title: P17MC.4G10


title: P17MC.4F7

status: Public on Apr 23 2019

type: SRA

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

library_source: transcriptomic

data_processing:
Demultiplexed FASTQ files were aligned to the mouse genome (mm10 build) using STAR version 2.5.2 (Dobin et al., 2013) with default options.
Reads aligned to each gene were counted using featureCounts version 1.5.1 (Liao et al., 2014)
Filtered out cells outside the limits of median ± 4 * median absolute deviations for both reads number and genes detected; and excluded cells with more than 10% of reads aligning to mitochondrial genes
Further downstream processing was performed using Seurat (version 2.3.1 (Butler et al., 2018)) and Monocle2 (version 2.6.4 (Qiu et al., 2017a, 2017b; Trapnell et al., 2014))
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files of raw count data
Supplementary_files_format_and_content: tab-delimited text files of normalised count data (log normalised, scaled by 10000)

molecule: polyA RNA

organism: Mus musculus

source_name: Cortex

growth_protocol: APPswe/PS1dE9 (APP/PS1) were crossed with a C57Bl/6-Apoenull breeder to obtain homozygous APP/PS1-Apoenull mice [Hudry et. al., submited)]. APP/PS1-Apoe(null) mice, along with parental APP/PS1 mice and the respective control strains C57Bl/6 and C57Bl/6-Apoe(null), were transferred from the Hyman lab to the De Strooper lab, and housed for at least 1 month before being used for experiments.

extract_protocol:
The dissection and microglia isolation steps were carried out on ice or at +4°C. Cortex and hippocampus were dissected and finely chopped, and transferred to a tuve containing ice-cold Hibernate A medium without phenol red. Single cell suspension prepared using the Adult Brain Dissociation kit. Single live microglia cells (CD11b+/DAPI-) were sorted using BD FACSAria III
Single cell retrotranscription and preparation of sequencing libraries was performed using a modified SmartSeq2 protocol (Picelli et al., 2013, 2014; Trombetta et al., 2014). We used 5’-biotinylated primers throughout the protocol

