title: repli-ATAC replicate 3 Nascent chromatin Unbound dTAG


title: repli-ATAC replicate 3 Post-replication chromatin DMSO 2

status: Public on Apr 17 2024

type: SRA

city: Utrecht

first: Francesca

last: Mattiroli

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

library_source: genomic

data_processing:
ATAC Libraries were sequenced 2x50 bp on Illumina NextSeq2000, scEdU-seq Libraries were sequenced 2x100 bp on Illumina NextSeq2000, VASA-seq libraries were sequenced 2x100bp on Illumina Nextseq2000, ChiC-seq libraries were sequenced 2x100bp on Illumina Nextseq2000
See Stewart-Morgan, K.R., et al., (Repli-ATAC 2023), van den Berg et al.,(scEdU-seq, 2022), Salmen et al.,(VASA-seq 2022), Zeller et al., (ChiC-seq 2022)
For Repli-ATAC, Bigwigs files were created using deepTools bamCoverage and bamCompare, with options `--binSize 15000 and a normalization scale factor was applied for spike in normalization. For VASA-seq, scEdU-seq, ChiC-seq,  see  Zeller et al, (ChIC-seq, 2022), van den Berg et al.,(scEdU-seq, 2022), Salmen et al.,(VASA-seq 2022)
Assembly: GRCh38 (Gencode) and dm6 (flybase)
Supplementary files format and content: BigWIg files (15Kb binned) & deduplicated single cell count tables (tsv.gz) & bed files (15kb bins)

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: Human TERT-RPE-1 cells (female) were cultured in Dulbecco’s Modified Eagle’s Medium/Nutrient Mixture F-12, GlutaMAX™ supplement (DMEM, Gibco) containing 10% Fetal Bovine Serum (FBS, Sigma Aldrich) and 100 U/mL penicillin/streptomycin (Gibco) at 37°C in 5% C02

extract_protocol:
Stewart-Morgan, K.R., et al., (Repli-ATAC 2023), van den Berg et al.,(scEdU-seq, 2022), Salmen et al.,(VASA-seq 2022) & Zeller et al., (ChIC-seq, 2022)
Stewart-Morgan, K.R., et al., (Repli-ATAC 2023), van den Berg et al.,(scEdU-seq, 2022), Salmen et al.,(VASA-seq 2022), Zeller et al., (ChIC-seq, 2022)
repli-ATAC-seq, scEdU-seq, VASA-seq & ChIC-seq

treatment_protocol: RPE1 cells were treated for inficiated times with 1 µM of dTAG-v1 molecule (Bio-Techne).

tag: cell line

tag: cell type

value: hTERT-immortalized retinal pigment epithelial cells

tag: treatment

value: DMSO


title: repli-ATAC replicate 3 Nascent chromatin Unbound DMSO


title: repli-ATAC replicate 3 Post-replication chromatin dTAG 2

value: dTAG


title: repli-ATAC replicate 3 Post-replication chromatin dTAG 1


title: dpb4D_BrdU rep4

city: New York

first: zhiguo

last: zhang

state: NY

address: 1130 St. Nicholas Avenue

department: Pediatric and Genetics and Development

country: USA

institute: Columbia University

description: synchronized to G2 ending, nascent DNA on S10 min

data_processing:
mapped to pombe reference genome by Bowtie2
Read coverage in a bin of 1bp was calculated from filtered bam files by deepTools2 and then normalized with total filtered reads number into reads per million (RPM).
Origins were called by MACS2 from BrdU-IP
Assembly: pombe, ASM294v2
Supplementary files format and content: bw, bigwig format, contains the read density at each genomic position

organism: Schizosaccharomyces pombe

source_name: fission yeast

growth_protocol: Strains containing the cdc25-22 temperature-sensitive mutant were first grown at permissive temperature (25°C) until the early-mid log phase (OD 0.2~0.4). Cultures were then incubated at 36°C for 4 hours to arrest cells at the G2 phase of the cell cycle. Cells were then shifted to 25°C to allow them to enter the S phase synchronously.

extract_protocol:
Cells were crosslinked at 60 minutes after temperature shift with the addition of 1% formaldehyde and incubated for 20 minutes with shaking at 25°C. Immunoprecipitation was performed as described in ChIP. Crosslinking was reversed by Chelex-100. Briefly, total and ChIP DNA were incubated at 100°C for 5 minutes and then immediately cooled on ice for 5 minutes. DNA was diluted ten times with BrdU IP buffer (PBS, 0.0625% Triton X-100(v/v)), and incubated with BrdU antibody (BD Bioscience 555627) for two hours at 4°C. Next, Sepharose Protein G beads (Cytiva 17-0618-01) were added and incubated for an additional one hour at 4°C. The beads were then washed three times with BrdU IP buffer and once with TE. Finally, DNA was eluted with TES and purified with the QIAGEN MinElute PCR Purification kit (Qiagen 28004).
AccelNGS 1S Plus DNA library kit (Swift Bioscience, 10096).
eSPAN-seq

treatment_protocol: BrdU was added to a final concentration of 650 μM at 25minutes after the temperature shift.

value: fission yeast

tag: strain

tag: genotype

value: BrdU


title: dpb4D_Input rep4

value: Input


title: repli-ATAC EdU Input CTRL replicate 2 Mature chromatin dTAG


title: dpb4D_H3K56ac_ChIP rep1


title: repli-ATAC replicate 3 Post-replication chromatin DMSO 1


title: dpb4D_BrdU rep3


title: repli-ATAC replicate 3 Mature 15h chromatin dTAG


title: dpb4D_Input rep3


title: dpb4D_H3K56ac_eSPAN rep1


title: repli-ATAC replicate 3 Mature 15h chromatin DMSO


title: repli-ATAC replicate 3 Mature 2h chromatin dTAG


title: repli-ATAC replicate 3 Mature 2h chromatin DMSO


title: WT_BrdU rep3

value: WT


title: repli-ATAC replicate 3 Nascent chromatin dTAG


title: WT_Input rep3


title: mcm22A_dpb4D_H3K4me3_eSPAN rep2


title: WT_H3K56ac_ChIP rep1


title: repli-ATAC replicate 2 Mature 2h chromatin DMSO


title: repli-ATAC replicate 3 Nascent chromatin DMSO


title: repli-ATAC replicate 2 Nascent chromatin dTAG


title: mcm22A_dpb4D_Input rep2


title: mcm22A_dpb4D_H3K4me3_ChIP rep2


title: mcm22A_dpb4D_BrdU rep2


title: repli-ATAC replicate 2 Nascent chromatin DMSO


title: mcm22A_dpb4D_H3K4me3_eSPAN rep1


title: repli-ATAC replicate 1 Mature 2h chromatin DMSO


title: repli-ATAC replicate 1 Mature 2h chromatin dTAG


title: mcm22A_dpb4D_BrdU rep1


title: mcm22A_dpb4D_Input rep1


title: WT_H3K56ac_eSPAN rep1


title: mcm22A_H3K4me3_eSPAN rep2


title: mcm22A_dpb4D_H3K4me3_ChIP rep1


title: repli-ATAC replicate 1 Nascent chromatin DMSO


title: mcm22A_H3K4me3_ChIP rep2


title: mcm22A_BrdU rep2


title: IGF1_rep3, miRNA-seq

city: Goiania

first: Bruno

middle: Oliveira Silva

last: Duran

state: GO

address: Esperança Avenue, Campus Samambaia, Biological Sciences Institute

department: Department of Histology, Embryology and Cell Biology

country: Brazil

institute: Federal University of Goias

library_source: transcriptomic

data_processing:
microRNAome was obtained through the HiSeq 4000 platform (Illumina, USA) with 50 base pairs, single-end, and 10 million reads per sample.
Adapters and low-quality reads were removed using in-house perl scripts. Unique sequences with length in 18-26 nucleotides were mapped to specific species precursors in miRBase 22.0 (https://www.mirbase.org/, accessed in December 2022) by BLAST search, to identify known miRNAs and novel 5p- and 3p- derived miRNAs candidates.
The normalized reads of each miRNA were used to differential expression. Differences between treatments were considered significant when corrected p-values (False Discovery Rate, FDR) were < 0.05.
Assembly: miRNA sequences of specific species in miRBase 22.0 (https://www.mirbase.org/). Astatotilapia burtoni, Danio rerio, Salmo salar, Oreochromis niloticus.
Supplementary files format and content: Matrix table (.xlsx) with normalized reads values for the identified miRNAs in each sample. Differences between treatments for each miRNA are indicated as p-value.

molecule: total RNA

organism: Sparus aurata

source_name: Fast-twitch skeletal muscle

growth_protocol: Cells were isolated from gilthead sea bream fast-twitch muscle and grown in complete medium until the 8th day of culture.

extract_protocol:
Total RNA was extracted using Trizol, as recommended by manufacturer. Approximately 1 ug of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits.
Small RNA library, size fractionaction.

treatment_protocol: C (control) group cells were cultured in nutrient restriction medium for 36 hours. AA (amino acids) group cells were cultured in nutrient restriction medium for 12 hours followed by 24 hours of AA supplementation. IGF1 (insulin-like growth factor 1) group cells were cultured in nutrient restriction medium for 12 hours followed by 24 hours of IGF1 supplementation.

tag: tissue

value: Fast-twitch skeletal muscle

value: Muscle cells

value: IGF1 treatment for 24 hours


title: Patients 1 Luminex_116

type: protein

city: Hiroshima-shi

first: Hikaru

last: Nakahara

address: kasumi 1-2-3, minami-ku

country: Japan

institute: Hiroshima University

scan_protocol: All materials were attached with bead cocktail and biotin antibody cocktail based on the principle of sandwich ELISA, and measured using Lumiex 200. Detailed protocols were implemented according to R&D.

data_processing: The raw data was quantified by quantitative analysis using Logistic 5P weighted using Luminex xPONENTversion 3.1Build971.

label: Luminex

molecule: protein

source_name: chronic liver disease without any tumor

value: serum

tag: status

value: unknown

tag: age

tag: Sex

value: Male


title: repli-ATAC replicate 2 Mature 2h chromatin dTAG


title: Patients 1 Luminex_114


title: IGF1_rep2, miRNA-seq


title: mcm22A_Input rep2


title: Patients 1 Luminex_113


title: Patients 1 Luminex_115


title: IGF1_rep1, miRNA-seq


title: Patients 1 Luminex_112


title: Patients 1 Luminex_111


title: mcm22A_H3K4me3_eSPAN rep1


title: AA_rep3, miRNA-seq

value: AA treatment for 24 hours


title: Patients 1 Luminex_110


title: mcm22A_H3K4me3_ChIP rep1


title: Patients 1 Luminex_109


title: AA_rep2, miRNA-seq


title: mcm22A_BrdU rep1


title: repli-ATAC replicate 1 Nascent chromatin dTAG


title: Patients 1 Luminex_107


title: Patients 1 Luminex_108

value: Female


title: AA_rep1, miRNA-seq


title: mcm22A_Input rep1


title: Patients 1 Luminex_105


title: C_rep3, miRNA-seq

value: Nutrient restriction for 36 hours (control)


title: dpb4D_H3K4me3_eSPAN rep2


title: Patients 1 Luminex_104


title: C_rep2, miRNA-seq


title: Patients 1 Luminex_103


title: dpb4D_H3K4me3_ChIP rep2


title: Patients 1 Luminex_102


title: dpb4D_BrdU rep2


title: Patients 1 Luminex_100


title: Patients 1 Luminex_101


title: Patients 1 Luminex_098


title: dpb4D_Input rep2


title: Patients 1 Luminex_097


title: Patients 1 Luminex_099


title: SARS_CoV2_2_3

type: RNA

city: Lucknow

first: Vikas

last: Agarwal

state: Uttar Pradesh

address: SGPGIMS, Raebareli road

department: Clinical Immunology

country: India

institute: Sanjay Gandhi Postgraduate Institute of Medical Sciences

description:
SARS_CoV2 2 Plate 3
Roche Lightcycler

data_processing: Matrix non-normalized was generated by calculating mean of CT values for each gene including housekeeping gene, GAPDH, for all the patients with SARS-CoV2 as well as all the  disease controls recruited in the study. Matrix normalized was generated by subtratcing the mean Ct value of GAPDH from the gene of interest (GOI). This yielded two normalized integers set, (mean CT GOI in patients with SARS-CoV2 -mean  CT housekeeping gene, GAPDH, in patients with SARS-CoV2) and (Mean Ct GOI disease controls - mean Ct  housekeeping gene, GAPDH, in disease  controls). These normalised values were referred to as delta Ct values. Delta delta Ct values for each GOI were calculated by subtracting delta ct  in SARS-CoV2 patient - delta Ct value in disease controls. Fold change of GOI was calculated by 2 (to the power delta delta Ct) for each gene.

