title: iWAT_Hiraf/f_Adipoq-Cre_HFD_rep2

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

description: Library name: Sample 16

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

source_name: inguinal white adipose tissue

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

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

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

value: inguinal white adipose tissue

value: Hira-/-

value: high-fat diet (8 weeks)

tag: time

value: 16 weeks


title: PoolCTL_A_LP6

status: Public on Jun 01 2026

type: SRA

city: Ghent

first: Xin

last: Wang

address: Corneel Heymanslaan 10, B

country: Belgium

institute: University Gent

description: Library name: RNA017657

library_source: other

data_processing:
High performance computing 3'-RNAseq analysis pipeline (Quantseq)
QC via FASTQC 0.11.9
Quality related trimming via bbduk (BBMap v38.87, k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20)
read mapping via STAR 2.7.6a
bam file indexing via SAMtools 1.15
count tables generated via HTSeq 0.11.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw count tables

molecule: other

organism: Homo sapiens

growth_protocol: HEK293T-dCas9 cells were maintained in RPMI medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin–streptomycin at 37 °C in the incubator with 5% CO₂.

extract_protocol:
Cells were lysed directly in the culture plate using the SingleShot™ Cell Lysis Kit (Bio-Rad) according to the manufacturer’s instructions. Cell lysates were used directly for downstream RNA-seq library preparation.
Libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen) .

treatment_protocol: Cells were transfected with a total of 40 ng purified sgRNA per well using Lipofectamine™ CRISPRMAX™ Cas9 Transfection Reagent (Invitrogen, Cat. #CMAX00003).

tag: cell line

tag: cell type

value: embryonic kidney cell

tag: genotype

tag: treatment

value: PoolCTL

tag: batch


title: S14_Healthy_Control_3

city: Lausanne

first: Evarist

last: Planet

state: Vaud

address: Route Cantonale

country: Switzerland

institute: EPFL

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger (v7.0.1, 10x Genomics) was used to align reads to the human reference genome (hg19)
Assembly: hg19

molecule: polyA RNA

source_name: PBMC

extract_protocol:
PBMCs were isolated from EDTA anticoagulated venous blood of SCADR patients and healthy volunteers after ficoll gradient sorting using 15 ml tubes (Corning) and resuspended in 1ml of ice-cold PBS containing 1% BSA and 0.25mM EDTA prior to FACS sorting of propidium negative (PI) cells using a Beckman Coulter MoFlo Astrios for dead cell removal. Sorted cells were immediately processed for scRNA-seq analysis. Skin biopsies were processed essentially as previously described by Kim D et al. (Nat Med. 2020;26(2):236-243. doi:10.1038/s41591-019-0733-7) with minor modifications. Skin isolated cells were not ACK treated after 40-μm cell strainers filtration and were resuspended in 0.5 ml ice-cold PBS containing 1% BSA and 0.25mM EDTA prior to cell sorting. Alive cells were isolated with Beckman Coulter MoFlo Astrios after PI and Hoecht staining and immediately processed for scRNA-seq analysis. After isolation, the cells were diluted at a concentration of 500-1000 cells/ml in PBS 2% FCS and checked for viability and absence of significant doublets or aggregates.
The cells were then loaded into a Chromium Single Cell Controller (10x Genomics, Pleasanton, CA) in a NextGEM chip G together with beads, master mix reagents (containing RT enzyme and poly-dt RT primers), and oil to generate single-cell-containing droplets. Single-cell Gene Expression libraries were then prepared using Chromium Next GEM Single Cell 3’ Kit v3.1 following the manufacturer’s instructions. Quality control was performed with a TapeStation 4200 (Agilent) and QuBit dsDNA high sensitivity assay (Thermo) following manufacturer instructions. With this procedure, the cDNAs from distinct droplets harbor a distinct and unique 10x “cell barcode”.

