title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_DMSO_D4_H3K27ac

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

description: Library name: Sample 30

data_processing:
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER (v2) with following configuration: For ChIP-seq of HIRA and SPT6, a window size of 50 bp, gap size of 50 bp, and a false discovery rate of 1E-10 were used. For S5P-Pol II, S2P-Pol II, and CDK9, a window size of 50 bp, gap size of 50 bp, and a false discovery rate of 1E-3 were used. For H3K27ac, a window size of 200 bp, gap size of 200 bp, and a false discovery rate of 1E-3 were used. The effective genome fraction of 0.8 was applied to all ChIP-Seq data.
Paired-end reads of RNA-seq were aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the reads per kilo base per million (RPKM) on exonic regions as expression measurements for each gene.
Assembly: mm9
Supplementary files format and content: wig files were generated using in-house script and the scores represent RPKM; tab-delimited text files include FPKM values for each gene.

growth_protocol: Mouse 3T3-L1 white preadipocytes were maintained in growth (DMEM +10%BS) medium

extract_protocol:
ChIP-Seq: Cells were cross-linked with 1.5% formaldehyde for 10 min and quenched by 125 mM glycine for 10 min. 10 million fixed cells were resuspended in ice cold buffer containing 5mM PIPES, pH 7.5, 85mM KCl, 1% NP-40 and protease inhibitors, incubated on ice for 15 min, and centrifuged at 500 g for 5 min at 4°C. Nuclei were resuspended with 1mL buffer containing 50mM Tris-HCl, pH8.0, 10mM EDTA, 0.1% SDS and protease inhibitors, and subjected to sonication. Sheared chromatin was clarified by centrifugation at 13,000 g for 10 min at 4°C. The supernatant was transferred to a new tube and further supplemented with 1% Triton-X100, 0.1% sodium deoxycholate and protease inhibitors. 2% of the mixture was set aside as input and 20ng of spike-in chromatin (Active Motif, #53083) was added to the rest. For each ChIP, 4 - 10 µg of target antibodies and 2μg of spike-in antibody (anti-H2Av, Active Motif, #61686) were added and incubated on a rotator at 4°C overnight. ChIP samples were added with 50μL prewashed protein A Dynabeads (ThermoFisher) and incubated for 3h at 4°C. Beads were then collected on a magnetic rack and washed twice with 1mL cold RIPA buffer, twice with 1mL cold RIPA buffer containing 300mM NaCl, twice with 1mL cold LiCl buffer and once with PBS. Beads were then eluted with 100 μL buffer containing 0.1M NaHCO3, 1% SDS, and 20μg Proteinase K at 65°C overnight. Input sample volumes were adjusted to 100μL with the elution buffer. Samples were then purified using QIAquick PCR purification kit (Qiagen) and eluted in 30 μL 10mM Tris-HCl.
ChIP-Seq: Libraries were prepared according to NEB (Illumina kit) instructions. DNA were used to construct libraries using NEBNext® Ultra™ II DNA Library Prep kit with AMPure XP magnetic beads (Beckman Coulter).
RNA-Seq: Total RNA was subjected to mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490).
RNA-Seq: Isolated mRNAs were reverse-transcribed into double stranded cDNA and subjected to sequencing library construction using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB, E7770) according to the manufacturer’s instructions.

treatment_protocol: For the adipogenesis assay, cells were plated in growth medium (DMEM plus 10% BS) 4 days before the induction and were induced with 10 μg/mL insulin, 0.5 mM IBMX and 1 μM DEX in FBS medium (DMEM plus 10% FBS) for 2 days. After 2 days of induction, the culture medium was changed to DMEM supplemented with FBS and insulin only.

value: Differentiating preadipocytes

value: wild type

value: adipogenic differentiation

tag: time

value: day 4

tag: chip antibody

value: Anti-H3K27ac (ab4729, Abcam)


title: Male KO Liver, Rep 4

status: Public on Jun 01 2026

type: SRA

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

country: USA

institute: Medical University of South Carolina

description: Library name: Sample 21

library_source: transcriptomic

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

molecule: polyA RNA

organism: Mus musculus

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.

tag: tissue

value: Liver

tag: cell line

value: 16-week old

tag: cell type

value: Bulk Tissue

tag: genotype


title: RNA24

city: Houston

first: Stephen

last: Wong

address: 6565 Fannin St

institute: Houston Methodist

description: Library name: DSP-1001660022159-B-F12

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

molecule: total RNA

organism: Homo sapiens

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: 3T3-L1_hHIRA-dTAG-HA_HiraKO_DMSO_D4_H3K4me1

description: Library name: Sample 29

library_source: genomic

molecule: genomic DNA

tag: treatment

value: Anti-H3K4me1 (13-0040, EpiCypher)


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_dTAG13_D7_input

description: Library name: Sample 28

value: Adipocyte

value: HIRA depleted

value: day 7


title: Male KO Liver, Rep 3

description: Library name: Sample 20


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_DMSO_D7_input

description: Library name: Sample 27


title: RNA23

description: Library name: DSP-1001660022159-B-G01


title: Male KO Liver, Rep 2

description: Library name: Sample 19


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_dTAG13_D4_input

description: Library name: Sample 26


title: RNA22

description: Library name: DSP-1001660022159-B-G02


title: Male KO Liver, Rep 1

description: Library name: Sample 18


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_dTAG13_D0_input

description: Library name: Sample 24

value: Preadipocyte

value: day 0


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_DMSO_D4_input

description: Library name: Sample 25


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_DMSO_D0_input

description: Library name: Sample 23


title: DREADD-CNO

city: Aurora

first: Tessa

last: Allen

state: CO

department: Cell and Developmental Biology

institute: University of Colorado, Anschutz

description: Library name: Sample 2

library_source: transcriptomic single cell

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

tag: strain

value: CNO


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_dTAG13_D7_HA

description: Library name: Sample 22

value: Anti-HA (13-2010, Epicypher)


title: thymus-Mettl3WT-TRB-RACE-rep1

city: Guangzhou

first: Hao

last: bingtao

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

country: China

institute: Southern Medical University

description: Library name: sample12

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: RNA27

description: Library name: DSP-1001660022159-B-F09


title: RNA54

description: Library name: DSP-1001660022159-B-D06

source_name: Chest Wall

value: Chest Wall


title: Male WT Liver, Rep 6

description: Library name: Sample 17

value: Liver


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_DMSO_D7_HA

description: Library name: Sample 21

value: wild type

value: adipogenic differentiation


title: thymus-Mettl3WT-TRB-RACE-rep2

description: Library name: sample13


title: RNA20

description: Library name: DSP-1001660022159-B-G04

value: Bone


title: Male WT Liver, Rep 5

description: Library name: Sample 16

value: 16-week old

value: Bulk Tissue


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_dTag13_D4_HA

description: Library name: Sample 20

value: Differentiating preadipocytes

value: HIRA depleted

value: day 4


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

city: Middlebury College

first: Amanda

last: Crocker

state: Vermont

address: 276 Bicentennial Way

department: Neuroscience

institute: Middlebury College

description:
Library name: 23248XR-01-56
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).

source_name: Cortex

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).

value: Cortex

value: Tau-MeCP2 Over-expression

tag: animal id


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_DMSO_D4_HA

description: Library name: Sample 19


title: Male WT Liver, Rep 4

description: Library name: Sample 15


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_dTag13_D0_HA

description: Library name: Sample 18

value: Preadipocyte

value: day 0


title: RNA18

description: Library name: DSP-1001660022159-B-G06


title: RNA19

description: Library name: DSP-1001660022159-B-G05


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_DMSO_D0_HA

description: Library name: Sample 17

value: Anti-HA (13-2010, Epicypher)


title: Male WT Liver, Rep 3

description: Library name: Sample 14


title: U2OS AR Dmon NT puro, 10 nM DHT 16h and 12.5 µM AI-14-91 16h, RNA-seq

city: Istanbul

first: Emirhan

last: Tekoglu

address: Rumelifeneri Yolu

country: Turkey

institute: Koc University

description:
Library name: RUNX024
CBFB_inh_counts.txt

data_processing:
Raw sequencing reads were aligned to the reference genome (GENCODE Release 47, GRCh38.p14) using the Minimap2 aligner (version 2.28). Read counting was performed with the Rsubread (version 2.22.1) package in R (version 4.5.0).
Assembly: hg38
Supplementary files format and content: txt: tab separated raw count tables

extract_protocol:
RNA was extracted with the RNeasy Plus Mini kit (Qiagen)
3′ mRNA (Oligo-dT) with unique molecular identifiers (UMIs) library prep and sequencing was performed using the ExpressoSeq rapid 3' RNA-Seq service (XPseq Analytics GmbH)

tag: genetic modification

value: stable expression of AR Dmon + non-targeting sgRNA


title: RNA17

description: Library name: DSP-1001660022159-B-G07


title: U2OS AR Dmon NT puro, DHT, RNA-seq, rep2

description:
Library name: RUNX023
CBFB_inh_counts.txt

value: 10nM DHT 16h


title: U2OS AR Dmon NT puro, DMSO, RNA-seq, rep2

description:
Library name: RUNX022
CBFB_inh_counts.txt

value: DMSO


title: Male WT Liver, Rep 1

description: Library name: Sample 12

value: Liver


title: U2OS AR WT NT puro, 10 nM DHT 16h, RNA-seq, rep2

description:
Library name: RUNX020
CBFB_inh_counts.txt

value: stable expression of AR WT + non-targeting sgRNA


title: RNA16

description: Library name: DSP-1001660022159-B-G08


title: U2OS AR WT NT puro, 10 nM DHT 16h and 12.5 µM AI-14-91 16h, RNA-seq

description:
Library name: RUNX021
CBFB_inh_counts.txt


title: U2OS AR WT NT puro, DMSO, RNA-seq, rep2

description:
Library name: RUNX019
CBFB_inh_counts.txt


title: RNA15

description: Library name: DSP-1001660022159-B-G09


title: Female KO Liver, Rep 6

description: Library name: Sample 11


title: U2OS AR Dmon NT puro siRUNX3, 10 nM DHT 16h, RNA-seq

description:
Library name: RUNX018
siRUNX3_counts.txt

value: stable expression of AR Dmon + non-targeting sgRNA + transient transfection of RUNX3 siRNA


title: RNA14

description: Library name: DSP-1001660022159-B-G10

value: Bone


title: U2OS AR Dmon NT puro siCTRL, 10 nM DHT 16h, RNA-seq

description:
Library name: RUNX017
siRUNX3_counts.txt

value: stable expression of AR Dmon + non-targeting sgRNA + transient transfection of non-targeting siRNA


title: U2OS AR WT NT puro siRUNX3,10 nM DHT 16h, RNA-seq

description:
Library name: RUNX015
siRUNX3_counts.txt

value: stable expression of AR WT + non-targeting sgRNA + transient transfection of RUNX3 siRNA


title: RNA13

description: Library name: DSP-1001660022159-B-G11


title: U2OS AR Dmon NT puro siCTRL, DMSO, RNA-seq

description:
Library name: RUNX016
siRUNX3_counts.txt


title: Female KO Liver, Rep 5

description: Library name: Sample 10

value: 16-week old

value: Bulk Tissue


title: Female KO Liver, Rep 4

description: Library name: Sample 9


title: U2OS AR WT NT puro siCTRL,10 nM DHT 16h, RNA-seq

description:
Library name: RUNX014
siRUNX3_counts.txt

value: stable expression of AR WT + non-targeting sgRNA + transient transfection of non-targeting siRNA