label: SYBR Green

source_name: Bone marrow

label_protocol: High capacity cDNA reverse transcriptions protocol, Applied Biosystems

extract_protocol: Trizol method

tag: age in years

tag: gender

value: M


title: Patients 1 Luminex_106


title: SARS_CoV2_1_3

description:
SARS_CoV2 1 Plate 3
Roche Lightcycler


title: dpb4D_H3K4me3_eSPAN rep1


title: Patients 1 Luminex_095

source_name: unresectable hepatocellular carcinoma

value: Alive


title: dpb4D_H3K4me3_ChIP rep1


title: Patients 1 Luminex_092

value: Dead


title: Patients 1 Luminex_096


title: Patients 1 Luminex_094


title: SARS_CoV2_1_2

description:
SARS_CoV2 1 Plate 2
Roche Lightcycler


title: Patients 1 Luminex_091


title: C_rep1, miRNA-seq


title: dpb4D_Input rep1


title: Patients 1 Luminex_090


title: Patients 1 Luminex_089


title: Patients 1 Luminex_088


title: WT_H3K4me3_eSPAN rep2


title: SARS_CoV2_2_1

description:
SARS_CoV2 2 Plate 1
Roche Lightcycler


title: WT_H3K4me3_ChIP rep2


title: Patients 1 Luminex_085


title: SARS_CoV2_1_1

description:
SARS_CoV2 1 Plate 1
Roche Lightcycler


title: Disease Control 2_3

description:
Disease Control 2 Plate 3
Roche Lightcycler


title: SARS_CoV2_2_2

description:
SARS_CoV2 2 Plate 2
Roche Lightcycler


title: Patients 1 Luminex_093


title: WT_BrdU rep2


title: Patients 1 Luminex_084


title: dpb4D_BrdU rep1


title: Patients 1 Luminex_083


title: WT_Input rep2


title: Disease Control 1_3

description:
Disease Control 1 Plate 3
Roche Lightcycler


title: Patients 1 Luminex_080


title: Patients 1 Luminex_081


title: Disease Control 2_2

description:
Disease Control 2 Plate 2
Roche Lightcycler


title: Patients 1 Luminex_078


title: WT_H3K4me3_eSPAN rep1


title: Disease Control 1_2

description:
Disease Control 1 Plate 2
Roche Lightcycler


title: Patients 1 Luminex_087


title: Patients 1 Luminex_086


title: WT_H3K4me3_ChIP rep1


title: Patients 1 Luminex_077


title: Patients 1 Luminex_079


title: WT_BrdU rep1


title: Disease Control 2_1

description:
Disease Control 2 Plate 1
Roche Lightcycler


title: Patients 1 Luminex_076


title: Disease Control 1_1

description:
Disease Control 1 Plate 1
Roche Lightcycler


title: WT_Input rep1


title: OCI-AML3 cells caspase-2 knockout clone 2 replicate 2 [AML3C23_1]

city: Houston

first: Lisa

last: Bouchier-Hayes

state: Texas

address: 1102 Bates Ave

institute: Baylor College of Medicine

data_processing:
BGISEQ-500 software version 0.3.8.1111
Bioinformatics analysis was carried out using Dr.Tom
Assembly: not provided

growth_protocol: OCI-AML2 and OCI-AML3 cells were grown in RPMI containing FBS (10% v/v), L-glutamine (2 mM), and penicillin/streptomycin (50 IU/mL/50 µg/mL) at 37C and 5%CO2

extract_protocol:
Total RNA was extracted from the cells using RNAeasy kit with QIAshredder (Qiagen) according to the manufacturer’s protocol. RNA was resuspended in diethylpyrocarbonate (DEPC) treated water and quantified using a NanoDrop 2000 spectrophotometer
RNA libraries were prepared by BGI Americas facility

treatment_protocol: Untreated cells in culture for less than two weeks

value: Acute myeloid leukemia

value: NPM1c+ Caspase-2 KO


title: Patients 1 Luminex_074


title: OCI-AML3 cells caspase-2 knockout clone 2 replicate 3 [AML3C23_2]


title: Patients 1 Luminex_071


title: Patients 1 Luminex_082


title: Patients 1 Luminex_072


title: Patients 1 Luminex_073


title: OCI-AML3 cells caspase-2 knockout clone 1 replicate 3 [AML3C9_2]


title: WT, Replicate #3

city: Daegu

first: Hong-Yeoul

last: Ryu

state: Buk-Gu

address: Daehak-ro 80

department: Biotechnology

country: South Korea

institute: Kyungpook National University

data_processing:
RNA-seq reads were timmed using Trim Galore (v0.5.0)
Trimmed reads were mapped to the sacCer3 reference genome using HISAT2 (v2.1.0)
Gene expression levels were quantified using StringTie (v1.3.3b) with gene models from SGD
DEGs were identified with DESeq2 (v1.22.1)
Assembly: sacCer3
Supplementary files format and content: csv; raw expression level counts for each gene in each group
Supplementary files format and content: xlsx; DEGs for each group compared to WT samples

organism: Saccharomyces cerevisiae

extract_protocol:
RNA was isolated using the Rneasy Mini Kit (74104, Qiagen)
RNA-seq libraries were prepared according to the Yale Center for Genome Analysis Guidelines


title: WT, Replicate #2


title: OCI-AML3 cells caspase-2 knockout clone 2 replicate 1 [AML3C23]


title: Patients 1 Luminex_068


title: WT, Replicate #1


title: Patients 1 Luminex_067


title: Patients 1 Luminex_070


title: Patients 1 Luminex_069


title: Patients 1 Luminex_075


title: OCI-AML3 cells caspase-2 knockout clone 1 replicate 2 [AML3C9_1]


title: OCI-AML3 cells caspase-2 knockout clone 1 replicate 1 [AML3C9]


title: Evolved ulp2D 500G #9, Replicate #2


title: OCI-AML3 cells caspase-2 WT replicate 3 [AML3WT_2]

value: NPM1c+ Caspase-2 WT


title: Evolved ulp2D 500G #9, Replicate #3


title: Patients 1 Luminex_065


title: Patients 1 Luminex_064


title: Patients 1 Luminex_060


title: Patients 1 Luminex_062


title: Patients 1 Luminex_061


title: Patients 1 Luminex_063


title: OCI-AML3 cells caspase-2 WT replicate 2 [AML3WT_1]


title: OCI-AML3 cells caspase-2 WT replicate 1 [AML3WT]


title: Patients 1 Luminex_059


title: Patients 1 Luminex_066


title: Evolved ulp2D 500G #6, Replicate #3


title: Patients 1 Luminex_058


title: Evolved ulp2D 500G #6, Replicate #2


title: Patients 1 Luminex_057


title: Patients 1 Luminex_056


title: OCI-AML2 cells caspase-2 knockout clone 2 replicate 2 [AML2C12_1]

value: NPM1WT Caspase-2 KO


title: Evolved ulp2D 500G #6, Replicate #1


title: Patients 1 Luminex_053


title: ulp2D, Replicate #3


title: OCI-AML2 cells caspase-2 knockout clone 2 replicate 3 [AML2C12_2]


title: Patients 1 Luminex_055


title: ulp2D, Replicate #2


title: OCI-AML2 cells caspase-2 knockout clone 2 replicate 1 [AML2C12]


title: Patients 1 Luminex_052


title: Patients 1 Luminex_051


title: Evolved ulp2D 500G #9, Replicate #1


title: Patients 1 Luminex_050


title: Patients 1 Luminex_049


title: OCI-AML2 cells caspase-2 knockout clone 1 replicate 3 [AML2C1_2]


title: OCI-AML2 cells caspase-2 knockout clone 1 replicate 2 [AML2C1_1]


title: ulp2D, Replicate #1


title: Patients 1 Luminex_048


title: Patients 1 Luminex_047


title: Microbiota of Saliva from subject HC_9

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
GM98

data_processing:
demultiplexing:  from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
primer check and trimming:  qiime cutadapt trim-paired  --i-demultiplexed-sequences demux-paired-end.qza --p-adapter-f  CCTACGGGNGGCWGCAG   --p-adapter-r  GACTACNVGGGTWTCTAATCC  –o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --verbose
quality check:  qiime demux summarize  --i-data trimmed-seqs.qza --o-visualization demux.qzv
ASV generation:  qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 250 --p-trunc-len-r 204 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 8
host read decontamination:  bowtie2 -x GRCh38_noalt_as -U dna-sequences.fasta --al eucar_contaminant_ASV.fasta -S bowtie2_SAM_output.txt -f -p 4 2> percentuals_aligned_bowtie2.txt
taxonomic assignment:  qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads decontaminated_rep-seqs.qza --o-classification taxonomy.qza
further analyses:  R software (see the relative script publicly available at github.com/LeandroD94)
Assembly: SILVA 138 (16S database)
Supplementary files format and content: dna-sequences.fasta: text containing every processed ASV code and sequence (already decontaminated through Bowtie2)
Supplementary files format and content: feature_abundance_table.tsv: TSV text file containing the abundance table
Library strategy: paired-end (2x300) amplicon sequencing

source_name: Saliva

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

value: Saliva

tag: patient id

tag: condition

value: Healthy


title: Patients 1 Luminex_046


title: Patients 1 Luminex_044


title: Patients 1 Luminex_045


title: OCI-AML2 cells caspase-2 knockout clone 1 replicate 1 [AML2C1]


title: Patients 1 Luminex_054


title: OCI-AML2 cells caspase-2 WT replicate 3 [AML2WT_2]

value: NPM1WT Caspase-2 WT


title: Microbiota of Saliva from subject HC_7

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
GM96


title: Lung, control, bulk RNA-seq,C5

city: hangzhou

first: kang

last: zhiying

address: 浙江省杭州市西湖区余杭塘路866号

country: China

institute: zhejiang universty

data_processing:
The sequencing data was filtered with SOAPnuke [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).The clean reads were mapped to the reference genome using HISAT2 [2]. After that, Ericscript (v0.5.5) [3] and rMATS (V3.2.5) [4] were used to detect fusion genes and differential splicing genes (DSGs), respectively. Bowtie2[5] was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.Expression level of gene was calculated by RSEM (v1.3.1) [6]. The heatmap was drawn by pheatmap (v1.0.8) [7] according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) [8] (or DEGseq[9] or PoissonDis[10])with Q value ≤ 0.05 (or FDR ≤ 0.001). To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) [11].
Assembly: GCF 000001635.26 GRCm38.p6
Supplementary files format and content: Tab-separated values files

organism: Mus musculus

source_name: Lung

extract_protocol:
Transfer appropriate sample to corresponding grinding tube. Add 1.5 mL TRIzol lysis buffer, transfer to the grinding machine, grind 30 s, stay at 5 min. Dispense 1.5 mL of TRIzol lysis buffer to a 2 mL tube. Take appropriate amount of tissue samples, grind the tissue samples into powder with liquid nitrogen and transfer into the lysis buffer. Stand flat for 5 min for the fully lysis of tissue cells. Add appropriate TRIzol lysis buffer into the cell sample tube (1 mL TRIzol for 1×106 cells). Centrifuge the tissue samples after grinding and crushing at 12000×g for 5 min in 4℃. Transfer the supernatant to the centrifuge tube with 300 µL Chloroform/isoamyl alcohol (24:1) mix thoroughly by upside down violent shaking. Centrifuge at 12000×g for 8 min in 4℃ (optional extraction with equal supernatant volume of chloroform/isoamyl alcohol (24:1) could be used if the middle layer is thick and the water phase turbidity). Transfer the supernatant to the 1.5 mL centrifuge tube, add 2/3 volume of Isopropyl alcohol, (optional 2µL 5 mg/mL glycogen for low-input tissue and cell sample to help precipitation). Gently invert and mix, place in -20℃ refrigerator for more than 2 h. Centrifuge at 17500×g for 25 min in 4℃. Discard the supernatant, wash with 0.9 mL 75% ethanol, suspend the precipitation by inverting. Centrifuge at 17500×g for 3 min in 4℃ (optional wash with 0.9 mL 75％ ethanol could be used, 17500×g for 3 min in 4℃). Discard the supernatant, centrifuge for a short time and use the tip to remove the residual liquid, air dry for 3-5 min. Dissolve the precipitation with 20-200 μL DEPC-H2O or RNase-free water.
Select the corresponding testing methods for quality inspection according to the requirements of samples and products.A certain amount of RNA samples are denatured at suitable temperature to open their secondary structure, and mRNA is enriched by oligo (dT) -attached magnetic beads.The reaction system is configured. After reacting at the suitable temperature for a fixed period of time, RNAs are fragmented.The first-strand synthesis reaction system is added to the interrupted mRNA, and the reaction procedure is set up to synthesize the first-strand cDNA. The second-strand synthesis reaction system (including dUTP) is prepared, and the reaction procedure is set up to synthesize the second-strand cDNA.After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs.The PCR reaction system and program are configured and set up to amplify the cDNAs.The corresponding library quality control protocol will be selected depending upon product requirements.Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested.Single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).

