title: AD_6

tag: strain


title: F741, Spinal, TL, Naive, 1w

status: Public on May 31 2022

type: SRA

city: Baltimore

first: Evelina

last: Mocci

state: MD

address: 655 W Lombard S

department: PTSS

country: USA

institute: SON

library_source: transcriptomic

data_processing:
We used FastQC and Trimmomatic  tools for evaluating the quality of the sequences, next we used HISAT2  software to align the sequences to the reference Rattus norvegicus (Norway rat) genome assembly Rnor_6.0 (rn6) from Rat Genome Sequencing Consortium [GCA_000001895.4 GCF_000001895.5]. Finally, gene expression was estimated using HTSeq(18) which considers a gene as the union of all exons regardless of the isoform and excludes reads that overlap multiple genes
Genome_build: rn6
Supplementary_files_format_and_content: batch effect corrected expression data have been uploaded to https://nemoanalytics.org/p?s=2f41a962

molecule: total RNA

organism: Rattus norvegicus

source_name: spinal

extract_protocol:
RNA was extracted from 4 type of tissues, including blood, colon, spinal, and dorsal root ganglia (DRG) at one week (week 1) and seven weeks (week 7) after the induction of stress
Libraries were prepared with NEB Ultra II Directional Library Prep kits. Samples at week 1 were sequenced on Illumina HiSeq 4000 platform using a 150 bp paired-end run (2 ´ 150), while samples at week7 were run on Illumina NovaSeq 6000 using a 150 bp paired-end run as well

treatment_protocol:
treatment protocol for stress (SIH). During the two hours, rats were tilted at a 45-degree angle head up or head down in 15 min blocks alternating with 15 min blocks in the horizontal position. The day after the last restraint session was designated Day 1
Rats were restrained in Broome style rodent restrainers (4.8 cm diameter, 20 cm length) preventing movement for 2 hours per day for 4 consecutive days
treatment protocol for comorbid rats. Masseter muscle inflammation: One day prior to starting the stress protocol, CPH rats were briefly sedated with isoflurane, and CFA (SigmaAldrich, F5881; 150 mL per side, 1:1 in saline) was injected bilaterally into the masseter muscles. This protocol (CFA+stress) produces the comorbid pain condition. We previously reported that saline injection into the masseter muscle followed by stress was similar to stress alone and CFA injection without stress did not induce visceral hypersensitivity

tag: Sex

value: female

tag: time

tag: tissue

value: spinal

tag: ID

tag: experimental group

value: Naive


title: 05_AD_23_NL

city: Copenhagen

first: Tu

last: Hu

address: 5 Artillerivej

department: Infectious Disease Immunology

country: Denmark

institute: Statens Serum Institut

data_processing:
Library strategy: BRB-Seq
Each BRB batch fastq file was demultiplexed using BRB-seq tool 1.6.0 Demultiplex function
To generate the count matrix, BRB-seq data was mapped by aligning reverse reads to human reference genome (GRCh38.105) by STAR(2.7.9a), then de-multiplexing by the forward read barcoding using BRB-seq tool 1.6.0.
Only expressed genes (mean count  > 1 across 80% samples) were included in the count matrix.
Assembly: human reference genome (GRCh38.105)
Supplementary files format and content: csv; The first column, gene_name, is the standard gene symbol (HGNC or MGI-approved gene symbols; if no official gene symbol exists, Havana clone-based name is used). The remaining columns contain the gene counts for each sample.

organism: Homo sapiens

source_name: skin

extract_protocol:
Total RNA was extracted from tape 5 to 8 from each skin site (RNAqueous, Life technologies) followed by digestion with DNase I.
Multiplexed cDNA libraries were generated using the BRB-seq workflow (Alpern et al. Genome Biology 2019;20:71.)

tag: visit

tag: group

value: AD

value: NL

tag: gender

tag: scorad

value: arm

value: skin


title: AD_4

city: Ultimo

first: Alison

last: Ricafrente

state: New South Wales

address: 15 Broadway

department: School of Life Sciences

country: Australia

institute: University of Technology Sydney

data_processing:
Sequenced reads were trimmed for adaptor sequences, masked for low quality reads and reads < 18 nt long
Cleaned reads were mapped to mature miRNA sequences of Fasciola hepatica derived from miRBase version 21 repositorry [Fhepatica_v1] and other published miRNAs featured in Ricafrente et al. 2021 using Bowtie version 1.3.0
Cleaned reads were analysed for novel miRNAs using MiRDeep2 (version 2.0.1.2) facilitated by inputs including F.hepatica genome (PRJEB25283); and reference mature miRNAs from F.hepatica miRBase repository [Fhepatica_v1] and other published miRNAs featured in Ricafrente et al. 2021, Schistosoma japonicum miRBase respository (ASM15177v1), Schistosoma mansoni miRBase repository (WTSI5) and  Caenorhabditis elegans miRBase respository(WBcel235)
Combined read counts of known/published and novel Fasciola hepatica miRNAs were normalised to counts per million (CPM)
Genome_build: F.hepatica genome (PRJEB25283)
Supplementary_files_format_and_content: Format is txt file tab delimited and contains raw read counts of Fasciola hepatica miRNAs of interest.

organism: Fasciola hepatica

source_name: Adult

extract_protocol:
Total RNA was extracted from the three F. hepatica life stages in triplicate using the miRNeasy mini kit (Qiagen) according to the manufacturer’s instructions, in a final elution of 50µl RNase-free water
Total RNA of each sample was used to prepare the miRNA sequencing library. After the completed libraries were quantified with Agilent 2100 Bioanalyzer, the DNA fragments in the libraries were denatured with 0.1M NaOH to generate single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ and finally sequenced for 51 cycles on Illumina NextSeq 500 according to the manufacturer’s instruction.The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 51 cycles on Illumina NextSeq per the manufacturer’s instructions.

value: Italian isolate

tag: time point

value: hepatic infection

value: Total tissue homogenisation


title: F741, Spinal, LS, Naive, 1w


title: 05_AD_12_LS

value: LS

value: leg


title: hs_GF_ASC_hnRNPA2B1_Sub3

city: orlando

first: Adeline

last: Divoux

state: FL

address: 301 E. Princeton St

department: Translational Research Institute

institute: Adventhealth

description: Subject3 hnRNPA2B1

library_source: genomic

data_processing:
Raw reads were aligned with Burrows-Wheeler Alignment (BWA) tool (v07.10)
BAM files were generated and filtered with SAMtools (v0.1.19)
To remove the artifacts from the predicted peaks, we used the blacklisted genomic regions of the Encyclopedia of DNA Elements (ENCODE)
Coverage (bigwig) files were created by bamCoverage in the deepTools program. RPKM normalisation was used.
Assembly: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: GF (gluteofemoral) adipose tissue

growth_protocol: Adipose–derived stem cells were cultured in aMEM medium (Gibco) supplemented with 2.5% FBS, EGF and FGF.

extract_protocol:
Fat biospsies were collected and SVF were isolated by centrifugation. Lysates were clarified from sonicated nuclei and hnRNPA2B1-chromatin complexes were isolated with antibody (Novus Biologicals NB120-6102).  DNA was purified with MinElute PCR Purification Kit (Qiagen).
ChIP-seq  libraries were prepared and sequenced using standard Illumina protocols for NovaSeq 6000 instrument with PE150.

value: GF (gluteofemoral) adipose tissue

tag: cell line

value: hASCs

tag: cell type

value: human adipose derived stem cells

tag: treatment

tag: chip antibody

value: hnRNPA2B1 (Novus Biologicals NB120-6102)


title: hs_GF_ASC_hnRNPA2B1_Sub4

description: Subject4 hnRNPA2B1


title: JUV_3

source_name: Juveniles

value: 21 d post infection


title: 05_AD_16_LS

value: male


title: 05_AD_02_NL

value: female


title: hs_GF_ASC_hnRNPA2B1_Sub2

description: Subject2 hnRNPA2B1


title: F741, Spinal, C, Naive, 1w

value: spinal

value: Naive


title: JUV_2


title: 05_AD_02_LS

value: AD


title: CAPAN-2 cells, SIRT4-3

city: Jinan

first: chuanxin

last: wang

address: 247 Beiyuan Street, Jinan 250033, Shandong, China,

country: China

institute: The Second Hospital of Shandong University

data_processing:
clean reads were aligned to the reference genome (hg38) with STAR
Read counts to each genomic feature were obtained with FeatureCounts from subread
The raw counts were normalized with DESeq2, followed by differential expression analysis with DESeq2.
Assembly: hg38
Supplementary files format and content: raw count

source_name: pancreatic cancer cell line

extract_protocol:
Total RNAs extracted from cells were using Trizol reagent.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)

tag: genotype

value: SIRT4 overexpression


title: F741, DRG, Naive, 1w

source_name: DRG

value: DRG


title: 05_AD_12_NL

value: NL

value: skin


title: 04_CO_46_HC

value: CO

value: HC

value: arm


title: hs_GF_ASC_hnRNPA2B1_Sub1

description: Subject1 hnRNPA2B1

value: GF (gluteofemoral) adipose tissue


title: 04_CO_56_HC


title: F741, COLON, P, Naive, 1w

source_name: colon

value: colon


title: NEJ_3

source_name: Newly excysted juveniles

value: Italian isolate

value: 24 hr post excystment

value: Total tissue homogenisation


title: F741, COLON, D, Naive, 1w


title: NEJ_2


title: NEJ_1


title: 04_CO_45_HC


title: CAPAN-2 cells, ctrl-3

value: control without SIRT4 overexpression


title: CAPAN-2 cells, SIRT4-1


title: F741, blood, Naive, 1w

source_name: blood

value: female

value: blood


title: 04_CO_43_HC


title: F740, Spinal, TL, Naive, 1w

value: spinal

value: Naive


title: CAPAN-2 cells, ctrl-2


title: 04_CO_33_HC


title: CAPAN-2 cells, ctrl-1


title: 04_AD_25_NL

value: AD

value: male


title: CAPAN-2 cells, SIRT4-2

value: SIRT4 overexpression


title: 04_AD_25_LS

value: LS

value: skin


title: F740, Spinal, LS, Naive, 1w


title: 04_AD_22_LS

value: leg


title: F740, Spinal, C, Naive, 1w


title: H460 cells,ISP-I (10μM) treatment for 48h,rep2

city: Shanghai

first: Tao

last: Ren

address: No. 600, Yi Shan Road

institute: Shanghai Jiao Tong University Affiliated Sixth People's Hospital

data_processing:
Illumina Novaseq 6000 system was used to generate 150bp pair-end reads
The reads, filtered by FastQC, were mapped to human genome (hg38) using HISAT2 software.
Read counts were calculated using HTSeq v0.9.1 and output as FPKM upon normalization.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA extraction from non-treated as well as ISP-I treated NSCLC cells (3 replicates per group) was done by TRIzol reagent (Invitrogen, Carlsbad, CA, USA)and RNeasy Mini Kit (Qiagen, Valencia, CA, USA). The concentrations, quality as well as integrity of extracted RNA were assessed by NanoDrop spectrophotometry (Thermo Scientific).
Sequencing libraries were constructed by TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA)

value: Human NSCLC cell lines

value: WT

value: ISP-I (10uM) treatment for 48h


title: H460 cells,ISP-I (10μM) treatment for 48h,rep3


title: 04_AD_15_NL

value: NL

value: arm


title: F740, COLON, M, Naive, 1w

value: colon


title: H460 cells,ISP-I (10μM) treatment for 48h,rep1


title: F740, COLON, P, Naive, 1w


title: F740, COLON, D, Naive, 1w


title: F740, DRG, Naive, 1w

value: DRG


title: F741, COLON, M, Naive, 1w

value: female


title: 04_AD_13_NL


title: A549 cells,ISP-I (10μM) treatment for 48h,rep3


title: F739, Spinal, TL, SIH, 1w

value: SIH


title: H460 cells,non-treated,rep1

value: non-treated


title: F739, Spinal, LS, SIH, 1w

value: spinal


title: 04_AD_13_LS

value: AD


title: H460 cells,non-treated,rep2


title: 04_AD_12_NL


title: A549 cells,ISP-I (10μM) treatment for 48h,rep2


title: 04_AD_22_NL

value: male


title: F739, Spinal, C, SIH, 1w


title: A549 cells,ISP-I (10μM) treatment for 48h,rep1


title: 04_AD_12_LS


title: H460 cells,non-treated,rep3


title: JUV_1

value: Italian isolate

value: 21 d post infection

value: Total tissue homogenisation


title: 04_AD_15_LS

value: LS

value: skin


title: 04_AD_06_NL


title: PS-ac-2

type: RNA

city: Duarte

first: Yi-Jia

last: Li

address: 1500 E Duarte Rd

institute: Beckman Research Institute at City of Hope Cancer Center

description: treatment

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions.
For the normalization it uses the average of three housekeeping genes: HPRT1, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
Excel software was used to perform all deltadeltaCt based fold-change calculations from  raw cycle data.