title: RNA12

description: Library name: DSP-1001660022159-B-G12


title: U2OS AR WT NT puro siCTRL, DMSO, RNA-seq

description:
Library name: RUNX013
siRUNX3_counts.txt


title: Female KO Liver, Rep 3

description: Library name: Sample 8


title: U2OS AR Dmon RUNX2 KO, 10 nM DHT 16h, RNA-seq

description:
Library name: RUNX012
RUNX1_2_KO_counts.txt

value: stable expression of AR Dmon + RUNX2 KO sgRNA


title: Female KO Liver, Rep 2

description: Library name: Sample 7


title: U2OS AR Dmon RUNX2 KO, DMSO, RNA-seq

description:
Library name: RUNX011
RUNX1_2_KO_counts.txt


title: RNA10

description: Library name: DSP-1001660022159-B-H02


title: RNA11

description: Library name: DSP-1001660022159-B-H01


title: U2OS AR Dmon RUNX1 KO, DMSO, RNA-seq

description:
Library name: RUNX009
RUNX1_2_KO_counts.txt

value: stable expression of AR Dmon + RUNX1 KO sgRNA


title: Female KO Liver, Rep 1

description: Library name: Sample 6


title: RNA9

description: Library name: DSP-1001660022159-B-H03


title: U2OS AR Dmon NT puro, DMSO, RNA-seq

description:
Library name: RUNX007
RUNX1_2_KO_counts.txt


title: U2OS AR WT RUNX2 KO, 10 nM DHT 16h, RNA-seq

description:
Library name: RUNX006
RUNX1_2_KO_counts.txt

value: stable expression of AR WT + RUNX2 KO sgRNA


title: RNA8

description: Library name: DSP-1001660022159-B-H04


title: Female WT Liver, Rep 5

description: Library name: Sample 5


title: U2OS AR WT RUNX2 KO, DMSO, RNA-seq

description:
Library name: RUNX005
RUNX1_2_KO_counts.txt


title: Female WT Liver, Rep 4

description: Library name: Sample 4


title: U2OS AR WT RUNX1 KO, 10 nM DHT 16h, RNA-seq

description:
Library name: RUNX004
RUNX1_2_KO_counts.txt

value: stable expression of AR WT + RUNX1 KO sgRNA


title: U2OS AR WT RUNX1 KO, DMSO, RNA-seq

description:
Library name: RUNX003
RUNX1_2_KO_counts.txt


title: ChoroidP_E17_biol rep 4

first: Hong

last: Liu

address: 9000 Rockville Pike

description:
Library name: sample 7
Column name in tpm_all_Samples.csv: ChoroidP_E17_5_tpm

data_processing:
Libraries were sequenced on an Illumina NovaSeq X apparatus at the NHLBI Genomics Facility at NIH. Reads of library were collected, converted by bcl2fastq (version 2) into fastq files and further analyzed for gene expression using Kallisto v0.51.1  (https://github.com/pachterlab/kallisto/releases)  given as TPM (transcripts per million read counts) according to the quantification of the reads on GRCm38/mm10 index.
Assembly: mm10
Supplementary files format and content: csv file include tpm values for each sample

source_name: choroid plexus

extract_protocol:
RNA from different samples was purified using an RNeasy plus mini or macro kit (Qiagen #74134 or #74034)
150 - 300 ng RNA per sample were used to construct libraries with a SMARTer total RNA sample prep kit (Takara #634875) following manufacture's protocol.

treatment_protocol: Meninges and choroid plexus tissues were micro-dissected from embryos and neonatal mice at the ages indicated, then immediately frozen on dry-ice in readiness for RNA extraction.

value: choroid plexus

value: embryonic day 17.5

value: wt


title: RNA6

description: Library name: DSP-1001660022159-B-H06


title: Female WT Liver, Rep 3

description: Library name: Sample 3


title: Female WT Liver, Rep 2

description: Library name: Sample 2


title: 4DR7F605OV_S60

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: 4DR7F605OV_S60_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 rat S1500+ manifest
Supplementary files format and content: tab-delimited text file includes attenuation-adjusted raw probe counts for each sample

organism: Rattus norvegicus

source_name: Ovary

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 Rat 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: Ovary

value: Sprague-Dawley

tag: Sex

value: female

tag: age

value: 9 weeks

tag: concentration (ppm)

tag: sample status

value: Used in Analysis

tag: qc issue


title: RNA5

description: Library name: DSP-1001660022159-B-H07

value: Bone


title: 4DR7F605LU_S134

description: Library name: 4DR7F605LU_S134_R1_001

source_name: Lung

value: Lung


title: Female WT Liver, Rep 1

description: Library name: Sample 1

value: Liver

value: 16-week old


title: 4DR7F605LI_S134

description: Library name: 4DR7F605LI_S134_R1_001

source_name: Liver Left Lobe

value: Liver Left Lobe


title: RNA4

description: Library name: DSP-1001660022159-B-H08


title: 4DR7F605KI_S124

description: Library name: 4DR7F605KI_S124_R1_001

source_name: Kidney

value: Kidney


title: Male KO Liver, Rep 3

description: Library name: Sample 12

data_processing:
Novogene performed data analysis in the Novogene platform
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Alignments were performed with HISAT2 v2.0.5 by Novogene
Differentially expressed genes were determined with the R package DESeq2
Assembly: mm39
Supplementary files format and content: spreadsheet containing gene counts

growth_protocol: Mice were maintained in co-housed cages on normal chow in controlled temperature and humidity until 16 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
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Bulk Tissue


title: 4DR7F605HE_S125

description: Library name: 4DR7F605HE_S125_R1_001

source_name: Heart

value: Heart


title: RNA3

description: Library name: DSP-1001660022159-B-H09


title: 4DR7F604OV_S77

description: Library name: 4DR7F604OV_S77_R1_001


title: Male KO Liver, Rep 2

description: Library name: Sample 11


title: ChoroidP_E14_biol rep 2

description:
Library name: sample 2
Column name in tpm_all_Samples.csv: ChoroidP_E14_2_tpm

value: embryonic day 14.5


title: 4DR7F604LU_S151

description: Library name: 4DR7F604LU_S151_R1_001


title: RNA2

description: Library name: DSP-1001660022159-B-H10


title: 4DR7F604LI_S151

description: Library name: 4DR7F604LI_S151_R1_001


title: Female WT Liver, Rep 3

description: Library name: Sample 10


title: RNA1

description: Library name: DSP-1001660022159-B-H11


title: 4DR7F604HE_S142

description: Library name: 4DR7F604HE_S142_R1_001


title: 4DR7F604KI_S141

description: Library name: 4DR7F604KI_S141_R1_001


title: Male WT Liver, Rep 3

description: Library name: Sample 9


title: 4DR7F603OV_S57

description: Library name: 4DR7F603OV_S57_R1_001


title: 4DR7F603LU_S131

description: Library name: 4DR7F603LU_S131_R1_001


title: 4DR7F603LI_S131

description: Library name: 4DR7F603LI_S131_R1_001


title: protein191

description:
Library name: DSP-1001660022162-A-A02
DSP-1001660022162-A-A02.dcc
DSP-1001660022162-A-A02.stats.txt

library_source: other

molecule: protein

source_name: Brain

value: Brain


title: 4DR7F603KI_S121

description: Library name: 4DR7F603KI_S121_R1_001


title: Male KO Liver, Rep 1

description: Library name: Sample 7


title: 4DR7F603HE_S122

description: Library name: 4DR7F603HE_S122_R1_001


title: protein190

description:
Library name: DSP-1001660022162-A-A03
DSP-1001660022162-A-A03.dcc
DSP-1001660022162-A-A03.stats.txt


title: 4DR7F602OV_S55

description: Library name: 4DR7F602OV_S55_R1_001


title: Male WT Liver, Rep 1

description: Library name: Sample 6


title: 4DR7F602LU_S129

description: Library name: 4DR7F602LU_S129_R1_001


title: protein189

description:
Library name: DSP-1001660022162-A-A04
DSP-1001660022162-A-A04.dcc
DSP-1001660022162-A-A04.stats.txt


title: 4DR7F602LI_S129

description: Library name: 4DR7F602LI_S129_R1_001


title: Female KO Liver, Rep 3

description: Library name: Sample 5


title: 4DR7F602KI_S119

description: Library name: 4DR7F602KI_S119_R1_001


title: protein188

description:
Library name: DSP-1001660022162-A-A05
DSP-1001660022162-A-A05.dcc
DSP-1001660022162-A-A05.stats.txt


title: 4DR7F602HE_S120

description: Library name: 4DR7F602HE_S120_R1_001


title: Female KO Liver, Rep 2

description: Library name: Sample 4


title: 4DR7F601OV_S59

description: Library name: 4DR7F601OV_S59_R1_001


title: protein187

description:
Library name: DSP-1001660022162-A-A06
DSP-1001660022162-A-A06.dcc
DSP-1001660022162-A-A06.stats.txt


title: 4DR7F601LU_S133

description: Library name: 4DR7F601LU_S133_R1_001


title: Female KO Liver, Rep 1

description: Library name: Sample 3


title: 4DR7F601LI_S133

description: Library name: 4DR7F601LI_S133_R1_001


title: RNA21

description: Library name: DSP-1001660022159-B-G03


title: protein186

description:
Library name: DSP-1001660022162-A-A07
DSP-1001660022162-A-A07.dcc
DSP-1001660022162-A-A07.stats.txt


title: 4DR7F601KI_S123

description: Library name: 4DR7F601KI_S123_R1_001


title: protein192

description:
Library name: DSP-1001660022162-A-A01
DSP-1001660022162-A-A01.dcc
DSP-1001660022162-A-A01.stats.txt


title: Female WT Liver, Rep 2

description: Library name: Sample 2


title: protein185

description:
Library name: DSP-1001660022162-A-A08
DSP-1001660022162-A-A08.dcc
DSP-1001660022162-A-A08.stats.txt


title: Male WT Liver, Rep 2

description: Library name: Sample 8


title: 4DR7F601HE_S124

description: Library name: 4DR7F601HE_S124_R1_001


title: 4DR6F505OV_S71

description: Library name: 4DR6F505OV_S71_R1_001


title: Female WT Liver, Rep 1

description: Library name: Sample 1


title: 4DR6F505LU_S145

description: Library name: 4DR6F505LU_S145_R1_001


title: protein184

description:
Library name: DSP-1001660022162-A-A09
DSP-1001660022162-A-A09.dcc
DSP-1001660022162-A-A09.stats.txt


title: 4DR6F505LI_S145

description: Library name: 4DR6F505LI_S145_R1_001


title: scTCR-seq of WT mouse 14 days post infected

city: Shanghai

first: Xiaoqian

last: Hu

address: No. 130, Dongan Road, Xuhui District, Shanghai

institute: Fudan University

description: Library name: D14_Tdg_260115N_S128_L005

data_processing:
Raw sequencing reads were processed using Cell Ranger V(D)J pipeline (10x Genomics). Sequencing reads were demultiplexed, aligned, and assembled to identify TCR gamma and delta chains. Cell barcodes and clonotype annotations were generated for downstream repertoire analysis.
Assembly: Mus musculus GRCm38
Supplementary files format and content: Processed files include TCR clonotype annotations, barcode-level TCR assignments, contig annotations, and clonotype frequency tables.
Library strategy: TCR-Seq

source_name: lung

extract_protocol:
For the inspection and counting of single-cell suspension, the survival rate of cells is generally required to be above 85%, and the qualified cells are prepared by washing and re-suspension into a suitable cell concentration of 700~1200 cells/µl
Single-cell gamma delta TCR libraries were generated using the 10x Genomics Chromium Single Cell V(D)J platform according to the manufacturer’s protocol. Single cells were encapsulated into Gel Beads in Emulsion (GEMs), followed by reverse transcription and barcode incorporation. Amplified cDNA was enriched for TCR gamma and delta receptor transcripts and used for library construction. Libraries were sequenced using paired-end sequencing on an Illumina platform.

