title: V6.5 cells, Ecad_KO_C

city: Pune

first: Deepa

last: Subramanyam

state: Maharashtra

address: National Centre For Cell Science, Sp Pune University, Ganeshkhind Road

country: India

institute: National Centre for Cell Science, SP Pune University Campus, Ganeshkhind, Pune - 411007, India

data_processing:
Adapters were trimmed from FASTQ files using cutadapt version 2.10 with default settings keeping a minimum read length of 20 bp.
Reads were mapped to the GRCm38 mouse genome keeping only uniquely mapping reads using STAR version 2.7.5b with the following settings “--outFilterMultimapNmax 1”.
Reads overlapping genes were then counted using featureCounts version 2.0.1 using the Gencode version 25 basic transcriptome annotation.
The count matrix was imported into R. Only genes with at least 1 count per million (CPM) across at least 3 samples were kept.
Genome_build: GRCm38
Supplementary_files_format_and_content: count matrix

source_name: Cdh1-/- V6.5 mouse embryonic stem cells

extract_protocol:
Total RNA was isolated using TRIzol (Life Technologies, cat no. 15596018)
Libraries were generated using the NEB ultra II directional RNA library prep kit.

tag: cell line

tag: cell type

value: embryonic stem cells


title: control_55 mRNA-seq

status: Public on Jul 01 2022

type: SRA

city: Aurora

first: Ivana

last: Yang

state: CO

country: USA

institute: University of Colorado Anschutz Medical Campus

description:
Yang_SysBio_control_55
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

library_source: transcriptomic

data_processing:
For RNA, RNA paired-end reads were aligned at the gene level to Ensembl GrCh38 using Kallisto {Bray, 2016, 27043002}. Genes and transcripts were detected in the mRNA dataset using hg38 Gencode v27 and filter of at least 6 reads in at least 20% of the samples, TMM normalized across all samples, and then inverse normalization transformed on a per-gene basis.
Genome_build: GRCh38
Supplementary_files_format_and_content: For RNA-seq, the gene-level filtered and normalized count file is included as a processed data file

molecule: total RNA

organism: Homo sapiens

source_name: tissue-Explant

extract_protocol:
RNA was isolated from the same sample of lung tissue using the AllPrep kit (Qiagen). Samples with RNA integrity number (RIN) and DNA integrity number (DIN) >5 were used.
mRNA libraries were prepared from 500 ng total RNA with TruSeq stranded mRNA library preparation kits (illumina) and sequenced at the average depth of 80M reads on the Illumina NovaSeq 6000 (illumina).

tag: tissue

value: lung

tag: center

value: Pittsburgh Lung Donor Core

tag: dx

value: normal

value: control

tag: rnaseqid

tag: age

tag: Sex

value: f

tag: race

value: white

tag: ethnicity

value: not hispanic or latino

value: N

tag: raw data disclaimer


title: DAM24.SALINE.P11

city: New York

first: Jordan

last: Marrocco

state: NY

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Illumina NovaSeq 6000
Quality control was performed on the reads.
Reads were aligned to the rn6 genome from the BSgenome.Rnorvegicus.UCSC.rn6.
The read counts were analyzed using the R/Bioconductor framework (www.R-project.org).
Differentially expressed gene (DEG) expression analysis was conducted using the DESeq2 package.
Assembly: rn6
Supplementary files format and content: DESeq2 files contain logFC (p<0.05) between Saline and LPS animals on P10 and on P11 along with rLog counts.

organism: Rattus norvegicus

source_name: Milk

growth_protocol: Sprague-Dawley rats were maintained at 20°C on a 12 h light/dark cycle (0700-1900 light) with ad libitum access to food and water.

extract_protocol:
2 and 24 hours after receieving either injection, dams were lightly anesthetized with isoflurane in O2, followed by the administration of 0.2 mL of oxytocin (20 USP/mL i.p). Distilled water was used to moisten the teats and milk obtained by gently squeezing its base to manually expel the sample for collection. A microhematocrit tube was used to collect ~20 ul of sample, and samples were stored at -80C until processing. For RNA isolation, milk was spun at 1,000 g to separate the fat layer from the whey. This fat layer was then mixed with an equal volume of PBS and spun again at 3,000 rpm to clean the fat of debris. The miRNeasy Mini Kit (QIAGEN, Cat. #217004) was used to isolate total RNA following the manufacturer’s directions. A NanoDrop 2000 spectrophotometer was used to quantify isolated RNA samples, which were then stored at -80C prior to sequencing.
A total of at least 190ng of RNA per replicate was prepared for sequencing by The New York Genomic Center using the Tru-Seq Stranded mRNA library preparation kit (Illumina, USA). Five biological replicates were used per experimental group. cDNA libraries were sequenced on an Illumina NovaSeq 6000 in two lanes to obtain 100-bp single-end reads at an approximate sequencing depth of 50 million reads per sample.

treatment_protocol: Rat mothers were injected with either lipolysaccharide or pyrogen-free saline on postnatal day 10.

tag: strain

value: Sprague-Dawley

tag: genotype

value: Wild Type

value: Milk

tag: agent

value: Saline


title: DAM2.LPS.P11

value: LPS


title: DAM1.SALINE.P11


title: V6.5 cells, WT_B

organism: Mus musculus

source_name: WT V6.5 mouse embryonic stem cells

value: WT


title: case_52 mRNA-seq

description:
Yang_SysBio_case_52
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: ipf

value: case

value: m

value: other

value: unknown


title: DAM21.LPS.P11


title: control_57 mRNA-seq

description:
Yang_SysBio_control_57
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: Y


title: V6.5 cells, Ecad_KO_A

value: embryonic stem cells


title: V6.5 cells, Ecad_KO_B


title: R108G_KY305

city: Houston

first: Brittney

last: Lozzi

state: TX

address: 1 Baylor Plaza

department: Cell & Gene Therapy

institute: Baylor College of Medicine

data_processing:
Quality control was performed on fastq files using fastQC. Paired end reads were mapped to the mouse genome (mm10) using STAR (v2.5.0a).
Reads Per Million (RPM) were calculated using GenomicAlignments (v1.16.0) and DESeq2 (v1.20.0) was used for read count normalization and differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each variant

molecule: polyA RNA

source_name: Cortical Brain Tumor

extract_protocol:
Bulk tissue was dissociated with QIAshredder column. RNA was isolated using trizol and chloroform and purified using the RNeasy Mini Kit (QIAGEN).
Illumina sequencing libraries were constructed from 500-900ng of total RNA using the TruSeq Stranded mRNA Library preperation kit (Illumina)

tag: disease state

value: Glioblastoma

value: Cortex

tag: egfr variant

value: post-natal day 70


title: V6.5 cells, WT_A


title: EGFR_KY23

value: wildtype EGFREGFR


title: mCherry_KY302

value: n/a (mCherry)


title: R108G_KY303


title: case_54 mRNA-seq

description:
Yang_SysBio_case_54
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: hispanic


title: DAM16.LPS.P10

value: Sprague-Dawley

value: Wild Type

value: Milk

value: LPS


title: EGFR_KY2


title: DAM20.LPS.P10


title: DAM17.SALINE.P11

value: Saline


title: control_53 mRNA-seq

description:
Yang_SysBio_control_53
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: Pittsburgh Lung Donor Core

value: f

value: black

value: unknown

value: N


title: DAM8.SALINE.P11


title: mCherry_KY4

value: Glioblastoma

value: Cortex


title: control_50 mRNA-seq

description:
Yang_SysBio_control_50
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: normal

value: control

value: white

value: not hispanic or latino


title: V6.5 cells, WT_C

value: WT

value: embryonic stem cells


title: R108G_KY306

value: post-natal day 70


title: DAM22.SALINE.P11

value: Sprague-Dawley

value: Wild Type

value: Milk


title: A289V_KY21


title: A289V_KY22


title: EGFR_KY1

value: wildtype EGFR


title: case_46 mRNA-seq

description:
Yang_SysBio_case_46
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: UCSF

value: ipf

value: case

value: m

value: Y


title: case_49 mRNA-seq

description:
Yang_SysBio_case_49
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***


title: mCherry_KY3

value: Glioblastoma

value: Cortex

value: n/a (mCherry)


title: DAM5.LPS.P10

value: LPS


title: DAM18.LPS.P10


title: Chol_BatchB_mCLB073

city: Ithaca

first: Monique

last: Theriault

address: 930 Campus Rd C5-105 VMC, Cornell University

department: Microbiology and Immunology

institute: Cornell University

data_processing:
Flexbar (v. 3.4) has been used to remove low quality reads and trim Illumina adapters.
rRNA reads have been removed using Bowtie2 (--sensitive mode)
rRNA filtered fastq files were split using Bowtie2 (--very-sensitive mode) into species-specific files using the two reference genomes, GRCh38.98 for Homo sapiens and NCBI assembly GCA_00668235.1 for Mtb Erdman
Hisat2 (v. 2.1.0) was used to align reads to the respective transcriptomes
Raw read counts for each sample were obtained using HTSeq (v. 0.11.0)
Genome_build: Genome_build: GRCh38.98 for Homo sapiens and NCBI assembly GCA_00668235.1 for Mtb Erdman

organism: Mycobacterium tuberculosis

source_name: Mtb cholesterol broth cultures

growth_protocol: Dual RNA-seq: Human monocyte derived macrophages (HMDMs) were infected with Erdman smyc’::mCherry reporter Mtb strain at MOI 2:1. Cholesterol RNA-Seq: Wildtype Erdman Mtb was grown in 7H9 OADC for 2 days in a roller bottle.

extract_protocol:
Dual RNA-Seq: To remove host RNA, Trizol samples were centrifuged and approximately 75% (~500 µL) of Trizol supernatant was transferred to a new tube. An additional 400 µL of Trizol and 150 µL of zirconia beads were added to the tubes containing the bacterial pellet and 25% of the remaining Trizol. These tubes were placed on a beat beater for two cycles of one minute each, with 2 minutes of rest on ice in between. After the bead beating, approximately 75% of host RNA in Trizol was added to be bacterial lysate tubes. Chloroform was added to Trizol tubes (200 µL of chloroform for 1 mL of Trizol) and tubes were mixed via shaking vigorously. Trizol:chloroform tubes were centrifuged for 15 minutes and the aqueous phase (~1 mL) was transferred to a fresh tube. 2 µL of glycoblue and 500uL of isopropanol were added to precipitate host and bacterial RNA. RNA was washed in 75% cold ethanol and RNA was eluted in 12 µL of NCFW. Cholesterol RNA-seq: Bacterial pellets in GTC buffer were washed with PBS + 0.05% Tween-80. Bacterial cells were lysed via 5mg/mL lysozyme treatment for 15 minutes at room temperature followed by hot Trizol bead beating for one cycle of 2 minutes. After bead beating, chloroform was added and the tubes were centrifuged to separate phases. The aqueous phase was then added to equal volume of pure ethanol. RNA was then purified using a Qiagen Rneasy Kit.
Sequencing libraries were generated using the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina (New England BioLabs). Libraries were sequenced on a HiSeq 4000 (Illumina) in multiple rounds until the desired sequencing depth for bacterial reads was reached.