value: Lung

value: Mice lung tissue


title: OCI-AML2 cells caspase-2 WT replicate 1 [AML2WT]


title: Microbiota of Saliva from subject HC_8

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
GM97


title: OCI-AML2 cells caspase-2 WT replicate 2 [AML2WT_1]


title: Microbiota of Saliva from subject HC_6

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
GM95


title: Lung, control, bulk RNA-seq,C4

address: 浙江省杭州市西湖区余杭塘路866号


title: Microbiota of Saliva from subject HC_4

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
GM93


title: Microbiota of Saliva from subject HC_5

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
GM94


title: Lung, control, bulk RNA-seq,C3

address: 浙江省杭州市西湖区余杭塘路866号


title: Microbiota of Saliva from subject HC_10

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
GM99


title: Patients 1 Luminex_042

value: serum


title: Patients 1 Luminex_041

value: Male


title: Microbiota of Saliva from subject HC_3

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
GM92


title: Patients 1 Luminex_034


title: Patients 1 Luminex_043


title: Patients 1 Luminex_036


title: Patients 1 Luminex_037


title: Microbiota of Saliva from subject HC_2

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
GM91


title: Patients 1 Luminex_032


title: Patients 1 Luminex_033


title: Patients 1 Luminex_040


title: Patients 1 Luminex_031


title: Patients 1 Luminex_039


title: Lung, control, bulk RNA-seq,C2

address: 浙江省杭州市西湖区余杭塘路866号


title: Patients 1 Luminex_035


title: Patients 1 Luminex_029


title: Patients 1 Luminex_038


title: Lung, control, bulk RNA-seq,C1

address: 浙江省杭州市西湖区余杭塘路866号


title: Microbiota of Saliva from subject HC_1

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
GM90


title: Patients 1 Luminex_028


title: Lung, extrapulmonary ALI, bulk RNA-seq,B5

address: 浙江省杭州市西湖区余杭塘路866号

value: LPS (25 mg/kg) to construct sepsisrelated ARDS


title: Patients 1 Luminex_027

value: Female


title: Microbiota of Stool from subject RCC_5

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
FL9

source_name: Stool

value: Stool

value: RCC


title: Microbiota of Saliva from subject RCC_4

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
FL8


title: Lung, extrapulmonary ALI, bulk RNA-seq,B3

address: 浙江省杭州市西湖区余杭塘路866号


title: Lung, extrapulmonary ALI, bulk RNA-seq,B4

address: 浙江省杭州市西湖区余杭塘路866号


title: Patients 1 Luminex_026

value: Alive


title: Microbiota of Stool from subject RCC_4

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
FL7


title: Patients 1 Luminex_030


title: Patients 1 Luminex_025


title: Lung, extrapulmonary ALI, bulk RNA-seq,B2

address: 浙江省杭州市西湖区余杭塘路866号


title: Lung, extrapulmonary ALI, bulk RNA-seq,B1

address: 浙江省杭州市西湖区余杭塘路866号


title: Patients 1 Luminex_023

value: Dead


title: Microbiota of Stool from subject RCC_3

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
FL5


title: Patients 1 Luminex_024


title: Patients 1 Luminex_022


title: Patients 1 Luminex_021


title: Lung, pulmonary ALI, bulk RNA-seq,A5

address: 浙江省杭州市西湖区余杭塘路866号

value: LPS (10 mg/kg, from Pseudomonas aeruginosa 27316, Sigma-Aldrich, USA, L9143)


title: Microbiota of Saliva from subject RCC_2

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
FL4


title: Patients 1 Luminex_020


title: Patients 1 Luminex_018


title: Patients 1 Luminex_017


title: Lung, pulmonary ALI, bulk RNA-seq,A4

address: 浙江省杭州市西湖区余杭塘路866号


title: Patients 1 Luminex_016


title: Patients 1 Luminex_015


title: Microbiota of Stool from subject RCC_2

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
FL3


title: Patients 1 Luminex_014


title: Lung, pulmonary ALI, bulk RNA-seq,A3

address: 浙江省杭州市西湖区余杭塘路866号


title: Patients 1 Luminex_013


title: Microbiota of Saliva from subject RCC_3

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
FL6


title: Microbiota of Saliva from subject RCC_10

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
FL19


title: Lung, pulmonary ALI, bulk RNA-seq,A2

address: 浙江省杭州市西湖区余杭塘路866号


title: Patients 1 Luminex_019


title: Lung, pulmonary ALI, bulk RNA-seq,A1

address: 浙江省杭州市西湖区余杭塘路866号


title: Patients 1 Luminex_010


title: P10_24 [Z10_B3_8_S88]

city: Ottawa

first: John

last: Stead

state: ON

address: 1125 Colonel By Drive

department: Department of Neuroscience

country: Canada

institute: Carleton University

data_processing:
Base calling was performed by bcl2fastq v 2.20
Quality trimming was performed using fastp v0.23.2
Alignment was performed using STAR v2.7.10a
Gene counts were performed with RSEM v1.3.3
Normalization was performed with DESeq2 v1.31.15
Assembly: Biospyder Zebrafish S1500+ Surrogate Gene Set
Supplementary files format and content: count_table.csv is a genes by samples count matrix of raw counts from the STAR alignments

organism: Danio rerio

growth_protocol: Zebrafish embryos were cultured in water from the ZebTEC housing system (Techniplast, Montreal, Canada) maintaining a temperature of 28 Celsius degrees, pH of 7.4, and conductivity of 2-400μS.

extract_protocol:
Total RNAs were extracted using a Qiagen Mini kit (Qiagen, Toronto, Canada), followed by the manufacter's protocol
RNA libraries were prepared in a 96-sample TempO-Seq S1500+ Zebrafish Surrogate Assay panel (BioSpyder Technologies, California, USA). Each sample was diluted with an equal volume of 2X Enhanced Lysis Buffer. All samples were annealed with detector oligo probes and sequentially processed in digestion, ligation, and amplification steps according to the manufacturer’s protocol. Equal amounts of each sample’s libraries were pooled in a 1.5 ml microtube and purified using NucleoSpin® Gel and PCR Cleanup Kits (Macherey-Nagel, Düren, Germany). Purified pooled libraries were sequenced on an Illumina NextSeq 2000 using a P2 Reagent kit and a 100 cycle flow cell (Illumina, USA).
TempO-Seq S1500+ Zebrafish Surrogate Assay - Index E set was used

treatment_protocol: Zebrafish embryos were exposed from 3-4 hours post fertilization (hpf) to 120 hpf in 16 ml Petri-dish of 0.1 % dimethylsulfoxide (DMSO) and chemical renewal of 8 ml was daily in every Petri-dish.

tag: developmental stage

value: 120-hours post fertilization

value: DMSO

tag: duration of_chemical_exposure

value: 5 days

tag: chemical

tag: chemical long_name

value: Dimethyl sulfoxide

tag: dose

tag: rna extraction_batch

tag: rna extraction_date

tag: chemical exposure_dates

tag: i7 index_id

value: GACTTCATT

tag: i5 index_id

tag: library well

tag: protocol

value: TempO-Seq


title: Patients 1 Luminex_011

tag: tissue

tag: status

tag: age

tag: Sex


title: Microbiota of Saliva from subject RCC_8

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
FL16

value: Saliva

tag: patient id

tag: condition


title: P10_23 [Z10_B3_7_S87]

tag: developmental stage

tag: treatment

tag: duration of_chemical_exposure


title: Microbiota of Stool from subject RCC_10

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
FL17


title: P10_22 [Z10_B3_6_S86]

tag: chemical

tag: chemical long_name

tag: dose


title: Microbiota of Saliva from subject RCC_9

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
FL18


title: Patients 1 Luminex_007


title: Patients 1 Luminex_004


title: Microbiota of Stool from subject RCC_8

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
FL15


title: Patients 1 Luminex_002


title: P10_21 [Z10_B3_5_S85]

tag: rna extraction_batch

tag: rna extraction_date

tag: chemical exposure_dates


title: Patients 1 Luminex_003


title: 82_heart_Male_WT_E5

city: Uppsala

first: Amir

last: Fallahshahroudi

address: Gropgränd 4

department: IMBIM

country: Sweden

institute: Uppsala University

description: longRNA-Seq

data_processing:
Raw reads from each library were aligned to the reference genome using STAR aligner v. 2.7.2b
The alignment process involved generating STAR indices, aligning reads to the reference genome in an annotation-aware manner, and quantifying the number of reads mapped to each gene using the --quantMode GeneCounts option in STAR
The resulting gene count matrices, along with a metadata file containing sample information and the GTF file, were used to create a RangedSummarizedExperiment object
This object was imported into DESeq2 v. 1.24.0 (ref. 47) for downstream analysis.
Raw short RNA-sequencing data were preprocessed using a custom Bash script. Adapter sequences were trimmed and reads were size-selected using Cutadapt version 4.4. The parameters set a maximum error rate of 0.25, targeted the adapter sequence “AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC” with a minimum overlap of 6 nucleotides, and allowed no indels, while selecting for read lengths between 19 and 26 nucleotides. After trimming and size selection, the reads were aligned to the chicken reference genome using STAR following the ENCODE miRNA-seq pipeline49 (www.encodeproject.org/microrna/microrna-seq-encode4/) (May 2017). This alignment process included mapping to the microRNA subset of the chicken GTF gene annotation and quantifying the number of aligned reads in STAR
Assembly: bGalGal1.mat.broiler.GRCg7b; GCA_016699485.1
Supplementary files format and content: DeSeq2 Object containing complete metadata and raw read counts for each gene.
Supplementary files format and content: DeSeq2 Object containing complete metadata and raw read counts for each microRNA..

molecule: polyA RNA

organism: Gallus gallus

source_name: heart

extract_protocol:
A total of 72 samples from E2, E3, and E5 embryos were used for the generation of RNA sequencing libraries. We extracted total RNA from whole embryos or dissected tissues using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen), following the manufacturer's protocols. The RNA quality was assessed using the Fragment Analyzer system (Agilent), and all RNA quality numbers (RQNs) were equal to 10, indicating a lack of degradation.
The RNA-seq libraries were prepared from 400 ng of RNA per sample using the NEBNext Ultra II RNA Library Prep Kit for Illumina sequencing was performed on an Illumina NextSeq 2000 system, using NextSeq 2000 P3 Reagents (100 Cycles), with samples multiplexed in two sets of 36. Additionally, we generated small RNA libraries using RNA derived from the same E5 male samples (i.e., those that were also used for the generation of RNA sequencing libraries). This included the generation of small RNA libraries for RNA derived from ZZ (2 replicates), ZKOZ (3 replicates), and ZKOZKO (3 replicates) for each tissue type (head, body, heart), respectively.
The RNA-seq libraries were prepared from 400 ng of RNA per sample using the NEBNext Ultra II RNA Library Prep Kit for Illumina sequencing was performed on an Illumina NextSeq 2000 system, using NextSeq 2000 P3 Reagents (100 Cycles), with samples multiplexed in two sets of 36. short RNA Seq libraries were prepared using the NEBNext Small RNA Library Prep Set for Illumina and were sequenced on an Illumina NextSeq 550 system using NextSeq 500/550 High Output Kit v2.5 (75 Cycles), with samples multiplexed in two sets of 12.

