title: Rv1_DKO_CDK19M_FBS_SNX631_3d_Rep3

value: CDK8/19-double kncokout, re-expressing human CDK19-D173A kinase-dead mutant

value: Rv1-dKO-CDK19M cells treated with 500 nM SNX631 for 72 hours, in FBS media


title: AM633_Fen_d1_Rep03 [AM6330051]

status: Public on Mar 31 2024

type: SRA

city: Indianapolis

first: Shreedharan

last: Sriram

address: 9330 Zionsville Road

country: USA

institute: Corteva Agriscience

library_source: transcriptomic

data_processing:
Adapter sequences remaining within the reads were trimmed (using parameters minlength=35 trimq=20 ktrim=r qtrim=rl k=23 mink=11 hdist=1) using the bbmap tool (v 38.18)
any reads aligning to Zebrafish rRNA sequences were removed using the bbmap tool (v38.18) from the JGI bbtools software package.
Zebrafish transcript abundances were calculated on a per sample basis using the Salmon software (v.1.2.0) 11 (with parameters “--seqBias --validateMappings --numBootstraps 100 --libType SR”) processed against the D. rerio GRCz11 reference genome and annotation 4 downloaded from Ensembl
Following transcript level abundance estimation, gene level expression counts were summarized from the salmon output using the tximport package (v1.26) 12 in R
any protein coding gene with less than an abundance count of ten across all samples were removed from further analysis
The DESeq2 analysis package (v1.34.0) in R 13 (version 4.1.3) was used for data normalization (using the variance stabilizing transformation (vst) method), handling batch effects and identification of differentially expressed genes between control groups and dose treatment groups for each molecule tested.
Assembly: D. rerio GRCz11 reference genome
Supplementary files format and content: tab-delimited text file which includes raw gene count values for each Sample
Supplementary files format and content: tab-delimited text file which includes vst-normalized and batch corrected gene expression table (filtered for low expressing genes)

molecule: total RNA

organism: Danio rerio

source_name: embryo

growth_protocol: Please refer to associated manuscript

extract_protocol:
Total RNA was isolated from zebrafish embryo samples from BioBide using the Qiagen RNeasy Mini kit following the manufacturer’s protocol. RNA samples had RNA Quality Scores ≥7 as determined with a 5200 Fragment Analyzer System (Agilent, Santa Clara, CA).
The Illumina Stranded mRNA Sample Preparation kit (Illumina, San Diego, California, U.S.A.) was used to generate RNAseq libraries following the manufacturer’s recommended protocol. First, poly-A containing mRNA was purified from 800 ng of total RNA using poly-T oligo-attached magnetic beads. Purified mRNA was fragmented to approximately 200 bp average length using divalent cations under high temperature. Following fragmentation, SuperScript II reverse transcriptase and random hexamers were used to synthesize first strand cDNA. Second strand synthesis was completed using dUTP-containing Second Strand Marking Master Mix. The resulting blunt end double stranded cDNA fragments underwent end repair, poly A-tailing, and ligation to Illumina index-anchors.  Anchor-ligated library products were enriched with dual-indexed Illumina adapters (IDT for Illumina DNA/RNA Indexes sets) with 13 cycles of PCR. Individual sample libraries were analyzed for fragment quality and quantity using a Tapestation 4200 with D1000 screentape.  Individual libraries were pooled together based on equal nmol amount.  The pooled library was quantitated by Qubit fluorometer (Thermo Scientific, Waltham, Massachusetts, U.S.A.) and further diluted to 2 nM. The normalized and pooled library was further diluted to 2 pM and loaded onto an Illumina NovaSeq6000 following manufacturer’s protocol and sequenced with single-read 100 bp configuration to generate raw RNAseq reads

treatment_protocol: Please refer to associated manuscript

tag: tissue

value: embryo

tag: developmental stage

value: 5 days post fertilization

tag: strain

value: Transgenic zebrafish (Danio rerio) Tg(cmlc2:CopEGFP)

tag: loading dose_level_(mg/kg)


title: AM633_Fen_d1_Rep01 [AM6330049]


title: AM633_Fen_d4_Rep03 [AM6330054]


title: AM633_Met_d1_Rep01 [AM6330058]


title: Rv1_DKO_CDK19M_FBS_SNX631_3d_Rep2

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

data_processing:
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by cutadapt (v 2.8) with parameters -m 75 -q 30
Reads were aligned to a hybrid reference genome consisting of both the human GRCh38.p13 primary assembly genome and the mouse GRCm39 primary assembly genome, utilizing STAR (v 2.7.2b) with parameter --outFilterMismatchNoverReadLmax 0.01 --outFilterMultimapNmax 1
Read counts over annotated genes were obtained using featureCount (subreads | version: 2.0.3) with parameters -T 12 -B -O --fraction -s 2 -p --countReadPairs -d 50 -D 800 -g gene_id
Assembly: GRCh38.p13 & GRCm39
Supplementary files format and content: tab-delimited text files include gene counts for each sample

organism: Homo sapiens

growth_protocol: 22Rv1 and its derivatives were cultured in RPMI-1640 media supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 1.5 g/L sodium bicarbonate, 10 mM HEPES, 0.45% D-glucose, and either 10% fetal bovine serum (FBS) or charcoal stripped FBS (CSS), plus 1% penicillin-streptomycin (P/S).

extract_protocol:
Total RNA was extracted using RNAeasy Mini Kit (Qiagen) and RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent)
Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library prep Kit

treatment_protocol: To evaluate effects of CDK8/19 inhibition under androgen-supplemented conditons, cells were seeded into 12-well plates at the density of 2 X 10^5/well in FBS media, incubated overnight, and then treated with 0.1% DMSO (vehicle control) or 500 nM SNX631 in FBS media for 3 days. To evaluate effects of CDK8/19 inhibition under androgen-deprived conditions, cells were first sub-cultured in CSS media for one passage (3-4 days) and then seeded into 12-well plates at the density of 3x10^5 /well in CSS media, incubated overnight, and then treated with 0.1% DMSO (vehicle control) or 500 nM SNX631 in CSS media for 3 days.

tag: cell line

tag: cell type

value: prostate cancer cells

tag: genotype

tag: treatment


title: Rv1_Luc_Int_SNX631_Rep2

data_processing:
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by cutadapt (v 2.8) with parameters -m 75 -q 30
Reads were aligned to a hybrid reference genome consisting of both the human GRCh38.p13 primary assembly genome and the mouse GRCm39 primary assembly genome, utilizing STAR (v 2.7.2b) with parameter --outFilterMismatchNoverReadLmax 0.01 --outFilterMultimapNmax 1
Read counts over annotated genes were obtained using featureCount (subreads | version: 2.0.3) with parameters -T 12 -B -O --fraction -s 2 -p --countReadPairs -d 50 -D 800 -g gene_id
Assembly: GRCh38.p13 & GRCm39
Supplementary files format and content: tab-delimited text files include human and mouse gene counts for each sample

source_name: xenograft

growth_protocol: 22Rv1 and its derivatives were cultured in RPMI-1640 media supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 1.5 g/L sodium bicarbonate, 10 mM HEPES, 0.45% D-glucose, and either 10% fetal bovine serum (FBS) or charcoal stripped FBS (CSS), plus 1% penicillin-streptomycin (P/S).   Cells were inoculated s.c. (2x10^6 cells in 0.1 mL 50% Matrigel per animal) in the right flank of intact or castrated male NSG mice to form xenograft tumors

extract_protocol:
Tumor tissues were first submerged in 500 μL RNA-Later stabilization solution (Thermo Fisher Scientific) at room temperature. After stabilization, RNA samples were extracted from tumor tissues using the mRNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol.  RNA quality was validated on RNA-1000 chip using Bioanalyzer (Agilent)
Sequencing libraries were generated using NEBNext Ultra II Directional RNA Library prep Kit

treatment_protocol: For SNX631 in vivo treatment, animals were randomly allocated to two study groups when the mean tumor size reached 100-200 mm^3. For Rv1-WT study, the treatment group received SNX631-medicated diet (500 ppm, producing 30-60 mg/kg/day dosage on average) and the control group received the control diet.  For Rv1-Luc study, the animals in the control group were dosed with vehicle (70% PEG-400/30% Propylene Glycol, 5 mL/kg, p.o., b.i.d.) and the treatment group was dosed with SNX631 (6 mg/mL solution in the vehicle, 5 mL/kg, p.o., b.i.d.) at 60 mg/kg/day.

value: xenograft

value: Luciferase-expressing

value: Rv1-Luc xenograft (Luc_Int_Snx_#5) growing intact NSG male mice, SNX631 treatment group (Int-Snx)


title: AM633_Cyh_d4_Rep02 [AM6330047]


title: AM633_Fen_d1_Rep02 [AM6330050]


title: AM633_Cyh_d4_Rep03 [AM6330048]


title: AM633_Cyh_d2_Rep03 [AM6330045]


title: Si8, replicate 1, scRNAseq

city: Beijing

first: Shao Jie

last: Qin

state: Beijing

address: No.5 Summer Palace Road, Yanyuan Street, Haidian District

country: China

institute: Peking University

description: 10ⅹGenomics single cell transcriptome sequencing project was undertook by BGI sequencing platform. The distribution of the fragments size was checked by the Agilent 2100 bioanalyzer and the final products were sequenced using the DNBSEQTM platform.

library_source: transcriptomic single cell

data_processing:
The original data we collected from sequencing is called Raw Reads, after we will split the Barcode, UMI and insertion of the reads according to the unique library structure of 10X Genomics’single cell RNA-Seq , and then the insertion will be compared to the reference genome, Then, the ratio of each region is compared and the expression statistics are performed; based on the expression results, cell clustering analysis is performed, and marker gene screening and identification are performed.
Differently expressed gene across different cell clusters were identified using the FindMarkers function in Seurat with parameters ‘logfc. Threshold >0.25, minPct>0.1 and Padj≤0.05’. KEGG (V93.0) pathway analysis was performed using phyper, a function of R. Hypergeometric tests was used to identify differential expressed genes that are significantly enriched compared to the background genes, and the corrected P value was Q value. KEGG pathways with Q value < =0.05 were considered to be significantly enriched.
Assembly: hg38

molecule: polyA RNA

source_name: breast

extract_protocol:
Pre-experiment utilizing Trypan Blue staining was conducted to ensure the viability of wtMCF7 cells was above 90% and cell was in optimal growth condition with confluency requirement of over 80%. Subsequently, the culture medium was washed off using Dulbecco's PBS (DPBS) buffer solution without calcium and magnesium, followed by digestion with 0.25% EDTA trypsin at 37℃ for 3 minutes. The detached cells were then collected by centrifugation at 500g for 5 minutes after being transferred to a centrifuge tube using culture medium. After resuspending the cells in DPBS buffer solution and performing cell counting, cells were finally diluted to density of 10e6 per milliliter. Once the cell preparation was completed, it needed to be immediately placed on ice for subsequent library construction using the 10xgenomics platform.
Frozen-stored cells were resuscitated rapidly and examined by microscope after 0.4% Trypan blue coloring. When the viability of cells was higher than 80 percent, the experiment of library construction was performed. Briefly, single cells, reagents and Gel Beads containing barcoded oligonucleotides were encapsulated into nanoliter-sized GEMs (Gel Bead in emulsion) using the GemCode Technology. Lysis and barcoded reverse transcription of polyadenylated mRNA from single cells were performed inside each GEM. Post RT-GEMs were cleaned up and cDNA were amplified. cDNA was fragmented and fragments end were repaired, as well A-tailing was added to the 3’ end. The adaptors were ligated to fragments which were double sided SPRI selected. Another double sided SPRI selecting was carried out after sample index PCR. The final library was quality and quantitated in two methods: check the distribution of the fragments size using the Agilent 2100 bioanalyzer, and quantify the library using real-time quantitative PCR (QPCR) (TaqMan Probe). The final products were sequenced using the DNBSEQTMplatform.

