title: iPSC-CM D-HCM_d51

first: Nobuyuki

last: Murakoshi

address: 1-1-1 Tennoudai

data_processing:
CLC Genomics Workbench v.22.0
Trimmed sequence reads were mapped to GRCh38/hg38 using CLC Genomics Workbench (parameter: mismatch cost: 2, insersion cost: 3, deletion cost: 3, length fraction: 0.8, similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC Genomics Workbench
Assembly: hg38
Supplementary files format and content: xlst files includes total counts, RPKM, TPM, and CPM

extract_protocol:
RNA was extracted from cell pellets using a RNeasy Mini Kit (QIAGEN).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina

tag: disease

value: dilated phase of hypertrophic cardiomyopathy

value: iPSC-derived cardiomyocytes

value: cardiomyocte differentiation


title: E5.5_Stat3null_3

status: Public on Apr 06 2025

type: SRA

city: Edinburgh

first: Takuya

last: Azami

address: Crewe Road

department: Institute of Genetics and Cancer

country: United Kingdom

institute: The University of Edinburgh

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low quality sequence using Trim Galore
Trimmed sequence reads were mapped to GRCm38/mm10 using HISAT2.
StringTie was used for gene counts.
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: postimplantation epiblast cell

growth_protocol: EpiSCs were cultured in N2B27 supplemented with FGF2, Activin A, and XAV-939 on fibronectin coated plate.

extract_protocol:
For low in put RNA-sequencing, RNA was isolated from indibidual epiblast usisng PicoPure RNA extraction kit (Thermo). Total RNA was isolated using Rneasy Mini Kit (QIAGEN) from EpiSCs.
SMARTer® Stranded Total RNA-Seq Kit v2 was used for the library construction from epiblast sample. NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® was used for the library construction from EpiSCs sample.

tag: tissue

value: postimplantation epiblast cell

tag: Stage

tag: genotype

value: Stat3 null


title: ifl_brm_rep2

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

data_processing:
Zebracall software used for basecalling.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using hisat2.
The expression of genes were obtained with the R package edgeR.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text file include normalized reads for each sample.

organism: Arabidopsis thaliana

source_name: Arabidopsis inflorescences

growth_protocol: Arabidopsis seeds were sown on the Murahsige and Skoog (MS) medium and stratified at 4 ℃ for 2 days. Subsequently, they were grown under long-day conditions (16 h of light at 23 ℃ and 8 h of darkness at 22 ℃).  Inflorescences of 4~5-week-old plants in soil were used for RNA-seq experiments.

extract_protocol:
Total RNA was extracted from Arabidopsis inflorescences with TRIzol reagent (Invitrogen, 15596018).
Sequencing libraries were built for RNA-seq (the single-end 50-bp strategy on the BGISEQ-500 platform).

value: Arabidopsis inflorescences

value: brm-/-


title: E5.5_Stat3null_2


title: iPSC-CM D-HCM_d45

city: Tsukuba

country: Japan

institute: University of Tsukuba

organism: Homo sapiens

tag: cell line

tag: cell type

value: WT

tag: treatment


title: ifl_brm_rep1


title: Ctrl1 ATAC-seq

city: Wuhan

first: Zhenli

last: Huang

address: 1277 Jiefang Avenue,

institute: Huazhong University of Science and Technology

library_source: genomic

data_processing:
The library products were enriched, quantified and sequenced on a DNBSEQ-T7 sequencer (MGI Tech Co., Ltd. China) with the PE150 model.
The quality control of raw data was performed by FastQC (version v0.11.5). Raw sequencing data were filtered through the Trimmomatic (version 0.36) to remove the adaptor and low-quality reads, and were further treated with FastUniq (version 1.1) to eliminate PCR duplications.
The deduplicated clean data were mapped reads to the reference genome Homo_sapiens.GRCh38 (ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/) by bowtie2 software (version 2.2.6). RSeQC（version 2.6）was used to evaluate the mapped reads distribution, coverage uniformity, and strand specificity. MACS2 software（Version 2.1.1）was used for peak calling.
Peak annotation and peak distribution were analyzed by using BedTools (Version 2.25.0). Motif enrichment was calculated using HOMER (version 4.10).
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: xls files with raw gene counts for every gene and every sample

molecule: genomic DNA

source_name: Peripheral blood

growth_protocol: Purified CD4+ T cells were isolated from the peripheral blood of healthy donors and cultured with X-VIVO15 supplemented with 10% fetal bovine serum in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
An ATAC assay was performed  to analyze CD4+GFP+ cell (50000 cells). Cells were treated with cell lysis buffer and nuclei were collected by centrifugation for 5min at 500×g.
The TruePrep DNA Library Prep Kit V2 for Illumina kit  was used for translocation and high-throughput DNA sequencing library construction.

treatment_protocol: Anti-CD3 mAb and anti-CD28 mAb were used to activate CD4+ T cells (1x106/mL), and IL-2 (10 ng/ml) was added into the medium for further culturing. After activation for 24 hours with anti-CD3/CD28 antibodies, CD4+ T cells were transfected with the SMAR1 lentivirus vector or empty vector carrying green fluorescent protein (GFP). GFP-positive cells were sorted by flow cytometry 5 days after transfection.

value: Peripheral blood

value: CD4+T cell

value: CD4+T cell were transfected with empty vector


title: OE2

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean data were mapped to the reference genome of  Homo_sapiens from GRCh38 (ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/) using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: xls files with raw gene counts for every gene and every sample

extract_protocol:
Total RNAs were extracted using TRIzol Reagent (Invitrogen).2 ug of total RNA was used for the construction of sequencing libraries.
2 ug of total RNA  was used for stranded RNA sequencing library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina®  following the manufacturer’s instruction.

treatment_protocol: Anti-CD3 mAb and anti-CD28 mAb were used to activate CD4+ T cells (1x106/mL), and IL-2 (10 ng/ml) was added into the medium for further culturing. After activation for 24 hours with anti-CD3/CD28 antibodies, CD4+ T cells were transfected with the SMAR1 lentivirus vector or empty vector.

value: CD4+T cell were transfected with SMAR1 lentivirus vector


title: iPSC-CM Ctrl_2_d51

value: healthy


title: E5.5_Stat3null_1


title: iPSC-CM D-HCM_d46


title: ifl_WT_rep3

value: wild type


title: Ctrl2


title: ifl_WT_rep2


title: Ctrl1


title: ifl_WT_rep1


title: iPSC-CM Ctrl_1_d51


title: Sirt7scKO, Male mouse, TA muscle, day 3 post injury, biol rep4

status: Public on Apr 05 2025

city: Kyoto

first: Tatsuya

last: Yoshizawa

state: Kyoto

address: 1－5 Shimogamohangi-cho, Sakyo-ku

institute: Kyoto Prefectural University of Medicine

description: Library name: Sirt7scKO4

data_processing:
Raw reads of fastq format were processed using the fastp program for quality control and removal of adapter sequences.
The processed reads were mapped to the mouse reference genome (UCSC GRCm38/mm10) using Bowtie2, and the mapped reads were counted using featureCounts.
Assembly: UCSC GRCm38/mm10
Supplementary files format and content: Excell file includes raw counts for each sample

source_name: TA muscle

extract_protocol:
Total RNA was extracted using a RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
Preparation of RNA library using NEBNext Ultra RNA Library Prep Kit for Illumina (#7530, NEB) and transcriptome sequencing using NovaSeq 6000 (Illumina, Inc) were conducted by a sequencing company, Novogene Co., LTD following Novogene's standard protocols.

treatment_protocol: TA muscle were collected from 7-week-old male WT; Pax7-CreERT2 (Control) and Sirt7fl/fl; Pax7-CreERT2 (Sirt7 scKO) mice at day 3 post injury by BaCl2.

value: TA muscle

value: Sirt7fl/fl; Pax7-CreERT2

tag: Sex

value: male

tag: age

value: day 3 post injury by BaCl2


title: Sirt7scKO, Male mouse, TA muscle, day 3 post injury, biol rep3

description: Library name: Sirt7scKO3


title: Sirt7scKO, Male mouse, TA muscle, day 3 post injury, biol rep2

description: Library name: Sirt7scKO2


title: iPSC-CM Ctrl_2_d48

value: iPSC-derived cardiomyocytes


title: Control, Male mouse, TA muscle, day 3 post injury, biol rep3

description: Library name: Control3

value: WT; Pax7-CreERT2


title: Control, Male mouse, TA muscle, day 3 post injury, biol rep1

description: Library name: Control1


title: RNA-seq Adult cortex CHD8 KI rep4

city: Kanazawa

first: Atsuki

last: Kawamura

state: Ishikawa

address: 13-1 Takaramachi

department: Department of Histology and Cell Biology

institute: Graduate School of Medical Sciences, Kanazawa University

description: Library name: Sample9

data_processing:
Trimming of adapter sequences was performed with Trimmomatic (version 0.39). The total amount of each mRNA was calculated with the use of a series of programs including HISAT2 (version 2.1.0), featureCounts (version 2.0.0), and DESeq2 (version 1.26.0). RNA-seq reads were mapped against the mouse (mm10) genome. GSEA was performed as described previously with the use of GSEA software version 4.3.2.
Assembly: mm10
Supplementary files format and content: Text file includes DESeq2 results

molecule: polyA RNA

source_name: Cortex

extract_protocol:
Total RNA was extracted from the cortex of a male mouse at 8 weeks of age with the use of the TRIzol reagent and PureLink RNA Mini Kit (Thermo Fisher Scientific).
Library preparation and sequencing analysis on an Illumina NovaSeq 6000 were conducted by Novogene Co., Ltd (Beijing, China).

value: Cortex

value: Chd8 KI


title: RNA-seq Adult cortex CHD8 WT rep5

description: Library name: Sample5

value: Wild-type


title: RNA-seq Adult cortex CHD8 KI rep5

description: Library name: Sample10


title: OE1


title: Control, Male mouse, TA muscle, day 3 post injury, biol rep2

description: Library name: Control2


title: RNA-seq Adult cortex CHD8 WT rep3

description: Library name: Sample3


title: RNA-seq Adult cortex CHD8 WT rep1

description: Library name: Sample1


title: RNA-seq Adult cortex CHD8 KI rep3

description: Library name: Sample8


title: ID8 cells, shUSP9X, rep2

city: Tianjin

first: Zhenlei

last: Zhang

address: Qixiangtai Road 22

institute: Tianjin Medical University

description:
Library name: Sample4
shUSP9X-22

data_processing:
Filtering of Clean Reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
Alignment with Ribosome RNA (rRNA). Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
Alignment with Reference Genome. An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
Quantification of Gene Abundance. The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Ensembl_release109
Supplementary files format and content: xls files include Counts and FPKM values for each sample

extract_protocol:
TRIzol (Invitrogen) was used to isolate total RNA from cells. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).And polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: mouse ovarian cancer cells

value: USP9X konckdown


title: ID8 cells, shUSP9X, rep1

description:
Library name: Sample3
shUSP9X-21


title: RNA-seq Adult cortex CHD8 WT rep2

description: Library name: Sample2


title: ID8 cells, shCtrl, rep2

description:
Library name: Sample2
shCtrl-2

value: WT


title: ID8 cells, shCtrl, rep1

description:
Library name: Sample1
shCtrl-1


title: ATAC-seq E14 forebrain CHD8 KI rep3

data_processing:
Trimming of adapter sequences was performed with Trimmomatic (version 0.39).
For RNA-seq analysis, the total amount of each mRNA was calculated with the use of a series of programs including HISAT2 (version 2.1.0), featureCounts (version 2.0.0), and DESeq2 (version 1.26.0). RNA-seq reads were mapped against the mouse (mm10) genome. GSEA was performed as described previously with the use of GSEA software version 4.3.2.
For ChIP-seq analysis, the reads were uniquely mapped to the mouse (mm10) genome with the use of Bowtie software (version 2.2.3), and duplicated reads were removed with samtools (version 1.9). BAM files for four replicates for each genotype were merged with samtools. Signal tracks were generated with bamCoverage in deepTools (3.5.4). S3norm method were used to normalize sequencing depths and signal-to-noise ratios in silico. Markedly enriched regions of the genome were identified with the use of the MACS peak caller (version 3.0.0, with cutoff of P < 1 × 10^–20). Heat map and density profiles were generated with plotHeatmap in deepTools. TOBIAS (Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal) was used for ATAC-seq footprinting analysis with JASPAR CORE 2024 motifs. For differentially accessible region analysis, read coverage for each BAM file were calculated with the use of featureCounts (version 2.0.0) followed by DESeq2 (version 1.26.0). GO analysis of differentially accessible regions (P < 0.01) was performed with the use of GREAT.
For ATAC-seq analysis, the paired-end reads were mapped to the mm10 genome with bowtie, and duplicated reads were removed with samtools (version 1.9). BAM files for four replicates for each genotype were merged with samtools. Signal tracks were generated with bamCoverage in deepTools. S3norm method were used to normalize sequencing depths and signal-to-noise ratios in silico. Markedly enriched regions of the genome were identified with the use of the MACS peak caller (P < 1 × 10^–12). Heat map and density profiles were generated with plotHeatmap in deepTools. Peak annotation was performed with ChIPseeker (1.22.1).
Assembly: mm10
Supplementary files format and content: bigwig files were generated using MACS2; text file includes DESeq2 results

