title: CEMBA3C_MacaqueM1_R1_P5-2-C21-I15


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-G3

status: Public on Oct 31 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 trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: Mmul_10 (rheMac10), annotation: Ensembl release 104
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: snmC-seq3

molecule: genomic DNA

organism: Macaca mulatta

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

treatment_protocol: For all snm3C-seq samples, in-situ 3C treatment was done during the nuclei preparation that allows capturing the chromatin conformation modality as described previously22. These steps were carried out using the Arima-3C BETA Kit (Arima Genomics). The nuclei were isolated and sorted into 384-well plates using previous methods21. Briefly, single-nuclei were stained with AlexaFluor488-conjugated anti-NeuN antibody (MAB377X, Millipore) and Hoechst 33342 (62249, ThermoFisher) followed by FANS using a BD Influx sorter with single-cell (1 drop single) mode.

tag: brain region

value: Motor cortex

tag: gender

value: M


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-H15


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-G16


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-I3


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-H4


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-H3


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-I16


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-F15


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-E3


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-F4


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-F3


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-G15


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-F16


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-B3


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-C16


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-C3


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-B4


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-D3


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-D16


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-C4


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-D4


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-C15


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-E15


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-D15


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-E16


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-B16


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-B15


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-A3


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-A15


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-A16


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-P13


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-P14


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-P1


title: CEMBA3C_MacaqueM1_R1_P5-2-C21-A4


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-M14


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-P2


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-O13


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-O14


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-N2


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-O2


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-O1


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-N14


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-N13


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-N1


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-M2


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-M1


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-J2


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-J14


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-K1


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-L1


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-L2


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-K14


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-K13


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-K2


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-L14


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-J13


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-L13


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-J1


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-I2


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-M13


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-I13


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-I1


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-I14


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-F13


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-E2


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-G1


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-H13


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-F1


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-G2


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-H2


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-F2


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-G14


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-H1


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-G13


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-H14


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-F14


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-E14


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-E1


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-E13


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-A14


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-D14


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-B1


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-C2


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-C14


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-D13


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-D1


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-A2


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-C1


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-B14


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-C13


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-B13


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-D2


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-A13


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-A1


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-O12


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-O24


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-O11


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-P23


title: CEMBA3C_MacaqueM1_R1_P5-1-C21-B2


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-N12


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-N11


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-P24


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-M24


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-N23


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-M23


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-P11


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-P12


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-O23


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-N24


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-K12


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-J23


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-M12


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-I24


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-H24


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-M11


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-I12


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-L11


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-L24


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-K23


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-J24


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-H11


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-H23


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-H12


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-G12


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-L23


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-G23


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-J11


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-K24


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-L12


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-J12


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-I23


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-K11


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-G24


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-I11


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-F11


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-F24


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-F12


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-F23


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-G11


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-E24


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-E23


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-A12


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-B23


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-D12


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-P22


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-P9


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-P10


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-A23


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-B24


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-B12


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-B11


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-C11


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-A11


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-D11


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-C23


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-C12


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-O21


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-C24


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-D23


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-E12


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-A24


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-D24


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-N9


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-O10


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-O9


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-N22


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-O22


title: CEMBA3C_MacaqueM1_R1_P4-6-M17-E11


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-P21


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-M9


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-M22


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-M10


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-N10


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-N21


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-M21


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-L21


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-L9


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-L22


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-J22


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-J21


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-L10


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-J9


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-K22


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-K9


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-K10


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-I9


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-I22


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-K21


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-I21


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-E9


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-E22


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-F9


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-G22


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-H10


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-H9


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-F10


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-G21


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-G9


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-H22


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-F21


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-J10


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-G10


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-H21


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-F22


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-E21


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-E10


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-D22


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-D9


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-C10


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-D21


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-C22


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-C9


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-B22


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-B9


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-B21


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-A9


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-B10


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-A21


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-A22


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-A10


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-P20


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-P8


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-O8


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-O19


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-O7


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-P7


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-O20


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-P19


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-C21


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-I10


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-M8


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-N8


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-M19


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-N20


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-N7


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-N19


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-M20


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-M7


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-K19


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-L8


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-K20


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-L7


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-L20


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-J7


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-L19


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-K8


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-J8


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-J19


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-I20


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-J20


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-I7


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-I8


title: CEMBA3C_MacaqueM1_R1_P4-5-M17-D10


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-I19


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-K7


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-H7


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-H20


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-G8


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-H19


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-H8


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-G20


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-G19


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-G7


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-F7


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-F8


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-E8


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-E7


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-E20


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-E19


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-C8


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-D19


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-C20


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-D8


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-D20


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-D7


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-C7


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-A8


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-B7


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-B19


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-B8


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-B20


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-C19


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-A7


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-F19


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-F20


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-A20


title: CEMBA3C_MacaqueM1_R1_P4-4-M17-A19


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-O17


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-O6


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-P6


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-P18


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-P5


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-P17


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-O18


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-O5


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-N18


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-M6


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-M18


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-L6


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-J18


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-N6


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-I6


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-I5


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-L18


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-L17


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-L5


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-K6


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-J6


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-K5


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-M17


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-J5


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-J17


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-I18


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-K17


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-I17


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-K18


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-M5


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-N17


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-H6


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-H17


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-G5


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-H18


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-H5


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-G6


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-G17


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-F6


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-G18


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-F18


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-P15


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-E5


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-E17


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-A18


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-A17


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-B18


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-C17


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-D5


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-A5


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-P16


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-D6


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-P4


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-P3


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-D17


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-B5


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-A6


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-E6


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-C5


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-F17


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-B17


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-D18


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-E18


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-C18


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-B6


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-C6


title: CEMBA3C_MacaqueM1_R1_P4-3-M17-F5


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-O4


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-O16


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-N4


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-O15


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-O3


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-G4


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-G3


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-G16


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-G15


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-J3


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-H15


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-K16


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-N16


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-I3


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-F4


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-M16


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-H16


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-J16


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-I15


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-K4


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-K15


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-L16


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-L4


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-H3


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-M3


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-H4


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-I4


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-M15


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-J4


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-M4


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-J15


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-N15


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-L3


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-L15


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-F3


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-F16


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-F15


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-I16


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-K3


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-E3


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-E15


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-D3


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-D16


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-D4


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-E16


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-P2


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-B16


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-P13


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-A4


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-A16


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-P1


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-C15


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-A15


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-B4


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-C16


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-C3


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-C4


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-A3


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-B3


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-N13


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-O13


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-O1


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-N2


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-O14


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-O2


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-N14


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-P14


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-B15


title: CEMBA3C_MacaqueM1_R1_P4-2-M17-D15


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-M2


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-N1


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-L2


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-M13


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-M1


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-M14


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-L14


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-I14


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-I1


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-H14


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-I13


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-H13


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-H2


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-J14


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-J1


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-K2


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-K13


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-K1


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-J2


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-J13


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-L13


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-K14


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-I2


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-L1


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-D14


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-G2


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-G13


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-F2


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-E2


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-D2


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-F14


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-G1


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-H1


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-E1


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-F13


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-G14


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-F1


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-E14


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-E13


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-D13


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-C14


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-C2


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-D1


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-C13


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-B2


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-B14


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-C1


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-P24


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-P23


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-A1


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-A13


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-B1


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-A14


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-A2


title: CEMBA3C_MacaqueM1_R1_P4-1-M17-B13


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-K12


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-L12


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-N24


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-N12


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-O11


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-K24


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-P11


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-M12


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-K11


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-M11


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-K23


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-O23


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-N23


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-P12


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-O12


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-L24


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-M24


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-L11


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-N11


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-J24


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-M23


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-L23


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-J23


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-J12


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-O24


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-I23


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-I24


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-I12


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-I11


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-H23


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-H11


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-E12


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-G23


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-F12


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-E11


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-E23


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-G12


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-E24


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-H12


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-G24


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-F11


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-F23


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-F24


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-D23


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-H24


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-G11


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-D24


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-C24


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-C12


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-D11


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-C11


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-C23


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-B24


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-B23


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-B12


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-D12


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-A24


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-B11


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-A12


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-A23


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-P9


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-P21


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-A11


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-P22


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-J22


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-I21


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-J10


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-I22


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-H9


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-K10


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-M10


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-I9


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-K9


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-M22


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-O10


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-O9


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-N22


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-O21


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-M9


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-K21


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-P10


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-J9


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-I10


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-J21


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-L9


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-N9


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-M21


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-L22


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-L10


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-N10


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-N21


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-O22


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-L21


title: CEMBA3C_MacaqueM1_R1_P3-6-K15-J11


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-H22


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-H21


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-H10


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-C21


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-B21


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-C10


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-A9


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-B22


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-B9


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-B10


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-A22


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-A21


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-E10


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-C22


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-D10


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-F21


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-G22


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-E9


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-F10


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-G21


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-E21


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-G10


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-F22


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-F9


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-D9


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-D22


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-D21


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-C9


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-G9


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-E22


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-P7


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-P8


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-P20


title: iPSC72 HCO, modified, BMP2, 35 day, Rep 3

city: Cincinnati

first: Daniel

middle: O.

