title: AAV-Clu,mouse heart,stero-seq

city: Shanghai

first: Qi

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Molecular Cell Science

data_processing:
Raw reads were aligned to the mm10/GRCm38 reference genome and generated a spot-gene matrix. Then, we convoluted into larger pseudo-spots of 50 × 50 square sizes (bin 50 for short), or more precisely, the 25 μm squares, and generated a new spot-gene matrix for further analysis.
Assembly: mm10
Supplementary files format and content: gem
Library strategy: stero-seq

source_name: heart

extract_protocol:
10-micron sections were taken from the largest cross-section, attached to the Stero-seq chip, and then incubated at 37°C for 3 min. Followed by 30 min fixation in methanol at -20 °C (Sigma, 34860), the ssDNA of tissues was stained with nucleic acid dye (Thermo, Q10212) and imaged. Tissue sections were permeabilized using 0.1% pepsin (Sigma, P7000) in 0.01M HCl buffer and incubated at 37°C for 15 min. DNA nanoballs (DNBs) on the chip captured released RNA from tissues, then were reverse transcribed at 42°C overnight. After reverse transcription, tissues were digested with tissue removal buffer (10 mM Tris-HCl, 25 mM EDTA, 100 mM NaCl, 0.5% SDS) at 37°C for 30 min
cDNA-containing chips were subjected to Exonuclease I (NEB, M0293L) at 37°C for 1h. PCR reactions with KAPA HiFi Hotstart Ready Mix (Roche, KK2602) were performed to amplify cDNAs. Qubit™ dsDNA Assay Kit (Thermo, Q32854) was used to quantify the concentrations of PCR products. cDNAs were fragmented with in-house Tn5 transposase at 55°C for 10 min, which was stopped by adding 0.02% SDS, then amplified using KAPA HiFi Hotstart Ready Mix. PCR products were purified and used to generate DNBs.

value: heart

value: Clu overexpressed

value: mouse heart

value: 3day post injury at P8


title: Wild-type, gd16.5, RNA-seq, replicate 1

status: Public on Nov 24 2025

type: SRA

city: Yangzhou

first: Yuchen

last: Tang

state: Jiangsu

address: Wenhui Road Yangzhou Citr No.48

country: China

institute: College of Veterinary Medicine Yangzhou University

description: Library name: wild-type gd16.5, RNA-seq, replicate 1

library_source: transcriptomic

data_processing:
RNA-seq reads were trimmed with Trim Galore v0.6.4., and then aligned to the mouse reference genome (GRCm38) using STAR v2.7.3a. Gene-level read counts were calculated by using the featureCount function of subread v2.0.0.
Assembly: GRCm38
Supplementary files format and content: tab-delimited table, gene-level read counts

molecule: polyA RNA

organism: Mus musculus

source_name: maternal-fetal interface

extract_protocol:
Total RNA was extracted using Trizol reagent (Qiagen, 74004) with on-column DNase digestion.
RNA-seq libraries were construction by using TruSeq stranded mRNA sample preparation kit (Illumina), and sequenced as 150 bp paired-end reads with HiSeq2500 (Illumina) platform.

tag: tissue

value: maternal-fetal interface

tag: genotype

value: wild-type


title: tropicalis NF33 fg mesendo RA LOF rep2

city: Cincinnati

first: Aaron

last: Zorn

state: OH

address: 240 Albert Sabin Way, Bld S

department: Developmental Biology

country: USA

institute: Cincinnati Children's Hospital and Medical Center

description:
Library name: tropicalis_NF33_fg_mesendo_RA_LOF_rep2
tropicalis_NF33_fg_mesendo_RA_LOF_rep1

data_processing:
Quality of reads was asessed with factqc
Quality trimmed reads in fastq format were mapped and quantified using RSEM (v1.3.0)  with bowtie2
Assembly: Xenopus Tropicalis v10
Supplementary files format and content: raw counts and TPM files in .txt format

molecule: total RNA

organism: Xenopus tropicalis

source_name: embryo

growth_protocol: embryos incubated at room temperature

extract_protocol:
RNA was extracted using the Macherey-Nagel Nucleospin RNA extraction kit according to manufacturer's insructions.
Library prep was performed using Illumina’s TruSeq stranded mRNA library preparation kit according to manufacturer's instructions.

treatment_protocol: 40uM cyclopamine (Tocris #1623), 100nM BMS493 (Tocris #3509) treatment from NF15-33.   1ng total Rfx6 ,morpholino oligo or 5bp mismatch oligo  (500pg per cell) injected at 2-cell stage.

value: embryo

tag: cell line

value: Xenopus Tropicalis, NXR_1018, Xtr.NigerianSt549

tag: cell type

value: dissected NF33 foregut tissue

tag: treatment

value: wild type

tag: batch


title: tropicalis NF33 fg mesendo RA LOF rep1

description:
Library name: tropicalis_NF33_fg_mesendo_RA_LOF_rep1
tropicalis_NF33_fg_mesendo_RA_LOF_rep1


title: VOF_Ctrl_1_mix2

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

data_processing:
Base-calling was performed with bcl2fastq program (v2.20).
By using the celseq2 pipeline (https://github.com/yanailab/celseq2), demultiplexing of the raw data was performed, and also UMI counts were calculated.
Using binomial statistics, the number of UMI was converted to transcript counts. The mathematical formula is described in "Validation of noise models for single-cell transcriptomics (PMID: 24747814)". In this calculation method, if the UMI is the maximum value of 4096, the transcriptome count diverges to infinity and cannot be converted, so 9genes (Fga, Mt-Rnr2, Mt-Nd4, Mt-Cytb, Mup14, Mup20, Mup8, Mup13, Mup15) with a UMI count of 4096 in at least one sample genes were excluded from the analysis.
Lowly expressed genes were filtered out, and batch correction of transcript counts was performed using Combat-Seq(PMID: 33015620). The numbers following the string “mix” at the end of each sample name are the same for the same batch, and this information was used for batch correction.
Assembly: GRCh38
Supplementary files format and content: Comma Separated Values files include Batch correlated transcript counts of all samples

source_name: Liver

growth_protocol: We bred wild-type C57BL/6 mice to ages of 11-14 weeks (young), 60 weeks (old), and 100 weeks (very old), and used them in the experiment.

extract_protocol:
Total RNA was extracted from mouse hepatocytes isolated from mouse livers using ISOGEN II (Nippongene), and purified using the RNeasy MinElute Cleanup Kit (Qiagen). The quality and concentration of the total RNA was evaluated using a NanoDrop 2000 (Thermo Fisher Scientific), and only RNA with an A260/A280 ratio of 2 or higher was used.
Detailed protocol is described in "CEL-Seq2: sensitive highly-multiplexed single-cell RNA-Seq (PMID: 27121950)".
OTHER: CEL-Seq2 (an RNA-seq protocol)

treatment_protocol: Detailed protocol of PH is described in "Partial hepatectomy in mice(PMID: 25835741)". The Sham surgery is performed under inhalation anesthesia with an abdominal median incision and suture closure. Hepatic cells were isolated from mouse livers by performing two-step collagenase digestion. Detailed protocol of hepatocyte isolation is described in "Hepatocyte suspensions and cultures as tools in experimental carcinogenesis (PMID: 224209)".

value: Liver

value: Primary Cells

value: Hepatocyte

value: WT

tag: time


title: YM_Ctrl_1X_mix1


title: YM_Ctrl_2X_mix1


title: C1qtnf6-KO, gd14.5, RNA-seq, replicate 5

description: Library name: C1qtnf6-KO gd14.5, RNA-seq, replicate 3


title: WildType_Mouse4

city: Los Angeles

first: Michel

middle: A

last: Zamojski

state: California

address: 8700 Beverly Boulevard

department: Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

description:
Library name: 033125-4-A6-2-1-WT-A
10X Genomics sc-ATAC assay

library_source: genomic single cell

data_processing:
Single Nuclei ATAC-seq sequencing data were processed using the CellRanger-ATAC pipeline version 2.2.0 with the provided mm10 reference genome.
Assembly: mm10
Supplementary files format and content: Peak-associated cut-site count matrices for cell-called barcodes in Hierarchical Data Format (HDF5)
Supplementary files format and content: Motif-overlapping cut-site count matrices for cell-called barcodes in Hierarchical Data Format (HDF5)
Supplementary files format and content: Lists of barcode-associated DNA fragments in BED-like tabular format
Supplementary files format and content: Peak to-gene annotations in tabular format
Supplementary files format and content: Peak to-motif associations in BED format
Supplementary files format and content: Lists of called-peaks in BED format
Supplementary files format and content: Per barcode QC and summary metrics in CSV format

molecule: genomic DNA

source_name: pituitary

growth_protocol: Animals were on a 12-hour on, 12-hour off light cycle, with lights on at 7 AM and off at 7 PM. Pituitaries were collected from male mice aged 8 weeks of C57BL/6 background strains.

extract_protocol:
Snap-frozen pituitaries were thawed on ice. For nuclei isolation, a modified protocol from Mathys et al Nat 2019 was followed, all on ice. RNAse inhibitor (NEB MO314L) was added to the homogenization buffer (0.32 M sucrose, 1 mM EDTA, 10 mM Tris-HCl, pH 7.4, 5mM CaCL2, 3mM Mg(Ac)2, 0.1% IGEPAL CA-630), 50% OptiPrep (Stock is 60% Media from Sigma; cat# D1556), 35% OptiPrep and 30% OptiPrep right before isolation. Each pituitary was homogenized with 10 strokes (loose pestle) in an individual autoclaved dounce glass homogenizer (1ml, VWR cat# 71000-514). The homogenate was filtered through a 40-micrometer cell strainer. The volume was measured and an equal volume of 50% OptiPrep was added. The gradient was centrifuged using an SW41 rotor at 9200 rpm and at 4C for 25 min. Nuclei were collected from the interphase between 30% and 35% OptiPrep. The nuclei were washed, resuspended either in 1x nuclei dilution buffer for snATACseq (10X Genomics) or in 1X PBS/0.04% BSA for snRNAseq, and counted on an Invitrogen Countess II cell counter. ii) Dissociated pituitary cells were cryopreserved in 90% FBS/10% DMSO and shipped to New York on dry-ice. Upon arrival, cells were stored in liquid nitrogen. On the day of an experiment, the vial was removed from liquid nitrogen on dry-ice, thawed quickly in a 37C waterbath, and cells were serially diluted with 10% FBS /DMEM until a minimum volume of 8ml was reached. Cells were centrifuged at 300xg for 5min, resuspended in 1ml of medium and counted. Nuclei were isolated from all cells remaining after the scGEM Drop-seq RNA-seq assay was done. Cells were centrifuged at 500g for 5min at 4C. The supernatant was carefully removed and 0.1X lysis buffer (1x: 10mM Tris-HCL pH 7.5, 10mM NaCl, 3mM MgCl2, nuclease-free H2O, 0.1% v/v NP-40, 0.1% v/v Tween-20, 0.01% v/v digitonin) was added. After 5min incubation on ice, 1ml of wash buffer was added. The nuclei were pelleted at 500xg for 5min at RT, resuspended either in 1X PBS/0.04% BSA for scGEM Drop-seq RNA-seq or in diluted nuclei buffer for snATAC-seq. Nuclei were counted and the concentration adjusted to run the given assay.
snATACseq was performed as described (10x Genomics), following the Chromium Single Cell ATAC Reagent Kits V1.1 User Guide. Nuclei were counted on a Nexclome instrument, and the final concentration was used to calculate the volume of nuclei stock to use. Transposition was performed in 10 microliter at 37C for 60min. Then the Chromium Chip E (PN-2000121) was loaded to target up to 10,000 nuclei. Barcoding was performed in the emulsion for 12 cycles following the Chromium protocol. Each library was tagged with a different index for multiplexing (Chromium i7 Sample Index N, Set A kit PN-3000262). Quality control and quantification of the libraries were assessed on a Bioanalyzer (High-Sensitivity DNA Bioanalyzer kit). Sequencing was carried out at the Cedars-Sinai Core on Illumina Novaseq X using 98+26 paired-end reads.

treatment_protocol: Nine-week-old male C57BL6/N mice were injected with a single dose of 20 mg/kg of IgG or Bimagrumab subcutaneously. Pituitary glands were flash-frozen in liquid N2 and subjected to snATAC-seq.