tag: genotype

tag: ngene

tag: nreads

tag: age

tag: Sex

value: M

tag: plateplus

tag: plate

tag: lane


title: P17MC.4H12


title: P17MC.4G1


title: P17MC.4F6


title: P17MC.4F5


title: P17MC.4F2


title: P17MC.4F3


title: P17MC.4F10


title: P17MC.4F11


title: P17MC.4F1


title: P17MC.4E8


title: P17MC.4E7


title: P17MC.4F12


title: P17MC.4E6


title: P17MC.4E9


title: P17MC.4E5


title: P17MC.4E12


title: P17MC.4E10


title: P17MC.4E11


title: P17MC.4E2


title: P17MC.4E3


title: P17MC.4E1


title: P17MC.4D9


title: P17MC.4D4


title: P17MC.4D7


title: P17MC.4D5


title: P17MC.4D6


title: P17MC.4F4


title: P17MC.4D2


title: P17MC.4D12


title: P17MC.4D1


title: P17MC.4C9


title: P17MC.4D3


title: P17MC.4E4


title: P17MC.4C7


title: P17MC.4D11


title: P17MC.4C5


title: P17MC.4C2


title: P17MC.4D10


title: P17MC.4C3


title: P17MC.4C6


title: P17MC.4C11


title: P17MC.4C8


title: P17MC.4C12


title: P17MC.4D8


title: P17MC.4B8


title: P17MC.4C1


title: P17MC.4B7


title: P17MC.4C4


title: P17MC.4C10


title: P17MC.4B5


title: P17MC.4B9


title: P17MC.4B6


title: P17MC.4B2


title: P17MC.4B3


title: P17MC.4B4


title: P17MC.4B11


title: P17MC.4B10


title: P17MC.4B12


title: P17MC.4B1


title: P17MC.4A7


title: P17MC.4A8


title: P17MC.4A9


title: P17MC.4A6


title: P17MC.4A4


title: P17MC.4A5


title: P17MC.4A3


title: P17MC.4A12


title: P17MC.4A11


title: P17MC.4A2


title: P17MC.4A1


title: P17MC.3H8


title: P17MC.3H6


title: P17MC.3H7


title: P17MC.3H3


title: P17MC.3H4


title: P17MC.3H2


title: P17MC.3H5


title: P17MC.3H11


title: P17MC.3G11


title: P17MC.3G5


title: P17MC.3G8


title: P17MC.3H10


title: P17MC.3G2


title: P17MC.3H1


title: P17MC.3G1


title: P17MC.4A10


title: P17MC.3G12


title: P17MC.3G3


title: P17MC.3G7


title: P17MC.3F8


title: P17MC.3G6


title: P17MC.3G10


title: P17MC.3F9


title: P17MC.3F4


title: P17MC.3F6


title: P17MC.3H9


title: P17MC.3F7


title: P17MC.3F5


title: P17MC.3H12


title: P17MC.3G9


title: P17MC.3F2


title: P17MC.3F12


title: P17MC.3F10


title: P17MC.3F3


title: P17MC.3G4


title: P17MC.3F1


title: P17MC.3E9


title: P17MC.3E6


title: P17MC.3E5


title: P17MC.3E8


title: P17MC.3E2


title: P17MC.3E4


title: P17MC.3E12


title: P17MC.3D9


title: P17MC.3E3


title: P17MC.3E10


title: P17MC.3E1


title: P17MC.3D8


title: P17MC.3F11


title: P17MC.3D6


title: P17MC.3D3


title: P17MC.3D5


title: P17MC.3D11


title: P17MC.3D7


title: P17MC.3D4


title: P17MC.3D2


title: P17MC.3D1


title: P17MC.3C8


title: P17MC.3C9


title: P17MC.3D10


title: P17MC.3C7


title: P17MC.3C6


title: P17MC.3C5


title: P17MC.3C4


title: P17MC.3E11


title: P17MC.3E7


title: P17MC.3C3


title: P17MC.3C2


title: P17MC.3C11


title: P17MC.3C10


title: P17MC.3C12


title: P17MC.3B9


title: P17MC.3C1


title: P17MC.3B5


title: P17MC.3B8


title: P17MC.3D12


title: P17MC.3B2


title: P17MC.3B7


title: P17MC.3B6


title: P17MC.3B12


title: P17MC.3B11


title: P17MC.3B4


title: P17MC.3A8


title: P17MC.3B10


title: P17MC.3A5


title: P17MC.3A9


title: P17MC.3B3


title: P17MC.3A4


title: P17MC.3A7


title: P17MC.3B1


title: P17MC.3A6


title: P17MC.3A12


title: P17MC.3A11


title: P17MC.3A3


title: P17MC.3A10


title: P17MC.2H8


title: P17MC.3A1


title: P17MC.2H9


title: P17MC.2H6


title: P17MC.2H7


title: P17MC.2H3


title: P17MC.2H5


title: P17MC.2H4


title: P17MC.2H11


title: P17MC.2H1


title: P17MC.2H2


title: P17MC.2G9


title: P17MC.2H12


title: P17MC.3A2


title: P17MC.2H10


title: P17MC.2G6


title: P17MC.2G2


title: P17MC.2G8


title: P17MC.2G3


title: P17MC.2G12


title: P17MC.2G4


title: P17MC.2G7


title: P17MC.2G11


title: P17MC.2F9


title: P17MC.2F8


title: P17MC.2G1


title: P17MC.2F6


title: P17MC.2F7


title: P17MC.2F5


title: P17MC.2F2


title: P17MC.2F3


title: P17MC.2F4


title: P17MC.2F1


title: P17MC.2F11


title: P17MC.2G5


title: P17MC.2F10


title: P17MC.2E9


title: P17MC.2E4


title: P17MC.2E5


title: P17MC.2E6


title: P17MC.2G10


title: P17MC.2E8


title: P17MC.2E3


title: P17MC.2E2


title: P17MC.2E11


title: P17MC.2E12


title: P17MC.2E1


title: P17MC.2D7


title: P17MC.2D9


title: P17MC.2D8


title: P17MC.2D5


title: P17MC.2D6


title: P17MC.2D2


title: P17MC.2D3


title: P17MC.2F12


title: P17MC.2D12


title: P17MC.2D11


title: P17MC.2E7


title: P17MC.2D10


title: P17MC.2E10


title: P17MC.2C8


title: P17MC.2C3


title: P17MC.2C4


title: P17MC.2C7


title: P17MC.2C9


title: P17MC.2C2


title: P17MC.2B9


title: P17MC.2C11


title: P17MC.2C5


title: P17MC.2B6


title: P17MC.2C1


title: P17MC.2C10


title: P17MC.2B7


title: P17MC.2C12


title: P17MC.2B5


title: P17MC.2B2


title: P17MC.2B3


title: P17MC.2D4


title: P17MC.2B12


title: P17MC.2B11


title: P17MC.2D1


title: P17MC.2B10


title: P17MC.2A9


title: P17MC.2B4


title: P17MC.2B8


title: P17MC.2A8


title: P17MC.2B1


title: P17MC.2C6


title: P17MC.2A6


title: P17MC.2A5


title: P17MC.2A4


title: P17MC.2A12


title: P17MC.2A3


title: P17MC.2A1


title: P17MC.1H7


title: P17MC.2A2


title: P17MC.1H9


title: P17MC.2A10


title: P17MC.1H12


title: P17MC.1H5


title: P17MC.1H4


title: P17MC.1H11


title: P17MC.1H10


title: P17MC.1H1


title: P17MC.1H3


title: P17MC.1G9


title: P17MC.1G6


title: P17MC.1G7


title: P17MC.1G8


title: P17MC.1G5


title: P17MC.2A7


title: P17MC.1G4


title: P17MC.2A11


title: P17MC.1G12


title: P17MC.1G11


title: P17MC.1H8


title: P17MC.1H6


title: P17MC.1H2


title: P17MC.1G10


title: P17MC.1F9


title: P17MC.1F5


title: P17MC.1F7


title: P17MC.1F11


title: P17MC.1F4


title: P17MC.1F10


title: P17MC.1E9


title: P17MC.1G3


title: P17MC.1F3


title: P17MC.1G2


title: P17MC.1F12


title: P17MC.1E8


title: P17MC.1E5


title: P17MC.1E7


title: P17MC.1F1


title: P17MC.1E6


title: P17MC.1E3


title: P17MC.1E2


title: P17MC.1E4


title: P17MC.1F6


title: P17MC.1F8


title: P17MC.1E12


title: P17MC.1D5


title: P17MC.1F2


title: P17MC.1E11


title: P17MC.1E1


title: P17MC.1D8


title: P17MC.1D9


title: P17MC.1D7


title: P17MC.1D6


title: P17MC.1D3


title: P17MC.1D11


title: P17MC.1D12


title: P17MC.1D4


title: P17MC.1D10


title: P17MC.1D1


title: P17MC.1C6


title: P17MC.1C7


title: P17MC.1E10


title: P17MC.1C4


title: P17MC.1C9


title: P17MC.1C5


title: P17MC.1C10


title: P17MC.1C1


title: P17MC.1C12


title: P17MC.1C11


title: P17MC.1C8


title: P17MC.1B7


title: P17MC.1B9


title: P17MC.1B8


title: P17MC.1C2


title: P17MC.1B6


title: P17MC.1B12


title: P17MC.1B3


title: P17MC.1B4


title: P17MC.1G1


title: P17MC.1B5


title: P17MC.1C3


title: P17MC.1B11


title: P17MC.1B10


title: P17MC.1B1


title: P17MC.1B2


title: P17MC.1A8


title: P17MC.1A7


title: P17MC.1A4


title: P17MC.1A5


title: P17MC.1A6


title: P17MC.1A12


title: P17MC.1A2


title: P17MC.1A3


title: P17MC.1A11


title: P17MC.1A10


title: E18MC.4H9


title: P17MC.1A1


title: E18MC.4H7


title: E18MC.4H8


title: E18MC.4H5


title: E18MC.4H4


title: E18MC.4H6


title: P17MC.1A9


title: E18MC.4H2


title: E18MC.4H3


title: E18MC.4H12


title: E18MC.4H1


title: E18MC.4G9


title: E18MC.4H11


title: E18MC.4G8


title: E18MC.4G6


title: E18MC.4G7


title: E18MC.4H10


title: P17MC.1D2


title: E18MC.4G5


title: E18MC.4G3


title: E18MC.4G12


title: E18MC.4G2


title: E18MC.4G4


title: E18MC.4G11


title: E18MC.4F9


title: E18MC.4G1


title: E18MC.4G10


title: E18MC.4F8


title: E18MC.4F4


title: E18MC.4F3


title: E18MC.4F5


title: E18MC.4F7


title: E18MC.4F6


title: E18MC.4F12


title: E18MC.4F11


title: E18MC.4F10


title: E18MC.4F1


title: E18MC.4E5


title: E18MC.4E6


title: E18MC.4E8


title: E18MC.4E7


title: E18MC.4E9


title: E18MC.4E12


title: E18MC.4E11


title: E18MC.4E4


title: E18MC.4E1


title: E18MC.4E10


title: E18MC.4D9


title: E18MC.4D8


title: E18MC.4D7


title: E18MC.4D6


title: E18MC.4D2


title: E18MC.4D3


title: E18MC.4D4


title: E18MC.4D5


title: E18MC.4F2


title: E18MC.4D12


title: E18MC.4C9


title: E18MC.4D10


title: E18MC.4C8


title: E18MC.4D11


title: E18MC.4D1


title: E18MC.4E3


title: E18MC.4C7


title: E18MC.4C5


title: E18MC.4E2


title: E18MC.4C6


title: E18MC.4C12


title: E18MC.4C10


title: E18MC.4C3


title: E18MC.4C2


title: E18MC.4C11


title: E18MC.4C1


title: E18MC.4B9


title: E18MC.4B6


title: E18MC.4B5


title: E18MC.4B7


title: E18MC.4B4


title: E18MC.4B3


title: E18MC.4B11


title: E18MC.4A9


title: E18MC.4B1


title: E18MC.4B2


title: E18MC.4A6


title: E18MC.4A8


title: E18MC.4A7


title: E18MC.4A5


title: E18MC.4A2


title: E18MC.4B8


title: E18MC.4A3


title: E18MC.4A4


title: E18MC.4A11


title: E18MC.4A10


title: E18MC.4A1


title: E18MC.4B12


title: E18MC.4A12


title: E18MC.3H7


title: E18MC.3H6


title: E18MC.4B10


title: E18MC.3H4


title: E18MC.3H3


title: E18MC.3H8


title: E18MC.3H11


title: E18MC.3H2


title: E18MC.3G8


title: E18MC.3H10


title: E18MC.3G7


title: E18MC.3G9


title: E18MC.3H1


title: E18MC.3G6


title: E18MC.3G5


title: E18MC.3G4


title: E18MC.3G2


title: E18MC.3G3


title: E18MC.3G12


title: E18MC.3G11


title: E18MC.3H9


title: E18MC.3G10


title: E18MC.3G1


title: E18MC.3F9


title: E18MC.3F7


title: E18MC.3H5


title: E18MC.3F5


title: E18MC.3F8


title: E18MC.3H12


title: E18MC.3F4


title: E18MC.3F3


title: E18MC.3F2


title: E18MC.3F11


title: E18MC.3F12


title: E18MC.3F10


title: E18MC.3F1


title: E18MC.3E7


title: E18MC.3E4


title: E18MC.3E9


title: E18MC.3E5


title: E18MC.3E8


title: E18MC.3E6


title: E18MC.3E12


title: E18MC.3E3


title: E18MC.3E2


title: E18MC.3D9


title: E18MC.3E11


title: E18MC.3E1


title: E18MC.3D8


title: E18MC.3F6


title: E18MC.3D7


title: E18MC.3D6


title: E18MC.3D4


title: E18MC.3D3


title: E18MC.3E10


title: E18MC.3D11


title: E18MC.3D12


title: E18MC.3D2


title: E18MC.3D10


title: E18MC.3C8


title: E18MC.3C9


title: E18MC.3C7


title: E18MC.3D5


title: E18MC.3C6


title: E18MC.3D1


title: E18MC.3C5


title: E18MC.3C2


title: E18MC.3C11


title: E18MC.3C4


title: E18MC.3C3


title: E18MC.3C10


title: E18MC.3C1


title: E18MC.3B5


title: E18MC.3B4


title: E18MC.3B6


title: E18MC.3B2


title: E18MC.3B3


title: E18MC.3B11


title: E18MC.3B8


title: E18MC.4C4


title: E18MC.3B12


title: E18MC.3A9


title: E18MC.3A8


title: E18MC.3A7


title: E18MC.3B10


title: E18MC.3A5


title: E18MC.3A3


title: E18MC.3A4


title: E18MC.3C12


title: E18MC.3B9


title: E18MC.3A11


title: E18MC.2H8


title: E18MC.3A2


title: E18MC.3A10


title: E18MC.3A1


title: E18MC.2H9


title: E18MC.2H7


title: E18MC.3B7


title: E18MC.2H5


title: E18MC.3B1


title: E18MC.2H4


title: E18MC.2H3


title: E18MC.2H1


title: E18MC.2H12


title: E18MC.2H11


title: E18MC.2H2


title: E18MC.2H10


title: E18MC.3A6


title: E18MC.2G9


title: E18MC.2G6


title: E18MC.2G8


title: E18MC.2G4


title: E18MC.3A12


title: E18MC.2G5


title: E18MC.2G7


title: E18MC.2G12


title: E18MC.2G3


title: E18MC.2G2


title: E18MC.2G11


title: E18MC.2G10


title: E18MC.2H6


title: E18MC.2G1


title: E18MC.2F9


title: E18MC.2F7


title: E18MC.2F4


title: E18MC.2F3


title: E18MC.2F2


title: E18MC.2F12


title: E18MC.2F11


title: E18MC.2E8


title: E18MC.2F10


title: E18MC.2E7


title: E18MC.2E6


title: E18MC.2F1


title: E18MC.2E5


title: E18MC.2E4


title: E18MC.2F8


title: E18MC.2E11


title: E18MC.2E1


title: E18MC.2E12


title: E18MC.2E3


title: E18MC.2E2


title: E18MC.2D9


title: E18MC.2F6


title: E18MC.2D5


title: E18MC.2F5


title: E18MC.2D4


title: E18MC.2D7


title: E18MC.2D3


title: E18MC.2D12


title: E18MC.2E9


title: E18MC.2C9


title: E18MC.2D10


title: E18MC.2D1


title: E18MC.2C8


title: E18MC.2C7


title: E18MC.2C6


title: E18MC.2C4


title: E18MC.2C5


title: E18MC.2E10


title: E18MC.2C3


title: E18MC.2C2


title: E18MC.2D6


title: E18MC.2C12


title: E18MC.2D8


title: E18MC.2C10


title: E18MC.2C1


title: E18MC.2B7


title: E18MC.2D2


title: E18MC.2B8


title: E18MC.2B9


title: E18MC.2C11


title: E18MC.2B4


title: E18MC.2B6


title: E18MC.2B2


title: E18MC.2B3


title: E18MC.2B5


title: E18MC.2B11


title: E18MC.2D11


title: E18MC.2A9


title: E18MC.2B10


title: E18MC.2A8


title: E18MC.2B1


title: E18MC.2A6


title: E18MC.2A5


title: E18MC.2A7


title: E18MC.2A4


title: E18MC.2A3


title: E18MC.2A2


title: E18MC.2A12


title: E18MC.2A11


title: E18MC.2B12


title: E18MC.2A1


title: E18MC.1H9


title: E18MC.1H7


title: E18MC.1H8


title: E18MC.2A10


title: E18MC.1H3


title: E18MC.1H5


title: E18MC.1H6


title: E18MC.1G8


title: E18MC.1H10


title: E18MC.1H12


title: E18MC.1G9


title: E18MC.1H11


title: E18MC.1G7


title: E18MC.1H2


title: E18MC.1H1


title: E18MC.1G5


title: E18MC.1G6


title: E18MC.1G4


title: E18MC.1G3


title: E18MC.1G2


title: E18MC.1G12


title: E18MC.1G1


title: E18MC.1F9


title: E18MC.1G10


title: E18MC.1F8


title: E18MC.1F7


title: E18MC.1F6


title: E18MC.1H4


title: E18MC.1F3


title: E18MC.1F5


title: E18MC.1F2


title: E18MC.1F4


title: E18MC.1F12


title: E18MC.1F11


title: E18MC.1F10


title: E18MC.1E7


title: E18MC.1E9


title: E18MC.1F1


title: E18MC.1E8


title: E18MC.1E5


title: E18MC.1E3


title: E18MC.1G11


title: E18MC.1E2


title: E18MC.1E12


title: E18MC.1E4


title: E18MC.1E10


title: E18MC.1E6


title: E18MC.1E1


title: E18MC.1D8


title: E18MC.1E11


title: E18MC.1D5


title: E18MC.1D6


title: E18MC.1D3


title: E18MC.1D7


title: E18MC.1D2


title: E18MC.1D4


title: E18MC.1D12


title: E18MC.1D10


title: E18MC.1C8


title: E18MC.1C9


title: E18MC.1D11


title: E18MC.1C7


title: E18MC.1D1


title: E18MC.1C6


title: E18MC.1C4


title: E18MC.1C3


title: E18MC.1C11


title: E18MC.1C12


title: E18MC.1C2


title: E18MC.1C5


title: E18MC.1C10


title: E18MC.1D9


title: E18MC.1B8


title: E18MC.1B7


title: E18MC.1B9


title: E18MC.1B3


title: E18MC.1B6


title: E18MC.1B4


title: E18MC.1B11


title: E18MC.1B12


title: E18MC.1B10


title: E18MC.1A9


title: E18MC.1A8


title: E18MC.1B1


title: E18MC.1A7


title: E18MC.1A4


title: E18MC.1A5


title: E18MC.1A12


title: E18MC.1A2


