title: AMB_201117_9mo_5E_6E_4_P5-2-I3-F3


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-H15

status: Public on Dec 17 2025

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

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

tag: strain

tag: age

value: 9 months

tag: brain region

value: CP

tag: gender

value: M


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-L16


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-E3


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-D4


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-F16


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-D16


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-F15


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-E4


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-D3


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-J16


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-E15


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-C15


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-D15


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-C4


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-C16


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-C3


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-B4


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-B3


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-B15


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-A16


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-A3


title: AMB_201117_9mo_5E_6E_4_P5-3-D10-G6


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-F4


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-B16


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-A15


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-P2


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-P13


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-P14


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-P1


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-E16


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-O2


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-O14


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-O13


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-O1


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-N14


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-N2


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-N1


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-M2


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-M14


title: AMB_201117_9mo_5E_6E_4_P5-2-I3-A4


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-M13


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-M1


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-L1


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-K14


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-L14


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-L2


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-K13


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-J2


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-J14


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-K1


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-J13


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-J1


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-I14


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-I2


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-I13


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-H2


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-H14


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-H1


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-H13


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-N13


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-G2


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-G13


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-G14


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-G1


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-F2


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-L13


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-K2


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-F14


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-F13


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-E1


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-E13


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-E14


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-D1


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-D14


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-E2


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-D13


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-C2


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-C13


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-C1


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-B14


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-I1


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-C14


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-B2


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-B13


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-A2


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-A13


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-B1


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-A14


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-A1


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-P24


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-P12


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-P11


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-F1


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-O24


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-P23


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-O23


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-O12


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-O11


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-N24


title: AMB_201117_9mo_5E_6E_4_P5-1-C21-D2


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-N12


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-N11


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-M24


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-L24


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-M11


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-M12


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-L11


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-K24


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-L12


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-K23


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-J24


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-J12


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-J23


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-I24


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-J11


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-I23


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-I12


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-H23


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-H24


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-H12


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-H11


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-I11


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-N23


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-G24


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-G23


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-G12


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-L23


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-G11


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-F12


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-F24


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-E24


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-E23


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-F11


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-K11


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-D24


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-E11


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-M23


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-K12


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-D23


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-D12


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-D11


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-C24


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-C23


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-C11


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-C12


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-B24


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-B12


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-B23


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-B11


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-A24


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-P9


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-A11


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-A23


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-F23


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-A12


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-P22


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-P21


title: AMB_201117_9mo_5E_6E_4_P4-6-M13-E12


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-O22


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-O9


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-O10


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-N9


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-P10


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-O21


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-N22


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-N10


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-M22


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-M9


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-K9


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-L10


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-M21


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-M10


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-L22


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-J9


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-K22


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-L21


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-K21


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-J22


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-J21


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-J10


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-I22


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-H9


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-I9


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-H10


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-G22


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-G21


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-H22


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-I21


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-N21


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-G9


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-G10


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-L9


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-F21


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-F22


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-K10


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-F9


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-E22


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-E9


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-H21


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-D9


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-E21


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-I10


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-D21


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-D22


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-B10


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-C10


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-B22


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-B9


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-C21


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-A9


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-C9


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-D10


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-C22


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-A22


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-P7


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-A10


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-A21


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-P20


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-F10


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-P8


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-E10


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-M7


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-O8


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-N19


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-N8


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-O7


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-N7


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-P19


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-O20


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-N20


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-M8


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-M20


title: AMB_201117_9mo_5E_6E_4_P4-5-D22-B21


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-L8


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-L7


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-L20


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-M19


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-K20


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-K7


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-L19


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-J20


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-K8


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-I8


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-J7


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-I7


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-J8


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-I20


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-J19


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-O19


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-H8


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-I19


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-H20


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-G7


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-G20


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-H7


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-G19


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-F7


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-G8


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-F20


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-F8


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-K19


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-F19


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-E8


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-E7


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-D7


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-D8


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-E20


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-D20


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-D19


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-C8


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-C7


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-C19


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-B7


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-B20


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-B8


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-H19


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-B19


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-A7


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-P6


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-A19


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-P5


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-A20


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-A8


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-P18


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-P17


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-O5


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-O17


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-O6


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-N6


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-O18


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-E19


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-N18


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-N5


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-N17


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-M17


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-M6


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-M18


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-L5


title: AMB_201117_9mo_5E_6E_4_P4-4-I15-C20


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-M5


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-L6


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-L18


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-K18


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-K17


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-J6


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-L17


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-J18


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-K6


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-J5


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-H6


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-H5


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-H17


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-H18


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-G6


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-G18


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-G5


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-I17


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-J17


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-I18


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-G17


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-F6


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-F17


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-F18


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-E18


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-K5


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-F5


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-E6


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-E5


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-E17


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-D18


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-D5


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-I6


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-D17


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-I5


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-D6


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-C17


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-C6


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-C18


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-B5


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-B18


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-B6


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-A18


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-A5


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-P15


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-O4


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-A6


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-B17


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-P4


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-O16


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-N16


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-A17


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-O3


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-N15


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-M3


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-N3


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-M16


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-M4


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-O15


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-N4


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-L4


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-L15


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-L3


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-M15


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-K4


title: AMB_201117_9mo_5E_6E_4_P4-3-I2-C5


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-P3


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-P16


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-J4


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-K3


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-J3


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-I4


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-J15


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-I3


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-K16


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-J16


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-H3


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-L16


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-G15


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-H4


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-G4


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-F3


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-I15


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-F4


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-G3


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-F15


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-G16


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-E3


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-F16


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-E16


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-D3


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-E15


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-K15


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-I16


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-D4


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-H15


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-H16


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-D16


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-C4


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-D15


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-E4


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-C16


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-B16


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-C15


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-B4


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-B15


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-A15


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-P14


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-P2


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-P13


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-A4


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-O2


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-A3


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-O14


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-A16


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-P1


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-O13


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-N2


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-N14


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-B3


