title: b16_mac_cKO_rep6


title: llc_mac_cKO_rep2

status: Public on Apr 10 2021

type: SRA

city: Bethesda

first: Chuanyuan

last: Chen

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

country: USA

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
For single cell RNAseq, 10X Genomics single cell RNA-seq data were aligned and quantified using the Cell Ranger Single-Cell Software Suit (version 3.0.2) against the mm10 reference genome.
For bulk RNAseq, The adaptor sequences were first trimmed from sequencing reads by using Trim Galore! with parameters --clip_R1 3, the remaining parameters default. Trimmed reads mapped to ribosomal RNA were removed using Bowtie2 (version 2.3.5). All remaining reads were mapped to the mouse genome mm9 using STAR (version 2.7.0f). Uniquely mapped reads were selected using SAMtools (version 1.9) with mapping quality ≥ 20.
For m6Aseq, Raw sequencing reads were trimmed by TrimGalore! with adjusting the parameter --clip_R1 3. Remaining trimmed reads were aligned to the mouse genome mm9 by STAR (version 2.7.0f). Uniquely mapped reads were selected using SAMtools (version 1.9) with mapping quality ≥ 20. The m6A-enriched regions (peaks) in each sample were detected by exomePeak R package (version2.16.0) with default paramters.
Genome_build: mm9

molecule: total RNA

organism: Mus musculus

source_name: tumor infiltrating macrophage

extract_protocol:
For RNA seq, total RNA was extracted using Trizol. For m6A seq, total RNA in macrophage was extracted using Trizol and polyadenylated RNA was purified using the Dynabeads mRNA Purification Kit (Invitrogen). Fragment the RNAs into ~100-nucleotide-long fragments by 10X Fragmentation Reagent(Invitrogen) at 94℃ for 45s and stop it using the 10X Stop Solution(Invitrogen). EpiMark N6-methyladenosine enrichment kit (NEB E1610S) was used for m6A immunoprecipitation (m6A-IP) to enrich the m6A marked RNAs followed by RNA extraction by Trizol.
For RNA seq and m6A seq, the library construction was performed with SMARTer Stranded Total RNA-Seq Kit (Takara). For single cell RNA seq, the library was performed using Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1(1000128) purchased from 10X Genomics according to the protocols provided by manufactures.

tag: technology

value: bulk RNA sequencing

tag: tumor type

value: LLC (Lewis lung carcinoma)

tag: day

tag: genotype

value: Mettl14 cKO


title: llc_mac_cKO_rep1


title: BMDMs polarized with IL4 (Polysome-associated mRNA) replicate 3

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

data_processing:
RNA sequencing reads were aligned to mm10 using HISAT2 (D. Kim, B. Langmead, S. L. Salzberg, HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12, 357-360 (2015)) and reads mapping to multiple locations in the genome were discarded.
Gene expression was quantified as described using default settings (D. Ramskold, E. T. Wang, C. B. Burge, R. Sandberg, An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol 5, e1000598 (2009).) and RefSeq gene definitions (N. R. Coordinators, Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 46, D8-D13 (2018).).
Only genes with <6 missing data points were included.
Raw counts were TMM normalized (M. D. Robinson, A. Oshlack, A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11, R25 (2010)) and log2 transformed using Voom (M. E. Ritchie et al., limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43, e47 (2015).) in R 3.5.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RNA sequencing counts and TMM-log2 normalized data

source_name: BMDM

growth_protocol: Bone marrow was extracted from naïve female FVB mice, differentiated into bone marrow-derived macrophages (BMDMs) as previously described (M. Wallerius et al., Cancer Res 76, 3166-3178 (2016).)

extract_protocol:
Polysome-profiling was performed  using polarized BMDMs. A fraction (~10%) of the obtained cell population was lysed in TRIzol reagent (ThermoFisher Scientific) and used for RNA sequencing with total RNA as input. Remaining cells were lysed in a hypotonic lysis buffer, as described and and lysates were  applied onto a 5%-50% (w/v) sucrose gradient, fractionated, and fractions corresponding to mRNA associated more than 3 ribosomes were collected in TRIzol reagent for subsequent RNA extraction. Such pooled samples were used for RNA sequencing of efficiently translated polysome-associated mRNA.
SmartSeq2 sequencing libraries were prepared

treatment_protocol: BMDMs were polarized with  IFNG (200 units/mL, Peprotech) or IL4 (40 ng/mL, Peprotech) for 4h.

tag: cell type

value: Polarized BMDMs

tag: rna source

value: Polysome-associated mRNA

tag: polarization

tag: replicate


title: H18574-L1_S6_L001

city: Kiel

first: Joana

middle: Pimenta

last: Bernardes

address: Am Botanischen Garten 11

department: Systems Immunology

country: Germany

institute: Institute of Clinical Molecular Biology

data_processing:
Merge re-sequenced FastQ files (cat)
Read QC (FastQC)
Adapter and quality trimming (Trim Galore!)
Removal of ribosomal RNA (SortMeRNA)
Alignment using  STAR
Sort and index alignments (SAMtools)
Duplicate read marking (picard MarkDuplicates)
Transcript assembly and quantification (StringTie)
Create bigWig coverage files (BEDTools, bedGraphToBigWig)
Present QC for raw read, alignment, gene biotype, sample similarity, and strand-specificity checks (MultiQC)
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts for individual samples
Supplementary_files_format_and_content: Metadata including Sample ID, demographics, histology and clinical information

organism: Homo sapiens

source_name: biopsy

extract_protocol:
Whole blood and sigmoid mucosal biopsy samples (collected from the most inflamed region within 30 cm of colon sigmoideum) were collected as a longitudinal dataset from which the RNA for transcriptome analyses was isolated.
Whole RNA libraries were prepared using TruSeq RNA Library Prep technology and samples were sequenced using HiSeq 4000 (2x75bp).

treatment_protocol: 600 mg of olamkicept were administered by intravenous infusion every 2 weeks for 12 weeks (i.e. 7 infusions).

tag: tissue

value: biopsy

tag: diagnosis

value: CD

tag: response

value: NoResp

tag: remission

value: NR

tag: patient

tag: timepoint

tag: location


title: llc_mac_WT_rep4

value: wild-type


title: BMDMs polarized with IL4 (total mRNA) replicate 2

value: total mRNA


title: llc_mac_WT_rep3


title: b16_mac_cKO_rep5


title: H18580-L1_S12_L002


title: llc_mac_WT_rep2


title: H18571-L1_S3_L001


title: H18570-L1_S2_L001


title: llc_mac_WT_rep1


title: macrophage_m6A_input_cKO_rep1

value: m6A sequencing


title: macrophage_m6A_IP_cKO_rep2


title: BMDMs polarized with IL4 (Polysome-associated mRNA) replicate 1


title: BMDMs polarized with IL4 (total mRNA) replicate 1


title: H18569-L1_S1_L001

value: UC


title: macrophage_m6A_IP_cKO_rep1


title: macrophage_m6A_input_WT_rep3


title: BMDMs polarized with INFG (Polysome-associated mRNA) replicate 1

value: INFG


title: BMDMs polarized with INFG (Polysome-associated mRNA) replicate 2


title: macrophage_m6A_input_WT_rep2


title: BMDMs polarized with INFG (total mRNA) replicate 2


title: macrophage_m6A_input_WT_rep1


title: BMDMs polarized with INFG (total mRNA) replicate 1


title: macrophage_m6A_IP_WT_rep3


title: macrophage_m6A_IP_WT_rep2


title: Mock-treated HCT116

city: Shinagawa-ku

first: Hideyuki

last: Takeshima

state: Tokyo

department: Institute for Advanced Life Sciences

country: Japan

institute: Hoshi University

data_processing:
Obtained sequence reads were de-multiplexed and mapped using the Cell Ranger software (10x Genomics, version 3.0.2).
Genome_build: The human genome (build hg38)
Supplementary_files_format_and_content: Count for all the cells.

source_name: Cell line

growth_protocol: Cells were cultured in McCoy's 5A+10% FBS medium.

extract_protocol:
Cells were trypsinized and used for the analysis.
A library was prepared using the Chromium Controller (10x Genomics, Pleasanton, CA) and Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3 (10x Genomics).

treatment_protocol: The cells were seeded on day 0, and treated with 0.5 µM of DAC on days 1 and 3.  The cells were placed in fresh medium without DAC on day 5, and harvested on day 7.

tag: cell line

tag: treatment

value: Mock


title: DAC-treated HCT116

value: DAC


title: macrophage_DN_rep2

description: CX3CR1+MHC II_DN_DP.raw_count.csv

tag: technology


title: macrophage_m6A_IP_WT_rep1

tag: tumor type


title: Huh7 cells-sh USP22

city: Shanghai

first: Jing

middle: tian

last: tian

address: Dongchuan Road

country: China

institute: Shanghai Jiaotong University

data_processing:
Clean data was generated by trimming the adaptor and filtering rRNAs using Seqtk (https://github.com/lh3/seqtk)
Clean reads were mapped to homo genome (GRCh37) with Hisat2(version:2.0.4)
The uniquely mapped fragments of genes were counted by Stringtie(version:1.3.0).
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include counts for each gene in each sample

source_name: human liver

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using VAHTS mRNA-seq V2 Library Prep Kit for Illumina

value: liver

value: USP22 knockdown


title: macrophage_m6A_input_cKO_rep2

value: LLC (Lewis lung carcinoma)

tag: day


title: Huh7 sh ctrl

value: control


title: Huh7 sh E2F6

value: E2F6 knockdown


title: Huh7 cells-sh ctrl


title: macrophage_DP_rep2

description: CX3CR1+MHC II_DN_DP.raw_count.csv

value: bulk RNA sequencing

tag: genotype


title: macrophage_DP_rep1

description: CX3CR1+MHC II_DN_DP.raw_count.csv


title: GRKO_Gasttoc_4

type: RNA

city: Cambridge

first: Scott

last: Jelinsky

state: MA

address: 610 Main Street

department: Inflammation and Immunology

institute: Pfizer

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: Biotin

source_name: GRKO_gastrocnemius muscle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were maintained in a temperature- and humidity-controlled animal facility, with a 12 hours  light/dark cycle.

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

tag: strain background

tag: genotype/variation

value: GR KO

value: gastrocnemius muscle


title: B16_scRNA_cKO

description:
b16_sc_gene_count_mtx.csv
b16_sc_cell_type_information.csv

source_name: tumor immune cells

value: single cell RNA sequencing

value: Mettl14 cKO


title: GRKO_Gasttoc_3


title: macrophage_DN_rep1

description: CX3CR1+MHC II_DN_DP.raw_count.csv


title: LLC_scRNA

description:
llc_sc_gene_count_mtx.csv
llc_sc_cell_type_information.csv

value: wild-type


title: GRKO_Gasttoc_2


title: Heart_2-methyl-2-thiazoline_2

city: Kyoto

first: Masahiro

last: Nishi

address: Kajii-cho 465, Kawaramachi Hirokoji, Kamigyo

department: Cardiology

institute: Kyoto prefectural university of medicine

description: Gene expression data from mouse heart treated with 2-methyl-2-thiazoline.

hyb_protocol: RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

label: biotin

source_name: Mouse heart treated with 2-methyl-2-thiazoline

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: 10-week-old C57BL/6 male mice were prepared.

treatment_protocol: Mouse hearts were excised 4 h after a subcutaneous injection of 2-methyl-2-thiazoline (50 mg/kg) and stored at -80℃.

tag: strain

value: Left ventricule tissue

tag: Sex

value: Male

tag: age

value: 10 weeks


title: fve-4_BS-Seq

first: Pei

last: Huang

address: Fenglin Road 300

institute: Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai

description: treated with bisulfite

library_source: genomic

data_processing:
Adapters were trimmed by cutadapt (version 1.16) and low-quality sequences (q < 20) using trimmomatic (version 0.36).
Clean reads were then mapped to the Arabidopsis thaliana TAIR 10 genome using BSMAP (2.90) with default parameters
methratio.py script was used to extract the methylation ratio from BSMAP mapping results, the option -r was used to remove potential PCR duplicates.
Genome_build: TAIR10
Supplementary_files_format_and_content: The bigWig files give methylation level for all Cs(three contexts). Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position ( unconverted_C / ( converted_C+ unconverted_C ) ).