value: pituitary

value: all pituitary cells

tag: strain

tag: Sex

value: Male

tag: age

value: 8 weeks

tag: genetic modification


title: tropicalis NF33 fg mesendo Hh LOF rep3

description:
Library name: tropicalis_NF33_fg_mesendo_Hh_LOF_rep3
tropicalis_NF33_fg_mesendo_Hh_LOF_rep3

value: 40uM cyclopamine (Tocris #1623)


title: Fshb-Enh2-KO_Mouse3

description:
Library name: 032525-3-A7-4-1-KO-A
10X Genomics sc-ATAC assay

value: KO of Fshb-Enhancer2


title: YF_Sh4d_2_mix4

value: Sham surgery


title: C1qtnf6-KO, gd14.5, RNA-seq, replicate 4

description: Library name: C1qtnf6-KO gd14.5, RNA-seq, replicate 2

value: maternal-fetal interface


title: tropicalis NF33 fg mesendo Hh LOF rep2

description:
Library name: tropicalis_NF33_fg_mesendo_Hh_LOF_rep2
tropicalis_NF33_fg_mesendo_Hh_LOF_rep2


title: C1qtnf6-KO, gd14.5, RNA-seq, replicate 3

description: Library name: C1qtnf6-KO gd14.5, RNA-seq, replicate 1


title: YF_Sh4d_1_mix4


title: Control+ TGFB1 2

city: Birmingham

first: Kelly

middle: Anne

last: Hyndman

state: Al

address: 1918 University BLVD

department: Medicine

institute: University of Alabama at Birmingham

description: Library name: TGFV2

data_processing:
GeneWiz provided fastq files to the lab.
Sequenced reads were trimmed for adaptor sequence with Trim_Galore v0.6.7, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using star2.7.3a.  Counts were generated with the subread v2.0.1 and the featureCounts" "-p" "--countReadPairs" "-t" "exon" "-g" "gene_id" "-a" "/RefGenomes/GRCr8/Rattus_norvegicus.GRCr8.114.gtf" "-o" "raw_counts.txt"
Count matrixes were then analyzed using DESeq2 v1.44 to caculate differentialy expressed genes and normalized counts
DeSeq2 Normalized counts were calcuated by counts divided by sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene
Assembly: GRCr8_114
Supplementary files format and content: raw_counts.csv
Supplementary files format and content: normalized_counts.csv

organism: Rattus norvegicus

source_name: NRK 49F

growth_protocol: cell were grown in standard conditions per ATCC instruction

extract_protocol:
Zymo Direct-Zol micro RNA isolation kit
RNA libraries were prepared for sequencing using standard Illumina protocols, and poly A selection by GeneWiz

treatment_protocol: cells were treated with 0.5% FBS media (vehicle) or 2 ng/ml TGFB1 (Abcam ab50036) for 24 hours in 0.5% FBS media

value: NRK 49F

value: Fibroblast

value: empty vector control


title: Control+ TGFB1 3

description: Library name: TGFV3


title: tropicalis NF33 fg mesendo Hh LOF rep1

description:
Library name: tropicalis_NF33_fg_mesendo_Hh_LOF_rep1
tropicalis_NF33_fg_mesendo_Hh_LOF_rep1

value: embryo

value: Xenopus Tropicalis, NXR_1018, Xtr.NigerianSt549

value: dissected NF33 foregut tissue


title: Control+ TGFB1 1

description: Library name: TGFV1


title: YF_4d_2_mix4

value: Liver

value: Primary Cells

value: PH


title: tropicalis NF33 pharynx mesendo control rep3

description:
Library name: tropicalis_NF33_pharynx_mesendo_control_rep3
tropicalis_NF33_pharynx_mesendo_control_rep3

value: dissected NF33 head+pharynx tissue

value: wild type

value: DMSO 0.1%


title: Wild-type, gd14.5, RNA-seq, replicate 3

description: Library name: wild-type gd14.5, RNA-seq, replicate 3

value: wild-type


title: HDAC1 Overexpressed + TGFB1 3

description: Library name: TGFHDAC3

value: HDAC1 overexpression


title: tropicalis NF33 pharynx mesendo control rep2

description:
Library name: tropicalis_NF33_pharynx_mesendo_control_rep2
tropicalis_NF33_pharynx_mesendo_control_rep2


title: Wild-type, gd14.5, RNA-seq, replicate 2

description: Library name: wild-type gd14.5, RNA-seq, replicate 2


title: YF_4d_1_mix4

value: Hepatocyte

value: WT


title: HDAC1 Overexpressed + TGFB1 2

description: Library name: TGFHDAC2


title: AAV-GFP,mouse heart,stero-seq

value: heart

value: GFP overexpressed

value: mouse heart

value: 3day post injury at P8


title: Wild-type, gd14.5, RNA-seq, replicate 1

description: Library name: wild-type gd14.5, RNA-seq, replicate 1

value: maternal-fetal interface


title: tropicalis NF33 pharynx mesendo control rep1

description:
Library name: tropicalis_NF33_pharynx_mesendo_control_rep1
tropicalis_NF33_pharynx_mesendo_control_rep1

value: embryo

value: Xenopus Tropicalis, NXR_1018, Xtr.NigerianSt549


title: YF_Sh2d_1_mix3

value: Liver

value: Sham surgery


title: HDAC1 Overexpressed + TGFB1 1

description: Library name: TGFHDAC1

value: NRK 49F

value: Fibroblast


title: C1qtnf6-KO, gd10.5, RNA-seq, replicate 5

description: Library name: C1qtnf6-KO gd10.5, RNA-seq, replicate 3


title: YF_52h_2_mix3

value: Primary Cells

value: PH


title: tropicalis NF33 hg mesendo control rep2

description:
Library name: tropicalis_NF33_hg_mesendo_control_rep2
tropicalis_NF33_hg_mesendo_control_rep2

value: dissected NF33 hindgut tissue

value: wild type

value: DMSO 0.1%


title: Control 2

description: Library name: NRKV2

value: empty vector control

value: vehicle


title: C1qtnf6-KO, gd10.5, RNA-seq, replicate 3

description: Library name: C1qtnf6-KO gd10.5, RNA-seq, replicate 1


title: YF_52h_1_mix3

value: Hepatocyte

value: WT


title: tropicalis NF33 hg mesendo control rep1

description:
Library name: tropicalis_NF33_hg_mesendo_control_rep1
tropicalis_NF33_hg_mesendo_control_rep1


title: Control 1

description: Library name: NRKV1


title: YF_Ctrl_3_mix2


title: Wild-type, gd10.5, RNA-seq, replicate 3

description: Library name: wild-type gd10.5, RNA-seq, replicate 3

value: wild-type


title: tropicalis NF33 fg mesendo control rep3

description:
Library name: tropicalis_NF33_fg_mesendo_control_rep3
tropicalis_NF33_fg_mesendo_control_rep3

value: dissected NF33 foregut tissue

value: DMSO 0.1% + 1ng mismatch MO


title: HDAC1 Overexpressed 3

description: Library name: NRKHDAC3

value: HDAC1 overexpression


title: YF_Ctrl_2_mix2

value: Liver


title: YF_Ctrl_1_mix2


title: YF_Sh2d_2_mix3

value: Sham surgery


title: Wild-type, gd10.5, RNA-seq, replicate 2

description: Library name: wild-type gd10.5, RNA-seq, replicate 2

value: maternal-fetal interface


title: HDAC1 Overexpressed 2

description: Library name: NRKHDAC2

value: NRK 49F

value: Fibroblast


title: tropicalis NF33 fg mesendo control rep1

description:
Library name: tropicalis_NF33_fg_mesendo_control_rep1
tropicalis_NF33_fg_mesendo_control_rep1

value: embryo

value: Xenopus Tropicalis, NXR_1018, Xtr.NigerianSt549


title: tropicalis NF33 fg mesendo control rep2

description:
Library name: tropicalis_NF33_fg_mesendo_control_rep2
tropicalis_NF33_fg_mesendo_control_rep2

value: wild type


title: Wild-type, gd10.5, RNA-seq, replicate 1

description: Library name: wild-type gd10.5, RNA-seq, replicate 1


title: HDAC1 Overexpressed 1

description: Library name: NRKHDAC1


title: PDGF+NC-3

status: Public on Nov 23 2025

city: Hangzhou

first: Sheng-an

last: Su

state: Zhejiang

address: No. 88 Jiefang Road

institute: Zhejiang University

description: Processed data column header: E3

data_processing:
A cDNA library constructed by technology from the pooled RNA from samples was sequenced run with Illumina Novaseq X Plus sequence platform.
We aligned reads of all samples to the mus musculus reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-2.1.6) with default parameters.
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software.
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: mm10
Supplementary files format and content: tab-delimited text file inculde gene count values of each sample
Supplementary files format and content: tab-delimited text file inculde transcript count values of each sample

source_name: Thoracic aortic tissue

growth_protocol: The SMCs isolated from mouse aorta were transfected with ITGAV silence RNA. Then the SMCs were stimulated by TGF-β or PDGFBB. Finally, the SMCs were harvested for bulk RNA sequencing.

extract_protocol:
RNA was harvested using Trizol and Invitrogen SuperScriptTM II Reverse Transcriptase Kit. 2.0ug of total RNA was used for the construction of sequencing libraries.
The cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase. The average insert size for the final cDNA librarys were 300±50 bp.

treatment_protocol: The SMCs isolated from mouse aorta were transfected with ITGAV silence RNA and stimulated by TGF-β or PDGFBB.

value: Thoracic aortic tissue

value: smooth muscle cell

value: PDGFBB+Scramble


title: Control 3

description: Library name: NRKV3

value: empty vector control

value: vehicle


title: C1qtnf6-KO, gd10.5, RNA-seq, replicate 4

description: Library name: C1qtnf6-KO gd10.5, RNA-seq, replicate 2


title: PDGF+Si-2

description: Processed data column header: F2

value: PDGFBB+ITGAV siRNA


title: PDGF+Si-1

description: Processed data column header: F1


title: PDGF+NC-2

description: Processed data column header: E2


title: PDGF+Si-3

description: Processed data column header: F3


title: PDGF+NC-1

description: Processed data column header: E1


title: tropicalis NF33 hg mesendo control rep3

description:
Library name: tropicalis_NF33_hg_mesendo_control_rep3
tropicalis_NF33_hg_mesendo_control_rep3

value: dissected NF33 hindgut tissue

value: DMSO 0.1%


title: TGFβ+Si-2

description: Processed data column header: D2

value: TGFBeta+ITGAV siRNA


title: TGFβ+NC-3

description: Processed data column header: C3

value: TGFBeta+Scramble


title: TGFβ+Si-3

description: Processed data column header: D3


title: TGFβ+Si-1

description: Processed data column header: D1


title: TGFβ+NC-1

description: Processed data column header: C1


title: Control+Si-3

description: Processed data column header: B3

value: ITGAV siRNA


title: Control+Si-1

description: Processed data column header: B1


title: Control+Si-2

description: Processed data column header: B2


title: Control+NC-3

description: Processed data column header: A3

value: Scramble


title: Control+NC-2

description: Processed data column header: A2


title: Control+NC-1

description: Processed data column header: A1


title: AMO-1/CFZ cell, P-gp LOW, rep2

city: Moscow

first: Natalia

last: Moiseeva

state: Moscow

address: Kashirskoe Shosse 24

country: Russia

institute: N.N. Blokhin National Medical Research Center of Oncology

description:
Library name: AMO1_CFZ_Pgp_LOW_2
Actual instrument model is the GeneMind SURFseq 5000.

data_processing:
Raw data quality control was performed using FastQC (FastQC, RRID:SCR_014583) and visualized by MultiQC (MultiQC, RRID:SCR_014982)
Read alignment was performed using STAR aligner (STAR, RRID:SCR_004463) with GRCh38 genome and Gencode annotations
The numbers of reads assigned to genomic features were calculated using featureCounts software (featureCounts, RRID:SCR_012919)
Subsequent analysis steps were performed using DESeq2 software (DESeq2, RRID:SCR_015687)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Homo sapiens

source_name: bone marrow

growth_protocol: The human multiple myeloma (MM) cell lines AMO-1 (obtained from the Leibniz Institute DSMZ) and resistant to carfilzomib AMO-1/CFZ were cultured in RPMI 1640 medium (PanEco, Russia) supplemented with 20% fetal bovine serum (Biowest, South America) and with 50 µg/mL streptomycin and 50 U/mL penicillin (PanEco, Russia)). Cells were maintained at 37 °C in a humidified atmosphere containing 5% CO2. The AMO-1/CFZ cell line was established by cultivation of AMO-1 cells with progressively increasing concentrations of carfilzomib

extract_protocol:
For RNA sequencing, the carfilzomib-resistant AMO-1/CFZ cells were stained for P-glycoprotein expression for subsequent sorting. Cells were stained with a FITC-conjugated mouse monoclonal antibody against human P-glycoprotein (clone 17F9; BD Biosciences, USA) for 30 minutes in the dark without prior fixation and then washed twice with PBS. Control AMO-1 cells (P-glycoprotein non-expressing) were used for RNA sequencing as an unsorted total lysate. Analysis and sorting of AMO-1/CFZ cells were performed on a FACSAria SORP instrument (BD Biosciences, USA). Based on the P-glycoprotein fluorescence intensity, stained AMO-1/CFZ cells were sorted into two distinct subpopulations: P-gp LOW and P-gp HIGH. The purity of the isolated subpopulations was confirmed by immediate post-sort analysis. Four independent biological replicates were performed. Data were acquired using BD FACSDiva 8.1.1 software and analyzed using FlowJo software (BD Biosciences, USA).
RNA libraries were synthesized using the NR605-02 VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (VAZYME, China) with indexed barcodes from the N809 VAHTS RNA Adapters Set 3 for Illumina (VAZYME, China) according to the manufacturer's protocols. Poly(A)+ RNA selection was performed with the N403-02 VAHTS mRNA Capture Beads 2.0 (VAZYME, China). RNA quality control was carried out using the C405110 Qsep400, R1 Cartridge (RNA Cartridge) (Bioptic Inc., Taiwan), and the quality of the final libraries was assessed with the C405105 Qsep400, N1 Cartridge (High Sensitivity Cartridge) (Bioptic Inc., Taiwan).

value: bone marrow

value: plasma cell


title: AMO-1 cell, control, rep3

description:
Library name: AMO1_CTRL_3
Actual instrument model is the GeneMind SURFseq 5000.


title: AMO-1 cell, control, rep4

description:
Library name: AMO1_CTRL_4
Actual instrument model is the GeneMind SURFseq 5000.


title: AMO-1 cell, control, rep2

description:
Library name: AMO1_CTRL_2
Actual instrument model is the GeneMind SURFseq 5000.


title: AMO-1 cell, control, rep1

description:
Library name: AMO1_CTRL_1
Actual instrument model is the GeneMind SURFseq 5000.


title: AMO-1/CFZ cell, P-gp LOW, rep1

description:
Library name: AMO1_CFZ_Pgp_LOW_1
Actual instrument model is the GeneMind SURFseq 5000.


title: AMO-1/CFZ cell, P-gp HIGH, rep4

description:
Library name: AMO1_CFZ_Pgp_HIGH_4
Actual instrument model is the GeneMind SURFseq 5000.


title: AMO-1/CFZ cell, P-gp HIGH, rep3

description:
Library name: AMO1_CFZ_Pgp_HIGH_3
Actual instrument model is the GeneMind SURFseq 5000.


