title: Fasting_V5

city: MADRID

first: ROBERTO

last: MARTIN-HERNANDEZ

address: CANTOBLANCO

department: BIOSTATISTICS AND BIOINFORMATICS UNIT

country: Spain

institute: IMDEA ALIMENTACION

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software.
HISAT2 v.2.1.0 was used to align paired end reads against the human “genome_snp_tran” index version GRCh38. The RNA strandness parameter was set to “FR”.
StringTie v.1.3.5 was used to assemble aligned reads into potential transcripts, and those were annotated based on GRCh38 v.94 genomic features.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes cpm read counts using normalized library sizes for all samples

source_name: PBMCs

extract_protocol:
9ml of blood from human volunteers were diluted 1:2 with PBS and layered onto half volume of Histopaque at room temperature. After centrifugation at 500 x g for 30 minutes at room temperature at the lowest acceleration and brake, the opaque interface containing the PBMCs was transferred with a Pasteur pipette to a clean tube, washed three times with PBS and the remaining pellet was resuspended with Tri-Reagent and kept at -80ºC until all samples were processed.
After mRNA enriched from organisms using oligo(dT) beads, library preparation was performed with NEB Next Ultra RNA Library Prep Kit. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina), dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, a ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment. The qualified libraries are fed into Illumina sequencers (Novaseq PE150) after pooling according to its effective concentration and expected data volume.

treatment_protocol: Blood samples were taken at IMDEA Food at 9:00 a.m. on day 1 (overnight fasting, V1 “Basal” point), and patients returned to their usual activities until 9:00 a.m. on day 2, when a second blood sample was taken at IMDEA Food (36 hours fasting, V2 “Fasting” point).

value: PBMCs


title: renal biopsy, control pt. 43 cel 31

status: Public on Jun 12 2022

type: RNA

city: Tucson

first: Nathan

last: Cherrington

state: Arizona

address: 1703 E. Mabel Street

department: Pharmacology & Toxicology

country: USA

institute: University of Arizona

description: Gene expression data from kidney biopsy

hyb_protocol: Once the labeling reaction was completed, 60uL was combined with the hybridization solution, then hybridized overnight for 17 hours on a Mouse Gene 1.0ST array in an Affymetrix GeneChip Hybridization Oven 640 (Affymetrix, Santa Clara, CA).

scan_protocol: arrays were scanned using the GeneChip Scanner 3000 with 7G upgrade (Thermo Scientific, Wilmington, DE)

data_processing: The image generated was analyzed using the GeneChip Expression Console (Affymetrix, Santa Clara, CA) were .DAT (image), .CEL (cell intensity data), .CHP (probe analysis data) files were generated.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: kidney FFPE neddgle biopsy

label_protocol: 10 ng of total RNA labeled according to GeneChip WT Pico Kit manufacturer's instructions

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

tag: tissue

value: Kidney

tag: disease state

value: normal


title: renal biopsy, control pt. 31 cel 4226

description: Gene expression data from kidney biopsy


title: Fasting_V4

type: SRA

library_source: transcriptomic

molecule: polyA RNA

tag: timepoint


title: Fasting_V10


title: Fasting_V11


title: Fasting_V9


title: MRT_hotair_nanopore_50s

city: New Haven

first: Li-Tao

last: Guo

state: Connecticut

address: 260 Whitney Ave

institute: Yale University

data_processing:
For nanopore sequencing, Guppy (v2.2.3) was used for base calling, Porechop (v0.2.4) for adapter removal, and ngmlr (v0.2.7) for alignment. Customized Python scripts were used for data analysis.
For Illumina TruSeq, cutadapt (v1.9.1) was used for adapter removal, HISAT2 (v2.1.0) used for alignment, and  RTEventsCounter.py used for data analysis

molecule: other

organism: synthetic construct

source_name: in vitro transcribed HOTAIR RNA

extract_protocol: cDNA was prepared using gene-specific RT primers. For nanopore sequencing, the cDNA was first converted to double-stranded DNA, and then Oxford Nanopore Ligation Sequencing Kit and Native Barcoding were used to construct the libraries. For Illumina TruSeq, Illumina TruSeq forward primer and indexed reverse primers were used to build the libraries.

tag: experiment goal

value: cDNA length measurement

tag: reverse transcriptase

value: MarathonRT, 50 sec extension

tag: molecule

value: in vitro transcribed HOTAIR RNA


title: MRT_hotair_nanopore_60s

value: MarathonRT, 60 sec extension


title: MRT_hotair_nanopore_65s

value: MarathonRT, 65 sec extension


title: MRT_hotair_nanopore_70s

value: MarathonRT, 70 sec extension


title: Aorta-Ovgp1 WT5

city: Peking

first: Zhengqin

last: Rong

address: Beiqing Road

country: China

institute: Basepedia

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: aorta

extract_protocol:
artoa were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: aorta

tag: cell line

tag: cell type

value: aorta cells

tag: genotype

value: wild type mice


title: MRT_hotair_nanopore_55s

value: MarathonRT, 55 sec extension


title: renal biopsy, control pt. 25 cel 2678

description: Gene expression data from kidney biopsy


title: renal biopsy, control pt. 21 cel 9

description: Gene expression data from kidney biopsy


title: Fasting_V8


title: Aorta-Ovgp1 WT4


title: MRT_hotair_nanopore_45s

value: MarathonRT, 45 sec extension


title: renal biopsy, control pt. 19 cel 1

description: Gene expression data from kidney biopsy


title: Fasting_V3


title: Aorta-Ovgp1 WT3


title: MRT_hotair_nanopore_40s

value: MarathonRT, 40 sec extension


title: MRT_hotair_nanopore_35s

value: MarathonRT, 35 sec extension


title: Fasting_V7


title: renal biopsy, control pt. 32 cel 38

description: Gene expression data from kidney biopsy


title: MRT_hotair_nanopore_30s

value: MarathonRT, 30 sec extension


title: MRT_hotair_nanopore_20s

value: MarathonRT, 20 sec extension


title: Aorta-Ovgp1 WT2


title: Fasting_V6

value: PBMCs


title: MRT_hotair_nanopore_25s

value: MarathonRT, 25 sec extension


title: renal biopsy, control pt. 17 cel 46

description: Gene expression data from kidney biopsy

value: Kidney

value: normal


title: MRT_hotair_nanopore_15s

value: cDNA length measurement

value: MarathonRT, 15 sec extension

value: in vitro transcribed HOTAIR RNA


title: Aorta-Ovgp1 WT1


title: MRT_hotair_nanopore_5s

value: MarathonRT, 5 sec extension


title: MRT_hotair_nanopore_10s

value: MarathonRT, 10 sec extension


title: Fasting_V2


title: Aorta-Ovgp1 KO5

value: aorta

value: aorta cells

value: Ovgp5 knock out mice


title: Fasting_V1


title: tgirt_rep1_gcsl

source_name: in vitro transcribed HOTAIR GCSL RNA

value: reverse transcription stop determination

value: TGIRT, replicate 1

value: in vitro transcribed HOTAIR GCSL RNA


title: tgirt_rep2_gcsl

value: TGIRT, replicate 2


title: ssiv_rep1_gcsl

value: SuperScript IV, replicate 1


title: Aorta-Ovgp1 KO4

value: Ovgp4 knock out mice


title: Basal_V11

value: PBMCs


title: ssiv_rep2_gcsl

value: SuperScript IV, replicate 2


title: Basal_V10


title: Aorta-Ovgp1 KO2

value: Ovgp2 knock out mice


title: Basal_V9


title: Aorta-Ovgp1 KO1

value: Ovgp1 knock out mice


title: mrt_rep1_gcsl

value: MarathonRT, replicate 1


title: Basal_V8


title: PB.rep2.RNA-seq

city: hangzhou

first: kuang

last: junqi

address: No.18 Shilongshan Road

institute: westlake University

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 vM13) transcriptome using Bowtie2 (v2.2.5) and RSEM (v1.3.0)
Genome_build: mm10

source_name: mouse embryonic stem cells(mESCs)

growth_protocol: Mouse ESCs were cultured on feeder free with mESC-2i medium (DMEM, 15%FBS, NEAA, GlutaMAX, PD0325901, Chir99021, LIF)

extract_protocol:
TRIzol, according to the manufacturers instructions
VAHTS mRNA-seq V2 Library Prep Kit for Illumina was used according to the manufacturer's instruction. Briefly, 1ug total RNA was used and mRNA was enriched using olig-dT dynabeads, followed by fragmentation by divalent cation at elevated temperature. First-strand cDNA synthesis by random hexamers and reverse transcriptase was followed by the second-strand cDNA synthesis. Then the reverse product was purified using AMPure XP beads. The cDNA was end repaired and a dA was added, followed by ligation, two round purification using AMPure XP beads, PCR amplification and PCR product purification. The library was quantified with an Invitrogen Qubit.

treatment_protocol: Treated with 2µg/ml doxycycline and/or PFI-3, BI-9564

value: OG2 transgenetic mouse embryonic stem cells(OG2ES)

tag: strain

tag: treatment

value: treated with doxycycline and PFI-3&BI-9564 for 6hrs

tag: passage


title: HCT116_3BKO_rH2AXChIP

city: Taipei

first: Wei-Yi

last: Chen

address: No. 155, Sec 2, Linong St.

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Yang Ming Chiao Tung University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the HG38 human genome assembly using bowtie version 1.12 with with parameters "-n 2 -m 1 -l 36 --best".
Potential PCR duplicates in ChIP-seq reads were removed using samtools rmdup command.
Tiled data files (TDF) were generated by igvtools with parameters "-z 5 -w 10 -e 200" for ChIP-seq.
The gene expression profiling was analyzed by HOMER software
Genome_build: HG38
Supplementary_files_format_and_content: Tiled data files (TDF) for input and ChIP samples.

molecule: genomic DNA

growth_protocol: The human HCT116 cell lines were grown in McCoy's 5A (Gibco) medium supplemented with 10% fetal bovine serum at 37 °C.

extract_protocol:
Chromatin lysates were prepared by sonication and protein-DNA complexes were isolated with indicated antibody.
Multiplexing libraries were prepared for sequencing using Illumina TruSeq Rapid SR Cluster Kit according to the standard protocol.

treatment_protocol: Cells were fixed and harvested at 80% confluency.

value: colorectal carcinoma

value: HCT116, DNMT3b-KO

tag: chip antibody

value: anti-phospho-Histone H2AX, Ser-139 (05-636, Millipore)


title: HCT116_WT_rH2AXChIP

value: HCT116, WT


title: PB.rep1.RNA-seq


title: Basal_V7


title: HCT116_WT_input


title: Basal_V6


title: Aorta-Ovgp1 KO3

value: aorta

value: aorta cells

value: Ovgp3 knock out mice


title: Basal_V5


title: Ablation Saline

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

description: RNA was isolated from the brains of 5 mice.

