title: Xyn6h_ii

status: Public on Sep 30 2022

type: SRA

city: Amsterdam

first: Biwen

last: Wang

address: Work, Science Park 904,1098 XH,Amsterdam,The Netherlands

department: Swammerdam Institute for Life Science

country: Netherlands

institute: University of Amsterdam

library_source: transcriptomic

data_processing:
Raw data were analyzed on the web-based platform Galaxy
Trimmomatic was applied to remove adaptors and filter bad reads
Bowtie2 was used to aligned trimed reads to reference genome fasta (NC_000964.3)
featureCounts was used to count reads for the gene features base on annotation GFF3 file (NC_000964.3) and using "locus_tag" as the GFF gene identifier
DEseq2 was used to normalized the count reads and compare the differences in the transcriptome between XynA overproducing (Xyn) and non-producing (Emp) samples
Assembly: NC_000964.3
Supplementary files format and content: tabular files include raw counts for each gene/RNA features for each sample
Supplementary files format and content: tabular files include normalized counts for each gene/RNA features for all samples
Supplementary files format and content: Matrix table with Gene Identifiers, Gene name, mean normalised counts, the logarithm (to basis 2) of fold change, standard error estimate for the log2 fold change estimate, Wald statistic, p value for the statistical significance of this change and p value adjusted for multiple testing with the Benjamini-Hochberg procedure which controls false discovery rate (FDR) for each gene/RNA features between samples.

molecule: total RNA

organism: Bacillus subtilis

source_name: Bacteria

growth_protocol: Cells were cultured at 37 °C in 10 ml LB medium with 50 μg/ml kanamycin in 125 ml flasks to 6 h growth (OD600 ~4).

extract_protocol:
Cell disruption was achieved by bead beating (Precellys 24). After centrifugation, the rough RNA in the upper aqueous phase was ethanol-precipitated, washed twice with 70% ethanol, dried and dissolved in water. DNA was removed by DNAseI (NEB) treatment; the pure total RNA was then extracted by a second-round of P/C/I extraction, following by ethonal-precipitation and 70% ethanol washing, and finally dissolved in water. The total RNA was subjected to MICROBExpress™ Bacterial mRNA Enrichment Kit (Thermo Fisher) to remove >95% of the 16S and 23S rRNA from total RNA.
Libraries were constructed using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs) and NEBNext® Multiplex Oligos for Illumina® (New England Biolabs), according to the manufacturer's protocol.

treatment_protocol: 2 mL cells were collected by centrifugation at 4°C, 20,000xrcf for 1 min. Cell pellets were resuspended in 0.4 ml ice-cold growth medium and added to a screw cap tube containing 1.5g glass beads(0.1 mm), 0.4 ml Phenol/ Chloroform / isoamyl alcohol mixture [P/C/I, 25:24:1, ROTH] and 50 ul 10% SDS, votex to mix, flash freeze in liquid nitrogen.

tag: growth phase

value: Stationaryl growth

tag: strain

tag: treatment

value: pCS58 (Xyn)


title: Emp6h_ii

value: pBW17 (Emp)


title: Xyn6h_i


title: UMA302_urea.1

city: Amherst

first: David

middle: A

last: Sela

state: Massachusetts

address: 102 Holdsworth Way

department: Food Science

country: USA

institute: University of Massachusetts Amherst

description: UMA302_raw countts.txt

data_processing:
Base calling was performed by RTA v2.
The quality of sequencing was checked by FastQC.
Raw sequenced reads were aligned to the Bifidobacterium longum subsp. infantis ATCC 15697 (NC_011593.1) using bowtie2/2-2.1.0
The resulting SAM files were converted to BAM files and sorted through samtools 1.2.
Counting of the number of reads that correspond to annotated gene was performed using HTSeq 0.6.1.
Genome_build: Bifidobacterium longum subsp. infantis ATCC 15697 (NC_011593.1)
Supplementary_files_format_and_content: tab-delimited text files of raw counts output from HTSeq 0.6.1

organism: Bifidobacterium longum subsp. infantis

source_name: Bifidobacterium.longum subsp infantis

growth_protocol: Bifidobacterium longum subsp. infantis (B. infantis) UMA 272, B. infantis UMA 299 and B. infantis UMA 302 were grown on modified MRS medium devoid of  nitrogen source and supplemented with 2% w/v urea, 2% w/v complex nitrogen source (control) or 0.15% w/v L-cysteine.

extract_protocol:
Bacteria cultures were harvested at mid-exponential phase and stored in RNAlater Ambion until use. Total RNA was extracted using Ambion RNAqeous kit (Thermo Fisher Scientific, Waltham, MA, US) according to manufacturer instructions with the addition of a bead-beating step (FastPrep-24Tm 5G MP Biomedicals Inc, Santa Ana, CA, US).
Ribosomal RNA was removed using the Ribo-Zero rRNA Removal kit, Bacteria (Illumina, San Diego, CA, US) following manufacturer instructions. rRNA-depleted RNA was purified with the RNeasy Minelute Cleanup kit (Qiagen, Valencia CA,US). Whole transcriptome libraries were constructed using TruSeq Stranded mRNA Library Preparation Kit (Illumina) following manufacturer instructions. Libraries were pooled in equimolar concentration and diluted to 4 nM and denatured immediately prior to sequencing on an Illumina NextSeq 500.

value: Bifidobacterium.longum subsp infantis UMA 302


title: UMA302_urea.2

description: UMA302_raw countts.txt


title: UMA299_urea.1

description: UMA299_raw counts.txt

value: Bifidobacterium.longum subsp infantis UMA 299


title: UMA299_urea.2

description: UMA299_raw counts.txt


title: UMA302_L-cysteine.2

description: UMA302_raw countts.txt


title: UMA299_control.2

description: UMA299_raw counts.txt


title: UMA299_L-cysteine.1

description: UMA299_raw counts.txt


title: UMA299_L-cysteine.2

description: UMA299_raw counts.txt


title: Emp6h_i


title: UMA302_control.2

description: UMA302_raw countts.txt


title: UMA272_L-cysteine.1

description: UMA272_raw counts.txt

value: Bifidobacterium.longum subsp infantis UMA 272


title: UMA302_control.1

description: UMA302_raw countts.txt


title: UMA272_urea.1

description: UMA272_raw counts.txt


title: UMA272_control.2

description: UMA272_raw counts.txt


title: UMA299_control.1

description: UMA299_raw counts.txt


title: UMA272_L-cysteine.2

description: UMA272_raw counts.txt


title: UMA272_control.1

description: UMA272_raw counts.txt


title: UMA302_L-cysteine.1

description: UMA302_raw countts.txt


title: UMA272_urea.2

description: UMA272_raw counts.txt


title: LSI_4mo_C

city: Camden

first: Jean-Pierre

last: Issa

state: NJ

address: 403 Haddon Ave

institute: Coriell Institute for Medical Research

data_processing:
BGI paired end sequencing
tophat2 --sensitive alignment of the reads in fastq files to mm9 and generating BAM files
ht-seq-count  with default settings to generate counts of each gene
Cuffdiff to generate FPKM and fold change of each condition compared to control, we filtered for genes that had 0 reads across all samples
Assembly: mm9
Supplementary files format and content: The processed file is plain text format. The first 9 columns are the FPKMs of the individual samples.

organism: Mus musculus

source_name: Lower Small Intestine Epithelium

growth_protocol: Mice were aged to time points 4 month, 12 month, 18 month 24 month

extract_protocol:
Cell Pellets were lysed in 1mL Trizol (Thermo Fisher, # 15596026) and 100 µL of bromo-chlorophenol (Fisher, # AC173530050) were added. Phase separation was done by centrifugation at 12,000 g for 15 min at 4°C. Supernatant containing RNA was collected, RNA precipitated with an equal volume of isopropanol, and washed with 1 ml 75% ethanol. RNA pellet was collected by centrifuging at 7500 g for 5 min and dissolving in 30 ul nuclease free water. RNA concentration was determined with Qubit RNA Broad range kit (Thermo Fisher, # Q10210) and RNA integrity score (RIN) was determined using Agilent RNA 6000 nano kit (Agilent, # 56067-1511). RNA was sent to BGI, who performed library preparation and sequencing.
BGI

treatment_protocol: No treatment

tag: cell type

value: Intestine epithelial cells


title: LSI_12mo_C


title: USI_12mo_B

source_name: Upper Small Intestine Epithelium


title: USI_24mo_B


title: USI_4mo_B


title: USI_12mo_C


title: LSI_24mo_B


title: adjacent normal tissues  1

type: RNA

city: Fuzhou

first: Zexi

last: Chen

state: Fujian

address: 1 Xue Yuan Road,University Town

country: China

institute: Fujian Medical University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.Scanned images were imported into Agilent Feature Extraction software for raw data extraction.

data_processing:
Data processing, including quantile normalization, was performed using R software.
CircRNAs that were significantly differentially expressed between the tumor and normal tissues were identified using a fold-change cut-off value

organism: Homo sapiens

source_name: adjacent normal tissues

label_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from samples using TRIzol™ reagent (Invitrogen; Thermo Fisher Scientific, Inc., Waltham, MA, USA) following the protocol provided by the manufacturer. Next, RNA was purified with the RNeasy Mini kit (Qiagen) according to the manufacturer's guidelines. A NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Inc.) was used to measure the concentration of RNA based on the OD260/OD280 ratio.

treatment_protocol: 2 pairs of tongue squamous cell carcinoma and their matched adjacent tissues taken were obtained from patients undergoing surgery at the Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Fujian Medical University. None of the patients received chemotherapy or radiotherapy before surgery. The experimental tissue specimens were diagnosed independently by two experienced clinical pathologists. Specimens were instantly stored in liquid nitrogen and then stored at -80°C after biopsy.

tag: gender

value: male

tag: age

value: 48 years

tag: tnm status

tag: tissue

value: tongue


title: USI_4mo_A


title: LSI_4mo_A


title: adjacent normal tissues  2

value: 57 years


title: tongue squamous cell carcinoma 1

source_name: tongue squamous cell carcinoma


title: LSI_12mo_B


title: USI_4mo_C


title: LSI_12mo_A


title: LSI_24mo_A


title: LSI_4mo_B


title: USI_12mo_A


title: USI_24mo_A


title: COL_12mo_B

source_name: Colon Epithelium


title: COL_4mo_A


title: COL_12mo_A


title: tongue squamous cell carcinoma 2


title: COL_4mo_C


title: COL_24mo_B


title: COL_24mo_A


title: COL_4mo_B


title: GC9961-Male-22months

city: Lausanne

first: Maroun

last: Bou Sleiman

state: Vaud

address: Rue Cantonale

department: IBI

country: Switzerland

institute: EPFL

data_processing:
The STAR reference genome was generated using STAR 2.6.0a using  Mus_musculus.GRCm38.dna.primary_assembly.fa and Mus_musculus.GRCm38.91.gtf as reference genomes and annotations. Command: STAR --runThreadN [#threads] --runMode genomeGenerate --genomeDir [stargenome_directory] --genomeFastaFiles Mus_musculus.GRCm38.dna.primary_assembly.fa --sjdbGTFfile Mus_musculus.GRCm38.91.gt --sjdbOverhang 99
Mapping for each sample was performed using this command: STAR --runThreadN [#threads] --genomeDir [stargenomedirectory] --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --readFilesIn [raw fq.gz files] --outFileNamePrefix [sample_id]
Reads were counted using htseq-count (Htseq framework version 0.10.0): htseq-count -f bam -r pos -s no -m union -t exon -i gene_id [BAM file] Mus_musculus.GRCm38.91.gtf
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated file with raw counts

source_name: Liver

growth_protocol: The UM-HET3 mice are genetically heterogeneous progeny of CByB6F1 females and C3D2F1 males. The mothers of the test mice were CByB6F1/J, JAX stock #100009, whose female parents are BALB/cByJ and whose male parents are C57BL/6J. The fathers of the test mice were C3D2F1/J, JAX stock #100004, whose mothers are C3H/HeJ and whose fathers are DBA/2J. The mice were aged at the Glenn Center at the University of Michigan.