value: breast

value: breast cancer

value: wt

value: no


title: Rv1_Luc_Int_Ctrl_Rep3

value: Rv1-Luc xenograft (Luc_Int_Ctrl_#2) growing intact NSG male mice, control group (Int-Ctrl)


title: Rv1_DKO_CDK19M_FBS_SNX631_3d_Rep1


title: AM633_Cyh_d2_Rep02 [AM6330044]


title: AM633_Cyh_d2_Rep01 [AM6330043]


title: Rv1_Luc_Int_Ctrl_Rep1

value: Rv1-Luc xenograft (Luc_Int_Ctrl_#5) growing intact NSG male mice, control group (Int-Ctrl)


title: AM633_Cyh_d1_Rep03 [AM6330042]


title: AM633_Cyh_d1_Rep02 [AM6330041]


title: SH-SY5Y, DNAJC12KO input, rep1

city: Shanghai

first: Xi

last: Mo

address: Dongfang Road

department: Pediatric Translational Medicine Institute

institute: Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine

library_source: genomic

data_processing:
For ChIP-seq data analysis, reads from ChIP-seq were aligned to the hg38 reference genome using Burrows-Wheeler Alignment tool v0.7.17-r1188. After filtering ambiguously-mapped and duplicates reads, MACS2 v2.2.6 was used to call the peaks with the following parameters, -f BAMPE -g hs -B. Results from the ChIP-seq data were visualized in Integrative Genomics Viewer v2.8.13.
Assembly: hg38
Supplementary files format and content: Peak file from MACS2 peak calling

molecule: genomic DNA

extract_protocol:
1 × 107 cells in culture dishes were fixed with 1 % formaldehyde at room temperature for 10 minutes, and the fixation was stopped via addition of 0.125 M glycine at room temperature for 5 minutes. The cells were washed with cold PBS and scraped into cold SDS lysis buffer from a ChIP Assay Kit (P2078, Beyotime, China). Then, the Covaris™ S220 (Covaris, Amercia) was used to sonicate the sample for a total of 8 minutes (with intervals) at 4 ℃.The chromatin pellets were extracted from cells by lysis buffer from a ChIP Assay Kit (P2078, Beyotime, China). Sonicated chromatin was then incubated with 2 μg of anti-histone H4K5la (PTM-1407RM, PTM BIO, China) or control IgG (66362S, CST, Amercia) precoated on Dynabeads protein G (10007D, Dynabeads protein G, Amercia) at 4 ℃ overnight. The spike-in antibody (61686, active motif, Amercia) and spike-in chromatin (53083, active motif, Amercia) were added as internal control. Immunoprecipitants were washed sequentially with low salt immune complex wash buffer, high salt immune complex wash buffer, LiCl immune complex wash buffer and TE buffer (P2078, Beyotime, China). Chromatin precipitated was then eluted by protease K digestion, cross-link reversed at 65 ℃ for 4 hours, and purified using a QIAquick PCR purification kit (51304, Qiagen, Germany).
DNA fragment Adjust the volume of the combined gDNA sample to a total volume of 41 μL using 1×TE and fragment the DNA to 300 bp using the Biorupter. Blunt-ended fragments are created by filling in or chewing back 3’ and 5’ overhangs. Phosphorylation of the 5’ ends ensures the fragments are suitable for ligation. The single A overhang enables ligation to adaptors with single T overhangs. Adaptor containing sequences required downstream in the sequencing workflow are ligated to the dA-tailed fragment.  The KAPA HiFi DNA Polymerase has been inactivated, enabling amplification of DNA.

value: neuroblastoma cells

tag: chip antibody


title: Rv1_DKO_CDK19M_FBS_Ctrl_3d_Rep3

value: Rv1-dKO-CDK19M cells treated with 0.1% DMSO (vehicle control) for 72 hours, in FBS media


title: SH-SY5Y, DNAJC12KO, rep1

value: anti-histone H4K5la (PTM-1407RM, PTM BIO, China)


title: AM633_Cyh_d1_Rep01 [AM6330040]


title: SH-SY5Y, WT, rep1

value: WT


title: Rv1_DKO_CDK19M_FBS_Ctrl_3d_Rep1

value: CDK8/19-double kncokout, re-expressing human CDK19-D173A kinase-dead mutant


title: Rv1_DKO_CDK19M_FBS_Ctrl_3d_Rep2


title: AM633_Top_d5000_Rep02 [AM6330038]

value: embryo

value: 5 days post fertilization


title: AM633_Top_d5000_Rep01 [AM6330037]

value: Transgenic zebrafish (Danio rerio) Tg(cmlc2:CopEGFP)


title: AM633_Cyh_d4_Rep01 [AM6330046]


title: AM633_Top_d1500_Rep02 [AM6330035]


title: Rv1_DKO_CDK19_FBS_SNX631_3d_Rep2

value: prostate cancer cells

value: CDK8/19-double kncokout, re-expressing human wt CDK19

value: Rv1-dKO-CDK19 cells treated with 500 nM SNX631 for 72 hours, in FBS media


title: AM633_Top_d1500_Rep03 [AM6330036]


title: AM633_Top_d500_Rep03 [AM6330033]


title: Rv1_DKO_CDK19_FBS_SNX631_3d_Rep1


title: AM633_Top_d1500_Rep01 [AM6330034]


title: SH-SY5Y, WT input, rep1


title: WSU-HN6, shCtrl, rep3

city: Wuhan

first: Shu-Jin

last: Li

state: Hubei

address: 237 Luoyu Road

institute: School & Hospital of Stomatology, Wuhan University

data_processing:
The image data obtained by the high-throughput sequencer is converted into sequence data (reads) by CASAVA base recognition, and the file is in fastq format, which mainly contains the sequence information of the sequenced fragments and their corresponding sequencing quality information.
The original data obtained by sequencing contains a small amount of reads with sequencing adapters or low sequencing quality. In order to ensure the quality and reliability of data analysis, it is necessary to filter the original data. Mainly include removing reads with adapters, removing reads containing N (N means unable to determine base information), and removing low-quality reads (reads with Qphred <=20 bases accounting for more than 50% of the entire read length). Fastp (0.23.2) is used for raw data filtering, and the parameters are “–cut_front --cut_tail --cut_window_size 4 -a auto --cut_mean_quality 20 --length_required 36”. All subsequent analyses are based on high-quality analysis of clean data.
Download the reference genome and gene model annotation file directly from the genome website. Use HISAT2 (v2.2.1) to build an index of the reference genome, and use HISAT2 (v2.2.1) to align paired-end clean reads with the reference genome, with parameters “–phred33 --no-mixed --no-discordant”.
featureCounts (v2.0.1) is used to calculate the number of reads mapped to each gene.
Assembly: GRCh38
Supplementary files format and content: counts for each sample

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
The library construction kit used in library construction is Illumina’s NEBNext® UltraTM RNA Library Prep Kit.

value: shCtrl


title: AM633_Top_d500_Rep01 [AM6330031]


title: AM633_Top_d5000_Rep03 [AM6330039]


title: Rv1_DKO_CDK19_FBS_Ctrl_3d_Rep2

value: Rv1-dKO-CDK19 cells treated with 0.1% DMSO (vehicle control) for 72 hours, in FBS media


title: Rv1_DKO_CDK19_FBS_Ctrl_3d_Rep3


title: AM633_Top_d100_Rep03 [AM6330030]


title: WSU-HN6, shCtrl, rep1


title: AM633_Top_d500_Rep02 [AM6330032]


title: Rv1_DKO_CDK19_FBS_SNX631_3d_Rep3


title: WSU-HN6, sh61A, rep2


title: Rv1_DKO_CDK19_FBS_Ctrl_3d_Rep1


title: AM633_Top_d100_Rep01 [AM6330028]


title: AM633_Mes_d5000_Rep02 [AM6330026]


title: CAL-27, sh61A, IFNγ, rep3

value: sh61A, IFNg


title: AM633_Mes_d5000_Rep01 [AM6330025]


title: WSU-HN6, sh61A, rep1


title: Rv1_DKO_CDK8M_FBS_SNX631_3d_Rep3

value: CDK8/19-double kncokout, re-expressing human CDK8-D173A kinase-dead mutant

value: Rv1-dKO-CDK8M cells treated with 500 nM SNX631 for 72 hours, in FBS media


title: AM633_Mes_d1500_Rep03 [AM6330024]


title: WSU-HN6, sh61A, rep3


title: CAL-27, sh61A, IFNγ, rep2


title: AM633_Mes_d1500_Rep02 [AM6330023]


title: Rv1_DKO_CDK8M_FBS_SNX631_3d_Rep2


title: WSU-HN6, shCtrl, rep2


title: AM633_Mes_d1500_Rep01 [AM6330022]


title: AM633_Top_d100_Rep02 [AM6330029]


title: CAL-27, sh61A, IFNγ, rep1


title: AM633_Mes_d500_Rep03 [AM6330021]


title: AM633_Mes_d5000_Rep03 [AM6330027]


title: Rv1_DKO_CDK8M_FBS_SNX631_3d_Rep1


title: AM633_Mes_d500_Rep01 [AM6330019]


title: Rv1_DKO_CDK8M_FBS_Ctrl_3d_Rep2

value: Rv1-dKO-CDK8M cells treated with 0.1% DMSO (vehicle control) for 72 hours, in FBS media


title: Rv1_DKO_CDK8M_FBS_Ctrl_3d_Rep3


title: AM633_Mes_d100_Rep03 [AM6330018]


title: AM633_Mes_d500_Rep02 [AM6330020]


title: AM633_Mes_d100_Rep02 [AM6330017]


title: CAL-27, shCtrl, IFNγ, rep3

value: shCtrl, IFNg


title: CAL-27, shCtrl, IFNγ, rep1


title: AM633_Mes_d100_Rep01 [AM6330016]


title: AM633_Aci_d0.002_Rep03 [AM6330015]


title: CAL-27, shCtrl, IFNγ, rep2


title: CAL-27, sh61A, PBS, rep3

value: sh61A, PBS


title: Rv1_DKO_CDK8M_FBS_Ctrl_3d_Rep1


title: AM633_Aci_d0.002_Rep01 [AM6330013]


title: Rv1_DKO_CDK8_FBS_SNX631_3d_Rep3

value: CDK8/19-double kncokout, re-expressing human wt CDK8

value: Rv1-dKO-CDK8 cells treated with 500 nM SNX631 for 72 hours, in FBS media


title: AM633_Aci_d0.0005_Rep02 [AM6330012]


title: AM633_Aci_d0.002_Rep02 [AM6330014]


title: CAL-27, sh61A, PBS, rep2


title: AM633_Aci_d0.0005_Rep01 [AM6330011]


title: Rv1_DKO_CDK8_FBS_SNX631_3d_Rep2


title: CAL-27, sh61A, PBS, rep1


title: AM633_Aci_d0.0001_Rep03 [AM6330009]


title: AM633_Aci_d0.0001_Rep02 [AM6330008]


title: Rv1_DKO_CDK8_FBS_SNX631_3d_Rep1


title: AM633_DMSO_d0.01_Rep03 [AM6330006]


title: AM633_Aci_d0.0001_Rep01 [AM6330007]


title: CAL-27, shCtrl, PBS, rep3

value: shCtrl, PBS


title: AM633_DMSO_d0.01_Rep01 [AM6330004]

value: embryo


title: AM633_DMSO_d0.01_Rep02 [AM6330005]

value: 5 days post fertilization


title: AM633_DMSO_d0.005_Rep03 [AM6330003]

value: Transgenic zebrafish (Danio rerio) Tg(cmlc2:CopEGFP)


title: Rv1_DKO_CDK8_FBS_Ctrl_3d_Rep3

value: prostate cancer cells

value: Rv1-dKO-CDK8 cells treated with 0.1% DMSO (vehicle control) for 72 hours, in FBS media


title: U87-WT-H

city: Tianjin

first: xudong

last: Wu

address: Qixiangtai Road

institute: Tianjin medical university

data_processing:
RNA-seq analysis was completed by BGI company(Shenzhen,China).
Genome_build: hg19
Supplementary_files_format_and_content: FPKM values for each Sample
Supplementary_files_format_and_content: bigwig file for each Sample

source_name: U87 WT Hypoxia

growth_protocol: All cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) and maintained at 37 °C with 5% CO2, but hypoxia experiments were performed inhypoxic incubator with 5% CO2 and 1% O2.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using NEBNext Ultra RNA library Prep Kit for Illumina.