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline with force_counts set to 2000. The output from the cellranger count pipeline for each sample has been uploaded as a folder containing count, barcode, and gene matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Compressed tar archives containing the raw UMI count matrices for each sample, as well as matrices with gene symbols and barcodes.

source_name: Mouse brain

growth_protocol: Not applicable

extract_protocol:
10x Genomics Chromium single cell preparation
NGS Illumina Next Seq

treatment_protocol: Injection of artificial CSF (sham), or injection of Visudyne (5 uL) followed by 5 steps of transcranial photoconversion (meningeal lymphatic vessel ablation). Each combined with i.p. injection of either 1μg IL-1β or saline vehicle.

tag: age

value: 3 months

tag: gender

value: male

value: Ablation Saline

value: brain


title: T48Ls-2

city: Lanzhou City

first: lu

last: zhao

state: Gansu Province

address: Yintan Road Street

institute: Gansu Agricultural University

data_processing:
The clean miRNA reads were obtained from raw reads after discarding sequences, adaptor-ligated contaminants, and reads shorter than 18 nt.
Clean reads were compared against small RNAs in Rfam database to identify and remove rRNA, scRNA, sonRNA, snRNA, and tRNA.
Known miRNAs were identified by aligning against the miRbase database (v.22), and unannotated reads were considered as novel miRNAs according to their genome positions and hairpin structures using Mireap_v0.2.
Assembly: miRbase database (v.22)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Oncorhynchus mykiss

source_name: liver tissues

extract_protocol:
The samples were collected immediately, then flash-frozen in liquid nitrogen,and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver tissues

value: IHNV infection

tag: phenotype

value: wild-type


title: BI.rep1.RNA-seq

value: treated with doxycycline and BI-9564 for 6hrs


title: mrt_rep2_gcsl

value: reverse transcription stop determination

value: MarathonRT, replicate 2

value: in vitro transcribed HOTAIR GCSL RNA


title: Ablation Il1b

value: Ablation Il1b


title: T48Ls-3


title: Basal_V4

value: PBMCs


title: Sham Il1b

value: Sham Il1b


title: T48Ls-1


title: Tissue_treated1_60d_rep1

city: Lanzhou

first: jiajia

last: liu

state: Gansu

address: Gansu university of traditional Chinese medicine

hyb_protocol: The labeled and concentrated RNA product was adjusted to 17 μL with water, and other ingredients were added and heated at 100 ° C for 5 min. Then transfer to the ice bath; assemble the hybridization device, add 45 μL of the hybridization solution to the hybrid cover slip; place the hybridization device in the Agilent hybridization oven for overnight hybridization (about 16 hr, 20 rpm);

scan_protocol: After the hybridization, the chip is removed, first Wash in 0.2% SDS, 2×SSC lotion I for 5 min at 42 °C, then wash in 0.2×SSC lotion II at room temperature for 5 min. After the slide is dried, it can be used for scanning; use Agilent chip Scanner (G2565CA) scans the cleaned chip

data_processing: Hybrid images were analyzed and extracted using Agilent Feature Extraction (v10.7) software. The analysis was then performed using the Boo Expression Profiling Chip Analyzer software (CBC Analyzer, an expression profiling process based on R Bioconductor and Perl).

source_name: liver after metformin treatment

label_protocol: Cyanine-5 (Cy5) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation And cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Groups of mice after fasting for 12 hours on the ice box broken neck death, put the liver tissue of mice in cryopreserved tubes, and then put into liquid nitrogen frozen, finally transferred to - 80 ℃ refrigerator.

extract_protocol: Total RNA from each group of mice was extracted using a Trizol kit and then processed using FeatureExtraction software to obtain raw data files (.txt). Import the raw data file (.txt) into GeneSpring software and write parameter information such as grouping. Data normalization and QC analysis were performed for each sample.

treatment_protocol: The liver tissues of each group were derived from natural aging mice, aging diabetic mice, mice treated with metformin in aging diabetes, and mice treated with astragalus polysaccharide and metformin in the treatment of aging diabetes.

tag: mouse group

value: Whole liver


title: Tissue_treated2_60d_rep1

institute: Gansu university of traditional Chinese medicine

source_name: liver in the treatment of astragalus polysaccharide combined with metformin

value: mice treated with astragalus polysaccharide and metformin in the treatment of aging diabetes.

tag: tissue


title: Basal_V3


title: Tissue_unprocessed_60d_rep1

description: S-G

source_name: liver without drug treatment

value: natural aging mice


title: Tissue_molded_60d_rep1

source_name: liver after modeling

value: aging diabetic mice


title: Sham Saline

value: 3 months

value: male

value: Sham Saline


title: DMSO.rep2.RNA-seq

value: OG2 transgenetic mouse embryonic stem cells(OG2ES)

value: treated with doxycycline and DMSO for 6hrs


title: C48Ls-3

value: liver tissues

value: control

value: wild-type


title: Aged Saline

treatment_protocol: injection i.p. with either 1μg IL-1β or saline vehicle

value: 24 months

value: Saline

value: brain


title: Basal_V2

value: PBMCs


title: Basal_V1


title: C48Ls-2


title: Aged Il1b


title: PFI.rep1.RNA-seq

value: treated with doxycycline and PFI-3 for 6hrs


title: C48Ls-1


title: DMSO.rep1.RNA-seq


title: DMS273-sgATG7-3

status: Public on Jun 11 2022

city: Chiyoda-ku

first: Shogo

last: Okazaki

state: Tokyo

address: 1-8-13 Kanda-Surugadai

department: School of Dentistry

country: Japan

institute: Nihon University

data_processing:
Sequenced reads were mapped to hg38 genome using HISAT2
Assembly: hg38
Supplementary files format and content: Gene expression data were calculated read counts and compared between samples by using NGS data analysis system MASER 5 Genome_build: hg38

growth_protocol: All cell lines were maintained under 5% CO2 at 37°C in RPMI 1640 medium (Nacalai) supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted and purified with the use of RNeasy Mini Kit (Qiagen).
400 ng of total RNA was treated with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) (NEB) to eliminate rRNA molecules and used for cDNA library preparation. cDNA synthesis followed by transcriptome library preparation were conducted by MGIEasy RNA Directional Library Prep Kit V2.0 (MGI tech), where dUTP were incorporated in the process of the 2nd strand cDNA synthesis, instead of dTTP, that block PCR amplification against the 2nd strand templates, enabling strand-specific transcriptome profiling. A 12-cycle PCR amplification was performed to increase library yield. Resulting transcriptome sequencing libraries were quantified by Qubit dsDNA HS Assay (Thermofisher) and their fragment size distribution was confirmed by TapeStation D1000 ScreenTape (Agilent).

treatment_protocol: We use CRISPRv2 to knock out ATG7 and SQSTM1 in small cell lung cancer cell lines.

value: SCLC cells

value: ATG7 KO


title: DMS273-sgATG7-SQSTM1-3

value: ATG7/SQSTM1 KO


title: BI.rep2.RNA-seq

value: treated with doxycycline and BI-9564 for 6hrs


title: DMS273-sgATG7-2


title: DMS273-sgATG7-SQSTM1-1


title: DMS273-sgScr-2

value: WT


title: DMS273-sgATG7-SQSTM1-2


title: DMS273-sgScr-3


title: DMS273-sgATG7-1


title: PFI.rep2.RNA-seq


title: DMS273-sgScr-1


title: Control of oscoi2 #2 leaves replicate 1

city: Utsunomiya

first: Koji

last: Miyamoto

state: Tochigi

address: 1-1 Toyosatodai

department: Department of Biosciences

institute: Teikyo University

description: Biological replicate 1 of 3.

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Agilent Technologies Scanner G2505C US22502560

data_processing: After data was analyzed by Fearure Extraction software (Agilent), data normalization was performed using Subio Platform with Basic Plug-in (Subio Inc).

organism: Oryza sativa

source_name: Control of oscoi2 #2 leaves

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

growth_protocol: Wild-type rice plants (Oryza sativa L., 'Nipponbare') and rice COI mutants were grown in a glass house under natural daylight.

extract_protocol: RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: The leaf disks (6 mmϕ) were excised from the uppermost rice leaf blades of 1 month-old plants. Then the leaf disks were floated on 0.1%(v/v) DMSO or 0.5 mM MeJA

tag: sample group

value: Control of oscoi2 #2 leaves


title: oscoi2 #2 leaves treated with 0.5 mM MeJA for 24 h replicate 1

description: Biological replicate 1 of 3.


title: Control of oscoi2 #1 leaves replicate 3

description: Biological replicate 3 of 3.

source_name: Control of oscoi2 #1 leaves

value: Control of oscoi2 #1 leaves


title: oscoi2 #1 leaves treated with 0.5 mM MeJA for 24 h replicate 2

description: Biological replicate 2 of 3.


title: Control of oscoi2 #2 leaves replicate 3

description: Biological replicate 3 of 3.


title: oscoi2 #2 leaves treated with 0.5 mM MeJA for 24 h replicate 2

description: Biological replicate 2 of 3.


title: oscoi2 #2 leaves treated with 0.5 mM MeJA for 24 h replicate 3

description: Biological replicate 3 of 3.


title: oscoi2 #1 leaves treated with 0.5 mM MeJA for 24 h replicate 3

description: Biological replicate 3 of 3.


title: oscoi1b #3 leaves treated with 0.5 mM MeJA for 24 h replicate 3

description: Biological replicate 3 of 3.


title: Control of oscoi2 #1 leaves replicate 1

description: Biological replicate 1 of 3.


title: oscoi2 #1 leaves treated with 0.5 mM MeJA for 24 h replicate 1

description: Biological replicate 1 of 3.


title: Control of oscoi1b #3 leaves replicate 1

description: Biological replicate 1 of 3.

source_name: Control of oscoi1b #3 leaves

value: Control of oscoi1b #3 leaves


title: Control of oscoi1b #2 leaves replicate 3

description: Biological replicate 3 of 3.

source_name: Control of oscoi1b #2 leaves

value: Control of oscoi1b #2 leaves


title: Control of oscoi1b #3 leaves replicate 3

description: Biological replicate 3 of 3.


title: oscoi1a #2 leaves treated with 0.5 mM MeJA for 24 h replicate 1

description: Biological replicate 1 of 3.


title: oscoi1b #2 leaves treated with 0.5 mM MeJA for 24 h replicate 2

description: Biological replicate 2 of 3.


title: Control of oscoi2 #2 leaves replicate 2

description: Biological replicate 2 of 3.


title: oscoi1a #2 leaves treated with 0.5 mM MeJA for 24 h replicate 3

description: Biological replicate 3 of 3.


title: oscoi1b #2 leaves treated with 0.5 mM MeJA for 24 h replicate 3

description: Biological replicate 3 of 3.


title: Control of oscoi1a #2 leaves replicate 1

description: Biological replicate 1 of 3.

source_name: Control of oscoi1a #2 leaves

value: Control of oscoi1a #2 leaves


title: oscoi1b #2 leaves treated with 0.5 mM MeJA for 24 h replicate 1

description: Biological replicate 1 of 3.


title: oscoi1b #3 leaves treated with 0.5 mM MeJA for 24 h replicate 1

description: Biological replicate 1 of 3.


title: oscoi1b #3 leaves treated with 0.5 mM MeJA for 24 h replicate 2

description: Biological replicate 2 of 3.


title: Control of oscoi1a #2 leaves replicate 3

description: Biological replicate 3 of 3.


title: Control of oscoi1b #3 leaves replicate 2

description: Biological replicate 2 of 3.


title: Control of oscoi1b #2 leaves replicate 1

description: Biological replicate 1 of 3.


title: Control of oscoi1b #2 leaves replicate 2

description: Biological replicate 2 of 3.


title: oscoi1a #2 leaves treated with 0.5 mM MeJA for 24 h replicate 2

description: Biological replicate 2 of 3.


