title: Pool2, CITE-seq, HTO, 3 replicates of WT IELs, 3 replicates of gdHYP IELS

first: Darwin

last: D'Souza

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

description:
Library name: AlonsoPool_2_H
Hashtag-derived oligonucleotide

data_processing:
Analysis of scRNA seq data was conducted in Python using Scanpy library with default parameters unless otherwise specified. Quality control and filtering steps were performed to remove low-quality cells and genes prior to analysis. Pre-processing including normalization, principal component analysis, and Leiden clustering were performed followed by UMAP for visualization. Leiden clusters were manually annotated as specific cell types based on expression of marker genes (Cd4, Cd8a, Cd8b, Trdc, Ki67). Cells were categorized into CD39neg , CD39int , and CD39hi groups based on normalized CD39 expression thresholds (0.15 <= x <= 3). gd IELs (CD8aa TCRgd Tcf7pos and CD8aa TCRgd Tcf7neg) were selected for further downstream analyses. DGE analysis was performed by aggregating raw counts into pseudobulk per sample, filtering out genes with fewer than 10 counts. The DESeq2 package was used for DGE analysis with WT as reference. Variance stabilizing transform (vst) was applied to the pseudobulk data using DESeq2 vst function. The top 500 genes were selected using median absolute dispersion score. Finally, the data was z-normalized before creating clustermap using Seaborn library.
cellranger-7.0.1
Assembly: mm10
Supplementary files format and content: ADT and HTO barcodes: feature_reference.csv
Supplementary files format and content: Cell Annotations in AnnData format: adata_w_conditions.h5ad
Supplementary files format and content: Cell Ranger arguments: AlonsoPool_*_cellranger_config.csv
Supplementary files format and content: Cell Ranger output filtered cells and hastag assignment: AlonsoPool_*_assignment_confidence_table.csv
Supplementary files format and content: Cell Ranger output raw matrix: AlonsoPool_*_raw_feature_bc_matrix.h5
Supplementary files format and content: HTO to sample mapping: AlonsoPool_*_sample_mapping.csv
Supplementary files format and content: HTO to sample mapping: sample_mapping.csv
Library strategy: CITE-seq

molecule: protein

source_name: Small intestine

extract_protocol:
Viability of single cells were assessed using Acridine Orange/Propidium Iodide viability staining reagent (Nexcelom), and debris-free suspensions of >80% viability were deemed suitable for the experiments. Three WT samples and three gdHYP samples were each labeled with a distinct Totalseq C mouse hashtag antibody (HTO-1 to HTO-6, Biolegend) to assign a unique sample identifier. All samples were subsequently pooled in equal proportions and stained with anti-CD39 antibody conjugated with oligonucleotide tags (Biolegend), following the manufacturer’s instructions. Unbound antibodies were washed away to minimize background signal. Subsequently, cells were encapsulated into Gel-Bead in Emulsions (GEMs) using the Chromium X platform (10x Genomics) with the 5’ gene expression (5’ GEX) V2 kit, with a targeted recovery of 20,000 cells per lane. During encapsulation, each cell was uniquely barcoded with a cell-specific barcode, allowing for the tracing of individual cells throughout the experiment. Cells were lysed within the GEMs, and both RNA and protein information were captured during reverse transcription (RT) and cDNA amplification steps, following 10x’s established protocols.
Resulting libraries contain information on gene expression (GEX), hashtag (HTO) and cell surface protein (ADT) levels for each cell. Libraries were quantified using TapeStation (Agilent) and QuBit (ThermoFisher) analyses and were sequenced in paired-end mode on a NovaSeq instrument (Illumina) targeting a depth of 25,000 reads per cell for GEX library and 5000 reads per cell for HTO and ADT libraries.

value: Small intestine

value: intraepithelial lymphocyte

value: mixed sample (WT and gdHYP)

tag: library type

value: HTO

tag: hto

value: Total-seq-C0301 anti-mouse Hashtag 1, Total-seq-C0302 anti-mouse Hashtag 2, Total-seq-C0303 anti-mouse Hashtag 3, Total-seq-C0304 anti-mouse Hashtag 4, Total-seq-C0305 anti-mouse Hashtag 5,Total-seq-C0306 anti-mouse Hashtag 6


title: Pool2, CITE-seq, GEX, 3 replicates of WT IELs, 3 replicates of gdHYP IELS

status: Public on Aug 05 2025

type: SRA

city: New York

state: NY

country: USA

description:
Library name: AlonsoPool_2_G
polyA RNA

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype

value: mRNA


title: Pool2, CITE-seq, ADT, 3 replicates of WT IELs, 3 replicates of gdHYP IELS

description:
Library name: AlonsoPool_2_F
Antibody-derived oligonucleotide

library_source: other

value: ADT

tag: adt

value: Totalseq-C0834 anti-mouse CD39


title: Pool1, CITE-seq, ADT, 3 replicates of WT IELs, 3 replicates of gdHYP IELS

description:
Library name: AlonsoPool_1_F
Antibody-derived oligonucleotide


title: [21] Young (6 months old); Lean (12% Kcal fat diet)

city: Fayetteville

first: Eleanor

last: Schrems

state: Arkansas

address: 155 Stadium Dr.

department: Health, Human Performance, and Recreation

institute: University of Arkansas

description: Library name: Sample 21

data_processing:
FASTQ files were aligned using STAR 2.78a index alignment – RefSeq: mus musculus (mouse) – mm39 GeneBank assembly. Pre-alignment QA/QC was done prior to STAR alignment and after to ensure the quality of raw, unaligned sequencing reads (quality score ~35.66). Samples were normalized by using the median ratio for DESeq2 in Partek, and a filter of 10 minimum reads across all samples was applied. Analysis of differentially expressed genes (DEGs) was done using DESeq2. In order to gain insight to the effects of obesity and age alone, as well as those purely unique to aged obesity (SO), DESeq2 was performed with separate comparisons of YO, AL, and AO groups against YL. Additional DESeq2 was performed for comparisons of AO against AL to gain insight to the effects of obesity in an aged condition. Finally, DESeq2 comparisons were made between AO and YO to gain insight to the effects of ageing with obesity, indicative of lifelong obesity.
Assembly: mm39 GeneBank Assembly
Supplementary files format and content: File Type: xlsx; Contents: Data for each individual sample, normalized by using the median ratio for DeSeq2 in Partek. Normalization was done following a filtering step to include genes with a minimum of 10 counts.

molecule: total RNA

source_name: Gastrocnemius muscle

extract_protocol:
Given the gastrocnemius is a muscle with a mixed fiber type and atrophied the most in the aged-obese (SO) animal group (Table 1), RNA from this muscle was chosen for sequencing. mRNA was isolated from the gastrocnemius muscle, where the muscle tissue was homogenized with Trizol (Life Technologies, Grand Island, NY, USA), and phenol–chloroform extraction was performed following homogenization. RNA was ethanol-precipitated and diluted in 70% of diethyl pyro carbonate-treated ethanol. Total RNA was isolated using an Invitro-gen PureLinkTM RNA Mini Kit (Invitrogen, Waltham, MA, USA; 12183018A). Total RNA was eluted in RNase-free water. RNA concentration and purity were measured using a BioTek Take3 micro-volume microplate with a BioTek Synergy HTX Multi-Mode Microplate Reader, IVD (Fisher Scientific, Waltham, MA, USA; BTS1LASI). A 260/280 nm ratio of >2 was utilized as an initial quality assessment(28). RNA concentration was assessed using a Qubit Fluorimeter, Fragment Analyzer, Nano Drop, and Microplate reader. RNA integrity and quality were assessed by quantifying the RNA integrity number (RIN) and the RNA quality number (RQN) using Agilent 2100 Bioanalyzer and Fragment Analyzer. RIN scores below 7 were excluded from subsequent analysis.
Single-end mRNA sequencing was completed at the BGI Hong Kong Tech Solution NGS Lab (Hong Kong, China) using MGISeq 2000 Transcriptome for library preparation.

value: Gastrocnemius muscle

tag: cell line

value: Male

value: 6 months old

tag: treatment

value: 12% Kcal from fat diet


title: 15-275, 2N, ChN, Batch 3, Medial Septal Neurons

city: Orangeburg

first: Stephen

middle: D.

last: Ginsberg

state: New York

address: 140 Old Orangeburg Road

department: Centre for Dementia Research

institute: Research Foundation for Mental Hygiene

description: Library name: 15-275

data_processing:
Quality Control was performed, and reads with any adapter contamination are trimmed using trimmomatic 0.39. The sequences are then decontaminated using Kraken2 to ensure host specificity.
The decontaminated sequences are then aligned to a reference genome using the STAR aligner. Gene counts were extracted using RSEM.
Downstream analysis was performed using R with the gene counts obtained from RSEM. Genes with over 0.1 counts per million were retained followed by TMM normalization.
Batch correction was performed using three different approaches then differential expression analysis was performed separately for each method, and DEGs common in 2 or more approaches are used for Downstream interpretation.
Assembly: GRCm39
Supplementary files format and content: tab delimited text files with gene counts of all samples in one file
Supplementary files format and content: tab delimited text files with gene counts of one sample per one file

source_name: Brain, basal forebrain

growth_protocol: Breeder pairs (female Ts65Dn and male C57Bl/6J Eicher x C3H/HeSnJ F1 mice) were purchased from Jackson Laboratories (Bar Harbor, ME, USA) and mated at the Nathan Kline Institute. Breeder pairs were assigned to receive one of two choline-controlled experimental diets: i) control rodent diet containing 1.1 g/kg choline chloride (AIN-76A; Dyets Inc., Bethlehem, PA), or ii) choline-supplemented diet containing 5.0 g/kg choline chloride (AIN-76A; Dyets Inc.). Tail clips were taken and genotyped  at weaning and mice were aged to ~10-12 MO, with the average age of ~11 MO.

extract_protocol:
A rapid staining protocol utilizing antibody against choline acetyltransferase (ChAT) (AB144P, Millipore, Burlington MA) was performed to detect cholinergic positive neurons while preserving intact RNA in the unfixed tissue. ChAT-immunoreactive (ir) neurons were identified within the medial septal (MS) region and isolated by LCM (LMD7000)RNA from ~500 MS neukrons was purified using miRNeasy Micro kit (Qiagen) according to manufacturers’ specifications. A DNase digestion was performed twice sequentially before the final washes and RNA purification. . Approximately 500 ChAT-ir neurons were isolated per brain before proceeding to RNA isolation and RNA-seq library preparation.
The SMARTer Stranded Total RNA-Seq kit-Pico input Mammalian (v1, Takara Bio, Mountain View, CA) was employed with minor modifications during step A to utilize full volume of isolated RNA. Samples were quantified (Agilent 2100 HS DNA kit), with samples showing no peak between 300-500bp re-isolated by LCM, with RNA isolation and library preparation repeated.  Samples were isolated and processed in three independent batches, batch 1 (2N, n=3; 2N+, n=5; Ts n=4, Ts+ n=5), batch 2 (2N, n=2; 2N+, n=2; Ts n=4, Ts+ n=2), batch 3 (2N, n=6; 2N+, n=5; Ts n=3, Ts+ n=3).  For each sample run (Batch 1, 2 and 3), library samples were pooled in equimolar concentrations and assayed on an HiSeq-4000 (Illumina, San Diego, CA) using a single read 50 cycle protocol at NYUGSOM Genome Technology Center (GTC).

treatment_protocol: see growth protocol.

value: Brain, basal forebrain

value: cholinergic neurons

value: Medial Septal Neurons

value: ChN

tag: batch

value: Batch 3


title: Pool1, CITE-seq, HTO, 3 replicates of WT IELs, 3 replicates of gdHYP IELS

description:
Library name: AlonsoPool_1_H
Hashtag-derived oligonucleotide

value: Small intestine


title: earlyOA8

city: Detroit

first: Shabana Amanda

last: Ali

state: Michigan

address: Integrative Biosciences Center, 6135 Woodward Avenue

department: Bone and Joint Center

institute: Henry Ford Health + Michigan State University Health Sciences

description:
Library name: Sample 14
Column name in allsamples_raw_counts.csv: earlyOA8

data_processing:
The raw microRNA sequences obtained after sequencing were aligned to miRBase v22.1 and the human reference genome (vGRCh38).
Abundant microRNAs, defined as those with at least 10 counts-per-million (CPM) in two or more samples, were selected, and the counts were normalized to total counts.
Differential expression analysis between groups was performed in a pairwise manner using a quasi-likelihood negative binomial model with trended dispersions, implemented in the edgeR package (v3.40.2).
Novel microRNA sequences were identified using miRDeep2.
Assembly: vGRCh38
Supplementary files format and content: allsamples_raw_counts cvs file includes raw counts for each sample

organism: Homo sapiens

source_name: Plasma

growth_protocol: No growth

extract_protocol:
Blood samples were collected in EDTA-coated vacutainers and fractionated by centrifugation. RNA was isolated from 250 μL plasma using the miRNeasy Serum/Plasma Advanced Kit (QIAGEN Inc.), following the manufacturer's instructions.
Library construction followed the QIAseq miRNA Library Kit (QIAGEN Inc.) protocol.

