title: Genomic DNA from 202242400013_R05C01

first: Maitreyi

last: Mazumdar

address: Department of Neurology

institute: Boston Children's Hospital & Harvard Medical School

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridised to the Illumina Infinium  MethylationEPIC Beadchips using the standard Illumina protocol.

scan_protocol: Arrays were imaged using an HiSCAN with standard recommended Illumina scanner settings.

data_processing:
See original publication
matrix processed value definition: Beta values with dasen + noob normalization, filtered for quality probes.
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

extract_protocol: Genomic DNA was extracted from four villi sites per placenta using a standard salting-out procedure, combined in equimolar amounts. The combined samples were purified using the Qiagen DNeasy Kit according to standard instructions.

tag: group

tag: depression

value: Non-Depressed

value: Non-Exposed

value: No

value: Vaginal

value: Male

value: Chorionic Villi

tag: trophoblasts

tag: stromal

tag: hofbauer

tag: endothelial

tag: nrbc

tag: syncytiotrophoblast


title: Genomic DNA from 202242400049_R02C01

status: Public on Jan 12 2023

type: genomic

city: Boston

state: MA

country: USA

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

value: Depressed

value: Female

tag: tissue


title: Genomic DNA from 202232290047_R04C01

value: Exposed


title: Genomic DNA from 202232290002_R05C01

value: Cesarean


title: Genomic DNA from 202242400050_R07C01


title: Genomic DNA from 202232290047_R01C01


title: Genomic DNA from 202240580237_R06C01


title: Genomic DNA from 202232290047_R03C01


title: Genomic DNA from 202242400013_R08C01


title: Genomic DNA from 202232290037_R08C01


title: Genomic DNA from 202232290037_R04C01


title: Genomic DNA from 202232290038_R03C01


title: Genomic DNA from 202232290038_R07C01


title: Genomic DNA from 202242400013_R06C01


title: Genomic DNA from 202232290037_R05C01


title: Genomic DNA from 202240580237_R07C01


title: Genomic DNA from 202242400049_R05C01


title: Genomic DNA from 202242400050_R06C01


title: Genomic DNA from 202232290037_R01C01


title: Genomic DNA from 202242400049_R01C01


title: Genomic DNA from 202232290032_R08C01


title: Genomic DNA from 202242400050_R02C01


title: Genomic DNA from 202242400013_R02C01


title: Genomic DNA from 202232290037_R02C01


title: Genomic DNA from 202232290038_R05C01


title: Genomic DNA from 202240580237_R08C01


title: Genomic DNA from 202242400013_R04C01


title: Genomic DNA from 202232290032_R04C01


title: Genomic DNA from 202232290038_R04C01


title: Genomic DNA from 202242400050_R01C01


title: Genomic DNA from 202232290002_R04C01


title: Genomic DNA from 202232290038_R08C01


title: Genomic DNA from 202242400049_R07C01


title: Genomic DNA from 202232290002_R02C01


title: Genomic DNA from 202242400013_R01C01


title: Genomic DNA from 202240580237_R04C01


title: Genomic DNA from 202232290032_R02C01


title: Genomic DNA from 202232290038_R02C01


title: Genomic DNA from 202242400050_R05C01


title: Genomic DNA from 202232290047_R08C01


title: Genomic DNA from 202242400049_R03C01


title: Genomic DNA from 202242400049_R08C01


title: Genomic DNA from 202240580237_R02C01


title: cDC2_MOCK_D602

status: Public on Jan 13 2023

type: SRA

city: Paris

first: Philippe

last: Benaroch

address: 12, rue Lhomond

department: INSERM U932 Immunity and Cancer

country: France

institute: Institut Curie

library_source: transcriptomic

data_processing:
Raw fastq reads were trimmed to remove remaining Illumina adaptors using TrimGalore v.0.6.2
A reference sequence for human (hg38) is built with STAR 2.7.3a
A reference sequence for the HIV genome is built with STAR 2.7.3a
Reads were first mapped on the human genome
Unmapped reads on the human genome were mapped on the HIV genome
Counting tables were obtained using featureCounts from Subread 1.5.1
Genome_build: GRCh38
Genome_build: NC_001802
Supplementary_files_format_and_content: tsv files containing human ENSEMBL IDs raw expression values
Supplementary_files_format_and_content: tsv file containing TPM normalized (Transcripts Per Million) expression matrix for human ENSEMBL IDs

molecule: total RNA

source_name: PBMC

growth_protocol: Isolated DC populations were cultured in Xvivo medium (Lonza)

extract_protocol:
SMART-Seq® v4 Ultra® Low Input RNA kit from Takara Bio
RNA libraries were prepared with KAPA HyperPlus kit from Roche

treatment_protocol: Cells were cultured with HIV-1 NL-AD8 complemented or not with Vpx (plasmid VPX-any-VPR),with or without azidothymidine (Azt, 25µM) and neverapin (Nvp, 5µM), for 24 hours

tag: cell type

tag: time point (hour)

tag: treatment

value: mock medium


title: Genomic DNA from 202232290038_R06C01


title: Genomic DNA from 202242400050_R08C01


title: Genomic DNA from 202232290047_R02C01


title: Genomic DNA from 202242400049_R06C01


title: Genomic DNA from 202240580237_R03C01


title: Genomic DNA from 202232290032_R06C01


title: Genomic DNA from 202232290032_R01C01


title: Genomic DNA from 202232290002_R08C01


title: Genomic DNA from 202242400050_R03C01


title: Genomic DNA from 202232290047_R05C01


title: Genomic DNA from 202232290037_R06C01


title: Genomic DNA from 202232290032_R07C01


title: Genomic DNA from 202232290032_R05C01


title: Genomic DNA from 202232290047_R07C01


title: Genomic DNA from 202232290032_R03C01


title: Genomic DNA from 202240580237_R01C01


title: PWOFC-2

city: Guangzhou

first: Xiaoyun

last: Wang

state: Guangdong

address: 190 Kaiyuan Avenue, Huangpu

department: Infection and Immunity

country: China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description:
The whole Drosophila were collected after FMT experiments
dmel-count.txt

data_processing:
All raw sequencing data were quality controlled by fastqc. Adapters, reads with more than 10% unknown nucleotide (N) content,  and reads with more than half low quality (Q-value <20) bases were removed.
For RNA-seq data, The clean reads were mapped to the dm6 Drosophila reference genome using HISAT2.
For RNA-seq data, The mapped reads of each sample were assembled and quantified by StringTie (version 1.3.1) in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated.
For RNA-seq data, RNA differential expression analyses among groups were performed by DESeq2 (version 1.36.0). The genes/transcripts with the a false discovery rate (FDR) < 0.05 and absolute fold change >2 were considered as differentially expressed genes/transcripts and used for downstream analyses.
Assembly: dm6
Supplementary files format and content: Tab-delimited text file (.txt) include raw read counts for the RNA-seq data of sterile samples

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Whole adult

growth_protocol: Drosophila melanogaster w1118 was reared at 25℃ under 12 h light/12 h dark cycles on yeast-glucose medium (1 L water, 100 g yeast, 100 g glucose, 1.2% agar, 0.1% potassium sorbate)

extract_protocol:
Total RNA of RNA-seq samples were homogenized in 1 ml TRIzol (Accurate Biotechnology) and precipitaed by isopropyl alcohol.
After total RNAs of each samples were extracted, the mRNAs enriched by Oligo(dT) beads were fragmented using fragmenta-tion buffer and reverse transcripted into cDNAs with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP, and buffer. The cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen), and were end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina NovaSeq 6000 by Berry Genomics.

treatment_protocol: adult Drosophila were cultured in a yeast-glucose based medium containing 250 μM rotenone (C23H22O6, dissolved in DMSO)

value: Whole adult

tag: growth protocol

value: Feeding with yeast-glucose medium

value: Parkinson's Drosophila without FMT from control Drosophila

tag: replicate


title: Genomic DNA from 202232290002_R07C01


title: Mouse RNA-seq - ISO 1hour rep4

city: Beijing

first: Di

last: Zhang

address: No.5 YiHeYuan Road, Haidian District

institute: Peking University

data_processing:
Data manipulation included removing reads containing adapter, reads containing poly-N, and low-quality reads from raw data.
Then the clean reads were mapped to the mouse reference genome GRCm38.p6 from the National Center for Biotechnology Information (NCBI) database using Hissat2 v2.0.5.
Genes with zero count in all samples were filtered out, leaving 24,188 genes under ISO treatment and 23,526 genes under PE treatment. The mRNA levels were normalized to gene length and total counts as transcripts per million (TPM).
Assembly: GRCm38.p6
Supplementary files format and content: Raw gene counts FPKM, and TPM values for every gene and every sample.

organism: Mus musculus

source_name: Heart

extract_protocol:
After 1 hour, 1 day, or 3 days, mice were euthanatized following anesthetization with an overdose of pentobarbital. The heart tissue was collected for further determination. A total amount of 1 μg RNA was used as input material for the RNA sample preparations. mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X).
First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using dNTP with DNA Polymerase I system. After adenylation of 3’ ends of DNA fragments, the adaptor with hairpin loop structure was ligated for hybridization. To select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA). After PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained. To ensure the quality of the library, the library was initially quantified by Qubit2.0 Fluorometer, then diluted to 1.5ng/ul, and the insert size of the library is detected by Agilent 2100 bioanalyzer. After insert size meets the expectation, qRT-PCR is used to accurately quantify the effective concentration of the library (the effective concentration of the library is higher than that of 2nM) to ensure the quality of the library.

treatment_protocol: All animal experiments were approved by Peking University Institutional Review Board Animal Welfare Committee (LA2021013) and conformed to the guidelines for animal experiments of Peking University Health Science center. The 12-week-old male C57BL/6N mice were bought from Vital River Laboratory Animal Technology Company (Beijing, China) and housed in a specific pathogen-free environment in the Animal Department of Peking University Health Science Center. Mice were randomly allocated into different groups and subcutaneously injected with a single dose of isoprenaline (ISO, 5 mg/kg) or phenylephrine (PE, 10 mg/kg). The dosage was chosen according to our previous studies.

tag: strain

tag: Sex

value: male

value: Heart

value: ISO treatment

tag: sampling time

value: 1 hour


title: Genomic DNA from 202242400049_R04C01

tag: group

value: Non-Depressed

value: Non-Exposed


title: Genomic DNA from 202240580237_R05C01

tag: depression

value: No


title: Genomic DNA from 202232290037_R07C01

value: Vaginal

tag: trophoblasts


title: genomic DNA from placental villous sample 22

city: Gainesville

first: Heather

middle: M

last: Brockway

state: FL

department: Physiology and Functional Genomics

institute: University of Florida

description: placental villous tissue

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human  EPIC 850KBeadchip using standard Illumina protocol

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

data_processing: Minfi v1.34.0, methylumi v2.34.0

label: Cy3 and Cy5

source_name: placental villous sample 22

extract_protocol: genomic DNA was extracted and purified from placenta villous tissue samples using Qiagen DNeasy Kit according to standard instructions

value: placental villous

tag: birth type

value: IAI

tag: fetal sex

value: M


title: genomic DNA from placental villous sample 19

description: placental villous tissue

source_name: placental villous sample 19

value: TB


title: genomic DNA from placental villous sample 15

description: placental villous tissue

source_name: placental villous sample 15

value: F


title: genomic DNA from placental villous sample 18

description: placental villous tissue

source_name: placental villous sample 18

value: PTB


title: genomic DNA from placental villous sample 25

description: placental villous tissue

source_name: placental villous sample 25


title: genomic DNA from placental villous sample 24

description: placental villous tissue

source_name: placental villous sample 24


title: genomic DNA from placental villous sample 6

description: placental villous tissue

source_name: placental villous sample 6


title: genomic DNA from placental villous sample 21

description: placental villous tissue

source_name: placental villous sample 21


title: genomic DNA from placental villous sample 23

description: placental villous tissue

source_name: placental villous sample 23


title: genomic DNA from placental villous sample 27

description: placental villous tissue

source_name: placental villous sample 27


title: genomic DNA from placental villous sample 14

description: placental villous tissue

source_name: placental villous sample 14


title: Genomic DNA from 202242400013_R03C01

value: Male

value: Chorionic Villi

tag: stromal

tag: hofbauer

tag: endothelial


title: pdx_breast_tumor_TNBC177

type: RNA

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

description: PDX tumor

hyb_protocol: The cRNA is hybridized to the oligonucleotide probes on the array.

