title: HctYH_OF3A_5-3-K9-O6


title: HctYH_OF3A_5-4-K9-A19

status: Public on Dec 15 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: OF3A human BA46

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

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

tag: age

tag: Sex

value: Female

tag: molecule subtype

value: nuclear RNA + genomic DNA


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title: HctYH_OF3A_4-6-C7-L24


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title: HctYH_OF3A_4-6-C7-L11


title: HctYH_OF3A_4-6-C7-K24


title: HctYH_OF3A_4-6-C7-J24


title: HctYH_OF3A_4-6-C7-O24


title: HctYH_OF3A_4-6-C7-K23


title: HctYH_OF3A_4-6-C7-J11


title: HctYH_OF3A_4-6-C7-P12


title: HctYH_OF3A_4-6-C7-K11


title: HctYH_OF3A_4-6-C7-I24


title: HctYH_OF3A_4-6-C7-J12


title: HctYH_OF3A_4-6-C7-I23


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title: HctYH_OF3A_4-6-C7-M12


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title: HctYH_OF3A_4-5-C7-A22


title: HctYH_OF3A_4-5-C7-A21


title: HctYH_OF3A_4-5-C7-D9


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title: HctYH_OF3A_4-4-C7-N7


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title: HctYH_OF3A_4-4-C7-M7


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title: HctYH_OF3A_3-5-O5-B21


title: HctYH_OF3A_3-4-O5-M19


title: HctYH_OF3A_3-4-O5-L8


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title: HctYH_OF3A_3-4-O5-L20


title: HctYH_OF3A_3-4-O5-L19


title: HctYH_OF3A_3-4-O5-K8


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title: HctYH_OF3A_3-4-O5-P20


title: HctYH_OF3A_3-4-O5-K20


title: HctYH_OF3A_3-4-O5-K19


title: HctYH_OF3A_3-4-O5-J8


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title: HctYH_OF3A_3-4-O5-I8


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title: HctYH_OF3A_3-4-O5-J20


title: HctYH_OF3A_3-4-O5-J7


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title: HctYH_OF3A_3-4-O5-H19


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title: HctYH_OF3A_3-4-O5-G19


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title: HctYH_OF3A_3-4-O5-G7


title: HctYH_OF3A_3-4-O5-F19


title: HctYH_OF3A_3-4-O5-E8


title: HctYH_OF3A_3-4-O5-E7


title: HctYH_OF3A_3-4-O5-D7


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title: HctYH_OF3A_3-4-O5-D8


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title: HctYH_OF3A_3-4-O5-D19


title: HctYH_OF3A_3-4-O5-D20


title: HctYH_OF3A_3-4-O5-C8


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title: HctYH_OF3A_3-4-O5-C7


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title: HctYH_OF3A_2-5-E5-D10


title: HctYH_OF3A_2-5-E5-F10


title: HctYH_OF3A_2-5-E5-D21


title: HctYH_OF3A_2-5-E5-C22


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title: HctYH_OF3A_2-5-E5-B22


