title: thymus-Mettl3KO-3CHTGTS-TEA-rep1

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

description: Library name: sample99

data_processing:
For ATAC-seq, The rawdata reads were first processed using fastp (version 0.20.0) to remove adapter sequences and low-quality reads. Following this quality control step, the filtered reads were aligned to the mouse reference genome (mm10) via Bowtie2 (version 2.4.5) with the parameters set as -p 8 –sensitive. PCR duplicate fragments were then eliminated using Picard (version 2.22.8). Further filtering was applied to exclude unmapped reads, multi-mapped reads, and those aligning to the mitochondrial chromosome (chrM). The Fragments Ratio in Peaks (FRiP) value— a key metric for assessing ChIP-seq data quality— was calculated through a combination of Bedtools (version 2.29.2) and awk (version 4.0.2). To facilitate visualization in the Integrative Genomics Viewer (IGV), deepTools (version 3.5.0) was employed to generate bigWig files normalized by Counts Per Million (CPM). For subsequent peak calling analyses, SAM files were converted to the binary BAM format using SAMtools (version 1.9). Peaks were identified using MACS2 (version 2.2.4) with the specified parameters: –nomodel –shift -100 –extsize 200 -B –keep-dup all –broad –broad-cutoff 0.1.
for merip-seq,Trimmomatic trimmed adapters; HISAT2 (v2.2.1) aligned reads to mm10. MeTPeak (v1.2) called m6A peaks; Homer (v4.11) performed motif analysis; Guitar (v1.26.0) assessed m6A distribution. Differential peaks were identified by DESeq2 (v1.38.3) or edgeR (v3.40.2; log2FC ≥ 0.58, FDR < 0.05).
for RNA-seq. Fastp (v0.20.0) performed quality control; reads were aligned to mm10 with HISAT2 (v2.2.1) and quantified with StringTie (v2.2.1). DESeq2 (v1.38.3) identified differentially expressed genes (padj < 0.05, log2FC ≥ 1). GO and GSEA used clusterProfiler (v4.8.3).
RIBO-seq.Sequencing: Illumina NovaSeq 6000 (150 bp PE). Translational efficiency was calculated as Ribo-seq reads / RNA-seq reads; differential analysis used DESeq2.
5'RACE. V(D)J usage, CDR3 length, and repertoire diversity were analysed with custom bioinformatics pipelines.
3C-HTGTS  Differential chromatin interactions were analysed with R.4Cker (k = 30 merged restriction fragments, DESeq2, P < 0.05).
Assembly: mm10
Supplementary files format and content: BigWig files were generated using bamCoverage with normalized values for each sample.

source_name: Thymus

growth_protocol: All experiments involving mice were performed using protocols approved by  Southern Medical University Animal Studies Committee. Mice were on a C57Bl/6 genetic background . Animals were housed and bred in a specific pathogen-free animal facility.

extract_protocol:
For ScRNA-seq, the  single-cell suspension was loaded onto a Chromium Single Cell Chip (Chromium Single Cell G Chip Kit, 10x Genomics, PN-1000120) according to the manufacturer’s instructions by Guangzhou Yiyue Biotechnology Co., Ltd with the use of a Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, for co-encapsulation with barcoded Gel Beads at a target capture rate of about 10000 individual cells per sample. We lysed captured cells and released RNA was barcoded through reverse-transcription in individual single-cell gel beads in the emulsion (GEMS). In each droplet, complementary DNA (cDNA) was generated and amplified through reverse-transcription on a T100 PCR Thermal Cycler (Bio Rad) at 53 ℃ for 45 min, followed by 85 ℃ for 5 min and a hold at 4 ℃. Then, cDNA concentration and quality were assessed using Qubit Fluorometer (Thermo Scientific) and bioanalyzer2100 (Agilent), respectively. According to the manufacturer’s introduction, scRNA-seq libraries were constructed and sequenced to a depth of 40000 reads per cell on illumina platform.
For meRIP-seq.Total RNA (10–50 μg) from FACS-sorted DP cells (1 × 107) was DNase I treated, fragmented by Zn2+ hydrolysis (0.2 M ZnCl2, 94°C, 50 s), and immunoprecipitated with 5 μg anti-m6A antibody (Abcam, ab151230) in IPP buffer at 4°C. Antibody-RNA complexes were captured with Dynabeads Protein A/G (Thermo Fisher), washed sequentially in IPP, high-salt IPP (400 mM NaCl), and low-detergent IPP buffers, then competitively eluted with m6A mononucleoside (Selleck, S3190, 1 mg/ml) at 37°C. Eluted and input RNA were used for stranded library construction (SMARTer Stranded Total RNA-Seq Kit v2-Pico, Takara) and sequenced on the Illumina NovaSeq 6000 (150 bp PE).
For RNA-seq.Total RNA from 1 × 107 FACS-sorted DP cells was extracted with TRIzol. Poly(A) RNA was selected with oligo(dT) beads, fragmented, reverse-transcribed with SuperScript IV, and second-strand synthesized. Following end repair, A-tailing, and adapter ligation, libraries were size-selected (200–500 bp), amplified (12 cycles), and sequenced on the Illumina NovaSeq 6000 (150 bp PE).
For ATAC-seq,  approximately 5 × 10⁴ cell pellets were washed once with cold phosphate-buffered saline (PBS). Cells were then lysed on ice for 3 minutes in 50 μL of ice-cold Lysis Buffer, which contained the following components: 10 mM Tris (pH 7.4), 10 mM NaCl, 3 mM MgCl₂, 0.1% NP-40, 0.1% TWEEN 20, and 0.01% Digitonin. Following lysis, the cell lysate was resuspended in 1 mL of ice-cold RBS-Wash Buffer (10 mM Tris [pH 7.4], 10 mM NaCl, 3 mM MgCl₂, and 0.1% TWEEN 20) and centrifuged at 4°C and 500 ×g for 5 minutes to pellet the cellular material. The tagmentation process was performed in 1× Tagmentation Buffer (comprising 10 mM Tris [pH 7.4], 5 mM MgCl₂, 10% dimethylformamide [DMF], 33% PBS, 0.1% TWEEN 20, and 0.01% Digitonin) with the addition of 100 nM Tn5 Transposase, and the reaction was incubated at 37°C for 30 minutes. Immediately after tagmentation, free DNA fragments were purified according to the standard protocol provided with the QIAquick PCR Purification Kit (QIAGEN, Cat. No. 28106, Germany). This purification step was followed by a final PCR amplification, which included 10–15 cycles using P5 and P7 primers. After post-amplification purification, the prepared libraries were subjected to sequencing on the Illumina NovaSeq 6000 platform to generate 150-bp paired-end reads (PE150).
For Ribo-seq,FACS-sorted DP cells (1 × 106) were CHX-treated (100 μg/ml, 5 min) and lysed in CHX-containing lysis buffer with Turbo DNase. After clarification (20,000g, 10 min, 4°C), RNase I digested unprotected RNA (45 min, room temperature). Ribosome-protected fragments (RPFs) were purified by sucrose cushion ultracentrifugation (1 M sucrose, 260,000g, 4 h, 4°C), extracted with TRIzol, and resolved on 15% TBE-urea gels. The 26-34 nt region was excised, RNA extracted overnight, and libraries constructed with the CATS Small RNA-seq Kit (Diagenode, C05010048).
For 5′RACE-seq,Total RNA from thymocytes (1 × 107) was reverse-transcribed using the SMARTer oligo and gene-specific primers for Tcra, Tcrb, or Tcrd with the HiScript III Kit (Vazyme, R312-01). cDNA was amplified by nested PCR with gene-specific and universal 5′ primers, gel-purified (Qiagen, 28704), and subjected to Illumina library preparation. Sequencing: NovaSeq 6000 (150 bp PE).
For HTGTS,Genomic DNA (10 μg) was sonicated (Qsonica Q800R3, 20% amplitude, 15s on / 25s off, 3 min total, 4°C). Sonicated DNA (2.5 μg) underwent 100 cycles of linear amplification with a biotinylated bait primer (Phanta Max Mix, Vazyme). Products were captured on Streptavidin C1 beads (Thermo Fisher, 65602), ligated to a bridge adapter (T4 DNA ligase, NEB, M0202, 16°C overnight), and amplified by indexed nested PCR. Libraries were purified, size-selected to 300-700 bp, and sequenced on the NovaSeq 6000 (150 bp PE).
For 3C-HTGTS,Thymocytes from anti-CD3-stimulated Rag1-D708A mice (1 × 107) were crosslinked with 1% formaldehyde (10 min, room temperature), quenched with glycine, and lysed. Chromatin was solubilized (0.1% SDS, 37°C), digested with DpnII (NEB, R0543, 37°C overnight), and ligated with T4 DNA ligase (16°C overnight). Crosslinks were reversed (Proteinase K, 65°C overnight); DNA was purified by phenol-chloroform extraction and ethanol precipitation. The resulting 3C libraries were processed through the HTGTS pipeline (Section 4.3.7) with Trav17 or Eα bait primers.
Construction of libraries were described as the above extract protocol

value: Thymus

value: Thymocyte


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 19

status: Public on Jun 01 2026

type: SRA

city: Middlebury College

first: Amanda

last: Crocker

state: Vermont

address: 276 Bicentennial Way

department: Neuroscience

country: USA

institute: Middlebury College

description: Library name: 23248XR-02-116

library_source: transcriptomic

data_processing:
Raw paired-end sequence data in Fastq format was initially trimmed using the Flexbar package with the adapters of read 1: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC and read 2: GATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGTCGCCGTATCATT. Trimmed reads were aligned to mm10 genome reference by STAR, version 2.7.10b  to generate the bam files. The featureCounts package with multimapping reads as counted was employed to count the reads inside the bam files that were aligned to the 6 categories/classes of small RNAs: circRNA, miRNA, piRNA, snoRNA, snRNA, and tRNA. The annotations of snoRNA and snRNA are extracted from the Gencode mm10 GTF file. The miRNA sequences and annotations are based on the miRBase database. The genomic tRNA database is the source of the tRNA information. The piRNABank is the sources of the empirically known sequences and other related information on piRNAs. The circRNA sequences and annotations are from the circAtlas 3.0 database.
Deseq2 was used for normalization and differential expression analysis.
Assembly: mm10
Supplementary files format and content: Raw_Counts_SmallRNA_CircRNA.txt (raw counts from featureCounts for all samples compiled in a table with library name as headers), Normalized_Counts_SmallRNA_CircRNA.txt (DESeq2 normalized counts for all samples compiled in a table with library name as headers), Raw_Counts_SmallRNA_miRNA.txt (raw counts from featureCounts for all samples compiled in a table with library name as headers), Normalized_Counts_SmallRNA_miRNA.txt (DESeq2 normalized counts for all samples compiled in a table with library name as headers), Raw_Counts_SmallRNA_piRNA.txt (raw counts from featureCounts for all samples compiled in a table with library name as headers), Normalized_Counts_SmallRNA_piRNA.txt (DESeq2 normalized counts for all samples compiled in a table with library name as headers), Raw_Counts_SmallRNA_snoRNA.txt (raw counts from featureCounts for all samples compiled in a table with library name as headers), Normalized_Counts_SmallRNA_snoRNA.txt (DESeq2 normalized counts for all samples compiled in a table with library name as headers), Raw_Counts_SmallRNA_snRNA.txt (raw counts from featureCounts for all samples compiled in a table with library name as headers), Normalized_Counts_SmallRNA_snRNA.txt (DESeq2 normalized counts for all samples compiled in a table with library name as headers), Raw_Counts_SmallRNA_tRNA.txt (raw counts from featureCounts for all samples compiled in a table with library name as headers), Normalized_Counts_SmallRNA_tRNA.txt (DESeq2 normalized counts for all samples compiled in a table with library name as headers)

