title: Morphant-XI

data_processing:
We analyzed the data using Partek Flow Genomic Analysis Software (https://www.partek.com/partek-flow/). We trimmed the adapter sequence “CTGTCTCTTATACACATCT” from the 3’ end using default parameters, before trimming bases from the 5’ end, selecting an end minimum quality value (Phred) score of 32, and a minimum read length of 65 bases. We aligned reads using default parameters and the STAR-2.6.1d algorithm. We normalized the log expression ratios using a Trimmed Means of M values (TMM) weighted algorithm. We performed differential expression analysis using the Gene Specific Analysis (GSA) algorithm in Partek Flow. The outcome of GSA was assessed by hierarchical clustering (heatmap) plotting, clustering by features, using average linkage and Euclidean cluster distance and point distance metrics respectively.
Assembly: Lawson Lab zebrafish transcriptome V4.3.2 (https://www.umassmed.edu/lawson-lab/reagents/zebrafish-transcriptome/)
Supplementary files format and content: Tab-separated differential expression analysis file comparing all uninjected control samples versus all hmx2;hmx3a DKD morphant embryos.

growth_protocol: The hmx2;hmx3a double knockdown (DKD) morphant embryos used in this study exhibit delayed development from somitogenesis stages onwards when compared to uninjected controls. To circumvent this, they were incubated at 32oC from 9 hours post fertilization (hpf) onwards. This ensured that control and injected embryos reached the desired developmental stage of 27 hpf at approximately the same time. The lateral line primordium does not migrate in DKD animals, so this could not be used to stage injected embryos. Instead, these embryos were visually inspected and processed for fluorescence-activated cell sorting (FACS) when they displayed the same head-trunk angle, head size and eye size as prim-staged uninjected control embryos.

extract_protocol:
Uninjected control embryos and hmx2;hmx3a DKD morphant embryos in the Tg(hmx CNEIII:cfos:GAL4-VP16,UAS:EGFP)SU41 background (generated as described above) were screened for fluorescence from 24 hpf onwards. Only EGFP-positive control and hmx2;hmx3a DKD morphant animals were used for dissociation and fluorescent activated cell sorting (FACS) at 27 hpf.   Embryos were deyolked, dissected and dissociated as described in GSE145916, with the following modifications: Trunk tissue was dissected anteriorly at the boundary between the hindbrain and spinal cord, and posteriorly, immediately above the end of the yolk extension. To ensure complete dissociation of trunk tissue with the Papain Dissociation System (Worthington Biochemical Corporation, LK003150), trunks were incubated in 1 ml Papain/DNase mix with gentle rocking at 28.5oC for 30 minutes. The digested tissue was then allowed to settle for 10 seconds before the Papain/DNase mix was carefully decanted until approximately 500 µl remained. Immediately after homogenising the digested tissue mixture with a sterile p200 tip, we passed each sample through a 40 µm Flowmi cell strainer (Merck, BAH136800040) into a sterile microcentrifuge tube. After Papain inactivation, samples were resuspended in 1 ml Leibovitz’s L-15 medium (ThermoFisher Scientific, 21083027) + 0.5% FBS and stored on ice. Immediately before FACS, DAPI (Merck, D9542) and Draq5 (BioLegend, 424101) were added at a final concentration of 5 µg/ml and 5 µM respectively.  FACS was performed using a Becton Dickinson FACS Aria III Cell Sorter at the SUNY Upstate Medical University Research Flow Core using the parameters described by Cerda et al., (2008) with the following modifications. Ice-cold samples were filtered through 35 µm mesh strainers in to 5 ml round-bottomed polystyrene tubes (Corning Falcon, 352235). All FAC-sorting and collection steps were performed at +4oC, using a 100 µm nozzle and 20 psi sort pressure. Successive doublet exclusion gates (forward scatter height x forward scatter width, followed by side scatter height x side scatter width) were used to finesse capture of real single cells. Accurate live/dead filtering was performed by selecting for DAPI-negative (sick cells are DAPI-permeant and excluded) and Draq-5 positive (only healthy nuclei are Draq-5 permeant) cells. Cells were sorted directly in to sterile 1.5 ml microcentrifuge tubes containing 100 µl of Buffer RLT (Qiagen RNeasy Micro Kit, 74004) plus 143 mMβ-mercaptoethanol. Sorted cells were stored at -80oC prior to RNA extraction.  Frozen FAC-sorted cell lysates were removed from storage at -80oC and thawed in a 37oC waterbath, before transferring to sterile microcentrifuge tubes. If necessary, sample volumes were completed to 250 µl with UltraPure DNase/RNase-Free distilled water (ThermoFisher Scientific, 10977035). 750 µl TRIzol LS Reagent (ThermoFisher Scientific, 10296028) was added to each 250 µl sample, before homogenising by gently pipetting up and down ten times with a sterile p1000 pipette tip. Samples were immediately transferred to Phasemaker tubes (which had been pre-centrifuged as per the manufacturer’s instructions (ThermoFisher Scientific, A33248)), before incubating for 5 minutes at room temperature. 200 µl chloroform was added to each sample. The tubes were then shaken vigorously for 15 seconds and incubated for a further 5 minutes at room temperature. The samples were then centrifuged for 5 minutes at 16,000 x g at 4oC, before transferring the RNA-containing upper aqueous phase to a sterile centrifuge tube and adding one volume of 70% RNase-free ethanol. Samples were inverted to mix thoroughly, and the supernatant immediately loaded to an RNEasy MinElute column (from the RNeasy Micro Kit, Qiagen, 74004), before centrifuging for 15 seconds at 10,000 rpm. Wash steps with RW1 buffer, RPE buffer and 80% RNase-free ethanol was performed as per the RNeasy Micro Kit instructions. Samples were eluted in 14 µl RNase-free water. RNA integrity was assessed with the Agilent RNA 6000 Pico chip (Agilent, 5067-1513) on an Agilent 2100 Bioanalyzer. Only samples with RNA integrity (RIN) values >9 were used for library preparation. RNA concentrations were measured with the Qubit RNA High-Sensitivity Assay Kit (ThermoFisher Scientific, Q32852) and a Qubit 3.0 fluorometer (ThermoFisher Scientific, Q33216).
cDNA was synthesised using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara, 634888), and used to make sequencing libraries with the Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024). cDNA and library quality were measured with the Agilent High Sensitivity DNA Kit (Agilent, 5067-4626) on an Agilent 2100 Bioanalyzer. Libraries were sequenced on an Illumina NextSeq500 to a depth of 20 million reads per sample (Illumina NextSeq 500/500 High Output Kit, v2.5, 75 cycles, 20024906).

treatment_protocol: The hmx2;hmx3a DKD morphant embryos used in this study were obtained by injecting 3.5 nl of a mixture containing 2 ng/nl each of a translation-blocking hmx2 morpholino (5’ TTCCGCTGTCCTCCGAATTATTCAT) and a translation-blocking hmx3a morpholino (5’ ACGTATCCTGTGTTGTTTCGGGCAT), plus 5 ng/nl of a control zebrafish p53 morpholino (5’ GCGCCATTGCTTTGCAAGAATTG)  into the single-cell of a one-cell stage Tg(hmx CNEIII:cfos:GAL4-VP16,UAS:EGFP)SU41 embryo (all morpholinos obtained from Gene Tools).   Morpholino injections always produce a spectrum of phenotypes, since it is hard to ensure that every cell receives the same dose. Therefore, prior to processing for FACS at 27 hpf, we removed any embryos with severely abnormal morphology (stunted length and/or severely developmentally delayed, likely caused by receiving too much morpholino). DKD morphant embryos display a slight curled-tail-down morphology. Embryos that lacked this morphology (and may therefore not have received any or sufficient morpholino) were also removed before processing for FACS.

value: V1 and dI2 spinal interneurons

value: hmx2;hmx3a double knockdowm morphant


title: 200722330021_R02C01

status: Public on Aug 09 2023

type: genomic

city: Baltimore

first: Yuba

middle: R

last: Bhandari

state: MD

address: 1650 Orleans Street

country: USA

institute: The Johns Hopkins University School of Medicine

description:
LESION: adenoma at baseline
AGE: age (years)
IS_FEMALE: 1=F, 0=M
ADEN_GRADE: grading score adenoma
ADEN_SIZE: size (mm)
ADEN_LEFT: adenoma located at left colon
ADEN_3PLUS: 3 or more adenomas in patient
ADEN_LT_1CM: adenoma larger than 1 cm
ADEN_HAS_HGD: adenoma has high grade dysplasia

hyb_protocol: not provided

scan_protocol: not provided

data_processing:
Data belonging to both 450K and EPIC platform was normalized using "preprocessFunnorm" subroutine from "Minfi" package version 1.42.0.
850k_matrix.txt: methylation β-values (ratio of the methylated probe intensity and the overall intensity)

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: FFPE sample

label_protocol: not provided

extract_protocol: DNA was extracted from 2-3 slices (10 µm) from the FFPE samples (Qiagen), quantified using PicoGreen and checked for quality using the Illumina FFPE QC Kit. The DNA was then subjected to bisulfite conversion (EZ DNA methylation kit, Zymo Research) and controlled by two in-house qPCRs. Next, 250 ng DNA was subjected to Illumina’s FFPE restoration protocol. Data were processed in two batches: the first batch was profiled on Illumina Infinium 450K beadchips, the second batch was run on Infinium EPIC (850K) beadchips.

tag: patientid

tag: lesion

tag: age

tag: bmi


title: Liver, BemA 10mg/kg diet + Lira injections_4

type: RNA

city: Hamilton

first: Dongdong

last: Wang

state: Ontario

address: 1200 Main Street West

department: Department of Medicine

country: Canada

institute: McMaster University

description: Data can be used by nSolver Software

hyb_protocol: Hyb protocol from NanoString Technologies, Inc.

scan_protocol: Scan protocol from NanoString Technologies, Inc.

data_processing: Gene expression data was normalized and log-transformed prior to differential gene expression analysis and pathway signature score computation using NanoString Technologies’ nSolver 4.0 software (version 4.0.70) and the embedded PLAGE algorithm.

label: Nanostring label

molecule: total RNA

organism: Mus musculus

source_name: Liver

label_protocol: Label protocol from NanoString Technologies, Inc.

extract_protocol: Liver tissue (~15 mg) was lysed in 1 mL TRIzol reagent (Invitrogen) using ceramic beads and a Precellys 24 homogenizer (Bertin Technologies). Samples were spun down for 10 mins at 12 000 g at 4 ºC. 200 µL of chloroform was added and shaken vigorously before spinning samples again at same settings. Supernatant was placed in new tubes and an equal amount of 70% ethanol was added then vortexed. Solutions were loaded onto RNeasy columns and manufacturer’s instructions were followed including a DNAse I digestion step (Qiagen).

treatment_protocol: At 8 weeks of age, mice were moved into specific-pathogen free (SPF) microisolators in a room maintained at ~29 ºC and fed a high-fat, high-fructose diet (NASH Diet; ND; 40% fat from mostly palm, 20% fructose, 0.02% cholesterol). Due to fructose being supplemented in the diet, diet was changed every few weeks. 16 weeks later, mice were grouped by matching body weight and adiposity randomly and placed on respective interventional arms. Adiposity was assessed based on time-domain NMR using a Bruker Minispec LF90II. Control mice were continued on diet alone, vehicle-treated mice (Vehicle) were given subcutaneous saline injections every second day 1-2 hrs before the dark cycle, bempedoic acid-treated mice (BemA) had the drug supplemented in the diet at a dose of 10 mg/kg, liraglutide-treated mice (Lira) were given subcutaneous injections of Victoza diluted in saline to a dose of 70 µg/kg every second day 1-2 hrs before the dark cycle, and combination-treated mice (Lira+BemA) were given subcutaneous injections of Victoza diluted in saline to a dose of 70 µg/kg every second day 1-2 hrs before the dark cycle with bempedoic acid supplemented in the diet at a dose of 10 mg/kg.

