title: AMB_200702_9mo_2A_3A_2_P6-1-C1-P14


title: AMB_200702_9mo_2A_3A_2_P6-1-C1-P13

status: Public on Dec 30 2025

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

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

tag: strain

tag: brain region

value: FC

tag: gender

value: M

tag: age

value: 9 months


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-D15


title: AMB_200702_9mo_2A_3A_2_P6-1-C1-P1


title: AMB_200702_9mo_2A_3A_2_P6-1-C1-O14


title: AMB_200702_9mo_2A_3A_2_P6-1-C1-O2


title: AMB_200702_9mo_2A_3A_2_P6-1-C1-O13


title: AMB_200702_9mo_2A_3A_2_P6-1-C1-N2


title: AMB_200702_9mo_2A_3A_2_P6-1-C1-N14


title: AMB_200702_9mo_2A_3A_2_P6-1-C1-O1


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-B4


title: AMB_200702_9mo_2A_3A_2_P6-2-L17-C3


title: AMB_200702_9mo_2A_3A_2_P6-1-C1-N1


title: AMB_200702_9mo_2A_3A_2_P6-1-C1-M2


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title: AMB_200702_9mo_2A_3A_2_P6-1-C1-N13


title: AMB_200702_9mo_2A_3A_2_P6-1-C1-M14


title: AMB_200702_9mo_2A_3A_2_P6-1-C1-L13


title: AMB_200702_9mo_2A_3A_2_P6-1-C1-L2


title: AMB_200702_9mo_2A_3A_2_P6-1-C1-K2


title: AMB_200702_9mo_2A_3A_2_P6-1-C1-L14


title: AMB_200702_9mo_2A_3A_2_P6-1-C1-L1


title: AMB_200702_9mo_2A_3A_2_P6-1-C1-K13


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title: AMB_200702_9mo_2A_3A_2_P5-4-D20-O20


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title: AMB_200702_9mo_2A_3A_2_P5-4-D20-H7


title: AMB_200702_9mo_2A_3A_2_P5-4-D20-H20


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title: AMB_200702_9mo_2A_3A_2_P5-4-D20-G7


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title: AMB_200630_9mo_2A_3A_1_P6-1-A9-P1


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-O2


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-P13


title: AMB_200630_9mo_2A_3A_1_P6-2-P5-C4


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-O14


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-O13


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-N14


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-N1


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-M14


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-O1


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-L14


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-L13


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-K2


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-L1


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-K1


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-K13


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-K14


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-M1


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-J2


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-J14


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-P2


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-J13


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-J1


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-I1


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-I2


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-I14


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-H2


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-I13


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-N13


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-N2


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-M2


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-M13


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-H1


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-G2


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-G13


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-H14


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-L2


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-H13


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-G14


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-F2


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-F1


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-F14


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-F13


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-E2


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-E1


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-E13


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-D14


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-D2


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-D1


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-D13


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-C1


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-B13


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-B1


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-A2


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-G1


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-C2


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-A14


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-C13


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-A1


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-P23


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-C14


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-P11


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-P12


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-E14


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-P24


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-O24


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-O12


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-O11


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-O23


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-N24


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-M24


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-N23


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-M12


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-M23


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-B14


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-L24


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-B2


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-L23


title: AMB_200630_9mo_2A_3A_1_P6-1-A9-A13


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-L11


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-K24


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-K12


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-L12


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-K23


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-K11


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-J24


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-J12


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-J23


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-J11


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-I24


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-I23


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-H23


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-H11


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-G24


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-I11


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-I12


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-G11


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-N11


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-F23


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-H24


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-F12


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-G23


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-G12


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-F24


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-M11


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-F11


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-E12


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-E23


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-E24


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-E11


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-D24


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-D12


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-D23


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-B23


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-D11


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-H12


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-C23


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-B12


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-A24


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-A23


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-A12


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-P21


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-O22


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-C24


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-A11


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-O10


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-P9


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-P22


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-N9


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-P10


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-N22


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-O9


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-O21


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-N21


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-B24


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-C12


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-M9


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-M22


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-C11


title: AMB_200630_9mo_2A_3A_1_P5-6-H20-B11


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-M21


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-L9


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-L22


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-M10


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-L21


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-L10


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-K21


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-K9


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-K22


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-J22


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-K10


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-J10


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-J21


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-I9


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-H9


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-I21


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-H21


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-I10


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-N10


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-H22


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-I22


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-G22


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-H10


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-G10


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-G9


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-G21


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-J9


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-E22


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-F22


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-F10


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-E21


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-E9


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-E10


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-D22


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-D21


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-C9


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-D9


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-C22


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-B9


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-D10


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-B21


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-B10


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-C10


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-B22


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-A9


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-A22


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-C21


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-A21


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-A10


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-P8


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-P7


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-F21


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-P20


title: AMB_200630_9mo_2A_3A_1_P5-5-N2-F9


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-O7


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-P19


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-O8


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-N8


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-O20


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-N7


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-O19


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-N20


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-N19


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-M19


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-L7


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-K8


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-L20


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-K20


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-J8


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-K19


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-K7


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-J7


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-J19


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-I8


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-I20


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-H8


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-I19


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-I7


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-H7


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-H19


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title: AMB_200630_9mo_2A_3A_1_P5-4-H7-M20


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title: AMB_200630_9mo_2A_3A_1_P5-4-H7-G8


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-F20


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-M8


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-H20


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-M7


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-G7


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title: AMB_200630_9mo_2A_3A_1_P5-4-H7-E19