molecule: total RNA

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
RNA was isolated from samples using Qiazol phase separation followed by cleanup with RNeasy 96 Kit per manufacturer’s instruction. Isolated RNA sample quality was assessed by both RNA Tapestation assay and High Sensitivity RNA Tapestation assay (Agilent Technologies Inc., California, USA and quantified by Infinite F Nano+ 200 Pro Tecan® (Tecan, Switzerland).
Library construction was prepared using NEBNext® Small RNA Library Prep Set for Illumina® (Multiplex Compatible) following the manufacturer's protocol (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation HSD1000 ScreenTape (Agilent Technologies Inc., California, USA). Final library size was about 250bp with an insert size of about 100bp. Illumina® 6-nt single-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq X Plus (Illumina, California, USA) with a read length configuration of 150 PE for 20M PE reads per sample (10M in each direction).

tag: tissue

value: Hippocampus

tag: genotype

tag: treatment

value: injected pbs controls

tag: animal id


title: 6957-JF-2

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

description: Library name: 6957-JF-2

library_source: transcriptomic single cell

data_processing:
CellRanger was used to map the reads (paired end) to the reference genome to generate the bam files.
Raw base call (BCL) files from the NovaSeq 6000 were converted and demultiplexed to sample-level FASTQ files using Illumina BCL Convert (or bcl2fastq2) with an Illumina SampleSheet specifying unique dual indexes. Default quality and index mismatch filters were applied, and per-lane FASTQs were concatenated by sample to produce a single FASTQ set per library for downstream single-cell RNA-seq analysis.
Assembly: hg38
Supplementary files format and content: cellranger output format

molecule: polyA RNA

organism: Homo sapiens

source_name: human skin

extract_protocol:
Skin samples are incubated with dispase overnight, followed by tissue dissociation using collagenase and trypsin-EDTA. The epidermis and dermis are minced, incubated with enzymes, and then processed through mesh filtration and centrifugation. After cell counting, the epidermal and dermal cells are recombined in a desired ratio for library preparation.
https://cdn.10xgenomics.com/image/upload/v1722287750/support-documents/CG000527_Chromium_FixedRNAProfiling_MultiplexedSamples_UserGuide_Rev_F.pdf

value: human skin

tag: cell type

value: a pool of single cells

tag: disease

value: Nonles AD


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 18

description: Library name: 23248XR-02-115


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 17

description: Library name: 23248XR-02-114


title: thymus-Mettl3KO-3CHTGTS-TEA-rep2

country: China

description: Library name: sample98

library_source: genomic

molecule: genomic DNA


title: 6957-JF-1

description: Library name: 6957-JF-1

value: Les AD


title: Hippocampus of Mecp2-KO, injected with PBS, control, biolrep 6

description: Library name: 23248XR-02-113


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 16

description: Library name: 23248XR-02-112


title: 6946-JF-2

description: Library name: 6946-JF-2


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 15

description: Library name: 23248XR-02-111


title: thymus-Mettl3WT-3CHTGTS-TEA-rep1

description: Library name: sample96


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 14

description: Library name: 23248XR-02-110


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 13

description: Library name: 23248XR-02-109


title: thymus-Mettl3WT-3CHTGTS-TEA-rep2

description: Library name: sample95


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 12

description: Library name: 23248XR-02-108


title: thymus-Mettl3WT-3CHTGTS-TEA-rep3

description: Library name: sample94


title: Hippocampus of Mecp2-KO, injected with PBS, control, biolrep 5

description: Library name: 23248XR-02-107


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 11

description: Library name: 23248XR-02-106


title: 6938-JF-1

description: Library name: 6938-JF-1


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 10

description: Library name: 23248XR-02-105


title: thymus-Mettl3KO-3CHTGTS-TRAV17-rep1

description: Library name: sample93


title: Hippocampus of Mecp2-KO, injected with PBS, control, biolrep 4

description: Library name: 23248XR-02-104


title: 6929-JF-1

description: Library name: 6929-JF-1


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 9

description: Library name: 23248XR-02-102


title: thymus-Mettl3KO-3CHTGTS-TEA-rep3

description: Library name: sample97


title: Hippocampus of Mecp2-KO, injected with PBS, control, biolrep 3

description: Library name: 23248XR-02-101


title: thymus-Mettl3KO-3CHTGTS-TRAV17-rep2

description: Library name: sample92


title: 6919-JF-2

description: Library name: 6919-JF-2


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 8

description: Library name: 23248XR-02-100


title: 6946-JF-1

description: Library name: 6946-JF-1


title: thymus-Mettl3KO-3CHTGTS-TRAV17-rep3

description: Library name: sample91


title: Hippocmapus of Mecp2-KO, injected with PBS, control, biolrep 2

description: Library name: 23248XR-02-99


title: 6911-JF-1

description: Library name: 6911-JF-1

value: Control


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 7

description: Library name: 23248XR-02-98


title: thymus-Mettl3WT-3CHTGTS-TRAV17-rep1

description: Library name: sample90


title: 6938-JF-2

description: Library name: 6938-JF-2


title: Hippocampus of Mecp2-KO, injected with PBS, control, biolrep 1

description: Library name: 23248XR-02-97


title: 6883-JF-2

description: Library name: 6883-JF-2


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 6

description: Library name: 23248XR-02-96


title: Hippocampus of Tau+/+, Control for Tau driven overexpression of Mecp2, biolrep 2

description: Library name: 23248XR-02-146

value: Tau-Wildtype Control


title: thymus-Mettl3WT-3CHTGTS-TRAV17-rep2

description: Library name: sample89


title: 6883-JF-1

description: Library name: 6883-JF-1


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 5

description: Library name: 23248XR-02-95


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 4

description: Library name: 23248XR-02-94


title: thymus-Mettl3WT-3CHTGTS-TRAV17-rep3

description: Library name: sample88


title: 7115-JF-4

description: Library name: 7115-JF-4


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 3

description: Library name: 23248XR-02-93


title: 7115-JF-2

description: Library name: 7115-JF-2


title: 6835-AB-2

description: Library name: 6835-AB-2


title: Hippocmapus of Mecp2-WT, injected with PBS, control, biolrep 2

description: Library name: 23248XR-02-92


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 1

description: Library name: 23248XR-02-91


title: CCI/P_FF_2

city: Washington

first: John

middle: R

last: Bethea

state: DC

address: 2300 I Street NW

institute: The George Washington University

description:
Library name: HC-236
Column name in Raw_Normalized_Counts_Genes_DESeq2_HTSEQ:HC-236_Raw.Read.Count

data_processing:
Raw fastq read quality was assessed using fastqC v0.11.8.
Adapter and low-quality reads were trimmed using fastq-mcf v1.05 and cutadapt v2.5.
Contaminant reads, including mitochondrial, ribosomal RNA, transfer RNA, and adapter sequences, were removed using Bowtie2 v2.5.1.
Paired-end reads were aligned to the mouse reference genome using STAR v2.7.3a with a two-pass mapping strategy.
Raw gene counts were generated using HTSeq v0.11.2; normalized counts and differential expression were generated using DESeq2, and FPKM values were generated using Cufflinks v2.2.1.
Assembly: GRCm38/mm10, Ensembl release 92; genome-build accession NCBI:GCA_000001635.8
Supplementary files format and content: csv files include FPKM values for each sample

source_name: Brain - Hippocampus

extract_protocol:
Total RNA was extracted with TRIzol (Thermo Fisher Scientific, Waltham, MA) according to the manufacturer’s instructions. RNA integrity was confirmed using an Agilent Bioanalyzer 2100; samples with RIN ≥ 7.0 were used.
RNA library for RNA-seq were prepared using Illumina TruSeq stranded mRNA kit following manufacturer's protocol

treatment_protocol: A TNFR2 agonist (10 mg/kg, i.p.), composed of a covalently stabilized TNFR2-selective single-chain TNF trimer fused to an effector-deficient Fc domain, was diluted in sterile PBS (Thermo Fisher J67670.K2) and administered on post-injury days (dpi) 7, 10, and 13 to half of the animal group. As control group, animals were treated with sterile PBS.