value: heart

tag: hh stage

tag: breed

value: Hy-Line

tag: genotype

value: WT


title: Patients 1 Luminex_012

tag: tissue

value: serum

tag: status

value: Male


title: Microbiota of Saliva from subject RCC_1

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
FL2


title: Patients 1 Luminex_009

tag: age

tag: Sex

value: Female


title: Microbiota of Saliva from subject RCC_7

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
FL14

tag: patient id

tag: condition

value: RCC


title: 82_head_Male_WT_E5

description: longRNA-Seq

source_name: head

value: head

tag: developmental stage


title: Microbiota of Stool from subject RCC_7

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
FL13

value: Stool


title: Patients 1 Luminex_001

value: Dead


title: 82_body_Male_WT_E5

description: longRNA-Seq

source_name: body

value: body


title: Patients 1 Luminex_008

value: Alive


title: Patients 1 Luminex_006


title: 81_heart_Male_WT_E5

description: longRNA-Seq


title: P10_19 [Z10_B3_3_S83]

value: 120-hours post fertilization

tag: treatment

value: DMSO

tag: duration of_chemical_exposure

value: 5 days

tag: i7 index_id

tag: i5 index_id

tag: library well

tag: protocol


title: Microbiota of Saliva from subject RCC_6

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
FL12


title: 81_head_Male_WT_E5

description: longRNA-Seq


title: Microbiota of Stool from subject RCC_6

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
FL11


title: 81_body_Male_WT_E5

description: longRNA-Seq


title: 76_head_Male_WT_E5

description: longRNA-Seq


title: P10_17 [Z10_B3_1_S81]

tag: chemical

tag: chemical long_name

value: Dimethyl sulfoxide

tag: dose

tag: rna extraction_batch

tag: rna extraction_date

tag: chemical exposure_dates

value: GACTTCATT

value: TempO-Seq


title: 56_heart_Male_KO_E5

description: longRNA-Seq

tag: tissue

value: heart

tag: hh stage

tag: breed

value: G2 Outcross

tag: genotype

value: KO


title: 76_body_Male_WT_E5

description: longRNA-Seq

tag: developmental stage

value: Hy-Line

value: WT

tag: Sex

value: Male


title: P10_18 [Z10_B3_2_S82]

tag: treatment

tag: duration of_chemical_exposure


title: P01_24 [Z1_B3_8_S72]

tag: i7 index_id

value: TAAGGTAGC

tag: i5 index_id


title: Microbiota of Saliva from subject RCC_5

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_abundance_table.tsv
FL10

value: Saliva

tag: patient id

tag: condition

value: RCC


title: Microbiota of Stool from subject RCC_1

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
FL1

value: Stool


title: 56_body_Male_KO_E5

description: longRNA-Seq

value: body


title: P01_23 [Z1_B3_7_S71]

value: 120-hours post fertilization

tag: chemical

tag: chemical long_name

tag: library well

tag: protocol


title: 433_heart_Male_HZ_E3

description: longRNA-Seq

value: HZ


title: P10_20 [Z10_B3_4_S84]

value: DMSO

value: 5 days

tag: dose

tag: rna extraction_batch

tag: rna extraction_date

tag: chemical exposure_dates


title: P01_22 [Z1_B3_6_S70]

tag: tissue

value: Dimethyl sulfoxide


title: 56_head_Male_KO_E5

description: longRNA-Seq

value: head

tag: developmental stage

tag: hh stage

tag: breed

tag: genotype


title: 433_head_Male_HZ_E3

description: longRNA-Seq

tag: Sex


title: Microbiota of Stool from subject HC_10

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
EN48

value: Healthy


title: 428_heart_Male_HZ_E3

description: longRNA-Seq

value: heart

value: G2 Outcross


title: 433_body_Male_HZ_E3

description: longRNA-Seq


title: 76_heart_Male_WT_E5

description: longRNA-Seq

value: Hy-Line


title: 428_head_Male_HZ_E3

description: longRNA-Seq


title: Microbiota of Stool from subject HC_8

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
EN46


title: P01_21 [Z1_B3_5_S69]

tag: treatment

tag: duration of_chemical_exposure

tag: i7 index_id

tag: i5 index_id

value: TempO-Seq


title: 421_heart_Male_WT_E3

description: longRNA-Seq

value: WT

value: Male


title: Patients 1 Luminex_005

value: serum

tag: status

value: Dead

tag: age

value: Female


title: P01_20 [Z1_B3_4_S68]

tag: chemical

tag: chemical long_name

value: TAAGGTAGC

tag: library well

tag: protocol


title: P01_19 [Z1_B3_3_S67]

value: 120-hours post fertilization

tag: dose

tag: rna extraction_batch

tag: rna extraction_date

tag: chemical exposure_dates


title: Microbiota of Stool from subject HC_6

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
EN41

tag: tissue

value: Stool

tag: patient id

tag: condition


title: Microbiota of Stool from subject HC_5

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
EN40


title: P01_18 [Z1_B3_2_S66]

tag: developmental stage

tag: treatment

value: DMSO


title: Microbiota of Stool from subject HC_7

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
EN43


title: 421_head_Male_WT_E3

description: longRNA-Seq

tag: hh stage

tag: breed

tag: genotype

tag: Sex


title: 420_heart_Male_WT_E3

description: longRNA-Seq


title: 420_body_Male_WT_E3

description: longRNA-Seq

value: body


title: 421_body_Male_WT_E3

description: longRNA-Seq


title: Microbiota of Stool from subject HC_4

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
EN29


title: P05_24 [Z5_B3_8_S80]

tag: duration of_chemical_exposure

value: 5 days

tag: chemical

value: Dimethyl sulfoxide

tag: i7 index_id

value: TGCATGACA

tag: i5 index_id


title: 413_head_Male_KO_E3

description: longRNA-Seq

value: head

value: KO


title: 413_heart_Male_KO_E3

description: longRNA-Seq

value: heart

value: G2 Outcross


title: Microbiota of Stool from subject HC_9

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
EN47

value: Healthy


title: 413_body_Male_KO_E3

description: longRNA-Seq

value: Male


title: 411_heart_Male_KO_E3

description: longRNA-Seq


title: P05_23 [Z5_B3_7_S79]

tag: chemical long_name

tag: dose

tag: library well

tag: protocol

value: TempO-Seq


title: 411_head_Male_KO_E3

description: longRNA-Seq

tag: tissue


title: Microbiota of Stool from subject HC_2

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
EN13

tag: patient id


title: P01_17 [Z1_B3_1_S65]

tag: rna extraction_batch

tag: rna extraction_date

tag: chemical exposure_dates


title: Microbiota of Stool from subject HC_3

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
EN28

tag: condition


title: 428_body_Male_HZ_E3

description: longRNA-Seq

tag: developmental stage

tag: hh stage

tag: breed

value: HZ


title: 411_body_Male_KO_E3

description: longRNA-Seq

tag: genotype

tag: Sex


title: P05_22 [Z5_B3_6_S78]

tag: treatment

tag: duration of_chemical_exposure

tag: chemical

tag: i7 index_id


title: Microbiota of Stool from subject HC_1

description:
16s rRNA v3-v4 sequencing of human Stool
feature_abundance_table.tsv
EN11


title: 408_head_Male_HZ_E3

description: longRNA-Seq


title: 408_heart_Male_HZ_E3

description: longRNA-Seq


title: 408_body_Male_HZ_E3

description: longRNA-Seq


title: 420_head_Male_WT_E3

description: longRNA-Seq

value: Hy-Line

value: WT


title: Biopsy from MAP Mouse, rep3

first: Pawel

last: Mazur

address: 6565 MD Anderson Blvd

institute: MD Anderson Cancer Center

data_processing:
Paired-end reads were processed and aligned to the murine GRCm38 genome using Hisat2. Gene counts for uniquely mapped reads were generated using featureCounts.
Assembly: GRCm38
Supplementary files format and content: CSV file includes raw counts for each sample

source_name: Pancreas (tumor)

extract_protocol:
Total RNA was extracted from wild-type pancreata or tumors from Men1 LoxP/LoxP;Atrx LoxP/LoxP;Pten LoxP/LoxP (MAP);Pdx1-CreER  mutant mice using Trizol reagent.
RNA libraries were prepared using the TruSeq Stranded Total RNA kit

value: Pancreas (tumor)

value: MAP


title: 406_head_Male_KO_E3

description: longRNA-Seq


title: Biopsy from MAP Mouse, rep2


title: P05_20 [Z5_B3_4_S76]

value: 120-hours post fertilization

value: DMSO

tag: chemical long_name

tag: dose

tag: i5 index_id

tag: library well


title: 406_heart_Male_KO_E3

description: longRNA-Seq

tag: tissue


title: 406_body_Male_KO_E3

description: longRNA-Seq

value: body


title: P05_19 [Z5_B3_3_S75]

value: 5 days

value: Dimethyl sulfoxide

tag: rna extraction_batch

tag: rna extraction_date

tag: protocol


title: Biopsy from MAP Mouse, rep1


title: 400_head_Male_WT_E3

description: longRNA-Seq

value: head

tag: developmental stage


title: P05_18 [Z5_B3_2_S74]

tag: chemical exposure_dates

value: TGCATGACA


title: 400_body_Male_WT_E3

description: longRNA-Seq

tag: hh stage

tag: breed


title: 38_heart_Male_KO_E5

description: longRNA-Seq

value: heart

tag: genotype

value: KO

tag: Sex


title: Biopsy from WT Mouse, rep3

source_name: Pancreas

value: Pancreas


title: Biopsy from WT Mouse, rep2


title: 38_body_Male_KO_E5

description: longRNA-Seq

value: G2 Outcross

value: Male


title: 38_head_Male_KO_E5

description: longRNA-Seq


title: P05_16 [Z5_B2_8_S48]

tag: treatment

tag: duration of_chemical_exposure

value: ACTCATGTA

value: TempO-Seq


title: 356_whole_Female_WT_E2

description: longRNA-Seq

source_name: whole

value: whole

value: Hy-Line

value: WT

value: Female


title: 368_whole_Female_WT_E2

description: longRNA-Seq


title: P05_21 [Z5_B3_5_S77]

value: 120-hours post fertilization

value: DMSO

tag: chemical

tag: i7 index_id


title: Biopsy from WT Mouse, rep1


title: P05_15 [Z5_B2_7_S47]

value: 5 days

tag: chemical long_name

tag: dose


title: 372_whole_Female_WT_E2

description: longRNA-Seq


title: 353_whole_Male_WT_E2

description: longRNA-Seq


title: HC2_1

description:
Healthy Control2 Plate 1
Roche Lightcycler

data_processing: Matrix non-normalized was generated by calculating mean of CT values for each gene including housekeeping gene, GAPDH, for all the patients with SARS-CoV2 as well as all the  healthy controls recruited in the study. Matrix normalized was generated by subtratcing the mean Ct value of GAPDH from the gene of interest (GOI). This yielded two normalized integers set, (mean CT GOI in patients with SARS-CoV2 -mean  CT housekeeping gene, GAPDH, in patients with SARS-CoV2) and (Mean Ct GOI healthy controls - mean Ct  housekeeping gene, GAPDH, in healthy  controls). These normalised values were referred to as delta Ct values. Delta delta Ct values for each GOI were calculated by subtracting delta ct  in SARS-CoV2 patient - delta Ct value in healthy controls. Fold change of GOI was calculated by 2 (to the power delta delta Ct) for each gene.

source_name: Peripheral Blood

tag: age in years

tag: gender


title: P05_14 [Z5_B2_6_S46]

tag: tissue

value: Dimethyl sulfoxide

tag: rna extraction_batch

tag: i5 index_id

tag: library well


title: 352_whole_Female_WT_E2

description: longRNA-Seq

tag: developmental stage


title: 400_heart_Male_WT_E3

description: longRNA-Seq

tag: hh stage


title: 344_whole_Male_KO_E2

description: longRNA-Seq

tag: breed


title: 345_whole_Female_WT_E2

description: longRNA-Seq

tag: genotype


title: HC1_1

description:
Healthy Control1 Plate 1
Roche Lightcycler


title: P05_12 [Z5_B2_4_S44]

tag: rna extraction_date

tag: chemical exposure_dates

tag: protocol


title: P05_13 [Z5_B2_5_S45]

tag: treatment

tag: duration of_chemical_exposure

tag: chemical


title: Delta_3_3

description:
Delta Patient_3 Plate 3
Roche Lightcycler


title: 339_whole_Female_KO_E2

description: longRNA-Seq

tag: Sex


title: P05_17 [Z5_B3_1_S73]

tag: chemical long_name

tag: dose

tag: i7 index_id


title: P05_11 [Z5_B2_3_S43]

tag: tissue

tag: rna extraction_batch


title: 333_whole_Male_HZ_E2

description: longRNA-Seq

value: HZ


title: 332_whole_Male_KO_E2

description: longRNA-Seq


title: P05_10 [Z5_B2_2_S42]

tag: i5 index_id

tag: library well


title: Delta_1_3

description:
Delta Patient_1 Plate 3
Roche Lightcycler

tag: age in years

tag: gender


title: Delta_2_3

description:
Delta Patient_2 Plate 3
Roche Lightcycler


title: 330_whole_Male_WT_E2

description: longRNA-Seq

tag: developmental stage

tag: hh stage

tag: breed

tag: genotype


title: 331_whole_Male_HZ_E2

description: longRNA-Seq


title: 355_whole_Male_WT_E2

description: longRNA-Seq


title: P05_9 [Z5_B2_1_S41]

tag: treatment

tag: rna extraction_date

tag: chemical exposure_dates

tag: protocol


title: Delta_3_2

description:
Delta Patient_3 Plate 2
Roche Lightcycler


title: 33_head_Male_HZ_E5

description: longRNA-Seq

value: head

tag: Sex


title: 33_heart_Male_HZ_E5

description: longRNA-Seq

value: heart


title: 33_body_Male_HZ_E5

description: longRNA-Seq

value: body


title: Delta_2_2

description:
Delta Patient_2 Plate 2
Roche Lightcycler


title: 32_heart_Male_KO_E5

description: longRNA-Seq

value: KO


title: P05_7 [Z5_B1_7_S15]

tag: duration of_chemical_exposure

tag: chemical

tag: chemical long_name

tag: dose

value: AAGACTCTT


title: P05_8 [Z5_B1_8_S16]

tag: tissue

tag: rna extraction_batch

tag: i7 index_id

tag: i5 index_id


title: 32_head_Male_KO_E5

description: longRNA-Seq

tag: developmental stage

value: G2 Outcross

value: Male


title: 318_whole_Male_HZ_E2

description: longRNA-Seq

tag: hh stage


title: Delta_1_2

description:
Delta Patient_1 Plate 2
Roche Lightcycler

tag: age in years

tag: gender


title: P05_5 [Z5_B1_5_S13]

