title: AMB_201013_8wk_2A_3A_2_P6-2-E8-L16


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-K4

status: Public on Dec 23 2025

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Library strategy: snmC-seq3
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: strain

tag: age

value: 8 weeks

tag: brain region

value: FC

tag: gender

value: M


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-K3


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-L15


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-K15


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-K16


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-I16


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-I3


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-J4


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-H16


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-H3


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-J3


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-H4


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-J16


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-I4


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-J15


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-O15


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-H15


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-I15


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-F3


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-F16


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-E16


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-E15


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-D4


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-G4


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-G3


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-G15


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-G16


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-F4


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-C4


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-E4


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-E3


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-D3


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-C15


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-B3


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-D15


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-A3


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-A4


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-A15


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-C16


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-B4


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-F15


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-B16


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-A16


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-B15


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-P14


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-D16


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-P1


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-P13


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-O13


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-N13


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-N2


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-N1


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-O1


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-O14


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-N14


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-L2


title: AMB_201013_8wk_2A_3A_2_P6-2-E8-C3


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-M13


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-L14


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-M1


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-L1


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-L13


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-P2


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-K2


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-K14


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-K13


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-O2


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-K1


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-J14


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-J1


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-J2


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-I14


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-M2


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-M14


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-I2


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-I1


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-J13


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-H1


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-H13


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-H14


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-F13


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-G1


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-G2


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-F14


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-G13


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-F1


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-D14


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-D13


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-D1


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-G14


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-F2


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-D2


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-E2


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-I13


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-H2


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-E13


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-E1


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-B2


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-B13


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-C2


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-C14


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-A13


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-C1


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-E14


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-B14


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-B1


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-A14


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-A1


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-P23


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-C13


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-P12


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-N23


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-N24


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-O12


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-O24


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-O11


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-P11


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-N11


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-N12


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-M24


title: AMB_201013_8wk_2A_3A_2_P6-1-C18-A2


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-M23


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-L23


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-K24


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-P24


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-M12


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-M11


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-L12


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-L24


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-K23


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-L11


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-O23


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-K12


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-J24


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-J23


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-K11


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-J11


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-I23


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-I12


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-H12


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-I11


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-G24


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-G23


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-H24


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-G12


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-F24


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-F11


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-J12


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-E23


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-H11


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-F12


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-F23


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-E24


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-D23


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-D24


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-I24


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-D12


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-D11


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-E12


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-E11


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-C24


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-H23


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-G11


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-C23


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-C11


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-C12


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-B24


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-B23


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-P21


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-P22


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-O21


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-L9


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-B12


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-A12


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-P9


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-O22


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-P10


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-A11


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-A23


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-L22


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-O9


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-A24


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-O10


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-L21


title: AMB_201013_8wk_2A_3A_2_P5-6-F6-B11


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-N22


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-L10


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-K10


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-N21


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-N10


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-M9


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-M22


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-M21


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-K9


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-K22


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-M10


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-J22


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-J21


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-N9


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-J10


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-I21


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-H9


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-H22


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-I22


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-G9


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-I10


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-K21


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-G22


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-G21


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-G10


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-H10


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-F9


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-F22


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-H21


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-F10


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-J9


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-F21


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-E9


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-E22


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-E21


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-E10


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-D9


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-I9


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-D21


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-D22


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-D10


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-C9


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-C21


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-C22


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-B9


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-A22


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-B22


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-P8


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-A21


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-P7


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-A9


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-A10


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-C10


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-B10


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-O20


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-P19


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-N7


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-P20


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-N8


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-O19


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-N20


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-M7


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-M8


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-M20


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-N19


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-M19


title: AMB_201013_8wk_2A_3A_2_P5-5-E5-B21


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-L7


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-L20


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-K8


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-L19


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-L8


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-K7


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-O8


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-K19


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-J20


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-K20


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-O7


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-J8


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-J19


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-J7


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-I8


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-I7


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-I19


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-I20


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-H7


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-H19


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-H20


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-H8


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-G7


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-G20


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-G19


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-F8


title: Biopsy_898_R2H

type: RNA

city: Toronto

first: Mingyao

last: Liu

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

description: Gene expression data from human lungs at R2H

hyb_protocol: According to manufacturer guidelines

scan_protocol: According to manufacturer guidelines

data_processing: Affymetrix CEL files were imported and processed using RMA in R version 3.5.1 with the affy package. We used Affymetrix Human Genome U133 Plus 2.0 Array annotation data (hgu133plus2.db package in R)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Biopsy, time point: R2H

label_protocol: According to manufacturer guidelines

extract_protocol: RNA was extracted from snap frozen samples using the RNeasy Mini Kit (Qiagen; Hilden, Germany). RNA quality was assessed using Nanodrop spectrophotometer (VWR; Radnor, PA) and Bioanalyzer (Agilent; Santa Clara, CA)