value: Brain - Hippocampus

value: TNFR2 F/F (FF)

value: CCI + PBS


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 6

description: Library name: 23248XR-02-137

value: MeCP2:-/Y rtt271a

value: injected rtt271 3e11


title: thymus-Mettl3KO-3CHTGTS-Ea-rep1

description: Library name: sample87


title: 6835-AB-1

description: Library name: 6835-AB-1


title: Hippocampus of Mecp2-KO, non-injected control, biolrep 2

description: Library name: 23248XR-02-90

value: non-injected ctrl


title: thymus-Mettl3KO-3CHTGTS-Ea-rep2

description: Library name: sample86


title: Hippocampus of Mecp2-KO, non-injected control, biolrep 1

description: Library name: 23248XR-02-89


title: 7063-JF-4

description: Library name: 7063-JF-4


title: 6830-AB-2

description: Library name: 6830-AB-2


title: Cortex of Tau+/+, Control for Tau driven overexpression of Mecp2, biolrep 7

description: Library name: 23248XR-02-70

source_name: Cortex

value: Cortex


title: thymus-Mettl3KO-3CHTGTS-Ea-rep3

description: Library name: sample85

value: Thymus


title: Cortex of Tau-/+, Tau driven overexpression of Mecp2, biolrep 7

description: Library name: 23248XR-02-69

value: Tau-MeCP2 Over-expression


title: Cortex of Tau+/+, Control for Tau driven overexpression of Mecp2, biolrep 6

description: Library name: 23248XR-02-68


title: 6830-AB-1

description: Library name: 6830-AB-1


title: thymus-Mettl3WT-3CHTGTS-Ea-rep1

description: Library name: sample84

value: Thymocyte


title: 6788-JF-4

description: Library name: 6788-JF-4


title: Cortex of Tau+/+, Control for Tau driven overexpression of Mecp2, biolrep 4

description: Library name: 23248XR-02-66


title: thymus-Mettl3WT-3CHTGTS-Ea-rep2

description: Library name: sample83


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 10

description: Library name: 23248XR-02-128

value: Hippocampus

value: injected rtt271 1e11


title: Cortex of Tau-/+, Tau driven overexpression of Mecp2, biolrep 6

description: Library name: 23248XR-02-64


title: Cortex of Tau+/+, Control for Tau driven overexpression of Mecp2, biolrep 5

description: Library name: 23248XR-02-67


title: Cortex of Tau-/+, Tau driven overexpression of Mecp2, biolrep 5

description: Library name: 23248XR-02-63


title: 6788-JF-2

description: Library name: 6788-JF-2

value: human skin

value: a pool of single cells


title: thymus-Mettl3WT-3CHTGTS-Ea-rep3

description: Library name: sample82


title: Cortex of Tau-/+, Tau driven overexpression of Mecp2, biolrep 4

description: Library name: 23248XR-02-62


title: Cortex of Tau-/+, Tau driven overexpression of Mecp2, biolrep 3

description: Library name: 23248XR-02-61


title: thymus-Mettl3WT-RAG1D708A-ChIP-input-rep3

description: Library name: sample81


title: 6788-JF-1

description: Library name: 6788-JF-1

value: Les AD


title: Cortex of Tau+/+, Control for Tau driven overexpression of Mecp2, biolrep 3

description: Library name: 23248XR-02-60


title: 6766-JF-2

description: Library name: 6766-JF-2

value: Nonles AD


title: Cortex of Tau-/+, Tau driven overexpression of Mecp2, biolrep 2

description: Library name: 23248XR-02-59


title: Cortex of Tau+/+, Control for Tau driven overexpression of Mecp2, biolrep 2

description: Library name: 23248XR-02-58

value: Tau-Wildtype Control


title: thymus-Mettl3WT-RAG1D708A-ChIP-H3K4me3-ip-rep3

description: Library name: sample80


title: 6766-JF-1

description: Library name: 6766-JF-1


title: Cortex of Tau+/+, Control for Tau driven overexpression of Mecp2, biolrep 1

description: Library name: 23248XR-02-57


title: thymus-Mettl3WT-RAG1D708A-ChIP-H3K27ac-ip-rep3

description: Library name: sample79


title: Cortex of Tau-/+, Tau driven overexpression of Mecp2, biolrep 1

description: Library name: 23248XR-02-56


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 4

description: Library name: 23248XR-02-122


title: 6733-JF-1

description: Library name: 6733-JF-1

value: Control


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 12

description: Library name: 23248XR-02-55


title: thymus-Mettl3KO-RAG1D708A-ChIP-input-rep3

description: Library name: sample78


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 11

description: Library name: 23248XR-02-54


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 2

description: Library name: 23248XR-02-120


title: 6726-JF-4

description: Library name: 6726-JF-4


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 10

description: Library name: 23248XR-02-53


title: thymus-Mettl3KO-RAG1D708A-ChIP-H3K4me3-ip-rep3

description: Library name: sample77


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 9

description: Library name: 23248XR-02-52


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 8

description: Library name: 23248XR-02-51


title: thymus-Mettl3KO-RAG1D708A-ChIP-H3K27ac-ip-rep3

description: Library name: sample76


title: 6726-JF-1

description: Library name: 6726-JF-1


title: 6726-JF-2

description: Library name: 6726-JF-2


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 7

description: Library name: 23248XR-02-50


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 6

description: Library name: 23248XR-02-49


title: thymus-Mettl3KO-RAG1D708A-ChIP-H3K27ac-ip-rep2

description: Library name: sample75


title: Hippocampus of Mecp2-WT, injected with PBS, control, biolrep 21

description: Library name: 23248XR-02-118

value: injected pbs controls


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 5

description: Library name: 23248XR-02-48


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 4

description: Library name: 23248XR-02-47


title: 6673-JF-2

description: Library name: 6673-JF-2


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 3

description: Library name: 23248XR-02-46


title: thymus-Mettl3KO-RAG1D708A-ChIP-H3K4me3-ip-rep2

description: Library name: sample74


title: 6673-JF-1

description: Library name: 6673-JF-1


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 2

description: Library name: 23248XR-02-45


title: thymus-Mettl3KO-RAG1D708A-ChIP-input-rep2

description: Library name: sample73


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biolrep 1

description: Library name: 23248XR-02-44


title: thymus-Mettl3WT-RAG1D708A-ChIP-H3K27ac-ip-rep2

description: Library name: sample72


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 13

description: Library name: 23248XR-02-43


title: 6636-JF-2

description: Library name: 6636-JF-2


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 12

description: Library name: 23248XR-02-42


title: 6636-JF-1

description: Library name: 6636-JF-1


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 11

description: Library name: 23248XR-02-41


title: thymus-Mettl3WT-RAG1D708A-ChIP-H3K4me3-ip-rep2

description: Library name: sample71


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 10

description: Library name: 23248XR-02-40


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 9

description: Library name: 23248XR-02-39


title: 6458-JF-2

description: Library name: 6458-JF-2


title: thymus-Mettl3WT-RAG1D708A-ChIP-input-rep2

description: Library name: sample70


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 8

description: Library name: 23248XR-02-38


title: 6458-JF-1

description: Library name: 6458-JF-1


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 7

description: Library name: 23248XR-02-37


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 6

description: Library name: 23248XR-02-36


title: 6425-JF-1

description: Library name: 6425-JF-1


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 5

description: Library name: 23248XR-02-35


title: thymus-Mettl3WT-RAG1D708A-ChIP-input-rep1

description: Library name: sample69


title: thymus-Mettl3WT-RAG1D708A-ChIP-H3K4me3-ip-rep1

description: Library name: sample68


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 4

description: Library name: 23248XR-02-34


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 3

description: Library name: 23248XR-02-33


title: 6372-AB-2

description: Library name: 6372-AB-2


title: thymus-Mettl3WT-RAG1D708A-ChIP-H3K27ac-ip-rep1

description: Library name: sample67


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 2

description: Library name: 23248XR-02-32


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biolrep 1

description: Library name: 23248XR-02-31


title: 6372-AB-1

description: Library name: 6372-AB-1


title: thymus-Mettl3KO-RAG1D708A-ChIP-input-rep1

description: Library name: sample66


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 21

description: Library name: 23248XR-02-30


title: 6359-AB-2

description: Library name: 6359-AB-2


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 20

description: Library name: 23248XR-02-29


title: thymus-Mettl3KO-RAG1D708A-ChIP-H3K4me3-ip-rep1

description: Library name: sample65


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 19

description: Library name: 23248XR-02-28


title: 6359-AB-1

description: Library name: 6359-AB-1


title: thymus-Mettl3KO-RAG1D708A-ChIP-H3K27ac-ip-rep1

description: Library name: sample64


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 17

description: Library name: 23248XR-02-26


title: Cortex of Mecp2-KO, injected with PBS, control, biolrep 6

description: Library name: 23248XR-02-25


title: 6201-AB-1

description: Library name: 6201-AB-1


title: thymus-Mettl3WT-Riboseq-count-rep1

description: Library name: sample63

data_processing:
For ATAC-seq, The rawdata reads were first processed using fastp (version 0.20.0) to remove adapter sequences and low-quality reads. Following this quality control step, the filtered reads were aligned to the mouse reference genome (mm10) via Bowtie2 (version 2.4.5) with the parameters set as -p 8 –sensitive. PCR duplicate fragments were then eliminated using Picard (version 2.22.8). Further filtering was applied to exclude unmapped reads, multi-mapped reads, and those aligning to the mitochondrial chromosome (chrM). The Fragments Ratio in Peaks (FRiP) value— a key metric for assessing ChIP-seq data quality— was calculated through a combination of Bedtools (version 2.29.2) and awk (version 4.0.2). To facilitate visualization in the Integrative Genomics Viewer (IGV), deepTools (version 3.5.0) was employed to generate bigWig files normalized by Counts Per Million (CPM). For subsequent peak calling analyses, SAM files were converted to the binary BAM format using SAMtools (version 1.9). Peaks were identified using MACS2 (version 2.2.4) with the specified parameters: –nomodel –shift -100 –extsize 200 -B –keep-dup all –broad –broad-cutoff 0.1.
for merip-seq,Trimmomatic trimmed adapters; HISAT2 (v2.2.1) aligned reads to mm10. MeTPeak (v1.2) called m6A peaks; Homer (v4.11) performed motif analysis; Guitar (v1.26.0) assessed m6A distribution. Differential peaks were identified by DESeq2 (v1.38.3) or edgeR (v3.40.2; log2FC ≥ 0.58, FDR < 0.05).
for RNA-seq. Fastp (v0.20.0) performed quality control; reads were aligned to mm10 with HISAT2 (v2.2.1) and quantified with StringTie (v2.2.1). DESeq2 (v1.38.3) identified differentially expressed genes (padj < 0.05, log2FC ≥ 1). GO and GSEA used clusterProfiler (v4.8.3).
RIBO-seq.Sequencing: Illumina NovaSeq 6000 (150 bp PE). Translational efficiency was calculated as Ribo-seq reads / RNA-seq reads; differential analysis used DESeq2.
5'RACE. V(D)J usage, CDR3 length, and repertoire diversity were analysed with custom bioinformatics pipelines.
3C-HTGTS  Differential chromatin interactions were analysed with R.4Cker (k = 30 merged restriction fragments, DESeq2, P < 0.05).
Assembly: mm10
Supplementary files format and content: BigWig files were generated using bamCoverage with normalized values for each sample.
Library strategy: Ribo-Seq