last: Kechele

state: OH

address: 3333 Burnet Ave Location R3.034

department: Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

description: IPSC72_HIOmod_HCOmod_HCO_35d_TPM_Matrix.txt

library_source: transcriptomic

data_processing:
For H1 RNA-seq, FASTQ data was evaluated using FASTQC. Tuxedo Suite was used for alignment and differential expression analysis. Reads were aligned to hg19 using TopHat v2.0.13 and Bowtie v2.2.5 using default parameters except "-2-very-sensitive", "-no-coverage-search", and "-no-novel-juncs". Cufflinks with"-mulit-read-correct", "-compatible-hits-norm", and "-upper-quartile -norm" to generate TPM matrix.
For iPSC72 RNA-seq, data was processed through BGI pipeline. Briefly, sequenced samples were filtered, trimmed of adapters and low-quality read, quality controlled, and aligned to hg38.
Assembly: hg19 H1 RNA-seq
Assembly: hg38 iPSC72 RNA-seq
Supplementary files format and content: tab-delimited text files including TPM per sample

molecule: total RNA

organism: Homo sapiens

source_name: hPSC-derived colonic organoid

extract_protocol:
RNA was extracted using RNA NucleoSpin kit (Macherey-Nagel) according to manufacturer's instructions. >300 ng/sample of RNA used to make RNA library.
For H1, library construction was performed by CCHMC DNA sequencing core using standard Illumina mRNA Stranded Library Preperation protocol. For iPSC72, library construction was performed by BGI.

tag: tissue

value: hPSC-derived colonic organoid

tag: cell line

value: hiPSC 72.3

tag: cell type

value: Pooled organoids epithelium and mesenchyme

tag: age

value: 35 days post-hPSC

tag: treatment

value: BMP2 Day 7-10


title: iPSC72 HIO, modified, NOGGIN, 35 day, Rep 2

source_name: hPSC-derived intestinal organoid

value: hPSC-derived intestinal organoid

value: NOGGIN Day 7-10


title: iPSC72 HCO, BMP2, 35 day, Rep 2


title: iPSC72 HCO, modified, BMP2, 35 day, Rep 2


title: iPSC72 HCO, BMP2, 35 day, Rep 1


title: iPSC72 HCO, modified, BMP2, 35 day, Rep 1


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-O8


title: Daidzein 2

city: Fukuoka

first: Kentaro

last: Nishi

address: 2-3-1 Matsukadai Higashi-ku

department: Life Science

country: Japan

institute: Kyushu sangyo university

description: Daidzein.xlsx

data_processing:
The libraries was subjected to sequencing using the DNBSEQ-G400 (MGISEQ-2000RS, MGI Tech) instrument.
The obtained reads were aligned using splitBarcode (https://github.com/MGI-tech-bioinformatics/splitBarcode).
The read data were downsized to 20 M read pairs using seqkit v0.13.0.
The adopter sequences were cleaned with cutadapt ver.2.10, the read data were mapped with HISAT v2.2.1.
The value of FPKMs (reads per kilobase of transcript per million reads mapped) of each gene was estimated with Cuffdiff v2.2.1.
FPKMs of E2, soy compounds, soymilk extracts and ctrl was used for the processed data files and E2/ctrl, soy compounds/ctrl or soymilk extracts/ctrl was used for caluculating log2.
Assembly: hg19
Supplementary files format and content: log2

source_name: Daidzein-treated cells

growth_protocol: MCF-7 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted using RNeasy mini kit (QIAGEN).
The DNA libraries for sequencing were constructed with Truseq Stranded mRNA Library Prep (Illumina,  San Diego, CA) and MGIEasy Universal Library Conversion Kit (MGI Tech, Shenzhen, PRC).

treatment_protocol: The cells were treated in RPMI1640 including 10 nM E2, 10 uM soy compounds, 10 ug/ml soymilk extracts or 0.1% DMSO (ctrl) for 3 more days.

value: Daidzein-treated cells

value: breast cancer cells

value: Daidzein


title: Daidzein 1

description: Daidzein.xlsx


title: iPSC72 HIO, modified, NOGGIN, 35 day, Rep 1


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-P19


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-O20


title: iPSC72 HCO, BMP2, 35 day, Rep 3


title: Daidzin 2

description: Daidzin.xlsx

source_name: Daidzin-treated cells

value: Daidzin-treated cells

value: Daidzin


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-N20


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-N19


title: CEMBA3C_MacaqueM1_R1_P3-5-K15-A10


title: Genistein 1

description: Genistein.xlsx

source_name: Genistein-treated cells

value: Genistein-treated cells

value: Genistein


title: Fermented Black Soybean 1

source_name: Fermented Black Soybean-treated cells

value: Fermented Black Soybean-treated cells

value: Fermented soymilk extract (Black Soybean)


title: Genistin 2

description: Genistin.xlsx

source_name: Genistin-treated cells

value: Genistin-treated cells

value: Genistin


title: Daidzin 1

description: Daidzin.xlsx


title: Fermented Black Soybean 2


title: Genistein 2

description: Genistein.xlsx


title: Genistin 1

description: Genistin.xlsx


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-M8

value: Motor cortex

value: M


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-M7


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-N8


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-O7


title: Unfermented Black Soybean 1

source_name: Unfermented Black Soybean-treated cells

value: Unfermented Black Soybean-treated cells

value: Unfermented soymilk extract (Black Soybean)


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-O19


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-N7


title: Unfermented Black Soybean 2


title: Fermented Yellow Soybean 1

source_name: Fermented Yellow Soybean-treated cells

value: Fermented Yellow Soybean-treated cells

value: Fermented soymilk extract (Yellow Soybean)


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-M20


title: Unfermented Yellow Soybean 2

source_name: Unfermented Yellow Soybean-treated cells

value: Unfermented soymilk extract (Yellow Soybean)


title: Ctrl 2

source_name: breast cancer cells

value: breast cancer cells


title: Ctrl 3


title: Ctrl 1


title: Fermented Yellow Soybean 2


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-L7


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-L20


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-M19


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-L19


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-J8


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-K20


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-K8


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-K7


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-J20


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-K19


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-J7


title: E2 3

source_name: E2-treated cells

value: E2-treated cells


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-L8


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-I8


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-I7


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-I20


title: Unfermented Yellow Soybean 1

value: Unfermented Yellow Soybean-treated cells


title: E2 2


title: E2 1


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-J19


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-H8


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-H20


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-I19


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-H19


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-H7


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-G19


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-G7


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-G8


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-F7


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-F20


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-F19


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-G20


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-F8


title: normal fat, NF7583_RO

type: RNA

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

hyb_protocol: cRNA was hybridized to U133A_2.0 expression arrays

scan_protocol: Fluorescent signal was measured by laser confocal scanning (Agilent) and converted to signal intesity (Affymetrix Microarray Suite)

data_processing: CEL files were processed and normalized using gcrma methods implemented in the BioConductor package gcrma. Citation: Wu J, Gentry RIwcfJMJ (2023). gcrma: Background Adjustment Using Sequence Information. R package version 2.72.0.