title: fetal cerebral cortex, KO_1

city: beijing

first: huiyang

last: Jia

state: Beijing

address: China

institute: Institute of Zoology, Chinese Academy of Sciences

description: Library name: Sample 4

data_processing:
We processed the raw 150-bp paired-end Illumina reads using CASAVA to generate FASTQ files, then removed adapter-contaminated reads, reads containing undetermined bases (N), and low-quality reads in which bases with Qphred  20 accounted for more than 50% of the read length; Q30 scores and GC content were calculated and all downstream analyses were based on these high-quality clean reads. Clean reads were aligned to the reference genome using HISAT2 (v2.0.5) with the corresponding gene model annotation, and gene expression levels were quantified as FPKM, taking both gene length and sequencing depth into account. Differential expression between sample groups was assessed with DESeq2 (or DESeq when biological replicates were not available) using a negative binomial model and Benjamini-Hochberg correction, designating genes with adjusted P  0.05 as differentially expressed. Differentially expressed genes were then subjected to GO and KEGG pathway enrichment analysis using the clusterProfiler package, and terms/pathways with P-value < 0.05 were considered significantly enriched.
Assembly: Mus_musculus.NCBI.GRCm39
Supplementary files format and content: KO_Control.matrix.txt (tab-delimited text file)

source_name: cortex

extract_protocol:
Total RNA was extracted using the TRIzol method
After quality assessment, poly(A)+^++ mRNA was enriched from total RNA using Oligo(dT) magnetic beads and fragmented with Fragmentation Buffer. First- and second-strand cDNA were synthesized from the fragmented mRNA, and the resulting double-stranded cDNA was purified, end repaired, A-tailed, ligated to sequencing adapters, and size-selected to obtain ~350 bp fragments.
The library was enriched by PCR and, for sequencing on the DNBSEQ-T7 platform, the double-stranded cDNA was thermally denatured to single-stranded DNA and circularized with a specific oligonucleotide to generate a single-stranded circular library. Libraries that passed quality control on a Qubit 3.0 fluorometer and an Agilent 2100 Bioanalyzer were subjected to high-throughput sequencing using a PE150 strategy.

value: cortex


title: fetal cerebral cortex, KO_3

description: Library name: Sample 6


title: fetal cerebral cortex, Control_1

description: Library name: Sample 1


title: fetal cerebral cortex, Control_3

description: Library name: Sample 3


title: Normal3_colon epithelium

description: Library name: Normal3_colon epithelium

data_processing:
We processed the raw 150-bp paired-end Illumina reads using CASAVA to generate FASTQ files, then removed adapter-contaminated reads, reads containing undetermined bases (N), and low-quality reads in which bases with Qphred  20 accounted for more than 50% of the read length; Q30 scores and GC content were calculated and all downstream analyses were based on these high-quality clean reads. Clean reads were aligned to the reference genome using HISAT2 (v2.0.5) with the corresponding gene model annotation, and gene expression levels were quantified as FPKM, taking both gene length and sequencing depth into account. Differential expression between sample groups was assessed with DESeq2 (or DESeq when biological replicates were not available) using a negative binomial model and Benjamini-Hochberg correction, designating genes with adjusted P  0.05 as differentially expressed. Differentially expressed genes were then subjected to GO and KEGG pathway enrichment analysis using the clusterProfiler package, and terms/pathways with P-value < 0.05 were considered significantly enriched.
Assembly: Mus_musculus.NCBI.GRCm39
Supplementary files format and content: Treated_Control.anno.txt (tab-delimited text file)

source_name: colon epithelium

value: colon epithelium


title: fetal cerebral cortex, KO_2

description: Library name: Sample 5


title: DSS3_colon epithelium

description: Library name: DSS3_colon epithelium


title: AMO-1/CFZ cell, P-gp HIGH, rep1

description:
Library name: AMO1_CFZ_Pgp_HIGH_1
Actual instrument model is the GeneMind SURFseq 5000.


title: AMO-1/CFZ cell, P-gp HIGH, rep2

description:
Library name: AMO1_CFZ_Pgp_HIGH_2
Actual instrument model is the GeneMind SURFseq 5000.


title: DSS1_colon epithelium

description: Library name: DSS1_colon epithelium


title: fetal cerebral cortex, Control_2

description: Library name: Sample 2


title: Liver_HFD_10epiPDX_Biorep3

city: Seoul

first: Nahyun

last: Kim

address: 120 Neungdong-ro, Gwangjin-gu, Seoul

country: South Korea

institute: Konkuk university

description: Library name: Sample9

data_processing:
Illumina NovaSeq 6000
Sequenced RNA-sequencing reads were trimmed for adapter seuquence, and processed for eliminating artifacts such as contaminant DNA or PCR duplicates using Trimmomatic 0.38 with parameters SLIDINGWINDOW:4:15 TRAILING:3 LEADING:3 MINLEN:36.
Trimmed reads were mapped to reference genome (UCSC GRCm38/mm10) using the Bowtie2 2.3.4.1 aligner.
Fragments per kilobase of transcript per million mapped reads (FPKM) was estimated with StringTie for mus musculus genes.
Assembly: mm10
Supplementary files format and content: GTF file contains the merged transcript annotations generated using StringTie

extract_protocol:
RNA was harvested using the PureLink™ RNA Mini Kit (Invitrogen) according to the manufacturer’s instructions
RNA libraries for RNA-seq were prepared using SureSlect XT RNA Direct Library Preparation Kit following manufacturer's protocols.

treatment_protocol: Diet-induced obese mice were treated with 10-epi PDX. Metabolic outcomes, including body weight, hepatic steatosis, adipose tissue inflammation, and insulin sensitivity, were monitored

value: Liver

value: Male

tag: diet

value: High fat diet

value: 10 epimer PDX


title: TGFβ+NC-2

description: Processed data column header: C2

value: Thoracic aortic tissue

value: smooth muscle cell


title: AMO-1/CFZ cell, P-gp LOW, rep3

description:
Library name: AMO1_CFZ_Pgp_LOW_3
Actual instrument model is the GeneMind SURFseq 5000.


title: DSS2_colon epithelium

description: Library name: DSS2_colon epithelium


title: Liver_HFD_10epiPDX_Biorep1

description: Library name: Sample7


title: Normal2_colon epithelium

description: Library name: Normal2_colon epithelium


title: Liver_HFD_Biorep3

description: Library name: Sample6

value: PBS


title: Liver_HFD_10epiPDX_Biorep2

description: Library name: Sample8


title: AMO-1/CFZ cell, P-gp LOW, rep4

description:
Library name: AMO1_CFZ_Pgp_LOW_4
Actual instrument model is the GeneMind SURFseq 5000.


title: Liver_HFD_Biorep2

description: Library name: Sample5


title: MMK-1-3

first: shuting

last: Yu

address: 320 Yueyang Road, Xuhui District

institute: Shanghai Institute of Nutrition and Health

description: Library name: Sample6

data_processing:
The libraries were sequenced using an Illumina Novaseq 6000 platform, generating 150 bp paired-end reads.
Raw reads in FASTQ format were processed using Fastp, and low-quality reads were removed to obtain clean reads.
Clean reads were mapped to the reference genome using HISAT2. The FPKM of each gene was calculated, and the read counts of each gene were obtained via HTSeq-count. PCA analyses were performed using R (v 3.2.0) to evaluate biological duplication of the samples.
Differential expression analysis was performed using the DESeq2. The threshold for significantly differentially expressed genes (DEGs) was set at a Q value of <0.05 and a fold change of >2 or <0.5.
Assembly: mm10
Supplementary files format and content: csv files include FPKM values for each Sample
Supplementary files format and content: csv files include raw counts for each Sample

source_name: small intestinal organoids

extract_protocol:
Small intestinal organoids derived from Fpr2f/f mice were treated with 1 μM MMK-1 for 5 days. 0.1% DMSO was used as the vehicle control.  Total RNA was extracted using Trizol.
The RNA libraries for RNA-seq were constructed using the VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions. RNA library construction, RNA-seq, and transcriptome analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: small intestinal organoids

value: 1 mM MMK-1

value: day 5


title: MMK-1-2

description: Library name: Sample5


title: MMK-1-1

description: Library name: Sample4


title: Liver_HFD_Biorep1

description: Library name: Sample4


title: Liver_ND_Biorep3

description: Library name: Sample3

value: Normal diet


title: Liver_ND_Biorep1

description: Library name: Sample1


title: Control-2

description: Library name: Sample2

value: 0.1% DMSO


title: Liver_ND_Biorep2

description: Library name: Sample2


title: Control-1

description: Library name: Sample1


title: Control-3

description: Library name: Sample3


title: 13w

city: Okayama

first: Ikue

last: Tosa

state: Okayama

address: Shikata-cho2-5-1, Kita-ku

institute: Okayama University

description:
Library name: 13w
10x Genomics

library_source: transcriptomic single cell

data_processing:
The sequencing data was first pre-processed using the 10X Genomics software Cell Ranger.
Assembly: GRCm39
Supplementary files format and content: Tab-sepalated values files and matrix files

source_name: TMJ

extract_protocol:
Mandibular condyles were collected from E16.5, P0, and 13-week-old mice, pooled within each age group (7-20 mice per group), and enzymatically digested in Dulbecco's Modified Eagle Medium (DMEM; Gibco, 11885084) containing 2 mg/mL collagenase A (Roche, 11088793001) and 4 mg/mL dispase 2 (Roche, 04942078001) at 37°C for 90 minutes. Cell suspensions were filtered through a 40-µm strainer (Corning, 352340) and stained with DAPI and Calcein AM (Invitrogen, C1430). Live cells (Calcein⁺DAPI⁻) were sorted using an Influx Cell Sorter (BD Biosciences).
Sorted cells were processed using the Chromium Next GEM Single Cell 3ʹ GEM kit v.3.1 (10X Genomics Inc.) following the manufacturer’s instruction.

value: TMJ

value: condylar cartilage cells

value: WT


title: E16.5

description:
Library name: E16.5
10x Genomics


title: scRNA_3dpmi_ho

city: shanghai

first: Zhongxiang

last: Chen

state: Shanghai

address: 浦东新区东方路1678号上海儿童医学中心

institute: shanghai children's medical center

description: Library name: scRNA_3dpmi_ho

data_processing:
Briefly, raw reads were processed using CellRanger. RNA Velocity was calculated using Velocyto. Gene-cell matrices was loaded to Scanpy framework for further analysis. BBKNN was used for batch correction, followed by leiden clustering with resolution of 0.4, 0.6, 0.8, 1, and 1.2. Subclusters were then organized hierarchically based on conventional cell type-specific genes.
Assembly: GRCm39
Supplementary files format and content: barcode, matrix, and features

extract_protocol:
The cardiac cell nuclei were isolated.
loaded into the 10X Genomics Chromium system for library construction using the Chromium Single Cell 5’ Reagent Kits v2 (10× Genomics), following the standard protocols provided by the manufacturer. The libraries were sequenced on NovaSeq6000 sequencer (Illumina).

value: heart

value: total cells


title: scRNA_3dpmi_wt

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: scRNA_3dpmi_wt

value: wild type


title: scRNA_homeo_ho

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: scRNA_homeo_ho

value: homeostasis


title: RNAseq_3dpmi_cm_ho_replicate1

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_3dpmi_cm_ho_replicate1

data_processing:
20 million pair-end reads were yield for each sample and aligned to mouse genes (GRCm39) using hisat2. Alternative spliced transcripts were quantified by Kallisto.
Assembly: GRCm39
Supplementary files format and content: raw counts in csv

extract_protocol:
The cardiac tissues and isolated cells were collected for RNA isolation using Trizol reagent (Invitrogen, 15596026) for bulk RNAseq.
For each sample, total amount of 2 μg RNA were subjected to library construction and Illumina sequencing.

value: cardiomyocytes


title: RNAseq_3dpmi_cm_wt_replicate3

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_3dpmi_cm_wt_replicate3


title: RNAseq_3dpmi_cm_ho_replicate2

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_3dpmi_cm_ho_replicate2


title: Normal1_colon epithelium

description: Library name: Normal1_colon epithelium

value: colon epithelium


title: RNAseq_3dpmi_cm_wt_replicate1

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_3dpmi_cm_wt_replicate1


title: RNAseq_homeo_cm_ho_replicate3

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_homeo_cm_ho_replicate3


title: RNAseq_homeo_cm_ho_replicate1

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_homeo_cm_ho_replicate1


title: RNAseq_homeo_cm_ho_replicate2

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_homeo_cm_ho_replicate2


title: P0

description:
Library name: P0
10x Genomics


title: RNAseq_homeo_cm_wt_replicate3

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_homeo_cm_wt_replicate3


title: RNAseq_3dpmi_ec_ho_replicate2

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_3dpmi_ec_ho_replicate2

value: endothelial cells


title: scRNA_homeo_wt

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: scRNA_homeo_wt


title: RNAseq_homeo_cm_wt_replicate1

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_homeo_cm_wt_replicate1


title: RNAseq_homeo_cm_wt_replicate2

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_homeo_cm_wt_replicate2


title: RNAseq_3dpmi_cm_ho_replicate3

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_3dpmi_cm_ho_replicate3


title: RNAseq_homeo_ec_ho_replicate2

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_homeo_ec_ho_replicate2


title: RNAseq_homeo_ec_ho_replicate1

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_homeo_ec_ho_replicate1


title: RNAseq_3dpmi_ec_wt_replicate2

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_3dpmi_ec_wt_replicate2


title: K562 DRB - input

city: Melbourne

first: Daniel

last: Neville

state: Victoria

address: 99 Commercial Road Level 6, Alfred Centre

department: Australian Centre for Blood Diseases

country: Australia

institute: Monash University

library_source: genomic

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were trimmed to remove adapter with cutadapt.
ChIPs were aligned using Bowtie2. Mouse cell lines were aligend to mm10 and human to Hg38
Sam files were converted into Bam files using samtools. Tdf files were generated using igvtools.
Assembly: mm10 and hg38
Supplementary files format and content: .

source_name: Blood

growth_protocol: Cells were cultured in RPMI-1640 supplemented with 2mM Glutamax, 100IU/ml Penicillin, 100 ug/ml Streptomycin and 10%HI-FCS in 5% CO2 37degrees.