label: SYBR green

source_name: breast cancer cells

label_protocol: PCR assays were performed using Human Fatty Acid and Lipid Metabolism Primer Library (HFLM-1; Realtimeprimers.com) following the Manufacturer’s instructions. Reverse transcription was performed from 1000 ng total RNA using iScript cDNA synthesis kit (1708891; Bio-Rad). Quantitative real-time PCR were performed (CFX96, Bio-Rad) with 45 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

growth_protocol: 5 millions of MDA-MB-231-R cells were injected into mammary fat pads of female NSG mice.

extract_protocol: RNA was isolated from pooled tumor tissues (n=4) by using RNeasy Plus Kits (Qiagen)

treatment_protocol: When tumors reached an average size of 80-100 mm3, mice (n=4) were intravenously treated with 1 mg/kg of PS-acet.-STAT3 peptide (AnaSpec, Fremont, CA, USA) or vehicle (HBSS; Thermo Fisher Scientific) every other day. Tumor growth was measured by a digital caliper every other day. To study the effects of the modified peptides at protein and gene levels, mice were euthanized when the tumor size reached to 500 mm3 in control groups.

value: 14 days

tag: agent

value: PS-acet-STAT3 peptide


title: PS-ac-3

description: treatment


title: F740, blood, Naive, 1w

value: blood

value: Naive


title: A549 cells,non-treated,rep2

value: Human NSCLC cell lines

value: WT


title: A549 cells,non-treated,rep3


title: 04_AD_06_LS

value: female

value: arm


title: A549 cells,non-treated,rep1

value: non-treated


title: 04_AD_02_NL

value: NL


title: F739, COLON, D, SIH, 1w

value: colon

value: SIH


title: F739, COLON, P, SIH, 1w


title: F739, COLON, M, SIH, 1w


title: KTB_V3_Live/Epithelial

city: San Francisco

first: Zev

last: Gartner

state: CA

address: 600 16th St. Room GH-N512E Box 2280

department: Pharmaceutical Chemistry

institute: University of California San Francisco

description:
Sample name: Set 22
KTB.raw.counts.matrix.rds
KTB.barcode.counts.rds
KTB.metadata.rds

data_processing:
Cell Ranger (10x Genomics V5.0.0) was used to align sequences, filter data and count unique molecular identifiers (UMIs). Data were mapped to the human reference genome GRCh37 (hg19).
For samples in the same batch run across multiple 10X lanes, the cellranger aggr pipeline (10X Genomics V5.0.0) was used to normalize read depth across droplet microfluidic lanes
For MULTI-seq barcode library pre-processing, raw barcode FASTQs were converted to barcode UMI count matrices as described in McGinnis et al., 2019.
For multiplexed samples, barcode UMI count matrices were used to classify cells using the MULTI-seq classification suite. To classify cells that were identified as unlabeled by MULTI-seq, we used the SoupOrCell pipeline (Heaton et al., 2020) to assign cells to different individuals based on single nucleotide polymorphisms (SNPs).
Cell type identification and data integration was performed using the Seurat package (version 3.1.5) in R.
Assembly: hg19
Supplementary files format and content: RDS files containing: 1) matrix tables with raw gene counts for each cell, 2) matrix tables with raw MULTIseq barcode counts (for multiplexed samples) for each cell, 3) sample metadata tables listing samples and relevant information (e.g. reproductive history, BMI, etc.), 4) a processed, integrated Seurat object for all reduction mammoplasty samples.
RM.raw.counts.matrix.rds (RDS - gene counts matrix table)
KTB.raw.counts.matrix.rds (RDS - gene counts matrix table)
RM.barcode.counts_Batch3_Live.rds (RDS - barcode counts matrix table)
RM.barcode.counts_Batch3_Epithelial.rds (RDS - barcode counts matrix table)
RM.barcode.counts_Batch4_Live.rds (RDS - barcode counts matrix table)
RM.barcode.counts_Batch4_Epithelial.rds (RDS - barcode counts matrix table)
KTB.barcode.counts.rds (RDS - barcode counts matrix table)
RM.metadata.rds (RDS - metadata table)
KTB.metadata.rds (RDS - metadata table)
breast.data.rds (RDS - processed seurat object)

source_name: reduction mammoplasty sample

extract_protocol:
Tissue was dissociated mechanically and enzymatically, collected after serial filtration to obtain epithelial-enriched tissue fragments, and cryopreserved until use. The day of sorting, the 150 µm fraction, or total banked material for the KTB samples, was thawed and digested to single cells by trituration in trypsin followed by dispase. For multiplexed experiments, samples were labeled by LMO MULTIseq barcodes. Single cells were sorted using the indicated sort gates.
Single cells were lysed in droplets using the 10X Chromium instrument. Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide v2 or 10X Chromium Single Cell 3' Reagent Kit User Guide v3. For multiplexed samples, library preparation was performed according to the 10X Chromium Single Cell 3' Reagent Kit User Guide Rev C and a MULTI-seq library preparation protocol (McGinnis et al.).

value: breast

value: untreated

tag: 10x chemistry

tag: sort gate

value: Live/Epithelial

value: primary breast cells

tag: multi-seq reagent

value: LMO

tag: number of multiplexed samples

tag: sample type

value: Pooled:Live singlet (50%) / Epithelial (Luminal + Basal/myoepithelial; 50%) sort gates


title: F739, blood, SIH, 1w

tag: Sex

tag: time

tag: tissue

tag: ID

tag: experimental group


title: Batch4_V3_Epithelial

description:
Sample name: Set 21
RM.raw.counts.matrix.rds
RM.barcode.counts_Batch4_Epithelial.rds
RM.metadata.rds
breast.data.rds

value: Epithelial

value: Luminal + Basal/myoepithelial sort gate


title: Batch4_V3_Live

description:
Sample name: Set 20
RM.raw.counts.matrix.rds
RM.barcode.counts_Batch4_Live.rds
RM.metadata.rds
breast.data.rds

value: Live

value: Pooled:Live singlet (90%) / CD45+ immune (10%) sort gates


title: 04_AD_02_LS

tag: visit

tag: group

value: AD

value: LS

tag: gender

tag: scorad

value: skin


title: HBSS-1

description: Control

tag: time point

value: 14 days

tag: cell line

value: HBSS


title: F739, DRG, SIH, 1w

value: female

value: DRG


title: 03_CO_54_HC

value: CO

value: HC

value: arm


title: 03_CO_56_HC

value: male


title: 03_CO_52_HC


title: F736, Spinal, LS, CPH, 1w

value: spinal

value: CPH


title: F736, Spinal, TL, CPH, 1w


title: 03_CO_48_HC


title: F736, Spinal, C, CPH, 1w


title: HBSS-3

description: Control

tag: agent


title: Batch3_V3_Epithelial

description:
Sample name: Set 19
RM.raw.counts.matrix.rds
RM.barcode.counts_Batch3_Epithelial.rds
RM.metadata.rds
breast.data.rds

value: breast

tag: treatment

value: untreated

tag: 10x chemistry

value: Epithelial

tag: cell type

value: primary breast cells

value: LMO


title: KR-2

description:
K685R STAT3
KR-STAT3-rep-2

growth_protocol: MDA-MB-231-R cells were maintained in DMEM media supplied with 50 nM of paclitaxel. WT or K685R mutant-STAT3 was expressed in MDA-MB-231-R cells through DNA transfection.

extract_protocol: RNA was isolated by using RNeasy Plus Kits (Qiagen)

tag: genotype

value: K685R STAT3


title: KR-3

description:
K685R STAT3
KR-STAT3-rep-3

treatment_protocol: WT or K685R mutant-STAT3 was expressed in MDA-MB-231-R cells through DNA transfection.


title: Batch3_V3_Live

description:
Sample name: Set 18
RM.raw.counts.matrix.rds
RM.barcode.counts_Batch3_Live.rds
RM.metadata.rds
breast.data.rds

tag: sort gate

value: Live

tag: multi-seq reagent

tag: number of multiplexed samples

tag: sample type

value: Live/singlet sort gate


title: PS-ac-1

description: treatment

value: 14 days

value: PS-acet-STAT3 peptide


title: KR-1

description:
K685R STAT3
KR-STAT3-rep-1


title: WT-3

description:
Wild type STAT3
WT-STAT3-rep 3

value: Wild type STAT3


title: 03_CO_39_HC

value: CO

value: female

tag: tissue

value: skin


title: F736, COLON, P, CPH, 1w

tag: Sex

tag: time

value: colon

tag: ID

tag: experimental group


title: RNA-seq G401 ACBI1 rep2

city: Nashville

first: Jing

last: Wang

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University Medical Center

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using STAR after adapter trimming, and quantified by featureCounts.
Differential analysis were performed by DESeq2.
ATAC-seq reads were aligned to the human genome hg19 using Bowtie2 (bowtie2 -p 8 -X 2000 --no-mixed --no-discordant).
Peaks were called using MACS2 with q-value of 0.05.
Differential enriched peaks were identified using DiffBind.
Assembly: hg19
Supplementary files format and content: RNA-seq: tab-delimited text file include raw counts for each Sample
Supplementary files format and content: ATAC-seq: one peak file per condition

source_name: G401 cells

growth_protocol: G401 cells were maintained in DMEM supplemented with 10% FBS and 1%Penicillin/Streptomycin. This maintenance media was also the same media that DMSO or ACBI1 was diluted in for all experiments.

extract_protocol:
For ATAC-seq, 75,000 cells were harvested and nuclei were treated with the Active Motif transposase included in the Active Motif ATAC-seq kit. All subsequent processing following the Active motif protocol, except final libraries were cleaned up using a PCR purification kit rather than SPRI beads. For RNA-seq, RNA was extracted using Trizol and the Direct-zol RNA mini prep kit by Zymo Research.
For ATAC-seq libraries were made using the Active Motif ATAC-seq kit, which included index primers and all PCR reagents. For RNA-seq, libraries were made at Vanderbilt University Medical Center VANTAGE core using their standard methods with ribosomal RNA depletion.

treatment_protocol: G401 cells were treated with DMSO or 250 nM ACBI1 for the following time periods:  ATAC-seq and RNA-seq were 24 hour timepoints.

value: G401 cells

value: 250 nM ACBI1

tag: passage


title: WT-2

description:
Wild type STAT3
WT-STAT3-rep 2


title: RNA-seq G401 ACBI1 rep1


title: 03_CO_33_HC

tag: visit

tag: group

value: HC

tag: gender

tag: scorad

value: arm


title: HBSS-2

description: Control

tag: time point

tag: cell line

tag: agent

value: HBSS


title: WT-1

description:
Wild type STAT3
WT-STAT3-rep 1

tag: genotype


title: 242-RNA

city: Melbourne

first: Deanna

middle: S

last: Deveson Lucas

state: Victoria

address: 15 Innovation walk, Monash University, Clayton

institute: Monash University

data_processing:
Raw fastq files have been analysed with RNAsik pipeline (Tsyganov et al. 2018) to produce raw genes count matrix and various quality control metrics.
For this analysis RNAsik pipeline (Tsyganov et al. 2018) ran with STAR aligner option (Dobin et al., 2013) and reads were quantified with featureCounts (Liao, Smyth, and Shi 2014).
Chelonia mydas reference genome rCheMyd1  (GCF_015237465.1 NCBI)
Raw counts were then analysed with Degust (Powell 2015) web tool to do differential expression analysis to produce list of differentially expressed genes and several quality plots including classical multidimensional scaling (MDS) and MA plots
In this analysis limma voom (Law et al. 2014) was used for differential expression analysis. Degust (Powell 2015) largely follows limma voom workflow with typical counts per million (CPM) library size normalisation and trimmed mean of M values (TMM) normalisation (Robinson and Oshlack 2010) for RNA composition normalisation.
Genome_build: rCheMyd1  (GCF_015237465.1 NCBI)
Supplementary_files_format_and_content: raw gene counts, text file, tab separated

organism: Chelonia mydas

source_name: 36hs H (Hypoxic)

growth_protocol: Embryos from the 0 h group were extracted immediately after arriving at the laboratory (see details below), within 1 h of oviposition. Eggs from the 36 h N group were buried in sand in a polystyrene container and incubated under normoxic conditions at 26-28 ⁰C in the laboratory. Eggs for the 36 h H group were incubated under hypoxic conditions in a sealed plastic bag filled with nitrogen (Pac Food Pty Ltd, Kunda Park, QLD, Australia), as described previously (Williamson et al., 2017c). This bag was in turn placed in a larger bag which was also filled with nitrogen gas and sealed. The bag was then buried in sand within a polystyrene container for incubation at 26-28 ⁰C in the laboratory. Embryos were removed after 36 h of incubation in normoxia or hypoxia.