tag: tissue

value: PBMC

tag: subject status

tag: gender

value: Female

tag: age


title: GAL4_B_LP6

description: Library name: RNA017656


title: S13_Healthy_Control_2

description: 10x Genomics


title: iWAT_Hiraf/f_Adipoq-Cre_HFD_rep1

country: USA

description: Library name: Sample 15

library_source: transcriptomic

organism: Mus musculus


title: AT2G00440-1-NBS_Biological-replicate-1

city: Gif Sur Yvette

first: Jeremie

last: Bazin

address: Bâtiment 630, rue de Noetzlin Plateau du Moulon

country: France

institute: CNRS

description: Library name: AT2G00440-1-NBS_Biological-replicate-1

data_processing:
Libraries were prepared using a Tru-Seq Stranded mRNA Sample Prep kit (Illumina®). Sequencing was performed using a paired-end protocol to a minimum depth of 40 million reads per sample on an DNB-seq 100nt paired end (BGI Genomics, China). Raw reads were quality-trimmed and adapter sequences removed using Cutadapt (5.1). Cleaned reads were aligned to the A. thaliana reference genome using STAR (2.7.11b), with minimum and maximum intron lengths set to 50 and 5000 nt, respectively. Only uniquely mapping reads were retained for downstream analysis. Gene-level expression quantification was performed using HTSeq (2.0.5) in union mode, using the Araport11 gene annotation. Differential gene expression analysis was carried out using DESeq2, with pairwise comparisons between genotypes. Genes were considered differentially expressed if they had a false discovery rate (FDR) < 0.01.
Transcript Quantification and Differential Alternative Splicing Analysis
Transcript-level abundance estimation was performed using Kallisto with 100 bootstrap. Quantification was based on the AtRTD2 reference transcriptome (R. Zhang et al. 2017). Differential alternative splicing (DAS) analysis was conducted using SUPPA2 (Trincado et al. 2018), using transcript per million (TPM) values from Kallisto. Splicing events were considered differentially regulated if they exhibited an absolute dPSI (|dPSI|) > 0.2 and FDR < 0.01.
Assembly: Tair10
Supplementary files format and content: Normalized (DEseq2) read counts over exons per genes for Transienty assay
Supplementary files format and content: Suppa2 alternative splicing results for Transienty assay
Supplementary files format and content: Normalized (DEseq2) read counts over exons per genes for transgenic lines
Supplementary files format and content: Suppa2 alternative splicing results for Transgenic lines

organism: Arabidopsis thaliana

source_name: 7th leaf

growth_protocol: Total RNA was extracted from individual seventh leaves of 37-day-old-plants grown in an Aralab climate chamber with long day conditions (16 h light/ 8 h dark, 20°C, 60% humidity).Total RNA was extracted from pools of 10-day-old seedlings for KD- and OE-ACHLYS. TURBO™ DNase (Life Technologies) treated RNA was purified using the RNA Cleanup protocol of the RNeasy Plant Mini Kit (QIAGEN) and used for Illumina® Stranded mRNA Prep (Illumina) following the manufacturer's instructions. We performed a second library clean up to reduce primer dimer contamination. Libraries were sequenced by BGI genomics (China).

extract_protocol:
Following the manufacturer's instructions total RNA was extracted using TRI REAGENT® (Molecular Research Center, Inc.). TURBO™ DNase (Life Technologies) treated RNA was purified using the RNA Cleanup protocol of the RNeasy Plant Mini Kit (QIAGEN) and used for Illumina® Stranded mRNA Prep (Illumina) following the manufacturer's instructions. We performed a second library clean up to reduce primer dimer contamination. Libraries were sequenced by BGI genomics (China)
Libraries were construted by Illumina® Stranded mRNA Prep (Illumina) following the manufacturer's instructions. We performed a second library clean up to reduce primer dimer contamination. Libraries were sequenced by BGI genomics (China)