treatment_protocol: No treatment

value: Plasma

tag: disease

value: Early OA


title: earlyOA2

description:
Library name: Sample 8
Column name in allsamples_raw_counts.csv: earlyOA2


title: Pool1, CITE-seq, GEX, 3 replicates of WT IELs, 3 replicates of gdHYP IELS

description:
Library name: AlonsoPool_1_G
polyA RNA

value: intraepithelial lymphocyte

value: mixed sample (WT and gdHYP)


title: 15-274, 2N, ChN, Batch 3, Medial Septal Neurons

description: Library name: 15-274


title: DAHB+O-treated rep1

first: Craig

last: Thompson

address: 411 East 67th Street RRL 469

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: DAHB+O1
RNA-seq on CD8+ T cells

data_processing:
RNA sequencing reads were 3’ trimmed for base quality (Q ≥15) and adapter sequences using TrimGalore v0.4.5. Reads were aligned to the Mus musculus reference genome (mm10) using STAR v2.4 with default parameters. Data quality and transcript coverage were assessed with the Picard tool CollectRNASeqMetrics (http://broadinstitute.github.io/picard/). Gene-level count tables were generated using HTSeq v0.9.1. Normalization and differential expression analysis were performed using DESeq2 with default parameters. Outliers were evaluated by principal component analysis (PCA) based on normalized expression values. The processed data file contains DESeq2-normalized gene expression counts.
Assembly: mm10
Supplementary files format and content: Excel file with normalized counts.

source_name: Spleen and lymph nodes

extract_protocol:
100,000 CD8 T cells were obtained from spleen/lymph nodes of mice and were activated with anti-CD3/anti-CD28 and treated as indicated.
Total RNA was isolated from cells using the RNeasy Plus Micro Kit (Qiagen) following the manufacturer’s protocol. Genomic DNA was removed using the gDNA Eliminator spin columns included in the kit. RNA concentration was measured using a NanoDrop spectrophotometer. Quality control and library preparation (poly(A) enrichment) were performed by the MSKCC Integrated Genomics Core.

value: Spleen and lymph nodes

value: CD8 T cells

value: Wild-type

value: DAHB+O


title: earlyOA1

description:
Library name: Sample 7
Column name in allsamples_raw_counts.csv: earlyOA1


title: DAHB+O-treated rep2

description:
Library name: DAHB+O2
RNA-seq on CD8+ T cells


title: DAHB+O-treated rep3

description:
Library name: DAHB+O3
RNA-seq on CD8+ T cells


title: DAHB-treated rep3

description:
Library name: DAHB3
RNA-seq on CD8+ T cells

value: DAHB


title: DAHB-treated rep2

description:
Library name: DAHB2
RNA-seq on CD8+ T cells


title: DAHB-treated rep1

description:
Library name: DAHB1
RNA-seq on CD8+ T cells


title: NaCl-treated rep3

description:
Library name: Ctrl3
RNA-seq on CD8+ T cells

value: NaCl


title: 15-136, 2N, ChN, Batch 3, Medial Septal Neurons

description: Library name: 15-136


title: 15-137, TS, ChN, Batch 3, Medial Septal Neurons

description: Library name: 15-137

value: TS


title: earlyRA4

description:
Library name: Sample 4
Column name in allsamples_raw_counts.csv: earlyRA4

value: Early RA


title: 14-163, TS, ChP, Batch 3, Medial Septal Neurons

description: Library name: 14-163

value: Brain, basal forebrain

value: cholinergic neurons

value: ChP


title: DAHB-treated rep1

description:
Library name: DAHB_1
RNA-seq on CD8+ T cells

data_processing:
RNA sequencing reads were trimmed for adapter sequences and low-quality bases using Trimmomatic v0.36, and aligned to the Mus musculus GRCm38 reference genome using STAR v2.5.2b. Only uniquely aligned reads were retained. Gene-level read counts were generated with featureCounts v1.5.2 using exon regions from the Ensembl annotation. If applicable, strand-specific counting was performed. Normalization and differential expression were evaluated with DESeq2 using default parameters.
Assembly: GRCm38
Supplementary files format and content: Excel file with normalized counts.

extract_protocol:
100,000 CD8 T cells were obtained from spleen/lymph nodes of mice and were activated with anti-CD3/anti-CD28 and treated as indicated.
Total RNA was isolated from cells using the RNeasy Plus Micro Kit (Qiagen) following the manufacturer’s protocol. Genomic DNA was removed using the gDNA Eliminator spin columns included in the kit. RNA concentration was measured using a NanoDrop spectrophotometer. Quality control and library preparation were performed by Azenta Life Sciences.

value: Az


title: DAHB-treated rep2

description:
Library name: DAHB_2
RNA-seq on CD8+ T cells


title: 14-160, TS, ChP, Batch 3, Medial Septal Neurons

description: Library name: 14-160

value: Medial Septal Neurons

value: Batch 3


title: DAHB-treated rep3

description:
Library name: DAHB_3
RNA-seq on CD8+ T cells


title: earlyRA2

description:
Library name: Sample 2
Column name in allsamples_raw_counts.csv: earlyRA2

value: Plasma


title: NaCl-treated rep3

description:
Library name: Ctrl_3
RNA-seq on CD8+ T cells


title: NaCl-treated rep2

description:
Library name: Ctrl2
RNA-seq on CD8+ T cells


title: NaCl-treated rep1

description:
Library name: Ctrl1
RNA-seq on CD8+ T cells


title: earlyRA1

description:
Library name: Sample 1
Column name in allsamples_raw_counts.csv: earlyRA1


title: earlyRA3

description:
Library name: Sample 3
Column name in allsamples_raw_counts.csv: earlyRA3


title: 14-114, 2N, ChP, Batch 3, Medial Septal Neurons

description: Library name: 14-114


title: NaCl-treated rep2

description:
Library name: Ctrl_2
RNA-seq on CD8+ T cells


title: NaCl-treated rep1

description:
Library name: Ctrl_1
RNA-seq on CD8+ T cells


title: 14-113, 2N, ChP, Batch 3, Medial Septal Neurons

description: Library name: 14-113


title: 15-232, 2N, ChN, Batch 3, Medial Septal Neurons

description: Library name: 15-232

value: ChN


title: 14-106, 2N, ChP, Batch 3, Medial Septal Neurons

description: Library name: 14-106


title: earlyRA5

description:
Library name: Sample 5
Column name in allsamples_raw_counts.csv: earlyRA5


title: HUDEP-2, Bcl11a enhancer KO, diff, clone 2

city: Utrecht

first: Richard

last: Gremmen

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

library_source: genomic

data_processing:
Sequencing libraries were pooled and pair-end (2 × 50 bp) sequenced on an Illumina Nextseq 2000 platform.
Reads were trimmed with cutadapt 4.4 with --minimum-length 10 and removal of adapters, aligned to the GRCh38.p14 reference genome with bowtie2 with parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail -X 1000.
Non-primary alignments, not-properly paired reads and alignments with mapping quality lower than 1 were filtered out with samtools 1.17 (view - F 260) and blacklisted against ENCODE Unified GRCh38 Blacklist ENCFF356LFX (https://www.encodeproject.org/files/ENCFF356LFX/) with bedtools 2.31.0.
Duplicates where removed with picard MarkDuplicates --REMOVE_DUPLICATES true (picard 2.27.5)
Bigwigs were created using bamCoverage (deeptools 3.5.5) with parameters bamCoverage --binSize 10 --normalizeUsing RPGC --ignoreForNormalization chrX chrM --extendReads
Assembly: GRCh38.p14
Supplementary files format and content: Bigwigs
Library strategy: Cut&Run

molecule: genomic DNA

source_name: umbilical cord blood

growth_protocol: Cells were cultured in Cellquin proliferation medium which consists of fully defined serum free Iscove’s Modified Dulbecco’s Medium (IMDM), supplemented with human holotransferrin (300 μg/ml), Insulin (10 μg/ml), Na-pyruvate (100 uM), Penicillin/Streptomycin (P/S, 100 U/mL), L-glutamine (2 mM), lipid mixture 1 (Sigma-Aldrich), Poly(vinyl alcohol) (1 g/L), EPO (2 U/mL), dexamethasone (1 μM), doxycycline (3-6 μg/mL), and human recombinant stem cell factor  (1:100). HUDEP-2 cells were differentiated by switching the medium to differentiation medium (Cellquin supplemented with doxycycline (2uG/mL), EPO (10U/mL), 3% human plasma and Heparin (2U/mL)). After 7 days, doxycycline was removed from the medium and the cells were cultured for an additional 3 days.

extract_protocol:
CUT&RUN was performed using the CUT&RUN Kit from Cell Signaling (catalog no. 86652S) according to the manufacturer’s instructions. Briefly, 0.5 million cells were harvested and washed twice in 1× wash buffer at room temperature and bound to 15 μl of Concanavalin A beads. Primary antibody incubation was performed in PCR tubes for 2 h at 4 °C with rotation. H3K4me3 antibody supplied by the kit was used (1:xyz). After two washes, pAG-MNase was added and incubated for 1 h at 4 °C with rotation. After three washes, cells were resuspended in 1× wash buffer and pAG-MNase digestion was activated by adding 2 mM CaCl2. Samples were incubated on ice for 45 min, then 2× stop buffer was added to end the reaction. The samples were incubated at 37 °C for 10 min to release the captured chromatin fragments
The sequencing libraries were prepared using the NEBNext Ultra II DNA Library (New England Biolabs, catalog no. E7645) with 15–30 ng of input DNA.

value: umbilical cord blood

value: Human erythroid progenitor cell line

tag: antibody

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb #9756

value: KO


title: earlyRA6

description:
Library name: Sample 6
Column name in allsamples_raw_counts.csv: earlyRA6


title: W439

city: Boston

first: Christina

last: Sharkey

address: 99 Brookline Ave

institute: Beth Israel Deaconess Medical Center

description: Library name: WT439

data_processing:
We used Novogene's Bioinformatics service for data processing. The workflow is the following: (1) Data quality check – a step where low confidence nucleotide base-calls can be identified and removed. (2) Map your data to reference genome. (3) Differential gene expression analysis, where we will visualize the distribution of differentially expressed genes across your samples using high-resolution and publication ready volcano plots and heatmaps. To annotate a function to your genes, one can then perform a (4) Functional analysis by mapping the reads against publicly available protein databases, such as the Gene Ontology db (GO enrichment analysis), Kyoto Encyclopedia of Genes and Genomes db (KEGG enrichment analysis), or perform a Gene Set Enrichment Analysis (GSEA) and Protein-Protein interaction studies. Lastly, (5) Structure analysis can also be performed to identify Single Nucleotide Polymorphisms (SNPs), investigate differences in distribution of indels and deletions across samples (InDel analysis), or analyze splice isoforms (Alternative splicing analysis).
Assembly: Mus Musculus (GRCm38/mm10)
Supplementary files format and content: Excel

source_name: Primary Mouse Prostate Tissue

extract_protocol:
Qiagen Rneasy Kit
polyA enrichment library preparation was used to construct 250-300 bp insert cDNA library.

value: Primary Mouse Prostate Tissue


title: HUDEP-2, Bcl11a enhancer KO, diff, clone 1

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb #9755


title: W423

description: Library name: WT423


title: W444

description: Library name: WT444


title: 16-22, TS, ChN, Batch 2, Medial Septal Neurons

description: Library name: 16-22

value: Batch 2


title: HUDEP-2, Del2Rec, diff, clone 2

description: HUDEP-2, Del2Rec, diff, clone 2

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb #9754

value: deletion clone


title: H417

description: Library name: Het417


title: K448

description: Library name: KO448


title: H470

description: Library name: Het470


title: 15-243, 2N, ChN, Batch 2, Medial Septal Neurons

description: Library name: 15-243

value: Brain, basal forebrain


title: HUDEP-2, WT, diff, rep1

description: HUDEP-2, WT, diff, rep1

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb #9751

value: WT


title: K416

description: Library name: KO416


title: 15-332, 2N, ChP, Batch 2, Medial Septal Neurons

description: Library name: 15-332

value: cholinergic neurons

value: ChP


title: HUDEP-2, WT, diff, rep2

description: HUDEP-2, WT, diff, rep2

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb #9752


title: K414

description: Library name: KO414


title: HUDEP-2, Del2Rec, diff, clone 1

description: HUDEP-2, Del2Rec, diff, clone 1

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb #9753


title: 15-325, TS, ChN, Batch 2, Medial Septal Neurons

description: Library name: 15-325

value: Medial Septal Neurons

value: TS

value: ChN


title: H472

description: Library name: Het472


title: 15-273, TS, ChN, Batch 2, Medial Septal Neurons

description: Library name: 15-273


title: 1469_SM/J_M

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

description:
Library name: 1469_SM/J_M
1469

data_processing:
FASTQ files were quantified with kallisto 0.46.1 against the Ensembl mouse transcriptome (v97)
Assembly: mm10
Supplementary files format and content: tab-delimited files contain counts and TPM values

source_name: subcutaneous adipose

extract_protocol:
Extractions were performed with the Qiagen Rneasy 96 kit (catalog number 74181) using the manufacturer's instructions.
Libraries were prepared with the KAPA mRNA HyperPrep Kit KK8581 and adapter kit KK8722 using manufacturer's instructions

value: subcutaneous adipose

tag: strain

value: SM/J

tag: Sex

value: male


title: 1464_AXB13/PgnJ_F

description:
Library name: 1464_AXB13/PgnJ_F
1464

value: female


title: HUDEP-2, WT, diff, rep1

description: HUDEP-2, WT, diff, rep1

data_processing:
trimmed with cutadapt 4.4 with --minimum-length 10 and removal of adapters
aligned to the GRCh38.p14 reference genome with bowtie2 (2.5.1) with parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --dovetail -X 1000
Non-primary alignments, not-properly paired reads (in case of PE reads) and alignments with mapping quality lower than 15 were filtered out with samtools 1.17 (view - F 260)
blacklisted against ENCODE Unified GRCh38 Blacklist ENCFF356LFX (https://www.encodeproject.org/files/ENCFF356LFX/) with bedtools 2.31.0
converted the bams to tagAlign BED files with bamtobed (bedtools 2.31.1) and created treatment bedgraphs during macs2 (2.2.9.1) peak calling, with artificial reads centralized  5bp up- and downstream of Tn5 transposase cutting sites, with parameters -f BED -g hs -p 0.01 --shift -75 --extsize 150 --nomodel --bdg --SPMR --keep-dup all.
Assembly: GRCh38.p14
Supplementary files format and content: bigwigs: Treatment bedgraphs were converted to bigwigs with bedGraphToBigWig (ucsc tools 3.3.5).