scan_protocol: Immediately following the hybridization, the hybridized probe arrays undergo an automated washing and staining protocol on the fluidic station and are then scanned on the GeneChip Scanner.

data_processing: RMA signal calculated using R/Bioconductor.

label: biotin

source_name: pdx established from pre-treatment breast tumor biopsy

label_protocol: We performed an in vitro transcription reaction to produce biotin-labeled cRNA from the cDNA.

growth_protocol: Tumor cells were engrafted into NOD/SCID mice and passaged through three generations.

extract_protocol: Fresh tumor core biopsies were placed into a 1.5 ml vial of RNAlater (Qiagen) at room temperature, then held in a 4°C refrigerator (6-72 hours) and after that stored frozen at -20°C until use.  RNA was extracted using PicoPure RNA isolation kit (ThermoFisher Scientific, Waltham, MA) following the manufacturer's instructions.

tag: xenograft

tag: disease state

value: breast cancer


title: genomic DNA from placental villous sample 10

description: placental villous tissue

source_name: placental villous sample 10

tag: tissue


title: genomic DNA from placental villous sample 5

description: placental villous tissue

source_name: placental villous sample 5


title: genomic DNA from placental villous sample 7

description: placental villous tissue

source_name: placental villous sample 7


title: genomic DNA from placental villous sample 13

description: placental villous tissue

source_name: placental villous sample 13


title: pdx_breast_tumor_TNBC299

description: PDX tumor


title: genomic DNA from placental villous sample 1

description: placental villous tissue

source_name: placental villous sample 1


title: pdx_breast_tumor_TNBC297

description: PDX tumor


title: genomic DNA from placental villous sample 12

description: placental villous tissue

source_name: placental villous sample 12


title: genomic DNA from placental villous sample 26

description: placental villous tissue

source_name: placental villous sample 26


title: genomic DNA from placental villous sample 9

description: placental villous tissue

source_name: placental villous sample 9


title: genomic DNA from placental villous sample 8

description: placental villous tissue

source_name: placental villous sample 8


title: pdx_breast_tumor_TNBC288

description: PDX tumor


title: genomic DNA from placental villous sample 20

description: placental villous tissue

source_name: placental villous sample 20


title: genomic DNA from placental villous sample 11

description: placental villous tissue

source_name: placental villous sample 11


title: pdx_breast_tumor_TNBC293

description: PDX tumor


title: pdx_breast_tumor_TNBC287

description: PDX tumor


title: pdx_breast_tumor_TNBC292

description: PDX tumor


title: pdx_breast_tumor_TNBC277

description: PDX tumor


title: genomic DNA from placental villous sample 16

description: placental villous tissue

source_name: placental villous sample 16


title: pdx_breast_tumor_TNBC284

description: PDX tumor


title: pdx_breast_tumor_TNBC271

description: PDX tumor


title: pdx_breast_tumor_TNBC274

description: PDX tumor


title: pdx_breast_tumor_TNBC270

description: PDX tumor


title: genomic DNA from placental villous sample 17

description: placental villous tissue

source_name: placental villous sample 17


title: pdx_breast_tumor_TNBC269

description: PDX tumor


title: pdx_breast_tumor_TNBC273

description: PDX tumor


title: pdx_breast_tumor_ATID003

description: PDX tumor


title: genomic DNA from placental villous sample 2

description: placental villous tissue

source_name: placental villous sample 2


title: pdx_breast_tumor_TNBC294

description: PDX tumor


title: pdx_breast_tumor_TNBC263

description: PDX tumor


title: pdx_breast_tumor_TNBC261

description: PDX tumor


title: pdx_breast_tumor_TNBC291

description: PDX tumor


title: pdx_breast_tumor_TNBC255

description: PDX tumor


title: pdx_breast_tumor_TNBC257

description: PDX tumor


title: genomic DNA from placental villous sample 3

description: placental villous tissue

source_name: placental villous sample 3


title: pdx_breast_tumor_TNBC251

description: PDX tumor


title: pdx_breast_tumor_TNBC289

description: PDX tumor


title: pdx_breast_tumor_TNBC253

description: PDX tumor


title: pdx_breast_tumor_TNBC249

description: PDX tumor


title: pdx_breast_tumor_TNBC286

description: PDX tumor


title: pdx_breast_tumor_TNBC244

description: PDX tumor


title: pdx_breast_tumor_TNBC237

description: PDX tumor


title: pdx_breast_tumor_TNBC275

description: PDX tumor


title: pdx_breast_tumor_TNBC267

description: PDX tumor


title: pdx_breast_tumor_TNBC266

description: PDX tumor


title: pdx_breast_tumor_TNBC238

description: PDX tumor


title: pdx_breast_tumor_TNBC234

description: PDX tumor


title: pdx_breast_tumor_TNBC276

description: PDX tumor


title: pdx_breast_tumor_TNBC259

description: PDX tumor


title: pdx_breast_tumor_TNBC254

description: PDX tumor


title: pdx_breast_tumor_TNBC298

description: PDX tumor


title: pdx_breast_tumor_TNBC226

description: PDX tumor


title: pdx_breast_tumor_TNBC223

description: PDX tumor


title: pdx_breast_tumor_TNBC221

description: PDX tumor


title: pdx_breast_tumor_TNBC233

description: PDX tumor


title: pdx_breast_tumor_TNBC247

description: PDX tumor


title: pdx_breast_tumor_TNBC241

description: PDX tumor


title: pdx_breast_tumor_TNBC240

description: PDX tumor


title: genomic DNA from placental villous sample 4

description: placental villous tissue

source_name: placental villous sample 4


title: pdx_breast_tumor_TNBC245

description: PDX tumor

source_name: pdx established from pre-treatment breast tumor biopsy


title: pdx_breast_tumor_TNBC229

description: PDX tumor


title: pdx_breast_tumor_TNBC228

description: PDX tumor


title: pdx_breast_tumor_TNBC283

description: PDX tumor


title: pdx_breast_tumor_TNBC231

description: PDX tumor


title: pdx_breast_tumor_TNBC222

description: PDX tumor


title: pdx_breast_tumor_TNBC235

description: PDX tumor


title: pdx_breast_tumor_TNBC224

description: PDX tumor


title: pdx_breast_tumor_TNBC225

description: PDX tumor


title: pdx_breast_tumor_TNBC220

description: PDX tumor


title: pdx_breast_tumor_TNBC290

description: PDX tumor


title: pdx_breast_tumor_TNBC250

description: PDX tumor


title: pdx_breast_tumor_TNBC211

description: PDX tumor


title: pdx_breast_tumor_TNBC209

description: PDX tumor


title: pdx_breast_tumor_TNBC199

description: PDX tumor


title: pdx_breast_tumor_TNBC217

description: PDX tumor


title: pdx_breast_tumor_TNBC218

description: PDX tumor


title: pdx_breast_tumor_TNBC216

description: PDX tumor


title: pdx_breast_tumor_TNBC197

description: PDX tumor


title: pdx_breast_tumor_TNBC195

description: PDX tumor


title: pdx_breast_tumor_TNBC215

description: PDX tumor


title: pdx_breast_tumor_TNBC208

description: PDX tumor


title: pdx_breast_tumor_TNBC213

description: PDX tumor


title: pdx_breast_tumor_TNBC210

description: PDX tumor


title: pdx_breast_tumor_TNBC191

description: PDX tumor


title: pdx_breast_tumor_TNBC193

description: PDX tumor


title: pdx_breast_tumor_TNBC200

description: PDX tumor


title: pdx_breast_tumor_TNBC192

description: PDX tumor


title: pdx_breast_tumor_TNBC180

description: PDX tumor


title: pdx_breast_tumor_TNBC205

description: PDX tumor


title: pdx_breast_tumor_TNBC173

description: PDX tumor


title: pdx_breast_tumor_TNBC179

description: PDX tumor


title: pdx_breast_tumor_TNBC190

description: PDX tumor


title: pdx_breast_tumor_TNBC168

description: PDX tumor


title: pdx_breast_tumor_TNBC186

description: PDX tumor


title: pdx_breast_tumor_TNBC175

description: PDX tumor


title: pdx_breast_tumor_TNBC165

description: PDX tumor


title: pdx_breast_tumor_TNBC172

description: PDX tumor


title: pdx_breast_tumor_TNBC164

description: PDX tumor


title: pdx_breast_tumor_TNBC170

description: PDX tumor


title: pdx_breast_tumor_TNBC181

description: PDX tumor


title: pdx_breast_tumor_TNBC185

description: PDX tumor


title: pdx_breast_tumor_TNBC182

description: PDX tumor


title: pdx_breast_tumor_TNBC174

description: PDX tumor


title: pdx_breast_tumor_TNBC163

description: PDX tumor


title: pdx_breast_tumor_TNBC166

description: PDX tumor


title: pdx_breast_tumor_TNBC187

description: PDX tumor


title: pdx_breast_tumor_TNBC161

description: PDX tumor


title: pdx_breast_tumor_TNBC151

description: PDX tumor


title: pdx_breast_tumor_TNBC160

description: PDX tumor


title: pdx_breast_tumor_TNBC154

description: PDX tumor


title: pdx_breast_tumor_TNBC152

description: PDX tumor


title: pdx_breast_tumor_TNBC157

description: PDX tumor


title: pdx_breast_tumor_TNBC159

description: PDX tumor


title: pdx_breast_tumor_TNBC155

description: PDX tumor


title: pdx_breast_tumor_TNBC145

description: PDX tumor


title: pdx_breast_tumor_TNBC140

description: PDX tumor


title: pdx_breast_tumor_TNBC149

description: PDX tumor


title: pdx_breast_tumor_TNBC158

description: PDX tumor


title: pdx_breast_tumor_TNBC130

description: PDX tumor


title: pdx_breast_tumor_TNBC150

description: PDX tumor


title: pdx_breast_tumor_TNBC127

description: PDX tumor


title: pdx_breast_tumor_TNBC124

description: PDX tumor


title: pdx_breast_tumor_TNBC125

description: PDX tumor


title: pdx_breast_tumor_TNBC178

description: PDX tumor


title: pdx_breast_tumor_TNBC136

description: PDX tumor


title: pdx_breast_tumor_TNBC139

description: PDX tumor


title: pdx_breast_tumor_TNBC143

description: PDX tumor


title: pdx_breast_tumor_TNBC128

description: PDX tumor


title: pdx_breast_tumor_TNBC122

description: PDX tumor


title: pdx_breast_tumor_TNBC142

description: PDX tumor


title: pdx_breast_tumor_TNBC137

description: PDX tumor


title: pdx_breast_tumor_TNBC141

description: PDX tumor


title: pdx_breast_tumor_TNBC119

description: PDX tumor


title: pdx_breast_tumor_TNBC117

description: PDX tumor


title: pdx_breast_tumor_TNBC113

description: PDX tumor


title: pdx_breast_tumor_TNBC121

description: PDX tumor


title: pdx_breast_tumor_TNBC144

description: PDX tumor


title: pdx_breast_tumor_TNBC115

description: PDX tumor


title: pdx_breast_tumor_TNBC116

description: PDX tumor


title: pdx_breast_tumor_TNBC134

description: PDX tumor


title: pdx_breast_tumor_TNBC135

description: PDX tumor


title: pdx_breast_tumor_TNBC110

description: PDX tumor


title: pdx_breast_tumor_TNBC109

description: PDX tumor


title: pdx_breast_tumor_TNBC108

description: PDX tumor


title: pdx_breast_tumor_TNBC106

description: PDX tumor


title: pdx_breast_tumor_TNBC105

description: PDX tumor


title: pdx_breast_tumor_TNBC098

description: PDX tumor


title: pdx_breast_tumor_TNBC094

description: PDX tumor


title: pdx_breast_tumor_TNBC093

description: PDX tumor


title: pdx_breast_tumor_TNBC103

description: PDX tumor