label: biotin

source_name: normal fat

label_protocol: cDNA was prepared by using oligo(dT)24-T7 (Genset Corp.), and cRNA was prepared by using biotinylated UTP and CTP

growth_protocol: not applicable (tissue samples)

extract_protocol: Cryomolds were prepared from tissue samples and macrodissected after evaluation by a sarcoma specific pathologist.  After histologic confirmation, RNA was prepared using Rneasy kits from QIAGEN and hybridization to U133A_2.0 gene expression arrays performed per standard protocols

value: normal fat

tag: tumor grade

value: not applicable


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-D7


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-E7


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-E8


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-E19


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-D8


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-E20


title: normal fat, NF687


title: normal fat, NF9548


title: normal fat, NF4640


title: normal fat, NF106


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-D20


title: desmoid tumor, DES970

source_name: desmoid tumor

value: desmoid tumor

value: low


title: desmoid tumor, DES932


title: desmoid tumor, DES982


title: desmoid tumor, DES958


title: normal fat, NF685


title: desmoid tumor, DES934


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-C7


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-C8


title: desmoid tumor, DES884


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-C20


title: normal fat, NF7583


title: desmoid tumor, DES953


title: normal fat, NF8293


title: desmoid tumor, DES925


title: desmoid tumor, DES948


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-D19


title: desmoid tumor, DES951


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-C19


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-B20


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-B7


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-B19


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-B8


title: normal fat, NF5821


title: desmoid tumor, DES929


title: normal fat, NF678


title: desmoid tumor, DES936


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-A19


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-A8


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-A7


title: CEMBA3C_MacaqueM1_R1_P3-4-K15-A20


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-P6


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-P5


title: desmoid tumor, DES930


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-P18


title: desmoid tumor, DES959


title: desmoid tumor, DES883


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-P17


title: desmoid tumor, DES952


title: desmoid tumor, DES974


title: desmoid tumor, DES981


title: desmoid tumor, DES1002


title: desmoid tumor, DES957


title: desmoid tumor, DES891


title: normal fat, NF6292


title: desmoid tumor, DES1003


title: desmoid tumor, DES950


title: desmoid tumor, DES885


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-O18


title: desmoid tumor, DES997


title: desmoid tumor, DES956


title: desmoid tumor, DES942


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-N6


title: desmoid tumor, DS891


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-O6


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-O5


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-N17


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-O17


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-N18


title: desmoid tumor, DES882


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-M6


title: desmoid tumor, DES924


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-M18


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-M5


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-M17


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-L5


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-K6


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-L6


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-L18


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-L17


title: desmoid tumor, DES888


title: desmoid tumor, DES983


title: desmoid tumor, DES896


title: desmoid tumor, DES949


title: desmoid tumor, DES999


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-K5


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-J17


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-J5


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-K17


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-J6


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-J18


title: desmoid tumor, DES977


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-K18


title: desmoid tumor, DES892


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-I6


title: desmoid tumor, DES1011


title: desmoid tumor, DES940


title: desmoid tumor, DES992


title: desmoid tumor, DES880


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-H6


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-I5


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-H18


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-I17


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-H5


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-H17


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-I18


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-G6


title: desmoid tumor, DES984


title: desmoid tumor, DES979


title: desmoid tumor, DES895


title: desmoid tumor, DES941


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-G18


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-G17


title: desmoid tumor, DES937


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-F6


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-G5


title: desmoid tumor, DES890


title: desmoid tumor, DES881


title: desmoid tumor, DES995


title: desmoid tumor, DES938


title: desmoid tumor, DES955


title: desmoid tumor, DES933


title: desmoid tumor, DES964


title: desmoid tumor, DES886


title: desmoid tumor, DES927


title: desmoid tumor, DES1001


title: desmoid tumor, DES894


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-F18


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-F17


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-E5


title: desmoid tumor, DES926


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-E18


title: desmoid tumor, DES961


title: desmoid tumor, DES969


title: desmoid tumor, DES923


title: desmoid tumor, DES889


title: normal muscle, NM1030

source_name: normal muscle

value: normal muscle


title: desmoid tumor, DES931


title: desmoid tumor, DES943


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-F5


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-E17


title: desmoid tumor, DES998


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-D5


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-D6


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-E6


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-D17


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-D18


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-C6


title: desmoid tumor, DES928


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-B17


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-C17


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-B6


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-C18


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-B18


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-B5


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-A5


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-A6


title: H3i, YPD, Sip4, biol rep2

city: Pathumthani

first: Peerapat

last: Khamwachirapithak

address: Phahonyothin Road, Khlong Luang

country: Thailand

institute: Thammasat University

data_processing:
FastQC
ChIP-seq reads were align to Saccer3 genome using the Bowtie2
Sorting and indexing using Samtools
Samtools depth was used to estimate depth of each sample, and used for normalization
Normalized ChIP-seq coverages were calculated by Bedtools and pseudocount was added, before being converted to bigWig files using WigtoBigWig
Assembly: Saccer3
Supplementary files format and content: bigWig

organism: Saccharomyces cerevisiae

source_name: Cell pellet

growth_protocol: Cells were cultured in YPGal medium at 30°C and 230 rpm before H3-shutoff experiment. The H3 inducible shut-off strain (i.e., “DGS200.1” or  “H3i”) from the YEF473A strain by knocking out the HHT1 gene (encoding H3), and replacing the native promoter of the HHT2 gene (the other H3-encoding gene) with an inducible Gal1 promoter.

extract_protocol:
Cell were fixed with 1% formaldehyde and quenched by Tris pH 8.  Genomic DNA was sonicated, and Rap1 binding DNA  was pulled down using anti-FLAG beads (Sigma, M8223)
ChIP libraries were prepared for sequencing using standard Illumina protocol

treatment_protocol: Switching media to from YPGal to YPD

value: Cell pellet

value: Yeast cell

tag: genotype

tag: antibody

value: anti-FLAG beads (Sigma, M8223)

value: YPD


title: H3i, YPD, Rme1, biol rep2


title: H3i, YPGal, Sip4, biol rep2

value: YPGal


title: WT, YPD, Sip4, biol rep2

value: WT


title: WT, YPGal, Sip4, biol rep2


title: H3i, YPD, Aft2, biol rep2


title: H3i, YPGal, Rox1, biol rep2


title: H3i, YPD, Rox1, biol rep2


title: WT, YPGal, Rme1, biol rep2


title: WT, YPGal, Rox1, biol rep2


title: WT, YPD, Rox1, biol rep2


title: H3i, YPGal, Rme1, biol rep2


title: WT, YPD, Rme1, biol rep2


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-A18

value: Motor cortex

value: M


title: normal muscle, NM1027


title: normal muscle, NM1021


title: normal muscle, NM1031


title: CEMBA3C_MacaqueM1_R1_P3-3-K15-A17


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-P16


title: WT, YPD, Aft2, biol rep2


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-P4


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-P3


title: H3i, YPD, Zms1, biol rep1


title: normal muscle, NM1025


title: WT, YPGal, Aft2, biol rep2


title: H3i, YPGal, Zms1, biol rep1


title: WT, YPD, Zms1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-O4


title: WT, YPGal, Zms1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-P15


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-O3


title: WT, YPD, Yox1, biol rep1


title: H3i, YPD, Yox1, biol rep1


title: WT, YPGal, Yox1, biol rep1


title: H3i, YPGal, Yox1, biol rep1


title: H3i, YPGal, Aft2, biol rep2


title: H3i, YPD, Yap1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-O16


title: normal muscle, NM1028


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-O15


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-N4


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-N16


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-N15


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-L3


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-M3


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-K3


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-M16


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-L16


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-L4


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-M4


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-K16


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-L15


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-K4


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-M15


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-K15


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-J4


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-J3


title: WT, YPD, Usv1, biol rep1


title: H3i, YPD, War1, biol rep1


title: WT, YPGal, War1, biol rep1


title: WT, YPD, Yap1, biol rep1


title: H3i, YPD, Xbp1, biol rep1


title: WT, YPGal, Xbp1, biol rep1


title: WT, YPD, War1, biol rep1


title: H3i, YPGal, Yap1, biol rep1


title: H3i, YPD, Usv1, biol rep1


title: H3i, YPGal, Xbp1, biol rep1


title: WT, YPGal, Yap1, biol rep1


title: WT, YPD, Xbp1, biol rep1


title: H3i, YPGal, War1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-J16


title: WT, YPD, Ume6, biol rep1


title: H3i, YPGal, Ume6, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-J15