title: HctYH_OF3A_2-4-E5-O7


title: HctYH_OF3A_2-5-E5-E22


title: HctYH_OF3A_2-5-E5-B21


title: HctYH_OF3A_2-5-E5-A9


title: HctYH_OF3A_2-4-E5-P19


title: HctYH_OF3A_2-5-E5-A21


title: HctYH_OF3A_2-4-E5-P8


title: HctYH_OF3A_2-4-E5-P7


title: HctYH_OF3A_2-4-E5-O20


title: HctYH_OF3A_2-4-E5-N7


title: HctYH_OF3A_2-4-E5-N8


title: HctYH_OF3A_2-4-E5-O19


title: HctYH_OF3A_2-4-E5-N19


title: HctYH_OF3A_2-4-E5-M8


title: HctYH_OF3A_2-4-E5-M20


title: HctYH_OF3A_2-4-E5-L8


title: HctYH_OF3A_2-4-E5-M19


title: HctYH_OF3A_2-4-E5-M7


title: HctYH_OF3A_2-5-E5-A22


title: HctYH_OF3A_2-4-E5-L20


title: HctYH_OF3A_2-4-E5-P20


title: HctYH_OF3A_2-4-E5-L19


title: HctYH_OF3A_2-4-E5-K20


title: HctYH_OF3A_2-4-E5-K7


title: HctYH_OF3A_2-4-E5-K19


title: HctYH_OF3A_2-4-E5-K8


title: HctYH_OF3A_2-4-E5-J20


title: HctYH_OF3A_2-4-E5-J8


title: HctYH_OF3A_2-4-E5-I8


title: HctYH_OF3A_2-4-E5-J19


title: HctYH_OF3A_2-4-E5-I20


title: HctYH_OF3A_2-4-E5-I7


title: HctYH_OF3A_2-4-E5-J7


title: HctYH_OF3A_2-4-E5-H8


title: HctYH_OF3A_2-4-E5-N20


title: HctYH_OF3A_2-4-E5-H20


title: HctYH_OF3A_2-4-E5-G8


title: HctYH_OF3A_2-4-E5-H19


title: HctYH_OF3A_2-4-E5-I19


title: HctYH_OF3A_2-4-E5-G20


title: HctYH_OF3A_2-4-E5-G19


title: HctYH_OF3A_2-4-E5-F8


title: HctYH_OF3A_2-4-E5-F19


title: HctYH_OF3A_2-4-E5-F20


title: HctYH_OF3A_2-4-E5-F7


title: HctYH_OF3A_2-4-E5-L7


title: HctYH_OF3A_2-4-E5-E8


title: HctYH_OF3A_2-4-E5-E20


title: HctYH_OF3A_2-4-E5-E19


title: HctYH_OF3A_2-4-E5-D8


title: HctYH_OF3A_2-4-E5-H7


title: HctYH_OF3A_2-4-E5-D7


title: HctYH_OF3A_2-4-E5-D20


title: HctYH_OF3A_2-4-E5-D19


title: HctYH_OF3A_2-4-E5-C8


title: HctYH_OF3A_2-4-E5-C7


title: HctYH_OF3A_2-4-E5-B7


title: HctYH_OF3A_2-4-E5-B19


title: HctYH_OF3A_2-4-E5-G7


title: HctYH_OF3A_2-4-E5-B8


title: HctYH_OF3A_2-4-E5-C19


title: HctYH_OF3A_2-4-E5-A8


title: HctYH_OF3A_2-4-E5-B20


title: HctYH_OF3A_2-4-E5-A7


title: HctYH_OF3A_2-4-E5-A20


title: HctYH_OF3A_2-3-E5-P6


title: HctYH_OF3A_2-3-E5-P17


title: HctYH_OF3A_2-3-E5-O6


title: HctYH_OF3A_2-3-E5-O18


title: HctYH_OF3A_2-3-E5-O17


title: HctYH_OF3A_2-3-E5-O5


title: HctYH_OF3A_2-3-E5-P5


title: HctYH_OF3A_2-3-E5-N6


title: HctYH_OF3A_2-4-E5-E7


title: HctYH_OF3A_2-3-E5-N5


title: HctYH_OF3A_2-3-E5-N18


title: HctYH_OF3A_2-4-E5-C20


title: HctYH_OF3A_2-3-E5-N17


title: HctYH_OF3A_2-3-E5-M5


title: HctYH_OF3A_2-3-E5-M6


title: HctYH_OF3A_2-3-E5-L6


title: HctYH_OF3A_2-3-E5-M18


title: HctYH_OF3A_2-3-E5-L5


title: HctYH_OF3A_2-3-E5-M17


title: HctYH_OF3A_2-3-E5-K6


title: HctYH_OF3A_2-3-E5-K5


title: HctYH_OF3A_2-3-E5-L18


title: HctYH_OF3A_2-4-E5-A19


title: HctYH_OF3A_2-3-E5-P18


title: HctYH_OF3A_2-3-E5-K17


title: HctYH_OF3A_2-3-E5-K18


title: HctYH_OF3A_2-3-E5-J5


title: HctYH_OF3A_2-3-E5-J6


title: HctYH_OF3A_2-3-E5-J18


title: HctYH_OF3A_2-3-E5-J17


title: HctYH_OF3A_2-3-E5-I5


title: HctYH_OF3A_2-3-E5-I17


title: HctYH_OF3A_2-3-E5-H6


title: HctYH_OF3A_2-3-E5-H5


title: HctYH_OF3A_2-3-E5-H18


title: HctYH_OF3A_2-3-E5-G5


title: HctYH_OF3A_2-3-E5-H17


title: HctYH_OF3A_2-3-E5-G6


title: HctYH_OF3A_2-3-E5-L17


title: HctYH_OF3A_2-3-E5-G18


title: HctYH_OF3A_2-3-E5-F18


title: HctYH_OF3A_2-3-E5-F17


title: HctYH_OF3A_2-3-E5-F5


title: HctYH_OF3A_2-3-E5-E5


title: HctYH_OF3A_2-3-E5-F6


title: HctYH_OF3A_2-3-E5-E6


title: HctYH_OF3A_2-3-E5-D6


title: HctYH_OF3A_2-3-E5-D5


title: HctYH_OF3A_2-3-E5-E18


title: HctYH_OF3A_2-3-E5-D17


title: HctYH_OF3A_2-3-E5-E17


title: HctYH_OF3A_2-3-E5-C6


title: HctYH_OF3A_2-3-E5-I6


title: HctYH_OF3A_2-3-E5-C18


title: HctYH_OF3A_2-3-E5-B18


title: HctYH_OF3A_2-3-E5-B17


title: HctYH_OF3A_2-3-E5-I18


title: HctYH_OF3A_2-3-E5-C17


title: HctYH_OF3A_2-3-E5-B5


title: HctYH_OF3A_2-3-E5-A5


title: HctYH_OF3A_2-3-E5-A6


title: HctYH_OF3A_2-2-E5-P4


title: HctYH_OF3A_2-3-E5-G17


title: HctYH_OF3A_2-3-E5-A17


title: HctYH_OF3A_2-2-E5-P3


title: HctYH_OF3A_2-2-E5-P16


title: HctYH_OF3A_2-3-E5-D18


title: HctYH_OF3A_2-2-E5-P15


title: HctYH_OF3A_2-3-E5-C5


title: HctYH_OF3A_2-2-E5-O3


title: HctYH_OF3A_2-2-E5-O15


title: HctYH_OF3A_2-2-E5-N4


title: HctYH_OF3A_2-2-E5-N15


title: HctYH_OF3A_2-3-E5-B6


title: HctYH_OF3A_2-2-E5-N16


title: HctYH_OF3A_2-2-E5-M16


title: HctYH_OF3A_2-2-E5-O4


title: HctYH_OF3A_2-2-E5-M4


title: HctYH_OF3A_2-2-E5-M15


title: HctYH_OF3A_2-2-E5-M3


title: HctYH_OF3A_2-2-E5-L4


title: HctYH_OF3A_2-3-E5-A18


title: HctYH_OF3A_2-2-E5-L15


title: HctYH_OF3A_2-2-E5-L16


title: HctYH_OF3A_2-2-E5-K4


title: HctYH_OF3A_2-2-E5-K3


title: HctYH_OF3A_2-2-E5-K16


title: HctYH_OF3A_2-2-E5-J4


title: HctYH_OF3A_2-2-E5-K15


title: HctYH_OF3A_2-2-E5-J16


title: HctYH_OF3A_2-2-E5-J3


title: HctYH_OF3A_2-2-E5-J15


title: HctYH_OF3A_2-2-E5-O16


title: HctYH_OF3A_2-2-E5-I3


title: HctYH_OF3A_2-2-E5-I15


title: HctYH_OF3A_2-2-E5-H4


title: HctYH_OF3A_2-2-E5-I16


title: HctYH_OF3A_2-2-E5-I4


title: HctYH_OF3A_2-2-E5-F4


title: HctYH_OF3A_2-2-E5-L3


title: HctYH_OF3A_2-2-E5-G16


title: HctYH_OF3A_2-2-E5-H16


title: HctYH_OF3A_2-2-E5-H3


title: HctYH_OF3A_2-2-E5-F3


title: HctYH_OF3A_2-2-E5-H15


title: HctYH_OF3A_2-2-E5-G3


title: HctYH_OF3A_2-2-E5-F15


title: HctYH_OF3A_2-2-E5-G15


title: HctYH_OF3A_2-2-E5-F16


title: HctYH_OF3A_2-2-E5-E4


title: HctYH_OF3A_2-2-E5-G4


title: HctYH_OF3A_2-2-E5-E16


title: HctYH_OF3A_2-2-E5-E3


title: HctYH_OF3A_2-2-E5-D4


title: HctYH_OF3A_2-2-E5-E15


title: HctYH_OF3A_2-2-E5-D3


title: HctYH_OF3A_2-2-E5-C4


title: HctYH_OF3A_2-2-E5-C16


title: HctYH_OF3A_2-2-E5-C15


title: HctYH_OF3A_2-2-E5-B4


title: HctYH_OF3A_2-2-E5-A4


title: HctYH_OF3A_2-2-E5-B16


title: HctYH_OF3A_2-2-E5-C3


title: HctYH_OF3A_2-2-E5-B15


title: HctYH_OF3A_2-2-E5-B3


title: HctYH_OF3A_2-2-E5-A15


title: HctYH_OF3A_2-1-E5-P13


title: HctYH_OF3A_2-1-E5-O14


title: HctYH_OF3A_2-2-E5-A3


title: HctYH_OF3A_2-1-E5-P1


title: HctYH_OF3A_2-1-E5-P14


title: HctYH_OF3A_2-2-E5-A16


title: HctYH_OF3A_2-1-E5-P2


title: HctYH_OF3A_2-1-E5-O1


title: HctYH_OF3A_2-2-E5-D16


title: HctYH_OF3A_2-1-E5-N14


title: HctYH_OF3A_2-2-E5-D15


title: HctYH_OF3A_2-1-E5-N1


title: HctYH_OF3A_2-1-E5-N2


title: HctYH_OF3A_2-1-E5-M2


title: HctYH_OF3A_2-1-E5-M14


title: HctYH_OF3A_2-1-E5-M1


title: HctYH_OF3A_2-1-E5-N13


title: HctYH_OF3A_2-1-E5-M13


title: HctYH_OF3A_2-1-E5-L2


title: HctYH_OF3A_2-1-E5-L1


title: HctYH_OF3A_2-1-E5-L14


title: HctYH_OF3A_2-1-E5-L13


title: HctYH_OF3A_2-1-E5-O2


title: HctYH_OF3A_2-1-E5-K2


title: HctYH_OF3A_2-1-E5-O13


title: HctYH_OF3A_2-1-E5-K14


title: HctYH_OF3A_2-1-E5-K13


title: HctYH_OF3A_2-1-E5-J14


title: HctYH_OF3A_2-1-E5-J1


title: HctYH_OF3A_2-1-E5-J2


title: snRNA-seq, D. sechellia central brain (noni supplemented), biol rep4

city: Suwon

first: Daehan

last: Lee

state: Gyeonggi

address: 2066 Seobu-ro

country: South Korea

institute: Sungkyunkwan University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw snRNA-seq data was first processed through Cell Ranger (v6.0.1, default parameters except --include-introns)
Assembly: D. simulans reference genome and transcriptome from FlyBase (release 2.02)
Supplementary files format and content: TSV files and matrix files

molecule: total RNA

organism: Drosophila sechellia

source_name: central brain

growth_protocol: Standard fly growth medium

extract_protocol:
Newly-eclosed 30-50 male and female adult flies were collected and placed together for mating, followed by sorting by sex on day 5. The central brains of 20 mated female flies were dissected and collected in 100 μl Schneider’s medium, flash-frozen in liquid nitrogen, and stored at -80ºC for nuclear extraction. Sample homogenization, single-nucleus suspension, and nuclear sorting were performed using the standard protocol described in the Fly Cell Atlas (Li et al. 2022)
To obtain sequencing data from 10,000 nuclei, 15-20,000 nuclei were collected and loaded onto the Chromium Next GEM Chip (10x Genomics). Sequencing libraries were prepared with the Chromium Single Cell 3ʹ reagent kit v3.1 dual index, strictly following the manufacturer’s recommendations.

tag: tissue

value: central brain

tag: genotype

tag: treatment

value: noni-paste supplemented


title: snRNA-seq, D. sechellia central brain (noni supplemented), biol rep6

description: 10x Genomics


title: snRNA-seq, D. sechellia central brain (noni supplemented), biol rep5

description: 10x Genomics


title: snRNA-seq, D. sechellia central brain (noni supplemented), biol rep2

description: 10x Genomics


title: HctYH_OF3A_2-1-E5-I2


title: HctYH_OF3A_2-1-E5-J13


title: snRNA-seq, D. sechellia central brain (noni supplemented), biol rep1

description: 10x Genomics


title: HctYH_OF3A_2-1-E5-I1


title: HctYH_OF3A_2-1-E5-I14


title: HctYH_OF3A_2-1-E5-I13


title: snRNA-seq, D. sechellia central brain (standard food), biol rep5

description: 10x Genomics

value: standard fly food


title: HctYH_OF3A_2-1-E5-H2


title: snRNA-seq, D. sechellia central brain (standard food), biol rep3

description: 10x Genomics


title: HctYH_OF3A_2-1-E5-H1


title: snRNA-seq, D. sechellia central brain (standard food), biol rep4

description: 10x Genomics


title: HctYH_OF3A_2-1-E5-H14


title: HctYH_OF3A_2-1-E5-K1


title: snRNA-seq, D. sechellia central brain (standard food), biol rep1

description: 10x Genomics


title: HctYH_OF3A_2-1-E5-H13


title: HctYH_OF3A_2-1-E5-G2


title: snRNA-seq, D. sechellia central brain (standard food), biol rep6

description: 10x Genomics


title: snRNA-seq, D. sechellia central brain (noni supplemented), biol rep3

description: 10x Genomics


title: HctYH_OF3A_2-1-E5-G1


title: Anxa1 WT AP, (2)

city: Fuzhou

first: Changgan

last: Chen

state: Fujian

address: #29 Xinquan Road, Fuzhou 350001, People’s Republic of China

country: China

institute: Fujian Medical University Union Hospital

library_source: transcriptomic

data_processing:
GO enrichment of cluster markers were performed using KOBAS software with Benjamini-Hochberg multiple testing adjustment.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus musculus

source_name: Pancreas

extract_protocol:
Pancreas tissues were ground and lysed with TRIzol (Invitrogen), and total RNA was extracted with RNA Extraction Kit (Vazyme), according to the manufacturer’s protocol.
The libraries were sequenced using an Illumina Novaseq6000 sequencer.

