title: PT16,ThymicCarcinoma,vdj_t

description:
Library name: PT16.S23.ThymicCarcinoma.Mixed.vdj_t
10x Genomics


title: C57_Kidney_WT_Male2

status: Public on Jul 31 2026

type: SRA

city: Hangzhou

first: Xiaoping

last: Han

state: Zhejiang

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

country: China

institute: Zhejiang University School of Medicine

description:
Library name: C57_Kidney_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

library_source: transcriptomic

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were then aligned to mm10 using STAR (v2.7.10a).
Read counts were generated using featureCounts.
Transcripts were quantified with Salmon (v1.10.3) in quasi-mapping-based mode.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw count values for individual samples.

molecule: polyA RNA

organism: Mus musculus

source_name: Kidney

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2-3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme). The extracted RNA was used for reverse transcription. Following the reaction, a PCR amplification program was performed. Purification was then conducted using 0.9× of VAHTS DNA Clean Beads. TruePrep DNA Library Prep Kit for MGI (Vazyme) was used for sequencing library construction.

tag: tissue

value: Kidney

tag: genotype

value: WT

tag: strain

tag: Sex

value: Male

tag: age

value: 10 weeks

tag: mouse id


title: PT16,Thymus_no_MG,vdj_t

city: Chicago

first: Yuanqing

last: Yan

state: IL

address: 303 E Superior Street

country: USA

institute: Northwestern University

description:
Library name: PT16.S22.Thymus_no_MG.Mixed.vdj_t
10x Genomics

data_processing:
For scRNA-seq, raw reads were demultiplexed with Cell Ranger (v6.0.0 or v7.1.0) and mapped to the human genome (GRCh38). Ambient RNA was removed using SoupX, and doublets were filtered with scDblFinder. Quality control in Seurat excluded cells with <200 or >7,500 unique features, <400 or >40,000 total RNA counts, or >10% mitochondrial content. For V(D)J sequencing, the djvdj (v0.1.0) package was utilized, retaining only cells with high-quality transcriptomic data. Samples with fewer than 10 cells were excluded for robustness. Clonotypes were defined by CDR3 amino acid sequences, and only those with exactly two chains were retained; cells without an assigned clonotype were removed. For Visium HD, images were aligned in Loupe Browser (v8.0.0), and Space Ranger (v3.1.0) was used for mapping. Bin2cell (v0.3.3) aggregated 2 μm bins to reconstruct single-cell-like profiles based on H&E morphology and gene expression at 0.5 μm per pixel resolution. Downstream analysis was performed in Scanpy, excluding cells with <100 or >40,000 features or >20% mitochondrial content.
Assembly: HG38
Supplementary files format and content: HDF5, csv and tsv of processed data
Library strategy: TCR-Seq

molecule: total RNA

organism: Homo sapiens

source_name: Thymus

extract_protocol:
Fresh thymus samples were obtained for scRNA-seq plus V(D)J sequencing and formalin-fixed, paraffin-embedded specimens were used for Visium HD spatial transcriptomics.
For scRNA-seq (3' v3) and scRNA-seq with V(D)J sequencing (5'), libraries were prepared using the 10x Genomics Chromium Single Cell 3' v3 or Single Cell 5' Expression Assay and sequenced on NextSeq 1000/2000 or Illumina NovaSeq 6000 instruments. For Visium HD, samples were sectioned at 5 μm and processed at the Northwestern University NUSeq Core following the manufacturer’s protocol (Visium HD v1). These libraries were subsequently sequenced on an Illumina NovaSeq X Plus.

tag: cell type

value: T cells

value: Thymus


title: 19_044K3_LN

city: Seattle

first: Sonali

last: Arora

state: WA

address: 1100 Fairview Ave N,

institute: FHCRC

description:
Library name: 19_044K3_LN
19_044K3_LN

library_source: transcriptomic single cell

data_processing:
The sequencing reads were analyzed with human reference genome GRCh38 using Cell Ranger v7.1.0 [1]. Introns were included in the analysis
raw bcl files were processed using cellranger mkfastq and cellranger count
Assembly: hg38
Supplementary files format and content: barcodes.tsv, genes.tsv and matrix.mtx ( 3 files per sample, output from cellranger count) are submitted as processed files. Additionally "possorted_genome_bam.bam" are submitted as raw files per sample.

molecule: nuclear RNA

extract_protocol:
We isolated nuclei from OCT-embedded frozen human bladder cancer tissue samples and constructed 3’ single-cell gene expression libraries (Next GEM v3.1) using the 10x Genomics Chromium system
RNA libraries were prepared for sequencing using Single Cell Library Kit from 10x Genomics (P/N 120218) according to manufacturer's guidelines.

tag: cell line


title: AML12-DEP-3

city: Changzhou

first: Yuancheng

last: Shao

address: No. 68, Gehu Middle Road, Wujin District, Changzhou City

institute: Changzhou No 2 People’s Hospital, the Affiliated Hospital of Nanjing Medical University

description:
Library name: Sample12
AML12-DEP-3

data_processing:
Raw reads generated during high-throughput sequencing were fastq format sequences. In order to get high-quality reads that could be used for later analysis, raw reads needed to be further quality filtered. Trimmomatic software was first used for adpter removing, And then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads.Using hisat2 to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment.
Assembly: GRCm39.110
Supplementary files format and content: processed data.xlsx

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.
RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded Total

value: Mouse hepatocytes

tag: treatment


title: C57_Kidney_WT_Female3

description:
Library name: C57_Kidney_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 7.5 months


title: 19_044G2_Liver

description:
Library name: 19_044G2_Liver
19_044G2_Liver


title: PT15,Thymus_MG,vdj_t

description:
Library name: PT15.S21.Thymus_MG.Mixed.vdj_t
10x Genomics


title: C57_Kidney_WT_Female2

description:
Library name: C57_Kidney_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: AML12-DEP-2

description:
Library name: Sample11
AML12-DEP-2


title: PT14,MetastasisTumor,vdj_t

description:
Library name: PT14.S20.MetastasisTumor.Mixed.vdj_t
10x Genomics


title: AML12-DEP-1

description:
Library name: Sample10
AML12-DEP-1


title: KO70_indexH3

city: New York

first: Justin

middle: J

last: Frere

state: NY

address: Alexandria Center for Life Sciences, West Tower, 430 E 29th St.

department: Microbiology

institute: NYU Langone Health

description: PolyA enriched and prepared using TruSeq Stranded mRNA library prep

data_processing:
Base calling and sample deconvolution performed via Illumina BaseSpace
Reads aligned to MesAur1.0 genome assembly using Ensembl GTF file and quantified using Salmon as made available in Illumina BaseSpace "RNA-Seq Alignment" application
Assembly: Mesocricetus Auratus MesAur1.0
Supplementary files format and content: .quant.genes.sf Salmon files (show raw and normalized read counts by gene)
Supplementary files format and content: .csv files show the read count for individual base calls compared to the viral reference sequence

organism: Mesocricetus auratus

source_name: Brain mock 3

growth_protocol: Golden hamstsers were housed in pairs in the ABSL3 facility of NYU-Langone/Mount Sinai Hospital, under 12 hour light/dark cycle. Water and Food (PicoLab Rodent Diet 20 5053) was provided ad libitum.

extract_protocol: RNA was extracted using Trizol reagent and following manufacturer's instructions. 100 ng of RNA were used for the construction ofn libraries.

treatment_protocol: Dexamethasone was prepared fresh each day at a dose of 1 mg/kg in 0.5 mL of 20% DMSO/60% PEG400/20% 2-hydroxypropyl-beta-cyclodextrin in water (w/w), and administered via subcutaneous injection.

value: Brain

tag: time

value: 3 dpi

value: MOCK


title: C57_Kidney_WT_Female1

description:
Library name: C57_Kidney_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 weeks


title: C57_Kidney_KO_Male5

description:
Library name: C57_Kidney_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: 7 weeks


title: KO67_indexE3

source_name: Kidney mock 3


title: AML12-DMSO-3

description:
Library name: Sample9
AML12-DMSO-3


title: KO69_indexG3

source_name: G.I. mock 3


title: AML12-DMSO-2

description:
Library name: Sample8
AML12-DMSO-2


title: PT14,PrimaryTumor,vdj_t

description:
Library name: PT14.S19.PrimaryTumor.Mixed.vdj_t
10x Genomics


title: C57_Kidney_KO_Male4

description:
Library name: C57_Kidney_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: KO66_indexD3

source_name: Liver mock 3

value: Liver


title: PT12,Thymoma_MG,vdj_t

description:
Library name: PT12.S17.Thymoma_MG.Mixed.vdj_t
10x Genomics


title: AML12-DMSO-1

description:
Library name: Sample7
AML12-DMSO-1


title: PT13,Thymoma_MG,vdj_t

description:
Library name: PT13.S18.Thymoma_MG.Mixed.vdj_t
10x Genomics


title: C57_Kidney_KO_Male2

description:
Library name: C57_Kidney_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: PT12,Thymus_MG,vdj_t

description:
Library name: PT12.S16.Thymus_MG.Mixed.vdj_t
10x Genomics


title: KO65_indexC3

source_name: Spleen mock 3

value: Spleen


title: iWAT-DEP-3

description:
Library name: Sample6
iWAT-DEP-3

source_name: iWAT

value: iWAT

value: Mouse adipocytes

value: DMEM+DEP


title: C57_Kidney_KO_Male1

description:
Library name: C57_Kidney_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Kidney

value: Male


title: PT11,Thymus_MG,vdj_t

description:
Library name: PT11.S15.Thymus_MG.Mixed.vdj_t
10x Genomics

value: T cells

value: Thymus


title: KO64_indexB3

source_name: Heart mock 3

value: Heart

value: WT


title: iWAT-DEP-2

description:
Library name: Sample5
iWAT-DEP-2


title: C57_Kidney_KO_Female2

description:
Library name: C57_Kidney_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 8 months


title: PT10,Thymoma_no_MG,vdj_t

description:
Library name: PT10.S14.Thymoma_no_MG.Mixed.vdj_t
10x Genomics


title: C57_Kidney_KO_Female1

description:
Library name: C57_Kidney_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: KO63_indexA3

source_name: Lung mock 3

value: Lung

value: 3 dpi

value: MOCK


title: PT9,MetastasisTumor2,vdj_b

description:
Library name: PT9.S13.MetastasisTumor2.Mixed.vdj_b
10x Genomics

data_processing:
For scRNA-seq, raw reads were demultiplexed with Cell Ranger (v6.0.0 or v7.1.0) and mapped to the human genome (GRCh38). Ambient RNA was removed using SoupX, and doublets were filtered with scDblFinder. Quality control in Seurat excluded cells with <200 or >7,500 unique features, <400 or >40,000 total RNA counts, or >10% mitochondrial content. For V(D)J sequencing, the djvdj (v0.1.0) package was utilized, retaining only cells with high-quality transcriptomic data. Samples with fewer than 10 cells were excluded for robustness. Clonotypes were defined by CDR3 amino acid sequences, and only those with exactly two chains were retained; cells without an assigned clonotype were removed. For Visium HD, images were aligned in Loupe Browser (v8.0.0), and Space Ranger (v3.1.0) was used for mapping. Bin2cell (v0.3.3) aggregated 2 μm bins to reconstruct single-cell-like profiles based on H&E morphology and gene expression at 0.5 μm per pixel resolution. Downstream analysis was performed in Scanpy, excluding cells with <100 or >40,000 features or >20% mitochondrial content.
Assembly: HG38
Supplementary files format and content: HDF5, csv and tsv of processed data
Library strategy: BCR-Seq