extract_protocol:
RNA was isolated using the RNeasy Micro Isolation Kit (Qiagen, Chadstone, Australia), following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Once extracted from eggs, embryos were immediately frozen in liquid nitrogen before being stored at -80 ⁰C.

value: embryo

tag: condition

value: incubated in hypoxia (<8 mmHg)


title: RNA-seq G401 DMSO rep3

tag: cell type

tag: treatment

value: DMSO


title: 03_AD_25_NL

value: AD

value: NL

value: male

tag: tissue


title: 194-RNA


title: F736, COLON, D, CPH, 1w

tag: Sex

value: CPH


title: F736, DRG, CPH, 1w

tag: time

value: DRG


title: RNA-seq G401 DMSO rep2


title: RNA-seq G401 ACBI1 rep3


title: 03_CO_45_HC

value: CO


title: 142-RNA


title: 94-RNA


title: F736, blood, CPH, 1w

value: female

value: blood

tag: ID


title: RNA-seq G401 DMSO rep1


title: 03_AD_22_LS

value: LS

value: leg

value: skin


title: 03_AD_23_LS


title: F732, SPINAL, LS, SIH, 1w

value: spinal

tag: experimental group

value: SIH


title: 03_AD_16_NL

value: arm


title: 03_AD_25_LS


title: 46-RNA

value: embryo


title: F736, COLON, M, CPH, 1w

value: colon


title: 235-RNA

source_name: 36hs N (Normal)

value: incubated in normoxia (oxygen tension ~159 mmHg)


title: F732, SPINAL, C, SIH, 1w


title: ATAC-seq G401 ACBI1 rep2

value: G401 cells

value: 250 nM ACBI1

tag: passage


title: 03_AD_16_LS

tag: visit

value: AD

value: male


title: ATAC-seq G401 DMSO rep3

value: DMSO


title: F732, DRG, SIH, 1w

value: DRG


title: ATAC-seq G401 ACBI1 rep3


title: 233-RNA


title: ATAC-seq G401 DMSO rep2


title: ATAC-seq G401 DMSO rep1


title: F732, SPINAL, TL, SIH, 1w

value: female


title: ATAC-seq G401 ACBI1 rep1


title: F732, COLON, D, SIH, 1w


title: 03_AD_15_LS

tag: group


title: 03_AD_13_LS

tag: gender


title: 03_AD_13_NL

value: NL

tag: scorad


title: Control blood smalld RNA-seq N6

city: Wuhan

first: Yong

last: Wu

address: Gongnongbing road 89#

institute: Wuhan Mental Health Center

data_processing:
The miRNAs were quantified by miRDeep2 (Friedlander et al., 2012) using human miRNAs from miRbase (http://www.mirbase.org/) (Kozomara et al., 2019) as reference.
Genome_build: GRCh38
Supplementary_files_format_and_content: VstNormalized_matrix_of_miRNA_all_Samples.csv: csv file includes normalized values by DESeq2 vst method for each miRNA sample.

source_name: Blood

extract_protocol:
The total RNA was extracted from the blood using the PAXgene® Blood RNA Kit (QIAGEN, Hombrechtikon, Switzerland) according to the handbook’s instructions
For the small RNA library, a total of 2 μg total RNA isolated from each sample using NEBNext® Multiplex Small RNA Library Prep Set For Illumina® (NEB, USA) according to the manufacturer’s instruction.

value: blood

tag: disease state

value: Control

tag: bmi

tag: age

tag: molecule type

value: small RNA


title: 135-RNA

tag: condition


title: F732, COLON, M, SIH, 1w


title: 133-RNA


title: F731, SPINAL, TL, SIH, 1w

value: spinal


title: 03_AD_06_NL

value: skin


title: Control blood smalld RNA-seq N7


title: 155-RNA

value: Freshly laid egg


title: 203-RNA

value: embryo


title: F731, SPINAL, LS, SIH, 1w

value: SIH


title: F731, SPINAL, C, SIH, 1w


title: 104-RNA


title: 03_AD_06_LS

value: LS

value: arm


title: 03_AD_02_NL


title: Control blood smalld RNA-seq N5


title: Control blood smalld RNA-seq N4


title: F731, DRG, SIH, 1w


title: 03_AD_02_LS


title: 02_CO_46_HC

value: CO

value: HC


title: Control blood smalld RNA-seq N3

value: male


title: F732, COLON, P, SIH, 1w

value: colon


title: 54-RNA


title: 8-RNA


title: 02_CO_45_HC


title: F731, COLON, P, SIH, 1w


title: 37-RNA

value: incubated in normoxia (oxygen tension ~159 mmHg)


title: F731, COLON, M, SIH, 1w

value: female


title: F731, COLON, D, SIH, 1w


title: Control blood smalld RNA-seq N2


title: Synechocystis sp. PCC6803 was treated by 3 μM of 4k Q3-3

first: Meng

last: Cai

state: Hubei

address: NO.152 Luoyu Road

institute: Central China Normal University

data_processing:
The raw paired end reads were trimmed and quality controlled by Trimmomatic with parameters (SLIDINGWINDOW:4:15 MINLEN:75) (version 0.36 http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic).Then clean reads were separately aligned to reference genome with orientation mode using Rockhopper (http://cs.wellesley.edu/~btjaden/Rockhopper/) software. Rockhopper was a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. As input, Rockhopper takes RNA sequencing reads generated by high-throughput sequencing technology. This software was used to calculate gene expression levels with default parameters.
To identify DEGs (differential expression genes) between the two different samples, the expression level for each transcript was calculated using the fragments per kilobase of read per million mapped reads (RPKM) method. edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html) was used for differential expression analysis. The DEGs between two samples were selected using the following criteria: i) the logarithmic of fold change was greater than 2 and the false discovery rate (FDR) should be less than 0.05. To understand the functions of the differential expressed genes, GO functional enrichment and KEGG pathway analysis were carried out by Goatools (https://github.com/tanghaibao/Goatools) and KOBAS(http://kobas.cbi.pku.edu.cn/home.do) respectively. DEGs were significantly enriched in GO terms and metabolic pathways when their Bonferroni-corrected P-value was less than 0.05.
Genome_build: GCF_018845095.1_ASM1884509v1
Supplementary_files_format_and_content: tab-delimited text files include reads count for each Sample

organism: Synechocystis sp. PCC 6803

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed usingDNase I (TaKara). Then RNA quality was determined using 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). High-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0,>10μg) is used to construct sequencing library.
RNA-seq strand-specific libraries were prepared following TruSeq RNA sample preparation Kit from Illumina (San Diego, CA), using 5μg of total RNA. Shortly, rRNA removal by RiboZero rRNA removal kit(Epicenter) , fragmented using fragmentation buffer. cDNA synthesis, end repair, A-base addition and ligation of the Illumina-indexed adaptors were performed according to Illumina’s protocol. Libraries were then size selected for cDNA target fragments of 200–300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by TBS380, Paired-end libraries were sequenced by Illumina NovaSeq 6000 sequencing (150bp*2.).

value: treated by 3 uM of 4k


title: F725, SPINAL, TL, Naive, 1w

value: Naive


title: 02_AD_25_NL

value: AD

value: NL


title: OUD blood small RNA-seq H7

value: blood

value: OUD

value: small RNA


title: Synechocystis sp. PCC6803 was treated by 3 μM of 4k Q3-1


title: 02_AD_23_NL

value: skin


title: Synechocystis sp. PCC6803 was treated by 1 μM of 4k Q2-3

value: treated by 1 uM of 4k


title: OUD blood small RNA-seq H6


title: 02_CO_42_HC


title: F725, SPINAL, LS, Naive, 1w

value: spinal


title: Synechocystis sp. PCC6803 was treated by 3 μM of 4k Q3-2


title: OUD blood small RNA-seq H5


title: Synechocystis sp. PCC6803 was treated by 1 μM of 4k Q2-2


title: F725, SPINAL, C, Naive, 1w


title: 02_AD_23_LS

value: LS

value: arm


title: OUD blood small RNA-seq H4


title: 02_AD_22_NL

value: leg


title: F725, DRG, Naive, 1w

value: DRG


title: OUD blood small RNA-seq H3

value: male


title: F725, COLON, P, Naive, 1w

value: colon


title: Synechocystis sp. PCC6803 was treated by DMSO Q1-3

value: treated by DMSO


title: Synechocystis sp. PCC6803 was treated by 1 μM of 4k Q2-1


title: OUD blood small RNA-seq H2


title: 02_AD_17_NL

value: female


title: Control blood smalld RNA-seq N1

value: Control


title: Synechocystis sp. PCC6803 was treated by DMSO Q1-2


title: 02_AD_17_LS

value: AD


title: OUD blood small RNA-seq H1


title: F725, COLON, D, Naive, 1w

value: Naive


title: Synechocystis sp. PCC6803 was treated by DMSO Q1-1


title: F725, COLON, M, Naive, 1w


title: CRMM2 cells, CuB 0.2 μM rep3

first: Jinlian

last: Wei

state: Shanghai

address: Meilong Road 130

institute: EAST CHINA UNIVERSITY OF SCIENCE AND TECHNOLOGY

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Homo sapiens whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.3.1 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

extract_protocol:
CRMM2 cells were removed, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CRMM2 cells were cultured in 10 cm dishes, and treated with DMSO, 0.1 μM or 0.2 μM CuB.