extract_protocol:
RNA extraction was performed on 10mg of powder from snap-frozen liver tissue using the Zymogen Direct-zol kit.
BGISEQ-500 library construction was performed by BGI

treatment_protocol: Mice were aged on Purina 5LG2 diet

tag: Sex

value: Male

value: Liver


title: COL_12mo_C


title: GC10906-Male-6months


title: GC8722-Female-22months

value: Female


title: GC8729-Female-22months


title: GC10955-Male-6months


title: GC8232-Male-22months


title: GC18029-Female-6months


title: GC8344-Female-22months


title: GC8953-Female-22months


title: GC8743-Female-22months


title: GC9387-Male-22months


title: GC8988-Female-22months


title: GC10878-Female-6months


title: GC8736-Female-22months


title: GC9828-Male-22months


title: GC8967-Female-22months


title: GC10871-Female-6months


title: GC8225-Male-22months


title: GC8351-Female-22months


title: GC9611-Male-22months


title: GC8652-Male-22months


title: GC10864-Female-6months


title: GC10857-Female-6months


title: GC9835-Male-22months


title: GC10822-Female-6months


title: GC10920-Male-6months


title: GC10913-Male-6months


title: GC10850-Male-6months


title: GC10808-Female-6months


title: GC10815-Female-6months


title: GC10843-Male-6months


title: GC10801-Male-6months


title: Input control Monkey 6 (3)

city: Guangzhou

first: Alexander

middle: V.

last: Strunnikov

state: Guangdong

address: 190 Kai Yuan Avenue

institute: GIBH

description: control

library_source: genomic

data_processing:
Paired end reads (R1 and R2 FASTQ files) were treated as single reads
R1 and R2 reads were cleaned using fastp application (github..com/OpenGene/fastp.git) . Reads were combined and aligned using bowtie-1.2.2 software with parameters: -best -m 5 -v 3
Peak calling was done with MACS2-2.1.1. software using a corresponding chromatin input file as a control
Peak calling was applied to the full genome assembly, including assembled chromosomes, and both placed and unplaced fragments
Bedgraph files were converted to bigWig files using bedGraphToBigWig script (ucsC utilities), excluding chromosome fragments
Genome_build: macFas5 (June 2013), Accession GCA_000364345.1 , NCBI Assembly 704988.
Supplementary_files_format_and_content: bigWig file is an indexed binary format file that displays continuous signal data as a graph.

molecule: genomic DNA

organism: Macaca fascicularis

source_name: dissected testis

extract_protocol:
Testis fractionation: Testis samples were placed on ice and cut into pieces with sterile scalpel. Homogenates were individually filtered through two mesh wire gauzes to remove large pieces of tissue fragments and the cells of stroma. Cells in filtered homogenates were extensively washed with cold PBS and fixed with 1% EM-grade formaldehyde/PBS for 15 min. Crosslinking was quenched with glycine (0.125M final concentration). Cells were centrifuged, resuspended in PBS/1 x proteinase inhibitor cocktail /10% glycerol, and kept at -80 degrees C. A modified ChIP version named ChEP (chromatin enriched for proteomics) was used to precipitate proteins of interest with specific antibodies.
DNA fragments were end-repaired and A-tailed according to Illumina protocol, and then ligated with adapters. DNA fragments that have adapter molecules on both ends were amplified by PCR. DNA concentration of the resulting sequencing libraries was measured with the Qubit 2.0 fluorometer dsDNA HS Assay (Thermo Fisher Scientific), while the size distribution was analyzed using Agilent BioAnalyzer 2100 (Agilent). Paired-end sequencing was performed using an Illumina HiSeq system with Illumina-provided protocols for paired-end sequencing.

value: testis

value: male germline cells

tag: antibody


title: Input control Monkey 6 (2)

description: control

data_processing:
Paired end reads (R1 and R2 FASTQ files) were treated as single reads
R1 and R2 reads were combined and aligned using bowtie-1.2.2 software with parameters: -best -m 5 -v 3 -5 10 -3 20
Peak calling was done with MACS2-2.1.1. software using a corresponding chromatin input file as a control
Peak calling was applied to the full genome assembly, including assembled chromosomes, and both placed and unplaced fragments
Bedgraph files were conversted to bigWig files using bedGraphToBigWig script (ucsC utilities), excluding chromsome fragments
Genome_build: macFas5 (June 2013), Accession GCA_000364345.1 , NCBI Assembly 704988
Supplementary_files_format_and_content: bigWig file is an indexed binary format file that displays continuous signal data as a graph.

extract_protocol:
Testis samples were placed on ice and cut into pieces with sterile scalpel. Homogenates were individually filtered through thwo mesh wire gauzes to remove large pieces of tissue fragments and the cells of stroma. Cells in filtered homogenates were extensively washed with cold PBS and fixed with 1% EM-grade formaldehyde/PBS for 15 min. Crosslinking was quenched with glycine (0.125M final concentration). Cells were centrifuged, resuspended in PBS/1 x proteinase inhibitor cocktail /10% glycerol, and kept at -80 degrres C. A modified ChIP version named ChEP (chromatin enriched for proteomics) was used to precipitate proteins of interest with specific antibodies.
DNA fragments were end-repaired and A-tailed according to Illumina protocol, and then ligated with adapters. DNA fragments that have adapter molecules on both ends were amplified by PCR. DNA concentration of the resulting sequencing libraries was measured with the Qubit 2.0 fluorometer dsDNA HS Assay (Thermo Fisher Scientific), while the size distribution was analyzed using Agilent BioAnalyzer 2100 (Agilent). Paired-end sequencing was performed using an Illumina HiSeq system with Illumina-provided protocols for paired-end sequencing.


title: RAD21L ChIP Monkey 3

description: bigWig: chr1-20,X

value: custom rabbit polyclonal anti-RAD21L


title: Input control Monkey 5 (3)

description: control


title: RAD21L ChIP Monkey 4

description: bigWig: chr1-20,X


title: Input control Monkey 4 (2)

description: control


title: STAG3 ChIP Monkey 3

description: bigWig: chr1-20,X

value: custom rabbit polyclonal anti-STAG3


title: REC8 ChIP Monkey 3

description: bigWig: chr1-20,X

value: custom rabbit polyclonal anti-REC8


title: CTCF ChIP Monkey 6

description: bigWig: chr1-20,X

value: Cell Signalling, D31H2 and D1A7


title: SMC1b ChIP Monkey 4

description: bigWig: chr1-20,X

value: custom rabbit polyclonal anti-SMC1b


title: REC8 ChIP Monkey 4

description: bigWig: chr1-20,X


title: BORIS ChIP Monkey 5

description: bigWig: chr1-20,X


title: GC10836-Male-6months


title: BORIS ChIP Monkey 6

description: bigWig: chr1-20,X


title: CTCF ChIP Monkey 5

description: bigWig: chr1-20,X


title: GC10787-Male-6months


title: STAG3 ChIP Monkey 4

description: bigWig: chr1-20,X


title: Input control Monkey 3 (2)

description: control


title: Input control Monkey 4 (1)

description: control


title: Input control Monkey 5 (2)

description: control


title: Input control Monkey 6 (1)

description: control


title: Input control Monkey 3 (1)

description: control


title: Input control Monkey 5 (1)

description: control


title: M0-2

city: Fort Collins

first: Steven

last: Dow

state: CO

address: 300 W Drake Rd

department: Clinical Sciences

institute: Colorado State University

description: ATE

data_processing:
Partek Flow software, version 7.0
Raw data were filtered by removing reads containing adapters and reads containing N > 10% and for Phred scores >30
Filtered reads were aligned with STAR 2.7.3a, CanFam3.1 genome assembly
Aligned reads were annotated and counted using HT-seq
Assembly: CanFam3.1

organism: Canis lupus familiaris

growth_protocol: canine PBMC extracted from whole blood using Ficol solution, monocytes isolated by adherance

extract_protocol:
Qiagen Rneasy
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purificatio

treatment_protocol: M0 macrophages differentiated with M-CSF, M1 inflmatory macrophage stimulated with IFNg, M2 macrophages derived using IL13 and IL4

value: primary cells

value: Monocyte-derived M0 macrophage

tag: breed

value: beagle

value: M-CSF


title: M0-3

description: KBS


title: M2-1

value: Monocyte-derived M2 macrophage


title: DMSO-treated SC5314 rep2

city: Kuala Lumpur

first: Sun Tee

last: Tay

state: W.P. Kuala Lumpur

address: Jalan Profesor Diraja Ungku Aziz

department: Medical Microbiology

country: Malaysia

institute: University of Malaya

data_processing:
The raw paired-end sequencing data were quality-checked using FastQC v0.11.8
Sequence reads were mapped to C. albicans SC5314 (GenBank accession: GCA_000182965.3) reference genome using STAR v2.7 with default parameters.
Enumeration of reads mapped to each gene was performed using featureCounts version 2.0.0 with the following parameters: -t gene -g gene_id -p -B -C.
Differential gene expression analysis was performed using the R package DESeq2. Nominal p-values were corrected for multiple testing using the Benjamini–Hochberg method.
Differentially expressed genes (DEGs) were identified using a false-discovery rate (FDR) of <0.001  and a minimum log2 fold change value of 1.
Genome_build: C. albicans SC5314 (GenBank accession: GCA_000182965.3)
Supplementary_files_format_and_content: Number of reads mapped to each gene in every sample
Supplementary_files_format_and_content: raw gene counts

organism: Candida albicans

source_name: Yeast

growth_protocol: The yeast cells were prepared by growing a mother culture of C. albicans yeast colony in 5 ml of yeast peptone dextrose (YPD) broth for 24 hours. 150 µl of mother culture was then diluted into 5 ml of fresh YPD broth to become 107 of cells and let to grow for 6 hours into 109 of cells.

extract_protocol:
After treatment, the yeast cells were harvested  and extracted using RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s protocol.
The total RNA was enriched prior double-stranded cDNA synthesis. Then, after a series of terminal repair, A ligation and sequencing adaptor ligation was performed, the double-stranded cDNA library was completed through size selection and PCR enrichment.

treatment_protocol: The yeast cells were exposed to Aureobasidin A in 1 µg/ml for 3 hours prior harvesting

value: DMSO-treated


title: HEKa treated with siLINC00958, biological rep4

city: Uppsala

first: Longlong

last: Luo

state: Sweden

address: BMC Husargatan 3 752 37 UPPSALA

country: Sweden

institute: Uppsala University

description:
Gene expression data from human epidermal keratinocytes transfected with siRNAs targeting LINC00958
Primary keratinocytes_siLINC00958-4

hyb_protocol: Following fragmentation, 5 micrograms of biotin-labeled sense-strand cDNA fragments in 200 µL of hybridization mix was loaded onto a human Clariom D array and hybridized to probes on the array in a GeneChip Hybridization Oven 645 (Affymetrix) for 16 h at 45°C with 60 rpm rotation.

scan_protocol: GeneChips were scanned using GeneArray G7 scanner (Affymetrix) and quantified into .CEL files with image and signal intensities. https://www.thermofisher.com/se/en/home/life-science/microarray-analysis.html

data_processing: Data were normalised (log2) and analyzed using Transcriptome Analysis Console (TAC) software (Thermo Fisher Scientific) using SST-RMA algorithm and annotated on exon/gene level with the library for Clariom D Array (human). Transcripts with fold-change greater than 1.5 and False Discovery Rate (FDR) < 0.05 were differentially expressed.

label: biotin

source_name: Human Epidermal Keratinocyte perform transfection with siRNAs targeting LINC00958

label_protocol: The fragmented cDNA was labeled by terminal deoxynucleotidyl transferase using the Affymetrix proprietary DNA labeling reagent, which is covalently linked to biotin.

growth_protocol: Primary human keratinocytes were cultured at 37 °C in 5% CO2 in EpiLife serum-free medium containing Human Keratinocyte Growth Supplement and penicillin/streptomycin antibiotics (Thermo Fisher Scientific).

