title: 207s_I18

description: Mouse non-parenchymal single cells


title: 207s_I24

status: Public on Apr 29 2023

type: SRA

city: Huddinge

first: Ping

last: Chen

address: Alfred Nobels allé 8

department: Department of Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description: Mouse non-parenchymal single cells

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were de-multiplexed and converted into fastq format for each cell by using Illumina bcl2fastq with default setting.
Reads were aligned to human genome mm10 using the STAR aligner.
Uniquely aligned reads mapping to the RefSeq gene annotations were used for gene expression estimates at reads per kilobase transcript and million mapped reads (RPKMs) using rpkmforgenes.
Low quality cells were excluded from downstream analysis when they failed to meet the following criteria for retaining cells: 1) >= 50,000 sequence reads; 2) >= 20% of reads uniquely aligned to the genome; 3) >= 40% of these reads mapping to RefSeq annotated exons; 4) >= 1000 genes with RPKM >= 1; and 5) < 25% of mitochondrial gene expression. In addition, doublets detected by Scrublet were further removed.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each single cell.

molecule: total RNA

organism: Mus musculus

source_name: Mouse non-parenchymal single cells

growth_protocol: Not applicable

extract_protocol:
Not applicable
The reverse-transcribed cDNA from single cells was amplified followed by tagmentation and a standard index PCR. The single cell libraries were prepared according to Smart-seq2 protocol. The sequencing was performed on HISEQ 3000 (IIlumina).
Smart-seq2 single cell RNA-Seq

treatment_protocol: Not applicable

tag: tissue

value: Liver

tag: disease state


title: 207s_I17

description: Mouse non-parenchymal single cells


title: 207s_H7

description: Mouse non-parenchymal single cells


title: 207s_I23

description: Mouse non-parenchymal single cells


title: 207s_I3

description: Mouse non-parenchymal single cells


title: 207s_I13

description: Mouse non-parenchymal single cells


title: 207s_I12

description: Mouse non-parenchymal single cells


title: 207s_K16

description: Mouse non-parenchymal single cells


title: 207s_I10

description: Mouse non-parenchymal single cells


title: 207s_H6

description: Mouse non-parenchymal single cells


title: 207s_I1

description: Mouse non-parenchymal single cells


title: 207s_H9

description: Mouse non-parenchymal single cells


title: 207s_H3

description: Mouse non-parenchymal single cells


title: 207s_I5

description: Mouse non-parenchymal single cells


title: 207s_H19

description: Mouse non-parenchymal single cells


title: 207s_H13

description: Mouse non-parenchymal single cells


title: 207s_H11

description: Mouse non-parenchymal single cells


title: 207s_H17

description: Mouse non-parenchymal single cells


title: 207s_G2

description: Mouse non-parenchymal single cells


title: 207s_H12

description: Mouse non-parenchymal single cells


title: 207s_G7

description: Mouse non-parenchymal single cells


title: 207s_G24

description: Mouse non-parenchymal single cells


title: 207s_G23

description: Mouse non-parenchymal single cells


title: 207s_G22

description: Mouse non-parenchymal single cells


title: 207s_G6

description: Mouse non-parenchymal single cells


title: 207s_G21

description: Mouse non-parenchymal single cells


title: 207s_G19

description: Mouse non-parenchymal single cells


title: 207s_G16

description: Mouse non-parenchymal single cells


title: 207s_G14

description: Mouse non-parenchymal single cells


title: 207s_G1

description: Mouse non-parenchymal single cells


title: 207s_F6

description: Mouse non-parenchymal single cells


title: 207s_F9

description: Mouse non-parenchymal single cells


title: 207s_G11

description: Mouse non-parenchymal single cells


title: 207s_F7

description: Mouse non-parenchymal single cells


title: 207s_F3

description: Mouse non-parenchymal single cells


title: 207s_G13

description: Mouse non-parenchymal single cells


title: 207s_G18

description: Mouse non-parenchymal single cells


title: 207s_F24

description: Mouse non-parenchymal single cells


title: 207s_F4

description: Mouse non-parenchymal single cells


title: 207s_F5

description: Mouse non-parenchymal single cells


title: 207s_F21

description: Mouse non-parenchymal single cells


title: 207s_H23

description: Mouse non-parenchymal single cells


title: 207s_F2

description: Mouse non-parenchymal single cells


title: 207s_F15

description: Mouse non-parenchymal single cells


title: 207s_F14

description: Mouse non-parenchymal single cells


title: 207s_F16

description: Mouse non-parenchymal single cells


title: 207s_F20

description: Mouse non-parenchymal single cells


title: 207s_F13

description: Mouse non-parenchymal single cells


title: 207s_F12

description: Mouse non-parenchymal single cells


title: 207s_F11

description: Mouse non-parenchymal single cells


title: 207s_E21

description: Mouse non-parenchymal single cells


title: 207s_F10

description: Mouse non-parenchymal single cells


title: 207s_H2

description: Mouse non-parenchymal single cells


title: 207s_G15

description: Mouse non-parenchymal single cells


title: 207s_F18

description: Mouse non-parenchymal single cells


title: 207s_E22

description: Mouse non-parenchymal single cells


title: 207s_E9

description: Mouse non-parenchymal single cells


title: 207s_E4

description: Mouse non-parenchymal single cells


title: 207s_E6

description: Mouse non-parenchymal single cells


title: 207s_E5

description: Mouse non-parenchymal single cells


title: 207s_E13

description: Mouse non-parenchymal single cells


title: 207s_E3

description: Mouse non-parenchymal single cells


title: 207s_E24

description: Mouse non-parenchymal single cells


title: 207s_E15

description: Mouse non-parenchymal single cells


title: 207s_E20

description: Mouse non-parenchymal single cells


title: 207s_E19

description: Mouse non-parenchymal single cells


title: 207s_E12

description: Mouse non-parenchymal single cells


title: 207s_E17

description: Mouse non-parenchymal single cells


title: 207s_E2

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_990

city: Cardiff

first: Jimena

last: Monzón-Sandoval

address: Maindy Road

country: United Kingdom

institute: UK Dementia Research Institute at Cardiff University

data_processing:
The quality of the sequences was assessed using FastQC (version 0.11.8) and results summarized using MultiQC.
After removing adapters by TrimGalore (version 0.5.0) transcript abundances was quantified using Kallisto (version 0.46.0)
The reference index used include the all cDNA, ncRNA sequences from Ensembl (release 99, GRCh38) as well as the Array Control RNA spike sequences from Thermo Fisher. Sequences in scaffold chromosomes were removed and we kept only chromosomes 1-22, X and Y.
We removed cells with less than 25% of reads mapping to protein coding genes and retained cells with at least half a million reads. We further removed an outlier sample from 12 PCW. We filtered out lowly expressed genes, keeping only those with more the 5 counts in at least 1% of the cells. The filtered dataset consisted of 14673 protein coding genes across 358 cells.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: MGE_counts_gene_level.txt: estimated counts per gene in tab separated values
Supplementary files format and content: MGE_metadata_filtered.txt metadata in tab separated values

molecule: polyA RNA

organism: Homo sapiens

source_name: medial ganglionic eminence (MGE)

extract_protocol:
Human fetal tissue was collected from medical terminations of pregnancy with full donor consent, through the SWIFT human fetal tissue bank (http://www.biobankswales.org.uk/swift-research-tissue-bank), under UK Human Tissue Authority research license (No. 12457) held by Cardiff University and with ethical approval of the project from the Bro Taf local research ethics committee. Gestational age was estimated through ultrasound scan prior to the procedure in combination with measurement of fetal regions. MGE tissue was harvested from seven fetuses corresponds to approximately 10, 12-15  post conception weeks (PCW). MGEs were individually incubated at 37°C for 20 min in TrypLE Express containing Donase-α. Tissue was dissociated by trituration in 200 μl of DMEM/D to obtain a quasi-single-cell suspension. The cell concentration was calculated by manual counting and viability measured by Trypan Blue assay.
Single cells were captured according to the manufacturer's protocol on a C1 Single-Cell IFC microfluidic chip designed for 10- to 17-μm cells (Fluidigm, Inc). This captured one cell in each of up to 96 capture chambers. Capture efficiency and cell viability was determined by microscopy before cDNA amplification and library preparation using the SMART-Seq 46 v4 Ultra Low Input RNA kit chemistry (Clontech) and Nextera XT DNA Library Prep Index Kit (Illumina). Single cell sequencing was carried out on HiSeq 4000 Illumina platform with the following parameters: paired-end reads, read length 2 x 75bp and read depth of approximately 1 million reads per cell.