tag: cell type

value: conjunctival cells

tag: cell line

value: CuB 0.2 μM


title: 02_AD_16_LS

tag: tissue


title: CRMM2 cells, CuB 0.2 μM rep2

tag: treatment


title: 02_AD_16_NL

value: NL


title: CRMM2 cells, CuB 0.2 μM rep1


title: 02_AD_15_NL

value: hand

value: skin


title: CRMM2 cells, CuB 0.1 μM rep3

value: CuB 0.1 μM


title: 02_AD_14_LS

value: LS


title: F724, SPINAL, C, SIH, 1w

tag: Sex

tag: time

value: spinal

value: SIH


title: 02_AD_22_LS

value: leg


title: 02_AD_13_NL

value: arm


title: F724, SPINAL, LS, SIH, 1w

tag: ID

tag: experimental group


title: F724, DRG, SIH, 1w

value: DRG


title: CRMM2 cells, CuB 0.1 μM rep1


title: 02_AD_13_LS

tag: visit


title: 02_AD_12_NL

tag: group


title: CRMM2 cells, Control rep3

value: DMSO


title: F724, COLON, M, SIH, 1w

value: female

value: colon


title: F724, COLON, D, SIH, 1w


title: 02_AD_12_LS

value: AD

tag: gender


title: SE60

city: Charlottesville

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

data_processing:
Quality control of raw reads by FastQC
TPM (Transcript per million counts of per kilobase transcript)
Assembly: GRCm38 (mm10)
Supplementary files format and content: raw reads counts and normalized gene expression values in .txt format

molecule: polyA RNA

organism: Mus musculus

source_name: lung

extract_protocol:
Total RNA from lung tissue was isolated by Trizol. One ug of RNA was used for cDNA library construction
Novogene NEBNext® Ultra 2 RNA Library Prep Kit

tag: strain

value: Female

value: Lung

value: cigarette smoke

tag: exposure time

value: exposure time:5mo

tag: surgery status

value: no surgery


title: F724, SPINAL, TL, SIH, 1w

source_name: spinal


title: CRMM2 cells, Control rep2

value: conjunctival cells


title: F721, SPINAL, TL, CPH, 1w

value: CPH


title: 02_AD_11_LS

source_name: skin

value: LS

tag: scorad

value: skin


title: CRMM2 cells, Control rep1


title: SE59


title: SE58


title: CRMM2 cells, CuB 0.1 μM rep2

value: CuB 0.1 μM


title: F721, SPINAL, LS, CPH, 1w

value: spinal


title: 02_AD_09_LS

value: arm


title: F724, COLON, P, SIH, 1w

value: SIH


title: 02_AD_06_LS


title: F721, SPINAL, C, CPH, 1w


title: SE57


title: F721, DRG, CPH, 1w

value: DRG


title: 02_AD_02_NL

value: NL

value: female


title: CE29

city: Valencia

first: Hortensia

last: Ferrero

state: Valencia

address: Avenida Fernando Abril Martorell 106, Torre A

department: Reproductive Medicine

country: Spain

institute: Instituto de Investigación Sanitaria La Fe / Fundación IVI

data_processing:
Sequenced reads were mapped to HG38 whole genome using STAR_2.5.2 mapping software with default settings.
For gene expression quantification, uniquely mapping reads were submitted to featureCounts algorithm  to obtain the count matrix. Genome reference annotation was extracted from Gencode 24, (Ensembl version 84). Sequencing the samples yielded an average of 30 million reads per sample.
Genome_build: HG38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Uterine myometrium

extract_protocol:
Total RNA from UL and MM tissues (n= 30) was extracted with TRIzol reagent (Fisher Scientific, Waltham, MA). Samples were quantified using TapeStation 4200 (Agilent, USA). cDNA synthesis and library generation were performed using TruSeq RNA Library Prep Kit v2 (Illumina, USA) according to manufacturer’s instructions. Samples were quantified using Bioanalyzer (Agilent, USA) and DNA pools generated were quantified using Qubit DNA HS assay kit (ThermoFisher Scientific, Waltham, MA, USA). Libraries were sequenced using Illumina NovaSeq 600 Instrument (Illumina, USA) with a in a paired-end design.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Uterine myometrium

value: Caucasian women

tag: patient

value: Patient 29

tag: age

tag: bmi


title: CE31

value: Patient 31


title: CE30

value: Patient 30


title: SE55

value: Male

value: Lung

value: cigarette smoke

value: exposure time:5mo

value: no surgery


title: F721, COLON, P, CPH, 1w

value: colon

value: CPH


title: 02_AD_02_LS

value: AD

value: LS

value: arm

value: skin


title: SE54


title: CE27

value: female

value: Patient 27


title: SE56

value: Female


title: F721, COLON, M, CPH, 1w


title: 01_CO_60_HC

value: CO

value: HC

value: male


title: F721, COLON, D, CPH, 1w


title: CE26

value: Uterine myometrium

value: Caucasian women

value: Patient 26


title: SE53

value: Male

value: Lung

value: cigarette smoke

value: exposure time:5mo


title: CE25

value: Patient 25


title: SE52

value: no surgery


title: F720, SPINAL, TL, CPH, 1w

value: spinal

value: CPH


title: 01_CO_53_HC

value: arm

value: skin


title: 01_CO_54_HC

value: female


title: 01_CO_56_HC

value: CO


title: CE24

value: Patient 24


title: F720, SPINAL, LS, CPH, 1w


title: F720, SPINAL, C, CPH, 1w


title: CE22

value: Patient 22


title: SE506

value: Female

value: room air


title: SE507


title: 01_CO_52_HC

value: HC


title: SE51

value: Male


title: F720, DRG, CPH, 1w

value: DRG


title: CE21

value: Uterine myometrium

value: Caucasian women

value: Patient 21


title: SE505

value: Lung

value: exposure time:5mo

value: no surgery


title: F720, COLON, P, CPH, 1w

value: colon

value: CPH


title: 01_CO_47_HC

value: female

value: arm

value: skin


title: CE19

value: Patient 19


title: F720, COLON, M, CPH, 1w


title: SE503


title: 01_CO_45_HC

value: CO


title: F720, COLON, D, CPH, 1w


title: 01_CO_48_HC


title: CE20

value: Patient 20


title: SE504

value: room air


title: CE23

value: Patient 23


title: CE18

value: Patient 18


title: SE502

value: Male


title: CE17

value: Uterine myometrium

value: Caucasian women

value: Patient 17


title: SB95

value: Female

value: Lung

value: cigarette smoke

value: exposure time:5mo

value: ovariectomie


title: 01_CO_49_HC

value: HC

value: female

value: arm


title: F719, SPINAL, C, CPH, 1w

value: spinal

value: CPH


title: 01_CO_32_HC

value: CO

value: elbow

value: skin


title: 01_CO_33_HC


title: SB93


title: SB94


title: 01_AD_30_NL

value: AD

value: NL


title: F719, DRG, CPH, 1w

value: DRG


title: SB92


title: CE13

value: Uterine myometrium

value: Caucasian women

value: Patient 13


title: CE15

value: Patient 15


title: 01_AD_30_LS

value: LS


title: F719, COLON, P, CPH, 1w

value: colon


title: CE12

value: Patient 12


title: F719, SPINAL, LS, CPH, 1w

value: female


title: F719, SPINAL, TL, CPH, 1w


title: F719, COLON, M, CPH, 1w


title: F719, COLON, D, CPH, 1w


title: CE16

value: Patient 16


title: SB40

value: Female

value: Lung

value: cigarette smoke

value: exposure time:5mo

value: sham surgery


title: 01_CO_43_HC

value: CO

value: HC

value: arm

value: skin


title: CE14

value: Uterine myometrium

value: Caucasian women

value: Patient 14


title: CE11

value: Patient 11


title: SB39


title: 01_AD_27_LS

value: AD

value: LS


title: CE10

value: female

value: Patient 10


title: SB38

value: Female


title: B149, Spinal, LS, 1w

value: spinal

value: Naive


title: 01_AD_26_NL

value: NL

value: male


title: SB37

value: Lung

value: cigarette smoke

value: exposure time:5mo

value: sham surgery


title: B149, Spinal, C, 1w


title: CE8

value: Uterine myometrium

value: Patient 8


title: 01_AD_26_LS

value: arm

value: skin


title: SB36


title: 01_AD_27_NL

value: AD


title: CE7

value: Caucasian women

value: Patient 7


title: SA998

value: exposure time:3mo

value: ovariectomie


title: CE6

value: female

value: Patient 6


title: 01_AD_25_LS

value: LS


title: B149, COLON, M, 1w

value: colon

value: Naive


title: SA997

value: Female

value: Lung

value: cigarette smoke


title: B149, COLON, P, 1w


title: 01_AD_22_NL

value: NL

value: male


title: CE5

value: Uterine myometrium

value: Patient 5


title: B149, COLON, D, 1w


title: SA996


title: CE9

value: Patient 9


title: 01_AD_22_LS

value: AD

value: skin


title: CE4

value: Caucasian women

value: Patient 4


title: SA909

value: exposure time:3mo

value: sham surgery


title: CE3

value: female

value: Patient 3


title: 01_AD_25_NL

value: arm


title: 01_AD_21_NL


title: B149, DRG, 1w

value: DRG

value: Naive


title: 01_AD_20_NL

value: hand


title: SA908

value: Female

value: Lung

value: cigarette smoke


title: 01_AD_19_NL

value: NL


title: IFN/LPS Control D

city: Chicago

first: Afsar

last: Naqvi

state: IL

address: 801 S Paulina, Room 561B

department: Periodontics

institute: University of Illinois at Chicago

description: Control mimic Transfected M1 macrophage

hyb_protocol: Hybridization was performed at 40°C for 16 hours on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://mirbase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide. After RNA hybridization, tag-conjugating Cy3 dye was circulated through the microfluidic chip for dye staining.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).

source_name: Primary human macrophages

label_protocol: A strand-labeling reaction was carried out with total RNA (1 ug), control oligo-nucleotides, App-Cap3 (5’-adenylated and 3’-dideoxy oligo-adaptor, Integrated DNA Technologies) and T4 RNA ligase (Rnl2tr-K227Q, New England BioLabs) in T4 RNA ligase buffer with PEG 8000 and RNase inhibitor (Promega).

growth_protocol: Primary human DC14+ monocytes were differentiated to M1 and M2 macrophages in the presence of GM-CSF and M-CSF for 7 days.

extract_protocol: Total RNA was isolated using miRNeasy kit Qiagen. Briefly, cells were lysed in Qiazol and then total RNA was purified using columns as per the manufacturer's instructions. RNA was eluted in 50 µl RNase-free water.

treatment_protocol: Cells were transfected with viral miRNA or control miRNA mimics using Lipofectamine 2000. After 4 hours, transfection media was replaced with complete media containing IFNγ+LPS (M1 macrophages) or IL4+IL13 (M2 macrophages). After 48 hours, cells were harvested for RNA isolation.

tag: cell type

value: M1 macrophage

tag: transfection

value: Control mimic


title: SA907

tag: tissue

tag: treatment


title: ME31

source_name: Uterine leiomyoma

value: Uterine leiomyoma

value: Patient 31


title: CE2

value: Uterine myometrium

value: Caucasian women

value: Patient 2


title: IFN/LPS Control C

description: Control mimic Transfected M1 macrophage


title: ME30

value: female

value: Patient 30


title: NILER_shCTR_MEKi_D5_CD45_plus_TCR

city: LOS ANGELES

first: Sixue

last: Liu

state: California

address: 10833 Le Conte Avenue

institute: UCLA

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #5

data_processing:
The reads are first mapped to Grcm38 using cellranger software from 10x Genomics
Single-cell, gene-level raw read counts are read from cellranger output and analyzed using Seurat
The normalized count from the Seurat object after NormalizeData step are provided as processed data file
Subsequent clustering analyses are descibed in the full manuscript
Assembly: GRCm38
Supplementary files format and content: Gene level expression matrix

source_name: NRAS mutant mouse melanoma model

extract_protocol:
Single Cell 5' Gene Expression Libraries v1.1; Single Cell V(D)J Libraries v1.1
10x Genomics single cell 5' RNA-Seq and V(D)J sequencing

value: Trametinib

value: V(D)J sequencing

tag: molecule type

value: V(D)J mRNA


title: NILER_shITCH_MEKi_D5_CD45_plus_TCR

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #6


title: CE1

value: Patient 1


title: IFN/LPS Control B

description: Control mimic Transfected M1 macrophage


title: 01_AD_17_LS

extract_protocol:
Total RNA was extracted from tape 5 to 8 from each skin site (RNAqueous, Life technologies) followed by digestion with DNase I.
Multiplexed cDNA libraries were generated using the BRB-seq workflow (Alpern et al. Genome Biology 2019;20:71.)