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-I16


title: H3i, YPD, Ume6, biol rep1


title: H3i, YPD, Tos8, biol rep1


title: WT, YPGal, Usv1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-I3


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-I4


title: H3i, YPGal, Usv1, biol rep1


title: WT, YPGal, Ume6, biol rep1


title: normal muscle, NM1023


title: WT, YPGal, Tos8, biol rep1


title: WT, YPD, Tos8, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-H16


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-H15


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-F3


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-E3


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-G3


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-H4


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-F16


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-G16


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-H3


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-F15


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-I15


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-F4


title: H3i, YPD, Tec1, biol rep1


title: H3i, YPD, Tbp1, biol rep1


title: WT, YPD, Tbp1, biol rep1


title: H3i, YPGal, Tec1, biol rep1


title: WT, YPGal, Tec1, biol rep1


title: H3i, YPGal, Tos8, biol rep1


title: H3i, YPGal, Tbp1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-G4


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-G15


title: WT, YPD, Tec1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-E16


title: H3i, YPGal, Skn7, biol rep1


title: H3i, YPD, Skn7, biol rep1


title: WT, YPGal, Tbp1, biol rep1


title: WT, YPD, Skn7, biol rep1


title: H3i, YPD, Sip4, biol rep1


title: WT, YPGal, Sip4, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-E15


title: WT, YPD, Sip4, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-D15


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-D4


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-D3


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-C15


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-D16


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-C16


title: WT, YPGal, Skn7, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-C4


title: H3i, YPGal, Sip4, biol rep1


title: WT, YPD, Sfl1, biol rep1


title: WT, YPD, Rsc30, biol rep1


title: H3i, YPGal, Sfl1, biol rep1


title: H3i, YPGal, Rsc30, biol rep1


title: H3i, YPD, Rsc30, biol rep1


title: WT, YPGal, Rsc30, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-B16


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-B3


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-B4


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-C3


title: H3i, YPD, Sfl1, biol rep1


title: WT, YPGal, Sfl1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-A4


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-B15


title: H3i, YPD, Rsc3, biol rep1


title: H3i, YPGal, Rsc3, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-A15


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-A3


title: H3i, YPGal, Rpn4, biol rep1


title: WT, YPGal, Rpn4, biol rep1


title: H3i, YPD, Rpn4, biol rep1


title: WT, YPGal, Rsc3, biol rep1


title: H3i, YPGal, Rox1, biol rep1


title: H3i, YPD, Rox1, biol rep1


title: WT, YPD, Rox1, biol rep1


title: WT, YPD, Rpn4, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-2-K15-A16


title: WT, YPGal, Rox1, biol rep1


title: H3i, YPGal, Rme1, biol rep1


title: WT, YPGal, Rme1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-P14


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-P2


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-O1


title: WT, YPD, Rsc3, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-N1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-O2


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-N14


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-N2


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-P13


title: WT, YPD, Rme1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-P1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-O14


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-O13


title: H3i, YPD, Rme1, biol rep1


title: WT, YPGal, Reb1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-M2


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-N13


title: normal muscle, NM1022


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-M13


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-M14


title: H3i, YPD, Reb1, biol rep1


title: H3i, YPGal, Put3, biol rep1


title: WT, YPD, Put3, biol rep1


title: H3i, YPGal, Reb1, biol rep1


title: WT, YPD, Reb1, biol rep1


title: WT, YPGal, Put3, biol rep1


title: H3i, YPGal, Pho4, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-M1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-L13


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-L2


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-J2


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-K13


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-K2


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-L14


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-K1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-L1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-J14


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-K14


title: H3i, YPD, Put3, biol rep1


title: H3i, YPD, Pho4, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-J13


title: WT, YPD, Pho4, biol rep1


title: H3i, YPD, Pho2, biol rep1


title: H3i, YPGal, Pho2, biol rep1


title: WT, YPD, Pho2, biol rep1


title: WT, YPGal, Pho4, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-J1


title: H3i, YPD, Phd1, biol rep1


title: WT, YPGal, Pho2, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-I2


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-I13


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-I14


title: H3i, YPD, Oaf1, biol rep1


title: H3i, YPGal, Oaf1, biol rep1


title: H3i, YPGal, Phd1, biol rep1


title: H3i, YPD, Msn4, biol rep1


title: WT, YPD, Msn4, biol rep1


title: WT, YPD, Phd1, biol rep1


title: WT, YPD, Oaf1, biol rep1


title: H3i, YPGal, Msn4, biol rep1


title: WT, YPGal, Oaf1, biol rep1


title: WT, YPGal, Phd1, biol rep1


title: WT, YPGal, Msn4, biol rep1


title: WT, YPD, Msn2, biol rep1


title: WT, YPGal, Msn2, biol rep1


title: H3i, YPD, Msn2, biol rep1


title: H3i, YPD, Mga1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-E2


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-H2


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-G2


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-F2


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-H13


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-H14


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-G1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-H1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-F13


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-G13


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-F14


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-G14


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-I1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-F1


title: H3i, YPGal, Msn2, biol rep1


title: WT, YPD, Mga1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-E1


title: H3i, YPGal, Mga1, biol rep1


title: WT, YPGal, Mga1, biol rep1


title: WT, YPGal, Mbp1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-E13


title: H3i, YPD, Ino4, biol rep1


title: H3i, YPGal, Mbp1, biol rep1


title: WT, YPGal, Ino4, biol rep1


title: H3i, YPGal, Ino4, biol rep1


title: WT, YPD, Ino4, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-C1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-C13


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-C2


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-D13


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-C14


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-E14


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-D2


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-D14


title: H3i, YPD, Htz1, biol rep1


title: H3i, YPGal, Htz1, biol rep1


title: WT, YPD, Htz1, biol rep1


title: WT, YPD, Mbp1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-D1


title: H3i, YPD, Mbp1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-A14


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-A2


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-B13


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-B14


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-A1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-B2


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-B1


title: CEMBA3C_MacaqueM1_R1_P3-1-K15-A13


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-P11


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-O12


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-O11


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-O24


title: H3i, YPD, Hap4, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-P24


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-P12


title: WT, YPGal, Hmra2, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-P23


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-O23


title: H3i, YPD, Hmra2, biol rep1


title: H3i, YPGal, Hsf1, biol rep1


title: WT, YPGal, Hsf1, biol rep1


title: H3i, YPGal, Hms2, biol rep1


title: WT, YPD, Hmra2, biol rep1


title: WT, YPGal, Htz1, biol rep1


title: WT, YPGal, Hms2, biol rep1


title: WT, YPD, Hsf1, biol rep1


title: WT, YPD, Hms2, biol rep1


title: H3i, YPD, Hsf1, biol rep1


title: H3i, YPD, Hms2, biol rep1


title: H3i, YPGal, Hmra2, biol rep1


title: H3i, YPD, Gln3, biol rep1


title: WT, YPD, Hap4, biol rep1


title: H3i, YPGal, Hap4, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-N11


title: WT, YPGal, Hap4, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-N24


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-N12


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-N23


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-M23


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-M24


title: H3i, YPGal, Gln3, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-M12