tag: diet

value: NASH diet

tag: treatment

value: Bempedoic acid (10 mg/kg) + Liraglutide (70 µg/kg)

tag: tissue

value: mouse liver


title: DA3/EPOR Escaped rep 2

type: SRA

city: Toronto

first: Sam

last: Benchimol

state: ON

address: 4700 Keele St.

institute: York University

library_source: transcriptomic

data_processing:
Genome Quebec performed base calling
First 13 bases of sequenced reads trimmed using Trimmomatic due to low-quality sequence, then mapped to grcm38 (mm10) whole genome using HiSAT2  --dta --rna-strandness RF -1.
Reads were counted using HTSEQ
Normalization of counts and differential expression was calculated using EdgeR, as described by Chen et al., (2008).
Genome_build: grcm38 (mm10)
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for read genes fo each Sample

source_name: DA3/EPOR cells

growth_protocol: DA3/EPOR cells were grown in RPMI 1640 supplemntented with 1U EPO and 10% FBS

extract_protocol:
Total RNA was isolated using Monarch Total RNA Miniprep Kit (New England BioLabs) as described by the manufacturer. A poly-A tail selection was performed by Genome Quebec
RNA libraries were prepared for sequencing by Genome Quebec

treatment_protocol: Senescent and Escaped DA3/EPOR cells were treated with 200ng/ml Doxorubicin for 24 hours and allowed to recover in Doxorubicin free media for 3 and 9 days, respectively.

tag: cell line

value: DA3/EPOR cells

tag: group

value: Escaped

tag: disease

value: Leukemia


title: DA3/EPOR Proliferating rep 3

value: Proliferating


title: Morphant-X

city: Syracuse

first: Samantha

middle: Jane

last: England

state: NY

address: 107 College Place

department: Biology

institute: Syracuse University

organism: Danio rerio

source_name: Spinal Cord

value: Spinal Cord

tag: cell type

tag: genotype


title: Liver, BemA 10mg/kg diet + Lira injections_3

description: Data can be used by nSolver Software


title: Liver, BemA 10mg/kg diet + Lira injections_2

description: Data can be used by nSolver Software


title: Morphant-IX


title: DA3/EPOR Proliferating rep 1


title: 200722330014_R07C01


title: Morphant-VIII


title: Morphant-VII


title: 200722330021_R04C01


title: sham control astrocyte #3

city: Stanford

first: Fangfei

last: Qu

state: CA California

address: SIM1 G2065, 265 Campus Drive

institute: Stanford University

data_processing:
RNA quantification done by salmon version 0.8.2
Differential expression analysis with DESeq2 version 1.28.1
Genome_build: mm10
Supplementary_files_format_and_content: quant.sf files are tab delimited text files

source_name: astrocytes isolated from sham brain injection control

extract_protocol:
Cells were flash frozen on dry ice and sent to Novogene for total RNA isolation and quality control.
Library preparation and sequencing were performed by Novogene using Illumina’s sequencing platform.

value: astrocyte

tag: microenvironment

value: sham injection


title: 200722330014_R08C01


title: DA3/EPOR Proliferating rep 2


title: DA3/EPOR Senescent rep 1

value: Senescent


title: sham control astrocyte #2


title: Control-XI

value: Wild type

value: Uninjected control


title: Liver, Bem A 10mg/kg_4

description: Data can be used by nSolver Software

value: Bempedoic acid (10 mg/kg)


title: Liver, Bem A 10mg/kg_5

description: Data can be used by nSolver Software


title: 200722330014_R06C01


title: 200722330014_R05C01


title: 200722330021_R01C01


title: sham control astrocyte #1


title: 200722330014_R04C01


title: Tumor-associated astrocyte #3

source_name: astrocytes isolated from SCLC brain allograft

value: SCLC brain allograft


title: Control-IX

value: V1 and dI2 spinal interneurons


title: Liver, Bem A 10mg/kg_3

description: Data can be used by nSolver Software


title: 200722330014_R03C01


title: Tumor-associated astrocyte #2


title: Control-VIII


title: Liver, Bem A 10mg/kg_2

description: Data can be used by nSolver Software


title: Liver, Bem A 10mg/kg_1

description: Data can be used by nSolver Software


title: 200722330014_R02C01


title: 200722330014_R01C01


title: Tumor-associated astrocyte #1


title: Liver, BemA 10mg/kg diet + Lira injections_1

description: Data can be used by nSolver Software


title: Control-VII


title: WT-LK-HIC-seq

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

country: China

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

description: WT-LK-HIC-seq

library_source: genomic

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq, ATAC-seq and HiC-seq reads  were aligned to the hg19 or mm9 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Assembly: mm9, hg19
Supplementary files format and content: tab-delimited text files include count values for RNA-seq, and peaks for ATAC-seq, and interaction contact file for HIC-seq samples.

organism: Mus

source_name: Bone marrow Lin-  Kit+ cells

growth_protocol: Total bone marrow LK cells were isolate from WT and NPM1C+ KI mice, and were sorted with Lin- and Kit+ markers.  Human OCI-AML3 leukemia cells were culture with alpha-MEM supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
RNA samples extracted with Trizon and treated with Dnase I.  ATAC-seq samples derived according to Nextera Tn5 Transposase kits. Hi-C assay was performed to generate a genome-wide interaction as described previously with Arima-HiC Kit (Cat: A410030) (https://arimagenomics.com/).
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594).  ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.  HiC-seq libraries were prepared according to KAPA HyperPrep Kits (KK8500).

treatment_protocol: Immediately extract total RNA from OCI-AML3 AML cells with and without Selinexor (KPT-330, XPO1 inhibitor) treatment.

tag: cell types

value: Mouse-derived Bone marrow cells

value: Bone marrow

tag: cell subtype

value: Lin-  Kit+ cells


title: ΔdgcO anaerobic 3

status: Public on Aug 08 2023

city: University Park

first: Emily

last: Weinert

state: PA

address: 306 Althouse Lab

department: Department of Biochemistry and Molecular Biology

institute: Penn State University

description:
Total RNA depleted of rRNA
FF-Pcc-Anaerobic-dGCS-3

data_processing:
Each sample was sequenced to an approximate depth of 25 million reads.
Quality control and adapter trimming was performed with bcl2fastq (ver. 2.20.0.445) on default parameters.
RNA-Seq reads were mapped to the GenBank assembly CP051652.1 using HISAT2 on default parameters + '--very-sensitive'
Read quantification was performed using Subread’s featureCounts functionality (ver. 2.0.1) on default parameters + '-Q 20'
Read counts loaded into R (ver. 4.0.2) and were normalized using edgeR’s Trimmed Mean of M values (TMM) algorithm (ver. 1.14.5) with default parameters.
Subsequent values were then converted to counts per million (cpm).
Differential expression analysis was performed using edgeR’s Quasi-Linear F-Test (qlfTest) functionality against treatment groups (ver. 1.14.5) with default parameters.
Assembly: The NCBI index (https://www.ncbi.nlm.nih.gov/assembly/GCF_013488035.1/) was used for gene annotation. The dgcO gene is annotated by the LocusTag HER17_08095.
Supplementary files format and content: Table with raw counts for each locus and sample
Supplementary files format and content: A table containing normalized read counts for each sample (in columns) and each annotated transcript (in rows). Includes statistics for differential expression between the following conditions: WT aerobic vs WT anaerobic, WT aerobic vs ΔdgcO aerobic, ΔdgcO aerobic vs ΔdgcO anaerobic, WT anaerobic vs ΔdgcO anaerobic

organism: Pectobacterium carotovorum subsp. carotovorum

source_name: P. carotovorum culture

growth_protocol: Overnight cultures of P. carotovorum subsp. carotovorum WPP14 WT and ΔdgcO cells were grown aerobically in 3 mL LB media. Cells were subcultured 1:100 in 5 mL of fresh LB media in 15 mL culture tubes and were grown at 30 °C with shaking aerobically. Additionally, the overnight cultures were subcultured 1:100 inton 5 ml degassed fresh LB media in an anaerobic glovebag (Coy). When cultures reached OD600 = 0.6-0.7. aerobically, and OD 600 = 0.2 anaerobically, samples were collected for RNA-seq and differential expression analysis.

extract_protocol:
Total RNA was extracted from the resuspended pellets using the Monarch® Total RNA Miniprep Kit #T2010S (NEB, Ipswich, MA, USA) following the manufacturer's instructions.
Extracted RNA was sent on dry ice to Seqcenter, LLC (Pittsburgh, PA, USA) where all following steps, incuding data processing, were completed. Samples were subjected to ribosomal RNA depletion using the Ribo-Zero™ Plus rRNA Removal Kit and complementary DNA (cDNA) libraries were then prepared with the Illumina Stranded RNA library preparation kit.

treatment_protocol: 1 mL of culture were collected at OD600 = 0.6-0.7 from aerobically growing cells and at OD600 = 0.2 for anaerobically growing cells, and cells were pelleted at 14000 x g for 2 min. Supernatant was removed and the pellets were either flash frozen in liquid nitrogen and stored at -80 °C or were immediately used for RNA extraction.

tag: background strain

tag: growth phase

value: Logarithmic


title: ΔdgcO aerobic 3

description:
Total RNA depleted of rRNA
FF-Pcc-Aerobic-dGCS-3


title: ΔdgcO anaerobic 1

description:
Total RNA depleted of rRNA
FF-Pcc-Anaerobic-dGCS-1


title: ΔdgcO aerobic 2

description:
Total RNA depleted of rRNA
FF-Pcc-Aerobic-dGCS-2


title: WT anaerobic 3

description:
Total RNA depleted of rRNA
FF-Pcc-Anaerobic-WT-3

value: WT


title: WT anaerobic 2

description:
Total RNA depleted of rRNA
FF-Pcc-Anaerobic-WT-2


title: WT aerobic 3

description:
Total RNA depleted of rRNA
pcc-WT-aerobic-3


title: Control-X


title: WT aerobic 1

description:
Total RNA depleted of rRNA
pcc-WT-aerobic-1


title: WT aerobic 2

description:
Total RNA depleted of rRNA
pcc-WT-aerobic-2


title: BigD-1-Replicate-4

city: Corvallis

first: Robyn

middle: Leigh

last: Tanguay

state: Oregon

department: Environmental Molecular Toxicology

institute: Oregon State University

data_processing:
SOAPnuke for read filter
HISAT2 for genome mapping
STAR for reference genome map
DEseq2 for differential expression
Assembly: GCF_000002035.6_GRCz11
Supplementary files format and content: .xlsx with read counts, filtered files and gene expression for all samples.