title: pdx_breast_tumor_TNBC101

description: PDX tumor


title: pdx_breast_tumor_TNBC104

description: PDX tumor


title: pdx_breast_tumor_TNBC083

description: PDX tumor


title: pdx_breast_tumor_TNBC107

description: PDX tumor


title: pdx_breast_tumor_TNBC079

description: PDX tumor


title: pdx_breast_tumor_TNBC081

description: PDX tumor


title: pdx_breast_tumor_TNBC084

description: PDX tumor


title: pdx_breast_tumor_TNBC102

description: PDX tumor


title: pdx_breast_tumor_TNBC091

description: PDX tumor


title: pdx_breast_tumor_TNBC090

description: PDX tumor


title: pdx_breast_tumor_TNBC082

description: PDX tumor


title: pdx_breast_tumor_TNBC077

description: PDX tumor


title: pdx_breast_tumor_TNBC076

description: PDX tumor


title: pdx_breast_tumor_TNBC111

description: PDX tumor


title: pdx_breast_tumor_TNBC074

description: PDX tumor


title: pdx_breast_tumor_TNBC088

description: PDX tumor


title: pdx_breast_tumor_TNBC085

description: PDX tumor


title: pdx_breast_tumor_TNBC086

description: PDX tumor


title: pdx_breast_tumor_TNBC073

description: PDX tumor


title: pdx_breast_tumor_TNBC069

description: PDX tumor


title: pdx_breast_tumor_TNBC087

description: PDX tumor


title: pdx_breast_tumor_TNBC067

description: PDX tumor


title: pdx_breast_tumor_TNBC072

description: PDX tumor


title: pdx_breast_tumor_TNBC057

description: PDX tumor


title: pdx_breast_tumor_TNBC059

description: PDX tumor


title: pdx_breast_tumor_TNBC070

description: PDX tumor


title: pdx_breast_tumor_TNBC061

description: PDX tumor


title: pdx_breast_tumor_TNBC055

description: PDX tumor


title: pdx_breast_tumor_TNBC052

description: PDX tumor


title: pdx_breast_tumor_TNBC043

description: PDX tumor


title: pdx_breast_tumor_TNBC054

description: PDX tumor


title: pdx_breast_tumor_TNBC046

description: PDX tumor


title: pdx_breast_tumor_TNBC063

description: PDX tumor


title: pdx_breast_tumor_TNBC047

description: PDX tumor


title: pdx_breast_tumor_TNBC056

description: PDX tumor


title: pdx_breast_tumor_TNBC040

description: PDX tumor


title: pdx_breast_tumor_TNBC042

description: PDX tumor


title: pdx_breast_tumor_TNBC051

description: PDX tumor


title: pdx_breast_tumor_TNBC035

description: PDX tumor


title: pdx_breast_tumor_TNBC050

description: PDX tumor


title: pdx_breast_tumor_TNBC053

description: PDX tumor


title: pdx_breast_tumor_TNBC033

description: PDX tumor


title: pdx_breast_tumor_TNBC030

description: PDX tumor


title: pdx_breast_tumor_TNBC034

description: PDX tumor


title: pdx_breast_tumor_TNBC039

description: PDX tumor


title: pdx_breast_tumor_TNBC026

description: PDX tumor


title: pdx_breast_tumor_TNBC032

description: PDX tumor


title: pdx_breast_tumor_TNBC041

description: PDX tumor


title: pdx_breast_tumor_TNBC022

description: PDX tumor


title: pdx_breast_tumor_TNBC024

description: PDX tumor


title: pdx_breast_tumor_TNBC029

description: PDX tumor


title: pdx_breast_tumor_TNBC023

description: PDX tumor


title: pdx_breast_tumor_TNBC017

description: PDX tumor


title: pdx_breast_tumor_TNBC015

description: PDX tumor


title: pdx_breast_tumor_TNBC016

description: PDX tumor


title: pdx_breast_tumor_TNBC025

description: PDX tumor


title: pdx_breast_tumor_TNBC009

description: PDX tumor


title: pdx_breast_tumor_TNBC014

description: PDX tumor


title: pdx_breast_tumor_TNBC112

description: PDX tumor


title: pdx_breast_tumor_TNBC020

description: PDX tumor


title: pdx_breast_tumor_TNBC007

description: PDX tumor


title: pdx_breast_tumor_TNBC001

description: PDX tumor


title: NPCs-m3C, Mettl8-cKO, rep3

city: Philadelphia

first: Feng

state: PA

address: 415 Curie Boulevard

department: Department of Neuroscience and Mahoney Institute for Neurosciences

institute: Perelman School for Medicine, University of Pennsylvania

description:
M3CNPC_KO3_S7_R1_001
Summary_cleavage_ratio_and_coverage_data.txt

data_processing:
Raw sequencing data were demultiplexed with bcl2fastq2 v2.17.1.14 (Illumina).
Adaptors were trimmed using Trimmomatic v0.32 software (parameter-TruSeq3-PE-2.fa:2:30:10 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:26).
Trimmed sequence reads were mapped to mouse reference genome GRCm38.p6 using STAR v2.5.2a (parameters-quantMode GeneCounts --outSAMattributes All --outFilterMultimapNmax 20 --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1).
All Cytosine sites were analyzed when their +1 bp downstream sites are a) within genomic regions with known features including genes and tRNAs, b) as the start end of more than one read in each WT sample, and c) with coverage in all samples. The cleavage ratio of sitei was calculated as the ratio of the number of reads starting at sitei+1 to the read depth of sitei+1.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files including the cleavage ratio and coverage data of 135582 analyzed Cytosine sites with more than one read in each WT sample in m3C-HAC-seq starting at their 1 bp downstream sites
Library strategy: m3C-HAC-seq

source_name: Cerebral cortex

growth_protocol: WT or Mettl8 cKO NPCs were maintained in plates pre-coated with 1% Matrigel and in the DMEM/F12 medium containing 2% B27 supplement, 1% N2 supplement, bFGF (20 ng/mL), EGF (20 ng/mL), 1% Glutamax, 1% P/S with digestion using Accutase for passaging

extract_protocol:
RNA was extracted using TRIZOL (Invitrogen) and the kit of Zymo RNA Clean & Concentrator™-5. 8000 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for m3C-seq were prepared based on m3C-specific Hydrazine-Aniline Cleavage sequencing (HAC-seq) method.

tag: cell type

value: Neural progenitor cells

value: Cerebral cortex

tag: developmental stage

value: Embryonic day 17.5

tag: genotype

value: Mettl8 knockout

tag: treatment

value: Cultured on Matrigel-coated plates


title: NPCs-m3C, WT, rep2

description:
M3CNPC_WT2_S2_R1_001
Summary_cleavage_ratio_and_coverage_data.txt

value: WT


title: NPCs-m3C, WT, rep1

description:
M3CNPC_WT1_S1_R1_001
Summary_cleavage_ratio_and_coverage_data.txt


title: NPCs-m3C, WT, rep3

description:
M3CNPC_WT3_S5_R1_001
Summary_cleavage_ratio_and_coverage_data.txt


title: NPCs-m3C, WT, rep4

description:
M3CNPC_WT4_S6_R1_001
Summary_cleavage_ratio_and_coverage_data.txt


title: mouse_intestine_E14.5_scRNAseq

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: Weill Hall, 237 Tower Road

department: Meinig School of Biomedical Engineering

institute: Cornell University

description: Singe-cell RNAseq of mouse mid-gut at embryonic stage E14.5

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: H5AD files containing gene expression matrices

source_name: mid-gut

extract_protocol:
Timed-pregnant C57BL/6J mice were purchased from Jackson's laboratory. We collected midguts - gut tubes extending from after the stomach to the end of the protruding midgut and the attached dorsal mesentery from E12.5 and E14.5 embryos. We collected 60 midguts at E12.5 and 35 midguts at E14.5. From E16.5, E18.5, and P1.5 stages, we dissected open the small intestine extending from after the stomach to the end of the ileum and flushed it with ice-cold PBS. The mesentery of the duodenum was disposed of to prevent sampling of the pancreas. We sampled small intestines from two animals each for stages E16.5, E18.5, and P1.5. Samples were stored in cold PBS on ice for not more than 30 minutes before processing. When enough samples of a particular stage were collected, the tissue was cut into ~1 mm pieces and transferred into a solution of Collagenase Type 1 (200 units/ml) and Hyaluronidase (100 units/ml) under mild agitation at 37°C. 5μl of the cell suspension was plated onto a hemocytometer every 5 minutes after 20 minutes of agitation and checked for the extent of dissociation. All samples reached a near single-cell suspension by the 35-40 minute mark and were passed through a 40 µm filter and centrifuged into a pellet. Following that, samples were resuspended in phosphate-buffered saline containing 0.04% bovine serum albumin. Before loading the cells on 10x Chromium, Trypan Blue-stained cells from each sample were counted on an automated cell counter to determine their viability. The samples' cell viability ranged from 83-88% after adjusting for the cell size threshold. In order to obtain the appropriate number of transcriptomes from viable cells (10,000 cells each for E12.5 and E14.5 stages, and 5000 each for E16.5, E18.5, and P1.5 stages), we adjusted the number of cells loaded on 10x Chromium using these cell viabilities.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).

value: mid-gut

tag: strain


title: mouse_intestine_E16.5_scRNAseq

description: Singe-cell RNAseq of mouse small intestine at embryonic stage E16.5

source_name: small intestine

value: small intestine


title: pdx_breast_tumor_TNBC005

description: PDX tumor


title: mouse_intestine_E12.5_scRNAseq

description: Singe-cell RNAseq of mouse mid-gut at embryonic stage E12.5


title: pdx_breast_tumor_ATID002

description: PDX tumor


title: pdx_breast_tumor_TNBC006

description: PDX tumor


title: NPCs-m3C, Mettl8-cKO, rep2

description:
M3CNPC_KO2_S4_R1_001
Summary_cleavage_ratio_and_coverage_data.txt


title: mouse_intestine_P1.5_scRNAseq

description: Singe-cell RNAseq of mouse small intestine at postnatal stage P1.5


title: mouse_intestine_E18.5_scRNAseq

description: Singe-cell RNAseq of mouse small intestine at embryonic stage E18.5


title: pdx_breast_tumor_TNBC004

description: PDX tumor


title: NPCs-m3C, Mettl8-cKO, rep1

description:
M3CNPC_KO1_S3_R1_001
Summary_cleavage_ratio_and_coverage_data.txt


title: NPCs, WT, rep6

description:
Me8NPC2_WT7_S12_R2_001
Raw_count_table_all_samples.txt

data_processing:
Raw sequencing data were demultiplexed with bcl2fastq2 v2.17.1.14 (Illumina).
Adaptors were trimmed using Trimmomatic v0.32 software (parameter-NexteraPE-PE.fa:2:30:10; TRAILING:3; SLIDINGWINDOW:4:15; MINLEN:18).
Trimmed sequence reads were mapped to mouse reference genome GRCm38 using STAR v2.5.2a (parameters-quantMode GeneCounts --outSAMattributes All --outFilterMultimapNmax 20 --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1).
Only uniquely mapped reads were quantified at the gene level and summarized to gene counts using STAR-quantMode (GeneCounts), with multimapping and chimeric alignments discarded.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files including the raw count of all genes for all the samples

growth_protocol: WT or Mettl8 cKO NPCs  were maintained in plates pre-coated with 1% Matrigel and in the DMEM/F12 medium containing 2% B27 supplement, 1% N2 supplement, bFGF (20 ng/mL), EGF (20 ng/mL), 1% Glutamax, 1% P/S with digestion using Accutase for passaging

extract_protocol:
RNA was extracted using TRIZOL (Invitrogen) and the kit of Zymo RNA Clean & Concentrator™-5. 300ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared based on SMART-seq2 method.