title: E18MC.1A6


title: E18MC.1C1


title: E18MC.1A3


title: E18MC.1B5


title: E18MC.1A1


title: E18MC.1A11


title: D18MH.4H9

source_name: Hippocampus


title: D18MH.4H8


title: D18MH.4H3


title: E18MC.1B2


title: D18MH.4H7


title: D18MH.4H4


title: D18MH.4H6


title: E18MC.1A10


title: D18MH.4H2


title: D18MH.4H5


title: D18MH.4H10


title: D18MH.4H12


title: D18MH.4H11


title: D18MH.4G9


title: D18MH.4G6


title: D18MH.4G7


title: D18MH.4G8


title: D18MH.4G5


title: D18MH.4G3


title: D18MH.4G4


title: D18MH.4G12


title: D18MH.4G2


title: D18MH.4F8


title: D18MH.4G11


title: D18MH.4H1


title: D18MH.4G1


title: D18MH.4F9


title: D18MH.4F12


title: D18MH.4F2


title: D18MH.4F5


title: D18MH.4F6


title: D18MH.4F10


title: D18MH.4F4


title: D18MH.4F3


title: D18MH.4E9


title: D18MH.4E6


title: D18MH.4G10


title: D18MH.4E8


title: D18MH.4F11


title: D18MH.4E5


title: D18MH.4E4


title: D18MH.4E3


title: D18MH.4E12


title: D18MH.4E11


title: D18MH.4F7


title: D18MH.4E10


title: D18MH.4E1


title: D18MH.4D9


title: D18MH.4F1


title: D18MH.4D8


title: D18MH.4E7


title: D18MH.4D6


title: D18MH.4D7


title: D18MH.4D5


title: D18MH.4D4


title: D18MH.4D2


title: D18MH.4D11


title: D18MH.4D1


title: D18MH.4C9


title: D18MH.4D10


title: D18MH.4D12


title: D18MH.4E2


title: D18MH.4C3


title: D18MH.4C4


title: D18MH.4C7


title: D18MH.4C12


title: D18MH.4C5


title: D18MH.4C10


title: D18MH.4C2


title: D18MH.4B9


title: D18MH.4C1


title: D18MH.4C6


title: D18MH.4C11


title: D18MH.4B8


title: D18MH.4B6


title: D18MH.4B7


title: D18MH.4B5


title: D18MH.4B4


title: D18MH.4B3


title: D18MH.4D3


title: D18MH.4C8


title: D18MH.4B11


title: D18MH.4B12


title: D18MH.4B2


title: D18MH.4A7


title: D18MH.4A6


title: D18MH.4A8


title: D18MH.4B10


title: D18MH.4A9


title: D18MH.4A5


title: D18MH.4B1


title: D18MH.4A4


title: D18MH.4A10


title: D18MH.4A3


title: D18MH.4A11


title: D18MH.3H7


title: D18MH.4A1


title: D18MH.4A12


title: D18MH.3H9


title: D18MH.3H8


title: D18MH.4A2


title: D18MH.3H6


title: D18MH.3H4


title: D18MH.3H5


title: D18MH.3H3


title: D18MH.3H2


title: D18MH.3H12


title: D18MH.3H10


title: D18MH.3H11


title: D18MH.3G8


title: D18MH.3G7


title: D18MH.3F9


title: D18MH.3G2


title: D18MH.3H1


title: D18MH.3G11


title: D18MH.3G10


title: D18MH.3G1


title: D18MH.3F6


title: D18MH.3F7


title: D18MH.3F4


title: D18MH.3F1


title: D18MH.3F8


title: D18MH.3E8


title: D18MH.3G9


title: D18MH.3E9


title: D18MH.3F3


title: D18MH.3F12


title: D18MH.3E7


title: D18MH.3E5


title: D18MH.3E6


title: D18MH.3G4


title: D18MH.3G6


title: D18MH.3G5


title: D18MH.3E2


title: D18MH.3E4


title: D18MH.3E3


title: D18MH.3E12


title: D18MH.3E11


title: D18MH.3F10


title: D18MH.3D9


title: D18MH.3F11


title: D18MH.3E1


title: D18MH.3D4


title: D18MH.3F5


title: D18MH.3D5


title: D18MH.3D2


title: D18MH.3D12


title: D18MH.3D7


title: D18MH.3D8


title: D18MH.3E10


title: D18MH.3D6


title: D18MH.3D10


title: D18MH.3D1


title: D18MH.3C9


title: D18MH.3C8


title: D18MH.3C7


title: D18MH.3C6


title: D18MH.3C5


title: D18MH.3C3


title: D18MH.3C2


title: D18MH.3C4


title: D18MH.3C12


title: D18MH.3C11


title: D18MH.3C1


title: D18MH.3D3


title: D18MH.3C10


title: D18MH.3D11


title: D18MH.3B9


title: D18MH.3B7


title: D18MH.3B4


title: D18MH.3B6


title: D18MH.3B5


title: D18MH.3B12


title: D18MH.3B1


title: D18MH.3B11


title: D18MH.3A9


title: D18MH.3A7


title: D18MH.3A6


title: D18MH.3A5


title: D18MH.3A4


title: D18MH.3A3


title: D18MH.3A10


title: D18MH.3A2


title: D18MH.3B8


title: D18MH.3A11


title: D18MH.3B2


title: D18MH.3A1


title: D18MH.3B3


title: D18MH.2H9


title: D18MH.3B10


title: D18MH.2H8


title: D18MH.2H7


title: D18MH.3A8


title: D18MH.2H2


title: D18MH.2H3


title: D18MH.2H4


title: D18MH.2H6


title: D18MH.2H10


title: D18MH.2H11


title: D18MH.2H1


title: D18MH.2G9


title: D18MH.2G8


title: D18MH.2G7


title: D18MH.3A12


title: D18MH.2G6


title: D18MH.2G3


title: D18MH.2G2


title: D18MH.2H5


title: D18MH.2G5


title: D18MH.2G12


title: D18MH.2G4


title: D18MH.2G10


title: D18MH.2F8


title: D18MH.2G1


title: D18MH.2H12


title: D18MH.2F7


title: D18MH.2F2


title: D18MH.2F5


title: D18MH.2F12


title: D18MH.2F6


title: D18MH.2F3


title: D18MH.2G11


title: D18MH.2F1


title: D18MH.2F10


title: D18MH.2F9


title: D18MH.2F11


title: D18MH.2E7


title: D18MH.2E9


title: D18MH.2E8


title: D18MH.2E6


title: D18MH.2E5


title: D18MH.2F4


title: D18MH.2E4


title: D18MH.2E12


title: D18MH.2E11


title: D18MH.2E3


title: D18MH.2E2


title: D18MH.2E1


title: D18MH.2E10


title: D18MH.2D9


title: D18MH.2D4


title: D18MH.2D8


title: D18MH.2D11


title: D18MH.2D2


title: D18MH.2D10


title: D18MH.2D6


title: D18MH.2C9


title: D18MH.2D5


title: D18MH.2D12


title: D18MH.2D3


title: D18MH.2D7


title: D18MH.2C6


title: D18MH.2D1


title: D18MH.2C4


title: D18MH.2C5


title: D18MH.2C8


title: D18MH.2C7


title: D18MH.2C3


title: D18MH.2C2


title: D18MH.2C12


title: D18MH.2C11


title: D18MH.2C10


title: D18MH.2C1


title: D18MH.2B9


title: D18MH.2B7


title: D18MH.2B8


title: D18MH.3F2


title: D18MH.2B6


title: D18MH.2B5


title: D18MH.2B10


title: D18MH.2A7


title: D18MH.2B4


title: D18MH.2A6


title: D18MH.2B3


title: D18MH.2B2


title: D18MH.2B12


title: D18MH.2A11


title: D18MH.2A2


title: D18MH.2B11


title: D18MH.2B1


title: D18MH.2A8


title: D18MH.2A9


title: D18MH.2A4


title: D18MH.1H9


title: D18MH.2A12


title: D18MH.2A3


title: D18MH.2A10


title: D18MH.1H5


title: D18MH.1H7


title: D18MH.1H6


title: D18MH.1H4


title: D18MH.1H2


title: D18MH.2A5


title: D18MH.1H3


title: D18MH.1H1


title: D18MH.1G8


title: D18MH.1H10


title: D18MH.1G9


title: D18MH.1G6


title: D18MH.2A1


title: D18MH.1H12


title: D18MH.1G3


title: D18MH.1G12


title: D18MH.1G2


title: D18MH.1G11


title: D18MH.1H11


title: D18MH.1H8


title: D18MH.1G10


title: D18MH.1G5


title: D18MH.1F9


title: D18MH.1G7


title: D18MH.1F8


title: D18MH.1F7


title: D18MH.1F6


title: D18MH.1F4


title: D18MH.1F5


title: D18MH.1F3


title: D18MH.1F2


title: D18MH.1F10


title: D18MH.1F1


title: D18MH.1F11


title: D18MH.1E9


title: D18MH.1F12


title: D18MH.1G4


title: D18MH.1E5


title: D18MH.1E4


title: D18MH.1E2


title: D18MH.1G1


title: D18MH.1E11


title: D18MH.1E6


title: D18MH.1E3


title: D18MH.1E10


title: D18MH.1E1


title: D18MH.1D7


title: D18MH.1E12


title: D18MH.1D8


title: D18MH.1D9


title: D18MH.1D4


title: D18MH.1D3


title: D18MH.1D6


title: D18MH.1D5


title: D18MH.1D2


title: D18MH.1E8


title: D18MH.1D11


title: D18MH.1D10


title: D18MH.1C7


title: D18MH.1C8


title: D18MH.1D1


title: D18MH.1C9


title: D18MH.1E7


title: D18MH.1C6


title: D18MH.1C5


title: D18MH.1C3


title: D18MH.1C2


title: D18MH.1C12


title: D18MH.1C4


title: D18MH.1C11


title: D18MH.1B9


title: D18MH.1C10


title: D18MH.1C1


title: D18MH.1B7


title: D18MH.1D12


title: D18MH.1B8


title: D18MH.1B5


title: D18MH.1B6


title: D18MH.1B12


title: D18MH.1B3


title: D18MH.1B2


title: Pig 6 DP

city: Los Angeles

first: Denis

last: Evseenko

state: CA

address: 1450 Biggy St

department: Orthopaedic Surgery

country: USA

institute: University of Southern  California

data_processing:
Reads were mapped to the pig genome (Ensembl 84) using STAR
Transcript estimation was performed using Partek E/M
Differenential expression was performed using ANOVA
Genome_build: Sus scrofa Ensembl84

molecule: total RNA

organism: Sus scrofa

source_name: Knee cartilage

extract_protocol:
Qiagen Micro kit
Library preparation with Nugen SoLo mRNA-Seq kit

tag: tissue

value: Knee cartilage

tag: developmental stage

value: Adult

tag: cell type

value: ITGA4 and BMPR1B positve sorted cells


title: D18MH.1B11


title: Pig 6 DN

value: ITGA4 and BMPR1B negative sorted cells


title: D18MH.1B10


title: Pig 6 B1B

value: BMPR1B positve sorted cells


title: Pig 6 A4

value: ITGA4 positive sorted cells


title: D18MH.1B1


title: D18MH.1A9


title: Pig 5 DP


title: D18MH.1A8


title: Pig 5 B1B


title: D18MH.1B4


title: D18MH.1A6


title: D18MH.1A5


title: Pig 5 MSC

source_name: Knee synovial pericyte

value: Knee synovial pericyte

value: CD146 Positive sorted cells


title: Pig 3 MSC


title: Pig 5 A4


title: Pig 4 MSC


title: D18MH.1A2


title: Pig 2 DN


title: D18MH.1A11


title: D18MH.1A10


title: D18MH.1A4


title: Pig 2 B1B


title: Pig 2 A4


title: D18MH.1A12


title: D18MH.1A1


title: D18MC.4H9


title: D18MH.1A3


title: Pig 2 DP


title: D18MC.4H8


title: gun1 fug1_2

city: Planegg

first: Tatjana

last: Kleine

address: Großhaderner Straße 2

department: Biologie I, Botanik

country: Germany

institute: Ludwig-Maximilians-Universität München

data_processing:
Galaxy platform
adaptors were removed with Trimmomatic (Bolger et al., 2014)
sequencing quality was accessed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were mapped to the Arabidopsis genome (TAIR10) with the gapped-read mapper TopHat 2.1.1 (Kim et al., 2013) set for Forward Read (FR) unstranded libraries and adjusting the maximum intron length to 5000 bp.
Reads were counted with featureCounts (Liao et al., 2014) with the help of the gene annotation in Araport11 (www.araport.org/data/araport11).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited files include read count values for each sample

organism: Arabidopsis thaliana

source_name: 4-d-old seedlings

growth_protocol: Surface-sterilized wild-type (Col-0) and mutant seeds were plated on one-half-strength Murashige and Skoog (MS) medium containing 1% (w/v) sucrose and 1% (w/v) agar. After stratification for 2 days in darkness at 4°C, plants were grown at 22°C under long-day conditions (LD, 16 h light/8 h dark) using white light (100 µmol m-2 s-1).

extract_protocol:
Total RNA from plants was isolated using Trizol (Invitrogen, Carlsbad, USA) and purified using Direct-zol™ RNA MiniPrep Plus columns (Zymo Research, Irvine, USA) according to the manufacturer’s instructions. RNA integrity and quality was assessed by an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, USA).
Illumina Tru-Seq

treatment_protocol: long-day conditions

value: gun1-103 fug1-3 mutant

value: 4-d-old seedlings


title: D18MC.4H7


title: gun1 fug1_3


title: D18MH.1A7


title: Pig 5 DN


title: fug1_3


title: gun1 fug1_1


title: D18MC.4H6


title: D18MC.4H5


title: fug1_2


title: fug1_1


title: D18MC.4H4


title: D18MC.4H3


title: gun1_3

value: gun1-103 (SAIL_742_A11) mutant


title: D18MC.4H2


title: gun1_2


title: D18MC.4H12


title: D18MC.4H11


title: Col_3

value: wild type


title: D18MC.4G5


title: D18MC.4G8


title: D18MC.4H10


title: D18MC.4G7


title: D18MC.4G9


title: D18MC.4G6


title: D18MC.4H1


title: D18MC.4G4


title: D18MC.4G3


title: gun1_1


title: D18MC.4G2


title: PKH26 Low single cell 42

city: Göteborg

first: Emma

last: Jonasson

address: Medicinaregatan 1F, floor 5

department: Sahlgrenska Center for Cancer Research

country: Sweden

institute: University of Gothenburg

data_processing:
Alignment was performed using STAR (with ERCC spike-in sequences included) with splice junctions supplied from the GENCODE V17 annotation
Gene expression was quantified using HTseq with the options “-s no” and “-m intersection-strict”
Genome_build: hg19
Supplementary_files_format_and_content: Excel file containing matrix of unnormalized reads mapped to each transcript (including ERCC spike-ins) as a result from HTseq analysis

organism: Homo sapiens

source_name: Breast cancer cell line

growth_protocol: MDA-MB-231 luciferase cells were cultured in DMEM medium supplied with 10% FBS, 1% penicillin/streptomycin, 1x MEM Non-essential Amino Acid Solution and 1% L-glutamine

extract_protocol:
Single-cells were sorted using FACS into 96-well plates pre-filled with 5µl lysis buffer (1 µg/µl BSA supplied in 2.5% glycerol and 0.2% Triton X-100). Plates were frozen on dry ice and stored in -80°C.
The library was generated using the Smart-seq2 protocol (Picelli, Faridani et al. 2014) with some modifications.

treatment_protocol:
Cell proliferation staining and mammosphere formation assay: Cells were stained with PKH26 Red Fluorescent Cell Linker Kit according to the manufacturer’s instructions with a concentration of 1µM PKH26. For non-adherent mammosphere formation assay, single-cells were seeded on cell cuclture flasks pre-coated with 1.2% poly(2-hydroxyethyl methacrylate) in 95% ethanol using 30 ml phenol-red free DMEM/F-12 medium supplied with 2% B-27 supplement, 1% penicillin/streptomycin and 20 ng/ml epidermal growth factor. After 120h, spheres were collected , centrifuged and disscoaiated using 0.25% trypsin before FACS sorting.
Cell cycle staining: Cells were stained with Vybrant DyeCycle Violet stain according to the manufacturer’s instructions with a concentration of 5µM.

tag: cell line

value: MDA-MB-231 luciferase

tag: cell culture method

value: Non-adherent (mammsophere assay)

tag: staining

value: PKH26, low intensity sorted


title: DMSO-3: Vehicle control rep3

city: Indianapolis

first: Xinxin

last: Huang

state: IN

address: 950 W. Walnut St R2 304

department: Microbiology and Immunology

institute: Indiana University School of Medicine

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NextSeq500
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to hg38 genes using featureCounts (from subread v1.5.1) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 4 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using likelihood ratio test method in edgeR (v3.20.8).
Genome_build: hg38
Supplementary_files_format_and_content: analysis with raw count (excel) from edgeR

source_name: Cord blood CD34+ cells

growth_protocol: CD34+ cells were isolated from human cord blood and culture in RPMI-1640 medium with 10% fetal bovine serum, 100 ng/mLSCF, TPO and Flt3L for 16 hours

extract_protocol:
RNA was extracted using the RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD34+ cells were treated with vehicle control (DMSO) or Riociguat for 16 hours