treatment_protocol: The transient expression in wild type (Columbia-0) or nsra A. thaliana leaves was performed according to Y. Zhang et al. 2020. Agrobacterium (GV3101 or AGL1) clones containing a vector to overexpress the lncRNA candidates, ASCO or GFP as control, were grown in liquid culture overnight (28°C). 200 µl of liquid culture was transferred to YEB-induced medium plates (0.2 mM acetosyringone) and incubated at 28°C for 36 h. Bacteria were scraped from the plate and resuspended in 2 ml washing solution (10 mM MgCl2, 100 μM acetosyringone) and diluted in infiltration solution (¼MS [pH = 6.0], 1% sucrose, 100 μM acetosyringone, 0.005%v/v Silwet L-77) to an OD600 of 0.5. The previously marked 7th leaf of 30-35-day-old plants (long day, day 20°C, night 18°C, 60% humidity) was infiltrated with agrobacteria using a 1-ml plastic syringe. The infiltrated plants were dried for 1h in the growth cabinet, incubated in the dark for 24 h and the samples were collected 88 h after infiltration.

value: 7th leaf

value: Plant


title: iWAT_Hiraf/f_HFD_rep2

description: Library name: Sample 14

value: wild type


title: AT2G00440-1-NBS_Biological-replicate-2

description: Library name: AT2G00440-1-NBS_Biological-replicate-2


title: GAL4_A_LP6

description: Library name: RNA017655


title: S12_Healthy_Control_1

description: 10x Genomics

value: Male


title: iWAT_Hiraf/f_HFD_rep1

description: Library name: Sample 13


title: Running_04

city: Daejeon

first: Jong-Eun

last: Park

address: 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description:
Library name: Running_04
10x Genomics

data_processing:
Sequence data were processed with CellRanger (v.6.0.2) to generate count matrices
Assembly: mm10
Supplementary files format and content: CellRanger filtered_feature_bc_matrix (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz)

molecule: total RNA

source_name: Hindpaw engrafted B16F10 melanoma

extract_protocol:
To make single cell suspension, freshly collected tumor tissues were chopped with scissors and enzymatically dissociated with tumor dissociation kit (Milteyni Biotec) and blood cells were RBC-lysed with RBC lysis buffer.
Library was constucted according to the manufacturer's instructions (10X 3' v3)