value: Pancreas

value: Anxa1 flox/flox

value: repeated injection of cerulein


title: Anxa1 WT AP, (4)


title: Anxa1 WT AP, (1)


title: Anxa1 WT AP, (3)


title: HctYH_OF3A_2-1-E5-G14


title: Anxa1 CKO AP, (2)

value: myeloid-specific Anxa1-knockout


title: Anxa1 CKO AP, (3)


title: HctYH_OF3A_2-1-E5-F1


title: HctYH_OF3A_2-1-E5-F14


title: KO_DC_4

city: Zurich

first: Ganesh

last: Pathare

state: Zürich

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

data_processing:
In brief, amplified cDNA samples were subjected to different quality control standards. RNA sample was used for library preparation using NEB Next® Ultra RNA Library Prep Kit for Illumina®.
Indices were included to multiplex multiple samples. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis.
The library was ready after end repair, A-tailing, adapter ligation, and size selection. After amplification and purification, the insert size of the library was validated on an Agilent 2100 and quantified using quantitative qPCR.
. Libraries were then sequenced on Illumina NovaSeq 6000 S4 flow cell with PE150 according to results from library quality control and expected data volume.
Assembly: mm10
Supplementary files format and content: .xls files included raw counts for each sample

source_name: Kidney

growth_protocol: 2 months old C57Bl6 mice under chow diet and normal drinking water were randomely selected for the experiment.

extract_protocol:
RNA was isolated from DC cells using a Nucleospin kit
RNA sample was used for library preparation using NEB Next® Ultra RNA Library Prep Kit for Illumina®.

treatment_protocol: DC cells were sorted using COPAS

value: Kidney

value: KO


title: HctYH_OF3A_2-1-E5-F2


title: Anxa1 CKO AP, (4)


title: HctYH_OF3A_2-1-E5-G13


title: HctYH_OF3A_2-1-E5-F13


title: snRNA-seq, D. sechellia central brain (standard food), biol rep2

description: 10x Genomics


title: KO_DC_3


title: HctYH_OF3A_2-1-E5-E1


title: HctYH_OF3A_2-1-E5-E2


title: KO_DC_1


title: HctYH_OF3A_2-1-E5-E14


title: Ctrl_DC_4

value: Ctrl


title: HctYH_OF3A_2-1-E5-E13


title: HctYH_OF3A_2-1-E5-D2


title: Ctrl_DC_3


title: Ctrl_DC_2


title: Ctrl_DC_1


title: HctYH_OF3A_2-1-E5-D1


title: HctYH_OF3A_2-1-E5-D14


title: Anxa1 CKO AP, (1)


title: HctYH_OF3A_2-1-E5-C2


title: HctYH_OF3A_2-1-E5-D13


title: HctYH_OF3A_2-1-E5-C14


title: HctYH_OF3A_2-1-E5-B2


title: Eosinophil-5N

city: IOWA CITY

first: Julia

last: Klesney-Tait

state: Iowa

address: 451 Newton Rd

department: Internal Medicine

institute: University of Iowa

data_processing:
Sequencing results were converted to the FastQ file format by the University of Iowa Next Generation Sequencing Core. Raw sequencing reads were pseudo-aligned to mouse genome GRCm39 using kallisto version 0.45.0.
Raw counts were filtered per EdgeR default settings and library sizes normalized by trimmed mean of M values.
Differential gene expression analysis was performed using RStudio, R Version 4.3.0, and the EdgeR 3.42.4 quasi-likelihood F-test pipeline. The Benjamini-Hochberg procedure was used to correct for multiple comparisons.
Assembly: Mouse genome GRCm39
Supplementary files format and content: Matrix of log(CPM). Created using edgeR following library normalization with prior count = 1.
Supplementary files format and content: Matrix of raw counts.

source_name: Lung lavage

extract_protocol:
Sorted eosinophils were centrifuged and RNA isolated with the Qiagen RNeasy RNA isolation kit per manufacturer’s instructions. RNA quantity and quality were assessed using Qubit RNA quantification and electropherogram analysis.
cDNA libraries were generated with the Illumina Stranded Total RNA Prep Ligation w/ RiboZero Plus kit. The libraries were multiplexed and 100bp paired-end sequencing performed in one lane of a NovaSeq 6000 SP flow cell using the Illumina XP workflow.

treatment_protocol: 8–12-week-old mice were sensitized with 20ug ovalbumin (Sigma) and 4mg Imject Alum (Thermo) on days 0 and 7. Mice were then whole-body exposed to nebulized 1% ovalbumin on days 16-18 for 40 minutes utilizing a Hudson RCI Micro Mist nebulizer at a flow rate of 5.5 liters per minute. Mice were harvested on day 19 for analysis.

value: Lung lavage

tag: strain

tag: cell type

value: Eosinophil

value: WT

value: Sorted TREM-1-


title: Eosinophil-3T

value: Sorted TREM-1+


title: HctYH_OF3A_2-1-E5-C13

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: Eosinophil-6T


title: Eosinophil-6N


title: KO_DC_2


title: HctYH_OF3A_2-1-E5-B1

value: nuclear RNA + genomic DNA


title: Eosinophil-3N


title: Eosinophil-2N


title: Eosinophil-2T


title: HctYH_OF3A_2-1-E5-B13


title: Eosinophil-4T


title: Eosinophil-4N


title: Eosinophil-5T


title: HctYH_OF3A_2-1-E5-A1


title: HctYH_OF3A_2-1-E5-A2


title: Eosinophil-1T


title: Eosinophil-1N


title: Liver_Resveratrol16wk_triplicate3

city: Toronto

first: Tianru

last: Jin

state: Ontario

address: 101 college street

department: Advanced Diagnostics

country: Canada

institute: University Health Network

data_processing:
Data processing was performed using RNA-seq IMmune Analysis Pipeline (RIMA, Yang et al. Nat Protoc. 2023)
…
.
..
….
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes tpm for each sample
Supplementary files format and content: Comma-delimited text file includes tpm for all samples

source_name: Liver

growth_protocol: Mice were maintained at ambient room temperature and relative humidity of 50%, with free access to food and water under a 12 h light:12 h darkness cycle.

extract_protocol:
Total RNA was harvested using Rneasy Mini Kit (QIAGEN) and was quantified and analysed using Nanodrop spectrophotometer and Bioanalyzer. One µg of total RNA was used for the construction of sequencing libraries, with the service provided by Center for Applied Genomics (Sickkids Hospital, Canada)
Libraries were loaded onto Illumina NovaSeq SP flow cells and paired-end sequencing was performed on Illumina NovaSeq SP sequencing instruments.

treatment_protocol: Mice were either fed LFD, High fat (60% fat) and High Fructose (20%) diet or HFHF with Resveratrol (0.5% in diet)

value: Liver

value: Wildtype

value: High fat high fructose diet with Resveratrol


title: HctYH_OF3A_2-1-E5-A14


title: HctYH_OF3A_1-6-I3-P24


title: HctYH_OF3A_2-1-E5-A13


title: Liver_Resveratrol16wk_triplicate2


title: HctYH_OF3A_2-1-E5-C1


title: HctYH_OF3A_1-6-I3-P23


title: Liver_Resveratrol16wk_triplicate1


title: Liver_HFHF16wk_triplicate 3

value: High fat high fructose diet


title: Liver_HFHF16wk_triplicate 2


title: HctYH_OF3A_1-6-I3-P12


title: Liver_LFD16w_Duplicate2

value: Chow diet


title: Liver_LFD16w_Duplicate1


title: Liver_HFHF16wk_triplicate 1


title: HctYH_OF3A_1-6-I3-O24


title: HctYH_OF3A_1-6-I3-P11


title: HctYH_OF3A_2-1-E5-B14


title: HctYH_OF3A_1-6-I3-O23


title: P5-V2 Lesional

city: London

first: Luc

last: Francis

address: Guy's Hospital, Great Maze Pond

country: United Kingdom

institute: King's College London

data_processing:
Sequencing output files were demultiplexed and coverted to fastq files using Cell Ranger v4.0.0 to v6.1.1 (10X genomics).
Cell Ranger was used to align demultiplexed reads to the reference genome, barcode counting, UMI counting and estimate the number of cells.
Assembly: Reference Genome GRCH38-2020-A
Supplementary files format and content: For each sample there are three associated files: tab-seperated values file containing barcdoes, tab-separated file containing annotated genes (features), matrix file containing UMI counts and indices for the barcode and gene tsv files

source_name: Skin biopsy

extract_protocol:
Skin biopsies were separated into dermis and epidermis. Single cell dissociation was performed. An equal number of dermis and epidermis cells were collected for analysis.
Libraries were prepared using the Chromium 10X Single Cell 3' reagent Kit v2, according to the manufacturer's instructions

value: Skin biopsy

tag: disease state

value: Day 3 Lesional Psoriasis Skin


title: P5-V3 Lesional

value: Day 14 Lesional Psoriasis Skin


title: P5-V1 Lesional

value: Baseline Lesional Psoriasis Skin


title: liver, PC_P55WT + TNF, replicate3

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

data_processing:
checking read quality with fastqc v0.12.1 – no quality based preprocessing required
data were mapped with the STAR (2.7.10a) to the mouse reference genome/transcriptome (mm39/gencode v28) using default paremeters with following additions: --clip5pNbases 12 to remove a strong sequence bias at the 5’ end, --quantMode GeneCounts to obtain read counts per sample immediatly from STAR
per sample read couns were merged into a count matrix and further processed in R using the DESeq2 libary
Assembly: mm39
Supplementary files format and content: tab delimited text file with raw counts as obtained with STAR from each sample

source_name: liver

growth_protocol: mice were kept in an SPF animal house with ad libitum access to food and water