extract_protocol:
ChIP DNA was purified using qiagen PCR clean up columns
Library prep was performed on ChIP DNA using NEB Ultra II kit

treatment_protocol: ~ 100x10^6 cells were fixed/sonicated and ChIP performed at indicated timepoints from approx- 20-30 million cells per ChIP

value: Blood

value: Myeloid


title: RNAseq_3dpmi_ec_wt_replicate1

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_3dpmi_ec_wt_replicate1


title: K562 DRB - DRB H3K27me3


title: RNAseq_3dpmi_ec_ho_replicate1

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_3dpmi_ec_ho_replicate1


title: K562 DRB - DRB H2AK119ub


title: RNAseq_homeo_ec_wt_replicate3

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_homeo_ec_wt_replicate3


title: RNAseq_homeo_ec_wt_replicate1

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_homeo_ec_wt_replicate1


title: RNAseq_homeo_ec_ho_replicate3

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_homeo_ec_ho_replicate3


title: RNAseq_30dpMI_ho_replicate4

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_30dpMI_ho_replicate4


title: RNAseq_3dpmi_cm_wt_replicate2

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_3dpmi_cm_wt_replicate2


title: K562 DRB - DMSO H2AK119ub


title: MOLM13 PB - DMSO H3K79me2

value: 96 hrs


title: MOLM13 PB - VTP50469 500 nM H3K79me2


title: MOLM13 PB - SGC0946 5uM H3K79me2


title: K562 DRB - DMSO H3K27me3


title: RNAseq_30dpMI_ho_replicate1

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_30dpMI_ho_replicate1


title: RNAseq_30dpMI_wt_replicate3

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_30dpMI_wt_replicate3


title: MOLM13 PB - input


title: MOLM13 NT - VTP50469 500 nM H3K79me2


title: MOLM13 NT - DMSO H3K79me2


title: RNAseq_30dpMI_wt_replicate1

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_30dpMI_wt_replicate1


title: RNAseq_7dpMI_ho_replicate4

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_7dpMI_ho_replicate4


title: RNAseq_30dpMI_wt_replicate2

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_30dpMI_wt_replicate2


title: MOLM13 NT - SGC0946 5uM H3K79me2


title: RNAseq_7dpMI_ho_replicate3

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_7dpMI_ho_replicate3


title: RNAseq_homeo_ec_wt_replicate2

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_homeo_ec_wt_replicate2


title: MOLM13 PB - SGC0946 5uM H2AK119ub


title: RNAseq_7dpMI_ho_replicate1

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_7dpMI_ho_replicate1


title: RNAseq_7dpMI_ho_replicate2

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_7dpMI_ho_replicate2


title: MOLM13 NT - input


title: MOLM13 PB - DMSO H2AK119ub


title: MOLM13 PB - VTP50469 500 nM H2AK119ub


title: RNAseq_30dpMI_ho_replicate3

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_30dpMI_ho_replicate3


title: RNAseq_7dpMI_wt_replicate4

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_7dpMI_wt_replicate4


title: RNAseq_7dpMI_wt_replicate3

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_7dpMI_wt_replicate3


title: MOLM13 NT - SGC0946 5uM H2AK119ub


title: RNAseq_30dpMI_ho_replicate2

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_30dpMI_ho_replicate2


title: RNAseq_7dpMI_wt_replicate2

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_7dpMI_wt_replicate2


title: RNAseq_7dpMI_wt_replicate1

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_7dpMI_wt_replicate1


title: MOLM13 NT - VTP50469 500 nM H2AK119ub


title: MOLM13 NT - DMSO H2AK119ub


title: RNAseq_homeo_ho_replicate3

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_homeo_ho_replicate3


title: RNAseq_homeo_ho_replicate2

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_homeo_ho_replicate2


title: MOLM13 PB - SGC0946 5uM H3K27me3


title: MOLM13 PB - VTP50469 500 nM H3K27me3


title: RNAseq_homeo_ho_replicate1

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_homeo_ho_replicate1


title: MOLM13 PB - DMSO H3K27me3


title: RNAseq_homeo_wt_replicate3

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_homeo_wt_replicate3


title: MOLM13 NT - SGC0946 5uM H3K27me3


title: RNAseq_homeo_wt_replicate1

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_homeo_wt_replicate1


title: MOLM13 NT - VTP50469 500 nM H3K27me3


title: MOLM13 NT - DMSO H3K27me3


title: p38a-ko-H9

city: Buffalo

first: Andrei

last: Bakin

address: Elm and Carlton streets

institute: Roswell Park Comprehensive Cancer Center

description:
Library name: p38a-ko-H9
10X Genomics

data_processing:
Raw sequence data demultiplexing, barcode processing, alignment (mm10) and filtering for true cells were performed using the Cell Ranger Single-Cell Software Suite (v6.0.0)
All downstream analysis was performed in RStudio Desktop v1.4 equipped with R v4.2.1. The filtered feature matrix containing gene counts, cell barcodes and gene names was utilized to construct a SingleCellExperiment object using SingleCellExperiment package. Per cell quality control was performed using the addPerCellQC function from Scater package. Cells with sequencing depth less than 1500 total counts, less than 300 detected genes, and more than 20% mitochondrial content were removed. Next, Per Gene QC was performed by examining the mean vs. variance relationship of gene counts in the log2 counts/million scale. Genes with variance of less than 0.5 log2 counts per million were removed. Dimensionality reduction was performed to visualize the data points in a 2D plane using t-distributed Stochastic Neighborhood Embedding (t-SNE) method as outlined in Scater package. Identity of immune cell types was determined using Single R package. Mouse immunological gene expression data from Immunological Genome Project (ImmGen) database  was used as reference and was accessed using Celldex package. About 20 different cell types (both immune and non-immune) were found to be present, from which non-immune cell types (Epithelial cells, Fibroblasts) were excluded from analysis. In addition, the immune cells that were less than 1% abundant i.e. Basophils, B cells, Mast cells and γδ T cells were excluded. The cell types that passed the criteria included T cells, Dendritic cells, Neutrophils, Monocytes, Macrophages, NK cells, NKT cells and Innate Lymphoid Cells.  Seurat v5 was used for further analysis. In some of these cell populations, differential gene expression analysis was performed between the groups using FindMarkers function from Seurat using the following cutoffs: logFC > 0 and p value < 0.05. Heatmaps were constructed as outlined in ComplexHeatmap package. The pathway enrichment analysis was performed using the fgsea package with NES defined as enrichment score normalized to mean enrichment of random samples of the same size.
Assembly: mm10
Supplementary files format and content: 10x Genomics cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Breast tumor (primary)

growth_protocol: 200,000 4T1-luc p38a wildtype cells or 4T1 cells with p38a inactivated by CRISPR-Cas9 (p38a knock-out; p38a-KO-H9) cells were resuspended in 100ul of PBS+matrigel solution (1:1 ratio of PBS and matrigel) and implanted into 4th mammary fat pad of 6-8 week old female BALB/c mice. The mice were monitored every day. Mouse weights and tumor volumes were recorded twice/week. Mice were euthanized on day 14 post tumor implantation. This time-frame was chosen as 4T1 tumors induce changes to myeloid compartment within 14 days before the metastasis is detectable.

extract_protocol:
At day 14 post implantation, tumors from 3 mice per group of comparable sizes were pooled together and single-cell suspensions were prepared by cold protease digestion methods. The cells were stained for CD45 (pan-immune cell marker) and 7AAD (live/dead). About 100,000 Live CD45+ cells (negative for 7AAD) were sorted using BDFACSAria II. The cells were resuspended in PBS+0.04% FBS solution at a concentration of 1000 cells per sample. Immediately following preparation, cells were provided to the Roswell Park Genomics Shared Resource (GSR) for further processing and single cell sequencing (10x Genomics).
single cell 3' protocol v2; 10X Genomics 3' RACE technology

treatment_protocol: On day 4 post tumor implantation (when the tumors became palpable), mice from p38WT cohort were divided in two groups and treated with vehicle control (DPBS) or p38 inhibitor (LY2228820; p38i; 30mg/kg daily gavage) for 10 days.

value: Breast tumor (primary)

value: Live CD45+ cells

value: Balb/c


title: HUDEP-2 - SGC0946 Undifferentiated rep3

description:
240717_hudep_diff_readspergene.tsv
HUDEP-Expansion-SGC-3_S72

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were aligned to mouse or human genome with STAR aligner
Differential expression analysis was performed using Degust (DEseq2)
Assembly: hg38
Supplementary files format and content: .

extract_protocol:
Bioline RNA extraction kit
3' Poolseq or 3' Lexogen library prep for Illumina

value: Erytheroid

value: 7 days + 72hrs


title: 4T1-Tu-plus-p38i

description:
Library name: 4T1-Tu-plus-p38i
10X Genomics

value: p38 inhibitor, LY2228820


title: 4T1-Tu

description:
Library name: 4T1-Tu
10X Genomics

value: Vehicle control (1X DPBS)


title: HUDEP-2 - SGC0946 Undifferentiated rep1

description:
240717_hudep_diff_readspergene.tsv
HUDEP-Expansion-SGC-1_S70


title: mESC DRB - input

source_name: Ectoderm

value: Ectoderm

value: mESC

value: Stem


title: HUDEP-2 - DMSO Undifferentiated rep3

description:
240717_hudep_diff_readspergene.tsv
HUDEP-Expansion-DMSO-3_S66


title: mESC DRB - DRB SUZ12


title: HUDEP-2 - DMSO Undifferentiated rep2

description:
240717_hudep_diff_readspergene.tsv
HUDEP-Expansion-DMSO-2_S65


title: HUDEP-2 - DMSO Undifferentiated rep1

description:
240717_hudep_diff_readspergene.tsv
HUDEP-Expansion-DMSO-1_S64


title: HUDEP-2 - SGC0946 Differentiation rep3

description:
240717_hudep_diff_readspergene.tsv
HUDEP-Differentiation-SGC-3_S75


title: mESC DRB - DRB H2AK119ub


title: mESC DRB - DRB H3K27me3


title: HUDEP-2 - SGC0946 Differentiation rep2

description:
240717_hudep_diff_readspergene.tsv
HUDEP-Differentiation-SGC-2_S74


title: mESC DRB - DMSO SUZ12


title: HUDEP-2 - SGC0946 Differentiation rep1

description:
240717_hudep_diff_readspergene.tsv
HUDEP-Differentiation-SGC-1_S73


title: HUDEP-2 - DMSO Differentation rep2

description:
240717_hudep_diff_readspergene.tsv
HUDEP-Differentiation-DMSO-2_S68


title: mESC DRB - DMSO H2AK119ub


title: HUDEP-2 - DMSO Differentation rep3

description:
240717_hudep_diff_readspergene.tsv
HUDEP-Differentiation-DMSO-3_S69


title: mESC DRB - DMSO H3K27me3


title: RNAseq_homeo_wt_replicate2

address: 浦东新区东方路1678号上海儿童医学中心

description: Library name: RNAseq_homeo_wt_replicate2

value: heart

value: total cells

value: wild type

value: homeostasis


title: HUDEP-2 - DMSO Differentation rep1

description:
240717_hudep_diff_readspergene.tsv
HUDEP-Differentiation-DMSO-1_S67

value: Blood


title: HUDEP-2 - SGC0946 Undifferentiated rep2

description:
240717_hudep_diff_readspergene.tsv
HUDEP-Expansion-SGC-2_S71


title: MLLAF9 Control - DMSO H2AK119ub rep3

value: Myeloid


title: MLLAF9 Control - SGC0946 5uM H2AK119ub rep3


title: MLLAF9 Control - VTP50469 500nM H2AK119ub rep3


title: K562 Control - SGC0946 5uM H3K79me2

value: SGC0946 treatment 7 days


title: K562 Control - SGC0946 5uM H2AK119ub


title: mESC DRB - DRB POL2


title: K562 Control - VTP50469 500nM H3K79me2

value: VTP50469 treatment 7 days


title: MLLAF9 Control - VTP50469 500nM BCOR


title: K562 Control - VTP50469 500nM H2AK119ub


title: MLLAF9 Control - SGC0946 5uM BCOR


title: K562 Control - DMSO H2KAK119ub

value: 7 days


title: MLLAF9 Control - SGC0946 5uM RING1B


title: K562 Control - DMSO H3K79me2


title: HUDEP-2 Control - SGC0946 5uM H3K79me2


title: MLLAF9 Control - VTP50469 500nM RING1B


title: mESC DRB - DMSO POL2


title: MLLAF9 Control - DMSO BCOR


title: K562 Control - DMSO input


title: MLLAF9 Control - DMSO RING1B rep2


title: MLLAF9 Control - input


title: HUDEP-2 Control - DMSO H3K79me2


title: HUDEP-2 Control - SGC0946 5uM H2AK119ub


title: MLLAF9 Control - SGC0946 5uM H3K27me3 rep2


title: MLLAF9 Control - VTP50469 500nM H3K27me3 rep2


title: MLLAF9 Control - DMSO H3K27me3 rep2


title: BAPN+SB273005-4

data_processing:
A cDNA library constructed by technology from the pooled RNA from samples was sequenced run with Illumina NovaseqTM 6000 sequence platform.
We aligned reads of all samples to the mus musculus reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.2.1) package.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-2.1.6) with default parameters.
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software.
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: mm10
Supplementary files format and content: tab-delimited text file inculde gene FPKM values of each sample
Supplementary files format and content: tab-delimited text file inculde transcript FPKM values of each sample

source_name: ascending aortic tissue

growth_protocol: The ascending TAA tissues of mice were harvested for bulk RNA sequencing.

treatment_protocol: Mice fed with BAPN and integrin αV inhibitors Cilengitide or SB273005, respectively and were sacrificed in the 6th week of modeling.

