title: WT input

city: Boulder

first: Jennifer

last: Kugel

state: Colorado

address: 3415 Colorado Ave

department: Biochemistry

institute: University of Colorado at Boulder

data_processing:
The sequencing quality was assessed using FastQC
Reads were mapped to the human genome using the hg19 assembly with Bowtie v1.2.2 in the -v alignment mode allowing one mismatch per read (-v1), mapping the first 50 nucleotides (--trim3 101), and only reporting reads that aligned to a unique position (-m1).
Tag directories were created in HOMER v4.9.1 from the .map files generated by Bowtie
HOMER v4.9.1 was used to create bedgraph files for visualization by using the makeUCSCfile command and forcing the file size to be 50mb (-fsize 50e6)
Tag directories were converted to BED file format in HOMER v4.9.1 and the Bedtools (v2.27.1) coverage command was used to determine Pol II occupancy in gene bodies.
DESeq2 (v1.26.0) was used to identify significant changes in gene body Pol II occupancy between mock and WT, and mock and n12 infections.
Genome_build: Hg19
Supplementary_files_format_and_content: Processed data files are bedgraph files of each biological replicate and input

source_name: Embryonic Kidney cells

growth_protocol: HEK 293 cells were grown in modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 mg/ml streptomycin at 37°C in 5% CO2.

extract_protocol:
Cells were crosslinked and chromatin was isolated and sheared. Pol II-DNA bound complexes were purified by antibody precipitation.
Libraries for Illumina sequencing were prepared from the Pol II ChIP eluates by the University of Colorado Anschutz Genomics and Microarray Core facility using the Tecan Ovation Ultralow DNA Library System. Sequencing was performed using an Illumina NovaSEQ6000, obtaining 2 × 150 bp reads.

treatment_protocol: Cells were treated in biological duplicate (rep 1 and rep 2) with indicated virus at an MOI of 10 pfu/cell with WT HSV-1, an equivalent viral load with n12, or with untreated media for 1h (mock). The inoculum was aspirated and replaced with fresh pre-warmed media for the remaining 3h of infection.

value: HEK 293

value: 4h infection with WT HSV-1 KOS strain


title: N3

status: Public on Jul 07 2021

type: SRA

city: wuxi

first: fangmei

last: an

state: jiangsu

address: NO 299,QingYang Road

country: China

institute: Wuxi Public Hospital

library_source: transcriptomic

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The remaining reads were filtered against the rRNA database to remove possible ribosomal RNA contamination,  and then mapped to the hg19 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM/counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: gastric mucosa

extract_protocol: Total RNA extraction

tag: tissue

value: gastric mucosa

tag: tissue type

value: chronic superficial gastritis


title: Jimbour_R_3

city: Penrith

first: Krista

last: Plett

state: NSW

address: Locked Bag 1797

department: Hawkesbury Institute for the Environment

country: Australia

institute: Western Sydney University

data_processing:
NovaSeq sequencing was performed at the Ramaciotti Centre for Genomics (University of New South Wales, Sydney, Australia)
Raw reads from the RNA-sequencing were trimmed and mapped to the C. arietinum genome (desi type - ICC4958) using CLC Workbench v.10. Genes that were not expressed or lowly expressed (<5 counts on average across each set of 3 replicates) were eliminated from the data set.
Genome_build: C. arietinum genome (desi type - ICC4958)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Cicer arietinum

source_name: Roots

growth_protocol: Chickpea seeds from three genotypes forming low numbers of nodules (Jimbour, Boundary, ICC11664) and three genotypes with high nodulation (ICC9002, ICC2072 and ICC1510) were sterilized in 10% bleach, rinsed in sterile water and planted into vermiculite for two weeks. Seedlings were transplanted to sterilized soil and acclimatised to the new soil for a day prior to inoculation.

extract_protocol:
RNA was extracted from the chickpea roots (3 biological replicates per condition) using the Isolate II RNA Plant kit (Bioline, London, U.K.) according to manufacturer’s instructions.
RNA libraries were constructed using the SENSE total RNA-Seq library prep kit (Lexogen, Vienna, Austria)

treatment_protocol: Actively growing cultures of M. ciceri (~10,000 CFU per plant) was applied to half of the chickpeas while a mock solution without rhizobia was applied to the other half. Chickpea roots were harvested and frozen in liquid nitrogen 3 days after addition of live M. ciceri cultures or mock controls.

tag: genotype

value: Jimbour

tag: agent

value: Mesorhizobium ciceri


title: TT-239_DMSO

city: South San Francisco

first: Farshad

last: Farshidfar

state: CA

address: 171 Oyster Point Blvd Ste 500

country: USA

institute: Tenaya Therapeutics Inc.

data_processing:
Read alignment by Salmon (ver. 1.3.0)
tximport to generate gene expression matrix in Transcript Per Million (TPM)
Protein-coding genes identification by Ensembl human reference genome release 100
Exclusion of mitochondrial genes and renormalization to TPM.
Genome_build: hg38 v.13
Supplementary_files_format_and_content: TXT

source_name: iPSC-CM

growth_protocol: iPSC Culture, iPSC-CM Differentiation, and Blasticidin Selection: WTC iPSCs and derivative lines were maintained under feeder-free conditions on growth factor-reduced Matrigel (BD Biosciences) and fed daily with E8 medium (STEMCELL Technologies) (Ludwig et al., 2006). Accutase (STEMCELL Technologies) was used to enzymatically dissociate iPSCs into single cells. To promote cell survival during enzymatic passaging, cells were passaged with p160-Rho-associated coiled-coil kinase (ROCK) inhibitor Y-27632 (10μM; Selleckchem) (Watanabe et al., 2007). iPSCs were frozen in 90% fetal bovine serum (HyClone) and 10% dimethyl sulfoxide (Sigma). iPSCs were differentiated into iPSC-CMs using the Wnt modulation-differentiation method (Lian et al., 2012) with 7μM CHIR (Selleckchem) and 5μM IWP2 (Sigma) in RPMI media supplemented with B27 (Thermo Fisher Scientific). iPSC-CMs were purified using 1μM blasticidin (Thermo Fisher Scientific). Then, 15 days after adding CHIR, iPSC-CMs were frozen in 90% fetal bovine serum (FBS) + 10% DMSO. iPSC-CMs were thawed in RPMI+B27+10% FBS directly onto Matrigel-coated 384-well plates at a density of 20,000 cells/well. The next day, the media was switched to Tenaya’s Cardiomyocyte (TCM) media for 6 days before screening. TCM media comprises Dulbecco's Modified Eagle Medium (DMEM) without glucose, 10% dialyzed FBS, 10mM D-(+)-galactose, and 1mM sodium pyruvate. Generation of Blasticidin-Selectable iPSC Line: A plasmid containing the Bsd open reading frame and a selectable marker containing Puromycin and green fluorescent protein was knocked into the 3’ end of the MYH6 locus of WTC iPSCs. Cells were selected with puromycin. After the first round of selection, the selectable marker was removed using a plasmid expressing Cre recombinase (Supplemental Figure 1A). Clones were isolated and verified using colony polymerase chain reaction (PCR) to ensure the presence of the Bsd marker and absence of the selectable cassette. Finalized clones showing the appropriate iPSC morphology were sent to WiCell for single-nucleotide polymorphism karyotyping (Figure S1B).

extract_protocol:
RNA Extraction: Approximately 10^5 to 10^6 iPSC-CMs were lysed with TRI Reagent (Zymo Research) and frozen at -80 °C to ensure complete cell lysis. Total RNA was extracted and washed from lysed cells using the Direct-zol-96 RNA Kit (Zymo Research) according to the manufacturer’s instructions. Samples were treated with DNase I for 15 minutes at room temperature. cDNA was reverse transcribed from 1 μg of RNA through random hexamers using the SuperScript-III kit (Invitrogen) according to the manufacturer’s instructions. Real-time qPCR reactions were performed using the TaqMan universal PCR master mix (Applied Biosystems) with the TaqMan probes listed in Table S5 (Life Technologies).
Library Preparation: 100ng total RNA was extracted via polyA-tail specific protocol according to Illumina protocol. RNA library preparation was achieved by using TruSeq Stranded mRNA kit (Illumina) which also removes ribosomal RNA. The libraries were sequenced as 100bp single-end reads using Illumina NovaSeq SP with an average of 30M reads per sample.

treatment_protocol: Approximately 10^5 iPSC-CMs exposed to cardiotoxic drugs for 4 days.

tag: treatment

value: DMSO

tag: media-timepoint

value: 0.1% DMSO

tag: cell type

value: iPSC cardiomyocytes


title: N1


title: H4K16ac ChIP MSL2 vir 2

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

library_source: genomic

data_processing:
Sequencing reads were aligned to the dm6 version of the D. melanogaster genome using bowtie2 (version 2.3.5) allowing only unique matches
Coverage vectors were generated by counting overlapping fragments at each genomic position
Genome_build: dm6 (mel) and caf1 (vir)
Supplementary_files_format_and_content: bigwig files with coverage

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: KC cells

growth_protocol: D. melanogaster embryonic Kc167 cell line was obtained from the Drosophila Genomic Resource Center (https://dgrc.bio.indiana.edu/Home). D. melanogaster S2 (subclone L2-4) cell line was a kind gift of P Heun (Villa et al., 2016). D. virilis 79f7Dv3 cell line was a kind gift of BV Adrianov (Albig et al., 2019). The identity of cell lines was verified by high-throughput sequencing. Cells were subjected to mycoplasma testing. Cells were maintained at 26°C in Schneider’s Drosophila Medium (Thermo-Fischer, Cat. No 21720024) supplemented with 10% FBS (Kc167 and S2) or 5% FBS (79f7Dv3) and 1% Penicillin-Streptomycin solution (Sigma-Aldrich, Cat No P-4333). Spodoptera frugiperda 21 (SF21) cells (Gibco) were used for amplification of recombinant baculoviruses and baculovirus-driven expression of recombinant proteins. SF21 cells were cultured at 26°C in Sf-900 II medium (Gibco) supplemented with 10% fetal calf serum and gentamycin.

extract_protocol:
Pellet from 6 × 107 S2 or virilis cells was suspended in 1.2 ml of lysis buffer (10 mM Tris pH 8, 100 mM NaCl, 25 mM EDTA pH 8, 0.5% SDS, 0.15 mg/ml of proteinase K) and incubated at 56°C overnight. After addition of sodium acetate to a final concentration of 0.3 M, the nucleic acids were extracted with phenol–chloroform and precipitated with an equal volume of isopropanol at −20°C for 1 h. Precipitated nucleic acids were centrifuged and washed with 70% ethanol. Dried pellets were resuspended in TE buffer and sonicated with Covaris AFA S220 (microTUBEs, Peak Incident Power 175 W, Duty Factor 10%, Cycles per Burst 200, 430 s) to generate 200 bp fragments. After RNAse digestion (0.1 mg/ml, 1 h at 37°C), DNA was purified with the GenElute kit (Sigma-Aldrich). DNA immunoprecipitation (DIP) experiments were performed as in (Villa et al. 2016) with few modifications. Briefly, 400 ng of genomic DNA (gDNA) was incubated with 80nM of recombinant proteins at 26°C for 30 min in 100 μl of binding buffer (100 mM KCl, 2 mM MgCl2, 2 mM Tris–HCl pH 7.5, 10% Glycerol, 10 μM ZnCl2). Ten percent of the reaction was taken as input material. DNA–protein complexes were immunoprecipitated using 30 μl of anti-FLAG M2 beads (SIGMA) and washed twice with 100 μl of binding buffer to eliminate unbound DNA. After proteinase K digestion (0.5 mg/ml, 1 h at 56°C), DNA was purified with AMPure beads (Beckman Coulter).
Libraries for sequencing were prepared using NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs, E7465).

treatment_protocol: Cells were transfected with the plasmid of interest plus 1:20 of pCoBlast (Thermo Fischer, Cat. No K5150-01) using Effectene transfection reagent (QIAgen, Cat. No 301425). 72h after transfection cells were diluted 2-3 times and Blasticidin was added to the medium at a final concentration of 50ng/ul for 7 or 10 days. For the DIP experiments in presence of RNA we pre-incubated the recombinant proteins with different amount of RB4 (GGUUAACGUUAUACAAGCCGAG) or ctrl (GACGUUGUAAUAUGUACGGGAU) RNA oligos and proceeded with the normal DIP protocol.

tag: ip target

tag: assay type

value: ChIP

tag: experimental series

tag: transfection

value: GFP-MSL2 vir


title: H4K16ac ChIP MSL2 mel 2

value: GFP-MSL2 mel


title: Jimbour_R_2


title: WT rep 2

tag: cell line

tag: chip antibody

value: Pol II (Rpb1 NTD (D8L4Y))


title: Boundary_R_1

value: PBA Boundary


title: SMC 5hmc 48hr replicate 2

city: Fukuoka

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

country: Japan

institute: Kyushu University

data_processing:
Targeted hydroxymethylome sequencing reads were mapped to the human reference genome sequence (hg19) using Bmap (http://itolab.med.kyushu-u.ac.jp/BMap/index.html).
Hydroxymethylation levels were calculated for individual CG sites.
Genome_build: hg19
Supplementary_files_format_and_content: BED files include chrmosome, position, strand, the number of hmC reads and the number of total reads.