title: NPCs, WT, rep5

description:
Me8NPC2_WT5_S10_R2_001
Raw_count_table_all_samples.txt


title: pdx_breast_tumor_TNBC010

description: PDX tumor


title: pdx_breast_tumor_TNBC078

description: PDX tumor


title: NPCs, Mettl8-cKO, rep5

description:
Me8NPC2_KO3_S8_R2_001
Raw_count_table_all_samples.txt


title: NPCs, Mettl8-cKO, rep6

description:
Me8NPC2_KO6_S11_R2_001
Raw_count_table_all_samples.txt


title: NPCs, Mettl8-cKO, rep4

description:
Me8NPC2_KO2_S7_R2_001
Raw_count_table_all_samples.txt


title: NPCs, WT, rep4

description:
Me8NPC2_WT4_S9_R2_001
Raw_count_table_all_samples.txt


title: NPCs, Mettl8-cKO, rep3

description:
Me8NPC2_KO1_S6_R2_001
Raw_count_table_all_samples.txt


title: NPCs, WT, rep3

description:
Me8NPC1_WT5_S5_R2_001
Raw_count_table_all_samples.txt


title: NPCs, Mettl8-cKO, rep2

description:
Me8NPC1_KO3_S3_R2_001
Raw_count_table_all_samples.txt


title: NPCs, WT, rep1

description:
Me8NPC1_WT1_S1_R2_001
Raw_count_table_all_samples.txt


title: NPCs, WT, rep2

description:
Me8NPC1_WT4_S4_R2_001
Raw_count_table_all_samples.txt


title: NPCs, Mettl8-cKO, rep1

description:
Me8NPC1_KO2_S2_R2_001
Raw_count_table_all_samples.txt


title: MSTO_B_2

city: Amsterdam

first: Jitendra

last: Badhai

address: Plesmanlaan 121

department: Division Molecular Genetics

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Sequencing libraries were constructed with a TruSeq mRNA Library Preparation Kit using poly-A-enriched RNA (Illumina, San Diego, CA, USA). The Samples were run on a HiSeq 2500 Illumina sequencer generating 65 base-pair single end reads. The sequence reads were mapped to the mouse genome (mm10) or hg 38, using TopHat (2.0.12). TopHat was run with default. Reads with mapping quality less than 10 and non-primary alignments were discarded. Remaining reads were counted using HTSeq-count. Statistical analysis of the differential expression of genes was performed using DESeq2
Assembly: mm10, Grcm38
Supplementary files format and content: read counts table
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: pleura

extract_protocol:
for RNA seq: RNA was isolated from tumor cell lines and mouse tumors with the Qiagen All Prep DNA/RNA kit. Quantification and quality assessment for RNA were performed with a Bioanalyzer (RIN >6.5) (Agilent, Santa Clara, CA, USA).
for RNAseq: Sequencing libraries were constructed with a TruSeq mRNA Library Preparation Kit using poly-A-enriched RNA (Illumina, San Diego, CA, USA). The Samples were run on a HiSeq 2500 Illumina sequencer generating 65 base-pair single end reads.

value: pleura

tag: cell line

value: BAP1 shRNA


title: MSTO_R_1

value: Random shRNA


title: H2810_B_2


title: MSTO_R_2


title: MSTO_B_1


title: H2810_B_1


title: H2810_R_1


title: H2810_R_2


title: CP-A TP53-/-, clone 3, control, rep2

city: Lausanne

first: Luca

last: Nanni

state: Vaud

address: Quartier Sorge

department: Computational Biology

country: Switzerland

institute: Université de Lausanne

library_source: genomic

data_processing:
Reads were mapped to the human hg19 reference genome using bwa mem version 0.7.17 and processed using the Juicer pipeline version 1.6. For each sample, Hi-C maps were generated at resolutions 10 kb, 20 kb, 25 kb, 50 kb, 100 kb, 250 kb, 500 kb, 1 Mb, and 10 Mb. Once assessed the concordance between replicas of the same biological condition, Hi-C maps of the same condition were merged using the mega.sh script provided by the Juicer pipeline. All Hi-C maps were normalized using the Knight-Ruiz method (KR) implemented in the Juicer pipeline.
Assembly: hg19
Supplementary files format and content: .hic files represent binarized Hi-C matrices built using Juicer using reads having MAPQ >= 30
Supplementary files format and content: .hic files named as "mega" represent the aggregation of multiple replicates of the same biological condition

source_name: esophageal epithelium

growth_protocol: RPE cells were grown in DMEM/F-12, GlutaMAX™ (catalogue no. 10565018) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific, catalogue no. 10270106) and 1% Antibiotic-Antimycotic (Thermo Fisher Scientific, catalogue no. 15240062). CP-A cells were grown in MCDB-153 medium (Sigma-Aldrich, catalogue no. M7403) supplemented with 20mg/L adenine (Sigma-Aldrich, catalogue no. A2786), 400µg/L hydrocortisone (Sigma-Aldrich, catalogue no. H0135), 50mg/L bovine pituitary extract (Thermo Fisher Scientific, catalogue no. 13028014), 1x Insulin-transferrin-sodium selenite media supplement (Sigma-Aldrich, catalogue no. I1884), 8.4 µg/L cholera toxin (Sigma-Aldrich, catalogue no. C8052), 4mM glutamine (Sigma-Aldrich, catalogue no. G7513), 5% foetal bovine serum, and 1% Antibiotic-Antimycotic. K562 (67, XX) was cultured in RPMI medium (Thermo Fisher Scientific, catalogue no. 11875093) supplemented with 10% foetal bovine serum and 1% Penicillin-Streptomycin (Thermo Fisher Scientific, catalogue no. 15140122).

extract_protocol:
1-2 million cells were collected and fixed with 2% formaldehyde (Thermo Fisher Scientific, catalogue no. 11483217). The reaction was quenched with 200mM glycine (VWR, catalogue no. 101194M) final concentration, cells were washed with PBS (Thermo Fisher Scientific, catalogue no. 10010023) and lysed in a solution containing 10mM Tris-HCl pH 8.0 (Thermo Fisher Scientific, catalogue no. 15568025), 10mM NaCl (Sigma-Aldrich, catalogue no. S6546), 0.2% Igepal CA-630 (Sigma-Aldich, catalogue no. I8896), and 1x Proteinase inhibitor cocktail (Roche, catalogue no. 11697498001) at 4°C for 30 minutes. Resulting nuclei were re-suspended in 1X NEB3.1 buffer (New England Biolabs, catalogue no. B7203S). Nuclei suspension was incubated with 0.11% SDS (Carl Roth, catalogue no. CN30) final concentration for 10 minutes at 65°C. Reaction was quenched with 1% Triton-X100 (AppliChem, catalogue no. A1388) and nuclei were digested with 100U MboI restriction enzyme (New England Biolabs, catalogue no. R0147) at 37°C overnight. Restriction enzyme was inactivated according to manufacturer’s specifications and digested nuclei were washed and re-suspended in 1x NEB3.1. Digested ends were then marked with biotin via incubation in 0.03mM biotin-14-dATP (Thermo Fisher Scientific, catalogue no. 19524016), 0.03mM dCTP, 0.03mM dGTP, 0.03mM dTTP (Promega, catalogue no. U1420) and 50U Klenow DNA polymerase I (New England Biolabs, catalogue no. M0210M) for 4 hours at room temperature. Resulting blunt-ends were proximally ligated with 50U T4 DNA Ligase (Thermo Fisher Scientific, catalogue no. EL0011), 1x T4 DNA ligase buffer (Thermo Fisher Scientific, catalogue no. B69), 5% PEG, 1% Triton-X100, 0.1mg/ml BSA (New England Biolabs, catalogue no. B9000S) for 4 hours at room temperature. Crosslink reversal was performed on the proximity-ligated chromatin through the incubation with 300mM NaCl and 1% SDS overnight, at 68°C. The sample was then treated with 50g/ml RNase A (Thermo Fisher Scientific, catalogue no. EN0531) for 30 minutes at 37°C, followed by 400ug/ml Proteinase K (Promega, catalogue no. V3021) at 65°C for one hour. DNA was purified via precipitation with 1.6 volumes of pure ethanol and 0.1 volumes of sodium acetate, pH 5.2 (Thermo Fisher Scientific, catalogue no. R1181) at -80°C. DNA was eluted and then fragmented by sonication at 80V peak incidence power, 10% duty factor, 200 cycles per burst, for 60-80 seconds with an E220 Focused-ultrasonicator (Covaris). Sheared DNA was size selected for library preparation using AMPure XP beads (Beckman Coulter, catalogue no. A63881).
Biotin-marked fragments were isolated with Dynabeads™ MyOne™ Streptavidin C1 (Thermo Fisher Scientific, catalogue no. 65001) and all subsequent steps were performed on the bead-bound DNA fraction. Hi-C library preparation continued with end polishing reaction, which involved incubation of DNA with 1x T4 ligase buffer (New England Biolabs, catalogue no. B0202S), 2.5mM each dNTP, 50U T4 Polynucleotide Kinase (New England Biolabs, catalogue no. M0201), 12U T4 DNA Polymerase (New England Biolabs, catalogue no. M0203), and 5U Klenow DNA polymerase I, at room temperature for 30 minutes. PolyA tail was added by incubating the DNA sample in 1X NEBuffer™ 2 (New Enlgand Biolabs, catalogue no. B7002S) with 0.5mM dATP and 25U Klenow Fragment (3'→5' exonuclease) (New England Biolabs, catalogue no. M0212) at 37°C for 30 minutes. DNA fragment ends were then ligated to Illumina TruSeq unique dual indexes (Integrated DNA Technologies) in 1X T4 Ligation buffer with 5% PEG and 15U T4 DNA Ligase for 2 hours at room temperature or overnight at 16°C. Lastly, libraries were PCR amplified using Illumina forward (AATGATACGGCGACCACCGAGATCTACAC) and reverse (CAAGCAGAAGACGGCATACGAGAT) primers and KAPA HiFi HotStart ReadyMix (Roche, catalogue no. KK2602) for 6-10 cycles. Resulting fragments were size-selected with AMPure XP beads.

treatment_protocol: For WGD in vitro in RPE TP53-/-, two methods were used to induce cytokinesis failure. Cells were incubated for 24 hours with 0.1ug/ml nocodazole (Sigma-Aldrich, catalogue no. M1404) containing medium. Following nocodazole treatment, the cells were exposed for an additional 24 hours to 4uM dihydrocytochalasin B (Cayman Chemical, catalogue no. 20845) and then were allowed to recover for 48 hours. Alternatively, cells were incubated for 24 hours with 9uM of the CDK1 inhibitor RO-3306 (Sigma-Aldrich, catalogue no. SML0569) for G2 synchronization. Drug was washed and cells were then treated with 4uM dihydrocytochalasin B for 24 hours. Cells were allowed to recover for 48 hours and tetraploid cells were sorted based on cell cycle staining with 1ug/ml Hoechst 33342 (Sigma-Aldrich, catalogue no. H1399). For mitotic slippage induction, 0.1ug/ml nocodazole (Sigma-Aldrich, catalogue no. M1404) was added to the growth medium to CP-A, CP-A TP53-/- and K562 cells, which were then incubated for 72, 72, and 48 hours, respectively. For cells with elongated G1 phase after tetraploidisation, CP-A TP53-/- cells were WGD induced with 0.1ug/ml nocodazole for 72 hours and treated with 0.5uM of the CDK4/6 inhibitor Palbociclib (Sigma-Aldrich, catalogue no. PZ0383) for the last 16 hours of the WGD induction. RPE TP53-/- and CP-A TP53-/- cells were then kept in culture for 20 weeks. RPE TP53-/- control and 20w pWGD cells were injected in NSG mice. After 6 weeks, only 20w pWGD injected mice formed tumours in vivo (T1, T2, T3), which were collected and dissociated into single cells with human Tumour Dissociation Kit (Miltenyi Biotec, catalogue no. 130-095-929) and Mouse Cell Depletion Kit (Miltenyi Biotec, catalogue no. 130-104-694) following manufacturer’s protocols. For CP-A TP53-/- control, 6w pWGD, and 20w pWGD, 100,000 cells were resuspended in complete MDCB-153 media were mixed in a 1:1 ratio with 0.7% sterile noble agar (Thermo Fisher Scientific, catalogue no. J10907), then plated on Costar® ultra-low attachment plates (Corning, catalogue no. 3473) on top of a mixture of 1:1 MCDB-153 media and 1.4% sterile noble agar. Mixture was allowed to solidify in a humidified atmosphere at 37 degrees C overnight, then fresh complete MCDB 153 media was added on top of the layers of agar. Samples were incubated for up to 10 weeks in normal conditions and media was replaced twice a week. Individual colonies were picked from the agar layer and cultured for downstream analysis. For CIN-only induction, RPE TP53-/- cells were synchronised at G1/S border with 5mM thymidine (Sigma-Aldrich, catalogue no. T9250) for 24 hours. Six hours after thymidine block release, the cells were treated with 500nM of the Mps1 inhibitor Reversine (Sigma-Aldrich, catalogue no. R3904) for 12 hours. Before processing for downstream analyses, cells were allowed to recover for six hours. For isolation of high ploidy cells, CP-A TP53-/- cells were stained with 1ug/ml Hoechst 33342 for cell cycle profiling. Dividing cells with high ploidy (high Hoechst 33342 signal, > 4N peak) were bulk sorted. Cells were allowed to recover overnight, and then fixed for downstream analyses.