title: HP5

city: Hefei

first: Yanfeng

last: Xue

state: Anhui

address: Changjiang Western Road 130

institute: Anhui Agricultural University

description: HP

data_processing:
The inhouse perl script was used to remove low-quality reads.
HISAT2 was used to align the remaining clean reads to the Ovis aries reference genome (Oar v3.1).
Moreover, in order to estimate the expression of each gene transcript, the software StringTie (version 1.3.4d) was applied and the fragments per kilobase of transcript per million fragments mapped value of each gene was calculated.
Genome_build: Oar v3.1
Supplementary_files_format_and_content: Excel; The symbol, ID, and FPKM value for each gene

organism: Ovis aries

source_name: Ruminal epithelium

extract_protocol:
Frozen ruminal epithelium samples were used to extact RNA using Trizol method.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hu-Lamb

tag: Sex

value: Male


title: WT2

city: St. Louis

first: Lite

last: Yang

address: 4922 Parkview Place

institute: Washington University in St. Louis

data_processing:
Raw fastq files are prepared by demultiplexing Illumina Nextseq runs using v3 indrops python scripts (github/indrops).
All  subsequent processing steps from fastq files to count matrixes were performed using a custom pipeline for inDrops data analysis (github.com/indrops), using the default version 3 parameters.
inDrops.py first filters reads based on information present in read files 2,3, and 4, for presence of i) two cell barcode sequences, ii) unique molecular identifier, iii) Illumina libray index. inDrops.py demultiplexes by Illumina library index (read 3).  For read 3, the library indices provided to the indrop.py custom pipeline are given in the yaml files. Libraries called "not_included_in_study_*" were not included in the study, but their indexes should be specified when using the indrop.py pipeline for demultiplexing.
inDrops.py then trims Read 1 using Trimmomatic (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
inDrops.py then matches cell barcodes (revealed by Read 2 and 4) against a list of the pre-determined barcodes. The reads were then split into barcode-specific files for mapping and UMI filtering.
inDrops.py then aligns the reads using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 70 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.81 or GRCh38.85) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes). The reference index is assembled using inDrops.py as described in the manual.
inDrops.py performs UMI correction and returns gene expression counts of UMI-filtered transcripts per gene. Resulting raw count files are provided and called  *.counts.tsv.gz.
Assembly: mm10
Supplementary files format and content: Raw counts tables from each sample were then combined by their respective experiment into the raw counts files available in GEO

source_name: Dorsal root ganglia

extract_protocol:
Mouse dorsal root ganglia were dissociated into a single nuclei suspension as described in Renthal et al. 2020 and Yang et al. 2021. Briefly, tissue was dissociated by dounce homogenization and clarified by ultracentrifugation through a Optiprep gradient based on a protocol (Mo et al. Neuron 2015) and modified in Renthal et al. 2020.
inDrops libraries were constructued as described in Zilionis et al., Nat. Protoc. 2017.

tag: assay

value: inDrops

tag: condition

value: No disease

tag: days after tamoxifen injection


title: PID21_1

value: PID


title: PID42_1


title: PID42_2


title: HP4

description: HP


title: HP2

description: HP


title: HP1

description: HP


title: PID21_2


title: Control of oscoi1a #1 leaves replicate 2

description: Biological replicate 2 of 3.

source_name: Control of oscoi1a #1 leaves

value: Control of oscoi1a #1 leaves


title: WT1


title: Bladder 463 CIE 4 wk

city: Aurora

first: Anna

last: Malykhina

state: CO

institute: University of Colorado

hyb_protocol: Hybridization of RNA with NanoString reporter codeset were performed according to manufacturer's recommended protocol

scan_protocol: After hybridization, samples were loaded into the cartridge which is installed into the digital analyzer. Scanning commenced according to manufactuerere recommendation

data_processing: Data processing were done by using the Rosalind Platform: https://nanostring.rosalind.bio/

source_name: urinary bladder CIE 4 weeks

label_protocol: Nanostring does not use labeling procedures

growth_protocol: No growth protocol used, as our experiment involved mouse tissues.

extract_protocol: The lumbosacral (L6-S2) spinal cord (SC) segments and urinary bladders (UB) were collected during acute stage of infection (1 wk), and at the first peak of demyelination (4 wks) after inoculation with the virus. Isolated tissues were immediately placed on dry ice for freezing, and then stored at -80 C. Total RNA was isolated using the Qiagen RNeasy MINI kit (Qiagen, Clifton Hill, Victoria, Australia) according to the manufacturer's instructions. The amount of total RNA was quantified on the NanoDrop Microvolume Spectrophotometer (Thermo Scientific NanoDrop Products)

treatment_protocol: The mice received either a single intracranial injection of 20 µl sterile saline (N=6, control group) or mouse hepatitis virus (MHV, A59 strain, 6000 PFU, N=20, experimental group) in 20 µl sterile saline under isoflurane anesthesia. After inoculation with the virus, mice were monitored daily for evaluation of neurological symptom development by using clinical symptoms score (CSS) system and weighed every day up to 4 wks post-inoculation.

value: male

value: 12 weeks

value: urinary bladder

value: CIE 4 weeks


title: SC 463 CIE 4 wk

source_name: spinal cord CIE 4 weeks

value: spinal cord


title: Control of oscoi2 #1 leaves replicate 2

description: Biological replicate 2 of 3.


title: Bladder 459 CIE 1 wk

source_name: urinary bladder CIE 1 week

value: CIE 1 week


title: Bladder 455 CIE 4 wk


title: Control of oscoi1a #2 leaves replicate 2

description: Biological replicate 2 of 3.


title: oscoi1a #1 leaves treated with 0.5 mM MeJA for 24 h replicate 3

description: Biological replicate 3 of 3.


title: Control of oscoi1a #1 leaves replicate 1

description: Biological replicate 1 of 3.


title: Wild-type rice leaves treated with 0.5 mM MeJA for 24 h replicate 3

description: Biological replicate 3 of 3.


title: Control of wild-type rice leaves replicate 3

description: Biological replicate 3 of 3.

source_name: Control of wild-type rice leaves

value: Control of wild-type rice leaves


title: Wild-type rice leaves treated with 0.5 mM MeJA for 24 h replicate 1

description: Biological replicate 1 of 3.


title: oscoi1a #1 leaves treated with 0.5 mM MeJA for 24 h replicate 1

description: Biological replicate 1 of 3.


title: Wild-type rice leaves treated with 0.5 mM MeJA for 24 h replicate 2

description: Biological replicate 2 of 3.


title: HG2

description: HG


title: HP3

description: HP


title: HG4

description: HG


title: CON4

description: CON


title: CON5

description: CON


title: Control of wild-type rice leaves replicate 1

description: Biological replicate 1 of 3.


title: Control of oscoi1a #1 leaves replicate 3

description: Biological replicate 3 of 3.


title: Bladder 406 Control

source_name: urinary bladder control

value: control


title: SC 459 CIE 1 wk

source_name: spinal cord CIE 1 week


title: Bladder 401 Control


title: SC 401 Control

source_name: spinal cord control


title: CON3

description: CON


title: HG3

description: HG


title: Bladder 469 CIE 1 wk


title: SC 469 CIE 1 wk


title: CON2

description: CON


title: HG1

description: HG


title: SC 454 CIE 4 wk


title: Bladder 456 1 wk


title: oscoi1a #1 leaves treated with 0.5 mM MeJA for 24 h replicate 2

description: Biological replicate 2 of 3.


title: CON1

description: CON


title: Control of wild-type rice leaves replicate 2

description: Biological replicate 2 of 3.


title: SC 456 1 wk


title: SC 403 Control


title: Bladder 458 CIE 1 wk


title: Bladder 454 CIE 4 wk


title: SC 472 CIE 1 wk


title: Bladder 472 CIE 1 wk


title: Bladder 403 Control


title: Rsv_1

city: Seoul

first: Seon-Yeong

last: Lee

address: 222 banpo-daero, seocho-gu

department: Rheumatism research center

country: South Korea

institute: the catholic university

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)

source_name: C54BL/6 WT mouse, CD4 T cells, 20 μM Rosuvastatin withTh17 condition, 3day culture

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

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

value: spleen

value: CD4 T cells


title: SC 458 CIE 1 wk


title: Eze_1

label: biotin-labeled with TdT (terminal deoxynucleotidyl transferase)

source_name: C54BL/6 WT mouse, CD4 T cells, 20 μM Ezetimibe withTh17 condition, 3day culture


title: Rsv


title: Rsv_2


title: Eze


title: Th17_2

source_name: C54BL/6 WT mouse, CD4 T cells, Th17 condition, 3day culture


title: Rsv_3


title: Pcan12_R2

city: Göttingen

first: Victor

last: Chano

address: Buesgenweg 2

department: Forest Genetics and Forest Tree Breeding

country: Germany

institute: University of Göttingen

description: Pc12R2 (Cy3) vs Pc12CR2 (Cy5)

hyb_protocol: Probes were mixed and hybridized to a 60K custom microarray (Agilent Technologies) for 17 hours at 65ºC in Gex Hybridization Buffer HI-RPM in a hybridization oven. Arrays were washed according to the manufacturer’s instructions, dried by centrifugation

scan_protocol: Arrays were scanned at 3 mm resolution on Agilent DNA Microarrays Scanner (G2565BA, Agilent Technologies) and the images were analyzed with Feature Extraction software (Agilent Technologies).

data_processing: For local background correction and normalization, the methods normexp and loess in LIMMA were used, respectively (Smyth and Speed 2003).

organism: Pinus canariensis

source_name: Pc12R2: Newly formed resprouts, including phloematic and meristematic tissues surrounding

label_protocol: The Low Input Quick Amp Labeling Kit, Two-Color generates fluorescent cRNA (complimentary RNA) with 200 ng of total RNA for two-color processing. The method uses T7 RNA Polymerase Blend (red cap), which simultaneously amplifies target material and incorporates Cyanine 3-CTP or Cyanine 5-CTP.

growth_protocol: Pines were grown in greenhouse, using 650 ml conical containers with 3:1 (v/v) peat:vermiculite. After the first year, trees were transferred to soil in experimental garden at UPM facilities, and grown under environmental conditions. At the moment of the beginning of this experiment, trees were 5 years old, approximately 2 m high and 7-10 cm diameter at the base.

extract_protocol: Total RNA was isolated from differentiating xylem samples stored at -80ºC, using the CTAB-LiCl precipitation method (Chang et al. 1993), and purified with the RNeasy Plant Mini Kit (Qiagen, CA, USA). Quantity of total RNA for each sample was measured with Nanodrop model ND-1000 (Thermo Scientific, MA, USA), and RNA quality was checked using the Experion Bioanalyzer (Bio-Rad, CA, USA).