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-E7


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-D8


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-E20


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-D19


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-C7


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-C8


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-C20


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-C19


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-B8


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-B7


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-B20


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-B19


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-A20


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-A8


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-A7


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-P6


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-P5


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-A19


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-P17


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-P18


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-O6


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-O5


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-N6


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-O17


title: AMB_200630_9mo_2A_3A_1_P5-4-H7-D20


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-O18


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-N5


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-N18


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-M5


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-L6


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-M17


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-M18


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-M6


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-N17


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-L18


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-L5


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-L17


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-K5


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-K6


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-K18


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-K17


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-J6


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-J5


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-J18


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-J17


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-I6


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-I5


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-I18


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-I17


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-H6


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-H5


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-H18


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-H17


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-G5


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-G17


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-G18


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-G6


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-F6


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-E18


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-F18


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-F17


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-D6


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-F5


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-E5


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-D17


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-D18


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-E6


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-E17


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-C6


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-C17


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-B6


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-B5


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-B18


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-C5


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-B17


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-C18


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-A5


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-A18


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-A17


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-A6


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-P16


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-P15


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-O4


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-O16


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-O3


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-P4


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-N3


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-N4


title: AMB_200630_9mo_2A_3A_1_P5-3-N14-D5


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-N15


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-M4


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-N16


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-M15


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-M16


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-L3


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-K3


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-K16


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-J4


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-J3


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-K4


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-K15


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-P3


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-J16


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-O15


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-H4


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-I16


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-J15


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-H3


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-H16


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-I3


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-G4


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-I15


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-H15


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-G3


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-L4


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-F4


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-G15


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-M3


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-F3


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-G16


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-L16


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-F15


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-F16


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-L15


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-E3


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-E16


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-D4


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-D16


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-D3


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-D15


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-I4


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-E4


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-C4


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-B4


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-C16


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-C15


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-B16


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-A3


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-A4


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-A16


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-B15


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-P2


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-P14


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-A15


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-E15


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-O14


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-O13


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-P13


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-O1


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-N2


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-N14


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-N1


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-M14


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-M2


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-M13


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-M1


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-C3


title: AMB_200630_9mo_2A_3A_1_P5-2-C12-B3


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-L2


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-L14


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-L1


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-K2


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-L13


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-K14


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-K1


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-P1


title: female_6

city: wuhan

first: xuemeng

last: han

address: shizishan street

country: China

institute: HZAU

description: Library name: female_6

library_source: transcriptomic

data_processing:
The filtered reads were then aligned and annotated to the M. incognita genome using HISAT2 (v2.2.1), with the following specific options: hisat2 -p [threads] -x [index] -S [output] -1 [read1] -2 [read2]. Transcript quantification was performed using StringTie (v2.2.1), followed by sorting the data, generating read counts with prepDE.py, and calculating gene expression levels with getTPM.py, which were expressed as transcripts per million (TPM). To identify expressed genes, we applied a threshold of TPM ≥ 1 at at least one time point.
Assembly: WHF4-1 assembled T2T genome version 1.0
Supplementary files format and content: The gene count dataset: transcript_counts and filtering_counts.

molecule: total RNA

organism: Meloidogyne incognita

source_name: single nematode

extract_protocol:
The washed nematodes were transferred into 90 mm glass Petri dishes. Individual nematodes were isolated under an inverted optical microscope (Mshot M152) equipped with a 10× eyepiece and a 4× objective lens, using a fine glass pipette, and transferred into fresh sterile water. Fresh eggs were collected and incubated in vitro to obtain pre_J2 nematodes after approximately 3 days. Ten individual nematodes were then manually picked under a microscope and classified into different developmental stages based on their morphology before immediate lysis. According to morphological characteristics, the nematodes at distinct developmental stages
The washed nematodes were transferred into 90 mm glass Petri dishes. Individual nematodes were picked under a microscope using a fine pipette and placed into fresh water. Each nematode was then transferred into a pre-labeled PCR microtube containing 1.5 μL of lysis buffer, prepared from 18 μL of 0.3% Triton-X 100 and 2 μL of RNase inhibitor. Under the microscope, each nematode was carefully punctured with a fine needle to release its contents. The microtubes were briefly centrifuged to collect the material at the bottom. The trace amounts of mRNA from each nematode were reverse transcribed into complementary DNA (cDNA).