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 15

description: Library name: 23248XR-02-23


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 18

description: Library name: 23248XR-02-27


title: 6178-AB-9

description: Library name: 6178-AB-9


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 16

description: Library name: 23248XR-02-24


title: thymus-Mettl3WT-Riboseq-count-rep2

description: Library name: sample62


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 14

description: Library name: 23248XR-02-22


title: 6178-AB-8

description: Library name: 6178-AB-8


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 13

description: Library name: 23248XR-02-21


title: thymus-Mettl3WT-Riboseq-count-rep3

description: Library name: sample61


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 12

description: Library name: 23248XR-02-20


title: 6138-AB-5

description: Library name: 6138-AB-5


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 11

description: Library name: 23248XR-02-18


title: Cortex of Mecp2-KO, injected with PBS, control, biolrep 5

description: Library name: 23248XR-02-19


title: thymus-Mettl3KO-Riboseq-count-rep1

description: Library name: sample60


title: 6138-AB-4

description: Library name: 6138-AB-4


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 10

description: Library name: 23248XR-02-17


title: HB34_IP_2

city: hangzhou

first: xiaoxiao

last: Li

address: #866 Yuhangtang Rd.

institute: zhejiang university

description: Library name: HB34_IP_2

data_processing:
The clean paired-end reads were mapped to the reference genome by Bowtie2 (Version 2.3.5) and reads with low mapping quality or multiple positions on the genome were identified and removed by SAMtools (version 1.9). Only perfectly and uniquely mapped reads were retained for further analysis.
Enriched peaks were called and annotated by MACS2 (Version 2.2.8) with the following parameters: “-f BAMPE -g 119145879 -q 0.01”. Peaks that were consistently found in two replicates were selected for further analyses. The generated data were imported into the Integrative Genomics Viewer (IGV) (James T Robinson, 2011) for visualization.
ComputeMatrix, plotProfile and plotHeatmap programs in deepTools (version 3.3.0) were used to compare the average enrichment at defined loci between YB2-FLAG and WT. To assign peaks to proximal genes, regions within 1.0 kb flanking the transcription start site (TSS) were extracted.
Assembly: TAIR10
Supplementary files format and content: bw files generated from SAMtools
Supplementary files format and content: peak files generated from MACS2

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: The stratified seeds were germinated in half-strength Murashige and Skoog (MS) medium for 10. Plants were grown under cool white light in a long-day condition (16 h light /8 h dark, 22 ºC).

extract_protocol:
Briefly, about 0.5-g 10-d-old seedlings were crosslinked with 1% formaldehyde and stopped with 125 mM glycine. Samples were ground and resuspended in the nuclei isolating buffer (10 mM Tris pH 8.0, 10 mM Sodium butyrate, 400 mM Sucrose, 0.1 mM PMSF, 5 mM β-mercaptoethanol, 1×cocktail protein inhibitor freshly). The isolated nuclei were resuspended with 1 mL lysis buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 10 mM Sodium butyrate, 0.1% deoxycholate, 0.1% SDS, 1% Triton X-100, 1 mM PMSF and 1×protease inhibitor cocktail freshly) and sonicated into 200-500 bp fragments by Diagenode Bioruptor (high setting, 18 cycles，30s on and 30s off). Subsequently, the sonicated chromatin was incubated with GFP-antibodies (Abcam, ab290) overnight at 4°C.
The recovered DNAs in ChIP assay were used to library construction with the Scale ssDNA-seq Lib Prep Kit (ABclonal, RK20228). High-throughput sequencing was carried out using Illumina Hiseq-PE150 by Novogene Corporation (Beijing, China).

value: leaves

tag: cell line

value: Columbia


title: Cortex of Mecp2-KO, injected with PBS, control, biolrep 4

description: Library name: 23248XR-02-16


title: 6138-AB-2

description: Library name: 6138-AB-2


title: thymus-Mettl3KO-Riboseq-count-rep2

description: Library name: sample59


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 9

description: Library name: 23248XR-02-14


title: thymus-Mettl3KO-Riboseq-count-rep3

description: Library name: sample58


title: Cortex of Mecp2-KO, injected with PBS, control, biolrep 3

description: Library name: 23248XR-02-13


title: 6138-AB-1

description: Library name: 6138-AB-1


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 8

description: Library name: 23248XR-02-12


title: DP-Mettl3KO-meRIPseq-input-rep1

description: Library name: sample57

data_processing:
For ATAC-seq, The rawdata reads were first processed using fastp (version 0.20.0) to remove adapter sequences and low-quality reads. Following this quality control step, the filtered reads were aligned to the mouse reference genome (mm10) via Bowtie2 (version 2.4.5) with the parameters set as -p 8 –sensitive. PCR duplicate fragments were then eliminated using Picard (version 2.22.8). Further filtering was applied to exclude unmapped reads, multi-mapped reads, and those aligning to the mitochondrial chromosome (chrM). The Fragments Ratio in Peaks (FRiP) value— a key metric for assessing ChIP-seq data quality— was calculated through a combination of Bedtools (version 2.29.2) and awk (version 4.0.2). To facilitate visualization in the Integrative Genomics Viewer (IGV), deepTools (version 3.5.0) was employed to generate bigWig files normalized by Counts Per Million (CPM). For subsequent peak calling analyses, SAM files were converted to the binary BAM format using SAMtools (version 1.9). Peaks were identified using MACS2 (version 2.2.4) with the specified parameters: –nomodel –shift -100 –extsize 200 -B –keep-dup all –broad –broad-cutoff 0.1.
for merip-seq,Trimmomatic trimmed adapters; HISAT2 (v2.2.1) aligned reads to mm10. MeTPeak (v1.2) called m6A peaks; Homer (v4.11) performed motif analysis; Guitar (v1.26.0) assessed m6A distribution. Differential peaks were identified by DESeq2 (v1.38.3) or edgeR (v3.40.2; log2FC ≥ 0.58, FDR < 0.05).
for RNA-seq. Fastp (v0.20.0) performed quality control; reads were aligned to mm10 with HISAT2 (v2.2.1) and quantified with StringTie (v2.2.1). DESeq2 (v1.38.3) identified differentially expressed genes (padj < 0.05, log2FC ≥ 1). GO and GSEA used clusterProfiler (v4.8.3).
RIBO-seq.Sequencing: Illumina NovaSeq 6000 (150 bp PE). Translational efficiency was calculated as Ribo-seq reads / RNA-seq reads; differential analysis used DESeq2.
5'RACE. V(D)J usage, CDR3 length, and repertoire diversity were analysed with custom bioinformatics pipelines.
3C-HTGTS  Differential chromatin interactions were analysed with R.4Cker (k = 30 merged restriction fragments, DESeq2, P < 0.05).
Assembly: mm10
Supplementary files format and content: BigWig files were generated using bamCoverage with normalized values for each sample.
Library strategy: MeRIP-Seq

value: DP


title: Cortex of Mecp2-KO, injected with PBS, control, biolrep 2

description: Library name: 23248XR-02-11


title: 5995-AB-2

description: Library name: 5995-AB-2


title: DP-Mettl3KO-meRIPseq-input-rep2

description: Library name: sample56


title: 5941-AB-1

description: Library name: 5941-AB-1


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 7

description: Library name: 23248XR-02-10


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 6

description: Library name: 23248XR-02-08


title: DP-Mettl3KO-meRIPseq-input-rep3

description: Library name: sample55


title: Cortex of Mecp2-KO, injected with PBS, control, biolrep 1

description: Library name: 23248XR-02-09


title: DP-Mettl3KO-meRIPseq-ip-rep1

description: Library name: sample54


title: 5917-AB-2

description: Library name: 5917-AB-2


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 5

description: Library name: 23248XR-02-07


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 3

description: Library name: 23248XR-02-05


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 4

description: Library name: 23248XR-02-06


title: RNA95

city: Houston

first: Stephen

last: Wong

address: 6565 Fannin St

institute: Houston Methodist

description: Library name: DSP-1001660022159-B-A01

data_processing:
Spatial proteogenomic and transcriptomic data were generated on the GeoMx DSP platform and processed with the GeoMxWorkflows R package (v1.0+) following the standard NanoString pipeline. Raw DCC files were imported with corresponding PKC files and sample annotations using readNanoStringGeoMxSet. Segment-level QC required: minimum total reads ≥1,000, trimmed reads ≥80%, stitched reads ≥80%, aligned reads ≥75%, sequencing saturation ≥50%, negative control counts ≥1, NTC counts ≤9,000, nuclei count ≥20, and segment area ≥1,000 μm². Probe-level QC was performed with setBioProbeQCFlags (minimum probe ratio 0.1; maximum percentage failing Grubbs test 20%; local outlier removal enabled), and probes failing these metrics or flagged as global Grubbs outliers were excluded. Probe counts were aggregated to genes with aggregateCounts. For each segment, the limit of quantification (LOQ) was defined as the geometric mean of negative controls plus 2 SD, with a minimum LOQ of 2 counts. Segments with <5% gene detection were removed, and genes detected above LOQ in <10% of segments were excluded (negative control probes retained for normalization). The final dataset comprised 7,709 genes across 65 high-quality segments. Spatial multi-omics data from all metastases samples were obtained from both PanCK+ tumor cell regions and CD45+ immune cell regions. Sample identifiers were standardized by combining scan names with ROI identifiers to ensure proper matching between expression data and metadata across both data modalities. Low-expression gene filtering was applied independently to brain and bone datasets using stringent criteria: genes were retained only if they showed ≥1 count in ≥3 samples per tissue type to ensure adequate gene coverage.
The PKC are
(v1.0) Human Procode NGS Core Protein (Lot Number: 519184)
(v1.1) Human Procode NGS IPA Protein (Lot Number: 512044)
(v1.0) Human NGS Whole Transcriptome Atlas RNA (Lot Number: HW0050423)
In the following link
https://brukerspatialbiology.com/products/geomx-digital-spatial-profiler/geomx-dsp-configuration-files/
Assembly: GRCh38
Supplementary files format and content: .csv, dcc
Supplementary files format and content: The RNA_Pro__Exp.csv, WTAONLY_Exp_NEW.csv files were generated from the .dcc file, the readout of gene expression and the protein (the first row =  the sample id,  and the first column = RNA/protein name).
Supplementary files format and content: When dcc was generated from merged/multiple samples, the file is linked to the first sample records and listed in the corresponding sample description field
Library strategy: Spatial Transcriptomics

source_name: Bone

extract_protocol:
We retrospectively collected metastatic tissue samples from six breast cancer patients with one or more metastatic lesions. The samples included two bone metastases, two brain metastases, one pericardial metastasis, and one chest wall metastasis. Formalin-fixed, paraffin-embedded (FFPE) tissue sections (5 μm) were mounted on standard microscope slides and processed for spatial proteogenomics analysis using the NanoString GeoMx Digital Spatial Profiler (DSP). To enable tissue compartmentalization and spatial segmentation, sections were stained with a panel of three fluorescently labeled morphological markers: anti-pancytokeratin (PanCK-AF532) to identify epithelial tumor cells, anti-CD45 (CD45-AF594) to delineate immune cell populations, and Syto13 nucleic acid stain to visualize nuclei and define cellular boundaries. Staining was performed according to standard immunofluorescence protocols with overnight incubation at 4°C.
DNA barcodes corresponding to RNA and protein targets were photocleaved and collected from each segmented AOI using sequential UV light exposure. Collected barcodes were processed using the GeoMx library preparation protocol with unique dual indexing (i7/i5) for each AOI to enable multiplexed analysis.