value: medial ganglionic eminence (MGE)

tag: group

tag: developmental stage_pcw

tag: batch

tag: sample id


title: MGE_B_12pcw_996


title: MGE_B_12pcw_999


title: MGE_B_12pcw_998


title: 207s_E8

description: Mouse non-parenchymal single cells


title: 207s_E18

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_992


title: MGE_B_12pcw_991


title: 207s_E23

description: Mouse non-parenchymal single cells


title: 207s_E11

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_989


title: MGE_B_12pcw_995


title: MGE_B_12pcw_987


title: MGE_B_12pcw_988


title: 207s_D9

description: Mouse non-parenchymal single cells


title: 207s_E10

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_997


title: 207s_D7

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_986


title: MGE_B_12pcw_984


title: 207s_D6

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_985


title: MGE_B_12pcw_993


title: MGE_B_12pcw_994


title: 207s_D21

description: Mouse non-parenchymal single cells


title: 207s_E16

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_982


title: 207s_E14

description: Mouse non-parenchymal single cells


title: 207s_D5

description: Mouse non-parenchymal single cells


title: 207s_D8

description: Mouse non-parenchymal single cells


title: 207s_D24

description: Mouse non-parenchymal single cells


title: 207s_D20

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_978


title: MGE_A_14pcw_979


title: 207s_D15

description: Mouse non-parenchymal single cells


title: 207s_D17

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_980


title: 207s_D14

description: Mouse non-parenchymal single cells


title: MGE_B_12pcw_981


title: MGE_A_14pcw_976


title: 207s_D11

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_973


title: MGE_A_14pcw_977


title: MGE_A_14pcw_974


title: MGE_A_14pcw_975


title: 207s_D1

description: Mouse non-parenchymal single cells


title: 207s_D13

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_971


title: 207s_C3

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_972


title: MGE_A_14pcw_970


title: MGE_B_12pcw_983


title: 207s_C9

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_969


title: 207s_C22

description: Mouse non-parenchymal single cells


title: 207s_C6

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_968


title: 207s_D12

description: Mouse non-parenchymal single cells


title: 207s_C20

description: Mouse non-parenchymal single cells


title: 207s_C23

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_963


title: MGE_A_14pcw_964


title: MGE_A_14pcw_965


title: 207s_C21

description: Mouse non-parenchymal single cells


title: 207s_C7

description: Mouse non-parenchymal single cells


title: 207s_C2

description: Mouse non-parenchymal single cells


title: 207s_C14

description: Mouse non-parenchymal single cells


title: 207s_C8

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_961


title: MGE_A_14pcw_960


title: 207s_C13

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_958


title: MGE_A_14pcw_962


title: 207s_C19

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_957


title: 207s_C16

description: Mouse non-parenchymal single cells


title: 207s_C24

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_956


title: 207s_C15

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_955


title: MGE_A_14pcw_967


title: MGE_A_14pcw_954


title: 207s_C11

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_966


title: MGE_A_14pcw_952


title: 207s_C10

description: Mouse non-parenchymal single cells


title: 207s_B5

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_951


title: MGE_A_14pcw_959


title: 207s_B22

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_950


title: 207s_B6

description: Mouse non-parenchymal single cells


title: 207s_B2

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_949


title: 207s_A9

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_945


title: 207s_A8

description: Mouse non-parenchymal single cells


title: 207s_B1

description: Mouse non-parenchymal single cells


title: 207s_B20

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_944


title: 207s_B23

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_947


title: 207s_A3

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_942


title: MGE_A_14pcw_943


title: MGE_A_14pcw_941


title: 207s_A21

description: Mouse non-parenchymal single cells


title: 207s_B9

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_953


title: 207s_A22

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_940


title: 207s_A19

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_939


title: 207s_A23

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_938


title: 207s_A6

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_948


title: MGE_A_14pcw_936


title: 207s_A4

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_937


title: 207s_A2

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_946


title: 207s_A24

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_932


title: 207s_A17

description: Mouse non-parenchymal single cells


title: 207s_A13

description: Mouse non-parenchymal single cells


title: 207s_A1

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_931


title: MGE_A_14pcw_933


title: MGE_A_14pcw_930


title: 207s_A16

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_928


title: 207s_A15

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_929


title: 206s_P9

description: Mouse non-parenchymal single cells


title: 206s_P8

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_925


title: 206s_P7

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_927


title: MGE_A_14pcw_926


title: 206s_P6

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_924


title: MGE_A_14pcw_923


title: MGE_A_14pcw_935


title: MGE_A_14pcw_921


title: 206s_P20

description: Mouse non-parenchymal single cells


title: 207s_A20

description: Mouse non-parenchymal single cells


title: 206s_P22

description: Mouse non-parenchymal single cells


title: 206s_P19

description: Mouse non-parenchymal single cells


title: 206s_P18

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_934


title: 206s_P2

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_920


title: MGE_A_14pcw_918


title: 206s_P12

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_917


title: MGE_A_14pcw_919


title: 206s_P13

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_914


title: MGE_A_10pcw_915


title: MGE_A_10pcw_916


title: 206s_P17

description: Mouse non-parenchymal single cells


title: 206s_P11

description: Mouse non-parenchymal single cells


title: 206s_P15

description: Mouse non-parenchymal single cells


title: 206s_P1

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_912


title: MGE_A_10pcw_911


title: 206s_P21

description: Mouse non-parenchymal single cells


title: MGE_A_14pcw_922


title: 206s_P16

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_910


title: 206s_O7

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_908


title: 206s_P3

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_907


title: MGE_A_10pcw_909


title: 206s_O4

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_906


title: 206s_O6

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_905


title: MGE_A_10pcw_904


title: 206s_O9

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_903


title: MGE_A_10pcw_902


title: 206s_O5

description: Mouse non-parenchymal single cells


title: 206s_O3

description: Mouse non-parenchymal single cells


title: 206s_O17

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_901


title: MGE_A_10pcw_913


title: 206s_O23

description: Mouse non-parenchymal single cells


title: 206s_O2

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_899


title: MGE_A_10pcw_898


title: MGE_A_10pcw_900


title: 206s_P10

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_897


title: 206s_O21

description: Mouse non-parenchymal single cells


title: 206s_O20

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_896


title: 206s_O12

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_894


title: 206s_O1

description: Mouse non-parenchymal single cells


title: 206s_O8

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_895


title: 206s_O11

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_893


title: 206s_O16

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_891


title: MGE_A_10pcw_892


title: 206s_N9

description: Mouse non-parenchymal single cells


title: 206s_O15

description: Mouse non-parenchymal single cells


title: 206s_N7

description: Mouse non-parenchymal single cells


title: 206s_O18

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_889


title: MGE_A_10pcw_890


title: 206s_N4

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_888


title: 206s_O13

description: Mouse non-parenchymal single cells


title: 206s_N5

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_885


title: 206s_N8

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_886


title: MGE_A_10pcw_887


title: 206s_N6

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_884


title: 206s_N3

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_883


title: 206s_N20

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_882


title: MGE_A_10pcw_880


title: MGE_A_10pcw_881


title: 206s_N18

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_879


title: 206s_N19

description: Mouse non-parenchymal single cells


title: 206s_N2

description: Mouse non-parenchymal single cells


title: 206s_N23

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_876


title: 206s_M9

description: Mouse non-parenchymal single cells


title: 206s_N21

description: Mouse non-parenchymal single cells


title: 206s_N15

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_874


title: MGE_A_10pcw_875


title: MGE_A_10pcw_873


title: 206s_N1

description: Mouse non-parenchymal single cells


title: 206s_N11

description: Mouse non-parenchymal single cells


title: 206s_N12

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_871


title: MGE_A_10pcw_872


title: 206s_N13

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_870


title: 206s_M7

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_869


title: 206s_M24

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_867


title: MGE_A_10pcw_868


title: 206s_M5

description: Mouse non-parenchymal single cells


title: 206s_M23

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_866


title: 206s_M16

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_865


title: MGE_A_10pcw_878


title: MGE_A_10pcw_877


title: 206s_M22

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_864


title: 206s_N10

description: Mouse non-parenchymal single cells


title: 206s_M15

description: Mouse non-parenchymal single cells


title: 206s_M2

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_862


title: MGE_A_10pcw_863


title: 206s_M21

description: Mouse non-parenchymal single cells


title: 206s_M18

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_861


title: MGE_A_10pcw_860


title: 206s_M17

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_859


title: 206s_M12

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_858


title: 206s_L7

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_857


title: 206s_M20

description: Mouse non-parenchymal single cells


title: 206s_L5

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_856


title: MGE_A_10pcw_855


title: MGE_A_10pcw_854


title: 206s_M10

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_853


title: 206s_M11

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_852


title: 206s_L6

description: Mouse non-parenchymal single cells


title: 206s_L9

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_851


title: MGE_A_10pcw_850


title: 206s_L21

description: Mouse non-parenchymal single cells


title: 206s_L23

description: Mouse non-parenchymal single cells


title: 206s_L24

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_849


title: MGE_A_10pcw_848


title: MGE_A_10pcw_847


title: 206s_L22

description: Mouse non-parenchymal single cells


title: 206s_L13

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_845


title: MGE_A_10pcw_844


title: 206s_L2

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_843


title: 206s_L18

description: Mouse non-parenchymal single cells


title: 206s_L16

description: Mouse non-parenchymal single cells


title: 206s_L12

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_842


title: 206s_L20

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_841


title: MGE_A_10pcw_840


title: MGE_A_10pcw_839


title: 206s_L11

description: Mouse non-parenchymal single cells


title: 206s_L15

description: Mouse non-parenchymal single cells


title: MGE_A_10pcw_838


title: MGE_A_15pcw_837


title: 206s_K24

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_835


title: 206s_K7

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_834


title: MGE_A_15pcw_832


title: MGE_A_10pcw_846


title: MGE_A_15pcw_833


title: 206s_L1

description: Mouse non-parenchymal single cells


title: 206s_L17

description: Mouse non-parenchymal single cells


title: 206s_K20

description: Mouse non-parenchymal single cells


title: 206s_K21

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_830


title: MGE_A_15pcw_829


title: MGE_A_15pcw_826


title: 206s_K11

description: Mouse non-parenchymal single cells


title: 206s_K1

description: Mouse non-parenchymal single cells


title: 206s_J8

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_825


title: MGE_A_15pcw_827


title: 206s_K13

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_824


title: 206s_K10