treatment_protocol: Dual RNA-seq: At 2 dpi, experimental compounds were administered at 10 µM, INH at 67.5 ng/mL, and EMB at 5 µg/mL. Infected HMDMs were treated for 48 hours prior to sorting. Cholesterol RNA seq: After 2 days of growth, drugs were administed at 10x EC50.

tag: bacterial strain

value: Erdman M. tuberculosis, pCherry3

tag: treatment

value: 20 µM mCLB073


title: Chol_BatchA_mCLB073


title: Chol_BatchB_DMSO

value: DMSO (untreated)


title: DAM15.SALINE.P10

value: Sprague-Dawley

value: Saline


title: case_47 mRNA-seq

description:
Yang_SysBio_case_47
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: f

value: white

value: not hispanic or latino


title: Chol_BatchA_DMSO


title: Chol_BatchB_sAEL057

value: 20 µM sAEL057


title: A289V_KY10

value: post-natal day 70


title: A289V_KY20


title: DAM22.SALINE.P10

value: Wild Type

value: Milk


title: control_44 mRNA-seq

description:
Yang_SysBio_control_44
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: m

value: N


title: case_45 mRNA-seq

description:
Yang_SysBio_case_45
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: ipf

value: case

value: other

value: unknown

value: Y


title: LY6

type: genomic

city: Vitoria-Gasteiz

first: Guiomar

last: Perez de Nanclares

state: Araba

address: Jose Atxotegi sn

department: (Epi)Genetics Lab

country: Spain

institute: Bioaraba Health Research Institute

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing:
Methilumi R-package
Average Beta

label: Cy3 and Cy5

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from PBL samples using Qiagen Mini Kit according to standard instructions

value: peripheral blood

value: Normal


title: Chol_BatchA_sAEL057

value: Erdman M. tuberculosis, pCherry3

value: 20 µM sAEL057


title: DAM3.SALINE.P10

value: Sprague-Dawley

value: Wild Type

value: Milk

value: Saline


title: A289I_KY311

value: Glioblastoma

value: Cortex

value: post-natal day 70


title: control_48 mRNA-seq

description:
Yang_SysBio_control_48
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: f

value: white

value: not hispanic or latino

value: N


title: DAM2.LPS.P10

value: LPS


title: A289I_KY310


title: LY5

value: peripheral blood

value: Normal


title: case_43 mRNA-seq

description:
Yang_SysBio_case_43
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: ipf

value: case

value: m

value: Y


title: A289I_KY309

value: Glioblastoma

value: Cortex

value: post-natal day 70


title: LY3


title: control_42 mRNA-seq

description:
Yang_SysBio_control_42
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: Pittsburgh Lung Donor Core

value: normal


title: LY2


title: DAM8.SALINE.P10

value: Sprague-Dawley

value: Wild Type

value: Milk

value: Saline


title: Chronic Carbon Fiber Stimulus [5123-QW-5]

city: East Lansing

first: Quentin

middle: Alexander

last: Whitsitt

state: Michigan

address: 775 Woodlot Dr.

department: Biomedical Engineering

institute: Michigan State University

data_processing:
Fastq files processed using Space Ranger pipeline version 1.3.1
Assembly: Rnor_6.0
Supplementary files format and content: .cloupe files meant for use in Loupe Browser (10x Genomics), spatial gene expression

source_name: Brain

extract_protocol: 10x Genomics, Visium spatial gene expression protocol

value: Brain

value: Long-evans Rat

value: Chronic stimulation (carbon fiber)


title: case_40 mRNA-seq

description:
Yang_SysBio_case_40
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: ipf

value: unknown

value: hispanic

value: N


title: A289I_KY307

value: Glioblastoma

value: Cortex


title: Chronic Microwire Stimulus [5123-QW-7]

value: Chronic no stimulation (microwire)


title: A289I_KY308

value: post-natal day 70


title: LSK_TP_3

city: Charlottesville

first: Golam

last: Mohi

state: Virginia

address: 1340 Jefferson Park Ave

department: Biochemistry and Molecular Genetics

institute: University of Virginia

data_processing:
Fastq files were aligned with mm10 using hisat2 2.1.0.
SAM files were converted to BAM files with samtools 1.9.0.
Gene counts were producing using R packages: GenomicAlignments 1.24.0 and TxDb.Mmusculus.UCSC.mm10.knownGene 3.10.0.
Differential analysis was performed using DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: LSK_TPvsVeh_genecounts.csv, LSK_TPvsVEHICLE.csv

source_name: BM LSK Cells

extract_protocol:
Bone marrow cells were harvested and lineage depleted by MACS mouse lineage depletion kit, and the LSK (Lin-Sca1+c-kit+) cell were sorted by flow cytometry.
Library prep was done according to protocol of NEB polyA-RNA magnetic isolation kit and then NEBNext Ultra II RNA Library Prep Kit for Illumina.

value: Mx1Cre; Jak2VF/VF

tag: cell type

value: Bone marrrow LSK cells


title: case_41 mRNA-seq

description:
Yang_SysBio_case_41
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: tissue

value: lung

value: case

value: m

value: Y


title: LSK_TP_2


title: Chronic Microwire No Stimulus [5123-QW-3]

value: Brain

value: Long-evans Rat

value: Chronic stimulation (microwire)


title: case_32 mRNA-seq

description:
Yang_SysBio_case_32
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: center

value: Vanderbilt

value: ipf

value: white

value: not hispanic or latino


title: LY1

value: peripheral blood

value: Normal


title: DAM24.SALINE.P10

value: Sprague-Dawley

value: Wild Type

value: Milk

value: Saline


title: Acute Stim - Replicate 2 [3962-QW-2]

value: Acute stimulation


title: case_31 mRNA-seq

description:
Yang_SysBio_case_31
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

tag: dx

value: case


title: Acute Stim - Replicate 1 [3962-QW-1]


title: CB62


title: LSK_TP_1

value: Mx1Cre; Jak2VF/VF

value: Bone marrrow LSK cells


title: CB49


title: LSK_Vehicle_3

value: PBS


title: control_30 mRNA-seq

description:
Yang_SysBio_control_30
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: normal

value: control

tag: rnaseqid

value: f

value: black

value: unknown

value: Y


title: control_28 mRNA-seq

description:
Yang_SysBio_control_28
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: age

value: m

value: N


title: Acute Craniotomy Control [4742-QW-1]

value: Brain

value: Long-evans Rat

value: Craniotomy control


title: CB93

value: peripheral blood

value: Normal


title: LY4


title: case_27 mRNA-seq

description:
Yang_SysBio_case_27
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: Vanderbilt

value: ipf

value: case

tag: Sex

value: white

value: not hispanic or latino


title: case_36 mRNA-seq

description:
Yang_SysBio_case_36
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

source_name: tissue-Unknown

value: National Jewish

tag: race


title: LSK_Vehicle_2

value: Mx1Cre; Jak2VF/VF

value: Bone marrrow LSK cells

value: PBS


title: CB90


title: control_26 mRNA-seq

description:
Yang_SysBio_control_26
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: UCSF

value: normal

value: control

value: m

value: black

tag: ethnicity

value: unknown

value: Y


title: Enriched 5

description: Enriched environment

data_processing:
Illumina NovaSeq 6000
Quality control was performed on the reads.
Reads were aligned to the rn6 genome from the BSgenome.Rnorvegicus.UCSC.rn6.
The read counts were analyzed using the R/Bioconductor framework (www.R-project.org).
Differentially expressed gene (DEG) expression analysis was conducted using the DESeq2 package.
Assembly: rn6
Supplementary files format and content: DESeq2 files contain logFC between SD and EE animals

extract_protocol:
Immediately following the separation period on P10, dams were lightly anesthetized with isoflurane in O2, followed by the administration of 0.2 mL of oxytocin (20 USP/mL i.p). Distilled water was used to moisten the teats and milk obtained by gently squeezing its base to manually expel the sample for collection. A microhematocrit tube was used to collect ~20 ul of sample, and samples were stored at -80C until processing. For RNA isolation, milk was spun at 1,000 g to separate the fat layer from the whey. This fat layer was then mixed with an equal volume of PBS and spun again at 3,000 rpm to clean the fat of debris. The miRNeasy Mini Kit (QIAGEN, Cat. #217004) was used to isolate total RNA following the manufacturer’s directions. A NanoDrop 2000 spectrophotometer was used to quantify isolated RNA samples, which were then stored at -80C prior to sequencing.
A total of at least 190ng of RNA per replicate was prepared for sequencing by The New York Genomic Center using the Tru-Seq Stranded mRNA library preparation kit (Illumina, USA). Five biological replicates were used per experimental group. cDNA libraries were sequenced on an Illumina NovaSeq 6000 in two lanes to obtain 100-bp single-end reads at an approximate sequencing depth of 50 million reads per sample.

treatment_protocol: Female rats were pair-housed in one of two conditions: environmental enrichment (EE; 91.5×64×159 cm), or standard laboratory cages (SD; 27×48×20 cm).

value: Sprague-Dawley

value: Wild Type

value: Milk


title: LSK_Vehicle_1


title: CB50

value: peripheral blood

value: Normal


title: case_25 mRNA-seq

description:
Yang_SysBio_case_25
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: Vanderbilt

value: ipf

value: case

value: white

value: not hispanic or latino

value: N

tag: raw data disclaimer


title: Enriched 3

description: Enriched environment

tag: strain


title: PLUS3

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

data_processing:
Raw reads were trimmed for quality and adaptors removal with cutadapt.  A sub set of randomly selected 15 million reads from each sample’s library (using seqtk package (https://github.com/lh3/seqtk)
Reads were mapped to Trypanosoma brucei genome (GCA_000002445.1_ASM244v1) with TopHat (v2.1.1)
Counts per gene quantification was performed using htseq-count
NA
NA
Genome_build: GCA_000002445.1_ASM244v1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Trypanosoma brucei brucei

source_name: UMSBP2 knock down

growth_protocol: Beck's Medium

extract_protocol:
PolyA
RNA libraries were prepared for sequencing using KAPA Stranded mRNA-Seq Kits

treatment_protocol: RNAi induction by Tetracycline

value: one complete parasite per sample

tag: Stage

value: parasite was collected from host at procyclic stage

tag: genotype

value: UMSBP2 knock down


title: CB48

tag: disease state


title: CB63


title: case_24 mRNA-seq

description:
Yang_SysBio_case_24
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: f


title: CB7


title: Enriched 2

description: Enriched environment


title: Standard 5

description: Standard housed


title: case_23 mRNA-seq

description:
Yang_SysBio_case_23
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m