value: esophageal epithelium

value: immortalized non-dysplastic metaplasia (Barrett's oesophagus) epithelial cells

tag: condition

value: control


title: CP-A TP53-/-, clone 19, WGD, rep2

value: WGD


title: CP-A TP53-/-, clone 3, WGD, rep1


title: CP-A TP53-/-, clone 19, control, rep2


title: CP-A TP53-/-, clone 19, control, rep1


title: CP-A TP53-/-, clone 3, WGD, rep2


title: H2731_replicate_2_GSK126

description: readcounts_human RNAseq_CRM.txt

value: Bap1 mutated

value: GSK126 treatment


title: H2731_replicate_1_GSK126

description: readcounts_human RNAseq_CRM.txt


title: H2731_replicate_2_DMSO

description: readcounts_human RNAseq_CRM.txt

value: DMSO treatment


title: H2731_replicate_1_DMSO

description: readcounts_human RNAseq_CRM.txt


title: H2810_replicate_1_GSK126

description: readcounts_human RNAseq_CRM.txt

value: Bap1 wildtype


title: H2810_replicate_2_GSK126

description: readcounts_human RNAseq_CRM.txt


title: H2810_replicate_2_DMSO

description: readcounts_human RNAseq_CRM.txt


title: H2810_replicate_1_DMSO

description: readcounts_human RNAseq_CRM.txt


title: PLC cells - H3K27ac

first: Li

last: Peng

address: No. 107 Yanjiang West Road

institute: Sun Yat-Sen Memorial Hospital

data_processing:
For the analysis of ChIP-seq data, Bowtie2 was used to align sequencing reads onto the human reference genome hg19.
MACS2 was used to call peaks, deeptools was used to rorate bigwig files, and ROSE was used to identify SEs.
Assembly: hg19
Supplementary files format and content: wig
Supplementary files format and content: peak text files

source_name: HCC cell lines

growth_protocol: Hepatocellular carcinoma (HCC) cell lines PLC were cultured in DMEM (Thermo, USA) supplemental with 10% FBS (Gibco, USA) and penicillin & streptomycin (Hyclone, USA) in an incubator with 5% CO2 at 37°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody histone-3-lysine-27 acetylation (H3K27ac).
The purified ChIP DNA samples and their input DNA were diluted and send to BGI Genomics for library construction and sequencing.

treatment_protocol: No special treatment

value: liver

value: PLC

tag: chip antibody

value: H3K27ac (ABCam, ab4729)

value: untreated


title: CP-A TP53-/-, clone 19, WGD, rep1


title: sgMETTL16+OE-METTL16.rep2

city: Monrovia

first: Jianjun

last: Chen

state: CA

department: Systems Biology

institute: Beckman Research Institute of City of Hope

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
RNA-seq reads were aligned to the GRCh38 genome assembly using STAR
The aligned reads were then assigned to genes using RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: table delimited text file containing the expression of genes

growth_protocol: The NOMO-1 cells infected with indicated lentivirus were expanded in RPMI1640 medium with 10% FBS, 1 X penicillin-streptomycin, plasmocin prophylactic, and 2 ug/ml puromycin for 1-2 weeks and the cells were collected.

extract_protocol:
Total RNAs were isolated from the whole cells with QIAzol and  ribosome RNA was depleted from total RNA using Ribo-Zero plus rRNA depletion kit; ribo-zero-RNA.
Both RNA samples were utilized for next-generation sequencing (NGS). The library preparation was constructed using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) and was quantified by BioAnalyzer High Sensitivity DNA chip, and then was deeply sequenced on the Illumina HiSeq 2500.

treatment_protocol: Without special treatment

value: Acute myeloid leukemia

value: METTL16 rescue


title: sgMETTL16+EV.rep2

value: METTL16 knockout


title: CP-A TP53-/-, clone 3, control, rep1


title: sgMETTL16-1. Input rep1

description:
sgMETTL16-1. Input rep1
sgNS.sgMETTL16-1.diff_peak.1.txt

data_processing:
sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
m6A-seq reads were aligned to the GRCh38 genome assembly using STAR
peaks were called using exomePeak.
the m6A peaks were annotated using an ad hoc perl script.
Genome_build: GRCh38
Supplementary_files_format_and_content: peak files were generated using exomePeak

growth_protocol: The NOMO-1 cells with METTL16 knockout were expanded in RPMI1640 medium with 10% FBS, 1 X penicillin-streptomycin, plasmocin prophylactic, and 2 ug/ml puromycin for 1-2 weeks and the cells were collected.

extract_protocol:
Total RNAs were isolated from the whole cells with QIAzol and poly(A) RNAs were enriched from total RNA with  oligo(dT) polystyrene beads.The anti-m6A antibody (202003, Synaptic Systems) was applied for m6A immunoprecipitation
Both input and m6A IP samples were utilized for next-generation sequencing (NGS). The library preparation was constructed using the TruSeq Stranded mRNA Sample Prep Kit (Illumina) and was quantified by BioAnalyzer High Sensitivity DNA chip, and then was deeply sequenced on the Illumina HiSeq 2500.

tag: merip antibody


title: sgNS.input rep1

description: Negative control sgNS.input rep1

value: sgNS


title: sgNS.input rep2

description: Negative control sgNS.input rep2


title: sgMETTL16+EV.rep1


title: sgMETTL16+OE-METTL16.rep1


title: sgMETTL16-2. IP rep1

description:
sgMETTL16-2. IP rep1
sgNS.sgMETTL16-2.diff_peak.1.txt

value: m6A antibody (Cat#:202003, Synaptic Systems)


title: sgMETTL16-2. Input rep2

description:
sgMETTL16-2. Input rep2
sgNS.sgMETTL16-2.diff_peak.2.txt


title: sgMETTL16-2. Input rep1

description:
sgMETTL16-2. Input rep1
sgNS.sgMETTL16-2.diff_peak.1.txt


title: sgNS.IP rep2

description: sgNS.IP rep2


title: sgMETTL16-2. IP rep2

description:
sgMETTL16-2. IP rep2
sgNS.sgMETTL16-2.diff_peak.2.txt


title: sgMETTL16-1. Input rep2

description:
sgMETTL16-1. Input rep2
sgNS.sgMETTL16-1.diff_peak.2.txt


title: sgNS+EV.rep1

value: sgNS+EV


title: pdx_breast_tumor_TNBC021

description: PDX tumor

value: breast cancer


title: DSM-53pos-ve_3: DMS53/tet-MUC1shRNA

city: Bostone

first: Atsushi

last: Fushimi

address: 450 Brookline Ave.

institute: Dana-Farber Cancer Institute

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).

growth_protocol: NCI-H69 cells were cultured in RPMI 1640 medium (Corning, Corning, NY, USA) supplemented with 10% FBS and 2 mM glutamine. DMS53 cells were cultured in Weymouth's medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% FBS.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

treatment_protocol: Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline.

value: small cell lung cancer

tag: genotype/resistance

value: puromycin resistance


title: DSM-53pos-ve_2: DMS53/tet-MUC1shRNA


title: DSM-53pos-ve_1: DMS53/tet-MUC1shRNA


title: DSM-53-ve_2: DMS53/tet-MUC1shRNA


title: sgMETTL16-1. IP rep2

description:
sgMETTL16-1. IP rep2
sgNS.sgMETTL16-1.diff_peak.2.txt


title: sgNS+EV.rep2

value: control


title: DSM-53-ve_1: DMS53/tet-MUC1shRNA


title: H69plusve_3: H69/tet-MUC1shRNA


title: sgMETTL16-1. IP rep1

description:
sgMETTL16-1. IP rep1
sgNS.sgMETTL16-1.diff_peak.1.txt


title: pdx_breast_tumor_TNBC044

description: PDX tumor


title: H69-ve_3: H69/tet-MUC1shRNA


title: H69-ve_1: H69/tet-MUC1shRNA


title: H69-ve_2: H69/tet-MUC1shRNA


title: DSM-53-ve_3: DMS53/tet-MUC1shRNA


title: pdx_breast_tumor_TNBC089

description: PDX tumor


title: SCC34-GefT3

city: Barcelona

first: Purificación

last: Muñoz

address: Av Gran Vía de L'Hospitalet 199-203

country: Spain

institute: IDIBELL

description:
H34E
2019-10-11_PMunoz_RNAseq_hg38_allsamples_raw_counts

data_processing:
Strand-specific 50-bp paired-end reads were generated using a HiSeq 2500 sequencer (Illumina).
The quality of the fastq files was checked using the FastQC and the Qualimap (rnseq module – version 2.2.1) software
An estimation of ribosomal RNA in the raw data was obtained with riboPicker (version 0.4.3)
Reads were aligned with the STAR mapper (version 2.5.2a) to release 88 of the Homo sapiens ENSEMBL version of the genome (GRCh38/hg38 assembly).
A raw count of reads per gene was also obtained with STAR (quantMode GeneCounts option).
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: From the fastq files were generated two excel files that contain the number of counts for each gene in the different analyzed samples. The file "2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts" contains the counts corresponding to the cSCC10-, cSCC16- and cSCC24-PDXs, and the file "2019-10-11_PMunoz_RNAseq_hg38_allsamples_raw_counts" contains the counts corresponding to the cSCC34-PDX. The RNA-seq of all the models analysed has been carried out by the same laboratory located at the Genomic Unit in the Genomic Regulation Center (CRG), Barcleona. All data was generated and processed under the same criteria and using the same tools as the models were generated

source_name: sorted cSCC-PDX cells

growth_protocol: cSCC-PDX samples were engrafted on NOD-scid IL2Rgamma null (NSG) mice and tumor volume was monitored every 2 days during the treatment

extract_protocol:
Total RNA was isolated from FACS-sorted tumor cells by using RNAesay Mini Kit (Qiagen). RNA quality was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina TruSeq protocols

treatment_protocol: When tumors were detectable (approximately 380 mm3), mice were randomly assigned to a control or inhibitor treatment group, and were orally treated with gefitinib, or vehicle every 48 hours. Intrinsically resistant cSCC34-PDXs were continuously treated with gefitinib. Mice carrying cSCC10-, cSCC16- and cSCC24-PDXs received 21 doses of gefitinib, which showed a stable and significant reduction of tumor growth. Then, treatment was halted in these mice, allowing tumor relapse. Samples of relapsed tumors were engrafted in new NSG mice, and when they were detectable were again treated with gefinitib for one or two cycles more to test the acquisition of gefitinib resistance.

tag: group

value: gefitinib-treated

value: Cutaneous squamous cell carcinoma

value: Tumor


title: SCC24-GefR2.1

description:
H24E
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts

value: gefitinib-resistant


title: SCC24-GefR2.2

description:
H24F
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: SCC34-GefT2.2

description:
H34D
2019-10-11_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: SCC34-PDX3

description:
H34C
2019-10-11_PMunoz_RNAseq_hg38_allsamples_raw_counts

value: Control


title: SCC24-GefR2

description:
H24D
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: SCC16-GefR2.2

description:
H16E
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: SCC16-GefR4

description:
H16F
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: SCC34-PDX1

description:
H34A
2019-10-11_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: SCC24-PDX3

description:
H24C
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: SCC16-GefR2.1

description:
H16D
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: H69plusve_2: H69/tet-MUC1shRNA


title: SCC24-PDX2

description:
H24B
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: SCC16-PDX2

description:
H16B
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: SCC16-PDX3

description:
H16C
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: SCC34-PDX2

description:
H34B
2019-10-11_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: SCC24-PDX1

description:
H24A
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: SCC16-PDX1

description:
H16A
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: SCC10-GefR3

description:
H10F
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: H69plusve_1: H69/tet-MUC1shRNA


title: sgNS.IP rep1

description: sgNS.IP rep1


title: SCC34-GefT4.1

description:
H34F
2019-10-11_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: Prototype TG 2

type: protein

city: Stanford

first: Allan

last: Feng

address: 269 Campus Dr

department: Imm/Rheum

institute: Stanford School of Medicine

description: Antibodies in samples bind to conjugated beads in array. The fluorescence measured as MFI from the secondary antibody was used to determine antibody reactivity.