extract_protocol:
ATAC-seq was performed using the Omni-ATAC protocol. Briefly, 200,000 cells were lysed with 0.1% NP-40, 0.1% Tween-20 and 0.01% digitonin, and incubated with homemade Tagment DNA Enzyme for 30 min at 37 °C. DNA was purified with QIAGEN MinElute Reaction Cleanup Kit
Library fragments were amplified using Phusion High-Fidelity PCR Master Mix with HF Buffer (Thermo Fisher Scientific, catalog no. F531S) and customized primers with unique single or dual indexes.

value: umbilical cord blood

value: Human erythroid progenitor cell line


title: 1474_NZB/BlNJ_M

description:
Library name: 1474_NZB/BlNJ_M
1474

value: NZB/BlNJ


title: 15-240, 2N, ChN, Batch 2, Medial Septal Neurons

description: Library name: 15-240

value: Brain, basal forebrain

value: Batch 2


title: 1446_I/LnJ_F

description:
Library name: 1446_I/LnJ_F
1446

value: I/LnJ


title: HUDEP-2, WT, diff, rep2

description: HUDEP-2, WT, diff, rep2

value: WT


title: HUDEP-2, Del2Rec, diff, clone 2

description: HUDEP-2, Del2Rec, diff, clone 2

value: deletion clone


title: 15-14, 2N, ChP, Batch 2, Medial Septal Neurons

description: Library name: 15-14

value: cholinergic neurons

value: ChP


title: 1477_NZB/BlNJ_F

description:
Library name: 1477_NZB/BlNJ_F
1477


title: 1435_A/J_F

description:
Library name: 1435_A/J_F
1435

value: A/J


title: 1451_I/LnJ_M

description:
Library name: 1451_I/LnJ_M
1451


title: 15-237, TS, ChP, Batch 2, Medial Septal Neurons

description: Library name: 15-237

value: Medial Septal Neurons

value: TS


title: 1441_CXB13/HiAJ_F

description:
Library name: 1441_CXB13/HiAJ_F
1441

value: subcutaneous adipose


title: 1430_A/J_M

description:
Library name: 1430_A/J_M
1430


title: 1434_MA/MyJ_F

description:
Library name: 1434_MA/MyJ_F
1434

value: MA/MyJ


title: HUDEP-2, Del2Rec, diff, clone 1

description: HUDEP-2, Del2Rec, diff, clone 1


title: 1425_BXA8/PgnJ_M

description:
Library name: 1425_BXA8/PgnJ_M
1425

value: male


description: HUDEP-2, Bcl11a enhancer KO, diff, clone 2

value: KO


title: 14-153, TS, ChP, Batch 2, Medial Septal Neurons

description: Library name: 14-153


title: 1411_PL/J_F

description:
Library name: 1411_PL/J_F
1411

value: PL/J

value: female


title: 14-59, TS, ChN, Batch 2, Medial Septal Neurons

description: Library name: 14-59

value: ChN


description: HUDEP-2, Bcl11a enhancer KO, diff, clone 1

value: umbilical cord blood

value: Human erythroid progenitor cell line


title: HUDEP-2, TFBS edit, diff, clone 1

description: HUDEP-2, TFBS edit, diff, clone 1

value: TFBS edit


title: 15-242, TS, ChN, Batch 1, Medial Septal Neurons

description: Library name: 15-242

value: Brain, basal forebrain

value: Batch 1


title: HUDEP-2, TFBS edit, diff, clone 2

description: HUDEP-2, TFBS edit, diff, clone 2


title: 1408_CE/J_F

description:
Library name: 1408_CE/J_F
1408

value: CE/J


title: 15-310, 2N, ChP, Batch 1, Medial Septal Neurons

description: Library name: 15-310

value: cholinergic neurons

value: ChP


title: 1391_SJL/J_M

description:
Library name: 1391_SJL/J_M
1391

value: SJL/J


title: 1386_AXB13/PgnJ_M

description:
Library name: 1386_AXB13/PgnJ_M
1386


title: 15-261, 2N, ChP, Batch 1, Medial Septal Neurons

description: Library name: 15-261

value: Medial Septal Neurons


title: 1398_AKR/J_M

description:
Library name: 1398_AKR/J_M
1398

value: subcutaneous adipose

value: AKR/J


title: 1394_SJL/J_F

description:
Library name: 1394_SJL/J_F
1394


title: 1367_AXB12/PgnJ_F

description:
Library name: 1367_AXB12/PgnJ_F
1367


title: 1405_AXB5/PgnJ_F

description:
Library name: 1405_AXB5/PgnJ_F
1405


title: RNA-seq NANOS1 mutant overexpression, BR1

city: Stanford

first: Abby

middle: R

last: Thurm

state: CA

address: 443 Via Ortega Rm 036

institute: Stanford University

description:
Library name: ART_L45
FL-OE_se_counts_20241104_REVISED.csv

data_processing:
HT-Recruit: https://github.com/bintulab/HT-recruit-Analyze/tree/main/Scripts; sequences were aligned to a reference library fasta using bowtie, then counts in each fraction were normalized and used to create log2 ratios of each library member in the unbound:bound samples
Cut&Run: https://github.com/bintulab/Spreading_Lensch_2022/tree/main/CUT%26RUN%20Analysis; reads were aligned to a custom human genome containing reporter locus using bowtie2, then duplicate reads were removed with Picard. Bedgraph files were generated using bedtools and normalized using total counts per sample (CPM)
RNA-seq: https://github.com/bintulab/Viral_Ludwig_2022/tree/main/final_April-2023/RNA-seq%20Scripts; reads were aligned to a reference transcriptome with hisat2, then samtools was used to convert SAM --> BAM --> sorting --> indexing steps. Differential expression analysis and downstream plotting was performed using DESeq2 from Bioconductor
Assembly: hg38 genome/transcriptome for Cut&Run + RNA-seq; custom library indices for HT-recruit
Supplementary files format and content: HT-Recruit: comma-delimited text file with raw counts for each of four samples included in an HT-Recruit assay (Unbound fraction, replicate 1; Bound fraction, replicate 1; Unbound fraction, replicate 2; Bound fraction, replicate 2)
Supplementary files format and content: Cut&Run: bedGraph files with read density per genomic location for each sample
Supplementary files format and content: RNA-seq: comma-delimited text file with raw read counts for each overexpression/RNA-seq sample

growth_protocol: K562 lympohblastic cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
HT-Recruit: genomic DNA was extracted after cell magnetic separation using the QiaAmp Blood+Tissue DNA Maxi kit; Cut&Run: genomic DNA was extracted and processed using the CUTANA CUT&RUN kit (Epicypher); RNA-seq: RNA was extracted using the Qiagen RNEasy and QiaShreeder kits
HT-Recruit: libraries were prepared via genomic PCR with custom primer sets to append Illumina-compatible barcodes; Cut&Run: libraries were prepared using the CUTANA CUT&RUN kit with subsequent NEB library prep protocol; RNA-seq: libraries were prepared using the NEBNext PolyA mRNA Magnetic Isolation Module and the NEBNext Ultra II Rna Library Prep Kit

treatment_protocol: For Cut&Run and RNA-seq experiments, TMP was added to stabilize degron-tagged constructs for 24-48 hours before assay endpoint.