source_name: SMC 5hmc 48hr

growth_protocol: hcSMCs (Human Coronary Artery Smooth Muscle Cells) were cultured in SMGM-2 (Smooth Muscle Growth Medium-2, Lonza) at 37C. After reaching confluent, hcSMCs were washed in PBS, and the culture medium was changed to DMEM low glucose, pyruvate with 0.2% fetal bovine serum for 48 hours. After this, cholesterol was delivered to cells by changing the medium to DMEM with water-soluble cholesterol at a final concentration 3.3 (µg/ml) [Chol:MβCD 75 (µg/ml)]. Cells were harvested at 24, 48, 72 hours after the cholesterol loading started.

extract_protocol:
Cultured hcSMCs were washed once with PBS and lysed directly with the lysis buffer in the flasks, and total RNA and DNA were extracted using RNA/DNA/Protein Purification Plus Kit (Norgen #47700). The DNA samples was quantified using Qubit® 2.0 Fluorometer (Life technologies).
One thousand ng of genomic DNA spiked with two pmol of biotinylated double-stranded oligonucleotides with 5-mC or 5-hmC modifications was treated with the 5mC Tet1 Oxidation Kit from Wise Gene according to the manufacture's instruction. After the reaction, DNA was purified using the QiaQuick PCR purification kit (Qiagen). The purified DNA was mixed with Dynabeads MyOne Streptavidin T1 and incubated at room temperature for 30 min with rocking. Both supernatant and beads were separately bisulfite-treated using EZ DNA Methylation-Gold Kit (Zymo Reesarch). The bisulfite-treated DNA from the beads was used for monitoring the conversion efficiency of 5-mC and 5-hmC. In contrast, the bisulfite-treated DNA from the supernatant was served for library preparation with the tPBAT protocol described in Miura F et al. (2019).

value: Cultured smooth muscle cells


title: WT rep 1


title: H4K16ac ChIP control 2


title: CAG+IM1

value: chronic atrophic gastritis + intestinal metaplasia


title: mock input

value: mock infection


title: TT-237_DMSO


title: Jimbour_C_3

value: Mock


title: Jimbour_R_1


title: SMC 5hmc 48hr replicate 1


title: H4K16ac ChIP Input 6


title: SMC 5hmc 24hr replicate 3

source_name: SMC 5hmc 24hr


title: H4K16ac ChIP Input 5


title: SMC 5hmc 24hr replicate 2


title: mock rep 2

value: HEK 293


title: Jimbour_C_2


title: mock rep 1


title: Jimbour_C_1


title: H4K16ac ChIP Input 4


title: n12 input

value: 4h infection with HSV-1 n12


title: SMC 5hmc 24hr replicate 1


title: H4K16ac ChIP control 1


title: SMC 5hmc 0hr replicate 3

source_name: SMC 5hmc 0hr


title: n12 rep 1


title: ICC09002_R_2


title: SMC 5hmc 0hr replicate 2


title: n12 rep 2


title: ICC09002_R_1


title: H4K16ac ChIP Input 3


title: SMC 5hmc 0hr replicate 1


title: H4K16ac ChIP Input 2


title: H4K16ac ChIP Input 1


title: huh7-WDR4-561

city: wuhan

first: xia

last: peng

state: hubei

address: zhongnan hospital

institute: wuhan university

data_processing:
llumina Novaseq 6000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: sh-WDR4-2 in Huh-7 cells, 48hr

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

tag: protocol

value: Human liver cancer cells

value: transfected with siWDR4


title: H4K16ac ChIP MSL2 vir 1


title: ICC09002_C_2


title: ICC09002_C_3


title: SMC 5mc 48hr replicate 3

data_processing:
Targeted methylome sequencing reads were mapped to the human reference genome sequence (hg19) using Bmap (http://itolab.med.kyushu-u.ac.jp/BMap/index.html).
Methylation levels were calculated for individual CG sites.
Genome_build: hg19
Supplementary_files_format_and_content: BED files include chrmosome, position, strand, the number of mC reads and the number of total reads.

source_name: SMC 5mc 48hr

extract_protocol:
Cultured hcSMCs were washed once with PBS and lysed directly with the lysis buffer in the flasks, and total RNA and DNA were extracted using RNA/DNA/Protein Purification Plus Kit (Norgen #47700). The DNA samples was quantified using Qubit® 2.0 Fluorometer (Life technologies).
One hundred ng of genomic DNA spiked with one ng of unmethylated lambda DNA (Promega) was served for tPBAT protocol (Miura F et al, 2019).


title: SMC 5mc 48hr replicate 2


title: ICC09002_C_1


title: huh7-WDR4-NC

source_name: sh-NC in Huh-7 cells, 48hr

value: transduced with sh-NC


title: H4K16ac ChIP MSL2 mel 1


title: HCC-LM3-NC

source_name: sh-NC in HCC-LM3 cells, 48hr

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


title: HCC-LM3-WDR4-561

source_name: sh-WDR4-2 in HCC-LM3 cells, 48hr

value: transduced with WDR4


title: ICC02072_R_3

value: Mesorhizobium ciceri


title: SMC 5mc 48hr replicate 1


title: VIR_Pbdrome DIP 4

source_name: S2 cells sheared genomic DNA

value: MSL2 virPbdrome

value: DIP


title: SMC 5mc 24hr replicate 3

source_name: SMC 5mc 24hr


title: EV_PRL_R3

city: RICHMOND

first: Alicia

middle: Eileen

last: Woock

state: VA

address: 1101 E Marshall St

department: Pathology

institute: Virginia Commonwealth University

data_processing:
Illumina NovaSEQ6000 System software was used for base-calling, generating ≥50 million 150 bp paired-end (PE) reads per sample
Sequenced reads were trimmed for adapters and any read that was trimmed to less than 30bp was removed with CutAdapt. FastqScreen of a randomly sampled subset of readsfrom each sample was aligned to multiple genomes, and results indicated that there was no contamination in any of the samples.
STAR v2.7.3a  was used to align the fastq files to the latest version of the human genome, GRCh38. Prior to transcript quantification, the GFFRead utility was used to create a transcriptome fasta file from the main reference genome fasta file.
Salmon v0.12.0 utilized the transcript fasta file to quantify each transcript from the STAR-aligned data.  Salmon’s “quant” mode was used with the library type set to “ISF”.  Salmon output included the raw count estimate, TPM value, and estimated transcript length for each gene.
The tximport R package was used to import the Salmon quantifications from each sample into R v3.6.0, identify the official gene symbol, and merge raw count and TPM values into a single matrix file
Genome_build: GRCh38
Supplementary_files_format_and_content: Salmon quant files contain the output of the Salmon 'quant' algorithm with estimated transcript length, TPM, and estimated read count.  The tab delimited text file contains the raw read count obtained from Salmon for all samples, summarized to a single matrix for input into downstream differential expression tools.

source_name: MCF7 cells

growth_protocol: MCF7 breast cancer cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S). Endogenous STAT5a was targeted by shRNA, and stable knockdown was achieved by viral transduction and antibiotic selection. These MCF7 cells with STAT5a knockdown were then rescued: stable rescue with indicated STAT5a species was done by viral transduction and antibiotic selection. Confirmation of rescues was performed by Western Blot. Cells were grown in an incubator at 37C with 5% CO2, and routinely passaged.

extract_protocol:
Cells were washed with 1x PBS, placed on ice, and RNA was harvested using Trizol reagent and the PureLink™ RNA Mini Kit (Thermo Fisher Scientific, 12183018A) with Dnase treatment.
mRNA library was prepared by polyA selection with ≥500 ng RNA using the Universal Plus mRNA-Seq Library Preparation Kit (NuGEN) following manufacturer’s protocol.

treatment_protocol: Following 24 hour serum starvation, (DMEM supplemented with 0.1% BSA), three biological replicates were treated with PRL (250 ng/ml) for two hours.

tag: stat5a knockdown

value: Endogenous STAT5a knockdown

tag: stat5a rescue

value: empty vector (EV) control

value: treated with PRL for 2 hours

tag: biological replicate

value: biological rep 3


title: ICC02072_R_2


title: VIR_Pbdrome DIP 3


title: ICC09002_R_3


title: SMC 5mc 24hr replicate 2

value: Cultured smooth muscle cells


title: EV_PRL_R2

value: biological rep 2


title: ICC02072_C_3


title: ICC02072_R_1


title: SMC 5mc 24hr replicate 1


title: VIR_CXCPbdrome DIP 1

value: MSL2 CXCPbdrome


title: VIR_CXCPbdrome DIP 2


title: EV_PRL_R1

value: biological rep 1


title: EV_0_R2

value: untreated


title: EV_0_R3


title: SMC 5mc 0hr replicate 2

source_name: SMC 5mc 0hr


title: ICC02072_C_2

value: Mock


title: ICC02072_C_1


title: SMC 5mc 0hr replicate 3


title: VIR_CXCdrome DIP 2

value: MSL2 virCXCdrome


title: SMC 5mc 0hr replicate 1


title: VIR_CXCdrome DIP 1


title: ICC01510_R_2


title: ICC01510_R_3


title: EV_0_R1


title: Ezh2 deficient spleen NK

city: beijing

first: Minghang

last: Yu

address: No.10 Xitoutiao, You An Men

institute: Capital Medical University

description: Ezh2fl/fl mice were crossed with Ncr1iCre mice to obtain Ezh2fl/fl; Ncr1iCre mice (Ezh2ΔNK)

data_processing:
Sequenced reads were aligned to the GRCm38 murine transcriptome(bowtie2)
Quantify the expression of transcripts in each cell using BD™ Rhapsody Whole Transcriptome Assay Analysis Pipeline
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Mus musculus

source_name: spleen

extract_protocol:
For cell sorting, the bulk spleen cells were used to isolate the CD45+CD3-CD19-NKp46+NK1.1+ cells for scRNA-seq experiments by BD FACSAria III, and the purity was generally above 95%
Library construction was performed using a BD Rhapsody™ Single-Cell Analysis System following a standard protocol provided by the manufacturer (BD Biosciences)

tag: strain

tag: tissue

value: spleen

tag: age

value: 6~8 week


title: WT spleen NK

tag: genotype

value: wild type


title: MSL2 dromeCXCvir DIP 1

value: MSL2 dromeCXCvir


title: MSL2 dromeCXCvir DIP 2


title: S780A_PRL_R2

value: point mutant S780A-STAT5a

tag: treatment


title: ICC01510_C_3

tag: agent


title: S780A_PRL_R1


title: ICC01510_C_2


title: S780A_0_R3


title: musAd002_UrF_re-analyzed

city: Dallas

first: Gervaise

middle: H.

last: Henry

state: Texas

address: 5323 Harry Hines Blvd, Mail Code:9110

department: Urology

institute: UT Southwestern Medical Center

description: re-analysis of GSM4338168

data_processing:
Illumina's RTA version 1.18.66.3 was used for basecalling
10x Genomics’ cellranger mkfastq version 4.0.0 was used to demultiplex fastqs using default settings
10x Genomics’ cellranger count version 4.0.0 was used to generate mapped bam files using default settings combining fastq's from NextSeq 500 and NovaSeq 6000
Genome_build: mm10
Supplementary_files_format_and_content: Genes-by-cells matrix in Hierarchical Data Format 5 File (H5)

source_name: Mouse urethra

extract_protocol:
Single-cell suspensions containing ~17400 cells were loaded on 10x Genomics Chromium single-cell Controller with 3’ library and gel bead kit v2 and v3  according to manufacture’s recommendations
According to 10x Genomics’ protocol, sequenced (R1=26cycles R2=58cycles, i7=8cycles on NextSeq 500) OR (PE150 on NovaSeq 6000)

treatment_protocol: Single-cells were dissociated from health adult mouse urethra

tag: digestion enzyme

value: 10mg/mL Cold Protease 1hr

tag: number of mice pooled

tag: macs strategy

tag: 10x library type


title: musAd004n5_UrF_re-analyzed

description: re-analysis of GSM4338169


title: S780A_0_R2

value: Endogenous STAT5a knockdown


title: MSL2vir DIP 3

tag: ip target

value: MSL2 Drosophila virilis

tag: assay type

value: DIP

tag: experimental series


title: musAd007_PrFcol_GEX (re-analyzed)

data_processing:
Illumina's RTA version 1.18.66.3 was used for basecalling
10x Genomics’ cellranger mkfastq version 4.0.0 was used to demultiplex fastqs using default settings
10x Genomics’ cellranger count version 4.0.0 was used to generate mapped bam files using default settingscombining fastq's from NextSeq 500 and NovaSeq 6000
Genome_build: mm10
Supplementary_files_format_and_content: Genes-by-cells matrix in Hierarchical Data Format 5 File (H5)

source_name: Mouse prostate

extract_protocol:
Single-cell suspensions containing ~17400 cells were loaded on 10x Genomics Chromium single-cell Controller with 3’ library and gel bead kit v2 and v3 according to manufacture’s recommendations
According to 10x Genomics’ protocol, sequenced (R1=26cycles R2=58cycles, i7=8cycles on NextSeq 500) OR (PE150 on NovaSeq 6000)
scRNA-seq

treatment_protocol: Single-cells were dissociated from health adult mouse prostates

value: prostate

tag: prostatic lobe

value: AP + VP + DLP

value: 1.5mg/mL Collagenase I 1hr


title: ICC01510_C_1

source_name: Roots


title: musAd003_PrF_St (re-analyzed)