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Plants were grown at 22°C in a growth chamber with 16 h of light and 8 h of darkness on 1/2 MS medium with 0.8% glucose.

extract_protocol: Genomic DNA was extracted from 14-d-old seedlings and sent to Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, CAS (Shanghai, China)  for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.

value: fve-4 mutant

tag: tissue

value: Seedlings


title: Col-0_BS-Seq

description: treated with bisulfite

value: Col-0 wild type


title: Heart_2-methyl-2-thiazoline_3


title: H17481-L1_S48_L007

source_name: blood

value: blood

tag: diagnosis

value: UC

tag: response

value: Resp

value: NR


title: nrpe1-11_BS-Seq

description: treated with bisulfite

value: nrpe1-11 mutant


title: Heart_2-methyl-2-thiazoline_1


title: nrpd1-3_BS-Seq

description: treated with bisulfite

value: nrpd1-3 mutant


title: WT_Gastroc_4

source_name: WT_gastrocnemius muscle

value: wild type


title: GRKO_Gasttoc_1

value: GR KO

value: gastrocnemius muscle


title: 13-P999993-S001-R01: cellbender counts

status: Public on Apr 09 2021

first: Caroline

last: Porter

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

description: Cellbender remove-background corrected single-cell or single nucleus RNA-Seq (10X) Cellranger counts, stored as an HDF5 file.

data_processing:
sc/snRNA-seq: 3' RNAseq (10x kit V3 chemistry)
sc/snRNA-seq: Demultiplexing is run using Cell Ranger mkfastq.
sc/snRNA-seq: Counts matrix is generated using the Cumulus cellranger_workflow in Terra.
sc/snRNA-seq: Ambient RNA is removed using Cellbender remove-background workflow in Terra.
bulk RNA-seq: Demultiplexing is run using bcl2fastq
bulk RNA-seq: Alignment peformed using STAR
bulk RNA-seq: Counts matrix generated using RSEM
Supplementary_files_format_and_content: Raw count or cellbender count matrices are in the HDF5 Feature Barcode Matrix Format used by 10x, bulk counts matrices are provided as an RSEM counts matrix, and metadata files are comma-delimited text.

source_name: COVID-19 autpsy tissue

extract_protocol:
Dissociated individual cells or isolated individual nuclei from fresh, frozen, or cryopreserved COVID-19 autopsy samples; bulk samples were lysed in RLT buffer + 1% beta mercaptoethanol
3' RNAseq (10x kit V3 chemistry) for sc/snRNA-seq; Smart-seq2 for bulk RNA-seq

value: heart

tag: disease state

tag: sampleID

tag: donor

tag: processing

value: nuclei


title: 13-P999994-S001-R01: cellbender counts

value: kidney


title: 13-P999999-S001-R01: cellbender counts


title: 13-P999994-S002-R01: cellbender counts


title: 13-P999996-S001-R01: cellbender counts


title: 13-P999997-S001-R01: cellbender counts


title: 13-P999998-S001-R01: cellbender counts


title: Heart_Saline_2

description: Gene expression data from mouse heart treated with saline.

source_name: Mouse heart treated with saline

value: Left ventricule tissue

value: Male

tag: treatment

value: Saline


title: WT_Gastroc_2


title: Heart_Saline_1

value: 10 weeks


title: Heart_Saline_3


title: WT_Gastroc_3


title: WT_Gastroc_1


title: 13-P999992-S001-R01: cellbender counts


title: 13-P999991-S001-R01: cellbender counts


title: 12-P890292-S003-R01: cellbender counts

value: liver


title: 12-P890292-S007-R01: cellbender counts

value: lung


title: 12-P890292-S009-R01: cellbender counts


title: 12-P852049-S007-R01: cellbender counts


title: 12-P617758-S008-R01: cellbender counts


title: 12-P617758-S012-R01: cellbender counts


title: 12-P852049-S011-R01: cellbender counts


title: 12-P852049-S003-R01: cellbender counts


title: 12-P617758-S006-R01: cellbender counts


title: 12-P485759-S020-R01: cellbender counts


title: 12-P617758-S003-R01: cellbender counts


title: 12-P485759-S016-R01: cellbender counts


title: 12-P485759-S012-R01: cellbender counts


title: 12-P485759-S008-R01: cellbender counts


title: 12-P230638-S003-R01: cellbender counts


title: 04-P079042-S079-R01: cellbender counts


title: 04-P054921-S040-R01: cellbender counts

value: spleen


title: 04-P079042-S055-R01: cellbender counts

value: trachea


title: 04-P103142-S049-R01: cellbender counts


title: 04-P054921-S064-R01: cellbender counts


title: 04-P103142-S059-R01: cellbender counts

value: LN


title: 04-P103142-S069-R01: cellbender counts


title: 04-P103142-S131-R01: cellbender counts


title: 04-P006354-S023-R01: cellbender counts


title: 04-P079042-S047-R01: cellbender counts


title: 04-P054921-S032-R01: cellbender counts


title: 04-P054921-S080-R01: cellbender counts


title: 04-P006354-S031-R01: cellbender counts


title: 02-P334354-S105-R01: cellbender counts

value: brain


title: 12-P890292-S006-R01: cellbender counts


title: 02-P334354-S027-R01: cellbender counts


title: 02-P334354-S065-R01: cellbender counts

value: airway


title: 12-P230638-S005-R01: cellbender counts


title: 04-P103142-S141-R01: cellbender counts


title: 02-P348762-S026-R01: cellbender counts


title: 02-P348762-S041-R01: cellbender counts


title: 02-P348762-S011-R01: cellbender counts


title: 02-P334354-S012-R01: cellbender counts


title: 02-P248880-S041-R01: cellbender counts


title: 02-P334354-S041-R01: cellbender counts


title: 02-P248880-S026-R01: cellbender counts


title: 02-P348762-S064-R01: cellbender counts


title: 02-P118946-S070-R01: cellbender counts


title: 02-P118946-S043-R01: cellbender counts


title: 13-P999999-S001-R01: cellranger counts

description: Single-cell or single nucleus RNA-Seq (10X) Cellranger counts, stored as an HDF5 file.


title: 13-P999997-S001-R01: cellranger counts


title: 13-P999994-S002-R01: cellranger counts


title: 13-P999993-S001-R01: cellranger counts


title: 13-P999992-S001-R01: cellranger counts


title: 13-P999994-S001-R01: cellranger counts


title: 02-P240970-S016-R01: cellbender counts


title: 02-P240970-S036-R01: cellbender counts


title: 02-P166169-S022-R01: cellbender counts


title: 02-P166169-S026-R01: cellbender counts


title: 02-P005175-S022-R01: cellbender counts


title: 13-P999998-S001-R01: cellranger counts


title: 12-P890292-S009-R01: cellranger counts


title: 02-P005175-S053-R01: cellbender counts


title: 12-P890292-S007-R01: cellranger counts


title: 02-P118946-S058-R01: cellbender counts


title: 12-P890292-S006-R01: cellranger counts


title: 02-P240970-S048-R01: cellbender counts


title: 12-P852049-S011-R01: cellranger counts


title: 12-P852049-S007-R01: cellranger counts


title: 12-P852049-S003-R01: cellranger counts


title: 12-P617758-S012-R01: cellranger counts


title: 12-P617758-S003-R01: cellranger counts


title: 12-P485759-S020-R01: cellranger counts


title: 12-P617758-S006-R01: cellranger counts


title: 02-P005175-S041-R01: cellbender counts


title: 12-P617758-S008-R01: cellranger counts


title: 12-P485759-S016-R01: cellranger counts


title: 12-P485759-S012-R01: cellranger counts


title: 12-P230638-S005-R01: cellranger counts


title: 13-P999991-S001-R01: cellranger counts


title: 12-P890292-S003-R01: cellranger counts


title: 12-P485759-S008-R01: cellranger counts


title: 13-P999996-S001-R01: cellranger counts


title: 04-P079042-S079-R01: cellranger counts


title: 04-P079042-S055-R01: cellranger counts


title: 04-P103142-S069-R01: cellranger counts


title: 04-P103142-S049-R01: cellranger counts


title: 12-P230638-S003-R01: cellranger counts


title: 04-P054921-S080-R01: cellranger counts


title: 04-P054921-S032-R01: cellranger counts


title: 04-P103142-S131-R01: cellranger counts


title: 04-P054921-S064-R01: cellranger counts


title: 04-P006354-S031-R01: cellranger counts


title: 04-P079042-S047-R01: cellranger counts


title: 04-P054921-S040-R01: cellranger counts


title: 02-P348762-S064-R01: cellranger counts


title: 02-P334354-S065-R01: cellranger counts


title: 02-P348762-S026-R01: cellranger counts


title: 02-P348762-S011-R01: cellranger counts


title: 02-P334354-S105-R01: cellranger counts


title: 04-P006354-S023-R01: cellranger counts


title: 02-P334354-S041-R01: cellranger counts


title: 04-P103142-S059-R01: cellranger counts


title: 04-P103142-S141-R01: cellranger counts


title: 02-P334354-S027-R01: cellranger counts


title: 02-P334354-S012-R01: cellranger counts


title: 02-P248880-S041-R01: cellranger counts


title: 02-P248880-S026-R01: cellranger counts


title: 02-P240970-S048-R01: cellranger counts


title: 02-P240970-S036-R01: cellranger counts


title: 02-P166169-S022-R01: cellranger counts


title: 02-P240970-S016-R01: cellranger counts


title: 02-P118946-S070-R01: cellranger counts


title: 02-P005175-S041-R01: cellranger counts


title: 02-P166169-S026-R01: cellranger counts


title: 02-P005175-S053-R01: cellranger counts


title: B16_scRNA_WT

tag: technology

value: single cell RNA sequencing

value: wild-type


title: 02-P005175-S022-R01: cellranger counts


title: 02-P118946-S043-R01: cellranger counts


title: 02-P118946-S058-R01: cellranger counts


title: 02-P348762-S041-R01: cellranger counts


title: HepG2_0.1% DMSO_48h_Rep3

city: Guangzhou

first: Lan

last: Tang

state: Guangdong

address: 1838  Guangzhou North Ave,

department: School of Pharmaceutical Science

institute: Southern Medical University

data_processing:
Illumina Casava1.8 software used for base-calling.
Reads containing adapter, reads containing ploy-N and low quality reads were trimmed.
STAR2.5.1b was used for alignment.
The counts and Fragments Per Kilobase of exon per Megabase of library size (FPKM) of genes were calculated and normalized by DESeq2 1.10.1.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include count or log2FPKM values for each Sample …

growth_protocol: culture medium: DMEM; growth: adherent

extract_protocol:
HepG2 cells upon treatment of the 10μM Oridonin or DMSO(0.1%) were grown on the 6-well cell culture plates,which were devided into two groups with 3 duplicate samples. Centrifugal column were used to extract total cellular RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: cell type

value: human liver carcinoma cells

tag: culture medium

value: DMEM


title: HepG2_10μM Oridonin_48h_Rep2

value: 10μM Oridonin_48h


title: HepG2_0.1% DMSO_48h_Rep2


title: HepG2_0.1% DMSO_48h_Rep1


title: CRO416A50: Tyk2  KO 0.1 ng/ml IFNL rep2

city: London

first: Andreas

last: Wack

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Adaptor removal and quality trimming done with Trimmomatic v 0.36
Read alingment and gene counts was performed with RSEM v 1.2.31 and STAR v 2.5.2a
Differential expression analysis was carried out with DESeq2 package ( version 1.20.0 ) with R version 3.5.1
Genome_build: Ensembl GRCm38 release 89
Supplementary_files_format_and_content: Tab-delimited text include normalized counts per gene and per sample (generated by DESeq2).

source_name: neutrophils

growth_protocol: Mouse neutrophils were isolated by negative selection from bone marrow of mice with the indicated genotypes using EasySep™ Mouse Neutrophil Enrichment Kit (STEMCELL Technologies) according to the manufacturer’s instructions

extract_protocol:
RNA was isolated  by  the Qiagen RNeasy mini kit
library was prepared using polyA KAPA mRNA Hyper Prep

treatment_protocol: Neutrophils  were either mock treated or treated with either IFNab (0.1ng/ml or 3 ng/ml) or IFNL (0.1ng/ml or 3 ng/ml)

tag: genotype

value: tyk2 KO

tag: passsage

value: primary

value: neutrophils


title: CRO416A49: Tyk2  KO 0.1 ng/ml IFNL rep1

tag: strain


title: CRO416A53: Tyk2  KO 3 ng/ml IFNL  rep2


title: CRO416A46: Tyk2 KO 3 ng/ml IFNaBD rep1


title: CRO416A51: Tyk2  KO 0.1 ng/ml IFNL rep3


title: CRO416A45: Tyk2 KO 0.1 ng/ml IFNaBD rep3


title: HepG2_10μM Oridonin_48h_Rep3


title: CRO416A54: Tyk2  KO 3 ng/ml IFNL  rep3


title: CRO416A52: Tyk2  KO 3 ng/ml IFNL  rep1


title: CRO416A48: Tyk2 KO 3 ng/ml IFNaBD rep3


title: HepG2_10μM Oridonin_48h_Rep1


title: CRO416A44: Tyk2 KO 0.1 ng/ml IFNaBD rep2


title: CRO416A43: Tyk2 KO 0.1 ng/ml IFNaBD rep1


title: CRO416A29: Tyk2 KO mock rep2


title: CRO416A28: Tyk2 KO mock rep1


title: CRO416A41: wt 3 ng/ml IFNL rep2

value: wt


title: CRO416A40: wt 3 ng/ml IFNL rep1


title: CRO416A42: wt 3 ng/ml IFNL rep3


title: CRO416A30: Tyk2 KO mock rep3


title: CRO416A39: wt 0.1 ng/ml IFNL rep3


title: CRO416A38: wt 0.1 ng/ml IFNL rep2


title: THP1_4hr_IMQ+X_rep1

city: Taoyuan City

first: Shih-Yi

last: Chuang

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

description:
Gene expression after 4hr in IMQ+X_THP1 cells
X

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction10.7.3.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process. 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

growth_protocol: Human promonocytic leukemia cells THP1 was maintained in RPMI 1640 (Gibco) supplemented with 10% heat-inactivated FBS, and 100 U/mL of penicillin and streptomycin.