value: Bone


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 2

description: Library name: 23248XR-02-04

value: Cortex


title: DP-Mettl3KO-meRIPseq-ip-rep2

description: Library name: sample53

value: Thymus


title: RNA94

description: Library name: DSP-1001660022159-B-A02


title: Cortex of Mecp2-WT, injected with PBS, control, biolrep 1

description: Library name: 23248XR-02-03


title: Cortex of Mecp2-KO, non-injected control, biolrep 2

description: Library name: 23248XR-02-02

value: non-injected ctrl


title: DP-Mettl3KO-meRIPseq-ip-rep3

description: Library name: sample52


title: RNA93

description: Library name: DSP-1001660022159-B-A03


title: Cortex of Mecp2-KO, non-injected control, biolrep 1

description: Library name: 23248XR-02-01


title: Hippocampus of Tau+/+, Control for Tau driven overexpression of Mecp2, biol rep 8

description:
Library name: 23248XR-01-158
Raw_counts.txt
Normalized_counts.txt

data_processing:
FastQC was employed to check the quality of raw reads.Sequences of poor quality were removed.
HiSAT2 was used for alignment of trimmed reads using mm39 build and GRCm39 GTF file. FeatureCounts was used for gene counts. Deseq2 was used for normalization and differential expression analysis.
Assembly: mm39
Supplementary files format and content: Raw_counts.txt (raw counts from FeatureCounts for all samples compiled in a table with library name as headers), Normalized_counts.txt (DESeq2 normalized counts for all samples compiled in a table with library name as headers),
Supplementary files format and content: RTT271_counts.txt (count table of RTT271 construct in RNA library for injected samples), MECP2_E2_CDS_Tau_counts.txt (count table for Tau overexpression contruct in Tau-driven Mecp2 overexpression and control lines).

extract_protocol:
RNA was isolated from samples using Qiazol phase separation followed by cleanup with RNeasy 96 Kit per manufacturer’s instruction. Isolated RNA sample quality was assessed by both RNA Tapestation assay and High Sensitivity RNA Tapestation assay (Agilent Technologies Inc., California, USA and quantified by Infinite F Nano+ 200 Pro Tecan® (Tecan, Switzerland)
Paramagnetic beads coupled with oligo d(T)25 are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual (New England BioLabs Inc., Massachusetts, USA). Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendations. The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 30 minutes at 42⁰C. All remaining steps for library construction were used according to the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation HSD1000 ScreenTape (Agilent Technologies Inc., California, USA). Final library size was about 450bp with an insert size of about 300bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq X Plus (Illumina, California, USA) with a read length configuration of 150 PE for 60M PE reads per sample (30M in each direction).


title: DP-Mettl3WT-meRIPseq-input-rep1

description: Library name: sample51


title: Hippocampus of Tau-/+, Tau driven overexpression of Mecp2, biol rep 7

description:
Library name: 23248XR-01-157
Raw_counts.txt
Normalized_counts.txt

value: Tau-MeCP2 Over-expression


title: RNA92

description: Library name: DSP-1001660022159-B-A04


title: Hippocampus of Tau+/+, Control for Tau driven overexpression of Mecp2, biol rep 7

description:
Library name: 23248XR-01-156
Raw_counts.txt
Normalized_counts.txt

value: Hippocampus


title: DP-Mettl3WT-meRIPseq-input-rep2

description: Library name: sample50


title: Hippocampus of Tau+/+, Control for Tau driven overexpression of Mecp2, biol rep 6

description:
Library name: 23248XR-01-155
Raw_counts.txt
Normalized_counts.txt


title: RNA91

description: Library name: DSP-1001660022159-B-A05


title: Hippocampus of Tau+/+, Control for Tau driven overexpression of Mecp2, biol rep 5

description:
Library name: 23248XR-01-154
Raw_counts.txt
Normalized_counts.txt


title: DP-Mettl3WT-meRIPseq-input-rep3

description: Library name: sample49


title: Hippocampus of Tau+/+, Control for Tau driven overexpression of Mecp2, biol rep 4

description:
Library name: 23248XR-01-153
Raw_counts.txt
Normalized_counts.txt


title: DP-Mettl3WT-meRIPseq-ip-rep1

description: Library name: sample48


title: RNA90

description: Library name: DSP-1001660022159-B-A06


title: Hippocampus of Tau-/+, Tau driven overexpression of Mecp2, biol rep 6

description:
Library name: 23248XR-01-152
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Tau-/+, Tau driven overexpression of Mecp2, biol rep 5

description:
Library name: 23248XR-01-151
Raw_counts.txt
Normalized_counts.txt


title: RNA89

description: Library name: DSP-1001660022159-B-A07


title: DP-Mettl3WT-meRIPseq-ip-rep2

description: Library name: sample47


title: Hippocampus of Tau-/+, Tau driven overexpression of Mecp2, biol rep 4

description:
Library name: 23248XR-01-150
Raw_counts.txt
Normalized_counts.txt


title: RNA88

description: Library name: DSP-1001660022159-B-A08


title: Hippocampus of Tau-/+, Tau driven overexpression of Mecp2, biol rep 3

description:
Library name: 23248XR-01-149
Raw_counts.txt
Normalized_counts.txt


title: DP-Mettl3WT-meRIPseq-ip-rep3

description: Library name: sample46


title: Hippocampus of Tau-/+, Tau driven overexpression of Mecp2, biol rep 2

description:
Library name: 23248XR-01-147
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Tau+/+, Control for Tau driven overexpression of Mecp2, biol rep 3

description:
Library name: 23248XR-01-148
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Tau+/+, Control for Tau driven overexpression of Mecp2, biol rep 2

description:
Library name: 23248XR-01-146
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3WT-RAG1D708A-ATAC-rep3

description: Library name: sample45

value: Thymocyte


title: Hippocampus of Tau+/+, Control for Tau driven overexpression of Mecp2, biol rep 1

description:
Library name: 23248XR-01-145
Raw_counts.txt
Normalized_counts.txt


title: RNA87

description: Library name: DSP-1001660022159-B-A09


title: RNA86

description: Library name: DSP-1001660022159-B-A10


title: Hippocampus of Tau-/+, Tau driven overexpression of Mecp2, biol rep 1

description:
Library name: 23248XR-01-144
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3WT-RAG1D708A-ATAC-rep2

description: Library name: sample44


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 12

description:
Library name: 23248XR-01-143
Raw_counts.txt
Normalized_counts.txt

value: MeCP2:-/Y rtt271a

value: injected rtt271 3e11


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 11

description:
Library name: 23248XR-01-142
Raw_counts.txt
Normalized_counts.txt


title: RNA85

description: Library name: DSP-1001660022159-B-A11


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 9

description:
Library name: 23248XR-01-140
Raw_counts.txt
Normalized_counts.txt


title: RNA84

description: Library name: DSP-1001660022159-B-A12


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 10

description:
Library name: 23248XR-01-141
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3WT-RAG1D708A-ATAC-rep1

description: Library name: sample43


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 8

description:
Library name: 23248XR-01-139
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3KO-RAG1D708A-ATAC-rep3

description: Library name: sample42


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 7

description:
Library name: 23248XR-01-138
Raw_counts.txt
Normalized_counts.txt


title: RNA82

description: Library name: DSP-1001660022159-B-B02


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 5

description:
Library name: 23248XR-01-136
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 4

description:
Library name: 23248XR-01-135
Raw_counts.txt
Normalized_counts.txt


title: DP-Mettl3WT-ATAC-rep3

description: Library name: sample39


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 1

description:
Library name: 23248XR-01-132
Raw_counts.txt
Normalized_counts.txt


title: RNA80

description: Library name: DSP-1001660022159-B-B04


title: DP-Mettl3WT-ATAC-rep2

description: Library name: sample38


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 3

description:
Library name: 23248XR-01-134
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 13

description:
Library name: 23248XR-01-131
Raw_counts.txt
Normalized_counts.txt

value: injected rtt271 1e11


title: RNA79

description: Library name: DSP-1001660022159-B-B05


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 12

description:
Library name: 23248XR-01-130
Raw_counts.txt
Normalized_counts.txt


title: DP-Mettl3WT-ATAC-rep1

description: Library name: sample37


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 11

description:
Library name: 23248XR-01-129
Raw_counts.txt
Normalized_counts.txt


title: RNA78

description: Library name: DSP-1001660022159-B-B06


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 10

description:
Library name: 23248XR-01-128
Raw_counts.txt
Normalized_counts.txt


title: RNA77

description: Library name: DSP-1001660022159-B-B07


title: DP-Mettl3KO-ATAC-rep3

description: Library name: sample36


title: Hippocmapus of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 8

description:
Library name: 23248XR-01-126
Raw_counts.txt
Normalized_counts.txt


title: DP-Mettl3KO-ATAC-rep2

description: Library name: sample35


title: RNA76

description: Library name: DSP-1001660022159-B-B08


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 6

description:
Library name: 23248XR-01-124
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 7

description:
Library name: 23248XR-01-125
Raw_counts.txt
Normalized_counts.txt


title: DP-Mettl3KO-ATAC-rep1

description: Library name: sample34


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 5

description:
Library name: 23248XR-01-123
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 4

description:
Library name: 23248XR-01-122
Raw_counts.txt
Normalized_counts.txt


title: Hippocmapus of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 3

description:
Library name: 23248XR-01-121
Raw_counts.txt
Normalized_counts.txt


title: DP-Mettl3WT-RNAseq-rep4

description: Library name: sample33


title: RNA75

description: Library name: DSP-1001660022159-B-B09


title: RNA74

description: Library name: DSP-1001660022159-B-B10


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 2

description:
Library name: 23248XR-01-120
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 1

description:
Library name: 23248XR-01-119
Raw_counts.txt
Normalized_counts.txt


title: DP-Mettl3WT-RNAseq-rep3

description: Library name: sample32


title: RNA73

description: Library name: DSP-1001660022159-B-B11


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 21

description:
Library name: 23248XR-01-118
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 20