value: hematopoietic stem and progenitor cells

tag: treatment

value: DMSO for 16 hours


title: RIO-1: Riociguat rep1

value: 10uM Riociguat for 16 hours


title: PKH26 Low single cell 45


title: PKH26 Low single cell 44


title: DMSO-1: Vehicle control rep1


title: RIO-3: Riociguat rep3


title: DMSO-2: Vehicle control rep2


title: RIO-2: Riociguat rep2


title: D18MC.4G12

value: M


title: Col_1


title: PKH26 Low single cell 41


title: D18MC.4G11


title: Col_2


title: PKH26 Low single cell 40


title: PKH26 Low single cell 39


title: PKH26 Low single cell 38


title: D18MC.4G1


title: D18MC.4F9


title: PKH26 Low single cell 37


title: PKH26 Low single cell 36


title: PKH26 Low single cell 43


title: D18MC.4F7


title: D18MC.4F6


title: PKH26 Low single cell 35


title: D18MC.4F5


title: D18MC.4F4


title: D18MC.4G10


title: PKH26 Low single cell 33


title: D18MC.4F11


title: D18MC.4F12


title: PKH26 Low single cell 31


title: PKH26 Low single cell 30


title: PKH26 Low single cell 29


title: D18MC.4F2


title: PKH26 Low single cell 32


title: D18MC.4F1


title: PKH26 Low single cell 28


title: D18MC.4F10


title: D18MC.4F8


title: D18MC.4E9


title: D18MC.4E8


title: PKH26 Low single cell 26


title: PKH26 Low single cell 25


title: D18MC.4E6


title: D18MC.4E7


title: PKH26 Low single cell 24


title: D18MC.4E5


title: D18MC.4F3


title: PKH26 Low single cell 34


title: PKH26 Low single cell 22


title: D18MC.4E2


title: D18MC.4E3


title: D18MC.4E12


title: PKH26 Low single cell 19


title: PKH26 Low single cell 18


title: PKH26 Low single cell 27


title: D18MC.4E11


title: D18MC.4E10


title: PKH26 Low single cell 16


title: D18MC.4E1


title: D18MC.4D9


title: D18MC.4D7


title: D18MC.4D8


title: PKH26 Low single cell 13


title: D18MC.4E4


title: PKH26 Low single cell 11


title: PKH26 Low single cell 23


title: PKH26 Low single cell 12


title: PKH26 Low single cell 21


title: PKH26 Low single cell 10


title: D18MC.4D4


title: PKH26 Low single cell 20


title: D18MC.4D5


title: PKH26 Low single cell 9


title: PKH26 Low single cell 17


title: D18MC.4D6


title: PKH26 Low single cell 15


title: D18MC.4D2


title: PKH26 Low single cell 8


title: D18MC.4D11


title: PKH26 Low single cell 6


title: PKH26 Low single cell 4


title: D18MC.4D3


title: PKH26 Low single cell 5


title: D18MC.4D12


title: D18MC.4D10


title: PKH26 Low single cell 14


title: D18MC.4D1


title: D18MC.4C9


title: PKH26 Low single cell 2


title: D18MC.4C8


title: PKH26 Low single cell 3


title: PKH26 Low single cell 1


title: D18MC.4C7


title: D18MC.4C6


title: PKH26 High single cell 45

value: PKH26, high intensity sorted


title: PKH26 High single cell 44


title: PKH26 High single cell 46


title: PKH26 Low single cell 7


title: PKH26 High single cell 43


title: D18MC.4C5


title: PKH26 High single cell 42


title: D18MC.4C4


title: D18MC.4C2


title: D18MC.4C3


title: PKH26 High single cell 40


title: PKH26 High single cell 39


title: D18MC.4C11


title: PKH26 High single cell 38


title: D18MC.4C10


title: D18MC.4B9


title: PKH26 High single cell 37


title: D18MC.4C12


title: PKH26 High single cell 36


title: PKH26 High single cell 35


title: D18MC.4B8


title: PKH26 High single cell 34


title: PKH26 High single cell 33


title: D18MC.4B6


title: D18MC.4B7


title: PKH26 High single cell 41


title: PKH26 High single cell 32


title: D18MC.4B5


title: PKH26 High single cell 31


title: D18MC.4B2


title: D18MC.4B4


title: PKH26 High single cell 30


title: D18MC.4B3


title: D18MC.4C1


title: PKH26 High single cell 29


title: D18MC.4B12


title: PKH26 High single cell 28


title: D18MC.4B10


title: D18MC.4B1


title: D18MC.4B11


title: D18MC.4A9


title: PKH26 High single cell 26


title: PKH26 High single cell 27


title: PKH26 High single cell 25


title: D18MC.4A8


title: PKH26 High single cell 23


title: PKH26 High single cell 24


title: D18MC.4A7


title: D18MC.4A5


title: D18MC.4A6


title: D18MC.4A4


title: PKH26 High single cell 22


title: PKH26 High single cell 20


title: PKH26 High single cell 21


title: PKH26 High single cell 19


title: D18MC.4A3


title: D18MC.4A2


title: PKH26 High single cell 17


title: PKH26 High single cell 18


title: D18MC.4A12


title: D18MC.4A11


title: PKH26 High single cell 16


title: PKH26 High single cell 15


title: D18MC.4A10


title: PKH26 High single cell 14


title: D18MC.3H8


title: D18MC.3H9


title: D18MC.3H6


title: D18MC.3H7


title: PKH26 High single cell 12


title: PKH26 High single cell 11


title: PKH26 High single cell 10


title: D18MC.3H4


title: D18MC.3H2


title: PKH26 High single cell 9


title: PKH26 High single cell 6


title: D18MC.3H11


title: PKH26 High single cell 3


title: PKH26 High single cell 4


title: D18MC.3H5


title: PKH26 High single cell 5


title: D18MC.3H10


title: PKH26 High single cell 2


title: PKH26 High single cell 1


title: D18MC.3H12


title: PKH26 High single cell 13


title: D18MC.3G9


title: D18MC.4A1


title: D18MC.3H1


title: G1 single cell 30

value: Adherent

value: Vybrant DyeCycle violet, low intensity sorted


title: D18MC.3G7


title: G1 single cell 28


title: G1 single cell 29


title: D18MC.3H3


title: PKH26 High single cell 7


title: PKH26 High single cell 8


title: D18MC.3G6


title: G1 single cell 27


title: D18MC.3G5


title: D18MH.3G3


title: D18MH.3G12


title: D18MC.3G4


title: G1 single cell 25


title: G1 single cell 24


title: D18MC.3G2


title: G1 single cell 23


title: G1 single cell 22


title: D18MC.3G11


title: G1 single cell 21


title: G1 single cell 20


title: D18MC.3G1


title: D18MC.3F8


title: D18MC.3F9


title: G1 single cell 19


title: G1 single cell 18


title: G1 single cell 17


title: D18MC.3G10


title: G1 single cell 15


title: G1 single cell 14


title: G1 single cell 26


title: D18MC.3F4


title: D18MC.3F5


title: G1 single cell 13


title: D18MC.3G8


title: D18MC.3F6


title: D18MC.3F2


title: D18MC.3G12


title: G1 single cell 16


title: G1 single cell 12


title: D18MC.3F12


title: D18MC.3F7


title: G1 single cell 11


title: G1 single cell 10


title: G1 single cell 8


title: G1 single cell 7


title: G1 single cell 9


title: D18MC.3F1


title: D18MC.3E7


title: D18MC.3E9


title: D18MC.3F10


title: D18MC.3E6


title: G1 single cell 3


title: G1 single cell 5


title: G1 single cell 4


title: D18MC.3E5


title: D18MC.3E4


title: HOM6

city: München

first: Friederike

last: Matheus

address: Ingolstädter Landstrasse 1

department: Institute for Stem Cell Research

institute: Helmholtz Center Munich

data_processing:
For Fastq manipulation steps, tools on the public server at usegalaxy.org were used.
Qualtiy was assessed using the FastQC tool (Galaxy platform)
Reads were mapped to the hg19 genome using TopHat for Illumina tool (Galaxy platform)
Read count was performed using the featureCounts (v1.5.0) function of the Subread package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes read counts for all samples

source_name: neural crest differentiation culture

growth_protocol: Human embryonic stem cell lines were differentiated according to a protocol by Bajpai et al (Nature 463, 958-962).

extract_protocol:
RNA was isolated from cultures at day 7 of neural crest differentiation using the Qiagen RNeasy Mini Kit (Cat.#4104). Illumina TruSeq RNA Sample Prep Kit (Cat. #RS-122-2301) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: embryonic stem cell-derived neuronal crest progenitor culture

tag: day of protocol

value: day 7

value: homozygous 500 bp deletion in ASXL1


title: D18MC.3E2


title: HOM7


title: HOM5


title: D18MC.3E12


title: D18MC.3E3


title: G1 single cell 1


title: HOM4


title: D18MC.3E10


title: D18MC.3E8


title: HOM3

value: compound heterozygous 500 bp deletion/inversion in ASXL1


title: D18MC.3E11


title: D18MC.3D9


title: D18MC.3D7


title: D18MC.3E1


title: HOM1


title: D18MC.3F11


title: WT3

value: wildtype


title: HOM2


title: D18MC.3D8


title: WT2


title: D18MC.3D6


title: WT1


title: D18MC.3D4


title: D18MC.3D3


title: G1 single cell 6


title: Tet3-Gfapcre 3

city: Burjassot

first: Sacri

middle: R.

last: Ferron

state: Valencia

address: Calle Doctor Moliner, 50

department: Cell Biology

country: Spain

institute: University of Valencia

description: RNAseq

data_processing:
The sequences were aligned to the mouse genome reference (GRCm38.p5) taken from Ensembl using the Subread package in Linux
The expression of every gene per sample was measured using a gtf annotation file (GRCm38.87) taken from Ensembl and the R package Rsubread.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes raw counts of sequencing reads of every gene per sample

source_name: Tet3-Gfap cre 3

growth_protocol: Isolation of NSCs from adult mice control or deficient for Tet3

extract_protocol:
Dissection pieces of the subventricular zone from the adult murine brain where incubated in papain solution for 20 min.
Libraries were generated from triplicated samples per condition using the Illumina TruSeq stranded mRNA Sample Preparation Kit v2 following the manufacturer’s protocol.

value: Tet3-Gfap cre


title: Tet3-Gfapcre 2

description: RNAseq

source_name: Tet3-Gfap cre 2


title: D18MC.3D12


title: Tet3-Gfapcre 1

description: RNAseq

source_name: Tet3-Gfap cre 1


title: D18MC.3D2


title: D18MC.3D11


title: Tet3-Gfapcontrol  3

description: RNAseq

source_name: Tet3-Gfap control  3

value: Tet3-Gfap control


title: Tet3-Gfapcontrol  2

description: RNAseq

source_name: Tet3-Gfap control  2


title: Tet3-Gfapcontrol  1

description: RNAseq

source_name: Tet3-Gfap control  1


title: D18MC.3F3


title: TMEV-infected mouse spinal cord at 35 days pi_5

city: Osakasayama

first: Seiichi

last: Omura

state: Osaka

address: 377-2 Ohnohigashi

department: Department of Microbiology

country: Japan

institute: Kindai University Faculty of Medicine

data_processing:
Basecalls performed using CASAVA
The raw sequence data were aligned to reference genome, Mus musculus GRCm38.75, downloaded from ENSEMBLE, using the Spliced Transcripts Alignment to a Reference (STAR)
The read count data were normalized with two methods: 1) read counts per kilobase (RPK) and 2) DEG elimination strategy (DEGES), using “R” and the package “tag count comparison (TCC)”
Genome_build: mm10
Supplementary_files_format_and_content: Normalized read counts

extract_protocol:
RNA was isolated using Tri-Reagent and RNeasy Mini Kit (QIAGEN). Illumina TruSeq Stranded Total RNA LT Sample Prep kit - Set A with Ribo-Zero Gold was used with 100 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Female 5-week-old SJL/J mice (Jackson Laboratory, Bar Harbor, ME) were infected intracerebrally with 2 x 10^5 plaque forming units (PFU) of the Daniels (DA) strain of TMEV.

tag: strain

value: SJL/J

value: Female

tag: infection

value: Intracerebral infection of TMEV

tag: time

value: 35 days p.i.

value: Spinal cord


title: D18MC.3D1

tag: genotype

tag: ngene

tag: nreads


title: D18MC.3D10

tag: age

tag: Sex

tag: plateplus


title: D18MC.3D5

tag: plate

tag: lane


title: TMEV-infected mouse spinal cord at 35 days pi_1

tag: tissue


title: G1 single cell 2

tag: cell line

value: MDA-MB-231 luciferase


title: TMEV-infected mouse spinal cord at 35 days pi_2


title: TMEV-infected mouse spinal cord at 35 days pi_4


title: TMEV-infected mouse spinal cord at 35 days pi_3


title: D18MC.3C4

value: M


title: D18MC.3C5


title: D18MC.3C8


title: Mock-infected mouse spinal cord at 35 days pi_4

value: Intracerebral injection of PBS


title: Mock-infected mouse spinal cord at 35 days pi_5


title: Mock-infected mouse spinal cord at 35 days pi_2


title: Mock-infected mouse spinal cord at 35 days pi_3


title: Mock-infected mouse spinal cord at 35 days pi_1


title: TMEV-infected mouse spinal cord at 7 days pi_5

value: 7 days p.i.


title: D18MC.3C7


title: TMEV-infected mouse spinal cord at 7 days pi_4


title: D18MC.3C2


title: D18MC.3C9


title: D18MC.3C3


title: TMEV-infected mouse spinal cord at 7 days pi_1


title: D18MC.3C1


title: D18MC.3B8


title: D18MC.3C10


title: D18MC.3C12


title: D18MC.3B9


title: Mock-infected mouse spinal cord at 7 days pi_4


title: D18MC.3C11


title: D18MC.3G3


title: Mock-infected mouse spinal cord at 7 days pi_3


title: Mock-infected mouse spinal cord at 7 days pi_5


title: D18MC.3B7


title: Mock-infected mouse spinal cord at 7 days pi_2


title: D18MC.3B5


title: D18MC.3B4


title: Mock-infected mouse spinal cord at 7 days pi_1


title: D18MC.3B3


title: D18MC.3B6


title: D18MC.3B2


title: TMEV-infected mouse spinal cord at 4 days pi_4

value: 4 days p.i.


title: TMEV-infected mouse spinal cord at 7 days pi_3


title: D18MC.3B12


title: TMEV-infected mouse spinal cord at 4 days pi_5


title: TMEV-infected mouse spinal cord at 7 days pi_2


title: TMEV-infected mouse spinal cord at 4 days pi_2


title: TMEV-infected mouse spinal cord at 4 days pi_3


title: D18MC.3B11


title: TMEV-infected mouse spinal cord at 4 days pi_1


title: D18MC.3B10


title: D18MC.3B1


title: D18MC.3A9


title: D18MC.3A7


title: D18MC.3A8


title: Mock-infected mouse spinal cord at 4 days pi_3


title: Mock-infected mouse spinal cord at 4 days pi_2


title: Mock-infected mouse spinal cord at 4 days pi_5


title: D18MC.3A6


title: Mock-infected mouse spinal cord at 4 days pi_1


title: D18MC.3A5


title: D18MC.3A4


title: D18MC.3A2


title: D18MC.3A3


title: D18MC.3A11


title: D18MC.3A10


title: D18MC.3C6


title: C18MC.4H9


title: D18MC.3A1


title: Mock-infected mouse spinal cord at 4 days pi_4


title: C18MC.4H7


title: C18MC.4H8


title: C18MC.4H5


title: C18MC.4H6


title: D18MC.3A12


title: C18MC.4H3


title: C18MC.4H4


title: KO_59

city: New York

first: Michael

middle: S

last: Breen

state: NY

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

data_processing:
All high-quality short reads were mapped to the rat reference genome rn4 using the STAR Aligner v2.4.0g1 (Dobin A et al. 2013) with 2-pass mapping strategy (--twopassMode Basic).
RNAseq read quality was checked with the FastQC and RNA-seqQC tools.
Uniquely mapped reads with overlapping genes were counted with featureCounts v1.4.4 (Liao Y et al. 2014) parameters (featureCounts -T 10 -p -t exon -g gene_id)
Filtered raw count data was subjected to conditional quantile normalization (CQN) (Hansen KD et al. 2012) to remove systematic bias introduced by GC-content and correct for global distortions
Normalized data were inspected for outlying samples using unsupervised clustering of samples (Pearson’s correlation coefficient and average distance metric) and principal component analysis to identify outliers outside two standard deviations from these grand averages. Based on these metrics, two outliers were removed from these data (WT=2).
Genome_build: mm4

organism: Rattus norvegicus

source_name: mPFC

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions. Subsequently, the quantity of all purified RNA samples was measured on a nanodrop (2.07±0.01 A260/280; 2.11±0.19 A260/230) and the quality and integrity were measured with the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). All RNA integrity numbers were greater than 9 (9.6±0.3).
1µg of total RNA was used for the preparation of the RNAseq library using the Illumina Genome Analyzer IIx TruSeq mRNA Seq Kit supplied by Illumina (Cat number: RS-122-2001). A poly-A-based mRNA enrichment step was carried out and cDNA was synthesized and used for library preparation using the Illumina TruSeqTM RNA sample preparation kit as previously described (Tariq MA et al. 2011), except for the following step: adapter-ligated DNA fragments were size-selected by gel-free size selection using appropriate concentration of SPRI AMPure beads to get an average 200bp peak size in adaptor ligated DNA. The size selected adaptor-ligated DNA fragments were amplified by LM-PCR. Then, Illumina recommended 6bp barcode bases were introduced at one end of the adaptors during PCR amplification step. The amplified PCR products were then purified with SPRI AMPure XP magnetic beads to get the final RNAseq library, which was used for high-throughput RNAseq. All samples were sequenced on the Illumina Genome Analyzer IIx.

value: Sprague Dawley

value: deletion of Fmr1 exon 8

value: medial prefrontal cortex (mPFC)

tag: sample preparation

value: whole lysate

value: 8 weeks

tag: batch

tag: parents

tag: rnaseqlane

tag: rin


title: KO_58

tag: strain


title: C18MC.4H2


title: C18MC.4H12


title: WT TH1 cells, biological rep1

type: RNA

city: Chongqing

first: Pengcheng

last: Wang

state: chongqing

address: gaotanyan street

department: Institute of Immunology

country: China

institute: Army Medical University

description: Gene exprssion data from TH1 cells. (CXCR5-SLAMhighCD4+ T cells from LCMV infected mice)

hyb_protocol: Standard Affymetrix

scan_protocol: Standard Affymetrix

label: biotin

source_name: mouse CXCR5-SLAMhighCD4+ T cells

label_protocol: RNA quality of all samples was confirmed by BioAnalyzer Nano gel (Agilent), then probes were generated from 30ng total RNA by single round linear amplification using the Ovation Pico system (Nugen).