treatment_protocol: Resprouting induced by wounding in the stem. Control samples collected from remote branches, avoiding the local effect of wouding

value: Phloem (control)

tag: Stage

source_name: Pc12CR2: Phloematic tissue with no resprouts from remote parts of the plant, used as control


title: M-smegmatis-pVV16-rv1339-3

city: London

first: Gerald

last: Larrouy-Maumus

address: Exhibition Road

country: United Kingdom

institute: Imperial College London

description:
S6
Raw_counts_msmeg.csv
Raw_counts_mtb.csv

data_processing:
Illumina HiSeq4000 SAV software was used for base-calling.
Sequences were aligned using BWA v0.7.17-r1188 using the mc2-155 M. smegmatis reference genome with the parameters bwa mem -t 6
Sequences were aligned using BWA v0.7.17-r1188 using the H37Rv M. tuberculosis reference genome with the parameters bwa mem -t 6
Genes were counted using featureCounts v1.6.0 and the mc2-155 M. smegmatis annotation with the following parameters -s 2 -t gene -g Name -a
Genes were counted using featureCounts v1.6.0 and the H37Rv M. tuberculosis annotation with the following parameters -s 2 -t gene -g ID -a
Count matrices for each sample were combined into a single count matrix (Raw_counts_msmeg.csv or Raw_counts_mtb.csv, depending on the reference genome used). Genes were normalised using the estimateSizeFactors() function, followed by logging the data for visualisation purposes before raw counts were filtered to remove low counts then analysed using DESeq2.
Genome_build: GCF_000015005.1_ASM1500v1 and GCF_000195955.2_ASM19595v2
Supplementary_files_format_and_content: Comma-delimited files containing samples across the columns and genes across the rows. Values are raw counts. s1, s2 and s3 correspond to the empty vector controls, while s4, s5 and s6 correspond to the Rv1339 over-expressor strain. Raw_counts_msmeg.csv includes raw gene counts for alignment to M. smegmatis reference sequence. Raw_counts_mtb.csv includes raw gene counts for alignment to M. tuberculosis reference sequence.

organism: Mycolicibacterium smegmatis

source_name: M. smegmatis strain

growth_protocol: Mycobacteria were cultured up to mid-exponential phase in 7H9 liquid medium supplemented with 0.5 g/l Fraction V bovine serum albumin, 0.05% tyloxapol, 0.2% dextrose, 0.2% glycerol, and 10 mM NaCl.

extract_protocol:
Bacteria were to mid-log phase (light transmittance at 600 nm ~0.6), washed twice with cold PBS at +4°C. Total RNA was extracted according to the FastRNA Pro Blue kit manual (MP). To remove genomic DNA, the samples were treated once with RNase-free DNase (Promega) for 3 h at 37°C and purified using RNeasy columns (Qiagen) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.
RNA-Seq on Illumina HiSeq4000.

tag: genotype/variation

value: Rv1339 expressing strain


title: Eze_2

tag: cell type


title: Pcan1_R1

description: Pc1R1 (Cy3) vs Pc1CR1 (Cy5)

source_name: Pc1R1: Newly formed resprouts, including phloematic and meristematic tissues surrounding

source_name: Pc1CR1: Phloematic tissue with no resprouts from remote parts of the plant, used as control


title: Eze_3

tag: strain


title: Th0_2

source_name: C54BL/6 WT mouse, CD4 T cells, Th0 condition, 3day culture


title: Th0_3


title: Th17


title: Pcan9_R2

description: Pc9R2 (Cy5) vs Pc9CR2 (Cy3)

source_name: Pc9R2: Newly formed resprouts, including phloematic and meristematic tissues surrounding

source_name: Pc9CR2: Phloematic tissue with no resprouts from remote parts of the plant, used as control


title: Pcan1_R0

description: Pc1R0 (Cy3) vs Pc1CR0 (Cy5)

source_name: Pc1R0: Newly formed resprouts, including phloematic and meristematic tissues surrounding

source_name: Pc1CR0: Phloematic tissue with no resprouts from remote parts of the plant, used as control


title: Pcan12_R1

description: Pc12R1 (Cy3) vs Pc12CR1 (Cy5)

source_name: Pc12R1: Newly formed resprouts, including phloematic and meristematic tissues surrounding

source_name: Pc12CR1: Phloematic tissue with no resprouts from remote parts of the plant, used as control


title: M-smegmatis-pVV16-3

description:
S3
Raw_counts_msmeg.csv
Raw_counts_mtb.csv

value: Empty vector control


title: Bladder 402 Control

source_name: urinary bladder control

tag: treatment


title: Pcan12_R0

description: Pc12R0 (Cy3) vs Pc12CR0 (Cy5)

source_name: Pc12R0: Newly formed resprouts, including phloematic and meristematic tissues surrounding

source_name: Pc12CR0: Phloematic tissue with no resprouts from remote parts of the plant, used as control


title: Pcan9_R1

description: Pc9R1 (Cy5) vs Pc9CR1 (Cy3)

source_name: Pc9R1: Newly formed resprouts, including phloematic and meristematic tissues surrounding

source_name: Pc9CR1: Phloematic tissue with no resprouts from remote parts of the plant, used as control


title: SC 402 Control

source_name: spinal cord control


title: Pcan1_R2

description: Pc1R2 (Cy3) vs Pc1CR2 (Cy5)

source_name: Pc1R2: Newly formed resprouts, including phloematic and meristematic tissues surrounding

source_name: Pc1CR2: Phloematic tissue with no resprouts from remote parts of the plant, used as control


title: Th0


title: Th17_1

source_name: C54BL/6 WT mouse, CD4 T cells, Th17 condition, 3day culture


title: Th0_1


title: M-smegmatis-pVV16-1

description:
S1
Raw_counts_msmeg.csv
Raw_counts_mtb.csv

source_name: M. smegmatis strain


title: Pcan9_R0

description: Pc9R0 (Cy5) vs Pc9CR0 (Cy3)

source_name: Pc9R0: Newly formed resprouts, including phloematic and meristematic tissues surrounding

source_name: Pc9CR0: Phloematic tissue with no resprouts from remote parts of the plant, used as control


title: M-smegmatis-pVV16-rv1339-1

description:
S4
Raw_counts_msmeg.csv
Raw_counts_mtb.csv


title: ZBP1-/-::ADARp150/P195A Mouse 4

city: Seattle

first: Andrew

last: Oberst

state: WA

address: 750 Republican St.

department: Department of Immunology

institute: University of Washington

data_processing:
Reads were pseudo aligned using kallisto v0.46.2 to GRCm39 transcripts using default parameters.
Quality control was performed on raw reads using fastqc and then combined with aligned reads using multiqc.
Assembly: GRCm39
Supplementary files format and content: Kallisto pseudo-align abundance h5 files

source_name: Spleen

extract_protocol:
Total RNA was added directly to lysis buffer from the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara).
RNA libraries for RNA-seq were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries. Libraries were pooled and quantified using a Qubit Fluorometer (Life Technologies). Dual-index, single-read sequencing of pooled libraries was carried out on a HiSeq2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS kits (Illumina) with a target depth of 10 million reads per sample.

value: Spleen

value: M

tag: age (days)

tag: genotype


title: ZBP1-/-::ADARp150/P195A Mouse 5

value: F


title: P195A/p150- PKR-/- Mouse 3


title: P195A/p150- PKR-/- Mouse 2


title: ZBP1-/-::ADARp150/P195A Mouse 2


title: ZBP1-/-::ADARp150/P195A Mouse 3


title: M-smegmatis-pVV16-rv1339-2

description:
S5
Raw_counts_msmeg.csv
Raw_counts_mtb.csv


title: P195A/p150- Mouse 4


title: M-smegmatis-pVV16-2

description:
S2
Raw_counts_msmeg.csv
Raw_counts_mtb.csv


title: P195A/p150- Mouse 3


title: Test 2

city: Rochester

first: Tianle

last: Ma

state: MI

address: 115 Library Dr

institute: Oakland University

data_processing:
STAR v2.7.7a alignment followed by RSEM v1.3.3 expression quantification
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to GRCh38.p13 (GENCODE release 36) using STAR v2.7.7a using default parameters
Read count extraction and normalization were performed using RSEM v1.3.3
Assembly: GRCh38.p13 (GENCODE release 36)
Supplementary files format and content: tab-delimited text files include expected count, TPM, RPKM values for each Sample

source_name: H1 and H9 human ES cells

growth_protocol: H1 and H9 human embryonic stem cells were cultured on Matrigel coated tissue culture plates with StemFlex Medium and maintained in cell culture incubators with high humidity and 5% CO2 at 37°C

extract_protocol:
RNA was harvested using the TruSeq Stranded mRNA LT Sample Prep Kit and >500 ng total RNA for the construction of sequencing library
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA-Seq Library preparation kit following manufacturer's protocol

treatment_protocol: Control groups were cultured under normal gravity whereas the test groups were exposed to simulated microgravity

tag: cell line

value: H1 and H9 human ES cells

value: Pluripotent stem cells

value: expesed to near zero gravity (microgravity)


title: P195A/p150- PKR-/- Mouse 4


title: ZBP1-/-::ADARp150/P195A Mouse 1


title: P195A/p150- Mouse 1


title: Test 3

value: exposed to near zero gravity (microgravity)


title: WT (B6/J) Mouse 3

value: WT


title: FP1_GEX

city: New York

first: Daylon

last: James

address: 515 East 71st

institute: Weill Cornell Medicine

library_source: transcriptomic single cell

data_processing:
fastq files were processed using CellRangr count and individual libraries were aggregated using CellRangr aggr
Resultant features/barcodes file was imported into R Studio and used to generate a Seurat Object in Seurat
Assembly: GRCh38
Supplementary files format and content: filtered feature matrix and barcodes

source_name: human antral follicle derived cells

growth_protocol: cells were isolated from primary patient derived ovarian follicles

extract_protocol:
cells were enzymatically separated and sorted by fluorescence activated cell sorting
RNA libraries were prepared for sequencing using version 3 10x Chromium library preparation kits

value: granulosa and stroma cells

tag: source

value: ovarian antral follicle

tag: follicle size

value: 3 mm


title: P195A/p150- PKR-/- Mouse 1


title: FP1_ATAC


title: Pt1_1

value: stromal cells


title: Control 1

value: exposed to normal gravity


title: WT (B6/J) Mouse 1


type: protein

city: Ulsan

first: Sook-Kyoung

last: Heo

address: 877 Bangeojinsunhwan-doro

department: Biomedical Research Center

institute: University of Ulsan College of Medicine

description: Cytokine Profiling Antibody Array (Fullmoon biosystems, Sunnyvale, CA)

hyb_protocol: The labeled sample was mixed in 6 ml of coupling solution. The blocked array slide was incubated with coupling mixture on shaker at 60 rpm for 2 hours at room temperature into  coupling dish. After coupling, the slide was washed 6 times with 30 ml of washing solution into petri dish on shaker at 60 rpm for 5 minutes. And the slide rinsed with Milli-Q grade.  The 30 ul of 0.5 mg/ml Cy3-streptavidin (GE Healthcare, Chalfont St. Giles, UK) was mixed in 30 ml of detection buffer. The coupled array slide was treated with detection mixture into petri  dish on shaker at 60 rpm for 20 minutes at room temperature. After detecting, the slide was washed 6 times with 30 ml of washing solution into petri dish on shaker at 60 rpm for 5 minutes.  And the slide rinsed with Milli-Q grade wate.

scan_protocol: The slide scanning was performed using GenePix 4100A scanner (Axon Instrument, USA).  The slides were absolutely dried before the scanning and scanned within 24-48 hours. The slides   were scanned at 10 um resolution, optimal laser power and PMT.

data_processing: After got the scan image, they were grided and quantified with GenePix 7.0 Software (Axon Instrument, USA).

molecule: protein

source_name: Plasma in patients with acute acute myeloid leukemia without aGVHD

label_protocol: The 50 ug of protein sample was filled up 75 ul with labeling buffer and treated 3 ul of the 10  ug/ul biotin/DMF solution.

growth_protocol: Plasma in patients with AML with aGVHD vs Plasma in patients with AML without aGVHD

extract_protocol: The protein was extracted by using protein extraction buffer (Fullmoon biosystems, Sunnyvale, CA). After extraction, the protein solution was purified using gel matrix column that was  included in antibody array assay kit (Fullmoon biosystems, Sunnyvale, CA). Debris was removed from tissue extract with centrifuge.

