title: Control-DMSO-Rep3


title: Aged_nphx_1075

status: Public on Apr 01 2023

type: SRA

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

description:
Aged_nphx_lec
Aged_nphx_normalized_expression_matrix.csv

library_source: transcriptomic

data_processing:
Demultiplexed fastq files were aligned to mm10 mouse reference genome by STAR aligner.
Raw read count matrix were made by featureCounts from Subread package
Raw read count matrix were read by Seurat (v4.1.0). Then, low quality cells (expressing less than 2000 genes), potential dead cells (>10% mitochondrial gene percentage) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control. Matrices were log normalized and variables such as number of UMIs, mitochondrial gene percentages, ribosomal gene module scores, and dissociation gene module scores were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for nasopharyngeal LECs

molecule: total RNA

organism: Mus musculus

growth_protocol: Smart-Seq3 single-cell RNA libraries

extract_protocol:
FACS sorted nasopharyngeal LECs (CD31+ PDPN+) were processed by Smart-Seq3 protocol
Libraries were generated following Smart-Seq3 protocol (Hagemann-Jensen M et al.,Single-cell RNA counting at allele and isoform resolution using Smartseq3. Nat Biotechnol 2020)

tag: strain

tag: cell type

value: FACS sorted


title: Control-DMSO-Rep2

city: Chicago

first: Marc

middle: L

last: Mendillo

state: IL

address: 303 E Superior St

country: USA

institute: Northwestern University

data_processing:
The quality of DNA reads, in fastq format, was evaluated using FastQC.  Adapters were trimmed, and reads of poor quality or aligning to rRNA sequences were filtered.  The cleaned reads were aligned to rat genome assembly rn6 using Tophat.  Gene counts were quantified from BAM files using htseq-counts.
Assembly: rn6
Supplementary files format and content: htseq counts tables provide normalized count estimates of uniquely mapped RNAseq reads

organism: Rattus norvegicus

source_name: brain, cerebral cortex

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit according to supplied protocol.
Llibraries were prepared from 150 ng RNA using the Illumina TruSeq Stranded mRNA Library Preparation Kit, according to supplied protocol.

tag: tissue

value: brain, cerebral cortex

value: primary glutamatergic  neurons and astrocytes

tag: genotype

value: Empty Vector

tag: treatment

value: DMSO


title: Plasma sEVs_non-R0_rep14

city: changsha

first: mu

last: Liu

address: No. 932, Lushan South Road, Yuelu District, Changsha City, Hunan Province

country: China

institute: Central South University

data_processing:
The raw reads were processed by filtering out containing adapter, poly ’N’, low quality, smaller than 17nt reads by FASTQC to get clean reads. Mapping reads were obtained by mapping clean reads to reference genome of by Bowtie.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA by BLAST. The miRNA expression was calculated by RPM (Reads Per Million) values (PRM=(number of reads mapping to miRNA/ number of reads in Clean data)×106 ).
The expression levels were normalized by RPM, RPM is equal to (number of reads mapping to miRNA/ number of reads in Clean data)×10^6. Differential expression between two sets of samples was calculated by the limma algorithm according to the criteria of |log2（Fold Change）|≥1 and P-value < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample

organism: Homo sapiens

source_name: Plasma sEVs

extract_protocol:
A total of 4mL of plasma was mixed with RiboTM Exosome Isolation Reagent, and exosome isolation was performed according to the manufacturer’s instructions (Ribobio, China). Exosomal RNA was extracted by the HiPure Liquid Plasma miRNA Kit (Megan, China). The quantity and integrity of Exosomal RNA yield were assessed by using the Qubit®2.0 (Life Technologies, USA) and Agilent 2200 TapeStation (Agilent Technologies, USA) separately.
50ng Exosomal RNA of each sample was used to prepare small RNA libraries by NEBNext® Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) according to manufacturer’s instructions. The libraries were sequenced by HiSeq 2500 (Illumina, USA) with single-end 50bp at Ribobio Co. Ltd (Ribobio, China).

value: Plasma sEV

tag: residual disease status

tag: figo stage

value: IIIC

tag: age

tag: serum ca-125

value: untreated


title: OVCAR8 Cas9-negative initial (adherent) condition replicate 1

city: Ottawa

first: Pirunthan

last: Perampalam

state: ON

address: 336 Drumlsih Lane

country: Canada

description:
GO-CRISPR screen sample
OVCAR8_TRACS.csv

data_processing:
Library strategy: GO-CRISPR
Raw read files (FASTQ) from GO-CRISPR screen were anlayzed using TRACS 1.1.3
TRACS 1.1.3 automatically does the following: FASTQ files are trimmed with Cutadapt 1.15; the reference sgRNA CSV file is converted to FASTA format; A Bowtie2 index is constructed using Bowtie 2.3.4.1; the initial plasmid library (L0) is aligned to the index and a BAM file is generated using Bowtie 2.3.4.1 and Samtools 1.7; Read counts are generated using MAGeCK 0.5.6; TRACS then runs the TRACS algorithm to determine gene essentiality.
Raw read files (FASTQ) from RNA-seq experiments were mapped using STAR 2.6.1 to get read counts. Then, differential expression was analyzed using BEAVR 1.0.9
Genome_build: Human GeCKO v2 library A+B reference sgRNA sequences
Supplementary_files_format_and_content: For GO-CRISPR, CSV files containing Enrichment Scores (ES) and Enrichment Ratios (ER) for each gene
Supplementary_files_format_and_content: For RNA-seq, CSV files containing transcript/gene read counts and metadata (sample info)

source_name: High-grade serous ovarian cancer

extract_protocol:
Cells were harvested and genomic DNA was extracted using QIAmp Blood Maxi Kits (QIAGEN #51194). Genomic encoded sgRNA sequences were PCR amplified with two rounds of PCR to increase abundance of the initial sgRNA population and insert sample barcodes necessary for identification of condition and replicate number. PCR products were gel purified, quantitated by Qubit (Invitrogen) and pooled prior to high throughput sequencing.
Pooled preparation containing all barcoded samples were sequenced using an Illumina NextSeq 550 75-cycle high output kit (#20024906). FASTQ files were obtained containing raw reads for all samples and were demultiplexed to obtain individual FASTQ files for each sample: one initial pooled sgRNA library file (L0), 3x Cas9-positive initial condition replicates (T0), 3x Cas9-positive final condition replicates (Tf), 3x Cas9-negative initial condition replicates (T0), 3x Cas9-negative final condition replicates (Tf).

tag: cas9 status

value: Cas9 negative

tag: go-crispr time point

tag: plate condition

value: Adherent

tag: replicate


title: Plasma sEVs_non-R0_rep13


title: Control-DMSO-Rep1


title: OVCAR8 Cas9-positive final (reattached spheroid) condition replicate 3

value: Cas9 positive

value: Tf

value: Reattached (Ultra low attachment)


title: Plasma sEVs_non-R0_rep12


title: OVCAR8 Cas9-positive final (reattached spheroid) condition replicate 2


title: Aged_nphx_1073


title: Plasma sEVs_non-R0_rep11


title: OVCAR8 Cas9-negative final (reattached spheroid) condition replicate 2


title: 21m_ICH_R-mRNA

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with Pvalue < =0.01 and Fold change >=2
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene RPKM values for each Sample

molecule: polyA RNA

source_name: Rat brain tissues

extract_protocol:
Total RNA was extracted from nine rat brains by using TRIzol Reagent (Ambion), and then pooled together an equal amount of total RNA from all samples to obtain the represented RNA mix. Total RNA was treated with RQ1 DNase (promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% Agarose gel electrophoresis.
For each sample, 10 μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo (dT)-conjugated magnetic beads (invitrogen) before being used for directional RNA-seq library preparation. Purified mRNAs were ion fragmented at 95℃ followed by end repair and 5' adaptor ligation. Then mRNA reverse transcription was performed with RT primer harboring 3' adaptor sequenceand randomized hexamer. The cDNAs were purified and amplified. And products corresponding to 200-500 bps were purified, quantified and stored at -80 ℃ before sequencing.

value: contralateral brain

value: 21 mon old

tag: disease

value: intracerebral hemorrhage


title: 21m_ICH_L-mRNA

value: ipsilateral brain


title: Aged_nphx_1072

value: FACS sorted


title: OVCAR8 Cas9-positive final (reattached spheroid) condition replicate 1


title: OVCAR8 Cas9-positive initial (adherent) condition replicate 3


title: OVCAR8 Cas9-positive initial (adherent) condition replicate 2


title: Plasma sEVs_non-R0_rep10


title: 13m_ICH_R-mRNA

value: 13 mon old


title: 13m_ICH_L-mRNA


title: HC_BC000001_MCPY_4_rep1

city: Boston

first: Xianjun

last: Dong

state: MA

address: 60 Fenwood Rd

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
RNA-seq raw files in FASTQ format were processed in a customized pipeline. For each sample, we first filtered out reads that failed vendor check or are too short (<15nt) after removing the low-quality ends or possible adaptor contamination by using fastq-mcf with options of “-t 0 –x 10 –l 15 –w 4 –q 10 –u”. We then checked the quality using FastQC and generated k-mer profile using kpal for the remaining reads. Reads were then mapped to the human genome (GRCh37/hg19) using Tophat (v2.0.8) by allowing up to 2 mismatches and 100 multiple hits. Reads mapped to ribosomal RNAs or to the mitochondrial genome were excluded from downstream analysis. Gene expression levels were quantified using FPKM (Fragments Per Kilobase of transcript per Million mapped reads). Only uniquely mapped reads were used to estimate FPKM. To calculate normalized FPKM, we first ran Cuffquant (v2.2.1) with default arguments for genes annotated in GENCODE (v19), and then ran Cuffnorm with parameters of “-total-hits-norm –library-norm-method quartile” on the CBX files generated from Cuffquant
For circRNA identification, we first extracted the chimerically aligned RNAseq reads using Tophat-fusion and then called circRNAs using circExplorer (v2.0). To identify circRNAs that are not back-spliced from a canonical exon border, we ran circExplorer2 with a customized gene annotation file and the “--low-confidence” option. CircRNAs with at least two unique back-spliced reads in overall samples are categorized as “being expressed” and kept as circRNA candidates. CircRNA expression is quantified by normalized reads per million (RPM) at the back-splicing sites for each sample
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPM values for each circRNA in each sample

source_name: Motor cortex pyramidal neuron

extract_protocol:
Total RNA was isolated and treated with DNase (Qiagen) using the Arcturus Picopure method (Applied Biosystems), yielding approximately 7-8 ng RNA per subject. Total RNA was linearly amplified into 5~10 µg of double-stranded cDNA using the validated, precise, isothermal RNA amplification method implemented in the Ovation RNA-seq System V2 (NuGen)
Sequencing libraries were generated from 500 ng of the double-stranded (ds) cDNA using the TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer's protocol. The cDNA was fragmented, and end repair, A-tailing, adapter ligation was performed for library construction.

tag: source sampleid

tag: source subjectid

tag: disease state

value: HC

value: MCPY

tag: batch


title: Plasma sEVs_non-R0_rep9


title: Aged_nphx_1070

tag: strain

tag: cell type


title: Plasma sEVs_R0_rep11

tag: tissue

value: IIIA


title: OVCAR8 Cas9-positive initial (adherent) condition replicate 1


title: Aged_nphx_1074


title: Srobleaf_PARE

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
Library strategy: PARE-Seq
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the sorghum genome (JGI database).
PARE: the adapter sequences were trimmed from raw sequence reads, and then the RNA sequences were trimmed to the lengths of 20 nucleotides. PARE reads were mapped to the sorghum genome (JGI database).
Genome_build: Sorghum bicolor (JGI database)
Supplementary_files_format_and_content: Tag count file

organism: Saccharum robustum

source_name: young leaf

extract_protocol: Small RNA libraries and PARE libraries were constructed from total RNA isolated from young leaves of sugarcane using Trizol Reagent (Invitrogen, Life Technologies, USA). The sRNA library preparation protocol is based on Illumina’s sRNA Sequencing Sample Preparation Guide (Illumina, San Diego, CA). And the PARE library preparation protocol is based on Illumina’s TruSeq RNA  Sequencing Sample Preparation Guide (Illumina, San Diego, CA) The libraries were sequenced on an Illumina GAII at the Delaware Biotechnology Institute (Newark, DE).