tag: sample type

value: RNA

tag: tissue

value: Lung


title: Biopsy_864_R2H


title: Biopsy_858_R2H


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-E8


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-E7


title: Biopsy_853_R2H


title: Biopsy_857_R2H


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-E20


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-E19


title: Biopsy_855_R2H


title: Biopsy_843_R2H


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-D8


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-D7


title: Biopsy_834_R2H


title: Biopsy_832_R2H


title: Biopsy_828_R2H


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-G8


title: Biopsy_824_R2H


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-D19


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-C7


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-F20


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-C20


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-C19


title: Biopsy_780_R2H


title: Biopsy_772_R2H


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-F19


title: Biopsy_758_R2H


title: Biopsy_796_R2H


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-F7


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-B7


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-B8


title: Biopsy_763_R2H


title: Biopsy_728_R2H


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-B19


title: Biopsy_747_R2H


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-A7


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-A8


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-A20


title: Biopsy_679_R2H


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-C8


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-D20


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-B20


title: AMB_201013_8wk_2A_3A_2_P5-4-J2-A19


title: Biopsy_717_R2H


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-P6


title: Biopsy_786_R2H


title: Biopsy_686_R2H


title: Biopsy_704_R2H


title: Biopsy_691_R2H


title: Biopsy_690_R2H


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-P18


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-P5


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-O6


title: Biopsy_692_R2H


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-O5


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-P17


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-O18


title: Biopsy_705_R2H


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-O17


title: Biopsy_699_R2H


title: Biopsy_667_R2H


title: Biopsy_654_R2H


title: Biopsy_659_R2H


title: Biopsy_695_R2H


title: Biopsy_645_R2H


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-N18


title: Biopsy_639_R2H


title: Biopsy_635_R2H


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-N5


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-N6


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-M18


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-N17


title: Biopsy_618_R2H


title: Biopsy_626_R2H


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-M17


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-M6


title: Biopsy_614_R2H


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-L6


title: Biopsy_606_R2H


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-L5


title: Biopsy_821_R2H


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-L18


title: Biopsy_833_R2H


title: Biopsy_571_R2H


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-K6


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-K5


title: Biopsy_793_R2H


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-M5


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-K17


title: Biopsy_740_R2H


title: Biopsy_719_R2H


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-J6


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-J5


title: Biopsy_652_R2H


title: Biopsy_684_R2H


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-I6


title: Biopsy_607_R2H


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-L17


title: Biopsy_589_R2H


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-I18


title: Biopsy_744_R2H


title: Biopsy_757_R2H


title: Biopsy_602_R2H


title: Biopsy_898_CIT

description: Gene expression data from human lungs at CIT

source_name: Biopsy, time point: CIT


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-J17


title: Biopsy_785_R2H


title: Biopsy_383_R2H


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-H5


title: Biopsy_864_CIT


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-K18


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-H6


title: Biopsy_858_CIT


title: Biopsy_857_CIT


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-H17


title: Biopsy_855_CIT


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-I5


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-G5


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-I17


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-G18


title: Biopsy_843_CIT


title: Biopsy_832_CIT


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-G17


title: Biopsy_834_CIT


title: Biopsy_828_CIT


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-F6


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-F18


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-F5


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-F17


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-H18


title: Biopsy_824_CIT


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-E6


title: Biopsy_780_CIT


title: Biopsy_796_CIT


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-G6


title: Biopsy_758_CIT


title: Biopsy_772_CIT


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-E5


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-E17


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-E18


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-D6


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-D5


title: Biopsy_763_CIT


title: Biopsy_728_CIT


title: Biopsy_747_CIT


title: Biopsy_853_CIT


title: Biopsy_717_CIT


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-D17


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-J18


title: Biopsy_695_CIT


title: Biopsy_786_CIT


title: Biopsy_679_CIT


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-C6


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-C5


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-C18


title: Biopsy_686_CIT


title: Biopsy_704_CIT


title: Biopsy_691_CIT


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-C17


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-B6


title: Biopsy_690_CIT


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-B5


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-B18


title: Biopsy_692_CIT


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-D18


title: Biopsy_705_CIT


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-B17


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-A5


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-A6


title: Biopsy_667_CIT


title: Biopsy_659_CIT


title: Biopsy_645_CIT


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-A17


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-P4


title: Biopsy_639_CIT


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-P3


title: Biopsy_635_CIT


title: Biopsy_626_CIT


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-P15


title: Biopsy_618_CIT


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-O4


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-O3


title: Biopsy_606_CIT


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-O16


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-O15


title: Biopsy_589_CIT


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-N4


title: Biopsy_571_CIT


title: AMB_201013_8wk_2A_3A_2_P5-3-K15-A18


title: Biopsy_821_CIT


title: Biopsy_793_CIT


title: Biopsy_699_CIT


title: Biopsy_833_CIT


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-M4


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-N16


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-N3


title: Biopsy_654_CIT


title: Biopsy_757_CIT


title: Biopsy_785_CIT


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-M3


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-N15


title: Biopsy_740_CIT


title: Biopsy_614_CIT


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-P16


title: Biopsy_719_CIT


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-M15


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-M16


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-L4


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-L3


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-L16


title: Biopsy_684_CIT


title: Biopsy_744_CIT


title: Biopsy_607_CIT


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-K4


title: Biopsy_602_CIT


title: Biopsy_383_CIT


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-K3


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-K16


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-L15


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-J3


title: Biopsy_652_CIT


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-K15


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-J4


title: Primary rat hepatocyte, 1-Nitropropane, 3uM, rep1

city: Durham

first: Rasim

last: Barutcu

state: NC

address: 6 Davis Drive

institute: ScitoVation

description: Library name: RTH2_Nitropropane_3_G01

library_source: transcriptomic

data_processing:
TempO-Seq data were analyzed using the TempO-SeqR software package, which is built on the R statistical computing environment. Each quality-filtered FASTQ file, by using the FastQC software, containing sequencing reads and quality scores, is aligned to a user-defined pseudo-transcriptome using the Bowtie algorithm. The output of the TempO-Seq data analysis is a table of gene expression counts, where each column represents a sample, and each row corresponds to a gene. This table is generated following the alignment and processing of the sequencing data, facilitating subsequent analyses such as differential gene expression and pathway evaluations. The gene count values were used for the subsequent differential gene expression analyses.
Counted reads for each annotated gene feature were analyzed for differential expression in R (v.3.5.3) using the BioConductor library DESeq2 (v.1.28.1) using TMM normalization. DESeq2 uses a dispersion correction of the count data based on the negative binomial distribution and a maximum likelihood model to impute the prior data distribution for statistical testing. Empirical Bayesian statistics are applied to linear combinations of factors to test differential expression for multiple contrasts simultaneously. To avoid bias in the dispersion correction, the data were pre-filtered to exclude any annotated genomic feature for which there were less than 10 counts in any biological sample. The final output of DESeq2 is a table of estimated Log2 fold change, p-values for the defined contrasts tested, as well as Benjamin Hochberg corrected false discovery p-values (FDR or adjusted p-value). A statistical criterion, the Benjamini and Hochberg step-up false discovery rate adjusted p-value of less than 0.05 (FDR<0.05), a commonly used threshold in whole transcriptomic analysis, was used in the analyses. Genes with fewer than 10 counts in all samples were excluded from the analysis. Additionally, it is useful to define a minimum magnitude of change in gene expression. Common values for differential expression experiments would be a change in expression (e.g., the ratio of the mean expression of treated samples relative to mean expression of control samples), up or down-regulated relative to controls of |logFC| > 1 fold. As treated samples can be either up-regulated (a positive fold change) or down-regulated (a negative fold change) relative to controls, this threshold was applied as the absolute value of estimated fold change (|log2FC|>1.0). Finally, the application of both a statistical threshold and a magnitude of change threshold (p-adjusted<0.05 & |log2FC|>1.0 fold) was used; these criteria produced the most robust gene lists relative to indicated functional enrichment with a known cellular gene ontology.
Assembly: GRCr8
Supplementary files format and content: csv file of gene count values

organism: Rattus norvegicus

source_name: Liver

growth_protocol: Primary hepatocytes from female Sprague-Dawley rats (BioIVT, Lot YPH) were used as the in vitro model for evaluating nitromethane (NM), nitroethane (NE), and 1-nitropropane (1NP) toxicity. Cells were cultured in 96-well plates (CytoOne, CC7682-7596) coated with 90 µg/mL type I collagen (Sigma-Aldrich, C3867) at a seeding density of 40,000 cells/well. Cells were maintained in Williams' E Medium (Thermo Fisher, A1217601) supplemented with 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, and insulin-transferrin-selenium (ITS, Thermo Fisher, 41400045) at 37°C, 5% CO₂.

extract_protocol:
RNA extraction was performed by using the TempO-seq platform (Biospyder) according to manufacturer's instructions.
Transcriptomic profiling was conducted using the BioSpyder TempO-Seq Human Whole Transcriptome targeted gene panel (version 2.0), which interrogates over 20,000 protein-coding genes according to the manufacturer’s protocol (BioSpyder Technologies, Carlsbad, CA, USA).  In TempO-Seq (Harril et al., 2021; Mav et al., 2018), each Detector Oligo (DO) contains a sequence complementary to an mRNA target and a universal primer binding site shared across all genes. DOs anneal to the RNA template at specific target sites and can be ligated together. Ligated DOs are then amplified using a single-plex PCR with a universal primer pair, incorporating both Illumina adaptors and sample-specific barcodes. This dual-index barcoding enables deconvolution of sample reads through standard Illumina software, producing a FASTQ file for each sample. For transcriptomic analysis, three biological replicates were profiled per concentration, per chemical, in addition to vehicle and positive control groups.

treatment_protocol: A dose range of 0.003–10 mM was selected based on preliminary cytotoxicity assessments. Cells were exposed to NM, NE, or 1NP at 0.003, 0.01, 0.03, 0.1, 0.3, 1, 3, and 10 mM for 24 hours. Controls included 0.2% DMSO (vehicle control), 10 mM formaldehyde (100% cytotoxicity control), and known nuclear receptor agonists such as benzo[a]pyrene (AhR activator), CITCO (CAR activator), and WY14643 (PPAR-α activator). CITCO, while a potent activator of human CAR, has reduced potency for rat CAR and was included here primarily as a general nuclear receptor activator reference rather than for species-specific CAR activation.