source_name: Forebrain

extract_protocol:
For RNA-seq, total RNA was extracted from the forebrain of a male mouse at E14.5 or E18.5 with the use of the TRIzol reagent and PureLink RNA Mini Kit (Thermo Fisher Scientific). Library preparation and sequencing analysis on an Illumina NovaSeq 6000 were conducted by Novogene Co., Ltd (Beijing, China). For ChIP-seq analysis, purified DNA was used to prepare a library with the use of SMARTer ThruPLEX DNA-Seq kit and SMARTer DNA unique dual index kit. For ATAC-seq analysis, nuclei were used prepare a library with the use of an ATAC-Seq Kit (Active Motif). Sequencing analysis on an Illumina NovaSeq 6000 were conducted by Novogene Co., Ltd.
RNA-seq, ChIP-seq, and ATAC-seq libraries were prepared for sequencing using standard protocols

value: Forebrain


title: ATAC-seq E14 forebrain CHD8 WT rep4


title: Sirt7scKO, Male mouse, TA muscle, day 3 post injury, biol rep1

description: Library name: Sirt7scKO1


title: ATAC-seq E14 forebrain CHD8 WT rep2


title: ATAC-seq E14 forebrain CHD8 KI rep2


title: ChIP-seq CHD8 E14 forebrain CHD8 KI rep3


title: ChIP-seq CHD8 E14 forebrain CHD8 KI rep2


title: RNA-seq Adult cortex CHD8 KI rep2

description: Library name: Sample7


title: RNA-seq Adult cortex CHD8 WT rep4

description: Library name: Sample4


title: ATAC-seq E14 forebrain CHD8 WT rep1


title: ATAC-seq E14 forebrain CHD8 KI rep1


title: ChIP-seq input E14 forebrain CHD8 KI rep3


title: ChIP-seq input E14 forebrain CHD8 WT rep3


title: ChIP-seq input E14 forebrain CHD8 KI rep1


title: ChIP-seq CHD8 E14 forebrain CHD8 WT rep2


title: ChIP-seq CHD8 E14 forebrain CHD8 WT rep3


title: ATAC-seq E14 forebrain CHD8 KI rep4


title: ChIP-seq input E14 forebrain CHD8 KI rep2


title: ChIP-seq input E14 forebrain CHD8 WT rep2


title: ATAC-seq E14 forebrain CHD8 WT rep3


title: ChIP-seq CHD8 E14 forebrain CHD8 KI rep1


title: ChIP-seq input E14 forebrain CHD8 WT rep1


title: RNA-seq Adult cortex CHD8 KI rep1

description: Library name: Sample6


title: RNA-seq E18 forebrain CHD8 KI rep5


title: RNA-seq E18 forebrain CHD8 KI rep4


title: ChIP-seq CHD8 E14 forebrain CHD8 WT rep1


title: RNA-seq E18 forebrain CHD8 KI rep3


title: RNA-seq E18 forebrain CHD8 KI rep2


title: RNA-seq E18 forebrain CHD8 KI rep1


title: RNA-seq E18 forebrain CHD8 WT rep5


title: RNA-seq E18 forebrain CHD8 WT rep1


title: RNA-seq E14 forebrain CHD8 KI rep3


title: RNA-seq E14 forebrain CHD8 KI rep1


title: RNA-seq E14 forebrain CHD8 KI rep4


title: DAC-untreated intracellular DNA

type: genomic

city: Fukui

first: Rie

last: Nishi

address: 23-3 Matsuokashimoaizuki, Eiheiji-cho, Yoshida-gun

institute: University of Fukui

description:
MDS-L
DAC-untreated intracellular DNA

hyb_protocol: Bisulfite converted DNA using the EZ DNA Methylation Kit (Zymo Research) was amplified, fragmented, and hybridized to Illumina Infinium Human Methylation 450 BeadChips using standard Illumina protocols.

scan_protocol: Data was obtained using GenomeStudio software.

data_processing: DNA methylation analysis (data quality control, data normalization, and output of numerical methylation data per region) was performed using the R package (RnBeads).

label: Biotin

source_name: MDS-L

label_protocol: Standard illumina Protocol

extract_protocol: The DNA was extracted from the cells by using a DNeasy Tissue kit (Qiagen)

value: Myelodysplastic syndromes

value: MDS-L

value: floating


title: RNA-seq E14 forebrain CHD8 WT rep3


title: RNA-seq E14 forebrain CHD8 WT rep1


title: RNA-seq E14 forebrain CHD8 WT rep2


title: 7-1

city: Shanghai

first: Yuping

state: Shanghai

department: Shanghai Institute of Immunity and Infection

institute: Chinese acadmy of sciences

description:
Library name: Sample 7
Column name in processed data.txt: WT_2h_1

data_processing:
Trim Galore
Raw sequencing reads were processed using Trim Galore to remove adapters and low-quality sequences.
The cleaned reads were then mapped to the C. auris B8441 genome (version s01-m01-r04, Candida Genome Database) using STAR
Gene expression levels were quantified using featureCounts, and differential expression analysis was performed using DESeq2
Assembly: GCA_002759435.3
Supplementary files format and content: processed data.txt includes raw counts for each sample

organism: Candidozyma auris

source_name: strain

growth_protocol: Isolates of C. auris CBS12767 and the gcn5Δ mutant (three independent clones each) were inoculated into 5 mL of YPD liquid medium and cultured overnight at 300C with shaking at 200 rpm until saturation. The cultures were then diluted to an OD600 of 0.1 in 10 mL of fresh YPD medium and grown at 300C with shaking at 200 rpm for 4 hours.

extract_protocol:
Following sample collection, 400 μL of ice-cold lysis buffer (composed of 0.1 M LiCl, 0.1 M Tris [pH 7.5], 5% SDS, and 2% β-mercaptoethanol) was added to resuspend the samples. Subsequently, 200 μL of acid-washed glass beads and 200 μL of PCIA (pH 4.5, P120617, Aladdin) were incorporated into the mixture. This combination was vortexed at maximum speed at 40C for 5 minutes, then placed on ice for an additional 5 minutes. Following this step, the mixture was centrifuged at maximum speed at 40C for 10 minutes, and the supernatant was carefully collected. To purify the supernatant, it was sequentially extracted with 200 μL of PCIA and then with 300 μL of chloroform. After purification, 1 mL of 100% ethanol was added to precipitate the RNA, which was then incubated at -800C for 30 minutes. The mixture was subsequently centrifuged at maximum speed at 40C for 10 minutes, and the resulting pellet was washed once with 75% ethanol. Finally, the pellet was dissolved in 40 μL of nuclease-free water.
1. Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; 2. mRNA molecules were fragmented into small pieces; 3. The fragmented mRNA was synthesized into first strand cDNA using random primers;  4. The second strand cDNA was synthesized with dUTP instead of dTTP; 5. The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 6. Digest the U-labeled second-strand template with Uracil-DNA-Glycosylase (UDG) and perform PCR amplification; 7. Library quality control; 8. Library circularization;

treatment_protocol: 5 mL of the culture was divided equally into two 15 mL centrifuge tubes. Each tube was treated with either 256 µg/mL fluconazole (FLC) or an equivalent volume of solvent. The cultures were incubated at 300C with shaking at 200 rpm for an additional 2 hours.

value: strain

value: WT cell

value: 256 μg/mL Fluconazole 2 hours


title: RNA-seq E18 forebrain CHD8 WT rep2


title: RNA-seq E14 forebrain CHD8 KI rep5


title: RNA-seq E14 forebrain CHD8 KI rep2


title: RNA-seq E14 forebrain CHD8 WT rep4


title: RNA-seq E18 forebrain CHD8 WT rep3


title: 12-3

description:
Library name: Sample 12
Column name in processed data.txt: gcn5_2h_3

value: mutant cells

value: GCN5 knockout


title: 7-2

description:
Library name: Sample 8
Column name in processed data.txt: WT_2h_2


title: DAC-treated intracellular DNA

description:
MDS-L-DAC
DAC-treated intracellular DNA

value: Long-term culture with DAC


title: 12-2

description:
Library name: Sample 11
Column name in processed data.txt: gcn5_2h_2


title: 12-1

description:
Library name: Sample 10
Column name in processed data.txt: gcn5_2h_1


title: 6-3

description:
Library name: Sample 6
Column name in processed data.txt: gcn5_0h_3

value: DMSO 2 hours


title: 7-3

description:
Library name: Sample 9
Column name in processed data.txt: WT_2h_3


title: 6-2

description:
Library name: Sample 5
Column name in processed data.txt: gcn5_0h_2


title: RNA-seq E18 forebrain CHD8 WT rep4


title: 6-1

description:
Library name: Sample 4
Column name in processed data.txt: gcn5_0h_1


title: 1-3

description:
Library name: Sample 3
Column name in processed data.txt: WT_0h_3

value: WT cells


title: 1-2

description:
Library name: Sample 2
Column name in processed data.txt: WT_0h_2


title: RNA-seq E14 forebrain CHD8 WT rep5


title: 1-1

description:
Library name: Sample 1
Column name in processed data.txt: WT_0h_1


title: Female, Old, B6xFVB, APP-PSEN1-Tardbp, Het, rep2

city: BAR HARBOR

first: Amy

middle: R

last: Dunn

state: ME

address: 600 Main St

country: USA

institute: The Jackson Laboratory

description: Library name: A52730

data_processing:
Rawdata (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: mm39
Supplementary files format and content: FPKM counts in csv format

extract_protocol:
Rneasy mini kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dTTP for non strand specific library or dUTP for strand specific library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: Cerebral cortex

value: Het

value: Female


title: Female, Young, B6xFVB, Control, WT, rep2

description: Library name: A52410


title: Male, Young, B6xWSB, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep1

description: Library name: A52387

value: Male


title: Male, Young, B6xWSB, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep2

description: Library name: A52382


title: Male, Old, B6xWSB, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep1

description: Library name: A52390


title: Female, Old, B6xWSB, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep1

description: Library name: A52372


title: Female, Young, B6xWSB, APP-PSEN1-Mapt-Tardbp-Apoe, Het

description: Library name: A52365


title: Male, Old, B6xWSB, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep2

description: Library name: A52394


title: Male, Old, B6xFVB, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep1

description: Library name: A52341


title: Female, Old, B6xFVB, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep2

description: Library name: A52358


title: Female, Young, B6xFVB, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep2

description: Library name: A52347


title: Male, Young, B6xFVB, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep2

description: Library name: A52334


title: Male, Old, B6xD2, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep2

description: Library name: A52323


title: Female, Old, B6xWSB, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep2

description: Library name: A52371


title: Female, Young, B6xFVB, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep1

description: Library name: A52352


title: Male, Old, B6xFVB, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep2

description: Library name: A52340


title: Female, Old, B6xWSB, Control, WT, rep1

description: Library name: A52407

source_name: Female, Old, B6xWSB, Control, WT, rep1

value: WT


title: Male, Old, B6xD2, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep1

description: Library name: A52322


title: Male, Young, B6xD2, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep1

description: Library name: A52316


title: Male, Young, B6xFVB, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep1

description: Library name: A52329


title: Male, Young, B6xD2, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep2

description: Library name: A52315


title: Female, Old, B6xD2, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep2

description: Library name: A52299


title: Female, Old, B6xD2, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep1

description: Library name: A52300


title: Female, Young, B6xD2, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep1

description: Library name: A52298


title: Male, Old, B6, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep1

description: Library name: A52281


title: Male, Young, B6, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep2

description: Library name: A52280


title: Female, Young, B6xD2, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep2

description: Library name: A52293


title: Male, Young, B6xD2, Control, WT, rep2

description: Library name: A52451

source_name: Male, Young, B6xD2, Control, WT, rep2


title: Female, Old, B6xFVB, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep1

description: Library name: A52353


title: Female, Old, B6, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep2

description: Library name: A52264


title: Female, Young, B6, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep1

description: Library name: A52256


title: Female, Old, B6, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep1

description: Library name: A52263


title: Male, Old, B6, APP-PSEN1-Mapt-Snca-Tardbp, Hom, rep2

description: Library name: A50883

value: Hom


title: Female, Old, B6, APP-PSEN1-Mapt-Snca-Tardbp, Hom, rep1

description: Library name: A50867


title: Male, Old, B6, APP-PSEN1-Mapt-Snca-Tardbp, Hom, rep1

description: Library name: A50882


title: Male, Young, B6xFVB, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep1

description: Library name: A50838


title: Male, Old, B6, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep1

description: Library name: A50402


title: Female, Old, B6, APP-PSEN1-Mapt-Snca-Tardbp, Hom, rep2

description: Library name: A50863


title: Male, Young, B6xD2, Control, WT, rep1

description: Library name: A50498

source_name: Male, Young, B6xD2, Control, WT, rep1


title: Male, Young, B6, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep1

description: Library name: A50396


title: Male, Old, B6, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep2

description: Library name: A50406


title: Female, Old, B6, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep1

description: Library name: A50387


title: Female, Old, B6, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep2

description: Library name: A50386


title: Male, Young, B6, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep2

description: Library name: A50395


title: Female, Young, B6, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep1