value: CML lymphoblast

value: WT

value: RNA-seq after 2 days of overexpression of full-length NANOS1 mutant


title: 1362_BXA11/PgnJ_M

description:
Library name: 1362_BXA11/PgnJ_M
1362

value: male


title: 1421_AXB5/PgnJ_M

description:
Library name: 1421_AXB5/PgnJ_M
1421


title: 1360_BXD85/RwwJ_F

description:
Library name: 1360_BXD85/RwwJ_F
1360

value: female


title: RNA-seq FIP1L1 mutant overexpression, BR1

description:
Library name: ART_L43
FL-OE_se_counts_20241104_REVISED.csv

value: RNA-seq after 2 days of overexpression of full-length FIP1L1 mutant


title: RNA-seq NANOS1 mutant overexpression, BR2

description:
Library name: ART_L46
FL-OE_se_counts_20241104_REVISED.csv


title: 1413_BXD15/TyJ_M

description:
Library name: 1413_BXD15/TyJ_M
1413


title: 1345_AXB12/PgnJ_M

description:
Library name: 1345_AXB12/PgnJ_M
1345


title: 15-236, 2N, ChN, Batch 1, Medial Septal Neurons

description: Library name: 15-236

value: ChN


title: RNA-seq FIP1L1 mutant overexpression, BR2

description:
Library name: ART_L44
FL-OE_se_counts_20241104_REVISED.csv


title: 15-167, TS, ChN, Batch 1, Medial Septal Neurons

description: Library name: 15-167

value: TS


title: 1355_BXA8/PgnJ_F

description:
Library name: 1355_BXA8/PgnJ_F
1355


title: 1349_SM/J_F

description:
Library name: 1349_SM/J_F
1349

value: SM/J


title: 15-241, TS, ChN, Batch 1, Medial Septal Neurons

description: Library name: 15-241

value: Brain, basal forebrain

value: Batch 1


title: 15-215, TS, ChP, Batch 1, Medial Septal Neurons

description: Library name: 15-215

value: cholinergic neurons


title: RNA-seq CPEB2 mutant overexpression, BR2

description:
Library name: ART_L42
FL-OE_se_counts_20241104_REVISED.csv

value: RNA-seq after 2 days of overexpression of full-length CPEB2 mutant


title: 1338_BXD38/TyJ_F

description:
Library name: 1338_BXD38/TyJ_F
1338


title: RNA-seq NANOS1 full-length overexpression, BR2

description:
Library name: ART_L40
FL-OE_se_counts_20241104_REVISED.csv

value: RNA-seq after 2 days of overexpression of full-length NANOS1


title: 1341_CE/J_M

description:
Library name: 1341_CE/J_M
1341

value: CE/J


title: 1365_129X1/SvJ_F

description:
Library name: 1365_129X1/SvJ_F
1365

value: subcutaneous adipose


title: 15-166, 2N, ChN, Batch 1, Medial Septal Neurons

description: Library name: 15-166

value: Medial Septal Neurons


title: 1320_BXD86/RwwJ_M

description:
Library name: 1320_BXD86/RwwJ_M
1320


title: RNA-seq CPEB2 mutant overexpression, BR1

description:
Library name: ART_L41
FL-OE_se_counts_20241104_REVISED.csv

value: CML lymphoblast


title: 15-15, 2N, ChP, Batch 1, Medial Septal Neurons

description: Library name: 15-15

value: ChP


title: 1315_BXD86/RwwJ_F

description:
Library name: 1315_BXD86/RwwJ_F
1315


title: 15-02, TS, ChP, Batch 1, Medial Septal Neurons

description: Library name: 15-02


title: 1324_KK/HlJ_F

description:
Library name: 1324_KK/HlJ_F
1324

value: KK/HlJ


title: 15-01, 2N, ChP, Batch 1, Medial Septal Neurons

description: Library name: 15-01


title: 1297_SWR/J_F

description:
Library name: 1297_SWR/J_F
1297

value: SWR/J


title: RNA-seq FIP1L1 full-length overexpression, BR2

description:
Library name: ART_L38
FL-OE_se_counts_20241104_REVISED.csv

value: WT

value: RNA-seq after 2 days of overexpression of full-length FIP1L1


title: RNA-seq NANOS1 full-length overexpression, BR1

description:
Library name: ART_L39
FL-OE_se_counts_20241104_REVISED.csv


title: 1308_KK/HlJ_M

description:
Library name: 1308_KK/HlJ_M
1308

value: male


title: 1293_C57BLKS/J_F

description:
Library name: 1293_C57BLKS/J_F
1293

value: female


title: RNA-seq FIP1L1 full-length overexpression, BR1

description:
Library name: ART_L37
FL-OE_se_counts_20241104_REVISED.csv


title: 14-60, 2N, ChN, Batch 1, Medial Septal Neurons

description: Library name: 14-60

value: ChN


title: 1285_SWR/J_M

description:
Library name: 1285_SWR/J_M
1285


title: 14-57, TS, ChN, Batch 1, Medial Septal Neurons

description: Library name: 14-57

value: Brain, basal forebrain

value: TS


title: 1281_AXB19a/PgnJ_M

description:
Library name: 1281_AXB19a/PgnJ_M
1281


title: 1290_C57BLKS/J_M

description:
Library name: 1290_C57BLKS/J_M
1290


title: RNA-seq CPEB2 full-length overexpression, BR2

description:
Library name: ART_L36
FL-OE_se_counts_20241104_REVISED.csv

value: RNA-seq after 2 days of overexpression of full-length CPEB2


title: 1278_AXB19b/PgnJ_F

description:
Library name: 1278_AXB19b/PgnJ_F
1278


title: 1332_BXD48/RwwJ_F

description:
Library name: 1332_BXD48/RwwJ_F
1332


title: 14-159, TS, ChP, Batch 1, Medial Septal Neurons

description: Library name: 14-159

value: cholinergic neurons

value: Batch 1


title: 1272_NZW/LacJ_F

description:
Library name: 1272_NZW/LacJ_F
1272

value: NZW/LacJ


title: RNA-seq RBFOX-NANOS over expression, BR2

description:
Library name: ART_L34
FL-OE_se_counts_20241104_REVISED.csv

value: RNA-seq after 2 days of overexpression of RBFOX2_RBD-NANOS1_003


title: 14-158, TS, ChP, Batch 1, Medial Septal Neurons

description: Library name: 14-158

value: Medial Septal Neurons


title: 1266_LP/J_F

description:
Library name: 1266_LP/J_F
1266

value: subcutaneous adipose

value: LP/J


title: 1257_BXD71/RwwJ_F

description:
Library name: 1257_BXD71/RwwJ_F
1257


title: RNA-seq RBFOX-NANOS over expression, BR1

description:
Library name: ART_L33
FL-OE_se_counts_20241104_REVISED.csv

value: CML lymphoblast


title: 1205_AXB19b/PgnJ_M

description:
Library name: 1205_AXB19b/PgnJ_M
1205


title: 1197_BXD85/RwwJ_M

description:
Library name: 1197_BXD85/RwwJ_M
1197


title: 14-116, TS, ChP, Batch 1, Medial Septal Neurons

description: Library name: 14-116

value: ChP


title: 1183_CXB6/ByJ_M

description:
Library name: 1183_CXB6/ByJ_M
1183


title: RNA-seq synNANOS over expression, BR2

description:
Library name: ART_L32
FL-OE_se_counts_20241104_REVISED.csv

value: WT

value: RNA-seq after 2 days of overexpression of DHFR-MCP-NANOS1_003


title: 1132_BXD44/RwwJ_F

description:
Library name: 1132_BXD44/RwwJ_F
1132


title: Rpp21-rep4

city: Riverside

first: Shiyang

last: He

address: 3401 Watkins Drive, Boyce Hall

department: Biochemistry

institute: UCR

description: Library name: Rpp21-rep4

data_processing:
When obtained the raw fastq file from the sequencers, FastQC was used to perform quality control.
STAR (v2.7.3a) were used to map the sequencing reads to mouse genome (mm10).
PCR duplications were removed with UMI-tools version(version 1.0.1).
Bedgraph files were generated from bedtools v2.29.2 and subsesquently transfromed to bigwig files with bedGraphToBigWig(V4).
Assembly: UCSC mm10
Supplementary files format and content: BigWig files for crosslinking events
Library strategy: iCLIP

source_name: E14 mESC

growth_protocol: mESC E14 cells were maintained in DMEM supplemented with 15% FBS (Cytiva, SH30910.03), 1% MEM NEAA (Gibco, 11140-050), 0.1% Beta-Mercaptoethanol (LifeTech, 21985-023), 106 U/ml LIF (MiltenyiBiotec, 130-095-775) and 100 U/ml Penicillin-Streptomycin (Gibco, 15140122) at 37oC and 5% CO2.

extract_protocol:
After partial RNase I digestion of cell lysates, immunoprecipitation was performed using anti-Flag or anti-PABPC1 antibodies, followed by 3' adapter ligation, SDS PAGE, and transfer of protein-RNA complexes to a nitrocellulose membrane from which RNA was extracted in the presence of proteinase K.
iCLIP libraries were constructed following the protocol described in Buchbender et al (Methods, 2020; PMID: 31610236)

value: E14 mESC

value: Embryonic stem cell

value: stably expressing Flag-tagged Rpp21


title: 1123_BXD84/RwwJ_F

description:
Library name: 1123_BXD84/RwwJ_F
1123

value: female


title: RNA-seq synNANOS over expression, BR1

description:
Library name: ART_L31
FL-OE_se_counts_20241104_REVISED.csv


title: 1129_BXD48/RwwJ_M

description:
Library name: 1129_BXD48/RwwJ_M
1129

value: male


title: Rpp21-rep3

description: Library name: Rpp21-rep3


title: 1121_BXD74/RwwJ_M

description:
Library name: 1121_BXD74/RwwJ_M
1121


title: 1118_BXD45/RwwJ_M

description:
Library name: 1118_BXD45/RwwJ_M
1118


title: RNA-seq MCP alone over expression, BR2

description:
Library name: ART_L30
FL-OE_se_counts_20241104_REVISED.csv

value: RNA-seq after 2 days of overexpression of MCP alone


title: Rpp21-rep2

description: Library name: Rpp21-rep2


title: RNA-seq MCP alone over expression, BR1

description:
Library name: ART_L29
FL-OE_se_counts_20241104_REVISED.csv


title: 1116_BXD45/RwwJ_F

description:
Library name: 1116_BXD45/RwwJ_F
1116


title: 1109_C3H/HeJ_F

description:
Library name: 1109_C3H/HeJ_F
1109


title: RNA-seq CPEB2 full-length overexpression, BR1

description:
Library name: ART_L35
FL-OE_se_counts_20241104_REVISED.csv

value: RNA-seq after 2 days of overexpression of full-length CPEB2


title: MCP-NANOS H3K9me3 C+R R2

description: Library name: ART_L28

data_processing:
HT-Recruit: https://github.com/bintulab/HT-recruit-Analyze/tree/main/Scripts; sequences were aligned to a reference library fasta using bowtie, then counts in each fraction were normalized and used to create log2 ratios of each library member in the unbound:bound samples
Cut&Run: https://github.com/bintulab/Spreading_Lensch_2022/tree/main/CUT%26RUN%20Analysis; reads were aligned to a custom human genome containing reporter locus using bowtie2, then duplicate reads were removed with Picard. Bedgraph files were generated using bedtools and normalized using total counts per sample (CPM)
RNA-seq: https://github.com/bintulab/Viral_Ludwig_2022/tree/main/final_April-2023/RNA-seq%20Scripts; reads were aligned to a reference transcriptome with hisat2, then samtools was used to convert SAM --> BAM --> sorting --> indexing steps. Differential expression analysis and downstream plotting was performed using DESeq2 from Bioconductor
Assembly: hg38 genome/transcriptome for Cut&Run + RNA-seq; custom library indices for HT-recruit
Supplementary files format and content: HT-Recruit: comma-delimited text file with raw counts for each of four samples included in an HT-Recruit assay (Unbound fraction, replicate 1; Bound fraction, replicate 1; Unbound fraction, replicate 2; Bound fraction, replicate 2)
Supplementary files format and content: Cut&Run: bedGraph files with read density per genomic location for each sample
Supplementary files format and content: RNA-seq: comma-delimited text file with raw read counts for each overexpression/RNA-seq sample
Library strategy: CUT&Run

value: CUT&RUN for H3K9me3 after 2 days of reporter recruitment with MCP-NANOS1_003


title: 1106_BXD60/RwwJ_M

description:
Library name: 1106_BXD60/RwwJ_M
1106


title: 14-118, 2N, ChP, Batch 1, Medial Septal Neurons

description: Library name: 14-118

value: Brain, basal forebrain

value: cholinergic neurons

value: Batch 1


title: 1269_NZW/LacJ_M

description:
Library name: 1269_NZW/LacJ_M
1269

value: subcutaneous adipose

value: NZW/LacJ


title: MCP-NANOS H3K9me3 C+R R1

description: Library name: ART_L27

value: CML lymphoblast


title: Rpp14-rep4

description: Library name: Rpp14-rep4

value: stably expressing Flag-tagged Rpp14


title: 1093_BXD87/RwwJ_F

description:
Library name: 1093_BXD87/RwwJ_F
1093


title: 1096_BXD87/RwwJ_M

description:
Library name: 1096_BXD87/RwwJ_M
1096


title: 1099_BXD55/RwwJ_F

description:
Library name: 1099_BXD55/RwwJ_F
1099


title: Rpp14-rep2

description: Library name: Rpp14-rep2


title: MCP-KRAB d1 H3K9me3 C+R R2

description: Library name: ART_L26

value: WT

value: CUT&RUN for H3K9me3 after 1 day of reporter recruitment with MCP-KRAB


title: MCP-KRAB d1 H3K9me3 C+R R1

description: Library name: ART_L25


title: Rpp14-rep1

description: Library name: Rpp14-rep1

value: E14 mESC


title: 1080_BXD75/RwwJ_M

description:
Library name: 1080_BXD75/RwwJ_M
1080


title: MCP-KRAB d0 H3K9me3 C+R R2

description: Library name: ART_L24

value: CUT&RUN for H3K9me3 before reporter recruitment with MCP-KRAB


title: 1087_BXD55/RwwJ_M

description:
Library name: 1087_BXD55/RwwJ_M
1087


title: 1076_BXD84/RwwJ_M

description:
Library name: 1076_BXD84/RwwJ_M
1076


title: Pop5_rep4

description: Library name: Pop5_rep4

value: Embryonic stem cell

value: stably expressing Flag-tagged Pop5


title: 1113_BXD64/RwwJ_M

description:
Library name: 1113_BXD64/RwwJ_M
1113

value: male


title: Rpp21-rep1

description: Library name: Rpp21-rep1

value: stably expressing Flag-tagged Rpp21


title: 1066_BXD71/RwwJ_M

description:
Library name: 1066_BXD71/RwwJ_M
1066


title: 1068_BXD74/RwwJ_F

description:
Library name: 1068_BXD74/RwwJ_F
1068

value: female


title: Pop5_rep3

description: Library name: Pop5_rep3


title: Pop5_rep2

description: Library name: Pop5_rep2


title: 1063_BXH8/TyJ_F

description:
Library name: 1063_BXH8/TyJ_F
1063


title: 1059_BXH8/TyJ_M

description:
Library name: 1059_BXH8/TyJ_M
1059


title: rTetR-KRAB H3K9me3 C+R R2

description: Library name: ART_L22

value: CUT&RUN for H3K9me3 after 1 day of reporter recruitment with rTetR-KRAB


title: rTetR-KRAB H3K9me3 C+R R1

description: Library name: ART_L21


title: 1103_BXD60/RwwJ_F

description:
Library name: 1103_BXD60/RwwJ_F
1103


title: Rpp14-rep3

description: Library name: Rpp14-rep3


title: 1057_BXD50/RwwJ_M

description:
Library name: 1057_BXD50/RwwJ_M
1057


title: Pop5_rep1

description: Library name: Pop5_rep1


title: 1055_BXD50/RwwJ_F

description:
Library name: 1055_BXD50/RwwJ_F
1055


title: 5' 7 SL RBP Hit Lib Screen R2 Bound

description:
Library name: ART_L20
RBP-HitLib_AT209_reseq_combo.csv

value: High-throughput recruitment assay to measure the effects on reporter RNA expression from tethering a 3,000 member library to a reporter RNA with 7 MS2 stem-loops in the 5' UTR.


title: 1054_BXH22/KccJ_F

description:
Library name: 1054_BXH22/KccJ_F
1054


title: Nepro-rep4

description: Library name: Nepro-rep4

value: stably expressing Flag-tagged Nepro


title: 1043_BXD79/RwwJ_M

description:
Library name: 1043_BXD79/RwwJ_M
1043


title: 1048_BXD62/RwwJ_F

description:
Library name: 1048_BXD62/RwwJ_F
1048


title: 5' 7 SL RBP Hit Lib Screen R2 Unbound

description:
Library name: ART_L19
RBP-HitLib_AT209_reseq_combo.csv


title: 5' 7 SL RBP Hit Lib Screen R1 Bound

description:
Library name: ART_L18
RBP-HitLib_AT209_reseq_combo.csv


title: Nepro-rep3

description: Library name: Nepro-rep3


title: 1088_BXD70/RwwJ_F

description:
Library name: 1088_BXD70/RwwJ_F
1088


title: 1038_129X1/SvJ_M

description:
Library name: 1038_129X1/SvJ_M
1038


title: MCP-KRAB d0 H3K9me3 C+R R1

description: Library name: ART_L23


title: 1029_BXD64/RwwJ_F

description:
Library name: 1029_BXD64/RwwJ_F
1029


title: 5' 7 SL RBP Hit Lib Screen R1 Unbound

description:
Library name: ART_L17
RBP-HitLib_AT209_reseq_combo.csv


title: 1027_BXD44/RwwJ_M

description:
Library name: 1027_BXD44/RwwJ_M
1027


title: 1049_BXD62/RwwJ_M

description:
Library name: 1049_BXD62/RwwJ_M
1049


title: Nepro-rep1

description: Library name: Nepro-rep1


title: 946_BXD43/RwwJ_F

description:
Library name: 946_BXD43/RwwJ_F
946


title: 941_BXD66/RwwJ_M

description:
Library name: 941_BXD66/RwwJ_M
941


title: DNA RBP Hit Lib Screen R2 Unbound

description:
Library name: ART_L16
JT126_RBP_Hit_combo.csv

value: High-throughput recruitment assay to measure the effects on reporter RNA expression from tethering a 3,000 member library to a reporter DNA with 9x TetO sites in the proximal enhancer.