extract_protocol:
RNA was extracted using the Aurum™ Total RNA Mini Kit according to the manufacturers instructions. RNA was shipped to VIB nucleomics core for library preparation and sequencing
RNA-seq libraries were prepared using the illumina TruSeq Stranded mRNA kit using the manufacturers instructions

treatment_protocol: Mice were divided in P55 KO (P55fl/fl DefaCre/+) and matich wild type littermates (P55fl/fl +/+) and streated with TNF/PBS of 18 hours. The liver was isolated and stored in RNAlater

value: liver

value: PC P55 WT

tag: treatment 1

value: 18h TNF


title: HctYH_OF3A_1-6-I3-O11


title: P5-V1 Non Lesional

value: Baseline Non Lesional Psoriasis Skin


title: liver, PC_P55WT + TNF, replicate2


title: HctYH_OF3A_1-6-I3-N24


title: P4-V3 Lesional


title: HctYH_OF3A_1-6-I3-N23


title: P4-V1 Lesional


title: liver, PC_P55WT + TNF, replicate1


title: P4-V2 Lesional


title: liver, PC_P55WT + PBS, replicate4

value: 18h PBS


title: P3-V2 Lesional


title: HctYH_OF3A_1-6-I3-N12

value: Dorsolateral Prefrontal cortex (Brodmann area 46)


title: HctYH_OF3A_1-6-I3-N11

value: Female


title: P3-V1 Non Lesional


title: P3-V1 Lesional


title: HctYH_OF3A_1-6-I3-O12

value: nuclear RNA + genomic DNA


title: liver, PC_P55WT + TNF, replicate4


title: liver, PC_P55WT + PBS, replicate3


title: liver, PC_P55WT + PBS, replicate2


title: HctYH_OF3A_1-6-I3-M24


title: P2-V2 Lesional


title: P1-V3 Lesional


title: P2-V1 Lesional


title: HctYH_OF3A_1-6-I3-M12


title: HctYH_OF3A_1-6-I3-M23


title: P1-V1 Non Lesional


title: P1-V2 Lesional


title: P2-V1 Non Lesional


title: P4-V1 Non Lesional


title: HctYH_OF3A_1-6-I3-M11


title: liver, PC_P55KO + TNF, replicate3

value: PC P55 KO


title: HctYH_OF3A_1-6-I3-L24


title: liver, PC_P55KO + TNF, replicate2


title: liver, PC_P55KO + TNF, replicate4


title: liver, PC_P55KO + TNF, replicate1


title: liver, PC_P55WT + PBS, replicate1


title: HctYH_OF3A_1-6-I3-L23


title: HctYH_OF3A_1-6-I3-L12


title: liver, PC_P55KO + PBS, replicate3


title: P2-V3 Lesional


title: HctYH_OF3A_1-6-I3-L11


title: HctYH_OF3A_1-6-I3-K24


title: Paneth cells, P55WT + TNF, replicate4

source_name: small intestine

extract_protocol:
RNA was extracted using the RNeasy Plus Micro Kit according to the manufacturers instructions. RNA was shipped to VIB nucleomics core for library preparation and sequencing
RNA-seq libraries were prepared using the illumina TruSeq Stranded mRNA kit using the manufacturers instructions

treatment_protocol: Mice were divided in P55 KO (P55fl/fl DefaCre/+) and matich wild type littermates (P55fl/fl +/+) and streated with TNF/PBS of 3 hours. The small intestine was extracted and panetch cells were purified using FACS (markers c-KIT and Cd24a). RNA was then axtracted from the purified Pcs

value: small intestine

value: Paneth cells (FACS purified)

value: P55 WT

value: 3h TNF


title: liver, PC_P55KO + PBS, replicate1


title: Paneth cells, P55WT + TNF, replicate3


title: HctYH_OF3A_1-6-I3-K11


title: Paneth cells, P55WT + TNF, replicate2


title: HctYH_OF3A_1-6-I3-K12


title: Paneth cells, P55WT + TNF, replicate1


title: HctYH_OF3A_1-6-I3-J24


title: Paneth cells, P55WT + PBS, replicate4

value: 3h PBS


title: HctYH_OF3A_1-6-I3-J12


title: HctYH_OF3A_1-6-I3-J11


title: P3-V3 Lesional

value: Skin biopsy


title: HctYH_OF3A_1-6-I3-I24


title: Paneth cells, P55KO + TNF, replicate4

value: P55 KO


title: Paneth cells, P55WT + PBS, replicate1


title: Paneth cells, P55KO + TNF, replicate3


title: HctYH_OF3A_1-6-I3-I11


title: HctYH_OF3A_1-6-I3-I12


title: liver, PC_P55KO + PBS, replicate2


title: HctYH_OF3A_1-6-I3-H24


title: Paneth cells, P55KO + TNF, replicate2


title: HctYH_OF3A_1-6-I3-H23


title: Paneth cells, P55KO + PBS, replicate4


title: Paneth cells, P55KO + TNF, replicate1


title: Paneth cells, P55KO + PBS, replicate3


title: HctYH_OF3A_1-6-I3-J23


title: Paneth cells, P55WT + PBS, replicate2


title: HctYH_OF3A_1-6-I3-H12


title: Paneth cells, P55KO + PBS, replicate1


title: Paneth cells, P55WT + PBS, replicate3


title: Paneth cells, P55KO + PBS, replicate2


title: HctYH_OF3A_1-6-I3-G24


title: HctYH_OF3A_1-6-I3-H11


title: HctYH_OF3A_1-6-I3-G23


title: Tfap2c_mzKO_8C_ATAC_rep2

city: Beijing

first: Lijia

last: Li

address: Haidian District

department: School of Life Science

institute: Tsinghua University

data_processing:
CUT&RUN reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
Assembly: mm9
Supplementary files format and content: Bigwig for CUT&RUN, ATAC-seq, ChIP-seq tracks, gene expression table for RNA-seq data

growth_protocol: Embryos were collected from mice induced to superovulation by injections of 5 IU of pregnant mare's serum gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) and 5 IU of human chorionic gonadotrophin (Ningbo Sansheng Pharmaceutical Co, Ltd) 44-48 hours

extract_protocol:
Cells or embyos were lysed in lysis buffer.
The ATAC-seq procedure was performed as previously described (Wu et al. 2018). Briefly, cells were transferred into 6 μl of lysis buffer [10 mM tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, and 0.02% digitonin) in ice for 10 min. The ATAC reaction was performed by adding 4 μl of ddH2O, 4 μl of 5× TTBL, and 5 μl TTE mix V5 (Vazyme Biotech Co.,Ltd, catalog no. TD502) at 37°C for 30 min and then stopped by adding 5 μl of 5× TS stop buffer at room temperature for 5 min. DNA was extracted by phenol chloroform and ethanol purification after adding 40 ng of carrier RNA and 103 μl of tris-EDTA. Then, DNA was PCR-amplified with 10 μl of index (Vazyme Biotech Co.,Ltd, catalog no. TD202), 10 μl of 5× TAB and 1 μl tris-acetate-EDTA (Vazyme Biotech Co.,Ltd, catalog no. TD502) with the program of 72°C for 3 min, 98°C for 30 s, (98°C for 15 s, 60°C for 30 s, and 72°C for 3 min) with 18 cycles, and 72°C for 5 min.

value: mix

tag: chip-antibody


title: Tfap2c_control_8C_ATAC_rep2

value: Tfap2c control


title: HctYH_OF3A_1-6-I3-G11


title: HctYH_OF3A_1-6-I3-I23


title: HctYH_OF3A_1-6-I3-G12


title: Tfap2c_mzKO_8C_ATAC_rep1

data_processing:
Assembly: mm9
Supplementary files format and content: Bigwig for CUT&RUN, ATAC-seq, ChIP-seq tracks, gene expression table for RNA-seq data


title: HctYH_OF3A_1-6-I3-F24


title: HctYH_OF3A_1-6-I3-F23


title: Tfap2c_control_8C_ATAC_rep1

data_processing:
bulk RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). scRNA-seq reads were mapped to mm9 genome by HISAT2 (version 2.1.0).The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
CUT&RUN reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
Assembly: mm9
Supplementary files format and content: Bigwig for CUT&RUN, ATAC-seq, ChIP-seq tracks, gene expression table for RNA-seq data


title: Sox2FKBP_D3_EpiLC_dTAGv_OE_Zic3_RNA_rep2

data_processing:
ChIP-seq reads were mapped to the mm9 reference genome using Bowtie2 with parameters -t -q -N 1 -L 25. All ummapped reads, non-uniqurely mapped reads and PCR duplicates were removed. For downstream analysis, we computed the numbers of reads per kilobase of bin per million reads sequenced (RPKM) which were further normalized by input. A resolution of 100bp bin in genome was used in the rpkm file.
bulk RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). scRNA-seq reads were mapped to mm9 genome by HISAT2 (version 2.1.0).The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
CUT&RUN reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
Assembly: mm9
Supplementary files format and content: Bigwig for CUT&RUN, ATAC-seq, ChIP-seq tracks, gene expression table for RNA-seq data

source_name: mESC-derived D3 EpiLC

growth_protocol: 2i ESC cells were plated on TC dishes pretreated with 1:100 matrigel in N2B27-based medium supplemented with 1% KSR (Invitrogen), 12 mg/ml bFGF (Peprotech) and 20 ng/ml Activin A (R&D Scientific) was added to induce EpiLCs.

extract_protocol:
Cells or embyos were lysed in lysis buffer containing RNase inhibitor.
The Smart-seq2 libraries of embryos were prepared as previously described (Picelli et al., 2014). Embryos were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before being subjected to sequencing.