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

treatment_protocol: For LINC00958 knockdown, 3 ng/ml pre-designed siPools with a pool of 30 different siRNAs (siTOOLs) targeting LINC00958 (siLINC00958) or non-targeting control (siControl) were transfected with RNAiMAX (Thermo Fisher Scientific) in primary keratinocytes for 48 hours.

value: Adult human skin

value: Human Epidermal Keratinocyte

tag: genotype


title: M2-2

description: ATE


title: AbA-treated SC5314 rep1

value: AbA-treated


title: M1-1

value: Monocyte-derived M1 macrophage

value: IFNg


title: M0-1


title: M2-3

description: KBS


title: M1-2

description: ATE


title: Raw mRNA data ∆NLS1, ∆NLS2 mutant replicate 3

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: cDNA labelling for ∆NLS1,  ∆NLS2 strain, Replicate 3

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. After quantification, filters were stripped by washing them by pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were either checked with a Geiger counter.

scan_protocol: Images were acquired using a Fujifilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for variable times.

data_processing:
Raw image quantization with background subtracted and Median Absolute Desviation normalization of each triplicate. The average processed value for each gene was corrected by percentage of guanines (RA data) or uracils (TR data) present in each probe-coding strand as described in García-Martinez et al. 2004.
Value in the processed data is the result of the Median Absolute Desviation normalization of each triplicate of the raw data.

organism: Saccharomyces cerevisiae

source_name: NLS1-NLS2 mutant

label_protocol: For GRO samples: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were frozen in liquid nitrogen. Samples were then permeabilized with 1 mL of 0.5% sarkosyl and cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix. For mRNA samples: cDNA was synthetized by reverse transcription of total mRNA using oligo d(T)15VN as primer and 33P-dCTP for labelling.

growth_protocol: Cells were grown in YPD at 30ºC for at least 15 hours to reach early exponential phase at 0.4-0.5 OD600. Then, cells were spun-down and collected. Each sample was done in triplicate.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.

value: NLS1-NLS2 mutant

tag: method

value: expression


title: M1-3

description: KBS


title: Raw mRNA data S454P mutant replicate 3

description: cDNA labelling for S454P strain, Replicate 3

source_name: S454P mutant

value: S454P mutant


title: HEKa treated with siLINC00958, biological rep3

description:
Gene expression data from human epidermal keratinocytes transfected with siRNAs targeting LINC00958
Primary keratinocytes_siLINC00958-3


title: DMSO-treated SC5314 rep1


title: Raw mRNA data ∆NLS1 mutant replicate 3

description: cDNA labelling for ∆NLS1 strain, Replicate 3

source_name: NLS1 mutant

value: NLS1 mutant


title: RevIH2i2-gDNA_nanopore_bio rep 2

city: CLERMONT-FERRAND

first: Emilie

last: BRASSET

address: 28 place Henri dunant

country: France

institute: CNRS 6293 INSERM U1103 Université Clermont Auvergne

data_processing:
Data Analysis Pipeline: guppy 4.3.4-1, Porechop 0.2.4
format: fastq; content: original sequence pass reads after adapter trimming.
Supplementary files format and content: The processed data were obtained from the raw fastq files by using Nucbase (Dufourt, J., Pouchin, P., Peyret, P., Brasset, E., and Vaury, C. (2013). NucBase, an easy to use read mapper for small RNAs. Mob. DNA 4, 1. https://doi.org/10.1186/1759-8753-4-1.). They contain all reads with the corresponding numbers of read counts.

organism: Drosophila melanogaster

source_name: all tissues

growth_protocol: Flies were kept at standard conditon at 25°C

extract_protocol:
Crush 150 frozen flies in 10mL of nuclear isolation buffer (0.35 M sucrose, 0.1 M EDTA, 50 mM Tris-HCl) and homogenise the sample using TissueRuptor II with 2 x 15 second pulses on speed 2. Place 2 layers of 200 μm nylon mesh into a fresh 15 ml Falcon tube. Using a 1 ml wide-bore tip, transfer the homogenised flies through the mesh into the Falcon tube. Wash the nylon mesh with 2 ml of the nuclear isolation buffer. Repeat this wash step one more time. Centrifuge the filtered solution at 3500 x g for 15 minutes at 4 o C. Discard the supernatant. Add 5 ml of Buffer G2 of the QIAGEN Blood and Cell Culture DNA Midi Kit and 95 μl of Proteinase K to the pellet and resuspend by pipetting up and down with a 200 μl wide-bore pipette tip. Incubate at 50 o C for 45 minutes with gentle mixing at 100 rpm. Equilibrate a QIAGEN Genomic-tip 100/G column with 4 ml of Buffer QBT. Pour the lysate through the column. Purify the lysate according to the standard protocol of the QIAGEN kit. Elution is in 150 μl TE buffer.
This work has benefited from the facilities and expertise of the high throughput sequencing core facility of I2BC (Centre de Recherche de Gif – http://www.i2bc.paris-saclay.fr/)
Instrument: GridION version GXB02022 – 21.02.5; Sequencing kit: SQK-LSK109; Flowcell type: flo-min106 (R9.4.1)

tag: time

value: 3-6 day old female

value: all tissues

value: RevI-H2i2 isogenic line


title: RevIH2i2-gDNA_nanopore_bio rep 1


title: Raw mRNA data ∆NLS1, ∆NLS2 mutant replicate 2

description: cDNA labelling for ∆NLS1,  ∆NLS2 strain, Replicate 2


title: Raw mRNA data ∆NLS1 mutant replicate 2

description: cDNA labelling for ∆NLS1 strain, Replicate 2


title: DMSO-treated SC5314 rep3


title: HEKa treated with siControl, biological rep4

description:
Gene expression data from human epidermal keratinocytes transfected with siRNA negative control
Primary keratinocytes_siControl-4

source_name: Human Epidermal Keratinocyte perform transfection with siRNA negative control

value: transfected with siRNA negative control


title: HEKa treated with siControl, biological rep3

description:
Gene expression data from human epidermal keratinocytes transfected with siRNA negative control
Primary keratinocytes_siControl-3


title: HEKa treated with siLINC00958, biological rep1

description:
Gene expression data from human epidermal keratinocytes transfected with siRNAs targeting LINC00958
Primary keratinocytes_siLINC00958-1


title: AbA-treated SC5314 rep3


title: HEKa treated with siControl, biological rep1

description:
Gene expression data from human epidermal keratinocytes transfected with siRNA negative control
Primary keratinocytes_siControl-1


title: Raw mRNA data wt replicate 3

description: cDNA labelling for wt strain. Replicate 3

source_name: wild type

value: wild type


title: Raw mRNA data ∆NLS1 mutant replicate 1

description: cDNA labelling for ∆NLS1 strain, Replicate 1


title: AbA-treated SC5314 rep2


title: Raw TR data S454P mutant replicate 2

description: GRO labelling for S454P strain, Replicate 2

value: GRO


title: HEKa treated with siLINC00958, biological rep2

description:
Gene expression data from human epidermal keratinocytes transfected with siRNAs targeting LINC00958
Primary keratinocytes_siLINC00958-2


title: Raw TR data ∆NLS1 mutant replicate 3

description: GRO labelling for ∆NLS1 strain, Replicate 3


title: Raw TR data wt replicate 3

description: GRO labelling for wt strain. Replicate 3


title: Raw mRNA data wt replicate 2

description: cDNA labelling for wt strain. Replicate 2


title: Raw mRNA data wt replicate 1

description: cDNA labelling for wt strain. Replicate 1


title: Raw TR data ∆NLS1, ∆NLS2 mutant replicate 3

description: GRO labelling for ∆NLS1,  ∆NLS2 strain, Replicate 3


title: Raw mRNA data ∆NLS1, ∆NLS2 mutant replicate 1

description: cDNA labelling for ∆NLS1,  ∆NLS2 strain, Replicate 1


title: HEKa treated with siControl, biological rep2

description:
Gene expression data from human epidermal keratinocytes transfected with siRNA negative control
Primary keratinocytes_siControl-2


title: Raw mRNA data S454P mutant replicate 1

description: cDNA labelling for S454P strain, Replicate 1


title: Raw mRNA data S454P mutant replicate 2

description: cDNA labelling for S454P strain, Replicate 2


title: Raw TR data ∆NLS1 mutant replicate 2

description: GRO labelling for ∆NLS1 strain, Replicate 2


title: Raw TR data wt replicate 2

description: GRO labelling for wt strain. Replicate 2


title: Raw TR data S454P mutant replicate 1

description: GRO labelling for S454P strain, Replicate 1


title: Raw TR data S454P mutant replicate 3

description: GRO labelling for S454P strain, Replicate 3


title: NOMe-Seq, budding yeast treated with GCMT

city: Kashiwa

first: Fumihito

last: Miura

state: Chiba

address: Kashiwanoha 5-1-5

department: Graduate School of Frontier Sciences

country: Japan

institute: The University of Tokyo

data_processing:
Library strategy: NOMe-seq
Reads were mapped with BMap
Alignments were summerized with MPTC
Methylation levels and read coverage were exported with MetExport
Genome_build: sacCer3
Supplementary_files_format_and_content: bedGraph

source_name: Budding yeast nuclei treated with GCMT

growth_protocol: The S288C strain was innoculated in YPD media, grown with shaking at 30°C

extract_protocol:
The genomic DNA was extracted from the methyltransferase-treated fixed yeast cells.
After bisulfite treatment with EZ methylation gold kit, and served for tPBAT protocol

treatment_protocol: The yeast cells were treated with Zymolyase 100T, fixed with 1% formaldehyde, treated with a solution containing 0.1% NP40. The nuclei was treated with M.CviPI or M.CviQIX.

value: GCMT (M.CviPI)

value: whole yeast cell


title: NOMe-Seq with CCMT

data_processing:
Reads were mapped with BMap
Alignments were summerized with MPTC
Methylation levels and read coverage were exported with MetExport
Assembly: sacCer3
Supplementary files format and content: bedGraph

source_name: Budding yeast nuclei treated with CCMT

treatment_protocol: The yeast cells were treated with Zymolyase 100T, fixed with 1% formaldehyde, treated with a solution containing 0.1% NP40. The nuclei was treated with M.CviQIX.

value: CCMT (M.CviQIX)


title: Raw TR data ∆NLS1 mutant replicate 1

description: GRO labelling for ∆NLS1 strain, Replicate 1


title: AEP288 (qtr2∆) + preQ1-L1, small RNAs, - rRNA, IP-control, rep3 (Expt2)

city: Berlin

first: Ann

last: Ehrenhofer-Murray

address: Philippstr. 13

department: Institut für Biologie

country: Germany

institute: Humboldt-Universität zu Berlin

data_processing:
Adapter-trimming was performed using Skewer version 0.2.2 and alignment to S. pombe RNAs (mRNA, ncRNA and tRNA; main and mitochondrial) from Pombase (https://www.pombase.org/) was achieved using Salmon version 14.0 and HISAT2 version 2.1.1, as a splice-site sensitive alignment program.
Conversion of sam to bam files was performed using SAMtools. Peak calling of aligned sequences was performed using the Bioconductor package exomePeak2 (adjusted P-value < 0.1).
Assembly: S.pombe genome version ASM294v2.29
Supplementary files format and content: comma-separated values files include read counts, log2-fold change, pvalues and the padj for IP (WT) and input (qtr2∆)

organism: Schizosaccharomyces pombe

source_name: AEP288 (qtr2{delta})

growth_protocol: Strains AEP1 and AEP288 were grown in full medium (YES) with 0.1 µM preQ1-L1. Cultures were inoculated at an OD600 of 0.2 and grown to an optical density of 1.0

extract_protocol:
Small RNAs were isolated using the PureLink™ miRNA Isolation Kit (Invitrogen) according to the manufacturer’s instructions. Ribosomal RNA depletion of 5S and 5.8S rRNA was achieved using reverse complementary oligonucleotides with a 5'-biotin tag as described before (Kraus et al. 2019). 8 µg small RNAs were used for hybridization with 100 µM oligonucleotides in 10 µL of formamide, 2.5 µL of 20 x SSC, 5 µL of 0.005 M EDTA, pH 8 with the following thermocycling: 80 °C for 5 min, ramp down to 25 °C at intervals of 5 °C per minute. The reaction was stopped with the addition of 2 µl RNAseOut ans 50 µl of 1 x SCC containing 20% formamide. Removal of rRNA/oligonucleotide hybrids was performed using DynabeadsTM MyOneTM Streptavidin C1 (ThermoFisher) according to the manufacturer’s instructions.
Library preparation of immunoprecipitated RNAs for deep sequencing was performed using the NEBNext Small RNA Library Prep Set for Illumina (Multiplex Compatible; New England Biolabs) according to the manufacturer's protocols.