description:
Library name: 23248XR-01-117
Raw_counts.txt
Normalized_counts.txt


title: RNA72

description: Library name: DSP-1001660022159-B-B12


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 19

description:
Library name: 23248XR-01-116
Raw_counts.txt
Normalized_counts.txt


title: DP-Mettl3WT-RNAseq-rep1

description: Library name: sample30


title: DP-Mettl3WT-RNAseq-rep2

description: Library name: sample31


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 18

description:
Library name: 23248XR-01-115
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 17

description:
Library name: 23248XR-01-114
Raw_counts.txt
Normalized_counts.txt


title: RNA71

description: Library name: DSP-1001660022159-B-C01


title: DP-Mettl3KO-RNAseq-rep3

description: Library name: sample29


title: Hippocampus of Mecp2-KO, injected with PBS, control, biol rep 6

description:
Library name: 23248XR-01-113
Raw_counts.txt
Normalized_counts.txt


title: RNA70

description: Library name: DSP-1001660022159-B-C02


title: RNA83

description: Library name: DSP-1001660022159-B-B01


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 16

description:
Library name: 23248XR-01-112
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3KO-RAG1D708A-ATAC-rep2

description: Library name: sample41


title: DP-Mettl3KO-RNAseq-rep2

description: Library name: sample28


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 15

description:
Library name: 23248XR-01-111
Raw_counts.txt
Normalized_counts.txt


title: RNA69

description: Library name: DSP-1001660022159-B-C03


title: DP-Mettl3KO-RNAseq-rep1

description: Library name: sample27


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 6

description:
Library name: 23248XR-01-137
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 13

description:
Library name: 23248XR-01-109
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 14

description:
Library name: 23248XR-01-110
Raw_counts.txt
Normalized_counts.txt


title: RNA68

description: Library name: DSP-1001660022159-B-C04


title: thymus-Mettl3KO-RAG1D708A-ATAC-rep1

description: Library name: sample40


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 12

description:
Library name: 23248XR-01-108
Raw_counts.txt
Normalized_counts.txt


title: RNA81

description: Library name: DSP-1001660022159-B-B03


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 2

description:
Library name: 23248XR-01-133
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3WT-TRAV14-HTGTS-rep3

description: Library name: sample26


title: Hippocampus of Mecp2-KO, injected with PBS, control, biol rep 5

description:
Library name: 23248XR-01-107
Raw_counts.txt
Normalized_counts.txt


title: RNA67

description: Library name: DSP-1001660022159-B-C05


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 11

description:
Library name: 23248XR-01-106
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 10

description:
Library name: 23248XR-01-105
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3WT-TRAV14-HTGTS-rep2

description: Library name: sample25


title: RNA66

description: Library name: DSP-1001660022159-B-C06


title: Hippocampus of Mecp2-KO, injected with PBS, control, biol rep 4

description:
Library name: 23248XR-01-104
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 9

description:
Library name: 23248XR-01-102
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3WT-TRAV14-HTGTS-rep1

description: Library name: sample24


title: RNA65

description: Library name: DSP-1001660022159-B-C07


title: Hippocampus of Mecp2-KO, injected with PBS, control, biol rep 3

description:
Library name: 23248XR-01-101
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3KO-TRAV14-HTGTS-rep3

description: Library name: sample23


title: RNA64

description: Library name: DSP-1001660022159-B-C08


title: Hippocampus of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 9

description:
Library name: 23248XR-01-127
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 8

description:
Library name: 23248XR-01-100
Raw_counts.txt
Normalized_counts.txt


title: Hippocmapus of Mecp2-KO, injected with PBS, control, biol rep 2

description:
Library name: 23248XR-01-99
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3KO-TRAV14-HTGTS-rep2

description: Library name: sample22


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 7

description:
Library name: 23248XR-01-98
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Mecp2-KO, injected with PBS, control, biol rep 1

description:
Library name: 23248XR-01-97
Raw_counts.txt
Normalized_counts.txt


title: RNA63

description: Library name: DSP-1001660022159-B-C09


title: thymus-Mettl3KO-TRAV14-HTGTS-rep1

description: Library name: sample21


title: RNA62

description: Library name: DSP-1001660022159-B-C10


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 6

description:
Library name: 23248XR-01-96
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 5

description:
Library name: 23248XR-01-95
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 4

description:
Library name: 23248XR-01-94
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3WT-TRD-RACE-rep3

description: Library name: sample20


title: RNA61

description: Library name: DSP-1001660022159-B-C11


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 3

description:
Library name: 23248XR-01-93
Raw_counts.txt
Normalized_counts.txt


title: Hippocmapus of Mecp2-WT, injected with PBS, control, biol rep 2

description:
Library name: 23248XR-01-92
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3WT-TRD-RACE-rep2

description: Library name: sample19


title: RNA60

description: Library name: DSP-1001660022159-B-C12


title: Hippocampus of Mecp2-WT, injected with PBS, control, biol rep 1

description:
Library name: 23248XR-01-91
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3WT-TRD-RACE-rep1

description: Library name: sample18


title: thymus-Mettl3KO-TRD-RACE-rep3

description: Library name: sample17


title: RNA59

description: Library name: DSP-1001660022159-B-D01

source_name: Chest Wall

value: Chest Wall


title: Hippocampus of Mecp2-KO, non-injected control, biol rep 1

description:
Library name: 23248XR-01-89
Raw_counts.txt
Normalized_counts.txt


title: Hippocampus of Mecp2-KO, non-injected control, biol rep 2

description:
Library name: 23248XR-01-90
Raw_counts.txt
Normalized_counts.txt


title: Cortex of Tau+/+, Control for Tau driven overexpression of Mecp2, biol rep 7

description:
Library name: 23248XR-01-70
Raw_counts.txt
Normalized_counts.txt

value: Tau-Wildtype Control


title: Cortex of Tau-/+, Tau driven overexpression of Mecp2, biol rep 7

description:
Library name: 23248XR-01-69
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3KO-TRD-RACE-rep2

description: Library name: sample16


title: Cortex of Tau+/+, Control for Tau driven overexpression of Mecp2, biol rep 6

description:
Library name: 23248XR-01-68
Raw_counts.txt
Normalized_counts.txt


title: Cortex of Tau+/+, Control for Tau driven overexpression of Mecp2, biol rep 5

description:
Library name: 23248XR-01-67
Raw_counts.txt
Normalized_counts.txt


title: RNA58

description: Library name: DSP-1001660022159-B-D02


title: Cortex of Tau+/+, Control for Tau driven overexpression of Mecp2, biol rep 4

description:
Library name: 23248XR-01-66
Raw_counts.txt
Normalized_counts.txt


title: Cortex of Tau-/+, Tau driven overexpression of Mecp2, biol rep 6

description:
Library name: 23248XR-01-64
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3WT-TRB-RACE-rep3

description: Library name: sample14


title: RNA56

description: Library name: DSP-1001660022159-B-D04


title: Cortex of Tau-/+, Tau driven overexpression of Mecp2, biol rep 5

description:
Library name: 23248XR-01-63
Raw_counts.txt
Normalized_counts.txt


title: Cortex of Tau-/+, Tau driven overexpression of Mecp2, biol rep 4

description:
Library name: 23248XR-01-62
Raw_counts.txt
Normalized_counts.txt


title: RNA55

description: Library name: DSP-1001660022159-B-D05


title: Cortex of Tau-/+, Tau driven overexpression of Mecp2, biol rep 3

description:
Library name: 23248XR-01-61
Raw_counts.txt
Normalized_counts.txt


title: Cortex of Tau+/+, Control for Tau driven overexpression of Mecp2, biol rep 3

description:
Library name: 23248XR-01-60
Raw_counts.txt
Normalized_counts.txt


title: Cortex of Tau-/+, Tau driven overexpression of Mecp2, biol rep 2

description:
Library name: 23248XR-01-59
Raw_counts.txt
Normalized_counts.txt


title: RNA53

description: Library name: DSP-1001660022159-B-D07


title: Cortex of Tau+/+, Control for Tau driven overexpression of Mecp2, biol rep 2

description:
Library name: 23248XR-01-58
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3KO-TRB-RACE-rep3

description: Library name: sample11


title: Cortex of Tau+/+, Control for Tau driven overexpression of Mecp2, biol rep 1

description:
Library name: 23248XR-01-57
Raw_counts.txt
Normalized_counts.txt


title: RNA52

description: Library name: DSP-1001660022159-B-D08


title: thymus-Mettl3KO-TRB-RACE-rep2

description: Library name: sample10


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 12

description:
Library name: 23248XR-01-55
Raw_counts.txt
Normalized_counts.txt


title: RNA51

description: Library name: DSP-1001660022159-B-D09


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 11

description:
Library name: 23248XR-01-54
Raw_counts.txt
Normalized_counts.txt


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 10

description:
Library name: 23248XR-01-53
Raw_counts.txt
Normalized_counts.txt


title: RNA50

description: Library name: DSP-1001660022159-B-D10


title: thymus-Mettl3KO-TRB-RACE-rep1

description: Library name: sample9


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 9

description:
Library name: 23248XR-01-52
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3WT-TRA-RACE-rep3

description: Library name: sample8


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 8

description:
Library name: 23248XR-01-51
Raw_counts.txt
Normalized_counts.txt


title: RNA49

description: Library name: DSP-1001660022159-B-D11


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 7

description:
Library name: 23248XR-01-50
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3WT-TRA-RACE-rep2

description: Library name: sample7


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 6

description:
Library name: 23248XR-01-49
Raw_counts.txt
Normalized_counts.txt


title: RNA48

description: Library name: DSP-1001660022159-B-D12


title: thymus-Mettl3WT-TRA-RACE-rep1

description: Library name: sample6


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 3

description:
Library name: 23248XR-01-46
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3KO-TRA-RACE-rep3

description: Library name: sample5


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 2

description:
Library name: 23248XR-01-45
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3KO-TRA-RACE-rep2

description: Library name: sample4


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 3e11, biol rep 1

description:
Library name: 23248XR-01-44
Raw_counts.txt
Normalized_counts.txt


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 13

description:
Library name: 23248XR-01-43
Raw_counts.txt
Normalized_counts.txt


title: RNA45

description: Library name: DSP-1001660022159-B-E03


title: J21

description: Library name: J21

value: human skin

value: a pool of single cells

value: Control


title: Ctrl_LNA_3

city: St. Louis

first: Dylan

last: Galloway

state: MO

address: 4370 Duncan Ave

department: Neurology

institute: Washington University in St. Louis

description: Library name: Scram_Ctrl_3

data_processing:
Reads aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1
Quantification via featureCounts
Assembly: GRCm38
Supplementary files format and content: Tab-delimited file with counts, CPM, and TPM

growth_protocol: Mice were housed on a standard 12hr light/dark cycle. Motor neurons were generated from mESCs using a standard -2/+4 protocol with retinoic acid and SAG. Motor neurons were cultured in growth factor supplemented neuronal media.