source_name: Zebrafish embryonic total RNA

extract_protocol: none provided

value: whole embryos


title: BigD-1-Replicate-2


title: BigD-1-Replicate-3


title: BigD-0-Replicate-3


title: BigD-0-Replicate-4


title: BigD-0-Replicate-2


title: BigD-0-Replicate-1


title: slincRosu3-1-Replicate-4


title: slincRosu3-1-Replicate-3


title: slincRosu3-1-Replicate-2


title: NPM1C-KI-LK-HIC-seq


title: slincRosu3-0-Replicate-4


title: slincRosu3-1-Replicate-1


title: slincRosu3-0-Replicate-3


title: slincRosu3-0-Replicate-2


title: ΔdgcO anaerobic 2

description:
Total RNA depleted of rRNA
FF-Pcc-Anaerobic-dGCS-2


title: slincRosu3-0-Replicate-1


title: ΔdgcO aerobic 1

description:
Total RNA depleted of rRNA
FF-Pcc-Aerobic-dGCS-1


title: WT anaerobic 1

description:
Total RNA depleted of rRNA
FF-Pcc-Anaerobic-WT-1


title: WT-1-Replicate-4


title: WT-1-Replicate-3


title: WT-1-Replicate-1


title: WT-0-Replicate-3


title: WT-0-Replicate-2


title: WT-0-Replicate-1


title: TLPH152 strains, vector control, 96h, rep2

city: Shanghai

first: Penghui

last: Dai

address: 800 Dongchuan Road

department: School of Life Sciences and Biotechnology

institute: Shanghai Jiao Tong University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit version 0.0.13 and Perl version 5.8.8
mRNA-seq reads were aligned to the Streptomyces xinghaiensis TL01 genome assembly using bowtie2 (version: 2-2.0.5).
Gene abundance measurements were generationed and normalized using BEDTools (version:2.16.1) ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Assembly: Streptomyces xinghaiensis TL01 (CP121002, not released yet).fasta
Supplementary files format and content: tab-delimited text files include FPKM values and raw fragment counts for each Sample

organism: Streptomyces xinghaiensis

source_name: Fermented cell culture

growth_protocol: All strains were grown in fermentation medium at 230 rpm and 30 °C for 96 h.

extract_protocol:
Total RNA was extracted using TransZol Up Plus RNA Kit（Cat#ER501-01，Trans)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 4200 TapeStation (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries for RNA-seq were prepared using  VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Samples (1.0 mL) of all strains were harvested at 96 h of fermentation, followed by centrifugation at 5,000 rpm for 3 min and discarding the supernatant. Subsequently, cells were washed three times with PBS buffer solution.

value: Fermented cell culture

tag: strain

value: Fermentation for 96 h


title: BigD-1-Replicate-1


title: TLPH152 strains, vector control, 96h, rep3


title: TLPH152 strains, vector control, 96h, rep1


title: TLPH17 strains, 96h, rep1

value: metK, adoK, metF and tylR overexpression


title: TLPH17 strains, 96h, rep3


title: TLPH11 strains, 96h, rep1

value: metK, adoK and metF overexpression


title: TLPH08-2 strains, 96h, rep3

value: tlrC overexpression


title: TLPH11 strains, 96h, rep3


title: TLPH11 strains, 96h, rep2


title: TLPH08-2 strains, 96h, rep2


title: TLPH08-2 strains, 96h, rep1


title: del(xpk)_Dark_12hr_biol_rep_2

city: Taipei

first: James

middle: C.

last: Liao

address: 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan

country: Taiwan

institute: Academia Sinica

data_processing:
bcl2fastq 2.1.8for base-calling
CLC Genomics Workbench 22.0 for differential gene expression
Supplementary files format and content: Differential gene expression between WT and Δxpk across all conditions (across group, ANOVA-like), with TMM-normalized CPM values

organism: Synechococcus elongatus

growth_protocol: Cultures were grown in standard BG11, at 30°C, 150rpm. Three cultures for each genotype, WT and Δxpk, were harvested at 4 different time points (Light 1 h: 1 hour after switching to light; Light 12 h: 12-hour illumination; Dark 1 h: 1 hour after switching to dark; Dark 12 h: 12-hour darkness) for a total of 24 samples. Each sample consisted of 5 mL of culture with an OD730~1. The cells were pelleted by full-speed centrifugation for 10 seconds, frozen with liquid nitrogen, and stored at -80°C until all time points were harvested.

extract_protocol:
For RNA extraction, the cell pellets were washed once with 300 µL of Qiagen RNAprotect® cell reagent, and the supernatant was removed after centrifugation. The cells were then once again frozen with liquid nitrogen and thawed by adding 350 µL of RLT solution from the Qiagen RNeasy kit. After 3 rounds of freeze-thaw-vortex steps, the samples were centrifuged at 15000g for 10 minutes. The supernatant was transferred to tubes and mixed with an equal volume of 100% ethanol before transferring to RNeasy mini-spin columns. The standard procedures of the Qiagen RNeasy kit were followed, and the Invitrogen TURBO DNA-free™ kit was used to remove DNA contamination.
For RNA-seq library preparation, RNA quality control was performed using the Agilent fragment analyzer 5200. Library preparation and rRNA depletion were performed using the Illumina Ribo-Zero Plus rRNA depletion kit. All sequencing was performed on Illumina Nextseq 2000 with P2 flowcell, 300 cycles, and pair-end 150 bp.
Standard Ribozero plus procedure

value: del(xpk)

value: Dark 12hr


title: del(xpk)_Dark_12hr_biol_rep_3


title: WT_Dark_12hr_biol_rep_3


title: WT-0-Replicate-4


title: WT-1-Replicate-2


title: del(xpk)_Dark_1hr_biol_rep_3

value: Dark 1hr


title: WT_Dark_1hr_biol_rep_2


title: WT_Dark_1hr_biol_rep_3


title: del(xpk)_Dark_1hr_biol_rep_2


title: del(xpk)_Dark_1hr_biol_rep_1


title: WT_Dark_12hr_biol_rep_1


title: del(xpk)_Light_12hr_biol_rep_2

value: Light 12 hr


title: WT_Dark_1hr_biol_rep_1


title: del(xpk)_Light_12hr_biol_rep_1


title: TLPH17 strains, 96h, rep2


title: del(xpk)_Light_12hr_biol_rep_3


title: WT_Light_12hr_biol_rep_3


title: WT_Light_12hr_biol_rep_1


title: WT_Light_12hr_biol_rep_2


title: del(xpk)_Light_1hr_biol_rep_3

value: Light 1hr


title: del(xpk)_Light_1hr_biol_rep_2


title: del(xpk)_Light_1hr_biol_rep_1


title: WT_Light_1hr_biol_rep_1


title: WT_Light_1hr_biol_rep_2


title: del(xpk)_Dark_12hr_biol_rep_1


title: Large yellow croaker, differentiation, Day6 rep3

first: 劳

last: 霁晖

address: 866 Yuhangtang Road, Xihu District

department: College of life sciences

institute: Zhejiang University

description: TPM_allsample.csv for all RNA-Seq sample

data_processing:
RNA-seq raw data was processed with Fastp (v 0.19.5).
TopHat (v 2.1.1) was used to align reads to NCBI reference genome L_crocea_2.0 (GCA_000972845.2,).
After alignment, transcripts were assembled using Cufflinks (v 2.2.1).
To annotate the gene functions, the integrated gene set was aligned against public databases, including NR, Swiss-Port, Pfam, EggNOG, GO and KEGG with BLAST+ (v 2.9.0).
Gene expression was measured using RSEM (v 1.3.3) with expression values normalized into transcripts per million (TPM).
DEseq2 (v 1.24.0) was used for differential expression analysis. When the log2FC cutoff value above 1 and P-adjust <0.05, genes were considered differentially expressed.
Assembly: L_crocea_2.0 (GCA_000972845.2)
Supplementary files format and content: CSV files include TPM values for each Sample

organism: Larimichthys crocea

source_name: PSCs

growth_protocol: Large yellow croaker muscle satellite cells were maintained in DMEM supplemented with 8% fetal bovine serum (FBS) ，10ng/ml bfgf and 1×PS in humidified atmosphere with 5% CO2 at 27C

extract_protocol:
RNA was harvested using Trizoln Kit
RNA libraries for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit following manufacturer's protocols.

treatment_protocol: Large yellow croaker muscle satellite cells were differentiated in F12 medium containing 8% HS, 10ng/ml IGF-1, 50 nM necrosulfonamide, 200 uM ascorbic acid , 1×PS, which was renewed half every 3 days.

value: PSCs

value: muscle satellite cell

value: myogenic differentiation

tag: time

value: Day 6


title: Large yellow croaker, differentiation, Day6 rep2


title: Large yellow croaker, differentiation, Day6 rep1


title: WT_Dark_12hr_biol_rep_2


title: Large yellow croaker, differentiation, Day3 rep2

value: Day 3


title: Large yellow croaker, differentiation, Day3 rep3

value: WT


title: Large yellow croaker, differentiation, Day3 rep1


title: Large yellow croaker, Control, Day0 rep3

value: Day 0


title: Large yellow croaker, Control, Day0 rep2


title: Large yellow croaker, Control, Day0 rep1


title: WT Peritoneal macrophage, LPS, 6 hours, rep2

city: Xiamen

first: yongyou

last: zhang

state: Fujian

address: Xiang'an South Road

institute: Xiamen University

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1)
Assembly: GCF_000001635.26_GRCm38.p6 for Mus musculus
Supplementary files format and content: csv files include read count values for each Sample

source_name: Peritoneal macrophage

growth_protocol: After LPS or PBS challenge, cells were conducted RNA extraction.

extract_protocol: The RNA was extracted using an RNA extraction reagent kit(TIANGEN, Cat#DP419). Three or four independent samples (biological replicates) were established for each group. The RNA sequencing library was prepared and sequenced on a BGISEQ-500 platform(BGI, China) by SE50 sequencing

treatment_protocol: Peritoneal macrophages were stimulated with or without LPS for 6 hours.

value: Peritoneal macrophage

value: LPS (1μg/mL) for 6 hours


title: Ythdf1 knockout Peritoneal macrophage, LPS, 6 hours, rep3

value: Ythdf1 knockout


title: Ythdf1 knockout Peritoneal macrophage, LPS, 6 hours, rep1


title: Ythdf1 knockout Peritoneal macrophage, PBS, 6 hours, rep2

value: PBS for 6 hours


title: Ythdf1 knockout Peritoneal macrophage, LPS, 6 hours, rep2


title: Ythdf1 knockout Peritoneal macrophage, PBS, 6 hours, rep3


title: WT Peritoneal macrophage, PBS, 6 hours, rep2


title: WT Peritoneal macrophage, LPS, 6 hours, rep3


title: Ythdf1 knockout Peritoneal macrophage, PBS, 6 hours, rep1


title: WT Peritoneal macrophage, PBS, 6 hours, rep3


title: WT Peritoneal macrophage, PBS, 6 hours, rep1


title: WT Peritoneal macrophage, LPS, 6 hours, rep1


title: WT_Light_1hr_biol_rep_3


title: Ythdf1 knockout, ConA, 8 hours, rep3

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1)
Assembly: GCF_000001635.26_GRCm38.p6 for Mus musculus
Supplementary files format and content: csv files include TPM values for each Sample

source_name: liver

growth_protocol: After ConA or saline injection, mice were euthanized and the liver were harvested for RNA extraction.

extract_protocol: The RNA was extracted using an RNA extraction reagent kit(TIANGEN, Cat#DP419). Three or four independent samples (biological replicates) were established for each group. The RNA sequencing library was prepared and sequenced on a BGISEQ-500 platform(BGI, China) by SE50 sequencing.

treatment_protocol: Mice were intravenously injected with or without ConA for 8 hours, then the livers were harvested.

