title: 3543_OF1A_3-5-C21-O9


title: 3543_OF1A_3-5-C21-P22

status: Public on Dec 13 2023

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:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
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.
Library strategy: snmCT-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: OF1A human BA46

extract_protocol: Library prepared following protocol discribed in Luo, Chongyuan, Hanqing Liu, Fangming Xie, Ethan J. Armand, Kimberly Siletti, Trygve E. Bakken, Rongxin Fang, et al. 2019. “Single Nucleus Multi-Omics Links Human Cortical Cell Regulatory Genome Diversity to Disease Risk Variants.” bioRxiv. https://doi.org/10.1101/2019.12.11.873398. https://www.protocols.io/view/snmcat-v1-bwubpesn

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: age

tag: Sex

value: Female

tag: molecule subtype

value: nuclear RNA + genomic DNA


title: 3543_OF1A_3-5-C21-O22


title: 3543_OF1A_3-5-C21-O21


title: 3543_OF1A_3-5-C21-O10


title: 3543_OF1A_3-5-C21-I10


title: 3543_OF1A_3-5-C21-M22


title: 3543_OF1A_3-5-C21-M9


title: 3543_OF1A_3-5-C21-H9


title: 3543_OF1A_3-5-C21-M21


title: 3543_OF1A_3-5-C21-L21


title: 3543_OF1A_3-5-C21-L9


title: 3543_OF1A_3-5-C21-L22


title: 3543_OF1A_3-5-C21-L10


title: 3543_OF1A_3-5-C21-H21


title: 3543_OF1A_3-5-C21-K21


title: 3543_OF1A_3-5-C21-K22


title: 3543_OF1A_3-5-C21-H22


title: 3543_OF1A_3-5-C21-J9


title: 3543_OF1A_3-5-C21-F22


title: 3543_OF1A_3-5-C21-E9


title: 3543_OF1A_3-5-C21-G10


title: 3543_OF1A_3-5-C21-I9


title: 3543_OF1A_3-5-C21-G21


title: 3543_OF1A_3-5-C21-I21


title: 3543_OF1A_3-5-C21-E10


title: 3543_OF1A_3-5-C21-I22


title: 3543_OF1A_3-5-C21-J21


title: 3543_OF1A_3-5-C21-D10


title: 3543_OF1A_3-5-C21-D21


title: 3543_OF1A_3-5-C21-H10


title: 3543_OF1A_3-5-C21-G9


title: 3543_OF1A_3-5-C21-G22


title: 3543_OF1A_3-5-C21-F21


title: 3543_OF1A_3-5-C21-F9


title: 3543_OF1A_3-5-C21-C21


title: 3543_OF1A_3-5-C21-C10


title: 3543_OF1A_3-5-C21-F10


title: 3543_OF1A_3-5-C21-E22


title: 3543_OF1A_3-5-C21-B9


title: 3543_OF1A_3-5-C21-E21


title: 3543_OF1A_3-5-C21-A9


title: 3543_OF1A_3-5-C21-A21


title: 3543_OF1A_3-5-C21-A22


title: 3543_OF1A_3-4-C21-P7


title: 3543_OF1A_3-4-C21-O7


title: 3543_OF1A_3-4-C21-N8


title: 3543_OF1A_3-5-C21-B21


title: 3543_OF1A_3-4-C21-O20


title: 3543_OF1A_3-4-C21-N20


title: 3543_OF1A_3-5-C21-A10


title: 3543_OF1A_3-4-C21-M19


title: 3543_OF1A_3-4-C21-L8


title: 3543_OF1A_3-4-C21-M7


title: 3543_OF1A_3-4-C21-L7


title: 3543_OF1A_3-5-C21-D9


title: 3543_OF1A_3-4-C21-L20


title: 3543_OF1A_3-4-C21-L19


title: 3543_OF1A_3-4-C21-J8


title: 3543_OF1A_3-4-C21-M20


title: 3543_OF1A_3-4-C21-J7


title: 3543_OF1A_3-4-C21-J20


title: 3543_OF1A_3-4-C21-I8


title: 3543_OF1A_3-4-C21-J19


title: 3543_OF1A_3-5-C21-C9


title: 3543_OF1A_3-4-C21-I7


title: 3543_OF1A_3-4-C21-P19


title: 3543_OF1A_3-4-C21-P20


title: 3543_OF1A_3-4-C21-P8


title: 3543_OF1A_3-5-C21-B22


title: 3543_OF1A_3-4-C21-H20


title: 3543_OF1A_3-4-C21-H19


title: 3543_OF1A_3-4-C21-G8


title: 3543_OF1A_3-5-C21-D22


title: 3543_OF1A_3-4-C21-G20


title: 3543_OF1A_3-5-C21-C22


title: 3543_OF1A_3-4-C21-O19


title: 3543_OF1A_3-4-C21-N7


title: 3543_OF1A_3-4-C21-H8


title: 3543_OF1A_3-4-C21-N19


title: 3543_OF1A_3-4-C21-E7


title: 3543_OF1A_3-4-C21-D8


title: 3543_OF1A_3-4-C21-M8


title: 3543_OF1A_3-4-C21-O8


title: 3543_OF1A_3-4-C21-D20


title: 3543_OF1A_3-4-C21-K8


title: 3543_OF1A_3-4-C21-K20


title: 3543_OF1A_3-4-C21-K7


title: 3543_OF1A_3-4-C21-K19


title: 3543_OF1A_3-4-C21-C20


title: 3543_OF1A_3-4-C21-C19


title: 3543_OF1A_3-4-C21-I20


title: 3543_OF1A_3-4-C21-F8


title: 3543_OF1A_3-4-C21-G7


title: 3543_OF1A_3-4-C21-F20


title: 3543_OF1A_3-4-C21-E8


title: 3543_OF1A_3-4-C21-F19


title: 3543_OF1A_3-4-C21-I19


title: 3543_OF1A_3-4-C21-H7


title: 3543_OF1A_3-4-C21-E20


title: 3543_OF1A_3-4-C21-F7


title: 3543_OF1A_3-4-C21-A7


title: 3543_OF1A_3-4-C21-E19


title: 3543_OF1A_3-4-C21-A20


title: 3543_OF1A_3-4-C21-D7


title: 3543_OF1A_3-3-C21-O5


title: 3543_OF1A_3-4-C21-C8


title: 3543_OF1A_3-4-C21-G19


title: 3543_OF1A_3-4-C21-C7


title: 3543_OF1A_3-4-C21-B8


title: 3543_OF1A_3-4-C21-B7


title: 3543_OF1A_3-4-C21-D19


title: 3543_OF1A_3-4-C21-A8


title: 3543_OF1A_3-3-C21-O18


title: 3543_OF1A_3-4-C21-B20


title: 3543_OF1A_3-4-C21-A19


title: 3543_OF1A_3-3-C21-P18


title: 3543_OF1A_3-3-C21-P5


title: 3543_OF1A_3-4-C21-B19


title: 3543_OF1A_3-3-C21-O17


title: 3543_OF1A_3-3-C21-N6


title: 3543_OF1A_3-3-C21-P17


title: 3543_OF1A_3-3-C21-L6


title: 3543_OF1A_3-3-C21-O6


title: 3543_OF1A_3-3-C21-N5


title: 3543_OF1A_3-3-C21-N18


title: 3543_OF1A_3-3-C21-P6


title: 3543_OF1A_3-3-C21-M5


title: 3543_OF1A_3-3-C21-M18


title: 3543_OF1A_3-3-C21-M17


title: 3543_OF1A_3-3-C21-M6


title: 3543_OF1A_3-3-C21-L5


title: 3543_OF1A_3-3-C21-L18


title: 3543_OF1A_3-3-C21-K18


title: 3543_OF1A_3-3-C21-J6


title: 3543_OF1A_3-3-C21-K5


title: 3543_OF1A_3-3-C21-J5


title: 3543_OF1A_3-3-C21-J17


title: 3543_OF1A_3-3-C21-K17


title: 3543_OF1A_3-3-C21-L17


title: 3543_OF1A_3-3-C21-K6


title: 3543_OF1A_3-3-C21-I5


title: 3543_OF1A_3-3-C21-I17


title: 3543_OF1A_3-3-C21-G18


title: 3543_OF1A_3-3-C21-F18


title: 3543_OF1A_3-3-C21-F17


title: 3543_OF1A_3-3-C21-G5


title: 3543_OF1A_3-3-C21-E17


title: 3543_OF1A_3-3-C21-D6


title: 3543_OF1A_3-3-C21-J18


title: 3543_OF1A_3-3-C21-N17


title: 3543_OF1A_3-3-C21-H5


title: 3543_OF1A_3-3-C21-H6


title: 3543_OF1A_3-3-C21-H18


title: 3543_OF1A_3-3-C21-H17


title: 3543_OF1A_3-3-C21-G6


title: 3543_OF1A_3-3-C21-G17


title: 3543_OF1A_3-3-C21-F6


title: 3543_OF1A_3-3-C21-F5


title: 3543_OF1A_3-3-C21-E5


title: 3543_OF1A_3-3-C21-I6


title: 3543_OF1A_3-3-C21-C18


title: 3543_OF1A_3-3-C21-D17


title: 3543_OF1A_3-3-C21-D5


title: 3543_OF1A_3-3-C21-A5


title: 3543_OF1A_3-3-C21-B18


title: 3543_OF1A_3-3-C21-A6


title: 3543_OF1A_3-3-C21-D18


title: 3543_OF1A_3-3-C21-C17


title: 3543_OF1A_3-3-C21-A18


title: 3543_OF1A_3-3-C21-C5


title: 3543_OF1A_3-3-C21-C6


title: 3543_OF1A_3-3-C21-E6


title: 3543_OF1A_3-3-C21-B6


title: 3543_OF1A_3-3-C21-E18


title: 3543_OF1A_3-3-C21-B17


title: 3543_OF1A_3-3-C21-A17


title: 3543_OF1A_3-2-C21-M3


title: 3543_OF1A_3-2-C21-O3


title: 3543_OF1A_3-2-C21-O15


title: 3543_OF1A_3-2-C21-P4


title: 3543_OF1A_3-2-C21-N4


title: 3543_OF1A_3-2-C21-O4


title: 3543_OF1A_3-2-C21-P16


title: 3543_OF1A_3-2-C21-P15


title: 3543_OF1A_3-2-C21-O16


title: 3543_OF1A_3-2-C21-P3


title: 3543_OF1A_3-2-C21-M16


title: 3543_OF1A_3-2-C21-M15


title: 3543_OF1A_3-2-C21-L15


title: 3543_OF1A_3-2-C21-K16


title: 3543_OF1A_3-2-C21-K15


title: 3543_OF1A_3-2-C21-J4


title: 3543_OF1A_3-2-C21-J3


title: 3543_OF1A_3-2-C21-N16


title: 3543_OF1A_3-3-C21-B5


title: 3543_OF1A_3-2-C21-M4


title: 3543_OF1A_3-2-C21-N3


title: 3543_OF1A_3-2-C21-L16


title: 3543_OF1A_3-2-C21-L4


title: 3543_OF1A_3-2-C21-N15


title: 3543_OF1A_3-2-C21-K3


title: 3543_OF1A_3-2-C21-L3


title: 3543_OF1A_3-2-C21-K4


title: 3543_OF1A_3-2-C21-I15


title: 3543_OF1A_3-2-C21-I16


title: 3543_OF1A_3-2-C21-G15


title: 3543_OF1A_3-2-C21-H3


title: 3543_OF1A_3-2-C21-J15


title: 3543_OF1A_3-2-C21-H16


title: 3543_OF1A_3-2-C21-J16


title: 3543_OF1A_3-2-C21-I4


title: 3543_OF1A_3-2-C21-I3


title: 3543_OF1A_3-2-C21-H15


title: 3543_OF1A_3-2-C21-H4


title: 3543_OF1A_3-2-C21-G3


title: 3543_OF1A_3-2-C21-G16


title: 3543_OF1A_3-2-C21-F4


title: 3543_OF1A_3-2-C21-F3


title: 3543_OF1A_3-2-C21-F16


title: 3543_OF1A_3-2-C21-D4


title: 3543_OF1A_3-2-C21-E3


title: 3543_OF1A_3-2-C21-E4


title: 3543_OF1A_3-2-C21-F15


title: 3543_OF1A_3-2-C21-E15


title: 3543_OF1A_3-2-C21-C16


title: 3543_OF1A_3-2-C21-E16


title: 3543_OF1A_3-2-C21-C15


title: 3543_OF1A_3-2-C21-D16


title: 3543_OF1A_3-2-C21-D3


title: 3543_OF1A_3-2-C21-D15


title: 3543_OF1A_3-2-C21-C4


title: 3543_OF1A_3-2-C21-B4


title: 3543_OF1A_3-2-C21-G4


title: 3543_OF1A_3-1-C21-O2


title: 3543_OF1A_3-2-C21-C3


title: 3543_OF1A_3-1-C21-P13


title: 3543_OF1A_3-2-C21-B3


title: 3543_OF1A_3-1-C21-O1


title: 3543_OF1A_3-2-C21-B15


title: 3543_OF1A_3-2-C21-B16


title: 3543_OF1A_3-2-C21-A15


title: 3543_OF1A_3-2-C21-A3


title: 3543_OF1A_3-1-C21-P2


title: 3543_OF1A_3-1-C21-P1


title: 3543_OF1A_3-1-C21-N2


title: 3543_OF1A_3-1-C21-P14


title: 3543_OF1A_3-1-C21-O14


title: 3543_OF1A_3-2-C21-A16


title: 3543_OF1A_3-1-C21-M1


title: 3543_OF1A_3-1-C21-O13


title: 3543_OF1A_3-1-C21-N13


title: 3543_OF1A_3-1-C21-N14


title: 3543_OF1A_3-1-C21-L2


title: 3543_OF1A_3-1-C21-M13


title: 3543_OF1A_3-1-C21-M14


title: 3543_OF1A_3-1-C21-M2


title: 3543_OF1A_3-2-C21-A4


title: 3543_OF1A_3-1-C21-L13


title: 3543_OF1A_3-1-C21-L1


title: 3543_OF1A_3-1-C21-J14


title: 3543_OF1A_3-1-C21-N1


title: 3543_OF1A_3-1-C21-K1


title: 3543_OF1A_3-1-C21-H2


title: 3543_OF1A_3-1-C21-K13


title: 3543_OF1A_3-1-C21-K14


title: 3543_OF1A_3-1-C21-J2


title: 3543_OF1A_3-1-C21-J13


title: 3543_OF1A_3-1-C21-J1