tag: sample type

value: Plasma from blood


title: Test 1


title: Control 3


title: Heart_T6V_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Heart

growth_protocol: 12hr/12hr light dark cycle, fed with normal chow diet

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: daily treated with vehicle or SR9009

tag: tissue

value: Heart

value: TAC 6 week+Vehicle


title: Adult, uninjured, rep2_4

city: Boulder

first: Jesse

last: Kurland

address: 1945 Colorado Ave

department: MCDB

institute: University of Colorado Boulder

description: cellular RNA

data_processing:
paired-end fastq files from the Illumina NovaSeq 6000
FastQC (v0.11.8) was used for initial quality control of Fastq files
transcript reads were mapped with the CellRanger Software Suite (10x Genomics, v3.0.1) using a  mm10 reference package
Assembly: mm10
Supplementary files format and content: raw_bc_matrix files from cellranger count

source_name: tibialis anterior muscle

growth_protocol: Mice were bred and housed according to National Institutes of Health (NIH) guidelines for the ethical treatment of animals in a pathogen-free facility at the University of Colorado at Boulder. University of Colorado Institutional Animal Care and Use Committee (IACUC) approved animal protocols and procedures.

extract_protocol:
TA muscles were dissected and placed into 400U/mL collagenase at 37°C for 1h with shaking and then placed into Ham’s F-12C supplemented with 15% horse serum to inactivate the collagenase. Cells were passed through three strainers of 100µm, 70µm, and 40µm (BD Falcon) and flow through was centrifuged at 1500×g for 5 min and the cell pellets were re-suspended in Ham’s F-12C. To remove dead cells and debris, cells were passed over the Miltenyi, dead cell removal kit columns (Cat# 130-090-101). To remove red blood cells (RBC), cells were incubated with antiTer119 micro magnetic beads and passed over a Miltenyi column (Cat#130-049-901). For the adult and aged uninjured TAs, 6 TA muscles (from 3 mice) were pooled together. For the injured TA muscles 2 TA muscles from 2 different mice were pooled together. Cells were then counted using a BioRad TC20 automated cell counter and processed with the 10X genomics single cell sequencing kit.
To capture, label, and generate transcriptome libraries of individual cells we used the 10X genomics Chromium Single Cell 3’ Library and Gel Bead Kit v2 (Cat #PN-120237) following the manufactures protocols.

treatment_protocol: Mice were anesthetized with isoflurane followed by injection with 50μl of 1.2% BaCl2 in normal saline into the TA and EDL muscles.

value: tibialis anterior muscle

tag: age

value: 3-4 months old

value: male

value: Wild type

value: Uninjured

value: mononuclear cell


title: Plasma in patients with AML with aGVHD

source_name: Plasma in patients with acute acute myeloid leukemia with aGVHD


title: P195A/p150- Mouse 2

value: Spleen

tag: Sex

value: M


title: Heart_T6V_2


title: WT (B6/J) Mouse 4

value: F

value: WT


title: HG5

description: HG

source_name: Ruminal epithelium

value: Hu-Lamb

value: Male


title: Control 2

value: H1 and H9 human ES cells

value: Pluripotent stem cells


title: Adult, uninjured, rep2_3

description: cellular RNA


title: Don1_6-11

value: granulosa and stroma cells

value: ovarian antral follicle


title: Heart_T1S_4

value: Heart

value: TAC 1 week+SR9009


title: Heart_T1S_3


title: Omicron_66_1st

city: Bethesda

first: Hye Kyung

state: MD

address: 8 CENTER DR RM 107

department: National Institute of Diabetes and Digestive and Kidney (NIDDK)

institute: National Institutes of Health (NIH)

data_processing:
RNA-seq data were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) and subsequently aligned to the reference genome hg19 applying STAR RNA-seq aligner (Dobin et al., Bioinformatics, 2013). HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
HTSeq(Anders et al., Bioinformatics, 2015) was applied for obtain HTSeq counts.
Trimmed RNA-seq data were aligned to the human V, D and J genes and obtained immune clonotypes using MiXCR (Bolotin et al., Nat Methods, 2015; Bolotin et al., Nat Biotechnol, 2017).
Assembly: hg19
Supplementary files format and content: HTSeq counts from RNA-seq samples

source_name: PBMCs

growth_protocol: Blood samples were collected from the COVID-19 patients infected by Omicron varient.

extract_protocol:
The buffy coat was extracted by centrifuge after blood sample collection and RBC was removed using RBC lysis buffer in the buffy coat. Total RNA was isolated using a Maxwell RSC simply RNA Blood purification kit.
Libraries for sequencing were prepared with TruSeq Stranded mRNA Kit following standard Illumina protocols.

tag: gender

value: Female

tag: group (by covid-19 vaccination, prior infection)

value: No vaccination, No prior infection

tag: omicron sublineage

tag: days after positive pcr results

value: day 0

tag: disease state

tag: geographical location

value: Austria

value: PBMC


title: Heart_T6S_3

tag: strain

value: TAC 6 week+SR9009


title: Omicron_70_1st

value: No vaccination, Prior infection

value: day 2

tag: cell type


title: Omicron_67_1st

value: day 3


title: Heart_T1S_2

tag: treatment


title: Omicron_68_1st


title: Heart_T6S_2


title: Heart_T6S_1


title: Omicron_65_1st

value: Vaccination, No prior infection

value: day 1


title: WT (B6/J) Mouse 2

value: Spleen

value: M

tag: age (days)

tag: genotype

value: WT


title: Heart_T6V_1

value: TAC 6 week+Vehicle


title: Heart_T1S_1

value: Heart


title: Adult, uninjured, rep2_1

description: cellular RNA

value: tibialis anterior muscle

value: 3-4 months old

value: male

value: Wild type

value: Uninjured

value: mononuclear cell


title: Biological Replicate 2 T47D Y537S DMSO

city: Madison

first: Kristine

last: Donahue

state: WI

address: 1111 Highland Ave.

institute: University of Wisconsin

data_processing:
Reads were aligned using RNA star to the GRCh38 genome assembly
Read counts were performed using HTSeq Count
Assembly: GRCh38.p10

source_name: breast

growth_protocol: T47D Y537S cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) 1% penicillin and streptomycin 1% HEPES, 1% L-glutamine, 1% sodium pyruvate in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was isolated using the Omega E.N.Z.A total RNA extraction kit, and performed according to the manufacturer's instructions
RNA libraries were prepared using the Illumina TruSeq RNA library prep kit following the manufacturer's instructions

treatment_protocol: Once cells reached 80% confluency, they were washed with phosphate buffered saline and hormone starved for 24 hours in phenol red-free RPMI supplemented with 5% charcoal-stripped FBS. Then, cells were treated with either DMSO or 10 μM diptoindonesin G for 24 hours.

value: breast

tag: cell line

value: epithelial cells

value: DMSO


title: Biological Replicate 2 T47D Y537S DIPG

value: 10 μM diptoindonesin G


title: Omicron_53_1st

value: Female

value: No vaccination, No prior infection

value: day 2

value: Austria

value: PBMC


title: Heart_T1V_4

value: TAC 1 week+Vehicle


title: Adult, uninjured, rep1_2

description: cellular RNA


title: Biological Replicate 1 T47D Y537S DMSO


title: Biological Replicate 1 T47D Y537S DIPG


title: Adult, uninjured, rep1_4

description: cellular RNA


title: Omicron_52_1st

value: Vaccination, Prior infection

value: day 5


title: Adult, uninjured, rep1_3

description: cellular RNA

value: tibialis anterior muscle

value: 3-4 months old


title: Adult, uninjured, rep1_1

description: cellular RNA

value: male

value: Wild type


title: Adult, 7 days post-injury rep2_4

description: cellular RNA

value: 7 days post-injury

value: mononuclear cell


title: Adult, uninjured, rep2_2

description: cellular RNA

value: Uninjured


title: Th17_3

value: spleen

value: CD4 T cells


title: WT

city: Philadelphia

first: Ting

last: Li

address: 422 Curie Blvd.

institute: University of Pennsylvania

description: 10x Genomics

data_processing:
Alignment of 3′ end counting libraries from scRNAseq analyses was completed using 10x Genomics Cell Ranger. The “Cell Ranger Aggr” function was used to normalize the number of confidently mapped reads per cell across the two libraries.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
To obtain tumor-infiltrating cells, tumors were digested in RPMI 1640 (Gibco) supplemented with 0.5 mg/ml collagenase type IV (Gibco) and 0.1 mg/ml DNase I (Sigma-Aldrich) for 20 min at 37°C. Tumors were then treated with Percoll(GE Healthcare Lifesciences, 17089101) and immune cells were isolated for flow cytometry and sorting. FACS-isolated CD45+ cells from the 5 pooled tumors from WT (LysM-cre x Rel+/+) or myeloid Rel knockout mice (LysM-cre x RelloxP/loxP) were washed once in PBS (calcium- and magnesium-free) containing 0.04% BSA and resuspended to a concentration of 700-1200 cells/ul.
The DNA libraries were prepared using the Chromium Single Cell 3′ Reagents Kits and 10x Genomics Chromium platform for droplet-enabled scRNAseq according to the manufacturer’s instructions. Each library was sequenced on the Illumina HiSeq 4000 platform to achieve an average of 10000 reads per cell.

value: tumor

value: introtumor viable CD45+ cells

value: LysM-cre x Rel+/+

value: tissue digestion and FACS sorting


title: Heart_T1V_3

value: Heart


title: Omicron_51_1st

value: Female

value: No vaccination, Prior infection

value: day 1

value: Austria

value: PBMC


title: Heart_T1V_2

value: TAC 1 week+Vehicle


title: Omicron_55_1st

value: No vaccination, No prior infection

value: day 2


title: Omicron_48_1st


title: Omicron_50_1st


title: Adult, 7 days post-injury rep2_2

description: cellular RNA

value: tibialis anterior muscle

value: 3-4 months old

value: male

value: Wild type

value: 7 days post-injury

value: mononuclear cell


title: Omicron_49_1st

value: day 0


title: Heart_Control_2

value: Control


title: RIF_B11

city: La Jolla

first: Igor

last: Segota

address: 9500 Gilman Drive

institute: University of California, San Diego

description: degradation rate experiment for C-limitation

data_processing:
Demultiplexed reads were trimmed for adapter sequences using Cutadapt (DOI:10.14806/ej.17.1.200 )
Reads were aligned to the E.coli MG1655 U00096.3 genome using bowtie v2.2.6
Read counts were obtained using Python HTSeq-count (HTSeq v0.6.1p2)
Assembly: E.coli MG1655 U00096.3
Supplementary files format and content: Excel workbook with data presented as fractional mRNA abundance for each gene. The column headers correspond to the sample title.

