title: P111

city: Szczecin

first: Tomasz

middle: K

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

institute: Pomeranian Medical University

description: peripheral blood from COVID-19 patient

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

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

data_processing: Data were processed in R using ChAMP package, normalized using BMIQ method.

label: Cy5 and Cy3

source_name: peripheral blood

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted using PureLink™ Genomic DNA Mini Kit.

tag: disease


title: BulkRNA hESCs, replicate C

status: Public on Jul 20 2022

type: SRA

city: Roma

first: Alessio

last: Colantoni

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

country: Italy

institute: "Sapienza" University of Rome

library_source: transcriptomic

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq v2.17 software. One mismatch was allowed for index sequence identification.
Adapter sequences and poor quality ends were removed using the Trimmomatic v0.39 software with parameters ILLUMINACLIP:/path/to/adapter:2:30:10:1:true  SLIDINGWINDOW:20:15 MINLEN:36.
Salmon v1.3.0 tool was employed to quantify transcript expression, producing isoform-level transcripts per million (TPM) values from a full decoy transcriptome index created using the GENCODE v35 transcriptome and the hg38 genome.
Assembly: hg38
Supplementary files format and content: Sample-specific Salmon quantification files

molecule: total RNA

organism: Homo sapiens

growth_protocol: H9 hESCs were routinely propagated feeder-free in mTeSR1 on cell culture plates previously coated with Matrigel following the manufacturer instructions. Undifferentiated hESCs were propagated and passed at least 3 times after thawing and plated for the differentiation when at 80% of confluence. Cells were maintained in culture and expanded at high quality with particular care to avoid any spontaneous differentiation, which would confound downstream differentiation. The day before the induction of the differentiation, hESCs were washed twice in PBS, dissociated with Accutase, plated in mTeSR1 + Rock Inhibitor (Y27632, 5uM) to promote cell survival and incubated for 12 hours at 37 °C, 5% CO2 for 12 hours. The day after, 30% confluent hESCs were induced to differentiate into definitive endoderm, by incubation with Medium A (Gibco cat. n. A30621-01) for 24 hours and with Medium B (Gibco cat. n. 30624-01) for the following 24 hours at 37 °C, 5% CO2. The third day DE was patterned into AFG by the addition of CDM2 medium with A-83-01, 1uM and DM3189, 250nM. The composition of CDM2 basal medium was as follows: 50% IMDM (+GlutaMAX, +HEPES, +Sodium Bicarbonate; Gibco, 31980-097) + 50% F12 (+GlutaMAX; Gibco, 31765-092) + 1 mg/mL polyvinyl alcohol (Sigma, P8136-250G) + 1% v/v concentrated lipids (Gibco, 11905-031) + 450 µM monothioglycerol (Sigma, M6145) + 0.7 µg/mL insulin (Roche, 1376497) + 15 µg/mL transferrin (Roche, 652202) and incubated at 37 °C, 5% CO2. From day four to day 5, Retinoic Acid 200 nM was added at the CDM2 medium with A-83-01, 1 uM and DM3189, 250 nM and medium was changed every 24 hours.

extract_protocol:
Total RNA from hESCs, DE, AFE, and PE cells was isolated by collecting cells using TRI Reagent (Zymo Research), followed by column purification and DNAse treatment using Direct-zol RNA MiniPrep Kit (Zymo Research), and quantification by Nanodrop (Thermo Scientific).
1 ug of RNA from three biological replicates of hESCs, DE, AFE and PE conditions was quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).  RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were initially enriched with Oligod(T) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNA were subsequently synthesized. cDNA fragments were end-repaired and adenylated at 3’ ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by PCR with limited cycles. The sequencing library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

tag: cell line

tag: cell type

value: Human Embryonic Stem cells (hESCs)

tag: time

value: Day 0


title: BSSE_QGF_130147_HHJWMBGXC_1_E09_Plate_B_1908Seq6_TTAACCTTCG_AGGCCAGACA_S165_R1_001_MM_1.fastq.gz

city: Basel

first: Tobias

last: Kull

address: Mattenstrasse 26

country: Switzerland

institute: ETH Zurich

description:
ID in processed data file:
E9_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

data_processing:
Illumina RTA Version: 2.4.11 used for basecalling.
Sequenced reads were mapped to M21 musmusculus whole genome using star 2.5.3a with --quantMode GeneCounts.
The resulting sam files were converted into bam files with samtools. R
Raw counts were extracted from bam files using  subread version 1.5.0 featureCount with parameters:-t gene -g gene_id
Assembly: M21 (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M21)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: The file "seq_metadata_column-sample-matching.xlsx" provides the column header ID for each sample in this data set. This information is also available in the 'Description' field above.

molecule: polyA RNA

organism: Mus musculus

source_name: GMP (ganulocyte monocyte progenitor)

extract_protocol:
Single GMP cells were isolated with a micromanipulator and immediately placed into lysis buffer at 4 degree Celsius. Then Smart-Seq2 in adaption from https://www.nature.com/articles/s41467-018-05347-6
Nextera DNA Flex Library Prep

tag: strain

tag: tissue

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)

tag: age

value: 12 - 19 weeks

tag: genotype

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: P104

type: genomic

country: Poland

description: peripheral blood from COVID-19 patient

molecule: genomic DNA

tag: Sex

value: M


title: P108

description: peripheral blood from COVID-19 patient

value: F


title: P85

description: peripheral blood from COVID-19 patient


title: P87

description: peripheral blood from COVID-19 patient


title: BulkRNA hESCs, replicate B


title: P101

description: peripheral blood from COVID-19 patient


title: P100

description: peripheral blood from COVID-19 patient


title: P58

description: peripheral blood from COVID-19 patient


title: P45

description: peripheral blood from COVID-19 patient


title: BSSE_QGF_130146_HHJWMBGXC_1_D09_Plate_B_1908Seq6_CGTGTACCAG_AGGATAAGTT_S164_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
D9_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130145_HHJWMBGXC_1_C09_Plate_B_1908Seq6_ACTTGTTATC_CGCGCCTAGA_S163_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
C9_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BulkRNA hESCs, replicate A


title: P106

description: peripheral blood from COVID-19 patient


title: P86

description: peripheral blood from COVID-19 patient


title: P71

description: peripheral blood from COVID-19 patient


title: P73

description: peripheral blood from COVID-19 patient


title: P105

description: peripheral blood from COVID-19 patient


title: P88

description: peripheral blood from COVID-19 patient


title: P65

description: peripheral blood from COVID-19 patient


title: P78

description: peripheral blood from COVID-19 patient


title: exp 3

city: chang sha

first: yuan

last: fang

address: 138 TongZiPo road

country: China

institute: The Third Xiangya Hospital of Central South Uniiversity

data_processing:
Library Preparation included: 1) 3’ -adapter ligation; 2) 5’-adapter ligation; 3) cDNA synthesis; 4) PCR amplification; 5) size selection of ~134-160bp PCR amplified fragments (corresponding to ~14-40nt small RNAs).
Completed libraries were quantified using an Agilent 2100 Bioanalyzer.
DNA fragments in well mixed libraries were denatured using 0.1M NaOH to generate single-stranded DNA molecules and loaded using the NextSeq 500/550 V2 kit (#FC-404-2005, Illumina) according to instructions provided by the manufacturer.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Rattus norvegicus

source_name: muscle

extract_protocol:
muscle were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. The NEBNext® Multiplex Small RNA Library Prep Set for Illumina® was used for library preparation. The NextSeq 500/550 V2 kit (#FC-404-2005, Illumina) was used for sequencing on the Illumina NextSeq 500.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lewis

tag: tissure

value: muscle

value: 6-8 weeks

tag: skin phenotype

value: UV damage


title: exp 1


title: exp 2


title: ChIP PE Input for H3K4Me1, replicate B

library_source: genomic

data_processing:
Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq v2.17 software.
Sequencing adapters and low-quality bases were trimmed using the Trimmomatic v0.39 software with parameters ILLUMINACLIP:/path/to/adapter:2:30:10:1:true SLIDINGWINDOW:20:15 MINLEN:36.
Preprocessed reads were then aligned to hg38 genome using Bowtie2 v2.3.4.1 with parameters --wrapper basic-0 --fr -X 2000.
Aligned reads were filtered using SAMtools v1.11 to keep only concordant primary alignments having a minimum mapping quality of 30. PCR or optical duplicates were marked using Picard v2.25.1 tool and removed. Reads mapping to mitochondrial DNA and to unplaced contigs were filtered out. Reads falling in ENCODE Blacklist regions were removed using BEDTools v2.30.0 pairToBed tool.
deepTools v3.5.1 bamCoverage tool was employed to convert BAM files to bigWig files with RPGC normalization and the genomic bin size set to 10 bp.
Chromatin state discovery was performed using the ChromHMM v1.22 software. As a first step, all the BAM files were binarized with the BinarizedBam module, using a bin size of 200 bp. Concatenated model learning was conducted with the LearnModel module, using the input samples as control data to adjust the binarization threshold locally. This module was employed to build models with a number of states ranging from 6 to 16. We decided to focus on a model with 10 states for the subsequent analyses, since it delivered a compact and meaningful representation of the main chromatin states that can be produced with the 4 histone marks under analysis. The LearnModel module produced 200 bp chromatin state calls for DE and PE cell types, that were renamed based on the function that is commonly associated to known HM combinations and on their overlap with annotated functional regions. The two quiescent states were collapsed into a single Quies state.
Assembly: hg38
Supplementary files format and content: Sample-specific read coverage tracks (bigWig format).
Supplementary files format and content: Expanded ChromHMM state calls for DE and PE (BED format).

source_name: Pharyngeal Endoderm (PE)

extract_protocol:
ChIP experiments were performed on chromatin extracts according to the manufacturer's protocol (MAGnify ChIP, Life Technologies Cat. n. 492024). For each immunoprecipitation reaction, 10ug of sheared chromatin from DE and PE  differentiated cells was used (two biological replicates per ChIP experiment). Sheared chromatin was incubated O.N. with 5μg of anti- H3K27me3 (Abcam Cat. n. ab6002), H3K4me3 (Active Motif Cat. n. 39159), H3K27ac (Active Motif Cat. n. 39133), or H3K4me1 (Abcam ab8895) antibodies.
Immunoprecipitated (IP) and input DNA samples were quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and the DNA integrity was checked with 4200 TapeStation (Agilent Technologies, Palo Alto, CA, USA). NEBNext Ultra DNA Library Preparation kit was used following the manufacturer’s recommendations (Illumina, San Diego, CA, USA). Briefly, the ChIP DNA was end-repaired and adapters were ligated after adenylation of the 3’ ends. Adapter-ligated DNA was size selected, followed by clean up, and limited cycle PCR enrichment. The ChIP library was validated using Agilent TapeStation and quantified using Qubit 2.0 Fluorometer as well as real time PCR (Applied Biosystems, Carlsbad, CA, USA).