tag: tissue

value: single nematode

tag: cell line

value: Adult female

tag: cell type


title: female_4

description: Library name: female_4


title: female_7

description: Library name: female_7


title: female_5

description: Library name: female_5


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-J14


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-J13


title: female_3

description: Library name: female_3


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-O2


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-J1


title: female_2

description: Library name: female_2


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-I2


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-N13


title: female_1

description: Library name: female_1


title: male_6

description: Library name: male_6


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-I14


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-I13


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-I1


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-K13


title: male_1

description: Library name: male_1


title: male_2

description: Library name: male_2


title: male_5

description: Library name: male_5


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-H2


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-G14


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-H14


title: J4_female_7

description: Library name: J4_female_7


title: male_3

description: Library name: male_3


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-H1


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-F2


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-J2


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-H13


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-G2


title: J4_female_8

description: Library name: J4_female_8


title: male_4

description: Library name: male_4


title: J4_female_6

description: Library name: J4_female_6


title: J4_female_4

description: Library name: J4_female_4


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-G1


title: J4_female_3

description: Library name: J4_female_3


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-F13


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-F14


title: J4_moulting_14

description: Library name: J4_moulting_14


title: J4_female_1

description: Library name: J4_female_1


title: male_7

description: Library name: male_7


title: J4_female_2

description: Library name: J4_female_2


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-E2


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-F1


title: J4_female_5

description: Library name: J4_female_5


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-G13


title: J4_moulting_13

description: Library name: J4_moulting_13


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-D13


title: J4_moulting_9

description: Library name: J4_moulting_9


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-D2


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-E14


title: J4_moulting_11

description: Library name: J4_moulting_11


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-D1


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-E13


title: J4_moulting_12

description: Library name: J4_moulting_12


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-D14


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-E1


title: J4_moulting_5

description: Library name: J4_moulting_5


title: J4_moulting_7

description: Library name: J4_moulting_7


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-C1


title: J4_moulting_3

description: Library name: J4_moulting_3


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-C13


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-C14


title: J4_moulting_8

description: Library name: J4_moulting_8


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-B2


title: J4_moulting_4

description: Library name: J4_moulting_4


title: J4_moulting_2

description: Library name: J4_moulting_2


title: J4_moulting_1

description: Library name: J4_moulting_1


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-B14


title: J4_8

description: Library name: J4_8


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-B13


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-B1


title: J4_7

description: Library name: J4_7


title: J4_moulting_10

description: Library name: J4_moulting_10


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-C2


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-A2


title: J4_moulting_6

description: Library name: J4_moulting_6


title: J4_6

description: Library name: J4_6


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-A14


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-A13


title: J4_5

description: Library name: J4_5


title: J4_3

description: Library name: J4_3


title: AMB_200630_9mo_2A_3A_1_P5-1-B22-A1


title: J4_2

description: Library name: J4_2


title: J4_1

description: Library name: J4_1


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-P12


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-P24


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-P23


title: J3_14

description: Library name: J3_14


title: J3_12

description: Library name: J3_12


title: J3_13

description: Library name: J3_13


title: J3_11

description: Library name: J3_11


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-O24


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-O23


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-O11


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-O12


title: J3_9

description: Library name: J3_9


title: J3_8

description: Library name: J3_8


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-N24


title: J3_7

description: Library name: J3_7


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-N23


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-N12


title: J3_5

description: Library name: J3_5


title: J3_6

description: Library name: J3_6


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-N11


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-M24


title: J4_4

description: Library name: J4_4


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-M23


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-P11


title: J3_3

description: Library name: J3_3


title: J3_4

description: Library name: J3_4


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-M12


title: J3_1

description: Library name: J3_1


title: par_J2_12

description: Library name: par_J2_12


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-L24


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-L23


title: par_J2_11

description: Library name: par_J2_11


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-M11


title: J3_10

description: Library name: J3_10


title: J3_2

description: Library name: J3_2


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-L11


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-L12


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-K24


title: par_J2_9

description: Library name: par_J2_9


title: par_J2_10

description: Library name: par_J2_10


title: par_J2_7

description: Library name: par_J2_7


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-K12


title: par_J2_6

description: Library name: par_J2_6


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-K11


title: par_J2_5

description: Library name: par_J2_5


title: par_J2_4

description: Library name: par_J2_4


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-J24


title: par_J2_3

description: Library name: par_J2_3


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-J23


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-J12


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-J11


title: pre_J2_4

description: Library name: pre_J2_4


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-I24


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-I11


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-I12


title: par_J2_2

description: Library name: par_J2_2


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-H24


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-I23


title: par_J2_8

description: Library name: par_J2_8


title: pre_J2_2

description: Library name: pre_J2_2


title: pre_J2_3

description: Library name: pre_J2_3


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-H23


title: Circadian Perturbed ZT = 16 (Extended Light, Light ON) Replicate 2

city: Richland

first: Lindsey

middle: N

last: Anderson

state: WA

address: 3300 Stevens Dr

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

description: Library name: 16Hr-lt-49

data_processing:
Read trimming / QC (TrimGalore v0.6.10; CutAdapt v5.0)
Read mapping & quantification (Rsubread v2.20)
Assembly: GCF_000011465.1 (26-JAN-2024)
Supplementary files format and content: .csv counts

organism: Prochlorococcus marinus

source_name: strain CCMP1986

growth_protocol: Prochlorococcus marinus MED4 was cultured in adapted Pro99 media prepared using Salish Seawater (Sequim, Washington) and 2X standard concentrations of Pro99 N/P sources, while maintaining 1× concentration of Pro99 trace metals.

extract_protocol:
RNA was extracted from exponentially growing cells using Qiagen Rneasy plus mini kit following manufacturer instructions. Samples underwent DNase treatment and rRNA depletion before paired-end sequencing
RNA-Seq with rRNA depletion

treatment_protocol: Cultures were acclimated to a circadian photoperiod of 12:12 h light:dark at an incident white-light intensity of 45 µmol photons m⁻² s⁻¹ and a temperature of 22 °C for XX days / generations prior to sampling. Accimaltion was performed in a single XL batch flask before splitting samples into individual 50mL tubes. Circadian perturbed samples were exposed to extended periods of light during circadian night (ZT = 14, 16h) or dark during circadian day (ZT = 2, 4h).

tag: genotype

value: WT

tag: treatment


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-K23


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-H12


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-H11


title: Circadian Perturbed ZT = 16 (Extended Light, Light ON) Replicate 1

description: Library name: 16Hr-lt-48


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-G24


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-G23


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-G12


title: Circadian Perturbed ZT = 14 (Extended Light, Light ON) Replicate 2

description: Library name: 14Hr-lt-46


title: Circadian Perturbed ZT = 14 (Extended Light, Light ON) Replicate 1

description: Library name: 14Hr-lt-45


title: Circadian Perturbed ZT = 4 (Extended Dark, Light OFF) Replicate 1

description: Library name: 4Hr-dk-43


title: Circadian Perturbed ZT = 4 (Extended Dark, Light OFF) Replicate 2

description: Library name: 4Hr-dk-44


title: Circadian Perturbed ZT = 2 (Extended Dark, Light OFF) Replicate 2

description: Library name: 2Hr-dk-42


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-F24


title: par_J2_1

description: Library name: par_J2_1


title: pre_J2_5

description: Library name: pre_J2_5


title: pre_J2_1

description: Library name: pre_J2_1


title: Circadian Perturbed ZT = 2 (Extended Dark, Light OFF) Replicate 1

description: Library name: 2Hr-dk-41


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-F23


title: Circadian ZT = 22 (Night, Light OFF) Replicate 3

description: Library name: 22Hr-36

value: Circadian ZT = 22 (Night, Light OFF)


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-E24


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-F12


title: Circadian ZT = 22 (Night, Light OFF) Replicate 1

description: Library name: 22Hr-34


title: Circadian ZT = 20 (Night, Light OFF) Replicate 3

description: Library name: 20Hr-33

value: Circadian ZT = 20 (Night, Light OFF)