organism: Escherichia coli K-12

growth_protocol: Description of media composition is found in the supplementary information of the associated manuscript as well as in the description tabs of the processed data files

extract_protocol:
Cells were pelleted and RNA was extracted using the TRIzol method
rRNA was removed using Ribo-Zero and libraries were constructed using the TruSeq kit (Illumina)

tag: supplement added


title: Heart_T1V_1

value: Heart


title: RIF_B9


title: Heart_Control_1


title: Adult, 7 days post-injury rep2_1

description: cellular RNA


title: RIF_B5


title: Adult, 7 days post-injury rep1_4

description: cellular RNA


title: Adult, 7 days post-injury rep2_3

description: cellular RNA


title: RIF_B7


title: Omicron_43_1st

value: Female


title: Myeloid specific c-Rel KO

description: 10x Genomics

value: tumor

value: introtumor viable CD45+ cells

value: LysM-cre x RelloxP/loxP

value: tissue digestion and FACS sorting


title: WT_ZT22_3

description: 8-week old

treatment_protocol: Reverb fl/fl and  Reverb fl/fl /MHC+

value: WT


title: RIF_B3


title: Omicron_38_1st

value: No vaccination, No prior infection

value: day 4

value: Austria

value: PBMC


title: Adult, 7 days post-injury rep1_2

description: cellular RNA

value: tibialis anterior muscle

value: 3-4 months old

value: male


title: Heart_Control_3


title: Adult, 7 days post-injury rep1_3

description: cellular RNA

value: Wild type

value: 7 days post-injury

value: mononuclear cell


title: Adult, 7 days post-injury rep1_1

description: cellular RNA


title: WT_ZT22_2

description: 8-week old

value: Heart


title: WT_ZT18_3

description: 8-week old


title: Omicron_42_1st

value: Male

value: No vaccination, Prior infection

value: day 3


title: WT_ZT18_2

description: 8-week old


title: Omicron_37_1st

value: day 5


title: RIF_B1


title: WT_ZT22_1

description: 8-week old


title: WT_ZT18_1

description: 8-week old


title: Omicron_33_1st

value: day 2


title: Omicron_35_1st

value: Female


title: Omicron_31_1st

value: No vaccination, No prior infection

value: day 1


title: RIF_A9

description: degradation rate experiment for reference growth


title: RIF_A7


title: RIF_B0


title: Adult, 4 days post-injury rep2_4

description: cellular RNA

value: 4 days post-injury


title: WT_ZT14_3

description: 8-week old

value: WT


title: Adult, 4 days post-injury rep2_1

description: cellular RNA

value: tibialis anterior muscle


title: RIF_B2


title: Adult, 4 days post-injury rep2_3

description: cellular RNA

value: 3-4 months old


title: Adult, 4 days post-injury rep2_2

description: cellular RNA

value: male


title: RIF_A11


title: Adult, 4 days post-injury rep1_4

description: cellular RNA

value: Wild type


title: Omicron_34_1st

value: day 0

value: Austria

value: PBMC


title: WT_ZT14_1

description: 8-week old

value: Heart


title: Omicron_28_1st

value: Male


title: RIF_A5


title: Adult, 4 days post-injury rep1_3

description: cellular RNA

value: mononuclear cell


title: RIF_A3


title: Omicron_27_1st


title: WT_ZT10_3

description: 8-week old


title: WT_ZT10_1

description: 8-week old


title: Adult, 4 days post-injury rep1_2

description: cellular RNA


title: Omicron_26_1st


title: RIF_A1


title: RIF_A2


title: Omicron_25_1st


title: Omicron_30_1st


title: WT_ZT10_2

description: 8-week old


title: RIF_A0


title: Adult, 4 days post-injury rep1_1

description: cellular RNA


title: Omicron_29_1st

value: day 4


title: WT_ZT14_2

description: 8-week old


title: bone marrow,HFD and Exercise,rep2

city: Shanghai

first: Jinwen

last: Luan

address: No. 200, Hengren Road

institute: Shanghai University of Sport

data_processing:
The quality of all libraries was assessed using FastQC   (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Reads with a poor sequencing qualities, together with the adapter sequences were then removed using fastp with default configurations.
The reads from rRNA species were removed by filtering reads with mappability to the rRNA sequences. Cleaned reads were then mapped to mouse genome GRCm38 using HiSAT2.
Coordinately aligned reads were filtered out using SAMtools.
Gene expression levels were quantified using the stringtie with Gencode vM25 annotation together with reads counts in each gene.
Differential expression analysis was then performed by DESeq2 package.
Assembly: GRCm38
Supplementary files format and content: tab-delimited ctab files include FPKM values for each Sample

source_name: bone marrow

growth_protocol: 8-week male C57/B6 mice were fed with HFD to establish an obese mice model

extract_protocol:
Tissue was homogenized with an RNase-free disposable pellet pestle (Fisher) and RNA was extracted using the commercially available RNeasy Lipid Tissue Mini Kit (Qiagen, Valencia, CA). Purification of the isolated RNA included treatment with DNase I (Qiagen, Valencia, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Total mice were randomly divided into 2 groups: the exercise and the control groups. The exercise group of mice was put on a moderate-intensity treadmill running for 12 weeks

value: bone marrow

value: mesenchymal stem cells

value: fibroblast

value: HFD feeding and Exercise


title: WT_ZT6_3

description: 8-week old


title: r4_1

description: Biological replicate of sample r4

value: 8 µM chloramphenicol


title: Omicron_24_1st

value: Female

value: No vaccination, No prior infection

value: day 2


title: bone marrow,HFD and Exercise,rep1


title: r2_1

description: Biological replicate of sample r2

value: 4 µM chloramphenicol


title: WT_ZT6_2

description: 8-week old

value: WT


title: Omicron_19_1st

value: Vaccination, No prior infection


title: WT_ZT2_3

description: 8-week old


title: Omicron_20_1st

value: day 1

value: Austria


title: r3_1

description: Biological replicate of sample r3

value: 6 µM chloramphenicol


title: WT_ZT6_1

description: 8-week old

value: Heart


title: r0_1

description: Biological replicate of sample r0


title: r1_1

description: Biological replicate of sample r1

value: 2 µM chloramphenicol


title: bone marrow,HFD,rep2

value: HFD feeding


title: Omicron_16_1st

value: Male

value: PBMC


title: Omicron_17_1st


title: WT_ZT2_2

description: 8-week old


title: bone marrow,HFD,rep1

value: bone marrow

value: mesenchymal stem cells

value: fibroblast


title: WT_ZT2_1

description: 8-week old


title: A005

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

description:
asthma patient
26

data_processing:
Data were analyzed in excel using Ct values for each sample,  normalized to global means, and fold changes were calculated using the 2-ΔΔCT method.
Matrix normalized template shows miRNA Ct values normalized to global mean ΔCt = (Ct_miRNA − Ct_global mean)
For fold change calculations, ΔΔCt based fold-change values were obtained using an average of control sample Ct values (2^-ΔΔCt, where -ΔΔCt = -[ΔCtsample -ΔCtavgcontrol])). A fold change of 50 was considered as cutoff.
Matrix non-normalized are raw Ct values. Matrix normalized are normalized to the global mean. Fold changes are calculated with the livak method (2^-ΔΔCt, where -ΔΔCt = -[ΔCttest -ΔCtcontrol])

label: SYBR Green

source_name: exhaled breath condensate

label_protocol: Small RNAs were retro-transcribed from 200 ng of total RNA using the miScript II RT kit (Qiagen). The expression of 1066 human miRNAs was assayed with the Human miRNome miScript® miRNA PCR Array (QIAGEN, MIHS-3216Z).

extract_protocol: MicroRNAs were purified from 0.5 mL of TAs with the Plasma/Serum RNA Purification Kit (Norgen Biotek Corp., Thorold, ON, Canada).

treatment_protocol: Tracheal aspirates were obtained from control patients (no lung disease, no prematurity), and premature patients with Bronchopulmonary dysplasia. Total RNA was purified from TAs and the expression of 1066 human miRNAs was detected with a PCR array.

value: exhaled breath condensate

tag: scd

value: no

tag: scd+asthma

tag: control

tag: asthma

value: yes


title: r5

description: Cloramphenicol (translational) inhibition

value: 9 µM chloramphenicol


title: KO_ZT22_3

city: Hefei

first: Yanfeng

institute: Anhui Agricultural University

description: 8-week old

tag: tissue

value: KO


title: Omicron_15_1st

tag: gender

value: Female

tag: age

tag: group (by covid-19 vaccination, prior infection)

value: Vaccination, No prior infection

value: day 3


title: A003

description:
asthma patient
25


title: KO_ZT22_2

description: 8-week old


title: r4

value: 8 µM chloramphenicol


title: A002

description:
asthma patient
24


title: Omicron_14_1st

tag: omicron sublineage

tag: days after positive pcr results

value: day 2

tag: disease state

value: Austria


title: r3

tag: strain

value: 6 µM chloramphenicol


title: r2

value: 4 µM chloramphenicol


title: A001

description:
Healthy control patient, no lung disease
23


title: Omicron_13_1st

value: Male

value: No vaccination, Prior infection

tag: geographical location

tag: cell type

value: PBMC


title: KO_ZT22_1

description: 8-week old

value: Heart

tag: genotype


title: Omicron_18_1st


title: C010

description:
Healthy control patient, no lung disease
22

value: exhaled breath condensate


title: r1

value: 2 µM chloramphenicol


title: C008

description:
Healthy control patient, no lung disease
21

value: no

value: yes


title: Omicron_12_1st


title: r0

description: NCM3722 (wild type) in MOPS medium


title: KO_ZT18_3

description: 8-week old

value: KO


title: Omicron_11_1st

value: Female

value: day 0


title: KO_ZT18_2

description: 8-week old


title: C007

description:
Healthy control patient, no lung disease
20


title: a4_1

description: Biological replicate of sample a4

value: 20 µM IPTG


title: C006

description:
Healthy control patient, no lung disease
19


title: KO_ZT18_1

description: 8-week old


title: KO_ZT14_3

description: 8-week old


title: Omicron_10_1st

value: Vaccination, No prior infection


title: KO_ZT14_1

description: 8-week old


title: C005

description:
Healthy control patient, no lung disease
18


title: a2_1

description: Biological replicate of sample a2

value: 40 µM IPTG


title: KO_ZT14_2

description: 8-week old


title: Omicron_9_1st

value: day 3

value: Austria


title: Omicron_8_1st

value: day 2


title: a1_1

description: Biological replicate of sample a1

value: 60 µM IPTG


title: Omicron_7_1st

value: Male


title: C004

description:
Healthy control patient, no lung disease
17


title: KO_ZT10_3

description: 8-week old


title: Omicron_6_1st

value: PBMC


title: KO_ZT10_2

description: 8-week old

value: Heart


title: C003

description:
Healthy control patient, no lung disease
16

value: exhaled breath condensate


title: a4

description: Titratable ammonia assimilation (Plac-GOGAT)


title: C002

description:
Healthy control patient, no lung disease
15


title: Omicron_5_1st


title: C001

description:
Healthy control patient, no lung disease
14


title: a3

value: 28 µM IPTG


title: Omicron_4_1st


title: KO_ZT10_1

description: 8-week old


title: a3_1

description: Biological replicate of sample a3

value: 30 µM IPTG


title: a2


title: KO_ZT6_3

description: 8-week old


title: SA003

description:
Sickle cell + asthma patient
12

value: no

value: yes


title: SA004

description:
Sickle cell + asthma patient
13


title: a1


title: Omicron_2_1st


title: Omicron_3_1st

value: Female


title: KO_ZT6_2

description: 8-week old

value: KO


title: c3_1

description: Biological replicate of sample c3

value: 400 µM 3MBA


title: c4_1

description: Biological replicate of sample c4

value: 40 µM 3MBA


title: Omicron_1_1st

value: Vaccination, No prior infection

value: day 0


title: KO_ZT2_3

description: 8-week old


title: KO_ZT6_1

description: 8-week old


title: Naive_30_Day0

value: Healthy control

value: Austria


title: KO_ZT2_2

description: 8-week old


title: Naive_29_Day0


title: SA001

description:
Sickle cell + asthma patient
10


title: S008

description:
Sickle cell patient
8


title: c4

description: Titratable glucose uptake (Pu-ptsG)


