL_tpm5.txt


title: PM-11

description:
CP-E_26
L2PM-L2AL_tpm5.txt


title: PM-9

description:
CP-E_24
L2PM-L2AL_tpm5.txt


title: PM-12

description:
CP-E_27
L2PM-L2AL_tpm5.txt


title: PM-10

description:
CP-E_25
L2PM-L2AL_tpm5.txt


title: AL-12

description:
CP-E_68
L2PM-L2AL_tpm5.txt


title: PM-6

description:
CP-E_21
L2PM-L2AL_tpm5.txt


title: PM-7

description:
CP-E_22
L2PM-L2AL_tpm5.txt


title: PM-5

description:
CP-E_20
L2PM-L2AL_tpm5.txt


title: PM-4

description:
CP-E_19
L2PM-L2AL_tpm5.txt


title: PM-3

description:
CP-E_18
L2PM-L2AL_tpm5.txt


title: PM-2

description:
CP-E_17
L2PM-L2AL_tpm5.txt


title: nc14_posterior_rep1

city: San Francisco

first: Michael

last: Stadler

state: California

address: 1519B York St.

data_processing:
Mapping with bowtie
All analyses with custom Python/R/Perl scripts
Genome_build: dm3 (R5_22)
Supplementary_files_format_and_content: Excel file of boundary calls by algorithm, manual, and merged.

organism: Drosophila melanogaster

growth_protocol: Flies were grown in a population cage, embryos were collected for one hour, aged appropriately at 25C.

extract_protocol:
Embryos were dounced multiple times, solubilized with SDS.
Standard Illumina: sonicate, repair ends, add A-overhanges, ligate adaptors, PCR.

treatment_protocol: Formaldehyde cross-linked

tag: developmental stage

value: nc14 (early cellularized embryo)

value: embryo posterior half


title: PM-24

description:
CP-G_68
L2PM-L2AL_tpm5.txt


title: L2Ant-34

description:
CP-F_92
V1L2Ant-V1L2Post_tpm5.txt

value: anterior primary visual cortex layer 2


title: L2Ant-35

description:
CP-F_93
V1L2Ant-V1L2Post_tpm5.txt


title: nc14_whole_rep1

value: whole embryo


title: nc14_anterior_rep1

value: embryo anterior half


title: L2Post-39

description:
CP-F_9
V1L2Ant-V1L2Post_tpm5.txt

value: posterior primary visual cortex layer 2


title: PM-8

description:
CP-E_23
L2PM-L2AL_tpm5.txt


title: L2Ant-33

description:
CP-F_91
V1L2Ant-V1L2Post_tpm5.txt


title: nc14_whole_rep2


title: nc12_whole_rep2


title: nc14_anterior_rep2


title: L2Ant-32

description:
CP-F_90
V1L2Ant-V1L2Post_tpm5.txt


title: L2Ant-29

description:
CP-F_87
V1L2Ant-V1L2Post_tpm5.txt


title: L2Ant-31

description:
CP-F_89
V1L2Ant-V1L2Post_tpm5.txt


title: nc14_posterior_rep2


title: CGN RNA_seq Kdm6b knockdown Rep3

city: Durham

first: Anne

last: West

state: NC

address: 311 research drive

department: Neurobiology

institute: Duke University

data_processing:
Hiseq 4000 reads were trimmed (Trimmomatic)
RNAseq were aligned to the mm9 genome (TopHat2),  counted for each gene (htseq-count) and compiled in the kdm6b_rna_counts.txt tsv
Read counts were analyzed by edgeR using DESeq2’s independent filtering method to determine the cutoff for the minimum read counts per sample.
For Kdm6b analysis, the model that edgeR tested included terms for batch effects between the replicates since they were not all generated at the same time. Kdm6b genes that were differentially expressed (FDR < 0.05) and expressed at biological relevant levels (absolute logFC > 0.5 and RPKM > 5).
Genome_build: mm9
Supplementary_files_format_and_content: text file on series record with raw read counts for all samples and bigwig files on each sample.