value: young leaf

tag: cultivar

value: mature plants


title: Aged_nphx_1069


title: Plasma sEVs_R0_rep10

value: Plasma sEV

tag: residual disease status

value: IIIC

tag: treatment

value: untreated


title: Cas9-negative final (reattached spheroid) condition replicate 3

data_processing:
Raw read files (FASTQ) were anlayzed using TRACS 1.1.3
TRACS 1.1.3 automatically does the following: FASTQ files are trimmed with Cutadapt 1.15; the reference sgRNA CSV file is converted to FASTA format; A Bowtie2 index is constructed using Bowtie 2.3.4.1; the initial plasmid library (L0) is aligned to the index and a BAM file is generated using Bowtie 2.3.4.1 and Samtools 1.7; Read counts are generated using MAGeCK 0.5.6; TRACS then runs the TRACS algorithm to determine gene essentiality.
Genome_build: Human GeCKO v2 library A+B reference sgRNA sequences
Supplementary_files_format_and_content: CSV file containing Enrichment Scores (ES) and Enrichment Ratios (ER) for each gene

extract_protocol:
At each time point indicated (either L0, T0, or Tf), cells were harvested and genomic DNA was extracted using QIAmp Blood Maxi Kits (QIAGEN #51194). Genomic encoded sgRNA sequences were PCR amplified with two rounds of PCR to increase abundance of the initial sgRNA population and insert sample barcodes necessary for identification of condition and replicate number. PCR products were gel purified, quantitated by Qubit (Invitrogen) and pooled prior to high throughput sequencing.
Pooled preparation containing all barcoded samples were sequenced using an Illumina NextSeq 550 75-cycle high output kit (#20024906). FASTQ files were obtained containing raw reads for all samples and were demultiplexed to obtain individual FASTQ files for each sample: one initial pooled sgRNA library file (L0), 3x Cas9-positive initial condition replicates (T0), 3x Cas9-positive final condition replicates (Tf), 3x Cas9-negative initial condition replicates (T0), 3x Cas9-negative final condition replicates (Tf).

value: Cas9 negative


title: Aged_nphx_1067


title: Plasma sEVs_R0_rep9

tag: figo stage

tag: age


title: Ssinleaf_PARE

organism: Saccharum sinense

value: Chukche


title: Aged_nphx_1068


title: Cas9-negative final (reattached spheroid) condition replicate 2

tag: cas9 status

value: Tf


title: Plasma sEVs_R0_rep8

value: IV

tag: serum ca-125


title: Aged_nphx_1066


title: Ssinleaf_sRNA

data_processing:
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the sorghum genome (JGI database).
PARE: the adapter sequences were trimmed from raw sequence reads, and then the RNA sequences were trimmed to the lengths of 20 nucleotides. PARE reads were mapped to the sorghum genome (JGI database).
Genome_build: Sorghum bicolor (JGI database)
Supplementary_files_format_and_content: Tag count file


title: Cas9-negative final (reattached spheroid) condition replicate 1

tag: go-crispr time point


title: Aged_nphx_1071


title: Aged_nphx_1065


title: Plasma sEVs_non-R0_rep8

data_processing:
The raw reads were processed by filtering out containing adapter, poly ’N’, low quality, smaller than 17nt reads by FASTQC to get clean reads. Mapping reads were obtained by mapping clean reads to reference genome of by Bowtie.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA by BLAST. The miRNA expression was calculated by RPM (Reads Per Million) values (PRM=(number of reads mapping to miRNA/ number of reads in Clean data)×106 ).
The expression levels were normalized by RPM, RPM is equal to (number of reads mapping to miRNA/ number of reads in Clean data)×10^6. Differential expression between two sets of samples was calculated by the limma algorithm according to the criteria of |log2（Fold Change）|≥1 and P-value < 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample


title: Tumor

type: genomic

city: Caserta

first: Francesco

last: Cecere

state: Caserta

address: Via A. Vivaldi, n. 43

department: DiStABiF

country: Italy

institute: University of Campania "Luigi Vanvitelli"

description:
methylation profiling using bisulfite converted
Infinium MethylationEPIC

hyb_protocol: 800 nanograms of genomic DNA was treated with sodium bisulfite by using the EZ DNA Methylation Kit (D5001, Zymo Research) following the manufacturer’s protocol. The bisulfite converted DNA was amplified, fragmented and hybridized to Infinium MethylationEPIC 850K Bead Chip (WG-317-1001, Illumina) using Illumina standard protocol.

scan_protocol: Fluorescence intensities were captured using Illumina HiScan SQ (Illumina)

data_processing:
Genome-wide methylation analysis was performed by the Illumina Infinium methylation Epic array on bisulfite converted DNA extracted from the three tissues of the patient. Data were analyzed using R version 4.1.0. Beta values (Bvalues) were derived from “idat” files by the “champ.load” module of the “ChAMP” R package (v.2.22.0), with quality control options set as default and array type as “EPIC.” To adjust the Bvalues of type 2 probes, we applied BMIQ normalization with the default options for array type as “EPIC.”
normalized data files contain: BMIQ normalized matrix
signal intensities file contains: Unmethylated signal (B) and methylated signal (A) intensities

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Colon Tissue

label_protocol: Standard llumina Protocol

extract_protocol: Genomic DNA was isolated from peripheral blood lymphocytes by using the salting-out method.

tag: gender

value: F

tag: condition

value: BWS-CRC

value: Colon

value: A


title: Cas9-negative initial (adherent) condition replicate 3


title: Aged_nphx_1064

value: FACS sorted


title: Plasma sEVs_non-R0_rep7


title: Peri_neoplastic


title: Aged_nphx_1063


title: Plasma sEVs_non-R0_rep6


title: Aged_nphx_1062


title: Cas9-negative initial (adherent) condition replicate 2


title: Srobleaf_sRNA


title: Cas9-negative initial (adherent) condition replicate 1


title: C11_reanalyzed

description:
methylation profiling using bisulfite converted
platform name: Infinium MethylationEPIC

source_name: Blood

value: control

value: blood

value: re-analyzed from GSE195873


title: C12_reanalyzed


title: Aged_nphx_1061


title: Plasma sEVs_non-R0_rep4


title: Plasma sEVs_non-R0_rep5


title: C10_reanalyzed

value: M


title: Aged_nphx_1060


title: Cas9-positive final (reattached spheroid) condition replicate 3

value: Cas9 positive


title: Cas9-positive final (reattached spheroid) condition replicate 2


title: Cas9-positive final (reattached spheroid) condition replicate 1


title: C9_reanalyzed


title: Cas9-positive initial (adherent) condition replicate 3


title: Aged_nphx_1058


title: C8_reanalyzed


title: Plasma sEVs_non-R0_rep3

value: Plasma sEV


title: Cas9-positive initial (adherent) condition replicate 2


title: C7_reanalyzed


title: Plasma sEVs_non-R0_rep2

value: IIIC


title: Aged_nphx_1057


title: Plasma sEVs_non-R0_rep1

value: untreated


title: C6_reanalyzed


title: Plasma sEVs_R0_rep7


title: Plasma sEVs_R0_rep6


title: C5_reanalyzed


title: Mouse_Tcells_2_S3_L004

city: Louisville

first: Jun

last: Yan

state: KY

address: 505 S Hancock Street

institute: University of Louisville

library_source: transcriptomic single cell

data_processing:
Illumina BaseSpace FastQ v1.0.0 used for basecalling
Files were demuliplexed to Fastq files using 10X Genomics Cellranger mkfastq
Raw sequences were checked for quality values using fastQC v0.10.1.  Quality trimming was not deemed necessary.
The sequences were directly aligned to the Mus musculus reference genome assembly (mm10) using 10X Genomics Cellranger
Read counts for gene regions were obtained with 10X Genomics Cellranger count
Assembly: mm10

source_name: Spleen and LN

extract_protocol: 3’ Gene Expression library preparation was performed following the protocol laid out in Step 3 (page 35) of the Chromium Single Cell 3’ Reagents Kits v3 Rev A User Guide.

value: Spleen and LN

value: gdT cells


title: Mouse_Tcells_2_S3_L003


title: (-)-borneol_rep2

type: RNA

city: Shiga

first: Junji

last: Takabayashi

address: 2-509-3 Hirano, Otsu

department: Center for Ecological Research

country: Japan

institute: Kyoto University

description:
Biological replicate 2 of 2
m2

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Agilent scanner model G2565

data_processing:
Data was analyzed by Fearure Extraction software (Agilent)
Normalized ProcessedSignal of Cy3

organism: Arabidopsis thaliana

source_name: WT Arabidopsis leaves

label_protocol: Low RNA input Linear Amplification/Labeling Kit (Agilent)

growth_protocol: The Arabidopsis thaliana accession Columbia-0 (Col-0)  seeds were germinated under sterile conditions, while the plants were grown at 23°C under a 16L-8D light regime (~100 µmol photons m-2 s-1) in a climate-controlled chamber.

extract_protocol: RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: Three days after germination of Arabidospsis thaliana (ecotype Col-0) seeds, the seedlings were treated with one of the enantiomers of borneol (25 mM) for 24 hours.

tag: ecotype

value: 25 mM (-)-borneol_24 h


title: Aged_nphx_1055


title: Plasma sEVs_R0_rep5

value: IIIA


title: (-)-borneol_rep1

description:
Biological replicate 1 of 2
m1


title: Plasma sEVs_R0_rep4

value: IIIB


title: Mouse_Tcells_2_S3_L002


title: Mouse_Tcells_2_S3_L001


title: Aged_nphx_1053


title: Aged_nphx_1052


title: (+)-borneol_rep3

description:
Biological replicate 3 of 3
p3

value: 25 mM (+)-borneol_24 h


title: Plasma sEVs_R0_rep1


title: Aged_nphx_1051


title: Plasma sEVs_R0_rep3


title: Aged_nphx_1059


title: Plasma sEVs_R0_rep2


title: Mouse_Tcells_1_S2_L004


title: Mouse_Tcells_1_S2_L003


title: Aged_nphx_1056


title: Aged_nphx_1050


title: Mouse_Tcells_1_S2_L002


title: (+)-borneol_rep1

description:
Biological replicate 1 of 3
p1


title: Cas9-positive initial (adherent) condition replicate 1


title: Aged_nphx_1049


title: control_mock_rep3

description:
Biological replicate 3 of 3
c3

value: mock_MeOH_24 h


title: PCa_PC3_Res_2

city: Ann Arbor

first: Evan

middle: T

last: Keller

state: MI

address: 2800 Plymouth Rd

institute: University of Michigan

data_processing:
Samples were sequenced on the Illumina HiSeq-2500 Rapid with single end option.
Samples were aligned to Human genome hg38 using bowtie alignment tool.
Genome_build: Human genome hg38
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts

growth_protocol: Cells were cultered in RPMI 1640 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
Cells were trypsinized in 0.05% Trypsin EDTA for 5-10 mins at 37°C and washed with media.
Libraries for each cell line was prepared using the SMART-seq mRNA Library kit (Takara Bio USA, Inc.).  RNA and library quality were tested using the Aqilent 2100 Bioanalyzer.

treatment_protocol: Docetaxel resistance was maintained with the addition of 10 nM docetaxel in DMSO in growth media while sensitive cells were maintained with the addition of a final concentration of 0.1% DMSO.