extract_protocol:
Norgen Total RNA Plus
KAPA RiboErase

treatment_protocol: Mice were divided by genotype, cells were transfected with Lipofectamine 2000 and 10nM of miR-146a LNA or control LNA (Qiagen) for 72hrs.

value: RW.4 mESC

value: Motor Neuron

value: Wild-type

value: Control LNA


title: 061522ICN_posterior

city: New Haven

first: Qian

last: Xu

state: Connecticut

address: 100 College

institute: Yale university

description:
Library name: sample3
10x genomics

data_processing:
Raw sequencing data were aligned to the mm10-2020-A mouse genome reference using the Cell Ranger software v.7.1.0 (10X Genomics). Cells were filtered using the following quality control thresholds: number of detected genes per cell > 2,500 and < 20,000; and percentage of mitochondria genes < 10%. To select neuronal populations, cells with Plp1 expression ³1 and Fabp7 ³1 were excluded, and those expressing Phox2b >0 and Snap25 >0 were retained. A total of 2,870 high-quality ICNs passed filtering (1,111 from mixed ganglia, 933 from anterior ganglia, and 826 from posterior ganglia). Filtered datasets were integrated and analyzed using the Seurat R package v.4.4.2. Dimensionality reduction was performed using the top 50 principal components, and UMAP was used for visualization. ICN cell types were annotated based on unsupervised clustering. DEGs between ICN subtypes were identified using the Seurat’s built-in likelihood-ratio test based on the bimod distribution.
Assembly: mouse mm10-2020
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Heart atria posterior section

extract_protocol:
ICNs were acutely isolated using a modified protocol for peripheral neurons. Briefly, hearts were harvested from 10 age- and sex-matched Baf53bGFP mice into ice-cold Leibovitz's L-15 Medium (GibcoTM). ICN-containing regions were identified and dissected under a Leica M205FCA Fluorescence Stereo Microscope. Tissues were trimmed into 1-3 mm2 pieces and incubated with 0.25% trypsin-EDTA (GibcoTM) at 37 ˚C for 25 minutes. After washing in L-15 medium supplemented with 10% fatal bovine serum (FBS), tissues were digested with 1 mg/mL Collagenase A (Sigma) and 3 mg/mL of Dispase II (Sigma) in 1 x Hank’s Balanced Salt Solution (HBSS, Stemcell Technologies) at 37°C for 40 minutes. Dissociated tissues were triturated using a series of three fire-polished Pasteur pipettes of decreasing opening size, then filtered through a 40 mm cell strainer (Corning). Cells were centrifuged at 200 x g for 10 minutes at 4°C and resuspended in 1x HBSS containing 0.04% BSA. For regional transcriptomic analysis, anterior and posterior ganglia were dissected and processed separately. For mixed ganglia samples, tissues were pooled. Fluorescently labelled cells were sorted using a BD FACS Aria cell sorter into ice-cold 1x HBSS with 0.04% BSA at the Yale Flow Cytometry Facility.
Approximately 5,000-10,000 sorted cells were loaded per channel on the 10x Genomics Chromium microfluidic device to target a recovery of 3,000-6,000 cells per sample. Single-cell cDNA libraries were prepared using the Chromium Single Cell 3’ V3 reagent kit at the Yale Center for Genomic Analysis (YCGA) and sequenced on an Illumina NovaSeq S4 sequencer at 150-300 million reads to achieve a target depth of 30,000-50,000 reads per cell.

value: Heart atria posterior section

value: neuron

tag: age

value: 4 months

tag: Sex

value: female and male


title: J6

description: Library name: J6

value: Les AD


title: miR-146a_LNA_2

description: Library name: LNA_146a_2

value: miR-146a LNA


title: J19

description: Library name: J19


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 12

description:
Library name: 23248XR-01-42
Raw_counts.txt
Normalized_counts.txt

value: Cortex

value: MeCP2:-/Y rtt271a


title: thymus-Mettl3KO-TRA-RACE-rep1

description: Library name: sample3

value: Thymus

value: Thymocyte


title: 8219_LS

description: Library name: 8219_LS

source_name: Spinal Cord

value: Spinal Cord

value: miR-146a KO


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 11

description:
Library name: 23248XR-01-41
Raw_counts.txt
Normalized_counts.txt

value: injected rtt271 1e11


title: RNA44

description: Library name: DSP-1001660022159-B-E04

value: Chest Wall


title: thymus-Mettl3KO-TRD-RACE-rep1

description: Library name: sample15


title: RNA57

description: Library name: DSP-1001660022159-B-D03


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 9

description:
Library name: 23248XR-01-39
Raw_counts.txt
Normalized_counts.txt


title: thymus-Mettl3KO-scRNAseq-rep1

description: Library name: sample1


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 7

description:
Library name: 23248XR-01-37
Raw_counts.txt
Normalized_counts.txt


title: RNA43

description: Library name: DSP-1001660022159-B-E05


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 6

description:
Library name: 23248XR-01-36
Raw_counts.txt
Normalized_counts.txt


title: RNA42

description: Library name: DSP-1001660022159-B-E06


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 5

description:
Library name: 23248XR-01-35
Raw_counts.txt
Normalized_counts.txt


title: White adipocytes, DICERKO, isoproterenol, biological replicate 3

city: Campinas

first: Marcelo

last: Mori

state: São Paulo

address: R. Monteiro Lobato

country: Brazil

institute: UNICAMP

description: Library name: 8249_S36

data_processing:
Quality control of raw reads was performed with FastQC. Low-quality sequences and adapters were removed using Trimmomatic. All steps were performed using the Galaxy platform.
Processed reads were aligned to the mouse reference genome mm10 using HISAT2 with default settings.
Read counts were quantified per genomic feature using featureCounts. Genes with fewer than 4 reads across all samples or variance lower than 5 were filtered out.
Differential expression analysis was performed using edgeR (via NetworkAnalyst 3.0) with TMM normalization. Differentially expressed genes were identified at FDR < 0.05.
Assembly: mm10 (GRCm38)
Supplementary files format and content: normalizedexpression.txt

source_name: Immortalized white subcutaneous preadipocyte cell line (Dicer1 flox/Cre-ERT2)

growth_protocol: Immortalized white subcutaneous preadipocytes (Dicer1 flox/flox, Cre-ERT2) were maintained in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. Cells were differentiated to mature adipocytes by sequential treatment: induction medium (DMEM, 10% FBS, 20 nM insulin, 2.8 uM rosiglitazone, 1 nM T3, 0.5 mM IBMX, 1 uM dexamethasone, 0.125 mM indomethacin) for 2 days, then maintenance medium (DMEM, 20 nM insulin, 2.8 uM rosiglitazone, 1 nM T3) for 2 days, followed by DMEM with 20 nM insulin and 2.8 uM rosiglitazone for 2 additional days.

extract_protocol:
Total RNA was extracted using Trizol reagent (Life Technologies) according to the manufacturer's protocol. RNA quality and integrity were assessed using the Bioanalyzer 2100 (Agilent Technologies).
RNA-seq libraries were prepared from poly(A)-enriched mRNA using the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs) following the manufacturer's protocol.

treatment_protocol: On day 6 of differentiation, DICER knockout was induced by 48-hour treatment with 10 uM 4-hydroxytamoxifen (4-OHT); control cells received ethanol vehicle. Following knockout induction, cells were stimulated with 10 uM isoproterenol for 6 hours to mimic cold/thermogenic activation.

value: White adipocytes (differentiated)

value: Dicer1 flox/flox (Cre-ERT2), 4-OHT-induced knockout

value: isoproterenol 10 uM, 6h


title: RNA41

description: Library name: DSP-1001660022159-B-E07


title: White adipocytes, DICERKO, isoproterenol, biological replicate 1

description: Library name: 8247_S34

value: Immortalized white subcutaneous preadipocyte cell line (Dicer1 flox/Cre-ERT2)


title: Cortex of Mecp2-KO, injected with AAV9-rrt271 1e11, biol rep 3

description:
Library name: 23248XR-01-33
Raw_counts.txt
Normalized_counts.txt


title: RNA40

description: Library name: DSP-1001660022159-B-E08


title: White adipocytes, DICERKO, isoproterenol, biological replicate 2

description: Library name: 8248_S35


title: White adipocytes, WT control, isoproterenol, biological replicate 3

description: Library name: 8246_S33

value: Dicer1 flox/flox (Cre-ERT2), vehicle (EtOH)


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 21

description:
Library name: 23248XR-01-30
Raw_counts.txt
Normalized_counts.txt

value: injected pbs controls


title: White adipocytes, WT control, isoproterenol, biological replicate 2

description: Library name: 8245_S32


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 20

description:
Library name: 23248XR-01-29
Raw_counts.txt
Normalized_counts.txt


title: RNA38

description: Library name: DSP-1001660022159-B-E10

value: Bone


title: RNA39

description: Library name: DSP-1001660022159-B-E09


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 19

description:
Library name: 23248XR-01-28
Raw_counts.txt
Normalized_counts.txt


title: 2DM1F6LU_S32

city: Durham

first: Scott

last: Auerbach

state: NC

address: 111 TW Alexander Drive

institute: Division of the National Toxicology Program at NIEHS

description: Library name: 2DM1F6LU_S32_R1_001

data_processing:
TempO-Seq sequences were aligned to the rat S1500+ probe sequences using Bowtie version 1.3.1. The Bowtie configuration allowed up to three mismatches and selected the single best alignment for reporting.
The aligned read counts for attenuated probes were properly readjusted to calculate unattenuated equivalent counts using the attenuation factors provided in the platform manifest.
Assembly: BioSpyder TempO-seq mouse S1500+ manifest
Supplementary files format and content: tab-delimited text file includes attenuation-adjusted raw probe counts for each sample

source_name: Lung

extract_protocol:
The majority of all tissues from all animals were collected within approximately 10 minutes of euthanasia. Tissue samples were collected following organ weight measurements in the following order: lung, heart, liver (left lobe), kidney, and ovary (no ovary weights were taken) from all remaining animals on study day 5 for transcriptomic analysis. Two samples of lung, heart, liver, and kidney tissue (approximately 5 mm3) were collected and placed into cryotubes containing RNAlater. The ovaries were collected whole bilaterally (one sample) and placed into cryotubes containing RNAlater. The tissue samples were stored at 2°C to 8°C for approximately 55 hours for rats or up to 48 hours for mice. The RNAlater was then removed and the samples were stored in a −85°C to −60°C freezer until processed for RNA isolation. Tissues were homogenized in QIAzol lysis buffer (Qiagen Inc., Valencia, CA) using the TissueLyser II bead-beating system followed by RNA extraction using the RNeasy 96 QIAcube HT kits (Qiagen Inc., Valencia, CA) with a DNA digestion step.
Isolated RNA was utilized for analysis using either the Mouse S1500+ v1.2 TempO-Seq (BioSpyder, Carlsbad, CA) platform with a minimum of 500 mapped read counts/transcript and approximately 1.5 million counts/sample. Work instructions developed by Battelle using the BioSpyder User Guide (https://www.biospyder.com/s/100802-TempO-Seq-User-Guide-rev-C-r8r7.pdf) were followed.