value: glioblastoma cell line

value: WT

value: hypoxia


title: CAL-27, shCtrl, PBS, rep2


title: AM633_DMSO_d0.005_Rep02 [AM6330002]


title: Rv1_DKO_CDK8_FBS_Ctrl_3d_Rep2


title: AL980_SXG_d20000_Rep03 [AL9800132]


title: CAL-27, shCtrl, PBS, rep1


title: AM633_DMSO_d0.005_Rep01 [AM6330001]


title: Rv1_DKO_CDK8_FBS_Ctrl_3d_Rep1


title: Hs, 293T, ANKRD11 KD, HDAC3, Cut&Tag, rep2

first: Shaobo

last: Liang

state: Hubei Sheng

address: BaYi Road, LUOJIA HILL

institute: Wuhan University

data_processing:
Raw reads were cleaned with trim-galore and mapped to the Drosophila melanogaster genome (dm6, FlyBase) and Homo sapiens genome (hg38, Ensembl) using STAR for mRNA sequencing and Bowtie2 for sequencing of CUT&Tag and ChIP assays.
For mRNA sequencing, the reads at the gene level were summarized by featureCounts, followed by DESeq2 R package for analysis of differential expression.
For CUT&Tag and ChIP sequencing, duplicate reads were removed by picard, and peaks were called using MACS2.
Supplementary files format and content: narrow peaks of Cut&Tag and ChIP sequencing
Supplementary files format and content: read count of RNAseq
Library strategy: Cut&Tag

extract_protocol:
RNA was harvested using TRI Reagent (Sigma-Aldrich). 1 ug of total RNA was used for the construction of sequencing libraries. ChIP DNA was pulled down by H3K9ac antibody in HEK293T cells. DNA for CUT&Tag-seq was cleavaged Under Target & Tagmentation by RNPC3 or HDAC3 antibody in HEK293T cells.
RNA libraries for RNA-seq were prepared using Fast RNA-seq Lib Prep Kit V2 following manufacturer's protocols. DNA libraries for CUT&Tag-seq were prepared using CUT&Tag Assay Kit (pAG-Tn5) following manufacturer's protocols. DNA libraries for ChIP-seq were prepared using Scale ssDNA-seq Lib Prep Kit following manufacturer's protocols.

value: HsANKRD11 KD

value: HDAC3 (10255-1-AP, Proteintech)


title: AL980_SXG_d20000_Rep02 [AL9800131]


title: AL980_SXG_d20000_Rep01 [AL9800130]


title: U87-WT-N

source_name: U87 WT Normoxia

value: normoxia


title: Rv1_Luc_CSS_SNX631_3d_Rep3

value: Luciferase-expressing

value: Rv1-Luc cells treated with 500 nM SNX631 for 72 hours, in CSS media


title: Rv1_Luc_CSS_SNX631_3d_Rep2


title: AL980_SXG_d5000_Rep03 [AL9800129]


title: AM633_Pro_d15_Rep01 [AM6330082]


title: AL980_SXG_d5000_Rep01 [AL9800127]


title: BB_rep3

first: Wenxing

last: Chen

address: No.1, Shizishan Street, Hongshan District

institute: Huazhong Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.8
The ChIP-seq reads were mapped to  apple whole genome (GDDH13_11.1) using Bowtie (Langmead, 2010) with up to two mismatches allowed
The raw sequencing reads were processed fastp with default parameter
The obtained clean reads were mapped to the apple genome with HISAT
StringTie and DESeq2 R package were used to estimate transcript abundances and identify differentially expressed genes with an FDR threshold of 0.05 in different samples.
Genome_build: apple genome (GDDH13_11.1, Daccord et al., 2017)

organism: Malus domestica

source_name: Flower buds

growth_protocol: The one-year old middle branches bearing flower buds at terminal position were sampled from apple trees (Malus×domestica Borkh. ‘Fuji’) grown at the experimental farm of the Department of Agriculture, Shinshu University (Nagano, Japan; 36’ N and 139’ E) on 11 November, 2016

extract_protocol:
Total RNA was isolated from frozen flesh samples using Trizol reagent. Three to four flower buds were used as one replicate.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The flower buds used for ChIP experiment were collected before incubation (before chilling, sample “BC”) and after chilling exposure for 60 d (after chilling, sample “AC”). After 60 d of chilling exposure, branches were then moved to forcing condition in a growth chamber, 22 °C under long-photoperiod conditions (16 h light/8 h dark) with a light intensity of 100 μmol m-2 s-1 provided by cool-white fluorescent lights.

value: terminal flower buds

value: approaching bud break

value: 22C for 9 days


title: BB_rep2


title: AL980_SXG_d5000_Rep02 [AL9800128]


title: AL980_SXG_d2000_Rep03 [AL9800126]


title: Rv1_Luc_CSS_Ctrl_3d_Rep3

value: Rv1-Luc cells treated with 0.1% DMSO (vehicle control) for 72 hours, in CSS media


title: BB_rep1


title: AL980_SXG_d2000_Rep01 [AL9800124]

value: embryo


title: AL980_SXG_d500_Rep03 [AL9800123]

value: 5 days post fertilization


title: Rv1_Luc_CSS_Ctrl_3d_Rep2


title: AL980_SXG_d500_Rep01 [AL9800121]

value: Transgenic zebrafish (Danio rerio) Tg(cmlc2:CopEGFP)


title: AC_rep2

value: after chilling exposure

value: 5C for 60 days


title: AL980_SXG_d250_Rep03 [AL9800120]


title: AL980_SXG_d250_Rep02 [AL9800119]


title: AC_rep3


title: AL980_SXG_d500_Rep02 [AL9800122]


title: Rv1_Luc_FBS_SNX631_3d_Rep2

value: prostate cancer cells

value: Rv1-Luc cells treated with 500 nM SNX631 for 72 hours, in FBS media


title: Rv1_Luc_FBS_SNX631_3d_Rep3


title: Rv1_Luc_CSS_SNX631_3d_Rep1


title: Rv1_Luc_CSS_Ctrl_3d_Rep1


title: BC_rep4

value: before chilling exposure

value: untreated


title: AL980_RA_d100_Rep02 [AL9800116]


title: Rv1_Luc_FBS_SNX631_3d_Rep1


title: AL980_SXG_d2000_Rep02 [AL9800125]


title: AC_rep1


title: AL980_RA_d100_Rep01 [AL9800115]


title: AL980_SXG_d250_Rep01 [AL9800118]


title: AL980_DMSO_d0.01_Rep03 [AL9800114]


title: Rv1_Luc_FBS_Ctrl_3d_Rep3

value: Rv1-Luc cells treated with 0.1% DMSO (vehicle control) for 72 hours, in FBS media


title: AL980_DMSO_d0.01_Rep02 [AL9800113]


title: BC_rep2


title: BC_rep3


title: Rv1_Luc_FBS_Ctrl_3d_Rep2


title: AL980_DMSO_d0.01_Rep01 [AL9800112]


title: AL980_DMSO_d0.005_Rep03 [AL9800111]


title: BC_rep1


title: AL980_RA_d100_Rep03 [AL9800117]


title: AL980_DMSO_d0.005_Rep02 [AL9800110]


title: Rv1_Luc_FBS_Ctrl_3d_Rep1


title: wt_P19_ECC_monolayer_+RA_24hrs_rep3

city: Nantes

first: Christine

last: Chauveau

address: 30 Boulevard Jean Monnet

country: France

institute: CR2TI UMR 1064

data_processing:
Base calling : bcl2fastq2 v2.20
Data filtering, alignment and UMI count done with SRP pipeline : Eric Charpentier, Marine Cornec, Solenne Dumont et al. 3’ RNA sequencing for robust and low-cost gene expression profiling, 28 January 2021, PROTOCOL (Version 1) available at Protocol Exchange [https://doi.org/10.21203/rs.3.pex-1336/v1]
read trimming: cutadapt v4.5
Alignment : bwa v0.7.17 ; bwa aln -M 0 | bwa samse
Read counts : custom python script count.py using pysam : https://bio.tools/3SRP
Assembly: mm10
Supplementary files format and content: Count matrix containing raw UMI counts, one sample per column for a total of 36 column, raw names are HGNC approved genes symbol

organism: Mus musculus

growth_protocol: wt and Tdg-null P19 mouse embryonal carcinoma cells (ECCs) were grown in cell culture plastic dishes in 10% FCS DMEM containing penicillin and streptomycin. To obtain aggregates, cells were grown in bacterial grade plastic dishes.

extract_protocol:
Total RNA was extracted using Trizol and RNA Integrity Number (RIN) score was determined with a 2100 Bioanalyzer (Agilent).
RNAseq library have been prepared following the 3’SRP method published by : Eric Charpentier, Marine Cornec, Solenne Dumont et al. 3’ RNA sequencing for robust and low-cost gene expression profiling, 28 January 2021, PROTOCOL (Version 1) available at Protocol Exchange [https://doi.org/10.21203/rs.3.pex-1336/v1]

treatment_protocol: To induce cell differentiation, cells were treated with 1 micromolar retinoic acid (RA) for the indicated time.

value: Embryonal carcinoma

value: WT

value: retinoic acid, 24hrs


title: AL980_HU_d20000_Rep03 [AL9800108]


title: AL980_DMSO_d0.005_Rep01 [AL9800109]


title: wt_P19_ECC_monolayer_+RA_24hrs_rep2


title: n92_responder_epidermis

city: Portland

first: Connie

last: Shao

state: OR

address: 3303 S Bond Ave Building 1

institute: Oregon Health & Science University

data_processing:
mRNA was sequenced by Novogene (Sacramento, CA). Briefly, short read sequencing assays (NovaSeq 6000, Illumina) were performed at a depth of 40 million reads per sample. Raw reads were postprocessed with fastp software and aligned to the human genome, version GRCh38, using Hisat2 (v2.0.5). A counts matrix was generated using featureCounts v1.5.0-p3. Differential expression analysis was conducted with the DESeq2 R package (v1.20.0) and reads were filtered by p < 0.05 after adjustment for the false discovery rate using the Benjamini and Hochberg approach. KEGG pathways (www.genome.jp/kegg) were analyzed using clusterProfiler R. Gene expression was compared between healthy controls and patients with PRP, and stratified by epidermis vs dermis, time on therapy (week-0, week-24, week-24) and response to therapy.
Assembly: GRCh38
Supplementary files format and content: bulk RNA-seq counts matrix in comma separated values format

source_name: epidermis

extract_protocol:
Skin punch biopsy samples were rinsed in sterile phosphate buffered saline without calcium or magnesium (HyClone Laboratories, GE Healthcare) and then incubated at room temperature in a 3.8% ammonium thiocyanate (Sigma Aldrich) in phosphate buffered saline without calcium or magnesium solution for 45 minutes. The epidermis and dermis were subsequently separated using sterile forceps, placed into separate RNase-free tubes containing 700 μL QIAzol (Qiagen), homogenized by hand using RNase-free pestles (Argos), and placed at −80 °C. All samples were collected, processed under sterile conditions, and stored within a 2-hour time frame. RNA was isolated using chloroform (Fisher Scientific), RNeasy Mini Kit (Qiagen), and RNase-free DNaseI (Qiagen). Briefly, 140 μL chloroform was added to each tube, the mixture was vortexed for 5 seconds, and the tubes were left to stand for 2 to 3 minutes at room temperature. After centrifugation at 12 000 g for 15 minutes at 4 °C, the top aqueous layer was transferred to a new tube and combined with an equal volume of 100% ethanol. Thereafter, the Qiagen RNeasy Mini Kit protocol was followed, ending with a 35 μL elution volume of RNase-free water. RNA quality was assessed on a Synergy H1 microplate reader (BioTek Instruments) with UV readings of 260 nm, 280 nm, 230 nm, and 320 nm. Purified RNA was stored at −80 °C until downstream analysis.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers,  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Guselkumab subcutaneous injections performed at the FDA-approved dosing schedule for psoriasis over a 24-week period

value: epidermis

value: responder


title: AL980_HU_d20000_Rep02 [AL9800107]


title: AL980_HU_d20000_Rep01 [AL9800106]


title: n91_responder_dermis

source_name: dermis

value: dermis


title: AL980_HU_d10000_Rep03 [AL9800105]


title: n89_responder_dermis


title: wt_P19_ECC_monolayer_+RA_24hrs_rep1


title: wt_P19_ECC_monolayer_+RA_12hrs_rep2

value: retinoic acid, 12hrs


title: n90_responder_epidermis


title: AL980_HU_d5000_Rep02 [AL9800101]

value: embryo


title: AL980_HU_d10000_Rep02 [AL9800104]

value: 5 days post fertilization


title: AL980_HU_d5000_Rep03 [AL9800102]

value: Transgenic zebrafish (Danio rerio) Tg(cmlc2:CopEGFP)


title: n88_responder_epidermis


title: AL980_HU_d2000_Rep03 [AL9800099]


title: AL980_HU_d10000_Rep01 [AL9800103]


title: AL980_HU_d2000_Rep02 [AL9800098]


title: AL980_HU_d5000_Rep01 [AL9800100]


title: wt_P19_ECC_monolayer_+RA_12hrs_rep1


title: n87_responder_dermis


title: AL980_HU_d2000_Rep01 [AL9800097]


title: n86_responder_epidermis


title: AL980_HU_d1000_Rep03 [AL9800096]


title: wt_P19_ECC_monolayer_+RA_6hrs_rep3

value: retinoic acid, 6hrs


title: wt_P19_ECC_monolayer_+RA_6hrs_rep2


title: wt_P19_ECC_monolayer_+RA_12hrs_rep3


title: AL980_HU_d1000_Rep02 [AL9800095]


title: AL980_HU_d1000_Rep01 [AL9800094]