hyb_protocol: A secondary antibody conjugated to a fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from samples.

scan_protocol: A Luminex FlexMAP 3D instrument was used to measure fluorescence (in MFI) from each  barcoded bead.

data_processing: Sample replicate MFI values were averaged for each antigen. The average barebead MFI was then subtracted from the average MFI of each sample and antigen.

label: R-PE conjugated goat anti-human IgG secondary antibody

molecule: protein

source_name: Serum/Plasma

extract_protocol: Blood was collected from patients and healthy controls. The blood was then processed into serum or plasma which was then run on our arrays.

value: Prototype Autoimmune Disease Sample


title: SCC10-GefR1.1

description:
H10E
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: SCC10-GefR1

description:
H10D
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: Prototype Ro 2

label_protocol: A secondary antibody conjugated to a fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from samples.


title: SCC10-PDX3

description:
H10C
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: Prototype RNP 2


title: SCC10-PDX1

description:
H10A
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: RPE TP53-/-, 20w pWGD tumor 1

data_processing:
The sequencing reads for all the samples were aligned using human reference transcriptome (hg19, Ensembl-87 build) with the 10x Genomics Cell Ranger pipeline (version 3.1.1) with default parameters. The Seurat R package (v3.1.5) was utilized for data processing. Raw UMI read counts data for each sample were read as Seurat data objects by keeping genes expressed in at least one cell. The intersection of genes present in all datasets was kept and the merge function from the library was applied to merge the data. Cells having less than 200 and more than 10000 genes expressed were removed from the analysis. Cells that had over 8% of mitochondrial UMIs genes expression were removed as well. At this stage, the library depths were standardized using the NormalizeData function from Seurat in which UMI counts for each cell divided by the total UMI counts for that cell with a scaling factor set at 10000. The expression matrix thus obtained was natural log-transformed.
Assembly: hg19
Supplementary files format and content: RPE_cells_metadata.tsv contains, for each cell, information about the sample it comes from and the infercnv cluster it was assigned
Supplementary files format and content: RPE_gene_expression.tsv contains the gene expression matrix as calcualted by cell-ranger

source_name: retinal epithelium

growth_protocol: RPE TP53-/- cells were grown in DMEM/F-12, GlutaMAX™ (catalogue no. 10565018) supplemented with 10% fetal bovine serum (Thermo Fisher Scientific, catalogue no. 10270106) and 1% Antibiotic-Antimycotic (Thermo Fisher Scientific, catalogue no. 15240062).

extract_protocol: Single-cell RNA sequencing was performed using Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10X Genomics) following manufacturer’s protocol. All conditions were sequenced in one replicate, with a target of 3000 cells per condition.

treatment_protocol: For WGD, RPE TP53-/- cells were incubated for 24 hours with 0.1ug/ml nocodazole (Sigma-Aldrich, catalogue no. M1404) containing medium. Following nocodazole treatment, the cells were exposed for an additional 24 hours to 4uM dihydrocytochalasin B (Cayman Chemical, catalogue no. 20845) and then were allowed to recover for 48 hours. Cells were then kept in culture for 6 weeks (6w pWGD) and 20 weeks (20w pWGD) in vitro. Control and 20w pWGD cells were injected in NSG mice. After 6 weeks, only 20w pWGD injected mice formed tumours (in vivo T1, T2, T3), which were collected and dissociated into single cells with human Tumour Dissociation Kit (Miltenyi Biotec, catalogue no. 130-095-929) and Mouse Cell Depletion Kit (Miltenyi Biotec, catalogue no. 130-104-694) following manufacturer’s protocols.

value: retinal epithelium

value: hTERT RPE-1

value: immortalized retinal epithelial cells grown subcutaneously in NSG mice

value: 20w pWGD T1, in vivo


title: Subject HC 33

value: Health Control


title: RPE TP53-/-, 20w pWGD tumor 3

value: 20w pWGD T3, in vivo


title: SCC10-PDX2

description:
H10B
2018-08-01_PMunoz_RNAseq_hg38_allsamples_raw_counts


title: Prototype Centromere 2


title: Subject HC 30


title: RPE TP53-/-, 20w pWGD

value: immortalized retinal epithelial cells

value: 20w pWGD


title: Subject HC 32


title: RPE TP53-/-, 6w pWGD

value: 6w pWGD


title: RPE TP53-/-, 20w pWGD tumor 2


title: RPE TP53-/-, control


title: Subject HC 29


title: Subject HC 27


title: Subject HC 31


title: Prototype Scl-70 2


title: Subject HC 26


title: Subject HC 25


title: Subject HC 24


title: Patient P1.1, mRNA-derived cDNA, scRNA-seq (capture reaction 2of2)

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

description:
10x Genomics
152of2_MPS12341081_G12_8139

data_processing:
QC: Sequence reads quality was assessed using BVAtools (https://bitbucket.org/mugqic/bvatools)
Pre-processing: Cell Ranger v3.0.1 for scRNA was used to map reads to the hg38 human reference genome assembly, perform filtering, and count barcodes and unique molecular indexes (UMIs).
Filtering: Genes that were not expressed in any of the datasets were discarded. Cells with >20% of mitochondrial genes were excluded. To filter out low quality cells and doublets, cells falling outside the [-1SD;+2.5SD] interval for the UMI and gene count distribution were excluded. To further identify and remove doublets, we first manually remove cells which co-express cell-specific markers (CD14, CD79A, TRBC1, HBA2 and LILRA4) then the DoubletFinder package v2.0.3 was used to identify and filter out remaining cell doublets (McGinnis et al., 2019).
Joint sample analysis: After dead cells and doublet removal, the patient and control samples were jointly analyzed using the Seurat v4.0.2 R package (Stuart et al., 2019) and cell clustering was performed using the Uniform Manifold Approximation and Projection dimension reduction method (Becht et al., 2019) using the most variable genes, but excluding mitochondrial and ribosomal protein genes, as well as sex-related genes since the two patients are females. Based on the clustering, we performed subclustering for the large immune cell lineages separately (myeloid/pDC, T/NK lymphocytes, and B cells) to identify residual remaining doublets, hence small residual cell clusters expressing multiple cell-specific markers were excluded. A final UMAP clustering identified fourteen distinct 11 T cell and 2 B cells; myeloid cells were excluded from further analyses because of the low number of cells found in patient samples, which is likely due to poor survival of these cells during sample freezing and shipping. The protein markers identified using CITE-seq were used to ascertain the cell identity to each cluster, in conjunction with the MAST approach (Finak et al., 2015) to identify the marker genes for each cluster, in conjunction with the MAST approach (Finak et al., 2015) to identify the marker genes for each cluster.
Differential gene expression analysis:  was performed using MAST for each lymphoid cell cluster by comparing the RNA expression from P1.2 and P2 vs the 5 healthy controls. Adjusted p-values were estimated using the Benjamini-Hochberg (BH) procedure. Every significant differentially expressed gene (absolute FC >=1.5 and adj-p-value ≤0.001) was extracted as down- or up-regulated and used for downstream analysis.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Whole blood

extract_protocol:
The frozen PBMCs were quickly thawed at 37°C and gently resuspended by serial additions of DMEM + 10% heat-inactivated FBS, for a final volume of 14ml. Following centrifugation at 300g for 5 min, cells were washed twice with 5ml DMEM + 10% HI-FBS to remove cell debris. Cell counting and viability assessment was done using the LIVE/DEAD™ Viability kit (ThermoFisher Scientific), according to manufacturer’s guidelines.
Single-cell library: The samples were loaded onto a 10X Genomics Chromium G chip aiming to capture 10,000 cells per samples. The reverse transcription and library preparation was performed using the Chromium Single Cell 3′ v2 Reagent Kits following manufacturers guidelines. The cDNA library quality was assessed using a TapeStation (Agilent).
Sequencing: The cDNA libraries were sequenced on a HiSeq 4000 sequencer.

tag: individual

value: Patient P1.1

value: Peripheral Blood Mononuclear Cells (PBMC)

value: Whole blood


title: MAC101, 4dpi, 3

city: Leiden

first: Herman

middle: Pieter

last: Spaink

address: Einsteinweg 55

department: Institute of Biology

institute: Leiden University

description:
150 nucleotides
Hu_Mac101 infection vs. pvp control_DEseq
Expression Browser.xlsx
HJ72FDSX3_104711-002-023_TCCACGTT-GTTCAACC_L004

data_processing:
RNAseq reads were aligned against the zebrafish genome (GRCz11) by using CLC genomic workbench software (QIAGEN, Cat. 832583).
Read mapping and statistical analyses were performed using the program CLC Genome Workbench version 21
Assembly: the zebrafish genome GRCz11
Supplementary files format and content: excel files include normalized read values per million for each Sample and ratios and P values of the infected version the uninfected situation for MAC101 and Mma20 respectively.
Supplementary files format and content: Total counts
Supplementary files format and content: RPKM
Supplementary files format and content: TPM
Supplementary files format and content: CPM

organism: Danio rerio

source_name: whole embryos

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://zfin.org).

extract_protocol:
Zebrafish larvae from  all groups  groups (n=4) were resuspended and crushed in 0.5 ml of TRIzol Reagent
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760S/L) was used to process the samples. Briefly, mRNA was isolated from total RNA using oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation of the sequencing adapters and PCR amplification of the resulting product. The quality and yield after sample preparation was measured with Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).

treatment_protocol:
Infection with bacteria
4500 CFU Mycobacterium avium strain Mac101 and 250 CFU M. marinum strain Mma20

value: AB/TL wild type

value: whole embryos

tag: time

value: 5 days post fertilization

tag: agent

value: Mycobacterium avium strain Mac101


title: Patient P1.1, mRNA-derived cDNA, scRNA-seq (capture reaction 1of2)

description:
10x Genomics
151of2_MPS12343356_C08_8139


title: MAC101, 4dpi, 2

description:
150 nucleotides
Hu_Mac101 infection vs. pvp control_DEseq
Expression Browser.xlsx
HJ5Y5DSX3_104711-002-022_GACGAACT-TCGCATTG_L001


title: Subject HC 23


title: MAC101, 4dpi, 4

description:
150 nucleotides
Hu_Mac101 infection vs. pvp control_DEseq
Expression Browser.xlsx
HJ72FDSX3_104711-002-024_AACCAGAG-AACCGAAG_L004


title: Subject UMR 45

value: COVID-19 Negative Patients from Marburg


title: MAC101, 4dpi, 1

description:
150 nucleotides
Hu_Mac101 infection vs. pvp control_DEseq
Expression Browser.xlsx
HJ72FDSX3_104711-002-021_CCGCTTAA-ACGATGAC_L004


title: Subject UMR 44


title: Subject HC 28


title: Mma20, 4dpi, 4

description:
150 nucleotides
Hu_Mma20 infection vs. pvp control_DEseq
Expression Browser.xlsx
HJ72FDSX3_104711-002-020_GACGTCAT-TCAACTGG_L004

value: Mycobacterium marinum strain Mma20


title: Mma20, 4dpi, 3

description:
150 nucleotides
Hu_Mma20 infection vs. pvp control_DEseq
Expression Browser.xlsx
HJ72FDSX3_104711-002-019_GGAGGAAT-AACCGTTC_L004


title: pdx_breast_tumor_TNBC013

description: PDX tumor

tag: xenograft

value: breast cancer


title: PVP Control, 4dpi, 4

description:
150 nucleotides
Hu_Mma20 infection vs. pvp control_DEseq
Hu_Mac101 infection vs. pvp control_DEseq
Expression Browser.xlsx
HJ72FDSX3_104711-002-016_ATCTGACC-AAGTCGAG_L004

value: PVP Control


title: Mma20, 4dpi, 2

description:
150 nucleotides
Hu_Mma20 infection vs. pvp control_DEseq
Expression Browser.xlsx
HJ5YMDSX3_104711-002-018R_CAACACAG-TGGCTATC_L004


title: PVP Control, 4dpi, 3

description:
150 nucleotides
Hu_Mma20 infection vs. pvp control_DEseq
Hu_Mac101 infection vs. pvp control_DEseq
Expression Browser.xlsx
HJ72FDSX3_104711-002-015_CTTAGGAC-CAGTGAAG_L004


title: PVP Control, 4dpi, 1

description:
150 nucleotides
Hu_Mma20 infection vs. pvp control_DEseq
Hu_Mac101 infection vs. pvp control_DEseq
Expression Browser.xlsx
HJ72FDSX3_104711-002-013_GAATCCGT-TGGAGTTG_L004


title: Subject UMR 43

description: Antibodies in samples bind to conjugated beads in array. The fluorescence measured as MFI from the secondary antibody was used to determine antibody reactivity.