title: 3543_OF1A_3-1-C21-L14


title: 3543_OF1A_3-1-C21-I13


title: 3543_OF1A_3-1-C21-H1


title: 3543_OF1A_3-1-C21-I2


title: 3543_OF1A_3-1-C21-G2


title: 3543_OF1A_3-1-C21-F1


title: 3543_OF1A_3-1-C21-H14


title: 3543_OF1A_3-1-C21-G14


title: 3543_OF1A_3-1-C21-I14


title: 3543_OF1A_3-1-C21-G1


title: 3543_OF1A_3-1-C21-G13


title: 3543_OF1A_3-1-C21-K2


title: 3543_OF1A_3-1-C21-F2


title: 3543_OF1A_3-1-C21-D1


title: 3543_OF1A_3-1-C21-E2


title: 3543_OF1A_3-1-C21-F13


title: 3543_OF1A_3-1-C21-E1


title: 3543_OF1A_3-1-C21-I1


title: 3543_OF1A_3-1-C21-E14


title: 3543_OF1A_3-1-C21-E13


title: 3543_OF1A_3-1-C21-C1


title: 3543_OF1A_3-1-C21-D2


title: 3543_OF1A_3-1-C21-B1


title: 3543_OF1A_3-1-C21-D14


title: 3543_OF1A_3-1-C21-H13


title: 3543_OF1A_3-1-C21-D13


title: 3543_OF1A_3-1-C21-A2


title: 3543_OF1A_3-1-C21-C2


title: 3543_OF1A_3-1-C21-C13


title: 3543_OF1A_3-1-C21-B2


title: 3543_OF1A_3-1-C21-C14


title: 3543_OF1A_3-1-C21-A1


title: 3543_OF1A_3-1-C21-A14


title: 3543_OF1A_3-1-C21-A13


title: 3543_OF1A_3-1-C21-B14


title: 3543_OF1A_3-1-C21-F14


title: 3543_OF1A_3-1-C21-B13


title: 3543_OF1A_2-6-M17-P12


title: 3543_OF1A_2-6-M17-P23


title: 3543_OF1A_2-6-M17-P11


title: 3543_OF1A_2-6-M17-N12


title: 3543_OF1A_2-6-M17-N23


title: 3543_OF1A_2-6-M17-O12


title: 3543_OF1A_2-6-M17-O23


title: 3543_OF1A_2-6-M17-O11


title: 3543_OF1A_2-6-M17-O24


title: 3543_OF1A_2-6-M17-N24


title: 3543_OF1A_2-6-M17-N11


title: 3543_OF1A_2-6-M17-M23


title: 3543_OF1A_2-6-M17-M12


title: 3543_OF1A_2-6-M17-M24


title: 3543_OF1A_2-6-M17-L24


title: 3543_OF1A_2-6-M17-M11


title: 3543_OF1A_2-6-M17-L12


title: 3543_OF1A_2-6-M17-K23


title: 3543_OF1A_2-6-M17-L11


title: 3543_OF1A_2-6-M17-K11


title: 3543_OF1A_2-6-M17-J12


title: 3543_OF1A_2-6-M17-L23


title: 3543_OF1A_2-6-M17-J24


title: 3543_OF1A_2-6-M17-P24


title: 3543_OF1A_2-6-M17-I24


title: 3543_OF1A_2-6-M17-I12


title: 3543_OF1A_2-6-M17-I23


title: 3543_OF1A_2-6-M17-I11


title: 3543_OF1A_2-6-M17-J23


title: 3543_OF1A_2-6-M17-H24


title: 3543_OF1A_2-6-M17-J11


title: 3543_OF1A_2-6-M17-G23


title: 3543_OF1A_2-6-M17-G24


title: 3543_OF1A_2-6-M17-H11


title: 3543_OF1A_2-6-M17-G12


title: 3543_OF1A_2-6-M17-H12


title: 3543_OF1A_2-6-M17-F24


title: 3543_OF1A_2-6-M17-F23


title: 3543_OF1A_2-6-M17-E24


title: 3543_OF1A_2-6-M17-K24


title: 3543_OF1A_2-6-M17-E23


title: 3543_OF1A_2-6-M17-F12


title: 3543_OF1A_2-6-M17-H23


title: 3543_OF1A_2-6-M17-G11


title: 3543_OF1A_2-6-M17-K12


title: 3543_OF1A_2-6-M17-E12


title: 3543_OF1A_2-6-M17-D12


title: 3543_OF1A_2-6-M17-E11


title: 3543_OF1A_2-6-M17-D24


title: 3543_OF1A_2-6-M17-C23


title: 3543_OF1A_2-6-M17-D11


title: 3543_OF1A_2-6-M17-C24


title: 3543_OF1A_2-6-M17-C12


title: 3543_OF1A_2-6-M17-B24


title: 3543_OF1A_2-6-M17-C11


title: 3543_OF1A_2-6-M17-B23


title: 3543_OF1A_2-6-M17-B12


title: 3543_OF1A_2-6-M17-B11


title: 3543_OF1A_2-6-M17-F11


title: 3543_OF1A_2-6-M17-A23


title: 3543_OF1A_2-6-M17-A11


title: 3543_OF1A_2-5-M17-P9


title: 3543_OF1A_2-5-M17-P22


title: 3543_OF1A_2-6-M17-A12


title: 3543_OF1A_2-5-M17-P10


title: 3543_OF1A_2-5-M17-P21


title: 3543_OF1A_2-5-M17-O22


title: 3543_OF1A_2-6-M17-D23


title: 3543_OF1A_2-5-M17-O10


title: 3543_OF1A_2-5-M17-O9


title: 3543_OF1A_2-5-M17-N9


title: 3543_OF1A_2-5-M17-O21


title: 3543_OF1A_2-5-M17-N10


title: 3543_OF1A_2-5-M17-N21


title: 3543_OF1A_2-5-M17-L9


title: 3543_OF1A_2-5-M17-L22


title: 3543_OF1A_2-5-M17-M10


title: 3543_OF1A_2-6-M17-A24


title: 3543_OF1A_2-5-M17-L21


title: 3543_OF1A_2-5-M17-L10


title: 3543_OF1A_2-5-M17-K9


title: 3543_OF1A_2-5-M17-K22


title: 3543_OF1A_2-5-M17-N22


title: 3543_OF1A_2-5-M17-M9


title: 3543_OF1A_2-5-M17-J10


title: 3543_OF1A_2-5-M17-I22


title: 3543_OF1A_2-5-M17-J21


title: 3543_OF1A_2-5-M17-I9


title: 3543_OF1A_2-5-M17-J9


title: 3543_OF1A_2-5-M17-I21


title: 3543_OF1A_2-5-M17-K21


title: 3543_OF1A_2-5-M17-I10


title: 3543_OF1A_2-5-M17-H22


title: 3543_OF1A_2-5-M17-M22


title: 3543_OF1A_2-5-M17-J22


title: 3543_OF1A_2-5-M17-H9


title: 3543_OF1A_2-5-M17-G9


title: 3543_OF1A_2-5-M17-H10


title: 3543_OF1A_2-5-M17-G21


title: 3543_OF1A_2-5-M17-F9


title: 3543_OF1A_2-5-M17-F22


title: 3543_OF1A_2-5-M17-M21


title: 3543_OF1A_2-5-M17-K10


title: 3543_OF1A_2-5-M17-G22


title: 3543_OF1A_2-5-M17-G10


title: 3543_OF1A_2-5-M17-F10


title: 3543_OF1A_2-5-M17-E10


title: 3543_OF1A_2-5-M17-F21


title: 3543_OF1A_2-5-M17-E9


title: 3543_OF1A_2-5-M17-E22


title: 3543_OF1A_2-5-M17-D9


title: 3543_OF1A_2-5-M17-H21


title: 3543_OF1A_2-5-M17-E21


title: 3543_OF1A_2-5-M17-C21


title: 3543_OF1A_2-5-M17-B22


title: 3543_OF1A_2-5-M17-D10


title: 3543_OF1A_2-5-M17-B21


title: 3543_OF1A_2-5-M17-D21


title: 3543_OF1A_2-5-M17-C22


title: 3543_OF1A_2-5-M17-C10


title: 3543_OF1A_2-5-M17-A22


title: 3543_OF1A_2-5-M17-C9


title: 3543_OF1A_2-5-M17-D22


title: 3543_OF1A_2-5-M17-A9


title: 3543_OF1A_2-5-M17-B10


title: 3543_OF1A_2-5-M17-A21


title: 3543_OF1A_2-4-M17-P8


title: 3543_OF1A_2-5-M17-A10


title: 3543_OF1A_2-4-M17-P7


title: 3543_OF1A_2-4-M17-P20


title: 3543_OF1A_2-4-M17-O7


title: 3543_OF1A_2-4-M17-P19


title: 3543_OF1A_2-4-M17-O8


title: 3543_OF1A_2-4-M17-N19


title: 3543_OF1A_2-5-M17-B9


title: 3543_OF1A_2-4-M17-N8


title: 3543_OF1A_2-4-M17-O20


title: 3543_OF1A_2-4-M17-N7


title: 3543_OF1A_2-4-M17-O19


title: 3543_OF1A_2-4-M17-M7


title: 3543_OF1A_2-4-M17-M8


title: 3543_OF1A_2-4-M17-L8


title: 3543_OF1A_2-4-M17-N20


title: 3543_OF1A_2-4-M17-L7


title: 3543_OF1A_2-4-M17-M20


title: 3543_OF1A_2-4-M17-M19


title: 3543_OF1A_2-4-M17-L19


title: 3543_OF1A_2-4-M17-K19


title: 3543_OF1A_2-4-M17-L20


title: 3543_OF1A_2-4-M17-J8


title: 3543_OF1A_2-4-M17-I7


title: 3543_OF1A_2-4-M17-I19


title: 3543_OF1A_2-4-M17-K8


title: 3543_OF1A_2-4-M17-K20


title: 3543_OF1A_2-4-M17-H8


title: 3543_OF1A_2-4-M17-J20


title: 3543_OF1A_2-4-M17-J7


title: 3543_OF1A_2-4-M17-H7


title: 3543_OF1A_2-4-M17-J19


title: 3543_OF1A_2-4-M17-I20


title: 3543_OF1A_2-4-M17-H20


title: 3543_OF1A_2-4-M17-G7


title: 3543_OF1A_2-4-M17-G8


title: 3543_OF1A_2-4-M17-K7


title: 3543_OF1A_2-4-M17-G20


title: 3543_OF1A_2-4-M17-F8


title: 3543_OF1A_2-4-M17-G19


title: 3543_OF1A_2-4-M17-F7


title: 3543_OF1A_2-4-M17-F19


title: 3543_OF1A_2-4-M17-E8


title: 3543_OF1A_2-4-M17-I8


title: 3543_OF1A_2-4-M17-D7


title: 3543_OF1A_2-4-M17-E19


title: 3543_OF1A_2-4-M17-D19


title: 3543_OF1A_2-4-M17-F20


title: 3543_OF1A_2-4-M17-E20


title: 3543_OF1A_2-4-M17-D20


title: 3543_OF1A_2-4-M17-C8


title: 3543_OF1A_2-4-M17-D8


title: 3543_OF1A_2-4-M17-C20


title: 3543_OF1A_2-4-M17-C19


title: 3543_OF1A_2-4-M17-B8


title: 3543_OF1A_2-4-M17-B20


title: 3543_OF1A_2-4-M17-B7


title: 3543_OF1A_2-4-M17-B19


title: 3543_OF1A_2-4-M17-C7


title: 3543_OF1A_2-4-M17-A8


title: 3543_OF1A_2-4-M17-H19


title: 3543_OF1A_2-4-M17-A7


title: 3543_OF1A_2-4-M17-E7


title: 3543_OF1A_2-4-M17-A20


title: 3543_OF1A_2-3-M17-P6


title: 3543_OF1A_2-4-M17-A19


title: 3543_OF1A_2-3-M17-P5


title: 3543_OF1A_2-3-M17-O5


title: 3543_OF1A_2-3-M17-O6


title: 3543_OF1A_2-3-M17-P17


title: 3543_OF1A_2-3-M17-P18


title: 3543_OF1A_2-3-M17-O17


title: 3543_OF1A_2-3-M17-N5


title: 3543_OF1A_2-3-M17-N17


title: 3543_OF1A_2-3-M17-M18


title: 3543_OF1A_2-3-M17-N6


title: 3543_OF1A_2-3-M17-N18


title: 3543_OF1A_2-3-M17-M17


title: 3543_OF1A_2-3-M17-M6


title: 3543_OF1A_2-3-M17-L6


title: 3543_OF1A_2-3-M17-L5


title: 3543_OF1A_2-3-M17-K5


title: 3543_OF1A_2-3-M17-J6


title: 3543_OF1A_2-3-M17-L17


title: 3543_OF1A_2-3-M17-L18


title: 3543_OF1A_2-3-M17-K18


title: 3543_OF1A_2-3-M17-K17


title: 3543_OF1A_2-3-M17-J5


title: 3543_OF1A_2-3-M17-O18


title: 3543_OF1A_2-3-M17-J17


title: 3543_OF1A_2-3-M17-I5


title: 3543_OF1A_2-3-M17-I6


title: 3543_OF1A_2-3-M17-I17


title: 3543_OF1A_2-3-M17-J18


title: 3543_OF1A_2-3-M17-H5


title: 3543_OF1A_2-3-M17-I18


title: 3543_OF1A_2-3-M17-H18


title: 3543_OF1A_2-3-M17-G6


title: 3543_OF1A_2-3-M17-G18


title: 3543_OF1A_2-3-M17-H6


title: 3543_OF1A_2-3-M17-K6


title: 3543_OF1A_2-3-M17-G17


title: 3543_OF1A_2-3-M17-G5


title: 3543_OF1A_2-3-M17-H17


title: 3543_OF1A_2-3-M17-F5


title: 3543_OF1A_2-3-M17-F6


title: 3543_OF1A_2-3-M17-M5


title: 3543_OF1A_2-3-M17-F17


title: 3543_OF1A_2-3-M17-D6


title: 3543_OF1A_2-3-M17-E18


title: 3543_OF1A_2-3-M17-E17


title: 3543_OF1A_2-3-M17-E6


title: 3543_OF1A_2-3-M17-D5


title: 3543_OF1A_2-3-M17-C6


title: 3543_OF1A_2-3-M17-C5


title: 3543_OF1A_2-3-M17-D18


title: 3543_OF1A_2-3-M17-C18


title: 3543_OF1A_2-3-M17-C17


title: 3543_OF1A_2-3-M17-F18


title: 3543_OF1A_2-3-M17-E5


title: 3543_OF1A_2-3-M17-B5


title: 3543_OF1A_2-3-M17-B6


title: 3543_OF1A_2-3-M17-A5


title: 3543_OF1A_2-3-M17-B17


title: 3543_OF1A_2-3-M17-A6


title: 3543_OF1A_2-3-M17-B18


title: 3543_OF1A_2-3-M17-A18


title: 3543_OF1A_2-2-M17-P4


title: 3543_OF1A_2-2-M17-O4


title: 3543_OF1A_2-3-M17-A17


title: 3543_OF1A_2-2-M17-O16


title: 3543_OF1A_2-2-M17-O3