title: n85_responder_dermis


title: AL980_CTZ_d1500_Rep03 [AL9800093]


title: wt_P19_ECC_monolayer_+RA_6hrs_rep1


title: AL980_CTZ_d1500_Rep02 [AL9800092]


title: AL980_CTZ_d1500_Rep01 [AL9800091]


title: wt_P19_ECC_monolayer_untreated_rep3


title: n84_responder_epidermis


title: wt_P19_ECC_monolayer_untreated_rep2


title: AL980_CTZ_d400_Rep01 [AL9800088]


title: n82_responder_epidermis


title: n83_responder_dermis


title: AL980_CTZ_d400_Rep03 [AL9800090]


title: TDG-null_P19_ECC_aggregates_+RA_48hrs_rep3

value: Tdg knock out

value: retinoic acid, 48hrs


title: AL980_CTZ_d100_Rep02 [AL9800086]


title: n81_responder_dermis


title: AL980_CTZ_d100_Rep01 [AL9800085]


title: AL980_5FU_d30000_Rep02 [AL9800083]


title: n79_responder_dermis


title: AL980_5FU_d10000_Rep03 [AL9800081]


title: TDG-null_P19_ECC_aggregates_+RA_48hrs_rep1


title: n78_responder_epidermis


title: AL980_CTZ_d400_Rep02 [AL9800089]


title: AL980_5FU_d10000_Rep02 [AL9800080]


title: AL980_CTZ_d100_Rep03 [AL9800087]


title: AL980_5FU_d30000_Rep01 [AL9800082]


title: TDG-null_P19_ECC_aggregates_+RA_48hrs_rep2


title: wt_P19_ECC_monolayer_untreated_rep1


title: n80_responder_epidermis


title: n77_nonresponder_dermis

value: nonresponder


title: AL980_5FU_d5000_Rep02 [AL9800077]


title: TDG-null_P19_ECC_aggregates_rep2


title: AL980_5FU_d5000_Rep01 [AL9800076]


title: AL980_5FU_d30000_Rep03 [AL9800084]


title: n75_nonresponder_epidermis


title: AL980_5FU_d2000_Rep02 [AL9800074]


title: n76_nonresponder_dermis


title: TDG-null_P19_ECC_monolayer_+RA_48hrs_rep3


title: AL980_5FU_d1000_Rep02 [AL9800071]


title: AL980_5FU_d2000_Rep01 [AL9800073]


title: AL980_5FU_d2000_Rep03 [AL9800075]


title: n74_nonresponder_dermis


title: TDG-null_P19_ECC_monolayer_+RA_48hrs_rep2


title: AL980_5FU_d1000_Rep03 [AL9800072]


title: AL980_5FU_d5000_Rep03 [AL9800078]


title: AL980_5FU_d10000_Rep01 [AL9800079]


title: AL980_5FU_d1000_Rep01 [AL9800070]


title: TDG-null_P19_ECC_monolayer_+RA_48hrs_rep1


title: AL980_MDNC_d0.1_Rep02 [AL9800068]


title: AL980_MDNC_d0.1_Rep03 [AL9800069]


title: n72_nonresponder_epidermis


title: n73_nonresponder_epidermis


title: TDG-null_P19_ECC_monolayer_rep3


title: n71_nonresponder_dermis


title: AL980_MDNC_d0.03_Rep02 [AL9800065]


title: TDG-null_P19_ECC_aggregates_rep1


title: AL980_MDNC_d0.03_Rep03 [AL9800066]


title: TDG-null_P19_ECC_monolayer_rep2


title: AL980_MDNC_d0.03_Rep01 [AL9800064]


title: AL980_MDNC_d0.01_Rep03 [AL9800063]


title: TDG-null_P19_ECC_monolayer_rep1


title: n69_nonresponder_epidermis


title: AL980_MDNC_d0.01_Rep01 [AL9800061]


title: AL980_MDNC_d0.01_Rep02 [AL9800062]


title: AL980_DNC_d0.1_Rep03 [AL9800060]


title: AL980_MDNC_d0.1_Rep01 [AL9800067]


title: wt_P19_ECC_aggregates_+RA_48hrs_rep3


title: AL980_DNC_d0.1_Rep01 [AL9800058]


title: AL980_DNC_d0.1_Rep02 [AL9800059]


title: n67_nonresponder_epidermis


title: AL980_DNC_d0.03_Rep03 [AL9800057]


title: AL980_DNC_d0.03_Rep02 [AL9800056]


title: wt_P19_ECC_aggregates_+RA_48hrs_rep1


title: AL980_DNC_d0.03_Rep01 [AL9800055]


title: n66_nonresponder_dermis


title: n68_nonresponder_dermis


title: wt_P19_ECC_aggregates_rep3


title: AL980_DNC_d0.01_Rep02 [AL9800053]


title: AL980_DNC_d0.01_Rep03 [AL9800054]


title: n70_nonresponder_epidermis


title: AL980_DNC_d0.01_Rep01 [AL9800052]


title: n64_nonresponder_dermis


title: wt_P19_ECC_aggregates_rep2


title: AL980_SAHA_d1000_Rep02 [AL9800050]


title: AL980_SAHA_d1000_Rep01 [AL9800049]


title: wt_P19_ECC_aggregates_rep1


title: wt_P19_ECC_aggregates_+RA_48hrs_rep2


title: AL980_SAHA_d300_Rep03 [AL9800048]


title: n63_responder_epidermis


title: n65_nonresponder_epidermis


title: AL980_SAHA_d300_Rep02 [AL9800047]


title: wt_P19_ECC_monolayer_+RA_48hrs_rep2


title: n62_responder_dermis


title: AL980_SAHA_d300_Rep01 [AL9800046]


title: n61_responder_epidermis


title: wt_P19_ECC_monolayer_+RA_48hrs_rep1


title: AL980_SAHA_d200_Rep03 [AL9800045]


title: AL980_SAHA_d200_Rep02 [AL9800044]


title: wt_P19_ECC_monolayer_rep3


title: n59_responder_epidermis


title: AL980_SAHA_d50_Rep03 [AL9800042]


title: AL980_SAHA_d50_Rep02 [AL9800041]


title: wt_P19_ECC_monolayer_rep2


title: n58_responder_dermis


title: AL980_SAHA_d50_Rep01 [AL9800040]


title: wt_P19_ECC_monolayer_+RA_48hrs_rep3


title: AL980_SAHA_d1000_Rep03 [AL9800051]


title: AL980_SAHA_d200_Rep01 [AL9800043]


title: AL980_MTX_d300_Rep03 [AL9800039]


title: AL980_MTX_d300_Rep02 [AL9800038]


title: AL980_MTX_d300_Rep01 [AL9800037]


title: AL980_MTX_d80_Rep02 [AL9800035]


title: HOM-L3 day 6

first: Domgmin

last: Yin

state: Shanghai

address: No.3663, Zhongshan North Road

institute: Shanghai Key Laboratory of Brain Functional Genomics

data_processing:
Paired-end reads were harvested from sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome with hisat2 software (v2.0.4).
Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization.
Differentially expressed mRNAs were identified by p-value and fold change. GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Assembly: mm10
Supplementary files format and content: The Excel contains the mRNA raw counts and normalized counts information

source_name: Hippocampus

extract_protocol:
Total RNA was extracted using Trizol reagent
total RNA was extracted with Trizol , and subjected to ribosomal RNA (rRNA) removal using GenSeq® rRNA Removal Kit (GenSeq, Inc., Shanghai, China). Then, the rRNA-depleted samples were used for library construction with GenSeq® Directional RNA Library Prep Kit (GenSeq, Inc., Shanghai, China) by following manufacturer’s recommendations. The RNA was fragmented into ~300 nt in length. The first-strand cDNA was synthesized from the RNA fragments by reverse transcriptase and random hexamer primers, and the second-strand cDNA was synthesized in 2nd Strand Synthesis Buffer with dUTP Mix. Then, the double stranded cDNA fragments were subjected to end-repair and dA-tailing, followed by adapter ligation. The adapter-ligated DNA samples were PCR amplified and purified to obtain sequencing libraries.

value: Hippocampus

tag: sample type

value: HOM

value: L day 6


title: HOM-C3 day 6

value: C day 6


title: n60_responder_dermis


title: AL980_MTX_d80_Rep01 [AL9800034]


title: AL980_MTX_d40_Rep03 [AL9800033]


title: AL980_MTX_d40_Rep02 [AL9800032]


title: n54_responder_dermis


title: AL980_MTX_d40_Rep01 [AL9800031]


title: HOM-C2 day 6


title: wt_P19_ECC_monolayer_rep1

value: Embryonal carcinoma

value: WT


title: AL980_MTX_d20_Rep02 [AL9800029]


title: HOM-L1 day 6


title: AL980_MTX_d10_Rep03 [AL9800027]


title: n52_responder_dermis


title: HOM-C1 day 6


title: n57_responder_dermis


title: AL980_MTX_d80_Rep03 [AL9800036]


title: n56_responder_dermis


title: AL980_MTX_d10_Rep02 [AL9800026]


title: AL980_MTX_d10_Rep01 [AL9800025]


title: AL980_MTX_d20_Rep01 [AL9800028]


title: SYN-L day 20

value: SYN

value: L day 20


title: n51_responder_epidermis

value: epidermis

value: responder


title: n55_responder_epidermis


title: n50_responder_dermis

value: dermis


title: AL980_PHT_d80_Rep02 [AL9800023]

value: embryo

value: 5 days post fertilization


title: SYN-C day 20

value: C day 20


title: HOM-L2 day 6


title: AL980_PHT_d80_Rep01 [AL9800022]

value: Transgenic zebrafish (Danio rerio) Tg(cmlc2:CopEGFP)


title: n53_responder_epidermis


title: AL980_PHT_d80_Rep03 [AL9800024]


title: AL980_MTX_d20_Rep03 [AL9800030]


title: AL980_PHT_d40_Rep03 [AL9800021]


title: SYN-L day 6


title: AL980_PHT_d40_Rep02 [AL9800020]


title: AL980_PHT_d40_Rep01 [AL9800019]


title: AL980_PHT_d20_Rep03 [AL9800018]


title: n47_responder_dermis


title: n46_responder_epidermis


title: AL980_PHT_d20_Rep02 [AL9800017]


title: AL980_PHT_d20_Rep01 [AL9800016]


title: SYN-L day 1

value: L day 1


title: AL980_PHT_d10_Rep03 [AL9800015]


title: AL980_PHT_d10_Rep02 [AL9800014]


title: AL980_PHT_d10_Rep01 [AL9800013]


title: n49_responder_epidermis


title: AL980_FPB_d1.2_Rep01 [AL9800010]


title: n44_responder_dermis


title: AL980_FPB_d1.2_Rep03 [AL9800012]


title: n45_responder_epidermis


title: AL980_FPB_d1.2_Rep02 [AL9800011]


title: n48_responder_epidermis


title: SYN-C day 6


title: n42_responder_epidermis


title: AL980_FPB_d0.6_Rep02 [AL9800008]


title: AL980_FPB_d0.6_Rep03 [AL9800009]


title: WT, cDC1, RNA-seq, WC_3

first: Tantan

last: Wang

address: Haidian  District

institute: Tsinghua University

data_processing:
The short sequence reads were aligned to  mm10 reference genome using STAR, then quantified by featureCounts. After obtaining the raw count matrix, the R package DESeq2 was used for differential gene expression analysis among subgroups and DEGs (pvalue < 0.05) between WT, KDM5A KO and/or KDM5A overexpression MDA-MB-231 cells with or without 10ng/ml IFN-γ treatment were identified. Gene Ontology (GO) analysis , KEGG analysis and GSEA (Gene Set Enrichment Analysis) were performed with the R package clusterProfiler.
Assembly: mm10
Supplementary files format and content: excel file includes fpkm values for each sample

source_name: cDC1 cells

extract_protocol:
RNA was extracted using the Trizol reagent (Ambion).
The reverse transcription, and cDNA library construction were then performed following the protocol of NEBNext Ultra RNA Library Prep Kit.