title: Subject UMR 42


title: Subject UMR 36


title: aged_rep_2

city: Chongqing

first: jiangyong

last: he

address: Tiansheng Li Street of Beibei District

institute: southwest university

description:
aged brain immune cells
sorted from 3 mixed zebrafish brain tissue

data_processing:
The cell Ranger software pipeline (version 5.0.0) provided by 10xGenomics was used to demultiplex cellular barcodes, map reads to the reference genome and generate  gene-cell matrices, the gene-cell matrices (named ‘raw_gene_bc_matrices’by 10x Genomics) generated by Cell Ranger served as input data for further analyses with Seurat v3
Genome_build: GRCz11
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: brain immune cells

extract_protocol:
Adult and aged zebrafish were anesthetized on ice. The whole brain was dissected in ice-cold PBS and collected into buffer (fresh PBS with 5% fetal bovine serum (FBS) and 0.1% DNaseI). The collected brains was cut into pieces, dissociated with digested buffer (0.25% trypsin in buffer) for 15 min and passed through a 26G needle 5 times to further smash the tissue. The processed cell samples were filtered with 40 uM cell strainer and collected with 800g at 4℃ for 5min, then resuspended to single-cell suspension with ice-cold 5% FBS. Next, cell sorting was performed by flow cytometry (Moflo XDP, Beckman) to gain GFP+ immunocytes.Then the collected single-cell products were performed 10X single cell RNA sequence
RNA libraries were prepared with Chromium Single cell 3` Reagent Kits (v3.1 chemistry, PN- 1000121) according to the manufacture`s protocol

value: WT

value: brain

tag: age

value: 26 months


title: Subject UMR 39


title: Subject UMR 38


title: Subject UMR 41


title: Subject UMR 40


title: human blood (PBMC), HTO-derived cDNA, rep 2

city: Berkeley

first: Iain

middle: Christopher

last: Clark

address: 374 Stanley Hall

institute: University of California, Berkeley

description:
Cell Hashing library: read1 file contains cell barcode and molecular index; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
TS20220816_HTO_FR_6

library_source: other

data_processing:
Barcode error correction on RNA and HTO FASTQs performed with PIPseeker V1.0.0, along with RNA matrix generation. HTO count matrices were generated using CITE-seq Count (v1.4.3). Background barcodes were excluded from the RNA matrices.
Further processing was done with Seurat v4.1.0 (demultiplexing, hashtag identification, clustering).
Assembly: GRCh38.p13
Supplementary files format and content: Zipped folders containing filtered gene expression (RNA) and hashtag oligonucleotide (HTO) matrices, consisting of:  barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: Single-cell RNA-Seq with hashtag oligonucleotide (HTO) workflow

source_name: Blood

growth_protocol: PBMCs (AllCells Lot #3082436) were thawed from a cryolot at 37C for 2 mins, then resuspended in RPMI-1640 (Thermofisher #11875093) supplemented with 10% FBS (ThermoFisher #A3840001) at 37C.

extract_protocol:
Libraries were prepared using Fluent BioSciences' PIPseq single-cell RNA-sequencing kit.
Libraries were prepared using Fluent BioSciences' PIPseq single-cell RNA-sequencing kit.

tag: tissue

value: Blood

value: PBMC (AllCells PBMC lot #3052467)

tag: library type

value: HTO

tag: antibodies/tags

value: TotalSeq-A anti-human antibody hash A0255


title: aged_rep_1

tag: genotype


title: Subject UMR 32


title: PVP Control, 4dpi, 2

description:
150 nucleotides
Hu_Mma20 infection vs. pvp control_DEseq
Hu_Mac101 infection vs. pvp control_DEseq
Expression Browser.xlsx
HJ72FDSX3_104711-002-014_CATGAGCA-GCAAGATC_L004


title: Subject UMR 31


title: Subject UMR 37


title: human blood (PBMC), mRNA-derived cDNA, rep 2

description:
3' mRNA library: read1 file contains cell barcode and molecular index; read2 file contains transcript
poly A RNA
TS20220816Gx_FR_6

tag: cell type

value: mRNA


title: Mma20, 4dpi, 1

description:
150 nucleotides
Hu_Mma20 infection vs. pvp control_DEseq
Expression Browser.xlsx
HJ5Y5DSX3_104711-002-017_TCCTCATG-AGGTGTAC_L001


title: human blood (PBMC), mRNA-derived cDNA, rep 1

description:
3' mRNA library: read1 file contains cell barcode and molecular index; read2 file contains transcript
poly A RNA
TS20220816Gx_FR_5

value: PBMC  (AllCells PBMC lot #3052467)


title: human blood (PBMC), HTO-derived cDNA, rep 1

description:
Cell Hashing library: read1 file contains cell barcode and molecular index; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)
TS20220816_HTO_FR_5

value: TotalSeq-A anti-human antibody hash A0253


title: Subject UMR 34


title: adult_rep_2

description:
adult brain immune cells
sorted from 3 mixed zebrafish brain tissue

value: 12 months


title: Subject UMR 33


title: Subject UMR 30


title: Subject UMR 35


title: Subject UMR 27


title: Subject UMR 29


title: Subject UGMLC 15

value: ARDS Patients from Giessen


title: Subject UGMLC 16


title: Fed

city: Jinan

first: Yuan

last: Detian

email: yuandt@sdu.edu.cn, lishiyang@sdu.edu.cn

address: Wenhuaxi Road 44

institute: Shandong University

description: 10x Genomics

data_processing:
Spaceranger software (version 2.0.0, 10x Genomics) was used to align and obtain raw counts from each of the spots on the Visium spatial transcriptomics slides against the mm10 mouse genome reference data.
Raw gene expression matrix, together with spatial location of spots and tissue H&E images, were used to create a Seurat object with a Load10X_spatial function, and normalisation was carried out by SCTransform.
Assembly: mm10
Library strategy: Visium Spatial gene expression

source_name: Liver

extract_protocol:
Livers were embedded in tissue-Tek (OCT) and snap-frozen using dry ice slurry. Cryosections were cut at 10-μm thickness, mounted onto the Visium Spatial Gene Expression Slide (10x Genomics, PN-2000233). Sections were placed on Thermocycler Adaptor with the active surface facing up, incubated for 1 min at 37 °C, and fixed for 30 min with methyl alcohol in –20 °C, followed by staining with H&E (Eosin, Dako CS701, Hematoxylin Dako S3309, bluing buffer CS702). The brightfield images were taken on VS120 (Olympus) whole-slide scanner.
Visium spatial gene expression was processed using Visium spatial gene expression slide and Reagent Kit (10× Genomics, PN-1000184). For each well, Slide Cassette was used to create leakproof wells for adding reagents. 70 μL Permeabilization enzyme was added and incubated at 37 °C for 20 min. Each well was washed with 100 μL SSC, and 75 μL reverse transcription Master Mix was added for cDNA Synthesis. At the end of first-strand synthesis, remove reverse transcription Master Mix from the wells. Add 75 μL 0.08 M KOH and incubate 5 min at room temperature, then remove the KOH from wells and wash with 100 μL EB buffer. Add 75 μL Second Strand Mix to each well for second-strand synthesis. cDNA amplification was performed on a S1000TM Touch Thermal Cycler (Bio Rad). According to the manufacture’s introduction, Visium spatial libraries were constructed using Visium spatial Library construction kit (10× Genomics, PN-1000184).

value: Liver

value: C57BL6J Wild type

tag: treatment

value: Fed


title: Refed

description: 10x Genomics

value: Fasted 16h then refed 6h


title: PBMC T100

description: Patient 34, replicate 1

data_processing:
The sample is aligned to human GRCh38.p13 with Salmon and quantified with alevin v1.2.0
Assembly: GRCh38.p13
Supplementary files format and content: Filtered gene expression matrices for AllCells PBMC lot #3052467, generated following alignment of paired-end fastqs using Salmon alevin. Background barcodes were excluded from the gene expression matrices.

source_name: human blood (PBMC)

growth_protocol: PBMCs (AllCells Lot #3052467) were thawed from a cryolot at 37C for 2 mins, then resuspended in RPMI-1640 (Thermofisher #11875093) supplemented with 10% FBS (ThermoFisher #A3840001) at 37C.

extract_protocol: Libraries were prepared using Fluent BioSciences' PIPseq single-cell RNA-sequencing kit.

value: blood, PBMC


title: Subject UGMLC 12


title: Subject UGMLC 14


title: Subject UGMLC 13


title: adult_rep_1

value: WT


title: Subject UGMLC 10


title: Subject UGMLC 11


title: Subject UMR 28

value: COVID-19 Negative Patients from Marburg


title: Subject UGMLC 17


title: MP001 T200

description: Patient 34, replicate 1

data_processing:
The sample is aligned to human GRCh38.p13 with Salmon and quantified with alevin v1.2.0
Assembly: GRCh38.p13
Supplementary files format and content: Filtered gene expression matrices for sample MP001, generated following alignment of paired-end fastqs using Salmon alevin. Background barcodes were excluded from the gene expression matrices.

source_name: Human breast tissue

extract_protocol:
Fresh reduction mammoplasty tissue was processed according to Murrow et al (2020) doi: https://doi.org/10.1101/430611
Libraries were prepared using Fluent BioSciences' PIPseq single-cell RNA-sequencing kit.

value: Breast tissue


title: Fasted

description: 10x Genomics

value: Fasted 16h


title: Subject UGMLC 8


title: D14_KO_Rep2

city: NanJing

first: Yumei

last: Jia

address: Xiaolingwei Street, Xuanwu District, Nanjing

institute: NanJing Agricultral University

data_processing:
The clean reads were mapped to the Mus musculus mm10 reference genome using HISAT2 v2.0.5.
Feature Counts (1.5.0-p3) is used to calculate the reads mapped to each gene. Then according to the length of the gene calculate the FPKM of each gene and calculate the reads mapped to that gene.
DESeq2 were used to identify differentially expressed genes.
Functional enrichment (GO annotation, KEGG) of gene sets with different expression patterns was performed using cluster Profiler.
Assembly: mm10
Supplementary files format and content: tab-delimited FPKM files include FPKM values for each Sample …

source_name: mouse differentiated cells from ESCs

growth_protocol: mESCs were cultured under 5% CO2 at 37 °C on plates were pre-coated with gelatin.mESCs cell culture medium consisting of knockout DMEM supplemented with 20% fetal bovine serum (FBS, ES quality, Hyclone), 1,000 U/ml leukemia inhibitory factor (LIF)(ESGRO, Chemicon), 0.1 mM non-essential amino acids, 0.1 mM β-mercaptoethanol, 2 mM L-glutamine, and penicillin (100 U/ml) and streptomycin (100 µg/ml). mESCs were cultured in medium without LIF as hanging drop for 3 days, and then transferred to microwell plates for 11 days.