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-F11


title: Circadian ZT = 22 (Night, Light OFF) Replicate 2

description: Library name: 22Hr-35


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-E23


title: Circadian ZT = 20 (Night, Light OFF) Replicate 2

description: Library name: 20Hr-32


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-E12


title: Circadian ZT = 20 (Night, Light OFF) Replicate 1

description: Library name: 20Hr-31


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-E11


title: Circadian ZT = 18 (Night, Light OFF) Replicate 3

description: Library name: 18Hr-30

value: Circadian ZT = 18 (Night, Light OFF)


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-D24


title: Circadian ZT = 18 (Night, Light OFF) Replicate 2

description: Library name: 18Hr-29


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-D23


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-G11


title: Circadian ZT = 18 (Night, Light OFF) Replicate 1

description: Library name: 18Hr-28


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-D12


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-C24


title: Circadian ZT = 16 (Night, Light OFF) Replicate 3

description: Library name: 16Hr-27

value: Circadian ZT = 16 (Night, Light OFF)


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-D11


title: Circadian ZT = 16 (Night, Light OFF) Replicate 2

description: Library name: 16Hr-26


title: Circadian ZT = 14 (Night, Light OFF) Replicate 3

description: Library name: 14Hr-24

value: Circadian ZT = 14 (Night, Light OFF)


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-C23


title: Circadian ZT = 16 (Night, Light OFF) Replicate 1

description: Library name: 16Hr-25


title: Circadian ZT = 14 (Night, Light OFF) Replicate 2

description: Library name: 14Hr-23


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-C11


title: Circadian ZT = 14 (Night, Light OFF) Replicate 1

description: Library name: 14Hr-22


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-C12


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-B24


title: Circadian ZT = 12 (Dusk, Light ON) Replicate 3

description: Library name: 12Hr-21

value: Circadian ZT = 12 (Dusk, Light ON)


title: Circadian ZT = 12 (Dusk, Light ON) Replicate 2

description: Library name: 12Hr-20


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-B11


title: Circadian ZT = 12 (Dusk, Light ON) Replicate 1

description: Library name: 12Hr-19


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-B23


title: Circadian ZT = 10 (Day, Light ON) Replicate 3

description: Library name: 10Hr-18

value: Circadian ZT = 10 (Day, Light ON)


title: Circadian ZT = 10 (Day, Light ON) Replicate 1

description: Library name: 10Hr-16


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-A24


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-B12


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-A23


title: Circadian ZT = 10 (Day, Light ON) Replicate 2

description: Library name: 10Hr-17


title: Circadian ZT = 8 (Day, Light ON) Replicate 3

description: Library name: 8Hr-15

value: Circadian ZT = 8 (Day, Light ON)


title: Circadian ZT = 8 (Day, Light ON) Replicate 2

description: Library name: 8Hr-14


title: Circadian ZT = 8 (Day, Light ON) Replicate 1

description: Library name: 8Hr-13


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-A11


title: AMB_200205_9mo_2A_3A_1_P2-6-L23-A12


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-P9


title: Circadian ZT = 6 (Day, Light ON) Replicate 3

description: Library name: 6Hr-12

value: Circadian ZT = 6 (Day, Light ON)


title: Circadian ZT = 6 (Day, Light ON) Replicate 2

description: Library name: 6Hr-11


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-P10


title: Circadian ZT = 4 (Day, Light ON) Replicate 3

description: Library name: 4Hr-9

value: Circadian ZT = 4 (Day, Light ON)


title: Circadian ZT = 6 (Day, Light ON) Replicate 1

description: Library name: 6Hr-10


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-O9


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-P21


title: Circadian ZT = 4 (Day, Light ON) Replicate 2

description: Library name: 4Hr-8


title: Circadian ZT = 4 (Day, Light ON) Replicate 1

description: Library name: 4Hr-7


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-O21


title: Circadian ZT = 2 (Day, Light ON) Replicate 3

description: Library name: 2Hr-6

value: Circadian ZT = 2 (Day, Light ON)


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-N9

value: FC


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-N22

value: M


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-O10

value: 9 months


title: Circadian ZT = 2 (Day, Light ON) Replicate 2

description: Library name: 2Hr-5


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-N10


title: Circadian ZT = 0 (Dawn, Light OFF) Replicate 2

description: Library name: 0Hr-2

value: Circadian ZT = 0 (Dawn, Light OFF)


title: Circadian ZT = 0 (Dawn, Light OFF) Replicate 3

description: Library name: 0Hr-3


title: Circadian ZT = 2 (Day, Light ON) Replicate 1

description: Library name: 2Hr-4


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-O22


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-N21


title: Circadian ZT = 0 (Dawn, Light OFF) Replicate 1

description: Library name: 0Hr-1


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-M9


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-M22


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-M21


title: OGDHL_KO_Res_dMTS_2

city: Los Angeles

first: Andrew

middle: Scott

last: Goldstein

address: 610 Charles E Young Dr East

department: Urology

institute: University of California, Los Angeles

description: Library name: sample8

data_processing:
The alignment was performed using STAR [2] with human reference genome GRCh38. The Ensembl Transcripts release GRCh38.107 GTF was used for gene feature annotation. For normalization of transcripts counts, TPM normalized counts were generated.
Assembly: GRch38
Supplementary files format and content: TXT files contain normalized TPM Values

organism: Homo sapiens

source_name: prostate cancer

growth_protocol: Cells were cultured in RPMI 1640 containing 10% FBS and 1% Pen-Strep.

extract_protocol:
RNA was isolated from cell pellets using the Qiagen RNeasy Plus Mini Kit according to manufacturer’s instructions. RNA quantity/ integrity was assessed with an Agilent Bioanalyzer.
Libraries for RNA-Seq were prepared with KAPA mRNA HyperPrep Kit. The workflow consists of mRNA enrichment and fragmentation, first strand cDNA synthesis using random priming followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporates dUTP into the second cDNA strand to maintain strand origin information. cDNA generation is followed by end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in a half lane. Sequencing was performed on Illumina NovaSeq X Plus for PE 2x50 run. Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.