value: ascending aortic tissue


title: BAPN+SB273005-3


title: BAPN+SB273005-1


title: BAPN+SB273005-2


title: BAPN+Cilengitide-3

value: BAPN+Cilengitide


title: Total RNA-sequencing of Aag2 cells infected with AWK mosquitoes

city: BOSTON

first: NELSON

middle: C

last: LAU

state: MA

address: 72 E Concord St K219, Dept of Biochemistry

department: Biochemistry and Cell Biology

institute: Boston University Chobanian & Avedisian School of Medicine

description: Library name: AeAeg_Aag2_AWK_lRNA

data_processing:
The Mosquioto Small RNA Genomics (MSRG)  pipeline published in PMIDs: 33419731 and 35796973. Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt and Trimmomator. Total RNA reads were also further trimmed by length to 35 nt to be compatable for processing with the MSRG pipeline
Assembly: AaegL5
Supplementary files format and content: tab-delimited text file with Excel extension includes processed counts for each Sample for microRNA genes or protein-coding genes. csv files include RPM values for each Sample mapped to viruses

organism: Aedes aegypti

extract_protocol:
RNA was harvested using the NEB Monarch Total RNA extration kit.  0.5 to 1.0ug of total RNA was used for the construction of sequencing libraries.
Total RNA libraries for RNA-seq were prepared using Zymo RiboFree Zymo-Seq Library Prep Kit following manufacturer's protocols.  Small RNA libraries for microRNA-seq were prepared with the NEBNext Small RNA Library prep kit according to the manufacturer's protocols.