title: 3543_OF1A_2-2-M17-P3


title: 3543_OF1A_2-2-M17-P16


title: 3543_OF1A_2-3-M17-D17


title: 3543_OF1A_2-2-M17-O15


title: 3543_OF1A_2-2-M17-N16


title: 3543_OF1A_2-2-M17-N4


title: 3543_OF1A_2-2-M17-M16


title: 3543_OF1A_2-2-M17-M4


title: 3543_OF1A_2-2-M17-M3


title: 3543_OF1A_2-2-M17-L4


title: 3543_OF1A_2-2-M17-N15


title: 3543_OF1A_2-2-M17-M15


title: 3543_OF1A_2-2-M17-L3


title: 3543_OF1A_2-2-M17-L15


title: 3543_OF1A_2-2-M17-L16


title: 3543_OF1A_2-2-M17-P15


title: 3543_OF1A_2-2-M17-K3


title: 3543_OF1A_2-2-M17-K16


title: 3543_OF1A_2-2-M17-K15


title: 3543_OF1A_2-2-M17-I4


title: 3543_OF1A_2-2-M17-J4


title: 3543_OF1A_2-2-M17-I16


title: 3543_OF1A_2-2-M17-I3


title: 3543_OF1A_2-2-M17-J15


title: 3543_OF1A_2-2-M17-J16


title: 3543_OF1A_2-2-M17-I15


title: 3543_OF1A_2-2-M17-H3


title: 3543_OF1A_2-2-M17-H16


title: 3543_OF1A_2-2-M17-N3


title: 3543_OF1A_2-2-M17-G4


title: 3543_OF1A_2-2-M17-G3


title: 3543_OF1A_2-2-M17-G16


title: 3543_OF1A_2-2-M17-H4


title: 3543_OF1A_2-2-M17-G15


title: 3543_OF1A_2-2-M17-F3


title: 3543_OF1A_2-2-M17-E4


title: 3543_OF1A_2-2-M17-K4


title: 3543_OF1A_2-2-M17-H15


title: 3543_OF1A_2-2-M17-F16


title: 3543_OF1A_2-2-M17-E3


title: 3543_OF1A_2-2-M17-J3


title: 3543_OF1A_2-2-M17-D4


title: 3543_OF1A_2-2-M17-E15


title: 3543_OF1A_2-2-M17-E16


title: 3543_OF1A_2-2-M17-D3


title: 3543_OF1A_2-2-M17-C16


title: 3543_OF1A_2-2-M17-C4


title: 3543_OF1A_2-2-M17-C3


title: 3543_OF1A_2-2-M17-D16


title: 3543_OF1A_2-2-M17-D15


title: 3543_OF1A_2-2-M17-C15


title: 3543_OF1A_2-2-M17-B16


title: 3543_OF1A_2-2-M17-B15


title: 3543_OF1A_2-2-M17-F4


title: 3543_OF1A_2-2-M17-A4


title: 3543_OF1A_2-2-M17-F15


title: 3543_OF1A_2-2-M17-A16


title: 3543_OF1A_2-2-M17-A3


title: 3543_OF1A_2-2-M17-A15


title: 3543_OF1A_2-1-M17-P14


title: 3543_OF1A_2-1-M17-P1


title: 3543_OF1A_2-1-M17-P13


title: 3543_OF1A_2-1-M17-P2


title: 3543_OF1A_2-1-M17-O2


title: 3543_OF1A_2-1-M17-O1


title: 3543_OF1A_2-1-M17-O13


title: 3543_OF1A_2-1-M17-O14


title: 3543_OF1A_2-1-M17-N2


title: 3543_OF1A_2-1-M17-N1


title: 3543_OF1A_2-1-M17-M2


title: 3543_OF1A_2-1-M17-N14


title: 3543_OF1A_2-2-M17-B3


title: 3543_OF1A_2-1-M17-N13


title: 3543_OF1A_2-2-M17-B4


title: 3543_OF1A_2-1-M17-M13


title: 3543_OF1A_2-1-M17-L1


title: 3543_OF1A_2-1-M17-M1


title: 3543_OF1A_2-1-M17-L14


title: 3543_OF1A_2-1-M17-L13


title: 3543_OF1A_2-1-M17-K2


title: 3543_OF1A_2-1-M17-M14


title: 3543_OF1A_2-1-M17-K1


title: 3543_OF1A_2-1-M17-K14


title: 3543_OF1A_2-1-M17-K13


title: 3543_OF1A_2-1-M17-J1


title: 3543_OF1A_2-1-M17-J2


title: 3543_OF1A_2-1-M17-J14


title: 3543_OF1A_2-1-M17-I1


title: 3543_OF1A_2-1-M17-I13


title: 3543_OF1A_2-1-M17-J13


title: 3543_OF1A_2-1-M17-I2


title: 3543_OF1A_2-1-M17-H2


title: 3543_OF1A_2-1-M17-H1


title: 3543_OF1A_2-1-M17-H14


title: 3543_OF1A_2-1-M17-H13


title: 3543_OF1A_2-1-M17-L2


title: 3543_OF1A_2-1-M17-G1


title: 3543_OF1A_2-1-M17-G2


title: 3543_OF1A_2-1-M17-F1


title: 3543_OF1A_2-1-M17-G14


title: 3543_OF1A_2-1-M17-F2


title: 3543_OF1A_2-1-M17-F13


title: 3543_OF1A_2-1-M17-G13


title: 3543_OF1A_2-1-M17-F14


title: 3543_OF1A_2-1-M17-E1


title: 3543_OF1A_2-1-M17-E14


title: 3543_OF1A_2-1-M17-E2


title: 3543_OF1A_2-1-M17-D2


title: 3543_OF1A_2-1-M17-D14


title: 3543_OF1A_2-1-M17-D13


title: 3543_OF1A_2-1-M17-C1


title: 3543_OF1A_2-1-M17-D1


title: 3543_OF1A_2-1-M17-I14


title: 3543_OF1A_2-1-M17-C14


title: 3543_OF1A_2-1-M17-C13


title: 3543_OF1A_2-1-M17-B1


title: 3543_OF1A_2-1-M17-A2


title: 3543_OF1A_2-1-M17-A1


title: 3543_OF1A_2-1-M17-B14


title: 3543_OF1A_2-1-M17-B13


title: 3543_OF1A_2-1-M17-A14


title: 3543_OF1A_2-1-M17-A13


title: 3543_OF1A_1-6-K15-P24


title: 3543_OF1A_2-1-M17-E13


title: 3543_OF1A_1-6-K15-P23


title: 3543_OF1A_1-6-K15-P12


title: 3543_OF1A_1-6-K15-O23


title: 3543_OF1A_1-6-K15-O24


title: 3543_OF1A_1-6-K15-P11


title: 3543_OF1A_1-6-K15-O12


title: 3543_OF1A_1-6-K15-N23


title: 3543_OF1A_1-6-K15-N11


title: 3543_OF1A_1-6-K15-M24


title: 3543_OF1A_1-6-K15-O11


title: 3543_OF1A_2-1-M17-C2


title: 3543_OF1A_1-6-K15-M23


title: 3543_OF1A_2-1-M17-B2


title: 3543_OF1A_1-6-K15-N24


title: 3543_OF1A_1-6-K15-M11


title: 3543_OF1A_1-6-K15-L24


title: 3543_OF1A_1-6-K15-M12


title: EV_ROM_BRD4_spikein

city: New York

first: Dimitris

last: Karagiannis

state: NY

institute: Columbia University

data_processing:
CUT&Tag reads of KP cell samples were mapped to the mouse genome assembly mm10 using Bowtie2 (v2.3.5.1, parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700). For H4ac spikein samples, reads werealso mapped to the Drosophila genome (Dmel_A4_1.0). For BRD4 spikein samples, reads also were mapped to the human genome (GRCh38).
Potential PCR duplicates were removed by the function "MarkDuplicates" (parameter: REMOVE_DUPLICATES=true) of Picard (v2.24.2). Genomic enrichments of CUT&Tag signals were generated using deeptools (v3.3.2, parameters bamCoverage --normalizeUsing CPM --binSize 25 --smoothLength 100) and visualized using IGV.
Peaks were called using MACS2 (parameters: --f BAMPE -g mm --broad). Consensuses of H3K27ac, H4ac and BRD4 peaks across conditions were generated by the ‘cat’ function (Linux) and ‘sort’ and ‘merge’ functions of bedtools (v2.27.1).
The read counts of H3K27ac, H4ac and BRD4 CUT&Tag data in genomic elements were measured by featureCounts (v2.0.0). Differential analysis was performed using DEseq2(v1.32.0).
Peak annotation was done using ChIPseeker56(v1.28.3). Heatmaps were generated using deeptools (v3.3.2) functions computeMatrix and plotHeatmap.
Assembly: mm10
Supplementary files format and content: bigWig for genomic distribution analysis, txt for spike-in scale factor determination

organism: Mus musculus

source_name: cell line

growth_protocol: KP cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics (P/S) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
CUT&Tag was performed as described previously23, with an additional step of light fixation to better preserve histone acetylation/TF binding. In brief, 1 × 105 cells were lightly fixed with 0.1% paraformaldehyde 5’, neutralized by Glycine 125mM, and washed once with 1 ml of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine (Sigma-Aldrich), 1× Protease inhibitor cocktail (Roche)). Concanavalin A-coated magnetic beads (Bangs Laboratories) were washed twice with binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM MnCl2, 1 mM CaCl2). 10 µl/sample of beads were added to cells in 400ul of wash buffer and incubated at room temperature for 15 min. Beads-bound cells were resuspended in 100 µl of antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.06% Digitonin (Sigma-Aldrich), 2 mM EDTA, 0.1% BSA, 1× Protease inhibitor cocktail and incubated with indicated antibodies (Supplementary Table 3) or normal rabbit IgG (Cell Signaling) at 4 degrees overnight on nutator. After being washed once with Dig-wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.05% Digitonin, 1× Protease inhibitor cocktail), beads-bound cells were incubated with 1 µl Guinea pig anti-rabbit secondary antibody (Antibodies Online ABIN101961) and 2 µl  Hyperactive pA-Tn5 Transposase adapter complex in 100 µl Dig-300 buffer (20 mM HEPES•NaOH, pH 7.5, 0.5 mM Spermidine, 1× Protease inhibitor cocktail, 300 mM NaCl, 0.01% Digitonin) at room temperature for 1 h. Cells were washed three times with Dig-300 buffer to remove unbound antibody and Tn5 and then resuspended in 300 µl of tagmentation buffer (10 mM MgCl2 in Dig-300 buffer) and incubated at 37 °C for 1 h. 10 µl of 0.5 M EDTA, 3 µl of 10% SDS and 5 µl of 10 mg/ml Proteinase K were added to each sample and incubated at 50 °C for 1 h to terminate tagmentation. DNA was purified using chloroform isoamyl alcohol (Sigma Aldrich) and eluted with 25 µl ddH2O. For H3K27ac, 2ul of SNAP-ChIP K-AcylStat panel nucleosomes (EpiCypher) was added as spike-in control at the primary antibody incubation step. For H4ac, 5000 S2 Drosophila cells were added at the cell-bead binding step. For BRD4, 10000 K562 cells were added at the cell-bead binding step.
For library amplification, 21 µl of DNA was mixed with 2µL i5 unique index primer (10 µM), 2 µL i7 unique index primer (10 µM) and 25 µL NEBNext High-Fidelity 2X PCR Master Mix (NEB) and subjected to the following PCR program: 72℃, 5 min; 98℃, 30 sec; 13 cycles of 98℃, 10 sec and 63℃, 10 sec; 72℃, 1 min and hold at 10℃. To purify the PCR products, 1.1× volumes of pre-warmed Ampure XP beads (Beckman Coulter) were added and incubated at room temperature for 10 min. Libraries were washed twice with 80% ethanol and eluted in 20 µl of 10 mM Tris-HCl, pH 8.  Libraries were sequenced on an NextSeq 550 platform (Illumina, 75 cycles High Output Kit v2.0) and 75-bp paired-end reads were generated. To determine global level differences in histone acetylation signal we used spike-in controls.  Files resulting from 4 sequencing lanes were concatenated into a single file for each condition.