description: Library name: A50385


title: Male, Old, B6xWSB, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep1

description: Library name: A50374


title: Male, Young, B6xWSB, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep1

description: Library name: A50362


title: Female, Old, B6xWSB, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep1

description: Library name: A50356


title: Male, Young, B6, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep1

description: Library name: A52275


title: Male, Old, B6, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep2

description: Library name: A52286


title: Male, Old, B6xWSB, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep2

description: Library name: A50373


title: Male, Young, B6xWSB, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep2

description: Library name: A50367


title: Female, Young, B6xWSB, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep2

description: Library name: A50344


title: Female, Young, B6xWSB, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep1

description: Library name: A50349


title: Female, Young, B6, APP-PSEN1-Mapt-Tardbp-Apoe, Het, rep2

description: Library name: A52261


title: Female, Old, B6xWSB, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep2

description: Library name: A50350


title: Male, Old, B6xFVB, APP-PSEN1-Mapt-Snca-Tardbp, Het

description: Library name: A50341


title: Male, Young, B6xFVB, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep2

description: Library name: A50333


title: Female, Young, B6xFVB, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep1

description: Library name: A50329


title: Male, Young, B6xFVB, Control, WT, rep1

description: Library name: A50425

source_name: Male, Young, B6xFVB, Control, WT, rep1


title: Female, Old, B6xFVB, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep2

description: Library name: A50331


title: Female, Young, B6xFVB, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep2

description: Library name: A50325


title: Male, Old, B6xD2, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep1

description: Library name: A50318


title: Male, Old, B6xD2, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep2

description: Library name: A50314


title: Male, Young, B6xD2, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep2

description: Library name: A50312


title: Female, Old, B6xFVB, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep1

description: Library name: A50332


title: Female, Old, B6xD2, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep2

description: Library name: A50295


title: Female, Young, B6xD2, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep2

description: Library name: A50293


title: Male, Young, B6, APP-PSEN1-Tardbp-Apoe, Hom, rep2

description: Library name: A50112


title: Female, Young, B6, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep2

description: Library name: A50379


title: Female, Young, B6, APP-PSEN1-Tardbp-Apoe, Hom, rep1

description: Library name: A50103


title: Female, Young, B6, APP-PSEN1-Tardbp-Apoe, Hom, rep2

description: Library name: A50104


title: Male, Young, B6, APP-PSEN1-Mapt-Tardbp-Apoe, Hom, rep2

description: Library name: A50089


title: Male, Young, B6, APP-PSEN1-Tardbp-Apoe, Hom, rep1

description: Library name: A50122


title: Female, Young, B6xD2, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep1

description: Library name: A50294


title: Female, Young, B6, APP-PSEN1-Mapt-Tardbp-Apoe, Hom, rep1

description: Library name: A50068


title: Male, Young, B6, hAPP, Hom, rep2

description: Library name: A49822

source_name: Male, Young, B6, hAPP, Hom, rep2


title: Female, Young, B6, APP-PSEN1-Mapt-Tardbp-Apoe, Hom, rep2

description: Library name: A50067


title: Male, Old, B6, Control, WT

description: Library name: A48296

source_name: Male, Old, B6, Control, WT


title: Male, Young, B6, Control, WT, rep2

description: Library name: A49911

source_name: Male, Young, B6, Control, WT, rep2


title: Male, Old, B6, hAPP, Hom, rep1

description: Library name: A48290

source_name: Male, Old, B6, hAPP, Hom, rep1


title: Male, Young, B6, APP-PSEN1-Mapt-Tardbp-Apoe, Hom, rep1

description: Library name: A50087


title: Male, Old, B6, hAPP, Hom, rep2

description: Library name: A48289

source_name: Male, Old, B6, hAPP, Hom, rep2


title: Female, Old, B6, hAPP, Hom, rep1

description: Library name: A48281

source_name: Female, Old, B6, hAPP, Hom, rep1


title: Female, Old, B6, hAPP, Hom, rep2

description: Library name: A48277

source_name: Female, Old, B6, hAPP, Hom, rep2


title: Female, Old, B6xD2, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep1