title: AMB_201117_9mo_5E_6E_4_P4-2-A22-C3


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-N1


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-O1


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-N13


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-M13


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-M2


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-M1


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-M14


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-L2


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-L13


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-K14


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-K13


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-K2


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-K1


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-J14


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-L14


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-J1


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-J2


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-I13


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-I14


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-I1


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-I2


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-J13


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-H13


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-H2


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-G14


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-G2


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-F14


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-G1


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-G13


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-H1


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-L1


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-E2


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-F13


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-F1


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-D13


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-E14


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-C2


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-C13


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-D14


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-D2


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-D1


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-E1


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-C1


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-B14


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-C14


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-B2


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-B13


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-A14


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-H14


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-A13


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-F2


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-B1


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-A1


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-P24


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-P23


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-P12


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-E13


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-P11


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-O24


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-O12


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-O23


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-O11


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-N24


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-N23


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-N11


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-N12


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-L24


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-M11


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-M23


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-M12


title: AMB_201117_9mo_5E_6E_4_P4-1-D8-A2


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-L12


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-L11


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-K24


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-K11


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-J24


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-K12


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-J23


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-K23


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-J12


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-J11


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-I23


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-I24


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-I11


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-H24


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-I12


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-H12


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-H23


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-G23


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-G11


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-M24


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-H11


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-L23


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-F24


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-G24


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-F23


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-F11


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-E23


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-F12


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-E11


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-D24


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-E12


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-D23


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-D12


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-D11


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-C24


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-C11


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-C12


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-B24


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-B23


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-B12


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-B11


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-G12


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-A24


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-A12


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-A11


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-A23


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-P21


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-P9


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-O9


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-P10


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-O22


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-N21


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-N22


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-N10


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-M9


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-C23


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-P22


title: AMB_201117_9mo_5E_6E_4_P3-6-D23-E24


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-M21


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-M10


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-L9


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-N9


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-L22


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-L10


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-K9


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-K21


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-M22


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-K22


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-K10


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-J9


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-J22


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-J10


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-J21


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-O10


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-O21


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-I22


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-I9


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-I21


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-I10


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-H9


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-H10


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-H21


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-G9


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-G21


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-G22


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-G10


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-L21


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-F22


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-E9


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-E22


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-E21


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-E10


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-F10


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-F21


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-D9


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-D22


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-D21


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-C9


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-D10


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-B9


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-B21


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-C21


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-B22


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-B10


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-C10


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-A22


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-H22


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-P8


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-A9


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-P19


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-P7


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-F9


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-A10


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-P20


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-O7


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-O8


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-O20


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-N8


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-O19


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-N7


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-N19


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-M7


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-N20


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-M8


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-L20


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-M19


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-K20


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-K7


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-C22


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-L7


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-I20


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-L8


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-M20


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-I7


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-H7


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-L19


title: AMB_201117_9mo_5E_6E_4_P3-5-F11-A21


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-K19


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-H20


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-G7


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-J8


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-J20


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-J19


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-K8


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-I8


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-I19


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-H19


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-E8


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-E7


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-G20


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-E20


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-G8


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-H8


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-G19


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-F7


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-F8


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-D19


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-D20


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-F20


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-J7


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-F19


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-E19


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-B8


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-B19


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-D8


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-D7


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-C8


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-C7


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-C20


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-C19


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-P17


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-P18


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-O6


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-O5


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-O18


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-N5


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-B20


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-N17


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-A8


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-B7


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-M5


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-A20


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-A7


title: AMB_201117_9mo_5E_6E_4_P3-4-K4-A19


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-L6


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-N6


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-N18


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-M17


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-O17


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-P5


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-M6


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-K6


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-P6


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-L17


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-K17


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-K18


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-I6


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-J18


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-J6


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-L5


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-M18


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-I18


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-I17


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-H6


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-H5


title: infx.5

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: infx.5

library_source: transcriptomic

data_processing:
Sequenced reads were aligned using RSEM along with Bowtie2 against the human genome (version: mm10)
DESeq2 was used to normalize the reads and obtain the differentially expressed genes
Assembly: mm10
Supplementary files format and content: RSEM Count file is in Text

molecule: polyA RNA

source_name: lung

extract_protocol:
RNA was extracted using Rneasy plus mini kit (Qiagen)
Done by Genomics core

treatment_protocol: DBA/2 mice were vaccinated with DNA vaccines pHAH1 or pVACC-NPH3. Control mice included mock (aka CTRL unvaccinated, uninfected) and naive (AKA INFX, no vaccine, infected).  Mice were infected 14 days later with 10 LD50 A/California/07/2009 X17A intranasally. Lungs were harvested 6 days post infection and fixed in formalin, paraffin-embedded (FFPE).

tag: tissue

value: lung

tag: treatment

value: unvaccinated, infected


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-K5


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-L18


title: infx.4

description: Library name: infx.4


title: infx.3

description: Library name: infx.3


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-I5


title: infx.1

description: Library name: infx.1


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-H18


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-G18


title: ctrl.5

description: Library name: ctrl.5

value: unvaccinated, uninfected


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-G17


title: infx.2

description: Library name: infx.2


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-F6


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-G5


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-H17


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-J5


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-J17


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-F18


title: ctrl.3

description: Library name: ctrl.3


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-F17


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-E6


title: ctrl.2

description: Library name: ctrl.2


title: T.NP.3

description: Library name: T.NP.3

value: pVACC-NPH3 vaccine


title: ctrl.1

description: Library name: ctrl.1


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-E5


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-G6


title: T.NP.2

description: Library name: T.NP.2


title: T.NP.1

description: Library name: T.NP.1


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-E17


title: T.Mon.3

description: Library name: T.Mon.3

value: DNA-encoded mAb


title: T.Mon.4

description: Library name: T.Mon.4


title: T.Mon.2

description: Library name: T.Mon.2


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-D6


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-D5


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-D18


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-D17


title: ctrl.4

description: Library name: ctrl.4


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-C5


title: p23081-s002_Human-Lung-Epi-2_S99

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

description:
Library name: p23081-s002_Human-Lung-Epi-2_S99
10x Genomics

library_source: transcriptomic single cell

data_processing:
Pre-processing of sequencing results to generate count matrices was performed using the 10x Genomics Cell Ranger v7.1.0 count pipeline and aligning to the GRCh38-2020-A human reference genome.
Assembly: GRCh38-2020-A
Supplementary files format and content: 10x Genomics mRNA output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

organism: Homo sapiens

source_name: Lung

extract_protocol:
At 18 hours post stimulation, epithelial cells were isolated from total human lung cells by FACS.
10x 5’ scRNA-seq libraries were generated using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (10x Genomics 1000263) according to the instructions provided.

treatment_protocol: Total human lung cells were stimulated with MHC I restricted influenza specific peptides in the presence/absence of anti-IFNg antibody to activate antigen specific CD8 T cells

value: Lung

tag: cell type

value: airway epithelial cells

tag: sorting markers

value: CD45-; CD31-; EpCAM+

value: influenza peptide stimulated + isotype control


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-C6


title: T.HA.3

description: Library name: T.HA.3

value: pHAH1 vaccine


title: p23081-s003_Human-Lung-Epi-3_S100

description:
Library name: p23081-s003_Human-Lung-Epi-3_S100
10x Genomics

value: influenza peptide stimulated +anti-IFN-gamma antibody


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-C18


title: p23081-s001_Human-Lung-Epi-1_S98

description:
Library name: p23081-s001_Human-Lung-Epi-1_S98
10x Genomics

value: unstimulated


title: T.Mon.1

description: Library name: T.Mon.1


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-C17


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-F5


title: T.HA.2

description: Library name: T.HA.2


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-B18


title: NK cells D1 from PDO7

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Library name: NK_D1_from_P7_co_S2

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Get raw counts with kallisto quant version 0.4.6.
CPM estimates, generated with cpm function from edgeR version 3.17
Assembly: GRCh38.p13
Supplementary files format and content: raw counts with kallisto quant version 0.4.6.
Supplementary files format and content: CPM estimates, generated with cpm function from edgeR version 3.17

molecule: total RNA

source_name: NK cells

growth_protocol: For regular NK cell/PDO co-cultures, cells were resuspended in BME and 6 BME domes (each 3-4 µl) were seeded in 24 well cell-culture plates. After incubation for 30 min at 37°C a 1:1 mixture of the in Zhan T, et al., (Nature Communications 10, 2197; 10.1038/s41467-019-09898-0 (2019)) described organoid medium without Nicotinamide and Y-27632, and RPMI supplemented with 10% FCS, 100 U/ml P/S, and 100 U IL-2 was added.

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Quiagen) according to the manufacturer’s instructions.
RNA libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs) with previous enrichment of mRNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs), both according to the manufacturers instructions.

treatment_protocol: NK cells were either cultured alone or co-cultured with PDO7 or PDO22 organoids

value: NK cells

value: Co-cultured with PDO7

tag: batch


title: T.HA.1

description: Library name: T.HA.1


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-E18

value: 9 months


title: Sample_92797_BTBR ob_Atra

city: Ann Arbor

first: Jennifer

last: Harder

state: Michigan

address: 1150 W. Medical Center Drive

department: Division of Nephrology

institute: The University of Michigan

description: Library name: Sample_92797

data_processing:
Alignment with STAR 1-pass mapping
Read counts were generated using Htseq
Genes filtered to average of >=10 across all conditions
Expression for PCA and correlation analysis was geenrated using DESeq2 rlog
DGE was performed using standard edgeR calcNormFactors and limma, starting from raw counts
Assembly: Mus_musculus.GRCm38.91
Supplementary files format and content: Log 2 transformed gene level CPM based on Htseq and voom

source_name: BTBR ob_Atra

growth_protocol: Kidney tissues from BTBR ob/ob mice were used. Breeding pairs of BTBR WT, BTBR/ob heterozygotes [BTBRob+/−; BTBR.V(B6)-Lepob/WiscJ; stock no. 004824]) were purchased from Jackson Laboratories (Bar Harbor, ME) and maintained in a specific pathogen–free facility with a 12-hour light cycle and with free access to standard diet and water.

extract_protocol:
BTBR WT mice (n=5) were sacrificed at the same age as controls for BTBR ob/ob. Total RNA was isolated from glomeruli enriched cortex tissue using RNeasy isolation kits (Qiagen). RNA quantity and integrity was confirmed on an Agilent 2100 bioanalyzer. RNA sequencing was performed on oligo(dT) purified poly(A)+ mRNA
A standard TruSeq mRNA library was constructed using TruSeq RNA Sample Prep Kit v2 (Illumina, Cat.# RS-122-2001). The library was sequenced by Illumina HiSeq 4000 using a single-end run (SE50 bases).

treatment_protocol: BTBR ob/ob were treated with saline (n=5) and atrasentan 5 mg/kg body weight per day (n=7) in drinking water. Atrasentanor saline treatment was initiated when animals were 18 weeks of age and continued for 6 weeks until 24 weeks of age.