value: Pharyngeal Endoderm (PE)

tag: chip antibody

value: Day 5 + RA

tag: sequencing run


title: P98

description: peripheral blood from COVID-19 patient


title: BSSE_QGF_130144_HHJWMBGXC_1_B09_Plate_B_1908Seq6_TTAACGGTGT_TCCTGACCGT_S162_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
B9_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: ChIP PE Input, replicate B


title: BSSE_QGF_130142_HHJWMBGXC_1_H08_Plate_B_1908Seq6_GTGACGGAGC_TGGCGGTCCA_S160_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
H8_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: ChIP PE Input for H3K4Me1, replicate A


title: P64

description: peripheral blood from COVID-19 patient


title: P54

description: peripheral blood from COVID-19 patient


title: P103

description: peripheral blood from COVID-19 patient


title: P47

description: peripheral blood from COVID-19 patient


title: BSSE_QGF_130143_HHJWMBGXC_1_A09_Plate_B_1908Seq6_AATTCCATCT_CTTCAGTTAC_S161_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
A9_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: P59

description: peripheral blood from COVID-19 patient


title: P66

description: peripheral blood from COVID-19 patient


title: Ad MSC CM-2 [IonXpress_RNA_022]

city: Indianapolis

first: Meijing

last: Wang

state: Indiana

address: 950 W Walnut St. R2 E319

department: Surgery

country: USA

institute: Indiana University School of Medicine

data_processing:
Sequence reads were aligned to the mouse reference genome mm10 with STAR-2.4.2a.
featureCounts (subread-1.5.0) was used to quantify gene expression (parameters applied: "“-s 1 –Q 10")
Gene expression profiling, conducted by means of RNA-Sequencing analysis, identified a limited number of genes that were significantly modulated (differentially expressed genes, False Discovery Rate < 0.1, |fold changes| ≥ 1.5) following 6h cold storage.
Using the Ingenuity Pathway Analysis of differentially expressed genes,  top canonical pathways and top inhibited and activated upstream regulators were identified.
Assembly: mm10
Supplementary files format and content: Excel tables including read counts for the genes used in generating the figures

source_name: heart tissue

growth_protocol: Mouse heart tissue samples

extract_protocol:
QIAGEN miRNeasy kit was used to prepare RNA samples
cDNA library preparation included polyA mRNA capture, enzymatic fragmentation, hybridization and ligation of adaptors, reverse transcription, size-selection, and amplification with barcode primers, following the Ion Total RNA-Seq Kit v2 User Guide

treatment_protocol: Isolated mouse hearts without ex vivo cold storage or stored in cold presrevation soultion +/- BM-MSC CM or Ad-MSC CM for 6 hours

value: heart tissue


title: ctrl 2

value: normal


title: ctrl 3


title: Ad MSC CM-3 [IonXpress_RNA_024]


title: Ad MSC CM-4 [IonXpress_RNA_026]


title: BSSE_QGF_130141_HHJWMBGXC_1_G08_Plate_B_1908Seq6_TCCGGACTAG_GACGAACAAT_S159_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
G8_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BM MSC CM-1 [IonXpress_RNA_018]


title: P102

description: peripheral blood from COVID-19 patient


title: P63

description: peripheral blood from COVID-19 patient


title: Ad MSC CM-1 [IonXpress_RNA_019]


title: BM MSC CM-3 [IonXpress_RNA_025]


title: ChIP PE Input, replicate A


title: ChIP PE H3K4me1, replicate B

value: H3K4me1 (Abcam ab8895


title: BSSE_QGF_130140_HHJWMBGXC_1_F08_Plate_B_1908Seq6_CGATGCGGTT_CCTGCTTGGT_S158_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
F8_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: ChIP PE H3K4me3, replicate B

value: H3K4me3 (Active Motif Cat. n. 39159)


title: baseline C-3' [IonXpress_RNA_029]


title: 6h-I -1' [IonXpress_RNA_017]


title: BSSE_QGF_130139_HHJWMBGXC_1_E08_Plate_B_1908Seq6_CTAGATTGCG_AGATATGGCG_S157_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
E8_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: P38

description: peripheral blood from COVID-19 patient


title: 6h-I -4' [IonXpress_RNA_030]


title: BSSE_QGF_130138_HHJWMBGXC_1_D08_Plate_B_1908Seq6_GCAATATTCA_GGCGCCAATT_S156_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
D8_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: 6h-I -3' [IonXpress_RNA_023]


title: ChIP PE H3K4me3, replicate A


title: BM MSC CM-2 [IonXpress_RNA_021]


title: ChIP PE H3K4me1, replicate A


title: ChIP PE H3K27me3, replicate A

value: H3K27me3 (Abcam Cat. n. ab6002)


title: 6h-I -2' [IonXpress_RNA_020]


title: BSSE_QGF_130137_HHJWMBGXC_1_C08_Plate_B_1908Seq6_ATAGCGGAAT_GCGCAGAGTA_S155_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
C8_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

value: bone marrow


title: BSSE_QGF_130136_HHJWMBGXC_1_B08_Plate_B_1908Seq6_GTTCGGAGTT_CGCCTTCTGA_S154_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
B8_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

value: GMP (ganulocyte monocyte progenitor)


title: BSSE_QGF_130135_HHJWMBGXC_1_A08_Plate_B_1908Seq6_CCACGCTGAA_TATTCCTCAG_S153_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
A8_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

value: 12 - 19 weeks


title: ctrl 1


title: 6h-I -3 [IonXpress_RNA_015]


title: ChIP PE H3K27me3, replicate B


title: baseline C-2' [IonXpress_RNA_028]


title: P34

description: peripheral blood from COVID-19 patient


title: BSSE_QGF_130134_HHJWMBGXC_1_H07_Plate_B_1908Seq6_CACAGCGGTC_ATTCCTATTG_S152_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
H7_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: P32

description: peripheral blood from COVID-19 patient


title: baseline C-1' [IonXpress_RNA_027]


title: ChIP PE H3K27ac, replicate B

value: H3K27ac (Active Motif Cat. n. 39133)


title: 6h ischemia + vehicle (6h-I) -1 [IonXpress_RNA_001]


title: ChIP PE H3K27ac, replicate A


title: baseline C-3 [IonXpress_RNA_012]


title: BSSE_QGF_130133_HHJWMBGXC_1_G07_Plate_B_1908Seq6_TTGTATCAGG_ACAGAGGCCA_S151_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
G7_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: 6h-I -2 [IonXpress_RNA_002]


title: BSSE_QGF_130132_HHJWMBGXC_1_F07_Plate_B_1908Seq6_TAGAGAATAC_TATAGATTCG_S150_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
F7_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: baseline C-2 [IonXpress_RNA_006]


title: P11

description: peripheral blood from COVID-19 patient

value: M


title: control, no ischemia (baseline C)-1 [IonXpress_RNA_004]


title: ChIP DE Input, replicate A

source_name: Definitive Endoderm (DE)

value: Definitive Endoderm (DE)

value: Day 2


title: baseline C-4 [IonXpress_RNA_013]


title: BSSE_QGF_130130_HHJWMBGXC_1_D07_Plate_B_1908Seq6_CCGCGTATAG_TAGGAACCGG_S148_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
D7_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130131_HHJWMBGXC_1_E07_Plate_B_1908Seq6_GATTCTGAAT_AGCGGTGGAC_S149_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
E7_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: P10

description: peripheral blood from COVID-19 patient

value: F


title: BSSE_QGF_130129_HHJWMBGXC_1_C07_Plate_B_1908Seq6_ACGTTCCTTA_GACCGCTGTG_S147_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
C7_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: P57

description: peripheral blood from COVID-19 patient


title: ChIP DE H3K4me3, replicate A


title: ChIP DE H3K4me1, replicate B


title: BSSE_QGF_130128_HHJWMBGXC_1_B07_Plate_B_1908Seq6_CGCAGCAATT_ATTCCGCTAT_S146_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
B7_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: ChIP DE H3K4me1, replicate A


title: BSSE_QGF_130127_HHJWMBGXC_1_A07_Plate_B_1908Seq6_TATGATGGCC_GATTGTCATA_S145_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
A7_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: Adherent_negative siRNA_rep 2

type: RNA

city: Edinburgh

first: Emma

middle: A

last: Hurst

address: Easter Bush Campus

country: United Kingdom

institute: University of Edinburgh

hyb_protocol: Samples were hybridised according to the standard protocol for Affymetrix Gene Titan hybridisation, using the Affymetrix Gene Titan Hybridization Wash & Stain Kit for WT Array Plates (PN 901622).

scan_protocol: Arrays were scanned with the GeneTitan scanner

data_processing: Data were processed using the Affymetrix Expression Console software version 1.1

label: biotin

organism: Canis lupus

source_name: K9TCC adhrent cells transfected with negative siRNA

label_protocol: The RNA from each experimental sample was reverse transcribed to complementary DNA (cDNA), fragmented and labelled with Biotin and amplified using the Ambion® WT Expression labelling kit using the standard protocol.

growth_protocol: The K9TCC adherent cells were grown in DMEM-F-12 cell culture medium containing HEPES and L-glutamine, supplemented with 10% fetal bovine serum and 100ug/mL penicillin and streptomycin. K9TCC cancer stem cell spheres were grown in ultralow attachment plates in serum-free condition N2 media (William’s E Medium with GlutaMAX supplemented with putrescine (100 μM), sodium selenite (30 nM), transferrin (25 μg/mL), insulin (20 μg/mL), human recombinant basic fibroblast growth factor (bFGF, 10 ng/mL) and epidermal growth factor (EGF, 10 ng/mL)) per well. Additional growth factors (EGF and bFGF, both at 100 μg/mL) were added to the media every other day. All cell cultures were maintained at 37°C in a humidified 5 % CO2 incubator.

extract_protocol: RNA was extracted using the RNeasy Mini Kit (Qiagen) and a Nanodrop (Nanodrop 1000, Thermo Scientific) was used to measure the yield of RNA from each extraction.

treatment_protocol: Mavacoxib (Trocoxil™, Zoetis) was dissolved in dimethyl sulfoxide (DMSO) and diluted in relevant cell culture media immediately before use. Relevant volumes were added to cell culture media to provide 0uM (DMSO-only) or 50uM mavacoxib treatment. For siRNA treatment, the forward transfection method was used. Both adherent cells and spheres were seeded in achorage dependent conditions the day prior to treatment. Trasnfection with either COX-2 siRNA or negative control siRNA was completed using Lipofectamine RNAiMAX reagent. Cells were incubated for 48 hours after transfection.

value: Bladder transitional cell carcinoma cell line K9TCC

value: adherent cells

tag: treatment

value: transfected with negative siRNA for 48 hours


title: ChIP DE H3K27me3, replicate B


title: ChIP DE Input, replicate B


title: Spheres_negative siRNA_rep 2

source_name: K9TCC cancer stem cell spheres transfected with negative siRNA

value: cancer stem cell spheres


title: BSSE_QGF_130126_HHJWMBGXC_1_H06_Plate_B_1908Seq6_AATCCAATTG_CATGTAGAGG_S144_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
H6_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: ChIP DE H3K4me3, replicate B


title: ChIP DE H3K27me3, replicate A

growth_protocol: H9 hESCs were routinely propagated feeder-free in mTeSR1 on cell culture plates previously coated with Matrigel following the manufacturer instructions. Undifferentiated hESCs were propagated and passed at least 3 times after thawing and plated for the differentiation when at 80% of confluence. Cells were maintained in culture and expanded at high quality with particular care to avoid any spontaneous differentiation, which would confound downstream differentiation. The day before the induction of the differentiation, hESCs were washed twice in PBS, dissociated with Accutase, plated in mTeSR1 + Rock Inhibitor (Y27632, 5uM) to promote cell survival and incubated for 12 hours at 37 °C, 5% CO2 for 12 hours. The day after, 30% confluent hESCs were induced to differentiate into definitive endoderm, by incubation with Medium A (Gibco cat. n. A30621-01) for 24 hours and with Medium B (Gibco cat. n. 30624-01) for the following 24 hours at 37 °C, 5% CO2. The third day DE was patterned into AFG by the addition of CDM2 medium with A-83-01, 1uM and DM3189, 250nM. The composition of CDM2 basal medium was as follows: 50% IMDM (+GlutaMAX, +HEPES, +Sodium Bicarbonate; Gibco, 31980-097) + 50% F12 (+GlutaMAX; Gibco, 31765-092) + 1 mg/mL polyvinyl alcohol (Sigma, P8136-250G) + 1% v/v concentrated lipids (Gibco, 11905-031) + 450 µM monothioglycerol (Sigma, M6145) + 0.7 µg/mL insulin (Roche, 1376497) + 15 µg/mL transferrin (Roche, 652202) and incubated at 37 °C, 5% CO2. From day four to day 5, Retinoic Acid 200 nM was added at the CDM2 medium with A-83-01, 1 uM and DM3189, 250 nM and medium was changed every 24 hours.