value: Y


title: Enriched 1

description: Enriched environment

value: Sprague-Dawley

value: Wild Type


title: Enriched 4

description: Enriched environment

value: Milk


title: CB8

value: peripheral blood

value: Normal


title: PLUS1


title: MINUS3

source_name: Wild type

value: Wild type


title: control_22 mRNA-seq

description:
Yang_SysBio_control_22
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: UCSF

value: normal

value: control

value: unknown

value: hispanic


title: MINUS4

value: one complete parasite per sample

value: parasite was collected from host at procyclic stage


title: Standard 4

description: Standard housed


title: PLUS4

value: UMSBP2 knock down


title: case_21 mRNA-seq

description:
Yang_SysBio_case_21
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Vanderbilt

value: ipf

value: case

value: m

value: white

value: not hispanic or latino


title: CB5

value: peripheral blood

value: Normal


title: CB233


title: Standard 3

description: Standard housed

value: Sprague-Dawley

value: Wild Type

value: Milk


title: MINUS1

value: Wild type


title: control_19 mRNA-seq

description:
Yang_SysBio_control_19
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: UCSF

value: normal

value: control

value: black

value: unknown

value: N


title: case_20 mRNA-seq

description:
Yang_SysBio_case_20
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Vanderbilt

value: ipf

value: case

value: Y


title: Standard 1

description: Standard housed


title: CB162

value: peripheral blood


title: case_16 mRNA-seq

description:
Yang_SysBio_case_16
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: m

value: white

value: not hispanic or latino


title: control_sample_2

city: Paris

first: Lasse

middle: van

last: Wijlick

address: 25-28 Rue du Dr Roux

department: Mycology

country: France

institute: Institut Pasteur

library_source: genomic

data_processing:
Reads were mapped on the available C. albicans genome sequence assembly 22 (candiagenome.org) using Hisat2
binding sites were identified using bPeaks
Assembly: Candida genome databse assembly 22
Supplementary files format and content: location of obtained binding peaks calculated with bPeaks in bedGraph format

organism: Candida albicans

source_name: control

extract_protocol:
Cells were mechanically opened in standard lysis buffer, with 0.5mm glasbeads during 6 rounds of 45s on a FasPrep at 6.5m speed.
The DNA library was prepared with the TruSeq ChIP library preparation kit from Illumina. 10 ng were used as starting material of each sample. Size selection of the corresponding library was performed by two consecutive AMPure XP bead (Beckman) steps

tag: strain background

value: BWP17 parental strain

value: ChIP antibody:anti-HA


title: Y32B_res

city: College Station

first: Michael

middle: Carey

last: Satterfield

address: 2471 TAMUS

department: Animals Science

institute: Texas A&M University

data_processing:
Libraries were multiplexed and sequenced from both directions as 75 base pair paired-end reads on one lane on a NextSeq500 instrument
Raw sequences (FASTQ) were subjected to quality check by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The program fqtrim (https://ccb.jhu.edu/software/fqtrim/) was used to remove adapters, perform quality trimming (phred score >30) by a sliding window scan (6 nucleotides) and select read length of 30 nucleotides or longer after trimming.
The reads obtained from the quality control step were mapped to the cattle reference genome (ARS-UCD1.2) by using Hisat2 aligner. The program FeatureCounts was used to quantify read counts by using the sequences alignment files of each sample.
Genes with evidence of expression (counts per million; rowSum >5) were used for model-based differential expression analysis using the edgeR robust method.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: CSV file with genes by row and samples by column, raw counts
Supplementary_files_format_and_content: Matrix file with normalized CPM from edgeR for all samples

organism: Bos taurus

source_name: longissimus dorsi muscle

extract_protocol:
Total RNA was extracted using Trizol reagent, treated with DNAse I, and purified using an RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Control dams were fed 100% of their NRC nutritional requirements from Day 158 of pregnancy to parturition. Nutrient restricted dams were fed 50% of their NRC nutritional requirements for the same time period. Offspring were all treated equally from birth to slaughter on post-natal day 485.

value: longissimus dorsi muscle

value: restricted

value: female


title: CB159

value: Normal


title: control_sample_3


title: control_sample_1


title: Y1A_res


title: Y2A_res


title: CB158


title: CB81


title: CB80


title: overexpression, TET-promoter, IRF1-HA 2

source_name: overexpression


title: Y19A_res


title: case_11 mRNA-seq

description:
Yang_SysBio_case_11
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: UCSF

value: f


title: overexpression, TET-promoter, IRF1-HA 1


title: control_10 mRNA-seq

description:
Yang_SysBio_control_10
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core

value: normal

value: control

value: N


title: Standard 2

description: Standard housed

value: Sprague-Dawley

value: Wild Type

value: Milk


title: CB170

value: peripheral blood


title: control_13 mRNA-seq

description:
Yang_SysBio_control_13
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: white

value: not hispanic or latino


title: Y15B_res

value: longissimus dorsi muscle


title: case_9 mRNA-seq

description:
Yang_SysBio_case_9
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf

value: case

value: m

value: Y


title: CB59

value: Normal


title: case_8 mRNA-seq

description:
Yang_SysBio_case_8
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: UCSF


title: case_15 mRNA-seq

description:
Yang_SysBio_case_15
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Vanderbilt


title: overexpression, TET-promoter, IRF1-HA 3

value: BWP17 parental strain

value: ChIP antibody:anti-HA


title: CB58


title: Y9A_con

value: control

value: female


title: CB41


title: case_7 mRNA-seq

description:
Yang_SysBio_case_7
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: White


title: Y5A_con


title: control_6 mRNA-seq

description:
Yang_SysBio_control_6
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core

value: normal


title: CB36

value: peripheral blood


title: case_5 mRNA-seq

description:
Yang_SysBio_case_5
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: white

value: not hispanic or latino


title: Y18A_res

value: longissimus dorsi muscle

value: restricted


title: CB60


title: case_4 mRNA-seq

description:
Yang_SysBio_case_4
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: ipf

value: case

value: m

value: N


title: Y37B_con


title: GS0081


title: Y45A_con


title: GS0079


title: Nfat1 -/- -SNL 1

type: RNA

city: nantong

first: Bao-Chun

last: Jiang

state: Jiangsu Province

address: 9 seyuan Road

country: China

institute: Nanytong University

description: Gene expression of Nfat1 -/- -SNL

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Spinal cord

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: Mice spinal cords were harvested and snap-frozen in liquid nitrogen following transcardial perfusion with PBS.

value: Spinal cord

value: 8 week

tag: gender

value: male

value: Nfat1 -/-

value: SNL


title: case_3 mRNA-seq

description:
Yang_SysBio_case_3
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: lung

value: UCSF


title: GS0084


title: R1B_res

tag: treatment

value: female


title: Nfat2 -/- -SNL 2

description: Gene expression of Nfat1 -/- -SNL


title: WT-SNL 2

description: Gene expression of WT-SNL 2

value: WT


title: Y22A_con

value: control


title: Z4B-6h-T47D-50-1

city: Shenzhen

first: Yan

last: Zhao

address: No. 1088,Xueyuandadao

department: BIology

institute: Southern University of Science and Technology

data_processing:
All sequencing data were aligned to the GRCh38 genome using the STAR package
Unique aligned reads were retained to obtain reads count matriceswith featureCounts
The Gene Transfer Format (GTF) file used for quantitative analysis is Ensembl release 90.
Genome_build: GRCh38
Supplementary_files_format_and_content: mRNA expression level generated by featureCounts

growth_protocol: Human cancer cells were purchased from ATCC. It was maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS) (gibco, #10270106) (v/v) in a CO2 incubator with 5% CO2. Culture media were also supplemented with 100IU/ml penicillin and 100lg/ml streptomycin gibco (Gibco #15070063). The culture meidum was replaced every other day. Cells at 70% confluence were used for all the assays.

extract_protocol:
Total RNA was extracted from the cells by Total RNA Extraction Reagent
Hieff NGS® MaxUp II Dual-mode mRNA Library Prep Kit for Illumina® MaxUp II

treatment_protocol: DMSO or Vinigrol(50uM) treatment 6 hrs in 4 cell lines

tag: cell line

value: vinigrol

tag: time

value: 6 hours


title: Z4B-6h-T47D-50-2


title: WT-SNL 1

description: Gene expression of WT-SNL 1

tag: tissue


title: case_2 mRNA-seq

description:
Yang_SysBio_case_2
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

tag: center

tag: dx

value: white

value: not hispanic or latino

value: Y


title: WT-Sham 1

description: Gene expression of WT-Sham 1

tag: age

value: sham


title: R8B_con

value: longissimus dorsi muscle

tag: Sex


title: Z4B-6h-T47D-0-2

value: DMSO


title: GS0089

value: peripheral blood


title: control_1 mRNA-seq

description:
Yang_SysBio_control_1
*** Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects. ***

value: Pittsburgh Lung Donor Core

value: normal

tag: rnaseqid

value: m

tag: race

value: N


title: R5A_con


title: GS0096


title: GS0098


title: MM300X Bromo+Cobi-2

city: San Francisoc

first: Mehdi

last: Nosrati

state: California

address: 475 Brannan, Suite 220

department: Research Institute

institute: California Pacific Medical Center

data_processing: The RNA-Seq data was aligned to the human reference genome (hg19) using the software STAR, followed by gene quantification in the software AltAnalyze to obtain gene-level RPKM values. Gene expression quantification (RPKM) was determined from exon-exon junctions and differential expression (fold>2, empirical Bayes moderated t-test p<0.05) was performed in AltAnalyze version 2.1.3 using the Ensembl 72 human database. Embedded gene-set enrichment analyses were performed using GO-Elite with default options.