source_name: Postnatal day 7 cerebellar granule neurons (kdm6b knockdown)

growth_protocol: Cerebella from a litter of P7 mice were chopped into small pieces then digested at 37°C for 30 min in 10 U/ml papain (Worthington), 200 µg/ml l-cysteine (Sigma), and 250 U/ml DNase (Sigma) in PBS. The tissue was mechanically triturated in PBS with trypsin inhibi-tor and 250 U/ml DNase then centrifuged and resuspended in PBS/BSA. The cell suspension was passed through a cell strainer (Becton Dickinson), layered on a step gradient of 35% and 65% Percoll (Sigma), and centrifuged at 2,500 rpm for 12 min at 25°C. GNPs were harvested from the 35/65% interface, washed in PBS/BSA, resuspended in neurobasal medium with B27 supplements and 2% FBS and plated on poly-d-lysine–coated dishes. In certain cases, as noted in the text, Brain-Derived Neurotrophic Factor (Peprotech) was added at 50 ng/ml.

extract_protocol:
RNA was harvested using Qiagen RNeasy Mini Kit (Cat# 74104).  Potential DNA contamination was removed by on-column DNase’s digestion using Qiagen’s RNase-free DNase Set (Cat# 79254).
Stranded mRNA-seq was done by Duke Sequencing core facility using the Kapa Stranded mRNA-Seq library prep kit to make sequencing libraries, which are typically sequenced on Illumina instruments with a 50 bp single end reads length.

treatment_protocol: RNA interference, we used shRNAs targeting non-overlapping sequences in mouse Kdm6b that were cloned in the lentiviral vector pLKO.1 (Thermo Scientific). Kdm6b shRNA (TRC#0000095266): GTTCGTTACAAGTGAGAACTC. Empty pLKO.1 vector was used as the control. Viral shRNAs were packaged as lentivirus in HEK293T cells (ATCC). Neurons in culture were infected with virus on DIV1.

value: Postnatal day 7

value: cerebellum

value: cerebellar granule neurons


title: CGN RNA_seq Kdm6b knockdown Rep1


title: PM-1

description:
CP-E_16
L2PM-L2AL_tpm5.txt

value: 129S2/SvPasCrl, CD-1 mix

value: postnatal day >p35


title: CGN RNA_seq Control Rep3

source_name: Postnatal day 7 cerebellar granule neurons (control)


title: L2Ant-28

description:
CP-F_86
V1L2Ant-V1L2Post_tpm5.txt

value: SepW1-Cre, WT


title: L2Post-38

description:
CP-F_85
V1L2Ant-V1L2Post_tpm5.txt


title: Stage5_whole_rep1

value: stage 5 (early cellularized embryo)