title: HctYH_OF3A_1-6-I3-F12


title: Sox2FKBP_D3_EpiLC_dTAGv_OE_Otx2_RNA_rep2


title: HctYH_OF3A_1-6-I3-F11


title: HctYH_OF3A_1-6-I3-K23


title: HctYH_OF3A_1-6-I3-E24


title: Sox2FKBP_D0_EpiLC_dTAGv_OE_RNA_rep2

source_name: mESC-derived D1 EpiLC


title: Sox2FKBP_D3_EpiLC_DMSO_OE_Zic3_RNA_rep2


title: HctYH_OF3A_1-6-I3-E23


title: HctYH_OF3A_1-6-I3-E12


title: Sox2FKBP_D3_EpiLC_DMSO_OE_Otx2_RNA_rep2

source_name: mESC-derived D2 EpiLC


title: HctYH_OF3A_1-6-I3-D23


title: Sox2FKBP_D0_EpiLC_DMSO_OE_RNA_rep2

source_name: mESC-derived D0 EpiLC


title: HctYH_OF3A_1-6-I3-D12


title: Sox2FKBP_D3_EpiLC_DMSO_OE_mCherry_RNA_rep2

extract_protocol:
Cells or embyos were lysed in lysis buffer.
The Smart-seq2 libraries of embryos were prepared as previously described (Picelli et al., 2014). Embryos were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before being subjected to sequencing.


title: Sox2FKBP_D3_EpiLC_dTAGv_OE_mCherry_RNA_rep1


title: Sox2FKBP_D3_EpiLC_dTAGv_OE_Zic3_RNA_rep1


title: HctYH_OF3A_1-6-I3-D11


title: HctYH_OF3A_1-6-I3-E11


title: Sox2FKBP_D0_EpiLC_dTAGv_OE_RNA_rep1


title: HctYH_OF3A_1-6-I3-D24


title: HctYH_OF3A_1-6-I3-C23


title: HctYH_OF3A_1-6-I3-C24


title: HctYH_OF3A_1-6-I3-C12


title: Sox2FKBP_D3_EpiLC_DMSO_OE_Zic3_RNA_rep1


title: Sox2FKBP_D3_EpiLC_DMSO_OE_Otx2_RNA_rep1


title: Sox2FKBP_D3_EpiLC_dTAGv_OE_mCherry_RNA_rep2


title: HctYH_OF3A_1-6-I3-B24


title: HctYH_OF3A_1-6-I3-B23


title: Sox2_mzKO_E45ICM_ATAC_rep1

source_name: E4.5 ICM

growth_protocol: For collection of wildtypes E4.5 ICM, 4–6-week-old C57BL/6J female mice were injected with pregnant mare serum gonadotropin followed by human chorionic gonadotropin (hCG; Ningbo Hormone Product Co., Cat # 110251283 Ltd., China 10 IU) 48 hours before being mated with PWK/PhJ mice. Fertilized 8 cell were flushed out from the oviduct with HEPES-buffered CZB medium at E2.5 (68-70h). In vitro cultured was carried out for one day with the 8-cell embryo in KSOM medium to get blastocyst.


title: HctYH_OF3A_1-6-I3-B12


title: Sox2_control_E45ICM_ATAC_rep1

value: Sox2 control


title: HctYH_OF3A_1-6-I3-B11


title: HctYH_OF3A_1-6-I3-A24


title: Sox2FKBP_D3_EpiLC_dTAGv_OE_Otx2_RNA_rep1


title: Sox2_control_E35ICM_ATAC_rep2

source_name: E3.5 ICM

growth_protocol: For collection of wildtypes E3.5 ICM, 4–6-week-old C57BL/6J female mice were injected with pregnant mare serum gonadotropin followed by human chorionic gonadotropin (hCG; Ningbo Hormone Product Co., Cat # 110251283 Ltd., China 10 IU) 48 hours before being䇦얿䇦䇦䇦얿鍖鍖鍠骟ᴠᴠᴠᴠ


title: HctYH_OF3A_1-6-I3-A12


title: Sox2_mzKO_E35ICM_ATAC_rep1

growth_protocol: For collection of wildtypes E3.5 ICM, 4–6-week-old C57BL/6J female mice were injected with pregnant mare serum gonadotropin followed by human chorionic gonadotropin (hCG; Ningbo Hormone Product Co., Cat # 110251283 Ltd., China 10 IU) 48 hours before being mated with PWK/PhJ mice. Fertilized 8 cell were flushed out from the oviduct with HEPES-buffered CZB medium at E2.5 (68-70h). In vitro cultured was carried out for one day with the 8-cell embryo in KSOM medium to get blastocyst.


title: Sox2_control_E35ICM_ATAC_rep1


title: HctYH_OF3A_1-5-I3-P9


title: HctYH_OF3A_1-5-I3-P22


title: Sox2FKBP_D3_EpiLC_DMSO_OE_mCherry_RNA_rep1


title: HctYH_OF3A_1-5-I3-P21


title: E45_Epi_SOX2_CR_rep2

data_processing:
ChIP-seq reads were mapped to the mm9 reference genome using Bowtie2 with parameters -t -q -N 1 -L 25. All ummapped reads, non-uniqurely mapped reads and PCR duplicates were removed. For downstream analysis, we computed the numbers of reads per kilobase of bin per million reads sequenced (RPKM) which were further normalized by input. A resolution of 100bp bin in genome was used in the rpkm file.
bulk RNA-seq reads were mapped to the mm9 reference genome using Tophat (version 2.0.11). scRNA-seq reads were mapped to mm9 genome by HISAT2 (version 2.1.0).The gene expression levels were calculated by Cufflinks (version 2.2.1). RefFlat database from UCSC genome browser was used with microRNA and repeats excluded.
CUT&RUN reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
Assembly: mm9
Supplementary files format and content: Bigwig for CUT&RUN, ATAC-seq, ChIP-seq tracks, gene expression table for RNA-seq data
Library strategy: CUT&RUN

extract_protocol:
Cells or embyos were lysed in wash buffer.
CUT&RUN was performed as previously reported (Skene et al., 2018; Skene and Henikoff, 2017) with modifications. Briefly, after removing the zona pellucida with Tyrode’s solution (Sigma-Aldrich, T1788) or 0.5% (m/v) Protease from Streptomyces griseus (Sigma-Aldrich, P8811), early embryos were incubated with Concanavalin-coated magnetic beads (Polyscience, 86057) for 10 min at room temperature on a thermomixer at 400 rpm. Samples were then incubated with primary antibody at a ratio of 1:100 at 4℃ for 3-5 hours on a thermomixer at 400 rpm. After washing for one time, beads were incubated with pA-MNase (to a final concentration of 400-700ng/mL) (a gift from Steven Henikoff lab) at 4℃ for 1 hours on a thermomixer at 400 rpm. After two times of washing, targeted digestion was performed by adding 2μL of 100mM CaCl2 for 30 mins on ice, followed by termination by adding an equal volume of 2  × stop buffer. Samples were then incubated at 37℃ for 20 mins for fragment releasing. The total samples or supernatants were digested with Proteinase K (NEB, P8107S) and purified using phenol:chloroform:isoamyl alcohol (25:24:1, v/v) followed by ethanol purification at -80℃ overnight. The next day, DNA was purified and subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Sequencing was done using the HiSeq X Ten system or  NovaSeq (Illumina) according to the manufacturer’s protocol.

value: wild type

value: C57BL/13J x  PWK/PhJ

value: Sox2 (Abclonal, A11936)