extract_protocol: Total cellular RNA was extracted using the Direct-zolTM MiniPrep RNA isolation kit with RNase-free DNase1 digestion to remove genomic DNA contamination according to the manufacturer’s instructions.

treatment_protocol: THP-1 was differentiated into macrophages by treating cells with 100 ng/ml of PMA for 24-36 h, followed by overnight incubation in fresh medium. THP1 cells were pretreated with DMD following in the presence of IMQ.

value: peripheral blood

value: Monocyte cell


title: THP1_4hr_Ctrl_rep1

description:
Gene expression after 4hr in normal THP1 cells
Ctrl


title: CRO416A37: wt 0.1 ng/ml IFNL rep1


title: THP1_4hr_IMQ_rep1

description:
Gene expression after 4hr in IMQ_THP1 cells
IMQ


title: CRO416A32: wt 0.1 ng/ml IFNaBD rep2


title: CRO416A47: Tyk2 KO 3 ng/ml IFNaBD rep2


title: CRO416A31: wt 0.1 ng/ml IFNaBD rep1


title: CRO416A33: wt 0.1 ng/ml IFNaBD rep3


title: CRO416A36: wt 3 ng/ml IFNaBD rep3


title: CRO416A27: wt mock rep3


title: CRO416A34: wt 3 ng/ml IFNaBD rep1


title: CRO416A35: wt 3 ng/ml IFNaBD rep2


title: CRO416A21: Tyk2 KO IFNab 0.3 ng/ml rep3

source_name: airway epithelia (AEC)

growth_protocol: Primary cells isolated from tracheas by enzymatic treatment were seeded onto 0.4 μm pore size clear polyester membrane  coated with a collagen solution. At confluence, media was removed from the upper chamber to establish an air- liquid interface (ALI). Fully differentiated, 10-14 days-old post ALI cultures were routinely used for experiments.

extract_protocol:
RNA was isolated from MTEC cultures by directly lysing the cells in the transwells, using the Qiagen RNeasy mini kit
library was prepared using polyA KAPA mRNA Hyper Prep kit  following manufacturer’s protocols

treatment_protocol: AEC were either mock treated or treated with either IFNab (0.3ng/ml) or IFNL (0.3/ml)

value: airway epithelial cells


title: CRO416A19: Tyk2 KO IFNab 0.3 ng/ml rep1


title: CRO416A24: Tyk2 KO IFNab 3 ng/ml rep3


title: CRO416A18: Tyk2 KO IFNL 0.3 ng/ml rep3


title: CRO416A25: wt mock rep1


title: CRO416A23: Tyk2 KO IFNab 3 ng/ml rep2


title: CRO416A17: Tyk2 KO IFNL 0.3 ng/ml rep2


title: CRO416A20: Tyk2 KO IFNab 0.3 ng/ml rep2


title: CRO416A26: wt mock rep2


title: CRO416A12: wt IFNab 3 ng/ml rep3


title: CRO416A8: wt IFNab 0.3 ng/ml rep2


title: CRO416A16: Tyk2 KO IFNL 0.3 ng/ml rep1


title: CRO416A15: Tyk2 KO mock rep3


title: CRO416A14: Tyk2 KO mock rep2


title: CRO416A10: wt IFNab 3 ng/ml rep1


title: CRO416A13: Tyk2 KO mock rep1


title: CRO416A7: wt IFNab 0.3 ng/ml rep1


title: CRO416A5: wt IFNL 0.3 ng/ml rep2


title: CRO416A11: wt IFNab 3 ng/ml rep2


title: CRO416A9: wt IFNab 0.3 ng/ml rep3


title: CRO416A6: wt IFNL 0.3 ng/ml rep3


title: CRO416A22: Tyk2 KO IFNab 3 ng/ml rep1


title: CRO416A2: wt mock rep2


title: CRO416A4: wt IFNL 0.3 ng/ml rep1


title: CRO416A1: wt mock rep1


title: HSV+IFNbeta_8dpi-3 (techn. Rep. 2)

city: Vienna

first: Veronica

last: Krenn

address: Dr. Bohr gasse 3

country: Austria

institute: Institute for Molecular Biotechnology (IMBA)

data_processing:
Bascalling performed using RTA 1.18.66.3
Technical replicates are merged with samtools (v1.4)
The strand specific reads were screened for ribosomal RNA by aligning with BWA (v0.7.12) against known rRNA sequences (RefSeq).
The rRNA subtracted reads were aligned with TopHat (v2.1.1) against the Homo sapiens genome (hg38). Microexon-search was enabled. Additionally, a gene model was provided as GTF (UCSC, 2015_01, hg38).
The aligned reads were counted with HTSeq (0.6.1p1).
Genome_build: hg38
Supplementary_files_format_and_content: Text file (txt) containing the raw gene counts of HTseq (columns: symbol, count)

molecule: polyA RNA

source_name: human induced pluripotent stem cells

growth_protocol: Human ESC H9 cells were differentiated to 3D brain organoids according to the original cerebral organoid protocol (Lancaster et al. Nature 2013)

extract_protocol:
RNA was isolated from a pool of 4 organoids at 4dpi and 8dpi using RNeasy Micro Kit (QIAGEN, cat. #74004) according to the manufacturers instructions. Before lysis in RLT buffer, organoids were incubated in cold Cell recovery solution (Corning BDC354253) on ice for 1h and washed twice with cold DEPC-treated PBS to remove excess of Matrigel.
RNA concentration and integrity was analysed on a Frgament Analyzer (Advanced Analytical Technologies, Inc.). Libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, cat. # E7420L). Barcoded samples were multiplexed and sequenced on four lanes of 50bp SE on a HighSeq2500 (Illumina). Sample preparation and sequencing was performed at the VBCF NGS Unit (www.vbcf.ac.at).

treatment_protocol: Day 11 organoids were exposed to MOCK or Herpex Simplex Virus 1 (HSV-1, strain F, MOI 0.001) for 1 day, embedded in Matrigel and then cultured for additional 7 days (8dpi). Treatment with human IFNalpha (10ng/ml) or human IFNbeta (10ng/ml) was applied at 2,4 and 6 dpi. In untreated samples, BSA 0.1% solution was used.

tag: stage for hsv exposure

value: day 11

tag: days post infection

value: 8 dpi

value: IFNbeta

tag: treatment applications


title: HSV+IFNbeta_8dpi-3 (techn. Rep. 1)


title: HSV+IFNalpha_8dpi-1 (techn. Rep. 1)

value: IFNalpha


title: HSV+IFNbeta_8dpi-1 (techn. Rep. 2)


title: HSV+IFNalpha_8dpi-2 (techn. Rep. 2)


title: HSV+IFNalpha_8dpi-3 (techn. Rep. 2)


title: HSV+IFNalpha_8dpi-2 (techn. Rep. 1)


title: HSV+IFNbeta_8dpi-1 (techn. Rep. 1)


title: HSV_8dpi-3 (techn. Rep. 2)

value: untreated


title: HSV_8dpi-2 (techn. Rep. 1)


title: MOCK+IFNbeta_8dpi-3 (techn. Rep. 2)


title: HSV+IFNalpha_8dpi-1 (techn. Rep. 2)


title: MOCK+IFNbeta_8dpi-2 (techn. Rep. 1)


title: CRO416A3: wt mock rep3


title: HSV_8dpi-1 (techn. Rep. 2)


title: HSV_8dpi-2 (techn. Rep. 2)


title: MOCK+IFNalpha_8dpi-3 (techn. Rep. 2)


title: MOCK+IFNbeta_8dpi-3 (techn. Rep. 1)


title: MOCK+IFNbeta_8dpi-2 (techn. Rep. 2)


title: MOCK+IFNbeta_8dpi-1 (techn. Rep. 2)


title: MOCK+IFNbeta_8dpi-1 (techn. Rep. 1)


title: HSV+IFNbeta_8dpi-2 (techn. Rep. 1)


title: HSV+IFNbeta_8dpi-2 (techn. Rep. 2)


title: HSV_8dpi-3 (techn. Rep. 1)


title: HSV+IFNalpha_8dpi-3 (techn. Rep. 1)


title: MOCK+IFNalpha_8dpi-3 (techn. Rep. 1)


title: MOCK+IFNalpha_8dpi-2 (techn. Rep. 1)


title: MOCK+IFNalpha_8dpi-1 (techn. Rep. 2)


title: HSV_8dpi-1 (techn. Rep. 1)


title: MOCK+IFNalpha_8dpi-1 (techn. Rep. 1)


title: MOCK_8dpi-1 (techn. Rep. 1)


title: HSV+IFNbeta_4dpi-3 (techn. Rep. 2)

value: 4 dpi

value: 2 dpi


title: MOCK_8dpi-2 (techn. Rep. 2)


title: MOCK_8dpi-3 (techn. Rep. 2)


title: MOCK_8dpi-2 (techn. Rep. 1)


title: MOCK_8dpi-1 (techn. Rep. 2)


title: HSV+IFNbeta_4dpi-2 (techn. Rep. 1)


title: HSV+IFNbeta_4dpi-2 (techn. Rep. 2)


title: HSV+IFNbeta_4dpi-3 (techn. Rep. 1)


title: HSV+IFNbeta_4dpi-1 (techn. Rep. 1)


title: HSV+IFNbeta_4dpi-1 (techn. Rep. 2)


title: HSV+IFNalpha_4dpi-3 (techn. Rep. 2)


title: HSV+IFNalpha_4dpi-1 (techn. Rep. 2)


title: MOCK+IFNalpha_8dpi-2 (techn. Rep. 2)


title: HSV_4dpi-3 (techn. Rep. 1)


title: HSV+IFNalpha_4dpi-2 (techn. Rep. 2)


title: HSV+IFNalpha_4dpi-3 (techn. Rep. 1)


title: HSV_4dpi-1 (techn. Rep. 1)


title: HSV_4dpi-2 (techn. Rep. 2)


title: MOCK+IFNbeta_4dpi-3 (techn. Rep. 2)


title: HSV_4dpi-2 (techn. Rep. 1)


title: HSV_4dpi-1 (techn. Rep. 2)


title: MOCK_8dpi-3 (techn. Rep. 1)


title: MOCK+IFNbeta_4dpi-2 (techn. Rep. 2)


title: MOCK+IFNbeta_4dpi-2 (techn. Rep. 1)


title: HSV+IFNalpha_4dpi-2 (techn. Rep. 1)


title: MOCK+IFNbeta_4dpi-1 (techn. Rep. 1)


title: HSV+IFNalpha_4dpi-1 (techn. Rep. 1)


title: HSV_4dpi-3 (techn. Rep. 2)


title: MOCK+IFNalpha_4dpi-2 (techn. Rep. 2)


title: MOCK+IFNalpha_4dpi-3 (techn. Rep. 1)


title: MOCK+IFNalpha_4dpi-1 (techn. Rep. 2)


title: MOCK_4dpi-2 (techn. Rep. 2)


title: MOCK+IFNalpha_4dpi-3 (techn. Rep. 2)


title: MOCK_4dpi-3 (techn. Rep. 1)


title: MOCK+IFNalpha_4dpi-2 (techn. Rep. 1)


title: MOCK_4dpi-1 (techn. Rep. 2)


title: MOCK+IFNalpha_4dpi-1 (techn. Rep. 1)


title: MOCK_4dpi-2 (techn. Rep. 1)


title: ZIKV+IFNbeta_12dpi-1 (techn. Rep. 1 & 2)

first: Thomas

middle: Rainer

last: Burkard

address: Dr. Bohrgasse 7

institute: IMBA

extract_protocol:
RNA was isolated from a pool of 3-4 organoids at 4dpi and 12dpi using RNeasy Micro Kit (QIAGEN, cat. #74004) according to the manufacturers instructions. Before lysis in RLT buffer, organoids were incubated in cold Cell recovery solution (Corning BDC354253) on ice for 1h and washed twice with cold DEPC-treated PBS.
RNA concentration and integrity was analysed on a Frgament Analyzer (Advanced Analytical Technologies, Inc.). Libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB, cat. # E7420L). Barcoded samples were multiplexed and sequenced on four lanes of 50bp SE on a HighSeq2500 (Illumina). Sample preparation and sequencing was performed at the VBCF NGS Unit (www.vbcf.ac.at).