treatment_protocol: Mattress or forced wheel running

value: Hindpaw engrafted B16F10 melanoma

value: Forced wheel running


title: NPC43-1-GRP7_Biological-replicate-4

description: Library name: NPC43-1-GRP7_Biological-replicate-4


title: Das_Alyona__BT2015050_2019_D1

city: Toronto

first: Alyona

last: Ivanova

state: ON

address: 686 Bay Street

country: Canada

institute: The Hospital for Sick Children

description:
Library name: IDH_mut/visium_raw/2019
FF trasncriptome sequencing

data_processing:
GeoMx: All computational analysis methods were run using defaults unless otherwise specified. Raw counts were grouped into a single dataset. The expression threshold used for this study is LOQ (limit of quantitation) = 2 and frequency of 10%. With these settings all targets with LOQ of 2 or greater in at least 10% of segments were kept. Filtering by LOQ gives confidence that the target is expressed above background levels and that it is accurately quantified. Remaining genes were normalized by Q3 normalization
Visium: Preliminary data processing, including demultiplexing, alignment to the GRCh38 reference genome (version 2020-A), and UMI counting, was performed using the Space Ranger pipeline (v2.0.1) from 10x Genomics. Spatial gene expression matrices were generated using the Visium Human Transcriptome Probe Set v2.0.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: spatial_enrichment.csv: feature spatial autocorrelation analysis using Moran's I in CSV format
Supplementary files format and content: cytassist_image.tiff: input CytAssist image in original resolution that can be used to re-run the pipeline
Supplementary files format and content: aligned_tissue_image.jpg: aligned CytAssist and Microscope QC image
Supplementary files format and content: filtered_feature_bc_matrix.h5: Same information as filtered_feature_bc_matrix/ but in HDF5 format.
Supplementary files format and content: metrics_summary.csv: run summary metrics in CSV format
Supplementary files format and content: molecule_info.h5: Contains per-molecule information for all molecules that contain a valid barcode, valid UMI, and were assigned with high confidence to a gene or protein barcode. This file is required for additional analysis spaceranger pipelines including aggr, targeted-compare and targeted-depth.
Supplementary files format and content: possorted_genome_bam.bam: indexed BAM file containing position-sorted reads aligned to the genome and transcriptome, annotated with barcode information
Supplementary files format and content: possorted_genome_bam.bam.bai: Index for possorted_genome_bam.bam. In cases where the reference transcriptome is generated from a genome with very long chromosomes (>512 Mbp), Space Ranger v2.0+ generates a possorted_genome_bam.bam.csi index file instead.
Supplementary files format and content: probe_set.csv: Copy of the input probe set reference CSV file
Supplementary files format and content: raw_feature_bc_matrix.h5:  Same information as raw_feature_bc_matrices/ in HDF5 format.
Supplementary files format and content: raw_probe_bc_matrix.h5: Contains UMI counts of each probe for all detected barcodes in HDF5 format. Only produced when running pipelines for probe-based assays.
Supplementary files format and content: cloupe.cloupe: Loupe Browser visualization and analysis file
Supplementary files format and content: Initial Dataset_GBM.xlsx: raw GeoMx dataset.
Supplementary files format and content: NGS QC_GBM.xlsx: dataset resulting from first QC step, this is the dataset after applying technical QC parameters to primarily evaluate library prep and sequencing performance
Supplementary files format and content: Filter_Segments_defaultLOQ.xlsx: dataset resulting from filtering. In this step we established an expression threshold and a frequency at which the targets are allowed to be below that threshold. The expression threshold used for this study is LOQ (limit of quantitation) = 2 and frequency of 10%. With these setting all targets with LOQ of 2 or greater in at least 10% of segments were kept. Filtering by LOQ gives confidence that the target is expressed above background levels and that it is accurately quantified.
Supplementary files format and content: Q3_Normalize copy.xlsx: dataset resulting from Q3 normalization. Input is the filter_segments_defaultLOQ.xlsx dataset
Supplementary files format and content: OME-TIFF: OME-TIFF files,  slide images containing embedded OME-XML metadata.
Supplementary files format and content: 15-1842_18-17149_BT 201503_C folder with tiff images of each ROI
Supplementary files format and content: DCC files and PKC configuration file (GNP_config.ini): raw data files generated by the GeoMx NGS Pipeline software from sequencer output (FASTQ files). PKC files are configuration files that accompany the DCC files. They contain metadata about the probes and targets used in the experiment, allowing the analysis software to correctly interpret the raw counts in the DCC files.
Supplementary files format and content: Biological Probe QC.xlsx - dataset resulting from second QC step, this is the dataset assess probe performance (uses Grubb's outlier test). Removes any probes classified as local or global outliers.
Library strategy: Spatial Transcriptomics

source_name: astrocytoma

extract_protocol:
FFPE tissue sections for GeoMx DSP experiments were cut to a thickness of 5μm using a microtome and mounted onto Superfrost Plus slides within 1 month of spatial transcriptomics analysis.  Fresh-frozen tissue sections for Visium (10 μm thickness) were mounted onto Visium CytAssist slides, with two samples per slide. Sample preparation—including H&E staining, imaging, probe hybridization, and library construction—was carried out following the manufacturer's protocol (10X Genomics, Visium Spatial Protocols – Tissue Preparation Guide, CG000240, and Visium CytAssist Spatial Gene Expression for Fresh Frozen – Tissue Preparation Guide, CG000636, Rev A).
For GeoMx,sequencing was performed on an Illumina NovaSeq 6000 and fastq files were processed into gene count data for each sample using the GeoMx® NGS Pipeline. Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction.