value: cDC1 cells


title: AL980_FPB_d0.3_Rep03 [AL9800006]


title: AL980_FPB_d0.3_Rep02 [AL9800005]


title: n41_responder_dermis


title: n40_nonresponder_epidermis

value: nonresponder


title: AL980_FPB_d0.3_Rep01 [AL9800004]


title: SYN-C day 1

value: Hippocampus

value: C day 1


title: AL980_FPB_d0.1_Rep03 [AL9800003]


title: WT, cDC1, RNA-seq, WC_2


title: B50, replicate 3, scRNA-seq

city: Nanjing

first: Gao

last: Lingyu

address: #12 Jiangwangmiao Street

department: Institute of Dermatology

institute: Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College

description: 10x genomic

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cell Ranger software v2.1.1
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: kidney

extract_protocol:
Freshly collected tubular epithelial cells and B cells from pristane-induced C57bl/6j mice were flushed with ice-cold HBSS. Singles cells RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA liibraries for RNA-seq were prepared using SMARTER Mrna-Seq Library Prep Kit following manufacter's protocols

value: kidney

value: renal tubular epithelial cells

value: epithelial cells

value: pristane-induced C57BL/6j lupus mice

value: FMT


title: n43_responder_dermis


title: n39_nonresponder_dermis


title: B48, replicate 2, scRNA-seq

description: 10x genomic


title: AL980_FPB_d0.1_Rep02 [AL9800002]


title: B42, replicate 1, scRNA-seq

description: 10x genomic


title: AL980_FPB_d0.1_Rep01 [AL9800001]


title: KDM5A knock out, cDC1, RNA-seq, KC_1

value: KDM5A knock out


title: n38_nonresponder_epidermis

value: epidermis


title: KDM5A knock out, cDC1, RNA-seq, KC_2


title: n37_nonresponder_dermis

value: dermis


title: C15, replicate 1, scRNA-seq

description: 10x genomic

value: Saline


title: bone tissue,fracture,day28,rep2

first: Shuhang

last: Guo

address: Xizhimen South Street

institute: Peking University People's Hospital

data_processing:
The sequencing data were filtered, and the low-quality data were removed. The clean reads of each sample were screened, and sRNA within a certain length range was selected for subsequent analysis. The distribution of small Rnas on the reference sequence was analyzed by positioning the length screened srnas to the reference sequence using bowtie.
Assembly: rattus_norvegicus_Ensembl_97
Supplementary files format and content: tab-delimited text file includes raw counts for all Samples (D0_1~D28_3)

organism: Rattus norvegicus

source_name: bone

extract_protocol:
Rats were anesthetized with 2.5% isoflurane/oxygen. Right L4-L6 spinal coad was taken from each rat, and the samples were frozen in liquid nitrogen within 3 minutes after leaving the body. The frozen samples were crushed and dissolved in TRIzol (Invitrogen). RNA was subsequently extracted from tissues and the RNA were subjected to strict quality control (Agilent 2100 bioanalyzer).
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9. After the completion of the library construction, Qubit 2.0 was used for preliminary quantification, diluting the library to 1.5ng/ul, and then Agilent 2100 was used to detect the Insert size of the library to ensure the quality of the library. After qualified library inspection, Illumina PE150 sequencing was conducted by pooling according to effective concentration of library and data output requirements.

value: SD

value: bone


title: bone tissue,fracture,day28,rep3


title: TDG-null_P19_ECC_aggregates_rep3

value: Embryonal carcinoma

value: Tdg knock out


title: n35_responder_dermis

value: responder


title: bone tissue,fracture,day28,rep1


title: Control TA, mouse 12

type: RNA

city: Campinas

first: Dimitrius Santiago

middle: Passos Simoes Froes

last: Guimaraes

state: Sao Paulo

address: Carl von Linneaus

department: BFM

country: Brazil

institute: Unicamp

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Transcriptome Analysis Console (TAC) software (v4.0.3, ThermoFisher Scientific) was used for the analysis of the microarray data. Signal values were log2-transformed, and quantile normalized using the Signal Space Transformation (SST-RMA) method. Paired comparisons of gene expression levels between sample groups were performed using moderated t-test as implemented in BioConductor package limma. P-values were adjusted for multiple testing using the Benjamini-Hochberg method.

label: biotin

source_name: control TA

label_protocol: Affymetrix Whole Transcript (WT) Assay kit probed in CGAS cartridge for Clariom S (mouse) following manufacturer’s instructions

growth_protocol: Mice had free access to water and food (standard chow diet) and were housed in a 12-h light/12-h dark cycle, 24 °C and 45% humidity

extract_protocol: Mice were euthanized by Avertin and the dissected TAs immediatelly frozen in liquid nitrogen, and stored in -80oC until extraction. RNA was extracted with TRIzol according to manufacturer's instructions and further purified with Rneasy.

tag: gender

value: male

value: adult

value: control

value: Electroporated mouse tibialis anterior


title: n34_responder_epidermis


title: WT Colon CD45+ scRNAseq replicate 2

city: New Haven

first: Yi

last: Luan

state: CT

address: 10 Amistad, Room 324

institute: Yale University

data_processing:
The sequencing reads of the single-cell RNA-seq (scRNA-seq) was mapped to mouse reference (mm10) followed by quantification of transcript expression using cellranger V7.0.0.
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Colon

extract_protocol:
Splenocytes were collected through mashing the spleen by using the plunger end of the syringe in 1 ml Facs buffer through placing the spleen into the cell strainer. Bone marrow cells were flushed from the femur and tibia bones. Peripheral blood (600–800µl) was collected by retro-orbital bleeding into tubes (BD 365965). Cells were then filtered through a 40μm cell strainer. Cells were centrifuged for 5 min at 500g. The red blood cells were then lysed with RBC lysis buffer for 3 min at room temperature. After centrifugation, cells were washed twice with Facs buffer and resuspended in Facs buffer. Mouse colons were surgically excised, flushed with PBS, then opened longitudinally and cut into approximately 0.5-cm-long pieces. The colon tissue was washed again with 10 ml PBS followed by incubation in 20 ml HBSS buffer containing 2% FBS, 1mM EDTA and 1mM DTT in 50 ml canonical tube, at 37 °C with constant shaking at 180 rpm for 20 min to release epithelial cells. The colon tissues were then washed with 10 ml HBSS buffer before being digested in 10 ml 1640 buffer containing 2% FBS, collagenase type II (2mg/ml), collagenase D (0.5mg/ml), DispaseII (3mg/ml) and DNase I (0.1mg/ml) at 37 °C with constant shaking at 180 rpm for 30 min in a 15ml tube. After digestion, the digested cells and remaining tissue fragments were vortexed intensely for 20 s before being passed through a 40 μm cell strainer. The filtered cell suspension was centrifuged at 600g, 4 °C for 5 min, then resuspended in 1 ml Facs buffer (2% FBS, 2mM EDTA in DPBS).
Viable cells were used for sequencing following the 10× Genomics protocol. Libraries were prepared using the Single Cell 5′ Library Kit V2 (10× Genomics). Transcriptome profiles of individual cells were determined by 10× Genomics-based droplet sequencing and libraries were sequenced with paired-end reads on an Illumina NovaSeq 6000

value: Colon

value: Colon CD45+ cells


title: Nr2f6 TA, mouse 12

source_name: Nr2f6 overexpression TA

value: Nr2f6 overexpression


title: Nr2f6 TA, mouse 11


title: bone tissue,fracture,day14,rep3


title: Wnt5 DKO Colon CD45+ scRNAseq replicate 2


title: D2, replicate 2, scRNA-seq

description: 10x genomic

value: kidney

value: renal tubular epithelial cells

value: epithelial cells

value: pristane-induced C57BL/6j lupus mice


title: AL980_FPB_d0.6_Rep01 [AL9800007]

data_processing:
Adapter sequences remaining within the reads were trimmed (using parameters minlength=35 trimq=20 ktrim=r qtrim=rl k=23 mink=11 hdist=1) using the bbmap tool (v 38.18)
any reads aligning to Zebrafish rRNA sequences were removed using the bbmap tool (v38.18) from the JGI bbtools software package.
Zebrafish transcript abundances were calculated on a per sample basis using the Salmon software (v.1.2.0) 11 (with parameters “--seqBias --validateMappings --numBootstraps 100 --libType SR”) processed against the D. rerio GRCz11 reference genome and annotation 4 downloaded from Ensembl
Following transcript level abundance estimation, gene level expression counts were summarized from the salmon output using the tximport package (v1.26) 12 in R
any protein coding gene with less than an abundance count of ten across all samples were removed from further analysis
The DESeq2 analysis package (v1.34.0) in R 13 (version 4.1.3) was used for data normalization (using the variance stabilizing transformation (vst) method), handling batch effects and identification of differentially expressed genes between control groups and dose treatment groups for each molecule tested.
Assembly: D. rerio GRCz11 reference genome
Supplementary files format and content: tab-delimited text file which includes raw gene count values for each Sample
Supplementary files format and content: tab-delimited text file which includes vst-normalized and batch corrected gene expression table (filtered for low expressing genes)

extract_protocol:
Total RNA was isolated from zebrafish embryo samples from BioBide using the Qiagen RNeasy Mini kit following the manufacturer’s protocol. RNA samples had RNA Quality Scores ≥7 as determined with a 5200 Fragment Analyzer System (Agilent, Santa Clara, CA).
The Illumina Stranded mRNA Sample Preparation kit (Illumina, San Diego, California, U.S.A.) was used to generate RNAseq libraries following the manufacturer’s recommended protocol. First, poly-A containing mRNA was purified from 800 ng of total RNA using poly-T oligo-attached magnetic beads. Purified mRNA was fragmented to approximately 200 bp average length using divalent cations under high temperature. Following fragmentation, SuperScript II reverse transcriptase and random hexamers were used to synthesize first strand cDNA. Second strand synthesis was completed using dUTP-containing Second Strand Marking Master Mix. The resulting blunt end double stranded cDNA fragments underwent end repair, poly A-tailing, and ligation to Illumina index-anchors.  Anchor-ligated library products were enriched with dual-indexed Illumina adapters (IDT for Illumina DNA/RNA Indexes sets) with 13 cycles of PCR. Individual sample libraries were analyzed for fragment quality and quantity using a Tapestation 4200 with D1000 screentape.  Individual libraries were pooled together based on equal nmol amount.  The pooled library was quantitated by Qubit fluorometer (Thermo Scientific, Waltham, Massachusetts, U.S.A.) and further diluted to 2 nM. The normalized and pooled library was further diluted to 2 pM and loaded onto an Illumina NovaSeq6000 following manufacturer’s protocol and sequenced with single-read 100 bp configuration to generate raw RNAseq reads

value: embryo

value: 5 days post fertilization

value: Transgenic zebrafish (Danio rerio) Tg(cmlc2:CopEGFP)


title: n33_responder_dermis

value: dermis


title: bone tissue,fracture,day14,rep2

value: SD

value: bone


title: Wnt5 DKO Colon CD45+ scRNAseq replicate 1


title: WT Colon CD45+ scRNAseq replicate 1


title: Nr2f6 TA, mouse 10

value: male


title: n32_control_epidermis

value: epidermis


title: Control TA, mouse 11

value: adult

value: control


title: n36_responder_epidermis

value: responder


title: TES-3

city: Lanzhou

first: shaoke

last: guo

state: Gansu

address: West Lake Street

department: Lanzhou institute of husbandry and pharmaceutical sciences

institute: Chinese Academy of Agricultural Sciences

description: cattle-yak

data_processing:
Pychopper was used to identify full-length sequences in valid sequencing data and NanoFilt was used to filter the full-length sequence.
Minimap2 was used to align the filtered full-length sequence with the reference gene and quickly construct a non-redundant transcript set.
The gffcompare was used to compare transcripts with known transcripts in the genome.
The alternative splicing types of each sample were obtained by suppa2.
Use Tofu (version: 13.0.0; parameter: default) alignment and search for fusion transcripts. Using MISA software for SSR prediction. The transcription factors were identified using the animal transcription factor database animalTFDB. TAPAS combined with the reference sequence of RefSeq database to identify APA.
Assembly: LU_Bosgru_v3.0
Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample.
Supplementary files format and content: Tab-delimited text files include DESeq2 results.
Supplementary files format and content: FASTA files

organism: Bos grunniens x Bos taurus

source_name: testis

growth_protocol: Five groups of 6-month-old (6M), 18-month-old (18M), 30-month-old (30M), 4-year-old (4Y) male yaks and 4-year-old adult male cattle-yak (TES) were selected from the same cooperative in Xiahe County (N34°51'50', E102°26'9') in Gannan Tibetan Autonomous Prefecture for castration.

extract_protocol:
Total RNA was extracted from each testicular sample using TRIzol reagent. RNA quality was assessed using Nanodrop-2000 and 1% agarose gel electrophoresis.
Qualified RNA was used to prepare 1μg total RNA for cDNA library construction by cDNA-PCR sequencing kit. The cDNA library was sequenced on PromethION sequencer (Oxford Nanopore Technologies, Oxford, UK). These testing processes were conducted according to the protocol of the manufacturer.

treatment_protocol: The testicular tissue was washed with PBS and quickly placed in a freezer tube, immediately stored in liquid nitrogen.