source_name: NSG mice bearing tumors from the MM-300 PDX line were

growth_protocol: DMEM-F12, EGF (50ng/mL), FGF (50ng/mL), 1x B-27 and 1x penicllin/streptomycin

extract_protocol: RNA was extracted from tumor samples using Qiagen RNEasy RNA extraction kit

treatment_protocol: Tumor bearing mice were treated with Vehicle or Bromosporine + Cobimetinib combination

tag: cell type

value: melanoma

value: Treated with bromosporine and cobimetinib


title: Z4B-6h-T47D-0-1


title: Z4B-6h-ADR-50-2

source_name: ADR

value: ADR


title: W4

city: Hong Kong

first: Qiuyu

last: JING

state: Hong Kong

address: Room 6202C, Academic Building, The Hong Kong University of Science and Technology

department: Division of Life Science

country: Hong Kong

data_processing:
library strategy: metagenomics DNA sequencing library
Illumina Casava1.7 software used for basecalling.
Raw reads were first trimmed to 2x75bp using Cutadapt (version 1.18) and rarefied to 30M to ensure equal library size except for non-template controls due to its low input. Duplicates were then removed using PRINSEQ (version 0.20.4) in a paired-end mode with entropy-based strategy. The threshold of entropy was set as 20. Adapters and bases with quality lower than 20 were then trimmed using BBMap (version 35.74). Reads shorter than 25bp were discarded.
Quality-controlled reads were mapped to human reference GRCh38 downloaded from NCBI RefSeq database using Bowtie2 (version 2.2.6) in a very-sensitive mode. Duplicates were marked and removed using Picard Tools (version 2.18.7). Then both mapped and unmapped reads were extracted using SAMtools (version 1.3.1) for analysis of human fragments and microbial compositions respectively.
Mapped human bam files were firstly sorted using SAMtools (version 1.3.1) and then converted to bed files using BEDtools (version 2.15.0). Human autosome reference was segmented into 1-megabase non-overlap bins using BEDtools. Ratio of fragments of different length overlapped with each bin were calculated using custom script.
Genome_build: GRCh38
Supplementary_files_format_and_content: text file containg the number of fragments with different length within 1M bins across autosomes

organism: blank sample

source_name: Water control

extract_protocol:
cfDNA was extracted from plasma using QIAamp circulating nucleic acid kit (QIAGEN)
single-strand DNA library preparation with custom sequencing primers

treatment_protocol: Plasma was separated from blood by centrifugation

tag: group

value: NTC

tag: time point

value: Water control

tag: molecule type

value: cell-free DNA


title: MM300X Bromo+Cobi-3


title: W6

institute: The Hong Kong University of Science and Technology


title: Z4B-6h-ADR-50-1

value: vinigrol

value: 6 hours


title: GS0099

tag: disease state


title: WT-Sham 2

description: Gene expression of WT-Sham 2

value: Spinal cord

value: 8 week

value: male

tag: genotype

value: WT


title: W3


title: Z4B-6h-ADR-0-2

value: DMSO


title: W2


title: GS0100

value: peripheral blood


title: MM300X Vehicle-3

value: Untreated


title: GS0082


title: GS0078


title: MM300X Vehicle-2


title: MM300X Vehicle-1


title: Wr


title: Z4B-6h-231-50-2


title: GS0074


title: DM1173

value: TND


title: Z4B-6h-ADR-0-1


title: Z4B-6h-231-0-2


title: Z4B-6h-231-50-1


title: C_W


title: 2217_B_abseq

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

country: Denmark

institute: Aarhus University

library_source: transcriptomic single cell

data_processing:
The raw sequencing dData were processed on the Seven Bridges Genomics platform using the BD Rhapsody Targeted Analysis Pipeline. "reference.zip" were used as reference, including immune panel and abseq information.
Supplementary files format and content: expression of immune panel and abseq in one matrix; and VDJ information in another matrix

source_name: spleen

extract_protocol:
For single-cell mRNA and repertoire sequencing, total splenocytes were purified from spleens of two no-bridge chimeras as indicated under Tissue Harvest and Preparation, followed by negative selection with biotinylated Ter-119, anti-biotin microbeads and magnetic separation. For one bridge chimera, the spleen was split in half, and one half was subjected to the same total splenocyte purification whereas the other half was used for purification of GC B cells using a PNA microbead kit (130-110-479, Miltenyi Biotec) according to the manufacturer’s instructions, and the two fractions were mixed to generate a GC B cell enriched splenocyte sample.
From each sample, 1*10^6 cells were added 100 µl of AbSeq staining mix containing a cocktail of 20 Abseq antibodies, and incubated for 60 minutes. Cells were washed three times with 2 ml BD staining buffer (250 g for 8 minutes centrifugation) and for each sample, 20,000 cells were loaded onto a BD Rhapsody cartridge and processed on the Rhapsody Express module following the manufacturer’s instructions. Each sample was subsequently split into two (A and B) to be able to verify technical reproducibility, and each subsample was used for generation of 4 libraries: (1) single-cell targeted library using the Mouse Immune Response Panel (Catalog No. 633753, BD) containing primer pairs targeting 397 genes commonly found in mouse immune cells and a BD Rhapsody Panel supplement (Part number 633742, BD) containing an additional 45 target genes, for a total of 442 targets; (2) Abseq library; (3) BCR V(D)J library; and (4) TCR V(D)J library.

value: spleen

value: bridge' chimeras


title: BHTB rep2

city: Newcastle upon Tyne

first: Katherine

last: James

address: Urban Sciences Building

department: School of Computing

country: United Kingdom

institute: Newcastle University

data_processing:
Prinseq-lite  was used to filter and trim raw read data by quality using the following parameters: –min_qual_mean 20 -min_len 50 -ns_max_p 5 -trim_qual_left 20 -trim_qual_right 20 -trim_ns_left 1 -trim_ns_right 1 -trim_qual_type min -trim_qual_rule lt -trim_tail_left 10 -trim_tail_right 10 –lc_method dust –lc_threshold 7 -out_format 3
Trinity v2.2.0 was used to assemble a single reference assembly using both paired, and unpaired data with default kmer value (k=25), and retaining all contigs with a minimum length of 300bp to produce  a de novo transcriptomes.
In both cases, DETONATE v1.11 and Transrate v1.0.0  were applied to filter chimeric, fragmented, or locally misassembled transcripts.
The cd-hit-est algorithm were used to cluster isoforms at a similarity threshold of 95% over at least 50% length of the shortest sequence (-c 0.95 –aS 50).
Annotation was carried out with the Trinotate pipeline v 3.0.1. Contigs with blast e-values < 1 x 10-10. Contigs identified as bacterial were discarded.
Expression analyses were conducted via the pipeline packaged with Trinity v2.2.0; preprocessed read data were aligned to the references, Scan_de_novo.fasta, using the bowtie2 option, and the RSEM option was used to estimate transcript abundance.
Assembly: Scan_de_novo.fasta
Supplementary files format and content: De novo assembly text files of tab-delimited TPM and FPKM files for each transcript
Supplementary files format and content: De novo assembly matrix file of raw counts for all samples
Supplementary files format and content: Fasta file of the de novo assembled contigs produced by Trinity (Scan_de_novo.fasta)

organism: Scyliorhinus canicula

source_name: Dental lamina, dentition and oral epithelium

extract_protocol:
The dental lamina and associated oral epithelium of 9 embryonic stage (33) small spotted catshark (Scyliorhinus canicula) were dissected in PBS at 4°C. The epithelia was removed from the jaws and the remaining soft tissue (including teeth) was flash frozen in liquid N2 in aluminum foil envelopes. Frozen tissue was pulverized with a hammer and total RNA was extracted using the Trizol® method employing a Qiagen TissueLyser II to complete the dissociation. The resulting total RNA was further purified using the Qiagen RNeasy kit. Quality and quantity were assessed with the Agilent Tapestation High Sensitivity RNA Screen Tape and only samples with RIN values > 8.0 were processed for sequencing.
Libraries were prepared using the Truseq RNA library preparation kit v2 (2 x 100bp, unstranded) and sequenced in a pooled lane on a HiSeq2000 sequencer on high-throughput mode generating 132,470,224 reads and 12.32Gbp (average read length = 93bp).

value: Dental lamina; Oral epithelia

tag: developmental stage

value: Stage 33/34

tag: compartment

value: BHTB


title: DM0724


title: Z4B-6h-231-0-1

tag: cell line

tag: treatment


title: BHTB rep1

tag: tissue


title: TTJ rep3

value: TTJ


title: 2217_A_abseq


title: MM300X Bromo+Cobi-1

value: melanoma

value: Treated with bromosporine and cobimetinib


title: DM0741


title: BHTB rep3


title: 1760_B_abseq

value: no bridge' chimeras


title: W1

value: NTC

value: Water control

value: cell-free DNA


title: MCF7_vinnigrol_treatment_rep2_3'-mRNA-seq

data_processing:
All sequencing data were aligned to the GRCh38 genome using the HISAT2 package
Unique aligned reads were retained to obtain reads count matriceswith featureCounts
The Gene Transfer Format (GTF) file used for quantitative analysis is Ensembl release 90.
Genome_build: GRCh38
Supplementary_files_format_and_content: mRNA expression level generated by featureCounts

growth_protocol: Human breast cancer cells MCF7 were purchased from ATCC. It was maintained in 1640 medium supplemented with 10% fetal bovine serum (FBS) (gibco, #10270106) (v/v) in a CO2 incubator with 5% CO2. Culture media were also supplemented with 100IU/ml penicillin and 100lg/ml streptomycin gibco (Gibco #15070063). The culture meidum was replaced every other day. Cells at 70% confluence were used for all the assays.

extract_protocol:
Total RNA was extracted from the MCF7 cells by Total RNA Extraction Reagent
The Lexogen QuantSeq 3'mRNA-seq library kit was used to prepare the RNA-seq library in this study.

treatment_protocol: DMSO or Vinigrol(50uM) treatment 6 hrs in MCF7 cells

value: vinigrol

tag: time


title: DM1170


title: TTJ rep2


title: MCF7_DMSO_control_rep2_3'-mRNA-seq

value: DMSO


title: MCF7_vinnigrol_treatment_rep1_3'-mRNA-seq


title: TTJ rep1


title: 1027_B_abseq


title: MCF7_DMSO_control_rep1_3'-mRNA-seq


title: non-metastasis 3

city: Jinan

first: Jing

last: Hu

address: Wenhua xi road

department: Department of Pathology

institute: Shandong University

description: mirna expression profile

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human miRNA Microarrays (8*60K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Arrays were scanned using an Agilent Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um . Dye channel was set to Green and Green PMT is set to 100%.

data_processing: The generated image files were analyzed using Agilent Feature Extraction Software (v 11.0.1.1). Using GemeSpring v12.1 software(Agilent) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: non-metastasis 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA Extraction was perforemd using TRIZOL following the manufacturer's recommendations.