treatment_protocol: Day 11 organoids were exposed to MOCK or ZIKV (MOI1,strain H/FP/2013) for 1 day and then cultured for additional 11 days (12dpi). Treatment with human IFNalpha (10ng/ml) or human IFNbeta (10ng/ml) was applied at 2,4,6 and 8 dpi. In untreated samples, BSA 0.1% solution was used.

tag: stage for zikv exposure

value: 12 dpi


title: ZIKV+IFNbeta_12dpi-2 (techn. Rep. 1 & 2)


title: ZIKV+IFNbeta_12dpi-3 (techn. Rep. 1 & 2)


title: MOCK+IFNbeta_4dpi-3 (techn. Rep. 1)


title: ZIKV+IFNalpha_12dpi-2 (techn. Rep. 1 & 2)

value: IFN alpha


title: ZIKV+IFNalpha_12dpi-1 (techn. Rep. 1, 2 & 3)


title: ZIKV_12dpi-4 (techn. Rep. 1 & 2)


title: MOCK+IFNbeta_12dpi-4 (techn. Rep. 1 & 2)


title: ZIKV_12dpi-2 (techn. Rep. 1 & 2)


title: ZIKV_12dpi-3 (techn. Rep. 1 & 2)


title: MOCK+IFNbeta_4dpi-1 (techn. Rep. 2)


title: MOCK+IFNbeta_12dpi-3 (techn. Rep. 1 & 2)


title: MOCK+IFNbeta_12dpi-2 (techn. Rep. 1 & 2)


title: MOCK_4dpi-3 (techn. Rep. 2)


title: MOCK+IFNalpha_12dpi-4 (techn. Rep. 1 & 2)


title: MOCK_4dpi-1 (techn. Rep. 1)


title: MOCK+IFNalpha_12dpi-2 (techn. Rep. 1 & 2)


title: MOCK_12dpi-4 (techn. Rep. 1 & 2)


title: ZIKV+IFNalpha_12dpi-3 (techn. Rep. 1 & 2)


title: MOCK_12dpi-3 (techn. Rep. 1 & 2)


title: ZIKV+IFNbeta_4dpi-1 (techn. Rep. 1 & 2)


title: ZIKV_4dpi-3 (techn. Rep. 1 & 2)


title: ZIKV+IFNalpha_4dpi-2 (techn. Rep. 1 & 2)


title: ZIKV+IFNalpha_4dpi-4 (techn. Rep. 1, 2, & 3)


title: ZIKV+IFNalpha_4dpi-3 (techn. Rep. 1 & 2)


title: MOCK+IFNbeta_4dpi-2 (techn. Rep. 1 & 2)


title: MOCK+IFNbeta_4dpi-1 (techn. Rep. 1 & 2)


title: ZIKV_4dpi-2 (techn. Rep. 1 & 2)


title: MOCK+IFNalpha_4dpi-2 (techn. Rep. 1 & 2)


title: MOCK+IFNalpha_4dpi-1 (techn. Rep. 1 & 2)


title: MOCK+IFNalpha_12dpi-3 (techn. Rep. 1 & 2)


title: MOCK_4dpi-3 (techn. Rep. 1 & 2)


title: MOCK_4dpi-2 (techn. Rep. 1 & 2)


title: MOCK_4dpi-1 (techn. Rep. 1 & 2)


title: MOCK_12dpi-2 (techn. Rep. 1 & 2)


title: ZIKV+IFNbeta_4dpi-2 (techn. Rep. 1 & 2)


title: ZIKV+IFNbeta_4dpi-4 (techn. Rep. 1 & 2)


title: MOCK+IFNbeta_4dpi-4 (techn. Rep. 1 & 2)


title: WM_CD19_30

city: Milano

first: Alessansdra

last: Trojani

address: Piazza dell'Ospedale Maggiore, 3

country: Italy

institute: Department of Hematology, ASST Grande Ospedale Metropolitano Niguarda

hyb_protocol: cDNA was hybridized to Affymetrix Human Genome U133 plus 2.0 array using the Gene Chip platform (Affymetrix, Santa Clara, Ca, USA) as we described in (http://dx.doi.org/10.17504/protocols.io.yncfvaw).

scan_protocol: Signals were scanned by Affymetrix Gene Chip Scanner 3000 according to the manufacturer’s instructions as we described in http://dx.doi.org/10.17504/protocols.io.yncfvaw.

data_processing: RMA

source_name: mononuclear cells  from bone marrow

label_protocol: We performed microarray experiments on the BM CD19+ and CD138+ cells. cDNA was prepared starting from the previously extracted RNA (50 ng) using Ovation Pico WTA System V2 kit (NuGEN, The Netherlands) and Encore Biotin Module Kit (NuGEN) following the manufacturer’s instructions (see http://dx.doi.org/10.17504/protocols.io.yncfvaw).

extract_protocol: BM CD19+ cells and BM CD138+ cells were isolated from WM,  IgM MGUS, and CTRLs. We isolated mononuclear cells (MNCs) from the BM blood samples (range, 4–6 ml) using Ficoll density gradient centrifugation at 800 rpm for 20 minutes. Immediately after, we selected BM CD19+ cells using Human CD19 MicroBeads; afterward, CD138 cells were positively isolated from the collected CD19- cells using Human CD138 Micro Beads according to the manufacturer’s instructions (Miltenyi Biotec). Total RNA was isolated from the BM CD19+ and BM CD138+ cells stored in RNAlater using MagMAX 96 Total RNA Isolation Kit (Thermo Fisher Scientific), according to the manufacturer’s instructions. The quality and the yield of the extracted RNA were measured using Nanodrop (Thermo Fisher Scientific).

tag: diagnosis

value: WM


title: WM_CD19_34


title: WM_CD19_28


title: WM_CD19_29


title: WM_CD19_33


title: WM_CD19_25


title: WM_CD19_27


title: MOCK+IFNalpha_4dpi-3 (techn. Rep. 1 & 2)


title: WM_CD19_24


title: WM_CD19_22


title: WM_CD19_16


title: WM_CD19_21


title: WM_CD19_11


title: WM_CD19_18


title: WM_CD19_31


title: WM_CD19_36


title: WM_CD19_20


title: WM_CD19_23


title: WM_CD19_17


title: WM_CD19_19


title: WM_CD19_26


title: WM_CD19_15


title: WM_CD19_10


title: WM_CD19_14


title: WM_CD19_12


title: WM_CD19_32


title: WM_CD19_13


title: WM_CD19_6


title: WM_CD19_5


title: WM_CD19_8


title: ZIKV_4dpi-1 (techn. Rep. 1 & 2)


title: WM_CD19_7


title: WM_CD19_1


title: WM_CD138_32


title: WM_CD138_27


title: WM_CD138_28


title: WM_CD138_30


title: WM_CD138_25


title: WM_CD138_26


title: WM_CD19_4


title: WM_CD138_23


title: WM_CD138_31


title: WM_CD138_29


title: WM_CD138_20


title: WM_CD19_2


title: WM_CD138_24


title: WM_CD138_18


title: WM_CD19_35


title: WM_CD138_19


title: WM_CD138_22


title: WM_CD138_21


title: WM_CD138_16


title: WM_CD138_17


title: WM_CD138_15


title: WM_CD19_3


title: WM_CD19_9


title: WM_CD138_14


title: WM_CD138_4


title: WM_CD138_12


title: WM_CD138_5


title: IgMMGUS_CD19_12

value: IgMMGUS


title: WM_CD138_13


title: WM_CD138_1


title: WM_CD138_11


title: IgMMGUS_CD19_11


title: WM_CD138_3


title: IgMMGUS_CD19_13


title: WM_CD138_6


title: WM_CD138_10


title: IgMMGUS_CD19_8


title: IgMMGUS_CD19_10


title: WM_CD138_9


title: IgMMGUS_CD138_10


title: IgMMGUS_CD19_6


title: WM_CD138_2


title: IgMMGUS_CD19_5


title: IgMMGUS_CD19_2


title: WM_CD138_8


title: IgMMGUS_CD138_8


title: IgMMGUS_CD19_3


title: IgMMGUS_CD19_1


title: IgMMGUS_CD19_4


title: IgMMGUS_CD19_7


title: IgMMGUS_CD19_9


title: IgMMGUS_CD138_7


title: IgMMGUS_CD138_9


title: WM_CD138_7


title: IgMMGUS_CD138_3


title: IgMMGUS_CD138_6


title: CTRL_CD19_6

value: CTRL


title: CTRL_CD19_3


title: CTRL_CD19_5


title: CTRL_CD19_1


title: IgMMGUS_CD138_4


title: CTRL_CD19_2


title: CTRL_CD138_7


title: CTRL_CD138_6


title: IgMMGUS_CD138_2


title: IgMMGUS_CD138_1


title: Control, low zinc, dermis, fish 5

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol for 4x44k microarrays

scan_protocol: Arrays were scanned with Agilent microarray scanner

data_processing: Global normalization was performed by equalizing the mean intensities of all microarrays. The individual values for each feature were divided to the mean value of all samples and expression ratios (ER) were calculated. Log2-ER were normalized with the locally weighted non-linear regression (Lowess)

organism: Salmo salar

source_name: Dermis

label_protocol: Amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon was fed with commercial feed