title: S780A_0_R1

tag: cell line

tag: stat5a knockdown


title: MSL2vir DIP 2


title: S780A_PRL_R3

tag: stat5a rescue

value: treated with PRL for 2 hours

tag: biological replicate

value: biological rep 3


title: MSL2vir DIP 1


title: S726A_PRL_R3

value: point mutant S726A-STAT5a


title: musAd002_PrF (re-analyzed)

tag: tissue


title: ICC01510_R_1

value: Mesorhizobium ciceri


title: DIP input 2

value: input control


title: DIP input 1


title: MSL2vir DIP 5


title: musAd001_PrF (re-analyzed)


title: GAT ILC2s - Ret KO 4

city: Lisboa

first: Ana

middle: Filipa Ribeiro

last: Cardoso

state: Lisboa

address: Avenida  Brasília, Fundação champalimaud, Immunophysiology lab

country: Portugal

institute: Fundação Champalimaud

description:
RET loss-of-function mutation
edgeR_ct-ko.txt

data_processing:
Data Filtering: raw data with adapter sequences or low-quality sequences was filtered. We first went   through a series of data processing to remove contamination and obtain valid data. This   step was completed by SOAPnuke software developed by BGI.  SOAPnuke software filter parameters：-n 0.001 -l 20 -q 0.4 -A 0.25 --cutAdaptor -Q 2 -G --minLen 100 , steps of  filtering:  1) Filter adapter: Delete the entire read if more than 25% match the adapter sequence;  2) Filter low-quality data: Delete the entire read if there are more than 50% bases having a quality value lower than 20;  3) Remove N: Delete the entire read if there are more than 5% N in the read;  4) Obtain clean reads .
Reads filtering  Sequencing Platform: BGISEQ  Sequencing length: PE100
We used HISAT to align the clean reads to the reference genome. Reference species  Species: Mus_musculus  Source: NCBI  Reference Genome Version: GCF_000001635.26_GRCm38.p6
We used Bowtie2 to align the clean reads to the reference genes.
We used EdgeR to normalize the read counts and determine any diferentially expressed genes.
Genome_build: Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary_files_format_and_content: Tab-delimited text files including read counts values for each sample, and statistics for RetMEN2B vs littermate controsl and for RetΔVav1 vs littermate controls.

source_name: Gonadal adipose tissue

extract_protocol:
For the isolation of adipose tissue cells, tissue was collected into PBS, cut into small pieces and incubated with Liberase TM (2.5µg/ml, Roche) and DNase I (20U/ml; Roche) for 1h at 37°C under gentle agitation. A single cell suspension was obtained by passage through a 100μm cell strainer (Thermo Fisher Scientific) and centrifugation was used to separate the stromal vascular fraction from the adipocyte fraction. Erythrocytes were lysed with red blood cell lysis buffer (eBioscience) and removed by centrifugation. Cell suspensions were stained and populations were gated on live cells and defined as ILC2: CD45+Lin-Thy1.2+Sca-1+KLRG1+. Cells were sorted using FACSFusion (BD Biosciences).  Total RNA from sorted or cultured cells was extracted using RNeasy micro kit or RNeasy mini kit (Qiagen) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Gonadal adipose tissue

tag: cell type


title: GAT ILC2s - Ret KO 3

tag: genotype


title: T3_10d

city: Hangzhou

first: Minjie

last: Huang

state: Zhejiang

address: No. 145 Shiqiao Road

department: Institute of Animal Husbandry and Veterinary Science

institute: Zhejiang Academy of Agricultural Sciences

data_processing:
Illumina Casava software used for basecalling.
Clean data were obtained after discarding the reads containing adapters, reads containing poly-Ns sequences (over 0.2%) and reads of low quality (over 50%) from the raw data.
The remaining clean data were aligned to the reference Apis mellifera genome. All mapped reads were assembled by StringTie
The transcripts obtained from splicing were merged by using Cuffmerge, and transcripts of less than 200 nt in length with an uncertain strand orientation were removed. The obtained sequences were subjected to Blasted searches against the reference database, and known transcripts were filtered out by Cuffcompare.
The expression levels of mRNAs and lncRNAs were calculated as fragments per kilobase of exon per million mapped fragments (FPKM) values.
Genome_build: GCF_003254395.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Apis mellifera

source_name: brain

growth_protocol: Dead bees were removed and the solution was replaced daily throughout the experiment.

extract_protocol:
Brains were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.A total of 3 µg RNA per sample was used to generate a complementary library with the NEBNext® UltraTM RNA Library Prep Kit for Illumina.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The bees were treated with 2 mL of 0.01 mg/L dinotefuran solution in the experimental group.he bees in control group were fed 2 mL of a 50% sucrose: water solution.

value: brain

tag: treatment

value: dinotefuran

tag: age


title: GAT ILC2s - Ret KO 2


title: MSL2vir DIP 4


title: musAd015_UrFcol_3GEX

description: Cells from one normal mouse urethral tissue

tag: digestion enzyme


title: T2_10d


title: GAT ILC2s - Ret KO 1


title: T1_10d


title: GAT ILC2s - Ret KO 5


title: GAT ILC2s - Ret Control 4

description:
Wild type control of RET loss-of-function mutation
edgeR_ct-ko.txt

value: Retfl littermate control


title: Young_Lung_scRNA-seq

city: St. Louis

first: Maxim

last: Artyomov

state: MO

address: 425 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St. Louis

description: infected chow-fed young mouse

data_processing:
Demultiplexing, barcode processing, single-cell 3' counting was performed with Cell Ranger Single-Cell Software Suite v3.0.2
Alignment was performed using Cell Ranger
See detailed methods in Ryu et al.
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: Filtered matrix of gene by cell expression, file with barcodes and file with expressed genes. Files are ready to be imported to Seurat package.

molecule: polyA RNA

source_name: whole lung from mCoV-A59 infected chow-fed young mouse

extract_protocol:
10x Genomics protocols
Single-cell libraries were prepared using standard 10x Genomics protocols.

tag: strain

tag: diet

value: chow

value: young


title: GAT ILC2s - Ret Control 3


title: C2_10d


title: S726A_0_R2

value: Endogenous STAT5a knockdown

value: untreated

value: biological rep 2


title: S726A_0_R1

value: biological rep 1


title: C3_10d


title: Y694F_PRL_R3

value: point mutant Y694F-STAT5a


title: Old-KD_Lung_scRNA-seq

description: infected KD-fed old mouse

source_name: whole lung from mCoV-A59 infected KD-fed old mouse

value: keto

value: old


title: GAT ILC2s - Ret Control 2


title: C1_10d


title: Old-Chow_Lung_scRNA-seq

description: infected chow-fed old mouse

source_name: whole lung from mCoV-A59 infected chow-fed old mouse


title: S726A_PRL_R2

value: treated with PRL for 2 hours


title: S726A_PRL_R1

value: point mutant S726A-STAT5a


title: Y694F_PRL_R2


title: T3_5d

value: 5 d


title: T-3: lung gdT chow bulkRNA-seq

description: 100bp paired-end sequencing

data_processing:
Fastq files for each sample were aligned to the mm10 genome (Gencode, release M25) using STAR (v2.7.3a)
Quality control was performed by FastQC (v0.11.8), MultiQC (v1.9), and Picard tools (v2.21.6).
Quantification was done using htseq-count function from HTSeq framework (v0.11.2)
Genome_build: mm10
Supplementary_files_format_and_content: excel spreadsheet of raw htseq counts

source_name: sorted gdT

extract_protocol:
Total RNA was extracted with RLT buffer
Bulk RNA libraries were prepared for sequencing using standard Illumina protocols.

value: lung gdT


title: GAT ILC2s - Ret Control 1

value: Gonadal adipose tissue


title: T2_5d

value: brain


title: T-2: lung gdT chow bulkRNA-seq

description: 100bp paired-end sequencing


title: Old_Lung_scRNA-seq

description: infected chow-fed old mouse


title: Y694F_0_R3

value: biological rep 3


title: S726A_0_R3


title: GAT ILC2s - Ret MEN2B 2

description:
RET gain-of-function mutation
edgeR_mut-wt.txt


title: T-1: lung gdT chow bulkRNA-seq

description: 100bp paired-end sequencing


title: Y694F_0_R2


title: GAT ILC2s - Ret MEN2B 1


title: T-6: lung gdT keto bulkRNA-seq

description: 100bp paired-end sequencing


title: Y694F_0_R1


title: C3_5d


title: C2_5d


title: T-5: lung gdT keto bulkRNA-seq

description: 100bp paired-end sequencing


title: GAT ILC2s - Ret WT 3

description:
Wild type control of RET gain-of-function mutation
edgeR_mut-wt.txt

value: RetWT littermate control


title: GAT ILC2s - Ret WT 2


title: T-4: lung gdT keto bulkRNA-seq

description: 100bp paired-end sequencing


title: WT_PRL_R3

value: wild type (WT)-STAT5a


title: GAT ILC2s - Ret MEN2B 3


title: Y694F_PRL_R1


title: T3_1d

value: dinotefuran

value: 1 d


title: C1_5d


title: GAT ILC2s - Ret WT 1


title: WT_PRL_R2

value: Endogenous STAT5a knockdown


title: WT_PRL_R1


title: T2_1d


title: WT_0_R3

value: untreated


title: T1_5d


title: miRVana screen_3

type: other

city: New York City

first: Coen

last: van Solingen

state: New York

address: 435 E30th street, Science Building 723T, Science Building 723T

department: Cardiology/Medicine

institute: NYU School of Medicine

description:
firefly_3
renilla_3

scan_protocol: Luciferase activity was read on a spectrophotometer (Envision).

data_processing:
PCSK9 3’UTR firefly luciferase values were normalized to those of control renilla luciferase values for each replicate
Raw data: Luciferase (firefly, renilla) activity in Relative Luciferase Units (RLU).  Six columns.
Normalized data: Ratio of average of firefly luciferase over average of renilla luciferase = ((firefly_1/renilla_1) + (firefly_2/renilla_2) + (firefly_3/renilla_3))/3.  One column.

molecule: other

growth_protocol: HEK293T cells  were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Corning) containing 10% Fetal Bovine Serum (FBS, Life Technologies) and 1% penicillin-streptomycin (pen-strep, Life Technologies).

extract_protocol: Luciferase activity was assayed with the Dual-Glo Luciferase Assay® (Promega) according to the manufacturer’s instructions.

treatment_protocol: HEK293T cells were seeded in a 384-well, white solid bottom polystyrene TC-treated microplates and co-transfected with 1.5 pmol of miRNA mimic, and 10 ng of total DNA plasmids composed of a 2:1 ratio of PCSK9 3’-UTR firefly luciferase reporter plasmid (Switchgear Genomics) to renilla luciferase control plasmid using Lipofectamine 2000 (Invitrogen).

tag: luciferase

value: Firefly luciferase, Renilla luciferase


title: T1_1d


title: miRVana screen_1

description:
firefly_1
renilla_1


title: WT_0_R1

value: biological rep 1


title: C2_1d


title: WT_0_R2

value: biological rep 2


title: Stretched Disease TPCs

city: Stanford

first: Christopher

last: Still

state: California

address: 443 Via Ortega, Room 376

institute: Stanford

description: Mechanical stimulus applied

data_processing:
10X Chromium libraries processed by Cellranger version 3.0.2.
Drop-seq libraries processed using the Drop-seq alignment cookbook. Hisat2 was used instead of the standard STAR aligner.
Cell hashing data was processed using CITE-seq-Count python package version 1.4.3
Genome_build: hg19
Supplementary_files_format_and_content: Drop-seq processed files are tab-delimited text files
Supplementary_files_format_and_content: Cell hashing processed files are csv files
Supplementary_files_format_and_content: 10X Chromium libraries are contained in standard cellranger output filtered_feature_bc_matrix

source_name: Tendon progenitor cells

growth_protocol: Following extraction of cells from tendon samples, cells were plated at low density (500 cells per cm^2) until confluent. All cells used in experiments started at passage 2. Cells were grown in low-glucose DMEM with 10% FBS, 50ug/ml ascorbic acid, and antibiotics.

extract_protocol:
Peritendous connective tissue was removed. Tendon tissue was then broken down by digestion with 0.1% type IV collagenase at 37°C with gentle agitation. Cells were then passed through a 70-micron filter to obtain a single cell suspension.
Drop-seq libraries were constructed as detailed in Macosko et al. 2015 with minor exceptions. A glass dolomite chip was used instead of the traditional PDMS chip. 10X Chromium Single Cell 3' V3 libraries were generated according to the standard protocol by the Stanford Functional Genomics Facility (SFGF). Cell Hashing libraries were generated according to the standard protocol by the SFGF.

treatment_protocol: Moderate strength cyclic stetch (6% end-to-end) for 12 hours a day, 3 days in a row followed by 1 day of rest.