tag: treatment

tag: library well

value: TempO-Seq


title: 32_body_Male_KO_E5

description: longRNA-Seq

tag: breed

tag: genotype


title: P05_6 [Z5_B1_6_S14]

tag: rna extraction_date

tag: chemical exposure_dates

tag: protocol


title: 338_whole_Female_KO_E2

description: longRNA-Seq

value: whole

tag: Sex


title: 317_whole_Female_KO_E2

description: longRNA-Seq


title: Delta_3_1

description:
Delta Patient_3 Plate 1
Roche Lightcycler


title: Delta_2_1

description:
Delta Patient_2 Plate 1
Roche Lightcycler


title: 313_whole_Male_KO_E2

description: longRNA-Seq


title: 312_whole_Female_WT_E2

description: longRNA-Seq


title: Delta_1_1

description:
Delta Patient_1 Plate 1
Roche Lightcycler


title: P05_4 [Z5_B1_4_S12]

tag: duration of_chemical_exposure

tag: chemical

tag: chemical long_name

tag: dose


title: USA300 LAC* cells, WT/m⏀11 biological replicate A

first: Alejandro

last: Pironti

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Raw reads were first trimmed by removing Illumina adapter sequences from 3′ ends using cutadapt,and by removing 3′ read sequences if more than 20 bases with Q≥20 were present. Paired-end reads were then mapped to the FPR3757 (NC_007793) reference genome using Bowtie2,and htseq-countwas used to produce strand-specific transcript count summaries. Raw fragment (i.e., paired-end read) counts were then combined into a numeric matrix, with genes in rows and samples in columns, and used as input for differential gene expression analysis with the limma R packagein Bioconductor.Normalization factors were computed on the data matrix using the weighted trimmed mean of M-values (TMM) method, followed by voommean-variance transformation in preparation for Limma linear modeling. Only genes with expression levels ≥1 FPKM (fragments per kb per million reads) in at least 50% of samples, and a length ≥200bp, were retained for further analysis. Filtered data were fitted to a design matrix containing all sample groups, and pairwise comparisons were performed between the groups of interest. Finally, eBayes adjusted P-values werecorrected for multiple testing using the Holm method and used to select genes with significant expression differences (q≤ 0.05).
Assembly: FPR3757 (NC_007793) + m⏀11
Supplementary files format and content: contrast_LAC_mosaic_phi11_6hrs_vs_LAC_6hrs_table_unfiltered.txt
Supplementary files format and content: counts_Harmanalysis.txt

organism: Staphylococcus aureus

source_name: USA300 LAC*

growth_protocol: overnight cultures of two separate single colonies of LAC* and LAC*/m⏀11 in TSB were diluted 1:100 into 5mL TSB and incubated at 37°C shaking 180 rpm for six hours to late exponential phase

extract_protocol:
For RNA extraction, cells were isolated with centrifugation and resuspended in 1 mL Trizol (Invitrogen, #15596026), then transferred to lysing matrix B (MP Biomedicals, #116911050) tubes for mechanical disruption at 6 m/s for 30 seconds three times. After disruption, samples were centrifuged for 10 minutes at 12,000 rpm at 4°C and the upper phase was transferred into a new RNA-free tube containing 500 µL ice cold Trizol, gently mixed, and incubated for 5 minutes at room temperature, then 200 µL chloroform was added and samples were centrifuged at 12000 rpm for 15 minutes at 4°C. The aqueous phase was mixed with 500 µL isopropanol and transferred to RNeasy column (Qiagen #74004) for washing and RNA elution per manufacturer protocol.
Extracted total RNA was visualized on the Agilent 2100 Bioanalyzer system using a Bioanalyzer Nanochip run with the Prokaryote setting. RIN scores for the total RNA measured from 9 to 10. Total RNA (500 ng per sample) was input into the Illumina stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit (96rxn, cat # 20040529). Libraries were prepared according to manufacturer’s instructions. PCR Amplification was run with 11 total cycles. Following completion of the preparation, library samples were visualized on the Agilent 4200 Tapestation System using High Sensitivity DNA Screentape. The concentration of each library was assessed by Qubit using the High Sensitivity DNA Kit. The samples were pooled equimolar and the pool was sequenced on the Illumina Novaseq 6000 system on one lane of the SP 100 cycle flow cell kit. The library pool was sequenced as paired end 50 bases.

tag: cell line

value: USA300 LAC*

value: USA300 LAC*/m{phi}11


title: P05_2 [Z5_B1_2_S10]

tag: tissue

tag: developmental stage

tag: rna extraction_batch

tag: i7 index_id

tag: i5 index_id


title: Recovered4_3

description:
Recovered patient_4 Plate 3
Roche Lightcycler

tag: age in years

tag: gender


title: USA300 LAC* cells, WT biological replicate B

tag: genotype


title: 25_heart_Male_HZ_E5

description: longRNA-Seq

tag: hh stage

tag: breed


title: USA300 LAC* cells, WT/m⏀11 biological replicate B


title: P05_1 [Z5_B1_1_S9]

tag: treatment

tag: rna extraction_date

tag: chemical exposure_dates

tag: library well

tag: protocol


title: P05_3 [Z5_B1_3_S11]

tag: duration of_chemical_exposure

tag: chemical

tag: chemical long_name

tag: dose


title: 25_head_Male_HZ_E5

description: longRNA-Seq

tag: tissue

tag: developmental stage

tag: Sex


title: 23_heart_Male_HZ_E5

description: longRNA-Seq


title: USA300 LAC* cells, WT biological replicate A

tag: cell line


title: 25_body_Male_HZ_E5

description: longRNA-Seq


title: P01_16 [Z1_B2_8_S40]

tag: rna extraction_batch

tag: i7 index_id

value: GTTTATACT

tag: i5 index_id


title: Recovered1_3

description:
Recovered patient_1 Plate 3
Roche Lightcycler

tag: age in years

tag: gender


title: WT::EV biological replicate B

data_processing:
Raw reads were mapped to the Staphylococcus aeureus LAC genome assembly (NCBI accession GCF_015475575) , pJC1111 and pamA using Bowtie2
featureCounts was used to generate a read count table.
Assembly: GCF_015475575 + pJC1111 + pamA
Supplementary files format and content: featureCounts.tsv contains the RNA sequencing reads.

growth_protocol: overnight cultures of separate single colonies of WT::pamA and WT::EV were diluted 1:100 in 15 mL RPMI medium and incubated at 37°C shaking 180 rpm for five hours to exponential growth (OD ~0.9).

treatment_protocol: not treated

tag: strain

tag: genotype

value: USA300 LAC*::EV


title: Recovered4_2

description:
Recovered patient_4 Plate 2
Roche Lightcycler


title: WT::pamA biological replicate C

value: USA300 LAC*::pamA


title: 23_head_Male_HZ_E5

description: longRNA-Seq

tag: hh stage

tag: breed


title: Recovered3_2

description:
Recovered patient_3 Plate 2
Roche Lightcycler


title: P01_15 [Z1_B2_7_S39]

value: 120-hours post fertilization

tag: treatment

value: DMSO

tag: duration of_chemical_exposure

value: 5 days

tag: rna extraction_date

tag: chemical exposure_dates

tag: library well

tag: protocol


title: P01_13 [Z1_B2_5_S37]

tag: tissue

tag: developmental stage

tag: chemical

tag: chemical long_name

value: Dimethyl sulfoxide

tag: dose


title: WT::pamA biological replicate B


title: Recovered3_3

description:
Recovered patient_3 Plate 3
Roche Lightcycler

tag: age in years


title: WT::pamA biological replicate A


title: P01_12 [Z1_B2_4_S36]

tag: rna extraction_batch

tag: i7 index_id

tag: i5 index_id


title: 23_body_Male_HZ_E5

description: longRNA-Seq

tag: hh stage

tag: genotype

value: HZ

tag: Sex


title: Recovered1_2

description:
Recovered patient_1 Plate 2
Roche Lightcycler

tag: gender


title: Recovered2_3

description:
Recovered patient_2 Plate 3
Roche Lightcycler

value: Female


title: P01_11 [Z1_B2_3_S35]

tag: treatment

tag: duration of_chemical_exposure

tag: rna extraction_date


title: Recovered4_1

description:
Recovered patient_4 Plate 1
Roche Lightcycler


title: Ubc9-RR, INPUT, Replicate 2

data_processing:
All FASTA RAW sequences were quality controlled using FastQC v0.11.7
ChIP-seq reads were trimmed using Trimmomatic v0.38
ChIP-seq reads were aligned to the sacCer3 reference genome using Bowtie v1.1.2
Peaks were called using MACS2 v2.1.1.20160309
Assembly: sacCer3
Supplementary files format and content: bigwig

extract_protocol:
Formaldehyde was added to mid-log phase cells at a final concentration of 1% for 20 min. After quenching and cell lysis, chromatin was sonicated using a VCX130 Ultrasonic processor (Sonics and Materials)
ChIP-seq libraries were prepared using the TruSeq DNA Sample prep kit according to manufacturer's guidelines

tag: cell type


title: WT::EV biological replicate A

tag: strain


title: Recovered3_1

description:
Recovered patient_3 Plate 1
Roche Lightcycler


title: Recovered2_2

description:
Recovered patient_2 Plate 2
Roche Lightcycler


title: Spatial_Transciptomics_Mouse_AicdaWT

city: Palermo

first: Claudio

last: Tripodo

address: Corso Tukory 211

department: PROMISE

institute: Univerisity of Palermo

description: Visium Spatial Gene expression for FFPE tissue Sequencing

data_processing:
Raw sequencing data were processed using 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger’s default setting
Gene expression level of Refseq coding genes were quantified using Space Ranger’s default setting
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducilas of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowers_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots

source_name: mesenteric lymph node

extract_protocol:
Tissues were decrosslinked and enzymatically permeabilized RNA libraries were prepared to add illumina indexes (i5 and i7) requested for sequencing, as reported in Visium Spatial Gene expression for FFPE protocol (10x Genomics Visium, CG000407)
RHS and LHS probes for mouse samples from the Mouse Transcriptome Probe Kit (10x PN 2000457 and 2000458) were added to the visium slide, following the manufacturer’s instructions, and then incubated for approximately 18 hours at 50 °C in a Thermocycler.

treatment_protocol: 4 um-thick FFPE sections were sectioned  and placed on Visium glass slide followed by HE staining

tag: tissue

value: mesenteric lymph node

value: B6N;129-Ilk tm1Star/J


title: P01_10 [Z1_B2_2_S34]

tag: developmental stage

tag: chemical

tag: chemical exposure_dates

tag: library well

tag: protocol


title: P01_8 [Z1_B1_8_S8]

tag: chemical long_name

tag: dose

tag: rna extraction_batch

tag: i7 index_id

value: TCCTCAGCC


title: P01_14 [Z1_B2_6_S38]

tag: i5 index_id


title: P01_9 [Z1_B2_1_S33]


title: Recovered2_1

description:
Recovered patient_2 Plate 1
Roche Lightcycler

tag: age in years

tag: gender


title: Spatial_Transciptomics_Mouse_AicdaKO

tag: genotype

value: B6.129P2-Aicda tm1(cre)Mnz/J


title: Mild3_3

description:
Mild_3 Plate 3
Roche Lightcycler

value: Male


title: Recovered1_1

description:
Recovered patient_1 Plate 1
Roche Lightcycler


title: WT, INPUT Replicate 2


title: Mild2_3

description:
Mild_2 Plate 3
Roche Lightcycler


title: Mild4_3

description:
Mild_4 Plate 3
Roche Lightcycler


title: Ubc9-RR, INPUT, Replicate 1


title: Pr14-59_MG430-2_06121310

city: Nara

first: Kazuki

last: Kurimoto

address: 840 Shijo-Cho, Kashihara

department: School of medicine

institute: Nara Medical University

description:
Gene expression data from a single primordial germ cell isolated using a glass capillary
Prdm14 (+/+) PGC at early-to-late bud stage (E7.25-E7.5)

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Genome 430 2.0 Array. Microarray data was processed using dChip (Ver.1.3) with the PM/MM difference model.  Expression level of Dppa3 (1424295_at) were investigated.