value: AEP288 (qtr2{delta})

value: FY7385;  h- SPAC2F3.13c (qtr2)::NatMX  leu1-32 ura4-D18 his3-D3

tag: growth condition

value: growth in full medium (YES) at 30C

value: metabolic labeling with preQ1-L1 dervitave

tag: experimental design

value: rRNA depletion and IP via strep-coated magnetic beads


title: AEP288 (qtr2∆) + preQ1-L1, small RNAs, - rRNA, IP-control, rep2 (Expt2)


title: Raw TR data ∆NLS1, ∆NLS2 mutant replicate 1

description: GRO labelling for ∆NLS1,  ∆NLS2 strain, Replicate 1

value: NLS1-NLS2 mutant


title: NOMe-Seq, budding yeast treated with CCMT


title: Raw TR data wt replicate 1

description: GRO labelling for wt strain. Replicate 1


title: AEP1 (WT) + preQ1-L1, small RNAs, - rRNA, IP, rep2 (Expt2)

source_name: AEP1 (WT)

value: AEP1 (WT)


title: AEP1 (WT) + preQ1-L1, small RNAs, - rRNA, IP, rep3 (Expt2)


title: AEP288 (qtr2∆) + preQ1-L1, small RNAs, - rRNA, IP-control, rep1 (Expt2)


title: AEP1 (WT) + preQ1-L1, small RNAs, - rRNA, IP, rep1 (Expt2)


title: AEP1 (WT) + preQ1-L1, IP, rep3 (Expt1)

extract_protocol:
Total RNA was isolated from 50 OD of cells. Cells were harvested and after addition of 1 mL of phenol, glass beads and vigorous shaking for 5 min, samples were centrifuged at 20.000 g for 5 min to clear the cell debris. Equal volume of phenol/chloroform/isoamylalcohol was added to the aqueous phase and centrifuged at 20.000 g for 5 min. After mixing the upper phase with an equal volume of chloroform followed by centrifugation at 20.000 g for 5 min, the RNA was precipitated.
Library preparation of immunoprecipitated RNAs for deep sequencing was performed using the NEBNext Small RNA Library Prep Set for Illumina (Multiplex Compatible; New England Biolabs) according to the manufacturer's protocols.

value: IP via strep-coated magnetic beads


title: AEP288 (qtr2∆) + preQ1-L1, IP-control, rep1 (Expt1)


title: AEP288 (qtr2∆) + preQ1-L1, IP-control, rep3 (Expt1)


title: AEP1 (WT) + preQ1-L1, IP, rep2 (Expt1)


title: AEP288 (qtr2∆) + preQ1-L1, IP-control, rep2 (Expt1)


title: AEP1 (WT) + preQ1-L1, IP, rep1 (Expt1)


title: CD8 High_2

city: Frankfurt am Main

first: Tobias

last: Burkard

address: Theodor-Stern-Kai 7

department: Institute of General Pharmacology and Toxicology

institute: Goethe University Frankfurt

data_processing:
The QuantSeq data analysis pipeline (Lexogen, Vienna, Austria) on BlueBee Genomics Platform was used for data processing.
Trimming (bbduk from the bbmap suite trimming)
Alignment (STAR v2.5.2a Aligner with modified ENCODE settings)
Gene read counting (HTSeq-count)
Assembly: GRCh38
Supplementary files format and content: text files include read counts for each sample.

source_name: blood

growth_protocol: Purified CD8+ T cells were maintained in RPMI without serum for starvation in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
mRNA isolation was immediately performed after sorting of CD8low and CD8high T cells using the RNeasy micro kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. 14ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QuantSeq 3’mRNA-Seq Library Prep Kit-FWD and UDI 12 nt Unique Dual Indexing Add-on kit (both Lexogen, Vienna, Austria) according to manufacturer’s instructions.

value: blood

value: CD8 T cell

tag: cd8 status

value: high

value: 40 h starvation


title: CD8 High_6


title: CD8 Low_6

value: low


title: CD8 High_3


title: CD8 High_4


title: CD8 Low_4


title: CD8 Low_5


title: CD8 High_5


title: CD8 Low_3


title: CD8 Low_2


title: CD8 High_1


title: 3C_S17_R1_001 (paired)

city: Aurora

first: Kelly

last: Doran

state: Colorado

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

data_processing:
CLC Genomics Workbench v 21.0.5
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Reads were aligned to the rRNA track of CP063198_sRNA and unmapped reads used for RNA-seq
Trimmed sequence reads were mapped first to mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Unmapped sequence reads were then mapped to CP063198_sRNA using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: CP063198_sRNA
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism:
Streptococcus agalactiae
Mus musculus

source_name: Skin

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).RNA was extracted from 2-3 mice before pooling RNA to form triplicate samples. For bacteria, we utilized three input controls as replicates and again pooled from 2-3 mice for all bacterial samples.
Samples were rRNA depleted using RiboZero Plus (Illumina) and libraries for the 12 mouse samples and 3 input bacteria cDNA samples were sequenced using the Illumina Stranded RNA sequencing platform.

value: Skin

value: Diabetic infected


title: 3B_S16_R1_001 (paired)


title: 3A_S15_R1_001 (paired)


title: CD8 Low_1


title: 1C_S11_R1_001 (paired)

value: Non-diabetic infected


title: InputC_S32_R1_001 (paired)

organism: Streptococcus agalactiae

source_name: cells

value: cells

value: Input


title: 1B_S10_R1_001 (paired)


title: 1A_S9_R1_001 (paired)


title: InputB_S31_R1_001 (paired)


title: Raw TR data ∆NLS1, ∆NLS2 mutant replicate 2

description: GRO labelling for ∆NLS1,  ∆NLS2 strain, Replicate 2

value: GRO


title: InputA_S30_R1_001 (paired)


title: CK-3

city: Yinchuan

first: Xiang

last: Xiao

state: Ningxia

address: Shengli Street

institute: Ningxia Medical University

data_processing:
Oxford Nanopore Technologies Long Read Processing: Raw reads were first filtered with minimum average read quality score=7 and minimum read length=500bp. Ribosomal RNA were discarded after mapping to rRNA database. Next, full-length, non-chemiric (FLNC) transcripts were determined by searching for primer at both ends of reads. Clusters of FLNC transcripts were obtained after mapping to reference genome with mimimap2, and consensus isoforms were obtained after polishing within each cluster by pinfish.
Remove redundant: Consensus sequences were mapped to reference genome using minimap2. Mapped reads were further collapsed by cDNA_Cupcake package with min-coverage=85% and min-identity=90%. 5’ difference was not considered when collapsing redundant transcripts.
Find fusion transcript:The criteria for fusion candidates is that a single transcript must:    (1) must map to 2 or more loci    (2) minimum coverage for each loci is 5% and minimum coverage in bp is >= 1 bp    (3) total coverage is >= 95%    (4) distance between the loci is at least 10kb
tab-delimited text files include CPM values for each Sample ...
Genome_build: http://ngs-data-archive.psc.riken.jp
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Glycyrrhiza uralensis

source_name: whole plant

growth_protocol: 60 water-absorbing, full-filled seeds were selected, blotted surface moisture, and sown evenly in each pot filled with 1900 g high-pressure sterilized and fully dried sand medium collected from native desert regions which do not contain any nutrients.

extract_protocol:
Glycyrrhiza uralensis Fisch. seedling were collected. Then RNA was extracted and its purity, concentration and integrity were tested. 1ug total RNA was prepared for cDNA libraries using protocol provided by Oxford Nanopore Technologies (ONT). Briefly, SuperScript IV First-Strand Synthesis System (Invitrogen) was used for full length mRNA reverse transcription and following cDNA PCR for 14 circles with LongAmp Tag (NEB). The PCR products were then subjected to FFPE DNA repair and end-repair (NEB) steps and following adaptor ligation using T4 DNA ligase (NEB). Agencourt XP beads was used for DNA purification according to ONT protocol. The final cDNA libraries were added to FLO-MIN109 flowcells and were run on PromethION platform at Biomarker Technology Company (Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: (ⅰ) Control group (CK), plants were watered to kept 65%-75% of saturation moisture content; (ⅱ) Drought stress group (D), plants were watered to kept 35%~45% of saturation moisture content; (ⅲ) Drought stress with G5 group (DB), plants were watered to kept 35%~45% of saturation moisture content and contained G5 (108 CFU mL−1); (ⅳ) Drought stress with Si group (DSi), plants were watered to kept 35%~45% of saturation moisture content and contained Si (2 mM); (v) Drought stress with G5 combined Si application group (DBSi)

value: whole plant

value: control treatment

value: 45 days

tag: stress

value: no stress


title: DBSi-1

value: drought with G5 combined Si treatment

value: drought stress


title: DB-1

value: drought with G5  reatment


title: DBSi-2


title: DBSi-3


title: DSi-3

value: drought with Si treatment


title: D-2

value: drought treatment


title: D-1


title: DB-3


title: DSi-1


title: CK-2


title: D-3


title: DSi-2


title: DB-2


title: CK-1


title: 5KO,DMSO,RNA,rep2

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

institute: RIKEN

data_processing:
Adaptor sequences and low quality bases in reads were trimmed using Trim Galore version 0.3.7
Mapping reads to genome or transcript by TopHat v2.1.1
BigWig files were produced by bamCoverage 2.5.4-1-eca29f6
Assembly: mm10
Supplementary files format and content: bigWIg

molecule: polyA RNA

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen)
500 ng of total RNA was used for RNA-seq library construction. RNA-seq library was constructed by KAPA mRNA Hyper Prep Kit (KAPA BIOSYSTEMS) and SeqCap Adapter Kit (Roche) according to manufacturer instructions.