growth_protocol: all infection were done by intraperitoneal injection of 2 x 10^5 plaque-forming units (PFU) of LCMV Armstrong strain per mouse. 2 x 10^5 naïve SMARTA CD4+T cells were adoptively transferred to recipient mice prior to LCMV infection. Spleens were harvested 6 days after LCMV infection.

extract_protocol: Sorted cells were lysed with TRIzol LS reagent (Life Technologies). Total RNA was extracted with isopropyl ethanol.

treatment_protocol: Splenocytes were isolated and antigen-specific CD4+ T cells were enriched using Biotin-labeled anti-CD19, anti-Ter119, anti-CD8, anti-CD11c, anti-CD11b, anti-NK1.1, anti-CD25 and magnetic bead purification (Beaver). Virus specific SMtg CD4+CD45.1+CD19-L/D- cells were then sorted into TFH and TH1 populations on the basis of CXCR5 and SLAM expression using a FACS Aria II (BD Bioscience).

value: spleen

tag: cell type

value: CD4 T cells

tag: cell subtype

value: WT


title: naïve CD4 T cells , biological rep1

description: Gene expression data from naïve CD4+ T cells. (CD44-CD62L+CD4+ T cells from uninfected mice)

source_name: mouse naïve CD4+ T cells

value: naïve CD4+ T cells

tag: genotype


title: WT TFH cells, biological rep2

description: Gene exprssion data from TFH cells. (CXCR5+SLAMlowCD4+ T cells from LCMV infected mice)

source_name: mouse CXCR5+SLAMlowCD4+ T cells

value: TFH


title: naïve CD4 T cells , biological rep2


title: WT TH1 cells, biological rep2


title: C18MC.4H10

source_name: Cortex

tag: ngene

tag: nreads


title: Tbx21-/- TFH cells, biological rep2


title: KO_62

tag: age


title: WT TFH cells, biological rep1


title: KO_71


title: WT_88

value: wild type


title: Tbx21-/- TH1 cells, biological rep2


title: Tbx21-/- TH1 cells, biological rep1


title: Tbx21-/- TFH cells, biological rep1


title: C18MC.4H1

tag: Sex

tag: plateplus


title: C18MC.4G9

tag: plate

tag: lane


title: WT_162

tag: tissue


title: C18MC.4G8


title: WT_167

tag: sample preparation


title: WT_169

tag: batch


title: KO_37

tag: parents


title: KO_39

tag: rnaseqlane


title: C18MC.4G7


title: WT_156

tag: rin


title: C18MC.4G6


title: WT_144

tag: strain


title: C18MC.4H11


title: WT_145


title: WT_170


title: C18MC.4G5


title: WT_137


title: C18MC.4G4


title: C18MC.4G2


title: WT_118


title: WT_123


title: C18MC.4G12


title: P_WT_947


title: P_WT_949


title: P_WT_827


title: C18MC.4G11


title: C18MC.4G1


title: C18MC.4G10


title: P_WT_806


title: C18MC.4F9


title: P_WT_805


title: P_WT_572


title: P_WT_570


title: C18MC.4F7


title: P_WT_549


title: C18MC.4F6


title: P_WT_542


title: P_WT_541


title: C18MC.4F4


title: C18MC.4F3


title: C18MC.4F2


title: C18MC.4F5


title: C18MC.4F8


title: C18MC.4G3


title: WT_97


title: C18MC.4F12


title: WT_92


title: C18MC.4F11


title: P_WT_826


title: C18MC.4F10


title: WT_83


title: C18MC.4F1


title: WT_82


title: C18MC.4E9


title: C18MC.4E8


title: C18MC.4E7


title: WT_73


title: P_WT_546


title: WT_60


title: WT_70


title: WT_61


title: C18MC.4E6


title: C18MC.4E4


title: WT_57


title: C18MC.4E5


title: KO_94


title: KO_85


title: WT_84


title: KO_95


title: C18MC.4E2


title: C18MC.4E3


title: KO_93


title: KO_72


title: C18MC.4E11


title: C18MC.4E10


title: KO_81


title: C18MC.4E12


title: C18MC.4D9


title: C18MC.4E1


title: C18MC.4D8


title: C18MC.4D6


title: C18MC.4D5


title: C18MC.4D7


title: C18MC.4D4


title: C18MC.4D3


title: C18MC.4D11


title: Fasting 3999853055_I

city: Warsaw

first: Agnieszka

last: Lugowska

address: Al. Sobieskiego 9

department: Department of Genetics

country: Poland

institute: Institute of Psychiatry and Neurology

description: Fasting

hyb_protocol: Illumina® Whole-Genome Gene Expression Direct Hybridization Assay, according to manufacturer's instructions

scan_protocol: HiScan SQ according to manufacturer's instructions

data_processing: The data was imported into Partek GS from Genoe Studio.

label: Biotin

source_name: skin fibroblasts

label_protocol: Ambion Illumina TotalPrep RNA Amplification Kit, according to manufacturer's instructions

growth_protocol: All cell lines were cultured in DMEM (Thermo Fisher Scientific Inc.) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin solution (Sigma-Aldrich Co. LLC., St. Louis, USA)  in a humidified atmosphere containing 5% CO2 at 37°C. Cells were harvested after trypsinization when the culture was confluent, immediately immersed in RNA Later (Qiagen), and stored at -70°C before further procedures.

extract_protocol: Total RNA samples were isolated from the cultured skin fibroblasts with the use of MagNa Pure Compact RNA Isolation Kit (Roche Applied Science, Mannheim, Germany). Quantity and quality of RNA samples were assessed using the NanoDrop instrument (Thermo Scientific) and evaluated with the RNA 6000 Nano Assay on the Agilent 2100 Bioanalyser (Agilent Technologies Inc., USA).

treatment_protocol: Fasting conditions - cells  were cultured in medium with lipoprotein deprived serum. LDL+LPDS - cells were cultured in medium with LPDS and then supplemented with LDL source.

tag: patient

tag: viability

value: alive

tag: condition

value: Control

tag: gender


title: C18MC.4C7

tag: genotype

tag: ngene

tag: nreads

value: M


title: C18MC.4C9

tag: age

tag: Sex

tag: plateplus


title: C18MC.4D1

tag: plate

tag: lane


title: C18MC.4D10


title: C18MC.4C8


title: C18MC.4C6


title: C18MC.4C5


title: Fasting 3999853055_D

description: Fasting

value: NPC-N


title: LDL+LPDS 3999853055_K

description: LDL+LPDS

value: ML

value: NPC(-)


title: C18MC.4C4


title: Fasting 3999853055_E

description: Fasting


title: C18MC.4D12


title: C18MC.4D2


title: Stand. 3999853055_H

description: Stand.


title: Fasting 3999853055_L

description: Fasting


title: LDL+LPDS 3999853055_F

description: LDL+LPDS


title: Fasting 3999853055_J

description: Fasting


title: LDL+LPDS 3999853055_G

description: LDL+LPDS

value: K


title: Stand. 3999853055_C

description: Stand.


title: LDL+LPDS 3999853054_K

description: LDL+LPDS


title: Fasting 3999853055_A

description: Fasting

value: SB

value: NPC-D


title: Fasting 3999853054_L

description: Fasting


title: Fasting 3999853055_B

description: Fasting

value: NPC-M


title: C18MC.4C3


title: C18MC.4C2


title: C18MC.4C10


title: C18MC.4C1


title: C18MC.4B8


title: C18MC.4B9


title: Stand. 3999853054_G

description: Stand.

value: ME

value: nie alive

value: Gaucher


title: Stand. 3999853054_H

description: Stand.

value: LA


title: C18MC.4C12


title: C18MC.4B6


title: C18MC.4B7


title: Stand. 3999853054_J

description: Stand.


title: LDL+LPDS 3999853054_F

description: LDL+LPDS


title: C18MC.4B5


title: N/A 3999853054_I


title: C18MC.4C11


title: C18MC.4B3


title: Stand. 3999853054_D

description: Stand.

value: MB


title: Stand. 3999853054_B

description: Stand.


title: C18MC.4B4


title: C18MC.4B2


title: Fasting 3999853053_K

description: Fasting


title: LDL+LPDS 3999853053_L

description: LDL+LPDS


title: Stand. 3999853053_J

description: Stand.


title: Fasting 3999853054_A

description: Fasting

value: NPC(-)-variant


title: Fasting 3999853053_H

description: Fasting


title: C18MC.4B12


title: C18MC.4B11


title: Fasting 3999853053_E

description: Fasting


title: Stand. 3999853053_D

description: Stand.


title: LDL+LPDS 3999853053_I

description: LDL+LPDS


title: C18MC.4A8


title: C18MC.4A9


title: LDL+LPDS 3999853053_C

description: LDL+LPDS


title: C18MC.4A7


title: Fasting 3999853053_B

description: Fasting


title: Stand. 3999853053_G

description: Stand.


title: LDL+LPDS 3999853053_F

description: LDL+LPDS


title: C18MC.4A5


title: C18MC.4A6


title: C18MC.4A4


title: C18MC.4A3


title: C18MC.4A2


title: C18MC.4B10


title: C18MC.4A12


title: C18MC.4B1


title: Stand. 3999853053_A

description: Stand.


title: C18MC.4A11


title: Stand. 3999853050_L

description: Stand.


title: LDL+LPDS 3999853050_K

description: LDL+LPDS

value: GP


title: LDL+LPDS 3999853050_I

description: LDL+LPDS

value: alive


title: C18MC.4A10


title: C18MC.4A1


title: Fasting 3999853050_J

description: Fasting


title: C18MC.3H9


title: C18MC.3H8


title: Fasting 3999853050_F

description: Fasting


title: LDL+LPDS 3999853050_G

description: LDL+LPDS


title: Stand. 3999853050_E

description: Stand.


title: Stand. 3999853050_C

description: Stand.

value: VA

value: Gaucher t.1


title: Fasting 3999853050_H

description: Fasting

value: Control


title: C18MC.3H7

value: M


title: C18MC.3H6


title: C18MC.3H5


title: C18MC.3H4


title: LDL+LPDS 3999853050_B

description: LDL+LPDS

value: NPC-N


title: Fasting 3999853050_A

description: Fasting


title: C18MC.3H3


title: Stand. 3999853046_K

description: Stand.


title: LDL+LPDS 3999853046_L

description: LDL+LPDS


title: C18MC.3H2


title: C18MC.3H12


title: LDL+LPDS 3999853046_J

description: LDL+LPDS


title: LDL+LPDS 3999853046_I

description: LDL+LPDS


title: C18MC.3H11


title: Stand. 3999853046_F

description: Stand.

value: K


title: Fasting 3999853046_G

description: Fasting


title: C18MC.3H10


title: Fasting 3999853046_H

description: Fasting


title: C18MC.3H1


title: C18MC.3G8


title: LDL+LPDS 3999853046_D

description: LDL+LPDS


title: C18MC.3G7


title: C18MC.3G6


title: C18MC.3G5


title: C18MC.3G4


title: Stand. 3999853046_B

description: Stand.


title: Stand. 3999853046_E

description: Stand.


title: Fasting 3999853037_K

description: Fasting


title: LDL+LPDS 3999853046_C

description: LDL+LPDS


title: LDL+LPDS 3999853037_I

description: LDL+LPDS


title: C18MC.3G9


title: C18MC.3G2


title: C18MC.3G3


title: C18MC.3G12


title: C18MC.3G11


title: C18MC.3G10


title: LDL+LPDS 3999853037_L

description: LDL+LPDS


title: C18MC.3G1


title: C18MC.3F9


title: Stand. 3999853037_G

description: Stand.


title: Fasting 3999853037_H

description: Fasting


title: C18MC.3F8


title: Stand. 3999853037_J

description: Stand.


title: LDL+LPDS 3999853037_F

description: LDL+LPDS


title: Fasting 3999853037_E

description: Fasting


title: LDL+LPDS 3999853046_A

description: LDL+LPDS

value: SB


title: C18MC.3F7


title: LDL+LPDS 3999853037_C

description: LDL+LPDS

value: NP


title: Stand. 3999853037_D

description: Stand.


title: C18MC.3F5


title: C18MC.3F6


title: Stand. 3999853037_A

description: Stand.


title: LDL+LPDS 3999844018_L

description: LDL+LPDS


title: Fasting 3999844018_K

description: Fasting


title: Stand. 3999844018_J

description: Stand.


title: C18MC.3F4


title: C18MC.3F2


title: C18MC.3F3


title: Fasting 3999853037_B

description: Fasting


title: C18MC.3F12


title: C18MC.3F11


title: LDL+LPDS 3999844018_I

description: LDL+LPDS


title: Fasting 3999853054_C

description: Fasting


title: Fasting 3999844018_H

description: Fasting


title: Stand. 3999853054_E

description: Stand.


title: Stand. 3999844018_G

description: Stand.


title: C18MC.3F10


title: C18MC.3E9


title: C18MC.3F1


title: Fasting 3999844018_E

description: Fasting

value: BB

value: NPC-NBP


title: Stand. 3999844018_D

description: Stand.


title: C18MC.3E7


title: C18MC.3E8


title: C18MC.3E6


title: C18MC.3E5


title: C18MC.3E4


title: LDL+LPDS 3999844018_C

description: LDL+LPDS

value: ZJ


title: Stand. 3999853050_D

description: Stand.

value: ZR


title: C18MC.3E3


title: C18MC.3E2


title: Fasting 3999844015_K

description: Fasting

value: deceased


title: LDL+LPDS 3999844015_L

description: LDL+LPDS


title: Fasting 3999844015_H

description: Fasting


title: LDL+LPDS 3999844018_F

description: LDL+LPDS


title: Stand. 3999844015_J

description: Stand.


title: Fasting 3999844018_B

description: Fasting


title: C18MC.3E12


title: C18MC.3E11


title: C18MC.3E10


title: C18MC.3E1


title: LDL+LPDS 3999844015_I

description: LDL+LPDS


title: LDL+LPDS 3999844015_C

description: LDL+LPDS


title: Fasting 3999844015_B

description: Fasting


title: Stand. 3999844015_D

description: Stand.