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-M11


title: WT, YPD, Gln3, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-J24


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-I24


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-L11


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-L23


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-I23


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-K11


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-J11


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-J12


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-K24


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-J23


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-L12


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-K12


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-K23


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-L24


title: H3i, YPD, Gat1, biol rep1


title: WT, YPD, Gis1, biol rep1


title: WT, YPD, Fhl1, biol rep1


title: H3i, YPD, Fhl1, biol rep1


title: H3i, YPGal, Fhl1, biol rep1


title: WT, YPD, Gcn4, biol rep1


title: H3i, YPGal, Gat1, biol rep1


title: WT, YPD, Gat1, biol rep1


title: H3i, YPD, Gcn4, biol rep1


title: WT, YPGal, Gis1, biol rep1


title: WT, YPGal, Gat1, biol rep1


title: WT, YPGal, Gln3, biol rep1


title: WT, YPGal, Gcn4, biol rep1


title: H3i, YPGal, Gis1, biol rep1


title: H3i, YPD, Gis1, biol rep1


title: H3i, YPGal, Gcn4, biol rep1


title: WT, YPGal, Fhl1, biol rep1


title: WT, YPD, Cup9, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-I12


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-I11


title: H3i, YPGal, Cup9, biol rep1


title: H3i, YPD, Cup9, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-G24


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-H11


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-H24


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-H12


title: WT, YPGal, Cup9, biol rep1


title: H3i, YPGal, Cst6, biol rep1


title: H3i, YPD, Cst6, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-H23


title: WT, YPD, Cst6, biol rep1


title: WT, YPD, Cin5, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-G12


title: H3i, YPGal, Cin5, biol rep1


title: WT, YPGal, Cin5, biol rep1


title: H3i, YPD, Cin5, biol rep1


title: H3i, YPD, Cbf1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-G11


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-G23


title: WT, YPGal, Cst6, biol rep1


title: H3i, YPGal, Azf1, biol rep1


title: WT, YPD, Cbf1, biol rep1


title: WT, YPGal, Cbf1, biol rep1


title: WT, YPGal, Azf1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-F11


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-F23


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-F12


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-E12


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-E11


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-E24


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-E23


title: WT, YPD, Azf1, biol rep1


title: H3i, YPD, Aft2, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-F24


title: H3i, YPGal, Cbf1, biol rep1


title: WT, YPD, Aft2, biol rep1


title: H3i, YPGal, Aft2, biol rep1


title: H3i, YPD, Azf1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-D11


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-C24


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-D12


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-C23


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-D23


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-C12


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-C11


title: H3i, YPD, Abf1, biol rep1


title: WT, YPGal, Aft2, biol rep1


title: WT, YPGal, Abf1, biol rep1


title: WT, YPD, Abf1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-B11


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-A24


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-D24


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-A23


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-A11


title: H3i, YPGal, inputRap1, biol rep1

data_processing:
FastQC
ChIP-seq reads were aligned to Saccer3 genome using the Bowtie2
Sorting and indexing using Samtools
Samtools depth was used to estimate depth of each sample, and used for normalization
Normalized ChIP-seq coverages were calculated by Bedtools and pseudocount was added, before being converted to bigWig files using WigtoBigWig
Assembly: Saccer3
Supplementary files format and content: bigWig

tag: chip antibody


title: H3i, YPD, inputRap1, biol rep1


title: WT, YPGal, inputRap1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-P22


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-P9


title: H3i, YPD, Rap1, biol rep2


title: H3i, YPGal, Rap1, biol rep2


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-A12


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-B23


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-B12


title: WT, YPD, inputRap1, biol rep1


title: H3i, YPGal, Abf1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-6-J11-B24


title: WT, YPD, Rap1, biol rep2


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-P10


title: H3i, YPGal, Rap1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-P21


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-O9


title: H3i, YPD, Rap1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-O22


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-O21


title: WT, YPD, Rap1, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-O10


title: WT, YPGal, Rap1, biol rep1


title: WT, YPGal, Rap1, biol rep2


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-N10


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-M22


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-N21


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-M10


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-M9


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-K9


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-L9


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-N9


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-L10


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-L22


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-M21


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-L21


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-N22


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-K21


title: H3i, YPGal, H3, biol rep1

data_processing:
FastQC
ChIP-seq reads were align to Saccer3 genome using the Bowtie2
Sorting and indexing using Samtools
Samtools depth was used to estimated depth of each sample, and used for spike-in normalization
Spike-in normalized ChIP-seq coverages were calculated by Bedtools and pseudocount was added, before being converted to bigWig files using WigtoBigWig
Assembly: Saccer3
Supplementary files format and content: bigWig

extract_protocol:
Cell were fixed with 1% formaldehyde and quenched by Tris pH 8.  Genomic DNA was fragmented by MNase enzyme, and H3-binding DNA pull down using anti-H3 antibody coupled with Dynabeads magnetic protein A beads
ChIP libraries were prepared for sequencing using standard Illumina protocol

value: Anti-histone H3 (Abcam, ab1791)


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-K22


title: WT, YPGal, H3, biol rep1


title: WT, YPD, input, biol rep1


title: WT, YPD, H3, biol rep1


title: H3i, YPD, H3, biol rep1


title: H3i, YPD, input, biol rep1


title: WT, YPGal, input, biol rep1


title: H3i, YPGal, input, biol rep1


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-K10


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-J21


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-J10


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-J22


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-J9


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-I9


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-I22


title: genomic DNA from NB62

type: genomic

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

description: biopsy gastric mucosa

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2
Average Beta or normalized (provide the normalization method) Average Beta
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from the clinical samples using QIAamp DNA FFPE Tissue Kit according to standard instructions

value: Male

tag: sample type

value: clinical sample

tag: disease state

value: normal


title: genomic DNA from NB61

description: biopsy gastric mucosa


title: genomic DNA from NB55

description: biopsy gastric mucosa


title: genomic DNA from NB56

description: biopsy gastric mucosa


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-I10


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-I21


title: genomic DNA from NB41

description: biopsy gastric mucosa


title: genomic DNA from NB53

description: biopsy gastric mucosa


title: EFL132488

city: Guiyang

first: Renxiang

last: Liu

state: Guizhou

address: Huaxi

country: China

institute: Guizhou University

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep(https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean reads were separately aligned to reference genome（https://solgenomics.net/organism/Nicotiana_tabacum/genome） with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)software.
The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) .
RSEM （http://deweylab.github.io/RSEM/）establishes the maximum likelihood abundance estimation model based on the maximum expectation algorithm, and considers the paid end reads, the length of reads, the length distribution of fragments, and the quality value to distinguish which transcripts are different subtypes of the same gene. The results of expression quantification are expressed in TPM/FPKM. The homogenization process of TPM/FPKM makes the total expression amount in different samples consistent.
Assembly: Tobacco K326 Reference Genome（https://solgenomics.net/organism/Nicotiana_tabacum/genome）
Supplementary files format and content: all_ express.txt includes 9 transcriptome sequencing materials and 69500 gene expressions. The file can be opened in Excel for viewing.

organism: Nicotiana tabacum

source_name: Young leaf

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) andquantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. After quantified by TBS380, paired-end RNA-seq  sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 ×  150bp read length)

tag: developmental stage

value: squaring period

value: Young leaf


title: EFL132491


title: EFL132485


title: EFL132486


title: EFL132487


title: EFL132484


title: EFL132490


title: EFL132483


title: EFL132489


title: genomic DNA from NB39

description: biopsy gastric mucosa

value: Female


title: ATF3-CKO_rGAS6, biological rep2

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

description: Gene expression data from rGAS6-stimulated BMDMs from ATF3-CKO mouse

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45℃ on [MTA-1_0] Affymetrix Mouse Transcriptome Array 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned by GeneChip® Scanner 3000.

data_processing:
The data were analyzed with Expression Console™, Version 1.3.1.
RMA signal intensity

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-8 ug total RNA

growth_protocol: BMDMs were isolated from the femurs and tibiae of adult mice and differentiated into macrophages in RPMI-1640 medium supplemented with 20 ng/mL recombinant murine macrophage colony-stimulating factor (M-CSF) (Peprotech, 315-02) for five days.

extract_protocol: For microarray profiling, the BMDMs total RNA was harvested using TRIzol reagent (Invitrogen, Carlsbad, Canada) and purified using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. The amount and quality of RNA were determined using UV-Vis Spectrophotometer (Thermo, NanoDrop 2000, USA) at the absorbance of 260 nm. The mRNA expression profiling was measured using Affymetrix ClariomTM D mouse Array (Affymetrix GeneChip, Santa Clara CA, USA), which contains 65957 gene-level probe sets.

treatment_protocol: GAS6-induced MerTK+ macrophages of WT or ATF3-CKO mice were harvested 24 hours following HR and performed to further analysis.