value: lung


title: 4DR6F505KI_S135

description: Library name: 4DR6F505KI_S135_R1_001


title: protein183

description:
Library name: DSP-1001660022162-A-A10
DSP-1001660022162-A-A10.dcc
DSP-1001660022162-A-A10.stats.txt


title: scTCR-seq of WT mouse 7 days post infected

description: Library name: D7_Tdg_260115N_S126_L005


title: 4DR6F505HE_S136

description: Library name: 4DR6F505HE_S136_R1_001


title: Male WT Liver, Rep 2

description: Library name: Sample 13


title: 4DR6F504OV_S76

description: Library name: 4DR6F504OV_S76_R1_001


title: protein182

description:
Library name: DSP-1001660022162-A-A11
DSP-1001660022162-A-A11.dcc
DSP-1001660022162-A-A11.stats.txt


title: 4DR6F504LU_S150

description: Library name: 4DR6F504LU_S150_R1_001

value: Not Used in Analysis

value: Outlier based on PCA/correlation


title: scTCR-seq of WT mouse

description: Library name: WT_Tdg_260115N_S127_L005


title: 4DR6F504LI_S150

description: Library name: 4DR6F504LI_S150_R1_001

value: Sprague-Dawley


title: protein181

description:
Library name: DSP-1001660022162-A-A12
DSP-1001660022162-A-A12.dcc
DSP-1001660022162-A-A12.stats.txt


title: 4DR6F504KI_S140

description: Library name: 4DR6F504KI_S140_R1_001

value: female


title: 6M-12W-Pit-CUMS4

first: Tiannuo

last: Yang

address: Meilong Road 130

institute: East China University of Science and Technology

description: Library name: Pit-H4

data_processing:
Samples are sequenced on the platform to getimage files, which are transformed by thesoftware of the sequencing platform, and theriginal data in FASTo format (Raw Data) isgenerated,Sequencing data contains a numberofconnectors,low-quality Reads, so we useastp(0,22.0)software to filter the sequencingdata to get high quality sequence (Clean Data)for further analysis .
Assembly: CSV file including Reads count for each sample
Supplementary files format and content: CSV file including FPKM for each sample

source_name: Pituitary

extract_protocol:
Total RNA was extracted by the chloroformmethod.
RNA-seg library was cunstructed by usingNEBNext Ultra ll RNA Library Prep Kit forlllumina.

value: Pituitary


title: 4DR6F504HE_S141

description: Library name: 4DR6F504HE_S141_R1_001

value: 9 weeks

value: Used in Analysis


title: protein180

description:
Library name: DSP-1001660022162-A-B01
DSP-1001660022162-A-B01.dcc
DSP-1001660022162-A-B01.stats.txt


title: 6M-12W-Pit-CUMS3

description: Library name: Pit-H3


title: 4DR6F503OV_S50

description: Library name: 4DR6F503OV_S50_R1_001

value: Ovary


title: 4DR6F503LU_S124

description: Library name: 4DR6F503LU_S124_R1_001

value: Lung


title: protein179

description:
Library name: DSP-1001660022162-A-B02
DSP-1001660022162-A-B02.dcc
DSP-1001660022162-A-B02.stats.txt


title: 4DR6F503LI_S124

description: Library name: 4DR6F503LI_S124_R1_001


title: 6M-12W-Pit-CUMS2

description: Library name: Pit-H2


title: 4DR6F503KI_S114

description: Library name: 4DR6F503KI_S114_R1_001


title: protein178

description:
Library name: DSP-1001660022162-A-B03
DSP-1001660022162-A-B03.dcc
DSP-1001660022162-A-B03.stats.txt


title: 6M-12W-Pit-CUMS1

description: Library name: Pit-H1


title: 4DR6F502OV_S82

description: Library name: 4DR6F502OV_S82_R1_001


title: 4DR6F503HE_S115

description: Library name: 4DR6F503HE_S115_R1_001


title: protein177

description:
Library name: DSP-1001660022162-A-B04
DSP-1001660022162-A-B04.dcc
DSP-1001660022162-A-B04.stats.txt


title: 4DR6F502LU_S156

description: Library name: 4DR6F502LU_S156_R1_001


title: 6M-12W-Pit-Ctrl4

description: Library name: Pit-G4


title: U2OS AR Dmon RUNX1 KO,10 nM DHT 16h, RNA-seq

description:
Library name: RUNX010
RUNX1_2_KO_counts.txt

value: stable expression of AR Dmon + RUNX1 KO sgRNA

value: 10nM DHT 16h


title: protein176

description:
Library name: DSP-1001660022162-A-B05
DSP-1001660022162-A-B05.dcc
DSP-1001660022162-A-B05.stats.txt


title: 4DR6F502LI_S156

description: Library name: 4DR6F502LI_S156_R1_001

value: Liver Left Lobe


title: U2OS AR Dmon NT puro, 10 nM DHT 16h, RNA-seq

description:
Library name: RUNX008
RUNX1_2_KO_counts.txt

value: stable expression of AR Dmon + non-targeting sgRNA


title: 4DR6F502KI_S146

description: Library name: 4DR6F502KI_S146_R1_001

value: Kidney


title: 6M-12W-Pit-Ctrl3

description: Library name: Pit-G3


title: 4DR6F502HE_S147

description: Library name: 4DR6F502HE_S147_R1_001

value: Heart


title: 6M-12W-Pit-Ctrl2

description: Library name: Pit-G2


title: 4DR6F501OV_S80

description: Library name: 4DR6F501OV_S80_R1_001


title: 4DR6F501LU_S154

description: Library name: 4DR6F501LU_S154_R1_001


title: protein174

description:
Library name: DSP-1001660022162-A-B07
DSP-1001660022162-A-B07.dcc
DSP-1001660022162-A-B07.stats.txt

value: Brain


title: 4DR6F501LI_S154

description: Library name: 4DR6F501LI_S154_R1_001


title: 6M-12W-Pit-Ctrl1

description: Library name: Pit-G1


title: 4DR6F501KI_S144

description: Library name: 4DR6F501KI_S144_R1_001


title: protein173

description:
Library name: DSP-1001660022162-A-B08
DSP-1001660022162-A-B08.dcc
DSP-1001660022162-A-B08.stats.txt


title: 4DR6F501HE_S145

description: Library name: 4DR6F501HE_S145_R1_001


title: RNA7

description: Library name: DSP-1001660022159-B-H05

value: Bone


title: 2M-8W-Pit-CUMS4

description: Library name: Pit-F4


title: 4DR5F405OV_S62

description: Library name: 4DR5F405OV_S62_R1_001


title: protein172

description:
Library name: DSP-1001660022162-A-B09
DSP-1001660022162-A-B09.dcc
DSP-1001660022162-A-B09.stats.txt


title: U2OS AR WT NT puro, DMSO, RNA-seq, rep1

description:
Library name: RUNX001
RUNX1_2_KO_counts.txt

value: stable expression of AR WT + non-targeting sgRNA

value: DMSO


title: 4DR5F405LU_S136

description: Library name: 4DR5F405LU_S136_R1_001

value: Sprague-Dawley


title: 2M-8W-Pit-CUMS3

description: Library name: Pit-F3


title: U2OS AR WT NT puro, 10 nM DHT 16h, RNA-seq, rep1

description:
Library name: RUNX002
RUNX1_2_KO_counts.txt


title: 4DR5F405LI_S136

description: Library name: 4DR5F405LI_S136_R1_001

value: female


title: protein171

description:
Library name: DSP-1001660022162-A-B10
DSP-1001660022162-A-B10.dcc
DSP-1001660022162-A-B10.stats.txt


title: 4DR5F405KI_S126

description: Library name: 4DR5F405KI_S126_R1_001


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

description:
Library name: 23248XR-01-47
Raw_counts.txt
Normalized_counts.txt

value: Cortex

value: MeCP2:-/Y rtt271a

value: injected rtt271 3e11


title: 2M-8W-Pit-CUMS2

description: Library name: Pit-F2

value: Pituitary


title: protein175

description:
Library name: DSP-1001660022162-A-B06
DSP-1001660022162-A-B06.dcc
DSP-1001660022162-A-B06.stats.txt


title: 4DR5F405HE_S127

description: Library name: 4DR5F405HE_S127_R1_001

value: 9 weeks

value: Used in Analysis


title: 4DR5F404OV_S52

description: Library name: 4DR5F404OV_S52_R1_001

value: Ovary


title: 2M-8W-Pit-CUMS1

description: Library name: Pit-F1


title: 4DR5F404LU_S126

description: Library name: 4DR5F404LU_S126_R1_001

value: Lung


title: protein170

description: Library name: DSP-1001660022162-A-B11


title: protein169

description:
Library name: DSP-1001660022162-A-B12
DSP-1001660022162-A-B12.dcc
DSP-1001660022162-A-B12.stats.txt


title: 4DR5F404LI_S126

description: Library name: 4DR5F404LI_S126_R1_001

value: Liver Left Lobe


title: 2M-8W-Pit-Ctrl4

description: Library name: Pit-E4


title: protein168

description:
Library name: DSP-1001660022162-A-C01
DSP-1001660022162-A-C01.dcc
DSP-1001660022162-A-C01.stats.txt


title: 4DR5F404KI_S116

description: Library name: 4DR5F404KI_S116_R1_001

value: Kidney


title: 4DR5F404HE_S117

description: Library name: 4DR5F404HE_S117_R1_001

value: Heart


title: 2M-8W-Pit-Ctrl3

description: Library name: Pit-E3


title: protein167

description:
Library name: DSP-1001660022162-A-C02
DSP-1001660022162-A-C02.dcc
DSP-1001660022162-A-C02.stats.txt

value: Brain


title: 2M-8W-Pit-Ctrl2

description: Library name: Pit-E2


title: 4DR5F403LU_S146

description: Library name: 4DR5F403LU_S146_R1_001


title: 4DR5F403OV_S72

description: Library name: 4DR5F403OV_S72_R1_001


title: 4DR5F403LI_S146

description: Library name: 4DR5F403LI_S146_R1_001


title: protein166

description:
Library name: DSP-1001660022162-A-C03
DSP-1001660022162-A-C03.dcc
DSP-1001660022162-A-C03.stats.txt


title: 4DR5F403HE_S137

description: Library name: 4DR5F403HE_S137_R1_001


title: 4DR5F403KI_S136

description: Library name: 4DR5F403KI_S136_R1_001


title: 2M-8W-Pit-Ctrl1

description: Library name: Pit-E1


title: protein165

description:
Library name: DSP-1001660022162-A-C04
DSP-1001660022162-A-C04.dcc
DSP-1001660022162-A-C04.stats.txt


title: 4DR5F402OV_S43

description: Library name: 4DR5F402OV_S43_R1_001


title: 2M-12W-Pit-CUMS4

description: Library name: Pit-T4


title: 4DR5F402LU_S117

description: Library name: 4DR5F402LU_S117_R1_001

value: Not Used in Analysis

value: SEQ DEPTH < 300000


title: 4DR5F402LI_S117

description: Library name: 4DR5F402LI_S117_R1_001


title: protein164

description:
Library name: DSP-1001660022162-A-C05
DSP-1001660022162-A-C05.dcc
DSP-1001660022162-A-C05.stats.txt