title: Stand. 3999844018_A

description: Stand.


title: Stand. 3999844015_F

description: Stand.

value: NPC-M


title: Stand. 3999844015_E

description: Stand.

value: ML

value: NPC(-)variant?


title: C18MC.3D9


title: C18MC.3D7


title: Stand. 3999844015_G

description: Stand.

value: alive


title: Stand. 3999844015_A

description: Stand.


title: C18MC.3D6


title: C18MC.3D5


title: C18MC.3D4


title: C18MC.3D3


title: Stand. 3999844014_J

description: Stand.


title: LDL+LPDS 3999844014_I

description: LDL+LPDS


title: C18MC.3D2


title: C18MC.3D11


title: C18MC.3D8


title: C18MC.3C8


title: C18MC.3D1


title: C18MC.3C9


title: Fasting 3999844014_H

description: Fasting


title: C18MC.3D10


title: C18MC.3C6


title: C18MC.3C5


title: LDL+LPDS 3999844014_L

description: LDL+LPDS


title: Stand. 3999844014_G

description: Stand.


title: C18MC.3D12


title: LDL+LPDS 3999844014_F

description: LDL+LPDS

value: KM

value: NPC?


title: Fasting 3999844014_E

description: Fasting


title: Fasting 3999844014_K

description: Fasting

value: Control


title: LDL+LPDS 3999844013_L

description: LDL+LPDS


title: C18MC.3C7

value: M


title: C18MC.3C2


title: LDL+LPDS 3999844014_C

description: LDL+LPDS

value: BE


title: Stand. 3999844014_D

description: Stand.


title: C18MC.3C12


title: Stand. 3999844014_A

description: Stand.

value: K


title: LDL+LPDS 3999844013_I

description: LDL+LPDS


title: C18MC.3C11


title: Fasting 3999844014_B

description: Fasting


title: Fasting 3999844013_H

description: Fasting


title: Fasting 3999844013_K

description: Fasting


title: Stand. 3999844013_J

description: Stand.


title: C18MC.3C10


title: C18MC.3C4


title: C18MC.3C3


title: LDL+LPDS 3999844013_F

description: LDL+LPDS

value: BZ


title: Fasting 3999844013_E

description: Fasting


title: C18MC.3B8


title: C18MC.3B9


title: C18MC.3B7


title: LDL+LPDS 3999844013_C

description: LDL+LPDS

value: WP

value: NPC-N


title: Fasting 3999844013_B

description: Fasting


title: Stand. 3999844013_G

description: Stand.


title: C18MC.3B6


title: Stand. 3999844013_D

description: Stand.


title: LDL+LPDS 3999844012_L

description: LDL+LPDS


title: Stand. 3999844013_A

description: Stand.


title: C18MC.3C1


title: C18MC.3B4


title: C18MC.3B3


title: C18MC.3B5


title: C18MC.3B12


title: C18MC.3B10


title: C18MC.3B1


title: LDL+LPDS 3999844012_I

description: LDL+LPDS


title: Stand. 3999844012_J

description: Stand.


title: Fasting 3999844012_K

description: Fasting


title: C18MC.3A9


title: C18MC.3A8


title: Fasting 3999844012_H

description: Fasting


title: LDL+LPDS 3999844012_F

description: LDL+LPDS

value: SP


title: Fasting 3999844012_E

description: Fasting


title: Stand. 3999844012_A

description: Stand.

value: DA

value: NPC-D


title: C18MC.3A7


title: C18MC.3A5


title: Fasting 3999844012_B

description: Fasting

value: deceased


title: Stand. 3999844010_L

description: Stand.


title: Stand. 3999844012_G

description: Stand.


title: C18MC.3B2


title: Stand. 3999844012_D

description: Stand.


title: Fasting 3999844010_J

description: Fasting


title: C18MC.3B11


title: Stand. 3999844010_I

description: Stand.


title: C18MC.3A4


title: C18MC.3A3


title: C18MC.3A2


title: C18MC.3A6


title: C18MC.3A12


title: LDL+LPDS 3999844010_K

description: LDL+LPDS


title: C18MC.3A11


title: C18MC.3A10


title: LDL+LPDS 3999844010_H

description: LDL+LPDS

value: SK


title: Stand. 3999844010_E

description: Stand.

value: SB


title: Fasting 3999844010_G

description: Fasting


title: LDL+LPDS 3999844012_C

description: LDL+LPDS


title: Stand. 3999844010_F

description: Stand.


title: L61A

city: Bologna

first: Daniel

last: Remondini

address: Viale Berti Pichat 6/2

department: Physics and Astronomy - DIFA

country: Italy

institute: Bologna University

data_processing:
Quality control of raw reads was carried out with FastQC.
PCR primers and Illumina adapter sequences were removed with Trimmomatic. Minimum base quality 15 over a 4-base sliding window was required, then only sequences longer than 36 nucleotides were included in the downstream analysis.
Read mapping with STAR aligner.
BAM file sorting and indexing with Samtools
Read counts per gene extracted with Htseq-count
Genome_build: Bos taurus UMD3.1.68
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

organism: Bos taurus

source_name: whole blood

extract_protocol:
Total RNA was extracted using the PAXgene® Blood miRNA Kit (PreAnalytiX GmbH) according to the manufacturer’s protocol. Total RNA was eluted in a final volume of 80 μL. RNA concentration was measured by NanoDrop™ 1000 spectrophotometer (Thermo Scientific) and RNA integrity was assessed with an Agilent 2200 TapeStation system (Agilent Technologies).
Libraries were prepared with the Illumina Truseq RNA sample prep kit (Illumina Inc., USA) following the manufacture’s protocol and the size and yield evaluated using an Agilent TapeStation 2200. Libraries were then quantified with an ABI9700 qPCR instrument using the KAPA Library Quantification Kit in triplicate, according to the manufacture’s protocol (Kapa Biosystems, Woburn, MA, USA) and then normalized to 10 nM as recommended by Illumina for cluster generation on the Hiseq2000. Fifteen libraries were prepared and equimolar amounts of 5 samples were mixed before NaOH denaturation. Each of the pools was run in a lane of a Hiseq Flowcell.

tag: tissue

value: whole blood

tag: race

value: frisona

value: 4 to 5 years old

tag: bcs

tag: dim

value: 170 to 190 days in milk

tag: group

value: Potentially exposed, negative to ELISA


title: C18MC.2H9

value: M


title: L66A


title: L43A


title: C18MC.3A1


title: L39A


title: L42A


title: L65A

value: Positive to ELISA


title: C18MC.2H6


title: C18MC.2H7


title: C18MC.2H5


title: C18MC.2H4


title: L44A


title: L47A


title: C18MC.2H3


title: LDL+LPDS 3999844010_C

description: LDL+LPDS

tag: patient

value: alive

value: Control


title: L41A


title: C18MC.2H12


title: C18MC.2H2


title: C18MC.2H8


title: L40A


title: Stand. 3999844010_A

description: Stand.

tag: viability


title: C18MC.2H10


title: Stand. 3999844010_D

description: Stand.

tag: condition


title: C18MC.2G8


title: C18MC.2H1


title: C18MC.2G7


title: C18MC.2G6


title: C18MC.2G9


title: Fasting 3999844010_B

description: Fasting

tag: gender


title: C18MC.2G4

tag: genotype


title: C18MC.2G3

tag: ngene


title: C18MC.2G5

tag: nreads


title: C18MC.2G12

tag: age


title: C18MC.2G10

tag: Sex


title: C18MC.2G1

tag: plateplus


title: C18MC.2H11

tag: plate


title: C18MC.2F9

tag: lane


title: C18MC.2F8


title: C18MC.2G2


title: trained Stau2 mice, replicate 1

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: R/Bioconductor, rma normalization, default parameters

source_name: trained Stau2 mice_brain tissue

label_protocol: Standard Affymetrix protocol.

growth_protocol: Adult male B6.129P2-Stau2Gt(RRG396)Byg mice and WT C57Bl/6J mice (16 weeks to 20 weeks) were housed in groups of 2-5 animals with a 12-h light, 12-h dark light cycle in individually ventilated cages. Mice had free excess to autoclaved water and food.

extract_protocol: Total mRNA was obtained from brain samples using TRIzol (Ambion) according to the manufacturer´s protocol. Genomic DNA was depleted using the Mini RNeasy kit (Qiagen). cDNA was synthesized from purified mRNA by reverse transcription using Superscript III reverse transcriptase (Invitrogen) according to the manufacturer´s manual

treatment_protocol: All behavioral tests were performed under identical environmental conditions. Between individual testing phases, animals were kept in their housing cages. 4 months old male Stau2GT and WT mice were exposed to a stimulation of exploratory and motor behavior for 4 consecutive weeks by different behavioral test (open field, novel object recognition/location, Barnes maze)

tag: strain background

tag: genotype/variation

value: 16-20 weeks

value: male

tag: time point

value: after behavioural training

tag: tissue

value: brain


title: trained Stau2 mice, replicate 2


title: C18MC.2F5


title: C18MC.2F7


title: hMSCs_ZIP13KD_rep2

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

country: South Korea

institute: POSTECH

description:
RNAs isolated from ZIP13-KD hMSCs
KO-3

hyb_protocol: RNA was hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST Arrays following manufacturers instructions

scan_protocol: Arrays were scanned following manufacturers instructions

data_processing: Affymetrix gene expression console was used to obtain pre-processed quantification data. Data was corrected and normalized using RMA.

source_name: siZIP13-treated human mesenchymal stem cells

label_protocol: Refer to the Affymetrix Gene Expression System Manual

growth_protocol: Human mesenchymal stem cells were purchased (Lonza), and maintained in DMEM medium (Gibco) with 10% FBS and antibiotics, at 37 ¬∞C.

extract_protocol: Total RNA was isolated from tissues using Qiazol (QIAGEN) following the manufacturers’ protocols.

treatment_protocol: siRNA transfection was performed with ON-TARGETplus SMARTpool siRNA (Life Technologies) using Lipofectamine RNAimax (Life Technologies) according to the manufacturer‚Äôs instructions.

tag: cell type

value: Human mesenchymal stem cells (hMSCs)


title: trained Stau2 mice, replicate 3


title: hMSCs_WT_rep2

description:
RNAs isolated from WT hMSCs
WT-2

source_name: WT human mesenchymal stem cells

value: WT


title: hMSCs_ZIP13KD_rep1

description:
RNAs isolated from ZIP13-KD hMSCs
KO-1


title: trained wildtype mice, replicate 2

source_name: trained wildtype mice_brain tissue

value: wild type


title: naive Stau2 mice, replicate 3

source_name: naive Stau2 mice_brain tissue

value: before behavioural training


title: C18MC.2F6


title: naive wildtype mice, replicate 2

source_name: naive wildtype mice_brain tissue


title: hMSCs_WT_rep1

description:
RNAs isolated from WT hMSCs
WT-1


title: naive Stau2 mice, replicate 2


title: naive wildtype mice, replicate 3


title: C18MC.2F4


title: C18MC.2F12


title: trained wildtype mice, replicate 3


title: C18MC.2F2


title: C18MC.2G11


title: C18MC.2F3


title: trained wildtype mice, replicate 1


title: C18MC.2F11


title: C18MC.2F10


title: naive wildtype mice, replicate 1


title: adult acinar cells, replicate 2

source_name: adult acinar cells

growth_protocol: embryonic acinar cells and adult acinar cells were freshly isolated by collagen-digestion and directly used for RNA extraction. acinar-to-ductal-metaplasia was cultivated in 3D-collagen for 7 days. Low-passage tumor cells were grown in standard medium.

extract_protocol: RNA was extracted with RNeasy Mini Kit from Qiagen according manufactures protocol.

treatment_protocol: acinar-to-ductal-metaplasia was additionally treated with 50 ng/ml Tgf-alpha.

tag: strain

value: C57Bl6/J wildtype

value: adult acinar cells

tag: replicate


title: C18MC.2E9


title: C18MC.2F1


title: C18MC.2E7


title: naive Stau2 mice, replicate 1


title: C18MC.2E8


title: adult acinar cells, replicate 3


title: C18MC.2E5


title: C18MC.2E6


title: adult acinar cells, replicate 1


title: embryonic acinar cells, replicate 3

source_name: embryonic acinar cells

value: embryonic acinar cells


title: C18MC.2E3


title: P9505_134

city: Stockholm

first: Mikael

last: Svensson

state: Stockholm

address: Solnavägen 30

department: Clinical neuroscience

institute: Karolinska Institutet

data_processing:
FastQC (v0.11.5)
Trim Galore! (v0.4.1)
Star (v2.5.1)
StringTie (v1.3.3)
Preseq (v0.1.0)
featureCounts (v1.5.1)
dupRadar (v1.0.0)
Picard MarkDuplicates (v2.0.1)
Nextflow (v0.25.7)
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include counts for each sample

source_name: Mesenchymal stem cells (MSC)

extract_protocol:
Trizol (manufacturer’s protocol). Contaminating genomic DNA was removed during the RNA isolation by on-column digestion with DNAse (DNAse I Qiagen, 79254). RNA clean-up was conducted using the RNeasy micro kit (Qiagen, 74004).
SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian kit (Clontech)

tag: exposure


title: embryonic acinar cells, replicate 2


title: P9505_135


title: tumor cells, replicate 3

source_name: tumor cells

value: tumor cells


title: acinar-to-ductal metaplasia, replicate 3

source_name: acinar-to-ductal metaplasia

value: acinar-to-ductal metaplasia


title: tumor cells, replicate 1


title: tumor cells, replicate 2


title: embryonic acinar cells, replicate 1


title: C18MC.2E2

value: M


title: C18MC.2E12


title: acinar-to-ductal metaplasia, replicate 2


title: C18MC.2E11


title: P9505_133


title: acinar-to-ductal metaplasia, replicate 1


title: P9505_132


title: P9505_131


title: C18MC.2E1


title: P9505_130


title: C18MC.2D9


title: C18MC.2E4


title: P9505_129


title: P9505_136


title: C18MC.2D8


title: P9505_126


title: P9505_127


title: P9505_125


title: C18MC.2D6


title: C18MC.2D5


title: C18MC.2D7


title: P9505_124


title: P9505_123


title: C18MC.2D4


title: P9505_122


title: P9505_108


title: C18MC.2E10


title: C18MC.2D3


title: P9505_106


title: C18MC.2D12


title: C18MC.2D10


title: P9505_105


title: C18MC.2C9


title: C18MC.2D1


title: P9505_104


title: C18MC.2C8


title: P9505_102


title: P9505_103


title: C18MC.2C7


title: P9505_101


title: C18MC.2C5


title: ko_nd_exp2_rep5

city: Milan

first: Jose

middle: Manuel

last: Garcia-Manteiga

address: Via Olgettina 58

department: Center for Translational Genomics and Bioinformatics

institute: OSR - San Raffaele Scientific Institute

data_processing:
alignment with STAR_2.5.3a (--outFilterMismatchNmax 14)
counting reads with featureCounts
Differential Gene Expression with LIMMA; ~ genotype (exp1) ~ genotype + treament (exp2)
[Filtering] Both experiments were filtered to obtain genes expressed to have at least 1 cpm (count per million) in at least 3 samples for experiment 1 and in at least 5 samples for experiment 2.
Genome_build: mm10 GRCm38; basic annotation mm10 GRCm38 M13 Gencode (genome annotation)
Supplementary_files_format_and_content: xls with two sheets of results, one for the first set of experiments with normal diet, the second with both normal and high fat diet for the genotype comparison (KO vs CONTROL)