tag: disease

value: prostate cancer

tag: gleason

value: Gleason 3+4


title: SL rep3

value: SL


title: 1027_A_abseq

value: spleen


title: SL rep2


title: Ko7_3

city: Chongqing

first: Zhon-gyi

last: qin

address: Changjiang Road, Yuzhong District

department: Gastroenterology

institute: Daping Hospital, Army Military Medical University (Third Military Medical University)

description: repeat 3

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HiSat2 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

growth_protocol: Human undifferentiated gastric cancer cell line HGC-27 was cultured in 20%FBS RPIM-1640 media. The surviving population of cells was grown to ~80% confluence and passaged twice to ensure viability.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: gastric cancer cell line


title: Ko7_2

description: repeat 2


title: bone metastais 4

description: mirna expression profile

source_name: bone metastais 4


title: non-metastasis 1

description: mirna expression profile

source_name: non-metastasis 1


title: 1760_A_abseq


title: HGC27_Snail_3

description: repeat 3

value: Snail-/-


title: Ko7_1

description: repeat 1


title: SL rep1

value: Dental lamina; Oral epithelia

value: Stage 33/34


title: LT rep2

value: LT


title: HGC27_Snail_2

description: repeat 2


title: LT rep3


title: bone metastais 3

description: mirna expression profile

source_name: bone metastais 3


title: LT rep1


title: RV3

city: New Delhi

first: G Aneeshkumar

last: Arimbasseri

state: Delhi

address: Aruna Asaf Ali Marg

department: Molecular Genetics Laboratory

institute: National Institute of Immunology

data_processing:
FastQC
Alignment using Bowtie2
Counting using HT-Seq
Differential expression using DEseq2
Genome_build: Ensembl ASM19595v2
Supplementary_files_format_and_content: tabular.txt files with raw read counts as calculated by Htseq-count

source_name: Mycobacterium tuberculosis 7H9 broth

growth_protocol: Mtb strains were grown in 7H9 media supplemented with10% ADC (NaCl, dextrose, bovine serum albumin, and catalase) and 0.2% glycerol and 0.1% Tween 80)

extract_protocol:
Isolation of RNA was performed using TRIzol reagent (Ambion). Cells equivalent to 10 O.D. of Rv, Rv∆embR, and Rv∆embR::embRstrains were harvested and resuspended in TRIzol reagent. The cells were lysed using 0.1 mm zirconium beads, following which RNA was extracted through chloroform, precipitated, and washed using 70% Ethanol (prepared in DEPC-water). The RNA was resuspended in the nuclease-free water and further purified using the RNeasy mini kit (Qiagen). The samples were treated with DNase I to remove any leftover DNA traces.
TruSeq RNA Library Prep Kit v2

value: WT


title: bone metastais 2

description: mirna expression profile

source_name: bone metastais 2


title: bone metastais 1

description: mirna expression profile

source_name: bone metastais 1


title: HGC27_Snail_1

description: repeat 1


title: RV1


title: ET rep3

value: ET


title: non-metastasis 2

description: mirna expression profile

source_name: non-metastasis 2


title: ET rep2


title: MOH cells, fb-PMT (30 µM) Rep. 2

city: Rensselaer

first: Sridar

middle: V

last: Chittur

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: 16 h to Affymetrix Clariom S Human arrays

scan_protocol: Affymetrix Scanner 3000 7G using AGCC software.

data_processing: CEL files were summarized using the Gene Level-SST RMA algorithm in Transcriptome Analysis Console v4.0.1.36 (Affymetrix) and the normalized data were subjected to one-way ANOVA with a p-value less than 0.05 . A 2-fold change was used to select entities that were statistically and differentially expressed between any two conditions.

label: biotin

source_name: MOH fb-PMT (30 µM)

label_protocol: Affymetrix Whole Transcript Sense Target labeling protocol

growth_protocol: Human glioblastoma multiforme MOH cells (ATCC, Manassas, VA) were cultured in RPMI medium containing 10% FBS at 37°C and 5% CO2/95% O2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cells were treated with fb-PMT (30 µM) for 24 h. Control cells were exposed to PBS, pH 7.4, for the same period of time.

value: MOH

value: Human glioblastoma multiforme cells

value: fb-PMT


title: WT_3

description: repeat 3

value: BRD4+/+ and Snail+/+


title: WT_2

description: repeat 2


title: KO4

value: EmbR KO


title: SUIT2 cells, UNTREATED Rep. 2

source_name: SUIT2 cells, UNTREATED

growth_protocol: Human glioblastoma multiforme SUIT2 cells, cells (ATCC, Manassas, VA) were cultured in RPMI medium containing 10% FBS at 37°C and 5% CO2/95% O2.

value: Control


title: MOH cells, fb-PMT (30 µM) Rep. 1


title: SUIT2 cells, UNTREATED Rep. 1


title: KO6


title: Mesocricetus auratus cell infected with Senecavirus A, 72hrs, rep3, MeRIP

status: Public on Jun 30 2022

city: Qingdao City

first: Bo

last: Ni

state: Shandong Province

address: No.369 Nanjing Road

institute: China Animal Health And Epidemiology Center

description: S-F-IP

data_processing:
library strategy: meRIP-seq
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
Clean reads of all libraries were aligned to the reference genome  by Hisat2 software (v2.0.4)
Methylated sites on RNAs (peaks) were identified by MACS software
Assembly: MesAur1.0 (for Mesocricetus auratus) and KX751945.1 (for Senecavirus A)
Supplementary files format and content: XLS sheet "Gene Expression Profiling.xlsx" illustrated the raw counts(column B to column G) and normalized score(column H to column M, calculated by edgeR) of each transcripts from the input samples. Additional gene annotation information was also provided in column N to column Q.
Supplementary files format and content: XLS sheet "Methylated_RNA_sites.mRNA.xlsx" illustrated the m6A methylation sites information,  including m6A peak start site, peak stop site, peak ID, m6A peak score, peak length, generated by MACS software(see column B to column F). Additional statistical enrichment information and gene annotation information was also provided
Supplementary files format and content: BED files that illustrated the m6A peak start site, peak stop site, peak ID, m6A peak score, generated by MACS software.

organism: Mesocricetus auratus

extract_protocol:
Total RNA was subjected to immunoprecipitation with the GenSeq® m6A-IP Kit (GenSeq Inc.) by following the manufacturer’s instructions. Briefly, RNA was randomly fragmented to ~200 nt by RNA Fragmentation Reagents. Protein A/G beads were coupled to the m6A antibody by rotating at room temperature for 1 h. The RNA fragments were incubated with the bead-linked antibodies and rotated at 4°C for 4 h. After incubation, the RNA/antibody complexes were washed for several times, and then, captured RNA was eluted from the complexes and purified.
RNA libraries for IP and input samples were then constructed with GenSeq® Low Input Whole RNA Library Prep Kit(GenSeq, Inc.) by following the manufacturer’s instructions. Libraries were qualified using Agilent 2100 bioanalyzer and then sequenced in a NovaSeq platform (Illumina).

treatment_protocol: BSR-T7/5 cells were seeded into two 12-well plates (4×10^6 cells/well, and 3 wells/plate) to allow cell adhesion inside an incubator for 3 hours. Six cell monolayers were independently inoculated with the passage-5 SVA (multiplicity of infection = 1) for further culturing at 37 °C. These two 12-well plates were separately removed from the incubator at 12 and 72 hpi for microscopy observation. The group 12 hpi contained sample-A, -B and -C (S-A, -B and -C); the group 72 hpi contained sample-D, -E and -F (S-D, -E and -F).

value: Senecavirus A infection

value: 72hrs post infection


title: Mesocricetus auratus cell infected with Senecavirus A, 72hrs, rep2, input

description: S-E-input


title: Mesocricetus auratus cell infected with Senecavirus A, 72hrs, rep1, input

description: S-D-input


title: Mesocricetus auratus cell infected with Senecavirus A, 12hrs, rep3, input

description: S-C-input

value: 12hrs post infection


title: Mesocricetus auratus cell infected with Senecavirus A, 12hrs, rep2, MeRIP

description: S-B-IP


title: Mesocricetus auratus cell infected with Senecavirus A, 72hrs, rep1, MeRIP

description: S-D-IP


title: Mesocricetus auratus cell infected with Senecavirus A, 12hrs, rep2, input

description: S-B-input


title: Mesocricetus auratus cell infected with Senecavirus A, 12hrs, rep1, MeRIP

description: S-A-IP


title: Mesocricetus auratus cell infected with Senecavirus A, 72hrs, rep3, input

description: S-F-input


title: Mesocricetus auratus cell infected with Senecavirus A, 72hrs, rep2, MeRIP

description: S-E-IP


title: Mesocricetus auratus cell infected with Senecavirus A, 12hrs, rep1, input

description: S-A-input


title: ET rep1


title: Mesocricetus auratus cell infected with Senecavirus A, 12hrs, rep3, MeRIP

description: S-C-IP


title: MOH cells, UNTREATED Rep. 1

source_name: MOH UNTREATED


title: WT_1

description: repeat 1


title: SUIT2 cells, fb-PMT (30 µM) Rep. 2

source_name: SUIT2 cells, fb-PMT (30 µM)


title: SUIT2 cells, fb-PMT (30 µM) Rep. 1


title: MOH cells, UNTREATED Rep. 2


title: RNA-seq PARENTAL rep1

city: Rome

first: Antonella

last: Sistigu

state: Rome

address: Viale Francesco Vito, 1

department: Translational Medicine and Surgery

country: Italy

institute: University of Rome Tor VergataUniversità Cattolica del Sacro Cuore

description: Parental Stem Cells

data_processing:
Alignment: the ATAC-seq paired-end 42 bp sequencing reads generated by Illumina sequencing (using NextSeq 500) were mapped to the genome using the BWA MEM algorithm, version 0.7.17 , with default settings. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis.
Processing: duplicate reads (“PCR duplicates”) are removed.
Peak Finding: the peak caller used for ATAC-Seq at Active Motif is MACS 2.1.0, using both Paired End reads from each aligned fragment.
Determination of Fragment Density: to identify the density of transposition events along the genome, the genome is divided into 32 bp bins and the number of fragments in each bin is determined. For this purpose, reads are extended to 200 bp in order to smooth the data.
Normalization: in the default analysis, the tag number of all samples is reduced (by random sampling) to the number of tags present in the smallest sample.
Merged Region Analysis: to compare peak metrics between 2 or more samples, overlapping Intervals are grouped into “Merged Regions”, which are defined by the start coordinate of the most upstream Interval and the end coordinate of the most downstream Interval (= union of overlapping Intervals).
Annotations: After defining the Intervals and Merged Regions, their genomic locations along with their proximities to gene annotations and other genomic features are determined.
Alignment RNA-seq: the RNA-seq paired-end 42bp sequencing reads generated by Illumina sequencing (using NextSeq 500) were trimmed for adaptor sequence then mapped to the genome using STAR aligner, version 2.7.3a, with the following parameters: --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.06 --outFilterMultimapNmax 20 --seedSearchStartLmax 25 --sjdbScore 2 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --limitOutSJcollapsed 2000000 --limitSjdbInsertNsj 1500000 --outFilterType BySJout --outSAMmapqUnique 60 --outSAMattributes NH HI AS --limitBAMsortRAM 12000000000 --chimSegmentMin 10 --chimOutType WithinBAM SoftClip Junctions --chimJunctionOverhangMin 10 --chimScoreMin 1 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentReadGapMax 3 --quantMode TranscriptomeSAM --quantTranscriptomeBAMcompression 9
Read counts were calculated using featureCounts, version 2.0.0.
Genome_build: mm10
Supplementary_files_format_and_content: 3627Cattolica_ATAC_mergedregs.xlsx: excel file with all Merged Regions (genomic regions containing 1 or multiple overlapping intervals).
Supplementary_files_format_and_content: gene_counts.txt: tab-delimited text files include read count values for each Sample.