title: DNA RBP Hit Lib Screen R2 Bound

description:
Library name: ART_L15
JT126_RBP_Hit_combo.csv


title: 951_BXD75/RwwJ_F

description:
Library name: 951_BXD75/RwwJ_F
951

value: subcutaneous adipose


title: M6_WT_I

city: St. Louis

first: Joanna

last: Jankowsky

state: MO

address: 660 S. Euclid Ave.

department: Neuroscience

institute: Washington University in St. Louis

data_processing:
Read quality control, mapping, and abundance measurements  were performed by Novogene (Beijing, CN).
Gene counts were normalized and analyzed using the EdgeR pipeline (v3.38.4) in R.
Assembly: mm10
Supplementary files format and content: Comma separated variable file of matrix table with raw gene counts for every gene and every sample, not normalized for library size

source_name: Brain

extract_protocol:
Brains were removed, flash frozen on dry ice, and RNA was harvested using an RNeasy kit (Qiagen, cat # 74106).
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene (Beijing, CN)

value: Brain

value: M

tag: age


title: M6_Tau_I

value: MAPT P301L PS19


title: 925_BXD79/RwwJ_F

description:
Library name: 925_BXD79/RwwJ_F
925


title: M6_KI_Tau

value: TMEM106b T186S KI x MAPT P301L PS19


title: 912_C3H/HeJ_M

description:
Library name: 912_C3H/HeJ_M
912


title: DNA RBP Hit Lib Screen R1 Unbound

description:
Library name: ART_L14
JT126_RBP_Hit_combo.csv

value: CML lymphoblast

value: WT


title: 905_BXD66/RwwJ_F

description:
Library name: 905_BXD66/RwwJ_F
905


title: Nepro-rep2

description: Library name: Nepro-rep2

value: E14 mESC


title: 1032_BXD73/RwwJ_M

description:
Library name: 1032_BXD73/RwwJ_M
1032


title: 893_BXD49/RwwJ_F

description:
Library name: 893_BXD49/RwwJ_F
893


title: 884_BXD49/RwwJ_M

description:
Library name: 884_BXD49/RwwJ_M
884


title: M5_WT_I


title: 901_DBA/2J_M

description:
Library name: 901_DBA/2J_M
901


title: 867_BXD43/RwwJ_M

description:
Library name: 867_BXD43/RwwJ_M
867


title: 3' RBP Hit Lib Screen R2 Unbound

description:
Library name: ART_L12
AT031_RBP_Hit_combo.csv

value: High-throughput recruitment assay to measure the effects on reporter RNA expression from tethering a 3,000 member library to a reporter RNA with 24 MS2 stem-loops in the 3' UTR.


title: M5_Tau_I


title: 857_AXB19a/PgnJ_F

description:
Library name: 857_AXB19a/PgnJ_F
857


title: M6_KI

value: KI

value: TMEM106b T186S KI


title: 881_BXD51/RwwJ_F

description:
Library name: 881_BXD51/RwwJ_F
881


title: M5_KI_Tau


title: 3' RBP Hit Lib Screen R1 Unbound

description:
Library name: ART_L10
AT031_RBP_Hit_combo.csv


title: 3' RBP Hit Lib Screen R1 Bound

description:
Library name: ART_L9
AT031_RBP_Hit_combo.csv


title: 878_BXD51/RwwJ_M

description:
Library name: 878_BXD51/RwwJ_M
878

value: male


title: 886_BXD69/RwwJ_F

description:
Library name: 886_BXD69/RwwJ_F
886

value: female


title: 846_BXD38/TyJ_M

description:
Library name: 846_BXD38/TyJ_M
846


title: M4_WT_I


title: 838_BXD12/TyJ_M

description:
Library name: 838_BXD12/TyJ_M
838


title: 907_MA/MyJ_M

description:
Library name: 907_MA/MyJ_M
907

value: MA/MyJ


title: DNA RBP Hit Lib Screen R1 Bound

description:
Library name: ART_L13
JT126_RBP_Hit_combo.csv


title: 3' RBP Lib Screen R2 Bound

description:
Library name: ART_L4
RBP_Lib_AT122_combo.csv

value: High-throughput recruitment assay to measure the effects on reporter RNA expression from tethering a 30,000 member library to a reporter RNA with 24 MS2 stem-loops in the 3' UTR.


title: 848_BXD11/TyJ_M

description:
Library name: 848_BXD11/TyJ_M
848


title: M5_KI


title: M4_Tau_I


title: 5' RBP Lib Screen R1 Unbound

description: Library name: ART_L5

value: High-throughput recruitment assay to measure the effects on reporter RNA expression from tethering a 30,000 member library to a reporter RNA with 24 MS2 stem-loops in the 5' UTR.


title: 3' RBP Hit Lib Screen R2 Bound

description:
Library name: ART_L11
AT031_RBP_Hit_combo.csv


title: 870_BXD56/RwwJ_M

description:
Library name: 870_BXD56/RwwJ_M
870


title: 837_BXD56/RwwJ_F

description:
Library name: 837_BXD56/RwwJ_F
837


title: 3' RBP Lib Screen R2 Unbound

description:
Library name: ART_L3
RBP_Lib_AT122_combo.csv


title: 850_C57BL/6J_M

description:
Library name: 850_C57BL/6J_M
850


title: 834_BXA2/PgnJ_F

description:
Library name: 834_BXA2/PgnJ_F
834


title: M4_KI_Tau


title: 3' RBP Lib Screen R1 Bound

description:
Library name: ART_L2
RBP_Lib_AT122_combo.csv


title: 823_BXA7/PgnJ_M

description:
Library name: 823_BXA7/PgnJ_M
823


title: M3_WT_O


title: 3' RBP Lib Screen R1 Unbound

description:
Library name: ART_L1
RBP_Lib_AT122_combo.csv


title: 812_CXB13/HiAJ_M

description:
Library name: 812_CXB13/HiAJ_M
812


title: 798_BXA7/PgnJ_F

description:
Library name: 798_BXA7/PgnJ_F
798


title: 808_BTBR T<+> tf/J_M

description:
Library name: 808_BTBR T_+_ tf/J_M
808

value: BTBR T<+> tf/J


title: M4_KI


title: KDM6A_786O_sgKDM6A_Normoxia_rep2

city: Beijing

first: Hua

last: Wang

address: 38 Xueyuan Rd

country: China

institute: Peking University

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 used for basecalling.
FASTQ reads were mapped to the GRCm38 (mm10) genome using Bowtie2 (v2.4.1) using the standard settings.
DeepTools (v3.3.0) was used to generate occupancy heat maps, and the resulting normalized occupancy matrix was used as input for custom R scripts to generate average profile plots and to calculate processivity indices.
Assembly: hg38
Supplementary files format and content: bw
Supplementary files format and content: All other processed data is made available as supplementary files to the manuscript

source_name: human cancer cell

growth_protocol: Cells were cultured in RPMI supplemented with 10% FBS v/v (Gibco), 100 U ml-1 penicillin and 100 µg ml-1 streptomycin (Pen/Strep) (Gibco).

extract_protocol:
Cells were cross-linked by the addition of 1% formaldehyde (Sigma-Aldrich, 252549-1L) in the dish for 10 minutes at RT before quenching with 0.125 M glycine. The fixed cells were washed with PBS and resuspended in SDS buffer (100 mM NaCl, 50 mM Tris-HCl pH 8.0, 5 mM EDTA, 0.5% SDS, 1x protease inhibitor cocktail from Roche). The resulting nuclei were spin down, resuspended in the immunoprecipitation buffer at 1 mL per 16 million cells (SDS buffer and Triton Dilution buffer (100 mM NaCl, 100 mM Tris-HCl pH 8.0, 5 mM EDTA, 5% Triton X-100) mixed in 2:1 ratio with the addition of 1x protease inhibitor cocktail from Roche) and processed on a Bioruptor Plus Sonicator (Diagenode) to achieve an average fragment length of 200-300 bps.
Libraries were constructed using NEBNext Ultra II DNA Library prep kit (NEB, E7645L).

treatment_protocol: LentiCas9-Blast was a gift from Feng Zhang (Addgene #52962) for KDM6A KO.

value: human cancer cell

tag: chip antibody


title: 801_BXD19/TyJ_M

description:
Library name: 801_BXD19/TyJ_M
801

value: subcutaneous adipose


title: 784_BALB/cJ_M

description:
Library name: 784_BALB/cJ_M
784

value: BALB/cJ


title: KDM6A_786O_sgKDM6A_Normoxia_rep1


title: M3_WT_I

value: Brain

value: M


title: KDM6A_786O_sgCtr_Normoxia_rep2

value: sgCtr


title: M3_Tau_I

value: MAPT P301L PS19


title: 765_BXD31/TyJ_M

description:
Library name: 765_BXD31/TyJ_M
765


title: 793_BTBR T<+> tf/J_F

description:
Library name: 793_BTBR T_+_ tf/J_F
793


title: M3_Tau_O


title: 772_SEA/GnJ_M

description:
Library name: 772_SEA/GnJ_M
772

value: SEA/GnJ


title: 780_BALB/cJ_F

description:
Library name: 780_BALB/cJ_F
780


title: KDM6A_786O_sgCtr_Normoxia_rep1


title: 760_AXB19/PgnJ_F

description:
Library name: 760_AXB19/PgnJ_F
760


title: 762_NOD/ShiLtJ_M

description:
Library name: 762_NOD/ShiLtJ_M
762

value: NOD/ShiLtJ


title: 757_AXB19/PgnJ_M

description:
Library name: 757_AXB19/PgnJ_M
757


title: Input_786O_sgCtr_Normoxia

value: Input


title: 748_CXB11/HiAJ_F

description:
Library name: 748_CXB11/HiAJ_F
748


title: M3_KO_Tau

value: TMEM106b KO x MAPT P301L PS19


title: M3_KI_Tau

value: TMEM106b T186S KI x MAPT P301L PS19


title: 745_BXD14/TyJ_M

description:
Library name: 745_BXD14/TyJ_M
745

value: male


title: M3_KO

value: KO

value: TMEM106B KO


title: 716_BXD40/TyJ_F

description:
Library name: 716_BXD40/TyJ_F
716

value: female


title: 816_BXA2/PgnJ_M

description:
Library name: 816_BXA2/PgnJ_M
816


title: M2_WT_I


title: Input_786O_sgKDM6A_Normoxia


title: M2_Tau_O


title: 754_BXH9/TyJ_M

description:
Library name: 754_BXH9/TyJ_M
754


title: 706_BXD6/TyJ_F

description:
Library name: 706_BXD6/TyJ_F
706


title: M3_KI

value: KI

value: TMEM106b T186S KI


title: 699_BXD24/TyJ-Cep290<rd16>/J_F

description:
Library name: 699_BXD24/TyJ-Cep290_rd16_/J_F
699

value: subcutaneous adipose


title: H3K27me3_CST_786O_sgKDM6A_Normoxia

value: human cancer cell


title: 741_BXD14/TyJ_F

description:
Library name: 741_BXD14/TyJ_F
741


title: 740_BXH6/TyJ_M

description:
Library name: 740_BXH6/TyJ_M
740


title: M2_WT_O

value: Brain


title: 703_BXD24/TyJ-Cep290<rd16>/J_M

description:
Library name: 703_BXD24/TyJ-Cep290_rd16_/J_M
703


title: 731_DBA/2J_F

description:
Library name: 731_DBA/2J_F
731


title: 714_BXD12/TyJ_F

description:
Library name: 714_BXD12/TyJ_F
714


title: M2_Tau_I

value: M


title: 691_CBA/J_M

description:
Library name: 691_CBA/J_M
691

value: CBA/J


title: 692_BXD21/TyJ_F

description:
Library name: 692_BXD21/TyJ_F
692


title: 686_CBA/J_F

description:
Library name: 686_CBA/J_F
686


title: 443_BXD34/TyJ_F

description:
Library name: 443_BXD34/TyJ_F
443


title: M2_KO


title: H3K27me3_CST_786O_sgCtr_Normoxia

value: sgCtr


title: 187_CXB11/HiAJ_M

description:
Library name: 187_CXB11/HiAJ_M
187


title: 191_BXD20/TyJ_M

description:
Library name: 191_BXD20/TyJ_M
191


title: M2_KI


title: 179_BXD8/TyJ_M

description:
Library name: 179_BXD8/TyJ_M
179


title: M2_KI_Tau


title: M2_KO_Tau


title: 174_BXD36/TyJ_M

description:
Library name: 174_BXD36/TyJ_M
174


title: Testis_Immature-1_Genotype-LL_Rep3

type: RNA

city: Helsinki

first: Ehsan

middle: Pashay

last: Ahi

address: Biocenter 1, Viikinkaari 9

country: Finland

institute: University of Helsinki

description: Nanostring data analysis on mRNA isolated from the Testis of Atlantic salmon (S-salar) in different maturation status with different vgll3 genotypes (EE or LL)

hyb_protocol: One hundred nanograms of total RNA were hybridized with the NanoString Technologies nCounter a Custom made Panel containing 342 unique pairs of 100bp reporter probes and biotin-labeled capture probes, including internal reference controls. Overnight hybridization occurred for 20 hours at 65°C, then reactions were held at 4°C until they were placed on the nCounter Prep Station. Wash protocol: Removal of excess probes with magnetic bead purification was performed on the nCounter Prep Station (software v4.0.11.2) on the High Sensitivity assay. Briefly, the probe-mRNA structure was affinity purified by its 3’ end to remove excess reporter probes, then by its 5’ end to remove excess capture probes. Once unbound probes were washed away, the tripartite structure was bound to the streptavidin-coated cartridge by the biotin capture probe, aligned by an electric current (negative to positive), and immobilized. Photobleaching and flurophore degradation was prevented with the addition of SlowFade.