source_name: BAT

growth_protocol: Brown adipose tissue was dissected and disgregated using Tyssue Lyser (Quiagen) in Trizol reagent (Life Technologies). RNA was then purified using RNA Spin columns

extract_protocol:
Total RNA was extracted using RNA spin columns (PureLink RNA Mini Kit, Ambion). RNA quantification was carried out using Qubit Fluorimetric Quantification (Life Technologies) and 500ng of RNA were used to prepare the library.
QuantSeq 3’ mRNA-Seq Library Prep Kit. The procedure was initiated by oligo-dT priming, then the First-strand synthesis and RNA removal was followed by random-primed synthesis of the complementary strand. The resulting double-stranded cDNA was purified with magnetic beads, in order to remove all reaction components. The adapter sequences were added by library PCR amplification, the proper cycle number was previously determined by qPCR. The library was purified from PCR components using purification beads

treatment_protocol: Mice in experiment 1 were fed with normal diet ad libitum. Mice for experiment 2 were fed ad libitum with either normal diet (ND) or high fat diet (HFD, 45 KJ%FAT) for 14 weeks.

value: ko

value: female

tag: age (at the time of sacrifice)

value: 21 weeks

tag: treatment

value: nd

value: Brown Adipose Tissue

tag: experiment


title: C18MC.2C6

extract_protocol:
The dissection and microglia isolation steps were carried out on ice or at +4°C. Cortex and hippocampus were dissected and finely chopped, and transferred to a tuve containing ice-cold Hibernate A medium without phenol red. Single cell suspension prepared using the Adult Brain Dissociation kit. Single live microglia cells (CD11b+/DAPI-) were sorted using BD FACSAria III
Single cell retrotranscription and preparation of sequencing libraries was performed using a modified SmartSeq2 protocol (Picelli et al., 2013, 2014; Trombetta et al., 2014). We used 5’-biotinylated primers throughout the protocol

tag: genotype

tag: ngene

tag: nreads


title: ko_hfd_exp2_rep5

tag: Sex

value: hfd


title: C18MC.2C4

tag: age

tag: plateplus

tag: plate


title: C18MC.2C3

tag: lane


title: ko_hfd_exp2_rep4


title: C18MC.2C2


title: C18MC.2D2


title: P9505_107


title: C18MC.2D11


title: C18MC.2C12


title: ko_hfd_exp2_rep2


title: ko_hfd_exp2_rep1


title: C18MC.2C10


title: C18MC.2C11


title: control_nd_exp2_rep5

value: control


title: C18MC.2C1


title: control_nd_exp2_rep4


title: C18MC.2B9


title: control_hfd_exp2_rep5


title: control_hfd_exp2_rep4


title: C18MC.2B8


title: C18MC.2B5


title: control_nd_exp2_rep1


title: C18MC.2B6


title: control_nd_exp2_rep3


title: control_hfd_exp2_rep3


title: control_nd_exp2_rep2


title: C18MC.2B7


title: ko_hfd_exp2_rep3


title: control_hfd_exp2_rep2


title: C18MC.2B3


title: control_hfd_exp2_rep1


title: C18MC.2B4


title: ko_nd_exp2_rep4


title: C18MC.2B2


title: ko_nd_exp2_rep2


title: C18MC.2B11


title: C18MC.2B12


title: ko_nd_exp2_rep3


title: control_nd_exp1_rep9

value: 4 weeks


title: C18MC.2B1


title: C18MC.2B10


title: ko_nd_exp2_rep1


title: C18MC.2A9


title: C18MC.2A8


title: control_nd_exp1_rep8


title: control_nd_exp1_rep7


title: control_nd_exp1_rep6

value: male


title: C18MC.2A4


title: control_nd_exp1_rep3


title: control_nd_exp1_rep4


title: C18MC.2A3


title: C18MC.2A5


title: C18MC.2A6


title: C18MC.2A7


title: ko_nd_exp1_rep6


title: ko_nd_exp1_rep4


title: C18MC.2A12


title: C18MC.2A2


title: ko_nd_exp1_rep5


title: ko_nd_exp1_rep3


title: C18MC.2A11


title: C18MC.2A10


title: C18MC.1H9


title: ko_nd_exp1_rep2


title: C18MC.2A1


title: control_nd_exp1_rep2


title: ko_nd_exp1_rep1


title: control_nd_exp1_rep1


title: C18MC.1H8


title: C18MC.1H7


title: Ba_DKO_a6neg_OHT rep4

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Human FAST DB v2016_1 were also provided

source_name: Mammary cells

growth_protocol: Mammary explants growth for 1 week at 37°C, 5%CO2; 5%FCs + 100mM 4-OHT

extract_protocol:
Qiagen micro-columns
RNA libraries were prepared for sequencing using SMARTer v4 protocol

treatment_protocol:
Isolated from tissue explants by FACs
Trypsine digestion/labelling/FACS sorting

tag: developmental stage

value: Mature Virgin

value: Mammary cells


title: control_nd_exp1_rep5

tag: tissue


title: C18MC.1H6

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

institute: KULeuven


title: C18MC.1H4


title: C18MC.1H5


title: Ba_DKO_a6neg_OHT rep1

tag: cell type


title: C18MC.1H12


title: C18MC.1H2


title: Ba_Ctrl_OHT rep2


title: C18MC.1H3


title: Ba_Ctrl_OHT rep4


title: Ba_Ctrl_OHT rep1


title: C18MC.1H10


title: C18MC.1H11


title: C18MC.1H1


title: Ba_Ctrl_OHT rep3


title: P9408: siPadi2-rep3

first: Eneritz

last: Agirre

address: Solnavägen 9

department: MBB

description: ATAC-seq

library_source: genomic

data_processing:
Paired-end ATAC-seq reads were trimmed  and aligned with Bowtie2 with TN5 shifted tagAlign for ATAC pipeline. Aligned reads were filtered and duplicates removes ( CutAdapt mark duplicates), more detail Kundaje Lab pipeline. Peaks were called with MACS2 , with specific parameters for ATAC-seq peak calling ( TN5 shifted tagAlign for ATAC pipeline). Peaks signal files were normalize to total number of reads per sample with DeepTools in order to visualize them.
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-seq peaks signal in bedGraph files normalized to total read count.

molecule: genomic DNA

source_name: oli-neu

growth_protocol: Oli-neu cells were grown in poly-L-lysine coated dishes and expanded in proliferation media consisting of DMEM ((life tec 41965062), N2 supplement, Pen/Strep Glu (life tec 10378016), T3 (sigma T6397) 340ng/ml, L-thyroxine (sigma 89430) 400 ng/ml, bFGF 10ng/ml and Pdgf-BB 1ng/ml. For Oli-neu differentiation, media without growth factors was added for 1 day in vitro and in the presence of 1μM of erb inhibitor (PD174265, St Cruz, ref sc-204170).

extract_protocol:
The cells were collected with accutase and lysed with ATAC-seq lysis buffer (0.1% IGEPAL)
ATAC-seq (Buenrostro et al., 2013)

treatment_protocol: Cells were transfected with siRNAs for 4 hours, after which the cells were kept for 24 hours in proliferation media and 24 hours in differentiation media.

value: oli-neu


title: C18MC.1G9

data_processing:
Demultiplexed FASTQ files were aligned to the mouse genome (mm10 build) using STAR version 2.5.2 (Dobin et al., 2013) with default options.
Reads aligned to each gene were counted using featureCounts version 1.5.1 (Liao et al., 2014)
Filtered out cells outside the limits of median ± 4 * median absolute deviations for both reads number and genes detected; and excluded cells with more than 10% of reads aligning to mitochondrial genes
Further downstream processing was performed using Seurat (version 2.3.1 (Butler et al., 2018)) and Monocle2 (version 2.6.4 (Qiu et al., 2017a, 2017b; Trapnell et al., 2014))
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files of raw count data
Supplementary_files_format_and_content: tab-delimited text files of normalised count data (log normalised, scaled by 10000)

source_name: Cortex


title: P9408: siPadi2-rep2

description: ATAC-seq


title: P7167: siPadi2-rep1

description: ATAC-seq


title: P9408: siCtr-rep3

description: ATAC-seq


title: C18MC.1G8


title: C18MC.1G7


title: P9408: siCtr-rep2

description: ATAC-seq


title: C18MC.1G5


title: P7167: siCtr-rep1

description: ATAC-seq

data_processing:
Paired-end ATAC-seq reads were trimmed  and aligned with Bowtie2. Aligned reads were filtered and duplicates were removed ( CutAdapt mark duplicates), more detail Kundaje Lab pipeline. Peaks were called with MACS2 , with specific parameters for ATAC-seq peak calling ( TN5 shifted tagAlign for ATAC pipeline). Peaks signal files were normalize to total number of reads per sample with DeepTools.
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-seq peaks signal in bedGraph files normalized to total read count.


title: C18MC.1G6


title: Ba_DKO_a6neg_OHT rep2


title: C18MC.1G4


title: C18MC.1G3


title: Uninduced_hepatocyte_6_2c96

city: Providence

first: Nicola

last: Neretti

state: RI

address: 70 Ship St

department: Department of Molecular Biology, Cell Biology & Biochemistry

institute: Brown University

description:
Single cell mRNA
Not included in downstream analysis

data_processing:
(Smart-seq2 time course experiment):Paired-end reads were quality trimmed using Trim galore and subsequently aligned to the human reference genome, hg19, and ERCC spike-in sequences using HISAT2. Cells that have less than 200,000 hg19 aligned reads, and a ratio of ERCC RNA spike-in control aligned reads to total aligned reads that is greater than 0.5 were filtered out. 232 IMR90 cells (100 growing cells, 41 day 2 cells, 43 day 4 cells and 48 senescent cells) passed this first filtering step. Subsequently, hg19 aligned reads were randomly downsampled to 200,000 reads. Genes were quantified using HTSeq-Count[25]. Cells that have more than 80,000 total gene counts and at least 500 genes with at least one count were used for downstream analysis. 224 IMR90 cells (100 Growing cells, 41 Day2 cells, 42 Day4 cells and 41 senescent cells) passed this second filtering step. Downstream analyses were done on the 224 cells as indicated in the sample description field
(10x Co-culture experiment): Cell Ranger 2.0.1 was used to align 10x Chromium RNA-seq reads  to hg19, TurboGFP and  puromycin sequence from pGIPZ and neomycin sequence from pLNCX2-ER-ras_neo, using the default parameters, and to generate gene-cell matrices. The data were subsequently processed using Seurat 2.3.0 to generate t-SNE plots and three clusters were identified using sparcl 1.0.3 (https://cran.r-project.org/web/packages/sparcl/index.html).
(Smart-seq2 hepatocyte): Paired-end reads were quality trimmed using Trim galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and subsequently aligned to the mouse reference genome mm10 and ERCC spike-in sequences using HISAT2. The mm10 aligned reads were randomly downsampled to 50,000 and cells that have less than 50,000 reads were removed. 75 single cells from the induced and uninduced hepatocyte passed this filter. Subsequently, cells that have less than 20,000 gene count and less than 500 genes with at least one read detected were removed. 43 single cells from the induced hepatocytes and 21 cells from the uninduced hepatocytes were retained. Lastly, cells with the log-transformed number of expressed genes and library size of 3 median absolute deviation below the median value were removed [19]. 39 single cells from the induced hepatocytes and 19 cells from the uninduced hepatocytes passed these filters.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: csv file contains FPKM values (Time_course_FPKM.csv) and tab-delimited files contain counts from HTSeq after downsampling (Hepatocyte_downsampled_Htseq.txt and Time_course_downsampled_HTSeq)
Supplementary_files_format_and_content: Mdm2_deleted_hepatocyte_HTSeq.txt: counts from HTSeq for cells that passed the filter (Induced_hepatocyte)
Supplementary_files_format_and_content: timecourse_HTSeq.txt: counts from HTSeq for cells that passed the filter
Supplementary_files_format_and_content: timecourse_FPKM.csv: FPKM for cells that passed the filter
Supplementary_files_format_and_content: Growing_Sen_10x_count.txt contains UMI counts from 10x dataset and Growing_Sen_10x_metadata.txt contains the metadata for the UMI counts

source_name: colony N4 C57/Bl6J  background

extract_protocol:
Single-cell RNA-seq was performed using Smart-seq2 or 10x chromium as indicated by each experiemnt
Smart-seq2 or 10x Genomics 3' expression protocol

treatment_protocol: (Smart-seq2 Time course experiment): ER:RasG12V -expressing cells were induced into senescence for 7 days with 4-hydroxytamoxifen (4-OHT) and were isolated as single cells using FACS. Single cells that were not induced with 4-OHT were used as control. Single cells were also collected at another two time points, day 2 and day 4, before they became fully senescent on day 7. (10x Co-culture experiment): GFP cells are co-cultured with ER:Ras expressing cells and were induced into senescence with 4-OHT. Single cell 3' gene expression was generated using 10x Genomics Chromium.  (Smart-seq2 Hepatocyte experiment): Ex vivo primary hepatocytes were isolated using a modified retrograde perfusion technique as previously described[27]. Briefly, following perfusion with Perfusion Medium (Gibco) for 5 min, and Liver Digest Medium (Gibco) for 10 min, the liver was excised and the capsule disrupted to yield a cell suspension that was collected in Williams' E Medium supplemented with 2% FCS. Hepatocytes were purified by pelleting through a 40% (v:v) percoll gradient prior to FACS analysis.