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_823


title: 206s_K6

description: Mouse non-parenchymal single cells


title: 206s_K19

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_822


title: 206s_K12

description: Mouse non-parenchymal single cells


title: 206s_K9

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_821


title: MGE_A_15pcw_820


title: 206s_K22

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_831


title: 206s_K18

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_818


title: 206s_K15

description: Mouse non-parenchymal single cells


title: 206s_J3

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_819


title: MGE_A_15pcw_816


title: 206s_J9

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_828


title: 206s_K23

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_814


title: MGE_A_15pcw_817


title: MGE_A_15pcw_813


title: 206s_J23

description: Mouse non-parenchymal single cells


title: 206s_J4

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_812


title: 206s_J22

description: Mouse non-parenchymal single cells


title: 206s_J6

description: Mouse non-parenchymal single cells


title: 206s_J24

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_811


title: 206s_J5

description: Mouse non-parenchymal single cells


title: 206s_J2

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_810


title: MGE_A_15pcw_809


title: 206s_J15

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_808


title: MGE_A_15pcw_807


title: 206s_J16

description: Mouse non-parenchymal single cells


title: 206s_J20

description: Mouse non-parenchymal single cells


title: 206s_J19

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_806


title: MGE_A_15pcw_805


title: 206s_J7

description: Mouse non-parenchymal single cells


title: 206s_J17

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_804


title: MGE_A_15pcw_815


title: MGE_A_15pcw_802


title: MGE_A_15pcw_803


title: 206s_J1

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_801


title: 206s_J12

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_799


title: MGE_A_15pcw_800


title: 206s_I7

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_798


title: MGE_A_15pcw_797


title: 206s_J10

description: Mouse non-parenchymal single cells


title: 206s_I4

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_796


title: MGE_A_15pcw_795


title: 206s_I12

description: Mouse non-parenchymal single cells


title: 206s_I5

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_794


title: 206s_I21

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_793


title: 206s_I6

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_792


title: 206s_I8

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_791


title: 206s_I19

description: Mouse non-parenchymal single cells


title: 206s_I20

description: Mouse non-parenchymal single cells


title: 206s_I10

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_789


title: MGE_A_15pcw_787


title: 206s_I11

description: Mouse non-parenchymal single cells


title: 206s_J11

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_788


title: 206s_I16

description: Mouse non-parenchymal single cells


title: 206s_I13

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_786


title: 206s_H9

description: Mouse non-parenchymal single cells


title: 206s_I1

description: Mouse non-parenchymal single cells


title: 206s_H24

description: Mouse non-parenchymal single cells


title: 206s_I9

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_783


title: 206s_H23

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_782


title: MGE_A_15pcw_780


title: MGE_A_15pcw_781


title: 206s_H16

description: Mouse non-parenchymal single cells


title: 206s_H6

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_779


title: 206s_H4

description: Mouse non-parenchymal single cells


title: 206s_H20

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_777


title: 206s_H22

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_790


title: MGE_A_15pcw_776


title: MGE_A_15pcw_778


title: 206s_H19

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_775


title: 206s_H15

description: Mouse non-parenchymal single cells


title: 206s_H17

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_773


title: MGE_A_15pcw_774


title: MGE_A_15pcw_785


title: 206s_G8

description: Mouse non-parenchymal single cells


title: MGE_A_15pcw_784


title: MGE_A_15pcw_771


title: MGE_A_13pcw_770


title: MGE_A_15pcw_772


title: 206s_G7

description: Mouse non-parenchymal single cells


title: 206s_H3

description: Mouse non-parenchymal single cells


title: 206s_G9

description: Mouse non-parenchymal single cells


title: 206s_H1

description: Mouse non-parenchymal single cells


title: 206s_G4

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_767


title: 206s_G5

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_766


title: MGE_A_13pcw_765


title: 206s_G2

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_764


title: MGE_A_13pcw_763


title: 206s_G22

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_761


title: MGE_A_13pcw_757


title: MGE_A_13pcw_760


title: MGE_A_13pcw_759


title: 206s_G23

description: Mouse non-parenchymal single cells


title: 206s_G24

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_758


title: MGE_A_13pcw_756


title: MGE_A_13pcw_754


title: 206s_G10

description: Mouse non-parenchymal single cells


title: 206s_G3

description: Mouse non-parenchymal single cells


title: 206s_G18

description: Mouse non-parenchymal single cells


title: 206s_G19

description: Mouse non-parenchymal single cells


title: 206s_G1

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_762


title: MGE_A_13pcw_753


title: 206s_G13

description: Mouse non-parenchymal single cells


title: 206s_G20

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_768


title: 206s_G15

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_751


title: 206s_G16

description: Mouse non-parenchymal single cells


title: 206s_G17

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_752


title: 206s_H10

description: Mouse non-parenchymal single cells


title: 206s_G6

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_755


title: 206s_G12

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_749


title: 206s_F9

description: Mouse non-parenchymal single cells


title: 206s_G11

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_747


title: MGE_A_13pcw_748


title: MGE_A_13pcw_745


title: 206s_F22

description: Mouse non-parenchymal single cells


title: 206s_F5

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_744


title: MGE_A_13pcw_743


title: MGE_A_13pcw_742


title: MGE_A_13pcw_740


title: 206s_F24

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_750


title: 206s_F6

description: Mouse non-parenchymal single cells


title: 206s_F4

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_741


title: 206s_F21

description: Mouse non-parenchymal single cells


title: 206s_F7

description: Mouse non-parenchymal single cells


title: 206s_F23

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_738


title: MGE_A_13pcw_739


title: MGE_A_13pcw_737


title: 206s_F18

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_736


title: MGE_A_13pcw_735


title: 206s_F19

description: Mouse non-parenchymal single cells


title: 206s_F16

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_746


title: MGE_A_13pcw_734


title: 206s_F2

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_733


title: 206s_F15

description: Mouse non-parenchymal single cells


title: 206s_F3

description: Mouse non-parenchymal single cells


title: 206s_F8

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_731


title: MGE_A_13pcw_732


title: 206s_F12

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_730


title: 206s_E9

description: Mouse non-parenchymal single cells


title: 206s_E8

description: Mouse non-parenchymal single cells


title: 206s_F13

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_728


title: 206s_F1

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_727


title: 206s_E7

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_725


title: MGE_A_13pcw_726


title: 206s_E3

description: Mouse non-parenchymal single cells


title: 206s_E23

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_724


title: MGE_A_13pcw_723


title: 206s_F10

description: Mouse non-parenchymal single cells


title: 206s_E6

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_722


title: MGE_A_13pcw_721


title: 206s_E4

description: Mouse non-parenchymal single cells


title: 206s_E24

description: Mouse non-parenchymal single cells


title: 206s_E22

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_719


title: MGE_A_13pcw_720


title: MGE_A_13pcw_717


title: 206s_E16

description: Mouse non-parenchymal single cells


title: 206s_E18

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_729


title: MGE_A_13pcw_716


title: 206s_E17

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_718


title: 206s_D24

description: Mouse non-parenchymal single cells


title: 206s_E2

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_714


title: MGE_A_13pcw_712


title: MGE_A_13pcw_715


title: 206s_D8

description: Mouse non-parenchymal single cells


title: 206s_E19

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_710


title: 206s_E11

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_711


title: 206s_D7

description: Mouse non-parenchymal single cells


title: 206s_D3

description: Mouse non-parenchymal single cells


title: 206s_E13

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_709


title: 206s_E1

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_708


title: MGE_A_13pcw_707


title: 206s_D4

description: Mouse non-parenchymal single cells


title: 206s_E10

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_705


title: 206s_D15

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_703


title: 206s_D6

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_702


title: 206s_D17

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_704


title: 206s_D19

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_701


title: MGE_A_13pcw_713


title: MGE_A_13pcw_700


title: 206s_D22

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_699


title: MGE_A_13pcw_698


title: 206s_D20

description: Mouse non-parenchymal single cells


title: 206s_D21

description: Mouse non-parenchymal single cells


title: 206s_D23

description: Mouse non-parenchymal single cells


title: 206s_D2

description: Mouse non-parenchymal single cells


title: 206s_D18

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_694


title: 206s_C9

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_695


title: 206s_D10

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_706


title: MGE_A_13pcw_693


title: MGE_A_13pcw_696


title: 206s_D13

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_692


title: MGE_A_13pcw_691


title: MGE_A_13pcw_690


title: 206s_C22

description: Mouse non-parenchymal single cells


title: 206s_C24

description: Mouse non-parenchymal single cells


title: 206s_C2

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_688


title: 206s_D11

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_687


title: MGE_A_12pcw_685


title: 206s_C21

description: Mouse non-parenchymal single cells


title: MGE_A_13pcw_689


title: 206s_C4

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_683


title: 206s_C18

description: Mouse non-parenchymal single cells


title: 206s_C23

description: Mouse non-parenchymal single cells


title: 206s_C19

description: Mouse non-parenchymal single cells


title: 206s_C5

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_681


title: MGE_A_13pcw_697


title: 206s_C15

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_679


title: 206s_C20

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_677


title: 206s_C12

description: Mouse non-parenchymal single cells


title: 206s_C10

description: Mouse non-parenchymal single cells


title: 206s_B7

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_675


title: 206s_B6

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_676


title: MGE_A_12pcw_674


title: 206s_B9

description: Mouse non-parenchymal single cells


title: 206s_B8

description: Mouse non-parenchymal single cells


title: 206s_B3

description: Mouse non-parenchymal single cells


title: 206s_C13

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_673


title: 206s_B24

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_672


title: Tissue_control_21days_rep1

type: RNA

city: Silver Spring

first: Sreenivas

last: Gannavaram

state: MD

address: 10903 New Hampshire Ave

department: DETTD

country: USA

institute: US FDA

description: 6-8 weeks old

hyb_protocol: Then nCounter Prep Station was used for probeset target RNA hybridization. For each hybridization reaction, probes were hybridized to 100ng between 16-24hrs at 65C, after which the specific transcripts were attached to a streptavidin coated cartridge and excess capture and reporter probes were removed.

scan_protocol: Next, nCounter Digital Analyzer was used to collect data, count inidividual flourescent barcodes and quantify the target RNA molecules.

data_processing: Normalization is aquired based on the standard curve that comes from exogenous control samples. Background hybridization signal is calculated from the provided negative controls. Any mRNA counts less than the mean background + 2 standard deviations are assigned as below the level of dection.

label: streptavidin coated cartridge

source_name: mouse ear tissue

label_protocol: The probes were hybridized up to 100ng of total RNA in each probeset-target reaction.