title: V1PM-41

description:
CP-N_92
V1ALPr-V1PMPr_tpm5.txt

value: primary visual cortex layer 2

tag: axonal projection

value: visual ctx layer 2 -> posterior medial


title: L2Post-35

description:
CP-F_82
V1L2Ant-V1L2Post_tpm5.txt


title: L2Post-34

description:
CP-F_81
V1L2Ant-V1L2Post_tpm5.txt


title: L2Post-32

description:
CP-F_8
V1L2Ant-V1L2Post_tpm5.txt


title: CGN RNA_seq Kdm6b knockdown Rep2


title: nc12_whole_rep1


title: CGN RNA_seq Control Rep2


title: L2Post-37

description:
CP-F_84
V1L2Ant-V1L2Post_tpm5.txt


title: L2Post-36

description:
CP-F_83
V1L2Ant-V1L2Post_tpm5.txt


title: CGN RNA_seq Control Rep1


title: V1AL-42

description:
CP-N_9
V1ALPr-V1PMPr_tpm5.txt

value: visual ctx layer 2 -> anterior lateral


title: L2Ant-30

description:
CP-F_88
V1L2Ant-V1L2Post_tpm5.txt


title: L2Post-33

description:
CP-F_80
V1L2Ant-V1L2Post_tpm5.txt


title: L2Post-29

description:
CP-F_77
V1L2Ant-V1L2Post_tpm5.txt


title: V1PM-40

description:
CP-N_91
V1ALPr-V1PMPr_tpm5.txt


title: V1AL-41

description:
CP-N_87
V1ALPr-V1PMPr_tpm5.txt


title: V1PM-37

description:
CP-N_88
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-30

description:
CP-F_78
V1L2Ant-V1L2Post_tpm5.txt


title: V1PM-39

description:
CP-N_90
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-28

description:
CP-F_76
V1L2Ant-V1L2Post_tpm5.txt


title: L2Post-27

description:
CP-F_75
V1L2Ant-V1L2Post_tpm5.txt


title: V1AL-39

description:
CP-N_85
V1ALPr-V1PMPr_tpm5.txt


title: V1AL-38

description:
CP-N_84
V1ALPr-V1PMPr_tpm5.txt


title: V1AL-37

description:
CP-N_83
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-31

description:
CP-F_79
V1L2Ant-V1L2Post_tpm5.txt


title: V1PM-36

description:
CP-N_80
V1ALPr-V1PMPr_tpm5.txt


title: V1PM-38

description:
CP-N_89
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-24

description:
CP-F_72
V1L2Ant-V1L2Post_tpm5.txt


title: V1AL-36

description:
CP-N_8
V1ALPr-V1PMPr_tpm5.txt


title: STEM-seq E7.5Ect rep3

status: Public on Dec 05 2017

city: Beijing

first: Wei

last: Xie

address: Zhongguancun north street

institute: Tsinghua University

description: Processed data file: stage.mCG.gz in STEM-seq-methylC_mCG.tar.

data_processing:
Base calls were performed using CASAVA version 1.8. Early embryo STEM-seq reads were aligned to the mm9 genome using BSseeker2.0.8. Replicates of same stage were pooled together and methylation values in wiggle files were computed for each single base. ES cell STEM-seq and MethylC-seq reads were aligned to the mm9 genome using BSseeker2.0.8. Replicates of same stage were pooled together and methylation values in wiggle files were computed by the number of reads falling into 1,000bp bin in the genome.
 Genome_build: mm9.
Supplementary_files_format_and_content: The bedgraph files counted the number of reads falling on each base or 1,000bp bin in the genome.

source_name: Postimplantation embryo

extract_protocol: Embryos were washed with PBS and incubated in lysis buffer. STEM-seq libraries were constructed following the protocol described in this study (Zhang et al., Nature Genetics, 2017).

treatment_protocol: C57BL/6N female mice were induced for superovulation by injections of 5 IU of pregnant mare’s serum gonadotrophin and 5 IU of human chorionic gonadotrophin (44-48 hours apart) and mated to DBA/2N males.