tag: strain

value: BMDMs


title: genomic DNA from NB33

description: biopsy gastric mucosa


title: WT_rGAS6, biological rep2

description: Gene expression data from rGAS6-stimulated BMDMs from WT mouse

source_name: rGAS6-stimulated BMDMs from WT mouse


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-H10


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-H21


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-G22


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-F9


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-H9


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-G21


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-G10


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-H22


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-G9


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-F22


title: genomic DNA from NB27

description: biopsy gastric mucosa


title: genomic DNA from NB24

description: biopsy gastric mucosa


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-F21


title: WT_rGAS6, biological rep3


title: genomic DNA from NB23

description: biopsy gastric mucosa


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-F10


title: genomic DNA from NB26

description: biopsy gastric mucosa


title: genomic DNA from NB25

description: biopsy gastric mucosa


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-E22


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-E9


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-E21


title: genomic DNA from NB31

description: biopsy gastric mucosa


title: genomic DNA from NB29

description: biopsy gastric mucosa


title: genomic DNA from NB28

description: biopsy gastric mucosa


title: genomic DNA from NB22

description: biopsy gastric mucosa


title: ATF3-CKO_rGAS6, biological rep1

source_name: rGAS6-stimulated BMDMs from ATF3-CKO mouse


title: WT_rGAS6, biological rep1


title: genomic DNA from NB21

description: biopsy gastric mucosa


title: genomic DNA from NB19

description: biopsy gastric mucosa


title: genomic DNA from NB20

description: biopsy gastric mucosa


title: genomic DNA from NB15

description: biopsy gastric mucosa


title: genomic DNA from NB17

description: biopsy gastric mucosa


title: genomic DNA from NB16

description: biopsy gastric mucosa


title: genomic DNA from NB14

description: biopsy gastric mucosa


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-D9


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-C21


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-C22


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-C9


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-D10


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-D22


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-E10


title: genomic DNA from NB18

description: biopsy gastric mucosa


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-D21


title: genomic DNA from NB8

description: biopsy gastric mucosa


title: genomic DNA from NB12

description: biopsy gastric mucosa


title: genomic DNA from NB6

description: biopsy gastric mucosa


title: genomic DNA from NB4

description: biopsy gastric mucosa


title: genomic DNA from NB9

description: biopsy gastric mucosa


title: genomic DNA from NB1

description: biopsy gastric mucosa


title: genomic DNA from NB11

description: biopsy gastric mucosa


title: genomic DNA from NB3

description: biopsy gastric mucosa


title: genomic DNA from NB2

description: biopsy gastric mucosa


title: genomic DNA from NB7

description: biopsy gastric mucosa


title: genomic DNA from NB10

description: biopsy gastric mucosa


title: genomic DNA from NB0

description: biopsy gastric mucosa


title: genomic DNA from C23

description: biopsy gastric mucosa


title: ATF3-CKO_rGAS6, biological rep3


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-P7


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-A21


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-A22


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-B9


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-P20


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-B22


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-B21


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-P19


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-O8


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-B10


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-O7


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-A9


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-A10


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-P8


title: CEMBA3C_MacaqueM1_R1_P2-5-J11-C10


title: genomic DNA from C19

description: biopsy gastric mucosa


title: genomic DNA from C14

description: biopsy gastric mucosa


title: genomic DNA from C9

description: biopsy gastric mucosa


title: genomic DNA from C15

description: biopsy gastric mucosa


title: genomic DNA from C6

description: biopsy gastric mucosa


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-O20


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-N19


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-N20


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-N7


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-O19


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-N8


title: genomic DNA from C2

description: biopsy gastric mucosa


title: genomic DNA from N63

description: gastric mucosa surrounding cancer


title: genomic DNA from N83

description: gastric mucosa surrounding cancer


title: genomic DNA from N60

description: gastric mucosa surrounding cancer


title: genomic DNA from C7

description: biopsy gastric mucosa


title: genomic DNA from N73

description: gastric mucosa surrounding cancer


title: genomic DNA from N68

description: gastric mucosa surrounding cancer


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-M20


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-M8


title: genomic DNA from N56

description: gastric mucosa surrounding cancer


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-M7


title: genomic DNA from C1

description: biopsy gastric mucosa


title: genomic DNA from N59

description: gastric mucosa surrounding cancer


title: genomic DNA from N33

description: gastric mucosa surrounding cancer


title: genomic DNA from N24

description: gastric mucosa surrounding cancer


title: genomic DNA from N31

description: gastric mucosa surrounding cancer


title: genomic DNA from N27

description: gastric mucosa surrounding cancer


title: genomic DNA from N30

description: gastric mucosa surrounding cancer


title: genomic DNA from N46

description: gastric mucosa surrounding cancer


title: genomic DNA from N43

description: gastric mucosa surrounding cancer


title: genomic DNA from N34

description: gastric mucosa surrounding cancer


title: genomic DNA from N29

description: gastric mucosa surrounding cancer


title: genomic DNA from N26

description: gastric mucosa surrounding cancer


title: genomic DNA from N25

description: gastric mucosa surrounding cancer


title: genomic DNA from N22

description: gastric mucosa surrounding cancer


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-J19


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-M19


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-J20


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-I20


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-K20


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-L19


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-I7


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-K19


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-K8


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-I8


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-L8


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-I19


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-J7


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-L7


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-J8


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-K7


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-L20


title: genomic DNA from N21

description: gastric mucosa surrounding cancer


title: genomic DNA from N16

description: gastric mucosa surrounding cancer


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-H8


title: genomic DNA from N17

description: gastric mucosa surrounding cancer


title: genomic DNA from N20

description: gastric mucosa surrounding cancer


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-H7


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-G7


title: genomic DNA from N10

description: gastric mucosa surrounding cancer


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-H19


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-H20


title: genomic DNA from NB13

description: biopsy gastric mucosa


title: genomic DNA from N8

description: gastric mucosa surrounding cancer


title: genomic DNA from N2

description: gastric mucosa surrounding cancer


title: genomic DNA from T68

description: gastric cancer

value: cancer


title: genomic DNA from N7

description: gastric mucosa surrounding cancer


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-G20


title: genomic DNA from T63

description: gastric cancer


title: genomic DNA from T74

description: gastric cancer


title: genomic DNA from T73

description: gastric cancer


title: genomic DNA from T60

description: gastric cancer


title: genomic DNA from T59

description: gastric cancer


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-G8


title: genomic DNA from T56

description: gastric cancer


title: genomic DNA from N15

description: gastric mucosa surrounding cancer


title: genomic DNA from T46

description: gastric cancer


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-E7


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-D7


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-D20


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-F7


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-E8


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-E19


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-F8


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-G19


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-F20


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-E20


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-D8


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-D19


title: genomic DNA from T34

description: gastric cancer


title: genomic DNA from T33

description: gastric cancer


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-C8


title: genomic DNA from T31

description: gastric cancer


title: genomic DNA from T43

description: gastric cancer


title: genomic DNA from T29

description: gastric cancer


title: genomic DNA from T27

description: gastric cancer


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-C7


title: genomic DNA from T25

description: gastric cancer


title: genomic DNA from T24

description: gastric cancer


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-C20


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-B7


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-C19


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-B20


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-B8


title: genomic DNA from T26

description: gastric cancer


title: genomic DNA from T30

description: gastric cancer


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-F19


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-B19


title: genomic DNA from T21

description: gastric cancer


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-A8


title: genomic DNA from T16

description: gastric cancer


title: genomic DNA from T15

description: gastric cancer


title: genomic DNA from T17

description: gastric cancer


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-A20


title: genomic DNA from T20

description: gastric cancer


title: genomic DNA from T8

description: gastric cancer


title: genomic DNA from T22

description: gastric cancer


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-A7


title: genomic DNA from T10

description: gastric cancer


title: genomic DNA from T2

description: gastric cancer


title: genomic DNA from T7

description: gastric cancer


title: genomic DNA from B68

description: biopsy gastric mucosa


title: genomic DNA from B63_1

description: biopsy gastric mucosa


title: genomic DNA from B47

description: biopsy gastric mucosa


title: genomic DNA from B63

description: biopsy gastric mucosa


title: genomic DNA from B46

description: biopsy gastric mucosa


title: genomic DNA from B43

description: biopsy gastric mucosa


title: genomic DNA from B38_1

description: biopsy gastric mucosa


title: genomic DNA from B35

description: biopsy gastric mucosa


title: genomic DNA from B33

description: biopsy gastric mucosa


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-P6


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-P5


title: CEMBA3C_MacaqueM1_R1_P2-4-J11-A19