value: astrocytoma


title: NEAT1_B_LP6

description: Library name: RNA017654


title: S11_MPR

description: 10x Genomics

value: MPR


title: NEAT1_A_LP6

description: Library name: RNA017653


title: NPC43-1-GRP7_Biological-replicate-3

description: Library name: NPC43-1-GRP7_Biological-replicate-3


title: AT3G05955-6-GRP7_Biological-replicate-1

description: Library name: AT3G05955-6-GRP7_Biological-replicate-1


title: iWAT_Hiraf/f_Adipoq-Cre_NCD23wk_rep1

description: Library name: Sample 11

value: normal chow

value: 23 weeks


title: S10_AGEP

description: 10x Genomics

value: AGEP


title: NPC43-1-GRP7_Biological-replicate-2

description: Library name: NPC43-1-GRP7_Biological-replicate-2


title: iWAT_Hiraf/f_Adipoq-Cre_NCD23wk_rep2

description: Library name: Sample 12

value: inguinal white adipose tissue

value: Hira-/-


title: DPH1_B_LP6

description: Library name: RNA017652

value: embryonic kidney cell


title: S9_SJS

description: 10x Genomics

value: SJS


title: 15-1842_18-17149_BT 201503_C

description:
Library name: IDH_mut/geomx_raw
FFPE transcriptome sequencing


title: NPC43-1-GRP7_Biological-replicate-1

description: Library name: NPC43-1-GRP7_Biological-replicate-1


title: iWAT_Hiraf/f_NCD23wk_rep2

description: Library name: Sample 10


title: DPH1_A_LP6

description: Library name: RNA017651


title: iWAT_Hiraf/f_NCD23wk_rep1

description: Library name: Sample 9


title: DANT2_D_LP6

description: Library name: RNA017650


title: MOS2039

city: Shanghai

first: meiyu

last: hu

address: 333 Nan Chen Road

country: China

institute: Shanghai University

description: Library name: sample24

data_processing:
Quality filtering, alignment to Mus musculus reference genome, gene quantification, and differential expression analysis were performed using standard RNA-seq pipelines.
Assembly: GRCm39
Supplementary files format and content: Processed data include gene expression matrix (counts and FPKM values), differentially expressed gene lists, and statistical analysis results. Files are provided in Microsoft Excel (.txt) format.

source_name: heart

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA quality and concentration were verified using a NanoDrop 2000 spectrophotometer and agarose gel electrophoresis.
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: heart

tag: group

value: AAV9-OE miR-21+Swim+MI-3W


title: S8_TEN

description: 10x Genomics

value: PBMC

value: TEN

value: Female


title: eWAT_Hiraf/f_Adipoq-Cre_HFD_rep2

description: Library name: Sample 8

source_name: epididymal white adipose tissue

value: epididymal white adipose tissue

value: high-fat diet (8 weeks)