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

description:
Library name: 23248XR-01-40
Raw_counts.txt
Normalized_counts.txt

value: injected rtt271 1e11


title: 2M-12W-Pit-CUMS3

description: Library name: Pit-T3


title: 4DR5F402KI_S147

description: Library name: 4DR5F402KI_S147_R1_001

value: Sprague-Dawley


title: protein163

description:
Library name: DSP-1001660022162-A-C06
DSP-1001660022162-A-C06.dcc
DSP-1001660022162-A-C06.stats.txt


title: 4DR5F402HE_S148

description: Library name: 4DR5F402HE_S148_R1_001

value: female


title: 2M-12W-Pit-CUMS2

description: Library name: Pit-T2


title: 4DR5F401OV_S81

description: Library name: 4DR5F401OV_S81_R1_001


title: protein162

description:
Library name: DSP-1001660022162-A-C07
DSP-1001660022162-A-C07.dcc
DSP-1001660022162-A-C07.stats.txt


title: 4DR5F401LU_S155

description: Library name: 4DR5F401LU_S155_R1_001


title: 2M-12W-Pit-CUMS1

description: Library name: Pit-T1


title: protein161

description:
Library name: DSP-1001660022162-A-C08
DSP-1001660022162-A-C08.dcc
DSP-1001660022162-A-C08.stats.txt


title: 4DR5F401LI_S155

description: Library name: 4DR5F401LI_S155_R1_001


title: 2M-12W-Pit-Ctrl4

description: Library name: Pit-S4


title: 4DR5F401KI_S145

description: Library name: 4DR5F401KI_S145_R1_001


title: 4DR5F401HE_S146

description: Library name: 4DR5F401HE_S146_R1_001


title: protein160

description:
Library name: DSP-1001660022162-A-C09
DSP-1001660022162-A-C09.dcc
DSP-1001660022162-A-C09.stats.txt


title: 4DR4F305OV_S56

description: Library name: 4DR4F305OV_S56_R1_001


title: 2M-12W-Pit-Ctrl3

description: Library name: Pit-S3


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

description:
Library name: 23248XR-01-32
Raw_counts.txt
Normalized_counts.txt

value: Cortex


title: protein159

description:
Library name: DSP-1001660022162-A-C10
DSP-1001660022162-A-C10.dcc
DSP-1001660022162-A-C10.stats.txt


title: 4DR4F305LU_S130

description: Library name: 4DR4F305LU_S130_R1_001


title: 2M-12W-Pit-Ctrl2

description: Library name: Pit-S2


title: 4DR4F305LI_S130

description: Library name: 4DR4F305LI_S130_R1_001


title: 4DR4F305KI_S120

description: Library name: 4DR4F305KI_S120_R1_001


title: protein158

description:
Library name: DSP-1001660022162-A-C11
DSP-1001660022162-A-C11.dcc
DSP-1001660022162-A-C11.stats.txt


title: 4DR4F305HE_S121

description: Library name: 4DR4F305HE_S121_R1_001


title: 4DR4F304OV_S51

description: Library name: 4DR4F304OV_S51_R1_001


title: 2M-12W-Pit-Ctrl1

description: Library name: Pit-S1


title: 6M-8W-Pit-CUMS4

description: Library name: Pit-L4


title: 4DR4F304LI_S125

description: Library name: 4DR4F304LI_S125_R1_001


title: 4DR4F304LU_S125

description: Library name: 4DR4F304LU_S125_R1_001


title: protein156

description:
Library name: DSP-1001660022162-A-D01
DSP-1001660022162-A-D01.dcc
DSP-1001660022162-A-D01.stats.txt


title: 6M-8W-Pit-CUMS3

description: Library name: Pit-L3


title: 4DR4F303OV_S78

description: Library name: 4DR4F303OV_S78_R1_001


title: 4DR4F304KI_S115

description: Library name: 4DR4F304KI_S115_R1_001


title: 4DR4F304HE_S116

description: Library name: 4DR4F304HE_S116_R1_001


title: 4DR4F303LU_S152

description: Library name: 4DR4F303LU_S152_R1_001


title: protein155

description:
Library name: DSP-1001660022162-A-D02
DSP-1001660022162-A-D02.dcc
DSP-1001660022162-A-D02.stats.txt


title: 4DR4F303LI_S152

description: Library name: 4DR4F303LI_S152_R1_001


title: protein154

description:
Library name: DSP-1001660022162-A-D03
DSP-1001660022162-A-D03.dcc
DSP-1001660022162-A-D03.stats.txt


title: 4DR4F303KI_S142

description: Library name: 4DR4F303KI_S142_R1_001


title: 6M-8W-Pit-CUMS1

description: Library name: Pit-L1


title: 6M-8W-Pit-Ctrl4

description: Library name: Pit-K4


title: protein153

description:
Library name: DSP-1001660022162-A-D04
DSP-1001660022162-A-D04.dcc
DSP-1001660022162-A-D04.stats.txt


title: 4DR4F302OV_S49

description: Library name: 4DR4F302OV_S49_R1_001


title: protein152

description:
Library name: DSP-1001660022162-A-D05
DSP-1001660022162-A-D05.dcc
DSP-1001660022162-A-D05.stats.txt


title: 4DR4F302LU_S123

description: Library name: 4DR4F302LU_S123_R1_001


title: 6M-8W-Pit-Ctrl3

description: Library name: Pit-K3


title: 4DR4F302LI_S123

description: Library name: 4DR4F302LI_S123_R1_001


title: 6M-8W-Pit-Ctrl2

description: Library name: Pit-K2


title: protein150

description:
Library name: DSP-1001660022162-A-D07
DSP-1001660022162-A-D07.dcc
DSP-1001660022162-A-D07.stats.txt


title: 4DR4F302HE_S114

description: Library name: 4DR4F302HE_S114_R1_001


title: 4DR4F301OV_S70

description: Library name: 4DR4F301OV_S70_R1_001


title: 6M-8W-Pit-Ctrl1

description: Library name: Pit-K1


title: protein149

description:
Library name: DSP-1001660022162-A-D08
DSP-1001660022162-A-D08.dcc
DSP-1001660022162-A-D08.stats.txt


title: 4DR4F301LI_S144

description: Library name: 4DR4F301LI_S144_R1_001


title: 4DR4F301KI_S134

description: Library name: 4DR4F301KI_S134_R1_001


title: protein148

description:
Library name: DSP-1001660022162-A-D09
DSP-1001660022162-A-D09.dcc
DSP-1001660022162-A-D09.stats.txt


title: 4DR4F301HE_S135

description: Library name: 4DR4F301HE_S135_R1_001


title: 6M-12W-Ova-CUMS3

description: Library name: Ova-H3


title: 4DR3F205OV_S65

description: Library name: 4DR3F205OV_S65_R1_001


title: protein147

description:
Library name: DSP-1001660022162-A-D10
DSP-1001660022162-A-D10.dcc
DSP-1001660022162-A-D10.stats.txt


title: 6M-12W-Ova-CUMS2

description: Library name: Ova-H2


title: 4DR3F205LU_S139

description: Library name: 4DR3F205LU_S139_R1_001


title: 4DR3F205LI_S139

description: Library name: 4DR3F205LI_S139_R1_001


title: protein146

description:
Library name: DSP-1001660022162-A-D11
DSP-1001660022162-A-D11.dcc
DSP-1001660022162-A-D11.stats.txt


title: 4DR3F205KI_S129

description: Library name: 4DR3F205KI_S129_R1_001


title: 4DR3F205HE_S130

description: Library name: 4DR3F205HE_S130_R1_001


title: protein145

description:
Library name: DSP-1001660022162-A-D12
DSP-1001660022162-A-D12.dcc
DSP-1001660022162-A-D12.stats.txt


title: 4DR3F204OV_S46

description: Library name: 4DR3F204OV_S46_R1_001


title: 6M-12W-Ova-Ctrl3

description: Library name: Ova-G3


title: 4DR3F204LU_S120

description: Library name: 4DR3F204LU_S120_R1_001


title: 4DR3F204LI_S120

description: Library name: 4DR3F204LI_S120_R1_001


title: 4DR3F204KI_S150

description: Library name: 4DR3F204KI_S150_R1_001


title: protein143

description:
Library name: DSP-1001660022162-A-E02
DSP-1001660022162-A-E02.dcc
DSP-1001660022162-A-E02.stats.txt


title: 6M-12W-Ova-Ctrl1

description: Library name: Ova-G1


title: 4DR3F203OV_S69

description: Library name: 4DR3F203OV_S69_R1_001


title: protein142

description:
Library name: DSP-1001660022162-A-E03
DSP-1001660022162-A-E03.dcc
DSP-1001660022162-A-E03.stats.txt


title: 4DR3F203LU_S143

description: Library name: 4DR3F203LU_S143_R1_001


title: 2M-8W-Ova-CUMS4

description: Library name: Ova-F4


title: 4DR3F203LI_S143

description: Library name: 4DR3F203LI_S143_R1_001


title: 4DR3F203KI_S133

description: Library name: 4DR3F203KI_S133_R1_001


title: 2M-8W-Ova-CUMS3

description: Library name: Ova-F3


title: 4DR3F202LU_S132

description: Library name: 4DR3F202LU_S132_R1_001


title: protein139

description:
Library name: DSP-1001660022162-A-E06
DSP-1001660022162-A-E06.dcc
DSP-1001660022162-A-E06.stats.txt


title: NPC patient 37

type: RNA

city: Hong Kong

first: Huaping

last: Li

address: 21 Sassoon Rd, Pok Fu Lam

country: Hong Kong

institute: The University of Hong Kong

hyb_protocol: Gene expression profiling was performed using the Nanostring PanCancer Immune Profiling Panel and 20 additional custom designed gene probes,

scan_protocol: standard protocol

data_processing:
The Nanostring nCounter expression profiling is optimized for FFPE samples, around 800 genes were profiled.
data were normalized based on NanoString housekeeping probes and the geNorm algorithm using RosalindÂ® Software (https://rosalind.onramp.bio/). Fold-changes and p-values were calculated using the fast method as described in the nCounterÂ® Advanced Analysis 2.0 User Manual. P-value adjustment was performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR).