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

value: low zinc

tag: infection

value: Control

tag: time

tag: tissue

value: Dermis


title: IgMMGUS_CD138_5


title: Control, low zinc, epidermis, fish 3

source_name: Epidermis

value: Epidermis


title: CTRL_CD19_7


title: Control, low zinc, epidermis, fish 6


title: Control, low zinc, epidermis, fish 1


title: CTRL_CD138_5


title: Control, low zinc, epidermis, fish 5


title: CTRL_CD138_3


title: CTRL_CD19_4


title: CTRL_CD138_4


title: Control, low zinc, dermis, fish 4


title: Control, low zinc, dermis, fish 3


title: Control, low zinc, epidermis, fish 4


title: Control, low zinc, epidermis, fish 2


title: CTRL_CD138_1


title: CTRL_CD138_2


title: Control, low zinc, dermis, fish 6


title: Control, high zinc, epidermis, fish 5

value: high zinc


title: Control, high zinc, epidermis, fish 6


title: Control, high zinc, epidermis, fish 1


title: Control, high zinc, dermis, fish 4


title: Control, high zinc, dermis, fish 6


title: Control, high zinc, epidermis, fish 2


title: Control, high zinc, dermis, fish 3


title: Control, high zinc, epidermis, fish 4


title: Control, low zinc, dermis, fish 1


title: Control, high zinc, dermis, fish 5


title: Control, high zinc, epidermis, fish 3


title: Control, low zinc, dermis, fish 2


title: Infected, 6 wpi, low zinc, ulcer, fish 21-7

source_name: Skin ulcer

value: Infected

value: 6 wpi

value: Skin ulcer


title: Control, high zinc, dermis, fish 1


title: Control, high zinc, dermis, fish 2


title: Infected, 6 wpi, high zinc, ulcer, fish 13-22


title: Infected, 6 wpi, low zinc, dermis, fish 20-4


title: Infected, 6 wpi, high zinc, dermis, fish 13-22


title: Infected, 6 wpi, low zinc, dermis, fish 20-8


title: Infected, 6 wpi, low zinc, ulcer, fish 21-11


title: Infected, 6 wpi, low zinc, ulcer, fish 21-5


title: Infected, 6 wpi, low zinc, dermis, fish 21-7


title: Infected, 6 wpi, low zinc, dermis, fish 21-5


title: Infected, 6 wpi, high zinc, ulcer, fish 13-11


title: Infected, 6 wpi, low zinc, ulcer, fish 20-8


title: Infected, 6 wpi, low zinc, ulcer, fish 20-7


title: Infected, 6 wpi, low zinc, dermis, fish 21-11


title: Infected, 6 wpi, high zinc, ulcer, fish 13-5


title: Infected, 6 wpi, high zinc, ulcer, fish 12-8


title: Infected, 6 wpi, low zinc, dermis, fish 20-7


title: Infected, 6 wpi, high zinc, dermis, fish 13-5


title: Infected, 6 wpi, high zinc, dermis, fish 13-11


title: Infected, 6 wpi, high zinc, ulcer, fish 12-6


title: Infected, 4 dpi, low zinc, epidermis, fish 6


title: Infected, 6 wpi, high zinc, dermis, fish 12-6


title: Infected, 6 wpi, high zinc, dermis, fish 12-2


title: Infected, 4 dpi, low zinc, epidermis, fish 9


title: Infected, 6 wpi, low zinc, ulcer, fish 20-4


title: Infected, 6 wpi, high zinc, dermis, fish 12-8


title: Infected, 4 dpi, low zinc, epidermis, fish 10


title: Infected, 4 dpi, low zinc, dermis, fish 2


title: Infected, 4 dpi, low zinc, epidermis, fish 4


title: Infected, 6 wpi, high zinc, ulcer, fish 12-2


title: Infected, 4 dpi, low zinc, epidermis, fish 2


title: Infected, 4 dpi, low zinc, dermis, fish 4


title: Infected, 4 dpi, low zinc, dermis, fish 6


title: Infected, 4 dpi, low zinc, epidermis, fish 1


title: Infected, 4 dpi, low zinc, dermis, fish 9


title: Infected, 4 dpi, low zinc, dermis, fish 10


title: Infected, 4 dpi, high zinc, dermis, fish 10


title: Infected, 4 dpi, high zinc, epidermis, fish 2


title: Infected, 4 dpi, low zinc, dermis, fish 3


title: Infected, 4 dpi, high zinc, epidermis, fish 5


title: Infected, 4 dpi, high zinc, epidermis, fish 4


title: Infected, 4 dpi, high zinc, epidermis, fish 3


title: Infected, 4 dpi, high zinc, epidermis, fish 10


title: Infected, 4 dpi, high zinc, dermis, fish 5


title: Infected, 4 dpi, high zinc, dermis, fish 6


title: Infected, 4 dpi, high zinc, dermis, fish 4


title: Infected, 4 dpi, high zinc, dermis, fish 3


title: Infected, 4 dpi, high zinc, epidermis, fish 6


title: Infected, 4 dpi, high zinc, dermis, fish 2


title: Infected, epidermis, freshwater, postsmolt, fish 1

value: epidermis

tag: water

value: fresh water

tag: Stage

value: postsmolt


title: Infected, epidermis, brackish water, postsmolt, fish 6

value: brackish water


title: Infected, epidermis, freshwater, postsmolt, fish 6


title: Infected, epidermis, freshwater, smolt, fish 5

value: smolt


title: Infected, epidermis, brackish water, postsmolt, fish 2


title: Infected, epidermis, brackish water, postsmolt, fish 4


title: Infected, epidermis, freshwater, postsmolt, fish 5


title: Infected, epidermis, brackish water, postsmolt, fish 5


title: Infected, epidermis, freshwater, smolt, fish 2


title: Infected, epidermis, freshwater, postsmolt, fish 2


title: Infected, epidermis, brackish water, postsmolt, fish 1


title: Infected, epidermis, freshwater, postsmolt, fish 3


title: Infected, dermis, brackish water, postsmolt, fish 7

value: dermis


title: Infected, dermis, brackish water, postsmolt, fish 2


title: Infected, epidermis, freshwater, postsmolt, fish 4


title: Infected, epidermis, brackish water, postsmolt, fish 3


title: Infected, dermis, brackish water, postsmolt, fish 6


title: Infected, dermis, freshwater, postsmolt, fish 6


title: Infected, epidermis, freshwater, smolt, fish 6


title: Infected, dermis, freshwater, postsmolt, fish 3


title: Infected, dermis, freshwater, postsmolt, fish 4


title: Infected, epidermis, freshwater, smolt, fish 1


title: Infected, dermis, brackish water, postsmolt, fish 5


title: Infected, epidermis, freshwater, smolt, fish 3


title: Infected, dermis, brackish water, postsmolt, fish 1


title: Infected, epidermis, freshwater, smolt, fish 4


title: Infected, dermis, brackish water, postsmolt, fish 4


title: Infected, dermis, brackish water, postsmolt, fish 3


title: Infected, dermis, freshwater, postsmolt, fish 5


title: Infected, dermis, freshwater, smolt, fish 1


title: Infected, dermis, freshwater, smolt, fish 5


title: Infected, dermis, freshwater, postsmolt, fish 1


title: Infected, dermis, freshwater, smolt, fish 6


title: Holding control, epidermis, fresh water, postsmolt, fish 9

value: Holding control


title: Holding control, epidermis, fresh water, smolt, fish 7


title: Holding control, epidermis, fresh water, smolt, fish 9


title: Infected, dermis, freshwater, postsmolt, fish 2


title: Holding control, epidermis, fresh water, postsmolt, fish 8


title: Infected, dermis, freshwater, smolt, fish 2


title: Holding control, epidermis, fresh water, postsmolt, fish 7


title: Infected, dermis, freshwater, smolt, fish 3


title: Holding control, epidermis, brackish water, smolt, fish 2


title: Holding control, epidermis, brackish water, smolt, fish 3


title: Holding control, epidermis, brackish water, postsmolt, fish 10


title: Holding control, epidermis, brackish water, postsmolt, fish 11


title: Infected, dermis, freshwater, smolt, fish 4


title: Holding control, epidermis, brackish water, smolt, fish 1


title: Holding control, epidermis, brackish water, postsmolt, fish 12


title: Holding control, epidermis, brackish water, postsmolt, fish 2


title: Series2_Hamster_Vehicle_CoV2-2

city: New York

first: Daniel

last: Blanco Melo

state: NY

address: One Gustave L. Levy Place, Box 1124

department: Microbiology

institute: Icahn School of Medicine at Mount Sina

description:
USA-WA1/2020
TruSeq Stranded mRNA Library Prep Kit
RawReadCounts_Hamster.tsv
RawReadCounts_Virus.tsv

data_processing:
cDNA libraries were sequenced using an Illumina NextSeq 500 platform
Raw sequencing reads were aligned to the human genome (hg19) or the Syrian golden hamster genome (MesAur1) using the RNA-Seq Alignment App (v2.0.1) on Basespace (Illumina, CA)
Differential gene expression analysis was performed using DESeq2 comparing amodiaquine traeted samples to vehicle treated sample
Raw sequencing reads were aligned to the SARS-CoV-2 genome using Bowtie2
Genome_build: human (hg19), hamster (MesAur1), SARS-CoV-2 (MN985325.1)
Supplementary_files_format_and_content: Tab separated value (tsv) matrix of raw read counts per gene/viral genome for each sample.

organism: Mesocricetus auratus

source_name: Vehicle treated Syrian golden hamster (SARS-CoV-2 infected)

extract_protocol:
Cells and tissues were homogenized in TRIzol reagent (invitrogen) and total RNA was extracted by phenol/chloroform extraction following manufacturer's protocol
TruSeq Stranded mRNA Library Prep Kit (Illumina)

value: Lung tissue

tag: treatment

value: Vehicle treated (-1dpi, 0dpi, 1dpi, 2dpi) SARS-CoV-2 infected (100PFU)

tag: time after treatment

value: 3 days post infection


title: Series2_Hamster_Amodiaquine_CoV2-2

source_name: Amodiaquine treated Syrian golden hamster (SARS-CoV-2 infected)

value: Amodiaquine treated (-1dpi, 0dpi, 1dpi, 2dpi) SARS-CoV-2 infected (100PFU)


title: Series2_Hamster_Amodiaquine_CoV2-3


title: Series2_Hamster_Vehicle_CoV2-3


title: Series2_Hamster_Vehicle_CoV2-1


title: Holding control, dermis, fresh water, smolt, fish 7


title: T2_3

city: taian

first: yanan

last: duan

address: 61 Daizong Street

institute: Shandong Agricultural University

data_processing:
Illumina Casava 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Malus domestica GDDH13 Whole Genome v1.1
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Malus domestica

source_name: Apple Rootstock

extract_protocol:
flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Hi-seq 6000 (Illumina, San Diego, CA)

tag: cultivar

value: F. Proliferatum infected

tag: disease

value: Apple replant disease

value: root


title: T2_2


title: Series2_Hamster_Amodiaquine_CoV2-1


title: T2_1


title: Holding control, dermis, fresh water, smolt, fish 9


title: Holding control, epidermis, fresh water, smolt, fish 8


title: T1_3

value: mock inoculated


title: Holding control, dermis, brackish water, smolt, fish 1


title: Holding control, epidermis, fresh water, postsmolt, fish 2


title: Holding control, epidermis, fresh water, postsmolt, fish 1


title: Holding control, epidermis, brackish water, postsmolt, fish 3


title: Holding control, dermis, fresh water, smolt, fish 8


title: Holding control, epidermis, fresh water, postsmolt, fish 3


title: Holding control, dermis, brackish water, smolt, fish 2


title: Holding control, dermis, fresh water, postsmolt, fish 9


title: Holding control, dermis, fresh water, postsmolt, fish 8


title: Holding control, dermis, brackish water, postsmolt, fish 4


title: Holding control, dermis, brackish water, postsmolt, fish 12


title: Holding control, dermis, brackish water, postsmolt, fish 11


title: T1_1


title: T1_2


title: M2_3


title: Holding control, dermis, fresh water, postsmolt, fish 7


title: Holding control, dermis, brackish water, smolt, fish 3


title: M2_2


title: M2_1


title: Holding control, dermis, brackish water, postsmolt, fish 10


title: M1_3


title: Holding control, dermis, brackish water, postsmolt, fish 3


title: M1_1


title: M1_2


title: Holding control, dermis, fresh water, postsmolt, fish 1


title: Holding control, dermis, fresh water, postsmolt, fish 2


title: Control, epidermis, brackish water, smolt, fish 6

value: Control


title: Control, epidermis, brackish water, smolt, fish 5


title: Psoriatic CD4+ T treated with DMSO (2)

city: Xi’an

first: Lin

last: Yiting

state: Shaanxi

address: 127 Changlexi Road

department: dermatology

institute: Xijing hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome
Feature Counts v2.0.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample

source_name: Peripheral blood CD4+ T cells

extract_protocol:
CD4+ T cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext Ultra RNA Library Prep Kit for Illumina (Cat#E7530S) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Illumina protocols

treatment_protocol: Psoriatic CD4+ T cells were isolated from PBMCs by magnetic cell sorting, and treated with CDK7 inhibitor THZ1 (10 nM) or DMSO for 24h

value: Peripheral blood CD4+ T cells

value: DMSO

tag: disease state

value: psoriasis


title: Psoriatic CD4+ T treated with THZ1 (1)

value: THZ1 (10 nM)


title: Psoriatic CD4+ T treated with DMSO (1)


title: Control, epidermis, fresh water, postsmolt, fish 6

value: epidermis

value: fresh water

value: postsmolt


title: Psoriatic CD4+ T treated with THZ1 (2)


title: o/e ALKBH3_1

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

description: All small RNA from 15 to 50 nt

data_processing:
The adapters were removed by using cutadapt
the reads were aligned to the human(hg38) genome
The tRNA annotations is download from GtRNAdb2.0(ref here)
Reads mapped to tRNA and were counted.
Genome_build: hg38
Supplementary_files_format_and_content: tRNA reads count

source_name: HeLa cells

growth_protocol: Human cancer cells HeLa  were purchased from American Type Culture Collection (ATCC, Manassas, VA) and maintained in our lab with Dulbecco’s modified Eagle medium (DMEM, GIBCO, Carlsbad, CA, USA) with 10 % fetal bovine serum, and 1 % penicillin/streptomycin (Invitrogen).

extract_protocol:
Total RNA (100 μg) were denatured at 70 °C for 5 min and separated by a 15% TBE-Urea gel with 20/100 or 10/60 oligo length standard ladder (Integrated DNA Technologies, Coralville, IA). After visualized by SYBR Gold (Ref. S11494 from Life Technologies), tRFs (15~50nt) in gels were cut according to sizes and recovered by small RNA PAGE recovery kit (Zymo Research, Irvine, CA, USA).
The recovered tRFs was used to establish the library by NEB small RNA library preparation kit (E7330S).

treatment_protocol: For cell lines stably overexpressed ALKBH3: HeLa  cells transfected with double-tagged ALKBH3 (N terminal Flag and HA in tandem) in pPB-CAG vector were selected by 2 μg/ml puromycin for two weeks. Control cell lines were created similarly with vector only expressing N-terminal Flag and HA in tandem. The ALKBH3 stable overexpression and control cells were cultured in medium supplemented with 2 μg/ml puromycin. Cells were incubated with medium without puromycin for four days before experiments.

