title: genomic DNA of peripheral blood of sample 1022_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-M20

status: Public on Jul 05 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Tab-delimited files (HIC files) describing the chromatin contacts will be generated with in-house developing package using the filtered BAM files
Assembly: hg38-donor-snp-substituted
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
Supplementary files format and content: tab-delimited files (HIC files) describing the chromatin contacts. Columns are: 1. Strand1, 2. Chromosome1, 3. Position1, 4. place holder column, always be 0, 5. Strand2, 6. Chromosome2, 7. Position2, 8. place holder column, always be 1.
Library strategy: snm3C-seq

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Dong-Sung Lee, Chongyuan Luo, Jingtian Zhou, Sahaana Chandran, Angeline Rivkin, Anna Bartlett, Joseph R. Nery, Conor Fitzpatrick, Carolyn O’Connor,Jesse R. Dixon, Joseph R. Ecker. 2019. “Simultaneous profiling of 3D genome structure and DNA methylation in single human cells.” Nat Methods. 16(10): 999–1006.

tag: brain region

value: SEP

tag: gender

value: M


title: genomic DNA of peripheral blood of sample 4010_2 at day 28

type: genomic

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

description: nonBPD peripheral blood sample at day 28

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

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

data_processing:
The raw IDAT files were read into R with the minfi package, the data was preprocessed with background and dye bias correction using the preprocessNoob method. The champ.runCombat function in ChAMP package was used to do batch ("Sentrix_ID" and "Sentrix_Position") correction on methylation array data. Prior to normalization, DNA methylation data were filtered based on the following quality control criteria, exclusion of:  arrays having more than 5% failed probes (1 array); all CpG probes on the X and Y chromosomes; and any probes containing single-nucleotide polymorphism with a minor allele frequency ≥ 1% (in EUR population of the 1000 Genomes Project) within 5 nucleotides to the CpG site. We also removed probes reported to hybridize to one or more non-target sites in the genome. There were 775,201 CpG probes remaining after exclusions.
Average Beta

label: Cy5 and Cy3

label_protocol: 100 to 500 ng of DNA was bisulfite converted using the EZ-DNA Methylation kit (Zymo Research)

extract_protocol: Blood samples were collected at birth in PAXgene reagent (Qiagen Inc., Valencia, CA) and snap frozen at -80°C. Samples were processed with PAXgene Blood miRNA Kit (PreAnalytix/Qiagen).  For DNA isolation, the isopropanol precipitants were loaded into the DNeasy Mini spin columns (DNeasy Blood & Tissue Kit, Qiagen). All extraction steps followed the manufacturer’s procedure.

value: nonBPD


title: genomic DNA of peripheral blood of sample 3011_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-M19


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-L7


title: genomic DNA of peripheral blood of sample 3009_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-L8


title: genomic DNA of peripheral blood of sample 3006_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-L19


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-K7


title: genomic DNA of peripheral blood of sample 3004_1 at day 28


title: genomic DNA of peripheral blood of sample 3005_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-K20


title: genomic DNA of peripheral blood of sample 1029_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-K19


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-N20


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-J7


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-J19


title: genomic DNA of peripheral blood of sample 1004_1 at day 28


title: genomic DNA of peripheral blood of sample 1002_1 at day 28


title: genomic DNA of peripheral blood of sample 3013_1 at day 28

description: BPD peripheral blood sample at day 28

value: BPD


title: genomic DNA of peripheral blood of sample 2014_1 at day 28

description: BPD peripheral blood sample at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-I19


title: genomic DNA of peripheral blood of sample 2012_1 at day 28

description: BPD peripheral blood sample at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-I7


title: genomic DNA of peripheral blood of sample 1012_1 at day 28

description: BPD peripheral blood sample at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-I8


title: genomic DNA of peripheral blood of sample 1001_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-L20


title: genomic DNA of peripheral blood of sample 3007_1 at day 28


title: genomic DNA of peripheral blood of sample 1009_2 at day 28

description: BPD peripheral blood sample at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-H20


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-H8


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-H19


title: genomic DNA of peripheral blood of sample 4015_1 at day 14

description: nonBPD peripheral blood sample at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-H7


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-G20


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-G19


title: genomic DNA of peripheral blood of sample 4013_1 at day 14


title: genomic DNA of peripheral blood of sample 4008_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-G8


title: genomic DNA of peripheral blood of sample 3003_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-G7


title: genomic DNA of peripheral blood of sample 4010_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-F20


title: genomic DNA of peripheral blood of sample 4009_1 at day 14


title: genomic DNA of peripheral blood of sample 3014_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-F8


title: genomic DNA of peripheral blood of sample 3018_1 at day 14


title: genomic DNA of peripheral blood of sample 3011_2 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-E8


title: genomic DNA of peripheral blood of sample 3015_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-F7


title: genomic DNA of peripheral blood of sample 3010_2 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-E20


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-E7


title: genomic DNA of peripheral blood of sample 3009_3 at day 14


title: genomic DNA of peripheral blood of sample 3009_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-D8


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-D7


title: genomic DNA of peripheral blood of sample 3005_1 at day 14


title: genomic DNA of peripheral blood of sample 4006_1 at day 14


title: genomic DNA of peripheral blood of sample 3002_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-C8


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-C7


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-D20


title: genomic DNA of peripheral blood of sample 2024_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-D19


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-C20


title: genomic DNA of peripheral blood of sample 2022_2 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-C19


title: genomic DNA of peripheral blood of sample 2022_1 at day 28


title: genomic DNA of peripheral blood of sample 2021_2 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-B8


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-B7


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-F19


title: genomic DNA of peripheral blood of sample 2018_1 at day 28


title: genomic DNA of peripheral blood of sample 2020_1 at day 28


title: genomic DNA of peripheral blood of sample 2016_1 at day 28


title: genomic DNA of peripheral blood of sample 2008_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-B19


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-A8


title: genomic DNA of peripheral blood of sample 3003_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-A7


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-A20


title: genomic DNA of peripheral blood of sample 2003_1 at day 28


title: genomic DNA of peripheral blood of sample 1033_1 at day 28


title: genomic DNA of peripheral blood of sample 1032_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-A19


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-P6


title: genomic DNA of peripheral blood of sample 2026_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-P5


title: genomic DNA of peripheral blood of sample 1030_2 at day 28


title: genomic DNA of peripheral blood of sample 1030_1 at day 28


title: genomic DNA of peripheral blood of sample 1029_2 at day 28


title: genomic DNA of peripheral blood of sample 1028_1 at day 28


title: genomic DNA of peripheral blood of sample 1027_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-O5


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-P18


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-P17


title: genomic DNA of peripheral blood of sample 1024_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-O18


title: genomic DNA of peripheral blood of sample 1020_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-O17


title: genomic DNA of peripheral blood of sample 1019_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-N6


title: genomic DNA of peripheral blood of sample 2005_2 at day 28


title: genomic DNA of peripheral blood of sample 1018_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-4-C23-B20


title: genomic DNA of peripheral blood of sample 1017_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-N18


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-N5


title: genomic DNA of peripheral blood of sample 1015_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-N17


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-M6


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-M5


title: genomic DNA of peripheral blood of sample 1003_1 at day 28


title: genomic DNA of peripheral blood of sample 3012_1 at day 28

description: BPD peripheral blood sample at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-O6


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-L6


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-M18


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-L5


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-L18


title: genomic DNA of peripheral blood of sample 1037_1 at day 28

description: BPD peripheral blood sample at day 28


title: genomic DNA of peripheral blood of sample 2017_1 at day 28

description: BPD peripheral blood sample at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-L17


title: genomic DNA of peripheral blood of sample 1007_1 at day 28

description: BPD peripheral blood sample at day 28


title: genomic DNA of peripheral blood of sample 4014_1 at day 14


title: genomic DNA of peripheral blood of sample 4012_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-K5


title: genomic DNA of peripheral blood of sample 4011_1 at day 14


title: genomic DNA of peripheral blood of sample 4007_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-K18


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-K17


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-J6


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-J5


title: genomic DNA of peripheral blood of sample 1010_1 at day 28


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-J18


title: genomic DNA of peripheral blood of sample 4006_2 at day 14


title: genomic DNA of peripheral blood of sample 1016_1 at day 28


title: genomic DNA of peripheral blood of sample 4002_1 at day 14


title: genomic DNA of peripheral blood of sample 3019_1 at day 14


title: genomic DNA of peripheral blood of sample 3016_1 at day 14


title: genomic DNA of peripheral blood of sample 3011_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-I6


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-I5


title: genomic DNA of peripheral blood of sample 2003_2 at day 28

description: BPD peripheral blood sample at day 28


title: genomic DNA of peripheral blood of sample 3012_1 at day 14

description: BPD peripheral blood sample at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-I18


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-K6


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-H6


title: genomic DNA of peripheral blood of sample 3006_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-H5


title: genomic DNA of peripheral blood of sample 3004_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-H18


title: genomic DNA of peripheral blood of sample 2024_1 at day 14


title: genomic DNA of peripheral blood of sample 2026_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-G5


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-G6


title: genomic DNA of peripheral blood of sample 3007_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-G18


title: genomic DNA of peripheral blood of sample 3008_1 at day 14


title: genomic DNA of peripheral blood of sample 2027_1 at day 14


title: genomic DNA of peripheral blood of sample 2023_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-J17


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-G17


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-F6


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-F18


title: genomic DNA of peripheral blood of sample 2022_2 at day 14


title: genomic DNA of peripheral blood of sample 2013_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-F5


title: genomic DNA of peripheral blood of sample 2019_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-E6


title: genomic DNA of peripheral blood of sample 2016_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-F17


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-E18


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-D6


title: genomic DNA of peripheral blood of sample 1035_1 at day 14


title: genomic DNA of peripheral blood of sample 2011_1 at day 14


title: genomic DNA of peripheral blood of sample 1039_1 at day 14


title: genomic DNA of peripheral blood of sample 1031_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-E5


title: genomic DNA of peripheral blood of sample 2026_2 at day 14


title: genomic DNA of peripheral blood of sample 2005_2 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-H17


title: genomic DNA of peripheral blood of sample 1032_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-C5