value: liver

value: ConA (8 mg/kg) for 8 hours


title: Ythdf1 knockout, ConA, 8 hours, rep4


title: Ythdf1 knockout, ConA, 8 hours, rep2


title: Ythdf1 knockout mice, 8 hours, rep2

value: saline for 8 hours


title: WT mice, saline, 8 hours, rep3


title: Ythdf1 knockout mice, 8 hours, rep1


title: WT mice, ConA, 8 hours, rep4


title: WT mice, ConA, 8 hours, rep3


title: WT mice, ConA, 8 hours, rep2


title: Wild-type yeast, 6 h in fermentative medium, rep1

city: Ikoma

first: Daisuke

last: Watanabe

state: Nara

address: 8916-5 Takayamacho

country: Japan

institute: Nara Institute of Science and Technology

data_processing:
Sequenced reads were trimmed of adapters and sequencing quality lower than 20 (using cutadapt and sickle).
The RNAseq reads were aligned to S. cerevisiae S288C whole genome using Hisat2.
Read Per Kilobase of transcript per Million (RPKM) was calculated using featureCounts with gene level and converted to TPM (Transcripts Per Million) by in-house script.
Assembly: Saccharomyces cerevisiae S288C; GenBank assembly accession: GCA_000146045.2
Supplementary files format and content: Tab-delimited text file contains raw reads, RPKM values, and TPM values.

organism: Saccharomyces cerevisiae

source_name: yeast cell

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit in QIAcube Connect (QIAGEN).
rRNA was removed by riboPool (siTOOLs Biotech), and then total RNA sample was subjected to library construction using MGIEasy RNA Directional Library Prep Set (MGI Tech Co Ltd) according to the manufacturers' manuals.

treatment_protocol: Yeast cells were statically incubated at 30 degree for 6 h in YPD20 medium.

value: yeast cell

value: 6 h in YPD20, statically incubated at 30 degree


title: WT mice, saline, 8 hours, rep1


title: Cdc55p-deficient yeast, 6 h in fermentative medium, rep1


title: msnsd-R3

city: Wuhan

first: Dan

last: Qin

address: Nanhu Avenue No.3

institute: Hubei Academy of Agricultural Universtiy

data_processing:
fastp: an ultra-fast all-in-one FASTQ preprocessor version 0.12.4
Processed data files were generated using fastp (parameters- length_required: 36 qualified quality phred: 20 unqualified percent limit: 50 n base limit: 5 compression level: 6)
-l, --length_required                reads shorter than length_required will be discarded, default is 15. (int [=15])
-q, --qualified_quality_phred        the quality value that a base is qualified. Default 15 means phred quality >=Q15 is qualified. (int [=15])
-u, --unqualified_percent_limit      how many percents of bases are allowed to be unqualified (0~100). Default 40 means 40% (int [=40])
-n, --n_base_limit                   if one read's number of N base is >n_base_limit, then this read/pair is discarded. Default is 5 (int [=5])
-z, --compression                    compression level for gzip output (1 ~ 9). 1 is fastest, 9 is smallest, default is 2. (int [=2])
Assembly: Morex V3 assembly
Supplementary files format and content: tab-delimited text files include TPM values for each sample and replicates

organism: Hordeum vulgare

source_name: 0.5-1cm young panicles

extract_protocol:
RNA was harvested using the TRIzol reagent (Tiangen). 1.5 μg of total RNA was used for the construction of sequencing libraries
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

value: 0.5-1cm young panicles

value: mutant


title: msnsd-R1


title: E934-R3

value: wild type


title: Ythdf1 knockout, ConA, 8 hours, rep1


title: 39b11 Transposon mutant rep 2

city: Rochester

first: Mikaeel

middle: Imran

last: Young

state: New York

address: 601 Elmwood Ave, Rm 211311B , MRBX

department: Microbiology and Immunology

institute: University of Rochester

data_processing:
Base calling performed using RTA3 software, sequence adapters removed and low quality reads filtered using fastQC software (v 0.11.9).
Reads were mapped to reference genome A.baumannii 17978 (ASM1542v1) by HISAT2 (v 2.2.1).
Assembled transcripts were generated and merged with StringTie (v 2.1.5).
Transcripts were quantified and gene expression levels determined using Cufflinks software (v 2.2.1).
Differential Gene Expression Analysis was conducted using DESeq software (v 3.14). A false detection rate (FDR) ≤ 0.05 and the absolute value of Log2 ratio ≥ 1 were used as the default threshold to identify significant Differentially Expressed Genes (DEGs)
DEGs were classified based on their Gene Ontology (GO) functional terms and KEGG pathway enrichment analysis using topGO software (v 3.14).
Genome_build: ASM1542v1
Supplementary_files_format_and_content: Raw counts and FPKM abundance counts in text document files. DEG analysis with KEGG GO annotations in Excel comma separated file.

organism: Acinetobacter baumannii

source_name: 39b11 transposon mutant bacterial cell

growth_protocol: A.baumannii wild type and 39b11 mutant (A1S_3277::Tn5) cells were grown for 6 hrs in 25 mL of human serum at 37 degrees celsius.

extract_protocol:
Cells were washed with TE buffer and total bacterial RNA was isolated using a Qiagen Rneasy kit according to the manufacturer's instructions. RNA was further Dnase treated and re-isolated with the Rneasy kit.
To construct sequencing libraries, cDNA synthesis was performed, the 3′ ends were adenylated and adaptors were ligated. Paired-end sequencing was performed with Illumina NovaSeq 6000.

treatment_protocol: A.baumannii wild type and 39b11 mutant (A1S_3277::Tn5) were treated with 0.15 µg/mL levofloxacin during 6hr growth period.

tag: transposon

value: 0.15 µg/mL levofloxacin for 6 hrs


title: 39b11 Transposon mutant rep 1


title: wild type rep 2

source_name: wild type bacterial cell


title: E934-R1


title: wild type rep 1


title: WT mice, ConA, 8 hours, rep1


title: WT mice, saline, 8 hours, rep2


title: olfactory epithelium, Ms4a cluster KO, rep3

city: Worcester

first: I-Hao

state: MA

address: 370 Sunderland Rd, Unit D24

department: PMM

institute: UMMS

description:
genes_expression_expected_count.tsv
CL3

data_processing:
Libraries were sequenced using paired-end 150 cycle reads on an Illumina Novaseq6000 (Novogene).
The sequencing reads were processed using the DolphinNext RNAseq pipeline (https://dolphinnext.umassmed.edu/index.php?np=1&id=732) (Yukselen et al., 2020). The default settings were employed, except that STAR v.2.6.1 and RSEM v.1.3.1 were used for alignment and quantification, respectively (Dobin et al., 2013; Li and Dewey, 2011). Transcriptome build: gencode M25.
The count matrix was loaded to R (v.4.0.0 or later), and DEseq2 (v.1.30.1) was used to normalize the matrix and perform differential gene expression analysis (Love et al. 2014)
Assembly: mm10
Supplementary files format and content: genes_expression_expected_count.tsv

molecule: polyA RNA

source_name: olfactory epithelium

growth_protocol: All animal care and use procedures were in accordance with federal guidelines (12 h light/12 h dark cycle, 20–23 °C, 30–70% humidity) and approved by the University of Massachusetts Medical School Institutional Animal Care and Use Committee (IACUC) (Protocol A-2645-18)

extract_protocol:
Three 8-12-week old Ms4a cluster knockout, Ms4a6c knockout, and littermate wild-type control mice were euthanized according to our IACUC protocol, and the main olfactory epithelium was dissected and immersed quickly in 0.6 ml of ice-cold Trizol (Invitrogen, #15596018). Olfactory epithelia were ground and homogenized with nuclease-free disposable pestles (Fisher Scientific, #12-141-368) in an Eppendorf tube (Eppendorf, #2231000347). The homogenized sample was incubated for 5 minutes at room temperature. 0.1 µL of chloroform was added to the sample and mixed by inverting for 20 seconds. The sample was then incubated for 3 minutes at RT. The sample was centrifuged at 12,000 xg for 15 minutes at 4 °C. The clear aqueous phase was collected into a nuclease-free Eppendorf tube, equal volume of 70% ethanol (Sigma-Aldrich, #E7023) was added and mixed. The sample was then loaded into RNeasy spin column and RNA was extracted with a RNeasy mini kit (Qiagen, #74104) following the manufacturer’s guidelines.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7490S and #E7760S) was used to construct sequencing libraries following the manufacturer’s guidelines with one alteration, which was to increase the insert length to around 300 bp.

value: olfactory epithelium

value: C57BL/6; Ms4a cluster-/-


title: db/db mouse cardiac tissue_DCM_rep3

city: Shijiazhuang

first: Lingling

last: Yuan

state: Hebei

address: No.215, Heping Road(West)

institute: The Second Hospital of Hebei Medical University

description: the enriched circular RNAs expression

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA Arrays V2 (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software. A series of data processing including quantile normalization were performed using the R software limma package. The circRNAs that at least 3 out of 6 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between two samples or two groups were identified using fold change cutoff or through Volcano Plot filtering respectively. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

source_name: cardiac apex, db/db, 21weeks

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

extract_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The purity and concentration of total RNA samples were determined with NanoDrop ND-1000.

treatment_protocol: Cardiac tissue samples were collected from db/db (n = 3) and C57BL/6 (n = 3) mice at age of 21 weeks.

value: cardiac apex

tag: age

value: at age of 21 weeks

value: db/db mice


title: olfactory epithelium, Ms4a cluster KO, rep1

description:
genes_expression_expected_count.tsv
CL1


title: db/db mouse cardiac tissue_DCM_rep2

description: the enriched circular RNAs expression


title: C57BL/6 mouse cardiac tissue_NC_rep1

description: the enriched circular RNAs expression

source_name: cardiac apex, C57BL/6, 21weeks

value: C57BL/6 mice


title: Ythdf1 knockout mice, 8 hours, rep3

value: Ythdf1 knockout


title: olfactory epithelium, Ms4a6c KO, rep3

description:
genes_expression_expected_count.tsv
C63


title: olfactory epithelium, Ms4a6c KO, rep2

description:
genes_expression_expected_count.tsv
C62


title: db/db mouse cardiac tissue_DCM_rep1

description: the enriched circular RNAs expression


title: olfactory epithelium, Ms4a cluster KO, rep2

description:
genes_expression_expected_count.tsv
CL2


title: olfactory epithelium, Ms4a6c KO, rep1

description:
genes_expression_expected_count.tsv
C61


title: C57BL/6 mouse cardiac tissue_NC_rep2

description: the enriched circular RNAs expression


title: C57BL/6 mouse cardiac tissue_NC_rep3

description: the enriched circular RNAs expression


title: olfactory epithelium, wild-type, rep1

description:
genes_expression_expected_count.tsv
WT1


title: olfactory epithelium, wild-type, rep2

description:
genes_expression_expected_count.tsv
WT2


title: olfactory epithelium, wild-type, rep3

description:
genes_expression_expected_count.tsv
WT3


title: msnsd-R2


title: E934-R2


title: ILC2,Mc5r-KO-2

first: yuying

last: huang

address: 320 Yue-Yang Road

institute: Center for Excellence in Molecular Cell Science, CAS

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: Lung

extract_protocol:
Total RNA was prepared, and RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies). Total RNA was subjected to reverse transcription and amplification using the Single Cell Full Length mRNA-Amplification Kit (Vazyme, N712-02).
A cDNA library was constructed with the TruePrepTM DNA Library Prep Kit V2 for Illumina® (Vazyme, TD503-01) according to the manufacturer’s protocol.