tag: cell line

value: HeLa cells

tag: cell type

value: Human cell line

tag: passages

tag: genotype/variation

value: ALKBH3 over expression


title: o/e ALKBH3_2

description: All small RNA from 15 to 50 nt


title: o/e control_2

description: All small RNA from 15 to 50 nt

value: control


title: Control, epidermis, brackish water, smolt, fish 4

value: brackish water

value: smolt


title: o/e control_1

description: All small RNA from 15 to 50 nt


title: Control, epidermis, brackish water, smolt, fish 3


title: Control, epidermis, brackish water, smolt, fish 2


title: Holding control, dermis, fresh water, postsmolt, fish 3

value: dermis

value: Holding control


title: Holding control, dermis, brackish water, postsmolt, fish 2


title: Control, epidermis, fresh water, postsmolt, fish 3


title: tKO26b/a1/a2 d15 neural cell small RNA miR-26a1/a2/b knockout CCC55A

city: Würzburg

first: Nina

last: Was

state: Bavaria

address: Zinklesweg 10

department: Institut für medizinische Strahlenkunde und Zellforschung

institute: Universität Würzburg

description: small RNA

data_processing:
Sequence reads were aligned to the  mouse genome (version mm10) using TopHat (Trapnell et al., 2012).
Transcripts were   quantified by Cufflinks and Cuffdiff and differential expression was determined  (Trapnell et al., 2012).
Small RNA seq reads were mapped against murine miR annotation database  (miRBase) using Burrow-Wheeler aligner. Each miR profile was normalized to relative   read frequencies (Farazi et al., 2012).
Genome_build: mouse genome (version mm10)
Supplementary_files_format_and_content: tab-delimited text files include miR Sequencing reads or output of cuffdiffs

source_name: Neural cell

growth_protocol: ESCs were differentiated into the neural lineage as described (Bibel et al., 2007b;  Wolber et al., 2013) with slight modifications. Briefly, 3x106 ESCs were plated into 10  cm petri dishes (Greiner Bio One) and cultured for 5 days under floating conditions in  ESC medium with 10% FCS and without LIF to allow for the formation of embryoid  bodies (EBs). To generate attached EBs (att. EBs), EBs in floating conditions were  transferred to tissue culture dishes on day 5 and cultured in serum-free neural selection  ITS-medium (DMEM/Ham’s F-12, 100 U/ml penicillin/streptomycin, 2mM L-glutamate,  5 μg/ml insulin, 50 μg/ml transferrin, 30 nM sodium selenite, 2.5 μg/ml fibronectin, and  1 μM retinoic acid). After 4 days, cells were trypsinized and further cultured (1,5x105  cells/cm2) on polyornithine- and laminin-coated dishes or coverslips in N2 medium  (DMEM/Ham’s F-12, 100 U/ml penicillin/streptomycin, 2 mM L-glutamate, 25 μg/ml  insulin, 50 μg/ml transferrin, 30 nM sodium selenite, 20 nM progesteron, and 100 μM  putrescin). Medium was replaced 2h and 24h post plating. Thereafter NPCs were  cultured in Neurobasal medium (Thermo-Fisher), supplemented with 100 U/ml  penicillin/streptomycin, 2mM L-glutamate, and 2% B27 supplement (Thermo-Fisher).  Medium was changed every 2nd day. Cells were cultured up to 15 days.

extract_protocol:
Total RNAs from two independent clones of WT and tKO26b/a1/a2 cell lines and two   biological replicates of NCs (day 15) were isolated using peqGold RNA pure   (PeqLab). rRNA was removed using the Ribo-Zero rRNA Removal Kit (Illumina).
cDNA library preparation using NEB Next Ultra Directional RNA Library  Prep Kit for Illumina (New England Biolabs). For small RNA sequencing total RNA was isolated and a 3´barcoded adapter was ligated usig truncated T4 RNA ligase (WT_R1_A: 5´-GTAGAGTGACTGTGGAATTCTC-3`; WT_R1B:5´-GTAGAGTCTGTGTGGAATTCTC-3´; WT_R1C:5´-GTCCGCTGACTGTGGAATTCTC-3´; WT_R1D:  5´- GTCCGCTCTGTGTGGAATTCTC-3´; CCC_22A:  5´-GTAGAGGCGATATGGAATTCTC-3´;  CCC_22B: 5´-GTCCGCTCATAGTGGAATTCTC-3´; CCC_55A: 5´-GTAGAGTCATAGTGGAATTCTC-3´; CCC_55B:5´-GTCCGCGCGATATGGAATTCTC-3´). Ligated RNAs were pooled and size selected. Small RNA cDNA libraries were generated  using SuperscriptIII (Invitrogen) and sequenced  by Illumina Sequencing.  (Hafner et al., 2010)

value: ES-derived neural cell

tag: genotype

value: miR-26a1/a2/b knockout CCC55A

tag: strain


title: Control, epidermis, fresh water, smolt, fish 3

value: Control


title: tKO26b/a1/a2 d15 neural cell small RNA miR-26a1/a2/b knockout CCC22B

description: small RNA

value: miR-26a1/a2/b knockout CCC22B


title: tKO26b/a1/a2 d15 neural cell small RNA miR-26a1/a2/b knockout CCC55B

description: small RNA

value: miR-26a1/a2/b knockout CCC55B


title: Control, epidermis, fresh water, postsmolt, fish 5


title: Control, epidermis, fresh water, postsmolt, fish 1


title: Control, epidermis, fresh water, postsmolt, fish 2


title: Control, epidermis, fresh water, smolt, fish 2


title: Control, epidermis, fresh water, postsmolt, fish 4


title: Control, dermis, brackish water, smolt, fish 5


title: Control, epidermis, fresh water, smolt, fish 5


title: Control, dermis, brackish water, smolt, fish 6


title: Control, epidermis, fresh water, smolt, fish 4


title: WT d15 neural cell small RNA rep4

description: small RNA

value: wildtype


title: tKO26b/a1/a2 d15 neural cell small RNA miR-26a1/a2/b knockout CCC22A

description: small RNA

value: miR-26a1/a2/b knockout CCC22A


title: WT d15 neural cell small RNA rep1

description: small RNA


title: WT d15 neural cell small RNA rep2

description: small RNA


title: Control, dermis, brackish water, smolt, fish 4


title: tKO26b/a1/a2 d15 neural cell miR-26a1/a2/b knockout CCC22

value: miR-26a1/a2/b knockout CCC22


title: tp53b-2

city: La Jolla

first: Wun Kiat Justin

last: Tan

state: California

address: 9500 Gilman Drive #0412, PFBH 414

institute: UCSD

data_processing:
Base calls were made on Illumina's BaseSpace
Sequenced reads were aligned to E. coli MG1655 (NC_000913.3) genome and plasmid sequences using Bowtie 2 ver. 2.1.0 into BAM files
BAM files were processed using HTSeq to generate raw read count files
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Comma-delimited raw read counts for all samples

organism: Escherichia coli

growth_protocol: Gly2 cells transformed with heterologous gene expressing plasmid were grown in M9 with 0.2% w/v glycerol as carbon source

extract_protocol:
Total RNA was isolated using Qiagens RNAProtect Bacteria Reagent kit
Ribosomal RNA was depleted using Illumina's Ribo-Zero rRNA removal kit and libraries were constructed using KAPA RNA-Seq Library Preparation kit

treatment_protocol: At A600 OD = 0.3 rhamnose was added to a final concentration of 1mM for induction of heterologous gene expression. Cells were harvested 2hrs after induction for total RNA extraction.

tag: induction concentration

value: 1mM Rhamnose

tag: induction od

tag: induction time


title: WT d15 neural cell


title: Control, epidermis, fresh water, smolt, fish 1

tag: tissue

value: epidermis

tag: infection

value: fresh water


title: tKO26b/a1/a2 d15 neural cell miR-26a1/a2/b knockout CCC55

value: miR-26a1/a2/b knockout CCC55


title: WT d15 neural cell small RNA rep3

description: small RNA


title: Control, dermis, brackish water, smolt, fish 3

tag: water

tag: Stage


title: tp53b-1


title: Control, dermis, fresh water, postsmolt, fish 3

value: postsmolt


title: Control, dermis, fresh water, postsmolt, fish 6


title: Control, dermis, fresh water, smolt, fish 6


title: Control, dermis, fresh water, postsmolt, fish 4


title: Control, dermis, fresh water, smolt, fish 3


title: Control, dermis, fresh water, postsmolt, fish 1


title: Control, dermis, fresh water, postsmolt, fish 2


title: ssDDC-2


title: Control, dermis, fresh water, postsmolt, fish 5


title: ssDDC-1


title: sgAANAT-D63G-2


title: Alkbh3-/-_2

description: All small RNA from 15 to 50 nt

data_processing:
The adapters were removed by using cutadapt
the reads were aligned to the mouse(mm10) genome
The tRNA annotations is download from GtRNAdb2.0(ref here)
Reads mapped to tRNA and were counted.
Genome_build: mm10
Supplementary_files_format_and_content: RNA reads count

source_name: Epididymis

growth_protocol: All animal studies were conducted in accordance with institutional guidelines for the care and use of experimental animals

treatment_protocol: No treatment

value: epididymis


title: sgAANAT-D63G-1


title: sfCOMT-2


title: Control, dermis, fresh water, smolt, fish 2

value: smolt


title: sfCOMT-1


title: Alkbh3-/-_1

description: All small RNA from 15 to 50 nt


title: Wild type

description: All small RNA from 15 to 50 nt

value: Wild type


title: saCOMT-T2A-1


title: saCOMT-T2A-2


title: rnTDC-trunc-2


title: rnTDC-2


title: rnTDC-trunc-1


title: rnTDC-1


title: HTO: 10x_5_TotalSeq-C_HTO_mLN

city: Planegg-Martinsried

first: Eduardo

last: Beltrán

state: Bayern

address: Großhaderner Str. 9

department: Institute of Clinical Neuroimmunology

institute: University Hospital, LMU Munich

description: TotalSeq-C Cell Hashing

data_processing:
Cell Ranger software (10x Genomics, v.3.1.0) was used to demultiplex samples, process raw data, align reads to the mm10 mouse reference genome and summarize unique molecular identifier (UMI) counts. Filtered gene-barcode and hashing-barcode matrices that contained only barcodes with UMI counts that passed the threshold for cell detection were used for further analysis.
Cell hashing analysis of libraries generated using the Chromium Single Cell 3' v2 kit, was performed using the CITE-seq-Count software version 1.4.3 (DOI 10.5281/zenodo.2590196).
We processed the filtered UMI count matrices using the R package Seurat (version 3.0). Cell hashing raw counts were normalized using centered log ratio (CLR) transformation, where counts were divided by the geometric mean of an HTO across cells and log-transformed.
As a QC steps we filtered out: doublets originating from two cells from different samples (one single barcoded cell was positive for two HTO) and cells where no HTO was detected. We further discarded cells where the number of detected genes was <200 or >5,000 and/or 10% of the counts belonged to mitochondrial genes. After QC, only raw gene counts in high-quality singlets were submitted to: log-normalization; identification of high variable genes by using the MeanVarPlot method; scaling; and regression against the number of UMIs and mitochondrial RNA content per cell.
Two clustering analysis were performed. For single cell gene expression analysis purpose, only cells analyzed in the 10x Chromium Single Cell 3' experiment were used for the first clustering analysis and identification of genes differentially expressed in each cluster-organ-stream combination. Additionally, for TCR analysis purpose, both 10x 3’ and 5’ datasets were merged. After merging, integration was performed to remove bath effects and the integrated assay was used for principal component analysis and unsupervised clustering. After marker identification for each cluster, only cells where a TCR clonotype was detected, were used for upstream analysis of TCR repertoire. Single-cell TCR annotation was performed using the 10x cellranger vdj pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: Filtered feature-barcode matrices containing only cellular barcodes in MEX and HDF5 format

source_name: photoconverted CD4+ T cells isolated from mesenteric lymph node + spleen + brain

extract_protocol: Two single-cell RNA experiments were performed. In the first, scRNA-seq and Cell Hashing libraries were prepared using the 10x Chromium Single Cell 3' Solution (Chromium Single Cell 3' v3 combined with Cell Hashing as per established protocols (doi: 10.1186/s13059-018-1603-1). In the second, scRNA-seq, scTCR-seq and Cell Hashing libraries were prepared using the 10x Chromium Single Cell 5' Solution (Chromium Next GEM Single Cell VDJ v1.1 with Feature Barcoding technology for Cell Surface Protein)

tag: cre reporter

value: T cell conditional mitoDendra2

tag: age

value: post natal 8 to 12 weeks

value: experimental autoimmune encephalomyelitis (EAE)


title: Control, dermis, fresh water, smolt, fish 4

value: dermis

value: Control


title: rnPNMT-2


title: Holding control, epidermis, brackish water, postsmolt, fish 4

value: Holding control

value: brackish water


title: G60, uninfected, spleen, fish 26

source_name: Spleen

tag: treatment

value: uninfected

value: Spleen


title: VDJ: 10x_5_VDJ_mLN

description: 10x Chromium Single Cell 5' + VDJ Solution

value: photoconverted CD4+ T cells isolated from mesenteric lymph node + spleen + brain

tag: disease


title: G60, uninfected, spleen, fish 19


title: Control, dermis, fresh water, smolt, fish 1


title: G100, uninfected, spleen, fish 20


title: rnPNMT-1

value: 1mM Rhamnose


title: G60, uninfected, spleen, fish 35


title: G100, uninfected, spleen, fish 8


title: G100, uninfected, spleen, fish 13


title: G60, uninfected, spleen, fish 24


title: Control, dermis, fresh water, smolt, fish 5

value: fresh water


title: RNA: 10x_5_GEX_mLN

description: 10x Chromium Single Cell 5' Solution


title: G100, uninfected, spleen, fish 3


title: G100, uninfected, spleen, fish 14


title: G60, uninfected, spleen, fish 25


title: G100, uninfected, spleen, fish 3-2


title: G100, infected, spleen, fish 49

value: infected


title: Maize_cytTC248_stress_rep3

city: Cluj-Napoca

first: Simona

last: Visan

state: Cluj

address: 34-36 Republicii

department: Functional Genomics, Proteomics and Experimental Pathology

country: Romania

institute: The Oncology Institute “Prof Dr. Ion Chiricuta”,

hyb_protocol: The probes were hybridized on Agilent maize custom arrays 4X180k. Hybridization was carried out for 17 hours at 65°C, followed by washing. In addition, to avoid the ozone effects on Cy-3 signal, a supplementary organic solvent containing an ozone scavenging compound dissolved in acetonitrile was used after washing step.