description: Library name: A50301


title: Male, Young, B6, hAPP, Hom, rep1

description: Library name: A48256

source_name: Male, Young, B6, hAPP, Hom, rep1


title: Male, Young, B6xD2, APP-PSEN1-Mapt-Snca-Tardbp, Het, rep1

description: Library name: A50307


title: Female, Old, B6, APP-PSEN1-Tardbp-Apoe, Hom, rep2

description: Library name: A48198


title: Female, Old, B6, APP-PSEN1-Tardbp-Apoe, Hom, rep1

description: Library name: A48196


title: Male, Old, B6, APP-PSEN1-Mapt-Tardbp-Apoe, Hom, rep1

description: Library name: A48229


title: Male, Old, B6, APP-PSEN1-Mapt-Tardbp-Apoe, Hom, rep2

description: Library name: A48222


title: Female, Old, B6, APP-PSEN1-Mapt-Tardbp-Apoe, Hom

description: Library name: A48213


title: Male, Old, B6, APP-PSEN1-Tardbp-Apoe, Hom, rep2

description: Library name: A48181


title: Male, Old, B6, APP-PSEN1-Tardbp-Apoe, Hom, rep1

description: Library name: A48184


title: Male, Young, B6, APP-PSEN1-Tardbp, Hom, rep2

description: Library name: A46985


title: Female, Young, B6, APP-PSEN1-Tardbp, Hom, rep1

description: Library name: A46971


title: Female, Young, B6, APP-PSEN1-Tardbp, Hom, rep2

description: Library name: A46972


title: Female, Young, B6, hAPP, Hom, rep1

description: Library name: A45968

source_name: Female, Young, B6, hAPP, Hom, rep1


title: Female, Young, B6, Control, WT, rep1

description: Library name: A45956

source_name: Female, Young, B6, Control, WT, rep1


title: Male, Young, B6, APP-PSEN1-Mapt-Tardbp, Hom, rep2

description: Library name: A44243


title: Male, Old, B6, APP-PSEN1-Tardbp, Hom, rep2

description: Library name: A45223


title: Female, Young, B6, APP-PSEN1-Mapt-Tardbp, Hom

description: Library name: A44242


title: Male, Young, B6, APP-PSEN1-Mapt, Hom, rep2

description: Library name: A44224


title: Male, Young, B6, APP-PSEN1-Mapt, Hom, rep1

description: Library name: A44227


title: Female, Young, B6, APP-PSEN1-Mapt, Hom, rep2

description: Library name: A44213


title: Female, Young, B6, APP-PSEN1-Mapt, Hom, rep1

description: Library name: A44201


title: Female, Old, B6, Control, WT, rep1

description: Library name: A48282

source_name: Female, Old, B6, Control, WT, rep1


title: Male, Young, B6, APP-PSEN1-Mapt-Tardbp, Hom, rep1

description: Library name: A44258


title: Male, Young, B6, APP-PSEN1-Snca, Hom, rep2

description: Library name: A44198


title: Male, Young, B6, APP-PSEN1-Snca, Hom, rep1

description: Library name: A44199


title: Female, Young, B6, APP-PSEN1-Snca, Hom, rep2

description: Library name: A44172


title: Female, Young, B6, Control, WT, rep2

description: Library name: A44128

source_name: Female, Young, B6, Control, WT, rep2


title: Male, Young, B6, APP-PSEN1-Tardbp-Apoe, Het, rep2

description: Library name: A44012


title: Male, Old, B6, APP-PSEN1-Tardbp-Apoe, Het, rep2

description: Library name: A44007


title: Female, Young, B6, APP-PSEN1-Snca, Hom, rep1

description: Library name: A44170


title: Male, Young, B6, APP-PSEN1-Tardbp-Apoe, Het, rep1

description: Library name: A44001


title: Male, Young, B6, APP-PSEN1-Tardbp, Hom, rep1

description: Library name: A46987


title: Female, Young, B6, hAPP, Hom, rep2

description: Library name: A44123

source_name: Female, Young, B6, hAPP, Hom, rep2


title: Female, Old, B6, APP-PSEN1-Tardbp-Apoe, Het

description: Library name: A43993


title: Male, Old, B6, APP-PSEN1-Tardbp, Hom, rep1

description: Library name: A45221


title: Male, Young, B6xFVB, APP-PSEN1-Tardbp-Apoe, Het, rep2

description: Library name: A43982


title: Male, Old, B6, APP-PSEN1-Tardbp-Apoe, Het, rep1

description: Library name: A44003


title: Female, Young, B6, APP-PSEN1-Tardbp-Apoe, Het, rep1

description: Library name: A43987


title: Male, Old, B6xFVB, APP-PSEN1-Tardbp-Apoe, Het, rep1

description: Library name: A43974


title: Male, Young, B6xFVB, APP-PSEN1-Tardbp-Apoe, Het, rep1

description: Library name: A43971


title: Male, Old, B6xFVB, APP-PSEN1-Tardbp-Apoe, Het, rep2

description: Library name: A43973


title: Female, Young, B6, APP-PSEN1-Tardbp-Apoe, Het, rep2

description: Library name: A43986


title: Female, Young, B6xFVB, APP-PSEN1-Tardbp-Apoe, Het, rep1

description: Library name: A43967


title: Female, Young, B6xFVB, APP-PSEN1-Tardbp-Apoe, Het, rep2

description: Library name: A43966


title: Female, Old, B6xFVB, APP-PSEN1-Tardbp-Apoe, Het, rep1

description: Library name: A43964


title: Female, Young, B6xD2, APP-PSEN1-Tardbp-Apoe, Het, rep2

description: Library name: A43937


title: Female, Young, B6xD2, APP-PSEN1-Tardbp-Apoe, Het, rep1

description: Library name: A43927


title: Male, Young, B6xWSB, APP-PSEN1-Tardbp-Apoe, Het, rep2

description: Library name: A43902


title: Male, Young, B6xD2, APP-PSEN1-Tardbp-Apoe, Het, rep2

description: Library name: A43955


title: Male, Young, B6xD2, APP-PSEN1-Tardbp-Apoe, Het, rep1

description: Library name: A43954


title: Male, Young, B6xWSB, APP-PSEN1-Tardbp-Apoe, Het, rep1

description: Library name: A43911


title: Female, Young, B6xWSB, APP-PSEN1-Tardbp-Apoe, Het, rep1

description: Library name: A43896


title: Female, Old, B6xWSB, APP-PSEN1-Tardbp-Apoe, Het

description: Library name: A43889


title: Male, Old, B6xD2, Control, WT

description: Library name: A43637

source_name: Male, Old, B6xD2, Control, WT


title: Female, Young, B6xWSB, APP-PSEN1-Tardbp-Apoe, Het, rep2

description: Library name: A43887


title: Female, Old, B6xD2, Control, WT, rep2

description: Library name: A43628

source_name: Female, Old, B6xD2, Control, WT, rep2


title: Female, Old, B6, Control, WT, rep2

description: Library name: A43394

source_name: Female, Old, B6, Control, WT, rep2


title: Male, Old, B6, APP-PSEN1-Mapt, Hom, rep1

description: Library name: A42458


title: Male, Old, B6, APP-PSEN1-Mapt, Hom, rep2

description: Library name: A42459


title: Male, Old, B6, APP-PSEN1-Snca, Hom, rep1

description: Library name: A42483


title: Female, Old, B6, APP-PSEN1-Mapt, Hom, rep1

description: Library name: A42441


title: Female, Old, B6xFVB, APP-PSEN1-Tardbp-Apoe, Het, rep2

description: Library name: A43963


title: Male, Old, B6, APP-PSEN1-Mapt-Tardbp, Hom, rep1

description: Library name: A42432


title: Female, Old, B6, APP-PSEN1-Mapt-Tardbp, Hom, rep1

description: Library name: A42406


title: Male, Old, B6xD2, APP-PSEN1-Snca, Het, rep2

description: Library name: A41873


title: Female, Old, B6, APP-PSEN1-Mapt, Hom, rep2

description: Library name: A42438


title: Male, Young, B6xD2, APP-PSEN1-Snca, Het, rep2

description: Library name: A41864


title: Female, Old, B6xD2, APP-PSEN1-Snca, Het, rep1

description: Library name: A41858


title: Male, Old, B6, APP-PSEN1-Snca, Het, rep2

description: Library name: A42033


title: Female, Young, B6xD2, APP-PSEN1-Snca, Het, rep1

description: Library name: A41857


title: Male, Old, B6xD2, APP-PSEN1-Snca, Het, rep1

description: Library name: A41863


title: Male, Young, B6xD2, APP-PSEN1-Snca, Het, rep1

description: Library name: A41868


title: Male, Old, B6xWSB, APP-PSEN1-Snca, Het, rep1

description: Library name: A41843


title: Female, Young, B6xD2, APP-PSEN1-Snca, Het, rep2

description: Library name: A41853


title: Male, Young, B6xWSB, APP-PSEN1-Snca, Het, rep2

description: Library name: A41834


title: Female, Old, B6xWSB, APP-PSEN1-Snca, Het, rep1

description: Library name: A41829


title: Male, Old, B6xWSB, APP-PSEN1-Snca, Het, rep2

description: Library name: A41833


title: Female, Young, B6xWSB, APP-PSEN1-Snca, Het, rep2

description: Library name: A41823


title: Male, Old, B6, APP-PSEN1-Mapt-Tardbp, Hom, rep2

description: Library name: A42428


title: Male, Old, B6, APP-PSEN1-Snca, Hom, rep2

description: Library name: A42481


title: Male, Young, B6xWSB, APP-PSEN1-Snca, Het, rep1

description: Library name: A41842


title: Female, Old, B6xWSB, APP-PSEN1-Snca, Het, rep2

description: Library name: A41817


title: Female, Old, B6xD2, APP-PSEN1-Snca, Het, rep2

description: Library name: A41847


title: Female, Young, B6xWSB, APP-PSEN1-Snca, Het, rep1

description: Library name: A41819


title: Male, Young, B6xFVB, APP-PSEN1-Snca, Het, rep1

description: Library name: A41796


title: Male, Young, B6xFVB, APP-PSEN1-Snca, Het, rep2

description: Library name: A41800


title: Male, Old, B6xFVB, APP-PSEN1-Snca, Het, rep1

description: Library name: A41790


title: Female, Old, B6, APP-PSEN1-Mapt-Tardbp, Hom, rep2

description: Library name: A42410


title: Female, Old, B6xFVB, APP-PSEN1-Snca, Het, rep1

description: Library name: A41776


title: Female, Young, B6xFVB, APP-PSEN1-Snca, Het, rep1

description: Library name: A41777


title: Male, Old, B6xFVB, APP-PSEN1-Snca, Het, rep2

description: Library name: A41791


title: Female, Old, B6xFVB, APP-PSEN1-Snca, Het, rep2

description: Library name: A41775


title: Male, Old, B6, APP-PSEN1-Snca, Het, rep1

description: Library name: A41771


title: Male, Young, B6, APP-PSEN1-Snca, Het, rep2

description: Library name: A41770


title: Female, Young, B6, APP-PSEN1-Snca, Het, rep2

description: Library name: A41757


title: Female, Young, B6, APP-PSEN1-Snca, Het, rep1

description: Library name: A41763


title: Male, Young, B6, APP-PSEN1-Snca, Het, rep1

description: Library name: A41767


title: Donor_2_17D_mock_2

city: Bethesda

first: Philip

last: Murphy

state: MD

address: 10 CENTER DR RM 11N111

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

description: Library name: Donor_2_17D_mock_2

data_processing:
Raw fastq files were trimmed to remove adapters and low-quality bases using Cutadapt v1.18
alignment to the GRCh38 reference genome and the Gencode v42 genome annotation using STAR v2.7.9a
PCR duplicates were marked using the MarkDuplicates tool from the Picard v3.1.0 (https://broadinstitute.github.io/picard/) software suite.
Raw gene counts were generated using RSEM v1.3.3 [82] and were filtered to include genes with >=1 count per million (CPM) in at least 2 samples.
Differential expression was evaluated using limma with TMM normalization
Assembly: GRCh38/Gencode v42
Supplementary files format and content: raw counts matrix at the gene level

source_name: Human monocyte-derived DCs

growth_protocol: plated human monocyte-derived DCs at 2x106 cells/well and mock-infected or infected with YFV-17D at an MOI of 0.1 in a small volume for 1 hour at 37˚C, 5% CO2 with occasional gentle rocking.

extract_protocol:
we mixed the samples with 200 µL of 1-bromo-3-chloropropane (Sigma Aldrich) and centrifuged at 4˚C for 15 minutes at 16,000 x g. We removed the aqueous phase and passed it through a QIAshredder column (Qiagen) at 21,000 x g for 2 minutes. RNA was extracted using the Qiagen AllPrep DNA/RNA system. An additional on-column DNase I treatment was performed for all extractions.
two hundred nanograms of RNA was used as the input for the Illumina stranded mRNA prep, ligation kit (Illumina) to generate sequencing libraries following the manufacturer’s protocol.

treatment_protocol: added fresh DC medium to the wells to the desired volume and MnTBAP (50 µM) or vehicle control was added to the appropriate wells at 0 and 24 h post-infection.

value: Human monocyte-derived DCs

value: 17D mock


title: Donor_2_Uninfected_MnTBAP_2

description: Library name: Donor_2_Uninfected_MnTBAP_2

value: Unifected MnTBAP


title: Donor_2_Uninfected_MnTBAP_1

description: Library name: Donor_2_Uninfected_MnTBAP_1


title: Donor_2_Uninfected_mock_2

description: Library name: Donor_2_Uninfected_mock_2

value: Unifected mock


title: Female, Old, B6, APP-PSEN1-Snca, Het, rep1

description: Library name: A41752


title: Donor_2_17D_MnTBAP_1

description: Library name: Donor_2_17D_MnTBAP_1

value: 17D MnTBAP


title: Female, Old, B6xD2, Control, WT, rep1

description: Library name: A41750

source_name: Female, Old, B6xD2, Control, WT, rep1


title: Donor_2_Uninfected_mock_1

description: Library name: Donor_2_Uninfected_mock_1


title: Male, Old, B6xFVB, Control, WT, rep1

description: Library name: A40730

source_name: Male, Old, B6xFVB, Control, WT, rep1


title: Female, Old, B6xFVB, Control, WT, rep1

description: Library name: A40724

source_name: Female, Old, B6xFVB, Control, WT, rep1


title: Female, Young, B6xFVB, Control, WT, rep1

description: Library name: A40721


title: Female, Young, B6xFVB, APP-PSEN1-Snca, Het, rep2

description: Library name: A41781


title: Donor_2_17D_MnTBAP_2

description: Library name: Donor_2_17D_MnTBAP_2


title: Female, Old, B6xWSB, Control, WT, rep2

description: Library name: A40715

source_name: Female, Old, B6xWSB, Control, WT, rep2


title: Donor_1_Uninfected_MnTBAP_2

description: Library name: Donor_1_Uninfected_MnTBAP_2


title: Male, Old, B6xWSB, Control, WT, rep1

description: Library name: A40719

source_name: Male, Old, B6xWSB, Control, WT, rep1


title: Donor_1_Uninfected_MnTBAP_1

description: Library name: Donor_1_Uninfected_MnTBAP_1


title: Male, Old, B6xWSB, APP-PSEN1-Mapt-Tardbp, Het, rep2

description: Library name: A40709


title: Donor_2_17D_mock_1

description: Library name: Donor_2_17D_mock_1


title: Donor_1_17D_mock_1

description: Library name: Donor_1_17D_mock_1


title: Donor_1_Uninfected_mock_2

description: Library name: Donor_1_Uninfected_mock_2


title: Donor_1_17D_mock_2

description: Library name: Donor_1_17D_mock_2


title: Male, Young, B6xWSB, APP-PSEN1-Mapt-Tardbp, Het, rep1

description: Library name: A40698


title: Female, Young, B6xWSB, Control, WT, rep1

description: Library name: A40711


title: Donor_1_Uninfected_mock_1

description: Library name: Donor_1_Uninfected_mock_1


title: Female, Old, B6xWSB, APP-PSEN1-Mapt-Tardbp, Het, rep1

description: Library name: A40696


title: Female, Young, B6xWSB, APP-PSEN1-Mapt-Tardbp, Het, rep1

description: Library name: A40683


title: 24h_Donor_3_hDC_17D_mock

description: Library name: 24h_Donor_3_hDC_17D_mock

value: 17D mock 24h


title: Female, Old, B6, APP-PSEN1-Snca, Het, rep2

description: Library name: A41751


title: 24h_Donor_3_hDC_Uninfected_MnTBAP

description: Library name: 24h_Donor_3_hDC_Uninfected_MnTBAP

value: Uninfected MnTBAP 24h


title: 24h_Donor_3_hDC_17D_MnTBAP

description: Library name: 24h_Donor_3_hDC_17D_MnTBAP

value: 17D MnTBAP 24h


title: Male, Old, B6xWSB, APP-PSEN1-Mapt-Tardbp, Het, rep1

description: Library name: A40708


title: 24h_Donor_3_hDC_Uninfected_mock

description: Library name: 24h_Donor_3_hDC_Uninfected_mock

value: Uninfected mock 24h


title: Donor_1_17D_MnTBAP_2

description: Library name: Donor_1_17D_MnTBAP_2


title: Female, Old, B6xWSB, APP-PSEN1-Mapt-Tardbp, Het, rep2

description: Library name: A40690


title: Male, Old, B6xFVB, APP-PSEN1-Mapt-Tardbp, Het, rep2

description: Library name: A40681


title: Donor_1_17D_MnTBAP_1

description: Library name: Donor_1_17D_MnTBAP_1


title: 24h_Donor_2_hDC_17D_mock

description: Library name: 24h_Donor_2_hDC_17D_mock


title: Male, Old, B6xFVB, APP-PSEN1-Mapt-Tardbp, Het, rep1

description: Library name: A40676


title: Female, Old, B6xFVB, APP-PSEN1-Mapt-Tardbp, Het, rep2

description: Library name: A40666


title: Male, Young, B6xFVB, APP-PSEN1-Mapt-Tardbp, Het, rep2

description: Library name: A40678


title: 24h_Donor_2_hDC_Uninfected_MnTBAP

description: Library name: 24h_Donor_2_hDC_Uninfected_MnTBAP


title: 24h_Donor_2_hDC_Uninfected_mock

description: Library name: 24h_Donor_2_hDC_Uninfected_mock


title: 48h_Donor_3_hDC_17D_MnTBAP

description: Library name: 48h_Donor_3_hDC_17D_MnTBAP

value: 17D MnTBAP 48h


title: 48h_Donor_3_hDC_17D_mock

description: Library name: 48h_Donor_3_hDC_17D_mock

value: 17D mock 48h


title: Female, Old, B6xFVB, APP-PSEN1-Mapt-Tardbp, Het, rep1

description: Library name: A40665

value: Cerebral cortex


title: 48h_Donor_3_hDC_Uninfected_mock

description: Library name: 48h_Donor_3_hDC_Uninfected_mock

value: Uninfected mock 48h


title: Female, Young, B6xFVB, APP-PSEN1-Mapt-Tardbp, Het, rep2

description: Library name: A40654

value: Het

value: Female


title: 48h_Donor_3_hDC_Uninfected_MnTBAP

description: Library name: 48h_Donor_3_hDC_Uninfected_MnTBAP

value: Uninfected MnTBAP 48h


title: Male, Old, B6xD2, APP-PSEN1-Mapt-Tardbp, Het, rep2

description: Library name: A40651

value: Male


title: Female, Young, B6xFVB, APP-PSEN1-Mapt-Tardbp, Het, rep1

description: Library name: A40663


title: 48h_Donor_2_hDC_17D_mock

description: Library name: 48h_Donor_2_hDC_17D_mock

value: Human monocyte-derived DCs


title: Male, Young, B6xD2, APP-PSEN1-Mapt-Tardbp, Het, rep2

description: Library name: A40649


title: 48h_Donor_2_hDC_Uninfected_MnTBAP

description: Library name: 48h_Donor_2_hDC_Uninfected_MnTBAP


title: Male, Old, B6xD2, APP-PSEN1-Mapt-Tardbp, Het, rep1

description: Library name: A40645


title: Male, Young, B6xD2, APP-PSEN1-Mapt-Tardbp, Het, rep1

description: Library name: A40639


title: 48h_Donor_2_hDC_Uninfected_mock

description: Library name: 48h_Donor_2_hDC_Uninfected_mock


title: 48h_Donor_1_hDC_17D_MnTBAP

description: Library name: 48h_Donor_1_hDC_17D_MnTBAP


title: 24h_Donor_2_hDC_17D_MnTBAP

description: Library name: 24h_Donor_2_hDC_17D_MnTBAP


title: Female, Old, B6xD2, APP-PSEN1-Mapt-Tardbp, Het, rep1

description: Library name: A40636


title: Female, Old, B6xD2, APP-PSEN1-Mapt-Tardbp, Het, rep2

description: Library name: A40635


title: 48h_Donor_1_hDC_Uninfected_MnTBAP

description: Library name: 48h_Donor_1_hDC_Uninfected_MnTBAP


title: 48h_Donor_1_hDC_17D_mock

description: Library name: 48h_Donor_1_hDC_17D_mock


title: Male, Old, B6, APP-PSEN1-Mapt-Tardbp, Het, rep1

description: Library name: A40616


title: 48h_Donor_1_hDC_Uninfected_mock

description: Library name: 48h_Donor_1_hDC_Uninfected_mock


title: Female, Young, B6xWSB, APP-PSEN1-Mapt-Tardbp, Het, rep2

description: Library name: A40694


title: Male, Young, B6xFVB, APP-PSEN1-Mapt-Tardbp, Het, rep1

description: Library name: A40669


title: Male, Old, B6, APP-PSEN1-Mapt-Tardbp, Het, rep2

description: Library name: A40615


title: Female, Old, B6, APP-PSEN1-Mapt-Tardbp, Het, rep1

description: Library name: A40605


title: A375-KD-1

first: Xunrui

last: Xunrui

address: No. 115, Jinzun Road, Beicai Town, Pudong New District

institute: Shanghai Jiao Tong University

description:
Library name: Sample10
A375_shVCX_rep1

data_processing:
Unique raw reads were mapped to the human reference genome using STAR
STAR parameters used: –twopassMode Basic –outSAMstrandField intronMotif –alignSJstitchMismatchNmax 5 -1 5 5
HTSeq was used to generate gene-level count tables for each sample
Assembly: Homo sapiens GRCh38(GENCODE v38)
Supplementary files format and content: Merged HTSeq counts matrix (.csv) with gene-level raw counts across all samples.