value: Lung

value: Mc5rfl/fl R5-/+

value: papin


title: ILC2,Mc5r-KO-1


title: ILC2,WT-1


title: ILC2,WT-2


title: naïve, ILC2 cells-2

value: WT

value: untreated


title: β cells sorted from TSA treated mouse islets_rep_3

city: Lille

first: Frederik

last: Oger

address: Faculté de Médecine - Pôle Recherche - 2eme etage - 1 place de Verdun

country: France

institute: Université de Lille

description: RNA polyA

data_processing:
The demultiplexing of sequence data (from BCL files generated by Illumina sequencing systems to standard FASTQ file formats) was performed using bcl2fastq Conversion Software (Illumina; version 2.19.1).
Trimming of residuals adapters and low-quality reads was performed using Cutadapt software (version 1.7.1).
Sequence reads from FASTQ files were mapped to the mouse genome (mm10) or human genome (Hg38) using STAR Aligner (version 2.5.2b). On average, 38M reads were generated per sample, and 93.5 % +/- 0.9% of them were accurately mapped.
The counting of the different genes and isoforms was performed using RSEM (version 1.3). Finally, differential expression was performed using DESeq2 package
Assembly: mm10 (mouse) and Hg38 (human)
Supplementary files format and content: Tab-delimited text files include TPM and FPKM values for each sample

source_name: β cells sorted from mouse pancreatic islets

growth_protocol: Mouse pancreas were digested using type V collagenase (Sigma, C9263-1G) for,10 min at 37°C. After digestion, the islets were separated in a density gradient medium (Histopaque, Sigma) and purified by handpicking under a macroscope. RNA was purified using Rneasy plus micro kit (Qiagen, 74034) following the manufacturer’s instruction. Total RNA sample concentrations were determined using a Nanodrop spectrophotometer (Implen, Nanophotometer N60 Touch)

extract_protocol:
Total RNA was extracted from EndoCβH1, Min6, mouse pancreatic islets and human pancreatic islets using RNeasy Plus mini kit (Qiagen, 74136) according to the manufacturer’s instructions. Total RNA sample concentrations were determined using a Nanodrop spectrophotometer (Implen). RNA quality was verified using RNA 6000 nanochips (Agilent, 5067-1511) on the Agilent 2100 bioanalyzer (Agilent, G2939A). 500 ng of purified RNA with RNA integrity number (RIN) ≥8 was subsequently used for library preparation
500 ng of purified RNA with RNA integrity number (RIN) ≥8 was subsequently used for library preparation with the TrueSeq Stranded mRNA library Prep (Illumina, 20020594) and sequenced in paired end 2x75 on the NextSeq device.
Libraries were prepared with the TruSeq Stranded mRNA library Prep (Illumina, #20020594) and sequenced on the Illumina NextSeq500 system using a paired-end 2×75 bp protocol.

treatment_protocol: EndoCβH1, Min6, mouse pancreatic islets and human pancreatic islets were treated either with DMSO (0.1%) or TSA (0.5µM) for 16h.

value: Ex vivo mouse beta cell


title: β cells sorted from TSA treated mouse islets_rep_2

description: RNA polyA


title: β cells sorted from TSA treated mouse islets_rep_1

description: RNA polyA


title: β cells sorted from DMSO treated mouse islets_rep_3

description: RNA polyA


title: naïve, ILC2 cells-1


title: β cells sorted from DMSO treated mouse islets_rep_2

description: RNA polyA


title: β cells sorted from DMSO treated mouse islets_rep_1

description: RNA polyA


title: NIH-3T3 cells, HSF4-Control

city: Tianjin

first: Heng

last: Zhang

address: 38 Rd.Tongyan

institute: Nankai University

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR)  primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format  were processed by Cutadapt[1]（version 1.9.1）to be high quality clean data.
Mapping: Firstly, mm10 reference genome sequences and gene model annotation files were  downloaded from UCSC. Secondly, bowtie2-build  is used to index reference genome sequence. Finally, clean data is aligned to reference genome via  software Bowtie2 (version 2.2.6).
Peaks analysis: Use MACS[2](V2) to analyze peaks quality control, peaks calling and peaks annotation.
Assembly: mm10
Supplementary files format and content: bw
Library strategy: CUT&RUN

growth_protocol: NIH-3T3 cells were maintained in DMEM medium supplemented with 10% fetal bovine serum and 100 U/mL penicillin, 100 mg/mL streptomycin.

extract_protocol:
The UVB lamp model NB-UVB311 (UVB Narrowband PL-L/PL-S, Philips) at 280-360 nm (peak 305-310 nm) with a power of 9 J/s was used for 10 minutes in the cell septum culture dish.Lysates were clarified from sonicated nuclei and HSF4-control-DNA, COIL-control-DNA, HSF4-UV-DNA or COIL-UV-DNA, complexes were isolated with antibody.
In this experiment, cut run kit was used to extract (CST, USA). In short, prepare an appropriate number of living cells. First, combine concanavalin A beads with the target primary antibody HSF4 and coil respectively. After binding overnight, elute the beads with PAG mnase enzyme to digest and release the eluted DNA. Finally, DNA Purification Kit (CST, USA) was used to purify the obtained DNA fragment bound to the target protein. The obtained DNA was stored in DNA Evolution Buffer (cell signaling, USA).

value: Fibroblast

tag: chip antibody

value: No treatment


title: NIH-3T3 cells, HSF4-UV

tag: treatment

value: Ultraviolet induced


title: Mouse Lung tissue_DicerS2D_rep1

city: Houston

first: Raisa

last: Reyes-Castro

state: Texas

address: 6767 Bertner Ave

department: Genetics

institute: UT Health MD Anderson Cancer Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
FASTQC files were processed using Cellranger v3.1.0 software
Clustering and cell population annotations were performed in R studio following Seurat algorithm.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung primary tumors

growth_protocol: Heterozygous phosphomimetic Dicer1 (Dicer1S2D/+) animals were crossed to  heterozygous Kras G12D (KrasLA1/+) animals to generate a cohort of Dicer1S2D/+, KrasLA1/+ and KrasLA1/+;Dicer1S2D/+ animals. Mice were euthanized at 39weeks of age for tissue collection.

extract_protocol:
Briefly, 39 weeks old mice were anesthetized using Avertin (Sigma, T4802), right heart ventricle was perfused with 1x PBS without calcium and magnesium (ThermoFisher, #100100023). Lungs were removed from the mouse and placed in Liebovitz media (Gibco, #21083-023). Lung tumors were identified and collected under the dissecting microscope. Tumors were minced with forceps and digested in the Liebovitz media with 2 mg/mL collagenase type I (Worthington CLS-1, LS004197), 0.5 mg/mL DNase I (Worthington D LS002007) and 2 mg/mL elastase (Worthington ESL LS002294) for 30 min at 37oC. Digestion was stopped with 20% Fetal bovine serum (FBS, Invitrogen 10082- 139). Cells were filtered using a 70 µm cell strainer (Falcon, 352350) on ice and transferred to a 2mL tube. Red blood cells were lysed using Red blood cells lysis buffer (Miltenyl Biotec 130-094-183), and the lysate centrifuged for 1 minute at 5000rpm. Supernatant was removed and cells in the pellet were washed twice with 1mL of ice-cold 1X Leibovitz plus 10% FBS. The cellular suspension was then filtered with a 40 µm cell strainer (Falcon #352340), centrifuged and cells resuspended in ice-cold 1X Leibovitz plus 10% FBS. Cell viability was evaluated using Trypan blue and counted with a hemocytometer. Samples with more than 70% of viable cells were submitted for scRNA-seq
After cell dissociation and counting, samples were centrifuged and re-suspended in 1X PBS with 0.04% BSA for single cell suspensions and processed for Chromium Single Cells Gene Expression Solution Platform (10x Chromium) with 3’v3 Library following manufacture instructions.

treatment_protocol: No treatment

tag: tissue

value: Lung primary tumors

tag: Sex

value: Male

tag: age in_weeks


title: NIH-3T3 cells, COIL-Control

tag: cell line

value: COIL (Cat No. 67218-1-Ig)


title: NIH-3T3 cells, COIL-UV

tag: cell type


title: Mouse Lung tumor_KrasLA1_rep2

description: 10x Genomics

tag: genotype


title: Mouse Lung tumor_KrasLA1_rep1

description: 10x Genomics


title: Mouse Lung tumor_KrasLA1;DicerS2D_rep1

description: 10x Genomics


title: ST I2

city: Manchester

first: Juan

middle: Fernando

last: Quintana

address: 2.18c CTF, Grafton Street

department: Lydia Becker Institute of Immunology and Inflammation

country: United Kingdom

institute: University of Manchester

description: Spatial transcriptome

data_processing:
For FASTQ generation and alignments, illumina basecall files (*.bcl) were converted to FASTQs using bcl2fastq
Gene counts were generated using CellRanger for single cell RNAseq (v.6.0.0) or SpaceRanger for spatial transcriptomics (v.1.2.2)
Mapping strategy was conducted on CellRanger or SpaceRanger against a combined Mus musculus (mm10) and Trypanosoma brucei (TREU927) transcriptome reference
After alignment, reads were grouped based on barcode sequences and demultiplexed using the Unique Molecular Identifiers (UMIs)
Assembly: mm10 + TREU927
Supplementary files format and content: .h5 files were generated as outputs from CellRanger or SpaceRanger. The filter matrices can be used for downstream analysis using the scripts available on https://zenodo.org/record/6387555#.Yksy3y8w1nk

source_name: Skin

growth_protocol: 6-8 weeks old mice were infected (i.p.) with 2,000 Trypanosoma brucei brucei strain Antat 1.1E. Mouse skin from naïve and infected mice were harvested for scRNAseq analysis. Skin sections were fixed in 4% PFA and prepared for spatial transcriptomics analysis

extract_protocol:
Single cell suspensions were obtained from murine skin using enzymatic dissociation, followed by library preparation using the 10X Chromium platform. Skin sections wre included in paraffin blocks, and 5 um sections were used for tissue analysis using the 10X Visium platform.
Illumina compatible, RNA libraries were prepared with the 10X Chromium technolgy

treatment_protocol: Two biological replicates per time point (naïve and 25 days post-infection) for single cell transcriptomics. One biological replicate for spatial transcriptomics

value: BALB/c

value: Female

value: 6-8 weeks old

value: Skin

value: 25 days post-infection


title: Mouse Lung tumor_KrasLA1;DicerS2D_rep2

description: 10x Genomics


title: ST N1

description: Spatial transcriptome

value: Naive


title: ST I1

description: Spatial transcriptome


title: ST N2

description: Spatial transcriptome


title: Infected-2_S9_L004

description: single cell RNA


title: Infected-2_S9_L001

description: single cell RNA


title: Infected-2_S12_L004

description: single cell RNA


title: Infected-2_S9_L002

description: single cell RNA


title: Infected-2_S12_L002

description: single cell RNA


title: Infected-2_S11_L001

description: single cell RNA


title: Infected-2_S10_L004

description: single cell RNA


title: Infected-2_S10_L002

description: single cell RNA


title: Infected-2_S11_L004

description: single cell RNA


title: Infected-2_S4_L003

description: single cell RNA


title: Infected-2_S4_L004

description: single cell RNA


title: Infected-2_S12_L001

description: single cell RNA


title: Infected-2_S11_L002

description: single cell RNA


title: Infected-2_S4_L002

description: single cell RNA


title: Infected-2_S4_L001

description: single cell RNA


title: Infected-2_S10_L001

description: single cell RNA


title: Infected-1_S40_L001

description: single cell RNA


title: Infected-1_S39_L002

description: single cell RNA


title: Infected-1_S40_L004

description: single cell RNA


title: Infected-1_S39_L001

description: single cell RNA


title: Infected-1_S37_L002

description: single cell RNA


title: Infected-1_S3_L004

description: single cell RNA


title: Infected-1_S38_L001

description: single cell RNA


title: Infected-1_S40_L002

description: single cell RNA


title: Infected-1_S39_L004

description: single cell RNA


title: Infected-1_S38_L004

description: single cell RNA


title: Infected-1_S2_L004

description: single cell RNA


title: Infected-1_S38_L002

description: single cell RNA


title: Infected-1_S2_L003

description: single cell RNA


title: Infected-1_S37_L004

description: single cell RNA


title: Naive-2_S24_L004

description: single cell RNA


title: Infected-1_S3_L002

description: single cell RNA


title: Infected-1_S3_L001

description: single cell RNA


title: Infected-1_S3_L003

description: single cell RNA


title: arabidopsis_5d_sh_a

city: Cold Spring Harbor

first: Ullas

middle: V.

last: Pedmale

address: 1 Bungtown RD

department: Pedmale

institute: Cold Spring Harbor Laboratory

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to either TAIR10 or ITAG4.1 whole genome using star v2.7.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated with cufflinks v2.1.1.