extract_protocol: Total RNA samples were analyzed using NanoString nCounter Immunology panel (NanoString Technologies, Seattle, WA).

treatment_protocol: RNA was extracted using PureLink RNA Mini Kit (cat# 12183020) and counted using NanoDrop 1000 Spectrophotometer (Thermo Scientific).

tag: strain

tag: Sex

value: female


title: Ear_Tissue_LmCen_treatment_21days_rep3

description: 6-8 weeks old immunized


title: 206s_B20

description: Mouse non-parenchymal single cells


title: Ear_Tissue_LmWT_treatment_21days_rep2

description: 6-8 weeks old infected


title: Ear_Tissue_LmWT_treatment_21days_rep3

description: 6-8 weeks old infected


title: 206s_C16

description: Mouse non-parenchymal single cells


title: Tissue_control_21days_rep3

description: 6-8 weeks old


title: Tissue_control_21days_rep2

description: 6-8 weeks old


title: Ear_Tissue_LmWT_treatment_21days_rep1

description: 6-8 weeks old infected


title: 206s_C6

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_671


title: Ear_Tissue_LmCen_treatment_21days_rep1

description: 6-8 weeks old immunized


title: Ear_Tissue_LmWT_treatment_7days_rep4

description: 6-8 weeks old infected


title: 206s_B2

description: Mouse non-parenchymal single cells


title: 206s_B23

description: Mouse non-parenchymal single cells


title: 206s_A9

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_670


title: 206s_B16

description: Mouse non-parenchymal single cells


title: Ear_Tissue_LmWT_treatment_7days_rep3

description: 6-8 weeks old infected


title: MGE_A_12pcw_668


title: 206s_B13

description: Mouse non-parenchymal single cells


title: Ear_Tissue_LmWT_treatment_7days_rep2

description: 6-8 weeks old infected


title: MGE_A_12pcw_669


title: Ear_Tissue_LmCen_treatment_21days_rep2

description: 6-8 weeks old immunized


title: 206s_B12

description: Mouse non-parenchymal single cells


title: 206s_B15

description: Mouse non-parenchymal single cells


title: 206s_B22

description: Mouse non-parenchymal single cells


title: Ear_Tissue_LmWT_treatment_7days_rep1

description: 6-8 weeks old infected


title: 206s_B18

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_667


title: MGE_A_12pcw_666


title: 206s_B11

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_665


title: 206s_B19

description: Mouse non-parenchymal single cells


title: 206s_A6

description: Mouse non-parenchymal single cells


title: Ear_Tissue_LmCen treatment_7days_rep3

description: 6-8 weeks old immunized


title: Ear_Tissue_LmCen treatment_7days_rep4

description: 6-8 weeks old immunized


title: MGE_A_12pcw_664


title: 206s_A5

description: Mouse non-parenchymal single cells


title: 206s_A8

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_663


title: 206s_B5

description: Mouse non-parenchymal single cells


title: 206s_A24

description: Mouse non-parenchymal single cells


title: 206s_A17

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_662


title: 206s_A23

description: Mouse non-parenchymal single cells


title: 206s_A19

description: Mouse non-parenchymal single cells


title: 206s_A16

description: Mouse non-parenchymal single cells


title: 206s_A3

description: Mouse non-parenchymal single cells


title: 206s_A21

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_660


title: MGE_A_12pcw_661


title: MGE_A_12pcw_659


title: 206s_B10

description: Mouse non-parenchymal single cells


title: 206s_A13

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_658


title: 206s_A18

description: Mouse non-parenchymal single cells


title: 206s_A1

description: Mouse non-parenchymal single cells


title: Ear_Tissue_LmCen treatment_7days_rep2

description: 6-8 weeks old immunized


title: Ear_Tissue_treatment_2days_rep4

description: 6-8 weeks old infected


title: Ear_Tissue_treatment_2days_rep2

description: 6-8 weeks old infected


title: Tissue_control_Naive4_rep4

description: 6-8 weeks old


title: Ear_Tissue_treatment_2days_rep3

description: 6-8 weeks old infected


title: Tissue_control_Naive3_rep3

description: 6-8 weeks old


title: Ear_Tissue_LmCen treatment_7days_rep1

description: 6-8 weeks old immunized


title: Ear_Tissue_treatment_2days_rep1

description: 6-8 weeks old infected


title: 206s_A10

description: Mouse non-parenchymal single cells


title: Tissue_control_Naive2_rep2

description: 6-8 weeks old


title: 206s_A12

description: Mouse non-parenchymal single cells


title: 206s_A2

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_657


title: 206s_A11

description: Mouse non-parenchymal single cells


title: 199s_P5

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_656


title: 199s_P22

description: Mouse non-parenchymal single cells


title: 199s_P4

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_655


title: 199s_P6

description: Mouse non-parenchymal single cells


title: 199s_P15

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_653


title: 199s_P17

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_654


title: 199s_P11

description: Mouse non-parenchymal single cells


title: Tissue_treatment_2days_rep3

description: 6-8 weeks old


title: MGE_A_12pcw_652


title: Tissue_treatment_2days_rep4

description: 6-8 weeks old


title: HiC for patient 2436, deep sequenced

city: Utrecht

first: Rico

last: Hagelaar

address: Heidelberglaan 25

country: Netherlands

institute: Princess Maxima Center

library_source: genomic

data_processing:
Mapping was done using BWA mem
Duplicates were removed using HICUP v0.5.10
Interaction matrices were generated using Juicer
Insulation scores were calculated using HiCExplorer
Genome_build: CRCh37
Supplementary_files_format_and_content: Hic file

molecule: genomic DNA

source_name: Patient

extract_protocol:
HiC was performed according to Rao et al. Cell, 2014. In short chromatin was crosslinked using formaldehyde, digested using MboI. Subsequently, ends were filled in using biotin labelled nucleotides and ligation was performed in situ. DNA was then extracted from the nuclei and purified. The DNA template was then sheared and a streptavidin pulldown was performed to enrich for DNA concatemers containing a ligation junction.
Illumina library prep was performed using custom adapters identical to those used in the illumina truseq kit and PCR amplified using adapter-overhang PCR.

tag: ctcf status

value: Deleted

tag: deep sequenced

value: Yes


title: 199s_P21

description: Mouse non-parenchymal single cells


title: HiC for patient 2436

value: No


title: MGE_A_12pcw_651


title: 199s_P13

description: Mouse non-parenchymal single cells


title: Tissue_treatment_2days_rep2

description: 6-8 weeks old


title: 199s_P8

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_650


title: Tissue_treatment_2days_rep1

description: 6-8 weeks old


title: 199s_P20

description: Mouse non-parenchymal single cells


title: HiC for patient 9757

value: Wild type


title: MGE_A_12pcw_649


title: 199s_P14

description: Mouse non-parenchymal single cells


title: 199s_P16

description: Mouse non-parenchymal single cells


title: Tissue_control_Naive1_rep1

description: 6-8 weeks old


title: 199s_P19

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_648


title: HiC for patient 9757, deep sequenced


title: 199s_O7

description: Mouse non-parenchymal single cells


title: 199s_P12

description: Mouse non-parenchymal single cells


title: HiC for patient 719


title: MGE_A_12pcw_647


title: 199s_P18

description: Mouse non-parenchymal single cells


title: 199s_P2

description: Mouse non-parenchymal single cells


title: 199s_O6

description: Mouse non-parenchymal single cells


title: 199s_P10

description: Mouse non-parenchymal single cells


title: 199s_O5

description: Mouse non-parenchymal single cells


title: 206s_A7

description: Mouse non-parenchymal single cells


title: HiC for patient 5676


title: MGE_A_12pcw_645


title: HiC for patient 1946

value: Mutant


title: HiC for patient 3770


title: 199s_P1

description: Mouse non-parenchymal single cells


title: 199s_O2

description: Mouse non-parenchymal single cells


title: 199s_O24

description: Mouse non-parenchymal single cells


title: 199s_O21

description: Mouse non-parenchymal single cells


title: Parental HPB-ALL

data_processing:
Data was processed into RDS files using the pipeline described in  Krijger, P.H.L., Geeven, G., Bianchi, V., Hilvering, C.R.E., and de Laat, W. (2020). 4C-seq   from beginning to end: A detailed protocol for sample preparation and data analysis.   Methods 170, 17-32.
Genome_build: CRCh37
Supplementary_files_format_and_content: RDS files are R objects and contain experiment parameters as well as calculated 4C signals.