title: Total RNA-sequencing of Aag2 cells infected with BZL mosquitoes

description: Library name: AeAeg_Aag2_BZL_lRNA


title: Total RNA-sequencing of whole mosquitoes: ZIK_LM_Fem_1

description: Library name: ZIK_LM_Fem_1_lRNA

source_name: whole mosquito

value: whole mosquito


title: Total RNA-sequencing of Aag2 cells uninfected

description: Library name: AeAeg_Aag2_Mock_lRNA


title: BAPN+Cilengitide-1


title: Total RNA-sequencing of Aag2 cells infected with KIN mosquitoes

description: Library name: AeAeg_Aag2_KIN_lRNA


title: BAPN+Cilengitide-2


title: BAPN-4

value: BAPN


title: BAPN-3


title: Total RNA-sequencing of whole mosquitoes: WynFL_MDC_Fem

description: Library name: WynFL_MDC_Fem_lRNA


title: Total RNA-sequencing of whole mosquitoes: TW_CC_Male_1

description: Library name: TW_CC_Male_1_lRNA


title: BAPN-2


title: Total RNA-sequencing of whole mosquitoes: TW_CC_Fem_1

description: Library name: TW_CC_Fem_1_lRNA


title: HUDEP-2 Control - DMSO H2KAK119ub

value: Erytheroid


title: BAPN-1


title: PBS-2

value: PBS


title: Total RNA-sequencing of whole mosquitoes: THI_LM_Male_1

description: Library name: THI_LM_Male_1_lRNA


title: Total RNA-sequencing of whole mosquitoes: TiresFL_MDC_Fem_1A

description: Library name: TiresFL_MDC_Fem_1A_lRNA


title: Total RNA-sequencing of whole mosquitoes: ThaiKP_LL_Male

description: Library name: ThaiKP_LL_Male_lRNA


title: PBS-3


title: Total RNA-sequencing of Aag2 cells infected with PZR mosquitoes

description: Library name: AeAeg_Aag2_PZR_lRNA


title: Total RNA-sequencing of whole mosquitoes: ZIK_LM_Male_1

description: Library name: ZIK_LM_Male_1_lRNA


title: PBS-1


title: Timecourse Control - DMSO H3K79me2


title: Total RNA-sequencing of whole mosquitoes: SMFL_MDC_Fem

description: Library name: SMFL_MDC_Fem_lRNA


title: Total RNA-sequencing of whole mosquitoes: PKT_LM_Male_1

description: Library name: PKT_LM_Male_1_lRNA


title: Total RNA-sequencing of whole mosquitoes: PineFL_MDC_Fem

description: Library name: PineFL_MDC_Fem_lRNA


title: Timecourse Control - DMSO input


title: Total RNA-sequencing of whole mosquitoes: ORL-Car_MY_Male_1

description: Library name: ORL-Car_MY_Male_1_lRNA

source_name: mosquito carcass

value: mosquito carcass


title: Timecourse Control - VTP50469 500nM 8h H3K79me2


title: Total RNA-sequencing of whole mosquitoes: THI_LM_Fem_1

description: Library name: THI_LM_Fem_1_lRNA


title: Total RNA-sequencing of whole mosquitoes: ORL-Abd_MY_Fem_1

description: Library name: ORL-Abd_MY_Fem_1_lRNA

source_name: mosquito abdomen

value: mosquito abdomen


title: Total RNA-sequencing of whole mosquitoes: ORL-Abd_MY_Male_1

description: Library name: ORL-Abd_MY_Male_1_lRNA


title: Timecourse Control - VTP50469 500nM 16h H3K79me2


title: Total RNA-sequencing of whole mosquitoes: ORL-Car_MY_Fem_1

description: Library name: ORL-Car_MY_Fem_1_lRNA


title: Total RNA-sequencing of whole mosquitoes: PKT_LM_Fem_1

description: Library name: PKT_LM_Fem_1_lRNA


title: Timecourse Control - VTP50469 500nM 24h H3K79me2


title: Timecourse Control - VTP50469 500nM 8h H3K27me3


title: Timecourse Control - DMSO H3K27me3


title: Timecourse Control - VTP50469 500nM 24h H2AK119ub


title: Total RNA-sequencing of whole mosquitoes: OHI_LM_Male_1

description: Library name: OHI_LM_Male_1_lRNA


title: Timecourse Control - VTP50469 500nM 8h H2AK119ub


title: Timecourse Control - DMSO H2AK119ub


title: Total RNA-sequencing of whole mosquitoes: ThaiKP_LL_Fem

description: Library name: ThaiKP_LL_Fem_lRNA


title: Total RNA-sequencing of whole mosquitoes: OHI_LM_Fem_1

description: Library name: OHI_LM_Fem_1_lRNA


title: NTvKO Control - VTP50469 500nM H3K79me2


title: Total RNA-sequencing of whole mosquitoes: OGD_LM_Male_1

description: Library name: OGD_LM_Male_1_lRNA


title: Timecourse Control - VTP50469 500nM 4h H3K79me2


title: NTvKO Control - SGC0946 5uM H3K79me2


title: Total RNA-sequencing of whole mosquitoes: OGD_LM_Fem_1

description: Library name: OGD_LM_Fem_1_lRNA


title: Total RNA-sequencing of whole mosquitoes: NGO_LM_Male_1

description: Library name: NGO_LM_Male_1_lRNA


title: Timecourse Control - VTP50469 500nM 24h H3K27me3


title: Total RNA-sequencing of whole mosquitoes: OpaFL_MDC_Fem

description: Library name: OpaFL_MDC_Fem_lRNA


title: Total RNA-sequencing of whole mosquitoes: NGO_LM_Fem_1

description: Library name: NGO_LM_Fem_1_lRNA


title: NTvKO PCGF1 KO VTP50469 500nM H3K79me2


title: NTvKO PCGF1 KO DMSO H3K79me2


title: Total RNA-sequencing of whole mosquitoes: Manz_AGS_Fem

description: Library name: Manz_AGS_Fem_lRNA


title: HUDEP-2 Control - DMSO input


title: Total RNA-sequencing of whole mosquitoes: LVP-Car_MY_Male_1

description: Library name: LVP-Car_MY_Male_1_lRNA


title: NTvKO Control - VTP50469 500nM H3K4me3


title: Total RNA-sequencing of whole mosquitoes: LVP-Car_MY_Fem_1

description: Library name: LVP-Car_MY_Fem_1_lRNA


title: NTvKO Control - SGC0946 5uM H3K4me3


title: NTvKO Control - DMSO H3K4me3


title: Total RNA-sequencing of whole mosquitoes: LVP-Abd_MY_Male_1

description: Library name: LVP-Abd_MY_Male_1_lRNA


title: Total RNA-sequencing of whole mosquitoes: LVP-Abd_MY_Fem_1

description: Library name: LVP-Abd_MY_Fem_1_lRNA


title: NTvKO PCGF1 KO VTP50469 500nM H3K4me3


title: Total RNA-sequencing of whole mosquitoes: Lope_LL_Male

description: Library name: Lope_LL_Male_lRNA


title: NTvKO PCGF1 KO DMSO H3K4me3


title: Total RNA-sequencing of whole mosquitoes: Lope_LL_Fem

description: Library name: Lope_LL_Fem_lRNA


title: Total RNA-sequencing of whole mosquitoes: LBV_LM_Male_1

description: Library name: LBV_LM_Male_1_lRNA


title: NTvKO Control - VTP50469 500nM H3K27me3


title: Total RNA-sequencing of whole mosquitoes: LBV_LM_Fem_1

description: Library name: LBV_LM_Fem_1_lRNA


title: NTvKO PCGF1 KO VTP50469 500nM H3K27me3


title: NTvKO Control - SGC0946 5uM H3K27me3


title: NTvKO Control - DMSO H3K27me3


title: NTvKO Control - DMSO H3K79me2


title: Total RNA-sequencing of whole mosquitoes: KUM_LM_Fem_1

description: Library name: KUM_LM_Fem_1_lRNA


title: NTvKO PCGF1 KO SGC0946 5uM H3K79me2


title: Total RNA-sequencing of whole mosquitoes: KIN_LM_Male_1

description: Library name: KIN_LM_Male_1_lRNA


title: Total RNA-sequencing of whole mosquitoes: Manz_AGS_Male

description: Library name: Manz_AGS_Male_lRNA


title: Total RNA-sequencing of whole mosquitoes: KUM_LM_Male_1

description: Library name: KUM_LM_Male_1_lRNA


title: Total RNA-sequencing of whole mosquitoes: KED_LM_Male_1

description: Library name: KED_LM_Male_1_lRNA


title: NTvKO PCGF1 KO DMSO H3K27me3


title: NTvKO Control - SGC0946 5uM H2AK119ub rep2


title: NTvKO PCGF1 KO SGC0946 5uM H3K27me3


title: NTvKO Control - VTP50469 500nM H2AK119ub rep2


title: Total RNA-sequencing of whole mosquitoes: KED_LM_Fem_1

description: Library name: KED_LM_Fem_1_lRNA


title: Total RNA-sequencing of whole mosquitoes: HibFL_MDC_Fem

description: Library name: HibFL_MDC_Fem_lRNA


title: NTvKO Control - DMSO H2AK119ub rep2


title: Total RNA-sequencing of whole mosquitoes: KIN_LM_Fem_1

description: Library name: KIN_LM_Fem_1_lRNA


title: Total RNA-sequencing of whole mosquitoes: HCMVN_AGS_Male_1

description: Library name: HCMVN_AGS_Male_1_lRNA


title: Total RNA-sequencing of whole mosquitoes: HCMVN_AGS_Fem_1

description: Library name: HCMVN_AGS_Fem_1_lRNA


title: NTvKO PCGF1 KO VTP50469 500nM H2AK119ub rep2


title: NTvKO PCGF1 KO SGC0946 5uM H3K4me3


title: NTvKO PCGF1 KO SGC0946 5uM H2AK119ub rep2


title: Total RNA-sequencing of whole mosquitoes: HCMVN_AGS_Fem_2

description: Library name: HCMVN_AGS_Fem_2_lRNA


title: NTvKO Control - DMSO input3


title: Total RNA-sequencing of whole mosquitoes: HanVN_AGS_Male_2

description: Library name: HanVN_AGS_Male_2_lRNA


title: NTvKO PCGF1 KO DMSO H2AK119ub rep2


title: NTvKO PCGF1 KO DMSO input


title: Total RNA-sequencing of whole mosquitoes: HanVN_AGS_Male_1

description: Library name: HanVN_AGS_Male_1_lRNA


title: NTvKO Control - DMSO input2


title: Total RNA-sequencing of whole mosquitoes: Guad_LL_Male

description: Library name: Guad_LL_Male_lRNA


title: Total RNA-sequencing of whole mosquitoes: HCMVN_AGS_Male_2

description: Library name: HCMVN_AGS_Male_2_lRNA


title: NTvKO Control - DMSO input1


title: Total RNA-sequencing of whole mosquitoes: HanVN_AGS_Fem_1

description: Library name: HanVN_AGS_Fem_1_lRNA


title: NTvKO Control - SGC0946 5uM H2AK119ub rep1


title: NTvKO PCGF1 KO VTP50469 500nM H2AK119ub rep1


title: NTvKO PCGF1 KO SGC0946 5uM H2AK119ub rep1


title: NTvKO Control - VTP50469 500nM H2AK119ub rep1


title: Total RNA-sequencing of whole mosquitoes: Guad_LL_Fem

description: Library name: Guad_LL_Fem_lRNA


title: Total RNA-sequencing of whole mosquitoes: FL_DB_Male

description: Library name: FL_DB_Male_lRNA


title: Total RNA-sequencing of whole mosquitoes: FL_DB_Fem

description: Library name: FL_DB_Fem_lRNA


title: NTvKO PCGF1 KO DMSO H2AK119ub rep1


title: Total RNA-sequencing of whole mosquitoes: HanVN_AGS_Fem_2

description: Library name: HanVN_AGS_Fem_2_lRNA


title: Total RNA-sequencing of whole mosquitoes: FL_BZ_Fem

description: Library name: FL_BZ_Fem_lRNA


title: Total RNA-sequencing of whole mosquitoes: FL_BZ_Male

description: Library name: FL_BZ_Male_lRNA


title: NTvKO Control - SGC0946 5uM H2AK119ub paired


title: NTvKO Control - DMSO input paired


title: Total RNA-sequencing of whole mosquitoes: FDOH_MDC_Fem_7

description: Library name: FDOH_MDC_Fem_7_lRNA


title: NTvKO Control - DMSO H2AK119ub rep1


title: NTvKO Control - DMSO H2AK119ub paired


title: NTvKO PCGF1 KO VTP50469 500nM H2AK119ub paired


title: Total RNA-sequencing of whole mosquitoes: FDOH_MDC_Fem_5

description: Library name: FDOH_MDC_Fem_5_lRNA


title: Total RNA-sequencing of whole mosquitoes: FDOH_MDC_Fem_6

description: Library name: FDOH_MDC_Fem_6_lRNA


title: Total RNA-sequencing of whole mosquitoes: FDOH_MDC_Fem_4

description: Library name: FDOH_MDC_Fem_4_lRNA


title: NTvKO PCGF1 KO SGC0946 5uM H2AK119ub paired


title: Total RNA-sequencing of mosquito eggs: FL-dorm_BZ_egg

description: Library name: FL-dorm_BZ_egg_lRNA

source_name: mosquito egg

value: mosquito egg


title: NTvKO PCGF1 KO DMSO input paired


title: Total RNA-sequencing of mosquito eggs: FL-active_BZ_egg

description: Library name: FL-active_BZ_egg_lRNA


title: NTvKO PCGF1 KO DMSO H2AK119ub paired


title: MLLAF9 Control - DMSO RING1B


title: NTvKO Control - VTP50469 500nM H2AK119ub paired


title: Total RNA-sequencing of whole mosquitoes: FDOH_MDC_Fem_2

description: Library name: FDOH_MDC_Fem_2_lRNA


title: Total RNA-sequencing of whole mosquitoes: FDOH_MDC_Fem_3

description: Library name: FDOH_MDC_Fem_3_lRNA


title: Total RNA-sequencing of whole mosquitoes: FDOH_MDC_Fem_1

description: Library name: FDOH_MDC_Fem_1_lRNA


title: MLLAF9 Control - VTP50469 500nM MLL1


title: Total RNA-sequencing of whole mosquitoes: FCV_LM_Male_1

description: Library name: FCV_LM_Male_1_lRNA


title: MLLAF9 Control - VTP50469 500nM KDM2B


title: Total RNA-sequencing of whole mosquitoes: FCV_LM_Fem_1

description: Library name: FCV_LM_Fem_1_lRNA


title: MLLAF9 Control - SGC0946 5uM MLL1


title: Total RNA-sequencing of whole mosquitoes: ENT_LM_Male_1

description: Library name: ENT_LM_Male_1_lRNA


title: Total RNA-sequencing of whole mosquitoes: ENT_LM_Fem_1

description: Library name: ENT_LM_Fem_1_lRNA


title: Total RNA-sequencing of whole mosquitoes: CVerd_LL_Fem

description: Library name: CVerd_LL_Fem_lRNA


title: MLLAF9 Control - DMSO KDM2B


title: Total RNA-sequencing of whole mosquitoes: Bangkok_AGS_Male

description: Library name: Bangkok_AGS_Male_lRNA


title: Total RNA-sequencing of whole mosquitoes: CVerd_LL_Male

description: Library name: CVerd_LL_Male_lRNA


title: Total RNA-sequencing of whole mosquitoes: Bangkok_AGS_Fem

description: Library name: Bangkok_AGS_Fem_lRNA


title: MLLAF9 Control - DMSO H3K9ac


title: MLLAF9 Control - SGC0946 5uM H3K9ac


title: MLLAF9 Control - VTP50469 500nM H3K79me2 rep2


title: Total RNA-sequencing of whole mosquitoes: AWK_LM_Male_1

description: Library name: AWK_LM_Male_1_lRNA


title: Total RNA-sequencing of whole mosquitoes: AWK_LM_Fem_1

description: Library name: AWK_LM_Fem_1_lRNA


title: MLLAF9 Control - SGC0946 5uM H3K79me2 rep2


title: MLLAF9 Control - DMSO H3K79me2 rep2


title: MLLAF9 Control - VTP50469 500nM H3K27ac


title: Small RNA-sequencing of Aag2 cells infected with KIN mosquitoes (rep2)

description: Library name: AeAeg_Aag2_KIN_4_sRNA

library_source: other

molecule: other


title: Small RNA-sequencing of Aag2 cells uninfected (rep3)

description: Library name: AeAeg_Aag2_Mock_3_sRNA


title: Small RNA-sequencing of Aag2 cells infected with PZR mosquitoes

description: Library name: AeAeg_Aag2_PZR_sRNA


title: MLLAF9 Control - DMSO H3K27ac


title: Small RNA-sequencing of Aag2 cells uninfected

description: Library name: AeAeg_Aag2_Mock_sRNA


title: MLLAF9 Control - SGC0946 5uM H3K27ac


title: MLLAF9 Control - VTP50469 500nM H3K9ac


title: MLLAF9 Control - DMSO MLL1


title: Small RNA-sequencing of Aag2 cells uninfected (rep4)

description: Library name: AeAeg_Aag2_Mock_4_sRNA


title: MLLAF9 Control - VTP50469 500nM H2AK120ub


title: MLLAF9 Control - SGC0946 5uM KDM2B


title: Small RNA-sequencing of Aag2 cells infected with KIN mosquitoes

description: Library name: AeAeg_Aag2_KIN_sRNA


title: MLLAF9 Control - DMSO H2AK120ub


title: MLLAF9 Control - SGC0946 5uM H2AK120ub


title: MLLAF9 Control - VTP50469 500nM H2AK119ub rep2


title: Small RNA-sequencing of Aag2 cells infected with AWK mosquitoes

description: Library name: AeAeg_Aag2_AWK_sRNA


title: Small RNA-sequencing of Aag2 cells infected with BZL mosquitoes (rep2)

description: Library name: AeAeg_Aag2_BZL_2_sRNA


title: Small RNA-sequencing of whole mosquito: ZIK_LM_Male_2

description: Library name: ZIK_LM_Male_2_sRNA


title: MLLAF9 Control - DMSO H2AK119ub rep2


title: MLLAF9 Control - SGC0946 5uM H2AK119ub rep2


title: Small RNA-sequencing of Aag2 cells infected with BZL mosquitoes

description: Library name: AeAeg_Aag2_BZL_sRNA


title: MLLAF9 Control - DMSO input for ac


title: Small RNA-sequencing of whole mosquito: ZIK_LM_Male_1

description: Library name: ZIK_LM_Male_1_sRNA


title: Small RNA-sequencing of whole mosquito: ZIK_LM_Fem_2

description: Library name: ZIK_LM_Fem_2_sRNA


title: Small RNA-sequencing of whole mosquito: ZIK_LM_Fem_1

description: Library name: ZIK_LM_Fem_1_sRNA


title: MLLAF9 Control - SGC0946 5uM H3K79me2


title: Small RNA-sequencing of whole mosquito: Yolo4CA_SW_Male

description: Library name: Yolo4CA_SW_Male_sRNA


title: MLLAF9 Control - VTP50469 500nM H3K79me2


title: Small RNA-sequencing of whole mosquito: Yolo3CA_SW_Fem

description: Library name: Yolo3CA_SW_Fem_sRNA


title: MLLAF9 Control - DMSO H3K79me2


title: Small RNA-sequencing of whole mosquito: WynFL_MDC_Fem

description: Library name: WynFL_MDC_Fem_sRNA


title: Small RNA-sequencing of whole mosquito: TW_CC_Fem_1

description: Library name: TW_CC_Fem_1_sRNA


title: MLLAF9 Control - VTP50469 500nM H3K27me3


title: MLLAF9 Control - SGC0946 5uM H3K27me3


title: MLLAF9 Control - SGC0946 5uM H2AK119ub


title: Small RNA-sequencing of whole mosquito: TVCA_AC_Male

description: Library name: TVCA_AC_Male_sRNA


title: Small RNA-sequencing of whole mosquito: TW_CC_Male_2

description: Library name: TW_CC_Male_2_sRNA


title: MLLAF9 Control - SGC0946 5uM VTP50469 500nM H2AK119ub


title: Small RNA-sequencing of whole mosquito: TW_CC_Male_1

description: Library name: TW_CC_Male_1_sRNA


title: Small RNA-sequencing of whole mosquito: TiresFL_MDC_Fem_2A

description: Library name: TiresFL_MDC_Fem_2A_sRNA


title: Small RNA-sequencing of whole mosquito: TiresFL_MDC_Fem_2B

description: Library name: TiresFL_MDC_Fem_2B_sRNA


title: Small RNA-sequencing of whole mosquito: TiresFL_MDC_Fem_2C

description: Library name: TiresFL_MDC_Fem_2C_sRNA


title: MLLAF9 Control - DMSO H3K27me3


title: Small RNA-sequencing of whole mosquito: TW_CC_Fem_2

description: Library name: TW_CC_Fem_2_sRNA


title: MLLAF9 Control - SGC0946 5uM VTP50469 500nM H3K27me3


title: MLLAF9 Control - VTP50469 500nM H2AK119ub


title: MLLAF9 Control - DMSO input for RING1B


title: Small RNA-sequencing of whole mosquito: TVCA_AC_Fem

description: Library name: TVCA_AC_Fem_sRNA


title: MLLAF9 Control - DMSO input

value: 3 days


title: Small RNA-sequencing of whole mosquito: TiresFL_MDC_Fem_1B

description: Library name: TiresFL_MDC_Fem_1B_sRNA


title: Small RNA-sequencing of whole mosquito: TiresFL_MDC_Fem_1C

description: Library name: TiresFL_MDC_Fem_1C_sRNA


title: MLLAF9 Control - DMSO input2


title: MLLAF9 Control - VTP50469 500nM FLAG


title: MLLAF9 Control - DMSO FLAG


title: MLLAF9 Control - DMSO H2AK119ub


title: Small RNA-sequencing of whole mosquito: TiresFL_MDC_Fem_1A

description: Library name: TiresFL_MDC_Fem_1A_sRNA


title: Small RNA-sequencing of whole mosquito: THI_LM_Male_1

description: Library name: THI_LM_Male_1_sRNA


title: ESC Control - SGC0946 5uM H2AK119ub

value: mESC

value: Stemcell


title: Small RNA-sequencing of whole mosquito: THI_LM_Fem_2

description: Library name: THI_LM_Fem_2_sRNA


title: ESC Control - SGC0946 5uM H3K79me2

value: Blood


title: Small RNA-sequencing of whole mosquito: THI_LM_Fem_1

description: Library name: THI_LM_Fem_1_sRNA


title: ESC Control - DMSO H3K79me2


title: Small RNA-sequencing of whole mosquito: THI_LM_Male_2

description: Library name: THI_LM_Male_2_sRNA


title: MV411 Control - VTP50469 500nM rep3

data_processing:
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were aligned to mouse or human genome with STAR aligner
Differential expression analysis was performed using Degust (DEseq2)
Assembly: mm10 and hg38
Supplementary files format and content: .