tag: docetaxel sensitivity

value: Resistant

value: Prostate cancer

tag: cell line


title: PCa_PC3_Res_1

tag: disease state


title: Mouse_Tcells_1_S2_L001

tag: strain


title: Aged_nphx_1054

tag: cell type

value: FACS sorted


title: Aged_nphx_1048


title: control_mock_rep2

description:
Biological replicate 2 of 3
c2


title: PCa_PC3_Sen_2

value: Sensitive


title: cDC2 untreated biol rep 4 [cDC2_unt_4]

first: Ulrich

last: von Andrian

address: 77 Ave Louis Pasteur

department: Immunology

institute: Harvard Medical School

data_processing:
Reads were aligned to the mouse genome (GENCODE GRCm38/mm10 primary assembly and gene annotations vM16; https://www.gencodegenes.org/mouse_releases/16.html) with STAR 2.5.4a (https://github.com/alexdobin/STAR/releases).
The ribosomal RNA gene annotations were removed from GTF (General Transfer Format) file.
The gene-level quantification was calculated by featureCounts (http://subread.sourceforge.net/).
Assembly: mm10
Supplementary files format and content: csv text file includes raw count table containing all samples

source_name: classical dendritic cell, type 2

growth_protocol: BM-DCs were differentiated in RPMI1640 medium with 10% FCS, penicillin-streptomycin, beta-mercaptoethanol, glutamine, and 100ng/ml Flt3L and harvested on day 9.

extract_protocol:
A thousand cells of each population were sorted directly into 5ul of lysis buffer (TCL Buffer (Qiagen) with 1% b‑mercaptoethanol)
Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′‑AAGCAGTGGTATCAACGCAGAGTACT30VN‑3′) and converted to cDNA via reverse transcription.

treatment_protocol: BM-DCs were cultured either in the presence of nociceptors or alone and treated with CGRP or SP neuropeptides overnight.

value: classical dendritic cell, type 2

tag: genotype

value: WT


title: control_mock_rep1

description:
Biological replicate 1 of 3
c1


title: Aged_nphx_1047


title: PCa_PC3_Sen_1


title: cDC2 untreated biol rep 3 [cDC2_unt_3]


title: Aged_nphx_1046


title: (+)-borneol_rep2

description:
Biological replicate 2 of 3
p2


title: PCa_DU145_Res_2


title: Aged_nphx_1045


title: cDC2 untreated biol rep 2 [cDC2_unt_2]


title: CYT_Rep4

city: Herlev

first: Joachim

last: Størling

address: Borgmester Ib Juuls Vej 83,

country: Denmark

institute: Steno Diabetes Center Copenhagen

data_processing:
RNA-seq libraries were sequenced on DNBseq platform to produce 100 bp long paired-end reads. An average of 45-50 million reads per replicate (EndoC-βH5 n=4) were obtained after pre-processing and QC (removal of low-quality reads and adapter sequences) using SOAPnuke software with following parameters: " -n 0.001 -l 20 -q 0.4 --adaMR 0.25 --ada_trim". Reads were aligned using TopHat (version 2.1.1) to GRCh38 genome with default parameters. Afterwards, reads were assigned to Ensembl version 107 gene annotation using htseq-count (version 0.9.1) with default parameters.
Genes with low expression were filtered based on a CPM cut-off of 0.5 in at least 4 samples. Differential gene expression analysis was performed on the two groups using the QL F-test in edgeR. Differentially expressed mRNAs were identified using a cut-off of abs(log2FC) > 0.5 and an FDR-adjusted p-value <0.05.
Assembly: GRCh38
Supplementary files format and content: Tab delimeted text files with CPM values of filtered genes for each sample

source_name: Human pancreatic cell line

growth_protocol: The EndoC-βH5 cells were seeded in appropriate plates coated with β-coat (Human Cell Design) and maintained in Ultiβ1 cell culture medium (Human Cell Design, Toulouse, France) containing 100 U/mL penicillin and 100 µg/mL streptomycin (Life Technologies). Cells were seeded in 24-well plates (200.000 cells/well) in duplicate and incubated in a humidified incubator at 37 °C with 5% CO2. Media change was carried out every 2-3 days.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA).
Libraries were prepared according to DNBSEQ Eukaryotic Strand-specific mRNA library kit

treatment_protocol: Cells were incubated for 48 hours in the presence or absence of recombinant human IL-1β (R&D systems), recombinant human IFNγ (PeproTech, Rocky Hill, NJ, USA) and/or recombinant human TNFα (R&D Systems).

tag: tissue

value: Human pancreatic cell line

tag: time

value: Cytokine-treated


title: CTRL_Rep4

tag: treatment

value: Control


title: Aged_nphx_1044


title: PCa_DU145_Res_1


title: PCa_DU145_Sen_2


title: CYT_Rep3


title: cDC2 untreated biol rep 1 [cDC2_unt_1]

value: untreated


title: PCa_DU145_Sen_1


title: cDC2 SP biol rep 4 [cDC2_SP_4]

value: 1nM Substance P


title: CTRL_Rep3


title: Aged_nphx_1043


title: Aged_nphx_1042


title: Aged_nphx_1041


title: CYT_Rep2


title: cDC2 SP biol rep 2 [cDC2_SP_2]


title: CTRL_Rep2


title: cDC2 SP biol rep 1 [cDC2_SP_1]


title: CYT_Rep1


title: CTRL_Rep1


title: cDC2 with nociceptors biol rep 2 [cDC2_DRG_2]

value: coculture with nociceptors


title: Aged_nphx_1038


title: Aged_nphx_1037


title: THZ531_1uM_R2

city: Leiden

first: Bob

last: van de Water

state: Leiden

address: Einsteinweg 55

country: Netherlands

institute: Leiden University

data_processing:
After sequencing, the raw reads were filtered by BGI. Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads.
Filtered reads were alligned to Grch38 using Hisat2 (v2.1.0)
Reads were counted using featureCounts.
Normalization and differential gene expression analysis was performed using DESeq2.
Assembly: Grch38
Supplementary files format and content: Raw counts .txt files

growth_protocol: Hs578T cells were maintained in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was isolated using RNeasy Plus Mini Kit (Qiagen)
Unstranded PolyA-selected libraries were prepared using the DNBseq platform and 50M 100bp paired-end reads were sequenced on a DNBSEQ-G400 sequencer by BGI Europe.

tag: replicate

value: human TNBC cell line

value: THZ531 1 uM


title: cDC2 SP biol rep 3 [cDC2_SP_3]


title: THZ531_1uM_R3


title: cDC2 with nociceptors biol rep 1 [cDC2_DRG_1]


title: Aged_nphx_1036

data_processing:
Demultiplexed fastq files were aligned to mm10 mouse reference genome by STAR aligner.
Raw read count matrix were made by featureCounts from Subread package
Raw read count matrix were read by Seurat (v4.1.0). Then, low quality cells (expressing less than 2000 genes), potential dead cells (>10% mitochondrial gene percentage) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
After quality control. Matrices were log normalized and variables such as number of UMIs, mitochondrial gene percentages, ribosomal gene module scores, and dissociation gene module scores were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for nasopharyngeal LECs


title: THZ531_1uM_R1


title: Aged_nphx_1035


title: cDC2 CGRP biol rep 4 [cDC2_CGRP_4]

value: 1nM Calcitonin gene-related peptide


title: THZ531_NIL_R3

value: THZ531 0.1 uM + Nilotinib 1 uM


title: cDC2 CGRP biol rep 3 [cDC2_CGRP_3]


title: Aged_nphx_1040


title: Aged_nphx_1039


title: NSC-56C-1 [Subline]

city: Tokyo

first: Masayuki

last: Komatsu

address: 5-1-1, Tsukiji, Chuo-ku

institute: National Cancer Center Research Institute

description: Subline

hyb_protocol: Following fragmentation, 10µg of cRNA were hybridized for 16 hr at 45ﾟC on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with GeneSpring version 14.9 using affymetrix expression analysis settings (Summarization algorithm: MAS5).

label: biotin

source_name: Gastric cancer cell line

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA by GeneChip 3' IVT Express Kit. The procedure was according to the standard Affymetrix protocol.

growth_protocol: Cells were maintained in 10% FBS-containing RPMI-1640 medium under an atmosphere of 5% CO2 and 95% air at 37˚C.

extract_protocol: Cultured cells were washed by D-PBS and lysed by ISOGEN solution. Extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: No specific treatment.


title: THZ531_NIL_R2


title: cDC2 with nociceptors biol rep 4 [cDC2_DRG_4]


title: cDC2 with nociceptors biol rep 3 [cDC2_DRG_3]


title: cDC2 CGRP biol rep 2 [cDC2_CGRP_2]


title: Aged_nphx_1033


title: NSC-47CX1F [Subline]

description: Subline


title: cDC2 CGRP biol rep 1 [cDC2_CGRP_1]


title: NSC-56C-2 [Parental line]

description: Parental line


title: NSC-40CX1a [Subline]

description: Subline


title: NSC-47C [Parental line]

description: Parental line


title: NIL_R3

value: Nilotinib 1 uM


title: Aged_nphx_1034


title: Aged_nphx_1031


title: Aged_nphx_1030


title: cDC1 untreated biol rep 4 [cDC1_unt_4]

source_name: classical dendritic cell, type 1

value: classical dendritic cell, type 1


title: cDC1 untreated biol rep 3 [cDC1_unt_3]


title: NIL_R1


title: Aged_nphx_1029


title: THZ531_LAP_R3

value: THZ531 0.1 uM + Lapatinib 3.16 uM


title: cDC1 untreated biol rep 1 [cDC1_unt_1]


title: cDC1 untreated biol rep 2 [cDC1_unt_2]


title: NSC-44CF [Parental line]

description: Parental line


title: Aged_nphx_1028

value: FACS sorted


title: NSC-44CX1a [Subline]

description: Subline


title: NSC-44CA [Subline]

description: Subline


title: NSC-40CX1 [Subline]

description: Subline


title: NSC-40C [Parental line]

description: Parental line


title: THZ531_NIL_R1


title: Aged_nphx_1032


title: NSC-44CX1 [Subline]

description: Subline


title: cDC1 SP biol rep 4 [cDC1_SP_4]


title: NIL_R2


title: Aged_nphx_1027


title: Aged_nphx_1026


title: cDC1 SP biol rep 3 [cDC1_SP_3]


title: cDC1 SP biol rep 2 [cDC1_SP_2]


title: KO-BMDMs-LPS_rep3

city: Wenzhou

first: guang

last: liang

state: Wenzhou

address: Wenzhou medical university of  higher education park  chashan town

department: School of Pharmaceutical Sciences

institute: Wenzhou Medical University

data_processing:
Illumina novaseq 6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: BMDMs

growth_protocol: BMDMs were collected and cultured in DMEM containing 20% L-929 culture medium and 10% fetal bovine serum, and 1% penicillin/streptomycin. On day 3 and day 5, fresh DMEM containing 20% L-929 culture medium and 10% fetal bovine serum was added. Cells were used for experiments on day 7.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT and Otud6a-/- BMDMs were plated at 300,000 cells/well in six-well plates. Cells were challenged with PBS or 100 ng/mL LPS for 6 h.