scan_protocol: The slides were scanned on Agilent Microarray Scanner (G2565CA) at 2 µm

data_processing: The scanned images were analyzed with Feature Extraction Software v.11 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 062494_D_F_20131129) to obtain median signal intensities. Data processing were done in R.Control features as well as saturated and non-uniformed features were removed. Data were normalized using quantile method.

organism: Zea mays

source_name: maize, cytTC248, stress, replicate 3

label_protocol: Cy-3 labeled microarray probes (cRNA-Cy3) were synthesized from 200 ng of total RNA using one-color Low Input Quick Amp Labeling Kit, according to Agilent manufacturer’s protocol. The quality of synthesized cRNAs was checked with Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies) considering a minimal yield of 1.65 μg and a specific activity of more than 6 pmol/μl Cy3/μg cRNA.

growth_protocol: 21 days with 16 h of light at 26 C and 8 h of dark at 20 C

extract_protocol: Total RNA was isolated with TriReagent (Sigma-Aldrich) and purified with RNeasy Mini Kit (Qiagen) according to the manufacture's protocol. The quality of the total RNA was evaluated with Bioanalyzer 2100 (Agilent Technologies) based on RNA integrity number (RIN). All samples had the RIN greater than 8.

treatment_protocol: 20 days with 16 h of light at 26 C and 8 h of dark at 20 C followed by 24 h at 40 C under the same light conditions

value: 3-leaf seedling

value: cytoplasm donor


title: Maize_cytTC248_stress_rep2

source_name: maize, cytTC248, stress, replicate 2


title: G100, infected, spleen, fish 47


title: rnCOMT-sol-1


title: Maize_cytTC248_stress_rep4

source_name: maize, cytTC248, stress, replicate 4


title: rnCOMT-sol-2


title: Maize_cytTC248_stress_rep1

source_name: maize, cytTC248, stress, replicate 1


title: pmTPH-2


title: G100, infected, spleen, fish 46


title: RNA: 10x_5_GEX_iLN

description: 10x Chromium Single Cell 5' Solution

source_name: photoconverted CD4+ T cells isolated from inguinal lymph node + spleen + brain


title: Maize_cytTC248_control_rep4

source_name: maize, cytTC248, replicate 4


title: HTO: 10x_5_TotalSeq-C_HTO_iLN

description: TotalSeq-C Cell Hashing

value: photoconverted CD4+ T cells isolated from inguinal lymph node + spleen + brain


title: VDJ: 10x_5_VDJ_iLN


title: pmTPH-1


title: HTO: 10x_3_TotalSeq-A_HTO

description: TotalSeq-A Cell Hashing

source_name: photoconverted CD4+ T cells isolated from inguinal lymph node + mesenteric lymph node + spleen + brain


title: Maize_cytTC248_control_rep3

source_name: maize, cytTC248, replicate 3


title: osTDC-L360V-2


title: osTDC-K374Q-2


title: G100, infected, spleen, fish 4


title: G60, infected, spleen, fish 60


title: G60, infected, spleen, fish 54


title: RNA: 10x_3_GEX

description: 10x Chromium Single Cell 3' Solution

value: photoconverted CD4+ T cells isolated from inguinal lymph node + mesenteric lymph node + spleen + brain


title: POAG 3

city: Muenster

first: Karoline

last: Walscheid

address: Hohenzollernring 74

institute: Department of Ophthalmology and Ophtha-Lab at St. Franziskus-Hospital

data_processing:
Analysis run on R version 3.2.3
RNA-seq reads were mapped to ENSEMBL Homo_sapiens GRCh38 version 83 primary transcript and transcript annotation file using Tophat2 v2.1.0 and Bowtie2 version 2.2.3.0
Number of genes with fewer than 1 read over all samples in HTSeq count matrix (removed before DE analysis)
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text file with differential gene expression results for every gene using DESeq2

source_name: Iris

extract_protocol:
Iris tissue was removed, shock frozen in liquid nitrogen and RNA was isolated using the RNeasy® Micro Kit (Quiagen GmbH).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: iris

tag: sample type

value: control sample


title: osTDC-K374L-2


title: Maize_cytTC248_control_rep1

source_name: maize, cytTC248, replicate 1

tag: cell type


title: POAG 2


title: osTDC-K374Q-1


title: G100, infected, spleen, fish 2


title: Maize_cytTC221_stress_rep4

source_name: maize, cytTC221, stress, replicate 4


title: POAG 4


title: Maize_cytTC248_control_rep2

source_name: maize, cytTC248, replicate 2


title: Maize_cytTC221_stress_rep2

source_name: maize, cytTC221, stress, replicate 2


title: G60, infected, spleen, fish 51


title: Maize_cytTC221_stress_rep3

source_name: maize, cytTC221, stress, replicate 3


title: G100, uninfected, gill, fish 20

source_name: Gill

value: Gill


title: G60, infected, spleen, fish 6


title: G60, infected, spleen, fish 7


title: osTDC-L360V-1


title: osTDC-K374L-1


title: Maize_cytTC221_stress_rep1

source_name: maize, cytTC221, stress, replicate 1


title: JIAU 4

value: study sample


title: G100, uninfected, gill, fish 14


title: POAG 1


title: osTDC-K374H-2


title: JIAU 3


title: JIAU 2


title: osTDC-K374H-1


title: ocAANAT-2


title: ocAANAT-1


title: Series1_A549-ACE2_Amodiaquine_CoV2-3

description:
USA-WA1/2020
TruSeq Stranded mRNA Library Prep Kit
RawReadCounts_Human.tsv
RawReadCounts_Virus.tsv

source_name: Amodiaquine treated A549-ACE2 cells  (SARS-CoV-2 infected)

value: Lung adenocarcinoma

value: Amodiaquine traetment (-1hpi) SARS-CoV-2 infected (MOI:0.1)

tag: time after treatment

value: 24 hours post infection


title: Series1_A549-ACE2_Amodiaquine_CoV2-2


title: Series1_A549-ACE2_Amodiaquine_CoV2-1


title: G100, uninfected, gill, fish 13

value: uninfected


title: G100, uninfected, gill, fish 8


title: msCOMT-2


title: G60, uninfected, gill, fish 26


title: msCOMT-1


title: G60, uninfected, gill, fish 35


title: G100, uninfected, gill, fish 3


title: hsTPH1-2


title: Maize_cytTC221_control_rep1

source_name: maize, cytTC221, replicate 1


title: Maize_cytTC221_control_rep2

source_name: maize, cytTC221, replicate 2


title: G60, uninfected, gill, fish 25


title: Maize_cytTC221_control_rep4


title: Maize_TC243_stress_rep4

source_name: maize, TC243, stress, replicate 4

value: nucleus donor


title: Maize_TC243_stress_rep1

source_name: maize, TC243, stress, replicate 1


title: JIAU 1


title: Father_stim_3

city: Vancouver

first: Stuart

middle: E

last: Turvey

state: British Columbia

address: A5-122 950 W 28th Avenue

department: Pediatrics

country: Canada

institute: The University of British Columbia

data_processing:
RNA was sequenced on the Illumina NextSeq 500 with Paired End 42bp x 42bp reads
Read sequences were aligned to the Homo sapiens reference sequence (UCSC hg19) using STAR aligner (version STAR_2.5.0b)
Assembly of transcripts and measurement of abundance was done using Cufflinks (Version 2.2.1)
TMM analysis using EdgeR was used for raw count normalization
Genome_build: Homo sapiens (UCSC hg19)
Supplementary_files_format_and_content: Raw counts and normalized counts are presented as .csv matrix files

source_name: lymphoblastoid cell lines

growth_protocol: PBMCs from each individual were cultured with complete RPM1-1640 media supplemented with tacrolimus, 10% heat inactivated fetal bovine serum, 2mM L-glutamine, and 1mM sodium pyruvate for 1h. Cells were then infected with supernatant from a viral replication-permissive marmoset cell line B95-8 until sufficient B cell blasts were generated. LCLs were propagated in complete RPMI-1640 media without tacrolimus.

extract_protocol:
RNA was extracted with a RNeasy Mini Plus Kit (Qiagen)
RNA samples were prepared following the standard protocol for the NEBnext Ultra ii Stranded mRNA (New England BioLabs)

treatment_protocol: Stimulated with 50 ng/mL PMA + 1 uM ionomycin for 4h

tag: replicate number

tag: unstim or stim (4hrs 50ng/ml pma + 1um ionomycin)

value: stimulated


title: Maize_cytTC221_control_rep3


title: Maize_TC243_control_rep2

source_name: maize, TC243, replicate 2


title: Maize_TC243_control_rep4

source_name: maize, TC243, replicate 4


title: G60, uninfected, gill, fish 24


title: Maize_TC243_control_rep3

source_name: maize, TC243, replicate 3


title: Father_stim_2


title: hsTPH1-1

tag: strain

value: 1mM Rhamnose


title: G60, uninfected, gill, fish 19


title: Maize_TC243_stress_rep2

source_name: maize, TC243, stress, replicate 2


title: Maize_TC243_stress_rep3

source_name: maize, TC243, stress, replicate 3


title: hsTPH-N158trunc-Set4-8

tag: induction concentration


title: Father_stim_1


title: Father_unstim_2

value: unstimulated


title: hsTPH-E2K-N91I-P99C-2

tag: induction od


title: hsTPH-N158trunc-Set4-7

tag: induction time


title: Father_unstim_3


title: Maize_TC243_control_rep1

source_name: maize, TC243, replicate 1

tag: tissue


title: Father_unstim_1


title: hsTPH-E2K-N91I-P99C-1


title: hsPNMT-mb-2


title: Mother_stim_3


title: hsPNMT-mb-1


title: G100, infected, gill, fish 49

tag: infection

value: infected


title: Mother_stim_2


title: G100, infected, gill, fish 2


title: G100, infected, gill, fish 4


title: hsASMT-2


title: G100, infected, gill, fish 47


title: G100, infected, gill, fish 46


title: Mother_stim_1


title: Tumor vs Normal patient ID 303

city: Villejuif

first: Shai

last: Magidi

address: rue Guy Moquet

country: France

institute: WIN Consortium

description:
Tumor vs Normal Lung 303
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)

hyb_protocol: Hybridizations were performed as dual-dye-swapped (direct and inversed labeling) experiments with direct cohybridization of equal amounts of labeled tumor and normal probes.

scan_protocol: Microarrays were read using the Agilent 2000 scanner version C.

data_processing: Data was processed with Agilent Feature extractions software

label: Cy5, Cy3

source_name: Cancer tissue

label_protocol: Of each tumor and normal tissue, 100 ng total RNA was used to generate double-stranded complementary DNA using MMLV reverse transcriptase and oligo DT primers coupled with the promoter sequence of T7 RNA. Probe labeling and linear amplification were generated using Agilent Technologies reagents and T7 RNA polymerase that generated labeled complementary labeled RNAs (tumor labeled with Cy5 and normal tissue with complementary RNAs with Cy3).

growth_protocol: storage protocol: All biopsies obtained were stored in cryogenic tubes containing RNAlater, a stabilizing reagent that prevents the degradation of nucleic acids (without the need for freezing in the imaging facilities) and preserves the structural morphology to enable subsequent pathology review.

extract_protocol: The tissue biopsies were lysed with a Polytron, by homogenization in the lysis buffer RLT Plus provided in the kit, and DNA was obtained with a specific affinity silica matrix column, specifically retaining the DNA, whereas RNAs and proteins were collected from the through flow. DNA was washed and eluted. The through flow containing RNAs was mixed with tri-reagent and, subsequently, RNA was obtained by isopropanol precipitation. This procedure enables the collection of all types of RNAs, including mRNAs and small microRNA species. RNAs pelleted through centrifugation were washed with ethanol 75% and solved in nuclease-free water

value: Lung

tag: gender

value: Female

tag: histology

value: Adenocarcinoma

label: Cy3, Cy5

source_name: Organ-matched normal tissue

value: Bronchial mucosa


title: Tumor vs Normal patient ID 284

description:
Tumor vs Normal Lung 284
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)

value: Male

tag: Stage


title: Tumor vs Normal patient ID 291

description:
Tumor vs Normal Lung 291
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)

tag: age


title: Tumor vs Normal patient ID 285

description:
Tumor vs Normal Lung 285
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: Tumor vs Normal patient ID 240

description:
Tumor vs Normal Lung 240
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: G60, infected, gill, fish 54

tag: treatment


title: Tumor vs Normal patient ID 241

description:
Tumor vs Normal Lung 241
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: HsAANAT-1


title: hsASMT-1


title: G60, infected, gill, fish 51


title: G60, infected, gill, fish 60


title: Tumor vs Normal patient ID 235

description:
Tumor vs Normal Lung 235
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: Mother_unstim_2


title: Mother_unstim_1


title: Mother_unstim_3


title: 12-P890292-S007-R02 [bulk_RNA-Seq]

city: Cambridge

first: Caroline

last: Porter

address: 415 Main Street

institute: Broad Institute

data_processing:
sc/snRNA-seq: 3' RNAseq (10x kit V3 chemistry)
sc/snRNA-seq: Demultiplexing is run using Cell Ranger mkfastq.
sc/snRNA-seq: Counts matrix is generated using the Cumulus cellranger_workflow in Terra.
sc/snRNA-seq: Ambient RNA is removed using Cellbender remove-background workflow in Terra.
bulk RNA-seq: Demultiplexing is run using bcl2fastq
bulk RNA-seq: Alignment peformed using STAR
bulk RNA-seq: Counts matrix generated using RSEM
Supplementary_files_format_and_content: Raw count or cellbender count matrices are in the HDF5 Feature Barcode Matrix Format used by 10x, bulk counts matrices are provided as an RSEM counts matrix, and metadata files are comma-delimited text.