value: Patellar Tendon

tag: disease status

value: Tendinopathy


title: C3_1d


title: C1_1d


title: HALO-VviNAC33

city: Verona

first: Nicola

last: Vitulo

state: Verona

address: Ca' Vignal 1, Strada Le Grazie 15

department: Department Biotechnology

country: Italy

institute: University of Verona

description: 1000ng of gDNA lilbrary

data_processing:
Library strategy: DAP-seq
Fastq files were trimmed using trimmomatic with the following parameters ILLUMINACLIP:TruSeq3- SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:50
Reads were mapped to the grape reference genome version 12X.2 using bowtie2 (version 2.3.4.3).
Reads mapping in multiple location were filtered removing all the reads with the XS:i field present in the BAM file
Peaks were called using GEM v3.4 with the following parameters: --d Read_Distribution_default.txt --k_min 6 --k_max 20 --outNP.
All the peaks with a ratio between sample/control lower than 5 fold were discarded
Genome_build: Association between the identified peaks and the nearest gene was performed using ChipSeeker R package using grape gene annotation V0 transposed on 12X.2 assembly
Supplementary_files_format_and_content: GEM event output file

organism: Vitis vinifera

source_name: Syrah leaves (wild type)

growth_protocol: The DAP-seq data were obtained using genomic DNA extracted from the young leaves of growth chamber-grown fruiting cuttings (Mullins et al., 1981) of Vitis vinifera cv. Syrah.

extract_protocol:
The genomic DNA was extracted from V. vinifera cv. Shiraz young leaves using a protocol adapted by Katsuhiro Matsui from Thomas et al., 1993.The leaves were harvested, frozen and ground in liquid nitrogen and stored at -80°C. Afterwards, 1g of powder was transferred to a 50ml falcon tube in which 12.5 ml of Crude Nuclei Buffer pH 7.6 (0.25M NaCl, 0.2M Tris-HCl pH 7.6, 2.5% PVP 40.000, 0.05M EDTA, 0.1% β-mercaptoethanol) were added. After a quick vortexing, the sample was centrifuged at 4°C for 10 minutes at 4000 rpm and the supernatant was discarded. The pellet was resuspended by vortexing with 5ml of DNA Extraction Buffer EtOH/Sark (0.5M NaCl, 0.2M Tris-HCl pH 8, 2.5% PVP 40.000, 0.05M EDTA pH 8, 3% N-Lauroylsarcosine, 20% EtHO,1% β -mercaptoethanol). The sample was left at 55°C for 30 minutes with frequent shacking and then added of 5ml chloroform. After vortexing, the solution was transferred into a 15 ml falcon tube and centrifuged at 20°C for 15 minutes at 5000 rpm. The upper phase was transferred into a new 50 ml falcon tube and 2.5 ml of isopropanol were added; the tube was mixed by inverting until a precipitate was seen and left at room temperature for 15 minutes. After a 15 minutes centrifuge at 5000 rpm and 20°C, the supernatant was poured off and the pellet was washed with 5 ml of 70% ethanol. The sample was re-centrifuged for 10 minutes at 5000 rpm and 20°C the pellet was air dried. Then, the dry pellet was resuspended in 600 µl of TE buffer (10mM Tris-HCl pH 8, 1mM EDTA pH 8) with 3 µl of RNase (stock 20mg/ml) and left overnight at 4°C. The solution was then transferred into a 1.5 ml collection tube and 300 µl of 7.5M NH4OAc were added. The DNA solution was centrifuged at room temperature for 10 minutes at 13.000 rpm, the supernatant was transferred into a new 1.5 ml tube and the DNA was precipitated with 0.5 ml of isopropanol. After another room temperature 10 minutes spin at 13.000 rpm, the pellet was washed again with 70% ethanol and let air dry. The DNA was finally resuspended in 300 µl of TE and its concentration was measured with the QubitTM dsDNA BR Assay kit (ThermoFisher).
For the DNA library preparation, the gDNA was fragmented and ligated with a truncated Illumina TruSeq adapter as described in Bartlett at al., 2017 and Galli et al., 2018. 7.5 µg of gDNA were diluted in 130 µl of EB (Qiagen), loaded into a Covaris microTUBE and sonicated using a Covaris S2 sonicator to obtain the fragments peak size of 200 bp. The sheared sample was then transferred into a 1.5 ml low-bind tube, cleaned with AMPure XP beads (Beckman Coulter) at a 2:1 ratio of gDNA:beads and eluted in EB. The end-repair reaction was set up using the End-It kit (Lucigen) and the cleaning was made with the Qiaquick PCR Purification kit (Qiagen). The end-repaired fragments were A-tailed using the Klenow Fragment 3’-5’ exo- (NEB) at 37°C for 30 minutes. After another Qiaquick purification, the truncated Illumina Y-adapter was ligated using the T4 DNA Ligase (NEB) at 16°C overnight. The enzyme was inactivated at 70°C for 10 minutes and then the sample was purified using a 1:1 ratio of library:beads. The final library was eluted in EB and quantified at the Qubit.

treatment_protocol: The previously isolated VviNAC33 ORF was transferred from the pENTR/D-TOPO (Invitrogen) entry vector into the Gateway-compatible pIX-HALO destination vector (Bartlett et al., 2017) using the GatewayTM LR Clonase II Enzyme mix (Invitrogen). The HALO-VviNAC33 fusion protein was then in vitro expressed using the TNTR SP6 Coupled Reticulocyte Lysate System (Promega) and 1 µg of pIX-HALO-ORF plasmid. An aliquot of the in vitro translation was conserved to verify the protein expression performing a Western blot analysis using the Promega Anti-Halotag monoclonal antibody.The assay was performed following the protocol of Bartlett et al., 2017.The remaining HALO-VviNAC33 fusion proteins TNT solution were at first immobilized on 1XPBS + NP40 (0.005%) washed Magne Halo Tag Beads (Promega) with 1 hour rotation at room temperature; in addition to the VviNAC33 sample, a HALO-GST in vitro expressed protein was also immobilized to be used as negative control. The beads were washed 4 times in 1XPBS + NP40 (0.005%) and resuspended in the same solution. 1000 ng of gDNA library were added to the protein bound beads and the samples were rotated for 1 hour at room temperature. The beads were washed 6 times in 1XPBS + NP40 (0.005%), transferred in a new tube and resuspended in EB. For the DNA release the beads were heated at 98°C for 10 minutes. Performing a 20 cycles PCR amplification with the Phusion High-Fidelity DNA Polymerase (NEB), the eluted DNA fragments were enriched and tagged with dual indexed multiplexing barcodes (Galli et al., 2018). Another 1:1 ratio AMPure XP beads purification was performed. Finally, the samples were quantified using the QubitTM dsDNA HS Assay kit (Invitrogen) and the absence of adapter dimers was checked using the KAPA Library Quantification kit (KAPA Biosystems). Samples were pooled and sequenced with 75 bp single end reads, obtaining a total of 3 million reads for each sample.

tag: cultivar

value: Syrah

tag: genotype/variation

value: HALO-VviNAC33 fusion protein

value: Young Leaves

tag: assay

value: DAP-seq

tag: tf in vitro translation kit


title: Stretched Normal TPCs

description: Mechanical stimulus applied

value: Normal


title: WT3_iTreg_DFMO

status: Public on Jul 06 2021

city: Berkeley

first: Allon

last: Wagner

address: 378 Stanley Hall

institute: UC Berkeley

data_processing:
All ATAC-Seq reads were trimmed using Trimmomatic (Bolger et al., 2014) to remove primer and low-quality bases. Reads < 36bp were dropped.
Reads were then passed to FastQC [http://www.bioinformatics.babraham.ac.uk/projects/fastqc/] to check the quality of the trimmed reads.
The paired-end reads were then aligned to the mm10 reference genome using bowtie2 (Langmead and Salzberg, 2012), allowing maximum insert sizes of 2000 bp, with the “--no-mixed” and “--no-discordant” parameters added. Reads with a mapping quality (MAPQ) below 30 were removed. Duplicates were removed with PicardTools, and the reads mapping to the blacklist regions and mitochondrial DNA were also removed.
Reads mapping to the positive strand were moved +4 bp, and reads mapping to the negative strand were moved -5bp following the procedure outlined in (Buenrostro et al., 2013) to account for the binding of the Tn5 transposase.
Peaks were called using macs2 on the aligned fragments (Zhang et al., 2008) with a qvalue cutoff of 0.001 and overlapping peaks among replicates were merged.
Genome_build: mm10

source_name: Spleen CD4+ T cells

growth_protocol: Naïve CD4+CD44-CD62L+CD25-T cells were sorted using BD FACSAria sorter and activated with plate-bound anti-CD3 (1µg/ml) and antiCD28 antibodies (1µg/ml) in the presence of cytokines at a concentration of 0.5 × 10^6cells/ml. For T cell differentiations the following combinations of cytokines were used: pathogenic Th17: 25ng/ml rmIL-6, 20ng/ml rmIL-1b (both Miltenyi Biotec) and 20ng/ml rmIL-23 (R&D systems); non-pathogenic Th17: 25ng/ml rmIL-6 and 2ng/ml of rhTGFb1 (Miltenyi Biotec); iTreg: 2ng/ml of rhTGFb1;

extract_protocol:
In vitro differentiated T-cells were sorted for live cells and stored in Bambanker freezing media (Thermo Fisher Scientific) at -80°C until further processing. Prior to library preparation, cells were thawed at 37  °C and washed with PBS.
Cell pellets were lysed and tagmented in 1X TD Buffer, 0.2ul TDE1 (Illumina), 0.01% digitonin, and 0.3X PBS in 40ul reaction volume following the protocol described in (Corces et al., 2016). Transposition reactions were incubated at 37 °C for 30 min at 300 rpm. The DNA was purified from the reaction using a MinElute PCR purification kit (QIAGEN). The whole resulting product was then PCR-amplified using indexed primers with NEBNext High-Fidelity 2X PCR Master Mix (NEB). First, we performed 5 cycles of pre-amplification. We sampled 10% of the pre-amplification reaction for SYBR Green quantitative PCR to assess the number of additional cycles needed for final amplification. After purifying the final library with the MinElute PCR purification kit (QIAGEN), the library was quantified for sequencing using qPCR and a Qubit dsDNA HS Assay kit (Invitrogen). Libraries were sequenced on an Illumina NextSeq 550 system with paired-end reads of 37 base pairs in length.

treatment_protocol: cells were harvested at 68 hours and were performed in the presence or absence of 100µM DFMO (Sigma)

value: iTreg

value: DFMO


title: WT2_Th17n_DFMO


title: WT1_Th17n_DFMO


title: WT2_iTreg_DFMO


title: WT3_Th17n_DFMO


title: WT1_iTreg

value: Vehicle


title: WT2_iTreg


title: WT3_iTreg


title: WT2_Th17n


title: WT1_iTreg_DFMO


title: WT1_Th17n


title: miRVana screen_2

description:
firefly_2
renilla_2

tag: cell line


title: HALO-GST_negative control

description: 1000ng of gDNA lilbrary

value: control

value: TNTR SP6 Coupled Reticulocyte Lysate System


title: 3-2, MUT REP2

type: RNA

city: Ardmore

first: Sheng

last: Ying

state: OK

address: 2510 Sam Noble Pkwy

institute: Noble Research Institute

data_processing:
Data normalization between chips was conducted using RMA (Robust Multichip Average) (Irizarry et al., 2003) implemented in Expression Console (Affymetrix).
Genes whose residuals between the compared sample pairs that are significantly higher than the measured background noise level were considered to be differentially expressed. A selection threshold of 2 for transcript ratios and a Bonferroni-corrected P value threshold of 2.19202E-06 were used (Dozmorov and Centola, 2003).

label: biotin

organism: Arabidopsis thaliana

source_name: Arabidosis root, MUT

label_protocol: Probe labeling, chip hybridization and scanning were performed according to the manufacturer’s instructions for 3' IVT PLUS Kit (Affymetrix).

growth_protocol: Arabidopsis seelings grow vertically on1/2 strength MS solid culture for 7 days

extract_protocol: Total RNA was isolated using RNeasy® plant mini kit (QIAGEN) following the manufacturer’s instructions. RNA was quantified and evaluated for purity using a Nanodrop Spectrophotometer ND-100 (NanoDrop Technologies) and Bioanalyzer 2100 (Agilent)

value: root

value: 7 days

value: AtRXR1 mutant


title: 3-1, MUT REP1

hyb_protocol: according to the manufacturer’s instructions for 3' IVT PLUS Kit (Affymetrix).


title: WT3_Th17n


title: 2-2, OX REP2

scan_protocol: according to the manufacturer’s instructions for 3' IVT PLUS Kit (Affymetrix).