source_name: Cell line

extract_protocol:
Libraries were generated according to the method described in Krijger, P.H.L., Geeven, G., Bianchi, V., Hilvering, C.R.E., and de Laat, W. (2020). 4C-seq   from beginning to end: A detailed protocol for sample preparation and data analysis.   Methods 170, 17-32. A combination of DpnII and Csp6I was used for 4C template generation.
Other: 4C

tag: cell line

value: HPB-ALL


title: MGE_A_12pcw_644


title: 199s_O23

description: Mouse non-parenchymal single cells


title: 199s_O3

description: Mouse non-parenchymal single cells


title: 199s_O19

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_642


title: HPB-ALL with CTCF overexpression, day 2


title: 199s_O20

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_643


title: MGE_A_12pcw_646


title: Patient 91 from BCL11B promotor viewpoint

tag: subect

value: Patient 91


title: MGE_A_12pcw_641


title: 199s_O12

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_640


title: 199s_O10

description: Mouse non-parenchymal single cells


title: 199s_O1

description: Mouse non-parenchymal single cells


title: 199s_O11

description: Mouse non-parenchymal single cells


title: 199s_O14

description: Mouse non-parenchymal single cells


title: Patient 71 from BCL11B promotor viewpoint

value: Patient 71


title: MGE_A_12pcw_639


title: MGE_A_12pcw_638


title: 199s_O18

description: Mouse non-parenchymal single cells


title: 199s_N8

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_637


title: 199s_N7

description: Mouse non-parenchymal single cells


title: Patient 332 from TLX3 viewpoint

tag: duplicate

value: Duplicate from ALL_331_TLX3

value: Patient 332


title: Patient 371 from BCL11B promotor viewpoint

value: Patient 371


title: MGE_A_12pcw_636


title: 199s_N5

description: Mouse non-parenchymal single cells


title: 199s_O22

description: Mouse non-parenchymal single cells


title: 199s_O13

description: Mouse non-parenchymal single cells


title: Patient 331 from TLX3 viewpoint

value: Patient 331


title: 199s_N4

description: Mouse non-parenchymal single cells


title: Patient 331 from BCL11B promotor viewpoint


title: 199s_N6

description: Mouse non-parenchymal single cells


title: 199s_N19

description: Mouse non-parenchymal single cells


title: 199s_N24

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_634


title: 199s_N3

description: Mouse non-parenchymal single cells


title: Patient 21 from BCL11B promotor viewpoint

value: Patient 21


title: Patient 391 from BCL11B promotor viewpoint

value: Patient 391


title: MGE_A_12pcw_633


title: 199s_N21

description: Mouse non-parenchymal single cells

value: Liver


title: 199s_N9

description: Mouse non-parenchymal single cells


title: Patient 51 from BCL11B promotor viewpoint

value: Patient 51


title: 199s_N20

description: Mouse non-parenchymal single cells


title: Patient 111 from BCL11B promotor viewpoint

value: Patient 111


title: 199s_N18

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_632

value: medial ganglionic eminence (MGE)


title: Patient 11 from BCL11B promotor viewpoint

value: Patient 11


title: 199s_M4

description: Mouse non-parenchymal single cells


title: Patient 111 from TLX3 viewpoint


title: MGE_A_12pcw_630


title: MGE_A_12pcw_631


title: 199s_O17

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_629


title: MGE_A_12pcw_635


title: 199s_M6

description: Mouse non-parenchymal single cells


title: Patient 392 from TLX3 viewpoint

value: Duplicate from ALL_391_TLX3

value: Patient 392


title: Patient 391 from TLX3 viewpoint


title: 199s_M7

description: Mouse non-parenchymal single cells


title: 199s_N10

description: Mouse non-parenchymal single cells


title: Patient 372 from TLX3 viewpoint

value: Duplicate from ALL_371_TLX3

value: Patient 372


title: 199s_N14

description: Mouse non-parenchymal single cells


title: 199s_N22

description: Mouse non-parenchymal single cells


title: 199s_M3

description: Mouse non-parenchymal single cells


title: 199s_M8

description: Mouse non-parenchymal single cells


title: Patient 371 from TLX3 viewpoint


title: 199s_M9

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_627


title: MGE_A_12pcw_626


title: 199s_N15

description: Mouse non-parenchymal single cells


title: Patient 22 from TLX3 viewpoint

value: Duplicate from ALL_21_TLX3

value: Patient 22


title: MGE_A_12pcw_625


title: 199s_N16

description: Mouse non-parenchymal single cells


title: 199s_N11

description: Mouse non-parenchymal single cells


title: 199s_N1

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1320


title: 199s_N12

description: Mouse non-parenchymal single cells


title: Patient 21 from TLX3 viewpoint


title: 199s_N13

description: Mouse non-parenchymal single cells


title: Patient 12 from TLX3 viewpoint

value: Duplicate from ALL_11_TLX3

value: Patient 12


title: 199s_N17

description: Mouse non-parenchymal single cells


title: 199s_M18

description: Mouse non-parenchymal single cells


title: MGE_A_12pcw_628


title: Patient 11 from TLX3 viewpoint


title: 199s_M20

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1318


title: 199s_M2

description: Mouse non-parenchymal single cells


title: 199s_M22

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1316


title: Patient 92 from TLX3 viewpoint

value: Duplicate from ALL_91_TLX3

value: Patient 92


title: 199s_M21

description: Mouse non-parenchymal single cells


title: 199s_M17

description: Mouse non-parenchymal single cells


title: 199s_M12

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1314


title: 199s_M23

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1310


title: MGE_B_13pcw_1308


title: 199s_M11

description: Mouse non-parenchymal single cells


title: 199s_M19

description: Mouse non-parenchymal single cells


title: Patient 91 from TLX3 viewpoint

value: Patient 91


title: 199s_M1

description: Mouse non-parenchymal single cells


title: 199s_M10

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1312


title: Patient 51 from TLX3 viewpoint


title: 199s_M14

description: Mouse non-parenchymal single cells


title: Patient 52 from TLX3 viewpoint

value: Duplicate from ALL_51_TLX3

value: Patient 52


title: MGE_B_13pcw_1306


title: Patient 72 from TLX3 viewpoint

value: Duplicate from ALL_71_TLX3

value: Patient 72


title: Patient 71 from TLX3 viewpoint

value: Patient 71


title: 199s_L24

description: Mouse non-parenchymal single cells

value: Liver


title: 199s_M16

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1304

value: medial ganglionic eminence (MGE)


title: 199s_M13

description: Mouse non-parenchymal single cells


title: 199s_L9

description: Mouse non-parenchymal single cells


title: Bulk cells from single cell clone G4 of HPB-ALL with overexpression of CTCF, from TLX3 viewpoint

value: HPB-ALL


title: Bulk cells from single cell clone G4 of HPB-ALL without overexpression of CTCF, from TLX3 viewpoint


title: MGE_B_13pcw_1302


title: 199s_L7

description: Mouse non-parenchymal single cells


title: 199s_M15

description: Mouse non-parenchymal single cells


title: 199s_L6

description: Mouse non-parenchymal single cells


title: 199s_L8

description: Mouse non-parenchymal single cells


title: Bulk cells from single cell clone E3 of HPB-ALL with overexpression of CTCF, from TLX3 viewpoint


title: MGE_B_13pcw_1298


title: Bulk cells from single cell clone E3 of HPB-ALL with overexpression of CTCF, from BCL11B promotor viewpoint


title: 199s_L18

description: Mouse non-parenchymal single cells


title: 199s_L22

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1296


title: 199s_L19

description: Mouse non-parenchymal single cells


title: 199s_L23

description: Mouse non-parenchymal single cells


title: Bulk cells from single cell clone E3 of HPB-ALL without overexpression of CTCF, from TLX3 viewpoint


title: Bulk cells from single cell clone E3 of HPB-ALL without overexpression of CTCF, from BCL11B promotor viewpoint


title: MGE_B_13pcw_1294


title: MGE_B_13pcw_1292


title: 199s_L2

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1290


title: 199s_L13

description: Mouse non-parenchymal single cells


title: 199s_K9

description: Mouse non-parenchymal single cells


title: Single cell clone E116 of HPB-ALL without overexpression of CTCF, from TLX3 viewpoint


title: 199s_L11

description: Mouse non-parenchymal single cells


title: Single cell clone E116 of HPB-ALL with overexpression of CTCF, from TLX3 viewpoint


title: MGE_B_13pcw_1300


title: MGE_B_13pcw_1288


title: 199s_K5

description: Mouse non-parenchymal single cells


title: 199s_K7

description: Mouse non-parenchymal single cells


title: 199s_L14

description: Mouse non-parenchymal single cells


title: Input DNA for cell line HPB-ALL

data_processing:
Reads were aligned to CRCh37, using BWA with default settings.
Peakcalling was done with MACS2, version 2.1.1.20160309, with the setting for narrowPeak calling. A q-value of 0.01 was applied while other settings were kept at default
Genome_build: CRCh37
Supplementary_files_format_and_content: narrowPeak peak text files

growth_protocol: Viably frozen diagnostic patient samples or patient-derived xenograft (PDX) cells were thawed

extract_protocol:
ChIP-seq was performed according to the SimpleChIP® Enzymatic Chromatin IP kit #9003 (Cell Signaling Technologies, Danvers, MA) procedure. The chromatin was sheared using the Biorupter Pico (Diagenode, Liege, Belgium; 7 cycles of 30’ on, 30’ off). After sonication, samples were divided and ~4x10e6 cells were used for each ChIP experiment. Antibodies were added to concentrations as recommended by the manufacturer and incubated overnight at 4°C under continuous rotation. Antibodies used are anti-CTCF (3418S) (Cell Signaling Technologies), anti-SMC3 (ab9263) (Abcam, Cambridge, UK) and normal rabbit IgG #2729 (Cell Signaling Technologies). DNA was pelleted with ChIP-grade Protein G Magnetic Beads #9006 (Cell Signaling Technologies) and washed according to the manufacturer’s protocol. After reverse cross-linking, DNA was purified with spin columns from the SimpleChIP kit or the Qiaquick PCR Purification Kit (Qiagen, Hilden, Germany). DNA concentrations were measured using the Qubit HS DNA sensitivity kit (ThermoFischer, Waltham, MA).
Libraries were prepared using the NEXTflex™ Rapid DNA Sequencing Kit (Bio Scientific). Samples were PCR amplified, checked for size and the absence of adaptor dimers on 2% agarose gel. Barcoded libraries were sequenced for 75 bp at a single end using the Illumina NextSeq500 sequencer.