title: Spheres_negative siRNA_rep 1


title: BSSE_QGF_130124_HHJWMBGXC_1_F06_Plate_B_1908Seq6_ACAACTACTG_AGTTATCACA_S142_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
F6_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: Adherent_COX-2 siRNA_rep 3

source_name: K9TCC adhrent cells transfected with COX-2 siRNA

value: transfected with COX-2 siRNA for 48 hours


title: Spheres_negative siRNA_rep 3


title: Adherent_negative siRNA_rep 3


title: BSSE_QGF_130123_HHJWMBGXC_1_E06_Plate_B_1908Seq6_CTTATTGGCC_GATAACAAGT_S141_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
E6_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: Spheres_COX-2 siRNA_rep 1

source_name: K9TCC cancer stem cell spheres transfected with COX-2 siRNA


title: Spheres_COX-2 siRNA_rep 3


title: Adherent_COX-2 siRNA_rep 1


title: Spheres_COX-2 siRNA_rep 2


title: Adherent_negative siRNA_rep 1


title: BSSE_QGF_130125_HHJWMBGXC_1_G06_Plate_B_1908Seq6_GTTGGATGAA_TTCCAGGTAA_S143_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
G6_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: ChIP DE H3K27ac, replicate B


title: BSSE_QGF_130122_HHJWMBGXC_1_D06_Plate_B_1908Seq6_TACGTGAAGG_CGGTTATTAG_S140_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
D6_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130121_HHJWMBGXC_1_C06_Plate_B_1908Seq6_GAATACCTAT_ACAATAGAGT_S139_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
C6_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: HEK-TIA1 4 h of relief

city: Hamburg

first: Zoya

last: Ignatova

address: Martin -Luther-King-Platz 6

country: Germany

institute: Universitaet Hamburg

description: total RNA in translating fraction

data_processing:
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 16
Genome read mapping using STAR (2.5.4b), parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 1
Read counting using HTSeq, version 0.9.1
Assembly: Homo sapiens Ensemble build GRCh38.p13
Supplementary files format and content: tab-delimited text files include RPKM for each sample

source_name: Human Embryonic Kidney 293 cells expressing N-terminally FLAG tagged TIA1

growth_protocol: HEK-TIA1 cells were cultured in DMEM (Panbiotech) medium supplemented with 10% fetal bovine serum and 2 mM glutamine at 37°C under a humidified environment with 5% CO2.

extract_protocol:
Cells were lysed in lysis buffer and fractionated on a 15-60% sucrose gradient. Total RNA in the translating fraction was collected and extracted. Spiked-in with standards and rRNA depleted with NEBNext® rRNA Depletion Kit
Isolation of mRNA-bound ribosome complexes,  RNA-size selection and generation of the cDNA libraries was performed as described (Guo et al, 2010; doi: 10.1038/nature09267 )

treatment_protocol: Cells were treated with 500µM Sodium Arsenite for 30 min and then fresh medium exchange to allow cell recovery; the fresh medium was supplemented with actinomycin D (0.5 µg/ml)

value: 500 microM AS treated then relieved; at the time of relief treated with actinomycin D


title: Adherent_COX-2 siRNA_rep 2


title: HEK-TIA1 30 min of relief

description: total RNA in translating fraction

value: expressing N-terminally FLAG tagged TIA1


title: BSSE_QGF_130120_HHJWMBGXC_1_B06_Plate_B_1908Seq6_GGCCAATATT_CGGTCCGATA_S138_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
B6_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: Spheres_0uM mavacoxib_rep 1

source_name: K9TCC cancer stem cell spheres treated with 0uM mavacoxib

value: 0uM mavacoxib for 24 hours


title: ChIP DE H3K27ac, replicate A


title: Spheres_50uM mavacoxib_rep 3

source_name: K9TCC cancer stem cell spheres treated with 50uM mavacoxib

value: 50uM mavacoxib for 24 hours


title: Spheres_50uM mavacoxib_rep 2


title: Spheres_0uM mavacoxib_rep 3


title: BSSE_QGF_130119_HHJWMBGXC_1_A06_Plate_B_1908Seq6_CCGGTTCCTA_TATATTCGAG_S137_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
A6_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)


title: Adherent_50uM mavacxib_rep 2

source_name: K9TCC adhrent cells treated with 50uM mavacoxib


title: Spheres_50uM mavacoxib_rep 1


title: Adherent_0uM mavacoxib_rep 2

source_name: K9TCC adhrent cells treated with 0uM mavacoxib


title: ECl_2.VN

city: Pretoria

first: John

last: Osei Sekyere

state: Gauteng

address: 05 Bopheloweg Off Dr. Savage Road

department: Department of Medical Microbiology

country: South Africa

institute: University of Pretoria

description:
MLST unknown
Samples were collected from Pregnant women who were at labour or just to have labour at the Steve Biko Academic Hospital. Rectal swabs were taken from the patients and brought to the laboratory for culturing and subsequent microbiological analysis

data_processing: All analysis was conducted within SMRTLINK v10.1

organism: Enterobacter roggenkampii

source_name: rectal swab of pregnant women

growth_protocol: isolates on the swabs were grown in an enrichment broth overnight prior to plating on a blood plate

extract_protocol:
Zymo DNA extraction kits were used to extract DNA for PCR confirmation of the resistance genes
HMW gDNA was isolated using NEB Mornach HMW DNA isolation kit (https://international.neb.com/protocols/2020/10/27/protocol-for-high-molecular-weight-dna-hmw-dna-extraction-from-bacteria). HMW gDNA was quantified using Qubit HS dsDNA Assay and qualified on Tapestation using genomics screentape. HMW gDNA was shared to ~10kb fragments using covaries g-Tubes and QC’d using the above method. SMRTbell libraries were performed using PacBio’s Microbial Multiplexing workflow (see attached)     The resulting libraries were size selected using BluePippin Size selection using U1 marker (10-18kb). QC was performed using the above method. Libraries were then prepared for sequencing following the online SMRTlink guided protocol (Binding kit 2.0 and Control 1.0, Sequel II Sequencing plate 2.0 and SMRT cell 8M.)
OTHER: size selection was done by Blue-Pippin and sequenced with PacBio for DNA WGS

treatment_protocol: The plates were impregnated with colistin and/ or carbapenems to inhibit all but carbapenem and/or colistin-resistant isolates

tag: source

value: Carbapenem and/or colistin resistant Enterobacterales isolated from pregnant women

tag: sample type

value: rectal swab isolate


title: ECl_3.VN


title: Spheres_0uM mavacoxib_rep 2


title: BSSE_QGF_130118_HHJWMBGXC_1_H05_Plate_B_1908Seq6_CCAGGCACCA_ACGCTAATTA_S136_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
H5_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

value: 12 - 19 weeks

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: Adherent_0uM mavacoxib_rep 3


title: Adherent_50uM mavacxib_rep 1


title: sgERN1 OC43 replicate 3

city: Chicago

first: Dongbo

last: Yang

state: IL

address: 929 E 57th St

institute: University of Chicago

data_processing:
The libraries were sequenced in two runs by a NovaSeq 6000 sequencer to generate paired-end 100bp reads.
For each sample, the reads from two flow cells were combined before downstream processing. Quality and adapter trimming were performed on the raw sequencing reads using Trim Galore! 0.6.3 (https://github.com/FelixKrueger/TrimGalore).
The reads were mapped to the human genome (UCSC hg19 with GENCODE annotation) using RNA STAR 2.7.1a.
The resulting mapped reads from each sample were counted by featureCounts  1.6.4 for per gene read counts.
The raw counts were analyzed for differential expression between experimental conditions using DESeq2  1.22.1 .
Assembly: Human (hg19)
Supplementary files format and content: Tab delimited text file containing a matrix table with raw gene counts for every gene and every sample

source_name: A549-ACE2 IRE1 KO

growth_protocol: ACE2-A549 control or IRE1 KO cells were cultured in 10% FBS RPMI to 70% confluence.

extract_protocol:
Cells were washed once with PBS and lysed using RLT Plus lysis buffer before genomic DNA removal and total RNA extraction by the Qiagen RNeasy Plus Mini Kit (Qiagen 74134).
RNA libraries were prepared for sequencing by the University of Chicago Genomics Facility following standard protocols.

treatment_protocol: Cells were washed once with PBS before being mock infected or infected with each virus at MOI = 1 for one hour in serum-free RPMI at 33C. Cells were then washed three times with PBS before 2% FBS RPMI was added. The cells were incubated for another 48 hours before sample collection.

tag: infection

value: OC43 MOI 1


title: Adherent_50uM mavacxib_rep 3


title: sgERN1 OC43 replicate 1


title: BSSE_QGF_130117_HHJWMBGXC_1_G05_Plate_B_1908Seq6_TGGCCTCTGT_TGAGACAGCG_S135_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
G5_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130116_HHJWMBGXC_1_F05_Plate_B_1908Seq6_TGGTGTTATG_TCCAATTCTA_S134_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
F5_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130115_HHJWMBGXC_1_E05_Plate_B_1908Seq6_AACGAGGCCG_ATACCTGGAT_S133_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
E5_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: sgERN1 SARS-CoV-2 replicate 3

value: SARS-CoV-2 MOI 1


title: sgERN1 mock replicate 2

value: Mock


title: Adherent_0uM mavacoxib_rep 1

value: Bladder transitional cell carcinoma cell line K9TCC

value: adherent cells


title: sgERN1 mock replicate 3


title: sgERN1 SARS-CoV-2 replicate 2


title: sgERN1 mock replicate 1


title: sgERN1 SARS-CoV-2 replicate 1


title: BSSE_QGF_130114_HHJWMBGXC_1_D05_Plate_B_1908Seq6_ATGTAACGTT_ACGATTGCTG_S132_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
D5_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: sgCTRL OC43 replicate 3

source_name: A549-ACE2 control


title: sgCTRL OC43 replicate 2


title: sgCTRL OC43 replicate 1


title: BSSE_QGF_130112_HHJWMBGXC_1_B05_Plate_B_1908Seq6_ATAGCCAAGA_AGTGCCACTG_S130_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
B5_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

source_name: GMP (ganulocyte monocyte progenitor)


title: sgERN1 OC43 replicate 2


title: sgCTRL SARS-CoV-2 replicate 2


title: BSSE_QGF_130111_HHJWMBGXC_1_A05_Plate_B_1908Seq6_TCTAGGCGCG_CGAAGGTTAA_S129_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
A5_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: sgCTRL mock replicate 3


title: sgCTRL SARS-CoV-2 replicate 3


title: BSSE_QGF_130109_HHJWMBGXC_1_G04_Plate_B_1908Seq6_GCTGACGTTG_TGTTCGCATT_S127_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
G4_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130110_HHJWMBGXC_1_H04_Plate_B_1908Seq6_CTAATAACCG_AACCGCATCG_S128_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
H4_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: sgCTRL mock replicate 1


title: sgCTRL SARS-CoV-2 replicate 1


title: HEK293 KO, MUL1(-/-), sample 3

city: Orlando

first: Antonis

last: Zervos

state: FL

address: 12722 Research Pkwy

department: Burnett School of Biomedical Sciences

institute: University of Central Florida

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
BAM files were generated as a result of this step.
Assembly: Homo sapiens GRCh38 reference genome (ENSEMBL)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: HEK293 wild type (WT) and HEK293 MUL1(-/-) cells were grown using DMEM supplemented with 10% fetal calf serum, 2 mM L-glutamine, 50 units/ml penicillin, and 50 μg/ml streptomycin