value: Liver

tag: cell type

value: Primary Hepatocytes

tag: treatment

value: Sprague-Dawley


title: Primary rat hepatocyte, 1-Nitropropane, 1uM, rep3

description: Library name: RTH2_Nitropropane_1_F03


title: Primary rat hepatocyte, 1-Nitropropane, 3uM, rep2

description: Library name: RTH2_Nitropropane_3_G02


title: Primary rat hepatocyte, 1-Nitropropane, 3uM, rep3

description: Library name: RTH2_Nitropropane_3_G03


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-J16


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-J15


title: Primary rat hepatocyte, 1-Nitropropane, 1uM, rep1

description: Library name: RTH2_Nitropropane_1_F01


title: Primary rat hepatocyte, 1-Nitropropane, 1uM, rep2

description: Library name: RTH2_Nitropropane_1_F02


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-I3


title: Primary rat hepatocyte, 1-Nitropropane, 10uM, rep3

description: Library name: RTH2_Nitropropane_10_H03


title: Primary rat hepatocyte, 1-Nitropropane, 10uM, rep2

description: Library name: RTH2_Nitropropane_10_H02


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-I16


title: Primary rat hepatocyte, 1-Nitropropane, 10uM, rep1

description: Library name: RTH2_Nitropropane_10_H01


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-I15


title: Primary rat hepatocyte, 1-Nitropropane, 0.3uM, rep3

description: Library name: RTH2_Nitropropane_0_3_E03


title: Primary rat hepatocyte, 1-Nitropropane, 0.3uM, rep2

description: Library name: RTH2_Nitropropane_0_3_E02


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-H4


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-H16


title: Primary rat hepatocyte, 1-Nitropropane, 0.3uM, rep1

description: Library name: RTH2_Nitropropane_0_3_E01


title: Primary rat hepatocyte, 1-Nitropropane, 0.1uM, rep3

description: Library name: RTH2_Nitropropane_0_1_D03


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-H15


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-G4


title: Primary rat hepatocyte, 1-Nitropropane, 0.03uM, rep3

description: Library name: RTH2_Nitropropane_0_03_C03


title: Primary rat hepatocyte, 1-Nitropropane, 0.1uM, rep1

description: Library name: RTH2_Nitropropane_0_1_D01


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-G3


title: Primary rat hepatocyte, 1-Nitropropane, 0.03uM, rep2

description: Library name: RTH2_Nitropropane_0_03_C02


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-G16


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-G15


title: Primary rat hepatocyte, 1-Nitropropane, 0.03uM, rep1

description: Library name: RTH2_Nitropropane_0_03_C01


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-F4


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-I4


title: Primary rat hepatocyte, 1-Nitropropane, 0.01uM, rep3

description: Library name: RTH2_Nitropropane_0_01_B03


title: Primary rat hepatocyte, 1-Nitropropane, 0.01uM, rep2

description: Library name: RTH2_Nitropropane_0_01_B02


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-F16


title: Primary rat hepatocyte, 1-Nitropropane, 0.01uM, rep1

description: Library name: RTH2_Nitropropane_0_01_B01


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-F3


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-E4


title: Primary rat hepatocyte, 1-Nitropropane, 0.003uM, rep2

description: Library name: RTH2_Nitropropane_0_003_A02


title: Primary rat hepatocyte, 1-Nitropropane, 0.003uM, rep3

description: Library name: RTH2_Nitropropane_0_003_A03


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-F15


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-E3


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-E16


title: Primary rat hepatocyte, 1-Nitropropane, 0.003uM, rep1

description: Library name: RTH2_Nitropropane_0_003_A01


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-H3


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-E15


title: Primary rat hepatocyte, Media, rep6

description: Library name: RTH2_Media_A06

value: Control


title: Primary rat hepatocyte, Media, rep5

description: Library name: RTH2_Media_A05


title: Primary rat hepatocyte, 1-Nitropropane, 0.1uM, rep2

description: Library name: RTH2_Nitropropane_0_1_D02


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-D4


title: Primary rat hepatocyte, Media, rep4

description: Library name: RTH2_Media_A04


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-D3


title: Primary rat hepatocyte, WY140, 50uM, rep6

description: Library name: RTH2_100uM_WY140_C06


title: Primary rat hepatocyte, WY140, 50uM, rep5

description: Library name: RTH2_100uM_WY140_C05


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-D16


title: Primary rat hepatocyte, WY140, 50uM, rep4

description: Library name: RTH2_100uM_WY140_C04


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-D15


title: Primary rat hepatocyte, DMSO, 0.5uM, rep6

description: Library name: RTH2_0_5_DMSO_B06

value: DMSO


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-C3


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-C4


title: Primary rat hepatocyte, DMSO, 0.5uM, rep4

description: Library name: RTH2_0_5_DMSO_B04


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-C16


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-B4


title: Primary rat hepatocyte, Nitromethane, 3uM, rep2

description: Library name: RTH1_Nitromethane_3_G05

value: Nitromethane


title: Primary rat hepatocyte, Nitromethane, 3uM, rep3

description: Library name: RTH1_Nitromethane_3_G06


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-B3


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-B15


title: Primary rat hepatocyte, Nitromethane, 3uM, rep1

description: Library name: RTH1_Nitromethane_3_G04


title: Primary rat hepatocyte, Nitromethane, 1uM, rep3

description: Library name: RTH1_Nitromethane_1_F06


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-B16


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-A4


title: Primary rat hepatocyte, Nitromethane, 1uM, rep2

description: Library name: RTH1_Nitromethane_1_F05


title: Primary rat hepatocyte, Nitromethane, 1uM, rep1

description: Library name: RTH1_Nitromethane_1_F04


title: Primary rat hepatocyte, Nitromethane, 10uM, rep2

description: Library name: RTH1_Nitromethane_10_H05


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-A15


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-A16


title: Primary rat hepatocyte, Nitromethane, 10uM, rep3

description: Library name: RTH1_Nitromethane_10_H06


title: Primary rat hepatocyte, Nitromethane, 10uM, rep1

description: Library name: RTH1_Nitromethane_10_H04


title: Primary rat hepatocyte, Nitromethane, 0.3uM, rep3

description: Library name: RTH1_Nitromethane_0_3_E06


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-P2


title: Primary rat hepatocyte, DMSO, 0.5uM, rep5

description: Library name: RTH2_0_5_DMSO_B05


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-P14


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-C15


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-P13


title: Primary rat hepatocyte, Nitromethane, 0.1uM, rep3

description: Library name: RTH1_Nitromethane_0_1_D06


title: Primary rat hepatocyte, Nitromethane, 0.3uM, rep1

description: Library name: RTH1_Nitromethane_0_3_E04


title: Primary rat hepatocyte, Nitromethane, 0.3uM, rep2

description: Library name: RTH1_Nitromethane_0_3_E05


title: Primary rat hepatocyte, Nitromethane, 0.1uM, rep2

description: Library name: RTH1_Nitromethane_0_1_D05


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-O14


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-P1


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-O2


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-O13


title: Primary rat hepatocyte, Nitromethane, 0.03uM, rep3

description: Library name: RTH1_Nitromethane_0_03_C06


title: Primary rat hepatocyte, Nitromethane, 0.1uM, rep1

description: Library name: RTH1_Nitromethane_0_1_D04


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-O1


title: Primary rat hepatocyte, Nitromethane, 0.03uM, rep2

description: Library name: RTH1_Nitromethane_0_03_C05


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-N2


title: AMB_201013_8wk_2A_3A_2_P5-2-C10-A3


title: Primary rat hepatocyte, Nitromethane, 0.03uM, rep1

description: Library name: RTH1_Nitromethane_0_03_C04


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-N13


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-N14


title: Primary rat hepatocyte, Nitromethane, 0.003uM, rep3

description: Library name: RTH1_Nitromethane_0_003_A06


title: Primary rat hepatocyte, Nitromethane, 0.01uM, rep1

description: Library name: RTH1_Nitromethane_0_01_B04


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-N1


title: Primary rat hepatocyte, Nitromethane, 0.01uM, rep2

description: Library name: RTH1_Nitromethane_0_01_B05


title: Primary rat hepatocyte, Nitromethane, 0.01uM, rep3

description: Library name: RTH1_Nitromethane_0_01_B06


title: Primary rat hepatocyte, Nitromethane, 0.003uM, rep2

description: Library name: RTH1_Nitromethane_0_003_A05


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-M2


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-M13


title: Primary rat hepatocyte, Nitromethane, 0.003uM, rep1

description: Library name: RTH1_Nitromethane_0_003_A04


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-M1


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-L2


title: Primary rat hepatocyte, Nitroethane, 3uM, rep3

description: Library name: RTH1_Nitroethane_3_G09

value: Nitroethane


title: Primary rat hepatocyte, Nitroethane, 3uM, rep2

description: Library name: RTH1_Nitroethane_3_G08


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-L14


title: Primary rat hepatocyte, Nitroethane, 1uM, rep3

description: Library name: RTH1_Nitroethane_1_F09


title: Primary rat hepatocyte, Nitroethane, 3uM, rep1

description: Library name: RTH1_Nitroethane_3_G07


title: Primary rat hepatocyte, Nitroethane, 1uM, rep2

description: Library name: RTH1_Nitroethane_1_F08


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-K2


title: Primary rat hepatocyte, Nitroethane, 10uM, rep3

description: Library name: RTH1_Nitroethane_10_H09


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-K13


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-K1


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-M14


title: Primary rat hepatocyte, Nitroethane, 10uM, rep1

description: Library name: RTH1_Nitroethane_10_H07


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-K14


title: Primary rat hepatocyte, Nitroethane, 0.3uM, rep3

description: Library name: RTH1_Nitroethane_0_3_E09


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-J13


title: Primary rat hepatocyte, Nitroethane, 0.3uM, rep1

description: Library name: RTH1_Nitroethane_0_3_E07


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-J1


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-L13


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-I2


title: Primary rat hepatocyte, Nitroethane, 0.1uM, rep3

description: Library name: RTH1_Nitroethane_0_1_D09


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-L1


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-I14


title: Primary rat hepatocyte, Nitroethane, 0.1uM, rep2

description: Library name: RTH1_Nitroethane_0_1_D08


title: Primary rat hepatocyte, Nitroethane, 0.1uM, rep1

description: Library name: RTH1_Nitroethane_0_1_D07


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-I13


title: Primary rat hepatocyte, Nitroethane, 0.03uM, rep1

description: Library name: RTH1_Nitroethane_0_03_C07


title: Primary rat hepatocyte, Nitroethane, 0.01uM, rep3

description: Library name: RTH1_Nitroethane_0_01_B09


title: Primary rat hepatocyte, Nitroethane, 1uM, rep1

description: Library name: RTH1_Nitroethane_1_F07


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-H14


title: Primary rat hepatocyte, Nitroethane, 10uM, rep2

description: Library name: RTH1_Nitroethane_10_H08


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-H2


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-H13


title: Primary rat hepatocyte, Nitroethane, 0.03uM, rep2

description: Library name: RTH1_Nitroethane_0_03_C08


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-J2


title: Primary rat hepatocyte, Nitroethane, 0.03uM, rep3

description: Library name: RTH1_Nitroethane_0_03_C09


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-I1


title: Primary rat hepatocyte, Nitroethane, 0.3uM, rep2

description: Library name: RTH1_Nitroethane_0_3_E08


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-H1


title: Primary rat hepatocyte, Nitroethane, 0.01uM, rep1

description: Library name: RTH1_Nitroethane_0_01_B07


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-J14


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-G2


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-G14


title: Primary rat hepatocyte, Nitroethane, 0.003uM, rep3

description: Library name: RTH1_Nitroethane_0_003_A09


title: Primary rat hepatocyte, Nitroethane, 0.01uM, rep2

description: Library name: RTH1_Nitroethane_0_01_B08


title: Primary rat hepatocyte, Nitroethane, 0.003uM, rep2

description: Library name: RTH1_Nitroethane_0_003_A08


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-G13


title: Primary rat hepatocyte, Nitroethane, 0.003uM, rep1

description: Library name: RTH1_Nitroethane_0_003_A07


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-G1


title: Primary rat hepatocyte, Media, rep3

description: Library name: RTH1_Media_A12


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-F2


title: Primary rat hepatocyte, Media, rep2

description: Library name: RTH1_Media_A11


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-F14


title: Primary rat hepatocyte, Media, rep1

description: Library name: RTH1_Media_A10


title: Primary rat hepatocyte, BAP, 50uM, rep3

description: Library name: RTH1_50uM_BAP_C12

value: BAP


title: Primary rat hepatocyte, WY140, 50uM, rep1

description: Library name: RTH1_50uM_WY140_F10


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-E14


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-F1


title: Primary rat hepatocyte, WY140, 50uM, rep2

description: Library name: RTH1_50uM_WY140_F11


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-E2


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-E13


title: Primary rat hepatocyte, BAP, 50uM, rep1

description: Library name: RTH1_50uM_BAP_C10


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-D2


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-E1


title: Primary rat hepatocyte, Rifampin, 40uM, rep3

description: Library name: RTH1_40uM_Rifampin_H03

value: Rifampin


title: Primary rat hepatocyte, Rifampin, 40uM, rep1

description: Library name: RTH1_40uM_Rifampin_H01


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-D14


title: Primary rat hepatocyte, Rifampin, 40uM, rep2

description: Library name: RTH1_40uM_Rifampin_H02


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-D1


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-D13


title: Primary rat hepatocyte, BAP, 50uM, rep2

description: Library name: RTH1_50uM_BAP_C11


title: Primary rat hepatocyte, Rifampin, 20uM, rep3

description: Library name: RTH1_20uM_Rifampin_E12


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-C2


title: Primary rat hepatocyte, Rifampin, 20uM, rep2

description: Library name: RTH1_20uM_Rifampin_E11


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-C14


title: Primary rat hepatocyte, WY140, 50uM, rep3

description: Library name: RTH1_50uM_WY140_F12


title: Primary rat hepatocyte, CITCO, 20uM, rep2

description: Library name: RTH1_20uM_CITCO_G02

value: CITCO


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-F13


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-B2


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-C13


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-C1


title: Primary rat hepatocyte, CITCO, 20uM, rep1

description: Library name: RTH1_20uM_CITCO_G01


title: Primary rat hepatocyte, CITCO, 10uM, rep3

description: Library name: RTH1_10uM_CITCO_D12


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-B14


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-B13


title: Primary rat hepatocyte, CITCO, 10uM, rep1

description: Library name: RTH1_10uM_CITCO_D10


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-A2


title: Primary rat hepatocyte, DMSO, 0.5uM, rep3

description: Library name: RTH1_0_5_DMSO_B12


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-A14


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-A1


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-A13


title: Primary rat hepatocyte, DMSO, 0.5uM, rep2

description: Library name: RTH1_0_5_DMSO_B11


title: Primary rat hepatocyte, DMSO, 0.5uM, rep1

description: Library name: RTH1_0_5_DMSO_B10


title: RNF125Dox3

city: Honolulu

first: Xue

last: Wang

state: HI

address: 701 Ilalo Street

department: Cancer Biology Program

institute: University of Hawaii Cancer Center

description:
Library name: RNF125Dox3
Column name in Processed data_fpkm.txt: RNF125Dox3