source_name: Arabidosis root, OX

value: AtRXR1 overexpression


title: 1-1, WT REP1

source_name: Arabidosis root, WT

value: WT


title: 1-2, WT REP2


title: 2-1, OX REP1


title: NM_02_130

city: Beijing

first: Ping

last: Lu

address: 5 Yiheyuan Road

institute: Peking University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
scRNA-Seq：Sequencing read pairs were split into single-cell RNA-seq read pairs according to the 8bp barcode of read2, followed by corresponding extraction of read1. Unique Molecular Identifiers (UMIs) were added to sequence identifier of read1 in order to correctly identify PCR duplicates later. We subsequently trimmed template switch oligo (TSO) sequence and ployA tail sequence in read1. After removing adapter contaminants and low-quality bases (N > 10%), we aligned clean reads to hg19 human reference genome from UCSC using TopHat (version 2.0.12). Then, the htseq-count script developed with HTSeq (version 0.6.0) was used to count uniquely aligned reads with genes. Transcripts of the same gene with identical UMIs were regarded as PCR duplicates and removed in this process.
Genome_build: hg19
Supplementary_files_format_and_content: A  comma-separated values (csv) file include UMI counts for each single cell RNA samples

source_name: kidney cancer patients’ paracancerous tissues

growth_protocol: Paracancerous tissues from renal carcinoma were diced and incubated with 0.5mg/ml type II (SIGMA, C6885) and 0.5mg/ml type IV (SIGMA, C5138) collagenase at 37℃ for 15 min. The glomeruli were transferred by pipetting to RPMI 1640 with 25 mM HEPES (Gibco, 22400-089) supplemented with 100 U/mL penicillin, 100 ug/mL streptomycin, 2 mM L-glutamine and 10% fetal bovine serum. After 7-10 days’ incubation, mesangial cells were seen at the edges of glomeruli that attached to the plate and passaged when confluent using 0.05% trypsin. Mesangial cells after 4~5 weeks of subculture still remains homogenous, the morphologically was characterized by phase contrast microscopy. Immunofluorescence staining of Desmin (Abcam, ab32362, 1:100) and Vimentin (Abcam, ab8978, 1:100) were used to identify mesangium. All experiments were performed using confluent mesangial cells from the 2nd to 4th passage. In an attempt to mimic the microenvironment around mesangial cells in vivo, mesangial cells were cultured with serum collected from normal volunteers or IgAN patients. In order to avoid influence of complement, all human serums were heat-inactivated by 56℃ water bath for 30 min before using.

extract_protocol:
Single-cell RNA sequencing was conducted using a modified high throughput STRT method. Single cell was transferred to lysis buffer containing a 25-bp RT primer that consists of poly T and a fragment of cell barcode and unique molecular identifier (UMI). The reverse transcription was then initiated by SSII, the synthesized cDNA was further amplified by 19 cycles of PCR to generate double-strand DNA. Then, the purified DNA was further amplified by another four cycles of PCR using a biotinylationed primer to add biotin modification to the 3’ terminal of the synthesized DNA. Subsequently, the modified double-strand DNA were fragmented to 300 bp by super sonication, the 3’ terminal fragments were then coupled to streptavidin C1 beads with one hour’s incubation. After washing by 2X B&W buffer, 3’ terminal of reverse transcribed DNA on C1 beads were used for library construction.
Preparation of library was based on the instruction of Kapa Hyper Prep Kit.
All sequencing data were generated by 150-bp pair-end sequencing through an Illumina Hiseq-4000 platform.

treatment_protocol: Sample collection procedure was approved by the Medicine Ethics Committee of the Chinese People’s Liberation Army General Hospital (S2017-102-01). 13 IgAN patients’ renal biopsies and 6 renal paracancerous tissue were collected. To capture cells inside glomerulus, renal biopsies were first cut into millimeter-sized pieces, the treated tissues were then transferred to 1ml 0.5mg/ml collagenase II and collagenase IV mixtures and digested for 5 min at 37°C with slight shaking. Digested tissues were then transferred to a 2 cm dish and diluted by 1 ml DMEM cell culture medium. Glomerulus were quickly picked using 100 µm inner-diameter mouth pipette and transferred to a 20 µl DPBS dro in 2 cm dish, after slightly treating with needle, the glomerulus were transferred to 200 µl mixtures containing 0.5mg/ml collagenase II, 0.5 mg/ml collagenase IV and 0.0125% tyrisin for 15 minutes’ digestion at 37°C with 900 rpm shaking. Meanwhile, the rest tissues were collected and centrifuged at 500g for 3min, after removing supernatant, tissues were resuspeded by 500 µl 0.5mg/ml collagenase II and collagenase IV mixtures and digested at 37°C with 900 rpm shaking for 10 min. After digestion, cells were centrifuged at 800g for 5min. For glomerulus cells, about 80~90 µl supernatant was discarded and resuspended by 200 µl DMEM culture medium. For the rest renal cells, all supernatant was removed and the pellets were then resuspended by 100 µl DMEM. To capture the major cell types, the non-glomerulus renal cells were first incubated with 100 µl buffer containing 10 µl CD14+ MicroBeads (Miltenyi, 130-050-021) for 15 min at 4°C. Cells were then washed by 1X DPBS and macrophages were isolated on magnetic rack using MS column, 300 µl DMEM was added to the column to flush out macrophages. The negative selected cells were then resuspended by 100 µl DMEM, after 15 min’s incubation with 100 µl buffer that contains 10 µl CD326 (EPCAM) beads at 4°C, epithelium were isolated using MS column on magnetic rack. To cover all the cell types, the last negative selected cells were also collected. All collected cells were diluted to 300 µl using DMEM. For monocytes collection, we took 5 ml peripheral blood from each of the 5 normal people and 5 of the 13 IgAN patients. Peripheral blood samples were collected into EDTA vacutainers. Peripheral blood monocytes were first isolated by Ficoll-Paque (Solarbio, P8680). The PBMC cell layer was collected and washed three times with PBS. After centrifugation with 800g for 5 min, cell pellets were resuspended in 300 µL buffer which contains 30 µl CD14+ beads and incubated for 15 min at 4℃. Cells were washed by PBS and monocytes were isolated using LS Column on MACS Separator (Miltenyi, 130-042-302). 5 mL of DMEM were added to the column to flush out positive cells using the plunger supplied with the column. Cell suspension was centrifuged and resuspended to 500 µl.