tag: cell line

value: iMEFs

value: DMSO


title: WT,DMSO,RNA,rep2

value: WT

tag: treatment


title: 5KO,DS,RNA,rep1

tag: cell type


title: WT,DMSO,RNA,rep1


title: 5KO,DS,RNA,rep2


title: 5KO,DMSO,RNA,rep1


title: WT,DS,RNA,rep1


title: WT,DS,RNA,rep2


title: SgPTEN

city: shenyang

first: Xin

address: No. 36, Sanhao Street

institute: Shengjing Hospital Affiliated to China Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: GL261 cells

growth_protocol: GL261 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA from GL261 cells were isolated by Trizol 1mL.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: GL261 cells

value: glioma cells

value: PTEN knockout


title: WT


title: 24 month Spleen_B

data_processing:
Fastq files were trimmed to remove Illumina adapters and aligned to the bisulfite-converted Homo sapiens genome (hg19) using Bismark v0.18.1  and Bowtie2.
Methylation values were extracted using Bismark v0.18.1.
We used methylKit v1.3.3 to analyze differential methylation.
Assembly: mm9
Supplementary files format and content: Bismark coverage files

source_name: Spleen

growth_protocol: Mice were aged to time points 4 month, 12 month, 18 month (Small Intestine and Colon) 24 month

extract_protocol:
tissues were lysed in 2% SDS and 25 mM EDTA overnight. Ammonium acetate (10M) was added to make the precipitate of SDS with proteins and was removed by centrifugation at 12,000 rpm. Next, DNA was precipitated using isopropanol, washed with 70% ethanol, and dissolved in dissolved in LTET (Tris 10 mM, EDTA, 0.1 mM + Tween 20,0.1% )
Biological duplicate samples of of all tissues were analyzed for DNA methylation changes by reduced representation bisulfite sequencing (RRBS) (Gu et al. Nature Protocols 2011, doi:10.1038/nprot.2010.190). We followed the NEB protocol for methylated adaptors. Briefly, 1 microgram of genomic DNA was spiked 100 picograms of lambda phage DNA as the unmethylated standard and digested with MspI. Ends of restriction fragments were filled in, 3’-dA tailed and methylated adaptors (NEB E7535) were ligated to the ends of restriction fragments. Bisulfite treatment using the Epitect kit (Qiagen) followed. Bisulfite-converted libraries were amplified using EpiMark Taq DNA polymerase (NEB) and primers with barcode indices. The libraries were pooled and sequenced at Fox Chase Cancer Center Genomics Facility/GENEWIZ/ Novogene on Illumina HiSeq2500 instrument using paired end reads of 80 bases (fox chase) and 150bp (Genewiz and Novogene). We used Bismark v0.18.1 to align the sequences to mm9 human genome assembly

value: Spleen

tag: strain


title: 24 month Spleen_F


title: 24 month Spleen_D


title: 24 month Spleen_C


title: 24 month Spleen_E


title: 12 month Spleen_D


title: 24 month Skeletal muscle_B

source_name: Skeletal muscle

value: Skeletal muscle


title: 24 month Skeletal muscle_A


title: 12 month Spleen_B


title: 4 month Spleen_C


title: 4 month Spleen_E


title: 12 month Spleen_C


title: 12 month Spleen_A


title: 4 month Spleen_B


title: 12 month Skeletal muscle_B


title: 4 month Spleen_D


title: 12 month Spleent_E


title: 4 month Spleen_A


title: 24 month Spleen_A


title: 12 month Skeletal muscle_A


title: 4 month Skeletal muscle_B


title: 24 month Lung_B

source_name: Lung

value: Lung


title: 4 month Skeletal muscle_A


title: 12 month Lung_A


title: 24 month Lung_A


title: 12 month Lung_B


title: 4 month Lung_B


title: 4 month Lung_A


title: VT-1_Liver, Surf4(fl/fl) Alb-Cre-, rep 1

city: Ann Arbor

first: Vi

last: Tamg

state: Michigan

address: 210 Washtenaw Ave

department: Molecular and Integrative Physiology

institute: University of Michigan

data_processing:
Demultiplexed fastq fiiles were aligned against the mouse reference genome (GRCm38.92) using STAR
Quantification was done using RSEM
Differential expression analysis was performed by DESeq2
Assembly: GRCm38.92
Supplementary files format and content: Comma separated values file with salmon count for each sample
Supplementary files format and content: Comma separated values file with Deseq output (basemean, log2fc, and adjusted p-values)

source_name: Liver

growth_protocol: Mice were housed in a controlled lighting (12h light/dark cycle) and temperature (22°C) environment and had free access to food (5L0D, LabDiet, St. Louis, MO) and water.

extract_protocol:
RNA was isolated using Rneasy Plus Mini Kit
Library prepartion was done by the University of Michigan Advanced Genomics Core

value: Liver

value: Surf4(fl/fl) Alb-Cre(-)

value: Male


title: VT-4_Liver, Surf4(fl/fl) Alb-Cre-, rep 2

value: Female


title: RTC41

city: Greifswald

first: Theresa

last: Kordaß

state: Mecklenburg-Vorpommern

address: Ferdinand-Sauerbruch Straße DZ7 5.05

department: Surgical Research Laboratory

institute: Univserity Medicine Greifswald

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Pre-processing of individual scRNA experiments
Reads were aligned to the hg_GRCm38 reference genome with Cell Ranger v6.1.1 (10X genomics) using default parameters to produce cell-by-gene unique molecular identifier (UMI) count matrices.
UMI count data was analyzed with Seurat R package v.4.0.5. Quality of datasets was assessed by UMI count, feature count and percentage of mitochondrial RNA reads. We filtered for high-quality cells based on feature count (above 1000) and percentage of mitochondrial reads (below 15%). Expression matrices of high-quality cells were log-normalized and scaled to a total expression of 1x10e5 UMIs for each cell. No regression of variables was applied.
Assembly: hg_GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: s.c. tumor

growth_protocol: Female C57BL/6J mice  were implanted s.c. with 4 x 105 EO771 cells into the right hind leg and the left flank, respectively one day apart. On day 18 tumors were collected for further processing.

extract_protocol:
Single cells suspensions of eight digested tumors per group were pooled. Afterwards, cells were incubated with LIVE/DEAD® Fixable Dead Cell Stain Kit (Thermo Fisher Scientific) diluted 1:1000 in PBS for 30 min at 4 °C and stained with PE Rat Anti-Mouse CD45 antibody (BD) in FACS buffer for 30 min at 4 °C. Sorting for viable CD45+ cells was performed with a BD FACS Aria III.   The cell suspension of CD45 positive cells was adjusted to a concentration of approximately 1000 cells/μl.
The cells were then loaded onto the 10x Genomics Chromium controller for droplet-enabled single cell RNA sequencing according to the manufacturer’s instruction manual. Library generation was performed following the Chromium Single Cell 3′ Reagents Kit version 3.1 user guide.

value: s.c. tumor

value: Immune cells

value: Radiation and anti-CTLA4 treatment Tumor 1

value: female


title: untreated

description: 10x Genomics

value: untreated Tumor 1


title: RT2

description: 10x Genomics

value: Radiation Tumor 2


title: RTC42

description: 10x Genomics

value: WT

value: Radiation and anti-CTLA4 treatment Tumor 2


title: VT-6_Liver, Surf4(fl/fl) Alb-Cre+, rep 3

value: Surf4(fl/fl) Alb-Cre(+)


title: RT1

description: 10x Genomics

value: Radiation Tumor 1


title: VT-2_Liver, Surf4(fl/fl) Alb-Cre+, rep 1


title: 12 month Liver_A

city: Camden

first: Jean-Pierre

last: Issa

address: 403 Haddon Ave

institute: Coriell Institute for Medical Research


title: 24 month Liver_A


title: 24 month Liver_B


title: spinal cord CD45+ cells_cDNA

city: Sapporo

first: Junichi

last: Kashiwakura

state: Hokkaido

address: 15-4-1, Maeda 7-jo, Teine-ku

institute: Hokkaido University of Science

description:
S4 flowcell
A0307 = Untreated C57BL/6 mouse, replicate 1, scRNAseq
A0308 = Untreated C57BL/6 mouse, replicate 2, scRNAseq
A0313 = Inhibitor-treated C57BL/6 mouse, replicate 1, scRNAseq
A0314 = Inhibitor-treated C57BL/6 mouse, replicate 2, scRNAseq
WTA2_S5

data_processing:
Demultiplexing of each cell by hashtag read count was performed according to the previous report.
Assembly: GRCm38 release-101
Supplementary files format and content: barcode sequence-separated values files and matrix files

source_name: spinal cords

extract_protocol:
hashtag-stained single cell suspension was pooled and approximately 28678 cells were loaded onto the BD Rhapsody system (BD Biosciences). After loading unique cell barcode-immobilized magnetic beads, cells were lysed, and reverse transcription of polyA RNA and hashtag oligos derived from each single cell were performed according to the manufacture’s instructions. Exonuclease I treatment and cDNA/hashtag amplification were performed by using TAS-Seq protocol.
Sequencing libraries were prepared by using NEBNext Ultra II FS library prep kit for Illumina (New England Biolabs) and quantified by KAPA library quantification kit (KAPA Biosystems) and a MultiNA system (Shimazu).

value: spinal cords

value: CD45+ cells

value: multiplexed sample:EAE induction, no inhibitor treatment or EAE induction, inhibitor treatment


title: 4 month Liver_B

value: Liver


title: spinal cord CD45+ cells_Tag

description:
S4 flowcell
A0307 = Untreated C57BL/6 mouse, replicate 1, scRNAseq
A0308 = Untreated C57BL/6 mouse, replicate 2, scRNAseq
A0313 = Inhibitor-treated C57BL/6 mouse, replicate 1, scRNAseq
A0314 = Inhibitor-treated C57BL/6 mouse, replicate 2, scRNAseq
Tag2_S6


title: 4 month Liver_A


title: 24 month Kidney_D

source_name: Kidney

value: Kidney


title: VT-5_Liver, Surf4(fl/fl) Alb-Cre-, rep 3

value: Surf4(fl/fl) Alb-Cre(-)

value: Male


title: 661W Cell-Light-2

city: Chengdu

first: Xiaoping

last: YU

state: State...

address: Chengdu Medical College, 610500, Sichuan Province, China

institute: Chengdu Medical College

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Assembly: mm10
Supplementary files format and content: FPKM values for each Sample

growth_protocol: 661W cells  were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
The animal total RNA was extracted according to the instruction manual of the TRlzol Reagent (Life technologies, California, USA).
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Light group: 661W cells were exposed to 2,000±100 lux cold white fluorescent lamp for 24 hours, Dark group: 661W cells were incubated in the dark for 24 hours. Total RNA was extracted for high-throughput sequencing to detect the expression of each gene.

value: photosensitive cells

value: 661W cells were exposed to 2,000+/-100 lux cold white fluorescent lamp for 24 hours


title: 661W Cell-Light-3


title: 661W Cell-Light-1


title: 661W Cell-Dark-3

value: 661W cells were incubated in the dark for 24 hours


title: 24 month Kidney_C


title: VT-3_Liver, Surf4(fl/fl) Alb-Cre+, rep 2

value: Female


title: 24 month Kidney_B


title: 661W Cell-Dark-2


title: 24 month Kidney_A


title: 661W Cell-Dark-1


title: 4 month Kidney_C


title: 12 month Kidney_B


title: 12 month Kidney_A


title: 12 month Kidney_C


title: 4 month Kidney_B


title: 27 month Heart_I

source_name: Heart

value: Heart


title: 26 month Heart_H


title: 4 month Kidney_A


title: 25 month Heart_G


title: si_lncPim1,replicate 1

city: Shanghai

first: Li

last: He

address: Xiangyin road of Yangpu district

institute: Second military medical university

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks.
and the read counts of each gene were obtained by htseq-count.
DEGs were identified using the DESeq (2012) R package functions estimate Size Factors and nbinomTest.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized FPKM values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA LTSample Prep Kit following manufacturer's protocols.

value: RNA interference of lncPim1


title: Control,,replicate 2

value: wild type


title: oe_lncPim1,replicate 1

value: over expression lncPim1


title: oe_lncPim1,replicate 2


title: si_lncPim1,replicate 2


title: Control,replicate 1


title: 24 month Heart_E


title: 24 month Heart_F


title: LPS and oxidized AAT [5105]

city: Hannover

first: Stephan

last: Immenschuh

state: Deutschland

address: Carl-Neuberg-Str. 1

department: Institute for Transfusion Medicine and Transplant Engineering

institute: Hannover Medical School

description: LPS and oxidized AAT, mice lung RNA

data_processing:
Sequencing was performed on a NovaSeq 6000 sequencer using 200 cycles in paired-end mode.
RNA-Seq data was quality control analysed with fastQC v0.11.8 and low quality 30 ends were removed using Trimmomatic v0.38.  (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and any adapter sequences and low quality 3′ ends were removed using Trimmomatic v0.36.
High-quality reads were mapped against GRCm38 (mm10) mouse genome using STAR v2.4.0.1 and mapping quality control was performed using RseQC v2.6.4.
Transcriptome prediction and gene/isoform quantification was calculated using HT-seq v0.11.1 based on GRCm38 (mm10) RefSeq reference genes
Assembly: GRCm38 (mm10)
Supplementary files format and content: Raw counts

source_name: Male Balb/c mouse

extract_protocol:
Total RNA was isolated from five mice samples per experimental group and qualitatively assessed by Agilent 2100 Bioanalyzer using Agilent RNA 6000 Nano Kit.
RNASeq libraries were prepared by using 200 ng RNA of each sample. TruSeq Stranded mRNA (Illumina Inc., USA) was used for library preparation according to the manufacturer protocol. Briefly, polyA-containing RNA molecules were purified using polyT oligo-attached magnetic beads followed by thermal fragmentation. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by a second strand cDNA synthesis, end repair process, adenylation of 30 ends and ligation of the adapters. The products were then purified with Ampure XP Beads (Beckman Coulter, Brea, CA), and enriched with 15 cycles of PCR to create the cDNA library.