data_processing:
Poor quality reads were trimmed using the fastq-mcf (v1.05). Reads quality was checked using the fastqc (v0.11.7).
Gene read counts were in Ensembl Gene ID and converted to Entrez Gene ID.
Corresponding Symbol annotations and full gene names were added using the “org.Hs.eg.db” library. NA (Not Annotated), duplicate Entrez IDs and genes without symbols were removed.
After removing the duplicated genes, the fragments per kilobase of transcript per million mapped reads (FPKM) were calculated.
Assembly: GRCh38
Supplementary files format and content: The tab-delimited text file includes FPKM values for each sample

source_name: HepG2 liver cancer cells

growth_protocol: pInducer20-RNF125 HepG2 cells were cultured in low glucose Dulbecco’s modified Eagle medium (DMEM) (Cat# 11885084, Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in an atmosphere of humidified air containing 5% CO2. Cell viability was more than 90% according to trypan blue exclusion analysis.

extract_protocol:
Total RNA was extracted from Cont (n=3) and Dox (n=3) groups using RNAiso Plus according to the manufacturer’s protocol.
RNA-seq libraries were prepared by poly(A) capture, followed by reverse transcription into cDNA.

treatment_protocol: pInducer20-RNF125 HepG2 cells were treated with or without 2 μM doxycycline hydrochloride (Dox) for 48 hours.

value: HepG2 liver cancer cells

tag: genotype

value: WT

value: total RNA


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-P24

value: 8 weeks

value: FC


title: Primary rat hepatocyte, CITCO, 20uM, rep3

description: Library name: RTH1_20uM_CITCO_G03


title: RNF125Dox2

description:
Library name: RNF125Dox2
Column name in Processed data_fpkm.txt: RNF125Dox2


title: Primary rat hepatocyte, Rifampin, 20uM, rep1

description: Library name: RTH1_20uM_Rifampin_E10


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-P23

value: M


title: RNF125Cont3

description:
Library name: RNF125Cont3
Column name in Processed data_fpkm.txt: RNF125Cont3


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-P11


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-P12


title: RNF125Cont2

description:
Library name: RNF125Cont2
Column name in Processed data_fpkm.txt: RNF125Cont2


title: RNF125Cont1

description:
Library name: RNF125Cont1
Column name in Processed data_fpkm.txt: RNF125Cont1


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-O23


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-O12


title: Primary rat hepatocyte, CITCO, 10uM, rep2

description: Library name: RTH1_10uM_CITCO_D11


title: AMB_201013_8wk_2A_3A_2_P5-1-E22-B1


title: iPSC-derived neurons, disomic, Cell line C9, Library C9N161224-4W-V-2

city: London

first: Michael

last: Lattke

address: Hammersmith Hospital Campus, Du Cane Road

department: Brain Sciences

country: United Kingdom

institute: Imperial College London

description:
Library name: C9N161224-4W-V-2
bulk RNA-seq (Singleron)
Bulk_Singleron_in_vitro_basic_char_v06_add_samples_counts_comb.csv

data_processing:
Raw sequencing data (fastq files) were demultiplexed, mapped to the human genome (GRCh38) and quantified by Singleron using the AccuraCode (v1.2.0) pipeline.
Assembly: GRCh38
Supplementary files format and content: Gene level count matrix of all samples combined samples

molecule: polyA RNA

growth_protocol: Two protocols were used to generate neural progenitor cells (iNPCs) and neurons (iNEU) from iPSCs as indicated in the sample metadata. A protocol used by the lab of Dean Nizetic (DN), based on the Gibco protocol (Thermo Fisher Scientific, MAN0008031), and protocol based on neurospheres developed by Su-Chun Zhang (SCZ; Wang et al., 2023). For the DN protocol, NPCs  between passages 6 and 10 were expanded in Geltrex-coated 6-well culture plates prepared by diluting a 60 μL Geltrex aliquot in 6 mL cold DMEM/F12, incubated at 37°C for at least 60 minutes. Cells were thawed, centrifuged at 300 × g for 5 minutes, and resuspended in Neural Expansion Medium (NEM) with 5 μM ROCK inhibitor Y27632 (STEMCELL Technologies) at a density of 1-2 million cells per well. Media changes were performed the next day with complete NEM, and then changed every other day thereafter. For neuronal differentiation, NPCs were dissociated with Accutase (Thermo Fisher Scientific) and seeded onto Poly-L-ornithine/Laminin-coated 24-well culture plates at a density of 70,000 cells per well in NEM with 5 μM Y27532. Media change was performed the next day with complete BrainPhys Neuronal Medium (STEMCELL Technologies), and then changed every four days for two weeks. After which, BrainPhys Neuronal Medium is supplemented with 2 μg/mL Laminin for media changes every four days till the desired experimental endpoint. For the SCZ protocol, iPSCs were transitioned to Neural Differentiation Medium (NDM), consisting of a 1:1 mixture of DMEM/F12 (Thermo Fisher Scientific) and Neurobasal medium (Thermo Fisher Scientific) supplemented with 1× GlutaMAX (Thermo Fisher Scientific), 0.5× N2 (STEMCELL Technologies), 0.5× B27 (STEMCELL Technologies), 100 μM ascorbic acid (Sigma-Aldrich). On the next day, dual SMAD inhibition was initiated by supplementing NDM with 10 μM SB431542 (Tocris) and 2 μM DMH1 (Tocris). Cells were cultured for seven days with daily medium changes. Cells were then dissociated with Versene and transferred to low attachment flasks in NDM supplemented with 10 ng/mL basic fibroblast growth factor (bFGF, STEMCELL Technologies) and 0.5 μM Thiazovivin to promote neurosphere formation. Neurospheres were maintained with medium changes every three days until the experimental endpoint. To differentiate neurons, neurospheres were dissociated using TrypLE (Thermo Fisher Scientific) and seeded onto Poly-L-ornithine/Laminin-coated 24-well culture plates at a density of 70,000 cells per well in Neuron Medium, composed of Neurobasal medium supplemented with 1× GlutaMAX, 1× B27 with vitamin A (STEMCELL Technologies), 10 ng/mL brain-derived neurotrophic factor (BDNF, Thermo Fisher Scientific), 10 ng/mL glial cell line-derived neurotrophic factor (GDNF, Thermo Fisher Scientific), 1 µM dibutyryl cyclic AMP (dbcAMP, STEMCELL Technologies), and 200 µM ascorbic acid. 0.1 µM Compound E (Merck Millipore) was added on the first day of plating and withdrawn during subsequent medium changes. Neuronal cultures were maintained with medium changes every four days until the indicated endpoint.

extract_protocol:
Total RNA was extracted from ~2-10 mg of fetal human brain tissue using the RNeasy Plus Micro kit (Qiagen) according to manufacturer’s instructions.
In vitro differentiated NPC or neuron cultures (neurons matured to day 30) were dissociated with Accutase, pelleted, and flash frozen. Samples were stored in -80C until further processing. Library preparation and bulk-RNA-seq were performed using AccuraCode® RNAseq Kit (Singleron Biotechnologies).

tag: cell line

value: iPSC-derived neurons

value: disomic

tag: sample id

tag: group

value: CON

tag: protocol

value: DN

tag: batch

tag: in final_analysis

value: TRUE


title: iPSC-derived neurons, disomic, Cell line C9, Library C9N061224-4W-V-3

description:
Library name: C9N061224-4W-V-3
bulk RNA-seq (Singleron)
Bulk_Singleron_in_vitro_basic_char_v06_add_samples_counts_comb.csv


title: iPSC-derived neurons, disomic, Cell line C9, Library C9N161224-4W-V-1

description:
Library name: C9N161224-4W-V-1
bulk RNA-seq (Singleron)
Bulk_Singleron_in_vitro_basic_char_v06_add_samples_counts_comb.csv


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-N24


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-O11


title: iPSC-derived neurons, disomic, Cell line C9, Library C9N061224-4W-V-2

description:
Library name: C9N061224-4W-V-2
bulk RNA-seq (Singleron)
Bulk_Singleron_in_vitro_basic_char_v06_add_samples_counts_comb.csv


title: iPSC-derived neurons, disomic, Cell line C9, Library C9N061224-4W-V-1

description:
Library name: C9N061224-4W-V-1
bulk RNA-seq (Singleron)
Bulk_Singleron_in_vitro_basic_char_v06_add_samples_counts_comb.csv


title: RNF125Dox1

description:
Library name: RNF125Dox1
Column name in Processed data_fpkm.txt: RNF125Dox1