source_name: skin

growth_protocol: PC9 and A375 cells were maintained in RPMI-1640 and DMEM medium, respectively, supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
Total RNA was extracted from PC9 and A375 stable cell lines using TRIzol (Takara Bio, USA).
The total RNA was extracted using the VAHTS Universal V6 RNA seq Library Prep Kit ( Vazyme, NR604-02, Nanjing, China）for Illumina to construct the cDNA library.

treatment_protocol: PC9 and A375 stable cell lines were transduced with lentiviral shRNA targeting the VCX gene family (shVCX) or with non-targeting control shRNA. Transduced cells were selected and expanded prior to RNA extraction.

value: skin

value: epithelial cell

value: wide type

value: sh-VCX family

tag: batch


title: A375-KD-3

description:
Library name: Sample12
A375_shVCX_rep3


title: Male, Young, B6xWSB, APP-PSEN1-Mapt-Tardbp, Het, rep2

description: Library name: A40612


title: 48h_Donor_2_hDC_17D_MnTBAP

description: Library name: 48h_Donor_2_hDC_17D_MnTBAP


title: A375-NC-3

description:
Library name: Sample9
A375_control_rep3

value: sh-Ctrl


title: Female, Old, B6, APP-PSEN1-Mapt-Tardbp, Het, rep2

description: Library name: A40606


title: A375-NC-2

description:
Library name: Sample8
A375_control_rep2


title: Female, Young, B6, APP-PSEN1-Mapt-Tardbp, Het, rep2

description: Library name: A40603


title: A375-NC-1

description:
Library name: Sample7
A375_control_rep1


title: A375-KD-2

description:
Library name: Sample11
A375_shVCX_rep2


title: Male, Old, B6, 5XFAD, Het, rep2

description: Library name: A40274

source_name: Male, Old, B6, 5XFAD, Het, rep2


title: PC9-NC-1

description:
Library name: Sample1
PC9_control_rep1

source_name: lung

value: lung


title: PC9-NC-3

description:
Library name: Sample3
PC9_control_rep3


title: Male, Young, B6, APP-PSEN1-Mapt, Het, rep1

description: Library name: A38014


title: Male, Young, B6xWSB, Control, WT, rep1

description: Library name: A38039

source_name: Male, Young, B6xWSB, Control, WT, rep1

value: WT


title: PC9-KD-2

description:
Library name: Sample5
PC9_shVCX_rep2


title: Male, Old, B6, APP-PSEN1-Mapt, Het, rep2

description: Library name: A38022


title: Male, Young, B6, APP-PSEN1-Mapt, Het, rep2

description: Library name: A38015


title: Female, Young, B6, APP-PSEN1-Mapt-Tardbp, Het, rep1

description: Library name: A40594


title: Female, Old, B6, APP-PSEN1-Mapt, Het

description: Library name: A38007

source_name: Female, Old, B6, APP-PSEN1-Mapt, Het


title: Follicular granulosa cells, Control9

city: Kunming

first: Xi

last: Luo

state: Yunnan Province

address: 157#, Jinbi Street

department: Reproductive Medicine

institute: First People’s Hospital of Yunnan Prov.

description: Library name: Control9

data_processing:
Quality assessment was performed using FastQC (v0.12.0) and adapter trimming with Trimmomatic (v0.39). High-quality reads were aligned to GRCh38 using STAR (v2.7.9a) and quantified with featureCounts (v2.0.8)
Assembly: GRCh38
Supplementary files format and content: csv files include count values for each sample

source_name: Ovaries

extract_protocol:
The total RNA was isolated and purified from the samples using TRIzol reagent (Thermo Fisher, 15596018) following the manufacturer’s protocol.
The quantity and purity of the total RNA were then assessed using the NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was evaluated using the Bioanalyzer 2100 (Agilent, CA, USA). Samples with a concentration >50 ng/μL, RIN value >7.0, and total RNA >1 μg were considered suitable for downstream experiments.
Polyadenylated mRNA was specifically captured using oligo(dT) magnetic beads (Dynabeads Oligo (dT), cat. 25-61005, Thermo Fisher, USA) through two rounds of purification. The captured mRNA was fragmented at high temperature using a magnesium RNA fragmentation kit (NEBNext® Magnesium RNA Fragmentation Module, cat. E6150S, USA) at 94°C for 5-7 minutes. The fragmented RNA was then reverse-transcribed into cDNA using SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, CA, USA). Subsequently, second-strand synthesis was performed using E. coli DNA polymerase I (NEB, cat. m0209, USA) and RNase H (NEB, cat. m0297, USA), converting the DNA-RNA hybrid into double-stranded DNA while incorporating dUTP Solution (Thermo Fisher, cat. R0133, CA, USA). The double-stranded DNA was end-repaired to generate blunt ends, followed by the addition of an “A” base to each end to enable ligation with T-tailed adapters. The fragments were then size-selected and purified using magnetic beads. The second strand was digested with UDG enzyme (NEB, cat. m0280, MA, USA), and PCR amplification was performed with the following conditions: initial denaturation at 95°C for 3 minutes, followed by 8 cycles of denaturation at 98°C for 15 seconds, annealing at 60°C for 15 seconds, and extension at 72°C for 30 seconds, with a final extension at 72°C for 5 minutes to generate a strand-specific library with fragment sizes of 300 bp ± 50 bp.

value: Ovaries

value: Follicular granulosa cells


title: Female, Young, B6, APP-PSEN1-Mapt, Het, rep1

description: Library name: A37999


title: Follicular granulosa cells, Control11

description: Library name: Control11


title: Follicular granulosa cells, Control8

description: Library name: Control8


title: Female, Young, B6, APP-PSEN1-Mapt, Het, rep2

description: Library name: A37995


title: Follicular granulosa cells, Control10

description: Library name: Control10


title: Male, Old, B6, APP-PSEN1-Mapt, Het, rep1

description: Library name: A38012


title: PC9-KD-3

description:
Library name: Sample6
PC9_shVCX_rep3


title: Follicular granulosa cells, Control7

description: Library name: Control7


title: Male, Young, B6xWSB, APP-PSEN1-Mapt, Het, rep1

description: Library name: A37985


title: Follicular granulosa cells, Control5

description: Library name: Control5


title: Male, Old, B6, 5XFAD, Het, rep1

description: Library name: A40275

source_name: Male, Old, B6, 5XFAD, Het, rep1


title: Follicular granulosa cells, Control4

description: Library name: Control4


title: Male, Old, B6xWSB, APP-PSEN1-Mapt, Het, rep1

description: Library name: A37992


title: Male, Young, B6xFVB, Control, WT, rep2

description: Library name: A38029

source_name: Male, Young, B6xFVB, Control, WT, rep2


title: Follicular granulosa cells, Control3

description: Library name: Control3


title: Male, Young, B6xWSB, APP-PSEN1-Mapt, Het, rep2

description: Library name: A37984


title: Follicular granulosa cells, Control2

description: Library name: Control2


title: PC9-NC-2

description:
Library name: Sample2
PC9_control_rep2


title: Male, Old, B6xWSB, APP-PSEN1-Mapt, Het, rep2

description: Library name: A37982


title: Female, Old, B6xWSB, APP-PSEN1-Mapt, Het, rep1

description: Library name: A37977


title: PC9-KD-1

description:
Library name: Sample4
PC9_shVCX_rep1


title: Female, Old, B6xWSB, APP-PSEN1-Mapt, Het, rep2

description: Library name: A37976


title: Follicular granulosa cells, PCOS9

description: Library name: PCOS9


title: Female, Young, B6xWSB, APP-PSEN1-Mapt, Het, rep2

description: Library name: A37969


title: Follicular granulosa cells, PCOS5

description: Library name: PCOS5


title: Female, Young, B6xWSB, APP-PSEN1-Mapt, Het, rep1

description: Library name: A37965


title: Follicular granulosa cells, PCOS6

description: Library name: PCOS6


title: Follicular granulosa cells, PCOS7

description: Library name: PCOS7


title: Male, Young, B6xFVB, APP-PSEN1-Mapt, Het, rep1

description: Library name: A37958


title: Male, Old, B6xFVB, APP-PSEN1-Mapt, Het, rep2

description: Library name: A37963


title: Male, Young, B6xFVB, APP-PSEN1-Mapt, Het, rep3

description: Library name: A37957


title: Follicular granulosa cells, PCOS3

description: Library name: PCOS3


title: Female, Young, B6xFVB, APP-PSEN1-Mapt, Het, rep2

description: Library name: A37944


title: Male, Old, B6xFVB, APP-PSEN1-Mapt, Het, rep1

description: Library name: A37956


title: Follicular granulosa cells, PCOS1

description: Library name: PCOS1


title: Female, Old, B6xFVB, APP-PSEN1-Mapt, Het, rep1

description: Library name: A37950


title: HEK293 PP1(H66K)-PNUTS_pdox_Ser5  Rep2 input

city: Aurora

first: David

last: Bentley

state: Colorado

department: BMG

institute: UCD AMC

description: Homemade, KAPA HiFi amplification

data_processing:
adapters were trimmed using bbtools bbkuk version 39.01
Reads were aligned using Bowtie2 version 2.3.2
PCR duplicates were removed using bbtools clumpify
Read coordinates were collapsed and centered using deeptools bamCoverage version 3.5.1.
Assembly: GRCh38/hg38 assembly
Supplementary files format and content: BigWig

extract_protocol:
Cross-linked chromatin was sonicated with a Covaris ME220 ultrasonicator
1-2 mg of cross-linked extract was immunoprecipitated, and prepared for illumina library construction by repair with Klenow, T4 DNA polymerase and T4 polynucleotide kinase, A-tailing with Klenow exo-, ligation to branched adaptors, SPRI bead purification of ~200bp fragments, and amplification (15-18 cycles) with Illumina Tru-seq primers using Phusion DNA polymerase.

tag: antibody

value: none (input)

value: DMEM 10% FCS,10ug/ml blasticidin, pen/strep,doxycycline (2.0 ug/ml) 24hr


title: Female, Old, B6xFVB, APP-PSEN1-Mapt, Het, rep2

description: Library name: A37940

value: Cerebral cortex


title: HEK293 PP1(H66K)-PNUTS_mdox_Ser5 Rep2 input

description: Homemade, KAPA HiFi amplification

value: DMEM 10% FCS,10ug/ml blasticidin, pen/strep


title: HEK293 PP1(H66K)-PNUTS_pdox_Ser5 Rep1 input

description: Homemade, KAPA HiFi amplification


title: HEK293 PP1(H66K)-PNUTS_mdox_Ser5 Rep1 input

description: Homemade, KAPA HiFi amplification


title: Male, Old, B6xD2, APP-PSEN1-Mapt, Het

description: Library name: A37925

source_name: Male, Old, B6xD2, APP-PSEN1-Mapt, Het

value: Het


title: Female, Young, B6xFVB, APP-PSEN1-Mapt, Het, rep1

description: Library name: A37938

value: Female


title: HEK293 PP1(H66K)-PNUTS_pDox_pol II_ChIPseq Rep2

description: Homemade, KAPA HiFi amplification

value: rabbit anti pan CTD (Schroeder etal Genes Dev. 14:2435, 2000)