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 2ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Human embryonic kidney

value: MUL1 KO


title: HEK293 KO, MUL1(-/-), sample 2


title: BSSE_QGF_130108_HHJWMBGXC_1_F04_Plate_B_1908Seq6_AGGAGGTATC_CCAGTTGGCA_S126_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
F4_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: HEK293 WT, control, sample 3

value: WT


title: BSSE_QGF_130113_HHJWMBGXC_1_C05_Plate_B_1908Seq6_TTCGGTGTGA_GAACAAGTAT_S131_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
C5_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130106_HHJWMBGXC_1_D04_Plate_B_1908Seq6_CTGCGTTACC_TATGGCTCGA_S124_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
D4_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: HEK293 WT, control, sample 2


title: BSSE_QGF_130107_HHJWMBGXC_1_E04_Plate_B_1908Seq6_AGGCCGTGGA_CTCGTGCGTT_S125_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
E4_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: HEK293 KO, MUL1(-/-), sample 1


title: HEK293 WT, control, sample 1


title: UM-UC-3, siControl, 2

city: Los Angeles

first: Hideki

last: Furuya

state: CA

address: 110 N. George Burns Road, Davis 2025

institute: Cedars Sinai Medical Center

data_processing:
Raw reads obtained from RNA-Seq were aligned to the transcriptome using STAR (version 2.5.0) / RSEM (version 1.2.25) with default parameters, using a custom human GRCh38 transcriptome reference downloaded from http://www.gencodegenes.org, containing all protein coding and long non-coding RNA genes based on human GENCODE version 23 (or Mouse GENCODE M8) annotation. Expression counts for each gene (TPM: transcripts per million) in all samples were normalized by the sequencing depth.
Assembly: human GRCh38
Supplementary files format and content: TPM
Supplementary files format and content: FPKM

growth_protocol: RT112 and UM-UC-3 cell lines were maintained in RPMI 1640 or DMEM media.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
Library construction was performed using the QIASeq Stranded mRNA Select kit (Qiagen, Hilden, Germany).

treatment_protocol: RT112 and UM-UC-3 cells were transfected with a pool of 3 synthesized commercial PAI-1 (sc-36179, Santa Cruz Biotechnology) (RT112KD-PAI1 and UM-UC-3KD-PAI1) or pool of 3 scrambled negative control siRNA (Scr, sc-37007, Santa Cruz Biotechnology) (RT112Scr and UM-UC-3Scr) in 6 well plates with a 100-pmol of siRNA and 9 μl of INTERFERin (Polyplus-transfection Inc., NY, USA) for 72 h according to manufacturer’s instruction.

value: Human bladder cancer


title: BSSE_QGF_130105_HHJWMBGXC_1_C04_Plate_B_1908Seq6_CGTACAGGAA_TAGGTTCTCT_S123_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
C4_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: RT112, siControl, 2


title: UM-UC-3, siControl, 1


title: UM-UC-3, siPAI-1, 2

value: PAI-1 knockdown


title: RT112, siControl, 1


title: BSSE_QGF_130104_HHJWMBGXC_1_B04_Plate_B_1908Seq6_GATATTGTGT_ACCACACGGT_S122_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
B4_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: RT112, siPAI-1, 2


title: RT112, siPAI-1, 1


title: BSSE_QGF_130103_HHJWMBGXC_1_A04_Plate_B_1908Seq6_AGAGAACCTA_GGTTATGCTA_S121_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
A4_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: KO_2Years

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

data_processing:
All raw FASTQs reads were aligned to Homo_sapiens : GRCh38 reference using the STAR algorithm and quantified through the 10X Genomics cellranger single cell pipeline, with default and recommended parameter. The outputs from the individual samples were combined using the CellRanger aggr function to normalize the sequencing depth and produce aggregated gene-cell UMI count matrix.
Genome_build: Homo_sapiens : GRCh38
Supplementary_files_format_and_content: Filtered feature - barcode HDF5 file output from CellRanger pipeline

source_name: testes

extract_protocol:
Human samples (homo sapiens) were obtained from the Fertility Preservation Program in Pittsburgh and processed at the University of Pittsburgh. Testes were collected from 1-, 2- and 7-year-old males through the University of Pittsburgh Health Sciences Tissue Bank and Center for Organ recovery under the University of Pittsburgh CORID 686. Human samples were enzymatically digested and processed as previously described (Shami et al. Dev Cell . 2020 Aug 24;54(4):529-547.e12). Human samples were processed with approval from the University of Pittsburgh Institutional Review Board (Protocol #STUDY09020220). Isolated primary human testicular cells were processed using Chromium TM Single Cell 3′ v3 Chemistry library prep kit according to the manufacturer’s instructions (10X Genomics, San Francisco, CA, USA).
Isolated primary human testicular cells were processed using Chromium TM Single Cell 3′ v3 Chemistry library prep kit according to the manufacturer’s instructions (10X Genomics, San Francisco, CA, USA). Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. A shallow sequencing was performed first using Illumina MiSeq SR50 to estimate the number of recovered cells in each sample (a total of 5089, 8447 and 7851 cells were collected from 1-, 2- and 7-year-old males, respectively). The sequencing of the libraries was performed a second time with a targeted sequencing depth of ~ 50,000 reads/cell using an Illumina NovaSeq 6000 sequencer (100pb single end reads) (CHGI, University of Calgary, Alberta, Canada). The raw reads were subsequently processed with a 10x Genomics CellRanger pipeline (version 3.1.0) using default settings. The outputs from the three human samples were combined using the CellRanger aggr function to normalize for the sequencing depth and produce aggregated gene-cell UMI count matrix for the downstream analysis.

value: 2 years


title: KO_1Year

value: 1 year


title: BSSE_QGF_130102_HHJWMBGXC_1_H03_Plate_B_1908Seq6_AGGACAGGCC_CATTCCAGCT_S120_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
H3_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)


title: BSSE_QGF_130100_HHJWMBGXC_1_F03_Plate_B_1908Seq6_ATACTTGTTC_TAACCGCCGA_S118_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
F3_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: KO_7Years

value: 7 years


title: BSSE_QGF_130101_HHJWMBGXC_1_G03_Plate_B_1908Seq6_TCCGCCAATT_CTCCGTGCTG_S119_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
G3_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

value: 12 - 19 weeks


title: BSSE_QGF_130099_HHJWMBGXC_1_E03_Plate_B_1908Seq6_CCGTGACCGA_CCGAACGTTG_S117_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
E3_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: BSSE_QGF_130098_HHJWMBGXC_1_D03_Plate_B_1908Seq6_ATCGGCGAAG_TCCAAGAATT_S116_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
D3_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130097_HHJWMBGXC_1_C03_Plate_B_1908Seq6_AGGCAGCTCT_CGGCTAACGT_S115_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
C3_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: UM-UC-3, siPAI-1, 1


title: BSSE_QGF_130096_HHJWMBGXC_1_B03_Plate_B_1908Seq6_TAGAATTGGA_GTTAATCTGA_S114_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
B3_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: MERS 36hpi replicate 3

data_processing:
The libraries were sequenced by a HiSeq 4000 to generate paired-end 150bp reads.
Raw sequencing reads from each sample were quality and adapter trimmed using BBDuk 38.73.
The reads were mapped to the human genome (hg38 with Ensembl V98 annotation) using RNA STAR 2.7.1a.
The resulting mapped reads from each sample were counted by featureCounts  1.6.4 for per gene read counts.
The raw counts were analyzed for differential expression between experimental conditions using DESeq2  1.22.1 .
Genome_build: Human (hg38)
Supplementary_files_format_and_content: Tab delimited text file containing a matrix table with raw gene counts for every gene and every sample

source_name: A549 cells with DPP4 overexpression

growth_protocol: Lung alveolar A549 cells expressing the MERS-CoV receptor DPP4 were cultured in 10% FBS RPMI media.

extract_protocol:
Cells were washed once with PBS and lysed using RLT Plus lysis buffer before genomic DNA removal and total RNA extraction by the Qiagen RNeasy Plus Mini Kit (Qiagen 74134).
RNA libraries were prepared for sequencing by GeneWiz following standard protocols.

treatment_protocol: At 70% cell confluence, cells were washed once with PBS before being mock infected or infected with MERS-CoV (EMC/2012) at MOI = 1. Virus was absorbed for 1 hour at 37 degrees Celsius in serum-free RPMI media. After one hour, virus was removed, cells washed three times with PBS, and 2% FBS RPMI was added. The cells were incubated for another 24 hours or 36 hours before sample collection.

value: MERS-CoV MOI 1

tag: time point


title: BSSE_QGF_130092_HHJWMBGXC_1_F02_Plate_B_1908Seq6_TAATTAGCGT_TGGTTAAGAA_S110_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
F2_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: MERS 24hpi replicate 3


title: MERS 24hpi replicate 2


title: BSSE_QGF_130094_HHJWMBGXC_1_H02_Plate_B_1908Seq6_TGATGGCTAC_CCAACAACAT_S112_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
H2_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130093_HHJWMBGXC_1_G02_Plate_B_1908Seq6_ATTAACAAGG_TGTTGTTCGT_S111_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
G2_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: MERS 36hpi replicate 2


title: MERS 36hpi replicate 1


title: BSSE_QGF_130090_HHJWMBGXC_1_D02_Plate_B_1908Seq6_AGTACTCATG_ATGTCGTGGT_S108_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
D2_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: Mock replicate 2


title: BSSE_QGF_130095_HHJWMBGXC_1_A03_Plate_B_1908Seq6_GAATTACAAG_ACCGGCTCAG_S113_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
A3_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: MERS 24hpi replicate 1


title: BSSE_QGF_130091_HHJWMBGXC_1_E02_Plate_B_1908Seq6_GGTAGAATTA_GTAGCCATCA_S109_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
E2_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130089_HHJWMBGXC_1_C02_Plate_B_1908Seq6_GAACGCAATA_ATCTTACTGT_S107_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
C2_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130088_HHJWMBGXC_1_B02_Plate_B_1908Seq6_TTCTGTAGAA_GAGCGCAATA_S106_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
B2_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: RNA_TranslatingFrac_4h_SR

description: total RNA in translating fraction

data_processing:
Quality trimming using FASTX-toolkit, version 0.0.13.2, parameters -v -t 20 -l 16
Genome read mapping using STAR (2.5.4b), parameters: --outFilterMultimapNmax 1 --outFilterMismatchNmax 1
Read counting using HTSeq, version 0.9.1
Genome_build: Homo sapiens Ensemble build GRCh38.p13
Supplementary_files_format_and_content: tab-delimited text files include unique read counts per gene per kilobase and million mapped reads RPKM for each sample

source_name: HEK-TIA1 4 h of relief

treatment_protocol: Cells were treated with 500µM Sodium Arsenite for 30 min and then fresh medium exchange to allow cell recovery

value: Human Embryonic Kidney 293 cells expressing N-terminally FLAG tagged TIA1

value: 500uM AS treated then relieved


title: Mock replicate 1

value: Mock


title: BSSE_QGF_130087_HHJWMBGXC_1_A02_Plate_B_1908Seq6_CAGCAATCGT_TGTGATGTAT_S105_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
A2_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: RNA_TranslatingFrac_30m_SR

description: total RNA in translating fraction

source_name: HEK-TIA1 30 min of relief

value: expressing N-terminally FLAG tagged TIA1


title: BSSE_QGF_130086_HHJWMBGXC_1_H01_Plate_B_1908Seq6_GGTCTATTAA_CCACGACACG_S104_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
H1_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130085_HHJWMBGXC_1_G01_Plate_B_1908Seq6_TCCGTTATGT_TTGTAGTGTA_S103_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
G1_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: Treated Replicate 1