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-C18


title: genomic DNA of peripheral blood of sample 2022_1 at day 14


title: genomic DNA of peripheral blood of sample 1033_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-E17


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-D18


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-D17


title: genomic DNA of peripheral blood of sample 1025_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-B6


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-C6


title: genomic DNA of peripheral blood of sample 2020_1 at day 14


title: genomic DNA of peripheral blood of sample 2021_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-B5


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-B18


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-D5


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-A6


title: genomic DNA of peripheral blood of sample 2021_2 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-B17


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-A18


title: genomic DNA of peripheral blood of sample 2015_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-A5


title: genomic DNA of peripheral blood of sample 1017_1 at day 14


title: genomic DNA of peripheral blood of sample 1024_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-P4


title: genomic DNA of peripheral blood of sample 1019_1 at day 14


title: genomic DNA of peripheral blood of sample 1010_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-P3


title: genomic DNA of peripheral blood of sample 1015_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-3-C23-A17


title: genomic DNA of peripheral blood of sample 1006_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-P16


title: genomic DNA of peripheral blood of sample 2005_1 at day 14


title: genomic DNA of peripheral blood of sample 2018_1 at day 14


title: genomic DNA of peripheral blood of sample 1011_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-O4


title: genomic DNA of peripheral blood of sample 2006_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-P15


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-O16


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-O15


title: genomic DNA of peripheral blood of sample 2003_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-O3


title: genomic DNA of peripheral blood of sample 2008_1 at day 14


title: genomic DNA of peripheral blood of sample 2006_1 at day 28


title: genomic DNA of peripheral blood of sample 1038_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-N3


title: genomic DNA of peripheral blood of sample 1030_2 at day 14


title: genomic DNA of peripheral blood of sample 1029_2 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-N16


title: genomic DNA of peripheral blood of sample 1029_1 at day 14


title: genomic DNA of peripheral blood of sample 1030_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-M4


title: genomic DNA of peripheral blood of sample 1027_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-M3


title: genomic DNA of peripheral blood of sample 1026_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-N15


title: genomic DNA of peripheral blood of sample 1022_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-M16


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-L4


title: genomic DNA of peripheral blood of sample 1020_1 at day 14


title: genomic DNA of peripheral blood of sample 1023_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-L15


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-N4


title: genomic DNA of peripheral blood of sample 1018_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-M15


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-L3


title: genomic DNA of peripheral blood of sample 1002_1 at day 14


title: genomic DNA of peripheral blood of sample 1004_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-K16


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-K15


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-L16


title: genomic DNA of peripheral blood of sample 1016_1 at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-K4


title: genomic DNA of peripheral blood of sample 1005_1 at day 14


title: genomic DNA of peripheral blood of sample 4005_1 at day 14

description: BPD peripheral blood sample at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-J4


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-J3


title: genomic DNA of peripheral blood of sample 2012_1 at day 14

description: BPD peripheral blood sample at day 14


title: genomic DNA of peripheral blood of sample 1012_1 at day 14

description: BPD peripheral blood sample at day 14


title: genomic DNA of peripheral blood of sample 2003_2 at day 14

description: BPD peripheral blood sample at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-I3


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-I16


title: genomic DNA of peripheral blood of sample 1003_1 at day 14


title: genomic DNA of peripheral blood of sample 1007_1 at day 14

description: BPD peripheral blood sample at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-I15


title: genomic DNA of peripheral blood of sample 3017_1 at day 14

description: BPD peripheral blood sample at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-K3


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-H3


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-H4


title: genomic DNA of peripheral blood of sample 1001_1 at day 14


title: genomic DNA of peripheral blood of sample 1037_1 at day 14

description: BPD peripheral blood sample at day 14


title: genomic DNA of peripheral blood of sample 3010_1 at day 28


title: genomic DNA of peripheral blood of sample 2017_1 at day 14

description: BPD peripheral blood sample at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-G4


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-H16


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-F4


title: genomic DNA of peripheral blood of sample 2014_1 at day 14

description: BPD peripheral blood sample at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-G3


title: iPSC Differentiated Endothelial Like Cells (ECs) from PAD08, A

city: Chicago

first: Yogesh

last: Goyal

state: IL

address: 303 E Superior St

institute: Northwestern University

description: Next Generation Sequencing

library_source: transcriptomic

data_processing:
RNA-seq reads were pseudo-aligned to the human transcriptome (GRCH38 cDNA) utilizing Kallisto v0.48.0 to generate estimated gene count matrices(3). Count matrices were normalized and differential gene expression analyses were done with DESeq2 v1.38.3 using R v4.2.3 for each subgrouping comparison (4).
The counts matrix was used to obtain tpm and other normalized values for each gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include tpm and raw counts  for each sample

molecule: total RNA

source_name: Vascular endothelial

extract_protocol:
Bulk paired end (61:8:8:61) RNA sequencing was done using MiRNeasy Micro Kit (Qiagen 217084) for extraction, NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490L), NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (E7770L), and NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1) (E7600S), as described previously (1,2). Prior to library preparation, the samples were randomized to avoid experimental and human biases. We started our experiments with a total of 24 samples (iPSCs and differentiated iPSCs-ECs) from healthy and disease patients. During library preparation, 2 DiPSC and 2 HiPSC-EC patient samples were excluded from sequencing due to insufficient RNA isolation. RNA-seq reads were pseudo-aligned to the human transcriptome (GRCH38 cDNA) utilizing Kallisto v0.48.0 to generate estimated gene count matrices(3). Count matrices were normalized and differential gene expression analyses were done with DESeq2 v1.38.3 using R v4.2.3 for each subgrouping comparison (4). The count matrix was further filtered for low expression counts such that any gene less than a total of 10 counts across samples cutoff were removed from downstream analysis. To compare between samples, differential gene expression data was extracted. The top 50 most up and down regulated genes (total 100, unless the number of differentially expressed genes were <100) were filtered utilizing an ordered Log2FC gene list and then used to generate corresponding comparisons within heat maps. GO analysis was performed using clusterProfiler in R. Scripts for all extraction and downstream differential expression analysis are provided at the Goyal laboratory GitHub: https://github.com/GoyalLab/Bulk-RNA-Jiang-Analysis.git .
Prior to extraction and library preparation, the samples were randomized to avoid any experimental and human biases.

tag: tissue

value: Vascular endothelial

tag: cell line

tag: cell type

value: Peripheral Artery Diseased Differentiated Endotheilial Like Cells

tag: genotype

value: WT

tag: treatment

value: Vasculife VEGF culture medium

tag: time

value: 2-3 days after differentiation


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-G16


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-H15


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-F16


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-F3


title: Induced Pluripotent Stem Cells (iPSCs) from PAD08, A

description: Next Generation Sequencing

value: Peripheral Artery Diseased Induced Pluripotent Stem Cells

value: Essential 8 Flex culture medium

value: 2-3 days after subculture


title: Induced Pluripotent Stem Cells (iPSCs) from PAD08, B

description: Next Generation Sequencing


title: genomic DNA of peripheral blood of sample 3013_1 at day 14

description: BPD peripheral blood sample at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-F15


title: iPSC Differentiated Endothelial Like Cells (ECs) from PAD07, B

description: Next Generation Sequencing


title: Induced Pluripotent Stem Cells (iPSCs) from PAD07, A

description: Next Generation Sequencing


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-E3


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-E4


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-J15


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-E16


title: iPSC Differentiated Endothelial Like Cells (ECs) from PAD02, B

description: Next Generation Sequencing


title: iPSC Differentiated Endothelial Like Cells (ECs) from PAD02, A

description: Next Generation Sequencing


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-E15


title: genomic DNA of peripheral blood of sample 1009_2 at day 14

description: BPD peripheral blood sample at day 14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-G15


title: iPSC Differentiated Endothelial Like Cells (ECs) from PAD08, B

description: Next Generation Sequencing


title: iPSC Differentiated Endothelial Like Cells (ECs) from PAD07, A

description: Next Generation Sequencing


title: Induced Pluripotent Stem Cells (iPSCs) from PAD02, B

description: Next Generation Sequencing


title: iPSC Differentiated Endothelial Like Cells (ECs) from AMH04, B

description: Next Generation Sequencing

value: Healthy Differentiated Endothelial Like Cells


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-D4


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-D3


title: Induced Pluripotent Stem Cells (iPSCs) from AMH04, A

description: Next Generation Sequencing

value: Healthy Induced Pluripotent Stem Cells


title: Induced Pluripotent Stem Cells (iPSCs) from AMH04, B

description: Next Generation Sequencing


title: iPSC Differentiated Endothelial Like Cells (ECs) from AMH02, B

description: Next Generation Sequencing


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-C16


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-C3


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-C15


title: Induced Pluripotent Stem Cells (iPSCs) from AMH01, A

description: Next Generation Sequencing


title: iPSC Differentiated Endothelial Like Cells (ECs) from AMH01, B

description: Next Generation Sequencing


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-A4


title: Induced Pluripotent Stem Cells (iPSCs) from AMH01, B

description: Next Generation Sequencing


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-D15


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-B15


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-A3


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-B3


title: Induced Pluripotent Stem Cells (iPSCs) from AMH02, B

description: Next Generation Sequencing


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-A16


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-A15


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-C4


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-B4


title: P9.10a.1

city: Raleigh

first: Ramsey

last: Lewis

address: 101 Derieux PI

department: Crop and Soil Sciences Department

institute: North Carolina State University

data_processing:
RNAseq reads were trimmed to remove poor quality bases using fastq-mcf with parameters of q=30, l=50 and P=30.
Reads were mapped against tobacco TN90 genome assembly Nitab-TN90 (GCF_000715135.1_Ntab-TN90_genomic.fna) using hisat2 version 2.1.0
Reads mapped to gene assembly were manipulated using samtools  for sorting/indexing
Raw count of reads mapped to annotated tobacco gene model (GCF_protein_coding_gene) were extracted using bedtools version 2.25.0
Assembly: Tobacco TN90 enome assembly Nitab4.5 (GCF_000715135.1_Ntab-TN90_genomic.fna)
Supplementary files format and content: tab-delimited text files include raw count values for each sample

organism: Nicotiana tabacum

source_name: Leaf

growth_protocol: Plants of each genotype were grown in field in Oxford, North Carolina State, USA.