value: kidney

tag: genotype

value: BTBR ob

value: Atra


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-B5

value: CP

value: M


title: NK cells D6 from PDO7

description: Library name: NK_D6_from_P7_co_S8


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-B17


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-A6


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-B6


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-A5


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-A18


title: NK cells D3 from PDO7

description: Library name: NK_D3_from_P7_co_S1


title: Sample_92808_ob/ob-d30_Saline

description: Library name: Sample_92808

value: Saline


title: NK cells D5 from PDO7

description: Library name: NK_D5_from_P7_co_S8


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-P3


title: Sample_92806_ob/ob-d30_Saline

description: Library name: Sample_92806


title: NK cells D2 from PDO7

description: Library name: NK_D2_from_P7_co_S2


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-O4


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-P16


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-P4


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-P15


title: AMB_201117_9mo_5E_6E_4_P3-3-M14-A17


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-O3


title: Sample_92801_BTBR ob_Atra

description: Library name: Sample_92801


title: Sample_92813_WT-d30_

description: Library name: Sample_92813


title: Sample_92795_BTBR ob_Atra

description: Library name: Sample_92795


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-O16


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-O15


title: NK cells D5 from PDO22

description: Library name: NK_D5_from_P22_co_S6

value: Co-cultured with PDO22


title: Sample_92811_WT-d30_

description: Library name: Sample_92811


title: NK cells D1 from PDO22

description: Library name: NK_D1_from_P22_co_S6


title: NK cells D3 from PDO22

description: Library name: NK_D3_from_P22_co_S5


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-N3


title: Sample_92800_BTBR ob_Atra

description: Library name: Sample_92800


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-N4


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-N16


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-M4


title: NK cells only D1

description: Library name: NK_cells_D1_S7

value: Ctrl


title: NK cells D2 from PDO22

description: Library name: NK_D2_from_P22_co_S4


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-M3


title: NK cells D6 from PDO22

description: Library name: NK_D6_from_P22_co_S2


title: Sample_92812_WT-d30_

description: Library name: Sample_92812


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-M16


title: NK cells only D6

description: Library name: NK_cells_D6_S3


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-M15


title: Sample_92810_WT-d30_

description: Library name: Sample_92810


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-L4


title: NK cells only D5

description: Library name: NK_cells_D5_S7


title: Sample_92805_ob/ob-d30_Saline

description: Library name: Sample_92805


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-L16


title: NK cells only D3

description: Library name: NK_cells_D3_S4


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-L15


title: NK cells only D2

description: Library name: NK_cells_D2_S5


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-K3


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-K4


title: Sample_92798_BTBR ob_Atra

description: Library name: Sample_92798


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-K15


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-K16


title: Sample_92796_BTBR ob_Atra

description: Library name: Sample_92796


title: Sample_92807_ob/ob-d30_Saline

description: Library name: Sample_92807


title: Sample_92814_WT-d30_

description: Library name: Sample_92814


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-J4


title: uninfected PHH, iwp2 treated, sequencing replicate 2

city: Nijmegen

first: Richard

last: Bartfai

state: Gelderland

address: Geert Grooteplein Zuid 28

department: Molecular Biology

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences

data_processing:
The sequencing endline fastq files were quality checked using FASTQC (ver. 0.11.9). The reads were subsequently trimmed for quality (-q 30) and adapter removal using the Trim_Galore software (ver. 0.6.7). The trimmed reads were aligned onto the Homo sapiens ver. 38 genome using STAR aligner (ver. 2.7.10a). The reads mapped onto the respective genomes were counted using the –quantMode GeneCounts option in STAR.
Reads mapping only to sense strand were corrected for batch effects stemming from different hepatocyte donors using the Combat-seq tool (sva package ver. 3.44.0). The batch corrected counts were used for subsequent differential expression analysis (for conditions/treatments) in DESEq2 package (ver. 1.36.0) in RStudio (ver. 4.2.2 “Innocent and Trusting”).
PCA plot for the various sequenced libraries/samples was generated using plotPCA command. Volcano plots for differentially expressed genes and genes of interest were generated using custom scripts and ggplot2 (ver. 3.4.2) in R.
Gene Ontology enrichment analysis was performed in using the clusterProfiler tool (ver. 4.4.4) with subsequent dot-plots generated using inbuilt functions in ggplot2. Heatmaps for differentially expressed genes were generated using the Morpheus online tool by Broad Institute.
Assembly: Plasmodium falciparum 3D7 genome version 59; Homo sapiens genome version GRCh38
Supplementary files format and content: tab-delimited txt files containing batch corrected Combat-seq counts for genes
Supplementary files format and content: tab-delimited txt files containing normalized counts for genes from DESeq2

source_name: primary human hepatocytes

extract_protocol:
Freshly isolated or in vitro cultured hepatocytes (mock or treatment) were homogenized in TRIzol solution and cryopreserved at -80°C. RNA was subsequently isolated using the Zymo research Direct zol RNA purification kit (Cat. No. #R2053)
RNA sequencing libraries from isolated/purified RNA were prepared using the Kapa mRNA Hyperprep Kit (Cat. No. #KK8581) using slight modifications of the manufacturer’s instructions for mRNA enrichment method. The input total RNA for the various libraries was selected between 150ng, 250ng or 500ng. The enriched mRNA was fragmented at 94°C  for 6min and dA tailing performed at 55°C for 15min. In order to better capture the AT rich Pf transcriptome we modified the PCR protocol as follows: Initial denaturation at 98°C for 2min; Cycling denaturation at 98°C for 20sec, annealing + extension at 62°C for 2min; final extension at 62°C for 3min. We selected PCR cycles for library amplification (12, 11 and 10 respectively) based on starting input total RNA amount.

value: primary human hepatocytes


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-N15


title: uninfected PHH, 5C treated, sequencing replicate 2


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-J3


title: Sample_92809_ob/ob-d30_Saline

description: Library name: Sample_92809


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-J16


title: uninfected PHH, mock treated, sequencing replicate 2

value: Mock


title: Sample_92799_BTBR ob_Atra

description: Library name: Sample_92799


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-I4


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-J15


title: uninfected PHH, 5C treated, sequencing replicate 1


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-L3


title: uninfected PHH, iwp2 treated, sequencing replicate 1


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-I16


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-I3


title: WT_placebo_rep4

city: Illkirch-Graffenstaden

first: Jocelyn

last: Laporte

address: 1 rue Laurent Fries

country: France

institute: IGBMC

description:
Library name: VWJQ77
library construction protocol: P2715

data_processing:
Image analysis and base calling were performed using RTA v.2.7.7 and bcl2fastq v.2.20.0.422.
First, adaptor, poly(A) and low-quality sequences (Phred quality score below 20) were removed using cutadapt (v.1.10). Reads shorter than 40 bases were excluded from further analysis. Using Bowtie v.1.2.2, we identified and removed reads mapping to External RNA Controls Consortium spike sequences.
Reads were mapped onto the mm39 assembly of Mus musculus genome using STAR v.2.5.3. Gene expression quantification was performed from uniquely aligned reads using htseq-count v.0.6.1p1, with annotations from Ensembl v.104 and union mode.
Assembly: mm39
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

source_name: Tibialis anterior muscle

extract_protocol:
RNA was isolated from TA muscle using TRI Reagent (Molecular Research Center).
P2715 : RNA-Seq libraries were generated from 300ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and IDT for Illumina - TruSeq RNA UD Indexes (96 Indexes, 96 Samples) (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using SPRI select beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.
P2895 : RNA-Seq libraries were generated from 350 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and IDT for Illumina - TruSeq RNA UD Indexes (96 Indexes, 96 Samples) (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 8 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using SPRI select beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: Tibialis anterior muscle

value: WT

value: placebo


title: Dnm2SL_tamox_rep4

description:
Library name: VWJQ52
library construction protocol: P2715

value: tamoxifen


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-H4


title: uninfected PHH, mock treated, sequencing replicate 1


title: freshly isolated hepatocytes, sequencing replicate 2

source_name: fresh hepatocytes

value: fresh hepatocytes


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-H3


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-H15


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-H16


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-G4


title: Dnm2SL_tamox_rep2

description:
Library name: VWJQ50
library construction protocol: P2715


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-G3


title: Dnm2SL_tamox_rep1

description:
Library name: VWJQ49
library construction protocol: P2715


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-G15


title: Dnm2SL_placebo_rep4

description:
Library name: VWJQ46
library construction protocol: P2715


title: LLC cells, brain metastasis, replicate 3

city: Pamplona

first: Karmele

last: Valencia

state: Navarra

address: Avenida Pío XII, 55

department: Innovación Terapéutica en Cáncer de Pulmón

country: Spain

institute: Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra

description:
Library name: Sample 12
Column name in mouse_featureCounts_1303.csv: LB3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
Trimmed sequence reads were mapped to GRCm39 using STAR.
Extraction of read counts and construction of the count matrix were performed using featureCounts.
Assembly: GRCm39
Supplementary files format and content: comma-delimited file cointaing raw counts for each sample

source_name: LLC

growth_protocol: LLC cells were mantained in RPMI medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37ºC.