tag: desease state

value: CTCF Deletion


title: 199s_K6

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1284


title: SMC3 pull down for cell line HPB-ALL

tag: antibody


title: 199s_L10

description: Mouse non-parenchymal single cells


title: CTCF pull down for cell line HPB-ALL

value: CTCF


title: MGE_B_13pcw_1282


title: 199s_L12

description: Mouse non-parenchymal single cells


title: 199s_K18

description: Mouse non-parenchymal single cells


title: 199s_K20

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1280


title: Input DNA for PDX sample 3977

source_name: Patient Derived Xenograft


title: 199s_K2

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1278


title: 199s_K17

description: Mouse non-parenchymal single cells


title: Input DNA for PDX sample 9248

value: CTCF Wild Type


title: 199s_K22

description: Mouse non-parenchymal single cells


title: 199s_K19

description: Mouse non-parenchymal single cells


title: 199s_K12

description: Mouse non-parenchymal single cells


title: Input DNA for PDX sample 419


title: Input DNA for PDX sample 5676


title: 199s_K10

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1274


title: 199s_L16

description: Mouse non-parenchymal single cells


title: 199s_J24

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1286


title: MGE_B_13pcw_1272


title: 199s_K15

description: Mouse non-parenchymal single cells


title: Input DNA for PDX sample 1946

value: CTCF Mutated


title: 199s_J3

description: Mouse non-parenchymal single cells


title: Input DNA for PDX sample 1179


title: 199s_L1

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1270


title: MGE_B_13pcw_1276


title: 199s_K11

description: Mouse non-parenchymal single cells


title: 199s_J23

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1268


title: Input DNA for PDX sample 719


title: Input DNA for PDX sample 634


title: MGE_B_13pcw_1266


title: 199s_J7

description: Mouse non-parenchymal single cells


title: SMC3 pull down for PDX sample 3977


title: 199s_J6

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1264


title: 199s_J16

description: Mouse non-parenchymal single cells


title: 199s_J4

description: Mouse non-parenchymal single cells


title: 199s_J19

description: Mouse non-parenchymal single cells


title: 199s_J21

description: Mouse non-parenchymal single cells


title: SMC3 pull down for PDX sample 9248


title: MGE_B_13pcw_1260


title: SMC3 pull down for PDX sample 5676


title: MGE_B_13pcw_1262


title: 199s_J22

description: Mouse non-parenchymal single cells


title: 199s_K16

description: Mouse non-parenchymal single cells


title: 199s_J17

description: Mouse non-parenchymal single cells


title: 199s_J18

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1256


title: MGE_B_13pcw_1258


title: 199s_J20

description: Mouse non-parenchymal single cells


title: SMC3 pull down for PDX sample 419


title: SMC3 pull down for PDX sample 1946


title: 199s_J2

description: Mouse non-parenchymal single cells


title: SMC3 pull down for PDX sample 1179


title: 199s_I7

description: Mouse non-parenchymal single cells


title: 199s_K13

description: Mouse non-parenchymal single cells


title: 199s_I23

description: Mouse non-parenchymal single cells


title: SMC3 pull down for PDX sample 634


title: 199s_J8

description: Mouse non-parenchymal single cells


title: 199s_I8

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1252


title: 199s_I3

description: Mouse non-parenchymal single cells


title: CTCF pull down for PDX sample 3977


title: MGE_B_13pcw_1250


title: 199s_I6

description: Mouse non-parenchymal single cells


title: CTCF pull down for PDX sample 5676


title: CTCF pull down for PDX sample 9248


title: 199s_J10

description: Mouse non-parenchymal single cells


title: 199s_J15

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1248


title: 199s_J12

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1246


title: 199s_J13

description: Mouse non-parenchymal single cells


title: 199s_J1

description: Mouse non-parenchymal single cells


title: CTCF pull down for PDX sample 419


title: MGE_B_13pcw_1244


title: 199s_I9

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1242


title: CTCF pull down for PDX sample 1946


title: 199s_I5

description: Mouse non-parenchymal single cells


title: 199s_J14

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1254


title: 199s_J11

description: Mouse non-parenchymal single cells


title: CTCF pull down for PDX sample 1179


title: 199s_I24

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1240


title: 199s_I17

description: Mouse non-parenchymal single cells


title: 199s_I4

description: Mouse non-parenchymal single cells


title: 199s_I19

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1238


title: 199s_I18

description: Mouse non-parenchymal single cells


title: Mix-H

city: wenhzou

first: liang

last: zhang

address: wenhzou

country: China

institute: wenzhou medical university

library_source: transcriptomic

data_processing:
Image analysis and base calling are performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8).
Sequencing quality are examined by FastQC  and trimmed reads (pass Illumina quality filter, trimmed 5', 3'-adaptor bases by cutadapt ) are aligned allowing for 1 mismatch only to the mature  tRNA sequences, then reads that do not map are aligned allowing for 1 mismatch only to precursor tRNA sequences with bowtie software .
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Plasma

extract_protocol:
Total RNA was isolated using Trizol  LS Reagentaccording to the manufacturer's standard procedures (Invitrogen Life Technologies, Carlsbad, CA, USA). RNA concentration and purity were determined using Nanodrop ® ND-1000, and RNA integrity was verified by denatured agarose gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Plasma

value: deep hypothermia circulatory arrest

tag: time point


title: MGE_B_13pcw_1234


title: 199s_I14

description: Mouse non-parenchymal single cells


title: Mix-F


title: MGE_B_13pcw_1236


title: MGE_B_13pcw_1232


title: 199s_H23

description: Mouse non-parenchymal single cells


title: 199s_I2

description: Mouse non-parenchymal single cells


title: 199s_I1

description: Mouse non-parenchymal single cells


title: Mix-E


title: 199s_H7

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1230


title: 199s_H3

description: Mouse non-parenchymal single cells


title: Mix-D


title: MGE_B_13pcw_1228


title: 199s_H9

description: Mouse non-parenchymal single cells


title: Mix-B


title: 199s_I20

description: Mouse non-parenchymal single cells


title: 199s_H21

description: Mouse non-parenchymal single cells


title: 199s_I11

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1226


title: 199s_I12

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1222


title: XDY-H


title: 199s_H8

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1220


title: CTCF pull down for PDX sample 719


title: CTCF pull down for PDX sample 634


title: MGE_B_13pcw_1224


title: 199s_I13

description: Mouse non-parenchymal single cells


title: 199s_H20

description: Mouse non-parenchymal single cells


title: 199s_H22

description: Mouse non-parenchymal single cells


title: XDY-E


title: 199s_H5

description: Mouse non-parenchymal single cells


title: 199s_H24

description: Mouse non-parenchymal single cells


title: 199s_H4

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1214


title: 199s_I15

description: Mouse non-parenchymal single cells


title: XDY-D


title: MGE_B_13pcw_1218


title: 199s_H18

description: Mouse non-parenchymal single cells


title: XBH-F


title: MGE_B_13pcw_1216


title: 199s_G5

description: Mouse non-parenchymal single cells


title: 199s_G21

description: Mouse non-parenchymal single cells


title: 199s_G6

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1212


title: XDY-F


title: 199s_G9

description: Mouse non-parenchymal single cells


title: 199s_G4

description: Mouse non-parenchymal single cells


title: XBH-E


title: MGE_B_13pcw_1210


title: MGE_B_13pcw_1208


title: XBH-D


title: 199s_H13

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1206


title: 199s_G23

description: Mouse non-parenchymal single cells


title: 199s_H11

description: Mouse non-parenchymal single cells


title: XBH-H


title: 199s_G8

description: Mouse non-parenchymal single cells


title: XDY-B


title: MGE_B_13pcw_1204


title: LGY-H


title: 199s_H15

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1202


title: 199s_H12

description: Mouse non-parenchymal single cells


title: 199s_G7

description: Mouse non-parenchymal single cells


title: LGY-F


title: LGY-E


title: 199s_H14

description: Mouse non-parenchymal single cells


title: 199s_H10

description: Mouse non-parenchymal single cells


title: 199s_H16

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1200


title: LGY-D


title: 199s_G2

description: Mouse non-parenchymal single cells


title: 199s_H1

description: Mouse non-parenchymal single cells


title: 199s_G18

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1198


title: LGY-B


title: MGE_B_13pcw_1196


title: 199s_F22

description: Mouse non-parenchymal single cells


title: 199s_F7

description: Mouse non-parenchymal single cells


title: XBH-B


title: 199s_G22

description: Mouse non-parenchymal single cells


title: FUJIOKA_MYB2

city: Birmingham

first: Carl

last: Ward

address: Edgbaston

institute: University of Birmingham

description: total RNA extraction 24h post siRNA transfection

data_processing:
base calling: HiSeq Control Software 2.2.58 / NextSeq Control Software 2.1.2
trim-galore (v0.5.0) --paired with cutadapt (v1.14)
rsem-calculate-expression (v1.2.22) --bowtie2 (v2.2.5) --bowtie2-sensitivity-level very_sensitive --paired-end --estimate-rspd
Genome_build: hg38 ensembl v81 gtf
Supplementary_files_format_and_content: Gene counts from rsem

source_name: Human FUJIOKA myelogenous leukaemia cell line

growth_protocol: MOLM14 and FUIOKAcells were cultured in RPMI-1640 medium supplemented with 10% foetal bovine serum (FBS), 50U/ml penicillin, 50µg/ml streptomycin, 2mM L-glutamine.  Cell were maintained at 0.5 x 106 cells/ml at 37°C with 5% CO2 in a humidified incubator and were washed with phosphate buffered saline solution between passages.

extract_protocol:
Total RNA was extracted 24h post transfection using QIAGEN Rneasy mini kit
Libraries were prepared via the Illumina TruSeq® Stranded mRNA library preparation protocol according to manufacturer's instructions

treatment_protocol: In total, 5 x 106 FUJIOKA, MOLM14, KASUMI1 or KG1a cells were electroporated using a EPI 3500 (Fischer, Germany) single 250 V pulse for 10ms with 300mM of MYB siRNA or a scrambled negative control siRNA (SIGMA ALDRICH) as previously reported in Clarke et al (Clarke et al., 2017). After electroporation, the cells were kept in the electroporation cuvette for 10 minutes after which cells were added RPMI-1640 with 10% FBS, supplemented with penicillin/streptomycin and L-glutamine at a concentration of cells per ml and returned to an incubator kept at 37°C and 5% CO2. After transfection cells were plated at a density 106 cells/ml and viable cells counted and passaged at a ratio of 1:2 every 24 hours for four consecutive days to determine their proliferative capacity. Assessment of differentiation at 96 hours post Myb reduction was achieved by flow cytometry of the cells with anti-CD11b PE-Cy7 and anti-CD14 APC. Acquisition and analysis of flow cytometric data was performed using Cyan ADP with Summit 4.4 software.