treatment_protocol: 200k KP cells were plated in 6-well plates in RPMI supplemented with 10% FBS and P/S. The next day cells were treated with DMSO or 5nM Romidepsin in RPMI for 16h. 3 biological replicates per condition are included

tag: tissue

value: cell line

tag: cell line

tag: cell type

value: LUAD

tag: genotype

value: Empty Vector

tag: treatment

value: ROM


title: NRF2_HDAC2

value: NRF2 OE

value: no treatment


title: 3543_OF1A_1-6-K15-L23


title: EV_DMSO_K27ac_newrep2

value: DMSO


title: EV_DMSO_BRD4_spikein


title: svLEC_tgfb1_4

city: Stockholm

first: Anastasios

middle: Erik

last: Damdimopoulos

state: Huddinge

address: Hälsovägen 7c

department: Department of Biosciences and Nutrition

country: Sweden

institute: Karolinska Institute

library_source: transcriptomic

data_processing:
Bcl files were converted and demultiplexed to fastq using the bcl2fastq (v2.20.0.422) program
STAR (2.7.3a) was used to index the mouse genome (GRCm38/mm10) and then map the fastq files.
featureCounts (v1.5.1) was used to count mapped reads in annotated exons using gene annotations from Ensembl.
Assembly: Mouse reference genome (GRCm38/mm10).
Supplementary files format and content: svLEC_counts.txt

molecule: polyA RNA

source_name: svLEC

growth_protocol: Mouse lymphatic endothelial cells (SV-LEC) (kindly provided by Dr Jonathan S. Alexander, Louisiana State University Health Sciences Center, Shreveport, Louisiana) were cultured in DMEM with high glucose supplemented with 10% FBS and 1% penicillin–streptomycin, and cultured in 37°C and 5% humidiﬁed CO2 incubator.

extract_protocol:
Total RNA was extracted from quadruplicate samples of svLEC cells that were either left untreated or treated for 72 h with 10 ng/ml TGFB1 (R&D Systems, Abingdon, UK), using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer´s protocol.
Libraries were prepared using TruSeq Stranded mRNA kit (Illumina) and sequenced on the Illumina Nextseq 550 platform, at single end mode and generating 75 bp reads.

treatment_protocol: Cell were either left untreated or treated for 72 h with 10 ng/ml TGFB1 (R&D Systems, Abingdon, UK)

value: svLEC

value: Lymphatic endothelial cell line isolated from mesenteric adventitial tissue

value: TGF-b1, 10ng/ml, 72 h


title: svLEC_tgfb1_3


title: svLEC_tgfb1_2


title: 3543_OF1A_1-6-K15-N12


title: 3543_OF1A_1-6-K15-K23


title: 3543_OF1A_1-6-K15-K24


title: 3543_OF1A_1-6-K15-K11


title: 3543_OF1A_1-6-K15-K12


title: svLEC_tgfb1_1


title: 3543_OF1A_1-6-K15-J23


title: svLEC_ctrl_2

value: Nontreated


title: 3543_OF1A_1-6-K15-J24


title: 3543_OF1A_1-6-K15-J12


title: 3543_OF1A_1-6-K15-J11


title: svLEC_ctrl_1


title: 3543_OF1A_1-6-K15-I24


title: HEK293T cells, UBR5KO, 6h IFNbeta

city: Farmington

first: Duomeng

last: Yang

address: 263 Farmington Avenue

institute: Uconn health

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using fastp v.0.23.1
UMI-based deduplication was performed using fastp v.0.23.1. Trimmed and deduplicated reads were then mapped to human reference assembly GRCh38 using the STAR aligner v.2.5.2b to generate BAM files.
Gene hit counts were calculated by using featureCounts from the Subread package
DESeq2 was used to perform differential expression analysis between the defined groups of samples.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes deseq2 result and raw counts for each sample

molecule: total RNA

extract_protocol:
RNA isolation from cells were performed using an RNA purification kit (Invitrogen, Cat# 12183018A). 1.5ug of total RNA was used for RNAseq libraries
RNA libraries for RNA-seq were prepared by GENWIZ with their own protocol and mRNA sequencing with Twist UMI system of their own.

value: Human embryonic kidney cells

value: IFN-beta


title: EV_ROM_K27ac_newrep2


title: 3543_OF1A_1-6-K15-L11


title: HEK293T cells, WT, 6h IFNbeta

value: WT


title: EV_HDAC2


title: 3543_OF1A_1-6-K15-I23

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_1-6-K15-L12

value: Female


title: 3543_OF1A_1-6-K15-I11

value: nuclear RNA + genomic DNA


title: HEK293T cells, TRIM28KO, 6h IFNbeta


title: HEK293T cells, TRIM28KO, 12h poly(I:C)

value: poly (I:C)


title: HEK293T cells, UBR5KO, 12h poly(I:C)


title: 3543_OF1A_1-6-K15-I12


title: svLEC_ctrl_4


title: svLEC_ctrl_3


title: 3543_OF1A_1-6-K15-H24


title: HEK293T cells, WT, 12h poly(I:C)


title: 3543_OF1A_1-6-K15-H23


title: HEK293T cells, UBR5KO, 0h

value: untreatment


title: 3543_OF1A_1-6-K15-H12


title: HEK293T cells, WT, 0h


title: Female naïve ESCs (UCLA1) R5

city: Los Angeles

first: Kathrin

last: Plath

institute: UCLA

description: 5iLAF-cultured, derived from the primed state, subclone 9, passage 8, replicate 1

data_processing:
Trim: RNA sequencing reads were trimmed using trim_galore (v0.4.1) with default parameters
Align: HISAT2 (v2.2.0) with default parameters was used to align RNA reads
Filter: Samtools (v1.9) was used to remove reads with mapping quality less than 30
Counts: HTSeq (v.0.6.1p1) with the following parameters “--format=bam --order=pos --stranded=reverse--minaqual=0 --type=exon --mode=union –idattr=gene_name" was used to calculate read counts overlapping with genes
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: All cells except HNES lines were cultured in 5iLAF naïve ESC medium (1:1 mixture of DMEM/F12 and Neurobasal supplemented with N2, B27, penicillin/streptomycin, nonessential amino acids, GlutaMAX, 0.5% KSR, 0.1mM β-mercaptoethanol, 50ug/ml bovine serum albumin, 20ng/ml rhLIF, 20ng/ml Activin A, 8ng/ml FGF2, 1uM MEK inhibitor PD0325901 0.5uM B-Raf inhibitor SB590885, 1uM GSK3-β inhibitor IM-12, 1uM Src inhibitor WH-4-023, and 10uM ROCK inhibitor Y-27632) and were cultured either in 5% CO2, 5% O2 (Hypoxia) at 37C or in 5% CO2 and atmospheric oxygen level (Normoxia) at 37C. HNES1 and HNES3 were cultured in naive ESC medium consisting of (1:1 mixture of DMEM/F12 and Neurobasal supplemented with N2, B27, penicillin/streptomycin, nonessential amino acids, GlutaMAX, 0.5% KSR, 0.1mM β-mercaptoethanol, 50ug/ml bovine serum albumin, 20ng/ml rhLIF, 2uM XAV939, 2uM Go6983, 1uM MEK inhibitor PD0325901, and 10uM ROCK inhibitor Y-27632) and were cultured in 5% CO2, 5% O2 at 37C)

extract_protocol:
RNA was isolated using Qiagen RNAeasy kit (#74104) according to manufacturer’s instructions
Libraries were prepared with the TruSeq Stranded mRNA Library Prep Kit (Illumina 20020594) according to manufacturer’s instructions. Library quality was assessed by TapeStation (Agilent) and subsequently quantified using the Qubit dsDNA High-Sensitivity Kit (Life Technologies)

treatment_protocol: Cells were washed with 1xPBS and dissociated with accutase for 5 minutes at 37C. Afterwards cells were resuspended in MEF media and span down at 1000 rpm for 5 minutes. Cell pallet was washed once with PBS+0.04% BSA and after 5 minute spin cell pallet was resuspended in Trizol reagent (Life Technologies #15596018) for RNA isolation

value: naive hESCs

tag: library strategy

value: RNA-seq

tag: origin

tag: culture condition

value: Normoxia


title: 3543_OF1A_1-6-K15-G24


title: Female naïve ESCs (UCLA1) R2

description: 5iLAF-cultured, derived from the primed state, subclone 12, passage 30, replicate 2


title: 3543_OF1A_1-6-K15-G23


title: Early female naïve (UCLA1 pre XIST) R2

description: 5iLAF-cultured, derived from the primed state, pre-XIST, subclone 4, passage 6, replicate 2


title: 3543_OF1A_1-6-K15-G12


title: 3543_OF1A_1-6-K15-G11


title: Early female naïve (UCLA1 pre XIST) R1

description: 5iLAF-cultured, derived from the primed state, pre-XIST, subclone 4, passage 6, replicate 1


title: eat-2(ad465);mxl-2(tm1516), pha-4 RNAi, adult day 2, replicate 3

city: Rochester

first: Andrew

middle: V

last: Samuelson

address: 601 Elmwood Ave

department: Biomedical Genetics

institute: University of Rochester Medical Center

description:
EAT-2_MXL-2_PHA-4_57
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt

data_processing:
Quality of the raw fastq files was summarized with FastQC (Andrews 2010) and reads were trimmed and filtered with Trimmomatic (Bolger et al. 2014). After filtering out low-quality reads, an average of 30.2 million reads per sample remained.
Samples were aligned to the C. elegans genome assembly WBcel235 with STAR 2.4.2a (Dobin et al. 2013) using gene annotation from Ensembl (version 82). An average of 94.7% of reads per sample were uniquely mapped to the genome.
Alignments were used as input to RSEM (version 1.2.23) for transcript-level quantification (Li and Dewey 2011) and featureCounts (version 1.4.6-p5) for gene-level counts (Liao et al. 2014). Ambiguous or multi-mapping reads, comprising an average of approximately 5% of the reads per sample, were not included in the gene-level count results.
Gene identifiers were updated from the Ensembl annotation used for mapping (version 82) to version 106 for further analysis. Genes with little evidence of expression were removed prior to analysis of the count-based data by filtering out genes with fewer than 10 reads in every sample. Removing the unexpressed genes left 17,907 genes across five gene types considered (16,883 protein coding, 794 pseudogenes, 136 ncRNA, 87 lincRNA, and 7 snRNA).
Assembly: C elegans WS235
Supplementary files format and content: Raw counts from FeatureCounts (Liao et al. Bioinformatics 30.7 (2014): 923-930.), filtered for genes with evidence of expression (counts ≥ 10 in at least one sample), and for genes with expected poly-adenylation. 17907 genes in total passed the filter criteria.
Supplementary files format and content: TPM (Transcripts Per Million) filtered for genes with evidence of expression (based on raw counts ≥ 10 in at least one sample), and for genes with expected poly-adenylation. 17907 genes in total passed the filter criteria. TPM calculated with RSEM (Li, Bo, and Colin N. Dewey. BMC bioinformatics 12.1 (2011): 1-16.)

organism: Caenorhabditis elegans

source_name: whole animal, hermaphrodites

growth_protocol: 10 cm RNAi agar plates were seeded with 1 mL of 20x concentrated bacteria from an overnight culture. Plates were allowed to dry for 1-2 days at room temperature, also providing time for the induction of dsRNA production before adding animals. Approximately 3,000 L1 animals were then added, split across multiple plates to prevent starvation and overcrowding, and kept at 16 °C until the L4 stage. When animals reached L4, 600 µL of 4 mg/mL 5-fluorodeoxyuridine (FUdR) was added to each plate to prevent production of progeny, and the plates were transferred to 20 °C (“day 0”). Developmental stage was assessed separately for each strain to account for shifts in developmental timing.

extract_protocol:
When animals reached day 2 of adulthood, they were washed off and collected from the plates in M9 buffer, followed by two washes in M9, and a final wash with DEPC-treated RNase-free water.  Approximately two times the volume of the animal pellet of TRIzol® reagent was added to each animal preparation, followed by brief mixing and freezing overnight at -80 °C. Tubes were then allowed to partially thaw, and were vortexed for five minutes to assist with disrupting the cuticle. Each sample was transferred to a new tube, and 200 µL of chloroform per 1 mL of TRIzol was added to each tube, followed by vortexing for 20 seconds, and the tubes were allowed to settle at room temperature for 10 minutes. The supernatants were transferred to new tubes, and an equal amount of 100% ethanol was added and mixed before proceeding to column purification with the Qiagen RNAeasy Mini kit according the manufacturer’s instructions. Samples were eluted with 30 – 50 µL of DEPC-treated water, and checked for initial concentration and quality with a Nanodrop ND-1000 spectrophotometer.
Isolated RNA was provided to the University of Rochester Genomics Research Center for library preparation and sequencing. Prior to library preparation, RNA integrity of all samples was confirmed on an Agilent 2100 Bioanalyzer. Libraries for sequencing were prepared with the Illumina TruSeq Stranded mRNA kit, according to the manufacturer’s instructions. Quality of the resulting libraries was checked again with a Bioanalyzer prior to sequencing to ensure integrity.