tag: patients

tag: disease state

value: kidney cancer

value: paracancerous tissues


title: NM_02_145

tag: tissue


title: NM_02_131


title: NM_02_128


title: NM_02_136


title: NM_02_148


title: NM_02_129


title: NM_02_134


title: NM_02_140


title: NM_02_147


title: NM_02_126


title: NM_02_149


title: NM_02_135


title: NM_02_141


title: NM_02_138


title: NM_02_132


title: NM_02_146


title: NM_02_127


title: NM_02_142


title: NM_02_139


title: NM_02_144


title: NM_02_143


title: NM_02_125


title: NM_02_133


title: NM_02_137


title: NM_02_124


title: NM_02_123


title: NM_02_122


title: NM_02_120


title: NM_02_121


title: NM_02_108


title: NM_02_102


title: NM_02_103


title: NM_02_110


title: NM_02_115


title: NM_02_117


title: NM_02_104


title: NM_02_097


title: NM_02_098


title: NM_02_099


title: NM_02_109


title: NM_02_111


title: NM_02_112


title: NM_02_094


title: NM_02_118


title: NM_02_096


title: NM_02_105


title: NM_02_106


title: NM_02_114


title: NM_02_113


title: NM_02_107


title: NM_02_093


title: NM_02_119


title: NM_02_116


title: NM_02_095


title: NM_02_092


title: NM_02_101


title: NM_02_091


title: NM_02_090


title: NM_02_100


title: NM_02_089


title: NM_02_088


title: NM_02_087


title: NM_02_086


title: NM_02_082


title: NM_02_084


title: NM_02_078


title: NM_02_083


title: NM_02_081


title: NM_02_080


title: NM_02_079


title: NM_02_077


title: NM_02_085


title: NM_02_076


title: NM_02_075


title: NM_02_072


title: NM_02_068


title: NM_02_069


title: NM_02_073


title: NM_02_074


title: NM_02_066


title: NM_02_067


title: NM_02_065


title: NM_02_064


title: NM_02_063


title: NM_02_062


title: NM_02_061


title: NM_02_060


title: NM_02_058


title: NM_02_071


title: NM_02_059


title: NM_02_070


title: NM_02_055


title: NM_02_056


title: NM_02_057


title: NM_02_054


title: NM_02_052


title: NM_02_050


title: NM_02_053


title: NM_02_048


title: NM_02_049


title: NM_02_047


title: NM_02_046


title: NM_02_045


title: NM_02_039


title: NM_02_038


title: NM_02_036


title: NM_02_037


title: NM_02_035


title: NM_02_042


title: NM_02_043


title: NM_02_044


title: NM_02_040


title: NM_02_034


title: NM_02_033


title: NM_02_029


title: NM_02_030


title: NM_02_051


title: NM_02_027


title: NM_02_031


title: NM_02_025


title: NM_02_032


title: NM_02_023


title: NM_02_028


title: NM_02_024


title: NM_02_026


title: NM_02_022


title: NM_02_041


title: NM_02_018


title: NM_02_019


title: NM_02_016


title: NM_02_017


title: NM_02_013


title: NM_02_015


title: NM_02_014


title: NM_02_010


title: NM_02_011


title: NM_02_009


title: NM_02_012


title: NM_02_006


title: NM_02_007


title: NM_02_021


title: NM_02_004


title: NM_01_119


title: NM_02_020


title: NM_01_116


title: NM_01_120


title: NM_01_118


title: NM_01_115


title: NM_01_114


title: NM_02_003


title: NM_02_001


title: NM_01_113


title: NM_01_117


title: NM_02_008


title: NM_01_112


title: NM_02_002


title: NM_01_111


title: NM_01_110


title: NM_02_005


title: NM_01_109


title: NM_01_108


title: NM_01_107


title: NM_01_106


title: NM_01_104


title: NM_01_100


title: NM_01_105


title: NM_01_101


title: NM_01_103


title: NM_01_099


title: NM_01_102


title: NM_01_098


title: NM_01_097


title: NM_01_096


title: NM_01_095


title: NM_01_092


title: NM_01_093


title: NM_01_094


title: NM_01_090


title: NM_01_089


title: NM_01_091


title: NM_01_087


title: NM_01_086


title: NM_01_088


title: NM_01_079


title: NM_01_081


title: NM_01_082


title: NM_01_083


title: NM_01_084


title: NM_01_085


title: NM_01_080


title: NM_01_077


title: NM_01_078


title: NM_01_076


title: NM_01_075


title: NM_01_073


title: NM_01_072


title: NM_01_070


title: NM_01_068


title: NM_01_071


title: NM_01_069


title: NM_01_067


title: NM_01_065


title: NM_01_066


title: NM_01_058


title: NM_01_054


title: NM_01_051


title: NM_01_057


title: NM_01_060


title: NM_01_050


title: NM_01_064


title: NM_01_062


title: NM_01_056


title: NM_01_055


title: NM_01_059


title: NM_01_063


title: NM_01_049


title: NM_01_053


title: NM_01_052


title: NM_01_061


title: NM_01_047


title: NM_01_074


title: NM_01_046


title: NM_01_044


title: NM_01_036


title: NM_01_041


title: NM_01_037


title: NM_01_043


title: NM_01_040


title: NM_01_042


title: NM_01_039


title: NM_01_033


title: NM_01_031


title: NM_01_028


title: NM_01_030


title: NM_01_029


title: NM_01_035


title: NM_01_024


title: NM_01_023


title: NM_01_022


title: NM_01_034


title: NM_01_025


title: NM_01_048


title: NM_01_026


title: NM_01_045


title: NM_01_021


title: NM_01_019


title: NM_01_038


title: NM_01_017


title: NM_01_018


title: NM_01_016


title: NM_01_013


title: NM_01_014


title: NM_01_015


title: NM_01_011


title: NM_01_012


title: NM_01_010


title: NM_01_032


title: NM_01_027


title: NM_01_020


title: NM_01_009


title: NM_01_006


title: NM_01_005


title: NM_01_008


title: NM_01_007


title: NM_01_004


title: NM_01_002


title: IgAN_20_069

source_name: IgAN patients’ renal biopsies

value: IgAN

value: renal biopsies


title: NM_01_003


title: NM_01_001


title: IgAN_20_067


title: IgAN_20_066


title: IgAN_20_065


title: IgAN_20_064


title: IgAN_20_063


title: IgAN_20_062


title: IgAN_20_058


title: IgAN_20_059


title: IgAN_20_056


title: IgAN_20_060


title: IgAN_20_057


title: IgAN_20_053


title: IgAN_20_052


title: IgAN_20_055


title: IgAN_20_050


title: IgAN_20_054


title: IgAN_20_070


title: IgAN_20_071


title: IgAN_20_072


title: IgAN_20_068


title: IgAN_20_048


title: IgAN_20_044


title: IgAN_20_046


title: IgAN_20_043


title: IgAN_20_049


title: IgAN_20_047


title: IgAN_20_042


title: IgAN_20_041


title: IgAN_20_038


title: IgAN_20_040


title: IgAN_20_061


title: IgAN_20_036


title: IgAN_20_034


title: IgAN_20_032


title: IgAN_20_031


title: IgAN_20_030


title: IgAN_20_033


title: IgAN_20_045


title: IgAN_20_051


title: IgAN_20_024


title: IgAN_20_027


title: IgAN_20_025


title: IgAN_20_026


title: IgAN_20_029


title: IgAN_20_028


title: IgAN_20_039


title: IgAN_20_023


title: IgAN_20_022


title: IgAN_20_020


title: IgAN_20_021


title: IgAN_20_019


title: IgAN_20_037


title: IgAN_20_012


title: IgAN_20_011


title: IgAN_20_013


title: IgAN_20_017


title: IgAN_20_015


title: IgAN_20_014


title: IgAN_20_035


title: IgAN_20_016


title: IgAN_20_010


title: IgAN_20_007


title: IgAN_20_009


title: IgAN_20_006


title: IgAN_20_008


title: IgAN_20_004


title: IgAN_20_003


title: IgAN_19_037


title: IgAN_20_001


title: IgAN_19_038


title: IgAN_20_002


title: IgAN_19_035


title: IgAN_20_018


title: IgAN_19_033


title: IgAN_19_031


title: IgAN_19_029


title: IgAN_19_032


title: IgAN_19_030


title: IgAN_19_034


title: IgAN_19_028


title: IgAN_19_026


title: IgAN_19_025


title: IgAN_19_023


title: IgAN_19_024


title: IgAN_19_022


title: IgAN_19_027


title: IgAN_19_021


title: IgAN_19_020


title: IgAN_20_005


title: IgAN_19_036


title: IgAN_19_016


title: IgAN_19_018


title: IgAN_19_017


title: IgAN_19_015


title: IgAN_19_013


title: IgAN_19_014


title: IgAN_19_004


title: IgAN_19_010


title: IgAN_19_006


title: IgAN_19_005


title: IgAN_19_002


title: IgAN_19_012


title: IgAN_19_008


title: IgAN_19_001


title: IgAN_18_012


title: IgAN_18_013


title: IgAN_19_007


title: IgAN_19_011


title: IgAN_19_009


title: IgAN_18_010


title: IgAN_18_007


title: IgAN_18_006


title: IgAN_18_014


title: IgAN_18_009


title: IgAN_18_011


title: IgAN_19_019


title: IgAN_18_008


title: IgAN_18_004


title: IgAN_18_001


title: IgAN_18_005


title: IgAN_18_003


title: IgAN_19_003


title: IgAN_18_002


title: IgAN_17_129


title: IgAN_17_128


title: IgAN_17_127


title: IgAN_17_126


title: IgAN_17_124


title: IgAN_17_123


title: IgAN_17_125


title: IgAN_17_121


title: IgAN_17_120


title: IgAN_17_118


title: IgAN_17_116


title: IgAN_17_115


title: IgAN_17_117


title: IgAN_17_114


title: IgAN_17_119


title: IgAN_17_113


title: IgAN_17_109


title: IgAN_17_111


title: IgAN_17_112


title: IgAN_17_110


title: IgAN_17_108


title: IgAN_17_104


title: IgAN_17_103


title: IgAN_17_105


title: IgAN_17_102


title: IgAN_17_106


title: IgAN_17_122


title: IgAN_17_098


title: IgAN_17_099


title: IgAN_17_101


title: IgAN_17_100


title: IgAN_17_097


title: IgAN_17_096


title: IgAN_17_095


title: IgAN_19_039


title: IgAN_17_093


title: IgAN_17_089


title: IgAN_17_091


title: IgAN_17_090


title: IgAN_17_086


title: IgAN_17_087


title: IgAN_17_085


title: IgAN_17_088


title: IgAN_17_107


title: IgAN_17_084


title: IgAN_17_081


title: IgAN_17_082


title: IgAN_17_083


title: IgAN_17_079


title: IgAN_17_080


title: IgAN_17_077


title: IgAN_17_094


title: IgAN_17_092


title: IgAN_17_076


title: IgAN_17_069


title: IgAN_17_073


title: IgAN_17_071


title: IgAN_17_072


title: IgAN_17_074


title: IgAN_17_070


title: IgAN_17_068


title: IgAN_17_067


title: IgAN_17_066


title: IgAN_17_065


title: IgAN_17_062


title: IgAN_17_064


title: IgAN_17_061


title: IgAN_17_058


title: IgAN_17_057


title: IgAN_17_060


title: IgAN_17_059


title: IgAN_17_055


title: IgAN_17_054


title: IgAN_17_078


title: IgAN_17_053


title: IgAN_17_075


title: IgAN_17_051


title: IgAN_17_052


title: IgAN_17_050


title: IgAN_17_049


title: IgAN_17_048


title: IgAN_17_047


title: IgAN_17_045


title: IgAN_17_038


title: IgAN_17_039


title: IgAN_17_042


title: IgAN_17_041


title: IgAN_17_043


title: IgAN_17_040


title: IgAN_17_046


title: IgAN_17_056


title: IgAN_17_044


title: IgAN_17_063


title: IgAN_17_037


title: IgAN_17_035


title: IgAN_17_032


title: IgAN_17_033


title: IgAN_17_036


title: IgAN_17_034


title: IgAN_17_031


title: IgAN_17_030


title: IgAN_17_029


title: IgAN_17_026


title: IgAN_17_027


title: IgAN_17_028


title: IgAN_17_025


title: IgAN_17_024


title: IgAN_17_023


title: IgAN_17_022


title: IgAN_17_021


title: IgAN_17_019


title: IgAN_17_020


title: IgAN_17_018


title: IgAN_17_017


title: IgAN_17_016


title: IgAN_17_014


title: IgAN_17_015


title: IgAN_17_009


title: IgAN_17_010


title: IgAN_17_008


title: IgAN_17_006


title: IgAN_17_004


title: IgAN_17_007


title: IgAN_17_013


title: IgAN_17_003


title: IgAN_17_011


title: IgAN_17_005


title: IgAN_17_001


title: IgAN_17_012


title: IgAN_17_002


title: IgAN_16_170


title: IgAN_16_171


title: IgAN_16_167


title: IgAN_16_169


title: IgAN_16_172


title: IgAN_16_168


title: IgAN_16_166


title: IgAN_16_165


title: IgAN_16_164


title: IgAN_16_163


title: IgAN_16_162


title: IgAN_16_159


title: IgAN_16_160


title: IgAN_16_157


title: IgAN_16_158


title: IgAN_16_173


title: IgAN_16_156


title: IgAN_16_153


title: IgAN_16_155


title: IgAN_16_152


title: IgAN_16_154


title: IgAN_16_148


title: IgAN_16_150


title: IgAN_16_147


title: IgAN_16_145


title: IgAN_16_149


title: IgAN_16_146


title: IgAN_16_151


title: IgAN_16_143


title: IgAN_16_138


title: IgAN_16_141


title: IgAN_16_139


title: IgAN_16_140


title: IgAN_16_137


title: IgAN_16_136


title: IgAN_16_135


title: IgAN_16_134


title: IgAN_16_161


title: IgAN_16_133


title: IgAN_16_144


title: IgAN_16_132


title: IgAN_16_130


title: IgAN_16_131


title: IgAN_16_128


title: IgAN_16_142


title: IgAN_16_125


title: IgAN_16_126


title: IgAN_16_124


title: IgAN_16_117


title: IgAN_16_119


title: IgAN_16_112


title: IgAN_16_121


title: IgAN_16_115


title: IgAN_16_116


title: IgAN_16_114


title: IgAN_16_111


title: IgAN_16_110


title: IgAN_16_122


title: IgAN_16_113


title: IgAN_16_123


title: IgAN_16_109


title: IgAN_16_120


title: IgAN_16_129


title: IgAN_16_105


title: IgAN_16_107


title: IgAN_16_108


title: IgAN_16_106


title: IgAN_16_104


title: IgAN_16_127


title: IgAN_16_101


title: IgAN_16_100


title: IgAN_16_098


title: IgAN_16_102


title: IgAN_16_099


title: IgAN_16_097


title: IgAN_16_118


title: IgAN_16_095


title: IgAN_16_090


title: IgAN_16_089


title: IgAN_16_091


title: IgAN_16_088


title: IgAN_16_094


title: IgAN_16_092


title: IgAN_16_087


title: IgAN_16_085


title: IgAN_16_084


title: IgAN_16_082


title: IgAN_16_103


title: IgAN_16_081


title: IgAN_16_079


title: IgAN_16_080


title: IgAN_16_078


title: IgAN_16_077


title: IgAN_16_076


title: IgAN_16_075


title: IgAN_16_096


title: IgAN_16_074


title: IgAN_16_073


title: IgAN_16_071


title: IgAN_16_070


title: IgAN_16_068


title: IgAN_16_072


title: IgAN_16_086


title: IgAN_16_093


title: IgAN_16_065


title: IgAN_16_066


title: IgAN_16_064


title: IgAN_16_059


title: IgAN_16_063


title: IgAN_16_060


title: IgAN_16_083


title: IgAN_16_058


title: IgAN_16_057


title: IgAN_16_055


title: IgAN_16_056


title: IgAN_16_054


title: IgAN_16_052


title: IgAN_16_051


title: IgAN_16_053


title: IgAN_16_050


title: IgAN_16_049


title: IgAN_16_069


title: IgAN_16_048


title: IgAN_16_046


title: IgAN_16_067


title: IgAN_16_047


title: IgAN_16_061


title: IgAN_16_044


title: IgAN_16_045


title: IgAN_16_062


title: IgAN_16_043


title: IgAN_16_041


title: IgAN_16_040


title: IgAN_16_042


title: IgAN_16_039


title: IgAN_16_037


title: IgAN_16_033


title: IgAN_16_032


title: IgAN_16_036


title: IgAN_16_030


title: IgAN_16_029


title: IgAN_16_023


title: IgAN_16_031


title: IgAN_16_025


title: IgAN_16_024


title: IgAN_16_027


title: IgAN_16_026


title: IgAN_16_028


title: IgAN_16_022


title: IgAN_16_021


title: IgAN_16_020


title: IgAN_16_019


title: IgAN_16_017


title: IgAN_16_034


title: IgAN_16_038


title: IgAN_16_035


title: IgAN_16_015


title: IgAN_16_016


title: PBM_IgAN_10_188

source_name: monocytes from IgAN patients' peripheral blood

tag: cell type

value: monocytes


title: PBM_IgAN_10_184