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

institute: University of Saskatchewan

data_processing:
fastq files were trimmed to remove adapter sequences and poor quality nucleotides using Trimmomatic v.0.36
STAR aligner v.2.5.2b was used to align the sequences to Homo sapiens GRCh38 reference genome
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was normalized using the DESeq2 package in R
Wald Test was used to calculate the log fold change and P-Value
Genome_build: Homo sapiens GRCh38 reference genome
Supplementary_files_format_and_content: tab-delimited text file containing the raw read counts.

source_name: Prostate Cancer Cell Line

growth_protocol: Standard culture conditions

extract_protocol:
Standard RNA extraction protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 48 hour treatment

value: Prostate

tag: cell line

value: Treated


title: Treated Replicate 2


title: BSSE_QGF_130084_HHJWMBGXC_1_F01_Plate_B_1908Seq6_ATGGCGCCTG_TCCACGGCCT_S102_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
F1_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

tag: cell type


title: Control Replicate 2

value: Control


title: Mock replicate 3


title: BSSE_QGF_130083_HHJWMBGXC_1_E01_Plate_B_1908Seq6_ATATGCATGT_TGGTGCCTGG_S101_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
E1_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: WT, non-diabetic, 479-4

city: New York City

first: Florencia

last: Schlamp

state: New York

address: 435 East 30th Street

institute: NYU Langone Health

data_processing:
FASTQ files were obtained, and low-quality bases as well as adapter sequences were trimmed using Cutadapt 1.18.
Reads were subsequently mapped to the Mus musculus GRCm38 transcriptome using Kallisto 0.46.2.
Raw counts per transcript were summed up at the gene level, and differential expression analysis was performed using edgeR 3.28.0.
RNA sequencing and differential gene expression analysis was performed by the NYU Genome Technology Center.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes counts for each sample

source_name: CD68+ cells from atherosclerotic plaque

growth_protocol: Bone marrow from WT and Prmt2-/- mice was transplanted into 8-week old Ldlr-/- mice. After 4 weeks of recovery, the mice were placed on a Western diet (21% [wt/wt] fat, 0.3% cholesterol [Research Diets ]) for 20 weeks to allow the development of atherosclerotic plaques.

extract_protocol:
Regression groups were sacrificed after 3 weeks on a chow diet. Mice were perfused with 10% sucrose/saline. Aortic roots were dissected and embedded in optimal cutting temperature compound medium (OCT), frozen immediately and stored at –80°C until further use. CD68+ cells were selected from atherosclerotic plaques by laser capture microdissection (LCM). All LCM procedures were performed under RNase-free conditions. Aortic root sections were stained with hematoxylin-eosin. Foam cells were identified under a microscope and verified by positive CD68 staining. For each animal, CD68+ cells were captured from 50–60 frozen sections.
RNA was isolated using the PicoPure Kit (Molecular Devices, Inc., Sunnyvale, CA), and quality and quantity were determined using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA). RNA-seq libraries were prepared using the Clontech SMARTer Stranded Total RNA Seq Kit -Pico Input Mammalian following the manufacturer’s protocol. Libraries were purified using AMPure beads, pooled equimolarly, and run on a HiSeq 4000 paired end reads.

treatment_protocol: Mice were injected IP with citrate buffer for 5 days to serve as control for diabetes mellitus. Regression was induced by reversal of hyperlipidemia using an apoB-antisense oligonucleotide (ASO) (Ionis Pharmaceuticals, 50 mg/kg; twice a week for 3 weeks) on a chow diet (13% fat kcal, 0% cholesterol).

value: CD68+ cells from atherosclerotic plaque

value: WT

value: apoB-ASO + citrate (nondiabetic)


title: BSSE_QGF_130079_HHJWMBGXC_1_A01_Plate_B_1908Seq6_TGCCGGTCAG_CCTGATACAA_S97_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
A1_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: BSSE_QGF_130080_HHJWMBGXC_1_B01_Plate_B_1908Seq6_CACTCAATTC_TTAAGTTGTG_S98_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
B1_Plate2
see PickedGMPs_PassedQC_190729TK20.csv


title: WT, non-diabetic, 941-4


title: KPF CAF-HIF2 KO rep3

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

description:
KO3
3prime scRNA-Seq

data_processing:
Basecalls performed using bcl2fastq to convert raw sequencing reads.
fastqs were aligned to the mm10 genome assembly using CellRanger.
CellRanger-generated matrix files were processed in R according to Methods described in the Manuscript text.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_filtered_gene_bc_matrices.tar: tar archives include files generated from fastq files via 10x Genomics CellRanger Count pipeline; barcodes.tsv, genes.tsv, matrix.mtx.

source_name: Pancreatic tumor

extract_protocol:
Tumors were harvested and single-cell suspensions were made by a combination of mincing, enzymatic digestion (Liberase and Accutase), and straining. Chromium Single Cell 3' Library & Gel Bead kit v2 (10X Genomics, Cat#PN-120237) and the 10X Genomics Chromium instrument were used to generate gel beads in emulsion and single-cell cDNA libraries, with 5,000 cells loaded per channel.
Single-cell cDNA libraries were prepared and sequenced using standard 10X Genomics and Illumina protocols.

treatment_protocol: KPF (FSF-Kras, p53 frt/frt, Pdx1-FlpO) CAF-HIF2 WT mice were fed normal chow and KPF CAF-HIF2 KO mice were fed tamoxifen chow once tumors were diagnosed by ultrasound.

value: C57BL/6 and 129 mix

tag: genetic background

value: FSF-Kras, p53 frt/frt, Pdx1-FlpO

value: Hif2a knockout

value: female

value: pancreas tumor

value: aSMA-expressing CAFs

tag: survival

value: 139 days


title: Lactobacillus-1

city: Louisville

first: Huang-Ge

last: Zhang

state: KY

address: 505 S Hancock Street

department: James Graham Brown Cancer Center

institute: University of Louisville

description: Bacteriophage

data_processing:
Basecalls performed using Illumina Casava1.7 software
To identify viral genomes, raw sequencing fastq files were first converted to fasta files and reduntant sequences were removed. Then, using BLASTn, viral genomes were searched to the NCBI complete RefSeq of viral sequences. Using in-house scripts, only perfectly matched sequences with 100 Percent identity and high similarity of E-value < 10-10 from BLASTn search were selected for further analysis.
For taxonomic classification, sequences were assigned to different viral families according to ICTV-defined families and Virus-Host DB.

organism: human feces metagenome

source_name: Feces

extract_protocol:
One gram of fecal sample was weighed and homogenized in 40 mL of PBS with a benchtop homogenizer (MP Biomedical). The sample was then centrifuged at 17,000x g for 5 min and the supernatant was filtered sequentially through a 2 μm and 0.45 μm filter. Phages were then concentrated using a polyethylene glycol (PEG) method(Luong et al., 2020). Briefly, one molar solid NaCl and 10% (v/v) PEG 8000 (Sigma) were dissolved in PBS and incubated overnight at 4°C as recommended for a constant and stable precipitation. The phages mixed in the solution were pelleted by centrifugation at 5,250x g for 1 h at 4°C and re-suspended in 500 μl of SM buffer (NaCl 100 mM, MgSO4.7H2O 8 mM, Tris-Cl 50 mM).
Phage DNA was sequenced with the Illumina MiSeq Nano V2 PE_250 bases method using the Nextera XT Kit with an input of 1 ng DNA. All samples were sequenced using paired-end reads
Genomic shotgun sequencning

value: Lactobacillus targetting


title: KPF CAF-HIF2 KO rep2

description:
KO2
3prime scRNA-Seq

tag: strain

tag: tissue

value: 89 days


title: BSSE_QGF_130082_HHJWMBGXC_1_D01_Plate_B_1908Seq6_TCAATGGAGA_GCACTACAAC_S100_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
D1_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

data_processing:
Illumina RTA Version: 2.4.11 used for basecalling.
Sequenced reads were mapped to M21 musmusculus whole genome using star 2.5.3a with --quantMode GeneCounts.
The resulting sam files were converted into bam files with samtools. R
Raw counts were extracted from bam files using  subread version 1.5.0 featureCount with parameters:-t gene -g gene_id
Assembly: M21 (ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M21)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: The file "seq_metadata_column-sample-matching.xlsx" provides the column header ID for each sample in this data set. This information is also available in the 'Description' field above.

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)

tag: age

value: 12 - 19 weeks

tag: genotype

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: PKO, non-diabetic, 5247-2

value: Prmt2 KO


title: Control Replicate 1

value: Prostate

value: Control


title: ID_Neonates1

data_processing:
All raw FASTQs reads were aligned to mm10 (GRCm38.p5) reference using the STAR algorithm and quantified through the 10X Genomics cellranger single cell pipeline, with default and recommended parameter. The outputs from the individual samples were combined using the CellRanger aggr function to normalize the sequencing depth and produce aggregated gene-cell UMI count matrix. Sequencing data was analyzed using the cell ranger pipeline. A total of 19,166 cells were included in the analysis and normalized to a read depth of 104,230 reads per cell.
Genome_build: mm10 (GRCm38.p5)
Supplementary_files_format_and_content: Filtered feature - barcode HDF5 file output from CellRanger pipeline

source_name: Testicular cells

extract_protocol:
Testicular cells were collected from 6-8 day (n=3) and 4-month-old mouse testes (n=2)  by 2 step enzymatic digestion as previously described (Yeh et al., 2007). Spermatogonia from 6-8 old mice were then isolated by size exclusion and granularity using FACS light scatter properties. The primary contaminating cell type in the enriched spermatogonia population were somatic peritubular myoid and Sertoli cells. Spermatogonia from 4-month-old  were isolated by fluorescence assisted cell sorting (FACS) (FACSAria II, BD Biosciences), using antibodies against GFR⍺1 ([1:100] Neuromics, goat polyclonal) and cKIT ([1:100] AbCam, rat polyclonal). The primary contaminating cell type in the enriched spermatogonia population after FACS was further differentiating germ cells (spermatocytes and round spermatids).   Isolated primary murine spermatogonia samples were resuspended in PBS supplemented with 1% BSA and 6000–10,000 cells per sample were processed using ChromiumTM Single Cell 3′ v2 Chemistry library prep kit according to the manufacturer’s instructions (10X Genomics, San Francisco, CA, USA). Samples were sequenced on an Illumina HiSeq4000 with paired-end 50 base pair reads by Genome Quebec (Montreal, QC, Canada).
Isolated primary murine spermatogonia samples were resuspended in PBS supplemented with 1% BSA and 6000–10,000 cells per sample were processed using ChromiumTM Single Cell 3′ v2 Chemistry library prep kit according to the manufacturer’s instructions (10X Genomics, San Francisco, CA, USA). Samples were sequenced on an Illumina HiSeq4000 with paired-end 50 base pair reads by Genome Quebec (Montreal, QC, Canada). Briefly, single cells were partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction.