tag: culture temperature

value: 16 °C until L4, then transferred to 20 °C

value: Adult D2

value: whole animal

tag: RNAi

tag: food source

value: HT115(DE3) E. coli


title: 3543_OF1A_1-6-K15-F24


title: eat-2(ad465);mxl-2(tm1516), pha-4 RNAi, adult day 2, replicate 2

description:
EAT-2_MXL-2_PHA-4_56
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: Female naïve ESCs (UCLA1) R1

description: 5iLAF-cultured, derived from the primed state, subclone 12, passage 8, replicate 1


title: 3543_OF1A_1-6-K15-F12


title: 3543_OF1A_1-6-K15-F11


title: eat-2(ad465);mxl-2(tm1516), pha-4 RNAi, adult day 2, replicate 1

description:
EAT-2_MXL-2_PHA-4_55
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: eat-2(ad465);mxl-2(tm1516), daf-16 RNAi, adult day 2, replicate 2

description:
EAT-2_MXL-2_DAF-16_53
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: 3543_OF1A_1-6-K15-F23


title: 3543_OF1A_1-6-K15-E24


title: 3543_OF1A_1-6-K15-E23


title: eat-2(ad465);mxl-2(tm1516), daf-16 RNAi, adult day 2, replicate 1

description:
EAT-2_MXL-2_DAF-16_52
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: 3543_OF1A_1-6-K15-H11


title: eat-2(ad465);mxl-2(tm1516), daf-16 RNAi, adult day 2, replicate 3

description:
EAT-2_MXL-2_DAF-16_54
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: eat-2(ad465);mxl-2(tm1516), EV RNAi, adult day 2, replicate 3

description:
EAT-2_MXL-2_EV_51
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt

value: empty vector (L4440)


title: eat-2(ad465);mxl-2(tm1516), EV RNAi, adult day 2, replicate 2

description:
EAT-2_MXL-2_EV_50
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: 3543_OF1A_1-6-K15-E11


title: 3543_OF1A_1-6-K15-E12


title: eat-2(ad465), pha-4 RNAi, adult day 2, replicate 2

description:
EAT-2_PHA-4_27
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: eat-2(ad465), pha-4 RNAi, adult day 2, replicate 1

description:
EAT-2_PHA-4_26
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: eat-2(ad465);mxl-2(tm1516), EV RNAi, adult day 2, replicate 1

description:
EAT-2_MXL-2_EV_49
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: 3543_OF1A_1-6-K15-D12


title: 3543_OF1A_1-6-K15-D23


title: 3543_OF1A_1-6-K15-D24


title: eat-2(ad465), daf-16 RNAi, adult day 2, replicate 1

description:
EAT-2_DAF-16_23
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: eat-2(ad465), EV RNAi, adult day 2, replicate 2

description:
EAT-2_EV_21
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: 3543_OF1A_1-6-K15-C24


title: 3543_OF1A_1-6-K15-C12


title: 3543_OF1A_1-6-K15-C23


title: 3543_OF1A_1-6-K15-C11


title: 3543_OF1A_1-6-K15-B24


title: eat-2(ad465), daf-16 RNAi, adult day 2, replicate 2

description:
EAT-2_DAF-16_24
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: eat-2(ad465), EV RNAi, adult day 2, replicate 1

description:
EAT-2_EV_19
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: 3543_OF1A_1-6-K15-B23


title: 3543_OF1A_1-6-K15-B12


title: mxl-2(tm1516), pha-4 RNAi, adult day 2, replicate 1

description:
MXL-2_PHA-4_16
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: mxl-2(tm1516), pha-4 RNAi, adult day 2, replicate 2

description:
MXL-2_PHA-4_17
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: mxl-2(tm1516), daf-16 RNAi, adult day 2, replicate 3

description:
MXL-2_DAF-16_15
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: 3543_OF1A_1-6-K15-B11


title: 3543_OF1A_1-6-K15-A24


title: mxl-2(tm1516), daf-16 RNAi, adult day 2, replicate 2

description:
MXL-2_DAF-16_14
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: mxl-2(tm1516), EV RNAi, adult day 2, replicate 3

description:
MXL-2_EV_12
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: mxl-2(tm1516), EV RNAi, adult day 2, replicate 2

description:
MXL-2_EV_11
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: 3543_OF1A_1-6-K15-A23


title: 3543_OF1A_1-6-K15-A12


title: 3543_OF1A_1-6-K15-A11


title: 3543_OF1A_1-6-K15-D11


title: 3543_OF1A_1-5-K15-P9


title: mxl-2(tm1516), EV RNAi, adult day 2, replicate 1

description:
MXL-2_EV_10
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: N2 (WT), pha-4 RNAi, adult day 2, replicate 3

description:
N2_PHA-4_9
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: mxl-2(tm1516), pha-4 RNAi, adult day 2, replicate 3

description:
MXL-2_PHA-4_18
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: 3543_OF1A_1-5-K15-P22


title: 3543_OF1A_1-5-K15-P21


title: 3543_OF1A_1-5-K15-P10


title: N2 (WT), pha-4 RNAi, adult day 2, replicate 1

description:
N2_PHA-4_7
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: N2 (WT), daf-16 RNAi, adult day 2, replicate 3

description:
N2_DAF-16_6
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: 3543_OF1A_1-5-K15-O9


title: 3543_OF1A_1-5-K15-O22


title: mxl-2(tm1516), daf-16 RNAi, adult day 2, replicate 1

description:
MXL-2_DAF-16_13
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: 3543_OF1A_1-5-K15-O21


title: N2 (WT), EV RNAi, adult day 2, replicate 3

description:
N2_EV_3
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: N2 (WT), daf-16 RNAi, adult day 2, replicate 2

description:
N2_DAF-16_5
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: 3543_OF1A_1-5-K15-O10


title: N2 (WT), daf-16 RNAi, adult day 2, replicate 1

description:
N2_DAF-16_4
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: N2 (WT), EV RNAi, adult day 2, replicate 1

description:
N2_EV_1
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: 3543_OF1A_1-5-K15-N21


title: 3543_OF1A_1-5-K15-N22


title: 3543_OF1A_1-5-K15-N9


title: N2 (WT), pha-4 RNAi, adult day 2, replicate 2

description:
N2_PHA-4_8
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: 3543_OF1A_1-5-K15-M22


title: 3543_OF1A_1-5-K15-M9


title: 3543_OF1A_1-5-K15-N10


title: Sfp1_wt_biol_rep_1

city: Burjassot

first: Antonio

last: Jordan

state: Valencia

address: Doctor Moliner 50

country: Spain

institute: Universitat de Valencia

data_processing:
CRAC processing from raw fastq files was done running the CRAC_pipeline_SE.py script, described in van Nues et al., 2017. For more information on the pipeline please visit https://git.ecdf.ed.ac.uk/sgrannem/crac_pipelines
Narrow CRAC peaks were identified using MACS2, using a p-value <0.05 criteria and without constructing a model.
Assembly: sacCer3 (R64)
Supplementary files format and content: bed files with coordinates of narrow peaks detected by MACS2
Library strategy: CRAC-seq

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown in Synthetic Complete Medium to a density of 1x107 cells per ml and UV cross-linked in the Vari-X-linker (McKellar et al JoVe 2020; HOW MANY mJ/cm2?) and harvested by rapid filtration (McKellar et al JoVe 2020)

extract_protocol:
Cell extracts were prepared essentially as previously described (van Nues et al 2017) except that the frozen cells were lysed by pulverising the liquid-nitrogen-frozen cells in a mixer mill.
Extract was subjected to tandem affinity purification, using IgG-sepharose beads followed by mild Rnase treatment, terminateion by 6M GuHCl followed by NTA beads purification; Dephosphorylate and add 3' adapter on beads; 5' phosphorylate using radioactive ATP; On-Bead 5’ Adapter ligation; Elute Sfp-23P-RNA and run on PAGE; Eloctrotransfer onto NC membrane and cut out the radioactive band followed by proteinase K and phenol:chloroform extraction; Reverse transcribe and PCR amplify. See Haag et al. 2017

value: 4741 derivative

value: MATa his3D1 leu2D0 met15D0 ura3D0 HTP::SFP1

value: UV irradiated in mid-log and harvested


title: Sfp1_delta_Rpb4_biol_rep_2

value: MATa his3D1 leu2D0 met15D0 ura3D0 HTP::SFP1 rpb4D


title: Sfp1_wt_biol_rep_2


title: 3543_OF1A_1-5-K15-M21

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: Sfp1_delta_Rpb4_biol_rep_1


title: LEC activated by Co-Colture replicate 3

city: Firenze

first: Gianluca

last: Mattei

state: FI

address: Via di S. Marta, 3

country: Italy

institute: Università degli Studi di Firenze

data_processing:
The library quality was assessed using Agilent DNA 7500 kit on an Agilent Bioanalyzer, followed by library quantification using 1X dsDNA High Sensitivity (HS) (ThermoFisher)
FastQC was used to verify the quality of the library
Salmon (v. 1.5.1) was used for sequencing and quantification of library transcripts
Differential expression analysis was executed, using DESeq2 (v. 1.30.1)
Assembly: GRCh38
Supplementary files format and content: normlized_counts.xlsx contains normalized counts by DESeq2
Supplementary files format and content: raw_counts.xlsx contains raw counts by Salmon
Supplementary files format and content: Salmon_DESeq2.xlsx contains log2FCs by DESeq2

source_name: LEC

extract_protocol:
Total RNA was extracted using ReliaPrepTM RNA Cell Miniprep System (Promega)
Library preparation was performed using the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina) according to manufacturer’s instruction, with initial input of 300 ng of total RNA.

value: LEC

value: Co-Colture


title: 3543_OF1A_1-5-K15-M10

value: Female

value: nuclear RNA + genomic DNA


title: LEC activated by Co-Colture replicate 2


title: non activated LEC replicate 2


title: non activated LEC replicate 1


title: LEC activated by Co-Colture replicate 1


title: N2 (WT), EV RNAi, adult day 2, replicate 2

description:
N2_EV_2
eat2_2023_bulk_rnaseq_filtered_counts.txt
eat2_2023_bulk_rnaseq_filtered_tpm.txt


title: 3543_OF1A_1-5-K15-L22


title: 3543_OF1A_1-5-K15-L9


title: LEC activated by FVS replicate 2

value: FVS


title: 3543_OF1A_1-5-K15-L10


title: LEC activated by FVS replicate 1


title: LEC activated by FVS replicate 3


title: 3543_OF1A_1-5-K15-K22


title: Human Female naive iPSC – XIST Pulldown

description: RAP-Seq using probes targeting Xist in naive iPSCs

data_processing:
Trim: trim_galore (v0.4.1) with default parameters was used to trim DNA sequencing reads
Align: Bowtie2 (v2.2.9) with the default parameters was used to align reads
Filter: Samtools (v1.9) was used to remove reads with mapping quality less than 30, or marked by Picard MarkDuplicates (v2.1.0) as PCR duplicates
Count: Bedtools (v2.26.0) intersect was used to count reads in each genomic region (either 100kb windows every 25kb, 1Mb every 250kb, or around transcription start site)
Enrichment: read counts in each window were normalized by the total read counts in each sample. The ratio of the normalized reads in the pulldown to the input were used as inputs
Peaks: MACS2 (v2.2.7.1) using broad and max-gap=100 was used to call peaks
Assembly: hg38
Supplementary files format and content: bedgraph files represent normalized enrichment ratios in windows across the genome (either 100kb windows every 25kb, 1Mb every 250kb, or around gene TSS). Is_unmappable=yes mark unmappable genomic regions
Supplementary files format and content: peak files represent broad peaks called for XIST pulldown files samples compared to input
Library strategy: RAP-seq

source_name: iPSC

growth_protocol: Naïve hESCs (UCLA1 and H9) and iPSCs were cultured in 5iLAF naïve ESC medium on irradiated male mouse embryonic fibroblasts (1:1 mixture of DMEM/F12 and Neurobasal supplemented with N2, B27, penicillin/streptomycin, nonessential amino acids, GlutaMAX, 0.5% KSR, 0.1mM β-mercaptoethanol, 50ug/ml bovine serum albumin, 20ng/ml rhLIF, 20ng/ml Activin A, 8ng/ml FGF2, 1uM MEK inhibitor PD0325901 0.5uM B-Raf inhibitor SB590885, 1uM GSK3-β inhibitor IM-12, 1uM Src inhibitor WH-4-023, and 10uM ROCK inhibitor Y-27632). NHDFs were cultured in DMEM, with 10% FBS, penicillin/streptomycin, nonessential amino acids, GlutaMAX and 0.1mM β-mercaptoethanol. H9 hESCs were cultured in 5% CO2, 5% O2 (Hypoxia) at 37C and UCLA1, iPSCs and NHDFs were cultured in normal atmospheric O2 and 5% CO2 at 37C.

extract_protocol:
After washing with PBS, 5-30 million cells were harvested from confluent cell cultures and incubated with freshly-made 10ml 2mM DSG in 1x PBS at room temperature for 45 minutes. Cells were subsequently crosslinked further at room temperature with 10ml 3% formaldehyde for 10 minutes, and the reaction was stopped by the addition of 2ml 2.5M glycine. Cells were pelleted at 4˚C, aliquoted into vials of 10 million cells, and subjected to lysate preparation as described by Engreitz et al. (Engreitz et al., 2013). Briefly, the cells were passively lysed in Cell Lysis Buffer (10mM HEPES at pH7.5, 20mM KCl, 2mM MgCl2, 1mM EDTA with 0.1% NP-40) for 10min on ice, then lysis was completed either with glass dounce homogenizer (UCLA1, naïve iPSCs and NHDFs) or without (naïve (WT and with XIST KO) and primed H9, and primed iPSCs). Nuclei were lysed in Nuclear Lysis Buffer (20mM HEPES at pH7.5, 50mM KCl, 1.5mM MnCl2, 1% NP-40, 0.4% Sodium deoxycholate, 0.1% N-lauroylsarcosine) for 10min on ice. Chromatin was solubilized by sonication. Briefly, for UCLA1, naïve iPSCs and NHDFs, five cycles of sonication were performed, with each cycle lasting 45 seconds on high power. For naïve and primed H9, and primed iPSCs sonication was done with a Misonix S-400 sonicator with microtip (model number: U1240A0418) at an amplitude of 12, total process time of 2 min with pulse on for 1sec and pulse off for 3sec. After sonication, chromatin was further segmented by incubating it with TURBO DNase digestion at a concentration of 0.1-0.4U/ul for 12-20min at 37C (time was optimized for each sample). The digestion was stop by the addition of DNase Stop Solution (mixture of EDTA and EGTA). XIST RNA pulldown from 5 million cells was done using 1ug (UCLA1, iPSCs, NHDF R1) or 50pmol (primed and naïve H9 and primed iPSCs) of non-overlapping 90nt long biotinylated oligonucleotide probes (Eurofins) (Table S3). To test the effect of higher concentration of the biotinylated oligonucleotides, a higher concentration was added to one replicate of NHDF (R2), using 5ug probes. 1mg (UCLA1, naïve iPSCs and NHDFs) or 0.6mg (naïve and primed H9, and primed iPSCs) of C1 Streptavidin beads were used. As a control, 5% of each sample was taken as an input control and the remaining sample was used for the pulldown. DNA was eluted by Rnase H digestion, and crosslinking was reversed via proteinase K digestion of eluted DNA at 60˚C 10-12 hours.
DNA libraries were prepared using NEBNext Ultra End Rpair/dA-Tailing Module (NEB) and TruSeq DNA adapters (Illumina) ligated using Quick Ligase (NEB). Libraries were amplified by KAPA HiFi Polymerase (Roche), pooled, and sequenced on the Illlumina HiSeq platform to generate 50bp single-end reads (UCLA1, naïve iPSCs and NHDFs) or pair-end reads (naïve and primed H9 and primed iPSCs).