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-N12


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-M24


title: iPSC-derived neurons, trisomy 21, Cell line C13, Library C13N161224-4W-V-3

description:
Library name: C13N161224-4W-V-3
bulk RNA-seq (Singleron)
Bulk_Singleron_in_vitro_basic_char_v06_add_samples_counts_comb.csv

value: trisomy 21

value: DS


title: iPSC-derived neurons, trisomy 21, Cell line C13, Library C13N161224-4W-V-2

description:
Library name: C13N161224-4W-V-2
bulk RNA-seq (Singleron)
Bulk_Singleron_in_vitro_basic_char_v06_add_samples_counts_comb.csv


title: iPSC-derived neurons, trisomy 21, Cell line C13, Library C13N161224-4W-V-1

description:
Library name: C13N161224-4W-V-1
bulk RNA-seq (Singleron)
Bulk_Singleron_in_vitro_basic_char_v06_add_samples_counts_comb.csv


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-N11


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-M23


title: iPSC-derived neurons, trisomy 21, Cell line C13, Library C13N061224-4W-V-3

description:
Library name: C13N061224-4W-V-3
bulk RNA-seq (Singleron)
Bulk_Singleron_in_vitro_basic_char_v06_add_samples_counts_comb.csv


title: iPSC-derived neurons, trisomy 21, Cell line C13, Library C13N061224-4W-V-1

description:
Library name: C13N061224-4W-V-1
bulk RNA-seq (Singleron)
Bulk_Singleron_in_vitro_basic_char_v06_add_samples_counts_comb.csv


title: iPSC-derived neurons, trisomy 21, Cell line C13, Library C13N061224-4W-V-2

description:
Library name: C13N061224-4W-V-2
bulk RNA-seq (Singleron)
Bulk_Singleron_in_vitro_basic_char_v06_add_samples_counts_comb.csv


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-M12


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-O24


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-L24


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-L23


title: Male, 10mpk, Asparagine, Rep3

city: NEW HAVEN

first: Oladimeji

last: Aladelokun

state: Connecticut

department: Environmental Health Sciences

institute: YALE UNIVERSITY

description:
Library name: 629
Column name in Male_ normalized.counts.txt: Male_10MPK_Asn_629

data_processing:
Signal intensities were converted to individual base calls during a run using the system’s Real Time Analysis (RTA) software
sample de-multiplexing and alignment to the human genome – was performed using Illumina’s CASAVA 1.8.2 software suite
Low quality reads with Phred quality score (Q) < 20 were trimmed, and adaptor contamination were removed using Trim Galore (v0.5.0)
Assembly: Trimmed reads were mapped to the human reference genome (hg38) using HISAT2 (v2.1.0)
Supplementary files format and content: tab-delimited text files include normalized counts for each sample

source_name: Tumor xenograft

growth_protocol: HCT116 cells were maintained in RPMI-1640 culture medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (Life Technologies, Carlsbad, CA, USA) and 1% penicillin/streptomycin (Life Technologies, Carlsbad, CA, USA) and 4 mM L-Glutamine (Life Technologies, Carlsbad, CA, USA). Cells were cultured at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated from tumors using the RNA isolation kit (Rneasy Mini Kit, QIAGEN, Hilden, Germany).  270 ng/ul of total RNA in 15 uL nuclease-free water was provided to Yale Centre for Genomic Analysis for construction of sequencing libraries
Libraries were prepared with equal amount of total RNA using the Total RNA TruSeq mRNA Stranded Library Prep Kit (Illumina, San Diego, CA, USA)

treatment_protocol: Mice were randomly separated into 6 groups of 5 for the tumor-specific survival experiment. HCT116 cancer cell xenograft establishment was confirmed as palpable tumors in all 30 mice. In group 1, female R2G2 mice received vehicle or control: PBS solution. Groups 2 and 3 represent female mice that were administered 1 mg/kg and 10 mg/kg asparagine respectively. In group 4, male R2G2 mice were administered PBS solution. In groups 5 and 6, male mice received 1 mg/kg and 10 mg/kg asparagine respectively

value: Tumor xenograft

value: Immortalized colon cancer

value: 10 mg/kg asparagine


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-L12


title: Male, 10mpk, Asparagine, Rep1

description:
Library name: 627
Column name in Male_ normalized.counts.txt: Male_10MPK_Asn_627


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-L11


title: Male, 1mpk, Asparagine, Rep3

description:
Library name: 624
Column name in Male_ normalized.counts.txt: Male_1MPK_Asn_624

value: 1 mg/kg asparagine


title: Male, 1mpk, Asparagine, Rep4

description:
Library name: 625
Column name in Male_ normalized.counts.txt: Male_1MPK_Asn_625


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-N23


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-K23


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-K12


title: Male, 1mpk, Asparagine, Rep2

description:
Library name: 622
Column name in Male_ normalized.counts.txt: Male_1MPK_Asn_622


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-K11


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-J24


title: Male, Vehicle, Rep3

description:
Library name: 618
Column name in Male_ normalized.counts.txt: Male_PBS_618

value: Phosphate buffered saline


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-J12


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-M11


title: Male, Vehicle, Rep4

description:
Library name: 620
Column name in Male_ normalized.counts.txt: Male_PBS_620

value: WT


title: Male, 10mpk, Asparagine, Rep4

description:
Library name: 630
Column name in Male_ normalized.counts.txt: Male_10MPK_Asn_630


title: Male, 1mpk, Asparagine, Rep1

description:
Library name: 621
Column name in Male_ normalized.counts.txt: Male_1MPK_Asn_621


title: Male, 10mpk, Asparagine, Rep2

description:
Library name: 628
Column name in Male_ normalized.counts.txt: Male_10MPK_Asn_628


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-J11


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-I23


title: Male, Vehicle, Rep1

description:
Library name: 616
Column name in Male_ normalized.counts.txt: Male_PBS_616


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-K24


title: Female, 10mpk, Asparagine, Rep4

description:
Library name: 615
Column name in Female_ normalized.counts.txt: Female_10MPK_Asn_615


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-J23


title: Female, 10mpk, Asparagine, Rep3

description:
Library name: 613
Column name in Female_ normalized.counts.txt: Female_10MPK_Asn_613


title: Male, Vehicle, Rep2

description:
Library name: 617
Column name in Male_ normalized.counts.txt: Male_PBS_617


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-I12


title: Female, 10mpk, Asparagine, Rep2

description:
Library name: 612
Column name in Female_ normalized.counts.txt: Female_10MPK_Asn_612


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-I24


title: Female, 10mpk, Asparagine, Rep1

description:
Library name: 611
Column name in Female_ normalized.counts.txt: Female_10MPK_Asn_611


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-I11


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-H24


title: Female, 1mpk, Asparagine, Rep4

description:
Library name: 610
Column name in Female_ normalized.counts.txt: Female_1MPK_Asn_610


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-H23


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-H12


title: Female, 1mpk, Asparagine, Rep3

description:
Library name: 608
Column name in Female_ normalized.counts.txt: Female_1MPK_Asn_608


title: Female, 1mpk, Asparagine, Rep1

description:
Library name: 606
Column name in Female_ normalized.counts.txt: Female_1MPK_Asn_606


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-G24


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-G23


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-G12


title: Female, Vehicle, Rep3

description:
Library name: 604
Column name in Female_ normalized.counts.txt: Female_PBS_604


title: Female, Vehicle, Rep1

description:
Library name: 601
Column name in Female_ normalized.counts.txt: Female_PBS_601


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-G11


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-F24


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-F23


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-F12


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-F11


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-E24


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-E11


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-H11


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-E23


title: HeLa, M, actD, 0 h

city: Cambridge

first: Ekaterina

last: Khalizeva

state: MA

address: 455 Main St

department: Biology

institute: Whitehead Institute

description: Library name: HeLa, M, actD, 0 h

data_processing:
poly(A) reads were trimmed using cutadapt (v4.8) with the parameters ‘--minimum-length 1 -a A{25} -A A{25}’.
Reads were then mapped to the human genome (Gencode release 25, GRCh38.p7, downloaded from the GENCODE website) using STAR (v2.7.1a; (Dobin et al, 2013) with the parameters ‘--runThreadN 24 --runMode alignReads --outFilterMultimapNmax 1 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate’
Exon mapping reads were quantified using htseq-count (v1.99.2; (Anders et al, 2015) with the parameters ‘-f bam -t exon -r pos -s reverse’.
A read cuttoff of ≥25 reads in each sample was applied for each gene.
Assembly: GRCh38.p7
Supplementary files format and content: All RNAseq processed data files are raw read counts as counted by htseq-count.

source_name: HeLa

extract_protocol:
Cells were washed in PBS and resuspended in TRIzol Reagent. All RNA isolations were performed with Phasemaker™ tubes according to the manufacturer’s protocol (Invitrogen, A33248). Total RNA was resuspended in water with 4 pg spike-in RNA (equal mixture of in vitro transcribed Fluc and Nluc) per 2 ug total RNA for experiments where spike-in RNA was used for normalization. For each sample, 500 ng total RNA was used for library prep.
For NOVASEQSP sequencing runs, libraries were prepared using the KAPAHyperRiboErase kit according to manufacturer's instructions. For AVITI sequencing runs, libraries were prepared using the Watchmaker QiaSeq FastSelect Ribodepletion kit according to manufacturer’s instructions.