value: AD

value: LS

value: skin


title: ME27

value: Patient 27


title: 01_AD_18_NL

value: NL

value: wrist


title: 01_AD_29_LS

value: male

value: arm


title: 01_AD_14_LS


title: 01_AD_19_LS

value: hand


title: ME29

value: Uterine leiomyoma

value: Caucasian women

value: Patient 29


title: 01_AD_13_NL

value: female


title: ME25

value: Patient 25


title: 01_AD_17_NL


title: IFN/LPS US4 A

description: hcmv miR-US4 Transfected M1 macrophage

value: M1 macrophage

value: hcmv miR-US4


title: NILER_shCTR_MEKi_D5_CD45_plus

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #3

value: Trametinib

value: 5' gene expression sequencing

value: 5' mRNA


title: IFN/LPS Control A

description: Control mimic Transfected M1 macrophage

value: Control mimic


title: IFN/LPS US4 D

description: hcmv miR-US4 Transfected M1 macrophage


title: IFN/LPS US4 B

description: hcmv miR-US4 Transfected M1 macrophage


title: IFN/LPS US4 C

description: hcmv miR-US4 Transfected M1 macrophage


title: ME23

value: Patient 23


title: ME26

value: Patient 26


title: 01_AD_11_LS

value: AD

value: LS

value: skin


title: 01_AD_10_NL

value: NL

value: wrist


title: 01_AD_13_LS

value: arm


title: IFN/LPS BART3 C

description: ebv BART3 Transfected M1 macrophage

value: ebv BART3


title: ME22

value: female

value: Uterine leiomyoma

value: Caucasian women

value: Patient 22


title: ME21

value: Patient 21


title: NILER_shITCH_MEKi_D5_CD45_plus

description: 10x Genomics single cell barcoded mRNA from CD45+ cells, Sample #4

value: Trametinib

value: 5' gene expression sequencing


title: 01_AD_11_NL


title: IFN/LPS BART3 A

description: ebv BART3 Transfected M1 macrophage

value: M1 macrophage


title: 01_AD_08_LS


title: 01_AD_10_LS


title: ME24

value: Patient 24


title: 01_AD_07_LS


title: ME20

value: Patient 20


title: ME17

value: Patient 17


title: IFN/LPS BART3 D

description: ebv BART3 Transfected M1 macrophage


title: ME18

value: Patient 18


title: ME16

value: Patient 16


title: IFN/LPS K12-4 C

description: kshv miR-K12-4 Transfected M1 macrophage

value: kshv miR-K12-4


title: B149, Spinal, TL, 1w

last: Mocci

address: 655 W Lombard S

institute: SON

data_processing:
We used FastQC and Trimmomatic  tools for evaluating the quality of the sequences, next we used HISAT2  software to align the sequences to the reference Rattus norvegicus (Norway rat) genome assembly Rnor_6.0 (rn6) from Rat Genome Sequencing Consortium [GCA_000001895.4 GCF_000001895.5]. Finally, gene expression was estimated using HTSeq(18) which considers a gene as the union of all exons regardless of the isoform and excludes reads that overlap multiple genes
Genome_build: rn6
Supplementary_files_format_and_content: batch effect corrected expression data have been uploaded to https://nemoanalytics.org/p?s=2f41a962

extract_protocol:
RNA was extracted from 4 type of tissues, including blood, colon, spinal, and dorsal root ganglia (DRG) at one week (week 1) and seven weeks (week 7) after the induction of stress
Libraries were prepared with NEB Ultra II Directional Library Prep kits. Samples at week 1 were sequenced on Illumina HiSeq 4000 platform using a 150 bp paired-end run (2 ´ 150), while samples at week7 were run on Illumina NovaSeq 6000 using a 150 bp paired-end run as well

tag: Sex

tag: time

value: spinal

tag: ID

value: Naive


title: IFN/LPS K12-4 D


title: IFN/LPS K12-3 D

description: kshv miR-K12-3 Transfected M1 macrophage

value: kshv miR-K12-3


title: ME19

value: female

tag: group

value: Patient 19


title: IFN/LPS K12-4 A


title: IFN/LPS K12-3 C


title: IFN/LPS K12-4 B


title: 01_AD_05_LS

last: Hu

address: 5 Artillerivej

institute: Statens Serum Institut

data_processing:
Library strategy: BRB-Seq
Each BRB batch fastq file was demultiplexed using BRB-seq tool 1.6.0 Demultiplex function
To generate the count matrix, BRB-seq data was mapped by aligning reverse reads to human reference genome (GRCh38.105) by STAR(2.7.9a), then de-multiplexing by the forward read barcoding using BRB-seq tool 1.6.0.
Only expressed genes (mean count  > 1 across 80% samples) were included in the count matrix.
Assembly: human reference genome (GRCh38.105)
Supplementary files format and content: csv; The first column, gene_name, is the standard gene symbol (HGNC or MGI-approved gene symbols; if no official gene symbol exists, Havana clone-based name is used). The remaining columns contain the gene counts for each sample.

tag: visit

value: AD

value: LS

tag: gender

value: hand

value: skin


title: 01_AD_05_NL

value: NL

value: arm


title: Lrp2sh2 rep1

city: Hong Kong

first: Wenjun

last: Xiong

state: Hong Kong SAR

address: Block2-315Room, To Yuen Building, City University, of  Hong Kong, 31 To Yuen Street, Kowloon Tong, Kowloon

country: Hong Kong

institute: City University of Hong Kong

description:
Lrp2sh2
Lrp2sh2

data_processing:
Basecalling is performed by Illumina RTA software in sequencer
Raw RNA sequencing reads were mapped to the mouse reference genome (GRCm38), followed by calculation of gene counts using STAR with the default parameter setting (version 2.7.3a), only the uniquely mapped reads were kept for the subsequent analyses.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include gene counts for each sample

extract_protocol:
RNAs were extracted from mouse RPE using Trizol (Thermofisher) followed by QuickRNA MicroPrep Kit (Zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: retinal

value: postnatal day 14


title: 01_AD_06_LS


title: ME14

value: Uterine leiomyoma

value: Caucasian women

value: Patient 14


title: GFP rep3

description:
GFP
GFP


title: IFN/LPS BART3 B

description: ebv BART3 Transfected M1 macrophage

value: M1 macrophage

value: ebv BART3


title: Lrp2sh2 rep3

description:
Lrp2sh2
Lrp2sh2


title: IFN/LPS K12-3 B


title: IFN/LPS K12-3 A


title: 01_AD_04_LS


title: ME13

value: Patient 13


title: 01_AD_03_LS


title: ME12

value: Patient 12


title: ME15

value: female

value: Patient 15


title: Lrp2sh2 rep2

description:
Lrp2sh2
Lrp2sh2


title: IFN/LPS H1 C

description: HSV1 miR-H1 Transfected M1 macrophage

value: HSV1 miR-H1


title: 01_AD_04_NL

value: AD


title: GFP rep1

description:
GFP
GFP


title: 01_AD_02_LS

value: LS


title: IFN/LPS H1 D

description: HSV1 miR-H1 Transfected M1 macrophage


title: ME10_3_S22

description: technical replicate

value: Patient 10


title: ME11

value: Patient 11


title: Laczsh rep3

description:
Laczsh
Laczsh


title: 01_AD_01_NL

value: NL

value: arm

value: skin


title: ME10_2_S17

description: technical replicate

value: Uterine leiomyoma


title: IFN/LPS H1 A

description: HSV1 miR-H1 Transfected M1 macrophage


title: 01_AD_01_LS


title: Laczsh rep1

description:
Laczsh
Laczsh

value: retinal

value: postnatal day 14


title: ME10_S3

value: Caucasian women


title: GFP rep2

description:
GFP
GFP


title: SB91

value: Female

value: Lung

value: cigarette smoke

tag: exposure time

value: exposure time:5mo

tag: surgery status

value: ovariectomie


title: IL4/IL13 Control D

description: Control mimic Transfected M2 macrophage

value: M2 macrophage

value: Control mimic


title: Lrp2sh1 rep3

description:
Lrp2sh1
Lrp2sh1


title: ME9

value: female

tag: patient

value: Patient 9


title: Lrp2sh1 rep2

description:
Lrp2sh1
Lrp2sh1

tag: age


title: ME8

value: Patient 8

tag: bmi


title: Laczsh rep2

description:
Laczsh
Laczsh


title: IFN/LPS H1 B

description: HSV1 miR-H1 Transfected M1 macrophage

tag: cell type

value: M1 macrophage

value: HSV1 miR-H1


title: IL4/IL13 Control C

description: Control mimic Transfected M2 macrophage

tag: transfection


title: IL4/IL13 US4 D

description: hcmv miR-US4 Transfected M2 macrophage

value: hcmv miR-US4


title: ME5

tag: tissue

value: Uterine leiomyoma

value: Patient 5


title: Uninjected rep3

description:
Uninjected
Uninjected

value: retinal

value: postnatal day 14


title: ME7

value: Caucasian women

value: Patient 7


title: nSrebp2 rep2

description:
nSrebp2
nSrebp2


title: Lrp2sh1 rep1

description:
Lrp2sh1
Lrp2sh1


title: IL4/IL13 Control A

description: Control mimic Transfected M2 macrophage


title: IL4/IL13 US4 C

description: hcmv miR-US4 Transfected M2 macrophage


title: radioresistant cells [MR]

city: Gyeongju

first: soyoung

last: Kim

address: Dongdae-ro 123

department: Department of Pharmacology

country: South Korea

institute: Dongguk university

hyb_protocol: Following fragmentation, 5.5 ug of framented cDNA were hybridized for about 17 hr at 45℃ on Human Gene 2.0 ST array. The hybridized probe arrays were stained and washed with GeneChip® Hybridization, Wash and Stain Kit(900720, Thermo Fisher Scientific) using the Fluidics Station 450(Affymetrix).

scan_protocol: The stained GeneChips were scanned with a GeneChip® Scanner 3000+ 7G(Affymetrix) a 570 nm.

data_processing: The RMA algorithm was used for expression summary and signal calculation of Human Gene 2.0 ST array data. Sketch Quantile normalization was performed for the signal normalization.

label: biotin

source_name: huamn HER2-positive brest cancer cells irradiated with 48 Gy

label_protocol: The GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription were performed according to the manufacturer's instructions from 200ng total RNA. Protocol performed using GeneChip™ WT PLUS Reagent Kit(902280, Thermo Fisher Scientific).

growth_protocol: Cell were cultured in Dulbecco Modified Eagle Medium (DMEM, Welgene) containing 10 % fetal bovine serum (Hyclone) and 1x Penicillin-Streptomycine solution (Welgene) using a 5% CO2 incubator at 37℃.

extract_protocol: Total RNA was extracted using easy-BLUE™ Total RNA Extraction kit (iNtRON Biotechnology Inc.) following to manufacturer’s instructions

treatment_protocol: Cells were exposed to 4 Gy twice a week and incubated for recovery from radiation-induced damage. Pre-SR and SR cells were exposed to 5 and 6 cycles of radiation, respectively.

tag: cell line source

value: Female,  mammary gland, derived from metastatic site:pleural effusion

tag: treatment

value: irradiated with 5 Gy twice a week


title: nSrebp2 rep3

description:
nSrebp2
nSrebp2


title: parental MCF-7 cells [WT]

source_name: human HER2-positive brest cancer cells


title: ME3

value: Patient 3


title: nSrebp2 rep1

description:
nSrebp2
nSrebp2


title: IL4/IL13 US4 B

description: hcmv miR-US4 Transfected M2 macrophage

value: M2 macrophage


title: Uninjected rep1

description:
Uninjected
Uninjected


title: ME4

value: Patient 4


title: ME6

value: female

value: Patient 6


title: IL4/IL13 BART3 B

description: ebv BART3 Transfected M2 macrophage

value: ebv BART3


title: IL4/IL13 BART3 C

description: ebv BART3 Transfected M2 macrophage


title: ME2

value: Patient 2


title: Uninjected rep2

description:
Uninjected
Uninjected


title: ME1

value: Patient 1


title: IL-1β + P. gingivalis persisters-treated HGECs - Td_3

first: Chuan

address: 34 Hospital Road, Sai Ying Pun

department: Faculty of Dentistry

institute: The University of Hong Kong

data_processing:
Raw reads generated by the Illumina NovaSeq 6000 were filtered by the useful Perl scripts to: 1) discard the reads if the length of trimmed reads is lower than 30bp after trimming Smart-seq2 public primer sequence from the Reads; 2) remove the contaminated reads for adapters if the read bases contained more than 5bp of adapter sequences; 3) remove the low quality reads containing more than 15 % bases with a quality value ≤ 19; 4) remove reads containing more than 5% ambiguous nucleotides.
After pre-processing, clean reads were obtained and aligned to the reference genome (GRCh38.p13) using HISAT2 v2.1.0 (Baltimore, MD, USA). The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index. Reads mapped to multiple locations and unmapped reads were excluded from gene expression analysis.
The gene expression level was estimated by the FPKM (Fragments per Kilobase per Million Mapped Fragments) method using HTSeq v0.6.0 (California Institute of Technology, Pasadena, CA, USA).
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: FPKM values for each gene and each sample

source_name: Human gingival epithelial cells

growth_protocol: Primary human gingival epithelial cells (HGECs) purchased from CELLnTEC (Stauffacherstrasse, Switzerland) were cultured in epithelial culture medium (CnT-prime, CELLnTEC, Stauffacherstrasse, Switzerland) supplemented with 100 μg/ml antimicrobial agent Primocin™ (InvivoGen, San Diego, CA, USA) in a humidified incubator at 37 °C with 5% CO2. The medium was changed every two days. The third to fifth passages of HGECs were used in all experiments of this study.