title: Male, Young, B6xD2, APP-PSEN1-Mapt, Het, rep1

description: Library name: A37928

value: Male


title: Male, Young, B6xD2, APP-PSEN1-Mapt, Het, rep2

description: Library name: A37923


title: HEK293 PP1(H66K)-PNUTS_mDox_pol II_ChIPseq Rep2

description: Homemade, KAPA HiFi amplification


title: Follicular granulosa cells, PCOS10

description: Library name: PCOS10


title: HEK293 PP1(H66K)-PNUTS_pDox_pol II_ChIPseq Rep1

description: Homemade, KAPA HiFi amplification


title: Female, Young, B6xD2, APP-PSEN1-Mapt, Het, rep2

description: Library name: A37916


title: HEK293 PP1(H66K)-PNUTS_mDox_pol II_ChIPseq Rep1

description: Homemade, KAPA HiFi amplification


title: Male, Young, B6, Control, WT, rep1

description: Library name: A37711

source_name: Male, Young, B6, Control, WT, rep1


title: HEK293 PP1(H66K)-PNUTSDWBD_pdox_Ser5 ChIPSeq Rep3

description: Homemade, KAPA HiFi amplification

value: monoclonal anti-Ser5P 4H8 Millipore


title: Follicular granulosa cells, PCOS4

description: Library name: PCOS4


title: Female, Old, B6xD2, APP-PSEN1-Mapt, Het, rep2

description: Library name: A37914


title: Female, Old, B6xD2, APP-PSEN1-Mapt, Het, rep1

description: Library name: A37913


title: Follicular granulosa cells, PCOS2

description: Library name: PCOS2


title: HEK293 PP1(WT)-PNUTS_pdox_Avitag ChIPSeq

description: Homemade, KAPA HiFi amplification

value: polyclonal rabbit anti Avitag


title: Female, Young, B6xD2, APP-PSEN1-Mapt, Het, rep1

description: Library name: A37912


title: HEK293 PP1(H66K)-PNUTS_pdox_Avitag ChIPSeq

description: Homemade, KAPA HiFi amplification


title: HEK293 PP1(H66K)-PNUTSDWBD_pdox_Ser5 ChIPSeq Rep1

description: Homemade, KAPA HiFi amplification

value: monoclonal anti-Ser5P 3E8 Chromotek


title: HEK293 PP1(H66K)-PNUTS_pdox_Ser5 ChIPSeq Rep3

description: Homemade, KAPA HiFi amplification


title: Male, Young, B6, APP-PSEN1-Tardbp, Het, rep2

description: Library name: A35786


title: Control 96hr rep1

city: New York

first: Megan

middle: D

last: Schertzer

state: New York

address: 101 Avenue of the Americas, 4th Floor, Knowles lab

institute: New York Genome Center

description:
Library name: 23c_rb2_empty_96hr
ribo-depleted

data_processing:
RNA-seq reads were aligned to hg38 genome using STAR v2.7.1 and ‘--twopassMode Basic’ and ‘--outSAMstrandField intronMotif’ parameters (Dobin et al. 2013).
Samtools v1.9 was used to filter for reads with a mapping quality greater than 20, sorted, and indexed (H. Li et al. 2009).
HEK293, hESC, and A375 junction counts (provided in Isoviz and used for non-sequence features in Figure 2) were generated using Regtools extract v0.5.2 (Cotto et al. 2023) with ‘-a 8 -m 50 -M 500000 -s 0’ parameters.
In RBFOX2 knockdown samples, differential splicing analysis was performed using rMATS v4.1.1 (Shen et al. 2014). First, we ran rMATS –task prep for each aligned bam across knockdown conditions and timepoints (--b1 all_bams.txt, -t single --libType fr-firststrand --readLength 158 --variable-read-length --allow-clipping). Next, we combined the prep results in a single post step (--task post). This generates a summary of all data across a single set of events with the same event IDs. Finally, at each timepoint, we statistically compared events in the control to each of the RBFOX2 knockdowns using prepare_stat_inputs.py for each comparison followed by rMATS with –task stat for the final output.
Assembly: hg38
Supplementary files format and content: Text file regtools junction count output for all samples.
Supplementary files format and content: rMATS combined output from JC.txt files for knockdown samples.

growth_protocol: A375 cells were acquired from American Type Culture Collection (ATCC Cat #CRL-1619). A375 cells were maintained at 37°C with 5% CO2 in DMEM media (ThermoFisher Cat #11965118) supplemented with 10% serum (Serum Plus II, Sigma-Aldrich, Cat #14009C).  HEK293 cells were acquired from ATCC (Cat #CRL-1573). HEK293 cells were maintained at 37°C with 5% CO2 in DMEM media (ThermoFisher Cat #11965118) supplemented with 10% serum (Serum Plus II, Sigma-Aldrich, Cat #14009C).  HUES66 human embryonic stem cells (hESCs) were obtained from Harvard University. Cells were maintained at 37°C with 5% CO2 in StemFlex media (ThermoFisher Cat #A3349401) and grown on Geltrex-coated plates (ThermoFisher Cat #A1413302). For passaging, Accutase (ThermoFisher Cat #A1110501) was used to dissociate cells and 10 µM ROCK inhibitor Y-27632 dihydrochloride (Tocris Cat #1254) was added to the media for plating.

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen #15596018) according to the manufacturer's protocol.  To isolate RNA from cytosolic and nuclear fractions, cells were washed twice with 1mL cold PBS and scraped in 1mL PBS + 1mM PMSF + 1:100 protease inhibitor cocktail (PIC, Sigma P8340). 200uL was removed at this step and added to 1mL Trizol (total RNA). The remaining cells were centrifuged at 1500xrcf. for 5 min, and resuspended in 250uL low salt solution (10mM KCl, 1.5mM MgCl2, 20mM Tris-HCl pH 7.5) supplemented with 1mM PMSF, 1mM DTT, and 1x PIC. Triton X-100 was added to a final concentration of 0.1% and cells were rotated for 10 min at 4C, then centrifuged for 5 min at 1500xrcf. 200uL of supernatant was removed and added to 1mL Trizol (cytosolic fraction). The remaining supernatant was discarded and the nuclear pellet was washed by rotating for 2min at 4C in low salt solution without Triton X-100 and centrifuged at 1300rpm for 10 min. Nuclear pellet was resuspended in 1mL Trizol (nuclear fraction). Isolation of RNA from Trizol was performed according to the manufacturer protocol.
Per RNA sample, we combined 1 µg of total RNA + 2 µl 1:100 ERCC RNA Spike-in Mix #1 (Invitrogen #4456740). Libraries were prepared using the Kapa RNA HyperPrep Kit with RiboErase (Roche #08098131702), pooled, and sequenced using the Nextseq 500/550 High Output Kit with 150 cycles (Illumina  #20024907).

value: 1ug/ml doxycycline

tag: timepoint

tag: replicate


title: RBFOX2 N-long KD 48hr rep1

description:
Library name: 23c_rb2_g5_48hr
ribo-depleted
rmats_empty_g5_48hr_combined_output.txt

value: RBFOX2 isoform knockdown


title: Female, Old, B6xWSB, APP-PSEN1-Tardbp, Het, rep1

description: Library name: A35818


title: Female, Old, B6xFVB, Control, WT, rep2

description: Library name: A35813

source_name: Female, Old, B6xFVB, Control, WT, rep2


title: RBFOX2 N-short KD 48hr rep1

description:
Library name: 23c_rb2_g3_48hr
ribo-depleted
rmats_empty_g3_48hr_combined_output.txt


title: HEK293 PP1(H66K)-PNUTSDWBD_mdox_Ser5 ChIPSeq Rep3

description: Homemade, KAPA HiFi amplification


title: Male, Old, B6xWSB, Control, WT, rep2

description: Library name: A35803

source_name: Male, Old, B6xWSB, Control, WT, rep2


title: HEK293 PP1(H66K)-PNUTSDWBD_pdox_Ser5 ChIPSeq Rep2

description: Homemade, KAPA HiFi amplification


title: HEK293 PP1(H66K)-PNUTS_mdox_Ser5 ChIPSeq Rep3

description: Homemade, KAPA HiFi amplification


title: HEK293 PP1(H66K)-PNUTSDWBD_mdox_Ser5 ChIPSeq Rep2

description: Homemade, KAPA HiFi amplification


title: RBFOX2 N-long KD 96hr rep1

description:
Library name: 23c_rb2_g5_96hr
ribo-depleted
rmats_empty_g5_96hr_combined_output.txt


title: Male, Old, B6, APP-PSEN1-Tardbp, Het, rep1

description: Library name: A35784


title: HEK293 PP1(H66K)-PNUTSDWBD_mdox_Ser5 ChIPSeq Rep1

description: Homemade, KAPA HiFi amplification


title: Female, Young, B6xWSB, Control, WT, rep2

description: Library name: A35796


title: Control 48hr rep1

description:
Library name: 23c_rb2_empty_48hr
ribo-depleted


title: RBFOX2 Total KD 96hr rep1

description:
Library name: 23c_rb2_g1_96hr
ribo-depleted
rmats_empty_g1_96hr_combined_output.txt

value: RBFOX2 total knockdown


title: HEK293 PP1(H66K)-PNUTS_mdox_Ser5 ChIPSeq Rep2

description: Homemade, KAPA HiFi amplification


title: RBFOX2 Total KD 48hr rep1

description:
Library name: 23c_rb2_g1_48hr
ribo-depleted
rmats_empty_g1_48hr_combined_output.txt


title: HEK293 PP1(H66K)-PNUTS_pdox_Ser5 ChIPSeq Rep2

description: Homemade, KAPA HiFi amplification


title: Male, Old, B6, APP-PSEN1-Tardbp, Het, rep2

description: Library name: A35783


title: Male, Young, B6xWSB, Control, WT, rep2

description: Library name: A35801

source_name: Male, Young, B6xWSB, Control, WT, rep2

value: WT


title: Male, Old, B6xFVB, Control, WT, rep2

description: Library name: A35808

source_name: Male, Old, B6xFVB, Control, WT, rep2


title: RBFOX2 N-long KD 24hr rep2

description:
Library name: 23b_rb_hesc_g5_rep2
ribo-depleted
rmats_empty_g5_24hr_combined_output.txt


title: Male, Young, B6, APP-PSEN1-Tardbp, Het, rep1

description: Library name: A35782


title: Female, Old, B6, APP-PSEN1-Tardbp, Het, rep1

description: Library name: A35778


title: HEK293 PP1(H66K)-PNUTS_mdox_Ser5 ChIPSeq Rep1

description: Homemade, KAPA HiFi amplification


title: Control 24hr rep2

description:
Library name: 23b_rb_hesc_empty_rep2
ribo-depleted


title: RBFOX2 N-short KD 24hr rep1

description:
Library name: 21c_RB2_g3
ribo-depleted
rmats_empty_g3_24hr_combined_output.txt


title: RBFOX2 Total KD 24hr rep1

description:
Library name: 21c_RB2_g1
ribo-depleted
rmats_empty_g1_24hr_combined_output.txt


title: RBFOX2 N-short KD 96hr rep1

description:
Library name: 23c_rb2_g3_96hr
ribo-depleted
rmats_empty_g3_96hr_combined_output.txt


title: HEK293 PP1(H66K)-PNUTS_pdox_Ser5 ChIPSeq Rep1

description: Homemade, KAPA HiFi amplification


title: Female, Young, B6, APP-PSEN1-Tardbp, Het, rep1

description: Library name: A35771


title: HEK293 PP1(H66K)-PNUTS_pDox_pol II_eNETseq Rep2

description: small RNA-seq

data_processing:
Adapters were trimmed using cutadapt version 2.3
Reads were aligned using Bowtie2 version 2.3.2
PCR duplicates were removed UMI-tools v0.5.4
Read coordinates were collapsed to a single base pair coordinate corresponding to the RNA 3' end
Assembly: GRCh38/hg38 assembly
Supplementary files format and content: BigWig

molecule: nuclear RNA

extract_protocol:
Pol II-associated nascent RNA was isolated by IP
10-20ng of RNA was used with the QIAseq miRNA UDI  kit (#331505) with 12 base UMI


title: Dorsal internal oblique muscles, IR-Atg200 (UAS-IR-FIP200), 3IL and APF of 1, 2, 3 and 4 day, rep1-4

city: Sumida-ku

first: Hiroki

last: Taoka

state: Tokyo

address: 2-1-3 Bunka

institute: Kao Corporation

description: Library name: IR-FIP200

data_processing:
Read1(10bp of UMI + 9bp of barcode) was assigned to Read2(insert read) by following command "umi_tools extract --bc-pattern=CCCCCCCCCCCCCCCCNNNNNNNNNN --stdin read1 --stdout read1_out --read2-in read2 --read2-out=read2_out  --whitelist=whitelist". To extract barcodes, umi_tools whitelist was used. Barcodes in the whitelist were validated by comparing them to barcodes used in the reverse transcription.
Reads were mapped to the BDGP6 reference using HISAT2 (ver.2.2.1).
Gene count was obtaind by featureCounts (ver.2.0.1).
The number of UMI was counted by using UMI tools (ver.1.1.2).
Assembly: BDGP6
Supplementary files format and content: compressed tab separated files(.tsv.gz)

organism: Drosophila melanogaster

source_name: Dorsal internal oblique muscles

extract_protocol:
RNA was extracted using ReliaPrep Tissue RNA Miniprep System (Promega).
Libraries were prepared by CEL-Seq2, a single-cell RNA-seq protocol (Hashimshony et al.) method. Individual samples were reverse transcribed using poly(T) primers with unique cell barcodes. Then replicate were mixed and amplified by PCR. 10nt of UMI followed by 9nt of cell barcode are in read1 and 81nt of RNA insert reads are in read2.