extract_protocol:
RNA extraction was performed using Macherey-Nagel RNA NucleoSpin kit.
Library preparation was performed using the Illumina Stranded mRNA Prep Ligation kit (Illumina) following the manufacturer’s protocol. All sequencing libraries were constructed from 100 ng of total RNA according to the manufacturer's instruction.

tag: cell line

value: LLC

value: cell line established from the lung of a C57BL mouse bearing a tumor resulting from an implantation of primary Lewis lung carcinoma


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-F4

value: 9 months


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-G16


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-F3


title: LLC cells, brain metastasis, replicate 1

description:
Library name: Sample 10
Column name in mouse_featureCounts_1303.csv: LB1


title: Dnm2SL_placebo_rep3

description:
Library name: VWJQ43
library construction protocol: P2715


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-F16


title: Dnm2SL_placebo_rep2

description:
Library name: VWJQ42
library construction protocol: P2715


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-I15


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-F15


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-E3


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-E16


title: LLC cells, bone metastasis, replicate 3

description:
Library name: Sample 9
Column name in mouse_featureCounts_1303.csv: LL3


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-E4


title: Dnm2SL_placebo_rep1

description:
Library name: VWJQ41
library construction protocol: P2715


title: LLC cells, bone metastasis, replicate 2

description:
Library name: Sample 8
Column name in mouse_featureCounts_1303.csv: LL2


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-E15


title: Dnm2SL_tamox_rep3

description:
Library name: VWJQ51
library construction protocol: P2715


title: freshly isolated hepatocytes, sequencing replicate 1


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-D4


title: LLC cells, bone metastasis, replicate 1

description:
Library name: Sample 7
Column name in mouse_featureCounts_1303.csv: LL1


title: WT_tamox_rep4

description:
Library name: VWJQ39
library construction protocol: P2715


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-D3


title: WT_tamox_rep3

description:
Library name: VWJQ38
library construction protocol: P2715


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-D16


title: LLC cells, circulating tumor cells, replicate 3

description:
Library name: Sample 6
Column name in mouse_featureCounts_1303.csv: LCTC3


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-D15


title: LLC cells, brain metastasis, replicate 2

description:
Library name: Sample 11
Column name in mouse_featureCounts_1303.csv: LB2


title: LLC cells, circulating tumor cells, replicate 2

description:
Library name: Sample 5
Column name in mouse_featureCounts_1303.csv: LCTC2


title: WT_tamox_rep1

description:
Library name: VWJQ36
library construction protocol: P2715


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-C16


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-C15


title: LLC cells, circulating tumor cells, replicate 1

description:
Library name: Sample 4
Column name in mouse_featureCounts_1303.csv: LCTC1


title: WT_placebo_rep3

description:
Library name: VWJQ33
library construction protocol: P2715


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-B4


title: LLC cells, parental, replicate 3

description:
Library name: Sample 3
Column name in mouse_featureCounts_1303.csv: LP3


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-B3


title: WT_placebo_rep2

description:
Library name: VWJQ31
library construction protocol: P2715


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-B16


title: WT_placebo_rep1

description:
Library name: VWJQ29
library construction protocol: P2715


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-A4


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-A3


title: WT_tamox_rep2

description:
Library name: VWJQ37
library construction protocol: P2715


title: 239032056BCD

city: Chengdu

first: Panwen

last: Tian

address: No. 37 Guoxue Lane, Wuhou District

country: China

institute: West China Hospital

description:
Library name: sample31
239032056BCD

data_processing:
The V and J gene segments were aligned using MIXCR and annotated with the IMGT (ImMunoGeneTics) database to identify TCR CDR3 sequences.
TCR data analysis was performed using the immunarch package, and visualizations were generated using R.
Assembly: GRCh38
Supplementary files format and content: TCR.xlsx     This file contains summary statistics of TCR repertoire profiling for each sample, including sequencing depth, clonotype counts, diversity indices (Shannon, Simpson, Gini-Simpson), clonality, and evenness.
Supplementary files format and content: xxxxxx.clones_filter_sampling_vjedit.tsv    This file contains processed TCR clonotype data for each sample.
Library strategy: TCR-Seq

source_name: peripheral blood

extract_protocol:
DNAs were extracted using the DNA FFPE Kit and the QIAamp DNA Blood Kit (Qiagen).
Multiplex primers were employed to amplify the CDR3 regions of the V and J genes segments from genomic DNA (gDNA). Paired-end 100 bp PCR products were generated and sequenced on an Illumina platform. TCR-Vβ sequencing was conducted in a CLIA/CAP-certified laboratory (Geneplus), with low-quality sequences filtered out during post-sequencing quality control.

value: peripheral blood


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-P2


title: 18month-old DIO+DHA mice6

first: María

middle: Jesús

last: Moreno-Aliaga

address: University of Navarra

department: Nutrition, Food Science and Physiology

institute: Centre for Nutrition Research

description: Library name: 18G6_S26_R3

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCm39 human assembly using STAR v2.7.9a with default parameters.
featureCounts v1.6.0 software and Gencode vM33 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: Liver

extract_protocol:
Total RNA from liver was extracted with QIAzol Lysis Reagent (Qiagen; Venlo, Limburg, The Netherlands). An RNA purification step was performed to prevent phenol carryover using the RNeasy Mini Kit (Qiagen; Venlo, Limburg, The Netherlands). RNA concentration was determined with the Nanodrop Spectrophotometer ND1000 (Nanodrop Technologies, Inc. Wilmington, NC, USA)
Library preparation was performed using the Nextera XT library preparation protocol which introduces i5-P5 and i7-P7 structure for massive parallel sequencing.

treatment_protocol: Two months-old C57BL/6J mice  were fed ad libi-tum for 4 months with high fat diet (HFD) containing as energy: 20% proteins, 35% carbohydrates, and 45% lipids (D12451 diet, Research Diets, Inc., New Brunswick, NJ USA). Then, DIO mice were divided into two groups: (1) the DIO group  continued with the HFD up to 18 months and (2) the DIO + DHA group, which was fed up to 18 months with the HFD containing a DHA-rich n-3 PUFA concentrate obtained from fish oil, replacing 15% wt/wt of dietary lipids (Research Diets Inc., New Brunswick, NJ, USA). The DHA-rich n-3 PUFA concentrate contained 683.4 mg DHA/g, 46.7 mg EPA/g, with a total content of n-3 PUFA of 838.9 mg/g as triglycerides.