treatment_protocol: Cells were maintained in 10uM Enzalutamide

value: prostate cancer

value: 16D CRPC

value: OGDHL KO + Res-dMTS OGDHL

value: Enzalutamide


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-M10


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-P22


title: OGDHL_KO_Res_dMTS_1

description: Library name: sample7


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-L9


title: OGDHL_KO_Res_FL_3

description: Library name: sample6

value: OGDHL KO + Res-FL OGDHL


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-L21


title: OGDHL_KO_Res_FL_1

description: Library name: sample4


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-L22


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-L10


title: OGDHL_KO_Res_FL_2

description: Library name: sample5


title: sgOGDHL_EGFP_3

description: Library name: sample3

value: OGDHL KO + eGFP


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-K9


title: sgOGDHL_EGFP_2

description: Library name: sample2


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-K22


title: sgOGDHL_EGFP_1

description: Library name: sample1


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-J22


title: OGDHL_KO_Res_dMTS_3

description: Library name: sample9


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-K10


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-J9


title: R1-RNA-seq

city: 广州

first: Chen

middle: Qian

last: Qian

state: 广东省

address: 天河区五山街道

institute: 华南农业大学

data_processing:
Illumina Casava software used for basecalling.
（1）Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted )（2）Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality).（3）Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%)
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
The GO （Gene Ontology, http://geneontology.org/）enrichment of DEGs was implemented by the hypergeometric test. GO terms with q<0.05 were considered to be significantly enriched.The KEGG PATHWAY enrichment of DEGs was implemented by the hypergeometric test. KEGG terms with q<0.05 were considered to be significantly enriched. genome build
Assembly: soybean nodule
Supplementary files format and content: tab-delimited text files include raw counts for each Sample .
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

organism: Glycine max

source_name: nodule

extract_protocol:
RNA was extracted from the sample by using Trizol Reagent (Invitrogen) , and then the RNA sample was strictly controlled.RNA purity was detected by NanoPhotometer® spectrophotometer (Thermo Fisher). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina NR604-01/02,

value: nodule

value: low nitrogen application with Bra.Q2 inoculation (R)


title: BR4-RNA-seq

value: low nitrogen application with Bac.B and Bra.Q2 inoculation  (BR)


title: dNCM_MEPC_plate119 (human)

city: Utrecht

first: Frank

last: Riemers

address: Uppsalalaan 8

country: Netherlands

institute: Utrecht University

description: Library name: S119

library_source: transcriptomic single cell

data_processing:
Mapping was performed against the canine reference genome (GRCh38)
Counts were assigned to of human or canine origin, based on the HLA signal the wells containing human cells were identified and removed from the dog data., whereas for the human data these wells were selected and kept.
Analysis was peformed in Seurat 5.3.0.
Assembly: GRCh38
Supplementary files format and content: Tab separated matrix, barcode and features

source_name: MEPCs derived from the Aggrecan-2A-mScarlet Reporter iPSC line intradiscally injected together with dNCM

extract_protocol:
Two-step enzymatic digestion, using the enzymes pronase (Roche, #11459643001) and collagenase type II (Worthington, #443E23628)
Single cell sequencing was peformed at Single Cell Discoveries (Utrecht, the Netherlands) according to the SORT-seq protocol, an adapted version of the CEL-seq2 protocol.


title: dNCM_MEPC_plate117 (human)

description: Library name: S117

value: MEPCs derived from the Aggrecan-2A-mScarlet Reporter iPSC line intradiscally injected together with dNCM


title: dNCM_MEPC_plate120 (human)

description: Library name: S120


title: dNCM_MEPC_plate118 (human)

description: Library name: S118


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-I22


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-I21


title: BR3-RNA-seq


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-I10


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-H9


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-I9


title: BR2-RNA-seq


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-H22


title: BR1-RNA-seq


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-H21


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-K21


title: 23_3_S21

city: Taipei

first: Po-Hsien

last: Chiu

address: No. 155, Sec. 2, Linong St. Beitou Dist., Taipei City 112304, Taiwan

country: Taiwan

institute: National Yang Ming Chiao Tung University

description:
Passage 23 (undergo Cetuximab 46 days)
GA1072_expected_count.txt
GA1072_FPKM.txt
GA1072_TPM.txt

data_processing:
Reads were trimmed and clipped for quality control in AfterQC v0.9.7.
Read quality was checked for each sample using FastQC v0.11.7.
High-quality reads were then imported into STAR v2.6.1a for alignment into BAM files.
BAM files were imported into the RSEM v1.3.1 for expected counts, FPKM and TPM estimation.
Expected counts table was extracted from each RSEM output .gene.results file.
Assembly: Expected counts table was imported into the DESeq2 v1.26.0 for rlog transformation.
Supplementary files format and content: hg38, GRCh38.94
Supplementary files format and content: Tab-delimited text file for expected counts of sample. Tab-delimited text file for FPKM of sample. Tab-delimited text file for TPM of sample. Tab-delimited text file for rlog of sample.

source_name: oral cavity

growth_protocol: OECM-1 cells were maintained in RPMI medium with 5% FBS and 1% P/S, all of them were placed in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Assay Method: Qubit fluorometer with Quant-iT RNA BR assay kit
Sample Prep. Kit : Illumina TruSeq Stranded mRNA Sample Prep Kit + limited cycles of PCR by KAPA HiFi Polymerase

treatment_protocol: Different passages of OECM-1 cells were all maintained in the medium containing Cetuximab (500μg/ml)

value: oral cavity

value: Cetuximab (500μg/ml)


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-H10


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-G9


title: 23_2_S20


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-J21


title: R4-RNA-seq


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-J10


title: 20_3_S18

description:
Passage 20 (undergo Cetuximab 40 days)
GA1072_expected_count.txt
GA1072_FPKM.txt
GA1072_TPM.txt