value: C57BL/6N x DBA/2N

value: Ectoderm


title: L2Post-23

description:
CP-F_71
V1L2Ant-V1L2Post_tpm5.txt


title: V1PM-35

description:
CP-N_79
V1ALPr-V1PMPr_tpm5.txt


title: V1AL-40

description:
CP-N_86
V1ALPr-V1PMPr_tpm5.txt


title: V1PM-33

description:
CP-N_77
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-20

description:
CP-F_69
V1L2Ant-V1L2Post_tpm5.txt


title: V1PM-34

description:
CP-N_78
V1ALPr-V1PMPr_tpm5.txt


title: V1PM-32

description:
CP-N_76
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-21

description:
CP-F_7
V1L2Ant-V1L2Post_tpm5.txt


title: V1PM-31

description:
CP-N_75
V1ALPr-V1PMPr_tpm5.txt


title: V1PM-29

description:
CP-N_73
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-19

description:
CP-F_68
V1L2Ant-V1L2Post_tpm5.txt


title: V1PM-30

description:
CP-N_74
V1ALPr-V1PMPr_tpm5.txt


title: V1PM-28

description:
CP-N_72
V1ALPr-V1PMPr_tpm5.txt


title: L2Ant-25

description:
CP-F_62
V1L2Ant-V1L2Post_tpm5.txt


title: V1PM-27

description:
CP-N_71
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-25

description:
CP-F_73
V1L2Ant-V1L2Post_tpm5.txt


title: L2Ant-26

description:
CP-F_63
V1L2Ant-V1L2Post_tpm5.txt


title: L2Post-26

description:
CP-F_74
V1L2Ant-V1L2Post_tpm5.txt


title: V1PM-26

description:
CP-N_70
V1ALPr-V1PMPr_tpm5.txt


title: L2Ant-24

description:
CP-F_61
V1L2Ant-V1L2Post_tpm5.txt


title: L2Ant-23

description:
CP-F_60
V1L2Ant-V1L2Post_tpm5.txt


title: L2Post-17

description:
CP-F_6
V1L2Ant-V1L2Post_tpm5.txt


title: L2Post-22

description:
CP-F_70
V1L2Ant-V1L2Post_tpm5.txt


title: L2Ant-21

description:
CP-F_58
V1L2Ant-V1L2Post_tpm5.txt


title: V1PM-25

description:
CP-N_69
V1ALPr-V1PMPr_tpm5.txt


title: V1PM-24

description:
CP-N_68
V1ALPr-V1PMPr_tpm5.txt


title: V1AL-35

description:
CP-N_7
V1ALPr-V1PMPr_tpm5.txt


title: V1PM-23

description:
CP-N_67
V1ALPr-V1PMPr_tpm5.txt


title: V1PM-22

description:
CP-N_66
V1ALPr-V1PMPr_tpm5.txt


title: L2Ant-20

description:
CP-F_57
V1L2Ant-V1L2Post_tpm5.txt


title: L2Ant-27

description:
CP-F_65
V1L2Ant-V1L2Post_tpm5.txt


title: L2Ant-19

description:
CP-F_56
V1L2Ant-V1L2Post_tpm5.txt


title: V1PM-20

description:
CP-N_63
V1ALPr-V1PMPr_tpm5.txt


title: PM-19

description:
CP-E_59
L2PM-L2AL_tpm5.txt

value: visual cortex posterior medial layer 2


title: L2Post-16

description:
CP-F_53
V1L2Ant-V1L2Post_tpm5.txt


title: L2Ant-18

description:
CP-F_55
V1L2Ant-V1L2Post_tpm5.txt

value: anterior primary visual cortex layer 2


title: V1AL-34

description:
CP-N_62
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-15

description:
CP-F_52
V1L2Ant-V1L2Post_tpm5.txt


title: L2Ant-17

description:
CP-F_54
V1L2Ant-V1L2Post_tpm5.txt


title: V1AL-33

description:
CP-N_61
V1ALPr-V1PMPr_tpm5.txt


title: V1AL-32

description:
CP-N_60
V1ALPr-V1PMPr_tpm5.txt


title: V1AL-31

description:
CP-N_6
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-12

description:
CP-F_5
V1L2Ant-V1L2Post_tpm5.txt


title: L2Post-13

description:
CP-F_50
V1L2Ant-V1L2Post_tpm5.txt


title: V1AL-30

description:
CP-N_59
V1ALPr-V1PMPr_tpm5.txt


title: L2Ant-22

description:
CP-F_59
V1L2Ant-V1L2Post_tpm5.txt


title: L2Post-14

description:
CP-F_51
V1L2Ant-V1L2Post_tpm5.txt


title: V1AL-29

description:
CP-N_58
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-11

description:
CP-F_49