title: S009

description:
Sickle cell patient
9


title: KO_ZT2_1

description: 8-week old


title: c0_1

description: Biological replicate of sample c5


title: Naive_28_Day0


title: c1_1

description: Biological replicate of sample c1

value: 300 µM 3MBA


title: SA002

description:
Sickle cell + asthma patient
11


title: Naive_26_Day0


title: c3

description: Titratable glucose uptake (Pu-ptsG)


title: Naive_27_Day0


title: c2

description: Titratable glucose uptake (Pu-ptsG)


title: S007

description:
Sickle cell patient
7


title: S006

description:
Sickle cell patient
6


title: S005

description:
Sickle cell patient
5


title: Naive_24_Day0


title: c2_1

description: Biological replicate of sample c2


title: Naive_17_Day0

value: Male


title: S004

description:
Sickle cell patient
4


title: Naive_18_Day0

value: PBMC


title: c1

description: Titratable glucose uptake (Pu-ptsG)


title: S002

description:
Sickle cell patient
2


title: Aortic smooth muscle cell KOmir21_12week_rep2

status: Public on Jun 10 2022

city: New Haven

first: Rolando

last: Garcia-Milian

state: CT

address: 333 Cedar St

department: CWML

institute: Yale University

data_processing:
Aligner used STAR v2.6 against mouse reference genome mm10
Quantification and annotation using Ensembl Transcripts release 91
DESeq2 normalization and differential expression
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Aortic smooth muscle cell

extract_protocol:
Cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Aorta

value: 12-weeks old

value: smooth muscle cell

tag: group


title: Aortic smooth muscle cell KOmir21_12week_rep3


title: Aortic smooth muscle cell WT_12week_rep3

value: WT/mTmG/ Myh11ERT2

value: control


title: Aortic smooth muscle cell KOmir21_12week_rep1


title: S003

description:
Sickle cell patient
3

value: exhaled breath condensate

value: yes

value: no


title: Aortic smooth muscle cell WT_12week_rep2


title: S001

description:
Sickle cell patient
1


title: Aortic smooth muscle cell KOmir21 rep1

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

value: 30-weeks old


title: Aortic smooth muscle cell KOmir21 rep2


title: Aortic smooth muscle cell WT rep2

value: WT


title: Aortic smooth muscle cell KOmir21 rep 3


title: Aortic smooth muscle cell WT rep1


title: Aortic smooth muscle cell WT_12week_rep1


title: KM63_2208L_3day_nt_CP-2133

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

data_processing:
Illumina Sequencing
FastQ files aligned using the STAR Aligner
Count data generated using Salmon
described in Hollern et al. 2019 Nov 14;179(5):1191-1206.e21.  doi: 10.1016/j.cell.2019.10.028.
Upper Quartile Normalization
Genome_build: Mm10
Supplementary_files_format_and_content: Data was normalized as described in Hollern et al. 2019 Nov 14;179(5):1191-1206.e21.

source_name: Mouse mammary tumor

growth_protocol: In Vivo- Murine

extract_protocol:
Total RNA isolated using Qiagen RNeasy Kit
Libraries for mRNA-seq were made using total RNA and the Illumina TruSeq mRNA sample preparation kit. This system uses Oligo-dT beads to capture polyA tails.

value: mouse mammary tumor

value: Balbc


title: KM58_2208L_3day_nt_CP-2130


title: KM59_2208L_3day_nt_CP-2131


title: DH659_2208L_PBS_CP-2028


title: DH662_2208L_PBS_CP-2027


title: DH678_2208L_pbs_CP-2032


title: c5

description: NCM3722 (wild type) in M9 medium

tag: supplement added


title: 2225L-T-Vivo_CP-3055


title: 2225L_ROSEN-3


title: 2208L_ROSEN-12


title: 2151R-53ca_CP-3502


title: 2151R-5310_CP-3501


title: BalbCp53null-T-11_CP-2205


title: 2151R-NT2_CP-3500


title: Aortic smooth muscle cell WT rep3


title: SCC3-ChIP-biological replicate 2

city: shanghai

first: Yu

last: Zhang

address: DongChuan Road No. 800

institute: Shanghai Jiaotong University

data_processing:
Low-quality and adapter sequences were trimmed from the reads using cutadapt (v1.18) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20, 20.
Then, the reads were mapped to the Arabidopsis thaliana TAIR10 genome using Bowtie2 (v2.3.4.3) with parameters: -N 0 --no-discordant --no-mixed --no-unal.
Samtools (v1.9) was used to transfer the mapping results from sam format to position sorted bam format.
Next, the duplicated reads were removed by markdup from sambamba (v0.6.8).
Bam files were then converted to bigwig files using bamCoverage from the deeptools suite (v3.1.3) with parameters: --normalize using RPKM --binSize 25.
Assembly: TAIR10
Supplementary files format and content: bigWig(bigWig is the binary version of WIG or bedGraph. BigWig stores interval axis information. And correlation score (SCORE), mainly used to view continuous density maps of data in the Genome Browser)

organism: Arabidopsis thaliana

source_name: the 7-day-old whole seedlings

growth_protocol: Plants were grown at 21℃ on MS agar plates supplemented with 1.5% sucrose and 0.8% agar.

extract_protocol:
Briefly, 10 g fresh 7-day-old whole seedlings were cross-linked in the cross-link buffer (0.4 M sucrose, 10m M Tris-HCl (pH8.0), 1m M PMSF, 1 m M EDTA, 1% formaldehyde) for 3×5min using vacuum infiltration and the reaction was terminated in 2 M glycine.
After reverse cross-link, DNA was extracted by phenol-chloroform method and sheared to an average size of 300 bp using a sonicator.Sequencing library was constructed according to the standard Illumina protocol.First,the end was supplemented, adenine was added in the 3 'segment, and then PCR amplification technology was used to build the library.

value: the 7-day-old whole seedlings

tag: chip antibody

value: anti-CSCC3(Abclonal #WG-02026D)


title: SCC3-ChIP-biological replicate 1


title: SYN4-ChIP-biological replicate 2

value: anti-GFP (Abcam #ab290)


title: SYN4-ChIP-biological replicate 1


title: DH677_2208L_pbs_CP-2031


title: P10 [INHIBITOR 2]

city: Lausanne

first: Mustafa

middle: Bilal

last: Bayazit

address: Rue du Bugnon 9

country: Switzerland

institute: University of Lausanne

description: Pancreatic islets from p10 rats

data_processing:
To determine transcript expression levels, reads were mapped to the rat transcriptome (ENSEMBL 92, rn6) using STAR (2.5.3a) and quantified with RSEM (1.3.0).
To identify differentially expressed genes, reads were mapped to the rat genome (rn6) using HISAT (2.1.0) and gene counts for rat genes (ENSEMBL 92, rn6) estimated using HTseq.
Genome_build: rn6
Supplementary_files_format_and_content: xlsx file that contains processed data from the RNA-Seq, RPKM values, gene names, and statistical comparisons.

organism: Rattus norvegicus

source_name: Pancreatic islet cells

growth_protocol: Pancreatic islets were isolated by collagenase digestion (Gotoh M et al., Transplantation, 1987) and Histopaque density gradient. Thereafter, islets were dissociated into single cells with trypsin-EDTA (Gibco) and cultured in RPMI 1640 GlutaMAX medium (Gibco) supplemented with 10% fetal bovine serum (Gibco), 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco), 1 mM sodium pyruvate (Sigma), and 10 mM Hepes (Sigma). Transfection was conducted using Lipofectamine 2000 with LNA inhibitor against either scrambled control or tiRNA-5HisGTG/GluCTC/GluTTC

extract_protocol: Total RNA was extracted with the miRNeasy micro kit (Qiagen).

value: Sprague Dawley

tag: agent

value: 20 pmol tiRNA-5 LNA inhibitor (HisGTG/GluCTC/GluTTC) - Total 60 pmol

value: Pancreatic islet cells


title: P10 [INHIBITOR 4]

description: Pancreatic islets from p10 rats


title: P10 [INHIBITOR 3]

description: Pancreatic islets from p10 rats


title: P10 [INHIBITOR 1]

description: Pancreatic islets from p10 rats


title: 2151R-NT_CP-3499


title: P10 [CONTROL 3]

description: Pancreatic islets from p10 rats

value: 60 pmol control LNA inhibitor


title: P10 [CONTROL 1]

description: Pancreatic islets from p10 rats


title: P10 [CONTROL 4]

description: Pancreatic islets from p10 rats


title: P10 [CONTROL 2]

description: Pancreatic islets from p10 rats


title: ADULT-2

description: Pancreatic islets from adult rats

data_processing:
To determine transcript expression levels, reads were mapped to the rat transcriptome (ENSEMBL 92, rn6) using STAR (2.5.3a) and quantified with RSEM (1.3.0).
To identify differentially expressed genes, reads were mapped to the rat genome (rn6) using HISAT (2.1.0) and gene counts for rat genes (ENSEMBL 92, rn6) estimated using HTseq.
Normalization and differential gene expression (FDR<0.05) were performed using DESeq2 (v.1.12.4).
Genome_build: rn6
Supplementary_files_format_and_content: xlsx file that contains catergorization of trna-derived fragments, their reads in TPM and statistical analysis on differential expression

growth_protocol: Pancreatic islets were isolated by collagenase digestion (Gotoh M et al., Transplantation, 1987) and Histopaque density gradient. Thereafter, islets were dissociated into single cells with trypsin-EDTA (Gibco) and cultured in RPMI 1640 GlutaMAX medium (Gibco) supplemented with 10% fetal bovine serum (Gibco), 100 U/mL penicillin and 100 µg/mL streptomycin (Gibco), 1 mM sodium pyruvate (Sigma), and 10 mM Hepes (Sigma).


title: ADULT-3

description: Pancreatic islets from adult rats


title: P10-1

description: Pancreatic islets from p10 rats


title: ADULT-1

description: Pancreatic islets from adult rats


title: P10-2

description: Pancreatic islets from p10 rats


title: BL21-N2 rep2

city: Wuhan

first: feng

last: chen

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

description: Gene expression data from N2 worms after fed with BL21

hyb_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000(Affymetrix)

data_processing: Affymetrix GeneChip Command Console (version 4.0, Affymetrix) was used to analyze array images to get raw data. Next, Genespring software (version 12.5; Agilent Technologies) was employed to finish the basic analysis with the raw data.

organism: Caenorhabditis elegans

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9ug total RNA.