scan_protocol: After hybridization, the sample strip was transferred to the nCounter Prep Station for purification and immobilization in a sample cartridge. After immobilization, the cartridge was analyzed with the nCounter Digital Analyzer by taking images of the immobilized fluorescent reporters. The number of images taken corresponded to the number of reporters counted. The raw count data was exported as a csv file.

data_processing: RCC files containing raw counts for 342 genes provided from nanostring were loaded into nSolver Analysis Software 4.0 and normalized for housekeeping genes and positive controls.

label: No label

organism: Salmo salar

source_name: Atlantic salmon Testis

label_protocol: Not applicable

growth_protocol: Described in Debes, P. V., N. Piavchenko, J. Erkinaro, and C. R. Primmer, 2020 Genetic growth potential, rather than phenotypic size, predicts migration phenotype in Atlantic salmon. Proc. R. Soc. B Biol. Sci. 287: 20200867.

extract_protocol: RNA was extracted from whole testis using a NucleoSpin RNA kit (Macherey-Nagel GmbH & Co. KG). The collected samples were transferred to tubes containing 1.4 mm ceramic beads from Omni International, along with Buffer RA1 and DDT (350 µl of RA1 and 3.5 µl of 1M DDT). Homogenization was performed using the Bead Ruptor Elite (Omni International) at a frequency of 30 Hz for a total of 2 min (in 6 cycles of 20 s each). The subsequent RNA extraction procedures adhered to the guidelines provided by the manufacturer, with the kit also including an integrated DNase stage to eliminate any remaining genomic DNA (gDNA). At the conclusion of this process, the RNA extracted from each individual sample was eluted using 50 µl of nuclease-free water. To assess RNA quantity, measurements were taken using the NanoDrop ND-1000 instrument (Thermo Scientific, Wilmington, DE, USA), while the quality of the RNA was evaluated through the employment of the 2100 BioAnalyzer system (Agilent Technologies, Santa Clara, CA, USA). The RNA integrity number (RIN) exceeded 7 for all samples.

treatment_protocol: Not applicable

value: Whole Testis

value: Male

tag: maturity

value: LL


title: 695_CXB6/ByJ_F

description:
Library name: 695_CXB6/ByJ_F
695


title: 125_BXD27/TyJ_F

description:
Library name: 125_BXD27/TyJ_F
125


title: Testis_Immature-2_Genotype-EE_Rep4

value: EE


title: Testis_Immature-1_Genotype-LL_Rep4


title: Testis_Mature_Genotype-LL_Rep4

value: Mature


title: M1_WT_O


title: Testis_Immature-2_Genotype-LL_Rep4


title: 143_PL/J_M

description:
Library name: 143_PL/J_M
143

value: PL/J

value: male


title: 119_BXA24/PgnJ_M

description:
Library name: 119_BXA24/PgnJ_M
119


title: Testis_Immature-2_Genotype-EE_Rep3


title: 121_BXD40/TyJ_M

description:
Library name: 121_BXD40/TyJ_M
121


title: M1_WT_I


title: Testis_Mature_Genotype-EE_Rep4


title: 55_FVB/NJ_M

description:
Library name: 55_FVB/NJ_M
55

value: FVB/NJ


title: 115_FVB/NJ_F

description:
Library name: 115_FVB/NJ_F
115

value: female


title: M1_Tau_O

value: MAPT P301L PS19


title: 24_C57BL/6J_F

description:
Library name: 24_C57BL/6J_F
24


title: muscle, trained, 72h post exercise, rep 3

city: Basel

first: Laura

middle: Maria

last: de Smalen

state: Basel-Stadt

address: Spitalstrasse 41

department: Biozentrum

country: Switzerland

institute: University of Basel

description:
Library name: Trained_72h_3
RNASeq

data_processing:
Reads were mapped to the mouse genome assembly GRCm39 using STAR v2.7.9.
Counts were quantified using salmon v1.5.0.
Differential expression analysis was performed with DESeq2 v3.16.
Assembly: GRCm39
Supplementary files format and content: RNA-seq_Count_Matrix_TPM_allconditions.tsv

source_name: quadriceps muscle

extract_protocol:
M. quadriceps muscles were crushed and tissue was further homogenized using Lysing matrix D tubes (MP Biomedicals) in TRI Reagent (Sigma). RNA was isolated and purified using RNeasy columns (Qiagen).
Libraries were prepared from total RNA using a TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: Mice underwent endurance training for 12 weeks by voluntary wheel running (Trained), or no training (Untrained). Untrained and Trained mice underwent one exhaustive bout of exercise and were sacrificed at 0h, 6h or 72h post-exercise. Sedentary mice performed no exercise.

value: quadriceps muscle

value: bulk tissue

value: wildtype

value: trained 72h post-exercise


title: muscle, trained, 72h post exercise, rep 2

description:
Library name: Trained_72h_2
RNASeq


title: M1_Tau_I

value: Brain

value: M


title: Testis_Immature-2_Genotype-LL_Rep3


title: M1_KO

value: KO

value: TMEM106B KO


title: muscle, trained, 72h post exercise, rep 1

description:
Library name: Trained_72h_1
RNASeq


title: Testis_Immature-2_Genotype-LL_Rep2

value: Whole Testis

value: Male


title: Testis_Mature_Genotype-LL_Rep3

value: LL


title: Testis_Mature_Genotype-LL_Rep1

value: Mature


title: Testis_Mature_Genotype-LL_Rep2


title: muscle, trained, 6h post exercise, rep 3

description:
Library name: Trained_6h_3
RNASeq

value: trained 6h post-exercise


title: muscle, trained, 6h post exercise, rep 2

description:
Library name: Trained_6h_2
RNASeq


title: M1_KI

value: KI

value: TMEM106b T186S KI


title: muscle, trained, 6h post exercise, rep 1

description:
Library name: Trained_6h_1
RNASeq


title: M1_KI_Tau

value: TMEM106b T186S KI x MAPT P301L PS19


title: muscle, trained, 0h post exercise, rep 2

description:
Library name: Trained_0h_2
RNASeq

value: trained 0h post-exercise


title: muscle, trained, 0h post exercise, rep 3

description:
Library name: Trained_0h_3
RNASeq

value: quadriceps muscle


title: muscle, trained, 0h post exercise, rep 1

description:
Library name: Trained_0h_1
RNASeq

value: bulk tissue


title: muscle, untrained, 72h post exercise, rep 3

description:
Library name: Untrained_72h_3
RNASeq

value: wildtype

value: untrained 72h post-exercise


title: M1_KO_Tau

value: Brain

value: TMEM106b KO x MAPT P301L PS19


title: muscle, untrained, 72h post exercise, rep 2

description:
Library name: Untrained_72h_2
RNASeq


title: muscle, untrained, 6h post exercise, rep 3

description:
Library name: Untrained_6h_3
RNASeq

value: untrained 6h post-exercise


title: Testis_Immature-1_Genotype-EE_Rep3

value: EE


title: Testis_Immature-1_Genotype-LL_Rep2

value: Whole Testis


title: Testis_Immature-1_Genotype-EE_Rep4

value: Male


title: muscle, untrained, 6h post exercise, rep 2

description:
Library name: Untrained_6h_2
RNASeq


title: F6_WT_I

value: F


title: muscle, untrained, 6h post exercise, rep 1

description:
Library name: Untrained_6h_1
RNASeq


title: F6_Tau_I

value: MAPT P301L PS19


title: muscle, untrained, 0h post exercise, rep 3

description:
Library name: Untrained_0h_3
RNASeq

value: untrained 0h post-exercise


title: muscle, untrained, 0h post exercise, rep 2

description:
Library name: Untrained_0h_2
RNASeq


title: muscle, sedentary, rep 3

description:
Library name: Sedentary_3
RNASeq

value: sedentary


title: muscle, untrained, 0h post exercise, rep 1

description:
Library name: Untrained_0h_1
RNASeq


title: F6_KI_Tau


title: Testis_Immature-1_Genotype-EE_Rep1


title: Testis_Immature-1_Genotype-EE_Rep2


title: Testis_Mature_Genotype-EE_Rep3

value: Mature


title: Testis_Immature-2_Genotype-LL_Rep1

value: LL


title: F7_KI_Tau

value: TMEM106b T186S KI x MAPT P301L PS19


title: muscle, sedentary, rep 1

description:
Library name: Sedentary_1
RNASeq

value: quadriceps muscle


title: F5_WT_I


title: muscle, sedentary, rep 2

description:
Library name: Sedentary_2
RNASeq

value: bulk tissue


title: muscle, untrained, 72h post exercise, rep 1

description:
Library name: Untrained_72h_1
RNASeq

value: wildtype


title: Testis_Immature-1_Genotype-LL_Rep1


title: Testis_Immature-2_Genotype-EE_Rep2


title: F5_KI

value: KI

value: TMEM106b T186S KI


title: F5_KI_Tau

value: Brain


title: F4_WT_I


title: Testis_Immature-2_Genotype-EE_Rep1


title: F4_Tau_I


title: Stem Node, Top Node, Rep 3

city: Columbia

first: Ashley

middle: N

last: Hostetler

address: 1201 Rollins St

institute: University of Missouri

description: Library name: P6N3

data_processing:
Read quality was assessed using FastQC (Galaxy version 0.74+galaxy1).
Raw reads were trimmed and filtered: PolyA, PolyG, and Illumina sequencing adapters were removed. Reads shorter than 20 nucleotides were discarded using Cutadapt (Galaxy version 4.9+galaxy1).
Reads were filtered using Fastp (Galaxy version 0.24.0+galaxy3) to remove those with ≥30% of bases having a Phred score <28.
High-quality reads were mapped to the Sorghum bicolor BTx623 v3.1.1 reference genome (McCormick et al., 2018) using HISAT2 (Galaxy version 2.2.1+galaxy1).
Uniquely mapped reads were quantified using featureCounts (Galaxy version 2.0.8+galaxy0).
Gene-level read counts were normalized using edgeR (version 4.4.2).
Assembly: Sorghum bicolor BTx623 v3.1.1
Supplementary files format and content: .tabular files contain gene counts for each individual sample

organism: Sorghum bicolor

source_name: Node3 - Third node above soil line

growth_protocol: Three Sorghum bicolor BTx623 seeds were planted in 3-gallon air pruning pots (Superoots Air-Pots) with BK55 Promix potting soil. Target growth conditions were 26.7℃ day/21.1℃ night with 16 h supplemental lighting provided by overhead HPS lamps (50 klux, PPFD ~ 925.93 μmol/m-2/s-1). From planting until tissue collection, plants were consistently watered so the soil remained wet and fertilized using a Dosatron (Ingersoll Rand) loaded with concentrated Peters Excel 15-5-15 fertilizer dispensed at a rate of 300 ppm N. At 36 days after planting (dap), when plants were at the V7-V8 stage, leaves were stripped from plant stems, and nodal tissue from the three lowest stem nodes above the soil line were collected. Stem nodes were dissected with a razor blade and the tissue was flash frozen in liquid nitrogen and stored at -80°C until RNA extractions.

extract_protocol:
Total RNA was isolated using the Quick-RNA Plant Miniprep Kit (Zymo Research) according to the manufacturer’s protocol.
Forward stranded 3’RNA-sequencing libraries were prepared using the 3’RNA-sequencing protocol of the YourSeq (FT & 3’DGE) Strand-Specific mRNA Library Prep Kit (Active Motif).