source_name: sarcoma cancer cells (MCA205)

growth_protocol: MCA205 PARENTAL mouse fibrosarcoma cell line was cultured in a Roswell Park Memorial Institute 1640 (RPMI 1640) growth medium supplemented with 10% (v/v) fetal bovine serum (FBS), 2 mM L-glutamine, 100 IU/mL penicillin G sodium salt and 100 µg/mL streptomycin sulfate.  FACS-sorted MCA205 CD44L and CD44 H IFN-CSCs were cultured in DMEM/F12-based culture medium was supplemented with 4 mg/mL bovine serum albumin (BSA), 1X Penicillin-Streptomycin-Amphotericin B (PSF), 0.13% NaHCO3, 6 mM Hepes, 2 mM L-glutamine, 0.1 mg/mL apotransferrin, 0.4 units heparin sodium salt, 1.1% glucose, 25 µg/mL insulin, 6.3 ng/mL progesterone, 9.7 µg/mL putrescine dihydrochloride, and 5.2 ng/mL sodium selenite and supplemented with 20 ng/mL human epidermal growth factor (EGF), 10 ng/mL human basic fibroblast growth factor (bFGF), and 10 mM nicotinamide. CSCs were passaged once/twice a week at dilution 1:2 by mechanical dissociation, through a micropipette, and incubated in standard culture conditions in ultra-low attachment tissue culture flasks.

extract_protocol:
ATAC-seq: 1 x 105 parental MCA205 cells and their IFN-CSC counterparts were treated with DNase I at 37°C for 30min. Cells were then washed and cryopreserved in culture medium containing FBS and 5% DMSO in 1,5 mL eppendorf microtubes. Cryopreserved cells were sent to Epigenetics Services Active Motif, Inc. (Carlsband, CA) to perform the ATAC-seq assay. Cells were thawed in a 37°C water bath, pelleted, washed with cold PBS, and tagmented. In details, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit. Tagmented DNA was then purified using the MinElute PCR purification kit, amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads. Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms, and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina). RNA-seq: 2.5 x 105 parental MCA205 cells and their IFN-CSC counterparts were harvested, washed and cryopreserved in 1,5 mL eppendorf microtubes. As above, RNA-seq analysis was performed by Epigenetics Services Active Motif, Inc. Total RNA was isolated from cells by using the RNeasy Mini Kit. For each sample, 2 µg of total RNA was then used in Illumina’s TruSeq Stranded mRNA Library kit.
Analysis of ATAC-seq data was performed as follows. Reads were aligned to the mouse genome (mm10) using the BWA algorithm. Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality ≥1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations. A peak re-calling strategy was used to reduce false positives. Analysis of RNA-seq: libraries were sequenced on Illumina NextSeq 500 as paired-end 42-nt reads. Sequence reads were analyzed with the STAR alignment – DESeq2, edgeR, limma-voom software pipelines.

treatment_protocol: To induce putative-CSCs (CD44H and CD44L IFN-CSCs), 1 x 105 MCA205 PARENTAL cells were cultured in 6-well plates in 2 mL of growth medium and treated 72h with purified mouse IFN-α/β (6000 U/mL)

value: Non-GMO. MCA-205 was derived from 3-methylcholanthrene-induced fibrosarcoma in C57BL/6 mice


title: RNA-seq CD44 HIGH rep2

description: CD133+ CD24+ CD44+ Cancer Stem Cells

source_name: FACS-sorted sarcoma cancer cells (MCA205)


title: ATAC-seq PARENTAL rep2

description: Parental Stem Cells


title: RNA-seq PARENTAL rep2

description: Parental Stem Cells


title: ATAC-seq CD44 HIGH rep1

description: CD133+ CD24+ CD44+ Cancer Stem Cells


title: ATAC-seq CD44 LOW rep1

description: CD133+ CD24+ CD44- Cancer Stem Cells


title: uninfected lung-Control LNA ASO rep3

city: Berkeley

first: Chi

last: Zhu

state: CA California

address: Morgan Hall, Rm238

department: Department of Nutritional Sciences & Toxicology

institute: University of California, Berkeley

description: Mice were treated with Saline or 400 ug LNA ASOs daily for three days

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome mm10 using STAR
Transcript abundance was calculated using Htseq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw count for each gene

source_name: uninfected lung-Control LNA ASO

extract_protocol:
lung lobes were collected 24 hrs after the last intranasal administration of Saline or LNA ASOs and tissues were lysed in DNA/RNA Shield (Zymo Research) and total RNA was extracted and cleaned by using RNeasy kit (Qiagen) according to the manufacturer’s protocol.
cDNA libraries were constructed from 500 ng of total RNA from lung tissues of mice according to the manufacturer’s protocol of Stranded mRNA-seq kit (KAPA). Briefly, mRNA was captured and fragmentized to 100~300 bp. library construction was performed undergoing end repair, A tailing, ligation of  unique dual-indexed adapters (KAPA) and amplification of 10 cycles to incorporate unique dual index sequences.

value: lung

tag: virus strain

value: No infection

tag: mouse strain

value: Control LNA ASO

tag: collection time

value: 24hrs after last treatment


title: ATAC-seq CD44 LOW rep2

description: CD133+ CD24+ CD44- Cancer Stem Cells


title: uninfected lung-Saline rep4

source_name: uninfected lung-Saline

value: Saline


title: RNA-seq CD44LOW rep1

description: CD133+ CD24+ CD44- Cancer Stem Cells


title: uninfected lung-Saline rep3


title: RNA-seq CD44 HIGH rep1

description: CD133+ CD24+ CD44+ Cancer Stem Cells


title: ATAC-seq CD44 HIGH rep2

description: CD133+ CD24+ CD44+ Cancer Stem Cells


title: uninfected lung-Saline rep1


title: RNA-seq CD44 LOW rep2

description: CD133+ CD24+ CD44- Cancer Stem Cells


title: uninfected lung-Saline rep2


title: M5_9: SARS-CoV-2-infected lung-5'-ASO#26 rep4

source_name: lung

extract_protocol:
lung lobes were collected at day 4 post-infection and tissues were lysed in DNA/RNA shield reagent (Zymo Research) and total RNA was extracted by using RNeasy kit (Qiagen) according to the manufacturer’s protocol.
cDNA libraries were constructed from 500 ng of total RNA from lung tissues of mice according to the manufacturer’s protocol of Stranded mRNA-seq kit (KAPA). Briefly, mRNA was captured and fragmentized to 100~300 bp. library construction was performed undergoing end repair, A tailing, ligation of  unique dual-indexed adapters (KAPA) and amplification of 10 cycles to incorporate unique dual index sequences.

value: Lung

value: SARS-CoV-2/WA1/2019 strain

value: LNA ASO

value: 4 days after infection


title: M5_6: SARS-CoV-2-infected lung-5'-ASO#26 rep1


title: M5_7: SARS-CoV-2-infected lung-5'-ASO#26 rep2


title: uninfected lung-Control LNA ASO rep1


title: M5_10: SARS-CoV-2-infected lung-5'-ASO#26 rep5


title: M5_2: SARS-CoV-2-infected lung-Saline rep2


title: M5_1: SARS-CoV-2-infected lung-Saline rep1


title: M5_8: SARS-CoV-2-infected lung-5'-ASO#26 rep3


title: uninfected lung-Control LNA ASO rep2


title: Somatic cell, secondary, rep40

status: Public on Jun 29 2022

city: Somerville

first: Daniela

middle: Dolores

last: Russo

state: Massachusetts

address: 5 Russell Rd

institute: Ragon Institute of MGH, MIT and Harvard

data_processing:
Raw sequencing data were demultiplexed and aligned to the GRCm38 genome using publicly available scripts on Terra (github.com/broadinstitute/TAG-public)
Cells expressing less than 500 genes were excluded from further analysis and genes were filtered to contain only those that were protein coding.
To filter for high-quality cells for each category, we utilized the AddModuleScore function in Seurat v4 (Hao et al., 2021) for scoring marker gene expression modules established from published datasets (Wang et al., 2020, Tharp et al., 2020, Zhang et al., 2018, Pangas et al., 2006) (Supplementary Table 1). Oocytes that scored highly for somatic cell gene expression (>2 standard deviations above the mean somatic cell module score) were removed. Similarly, somatic cells that scored highly for oocyte gene expression were also excluded.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated counts and tpm files

source_name: Somatic cell

extract_protocol:
Follicles were incubated in Accutase solution (Stemcell Technologies, Canada) (Zhang et al., 2018) until somatic cells partially detached from each other. Specifically, primordial and transitioning follicles were incubated in Accutase solution for 5 minutes, and primary and secondary follicles were incubated in Accutase solution for 10 minutes on 37 °C heated stage following agitation to dissociate somatic cells from the oocyte. Primordial and transitioning follicles were pipetted with 20 μm Pasteur pipet prepared by a micropipette puller (Sutter Instrument, CA, USA), primary follicle with a 30 μm Pasteur pipet and secondary follicle with a 50 μm stripper tip (Origio Inc.). Single cells were washed in three drops of 50 μL L-15/PVA with 100 μL/mL FBS.
scRNA-seq libraries were generated using SMART-Seq2 protocol (Trombetta et al., 2014). Briefly, cDNA was reversed transcribed from single cells using Maxima RT (Thermo Fisher Scientific) and whole transcriptome amplification (WTA) was performed. WTA products were purified using the Agencourt AMPure XP beads (Beckman Coulter, IN, USA) and used to prepare paired-end libraries with Nextera XT  (Illumina, CA, USA).