extract_protocol:
Total RNA was purified with RNeasy Plus Mini Kit (Qiagen, Benelux BV Qiagen GmbH, Hilden, Germany) according to the standard procedures.
RNA libraries were prepared for sequencing using standard Illumina protocols. Briefly, NanoPhotometer® spectrometer (IMPLEN, CA, USA) was used to detect the quantity and quality of the RNA. RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA) was used to analyze the RNA fragment size. Poly-T oligo-attached magnetic beads were used to purify mRNA from total RNA. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) and index codes were added to attribute sequences to each sample. Library RNA concentration was measured using Qubit® RNA Assay Kit (Life technologies, Waltham, MA, USA) in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA), and qualified insert size was accurately quantified using CFX96 Real-Time PCR System (Bio-Rad Laboratories, Hercules, CA, USA) to make sure it match the library valid concentration (＞10 nM). The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina, Santiago, CA, USA). After cluster generation, the libraries were sequenced on a NovaSeq 6000 platform (Illumina, Santiago, CA, USA), and 150 bp paired-end reads were generated.

treatment_protocol: HGECs were seeded onto suitable vessels with appropriate density. After adherence, cells were washed twice with Hank's balanced salt solution (HBSS, Gibco-BRL, Invitrogen), cultured with CnT-PR medium without antibiotics and treated with 1 ng/ml IL-1β or not. Those only cultured by CnT-PR medium without any treatments were regarded as blank group (BL). Four hours after IL-1β treatment, cells were treated with 1 μM FOXO1 inhibitor (Fi) AS1842856 (Selleckchem, Houston, TX, USA) or not. After another 2 hours, cells were infected with M-PgPs or P. gingivalis (MOI: 100) for 24 hours. Total RNAs were collected for the following tests.


title: IL4/IL13 Control B

description: Control mimic Transfected M2 macrophage

value: Control mimic


title: IL-1β + P. gingivalis persisters-treated HGECs - Td_2

value: Primary human gingival epithelial cells (HGECs)


title: IL4/IL13 BART3 A

description: ebv BART3 Transfected M2 macrophage


title: IL4/IL13 US4 A

description: hcmv miR-US4 Transfected M2 macrophage

value: hcmv miR-US4


title: IL-1β + P. gingivalis-treated HGECs - Tc_3

value: IL-1β + P. gingivalis-treated


title: Treated TGF-B HMEC siZNF827 R2

city: Odense M

first: Vijay

last: Tiwari

state: Denmark

address: Campusvej 55

department: Institut for Molekylær Medicin (IMM)

institute: Queen’s University Belfast

description:
All_samples_HMEC_TPM.txt.gz
VT413

data_processing:
Low quality bases were trimmed from pre-aligned reads, then aligned to hg19 reference genome using STAR v2.7, followed by quantification using salmon v1.4.
Raw read counts were filtered to remove counts where maximum <=1. Differential analysis was performed with DESeq2 (R, v3.14) with default parameters, with the median of ratios method of normalisation performed prior to differntial analysis.
After library size normalization using DESeq (v3.14), expression was quantified and differential expression analysis was performed using DESeq2.
Gene set enrichment analysis for biological processes was performed using GSEA Preranked module
Genome_build: hg19
Supplementary_files_format_and_content: [RNA-seq] Matrix table with gene counts from DESeq2, for every gene and every sample
Supplementary_files_format_and_content: [ChIP-seq]  Peak, Bigwig

growth_protocol: Cells were seeded at the same starting density (200K per well of six well plate) 16 hours before treatment

extract_protocol:
RNA was extracted using Trizol, isolated using chloroform, precipitated using isopropanol and the RNA pellet washed with ethanol before re-suspension in DEPC water
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with siRNA at the same time as TGF-beta induction (16 hours after plating), with TGF-beta and siRNA replenishment and medium changed on day 2

tag: cell line

value: HMEC

value: siRNA mediated ZNF827 knockdown in HMEC cells after TGF-beta induction (d4)


title: d8 TGF-B Input

growth_protocol: Cells were plated at 70% confluency 16 hours before treatment

extract_protocol:
ChIP were performed according to standard protocol
ChIP libraries were prepared using standard Illumina protocols

treatment_protocol: Cells were transfected with plasmid containing Flag-HA ZNF827 and induce with TGFbeta

value: HMLE

value: HMLE cells, Input, induced with TGF-beta

tag: chip antibody

value: none (input)


title: IL-1β + P. gingivalis persisters-treated HGECs - Td_1


title: d8 TGF-B ZNF827_2

value: HMLE cells transfected with Flag HA tagged construct, induced with TGF-beta

value: Flag M2 (Sigma)


title: IL4/IL13 BART3 D

description: ebv BART3 Transfected M2 macrophage

value: M2 macrophage


title: d8 TGF-B ZNF827_1


title: IL4/IL13 K12-4 D

description: kshv miR-K12-4 Transfected M2 macrophage

value: kshv miR-K12-4


title: IL-1β + P. gingivalis-treated HGECs - Tc_2


title: IL4/IL13 K12-4 B


title: IL4/IL13 K12-4 C


title: IL4/IL13 K12-3 D

description: kshv miR-K12-3 Transfected M2 macrophage

value: kshv miR-K12-3


title: IL4/IL13 K12-4 A


title: Injured urethra 3A [miRNA-seq]

city: Kunming

first: Han

last: Lin

state: Yunnan

address: No. 295, Xichang Road

department: Department of Urology

institute: The First Affiliated Hospital of Kunming Medical University

data_processing:
Remove low quality reads with nucleotides of scores lower than 30 in the first 25 nucleotides.
Keep the sequences with lengths are greater than or equal to 18 bp (the 3' adapter sequence of reads had been removed by the sequencing facility).
Sort and remove repetitive sequences.
Calculate the counts of unique sequences.
The unique sequences were aligned to assembled genome with BLAST.
Genome_build: miRBase 22.1
Supplementary_files_format_and_content: normal_vs_injured-miRNA-expression-levels.xlsx: Excel file includes sequences and count values.

source_name: Urethral tissue

growth_protocol: SD rats in the urethral injury group and the control group were separately raised in two cages. All rats were raised in SPF barrier environment, with the temperature range of 20 ℃ ~ 25 ℃, relative humidity range of 50% ~ 70%, 12 hours of alternate light and dark, good ventilation, free drinking of sterilized water and free feeding of sterilized feed.

extract_protocol:
Total RNA was extracted from the urethral tissue of the injured and normal rats using the Trizol reagent.
Library was prepared with 1 μg total RNA for each sample. Total RNA was purified by electrophoretic separation on a 15% urea denaturing polyacrylamide gel electrophoresis (PAGE) gel and small RNA regions corresponding to the 18–30 nt bands in the marker lane (14-30 ssRNA Ladder Marker, TAKARA) were excised and recovered. Then the 18–30 nt small RNAs were ligated to adenylated 3’ adapters annealed to unique molecular identifiers (UMI), followed by the ligation of 5’adapters. The adapter-ligated small RNAs were subsequently transcribed into cDNA by SuperScript II Reverse Transcriptase (Invitrogen, USA) and then several rounds of PCR amplification with PCR Primer Cocktail and PCR Mix were performed to enrich the cDNA fragments. The PCR products were selected by agarose gel electrophoresis with target fragments 110~130 bp, and then purified by QIAquick Gel Extraction Kit (QIAGEN, Valencia, CA). The library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The final ligation PCR products were sequenced using the BGISEQ-500 platform (BGI-Shenzhen, China).

treatment_protocol: After successful anesthesia, the rats were fixed on the constant temperature pad of the small animals on the operating table in a supine position, the perineal hair was removed, the perineal skin was carefully disinfected with Iodophor, and then the sheet was laid. The skin of the ventral penis was cut to expose the urethra. A small opening was cut at the urethral orifice with ophthalmic scissors. The urethral orifice was pulled open with three vascular forceps, and the rat urethra was slightly expanded with a certain round end iron rod. The round end of the customized iron bar was roasted on the external flame of alcohol lamp for 6 ~ 7 seconds and then inserted into the urethra, with the insertion depth of about 26 mm. After each withdrawal, the customized iron bar was roasted for 6 ~ 7 seconds and inserted again, so as to scald the urethral mucosa for 2 ~ 3 times. Then remove the tourniquet, 5-0 absorbable suture penis skin. On the third day after modeling of urethral injury, the rats were killed and the urethral tissue was removed.

value: Sprague Dawley

tag: Sex

value: Male

value: 2 months after birth

value: Injured urethra


title: Treated TGF-B HMEC siZNF827 R1

description:
All_samples_HMEC_TPM.txt.gz
VT412


title: IL-1β-treated HGECs - NC_3

value: Primary human gingival epithelial cells (HGECs)


title: Treated TGF-B HMEC siControl R2

description:
All_samples_HMEC_TPM.txt.gz
VT411

value: Non-targeting control in HMEC cells after TGF-beta induction (d4)


title: IL-1β-treated HGECs - NC_1


title: Treated TGF-B HMEC siControl R1

description:
All_samples_HMEC_TPM.txt.gz
VT410


title: IL-1β + P. gingivalis-treated HGECs - Tc_1

value: IL-1β + P. gingivalis-treated


title: IL-1β-treated HGECs - NC_2


title: Injured urethra 4A [miRNA-seq]


title: Injured urethra 4A [RNA-seq]

data_processing:
Hisat2 version 2.1.0 was used to aligned the obtained reads to the genome of Rattus norvegicus.
Stringtie version 2.1.6 was used to merge the transcripts.
Gffcompare version 0.12.2 was used to compare the merged transcripts to the annotated transcripts in the Rattus norvegicus database.
Cuffquant version 2.2.1 was used to quantify the expression levels (FPKM) values of transcripts.
Cuffnorm version 2.2.1 was used to normalize the FPKM values of transcripts.
Genome_build: rn7
Supplementary_files_format_and_content: tab-delimited excel files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted from  the urethral tissue of the injured and normal rats using the Trizol reagent.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: After successful anesthesia, the rats were fixed on the constant temperature pad of the small animals on the operating table in a supine position, the perineal hair was removed, the perineal skin was carefully disinfected with Iodophor, and then the sheet was laid. The skin of the ventral penis was cut to expose the urethra. A small opening was cut at the urethral orifice with ophthalmic scissors. The urethral orifice was pulled open with three vascular forceps, and the rat urethra was slightly expanded with a certain round end iron rod, The round end of the customized iron bar was roasted on the external flame of alcohol lamp for 6 ~ 7 seconds and then inserted into the urethra, with the insertion depth of about 26 mm. After each withdrawal, the customized iron bar was roasted for 6 ~ 7 seconds and inserted again, so as to scald the urethral mucosa for 2 ~ 3 times. Then remove the tourniquet, 5-0 absorbable suture penis skin. On the third day after modeling of urethral injury, the rats were killed and the urethral tissue was removed.