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-G22


title: R3-RNA-seq


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-G21


title: 23_1_S19


title: 20_2_S17


title: 20_1_S16


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-G10


title: 18_3_S15

description:
Passage 18 (undergo Cetuximab 36 days)
GA1072_expected_count.txt
GA1072_FPKM.txt
GA1072_TPM.txt


title: 18_1_S13


title: 15_3_S12

description:
Passage 15 (undergo Cetuximab 30 days)
GA1072_expected_count.txt
GA1072_FPKM.txt
GA1072_TPM.txt


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-F21


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-E9


title: 18_2_S14


title: 15_1_S10


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-F9


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-F22


title: R2-RNA-seq


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-E22


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-F10


title: 12_3_S9

description:
Passage 12 (undergo Cetuximab 24 days)
GA1072_expected_count.txt
GA1072_FPKM.txt
GA1072_TPM.txt


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-E21


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-E10


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-D9


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-D22


title: 8_3_S6

description:
Passage 8 (undergo Cetuximab 16 days)
GA1072_expected_count.txt
GA1072_FPKM.txt
GA1072_TPM.txt


title: 8_1_S4


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-D10


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-D21


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-C9


title: 0_3_S3

description:
GA1072_expected_count.txt
GA1072_FPKM.txt
GA1072_TPM.txt


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-C22


title: 15_2_S11


title: 0_1_S1


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-C21


title: S107-74295A (post)

description: Post

source_name: Right buccal (Soft palate)

growth_protocol: Those samples were obtained from patients' tissue, Without the process of maintenance

treatment_protocol: Those post samples were collected after cetuximab treatment and extracted RNA by Trizol.

value: Right buccal (Soft palate)

value: total treatment of Cetuximab:3600 MG ( in 6 times)


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-B9

value: FC

value: M


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-C10

value: 9 months


title: S108-56351A (post)

description: Post

source_name: Retromolar area (Left lip)

value: Retromolar area (Left lip)

value: total treatment of Cetuximab:1400 MG ( in 2 times)


title: S108-24250A (pre)

description: Pre

source_name: left lateral tongue border (Left oral tongue)


title: S110-03358A (post)

description: Post

source_name: Left lateral tongue border (Floor of mouth)

value: total treatment of Cetuximab:4700 MG ( in 8 times)


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-B22


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-B21


title: 12_1_S7


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-A9


title: S108-06850B (pre)

description: Pre

source_name: Right buccal (Lymph node)

value: Right buccal (Lymph node)


title: S108-57759E (post)

description: Post

source_name: Right buccal (Left lower lip and gingiva)

value: total treatment of Cetuximab:4600 MG ( in 11 times)


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-A22


title: 12_2_S8


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-B10


title: S106-35159E

description: Post

source_name: Tongue (Posterior pharyngeal wall)

value: Tongue (Posterior pharyngeal wall)

value: total treatment of Cetuximab:4000 MG (in 9 times)


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-A10


title: S105-85480E (Pre)

description: Pre

source_name: Tongue (Right lateral tongue border)

value: Tongue (Right lateral tongue border)


title: cal-27-ER_S2

data_processing:
Reads were trimmed and clipped for quality control in AfterQC v0.9.7.
Read quality was checked for each sample using FastQC v0.11.7.
High-quality reads were then imported into STAR v2.6.1a for alignment into BAM files.
BAM files were imported into the RSEM v1.3.1 for expected counts, FPKM and TPM estimation.
Expected counts table was extracted from each RSEM output .gene.results file.
Assembly: Expected counts table was imported into the DESeq2 v1.26.0 for rlog transformation.
Supplementary files format and content: hg38, GRCh38.94
Supplementary files format and content: Tab-delimited text file for expected counts of sample. Tab-delimited text file for FPKM of sample. Tab-delimited text file for TPM of sample.

source_name: tongue

growth_protocol: CAL27 parental and resistant cells were cultured in DMEM medium with 5% FBS and 1% P/S, while OECM-1 cells were maintained in RPMI medium with 5% FBS and 1% P/S, all of them were placed in a humidified atmosphere with 5% CO2 at 37°C.

treatment_protocol: Those resistant cell lines were cultured for 30 passages with cetuximab (500μg/ml), and collected RNA by Trizol.

value: tongue

value: ERCTX


title: 8_2_S5

value: oral cavity


title: AMB_200205_9mo_2A_3A_1_P2-5-E15-A21


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-P8


title: cal-27-WT_S1

value: WT


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-P7


title: 0_2_S2


title: OECM-1-WT_S3


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-P20


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-O7


title: BCR_S4: CMA (XBB.1.5)

city: Boston

first: Duane

middle: R.

last: Wesemann

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine, Division of Allergy and Clinical Immunology

institute: Brigham and Women's Hospital

description:
Library name: WL-167-BCR
5’ BCR seq

library_source: other

data_processing:
CellRanger count and vdj to process raw fastq files into a set of seven files per each sample: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, all_contig.fasta, filtered_contig.fasta, all_contig_annotations.csv, filtered_contig_annotations.csv v8.0.1
Assembly: GRCm39-2024-A
Supplementary files format and content: CellRanger count output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger vdj output files: all_contig.fasta, filtered_contig.fasta, all_contig_annotations.csv, filtered_contig_annotations.csv
Library strategy: CITE-seq

molecule: other

source_name: Lymph node

extract_protocol:
Single cells after sorting were encapsulated in Gel beads in Emulsion (GEM) using the 10X Controller with a Chromium Next GEM Single Cell 5' Kit v3, Chromium Single Cell Mouse BCR Amplification Kit, and Chromium 5’ Feature Barcode Kit.
library preparation using Chromium GEM-X Single Cell 5' Reagent Kits v3 (10X Genomics) according to the manufacturer’s protocol. Briefly, after gel-beads in emulsion (GEMs) generation, RT-PCR, cDNA amplification, fragmentation, end repair, A-tailing and sample indexing were performed.