label: oligonucleotide probe

source_name: locoregionally advanced NPC FFPE sample

label_protocol: Purity of End of expansion CAR-iNKT was >90%. No further label/purification step was required

extract_protocol: RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: gender

value: M

value: locoregionally advanced NPC FFPE sample


title: NPC patient 40


title: 2M-8W-Ova-CUMS1

description: Library name: Ova-F1


title: 4DR3F202KI_S122

description: Library name: 4DR3F202KI_S122_R1_001


title: protein138

description:
Library name: DSP-1001660022162-A-E07
DSP-1001660022162-A-E07.dcc
DSP-1001660022162-A-E07.stats.txt


title: 4DR3F202HE_S123

description: Library name: 4DR3F202HE_S123_R1_001


title: 2M-8W-Ova-Ctrl4

description: Library name: Ova-E4


title: protein157

description:
Library name: DSP-1001660022162-A-C12
DSP-1001660022162-A-C12.dcc
DSP-1001660022162-A-C12.stats.txt


title: 6M-8W-Pit-CUMS2

description: Library name: Pit-L2

value: Pituitary


title: 4DR3F201OV_S64

description: Library name: 4DR3F201OV_S64_R1_001

value: 9 weeks


title: 4DR3F202LI_S132

description: Library name: 4DR3F202LI_S132_R1_001

value: Used in Analysis


title: 4DR4F303HE_S143

description: Library name: 4DR4F303HE_S143_R1_001


title: 4DR3F201LU_S138

description: Library name: 4DR3F201LU_S138_R1_001


title: protein137

description:
Library name: DSP-1001660022162-A-E08
DSP-1001660022162-A-E08.dcc
DSP-1001660022162-A-E08.stats.txt


title: 2M-8W-Ova-Ctrl3

description: Library name: Ova-E3

value: Ovary


title: 4DR3F201LI_S138

description: Library name: 4DR3F201LI_S138_R1_001


title: 4DR4F302KI_S113

description: Library name: 4DR4F302KI_S113_R1_001


title: protein151

description:
Library name: DSP-1001660022162-A-D06
DSP-1001660022162-A-D06.dcc
DSP-1001660022162-A-D06.stats.txt


title: protein136

description:
Library name: DSP-1001660022162-A-E09
DSP-1001660022162-A-E09.dcc
DSP-1001660022162-A-E09.stats.txt


title: 4DR3F201KI_S128

description: Library name: 4DR3F201KI_S128_R1_001


title: 2M-8W-Ova-Ctrl2

description: Library name: Ova-E2


title: 4DR3F201HE_S129

description: Library name: 4DR3F201HE_S129_R1_001


title: 4DR4F301LU_S144

description: Library name: 4DR4F301LU_S144_R1_001

value: Lung


title: protein135

description:
Library name: DSP-1001660022162-A-E10
DSP-1001660022162-A-E10.dcc
DSP-1001660022162-A-E10.stats.txt


title: 6M-12W-Ova-CUMS4

description: Library name: Ova-H4


title: 4DR2F105OV_S48

description: Library name: 4DR2F105OV_S48_R1_001


title: 2M-8W-Ova-Ctrl1

description: Library name: Ova-E1


title: 4DR2F105LU_S122

description: Library name: 4DR2F105LU_S122_R1_001


title: protein134

description:
Library name: DSP-1001660022162-A-E11
DSP-1001660022162-A-E11.dcc
DSP-1001660022162-A-E11.stats.txt


title: 4DR2F105LI_S122

description: Library name: 4DR2F105LI_S122_R1_001

value: Liver Left Lobe


title: 4DR2F105HE_S113

description: Library name: 4DR2F105HE_S113_R1_001


title: 2M-12W-Ova-CUMS4

description: Library name: Ova-T4


title: protein133

description:
Library name: DSP-1001660022162-A-E12
DSP-1001660022162-A-E12.dcc
DSP-1001660022162-A-E12.stats.txt


title: 4DR2F104OV_S54

description: Library name: 4DR2F104OV_S54_R1_001


title: 6M-12W-Ova-CUMS1

description: Library name: Ova-H1


title: 4DR2F104LU_S128

description: Library name: 4DR2F104LU_S128_R1_001


title: protein132

description:
Library name: DSP-1001660022162-A-F01
DSP-1001660022162-A-F01.dcc
DSP-1001660022162-A-F01.stats.txt


title: 4DR2F104LI_S128

description: Library name: 4DR2F104LI_S128_R1_001


title: 2M-12W-Ova-CUMS2

description: Library name: Ova-T2


title: 2M-12W-Ova-CUMS3

description: Library name: Ova-T3


title: 4DR2F104KI_S118

description: Library name: 4DR2F104KI_S118_R1_001

value: Kidney


title: 4DR2F104HE_S119

description: Library name: 4DR2F104HE_S119_R1_001

value: Heart


title: protein144

description:
Library name: DSP-1001660022162-A-E01
DSP-1001660022162-A-E01.dcc
DSP-1001660022162-A-E01.stats.txt

value: Brain


title: protein131

description:
Library name: DSP-1001660022162-A-F02
DSP-1001660022162-A-F02.dcc
DSP-1001660022162-A-F02.stats.txt


title: 2M-12W-Ova-CUMS1

description: Library name: Ova-T1


title: 4DR2F103OV_S79

description: Library name: 4DR2F103OV_S79_R1_001


title: 6M-12W-Ova-Ctrl2

description: Library name: Ova-G2


title: 4DR2F103LU_S153

description: Library name: 4DR2F103LU_S153_R1_001


title: 2M-12W-Ova-Ctrl4

description: Library name: Ova-S4


title: 4DR2F103LI_S153

description: Library name: 4DR2F103LI_S153_R1_001


title: protein130

description:
Library name: DSP-1001660022162-A-F03
DSP-1001660022162-A-F03.dcc
DSP-1001660022162-A-F03.stats.txt


title: protein129

description:
Library name: DSP-1001660022162-A-F04
DSP-1001660022162-A-F04.dcc
DSP-1001660022162-A-F04.stats.txt


title: 4DR3F204HE_S151

description: Library name: 4DR3F204HE_S151_R1_001


title: 4DR2F103KI_S143

description: Library name: 4DR2F103KI_S143_R1_001


title: 2M-12W-Ova-Ctrl3

description: Library name: Ova-S3


title: 4DR2F103HE_S144

description: Library name: 4DR2F103HE_S144_R1_001


title: protein128

description:
Library name: DSP-1001660022162-A-F05
DSP-1001660022162-A-F05.dcc
DSP-1001660022162-A-F05.stats.txt


title: 4DR2F102OV_S47

description: Library name: 4DR2F102OV_S47_R1_001


title: 2M-12W-Ova-Ctrl2

description: Library name: Ova-S2


title: 4DR2F102LU_S121

description: Library name: 4DR2F102LU_S121_R1_001

value: Not Used in Analysis


title: protein127

description:
Library name: DSP-1001660022162-A-F06
DSP-1001660022162-A-F06.dcc
DSP-1001660022162-A-F06.stats.txt


title: 4DR2F102HE_S152

description: Library name: 4DR2F102HE_S152_R1_001


title: 2M-12W-Ova-Ctrl1

description: Library name: Ova-S1


title: protein126

description:
Library name: DSP-1001660022162-A-F07
DSP-1001660022162-A-F07.dcc
DSP-1001660022162-A-F07.stats.txt


title: 4DR2F102LI_S121

description: Library name: 4DR2F102LI_S121_R1_001


title: 6M-8W-Ova-CUMS4

description: Library name: Ova-L4


title: 4DR3F203HE_S134

description: Library name: 4DR3F203HE_S134_R1_001


title: 4DR2F101OV_S75

description: Library name: 4DR2F101OV_S75_R1_001


title: protein125

description:
Library name: DSP-1001660022162-A-F08
DSP-1001660022162-A-F08.dcc
DSP-1001660022162-A-F08.stats.txt


title: 4DR2F101LU_S149

description: Library name: 4DR2F101LU_S149_R1_001


title: 6M-8W-Ova-CUMS3

description: Library name: Ova-L3


title: 4DR2F102KI_S151

description: Library name: 4DR2F102KI_S151_R1_001


title: 4DR2F101LI_S149

description: Library name: 4DR2F101LI_S149_R1_001


title: protein124

description:
Library name: DSP-1001660022162-A-F09
DSP-1001660022162-A-F09.dcc
DSP-1001660022162-A-F09.stats.txt


title: 4DR2F101KI_S139

description: Library name: 4DR2F101KI_S139_R1_001


title: 6M-8W-Ova-CUMS2

description: Library name: Ova-L2


title: 4DR3F202OV_S58

description: Library name: 4DR3F202OV_S58_R1_001


title: protein140

description:
Library name: DSP-1001660022162-A-E05
DSP-1001660022162-A-E05.dcc
DSP-1001660022162-A-E05.stats.txt


title: protein141

description:
Library name: DSP-1001660022162-A-E04
DSP-1001660022162-A-E04.dcc
DSP-1001660022162-A-E04.stats.txt


title: 4DR2F101HE_S140

description: Library name: 4DR2F101HE_S140_R1_001


title: 4DR1F9OV_S68

description: Library name: 4DR1F9OV_S68_R1_001


title: protein123

description:
Library name: DSP-1001660022162-A-F10
DSP-1001660022162-A-F10.dcc
DSP-1001660022162-A-F10.stats.txt


title: 6M-8W-Ova-CUMS1

description: Library name: Ova-L1


title: 4DR1F9LU_S142

description: Library name: 4DR1F9LU_S142_R1_001


title: 2M-8W-Ova-CUMS2

description: Library name: Ova-F2


title: protein122

description:
Library name: DSP-1001660022162-A-F11
DSP-1001660022162-A-F11.dcc
DSP-1001660022162-A-F11.stats.txt


title: 6M-8W-Ova-Ctrl4

description: Library name: Ova-K4


title: 4DR1F9LI_S142

description: Library name: 4DR1F9LI_S142_R1_001


title: 4DR1F9KI_S132

description: Library name: 4DR1F9KI_S132_R1_001


title: protein121

description:
Library name: DSP-1001660022162-A-F12
DSP-1001660022162-A-F12.dcc
DSP-1001660022162-A-F12.stats.txt


title: 4DR1F9HE_S133

description: Library name: 4DR1F9HE_S133_R1_001


title: 6M-8W-Ova-Ctrl3

description: Library name: Ova-K3


title: 4DR1F8OV_S45

description: Library name: 4DR1F8OV_S45_R1_001


title: protein120

description:
Library name: DSP-1001660022162-A-G01
DSP-1001660022162-A-G01.dcc
DSP-1001660022162-A-G01.stats.txt


title: 4DR1F8LU_S119

description: Library name: 4DR1F8LU_S119_R1_001

value: SEQ DEPTH < 300000


title: 4DR1F8LI_S119

description: Library name: 4DR1F8LI_S119_R1_001


title: protein119

description:
Library name: DSP-1001660022162-A-G02
DSP-1001660022162-A-G02.dcc
DSP-1001660022162-A-G02.stats.txt


title: 4DR1F8HE_S150

description: Library name: 4DR1F8HE_S150_R1_001


title: 4DR1F8KI_S149

description: Library name: 4DR1F8KI_S149_R1_001


title: protein118

description:
Library name: DSP-1001660022162-A-G03
DSP-1001660022162-A-G03.dcc
DSP-1001660022162-A-G03.stats.txt


title: 6M-8W-Ova-Ctrl1

description: Library name: Ova-K1


title: 4DR1F7OV_S61

description: Library name: 4DR1F7OV_S61_R1_001


title: SMARCC2kd_4

city: Buffalo

first: Zhen

last: Yan

state: NY

address: 955 Main St

department: Physiology and Biophysics

institute: University at Buffalo

description: Library name: SM4

data_processing:
deseq2
Assembly: mm39, hg38
Supplementary files format and content: count matrix

source_name: prefrontal cortex

extract_protocol:
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature.
The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

value: prefrontal cortex

tag: disease

value: Smarcc2 knockdown

value: mouse


title: NPC patient 41


title: protein117

description:
Library name: DSP-1001660022162-A-G04
DSP-1001660022162-A-G04.dcc
DSP-1001660022162-A-G04.stats.txt