value: myelogenous leukaemia cell line

value: FUJIOKA

tag: mutational status

value: complex karyotype

tag: genotype/variation

value: MYB knock-down


title: 199s_G12

description: Mouse non-parenchymal single cells

tag: tissue

tag: disease state


title: FUJIOKA_MYB1


title: MGE_B_13pcw_1194

tag: group

tag: developmental stage_pcw


title: 199s_G17

description: Mouse non-parenchymal single cells


title: 199s_F21

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1192

tag: batch

tag: sample id


title: FUJIOKA_NEG2

value: control


title: 199s_G14

description: Mouse non-parenchymal single cells


title: 199s_G15

description: Mouse non-parenchymal single cells


title: FUJIOKA_NEG1


title: 199s_F23

description: Mouse non-parenchymal single cells


title: 199s_F8

description: Mouse non-parenchymal single cells


title: 199s_G11

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1186


title: 199s_F9

description: Mouse non-parenchymal single cells


title: 199s_F3

description: Mouse non-parenchymal single cells


title: MOLM14_MYB2

source_name: Human MOLM14 myelogenous leukaemia cell line

value: MLL translocation


title: 199s_F2

description: Mouse non-parenchymal single cells


title: MOLM14_MYB1


title: MGE_B_13pcw_1184


title: 199s_F20

description: Mouse non-parenchymal single cells


title: 199s_F4

description: Mouse non-parenchymal single cells


title: 199s_F24

description: Mouse non-parenchymal single cells


title: MOLM14_NEG2


title: MOLM14_NEG1


title: MGE_B_13pcw_1180


title: 199s_F15

description: Mouse non-parenchymal single cells


title: 199s_F19

description: Mouse non-parenchymal single cells


title: 199s_E6

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1188


title: 199s_E4

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1178


title: MGE_B_13pcw_1190


title: 199s_E3

description: Mouse non-parenchymal single cells


title: 199s_E8

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1176


title: MGE_B_13pcw_1174


title: 199s_F16

description: Mouse non-parenchymal single cells


title: MGE_B_13pcw_1172


title: MGE_B_13pcw_1170


title: MGE_B_13pcw_1182


title: RNAseq_ESC_dTrim24_DegrAct_12h_r2

city: Adelaide

first: Luke

middle: Thomas

last: Isbel

state: South Australia

address: 4 North Terrace, AHMS, Lvl 9

country: Australia

institute: SAiGENCI

data_processing:
Illumina RTA 1.18.64 and bcl2fastq2 v2.17 was used for basecalling and demultiplexing samples generated by Illumina HiSeq sequencing. Illumina RTA 3.4.4 and bcl2fastq2 v2.20 was used for basecalling and demultiplexing samples generated by Illumina NovaSeq sequencing. RNA-seq reads were mapped to mm10 using STAR aligner (Dobin et al, Bioinformatics 2013).
Assembly: mm10
Supplementary files format and content: Alignments overlapping the exon of a gene (gene annotation from the GENCODE release M25) were counted using the featureCounts function from the Rsubread Bioconductor package by gene_name (Liao et al, Nucleic Acids Research, 2019) with default parameters. Only protein coding genes were retained and excluding predicted genes (beginning Gm#####).  Count matrixes were generated and TMM-normalized by the DGEList and calcNormFactors functions from the edgeR (Robinson et al, Bioinformatics, 2010), and finally, counts per million (CPM) were generated using the cpm function from edgeR and adding a pseudocount of 8 and log2 transforming the data.

source_name: embryonic stem cells

growth_protocol: Mouse ES cells were cultured as previously described (Mohn, F. et al. Mol. Cell, 2008). Briefly, cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Invitrogen), supplemented with 15 % Fetal Calf Serum (Invitrogen), L-Glutamine (Gibco) and nonessential amino acids (Gibco), betamercaptoethanol (Sigma) and leukemia inhibitory factor (LIF; produced in-house). All experiments were performed with cells grown for several passages on plates coated with 0.2% gelatin (Sigma).

extract_protocol:
RNA for RNA-seq was isolated using Direct-zol RNA Purification Kit (Zymo), following the manufacturer’s instructions.
Sequencing libraries were prepared from 100ng of purified total RNA for biological replicates using TruSeq stranded Total RNA Library Prep (Illumina).

treatment_protocol: Cells (0.25x10^6) were seeded into 6-well plates the day before the experiment. Doxorubicin (1uM) or dTAG13 (500nM) compound were added to specific samples to activate p53 or degrade degron tagged alleles.

tag: cell type

value: embryonic stem cells

tag: genotype

value: degron-tagged Trim24

tag: strain

tag: treatment condition

value: degraded Trim24; activated p53 - 12 hours


title: RNAseq_ESC_dTrim24_DegrAct_12h_r1


title: 199s_F11

description: Mouse non-parenchymal single cells

value: Liver


title: MGE_B_13pcw_1168

value: medial ganglionic eminence (MGE)