value: 6-8 days old


title: PKO, non-diabetic, 927-4

value: CD68+ cells from atherosclerotic plaque

value: apoB-ASO + citrate (nondiabetic)


title: KPF CAF-HIF2 KO rep1

description:
KO1
3prime scRNA-Seq

value: C57BL/6 and 129 mix

value: FSF-Kras, p53 frt/frt, Pdx1-FlpO

value: Hif2a knockout

tag: Sex

value: 114 days


title: PKO, non-diabetic, 925_4


title: TSD-27-2

description: Bacteriophage

value: TSD-27 targetting


title: ID_Neonates2


title: TSD-27-1

description: Bacteriophage


title: Older2

description: Bacteriophage

value: Health old people


title: KPF CAF-HIF2 WT rep2

description:
Ctrl2
3prime scRNA-Seq

value: Hif2a wild type

value: male

value: pancreas tumor

value: aSMA-expressing CAFs

value: 105 days


title: Older1

description: Bacteriophage


title: BSSE_QGF_130081_HHJWMBGXC_1_C01_Plate_B_1908Seq6_TCTCACACGC_CGGACAGTGA_S99_R1_001_MM_1.fastq.gz

description:
ID in processed data file:
C1_Plate2
see PickedGMPs_PassedQC_190729TK20.csv

extract_protocol:
Single GMP cells were isolated with a micromanipulator and immediately placed into lysis buffer at 4 degree Celsius. Then Smart-Seq2 in adaption from https://www.nature.com/articles/s41467-018-05347-6
Nextera DNA Flex Library Prep

value: bone marrow

value: GMP (ganulocyte monocyte progenitor)

value: 12 - 19 weeks

value: GFP-p65 homozygous /H2BmCherry heterozygous


title: KPF CAF-HIF2 WT rep1

description:
Ctrl1
3prime scRNA-Seq

value: female

value: 84 days


title: ID_Neonates3

value: 6-8 days old


title: Young2

description: Bacteriophage

value: Health young people


title: WT, non-diabetic, 941-1

value: CD68+ cells from atherosclerotic plaque

value: WT

value: apoB-ASO + citrate (nondiabetic)


title: Lactobacillus-2

description: Bacteriophage

value: Lactobacillus targetting


title: ID_Adult2

value: 4 months


title: ID_Adult1


title: ipsilateral microglia replicate6

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

description:
counts.matrix.norm_anno
sPC_6

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Trimmomatic version 0.38 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.6.1d with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.6.3 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.18.1 .
Genome_build: mm10
Supplementary_files_format_and_content: library size normalized counts

source_name: ipsilateral hemisphisphere

extract_protocol:
RNA was isolated using miRNeasy micro Kit (Qiagen).
Approx. 250pg of total RNA was used as input for SMART®-Seq HT Kit (Takara Clontech).

value: ipsilateral microglia


title: ipsilateral microglia replicate4

description:
counts.matrix.norm_anno
sPC_4


title: ipsilateral microglia replicate5

description:
counts.matrix.norm_anno
sPC_5


title: hind muscle unloaded treated with 4-phenyl butyrate 3

city: Sharjah

first: Amir

middle: Ali

last: Khan

address: Emirates of Sharjah

department: Department of Applied Biology

country: United Arab Emirates

institute: University of Sharjah

data_processing:
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR exhibits better alignment precision and sensitivity than other RNA-seq aligners for both experimental and simulate
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count.
Genome_build: mice
Supplementary_files_format_and_content: excel sheet of read counts

source_name: Gastrocnemius muscles

growth_protocol: 4-month-old, male c57BL/6j mice into ground-based controls (n = 3) and Hind limb uploaded (HU) mice. HU mice were further divided into two groups and treated with either PBS as the vehicle (HU-v; n = 3) or 4-PBA (HU-t; 100mg/kg/d via intraperitoneal injections) (n = 3).

extract_protocol:
Total mRNAs were extracted from gastrocnemius muscles of the three groups of mice
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional.

treatment_protocol: HU (n=3) mice were injected with 4-PBA (HU-t; 100mg/kg/d via intraperitoneal injections)

value: hind muscle

value: 4-phenyl butyrate


title: KPF CAF-HIF2 WT rep3

description:
Ctrl3
3prime scRNA-Seq

value: C57BL/6 and 129 mix

value: FSF-Kras, p53 frt/frt, Pdx1-FlpO

value: Hif2a wild type

value: male

value: pancreas tumor

value: aSMA-expressing CAFs

value: 83 days


title: hind muscle unloaded treated with 4-phenyl butyrate 2


title: Hu95

description: 16S rRNA

data_processing:
3 μL of each library was pooled together into one tube.
The pooled library concentration was measured in ng/μL using the Qubit DNA HS assay.
Quality of the pooled library was checked using a Bioanalyzer. Size was measured at 636bp.
The pooled library was diluted to 10 nM using 10 mM Tris-HCl pH 8.5 0.1% Tween 20 buffer.
Sequencing was done on a Nano-300 cycle test chip (MS-103-1001) to confirm coverage of all libraries. Libraries with low reads were spiked in at higher concentrations to increase coverage. The re-pooled library was then ran on the MiSeq using an Illumina MiSeq Reagents kit v3 (600 cycles) (MS-102-3003) at 10 pM set at the below parameters according to kit instructions:
The 24 paired-end raw sequencing files (.fastq) representing two groups were generated in Genomics facility core, Univeristy of Louisville and downloaded from Illumina’s BaseSpace (https://basespace.illumina.com/) onto the KBRIN server for analysis using the script
The samples was further trimmed and analyzed using QIIME 2
Supplementary_files_format_and_content: The relative abundances of specific bacteria indicated in "16s seq processing data Hu.xlsx" were generated by each taxonomic raw reads divided by whole reads on all samples

organism: feces metagenome

extract_protocol:
Fecal DNA extract from 5 g feces of human using the QIAamp DNA Stool Mini Kit (Qiagen) according the instruction of manufactory.
QIAseq 16S/ITS 96-Index I (384) (Cat# 333825) and QIAseq 16S/ITS Screening Panel (24) (Cat# 333812)
3 μL of each library was pooled together into one tube.
The pooled library concentration was measured in ng/μL using the Qubit DNA HS assay.
Quality of the pooled library was checked using a Bioanalyzer. Size was measured at 636bp.
The pooled library was diluted to 10 nM using 10 mM Tris-HCl pH 8.5 0.1% Tween 20 buffer.
Sequencing was done on a Nano-300 cycle test chip (MS-103-1001) to confirm coverage of all libraries. Libraries with low reads were spiked in at higher concentrations to increase coverage. The re-pooled library was then ran on the MiSeq using an Illumina MiSeq Reagents kit v3 (600 cycles) (MS-102-3003) at 10 pM set at the below parameters according to kit instructions:
16s rRNA sequencing

treatment_protocol: No treatment

tag: developmental stage

value: Aged

value: Human Feces


title: hind muscle unloaded treated with 4-phenyl butyrate 1


title: Hu96

description: 16S rRNA


title: Hu94

description: 16S rRNA


title: ipsilateral microglia replicate3

description:
counts.matrix.norm_anno
sPC_3


title: ipsilateral microglia replicate2

description:
counts.matrix.norm_anno
sPC_2


title: hind muscle unloaded treated with vehicle 3

value: vehicle


title: ipsilateral microglia replicate1

description:
counts.matrix.norm_anno
sPC_1


title: hind muscle unloaded treated with vehicle 2


title: ipsilateral pericyte replicate6

description:
counts.matrix.norm_anno
sMG_6

value: ipsilateral pericyte


title: Hu93

description: 16S rRNA


title: ipsilateral pericyte replicate5

description:
counts.matrix.norm_anno
sMG_5


title: Ground-based controls 3


title: Hu91

description: 16S rRNA

value: Young


title: hind muscle unloaded treated with vehicle 1


title: Hu92

description: 16S rRNA


title: ipsilateral pericyte replicate4

description:
counts.matrix.norm_anno
sMG_4


title: Hu90

description: 16S rRNA


title: Ground-based controls 2


title: ipsilateral pericyte replicate2

description:
counts.matrix.norm_anno
sMG_2


title: hu89

description: 16S rRNA


title: ipsilateral pericyte replicate3

description:
counts.matrix.norm_anno
sMG_3


title: Hu88

description: 16S rRNA


title: Microdissected Rat Renal CCD, LPS_3_3Hr, RNA-Seq, Transcriptome 03

city: Taipei

first: Chih-Chien

last: Sung

state: Taipei

address: No 325, Section 2, Cheng-Kung Road,Neihu

department: Department of Medicine

country: Taiwan

institute: Tri-Service General Hospital, National Defense Medical Center

data_processing:
Sequenced reads were mapped to Ensembl rat gene set (Rnor_6.0) using STAR v2.7.9a
Transcript abundances in TPM were caculated by RSEM/1.3.3
Assembly: Rnor_6.0 (Ensembl)
Supplementary files format and content: tab-delimited text files include TPM  for each sample

source_name: Kidney

growth_protocol: Pathogen-free male Sprague-Dawley rats had free access to ad libitum drinking water and normal rodent chow before experiment. The rats were housed one per cage, maintained on a 12:12-h light-dark cycle, and acclimated to the housing conditions for 2 days before the experimental procedures.

extract_protocol:
For microdissecting cortical collecting duct,  total RNA were extracted using the Direct-zol™ RNA Kits (Zymo Research) and cDNA was synthesized by SMARTer V4 Ultra Low RNA kit (Clontech). The cDNA was then amplified for 15 PCR cycles, purified by AmPure XP magnetic beads (Beckman Coulter Genomics), and eluted with 15 μL Elution Buffer. The purified cDNA was further quantified by Qubit. Library size distribution was determined using the Agilent 2100 bioanalyzer using High-Sensitive DNA kit. The Nextera XT DNA Library Preparation Kits (Illumina) was used to generate the libraries with input of 1 ng.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cortical collecting ducts were microdissected from the kidneys 3 hours after intraperitoneal injection with lipopolysaccharide (LPS) or Vehicle (normal saline) (n=3 versus n=3, paired). Microdissected tubules were subjected to small sample RNA-Seq analysis as previously described (PMID: 31146973).