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Arabidopsis seedlings were grown in half-strength MS agar plates under constant white light for 5 days and subsequently kept in unshaded conditions or transfered to shade for the indicated time. Roots were harvested and immediately frozen in liquid nitrogen for RNA extraction. Tomato seedlings were grown in white light for 7 days under the same conditions and treatments described for Arabidopsis.

extract_protocol:
Arabidopsis total RNA was extracted with trizol-chloroform protocol. Tomato total RNA was extracted with a Promega ReliaPrep RNA miniprep System following manufacturer instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: root

tag: ecotype/cultivar

value: shaded root 5d


title: arabidopsis_1d_sh_b

value: shaded root 1d


title: Infected-1_S37_L001

description: single cell RNA


title: arabidopsis_3d_sh_b

value: shaded root 3d


title: Naive-2_S24_L001

description: single cell RNA


title: Infected-1_S2_L002

description: single cell RNA


title: Naive-2_S24_L002

description: single cell RNA


title: arabidopsis_3d_sh_a


title: arabidopsis_5d_sh_b


title: Infected-1_S2_L001

description: single cell RNA


title: Naive-2_S23_L004

description: single cell RNA


title: arabidopsis_1d_sh_a


title: Naive-2_S22_L004

description: single cell RNA


title: arabidopsis_3h_sh_b

value: shaded root 3h


title: Naive-2_S23_L002

description: single cell RNA


title: Naive-2_S22_L001

description: single cell RNA


title: arabidopsis_7h_sh_b

value: shaded root 7h


title: Naive-2_S21_L004

description: single cell RNA


title: Naive-2_S23_L001

description: single cell RNA


title: arabidopsis_30min_sh_b

value: shaded root 30min


title: arabidopsis_3h_sh_a


title: Naive-2_S22_L002

description: single cell RNA


title: arabidopsis_7h_sh_a


title: Naive-2_S21_L002

description: single cell RNA


title: Naive-2_S21_L001

description: single cell RNA


title: arabidopsis_5d_wl_a

value: unshaded root 5d


title: Naive-2_S2_L004

description: single cell RNA


title: Naive-2_S2_L003

description: single cell RNA


title: Naive-2_S1_L004

description: single cell RNA


title: arabidopsis_3d_wl_b

value: unshaded root 3d


title: Naive-2_S2_L002

description: single cell RNA


title: arabidopsis_3d_wl_a


title: Naive-2_S2_L001

description: single cell RNA


title: arabidopsis_1d_wl_a

value: unshaded root 1d


title: arabidopsis_7h_wl_b

value: unshaded root 7h


title: arabidopsis_7h_wl_a


title: arabidopsis_1d_wl_b


title: Naive-2_S1_L003

description: single cell RNA

value: BALB/c


title: Naive-2_S1_L002

description: single cell RNA

value: Female


title: Naive-2_S1_L001

description: single cell RNA

value: 6-8 weeks old


title: arabidopsis_30min_sh_a


title: Naive-1_S36_L002

description: single cell RNA

value: Skin


title: Naive-1_S36_L004

description: single cell RNA


title: arabidopsis_30min_wl_a

value: unshaded root 30min


title: Naive-1_S36_L001

description: single cell RNA

value: Naive


title: Naive-1_S35_L002

description: single cell RNA


title: arabidopsis_5d_wl_b

value: root


title: arabidopsis_30min_wl_b


title: Naive-1_S35_L004

description: single cell RNA


title: Naive-1_S35_L001

description: single cell RNA


title: RNA-seq of K562 cell line: 50nM dasatinib resistant

city: Adelaide

first: Benjamin

middle: Chia Sing

last: Leow

state: South Australia

address: SAHMRI North Terrace

department: Cancer Theme

country: Australia

institute: SAHMRI

data_processing:
Sequencing data was uploaded to the Illumina BaseSpace Sequencing Hub (Illumina Inc.), which was used for FastQC quality control. Results were used for differential gene expression analysis (EdgeR).
Raw counts for each samples were obtained by using featureCounts with default parameters
Assembly: Hg19
Supplementary files format and content: rawcounts_featurecounts.txt - raw counts from featureCounts with NCBI gene ID
Supplementary files format and content: DE_50_200.txt - a list of differentially expressed genes compared between the controls and DAS 50 and DAS 200
Supplementary files format and content: DE_10_15_25.txt - a list of differentially expressed genes compared between the controls and DAS 10, DAS 15 and DAS 25

extract_protocol:
Total RNA was extracted using the Phenol:Chloroform method, followed by ribosomal and non-coding RNA depletion.
Sequencing libraries were prepared using the NEXTFlex Rapid Directional RNA Seq Library Prep Kit (Perkin Elmer, Inc., Waltham, MA), depleting ribosomal and non-coding RNA.
Quality control of RNA was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA), using the Bioanalyzer RNA 6000 Nano assay. Libraries were sequenced on the Illumina MiSeq instrument (Illumina Inc., San Diego, CA), using a 150 cycle to produce 2x75 bp paired end reads.

value: Erythroblast

value: Long-term dasatinib co-culture


title: RNA-seq of K562 cell line: 25nM dasatinib resistant


title: RNA-seq of K562 cell line: 15nM dasatinib resistant


title: RNA-seq of K562 cell line: 200nM dasatinib resistant


title: Naive-1_S34_L004

description: single cell RNA


title: RNA-seq of K562 cell line: DMSO control

value: DMSO vehicle control


title: RNA-seq of K562 cell line: 10nM dasatinib resistant


title: Naive-1_S34_L002

description: single cell RNA


title: Naive-1_S34_L001

description: single cell RNA


title: arabidopsis_3h_wl_b

value: unshaded root 3h


title: RNA-seq of K562 cell line

value: Drug-naive control


title: 1663-PBL-Pop4

city: Atlanta

first: Weirong

last: Chen

state: GA

address: 615 Michael Street

department: School of Medicine

institute: Emory University

description:
S15
1663.txt

data_processing:
*library strategy: adaptive immune receptor response sequence (AIRR-seq)
Sequences were quality filtered and aligned with IMGT.org/HighV-quest.
Sequences were then analyzed for V region mutations and clonality using programs developed in-house and made previously available for public use.
All clonal assignments were based on matching V and J regions, matching CDR3 length, and 85% CDR3 homology.
Custom scripts and in-house developed analysis software were used with R, Matlab or Circos tools for visualization, and the scripts are available through the previous publication (Tipton et al, Nat Immunol 2015).
Supplementary files format and content: Tab delimited text file include sequences from all ASC subsets

source_name: Peripheral Blood

extract_protocol:
Sorted ASC populations (Pop 2, Pop 3, Pop 4 and Pop 5) from active SLE patients were used to extract the total cellular RNA by using the RNeasy Mini Kit (Qiagen, Inc. Valencia, CA) according to the manufacturer's protocol.
Approximately 400 pg of RNA was subjected to reverse transcription using the iScript RT kit (BioRad, Inc., Hercules, CA). Resulting cDNA products were combined with 50 nM VH1- VH6 specific primers and 250 nM Ca, Cm, and Cg specific primers in a 25 μl PCR reaction using High Fidelity Platinum PCR Supermix (Life Technologies, Carlsbad, CA).

value: Peripheral Blood

tag: subject status

value: active SLE patient

tag: subject id

value: PBL

tag: population


title: 1663-PBL-Pop5

description:
S16
1663.txt


title: 1663-PBL-Pop3

description:
S14
1663.txt


title: Naive-1_S1_L004

description: single cell RNA


title: Naive-1_S33_L002

description: single cell RNA


title: Naive-1_S33_L001

description: single cell RNA


title: 1663-PBL-Pop2

description:
S13
1663.txt


title: arabidopsis_3h_wl_a


title: Naive-1_S1_L003

description: single cell RNA


title: Naive-1_S1_L002

description: single cell RNA


title: Naive-1_S1_L001

description: single cell RNA


title: 1495-PBL-Pop4

description:
S11
1495.txt


title: 1495-PBL-Pop2

description:
S9
1495.txt


title: WT, replicate 3, scRNAseq

city: San Francisco

first: Min

state: CA

address: Fourth St.

institute: University of California

description:
10x Genomics
701

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Subcutaneous Inguinal adipose depot

extract_protocol:
SVF was isolated from the subcutaneous white adipose depots of 8-week old male wild-typeC57Bl/6J mice. Briefly, the adipose depots were dissected and then manually minced in DMEM/F12 and digested with collagenase 2 (1.5 units/ml; Roche). They were then incubated at 37°Cwith agitation for 60 min and vortexing for 10s every 10-15mins. HBSS with 2% FBS was addedand the dissociated cells were centrifuged at 350 × g for 5 min. Floating mature lipid-filledadipocytes were aspirated and the cell pellets were resuspended in ACK lysis buffer to removethe red blood cells, followed by the addition of HBSS with 2% FBS. The cells were then filteredthrough a 40-mM filter and pelleted by centrifugation at 350 × g for 5 min. Cell pellets wereresuspended in 200ul FACS staining buffer (5-10 x 105 cells/tube) and incubated with thefollowing antibodies for 30 min at 4°C protected from light. Cells were washed twice with FACSbuffer to remove unbound antibodies. The cells were sorted using a BD FACS Aria cell sorter (BD Biosciences). Cellss were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Adipocyte progenitors

value: Subcutaneous Inguinal adipose depot

value: 8 weeks old


title: WT, replicate 2, scRNAseq

description:
10x Genomics
470


title: 1382-PBL-Pop5

description:
S8
1382.txt


title: Naive-1_S33_L004

description: single cell RNA

value: BALB/c

value: Female


title: 1382-PBL-Pop4

description:
S7
1382.txt


title: WT, replicate 1, scRNAseq

description:
10x Genomics
463


title: Mouse #7651, replicate 4

city: Irvine

first: Scott

last: Atwood

address: 4238 McGaugh Hall

department: Department of Developmental and Cell Biology

institute: University of California, Irvine

description:
LT-4
10x Genomics

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed fastq files, and the CellRanger Pipeline (10x Genomics) was used to align reads and generate count matrices, against the mouse genome GRCm38/mm10. For downstream analysis, the Seurat (v4.3.0) R package (Hao et al., 2021) was used to combine the 4 cell libraries and a merged Seurat object was generated. Genes detected in <3 cells were removed. Low-quality cells were further filtered on the basis of total UMI counts per cell (>900 and <80,000), number of detected genes (>200 and <7,000) and mitochondrial genes fraction (<15%). Applying these filters resulted in a final data-set of 1,066 single cell transcriptomes.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Dorsal skin