V1L2Ant-V1L2Post_tpm5.txt


title: V1AL-28

description:
CP-N_57
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-9

description:
CP-F_47
V1L2Ant-V1L2Post_tpm5.txt


title: V1AL-27

description:
CP-N_56
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-10

description:
CP-F_48
V1L2Ant-V1L2Post_tpm5.txt


title: V1PM-21

description:
CP-N_65
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-8

description:
CP-F_46
V1L2Ant-V1L2Post_tpm5.txt


title: L2Post-7

description:
CP-F_44
V1L2Ant-V1L2Post_tpm5.txt


title: V1AL-25

description:
CP-N_54
V1ALPr-V1PMPr_tpm5.txt


title: V1AL-24

description:
CP-N_53
V1ALPr-V1PMPr_tpm5.txt


title: V1AL-26

description:
CP-N_55
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-5

description:
CP-F_42
V1L2Ant-V1L2Post_tpm5.txt


title: L2Post-18

description:
CP-F_66
V1L2Ant-V1L2Post_tpm5.txt


title: L2Post-4

description:
CP-F_3
V1L2Ant-V1L2Post_tpm5.txt


title: L2Ant-16

description:
CP-F_26
V1L2Ant-V1L2Post_tpm5.txt


title: L2Ant-15

description:
CP-F_25
V1L2Ant-V1L2Post_tpm5.txt


title: V1AL-20

description:
CP-N_5
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-6

description:
CP-F_43
V1L2Ant-V1L2Post_tpm5.txt


title: V1AL-19

description:
CP-N_49
V1ALPr-V1PMPr_tpm5.txt


title: V1AL-22

description:
CP-N_51
V1ALPr-V1PMPr_tpm5.txt


title: L2Ant-14

description:
CP-F_24
V1L2Ant-V1L2Post_tpm5.txt


title: V1AL-17

description:
CP-N_47
V1ALPr-V1PMPr_tpm5.txt


title: V1AL-21

description:
CP-N_50
V1ALPr-V1PMPr_tpm5.txt


title: V1AL-16

description:
CP-N_46
V1ALPr-V1PMPr_tpm5.txt


title: L2Ant-12

description:
CP-F_22
V1L2Ant-V1L2Post_tpm5.txt


title: V1AL-18

description:
CP-N_48
V1ALPr-V1PMPr_tpm5.txt


title: L2Ant-13

description:
CP-F_23
V1L2Ant-V1L2Post_tpm5.txt


title: L2Ant-11

description:
CP-F_21
V1L2Ant-V1L2Post_tpm5.txt


title: V1AL-15

description:
CP-N_45
V1ALPr-V1PMPr_tpm5.txt


title: L2Ant-10

description:
CP-F_20
V1L2Ant-V1L2Post_tpm5.txt


title: V1AL-14

description:
CP-N_43
V1ALPr-V1PMPr_tpm5.txt


title: V1PM-19

description:
CP-N_42
V1ALPr-V1PMPr_tpm5.txt


title: V1PM-18

description:
CP-N_41
V1ALPr-V1PMPr_tpm5.txt


title: L2Ant-9

description:
CP-F_19
V1L2Ant-V1L2Post_tpm5.txt


title: L2Ant-8

description:
CP-F_18
V1L2Ant-V1L2Post_tpm5.txt


title: V1AL-23

description:
CP-N_52
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-3

description:
CP-F_2
V1L2Ant-V1L2Post_tpm5.txt


title: L2Ant-6

description:
CP-F_16
V1L2Ant-V1L2Post_tpm5.txt


title: V1AL-13

description:
CP-N_4
V1ALPr-V1PMPr_tpm5.txt


title: V1PM-17

description:
CP-N_40
V1ALPr-V1PMPr_tpm5.txt


title: V1PM-16

description:
CP-N_37
V1ALPr-V1PMPr_tpm5.txt


title: L2Ant-7

description:
CP-F_17
V1L2Ant-V1L2Post_tpm5.txt


title: V1PM-15

description:
CP-N_36
V1ALPr-V1PMPr_tpm5.txt


title: V1PM-14

description:
CP-N_35
V1ALPr-V1PMPr_tpm5.txt


title: L2Ant-4

description:
CP-F_14
V1L2Ant-V1L2Post_tpm5.txt


title: L2Ant-3

description:
CP-F_13
V1L2Ant-V1L2Post_tpm5.txt


title: V1PM-13

description:
CP-N_34
V1ALPr-V1PMPr_tpm5.txt


title: V1PM-10

description:
CP-N_31
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-1

description:
CP-F_1
V1L2Ant-V1L2Post_tpm5.txt


title: V1PM-12

description:
CP-N_33
V1ALPr-V1PMPr_tpm5.txt


title: V1AL-12

description:
CP-N_3
V1ALPr-V1PMPr_tpm5.txt


title: L2Post-2

description:
CP-F_10
V1L2Ant-V1L2Post_tpm5.txt