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

tag: Stage

value: L4 stage worm

tag: diet


title: Cry5Ba-BL21 RB1884-rep2

description: Gene expression data from RB1884 worms after fed with CryBa/BL21


title: BL21-RB1884 rep1

description: Gene expression data from RB1884 worms after fed with BL21


title: BL21-RB1884 rep2


title: BL21-N2 rep1


title: P10-3

description: Pancreatic islets from p10 rats


title: Cry5Ba-BL21 RB1884-rep1


title: 5995-4: normal_rep4

city: Gainesville

first: Dawei

last: Dai

state: Florida

address: 2550 Hull Rd

department: Horticultural Sciences

institute: University of Florida

data_processing:
Raw RNA-seq data were screened to remove adapter sequences using  Cutadapt v1.1 (Martin, 2011) with the following parameters: error  rate = 0.1, times = 1, overlap = 5, andminimum length = 0. Adapter  trimmed sequences were quality trimmed with Trimmomatic v0.22 (Bolger  et al., 2014) using parameters (HEADCROP:0, LEADING:3, TRAILING:3,  SLIDINGWINDOW:4:15, and MINLEN:40) to truncate reads for base quality  <15 within 4 base windows and kept only reads >=40 bases after trimming.
Reads were uniquely aligned to the B73 RefGen_v2 maize (Zea mays)  genome assembly with GSNAP (Version 2013-07-20) using the following  parameters: orientation = FR, batch = 5, suboptimal levels = 0, novel  splicing = 1, local-splice dist = 8000, local-splice penalty = 0, distant-splice  penalty = 4, quality protocol = sanger, npaths = 1, quiet-if-excessive–  max-mismatches = 0.02, no fails-format = sam, sam-multipleprimaries–  pairmax-rna = 8000, pair expect = 200, pair dev = 150,  nthreads = 4.
Genome_build: B73 RefGen_v2 maize
Supplementary_files_format_and_content: Excel processed data file shows values of transcript per million (TPM), log2FoldChange(ded1-ref/normal), and adjusted p.

organism: Zea mays

source_name: endosperm

extract_protocol:
total RNA was extracted from 12 DAP normal and ded1-ref endosperms
RNA was extracted with Trizol reagent (Ambion, Thermo Fisher), followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.
Non-strand-specific TruSeq (Illumina) cDNA libraries were  prepared from 1 mg total RNA input with a 200 bp median insert length as described in Bai et al., 2019

tag: developmental stage

value: 12 DAP

tag: gene id (v3)

tag: tissue

value: kernel

value: normal


title: 5995-5: ded1-ref_rep3


title: 5996-8: normal_rep2


title: Cry5Ba-BL21 N2-rep2

description: Gene expression data from N2 worms after fed with CryBa/BL21


title: 5995-11: normal_rep1


title: Cry5Ba-BL21 N2-rep1


title: 5995-5: normal_rep3


title: 5995-4: ded1-ref_rep4


title: 5996-8: ded1-ref_rep2


title: HCT116 cells, shCtrl, biol rep 2

first: Deji

last: Ye

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health, Chlinese Academy of Sciences

data_processing:
Illumina Novaseq 6000 reads were trimmed and clipped for quality control in Trimmomatic v0.27
Read quality was checked for each sample using Fastp v0.19.5.
High-quality reads were then imported into TopHat v2.1.1 for alignment into BAM files.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: McCoy's 5a medium, 10% fetal bovine serum. Cells were cultured at 37C at 5% CO2.

extract_protocol:
HCT116 Cells were harvested and RNAiso Plus (9109, TaKaRa) was used to extract total RNA according to the manufacturer’s protocol. 1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 15 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x150 paired end flow cell.
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit following manufacturer's protocols.

tag: cell line

value: colorectal cancer cells


title: HCT116 cells, GMDS-AS1 shRNA2, biol rep 2

value: GMDS-AS1 knockdown


title: 5995-11: ded1-ref_rep1


title: LM3-CON_rep2

first: Xuewu

address: Tongji Hospital, Jiefang Avenue

institute: Huazhong University of Science and Technology

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray (G2534A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: LM3-CON control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low Input Quick-Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Stable cell lines were established by lentivirus-mediated transduction and puromycin selection. Cells were plated and cultured for  48 hours at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the QIAGEN RNeasy Mini Kit following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: No treatment

value: hepatocellular carcinoma (HCC) cell line

tag: genotype/variation

value: control


title: LM3-shSMAD3_rep2

source_name: LM3-shSMAD3 knockdown

value: shSMAD3 knockdown


title: LM3-CON_rep3


title: LM3-shSMAD3_rep3


title: 7721-SMAD3_rep2

source_name: 7721-SMAD3 overexpression

value: SMAD3 overexpression


title: 7721-SMAD3_rep3


title: 7721-VEC_rep1

source_name: 7721-VEC control

value: vector control


title: 7721-VEC_rep3


title: HCT116 cells, GMDS-AS1 shRNA2, biol rep 3


title: LM3-shSMAD3_rep1


title: HCT116 cells, shCtrl, biol rep 3

value: WT


title: HCT116 cells, GMDS-AS1 shRNA2, biol rep 1


title: Ery rep2 tech2

city: Seoul

first: Sungmin

last: Hwang

address: Hwarangno 14-gil 5, Seongbuk-gu

institute: Korea Institute of Science and Technology

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis).
The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq. Adapters are not trimmed away from the reads.
The sequencing artifacts and contamination of raw sequencing reads were assessed by FastQC v.0.11.9 and further adapter, poor-quality or short reads (< 10 bp) were trimmed by Cutadapt v.1.18.
The number of reads mapped to each transcript was counted by HTSeq v.0.11.0
Assembly: The preprocessed reads were aligned to the reference genome of GCF_002234675.1_ASM223467v1_genomic.gff by Tophat v.2.0.13.
Supplementary files format and content: The identification of differentially expressed genes (DEGs) with a default options of Cuffdiff v.2.2.0

organism: Oryzias latipes

source_name: three fish of Oryzias latifes

growth_protocol: Add 4 L of aerated dechlorinated tap water to three about 5 L (15 cm long, 22 cm wide, 17 cm deep) glass tanks. Using antibiotics stock, made three water condition: Non-treated, Ery 3.9 μg/ml and Amp 3.125 μg/ml. Ricefish were exposed to three condition (Control, Ery, Amp) of antibiotics during thirty days under a semi-static condition. The tank water was refreshed twice a week by discarding 2 L of the old breeding water and adding 2 L of the new breeding water with same antibiotics concentration as the old one. And every two weeks, all breeding water was refreshed. During the exposure, fish were fed with a commercial diet (PROPAC, Italy) once per day.

extract_protocol:
The RNA was extracted using TRI Reagent.
The purified total RNA was further processed to construct mRNA sequencing library according to the manufacturer’s instructions (Illumina Truseq stranded mRNA library prep kit, San Diego, CA, USA). mRNA was purified and fragmented from total RNA (1 μg) using poly-T oligo-attached magnetic beads, then reverse transcribed into cDNA with adapters.

value: wt

tag: treatment

value: Ery


title: HCT116 cells, shCtrl, biol rep 1


title: Ery rep1 tech1


title: hPSCs Day8

city: Syracuse

first: Yi

last: Zheng

state: New York

address: 900 S Crouse Ave

department: Biomedical and Chemical Engineering

institute: Syracuse University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v.3.1.0
Assembly: GRCh38.p13 from ENSEMBL
Supplementary files format and content: .rds files are the output of R Studio containing the data anlaysis ressults.

source_name: in vitro

extract_protocol:
Accutase for 1 h at 37°C
10X Genomics v.3 libraries were prepared according to the manufacturer’s instructions.

value: in vitro

value: human pluripotent stem cells (hPSCs)

tag: timepoint


title: Amp rep2 tech1

tag: strain

value: Amp


title: 7721-SMAD3_rep1


title: hPSCs Day3

description: 10x Genomics


title: Ery rep3 tech1


title: Ery rep3 tech2


title: Ery rep1 tech2


title: untreated rep3 tech1

value: untreated


title: untreated rep1 tech2


title: Ery rep2 tech1


title: untreated rep1 tech1


title: mock, 150mM, root, sample 3

city: Taipei

first: Shu-Yi

last: Yang

address: Life Science Building, NTU. No. 1, Sec. 4, Roosevelt Rd

institute: Institute of Plant Biology

data_processing:
The quality control of raw reads was evaluated using FastQC software v0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The low-quality reads (Q-value < 20) and adaptors were removed using the sequence preprocessing tool Trimmomatic v0.39 (Bolger et al., 2014). After low-quality reads and adaptors were removed, all cleaned reads were assembled into contigs using Trinity (Grabherr et al., 2011).
To get a more specific gene list, we used CD-HIT-EST version CD-HIT4 to cluster the redundancy of transcripts and removed the shorter redundant transcripts (Li and Godzik, 2006;Fu et al., 2012).
In this analysis, Bowtie2 version V2.3.2 and RSEM version v1.2.31 software were used to map short reads to the Trinity de novo assembly and quantify the read counts that matched to each contig (Li and Dewey, 2011;Langmead and Salzberg, 2012). Then, Transdecoder was used to identify candidate coding regions for gene prediction.
Next, to distinguish the de novo assembled sequences between those of the rice and fungal species, the Basic Local Alignment Search Tool (BLAST) searches against the Orygenes database (https://orygenesdb.cirad.fr/) for rice (O. sativa) and the National Center for Biotechnology Information (NCBI) database for AM fungi (R. irregularis), was performed for annotation, respectively (Altschul et al., 1990;Droc et al., 2006;Coordinators, 2016).
Assembly: Orygenes database (https://orygenesdb.cirad.fr/) for rice (O. sativa) and the National Center for Biotechnology Information (NCBI) database for AM fungi (R. irregularis)
Supplementary files format and content: tab-delimited excel files include raw count values for each Sample

source_name: root

extract_protocol:
Total RNA was extracted from 100 mg shoot or root tissue by using TRIzol Reagent (Invitrogen™) following the manufacturer’s instructions. A total amount of RNA (≥ 4 μg) per sample were used for transcriptome sequencing.
Strand-specific sequencing libraries were obtained following the handbook for the NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

value: root

value: wild type

value: mock

value: 150mM NaCl

tag: time

value: 8 weeks post inoculation


title: Amp rep1 tech1


title: radiation-8w rep3

city: Guangzhou

first: Yanmei

last: Cui

address: Yuancun erheng Road

institute: Sun Yat-sen University

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M8w-R3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts and fpkms for every gene and every sample

source_name: rectal tissue

extract_protocol:
Total RNA from the rectal tissues of mice in both irradiated and control group at 4 hours, 1 day, 3 days, 2 weeks and 8 weeks post-irradiation was extracted using Trizol reagent (Invitrogen, Carlsbad, CA). The mRNA was isolated by NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB, E7490).
The cDNA library was constructed following the manufacturer’s instructions of NEBNext Ultra RNA Library Prep Kit for Illumina（NEB, E7530）and NEBNext Multiplex Oligos for Illumina（NEB, E7500).

value: rectal tissue

value: 25Gy rectal radiation


title: untreated rep2 tech2


title: radiation-8w rep1

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M8w-R1


title: untreated rep3 tech2


title: 7721-VEC_rep2

tag: cell type

value: hepatocellular carcinoma (HCC) cell line


title: Amp rep1 tech2


title: control-8w rep3

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M8w-C3

value: sham-radiation


title: Amp rep2 tech2


title: radiation-2w rep3

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M2w-R3


title: untreated rep2 tech1


title: radiation-8w rep2

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M8w-R2


title: radiation-2w rep1

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M2w-R1


title: Amp rep3 tech2


title: control-8w rep2

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M8w-C2


title: Amp rep3 tech1


title: control-2w rep1

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M2w-C1


title: radiation-3d rep1

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M3d-R1


title: radiation-3d rep2

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M3d-R2


title: control-8w rep1

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M8w-C1


title: radiation-2w rep2

description:
All_gene_counts.list.xls
All_gene_fpkm.list.xls
M2w-R2