extract_protocol:
Label-on PPARG;YFP male mouse #7651 was euthanized at 8 weeks of age, and dorsal skin was shaved and removed. Epidermal cells were obtained by overnight trypsinization (0.25% trypsin, Invitrogen). Single cells were resuspended in 2% BSA/HBSS, stained with DAPI to exclude dead cells, and sorted using a SH800 cell sorter (Sony). 60,000 YFP+ cells were sorted for single cell analysis into 2% BSA/HBSS buffer, at a ratio of 3:1 FSC/BSC-high:FSC/BSC-low, where “high” cells represented the largest ~10% of cells by FSC/BSC.
Single cell suspensions were subjected to counting on the LUNA Fx7 Automated Cell Counter (Logos Biosystems) and diluted to a concentration of 300 cells/μL. Single nuclei 3’ Gene Expression LT libraries were generated using the 10x Genomics Chromium instrument following the manufacturer’s protocol (Chromium Next GEM Single Cell 3’ LT Kit v3.1). In brief, suspensions were loaded onto the 10x chip along with reverse transcription (RT) master mix and appropriate gel beads. Following generation of single-cell gel bead-in-emulsions (GEMs), reverse transcription was performed, and the resulting Post GEM-RT product was cleaned up and the cDNA is amplified. cDNA was subjected to enzymatic fragmentation and size selection to optimize the cDNA size prior to final library construction following the manufacturer’s protocol (10x Genomics). Final library quality was assessed using the LabChip GX (PerkinElmer). Libraries were then subjected to paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq 6000). Four LT reactions were run in parallel (LT1-4) from the same animal.

value: Sebaceous gland

value: Dorsal skin

value: PPARG;YFP label-on

value: 8 weeks

value: Male


title: Mouse #7651, replicate 3

description:
LT-3
10x Genomics


title: 1382-PBL-Pop2

description:
S5
1382.txt


title: Mouse #7651, replicate 2

description:
LT-2
10x Genomics


title: 1099-PBL-Pop4

description:
S3
1099.txt


title: 1099-PBL-Pop3

description:
S2
1099.txt


title: CXCR6KO OT-1 CD8 T cells from vaccinia-OVA infected skin

city: New York

first: Amanda

last: Lund

address: 522 First Ave

institute: NYU Langone Health

description: 10x Genomics

data_processing:
The barcoded processing, gene counting were made using the Cell Ranger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skin/Ear

extract_protocol: WT and CXCR6KO OT1 CD8 T cells were isolated from mouse ears 21 days post ear infection with vaccinia-OVA. Mouse ears were incubated with collagenase D for 1 hour and then smashed on a scored plate. Ear suspension was filtered and then cells were stained with CD8 PE. Cells were then CD8 enriched using Miltenyi magnetic enrichment kit. WT and CXCR6KO OT1 CD8 T cells were then fluorescence activated cell sorted for CD8+, CD45 intravenous negative, CD44+, ZombieRed- and congenic marker (WT=CD45.1, CXCR6KO =CD90.1/GFP)

value: Skin/Ear

value: CD8 T cell

value: CXCR6KO OT-1 CD90.1 Female

tag: agent

value: vaccinia-OVA


title: WT OT-1 CD8 T cells from vaccinia-OVA infected skin

description: 10x Genomics

value: WT OT-1 CD45.1 Female


title: NPs

city: Beijing

first: Zhenyu

last: Zhu

state: Beijing

address: 38 Xueyuan Road, Haidian

institute: Peking University

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Lymphocytes

extract_protocol:
RNA was purified using Trizol reagent and the integrity was assessed by the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
The trancriptome libraries were prepared using Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) and sequenced by the Illumina NovaSeq 6000

treatment_protocol: Cells were treated with NPs or NP-IDO-APT  for six days

value: Lymphocytes

value: WT

value: NPs


title: NP-IDO-APT

value: NP-IDO-APT


title: 1495-PBL-Pop5

description:
S12
1495.txt

value: Peripheral Blood

value: active SLE patient

value: PBL


title: pancreatic islets from CtBP2 flox 4

city: Tsukuba

first: Motohiro

last: Sekiya

address: 1-1-1 Tennodai

institute: University of Tsukuba

data_processing:
Sequencing reads were mapped to mm10 mouse reference genome.
The quality of the sequence reads was assessed with FastQC (version 0.11.7).
Low quality (<20) bases and adapter sequences were trimmed by Trimmomatic software (version 0.38).
The trimmed reads were aligned to the reference genome using RNA-seq aligner HISAT2 (version 2.1.0).
The SAM file generated by HISAT2 were converted into BAM files with Samtools (version 1.9).
Assembly: mouse reference genome mm10
Supplementary files format and content: bigWig files

source_name: pancreatic islet

extract_protocol:
CtBP2 flox mice were crossed with BAC INS1-Cre (Hasegawa Y et al. Experimental Animals 2014) to generate pancreatic beta cell specific CtBP2 KO mice. Mice were euthanized at 12-16 weeks of age. Pancreatic islets were isolated and subjected to RNA extraction using a kit (RNeasy micro kit, QIAGEN).
The library was prepared using NEBNext UltraII Directional RNA Library Prep Kit.
Sequencing was performed using NovaSeq6000 (Illumina).

value: pancreatic islet

value: flox

value: normal chow


title: 1495-PBL-Pop3

description:
S10
1495.txt


title: serial dilutions data set 2(250rep)

city: Cambridge

first: Aimin

last: Yan

address: One Kendall Square Building 300 Suite 201

institute: AVROBIO, Inc.

description: clonal dilution

data_processing:
bcl22fastq
IS-Seq pipeline
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw abundance values for each Sample
Library strategy: IS-Seq

source_name: HL60 cell line

growth_protocol: On Day 0, HL60 cells were seeded at 1,000,000 cells/mL with IMDM in the presence of 20% FBS and 1% Pen/Strep in 6-well plates

extract_protocol:
Genomic DNA (gDNA) isolation from single cell clones was performed using a QIAamp 96 DNA QIAcube HT Kit (Qiagen)
Linear - amplification mediated PCR(LAM-PCR)

treatment_protocol: HL60 WT cells were then transduced with a lentiviral vector encoding for the GFP marker gene at the following Multiplicity Of Infection(MOI) of 5,10,20,30 and 50

tag: sample type

value: serial dilutions data set 2(250rep)


title: single cell clone data set

description: single cell clones

value: single cell clone data set


title: serial dilutions data set 1(250+500)

description: clonal dilution

value: serial dilutions data set 1(250+500)


title: pancreatic islets from CtBP2 flox 2


title: pancreatic islets from CtBP2 flox 3


title: CI_2_P4_2

city: Chiba

first: Ichiro

last: Manabe

address: 1-8-1 Inohana, Chuo

institute: Chiba University

data_processing:
Reads were aligned to the hg38 human genome using STAR.
Assembly: hg38
Supplementary files format and content: bedGraph files were generated using Homer.

source_name: human uterine cervical fibroblast

growth_protocol: We prepared cervical fibroblasts from uterine tissue collected with appropriate informed consent. After delivery of the fetus and placenta in a scheduled cesarean section before the onset of labor, we identified the closed endocervix through the uterine wound and collected 5 mm of cervical tissue. The study protocol was approved by the Nippon Medical School Hospital institutional committee and performed in accordance with Ethical Guidelines for Medical and Biological Research Involving Human Subjects. Uterine cervical tissue was cut into small pieces and incubated Dulbecco’s modified Eagle’s medium (Gibco/Invitrogen, Carlsbad, CA, USA) containing 10% fetal bovine serum (HyClone, Logan, UT, USA) in a humidified atmosphere of 5% CO2 and 95% air at 37 °C. The culture medium was changed twice a week. Once confluent, fibroblasts were enzymatically detached with 0.25% trypsin (Gibco) and cultured in 10cm culture plates.

extract_protocol:
Total RNA was extracted from cells and purified using an RNeasy Mini Kit (Qiagen)
Poly-A mRNA was extracted from the total RNA using oligo-dT beads in a NEBNext Poly (A) RNA Magnetic Isolation Module (New England Biolabs), after which, RNA-seq libraries were prepared using the RNA-Seq library preparation kit for Illumina (New England Biolabs), according to the manufacturer’s protocols.

treatment_protocol: Each fibroblasts derived from control and CI were precultured with E2 in duplicate for 24 hours, then incubated with progesterone (1 μM) or EtOH (solvent) alone for 6 hours.

tag: condition

value: progesterone treated cells derived from cervical insufficiency

value: human uterine cervical fibroblast

tag: passage

value: progesterone treated


title: pancreatic islets from CtBP2 knockout 4

value: CtBP2 KO


title: pancreatic islets from CtBP2 flox 1


title: 1382-PBL-Pop3

description:
S6
1382.txt


title: 1099-PBL-Pop5

description:
S4
1099.txt


title: pancreatic islets from CtBP2 knockout 3


title: CI_2_notx_1

value: untreated cells derived from cervical insufficiency

value: untreated


title: CI_2_notx_2


title: CI_1_P4_2


title: CI_1_P4_1


title: CI_1_notx_2


title: pancreatic islets from CtBP2 knockout 1


title: 1099-PBL-Pop2

description:
S1
1099.txt


title: control_2_P4_2

value: progesterone treated cells derived from unripend cervix


title: CI_1_notx_1


title: Liver, CR group, 30 weeks old, rep4

city: Shanghai

first: Jiteng

last: Fan

state: Shanghai

address: 130 Dongan Road

institute: Fudan university

data_processing:
Illumina Casava 2.19 used for base-calling.
Clean data(clean reads) were obtainedl by removing reads containing adapter, reads containing ploy-N and low quality reads fromraw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include fpkm values for each sample

source_name: liver

extract_protocol:
RNA was harvested using Trizol regent.Illumina TruSeq RNA Sample Prep Kit was uesd. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

value: 30percent CR diet


title: Liver, CR group, 30 weeks old, rep3


title: Liver, CR group, 30 weeks old, rep1


title: control_2_P4_1


title: Liver, CR group, 30 weeks old, rep2


title: control_2_notx_2

value: untreated cells derived from unripend cervix


title: CI_2_P4_1


title: Liver, AL group, 30 weeks old, rep3

value: AL diet


title: control_1_P4_2


title: control_2_notx_1


title: Liver, AL group, 30 weeks old, rep2


title: Liver, AL group, 30 weeks old, rep1


title: pancreatic islets from CtBP2 knockout 2

value: pancreatic islet


title: control_1_notx_1


title: BEC_3

city: Philadelphia

first: Takeshi

last: Katsuda

address: 421 Curie Blvd, BRB II/III Rm531

department: Perelman School of Medicine

institute: University of Pennsylvania

data_processing:
Reads were mapped to GRCm39 mouse genome using the STAR aligner (version 2.7.10b).
Read counts were obtained using the featureCounts package (v2.0.1)
Read counts were imported to DESeq2, and normalization was performed using the "median of ratios normalization" method.
Assembly: GRCm39
Supplementary files format and content: Tab-delimited normalized data including all the samples.