title: E45_Epi_SOX2_CR_rep1

value: C57BL/12J x  PWK/PhJ


title: HctYH_OF3A_1-5-I3-P10

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: HctYH_OF3A_1-5-I3-O9

value: nuclear RNA + genomic DNA


title: HctYH_OF3A_1-6-I3-C11


title: Sox2FKBP_D0_EpiLC_DMSO_OE_RNA_rep1


title: HctYH_OF3A_1-5-I3-O21


title: HctYH_OF3A_1-5-I3-O10


title: HctYH_OF3A_1-5-I3-N9


title: HctYH_OF3A_1-5-I3-N21


title: Sox2_mzKO_E35ICM_ATAC_rep2


title: HctYH_OF3A_1-5-I3-N22


title: HctYH_OF3A_1-5-I3-N10


title: HctYH_OF3A_1-5-I3-M9


title: HctYH_OF3A_1-6-I3-A23


title: HctYH_OF3A_1-5-I3-M21


title: HctYH_OF3A_1-5-I3-L9


title: HctYH_OF3A_1-5-I3-L22


title: HctYH_OF3A_1-5-I3-M10


title: HctYH_OF3A_1-6-I3-A11


title: HctYH_OF3A_1-5-I3-L21


title: HctYH_OF3A_1-5-I3-L10


title: HctYH_OF3A_1-5-I3-O22


title: HctYH_OF3A_1-5-I3-K9


title: HctYH_OF3A_1-5-I3-K22


title: HctYH_OF3A_1-5-I3-K21


title: HctYH_OF3A_1-5-I3-I22


title: HctYH_OF3A_1-5-I3-I21


title: HctYH_OF3A_1-5-I3-I9


title: HctYH_OF3A_1-5-I3-J10


title: HctYH_OF3A_1-5-I3-K10


title: HctYH_OF3A_1-5-I3-J9


title: HctYH_OF3A_1-5-I3-I10


title: HctYH_OF3A_1-5-I3-J21


title: HctYH_OF3A_1-5-I3-H22


title: HctYH_OF3A_1-5-I3-H9


title: HctYH_OF3A_1-5-I3-M22


title: HctYH_OF3A_1-5-I3-H21


title: HctYH_OF3A_1-5-I3-H10


title: HctYH_OF3A_1-5-I3-G9


title: HctYH_OF3A_1-5-I3-G22


title: HctYH_OF3A_1-5-I3-G21


title: HctYH_OF3A_1-5-I3-G10


title: HctYH_OF3A_1-5-I3-F22


title: HctYH_OF3A_1-5-I3-E22


title: HctYH_OF3A_1-5-I3-E9


title: HctYH_OF3A_1-5-I3-F9


title: HctYH_OF3A_1-5-I3-E21


title: HctYH_OF3A_1-5-I3-E10


title: HctYH_OF3A_1-5-I3-J22


title: HctYH_OF3A_1-5-I3-F21


title: HctYH_OF3A_1-5-I3-D9


title: HctYH_OF3A_1-5-I3-D22


title: HctYH_OF3A_1-5-I3-D10


title: HctYH_OF3A_1-5-I3-D21


title: P1-V1 Lesional

value: Baseline Lesional Psoriasis Skin


title: HctYH_OF3A_1-5-I3-C9


title: HctYH_OF3A_1-5-I3-C10


title: Intestine_10Gy_rep4

type: RNA

city: Hirosaki

first: Mitsuru

last: Chiba

state: Aomori

address: 66-1 Hon-cho

department: Graduate School of Health Sciences

country: Japan

institute: Hirosaki University

description: exposed to 10 Gy of X-rays

hyb_protocol: SurePrint G3 mouse miRNA microarray slides (8 × 60 K, Ver.21.0) were hybridized with the Cy3-labeled miRNA in a hybridization solution prepared with a Gene Expression Hybridization Kit (Agilent Technologies) for 20 hours at 55°C in a rotating hybridization oven (Agilent Technologies), according to the manufacturer’s instructions. After hybridization, microarray slides were washed for 5 min at room temperature with GE Wash Buffer 1 (Agilent Technologies) and for 5 min at 37°C with GE Wash buffer 2 (Agilent Technologies), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarray Scanner (G4900DA) (Agilent Technologies) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 2 μm high sensitivity, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5 (Agilent Technologies) using default parameters (Protocol name: miRNA_1105_Oct12 and Grid name: 070155_D_F_20141006) to obtain background subtracted and spatially detrended Processed Signal intensities. The expression data obtained were processed using the GeneSpring GX14.5 software (Agilent Technologies) to normalize all values to 90% percentile shift on the respective microarrays, followed by normalization of the median expression level of all samples. The increase and decrease of more than 2.0-fold miRNAs at 10 Gy against 0 Gy were selected.

source_name: Intestine

label_protocol: Cyanine 3(Cy3)-labeled miRNAs were synthesized from total RNA of irradiated (10 Gy) and non-irradiated (0 Gy) samples (small intestine, serum and feces) using a miRNA Complete Labeling Reagent and Hyb kit (Agilent Technologies)., according to the manufacturer’s instructions.

extract_protocol: Total RNAs from the small intestine, serum, and feces were extracted using the Isogen II reagent and ethachinmate (Nippongene,) according to the manufacturer’s instructions. RNA concentration from the small intestine was assessed using the NanoDrop spectrophotometer (NanoDrop Technologies). RNA samples had 260/280 nm absorbance ratios of 1.8–2.0. RNA concentration of serum and feces was measured using a Quant-iT RiboGreen RNA Reagent and kit (Thermo Fisher Scientific) and Fluoroskan Ascent (Thermo Fisher Scientific) according to manufacturer’s instructions. The quality of total RNAs was confirmed using Agilent 2100 Bioanalyzer and Agilent RNA 6000 Pico kit (both Agilent Technologies), according to the manufacturer’s instructions.

treatment_protocol: Eight-week-old mice were exposed to X-rays (MBR-1520R-3 X-ray machine, Hitachi Medical Corporation) at a dose rate of 1.0 Gy/min (150 kVp, 20 mA, 0.5 mm aluminum and 0.3 mm copper filters). Blood obtained from the heart was collected in BD Microtainer tubes with serum separator additive BD Microgard closure (Becton Dickinson Biosciences). Blood was then centrifuged at 6000 × G at room temperature for 3 min, and serum was collected. Feces were directly collected in tubes. Small intestines were collected and stored at -80°C before use.

tag: gender

value: male

value: 8 weeks


title: Intestine_10Gy_rep2

description: exposed to 10 Gy of X-rays


title: Intestine_10Gy_rep1

description: exposed to 10 Gy of X-rays


title: Intestine_0Gy_rep4

description: exposed to 0 Gy of X-rays


title: Intestine_0Gy_rep3

description: exposed to 0 Gy of X-rays


title: HctYH_OF3A_1-5-I3-B9


title: Serum_10Gy_rep4

description: exposed to 10 Gy of X-rays

source_name: Serum


title: Intestine_0Gy_rep1

description: exposed to 0 Gy of X-rays


title: HctYH_OF3A_1-5-I3-C21

source_name: OF3A human BA46


title: Serum_10Gy_rep2

description: exposed to 10 Gy of X-rays


title: Serum_0Gy_rep1

description: exposed to 0 Gy of X-rays


title: Intestine_10Gy_rep3

description: exposed to 10 Gy of X-rays


title: Feces_10Gy_rep2

description: exposed to 10 Gy of X-rays

source_name: Feces


title: Serum_10Gy_rep3

description: exposed to 10 Gy of X-rays


title: Serum_10Gy_rep1

description: exposed to 10 Gy of X-rays


title: HctYH_OF3A_1-5-I3-B22


title: Feces_10Gy_rep3

description: exposed to 10 Gy of X-rays


title: Intestine_0Gy_rep2

description: exposed to 0 Gy of X-rays


title: Feces_0Gy_rep3

description: exposed to 0 Gy of X-rays


title: Serum_0Gy_rep2

description: exposed to 0 Gy of X-rays


title: Feces_0Gy_rep4

description: exposed to 0 Gy of X-rays


title: Feces_10Gy_rep4

description: exposed to 10 Gy of X-rays


title: HctYH_OF3A_1-5-I3-C22


title: 39db/db-Female-5

city: Tuskegee

first: Sunila

last: Mahavadi

state: Alabama

address: 1200 W. Montgomery Rd, Carver Research Building, Room #1

department: Biology

institute: Tuskegee University

data_processing:
*library strategy: Targeted bisulfite Seq
MiSeq Control Software, MiSeq Reporter Software, Bismark
Low quality nucleotides and adapter sequences were trimmed off during analysis QC MiSeq Reporter Software
Sequence reads were aligned back to the reference genome using Bismark. Index files were constructed using the bismark_genome_preparation command and the entire reference genome. The non-directional parameter was applied while running Bismark. All other parameters were set to default.
Nucleotides and amplicons were trimmed off during methylation calling. The methylation level of each sampled cytosine was estimated as the number of reporting a C, divided by the total number or reads reporting C or T.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files includes raw counts for each sample

source_name: Colon

extract_protocol:
The DNA was extracted and the samples were bisulfite converted by using EZ DNA Methylation-Lightning ™ Kit according to manufacturer's instructions. The samples were pooled, purified using DNA Clean & Concentration ™ Kit.
DNA methylation was assessed by EZ DNA Methylation-Lighning ™ Kit (Zymo Research, D5030), according to the manufacturer's instruction.

value: Colon

value: db/db (Type II)


title: HctYH_OF3A_1-5-I3-B21


title: Feces_10Gy_rep1

description: exposed to 10 Gy of X-rays


title: 40db/db-Female-6


title: HctYH_OF3A_1-5-I3-A9


title: 37db/db-Female-3


title: 38db/db-Female-4


title: HctYH_OF3A_1-5-I3-A22


title: 36db/db-Female-2


title: HctYH_OF3A_1-5-I3-B10


title: 34db/db-Female-6

source_name: Stomach

value: Stomach


title: 31db/db-Female-3


title: 33db/db-Female-5


title: Feces_0Gy_rep1

description: exposed to 0 Gy of X-rays


title: HctYH_OF3A_1-4-I3-P8


title: HctYH_OF3A_1-5-I3-A10


title: 32db/db-Female-4


title: HctYH_OF3A_1-5-I3-A21


title: Feces_0Gy_rep2

description: exposed to 0 Gy of X-rays


title: 30db/db-Female-2


title: 27WT-Female-3

value: Wild-type


title: HctYH_OF3A_1-4-I3-P7


title: 25WT-Female-1


title: 26WT-Female-2


title: HctYH_OF3A_1-4-I3-P20


title: 23WT-Female-3


title: 24WT-Female-4


title: 35db/db-Female-1


title: 22WT-Female-2


title: 21WT-Female-1


title: HctYH_OF3A_1-4-I3-P19


title: 19db/db-Male-4


title: HctYH_OF3A_1-4-I3-O8


title: 18db/db-Male-3


title: 20db/db-Male-5


title: 16db/db-Male-1


title: 28WT-Female-4


title: 13db/db-Male-3


title: 11db/db-Male-1


title: 12db/db-Male-2


title: 17db/db-Male-2


title: HctYH_OF3A_1-4-I3-O20


title: HctYH_OF3A_1-4-I3-O19


title: HctYH_OF3A_1-4-I3-N7


title: HctYH_OF3A_1-4-I3-N8


title: 10WT-Male-5


title: 29db/db-Female-1


title: 8WT-Male-3


title: 14db/db-Male-4


title: HctYH_OF3A_1-4-I3-N20


title: HctYH_OF3A_1-4-I3-O7


title: 6WT-Male-1


title: 9WT-Male-4


title: 15db/db-Male-5


title: 4WT-Male-4

source_name: stomach

value: stomach


title: Sorted CD45+TER119- Kaede-red cells from tumour-draining LN, isotype control treated tumours

city: Cambridge

first: Colin

middle: YC

address: Wellcome Genome Campus, Hinxton

institute: Molecular Immunity Unit

description: 10x Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x CellRanger software v6.1.2 according to the manufacturer's workflow.
Assembly: mm10
Supplementary files format and content: 10x Genomics CellRanger output: Tab-separated values files and matrix files

growth_protocol: 2.5e5 cells were subcutaneously injected into the pre-shaved left frank area of transgenic Kaede C57BL/6 mice under anaesthesia. Tumours were photoconverted on day 13. Mice were sacrificed on day 15.