label: biotin

source_name: Prdm14 (+/+) PGC at early-to-late bud stage (E7.25-E7.5), single cell

label_protocol: not provided

extract_protocol: C57BL/6 mice with the Prdm14 (+/-) genotype (Yamaji et al., Nature Genetics, 2008) were crossed. Pregnant mice were sacrificed at embryonic day (E) 7.25 - 7.5 and embryos at the early-to-mid allantois bud stage were isolated. The base of the allantois bud, where primordial germ cells (PGCs) were clustered, was dissected using a glass knife and cells were dissociated with trypsin as described (Kurimoto et al., Genes and Development, 2008). Single cells were randomly isolated manually using a glass capillary as described (Kurimoto et al., Nature Protocols, 2007) and directly subjected to cDNA amplification (Kurimoto et al., Nucleic Acids Research, 2006). cDNAs of PGCs were identified based on Prdm1 expression using targeted PCR as described (Kurimoto et al., Genes and Development, 2008). Genotypes of Prdm14 were identified by PCR as described (Yamaji et al., Nature Genetics, 2008). cDNAs of PGCs with Prdm14 (+/+), (+/-), and (-/-) genotypes were then subjected to microarray analysis using the Affymetrix GeneChip Mouse Genome 430 2.0 Array.

value: single primordial germ cell


title: Pr14-61_MG430-2_06121401


title: P01_7 [Z1_B1_7_S7]

tag: treatment

tag: duration of_chemical_exposure

tag: rna extraction_date

value: TempO-Seq


title: Pr14-64_MG430-2_06121402

tag: cell type


title: Pr14-65_MG430-2_06121403


title: P01_6 [Z1_B1_6_S6]

tag: tissue

tag: developmental stage


title: WT, INPUT, Replicate 1


title: Pr14-56_MG430-2_06121309


title: Pr14-50_MG430-2_06121307


title: Ubc9-RR, Smt3, ChIP, Replicate 2

tag: antibody


title: Ubc9-RR, Smt3, ChIP, Replicate 1


title: Mild1_3

description:
Mild_1 Plate 3
Roche Lightcycler


title: Pr14-51_MG430-2_06121308


title: Pr14-49_MG430-2_06121306


title: P01_4 [Z1_B1_4_S4]

tag: chemical

tag: chemical exposure_dates

tag: library well


title: Mild4_2

description:
Mild_4 Plate 2
Roche Lightcycler


title: P01_3 [Z1_B1_3_S3]

tag: chemical long_name

tag: dose

tag: protocol


title: P01_2 [Z1_B1_2_S2]

tag: rna extraction_batch

tag: i7 index_id

tag: i5 index_id


title: WT, Smt3, ChIP, Replicate 2


title: WT, Smt3, ChIP, Replicate 1


title: Pr14-31_MG430-2_06121303

tag: genotype


title: Mild3_2

description:
Mild_3 Plate 2
Roche Lightcycler

tag: age in years

tag: gender


title: Pr14-33_MG430-2_06121304


title: Mild2_2

description:
Mild_2 Plate 2
Roche Lightcycler


title: P20_23 [Z20_B3_7_S95]

tag: treatment

tag: duration of_chemical_exposure

tag: rna extraction_date

value: TAGCTCTTC


title: P20_22 [Z20_B3_6_S94]

tag: tissue

tag: developmental stage


title: P01_5 [Z1_B1_5_S5]

tag: chemical


title: Pr14-28_MG430-2_06121302

tag: cell type


title: Mild1_2

description:
Mild_1 Plate 2
Roche Lightcycler


title: Mild3_1

description:
Mild_3 Plate 1
Roche Lightcycler


title: Mild4_1

description:
Mild_4 Plate 1
Roche Lightcycler


title: Pr14-48_MG430-2_06121305


title: P01_1 [Z1_B1_1_S1]

tag: chemical exposure_dates

tag: library well


title: P20_24 [Z20_B3_8_S96]

tag: chemical long_name

tag: dose


title: Mild2_1

description:
Mild_2 Plate 1
Roche Lightcycler


title: P20_20 [Z20_B3_4_S92]

tag: rna extraction_batch

tag: protocol


title: Mild1_1

description:
Mild_1 Plate 1
Roche Lightcycler


title: P20_19 [Z20_B3_3_S91]

tag: i7 index_id

tag: i5 index_id


title: Pr14-119_MG430-2_06121506

description:
Gene expression data from a single primordial germ cell isolated using a glass capillary
Prdm14 (+/-) PGC at early-to-late bud stage (E7.25-E7.5)

source_name: Prdm14 (+/-) PGC at early-to-late bud stage (E7.25-E7.5), single cell

tag: genotype


title: Pr14-100_MG430-2_06121504


title: Pr14-25_MG430-2_06121301


title: Severe4-3

description:
Severe SARS_CoV2_4 Plate 3
Roche Lightcycler

tag: age in years

tag: gender


title: Severe3-3

description:
Severe SARS_CoV2_3 Plate 3
Roche Lightcycler


title: P20_18 [Z20_B3_2_S90]

tag: treatment

tag: duration of_chemical_exposure


title: Severe2-3

description:
Severe SARS_CoV2_2 Plate 3
Roche Lightcycler


title: BRC patient P4, tumour breast tissue, MNase-seq

city: Colchester

first: Vladimir

middle: B

last: Teif

address: Wivenhoe Park

department: School of Life Sciences

country: United Kingdom

institute: University of Essex

data_processing:
Breast tissue samples for patients P1-P3 were sequenced on Illumina NovaSeq S4, TruSeq ChIP Library Prep Kit (IP-202-1012), 2 x 100 bp paired-end mode. cfDNA samples for patients P1 and P3 were sequenced as above, but in 2 x 150 bp paired-end mode. Samples for patient P4 were sequenced on Illumina HiSeq 2500 sequencer, 2 x 75 bp paired-end mode, using NEBNext Ultra II Kit from NEB for library preparation. Paired-end sequenced reads were mapped with Bowtie  to human genome hg19, considering only uniquely mapped reads and allowing up to one mismatch. This resulted in ~500 million mapped reads per sample (see details in Supplementary Table S1). NucTools pipeline was used to obtain BED files with mapped nucleosomal DNA fragments including information about DNA fragment sizes. A set of Perl scripts called cfDNAtools developed for the next steps of analysis reported here is available at https://github.com/TeifLab/cfDNAtools. cfDNAtools script extract_nuc_sizes.pl  was used to extract fractions with DNA fragments with sizes between 100-120 bp, 120-140 bp, 140-160 bp, 160-180 bp and 180 -200 bp. Intersections between regions of interest were done using BEDTools (Quinlan, 2014).
DNA fragments with sizes 120-180bp are included in this dataset
Assembly: hg19
Supplementary files format and content: BED files containing all mapped reads within size range 120-180bp. The FED file contains the following columns: chromosome, start coordinate, end coordinate, fragment size (bp)
Supplementary files format and content: BigWig files for visualisation in the genome browser

source_name: breast

extract_protocol:
MNase-seq and MNase-assisted histone H3 ChIP-seq  Chromatin extraction. Paired normal and tumour breast tissues extracted during surgery were stored at -80  ͦC. Frozen tissue was first ground into fine powder in liquid nitrogen. It was further homogenized by manual douncing in 5 ml ice-cold Buffer I (0.3 M Sucrose in 60 mM KCl, 15 mM NaCl, 5mM MgCl2, 0.1 mM EGTA, 15 mM Tris-HCl (pH 7.5) with freshly added 0.5 mM DTT, 0.1 mM PMSF and 1XProtease Inhibitor Cocktail, Thermo Scientific Halt Protease Inhibitor Single-use Cocktail (100X). The homogenized cell suspension was centrifuged in a 15 ml Falcon conical centrifuge tube at 6000 g for 10 minutes at 4  ͦC. The precipitated cells were re-suspended in 500 µL of Buffer I, then 500 µL of Buffer II (same as Buffer I, but with freshly added 0.4 % (v/v) IGEPAL CA-630) was gently added on top and the lysate was incubated on ice for 3 minutes, followed by centrifugation at 3000 g for 3 minutes at 4  ͦC. The pellet was re-suspended in 1 ml of ice-cold NBR Buffer (85 mM NaCl, 5.5 % Sucrose, 10 mM Tris-HCl pH 7.5, 3 mM MgCl2, 1.5 mM CaCl2 with freshly added 0.2 mM phenylmethylsulfonyl fluoride (PMSF) and 1 mM DTT) and centrifuged at 3000 g for 3 minutes at 4  ͦC. The pellet then was re-suspended in 200 µl of NBR buffer. Samples were treated with 1 µl RNAseA (10 mg/ml) per 100 µl of nuclear lysate for 5 minutes at room temperature.     MNase digestion. MNase restriction enzyme (Sigma, Cat No: N5386-500UN) was diluted to 1U (Sigma Boehringer Units) in MNase buffer (50 % Glycerol, 10 mM Tris p H7.6 and 50 mM NaCl). The pellets re-suspended in 200 µl of NBR buffer in the chromatin extraction step were digested with MNase enzyme as follows. Chromatin derived from paired normal and tumour tissue was diluted with NBR buffer to keep the same concentration in both preparations.  A 20 µl aliquot of purified nuclei was test digested with 1 µl MNase for 7 min at room temperature to assess the optimal digestion time and enzyme concentrations. 1 µg of chromatin was digested with 1U of MNase for 7 minutes at room temperature to achieve 80:20 relative abundance of mono- and di-nucleosome fractions on agarose gel. The MNase digestion was stopped by addition of equal volume (NBR:STOP, 1:1) of STOP Buffer (215  mM NaCl, 10 mM TrisHCl pH 8, 20 mM EDTA, 5.5 % Sucrose, 2 % TritonX 100 with freshly added 0.2 mM PMSF, 1 mM DTT and 2X Protease Inhibitors). After digestion, chromatin was incubated on ice in the fridge at 4  ͦC overnight to release the digested chromatin.     Chromatin Immunoprecipitation (ChIP). 10 µl of Protein A beads (DynabeadsTM Protein A; Invitrogen) equivalent to 10 µl bed volume of slurry were prepared per each ChIP reaction. Bead storage buffer was aspirated, and the beads were washed twice in 500 µl in Block solution (0.5 % BSA (w/v) in PBS supplemented with 0.1 mM PMSF). Beads sufficient for 4 ChIP samples were all combined and dissolved in 600 µl of Block solution with addition of 5 µg of anti-H3 antibody Abcam AB1791 per ChIP reaction (20 µg for 40 µl of beads for 4 ChIP samples). The antibody-bead solution was incubated on a slow rotating wheel at 4  ͦC for two hours. After incubation, the beads were again washed in 600 µl block solution to remove un-bound antibody. The chromatin incubated overnight after MNase digestion, was then centrifuged for 10 minutes at max speed 9800 g at 4  ͦC. The supernatant with released chromatin was collected and stored at -20  ͦC and used for ChIP experiment. 5 % of chromatin volume used for MNase-assisted ChIP-seq was frozen at -20  ͦC as Input and used for MNase-seq. 300 µl of chromatin was incubated with the antibody bound Protein A beads for 3 hours on a rotating wheel at 4  ͦC. Unbound chromatin was washed 4 times  in 1 ml volume of ChIP-Wash buffer (150 mM NaCl, 10 mM Tris-HCl pH 8, 2 mM EDTA, 1 % NP40, 1 % Nadeoxycholate with freshly added 0.5 mM DTT, 0.1 mM PMSF and 1XProtease Inhibitor Cocktail). The initial wash of bound beads was done by gently mixing beads in the ChIP-Wash buffer for one min. For subsequent 3 washes: the tube was rotated for 5 minutes at 4  ͦC on a rotating wheel, then placed in magnetic rack for 1 min at 4  ͦC and then the supernatant was withdrawn.  After two washes the beads with wash buffer were transferred to new tubes. And as a final step, the beads were washed with 1 ml of filtered 1x TE buffer (10 mM Tris-HCl containing 1 mM EDTA) at room temperature, after which the TE buffer was removed as above. The elution of bound chromatin was performed with 100 µl of Elution buffer (0.1 M NaHCO3, 1 % SDS) supplemented with 2 µl of Proteinase K per ChIP sample tube. The beads were incubated with the elution buffer for 6-12 hours at 55  ͦC. Similarly, 2 µl of Proteinase K were added to Input material and incubated at 55  ͦC for 6-12 hours. The incubated beads were briefly vortexed and supernatant collected by placing the tubes in a magnetic rack. The beads were additionally washed in 20 µl of elution buffer and supernatant collected as above. The eluants were further purified with PCR purification columns according to manufacturer’s instructions and eluted in 20 µl volume of elution buffer of the kit. These final eluants were stored at -20  ͦC ready for library preparation step.   cfDNA extraction. Cell-free DNA was extracted from 500 µl of blood plasma or serum as detailed below, following the instructions of the purification kits. For patient P1, cfDNA was extracted from 500 µl of blood serum using Plasma/serum Cell-Free Circulating DNA purification Mini Kit  (Norgen Biotek Corp). For patient P2, cfDNA was extracted from 500 µl
The libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs, NEB #E7103) according to the manufacturer’s instructions.
NEBNext Ultra II DNA Library Prep Kit (New England Biolabs, NEB #E7103)

tag: tissue

value: breast

tag: condition

value: tumour


title: P20_16 [Z20_B2_8_S64]