tag: cell type

value: Somatic cell


title: Somatic cell, secondary, rep39


title: M5_4: SARS-CoV-2-infected lung-Saline rep4


title: ATAC-seq PARENTAL rep1

description: Parental Stem Cells


title: M5_5: SARS-CoV-2-infected lung-Saline rep5


title: uninfected lung-Control LNA ASO rep4


title: Somatic cell, secondary, rep35


title: Somatic cell, secondary, rep29


title: Somatic cell, secondary, rep38


title: Somatic cell, secondary, rep27


title: Somatic cell, secondary, rep42


title: M5_3: SARS-CoV-2-infected lung-Saline rep3


title: Somatic cell, secondary, rep33


title: Somatic cell, secondary, rep36


title: Somatic cell, secondary, rep37


title: Somatic cell, secondary, rep34


title: Somatic cell, secondary, rep41


title: Somatic cell, secondary, rep31


title: Somatic cell, secondary, rep32


title: Somatic cell, secondary, rep30


title: Somatic cell, secondary, rep21


title: Somatic cell, secondary, rep22


title: Somatic cell, secondary, rep28


title: Somatic cell, secondary, rep25


title: Somatic cell, secondary, rep24


title: Somatic cell, secondary, rep18


title: Somatic cell, secondary, rep17


title: Somatic cell, secondary, rep16


title: Somatic cell, secondary, rep19


title: Somatic cell, secondary, rep20


title: Somatic cell, secondary, rep15


title: Somatic cell, secondary, rep12


title: Somatic cell, secondary, rep26


title: Somatic cell, secondary, rep14


title: Somatic cell, secondary, rep13


title: Somatic cell, secondary, rep8


title: Somatic cell, secondary, rep6


title: Somatic cell, secondary, rep5


title: Somatic cell, secondary, rep7


title: Somatic cell, secondary, rep3


title: Somatic cell, secondary, rep23


title: Somatic cell, primary, rep56


title: Somatic cell, secondary, rep4


title: Somatic cell, secondary, rep1


title: Somatic cell, primary, rep53


title: Somatic cell, primary, rep55


title: Somatic cell, primary, rep49


title: Somatic cell, primary, rep51


title: Somatic cell, primary, rep54


title: Somatic cell, primary, rep50


title: Somatic cell, primary, rep48


title: Somatic cell, secondary, rep11


title: Somatic cell, secondary, rep9


title: Somatic cell, primary, rep44


title: Somatic cell, primary, rep45


title: Somatic cell, primary, rep43


title: Somatic cell, primary, rep42


title: Somatic cell, secondary, rep2


title: Somatic cell, primary, rep41


title: Somatic cell, primary, rep39


title: Somatic cell, primary, rep40


title: Somatic cell, primary, rep38


title: Somatic cell, primary, rep52


title: Somatic cell, primary, rep37


title: Somatic cell, primary, rep34


title: Somatic cell, primary, rep33


title: Somatic cell, primary, rep35


title: Somatic cell, primary, rep31


title: Somatic cell, primary, rep36


title: Somatic cell, primary, rep46


title: Somatic cell, primary, rep32


title: Somatic cell, primary, rep29


title: Somatic cell, primary, rep30


title: Somatic cell, primary, rep47


title: Somatic cell, primary, rep27


title: Somatic cell, primary, rep28


title: Somatic cell, primary, rep26


title: Somatic cell, primary, rep25


title: Somatic cell, primary, rep24


title: Somatic cell, primary, rep23


title: Somatic cell, secondary, rep10


title: Somatic cell, primary, rep22


title: Somatic cell, primary, rep16


title: Somatic cell, primary, rep20


title: Somatic cell, primary, rep18


title: Somatic cell, primary, rep17


title: Somatic cell, primary, rep21


title: Somatic cell, primary, rep15


title: Somatic cell, primary, rep14


title: Somatic cell, primary, rep12


title: Somatic cell, primary, rep10


title: Somatic cell, primary, rep13


title: Somatic cell, primary, rep6


title: Somatic cell, primary, rep5


title: Somatic cell, primary, rep11


title: Somatic cell, primary, rep8


title: Somatic cell, primary, rep4


title: Somatic cell, primary, rep7


title: Somatic cell, primary, rep19


title: Somatic cell, primary, rep1


title: Somatic cell, transitioning to primary, rep45


title: Somatic cell, transitioning to primary, rep46


title: Somatic cell, transitioning to primary, rep43


title: Somatic cell, primary, rep2


title: Somatic cell, transitioning to primary, rep39


title: Somatic cell, transitioning to primary, rep47


title: Somatic cell, transitioning to primary, rep42


title: Somatic cell, transitioning to primary, rep44


title: Somatic cell, transitioning to primary, rep38


title: Somatic cell, transitioning to primary, rep40


title: Somatic cell, transitioning to primary, rep37


title: Somatic cell, primary, rep9


title: Somatic cell, transitioning to primary, rep36


title: Somatic cell, primary, rep3


title: Somatic cell, transitioning to primary, rep35


title: Somatic cell, transitioning to primary, rep30


title: Somatic cell, transitioning to primary, rep33


title: Somatic cell, transitioning to primary, rep29


title: Somatic cell, transitioning to primary, rep28


title: Somatic cell, transitioning to primary, rep41


title: Somatic cell, transitioning to primary, rep25


title: Somatic cell, transitioning to primary, rep27


title: Somatic cell, transitioning to primary, rep34


title: Somatic cell, transitioning to primary, rep23


title: Somatic cell, transitioning to primary, rep31


title: Somatic cell, transitioning to primary, rep24


title: Somatic cell, transitioning to primary, rep19


title: Somatic cell, transitioning to primary, rep26


title: Somatic cell, transitioning to primary, rep22


title: Somatic cell, transitioning to primary, rep21


title: Somatic cell, transitioning to primary, rep17


title: Somatic cell, transitioning to primary, rep16


title: Somatic cell, transitioning to primary, rep18


title: Somatic cell, transitioning to primary, rep15


title: Somatic cell, transitioning to primary, rep9


title: Somatic cell, transitioning to primary, rep14


title: Somatic cell, transitioning to primary, rep12


title: Somatic cell, transitioning to primary, rep32


title: Somatic cell, transitioning to primary, rep8


title: Somatic cell, transitioning to primary, rep13


title: Somatic cell, transitioning to primary, rep7


title: Somatic cell, transitioning to primary, rep11


title: Somatic cell, transitioning to primary, rep10


title: Somatic cell, transitioning to primary, rep6


title: Somatic cell, transitioning to primary, rep4


title: Somatic cell, transitioning to primary, rep3


title: Somatic cell, transitioning to primary, rep5


title: Somatic cell, transitioning to primary, rep1


title: Somatic cell, transitioning to primary, rep20


title: Somatic cell, primordial, rep38


title: Somatic cell, primordial, rep40


title: Somatic cell, primordial, rep39


title: Somatic cell, primordial, rep36


title: Somatic cell, primordial, rep35


title: Somatic cell, primordial, rep33


title: Somatic cell, primordial, rep32


title: Somatic cell, primordial, rep31


title: Somatic cell, primordial, rep30


title: Somatic cell, primordial, rep29


title: Somatic cell, primordial, rep28


title: Somatic cell, primordial, rep27


title: Somatic cell, primordial, rep26


title: Somatic cell, primordial, rep23


title: Somatic cell, primordial, rep24


title: Somatic cell, primordial, rep21


title: Somatic cell, primordial, rep19


title: Somatic cell, primordial, rep22


title: Somatic cell, transitioning to primary, rep2


title: Somatic cell, primordial, rep20


title: Somatic cell, primordial, rep37


title: Somatic cell, primordial, rep34


title: Somatic cell, primordial, rep17


title: Somatic cell, primordial, rep16


title: Somatic cell, primordial, rep14


title: Somatic cell, primordial, rep15


title: Somatic cell, primordial, rep12


title: Somatic cell, primordial, rep13


title: Somatic cell, primordial, rep10


title: Somatic cell, primordial, rep8


title: Somatic cell, primordial, rep6


title: Somatic cell, primordial, rep9


title: Somatic cell, primordial, rep5


title: Somatic cell, primordial, rep11


title: Somatic cell, primordial, rep1


title: Somatic cell, primordial, rep2


title: Somatic cell, primordial, rep3


title: Somatic cell, primordial, rep7


title: Somatic cell, primordial, rep18


title: Oocyte, secondary, rep7

source_name: Oocyte

value: Oocyte


title: Oocyte, secondary, rep3


title: Oocyte, secondary, rep2


title: Oocyte, secondary, rep6


title: Oocyte, primary, rep19


title: Oocyte, secondary, rep1


title: Oocyte, primary, rep20


title: Oocyte, secondary, rep5


title: Somatic cell, primordial, rep25


title: Oocyte, primary, rep18


title: Oocyte, primary, rep17


title: Somatic cell, primordial, rep4


title: Oocyte, primary, rep15


title: Oocyte, primary, rep16


title: Oocyte, secondary, rep4


title: Oocyte, primary, rep10


title: Oocyte, primary, rep11


title: Oocyte, primary, rep13


title: Oocyte, primary, rep14


title: Oocyte, primary, rep12


title: Oocyte, primary, rep8


title: Oocyte, primary, rep6


title: Oocyte, primary, rep5


title: Oocyte, primary, rep7


title: Oocyte, primary, rep3


title: Oocyte, primary, rep2


title: Oocyte, primary, rep1


title: Oocyte, transitioning to primary, rep19


title: Oocyte, transitioning to primary, rep18


title: Oocyte, transitioning to primary, rep17


title: Oocyte, transitioning to primary, rep13


title: Oocyte, transitioning to primary, rep16


title: Oocyte, transitioning to primary, rep15


title: Oocyte, transitioning to primary, rep14


title: Oocyte, transitioning to primary, rep12


title: Oocyte, transitioning to primary, rep10


title: Oocyte, primary, rep9


title: Oocyte, transitioning to primary, rep9


title: Oocyte, transitioning to primary, rep11


title: Oocyte, transitioning to primary, rep7


title: Oocyte, transitioning to primary, rep5


title: Oocyte, transitioning to primary, rep8


title: Oocyte, transitioning to primary, rep4


title: Oocyte, transitioning to primary, rep6


title: Oocyte, primary, rep4


title: Oocyte, transitioning to primary, rep1


title: Oocyte, primordial, rep11


title: Oocyte, primordial, rep12


title: Oocyte, transitioning to primary, rep2


title: Oocyte, primordial, rep13


title: Oocyte, transitioning to primary, rep3


title: Oocyte, primordial, rep6


title: Oocyte, primordial, rep7


title: Oocyte, primordial, rep10


title: Oocyte, primordial, rep9


title: Oocyte, primordial, rep5


title: Oocyte, primordial, rep3


title: Oocyte, primordial, rep4


title: Oocyte, primordial, rep8


title: Oocyte, primordial, rep2


title: Group C - Patient 2-Feature

city: Stanford

first: Han

state: CA

address: G1105, 265 Campus Drive

department: Cardiovascular Medicine

institute: Stanford University

description:
CITE-seq data
Processed data included on GSM5449982:
MCE2-filtered_feature_bc_matrix.tar
MCE2-Feature

data_processing:
Library strategy: CITE-seq
Raw single-cell RNA-seq data were processed using 10x Genomics Cell Ranger (4.0.3) to demultiplex the FASTQ reads in order to align them to the human reference genome (GRCh38, v4.0.0, from 10X Genomics) and count the unique molecular identifier (UMI) (through the “cellranger count” function).
Raw T cell receptor (TCR) sequencing data were processed using 10x Genomics Cell Ranger (v4.0.3). In summary, the algorithm aligned FASTQ reads to human GRCh38 V(D)J reference genome (v4.0.0, from 10X Genomics) by using the “cellranger vdj” function, resulting in the assembly of V(D)J sequences and clonotypes (38).
Individual sample gene expression matrices were loaded into Seurat v4.0.0 R package (https://satijalab.org/seurat/) for further analysis.
To filter out poor quality data from cells with high mitochondrial gene expression likely to be dead/damaged cells (59), we removed cells with greater than >15% mitochondrial genes present (60). Additionally, we removed cells for which less than 500 genes were detected.
Genome_build: h38
Supplementary_files_format_and_content: Cell Ranger output

source_name: Human PBMCs

extract_protocol:
Frozen PBMCs were removed from liquid nitrogen and resuspended in warm RPMI media + 10% FBS (@ 37ºC) by adding 1 mL, 3 mL, 4 mL, 8 mL 16 mL media at 30-60 second intervals. Cells were washed and passed through a 40 um filter, centrifuged @ 300 rcf x 5 min and resuspended in PBS with 50 ul 1% BSA and Biolegend Fc Receptor Blocking Solution (Human TrueStain FcX (Cat. No. 422301) for 20 minutes. Afterwards, another 50 uL of antibody mastermix containing Biolegend TotalSeq-C antibodies for staining (Biolegend TotalSeq™-C0063 anti-human CD45RA Antibody Cat. No. 304163; Biolegend TotalSeq™-C0072 anti-human CD4 Antibody Cat. No. 300567; Biolegend TotalSeq™-C0046 anti-human CD8 Antibody Cat. No. 344753) for final manufacture-recommended concentration of 1.0 ug of antibody in 100 ul of staining buffer for every 1 million cells for a total of 10-15 minutes incubation. After incubation, cells were washed 2x by resuspending in 1.5 mL PBS + 1% RNase-free BSA (MACS BSA Stock Solution No. 130-091-376) and then 1 mL PBS + 0.04% BSA. 10 uL of cell suspension was then taken for counting and appropriate volume of PSA + 0.04% BSA was added (200-500 uL) to aim for final target concentration of 1 million cells/mL). Cells were then loaded into Chromium Next GEM Chip G (10x PN 2000177) to achieve 6000-8000 target cell recovery per sample according to the manufacture’s protocol.
All steps from cDNA isolation to library preparation were completed according to 10x’s manufacturing protocols for the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1. Isolated cDNA was amplified (14 cycles), and then cDNA was allocated for TCR enrichment, feature barcode library generation, and 5’ cDNA library generation. cDNA and library quality was evaluated using the high sensitivity DNA kit on the Agilent 2100 Bioanalyzer.