tag: background strain

value: Hepatocyte

tag: protocol used


title: Uninduced_hepatocyte_6_2c95


title: C18MC.1G2


title: C18MC.1G12


title: Ba_DKO_a6neg_OHT rep3


title: C18MC.1G11


title: C18MC.1G1


title: C18MC.1F8


title: Uninduced_hepatocyte_6_2c89


title: C18MC.1F9


title: Uninduced_hepatocyte_6_2c90


title: C18MC.1F7


title: C18MC.1F5


title: C18MC.1F4


title: Uninduced_hepatocyte_6_2c84


title: Uninduced_hepatocyte_6_2c87


title: C18MC.1F6


title: C18MC.1F3


title: Uninduced_hepatocyte_6_2c85


title: Uninduced_hepatocyte_6_2c86


title: Uninduced_hepatocyte_6_2c94


title: C18MC.1F12


title: Uninduced_hepatocyte_6_2c82


title: Uninduced_hepatocyte_6_2c81


title: C18MC.1F2


title: Uninduced_hepatocyte_6_2c83


title: Uninduced_hepatocyte_6_2c92


title: Uninduced_hepatocyte_6_2c91


title: Uninduced_hepatocyte_6_2c93


title: Uninduced_hepatocyte_6_2c80


title: C18MC.1F10


title: Uninduced_hepatocyte_6_2c9


title: C18MC.1G10


title: C18MC.1F11


title: Uninduced_hepatocyte_6_2c8


title: Uninduced_hepatocyte_6_2c88


title: C18MC.1F1


title: C18MC.1E8


title: C18MC.1E9


title: Uninduced_hepatocyte_6_2c78


title: Uninduced_hepatocyte_6_2c76


title: C18MC.1E6


title: C18MC.1E4


title: C18MC.1E7


title: Uninduced_hepatocyte_6_2c74


title: Uninduced_hepatocyte_6_2c75


title: Uninduced_hepatocyte_6_2c73


title: C18MC.1E5


title: Uninduced_hepatocyte_6_2c72


title: C18MC.1E3


title: C18MC.1E2


title: Uninduced_hepatocyte_6_2c71


title: C18MC.1E11


title: C18MC.1E10


title: C18MC.1E12


title: Uninduced_hepatocyte_6_2c70


title: Uninduced_hepatocyte_6_2c69


title: Uninduced_hepatocyte_6_2c68


title: C18MC.1E1


title: C18MC.1D9


title: Uninduced_hepatocyte_6_2c7


title: Uninduced_hepatocyte_6_2c66


title: C18MC.1D7


title: Uninduced_hepatocyte_6_2c67


title: Uninduced_hepatocyte_6_2c79


title: C18MC.1D6


title: Uninduced_hepatocyte_6_2c64


title: C18MC.1D8


title: Uninduced_hepatocyte_6_2c77


title: Uninduced_hepatocyte_6_2c62


title: Uninduced_hepatocyte_6_2c63


title: C18MC.1D4


title: C18MC.1D3


title: C18MC.1D2


title: Uninduced_hepatocyte_6_2c60


title: Uninduced_hepatocyte_6_2c6


title: C18MC.1D12


title: Uninduced_hepatocyte_6_2c58


title: C18MC.1D10


title: C18MC.1D1


title: Uninduced_hepatocyte_6_2c59


title: C18MC.1C9


title: C18MC.1C7


title: C18MC.1C8


title: Uninduced_hepatocyte_6_2c56


title: Uninduced_hepatocyte_6_2c54


title: Uninduced_hepatocyte_6_2c55


title: C18MC.1C6


title: Uninduced_hepatocyte_6_2c57


title: Uninduced_hepatocyte_6_2c65


title: C18MC.1C5


title: C18MC.1C4


title: Uninduced_hepatocyte_6_2c53


title: Uninduced_hepatocyte_6_2c52


title: Uninduced_hepatocyte_6_2c51


title: C18MC.1C3


title: C18MC.1D5


title: Uninduced_hepatocyte_6_2c61


title: Uninduced_hepatocyte_6_2c50


title: Uninduced_hepatocyte_6_2c49


title: C18MC.1C12


title: C18MC.1D11


title: C18MC.1C11


title: Uninduced_hepatocyte_6_2c48


title: C18MC.1C10


title: C18MC.1C1


title: C18MC.1B9


title: C18MC.1B8


title: Uninduced_hepatocyte_6_2c45


title: Uninduced_hepatocyte_6_2c47


title: Uninduced_hepatocyte_6_2c46


title: Uninduced_hepatocyte_6_2c44


title: Uninduced_hepatocyte_6_2c43


title: Uninduced_hepatocyte_6_2c40


title: C18MC.1B3


title: Uninduced_hepatocyte_6_2c42


title: C18MC.1B4


title: C18MC.1B6


title: C18MC.1B7


title: Uninduced_hepatocyte_6_2c41


title: C18MC.1B5


title: C18MC.1B2


title: C18MC.1C2


title: Uninduced_hepatocyte_6_2c39


title: Uninduced_hepatocyte_6_2c5


title: C18MC.1B11


title: C18MC.1B10


title: C18MC.1B12


title: Uninduced_hepatocyte_6_2c38


title: Uninduced_hepatocyte_6_2c36


title: C18MC.1B1


title: Uninduced_hepatocyte_6_2c35


title: Uninduced_hepatocyte_6_2c34


title: C18MC.1A8


title: C18MC.1A7


title: Uninduced_hepatocyte_6_2c33


title: Uninduced_hepatocyte_6_2c32


title: Uninduced_hepatocyte_6_2c4


title: Uninduced_hepatocyte_6_2c31


title: C18MC.1A5


title: Uninduced_hepatocyte_6_2c3


title: Uninduced_hepatocyte_6_2c29


title: C18MC.1A4


title: Uninduced_hepatocyte_6_2c37


title: C18MC.1A12


title: C18MC.1A11


title: C18MC.1A10


title: C18MC.1A2


title: Uninduced_hepatocyte_6_2c28


title: Uninduced_hepatocyte_6_2c27


title: Uninduced_hepatocyte_6_2c24


title: C18MC.1A3


title: C18MC.1A1


title: C18MC.1A9


title: P18MC.2H9


title: Uninduced_hepatocyte_6_2c22


title: Uninduced_hepatocyte_6_2c21


title: P18MC.2H8


title: Uninduced_hepatocyte_6_2c23


title: Uninduced_hepatocyte_6_2c25


title: C18MC.1A6


title: P18MC.2H7


title: Uninduced_hepatocyte_6_2c20


title: P18MC.2H4


title: P18MC.2H5


title: Uninduced_hepatocyte_6_2c2


title: Uninduced_hepatocyte_6_2c19


title: Uninduced_hepatocyte_6_2c18


title: P18MC.2H3


title: P18MC.2H2


title: Uninduced_hepatocyte_6_2c26


title: Uninduced_hepatocyte_6_2c16


title: Uninduced_hepatocyte_6_2c13


title: P18MC.2H10


title: P18MC.2H11


title: Uninduced_hepatocyte_6_2c14


title: P18MC.2G9


title: P18MC.2H12


title: P18MC.2H1


title: Uninduced_hepatocyte_6_2c11


title: Uninduced_hepatocyte_6_2c12


title: Uninduced_hepatocyte_6_2c1


title: Uninduced_hepatocyte_6_2b96


title: P18MC.2G8


title: Uninduced_hepatocyte_6_2c10


title: P18MC.2H6


title: P18MC.2G7


title: P18MC.2G6


title: Uninduced_hepatocyte_6_2c15


title: Uninduced_hepatocyte_6_2b94


title: P18MC.2G4


title: P18MC.2G3


title: Uninduced_hepatocyte_6_2b93


title: P18MC.2G5


title: Uninduced_hepatocyte_6_2b91


title: P18MC.2G2


title: Uninduced_hepatocyte_6_2c17


title: Uninduced_hepatocyte_6_2b90


title: P18MC.2G12


title: P18MC.2G11


title: Uninduced_hepatocyte_6_2b88


title: Uninduced_hepatocyte_6_2b85


title: P18MC.2G1


title: P18MC.2G10


title: Uninduced_hepatocyte_6_2b87


title: Uninduced_hepatocyte_6_2b86


title: Uninduced_hepatocyte_6_2b84


title: P18MC.2F7


title: P18MC.2F6


title: Uninduced_hepatocyte_6_2b82


title: P18MC.2F5


title: Uninduced_hepatocyte_6_2b81


title: P18MC.2F3


title: Uninduced_hepatocyte_6_2b80


title: P18MC.2F4


title: Uninduced_hepatocyte_6_2b8


title: P18MC.2F2


title: Uninduced_hepatocyte_6_2b9


title: Uninduced_hepatocyte_6_2b79


title: P18MC.2F12


title: Uninduced_hepatocyte_6_2b77


title: P18MC.2F11


title: Uninduced_hepatocyte_6_2b75


title: Uninduced_hepatocyte_6_2b73


title: Uninduced_hepatocyte_6_2b71


title: P18MC.2F10


title: P18MC.2F8


title: P18MC.2F9


title: Uninduced_hepatocyte_6_2b69


title: Uninduced_hepatocyte_6_2b70


title: Uninduced_hepatocyte_6_2b83


title: P18MC.2E7


title: Uninduced_hepatocyte_6_2b68


title: P18MC.2E5


title: Uninduced_hepatocyte_6_2b66


title: P18MC.2E4


title: P18MC.2E9


title: Uninduced_hepatocyte_6_2b65


title: P18MC.2E3


title: Uninduced_hepatocyte_6_2b64


title: P18MC.2E8


title: Uninduced_hepatocyte_6_2b67


title: Uninduced_hepatocyte_6_2b61


title: P18MC.2E12


title: P18MC.2E2


title: P18MC.2F1


title: Uninduced_hepatocyte_6_2b63


title: Uninduced_hepatocyte_6_2b60


title: P18MC.2E6


title: P18MC.2E11


title: Uninduced_hepatocyte_6_2b6


title: P18MC.2E1


title: P18MC.2E10


title: Uninduced_hepatocyte_6_2b59


title: P18MC.2D9


title: P18MC.2D8


title: Uninduced_hepatocyte_6_2b58


title: Uninduced_hepatocyte_6_2b57


title: Uninduced_hepatocyte_6_2b54


title: P18MC.2D7


title: P18MC.2D5


title: Uninduced_hepatocyte_6_2b56


title: P18MC.2D6


title: Uninduced_hepatocyte_6_2b53


title: P18MC.2D4


title: Uninduced_hepatocyte_6_2b52


title: P18MC.2D12


title: P18MC.2D3


title: Uninduced_hepatocyte_6_2b50


title: P18MC.2D2


title: Uninduced_hepatocyte_6_2b5


title: P18MC.2D11


title: P18MC.2D1


title: Uninduced_hepatocyte_6_2b47


title: P18MC.2D10


title: P18MC.2C9


title: Uninduced_hepatocyte_6_2b46


title: Uninduced_hepatocyte_6_2b45


title: P18MC.2C8


title: P18MC.2C6


title: Uninduced_hepatocyte_6_2b44


title: P18MC.2C7


title: Uninduced_hepatocyte_6_2b43


title: Uninduced_hepatocyte_6_2b42


title: P18MC.2C5


title: Uninduced_hepatocyte_6_2b51


title: P18MC.2C4


title: P18MC.2C3


title: P18MC.2C2


title: Uninduced_hepatocyte_6_2b41


title: Uninduced_hepatocyte_6_2b4


title: Uninduced_hepatocyte_6_2b37


title: P18MC.2C12


title: Uninduced_hepatocyte_6_2b49


title: Uninduced_hepatocyte_6_2b36


title: Uninduced_hepatocyte_6_2b35


title: P18MC.2C11


title: Uninduced_hepatocyte_6_2b34


title: P18MC.2C10


title: P18MC.2C1


title: P18MC.2B9


title: Uninduced_hepatocyte_6_2b33


title: P18MC.2B8


title: P18MC.2B7


title: P18MC.2B6


title: Uninduced_hepatocyte_6_2b29


title: Uninduced_hepatocyte_6_2b31


title: P18MC.2B5


title: Uninduced_hepatocyte_6_2b30


title: Uninduced_hepatocyte_6_2b26


title: Uninduced_hepatocyte_6_2b48


title: P18MC.2B3


title: Uninduced_hepatocyte_6_2b25


title: P18MC.2B4


title: Uninduced_hepatocyte_6_2b23


title: P18MC.2B2


title: Uninduced_hepatocyte_6_2b24


title: P18MC.2B12


title: Uninduced_hepatocyte_6_2b21


title: Uninduced_hepatocyte_6_2b22


title: Uninduced_hepatocyte_6_2b20


title: Uninduced_hepatocyte_6_2b18


title: Uninduced_hepatocyte_6_2b16


title: P18MC.2B10


title: P18MC.2A9


title: P18MC.2B1


title: Uninduced_hepatocyte_6_2b32


title: Uninduced_hepatocyte_6_2b13


title: P18MC.2A8


title: Uninduced_hepatocyte_6_2b92


title: P18MC.2A4


title: P18MC.2A3


title: Uninduced_hepatocyte_6_2b10


title: P18MC.2A2


title: Uninduced_hepatocyte_6_2b39


title: P18MC.2A12


title: Uninduced_hepatocyte_6_2b55


title: Uninduced_hepatocyte_6_2b17


title: P18MC.2B11


title: Uninduced_hepatocyte_6_2b89

description:
Single cell mRNA
Uninduced


title: P18MC.2A10


title: P18MC.2A1


title: P18MC.1H9


title: Uninduced_hepatocyte_6_2b78

description:
Single cell mRNA
Uninduced


title: Uninduced_hepatocyte_6_2b76

description:
Single cell mRNA
Uninduced


title: P18MC.2A7


title: P18MC.1H7


title: P18MC.1H5


title: P18MC.1H8


title: Uninduced_hepatocyte_6_2b7

description:
Single cell mRNA
Uninduced


title: Uninduced_hepatocyte_6_2b62

description:
Single cell mRNA
Uninduced


title: P18MC.2A6


title: Uninduced_hepatocyte_6_2c30


title: Uninduced_hepatocyte_6_2b74

description:
Single cell mRNA
Uninduced


title: P18MC.2A5


title: Uninduced_hepatocyte_6_2b72


title: Uninduced_hepatocyte_6_2b40

description:
Single cell mRNA
Uninduced


title: P18MC.1H6