value: C57BL/6 Otud6a-/-

value: macrophage

value: treated with LPS(100ng/ml) for 6 hours


title: cDC1 SP biol rep 1 [cDC1_SP_1]

value: WT


title: KO-BMDMs-LPS_rep2


title: NSC-38C-2 [Subline]

description: Subline


title: NSC-35C-1 [Parental line]

description: Parental line


title: NSC-38C-1 [Parental line]

description: Parental line


title: NSC-35C-2 [Subline]

description: Subline


title: cDC1 with nociceptors biol rep 4 [cDC1_DRG_4]


title: NSC-32CX1 [Subline]

description: Subline


title: LAP_R3

value: Lapatinib 3.16 uM


title: LAP_R2


title: THZ531_LAP_R2


title: LAP_R1


title: THZ531_0.1uM_R3


title: cDC1 with nociceptors biol rep 3 [cDC1_DRG_3]


title: THZ531_LAP_R1


title: THZ531_0.1uM_R2


title: NSC-32CX1a [Subline]

description: Subline


title: cDC1 with nociceptors biol rep 1 [cDC1_DRG_1]


title: KO-BMDMs-control_rep3


title: cDC1 with nociceptors biol rep 2 [cDC1_DRG_2]


title: KO-BMDMs-control_rep2


title: NSC-32C [Parental line]

description: Parental line


title: THZ531_0.1uM_R1


title: NSC-28CX1a [Subline]

description: Subline


title: KO-BMDMs-control_rep1


title: DMSO_R3

value: DMSO


title: cDC1 CGRP biol rep 4 [cDC1_CGRP_4]


title: NSC-28CX1 [Subline]

description: Subline


title: NSC-28C [Parental line]

description: Parental line


title: WT-BMDMs-LPS_rep3

value: C57BL/6 wild-type


title: DMSO_R2


title: NSC-26C-2 [Subline]

description: Subline


title: cDC1 CGRP biol rep 3 [cDC1_CGRP_3]


title: DMSO_R1


title: cDC1 CGRP biol rep 2 [cDC1_CGRP_2]


title: WT-BMDMs-control_rep3

value: untreated


title: mets_25

city: DaeJeon

first: Hee Jeong

last: Jin

address: 672 Yuseong-daero

department: Korean Medicine (KM) Data Division

institute: Korea Institute of Oriental Medicine

data_processing:
read trimming: skewer
mapping: STAR
quantification: Cuffquant
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was isolated from   PBMC cell using TRIzol® RNA Isolation Reagents (Life technologies, Carlsbad, CA) based method. The quantity and quality of the RNA were evaluated using Agilent Nono Kit and assessing the RNA integrity number (RIN >7). One mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard MGI protocols

value: PBMC

tag: Sex

value: Female

tag: diagnosis


title: premets_42

value: Male


title: cDC1 CGRP biol rep 1 [cDC1_CGRP_1]

value: 1nM Calcitonin gene-related peptide


title: NSC-24CX1a [Subline]

description: Subline


title: cDC2 with nociceptors capsaicin biol rep 4

treatment_protocol: BM-DCs were cultured either alone or in the presence of nociceptors overnight and treated with imiquimod or capsaicin as indicated

value: classical dendritic cell, type 2

value: coculture with nociceptors + 1uM capsaicin


title: WT-BMDMs-control_rep2


title: premets_41


title: NSC-26C-1 [Parental line]

description: Parental line


title: NSC-20CX2a [Subline]

description: Subline


title: KO-BMDMs-LPS_rep1


title: pDC with nociceptors capsaicin biol rep 4

source_name: plasmacytoid dendritic cell

value: plasmacytoid dendritic cell


title: WT-BMDMs-control_rep1


title: premets_40


title: WT-BMDMs-LPS_rep2


title: NSC-20CX2 [Subline]

description: Subline


title: NSC-20CX1a [Subline]

description: Subline


title: cDC1 with nociceptors capsaicin biol rep 4

value: classical dendritic cell, type 1


title: pDC with nociceptors IMQ biol rep 4

value: coculture with nociceptors + 1ug/ml Imiquimod


title: WT-BMDMs-LPS_rep1


title: mets_24


title: normal_33

description: Normal

source_name: Normal

value: Normal


title: cDC2 with nociceptors IMQ biol rep 4


title: R2

city: Jinan

first: Jianxiong

last: Ji

state: Shandong

address: 107 Wenhua Xi Road

department: Department of Neurosurgery

institute: Department of Neurosurgery, Qilu Hospital of Shandong University

description: 10x Genomics

data_processing:
Sequencing depth was normalized by using CellRanger (version v3.1.0).
We used Seurat package (version 3.0)  in R (version 3.5.3) to perform data filtering (both gene and cell), normalization, PCA and t-SNE.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: Mouse whole brain

extract_protocol:
Mouse whole brains were removed, flash frozen on dry ice. Cell nucleus were extracted and sorted by 10x Genomics Chromium
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: Mouse whole brain

value: mouse brain cells

value: whole-brain irradiation (2 Gy x 5)

tag: harvest time

value: 28 days post treatment


title: N2

description: 10x Genomics


title: normal_32

description: Normal


title: T cells, sodium acetate, 2 millimolar, rep3

city: Erlangen

first: Michael

last: Frech

address: Ulmenweg 18

department: Department of Internal Medicine 3 - Rheumatology and Immunology

country: Germany

institute: University Hospital Erlangen

data_processing:
Raw reads of fastq format were firstly processed through perl scripts. In this step, clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Paired-end clean reads were aligned to the reference genome (GrCM38/mm10 ) using Hisat2 v2.0.5
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
The count output was utilized to identify differentially expressed genes using DESeq2 version v1.26.0.
Assembly: mm10
Supplementary files format and content: FPKM values per sample in tab-delimited format

source_name: spleen

extract_protocol:
RNA was extracted using a RNeasy Mini kit (qiagen, USA) according to the manufacturer's instructions.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. RNA sample was used for library preparation using NEB Next® Ultra RNA Library Prep Kit for Illumina®. Indices were included to multiplex multiple samples.

value: spleen

value: T cells

value: WT

value: 2 mM sodium-acetate treated, 4 h


title: cDC1 with nociceptors IMQ biol rep 4


title: mets_23

value: PBMC

value: Female


title: pDC with nociceptors biol rep 4

value: coculture with nociceptors


title: T cells, sodium acetate, 2 millimolar, rep2


title: T cells, sodium acetate, 2 millimolar, rep1


title: premets_39

value: Male


title: T cells, control, rep3

value: No treatment


title: NSC-24C [Parental line]

description: Parental line


title: NSC-20C [Parental line]

description: Parental line


title: NSC-20CX1 [Subline]

description: Subline


title: NSC-18C-3 [Subline]

description: Subline


title: mets_22


title: cDC2 with nociceptors biol rep 4

value: classical dendritic cell, type 2


title: NSC-18C-2 [Subline]

description: Subline


title: T cells, control, rep2


title: T cells, control, rep1


title: cDC1 with nociceptors biol rep 4

value: classical dendritic cell, type 1


title: normal_31

description: Normal


title: mets_21


title: pDC with nociceptors capsaicin biol rep 3

value: plasmacytoid dendritic cell

value: coculture with nociceptors + 1uM capsaicin


title: Microglia, WT_Control, R14

city: London

first: George

last: Sideris-Lampretsas

address: 20 Newcomen Street

department: Wolfson CARD

country: United Kingdom

institute: King's College London

data_processing:
FastQC (v0.11.9)
HiSat2(version 2.1), aligned to mm39 (GRCm39.104)
Read count extraction with featureCounts (version 1.5.2)
quality check with Picard (http://broadinstitute.github.io/picard/)
Assembly: mm39/GRCm39.104
Supplementary files format and content: tab-delimited text file includes normalised count values (DESeq2-vst) for each Sample

source_name: Dorsal Lumbar Spinal Cord

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). For library preparation, 1 ng cDNA per sample was used.
RNA libraries for RNA-seq were prepared using NEBNext® UltraTM RNA Library Prep Kit (New England Biolabs, Ipswich, USA) following the manufacturer’s recommendation

treatment_protocol: Microglia were isolated from the dorsal lumbar spinal cord using FACS according to Bennett et al 2016 (PMID: 26884166). Briefly, RNA was extracted from 2000 CD45low/CD11b+/CX3CR1+ cells per sample using RNeasy Micro Kit (QIAGEN 74004) and eluted with 14ul nuclease-free water.

value: Dorsal Lumbar Spinal Cord

value: Microglia

value: Control Serum


title: cDC2 with nociceptors capsaicin biol rep 3


title: NSC-18C-1 [Parental line]

description: Parental line


title: normal_30

description: Normal

value: Normal


title: NSC-17CF [Subline]

description: Subline


title: cDC1 with nociceptors capsaicin biol rep 3


title: normal_29

description: Normal


title: Microglia, WT_Control, R12


title: pDC with nociceptors IMQ biol rep 3

value: coculture with nociceptors + 1ug/ml Imiquimod


title: Microglia, WT_Control, R13


title: NSC-17CA [Parental line]

description: Parental line


title: NSC-16CX1F [Subline]

description: Subline


title: premets_37


title: cDC2 with nociceptors IMQ biol rep 3


title: Microglia, WT_KBxN, R11

value: K/BxN Serum


title: Microglia, WT_KBxN, R10

value: WT


title: cDC1 with nociceptors IMQ biol rep 3


title: NSC-15CF [Parental line]

description: Parental line


title: pDC with nociceptors biol rep 3


title: normal_28

description: Normal


title: normal_27

description: Normal


title: Microglia, WT_KBxN, R9


title: NSC-15CA [Subline]

description: Subline


title: Microglia, WT_KBxN, R8


title: cDC2 with nociceptors biol rep 3


title: mets_20


title: normal_26

description: Normal


title: premets_38


title: cDC1 with nociceptors biol rep 3


title: Microglia, TASTPM_Control, R7

value: TASTPM


title: premets_36

value: PBMC


title: mets_19


title: pDC capsaicin biol rep 4

value: 1uM capsaicin


title: NSC-16C [Parental line]

description: Parental line


title: Microglia, TASTPM_Control, R6


title: Microglia, TASTPM_Control, R5


title: cDC2 capsaicin biol rep 4


title: NSC-11X1 [Subline]

description: Subline


title: NSC-11C [Parental line]

description: Parental line


title: cDC1 capsaicin biol rep 4


title: Microglia, TASTPM_KBxN, R4


title: normal_25

description: Normal

value: Female


title: NSC-10X1F

description: Subline


title: NSC-11X1a [Subline]

description: Subline


title: Microglia, TASTPM_KBxN, R2


title: Microglia, TASTPM_KBxN, R3


title: NSC-10X1aX1a

description: Subline


title: normal_24

description: Normal


title: normal_23

description: Normal

value: Male


title: NSC-10X1aF

description: Subline


title: Microglia, TASTPM_KBxN, R1


title: premets_35


title: circular RNA 180640A&B_3d-3

city: Nantong

first: baolan

last: sun

address: 20 Xisi Road

institute: Affiliated Hospital of Nantong University

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 Rnor_6.0 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Rnor_6.0

source_name: whole blood

growth_protocol: Sprague-Dawley (SD) male rats, weighing 250 to 300 g and 6 to 8 weeks in age, were fed conventionally. Animal feeding environment: 12 hours of day and night alternately, constant humidity (50 ± 5)%, temperature 20 ~ 25 ℃.

extract_protocol:
Whole blood were collected in PAXgene blood RNA tube, stored in -80℃, and RNA was harvested using PAXgene method. NEBNext Ultra RNA Library Prep Kit for Illumina  (Cat#E75305) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Pair end 150bp

value: 72 h after modeling

value: blood


title: pDC untreated biol rep 4

value: untreated


title: circular RNA 180640A&B_3d-2


title: NSC-10X1A

description: Subline


title: Mouse lung, Bleomycin, Ad-ATP12A 2, Batch 2 [9BA2]

city: GRAND RAPIDS

first: Xiaopeng

last: Li

address: 400 Monroe Ave NW

department: Pediatrics & Human Development

institute: Michigan State University

data_processing:
RNA-Seq reads were mapped on mm39 transcriptome using the ENSEMBL GRCm39  annotation with the STAR aligner and further processed using RSEM.
Assembly: mm39
Supplementary files format and content: comma-separated file includes Mouse ensembl_gene_id as rows and log2 transformed TPM values for each sample as columns

source_name: Mouse Lung

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using by the Genomics Core at the Van Andel Institute using 0.6 ug of total RNA

value: Mouse Lung

value: Bleomycin, Ad-ATP12A


title: GC025

description: Primary cancer cells


title: NSC-10X1aX1

description: Subline


title: NSC-10C [parental line]

description: Parental line


title: pDC IMQ biol rep 4

value: plasmacytoid dendritic cell

value: 1ug/ml Imiquimod


title: circular RNA 180640A&B_3d-1


title: premets_34


title: cDC2 untreated biol rep 4

value: classical dendritic cell, type 2


title: circular RNA 180640C_12H-3

value: 12 h after modeling


title: cDC2 IMQ biol rep 4


title: normal_21

description: Normal

value: Normal


title: circular RNA 180640C_12H-2


title: pDC capsaicin biol rep 3


title: NSC-10X1aA

description: Subline


title: normal_20

description: Normal


title: Mouse lung, Bleomycin, Ad-GFP 1, Batch 2 [9BG1]