value: urethra

value: male


title: IL4/IL13 K12-3 C


title: P. gingivalis persisters-treated HGECs - Tb_2

value: P. gingivalis persisters-treated


title: Treated TGF-B siZNF827 HMLE R2

description:
All_samples_HMLE_TPM.txt.gz
VT1023

source_name: Treated TGF-B_siZNF827_HMLE

value: HMLE

value: siRNA mediated ZNF827 knockdown in HMLE cells after TGF-beta induction (d4)


title: IL4/IL13 K12-3 B


title: Normal urethra 3A [RNA-seq]


title: Injured urethra 3A [RNA-seq]


title: P. gingivalis persisters-treated HGECs - Tb_3


title: Normal urethra 2A [miRNA-seq]

value: Normal Urethra


title: IL4/IL13 K12-3 A


title: IL4/IL13 H1 D

description: HSV1 miR-H1 Transfected M2 macrophage

value: HSV1 miR-H1


title: Treated TGF-B siZNF827 HMLE R1

description:
All_samples_HMLE_TPM.txt.gz
VT1022


title: Normal urethra 2A [RNA-seq]


title: P. gingivalis persisters-treated HGECs - Tb_1


title: Treated TGF-B siControl HMLE R3

description:
All_samples_HMLE_TPM.txt.gz
VT1021

source_name: Treated TGF-B_siControl_HMLE

value: Non-targeting control in HMLE cells after TGF-beta induction (d4)


title: IL4/IL13 H1 B

description: HSV1 miR-H1 Transfected M2 macrophage

value: M2 macrophage


title: Treated TGF-B siControl HMLE R2

description:
All_samples_HMLE_TPM.txt.gz
VT1020


title: P. gingivalis-treated HGECs - Ta_3

value: P. gingivalis-treated


title: Treated TGF-B siZNF827 HMLE R3

description:
All_samples_HMLE_TPM.txt.gz
VT1024


title: Treated TGF-B siControl HMLE R1

description:
All_samples_HMLE_TPM.txt.gz
VT1019


title: IL4/IL13 H1 C

description: HSV1 miR-H1 Transfected M2 macrophage


title: IL4/IL13 H1 A

description: HSV1 miR-H1 Transfected M2 macrophage


title: P. gingivalis-treated HGECs - Ta_1


title: P. gingivalis-treated HGECs - Ta_2


title: Untreated HMLE R2

description:
All_samples_HMLE_TPM.txt.gz
VT1017

value: Untreated HMLE


title: Normal urethra 3A [miRNA-seq]

value: Sprague Dawley

value: Male


title: Untreated HMLE R3

description:
All_samples_HMLE_TPM.txt.gz
VT1018


title: CUT&RUNseq_H3K36me3_F2_K27me3_GMpGPm_hermaphrodite_germline_rep2

city: Santa Cruz

first: Susan

last: Strome

address: 1156 High St

department: MCD Biology

institute: UC Santa Cruz

description:
CRseq_rawCounts.matrix.txt
CRseq_zscores.matrix.txt

data_processing:
library strategy: Cut&Run
Libraries sequenced on the NovaSeq platform were sequenced and demultiplexed at the QB3 Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley. Libraries sequenced on the NextSeq platform were sequenced and demultiplexed at UC Santa Cruz.
Illumina reads longer than 50 bp were trimmed to 50 bp. 50 bp reads were mapped to the Bristol (N2) genome version WS220 using tophat2 (v2.1.1) with bowtie2 (2.3.5.1).
For RNA-seq samples, R1 and R2 reads were mapped 3 ways: as single-end reads allowing 1 mismatch (mm1), as single-end reads allowing 0 mismatches (mm0) and as paired-end reads allowing 1 mismatch using -g 1 (1 max multihit) with a mate inner distance set to 200, a mate standard deviation of 50, and a segment length of 25.   For CUT&RUN samples, R1 and R2 reads were mapped 2 ways: as single-end reads allowing 1 mismatch (mm1) and as single-end reads allowing 0 mismatches (mm0).  For all samples, reads per transcript or gene body were counted using htseq and a gtf file specifying transcript/gene body (union of all exons) or SNP locations per transcript/gene body.
To determine RPKM for all reads that mapped to a transcript or gene body,  only the first mate (R1) of paired-end Illumina reads that mapped allowing 1 mismatch was used. RPKM was calculated by first scaling total reads used to 1 million, then dividing by transcript length in kb (union of all exons).   To determine allele-specific transcript and gene body reads, both mates of paired-end reads were mapped as single-end reads from which only SNP-containing reads were used for further SNP analysis. Reads that emanated from the sperm allele (N2 background) were SNP-containing reads that mapped to the N2 genome when allowing 0 mismatches. Reads that emanated from the oocyte allele (CB4856 background) were SNP-containing reads that mapped to the N2 genome when allowing 1 mismatch but not 0 mismatches. RPSM (reads per SNP per million) was calculated by scaling total SNP-containing reads to 1 million, then dividing transcript or gene body SNP-containing reads (reads per million) by the number of SNP locations in the transcript or gene body (per SNP).  To perform differential gene expression analysis, reads that were mapped paired-end using -g 1 (1 max multihit) with a mate inner distance set to 200, a mate standard deviation of 50, and a segment length of 25 were used to calculate significantly misexpressed genes using the differential analysis program DESeq2 (1.22.2).
Assembly: ce10
Supplementary files format and content: RNAseq_rawCounts.matrix.txt and CRseq_rawCounts.matrix.txt  are matrices containing raw gene-level counts over exons annotated in a Ensembl ce10 (WS220) GTF file. Counts were generated using HTseq from 1) R1 and R2 reads mapped as pairs for downstream differential expression analysis, 2) from R1 reads mapped as single end reads for RPKM calculations or 3) R1 and R2 reads mapped as single end reads and filtered for reads overalpping SNPs between Bristol (N2) and Hawaii (CB4856) genomes. RNAseq_DEGs_RPKM_RSPM.matrix.txt is a matrix containing log2 fold changes and adjusted p values generated with DESeq as well as transcript reads per kilobase per million (RPKM) and gamete-specific transcript reads per SNP per million SNPs (RSPM). CRseq_zscores.matrix.txt is a matrix containing H3K27me3 and H3K36me3 zscores calculated over exons and gamete-specific zscores.

organism: Caenorhabditis elegans

source_name: distal half of hermaphrodite germline

growth_protocol: All strains were maintained on nematode growth medium (NGM) agar plates seeded with a lawn of Escherichia coli OP50 and maintained at 20˚C except for fem-2 containing strains, which were maintained at 15˚C. To generate females, fem-2 containing strains were raised at 25˚C until they developed to the L4 stage

extract_protocol:
For germline collections, worms were selected at the L4 stage and allowed to develop 1 day at 20˚C to reach the 1st day of adulthood. Worms were decapitated to extrude the germlines. The distal halves of the germlines were collected by cutting the germline at the bend and transferring to ice-cold TRIzol reagent to reach a total of 30-50 germlines. Biological replicates of germlines in TRIzol were stored at -80˚C for later use in RNA sequencing library preparation.  2-4 biological replicates were collected for each genotype.   For L1 collections, gravid mothers were allowed to lay eggs overnight at 20˚C. The next day, late-stage embryos along with some bacteria were transferred to 50 uL drops of S Basal on gelatin chrom alum-coated slides. After 2 hours at room temperature, newly hatched L1 larvae were transferred to ice-cold TRIzol. This process of transferring embryos to S basal, incubating 2 hours, and transferring newly hatched L1 larvae to TRizol was repeated throughout the day to reach a final collection of ~100 newly hatched larvae per replicate. Biological replicates of L1 larvae in TRIzol were stored at -80˚C for later use in RNA sequencing library preparation. 3 biological replicates were collected for each genotype.
Libraries were prepared according to manufacturer's instructions.  For transcript analysis, RNA was polyA-selected (NEB #E7490) and libraries prepared (NEB #E7530). For CUT&RUN library preparation, DNA associated with H3K27me3 and H3K36me3 was collected via CUT&RUN method (Skene and Henikoff 2017; Skene et al. 2018) and libraries prepared (Tecan Genomics #0344NB-32).

tag: genotype

tag: mother genotype

tag: father genotype

value: no father

tag: molecule subtype

value: DNA associated with H3K36me3


title: HGECs - BL_1

value: Primary human gingival epithelial cells (HGECs)

value: untreated


title: CUT&RUNseq_H3K27me3_F2_K27me3_GMpGPm_hermaphrodite_germline_rep2

value: DNA associated with H3K27me3


title: CUT&RUNseq_H3K36me3_F2_K27me3_GMpGPm_hermaphrodite_germline_rep1


title: HGECs - BL_2


title: Untreated HMLE R1

description:
All_samples_HMLE_TPM.txt.gz
VT1016


title: CUT&RUNseq_H3K27me3_F1_K27me3_MpPp_hermaphrodite_germline_rep2

value: fem-2(b245ts) (CB4856 background)


title: dof4-1, replicate 2

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

institute: IBMCP

data_processing:
adaptor removal and low-quality trimming of raw reads with Cutadapt, clean reads  quality assessed with FastQC
reads mapped to Arabidopsis thaliana genome using HISAT2
gene counts obtained with Htseq-count and used for differential expression analysis using DESeq2
Assembly: TAIR 10
Supplementary files format and content: Excel file includes count  values for each sample

organism: Arabidopsis thaliana

source_name: seeds

extract_protocol:
Seed total RNA extraction was performed according to Oñate-Sánchez and Vicente-Carbajosa (2008). DNA removal was performed with DNAse kit (E.Z.N.A).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: background ecotype

tag: tissuie

value: seeds

value: 9 days after polinization


title: CUT&RUNseq_H3K27me3_F1_K27me3_MpPp_hermaphrodite_germline_rep1


title: dof4-1, replicate 3


title: dof4-1, replicate 1


title: CUT&RUNseq_H3K36me3_F1_K27me3_MpPm_hermaphrodite_germline_rep2


title: wild type Col-0, replicate 2

value: wild type


title: covid-19_lung_cov60

city: Karimnagar

first: Abhilash

last: Dasari

state: Telangana

address: H.No:8-4-652/3/1/1, Hanuman Nagar, Karimnagar

department: Biochemical engineering and biotechnology

country: India

institute: IIT Delhi

data_processing:
Quality test is performed using FastQC (version 0.11.9)
Using Trimmomatic (version 0.39) adaptor content and low quality bases are removed.
star aligner (version 2.7.8a) is used to align the reads.
Feature counts subreads package (version 2.0.1) is used to estimate the expression values of genes
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include read values for each Sample ...
Supplementary_files_format_and_content: Matrix table with compiled raw counts of all samples in csv file

source_name: Dead covid-19 patient lung

growth_protocol: Samples are extracted from  the parenchyma region of human lungs, these tissues are not grown invitro.

extract_protocol:
Lung tissue was harvested from the parenchyma region using standard protocol for histology and snap frozen within two hours for RNA extraction is done.
Total RNA was extracted from lung tissue using the Maxwell automated instrument and the Maxwell® RSC Viral Total Nucleic Acid Purification Kit (Promega)

treatment_protocol: samples are extracted from  the parenchyma region of human lungs, we haven't performed any specific treatment on extracted samples

value: lung tissue

tag: gender

tag: disease state


title: CUT&RUNseq_H3K27me3_F2_K27me3_GMpGPm_hermaphrodite_germline_rep1


title: CUT&RUNseq_H3K27me3_F1_K27me3_MpPm_hermaphrodite_germline_rep2


title: covid-19_lung_cov54


title: wild type Col-0, replicate 1

tag: age


title: HepAD38 without DOX  RNA-seq rep3

city: Beijing

first: Xiong

last: Ji

address: Yiheyuan Road

department: School of life science

institute: Peking University

data_processing:
Sequenced reads were removed adaptor and low-quality reads with cutadapt.
The remaining reads were mapped to human genome hg19 with hisat2 (version 2.1.0)
Transcript abundance values were quantified by htseq-count(Anders et al., 2015).
Differential expression analysis was performed with DESeq2 (Love et al., 2014).
To find the genes effected by the HBV cccDNA we selected the genes overlapped with the 4C reads, then visualized with the volcano plot (FDR<0.05 and log2(FC) > 1 as the cutoff)
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq raw counts and DESeq2 results for each sample

source_name: HepG2 cell

growth_protocol: Grow HepAD38 cells in a 10-cm plate with DMEM/F-12/ PS/G418/Dox.

extract_protocol:
RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China).RNA integrity and concentration was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 2 μg RNA per sample was used as input material for the RNA  sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair,A-tailing and adapter added were implemented. The aimed products were retrieved and PCR was performed, then the library was completed.

treatment_protocol: Change the medium to DMEM/F-12 containing ,10% tet-free FBS, PS, and G418, and allow the cells to propagate for 15 days.