extract_protocol:
Snap29 KO and WT mESCs and differentiated cells were washed by PBS and trypsinized to single cells, and then were committed to RNA extraction
The initial RNA for library construction is total RNA, and the mRNA with poly A tail is enriched by Oligo (dT) magnetic beads. Using fragmented mRNA as a template and random oligonucleotides as primers, the first strand of cDNA is synthesized in the M-MuLV reverse transcriptase system, which was followed by second strand cDNA synthesis. The cDNA fragments were added by a single “A” base and subsequently ligated with the adapter. The products were then purified and enriched with PCR amplification. PCR yield was quantified and samples were pooled together to make a single-strand DNA circle (ssDNA circle), generating the final library.

tag: cell line

tag: strain

value: Snap29 knockout


title: Patient 873 time point 2 replicate 2

description: Patient 873 time point 2 replicate 2

data_processing:
The sample is aligned to human GRCh38.p13 with Salmon and quantified with alevin v1.2.0
Assembly: GRCh38.p13
Supplementary files format and content: Matrices are zipped folders of 3 files: (1) sparse matrix, (2) barcodes file, (3) genes file. Raw data are gzipped fastqs, most of which have four files per sample: 2 lanes from 2 reads. Two samples were sequenced on a single lane NovaSeq run, and therefore only have the two reads from a single lane.

source_name: Mixed phenotype acute leukemia (MPAL)

growth_protocol: Patient samples

extract_protocol:
Cryopreserved peripheral blood mononuclear cells and peripheral bone marrow mononuclear cell samples
PIP-seq single cell library prep

treatment_protocol: Patients before and after chemotherapy

tag: sample type

value: B/Myeloid diagnosis -

tag: Sex

value: Female


title: D14_KO_Rep1

treatment_protocol: Snap29 KO and WT mESCs and differentiated cells were washed by PBS and trypsinized to single cells, and then were committed to RNA extraction


title: Subject UGMLC 5

tag: condition


title: Subject UGMLC 3


title: D14_WT_Rep3


title: Subject UGMLC 6


title: Subject UGMLC 7


title: Patient 873 time point 2 replicate 1

description: Patient 873 time point 2 replicate 1


title: D14_WT_Rep2


title: Subject UGMLC 2


title: Subject UGMLC 4


title: Patient 65 time point 2 replicate 2

description: Patient 65 time point 2 replicate 2

value: Male


title: Subject UGMLC 1


title: Subject AA40 T3

value: Influenza Patients from Athens


title: Subject UGMLC 9


title: D14_WT_Rep1


title: KO_Rep3

source_name: mouse ESCs


title: Patient 65 time point 1 replicate 2

description: Patient 65 time point 1 replicate 2


title: D14_KO_Rep3


title: Patient 65 time point 1 replicate 1

description: Patient 65 time point 1 replicate 1


title: Subject AA40 T1


title: Subject AA39 T2


title: Subject AA39 T1


title: Subject AA39 T3


title: Subject AA38 T2


title: Subject AA38 T3


title: KO_Rep2


title: DR3

city: Taigu

first: Chunlei

last: Zou

address: No.1 Mingxian Road

institute: Shanxi Agricultural University

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly
Stringtie-1.3.3b was used to count the read numbers mapped to each gene.
Differential expression analysis of two conditions/groups was performed using the edgeR.
Assembly: beta_vulgaris_Ensembl_44
Supplementary files format and content: filterstat.txt
Supplementary files format and content: transcripts.FPKM.xlsx

organism: Beta vulgaris

source_name: Sugar beet leaves, drought stress

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Strand-specific libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: leaves

value: Drought stress


title: KO_Rep1


title: DR2


title: Subject AA38 T1


title: WT_Rep2


title: Subject AA37 T1


title: Subject AA37 T2


title: Patient 65 time point 2 replicate 1

description: Patient 65 time point 2 replicate 1


title: Subject AA40 T2


title: WT_Rep1


title: CK3

source_name: Sugar beet leaves, well-watered

value: Well-watered


title: Subject AA36 T3


title: Subject AA36 T2


title: Subject AA37 T3


title: Post-ODASS_mPFC_Perseverer_rep3

city: Carouge GE

first: ridouane

last: achargui

address: Rue de la Fontenette, 18BIS

institute: UNIGE

description:
postODASS_mPFC_rawCounts.txt
T125

data_processing:
Quality control, pre-processing and mapping on galaxy platform (https://usegalaxy.org).
Sequencing quality was checked with FASTQC software (0.11.8).
Reads were clipped according to their respective adaptor sequence and trimmed according to their per base sequence quality for each library. Pre-processed reads were aligned to the mm10 mouse downloaded from UCSC genome using RNAstar.
Reads were assigned to genes using Rsubread (v 2.8.1)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each group

source_name: mPFC dissected bulk tissue

extract_protocol:
OFC or mPFC dissection as well as brain tissue imprints were collected in RLT plus buffer and total RNA was extracted following manufacturer's protocol (Qiagen micro elute kit)
RNA libraries were prepared for sequencing using Smartseq v4 ultra low  and Nextera kit from illumina.

tag: line

value: DAT-cre

value: brain

tag: brain area

value: mPFC


title: Subject AA36 T1


title: Post-ODASS_mPFC_Perseverer_rep2

description:
postODASS_mPFC_rawCounts.txt
T112


title: Subject AA35 T3


title: CK1


title: DR1


title: Subject AA35 T2


title: Subject AA35 T1


title: WT_Rep3


title: single-embryo Library 2

city: Grand Rapids

first: Adelheid

last: Lempradl

state: Michigan

address: 333 Bostwick Ave NE

department: Metabolism and Nutritional Programing

institute: Van Andel Institute

data_processing:
RNA-seq reads were demultiplexed, mapped, UMI-deduplicated, and counted using STAR 2.7.8a (mode STARsolo).
Raw gene counts files were merged into a single file and gene symbols were updated using the 'merge' function in base R and release FB2022_04.
The gene counts were analyzed using the RaceID3/StemID2/FateID workflow (Herman et al. 2018). Embryos with less than 250,000 reads or transcripts with < 3 read counts on < 5 samples were filtered out from the analysis (n=122). Unfertilized eggs (n=117) and embryos older than 3h were removed, leaving a total of 84 embryos in the final pseudo-time analysis. Well IDs were converted to embryo IDs based on the meta data described in the paper.
Assembly: Berkeley Drosophila Genome Project assembly release 6.28
Supplementary files format and content: Tab-delimited files containing the raw gene count files.
Supplementary files format and content: comma-separated file containing the normalized counts used for pseudotime analysis.

source_name: single-embryo

growth_protocol: Drosophila genetic reference panel (DGRP) 737 line from Bloomington Stock Center (#83729) was kept in incubators at 25 °C with 60% humidity and a 12-hour light-dark cycle. All flies were raised at constant densities on standardized cornmeal food (Bloomington recipe), Fly food M (LabExpress, Michigan, USA), and transferred into cages 1-2 days after eclosion.

extract_protocol:
Single embryos were homogenized in 500 µL TRIzol™ (Invitrogen, USA) by bead-beating with 0.2 g lysing matrix D beads (MP Biomedicals, USA) at 6 m/s for 30 seconds using the FastPrep-24™ instrument (MP Biomedicals, USA). RNA was then isolated following a miniaturized version of the manufacturer's instructions. Briefly, 100 µL chloroform (Sigma-Aldrich, USA) was added, samples mixed by vortex, incubated 2 min at room temperature (RT), and centrifuged for 15 minutes at 12,000 × g at 4 °C to recover RNA-containing aqueous phase in a fresh 1.5 ml microtube. RNA was precipitated by adding 250 µL ice-cold isopropanol (Sigma-Aldrich, USA) and 2 µL GlycoBlue™ (Thermo Fisher, USA), samples mixed by hand, incubated for 10 min at RT, and centrifuged for 10 minutes at 12,000 × g at 4°C. RNA pellets were washed with 1 ml 75% (v/v) ethanol (Pharmco, USA), dried and stored at -80 °C until further use. This same protocol was followed to isolate RNA from fixed embryos using 1 ml TRIzol™ and proportional changes in chloroform and isopropanol.
RNA-seq was carried out following a miniaturized version of the sensitive highly-multiplexed single-cell RNA-seq (CEL-Seq2) protocol (Hashimshony et al. 2016)  using the I.DOT liquid handler (CELLINK). Dried RNA was resuspended in 8 µL nuclease-free water (Invitrogen, USA) and 120 nL dispensed into a 384-well plate holding 240 nL of primer-mix including 192 different cell barcodes with unique molecular identifiers (UMI). Subsequent steps and reagents are detailed in Sagar et al., 2018, except that libraries were diluted 1:10 (cDNA:H2O) before an 11-cycle amplification.
Modified CelSeq2 protocol

value: single-embryo

tag: developmental stage

value: early development (less than or equal to 3 hours)


title: Subject AA34 T1


title: single-embryo Library 1

value: WT


title: Subject AA33 T1


title: Subject AA33 T2


title: Post-ODASS_mPFC_Renouncer_rep2

description:
postODASS_mPFC_rawCounts.txt
T114


title: Post-ODASS_mPFC_Renouncer_rep1

description:
postODASS_mPFC_rawCounts.txt
T97


title: Subject AA32 T1


title: Subject AA32 T2


title: Subject AA31 T1


title: Post-ODASS_mPFC_Perseverer_rep1

description:
postODASS_mPFC_rawCounts.txt
T94


title: Subject AA30 T1


title: CK2


title: Subject AA31 T2


title: Post-ODASS_mPFC_Renouncer_rep3

description:
postODASS_mPFC_rawCounts.txt
T120


title: Subject AA29 T3


title: Post-ODASS_OFC_Perseverer_rep2

description:
postODASS_OFC_rawCounts.txt
T111

source_name: dissected bulk tissue

value: OFC


title: Post-ODASS_OFC_Perseverer_rep3

description:
postODASS_OFC_rawCounts.txt
T124


title: Serum Exo-RNA 33-1

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: primary lung cancer

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

extract_protocol: Exosomes were obtained from the serum of NSCLC patients using ExoQuickTM (System Biosciences, LLC, Palo Alto, CA, USA). Total RNA was extracted using TRIzol reagent (Thermo Fisher Scientific, Waltham, MA, USA) from  isolated exosomes.

value: primary lung cancer

tag: response

value: Responder


title: Post-ODASS_OFC_Perseverer_rep1

description:
postODASS_OFC_rawCounts.txt
T95


title: Serum Exo-RNA 31-1


title: Subject AA29 T1

source_name: Serum/Plasma


title: Subject AA27 T2


title: Subject AA28 T1


title: Subject AA27 T1


title: Serum Exo-RNA 29-1


title: Subject AA32 T3


title: Subject AA26 T2


title: Subject AA26 T1


title: Subject AA25 T1


title: Post-ODASS_OFC_Renouncer_rep2

description:
postODASS_OFC_rawCounts.txt
T115


title: Subject AA24 T1


title: Serum Exo-RNA 28-1

value: Non-responder


title: Serum Exo-RNA 30-1


title: Serum Exo-RNA 26-1


title: Serum Exo-RNA 25-1


title: Subject AA23 T3


title: Subject AA29 T2


title: Post-ODASS_OFC_Renouncer_rep1

description:
postODASS_OFC_rawCounts.txt
T96


title: Pre-ODASS_OFC_Perseverer_rep1

description:
preODASS_OFC_rawCounts.txt
T83

source_name: brain tissue imprint


title: Post-ODASS_OFC_Renouncer_rep3

description:
postODASS_OFC_rawCounts.txt
T119


title: Pre-ODASS_OFC_Perseverer_rep2

description:
preODASS_OFC_rawCounts.txt
T104


title: Subject AA23 T1


title: Pre-ODASS_OFC_Renouncer_rep3

description:
preODASS_OFC_rawCounts.txt
T108


title: Subject AA21 T2


title: Subject AA21 T3


title: Serum Exo-RNA 24-1


title: Subject AA22 T1


title: Subject AA22 T2


title: Subject AA20 T2


title: Pre-ODASS_OFC_Renouncer_rep2

description:
preODASS_OFC_rawCounts.txt
T106


title: Subject AA21 T1


title: Serum Exo-RNA 21-1


title: Subject AA20 T1


title: Serum Exo-RNA 23-1


title: Pre-ODASS_OFC_Renouncer_rep1

description:
preODASS_OFC_rawCounts.txt
T84


title: Subject AA19 T3


title: Subject AA19 T2


title: Serum Exo-RNA 20-1