value: Bleomycin, Ad-GFP


title: cDC1 IMQ biol rep 4

value: classical dendritic cell, type 1

value: WT


title: Mouse lung, Bleomycin 2, Batch 2 [9B2]

value: Bleomycin


title: circular RNA 180640C_12H-1


title: cDC1 capsaicin biol rep 3

value: 1uM capsaicin


title: Mouse lung, Bleomycin 1, Batch 2 [9B1]


title: mets_18

value: PBMC

value: Female


title: Mouse lung, Bleomycin, Ad-ATP12A 1, Batch 2 [9BA1]


title: circular RNA 180640C_6H-3

value: 6 h after modeling


title: premets_33

value: Male


title: cDC1 untreated biol rep 4

value: untreated


title: cDC2 IMQ biol rep 3


title: Mouse lung, Control 1, Batch 2 [9C1]

value: Mouse Lung

value: Control


title: cDC1 IMQ biol rep 3


title: circular RNA 180640C_6H-1

value: blood


title: normal_18

description: Normal


title: Mouse lung, Control 2, Batch 2 [9C2]


title: circular RNA 180640C_6H-2


title: Mouse lung, Bleomycin, Ad-ATP12A 2, Batch 1 [11BA2]

value: Bleomycin, Ad-ATP12A


title: normal_17

description: Normal


title: circular RNA 180640A&B_T1-2

value: 1 h after modeling


title: pDC untreated biol rep 3

value: plasmacytoid dendritic cell


title: circular RNA 180640A&B_T1-3


title: Mouse lung, Bleomycin, Ad-GFP 2, Batch 1 [11BG2]


title: Mouse lung, Bleomycin, Ad-ATP12A 1, Batch 1 [11BA1]


title: cDC2 untreated biol rep 3

value: classical dendritic cell, type 2


title: premets_32


title: cDC1 untreated biol rep 3


title: pDC IMQ biol rep 3

value: 1ug/ml Imiquimod


title: circular RNA 180640A&B_T1-1


title: Mouse lung, Bleomycin, Ad-GFP 1, Batch 1 [11BG1]

value: Bleomycin, Ad-GFP


title: Mouse lung, Bleomycin 2, Batch 1 [11B2]


title: circular RNA 180640A&B_Sham-2

value: 0 h after modeling


title: normal_19

description: Normal

value: Normal


title: pDC with nociceptors capsaicin biol rep 2

value: WT

value: coculture with nociceptors + 1uM capsaicin


title: premets_31

value: PBMC

value: Female


title: cDC2 with nociceptors capsaicin biol rep 2


title: circular RNA 180640A&B_Sham-1


title: Mouse lung, Bleomycin 1, Batch 1 [11B1]

value: Bleomycin


title: cDC1 with nociceptors capsaicin biol rep 2

value: classical dendritic cell, type 1


title: premets_30


title: Mouse lung, Control 2, Batch 1 [11C2]

value: Mouse Lung


title: premets_29


title: mets_17


title: cDC2 with nociceptors IMQ biol rep 2

value: coculture with nociceptors + 1ug/ml Imiquimod


title: Mouse lung, Control 1, Batch 1 [11C1]

value: Control


title: RNA 180640A&B_3d-2

value: 72 h after modeling

value: blood


title: RNA 180640A&B_3d-3


title: pDC with nociceptors IMQ biol rep 2

value: plasmacytoid dendritic cell


title: mets_16


title: circular RNA 180640A&B_Sham-3


title: 11_RAW_shGIV_LPS_5h_set2

city: LA JOLLA

first: Sahar

last: Taheri

state: California

address: 9500 GILMAN DR.

institute: UCSD

data_processing:
RNASeq data was processed using kallisto (version 0.45.0). Gene-level TPM values and gene annotations were computed using a custom Perl Script.
Assembly: Mus_musculus genome build GRCm38.94
Supplementary files format and content: tab-delimited text file includes log2 of TPM values

source_name: RAW

extract_protocol: RNA sequencing libraries were generated using the Illumina TruSeq Stranded Total RNA Library Prep Gold with TruSeq Unique Dual Indexes (Illumina, San Diego, CA). Samples were processed following manufacturer’s instructions, except modifying RNA shear time to five minutes. Resulting libraries were multiplexed and sequenced with 100 basepair (bp) Paired End (PE100) to a depth of approximately 25-40 million reads per sample on an Illumina NovaSeq 6000. Samples were demuxltiplexed using bcl2fastq v2.20 Conversion Software (Illumina, San Diego, CA).

treatment_protocol: Samples were treated with LPS for 5 h, 100 ng/ml

tag: sample code

value: RAW

tag: type

value: shGIV

tag: protocol

tag: udf/conc (ng.ul)


title: mets_15

value: Male


title: 17_RAW_shGIV_LPS_5h_set3


title: premets_28


title: cDC1 with nociceptors IMQ biol rep 2

city: Boston


title: premets_27


title: pDC with nociceptors biol rep 2

value: coculture with nociceptors


title: 16_RAW_shGIV_LPS_0h_set3


title: 14_RAW_shC_LPS_5h_set3

value: shC


title: premets_26


title: RNA 180640C_12H-2

value: 12 h after modeling


title: RNA 180640C_12H-1


title: cDC2 with nociceptors biol rep 2

value: classical dendritic cell, type 2

value: WT


title: premets_25

value: PBMC


title: cDC1 with nociceptors biol rep 2


title: 13_RAW_shC_LPS_0h_set3


title: RNA 180640C_6H-3

value: 6 h after modeling


title: RNA 180640A&B_3d-1


title: premets_24

value: Female


title: pDC with nociceptors capsaicin biol rep 1

value: coculture with nociceptors + 1uM capsaicin


title: cDC2 with nociceptors capsaicin biol rep 1


title: mets_14


title: 8_RAW_sh_C_LPS_5h_set2


title: RNA 180640C_6H-2


title: RNA 180640C_6H-1


title: RNA 180640C_12H-3


title: normal_16

description: Normal

value: Normal


title: 7_RAW_shC_LPS_0h_set2


title: mets_13


title: RNA 180640A&B_T1-3

value: 1 h after modeling


title: pDC with nociceptors IMQ biol rep 1

value: coculture with nociceptors + 1ug/ml Imiquimod


title: cDC1 with nociceptors capsaicin biol rep 1

value: classical dendritic cell, type 1


title: RNA 180640A&B_T1-2

value: blood


title: 5_RAW_shGIV_LPS_5h_set1

value: RAW


title: normal_15

description: Normal


title: RNA 180640A&B_T1-1


title: cDC2 with nociceptors IMQ biol rep 1


title: 4_RAW_shGIV_LPS_0h_set1

value: shGIV


title: mets_12

value: Male


title: cDC1 with nociceptors IMQ biol rep 1


title: 1_RAW_shC_LPS_0h_set_1


title: mets_11


title: 10_RAW_shGIV_LPS_0h_set2


title: HCC4087 + HCC4210F + Mouse Macrophages

city: Dallas

first: Luc

last: Girard

state: TX

address: 5323 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

institute: UT Southwestern Medical Center

data_processing:
Illumina sequencer from UTSW Sequencing Core (single-end) or Novogene (paired-end)
fastq files were aligned to GRCm38 (mouse) or GRCh38 (human) reference genome using STAR v2.7.1a
bam files were processed to remove read duplicates using Picard MarkDuplicates from GATK v4.1.2. Human reads were filtered out in the co-culture samples.
FPKM values were obtained using Cufflinks v2.2.1
FPKM values were upper-quartile normalized, then log-transformed
Assembly: Genome_build: GRCm38 (mouse) or GRCh38 (human)

growth_protocol: See publication

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
Library preparation was done with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina or according to Novogene specifications (https://en.novogene.com)

treatment_protocol: See publication

value: NSCLC

tag: co-culture

value: Yes


title: pDC with nociceptors biol rep 1

value: plasmacytoid dendritic cell

value: coculture with nociceptors


title: RNA 180640A&B_Sham-2

value: 0 h after modeling


title: premets_23

value: PBMC


title: cDC2 with nociceptors biol rep 1

value: classical dendritic cell, type 2

value: WT


title: HCC366 + HCC4210F + Mouse Macrophages

tag: cell line


title: normal_14

description: Normal

value: Female


title: H2085 + HCC4210F + Mouse Macrophages


title: cDC1 with nociceptors biol rep 1


title: pDC capsaicin biol rep 2

value: 1uM capsaicin


title: H2073 + HCC4210F + Mouse Macrophages biol rep 4


title: normal_13

description: Normal

value: Normal


title: premets_22


title: cDC2 capsaicin biol rep 2


title: RNA 180640A&B_Sham-3


title: H2073 + HCC4210F + Mouse Macrophages biol rep 3


title: cDC1 capsaicin biol rep 2


title: mets_10


title: H2073 + HCC4210F + Mouse Macrophages biol rep 2


title: normal_12

description: Normal


title: pDC IMQ biol rep 2

value: 1ug/ml Imiquimod


title: RNA 180640A&B_Sham-1


title: H2073 + HCC4210F + Mouse Macrophages biol rep 1


title: premets_21


title: cho2set2KO-rep2

city: Hangzhou

first: Zhu

last: Yibing

state: Zhe Jiang

address: Xihu

department: Life Of Science

institute: Zhejiang University

data_processing:
Pass filter data of fastq format were processed by Cutadapt (V1.9.1).
Reference genome sequences and gene model annotation files of relative species were downloaded from genome website UCSC. Then Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Genome_build: sacCer3
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample in Excel file

organism: Saccharomyces cerevisiae

source_name: cell

growth_protocol: Yeast cells growed to log phase in YPL meidum from 0.1 OD.

extract_protocol:
RNA was harvested using Lucigen MasterPure Yeast RNA Purification Kit
1 μg total RNA was used for following library preparation. Next generation sequencing library preparations were constructed according to the Illumina protocol

treatment_protocol: Cells were washed with SL medium once and then transferred to SL medium for culturing 1h.

tag: background

value: cho2set2 delta

value: switch to minimal medium for 1h


title: cDC2 IMQ biol rep 2


title: H1993 + HCC4210F + Mouse Macrophages biol rep 2


title: opi1set2KO-rep2

value: opi1set2 delta


title: cho2set2KO-rep1


title: cDC1 IMQ biol rep 2

value: classical dendritic cell, type 1


title: mets_9

value: Male


title: cho2KO-rep2

value: cho2 delta


title: opi1set2KO-rep1


title: mets_8


title: pDC untreated biol rep 2

value: untreated


title: H1666 + HCC4210F + Mouse Macrophages biol rep 2

value: NSCLC

value: Yes


title: opi1KO-rep2

value: opi1 delta


title: cho2KO-rep1


title: premets_20

value: PBMC


title: opi1KO-rep1


title: cDC2 untreated biol rep 2

value: classical dendritic cell, type 2


title: H522 + HCC4210F + Mouse Macrophages


title: premets_19


title: cDC1 untreated biol rep 2

value: WT


title: normal_11

description: Normal

value: Female


title: H441 + HCC4210F + Mouse Macrophages biol rep 3


title: WT-rep2


title: pDC capsaicin biol rep 1

value: plasmacytoid dendritic cell

value: 1uM capsaicin


title: normal_10

description: Normal

value: Normal


title: cDC2 capsaicin biol rep 1


title: H1734 + HCC4210F + Mouse Macrophages


title: H441 + HCC4210F + Mouse Macrophages biol rep 2


title: normal_9

description: Normal


title: cDC1 capsaicin biol rep 1


title: premets_18


title: MIG-EV, rep 3

city: Melbourne

first: Kevin

middle: Robert

last: Gillinder

state: Victoria

address: 99 Commercial Road

department: Australian Centre for Blood Diseases

country: Australia

institute: Monash University

description: HPC7 cells transduced with an empty retroviral vector as a transduction control

library_source: genomic

data_processing:
Reads were filtered with FASTP (Chen et. al., 2018) using the parameters - fastp -l 35 -W 3 -5 -3
Singleton reads were discarded (fastq-pair)
Paired-end reads were aligned using Bowtie2 (Langmead and Salzberg, 2012) to the reference genome (mm10)
Aligned reads were filtered for optical and PCR duplicates (Picard Tools)
Reads aligning to ENCODE blacklisted regions (Amemiya et. al., 2019), mitochondrial genome, improper pairs, and mapping quality <20 were discarded
Analysis of differential enrichment at promoter regions (-1kb to 100bp around the TSS) was performed using DiffBind (Stark et al 2011)
Genome_build: Illumina iGenomes UCSC reference genome (mm10) & gene annotation
Supplementary_files_format_and_content: CSV file was generated from DiffBind (Bioconductor R) and contains results of differential enrichment analysis at gene promoters

source_name: Hematopoietic progenitor cells

growth_protocol: HPC7 cells were maintained in IMDM supplemented with 10% fetal bovine serum (Sigma), penicillin (100 U/ml), streptomycin (100 µg/ml), 2 mM L-glutamine (Gibco), 0.05 mM 2-mercaptoethanol and 100 µg/ml mSCF (Peprotech).