value: testis

tag: Sex

tag: age

value: four years


title: n31_control_dermis


title: bone tissue,fracture,day14,rep1


title: Wnt5 DKO BM CD45+ scRNAseq

source_name: Bone Marrow

value: Bone Marrow

value: Bone Marrow CD45+ cells


title: Nr2f6 TA, mouse 9

value: Nr2f6 overexpression

value: Electroporated mouse tibialis anterior


title: Control TA, mouse 10


title: WT BM CD45+ scRNAseq


title: bone tissue,fracture,day7,rep3


title: TES-2

description: cattle-yak


title: Empty vector TA, mouse 9


title: n30_control_epidermis


title: bone tissue,fracture,day7,rep2


title: bone tissue,fracture,day7,rep1


title: Wnt5 DKO Blood CD45+ scRNAseq

source_name: Periphral Blood

value: Periphral Blood

value: Blood CD45+ cells


title: bone tissue,fracture,day3,rep3


title: n29_control_dermis


title: iEHM1innervatedheartmuscle5K, rep4

city: Göttingen

first: André

last: Fischer

state: Niedersachsen

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

country: Germany

institute: Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE)

description:
PatapiaiEHM1innervatedheartmuscle5KSakib, rep4
3’ mRNA
PatapiaiEHM1innervatedheartmuscle5KSakib_raw_feature_bc_matrix.tar.gz
PatapiaiEHM1innervatedheartmuscle5KSakib_filtered_feature_bc_matrix.tar.gz

data_processing:
Raw BCL files weredemultiplexed (using cellranger mkfastq), mapped and counts files were generated using cellranger count (cellranger-4.0.0), using default settings.
Assembly: hg38 pre-mRNA
Supplementary files format and content: The processed data files include unfiltered (raw) and filtered feature-barcode matrices in the MEX (Market Exchange) file format ouputted by CellRanger.

source_name: innervated engineered human myocardium (iEHM)

extract_protocol:
Frozen iEHMs were used to isolate nuclei, adapted from Sakib et. al. [PMID: 33554149] with modifications. In brief, 500 µL EZ prep nuclei lysis buffer (Sigma, #NUC101) were added to the frozen samples and dounce homogenized for 40-60 strokes (until not big tissue chunks were seen) using plastic pestles in a 1.5 mL DNA low bind tube. Lysates were transferred into a 2 mL DNA low bind tube and additional lysis buffer were supplemented to fill up to 2 mL mark. Samples were incubated for 5 minutes on ice and later centrifuged for 500 xg for 5 minutes at 4 °C. Supernatants were discarded and the nuclei pellets were resuspended into 2 mL lysis buffer, and incubated on ice for 5 minutes. After centrifugation (500 xg, 5 minutes, 4 °C), the pellet was resuspended into Nuclei Suspension buffer, NSB (0.5% OmniPur BSA (Merck Millipore, #2905), 1:200 RNasin® Ribonuclease Inhibitor (Promega, #N2615), 1x cOmplete™, EDTA-free Protease Inhibitor Cocktail (Roche, #04693132001), dissolved in 1x PBS (RNAse free, Invitrogen, #AM9624). Filtered through 0.22 µm Syringe Filter Unit (Millipore, #SLGVR33RB)). It was centrifuged again for 500 xg, 5 minutes at 4 °C, and resuspended into 500 µL NSB. The lysate was strained through 40 µM Flowmi® Cell Strainers (Sigma, #BAH136800040) into a FACS tube. 1:500 of 7-AAD (Invitrogen, #00-6993-50) nuclei staining solution was added and nuclei were gated from the debris (Supplementary Figure 8) and sorted with a BD FACSaria III with 85 µM Nozzle, in a 15 mL falcon tube, coated with and containing 1 mL NSB. Around 200,000 nuclei were sorted per sample.
Sorted iEHM nuclei were immediately taken to process for single nuclei barcoding using 10X Genomics Chromium Single Cell 3' Reagent Kits (v3 Chemistry). 5000 nuclei were subjected to GEM generation and barcoding using Chromium Controller, according to the manufacturer’s protocol. For cDNA amplification, 14 PCR cycles were used. Indexed cDNA libraries were pooled into a single pool and sequenced 4 times in IlluminaNextSeq550 to achieve >50,000reads/nuclei.
snRNA-seq


title: WT Blood CD45+ scRNAseq


title: n27_control_dermis


title: bone tissue,fracture,day3,rep2


title: TES-1

description: cattle-yak


title: Wnt5 DKO Spleen CD45+ scRNAseq

source_name: Spleen

value: Spleen

value: Spleen CD45+ cells


title: iEHM1innervatedheartmuscle5K, rep3

description:
PatapiaiEHM1innervatedheartmuscle5KSakib, rep3
3’ mRNA
PatapiaiEHM1innervatedheartmuscle5KSakib_raw_feature_bc_matrix.tar.gz
PatapiaiEHM1innervatedheartmuscle5KSakib_filtered_feature_bc_matrix.tar.gz

value: innervated engineered human myocardium (iEHM)


title: iEHM1innervatedheartmuscle5K, rep2

description:
PatapiaiEHM1innervatedheartmuscle5KSakib, rep2
3’ mRNA
PatapiaiEHM1innervatedheartmuscle5KSakib_raw_feature_bc_matrix.tar.gz
PatapiaiEHM1innervatedheartmuscle5KSakib_filtered_feature_bc_matrix.tar.gz


title: n28_control _dermis

value: dermis


title: WT Spleen CD45+ scRNAseq


title: Homozygous Dab2 cKO mouse HFSCs at PD 68, biological replicate 3

city: Navi Mumbai

first: SANJEEV

middle: K

last: WAGHMARE

state: MAHARASHTRA

address: Sector 22, Kharghar

department: STEM CELL BIOLOGY GROUP

country: India

institute: ACTREC, TATA MEMORIAL CENTRE

data_processing:
The quality of generated data was tested using FastQC version 0.11.9
Read trimming was carried out using fastp version 0.23.4 (q limit- 30, length >= 50)
The alignment of reads was carried out against a mouse genome assembly (GrCm39) obtained from Ensembl using HISAT2 version 2.2.1
The SAM to BAM conversion and sorting (by read name) of the HISAT2 output files was carried out using SAMtools version 1.6
The mapped reads were counted using featureCounts version 2.0.6
Normalization and diiferential expresion analysis was carried out using DESeq2 R package version 1.42.0
Assembly: GrCm39
Supplementary files format and content: CSV file containing raw counts for all samples
Supplementary files format and content: CSV file containing DESeq2 output (with normalized counts) for all samples

source_name: Skin

growth_protocol: Dab2 fl/fl mice and K14 Cre mice were imported from Jackson laboratories. Dab2 fl/ fl mice were crossed with K14 Cre for multiple generations to obtain K14 Cre- Dab2fl/fl (WT) and K14 Cre+ Dab2fl/fl (Dab2 cKO). To activate Cre expression, mice were treated with tamoxifen intraperitoneally for 5 consecutive days at 75mg/kg body weight per day.

extract_protocol:
RNA extraction from FACS purified HFSCs was done using the absolutely RNA miniprep kit as described in the manufacturer’s procedure (Agilent technologies). The RNA quality was assessed by Agilent RNA 6000 Pico kit on the Agilent 2100 bioanalyzer. 5 ng of total RNA was used for construction of sequencing libraries
RNA libraries were prepeared using SMARTer Stranded total RNA-seq kit v3- pico input mammalian (Cat. No. 634485)  from Takara Bio Inc. following instructions from the manufacturer.

treatment_protocol: Dorsal skin sections of WT and Dab2 cKO mice at were collected at PD68 and incubated in 0.25% trypsin EDTA O/N. Next day, epidermis was separated from the dermis and single cell suspension was prepared.  The cells were centrifuged at 2000 rpm for five min. at 4°C. The cell pellet was washed by using ice-cold 1X 476 PBS and centrifuged again. The cell pellet was then dissolved in 750ul- 1ml of 5% chelated FBS in 1X PBS (FACS buffer) and stained with the anti- CD34 and anti-α6-Integrin to sort HFSCs using FACS Aria machine (BD Biosciences). The HFSCs were collected directly into 1.5 ml eppendorf tubes containing  into the RNA lysis buffer for RNA extraction.

value: Skin

value: Hair Follicle Stem Cells

value: DAB2 cKO

value: Postnatal Day 68

value: Female


title: n26_control_epidermis

value: epidermis

value: control


title: bone tissue,fracture,day3,rep1

value: SD

value: bone


title: n25_control_dermis


title: iEHM1innervatedheartmuscle5K, rep1

description:
PatapiaiEHM1innervatedheartmuscle5KSakib, rep1
3' mRNA
PatapiaiEHM1innervatedheartmuscle5KSakib_raw_feature_bc_matrix.tar.gz
PatapiaiEHM1innervatedheartmuscle5KSakib_filtered_feature_bc_matrix.tar.gz


title: bone tissue,fracture,day0,rep2


title: bone tissue,fracture,day0,rep3


title: Homozygous Dab2 cKO mouse HFSCs at PD 68, biological replicate 2


title: n24_control_epidermis


title: Dm, adult, ANKRD11 KO, rep2

data_processing:
Raw reads were cleaned with trim-galore and mapped to the Drosophila melanogaster genome (dm6, FlyBase) and Homo sapiens genome (hg38, Ensembl) using STAR for mRNA sequencing and Bowtie2 for sequencing of CUT&Tag and ChIP assays.
For mRNA sequencing, the reads at the gene level were summarized by featureCounts, followed by DESeq2 R package for analysis of differential expression.
For CUT&Tag and ChIP sequencing, duplicate reads were removed by picard, and peaks were called using MACS2.
Supplementary files format and content: narrow peaks of Cut&Tag and ChIP sequencing
Supplementary files format and content: read count of RNAseq

organism: Drosophila melanogaster

source_name: adult

value: adult

value: ANKRD11 KD


title: Homozygous Dab2 cKO mouse HFSCs at PD 68, biological replicate 1


title: n23_control _dermis


title: Wild type mouse HFSCs at PD 68, biological replicate 3

value: WT


title: Dm, adult, ANKRD11 KO, rep1


title: n22_control_epidermis


title: Dm, adult, 65K KO, rep3

value: Dm65K KD


title: Wild type mouse HFSCs at PD 68, biological replicate 2


title: Wild type mouse HFSCs at PD 68, biological replicate 1


title: bone tissue,fracture,day0,rep1


title: Dm, adult, 65K KO, rep2


title: n20_control_epidermis


title: VBDO young

city: Zhuhai

first: Liangyu

last: Zhao

state: Guangdong

address: 52th Meihua Road, Zhuhai, China

institute: Shanghai Jiao Tong University School of Medicinethe Fifth Affiliated Hospital of Sun Yat-sen University

description: 10X Genomic

data_processing:
The raw sequencing reads were processed by Cell Ranger (v.3.1.0) with the default parameters. The reference genome was mRatBN7.2.106
Assembly: mRatBN7.2.106
Supplementary files format and content: cell and gene martrix

source_name: urethra

extract_protocol:
Fresh urethra tissue samples of about 1×1-cm size were first immersed in 15 ml PBS with vigorous shaking to remove residual blood cells. Then, tissues were cut into pieces of 1×1-mm size and enzymatically digested with 2.5 mg/ml collagenase type I (17104-019, gibco), 4 mg/ml collagenase type IV (17018029, gibco), 0.1 mg/ml neutral protease, and 2 mg/ml DNase I (#AMPD1, Sigma-Aldrich) at 37°C for 40 min. Subsequently, the cell suspension was filtered through a 40-mm nylon mesh, and the cells were sorted by MACS with a Dead Cell Removal Kit (130-090-101, Miltenyi Biotec) to remove dead cells. The cells were resuspended in 0.05% BSA/PBS buffer before 10× Genomics library preparation.
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead Kit v3 (PN-1000094, 10× Genomics) according to the manufacturer’s instructions. Final libraries were sequenced on an Illumina NovaSeq 6000.