treatment_protocol: In addition to growing each cell type in appropriate media condition, cells were not treated with any additional agent(s).

value: iPSC

value: Naive iPSCs

value: RAP-Seq

tag: experiment type

value: XIST RAP


title: 3543_OF1A_1-5-K15-K21


title: Human Female naive iPSC – Input

description: Input DNA in naive iPSCs

value: Input


title: 3543_OF1A_1-5-K15-K10


title: 3543_OF1A_1-5-K15-J9


title: Human Female naive hESC UCLA1 – XIST Pulldown

description: RAP-Seq using probes targeting Xist in naive hESCs (UCLA1)

value: Naive hESC


title: 3543_OF1A_1-5-K15-J22


title: Human Female naive hESC UCLA1 – Input

description: Input DNA in naive hESCs (UCLA1)


title: 3543_OF1A_1-5-K15-J21


title: Human Female NHDF R2 – XIST Pulldown

description: RAP-Seq using probes targeting Xist in NHDFs (Rep2)

source_name: NHDF

value: NHDF

value: Somatic


title: Human Female NHDF R1 – XIST Pulldown

description: RAP-Seq using probes targeting Xist in NHDFs (Rep1)


title: 3543_OF1A_1-5-K15-J10


title: 3543_OF1A_1-5-K15-I9


title: 3543_OF1A_1-5-K15-L21


title: 3543_OF1A_1-5-K15-I21


title: 3543_OF1A_1-5-K15-I10


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23032161LR01-Day14-GC7-2]

city: Houston

first: yi

last: chai

address: pgpr

institute: Biostate AI

description: Valproate, 500 mg/kg, Day 14, Repeat 2

data_processing:
Raw data from Illumina sequencer
illumina Adaptor Trim
HISAT2 Alignment
Assembly: NCBI GCF_015227675.2, Genome assembly mRatBN7.2
Supplementary files format and content: csv

organism: Rattus norvegicus

source_name: Blood

growth_protocol: Animals were kept under a standard condition with room temperature at 21-23 ºC, 40-70% relative humidity, and a 12/12h light: dark cycle. Chow and water are available ad libitum.

extract_protocol:
Trizol based total RNA extraction method
RNA libraries for RNA-Seq were prepared by using mRNA capture based standard library preparation kit (Vazyme) following manufacturer's protocol.

value: 8-9 months

value: male

value: whole blood

value: Valproate, 500 mg/kg, Day 14, Repeat 2


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23032162LR01-Day14-GC7-3]

description: Valproate, 500 mg/kg, Day 14, Repeat 3

value: Valproate, 500 mg/kg, Day 14, Repeat 3


title: 3543_OF1A_1-5-K15-H9

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23032160LR01-Day14-GC7-1]

description: Valproate, 500 mg/kg, Day 14, Repeat 1

value: Valproate, 500 mg/kg, Day 14, Repeat 1


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23032163LR01-Day14-GC7-5]

description: Valproate, 500 mg/kg, Day 14, Repeat 5

value: Valproate, 500 mg/kg, Day 14, Repeat 5


title: 3543_OF1A_1-5-K15-H22

value: Female

value: nuclear RNA + genomic DNA


title: 3543_OF1A_1-5-K15-I22


title: 3543_OF1A_1-5-K15-H21


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23032159LR01-Day14-GC6-5]

description: Valproate, 500 mg/kg, Day 14, Repeat 5

value: 8 wks


title: 3543_OF1A_1-5-K15-H10


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23032157LR01-Day14-GC6-2]

description: Valproate, 500 mg/kg, Day 14, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23032158LR01-Day14-GC6-4]

description: Valproate, 500 mg/kg, Day 14, Repeat 4

value: Valproate, 500 mg/kg, Day 14, Repeat 4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23032156LR01-Day14-GC6-1]

description: Valproate, 500 mg/kg, Day 14, Repeat 1


title: 3543_OF1A_1-5-K15-K9


title: 3543_OF1A_1-5-K15-G9


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032155LR01-Day14-GC5-5]

description: Valproate, 500 mg/kg, Day 14, Repeat 5

value: 3-4 wks


title: 3543_OF1A_1-5-K15-G22


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032154LR02-Day14-GC5-4]

description: Valproate, 500 mg/kg, Day 14, Repeat 4


title: Human Female NHDF – Input

description: Input DNA in NHDFs

value: RAP-Seq

value: Input


title: 3543_OF1A_1-5-K15-G10


title: 3543_OF1A_1-5-K15-G21


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032152LR01-Day14-GC5-2]

description: Valproate, 500 mg/kg, Day 14, Repeat 2


title: 3543_OF1A_1-5-K15-F9


title: 3543_OF1A_1-5-K15-F22


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032151LR01-Day14-GC5-1]

description: Valproate, 500 mg/kg, Day 14, Repeat 1


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23032150LR01-Day13-GC7-5]

description: Valproate, 500 mg/kg, Day 13, Repeat 5

value: Valproate, 500 mg/kg, Day 13, Repeat 5


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23032149LR01-Day13-GC7-3]

description: Valproate, 500 mg/kg, Day 13, Repeat 3

value: Valproate, 500 mg/kg, Day 13, Repeat 3


title: 3543_OF1A_1-5-K15-F10


title: 3543_OF1A_1-5-K15-F21


title: 3543_OF1A_1-5-K15-E9


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23032148LR01-Day13-GC7-2]

description: Valproate, 500 mg/kg, Day 13, Repeat 2

value: 8-9 months

value: Valproate, 500 mg/kg, Day 13, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23032146LR01-Day13-GC6-5]

description: Valproate, 500 mg/kg, Day 13, Repeat 5

value: male

value: whole blood


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23032147LR01-Day13-GC7-1]

description: Valproate, 500 mg/kg, Day 13, Repeat 1

value: Valproate, 500 mg/kg, Day 13, Repeat 1


title: 3543_OF1A_1-5-K15-E22

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_1-5-K15-E10


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23032145LR01-Day13-GC6-4]

description: Valproate, 500 mg/kg, Day 13, Repeat 4

value: Valproate, 500 mg/kg, Day 13, Repeat 4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23032143LR01-Day13-GC6-1]

description: Valproate, 500 mg/kg, Day 13, Repeat 1


title: 3543_OF1A_1-5-K15-D22


title: 3543_OF1A_1-5-K15-D21


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23032144LR01-Day13-GC6-2]

description: Valproate, 500 mg/kg, Day 13, Repeat 2


title: 3543_OF1A_1-5-K15-D10


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032153LR01-Day14-GC5-3]

description: Valproate, 500 mg/kg, Day 14, Repeat 3

value: Valproate, 500 mg/kg, Day 14, Repeat 3


title: 3543_OF1A_1-5-K15-D9

value: Female


title: 3543_OF1A_1-5-K15-C9

value: nuclear RNA + genomic DNA


title: 3543_OF1A_1-5-K15-C22


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032139LR01-Day13-GC5-2]

description: Valproate, 500 mg/kg, Day 13, Repeat 2


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032141LR01-Day13-GC5-4]

description: Valproate, 500 mg/kg, Day 13, Repeat 4


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032138LR01-Day13-GC5-1]

description: Valproate, 500 mg/kg, Day 13, Repeat 1


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23032136LR01-Day12-GC7-3]

description: Valproate, 500 mg/kg, Day 12, Repeat 3

value: Valproate, 500 mg/kg, Day 12, Repeat 3


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23032137LR01-Day12-GC7-5]

description: Valproate, 500 mg/kg, Day 12, Repeat 5

value: Valproate, 500 mg/kg, Day 12, Repeat 5


title: 3543_OF1A_1-5-K15-C10


title: 3543_OF1A_1-5-K15-C21


title: 3543_OF1A_1-5-K15-B9


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23032135LR01-Day12-GC7-2]

description: Valproate, 500 mg/kg, Day 12, Repeat 2

value: Valproate, 500 mg/kg, Day 12, Repeat 2


title: 3543_OF1A_1-5-K15-E21


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032142LR01-Day13-GC5-5]

description: Valproate, 500 mg/kg, Day 13, Repeat 5

value: 3-4 wks


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23032134LR01-Day12-GC7-1]

description: Valproate, 500 mg/kg, Day 12, Repeat 1

value: Valproate, 500 mg/kg, Day 12, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23032133LR01-Day12-GC6-5]

description: Valproate, 500 mg/kg, Day 12, Repeat 5

value: 8 wks


title: 3543_OF1A_1-5-K15-B21


title: 3543_OF1A_1-5-K15-B10


title: 3543_OF1A_1-5-K15-A22


title: 3543_OF1A_1-5-K15-A9


title: 3543_OF1A_1-5-K15-A21


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032129LR01-Day12-GC5-5]

description: Valproate, 500 mg/kg, Day 12, Repeat 5


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23032130LR01-Day12-GC6-1]

description: Valproate, 500 mg/kg, Day 12, Repeat 1


title: 3543_OF1A_1-4-K15-P8


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23032132LR01-Day12-GC6-4]

description: Valproate, 500 mg/kg, Day 12, Repeat 4

value: Valproate, 500 mg/kg, Day 12, Repeat 4


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032140LR01-Day13-GC5-3]

description: Valproate, 500 mg/kg, Day 13, Repeat 3

value: Valproate, 500 mg/kg, Day 13, Repeat 3


title: 3543_OF1A_1-4-K15-P7


title: 3543_OF1A_1-5-K15-A10


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032127LR01-Day12-GC5-3]

description: Valproate, 500 mg/kg, Day 12, Repeat 3


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032125LR01-Day12-GC5-1]

description: Valproate, 500 mg/kg, Day 12, Repeat 1


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032126LR01-Day12-GC5-2]

description: Valproate, 500 mg/kg, Day 12, Repeat 2


title: 3543_OF1A_1-4-K15-P20


title: 3543_OF1A_1-4-K15-P19


title: 3543_OF1A_1-5-K15-B22


title: 3543_OF1A_1-4-K15-O7


title: 3543_OF1A_1-4-K15-O8


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23032122LR01-Day11-GC7-2]

description: Valproate, 500 mg/kg, Day 11, Repeat 2

value: 8-9 months

value: Valproate, 500 mg/kg, Day 11, Repeat 2


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23032121LR01-Day11-GC7-1]

description: Valproate, 500 mg/kg, Day 11, Repeat 1

value: male

value: whole blood

value: Valproate, 500 mg/kg, Day 11, Repeat 1


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23032124LR01-Day11-GC7-5]

description: Valproate, 500 mg/kg, Day 11, Repeat 5

value: Valproate, 500 mg/kg, Day 11, Repeat 5


title: 3543_OF1A_1-4-K15-O20

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23032123LR01-Day11-GC7-3]

description: Valproate, 500 mg/kg, Day 11, Repeat 3

value: Valproate, 500 mg/kg, Day 11, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23032120LR01-Day11-GC6-5]

description: Valproate, 500 mg/kg, Day 11, Repeat 5


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032128LR01-Day12-GC5-4]

description: Valproate, 500 mg/kg, Day 12, Repeat 4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23032118LR01-Day11-GC6-2]

description: Valproate, 500 mg/kg, Day 11, Repeat 2


title: 3543_OF1A_1-4-K15-N8

value: Female

value: nuclear RNA + genomic DNA


title: 3543_OF1A_1-4-K15-O19


title: 3543_OF1A_1-4-K15-N20


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23032117LR01-Day11-GC6-1]

description: Valproate, 500 mg/kg, Day 11, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23032131LR01-Day12-GC6-2]

description: Valproate, 500 mg/kg, Day 12, Repeat 2


title: 3543_OF1A_1-4-K15-N7


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032116LR01-Day11-GC5-5]

description: Valproate, 500 mg/kg, Day 11, Repeat 5


title: 3543_OF1A_1-4-K15-M7


title: 3543_OF1A_1-4-K15-N19


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032114LR01-Day11-GC5-3]

description: Valproate, 500 mg/kg, Day 11, Repeat 3


title: 3543_OF1A_1-4-K15-M8


title: 3543_OF1A_1-4-K15-M20


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032115LR01-Day11-GC5-4]

description: Valproate, 500 mg/kg, Day 11, Repeat 4

value: Valproate, 500 mg/kg, Day 11, Repeat 4


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032112LR01-Day11-GC5-1]

description: Valproate, 500 mg/kg, Day 11, Repeat 1


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23032113LR01-Day11-GC5-2]

description: Valproate, 500 mg/kg, Day 11, Repeat 2


title: 3543_OF1A_1-4-K15-L8


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23031544LR01-Day10-GC7-5]

description: Valproate, 500 mg/kg, Day 10, Repeat 5

value: Valproate, 500 mg/kg, Day 10, Repeat 5


title: 3543_OF1A_1-4-K15-L7


title: 3543_OF1A_1-4-K15-L19


title: 3543_OF1A_1-4-K15-L20


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23032119LR01-Day11-GC6-4]

description: Valproate, 500 mg/kg, Day 11, Repeat 4


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23031542LR01-Day10-GC7-2]

description: Valproate, 500 mg/kg, Day 10, Repeat 2

value: Valproate, 500 mg/kg, Day 10, Repeat 2


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23031541LR01-Day10-GC7-1]