source_name: Liver

extract_protocol:
RNA was isolated with Nucleospin RNA kit (Takara)
Library was prepared by Novogene (Sacramento, CA)

treatment_protocol: Mice were injected with AAV8-TBG-Cre for lineage trace hepatocytes. One week after AAV injection, biliary reprogramming was induced by challenging the mice with diet containing 0.1% 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC). After 8 weeks, cells were harvested, FACS-sorted, and RNA was isolated from them.

value: Liver

value: EGFP- Epcam+ cells

value: WT

value: AAV8-TBG-Cre injected; challenged with 0.1% DDC for 8 weeks

tag: Stage

value: BEC


title: BEC_2


title: BEC_1


title: Rep_full_3

value: EGFP+ Cd24+ Epcam+ cells


title: Rep_full_2


title: Kidney cortex biopsy_baboon_male_15072

city: Winston Salem

first: Laura

middle: A

last: Cox

state: NC

address: 1 Medical Center Blvd

department: Internal Medicine

institute: Wake Forest School of Medicine

data_processing:
Female and male transcripts were processed together in Partek Flow with an average read length of 93.58± 1.52 (minimum=25) and an average Phred score of 36.46 ± 0.54 (minimum=30).
Reads were aligned to the olive baboon genome (papAnu2.0; March 2012) with 57,005 transcripts represented by an average of 11,161,874 ± 3,684,392 total reads and 5.80 ± 1.88% coverage and 16.23 ± 2.71 depth.
Transcripts were excluded where the sum was less than or equal to 5 among all samples and normalized using TMM with a +1 offset to eliminate zeros for downstream analyses.
The full transcript list generated in Partek Flow was imported into Partek Genomics Suite for principal component analysis (PCA) (Partek®, Inc).
Transcripts were filtered for expression values totaling <17 among all samples and filtered based on coefficient of variation for values equal to 0 prior to sex-specific WGCNA.
The R package WGCNA was run as a Pearson’s correlation with default settings as described by Langfelder and Horvath34.
Genome_build: papAnu2.0
Supplementary_files_format_and_content: Matrix table with annotated normalized transcript counts for every transcript and WGCNA results from male samples.
Supplementary_files_format_and_content: Matrix table with annotated normalized transcript counts for every transcript and WGCNA results from female samples.

organism: Papio hamadryas

source_name: Kidney cortex biopsy

growth_protocol: Animals were maintained on a low salt chow diet their whole life leading up to the study.

extract_protocol:
RNA was isolated from kidney biopsy samples using the Direct-zol RNA Miniprep Plus Kit (Zymo Research). Tissue was homogenized in 600 μL of TRI reagent (Zymo Research) using a BeadBeater for 3 x 30 sec with RNA purification according to the Direct-zol RNA Miniprep Plus Kit instructions. RNA was quantified by Qubit RNA BR Assay Kit (Invitrogen) and RIN was determined by with an RNA ScreenTape Kit on the Tapestation 2200 (Agilent).
cDNA libraries were prepared using the KAPA Stranded mRNA-Seq Kit (Roche). Libraries were quantified by Qubit dsDNA Assay Kit (Invitrogen) and quality was determined by with a DNA ScreenTape Kit on the Tapestation 2200 (Agilent).

tag: animal id

tag: sample name

tag: diet

value: low salt control chow

value: male

tag: age

tag: colony

value: Southwest national primate research center

tag: collection

value: Ultrasound guided biopsy into liquid nitrogen

tag: surgery anesthetic

value: Animals were sedated with ketamine (10mg/kg, IM) and maintained on isoflurane (1.3-3.0%) anesthetic throughout the procedures. Buprenorphine (0.2 mg/kg, SQ) was administered for post operative pain relief after surgery and as needed over 24-48 hour period.

value: Kidney cortex biopsy


title: Kidney cortex biopsy_baboon_male_11184

tag: Sex

tag: tissue


title: Rep_intermed_2

tag: cell type

value: EGFP+ Cd24+ Epcam- cells

tag: genotype

tag: treatment


title: Rep_intermed_1


title: Kidney cortex biopsy_baboon_male_14460


title: Rep_intermed_3


title: Rep_full_1


title: Kidney cortex biopsy_baboon_male_14812


title: Kidney cortex biopsy_baboon_male_14027


title: Kidney cortex biopsy_baboon_male_14277


title: control_1_P4_1

value: progesterone treated cells derived from unripend cervix

value: human uterine cervical fibroblast

value: progesterone treated


title: Rep_early_1

value: EGFP+ Cd24- Epcam- cells


title: Rep_early_2

value: Liver


title: Rep_early_3


title: Kidney cortex biopsy_baboon_female_15562

value: female


title: Kidney cortex biopsy_baboon_male_15058


title: Kidney cortex biopsy_baboon_female_17174


title: control_1_notx_2

value: untreated cells derived from unripend cervix

value: untreated


title: Kidney cortex biopsy_baboon_male_14930


title: Kidney cortex biopsy_baboon_female_15122


title: CRPR2, cRNAseq

first: Shengzhe

state: TX

address: 6565 MD Anderson Blvd

department: Experimental Radiation Oncology

institute: MD Anderson Cancer Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The Seurat (v1.8.2) R package and Python (v3.8.12) package Scanpy (v1.8.2) were used for pre-processing and clustering of scRNA-seq data.
Assembly: mm10
Supplementary files format and content: Matrix files

extract_protocol:
Freshly collected mouse SCLC tumors and allograft tumors were transferred to a dry dish and minced into pieces with blades. The tissue was digested in Leibovitz’s medium (Invitrogen) with 2 mg/mL Collagenase Type I (Worthington), 2 mg/mL Elastase (Worthington) and 2 mg/mL DNaseI (Worthington) at 37 °C for 45 min. The tissue was triturated with pipet every 15 min of digestion until homogenous. The digestion was stopped with FBS (Invitrogen) to a final concentration of 20%. The cells were filtered with a 70 μm cell strainer (Falcon) and spun down at 5000 rpm for 1 min. The cell pellet was resuspended in red blood cell lysing buffer (Sigma) for 3 min, spun down at 5000 rpm for 1 min and washed with 1 mL ice-cold Leibovitz’s medium with 10% FBS. Cells were resuspended in 1 mL ice-cold Leibovitz’s medium with 10% FBS and filtered with a cell strainer (20 μm). Dead cells were removed with Dead Cell Removal Kit (Miltenyi Biotec) according to the manufacturer's instructions. Live cells were collected for 10x Genomics library preparation.
Single-cell Gene Expression Library was prepared according to the Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics). Briefly, single cells, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single-cell GEMS (Gel Beads-In-Emulsions), where full-length cDNA was synthesized and barcoded for each single cell. Subsequently, the GEMS were broken and cDNAs from each single cell were pooled, followed by cleanup using Dynabeads MyOne Silane Beads and cDNA amplification by PCR. The amplified product was then fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. The final library was generated by amplification.

value: Lung


title: preSC_CracdKO, cRNAseq

description: 10x Genomics

source_name: allograft

value: allograft

tag: cell line

value: preSC

value: CracdKO


title: Presc_WT, cRNAseq

description: 10x Genomics

value: WT


title: Kidney cortex biopsy_baboon_female_15113

value: low salt control chow

value: Southwest national primate research center

value: Ultrasound guided biopsy into liquid nitrogen


title: Kidney cortex biopsy_baboon_female_14740

value: Animals were sedated with ketamine (10mg/kg, IM) and maintained on isoflurane (1.3-3.0%) anesthetic throughout the procedures. Buprenorphine (0.2 mg/kg, SQ) was administered for post operative pain relief after surgery and as needed over 24-48 hour period.

value: Kidney cortex biopsy


title: RPR2, cRNAseq

description: 10x Genomics

source_name: Lung


title: Kidney cortex biopsy_baboon_female_14690


title: male not infected

city: La Jolla

first: Li-Fan

last: Lu

address: 9500 Gilman Dr., NSB 5314

department: Biological Sciences

institute: University of California, San Diego

description: 10x Genomics

data_processing:
Illumina’s bcl2fastq software was used for demultiplexing index 1 i7 for each of the four samples.
The fastq files were aligned to the mm10 mouse genome using the Cell Ranger (7.0.0) pipeline, including intronic reads.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: large intestine lamina propria

extract_protocol:
After perfusion, large intestines were harvested and minced before transferring to conical tubes. The minced pieces were resuspended in 10ml of complete RPMI-1640 containing 1% P/S, 20mM HEPES, 0.05 mg/ml Liberase TL (Roche), 0.05% DNaseI (Roche) and shaken at 200 rpm for 30 min at 37°C in 50-ml Falcon tubes. The tissue suspension was collected and passed through a 70 mm cell strainer and the cells were pelleted by centrifugation at 1500 rpm. The cells were then resuspended and purified by 47% Percoll and centrifuged at 1500 rpm for 10 min. The pellet were collected, washed and resuspended in complete RPMI media. CD45+ immune cells were then enriched for by Miltenyi Beads.
Library was performed according to the manufacter’s instructions (SC RNA3’ V3.1, 10X Genomics) GEMS were generated, poly-A RNA in every GEM was retrotranscripted to cDNA, cleaned up with Dynabeads, amplified by PCR and the appropriate sized fragments were selected with SPRIselect for library constrution. A sample index (i7) was added to each of the four samples during library construction.

value: large intestine lamina propria

value: 2-3 months

value: M

value: immune cells

value: not infected


title: male infected with Citrobacter rodentium

description: 10x Genomics

value: infected with 5.0 x 109 CFU of Citrobacter Rodentium strain DBS100


title: female not infected

description: 10x Genomics

value: F


title: breast, 2-3

city: shanghai

first: zhangjingnan

middle: zhangjinnan

last: zhangjinnan

address: cailunroad 1200

institute: Shanghai University of Traditional Chinese medicine

data_processing:
To be updated.
Assembly: mm10
Supplementary files format and content: The FPKM of gene in samples.

source_name: breast

growth_protocol: Mice were supplied with standard laboratory diet and water ad libitum at a temperature 22±1 °C with a 12 h light–dark cycle (6:00–18:00) and 65±5% humidity. All mice were received humane care in compliance with the institutional animal care guidelines approved by the Experimental Animal Ethical Committee, Shanghai University of Traditional Chinese Medicine.

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
1) RNA product after fragmentation mRNA enrichment (or rRNA removal) treatment.
2) Reverse transcription to generate first-strand cDNA:
3) Synthesis of double-stranded cDNA by dUTP addition:
4) End repair of double-stranded cDNA by each polymerase:
5) Ligase ligation of Illumina-specific connectors.
(6) PCR amplification and purification to obtain the final RNA sequencing library.
The constructed libraries were quality checked by Agilent 2100 Bioanalyzer (library concentration, fragment size 400-600bp, presence of splice, etc.) and final quantification of the libraries was performed by 9PCR method. The libraries were mixed according to the quantification results and the final sequencing data volume required to enter the sequencing process.

treatment_protocol: Six balb/c male mice were randomly divided into 2 groups: (1) vehicle control (n=3) and (2) 1 mg/kg ITSN (n=3), where mice were given ITSN orally (1 mg/kg/day, administered intragastrically).

value: breast

tag: strain

value: Balb/c

value: ITSN


title: Kidney cortex biopsy_baboon_male_14243

value: male