title: PBM_IgAN_10_185


title: PBM_IgAN_10_186


title: PBM_IgAN_10_187


title: PBM_IgAN_10_183


title: PBM_IgAN_10_182


title: PBM_IgAN_10_180


title: PBM_IgAN_10_181


title: IgAN_16_018


title: PBM_IgAN_10_177


title: PBM_IgAN_10_173


title: PBM_IgAN_10_178


title: PBM_IgAN_10_172


title: PBM_IgAN_10_174


title: PBM_IgAN_10_176


title: PBM_IgAN_10_171


title: PBM_IgAN_10_175


title: PBM_IgAN_10_166


title: PBM_IgAN_10_165


title: PBM_IgAN_10_168


title: PBM_IgAN_10_163


title: PBM_IgAN_10_162


title: PBM_IgAN_10_167


title: PBM_IgAN_10_169


title: PBM_IgAN_10_160


title: PBM_IgAN_10_161


title: PBM_IgAN_10_164


title: PBM_IgAN_10_158


title: PBM_IgAN_10_159


title: PBM_IgAN_10_156


title: PBM_IgAN_10_157


title: PBM_IgAN_10_154


title: PBM_IgAN_10_155


title: PBM_IgAN_10_153


title: PBM_IgAN_10_179


title: PBM_IgAN_10_152


title: PBM_IgAN_10_151


title: PBM_IgAN_10_170


title: PBM_IgAN_10_146


title: PBM_IgAN_10_149


title: PBM_IgAN_10_150


title: PBM_IgAN_10_148


title: PBM_IgAN_10_145


title: PBM_IgAN_10_147


title: PBM_IgAN_10_136


title: PBM_IgAN_10_141


title: PBM_IgAN_10_139


title: PBM_IgAN_10_142


title: PBM_IgAN_10_138


title: PBM_IgAN_10_140


title: PBM_IgAN_10_135


title: PBM_IgAN_10_143


title: PBM_IgAN_10_144


title: PBM_IgAN_10_137


title: PBM_IgAN_10_132


title: PBM_IgAN_10_134


title: PBM_IgAN_10_131


title: PBM_IgAN_10_130


title: PBM_IgAN_10_128


title: PBM_IgAN_10_129


title: PBM_IgAN_10_127


title: PBM_IgAN_10_126


title: PBM_IgAN_10_125


title: PBM_IgAN_10_123


title: PBM_IgAN_10_121


title: PBM_IgAN_10_124


title: PBM_IgAN_10_119


title: PBM_IgAN_10_122


title: PBM_IgAN_10_118


title: PBM_IgAN_10_117


title: PBM_IgAN_10_133


title: PBM_IgAN_10_115


title: PBM_IgAN_10_113


title: PBM_IgAN_10_112


title: PBM_IgAN_10_110


title: PBM_IgAN_10_109


title: PBM_IgAN_10_114


title: PBM_IgAN_10_104


title: PBM_IgAN_10_106


title: PBM_IgAN_10_103


title: PBM_IgAN_10_108


title: PBM_IgAN_10_107


title: PBM_IgAN_10_105


title: PBM_IgAN_10_101


title: PBM_IgAN_10_102


title: PBM_IgAN_10_100


title: PBM_IgAN_10_099


title: PBM_IgAN_10_097


title: PBM_IgAN_10_095


title: PBM_IgAN_10_120


title: PBM_IgAN_10_094


title: PBM_IgAN_10_093


title: PBM_IgAN_10_116


title: PBM_IgAN_10_091


title: PBM_IgAN_10_092


title: PBM_IgAN_10_111


title: PBM_IgAN_10_088


title: PBM_IgAN_10_090


title: PBM_IgAN_10_089


title: PBM_IgAN_10_087


title: PBM_IgAN_10_083


title: PBM_IgAN_10_086


title: PBM_IgAN_10_085


title: PBM_IgAN_10_081


title: PBM_IgAN_10_079


title: PBM_IgAN_10_076


title: PBM_IgAN_10_080


title: PBM_IgAN_10_084


title: PBM_IgAN_10_082


title: PBM_IgAN_10_078


title: PBM_IgAN_10_077


title: PBM_IgAN_10_098


title: PBM_IgAN_10_073


title: PBM_IgAN_10_075


title: PBM_IgAN_10_096


title: PBM_IgAN_10_072


title: PBM_IgAN_10_071


title: PBM_IgAN_10_069


title: PBM_IgAN_10_068


title: PBM_IgAN_10_067


title: PBM_IgAN_10_065


title: PBM_IgAN_10_066


title: PBM_IgAN_10_064


title: PBM_IgAN_10_063


title: PBM_IgAN_10_060


title: PBM_IgAN_10_061


title: PBM_IgAN_10_059


title: PBM_IgAN_10_057


title: PBM_IgAN_10_056


title: PBM_IgAN_10_052


title: PBM_IgAN_10_062


title: PBM_IgAN_10_058


title: PBM_IgAN_10_048


title: PBM_IgAN_10_074


title: PBM_IgAN_10_053


title: PBM_IgAN_10_055


title: PBM_IgAN_10_047


title: PBM_IgAN_10_051


title: PBM_IgAN_10_050


title: PBM_IgAN_10_049


title: PBM_IgAN_10_054


title: PBM_IgAN_10_045


title: PBM_IgAN_10_070


title: PBM_IgAN_10_043


title: PBM_IgAN_10_044


title: PBM_IgAN_10_046


title: PBM_IgAN_10_042


title: PBM_IgAN_10_041


title: PBM_IgAN_10_040


title: PBM_IgAN_10_039


title: PBM_IgAN_10_038


title: PBM_IgAN_10_037


title: PBM_IgAN_10_036


title: PBM_IgAN_10_035


title: PBM_IgAN_10_031


title: PBM_IgAN_10_034


title: PBM_IgAN_10_032


title: PBM_IgAN_10_033


title: PBM_IgAN_10_030


title: PBM_IgAN_10_027


title: PBM_IgAN_10_023


title: PBM_IgAN_10_029


title: PBM_IgAN_10_028


title: PBM_IgAN_10_026


title: PBM_IgAN_10_017


title: PBM_IgAN_10_016


title: PBM_IgAN_10_018


title: PBM_IgAN_10_025


title: PBM_IgAN_10_014


title: PBM_IgAN_10_019


title: PBM_IgAN_10_022


title: PBM_IgAN_10_021


title: PBM_IgAN_10_012


title: PBM_IgAN_10_024


title: PBM_IgAN_10_011


title: PBM_IgAN_10_010


title: PBM_IgAN_10_013


title: PBM_IgAN_10_015


title: PBM_IgAN_10_009


title: PBM_IgAN_10_008


title: PBM_IgAN_10_007


title: PBM_IgAN_10_006


title: PBM_IgAN_10_005


title: PBM_IgAN_10_020


title: PBM_IgAN_10_001


title: NM_09_080


title: PBM_IgAN_10_004


title: PBM_IgAN_10_002


title: NM_09_079


title: NM_09_078


title: NM_09_077


title: NM_09_071


title: NM_09_073


title: NM_09_067


title: NM_09_070


title: NM_09_068


title: NM_09_076


title: NM_09_069


title: NM_09_074


title: NM_09_063


title: NM_09_059


title: NM_09_062


title: NM_09_061


title: NM_09_065


title: NM_09_066


title: NM_09_064


title: PBM_IgAN_10_003


title: NM_09_060


title: NM_09_057


title: NM_09_058


title: NM_09_053


title: NM_09_052


title: NM_09_072


title: NM_09_075


title: NM_09_054


title: NM_09_056


title: NM_09_049


title: NM_09_055


title: NM_09_050


title: NM_09_047


title: NM_09_046


title: NM_09_045


title: NM_09_041


title: NM_09_042


title: NM_09_040


title: NM_09_044


title: NM_09_043


title: NM_09_038


title: NM_09_037


title: NM_09_039


title: NM_09_032


title: NM_09_036


title: NM_09_033


title: NM_09_035


title: NM_09_051


title: NM_09_048


title: NM_09_026


title: NM_09_027


title: NM_09_029


title: NM_09_025


title: NM_09_031


title: NM_09_023


title: NM_09_021


title: NM_09_020


title: NM_09_022


title: NM_09_024


title: NM_09_018


title: NM_09_019


title: NM_09_017


title: NM_09_012


title: NM_09_014


title: NM_09_016


title: NM_09_015


title: NM_09_034


title: NM_09_013


title: NM_09_030


title: NM_09_009


title: NM_09_008


title: NM_09_004


title: NM_09_006


title: NM_09_005


title: NM_09_028


title: NM_09_003


title: NM_09_002


title: NM_08_093


title: NM_08_091


title: NM_08_092


title: NM_08_089


title: NM_08_090


title: NM_08_086


title: NM_08_087


title: NM_08_085


title: NM_08_084


title: NM_08_083


title: NM_08_082


title: NM_08_079


title: NM_09_011


title: NM_09_010


title: NM_08_078


title: NM_09_007


title: NM_08_077


title: NM_08_075


title: NM_08_073


title: NM_08_074


title: NM_08_076


title: NM_08_072


title: NM_08_070


title: NM_09_001


title: NM_08_071


title: NM_08_069


title: NM_08_088


title: NM_08_065


title: NM_08_064


title: NM_08_068


title: NM_08_066


title: NM_08_067


title: NM_08_062


title: NM_08_059


title: NM_08_063


title: NM_08_080


title: NM_08_081


title: NM_08_057


title: NM_08_060


title: NM_08_054


title: NM_08_056


title: NM_08_055


title: NM_08_053


title: NM_08_052


title: NM_08_051


title: NM_08_050


title: NM_08_049


title: NM_08_044


title: NM_08_046


title: NM_08_045


title: NM_08_047


title: NM_08_048


title: NM_08_061


title: NM_08_041


title: NM_08_042


title: NM_08_039


title: NM_08_038


title: NM_08_037


title: NM_08_040


title: NM_08_036


title: NM_08_033


title: NM_08_058


title: NM_08_034


title: NM_08_032


title: NM_08_030


title: NM_08_029


title: NM_08_031


title: NM_08_028


title: NM_08_027


title: NM_08_026


title: NM_08_025


title: NM_08_024


title: NM_08_023


title: NM_08_016


title: NM_08_019


title: NM_08_021


title: NM_08_018


title: NM_08_043


title: NM_08_020


title: NM_08_013


title: NM_08_015


title: NM_08_014


title: NM_08_017


title: NM_08_012


title: NM_08_035


title: NM_08_007


title: NM_08_006


title: NM_08_005


title: NM_08_004


title: NM_08_009


title: NM_08_008


title: NM_08_001


title: NM_08_003


title: NM_08_002


title: NM_08_022


title: NM_07_093


title: NM_07_091


title: NM_07_092


title: NM_07_090


title: NM_07_094


title: NM_07_089


title: NM_07_086


title: NM_07_087


title: NM_07_088


title: NM_07_084


title: NM_07_083


title: NM_07_085


title: NM_07_081


title: NM_08_010


title: NM_07_077


title: NM_07_082


title: NM_07_078


title: NM_07_072


title: NM_07_080


title: NM_07_079


title: NM_07_071


title: NM_07_075


title: NM_07_073


title: NM_07_074


title: NM_07_070


title: NM_07_068


title: NM_07_076


title: NM_07_064


title: NM_07_063


title: NM_07_069


title: NM_07_067


title: NM_07_062


title: NM_07_065


title: NM_07_061


title: NM_07_060


title: NM_07_058


title: NM_07_057


title: NM_07_056


title: NM_07_055


title: NM_07_054


title: NM_07_053


title: NM_07_052


title: NM_07_051


title: NM_08_011


title: NM_07_050


title: NM_07_047


title: NM_07_049


title: NM_07_045


title: NM_07_042


title: NM_07_043


title: NM_07_048


title: NM_07_044


title: NM_07_041


title: NM_07_039


title: NM_07_038


title: NM_07_066


title: NM_07_036


title: NM_07_035


title: NM_07_034


title: NM_07_059


title: NM_07_031


title: NM_07_032


title: NM_07_028


title: NM_07_030


title: NM_07_027


title: NM_07_029


title: NM_07_026


title: NM_07_024


title: NM_07_046


title: NM_07_025


title: NM_07_023


title: NM_07_021


title: NM_07_040


title: NM_07_022


title: NM_07_015


title: NM_07_016


title: NM_07_020


title: NM_07_019


title: NM_07_018


title: NM_07_033


title: NM_07_013


title: NM_07_011


title: NM_07_012


title: NM_07_009


title: NM_07_037


title: NM_07_008


title: NM_07_010


title: NM_07_007


title: NM_07_006


title: NM_07_004


title: NM_07_005


title: NM_07_002


title: NM_07_003


title: NM_07_001


title: NM_03_067


title: NM_07_017


title: NM_03_064


title: NM_03_066


title: NM_03_065


title: NM_07_014


title: NM_03_062


title: NM_03_061


title: NM_03_060


title: NM_03_063


title: NM_03_059


title: NM_03_058


title: NM_03_057


title: NM_03_056


title: NM_03_054


title: NM_03_052


title: NM_03_055


title: NM_03_051


title: NM_03_049


title: NM_03_053


title: NM_03_050


title: NM_03_048


title: NM_03_046


title: NM_03_047


title: NM_03_044


title: NM_03_045


title: NM_03_043


title: NM_03_041


title: NM_03_042


title: NM_03_036


title: NM_03_039


title: NM_03_040


title: NM_03_038


title: NM_03_037


title: NM_03_035


title: NM_03_034


title: NM_03_033


title: NM_03_032


title: NM_03_030


title: NM_03_029


title: NM_03_028


title: NM_03_026


title: NM_03_022


title: NM_03_023


title: NM_03_020


title: NM_03_019


title: NM_03_024


title: NM_03_025


title: NM_03_021


title: NM_03_027


title: NM_03_017


title: NM_03_015


title: NM_03_013


title: NM_03_011


title: NM_03_012


title: NM_03_018


title: NM_03_016


title: NM_03_009


title: NM_03_007


title: NM_03_005


title: NM_03_006


title: NM_03_008


title: NM_03_031


title: NM_03_010


title: NM_03_004


title: NM_03_002


title: NM_02_309


title: NM_03_003


title: NM_03_001


title: NM_02_308


title: NM_02_307


title: NM_02_306


title: NM_02_305


title: NM_02_304


title: NM_02_302


title: NM_02_301


title: NM_02_300


title: NM_03_014


title: NM_02_298


title: NM_02_303


title: NM_02_297


title: NM_02_295


title: NM_02_294


title: NM_02_293


title: NM_02_292


title: NM_02_291


title: NM_02_288


title: NM_02_290


title: NM_02_287


title: NM_02_289


title: NM_02_286


title: NM_02_284


title: NM_02_283


title: NM_02_282


title: NM_02_281


title: NM_02_279


title: NM_02_280


title: NM_02_278


title: NM_02_274


title: NM_02_276


title: NM_02_277


title: NM_02_299


title: NM_02_296


title: NM_02_272


title: NM_02_273


title: NM_02_275


title: NM_02_269


title: NM_02_267


title: NM_02_266


title: NM_02_270


title: NM_02_285


title: NM_02_264


title: NM_02_271


title: NM_02_263


title: NM_02_262


title: NM_02_258


title: NM_02_261


title: NM_02_259


title: NM_02_257


title: NM_02_260


title: NM_02_255


title: NM_02_256


title: NM_02_253


title: NM_02_249


title: NM_02_251


title: NM_02_247


title: NM_02_246


title: NM_02_268


title: NM_02_250


title: NM_02_245


title: NM_02_265


title: NM_02_241


title: NM_02_240


title: NM_02_239


title: NM_02_244


title: NM_02_237


title: NM_02_238


title: NM_02_236


title: NM_02_235


title: NM_02_234


title: NM_02_233


title: NM_02_232


title: NM_02_230


title: NM_02_252


title: NM_02_231


title: NM_02_254


title: NM_02_227


title: NM_02_248


title: NM_02_224


title: NM_02_243


title: NM_02_221


title: NM_02_222


title: NM_02_242


title: NM_02_223


title: NM_02_218


title: NM_02_220


title: NM_02_219


title: NM_02_216


title: NM_02_215


title: NM_02_214


title: NM_02_211


title: NM_02_229


title: NM_02_213


title: NM_02_228


title: NM_02_212


title: NM_02_210


title: NM_02_206


title: NM_02_209


title: NM_02_226


title: NM_02_207


title: NM_02_208


title: NM_02_203


title: NM_02_225


title: NM_02_201


title: NM_02_205


title: NM_02_204


title: NM_02_202


title: NM_02_199


title: NM_02_197


title: NM_02_198


title: NM_02_194


title: NM_02_195


title: NM_02_217


title: NM_02_196


title: NM_02_192


title: NM_02_193


title: NM_02_190


title: NM_02_189


title: NM_02_188


title: NM_02_185


title: NM_02_183


title: NM_02_184


title: NM_02_186


title: NM_02_179


title: NM_02_177


title: NM_02_176


title: NM_02_174


title: NM_02_175


title: NM_02_187


title: NM_02_200


title: NM_02_173


title: NM_02_172


title: NM_02_182


title: NM_02_178


title: NM_02_180


title: NM_02_171


title: NM_02_167


title: NM_02_168


title: NM_02_169


title: NM_02_166


title: NM_02_165


title: NM_02_170


title: NM_02_164


title: NM_02_162


title: NM_02_191


title: NM_02_161


title: NM_02_163


title: NM_02_160


title: NM_02_159


title: NM_02_181


title: NM_02_157


title: NM_02_155


title: NM_02_154


title: NM_02_152


title: NM_02_151


title: NM_02_150


title: NM_02_153


title: uninfected A549 cells rep2 (mRNA and circRNA)