value: B cells


title: KO62_indexH2

source_name: Brain mock 2

value: Brain


title: iWAT-DMSO-3

description:
Library name: Sample3
iWAT-DMSO-3

value: DMEM


title: C57_Heart_WT_Male6

description:
Library name: C57_Heart_WT_Male6_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Heart

value: 9 weeks


title: KO61_indexG2

source_name: G.I. mock 2


title: iWAT-DEP-1

description:
Library name: Sample4
iWAT-DEP-1

value: iWAT

value: Mouse adipocytes


title: PT9,Thymoma_MG,vdj_b

description:
Library name: PT9.S12.Thymoma_MG.Mixed.vdj_b
10x Genomics


title: iWAT-DMSO-2

description:
Library name: Sample2
iWAT-DMSO-2


title: C57_Heart_WT_Male5

description:
Library name: C57_Heart_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 weeks


title: iWAT-DMSO-1

description:
Library name: Sample1
iWAT-DMSO-1


title: KO60_indexF2

description: PolyA enriched and prepared using TruSeq Stranded mRNA library prep

source_name: Pancreas mock 2

value: Pancreas


title: C57_Heart_WT_Male4

description:
Library name: C57_Heart_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male


title: PT9,MetastasisTumor1,vdj_b

description:
Library name: PT9.S11.MetastasisTumor1.Mixed.vdj_b
10x Genomics

value: Thymus


title: PT9,Thymus_MG,vdj_b

description:
Library name: PT9.S10.Thymus_MG.Mixed.vdj_b
10x Genomics


title: KO59_indexE2

source_name: Kidney mock 2

value: Kidney


title: Brain tissuse,Model2 treatment with Thalidomide,rep3

city: Beijing

first: Hongyun

last: Zhang

state: Dr

address: 45 Changchun ST

institute: CCMU

description: Library name: THA3

data_processing:
Raw data (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.
Reference genome and gene model annotation files were downloaded from genome website. Use HISAT2 (2.2.1) to build the index of the reference genome, and use HISAT2 to align paired-end clean reads to the reference genome. HISAT2 can use the gene model annotation file to create splice-aware alignments, providing better alignment accuracy compared to other non-splice alignment tools
featureCounts (2.0.6) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: Mus Musculus(GRCm38/mm10)
Supplementary files format and content: csv files include counts values lor each Sample

source_name: Brain tissue

extract_protocol:
RNA was extracted from the tissue using the standard extraction method, and then the RNA samples were subjected to strict quality control. The quality control method mainly involved using the Agilent 2100 bioanalyzer to precisely assess the integrity of the RNA.
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. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Brain tissue

value: Thalidomide


title: Brain tissuse,Model2 treatment with Thalidomide,rep2

description: Library name: THA2


title: KO58_indexD2

source_name: Liver mock 2

value: Liver

value: WT


title: C57_Heart_WT_Male2

description:
Library name: C57_Heart_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Heart

value: 10 weeks


title: PT7,Thymus_MG,vdj_b

description:
Library name: PT7.S8.Thymus_MG.Mixed.vdj_b
10x Genomics

value: B cells


title: C57_Heart_WT_Male3

description:
Library name: C57_Heart_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: PT8,Thymus_no_MG,vdj_b

description:
Library name: PT8.S9.Thymus_no_MG.Mixed.vdj_b
10x Genomics


title: KO57_indexC2

source_name: Spleen mock 2

value: Spleen

value: 3 dpi

value: MOCK


title: Brain tissuse,Model2 treatment with Thalidomide,rep1

description: Library name: THA1


title: C57_LargeIntestine_KO_Male2

description:
Library name: C57_LargeIntestine_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: LargeIntestine

value: LargeIntestine

value: Mecp2 KO

value: 9 weeks


title: cDC1, Clec1a KO7_n2_necro

city: Nantes

first: Elise

last: Chiffoleau

address: 30 Bd jean Monnet CHU

country: France

description:
Library name: Sample 8
TO239_DGEseq.unq.refseq.umi.dat

data_processing:
An average of 5 million 75 bp single-end reads were obtained for each sample.
Samples were demultiplexed and aligned to the GRCm38 (mm10) genome using the DGE bioinformatics pipeline.
Post-sequencing, data demultiplexing was performed using Illumina bcl2fastq.
The resulting FASTQ files were analyzed using the 3’ Sequencing RNA Profiling (SRP) pipeline
Assembly: mm10
Supplementary files format and content: Digital gene expression (DGE) profiles were generated by counting the number of unique UMIs associated with each RefSeq gene for each sample and expressed in .dat format

source_name: spleen

extract_protocol:
5,000 cells were incubated in lysis buffer containing 0.16uL 10% Triton X-100, 0.08 uL RNAse Out (40U/µL, Invitrogen) and 3.75 µL RNAse DNAse free water
Lyzed cells were loaded on a 96-plate using an OT-2 library prep robot (Opentrons). 1uL barcoded RT-primers with universal adapters, well-specific barcodes, and unique molecular identifiers were then added to the wells and incubated at 72°C for 3 min before reverse transcription. Barcoded complementary DNAs from multiple samples were then pooled, amplified, and tagmented using a transposon fragmentation approach which enriches for 3′ ends of complementary DNA.

treatment_protocol: Spleen from WT and Clec1a KO mice were recovered, minced and incubated with collagenase IV for 45 minutes at 37°C (Roche, cat: 11088882001). The resulting cell suspension was then enriched in cDC1s by incubation with a DC isolation kit (Milteny, cat: 130-091-169) and sorted with an AutoMACS separator. The resulting cell suspension was then stained with fluorochrome-conjugated antibodies and purified cDC1s were sorted by FACS (based on the expression of CD11c, MHC-II and XCR1) using a Cytek Aurora spectral flow cytometer. Purified cDC1s were then plated in flat-bottom 96-well plates and stimulated with E. coli (MOI = 10), MCA-OVA UV-treated cells (ratio 1:10) or recombinant mouse IFNβ (1000 U/ml, BioTechne R&D Systems cat: 8234-MB-010) for 6h. Then, cells were extensively washed and harvested for RNAseq experiments.

value: spleen

value: C57BL/6NCrl-Clec1atm1(EGFP,-cre/ERT2)Djr or WT littermates

value: 8-12 weeks old

value: type 1 conventional dendritic cells

value: Clec1a KO

value: stimulated with necrotic cells


title: PT6,Thymus_MG,vdj_b

description:
Library name: PT6.S7.Thymus_MG.Mixed.vdj_b
10x Genomics

source_name: Thymus

value: Thymus


title: C57_Heart_WT_Female3

description:
Library name: C57_Heart_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: WT

value: Female

value: 7.5 months


title: C57_Heart_WT_Female2

description:
Library name: C57_Heart_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Heart


title: Brain tissuse,Model2 treatment with DMSO,rep3

description: Library name: DMSO 3

value: Brain tissue

value: DMSO


title: KO55_indexA2

source_name: Lung mock 2

value: Lung

value: 3 dpi

value: MOCK


title: PT5,Thymus_MG,vdj_b

description:
Library name: PT5.S6.Thymus_MG.Mixed.vdj_b
10x Genomics

value: B cells


title: KO56_indexB2

source_name: Heart mock 2


title: Brain tissuse,Model2 treatment with DMSO,rep2

description: Library name: DMSO 2


title: C57_Heart_WT_Female1

description:
Library name: C57_Heart_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 weeks


title: PT16,ThymicCarcinoma,vdj_b

description:
Library name: PT16.S23.ThymicCarcinoma.Mixed.vdj_b
10x Genomics


title: KO54_indexH1

source_name: Brain mock 1

value: Brain


title: Brain tissuse,Model2 treatment with DMSO,rep1

description: Library name: DMSO 1


title: C57_Heart_KO_Male6

description:
Library name: C57_Heart_KO_Male6_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: Male


title: PT16,Thymus_no_MG,vdj_b

description:
Library name: PT16.S22.Thymus_no_MG.Mixed.vdj_b
10x Genomics


title: Brain tissuse,stereotactic intracranial AAV-BR1-KRASG12V injection,rep3

description: Library name: Model2-3


title: C57_Heart_KO_Male5

description:
Library name: C57_Heart_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7 weeks


title: PT15,Thymus_MG,vdj_b

description:
Library name: PT15.S21.Thymus_MG.Mixed.vdj_b
10x Genomics


title: KO53_indexG1

description: PolyA enriched and prepared using TruSeq Stranded mRNA library prep

source_name: G.I. mock 1


title: KO51_indexE1

source_name: Kidney mock 1

value: Kidney


title: Brain tissuse,stereotactic intracranial AAV-BR1-KRASG12V injection,rep2

description: Library name: Model2-2


title: PT14,MetastasisTumor,vdj_b

description:
Library name: PT14.S20.MetastasisTumor.Mixed.vdj_b
10x Genomics

value: Thymus


title: C57_Heart_KO_Male4

description:
Library name: C57_Heart_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: C57_Heart_KO_Male2

description:
Library name: C57_Heart_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: KO50_indexD1

source_name: Liver mock 1

value: Liver

value: WT


title: PT14,PrimaryTumor,vdj_b

description:
Library name: PT14.S19.PrimaryTumor.Mixed.vdj_b
10x Genomics


title: Brain tissuse,stereotactic intracranial AAV-BR1-KRASG12V injection,rep1

description: Library name: Model2-1


title: KO49_indexC1

source_name: Spleen mock 1

value: Spleen


title: Brain tissuse,stereotactic intracranial AAV-BR1 injection,rep3

description: Library name: Ctrl 6

value: Brain tissue

value: stereotactic intracranial AAV-BR1


title: C57_Heart_KO_Male1

description:
Library name: C57_Heart_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Heart

value: Heart


title: PT13,Thymoma_MG,vdj_b

description:
Library name: PT13.S18.Thymoma_MG.Mixed.vdj_b
10x Genomics


title: Brain tissuse,stereotactic intracranial AAV-BR1 injection,rep2

description: Library name: Ctrl 5


title: KO48_indexB1

source_name: Heart mock 1

value: 3 dpi


title: C57_Heart_KO_Female2

description:
Library name: C57_Heart_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 8 months


title: KO47_indexA1

source_name: Lung mock 1

value: Lung

value: MOCK


title: Brain tissuse,stereotactic intracranial AAV-BR1 injection,rep1

description: Library name: Ctrl 4


title: C57_Heart_KO_Female1

description:
Library name: C57_Heart_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO


title: PT12,Thymoma_MG,vdj_b

description:
Library name: PT12.S17.Thymoma_MG.Mixed.vdj_b
10x Genomics

value: B cells


title: PT12,Thymus_MG,vdj_b

description:
Library name: PT12.S16.Thymus_MG.Mixed.vdj_b
10x Genomics


title: KO102_IndexF7

source_name: O.B., SARS-CoV-2, I.N., 3dpi, 3

value: Olfactory bulb

value: 1000 PFU SARSCOV2 IN


title: Brain tissuse, intravenous AAV-BR1-KRASG12V injection,rep3

description: Library name: Model1-3

source_name: Brain tissue

value: intravenous AAV-BR1-KRASG12V injection


title: C57_Eye_WT_Male5

description:
Library name: C57_Eye_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Eye