title: 4DR1F7LU_S135

description: Library name: 4DR1F7LU_S135_R1_001

value: Sprague-Dawley

value: female


title: 4DR1F7LI_S135

description: Library name: 4DR1F7LI_S135_R1_001


title: SMARCC2kd_3

description: Library name: SM3


title: 4DR1F7KI_S125

description: Library name: 4DR1F7KI_S125_R1_001


title: protein116

description:
Library name: DSP-1001660022162-A-G05
DSP-1001660022162-A-G05.dcc
DSP-1001660022162-A-G05.stats.txt


title: 4DR1F7HE_S126

description: Library name: 4DR1F7HE_S126_R1_001


title: SMARCC2kd_2

description: Library name: SM2


title: protein115

description:
Library name: DSP-1001660022162-A-G06
DSP-1001660022162-A-G06.dcc
DSP-1001660022162-A-G06.stats.txt


title: 4DR1F6LU_S148

description: Library name: 4DR1F6LU_S148_R1_001


title: SMARCC2kd_1

description: Library name: SM1


title: GFP_4

description: Library name: GF4

value: control (mouse)


title: 4DR1F6KI_S138

description: Library name: 4DR1F6KI_S138_R1_001


title: 4DR1F6HE_S139

description: Library name: 4DR1F6HE_S139_R1_001


title: protein113

description:
Library name: DSP-1001660022162-A-G08
DSP-1001660022162-A-G08.dcc
DSP-1001660022162-A-G08.stats.txt


title: protein114

description:
Library name: DSP-1001660022162-A-G07
DSP-1001660022162-A-G07.dcc
DSP-1001660022162-A-G07.stats.txt


title: 4DR1F5OV_S73

description: Library name: 4DR1F5OV_S73_R1_001


title: GFP_3

description: Library name: GF3


title: protein112

description:
Library name: DSP-1001660022162-A-G09
DSP-1001660022162-A-G09.dcc
DSP-1001660022162-A-G09.stats.txt


title: GFP_2

description: Library name: GF2


title: 4DR1F6LI_S148

description: Library name: 4DR1F6LI_S148_R1_001


title: 4DR1F5KI_S137

description: Library name: 4DR1F5KI_S137_R1_001


title: protein111

description:
Library name: DSP-1001660022162-A-G10
DSP-1001660022162-A-G10.dcc
DSP-1001660022162-A-G10.stats.txt


title: 4DR1F5HE_S138

description: Library name: 4DR1F5HE_S138_R1_001


title: GFP_1

description: Library name: GF1


title: 4DR1F4OV_S63

description: Library name: 4DR1F4OV_S63_R1_001


title: protein110

description:
Library name: DSP-1001660022162-A-G11
DSP-1001660022162-A-G11.dcc
DSP-1001660022162-A-G11.stats.txt


title: 4DR1F4LU_S137

description: Library name: 4DR1F4LU_S137_R1_001


title: Alcam_BLC_rep3

city: Fukuoka

first: Hisayuki

last: Yao

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

country: Japan

institute: Kyushu University

description: Library name: Alcam_BLC_rep3

data_processing:
Dual-index barcoding with 10-bp i7 and i5 indices was employed for accurate sample demultiplexing. Single-cell RNA-seq FASTQ files were aligned to the mouse mm10 reference genome and processed into gene-cell count matrices using Cell Ranger v7.1.0 (10x Genomics). Three independent replicates from Alcam⁺Sca-1⁻ BLCs (total n = 25,704 cells) were then merged using the cellranger aggr pipeline with default normalization to generate an integrated feature-barcode matrix.
Assembly: Mouse mm10
Supplementary files format and content: filtered_feature_bc_matrix.h5: HDF5-format gene-cell UMI count matrix (25,704 filtered cells); also provided as matrix.mtx.gz, barcodes.tsv.gz, features.tsv.gz.

source_name: bone marrow

extract_protocol:
Femora, tibias and iliac bones were fragmented into small pieces after flushing out the BM cells. The bone fragments were incubated at 37°C for 90 min in collagenase solution containing type I collagenase (2.5 mg/mL, Worthington Biochemical), 20% fetal calf serum (FCS) and 250 units of DNase (Sigma) in DMEM. After the incubation, cells were treated with ACK lysing buffer (160 mM ammonium chloride, 10 mM potassium bicarbonate, 0.1 mM EDTA) to lyse red blood cells, and collected BLCs. BLCs were stained with anti-CD45, -Ter119, -CD31, -Alcam, -Sca-1 antibodies and PI, and were sorted using FACS Aria III (BD Biosciences).
Single-cell RNA-seq libraries were generated with the Chromium Next GEM Single Cell 3ʹ Reagent Kit v3.1 (10x Genomics, Pleasanton) following the manufacturer’s protocol.

value: bone marrow

value: WT


title: 4DR1F4LI_S137

description: Library name: 4DR1F4LI_S137_R1_001

value: 9 weeks

value: Used in Analysis


title: protein109

description:
Library name: DSP-1001660022162-A-G12
DSP-1001660022162-A-G12.dcc
DSP-1001660022162-A-G12.stats.txt


title: Alcam_BLC_rep2

description: Library name: Alcam_BLC_rep2


title: protein108

description:
Library name: DSP-1001660022162-A-H01
DSP-1001660022162-A-H01.dcc
DSP-1001660022162-A-H01.stats.txt


title: 4DR1F4HE_S128

description: Library name: 4DR1F4HE_S128_R1_001


title: 4DR1F3OV_S66

description: Library name: 4DR1F3OV_S66_R1_001

value: Ovary


title: 4DR1F3LU_S140

description: Library name: 4DR1F3LU_S140_R1_001

value: Lung


title: 4DR1F3LI_S140

description: Library name: 4DR1F3LI_S140_R1_001

value: Liver Left Lobe


title: protein107

description:
Library name: DSP-1001660022162-A-H02
DSP-1001660022162-A-H02.dcc
DSP-1001660022162-A-H02.stats.txt


title: S3-LCM74

city: San Diego

first: Young Chul

last: Kim

address: 3350 La Jolla Village Dr

institute: University of California-San Diego

description: Library name: S3-LCM74

data_processing:
nf-core/rnaseq analysis pipeline (v3.16.0) with the Nextflow workflow manager (v23.10.0)
Assembly: GRCm38, Ensembl release 101
Supplementary files format and content: txt file with log10 (TPM) of genes for each sample

extract_protocol:
Total RNA was isolated from 70-80 microdissected SGLT2-negative LTL-positive tubules per sample using Arcturus PicoPure frozen RNA isolation kit and additional gDNA digestion was performed via Arcticzymes Heat & Run gDNA removal kit.
Quality and quantity of total RNA were determined by High Sensitive Tape Analysis, and cDNA library was prepared using SMARTer Stranded Total RNA-seq Kit v3-Pico Input Mammalian with 0.5 ng total RNA (DV200>30%).

treatment_protocol: Experimental mice were treated with vehicle, dapagliflozin (10mg/kg diet) or semaglutide (3nmol/kg body weight per day) for 2 weeks.

value: Kidney

value: Sglt1 KO/Akita

value: Dapagliflozin


title: protein106

description:
Library name: DSP-1001660022162-A-H03
DSP-1001660022162-A-H03.dcc
DSP-1001660022162-A-H03.stats.txt

value: Brain


title: 4DR1F3HE_S131

description: Library name: 4DR1F3HE_S131_R1_001

value: Heart


title: S3-LCM66

description: Library name: S3-LCM66


title: 4DR1F2OV_S44

description: Library name: 4DR1F2OV_S44_R1_001


title: protein105

description:
Library name: DSP-1001660022162-A-H04
DSP-1001660022162-A-H04.dcc
DSP-1001660022162-A-H04.stats.txt


title: 4DR1F2LU_S118

description: Library name: 4DR1F2LU_S118_R1_001

value: Not Used in Analysis

value: SEQ DEPTH < 300000


title: 4DR1F2LI_S118

description: Library name: 4DR1F2LI_S118_R1_001

value: Sprague-Dawley


title: S3-LCM6

description: Library name: S3-LCM6


title: 4DR1F2HE_S149

description: Library name: 4DR1F2HE_S149_R1_001

value: female


title: 4DR1F1OV_S53

description: Library name: 4DR1F1OV_S53_R1_001


title: 4DR1F1LU_S127

description: Library name: 4DR1F1LU_S127_R1_001


title: S3-LCM101

description: Library name: S3-LCM101


title: 4DR1F1KI_S117

description: Library name: 4DR1F1KI_S117_R1_001


title: 4DR1F1HE_S118

description: Library name: 4DR1F1HE_S118_R1_001


title: S3-LCM78

description: Library name: S3-LCM78

value: Sglt1 WT/Akita


title: 4DR1F10OV_S67

description: Library name: 4DR1F10OV_S67_R1_001


title: protein99

description:
Library name: DSP-1001660022162-A-H10
DSP-1001660022162-A-H10.dcc
DSP-1001660022162-A-H10.stats.txt


title: 4DR1F10KI_S131

description: Library name: 4DR1F10KI_S131_R1_001


title: S3-LCM70

description: Library name: S3-LCM70


title: 4DR1F2KI_S148

description: Library name: 4DR1F2KI_S148_R1_001


title: S3-LCM19

description: Library name: S3-LCM19


title: protein103

description:
Library name: DSP-1001660022162-A-H06
DSP-1001660022162-A-H06.dcc
DSP-1001660022162-A-H06.stats.txt


title: 4DR1F1LI_S127

description: Library name: 4DR1F1LI_S127_R1_001


title: protein98

description:
Library name: DSP-1001660022162-A-H11
DSP-1001660022162-A-H11.dcc
DSP-1001660022162-A-H11.stats.txt


title: 2DR7F605OV_S19

description: Library name: 2DR7F605OV_S19_R1_001


title: S3-LCM43

description: Library name: S3-LCM43


title: 2DR7F605LU_S93

description: Library name: 2DR7F605LU_S93_R1_001


title: 4DR1F10LU_S141

description: Library name: 4DR1F10LU_S141_R1_001


title: S3-LCM71

description: Library name: S3-LCM71


title: 2DR7F605LI_S93

description: Library name: 2DR7F605LI_S93_R1_001


title: S3-LCM4

description: Library name: S3-LCM4


title: 4DR1F10LI_S141

description: Library name: 4DR1F10LI_S141_R1_001


title: 2DR7F605KI_S85

description: Library name: 2DR7F605KI_S85_R1_001


title: protein96

description:
Library name: DSP-1001660022162-A-A01-Y
DSP-1001660022162-A-A01.stats.txt
DSP-1001660022162-A-A01.dcc


title: 2DR7F605HE_S85

description: Library name: 2DR7F605HE_S85_R1_001


title: 2DR7F604OV_S36

description: Library name: 2DR7F604OV_S36_R1_001


title: protein95

description:
Library name: DSP-1001660022162-A-A02-Y
DSP-1001660022162-A-A02.stats.txt
DSP-1001660022162-A-A02.dcc


title: 2DR7F604LU_S110

description: Library name: 2DR7F604LU_S110_R1_001


title: S3-LCM99

description: Library name: S3-LCM99

value: Semaglutide


title: 2DR7F604LI_S110

description: Library name: 2DR7F604LI_S110_R1_001


title: protein94

description:
Library name: DSP-1001660022162-A-A03-Y
DSP-1001660022162-A-A03.stats.txt
DSP-1001660022162-A-A03.dcc