value: urethra

value: primary cell

value: urethra cells

value: ovariectomy and urethral dilatation


title: Dm, adult, ANKRD11 KO, rep3


title: VBDO midage

description: 10X Genomic


title: W2, Visium

city: Birmingham

first: James

middle: F

last: George

state: Alabama

address: 1720 2nd Ave South

institute: University of Alabama at Birmingham

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0, samples were analyzed using Seurat v4.3.0. Kidney resident macrophages were identified via expression of C1qa, CD4 T cells were identified by Cd3e and Cd4
Unhashed, W2_m1_CD45 hashed with Biolegend B301 Cat 155831, W2_m2_CD45 hashed with Biolegend B305,Cat 155839
Raw files in W2_m1_CD45 contain the fastq files for both W2_m1 and W2_m2. They can be separated with the hashing antibodies listed above
Assembly: mm10

extract_protocol:
Freshly collected immune cells were isolated from human kidneys. Cross sections of kidney were digested in the commercially available collagenase, Liberase, for 30 minutes at 37 degrees Celsius. Red blood cells were lysed and the samples were resuspended in PBS. Samples were stained for Viability and resuspended in FACS Buffer (PBS, 5% FBS, 5% EDTA) and stained with CD45-FITC antibody. Samples were identified as being FITC positive using FACS (Aria, BD) and unstained samples were used as a negative control.
RNA was isolated according to manufacturer's instructions for 3' Chromium gene expression and Visium spatial transcriptomics kits

value: kidney

value: mesenchymal stem cells

value: AAN CKD

tag: time

value: Week 2


title: n19_control_dermis

value: dermis


title: Dm, adult, 65K KO, rep1


title: sham young

description: 10X Genomic

value: sham


title: n18_control _epidermis

source_name: epidermis

value: epidermis

value: control


title: sham midage

description: 10X Genomic


title: W1 and W2, Mouse 1, CD45+, single cell sequening

description: 10X Genomics


title: MAP midage

description: 10X Genomic

value: ovariectomy and urethral dilatation and BAPN and MAP


title: Dm, adult, Ctrl, rep3

value: adult

value: Ctrl


title: n17_control_dermis

source_name: dermis


title: Dm, adult, Ctrl, rep2


title: MAP young

description: 10X Genomic

value: WT


title: App_hip_mic_9m_tg_4

city: Groningen

first: Takuya

last: Oshima

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences of Cells & Systems

country: Netherlands

institute: University Medical Center Groningen

data_processing:
Quality control was performed using third-party (FastQC v0.11.9) and in-house (FastQA v3.1.25) QC tools.
Sequence reads were trimmed to remove possible adapter sequences using cutadapt v2.10.
The trimmed reads were mapped to the mouse GRCm39 (Mus_musculus.GRCm39.dna.primary_assembly.fa) provided in the References directory. The reads were mapped to the reference sequence using a short read aligner based on Burrows-Wheeler Transform (Tophat v2-2.1) with default settings.
The alignment files were sorted and indexed with the samtools v1.10 package
After alignment duplicate reads were marked and removed with MarkDuplicates of the Picard v2.13.2 package.
Based on the mapped locations in the alignment file the frequency of how often a read was mapped on a transcript was determined with HTSeq v0.11.0.
Assembly: mouse GRCm39 (Mus_musculus.GRCm39.dna.primary_assembly.fa)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: brain

extract_protocol:
Microglia were isolated using an enzymatic protocol at 4°C as previously described (Talma et al., 2021). Microglia were sorted by gating the PIneg DRAQ5pos CD11bhigh CD45int CD49dneg cells with FACS. Total RNA was isolated using RNeasy Micro Kit (Qiagen, cat# 74004) according to the manufacturer’s instructions.
Sequencing libraries were generated using the NEBNext Low Input RNA Library Prep Kit for Illumina (New England Biolabs, cat# E6420S/L).
DNA sequencing was performed using a NovaSeq6000 according to the manufacturer's protocols. NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

value: brain

value: male

tag: region

value: hippocampus

value: microglia

value: tg

value: 9 month old


title: Dm, adult, Ctrl, rep1

extract_protocol:
RNA was harvested using TRI Reagent (Sigma-Aldrich). 1 ug of total RNA was used for the construction of sequencing libraries. ChIP DNA was pulled down by H3K9ac antibody in HEK293T cells. DNA for CUT&Tag-seq was cleavaged Under Target & Tagmentation by RNPC3 or HDAC3 antibody in HEK293T cells.
RNA libraries for RNA-seq were prepared using Fast RNA-seq Lib Prep Kit V2 following manufacturer's protocols. DNA libraries for CUT&Tag-seq were prepared using CUT&Tag Assay Kit (pAG-Tn5) following manufacturer's protocols. DNA libraries for ChIP-seq were prepared using Scale ssDNA-seq Lib Prep Kit following manufacturer's protocols.


title: n16_control_dermis


title: App_hip_mic_9m_tg_2


title: Dm, head, ANKRD11 KO, rep3

source_name: head

value: head

value: ANKRD11 KD


title: n15_control_epidermis


title: BAPN young

description: 10X Genomic

value: urethra

value: primary cell

value: urethra cells

value: ovariectomy and urethral dilatation and BAPN


title: BAPN midage

description: 10X Genomic


title: App_hip_mic_9m_tg_1


title: Dm, head, ANKRD11 KO, rep2


title: n14_control_dermis

value: dermis

value: control


title: 8_Rnf20-siRNA-Trained

city: Blacksburg

first: Timothy

last: Jarome

state: VA

address: 175 W Campus Dr

institute: Virginia Polytechnic Institute and State University

data_processing:
Sequence read is trimmed using trimgalore (--paired --phred33 --fastqc --illumina -q 30 --length 30)
Trimmed sequence is mapped to Rat genome (Rattus_norvegicus.Rnor_6.0.99)
featureCounts v2.0.1 is used to quantify the mapping results (featureCounts" "-T" "32" "-p" "-t" "exon" "-g" "gene_id" "-a) and generate count matrix
Assembly: Rattus_norvegicus.Rnor_6.0.99
Supplementary files format and content: comma-separated values file includes the raw count for each sample
Supplementary files format and content: comma-separated values file includes the DESeq2 normalized count for each sample

growth_protocol: Frozen brain tissue, from 8-9 week old Sprague Dawley rats

extract_protocol:
RNA was extracted usin Rneasy mini plus kit (Qiagen)
Illumina TruSeq Stranded mRNA HT Sample Prep Kit, enriched by 14 cycles of PCR, validated using Agilent TapeStation and quantified by qPCR

treatment_protocol: Streotaxic injection of siRNAs into dorsal CA1 area of the hippocampus

value: Sprague-Dawley

value: Male

value: All brain cell types


title: App_hip_mic_9m_wt_5

value: brain

value: wt


title: n13_control _dermis


title: Dm, head, ANKRD11 KO, rep1

first: Shaobo

last: Liang

address: BaYi Road, LUOJIA HILL

institute: Wuhan University


title: Dm, head, 65K KO, rep3

value: Dm65K KD


title: n12_control _dermis


title: App_hip_mic_9m_wt_3

value: male

value: hippocampus

value: microglia


title: 4_Rnf20-siRNA-Trained

value: WT


title: Dm, head, 65K KO, rep1

value: head


title: n11_control _dermis


title: App_hip_mic_9m_tg_3

value: tg

value: 9 month old


title: Dm, head, Ctrl, rep3

value: Ctrl


title: Dm, head, 65K KO, rep2


title: App_hip_mic_9m_wt_2_4


title: 14_Rnf20-siRNA-Trained


title: App_hip_mic_6m_tg_4

value: 6 month old


title: App_hip_mic_6m_tg_3


title: n10_responder_epidermis

value: epidermis

value: responder


title: n8_responder_epidermis


title: 20_Rnf20-siRNA-Trained

value: Sprague-Dawley


title: App_hip_mic_9m_wt_1


title: Dm, head, Ctrl, rep2


title: 5_Scr-siRNA-Trained

value: Male

value: Scr-siRNA-Trained


title: Dm, head, Ctrl, rep1


title: n9_responder_epidermis


title: 10_Scr-siRNA-Trained

value: All brain cell types


title: n7_responder_dermis

value: dermis


title: 6_Scr-siRNA-Trained


title: App_hip_mic_6m_tg_2

value: brain


title: 18_Rnf20-siRNA-Trained


title: 16_Scr-siRNA-Trained


title: WT4_hippo_CD11c_neg_8_3_S9

data_processing:
Raw reads were demultiplexed with UMI-tools (v0.5.3).
A cell barcode whitelist with the known barcodes was used to filter the reads.
Reads were aligned with HISAT2 (v2.1.0) to the Ensembl genome Mus musculus (GRCm38, mm10) using default parameters.
Quantification was done with featureCounts (v1.6.0) using the flag -primary.
The unique molecules per gene and per cell were quantified using the UMI-tools function count.
Assembly: mouse GRCm38 (mm10)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

extract_protocol:
Microglia were isolated using a mechanical protocol with a Tissue Grinder Potter-Elvehjem at 4°C as previously described (Galatro et al., 2017). Microglia were sorted by gating the DAPIneg DRAQ5pos CD11bhigh CD45int CD11cneg/pos cells with FACS. Microglia were collected in 384-well PCR plates containing cell lysis buffer.
Sequencing libraries were generated based on the Smart-seq2 protocol as previously described (Alsema et al., 2020).
DNA sequencing was performed using a Illumina NextSeq 500 system at a final concentration of 2 pM with a 7% spike in PhiX DNA.

value: male

value: wt

value: negative


title: n6_responder_epidermis

data_processing:
mRNA was sequenced by Novogene (Sacramento, CA). Briefly, short read sequencing assays (NovaSeq 6000, Illumina) were performed at a depth of 40 million reads per sample. Raw reads were postprocessed with fastp software and aligned to the human genome, version GRCh38, using Hisat2 (v2.0.5). A counts matrix was generated using featureCounts v1.5.0-p3. Differential expression analysis was conducted with the DESeq2 R package (v1.20.0) and reads were filtered by p < 0.05 after adjustment for the false discovery rate using the Benjamini and Hochberg approach. KEGG pathways (www.genome.jp/kegg) were analyzed using clusterProfiler R. Gene expression was compared between healthy controls and patients with PRP, and stratified by epidermis vs dermis, time on therapy (week-0, week-24, week-24) and response to therapy.
Assembly: GRCh38
Supplementary files format and content: bulk RNA-seq counts matrix in comma separated values format

extract_protocol:
Skin punch biopsy samples were rinsed in sterile phosphate buffered saline without calcium or magnesium (HyClone Laboratories, GE Healthcare) and then incubated at room temperature in a 3.8% ammonium thiocyanate (Sigma Aldrich) in phosphate buffered saline without calcium or magnesium solution for 45 minutes. The epidermis and dermis were subsequently separated using sterile forceps, placed into separate RNase-free tubes containing 700 μL QIAzol (Qiagen), homogenized by hand using RNase-free pestles (Argos), and placed at −80 °C. All samples were collected, processed under sterile conditions, and stored within a 2-hour time frame. RNA was isolated using chloroform (Fisher Scientific), RNeasy Mini Kit (Qiagen), and RNase-free DNaseI (Qiagen). Briefly, 140 μL chloroform was added to each tube, the mixture was vortexed for 5 seconds, and the tubes were left to stand for 2 to 3 minutes at room temperature. After centrifugation at 12 000 g for 15 minutes at 4 °C, the top aqueous layer was transferred to a new tube and combined with an equal volume of 100% ethanol. Thereafter, the Qiagen RNeasy Mini Kit protocol was followed, ending with a 35 μL elution volume of RNase-free water. RNA quality was assessed on a Synergy H1 microplate reader (BioTek Instruments) with UV readings of 260 nm, 280 nm, 230 nm, and 320 nm. Purified RNA was stored at −80 °C until downstream analysis.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers,  followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.  For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.


title: App_hip_mic_6m_tg_1

value: hippocampus

value: microglia


title: App_hip_mic_6m_wt_4


title: n5_control_epidermis

value: control


title: WT4_cortex_CD11c_neg_2_3_S2

value: cortex


title: 15_Scr-siRNA-Trained

value: WT


title: WT3_hippo_CD11c_neg_8_2_S8

value: 6 month old


title: n4_control_epidermis

value: epidermis


title: App_hip_mic_6m_wt_2


title: WT3_hippo_CD11c_neg_8_1_S8


title: 1_Scr-siRNA-Naïve

value: Scr-siRNA-Naive


title: App_hip_mic_6m_wt_3


title: 9_Scr-siRNA-Naïve

value: Sprague-Dawley


title: WT3_cortex_CD11c_neg_2_1_S2

value: tg


title: App_hip_mic_6m_wt_1


title: 2_Scr-siRNA-Naïve

value: Male


title: 12_Scr-siRNA-Naïve

value: All brain cell types


title: App_hip_mic_4m_tg_4

value: 4 month old


title: n1_control _epidermis


title: 11_Scr-siRNA-Naïve


title: App_hip_mic_4m_tg_3

value: brain


title: App_hip_mic_4m_tg_2

value: male


title: D15 kidney, AKI,  visium

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Space Ranger software, samples were analyzed using Seurat v4.3.0.
Assembly: human GRCh38 (GCA_000001405.28)

source_name: kidney

extract_protocol:
Human kidney sections were frozen in OCT. 10 micron sections were cut and processed according to the Visium platform protocol
RNA was isolated according to manufacturer's instructions for 3' Chromium gene expression and Visium spatial transcriptomics kits

value: kidney

tag: disease state

value: Acute Kidney Injury


title: WT2_cortex_CD11c_neg_1_3_S1

value: negative


title: WT1_hippo_CD11c_neg_7_2_S7

value: hippocampus

value: microglia


title: n2_control_epidermis

value: control


title: App_hip_mic_4m_tg_1


title: WT1_hippo_CD11c_neg_7_1_S7

value: wt


title: D1 kidney, AKI,  visium

description: 10X Genomics


title: Muscle, Chow diet, female, rep5

city: Oklahoma City

first: Michael

middle: C.