value: Eye

value: Male

value: 8 weeks


title: PT11,Thymus_MG,vdj_b

description:
Library name: PT11.S15.Thymus_MG.Mixed.vdj_b
10x Genomics

value: Thymus


title: KO101_IndexE7

source_name: O.B., SARS-CoV-2, I.N., 3dpi, 2

value: WT


title: Brain tissuse,intravenous AAV-BR1-KRASG12V injection,rep2

description: Library name: Model1-2

value: Brain tissue


title: C57_Eye_WT_Male4

description:
Library name: C57_Eye_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: Brain tissuse,intravenous AAV-BR1-KRASG12V injection,rep1

description: Library name: Model1-1


title: C57_Eye_WT_Male3

description:
Library name: C57_Eye_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: PT10,Thymoma_no_MG,vdj_b

description:
Library name: PT10.S14.Thymoma_no_MG.Mixed.vdj_b
10x Genomics


title: PT9,MetastasisTumor2, scRNA-seq

description:
Library name: PT9.S13.MetastasisTumor2.Mixed
10x Genomics

data_processing:
For scRNA-seq, raw reads were demultiplexed with Cell Ranger (v6.0.0 or v7.1.0) and mapped to the human genome (GRCh38). Ambient RNA was removed using SoupX, and doublets were filtered with scDblFinder. Quality control in Seurat excluded cells with <200 or >7,500 unique features, <400 or >40,000 total RNA counts, or >10% mitochondrial content. For V(D)J sequencing, the djvdj (v0.1.0) package was utilized, retaining only cells with high-quality transcriptomic data. Samples with fewer than 10 cells were excluded for robustness. Clonotypes were defined by CDR3 amino acid sequences, and only those with exactly two chains were retained; cells without an assigned clonotype were removed. For Visium HD, images were aligned in Loupe Browser (v8.0.0), and Space Ranger (v3.1.0) was used for mapping. Bin2cell (v0.3.3) aggregated 2 μm bins to reconstruct single-cell-like profiles based on H&E morphology and gene expression at 0.5 μm per pixel resolution. Downstream analysis was performed in Scanpy, excluding cells with <100 or >40,000 features or >20% mitochondrial content.
Assembly: HG38
Supplementary files format and content: HDF5, csv and tsv of processed data

value: all Thymus cells


title: KO99_indexC7

description: PolyA enriched and prepared using TruSeq Stranded mRNA library prep

source_name: O.B. mock 3

value: 3 dpi


title: Brain tissuse,intravenous AAV-BR1 injection,rep3

description: Library name: Ctrl 3

value: intravenous AAV-BR1


title: C57_Eye_WT_Male2

description:
Library name: C57_Eye_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 10 weeks


title: PT9,Thymoma_MG, scRNA-seq

description:
Library name: PT9.S12.Thymoma_MG.Mixed
10x Genomics


title: KO98_indexB7

source_name: O.B. mock 2


title: Brain tissuse,intravenous AAV-BR1 injection,rep2

description: Library name: Ctrl 2


title: Brain tissuse,intravenous AAV-BR1 injection,rep1

description: Library name: Ctrl 1


title: C57_Eye_WT_Female2

description:
Library name: C57_Eye_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 7.5 months


title: KO97_indexA7

source_name: O.B. mock 1

value: MOCK


title: Microbiota of stool EG37 – control male

city: Florence

first: Sara

last: Bertorello

address: Viale Gaetano Pieraccini 6

country: Italy

institute: University of Florence

description:
Library name: EG37
16s  rRNA v3-v4 sequencing of mice stool

library_source: genomic

data_processing:
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 7 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --p-minimum-length 100 –verbose
qiime demux summarize  --i-data trim-seqs.qza --o-visualization quality.qzv
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 224 --p-trunc-len-r 218 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 7
bowtie2 -x INDEXED_mouse_GRCm39_BOWTIE2/GRCm39  -U dna-sequences.fasta --un filtered.fasta
qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
R software for further analysis
Supplementary files format and content: filtered.fasta: text containing every processed ASV code and sequence
Supplementary files format and content: otu_table.csv: CSV text file containing the abundance table
Supplementary files format and content: tax.csv: CSV text file containing the complete taxonomic classification of the reference sequence
Library strategy: 16S rRNA-seq

molecule: genomic DNA

source_name: Stool

extract_protocol:
Total DNA was extracted from stools, amplified to collect amplicons of variable V3–V4 region of the bacterial 16S rRNA gene were sequenced in paired-end mode (2 × 250 cycles) with Illumina Novaseq.
For detailed library preparation please contact IGA Technology Services (Udine, Italy)

value: Stool

tag: group

value: control

value: male


title: KO96_indexH6

source_name: Brain, SARS-CoV-2, I.N., 3dpi, 3

value: Brain

value: 1000 PFU SARSCOV2 IN


title: C57_Eye_WT_Female1

description:
Library name: C57_Eye_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Eye


title: PT8,Thymus_no_MG, scRNA-seq

description:
Library name: PT8.S9.Thymus_no_MG.Mixed
10x Genomics

source_name: Thymus


title: neural_SpinalCord_KO_rep1

description:
Library name: neural_SpinalCord_KO_rep1_scATAC-seq
UUATAC-seq

library_source: genomic single cell

data_processing:
Raw FASTQ files were split by i7 indexes of DNBSEQ-T7 using splitBarcode (v0.1.6) then converted to BAM format. The 30-bp barcodes were tagged and reads with low quality were removed. Barcodes were next corrected and combined with the i7 indexes to label cells. The barcode-corrected BAM files were split by barcode 3 which label samples. Cell barcodes (i7 indexes + 30-bp barcodes) were added to the query name of each read. BAM files were then converted to FASTQ files with 30-bp barcodes and reverse complementary mosaic end (ME) sequences trimmed. Reads were aligned to mm10 using BWA (version 0.7.15) in paired-end mode. The aligned and sorted BAM files were shifted using the alignmentSieve function in deepTools (version 3.5.1) to correct the 9-bp gap. The shifted BAM files were next merged per sample and converted to BEDPE files (BED format). BEDPE files were cleaned to fragment files for subsequent analyses.
Assembly: mm10
Supplementary files format and content: Compressed BED  files containing sorted fragments
Supplementary files format and content: Compressed Tab-delimited text files containing metadata of cells analyzed

source_name: SpinalCord

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2-3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Library preparations were performed with the UUATAC-seq protocol

value: SpinalCord

value: Mecp2 KO

value: Male

value: 8 weeks


title: KO95_indexG6

source_name: G.I., SARS-CoV-2, I.N., 3dpi, 3

value: WT


title: C57_Eye_KO_Male5

description:
Library name: C57_Eye_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7 weeks


title: KO94_indexF6

source_name: Pancreas, SARS-CoV-2, I.N., 3dpi, 3

value: Pancreas

value: 3 dpi


title: Microbiota of stool EG36 – control male

description:
Library name: EG36
16s  rRNA v3-v4 sequencing of mice stool


title: C57_Eye_KO_Male2

description:
Library name: C57_Eye_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: Microbiota of stool EG34 – control female

description:
Library name: EG34
16s rRNA v3-v4 sequencing of mice stool

value: female


title: Microbiota of stool EG35 – control male

description:
Library name: EG35
16s rRNA v3-v4 sequencing of mice stool


title: PT6,Thymus_MG, scRNA-seq

description:
Library name: PT6.S7.Thymus_MG.Mixed
10x Genomics

value: all Thymus cells

value: Thymus


title: KO93_indexE6

source_name: Kidney, SARS-CoV-2, I.N., 3dpi, 3

value: Kidney


title: C57_Eye_KO_Male1

description:
Library name: C57_Eye_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: PT16,ThymicCarcinoma, scRNA-seq

description:
Library name: PT16.S23.ThymicCarcinoma.Mixed
10x Genomics


title: KO92_indexD6

source_name: Liver, SARS-CoV-2, I.N., 3dpi, 3

value: Liver


title: Microbiota of stool EG33 – control male

description:
Library name: EG33
16s  rRNA v3-v4 sequencing of mice stool

value: Stool

value: control

value: male


title: Microbiota of stool EG32 – control male

description:
Library name: EG32
16s rRNA v3-v4 sequencing of mice stool


title: PT16,Thymus_no_MG, scRNA-seq

description:
Library name: PT16.S22.Thymus_no_MG.Mixed
10x Genomics


title: Microbiota of stool EG31 – control male

description:
Library name: EG31
16s rRNA v3-v4 sequencing of mice stool


title: C57_Eye_KO_Female1

description:
Library name: C57_Eye_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Eye

value: Female


title: PT15,Thymus_MG, scRNA-seq

description:
Library name: PT15.S21.Thymus_MG.Mixed
10x Genomics


title: KO90_indexB6

description: PolyA enriched and prepared using TruSeq Stranded mRNA library prep

source_name: Heart, SARS-CoV-2, I.N., 3dpi, 3

value: Heart

value: 1000 PFU SARSCOV2 IN


title: Microbiota of stool EG30 –  control female

description:
Library name: EG30
16s  rRNA v3-v4 sequencing of mice stool


title: KO89_indexA6

source_name: Lung, SARS-CoV-2, I.N., 3dpi, 3

value: Lung

value: WT


title: C57_Eye_KO_Female2

description:
Library name: C57_Eye_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: 8 months


title: PT14,MetastasisTumor, scRNA-seq

description:
Library name: PT14.S20.MetastasisTumor.Mixed
10x Genomics


title: Microbiota of stool EG29 –  PAE female

description:
Library name: EG29
16s rRNA v3-v4 sequencing of mice stool

value: PAE


title: C57_Epididymis_WT_Male3

description:
Library name: C57_Epididymis_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Epididymis

value: Epididymis

value: Male

value: 8 weeks


title: PT14,PrimaryTumor, scRNA-seq

description:
Library name: PT14.S19.PrimaryTumor.Mixed
10x Genomics

value: all Thymus cells

value: Thymus


title: Microbiota of stool EG28 –  PAE female

description:
Library name: EG28
16s rRNA v3-v4 sequencing of mice stool

value: Stool

value: female


title: KO87_indexG5

source_name: G.I., SARS-CoV-2, I.N., 3dpi, 2

value: 3 dpi


title: KO86_indexF5

source_name: Pancreas, SARS-CoV-2, I.N., 3dpi, 2

value: Pancreas


title: Microbiota of stool EG27 –  PAE female

description:
Library name: EG27
16s  rRNA v3-v4 sequencing of mice stool


title: C57_Epididymis_WT_Male2

description:
Library name: C57_Epididymis_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 10 weeks


title: KO85_indexE5

source_name: Kidney, SARS-CoV-2, I.N., 3dpi, 2

value: Kidney


title: PT12,Thymoma_MG, scRNA-seq

description:
Library name: PT12.S17.Thymoma_MG.Mixed
10x Genomics


title: C57_Epididymis_KO_Male5

description:
Library name: C57_Epididymis_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7 weeks


title: C57_Epididymis_KO_Male4

description:
Library name: C57_Epididymis_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: PT12,Thymus_MG, scRNA-seq