title: V1PM-9

description:
CP-N_30
V1ALPr-V1PMPr_tpm5.txt


title: L3L2-37

description:
CP-H_93
L2-L3_tpm5.txt

value: visual cortex layer 3


title: L3L2-36

description:
CP-H_92
L2-L3_tpm5.txt


title: V1PM-8

description:
CP-N_29
V1ALPr-V1PMPr_tpm5.txt


title: V1PM-7

description:
CP-N_28
V1ALPr-V1PMPr_tpm5.txt


title: V1PM-6

description:
CP-N_27
V1ALPr-V1PMPr_tpm5.txt


title: L3L2-34

description:
CP-H_90
L2-L3_tpm5.txt


title: V1PM-5

description:
CP-N_26
V1ALPr-V1PMPr_tpm5.txt


title: L3L2-35

description:
CP-H_91
L2-L3_tpm5.txt


title: L2Ant-5

description:
CP-F_15
V1L2Ant-V1L2Post_tpm5.txt


title: V1PM-4

description:
CP-N_25
V1ALPr-V1PMPr_tpm5.txt


title: L3L2-33

description:
CP-H_89
L2-L3_tpm5.txt


title: V1PM-3

description:
CP-N_24
V1ALPr-V1PMPr_tpm5.txt


title: L2L3-37

description:
CP-H_87
L2-L3_tpm5.txt

value: visual cortex layer 2


title: L2L3-38

description:
CP-H_88
L2-L3_tpm5.txt


title: L2L3-36

description:
CP-H_86
L2-L3_tpm5.txt


title: V1PM-2

description:
CP-N_23
V1ALPr-V1PMPr_tpm5.txt


title: L2L3-35

description:
CP-H_85
L2-L3_tpm5.txt


title: L2Ant-2

description:
CP-F_12
V1L2Ant-V1L2Post_tpm5.txt


title: L2Ant-1

description:
CP-F_11
V1L2Ant-V1L2Post_tpm5.txt


title: V1PM-1

description:
CP-N_22
V1ALPr-V1PMPr_tpm5.txt


title: L2L3-34

description:
CP-H_84
L2-L3_tpm5.txt


title: V1PM-11

description:
CP-N_32
V1ALPr-V1PMPr_tpm5.txt


title: V1AL-11

description:
CP-N_21
V1ALPr-V1PMPr_tpm5.txt


title: L3L2-32

description:
CP-H_83
L2-L3_tpm5.txt


title: V1AL-10

description:
CP-N_2
V1ALPr-V1PMPr_tpm5.txt


title: V1AL-9

description:
CP-N_19
V1ALPr-V1PMPr_tpm5.txt


title: L3L2-30

description:
CP-H_81
L2-L3_tpm5.txt


title: L3L2-31

description:
CP-H_82
L2-L3_tpm5.txt


title: L3L2-29

description:
CP-H_80
L2-L3_tpm5.txt


title: V1AL-8

description:
CP-N_18
V1ALPr-V1PMPr_tpm5.txt


title: V1AL-7

description:
CP-N_17
V1ALPr-V1PMPr_tpm5.txt


title: L3L2-28

description:
CP-H_79
L2-L3_tpm5.txt


title: L2L3-33

description:
CP-H_78
L2-L3_tpm5.txt


title: V1AL-5

description:
CP-N_15
V1ALPr-V1PMPr_tpm5.txt


title: V1AL-6

description:
CP-N_16
V1ALPr-V1PMPr_tpm5.txt


title: V1AL-4

description:
CP-N_14
V1ALPr-V1PMPr_tpm5.txt


title: L2L3-32

description:
CP-H_77
L2-L3_tpm5.txt


title: V1AL-3

description:
CP-N_13
V1ALPr-V1PMPr_tpm5.txt


title: L2L3-31

description:
CP-H_76
L2-L3_tpm5.txt


title: L2L3-30

description:
CP-H_75
L2-L3_tpm5.txt


title: V1AL-1

description:
CP-N_1
V1ALPr-V1PMPr_tpm5.txt


title: L2L3-29

description:
CP-H_74
L2-L3_tpm5.txt


title: L5Cal-29

description:
CP-T_9
L5Cal-L5Front_tpm5.txt

value: visual cortex layer 5

value: layer 5 -> contralateral ctx


title: L3L2-26

description:
CP-H_72
L2-L3_tpm5.txt


title: L3L2-24

description:
CP-H_70
L2-L3_tpm5.txt


title: L5Front-51

description:
CP-T_87
L5Cal-L5Front_tpm5.txt

value: layer 5 -> frontal ctx


title: L5Front-50

description:
CP-T_85
L5Cal-L5Front_tpm5.txt


title: L3L2-25

description:
CP-H_71
L2-L3_tpm5.txt


title: L3L2-23

description:
CP-H_69
L2-L3_tpm5.txt


title: L5Front-49

description:
CP-T_84
L5Cal-L5Front_tpm5.txt


title: L2L3-28

description:
CP-H_68
L2-L3_tpm5.txt


title: L5Front-48

description:
CP-T_83
L5Cal-L5Front_tpm5.txt


title: L5Front-47

description:
CP-T_82
L5Cal-L5Front_tpm5.txt


title: L5Front-44

description:
CP-T_79
L5Cal-L5Front_tpm5.txt