tag: developmental stage

tag: chemical

tag: rna extraction_date

value: TCAGTACAT


title: BRC patient P4, tumour breast tissue, MNase-assisted H3 ChIP-seq

tag: cell type

tag: antibody

value: histone H3


title: P20_21 [Z20_B3_5_S93]

value: 120-hours post fertilization

value: DMSO

tag: chemical long_name

tag: dose

tag: chemical exposure_dates

tag: library well


title: Severe1-3

description:
Severe SARS_CoV2_1 Plate 3
Roche Lightcycler


title: BRC patient P4, normal breast tissue, MNase-seq

value: normal


title: P20_15 [Z20_B2_7_S63]

value: 5 days

value: Dimethyl sulfoxide

tag: rna extraction_batch

tag: i7 index_id

tag: i5 index_id

tag: protocol


title: Severe4-2

description:
Severe SARS_CoV2_4 Plate 2
Roche Lightcycler

tag: age in years

tag: gender


title: P20_14 [Z20_B2_6_S62]

tag: tissue

tag: treatment

tag: duration of_chemical_exposure


title: BRC patient P4, normal breast tissue, MNase-assisted H3 ChIP-seq

tag: condition


title: Pr14-98_MG430-2_06121502

tag: genotype


title: Pr14-91_MG430-2_06121410

tag: cell type


title: P20_17 [Z20_B3_1_S89]

tag: developmental stage

tag: chemical

tag: rna extraction_date


title: P20_13 [Z20_B2_5_S61]

tag: chemical long_name

tag: dose

tag: chemical exposure_dates


title: P20_12 [Z20_B2_4_S60]

tag: rna extraction_batch

tag: i7 index_id

tag: library well


title: Pr14-89_MG430-2_06121409


title: Severe2-2

description:
Severe SARS_CoV2_2 Plate 2
Roche Lightcycler

tag: age in years


title: Pr14-118_MG430-2_06121505


title: Pr14-97_MG430-2_06121501


title: Pr14-99_MG430-2_06121503


title: 104_13_IPS_dox_2 [S5_dox]

city: Boston

first: Edroaldo

last: Lummertz da Rocha

state: MA

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Boston Children's Hospital

data_processing:
RNA-seq reads were trimmed for adaptor sequence using Trimmomatic and aligned to the human genome hg38 using Bowtie/Tophat.
Counts were generated using featureCounts.
Normalization was performed with DESeq2.
Assembly: hg38
Supplementary files format and content: rawcounts.txt: Tab-separated text file containing gene expression counts.

source_name: HSPCs

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen) per the manufacturer’s protocol. Purified RNA was subjected to polyA selection using the NEBNext Polyadenylated mRNA Magnetic Isolation Module and subsequently used for library preparation with the NEBNext Ultra RNA Library Prep Kit (both from New England Biolabs). Libraries were analyzed on a Tapestation (Agilent) for quality control, quantified using the Qubit dsDNA HS Assay (Invitrogen) and equimolar pools were sequenced on HiSeq 2500 using 75-bp single-end protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: HSPCs


title: Severe1-2

description:
Severe SARS_CoV2_1 Plate 2
Roche Lightcycler

tag: gender


title: 104_13_IPS_nodox_2 [S6_nodox]


title: Pr14-79_MG430-2_06121407


title: Pr14-88_MG430-2_06121408


title: Pr14-76_MG430-2_06121405


title: Pr14-78_MG430-2_06121406


title: Severe4-1

description:
Severe SARS_CoV2_4 Plate 1
Roche Lightcycler


title: 104_13_IPS_dox [S3_dox]


title: P20_11 [Z20_B2_3_S59]

tag: tissue

tag: i5 index_id

tag: protocol


title: 104_13_IPS_nodox [S4_nodox]


title: Severe3-2

description:
Severe SARS_CoV2_3 Plate 2
Roche Lightcycler


title: P20_10 [Z20_B2_2_S58]

tag: treatment

tag: duration of_chemical_exposure


title: Pr14-66_MG430-2_06121404

tag: cell type

tag: genotype


title: Severe3-1

description:
Severe SARS_CoV2_3 Plate 1
Roche Lightcycler


title: P20_9 [Z20_B2_1_S57]

tag: developmental stage

tag: chemical


title: P10_16 [Z10_B2_8_S56]

tag: chemical long_name

tag: rna extraction_date

value: ATTCGCTCT


title: 106_IPS_nodox [S2_nodox]


title: Pr14-18_MG430-2_06121508

description:
Gene expression data from a single primordial germ cell isolated using a glass capillary
Prdm14 KO PGC

source_name: Prdm14 (-/-) PGC at early-to-late bud stage (E7.25-E7.5), single cell


title: P10_15 [Z10_B2_7_S55]

tag: dose

tag: chemical exposure_dates


title: Severe1-1

description:
Severe SARS_CoV2_1 Plate 1
Roche Lightcycler


title: Fanconi [GR16_FAL]


title: Fanconi [GR12_FAL]


title: Fanconi [GR21_FAL]


title: P10_13 [Z10_B2_5_S53]

tag: rna extraction_batch

tag: i7 index_id


title: HC4_3

description:
Healthy Control4 Plate 3
Roche Lightcycler

tag: age in years


title: P10_14 [Z10_B2_6_S54]

tag: library well


title: Pr14-81_MG430-2_06121510


title: HC2_3

description:
Healthy Control2 Plate 3
Roche Lightcycler

tag: gender


title: HC3_3

description:
Healthy Control3 Plate 3
Roche Lightcycler


title: Pr14-21_MG430-2_06121509


title: Severe2-1

description:
Severe SARS_CoV2_2 Plate 1
Roche Lightcycler


title: Pr14-08_MG430-2_06121507


title: MDS [GR7_MDS]


title: P10_12 [Z10_B2_4_S52]

tag: tissue

tag: i5 index_id


title: 106_IPS_dox [S1_dox]


title: MDS [GR6_MDS]


title: HC4_2

description:
Healthy Control4 Plate 2
Roche Lightcycler


title: P10_11 [Z10_B2_3_S51]

tag: treatment

tag: protocol


title: P10_10 [Z10_B2_2_S50]

tag: duration of_chemical_exposure


title: MDS [GR5_MDS]

tag: cell type


title: 3W Minoxidil (MXD) - 3W Control (Cy5) x 3W MXD (Cy3)

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

description:
3W Minoxidil (MXD)
0031_1_4
Dye-swap (Cy3/Cy5) of Cont vs N-CE 3W mouse back skin

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2600D SG17204584

data_processing: Software: Feature Extraction ver 12.0.3.1

source_name: 3W 3% Minoxidil-treated back skin Cy3

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: Experimental protocols were reviewed and approved by the Animal Care Committee of Hoshi University School of Pharmacy and Pharmaceutical Sciences. Male C57BL/6 mice (8 weeks-old) purchased from Tokyo Laboratory Animals Science Co., Ltd. (Tokyo, Japan). The animals were housed at the Animal Institution in Hoshi University. They were maintained in cages in a ventilated animal room with controlled temperature and relative humidity with a 12 h light : 12 h dark cycle with free access to water and rodent chow.

extract_protocol: QIAGEN, Rneasy Micro kit

treatment_protocol: Preliminary experiments were conducted with WO at 5, 10, and 20% concentrations. C57BL/6 mice were divided into 3 groups (6 mice per group): WO 20%, MXD 3%, and VC (propylene glycol: ethanol: water (5:3:2) was used as the vehicle control group). Briefly, starting the day after shaving, 200 μL of the adjusted sample was applied daily to the backs of the mice for observation and photography, and sampling.

tag: strain

value: back skin

source_name: 3W Vehicle-treated back skin Cy5


title: HC2_2

description:
Healthy Control2 Plate 2
Roche Lightcycler


title: P20_8 [Z20_B1_8_S32]

tag: developmental stage

tag: chemical

value: GAACTGTAT


title: RNA Individual 6 skin fibroblast cells, Dexamethasone, Time48

city: Los Angeles

first: Marcelo

last: Francia

state: CA

address: 1771 Beloit Avenue, Unit 204

department: Neuroscience

institute: University of California, Los Angeles

data_processing:
Fastqc software was used to assess the quality of the raw files. Low quality reads were trimmed using TrimGalore and Cutadapt.
Alignment of reads was performed with the STAR software and to human gene ensembl version GrCh38. STAR was indexed to the genome using the –runMode genomeGenerate function. For aligning, STAR was run with the parameters –outFilterType BySJout –outFilterMultimapNmax 20 –alignSJoverhangMin 8 –alignSJDBoverhangMin 1 –outFilterMismatchNmax 999 -outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 -alignIntronMax 1000000 -alignMatesGapMax 1000000.
Samtools was used to index the aligned files from STAR
Read counts were associated with genes using featureCounts software with the NCBI GRCh38 gene annotation file
Assembly: GrCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Skin

growth_protocol: Fibroblast cell lines were thawed out and grown to confluence in T75 culture flasks in standard culture media (DMEM containing 10% fetal bovine serum (FBS) and 1x Penicillin-Streptomycin)

extract_protocol:
RNA from cell lysates was extracted using the Qiagen RNeasy mini kit (Qiagen 74106). Cell lysates were extracted in a randomized order to prevent batch effects in downstream analysis. In order to collect total RNA including small RNAs, the standard extraction protocol (Purification of Total RNA from Animal Cells using Spin Technology) was adjusted by making the following changes: (i) adding 1.5 volumes of 100% ethanol, instead of 70%, after the lysis step (step 4 in handbook protocol) and (ii) adding 700 mL of buffer RWT (Qiagen 1067933) instead of the provided RW1 (step 6 in handbook protocol).
RNA library preps were made using the Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit

treatment_protocol: 5 days after being plated the cells were treated  with 100 nM Dexamethasone for 30 min. Cells were then washed with PBS and switched to collection media (DMEM containing 5% FBS and 1x Penicillin-Streptomycin). Collection started 12 hours after Dexamethasone treatment, and continued every 4 hours for a 48 hour period

value: Skin

value: Fibroblast cells

value: Dexamethasone

tag: time

value: Time 48


title: HC1_3

description:
Healthy Control1 Plate 3
Roche Lightcycler

value: Female


title: RNA Individual 6 skin fibroblast cells, Dexamethasone, Time44

value: Time 44


title: HC1_2

description:
Healthy Control1 Plate 2
Roche Lightcycler


title: 1W Minoxidil (MXD) - 1W Control (Cy5) x 1W MXD (Cy3)

description:
1W Minoxidil (MXD)
0027_1_4
Dye-swap (Cy3/Cy5) of Cont vs N-CE 1W mouse back skin

source_name: 1W 3% Minoxidil-treated back skin Cy3

source_name: 1W Vehicle-treated back skin Cy5


title: 3W Whale Oil (WO) - 3W Control (Cy3) x 3W WO (Cy5)

description:
3W Whale Oil (WO)
0031_1_1
Dye-swap (Cy3/Cy5) of Cont vs MXD 3W mouse back skin

source_name: 3W Vehicle-treated back skin Cy3

source_name: 3W 20% Whale Oil-treated back skin Cy5


title: P20_7 [Z20_B1_7_S31]

tag: chemical long_name

tag: dose

tag: rna extraction_date

value: TempO-Seq


title: HC4_1

description:
Healthy Control4 Plate 1
Roche Lightcycler

value: Male


title: 1W Minoxidil (MXD) - 1W Control (Cy3) x 1W MXD (Cy5)

description:
1W Minoxidil (MXD)
0027_1_3
Dye-swap (Cy3/Cy5) of Cont vs N-CE 1W mouse back skin

source_name: 1W Vehicle-treated back skin Cy3

source_name: 1W 3% Minoxidil-treated back skin Cy5


title: P20_6 [Z20_B1_6_S30]

value: 120-hours post fertilization

tag: rna extraction_batch

tag: chemical exposure_dates

tag: i7 index_id


title: RNA Individual 6 skin fibroblast cells, Dexamethasone, Time40

value: Time 40


title: RNA Individual 6 skin fibroblast cells, Dexamethasone, Time36

value: Time 36


title: RNA Individual 6 skin fibroblast cells, Dexamethasone, Time32

value: Time 32


title: HC3_1

description:
Healthy Control3 Plate 1
Roche Lightcycler

source_name: Peripheral Blood

tag: age in years

tag: gender


title: HC3_2

description:
Healthy Control3 Plate 2
Roche Lightcycler


title: GEX_hFOB 1.19, transfected with custom CRISPRi sgRNA pool 7

city: Philadelphia

first: Mitchell

middle: L

last: Conery

state: PA

address: 3615 Civic Center Blvd

department: Center for Spatial and Functional Genomics

institute: Children's Hospital of Philadelphia

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Single-cell FASTQs were initially processed using the CellRanger pipeline (10x Genomics Cell Ranger 3.0.0) with default settings.
We then used CellBender to denoise and filter the raw CellRanger outputs separately for each of the eight pools.
The number of droplets and expected number of cells were visually estimated from each pool’s unique molecular identifier (UMI) curve, and we ran Cellbender with a learning rate of 0.00005, 150 training epochs, and a false-positive rate of 1%.
After CellBender we used UMAP projections and violin plots implemented in Scanpy to visualize the remaining droplets for each pool and quickly recognized that all pools but the second contained two clusters of droplets, one with a high number of UMIs and genes per droplet and the other with a low level of cellular complexity. The second pool had an overall low level of complexity indicative of mostly empty droplets and was discarded.
For the remaining pools we used the Leiden algorithm to cluster the cells and retained only the high complexity cluster.
The remaining droplets were then combined across pools and visualized using UMAP and violin plots. We discarded droplets with >10% mitochondrial reads and >90,000 UMI to remove suspected dying cells and doublets respectively.
Assembly: hg19
Supplementary files format and content: Standardized h5seurat single-cell output file of QCed cells and tab-delimited file of sgRNAs per cell.