value: 16 weeks


title: S7_Healthy_Control_3

description: 10x Genomics

source_name: Skin

value: Skin


title: DANT2_C_LP6

description: Library name: RNA017649


title: S6_Healthy_Control_2

description: 10x Genomics


title: MOS2038

description: Library name: sample23


title: eWAT_Hiraf/f_Adipoq-Cre_HFD_rep1

description: Library name: Sample 7


title: DANT2_B_LP6

description: Library name: RNA017648


title: AT2G01422-2-NBS_Biological-replicate-2

description: Library name: AT2G01422-2-NBS_Biological-replicate-2

value: 7th leaf

value: Plant


title: S5_Healthy_Control_1

description: 10x Genomics

value: Male


title: MOS2037

description: Library name: sample22


title: eWAT_Hiraf/f_HFD_rep2

description: Library name: Sample 6

value: wild type


title: MOS2036

description: Library name: sample21


title: DANT2_A_LP6

description: Library name: RNA017647


title: S4_MPR

description: 10x Genomics

value: MPR


title: eWAT_Hiraf/f_HFD_rep1

description: Library name: Sample 5


title: SNHG25_D_LP6

description: Library name: RNA017646


title: MOS1369

description: Library name: sample20


title: eWAT_Hiraf/f_Adipoq-Cre_NCD23wk_rep2

description: Library name: Sample 4

value: Hira-/-

value: normal chow

value: 23 weeks


title: SNHG25_C_LP6

description: Library name: RNA017645

value: embryonic kidney cell


title: MOS1367

description: Library name: sample19

value: heart

value: AAV9-OE miR-21+Swim+MI-3W


title: S3_AGEP

description: 10x Genomics

value: AGEP


title: S2_SJS

description: 10x Genomics

value: SJS


title: eWAT_Hiraf/f_Adipoq-Cre_NCD23wk_rep1

description: Library name: Sample 3

value: epididymal white adipose tissue


title: MOC1353

description: Library name: sample18

value: AAV9-OE miR-21+Control+MI-3W


title: S1_TEN

description: 10x Genomics

value: TEN

value: Female


title: SNHG25_B_LP6

description: Library name: RNA017644


title: eWAT_Hiraf/f_NCD23wk_rep2

description: Library name: Sample 2


title: MOC1352

description: Library name: sample17


title: SNHG25_A_LP6

description: Library name: RNA017643


title: IP XL2 (DHX9)

city: Singapore

first: jinghe

last: xie

address: 21 Lower Kent Ridge Road

country: Singapore

institute: nuh

data_processing:
using eclipdemux to get barcode information of each sample. Using cutadapt to cut the adapter of fastq files. Using Fastqc  to check the quality of trrimed fastq files.
using STAR to finish the alignment.
Barcode_collapse_pe (PE): takes output from STAR genome mapping.
using Samtools to takes output from sortSam, makes bam index for use downstream.  Merges the two technical replicates for further downstream analysis.
using Clipper to call peaks on those files.
Assembly: hg19
Supplementary files format and content: eclip peaks of each sample

extract_protocol:
Cells were UV-crosslinked to fix ribonucleoprotein complexes. Cells were lysed and helicase-bound RNA molecules were captured using an antibody specific to the helicase of interest. These bound RNA were subjected to a series of linker ligation and purification steps according to the eCLIP-seq protocol.
The cDNA library was PCR amplified using a specfic cycle number depending on the level of qPCR fold enrichment of XLs relative to the IgG control. The PCR amplified libraries were then purified using AmpureXP beads. The products were subsequently gel purified using Qiagen Gel Extraction Kit prior to sequencing.

value: human esophageal squamous carcinoma cells

value: WT

value: No treatment

value: Day 0


title: MOC1349

description: Library name: sample16


title: eWAT_Hiraf/f_NCD23wk_rep1

description: Library name: Sample 1

value: wild type


title: MSTRG.57220_D_LP6

description: Library name: RNA017642


title: IP XL1 (DHX9)


title: O9-1 neural crest cells, d5 siY/T with FGF2, rep3

city: Houston

first: Jun

state: TX

address: 6431 Fannin Street

department: Department of Pediatrics  MSB.3.236B

institute: The University of Texas Health Science Center at Houston

description: Library name: O9-1_d5_siY/T_with_FGF2_rep3

data_processing:
The raw reads in FASTQ format were assessed for quality using FastQC, followed by trimming of low-quality bases and adapter sequences with Trimmoatic to ensure high-quality data for downstream analysis.
The reference genome mm10 was indexed using STAR's genome index generation function with a corresponding GTF annotation file. The cleaned reads were then aligned to the indexed genome using STAR, employing --outSAMtype BAM SortedByCoordinate for generating sorted BAM files. The duplicate reads were marked and removed using Picard tools,  and the final BAM files were used for downstream processing.
Gene expression quantification was performed using featureCounts to generate read counts for each gene based on the GTF annotation.
Assembly: mm10
Supplementary files format and content: Raw read counts in txt

source_name: O9-1 cells

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of mRNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: O9-1 cells

value: Neural crest cells

value: Wildtype

value: siY/T with FGF2

value: Day 5


title: MOC1348

description: Library name: sample15

value: heart


title: IP IgG (DHX9)


title: MSTRG.57220_C_LP6

description: Library name: RNA017641

value: embryonic kidney cell


title: O9-1 neural crest cells, d5 siY/T with FGF2, rep2

description: Library name: O9-1_d5_siY/T_with_FGF2_rep2


title: MOC1347

description: Library name: sample14


title: MSTRG.57220_B_LP6

description: Library name: RNA017640


title: Input XL2 (DHX9)