description:
Library name: PT12.S16.Thymus_MG.Mixed
10x Genomics


title: KO84_indexD5

source_name: Liver, SARS-CoV-2, I.N., 3dpi, 2

value: Liver

value: 1000 PFU SARSCOV2 IN


title: PT11,Thymus_MG, scRNA-seq

description:
Library name: PT11.S15.Thymus_MG.Mixed
10x Genomics


title: KO83_indexC5

source_name: Spleen, SARS-CoV-2, I.N., 3dpi, 2

value: Spleen

value: WT


title: Microbiota of stool EG24 – PAE male

description:
Library name: EG24
16s  rRNA v3-v4 sequencing of mice stool

value: PAE

value: male


title: C57_Epididymis_KO_Male2

description:
Library name: C57_Epididymis_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Epididymis

value: Mecp2 KO

value: Male

value: 9 weeks


title: Microbiota of stool EG23 – PAE male

description:
Library name: EG23
16s rRNA v3-v4 sequencing of mice stool

value: Stool


title: PT10,Thymoma_no_MG, scRNA-seq

description:
Library name: PT10.S14.Thymoma_no_MG.Mixed
10x Genomics

value: all Thymus cells

value: Thymus


title: KO82_indexB5

description: PolyA enriched and prepared using TruSeq Stranded mRNA library prep

source_name: Heart, SARS-CoV-2, I.N., 3dpi, 2

value: Heart

value: 3 dpi


title: C57_Epididymis_KO_Male1

description:
Library name: C57_Epididymis_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: KO81_indexA5

source_name: Lung, SARS-CoV-2, I.N., 3dpi, 2

value: Lung


title: Microbiota of stool EG22 – PAE male

description:
Library name: EG22
16s rRNA v3-v4 sequencing of mice stool

source_name: Stool


title: 92.1 cells, VE-822 treated sample 3

city: Nashville

first: Michael

middle: L

last: Freeman

address: 2220Pierce Ave

department: Radiation Oncology

institute: Vanderbilt University Medical Center

description: Library name: ATRi_3

data_processing:
Real Time Analysis Software (RTA) and NovaSeq Control Software (NCS 1.8.0; Illumina) were used for base calling. MultiQC (v1.7; Illumina) was used for data quality assessments.).
Reads were trimmed to remove adapter sequences using Cutadapt (v4.8)
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC (v0.12.1)
Reads were aligned to the Gencode GRCh38.p13 genome using STAR (v2.7.11a). Gencode v38 gene annotations were provided to STAR to improve the accuracy of mapping. featureCounts (v2.0.6) was used to count the number of mapped reads to each gene.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file of raw counts for each sample
Supplementary files format and content: TXV files with FPKM values for each sample

source_name: Uveal melanoma

extract_protocol:
Pelleted cells were lysed in RNAProtect (Qiagen). A Quality Control analysis was performed on the RNA samples using the Agilent Bioanalyzer to assess quality and an RNA Qubit assay was used to determine quantity.  Poly(A) RNA enrichment was conducted using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB), and the sequencing library was constructed by using the NEBNext Ultra II RNA Library Prep Kit (NEB) (P/N: E7765L, NEB, Ipswich, MA) following the manufacturer’s instructions
End repair, A-tailing, and adapter ligation was performed to generate the final cDNA library.

value: Uveal melanoma


title: Microbiota of stool EG21 – PAE male

description:
Library name: EG21
16s  rRNA v3-v4 sequencing of mice stool


title: C57_Diencephalon_WT_Male5

description:
Library name: C57_Diencephalon_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Diencephalon

value: Diencephalon

value: 8 weeks


title: PT5,Thymus_MG, scRNA-seq

description:
Library name: PT5.S6.Thymus_MG.Mixed
10x Genomics

source_name: Thymus


title: PT1,Thymoma_no_MG,thymocytes, scRNA-seq

description:
Library name: PT1.S1.Thymoma_no_MG.thymocytes
10x Genomics

value: thymocytes


title: C57_Diencephalon_WT_Male4

description:
Library name: C57_Diencephalon_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: WT


title: 92.1 cells, VE-822 treated sample 2

description: Library name: ATRi_2


title: KO78_indexF4

source_name: Pancreas, SARS-CoV-2, I.N., 3dpi, 1

value: Pancreas

value: 1000 PFU SARSCOV2 IN


title: C57_Diencephalon_WT_Male3

description:
Library name: C57_Diencephalon_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: 92.1 cells, VE-822 treated sample 1

description: Library name: ATRi_1


title: Microbiota of stool EG19 – PAE male

description:
Library name: EG19
16s rRNA v3-v4 sequencing of mice stool

value: PAE

value: male


title: C57_Diencephalon_WT_Male2

description:
Library name: C57_Diencephalon_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male

value: 10 weeks


title: KO76_indexD4

source_name: Liver, SARS-CoV-2, I.N., 3dpi, 1

value: Liver


title: 92.1 cells, DMSO treated, sample 3

description: Library name: DMSO_3


title: C57_Diencephalon_WT_Female3

description:
Library name: C57_Diencephalon_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 7.5 months


title: 92.1 cells, DMSO treated, sample 2

description: Library name: DMSO_2


title: KO75_indexC4

source_name: Spleen, SARS-CoV-2, I.N., 3dpi, 1

value: Spleen


title: Microbiota of stool EG17 – PAE male

description:
Library name: EG17
16s rRNA v3-v4 sequencing of mice stool

value: Stool


title: C57_Diencephalon_WT_Female2

description:
Library name: C57_Diencephalon_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: Microbiota of stool EG16 – PAE male

description:
Library name: EG16
16s rRNA v3-v4 sequencing of mice stool


title: KO74_indexB4

source_name: Heart, SARS-CoV-2, I.N., 3dpi, 1

value: Heart

value: 3 dpi


title: C57_Diencephalon_WT_Female1

description:
Library name: C57_Diencephalon_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Diencephalon


title: KO73_indexA4

source_name: Lung, SARS-CoV-2, I.N., 3dpi, 1

value: Lung


title: MP38 cells, VE-822 treated sample 3

description: Library name: VE822_3

value: Uveal melanoma


title: Microbiota of stool EG15 – PAE female

description:
Library name: EG15
16s  rRNA v3-v4 sequencing of mice stool

value: female


title: Microbiota of stool EG20 – PAE male

description:
Library name: EG20
16s rRNA v3-v4 sequencing of mice stool


title: C57_Diencephalon_KO_Male5

description:
Library name: C57_Diencephalon_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: 7 weeks


title: MP38 cells, VE-822 treated sample 2

description: Library name: VE822_2


title: KO77indexE4

description: PolyA enriched and prepared using TruSeq Stranded mRNA library prep

source_name: Kidney, SARS-CoV-2, I.N., 3dpi, 1

value: Kidney

value: WT

value: 1000 PFU SARSCOV2 IN


title: znf804a-2dpf,het,rep3

city: Worcester

first: Summer

last: Thyme

state: MA

address: 364 Plantation St

institute: UMass Chan Medical School

description: Library name: Sample 30

data_processing:
Paired-end and single-end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner (2.7.3a-GCC-6.4.0-2.28).
The raw counts files from STAR, in this record, were normalized using the rlog method in DESeq2 for subsequent published analysis.
To analyze splicing and produce the sample_#.isoforms.results.gz files, rsem-calculate-expression from the 1.3.3 version was run with the following commands:   --paired-end \   --bam \   --calc-pme \   --num-threads 4 \
Assembly: GRCz11
Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2.
Supplementary files format and content: Isoform quantification from RSEM

organism: Danio rerio

source_name: 2 dpf head with eyes, 3 heads combined

extract_protocol:
RNA was extracted using the MicroElute Total RNA Kit (Omega Bio-Tek R6834-02), with a 15-min incubation with Dnase I.
Libraries were constructed using an in-house protocol based on SMART-Seq2, followed by Nextera XT Library Preparation (FC-131-1096).

value: 2 dpf head with eyes, 3 heads combined

value: znf804a heterozygous mutant

tag: sample group


title: Microbiota of stool EG14 – PAE female

description:
Library name: EG14
16s rRNA v3-v4 sequencing of mice stool

value: PAE


title: C57_Diencephalon_KO_Male4

description:
Library name: C57_Diencephalon_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male

value: 8 weeks


title: MP38 cells, VE-822 treated sample 1

description: Library name: VE822_1


title: Microbiota of stool EG18 – PAE male

description:
Library name: EG18
16s  rRNA v3-v4 sequencing of mice stool

value: Stool

value: male


title: znf804a-2dpf,het,rep2

description: Library name: Sample 29


title: Microbiota of stool EG13 – PAE female

description:
Library name: EG13
16s rRNA v3-v4 sequencing of mice stool


title: C57_Diencephalon_KO_Male2

description:
Library name: C57_Diencephalon_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: MP38 cells, DMSO treated, sample 3

description: Library name: Control_3


title: KO100_indexD7

source_name: O.B., SARS-CoV-2, I.N., 3dpi, 1

value: Olfactory bulb

value: 3 dpi


title: znf804a-2dpf,het,rep1

description: Library name: Sample 28


title: C57_Diencephalon_KO_Male1

description:
Library name: C57_Diencephalon_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Diencephalon


title: Microbiota of stool EG12 –PAE female

description:
Library name: EG12
16s  rRNA v3-v4 sequencing of mice stool

value: female


title: PT9,MetastasisTumor1, scRNA-seq

description:
Library name: PT9.S11.MetastasisTumor1.Mixed
10x Genomics

value: all Thymus cells

value: Thymus


title: C57_Eye_WT_Female3

description:
Library name: C57_Eye_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Eye

value: Eye

value: Female

value: 7.5 months


title: PT9,Thymus_MG, scRNA-seq

description:
Library name: PT9.S10.Thymus_MG.Mixed
10x Genomics


title: MP38 cells, DMSO treated, sample 2

description: Library name: Control_2

value: Uveal melanoma


title: znf804a-2dpf,hom,rep3

description: Library name: Sample 27

value: 2 dpf head with eyes, 3 heads combined

value: znf804a homozygous mutant


title: Microbiota of stool EG11 – PAE female

description:
Library name: EG11
16s rRNA v3-v4 sequencing of mice stool

value: PAE


title: 92.1 cells, DMSO treated, sample 1

description: Library name: DMSO_1


title: C57_Diencephalon_KO_Female3

description:
Library name: C57_Diencephalon_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO


title: MP38 cells, DMSO treated, sample 1

description: Library name: Control_1


title: znf804a-2dpf,hom,rep2

description: Library name: Sample 26


title: PT7,Thymus_M, scRNA-seq

description:
Library name: PT7.S8.Thymus_MG.Mixed
10x Genomics


title: Microbiota of stool EG10 – control female

description:
Library name: EG10
16s rRNA v3-v4 sequencing of mice stool

value: Stool

value: control


title: C57_Diencephalon_KO_Female2

description:
Library name: C57_Diencephalon_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 months


title: MV3 tumor biol rep 2

city: miami

first: RIMPI

last: KHURANA

state: FL

address: Room 6112B, Rosenstiel Medical Science Building (RMSB),1600 NW 10th Avenue

institute: University of miami

description:
Library name: MV_3
Human tumor reads from xenograft

data_processing:
Reads were pre-processed using Xenome to separate human tumor reads from mouse stromal reads in xenograft samples
Reads were aligned to the human reference genome using STAR.
Gene-level counts were generated and normalized using variance-stabilizing transformation (VST).
Differential expression analysis was performed with DESeq2, using adjusted p<0.05 and |log2FC|>1 as significance thresholds.
Pathway analysis was conducted using GO, KEGG, and Ingenuity Pathway Analysis (IPA).
Assembly: Homo sapiens reference genome (e.g., GRCh38/hg38). If a specific Novogene build was used, this can be updated.
Supplementary files format and content: Normalized gene expression matrix (variance-stabilized counts) in tab-delimited text format. Includes gene identifiers, normalized expression values for each sample, and sample metadata.