description: Valproate, 500 mg/kg, Day 10, Repeat 1

value: Valproate, 500 mg/kg, Day 10, Repeat 1


title: 3543_OF1A_1-4-K15-K8


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23031540LR01-Day10-GC6-5]

description: Valproate, 500 mg/kg, Day 10, Repeat 5

value: 8 wks


title: 3543_OF1A_1-4-K15-K20


title: 3543_OF1A_1-4-K15-K7


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23031538LR01-Day10-GC6-2]

description: Valproate, 500 mg/kg, Day 10, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23031539LR01-Day10-GC6-4]

description: Valproate, 500 mg/kg, Day 10, Repeat 4

value: Valproate, 500 mg/kg, Day 10, Repeat 4


title: 3543_OF1A_1-4-K15-K19


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23031537LR01-Day10-GC6-1]

description: Valproate, 500 mg/kg, Day 10, Repeat 1


title: 3543_OF1A_1-4-K15-J8


title: 3543_OF1A_1-4-K15-M19


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23031536LR01-Day10-GC5-5]

description: Valproate, 500 mg/kg, Day 10, Repeat 5

value: 3-4 wks


title: 3543_OF1A_1-4-K15-J7


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23031535LR01-Day10-GC5-4]

description: Valproate, 500 mg/kg, Day 10, Repeat 4


title: 3543_OF1A_1-4-K15-J20


title: 3543_OF1A_1-4-K15-J19


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23031533LR01-Day10-GC5-2]

description: Valproate, 500 mg/kg, Day 10, Repeat 2


title: 3543_OF1A_1-4-K15-I7


title: 3543_OF1A_1-4-K15-I8


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23031534LR01-Day10-GC5-3]

description: Valproate, 500 mg/kg, Day 10, Repeat 3

value: Valproate, 500 mg/kg, Day 10, Repeat 3


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23031543LR01-Day10-GC7-3]

description: Valproate, 500 mg/kg, Day 10, Repeat 3

value: 8-9 months


title: 3543_OF1A_1-4-K15-I19


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23031449LR01-Day9-GC7-3]

description: Valproate, 500 mg/kg, Day 9, Repeat 3

value: male

value: Valproate, 500 mg/kg, Day 9, Repeat 3


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23031450LR01-Day9-GC7-5]

description: Valproate, 500 mg/kg, Day 9, Repeat 5

value: whole blood

value: Valproate, 500 mg/kg, Day 9, Repeat 5


title: 3543_OF1A_1-4-K15-I20

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23031448LR01-Day9-GC7-2]

description: Valproate, 500 mg/kg, Day 9, Repeat 2

value: Valproate, 500 mg/kg, Day 9, Repeat 2


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23031447LR01-Day9-GC7-1]

description: Valproate, 500 mg/kg, Day 9, Repeat 1

value: Valproate, 500 mg/kg, Day 9, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23031445LR01-Day9-GC6-4]

description: Valproate, 500 mg/kg, Day 9, Repeat 4

value: Valproate, 500 mg/kg, Day 9, Repeat 4


title: 3543_OF1A_1-4-K15-H8

value: Female

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23031446LR01-Day9-GC6-5]

description: Valproate, 500 mg/kg, Day 9, Repeat 5


title: 3543_OF1A_1-4-K15-H19


title: 3543_OF1A_1-4-K15-G8


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23031443LR01-Day9-GC6-2]

description: Valproate, 500 mg/kg, Day 9, Repeat 2


title: 3543_OF1A_1-4-K15-G7


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23031442LR01-Day9-GC6-1]

description: Valproate, 500 mg/kg, Day 9, Repeat 1


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23031532LR01-Day10-GC5-1]

description: Valproate, 500 mg/kg, Day 10, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23031444LR01-Day9-GC6-3]

description: Valproate, 500 mg/kg, Day 9, Repeat 3


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23031440LR01-Day9-GC5-4]

description: Valproate, 500 mg/kg, Day 9, Repeat 4


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23031441LR01-Day9-GC5-5]

description: Valproate, 500 mg/kg, Day 9, Repeat 5


title: 3543_OF1A_1-4-K15-G20


title: 3543_OF1A_1-4-K15-F7


title: 3543_OF1A_1-4-K15-F8


title: 3543_OF1A_1-4-K15-G19


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23031438LR01-Day9-GC5-2]

description: Valproate, 500 mg/kg, Day 9, Repeat 2


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23031439LR01-Day9-GC5-3]

description: Valproate, 500 mg/kg, Day 9, Repeat 3


title: 3543_OF1A_1-4-K15-F20


title: 3543_OF1A_1-4-K15-H7


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23031406LR01-Day8-GC7-2]

description: Valproate, 500 mg/kg, Day 8, Repeat 2

value: Valproate, 500 mg/kg, Day 8, Repeat 2


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23031405LR01-Day8-GC7-1]

description: Valproate, 500 mg/kg, Day 8, Repeat 1

value: Valproate, 500 mg/kg, Day 8, Repeat 1


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23031407LR01-Day8-GC7-3]

description: Valproate, 500 mg/kg, Day 8, Repeat 3

value: Valproate, 500 mg/kg, Day 8, Repeat 3


title: 3543_OF1A_1-4-K15-F19


title: 3543_OF1A_1-4-K15-E7


title: 3543_OF1A_1-4-K15-E8


title: 3543_OF1A_1-4-K15-H20


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23031408LR01-Day8-GC7-4]

description: Valproate, 500 mg/kg, Day 8, Repeat 4

value: Valproate, 500 mg/kg, Day 8, Repeat 4


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23031409LR01-Day8-GC7-5]

description: Valproate, 500 mg/kg, Day 8, Repeat 5

value: Valproate, 500 mg/kg, Day 8, Repeat 5


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23031404LR01-Day8-GC6-5]

description: Valproate, 500 mg/kg, Day 8, Repeat 5

value: 8 wks


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23031402LR01-Day8-GC6-3]

description: Valproate, 500 mg/kg, Day 8, Repeat 3


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23031403LR01-Day8-GC6-4]

description: Valproate, 500 mg/kg, Day 8, Repeat 4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23031401LR01-Day8-GC6-2]

description: Valproate, 500 mg/kg, Day 8, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23031400LR01-Day8-GC6-1]

description: Valproate, 500 mg/kg, Day 8, Repeat 1


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23031399LR01-Day8-GC5-5]

description: Valproate, 500 mg/kg, Day 8, Repeat 5

value: 3-4 wks


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23031397LR01-Day8-GC5-3]

description: Valproate, 500 mg/kg, Day 8, Repeat 3

value: male


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23031398LR01-Day8-GC5-4]

description: Valproate, 500 mg/kg, Day 8, Repeat 4


title: 3543_OF1A_1-4-K15-E19


title: 3543_OF1A_1-4-K15-C7


title: 3543_OF1A_1-4-K15-D20


title: 3543_OF1A_1-4-K15-C19


title: 3543_OF1A_1-4-K15-D8


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23031437LR01-Day9-GC5-1]

description: Valproate, 500 mg/kg, Day 9, Repeat 1


title: 3543_OF1A_1-4-K15-E20


title: 3543_OF1A_1-4-K15-D19


title: 3543_OF1A_1-4-K15-B8


title: 3543_OF1A_1-4-K15-D7


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23031396LR01-Day8-GC5-2]

description: Valproate, 500 mg/kg, Day 8, Repeat 2


title: 3543_OF1A_1-4-K15-B7


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030976LR01-Day7-GC7-5]

description: Valproate, 500 mg/kg, Day 7, Repeat 5

value: 8-9 months

value: Valproate, 500 mg/kg, Day 7, Repeat 5


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030975LR01-Day7-GC7-4]

description: Valproate, 500 mg/kg, Day 7, Repeat 4

value: whole blood

value: Valproate, 500 mg/kg, Day 7, Repeat 4


title: 3543_OF1A_1-4-K15-B20

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_1-4-K15-C8


title: 3543_OF1A_1-4-K15-A8


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030973LR01-Day7-GC7-2]

description: Valproate, 500 mg/kg, Day 7, Repeat 2

value: Valproate, 500 mg/kg, Day 7, Repeat 2


title: 3543_OF1A_1-4-K15-A7


title: 3543_OF1A_1-4-K15-C20


title: 3543_OF1A_1-4-K15-A20


title: 3543_OF1A_1-3-K15-P6


title: 3543_OF1A_1-3-K15-P5


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030972LR01-Day7-GC7-1]

description: Valproate, 500 mg/kg, Day 7, Repeat 1

value: Valproate, 500 mg/kg, Day 7, Repeat 1


title: 3543_OF1A_1-4-K15-A19

value: Female


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030971LR01-Day7-GC6-5]

description: Valproate, 500 mg/kg, Day 7, Repeat 5


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030970LR01-Day7-GC6-4]

description: Valproate, 500 mg/kg, Day 7, Repeat 4


title: 3543_OF1A_1-3-K15-P17

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030968LR01-Day7-GC6-2]

description: Valproate, 500 mg/kg, Day 7, Repeat 2


title: 3543_OF1A_1-3-K15-P18


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030966LR01-Day7-GC5-5]

description: Valproate, 500 mg/kg, Day 7, Repeat 5


title: 3543_OF1A_1-3-K15-O6


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030965LR01-Day7-GC5-4]

description: Valproate, 500 mg/kg, Day 7, Repeat 4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030967LR01-Day7-GC6-1]

description: Valproate, 500 mg/kg, Day 7, Repeat 1


title: 3543_OF1A_1-4-K15-B19


title: 3543_OF1A_1-3-K15-O18


title: 3543_OF1A_1-3-K15-O5


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23031395LR01-Day8-GC5-1]

description: Valproate, 500 mg/kg, Day 8, Repeat 1


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030974LR01-Day7-GC7-3]

description: Valproate, 500 mg/kg, Day 7, Repeat 3

value: Valproate, 500 mg/kg, Day 7, Repeat 3


title: 3543_OF1A_1-3-K15-O17


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030963LR01-Day7-GC5-2]

description: Valproate, 500 mg/kg, Day 7, Repeat 2


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030962LR01-Day7-GC5-1]

description: Valproate, 500 mg/kg, Day 7, Repeat 1


title: 3543_OF1A_1-3-K15-N6


title: 3543_OF1A_1-3-K15-N5


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030964LR01-Day7-GC5-3]

description: Valproate, 500 mg/kg, Day 7, Repeat 3


title: 3543_OF1A_1-3-K15-N18


title: 3543_OF1A_1-3-K15-N17


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030888LR01-Day6-GC7-4]

description: Valproate, 500 mg/kg, Day 6, Repeat 4

value: Valproate, 500 mg/kg, Day 6, Repeat 4


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030887LR01-Day6-GC7-3]

description: Valproate, 500 mg/kg, Day 6, Repeat 3

value: Valproate, 500 mg/kg, Day 6, Repeat 3


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030889LR01-Day6-GC7-5]

description: Valproate, 500 mg/kg, Day 6, Repeat 5

value: Valproate, 500 mg/kg, Day 6, Repeat 5


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030969LR01-Day7-GC6-3]

description: Valproate, 500 mg/kg, Day 7, Repeat 3


title: 3543_OF1A_1-3-K15-M6


title: 3543_OF1A_1-3-K15-M18


title: 3543_OF1A_1-3-K15-M5


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030886LR01-Day6-GC7-2]

description: Valproate, 500 mg/kg, Day 6, Repeat 2

value: Valproate, 500 mg/kg, Day 6, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030884LR01-Day6-GC6-5]

description: Valproate, 500 mg/kg, Day 6, Repeat 5

value: 8 wks


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030885LR01-Day6-GC7-1]

description: Valproate, 500 mg/kg, Day 6, Repeat 1

value: Valproate, 500 mg/kg, Day 6, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030883LR01-Day6-GC6-4]

description: Valproate, 500 mg/kg, Day 6, Repeat 4

value: male


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030882LR01-Day6-GC6-3]

description: Valproate, 500 mg/kg, Day 6, Repeat 3


title: 3543_OF1A_1-3-K15-M17


title: 3543_OF1A_1-3-K15-L5


title: 3543_OF1A_1-3-K15-L6


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030880LR01-Day6-GC6-1]

description: Valproate, 500 mg/kg, Day 6, Repeat 1


title: 3543_OF1A_1-3-K15-K6


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030879LR01-Day6-GC5-5]

description: Valproate, 500 mg/kg, Day 6, Repeat 5

value: 3-4 wks


title: 3543_OF1A_1-3-K15-L17


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030878LR01-Day6-GC5-4]

description: Valproate, 500 mg/kg, Day 6, Repeat 4


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030876LR01-Day6-GC5-2]

description: Valproate, 500 mg/kg, Day 6, Repeat 2


title: 3543_OF1A_1-3-K15-K5


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030875LR01-Day6-GC5-1]

description: Valproate, 500 mg/kg, Day 6, Repeat 1


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030754LR01-Day5-GC7-5]

description: Valproate, 500 mg/kg, Day 5, Repeat 5

value: 8-9 months

value: Valproate, 500 mg/kg, Day 5, Repeat 5


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030877LR01-Day6-GC5-3]

description: Valproate, 500 mg/kg, Day 6, Repeat 3

value: whole blood


title: 3543_OF1A_1-3-K15-K17

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_1-3-K15-K18


title: 3543_OF1A_1-3-K15-J5


title: 3543_OF1A_1-3-K15-J18


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030753LR01-Day5-GC7-4]

description: Valproate, 500 mg/kg, Day 5, Repeat 4

value: Valproate, 500 mg/kg, Day 5, Repeat 4


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030752LR01-Day5-GC7-3]

description: Valproate, 500 mg/kg, Day 5, Repeat 3

value: Valproate, 500 mg/kg, Day 5, Repeat 3


title: 3543_OF1A_1-3-K15-I5

value: Female


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030750LR01-Day5-GC7-1]

description: Valproate, 500 mg/kg, Day 5, Repeat 1

value: Valproate, 500 mg/kg, Day 5, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030749LR01-Day5-GC6-5]

description: Valproate, 500 mg/kg, Day 5, Repeat 5


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030751LR01-Day5-GC7-2]