city: Harbin

first: Zhiyuan

last: Qu

address: Haping road 678

department: State Key Laboratory of Veterinary Biotechnology

institute: Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.Bowtie2(2.2.8) was used for mapping reads to ribosome RNA database.The remaining reads were further used in assembly and analysis of mRNAs and circRNAs.
The rRNA removed reads of each sample were then mapped to reference genome by Tophat2(2.1.1). The alignment parameters were as follows: 1) maximum read mismatch is 2. 2) Diables the coverage based search for junctions. 3) The distance between mate-pair reads is 50 bp. 4) The standard deviation for the distribution on inner distance between mate-pair reads is 80 bp. The mapped reads were used for mRNA analysis and the unmapped reads were used for circRNA analysis
The reconstruction of mRNA was carried out with software Cufflinks(2.2.1), and then we used Cuffmerge to merge mRNA from different replicas of a group into comprehensive set of mRNA, and then merge the mRNA for further downstream differential expression analysis
20mers from both ends of the unmapped reads that aligned to GRCh38.p12 in the reversed orientation (head-to-tail) were extracted and then were subjected to find_circ to identify circRNAs
All of the clean tags of miRNA were then searched against miRBase database (release 21) to identify known miRNAs.
The mRNA expression level was normalized by using FPKM (Fragments per kilobase of transcript per million mapped reads) and the circRNAs expression level was normalized by RPM (Reads per million mapped reads). The miRNA expression level was calculated and normalized to TPM (transcripts per million).
The edge R package was used for differentially expression of mRNAs and circRNAs and miRNAs.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each mRNA Sample.
tab-delimited text files include RPM values for each circRNA Sample.
tab-delimited text files include TPM values for each miRNA Sample.

source_name: A549 cells

growth_protocol: A549 cells were grown in nutrient mixture F-12 Ham Kaighn’s modified medium or Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum  at 37℃ in a humidified 5% CO2 atmosphere.

extract_protocol:
RNA was harvested using Trizol reagent.
After removing the rRNAs, half of the total enriched RNA was used for circRNA and mRNA library construction, and the other half was size-selected by polyacrylamide gel electrophoresis to enrich for 18–30 nt RNAs for small RNA library construction. To construct circRNA and mRNA libraries, fragmented RNAs were reverse-transcribed into cDNA by using random primers, and the cDNA fragments were purified with a QiaQuick PCR extraction kit, end repaired, poly(A) added, and ligated to illumina sequencing adapters. Then, Uracil-N-Glycosylase was used to digest the second-strand cDNA. The digested products were amplified by PCR.To construct the small RNA library, the 3’ and 5’ illumina sequencing adaptors were ligated to the RNAs, and the ligation products were reverse-transcribed, amplified.

treatment_protocol: A549 cells were mock-infected or infected with H9N2 virus for 12 h

tag: infection

value: untreated


title: uninfected A549 cells rep3 (mRNA and circRNA)


title: infected A549 cells rep1 (mRNA and circRNA)

value: H9N2 virus infected for 12 h


title: uninfected A549 cells rep1 (mRNA and circRNA)


title: infected A549 cells rep3 (mRNA and circRNA)


title: infected A549 cells rep2 (mRNA and circRNA)


title: NM_02_156


title: NM_02_158


title: PBM_NM_05_014

source_name: monocytes from normal persons' peripheral blood

value: normal


title: PBM_NM_05_013


title: PBM_NM_05_016


title: PBM_NM_05_015


title: PBM_NM_05_018


title: PBM_NM_05_010


title: PBM_NM_05_008


title: PBM_NM_05_009


title: PBM_NM_05_017


title: PBM_NM_05_019


title: PBM_NM_05_020


title: PBM_NM_05_011


title: PBM_NM_05_012


title: PBM_NM_05_006


title: PBM_NM_05_007


title: PBM_NM_05_005


title: PBM_NM_05_002


title: PBM_NM_05_004


title: PBM_NM_05_003


title: PBM_NM_05_001


title: PBM_NM_04_015


title: PBM_NM_04_016


title: PBM_NM_04_014


title: PBM_NM_04_013


title: PBM_NM_04_012


title: PBM_NM_04_011


title: PBM_NM_04_010


title: PBM_NM_04_009


title: PBM_NM_04_004


title: PBM_NM_04_006


title: PBM_NM_04_007


title: PBM_NM_04_005


title: PBM_NM_04_008


title: PBM_NM_04_003


title: PBM_NM_03_010


title: PBM_NM_03_001


title: PBM_NM_03_007


title: PBM_NM_03_006


title: PBM_NM_03_003


title: PBM_NM_03_008


title: PBM_NM_04_002


title: PBM_NM_03_002


title: PBM_NM_02_120


title: PBM_NM_02_121


title: PBM_NM_02_117


title: PBM_NM_02_118


title: PBM_NM_03_005


title: PBM_NM_02_119


title: PBM_NM_04_001


title: PBM_NM_02_116


title: PBM_NM_02_114


title: PBM_NM_02_115


title: PBM_NM_02_112


title: PBM_NM_02_111


title: PBM_NM_03_004


title: PBM_NM_03_009


title: PBM_NM_02_109


title: PBM_NM_02_108


title: PBM_NM_02_107


title: PBM_NM_02_102


title: PBM_NM_02_101


title: PBM_NM_02_113


title: PBM_NM_02_098


title: PBM_NM_02_100


title: PBM_NM_02_104


title: PBM_NM_02_099


title: PBM_NM_02_093


title: PBM_NM_02_103


title: PBM_NM_02_105


title: PBM_NM_02_096


title: PBM_NM_02_094


title: PBM_NM_02_097


title: PBM_NM_02_090


title: PBM_NM_02_091


title: PBM_NM_02_088


title: PBM_NM_02_092


title: PBM_NM_02_110


title: PBM_NM_02_085


title: PBM_NM_02_086


title: PBM_NM_02_106


title: PBM_NM_02_082


title: PBM_NM_02_079


title: PBM_NM_02_084


title: PBM_NM_02_081


title: PBM_NM_02_080


title: PBM_NM_02_095


title: PBM_NM_02_089


title: PBM_NM_02_083


title: PBM_NM_02_077


title: PBM_NM_02_078


title: PBM_NM_02_076


title: PBM_NM_02_087


title: PBM_NM_02_074


title: PBM_NM_02_073


title: PBM_NM_02_075


title: PBM_NM_02_072


title: PBM_NM_02_064


title: PBM_NM_02_065


title: PBM_NM_02_071


title: PBM_NM_02_070


title: PBM_NM_02_060


title: PBM_NM_02_063


title: PBM_NM_02_066


title: PBM_NM_02_068


title: PBM_NM_02_067


title: PBM_NM_02_061


title: PBM_NM_02_062


title: PBM_NM_02_069


title: PBM_NM_02_059


title: PBM_NM_02_058


title: PBM_NM_02_057


title: PBM_NM_02_054


title: PBM_NM_02_056


title: PBM_NM_02_053


title: PBM_NM_02_052


title: PBM_NM_02_050


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title: PBM_NM_02_048


title: PBM_NM_02_047


title: PBM_NM_02_043


title: PBM_NM_02_044


title: PBM_NM_02_046


title: PBM_NM_02_040


title: PBM_NM_02_045


title: PBM_NM_02_042


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title: PBM_NM_02_038


title: PBM_NM_02_033


title: PBM_NM_02_031


title: PBM_NM_02_037


title: PBM_NM_02_030


title: PBM_NM_02_035


title: PBM_NM_02_055


title: PBM_NM_02_036


title: PBM_NM_02_034


title: PBM_NM_02_032


title: PBM_NM_02_028


title: PBM_NM_02_026


title: PBM_NM_02_027


title: PBM_NM_02_024


title: PBM_NM_02_023


title: PBM_NM_02_025


title: PBM_NM_02_022


title: PBM_NM_02_021


title: PBM_NM_02_014


title: PBM_NM_02_008


title: PBM_NM_02_016


title: PBM_NM_02_018


title: PBM_NM_02_013


title: PBM_NM_02_011


title: PBM_NM_02_020


title: PBM_NM_02_019


title: PBM_NM_02_012


title: PBM_NM_02_015


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title: PBM_NM_02_017


title: PBM_NM_02_005


title: PBM_NM_02_007


title: PBM_NM_02_029


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title: PBM_NM_02_003


title: PBM_NM_02_006


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title: PBM_IgAN_20_093


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title: PBM_IgAN_20_088


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title: PBM_IgAN_20_080


title: PBM_IgAN_20_082


title: PBM_IgAN_20_085


title: PBM_IgAN_20_084


title: PBM_IgAN_20_083


title: PBM_IgAN_20_081


title: PBM_IgAN_20_099


title: PBM_IgAN_20_077


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title: PBM_IgAN_20_079


title: PBM_IgAN_20_075


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title: PBM_IgAN_20_072


title: PBM_IgAN_20_089


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title: PBM_IgAN_20_068


title: PBM_IgAN_20_066


title: PBM_IgAN_20_065


title: PBM_IgAN_20_086


title: PBM_IgAN_20_064


title: PBM_IgAN_20_063


title: PBM_IgAN_20_062


title: PBM_IgAN_20_060


title: PBM_IgAN_20_059


title: PBM_IgAN_20_056


title: PBM_IgAN_20_057


title: PBM_IgAN_20_071


title: PBM_IgAN_20_070


title: PBM_IgAN_20_048


title: PBM_IgAN_20_051


title: PBM_IgAN_20_052


title: PBM_IgAN_20_053


title: PBM_IgAN_20_067


title: PBM_IgAN_20_049


title: PBM_IgAN_20_046


title: PBM_IgAN_20_047


title: PBM_IgAN_20_045


title: PBM_IgAN_20_042


title: PBM_IgAN_20_041


title: PBM_IgAN_20_044


title: PBM_IgAN_20_038


title: PBM_IgAN_20_037


title: PBM_IgAN_20_043


title: PBM_IgAN_20_061


title: PBM_IgAN_20_039


title: PBM_IgAN_20_040


title: PBM_IgAN_20_036


title: PBM_IgAN_20_035


title: PBM_IgAN_20_034


title: PBM_IgAN_20_055


title: PBM_IgAN_20_058


title: PBM_IgAN_20_054


title: PBM_IgAN_20_050


title: PBM_IgAN_20_033


title: PBM_IgAN_20_030


title: PBM_IgAN_20_027


title: PBM_IgAN_20_028


title: PBM_IgAN_20_024


title: PBM_IgAN_20_029


title: PBM_IgAN_20_026


title: PBM_IgAN_20_023


title: PBM_IgAN_20_025


title: PBM_IgAN_20_022


title: PBM_IgAN_20_031


title: PBM_IgAN_20_032


title: PBM_IgAN_20_021


title: PBM_IgAN_20_020


title: PBM_IgAN_20_016


title: PBM_IgAN_20_019


title: PBM_IgAN_20_017


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title: PBM_IgAN_20_015


title: PBM_IgAN_20_013


title: PBM_IgAN_20_012


title: PBM_IgAN_20_008


title: PBM_IgAN_20_006


title: PBM_IgAN_20_011


title: PBM_IgAN_20_010


title: PBM_IgAN_20_007


title: PBM_IgAN_20_003


title: PBM_IgAN_20_004


title: PBM_IgAN_20_005


title: PBM_IgAN_19_123


title: PBM_IgAN_20_001


title: PBM_IgAN_19_124


title: PBM_IgAN_19_121


title: PBM_IgAN_19_127


title: PBM_IgAN_19_125


title: PBM_IgAN_19_117


title: PBM_IgAN_19_122


title: PBM_IgAN_20_002


title: PBM_IgAN_19_115


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title: PBM_IgAN_19_126


title: PBM_IgAN_19_109


title: PBM_IgAN_19_106


title: PBM_IgAN_19_108


title: PBM_IgAN_19_110


title: PBM_IgAN_19_105


title: PBM_IgAN_20_009


title: PBM_IgAN_19_104


title: PBM_IgAN_19_103


title: PBM_IgAN_19_111


title: PBM_IgAN_19_102


title: PBM_IgAN_19_118


title: PBM_IgAN_19_119


title: PBM_IgAN_19_107


title: PBM_IgAN_19_099


title: PBM_IgAN_19_097


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title: PBM_IgAN_19_101


title: PBM_IgAN_19_093


title: PBM_IgAN_19_094


title: PBM_IgAN_19_096


title: PBM_IgAN_19_098


title: PBM_IgAN_19_083


title: PBM_IgAN_19_084


title: PBM_IgAN_19_082


title: PBM_IgAN_19_092


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title: PBM_IgAN_19_089


title: PBM_IgAN_19_088


title: PBM_IgAN_19_077


title: PBM_IgAN_19_081


title: PBM_IgAN_19_086


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title: PBM_IgAN_19_074


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title: PBM_IgAN_19_072


title: PBM_IgAN_19_078


title: PBM_IgAN_19_070


title: PBM_IgAN_19_071


title: PBM_IgAN_19_068


title: PBM_IgAN_19_067