value: Sprague Dawley

value: Kidney


title: Hu87

description: 16S rRNA


title: Young1

description: Bacteriophage

value: Health young people


title: ipsilateral pericyte replicate1

description:
counts.matrix.norm_anno
sMG_1


title: Hu86

description: 16S rRNA


title: ipsilateral endothelial cell replicate6

description:
counts.matrix.norm_anno
sEC_6

value: ipsilateral endothelial cell


title: ipsilateral endothelial cell replicate4

description:
counts.matrix.norm_anno
sEC_4


title: Hu84

description: 16S rRNA


title: Hu85

description: 16S rRNA


title: Microdissected Rat Renal CCD, LPS_2_3Hr, RNA-Seq, Transcriptome 02


title: Microdissected Rat Renal CCD, LPS_2_3Hr, RNA-Seq, Transcriptome 03


title: ipsilateral endothelial cell replicate3

description:
counts.matrix.norm_anno
sEC_3


title: Microdissected Rat Renal CCD, LPS_2_3Hr, RNA-Seq, Transcriptome 01


title: Microdissected Rat Renal CCD, LPS_1_3Hr, RNA-Seq, Transcriptome 03


title: Hu81

description: 16S rRNA


title: Hu82

description: 16S rRNA


title: ipsilateral endothelial cell replicate2

description:
counts.matrix.norm_anno
sEC_2


title: ipsilateral endothelial cell replicate1

description:
counts.matrix.norm_anno
sEC_1


title: Ground-based controls 1

value: hind muscle


title: Microdissected Rat Renal CCD, LPS_1_3Hr, RNA-Seq, Transcriptome 02


title: Microdissected Rat Renal CCD, LPS_3_3Hr, RNA-Seq, Transcriptome 02


title: Hu80

description: 16S rRNA


title: Hu79

description: 16S rRNA


title: ipsilateral astrocyte replicate6

description:
counts.matrix.norm_anno
sAC_6

value: ipsilateral astrocyte


title: Microdissected Rat Renal CCD, LPS_1_3Hr, RNA-Seq, Transcriptome 01


title: sgCTRL mock replicate 2

value: Mock


title: ipsilateral astrocyte replicate4

description:
counts.matrix.norm_anno
sAC_4


title: ipsilateral astrocyte replicate5

description:
counts.matrix.norm_anno
sAC_5


title: Hu78

description: 16S rRNA


title: Hu83

description: 16S rRNA


title: Microdissected Rat Renal CCD, Vehicle_3_3Hr, RNA-Seq, Transcriptome 02


title: Hu77

description: 16S rRNA


title: ipsilateral astrocyte replicate3

description:
counts.matrix.norm_anno
sAC_3


title: Microdissected Rat Renal CCD, Vehicle_3_3Hr, RNA-Seq, Transcriptome 03


title: Hu74

description: 16S rRNA


title: ipsilateral astrocyte replicate1

description:
counts.matrix.norm_anno
sAC_1


title: Microdissected Rat Renal CCD, LPS_3_3Hr, RNA-Seq, Transcriptome 01


title: Hu76

description: 16S rRNA


title: ipsilateral astrocyte replicate2

description:
counts.matrix.norm_anno
sAC_2


title: Microdissected Rat Renal CCD, Vehicle_2_3Hr, RNA-Seq, Transcriptome 03


title: Hu73

description: 16S rRNA


title: Microdissected Rat Renal CCD, Vehicle_2_3Hr, RNA-Seq, Transcriptome 01


title: contralateral pericyte replicate6

description:
counts.matrix.norm_anno
cPC_6

source_name: contralateral hemisphisphere

value: contralateral pericyte


title: Microdissected Rat Renal CCD, Vehicle_1_3Hr, RNA-Seq, Transcriptome 03


title: ipsilateral endothelial cell replicate5

description:
counts.matrix.norm_anno
sEC_5


title: contralateral pericyte replicate4

description:
counts.matrix.norm_anno
cPC_4


title: Hu70

description: 16S rRNA


title: contralateral pericyte replicate5

description:
counts.matrix.norm_anno
cPC_5


title: Microdissected Rat Renal CCD, Vehicle_2_3Hr, RNA-Seq, Transcriptome 02


title: Microdissected Rat Renal CCD, Vehicle_1_3Hr, RNA-Seq, Transcriptome 02


title: contralateral pericyte replicate3

description:
counts.matrix.norm_anno
cPC_3


title: Microdissected Rat Renal CCD, Vehicle_1_3Hr, RNA-Seq, Transcriptome 01


title: Cumulus_MG_1

city: East Lansing

first: Peter

last: Schall

state: MI

address: 474 S. Shaw Lane

department: CMIB ANS

institute: Michigan State University

data_processing:
Illumina Real Time Analysis (RTA) v2.7.7 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1.
Trimming was conducted utilizing Fastp (v0.20.0) with the following settings: minimum quality threshold of 20, minimum length of 20, removal of low complexity/poly-nucleotide reads, and hard trim first three basepairs on each read due to abnormal nucleotide distribution discovered via FastQC.
The cow cDNA genome (ARS-UCD1.20, build 100) was downloaded from Ensembl and indexed and transcript abundance quantified with Kallisto (v0.44.0), using standard settings.
Genome_build: ARS-UCD1.20
Supplementary_files_format_and_content: *_abundance.tsv: Tab-delimited Kallisto output files for each sample.

organism: Bos taurus

source_name: Cumulus

growth_protocol: Multiparous lactating dairy cows from May to August 2019 at a commercial dairy farm (Nobis Dairy Farm, St. Johns, MI, USA). Cows were housed in free stall barns, fed a mixed ration once daily, and had free access to water and feed. The mixed ration consisted of wheat, corn, corn-soybean meal-based concentrations, and alfalfa silages that were formulated to meet nutrient recommendations for lactating dairy cows. Cows were divided into two groups based on body condition change following parturition. Body condition of all multiparous cows < 2 weeks prior to expected time of parturition was evaluated according to a 5-point scale with 0.1-point increments and conducted weekly (Middleton et al., 2019). Body condition scores assessed within one week of calving (baseline) and again at 27-33 days in milk (DIM) were utilized to determine change in body condition during the first month of lactation. Cows that had a body condition score loss following parturition to 27-33 DIM were placed into the loss (L) group (n = 10). All cows in this group had a > 0.5-point BC loss with the exception of one cow with a 0.3 point-loss during this period. Cows that maintained or increased their body condition (> 0.1 point) from parturition to 27-33 DIM were placed in the maintained / gained (M/G) group (n = 8; Figure 1). Cumulus-oocyte complexes were retrieved by ovum pickup.

extract_protocol:
Total RNA was isolated from each oocyte using PicoPure™ RNA Extraction kit total RNA following the manufacturer’s protocol, including a DNase digestion (RNase-Free DNase Set; Qiagen, Hilden, Germany) to remove contaminating DNA.
Oocyte libraries were constructed using Ovation® SoLo RNA-Seq System (NuGEN, now TECAN, Redwood, CA), including a bead purification, end repair, adaptor ligation and first round library amplification and purification steps. Then 20–30 ng of each library was used for the remainder of library preparation, which included use of AnyDeplete bovine primers for rRNA depletion, and a second round of library amplification and purification. Enzymatic shearing was applied rendering all RNA-seq libraries between 300 and 350 bp in length. Barcoded libraries were pooled and sequenced on an Illumina HiSeq 4000 (Illumina, San Diego, CA, USA) at the Michigan State University- Genomics Core. Cumulus cell libraries were constructed using the Nugen (TECAN) Universal RNA-Seq with NuQuant kit.

value: Cumulus

tag: condition

value: L


title: contralateral pericyte replicate2

description:
counts.matrix.norm_anno
cPC_2


title: Microdissected Rat Renal CCD, Vehicle_3_3Hr, RNA-Seq, Transcriptome 01


title: Cumulus_MG_2


title: contralateral pericyte replicate1

description:
counts.matrix.norm_anno
cPC_1


title: Microdissected Rat Renal CCD, UUO_4_30mins, RNA-Seq, Transcriptome 02

data_processing:
Sequenced reads were mapped to Ensembl rat gene set (Rnor_6.0) using STAR v2.7.3
Transcript abundances in TPM were caculated by RSEM/1.3.3
Genome_build: Rnor_6.0 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text files include TPM  for each sample

growth_protocol: Pathogen-free male Sprague-Dawley rats weighing 120-160 g had free access to ad libitum drinking water and normal rodent chow before experiment. The rats were housed one per cage, maintained on a 12:12-h light-dark cycle, and acclimated to the housing conditions for 2 days before the experimental procedures.

extract_protocol:
For bulk kidney, obstructed kidneys from animals were rapidly removed and be processed individually by homogenizing in Trizol, then transferred to a 2.0 mL microcentrifuge tube for RNA extraction and library construction (TruSeq Stranded mRNA Library Prep Kit, Illumina) according to the manufacturer’s protocol. For microdissecting cortical collecting duct and cortical TAL,  total RNA were extracted using the Direct-zol™ RNA Kits (Zymo Research) and cDNA was synthesized by SMARTer V4 Ultra Low RNA kit (Clontech). The cDNA was then amplified for 15 PCR cycles, purified by AmPure XP magnetic beads (Beckman Coulter Genomics), and eluted with 15 μL Elution Buffer. The purified cDNA was further quantified by Qubit. Library size distribution was determined using the Agilent 2100 bioanalyzer using High-Sensitive DNA kit. The Nextera XT DNA Library Preparation Kits (Illumina) was used to generate the libraries with input of 1 ng.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the unilateral ureteral obstruction (UUO) group, rats were anesthetized and the left ureter was exposed and separated through a flank incision. The left ureter was ligated with 4-0 silk at near the renal pelvis. For the sham control group, surgical procedures were the same as for UUO animals except that the ureter was not ligated.

tag: group

value: UUO


title: Cumulus_L_3

value: MG


title: Microdissected Rat Renal cTALs, UUO_4_30mins, RNA-Seq, Transcriptome 01


title: contralateral microglia replicate6

description:
counts.matrix.norm_anno
cMG_6

value: contralateral microglia


title: Microdissected Rat Renal CCD, UUO_4_30mins, RNA-Seq, Transcriptome 01


title: contralateral microglia replicate5

description:
counts.matrix.norm_anno
cMG_5


title: Microdissected Rat Renal cTALs, UUO_3_30mins, RNA-Seq, Transcriptome 01


title: contralateral microglia replicate4

description:
counts.matrix.norm_anno
cMG_4


title: Cumulus_L_1


title: Oocyte_MG_3

source_name: Oocyte

value: Oocyte


title: Cumulus_MG_3


title: Microdissected Rat Renal CCD, UUO_3_30mins, RNA-Seq, Transcriptome 01


title: Oocyte_MG_1


title: contralateral microglia replicate2

description:
counts.matrix.norm_anno
cMG_2


title: Microdissected Rat Renal cTALs, UUO_2_30mins, RNA-Seq, Transcriptome 01


title: contralateral microglia replicate1

description:
counts.matrix.norm_anno
cMG_1


title: Oocyte_L_3


title: Microdissected Rat Renal CCD, UUO_2_30mins, RNA-Seq, Transcriptome 02


title: contralateral endothelial cell replicate6

description:
counts.matrix.norm_anno
cEC_6

value: contralateral endothelial cell


title: Oocyte_L_2


title: Microdissected Rat Renal CCD, UUO_2_30mins, RNA-Seq, Transcriptome 01


title: Cumulus_L_2


title: Microdissected Rat Renal cTALs, UUO_1_30mins, RNA-Seq, Transcriptome 01


title: contralateral endothelial cell replicate4

description:
counts.matrix.norm_anno
cEC_4


title: Oocyte_L_1


title: Microdissected Rat Renal CCD, UUO_1_30mins, RNA-Seq, Transcriptome 01


title: contralateral microglia replicate3

description:
counts.matrix.norm_anno
cMG_3


title: SRC23 KO_IL6/1β/23_2

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

description: SRC23 KO_IL6/1β/23_2

data_processing:
Low quality reads and adaptor sequences were removed by Trim Galore v0.4.4
Clean reads were mapped to mm10 using hisat2
Counts per gene were obtained using subread's fucntion featureCounts
Differentially expressed genes (DEG) were calculated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each Sample

growth_protocol: Naïve CD4+ T cells were activated with coated anti-CD3 and anti-CD28 and cultured in the presence of TGF-β+IL-6 or IL-6+IL-1β+IL23 for 4 days.