extract_protocol:
Leaf samples were collected and frozen and ground in liquid nitrogen, and RNA was purified using Plant Rneasy mini kit of Qiagen.
100 ng total RNA samples was used for RNA-seq library construction using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA)  followed the protocol for long size insertions.

treatment_protocol: Prior to leaf maturity in the Oxford field experiment, frozen top leaf samples were collected from three biological replicates of TN 90LC and green stem segregants derived from primary transformants TN 90LC + 35S:Yb1 P2 4a,  TN 90LC + 35S:Yb1 P9 10a, and TN 90LC + 35S:Yb1 P3 4a. isolate maintained at N.C. State University. A separate set of eighteen plants of each plant genotype was treated with 10 mL of the suspension buffer (without zoospores) and maintained as uninoculated control plants. All plants were maintained with sub-irrigation for 42 hours post-inoculation, at which time roots were carefully rinsed to remove growth media, excised, transferred to liquid nitrogen for rapid freezing, and eventually stored at -80°C until RNA purification.

value: Leaf

tag: cultivar

tag: line

value: Transgenic plant with overexpressed of NtYb1

tag: genetic modification

value: Transformed with NtYb1 (EGY2) transgene driven by 35S CMV promoter


title: P2.4a.3


title: P9.10a.2


title: iPSC Differentiated Endothelial Like Cells (ECs) from AMH02, A

description: Next Generation Sequencing


title: P2.4a.2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-P2

value: SEP


title: Induced Pluripotent Stem Cells (iPSCs) from AMH02, A

description: Next Generation Sequencing


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-P14

value: M


title: P2.4a.1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-2-C23-B16


title: P9.10a.3


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-P13


title: P3.9a.2


title: P3.9a.1


title: P3.9a.3


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-O2


title: CK.3

value: CK

value: Wild type


title: CK.2


title: CK.1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-O14


title: P44_WT2

city: Jinan

first: Rusong

last: Zhao

state: Shandong

address: 44 Wenhua xi Road

department: Center for Reproductive Medicine

country: China

institute: Shandong University

data_processing:
The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) [5] (or DEGseq[6] or PoissonDis[7])with Q value ≤ 0.05 (or FDR ≤ 0.001).
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05)
Assembly: mm10

organism: Mus musculus

source_name: Ovary

extract_protocol:
We used WT and TG ovaries to extract total RNA with an RNAprep Pure Tissue Kit (ES Science, RN001plus) according to the manufacturer’s instructions. RNA sequencing (RNA-seq) data were processed using standard procedures as previously described .
After fragment screening, library building, and PCR product purification, the samples were sequenced on a BGISEQ-500 platform at the BGI Bioinformatics Corporation (Wuhan, China).

value: Ovary

value: the injection of 44 hours of PMSG


title: P44_WT1

value: WT


title: P44_WT3


title: MDA231_P50_2_S6.bam

city: new orleans

first: Hui

last: Lyu

state: LA

address: 1700 Tulane Ave

institute: LSU

data_processing:
FASTQC was used to perform quality control on the raw data to ensure its reliability.
star v2.7.8a is to align the high-quality reads to a reference genome or transcriptome
feature count was used to assign the aligned reads to genes or transcripts to determine their expression levels.
Supplementary files format and content: GRCh38.p14

growth_protocol: MDA-MB-231 cellswere maintained in DMEM/F-12 (1:1) medium  containing 10% FBS and cultured in a 37°C humidified atmosphere containing 95% air and 5% CO2

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN).1mg total RNA was used for construction of sequence library
RNA library for RNA-seq was prepared using  Illumina Stranded mRNA Prep kit following manufacturer's protocol

treatment_protocol: cells were treated with DMSO or Panobinostat(50nM) for 24hrs

value: Breast cancer cell

value: Panobibostat


title: MDA231_P0_1_S1.bam

value: DMSO


title: P44_TG2


title: MDA231_P50_4_S8.bam


title: P44_TG3


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-O13


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-N14


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-N2


title: P44_TG1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-P1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-N1


title: MDA231_P0_3_S3.bam


title: HT29 Krt20-GFP Replicate 2

city: Boston

first: David

last: Chen

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana Farber Cancer Institute

library_source: other

data_processing:
Demultiplexing based on read primer sequence into sorted cell fractions using custom demultiplexing script, allowing up to one mismatch for assignment.
Read counting based on sgRNA sequence to measure abundance of 542 sgRNA in  library using custom read counting script, allowing up to one mismatch for assignment.
Supplementary files format and content: Excel file of raw read counts from each flow-sorted cell fraction of each knock-in endogenous reporter cell line replicate.

molecule: other

growth_protocol: HT-29 cells were plated two days before transfection, to reach 70–80% confluency at the time of transfection. 0.5 × 106 cells per transfection were collected for each condition. Cells were transfected with RNP complex and HDR templates by nucleofection with SF Cell Line 4D-Nucleofector X Kit (Lonza) using 20-ml Nucleocuvette Strips, as described by the manufacturer (Program FF137). Cells were immediately resuspended in 100 ul of culturing medium and plated into 1.5 ml of pre-warmed culturing medium in 24-well tissue culture plates. T7E1 assay, and site-specific PCR reactions were performed 72 h after nucleofection in order to check cleavage efficiency and integration, respectively. After confirming the correct integration and one-week regeneration cells were plated into 15 cm dish. The next day media was changed to antibiotic containing media (500 ug/ml neomycin and 20 ug/ul blasticidin) and antibiotic selection was performed.

extract_protocol:
Formed colonies were collected by trypsinization and resuspended in culture media. After regeneration culturing period (3-5 days), cell lines were tested by FACS analysis and site-specific PCR.
The pCC_01 - hU6-BsmBI-sgRNA(E+F)-barcode-EFS-Cas9-NLS-2A-Puro-WPRE plasmid (Addgene #139086) was used for CRISPR screen and validation. Briefly the plasmid was digested with Esp3I (NEB#R0734) at 37oc overnight. The 13 kb band was purified with gel purification kit (Takara Nucleospin® Gel and PCR Clean-up Midi). Eighty-two base pair single stranded oligos were designed.31 base pair 5` constant sequence compatible with the linearized (Esp3I) pCC_01 vector (3` end of the U6 promoter) followed by the 19 bp sgRNA sequence adding an extra g base for the proper sgRNA transcription, followed by the 3`vector compatible (5` end of the sgRNA scaffold) sequence. Single stranded oligo pools were ordered from IDT (oPools™ Oligo Pools) and built into the digested PCC_01 vector using NEBuilder HiFi DNA Assembly Master Mix (E2621L, New England Biolabs) according to the manufacturer`s instruction. The list of all oligos can be found in the Supplementary Table 3. Assembled gRNA libraries were purified by AMPure XP magnetic beads (Beckman Coulter)
Deep amplicon sequencing

value: Epithelial cells


title: HT29 Sox9-mKate2 Replicate 2


title: HT29 Sox9-mKate2 Krt20-GFP Replicate 2

value: Sox9-mKate2 Krt20-GFP


title: WetA_5d_3

city: Kunming

last: Bai

address: No. 2, Cuihu North Road

institute: Yunnan University

description: Submitter provided organism name: Arthrobotrys oligospora

data_processing:
fastx_toolkit
read alignment with: Bowtie2, hisat2, TopHat, and STAR
statistical analysis software include RSEM, Blast2go, KEGG database, GO database
Assembly: ADOT00000000.1

organism: Orbilia oligospora

source_name: Fungal hyphae cells  ADOT00000000.1

growth_protocol: WT, ΔAomedA and ΔAowetA strains grown on cellophane-overlaid CMY plates at 28°C for 5 days.

extract_protocol: After collecting the samples, RNA was extracted with the AxyPrep Multisource RNA Miniprep Kit (Axygen, Jiangsu, China)

treatment_protocol: Three replicates were used for each sample.

value: Fungal hyphae

tag: strain

value: delta AowetA


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-N13


title: HT29 Sox9-mKate2 Krt20-GFP Replicate 1


title: HT29 Sox9-mKate2 Replicate 1


title: WetA_5d_2


title: MDA231_P50_1_S5.bam


title: MedA_5d_2

value: delta AomedA


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-M14


title: MedA_5d_3


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-M2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-M1


title: MDA231_P0_2_S2.bam


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-M13


title: MedA_5d_1


title: AOB_5d_3


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-L2


title: AOB_5d_1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-L14


title: AOB_5d_2


title: AO_5d_3


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-L13


title: AO_5d_2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-L1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-K2


title: HT29 Krt20-GFP Replicate 1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-K1


title: tup1cyc8-3 (Biol rep 3)

city: Dublin 2

first: Alastair

last: Fleming

address: College Green

department: Microbiology Dept.

country: Ireland

institute: Trinity College Dublin

description:
tup1 cyc8 raw_counts
tup1 cyc8 normalized_counts

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Saccharomyces cerevisiae S288c reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2.
Assembly: Saccharomyces cerevisiae S288c reference genome
Supplementary files format and content: Raw alignment counts for genes in a tab-delimited text file
Supplementary files format and content: Normalised counts (generated using DESeq2) for genes in a tab-delimited text file

organism: Saccharomyces cerevisiae

source_name: log phase yeast cells (BY4741)

growth_protocol: Cells were grown overnight in 5 ml YPD (2% glucose) media and this was then used to innoculate a 50 ml culture of YPD (2% glucose). Log phase samples were collected when cultures reached OD600 0.6-0.8. Total RNA was extracted using the hot phenol method

extract_protocol:
Total RNA was extracted using the hot phenol method, followed by DNase treatment and purification using the RNeasy Minelute Cleanup Kit (Qiagen).
Strand-specific RNA sequencing with rRNA depletion

value: log phase yeast cells

value: tup1::KAN, cyc8::URA3 double mutant in BY4741 background


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-J2

value: SEP


title: tup1cyc8-2 (Biol rep 2)