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-P18


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-N5


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-O18


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-O17


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-L5


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-M18


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-L6


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-P17


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-O6


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-O5


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-N17


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-M6


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-N18


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-M17


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-M5


title: genomic DNA from B29

description: biopsy gastric mucosa


title: genomic DNA from B32

description: biopsy gastric mucosa


title: genomic DNA from B30

description: biopsy gastric mucosa


title: genomic DNA from B31

description: biopsy gastric mucosa


title: genomic DNA from B26

description: biopsy gastric mucosa


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-K6


title: genomic DNA from B25_1

description: biopsy gastric mucosa


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-N6


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-L18


title: genomic DNA from B21_2

description: biopsy gastric mucosa


title: genomic DNA from B27_2

description: biopsy gastric mucosa


title: genomic DNA from B21_1

description: biopsy gastric mucosa


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-K17


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-K18


title: genomic DNA from B17_1

description: biopsy gastric mucosa


title: genomic DNA from UT36N

description: gastric mucosa surrounding cancer


title: genomic DNA from B15_1

description: biopsy gastric mucosa


title: genomic DNA from B10_2

description: biopsy gastric mucosa


title: genomic DNA from B11

description: biopsy gastric mucosa


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-J18


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-J6


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-J17


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-L17


title: genomic DNA from B11_1

description: biopsy gastric mucosa


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-J5


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-I5


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-I6


title: genomic DNA from UT34T

description: gastric cancer


title: genomic DNA from UT34N

description: gastric mucosa surrounding cancer


title: genomic DNA from UT33N

description: gastric mucosa surrounding cancer


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-I18


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-K5


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-H6


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-H18


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-H5


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-I17


title: genomic DNA from UT36T

description: gastric cancer


title: genomic DNA from B16

description: biopsy gastric mucosa


title: genomic DNA from UT32N

description: gastric mucosa surrounding cancer


title: genomic DNA from UT31N

description: gastric mucosa surrounding cancer


title: genomic DNA from UT30N

description: gastric mucosa surrounding cancer


title: genomic DNA from UT30T

description: gastric cancer


title: genomic DNA from UT32T

description: gastric cancer


title: genomic DNA from UT31T

description: gastric cancer


title: genomic DNA from UT29T

description: gastric cancer


title: genomic DNA from UT27N

description: gastric mucosa surrounding cancer


title: genomic DNA from UT28N

description: gastric mucosa surrounding cancer


title: genomic DNA from UT33T

description: gastric cancer


title: genomic DNA from UT29N

description: gastric mucosa surrounding cancer


title: genomic DNA from UT27T

description: gastric cancer


title: genomic DNA from UT26N

description: gastric mucosa surrounding cancer


title: genomic DNA from UT25T

description: gastric cancer


title: genomic DNA from UT24N

description: gastric mucosa surrounding cancer


title: genomic DNA from UT24T

description: gastric cancer


title: genomic DNA from UT22N

description: gastric mucosa surrounding cancer


title: genomic DNA from UT22T

description: gastric cancer


title: genomic DNA from UT26T

description: gastric cancer


title: genomic DNA from UT20T

description: gastric cancer


title: genomic DNA from UT19T

description: gastric cancer


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-D18


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-E6


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-G6


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-C5


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-E5


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-C17


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-F5


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-G5


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-H17


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-D5


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-C6


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-D17


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-F6


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-F17


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-E17


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-C18


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-G18


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-B6


title: genomic DNA from UT18T

description: gastric cancer


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-D6


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-E18


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-F18


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-B5


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-G17


title: genomic DNA from UT16N

description: gastric mucosa surrounding cancer


title: genomic DNA from UT17T

description: gastric cancer


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-B18


title: genomic DNA from UT25N

description: gastric mucosa surrounding cancer


title: genomic DNA from UT16T

description: gastric cancer


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-A6


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-B17


title: genomic DNA from UT3N

description: gastric mucosa surrounding cancer


title: genomic DNA from UT11T

description: gastric cancer


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-A5


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-P16


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-P4


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-P3


title: genomic DNA from UT5N

description: gastric mucosa surrounding cancer


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-A18


title: genomic DNA from UT1T

description: gastric cancer


title: genomic DNA from UT1N

description: gastric mucosa surrounding cancer


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-N3


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-N16


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-P15


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-O3


title: genomic DNA from UT13T

description: gastric cancer


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-N4


title: CEMBA3C_MacaqueM1_R1_P2-3-J11-A17


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-O4


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-O16


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-O15


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-L4


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-M3


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-N15


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-M16


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-M4


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-M15


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-L16


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-L3


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-L15


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-K3


title: RNA-Seq CardiacProgenitor_WT_rep3

city: Boston

first: Syndi

last: Barish

state: MA

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

data_processing:
Sequences mapped using Kallisto
Differential gene expression of each sample was determined using Sleuth
Assembly: hg38
Supplementary files format and content: tab deliminated text files containing all sleuth output fields

growth_protocol: iPSCs were maintained in feeder-free conditions on matrigel coated plates and fed mTESR. Cardiomyocytes were made according to Lian et al., 2012.

extract_protocol:
Qiagen RNeasy mini kit with the RNase-Free DNase Set
Poly-A selection

value: iPSC-derived Cardiac Progenitor

value: wild type


title: RNA-Seq CardiacMesoderm_WT_rep2

value: iPSC-derived Cardiac Mesoderm


title: RNA-Seq Cardiomyocyte_UBE2B-/-1_rep2

value: iPSC-derived Cardiomyocyte

value: UBE2B-/- strain 1


title: RNA-Seq Cardiomyocyte_UBE2B-/-1_rep1


title: RNA-Seq Cardiomyocyte_UBE2B-/-2_rep3

value: UBE2B-/- strain 2


title: RNA-Seq Cardiomyocyte_UBE2B-/-2_rep1


title: RNA-Seq CardiacProgenitor_WT_rep1


title: RNA-Seq CardiacProgenitor_WT_rep2


title: RNA-Seq CardiacMesoderm_WT_rep1


title: RNA-Seq Cardiomyocyte_UBE2B-/-2_rep2


title: RNA-Seq Cardiomyocyte_UBE2B-/-1_rep3


title: RNA-Seq Cardiomyocyte_WT_rep3


title: RNA-Seq CardiacMesoderm_WT_rep3


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-K16

value: Motor cortex


title: rRNA2

city: cambridge

first: Jonathan

middle: Lewis

last: Price

address: The Sanger Building Tennis Court Road

department: Biochemistry

country: United Kingdom

institute: University of Cambridge

description: Unenriched COMRADES sample data

data_processing:
Trim adaptors - Cutadapt (params -b AGATCGGAAGAGCACACGTCTGAACTCCAGTC, -B AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT)
Merge Reads - Pear - https://cme.h-its.org/exelixis/web/software/pear/ (params: min-assembly-length 20, -v 7, and -j 5)
Merge UMI - https://gitlab.com/tdido/tstk (Params - --minreads 1)
Trim UMI - Cutadapt (params -m 10, -u 6)
STAR (https://github.com/alexdobin/STAR) (params: runThreadN 5, --genomeLoad NoSharedMemory, --outReadsUnmapped Fastx, --outFilterMultimapNmax 10000, --outFilterScoreMinOverLread 0, --outFilterMatchNminOverLread 0, --outSAMattributes All, --outSAMtype BAM SortedByCoordinate, --alignIntronMin 5, --alignIntronMax 3900000000, --seedSearchStartLmax 14, --seedSplitMin 14, --scoreGap 0, --scoreGapNoncan 0, --scoreGapGCAG 0, --scoreGapATAC 0, --scoreGenomicLengthLog2scale -0.1, --chimFilter None, --chimOutType WithinBAM HardClip, --chimSegmentMin 7, --chimJunctionOverhangMin 8, --chimScoreJunctionNonGTAG 0, --chimScoreDropMax 150, and --chimMainSegmentMultNmax 10000_
Assembly: hg38
Supplementary files format and content: Processed data as outputted from the nextflow pipeline, these are the input for the comradesOO R packge. TSV file with mapping locations of reads.

source_name: Huh-7 cells

extract_protocol:
The COMRADES assay was performed as described previously (Ziv et al., 2018). In brief, RNA was fragmented using RNase III (Ambion) and biotin was attached to crosslinked RNA duplexes using Click-IT Biotin sDIBO Alkyne (Life technologies). Biotinylated RNA duplexes were enriched using Dynabeads MyOne Streptavidin C1(Invitrogen) at the following reaction conditions: 100 mM Tris-Cl pH 7.5, 10 mM EDTA, 1 M NaCl, 0.1% Tween-20, 0.5 unit/µl Superase-In. Beads were washed 5 times on a magnet with 100 mM Tris-HCl pH 7.5, 10 mM EDTA, 3.5M NaCl, 0.1% Tween-20. RNA was eluted by adding 95% Formamide, 10 mM EDTA solution preheated to 65oC and purified using RNA Clean & Concentrator (Zymo Research). Each RNA sample was divided in two: one half was used for proximity ligation and then crosslink reversal (i.e. COMRADES sample), while in the other half, crosslink reversal was done before proximity ligation (i.e. control sample). Prior to proximity ligation, RNA was denatured by briefly heating to 95 °C. Proximity ligation was done under the following conditions: 1 unit/µl RNA ligase 1 (New England Biolabs), 1x RNA ligase buffer, 50 mM ATP, 1 unit/µl Superase-in (Invitrogen), final volume: 200 µl. Reaction was incubated for 16 hours at 16 °C and was terminated by cleaning with RNA Clean & Concentrator (Zymo Research). Crosslink reversal was done by irradiating the RNA on ice with 2.5KJ/m2 UVC.
Library preparation was done as described in(Ziv et al., 2018), using 6N unique molecular identifiers to eliminate PCR biases. Pre-adenylated adapters were used and all ligation reactions were carried without ATP to reduce ligation artefacts. All libraries and controls went through 13 PCR cycles using KAPA HiFi HotStart Ready Mix (KAPA Biosystems). PCR products were size-selected on a 1.8% agarose gel before loading on a Novaseq (Illumina) for paired-end 150 bp runs