treatment_protocol: On days one, two, and three mice were exposed for 10 min to clean air or aerosol LPS (0.21 mg/ml). One hour after each challenge, animals were treated i.p. with saline or with (4 mg/kg body weight) one of the AAT preparations: native (nAAT), oxidized (oxAAT), recombinant (recAAT) or peptide of AAT (C-36). Experiments were terminated 6 h after the last dose of AATs.

value: lung

tag: agent

value: LPS + oxAAT

value: male

value: Balb/c


title: LPS and recombinant AAT [6103]

description: LPS and recombinant AAT, mice lung RNA

value: LPS + recAAT


title: LPS and recombinant AAT [6105]

description: LPS and recombinant AAT, mice lung RNA


title: LPS and oxidized AAT [5104]

description: LPS and oxidized AAT, mice lung RNA


title: LPS and recombinant AAT [6101]

description: LPS and recombinant AAT, mice lung RNA


title: 24 month Heart_D

state: NJ


title: LPS and recombinant AAT [6104]

description: LPS and recombinant AAT, mice lung RNA


title: LPS and oxidized AAT [5103]

description: LPS and oxidized AAT, mice lung RNA


title: 24 month Heart_C


title: 24 month Heart_B


title: 28 month Heart_J


title: LPS and recombinant AAT [6102]

description: LPS and recombinant AAT, mice lung RNA


title: LPS and oxidized AAT [5101]

description: LPS and oxidized AAT, mice lung RNA


title: LPS and native AAT [4103]

description: LPS and native AAT, mice lung RNA

value: LPS + nAAT


title: LPS and native AAT [4105]

description: LPS and native AAT, mice lung RNA


title: 12 month Heart_F


title: 12 month Heart_D


title: 12 month Heart_C


title: LPS and native AAT [4104]

description: LPS and native AAT, mice lung RNA


title: Control (Clean air) [2102]

description: Control (Clean air), mice lung RNA

value: Clean Air


title: LPS and oxidized AAT [5102]

description: LPS and oxidized AAT, mice lung RNA


title: 12 month Heart_B


title: 4 month Heart_E


title: 4 month Heart_B


title: LPS and native AAT [4102]

description: LPS and native AAT, mice lung RNA


title: 4 month Heart_F


title: Control (Clean air) [2105]

description: Control (Clean air), mice lung RNA


title: LPS and native AAT [4101]

description: LPS and native AAT, mice lung RNA


title: 4 month Heart_C


title: Control (Clean air) [2101]

description: Control (Clean air), mice lung RNA


title: 4 month Heart_A


title: 12 month Heart_E


title: LPS only [1105]

description: LPS only, mice lung RNA

value: LPS


title: 24 month Heart_A


title: 4 month Heart_D


title: 12 month Heart_A


title: LPS only [1101]

description: LPS only, mice lung RNA


title: LPS only [1103]

description: LPS only, mice lung RNA


title: 12 month whole blood_C

source_name: Whole Blood

value: Whole Blood


title: 24 month whole blood_D


title: female C57BL/6 +  sCD83 rep2

first: Maximilian

last: Fuchs

department: IMTTS

institute: Hanover Medical School

data_processing:
Read mapping using Rsubread
Read quantification using Rsubread
Assembly: Mus musculus dna primary assembly
Supplementary files format and content: csv file containing raw read counts

source_name: skin

extract_protocol: Total RNA was isolated using RNeasy Plus Mini Kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries by Novogene.

treatment_protocol: mice were treated with 100µg sCD83 or PBS for control

value: skin

value: tissue extract

value: WT


title: female C57BL/6 +  PBS rep2

value: Mock


title: LPS only [1104]

description: LPS only, mice lung RNA


title: female C57BL/6 +  PBS rep3


title: 12 month whole blood_B


title: LPS only [1102]

description: LPS only, mice lung RNA


title: 24 month whole blood_B


title: female C57BL/6 +  sCD83 rep3


title: female C57BL/6 +  PBS rep1


title: 24 month COL_GFP+_A

source_name: Colon Epithelium

value: Intestine epithelial cells


title: female C57BL/6 + sCD83 rep1


title: 12 month whole blood_A


title: 24 month COL_GFP-_B


title: 24 month USI_GFP+_B

source_name: Upper Small Intestine Epithelium


title: 24 month whole blood_C


title: J774 cells, siControl biol rep 3

city: Seoul

first: Moon-Suhn

last: Ryu

address: 50 Yonsei-ro, Seodaemun-gu

department: Food and Nutrition

country: South Korea

institute: Yonsei University

data_processing:
151bp paired-end reads for 6 samples (n=24.0 Million reads average per sample) were trimmed using Trimmomatic (v 0.33) enabled with the optional “-q” option; 3bp sliding-window trimming from 3’ end requiring minimum Q30.
Quality control on raw sequence data for each sample was performed with FastQC. Read mapping was performed via Hisat2 (v2.1.0) using the mouse genome (mm10) as reference.
Gene quantification was done via Feature Counts for raw read counts. Differentially expressed genes were identified using the edgeR (negative binomial) feature in CLCGWB (Qiagen, Redwood City, CA) using raw read counts.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

growth_protocol: J774 mouse macrophage cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using Direct-zol RNA Miniprep Kit (Zymo Research)
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA library prep kit following manufacturer's protocols.

treatment_protocol: Gene knockdown was accomplished via liposome-mediated delivery of siRNA into cells

value: macrophages

value: control

value: control siRNA


title: J774 cells, siControl biol rep 1


title: J774 cells, siNCOA4 biol rep 3

value: NCOA4 knockdown

value: NCOA4 siRNA


title: 24 month USI_GFP-_B


title: 4 month whole blood_C


title: J774 cells, siNCOA4 biol rep 2


title: 4 month whole blood_A


title: J774 cells, siNCOA4 biol rep 1


title: J774 cells, siControl biol rep 2


title: 24 month COL_GFP-_A


title: mouse kidney, RC-Casp1KO, rep 2

city: Kansas City

first: Timothy

middle: Allen

last: Fields

state: KS

address: 3901 Rainbow Blvd

department: Pathology

institute: University of Kansas Medical Center

data_processing:
Base calling by CASAVA 1.8
Data filtering: (1) Remove reads containing adaptors;  (2) Remove reads containing N > 10% (N = base that could not be determined); (3) The Qscore (Quality value) of over 50% bases of the read is <= 5.
Map read to reference transcriptome: Spliced Transcripts Alignment to a Reference (STAR) software
Assembly: mm10
Supplementary files format and content: Tab-delimited text file with FPKMs for each sample and comparisons between groups.

source_name: kidney

extract_protocol:
RNA was harvested using TRIZOL, followed by DNase  treatment, followed by cleanup with RNeasy column (Qiagen). 5 µg of total RNA was used for the construction of sequencing libraries.
mRNA was purified from total RNA using poly-T magnetic beads. The mRNA was fragmented, and first strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was performed using DNA Polymerase I and RNase H. Double-stranded cDNA was purified using AMPure XP beads (Beckman Coulter). Remaining overhangs of the purified double-stranded cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. Library fragments were purified with AMPure XP system (Beckman Coulter) to select cDNA fragments ~150-200 bp. The final library was generated by PCR amplification and purification of PCR products by AMPure XP beads.

value: kidney

value: Female

tag: age

value: 6 months old

tag: disease state

value: mouse model of PKD


title: HiC of Dmrt1 -/- P7 Sertoli Cells rep 1a

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description:
HiC_Dmrt1_null_null_rep_1a
AB_Compartments_Dmrt1_null_null_p7_Sertoli.bigWig
HiC_interactions_Dmrt1_null_null_p7_Sertoli.bedpe

data_processing:
For each of the experiments, reads were trimmed using Trim Galore (v0.6.0) and cutadapt (v1.18) and assessed for quality with FastQC (v0.11.8). STAR (v2.7.2a), BWA mem (v0.7.12) and HiC-Pro (v3.1.0) were used to map transcriptomic (RNA-seq), genomic (ChIP-seq),and 3D (Hi-C) trimmed reads to the GRCm38 (mm10) genome respectively
The GENCODE M25 gene annotation set was used to estimate strand-specific gene expression data in the RNA-seq data with the Bioconductor package RSubread (v1.28.1) and to assign the locations of nearby genes in the ChIP-seq datasets. For paired-end ChIP-seq experiments, duplicated reads were removed with Picard MarkDuplicates (v2.17.10) and low quality reads (MAPQ < 55) or reads that mapped to the mitochondrial genome were removed with SAMtools (v1.0).
Assembly: GRCm38/mm10
Supplementary files format and content: Tables of expression counts and bigWig Coverage files and called HiC compartments and interactions.

source_name: Sertoli Cells

extract_protocol: Hi-C were performed for each cell type on  about 1 million primary granulosa cells using the Arima Hi-C Kit (#A510008).  Cells were fixed in 2% methanol-free formaldehyde in PBS at RT for ten min. with occasional mixing then quenched by addition of glycine to 0.125M with occasional mixing for 5 min.. Cells were placed on ice for 15 min. prior to washing with 1X PBS and stored at -80o C.  Hi-C was performed according to Arima Genomics (Document part # A160134 v00).  Sequencing libraries were prepared using the KAPA Hyper Prep Kit and xGen Duplex Seq adapters (Integrated DNA Techologies) according to Arima Genomics (Document part # A160139 v00).

tag: tissue

value: Sertoli Cells

value: Mixed 129Sv and C57Bl/6J

value: Dmrt1 -/-


title: 24 month USI_GFP-_A


title: 24 month COL_GFP+_B


title: 24 monthUSI_GFP+_A


title: HiC of Dmrt1 -/- P7 Sertoli Cells rep 2a

description:
HiC_Dmrt1_null_null_rep_2a
AB_Compartments_Dmrt1_null_null_p7_Sertoli.bigWig
HiC_interactions_Dmrt1_null_null_p7_Sertoli.bedpe


title: mouse kidney, RC-Casp1KO, rep 3

tag: Sex

value: Male


title: 4 month whole blood_B

value: Whole Blood


title: mouse kidney, RC-Casp1KO, rep 1


title: mouse kidney, RC, rep 4


title: 24 month whole blood_A


title: 24 month LSI_GFP+_A

source_name: Lower Small Intestine Epithelium


title: mouse kidney, RC-Casp1KO, rep 4


title: 24 month LSI_GFP-_B


title: mouse kidney, RC, rep 3


title: mouse kidney, RC, rep 2


title: mouse kidney, WT, rep 4

value: WT


title: mouse kidney, WT, rep 2


title: mouse kidney, RC, rep 1


title: mouse kidney, WT, rep 3


title: 18 month USI_GFP-_B


title: 18 monthUSI_GFP+_A


title: 18 month COL_GFP+_A


title: 18 month USI_GFP-_A


title: mouse kidney, WT, rep 1


title: 18 month USI_GFP+_B


title: Kidney_WT_VDR_Veh_rep9

city: Madison

first: Mark

middle: B

last: Meyer

state: WI

address: 1415 Linden Dr.