treatment_protocol: Single-cell RNA sequencing (scRNA-seq) coupled with single-cell B cell receptor sequencing (scBCR-seq) in mice that received Comirnaty alone or Comirnaty formulated with mannadjuvant. As an additional group for direct comparison of B cell responses, mice were immunized with a monovalent Comirnaty vaccine developed against the spike protein of XBB.1.5 (hereafter referred to as XBB.1.5-Comirnaty)

value: Lymph node

value: GC B cell

value: Comirnaty and Mannadjuvant

tag: library type

value: BCR


title: GEX_S4: CMA (XBB.1.5)

description:
Library name: WL-165-GEX
5’ polyA RNA

molecule: polyA RNA

value: mRNA


title: ADT_S4: CMA (XBB.1.5)

description:
Library name: WL-166-ADT
Hashtag-derived oligonucleotide (HTO)

molecule: protein

value: ADT

tag: hto

value: TotalSeq-C0304 anti-mouse Hashtag 4 (mouse 4), TotalSeq-C0305 anti-mouse Hashtag 5 (mouse 5), TotalSeq-C0306 anti-mouse Hashtag 6 (mouse 6)


title: ADT_S3: XBB.1.5-C (XBB.1.5)

description:
Library name: WL-163-ADT
Hashtag-derived oligonucleotide (HTO)

value: XBB.1.5 Comirnaty

value: TotalSeq-C0310 anti-mouse Hashtag 10 (mouse 10), TotalSeq-C0311 anti-mouse Hashtag 11 (mouse 11), TotalSeq-C0312 anti-mouse Hashtag 12 (mouse 12)


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-N8

value: FC

value: M

value: 9 months


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-N7


title: ADT_S2: C (WA1)

description:
Library name: WL-158-ADT
Hashtag-derived oligonucleotide (HTO)

value: Comirnaty

value: TotalSeq-C0301 anti-mouse Hashtag 1 (mouse 1), TotalSeq-C0302 anti-mouse Hashtag 2 (mouse 2), TotalSeq-C0303 anti-mouse Hashtag 3 (mouse 3)


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-O20


title: GEX_S3: XBB.1.5-C (XBB.1.5)

description:
Library name: WL-162-GEX
5’ polyA RNA


title: BCR_S2: C (WA1)

description:
Library name: WL-159-BCR
5’ BCR seq


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-N19


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-M8


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-N20


title: OECM-1-ERCTX_S4

value: ERCTX

value: Cetuximab (500μg/ml)


title: BCR_S1: CMA (WA1)

description:
Library name: WL-156-BCR
5’ BCR seq


title: ADT_S1: CMA (WA1)

description:
Library name: WL-155-ADT
Hashtag-derived oligonucleotide (HTO)

value: TotalSeq-C0307 anti-mouse Hashtag 7 (mouse 7), TotalSeq-C0308 anti-mouse Hashtag 8 (mouse 8), TotalSeq-C0309 anti-mouse Hashtag 9 (mouse 9)


title: GEX_S2: C (WA1)

description:
Library name: WL-157-GEX
5’ polyA RNA

value: Lymph node


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-M20


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-M19


title: GEX_S1: CMA (WA1)

description:
Library name: WL-154-GEX
5’ polyA RNA

value: GC B cell


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-M7


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-L8


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-P19


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-L7


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-O8


title: OM217 - ChD - C/D

city: Rio de Janeiro

first: Eric

middle: Henrique

last: Roma

state: Rio de Janeiro

address: Av. Brasil, 4365

department: Instituto Nacional de Infectologia

country: Brazil

institute: Fundação Oswaldo Cruz

description:
Library name: Sample 192
Column name in normalized_counts.csv: OM217

data_processing:
CLC Genomics Workbench software version 25 (Qiagen), with quality limit set to 0.05
miRNA counts were generated using the CLC Genomics Workbench software version 25.
Normalized counts were generated with DEseq2 package from R software environment  using Trimmed Mean of M-values (TMM) as method to normalize the miRNA-seq data.
Assembly: The generated reads were trimmed and aligned with the human mirBase v22
Supplementary files format and content: Comma-separated Values file include normalized counts for each sample
Supplementary files format and content: csv files include TMM of sequenced miRNAs for each sample.

source_name: blood serum

extract_protocol:
miRNA from 200ul of human serum samples were extracted using the miRNeasy Serum/Plasma Advanced kit from Qiagen and stored at at -80°C until use.
Five microliters of the extracted miRNA were used for library preparation for miRNA sequencing with the QIAseq miRNA Library kit (Qiagen) following the manufacturer's recommendations. After library preparation, the quality and quantification of the libraries were assessed using the TapeStation system (Agilent, Santa Clara, USA) with the High Sensitivity DNA 1000 kit (Agilent).

value: blood serum

tag: chagas disease?

value: Yes

tag: chagas disease_form

value: Chronic Chagas cardiomyopathy

tag: chronic chagas_cardiomyopathy_severity

value: severe

value: female


title: OM194 - ChD - C/D

description:
Library name: Sample 191
Column name in normalized_counts.csv: OM194


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-O19


title: OM186 - ChD - C/D

description:
Library name: Sample 190
Column name in normalized_counts.csv: OM186

value: male


title: BCR_S3: XBB.1.5-C (XBB.1.5)

description:
Library name: WL-164-BCR
5’ BCR seq

value: XBB.1.5 Comirnaty

value: BCR


title: OM160 - ChD - C/D

description:
Library name: Sample 189
Column name in normalized_counts.csv: OM160


title: OM156 - ChD - C/D

description:
Library name: Sample 188
Column name in normalized_counts.csv: OM156


title: OM149 - ChD - C/D

description:
Library name: Sample 187
Column name in normalized_counts.csv: OM149


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-L19

value: FC

value: M


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-K7

value: 9 months


title: OM129 - ChD - C/D

description:
Library name: Sample 184
Column name in normalized_counts.csv: OM129


title: OM137 - ChD - C/D

description:
Library name: Sample 185
Column name in normalized_counts.csv: OM137