title: 2DR7F604KI_S102

description: Library name: 2DR7F604KI_S102_R1_001


title: S3-LCM92

description: Library name: S3-LCM92


title: 2DR7F604HE_S102

description: Library name: 2DR7F604HE_S102_R1_001


title: protein93

description:
Library name: DSP-1001660022162-A-A04-Y
DSP-1001660022162-A-A04.stats.txt
DSP-1001660022162-A-A04.dcc


title: 2DR7F603OV_S16

description: Library name: 2DR7F603OV_S16_R1_001


title: 4DR1F10HE_S132

description: Library name: 4DR1F10HE_S132_R1_001


title: S3-LCM91

description: Library name: S3-LCM91


title: 2DR7F603LU_S90

description: Library name: 2DR7F603LU_S90_R1_001


title: protein92

description:
Library name: DSP-1001660022162-A-A05-Y
DSP-1001660022162-A-A05.stats.txt
DSP-1001660022162-A-A05.dcc


title: 2DR7F603LI_S90

description: Library name: 2DR7F603LI_S90_R1_001


title: S3-LCM90

description: Library name: S3-LCM90


title: 2DR7F603KI_S82

description: Library name: 2DR7F603KI_S82_R1_001


title: 6M-8W-Ova-Ctrl2

description: Library name: Ova-K2


title: RNA46

description: Library name: DSP-1001660022159-B-E02

value: Chest Wall


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

description:
Library name: 23248XR-01-48
Raw_counts.txt
Normalized_counts.txt

value: Cortex

value: MeCP2:-/Y rtt271a

value: injected rtt271 3e11


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

description:
Library name: 23248XR-01-38
Raw_counts.txt
Normalized_counts.txt

value: injected rtt271 1e11


title: RNA47

description: Library name: DSP-1001660022159-B-E01


title: protein91

description:
Library name: DSP-1001660022162-A-A06-Y
DSP-1001660022162-A-A06.stats.txt
DSP-1001660022162-A-A06.dcc


title: 2DR7F603HE_S82

description: Library name: 2DR7F603HE_S82_R1_001

value: 9 weeks

value: Used in Analysis


title: protein97

description:
Library name: DSP-1001660022162-A-H12
DSP-1001660022162-A-H12.dcc
DSP-1001660022162-A-H12.stats.txt


title: 2DR7F602OV_S14

description: Library name: 2DR7F602OV_S14_R1_001

value: Ovary


title: protein90

description:
Library name: DSP-1001660022162-A-A07-Y
DSP-1001660022162-A-A07.stats.txt
DSP-1001660022162-A-A07.dcc


title: 4DR1F6OV_S74

description: Library name: 4DR1F6OV_S74_R1_001


title: S3-LCM85

description: Library name: S3-LCM85

value: Kidney


title: 2DR7F602LU_S88

description: Library name: 2DR7F602LU_S88_R1_001

value: Lung


title: 2DR7F602LI_S88

description: Library name: 2DR7F602LI_S88_R1_001

value: Liver Left Lobe


title: protein89

description:
Library name: DSP-1001660022162-A-A08-Y
DSP-1001660022162-A-A08.stats.txt
DSP-1001660022162-A-A08.dcc

value: Brain


title: 2DR7F602KI_S80

description: Library name: 2DR7F602KI_S80_R1_001


title: S3-LCM86

description: Library name: S3-LCM86

value: Sglt1 KO/Akita

value: Vehicle


title: 2DR7F602HE_S80

description: Library name: 2DR7F602HE_S80_R1_001

value: Heart

value: Sprague-Dawley

value: female


title: S3-LCM88

description: Library name: S3-LCM88

value: Sglt1 WT/Akita

value: Semaglutide


title: 4DR1F5LU_S147

description: Library name: 4DR1F5LU_S147_R1_001


title: protein88

description:
Library name: DSP-1001660022162-A-A09-Y
DSP-1001660022162-A-A09.stats.txt
DSP-1001660022162-A-A09.dcc


title: 2DR7F601OV_S18

description: Library name: 2DR7F601OV_S18_R1_001


title: S3-LCM7

description: Library name: S3-LCM7


title: protein87

description:
Library name: DSP-1001660022162-A-A10-Y
DSP-1001660022162-A-A10.stats.txt
DSP-1001660022162-A-A10.dcc


title: 2DR7F601LU_S92

description: Library name: 2DR7F601LU_S92_R1_001

value: Not Used in Analysis

value: TOTAL ALIGNMENT RATE < 40%


title: 4DR1F5LI_S147

description: Library name: 4DR1F5LI_S147_R1_001


title: 2DR7F601LI_S92

description: Library name: 2DR7F601LI_S92_R1_001


title: S3-LCM69

description: Library name: S3-LCM69


title: S3-LCM17

description: Library name: S3-LCM17

value: Dapagliflozin


title: 2DR7F601HE_S84

description: Library name: 2DR7F601HE_S84_R1_001

value: 9 weeks


title: S3-LCM57

description: Library name: S3-LCM57


title: 2DR7F601KI_S84

description: Library name: 2DR7F601KI_S84_R1_001

value: Used in Analysis


title: 2DR6F505OV_S30

description: Library name: 2DR6F505OV_S30_R1_001

value: Ovary


title: protein86

description:
Library name: DSP-1001660022162-A-A11-Y
DSP-1001660022162-A-A11.stats.txt
DSP-1001660022162-A-A11.dcc


title: protein85

description:
Library name: DSP-1001660022162-A-A12-Y
DSP-1001660022162-A-A12.stats.txt
DSP-1001660022162-A-A12.dcc


title: Alcam_BLC_rep1

description: Library name: Alcam_BLC_rep1

value: bone marrow

value: WT


title: S3-LCM51

description: Library name: S3-LCM51

value: Kidney


title: 2DR6F505LU_S104

description: Library name: 2DR6F505LU_S104_R1_001

value: Lung


title: 2DR6F505LI_S104

description: Library name: 2DR6F505LI_S104_R1_001

value: Liver Left Lobe


title: 4DR1F4KI_S127

description: Library name: 4DR1F4KI_S127_R1_001


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

description:
Library name: 23248XR-01-34
Raw_counts.txt
Normalized_counts.txt

value: Cortex

value: MeCP2:-/Y rtt271a

value: injected rtt271 1e11


title: protein84

description:
Library name: DSP-1001660022162-A-B01-Y
DSP-1001660022162-A-B01.stats.txt
DSP-1001660022162-A-B01.dcc

value: Brain


title: 2DR6F505KI_S96

description: Library name: 2DR6F505KI_S96_R1_001

value: Sprague-Dawley

value: female


title: S3-LCM15

description: Library name: S3-LCM15

value: Sglt1 KO/Akita

value: Vehicle


title: protein83

description:
Library name: DSP-1001660022162-A-B02-Y
DSP-1001660022162-A-B02.stats.txt
DSP-1001660022162-A-B02.dcc


title: 4DR1F3KI_S130

description: Library name: 4DR1F3KI_S130_R1_001


title: S3-LCM82

description: Library name: S3-LCM82

value: Sglt1 WT/Akita


title: 2DR6F505HE_S96

description: Library name: 2DR6F505HE_S96_R1_001

value: Heart

value: 9 weeks


title: 2DR6F504OV_S35

description: Library name: 2DR6F504OV_S35_R1_001

value: Ovary

value: Used in Analysis


title: S3-LCM8

description: Library name: S3-LCM8


title: 2DR6F504LU_S109

description: Library name: 2DR6F504LU_S109_R1_001


title: 2DR6F504LI_S109

description: Library name: 2DR6F504LI_S109_R1_001


title: 2DR6F504KI_S101

description: Library name: 2DR6F504KI_S101_R1_001


title: protein82

description:
Library name: DSP-1001660022162-A-B03-Y
DSP-1001660022162-A-B03.stats.txt
DSP-1001660022162-A-B03.dcc


title: protein104

description:
Library name: DSP-1001660022162-A-H05
DSP-1001660022162-A-H05.dcc
DSP-1001660022162-A-H05.stats.txt


title: protein81

description:
Library name: DSP-1001660022162-A-B04-Y
DSP-1001660022162-A-B04.stats.txt
DSP-1001660022162-A-B04.dcc


title: S3-LCM76

description: Library name: S3-LCM76


title: protein80

description:
Library name: DSP-1001660022162-A-B05-Y
DSP-1001660022162-A-B05.stats.txt
DSP-1001660022162-A-B05.dcc


title: 2DR6F504HE_S101

description: Library name: 2DR6F504HE_S101_R1_001


title: 2DR6F503LU_S83

description: Library name: 2DR6F503LU_S83_R1_001


title: 2DR6F503KI_S75

description: Library name: 2DR6F503KI_S75_R1_001


title: protein79

description:
Library name: DSP-1001660022162-A-B06-Y
DSP-1001660022162-A-B06.stats.txt
DSP-1001660022162-A-B06.dcc


title: S3-LCM30

description: Library name: S3-LCM30


title: 2DR6F503HE_S75

description: Library name: 2DR6F503HE_S75_R1_001


title: protein78

description:
Library name: DSP-1001660022162-A-B07-Y
DSP-1001660022162-A-B07.stats.txt
DSP-1001660022162-A-B07.dcc


title: S3-LCM1

description: Library name: S3-LCM1


title: 2DR6F502OV_S41

description: Library name: 2DR6F502OV_S41_R1_001


title: protein77

description:
Library name: DSP-1001660022162-A-B08-Y
DSP-1001660022162-A-B08.stats.txt
DSP-1001660022162-A-B08.dcc


title: 2DR6F502LI_S115

description: Library name: 2DR6F502LI_S115_R1_001


title: S3-LCM98

description: Library name: S3-LCM98

value: Sglt1 KO

value: Dapagliflozin


title: 2DR6F502KI_S107

description: Library name: 2DR6F502KI_S107_R1_001

value: Kidney


title: 2DR6F502LU_S115

description: Library name: 2DR6F502LU_S115_R1_001

value: Lung


title: 2DR6F502HE_S107

description: Library name: 2DR6F502HE_S107_R1_001


title: protein76

description:
Library name: DSP-1001660022162-A-B09-Y
DSP-1001660022162-A-B09.stats.txt
DSP-1001660022162-A-B09.dcc


title: S3-LCM97

description: Library name: S3-LCM97


title: 2DR6F501OV_S39

description: Library name: 2DR6F501OV_S39_R1_001


title: S3-LCM96

description: Library name: S3-LCM96


title: 2DR6F501LI_S113

description: Library name: 2DR6F501LI_S113_R1_001

value: Liver Left Lobe


title: protein74

description: Library name: DSP-1001660022162-A-B11-Y


title: 2DR6F501HE_S105

description: Library name: 2DR6F501HE_S105_R1_001


title: S3-LCM9

description: Library name: S3-LCM9


title: protein73

description:
Library name: DSP-1001660022162-A-B12-Y
DSP-1001660022162-A-B12.stats.txt
DSP-1001660022162-A-B12.dcc