value: HeLa

tag: cell cycle_stage

value: actD


title: HeLa, G1, actD, 6 h

description: Library name: HeLa, G1, actD, 6 h


title: HeLa, G1, actD, 3 h

description: Library name: HeLa, G1, actD, 3 h


title: HeLa, M, actD, 1 h

description: Library name: HeLa, M, actD, 1 h


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-E12

value: 8 weeks

value: FC


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-D24

value: M


title: HeLa, STLC, THZ1, 6 h

description: Library name: HeLa, STLC, THZ1, 6 h


title: HeLa, M, actD, 3 h

description: Library name: HeLa, M, actD, 3 h


title: HeLa, G1, actD, 1 h

description: Library name: HeLa, G1, actD, 1 h


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-D12


title: Female, 1mpk, Asparagine, Rep2

description:
Library name: 607
Column name in Female_ normalized.counts.txt: Female_1MPK_Asn_607


title: HeLa, G1, actD, 0 h

description: Library name: HeLa, G1, actD, 0 h


title: HeLa, STLC, THZ1, 2 h

description: Library name: HeLa, STLC, THZ1, 2 h


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-D23


title: HeLa, M, actD, 6 h

description: Library name: HeLa, M, actD, 6 h


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-C23


title: Female, Vehicle, Rep4

description:
Library name: 605
Column name in Female_ normalized.counts.txt: Female_PBS_605


title: HeLa, STLC, THZ1, 4 h

description: Library name: HeLa, STLC, THZ1, 4 h


title: Female, Vehicle, Rep2

description:
Library name: 602
Column name in Female_ normalized.counts.txt: Female_PBS_602


title: HeLa, RO3306, THZ1, 6 h

description: Library name: HeLa, RO3306, THZ1, 6 h


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-D11


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-C11


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-C24


title: HeLa, STLC, THZ1, 1 h

description: Library name: HeLa, STLC, THZ1, 1 h


title: HeLa, STLC, THZ1, 0 h

description: Library name: HeLa, STLC, THZ1, 0 h


title: HeLa, RO3306, THZ1, 4 h

description: Library name: HeLa, RO3306, THZ1, 4 h


title: HeLa, RO3306, THZ1, 2 h

description: Library name: HeLa, RO3306, THZ1, 2 h


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-B23


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-B11


title: HeLa, STLC, actD, 3 h, bio rep 2

description: Library name: HeLa, STLC, actD, 3 h, bio rep 2


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-B12


title: HeLa, RO3306, THZ1, 1 h

description: Library name: HeLa, RO3306, THZ1, 1 h


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-C12


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-A24


title: HeLa, RO3306, THZ1, 0 h

description: Library name: HeLa, RO3306, THZ1, 0 h


title: HeLa, STLC, actD, 6 h, bio rep 1

description: Library name: HeLa, STLC, actD, 6 h, bio rep 1


title: HeLa, STLC, actD, 6 h, bio rep 2

description: Library name: HeLa, STLC, actD, 6 h, bio rep 2


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-A12


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-B24


title: HeLa, STLC, actD, 3 h, bio rep 1

description: Library name: HeLa, STLC, actD, 3 h, bio rep 1


title: HeLa, STLC, actD, 1 h, bio rep 2

description: Library name: HeLa, STLC, actD, 1 h, bio rep 2


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-A23


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-P9


title: AMB_201013_8wk_2A_3A_2_P10-6-J1-A11


title: HeLa, STLC, actD, 0 h, bio rep 2

description: Library name: HeLa, STLC, actD, 0 h, bio rep 2


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-P22


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-P21


title: HeLa, RO3306, actD, 6 h, bio rep 2

description: Library name: HeLa, RO3306, actD, 6 h, bio rep 2


title: HeLa, STLC, actD, 0 h, bio rep 1

description: Library name: HeLa, STLC, actD, 0 h, bio rep 1


title: HeLa, RO3306, actD, 6 h, bio rep 1

description: Library name: HeLa, RO3306, actD, 6 h, bio rep 1


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-O9


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-O22


title: HeLa, RO3306, actD, 3 h, bio rep 1

description: Library name: HeLa, RO3306, actD, 3 h, bio rep 1


title: HeLa, RO3306, actD, 3 h, bio rep 2

description: Library name: HeLa, RO3306, actD, 3 h, bio rep 2


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-O10


title: HeLa, RO3306, actD, 1 h, bio rep 1

description: Library name: HeLa, RO3306, actD, 1 h, bio rep 1


title: HeLa, RO3306, actD, 1 h, bio rep 2

description: Library name: HeLa, RO3306, actD, 1 h, bio rep 2


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-N22


title: HeLa, RO3306, actD, 0 h, bio rep 1

description: Library name: HeLa, RO3306, actD, 0 h, bio rep 1


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-O21


title: HeLa, RO3306, actD, 0 h, bio rep 2

description: Library name: HeLa, RO3306, actD, 0 h, bio rep 2


title: HeLa, STLC, actD, 1 h, bio rep 1

description: Library name: HeLa, STLC, actD, 1 h, bio rep 1


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-N10


title: HeLa, STLC 24 h, bio rep 2

description: Library name: HeLa, STLC 24 h, bio rep 2


title: HeLa, STLC 6 h, bio rep 1

description: Library name: HeLa, STLC 6 h, bio rep 1


title: HeLa, STLC 24 h, bio rep 1

description: Library name: HeLa, STLC 24 h, bio rep 1


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-M9


title: HeLa, STLC 6 h, bio rep 2

description: Library name: HeLa, STLC 6 h, bio rep 2


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-M22


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-M21


title: HeLa, STLC 0 h, bio rep 2

description: Library name: HeLa, STLC 0 h, bio rep 2


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-M10


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-P10


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-L9


title: HeLa, STLC 0 h, bio rep 1

description: Library name: HeLa, STLC 0 h, bio rep 1


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-L22


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_22

city: Heidelberg

first: Tang

last: Yiheng

address: Im Neuenheimer Feld 224

department: Department of Neuropathology

country: Germany

institute: Heidelberg University Hospital

data_processing:
Space Ranger v4.0.1
Assembly: GRCh38
Supplementary files format and content: H5/HDF5 archives
Supplementary files format and content: Tar archives of processed Visium data files
Library strategy: Spatial Transcriptomics

source_name: Meningioma

extract_protocol:
Preparation of FFPE and fresh frozen samples for spatial transcriptomics followed protocols from 10X Genomics.
Samples were sequenced on an Illumina NovaSeq 6000 (FFPE) or NextSeq 500 (fresh frozen).

value: Meningioma


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-L21


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-N21


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-L10


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_19


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-K22


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_20


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-N9


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_16


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-K21


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_18


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_17


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-J9


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_21


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_14


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_15


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-J21


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_13


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-J22


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-J10


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_11


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-I9


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-I22


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_09


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-I21


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_10


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-I10


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-K10


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_07


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-K9


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-H9


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-H22


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-H21


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_05


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_02


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_03


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-H10


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_04


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-G9


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_12


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_01


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-G22


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_08


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_47 Slide 4


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-G21


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_70


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-G10


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-F22


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_47 Slide 3


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-F9


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-F21


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_47 Slide 2


title: Spatial transcriptomic profiling of meningioma sample MNG_Sample_06


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_30


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_31


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-E9


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-F10


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_03 Slide 2


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-E22


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_47 Slide 1


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-E21


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-E10


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_02 Slide 2


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-D9


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_02 Slide 1


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_01


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_45 (class mal)

library_source: transcriptomic single cell

data_processing:
Cell Ranger v4.0.0
Assembly: GRCh38
Supplementary files format and content: H5/HDF5 archives

molecule: nuclear RNA

extract_protocol:
Single nuclei were extracted from fresh frozen tissue as described by Dogan et al. (2022).
The single-nuclei transcriptomics workflow was performed using the CG000315 Rev C 10X Genomics protocol. Sequencing was performed on the Illumina Novaseq 6000 platform.


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-D22


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_29 (class int-A)


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-D10


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_26 (class ben-1)


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-C9


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_41 (class mal)


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-C21


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_40 (class ben-1)


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-C10


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_24 (class int-A)


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-B9


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-B21


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_39 (class mal)


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-B10


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-D21


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-A9


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_32 (class ben-1)


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-B22


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-A22


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_35 (class mal)


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_44 (class mal)


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-A21


title: Spatial transcriptomic profiling of meningioma sample SC_Cohort_03 Slide 1


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-A10


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_18 (class ben-1)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-P7


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_37 (class int-B)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-P8


title: AMB_201013_8wk_2A_3A_2_P10-5-L24-C22


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-P20


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-P19


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-O8


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_10 (class ben-1)


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_16 (class ben-2)


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_14 (class mal)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-O7


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_38 (class mal)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-O20


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_33 (class int-A)


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_23 (class ben-2)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-N8


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_46 (class mal)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-O19


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_34 (class int-A)


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_05 (class ben-1)


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_06 (class ben-1)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-N20


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_43 (class mal)


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_42 (class int-B)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-N7


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-N19


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_36 (class int-A)


title: Single-nuclei RNA-seq of meningioma sample SC_Cohort_11 (class ben-2)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-M8