description: Valproate, 500 mg/kg, Day 5, Repeat 2

value: Valproate, 500 mg/kg, Day 5, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030881LR01-Day6-GC6-2]

description: Valproate, 500 mg/kg, Day 6, Repeat 2


title: 3543_OF1A_1-3-K15-I18

value: nuclear RNA + genomic DNA


title: 3543_OF1A_1-3-K15-I6


title: 3543_OF1A_1-3-K15-L18


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030747LR01-Day5-GC6-3]

description: Valproate, 500 mg/kg, Day 5, Repeat 3


title: 3543_OF1A_1-3-K15-I17


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030748LR01-Day5-GC6-4]

description: Valproate, 500 mg/kg, Day 5, Repeat 4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030746LR01-Day5-GC6-2]

description: Valproate, 500 mg/kg, Day 5, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030745LR01-Day5-GC6-1]

description: Valproate, 500 mg/kg, Day 5, Repeat 1


title: 3543_OF1A_1-3-K15-H5


title: 3543_OF1A_1-3-K15-H18


title: 3543_OF1A_1-3-K15-J6


title: 3543_OF1A_1-3-K15-H17


title: 3543_OF1A_1-3-K15-G6


title: 3543_OF1A_1-3-K15-G5


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030743LR01-Day5-GC5-4]

description: Valproate, 500 mg/kg, Day 5, Repeat 4


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030741LR01-Day5-GC5-2]

description: Valproate, 500 mg/kg, Day 5, Repeat 2


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030742LR01-Day5-GC5-3]

description: Valproate, 500 mg/kg, Day 5, Repeat 3


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030744LR01-Day5-GC5-5]

description: Valproate, 500 mg/kg, Day 5, Repeat 5


title: 3543_OF1A_1-3-K15-J17


title: 3543_OF1A_1-3-K15-G17


title: 3543_OF1A_1-3-K15-F6


title: 3543_OF1A_1-3-K15-F5


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030655LR01-Day4-GC7-4]

description: Valproate, 500 mg/kg, Day 4, Repeat 4

value: Valproate, 500 mg/kg, Day 4, Repeat 4


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030740LR01-Day5-GC5-1]

description: Valproate, 500 mg/kg, Day 5, Repeat 1


title: 3543_OF1A_1-3-K15-F18


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030654LR01-Day4-GC7-3]

description: Valproate, 500 mg/kg, Day 4, Repeat 3

value: Valproate, 500 mg/kg, Day 4, Repeat 3


title: 3543_OF1A_1-3-K15-G18


title: 3543_OF1A_1-3-K15-H6


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030652LR01-Day4-GC7-1]

description: Valproate, 500 mg/kg, Day 4, Repeat 1

value: Valproate, 500 mg/kg, Day 4, Repeat 1


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030653LR01-Day4-GC7-2]

description: Valproate, 500 mg/kg, Day 4, Repeat 2

value: Valproate, 500 mg/kg, Day 4, Repeat 2


title: 3543_OF1A_1-3-K15-E6


title: 3543_OF1A_1-3-K15-F17


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030651LR01-Day4-GC6-5]

description: Valproate, 500 mg/kg, Day 4, Repeat 5

value: 8 wks

value: Valproate, 500 mg/kg, Day 4, Repeat 5


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030649LR01-Day4-GC6-3]

description: Valproate, 500 mg/kg, Day 4, Repeat 3

value: male


title: 3543_OF1A_1-3-K15-E5


title: 3543_OF1A_1-3-K15-E18


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030650LR01-Day4-GC6-4]

description: Valproate, 500 mg/kg, Day 4, Repeat 4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030648LR01-Day4-GC6-2]

description: Valproate, 500 mg/kg, Day 4, Repeat 2


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030647LR01-Day4-GC6-1]

description: Valproate, 500 mg/kg, Day 4, Repeat 1


title: 3543_OF1A_1-3-K15-D6


title: 3543_OF1A_1-3-K15-E17


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030646LR01-Day4-GC5-5]

description: Valproate, 500 mg/kg, Day 4, Repeat 5

value: 3-4 wks


title: 3543_OF1A_1-3-K15-D5


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030656LR01-Day4-GC7-5]

description: Valproate, 500 mg/kg, Day 4, Repeat 5

value: 8-9 months


title: 3543_OF1A_1-3-K15-D18


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030644LR01-Day4-GC5-3]

description: Valproate, 500 mg/kg, Day 4, Repeat 3

value: whole blood


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030645LR01-Day4-GC5-4]

description: Valproate, 500 mg/kg, Day 4, Repeat 4


title: 3543_OF1A_1-3-K15-D17

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_1-3-K15-C6


title: 3543_OF1A_1-3-K15-C5


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030643LR01-Day4-GC5-2]

description: Valproate, 500 mg/kg, Day 4, Repeat 2


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030642LR01-Day4-GC5-1]

description: Valproate, 500 mg/kg, Day 4, Repeat 1


title: 3543_OF1A_1-3-K15-C17


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030598LR01-Day3-GC7-5]

description: Valproate, 500 mg/kg, Day 3, Repeat 5

value: Valproate, 500 mg/kg, Day 3, Repeat 5


title: 3543_OF1A_1-3-K15-C18


title: 3543_OF1A_1-3-K15-B5


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030596LR01-Day3-GC7-3]

description: Valproate, 500 mg/kg, Day 3, Repeat 3

value: Valproate, 500 mg/kg, Day 3, Repeat 3


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030595LR01-Day3-GC7-2]

description: Valproate, 500 mg/kg, Day 3, Repeat 2

value: Valproate, 500 mg/kg, Day 3, Repeat 2


title: 3543_OF1A_1-3-K15-A6

value: Female


title: 3543_OF1A_1-3-K15-B17


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030592LR01-Day3-GC6-4]

description: Valproate, 500 mg/kg, Day 3, Repeat 4

value: Valproate, 500 mg/kg, Day 3, Repeat 4


title: 3543_OF1A_1-3-K15-B18

value: nuclear RNA + genomic DNA


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030591LR01-Day3-GC6-3]

description: Valproate, 500 mg/kg, Day 3, Repeat 3


title: 3543_OF1A_1-3-K15-B6


title: 3543_OF1A_1-3-K15-A17


title: 3543_OF1A_1-3-K15-A5


title: 3543_OF1A_1-2-K15-P4


title: 3543_OF1A_1-2-K15-P3


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030588LR01-Day3-GC5-5]

description: Valproate, 500 mg/kg, Day 3, Repeat 5


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030586LR01-Day3-GC5-3]

description: Valproate, 500 mg/kg, Day 3, Repeat 3


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030587LR01-Day3-GC5-4]

description: Valproate, 500 mg/kg, Day 3, Repeat 4


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030594LR01-Day3-GC7-1]

description: Valproate, 500 mg/kg, Day 3, Repeat 1

value: Valproate, 500 mg/kg, Day 3, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030590LR01-Day3-GC6-2]

description: Valproate, 500 mg/kg, Day 3, Repeat 2


title: 3543_OF1A_1-2-K15-P16


title: 3543_OF1A_1-2-K15-P15


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030597LR01-Day3-GC7-4]

description: Valproate, 500 mg/kg, Day 3, Repeat 4


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030585LR01-Day3-GC5-2]

description: Valproate, 500 mg/kg, Day 3, Repeat 2


title: 3543_OF1A_1-2-K15-O4


title: 3543_OF1A_1-2-K15-O3


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030584LR01-Day3-GC5-1]

description: Valproate, 500 mg/kg, Day 3, Repeat 1


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030459LR01-Day2-GC7-5]

description: Valproate, 500 mg/kg, Day 2, Repeat 5

value: Valproate, 500 mg/kg, Day 2, Repeat 5


title: 3543_OF1A_1-2-K15-O16


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030458LR01-Day2-GC7-4]

description: Valproate, 500 mg/kg, Day 2, Repeat 4

value: Valproate, 500 mg/kg, Day 2, Repeat 4


title: 3543_OF1A_1-2-K15-O15


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030457LR01-Day2-GC7-3]

description: Valproate, 500 mg/kg, Day 2, Repeat 3

value: Valproate, 500 mg/kg, Day 2, Repeat 3


title: 3543_OF1A_1-2-K15-N3


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030456LR01-Day2-GC7-2]

description: Valproate, 500 mg/kg, Day 2, Repeat 2

value: Valproate, 500 mg/kg, Day 2, Repeat 2


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030455LR01-Day2-GC7-1]

description: Valproate, 500 mg/kg, Day 2, Repeat 1

value: Valproate, 500 mg/kg, Day 2, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030589LR01-Day3-GC6-1]

description: Valproate, 500 mg/kg, Day 3, Repeat 1

value: 8 wks

value: male


title: 3543_OF1A_1-2-K15-N16


title: 3543_OF1A_1-2-K15-N15


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030453LR01-Day2-GC6-4]

description: Valproate, 500 mg/kg, Day 2, Repeat 4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030593LR01-Day3-GC6-5]

description: Valproate, 500 mg/kg, Day 3, Repeat 5


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030452LR01-Day2-GC6-3]

description: Valproate, 500 mg/kg, Day 2, Repeat 3


title: 3543_OF1A_1-3-K15-A18


title: 3543_OF1A_1-2-K15-M4


title: 3543_OF1A_1-2-K15-M16


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030450LR01-Day2-GC6-1]

description: Valproate, 500 mg/kg, Day 2, Repeat 1


title: 3543_OF1A_1-2-K15-M3


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030449LR01-Day2-GC5-5]

description: Valproate, 500 mg/kg, Day 2, Repeat 5

value: 3-4 wks


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030451LR01-Day2-GC6-2]

description: Valproate, 500 mg/kg, Day 2, Repeat 2

value: whole blood


title: 3543_OF1A_1-2-K15-L4

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: 3543_OF1A_1-2-K15-M15


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030448LR01-Day2-GC5-4]

description: Valproate, 500 mg/kg, Day 2, Repeat 4


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030446LR01-Day2-GC5-2]

description: Valproate, 500 mg/kg, Day 2, Repeat 2


title: 3543_OF1A_1-2-K15-L3


title: 3543_OF1A_1-2-K15-N4


title: 3543_OF1A_1-2-K15-K4


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030447LR01-Day2-GC5-3]

description: Valproate, 500 mg/kg, Day 2, Repeat 3


title: 3543_OF1A_1-2-K15-L16


title: 3543_OF1A_1-2-K15-L15


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030454LR01-Day2-GC6-5]

description: Valproate, 500 mg/kg, Day 2, Repeat 5


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030287LR01-Day1-GC7-5]

description: Valproate, 500 mg/kg, Day 1, Repeat 5

value: 8-9 months

value: Valproate, 500 mg/kg, Day 1, Repeat 5


title: 3543_OF1A_1-2-K15-K3


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030286LR01-Day1-GC7-4]

description: Valproate, 500 mg/kg, Day 1, Repeat 4

value: Valproate, 500 mg/kg, Day 1, Repeat 4


title: 3543_OF1A_1-2-K15-K16

value: Female


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030285LR01-Day1-GC7-3]

description: Valproate, 500 mg/kg, Day 1, Repeat 3

value: Valproate, 500 mg/kg, Day 1, Repeat 3


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030284LR01-Day1-GC7-2]

description: Valproate, 500 mg/kg, Day 1, Repeat 2

value: Valproate, 500 mg/kg, Day 1, Repeat 2


title: 3543_OF1A_1-2-K15-K15

value: nuclear RNA + genomic DNA


title: 3543_OF1A_1-2-K15-J4


title: 3543_OF1A_1-2-K15-J3


title: 3543_OF1A_1-2-K15-J16


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030279LR01-Day1-GC6-2]

description: Valproate, 500 mg/kg, Day 1, Repeat 2


title: 3543_OF1A_1-2-K15-I4


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030282LR01-Day1-GC6-5]

description: Valproate, 500 mg/kg, Day 1, Repeat 5


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030445LR01-Day2-GC5-1]

description: Valproate, 500 mg/kg, Day 2, Repeat 1


title: 3543_OF1A_1-2-K15-I3


title: 3543_OF1A_1-2-K15-J15


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030278LR01-Day1-GC6-1]

description: Valproate, 500 mg/kg, Day 1, Repeat 1

value: Valproate, 500 mg/kg, Day 1, Repeat 1


title: RNA-Seq of rattus norvegicus: 8 wks male whole blood [Sample_R23030281LR01-Day1-GC6-4]

description: Valproate, 500 mg/kg, Day 1, Repeat 4


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030276LR01-Day1-GC5-4]

description: Valproate, 500 mg/kg, Day 1, Repeat 4


title: 3543_OF1A_1-2-K15-H4


title: 3543_OF1A_1-2-K15-I16


title: 3543_OF1A_1-2-K15-H3


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027081LR01-GD4-3]

description: Tetracyclin, 200 mg/kg, Day 10, Repeat 3

value: 6 wks


title: 3543_OF1A_1-2-K15-G4


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030273LR01-Day1-GC5-1]

description: Valproate, 500 mg/kg, Day 1, Repeat 1


title: RNA-Seq of rattus norvegicus: 8-9 months male whole blood [Sample_R23030283LR01-Day1-GC7-1]

description: Valproate, 500 mg/kg, Day 1, Repeat 1


title: 3543_OF1A_1-2-K15-H16


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030277LR01-Day1-GC5-5]

description: Valproate, 500 mg/kg, Day 1, Repeat 5


title: RNA-Seq of rattus norvegicus: 3-4 wks male whole blood [Sample_R23030274LR01-Day1-GC5-2]

description: Valproate, 500 mg/kg, Day 1, Repeat 2


title: 3543_OF1A_1-2-K15-G3


title: 3543_OF1A_1-2-K15-H15


title: RNA-Seq of rattus norvegicus: 6 wks male whole blood [Sample_R23027080LR01-GD4-2]

description: Tetracyclin, 200 mg/kg, Day 10, Repeat 2


title: 3543_OF1A_1-2-K15-G16


title: 3543_OF1A_1-2-K15-G15