value: Dorsal internal oblique muscles


title: Dorsal internal oblique muscles, IR-Stx17 (UAS-IR-Stx17), 3IL and APF of 1, 2, 3 and 4 day, rep1-4

description: Library name: IR-Stx17


title: Female, Young, B6, APP-PSEN1-Tardbp, Het, rep2

description: Library name: A35767


title: HEK293 PP1(H66K)-PNUTS_pDox_pol II_eNETseq Rep1

description: small RNA-seq


title: Male, Old, B6xWSB, APP-PSEN1-Tardbp, Het, rep1

description: Library name: A35764


title: RBFOX2 N-short KD 24hr rep2

description:
Library name: 23b_rb_hesc_g3_rep2
ribo-depleted
rmats_empty_g3_24hr_combined_output.txt


title: Dorsal internal oblique muscles, Control (UAS-LacZ), 3IL and APF of 1, 2, 3 and 4 day, rep1-4

description: Library name: Control


title: Dorsal internal oblique muscles, IR-Atg18 (UAS-IR-Atg18), 3IL and APF of 1, 2, 3 and 4 day, rep1-4

description: Library name: IR-Atg18


title: Taf13 HET, E6.5, 9

city: Amherst

first: Jesse

last: Mager

state: Massachusetts

address: 661 N Pleasant St

department: Veterinary and Animal Sciences

institute: University of Massachusetts Amherst

data_processing:
Raw reads were trimmed for sequence quality and to remove adapters or primers using trimmomatic (v0.39), and the quality was evaluated by fastqc (v0.11.9). Trimmed reads were aligned to the mouse genome assembly GRCm39 using STAR (v2.7.6a). Single embryo genotypes were confirmed by viewing read alignment to genes/exons targeted for knockout on IGV (v2.16.2).
Differential gene expression analysis was performed in R (v4.2.1) using DESeq2 (v1.36.0). Adjusted p-values were calculated by DEseq2 using the Benjamini-Hochberg method.
Assembly: Mus Musculus(GRCm39)
Supplementary files format and content: FPKM_summary.xlsx contains normalized read counts. DEGs_summary.xlsx contains differential gene expression results between MUT embryos compared to WT or HET embryos.

source_name: Single embryo

growth_protocol: For OG samples, Blastocysts were harvested at E3.5 and cultured individually in iBiTreat dishes with DMEM containing 10% fetal bovine serum. Embryos were kept in culture for 72 hrs at 37°C and 5% CO2  atmosphere in a humidified incubator.

extract_protocol:
RNA was extracted from E3.5, E6.5, or OG embryos individually using the Zymo kit as previously described. Total RNA was analyzed using the Agilent 2100 Bioanalyzer using the Eukaryote Total RNA Pico assay. RNaseq libraries were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina following manufacturer instructions. The quantity of library was assayed using the Qubit DNA HS assay, and quality was analyzed on Bioanalyzer.
Libraries were sequenced on Illumina NextSeq 500 platform using NextSeq 500/550 Mid Output v2.5 kit (150 cycles) with 76 bp paired-end sequencing chemistry. RNAseq library preparation and Illumina Next-Generation Sequencing was performed at Genomics Resource Laboratory (RRID:SCR_017907), Institute for Applied Life Sciences, University of Massachusetts Amherst, MA.

tag: time

value: Single embryo

value: Taf13 HET


title: Taf13 MUT, E6.5, 1

value: Taf13 MUT


title: Taf13 HET, E6.5, 8


title: Male, Young, B6xWSB, APP-PSEN1-Tardbp, Het, rep2

description: Library name: A35762

value: Cerebral cortex


title: Taf13 HET, E6.5, 7


title: Taf13 MUT, E6.5, 2


title: HEK293 PP1(H66K)-PNUTS_pDox_Ser5P_eNETseq Rep1

description: small RNA-seq

value: DMEM 10% FCS,10ug/ml blasticidin, pen/strep,doxycycline (2.0 ug/ml) 24hr


title: Taf13 HET, E6.5, 6


title: HEK293 PP1(H66K)-PNUTS_pDox_Ser5P_eNETseq Rep2

description: small RNA-seq


title: Taf13 HET, E6.5, 5


title: Male, Young, B6xWSB, APP-PSEN1-Tardbp, Het, rep1

description: Library name: A35757

value: Het


title: RBFOX2 N-long KD 24hr rep1

description:
Library name: 21c_RB2_g5
ribo-depleted
rmats_empty_g5_24hr_combined_output.txt


title: Taf13 HET, E6.5, 4


title: Female, Old, B6, APP-PSEN1-Tardbp, Het, rep2

description: Library name: A35768

value: Female


title: HEK293 PP1(H66K)-PNUTS_mDox_pol II_eNETseq Rep1

description: small RNA-seq

value: rabbit anti pan CTD (Schroeder etal Genes Dev. 14:2435, 2000)

value: DMEM 10% FCS,10ug/ml blasticidin, pen/strep


title: Taf13 HET, E6.5, 2


title: HEK293 PP1(H66K)-PNUTS_mDox_Ser5P_eNETseq Rep2

description: small RNA-seq


title: Female, Old, B6xWSB, APP-PSEN1-Tardbp, Het, rep2

description: Library name: A35754


title: Taf13 HET, E6.5, 1


title: Taf13 WT, E6.5, 4

value: Taf13 WT


title: HEK293 PP1(H66K)-PNUTS_mDox_Ser5P_eNETseq Rep1

description: small RNA-seq


title: Female, Young, B6xWSB, APP-PSEN1-Tardbp, Het, rep2

description: Library name: A35748


title: Taf13 WT, E6.5, 2


title: Taf13 WT, E6.5, 3


title: HEK293FlpIN_pol II_eNETseq Rep2

description: small RNA-seq

value: DMEM 10% FCS, pen/strep


title: Taf13 WT, E6.5, 1


title: HEK293FlpIN_pol II_eNETseq Rep1

description: small RNA-seq


title: Male, Old, B6xWSB, APP-PSEN1-Tardbp, Het, rep2

description: Library name: A35760

value: Male


title: Taf13 MUT, E3.5, 3


title: Taf13 MUT, E3.5, 2


title: HEK293FlpIN_Ser5P_eNETseq Rep2

description: small RNA-seq

value: monoclonal anti-Ser5P 3E8 Chromotek


title: Male, Old, B6xFVB, APP-PSEN1-Tardbp, Het, rep1

description: Library name: A35734


title: Taf13 HET, E3.5, 4


title: Male, Old, B6xFVB, APP-PSEN1-Tardbp, Het, rep2

description: Library name: A35745


title: Taf13 HET, E3.5, 3


title: HEK293 PP1(H66K)-PNUTS_mDox_pol II_eNETseq Rep2

description: small RNA-seq


title: Taf13 HET, E3.5, 1


title: Male, Young, B6xFVB, APP-PSEN1-Tardbp, Het

description: Library name: A35733


title: HEK293 PP1(H66K)-PNUTSDIPLD_pdox_BruSeq Rep3

data_processing:
adapters were trimmed using bbtools bbkuk version 39.01
Reads were aligned using Bowtie2 version 2.3.2
PCR duplicates were removed using bbtools clumpify
Assembly: GRCh38/hg38 assembly
Supplementary files format and content: BigWig

extract_protocol:
BrU-labeled RNA 2mM 20 min, was fragmented by hydrolysis ,  isolated by IP
20-100 ng of RNA was used with the KAPA RNA HyperPrep Kit (KR1350) to make strand-specific RNA-seq libraries

value: monoclonal anti-BrdU 3D4 (Pharmingen Cat 555627)


title: Taf13 HET, E6.5, 3


title: Taf13 HET, E3.5, 2


title: Female, Young, B6xFVB, APP-PSEN1-Tardbp, Het

description: Library name: A35723


title: Female, Young, B6xWSB, APP-PSEN1-Tardbp, Het, rep1

description: Library name: A35752


title: HEK293 PP1(H66K)-PNUTSDIPLD_pdox_BruSeq Rep2


title: Taf13 WT, E3.5, 4


title: Taf13 WT, E3.5, 2


title: Taf13 WT, E3.5, 3


title: Male, Old, B6xD2, APP-PSEN1-Tardbp, Het, rep2

description: Library name: A35715


title: HEK293 PP1(H66K)-PNUTSDIPLD_pdox_BruSeq Rep1


title: Taf12 MUT, OG, 4

value: OG

value: Taf12 MUT


title: Taf13 WT, E3.5, 1


title: HEK293 PP1(H66K)-PNUTSDIPLD_mdox_BruSeq Rep1


title: Taf13 MUT, E3.5, 1


title: Male, Young, B6xD2, APP-PSEN1-Tardbp, Het, rep2

description: Library name: A35707


title: Taf12 MUT, OG, 2


title: Taf12 MUT, OG, 3


title: HEK293 PP1(H66K)-PNUTSDWBD_pdox_BruSeq Rep2


title: Taf12 HET, OG, 3

value: Taf12 HET


title: Taf12 MUT, OG, 1

value: Single embryo


title: HEK293 PP1(H66K)-PNUTSDWBD_pdox_BruSeq Rep1


title: HEK293FlpIN_Ser5P_eNETseq Rep1

description: small RNA-seq


title: Taf12 HET, OG, 2


title: Taf12 HET, OG, 1


title: Male, Old, B6xD2, APP-PSEN1-Tardbp, Het, rep1

description: Library name: A35704


title: HEK293 PP1(H66K)-PNUTSDWBD_mdox_BruSeq Rep1


title: Female, Young, B6xD2, APP-PSEN1-Tardbp, Het, rep1

description: Library name: A35692


title: Taf12 WT, OG, 3

value: Taf12 WT


title: HEK293 PP1(H66K)-PNUTS_pdox_DRB15'BruSeq Rep2

extract_protocol:
BrU-labeled RNA 2mM 10 min, was fragmented by hydrolysis ,  isolated by IP
20-100 ng of RNA was used with the KAPA RNA HyperPrep Kit (KR1350) to make strand-specific RNA-seq libraries


title: Taf12 WT, OG, 2


title: Taf12 WT, OG, 4


title: Female, Old, B6xFVB, APP-PSEN1-Tardbp, Het, rep1

description: Library name: A35719


title: Female, Young, B6xD2, APP-PSEN1-Tardbp, Het, rep2

description: Library name: A35690


title: Taf12 MUT, E3.5, 3


title: HEK293 PP1(H66K)-PNUTS_mdox_DRB15'BruSeq Rep2


title: Taf12 WT, OG, 1


title: Female, Old, B6xD2, APP-PSEN1-Tardbp, Het

description: Library name: A35689


title: Taf12 MUT, E3.5, 1


title: Taf12 MUT, E3.5, 2


title: HEK293 PP1(H66K)-PNUTS_pdox_DRB15'BruSeq Rep1


title: Taf12 HET, E3.5, 5


title: HEK293 PP1(H66K)-PNUTS_mdox_DRB15'BruSeq Rep1


title: Taf12 HET, E3.5, 4


title: Female, Young, B6xD2, APP-PSEN1-Tardbp, Het, rep3

description: Library name: A35687


title: daf-16; daf-18 rep C

city: Durham

first: L. Ryan

last: Baugh

state: North Carolina

address: 124 Science Dr, FFSC 4336

department: Biology

institute: Duke University

data_processing:
bowtie2-2.3.3.1-linux-x86_64 (Langmead & Salzberg, 2012) was used to map paired-end reads with the command bowtie2 -p 2 -k 1 -S.1 -m 2 -S -p 2. HTSeq python-htseq 0.6.1p1-4build1 (amd64 binary) in ubuntu bionic (Anders et al., 2015) was used to count reads against C. elegans genome version WS273.
Assembly: WBcel235
Supplementary files format and content: counts files contain genes' WormBase IDs and read counts in each library.