value: Blood

value: PBMC

value: Immune Checkpoint Inhibitor

value: Myocarditis irAE

tag: molecule subtype

value: Surface Protein Feature Barcode Sequence


title: Group C - Patient 1 Early-Feature

description:
CITE-seq data
Processed data included on GSM5449981:
MCE1-filtered_feature_bc_matrix.tar
MCE1-Feature


title: Group C - Patient 1 Late-Feature

description:
CITE-seq data
Processed data included on GSM5449984:
MCL1-filtered_feature_bc_matrix.tar
MCL1-Feature


title: Group B - Patient 3-Feature

description:
CITE-seq data
Processed data included on GSM5449980:
B3-filtered_feature_bc_matrix.tar
B3-Feature

value: Non-Myocarditis irAE


title: Group A - Patient 3-Feature

description:
CITE-seq data
Processed data included on GSM5449976:
A3-filtered_feature_bc_matrix.tar
A3-Feature

value: No irAE


title: Group B - Patient 2-TCR

description:
single-cell TCR seq
B2-TCR

data_processing:
Library strategy: TCR-seq
Raw single-cell RNA-seq data were processed using 10x Genomics Cell Ranger (4.0.3) to demultiplex the FASTQ reads in order to align them to the human reference genome (GRCh38, v4.0.0, from 10X Genomics) and count the unique molecular identifier (UMI) (through the “cellranger count” function).
Raw T cell receptor (TCR) sequencing data were processed using 10x Genomics Cell Ranger (v4.0.3). In summary, the algorithm aligned FASTQ reads to human GRCh38 V(D)J reference genome (v4.0.0, from 10X Genomics) by using the “cellranger vdj” function, resulting in the assembly of V(D)J sequences and clonotypes (38).
Individual sample gene expression matrices were loaded into Seurat v4.0.0 R package (https://satijalab.org/seurat/) for further analysis.
To filter out poor quality data from cells with high mitochondrial gene expression likely to be dead/damaged cells (59), we removed cells with greater than >15% mitochondrial genes present (60). Additionally, we removed cells for which less than 500 genes were detected.
Genome_build: h38
Supplementary_files_format_and_content: Cell Ranger output

value: Total TCR sequences


title: Group A - Patient 1-TCR

description:
single-cell TCR seq
A1-TCR


title: Group A - Patient 2-TCR

description:
single-cell TCR seq
A2-TCR


title: Group C - Patient 2-TCR

description:
single-cell TCR seq
MCE2-TCR


title: Group A - Patient 2-Feature

description:
CITE-seq data
Processed data included on GSM5449975:
A2-filtered_feature_bc_matrix.tar
A2-Feature


title: Group A - Patient 1-Feature

description:
CITE-seq data
Processed data included on GSM5449974
A1-filtered_feature_bc_matrix.tar
A1-Feature


title: Group B - Patient 1-TCR

description:
single-cell TCR seq
B1-TCR


title: Group B - Patient 1-Feature

description:
CITE-seq data
Processed data included on GSM5449978:
B1-filtered_feature_bc_matrix.tar
B1-Feature


title: Group C - Patient 1 Early-TCR

description:
single-cell TCR seq
MCE1-TCR


title: Group B - Patient 3-TCR

description:
single-cell TCR seq
B3-TCR


title: Group A - Patient 3-TCR

description:
single-cell TCR seq
A3-TCR


title: Group C - Patient 3-TCR

description:
single-cell TCR seq
MCL3-TCR


title: Oocyte, primordial, rep1


title: Group B - Patient 3

description:
scRNA-seq data
B3

data_processing:
Raw single-cell RNA-seq data were processed using 10x Genomics Cell Ranger (4.0.3) to demultiplex the FASTQ reads in order to align them to the human reference genome (GRCh38, v4.0.0, from 10X Genomics) and count the unique molecular identifier (UMI) (through the “cellranger count” function).
Raw T cell receptor (TCR) sequencing data were processed using 10x Genomics Cell Ranger (v4.0.3). In summary, the algorithm aligned FASTQ reads to human GRCh38 V(D)J reference genome (v4.0.0, from 10X Genomics) by using the “cellranger vdj” function, resulting in the assembly of V(D)J sequences and clonotypes (38).
Individual sample gene expression matrices were loaded into Seurat v4.0.0 R package (https://satijalab.org/seurat/) for further analysis.
To filter out poor quality data from cells with high mitochondrial gene expression likely to be dead/damaged cells (59), we removed cells with greater than >15% mitochondrial genes present (60). Additionally, we removed cells for which less than 500 genes were detected.
Genome_build: h38
Supplementary_files_format_and_content: Cell Ranger output

value: Total RNA


title: Group C - Patient 2

description:
scRNA-seq data
MCE2


title: Group C - Patient 1 Late-TCR

description:
single-cell TCR seq
MCL1-TCR


title: Group C - Patient 3-Feature

description:
CITE-seq data
Processed data included on GSM5449985:
MCL3-filtered_feature_bc_matrix.tar
MCL3-Feature


title: Group C - Patient 1 Late

description:
scRNA-seq data
MCL1


title: Group A - Patient 3

description:
scRNA-seq data
A3


title: Group B - Patient 2

description:
scRNA-seq data
B2


title: Group C - Patient 1 Early

description:
scRNA-seq data
MCE1


title: Group B - Patient 2-Feature

description:
CITE-seq data
Processed data included on GSM5449979:
B2-filtered_feature_bc_matrix.tar
B2-Feature


title: Group B - Patient 1

description:
scRNA-seq data
B1


title: Group C - Patient 3

description:
scRNA-seq data
MCL3


title: CUTRUN_H3K4me3_PRC1ctrl_rep2

status: Public on Jun 26 2022

city: Davis

first: Satoshi

last: Namekawa

address: One Shields Avenue

institute: UC Davis

data_processing:
Library strategy: CUT&RUN
Raw RNA-seq reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.6) with the parameter ‘--paired’ were aligned to the mouse (GRCm38/mm10) genome using HISAT2(38) (version 2.2.1) with default parameters.  All unmapped reads, non-uniquely mapped reads, reads with low mapping quality (MAPQ < 30) were filtered out by samtools(39) (version 1.9) with the parameter '-q 30' before being subjected to downstream analyses.  To identify differentially expressed genes in RNA-seq, raw read counts for each gene were generated using htseq-count function, part of the HTSeq package (40) (version 1.6.0) based on the mouse gene annotation (gencode.vM24.annotation.gtf, GRCm38/mm10). DESeq2 (41) (version 1.28.1) was used for differential gene expression analyses with cutoffs FC > 2  and Padj value < 0.05. The TPM values of each gene were generated using RSEM (42)(version 1.3.3) for comparative expression analyses and computing the Pearson correlation coefficient between biological replicates.
For CUT&RUN data processing, we basically followed the online tutorial posted by Henikoff Lab (https://protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-bjk2kkye.html). Briefly, raw paired-end reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.6) were aligned mouse (GRCm38/mm10) genome using Bowtie2(44) (version 2.4.2) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. E. coli DNA carried along with bacterially-produced pAG-MNase protein brings along a fixed amount of E. coli DNA and can be used as spike-in DNA.  For mapping E.coli spike-in fragments, we also use the --no-overlap --no-dovetail options to avoid cross-mapping. PCR duplicates were removed from low-cell-number data using the ‘MarkDuplicates’ command in Picard tools (version 2.23.8) (https://broadinstitute.github.io/picard/ ).  To compare replicates, Pearson correlation coefficients were calculated and plotted by multiBamSummary bins and plot correlation from deepTools(45) (version 3.5.0).  Biological replicates were pooled for the visualization and other analyses after validation of the reproducibility (Pearson correlation coefficient > 0.85).  Spike-in normalization was implemented using the exogenous scaling factor computed from the E.coli mapping files (the formula used for calculation of scaling factors = 1/ (spike-in reads/100,000)).  For visualization of CUT&RUN using the Integrative Genomics Viewer(46) (version 2.5.3), spike-in normalized genome coverage tracks were generated using genomecov function of bedtools(47) (version 2.29.2) with ‘-bg -scale $scale_factor’ parameter. SEACR (48) (https://seacr.fredhutch.org/ ) was used for peak calling. The program ngs.plot(49) (version 2.63) was used to draw tag density plots and heatmaps for read enrichments.  The FPKM values of each gene’s promoter region (TSS±2kb) were generated using Bamscale package (50)(version 0.0.5) for comparative expression analyses.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample from RNA-seq analyses.bedgraph files were generated using bedtools; Scores represent spike-in normalized read counts.

source_name: CUTRUN

extract_protocol: CUT&RUN libraries of PRC1ctrl, PRC1cKO, and stella-GFP oocytes were conducted as previously described(30).  ~500 non-growing oocytes isolated from P1 ovaries were pooled as one replicate, and two independent biological replicates were used for CUT&RUN library generation.  The antibodies used were rabbit anti-H2AK119ub1 (1/100; Cell Signaling Technology; 8240), rabbit anti-H3K4me3 (1/100; Cell Signaling Technology; 9751), and rabbit anti-H3K27me3 antibody (1/100; Cell Signaling Technology; 9733).  Libraries were constructed using NEBNext® Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S).  Prepared CUT&RUN libraries were sequenced on the NovaSeq 6000 system (Illumina) with paired-ended 100-bp or 50-bp reads.

tag: strain

value: C57BL/6 X FVB/NJ

value: ovary

tag: age

value: post natal day 1

value: Ring1-/-; Rnf2F/+; Ddx4-Cre

tag: cut&run antibody