source_name: COVID-19 autpsy tissue

extract_protocol:
Dissociated individual cells or isolated individual nuclei from fresh, frozen, or cryopreserved COVID-19 autopsy samples; bulk samples were lysed in RLT buffer + 1% beta mercaptoethanol
3' RNAseq (10x kit V3 chemistry) for sc/snRNA-seq; Smart-seq2 for bulk RNA-seq

tag: disease state

tag: sampleID

tag: donor

tag: processing

value: cryo


title: G60, infected, gill, fish 6

source_name: Gill

value: Gill


title: ggTPH-2


title: Tumor vs Normal patient ID 220

description:
Tumor vs Normal Lung 220
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: Tumor vs Normal patient ID 212

description:
Tumor vs Normal Lung 212
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: ggTPH-1


title: 12-P852049-S007-R02 [bulk_RNA-Seq]


title: P2_stim_2

tag: replicate number


title: P2_stim_3

tag: unstim or stim (4hrs 50ng/ml pma + 1um ionomycin)


title: G60, infected, gill, fish 7


title: 12-P617758-S008-R02 [bulk_RNA-Seq]


title: ggAANAT-2

tag: strain


title: ggAANAT-1

tag: induction concentration


title: 12-P485759-S008-R02 [bulk_RNA-Seq]


title: P2_unstim_3


title: P2_stim_1


title: 12-P230638-S005-R02 [bulk_RNA-Seq]


title: cvPhhB_2

tag: induction od


title: 04-P103142-S090-R01 [bulk_RNA-Seq]


title: P2_unstim_2


title: Tumor vs Normal patient ID 165

description:
Tumor vs Normal Lung 165
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: hsAANAT-2

tag: induction time


title: Tumor vs Normal patient ID 156

description:
Tumor vs Normal Lung 156
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)

tag: tissue


title: Tumor vs Normal patient ID 209

description:
Tumor vs Normal Lung 209
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: Tumor vs Normal patient ID 188

description:
Tumor vs Normal Lung 188
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: cvPhhB_1


title: 04-P054921-S029-R01 [bulk_RNA-Seq]


title: cobPNMT-1


title: P1_stim_3


title: Tumor vs Normal patient ID 154

description:
Tumor vs Normal Lung 154
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: cobPNMT-2


title: 04-P079042-S023-R01 [bulk_RNA-Seq]


title: Tumor vs Normal patient ID 150

description:
Tumor vs Normal Lung 150
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: P1_stim_1


title: ckDDC_2


title: 04-P006354-S016-R01 [bulk_RNA-Seq]


title: P1_stim_2


title: ckDDC_1


title: 02-P348762-S057-R01 [bulk_RNA-Seq]


title: 04-P054921-S028-R01 [bulk_RNA-Seq]


title: 02-P334354-S106-R01 [bulk_RNA-Seq]

value: Brain


title: Tumor vs Normal patient ID 136

description:
Tumor vs Normal Lung 136
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: CcCOMT-2


title: Tumor vs Normal patient ID 130

description:
Tumor vs Normal Lung 130
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: Tumor vs Normal patient ID 131

description:
Tumor vs Normal Lung 131
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: ccCOMT-1


title: P2_unstim_1


title: P1_unstim_2


title: P1_unstim_1


title: Tumor vs Normal patient ID 190

description:
Tumor vs Normal Lung 190
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: 02-P334354-S088-R01 [bulk_RNA-Seq]


title: 02-P334354-S066-R01 [bulk_RNA-Seq]


title: 139

city: Birmingham

first: Martin

last: Young

state: Alabama

address: 703 19th Street S

department: Medicine

institute: University of Alabama at Birmingham

description: rawCounts.xlsx

data_processing:
Basecalling performed using Illumina bcl2fastq version 2.18.0.12.
Raw sequence FASTQ files were aligned using STAR version 2.7.3a using parameters --outReadsUnmapped Fastx --outSAMtype BAM sortedByCoordinate --outSAMattributes All
Transcript abundances were calculated using HTSeq-count version 0.12.3 using parameters -r pos -t exon -i gene_id -a 10 -s no -f bam
Normalization was performed using DESeq2 version 1.28.1 using default parameters in their vignette.
Genome_build: Gencode GRCm38 p6 Release M24
Supplementary_files_format_and_content: rawCounts.xlsx: Excel file containing Ensembl ID and raw counts for each gene in each sample.

source_name: Heart

extract_protocol: RNA was extracted using TriZol.

treatment_protocol: Mice were fed either a control diet or a high fat diet for 20 weeks, after which hearts were isolated at 6 distinct times of the day (ZT1, ZT5, ZT9, ZT13, ZT17, ZT21). Following RNA isolation, RNAseq was performed.

value: Heart

tag: diet

value: High Fat

tag: zietgeber time


title: btASMT_1


title: btASMT_2


title: Tumor vs Normal patient ID 133

description:
Tumor vs Normal Lung 133
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)

tag: gender

tag: histology


title: Tumor vs Normal patient ID 106

description:
Tumor vs Normal Lung 106
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)

tag: Stage

tag: age


title: 138

description: rawCounts.xlsx

value: Control


title: 02-P248880-S087-R01 [bulk_RNA-Seq]

tag: disease state


title: btAANAT_2


title: 128

description: rawCounts.xlsx


title: Tumor vs Normal patient ID 100

description:
Tumor vs Normal Lung 100
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: Tumor vs Normal patient ID 101

description:
Tumor vs Normal Lung 101
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: P1_unstim_3


title: 127

description: rawCounts.xlsx


title: 02-P240970-S009-R01 [bulk_RNA-Seq]

tag: sampleID


title: 02-P166169-S038-R01 [bulk_RNA-Seq]

tag: donor


title: 02-P166169-S027-R01 [bulk_RNA-Seq]

tag: processing


title: 124

description: rawCounts.xlsx


title: 126

description: rawCounts.xlsx


title: bpTDC-1


title: bpTDC-2


title: 02-P118946-S059-R01 [bulk_RNA-Seq]


title: Tumor vs Normal patient ID 089

description:
Tumor vs Normal Lung 089
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)

value: Undifferentiated large cell carcinoma


title: atASMT-325G-2


title: 123

description: rawCounts.xlsx


title: Tumor vs Normal patient ID 098

description:
Tumor vs Normal Lung 098
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: 112

description: rawCounts.xlsx


title: 02-P005175-S054-R01 [bulk_RNA-Seq]


title: btAANAT_1


title: 04-P103142-S150-R01: cellbender counts

description: Cellbender remove-background corrected single-cell or single nucleus RNA-Seq (10X) Cellranger counts, stored as an HDF5 file.

value: lung

value: fresh


title: Tumor vs Normal patient ID 118

description:
Tumor vs Normal Lung 118
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: Tumor vs Normal patient ID 085

description:
Tumor vs Normal Lung 085
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)

value: Large cell neuroendocrine carcinoma


title: Tumor vs Normal patient ID 088

description:
Tumor vs Normal Lung 088
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: 111

description: rawCounts.xlsx


title: Tumor vs Normal patient ID 066

description:
Tumor vs Normal Lung 066
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: HsTPH-2

value: 1mM Rhamnose


title: 04-P103142-S149-R01: cellbender counts


title: Tumor vs Normal patient ID 096

description:
Tumor vs Normal Lung 096
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)


title: 110

description: rawCounts.xlsx


title: 04-P103142-S148-R01: cellbender counts


title: hsTPH_E2K-2


title: 107

description: rawCounts.xlsx


title: atASMT-325G-1


title: 105

description: rawCounts.xlsx


title: VT3797_rep_A [RNA-seq]

city: Worcester

first: Ye

last: Duan

state: MASSACHUSETTS

address: 373 Plantation Street, Biotech Two, Suite 306

department: Program of Molecular Medicine

institute: Umass Medical School

description:
U18A
RNA.raw.reads.VT1367_VT3797.csv

data_processing:
Adaptor removal and size filtering by Cutadapt/1.9
rRNA/tRNA/srpR removal by Bowtie2/2.3.4.3
Genome mapping by Star/2.5.3
Gene counting by featureCounts(subread/1.6.2)
Genome_build: WBCel235
Supplementary_files_format_and_content: comma-seperated values of gene counts

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C.elegans were cultured on nematode growth medium (NGM) and fed with E. coli HB101 unless specified. To obtain populations of synchronized developing worms, gravid adults were collected and washed twice with water. Pellets of centrifuged worms were treated with 5 ml 1N NaOH and 1% (v/v) sodium hypochlorite for 5 min with shaking to obtain embryos, and the embryos were rinsed with M9 buffer three times. The embryos were hatched in 10 ml M9 buffer at 20°C for 16-18 hrs with mild shaking. Hatched L1 larvae were transferred to plates at 30-50 worms per plate and replicate plates were cultured  for defined periods; samples of the population were examined by microscopy to confirm the developmental stage at the time of harvest.

extract_protocol:
Harvested worms were washed with M9 medium, centrifuged, and the worm pellets were flash-frozen in liquid nitrogen. The worm pellets were thawed and lysed by adding 4X volumes of QIAzol (Qiagen, Cat: 79306) and shaking vigorously at room temperature for 15 min. The total RNA was extracted by the addition of 0.85X volume chloroform, centrifugation, and recovery of the aqueous phase, which was then re-extracted with 1 volume phenol:chloroform:isoamyl alcohol (25:24:1, pH = 5.5). Total RNA was then precipitated by add 1 volume of isopropanol and 0.5 µl GlycoBlue (Invitrogen, Cat: AM9516), followed by incubation at -80oC for at least 30 min, and recovery by centrifugation at 25,000 rcf for 10 min at 4 °C. The supernatants were then removed, and the RNA pellets were subsequently washed twice by 70% (v/v) ethanol, dried in air for 5 min, dissolved in water, and stored at -80 °C. Worm samples for RNA-seq were aliquoted from the ribosome profiling harvests before the lysis step and frozen separately. The total RNA was extracted as described above. To enrich for mRNA, rRNA was depleted as described in detail elsewhere (Duan et al., 2020b). rRNA-depleted mRNA samples were then purified by RNA Clean & Concentrator-5 Kit (ZYMO, Cat: R1015)
Libraries were constructed by NEBNext Ultra II RNA Library Prep kit (NEB, Cat: E7775, E7335, E7500) and sequenced by Illumina NextSeq 500 system

treatment_protocol: Synchronized populations of developing worms were cultured at 20 °C for 45 hrs after feeding. Harvested worms were washed with water three times and incubated at room temperature for 10 min to allow digestion of intestinal bacteria. Worms were then pelleted by centrifuge at 4,500 rcf for 2 min at room temperature and residual water was removed until the total volumes were twice as the worm pellets. The samples were then flashed frozen by liquid nitrogen and stored at -80 °C.

tag: genotype

value: mid L4

tag: temperature


title: VT3797_rep_B [RNA-seq]

description:
U18A
RNA.raw.reads.VT1367_VT3797.csv


title: 04-P103142-S109-R01: cellbender counts

value: nuclei


title: 04-P103142-S089-R01: cellbender counts


title: hsTPH_E2K-1

tag: strain


title: VT1367_rep_C [RNA-seq]

description:
WT for U18A
RNA.raw.reads.VT1367_VT3797.csv


title: 95

description: rawCounts.xlsx


title: 04-P079042-S071-R01: cellbender counts

value: heart


title: Tumor vs Normal patient ID 005

description:
Tumor vs Normal Lung 005
AFE_xxx files are Cy5/Cy3 (Tumor/Normal)
AFE_xxx_Rev files are Cy3/Cy5 (Normal/Tumor)

value: Lung

value: Adenocarcinoma


title: VT1367_rep_B [RNA-seq]


title: HsTPH-1

tag: induction concentration


title: VT3797_rep_C [RNA-seq]

description:
U18A
RNA.raw.reads.VT1367_VT3797.csv


title: hsTPH_Ntermtrunc-2

tag: induction od


title: 04-P079042-S015-R01: cellbender counts


title: hsTPH_N174trunc-2

tag: induction time


title: 94

description: rawCounts.xlsx

tag: tissue