value: Lung

value: B6D2F1/Crl (BDF-1)

value: female

value: 9 weeks

tag: concentration (ppm)

tag: sample status

value: Used in Analysis

tag: qc issue


title: White adipocytes, WT control, isoproterenol, biological replicate 1

description: Library name: 8244_S31


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 18

description:
Library name: 23248XR-01-27
Raw_counts.txt
Normalized_counts.txt

value: Cortex


title: RNA37

description: Library name: DSP-1001660022159-B-E11


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 17

description:
Library name: 23248XR-01-26
Raw_counts.txt
Normalized_counts.txt


title: hippocampal tissues of AAV-vehicle injected Bcas2F/F mice

city: Beijing

first: Hai

middle: xia

last: Ma

address: Changchun street NO.45

institute: Xuanwu Hospital

description: Library name: Sample2

data_processing:
Results from Illumina sequencing offline were converted to FASTQ format using bcl2fastq software (version 5.0.1). The scRNA-seq sequencing data were compared to reference genome using CellRanger software, and cellular and individual cellular 3' end transcripts were identified and counted in the sequenced samples.
The output CellRanger expression profile matrix was loaded into Seurat (version 4.1.0) for filtering of low quality cells from scRNA-seq data, and the filtered data was downscaled and clustered. Filtering low cell quality thresholds: number of genes expressed per cell >500, mitochondrial genes expressed in <25% of cells. Cells were projected into 2D space using t-SNE or UMAP.
Assembly: GRCm39
Supplementary files format and content: a differential expression test between each cluster

molecule: nuclear RNA

source_name: hippocampus

extract_protocol:
Tissue was added to 1 ml of pre-chilled lysate, sheared into small pieces of approximately 1 mm, 2 ml of pre-chilled lysate was added, transferred to a tissue homogenizer (885300-0007; Kimble Dounce Homogenizer ), and ground slowly 5 times. The tissue was incubated on ice for 5 min, followed by the addition of 4 ml of pre-cooled 2% BSA dilution, and the reaction was terminated by pipetting with a barrel pipette. Samples were passed through a 30um cell sieve, and the filtrate was collected and centrifuged at 300 g for 5 min at 4°C. The supernatant was discarded. The cells were resuspended with 5 ml of 2% BSA, centrifuged at 4°C for 5 min at 300 g. The supernatant was discarded and the cells were resuspended with 500 ul of resuspension solution (1xPBS, 2% BSA, 0.1% RNase inhibitor). Stain with PI (Propidium Iodide) and sort to remove debris impurities using a BD FACSAria II flow cytometer. Cells were collected and counted.
Single-cell nuclear suspension was added to the 10x Chromium chip according to the instructions for the 10X Genomics Chromium Single-Cell 3' kit (V3), with the expectation of capturing 8,000 cells. cDNA amplification and library construction were performed according to standard protocols. Libraries were sequenced by LC-Bio Technology (Hangzhou, China) on an Illumina NovaSeq 6000 sequencing system (double-end sequencing, 150 bp) at a minimum depth of 20,000 reads per cell.

value: hippocampus

value: WT


title: RNA36

description: Library name: DSP-1001660022159-B-E12


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 16

description:
Library name: 23248XR-01-24
Raw_counts.txt
Normalized_counts.txt


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 15

description:
Library name: 23248XR-01-23
Raw_counts.txt
Normalized_counts.txt


title: hippocampal tissues of AAV2/9-Syn-cre injected Bcas2F/F mice

description: Library name: Sample1

value: Bcas2 knockdown


title: Cortex of Mecp2-KO, injected with PBS, control, biol rep 6

description:
Library name: 23248XR-01-25
Raw_counts.txt
Normalized_counts.txt


title: RNA35

description: Library name: DSP-1001660022159-B-F01


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 14

description:
Library name: 23248XR-01-22
Raw_counts.txt
Normalized_counts.txt


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 13

description:
Library name: 23248XR-01-21
Raw_counts.txt
Normalized_counts.txt


title: RNA34

description: Library name: DSP-1001660022159-B-F02


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 12

description:
Library name: 23248XR-01-20
Raw_counts.txt
Normalized_counts.txt


title: Cortex of Mecp2-KO, injected with PBS, control, biol rep 5

description:
Library name: 23248XR-01-19
Raw_counts.txt
Normalized_counts.txt


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 11

description:
Library name: 23248XR-01-18
Raw_counts.txt
Normalized_counts.txt


title: hippocampal tissues of AAV-vehicle injected Bcas2F/F mice 1

description: Library name: WT_1

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCm39
Supplementary files format and content: FPKM, count values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 10

description:
Library name: 23248XR-01-17
Raw_counts.txt
Normalized_counts.txt


title: RNA33

description: Library name: DSP-1001660022159-B-F03


title: hippocampal tissues of AAV-vehicle injected Bcas2F/F mice 2

description: Library name: WT_2


title: Cortex of Mecp2-KO, injected with PBS, control, biol rep 4

description:
Library name: 23248XR-01-16
Raw_counts.txt
Normalized_counts.txt


title: hippocampal tissues of AAV2/9-Syn-cre injected Bcas2F/F mice 3

description: Library name: BKO_3


title: RNA31

description: Library name: DSP-1001660022159-B-F05


title: Cortex of Mecp2-KO, injected with PBS, control, biol rep 3

description:
Library name: 23248XR-01-13
Raw_counts.txt
Normalized_counts.txt


title: hippocampal tissues of AAV2/9-Syn-cre injected Bcas2F/F mice 2

description: Library name: BKO_2


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 8

description:
Library name: 23248XR-01-12
Raw_counts.txt
Normalized_counts.txt


title: RNA30

description: Library name: DSP-1001660022159-B-F06


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 7

description:
Library name: 23248XR-01-10
Raw_counts.txt
Normalized_counts.txt


title: Cortex of Mecp2-KO, injected with PBS, control, biol rep 2

description:
Library name: 23248XR-01-11
Raw_counts.txt
Normalized_counts.txt


title: RNA29

description: Library name: DSP-1001660022159-B-F07


title: Cortex of Mecp2-KO, injected with PBS, control, biol rep 1

description:
Library name: 23248XR-01-09
Raw_counts.txt
Normalized_counts.txt


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 6

description:
Library name: 23248XR-01-08
Raw_counts.txt
Normalized_counts.txt


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 5

description:
Library name: 23248XR-01-07
Raw_counts.txt
Normalized_counts.txt


title: RNA28

description: Library name: DSP-1001660022159-B-F08


title: WT-CNO

city: Aurora

first: Tessa

last: Allen

state: CO

department: Cell and Developmental Biology

institute: University of Colorado, Anschutz

description: Library name: Sample 1

data_processing:
cellranger-7.1.0
Assembly: Genome Reference Consortium Mouse Build 38
Supplementary files format and content: matrix
Supplementary files format and content: features
Supplementary files format and content: barcode

source_name: brain

extract_protocol:
brains were disected from P8 pups. Cortex and Corpus callosum were disected and cells were dissociated using papain (Worthington Biochemical). Oligodendrocytes were isolated using PDGFRα and O4-positive selection magnetic microbeads (Miltenyi).
Single Cell 3' v3

value: brain

value: oligodendrocytes

value: wildtype

tag: strain

value: CNO


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 4

description:
Library name: 23248XR-01-06
Raw_counts.txt
Normalized_counts.txt


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 3

description:
Library name: 23248XR-01-05
Raw_counts.txt
Normalized_counts.txt


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 2

description:
Library name: 23248XR-01-04
Raw_counts.txt
Normalized_counts.txt


title: Male KO Liver, Rep 6

city: Charleston

first: Jessica

middle: H

last: Hartman

state: South Carolina

address: 70 President St., Drug Discovery Bldg/Rm DD220

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

description: Library name: Sample 23

data_processing:
Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers,  and grouped by gene_id. Final gene counts were annotated with gene biotype and  other metadata extracted from the reference GTF file.  Sample-sample correlations for sample-sample heatmap and PCA were calculated on normalized counts  (TMM, trimmed mean of M-values) using Pearson correlation.
Assembly: mm39
Supplementary files format and content: spreadsheet containing raw and normalized gene counts

source_name: Liver

growth_protocol: Mice were maintained in co-housed cages on normal chow in controlled temperature and humidity until 12-13 weeks of age.

extract_protocol:
Liver lysates were prepared by homogenization in the bullet blender and RNA was isolated using the RNeasy Qiagen kit with the optional DNaseI on-column digestion step
Plasmidsaurus RNA-Seq utilizes Illumina sequencing and a 3’ end counting approach. We sent extracted total RNA on dry ice. They assessed RNA concentration using a fluorescence based plate reader assay and normalized sample concentrations before proceeding. For sequencing library preparation, they converted mRNA into complementary DNA (cDNA) via reverse transcription and second-strand synthesis, followed by tagmentation, library indexing, and amplification. Their approach uses 3’ end counting to capture differential gene expression.

value: Liver

value: 16-week old

value: Bulk Tissue


title: RNA26

description: Library name: DSP-1001660022159-B-F10

value: Bone


title: Cortex of Mecp2-WT, injected with PBS, control, biol rep 1

description:
Library name: 23248XR-01-03
Raw_counts.txt
Normalized_counts.txt

value: injected pbs controls


title: Male KO Liver, Rep 5

description: Library name: Sample 22


title: Cortex of Mecp2-KO, non-injected control, biol rep 2

description:
Library name: 23248XR-01-02
Raw_counts.txt
Normalized_counts.txt

value: non-injected ctrl


title: RNA25

description: Library name: DSP-1001660022159-B-F11


title: Cortex of Mecp2-KO, non-injected control, biol rep 1

description:
Library name: 23248XR-01-01
Raw_counts.txt
Normalized_counts.txt