extract_protocol:
The total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions
RNA-seq library was constructed for deep sequencing by BGI Genomics.

treatment_protocol: The cells were restimulated with plate-bound anti-CD3 for 4hrs before RNA extraction

value: in vitro Th17

value: Src2/3 DKO


title: contralateral endothelial cell replicate3

description:
counts.matrix.norm_anno
cEC_3


title: Microdissected Rat Renal CCD, UUO_3_30mins, RNA-Seq, Transcriptome 02

value: Sprague Dawley


title: Microdissected Rat Renal CCD, UUO_1_30mins, RNA-Seq, Transcriptome 02

value: Kidney


title: contralateral endothelial cell replicate1

description:
counts.matrix.norm_anno
cEC_1


title: SRC2 KO_IL6/1β/23_2

description: SRC2 KO_IL6/1β/23_2

value: Src2 KO


title: Microdissected Rat Renal cTALs, Sham Control_4_30mins, RNA-Seq, Transcriptome 01

value: sham


title: Oocyte_MG_2


title: Microdissected Rat Renal CCD, Sham Control_4_30mins, RNA-Seq, Transcriptome 02


title: AML9

city: Suzhou

first: Fang

last: Fang

state: Jiangsu

address: 92 Zhongnan street

institute: Children’s Hospital of Soochow University

description: AML sample with no treatment

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each sample

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bone marrow

tag: disease state

value: AML

tag: treatment


title: contralateral endothelial cell replicate2

description:
counts.matrix.norm_anno
cEC_2


title: AML7

description: AML sample with no treatment


title: AML6

description: AML sample with no treatment


title: contralateral astrocyte replicate6

description:
counts.matrix.norm_anno
cAC_6

value: contralateral astrocyte


title: Microdissected Rat Renal CCD, Sham Control_4_30mins, RNA-Seq, Transcriptome 01


title: SRC2 KO_IL6/1β/23_1

description: SRC2 KO_IL6/1β/23_1


title: AML5

description: AML sample with no treatment


title: WT_IL6/1β/23_2

value: wild type


title: contralateral astrocyte replicate5

description:
counts.matrix.norm_anno
cAC_5


title: SRC23 KO_TGFβ/IL6_2

description: SRC23 KO_TGFβ/IL6_2


title: contralateral astrocyte replicate4

description:
counts.matrix.norm_anno
cAC_4


title: WT_IL6/1β/23_1


title: AML8

description: AML sample with no treatment


title: SRC23 KO_IL6/1β/23_1

description: SRC23 KO_IL6/1β/23_1


title: AML4

description: AML sample with no treatment


title: contralateral endothelial cell replicate5

description:
counts.matrix.norm_anno
cEC_5


title: AML3

description: AML sample with no treatment


title: contralateral astrocyte replicate3

description:
counts.matrix.norm_anno
cAC_3


title: SRC2 KO_TGFβ/IL6_2

description: SRC2 KO_TGFβ/IL6_2


title: contralateral astrocyte replicate2

description:
counts.matrix.norm_anno
cAC_2


title: SRC23 KO_TGFβ/IL6_1

description: SRC23 KO_TGFβ/IL6_1


title: AML2

description: AML sample with no treatment


title: Microdissected Rat Renal cTALs, Sham Control_2_30mins, RNA-Seq, Transcriptome 01


title: Microdissected Rat Renal CCD, Sham Control_3_30mins, RNA-Seq, Transcriptome 01


title: AML1

description: AML sample with no treatment


title: WT_TGFβ/IL6_2


title: contralateral astrocyte replicate1

description:
counts.matrix.norm_anno
cAC_1


title: Microdissected Rat Renal CCD, Sham Control_2_30mins, RNA-Seq, Transcriptome 02


title: Microdissected Rat Renal CCD, Sham Control_2_30mins, RNA-Seq, Transcriptome 01


title: T87

city: Guangzhou

first: Jun

last: Ma

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

data_processing:
For RNA sequencing, the libraries (2μg RNA) were constructed using the TruSeq RNA Sample Preparation Kit (Illumina, CA, USA) and sequenced on an Illumina NovaSeq 6000 platform at the PGEM Biotechnology Co., Ltd (Guangzhou, China).
Fragments were mapped to the human genome using Hisat2 (v2.0.5), and gene abundance was reported as read counts.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human tissue

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tmn

value: Nasopharyngeal carcinoma

value: High


title: T665


title: Microdissected Rat Renal CCD, Sham Control_3_30mins, RNA-Seq, Transcriptome 02


title: AML11-Input

data_processing:
Raw data of ChIP-Seq was aligned to the reference genome (UCSC hg38) using Bowtie2 (v 2.3.5)
Peaks were identified using MACS2 (v2.0.9)
Genome_build: hg38
Supplementary_files_format_and_content: peak text files

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions

tag: chip antibody

tag: disease


title: Microdissected Rat Renal cTALs, Sham Control_1_30mins, RNA-Seq, Transcriptome 01


title: WT_TGFβ/IL6_1


title: AML10-Input


title: T629

value: Low


title: Irf8-/-  LT-HSC ATAC_seq_rep1

city: Shanghai

first: Qingsong

last: Qiu

address: Ruijin er road No.197

institute: SIH

data_processing:
Basecalls performed using bcl2fastq version 2.17
Using software trimmomatic version 0.36 removes the bad sequence from the pair-end sequence
ATAC-seq reads were aligned to the mouse genome mm10 assembly using bowtie2(version 2.2.9)
Data were filtered using picard version 1.141
Using software subread version 1.5 version counts the amount of every gene`s reads according to gene`s feature
The BAM files from each genotype were merged for peaking calling by macs2 (version 2.1.1.20160309)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deepTools; Scores represent Reads Per Kilobase per Million mapped reads

source_name: Long-term hematopoitic stem cell

extract_protocol:
1. Prepare nuclei. To prepare nuclei, we spun 50,000 cells at 500g for 5 min, which was followed by a wash using 50 μL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge.
1. Prepare nuclei. To prepare nuclei, we spun 50,000 cells at 500g for 5 min, which was followed by a wash using 50 μL of cold 1× PBS and centrifugation at 500g for 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500g for 10 min using a refrigerated centrifuge.  To avoid losing cells during the nuclei prep, we used a fixed-angle centrifuge and carefully pipetted away from the pellet after centrifugations.  2. Transpose and purify. Immediately following the nuclei prep, the pellet was resuspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (Illumina) and 22.5 μL nuclease-free water). The transposition reaction was carried out for 30 min at 37 °C. Directly following transposition the sample was purified using a Qiagen MinElute kit.  3. PCR. Following purification, we amplified library fragments using 1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 3 to 6(SEQ3309 for primer 3: AGGCAGAA, SEQ3310 for primer 4: TCCTGAGC, SEQ3740 for primer 5: GGACTCCT, SEQ3741 for primer 6: TAGGCATG), using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. To reduce GC and size bias in our PCR, we monitored the PCR reaction using qPCR in order to stop amplification before saturation. To do this, we amplified the full libraries for five cycles, after which we took an aliquot of the PCR reaction and added 10 μl of the PCR cocktail with Sybr Green at a final concentration of 0.6×. We ran this reaction for 20 cycles to determine the additional number of cycles needed for the remaining 45-μL reaction. The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ~30 nM in 20 μL. Libraries were amplified for a total of 10–12 cycles.

value: BM-derived Long-term hematopoitic stem cell

tag: development stage

value: 3 weeks


title: Irf8+/+  LT-HSC ATAC_seq_rep1

tag: cell type


title: Irf8+/+  LT-HSC ATAC_seq_rep2


title: T590


title: Microdissected Rat Renal CCD, Sham Control_1_30mins, RNA-Seq, Transcriptome 02


title: Microdissected Rat Renal CCD, Sham Control_1_30mins, RNA-Seq, Transcriptome 01


title: SRC2 KO_TGFβ/IL6_1

description: SRC2 KO_TGFβ/IL6_1


title: Microdissected Rat Renal cTALs, UUO_4_3Hr, RNA-Seq, Transcriptome 01

value: UUO


title: T550


title: Wt_M_Dark_R4 [VEG_WD4]

city: Sevilla

first: Gabriel

last: Gutierrez

address: PO BOX 1095

department: Genetics

country: Spain

institute: University of Seville

description:
RNA isolated from vegetative mycelium grown for 24h on vogel´s liquid flask under dark conditions with shaking (150 rpm)
VEG_WD4

data_processing:
libraries were run on Illumina Genome Analyzer (Illumina HiSeqV4).
Single end-reads of 100 nucleotide each were mapped against the N. crassa OR74A genome by using Tophat 2.11
quality was checked using FastQC
automatic preprocessing of the reads was carried out with AFTERQC 0.9.6
SeqMonk was used for visualization and quantification
Supplementary_files_format_and_content: raw counts, matrix text format

organism: Neurospora crassa

growth_protocol: dishes containing 25ml of Vogel´s liquid medium, were inoculated to a final concentration of 105 conidia/ml

extract_protocol:
Total RNA was isolated from frozen mycelia (approximately 100 mg) using 1g of Zirconia/Silica Beads (product number) with RLC extraction Buffer by using RNeasy Plant Mini Kit (Qiagen), following the manufacturer procedure. RNA was treated with on-column DNA digestion during RNA purification using RNAseq-free DNA set (Qiagen).
Poly-A selection and cDNA libraries preparation for RNA were prepared according to the Illumina mRNA Sample Preparation Guide

treatment_protocol: 48h at 22° in complete darkness.For light induction, cultures were exposed to white light for 30 min

tag: strain background

value: Wild-type

value: Dark

value: mycelia


title: Wt_M_Dark_R3 [VEG_WD3]

description:
RNA isolated from vegetative mycelium grown for 24h on vogel´s liquid flask under dark conditions with shaking (150 rpm)
VEG_WD3


title: Irf8-/-  LT-HSC ATAC_seq_rep2


title: Microdissected Rat Renal cTALs, Sham Control_3_30mins, RNA-Seq, Transcriptome 01

value: Sprague Dawley


title: Wt_M_Dark_R2 [VEG_WD2]

description:
RNA isolated from vegetative mycelium grown for 24h on vogel´s liquid flask under dark conditions with shaking (150 rpm)
VEG_WD2


title: T201


title: AML7-Input


title: Microdissected Rat Renal CCD, UUO_4_3Hr, RNA-Seq, Transcriptome 01

value: Kidney


title: AML6-Input


title: Wt_M_Dark_R1 [VEG_WD1]

description:
RNA isolated from vegetative mycelium grown for 24h on vogel´s liquid flask under dark conditions with shaking (150 rpm)
VEG_WD1


title: T1412


title: Microdissected Rat Renal cTALs, Sham Control_4_3Hr, RNA-Seq, Transcriptome 01


title: AML9-Input


title: AML5-Input


title: Microdissected Rat Renal CCD, Sham Control_4_3Hr, RNA-Seq, Transcriptome 02


title: T1029