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: All strains assayed in this study were maintained with Escherichia coli OP50 on nematode growth medium (NGM) plates and were well-fed for at least three generations before being used in experiments. All steps were done at 20 °C unless otherwise stated. For each biological replicate and each genotype, seven L4 worms were picked onto four 10 cm NGM plates seeded with OP50 (total: 28 L4 larvae). 96 hr later, those large plates were hypochlorite treated. Three biological replicates were performed.

extract_protocol:
RNA was extracted using TRIzol Reagent (Invitrogen#15596026) using the manufacturer’s protocol with some exceptions. 100 uL of acid-washed sand (Sigma-Aldrich#27439) was added to each sample at the beginning of the extraction protocol to aid with homogenization. RNA was eluted in nuclease-free water and stored at -80C until further use.
Libraries were prepared for sequencing using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs# E7775) starting with 50ng of total RNA per sample as input and 14 cycles of PCR. Barcoded libraries were pooled and sequenced on the NovaSeq 6000 S-Prime flow cell to obtain 50bp paired-end reads.

treatment_protocol: Wild type N2, daf-16(mu86), daf-18(ok480) and daf-16(mu86); daf-18(ok480)  were hypochlorite-treated and resuspended in virgin S-basal with 0.1% EtOH at 1/uL at 20 °C in the shaker at 180 rpm.Three biological replicates were fone. Approximately 20,000 starved L1s were collected at 16 hr after hypochlorite treatment for each genotype for each biological replicate, by spinning down, flash freezing, and storing at -80C.

value: whole worm

value: Starved in virgin S-basal with 0.1% EtOH for about 4 hours at 20 °C


title: Male, Young, B6xD2, APP-PSEN1-Tardbp, Het, rep1

description: Library name: A35703

value: Cerebral cortex


title: HEK293 PP1(H66K)-PNUTS_pdox_BruSeq Rep4

value: DMEM 10% FCS,10ug/ml blasticidin, pen/strep,doxycycline (2.0 ug/ml) 24hr


title: Taf12 HET, E3.5, 3


title: daf-16; daf-18 rep B


title: Taf12 HET, E3.5, 1


title: HEK293 PP1(H66K)-PNUTS_pdox_BruSeq Rep3


title: Taf12 HET, E3.5, 2


title: daf-16; daf-18 rep A


title: Taf12 WT, E3.5, 4


title: HEK293 PP1(H66K)-PNUTS_mdox_BruSeq Rep3


title: daf-18 rep C


title: Taf12 WT, E3.5, 3


title: HEK293 PP1(H66K)-PNUTS_pdox_BruSeq Rep2


title: daf-18 rep B


title: Taf12 WT, E3.5, 1


title: KPM1 sh IKKb

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

country: Germany

institute: Helmholz Zentrum Munich

description: KPM1 sh IKKb

data_processing:
base calling was performed with Miseq
alignment was performed with STAR
Reads Per Kilobase of exon per Megabase of library size (CPM) were calculated using FeuturesCounts funtion from Subread software
The data were filtered, normalized and the differential gene expression was computed using the packages limma (https://bioconductor.org/packages/release/bioc/html/limma.html) and edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) on R
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

source_name: Mouse malignant mesothelioma model cell line

growth_protocol: cells were cultured in minimum supplemented medium (DMEM+10% FBS + 1% PEN/STREP) for over 12 months or over 60 passages

extract_protocol:
Total RNA from the cells was extracted with the Trizol protocol followed by Qiagen RNeasy Mini Kit
Libraries were prepared according to Illumina specifications

treatment_protocol: silencing for both IKKs in AE17, AB2 and KPM1 cells using lentiviral shRNA pools

tag: background strain

tag: passages

value: more than 60

tag: knockdown

value: sh IKKb


title: Taf12 WT, E3.5, 2


title: KPM1 sh IKKa

description: KPM1 sh IKKa

value: Mouse malignant mesothelioma model cell line

value: sh IKKa


title: HEK293 PP1(H66K)-PNUTS_mdox_BruSeq Rep2

value: DMEM 10% FCS,10ug/ml blasticidin, pen/strep


title: KPM1 sh CTRL

description: KPM1 sh CTRL

value: sh CTRL


title: HEK293 PP1(H66K)-PNUTS_pdox_BruSeq Rep1


title: daf-18 rep A


title: daf-16 rep C


title: Taf5 MUT, E3.5, 3

value: Taf5 MUT


title: daf-16 rep B


title: HEK293 PP1(H66K)-PNUTS_mdox_BruSeq Rep1

value: monoclonal anti-BrdU 3D4 (Pharmingen Cat 555627)


title: Taf12 WT, E3.5, 5


title: Taf5 MUT, E3.5, 2


title: AE17 sh IKKb

description: AE17 sh IKKb

source_name: Mouse malignant mesothelioma cell line

value: Mouse malignant mesothelioma cell line


title: AE17 sh IKKa

description: AE17 sh IKKa


title: daf-16 rep A


title: AE17 sh CTRL

description: AE17 sh CTRL


title: Taf5 WT, E3.5, 3

value: Taf5 WT


title: Taf5 MUT, E3.5, 1


title: HEK293 PP1(WT)-PNUTS_pdox_BruSeq Rep2


title: Taf5 WT, E3.5, 2


title: wild type rep B

value: wild type (N2)


title: AB2 sh IKKb

description: AB2 sh IKKb


title: HEK293 PP1(WT)-PNUTS_mdox_BruSeq Rep1


title: AB2 sh IKKa

description: AB2 sh IKKa


title: wild type rep A


title: wild type rep C


title: TILs PTIR1-

city: Beijing

first: Jia

last: Song

state: China

address: Peking University School of Medicine, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

data_processing:
The Cell ranger software pipeline (version 6.0.1) provided by 10xGenomics was used to demultiplex cellular barcodes,map reads to the transcriptome, control quality and generate quantitative matrix.
The R package Seurat (version 4.0.3) was used for generation of Seurat object.
Low-quality cells with UMI numbers greater than 8000 or less than 1000, or having over 10% mitochondrial-derived UMI counts were removed.
The count matrix was normalized with SCTransform function.
IntegrateData function was used to integrate data and create a new matrix with 3000 features.
PCA was performed by R package Seurat (version 4.0.3). Top 50 PCs were used for tSNE and UMAP.
tSNE and UMAP were performed by R package Seurat (version 4.0.3).
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.

source_name: tumor infiltration lymphocytes

extract_protocol:
Single cells were mixed with Gel Beads, Partitioning Oil and glycerol, using for preparation of GEMs with ChromiumTM Next GEM Chip G Single Cell Kit. The GEMs were subjected to RT-PCR, and the products were purified with Dynabeads, followed by cDNA amplification.
RNA libraries were prepared with ChromiumTM Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 according to the manufacturer's protocol.

tag: disease state

value: colon cancer

value: colon

value: tumor infiltration lymphocytes

tag: cell population


title: AB2 sh CTRL

description: AB2 sh CTRL


title: EC, CD45-targeted radioimmunotherapy, rep 2

status: Public on Apr 04 2025

city: Seattle

first: Matthew

last: Hagen

state: WA

address: 1100 Fairview Ave N.

department: Translational Science and Therapeutics

institute: Fred Hutchinson Cancer Center

description: Library name: 16_MH

data_processing:
STAR v2.7.7a 2-pass mapping was used to align paired-end reads to hg38+HIV integrated reference with gene-level read quantification.
QC by FastQC 0.11.9, RNA-SeQC 2.3.4, RSeQC 4.0.0.
Bioconductor package edgeR 3.36.0 for DEG identification. Genes with low expression were excluded using edgeR function filterByExpr with min.count=10 and min.total.count = 15.
Filtered expression matrix was normalized by TMM method and subject to significance testing using quasi-likelihood pipeline implemented in edgeR. A gene was deemed differentially expressed if meeting the cutoffs of log2 fold change and Benjamini-Hochberg adjusted p-values.
Assembly: hg38+HIV integrated reference
Supplementary files format and content: all_samples.raw_counts.txt tab-delimited text file containing one column per sample.

source_name: Bone marrow endothelium

extract_protocol:
Qiagen microPrep kit per manufacturer instructons
SMART-Seq v4 Ultra Low Input RNA kit followed by Illumina NexteraXT DNA library prep kit

treatment_protocol: Endothelial reporter mice (Cdh5 CRE Rosa26 TdTomato) mice were non-treated, treated with total body irradiation, or treated with one of two radioimmunotheraphy protocols 8 days prior to harvest

tag: tissue

value: Bone marrow endothelium

value: Lineage- CD45- TdTomato+ FACS-sorted endothelial cells

value: Cdh5 CRE Rosa26 TdTomato

value: CD45-targeted radioimmunotherapy


title: TILs PTIR1+


title: Taf5 MUT, E3.5, 4

value: Single embryo

tag: genotype


title: EC, IgG non-targeted radioimmunotherapy, rep 2

description: Library name: 12_MH

value: IgG non-targeted radioimmunotherapy


title: EC, CD45-targeted radioimmunotherapy, rep 1

description: Library name: 15_MH


title: EC, IgG non-targeted radioimmunotherapy, rep 3

description: Library name: 13_MH


title: EC, Cesium TBI, rep 6

description: Library name: 10_MH

value: 500 cGy Cesium total body irradiation


title: EC, Cesium TBI, rep 5

description: Library name: 9_MH


title: EC, non-treated, rep 4

description: Library name: 7_MH

value: Non-treated control


title: EC, non-treated, rep 3

description: Library name: 6_MH


title: EC, Cesium TBI, rep 4

description: Library name: 8_MH


title: EC, Cesium TBI, rep 3

description: Library name: 5_MH


title: HEK293 PP1(WT)-PNUTS_pdox_BruSeq Rep1

tag: cell line

value: DMEM 10% FCS,10ug/ml blasticidin, pen/strep,doxycycline (2.0 ug/ml) 24hr


title: EC, non-treated, rep 2

description: Library name: 3_MH

tag: cell type


title: EC, Cesium TBI, rep 1

description: Library name: 1_MH

tag: treatment


title: Taf5 WT, E3.5, 1


title: HFD+2% DSS, liver, Sample 3

first: Tian

last: Xu

state: Beijing

address: No.1 Shuaifuyuan, Dongcheng District, Beijing,China

institute: Peking Union Medical College Hospital

description:
Library name: Sample 12
HFDDSS3

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libranes.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols

value: liver

value: WT

value: HFD+2% DSS

tag: strain


title: CD+2% DSS, liver, Sample 3

description:
Library name: Sample 9
CDDSS3

value: CD+2% DSS


title: CD+2% DSS, liver, Sample 2

description:
Library name: Sample 8
CDDSS2


title: HFD, liver, Sample 3

description:
Library name: Sample 6
HFD3

value: HFD


title: HFD+2% DSS, liver, Sample 1

description:
Library name: Sample 10
HFDDSS1


title: HFD, liver, Sample 2

description:
Library name: Sample 5
HFD2


title: CD+2% DSS, liver, Sample 1

description:
Library name: Sample 7
CDDSS1


title: HFD, liver, Sample 1

description:
Library name: Sample 4
HFD1


title: CD, liver, Sample 1

description:
Library name: Sample 1
CD1

value: CD


title: CD, liver, Sample 2

description:
Library name: Sample 2
CD2


title: CD, liver, Sample 3

description:
Library name: Sample 3
CD3


title: EC, IgG non-targeted radioimmunotherapy, rep 1

description: Library name: 11_MH


title: Murine cornea, 3 months, before abrasion, ipsilateral, replicate #5

city: Montpellier

first: Frederic

last: Michon

address: 80, rue Augustin Fliche

department: Institute for Neurosciences of Montpellier

country: France

institute: Inserm

description: Library name: N5R_S60

data_processing:
bcl2fastq2 Conversion Software was used to convert BCL files to FASTQ file format and demultiplex samples.
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence using Trimmomatic. Parameters used: :2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to GENCODE mouse Release M30 reference genome (GRCm39) and annotation files using STAR aligner with parameters  --runThreadN 20 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJstitchMismatchNmax 5 -1 5 5 --outFilterType BySJout --outFilterMismatchNmax 999 --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMmapqUnique 60 --quantMode GeneCounts --twopassMode Basic
Counts per gene were calculated using featureCounts software. Parameters used: -s 2 -T 20 -t exon -g gene_id
Differential expression analysis used the DESeq2 software in R environment. Procedures included: Normalization of count values between samples using a geometric means, using negative binomial linear model and Wald test to produce p-values, removal of low-expression outliers (using Cook's distance)  to optimize for p-value adjustment and finally, multiple testing adjustment of p-values with Benjamini-Hochberg procedure.
Assembly: GENCODE mouse Release M30 reference genome (GRCm39)
Supplementary files format and content: tab delimited count files

source_name: Cornea

extract_protocol:
Trizol + QIAGEN Rneasy extraction kit
Illumina Stranded Total RNA Prep with Ribo-Zero Plus

value: Cornea

value: Before mechanical abrasion


title: Murine cornea, 3 months, before abrasion, contralateral, replicate #5

description: Library name: N5L_S55


title: Murine cornea, 3 months, before abrasion, ipsilateral, replicate #4

description: Library name: N4R_S59


title: Murine cornea, 3 months, before abrasion, ipsilateral, replicate #3

description: Library name: N3R_S58


title: Murine cornea, 3 months, before abrasion, contralateral, replicate #3

description: Library name: N3L_S53


title: Murine cornea, 3 months, before abrasion, ipsilateral, replicate #2

description: Library name: N2R_S57


title: Murine cornea, 3 months, before abrasion, contralateral, replicate #4

description: Library name: N4L_S54


title: Murine cornea, 3 months, before abrasion, contralateral, replicate #1

description: Library name: N1L_S51


title: Murine cornea, 3 months, before abrasion, ipsilateral, replicate #1

description: Library name: N1R_S56


title: EC, non-treated, rep 1

description: Library name: 2_MH

value: Bone marrow endothelium


title: Murine cornea, 3 months, before abrasion, contralateral, replicate #2

description: Library name: N2L_S52


title: HFD+2% DSS, liver, Sample 2

description:
Library name: Sample 11
HFDDSS2


title: Murine cornea, 3 months, 48 hours post-abrasion, contralateral, replicate #5

description: Library name: E5L_S45

value: 48 hours after mechanical abrasion


title: Murine cornea, 3 months, 48 hours post-abrasion, ipsilateral, replicate #5

description: Library name: E5R_S50


title: Murine cornea, 3 months, 48 hours post-abrasion, ipsilateral, replicate #3

description: Library name: E3R_S48


title: Murine cornea, 3 months, 48 hours post-abrasion, ipsilateral, replicate #4

description: Library name: E4R_S49


title: Murine cornea, 3 months, 48 hours post-abrasion, contralateral, replicate #4

description: Library name: E4L_S44