value: Liver


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-A15

value: CP


title: LLC cells, parental, replicate 1

description:
Library name: Sample 1
Column name in mouse_featureCounts_1303.csv: LP1


title: 239033053BCD

description:
Library name: sample32
239033053BCD


title: 239023745BCD

description:
Library name: sample30
239023745BCD


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-A16

value: M


title: 239021695BCD

description:
Library name: sample29
239021695BCD


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-P14


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-C3


title: 18 month-old DIO+DHA mice5

description: Library name: 18G5_S25_R3


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-C4


title: 18 month-old DIO+DHA mice4

description: Library name: 18G4_S24_R3


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-P13


title: LLC cells, parental, replicate 2

description:
Library name: Sample 2
Column name in mouse_featureCounts_1303.csv: LP2


title: AMB_201117_9mo_5E_6E_4_P3-2-K18-B15


title: 239019143BCDR1

description:
Library name: sample28
239019143BCDR1


title: 18 month-old DIO+DHA mice2

description: Library name: 18G2_S23_R3


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-O13


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-O2


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-P1


title: 239018171BCD

description:
Library name: sample27
239018171BCD


title: 18 month-old DIO+DHA mice1

description: Library name: 18G1_S22_R3


title: 18 month-old DIO mice5

description: Library name: 18D5_S21_R3


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-O1


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-N14


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-N2


title: 18 month-old DIO mice4

description: Library name: 18D4_S20_R3


title: 239010876BCDR1

description:
Library name: sample26
239010876BCDR1


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-M2


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-N13


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-M14


title: 239006781BCD

description:
Library name: sample24
239006781BCD


title: 18 month-old DIO mice1

description: Library name: 18D1_S19_R3


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-M13


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-O14


title: 239030852BCD

description:
Library name: sample23
239030852BCD


title: ATAC-seq_shPHF8_rep2

city: Barcelona

first: Marta

middle: Artés

last: Hernández

address: Baldiri Reixac 15

institute: IBMB-CSIC

description:
Library name: shPHF8_2
NSCs were infected with lentiviral shRNA against PHF8 (shPHF8). Cells were scrapped and resuspended in RBS buffer and then Igepal CA-630 0.1% was added to achieve cell lysis. Transposition reaction with Transposes enzyme and buffer kits (Illumina, FC-121-1030) and immediately following transposition, DNA was purified. Nextera DNA Library Prep Kit (FC-121-1030), along with unique dual index barcodes for each sample and NEBNext High-Fidelity 2x PCR Master Mix (New England Lab, M0541) were used. Ampure XP beads (Beckman Coulter, A63880) were prepared for size selection. Libraries were then pair-end sequenced using NextSeq2000 and approximately 50M reads per sample were obtained

data_processing:
For RNA-seq, alignment was performed using HISAT2. Assignment of aligned reads to genes using HTSeq.Differential expression analysis using DESeq2
For ChIP-seq, single-end reads were aligned to the mouse mm10 reference genome using Bowtie2 (v2.3.5.1) with default options. SAMtools (v1.9) was used to filter out the low-quality alignments using the flag 3844. The resulting BAM files were sorted and deepTools was used to generate input-subtracted and counts per million (CPM) normalized signal tracks (bamCompare -- operation subtract -- normalizeUsing CPM --scaleFactorsMethod None) in bigWig format.
For ATAC-seq, paired-end reads were aligned to the mouse mm10 reference genome using Bowtie2 (v2.3.5.1) and specifying the "--very-sensitive-local" mode. SAMtools (v1.9) was used to filter out the low-quality reads with the flag 1796, remove reads mapped in the mitochondrial chromosome, and discard those with a MAPQ score below 20. The resulting BAM files were sorted and deepTools was used to generate counts per million (CPM) normalized signal tracks (bamCoverage --samFlagInclude 64 --normalizeUsing CPM) in bigWig format. The peak calling was performed with MACS2 (v.2.1.2) by specifying the -BAMPEmode.
Assembly: mm10
Supplementary files format and content: Bed files contain genomic coordinates. BigWig files contain the information for displaying graphs.

source_name: cerebral cortex

growth_protocol: NSCs were cultured in a poly-D-lysine (5 mg/ml, 2 hours at 37°C) and laminin (5 mg/ml, 4 hours at 37°C) pre-coated dishes growing with a media comprising equal parts DMEM F12 (without Phenol Red, Gibco) and Neural Basal Media (Gibco) containing penicillin/streptomycin and Glutamax (1%), N2 and B27 supplements (Gibco), non essential amino acids (0.1 mM), sodium pyruvate (1 mM), Hepes (5 mM), heparin (2 mg/l), bovine serum albumin (25 mg/l) and -mercaptoethanol (0.01 mM). We added fresh recombinant human EGF (R&D Systems) and FGF (Invitrogen) to 20 ng/ml and 10 ng/ml final, respectively.

extract_protocol:
For RNA-seq, RNA was extracted using High pure RNA isolation kit from Roche followed by DnaseI treatment.
For ChIP-seq, NSCs were cross-linked with Cross-link Gold 0.4% (Diagenode, C01019027) in PBS 30 minutes, and then fixed with methanol-free formaldehyde 1% for 10 min and stopped with 0.125 mM glycine for 10 minutes. Sonication was performed using a Bioruptor sonicator.
For ATAC-seq, cells were scrapped and resuspended in RBS buffer and then Igepal CA-630 0.1% was added to achieve cell lysis. Transposition reaction with Transposes enzyme and buffer kits (Illumina, FC-121-1030) and immediately following transposition, DNA was purified.
For RNA-seq, libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit with Ribo-Zero Human/Mouse/Rat Kit (ref. RS-122-2201/2, Illumina) according to the manufacturer's protocol. Briefly, 500 ng of total RNA was used for ribosomal RNA depletion RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina High HiSeq 2500)
For ChIP-seq, the libraries were prepared and amplified to make DNA NanoBall (DNB). Libraries were loaded into a nanoarray and single end 50 base pairs reads were generated by combinatorial Probe-Anchor synthesis (cPAS)
For ATAC-seq, Nextera DNA Library Prep Kit (FC-121-1030), along with unique dual index barcodes for each sample and NEBNext High-Fidelity 2x PCR Master Mix (New England Lab, M0541) were used. Ampure XP beads (Beckman Coulter, A63880) were prepared for size selection. Libraries were then pair-end sequenced using NextSeq2000 and approximately 50M reads per sample were obtained.

treatment_protocol: Cells were infected with lentiviral shRNA either scramble (control) or against PHF8 (shPHF8)

value: cerebral cortex

value: neural stem cells

value: PHF8 knockdown

value: lentiviral transduction


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-M1


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-L2


title: ATAC-seq_shPHF8_rep1

description:
Library name: shPHF8_1
NSCs were infected with lentiviral shRNA against PHF8 (shPHF8). Cells were scrapped and resuspended in RBS buffer and then Igepal CA-630 0.1% was added to achieve cell lysis. Transposition reaction with Transposes enzyme and buffer kits (Illumina, FC-121-1030) and immediately following transposition, DNA was purified. Nextera DNA Library Prep Kit (FC-121-1030), along with unique dual index barcodes for each sample and NEBNext High-Fidelity 2x PCR Master Mix (New England Lab, M0541) were used. Ampure XP beads (Beckman Coulter, A63880) were prepared for size selection. Libraries were then pair-end sequenced using NextSeq2000 and approximately 50M reads per sample were obtained


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-L14


title: 239029665BCD

description:
Library name: sample22
239029665BCD


title: ATAC-seq_shCTR_rep1

description:
Library name: shCTR_1
NSCs were infected with lentiviral shRNA scramble (shCTR). Cells were scrapped and resuspended in RBS buffer and then Igepal CA-630 0.1% was added to achieve cell lysis. Transposition reaction with Transposes enzyme and buffer kits (Illumina, FC-121-1030) and immediately following transposition, DNA was purified. Nextera DNA Library Prep Kit (FC-121-1030), along with unique dual index barcodes for each sample and NEBNext High-Fidelity 2x PCR Master Mix (New England Lab, M0541) were used. Ampure XP beads (Beckman Coulter, A63880) were prepared for size selection. Libraries were then pair-end sequenced using NextSeq2000 and approximately 50M reads per sample were obtained

value: CTR


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-L13


title: 239019831BCD

description:
Library name: sample21
239019831BCD


title: 239018274BD

description:
Library name: sample20
239018274BD


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-K13


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-K2


title: Ubc9 fl/fl; AdipoQ-cre+ E2

city: Pittsburgh

first: Bokai

last: Zhu

address: Bridgeside Point 1, 5th Floor, 100 Technology Drive

institute: Aging Institute of UPMC/University of Pittsburgh School of Medicine

description: Library name: 20i

data_processing:
Trim Galore (Galaxy)
RNA STAR (Galaxy)
htseq-count (Galaxy)
Cufflinks (Galaxy)
DESeq2 (Galaxy)
Assembly: mm10
Supplementary files format and content: Tabular files with FPKM values

source_name: Subcutaneous Adipose Tissue

growth_protocol: Mice fed ad libitum on normal chow

extract_protocol:
Tissue was weighed and 30-50mg of tissue was used for RNA extraction. RNA was extracted using RNeasy Lipid Tissue kit (Qiagen: 74804) along with Rnase-free DNase set (Qiagen:  79254) for DNA digestion.
Illumina Stranded Total Library Prep kit (Illumina: 20040529)
Illumina NextSeq 2000

treatment_protocol: Snap frozen and storage at -80 until it cut for RNA extraction