extract_protocol:
100,000 cells were collected and washed with PBS and pelleted by centrifugation (300 g). Cells were then washed with lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20) following a 3 min incubation on ice.
The tagmentation reaction was performed in a thermocycler for 30 mins at 37°C with 1x TD buffer, 0.3x PBS, 0.1% Tween 20, 2.5 µl Tn5 (Illumina) in a 50 µl volume as previously described (Corces et al. 2017).

tag: parental cell line

value: MIG-EV, rep 3-HPC7


title: WT-rep1

value: switch to minimal medium for 1h


title: H441 + HCC4210F + Mouse Macrophages biol rep 1

tag: cell type


title: H647 + HCC4210F + Mouse Macrophages


title: MIG-EV, rep 2

value: MIG-EV, rep 2-HPC7


title: H23 + HCC4210F + Mouse Macrophages


title: cDC2 IMQ biol rep 1

tag: genotype

value: 1ug/ml Imiquimod


title: set2KO-rep2

value: set2 delta


title: premets_17

value: Male


title: A427 + HCC4210F + Mouse Macrophages biol rep 2


title: MIG-EV, rep 1

value: MIG-EV, rep 1-HPC7


title: cDC2 capsaicin biol rep 3


title: pDC IMQ biol rep 1


title: premets_16


title: Mouse Macrophages biol rep 2

source_name: Mouse Macrophage

value: Mouse Macrophage

value: No


title: set2KO-rep1


title: MIG-mut5Snai1, rep3

description: HPC7 cells transduced with a retroviral vector for ectopic expression of mutant Snai1

value: MIG-mut5Snai1, rep3-HPC7


title: premets_15

value: PBMC


title: pDC untreated biol rep 1

value: untreated


title: MIG-mut5Snai1, rep2

value: MIG-mut5Snai1, rep2-HPC7


title: Mouse Macrophages biol rep 1


title: premets_14


title: cDC2 untreated biol rep 1

value: classical dendritic cell, type 2

value: WT


title: MIG-mut5Snai1, rep1

value: MIG-mut5Snai1, rep1-HPC7


title: Day10, ATDC5, rep2

city: Saskatoon

first: Christopher

middle: H.

last: Eskiw

state: SK

address: 51 Campus Drive

department: Food and Bioproduct Science

institute: University of Saskatchewan

data_processing:
TrimGalore! for trimming
reads mapped with HISTA2
Peak Calling using MAC2
Normalization using RPM
Assembly: mm10
Supplementary files format and content: text formatted to NARROWPEAK

growth_protocol: ATDC5 cells were initial grown in DME/F12 media containing 5% FBS until 70% confluent. For undifferentiated cells, cultures where maintained by serial passaging.

extract_protocol:
Unfixed cells at day 0, 3 and 10 of differentiation were scrapped into cold DME/F12 media and collected in 1.5mL centrifuge tubes. Cells were pelleted (300 X g, 4 oC, 5min), the supernatant removed, and snap frozen in liquid nitrogen. Tn5 reactions were performed on 2 independent biological replicates for each time point and sequencing was performed the Princess Margret Genomics Center (Toronto, Canada).
Sequencing was performed using the Illumina Novoseq protocol and generated 75bp single end reads.

treatment_protocol: To differentiate the cells for day 0, 3 and 10 time points, 10ul droplets of cells at a density of 3000 cell/ul were spotted into 10cm culture dishes and allowed to attach for 24h. Cells differentiated by the addition of DEM/F12 media containing 10mM bGP and 50mg/ml L-acorbate-2-phosphate. Media was change every 2-3 days to maintain nutrient levels.

value: pre-chondrocyte

tag: treatment protocol

value: differentiation


title: normal_22

description: Normal

value: Female

value: Normal


title: premets_13


title: Day10, ATDC5, rep1

tag: time


title: cDC1 untreated biol rep 1

data_processing:
Reads were aligned to the mouse genome (GENCODE GRCm38/mm10 primary assembly and gene annotations vM16; https://www.gencodegenes.org/mouse_releases/16.html) with STAR 2.5.4a (https://github.com/alexdobin/STAR/releases).
The ribosomal RNA gene annotations were removed from GTF (General Transfer Format) file.
The gene-level quantification was calculated by featureCounts (http://subread.sourceforge.net/).
Assembly: mm10
Supplementary files format and content: csv text file includes raw count table containing all samples

value: classical dendritic cell, type 1

tag: treatment


title: Mouse lung, Bleomycin, Ad-GFP 2, Batch 2 [9BG2]

tag: tissue

value: Mouse Lung

value: Bleomycin, Ad-GFP


title: Day0, ATDC5, rep2

value: control


title: Drp1-KO C2C12 cells after differentiaiton

city: Toyonaka

first: Naotada

last: Ishihara

state: Osaka

address: 1-1, Machikaneyamacho

institute: Osaka University

data_processing:
Basecalls were performed using ZebraCall v2_1.0.8.208
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt v 1.9.1 (parameter-default)/sickle v 1.33 (parameter- qual-threshold:20 length-threshold:40)
Trimmed sequence reads were mapped to GRCm39 using hisat2 v 2.2.1 (parameter-default)
Read count extraction was performed using featureCounts v 2.0.0 (parameters-assigns-reads-to-all-their-overlapping-meta-features:True strand-specific-read-counting:2)
Read count normalization was performed with Reads Per Kilobase Million (RPKM) and Transcripts Per Million (TPM) method using custum R scripts
Assembly: mm39
Supplementary files format and content: tab-delimited text files include RPKM and TPM values for each Sample

extract_protocol:
RNA was harvested using TRIzol Reagents (ThermoFisher Scientific) following manufacturer's protocol.
RNA libraries for RNA-seq were prepared using DNBSEQ-G400RS High-throughput Sequencing Kit (MGI Tech Co., Ltd.) following manufacturer's protocols.

value: immortalized myoblasts

value: Drp1 knockout

value: myogenic differentiation


title: Day3, ATDC5, rep1


title: premets_12

value: PBMC

tag: Sex


title: ST/IL17rb null Rep 4

city: Clayton

first: Nicholas

middle: C

last: Wong

address: Wellington Road

department: Monash Bioinformatics Platform, Central Clinical School

description:
ST2IL17rbko_UPJEJ_IEC-4_S14
Kapa Library Prep
NonStrandedCounts-withNames-proteinCoding.txt

data_processing:
Data was processing using in-house pipeline called RNASik v 1.4.7, https://monashbioinformaticsplatform.github.io/RNAsik-pipe/ to generate a counts matrix from fastq files.
Counts matrix was then loaded into Degust for differential gene expression analysis (DOI: 10.5281/zenodo.3258932).
Assembly: GRCm10
Supplementary files format and content: Gene counts matrix containing read counts across samples and with genes

source_name: proximal jejunum

extract_protocol:
QIAGEN RNA-easy universal kit
TruSeq stranded mRNA kit or Kapa RNA HyperPrep with RiboErase” kit

value: proximal jejunum

value: Lamina Propria


title: ST/IL17rb null Rep 3

description:
ST2IL17rbko_UPJEJ_IEC-3_S13
Kapa Library Prep
NonStrandedCounts-withNames-proteinCoding.txt


title: mets_7

value: Male

tag: diagnosis


title: cDC1 IMQ biol rep 1

first: Ulrich

last: von Andrian

address: 77 Ave Louis Pasteur

institute: Harvard Medical School

extract_protocol:
A thousand cells of each population were sorted directly into 5ul of lysis buffer (TCL Buffer (Qiagen) with 1% b‑mercaptoethanol)
Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′‑AAGCAGTGGTATCAACGCAGAGTACT30VN‑3′) and converted to cDNA via reverse transcription.

value: WT

value: 1ug/ml Imiquimod


title: Day0, ATDC5, rep1

value: pre-chondrocyte


title: normal_8

description: Normal


title: normal_7

description: Normal


title: ST/IL17rb null Rep 1

description:
ST2IL17rbko_UPJEJ_IEC-1_S11
Kapa Library Prep
NonStrandedCounts-withNames-proteinCoding.txt


title: Day3, ATDC5, rep2

value: differentiation


title: 42: soleus, knockout

city: Saint Louis

first: Rita

last: Brookheart

address: 660 S. Euclid Ave

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCm38.76
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: skeletal muscle

extract_protocol:
Muscle were harvested and immediately snap frozen in liquid nitrogen. Total RNA was isolated using RNA STAT-60 as per manufacterer's instructions. RNA  was DNase I treated as per manufacturer’s instructions (RNase-Free DNase Set, Qiagen) then cleaned up and eluted with RNAse and DNAse free molecular grade water (RNeasy MinElute Cleanup Kit, Qiagen), followed by quantification.
KAPA RiboErase

tag: strain

value: Site-1 Protease knockout

value: soleus

tag: age

value: 12 weeks


title: GATA1 Rep 5

description:
dbl_GATA1_UPJEJ_IEC-5_S10
Kapa Library Prep
NonStrandedCounts-withNames-proteinCoding.txt


title: TuYV-72h aphids_rep3

city: Strasbourg

first: Veronique

last: Ziegler-Graff

address: rue du general Zimmer

department: INSB

country: France

institute: CNRS

data_processing:
no trimming
mapping using HiSAT2 version 2.0.5
quantification using HTseq-count version 0.6.1
Assembly: TAIR 10
Supplementary files format and content: counts

source_name: rosette leaves

growth_protocol: leaves from treated plants (virus and/or aphids)

extract_protocol:
Trizol extraction
Library preparation using illumina TruSeq stranded mRNA kit

treatment_protocol: Total RNA from infected leaves

value: rosette leaves

tag: ecotype

value: TuYV-72h aphids


title: ST/IL17rb null Rep 2

description:
ST2IL17rbko_UPJEJ_IEC-2_S12
Kapa Library Prep
NonStrandedCounts-withNames-proteinCoding.txt


title: Drp1-KO C2C12 cells transiently expressing FLAG-Drp1after differentiaiton

value: Drp1 knockout expressing FLAG-Drp1


title: MIG-Snai1, rep1

description: HPC7 cells transduced with a retroviral vector for ectopic expression of wildtype Snai1

value: MIG-Snai1, rep1-HPC7


title: premets_11

value: Female


title: TuYV-72h aphids_rep1


title: GATA1 Rep 3

description:
dbl_GATA1_UPJEJ_IEC-3_S8
Kapa Library Prep
NonStrandedCounts-withNames-proteinCoding.txt


title: 40: soleus, knockout


title: GATA1 Rep 4

description:
dbl_GATA1_UPJEJ_IEC-4_S9
Kapa Library Prep
NonStrandedCounts-withNames-proteinCoding.txt