value: Myeloid


title: Small RNA-sequencing of whole mosquito: ThaiKP_LL_Fem

description: Library name: ThaiKP_LL_Fem_sRNA


title: Small RNA-sequencing of whole mosquito: Tap_KO_abd_NF_1

description: Library name: Tap_KO_abd_NF_1_sRNA


title: ESC Control - DMSO input


title: MV411 Control - VTP50469 500nM rep2


title: MV411 Control - VTP50469 500nM rep1


title: Small RNA-sequencing of whole mosquito: Tap_KO_abd_NF_2

description: Library name: Tap_KO_abd_NF_2_sRNA


title: Small RNA-sequencing of whole mosquito: Tap_KO_abd_24pBF_1

description: Library name: Tap_KO_abd_24pBF_1_sRNA


title: MV411 Control - SGC0946 5uM rep2


title: MLLAF9 Control - SGC0946 5uM FLAG


title: Small RNA-sequencing of whole mosquito: SMFL_MDC_Fem

description: Library name: SMFL_MDC_Fem_sRNA


title: MV411 Control - DMSO rep3


title: Small RNA-sequencing of whole mosquito: Sac09CA_SW_Fem

description: Library name: Sac09CA_SW_Fem_sRNA


title: Small RNA-sequencing of whole mosquito: Sac11CA_SW_Fem

description: Library name: Sac11CA_SW_Fem_sRNA


title: MV411 Control - SGC0946 5uM rep1


title: ESC Control - DMSO H2KAK119ub


title: Small RNA-sequencing of whole mosquito: ThaiKP_LL_Male

description: Library name: ThaiKP_LL_Male_sRNA


title: MV411 Control - DMSO rep1


title: Small RNA-sequencing of whole mosquito: Riv4CA_AC_Fem

description: Library name: Riv4CA_AC_Fem_sRNA


title: MV411 Control - DMSO rep2


title: Small RNA-sequencing of whole mosquito: Sac07CA_SW_Fem

description: Library name: Sac07CA_SW_Fem_sRNA


title: MV411 PCGF1 KO VTP50469 500nM rep3


title: MV411 PCGF1 KO VTP50469 500nM rep2


title: MV411 Control - SGC0946 5uM rep3


title: Small RNA-sequencing of whole mosquito: Riv2CA_AC_Fem

description: Library name: Riv2CA_AC_Fem_sRNA


title: MV411 PCGF1 KO VTP50469 500nM rep1


title: Small RNA-sequencing of whole mosquito: Rec_KO_mgt_48pBF_123

description: Library name: Rec_KO_mgt_48pBF_123_sRNA

source_name: mosquito midgut

value: mosquito midgut


title: Small RNA-sequencing of whole mosquito: Rec_KO_abd_NF_123

description: Library name: Rec_KO_abd_NF_123_sRNA


title: MV411 PCGF1 KO SGC0946 5uM rep3


title: Small RNA-sequencing of whole mosquito: Tap_KO_abd_24pBF_2

description: Library name: Tap_KO_abd_24pBF_2_sRNA


title: Small RNA-sequencing of whole mosquito: Rec_KO_mgt_NF_123

description: Library name: Rec_KO_mgt_NF_123_sRNA


title: Small RNA-sequencing of whole mosquito: Rec_KO_abd_48pBF_123

description: Library name: Rec_KO_abd_48pBF_123_sRNA


title: Small RNA-sequencing of whole mosquito: PZR_KO_mgt_NF_123

description: Library name: PZR_KO_mgt_NF_123_sRNA


title: MV411 PCGF1 KO SGC0946 5uM rep2


title: MV411 PCGF1 KO DMSO rep3


title: MV411 PCGF1 KO SGC0946 5uM rep1


title: MV411 PCGF1 KO DMSO rep2


title: Small RNA-sequencing of whole mosquito: PZR_KO_mgt_48pBF_123

description: Library name: PZR_KO_mgt_48pBF_123_sRNA


title: Small RNA-sequencing of whole mosquito: PZR_KO_abd_NF_123

description: Library name: PZR_KO_abd_NF_123_sRNA


title: Small RNA-sequencing of whole mosquito: PZR_KO_abd_48pBF_123

description: Library name: PZR_KO_abd_48pBF_123_sRNA


title: Small RNA-sequencing of whole mosquito: PKT_LM_Male_2

description: Library name: PKT_LM_Male_2_sRNA


title: MV411 BCOR KO VTP50469 500nM rep2


title: MV411 BCOR KO VTP50469 500nM rep3


title: MV411 BCOR KO SGC0946 5uM rep3


title: Small RNA-sequencing of whole mosquito: PKT_LM_Male_1

description: Library name: PKT_LM_Male_1_sRNA


title: Small RNA-sequencing of whole mosquito: PineFL_MDC_Fem

description: Library name: PineFL_MDC_Fem_sRNA


title: MV411 BCOR KO SGC0946 5uM rep2


title: Small RNA-sequencing of whole mosquito: PKT_LM_Fem_1

description: Library name: PKT_LM_Fem_1_sRNA


title: Small RNA-sequencing of whole mosquito: PKT_LM_Fem_2

description: Library name: PKT_LM_Fem_2_sRNA


title: MV411 BCOR KO DMSO rep2


title: MV411 BCOR KO VTP50469 500nM rep1


title: Small RNA-sequencing of whole mosquito: ORL-Car_MY_Male_2

description: Library name: ORL-Car_MY_Male_2_sRNA


title: MV411 BCOR KO SGC0946 5uM rep1


title: MV411 BCOR KO DMSO rep3


title: Small RNA-sequencing of whole mosquito: ORL-Abd_MY_Male_2

description: Library name: ORL-Abd_MY_Male_2_sRNA


title: Small RNA-sequencing of whole mosquito: ORL-Car_MY_Fem_2

description: Library name: ORL-Car_MY_Fem_2_sRNA


title: ESC Control - SGC0946 5uM rep3


title: Small RNA-sequencing of whole mosquito: ORL-Car_MY_Fem_1

description: Library name: ORL-Car_MY_Fem_1_sRNA


title: Small RNA-sequencing of whole mosquito: ORL-Abd_MY_Male_1

description: Library name: ORL-Abd_MY_Male_1_sRNA


title: Small RNA-sequencing of whole mosquito: ORL-Car_MY_Male_1

description: Library name: ORL-Car_MY_Male_1_sRNA


title: ESC Control - SGC0946 5uM rep2


title: ESC Control - SGC0946 5uM rep1


title: Small RNA-sequencing of whole mosquito: ORL-Abd_MY_Fem_1

description: Library name: ORL-Abd_MY_Fem_1_sRNA


title: ESC Control - DMSO rep4


title: Small RNA-sequencing of whole mosquito: OpaFL_MDC_Fem

description: Library name: OpaFL_MDC_Fem_sRNA


title: Small RNA-sequencing of whole mosquito: ORL-Abd_MY_Fem_2

description: Library name: ORL-Abd_MY_Fem_2_sRNA


title: ESC Control - DMSO rep3


title: Small RNA-sequencing of whole mosquito: OHI_LM_Male_2

description: Library name: OHI_LM_Male_2_sRNA


title: ESC Control - DMSO rep2


title: ESC Control - DMSO rep1


title: Small RNA-sequencing of whole mosquito: OHI_LM_Fem_2

description: Library name: OHI_LM_Fem_2_sRNA


title: MOLM13 PCGF1/BCOR KO VTP50469 96h 500nM rep3


title: MV411 BCOR KO DMSO rep1


title: ESC Control - SGC0946 5uM rep4


title: Small RNA-sequencing of whole mosquito: OGD_LM_Male_2

description: Library name: OGD_LM_Male_2_sRNA


title: MOLM13 PCGF1/BCOR KO VTP50469 96+48w 500nM rep3


title: MV411 PCGF1 KO DMSO rep1


title: Small RNA-sequencing of whole mosquito: OGD_LM_Fem_2

description: Library name: OGD_LM_Fem_2_sRNA


title: Small RNA-sequencing of whole mosquito: OHI_LM_Male_1

description: Library name: OHI_LM_Male_1_sRNA


title: Small RNA-sequencing of whole mosquito: OGD_LM_Fem_1

description: Library name: OGD_LM_Fem_1_sRNA


title: Small RNA-sequencing of whole mosquito: OHI_LM_Fem_1

description: Library name: OHI_LM_Fem_1_sRNA


title: MOLM13 PCGF1/BCOR KO Washout DMSO rep3


title: MOLM13 PCGF1/BCOR KO VTP50469 96+96w 500nM rep3


title: MOLM13 Control - VTP50469 96+96w 500nM rep3


title: MOLM13 Control - VTP50469 96+48w 500nM rep3


title: Small RNA-sequencing of whole mosquito: NolaJ1-Ov_TC_Fem

description: Library name: NolaJ1-Ov_TC_Fem_sRNA

source_name: mosquito ovary

value: mosquito ovary


title: Small RNA-sequencing of whole mosquito: NGO_LM_Male_1

description: Library name: NGO_LM_Male_1_sRNA


title: MOLM13 PCGF1/BCOR KO VTP50469 96h 500nM rep2


title: MOLM13 Control - VTP50469 96h 500nM rep2


title: Small RNA-sequencing of whole mosquito: OGD_LM_Male_1

description: Library name: OGD_LM_Male_1_sRNA


title: Small RNA-sequencing of whole mosquito: NGO_LM_Male_2

description: Library name: NGO_LM_Male_2_sRNA


title: MOLM13 Control - VTP50469 96+48w 500nM rep2


title: Small RNA-sequencing of whole mosquito: Manz_AGS_Male

description: Library name: Manz_AGS_Male_sRNA


title: Small RNA-sequencing of whole mosquito: NGO_LM_Fem_2

description: Library name: NGO_LM_Fem_2_sRNA


title: MOLM13 PCGF1/BCOR KO VTP50469 96+96w 500nM rep2


title: Small RNA-sequencing of whole mosquito: NGO_LM_Fem_1

description: Library name: NGO_LM_Fem_1_sRNA


title: Small RNA-sequencing of whole mosquito: MiaFL_MD_Fem

description: Library name: MiaFL_MD_Fem_sRNA


title: MOLM13 Control - VTP50469 96+96w 500nM rep2


title: MOLM13 Control - Washout DMSO rep3


title: MOLM13 PCGF1/BCOR KO VTP50469 96+96w 500nM rep1


title: MOLM13 PCGF1/BCOR KO VTP50469 96+48w 500nM rep2


title: MOLM13 PCGF1/BCOR KO VTP50469 96+48w 500nM rep1


title: Small RNA-sequencing of whole mosquito: Manz_AGS_Fem

description: Library name: Manz_AGS_Fem_sRNA


title: MOLM13 PCGF1/BCOR KO Washout DMSO rep2


title: MOLM13 PCGF1/BCOR KO Washout DMSO rep1


title: Small RNA-sequencing of whole mosquito: Mad9CA_TR_Fem

description: Library name: Mad9CA_TR_Fem_sRNA


title: Small RNA-sequencing of whole mosquito: MiaFL_MD_Male

description: Library name: MiaFL_MD_Male_sRNA


title: MOLM13 Control - VTP50469 96h 500nM rep3


title: MOLM13 Control - Washout DMSO rep2


title: Small RNA-sequencing of whole mosquito: Mad8CA_TR_Male

description: Library name: Mad8CA_TR_Male_sRNA


title: MOLM13 PCGF1/BCOR KO VTP50469 96h 500nM rep1


title: Small RNA-sequencing of whole mosquito: Mad7CA_TR_Fem

description: Library name: Mad7CA_TR_Fem_sRNA


title: Small RNA-sequencing of whole mosquito: Mad6CA_TR_Male

description: Library name: Mad6CA_TR_Male_sRNA


title: MOLM13 Control - VTP50469 96h 500nM rep1


title: Small RNA-sequencing of whole mosquito: Mad5CA_TR_Male

description: Library name: Mad5CA_TR_Male_sRNA


title: MOLM13 Control - VTP50469 96+48w 500nM rep1


title: Small RNA-sequencing of whole mosquito: Mad11CA_TR_Fem

description: Library name: Mad11CA_TR_Fem_sRNA


title: Small RNA-sequencing of whole mosquito: Mad10CA_TR_Male

description: Library name: Mad10CA_TR_Male_sRNA


title: Small RNA-sequencing of whole mosquito: Mad3CA_TR_Fem

description: Library name: Mad3CA_TR_Fem_sRNA


title: MOLM13 Control - VTP50469 96+96w 500nM rep1


title: MOLM13 PCGF1 KO VTP50469 500nM rep1


title: Small RNA-sequencing of whole mosquito: Mad4CA_TR_Fem

description: Library name: Mad4CA_TR_Fem_sRNA


title: Small RNA-sequencing of whole mosquito: LVP-Car_MY_Male_2

description: Library name: LVP-Car_MY_Male_2_sRNA


title: MOLM13 Control - Washout DMSO rep1


title: Small RNA-sequencing of whole mosquito: Mad2CA_TR_Male

description: Library name: Mad2CA_TR_Male_sRNA


title: Small RNA-sequencing of whole mosquito: LVP-Car_MY_Male_1

description: Library name: LVP-Car_MY_Male_1_sRNA


title: Small RNA-sequencing of whole mosquito: LVP-Car_MY_Fem_2

description: Library name: LVP-Car_MY_Fem_2_sRNA


title: Small RNA-sequencing of whole mosquito: LVP-Abd_MY_Male_2

description: Library name: LVP-Abd_MY_Male_2_sRNA


title: MOLM13 PCGF1 KO DMSO rep3


title: Small RNA-sequencing of whole mosquito: LVP-Abd_MY_Male_1

description: Library name: LVP-Abd_MY_Male_1_sRNA


title: MOLM13 PCGF1 KO VTP50469 500nM rep2


title: MOLM13 PCGF1 KO SGC0946 5uM rep2


title: MOLM13 PCGF1 KO SGC0946 5uM rep1


title: MOLM13 PCGF1 KO DMSO rep2


title: MOLM13 PCGF1 KO DMSO rep1


title: Small RNA-sequencing of whole mosquito: LVP-Abd_MY_Fem_2

description: Library name: LVP-Abd_MY_Fem_2_sRNA


title: Small RNA-sequencing of whole mosquito: LVP-Abd_MY_Fem_1

description: Library name: LVP-Abd_MY_Fem_1_sRNA


title: MOLM13 PCGF1 KO VTP50469 500nM rep3


title: Small RNA-sequencing of whole mosquito: Mad1CA_TR_Fem

description: Library name: Mad1CA_TR_Fem_sRNA


title: Small RNA-sequencing of whole mosquito: Lope_LL_Male

description: Library name: Lope_LL_Male_sRNA


title: Small RNA-sequencing of whole mosquito: Lope_LL_Fem

description: Library name: Lope_LL_Fem_sRNA


title: MOLM13 Control - VTP50469 500nM rep2


title: MOLM13 PCGF1 KO SGC0946 5uM rep3


title: MOLM13 Control - VTP50469 500nM rep1


title: MOLM13 Control - SGC0946 5uM rep3


title: Small RNA-sequencing of whole mosquito: LBV_LM_Male_1

description: Library name: LBV_LM_Male_1_sRNA


title: Small RNA-sequencing of whole mosquito: LBV_LM_Male_2

description: Library name: LBV_LM_Male_2_sRNA


title: MOLM13 Control - SGC0946 5uM rep2


title: Small RNA-sequencing of whole mosquito: LBV_LM_Fem_2

description: Library name: LBV_LM_Fem_2_sRNA


title: MOLM13 Control - SGC0946 5uM rep1


title: Small RNA-sequencing of whole mosquito: KUM_LM_Male_2

description: Library name: KUM_LM_Male_2_sRNA


title: Small RNA-sequencing of whole mosquito: LBV_LM_Fem_1

description: Library name: LBV_LM_Fem_1_sRNA


title: MOLM13 Control - DMSO rep3


title: Small RNA-sequencing of whole mosquito: LVP-Car_MY_Fem_1

description: Library name: LVP-Car_MY_Fem_1_sRNA


title: MOLM13 Control - DMSO rep1


title: MOLM13 Control - DMSO rep2