value: Node3 - Third node above soil line


title: Stem Node, Middle Node, Rep 3

description: Library name: P6N2

source_name: Node2 - Second node above soil line

value: Node2 - Second node above soil line


title: Testis_Mature_Genotype-EE_Rep1

value: Whole Testis

value: EE


title: Testis_Mature_Genotype-EE_Rep2

value: Male


title: Stem Node, Top Node, Rep 2

description: Library name: P4N3


title: F4_KI_Tau

value: F


title: F4_KI


title: F3_WT_O


title: Stem Node, Bottom Node, Rep 3

description: Library name: P6N1

source_name: Node1 - First node above soil line

value: Node1 - First node above soil line


title: Stem Node, Middle Node, Rep 2

description: Library name: P4N2


title: F3_WT_I


title: F5_Tau_I

value: MAPT P301L PS19


title: F3_Tau_O


title: F3_Tau_I


title: Mouse hippocampal microdissected CA1 region, 60min post LTP, biological replicate 3

city: Austin

first: Vighnesh

middle: Vijay

last: Ghatpande

state: Austin

address: 2500 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

description:
Library name: 20240339_WT_CA1_60min_ITP_E
CA1_60min_biol rep3

data_processing:
Ribosome profiling data were processed using RiboFlow. We extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools with the following parameters: 'umi_tools extract -p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex'. The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step. We clipped the 3’ adapter AAAAAAAAAACAAAAAAAAAA using cutadapt with the parameters “-a AAAAAAAAAACAAAAAAAAAA --overlap=4 --trimmed-only --maximum-length=56 --minimum-length=31 --quality-cutoff=28”. After UMI extraction and adapter trimming, reads were aligned to ribosomal and transfer RNAs using Bowtie2 with the parameters "-L 15 --no-unal --norc". The unaligned reads were mapped to a manually-curated transcriptome with the parameters "-L 15 --norc --no-unal". We retained alignments with mapping quality greater than 10 followed by deduplication using UMI-tools. As the last step, .ribo files are created. Supplementary files format and content: .ribo HDF5-formatted files contain ribosome occupancy at nucleotide resolution for lengths from 21 to 40. See https://ribopy.readthedocs.io/en/latest/ribo_file_format.html for a detailed description of the ribo format.
Assembly: Assembly: A curated transcriptome of primary transcripts was used for alignment. Reference files for use with RiboFlow are located at https://github.com/ribosomeprofiling/yeast_reference
Supplementary files format and content: .ribo HDF5-formatted files contain ribosome occupancy at nucleotide resolution for lengths from 21 to 40. See https://ribopy.readthedocs.io/en/latest/ribo_file_format.html for a detailed description of the ribo format.
Library strategy: Ribo-Seq

source_name: hippocampus

extract_protocol:
Flash-frozen single embryos were thawed on ice, 5µL of ITP lysis buffer (20 mM BisTris pH 7.2, 1.0% Triton-X100, 5mM MgCl2, 2.5 mM CaCl2, 100mM NaCl, 1 mM DTT, 0.1 mg/ml cycloheximide) was added to the droplet containing the embryo on the wall of the tube. Flash-frozen microdissected hippocampal tissue was thawed on ice and 10uL of lysis buffer (1% TritonX100, 50mM MgCl2, 0.1 mg/mL cycloheximide) was added to it. The tissue was homogenized with a pestle () until the solution was visibly clear. 4uL of the lysate was transferred to a 0.2mL PCR tube containing 1uL of 5X ITP lysis buffer (100 mM BisTris pH 7.2, 5.0% Triton-X100, 25mM MgCl2, 12.5 mM CaCl2, 500mM NaCl, 5 mM DTT, 0.5 mg/ml cycloheximide). For both the lysates, 1µL of RNaseI diluted 1:300 in the ITP lysis buffer was added and incubated at 37°C for 30 mins. 1µL of 0.7% SDS was added to stop RNaseI followed by running the lysate on an ITP chip. Ribosome footprints were eluted by collecting the RNA fragments between 19nt and 36nt markers on the ITP chip.
Ribosome profiling libraries were made using D-Plex Small RNA-Seq Kit (Diagenode) with the following modifications, a. 0.5µL PNK enzyme (NEB) was added along with the dephosphorylation reagent, b. The TSO was diluted 1:5, c. The cDNA was amplified for 16 cycles. The resulting libraries were analyzed with the Agilent High Sensitivity DNA Kit (Agilent). Each library was mixed in equimolar proportion and cleaned up with AmpureXP beads (1.5X) and PAGE purified on a 10% PAGE. Resulting libraries were sequenced on NovaSeq 6000 SP PE.

treatment_protocol: For the mouse embryos, of the appropriate stages were treated with either 2ug/ml Harringtonine or DMSO for 30mins following which they were transferred to eppendorf tubes and flash frozen. For the mouse acute hippocampal sections, LTP was induced in areaCA1 region of the section by TBS stimulation and the induced regions were microdissected at mentioned time points. These microdissected tissues were transferred to 1.5ml eppendorf tubes and flash frozen.

value: hippocampus

value: LTP induced

tag: time


title: Mouse hippocampal microdissected CA1 region, 60min post LTP, biological replicate 2

description:
Library name: 20240339_WT_CA1_60min_ITP_D
CA1_60min_biol rep2


title: F3_KO

value: KO

value: TMEM106B KO


title: F3_KI


title: Stem Node, Bottom Node, Rep 2

description: Library name: P4N1


title: Mouse hippocampal microdissected CA1 region, 30min post LTP, biological replicate 2

description:
Library name: 20240339_WT_CA1_30min_ITP_D
CA1_30min_biol rep2


title: Mouse hippocampal microdissected CA1 region, 30min post LTP, biological replicate 3

description:
Library name: 20240339_WT_CA1_30min_ITP_E
CA1_30min_biol rep3


title: Mouse hippocampal microdissected CA1 region, 30min post LTP, biological replicate 1

description:
Library name: 20220323_WT_CA1_30min_ITP_A
CA1_30min_biol rep1


title: Stem Node, Top Node, Rep 1

description: Library name: P2N3


title: F3_KI_Tau

value: TMEM106b T186S KI x MAPT P301L PS19


title: DLD-1 cell,anti-RPB1(CUT&Tag),Rep1

city: Xiamen

first: yongyou

last: zhang

state: Fujian

address: Xiang'an South Road

institute: Xiamen University

description: Library name: DLD1_WT_anti-RPB1-Rep1

data_processing:
Raw reads were filtered to remove adapter sequences and low-quality sequences using fastp (version 0.20).
Clean reads were mapped to the mouse mm10 or human hg19 reference genome using Bowtie2 (version 2.4) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -l 10 -X 700.
Duplicate reads were removed using Picard MarkDuplicates (version 2.27). Mitochondrial reads, unmapped reads, and reads with mapping quality <30 were filtered out using SAMtools (version 1.15).
BigWig files were generated using deepTools bamCoverage (version 3.3.1) with options: --binSize 10 --normalizeUsing RPGC.
Peaks were called for each sample using MACS2 callpeak (version 2.2) with options: --bdg --SPMR --gsize hs --keepdup all --gvalue 0.05 --shift -75 --extsize 150 --nomodel --call-summits --nolambda.
Assembly: hg19,mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: colon

extract_protocol:
For cell samples, digestion followed by permeabilization is sufficient. For mouse liver tissue, 0.1-0.2 g of liver tissue was excised and washed with 2 mL of swelling buffer (10 mM Tric-HCl pH 7.5, 2 Mm MgCl2, 3 mM CaCl2, 1×Protease inhibitor cocktail). The liver was then dounced in 1 ml of swelling buffer (dounced 10 times, piston A) and incubated at 4°C for 20 min. Afterward, the liver was dounced again 20 times (piston B), and 1 mL of swelling buffer was added. The cells were filtered using a 100 μm cell strainer and spun at 400×g at 4°C for 10 min. The supernatant was removed, and the cells were resuspended in 0.5 ml of swelling buffer + 10% glycerol. Slowly vortex while adding drop by drop 0.5 mL of lysis buffer (Swelling buffer + 10% glycerol + 1% NP-40). Incubate for 5 min at 4°C and add 1.5 mL of lysis buffer. Spin at 600×g at 4°C for 5 min, remove the supernatant, and wash the nuclei again with 1.5 mL of lysis buffer. Spin at 600 g at 4°C for 5 min, remove the supernatant, and resuspend the nuclei in 1 mL of freezing buffer. Finally, the nuclei were stained with DAPI and counted.
Following cell or nucleus counting, permeabilization is performed without the addition of antibodies. The permeabilized samples are incubated with LgBiT-Tn5 or NbALFA-Tn5, and unbound proteins are subsequently removed. A transposition activation reaction is then conducted to fragment intracellular DNA, which is extracted for downstream library preparation. Indexed libraries are generated using universal i5 primers and unique barcoded i7 primers, with each sample assigned a distinct barcode. The libraries are amplified through 15 cycles of PCR, and the resulting DNA is purified for high-throughput sequencing.

value: colon

value: epithelial

value: WT


title: Mouse hippocampal microdissected CA1 region, 60min post LTP, biological replicate 1

description:
Library name: 20220323_WT_CA1_1hr_ITP_A
CA1_60min_biol rep1


title: Mouse hippocampal microdissected CA1 region, 10min post LTP, biological replicate 3

description:
Library name: 20240339_WT_CA1_10min_ITP_E
CA1_10min_biol rep3


title: Mouse hippocampal microdissected CA1 region, 10min post LTP, biological replicate 2

description:
Library name: 20240339_WT_CA1_10min_ITP_D
CA1_10min_biol rep2


title: F3_KO_Tau

value: Brain

value: TMEM106b KO x MAPT P301L PS19


title: Mouse hippocampal microdissected CA1 region, noLTP, biological replicate 3

description:
Library name: 20240339_WT_CA1_NoLTP_ITP_E
CA1_NoLTP_biol rep3

value: uninduced


title: Mouse hippocampal microdissected CA1 region, 10min post LTP, biological replicate 1

description:
Library name: 20220323_WT_CA1_10min_ITP_A
CA1_10min_biol rep1


title: SW480 cell,KI-CTCT-HiBiT,nano-Tn5_anti-HiBiT(nano-CUT&Tag),Rep2

description: Library name: SW480_CTCF-HiBiT_nano-Tn5_anti-HiBiT-Rep2

value: anti-HiBiT


title: SW480 cell,KI-CTCT-HiBiT,nano-Tn5_anti-HiBiT(nano-CUT&Tag),Rep1

description: Library name: SW480_CTCF-HiBiT_nano-Tn5_anti-HiBiT-Rep1


title: Mouse hippocampal microdissected CA1 region, noLTP, biological replicate 2

description:
Library name: 20240339_WT_CA1_NoLTP_ITP_D
CA1_NoLTP_biol rep2


title: F2_WT_I


title: Stem Node, Middle Node, Rep 1

description: Library name: P2N2

value: Node2 - Second node above soil line


title: SW480 cell,KI-CTCT-HiBiT,nano-Tn5_anti-HiBiT(nano-CUT&Tag),Rep3

description: Library name: SW480_CTCF-HiBiT_nano-Tn5_anti-HiBiT-Rep3


title: hESC3_D+O

city: Hong Kong

first: Yimeng

last: Li

address: 21 Sassoon Road, Pokfulam Hong Kong

institute: The university of Hong Kong

description:
Library name: sample 9
Column name in Counts_normalized.txt: hESC3_D+O-FPKM

data_processing:
Low-quality reads were removed by fastp with default parameters
Remaining clean reads were align to GRCh38 by hisat2 with default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: GRCh38
Supplementary files format and content: Matrix tables with raw gene counts or normalized gene counts for every gene and every sample

source_name: human endometrial stromal cells

extract_protocol:
hESCs cultured to 80%-100% confluence in 10-12 wells were digested with 300 μl of collagenase (1 mg/ml) for 30 minutes at 37℃. This was followed by a 5-minute incubation at 37℃ with 500 μl of Trypsin-EDTA and 50 μl of DNase, shaken at 1,000 rpm. The reaction was halted with 50 μl of 100% FBS. The cells were then washed with PBS and filtered through a 40 μm cell strainer to remove clumps, resulting in a single-cell suspension, which were collected into 900 μl of the RNAiso Plus solution (TaKaRa) for RNA extraction.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China), where poly(A)+ RNA was enriched with oligo(dT) beads, fragmented, and converted to double-stranded cDNA with dUTP incorporation for strand specificity. Following end repair, A-tailing, and adapter ligation, the library was PCR-amplified, circularized, and transformed into DNA nanoballs (DNBs) via rolling circle amplification. These DNBs were then sequenced on BGI's DNBSEQ-G400 platform.