tag: with dox or not

value: without DOX

tag: hbv replication

value: Yes


title: covid-19_lung_cov55

tag: tissue

value: Female


title: HGECs - BL_3

last: Wang

tag: cell type


title: jao2-1_Bc_rep3

city: Strasbourg

first: Thierry

last: HEITZ

address: 12 rue du General Zimmer

department: IBMP

country: France

institute: CNRS

data_processing:
Quality check with fastQC version0.11.5
Mapping to the TAIR10 (Araport11) reference genome with Hisat2 v2.1.0
Aligned reads were summarized over annotated gene models using HTSeq-counts v0.9.9
Differentially expression analysis was performed with DESeq2 (package R) version v1.18.1
Genome_build: TAIR10 (Araport11)
Supplementary_files_format_and_content: csv files with differentially expressed genes between the two analysed conditions

source_name: rosette leaves

growth_protocol: Plants were grown in individual pots under 12h/12h photoperiod

extract_protocol:
Total RNA was extracted with NucleoSpin RNA Plant kit (Macherey-Nagel). After DNAse treatment, RNA was purified using NucleoSpin RNA Clean-up kit (Macherey-Nagel).
After analysis with an Agilent 2 100 Bioanalyzer, all samples had a RIN value ≥ 6.
DNBSEQ™ Technology Platform, performed by BGI

treatment_protocol: Plants were either non-treated or inoculated with spores of Botrytis cinerea (strain B05.10), two sites per leaf. Four plants were used per biological replicate, and 4 leaves were collected per plant.

value: leaf

tag: treatment


title: covid-19_lung_cov53


title: CUT&RUNseq_H3K36me3_F1_K27me3_MpPp_hermaphrodite_germline_rep1


title: covid-19_lung_cov50


title: jao2-1_Bc_rep2


title: CUT&RUNseq_H3K36me3_F1_K27me3_MpPp_hermaphrodite_germline_rep2


title: jao2-1_Bc_rep1


title: CUT&RUNseq_H3K36me3_F1_K27me3_MpPm_hermaphrodite_germline_rep1


title: HepAD38 without DOX  RNA-seq rep2

tag: cell line


title: covid-19_lung_cov48


title: CUT&RUNseq_H3K36me3_him8_male_germline_rep1

source_name: distal half of male germline


title: CUT&RUNseq_H3K27me3_him8_male_germline_rep2


title: covid-19_lung_cov47


title: HepAD38 with DOX  RNA-seq rep3

value: with DOX

value: No


title: CUT&RUNseq_H3K36me3_him8_male_germline_rep2


title: HepAD38 without DOX  RNA-seq rep1


title: WT_Bc_rep2


title: CUT&RUNseq_H3K27me3_him8_male_germline_rep1


title: CUT&RUNseq_H3K27me3_F1_K27me3_MpPm_hermaphrodite_germline_rep1


title: WT_Bc__rep1


title: CUT&RUNseq_H3K36me3_K27me3_MpPp_hermaphrodite_germline_rep2

value: mes-3(bn35)/hT2-GFP; him-8(e1489) (N2 background)


title: covid-19_lung_cov42

value: Male


title: HepAD38 with DOX  RNA-seq rep2


title: covid-19_lung_cov41


title: HepAD38 with DOX  RNA-seq rep1


title: CUT&RUNseq_H3K27me3_K27me3_MpPp_hermaphrodite_germline_rep2


title: HepAD38 control 3C-HTGTS

data_processing:
library strategy: 4C
Pair-end Illumina sequencing fastq data were remove adaptor and low-quality reads with cutadapt and then demultiplexing with fastq-multx (-m 0).
Pair-end reads without enzyme site or bait site were filtered (enzyme sites were filtered with trimLinker, one tools form ChIA-PET2, with parameters -t 12 -m 2 -k 1 -l 16).
The R2 end of the remaining reads were mapped to human genome hg19 with bowtie2 ("--very-sensitive-local -L 30 --score-min G,20,8).
The mapping reads were filtered the duplicated reads, self-ligation reads, relegation reads and dumped reads.
For visualization, we convert the final bam files into bigwig file with bamCoverage (--binSize 10 --normalizeUsing RPKM), and then upload the bigwig file to UCSC genome browser. For the visualization in Fig. 6, supplementary information, Fig S6, to get a more accurate view of the contacts, we also normalized the bias caused by restriction sites with 4C-ker.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files, which contain the normalized tags (RPKM).
Supplementary_files_format_and_content: bedGraph files, which contain the normalized tags with 4C-ker.

growth_protocol: HepAD38 cells were maintained in Dulbecco's modified Eagle medium/ F-12 with 10% FBS,DOX. HepG2-NTCP cells (AC12 clone) derive from HepG2 cells overexpressing human sodium taurocholate co-transporting polypeptide (NTCP). HepG2-NTCP cells are grown in DMEM with 10% FBS.

extract_protocol:
3C libraries were generated as previously described. Briefly, 10 million cells were cross-linked with 1% (v/v) formaldehyde for 10’ at room temperature, followed by quenching with glycine at a final concentration of 125 mM. Cells were lysed in 50 mM Tris-HCl, pH 7.5, containing 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100 and protease inhibitors. Nuclei were digested with 500 units of AluI restriction enzyme at 37℃ overnight, followed by ligation under dilute conditions overnight. Crosslinks were reversed and samples were treated with Proteinase K and RNase A prior to DNA precipitation.
The 3C libraries were sonicated for 30 s ON and 60 s OFF for two cycles on a Bioruptor Sonicator. Sonicated DNA was linearly amplified with a biotinylated primer. The biotin-labeled single-stranded DNA products were enriched with streptavidin C1 beads, and 3’ ends were ligated with the bridge adaptor containing a 6-nucleotide overhang. The adaptor-ligated products were amplified by a nested primer and an adaptor-complementary primer.

treatment_protocol: For infection, only enveloped DNA-containing viral particles (vp) were taken into account to determine the multiplicity of infection (MOI). AC12s were infected for 6 days with normalized amounts of virus at an MOI of 500 vp/cell.

tag: cell line source

tag: genotype/phenotype

value: HepAD38 replicates human hepatitis B virus (HBV) under conditions that can be regulated with tetracycline.

tag: primer

value: primer control

tag: restriction enzyme

value: AluI


title: jao2-1_rep3

tag: genotype


title: jao2-1_rep2


title: covid-19_lung_cov49


title: CUT&RUNseq_H3K36me3_K27me3_MpPm_hermaphrodite_germline_rep2

tag: mother genotype

tag: father genotype

value: mes-3(bn35); him-8(e1489) (N2 background)

tag: molecule subtype

value: DNA associated with H3K36me3


title: jao2-1_rep1


title: covid-19_lung_cov39

tag: gender


title: HepAD38 with DOX #2 3C-HTGTS

value: primer #2


title: HepAD38 with DOX #1 3C-HTGTS

value: primer #1


title: covid-19_lung_cov38

tag: disease state


title: HepG2-NTCP with HBV #2 3C-HTGTS

value: HepG2-NTCP cells (AC12 clone)

value: Expressing human NTCP in human hepatoma HepG2 cells (HepG2-NTCP) renders these cells susceptible for HBV infection.


title: WT_rep3


title: RNAseq_mes3_MpZm_him8_male_germline_rep3

description:
RNAseq_rawCounts.matrix.txt
RNAseq_DEGs_RPKM_RSPM.matrix.txt

data_processing:
Libraries sequenced on the NovaSeq platform were sequenced and demultiplexed at the QB3 Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley. Libraries sequenced on the NextSeq platform were sequenced and demultiplexed at UC Santa Cruz.
Illumina reads longer than 50 bp were trimmed to 50 bp. 50 bp reads were mapped to the Bristol (N2) genome version WS220 using tophat2 (v2.1.1) with bowtie2 (2.3.5.1).
For RNA-seq samples, R1 and R2 reads were mapped 3 ways: as single-end reads allowing 1 mismatch (mm1), as single-end reads allowing 0 mismatches (mm0) and as paired-end reads allowing 1 mismatch using -g 1 (1 max multihit) with a mate inner distance set to 200, a mate standard deviation of 50, and a segment length of 25.   For CUT&RUN samples, R1 and R2 reads were mapped 2 ways: as single-end reads allowing 1 mismatch (mm1) and as single-end reads allowing 0 mismatches (mm0).  For all samples, reads per transcript or gene body were counted using htseq and a gtf file specifying transcript/gene body (union of all exons) or SNP locations per transcript/gene body.
To determine RPKM for all reads that mapped to a transcript or gene body,  only the first mate (R1) of paired-end Illumina reads that mapped allowing 1 mismatch was used. RPKM was calculated by first scaling total reads used to 1 million, then dividing by transcript length in kb (union of all exons).   To determine allele-specific transcript and gene body reads, both mates of paired-end reads were mapped as single-end reads from which only SNP-containing reads were used for further SNP analysis. Reads that emanated from the sperm allele (N2 background) were SNP-containing reads that mapped to the N2 genome when allowing 0 mismatches. Reads that emanated from the oocyte allele (CB4856 background) were SNP-containing reads that mapped to the N2 genome when allowing 1 mismatch but not 0 mismatches. RPSM (reads per SNP per million) was calculated by scaling total SNP-containing reads to 1 million, then dividing transcript or gene body SNP-containing reads (reads per million) by the number of SNP locations in the transcript or gene body (per SNP).  To perform differential gene expression analysis, reads that were mapped paired-end using -g 1 (1 max multihit) with a mate inner distance set to 200, a mate standard deviation of 50, and a segment length of 25 were used to calculate significantly misexpressed genes using the differential analysis program DESeq2 (1.22.2).
Assembly: ce10
Supplementary files format and content: RNAseq_rawCounts.matrix.txt and CRseq_rawCounts.matrix.txt  are matrices containing raw gene-level counts over exons annotated in a Ensembl ce10 (WS220) GTF file. Counts were generated using HTseq from 1) R1 and R2 reads mapped as pairs for downstream differential expression analysis, 2) from R1 reads mapped as single end reads for RPKM calculations or 3) R1 and R2 reads mapped as single end reads and filtered for reads overalpping SNPs between Bristol (N2) and Hawaii (CB4856) genomes. RNAseq_DEGs_RPKM_RSPM.matrix.txt is a matrix containing log2 fold changes and adjusted p values generated with DESeq as well as transcript reads per kilobase per million (RPKM) and gamete-specific transcript reads per SNP per million SNPs (RSPM). CRseq_zscores.matrix.txt is a matrix containing H3K27me3 and H3K36me3 zscores calculated over exons and gamete-specific zscores.

value: no father


title: covid-19_lung_cov36

value: lung tissue


title: covid-19_lung_cov33


title: WT_rep2


title: HepG2-NTCP with HBV #1 3C-HTGTS


title: WT_rep1


title: RNAseq_mes3_MpZm_him8_male_germline_rep2


title: FN ribDKO rep3

city: Ube-shi

first: Kensuke

last: Shibata

state: Yamaguchi

address: 1-1 Minami-Kogushi 1-chome

country: Japan

institute: Yamaguchi univeristy

description: Sample 6

data_processing:
Illumina RTA3 software used for basecalling.
Quality trimming and adapter clipping were performed using fastp v0.20.1 with parameters -3 -q 15 -n 0 -t 1 -l 50 -w 8.
Trimmed reads were mapped to transcripts in the reference Francisella tularensis subsp. novicida U112 chromosome (NZ_CP009633.1) using Bowtie2 aligner within RSEM v1.3.1 (Robinson et al., 2009). RSEM performed the estimation of the abundance of genes and isoforms and  generated raw counts.
The EdgeR v3.32.1 software program (Li et al., 2011) was used to normalize and detect the differentially expressed genes (DEGs).
Genome_build: NZ_CP009633.1
Supplementary_files_format_and_content: tab-delimited text file includes normalized count values for each sample.

source_name: Francisella novicida U112 mutant of ribD gene replicate 3

growth_protocol: Francisella strains were cultured  to exponential phase at 37 °C in a  brain heart infusion broth (Becton, Dickinson and Company, Franklin Lakes, NJ) supplemented with cysteine.

extract_protocol:
After the culture of Francisella strains in the growth media, cell pellets were harvested using NucleoSpin RNA (Takara Bio, Cat#740955). After removal of rRNA using Illumina Ribo-Zero Plus rRNA Depletion Kit(Cat#20037135), TruSeq Stranded mRNA Library Prep Kit(Cat#20020595) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: mutant of ribD gene


title: covid-19_lung_cov32

value: Female


title: RNAseq_mes3_MpZm_him8_male_germline_rep1


title: RNAseq_him8_male_germline_rep3


title: covid-19_lung_cov25


title: RNAseq_him8_male_germline_rep2


title: WT_Bc_rep3

value: leaf


title: FN ribDKO rep2

description: Sample 5

organism: Francisella tularensis subsp. novicida U112

source_name: Francisella novicida U112 mutant of ribD gene replicate 2