title: 199s_F12

description: Mouse non-parenchymal single cells


title: 199s_E7

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_DegrAct_8h_r3

value: degraded Trim24; activated p53 - 8 hours


title: 199s_F17

description: Mouse non-parenchymal single cells


title: 199s_F13

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_DegrAct_8h_r2


title: MGE_B_15pcw_1166


title: RNAseq_ESC_dTrim24_DegrAct_8h_r1


title: RNAseq_ESC_dTrim24_DegrAct_12h_r3


title: RNAseq_ESC_dTrim24_DegrAct_4h_r3

value: degraded Trim24; activated p53 - 4 hours


title: 199s_F14

description: Mouse non-parenchymal single cells


title: 199s_E21

description: Mouse non-parenchymal single cells


title: 199s_E23

description: Mouse non-parenchymal single cells


title: 199s_F10

description: Mouse non-parenchymal single cells


title: 199s_E5

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1164


title: 199s_E2

description: Mouse non-parenchymal single cells


title: 199s_E9

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1160


title: RNAseq_ESC_dTrim24_DegrAct_4h_r2


title: 199s_E22

description: Mouse non-parenchymal single cells


title: 199s_F1

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_DegrAct_4h_r1


title: MGE_B_15pcw_1158


title: 199s_E24

description: Mouse non-parenchymal single cells


title: 199s_E19

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_DegrAct_2h_r3

value: degraded Trim24; activated p53 - 2 hours


title: MGE_B_15pcw_1156


title: 199s_E20

description: Mouse non-parenchymal single cells


title: 199s_E17

description: Mouse non-parenchymal single cells


title: 199s_E18

description: Mouse non-parenchymal single cells


title: 199s_E16

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_DegrAct_2h_r2


title: 199s_E13

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_DegrAct_2h_r1


title: MGE_B_15pcw_1154


title: MGE_B_15pcw_1162


title: 199s_D22

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1152


title: 199s_E1

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_Act_12h_r3

value: activated p53 - 12 hours


title: MGE_B_15pcw_1151


title: 199s_D21

description: Mouse non-parenchymal single cells


title: 199s_D9

description: Mouse non-parenchymal single cells


title: 199s_E11

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1149


title: RNAseq_ESC_dTrim24_Act_12h_r1


title: MGE_B_10pcw_1148


title: RNAseq_ESC_dTrim24_Act_12h_r2


title: 199s_E14

description: Mouse non-parenchymal single cells


title: 199s_D3

description: Mouse non-parenchymal single cells


title: 199s_E15

description: Mouse non-parenchymal single cells


title: 199s_D20

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_Act_8h_r3

value: activated p53 - 8 hours


title: MGE_B_15pcw_1147


title: 199s_D4

description: Mouse non-parenchymal single cells


title: 199s_D2

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1146


title: 199s_D5

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_Act_8h_r2


title: RNAseq_ESC_dTrim24_Act_8h_r1


title: RNAseq_ESC_dTrim24_Act_4h_r3

value: activated p53 - 4 hours


title: 199s_D8

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1145


title: MGE_B_10pcw_1144


title: 199s_D18

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_Act_4h_r2


title: 199s_D19

description: Mouse non-parenchymal single cells


title: 199s_D7

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1143


title: 199s_D11

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_Act_4h_r1


title: 199s_D1

description: Mouse non-parenchymal single cells


title: 199s_D14

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1142


title: MGE_B_15pcw_1141


title: RNAseq_ESC_dTrim24_Act_2h_r3

value: activated p53 - 2 hours


title: 199s_D12

description: Mouse non-parenchymal single cells


title: 199s_D15

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_Act_2h_r2


title: MGE_B_10pcw_1140


title: 199s_D10

description: Mouse non-parenchymal single cells


title: 199s_D17

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_Act_2h_r1


title: 199s_D16

description: Mouse non-parenchymal single cells


title: 199s_D6

description: Mouse non-parenchymal single cells


title: 199s_D13

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_Unt_0h_r3

value: basal p53


title: RNAseq_ESC_dTrim24_Unt_0h_r2


title: MGE_B_15pcw_1139


title: 199s_C8

description: Mouse non-parenchymal single cells


title: 199s_C6

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1138


title: 199s_C7

description: Mouse non-parenchymal single cells


title: 199s_C4

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_Unt_0h_r1


title: MGE_B_10pcw_1136


title: MGE_B_15pcw_1137


title: RNAseq_ESC_dTrim24_Unt_r3

value: activated p53


title: MGE_B_15pcw_1135


title: RNAseq_ESC_dTrim24_Unt_r2


title: 199s_C20

description: Mouse non-parenchymal single cells


title: 199s_C22

description: Mouse non-parenchymal single cells


title: 199s_C24

description: Mouse non-parenchymal single cells


title: 199s_C21

description: Mouse non-parenchymal single cells


title: 199s_C23

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_Unt_r1


title: 199s_C2

description: Mouse non-parenchymal single cells


title: 199s_C19

description: Mouse non-parenchymal single cells


title: 199s_C17

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_Degr_r3

value: degraded Trim24


title: MGE_B_10pcw_1132


title: 199s_C18

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_dTrim24_Degr_r2


title: 199s_C14

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1131


title: RNAseq_ESC_dTrim24_Degr_r1


title: 199s_C11

description: Mouse non-parenchymal single cells


title: 199s_C10

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_wt_Act_r2

value: wild type


title: 199s_C3

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1130


title: 199s_C1

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1129


title: 199s_B9

description: Mouse non-parenchymal single cells


title: 199s_B8

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1134


title: MGE_B_15pcw_1133


title: 199s_B7

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1128


title: 199s_B23

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_wt_Act_r1


title: RNAseq_ESC_wt_Unt_r1


title: 199s_B4

description: Mouse non-parenchymal single cells


title: 199s_B5

description: Mouse non-parenchymal single cells


title: 199s_B21

description: Mouse non-parenchymal single cells


title: RNAseq_ESC_wt_Unt_r2


title: MGE_B_10pcw_1126


title: 199s_B19

description: Mouse non-parenchymal single cells


title: 199s_B2

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1124


title: 199s_B17

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1125


title: 199s_B20

description: Mouse non-parenchymal single cells


title: 199s_B16

description: Mouse non-parenchymal single cells


title: 199s_B13

description: Mouse non-parenchymal single cells


title: 199s_B11

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1122


title: 199s_B12

description: Mouse non-parenchymal single cells


title: 199s_B1

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1121


title: 199s_B10

description: Mouse non-parenchymal single cells


title: 199s_A8

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1120


title: 199s_A7

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1127


title: 199s_A5

description: Mouse non-parenchymal single cells


title: 199s_A6

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1119


title: 199s_A4

description: Mouse non-parenchymal single cells


title: 199s_A3

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1117


title: 199s_A23

description: Mouse non-parenchymal single cells


title: 199s_A20

description: Mouse non-parenchymal single cells


title: 199s_A19

description: Mouse non-parenchymal single cells


title: 199s_A14

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1123


title: MGE_B_15pcw_1114


title: 199s_A17

description: Mouse non-parenchymal single cells


title: 199s_B14

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1113


title: 200s_P7

description: Mouse non-parenchymal single cells


title: 199s_A13

description: Mouse non-parenchymal single cells


title: 199s_A12

description: Mouse non-parenchymal single cells


title: 200s_P3

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1112


title: MGE_B_10pcw_1111


title: 200s_P21

description: Mouse non-parenchymal single cells


title: 200s_P17

description: Mouse non-parenchymal single cells


title: 200s_P19

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1118


title: MGE_B_15pcw_1116


title: 200s_O8

description: Mouse non-parenchymal single cells


title: 200s_P15

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1110


title: MGE_B_10pcw_1109


title: 200s_O6

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1108


title: 200s_P9

description: Mouse non-parenchymal single cells


title: 200s_O4

description: Mouse non-parenchymal single cells


title: 200s_O9

description: Mouse non-parenchymal single cells


title: 199s_A16

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1107


title: 200s_O22

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1115


title: 200s_O2

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1106


title: 200s_O18

description: Mouse non-parenchymal single cells


title: 200s_O19

description: Mouse non-parenchymal single cells


title: 200s_O17

description: Mouse non-parenchymal single cells


title: 200s_O13

description: Mouse non-parenchymal single cells


title: 200s_O11

description: Mouse non-parenchymal single cells


title: 200s_O10

description: Mouse non-parenchymal single cells


title: 200s_O12

description: Mouse non-parenchymal single cells


title: 200s_N9

description: Mouse non-parenchymal single cells


title: 200s_O5

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1103


title: MGE_B_10pcw_1102


title: 200s_N7

description: Mouse non-parenchymal single cells


title: 200s_N3

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1101


title: 200s_N20

description: Mouse non-parenchymal single cells


title: 200s_N18

description: Mouse non-parenchymal single cells


title: 200s_N17

description: Mouse non-parenchymal single cells


title: 200s_N5

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1100


title: 200s_O24

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1099


title: 200s_N16

description: Mouse non-parenchymal single cells


title: 200s_N13

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1098


title: 200s_N11

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1105


title: MGE_B_15pcw_1097


title: MGE_B_10pcw_1104


title: 200s_M4

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1096


title: 200s_M6

description: Mouse non-parenchymal single cells


title: 200s_M9

description: Mouse non-parenchymal single cells


title: 200s_M3

description: Mouse non-parenchymal single cells


title: 200s_M22

description: Mouse non-parenchymal single cells


title: 200s_M20

description: Mouse non-parenchymal single cells


title: 200s_M2

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1094


title: MGE_B_15pcw_1093


title: 200s_M21

description: Mouse non-parenchymal single cells


title: 200s_M19

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1095


title: 200s_M16

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1092


title: 200s_M13

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1090


title: MGE_B_15pcw_1089


title: 200s_M11

description: Mouse non-parenchymal single cells


title: 200s_M1

description: Mouse non-parenchymal single cells


title: 200s_L9

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1088


title: 200s_M10

description: Mouse non-parenchymal single cells


title: 200s_M23

description: Mouse non-parenchymal single cells


title: 200s_L5

description: Mouse non-parenchymal single cells


title: 200s_L3

description: Mouse non-parenchymal single cells


title: 200s_L20

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1086


title: MGE_B_15pcw_1087


title: MGE_B_15pcw_1091


title: 200s_M15

description: Mouse non-parenchymal single cells


title: 200s_M18

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1085


title: 200s_L19

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1084


title: 200s_L18

description: Mouse non-parenchymal single cells


title: 200s_M14

description: Mouse non-parenchymal single cells


title: 200s_L17

description: Mouse non-parenchymal single cells


title: 200s_K7

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1083


title: 200s_K8

description: Mouse non-parenchymal single cells


title: 200s_K4

description: Mouse non-parenchymal single cells


title: 200s_K5

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1082


title: 200s_K3

description: Mouse non-parenchymal single cells


title: 200s_K24

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1081


title: 200s_L7

description: Mouse non-parenchymal single cells


title: 200s_K21

description: Mouse non-parenchymal single cells


title: 200s_L21

description: Mouse non-parenchymal single cells


title: 200s_K22

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1080


title: 200s_K20

description: Mouse non-parenchymal single cells


title: 200s_K17

description: Mouse non-parenchymal single cells


title: 200s_K19

description: Mouse non-parenchymal single cells


title: arrayCGH data from patient 585

type: genomic

hyb_protocol: The hybridization mixtures were denatured at 95°C for 3 minutes, preincubated at 37°C for 30 minutes, and hybridized to the array in a microarray hybridization chamber (Agilent Technologies) for 14 to 18 hours at 65°C in a rotating oven (Robbins Scientific, Mountain View, CA). The array slides were washed in 0.5x SSC/0.005% Triton X-102 at room temperature for 5 minutes, followed by 5 minutes at 37°C in 0.1x SSC/0.005% Triton X-102.

scan_protocol: TIF images were obtained using Agilent scanner (model B and C)

data_processing: Images were analyzed using Cytogenomics v.50.0.38 software with the default analysis method: CGH v2 (ADM-2 algortihm). Threshold of 6.0, with a minimum of 3 consecutive aberrant probes and a minimum absolute amplification/deletion average of 0.25 log2ratio

source_name: pediatric patient samples

label_protocol: Labeling reactions with Cy5-dUTP and Cy3-dUTP (PerkinElmer, Wellesley, MA) were performed with 5 μg purified restricted DNA using the Bioprime labeling kit (Invitrogen, Paisley, United Kingdom) according to the manufacturer's instructions. Experimental and reference targets for each hybridization were pooled and mixed with 50 μg human Cot-1 DNA (Invitrogen), 100 μg yeast tRNA (Invitrogen), and 1x hybridization control targets (SP310; Operon Technologies, Alameda, CA) in a final volume of 500 μL in situ hybridization buffer (Agilent Technologies).

extract_protocol: 10 μg genomic reference or patient DNA was digested with AluI (20 U) and RsaI (20 U) (Invitrogen) overnight at 37°C. Patient genomic DNA (2 μg) and male/female reference DNA (2 μg; Promega) were fragmented by sonification (VibraCell Model VC130; Sonics & Materials, Newtown, CT). DNA fragmentation was verified by agarose gel electrophoresis. Individual reference and experimental samples were then purified using the QIAQuick polymerase chain reaction (PCR) clean-up kit (Qiagen, Valencia, CA).

tag: subarray

tag: subject

value: patient 585

value: control


title: MGE_B_15pcw_1079


title: arrayCGH data from patient 2722

value: patient 2722


title: 200s_K16

description: Mouse non-parenchymal single cells


title: 200s_K13

description: Mouse non-parenchymal single cells


title: 200s_K15

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1077


title: MGE_B_10pcw_1078


title: 200s_K1

description: Mouse non-parenchymal single cells


title: 200s_J7

description: Mouse non-parenchymal single cells


title: MGE_B_10pcw_1076


title: 200s_J5

description: Mouse non-parenchymal single cells


title: 200s_J3

description: Mouse non-parenchymal single cells


title: 200s_J17

description: Mouse non-parenchymal single cells


title: 200s_J19

description: Mouse non-parenchymal single cells


title: 200s_J21

description: Mouse non-parenchymal single cells


title: 200s_J15

description: Mouse non-parenchymal single cells


title: 200s_J13

description: Mouse non-parenchymal single cells


title: MGE_B_15pcw_1075


title: MGE_B_10pcw_1072


title: 200s_J12

description: Mouse non-parenchymal single cells