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-K14

value: M


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-J14


title: WetA_5d_1


title: tup1cyc8-1 (Biol rep 1)


title: cyc8-3 (Biol rep 3)

description:
cyc8 raw_counts
cyc8 normalized_counts

value: cyc8::KAN mutant in BY4741 background


title: cyc8-1 (Biol rep 1)

description:
cyc8 raw_counts
cyc8 normalized_counts


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-I2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-I14


title: cyc8-2 (Biol rep 2)

description:
cyc8 raw_counts
cyc8 normalized_counts


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-I13


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-I1


title: tup1-3 (Biol rep 3)

description:
tup1_raw_counts
tup1_normalized_counts

value: tup1::KAN mutant in BY4741 background


title: tup1-2 (Biol rep 2)

description:
tup1_raw_counts
tup1_normalized_counts


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-H13


title: AO_5d_1


title: R35A3_PU.1_rep1

city: Barcelona

first: Thomas

last: Graf

address: Carrer del Dr. Aiguader, 88

country: Spain

institute: Center for Genomic Regulation

data_processing:
Read quality was assessed with FastQC version v.0.11.3. Adaptors were removed using Cutadapt (version 0.4.2_dev) TrimGalore! In paired end mode (--340 paired –nextera). Reads were aligned to the mm10 genome using bowtie2 (v 2.2.4) in paired end mode with standard parameters. Output SAM files were converted to BAM files using samtools (v 0.1.19). BAM files were sorted and indexed using the samtools commands sort and index, respectively. Low quality reads and reads associated with a not primary or supplementary alignment SAM flag were filtered out using the samtools command “samtools view -F 2304 -b -q 10”. PCR duplicates were removed with Picard MarkDuplicates (version 2.3.0) with the following options: “REMOVE_DUPLICATES=true ASSUME_SORTED=true VERBOSITY=WARNING”. Filtered BAM files were indexed with samtools index and were used as input in the bamCoverage command of deeptools (v3.0.1) in order to generate bigwig files. bamCoverage was used with the options – binSize 1 –normalizeUsing RPKM –effectiveGenomeSize 2150570000 –extendReads –outFileFormat bigwig.
Assembly: mm10
Supplementary files format and content: bigWig

source_name: B-cells

growth_protocol: Freshly isolated B cells were infected with C/EBPα-ER-hCD4 retrovirus and hCD4 positive cells were plated at 500 cells/cm2 in gelatinized 12-well plates onto wild type inactivated MEF feeders in 20%-FBS (10270-106, GIBCO) RPMI medium (12633012, GIBCO) with 10 ng/mL IL-7(217-17, Preprotech)

extract_protocol:
To obtain samples for the ChiP-seq experiments biological duplicates of primary B cells expressing either C/EBPαWT ER or C/EBPαR35A ER were induced for 3h with E2 and 100,000 cells per sample processed by ChIPmentation, as described (Schmidl et al., 2015) (https://www.nature.com/articles/nmeth.3542). Three µl of anti-C/EBPa antibody (Santa Cruz sc-61 14AA) or anti-PU1 (Santa Cruz sc-352 T21) were used per immunoprecipitation. Tagmentation of immobilized C/EBPa or PU1 enriched chromatin was performed for 5 min at 37 degrees in a 25µL transposition reaction mix
Libraries were prepared with an Illumina TruSeq ChIP Library Preparation Kit and after quality control on Bioanalyzer sequenced (1 × 50 bp) on an Illumina HiSeq2500 instrument.

treatment_protocol: B cell infection with C/EBPα-ER-hCD4 retrovirus as described in (Di Stefano et al., 2014).

value: B-cells

value: Transdifferentiation


title: WT3_PU.1_rep1


title: WT3_PU.1_rep2


title: R35A3_PU.1_rep2


title: wt-3 (Biol rep 3)

value: BY4741 wt


title: R35A3_C/EBPa_rep2


title: wt-2 (Biol rep 2)


title: R35A3_C/EBPa_rep1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-J1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-G2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-G14


title: wt-1 (Biol rep 1)


title: WT3_C/EBPa_rep2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-G13


title: WT3_C/EBPa_rep1


title: RNAPII_creAF10_rep2

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

data_processing:
Reads were aligned mm9 mouse genome with Bowtie2
Samtools-1.2 was used to convert .sam files into .bam files using “view” and then sort .bam files with the “sort” command.
Spike-in normalization was calculated by isolating reads that did not align to the mouse genome from sorted bam files with Sam-1.2 “view -f4”. These unmapped reads were converted to fastq files with Samtools-1.2 “bam2fq” and aligned to hg19 using the Bowtie2 and Samtools-1.2 as above. Samtools-1.2 “flagstat” was used to calculate the number of reads that uniquely map to the human genome, which was used as a scaling factor for generation of bigwig files.
Deeptools was used to generate bigwig files that were normalized to the human spike-in scaling factor with: bamCoverage --binSize 10 --scaleFactor  --ignoreForNormalization chrX, and used to make metaplots.
H3K79me enrichment per gene body was calculated with BEDTools2.0 “multibamCov”. Reads were normalized per human spike-in scaling factor.
Assembly: mm9
Supplementary files format and content: bigwig

source_name: Mouse embryonic fibroblast

growth_protocol: MEFs were maintained in MEF media (DMEM, 10% FBS, 1x non-essential amino acids, 1x glutamax, 1x penicillin/streptomycin, and 2-Mercaptoethanol - 4 μl/500ml) and reprogramming cells were grown in ESC media (knock-out DMEM, 15% FBS, 1x non-essential amino acids, 1x glutamax, 1x penicillin/streptomycin, 2-Mercaptoethanol - 4 μl/525ml, and leukemia inhibitory factor) on plates coated with 0.1% porcine gelatin and DR4 feeder MEFs. All cells were maintained in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were fixed for 10 minutes with 1% formaldehyde, in solution, rotating at room temperature. Fixing was quenched with 0.14 M glycine for 5 minutes, and the cells were spun down at 300xg for 3 minutes. Cells were washed 3 times with PBS and flash frozen. 25-30 million cells were resuspended in 1 mL lysis buffer (1% SDS, 50 mM Tris-HCl pH 8, 20 mM EDTA, 1x cOmplete (Roche, 4693132001) protease inhibitor), and sonicated on a Covaris S220 Focused-ultrasonicator with the following parameters: 21 cycles of 45 seconds ON (peak 170, duty factor 5, cycles/burst 200), 45 seconds OFF (rest) in 6-8°C degassed water to generate fragments of 200-400 bp. Sonicated DNA was quantified with Qubit dsDNA HS (ThermoFisher Scientific, Q32854), aliquoted, and stored at -80°C. The H3K79me1/2 immunoprecipitations were set up with 7.1 ug of reprogramming day 4 chromatin plus 1:53 (133 ng) of human 293T spike in chromatin for normalization, generated as above. The RNAPII immunoprecipitation was set up with 13 ug of reprogramming day 4 chromatin plus 1:53 (247 ng) of human 293T spike-in chromatin. Chromatin was diluted 1:10 with dilution buffer (16.7 mM Tris-HCl pH 8, 0.01% SDS, 1.1% Trition-X, 1.2 mM EDTA, and 167 mM NaCl), and immunoprecipitated with 5 ug H3K79me1 (Abcam, ab2886, Lot GR274715-4), 5 ug H3K79me2 (Active Motif, 39143, Lot 16918002), or 10 ul of RPB1 NTD D8L4Y (Cell Signaling Technology, 14958S) antibody for 16 hours, rotating at 4°C. 25 μL of Protein A (ThermoFisher Scientific, 10002D) and 25 μL of Protein G (ThermoFisher Scientific, 10004D) Dynabeads that were washed once in PBS, 0.02% Tween-20 and once in dilution buffer, were added. Chromatin was incubated, rotating, with beads for 2 hours at 4°C. Beads were washed twice, rotating at 4°C for 5 minutes, with 1 mL of each of the following buffers: Low salt (50 mM HEPES pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1 mM EDTA pH 8.0, 140 mM NaCl), High salt (50 mM HEPES pH 7.9, 0.1% SDS, 1% Triton X-100, 0.1% Deoxycholate, 1 mM EDTA pH 8.0, 500 mM NaCl), LiCl (20 mM Tris-HCl pH 8, 0.5% NP-40, 0.5% Deoxycholate, 1 mM EDTA pH 8.0, 250 mM LiCl), and TE (10 mM Tris-HCl pH 8, 1 mM EDTA pH 8) using a magnetic rack. Beads were incubated with 250 μL elution buffer (50 mM Tris-HCl pH 8, 1 mM EDTA pH 8, 1% SDS) for 10 minutes at 65°C, shaking. 200 μL of TE with 0.67% SDS was added, and incubated shaking at 65°C for 10 minutes. 10 μg RNase A was added and incubated at 37°C for 30 minutes. 40 μg of Proteinase K was added, and incubated for 12-16 hours at 65°C to reverse crosslinks. DNA was cleaned with phenol-chloroform phase separation with phase lock tubes (VWR, 10847-802). DNA was precipitated with 1 volume isopropanol, 1/10th volume of 3M NaActate, and 20 μg glycogen, and washed with 70% ethanol. DNA was dissolved in 30 μL ultrapure water and concentrated to 5 μL using a SpeedVac for library preparation.
The entire ChIP sample was used as starting material for library construction with Ovation Ultralow System V2 using reagents at 0.5x and adapters diluted 1/5 in water, following the manufacturer’s instructions (NuGEN, 0344). The libraries were separated on an 1.5% agarose gel, cut from 200-400 bp for an additional size selection step. The gel fragment was purified using the MinElute Gel Extraction Kit (Qiagen, 28604).

treatment_protocol: Cells were infected with Cre recombinase (Ad5-CMV-Cre) and empty control (Ad5-CMV-Empty) purchased from the Vector Development Lab (Baylor College of Medicine) to delete AF10. 2.4e9 pfu of virus was resuspended in 5 mL of serum-free DMEM and added to 1-2 million MEFs in a 10-cm dish. Virus containing media was removed after 1 hour and replaced with MEF media. Reprogramming was initiated 2 days post-transduction with with 2 μg/mL doxycycline hyclate (Sigma-Aldrich, D9891), and replaced every 48 hours.

value: Mouse embryonic fibroblast

value: Conditional AF10

value: Day 4 reprogramming

value: AF10 -/-, OSKM, rtTA

value: CRE, dox

tag: chip antibody


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-F2


title: RNAPII_creAF10_rep1

value: RPB1 NTD D8L4Y (Cell Signaling Technology, 14958S)


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-G1


title: UGM, Male rep1

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

data_processing:
Raw reads were cleaned (adpater trimming, quality-trimming, removal of reads less than 50bp) was performed using Fastp toolkit.
Quality trimmed reads were mapped against the indexed ENSEMBL Rnor_6.0 reference genome using STAR3 aligner (v2.7.10a).
STAR derived mapping results and annotation (GTF) file were fed into the Htseq version 0.7.0.
Differential expression analysis was performed with Bioconductor package DESeq2 (version 1.22.2)
Pathway analysis was performed using ClusterProfiler
Assembly: ENSEMBL Rnor_6.0
Supplementary files format and content: Tab delimited text file containing raw counts for each sample

organism: Rattus norvegicus

source_name: urogenital sinus mesenchyme

growth_protocol: All animal experiments were performed in accordance with the Animal Welfare Ethical Review Board at Newcastle University or the Institutional Animal Care and Use Committee at Northshore University HealthSystem Research Institute. Embryonic male UGS was micro-dissected from E18 Sprague-Dawley rats (Harlan Laboratories Inc.) and neonatal P0 SVs were isolated from Wistar Han IGS outbred rats (Charles River Laboratories) as described previously (Hepburn et al., 2020; Lawrence et al., 2013).