value: human endometrial stromal cells

value: decidualization induction with hEO co-culture


title: Mouse hippocampal microdissected CA1 region, noLTP, biological replicate 1

description:
Library name: 20220323_WT_CA1_NoLTP_ITP_A
CA1_NoLTP_biol rep1


title: Stem Node, Bottom Node, Rep 1

description: Library name: P2N1

value: Node1 - First node above soil line


title: DLD-1 cell,anti-RPB1(CUT&Tag),Rep2

description: Library name: DLD1_WT_anti-RPB1-Rep2


title: hESC3_DEC

description:
Library name: sample 8
Column name in Counts_normalized.txt: hESC3_DEC-FPKM

value: hESCs treated with decidualization inducer


title: F2_Tau_I

value: F

value: MAPT P301L PS19


title: hESC3_CTRL

description:
Library name: sample 7
Column name in Counts_normalized.txt: hESC3_CTRL-FPKM

value: hESCs cultured alone without decidualization


title: F2_KO_Tau_corrected


title: 32 cell mouse embryo ribosome profiling, harringtonine treated, biological replicate 3

description:
Library name: 09072023_ITP_32cell_Harr_B
32cell_embryo_harringtonine_biol rep3

source_name: preimplantation embryo

value: preimplantation embryo

value: Harringtonine (2µg/ml)


title: 32 cell mouse embryo ribosome profiling, harringtonine treated, biological replicate 4

description:
Library name: 09072023_ITP_32cell_Harr_C
32cell_embryo_harringtonine_biol rep4


title: SW480 cell,WT,LgBiT-Tn5(Af-CUT&Tag)

description: Library name: SW480_WT_LgBiT-Tn5

value: colon


title: F2_KO

value: KO

value: TMEM106B KO


title: F2_KO_corrected

value: Brain


title: F2_KI

value: KI

value: TMEM106b T186S KI


title: SW480 cell,WT,NbALFA-Tn5(Af-CUT&Tag)

description: Library name: SW480_WT_NbALFA-Tn5

value: epithelial

value: WT


title: SW480 cell,KI-CTCF-ALFA,NbALFA-Tn5(Af-CUT&Tag),Rep3

description: Library name: SW480_CTCF-ALFA-NbALFA-Tn5-Rep3


title: 32 cell mouse embryo ribosome profiling, harringtonine treated, biological replicate 2

description:
Library name: 20221004_ITP_32cell_control_B
32cell_embryo_harringtonine_biol rep2


title: hESC2_DEC

description:
Library name: sample 5
Column name in Counts_normalized.txt: hESC2_DEC-FPKM

value: human endometrial stromal cells


title: F2_KI_Tau

value: TMEM106b T186S KI x MAPT P301L PS19


title: 32 cell mouse embryo ribosome profiling, harringtonine treated, biological replicate 1

description:
Library name: 20221004_ITP_32cell_Harr_30min_A
32cell_embryo_harringtonine_biol rep1


title: 32 cell mouse embryo ribosome profiling, DMSO treated, biological replicate 1

description:
Library name: 20221004_ITP_32cell_Harr_30min_B
32cell_embryo_control_biol rep1

value: DMSO


title: hESC2_CTRL

description:
Library name: sample 4
Column name in Counts_normalized.txt: hESC2_CTRL-FPKM


title: F2_KO_Tau

value: TMEM106b KO x MAPT P301L PS19


title: SW480 cell,KI-CTCT-HiBiT,nano-Tn5_anti-CTCF(nano-CUT&Tag),Rep3

description: Library name: SW480_CTCF-HiBiT_nano-Tn5_anti-CTCF-Rep3

value: anti-CTCF


title: SW480 cell,anti-CTCF(CUT&Tag),Rep2

description: Library name: SW480_WT_anti-CTCF-Rep2


title: 32 cell mouse embryo ribosome profiling, DMSO treated, biological replicate 2

description:
Library name: 09072023_ITP_32cell_control_C
32cell_embryo_control_biol rep2


title: SW480 cell,KI-CTCF-HiBiT,LgBiT-Tn5(Af-CUT&Tag),Rep3

description: Library name: SW480_CTCF-HiBiT_LgBiT-Tn5-Rep3


title: hESC2_D+O

description:
Library name: sample 6
Column name in Counts_normalized.txt: hESC2_D+O-FPKM

value: decidualization induction with hEO co-culture


title: hESC1_D+O

description:
Library name: sample 3
Column name in Counts_normalized.txt: hESC1_D+O-FPKM


title: hESC1_CTRL

description:
Library name: sample 1
Column name in Counts_normalized.txt: hESC1_CTRL-FPKM

value: hESCs cultured alone without decidualization


title: SW480 cell,anti-RPB1(CUT&Tag),Rep2

description: Library name: SW480_WT_anti-RPB1-Rep2


title: SW480 cell,anti-CTCF(CUT&Tag),Rep1

description: Library name: SW480_WT_anti-CTCF-Rep1


title: hESC1_DEC

description:
Library name: sample 2
Column name in Counts_normalized.txt: hESC1_DEC-FPKM

value: hESCs treated with decidualization inducer


title: F1_WT_O

value: F


title: F1_Tau_O

value: MAPT P301L PS19


title: 16 cell mouse embryo ribosome profiling, harringtonine treated, biological replicate 5

description:
Library name: 09072023_ITP_16cell_Harr_B
16cell_embryo_harringtonine_biol rep5

value: preimplantation embryo

value: Harringtonine (2µg/ml)


title: F1_WT_I

value: Brain


title: Slc17a5 OE M2-6

first: Shaorong

address: Tian Tan Xi Li No. 4

institute: Capital Mecidal University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Monocyte

value: Slc17a5 overexpression plasmid transfection


title: 16 cell mouse embryo ribosome profiling, harringtonine treated, biological replicate 4

description:
Library name: 09072023_ITP_16cell_Harr_A
16cell_embryo_harringtonine_biol rep4


title: SW480 cell,anti-RPB1(CUT&Tag),Rep1

description: Library name: SW480_WT_anti-RPB1-Rep1

value: colon

value: epithelial


title: 16 cell mouse embryo ribosome profiling, harringtonine treated, biological replicate 3

description:
Library name: 20221004_ITP_16cell_Harr_30min_A
16cell_embryo_harringtonine_biol rep3


title: Slc17a5 OE M2-5


title: 16 cell mouse embryo ribosome profiling, harringtonine treated, biological replicate 2

description:
Library name: 20221004_ITP_16cell_Harr_15min_B
16cell_embryo_harringtonine_biol rep2


title: F1_Tau_I


title: Slc17a5 OE M2-4


title: hiPSC-spNeuron_Day18

first: Miao

last: Xu

address: No. 31 Huatuo St., Daxing District, Beijing, P.R.China

institute: National Institutes for Food and Drug Control

description: Library name: Sample5

library_source: transcriptomic single cell

data_processing:
①A CeleScope v2.2.0dev1 (Singleron Biotechnologies, Nanjing, China) pipeline (https://github.com/singleron-RD/CeleScope/blob/master/doc/user_guide.md) was applied to transform raw data, delete low quality reads and align to the GRCh38 reference genome. ②The demultiplexing, barcoded processing, gene counting and aggregation weremade using the Cell Ranger software v7.1.0 (10x Genomics, USA) (https:/support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The cell barcodes, unique molecular identifiers (UMIs) and expression matrix files were obtained for subsequent bioinformatics analysis using R package Seurat (v4.4.0).
Assembly: Human; GRCh38
Supplementary files format and content: matrix table with raw gene counts for every gene and every cell

source_name: iPSC-derived spinal neuron_day18

extract_protocol:
①Cells in different time points (day-1, 3, 6, 12, 18) during differentation were digested by 0.75X TripLE and harvested, then washed and resuspended in DPBS prior to scRNA-seq using Singleron GEXSCOPE® protocol. ②After iPSC-spNPG transplantation into SCI mice, chimeric spinal tissue containing injury lesions and grafted iPSC-spNPG cells were collected and immediately snap frozen in liquid nitrogen. Following nuclei isolation, Hochest+ nuclei were sorted into wash buffer and transferred immediately for loading onto the 10X Chromium instrument to perform snRNA-seq.
①Cells were sampled at distinct time points (day-1, 3, 6, 12 and 18) and processed for scRNA-seq libraries construction using Singleron GEXSCOPE® protocol (Singleron). Single-cell suspensions were loaded onto a SCOPE-chip microfluidic device. Through gravity-based sedimentation under Poisson distribution principles, individual cells were isolated into customized microwells. PolyT-conjugated molecularly barcoded beads (containing unique Cell Barcode and UMI sequences) were subsequently added to each well, ensuring one bead per cell 168. Cells were lysed in situ, and mRNA was captured by hybridization of the poly(A) tail to the bead’s polyT oligonucleotides. Reverse transcription was performed to generate barcoded cDNA, incorporating Illumina R1 primer sequences, UMI, and Singleron Barcode.The pooled barcoded cDNA was purified using magnetic beads, amplified by PCR, and size-selected with SPRIselect reagent. During library construction, Illumina R2 primer sequences, P5/P7 adapters, and sample indexes were added to generate paired-end sequencing libraries compatible with Illumina platforms. ②Library was performed according to the manufacter's instructions (single cell 3’v2protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix andloaded together with partitioning oil and gel beads into the chip to generate the gelbead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in everysingle GEM was retrotranscripted to cDNA, which contains an llumina R1 primersequence, Unique Molecular ldentifier (UMl) and the 10x Barcode. The pooledbarcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCRand the apropiated sized fragments were selected with SPRlselect reagent forsubsequent library construction. During the library construction llumina R2 primersequence, paired-end constructs with P5 and P7 sequences and a sample indexwere added.

treatment_protocol: In vitro differentiation of spinal neuron from iPSC; Spinal neural progenitor cell transplantation into SCI mice model

value: iPSC-derived spinal neuron

value: Neuron

value: Differentiation


title: SW480 cell,KI-CTCF-HiBiT,ATAC

description: Library name: SW480_CTCF-HiBiT_ATAC_seq

data_processing:
Raw reads were filtered to remove adapter sequences and low-quality sequences using fastp (version 0.20).
Clean reads were mapped to the mouse mm10 or human hg19 reference genome using Bowtie2 (version 2.4) with options: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -l 10 -X 700.
Duplicate reads were removed using Picard MarkDuplicates (version 2.27). Mitochondrial reads, unmapped reads, and reads with mapping quality <30 were filtered out using SAMtools (version 1.15).
BigWig files were generated using deepTools bamCoverage (version 3.3.1) with options: --binSize 10 --normalizeUsing RPGC.
Peaks were called for each sample using MACS2 callpeak (version 2.2) with options: --bdg --SPMR --gsize hs --keepdup all --gvalue 0.05 --shift -75 --extsize 150 --nomodel --call-summits --nolambda.
Assembly: hg19,mm10
Supplementary files format and content: bigWig

extract_protocol:
For cell samples, digestion followed by permeabilization is sufficient. For mouse liver tissue, 0.1-0.2 g of liver tissue was excised and washed with 2 mL of swelling buffer (10 mM Tric-HCl pH 7.5, 2 Mm MgCl2, 3 mM CaCl2, 1×Protease inhibitor cocktail). The liver was then dounced in 1 ml of swelling buffer (dounced 10 times, piston A) and incubated at 4°C for 20 min. Afterward, the liver was dounced again 20 times (piston B), and 1 mL of swelling buffer was added. The cells were filtered using a 100 μm cell strainer and spun at 400×g at 4°C for 10 min. The supernatant was removed, and the cells were resuspended in 0.5 ml of swelling buffer + 10% glycerol. Slowly vortex while adding drop by drop 0.5 mL of lysis buffer (Swelling buffer + 10% glycerol + 1% NP-40). Incubate for 5 min at 4°C and add 1.5 mL of lysis buffer. Spin at 600×g at 4°C for 5 min, remove the supernatant, and wash the nuclei again with 1.5 mL of lysis buffer. Spin at 600 g at 4°C for 5 min, remove the supernatant, and resuspend the nuclei in 1 mL of freezing buffer. Finally, the nuclei were stained with DAPI and counted.
Harvest cells by centrifuging at 600×g for 5 minutes, discard the supernatant, and resuspend in PBS. Centrifuge a single-cell suspension containing the desired number of target cells at 600×g for 5 minutes, discard the supernatant, and resuspend in 50 µL of pre-cooled lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.02% digitonin, 0.1% Tween-20). Allow the cells to lyse by placing them on ice for 5 minutes. Centrifuge at 500×g for 10 minutes at 4°C to collect the cell nuclei and immediately continue to transposition reaction. To make the transposition reaction mix, combine the following: 10 μL 5×TD Buffer (50 mM Tris pH 7.5, 25 mM MgCl2, and 50% dimethylformamide), 16.5 µL PBS, 0.5 µL 10% Tween-20, 0.5 µL 1% digitonin 18.5 ddH2O and 4 µL LgBiT/NbALFA-Tn5 Transposase (~1 µM). Resuspend nuclei in the transposition reaction mix and incubate the transposition reaction at 37°C for 30 min. PCR mix (Vazyme#TD601) and adapters (VazymeTD#202) were used for library amplification, the total volume is 50 µL. The fragmented DNA library was initially incubated with a 0.55× (27.5 µL) volume of DNA purification magnetic beads (Vazyme#N411). After discarding the magnetic beads, the supernatant was retained, and a 1.2× (60 µL) volume of DNA magnetic beads was added to further purify the DNA fragment library.

value: KI-CTCF-HiBiT


title: 16 cell mouse embryo ribosome profiling, harringtonine treated, biological replicate 1

description:
Library name: 20221004_ITP_16cell_Harr_15min_A
16cell_embryo_harringtonine_biol rep1


title: Slc17a5 OE M2-3


title: hiPSC-spNPG_Day 12

description: Library name: Sample4

source_name: iPSC-derived spinal neural progenitor cells_day12

value: Neural progenitor cell


title: Slc17a5 OE M2-2


title: F1_KI_corrected

value: KI

value: TMEM106b T186S KI


title: 16 cell mouse embryo ribosome profiling, DMSO treated, biological replicate 4

description:
Library name: 09072023_ITP_16cell_control_B
16cell_embryo_control_biol rep4

value: DMSO


title: 16 cell mouse embryo ribosome profiling, DMSO treated, biological replicate 3

description:
Library name: 09072023_ITP_16cell_control_A
16cell_embryo_control_biol rep3


title: hiPSC-NMP_Day3

description: Library name: Sample2

source_name: iPSC-derived Neuromesodermal progenitor cells_day3

value: Pluripotent stem cell


title: Slc17a5 OE M2-1


title: Slc17a5 OE M1-6

value: LPS+IFNg