extract_protocol:
Tumours were cut into small pieces using surgical scissors then digested using Miltenyi Biotec Tumour Dissociation Kit using a gentleMACS Dissociator for 40 minutes at 37C, as per manufacturer's protocol. Subsequently, the sample was filtered through a 70 μm strainer to remove undigested tissue debris. Next, using Miltenyi Biotech Dead Cell Removal Kit and LS Columns, as per manufacturer's instructions, dead cells were removed from samples. Lymph nodes were cleaned and dissected in RPMI 1640 medium and crushed through a 70 μm strainer. Thereafter, cells were stained for surface markers and LIVE/DEAD viability dye before being centrifuged at 400 g at 4°C for 5 min and resuspended in FACS staining buffer for sorting (BD FACS Aria II Cell Sorter).
Gene expression libraries from were prepared from FACS-sorted populations of single cells using the Chromium Controller and Single Cell 3’ Reagent Kits v3 (10x genomics, Inc.) according to the manufacturer’s protocol. The resulting sequencing libraries comprised of standard Illumina paired-end constructs flanked with P5 and P7 sequences. The 16 bp 10x barcode and 10 bp UMI were encoded in read 1, while read 2 was used to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read.
scRNA-seq, 10x Genomics Chromium GEM 3' v3; 2 x 150bp paired-end sequencing performed on NovaSeq 6000 (Illumina)

treatment_protocol: Anti-PD-L1 mouse IgG1 (Clone 80, SP16-260; AstraZeneca) or NIP228 isotype control mouse IgG1 (SP16-017; Astra Zeneca) were administered on day 7, 10, and 13 after tumour injection by intraperitoneal injection. Each dose consisted of 100 ug antibodies diluted in 200 uL PBS (10 mg/kg bw).

value: Tumour-draining lymph node

tag: cell line

value: MC38-Ova tumours

value: CD45+ cells

value: WT C57BL/6 Kaede

value: Isotype control


title: Sorted Kaede-red myeloid cells, anti-PD-L1 treated tumours

description: 10x Genomics

value: Subcutaneous tumour

value: Myeloid cells

value: Anti-PD-L1 treated


title: HctYH_OF3A_1-4-I3-N19

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female

value: nuclear RNA + genomic DNA


title: 7WT-Male-2


title: HctYH_OF3A_1-4-I3-M7


title: 5WT-Male-5


title: 3WT-Male-3


title: NonTControlLN

description: 10x Genomics

source_name: Sorted Kaede+TER119-CD11c+B220-, Kaede+TER119-CD11c-B220+, and Kaede+TER119-CD11c-B220- cell mixture at 1:1:1 ratio, from control LN, no tumour

value: Control lymph node

value: Immune cells


title: 2WT-Male-2


title: Sorted Kaede-red myeloid cells, isotype control treated tumours

description: 10x Genomics


title: 1WT-Male-1


title: IPSC-CM+KDM5-C70-3 (RNA-seq)

city: Houston

first: Priyatansh

last: Gurha

state: Texas

address: 6770 Bertner Ave

department: School of Medicine

institute: UTHealth

data_processing:
FASTQC was used for the quality control check.
DESeq2 was used to identify differentially expressed genes.
Assembly: human genome build Hg38
Supplementary files format and content: text file with raw gene read counts

source_name: iPSC

growth_protocol: mTeSR1 medium (STEMCELL Technologies, catalog # 85850) in a six-well dish coated with 300µg/ml Matrigel

extract_protocol:
RNA was isolated using qiagen RNA easy kit
Strand-specific ribosomal RNA depleted sequencing libraries were generated using TruSeq stranded total RNA library preparation kit . The libraries were sequenced on  NextSeq500 instrument with  High Output 75nt PE sequencing
Ribosomal RNA depleted Total RNA seq  (Paired end)

treatment_protocol: After differentiation, iPSC-CMs were maintained in RPMI/B27+ medium . Twenty four hours later, cells were treated a pan-KDM5 inhibitor KDM5-C70

value: iPSC

value: induced pluripotent stem cells


title: IPSC-CM+KDM5-C70-2 (RNA-seq)


title: Sorted Kaede-green myeloid cells, anti-PD-L1 treated tumours

description: 10x Genomics


title: IPSC-CM+KDM5-C70-1 (RNA-seq)


title: HctYH_OF3A_1-4-I3-M20

data_processing:
Reads trimmed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted hg38 reference genome using Hisat-3n.
The raw BAM files were filtered using samtools to keep only uniquely mapped reads and use Picard to remove PCR duplicates.
From the filtered BAM file, DNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction < 0.5, selected reads will be processed by ALLCools package to produce ALLC files (allcools allc-to-bam function). The ALLC files are Tab-delimited files describing the quantity of unmethylated and methylated cytosine base calls.
Trimmed reads will also be mapped by Hisat2 to map to hg38 reference genome with GENCODE human v37 gene annotation. RNA reads are selected by read-level mCH base coverage >= 3 and read-level mCH fraction > 0.9, selected reads will be processed by featureCount to quantify gene level (exon + intron) RNA counts.
Assembly: hg38
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.
Library strategy: snmCT-seq

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


title: IPSC-CM+DMSO3 (RNA-seq)

value: DMSO


title: IPSC-CM+DMSO2 (RNA-seq)


title: HctYH_OF3A_1-4-I3-M19


title: TGFb48h_rep3, iCLIP

city: Seville

first: Jose

middle: Antonio

last: Guerrero-Martinez

state: Seville

address: Av. Americo Vespucio, N 24

department: Genome Biology

country: Spain

institute: CABIMER

data_processing:
RNA-Seq data were primarily filtered using the FASTQ Toolkit v1.0.0 program
Data were aligned using STAR  software, to map reads to the mm9 mouse reference genome, specifying strand information as reverse ®
BigWig files was generated using bamCoverage command from deeptools
Assembly: mm9 mouse reference genome
Supplementary files format and content: BigWig files

source_name: NMuMG

growth_protocol: Normal murine mammary gland NMuMG epithelial cells were cultured in Dulbecco's modified Eagle's medium containing 10% serum and 10 μg/ml insulin, until reaching 70–80% confluency

extract_protocol:
Individual Crosslinking Immunoprecipitation (iCLIP) technique identifies protein-RNA crosslink sites on a genome wide scale. iCLIP starts with ultraviolet (UV) irradiation followed by cell lysis and partial RNase digestion. Then, the complexes are purified using a specific antibody and an adaptor is ligated to the co-purified RNAs. The complexes are run on an SDS-PAGE and transferred to a nitrocellulose membrana.
Proteinase K digestion is applied to extract the crosslinked RNAs. RNAs are reverse transcribed. The resulting cDNA are size-selected and circularized. Finally, the iCLIP library is done by high-throghput sequencing.

treatment_protocol: For TGFβ treatment, cells were treated with 5 ng/ml TGFβ1 diluted in 4 mM HCl, 1 mg/ml BSA (240-B, R&D Systems) for the indicated time; or 4 mM HCl 1 mg/ml BSA as control.

value: NMuMG

value: TGFb for 48h

tag: tissue origin

value: mammary gland

value: glandular epithelial cells

tag: iclip antibody


title: HctYH_OF3A_1-4-I3-L7


title: HctYH_OF3A_1-4-I3-L8


title: TGFb48h_rep2, iCLIP


title: IPSC-CM+DMSO1 (RNA-seq)


title: IPSC-CM3 (RNA-seq)


title: IPSC-CM2 (RNA-seq)


title: HctYH_OF3A_1-4-I3-L20


title: IPSC-CM1 (RNA-seq)


title: HctYH_OF3A_1-4-I3-M8


title: TGFb48h_rep1, iCLIP


title: HctYH_OF3A_1-4-I3-L19


title: HctYH_OF3A_1-4-I3-K8


title: TGFb4h_rep2, iCLIP

value: TGFb for 4h


title: IPSC-CM-3 (Cut&Run)

data_processing:
SEACR for peak calling35. Consensus peaks from all samples were determined with minimum overlap set of 2 and differential expression of peak counts was performed using Diffbind (summit size 500bp) on local galaxy instance
human genome build Hg38
bed file
Library strategy: CUT&RUN

extract_protocol:
The CUT-and-RUN assay was performed at a MD anderson Core laboratory . Briefly, ~500,000 untreated and KDM5-C70 treated iPSC-CMs were harvested, washed, and attached to activated Concanavalin A-coated magnetic beads, then permeabilized with wash buffer containing 0.05% digitonin.
Then cells were incubated with an H3K4me3 antibody, the protein-DNA complex was precipitated, and the DNA was released, purified and used to generate libraries using NEB Ultra II Library prep kit following manufacturer’s instructions. Size distribution of the libraries was determined using the Agilent 4200 TapeStation and libraries were multiplexed to achieve uniform representation.
FASTQC was used for the quality control check.