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Micro Kit
Illumina Tru-Seq

treatment_protocol: After separation of mesenchymal and epithelial subsets, UGM and SVM were incubated for four hours in DMEM/F12 medium containing 2% ITS and 10nM DHT, while UGE and SVE were incubated in the same medium without the addition of DHT.

value: urogenital sinus mesenchyme

tag: Sex

value: male

tag: age

value: no treatment


title: UGM, Male rep3

value: Sprague-Dawley rats (Harlan Laboratories Inc.)


title: UGE rep3

source_name: urogenital sinus epithelium

value: urogenital sinus epithelium

value: male/female


title: UGE rep2


title: tup1-1 (Biol rep 1)

description:
tup1_raw_counts
tup1_normalized_counts

value: log phase yeast cells


title: RNA-seq R35K_120h_rep2

data_processing:
Quality control of FASTQ reads was performed using FastQC version v.0.11.3. Reads were aligned to the mm10 genome using STAR version 2.5.0a. Gene counts were quantified using STAR (--quantMode GeneCounts). Normalized counts were calculated out using DESeq2 version 1.14.1 and were log2 transformed.
Assembly: mm10
Supplementary files format and content: log2(DESeq2 Normalized Counts) for each gene and each experiment are provided as a tab-delimited file.
Supplementary files format and content: Raw Counts for each gene and each experiment are provided as a tab-delimited file.

source_name: Macrophages

extract_protocol:
B cells were harvested by trypsinization followed by removal of feeder cells through differential adherence to tissue culture dishes for 40 minutes. RNA was extracted from B cells with a miRNeasy mini kit (217004, Qiagen), quantified with a NanoDrop spectrophotometer and its quality examined in a fragment Bioanalyzer (Aligent 2100 Bioanalyzer DNA 7500 assay).
For RNA-sequencing (RNA-seq), libraries were prepared with a TruSeq Stranded mRNA Library Preparation Kit (Illumina) followed by single-end sequencing (50 bp) on a HiSeq2500 instrument (Illumina), obtaining at least 40 million reads per sample.

value: Macrophages


title: RNAPII_fl_rep2

value: AF10 fl/fl, OSKM, rtTA

value: Control, dox


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-H1

value: SEP

value: M


title: UGE rep1


title: RNA-seq R35K_120h_rep1

value: Transdifferentiation


title: UGM, Male rep2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-F14


title: SVM rep3

source_name: seminal vesicle mesenchyme

value: seminal vesicle mesenchyme

value: Wistar Han IGS outbred rats (Charles River Laboratories)


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-F1


title: RNAPII_fl_rep1

value: Mouse embryonic fibroblast

value: Conditional AF10

value: Day 4 reprogramming


title: SVM rep2

value: male


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-E2


title: RNA-seq R35K_6h_rep2

value: B-cells


title: CM4Input

city: Oklahoma City

first: Willard

last: Freeman

address: 825 NE 13th St

institute: Oklahoma Medical Research Foundation

description:
CM4_Input_S62
APP_PSEN1_input_fraction_data_matrix.txt

data_processing:
Strand NGS software package (v4.0; Strand Life Sciences)
Alignment and filtering criteria included the following: adapter trimming, fixed 2-bp trim from 5′ and 2 bp from 3′ ends, a maximum number of one novel splice allowed per read, a minimum of 90% identity with the reference sequence, a maximum 5% gap, and trimming of 3′ ends with Q < 30.
Normalization was performed with the DESeq2 algorithm
For statistical analysis of differential expression, a t-test between control and APP-PSEN1 with Benjamini–Hochberg multiple testing correction (BHMTC) was performed
Visualizations of hierarchical clustering and principal component analyses (PCAs) were performed in Strand NGS
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing raw and normalized FPKM data for each sample

source_name: Hippocampus

extract_protocol:
The hippocampi of the mice were dissected and processed through the Adult Brain Dissociation Kit, mouse and rat (#130-107-677, Miltenyi), according to manufacturer's instructions. Following the dissociation and debris removal, samples were incubated with Cd11b (microglia) microbeads (#130-093-634, Miltenyi) for magnetic separation using the autoMACS Separator (Miltenyi). Prior to the sort, an aliquot of cells from each sample was taken for the "Input" fraction. The sort was conducted using the "Posseld" program on the machine. Following the sort, cells were lysed in 350 uL of Buffer RLT (Qiagen) supplemented with 3.5 uL 2-β mercaptoethanol. 350 uL of 100% ethanol was added to the tube containing cells and then loaded onto an RNeasy Mini spin column. RNA was isolated using RNeasy Mini Kit (#74104, Qiagen), according to manufacturer’s instructions. RNA was quantified with a Nanodrop 2000c spectrophotometer (Thermofisher Scientific) and its quality assessed by HSRNA screentape with a 2200 Tapestation analyzer (Agilent Technologies)
The NEBNext Ultra II Directional Library Prep Kit for Illumina (#NEBE7760L; New England Biolabs Inc., Ipswich, MA) was used for the preparation of strand-specific sequencing libraries from each autoMACS-sorted RNA sample (input and positive fraction), according to manufacturer's instructions. Briefly, polyA containing mRNA was purified using oligo-dT attached magnetic beads. mRNA was chemically fragmented and cDNA synthesized. For strand-specificity, the incorporation of dUTP instead of dTTP in the second strand cDNA synthesis does not allow amplification past this dUTP with the polymerase. Following cDNA synthesis, each product underwent end repair process, the addition of a single ‘A’ base, and finally ligation of adapters. The cDNA products were further purified and enriched using PCR to make the final library for sequencing. Library sizing was performed with HS DNA ScreenTape (#5067-5582; Agilent Technologies) and libraries were quantified by Qubit dsDNA HS Assay Kit (ThermoFisher Scientific). The libraries for each sample were pooled at 4 nM concentration and sequenced using an Illumina NextSeq 6000 system (PE75bp) at the Oklahoma Medical Research Foundation Genomics Facility.

value: Hippocampus

value: Microglia

value: WT

tag: fraction

value: Input

tag: library prep_kit

value: NEBNext Ultra II Directional RNA Library Prep Kit for Illumina


title: RNA-seq R35K_18h_rep2


title: RNA-seq R35K_6h_rep1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-E14

tag: brain region


title: CM4Pos

description:
CM4_Pos_S52
APP_PSEN1_pos_fraction_data_matrix.txt

value: Positive


title: SVE rep3

source_name: seminal vesicle epithelium

value: seminal vesicle epithelium

value: no treatment


title: CM3Pos

description:
CM3_Pos_S49
APP_PSEN1_pos_fraction_data_matrix.txt


title: RNA-seq R35K_3h_rep2


title: RNA-seq R35K_3h_rep1


title: CM2Pos

description:
CM2_Pos_S39
APP_PSEN1_pos_fraction_data_matrix.txt


title: RNA-seq R35K_1h_rep2


title: SVE rep2


title: SVE rep 1


title: RNA-seq R35K_18h_rep1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-D2

value: SEP

tag: gender

value: M


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-E1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-F13


title: RNA-seq R35K_1h_rep1

value: Transdifferentiation


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-D14


title: CF4Pos

description:
CF4_Pos_S58
APP_PSEN1_pos_fraction_data_matrix.txt

tag: tissue


title: SVM rep 1

value: seminal vesicle mesenchyme

value: Wistar Han IGS outbred rats (Charles River Laboratories)


title: Adult_sham, scRNA seq

city: Bangalore

first: Soumyashree

last: Das

address: Rajiv gandhi nagar

country: India

institute: National Centre for Biological Sciences

description: 10x Genomics

data_processing:
raw illumina reads were processed in Cell Ranger (10X Genomics)
BCL files were demultiplexed and converted to FASTQ files using the mkfastq in Cell Ranger function
reads were aligned to the mouse genome (mm10) as well as tdTomato sequences using the count function
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart

extract_protocol:
10x gel bead, Libraries were constructed using the Chromium Single Cell 3' Reagent Kits acording to manufacturer instructions
Libraries were constructed using the Chromium Single Cell 3' Reagent Kits acording to manufacturer instructions

treatment_protocol: Hearts were digested to a single cell suspension and FACS sorted to purify lineage traced coronary cells