title: normal_6

description: Normal

value: Normal


title: TuYV-72h aphids_rep2


title: premets_10

value: PBMC


title: 41: soleus, control

value: Site-1 Protease floxed


title: WT C2C12 cells after differentiaiton

value: immortalized myoblasts

value: myogenic differentiation


title: premets_9

value: Male


title: TuYV-6h aphids_rep2

value: TuYV-6h aphids


title: 39: soleus, knockout


title: GATA1 Rep 1

description:
dbl_GATA1_UPJEJ_IEC-1_S6
Kapa Library Prep
NonStrandedCounts-withNames-proteinCoding.txt

value: proximal jejunum

value: Lamina Propria


title: GATA1 Rep 2

description:
dbl_GATA1_UPJEJ_IEC-2_S7
Kapa Library Prep
NonStrandedCounts-withNames-proteinCoding.txt


title: Balbc non-IEC Rep 5

description:
Balbc_UPJEJ_IEC-5_S5
Kapa Library Prep
NonStrandedCounts-withNames-proteinCoding.txt

value: BALB/cJ


title: 38: soleus, control

value: soleus


title: TuYV-6h aphids_rep1


title: premets_8


title: TuYV-0h aphids_rep3

value: TuYV-0h aphids


title: mets_6


title: 37: soleus, control

value: 12 weeks


title: normal_5

description: Normal


title: Balbc non-IEC Rep 3

description:
Balbc_UPJEJ_IEC-3_S3
Kapa Library Prep
NonStrandedCounts-withNames-proteinCoding.txt


title: TuYV-0h aphids_rep2

value: rosette leaves


title: Balbc non-IEC Rep 4

description:
Balbc_UPJEJ_IEC-4_S4
Kapa Library Prep
NonStrandedCounts-withNames-proteinCoding.txt


title: 36: soleus, control


title: 34: soleus, control


title: premets_7


title: 35: soleus, knockout

value: Site-1 Protease knockout


title: Mock-72h aphids_rep3

value: Mock-72h aphids


title: TuYV-6h aphids_rep3


title: normal_4

description: Normal


title: TuYV-0h aphids_rep1


title: Balbc non-IEC Rep 2

description:
Balbc_UPJEJ_IEC-2_S2
Kapa Library Prep
NonStrandedCounts-withNames-proteinCoding.txt


title: mets_5


title: Mock-72h aphids_rep2


title: 9: gastrocnemius, knockout

value: gastrocnemius


title: normal_3

description: Normal

value: Normal


title: 8: gastrocnemius, control


title: Mock-72h aphids_rep1


title: GATA1 IEC Rep4

description:
dbl_GATA1_UPJEJ_IEC_fraction_4_S9
Tru Seq Library Prep
ReverseStrandedCounts-withNames.txt

value: Epithelial Fraction


title: mets_4

value: PBMC

value: Female


title: 6: gastrocnemius, knockout


title: mets_3


title: premets_6


title: GATA1 IEC Rep3

description:
dbl_GATA1_UPJEJ_IEC_fraction_3_S8
Tru Seq Library Prep
ReverseStrandedCounts-withNames.txt


title: 7: gastrocnemius, knockout


title: premets_5


title: GATA1 IEC Rep2

description:
dbl_GATA1_UPJEJ_IEC_fraction_2_S7
Tru Seq Library Prep
ReverseStrandedCounts-withNames.txt


title: Mock-6h aphids_rep3

value: Mock-6h aphids


title: Balbc non-IEC Rep 1

description:
Balbc_UPJEJ_IEC-1_S1
Kapa Library Prep
NonStrandedCounts-withNames-proteinCoding.txt


title: 5: gastrocnemius, control

value: Site-1 Protease floxed


title: Mock-6h aphids_rep2


title: premets_4


title: Mock-0h aphids_rep3

value: Mock-0h aphids


title: 3: gastrocnemius, control


title: Mock-6h aphids_rep1


title: normal_2

description: Normal


title: Balbc IEC Rep 5

description:
Balbc_UPJEJ_IEC_fraction_5_S5
Tru Seq Library Prep
ReverseStrandedCounts-withNames.txt

value: proximal jejunum


title: Balbc IEC Rep 4

description:
Balbc_UPJEJ_IEC_fraction_4_S4
Tru Seq Library Prep
ReverseStrandedCounts-withNames.txt


title: 2: gastrocnemius, knockout


title: premets_3


title: Mock-0h aphids_rep1


title: GATA1 IEC Rep5

description:
dbl_GATA1_UPJEJ_IEC_fraction_5_S10
Kapa Library Prep
NonStrandedCounts-withNames-proteinCoding.txt


title: Balbc IEC Rep 3

description:
Balbc_UPJEJ_IEC_fraction_3_S3
Tru Seq Library Prep
ReverseStrandedCounts-withNames.txt


title: Mock-0h aphids_rep2


title: 1: gastrocnemius, control


title: normal_1

description: Normal


title: GATA1 IEC Rep1

description:
dbl_GATA1_UPJEJ_IEC_fraction_1_S6
Tru Seq Library Prep
ReverseStrandedCounts-withNames.txt


title: FM014_MINOR_7

city: stony brook

first: Fu

last: Luo

state: New York

address: 100 Nicholls Road

institute: Stony Brook University

description: Bulk RNA-seq from minor NPK clones

data_processing:
For single cell RNA-seq samples, FASTQ files were processed using the entire Cell Ranger (v3.0.2) single-cell analysis pipeline (10x Genomics). This pipeline includes both a ‘count’ and ‘aggregate’ step. Briefly, data were aligned with the 10x Genomics pre-built mouse genome for filtering, barcode counting, and UMI counting using default parameters.
For bulk RNA-seq samples, RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.17) for conversion of BCL to fastq format, coupled with adaptor trimming. Reads were mapped to the mouse genome (UCSC/mm10) using STAR (2.5.2b) and FeatureCounts (v1.5.0-p3).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample or every cell

source_name: Prostate luminal cancer cells

extract_protocol:
Library preparation was done using a Clontech’s SMART-seq v4 Ultra Low Input RNA Kit to create amplified cDNA, followed by library preparation using Illumina’s Nextera XT kit.
Briefly, mouse prostate tissue from AP lobes was dissected in cold phosphate buffered saline (PBS) and minced with scissors, followed by incubation in DMEM/F12 (Gibco) supplemented with 5% FBS and 0.1% collagenase/hyaluronidase (STEMCELL Technologies) at 37°C for 2 hours. Dissociated tissues were spun at 350 g for 5 min and resuspended in TrypLE (Gibco), followed by incubation at 37°C for 20 minutes. After centrifugation at 350 g, pelleted cells were resuspended with pre-warmed 5 mg/ml dispase (STEMCELL Technologies) and, if necessary, incubated for an additional 20 minutes at 37°C. The cell suspension was then supplemented with 1:10 dilution of 1 mg/ml DNase I (STEMCELL Technologies) and triturated vigorously for 2 min. Enzymes were deactivated and diluted by addition of HBSS/2% FBS. Finally, the resulting cell suspension was passed through a 40 μm cell strainer (Falcon) to remove any large clumps of cells remaining. Filtered single cells were resuspended in Opti-MEM (Gibco) and flow sorted based on RFP, CFP or YFP expression on a BD FACS Aria II instrument. The Confetti+ FACS sorted cells were processed for single cell RNAseq on a 10x Genomics platform. Similarly collected cells were also flash-frozen in liquid nitrogen and stored at −80 °C for subsequent RNA processing.
Protocols applicable to each sample are included in the SAMPLES section

value: prostate

value: Nkx3.1CreERT2/+; Ptenflox/flox; K-RasLSLG12D/+; R26r-Confetti

value: 3 month


title: Balbc IEC Rep 2

description:
Balbc_UPJEJ_IEC_fraction_2_S2
Tru Seq Library Prep
ReverseStrandedCounts-withNames.txt

value: BALB/cJ


title: 4: gastrocnemius, control

value: 12 weeks


title: FM012_DOMINANT_5

description: Bulk RNA-seq from dominant NPK clones


title: RNA_seq_WT_pregnant-dpc8_biliary epitheial cells_ex3

city: Bunkyo-ku

first: Fumiko

last: Toyoshima

state: Tokyo

address: 1-5-45 Yushima

department: Medical Research Laboratory

institute: Institute of Science Tokyo

data_processing:
The sequenced reads were mapped to the mm10 mouse reference genome using STATR  (version STAR-2.7.9a) with the GENCODE  vM23 annotation gtf file after trimming the adaptor sequences and low-quality bases using cutadapt-3.4.
The uniquely mapped reads were counted at the gene level (protein coding) using HTSeq-count v0.13.5 and the GENCODE vM25 annotation file. The expression levels were caluculated as FPKM usign DEseq2 (v. 1.30.1) and GenomicFeatures packages.
Genome_build: mm10
Supplementary_files_format_and_content: A tsv file includes FPKM values for each sample.

source_name: BECs in liver from pregnant-dpc8 mice

extract_protocol:
Mice were laparotomized under isoflurane inhalation anesthesia, and the portal vein was cannulated and perfused with liver perfusion medium. Then, the liver was perfused with liver digestion medium. To isolate BECs, remaining undigested liver pieces were further treated with collagenase, DNase I, and Dispase. The cell suspension was filtered with 70 micrometer cell strainer, then the filtrates were centrifugation at 50g to remove the parenchymal fraction. The non-parenchymal fraction in the supernatant was stained with anti-FcR antibody (rat, 1:100, Bio Legend, 101302), followed by staining with the fluorescence-conjugated antibodies for 1 h. After wash with PBS plus 1 % BSA, the cells were sorted by FACS. RNA was extracted from the FACS-sorted BECs by using an RNeasy Micro Kit (Qiagen).
50 ng Total RNA was used to generate RNA-seq libraries using KAPA RNA HyperPrep Kit with RiboErase (Roche).

value: WT

value: female

value: liver

tag: condition

value: pregnant at dpc8

value: biliary epithelial cells


title: H-88-78-1

city: Gandarbal

first: Basharat

middle: Ahmad

last: Bhat

state: Kashmir

address: Shuhama

department: Animal Biotechnology

country: India

institute: Sher-e-Kashmir University of Agricultural Sciences and Technology

description:
KM_TMRL_02
Solanum habrochaites

data_processing:
Illumina platform used for base calling
TASSEL5 GBSv2 pipeline was used for identification of tags at cut sites and SNPs located across reference genome.
The fastq files were aligned against the tomato reference genome using the Bowtie2 tool version 2.2.9. The .sam file created from the Bowtie2 aligner program was used through SAMToGBSdbPlugin()
DiscoverySNPCallerPluginV2 took a GBSv2 database file as input and identified SNPs from the aligned tags.
Assembly: mm9
Supplementary files format and content: The VCF file generated from tassel pipeline was generated.
Supplementary files format and content: After filtration SNPs were retained provided in hapmap (hmp) format.

organism: Solanum habrochaites

source_name: Leaf

extract_protocol:
gDNA was isolated from leaf samples by using Xcelgen Plant gDNA Isolation Kit (XG2611-01) as per the protocol described. The DNA was eluted in 50µl Nuclease-Free Water. The samples were quantified using Qubit Fluorometer. For determining A260/280 ratio, 1µl of sample was loaded in Nanodrop8000 spectrophotometer. The quality of samples was checked in 0.8% Agarose gel electrophoresis along with Hind III marker for the presence of intact bands.
To 100ng of gDNA, barcoded adapters (~0.1pM) were added and digested with Apek1 enzyme for 12h at 75oC. The barcoded and common adapters were ligated to the sticky ends of the digested DNA with T4 DNA Ligase enzyme at 22oC for 180 mins, followed by heat inactivation. The ligated products were pooled into 12 groups of 12 samples each group. The pool was PCR amplified to generate the final library pool.
High Sensitivity (HS) DNA chip and library pool was sequenced on Illumina platform to generate ~ 3 million reads/sample.