value: Subcutaneous Adipose Tissue

value: Ubc9 fl/fl; AdipoQ-cre+

value: Knockout


title: Ubc9 fl/fl; AdipoQ-cre+ D2

description: Library name: 19i


title: 239018350BCD

description:
Library name: sample19
239018350BCD


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-K1


title: 239010875BCDR1

description:
Library name: sample25
239010875BCDR1


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-N1


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-J2


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-J14


title: Ubc9 fl/fl; AdipoQ-cre+ C2

description: Library name: 18i


title: Ubc9 fl/fl; AdipoQ-cre+ B2

description: Library name: 17i


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-J1


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-J13


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-I2


title: Ubc9 fl/fl; AdipoQ-cre+ A2

description: Library name: 16i


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-K14


title: 239002377BCD

description:
Library name: sample15
239002377BCD


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-I13


title: Ubc9 fl/fl E2

description: Library name: 15i

value: Ubc9 fl/fl

value: Control


title: Ubc9 fl/fl D2

description: Library name: 14i


title: 239010561BCD

description:
Library name: sample16
239010561BCD


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-H14


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-I14


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-L1


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-I1


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-H2


title: 239000312BCD

description:
Library name: sample14
239000312BCD


title: Ubc9 fl/fl C2

description: Library name: 13i


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-H13


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-H1


title: Ubc9 fl/fl B2

description: Library name: 12i


title: 239000985BCDR1

description:
Library name: sample13
239000985BCDR1


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-G2


title: 239018251BCD

description:
Library name: sample18
239018251BCD


title: 239018350FD

description:
Library name: sample12
239018350FD

source_name: lung tumor biopsy

value: lung tumor biopsy

value: C1D1 ICI-PD


title: 239014968BCD

description:
Library name: sample17
239014968BCD


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-G14

value: 9 months


title: Ubc9 fl/fl A2

description: Library name: 11i


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-G1


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-G13


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-F2


title: 239030035FD

description:
Library name: sample11
239030035FD

source_name: FFPE lung tumor tissue

value: FFPE lung tumor tissue


title: Ubc9 fl/fl; AdipoQ-cre+ E1

description: Library name: 10e

source_name: Visceral adipose tissue

value: Visceral adipose tissue


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-F14

value: CP


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-F1

value: M


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-E2


title: Ubc9 fl/fl; AdipoQ-cre+ D1

description: Library name: 9e


title: Ubc9 fl/fl; AdipoQ-cre+ C1

description: Library name: 8e


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-E14


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-D2


title: 239010842FD

description:
Library name: sample9
239010842FD


title: 239019031FD

description:
Library name: sample8
239019031FD


title: Ubc9 fl/fl; AdipoQ-cre+ B1

description: Library name: 7e


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-E1


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-D14


title: 239000291FDR2

description:
Library name: sample7
239000291FDR2


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-D13


title: Ubc9 fl/fl E1

description: Library name: 5e


title: 239030852FDR2

description:
Library name: sample5
239030852FDR2

value: treatment-naïve


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-D1


title: 239000757FDR2

description:
Library name: sample6
239000757FDR2


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-C2


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-E13


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-C14


title: Ubc9 fl/fl D1

description: Library name: 4e


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-C13


title: Ubc9 fl/fl C1

description: Library name: 3e


title: 239026191FD

description:
Library name: sample4
239026191FD


title: 239030034FD

description:
Library name: sample10
239030034FD


title: 239021176FD

description:
Library name: sample3
239021176FD


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-F13


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-B2


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-B14


title: 239018274FD

description:
Library name: sample2
239018274FD


title: Ubc9 fl/fl B1

description: Library name: 2e


title: Ubc9 fl/fl; AdipoQ-cre+ A1

description: Library name: 6e


title: Ubc9 fl/fl A1

description: Library name: 1e


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-B13


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-A2


title: 241900044FD

description:
Library name: sample1
241900044FD


title: WT_placebo_rep8

description:
Library name: VHXT127
library construction protocol: P2895

value: Tibialis anterior muscle

value: WT

value: placebo


title: PHH cells, FRG, sample 3

city: Seattle

first: Keylie

last: Gibson

state: Washington

address: 188 East Blaine Street Suite 400

institute: Sana Biotechnology

data_processing:
Sequencing reads were checked with MultiQC v1.14 and trimmed with Cutadapt v4.4 and fastp v0.23.2.
Trimmed reads were mapped to the human genome reference only (GENCODE GRCh38 v43) using STAR v2.7.10b aligner and quantified with salmon v1.9.0. The PHH-FRG samples were mapped to the human genome reference and the mouse genome reference (GENCODE GRCm39 v32) and only the human genes were used in subsequent analyses for these samples.
Read count normalization and differential expression analyses for pairwise comparisons were processed using DESeq2 v1.40.2 in R v4.3.0.
Assembly: GENCODE GRCh38 v43
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes DESeq2 normalized counts for each sample
Supplementary files format and content: tab-delimited text file includes DESeq2 diffexp between CRYO and FRG samples
Supplementary files format and content: tab-delimited text file includes DESeq2 diffexp between CRYO and 24h samples

source_name: liver

growth_protocol: Primary human hepatocytes were cultured in HBM medium + supplement. FRG humanized liver mouse model was used to assess vector potential to transduce human hepatocytes in vivo. Mice were maintained and the study was conducted through Yecuris (Oregon, USA). The FRG mice have a FAH-/- mutation, which enables ablation of the murine hepatocytes, creating a niche for engraftment of donor hepatocytes. They also have Rag2 -/- IL2rg-/- immunodeficiency mutations which allow persistence and expansion of engrafted human hepatocytes. Hepatocytes were isolated from FRG mice.

extract_protocol:
Samples were sent to GENEWIZ (Azenta Life Sciences) where total RNA was extracted from each sample and sequenced with 150bp paired-end reads on an Illumina HiSeq platform.
Library prep for the samples occurred at GENEWIZ (Azenta Life Sciences).

treatment_protocol: Three different PHH cells: freshly thawed after cryopreservation (CRYO), thawed and cultured for 24h (24h) and isolated from FRG mice (FRG).

value: liver

value: PHH

value: Primary Human Hepatocytes

value: FRG

value: Isolated from FRG mice


title: WT_placebo_rep7

description:
Library name: VHXT126
library construction protocol: P2895


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-A14


title: PHH cells, FRG, sample 2


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-C1


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-P24


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-P23


title: WT_placebo_rep6

description:
Library name: VHXT125
library construction protocol: P2895


title: PHH cells, FRG, sample 1


title: WT_placebo_rep5

description:
Library name: VHXT124
library construction protocol: P2895


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-P12


title: Bin1KO_tamox_rep4

description:
Library name: VHXT113
library construction protocol: P2895

value: Bin1 mck-/-

value: tamoxifen


title: PHH cells, 24h, sample 3

value: Cultured for 24h


title: PHH cells, 24h, sample 2


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-O24

value: 9 months


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-O23


title: PHH cells, 24h, sample 1


title: Bin1KO_tamox_rep2

description:
Library name: VHXT111
library construction protocol: P2895


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-B1


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-N24


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-A13


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-O11


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-O12


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-N23


title: AMB_201117_9mo_5E_6E_4_P3-1-J3-A1


title: Bin1KO_tamox_rep3

description:
Library name: VHXT112
library construction protocol: P2895


title: PHH cells, Cryo D0, sample 3

value: CRYO

value: Thawed


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-N12

value: CP


title: Bin1KO_tamox_rep1

description:
Library name: VHXT110
library construction protocol: P2895


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-M24

value: M


title: Bin1KO_placebo_rep4

description:
Library name: VHXT107
library construction protocol: P2895


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-P11


title: PHH cells, Cryo D0, sample 1


title: Bin1KO_placebo_rep3

description:
Library name: VHXT106
library construction protocol: P2895


title: Renal Epithelial

data_processing:
All data processing was completed by GENEWIZ (Azenta Life Sciences).
The RNA-seq reads were processed by GENEWIZ, where the reads were mapped to the human genome reference (GRCh38) using STAR aligner.
Assembly: GRCh38
Supplementary files format and content: comma-separated text file includes raw counts for each sample
Supplementary files format and content: comma-separated text file includes CPM normalized counts for each sample
Supplementary files format and content: Metdata text file for samples

source_name: kidney

growth_protocol: SupT1 and Raji cell lines were cultured in RPMI media + 10% FBS. HEK-293 Lenti-X cell lines were cultured in DMEM+10% FBS. Hulec-5a cell lines were cultured in MCDB131 media, without L-glutamine, supplemented with 10ng/mL Epidermal Growth Factor, 1ug/mL Hydrocortisone, 10mM Glutamine, and 10% FBS. Huvec cell lines were cultured in Vasculife media + vasculife supplement. Human Pulmonary Alveolar Epithelial cells were cultured on lysine-coated plates in Alveolar (AEpiCM) media supplemented by FBS, ECGS, and PS. Human renal epithelial cells were cultured on lysine-coated plates in EpiCM media supplemented by FBS, ECGS, and PS. HLEC and Human Lymphatic Endothelial cells were cultured on fibronectin-coated plates in ECM media supplemented with FBS, ECGS, and PS. Human Aortic Endothelial, Human Pulmonary Artery Endothelial, and Human Coronary Artery Endothelial cells  were cultured in Vasculife medium + supplement.