value: Heart

value: ~2 months

value: Cx40CreER; Rosa26TdTomato


title: Adult_MI, scRNA seq

description: 10x Genomics


title: CF4Input

description:
CF4_Input_S66
APP_PSEN1_input_fraction_data_matrix.txt


title: RNA-seq R35K_0h_rep1

value: B-cells


title: CF3Pos

description:
CF3_Pos_S55
APP_PSEN1_pos_fraction_data_matrix.txt

value: Hippocampus


title: CM3Input

description:
CM3_Input_S60
APP_PSEN1_input_fraction_data_matrix.txt

value: Microglia


title: Neonate_MI, scRNA seq

description: 10x Genomics


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-D1


title: Neonate_sham, scRNA seq

description: 10x Genomics


title: CM2Input

description:
CM2_Input_S50
APP_PSEN1_input_fraction_data_matrix.txt

value: WT


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-D13


title: ATAC-Seq R35K_120h_rep2

data_processing:
Read quality was assessed with FastQC version v.0.11.3. Adaptors were removed using Cutadapt (version 0.4.2_dev) TrimGalore! In paired end mode (--340 paired –nextera). Reads were aligned to the mm10 genome using bowtie2 (v 2.2.4) in paired end mode with standard parameters. Output SAM files were converted to BAM files using samtools (v 0.1.19). BAM files were sorted and indexed using the samtools commands sort and index, respectively. Low quality reads and reads associated with a not primary or supplementary alignment SAM flag were filtered out using the samtools command “samtools view -F 2304 -b -q 10”. PCR duplicates were removed with Picard MarkDuplicates (version 2.3.0) with the following options: “REMOVE_DUPLICATES=true ASSUME_SORTED=true VERBOSITY=WARNING”. Filtered BAM files were indexed with samtools index and were used as input in the bamCoverage command of deeptools (v3.0.1) in order to generate bigwig files. bamCoverage was used with the options – binSize 1 –normalizeUsing RPGC –effectiveGenomeSize 2150570000 –extendReads –outFileFormat bigwig.
Supplementary files format and content: mm10
Supplementary files format and content: bigWig

extract_protocol:
ATAC-seq was performed as previously published (Buenrostro et al., 2015). Briefly, cells were harvested at the mentioned timepoints, feeder-depleted and lysed at 50.000 cells per condition. Immediately, transposition was performed using Nextera Tn5 Transposase (15027865, Illumina) at 37ºC for 30 minutes. Chromatin was then purified using Qiagen MinElute PCR Purification Kit (28004, Qiagen).
DNA was then amplified using NEBNext High Fidelity PCR Master Mix (M0541S, New England Biolabs Inc.) and barcoded primers (see table MMX). qPCR was performed to determine the optimal number of cycles for each condition to stop amplification prior to saturation. Quality was analyzed by gel electrophoresis and in a fragment Bioanalyzer (Agilent 2100 Bioanalyzer DNA 7500 assay).

value: Macrophages


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-E13


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-C2


title: Chir_Tils_mRNA_VDJ

city: DIJON

first: François

last: Ghiringhelli

address: 1 rue du Professeur Marion

country: France

institute: UMR INSERM 1231

library_source: transcriptomic single cell

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
CellRanger (v3.1.0) was used for raw data preprocessing. Fastq files were generated with cellranger mkfast and further data with cellranger count or VDJ.
Assembly: hg38
Supplementary files format and content: Comma separated files and matrix files.

source_name: Tumor

extract_protocol:
Tumor was mechanically and enzymatically dissociated using a human tumor dissociation kit, according to the manufacturer's instructions (130-095-929, Miltenyi Biotec). In brief, tumor was cut into small pieces and transferred into gentleMACS C tubes containing the enzyme mix. The dissociation was performed using the gentleMACS Octo Dissociator with heaters and with the human tumor dissociation 37C_h_TDK_1 program. Samples were homogenized before being applied to a MACS SmartStrainer 70µM (130-110-916, Miltenyi Biotec) placed on a 50 mL tube. Filters were washed with 20 mL serum-free RPMI (L0500-500, Dutscher) and then centrifuged at 300g for 7 minutes. After complete aspiration of the supernatant, tumor cell suspensions were resuspended in RPMI and counted with trypan blue to remove dead cells. Cells were frozen in a solution of 50% FBS (Dutscher), 40% RPMI and 10% DMSO (P60-36720100, Dutscher) until further use. PBMC were isolated and frozen as described above. On the day of the single cell experiment, the samples first underwent a specific preparation protocol. Briefly, the samples were thawed following the 10X genomics thawing protocol based on cascade dilutions. Dead cells were then removed with the Dead Cell Removal kit according the manufacturer’s instructions (130-090-101, Miltenyi Biotec). CD3 T cells were then isolated for each sample on a magnetic column after labelling with CD3 MicroBeads (130-050-101, Miltenyi Biotec). To better purify CD3 T cells, we labelled the samples with an anti-TCRαβ-PE (Clone IP26A, Beckman Coulter) and an anti-TCRγδ (Clone IMMU510, Beckman Coulter) in order to sort the positive cells for one of these two markers with an ARIA Fusion sorter. Finally, we resuspended the cells at 1000 cells/µL before proceeding with the cell encapsulation step according to the manufacturer’s instructions via the Chromium device (10X genomics).
Library preparation was performed using library prep for 5'mRNA and VDJ (10X Genomics)

value: Tumor

value: Tumor at time of surgery


title: ATAC-Seq R35K_120h_rep1


title: CF2Input

description:
CF2_Input_S56
APP_PSEN1_input_fraction_data_matrix.txt

value: Input

value: NEBNext Ultra II Directional RNA Library Prep Kit for Illumina


title: CF2Pos

description:
CF2_Pos_S45
APP_PSEN1_pos_fraction_data_matrix.txt

value: Positive


title: Chir_Tils_mRNA_5prime


title: ATAC-Seq R35K_18h_rep2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-C13

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Tab-delimited files (HIC files) describing the chromatin contacts will be generated with in-house developing package using the filtered BAM files
Assembly: hg38-donor-snp-substituted
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
Supplementary files format and content: tab-delimited files (HIC files) describing the chromatin contacts. Columns are: 1. Strand1, 2. Chromosome1, 3. Position1, 4. place holder column, always be 0, 5. Strand2, 6. Chromosome2, 7. Position2, 8. place holder column, always be 1.
Library strategy: snm3C-seq

extract_protocol:
Regions of human brains were dissected.
Library prepared following protocol discribed in Dong-Sung Lee, Chongyuan Luo, Jingtian Zhou, Sahaana Chandran, Angeline Rivkin, Anna Bartlett, Joseph R. Nery, Conor Fitzpatrick, Carolyn O’Connor,Jesse R. Dixon, Joseph R. Ecker. 2019. “Simultaneous profiling of 3D genome structure and DNA methylation in single human cells.” Nat Methods. 16(10): 999–1006.

value: SEP

value: M


title: Chir_PBMC_mRNA_VDJ

source_name: PBMC

value: PBMC

value: PBMC at time of surgery


title: ADM4Pos

description:
ADM4_Pos_S46
APP_PSEN1_pos_fraction_data_matrix.txt


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-C1


title: ATAC-Seq R35K_18h_rep1

value: Transdifferentiation


title: Chir_PBMC_mRNA_5prime


title: RNA-seq R35K_0h_rep2


title: ATAC-Seq R35K_6h_rep2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-C14


title: ADM4Input

description:
ADM4_Input_S57
APP_PSEN1_input_fraction_data_matrix.txt


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-B2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-B14


title: ATAC-Seq R35K_6h_rep1


title: CF3Input

description:
CF3_Input_S64
APP_PSEN1_input_fraction_data_matrix.txt


title: ADM3Pos

description:
ADM3_Pos_S43
APP_PSEN1_pos_fraction_data_matrix.txt


title: C2_mRNA_5prime

value: PBMC at cycle 2


title: ADM3Input

description:
ADM3_Input_S54
APP_PSEN1_input_fraction_data_matrix.txt


title: ATAC-Seq R35K_3h_rep2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-B13


title: ATAC-Seq R35K_3h_rep1


title: C1_mRNA_VDJ

value: PBMC at cycle 1


title: ADM2Pos

description:
ADM2_Pos_S65
APP_PSEN1_pos_fraction_data_matrix.txt


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-B1


title: ADM2Input

description:
ADM2_Input_S44
APP_PSEN1_input_fraction_data_matrix.txt


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-A2


title: ADM1Pos

description:
ADM1_Pos_S61
APP_PSEN1_pos_fraction_data_matrix.txt


title: HEK293, WT, MondoA ChIP, Replicate 2

city: Oberschleißheim

first: Robert

last: Schneider

address: Ingolstädter Landstraße 1

department: Institute of Functional Epigenetics

country: Germany

institute: Helmholtz Zentrum München

data_processing:
Adapter sequences were trimmed away from the sequenced ChIP-seq reads using cutadapt (v3.4) with quality cutoff of 20, discarding reads shorter than 36 bases.
ChIP-seq reads were aligned to a chimeric hg38+dm6 reference genome using bowtie2 (2.4.4) using parameters --seed 1 --mm --very-sensitive
Reads aligned to the hg38 and dm6 proportions of the chimeric genome were separated. Improperly paired reads, reads overlapping with blacklisted regions, and reads  with MAPQ <20 were filtered out.
MACS2 (2.2.7.1) was used to call peaks on endogenously aligned reads, with the settings --qvalue 0.001 -f BAMPE -g 2913022398 for transcription factors, and an additional setting of --min-length 400 --max-gap 800  for histone modifications.
bigWig read profiles were generated using deeptools bamCoverage (v3.5.1). The bigWig files are normalised per million reads in exogenous genome (H3K9ac, H3K4me3, Input) or per million reads in endogenous genome (MondoA, MLX).
Assembly: hg38, dm6
Supplementary files format and content: bigWig, narrowPeak (except for input sample)

growth_protocol: HEK293 cell line was cultured in DMEM (Sigma, 1 g glucose/L) supplemented with 10% FBS (Gibco), 2 mM L-glutamine, 1% Pen/Strep, 1 mM sodium pyruvate and non-essential amino acids and maintained at 37°C. Drosophila Schneider 2 cells were cultured at 27°C, in Schneider medium (Thermo Fisher) supplemented with 10% heat-inactivated FBS (Gibco) and 0.5% Pen/Strep.