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-J8


title: OM122 - ChD - C/D

description:
Library name: Sample 183
Column name in normalized_counts.csv: OM122


title: OM108 - ChD - C/D

description:
Library name: Sample 182
Column name in normalized_counts.csv: OM108


title: OM104 - ChD - C/D

description:
Library name: Sample 181
Column name in normalized_counts.csv: OM104


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-J7


title: OM96 - ChD - C/D

description:
Library name: Sample 180
Column name in normalized_counts.csv: OM96


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-K19


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-J20


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-I8


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-J19


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-I7


title: OM92 - ChD - C/D

description:
Library name: Sample 179
Column name in normalized_counts.csv: OM92


title: OM91 - ChD - C/D

description:
Library name: Sample 178
Column name in normalized_counts.csv: OM91


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-L20


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-I20


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-I19


title: OM90 - ChD - C/D

description:
Library name: Sample 177
Column name in normalized_counts.csv: OM90


title: OM81 - ChD - C/D

description:
Library name: Sample 175
Column name in normalized_counts.csv: OM81


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-H8


title: OM84 - ChD - C/D

description:
Library name: Sample 176
Column name in normalized_counts.csv: OM84


title: OM148 - ChD - C/D

description:
Library name: Sample 186
Column name in normalized_counts.csv: OM148


title: OM78 - ChD - C/D

description:
Library name: Sample 174
Column name in normalized_counts.csv: OM78


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-K20


title: OM74 - ChD - C/D

description:
Library name: Sample 173
Column name in normalized_counts.csv: OM74


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-H19


title: OM60 - ChD - C/D

description:
Library name: Sample 172
Column name in normalized_counts.csv: OM60


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-H20


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-G8


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-G7


title: OM40 - ChD - C/D

description:
Library name: Sample 170
Column name in normalized_counts.csv: OM40


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-G19


title: OM37 - ChD - C/D

description:
Library name: Sample 168
Column name in normalized_counts.csv: OM37


title: OM39 - ChD - C/D

description:
Library name: Sample 169
Column name in normalized_counts.csv: OM39


title: OM33 - ChD - C/D

description:
Library name: Sample 167
Column name in normalized_counts.csv: OM33


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-F8


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-F7


title: OM10 - ChD - C/D

description:
Library name: Sample 166
Column name in normalized_counts.csv: OM10


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-F19


title: OM5 - ChD - C/D

description:
Library name: Sample 165
Column name in normalized_counts.csv: OM5


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-F20


title: OM2 - ChD - C/D

description:
Library name: Sample 164
Column name in normalized_counts.csv: OM2


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-K8


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-E20


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-E7


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-E8


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-E19


title: OM1 - ChD - C/D

description:
Library name: Sample 163
Column name in normalized_counts.csv: OM1


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-H7


title: OM185 - ChD - B1/B2

description:
Library name: Sample 160
Column name in normalized_counts.csv: OM185

value: moderate


title: OM205 - ChD - B1/B2

description:
Library name: Sample 162
Column name in normalized_counts.csv: OM205


title: OM203 - ChD - B1/B2

description:
Library name: Sample 161
Column name in normalized_counts.csv: OM203


title: OM51 - ChD - C/D

description:
Library name: Sample 171
Column name in normalized_counts.csv: OM51


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-D7


title: OM184 - ChD - B1/B2

description:
Library name: Sample 159
Column name in normalized_counts.csv: OM184


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-G20


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-D20


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-D19


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-D8


title: OM182 - ChD - B1/B2

description:
Library name: Sample 158
Column name in normalized_counts.csv: OM182


title: OM173 - ChD - B1/B2

description:
Library name: Sample 156
Column name in normalized_counts.csv: OM173


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-C8


title: OM175 - ChD - B1/B2

description:
Library name: Sample 157
Column name in normalized_counts.csv: OM175


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-C7


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-C20


title: OM153 - ChD - B1/B2

description:
Library name: Sample 153
Column name in normalized_counts.csv: OM153


title: OM162 - ChD - B1/B2

description:
Library name: Sample 155
Column name in normalized_counts.csv: OM162


title: OM158 - ChD - B1/B2

description:
Library name: Sample 154
Column name in normalized_counts.csv: OM158


title: OM146 - ChD - B1/B2

description:
Library name: Sample 152
Column name in normalized_counts.csv: OM146


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-C19


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-B8


title: OM143 - ChD - B1/B2

description:
Library name: Sample 151
Column name in normalized_counts.csv: OM143


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-B7


title: OM130 - ChD - B1/B2

description:
Library name: Sample 150
Column name in normalized_counts.csv: OM130


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-B20


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-B19


title: OM99 - ChD - B1/B2

description:
Library name: Sample 147
Column name in normalized_counts.csv: OM99


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-A8


title: OM112 - ChD - B1/B2

description:
Library name: Sample 149
Column name in normalized_counts.csv: OM112


title: OM94 - ChD - B1/B2

description:
Library name: Sample 146
Column name in normalized_counts.csv: OM94


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-A20


title: OM86 - ChD - B1/B2

description:
Library name: Sample 145
Column name in normalized_counts.csv: OM86


title: OM85 - ChD - B1/B2

description:
Library name: Sample 144
Column name in normalized_counts.csv: OM85


title: OM76 - ChD - B1/B2

description:
Library name: Sample 143
Column name in normalized_counts.csv: OM76


title: OM71 - ChD - B1/B2

description:
Library name: Sample 142
Column name in normalized_counts.csv: OM71


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-P5


title: AMB_200205_9mo_2A_3A_1_P2-4-H24-A19


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-P18


title: OM68 - ChD - B1/B2

description:
Library name: Sample 141
Column name in normalized_counts.csv: OM68


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-P17


title: AMB_200205_9mo_2A_3A_1_P2-3-D19-O6


title: OM54 - ChD - B1/B2

description:
Library name: Sample 139
Column name in normalized_counts.csv: OM54


title: OM55 - ChD - B1/B2

description:
Library name: Sample 140
Column name in normalized_counts.csv: OM55