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

description:
Library name: 23248XR-01-14
Raw_counts.txt
Normalized_counts.txt

value: Cortex

value: injected pbs controls


title: 2DR5F405LU_S95

description: Library name: 2DR5F405LU_S95_R1_001


title: S3-LCM61

description: Library name: S3-LCM61


title: 2DR5F405LI_S95

description: Library name: 2DR5F405LI_S95_R1_001


title: 2DR5F405OV_S21

description: Library name: 2DR5F405OV_S21_R1_001


title: 2DR5F405KI_S87

description: Library name: 2DR5F405KI_S87_R1_001


title: protein72

description:
Library name: DSP-1001660022162-A-C01-Y
DSP-1001660022162-A-C01.stats.txt
DSP-1001660022162-A-C01.dcc

value: Brain


title: 2DR5F405HE_S87

description: Library name: 2DR5F405HE_S87_R1_001

value: Sprague-Dawley


title: S3-LCM72

description: Library name: S3-LCM72

value: Sglt1 WT


title: 2DR5F404OV_S11

description: Library name: 2DR5F404OV_S11_R1_001

value: female


title: 2DR5F404LU_S85

description: Library name: 2DR5F404LU_S85_R1_001


title: 2DR5F404LI_S85

description: Library name: 2DR5F404LI_S85_R1_001


title: S3-LCM44

description: Library name: S3-LCM44


title: protein69

description:
Library name: DSP-1001660022162-A-C04-Y
DSP-1001660022162-A-C04.stats.txt
DSP-1001660022162-A-C04.dcc


title: S3-LCM18

description: Library name: S3-LCM18


title: 2DR5F403LU_S105

description: Library name: 2DR5F403LU_S105_R1_001


title: protein68

description:
Library name: DSP-1001660022162-A-C05-Y
DSP-1001660022162-A-C05.stats.txt
DSP-1001660022162-A-C05.dcc


title: 2DR5F403LI_S105

description: Library name: 2DR5F403LI_S105_R1_001


title: 2DR5F403KI_S97

description: Library name: 2DR5F403KI_S97_R1_001


title: protein66

description:
Library name: DSP-1001660022162-A-C07-Y
DSP-1001660022162-A-C07.stats.txt
DSP-1001660022162-A-C07.dcc


title: S3-LCM10

description: Library name: S3-LCM10


title: 2DR5F402OV_S2

description: Library name: 2DR5F402OV_S2_R1_001


title: 2DR5F402LU_S76

description: Library name: 2DR5F402LU_S76_R1_001


title: S3-LCM95

description: Library name: S3-LCM95

value: Vehicle


title: 2DR5F402LI_S76

description: Library name: 2DR5F402LI_S76_R1_001


title: protein64

description:
Library name: DSP-1001660022162-A-C09-Y
DSP-1001660022162-A-C09.stats.txt
DSP-1001660022162-A-C09.dcc


title: 2DR5F402KI_S108

description: Library name: 2DR5F402KI_S108_R1_001


title: S3-LCM94

description: Library name: S3-LCM94


title: 2DR5F402HE_S108

description: Library name: 2DR5F402HE_S108_R1_001


title: protein63

description:
Library name: DSP-1001660022162-A-C10-Y
DSP-1001660022162-A-C10.stats.txt
DSP-1001660022162-A-C10.dcc


title: 2DR5F401OV_S40

description: Library name: 2DR5F401OV_S40_R1_001


title: S3-LCM87

description: Library name: S3-LCM87


title: 2DR5F401LU_S114

description: Library name: 2DR5F401LU_S114_R1_001


title: protein62

description:
Library name: DSP-1001660022162-A-C11-Y
DSP-1001660022162-A-C11.stats.txt
DSP-1001660022162-A-C11.dcc


title: 2DR5F401KI_S106

description: Library name: 2DR5F401KI_S106_R1_001


title: protein71

description:
Library name: DSP-1001660022162-A-C02-Y
DSP-1001660022162-A-C02.stats.txt
DSP-1001660022162-A-C02.dcc


title: protein70

description:
Library name: DSP-1001660022162-A-C03-Y
DSP-1001660022162-A-C03.stats.txt
DSP-1001660022162-A-C03.dcc


title: protein61

description:
Library name: DSP-1001660022162-A-C12-Y
DSP-1001660022162-A-C12.stats.txt
DSP-1001660022162-A-C12.dcc


title: S3-LCM55

description: Library name: S3-LCM55


title: S3-LCM42

description: Library name: S3-LCM42


title: 2DR4F305OV_S15

description: Library name: 2DR4F305OV_S15_R1_001


title: 2DR5F404HE_S77

description: Library name: 2DR5F404HE_S77_R1_001


title: protein67

description:
Library name: DSP-1001660022162-A-C06-Y
DSP-1001660022162-A-C06.stats.txt
DSP-1001660022162-A-C06.dcc


title: protein60

description:
Library name: DSP-1001660022162-A-D01-Y
DSP-1001660022162-A-D01.stats.txt
DSP-1001660022162-A-D01.dcc


title: 2DR4F305LU_S89

description: Library name: 2DR4F305LU_S89_R1_001


title: 2DR4F305LI_S89

description: Library name: 2DR4F305LI_S89_R1_001


title: 2DR5F403HE_S97

description: Library name: 2DR5F403HE_S97_R1_001


title: protein59

description:
Library name: DSP-1001660022162-A-D02-Y
DSP-1001660022162-A-D02.stats.txt
DSP-1001660022162-A-D02.dcc


title: 2DR4F305KI_S81

description: Library name: 2DR4F305KI_S81_R1_001


title: S3-LCM84

description: Library name: S3-LCM84


title: protein58

description:
Library name: DSP-1001660022162-A-D03-Y
DSP-1001660022162-A-D03.stats.txt
DSP-1001660022162-A-D03.dcc


title: protein57

description:
Library name: DSP-1001660022162-A-D04-Y
DSP-1001660022162-A-D04.stats.txt
DSP-1001660022162-A-D04.dcc


title: 2DR4F304LU_S84

description: Library name: 2DR4F304LU_S84_R1_001


title: S3-LCM83

description: Library name: S3-LCM83


title: 2DR4F304LI_S84

description: Library name: 2DR4F304LI_S84_R1_001


title: S3-LCM75

description: Library name: S3-LCM75


title: 2DR4F304KI_S76

description: Library name: 2DR4F304KI_S76_R1_001


title: protein56

description:
Library name: DSP-1001660022162-A-D05-Y
DSP-1001660022162-A-D05.stats.txt
DSP-1001660022162-A-D05.dcc


title: 2DR4F304HE_S76

description: Library name: 2DR4F304HE_S76_R1_001


title: S3-LCM67

description: Library name: S3-LCM67


title: 2DR4F303LU_S111

description: Library name: 2DR4F303LU_S111_R1_001


title: protein55

description:
Library name: DSP-1001660022162-A-D06-Y
DSP-1001660022162-A-D06.stats.txt
DSP-1001660022162-A-D06.dcc


title: S3-LCM58

description: Library name: S3-LCM58


title: 2DR4F303LI_S111

description: Library name: 2DR4F303LI_S111_R1_001


title: protein54

description:
Library name: DSP-1001660022162-A-D07-Y
DSP-1001660022162-A-D07.stats.txt
DSP-1001660022162-A-D07.dcc


title: 2DR4F303KI_S103

description: Library name: 2DR4F303KI_S103_R1_001


title: 2DR4F303HE_S103

description: Library name: 2DR4F303HE_S103_R1_001


title: S3-LCM54

description: Library name: S3-LCM54


title: S3-LCM2

description: Library name: S3-LCM2


title: protein53

description:
Library name: DSP-1001660022162-A-D08-Y
DSP-1001660022162-A-D08.stats.txt
DSP-1001660022162-A-D08.dcc

source_name: Bone

value: Bone


title: 2DR4F302OV_S8

description: Library name: 2DR4F302OV_S8_R1_001


title: 2DR4F302LU_S82

description: Library name: 2DR4F302LU_S82_R1_001


title: Homozygous LAKI treated with CHBA biological replicate 7

first: Stelios

middle: T.

last: Andreadis

address: 908 Furnas Hall

department: Chemical and Biological Engineering

description: Library name: LAKI-CHBA_7

data_processing:
Sequenced reads were processed using nf-core/rnaseq (v3.14.0) pipeline.
Quality of the reads was assessed using FastQC (v0.12.1). Sequencing reads were trimmed using Trim Galore (v0.6.7) to filter reads that were shorter than 20 bp.
The filtered reads were then mapped to the mouse genome (GRCm39, Ensembl) using STAR (v2.7.9a) and quantified using Salmon (v1.10.1).
The abundance estimates were imported into R using tximport (v1.26.1) package. The resulting gene-level counts were used for differential gene expression and PCA analysis using the DESeq2 (v1.38.3) package.
Assembly: GRCm39
Supplementary files format and content: csv file of raw counts suitable for differential expression analysis with DESeq2.

source_name: Gastrocnemius

extract_protocol:
RNA was extracted from 10 mg of GA muscle tissue using the RNeasy Fibrous Tissue Mini Kit (Qiagen)
Sequencing libraries were prepared as per standard Illumina protocols (Illumina Stranded Total RNA Prep with Ribo-Zero Plus), quality checked and quantified by Kapa Biosystems qPCR.

treatment_protocol: Mixed sex homozygous LAKI mice were used in the study. Young wildtype (WT) mice of similar age were used as controls.  LAKI mice were intraperitoneally injected with CHBA (10 mg/kg dissolved in 5% (v/v) DMSO in corn oil; abbreviated as LAKI-CHBA: 7 males and 6 females) or vehicle control (5% (v/v) DMSO in corn oil; LAKI: 7 females and 6 males), three times a week for 4 weeks. Young WT mice (WT: 2 females, 3 males) were also administered vehicle (5% (v/v) DMSO in corn oil). Injections were started when the mice were 2.5 months or 10 weeks old.

value: Gastrocnemius

value: 3-chloro-5-hydroxy BA (CHBA)


title: 2DR4F305HE_S81

description: Library name: 2DR4F305HE_S81_R1_001

value: Heart

value: 9 weeks


title: protein52

description:
Library name: DSP-1001660022162-A-D09-Y
DSP-1001660022162-A-D09.stats.txt
DSP-1001660022162-A-D09.dcc


title: 2DR4F304OV_S10

description: Library name: 2DR4F304OV_S10_R1_001

value: Ovary

value: Used in Analysis


title: 2DR4F302LI_S82

description: Library name: 2DR4F302LI_S82_R1_001


title: Homozygous LAKI treated with CHBA biological replicate 6

description: Library name: LAKI-CHBA_6


title: 2DR4F302KI_S74

description: Library name: 2DR4F302KI_S74_R1_001

value: Kidney


title: protein51

description:
Library name: DSP-1001660022162-A-D10-Y
DSP-1001660022162-A-D10.stats.txt
DSP-1001660022162-A-D10.dcc


title: 2DR6F503LI_S83

description: Library name: 2DR6F503LI_S83_R1_001


title: 2DR6F503OV_S9

description: Library name: 2DR6F503OV_S9_R1_001


title: S3-LCM40

description: Library name: S3-LCM40

value: Sglt1 WT/Akita


title: 2DR4F302HE_S74

description: Library name: 2DR4F302HE_S74_R1_001


title: Homozygous LAKI treated with CHBA biological replicate 5

description: Library name: LAKI-CHBA_5


title: 2DR4F301OV_S29

description: Library name: 2DR4F301OV_S29_R1_001


title: protein50

description:
Library name: DSP-1001660022162-A-D11-Y
DSP-1001660022162-A-D11.stats.txt
DSP-1001660022162-A-D11.dcc


title: Homozygous LAKI treated with CHBA biological replicate 4

description: Library name: LAKI-CHBA_4