source_name: Tumor xenograft

growth_protocol: HT-29 human colorectal cancer cells were implanted subcutaneously into 5–6-week-old male and female NSG mice. For RNA-seq experiments, 1.5×10^6 HT-29 cells were injected into the right flank. Tumors were allowed to grow until they reached ~150 mm³ before randomization and treatment.

extract_protocol:
Tumors were dissected and homogenized. Total RNA was isolated using the KingFisher Apex automated system (ThermoFisher) with Zymo Direct-zol Mag-Bead chemistry. RNA purity and integrity were verified using the Agilent Fragment Analyzer. Only high-quality RNA was used for library preparation.
RNA samples were submitted to Novogene. Poly-A–selected, non-directional cDNA libraries were prepared according to the Novogene standard mRNA-seq workflow. Libraries were sequenced on the Illumina NovaSeq X Plus platform.

treatment_protocol: Mice were randomized into four groups: (1) vehicle control, (2) MV-CD46-muPA (1.5×10^6 TCID50) administered via tail vein twice every other day, (3) Minnelide (0.21 mg/kg) administered intraperitoneally once daily, or (4) combination of MV-CD46-muPA plus Minnelide. Treatments were given for 7 days. Tumors were collected immediately after the final Minnelide treatment.

value: Tumor xenograft

value: epithelial

tag: batch


title: znf804a-2dpf,hom,rep1

description: Library name: Sample 25


title: Microbiota of stool EG9 –  control female

description:
Library name: EG9
16s  rRNA v3-v4 sequencing of mice stool


title: C57_Diencephalon_KO_Female1

description:
Library name: C57_Diencephalon_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Diencephalon

value: 9 weeks


title: C57_Eye_KO_Female3

description:
Library name: C57_Eye_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: MV2 tumor biol rep 1

description:
Library name: MV_2
Human tumor reads from xenograft


title: FACS-purified MG and their neuronal progeny 1 month after sodium iodate and TDI-011536 treatment

city: Hengyang

first: Houjian

state: Hunan

address: Shigu District Chuanshan Road

institute: The First Affiliated Hospital of University of South China

description:
Library name: Sample 1
10x Genomics

data_processing:
The raw sequencing data were processed using 10x Genomics' official analysis software, Cell Ranger, which performed data filtering, genome alignment, transcript quantification, and cell identification. This pipeline ultimately generated the gene expression matrix for each individual cell.
Subsequent analysis was performed using Seurat for further cell filtering, standardization of cell expression quantification, cell subpopulation classification, differential gene expression analysis across subpopulations, and marker gene screening.
Assembly: Mus musculus GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: retina

extract_protocol:
Cell quality control adjust the cell concentration to the optimal level, typically 1000 cells/μL. 10X Barcoding of cDNA Fragments Gel beads carrying barcode information are combined with a mixture of cells and enzymes, then encapsulated by oil-surfactant droplets within a microfluidic system to form GEMs. The GEMs flow into a collection reservoir, where the gel beads dissolve to release the barcode sequences. Reverse transcription is performed to generate cDNA fragments, and samples are labeled. The gel beads are then disrupted and the oil droplets are broken. Using the cDNA as a template, PCR amplification is carried out. The products from all GEMs are pooled to construct a standard sequencing library.
The cDNA is enzymatically fragmented into segments of approximately 200-300 bp. This is followed by traditional second-generation sequencing library preparation steps, such as the addition of sequencing adapters and primers. Finally, PCR amplification is performed to obtain the DNA library.

value: retina

value: Muller glia

value: GlastCreERT2+/tg; ROSA26R-tdTomato+/tg

value: sodium iodate and TDI-011536


title: KO91_indexC6

description: PolyA enriched and prepared using TruSeq Stranded mRNA library prep

source_name: Spleen, SARS-CoV-2, I.N., 3dpi, 3

value: Spleen

value: 3 dpi

value: WT

value: 1000 PFU SARSCOV2 IN


title: Microbiota of stool EG8 –  control female

description:
Library name: EG8
16s rRNA v3-v4 sequencing of mice stool

value: female


title: Minnelide4 tumor biol rep 4

description:
Library name: Minnelide_4
Human tumor reads from xenograft

value: Minnelide


title: C57_Cerebellum_WT_Male5

description:
Library name: C57_Cerebellum_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Cerebellum

value: Cerebellum

value: Male

value: 8 weeks


title: Wildtype GV oocyte Replicate 7

city: Copenhagen N

first: Daniel

middle: Martin

last: Messerschmidt

state: Zealand

address: 3C Blegdamsvej, Building 18

department: Faculty of Health and Medical Sciences

country: Denmark

institute: University of Copenhagen

description: Library name: wt_08

data_processing:
RNA-seq analysis was performed on the Galaxy platform. Sequence reads were mapped to the mouse genome build GRCm38.p6 (mm10) using STAR (Galaxy Version 2.7.11a), and gene-level transcript abundances were quantified by featureCounts (Galaxy Version 2.0.3) against the built-in gene annotation file (NCBI RefSeq)
Assembly: mm10/GRCm38
Supplementary files format and content: bigwig (signal tracks)

source_name: GV oocyte

extract_protocol:
For RNA-seq of knock out and wildtype oocytes, single oocytes were extrated as described previously Han et al. (2020) following the protocol by Picelli et al. (2014).
GV oocytes were individually snap frozen in 4 ul lysis buffer containing dNTP mix, oligo-dT primer and SUPERase-In RNase inhibitor (Invitrogen). RNA-seq library preparation was performed according to the Smart-seq2 protocol with slight modifications. 10 cycles of PCR pre-amplification were carried out. 1 ng of cDNA was used for tagmentation with the Nextera XT DNA Library Prep Kit (Illumina). Final libraries were amplified and pooled for single-end Illumina sequencing.

value: GV oocyte

value: wildtype


title: C57_Cerebellum_WT_Male4

description:
Library name: C57_Cerebellum_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: Minnelide3 tumor biol rep 3

description:
Library name: Minnelide_3
Human tumor reads from xenograft

value: Tumor xenograft

value: epithelial


title: Microbiota of stool EG7 – control male

description:
Library name: EG7
16s rRNA v3-v4 sequencing of mice stool

source_name: Stool

value: Stool

value: control

value: male


title: Microbiota of stool EG5 – control male

description:
Library name: EG6
16s  rRNA v3-v4 sequencing of mice stool


title: Wildtype GV oocyte Replicate 6

description: Library name: wt_07


title: C57_Cerebellum_WT_Male3

description:
Library name: C57_Cerebellum_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: Wildtype GV oocyte Replicate 5

description: Library name: wt_06


title: C57_Epididymis_WT_Male5

description:
Library name: C57_Epididymis_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Epididymis

value: Epididymis


title: C57_Cerebellum_WT_Male2

description:
Library name: C57_Cerebellum_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 10 weeks


title: Minnelide1 tumor biol rep 1

description:
Library name: Minnelide_1
Human tumor reads from xenograft


title: Microbiota of stool EG6 – control male

description:
Library name: EG5
16s rRNA v3-v4 sequencing of mice stool


title: Minnelide2 tumor biol rep 2

description:
Library name: Minnelide_2
Human tumor reads from xenograft


title: Wildtype GV oocyte Replicate 4

description: Library name: wt_05


title: Microbiota of stool EG4 –  control female

description:
Library name: EG4
16s rRNA v3-v4 sequencing of mice stool


title: C57_Cerebellum_WT_Female3

description:
Library name: C57_Cerebellum_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 7.5 months


title: Control4 tumor biol rep 4

description:
Library name: Control_4
Human tumor reads from xenograft

value: Vehicle / No treatment


title: Wildtype GV oocyte Replicate 3

description: Library name: wt_03


title: Microbiota of stool EG3 –  control female

description:
Library name: EG3
16s  rRNA v3-v4 sequencing of mice stool

value: female


title: KO88_indexH5

description: PolyA enriched and prepared using TruSeq Stranded mRNA library prep

source_name: Brain, SARS-CoV-2, I.N., 3dpi, 2

value: Brain

value: 3 dpi

value: WT

value: 1000 PFU SARSCOV2 IN


title: Control3 tumor biol rep 3

description:
Library name: Control_3
Human tumor reads from xenograft


title: C57_Cerebellum_WT_Female2

description:
Library name: C57_Cerebellum_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Cerebellum


title: PT13,Thymoma_MG, scRNA-seq

description:
Library name: PT13.S18.Thymoma_MG.Mixed
10x Genomics

source_name: Thymus

value: all Thymus cells

value: Thymus


title: Wildtype GV oocyte Replicate 2

description: Library name: wt_02

value: GV oocyte

value: wildtype


title: Microbiota of stool EG2 –  control male

description:
Library name: EG2
16s rRNA v3-v4 sequencing of mice stool

value: Stool

value: control


title: Control2 tumor biol rep 2

description:
Library name: Control_2
Human tumor reads from xenograft

value: Tumor xenograft

value: epithelial


title: Microbiota of stool EG1 –  control male

description:
Library name: EG1
16s rRNA v3-v4 sequencing of mice stool

value: male


title: Wildtype GV oocyte Replicate 1

description: Library name: wt_01


title: C57_Cerebellum_WT_Female1

description:
Library name: C57_Cerebellum_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 8 weeks


title: C57_Cerebellum_KO_Male5

description:
Library name: C57_Cerebellum_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: Male

value: 7 weeks


title: MPC5  Setdb2KO  high-glucose, rep3

first: Lanfang

last: Li

state: State...

address: China-japan Friendship Hospital

institute: China-japan Friendship Hospital

description: Library name: Sample 6

data_processing:
Rawreads of fastqformatwere firstly processed using fastp and the low quality reads were removed to obtainthecleanreads.Then reads for each sample were retained for subsequent analyses. Thecleanreads were mapped to the reference genome using HISAT. FPKM of each gene was calculatedandthe read counts of each gene were obtained by HTSeq-count. PCA analysis were performedusingR(v 3.2.0) to evaluate the biological duplication of samples.
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: mouse podocyte

value: KO

value: high-glucose


title: C57_Cerebellum_KO_Male4

description:
Library name: C57_Cerebellum_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were then aligned to mm10 using STAR (v2.7.10a).
Read counts were generated using featureCounts.
Transcripts were quantified with Salmon (v1.10.3) in quasi-mapping-based mode.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw count values for individual samples.