department: Nutritional Sciences

institute: University of Wisconsin-Madison

data_processing:
Data was processed from NovaSeq 6000 with bcl2fastq
ChIP-seq raw files were mapped using bowtie2 with standard parameters ( -x input file) with sam file output.
Sam files were converted with samtools into sorted and indexed bam files
HOMER was used to process the bam files, find peaks, and create the bigWig files.
bigWig files were averaged using the wiggletools mean function: wiggletools mean file1.bigWig file2.bigWig, file3.bigWig | wigToBigWig stdin chrom.sizes *_averaged.bigWig
Assembly: mm9
Supplementary files format and content: bigWig

source_name: kidney tissue

growth_protocol: C57BL/6 mice aged 8-9 wk (The Jackson Laboratory, Bar Harbor, ME) were housed in high density ventilated caging in the Animal Research Facility of University of Wisconsin-Madison under 12-hour light/dark cycles at 72°F and 45% humidity. All mice used in this study were maintained on a standard rodent chow diet (5008, Lab Diet, St. Louis, MO). All experiments and tissue collections were performed in the procedure rooms in the Research Animal Facility of University of Wisconsin-Madison. All animal studies were reviewed and approved by the Research Animal Care and Use Committee of University of Wisconsin-Madison under protocol A005478.

extract_protocol:
The kidneys were isolated, rinsed with cold 1× phosphate-buffered saline, and subjected to a cross-linking reaction for 10 min with 1.5% formaldehyde. After the fixative was neutralized for 5 min with glycine (0.125 m final concentration), the kidney tissue was homogenized briefly in phosphate-buffered saline using a loose fitting Dounce pestle, and the cells were collected via 70-μm nylon cell strainers (BD Falcon). Cells were then subjected to ChIP analysis as described previously (Yamamoto H, 2003, Journal Biol Chem).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA kit (NEB, #E7645S) with the NEBNext Multiplex Oligos for Illumina (NEB, #E6440S) according to the manufacturer’s protocols. Libraries were submitted to the University of Wisconsin – Madison Biotechnology Center’s DNA Sequencing Facility (Research Resource Identifier – RRID:SCR_017759). Libraries were sequenced on a NovaSeq 6000. Paired end, 250 bp sequencing with a target of 20+ million reads was performed.

treatment_protocol: Animals were subjected to intraperitoneal injection of 10 mg/kg body weight (bw) 1,25(OH)2D3 (in propylene glycol), 230 mg/kg bw PTH (1–84) (in phosphate buffered saline (PBS)), 50 mg/kg bw FGF23 (in PBS + 0.1% BSA), 30 mg/kg YKL-05-099 (PBS + 25mM HCl), 40 mg/kg SK-124 (15% HPBCD (hydroxypropyl β-cyclodextrin)), or vehicle (EtOH, PBS, or HPBCD). Animals were sacrificed and tissues collected at 30 min (PTH) or 60 min (all other treatments) and subjected to ChIP followed by ChIP-seq.

value: wild type C57BL6

value: vehicle (EtOH, PBS)

tag: antibody

value: VDR (Santa Cruz, C-20, sc-1008, lot# H1216)


title: 24 month LSI_GFP-_A

value: Intestine epithelial cells


title: Kidney_WT_VDR_Veh_rep7

tag: genotype


title: 18 month COL_GFP-_A


title: 24 month LSI_GFP+_B


title: Kidney_WT_VDR_125_rep8


title: 18 month LSI_GFP+_A


title: Kidney_WT_VDR_125_rep9


title: 18 month LSI_GFP+_B


title: 18 month LSI_GFP-_B


title: 12 month COL_GFP+_A


title: Kidney_WT_SRC3_YKL_rep2

value: SRC3 (Cell Signaling, 5E11, 2126S, lot# 4)


title: 18 month COL_GFP-_B


title: 12 month COL_GFP-_A


title: 18 month COL_GFP+_B


title: 12 month USI_GFP-_B


title: 12 month USI_GFP-_A


title: Kidney_WT_SRC3_Veh_rep3


title: Kidney_WT_VDR_Veh_rep8


title: Kidney_WT_SRC3_YKL_rep1


title: Kidney_WT_SRC3_Veh_rep2


title: Kidney_WT_SRC3_Veh_rep1


title: Kidney_WT_VDR_125_rep7


title: Kidney_WT_SRC3_YKL_rep3


title: Kidney_WT_SRC3_SK124_rep2

value: 40 ng/g bw SK-124


title: 12 month COL_GFP+_B


title: Kidney_WT_SRC3_PTH30_rep3

value: 230 ng/g bw PTH (30 min)


title: 12 month COL_GFP-_B


title: Kidney_WT_SRC3_SK124_rep3


title: 18 month LSI_GFP-_A


title: Kidney_WT_SRC3_PTH30_rep2


title: 12 month LSI_GFP-_B


title: 4 month COL_GFP+_A


title: 12 month Liver_B

value: Liver


title: 4 month COL_GFP-_B


title: 12 month LSI_GFP-_A


title: 4 month COL_GFP-_A


title: Kidney_WT_SRC3_SK124_rep1


title: Kidney_WT_SRC3_FGF23_rep1

value: 50 ng/g bw FGF23


title: 4 monthUSI_GFP+_A


title: 4 month USI_GFP+_B


title: 4 month COL_GFP+_B


title: Kidney_WT_SRC3_125_rep3


title: 4 month LSI_GFP+_A


title: Kidney_WT_SRC3_FGF23_rep2


title: Kidney, rilmenidine, rep 4

city: Boston

first: Alexander

last: Tyshkovskiy

state: Massachusetts

address: 77 Avenue Louis Pasteur

institute: Brigham & Women's Hospital, Harvard Medical School

data_processing:
HiSeq Control Software v2.2 was used for system control and base calling through an integrated primary analysis software RTA (Real Time Analysis. v1.18). The BCL (base calls) binary was converted into FASTQ utilizing illumina package bcl2fastq (v1.8.4).
Quality filtering and adapter removal were performed using Trimmomatic version 0.32.
Reads were mapped to mm10 mouse genome using STAR (version 2.5.2b). Genes were counted via featureCounts (version 1.5).
Assembly: mm10
Supplementary files format and content: comma-separated values file includes gene counts for each sample

extract_protocol:
After sacrifice, liver was removed and frozen on dry ice. RNA was extracted from liver tissues with PureLink RNA Mini Kit.
Sequencing libraries were prepared as described in (Hashimshony et al., 2016).

treatment_protocol: 3-month old male mice were kept on control diet (Purina 5LG6) or the same diet supplied with the 10 ppm of rilmenidine for 1 month.

value: Kidney

value: Rilmenidine

tag: dose

value: 10 ppm

value: 4 months


title: Kidney_WT_SRC3_PTH30_rep1


title: 4 month USI_GFP-_A


title: Kidney_WT_SRC1_YKL_rep1

value: SRC1 (Cell Signaling, 128E7, 2191S, lot# 2)


title: Kidney_WT_SRC1_Veh_rep3


title: Kidney_WT_SRC3_125_rep1


title: Kidney_WT_SRC3_125_rep2


title: Kidney, rilmenidine, rep 2

value: Male


title: 4 month USI_GFP-_B


title: Kidney_WT_SRC1_YKL_rep2


title: Kidney, rilmenidine, rep 3


title: Kidney_WT_SRC1_Veh_rep1


title: 4 month LSI_GFP-_B


title: Kidney, rilmenidine, rep 1


title: Kidney, control, rep 6

value: Control


title: 4 month LSI_GFP+_B


title: Kidney_WT_SRC3_FGF23_rep3


title: Kidney_WT_SRC1_YKL_rep3


title: Kidney_WT_SRC1_Veh_rep2


title: 4 month LSI_GFP-_A


title: Kidney_WT_SRC1_SK124_rep1


title: Kidney_WT_SRC1_SK124_rep3


title: Kidney_WT_SRC1_PTH30_rep2


title: Kidney_WT_SRC1_PTH30_rep1


title: Kidney, control, rep 1


title: GF_L1_3

city: Beijing

first: Jing

last: Li

state: Beijing

address: Beilishi Road 167, Xicheng District,

department: Department of Hypertension Center

institute: FuWai Hospital, National Center for Cardiovascular Diseases,  Peking Union Medical College & Chinese Academy of Medical Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (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. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database  of splice junctions based on the gene model annotation file and thus a better mapping  result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene. FPKM, expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and is  currently the most commonly used method for estimating gene expression levels
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the  DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining  differential expression in digital gene expression data using a model based on the  negative binomial distribution. The resulting P-values were adjusted using the  Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes  with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially  expressed
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Renal tissues were collected, and RNA was extracted using the RNeasy (Qiagen) kit with DNase. RNA quality was assessed on a NanoPhotometer spectrophotometer and Agilent 2100 bioanalyzer. Total RNA underwent mRNA enrichment with the NEBNext Poly (A) mRNA Magnetic Isolation Module, followed by library preparation with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina. Libraries were validated with the MultiNA Bioanalyzer, and barcoded samples were pooled to equimolar concentrations before sequencing. Cluster generation was performed with HiSeq 2500. Paired-end sequencing was performed at Novogene Bioinformatics Technology Co., Ltd. Cleaned RNA sequencing reads were obtained through quality control and blasted with a mice genome in HISAT2 software
Library preparation was performed with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina

value: kidney

value: wild type


title: Kidney, control, rep 3


title: Kidney_WT_SRC1_SK124_rep2

value: wild type C57BL6


title: GF_L1_2


title: Kidney_WT_SRC1_FGF23_rep1


title: Kidney, control, rep 5


title: Kidney_WT_SRC1_FGF23_rep2


title: Kidney_WT_SRC1_125_rep3


title: Kidney, control, rep 2


title: Kidney_WT_SRC1_PTH30_rep3


title: Kidney_WT_SRC1_125_rep2


title: GF_K1_1


title: Kidney, control, rep 4


title: Kidney_WT_SRC1_FGF23_rep3


title: GF_L1_1


title: GF_K1_3


title: Kidney_WT_SRC1_125_rep1


title: GF_L1_4


title: Kidney_WT_RXR_Veh_rep2

value: vehicle (EtOH, PBS)

value: RXR (Santa Cruz, N-197, sc-774, lot# D0815)


title: Kidney_WT_RXR_Veh_rep3


title: ABX_L1_3


title: GF_K1_2


title: ABX_L1_1


title: ABX_K1_3


title: Kidney_WT_RXR_125_rep1


title: Kidney_WT_RXR_Veh_rep1


title: ABX_L1_2


title: Kidney_WT_RNAPol2_YKL_rep2

value: RNA Polymerase II (Covance, 8WG16, lot #52)


title: S148 Glomeruli: muse Esm-1 + DM

city: Palo Alto

first: Xiaoyi

last: Zheng

state: California

address: 1701 Page Mill Rd

department: Med/Nephrology

institute: Stanford University

data_processing:
Raw paired-end FASTQ files were trimmed using Trimmomatic v0.36 as described in Bolger et al., Bioinformatics, 2014.
RNA-Seq alignment to the reference was performed using STAR v2.5.3a using default conditions as described in Dobin et al., Bioinformatics, 2013.
Gene counts were filtered for lowly expressed genes and differential expression analyses for RNA-Seq were performed using the DESeq2 v1.28.1 R
Package installed in R v4.0.2, using default conditions and batch correction incorporated in the design formula, as described in Love et al., Genome Biology, 2014.
Exploration, analysis, and visualization of results were performed using the DESeq2 R package and Integrative Genomics Viewer as described in
Robinson et al., Nature Biotechnology, 2011.
Genome_build: mm9

source_name: Glomeruli

extract_protocol:
Mice were sacrificed by cardiac perfusion. Kidneys were extracted and digested by GentleMACS. Digested kidneys were further treated by collagenase and hyaluronidase and passed through cell strainers. The glomeruli were collected and lysed in lysis buffer using an RNA isolation kit (Zymoresearch).
The second strand cDNA synthesis was performed using DNA Polymerase I and RNase H. The synthesized cDNA was fragmented randomly and the fragments are purified and resolved with EB buffer for end repair and single nucleotide A (adenine) addition. Thereafter, the short fragments were connected with sequencing adapters. The double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: DBA/2J mice were acclimated for one week in the animal facility. Seven week-old mice were hydrodynamically injected with saline or plasmids expressing mouse Esm-1 plasmid and Sleeping Beauty transposase for prolonged over-expression. At eight weeks of age, mice received daily, consecutive low dose streptozotocin (or vehicle) injections intraperitoneally as indicated to induce diabetes mellitus. Four weeks later, diabetic mice were additionally provided a 60% high fat diet for an additional 5 weeks. At week 17, mice were sacrificed and glomeruli were isolated and stored for analysis.