treatment_protocol: No treatment. All cell lines where thawed and then sent for processing and sequencing.

value: kidney

value: Human renal epithelial cells

value: cultured, untreated


title: Bin1KO_placebo_rep2

description:
Library name: VHXT105
library construction protocol: P2895

value: Tibialis anterior muscle

value: placebo


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-M12


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-M11


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-L23


title: Coronary Endothelial

source_name: cardiovascular

value: cardiovascular

value: Human Coronary Artery Endothelial cells


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-L12


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-M23


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-L11


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-K24


title: Pulmonary Endothelial

source_name: lung

value: lung

value: Human Pulmonary Alveolar Epithelial cells


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-K23


title: Aortic Endothelial

source_name: heart

value: heart

value: Human Aortic Endothelial cells


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-K12


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-K11


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-J24


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-N11


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-J23


title: Liver Endothelial

value: liver

value: Human Liver Endothelial cells


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-J12

value: 9 months


title: Lymphatic Endothelial

source_name: lymphatic

value: lymphatic

value: Human Lymphatic Endothelial cells


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-L24

value: CP

value: M


title: PHH cells, Cryo D0, sample 2

value: PHH

value: Primary Human Hepatocytes

value: CRYO

value: Thawed


title: HA-SL CD22-CAR transduced, post-thaw, 24hr stim, tr2

city: Aurora

first: Terry

last: Fry

state: CO

institute: University of of Colorado Denver and Children's Hospital Col

description:
Library name: Sample 11
10X Genomics OCM

data_processing:
Reads were demultiplexed and mapped to the human genome (GRCh38) using 10X cellranger (v9.0.1) before analysis with Seurat (v5.3.0)34. Cells with fewer than 7% mitochondrial reads and between 1000 and 7000 unique genes were included for subsequent comparisons. Data from cells in both replicates of rest (“Rest”) and stimulation (“Stim”) conditions were log normalized and scaled using all genes before processing with principal component analysis. The first 10 principal components were used to find neighbors, before clustering at a resolution of 0.5, and UMAP dimensional reduction using the 20 nearest neighbors. Subsets of CD4 and CD8 T cells were selected by normalized expression levels of CD4 and CD8A/CD8B. Gene expression comparisons were made between groups of CD4 or CD8 cells expressing different CARs with Seurat function FindMarkers using the MAST test including the replicate as a latent variable and a cutoff of >1.5 fold-change. Z-scores for genes with an adjusted p-value < 0.1 in at least one comparison were generated with SeuratExtend (v1.2.5) function CalcStats35 and plotted as heatmaps with ComplexHeatmap36.
Assembly: Human GRCh38
Supplementary files format and content: Tab separated values files

source_name: PBMC

extract_protocol:
At the end of the assay, dead cells were depleted using a Dead Cell Removal Kit (Miltenyi Biotec, Cat #130-090-101) to achieve greater than 90% viability, and cells were resuspended at 1.25e6/mL. Following manufacturer recommendations, emulsion droplets were constructed using 10X Genomics Chromium X controller with the 3’ scRNA-seq On-Chip Multiplexing (OCM) workflow to target 5,000 single cells per condition.
Gene expression library preparation was performed using the 10X Genomics Chromium Single Cell OCM 3′ Reagent Kit. Quality control on the generated cDNA was performed using an Agilent 2100 Bioanalyzer using a High Sensitivity DNA Kit (Agilent Technologies). One quarter of the cDNA was used to build the gene expression libraries, and indexed using the 10X, Set TT A index plate. Gene Expression libraries were pooled based off the projected number of cells captured and sequenced using a NextSeq 2000 P4 100c flow cell, aiming for 20,000 reads per sample. Two experimental replicates were performed.

treatment_protocol: Following CAR transduction and removal from beads, T cells were magnetically selected using unconjugated CD22 Protein Fc to obtain >98% pure CAR+ T cells and frozen down after 5 days of additional expansion in IL-2 as described above. 24-well plates were coated overnight using CD22 Protein Fc (3ug/mL in PBS) or PBS alone (no antigen)33. For stimulation, T cells were thawed, and allowed to rest in 100IU/mL IL-2 overnight, then cultured for 24 hours with or without plate-bound antigen.

value: PBMC

value: CD3+ T cell


title: SA-SL CD22-CAR transduced, post-thaw, 24hr stim, tr2

description:
Library name: Sample 10
10X Genomics OCM


title: HA-LL CD22-CAR transduced, post-thaw, 24hr rest, tr2

description:
Library name: Sample 9
10X Genomics OCM


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-I24


title: HA-LL CD22-CAR transduced, post-thaw, 24hr stim, tr2

description:
Library name: Sample 12
10X Genomics OCM


title: Raji

source_name: immune cells

value: immune cells

value: Raji

value: lymphoblast-like cells

value: cultured, untreated


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-I12


title: SA-SL CD22-CAR transduced, post-thaw, 24hr rest, tr2

description:
Library name: Sample 7
10X Genomics OCM


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-I11


title: Huvec

source_name: umbilical vein

value: umbilical vein

value: Huvec

value: Human umbilical vein endothelial cells


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-J11

value: 9 months


title: HA-SL CD22-CAR transduced, post-thaw, 24hr rest, tr2

description:
Library name: Sample 8
10X Genomics OCM


title: SupT1

value: T lymphoblast


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-I23

value: CP


title: Bin1KO_placebo_rep1

description:
Library name: VHXT104
library construction protocol: P2895

source_name: Tibialis anterior muscle

value: Tibialis anterior muscle

value: Bin1 mck-/-

value: placebo


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-H24

value: M


title: Hulec-5a

source_name: microvascular endothelium

value: microvascular endothelium

value: microvascular endothelial cell


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-H23


title: HA-LL CD22-CAR transduced, post-thaw, 24hr stim, tr1

description:
Library name: Sample 6
10X Genomics OCM

value: PBMC

value: CD3+ T cell


title: HEK293-LX

source_name: human embryonic kidney cells

value: human embryonic kidney cells

value: HEK-293T Lenti-X


title: HA-SL CD22-CAR transduced, post-thaw, 24hr stim, tr1

description:
Library name: Sample 5
10X Genomics OCM


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-H11


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-H12


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-G24


title: HA-LL CD22-CAR transduced, post-thaw, 24hr rest, tr1

description:
Library name: Sample 3
10X Genomics OCM


title: SA-SL CD22-CAR transduced, post-thaw, 24hr stim, tr1

description:
Library name: Sample 4
10X Genomics OCM


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-G12


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-G23


title: Metaphase Hela S3 Chemical map Rep2

city: Evanston

first: Xiaozhong

last: Wang

state: IL

address: 2200 Campus Dr

department: Molecular Biosciences

institute: Northwestern University

data_processing:
For chemical mapping, we sequenced two replicates for each state: interphase and metaphase. The resulting reads were mapped to Ensembl Genome assembly GRCh38.p13 (GCA_000001405.28, Release 108) using STAR software tool, and the only reads mapped to <=10 sites were used to calculate the chemical cleavage. Non-uniquely mapped reads are evenly divided among the mapped sites when calculating coverage.
For chemical maps, the resulting cleavage frequencies from the two replicates of each condition were merged for downstream analysis.
We  identified the cleavage pattern around the dyad, and the R package NuCMap that implements the deconvolution algorithm was used to compute the nucleosome center positioning (NCP) score at every genomic location (https://github.com/jipingw/NuCMap). We defined the unique nucleosome map based on the magnitude of NCP scores using a greedy algorithm, by requiring two neighboring dyad positions to be spaced >= 120 bp
Based on all defined nucleosomes, we selected the top 90% as our unique nucleosome set/map that represents the most prominent dyad positions.
Assembly: GCA_000001405.28, Release 108
Supplementary files format and content: bigwig tracks displaying corrected NCP score for each genomic position
Supplementary files format and content: bigwig track displaying unique nucleosome set position and associated score
Library strategy: Chemical Mapping

source_name: Hela S3

growth_protocol: HeLa S3 derived cell lines were cultured in high glucose Dulbecco’s modified Eagle’s (DMEM) (Corning) medium supplemented with 10% fetal bovine serum (FBS), 1% (v/v) Penicillin/Streptomycin, 1% (v/v) Glutamine, and 1 mM sodium pyruvate.