value: Cerebellum


title: Knock out GV oocyte Replicate 7

description: Library name: Obi1_KO_08

value: Knock out


title: Combination4 tumor biol rep 4

description:
Library name: Combination4
Human tumor reads from xenograft

value: MV + Minnelide (Combination)


title: Knock out GV oocyte Replicate 6

description: Library name: Obi1_KO_07

value: GV oocyte


title: C57_Cerebellum_KO_Male3

description:
Library name: C57_Cerebellum_KO_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: MPC5  Setdb2KO  high-glucose, rep2

description: Library name: Sample 5


title: MPC5  Setdb2KO  high-glucose, rep1

description: Library name: Sample 4


title: Combination3 tumor biol rep 3

description:
Library name: Combination3
Human tumor reads from xenograft


title: Knock out GV oocyte Replicate 5

description: Library name: Obi1_KO_06


title: Knock out GV oocyte Replicate 4

description: Library name: Obi1_KO_05


title: Combination2 tumor biol rep 2

description:
Library name: Combination2
Human tumor reads from xenograft


title: C57_Cerebellum_KO_Male2

description:
Library name: C57_Cerebellum_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: C57_Cerebellum_KO_Male1

description:
Library name: C57_Cerebellum_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: MPC5  Setdb2WT  high-glucose, rep3

description: Library name: Sample 3

value: WT


title: MPC5  Setdb2WT  high-glucose, rep2

description: Library name: Sample 2


title: C57_Cerebellum_KO_Female3

description:
Library name: C57_Cerebellum_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 7.5 months


title: Knock out GV oocyte Replicate 3

description: Library name: Obi1_KO_03


title: Combination1 tumor biol rep 1

description:
Library name: Combination1
Human tumor reads from xenograft

value: Tumor xenograft

value: epithelial


title: Peripheral CD8+ T cells, siControl transfected, anti-CD3/CD28 activated, 24-hours, healthy donor 3 (ATAC-16)

city: Rochester

first: Emilia

middle: R

last: Dellacecca

state: MN

address: 200 First Street SW, Kellen Building 02-102

department: Immunology

institute: Mayo Clinic

description: Library name: ATAC-16

data_processing:
Paired-end reads were aligned to human genome (hg38) using Burrows-Wheeler Aligner (v0.5.9) and PCR duplicates were removed with Picard MarkDuplicates (v1.67).
Peaks were called with MAC2 (v2.0.10) using default parameters.
Assembly: hg38
Supplementary files format and content: bigWig format

source_name: Peripheral blood

growth_protocol: CD8+ T cells were maintained in RPMI 1640 + 10% fetal bovine serum, 20 mM HEPES buffer, and 1X penicillin/streptomycin at 37 degrees Celsius with 5% CO2.

extract_protocol:
100,00 nucleofected CD8+ T cells were prepped following the published OMNI ATAC-seq protocol.
Amplified libraries were purified and the size of library DNA was determined with a fragment analyzer (Advanced Analytical Technologies) using the High Sensitivity NGS Fragment Analysis Kit (Advanced Analytical Technologies). Enrichment of accessible regions was determined by the fold difference between positive and negative genomic loci using real-time PCR. The libraries were sequenced to 51 base pairs from both ends.

treatment_protocol: CD8+ T cells were transfected with DUSP2-targeting siRNA (Horizon Discovery, Dharmacon) or negative control siRNA (Horizon DIscovery, Dharmacon) by nucleofection (Lonza) and activated with anti-CD3/CD28 soluble antibodies (STEMCELL Technologies) for 48-hours, rested cells were maintained under the same conditions without addition of activating antibodies.

value: Peripheral blood

value: CD8+ T cells

value: siControl, activated with anti-CD3/CD28

value: 66 years


title: Knock out GV oocyte Replicate 2

description: Library name: Obi1_KO_02


title: C57_Cerebellum_KO_Female2

description:
Library name: C57_Cerebellum_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: Female

value: 8 months


title: Peripheral CD8+ T cells, siControl transfected, healthy donor 3 (ATAC-15)

description: Library name: ATAC-15

value: siControl

value: Male


title: Knock out GV oocyte Replicate 1

description: Library name: Obi1_KO_01

value: Knock out


title: C57_Cerebellum_KO_Female1

description:
Library name: C57_Cerebellum_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Cerebellum


title: C57_Thymus_KO_Male5

description:
Library name: C57_Thymus_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Thymus

value: 7 weeks


title: M1C+H1930002 (M1C_3C_002_Plate4)

city: La Jolla

first: Joseph

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: Library name: M1C_and_H1930002_M1C_3C_002_Plate4

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)  The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.         The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates.      Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files. Tab-delimited files (HIC files) describing the chromatin contacts will be generated with in-house developing package using the filtered BAM files.
Assembly: hg38
Supplementary files format and content: An ALLC file contains 7 columns with DNA methylation information of a single cell at single base resolution. The columns are 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column.   A contact file contains long range chromatin contacts of a single cell after removing the ones overlapping blacklists. The columns are 1. Strand1, 2. Chromosome1, 3. Position1, 4. place holder column, always be 0, 5. Strand2, 6. Chromosome2, 7. Position2, 8. place holder column, always be 1.
Library strategy: snm3C-seq

source_name: Primary Motor Cortex

extract_protocol:
Nuclei extraction protocol can be found at https://www.protocols.io/view/snm3c-seq3-kqdg3x6ezg25/v1
Library preparation protocol can be found at https://www.protocols.io/view/snm3c-seq3-kqdg3x6ezg25/v1

value: Primary Motor Cortex


title: 21222X8 GAN KO

city: Salt Lake City

first: Dipayan

last: Chaudhuri

state: UT

institute: University of Utah

description: Library name: Sample 18

data_processing:
The mouse GRCm39 genome and gene annotation files were downloaded from Ensembl release 110 and a reference database was created using STAR version 2.7.9a
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Assembly: GRCm39
Supplementary files format and content: featureCount output files combined into a single tab-delimited matrix

source_name: Liver tissue

extract_protocol:
Livers were treated with trizole and then extracted using the Zymo RNA extraction kit (Cat #R2062)
Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold. Total RNA samples (100-500 ng) were hybridized with Ribo-Zero Gold to substantially deplete cytoplasmic and mitochondrial rRNA from the samples.  Stranded RNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded Total RNA Library Prep Gold kit (20020598) with TruSeq RNA UD Indexes (20022371).  Purified libraries were qualified on an Agilent Technologies 4150 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 1.30 nM in preparation for Illumina sequence analysis.

treatment_protocol: C57BL/6 mice we fed either a CHOW or a GAN diet for 28 weeks (diet begun at 8 weeks). At 28 weeks post diet, mice were sacrificed and their livers removed.

value: Liver tissue

value: EFHD1 KO

value: GAN diet, 28 weeks


title: C57_BrownFat_WT_Male5

first: Xiaoping

description:
Library name: C57_BrownFat_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: BrownFat

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2-3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme). The extracted RNA was used for reverse transcription. Following the reaction, a PCR amplification program was performed. Purification was then conducted using 0.9× of VAHTS DNA Clean Beads. TruePrep DNA Library Prep Kit for MGI (Vazyme) was used for sequencing library construction.

value: BrownFat

value: WT

value: 8 weeks


title: Peripheral CD8+ T cells, siDUSP2 transfected, anti-CD3/CD28 activated, 24-hours, healthy donor 3 (ATAC-14)

description: Library name: ATAC-14

value: Peripheral blood

value: CD8+ T cells

value: siDUSP2, activated with anti-CD3/CD28

value: 66 years


title: Peripheral CD8+ T cells, siDUSP2 transfected, healthy donor 3 (ATAC-13)

description: Library name: ATAC-13


title: Peripheral CD8+ T cells, siControl transfected, anti-CD3/CD28 activated, 24-hours, healthy donor 2 (ATAC-10)

description: Library name: ATAC-10

value: siControl, activated with anti-CD3/CD28

value: 64 years


title: 21222X7 GAN KO

description: Library name: Sample 17


title: C57_BrownFat_WT_Male4

description:
Library name: C57_BrownFat_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Male


title: HA-ZFPOBI1 OE H3K9me3_ChIP replicate 2

description: Library name: clK9_2

data_processing:
Raw reads were aligned to mm10 genome using Bowtie2 (default parameters), before sorting the bam files with samtools sort.Bigwig files were generated with the bamCoverage fonction of deeptools2.0, using the options --normalizeUsing RPKM --binSize 25 --smoothLength 100. Peaks were called with Macs2 callpeak (default parameters).
Assembly: mm10
Supplementary files format and content: bigwig files showing read coverage

source_name: mouse embryonic stem cell

growth_protocol: Embryonic stem cells were cultured under standard LIF/FCS conditions.

extract_protocol:
genomic DNA
ChIP was performed as previously described {Guccione:2007dy}. Chromatin was fragmented using a BRANSON Digital Sonifier (#S540D) to 250-1000bp fragments, precleared and incubated with antibodies overnight. Antibody/chromatin complexes were incubated for 50% Protein-G Sepharose slurry and washed before elution/decrosslinking in 1% SDS and 0.1 M NaHCO3. DNA was column purified with QIAquick PCR purification Kit, Qiagen.ChIP DNA concentrations were measured with the Qubit dsDNA HS Assay kit (Thermo Fisher Scientific). Libraries were prepared with the NEBNext Ultra II DNA Library Preparation Kit for Illumina (NEB), following manufacturer’s instructions. PCR conditions were adjusted to starting material concentrations and final elution volumes were reduced. Libraries were quantified by Bioanalyzer (High Sensitivity DNA Kit, Agilent) and PCR (KAPA Library Quantification Kit for Illumina, Roche). ChIP-Seq libraries were pooled and sequenced on the NextSeq500, as a single end (76bp) run

value: mouse embryonic stem cell

value: antibody:alpha-H3K9me3, Abcam, ab8898, 3 ug


title: 21222X6 GAN KO

description: Library name: Sample 16


title: HA-ZFPOBI1 OE H3K9me3_ChIP replicate 1

description: Library name: clK9_1


title: Peripheral CD8+ T cells, siControl transfected, healthy donor 2 (ATAC-9)

description: Library name: ATAC-9

value: siControl


title: 21222X5 GAN KO

description: Library name: Sample 15


title: C57_BrownFat_WT_Male2

description:
Library name: C57_BrownFat_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 10 weeks


title: Peripheral CD8+ T cells, siDUSP2 transfected, anti-CD3/CD28 activated, 24-hours, healthy donor 2 (ATAC-8)

description: Library name: ATAC-8


title: HA-ZFPOBI1 OE TRIM28-ChIP replicate 2

description: Library name: clTR28_2

value: antibody:alpha-TRIM28, Abcam ab10484, 5ug


title: 21222X4 GAN WT

description: Library name: Sample 14

value: Liver tissue

value: WT (6NJ)


title: 21222X3 GAN WT

description: Library name: Sample 13

value: GAN diet, 28 weeks


title: HA-ZFPOBI1 OE TRIM28-ChIP replicate 1

description: Library name: clTR28_1


title: C57_BrownFat_WT_Female3

description:
Library name: C57_BrownFat_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: BrownFat

value: WT

value: Female

value: 7.5 months


title: C57_BrownFat_WT_Female2

description:
Library name: C57_BrownFat_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: Peripheral CD8+ T cells, siControl transfected, anti-CD3/CD28 activated, 24-hours, healthy donor 1 (ATAC-4)

description: Library name: ATAC-4

value: Peripheral blood

value: CD8+ T cells

value: 68 years


title: 21222X2 GAN WT

description: Library name: Sample 12


title: C57_BrownFat_WT_Female1

description:
Library name: C57_BrownFat_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 weeks


title: 21222X1 GAN WT

description: Library name: Sample 11


title: C57_BrownFat_KO_Male5

description:
Library name: C57_BrownFat_KO_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: Male

value: 7 weeks


title: HA-ZFPOBI1 OE HA-ChIP replicate 1

description: Library name: clHA_1

value: mouse embryonic stem cell

value: antibody:alpha-HA, Abcm, ab9110, 5 ug


title: Peripheral CD8+ T cells, siDUSP2 transfected, anti-CD3/CD28 activated, 24-hours, healthy donor 1 (ATAC-2)