tag: domestication

value: Cultivated

value: Leaf


title: premets_2

city: DaeJeon

first: Hee Jeong

last: Jin

address: 672 Yuseong-daero

institute: Korea Institute of Oriental Medicine

data_processing:
read trimming: skewer
mapping: STAR
quantification: Cuffquant
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was isolated from   PBMC cell using TRIzol® RNA Isolation Reagents (Life technologies, Carlsbad, CA) based method. The quantity and quality of the RNA were evaluated using Agilent Nono Kit and assessing the RNA integrity number (RIN >7). One mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard MGI protocols

value: PBMC

value: Female


title: premets_1

value: Male


title: mets_1


title: RNA_seq_WT_pregnant-dpc8_biliary epitheial cells_ex2


title: FM011_MINOR_6

description: Bulk RNA-seq from minor NPK clones


title: P2P5_109

city: Jena

first: Axel

last: Mithöfer

state: Thuringia

address: Hans-Knöll-Straße 8

department: Plant Defense Physiology

institute: Max-Planck-Institute for Chemical Ecology

data_processing:
Raw reads were trimmed by in-house scripts.
Assembly: The clean reads were mapped onto Ipomoea trifida reference genome (http://sweetpotato.uga.edu/), using HISAT2 V2.0.5 with default parameter. HTSeq V0.6.1 software was used with the union mode to count read numbers mapped of genes for each sample.
Supplementary files format and content: Data matrix with read counts for further analysis with DESeq2 V1.22.2

organism: Ipomoea batatas

source_name: I. batatas 3rd leaves, 1 h IbPep1 treatment

growth_protocol: Sweet potato scions (Ipomoea batatas Lam.; cultivar Tainong 57) were grown in phytochambers under long day conditions (16 h light : 8 h dark) at 28 °C (day) and 25°C (night) in 70% relative humidity for 3 weeks

extract_protocol:
RNA was extracted according to 1 using TRIzol Reagent (Invitrogen, USA). 1 Meents, A. K. et al. Volatile DMNT systemically induces jasmonate-independent direct anti-herbivore defense in leaves of sweet potato (Ipomoea batatas) plants. Scientific Reports 9, doi:10.1038/s41598-019-53946-0 (2019).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendationsies for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Sweet potatoe leaves were treated for 1 h with IbHypSysIV, IbPep1 or water (control)

value: 3rd leave


title: P2P4_108

value: Ipomoea batatas Lam.; cultivar Tainong 57


title: P2P2_106


title: P2P1_105


title: RNA_seq_WT_pregnant-dpc8_biliary epitheial cells_ex1


title: FM008_MINOR_5

description: Bulk RNA-seq from minor NPK clones

value: prostate


title: 2805

organism: Solanum peruvianum

value: Wild


title: Balbc IEC Rep 1

description:
Balbc_UPJEJ_IEC_fraction_1_S1
Tru Seq Library Prep
ReverseStrandedCounts-withNames.txt

value: proximal jejunum

value: Epithelial Fraction


title: RNA_seq_WT_non-pregnant_biliary epitheial cells_ex3

source_name: BECs in liver from non-pregnant mice

value: non-pregnant


title: HS4P8_86

source_name: I. batatas 3rd leaves, 1 h IbHypSysIV treatment

value: IbHypSysIV


title: FM007_MINOR_4

description: Bulk RNA-seq from minor NPK clones

value: Nkx3.1CreERT2/+; Ptenflox/flox; K-RasLSLG12D/+; R26r-Confetti

value: 3 month


title: WIR-3957


title: HS4P7_85


title: mets_2


title: HS4P4_82


title: RNA_seq_WT_non-pregnant_biliary epitheial cells_ex1

value: WT

value: female

value: liver


title: FM005_MINOR_3

description: Bulk RNA-seq from minor NPK clones


title: FM009_DOMINANT_4

description: Bulk RNA-seq from dominant NPK clones


title: Initial plasmid library

city: Ottawa

first: Pirunthan

last: Perampalam

state: ON

address: 336 Drumlsih Lane

description: This is the initial sgRNA libray preparation (L0). The plasmid DNA from the pooled sgRNA preperation was extracted as described in the extraction protocol then submitted for high throughput sequencing.

data_processing:
Raw read files (FASTQ) were anlayzed using TRACS 1.1.3
TRACS 1.1.3 automatically does the following: FASTQ files are trimmed with Cutadapt 1.15; the reference sgRNA CSV file is converted to FASTA format; A Bowtie2 index is constructed using Bowtie 2.3.4.1; the initial plasmid library (L0) is aligned to the index and a BAM file is generated using Bowtie 2.3.4.1 and Samtools 1.7; Read counts are generated using MAGeCK 0.5.6; TRACS then runs the TRACS algorithm to determine gene essentiality.
Genome_build: Human GeCKO v2 library A+B reference sgRNA sequences
Supplementary_files_format_and_content: CSV file containing Enrichment Scores (ES) and Enrichment Ratios (ER) for each gene

organism: unidentified plasmid

source_name: not available

extract_protocol:
At each time point indicated (either L0, T0, or Tf), cells were harvested and genomic DNA was extracted using QIAmp Blood Maxi Kits (QIAGEN #51194). Genomic encoded sgRNA sequences were PCR amplified with two rounds of PCR to increase abundance of the initial sgRNA population and insert sample barcodes necessary for identification of condition and replicate number. PCR products were gel purified, quantitated by Qubit (Invitrogen) and pooled prior to high throughput sequencing.
Pooled preparation containing all barcoded samples were sequenced using an Illumina NextSeq 550 75-cycle high output kit (#20024906). FASTQ files were obtained containing raw reads for all samples and were demultiplexed to obtain individual FASTQ files for each sample: one initial pooled sgRNA library file (L0), 3x Cas9-positive initial condition replicates (T0), 3x Cas9-positive final condition replicates (Tf), 3x Cas9-negative initial condition replicates (T0), 3x Cas9-negative final condition replicates (Tf).

tag: go-crispr time point


title: HS4P1_79


title: D-lactic acid-producing Pichia pastoris without ScFLO1 overexpression, replicate 2

city: Khlong Luang

first: Wuttichai

last: Mhuantong

state: Pathum Thani

address: National Center for Genetic Engineering and Biotechnology (BIOTEC)

country: Thailand

institute: BIOTEC

data_processing:
The raw reads were processed using FASTP software. Clean reads were obtained from removing low quality reads from raw data using default parameters (the quality score cutoff of 20).
Assembly: Komagataella phaffii GS115 (GCF_000027005.1_ASM2700v1_genomic.fna)
Supplementary files format and content: normalizedReadCount.csv

organism: Komagataella pastoris

source_name: cell pellets

extract_protocol:
The pellets were washed with 5 mL of distilled water. Total RNA was extracted using the QIAgen RNeasy Kit following the manufacturer's protocol. Contaminating genomic DNA was removed from the RNA samples by DNaseI (NEB) digestion using the manufacturer's protocol.
The RNA quantity was analyzed using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies), and samples were stored at -80 °C until transcriptomics analysis. RNA Integrity Numbers (RIN) for the purified RNA samples were obtained using an Agilent 2100 Bioanalyzer (Agilent Technologies). All purified RNA samples had a RIN number higher than 8.0 and were sequenced by NovogeneAIT (Tianjin, China).
Paired-end 150bp

value: cell pellets


title: slick rep7

city: GAINESVILLE

first: FAHONG

last: YU

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: UNIVERSITY OF FLORIDA

data_processing:
Illumina basespace  used for basecalling.
Reads acquired from the Illumina NovaSeq 6000 platform were cleaned up with the cutadapt program to trim off sequencing adaptors and low-quality bases with a quality phred-like score <20. Reads <40 bases were excluded from RNA-seq analysis.
The genome of Bos taurus from JGI  was used as the reference sequences for RNA-seq analysis. The cleaned reads of each sample were mapped individually to the reference sequences using the read mapper of the STAR package were done to visualize differential gene expression for each treatment with in-house R scripts. In addition, we also conducted a multi-factor analysis (e.g., control, treatment, and age) for differences between the samples while estimating the effect of the treatment on an individual animal.
Pathway enrichment analysis were done with GSEA , which is an essential computational method for determining the statistical and concordant differences of the defined set of genes between two phenotypes. The log2 fold-change between the genotypes were ranked and run through the GSEA using the clusterProfiler (v3.16.1) package in R (v.4.1.3) against the information of Bos taurus in the MSigDB , the ‘org.Bt.eg.db’ in Bioconductor, and the ‘Bos_taurus.gmt’ in WikiPathways. The GO and KEGG enrichment analysis of differentially expressed genes (DEGs) (p-value <0.05, log2 fold change > |1.5|) between phenotypes were also conducted based on the MSigDB search.
Assembly: Bos_taurus.ARS-UCD1.2.dna.toplevel.fa
Supplementary files format and content: tab-delimited text files include the gene names and the mapped read counts for each Sample

organism: Bos taurus

source_name: skin

extract_protocol:
RNA extraction was performed with the Qiagen RNeasy Mini kit (Germantown MD, USA) according to the user’s guide. Quantity of RNA was determined using the QUBIT fluorescent method (Invitrogen, Carlsbad, CA, USA) and Agilent Bioanalyzer (Santa Clara, CA, USA).
An amount of 100 ng of high quality of total RNA with RIN of 7 or higher was used for library construction using the reagents provided in the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA) and the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs) according to the manufacturer's instructions. Briefly, 100 ng total RNA was used for mRNA isolation using the NEBNext Poly(A) mRNA Magnetic Isolation Module. Then the poly A enriched RNA was fragmented in NEBNext First Strand Synthesis Buffer via incubation at 94 °C for the desired time. Synthesis of ds cDNA was done using the 2nd strand master mix provided in the kit, followed by end-repair and dA-tailing.  At this point, Illumina adaptors were ligated to the sample. Finally, library was amplified and then purified with AMPure beads (Beckman Coulter, Brea, CA, USA).  Library size and mass were assessed by analysis in the Agilent TapeStation using a DNA5000 Screen Tape.  Quantitative PCR was used to validate the library's functionality using the KAPA library quantification kit (Kapa Biosystems, Wilmington, MA, USA) and monitoring on the BioRad CFX 96 real-time PCR system (Richmond, CA, USA). Twelve barcoded libraries were pooled equimolarly for sequencing simultaneously for 0.23 lanes using the Illumina NovaSeq6000. Normalized libraries were submitted to the Illumina  Free Adapter Blocking Reagent protocol to minimize presence of adaptor-dimers and index hopping rates.  The library pool was diluted to 0.8 nM and sequenced on one S4 flow cell lane (2x150 cycles) of the Illumina NovaSeq6000. The instrument’s computer utilized the NovaSeq Control Software v1.6. Cluster and SBS consumables were v1.5. The final loading concentration of the library was 120 pM with 1% PhiX spike-in control. One lane generated 2.5-3 billion paired-end reads (~950Gb) with an average Q30%>= 92.5% and Cluster PF= 85.4%.

treatment_protocol: Heifers were genotyped for the SLICK1 mutation in PRLR using either the CLARIFIDEÒ Plus platform from Zoetis (Parsippany, NJ, USA) or ta KASP-PCR procedure. All heifers were sired by one of two SL+/- Holstein bulls [Slick-Gator Blanco 551HO03574) or Slick-Gator Lone Ranger (047HO01029)] .Skin biopsy from the shoulder area was performed while the animal was restrained in a head chute. The skin sample was collected by rotating a 5 mm skin punch (Integra™ Miltex™ Standard Biopsy Punch, Fisher Scientific, Pittsburgh, PA, USA) while pressing downwards with mild force, and then the skin sample was taken from the skin punch using a tweezer and placed into a cassette between sponges. A sterile gauze was placed on the biopsy site to remove excess blood or stop bleeding, and subsequently the wound site was closed with super glue. A tick spray consisting of 0.5% (w/v) permethrin (Neogen, Lansing, MI, USA) was applied around the biopsy site.

value: skin

tag: geographic location

value: USA:Basinger, FL

value: 46 weeks

value: slick mutation


title: D-lactic acid-producing Pichia pastoris without ScFLO1 overexpression, replicate 3


title: C4_66

source_name: I. batatas 3rd leaves, 1 h water treatment

value: 3rd leave

value: Ipomoea batatas Lam.; cultivar Tainong 57

value: Control