last: Rudolph

state: OK

address: 975 NE 10th St. BRC North rm 364

department: Biochemistry and Physiology

institute: OUHSC

data_processing:
Following sequencing and demultiplexing, reads were trimmed for adapters and filtered based on quality score using Fastp
High quality reads were aligned to the rat genome (rn6)using STAR (ver 2.7.6a)
resulting read alignments file for each sample was imported in Seqmonk (ver 1.48.1)
raw counts matrix of all genes was imported into DESeq2 (DESeq2 version 1.30.1) in R (ver 4.1)
Assembly: Rn 6
Supplementary files format and content: raw counts matrix of all genes in al samples

source_name: Gastronemius

extract_protocol:
gastrocnemius tissue (50-100 mg) was homogenized in 1 mL of Trizol using the Bead Mill 24 . Total RNA was isolated using a combination of TRI reagent  and RNeasy-mini columns, including on-column deoxyribonuclease digestion.
cDNA libraries for mRNA-sequencing were prepared using polyA-mRNA from individual RNA samples using Illumina TruSeq reagents

value: Gastronemius

value: Wistar

value: Female

value: Chow


title: App_hip_mic_4m_wt_4


title: WT1_cortex_CD11c_neg_1_2_S1

value: 6 month old

value: cortex


title: App_hip_mic_4m_wt_3


title: n3_control_epidermis

value: epidermis


title: n21_control_dermis

value: dermis


title: 24856-normal-tissue

city: New York

first: Yifei

last: Sun

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
fastq files were generated with bcl2fastq(v2.0)
Sequence reads were trimmed for adaptor sequence and low-quality sequence(Q30) and mapped to GRCh38/hg38 (parameters- --outFilterMismatchNoverReadLmax 0.04,) with STAR v2.7
featureCounts was used to summerize raw counts(subread v1.6)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: breast

extract_protocol:
RNA was harvested using RNeasy midi Kit(Qiagen).
RNA libraries for mRNA-seq were prepared using QIAseq Stranded mRNA Select Kit and QIAseq Stranded RNA Library Kit

value: breast

value: normal

tag: er

value: Positive

tag: pr

value: Negative

tag: treatment type

value: No

tag: menopause status

value: Pre


title: Muscle, Chow diet, female, rep4

tag: tissue

tag: strain


title: WT1_cortex_CD11c_neg_1_1_S1

value: brain

value: male

tag: cell type

value: microglia

value: negative


title: 24823-tumor-tissue

tag: genotype

value: tumor

value: Post


title: Muscle, Chow diet, female, rep3

value: Gastronemius

value: Wistar

value: Female

tag: treatment

value: Chow


title: App_hip_mic_4m_wt_2

value: hippocampus

value: wt

value: 4 month old


title: WT2_hippo_CD11c_neg_7_3_S8

value: 6 month old

value: tg


title: APP4_hippo_CD11c_pos_12_1_S12

value: positive


title: 24823-normal-tissue

value: breast

value: normal

value: Negative

value: No


title: APP4_hippo_CD11c_neg_10_3_S11

value: brain

value: male

value: microglia

value: negative


title: 24760-tumor-tissue

value: tumor


title: App_hip_mic_4m_wt_1


title: Muscle, HSHS, female, rep5

value: Gastronemius

value: Wistar

value: Female

value: HFHS


title: 24760-normal-tissue


title: APP4_cortex_CD11c_pos_6_3_S6

value: cortex


title: Testes,Srsf1cKO-3, P10

city: Beijing

first: Wenlong

last: Lei

state: 北京

address: 北京市朝阳区北辰西路1号院5号

institute: 中国科学院

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp
Trimmed sequence reads were mapped to mm9 using HISAT2
Differential expressed analysis were performed by DESeq2
Alternative splicing were identified by rMAST
Assembly: mm9
Supplementary files format and content: bigwig

source_name: testes

extract_protocol:
One Total RNA was extracted from whole testes using TRNzol Universal Reagent (cat. # DP424, Tiangen, China) according to the manufacturer’s instructions. The quality of RNA samples was examined by NanoDrop 2000&8000 and Agilent 2100 Bioanalyzer，Agilent RNA 6000 Nano Kit. The high-quality RNAs were used to prepare the libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Total testes samples were used from P10 Srsf1WT and Srsf1cKO male mice according to three individual collections.

value: testes


title: 24732-tumor-tissue

value: Positive

value: TCHP

value: Post


title: Muscle, HSHS, female, rep4


title: Testes,Srsf1cKO-1, P10

address: 北京市朝阳区北辰西路1号院5号


title: APP4_cortex_CD11c_neg_6_1_S6

value: 6 month old

value: tg


title: 24732-normal-tissue

value: breast

value: normal

value: Negative


title: Muscle, HSHS, female, rep3


title: Muscle, HSHS, female, rep2


title: 24573-tumor-tissue

value: ACT


title: APP3_hippo_CD11c_neg_10_2_S10

value: brain

value: male

value: wt

value: hippocampus

value: microglia

value: negative


title: Muscle, Chow diet, female, rep2

value: Gastronemius

value: Wistar

value: Female

value: Chow


title: Testes,Srsf1WT-3, P10

address: 北京市朝阳区北辰西路1号院5号

value: testes

value: WT


title: Testes,Srsf1WT-2, P10

address: 北京市朝阳区北辰西路1号院5号


title: Muscle, HSHS, female, rep1

value: HFHS


title: APP3_hippo_CD11c_neg_10_1_S10

value: 6 month old


title: APP3_cortex_CD11c_pos_5_4_S5

value: cortex

value: positive


title: APP4_cortex_CD11c_pos_6_4_S7

value: tg


title: Muscle, Chow diet, male, rep6

value: Male


title: 24548-tumor-tissue

value: breast

value: tumor

value: Positive

value: Negative

value: No

value: Post


title: APP3_cortex_CD11c_pos_5_3_S6

value: brain

value: male

value: wt

value: microglia


title: Testes,Srsf1WT-1, P10

address: 北京市朝阳区北辰西路1号院5号

value: testes

value: WT


title: TSA3

city: Hyderabad

first: Lava

middle: Kumar

last: Surarapu

state: Telangana

address: NIAB, Gowlidoddi, Gachiboli, Hyderabad, Telangana

institute: National Institute of Animal Biotechnology

data_processing:
FastQC (v0.11.9) was used to analyze the raw reads base quality and adapter content. Fastp (v0.12.4) was used to trim the adapter and low-quality bases
After trimming, reads were aligned to total transcripts of Mus musculus (GRCm39, Ensemble release 106 - Apr 2022) using Salmon (v0.12.0)
Transcript levels were imported into gene-level counts using Tximport (v1.22.0), and differential gene expression was done using DESeq2 (v1.34.0)
DE genes were used for Gene Ontology and KEGG enrichment using the R package cluster profile (v4.4.2) and plotted using enrichplot (v1.14.2)
Assembly: total transcripts of Mus musculus (GRCm39, Ensembl release 106 - Apr 2022)

source_name: Testes

extract_protocol:
Whole testes RNA was isolated using the TRIZOL method (Invitrogen) and purified using a Nucleospin Purification kit (Quiagen)
llumina RNA library preparation kit; NovaSeq6000 S4 reagent kitVl.5

value: Testes

value: TSA


title: Muscle, Chow diet, male, rep5

value: Gastronemius

value: Wistar

value: Chow


title: TSA2


title: 24484-tumor-tissue

value: breast

value: ACT

value: Pre


title: Muscle, Chow diet, female, rep6

value: Female


title: TSA1


title: Muscle, Chow diet, male, rep4

value: Male


title: 24484-normal-tissue

value: normal

value: Negative


title: Testes,Srsf1cKO-2, P10

address: 北京市朝阳区北辰西路1号院5号


title: 24573-normal-tissue

value: Positive

value: Post


title: APP2_hippo_CD11c_neg_9_3_S10

value: brain

value: male

value: 6 month old

value: tg

value: hippocampus

value: microglia

value: negative


title: 24466-tumor-tissue

value: tumor

value: Anastrozole


title: APP2_cortex_CD11c_pos_4_3_S4

value: cortex

value: positive


title: AA2

value: Testes

value: AA


title: Muscle, Chow diet, male, rep2

value: Gastronemius

value: Wistar

value: Male

value: Chow


title: 24466-normal-tissue

value: breast

value: normal

value: Positive

value: Negative

value: Post


title: Muscle, Chow diet, male, rep1


title: 24548-normal-tissue

value: No


title: Muscle, HFHS diet, male, rep6

value: HFHS


title: APP2_cortex_CD11c_neg_4_2_S5

value: brain

value: male

value: 6 month old

value: wt

value: microglia

value: negative


title: APP2_cortex_CD11c_neg_4_1_S3

value: cortex


title: 24455-normal-tissue

value: ACT

value: Pre


title: 24856-tumor-tissue

value: tumor


title: Muscle, HFHS diet, male, rep5

value: Gastronemius

value: Wistar

value: Male


title: 24449-tumor-tissue

value: breast

value: Positive

value: Negative


title: Muscle, Chow diet, male, rep3

value: Chow


title: HMS-I1-2

value: Testes


title: HMS-I1-1


title: APP2-3_hippo_CD11c_pos_11_4_S12

value: brain

value: male

value: hippocampus

value: positive


title: APP2_cortex_CD11c_pos_4_4_S4

value: 6 month old

value: tg

value: microglia


title: APP2-3_hippo_CD11c_pos_11_3_S12

value: wt


title: 24449-normal-tissue

value: normal

value: No

value: Post


title: Muscle, HFHS diet, male, rep3

value: Gastronemius

value: Wistar

value: Male

value: HFHS


title: APP1_hippo_CD11c_neg_9_2_S9

value: negative


title: MTX3

value: Testes

value: MTX


title: Muscle, HFHS diet, male,rep2


title: MTX2


title: APP1_hippo_CD11c_neg_9_1_S9

value: brain

value: male


title: APP3_cortex_CD11c_neg_5_1_S5

value: cortex


title: 24455-tumor-tissue

value: breast

value: tumor

value: Positive

value: Negative

value: ACT

value: Pre


title: 24444-normal-tissue

value: normal

value: No


title: AA1

value: AA


title: Muscle, HFHS diet, male, rep1

value: Gastronemius

value: Wistar

value: Male


title: MTX1

value: Testes


title: HMS-I1-3


title: APP1_cortex_CD11c_pos_3_4_S4

value: 6 month old

value: tg

value: microglia

value: positive


title: 24433-tumor-tissue

value: breast


title: T2

first: Lufeng

last: Zheng

state: Jiangsu

address: Tongjia Xiang 24

department: School of Life Science and Technology, Jiangsu Key Laboratory of Carcinogenesis and Intervention

institute: China Pharmaceutical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Rrattus_CSIRO_v1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample …

source_name: Rat cardiac myocytes H9C2

growth_protocol: Cells were cultured in DMEM medium (Gibco, Grand Island, NY, USA) at 37 °C under a humidified atmosphere with 5% CO2, and supplemented with 10% FBS (Gibco), 80 U/ml penicillin, and 0.08 mg/ml streptomycin.

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

treatment_protocol: H9C2 cells were treated with or without PAGln (100 μM) for 48 h and subjected to  deep sequencing, in triplicate, using  Illumina NovaSeq 6000.

tag: cell line

value: Rat cardiac myocytes

value: PAGln


title: APP1_cortex_CD11c_pos_3_3_S2

value: brain

value: male

value: cortex


title: Muscle, HFHS diet, male, rep4

value: HFHS


title: AA3


title: T1


title: 24433-normal-tissue

value: normal


title: APP1_cortex_CD11c_neg_3_2_S3

value: wt

value: negative


title: 24387-tumor-tissue

value: tumor


title: C2

value: Control


title: APP1_cortex_CD11c_neg_3_1_S3


title: Control1

value: Testes


title: 24444-tumor-tissue

value: Positive

value: Negative

value: No

value: Pre


title: 24387-normal-tissue

value: breast


title: C1

value: Rat cardiac myocytes


title: 24272-tumor-tissue