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-M7


title: fetal brain, trisomy 21, Library B20D1B_atac, Chromatin Accessibility

description:
Library name: B20D1B_atac
10X Multiome (scRNA/ATAC-seq)

data_processing:
Raw demultiplexed sequencing data (fastq files) were mapped to the human genome (GRCh38) and quantified using cellranger-arc (v2.0.2; 10X Genomics)
Cellranger output was loaded, merged and further processed in an R environment (R v4.3.3), using the Seurat single cell analysis package v5.1.052,53 , with the Signac extension (v1.13.0). The detailed analysis pipeline can be found here: https://github.com/lattkem1/Down_Syndrome_Multiome
Assembly: GRCh38
Supplementary files format and content: Compressed cellranger-arc count matrices, features and cell barcodes
Supplementary files format and content: rda files containing the Seurat objects with labelled cell clusters and sample metadata (for complete dataset and filtered excitatory lineage cells)

source_name: fetal brain

extract_protocol:
Fresh-frozen fetal tissue from surgical terminations of pregancy from UK hospitals was collected by the "Human Developmental Biology Resource" (HDBR, https://www.hdbr.org/). 10-50 mg of fetal tissue were processed using a protocol based on dx.doi.org/10.17504/protocols.io.bvhhn336. After removal from dry ice, tissue was immediately suspended in Homogenisation Buffer (10 mM Tris-HCl pH7.4, 320 mM Sucrose, 3 mM CaCl2, 3 mM MgCl2), supplemented freshly with 0.1% NP-40, 1 mM DTT and 1 U/µl RNAse inhibitor (Protector (Sigma #3335402001), RiboLock (Thermo Fisher, PN-EO0382), or RNaseOUT (Thermo Fisher, 10777019) RNase inhibitor). The tissue was then immediately homogenised using a 1-ml dounce homogeniser and exactly after 5 min diluted with 1 volume of Homogenisation Buffer (without NP-40), filtered (30 µm mesh size) to remove large debris, and centrifuged (500g, 5 min, 4°C) to collect raw nuclei. Raw nuclei were resuspended in Homogenisation Buffer (without NP-40) and mixed with 1 volume 50% iodixanol buffer (10 mM Tris-HCl pH7.4, 3 mM CaCl2, 3 mM MgCl2, 1 mM DTT, 0.5 U/µl RNAse inhibitor). This suspension was carefully overlaid on a 29% iodixanol buffer (as above + 160 mM sucrose), and centrifuged (6000g, 30 min, 4°C). The nuclei pellet was resuspended in a Lysis Buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 1 mM DTT, 0.5 U/µl RNAse inhibitor, 0.1% Tween-20, 0.1% NP-40, 0.001% digitonin), and after exactly 2 min nuclei were diluted in 10 volumes wash buffer (lysis buffer without NP-40, digitonin), and centrifuged (500g, 5 min, 4°C) to collect the nuclei, which were then resuspended in 1x Nuclei Buffer (from the “Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle”; 10X Genomics PN-1000283/PN-1000285; supplemented with 1 mM DTT, 0.5 U/µl RNAse inhibitor).
snRNA-seq and snATAC-seq libraries were prepared using a 10X Genomics Chromium X and the “Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle” (10X Genomics PN-1000283/PN-1000285) according to manufacturer’s instructions. Libraries were sequenced using Illumina Nextseq2000 or Novaseq6000 sequencers.

value: fetal brain

tag: name

tag: library igf_id

tag: dev stage_pcw

tag: Sex

value: male

tag: library type

value: Chromatin Accessibility


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-M19

tag: strain

tag: age

tag: brain region

tag: gender


title: fetal brain, trisomy 21, Library B20D1B_gex, Gene Expression

description:
Library name: B20D1B_gex
10X Multiome (scRNA/ATAC-seq)

tag: tissue

tag: genotype

value: trisomy 21

value: Gene Expression

value: TRUE


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-M20


title: fetal brain, disomic, Library B20C2E_gex, Gene Expression

description:
Library name: B20C2E_gex
10X Multiome (scRNA/ATAC-seq)

value: disomic

tag: sample id

value: CON


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-L8


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-L7


title: fetal brain, trisomy 21, Library B18D1Q_gex, Gene Expression

description:
Library name: B18D1Q_gex
10X Multiome (scRNA/ATAC-seq)

tag: group

value: DS

value: female


title: fetal brain, trisomy 21, Library B18D2L_atac, Chromatin Accessibility

description:
Library name: B18D2L_atac
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, trisomy 21, Library B18D2L_gex, Gene Expression

description:
Library name: B18D2L_gex
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-L19


title: fetal brain, disomic, Library B20C2E_atac, Chromatin Accessibility

description:
Library name: B20C2E_atac
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-K7


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-K8


title: fetal brain, disomic, Library B18C1P_atac, Chromatin Accessibility

description:
Library name: B18C1P_atac
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, disomic, Library B18C1P_gex, Gene Expression

description:
Library name: B18C1P_gex
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-K20


title: fetal brain, trisomy 21, Library B17D2F_gex, Gene Expression, low quality/non-cortical, NOT IN FINAL ANALYSIS

description:
Library name: B17D2F_gex
10X Multiome (scRNA/ATAC-seq)

value: FALSE


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-K19


title: fetal brain, trisomy 21, Library B17D2F_atac, Chromatin Accessibility, low quality/non-cortical, NOT IN FINAL ANALYSIS

description:
Library name: B17D2F_atac
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, disomic, Library B17C1J_gex, Gene Expression

description:
Library name: B17C1J_gex
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-J8


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-J20


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-J7


title: fetal brain, disomic, Library B17C1J_atac, Chromatin Accessibility

description:
Library name: B17C1J_atac
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-J19


title: fetal brain, disomic, Library B16C1H_gex, Gene Expression

description:
Library name: B16C1H_gex
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, trisomy 21, Library B16D1L_gex, Gene Expression

description:
Library name: B16D1L_gex
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-L20


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-I7


title: fetal brain, trisomy 21, Library B15D1K_gex, Gene Expression

description:
Library name: B15D1K_gex
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-I19


title: fetal brain, disomic, Library B16C1H_atac, Chromatin Accessibility

description:
Library name: B16C1H_atac
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, trisomy 21, Library B18D1Q_atac, Chromatin Accessibility

description:
Library name: B18D1Q_atac
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, trisomy 21, Library B15D1K_atac, Chromatin Accessibility

description:
Library name: B15D1K_atac
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-I20


title: fetal brain, disomic, Library B15C1H_gex, Gene Expression, low quality/non-cortical, NOT IN FINAL ANALYSIS

description:
Library name: B15C1H_gex
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-H7


title: fetal brain, trisomy 21, Library B14D1H_gex, Gene Expression, low quality/non-cortical, NOT IN FINAL ANALYSIS

description:
Library name: B14D1H_gex
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-H19


title: fetal brain, disomic, Library B15C1H_atac, Chromatin Accessibility, low quality/non-cortical, NOT IN FINAL ANALYSIS

description:
Library name: B15C1H_atac
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, disomic, Library B14C1G_gex, Gene Expression

description:
Library name: B14C1G_gex
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-G8


title: fetal brain, disomic, Library B14C1G_atac, Chromatin Accessibility

description:
Library name: B14C1G_atac
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, trisomy 21, Library B16D1L_atac, Chromatin Accessibility

description:
Library name: B16D1L_atac
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-I8


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-G7


title: fetal brain, trisomy 21, Library B13D3G_atac, Chromatin Accessibility

description:
Library name: B13D3G_atac
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, trisomy 21, Library B13D3G_gex, Gene Expression

description:
Library name: B13D3G_gex
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-G19


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-H8


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-F20


title: fetal brain, trisomy 21, Library B12D4H_atac, Chromatin Accessibility, low quality/non-cortical, NOT IN FINAL ANALYSIS

description:
Library name: B12D4H_atac
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-F7


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-G20


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-F19


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-E7


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-E20


title: fetal brain, trisomy 21, Library B12D3C_gex, Gene Expression

description:
Library name: B12D3C_gex
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, trisomy 21, Library B12D3C_atac, Chromatin Accessibility

description:
Library name: B12D3C_atac
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, disomic, Library B12C4E_atac, Chromatin Accessibility

description:
Library name: B12C4E_atac
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, disomic, Library B12C4E_gex, Gene Expression

description:
Library name: B12C4E_gex
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-H20


title: fetal brain, trisomy 21, Library B14D1H_atac, Chromatin Accessibility, low quality/non-cortical, NOT IN FINAL ANALYSIS

description:
Library name: B14D1H_atac
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-E8


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-E19


title: fetal brain, disomic, Library B12C3B_atac, Chromatin Accessibility

description:
Library name: B12C3B_atac
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-F8


title: fetal brain, trisomy 21, Library B11D2F_gex, Gene Expression

description:
Library name: B11D2F_gex
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-D7


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-D8


title: fetal brain, trisomy 21, Library B12D4H_gex, Gene Expression, low quality/non-cortical, NOT IN FINAL ANALYSIS

description:
Library name: B12D4H_gex
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, trisomy 21, Library B11D1B_gex, Gene Expression

description:
Library name: B11D1B_gex
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-D19


title: fetal brain, disomic, Library B11C2H_gex, Gene Expression

description:
Library name: B11C2H_gex
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-D20


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-C8


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-C19


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-C7


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-C20


title: fetal brain, trisomy 21, Library B11D1B_atac, Chromatin Accessibility

description:
Library name: B11D1B_atac
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-B8


title: fetal brain, trisomy 21, Library B10D1N_atac, Chromatin Accessibility

description:
Library name: B10D1N_atac
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, disomic, Library B11C1A_gex, Gene Expression

description:
Library name: B11C1A_gex
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, disomic, Library B10C1Q_gex, Gene Expression

description:
Library name: B10C1Q_gex
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, trisomy 21, Library B10D1N_gex, Gene Expression

description:
Library name: B10D1N_gex
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-B20


title: fetal brain, disomic, Library B12C3B_gex, Gene Expression

description:
Library name: B12C3B_gex
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, disomic, Library B11C1A_atac, Chromatin Accessibility

description:
Library name: B11C1A_atac
10X Multiome (scRNA/ATAC-seq)


title: fetal brain, disomic, Library B11C2H_atac, Chromatin Accessibility

description:
Library name: B11C2H_atac
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-B19


title: fetal brain, disomic, Library B10C1Q_atac, Chromatin Accessibility

description:
Library name: B10C1Q_atac
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-B7


title: fetal brain, trisomy 21, Library B11D2F_atac, Chromatin Accessibility

description:
Library name: B11D2F_atac
10X Multiome (scRNA/ATAC-seq)