value: Glomeruli

value: 17 weeks

value: Wildtype

tag: susceptibility

value: DKD-susceptible

value: Streptozotocin

tag: in vivo over-expression

value: Esm-1 over-expression


title: ABX_K1_1


title: Kidney_WT_RNAPol2_Veh_rep1


title: ABX_K1_2


title: Kidney_WT_RNAPol2_SK124_rep2

value: 40 ng/g bw SK-124


title: S144 Glomeruli: Saline + DM

value: Saline control


title: Kidney_WT_RNAPol2_SK124_rep1


title: Kidney_WT_RNAPol2_YKL_rep3


title: Kidney_WT_RNAPol2_PTH30_rep1

value: 230 ng/g bw PTH (30 min)


title: S147 Glomeruli: mouse Esm-1 + DM


title: Kidney_WT_RNAPol2_YKL_rep1


title: Kidney_WT_RNAPol2_Veh_rep3


title: S30 Glomeruli: Saline + Control

value: Vehicle


title: Kidney_WT_RNAPol2_Veh_rep2


title: Kidney_WT_RNAPol2_SK124_rep3


title: S16 Glomeruli: Saline + DM


title: Kidney_WT_RNAPol2_FGF23_rep3

value: 50 ng/g bw FGF23


title: Kidney_WT_RNAPol2_FGF23_rep2


title: Kidney_WT_RNAPol2_PTH30_rep3


title: S141 Glomeruli: Saline + Control


title: Kidney_WT_RXR_125_rep2


title: 26341

city: Munich

first: Irmela

last: Jeremias

address: Feodor-Lynenstr. 21

department: Research Unit Apoptosis in Hematopoietic Stem Cells

institute: Helmholtz Zentrum München, German Center for Environmental Health (HMGU), Munich, Germany

description: GCGTAGTAATGAAT

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
Reads were mapped to a concatenated genome of human and mouse (hg38, mm10).
Quantification was done with ENSEMBL gene models (Homo_sapiens:GRCh38.84, Mus_musculus:GRCm38.85)
Mouse reads were excluded for further analysis
Supplementary files format and content: cell (columns) and gene (rows) -wise UMI expression table

source_name: ALL PDX line

growth_protocol: PDX cells were injected into NSG mice

extract_protocol:
prime-seq
Library was constructed using the prime-seq protocol

treatment_protocol: Mice were treated with 70 mg/kg Cyclophosphamide i.p. and 0.15 mg/kg Vincristin i.v. per week.

tag: disease stage

value: R

value: patient derived xenograft cells

tag: disease

value: acute lymphoblastic leukemia


title: S146 Glomeruli: mouse Esm-1 + DM


title: S143 Glomeruli: Saline + DM


title: 46741

description: GCGTAGTACCCTGG


title: S145 Glomeruli: Saline + DM


title: 46438

description: GCGTAGTAAAAGTT


title: 26342

description: GCGTAGTAAAATTG


title: S140 Glomeruli: Saline + Control


title: Kidney_WT_RXR_125_rep3

value: wild type C57BL6


title: 45994

description: GCGTAGTACTGCGG


title: Kidney_WT_RNAPol2_125_rep1


title: 45544

description: GCGTAGTATAATGA


title: Kidney_WT_pCREB_YKL_rep3


title: Kidney_WT_RNAPol2_PTH30_rep2


title: Kidney_WT_pCREB_YKL_rep2


title: Kidney_WT_pCREB_YKL_rep1


title: 35321

description: GCGTAGTAGTTCGA


title: Kidney_WT_RNAPol2_125_rep3


title: 41505

description: GCGTAGTAAAAACT


title: 35045

description: GCGTAGTACCCACG


title: 46455

description: GCGTAGTAGCTCGC


title: Kidney_WT_pCREB_SK124_rep3


title: Kidney_WT_RNAPol2_125_rep2


title: 35022

description: GCGTAGTAGGCCAC


title: Kidney_WT_pCREB_SK124_rep1


title: 41930-25

description: GCGTAGTACGGTGG


title: Kidney_WT_pCREB_Veh_rep5

value: vehicle (EtOH, PBS)


title: 45572

description: GCGTAGTATTATTG


title: Kidney_WT_RNAPol2_FGF23_rep1

value: RNA Polymerase II (Covance, 8WG16, lot #52)


title: 35023

description: GCGTAGTAATTACT


title: Kidney_WT_pCREB_Veh_rep4


title: Kidney_WT_pCREB_Veh_rep6


title: Kidney_WT_pCREB_PTH30_rep3


title: 41921-16

description: GCGTAGTAGGGATT


title: 35018

description: GCGTAGTAGCTAGA


title: 41922-17

description: GCGTAGTAATATAG


title: 35020

description: GCGTAGTATTAGTT


title: Kidney_WT_pCREB_PTH15_rep2

value: 230 ng/g bw PTH (15 min)


title: Kidney_WT_pCREB_PTH30_rep2


title: 35320

description: GCGTAGTATAAGAT


title: 35019

description: GCGTAGTATGTTTA


title: Kidney_WT_pCREB_PTH15_rep1


title: Kidney_WT_pCREB_FGF23YKL_rep3

value: 50 ng/g bw FGF23 + 30 ng/g bw YKL-05-099


title: Kidney_WT_pCREB_SK124_rep2


title: Kidney_WT_pCREB_PTH30_rep1


title: Kidney_WT_pCREB_FGF23YKL_rep1


title: Kidney_WT_pCREB_FGF23PTH30_rep2

value: 50 ng/g bw FGF23 + 230 ng/g bw PTH (30 min)


title: 31253

description: CCCACG


title: 31262

description: CCCCGT


title: Kidney_WT_pCREB_FGF23YKL_rep2


title: 31290

description: TTAGTT


title: 31264

description: GTTTAT


title: 31272

description: TACGCTGCAAATTG


title: 31231

description: GTTCGA

value: P


title: 31271

description: GCGTAGTACCCCGT


title: Kidney_WT_pCREB_PTH15_rep3


title: Kidney_WT_pCREB_FGF23_rep2


title: 32217-78

description: GCGTAGTATTAATC


title: 31280

description: TACGCTGCAAAGTT


title: 31279

description: TGTTTA


title: 32221-82

description: GCTCGC


title: 32220-81

description: GCGTAGTAGGAGCC


title: Kidney_WT_pCREB_125YKL_rep1


title: Kidney_WT_pCREB_FGF23PTH30_rep3


title: 31273

description: TACGCTGCTAAAGT


title: Kidney_WT_pCREB_FGF23PTH30_rep1


title: Kidney_WT_pCREB_125YKL_rep3


title: Kidney_WT_pCREB_FGF23_rep1


title: Kidney_WT_pCREB_125YKL_rep2


title: 32213-74 #2

description: GCGTAGTAGTTTAT

value: S


title: 31251

description: GCGTAGTACGTGGG


title: Kidney_WT_pCREB_125PTH30_rep2


title: Kidney_WT_pCREB_125PTH30_rep1


title: Kidney_WT_pCREB_FGF23_rep3


title: 32214-75

description: TACGCTGCCCCTGG


title: Kidney_WT_pCREB_125_rep3


title: Kidney_WT_pCREB_125_rep2


title: 32213-74 #1

description: GCTAGA


title: 32212-73 #2

description: TACGCTGCTTAATC


title: Kidney_WT_pCREB_125PTH30_rep3


title: 32210-71

description: GGGATT


title: 31356

description: ATCAAA

value: U


title: Kidney_WT_H3K9ac_Veh_rep5


title: 32211-72

description: CGGTGG


title: 31265

description: TAAGAT


title: Kidney_WT_H3K9ac_PTH30_rep3


title: 31270

description: TACGCTGCATGAAT


title: Kidney_WT_H3K9ac_Veh_rep4


title: Kidney_WT_H3K9ac_Veh_rep6


title: 31358

description: AAAACT


title: Kidney_WT_pCREB_125_rep1


title: 31233

description: ATATAG


title: Kidney_WT_H3K9ac_PTH30_rep1


title: Kidney_WT_H3K9ac_PTH30_rep2


title: Kidney_WT_H3K36me3_YKL_rep3


title: 32212-73 #1

description: GCGTAGTATAAAGT


title: 32227-88

description: GGAGCC


title: 31357

description: CGTGGG


title: Kidney_WT_H3K36me3_YKL_rep1


title: Kidney_WT_H3K36me3_YKL_rep2


title: 26669

description: GCGTAGTAAAGATT

value: other


title: Kidney_WT_H3K36me3_Veh_rep5


title: Kidney_WT_H3K36me3_Veh_rep6


title: Kidney_WT_H3K36me3_Veh_rep4


title: Kidney_WT_H3K36me3_PTH30_rep2


title: Kidney_WT_H3K36me3_PTH30_rep3


title: PD Patient_14 (Female)

city: Seongnam-si

first: Minsoo

last: Kwon

address: 335 Pangyo-ro

department: Pharmacology

institute: CHA University

data_processing:
Trimming with Average Q20 using BBDuk
Mapping using Bowtie2 to reference genome
Calculation read count using Bedtools
TMM + CPM normalization using EdgeR
Assembly: Human hg19 UCSC
Supplementary files format and content: Normalized counts.csv

source_name: Peripheral blood

extract_protocol:
RNA quality was assessed with an Agilent 2100 bioanalyzer using an RNA 6000 Nano Chip (Agilent Technolo- gies, Amstelveen, Netherlands).
The library construction was performed using a QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria

value: Peripheral blood

value: panic disorder

value: PBMC-derived microglia-like cell

value: Female


title: PD Patient_10 (Male)

value: Male


title: Kidney_WT_H3K27ac_Veh_rep6


title: PD Patient_16 (Female)


title: PD Patient_9 (Male)


title: PD Patient_11 (Female)


title: PD Patient_12 (Female)


title: Kidney_WT_H3K27ac_PTH30_rep2

value: 230 ng/g bw PTH (30 min)


title: PD Patient_17 (Male)


title: Kidney_WT_H3K27ac_Veh_rep4


title: PD Patient_8 (Male)


title: Kidney_WT_H3K27ac_PTH30_rep3


title: PD Patient_7 (Female)


title: PD Patient_4 (Female)


title: PD Patient_15 (Female)


title: Kidney_WT_CRTC2_YKL_rep2

value: CRTC2 (Bethyl Labs, A300-737A, lot# 1)


title: Kidney_WT_CRTC2_YKL_rep1

value: wild type C57BL6


title: Healthy CON_13 (Female)

value: healthy


title: Kidney_WT_H3K27ac_PTH30_rep1


title: PD Patient_1 (Female)


title: PD Patient_6 (Male)


title: PD Patient_3 (Female)


title: Kidney_WT_CRTC2_Veh_rep3

value: vehicle (EtOH, PBS)


title: Kidney_WT_H3K36me3_PTH30_rep1


title: Kidney_WT_CRTC2_Veh_rep2


title: Kidney_WT_CRTC2_YKL_rep3


title: Kidney_WT_H3K27ac_Veh_rep5


title: Healthy CON_12 (Male)


title: Kidney_WT_CRTC2_Veh_rep1


title: Healthy CON_9 (Female)


title: Healthy CON_3 (Female)


title: Kidney_WT_CRTC2_SK124_rep1

value: 40 ng/g bw SK-124


title: Kidney_WT_CRTC2_PTH30_rep3


title: Healthy CON_2 (Male)


title: Kidney_WT_CRTC2_PTH15_rep2

value: 230 ng/g bw PTH (15 min)


title: Healthy CON_8 (Male)


title: Healthy CON_1 (Male)