extract_protocol:
Cells were fixed with 1% formaldehyde for 5 min. After quenching and cell lysis chromatin was fragmented using QSonica Q800R sonicator. Total amount of 5 ug of human chromatin and 100 ng of Drosophila chromatin was used for IP.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit with the adapter dilution 1:25 and 5 uL pre-mixed forward/reverse primer solution. The starting mass of DNA for the library preparation was 5 ng. Libraries were amplified in 11 PCR cycles. Double size selection of DNA fragments of a size 200-600 bp was performed using magnetic AMPure XP beads (Beckman Coulter) and validated using Bioanalyzer High Sensitivity Chip (Agilent).

treatment_protocol: Stable knockdown in HEK293 cells was generated using lentiviral-delivered shRNA (TRCN0000196588) inserted into pLKO.1-puro plasmid (Addgene #8453).

tag: cell line

value: Human embryonic kidney

tag: knockdown

value: MondoA (Proteintech 13614-1-AP)

tag: replicate

tag: batch


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-A14


title: ATAC-Seq R35K_1h_rep1

value: B-cells

tag: treatment

tag: time


title: HEK293, WT, MondoA ChIP, Replicate 1

tag: cell type

value: WT


title: ATAC-Seq R35K_0h_rep2


title: C2_mRNA_VDJ


title: HEK293, PKM KD, MondoA ChIP, Replicate 2

value: PKM


title: ATAC-Seq R35K_0h_rep1


title: ADF4Pos

description:
ADF4_Pos_S40
APP_PSEN1_pos_fraction_data_matrix.txt

value: Hippocampus

value: Microglia

tag: genotype


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-A1


title: ADF4Input

description:
ADF4_Input_S51
APP_PSEN1_input_fraction_data_matrix.txt

value: Input


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-P24


title: OLG3

city: Zhengzhou

first: cancan

last: zhang

state: henan

address: 100 Science Road

institute: Zhengzhou university

data_processing:
We use Cutadapt (v1.15) software to filter the sequencing data to get high quality sequence（Clean Data）for further analysis .
The reference genome and gene annotation files were downloaded from genome website.The filtered reads were mapping to the reference genome using HISAT2 v2.0.5.
We used HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Assembly: mm39
Supplementary files format and content: tab-delimited text files includes FPKM values for each Sample

source_name: trachea

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), 0.75μg of total RNA was used for the construction of sequencing libraries.
Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA was disrupted to 200-300bp fragments by ion disruption
To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA).DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction
Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent). The sequencing library was then sequenced on NovaSeq 6000 platform (Illumina) by Suzhou PANOMIX Biomedical Tech Co.LTD.

value: trachea

tag: group

value: OLG


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-P23

city: La Jolla

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

value: SEP


title: OLG4


title: HEK293, WT, MLX ChIP, Replicate 2

tag: chip antibody

value: MLX (Cell Signaling #85570)


title: C1_mRNA_5prime

value: PBMC


title: ADF3Pos

description:
ADF3_Pos_S37
APP_PSEN1_pos_fraction_data_matrix.txt

value: Positive

value: NEBNext Ultra II Directional RNA Library Prep Kit for Illumina


title: OLG2


title: HEK293, WT, MLX ChIP, Replicate 1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-P12

value: M


title: ADF3Input

description:
ADF3_Input_S48
APP_PSEN1_input_fraction_data_matrix.txt


title: ATAC-Seq R35K_1h_rep2

value: Transdifferentiation


title: HEK293, PKM KD, MLX ChIP, Replicate 2

value: Human embryonic kidney


title: ADF2Pos

description:
ADF2_Pos_S63
APP_PSEN1_pos_fraction_data_matrix.txt


title: OLG1


title: ADM1Input

description:
ADM1_Input_S38
APP_PSEN1_input_fraction_data_matrix.txt


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-P11


title: ADF2Input

description:
ADF2_Input_S41
APP_PSEN1_input_fraction_data_matrix.txt


title: HEK293, PKM KD, MLX ChIP, Replicate 1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P5-1-C23-A13


title: OL78

value: OL


title: HEK293, WT, Input, Batch 2, Replicate 1&2


title: ADF1Pos

description:
ADF1_Pos_S59
APP_PSEN1_pos_fraction_data_matrix.txt


title: OL56


title: HEK293, PKM KD, Input, Batch 2, Replicate 1&2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-O23


title: HEK293, PKM KD, MondoA ChIP, Replicate 1

value: MondoA (Proteintech 13614-1-AP)


title: ADF1Input

description:
ADF1_Input_S35
APP_PSEN1_input_fraction_data_matrix.txt


title: OL34

value: WT


title: HEK293, WT, Replicate 2.2

description:
HEK293.xlsx
MUC13541

data_processing:
Residual adapter sequences and low-quality segments (<20) were trimmed out of the RNA-seq reads using Trim Galore (v0.6.7).
Resulting sequences were quantified against the hg38 transcriptome index from refgenie (hg38/salmon_sa_index, asset digest 4258fa823e3c92b4285b48efa2ce3da0) using salmon (v1.5.2) with  --seqBias --gcBias –validateMappings options
A differential expression analysis between WT and KD samples has been performed using DESeq2 (v1.32.0), with local fit for dispersion estimates and dispersion outlier filtering disabled. Only genes that had at least 10 reads mapped to them in all samples were considered
Resulting differentially expressed genes (Wald test, FDR 0.05) have been divided into categories based on their confident effect sizes. MCF-7 and HEK293 datasets were analysed independently.
Assembly: hg38
Supplementary files format and content: gzipped salmon quant.sf outputs
Supplementary files format and content: postprocessed excel file with differential analysis results

source_name: Human embryonic kidney

growth_protocol: HEK293 and MCF-7 cell lines were cultured in DMEM (Sigma, 1 g glucose/L) supplemented with 10% FBS (Gibco), 2 mM L-glutamine, 1% Pen/Strep, 1 mM sodium pyruvate and non-essential amino acids and maintained at 37°C.

extract_protocol:
Total RNA was extracted using Quick-RNA Miniprep Kit (Zymo Research). The integrity of RNA was checked on the Bioanalyzer 6000 Nano Chip (Agilent).
RNA-seq libraries were prepared using TruSeq Stranded Total RNA.

treatment_protocol: Stable knockdown in HEK293 and MCF-7 cells was generated using lentiviral-delivered shRNA (TRCN0000196588) inserted into pLKO.1-puro plasmid (Addgene #8453).

tag: biological replicate

tag: technical replicate


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-O12


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-O11


title: bld_GEX_Spt

first: Jenna

middle: Lynn

last: Collier

state: Massachusetts

address: 77 Avenue Louis Pasteur

department: Immunology

institute: Harvard University

description: Sorted TCR-beta+CD11a+ T cells from the peripheral blood from spontaneously diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the gene expression data.

data_processing:
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting, and csv files of TCR clonality were performed using the Cell Ranger analysis MULTI pipeline (v3.0.2)
Data normalization, dimension reduction, and differential expression analysis were performed using R version 4.0.3 and the Seurat R package (version 4.0.2)
Tissues were integrated across anchors (Stuart T, Butler A, et al. Cell. 2019;177:1888-1902)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files. Integrated .rds files contain Seurat objects with the count matrix as an RNA assay, and the TCR data, matching status, and other data in the @meta.data field.

molecule: polyA RNA

source_name: peripheral blood

growth_protocol: Peripheral blood was isolated using retroorbital collection prior to euthanasia, and the pancreatic lymph nodes and pancreas were collected from the same mice after euthanasia. Leukocytes were enriched from peripheral blood using histopaque gradients. Pancreas-infiltrating lymphocytes were enriched from pancreas samples by performing digestion with collagenase I and DNAse I followed by discontinous percoll gradient. TCR-beta+CD11a+ T cells were sorted using a BD Aria sorter prior to performing 10X library generation.

extract_protocol:
Sorted TCR-beta+CD11A+ T cells from peripheral blood, pancreas, and pancreatic lymph nodes were loaded into the 10X Chromium Controller using the Chromium Single Cell 5' Library and Gel Bead Kit (10X Genomics)
Protocol number CG000330 RevE from 10X Genomics (User Guide, Chromium Next GEM Single Cell V(D)J Reagent Kits v2 with Feature Barcoding technology for Cell Surface Protein) was used.
10X Chromium Single Cell V(D)J kits (5' v2 gene expression with paired T cell receptor sequencing and Feature Barcode detection)

treatment_protocol: Spontaneously diabetic mice received no treatment. Anti-PD-1 and isotype control treated mice received two doses of 0.2mg of antibody by intraperitoneal injection on days -4 and -2 before sacrifice. Three individual mice from each group were stained with hashtag antibodies before pooling for sequencing.

value: peripheral blood

value: TCR-beta+CD11A+ T cells

value: NOD/ShiLtJ

tag: age

value: 18 weeks

tag: Sex

value: Female

tag: disease

value: Diabetes


title: HEK293, WT, Replicate 2.3

description:
HEK293.xlsx
MUC13542


title: OL12

value: trachea


title: bld_GEX_PD1

description: Sorted TCR-beta+CD11a+ T cells from the peripheral blood from anti-PD-1-treated diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the gene expression data.

value: IP injection of 0.2mg anti-mouse PD-1 (clone:29F.1A12) on days -4, -2 before analysis

value: 16 weeks


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-O24

first: Joseph

tag: brain region

value: SEP

tag: gender


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-N23


title: bld_GEX_IgG

description: Sorted TCR-beta+CD11a+ T cells from the peripheral blood from isotype antibody-treated non-diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the gene expression data.

tag: tissue

value: IP injection of 0.2mg IgG2a isotype control (clone:2A3) on days -4, -2 before analysis


title: PBS3

value: PBS


title: PBS2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-N24

value: M


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-N12


title: HEK293, PKM KD, Replicate 2.2

description:
HEK293.xlsx
MUC13535

value: Human embryonic kidney

tag: knockdown

value: PKM


title: PBS1


title: bld_TCR_Spt

description: Sorted TCR-beta+CD11a+ T cells from the peripheral blood from spontaneously diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the TCR sequencing data.