source_name: hFOB 1.19, transfected with custom CRISPRi sgRNA pool, differentiated 5 days

growth_protocol: Stock hFOB-CRISPRi-KRAB-Pooled-sgRNA cells were grown in 100mm plates under Blasticidin/Puromycin selection for 2 days at 33.5°C, then differentiated for 5 days at 39.5°C.

extract_protocol:
Cells were removed from plates with TrypLE, counted, and diluted to 1000cells/ul in DPBS+1% FBS. RNA was extracted from cells and sgRNAs were barcode captured following manufacturer's instructions as part of 10X Genomics sequencing.
Library was constructed according to the manufacturer's instructions (10X Genomics scRNA-seq, GEX libraries) and Feature Barcoded CRIPSR Capture (CRISPR Capture libraries) at the CHOP Center for Applied Genomics.

treatment_protocol: To generate the hFOBs containing our custom sgRNAs, the same helper hFOB-dCas9-CRISPRi-KRAB cells were used for transduction. Cells were transduced at low MOI (0.2) plus polybrene (8ug/ml) with a Sigma-Aldrich custom sgRNA lentiviral pool (titer = 5.3 x 108 TU/ml).

tag: cell line

value: hFOB1.19 cells

value: human fetal osteoblasts

value: transfected with custom 296-sgRNA pool

value: differentiated 5 days

tag: pool

tag: library type

value: GEX


title: P20_5 [Z20_B1_5_S29]

tag: tissue

tag: treatment

value: DMSO

tag: duration of_chemical_exposure

value: 5 days

value: Dimethyl sulfoxide

value: GAACTGTAT

tag: i5 index_id

tag: library well

tag: protocol


title: GEX_hFOB 1.19, transfected with custom CRISPRi sgRNA pool 8

description: 10x Genomics

tag: cell type

tag: time


title: P20_4 [Z20_B1_4_S28]

tag: developmental stage

tag: chemical

tag: chemical long_name

tag: dose

tag: rna extraction_date


title: P10_9 [Z10_B2_1_S49]

tag: rna extraction_batch

tag: chemical exposure_dates

tag: i7 index_id

value: ATTCGCTCT


title: RNA Individual 6 skin fibroblast cells, Dexamethasone, Time28

value: Skin

value: Fibroblast cells

value: Dexamethasone

value: Time 28


title: P20_3 [Z20_B1_3_S27]

value: 120-hours post fertilization

value: TempO-Seq


title: 1W Whale Oil (WO) - 1W Control (Cy3) x 1W WO (Cy5)

description:
1W Whale Oil (WO)
0027_1_1
Dye-swap (Cy3/Cy5) of Cont vs MXD 1W mouse back skin

tag: strain

value: back skin

source_name: 1W 20% Whale Oil-treated back skin Cy5


title: RNA Individual 6 skin fibroblast cells, Dexamethasone, Time24

tag: tissue

value: Time 24


title: A549 cells, VILMIRg1, 1 ng/mL IFN, rep2

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

institute: NC State

data_processing:
Illumina RNA-seq reads were mapped against the human genome assembly version 38 (Hg38) using STAR version 2.7.9a. Custom STAR parameters were set as follows: limitOutSAMoneReadBytes: 1000000, outSAMprimaryFlag: AllBestScore, outFilterType: BySJout, alignSJoverhangMin: 8, alignSJDBoverhangMin: 3, outFilterMismatchNmax: 999, alignIntronMin: 20, alignIntronMax: 1000000, alignMatesGapMax: 1000000, outFilterMultimapNmax: 20; otherwise, default STAR parameters were used.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample as generated by STAR

growth_protocol: A549 cell lines were maintained in F-12K media with 10% fetal bovine serum (FBS) at 37°C in a 5% CO2 incubator.

extract_protocol:
Total RNA was isolated from cells following the TRIzol isolation method (Invitrogen). All samples were quantified and assayed to confirm minimum RNA integrity number of at least 9.4 using an Agilent Bioanalyzer (RNA 6000 Pico Kit, catalog no. 5067-1513).
500 ng of total RNA per sample underwent mRNA capture and was then fragmented at 94°C for 6 min. Sequencing libraries were prepared according to the manufacturer’s protocol using eleven cycles of final amplification (KAPA mRNA HyperPrep Kit, catalog no. KK8580 and KAPA UDI Adapter Kit, catalog no. KK8727). Libraries underwent QC prior to sequencing using an Agilent Bioanalyzer (High Sensitivity DNA Kit, catalog no. 5067-4626).

treatment_protocol: A549 cells were seeded overnight at 150,000 cells per well in 12-well plates in 1.5 mL media to reach ~80% confluency the next day. The media was then removed, and the cell monolayer was washed with 1X DPBS prior to interferon treatment. Cells were treated with fresh A549 media with or without human IFN-β recombinant protein (R&D Systems™ 8499IF010) at 1 ng/mL or 10 ng/mL for 6 hours.

tag: cell line

value: epithelial cell

tag: genotype

value: VILMIR knockdown

tag: treatment

value: 1 ng/mL IFN-B


title: GEX_hFOB 1.19, transfected with custom CRISPRi sgRNA pool 4

description: 10x Genomics

value: hFOB1.19 cells

value: human fetal osteoblasts

value: transfected with custom 296-sgRNA pool

value: differentiated 5 days

tag: pool

tag: library type

value: GEX


title: GEX_hFOB 1.19, transfected with custom CRISPRi sgRNA pool 5

description: 10x Genomics

tag: cell type


title: P20_2 [Z20_B1_2_S26]

value: DMSO

tag: duration of_chemical_exposure

value: 5 days

value: Dimethyl sulfoxide

value: GAACTGTAT

tag: i5 index_id

tag: library well

tag: protocol


title: P20_1 [Z20_B1_1_S25]

tag: developmental stage

tag: chemical

tag: chemical long_name

tag: dose


title: A549 cells, VILMIRg1, mock, rep3

value: mock


title: RNA Individual 6 skin fibroblast cells, Dexamethasone, Time16

value: Skin

value: Fibroblast cells

value: Dexamethasone

tag: time

value: Time 16


title: 1W Whale Oil (WO) - 1W Control (Cy5) x 1W WO (Cy3)

description:
1W Whale Oil (WO)
0027_1_2
Dye-swap (Cy3/Cy5) of Cont vs MXD 1W mouse back skin

source_name: 1W 20% Whale Oil-treated back skin Cy3

tag: strain

value: back skin


title: RNA Individual 6 skin fibroblast cells, Dexamethasone, Time12

tag: tissue

value: Time 12


title: P10_8 [Z10_B1_8_S24]

value: 120-hours post fertilization

tag: rna extraction_batch

tag: rna extraction_date

tag: chemical exposure_dates

tag: i7 index_id

value: GGGTTGTTA

value: TempO-Seq


title: GEX_hFOB 1.19, transfected with custom CRISPRi sgRNA pool 2

description: 10x Genomics

tag: cell line

value: hFOB1.19 cells

value: human fetal osteoblasts

tag: treatment

value: transfected with custom 296-sgRNA pool

tag: pool

tag: library type


title: GEX_hFOB 1.19, transfected with custom CRISPRi sgRNA pool 3

description: 10x Genomics

tag: cell type

value: differentiated 5 days

value: GEX


title: A549 cells, STAT1g1, 10 ng/mL IFN, rep3

value: epithelial cell

tag: genotype

value: STAT1 knockdown

value: 10 ng/mL IFN-B


title: C3 KO colon_No treatment

city: Miryang-si/Gyeongsangnam-do

first: Dae Youn

last: Hwang

address: 50 Cheonghak-ri, Samnangjin-eup

institute: Pusan National University

description: Gene expression data from 16-weeks-old C3 KO mice

hyb_protocol: Approximately 5.5 μg of the labeled DNA target was hybridized to the Affymetrix GeneChipTM Mouse 2.0 ST Array (ThermoFisher Scientific Inc.) at 45°C for 16 h.

scan_protocol: The hybridized arrays were washed, stained on a GeneChipTM Fluidics Station 450 (ThermoFisher Scientific Inc.), and scanned on a GCS3000 Scanner (Affymetrix, Santa Clara, CA, USA).

data_processing: The signal values were calculated using the Affymetrix® GeneChip™ Command Console® Software (AGCC).

label: Biotin

source_name: FVB background C3 KO mice colon tissue, No treatment

label_protocol: The sense cDNA was fragmented and biotin-labeled with terminal deoxynucleotidyl transferase (TdT) using the GeneChipTM HT WT Terminal Labeling Kit (ThermoFisher Scientific Inc.).

growth_protocol: The experimental protocols for wild type (WT) and C3 KO mice were reviewed and approved by the Pusan National University-Institutional Animal Care and Use Committee (PNU-IACUC; Approval Number PNU-2023-0407)

extract_protocol: The total RNAs were purified from the frozen mid colon tissue (100 mg) using TransZol (TransGen Biotech Co. LTD, Beijing, China) (1 mL) solution based on the manufacturer’s protocol.

treatment_protocol: No treatment

value: Distal colon

tag: age

value: 16 weeks

value: C3 KO


title: P10_7 [Z10_B1_7_S23]

tag: developmental stage

value: DMSO

tag: duration of_chemical_exposure

value: 5 days

tag: chemical

value: Dimethyl sulfoxide

tag: i5 index_id

tag: library well

tag: protocol


title: GEX_hFOB 1.19, transfected with custom CRISPRi sgRNA pool 6

description: 10x Genomics

tag: time


title: P10_6 [Z10_B1_6_S22]

tag: tissue

value: 120-hours post fertilization

tag: chemical long_name

tag: dose

tag: rna extraction_batch

tag: rna extraction_date


title: WT colon_No treatment

description: Gene expression data from 16-weeks-old WT mice

source_name: FVB mice colon tissue, No treatment

value: WT


title: A549 cells, STAT1g1, 1 ng/mL IFN, rep3

tag: cell line

tag: treatment

value: 1 ng/mL IFN-B


title: GEX_hFOB 1.19, transfected with custom CRISPRi sgRNA pool 1

description: 10x Genomics

value: hFOB1.19 cells

tag: cell type

tag: pool

tag: library type


title: RNA Individual 6 skin fibroblast cells, Dexamethasone, Time4

value: Skin

value: Fibroblast cells

value: Dexamethasone

value: Time 4


title: GDO_hFOB 1.19, transfected with custom CRISPRi sgRNA pool 8

description: 10x Genomics

data_processing:
Single-cell FASTQs were initially processed using the CellRanger pipeline (10x Genomics Cell Ranger 3.0.0) with default settings.
We then used CellBender to denoise and filter the raw CellRanger outputs separately for each of the eight pools.
The number of droplets and expected number of cells were visually estimated from each pool’s unique molecular identifier (UMI) curve, and we ran Cellbender with a learning rate of 0.00005, 150 training epochs, and a false-positive rate of 1%.
After CellBender we used UMAP projections and violin plots implemented in Scanpy to visualize the remaining droplets for each pool and quickly recognized that all pools but the second contained two clusters of droplets, one with a high number of UMIs and genes per droplet and the other with a low level of cellular complexity. The second pool had an overall low level of complexity indicative of mostly empty droplets and was discarded.
For the remaining pools we used the Leiden algorithm to cluster the cells and retained only the high complexity cluster.
The remaining droplets were then combined across pools and visualized using UMAP and violin plots. We discarded droplets with >10% mitochondrial reads and >90,000 UMI to remove suspected dying cells and doublets respectively.
Assembly: hg19
Supplementary files format and content: Standardized h5seurat single-cell output file of QCed cells and tab-delimited file of sgRNAs per cell.
Library strategy: scCRISPR screen

value: human fetal osteoblasts

value: transfected with custom 296-sgRNA pool

value: differentiated 5 days

value: GDO


title: RNA Individual 6 skin fibroblast cells, Dexamethasone, Time8

value: Time 8


title: RNA Individual 6 skin fibroblast cells, Dexamethasone, Time20

value: Time 20


title: A549 cells, STAT1g1, mock, rep3

value: epithelial cell

tag: genotype

value: STAT1 knockdown

value: mock