description: Library name: ATAC-2

value: siDUSP2, activated with anti-CD3/CD28


title: C57_BrownFat_KO_Male4

description:
Library name: C57_BrownFat_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: Peripheral CD8+ T cells, siDUSP2 transfected, healthy donor 1 (ATAC-1)

description: Library name: ATAC-1


title: HA-ZFPOBI1 OE INPUT

description: Library name: clINP


title: C57_BrownFat_KO_Male2

description:
Library name: C57_BrownFat_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: 18513X15 CHOW WT

description: Library name: Sample 8

value: Liver tissue

value: WT (6NJ)

value: CHOW diet control


title: C57_BrownFat_KO_Male1

description:
Library name: C57_BrownFat_KO_Male1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: BrownFat


title: vector control H3K9me3_ChIP replicate 3

description: Library name: vecK9_3

value: antibody:alpha-H3K9me3, Abcam, ab8898, 3 ug


title: Peripheral CD8+ T cells, siControl transfected_healthy donor 3

description: Library name: 15_66M_siCnt_R

data_processing:
Data was processed throught the HiChIP pipeline.
Reads were aligned to genome build (hg38) with Burrows-Wheeler Aligner (v0.5.9) and PCR duplicates were removed using Picard MarkDuplicates (v1.67).
Peaks were called with MACS2 (v2.0.10) at a relaxed significance threshold of q<0.1 to maximize sensitivity for ETS1 binding regions.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
1x106 nucleofected CD8+ T cells were fixed with 1% formaldehyde for 10 minutes, then quenched with glycine, and lysed in RIPA prior to sonication. Partially fragmented chromatin was then incubated with ETS1 (clone [D8O8A], Cell Signaling TECHNOLOGY) coupled Protein A and G Dynabeads (Invitrogen) overnight prior to magnetic bead separation and subjected to tagmentation (Illumina Tagment Kit) for 40 minutes at 37 degrees Celsius and overnight proteinase K (Thermo Scientific) treatment. The aqueous phase was then extracted by phenol:chloroform and precipitated with sodium acetation, glycogen, and ethanol incubated overnight prior to pelleting and resuspension in TE buffer.
DNA was amplified with a High-Fidelity PCR Mix (NEW ENGLAND Bilabs) and 0.4 uM of primers for 12 cycles. Libraries were measured for concentration and quality by Qubit fluorometry and the Agilent Fragment Analyzer and normalized to 1.6 nM. Libraries were pooled and loaded onto a NovaSeq SP flow cell at a final concentration of 320 pM and the flow cell was sequenced as 50 x 2 paired end reads.

tag: individual

value: healthy donor 3

value: siCnt

value: siControl, not activated

value: 66 years


title: C57_BrownFat_KO_Female3

description:
Library name: C57_BrownFat_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 7.5 months


title: Peripheral CD8+ T cells, siDUSP2 transfected, anti-CD3/CD28 activated, 24-hours_healthy donor 3

description: Library name: 14_66M_siDUSP2_A

value: Peripheral blood

value: CD8+ T cells

value: siDUSP2,  activated with anti-CD3/CD28

value: Male


title: vector control H3K9me3_ChIP replicate 1

description: Library name: vecK9_1

value: mouse embryonic stem cell


title: 18513X11 CHOW WT

description: Library name: Sample 6


title: C57_BrownFat_KO_Female2

description:
Library name: C57_BrownFat_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Mecp2 KO

value: 8 months


title: Peripheral CD8+ T cells, siDUSP2 transfected_healthy donor 3

description: Library name: 13_66M_siDUSP2_R

value: siDUSP2, not activated


title: 18513X9 CHOW WT

description: Library name: Sample 5

value: Liver tissue

value: WT (6NJ)

value: CHOW diet control


title: C57_BrownFat_KO_Female1

description:
Library name: C57_BrownFat_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: BrownFat

value: 9 weeks


title: Peripheral CD8+ T cells, siControl transfected, anti-CD3/CD28 activated, 24-hours_healthy donor 2

description: Library name: 10_64M_siCnt_A

value: healthy donor 2

value: siCnt

value: siControl,  activated with anti-CD3/CD28

value: 64 years


title: vector control TRIM28-ChIP replicate 2

description: Library name: vecTR28_2

value: antibody:alpha-TRIM28, Abcam ab10484, 5ug


title: 18513X7 CHOW WT

description: Library name: Sample 4


title: Peripheral CD8+ T cells, siControl transfected_healthy donor 2

description: Library name: 9_64M_siCnt_R

value: Peripheral blood

value: CD8+ T cells

value: siControl, not activated


title: C57_Breast_WT_Female3

description:
Library name: C57_Breast_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: Breast

value: Breast

value: WT

value: Female

value: 7.5 months


title: 18513X5 CHOW KO

description: Library name: Sample 3

value: Liver tissue

value: EFHD1 KO


title: C57_Breast_WT_Female2

description:
Library name: C57_Breast_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues


title: vector control HA-ChIP replicate 3

description: Library name: vecHA_3

value: mouse embryonic stem cell

value: antibody:alpha-HA, Abcm, ab9110, 5 ug


title: 18513X3 CHOW KO

description: Library name: Sample 2

value: CHOW diet control


title: C57_Breast_WT_Female1

description:
Library name: C57_Breast_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 weeks


title: Peripheral CD8+ T cells, siDUSP2 transfected_healthy donor 2

description: Library name: 7_64M_siDUSP2_R

value: healthy donor 2

value: siDUSP2, not activated

value: Male


title: Control1 tumor biol rep 1

description:
Library name: Control_1
Human tumor reads from xenograft

value: Tumor xenograft

value: epithelial

value: Vehicle / No treatment


title: vector control TRIM28-ChIP replicate 1

description: Library name: vecTR28_1

value: antibody:alpha-TRIM28, Abcam ab10484, 5ug


title: vector control HA-ChIP replicate 2

description: Library name: vecHA_2


title: 18513X1 CHOW KO

description: Library name: Sample 1


title: C57_Breast_KO_Female3

description:
Library name: C57_Breast_KO_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Breast

value: Mecp2 KO


title: MPC5  Setdb2WT  high-glucose, rep1

description: Library name: Sample 1

value: mouse podocyte

value: WT

value: high-glucose


title: Peripheral CD8+ T cells, siDUSP2 transfected, anti-CD3/CD28 activated, 24-hours_healthy donor 2

description: Library name: 8_64M_siDUSP2_A

value: Peripheral blood

value: CD8+ T cells

value: siDUSP2,  activated with anti-CD3/CD28

value: 64 years


title: Peripheral CD8+ T cells, siControl transfected, anti-CD3/CD28 activated, 24-hours_healthy donor 1

description: Library name: 4_68F_siCnt_A

value: healthy donor 1

value: siCnt

value: siControl,  activated with anti-CD3/CD28

value: Female

value: 68 years


title: HA-ZFPOBI1 OE H3K9me3_ChIP replicate 3

description: Library name: clK9_3

value: mouse embryonic stem cell

value: antibody:alpha-H3K9me3, Abcam, ab8898, 3 ug


title: 21222X9 GAN KO

description: Library name: Sample 19

value: Liver tissue

value: EFHD1 KO

value: GAN diet, 28 weeks


title: vector control HA-ChIP replicate 1

description: Library name: vecHA_1

value: antibody:alpha-HA, Abcm, ab9110, 5 ug


title: FAD_S_nega

city: Kodaira

first: Fumio

last: Takahashi

address: 4-1-1 Ogawahigashi

country: Japan

institute: National Center of Neurology and Psychiatry

description: Library name: PR3555_gene_expression_6

data_processing:
edgeR (Version 3.26.8)
Assembly: m28
Supplementary files format and content: csv files include TMP values for each sample

source_name: Brain

extract_protocol:
Brain and spinal cords dissected from 3 months-old mice were digested with GentleMACS Octo Dissociator. Neurons were isolated by using MACS® adult brain dissociation kit. Total RNA was extracted from isolated neurons using RNeasy Mini Kit (Qiagen)
SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing, Nextera XT DNA Library Prep Kit and IDT for Illumina - DNA/RNA UD Indexes, Tagmentation

value: Brain

value: Neuron

value: L1-GFP reporter/5xFAD


title: Peripheral CD8+ T cells, siControl transfected_healthy donor 1

description: Library name: 3_68F_siCnt_R

value: Peripheral blood

value: CD8+ T cells

value: siControl, not activated


title: C57_Breast_KO_Female2

city: Hangzhou

last: Han

address: Yuhangtang Road 866

institute: Zhejiang University School of Medicine

description:
Library name: C57_Breast_KO_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Breast

value: Mecp2 KO

value: 8 months


title: vector control INPUT

description: Library name: vecINP


title: HA-ZFPOBI1 OE TRIM28-ChIP replicate 3

description: Library name: clTR28_3

value: antibody:alpha-TRIM28, Abcam ab10484, 5ug


title: C57_Breast_KO_Female1

description:
Library name: C57_Breast_KO_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: Female

value: 9 weeks


title: C57_BrownFat_WT_Male3

description:
Library name: C57_BrownFat_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: BrownFat

value: WT

value: Male

value: 8 weeks


title: Peripheral CD8+ T cells, siDUSP2 transfected, anti-CD3/CD28 activated, 24-hours_healthy donor 1

description: Library name: 2_68F_siDUSP2_A

value: healthy donor 1

value: siDUSP2,  activated with anti-CD3/CD28

value: 68 years


title: FAD_S_posi

description: Library name: PR3555_gene_expression_5

value: Brain

value: Neuron

value: L1-GFP reporter/5xFAD


title: P20 mouse cortex [normoxia]

city: Tainan

first: Chih-Yen Wang

last: Wang

address: No.1, University Rd

department: Biotechnology and Bioindustry Sciences

country: Taiwan

institute: National Cheng Kung University

description: Library name: P20_normoxia

data_processing:
The scRNA-seq data were processed with Cell Ranger Count v7.1.0 (refdata-gex-mm10-2020-A), followed by unbiased clustering using Seurat package in R.
Assembly: mm10
Supplementary files format and content: rds file with integrated data of 2 samples

source_name: brain

extract_protocol:
P20 mouse cortical tissues (3 animals combined per group) were treated with papain and DNase I at 37 degree for 30 min. Unhealthy cells were removed using debris and dead cell removal kit with MS separation columns.
The cell suspension was prepared using single-cell 3’ Library and Gel Bead Kit V3.1 and the Chromium Single Cell G Chip Kit, and then loaded onto the Chromium Single Cell Controller (10x Genomics) to generate single-cell beads in the emulsion according to the manufacturer's protocol.