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-A7


title: neural graft, disomic, Library S388, Gene Expression

description:
Library name: S388
Singleron Celescope (snRNA-seq)

data_processing:
Raw demultiplexed sequencing data (fastq files) were mapped to the human genome (GRCh38) and quantified by Singleron using the Celescope snRNA-seq mapping software version 2.0.7
Celescope-generated count matrices were loaded, merged and further processed in an R environment (R v4.3.3), using the Seurat single cell analysis package v5.1.052,53 , with the Signac extension (v1.13.0). The detailed analysis pipeline can be found here: https://github.com/lattkem1/Down_Syndrome_Multiome
Assembly: GRCh38
Supplementary files format and content: Compressed Celescope count matrices, features and cell barcodes
Supplementary files format and content: rda files containing the Seurat objects with cells mapped to fetal cortex cell clusters, or to subsetted excitatory lineage clusters of the fetal tissue (including data from additonal cells analysed with 10X Multiome technology, excluding low quality cells and samples)

source_name: neural graft

growth_protocol: iPSCs were differentiated to cortical progenitors and injected into the brains of adult immunodeficient mice. Grafts were dissected 12-24 weeks after transplantation.

extract_protocol:
~10-50 mg of graft tissue were processed by Singleron for nuclei extraction; in some cases, grafts from multiple mice were pooled to get enough tissue for nuclei isolation.
snRNA-seq alibraries were prepared by Singleron using CeleScope scopeV3.0.1 (kit V2) technology.

value: neural graft

tag: cell line

tag: cell type

value: neural cells

tag: weeks post_transplantation


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-A8

value: 8 weeks


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-A20

value: FC


title: neural graft, trisomy 21, Library S385_386, Gene Expression, low quality, NOT IN FINAL ANALYSIS

description:
Library name: S385_386
Singleron Celescope (snRNA-seq)

tag: in final_analysis


title: AMB_201013_8wk_2A_3A_2_P10-4-D21-A19

value: M


title: neural graft, disomic, Library S387, Gene Expression

description:
Library name: S387
Singleron Celescope (snRNA-seq)

tag: name


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-P6


title: neural graft, disomic, Library S384, Gene Expression

description:
Library name: S384
Singleron Celescope (snRNA-seq)


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-P5


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-P18


title: neural graft, disomic, Library S383, Gene Expression

description:
Library name: S383
Singleron Celescope (snRNA-seq)


title: neural graft, trisomy 21, Library S382, Gene Expression

description:
Library name: S382
Singleron Celescope (snRNA-seq)


title: neural graft, trisomy 21, Library S381, Gene Expression

description:
Library name: S381
Singleron Celescope (snRNA-seq)


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-P17


title: neural graft, disomic, Library S380, Gene Expression

description:
Library name: S380
Singleron Celescope (snRNA-seq)


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-O6


title: neural graft, trisomy 21, Library S389_390, Gene Expression, low quality, NOT IN FINAL ANALYSIS

description:
Library name: S389_390
Singleron Celescope (snRNA-seq)


title: iPSC-derived neural progenitors, disomic, Cell line DS2U, Library DS2U_P8_3

description:
Library name: DS2U_P8_3
bulk RNA-seq (Singleron)

value: iPSC-derived neural progenitors

tag: protocol

value: SCZ

tag: batch


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-O17


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-N5


title: iPSC-derived neural progenitors, disomic, Cell line DS2U, Library DS2U_P8_1

description:
Library name: DS2U_P8_1
bulk RNA-seq (Singleron)

value: DN


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-O18


title: iPSC-derived neural progenitors, disomic, Cell line DS2U, Library DS2U_P8_4

description:
Library name: DS2U_P8_4
bulk RNA-seq (Singleron)


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-N18


title: iPSC-derived neural progenitors, disomic, Cell line DS2U, Library DS2U_P8_2

description:
Library name: DS2U_P8_2
bulk RNA-seq (Singleron)


title: iPSC-derived neural progenitors, disomic, Cell line DS2U, Library DS2U_NT_4

description:
Library name: DS2U_NT_4
bulk RNA-seq (Singleron)


title: iPSC-derived neural progenitors, disomic, Cell line DS2U, Library DS2U_NT_3

description:
Library name: DS2U_NT_3
bulk RNA-seq (Singleron)


title: iPSC-derived neural progenitors, disomic, Cell line DS2U, Library DS2U_NT_2

description:
Library name: DS2U_NT_2
bulk RNA-seq (Singleron)


title: iPSC-derived neural progenitors, disomic, Cell line DS2U, Library DS2U_NT_1

description:
Library name: DS2U_NT_1
bulk RNA-seq (Singleron)


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-M5


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-M18


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-M6


title: iPSC-derived neurons, disomic, Cell line DS2U, Library DS2U_D31_3

description:
Library name: DS2U_D31_3
bulk RNA-seq (Singleron)

value: iPSC-derived neurons


title: iPSC-derived neurons, disomic, Cell line DS2U, Library DS2U_D31_2

description:
Library name: DS2U_D31_2
bulk RNA-seq (Singleron)


title: iPSC-derived neurons, disomic, Cell line DS2U, Library DS2U_D31_1

description:
Library name: DS2U_D31_1
bulk RNA-seq (Singleron)


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-O5


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-N6


title: iPSC-derived neural progenitors, trisomy 21, Cell line DS1, Library DS1_P6_4

description:
Library name: DS1_P6_4
bulk RNA-seq (Singleron)

value: trisomy 21


title: neural graft, disomic, Library S379, Gene Expression

description:
Library name: S379
Singleron Celescope (snRNA-seq)

tag: Sex

value: male

value: Gene Expression


title: iPSC-derived neural progenitors, trisomy 21, Cell line DS1, Library DS1_P6_3

description:
Library name: DS1_P6_3
bulk RNA-seq (Singleron)

value: TRUE


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-L5


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-L6


title: iPSC-derived neural progenitors, trisomy 21, Cell line DS1, Library DS1_P6_2

description:
Library name: DS1_P6_2
bulk RNA-seq (Singleron)


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-L18


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-L17


title: iPSC-derived neural progenitors, trisomy 21, Cell line DS1, Library DS1_P6_1

description:
Library name: DS1_P6_1
bulk RNA-seq (Singleron)


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-K5


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-K6


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-K18


title: iPSC-derived neural progenitors, trisomy 21, Cell line DS1, Library DS1_NT_4

description:
Library name: DS1_NT_4
bulk RNA-seq (Singleron)


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-N17


title: iPSC-derived neural progenitors, trisomy 21, Cell line DS1, Library DS1_NT_2

description:
Library name: DS1_NT_2
bulk RNA-seq (Singleron)


title: iPSC-derived neural progenitors, trisomy 21, Cell line DS1, Library DS1_NT_3

description:
Library name: DS1_NT_3
bulk RNA-seq (Singleron)


title: iPSC-derived neural progenitors, trisomy 21, Cell line DS1, Library DS1_NT_1

description:
Library name: DS1_NT_1
bulk RNA-seq (Singleron)


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-J5


title: iPSC-derived neurons, trisomy 21, Cell line DS1, Library DS1_D31_3

description:
Library name: DS1_D31_3
bulk RNA-seq (Singleron)


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-K17


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-J6


title: iPSC-derived neurons, trisomy 21, Cell line DS1, Library DS1_D31_2

description:
Library name: DS1_D31_2
bulk RNA-seq (Singleron)


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-J18


title: iPSC-derived neurons, trisomy 21, Cell line DS1, Library DS1_D31_1

description:
Library name: DS1_D31_1
bulk RNA-seq (Singleron)


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-J17


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-M17


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-I6


title: iPSC-derived neural progenitors, disomic, Cell line C9, Library C9_P7_3

description:
Library name: C9_P7_3
bulk RNA-seq (Singleron)

value: disomic

value: CON


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-I5


title: iPSC-derived neural progenitors, disomic, Cell line C9, Library C9_P7_2

description:
Library name: C9_P7_2
bulk RNA-seq (Singleron)


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-I18


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-I17


title: iPSC-derived neural progenitors, disomic, Cell line C9, Library C9_P7_1

description:
Library name: C9_P7_1
bulk RNA-seq (Singleron)


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-H5


title: iPSC-derived neurons, disomic, Cell line C9, Library C9_D31_3

description:
Library name: C9_D31_3
bulk RNA-seq (Singleron)


title: iPSC-derived neurons, disomic, Cell line C9, Library C9_D31_2

description:
Library name: C9_D31_2
bulk RNA-seq (Singleron)


title: iPSC-derived neurons, disomic, Cell line C9, Library C9_D31_1

description:
Library name: C9_D31_1
bulk RNA-seq (Singleron)


title: iPSC-derived neural progenitors, trisomy 21, Cell line C13, Library C13_P7_1

description:
Library name: C13_P7_1
bulk RNA-seq (Singleron)

value: DS


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-H18


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-H17


title: iPSC-derived neural progenitors, trisomy 21, Cell line C13, Library C13_P7_3

description:
Library name: C13_P7_3
bulk RNA-seq (Singleron)


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-H6


title: iPSC-derived neural progenitors, trisomy 21, Cell line C13, Library C13_P7_2

description:
Library name: C13_P7_2
bulk RNA-seq (Singleron)


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-G18


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-G5


title: iPSC-derived neurons, trisomy 21, Cell line C13, Library C13_D31_1

description:
Library name: C13_D31_1
bulk RNA-seq (Singleron)


title: iPSC-derived neurons, trisomy 21, Cell line C13, Library C13_D31_3

description:
Library name: C13_D31_3
bulk RNA-seq (Singleron)


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-G6


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-F18


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-F6


title: AMB_201013_8wk_2A_3A_2_P10-3-P12-F5