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-M24


title: bld_TCR_IgG

description: Sorted TCR-beta+CD11a+ T cells from the peripheral blood from isotype antibody-treated non-diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the TCR sequencing data.


title: RNA-Seq R35A_120h_rep1

value: Macrophages

value: Transdifferentiation


title: bld_TCR_PD1

description: Sorted TCR-beta+CD11a+ T cells from the peripheral blood from anti-PD-1-treated diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the TCR sequencing data.

value: peripheral blood


title: RNA-Seq R35A_120h_rep2


title: HEK293, PKM KD, Replicate 2.1

description:
HEK293.xlsx
MUC13534


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-M23


title: bld_FB_Spt

description:
Sorted TCR-beta+CD11a+ T cells from the peripheral blood from spontaneously diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the CITE-seq data.
bld_Spt_barcodes.tsv.gz
bld_Spt_features.tsv.gz
bld_Spt_matrix.mtx.gz

value: TCR-beta+CD11A+ T cells


title: RNA-Seq R35A_18h_rep2

value: B-cells


title: HEK293, PKM KD, Replicate 1.1

description:
HEK293.xlsx
MUC10350


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-M12


title: HEK293, WT, Replicate 2.1

description:
HEK293.xlsx
MUC13540

value: WT


title: bld_FB_PD1

description:
Sorted TCR-beta+CD11a+ T cells from the peripheral blood from anti-PD-1-treated diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the CITE-seq data.
bld_PD1_barcodes.tsv.gz
bld_PD1_features.tsv.gz
bld_PD1_matrix.mtx.gz

value: NOD/ShiLtJ

value: Female


title: HEK293, PKM KD, Replicate 1.2

description:
HEK293.xlsx
MUC10351


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-M11


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-L24


title: RNA-Seq R35A_6h_rep2


title: RNA-Seq R35A_6h_rep1


title: RNA-Seq R35A_18h_rep1


title: HEK293, WT, Replicate 1.1

description:
HEK293.xlsx
MUC10353


title: pLN_GEX_Spt

description: Sorted TCR-beta+CD11a+ T cells from the pancreatic lymph nodes from spontaneously diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the gene expression data.

source_name: pancreatic lymph nodes

value: pancreatic lymph nodes

value: 18 weeks

value: Diabetes


title: pLN_GEX_PD1

description: Sorted TCR-beta+CD11a+ T cells from the pancreatic lymph nodes from anti-PD-1-treated diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the gene expression data.

value: IP injection of 0.2mg anti-mouse PD-1 (clone:29F.1A12) on days -4, -2 before analysis

value: 16 weeks


title: bld_FB_IgG

description:
Sorted TCR-beta+CD11a+ T cells from the peripheral blood from isotype antibody-treated non-diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the CITE-seq data.
bld_IgG_barcodes.tsv.gz
bld_IgG_features.tsv.gz
bld_IgG_matrix.mtx.gz

value: IP injection of 0.2mg IgG2a isotype control (clone:2A3) on days -4, -2 before analysis


title: HEK293, PKM KD, Replicate 2.3

description:
HEK293.xlsx
MUC13536


title: HEK293, WT, Replicate 1.3

description:
HEK293.xlsx
MUC10355


title: pLN_GEX_IgG

description: Sorted TCR-beta+CD11a+ T cells from the pancreatic lymph nodes from isotype antibody-treated non-diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the gene expression data.


title: RNA-Seq R35A_1h_rep2


title: HEK293, WT, Replicate 1.2

description:
HEK293.xlsx
MUC10354


title: eIF4E1c input biol rep 3

city: Vienna

first: Laura

last: Lorenzo-Orts

address: Institute of Molecular Pathology (IMP), Campus Vienna Biocenter 1

country: Austria

institute: IMP

data_processing:
RNA-seq reads were trimmed using trim-galore v0.5.0, and reads mapping to abundant sequences (Dr mitochondrial chromosome, SILVA Dr ribosomal RNA, phiX174 genome) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were analyzed using genome and gene annotation for the GRCz11 assembly obtained from Danio rerio Ensembl release 104. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts with parameter -s 0 for unstranded analysis (subread v1.6.2).
Differential gene expression analysis on raw counts and variance-stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1.
Functional annotation enrichment analysis of differentially expressed genes was conducted using clusterprofiler v3.6.0 in R v3.4.1.
Assembly: GRCz11
Supplementary files format and content: Tab-delimited text files with per gene read counts

organism: Danio rerio

source_name: Whole embryo lysate

extract_protocol:
RNA Clean & Concentrator kit (Zymo Research) of RIP and input samples
SMARTerStrandedRNA library (Ribo-Zero) for input samples; SMARTer ultra low RNA kit for RIP samples
RNA-Seq (RIP) and ssRNA-seq (Ribo-Ziro)

value: Whole embryo lysate

value: 8-cell stage


title: eIF4E1c input biol rep 2


title: RNA-Seq R35A_3h_rep2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-L23

value: SEP

value: M


title: pLN_TCR_PD1

description: Sorted TCR-beta+CD11a+ T cells from the pancreatic lymph nodes from anti-PD-1-treated diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the TCR sequencing data.


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-L12


title: RNA-Seq R35A_1h_rep1

value: Transdifferentiation


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-L11


title: pLN_TCR_Spt

description: Sorted TCR-beta+CD11a+ T cells from the pancreatic lymph nodes from spontaneously diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the TCR sequencing data.


title: RNA-Seq R35A_3h_rep1


title: HEK293, PKM KD, Replicate 1.3

description:
HEK293.xlsx
MUC10352

value: Human embryonic kidney

value: PKM


title: pLN_FB_Spt

description:
Sorted TCR-beta+CD11a+ T cells from the pancreatic lymph nodes from spontaneously diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the CITE-seq data.
pLN_Spt_barcodes.tsv.gz
pLN_Spt_features.tsv.gz
pLN_Spt_matrix.mtx.gz

value: TCR-beta+CD11A+ T cells


title: eIF4E1b input biol rep 1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-J24


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-K23


title: eIF4E1c input biol rep 1


title: pLN_TCR_IgG

description: Sorted TCR-beta+CD11a+ T cells from the pancreatic lymph nodes from isotype antibody-treated non-diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the TCR sequencing data.


title: RNA-Seq R35A_0h_rep2

value: B-cells


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-K12


title: eIF4E1b input biol rep 3


title: eIF4E1c RIP biol rep 1

source_name: Embryo lysate RIP

value: Embryo lysate RIP


title: eIF4E1b RIP biol rep 3


title: eIF4E1b input biol rep 2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-K11


title: RNA-Seq WT_6h_rep2

source_name: B-cells


title: pLN_FB_PD1

description:
Sorted TCR-beta+CD11a+ T cells from the pancreatic lymph nodes from anti-PD-1-treated diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the CITE-seq data.
pLN_PD1_barcodes.tsv.gz
pLN_PD1_features.tsv.gz
pLN_PD1_matrix.mtx.gz

value: NOD/ShiLtJ

value: Female


title: RNA-Seq R35A_0h_rep1


title: RNA-Seq WT_120h_rep2

value: Macrophages


title: pLN_FB_IgG

description:
Sorted TCR-beta+CD11a+ T cells from the pancreatic lymph nodes from isotype antibody-treated non-diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the CITE-seq data.
pLN_IgG_barcodes.tsv.gz
pLN_IgG_features.tsv.gz
pLN_IgG_matrix.mtx.gz

value: pancreatic lymph nodes


title: pan_GEX_Spt

description: Sorted TCR-beta+CD11a+ T cells from the pancreases from spontaneously diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the gene expression data.

source_name: pancreas

value: pancreas

value: 18 weeks

value: Diabetes


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-K24


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-J23


title: pan_TCR_Spt

description: Sorted TCR-beta+CD11a+ T cells from the pancreases from spontaneously diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the TCR sequencing data.


title: RNA-Seq WT_18h_rep2


title: RNA-Seq WT_6h_rep1


title: pan_GEX_PD1

description: Sorted TCR-beta+CD11a+ T cells from the pancreases from anti-PD-1-treated diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the gene expression data.

value: IP injection of 0.2mg anti-mouse PD-1 (clone:29F.1A12) on days -4, -2 before analysis

value: 16 weeks


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-J12

value: SEP


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-I12

value: M


title: RNA-Seq WT_3h_rep2

value: Transdifferentiation


title: RNA-Seq WT_18h_rep1


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-I11


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-J11


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-I24


title: pan_TCR_IgG

description: Sorted TCR-beta+CD11a+ T cells from the pancreases from isotype antibody-treated non-diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the TCR sequencing data.

value: IP injection of 0.2mg IgG2a isotype control (clone:2A3) on days -4, -2 before analysis


title: pan_GEX_IgG

description: Sorted TCR-beta+CD11a+ T cells from the pancreases from isotype antibody-treated non-diabetic mice. 10X 5' gene expression and paired T cell receptor sequencing were performed. CITE-seq was also used to detect Feature Barcodes for hashtag antibodies. These files contain the gene expression data.


title: eIF4E1b RIP biol rep 2

value: 8-cell stage


title: RNA-Seq WT_1h_rep2


title: HBA_220322_H1930001_CX46_SEP_3C_1_P4-6-O21-H12


title: RNA-Seq WT_1h_rep1


title: Cow 4 Day 3 Evening

city: Zurich

first: Maria

middle: Desemparats

last: Saenz-de-Juano

address: Universitatstrasse 2

country: Switzerland

institute: ETH Zurich

data_processing:
Remove Adapter: Tool “Clip” from Galaxy
Remove short reads (<25 nucleotides): Tool “Clip” from Galaxy
Remove Low Quality reads: Tool "FASTQ Quality Trimmer" from galaxy
Remove PCR duplicates: Tool “Collapse” from galaxy
Filtering: "Count Per Million (CPM) Filter" from Galaxy
Assembly: miRBase database v22.1
Supplementary files format and content: Normalization of read count using TMM and GLM robust (estimateGLMRobustDisp) included in edgeR

organism: Bos taurus

source_name: skimmed milk

extract_protocol:
miRNeasy MicroKit  (QIAGEN) following manufacturer's instructions
NEXTflex™ Small RNA-Seq Kit v3 (Bioo Scientific)  following manufacturer's instructions

tag: subject

value: Cow 4

tag: timepoint

value: Evening

tag: scc (cells/ml_of_milk)

value: skimmed milk


title: RNA-Seq WT_0h_rep2

value: B-cells

tag: treatment

tag: time


title: RNA-Seq WT_0h_rep1

tag: cell type