title: MOLM13 BCOR KO VTP50469 500nM rep2


title: Small RNA-sequencing of whole mosquito: KUM_LM_Male_1

description: Library name: KUM_LM_Male_1_sRNA


title: Small RNA-sequencing of whole mosquito: KUM_LM_Fem_2

description: Library name: KUM_LM_Fem_2_sRNA


title: MOLM13 BCOR KO VTP50469 500nM rep3


title: Small RNA-sequencing of whole mosquito: KIN_LM_Male_2

description: Library name: KIN_LM_Male_2_sRNA


title: Small RNA-sequencing of whole mosquito: KUM_LM_Fem_1

description: Library name: KUM_LM_Fem_1_sRNA


title: MOLM13 BCOR KO VTP50469 500nM rep1


title: MOLM13 Control - VTP50469 500nM rep3


title: Small RNA-sequencing of whole mosquito: KIN_LM_Fem_2

description: Library name: KIN_LM_Fem_2_sRNA


title: MOLM13 BCOR KO SGC0946 5uM rep3


title: MOLM13 BCOR KO SGC0946 5uM rep2


title: Small RNA-sequencing of whole mosquito: KED_LM_Male_1

description: Library name: KED_LM_Male_1_sRNA


title: Small RNA-sequencing of whole mosquito: KED_LM_Male_2

description: Library name: KED_LM_Male_2_sRNA


title: MOLM13 BCOR KO DMSO rep3


title: MOLM13 BCOR KO DMSO rep2


title: K562 Control - SGC0946 5uM rep4


title: Small RNA-sequencing of whole mosquito: KED_LM_Fem_1

description: Library name: KED_LM_Fem_1_sRNA


title: Small RNA-sequencing of whole mosquito: KED_LM_Fem_2

description: Library name: KED_LM_Fem_2_sRNA


title: K562 Control - SGC0946 5uM rep3


title: K562 Control - SGC0946 5uM rep2


title: Small RNA-sequencing of whole mosquito: JVCA_AC_Fem

description: Library name: JVCA_AC_Fem_sRNA


title: Small RNA-sequencing of whole mosquito: JVCA_AC_Male

description: Library name: JVCA_AC_Male_sRNA


title: K562 Control - SGC0946 5uM rep1


title: Small RNA-sequencing of whole mosquito: HibFL_MDC_Fem

description: Library name: HibFL_MDC_Fem_sRNA


title: K562 Control - DMSO rep4


title: Small RNA-sequencing of whole mosquito: HGCA_AC_Fem

description: Library name: HGCA_AC_Fem_sRNA


title: Small RNA-sequencing of whole mosquito: HGCA_AC_Male

description: Library name: HGCA_AC_Male_sRNA


title: Small RNA-sequencing of whole mosquito: HCMVN_AGS_Male_2

description: Library name: HCMVN_AGS_Male_2_sRNA


title: Small RNA-sequencing of whole mosquito: KIN_LM_Male_1

description: Library name: KIN_LM_Male_1_sRNA


title: K562 Control - DMSO rep3


title: Small RNA-sequencing of whole mosquito: HCMVN_AGS_Male_1

description: Library name: HCMVN_AGS_Male_1_sRNA


title: K562 Control - DMSO rep2


title: Small RNA-sequencing of whole mosquito: HCMVN_AGS_Fem_2

description: Library name: HCMVN_AGS_Fem_2_sRNA


title: HUDEP-2 Control - SGC0946 5uM rep4


title: K562 Control - DMSO rep1


title: HUDEP-2 Control - SGC0946 5uM rep3


title: MOLM13 BCOR KO SGC0946 5uM rep1


title: Small RNA-sequencing of whole mosquito: HCMVN_AGS_Fem_1

description: Library name: HCMVN_AGS_Fem_1_sRNA


title: Small RNA-sequencing of whole mosquito: HanVN_AGS_Male_2

description: Library name: HanVN_AGS_Male_2_sRNA


title: Small RNA-sequencing of whole mosquito: KIN_LM_Fem_1

description: Library name: KIN_LM_Fem_1_sRNA


title: MOLM13 BCOR KO DMSO rep1


title: Small RNA-sequencing of whole mosquito: HanVN_AGS_Male_1

description: Library name: HanVN_AGS_Male_1_sRNA


title: Small RNA-sequencing of whole mosquito: HanVN_AGS_Fem_2

description: Library name: HanVN_AGS_Fem_2_sRNA


title: HUDEP-2 Control - SGC0946 5uM rep1


title: HUDEP-2 Control - DMSO rep4


title: Small RNA-sequencing of whole mosquito: HanVN_AGS_Fem_1

description: Library name: HanVN_AGS_Fem_1_sRNA


title: Small RNA-sequencing of whole mosquito: Guad_LL_Male

description: Library name: Guad_LL_Male_sRNA


title: Small RNA-sequencing of whole mosquito: Guad_LL_Fem

description: Library name: Guad_LL_Fem_sRNA


title: HUDEP-2 Control - DMSO rep1


title: Control - VTP50469 300nM 8h rep3


title: HUDEP-2 Control - DMSO rep2


title: Small RNA-sequencing of whole mosquito: GDLS_KO_abd_24pBF_2

description: Library name: GDLS_KO_abd_24pBF_2_sRNA


title: Small RNA-sequencing of whole mosquito: GDLS_KO_abd_NF_2

description: Library name: GDLS_KO_abd_NF_2_sRNA


title: Small RNA-sequencing of whole mosquito: GDLS_KO_abd_24pBF_1

description: Library name: GDLS_KO_abd_24pBF_1_sRNA


title: Small RNA-sequencing of whole mosquito: GDLS_KO_abd_NF_1

description: Library name: GDLS_KO_abd_NF_1_sRNA


title: Control - VTP50469 300nM 48+72w rep3


title: Control - VTP50469 300nM 48h rep3


title: Small RNA-sequencing of whole mosquito: freret_KO_abd_field_3

description: Library name: freret_KO_abd_field_3_sRNA


title: Control - VTP50469 300nM 48+48w rep3


title: Small RNA-sequencing of whole mosquito: freret_KO_abd_field_2

description: Library name: freret_KO_abd_field_2_sRNA


title: HUDEP-2 Control - DMSO rep3


title: HUDEP-2 Control - SGC0946 5uM rep2


title: Control - Washout DMSO rep3


title: Small RNA-sequencing of whole mosquito: freret_KO_abd_field_1

description: Library name: freret_KO_abd_field_1_sRNA


title: Small RNA-sequencing of whole mosquito: FL-Rlater_BZ_Fem

description: Library name: FL-Rlater_BZ_Fem_sRNA


title: Small RNA-sequencing of whole mosquito: FL-Rlater_BZ_Male

description: Library name: FL-Rlater_BZ_Male_sRNA


title: PCGF1 KO VTP50469 300nM 48h rep3


title: PCGF1 KO VTP50469 300nM 8h rep3


title: Small RNA-sequencing of whole mosquito: FL-Freeze_BZ_Male

description: Library name: FL-Freeze_BZ_Male_sRNA


title: PCGF1 KO VTP50469 300nM 8+24w rep3


title: PCGF1 KO VTP50469 300nM 48+72w rep3


title: Small RNA-sequencing of whole mosquito: FL-Freeze_BZ_Fem

description: Library name: FL-Freeze_BZ_Fem_sRNA


title: Control - VTP50469 300nM 8+24w rep3


title: Small RNA-sequencing of mosquito eggs: FL-active_BZ_egg

description: Library name: FL-active_BZ_egg_sRNA


title: PCGF1 KO VTP50469 300nM 48+48w rep3


title: PCGF1 KO VTP50469 300nM 48+24w rep3


title: PCGF1 KO Washout DMSO rep3


title: Small RNA-sequencing of whole mosquito: FL_DB_Fem

description: Library name: FL_DB_Fem_sRNA


title: Small RNA-sequencing of whole mosquito: FL_BZ_Male

description: Library name: FL_BZ_Male_sRNA


title: Small RNA-sequencing of whole mosquito: FL_BZ_Fem

description: Library name: FL_BZ_Fem_sRNA


title: Control - VTP50469 300nM 8h rep2


title: Control - VTP50469 300nM 48+24w rep3


title: Control - VTP50469 300nM 8+24w rep2


title: Control - VTP50469 300nM 48h rep2


title: Control - VTP50469 300nM 48+72w rep2


title: Small RNA-sequencing of whole mosquito: FDOH_MDC_Fem_7

description: Library name: FDOH_MDC_Fem_7_sRNA


title: Small RNA-sequencing of whole mosquito: FDOH_MDC_Fem_6

description: Library name: FDOH_MDC_Fem_6_sRNA


title: Small RNA-sequencing of whole mosquito: FDOH_MDC_Fem_5

description: Library name: FDOH_MDC_Fem_5_sRNA


title: Control - VTP50469 300nM 48+48w rep2


title: Control - VTP50469 300nM 48+24w rep2


title: Small RNA-sequencing of mosquito eggs: FL-dorm_BZ_egg

description: Library name: FL-dorm_BZ_egg_sRNA


title: PCGF1 KO VTP50469 300nM 8h rep2


title: Small RNA-sequencing of whole mosquito: FDOH_MDC_Fem_1

description: Library name: FDOH_MDC_Fem_1_sRNA


title: Control - Washout DMSO rep2


title: PCGF1 KO VTP50469 300nM 8+24w rep2


title: Small RNA-sequencing of whole mosquito: FDOH_MDC_Fem_2

description: Library name: FDOH_MDC_Fem_2_sRNA


title: Small RNA-sequencing of whole mosquito: FDOH_MDC_Fem_4

description: Library name: FDOH_MDC_Fem_4_sRNA


title: Small RNA-sequencing of whole mosquito: FL_DB_Male

description: Library name: FL_DB_Male_sRNA


title: Small RNA-sequencing of whole mosquito: FCV_LM_Male_2

description: Library name: FCV_LM_Male_2_sRNA


title: PCGF1 KO VTP50469 300nM 48+72w rep2


title: Small RNA-sequencing of whole mosquito: FCV_LM_Male_1

description: Library name: FCV_LM_Male_1_sRNA


title: PCGF1 KO VTP50469 300nM 48+48w rep2


title: PCGF1 KO VTP50469 300nM 48h rep2


title: PCGF1 KO VTP50469 300nM 48+24w rep2


title: Small RNA-sequencing of whole mosquito: FCV_LM_Fem_2

description: Library name: FCV_LM_Fem_2_sRNA


title: Small RNA-sequencing of whole mosquito: FCV_LM_Fem_1

description: Library name: FCV_LM_Fem_1_sRNA


title: Small RNA-sequencing of whole mosquito: ENT_LM_Male_2

description: Library name: ENT_LM_Male_2_sRNA


title: Small RNA-sequencing of whole mosquito: ENT_LM_Male_1

description: Library name: ENT_LM_Male_1_sRNA


title: Control - VTP50469 300nM 8+24w rep1


title: PCGF1 KO Washout DMSO rep2


title: Small RNA-sequencing of whole mosquito: ENT_LM_Fem_2

description: Library name: ENT_LM_Fem_2_sRNA


title: Control - VTP50469 300nM 48h rep1


title: Small RNA-sequencing of whole mosquito: ENT_LM_Fem_1

description: Library name: ENT_LM_Fem_1_sRNA


title: Control - VTP50469 300nM 8h rep1


title: Small RNA-sequencing of whole mosquito: FDOH_MDC_Fem_3

description: Library name: FDOH_MDC_Fem_3_sRNA


title: Control - VTP50469 300nM 48+72w rep1


title: Control - VTP50469 300nM 48+48w rep1


title: Small RNA-sequencing of whole mosquito: CVerd_LL_Fem

description: Library name: CVerd_LL_Fem_sRNA


title: Control - VTP50469 300nM 48+24w rep1


title: Small RNA-sequencing of whole mosquito: CamPP_MC_Male

description: Library name: CamPP_MC_Male_sRNA


title: Small RNA-sequencing of whole mosquito: CVerd_LL_Male

description: Library name: CVerd_LL_Male_sRNA


title: Control - Washout DMSO rep1


title: PCGF1 KO VTP50469 300nM 8h rep1


title: Small RNA-sequencing of whole mosquito: CamKS_MC_Male

description: Library name: CamKS_MC_Male_sRNA


title: Small RNA-sequencing of whole mosquito: CamKS_MC_Fem

description: Library name: CamKS_MC_Fem_sRNA


title: PCGF1 KO VTP50469 300nM 8+24w rep1


title: Small RNA-sequencing of whole mosquito: burdette_KO_abd_field_2

description: Library name: burdette_KO_abd_field_2_sRNA


title: PCGF1 KO VTP50469 300nM 48+72w rep1


title: Small RNA-sequencing of whole mosquito: burdette_KO_abd_field_1

description: Library name: burdette_KO_abd_field_1_sRNA


title: Small RNA-sequencing of whole mosquito: Bangkok_AGS_Fem

description: Library name: Bangkok_AGS_Fem_sRNA


title: PCGF1 KO Washout DMSO rep1


title: NTVKO Control - VTP50469 8h 300nM rep3


title: Total RNA-sequencing of C636-NL cells infected with PZR mosquitoes

description: Library name: AeAlb_C636_PZR_lRNA

organism: Aedes albopictus


title: Small RNA-sequencing of whole mosquito: AWK_LM_Male_2

description: Library name: AWK_LM_Male_2_sRNA


title: Total RNA-sequencing of C636-NL cells infected with KIN mosquitoes

description: Library name: AeAlb_C636_KIN_lRNA


title: Small RNA-sequencing of whole mosquito: AWK_LM_Male_1

description: Library name: AWK_LM_Male_1_sRNA


title: Small RNA-sequencing of whole mosquito: AWK_LM_Fem_2

description: Library name: AWK_LM_Fem_2_sRNA


title: Small RNA-sequencing of whole mosquito: CamPP_MC_Fem

description: Library name: CamPP_MC_Fem_sRNA


title: Small RNA-sequencing of C636-ATCC cells infected with PZR mosquitoes

description: Library name: AeAlb_C636-ATCC_PZR_sRNA


title: Small RNA-sequencing of whole mosquito: AWK_LM_Fem_1

description: Library name: AWK_LM_Fem_1_sRNA


title: Small RNA-sequencing of C636-ATCC cells infected with AWK mosquitoes

description: Library name: AeAlb_C636-ATCC_AWK_sRNA


title: NTVKO Control - DMSO rep3


title: NTVKO Control - SGC0946 3uM rep3


title: Small RNA-sequencing of whole mosquito: Bangkok_AGS_Male

description: Library name: Bangkok_AGS_Male_sRNA


title: PCGF1 KO VTP50469 300nM 48+48w rep1


title: Small RNA-sequencing of C636-ATCC cells infected with BZL mosquitoes

description: Library name: AeAlb_C636-ATCC_BZL_sRNA


title: Small RNA-sequencing of C636-ATCC cells infected with KIN mosquitoes

description: Library name: AeAlb_C636-ATCC_KIN_sRNA


title: PCGF1 KO VTP50469 300nM 48h rep1


title: Small RNA-sequencing of whole mosquito: AutoFL_MDC_Fem_1B

description: Library name: AutoFL_MDC_Fem_1B_sRNA


title: Small RNA-sequencing of C636-ATCC cells infected with no infection

description: Library name: AeAlb_C636-ATCC_Mock_sRNA


title: NTVKO PCGF1 KO VTP50469 8h 300nM rep3


title: NTVKO Control - VTP50469 48h 300nM rep3


title: PCGF1 KO VTP50469 300nM 48+24w rep1