extract_protocol:
Cleaved genomic DNA was extracted from the rinsed cell pellets using proteinase K digestion followed by phenol/chloroform extraction, ethanol precipitation. The purified DNA was resolved on a 1.8% NuSieve 3:1 (Lonza) agarose gel. DNA fragments (~100 to 300 bp) were gel-purified and prepared for paired-end sequencing
the Illumina TrueSeq DNA PCR-Free kit

treatment_protocol: For synchronization of HeLa S3 cells to prometaphase, 2 x10 6 cells per 10cm cell culture plate seeded on the previous day were synchronized to early S phase by double thymidine (2 mM) treatment over the course of two days. This was followed by a 5-hour release in fresh media and an 8-hour nocodazole arrest at a final concentration of 100 ng/ml. Mitotic cells were then collected by shaking off and centrifugation.

value: Hela S3

value: double thymidine + nocodazole


title: HA-SL CD22-CAR transduced, post-thaw, 24hr rest, tr1

description:
Library name: Sample 2
10X Genomics OCM


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-G11


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-F24


title: SA-SL CD22-CAR transduced, post-thaw, 24hr rest, tr1

description:
Library name: Sample 1
10X Genomics OCM


title: Interphase Hela S3 Chemical map Rep2


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-F23


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-F12


title: Interphase Hela S3 Chemical map Rep1


title: A549 cells, adrenal gland metastasis, replicate 3

description:
Library name: Sample 12
Column name in human_countmatrix_030325.csv: AAG3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
Trimmed sequence reads were mapped to GRCh38.113 using STAR.
Extraction of read counts and construction of the count matrix were performed using featureCounts.
Assembly: GRCh38
Supplementary files format and content: comma-delimited file cointaing raw counts for each sample

growth_protocol: A549 cells were mantained in RPMI medium supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37ºC.

value: immortalized human cell line isolated from pulmonary adenocarcinoma

value: WT


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-E23

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

value: 9 months


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-E24


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-F11


title: Metaphase Hela S3 RNA-Seq

data_processing:
reads were aligned to Ensembl Genome assembly GRCh38.p13 (GCA_000001405.28, Release 108) using STAR software tool to generate reads per gene count output
Assembly: GCA_000001405.28, Release 108
Supplementary files format and content: tab delimited format files containing raw counts per gene

extract_protocol:
Total RNA was extracted from cultured HeLa cells using TRIzol Reagent (Life Technologies) following the manufacturer’s protocol.
For RNA-seq analysis, total RNA samples from different cell cycle phases were utilized to construct RNA-seq libraries using a TruSeq Stranded Total RNA Library Prep Kit (Illumina).


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-E12


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-E11


title: Interphase Hela S3 RNA-Seq


title: Metaphase Hela S3 Chemical map Rep1


title: A549 cells, adrenal gland metastasis, replicate 1

description:
Library name: Sample 10
Column name in human_countmatrix_030325.csv: AAG1


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-D24


title: A549 cells, adrenal gland metastasis, replicate 2

description:
Library name: Sample 11
Column name in human_countmatrix_030325.csv: AAG2


title: Interphase Hela S3 Mnase-Seq

data_processing:
The resulting reads were mapped to Ensembl Genome assembly GRCh38.p13 (GCA_000001405.28, Release 108) using STAR software tool, uniquely mapped reads were used.
Nucleosome occupancy is a center weighted occupancy calculated as described in methods using the NuCMap R package (https://github.com/jipingw/numap)
Assembly: GCA_000001405.28, Release 108
Supplementary files format and content: bigwig tracks displaying center weighted nucleosome occupancy score
Supplementary files format and content: bigwig tracks displaying unique nucleosome set and associated center weighted nucleosome occupancy score

extract_protocol:
The digested genomic DNA was purified followed by an overnight proteinase K digestion. Mononucleosomal DNA fragments were resolved on a 1.5% agarose gel and gel-purified for sequencing
TruSeq DNA PCR-Free kit


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-D12

extract_protocol:
Regions of mouse brain 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.


title: A549 cells, bone metastasis, replicate 3

description:
Library name: Sample 9
Column name in human_countmatrix_030325.csv: AL3


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-D11


title: A549 cells, bone metastasis, replicate 2

description:
Library name: Sample 8
Column name in human_countmatrix_030325.csv: AL2


title: Metaphase Hela S3 Mnase-Seq


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-C24


title: A549 cells, bone metastasis, replicate 1

description:
Library name: Sample 7
Column name in human_countmatrix_030325.csv: AL1


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-C12


title: WT, Maturation (28 mm) heart ventricles

city: Montreal

first: Rubén

last: Marín-Juez

address: 3175 Chem. de la Côte-Sainte-Catherine

country: Canada

institute: CHU Sainte-Justine

description:
Library name: WT-Maturation_28 mm
10x Genomics

data_processing:
FASTQ files were processed individually in 10x Genomics Cloud Analysis using the Cell Ranger Count v6.1.2 pipeline and reads were aligned to GRCz11 v4.3.2 reference genome. Filtered gene expression matrices were imported and further processed in Seurat v4. Samples were integrated to create a single aggregated Seurat object, and low-quality cells containing less than 200 unique features were removed. Batch effect correction was performed using the data integration and ScTransform functions in Seurat.
Assembly: GRCz11 v4.3.2 reference genome
Supplementary files format and content: Tab separated values files and matrix files

organism: Danio rerio

source_name: Heart ventricle

extract_protocol:
One pool of ventricles per developmental stage, initiation (10 mm) 25 ventricles, establishment (14 mm) 18 ventricles, expansion (18 mm) 12 ventricles and maturation (28 mm) 5 ventricles) was prepared using WT zebrafish. Euthanatized fish were dissected, and ventricles were extracted in calcium- , magnesium-free HBSS (Sigma, Cat. no. H9394) supplemented with 20 U/ml of heparin (Sigma, Cat no. H3393). Ventricles were washed in fresh HBSS and transferred into 1 ml of 1 mg/ml of collagenase (Gibco, Cat. no. 17101015) dissolved in HBSS for around 30 min digestion on a thermal mixer at 32 ⁰C and 700 rpm. Ventricles were mechanically disrupted by pipetting every 10 min. Samples were centrifuged at 2000 rpm for 5 min at RT and supernatants discarded. Cells were digested with 1 ml of 1x TrypLE Express Enzyme (Gibco, Cat. no. 12605010) for 15 min on a thermal mixer at 32 ⁰C and 700 rpm and pipetted every 5 min. Enzymatic digestion was stopped by adding 1 ml of 20% fetal bovine serum (Thermo, Cat no. A3160701) in HBSS to extracts. Tissue extracts were strained through a 70 μm cell strainer and centrifuged at 2000 rpm for 5 min at RT. The supernatants were discarded, and pellets were washed with 1 ml of 20% fetal bovine serum in HBSS. After centrifuge at 2000 rpm for 5 min at RT, cells were resuspended in 80 μl of 20% fetal bovine serum in HBSS and strained through a 40 μm cell strainer. Cells were counted and viability (>85%) was assessed using 0.4% Trypan Blue (Sigma, T8154). Cells were kept on ice and immediately processed for scRNA-seq.
For scRNA-seq experiment, 14000 cells were used for each sample and the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10x Genomics, Cat. no. PN-1000269) was used following manufacturer’s protocol. Each sample was indexed individually using the Dual Index Kit TT Set A (10x Genomics, Cat. no. PN-1000215).

value: Heart ventricle

value: 8 months old

value: AB


title: AMB_201117_9mo_5E_6E_4_P2-6-L4-B24

value: CP