value: Huh-7 cells

tag: group

value: Unenriched COMRADES sample


title: rRNA1C

description: Unenriched COMRADES control data

value: Unenriched COMRADES control


title: rRNA2C

description: Unenriched COMRADES control data


title: rRNA3

description: Unenriched COMRADES sample data


title: RNA-Seq Cardiomyocyte_WT_rep2


title: rRNA3C

description: Unenriched COMRADES control data


title: RNA-Seq Cardiomyocyte_WT_rep1


title: RNA-Seq Mesoderm_WT_rep3

value: iPSC-derived Mesoderm


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-K4

value: M


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-J4


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-J3


title: rRNA1

description: Unenriched COMRADES sample data


title: RNA-Seq Mesoderm_WT_rep1


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-J16


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-K15


title: ChIP-Seq Cardiomyocyte_UBE2B-/-1_Input_rep1

data_processing:
trimmed reads using FASTX-Toolkit
aligned using BWA Mem algorithm
peaks identified using Model-based Analysis of ChIP-seq (MACS) (version 2.1.1.20160309) using the BAMPE option, the nomodel option, and the broad option (with a cutoff of 0.2)
differentially bound sites were obtained using the "DiffBind" package in R, with a maximum q value of 0.05 and a minimum absolute fold change of 1.5
nearest genes to the differentially bound sites were obtained using the "ChIPseeker" package in R
Assembly: hg38
Supplementary files format and content: bigwig files were generated using fold enrichments as scores

extract_protocol:
frozen tissue were ground, DNA was sonicated on Bioruptor Pico sonicator, and precipitated with H2Bub1 antibody
Illumina protocol


title: RNA-Seq iPSC_WT_rep1

value: iPSC


title: ChIP-Seq Cardiomyocyte_UBE2B-/-1_Input_rep3


title: ChIP-Seq Cardiomyocyte_UBE2B-/-1_Input_rep2


title: ChIP-Seq Cardiomyocyte_UBE2B-/-2_Input_rep3


title: ChIP-Seq Cardiomyocyte_WT_Input_rep3


title: ChIP-Seq Cardiomyocyte_UBE2B-/-2_Input_rep1


title: RNA-Seq iPSC_WT_rep3


title: ChIP-Seq Cardiomyocyte_UBE2B-/-2_Input_rep2


title: RNA-Seq iPSC_WT_rep2


title: ChIP-Seq Cardiomyocyte_WT_Input_rep2


title: RNA-Seq Mesoderm_WT_rep2


title: ChIP-Seq Cardiomyocyte_WT_Input_rep1


title: ChIP-Seq CardiacProgenitor_WT_Input_rep2


title: ChIP-Seq CardiacProgenitor_WT_Input_rep1


title: ChIP-Seq CardiacMesoderm_WT_Input_rep2


title: ChIP-Seq CardiacMesoderm_WT_Input_rep1


title: ChIP-Seq Mesoderm_WT_Input_rep3


title: ChIP-Seq Mesoderm_WT_Input_rep2


title: ChIP-Seq CardiacMesoderm_WT_Input_rep3


title: ChIP-Seq CardiacProgenitor_WT_Input_rep3


title: ChIP-Seq Mesoderm_WT_Input_rep1


title: ChIP-Seq iPSC_WT_Input_rep3


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-F16


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-F15


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-F4


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-E16


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-G4


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-H3


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-E4


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-G15


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-I3


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-I4


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-H4


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-E15


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-G3


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-I16


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-E3


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-D4


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-F3


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-G16


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-H16


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-J15


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-H15


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-D3


title: ChIP-Seq iPSC_WT_Input_rep1


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-D16


title: ChIP-Seq iPSC_WT_Input_rep2


title: ChIP-Seq Cardiomyocyte_UBE2B-/-2_rep2


title: ChIP-Seq Cardiomyocyte_UBE2B-/-2_rep3


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-D15


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-C4


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-I15


title: ChIP-Seq Cardiomyocyte_UBE2B-/-1_rep1


title: ChIP-Seq Cardiomyocyte_UBE2B-/-2_rep1


title: ChIP-Seq Cardiomyocyte_WT_rep1


title: ChIP-Seq Cardiomyocyte_UBE2B-/-1_rep3


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-C3


title: ChIP-Seq Cardiomyocyte_UBE2B-/-1_rep2


title: ChIP-Seq Cardiomyocyte_WT_rep3


title: ChIP-Seq Cardiomyocyte_WT_rep2


title: ChIP-Seq Mesoderm_WT_rep3


title: ChIP-Seq CardiacMesoderm_WT_rep2


title: ChIP-Seq CardiacMesoderm_WT_rep1


title: ChIP-Seq CardiacProgenitor_WT_rep2


title: ChIP-Seq CardiacProgenitor_WT_rep3


title: ChIP-Seq CardiacMesoderm_WT_rep3


title: ChIP-Seq Mesoderm_WT_rep2


title: ChIP-Seq Mesoderm_WT_rep1


title: ChIP-Seq CardiacProgenitor_WT_rep1


title: ChIP-Seq iPSC_WT_rep1


title: ChIP-Seq iPSC_WT_rep2


title: ChIP-Seq iPSC_WT_rep3


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-O2


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-N1


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-P14


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-C15


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-P13


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-A4


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-N13


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-B3


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-B16


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-O14


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-M2


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-A3


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-A16


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-O13


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-P1


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-C16


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-O1


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-B15


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-P2


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-N2


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-M14


title: anti-CD33 CAR T-cell co-incubated with MOLM13-TP53+/+, replicate 2

city: Zurich

first: Roman

middle: Raffael

last: Schimmer

state: Zurich

address: Raemistrasse 100

department: Department of Medical Oncology and Hematology

country: Switzerland

institute: University Hospital Zurich and University of Zurich

data_processing:
Quality control, mapping and differential gene expression analysis was performed using the SUSHI bioinformatics pipeline
Gene set enrichment analysis (GSEA) was performed using the GSEA software jointly developed by UC San Diego and the Broad Institute
Assembly: hg18
Supplementary files format and content: excel file including all genes analysed (gene name, transcript ID, etc) and normalized counts for each above listed sample

source_name: Blood

growth_protocol: Isogenic MOLM13 cells harboring wildtype TP53 (MOLM13-TP53+/+) or knockout TP53 (MOLM13-TP53-/-) were cultured in RPMI medium supplemented with GlutaMAX™ (Gibco™, #61870010), 100 U ml-1 of penicillin and 100 mg ml-1 of streptomycin (Penicillin-Streptomycin 5’000 U/mL, Cat. No. 15070063), and 10% FCS (Gibco™, #16000044))

extract_protocol:
RNA was harvested with PicoPure™ RNA isolation kit (Thermo Fisher, #KIT0204) according to the manufacturer's instructions.
RNA libraries were constructed using the Illumina Truseq RNA Library Prep Kit V2

treatment_protocol: MOLM13-TP53 cells were incubated with anti-CD33 CAR T-cells for 6 days at an effector-to-target ratio resulting in incomplete target killing

value: Blood

value: T-cell

value: CAR T-cell therapy


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-B4


title: anti-CD33 CAR T-cell co-incubated with MOLM13-TP53-/-, replicate 1


title: anti-CD33 CAR T-cell co-incubated with MOLM13-TP53-/-, replicate 3


title: anti-CD33 CAR T-cell co-incubated with MOLM13-TP53-/-, replicate 2


title: anti-CD33 CAR T-cell co-incubated with MOLM13-TP53+/+, replicate 1


title: CEMBA3C_MacaqueM1_R1_P2-2-J11-A15


title: anti-CD33 CAR T-cell co-incubated with MOLM13-TP53+/+, replicate 3


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-N14


title: anti-CD33 CAR T-cell, resting, replicate 3


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-L1


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-L14


title: CEMBA3C_MacaqueM1_R1_P2-1-J11-K14