treatment_protocol: After differentiation, iPSC-CMs were maintained in  RPMI/B27+ medium . Twenty four hours later, cells were treated with a series of concentrations of pan-KDM5 inhibitor KDM5-C70


title: IPSC-CM-2 (Cut&Run)


title: IPSC-CM-4 (Cut&Run)


title: TGFb4h_rep3, iCLIP


title: IPSC-CM-1 (Cut&Run)


title: IPSC-CM+KDM5-C70-4 (Cut&Run)


title: TGFb4h_rep1, iCLIP


title: IPSC-CM+KDM5-C70-3 (Cut&Run)


title: HctYH_OF3A_1-4-I3-K7


title: IPSC-CM+KDM5-C70-2 (Cut&Run)


title: HctYH_OF3A_1-4-I3-K20


title: IPSC-CM+KDM5-C70-1 (Cut&Run)


title: control_rep3, iCLIP

value: Control cells


title: Sorted Kaede-green myeloid cells, isotype control treated tumours

description: 10x Genomics

value: Subcutaneous tumour

value: MC38-Ova tumours

value: WT C57BL/6 Kaede

value: Isotype control


title: HctYH_OF3A_1-4-I3-K19

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: HctYH_OF3A_1-4-I3-J8

value: nuclear RNA + genomic DNA


title: control_rep1, iCLIP


title: Tra2b_rep2

data_processing:
RNA-Seq data were primarily filtered using the FASTQ Toolkit v1.0.0 program
Data were aligned using HISAT2 software from Galaxy, to map reads to the mm35 mouse reference genome, specifying strand information as reverse (R). Limma-voom from galaxy was used to study differential expression of each gene
Assembly: mm35 mouse reference genome
Supplementary files format and content: Raw counts per ENSEMBL GENCODE genes at exon level for all treatments.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen)
The libraries were prepared with the TruSeq Stranded TOTAL RNA kit (Illumina, San Diego, CA, USA) and the sequencing was performed with the Illumina NovaSeq 6000 SP 2x75 bp

treatment_protocol: NMuMG cell which overexpress mRNA Serpine1 or Tra2b using lentiviral and retriviral viruses, respectively

value: Tra2b overexpression


title: Tra2b_rep1


title: HctYH_OF3A_1-4-I3-J20


title: S1_rep2

value: Serpine1 overexpression


title: HctYH_OF3A_1-4-I3-J19


title: HctYH_OF3A_1-4-I3-J7


title: S1_rep1


title: HctYH_OF3A_1-4-I3-I8


title: HctYH_OF3A_1-4-I3-I7


title: R1_rep2


title: HctYH_OF3A_1-4-I3-I20


title: R1_rep1


title: WGS, Ex37-38Del, rep3

city: Adelaide

first: Alison

last: Gardner

state: SA

address: AHMS, Uni of Adelaide, North Terrace

department: Faculty of Health and Medical Sciences

country: Australia

institute: University of Adelaide

data_processing:
library strategy: WGS
Aligned RNAseq with hisat2 using grcm38_tran & then ran salmon using Mus_musculus.GRCm38.gencode.vM25.chr_patch_hapl_scaff.annotation.gtf
Please note that sample 06-WT-14 was an outlier and removed from data processing.
Assembly: mm10
Supplementary files format and content: rnaseq gene counts, rnaseq transcript counts

source_name: Ear

extract_protocol:
Total RNAs were extracted from the E14.5, E18.5 and P10 Thoc2Δ/Y and Thoc2+/Y mouse brain dorsal cortices using our in-house protocol that uses combination of TRIzol Reagent (Invitrogen) and RNeasy Mini Kit (Qiagen) and quantified and qualified by NanoDrop (Thermo Fisher Scientific Inc.), Agilent 2100 Bioanalyzer (Agilent Technologies, USA), and 1% agarose gel.
1 μg total RNA from each sample with RNA integrity number (RIN) value ≥7 was used for library preparation. Next generation sequencing libraries were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina as per manufacturer’s protocol (Vazyme Biotech). Briefly, the poly(A) mRNAs were isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB). The mRNA fragmentation and priming were performed using NEBNext First Strand Synthesis Reaction Buffer and Random Primer mix. The first strand cDNA was synthesized using NEB ProtoScript II Reverse Transcriptase and the second-strand cDNA using Second Strand Synthesis Enzyme Mix. The double-stranded cDNAs were purified using AxyPrep Mag PCR Clean-up (Axygen) and treated with NEBNext Ultra End Repair/dA-Tailing mix to convert fragmented DNA to repaired DNA and add dA-tails to both ends, followed by T-A ligation using NEBNxt Ultra II Ligation Module to add adaptors to both the ends. The adaptor-ligated DNAs were size selected for fragments of ~360 bp (with ~300 bp inserts) using AxyPrep Mag PCR Clean-Up kit (Axygen). Each sample was amplified by PCR for 11 cycles using P5 and P7 primers; both primers carried sequences that can anneal with flow cell to perform bridge PCR and P7 primer with a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-Up Kit (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, USA). The libraries with different indices were multiplexed and loaded on an Illumina NovaSeq 6000 (Illumina, USA). Strand-specific sequencing at 80 million 2×150bp paired-end reads per sample was carried out.

value: Ear

value: 60 days

value: male


title: Sorted Kaede-red TILs, isotype control treated tumours

description: 10x Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x CellRanger software v6.1.2 according to the manufacturer's workflow.
Assembly: mm10
Supplementary files format and content: 10x Genomics CellRanger output (filtered feature matrices): Tab-separated values files and matrix files

source_name: Subcutaneous tumour

extract_protocol:
Tumours were cut into small pieces using surgical scissors then digested using Miltenyi Biotec Tumour Dissociation Kit using a gentleMACS Dissociator for 40 minutes at 37C, as per manufacturer's protocol. Subsequently, the sample was filtered through a 70 μm strainer to remove undigested tissue debris. Next, using Miltenyi Biotech Dead Cell Removal Kit and LS Columns, as per manufacturer's instructions, dead cells were removed from samples. Thereafter, cells were stained for surface markers and LIVE/DEAD viability dye before being centrifuged at 400 g at 4°C for 5 min and resuspended in FACS staining buffer for sorting (BD FACS Aria II Cell Sorter).
Gene expression libraries from were prepared from FACS-sorted populations of single cells using the Chromium Controller and Single Cell 3’ Reagent Kits v3 (10x genomics, Inc.) according to the manufacturer’s protocol. The resulting sequencing libraries comprised of standard Illumina paired-end constructs flanked with P5 and P7 sequences. The 16 bp 10x barcode and 10 bp UMI were encoded in read 1, while read 2 was used to sequence the cDNA fragment. Sample index sequences were incorporated as the i7 index read.
scRNA-seq, 10x Genomics Chromium GEM 3' v3; 2 x 150bp paired-end sequencing performed on NovaSeq 6000 (Illumina)

value: Tumour-infiltrating lymphocyte

tag: cell fraction

value: Kaede-red


title: WGS, Ex37-38Del, rep2


title: WGS, Ex37-38Del, rep4


title: Hemi-E14, rep5

data_processing:
Aligned RNAseq with hisat2 using grcm38_tran & then ran salmon using Mus_musculus.GRCm38.gencode.vM25.chr_patch_hapl_scaff.annotation.gtf
Please note that sample 06-WT-14 was an outlier and removed from data processing.
Assembly: mm10
Supplementary files format and content: rnaseq gene counts, rnaseq transcript counts

source_name: Brain

value: Brain


title: WGS, Ex37-38Del, rep1


title: control_rep2, iCLIP

value: NMuMG

value: mammary gland

value: glandular epithelial cells


title: WT-E14, rep5

value: WT


title: WT-E14, rep4


title: Sorted Kaede-green TILs, isotype control treated tumours (biol rep 2)

description: 10x Genomics

value: Subcutaneous tumour

value: WT C57BL/6 Kaede

value: Kaede-green


title: WT-E14, rep3


title: Sorted Kaede-green TILs, isotype control treated tumours (biol rep 1)

description: 10x Genomics


title: Hemi-E14, rep4


title: HctYH_OF3A_1-4-I3-H20

tag: brain region

value: Dorsolateral Prefrontal cortex (Brodmann area 46)

value: Female


title: Old_5

city: Nashville

first: Ananya

last: Nandy

state: Tennessee

address: 2215 Garland Ave

department: Clinical Pharmacology

institute: VUMC

data_processing:
Cutadapt (https://github.com/marcelm/cutadapt) was used to trim adapters.
STAR was used to map reads to the human reference genome.
DESeq2 was used to detect differential expression between conditions.
Assembly: hg38
Supplementary files format and content: A raw count table that provides complete data with values for all features and all samples

source_name: Femur

extract_protocol:
Femurs were removed, flash frozen on liquid nitrogen, pulverized to powder using Freezer mill and RNA was harvested using Trizol reagent. NovaSeq 6000  (version 2.4.11; Illumina) was used for preparing library
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone

tag: age

value: 22 months

value: enriched mRNA


title: HctYH_OF3A_1-4-I3-H19

tag: Sex

value: nuclear RNA + genomic DNA


title: WT-E14, rep2

value: male


title: WT-P10, rep5


title: Old_4

tag: molecule subtype


title: WT-E14, rep1

tag: tissue


title: Old_3


title: Hemi-E14, rep3

tag: genotype


title: WT-P10, rep4


title: HctYH_OF3A_1-4-I3-G7