treatment_protocol: 10.5% oxygen incubation from P3 to P11

value: brain


title: Peripheral CD8+ T cells, siDUSP2 transfected, healthy donor 2 (ATAC-7)

description: Library name: ATAC-7

value: Peripheral blood

value: CD8+ T cells

value: 64 years


title: Litter_S_nega

description: Library name: PR3555_gene_expression_2

value: L1-GFP reporter/WT


title: C57_BrainStem_WT_Male5

description:
Library name: C57_BrainStem_WT_Male5_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

source_name: BrainStem

value: BrainStem


title: Peripheral CD8+ T cells, siDUSP2 transfected_healthy donor 1

description: Library name: 1_68F_siDUSP2_R

value: siDUSP2, not activated

value: Female


title: HA-ZFPOBI1 OE HA-ChIP replicate 3

description: Library name: clHA_3

value: mouse embryonic stem cell

value: antibody:alpha-HA, Abcm, ab9110, 5 ug


title: Peripheral CD8+ T cells, siControl transfected, healthy donor 1 (ATAC-3)

description: Library name: ATAC-3

value: siControl


title: C57_BrainStem_WT_Male4

description:
Library name: C57_BrainStem_WT_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: WT

value: Male

value: 8 weeks


title: P7, mixed brain cell population, w/o treatment, rep 1

city: Paris

first: Tabitha

last: Rücker

address: 25, rue du Docteur Roux

institute: Institut Pasteur

data_processing:
Adapter trimming was performed with cutadapt v. 3.1 (parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA x.fastq). Trimmed sequences were aligned using RNA STAR aligner (v. 2.7.8a) against the GRCm38/mm10 reference. For Gap-aware read counting featureCounts (v. 2.0.1) was applied.
Read counts were normalized by rlog transformation with DESeq2 and subjected to downstream analyses.
Assembly: mm10
Supplementary files format and content: comma-separated value file includes raw counts for each sample (countTable_RNAseq.csv).
Supplementary files format and content: comma-separated value file includes normalized counts of each sample (rld_transformed_counts.csv).

source_name: cerebral cortex

extract_protocol:
Total RNA was extracted from frozen aliquots of 10,000 sorted cells using the RNeasy® Micro Kit (Qiagen, #74004).
From total RNA cDNA was synthesized, PolyA enriched and amplified using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Clontech Laboratories, # 634891). cDNA was then further processed with the Nextera XT DNA Library Preparation Kit (Illumina, #FC-131-1096).

value: cerebral cortex

value: neuronal cells

tag: transgene constructs

value: pCAG-tDimer

value: 7 days old puppy (P7)

value: w/o

tag: harvest mode


title: P7, pNeuroD cell population, w/o treatment, rep 1

value: mixed population of brain cells

value: pNeuroD-eGFP/pCAG-tDimer


title: HA-ZFPOBI1 OE HA-ChIP replicate 2

description: Library name: clHA_2


title: Peripheral CD8+ T cells, siControl transfected, anti-CD3/CD28 activated, 24-hours, healthy donor 2

description:
Library name: 42F siCont 24HR
Human RNA-seq Activated counts and FPKM.txt

data_processing:
Raw RNA sequencing paired-end reads were processed through Mayo RNA-Seq bioinformatics pipeline, MAP-Rseq (v3.1.4) to align to genome build hg38.
Variants were called using the RVBoost module from MAPR-seq.
Gene and exon expression quantification were performed using the Subread package to obtain both raw and normalized (FPKM) reads.
FASTQC, MultiQC, and RSEQC tools were used for comprehensive quality control assessment of the aliqned reads.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including raw counts and FPKM for each sample

extract_protocol:
Total RNA was isolated with TRIzol Reagent (Invitrogen), prior to inclusion in spin-column based isolation (Zymo Research). 250 ng of total RNA was used for construction of cDNA libraies.
Libraries were prepared with Illumina TruSeq Stranded mRNA Prep kit following manufacturer's instructions. The concentration and size distribution of the completed libraries were determined with the Agilent TapeStation's D1000 ScreenTape and Qubit fluorometry.

treatment_protocol: CD8+ T cells were transfected with DUSP2-targeting siRNA (Horizon Discovery, Dharmacon) or negative control siRNA (Horizon DIscovery, Dharmacon) by nucleofection (Lonza) and activated with anti-CD3/CD28 soluble antibodies (STEMCELL Technologies) for 24-hours, rested cells were maintained under the same conditions without addition of activating antibodies.

value: healthy donor 2

value: Peripheral blood

value: CD8+ T cells

value: siCont

value: Activated with anti-CD3/CD28

value: 42 years


title: Litter_S_posi

description: Library name: PR3555_gene_expression_1

value: Brain

value: Neuron

value: L1-GFP reporter/WT


title: 18513X19 CHOW WT

description: Library name: Sample 10

value: Liver tissue

value: WT (6NJ)

value: CHOW diet control


title: C57_BrainStem_WT_Male3

description:
Library name: C57_BrainStem_WT_Male3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: BrainStem

value: WT

value: Male

value: 8 weeks


title: Peripheral CD8+ T cells, siDUSP2 transfected, anti-CD3/CD28 activated, 24-hours, healthy donor 2

description:
Library name: 42F siDUSP2 24HR
Human RNA-seq Activated counts and FPKM.txt

value: Female


title: P5, pNeuroD cell population, w/o treatment, rep 2

value: cerebral cortex

value: neuronal cells

value: pNeuroD-eGFP/pCAG-tDimer

value: 5 days old puppy (P5)

value: w/o


title: C57_BrainStem_WT_Male2

description:
Library name: C57_BrainStem_WT_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 10 weeks


title: P5, pNeuroD cell population, w/o treatment, rep 1


title: Peripheral CD8+ T cells, siControl transfected, anti-CD3/CD28 activated, 24-hours, healthy donor 1

description:
Library name: 39M siCont 24HR
Human RNA-seq Activated counts and FPKM.txt

value: healthy donor 1

value: Peripheral blood

value: CD8+ T cells

value: siCont

value: Activated with anti-CD3/CD28

value: 39 years


title: C57_BrainStem_WT_Female3

description:
Library name: C57_BrainStem_WT_Female3_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: BrainStem

value: 7.5 months


title: miR-29a-3p_2

city: Nanjing

first: Huichen

last: Song

state: Jiangsu

address: Qixia District, Xianlin Road No.163

institute: Nanjing university

description: Library name: SAMPLES5

data_processing:
Illumina Casava1.7 software used for basecalling.
The remaining reads that passed all the filtering steps was counted  as clean reads and all subsequent analyses were based on this. Finally, we  used FastQC to perform basic statistics on the quality of the clean data reads
Bismark software was used to  perform alignments of bisulfite-treated reads to a reference genome . The reference genome was firstly transformed into bisulfiteconverted version (C-to-T and G-to-A converted) and then indexed using bowtie2. Clean reads were also transformed into fully bisulfite-converted versions (C-to-T and G-to- A converted) before being aligned to the similarly converted versions of the genome in a directional manner. Sequence reads that produce a unique best alignment from the two alignment processes (original top and bottom strand) were then compared to the normal genomic sequence and the methylation state of all cytosine positions was inferred.
Assembly: GRCm38_Ensembl_104
Supplementary files format and content: Methylated sites were identified with a binomial test using the methylated counts (mC), totols counts (mC+umC) and the non-conversion rate (r)

source_name: liver

extract_protocol:
After samples DNA testing, positive control DNAs were added into the DNAs,  Next, ssDNA fragements were Bisulfite treated. After BS treatment, unmethylated Cytosine will change into Uracil, while methylated Cytosine will stay unchanged. Then, methylation sequencing adapters ligation, size selection and PCR amplification steps were performed to the DNA fragmentszol reagent. I
llumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

value: liver

value: injected with extracellular vesicles rich in miR-29a-3p


title: miR-29a-3p_3

description: Library name: SAMPLES6


title: miR-29a-3p_1

description: Library name: SAMPLES4


title: 18513X17 CHOW KO

description: Library name: Sample 9

value: Liver tissue

value: EFHD1 KO

value: CHOW diet control


title: P5, mixed brain cell population, w/o treatment, rep 2

value: cerebral cortex

value: mixed population of brain cells

value: pCAG-tDimer


title: Peripheral CD8+ T cells, siDUSP2 transfected, anti-CD3/CD28 activated, 24-hours, healthy donor 1

description:
Library name: 39M siDUSP2 24HR
Human RNA-seq Activated counts and FPKM.txt

value: Male


title: NC_3

description: Library name: SAMPLES3

value: injected with extracellular vesicles rich in NC


title: Peripheral CD8+ T cells, siControl transfected, anti-CD3/CD28 activated, 24-hours_healthy donor 3

description: Library name: 16_66M_siCnt_A

value: healthy donor 3

value: Peripheral blood

value: siCnt

value: siControl,  activated with anti-CD3/CD28

value: 66 years


title: Microbiota of stool EG25 – PAE male

description:
Library name: EG25
16s rRNA v3-v4 sequencing of mice stool

data_processing:
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 7 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --p-minimum-length 100 –verbose
qiime demux summarize  --i-data trim-seqs.qza --o-visualization quality.qzv
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 224 --p-trunc-len-r 218 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 7
bowtie2 -x INDEXED_mouse_GRCm39_BOWTIE2/GRCm39  -U dna-sequences.fasta --un filtered.fasta
qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
R software for further analysis
Supplementary files format and content: filtered.fasta: text containing every processed ASV code and sequence
Supplementary files format and content: otu_table.csv: CSV text file containing the abundance table
Supplementary files format and content: tax.csv: CSV text file containing the complete taxonomic classification of the reference sequence
Library strategy: 16S rRNA-seq

extract_protocol:
Total DNA was extracted from stools, amplified to collect amplicons of variable V3–V4 region of the bacterial 16S rRNA gene were sequenced in paired-end mode (2 × 250 cycles) with Illumina Novaseq.
For detailed library preparation please contact IGA Technology Services (Udine, Italy)

value: Stool

value: PAE

value: male


title: C57_BrainStem_WT_Female2

description:
Library name: C57_BrainStem_WT_Female2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: BrainStem

value: WT

value: Female

value: 7.5 months


title: Peripheral CD8+ T cells, siControl transfected, healthy donor 2

description:
Library name: 42F siCont BL
Human RNA-seq Baseline counts and FPKM.txt

value: healthy donor 2

value: CD8+ T cells

value: siCont

value: not activated

value: 42 years


title: P5, mixed brain cell population, w/o treatment, rep 1

value: cerebral cortex

value: mixed population of brain cells

value: pCAG-tDimer

value: 5 days old puppy (P5)

value: w/o


title: NC_2

description: Library name: SAMPLES2

value: liver

value: injected with extracellular vesicles rich in NC


title: C57_BrainStem_WT_Female1

description:
Library name: C57_BrainStem_WT_Female1_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 8 weeks


title: P3, pNeuroD cell population, PolyI:C treatment, rep 4

value: neuronal cells

value: pNeuroD-eGFP/pCAG-tDimer

value: 3 days old puppy (P3)


title: Peripheral CD8+ T cells, siDUSP2 transfected, healthy donor 2

description:
Library name: 42F siDUSP2 BL
Human RNA-seq Baseline counts and FPKM.txt

value: Peripheral blood

value: Female


title: C57_BrainStem_KO_Male4

description:
Library name: C57_BrainStem_KO_Male4_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: BrainStem

value: Mecp2 KO

value: Male


title: Peripheral CD8+ T cells, siControl transfected, healthy donor 1

description:
Library name: 39M siCont BL
Human RNA-seq Baseline counts and FPKM.txt

value: healthy donor 1

value: CD8+ T cells

value: siCont

value: not activated

value: 39 years


title: vector control H3K9me3_ChIP replicate 2

description: Library name: vecK9_2

value: mouse embryonic stem cell

value: antibody:alpha-H3K9me3, Abcam, ab8898, 3 ug


title: C57_BrainStem_KO_Male2

description:
Library name: C57_BrainStem_KO_Male2_RNA-seq
RNA-seq counts of Mecp2 KO and WT tissues

value: 9 weeks


title: P3, pNeuroD cell population, PolyI:C treatment, rep 3

value: cerebral cortex