title: O9-1 neural crest cells, d5 siY/T with FGF2, rep1

description: Library name: O9-1_d5_siY/T_with_FGF2_rep1


title: MOC1346

description: Library name: sample13


title: MSTRG.57220_A_LP6

description: Library name: RNA017639


title: Input XL1 (DHX9)


title: MES2034

description: Library name: sample12


title: O9-1 neural crest cells, d5 siCtrl with FGF2, rep3

description: Library name: O9-1_d5_siCtrl_with_FGF2_rep3

value: siCtrl with FGF2


title: Input IgG (DHX9)


title: SNHG15_D_LP6

description: Library name: RNA017638


title: O9-1 neural crest cells, d5 siCtrl with FGF2, rep2

description: Library name: O9-1_d5_siCtrl_with_FGF2_rep2


title: MES2033

description: Library name: sample11


title: SNHG15_C_LP6

description: Library name: RNA017637


title: MES2032

description: Library name: sample10


title: IP XL2 (DDX21)


title: O9-1 neural crest cells, d5 siCtrl with FGF2, rep1

description: Library name: O9-1_d5_siCtrl_with_FGF2_rep1


title: SNHG15_B_LP6

description: Library name: RNA017636


title: O9-1 neural crest cells, d5 siCtrl no FGF2, rep3

description: Library name: O9-1_d5_siCtrl_no_FGF2_rep3

value: siCtrl no FGF2


title: IP XL1 (DDX21)


title: MES2031

description: Library name: sample9


title: SNHG15_A_LP6

description: Library name: RNA017635


title: IP IgG (DDX21)


title: MES2030

description: Library name: sample8


title: MSTRG.47058_D_LP6

description: Library name: RNA017634


title: O9-1 neural crest cells, d5 siCtrl no FGF2, rep2

description: Library name: O9-1_d5_siCtrl_no_FGF2_rep2


title: MES2027

description: Library name: sample7


title: O9-1 neural crest cells, d5 siCtrl no FGF2, rep1

description: Library name: O9-1_d5_siCtrl_no_FGF2_rep1


title: Input XL1 (DDX21)


title: MSTRG.47058_C_LP6

description: Library name: RNA017633


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_Scan2 | 011 | Full ROI

city: Boston

first: Emmanuel

last: Ogbonna

state: MA

address: 200 Longwood Ave

department: Laboratory of Systems Pharmacology

institute: Harvard Medical School; Tufts University School of Medicine

description:
Library name: LSP16102_Scan2 | 011 | Full ROI
FFPE

data_processing:
Raw sequencing data were processed to generate FASTQ files
demultiplexed fastqs according to nanostring pipeline
Process FASTQ files through GeoMx NGS pipeline and convert to DCC files
Retreive DCC files
Transfer DCC files to GeoMx DSP for QC and normalisation by DSP software
Then we have Q3 normalised count matrix file (available with the publication as Supplementary File)
Supplementary files format and content: DCC files are digital count files which have been processed from FASTQ files by nanostring pipeline
Library strategy: Spatial Transcriptomics

source_name: tuberculosis-infected human lung tissue

extract_protocol:
5uM thickness section was processed according to GeoMx protocol provided by Nanostring
the libraries were prepared according to manufacturer's protocol (Nanostring)

value: tuberculosis-infected human lung tissue

tag: histopathological region

value: TLS

tag: patient id


title: MEC1344

description: Library name: sample6


title: O9-1 neural crest cells, d2.5 siY/T with FGF2, rep3

description: Library name: O9-1_d2.5_siY/T_with_FGF2_rep3

value: Day 2.5


title: MSTRG.47058_B_LP6

description: Library name: RNA017632


title: O9-1 neural crest cells, d2.5 siY/T with FGF2, rep2

description: Library name: O9-1_d2.5_siY/T_with_FGF2_rep2


title: MEC1343

description: Library name: sample5


title: Input IgG (DDX21)

value: human esophageal squamous carcinoma cells


title: MSTRG.47058_A_LP6

description: Library name: RNA017631


title: IP XL2 (DDX3X)

value: WT


title: MEC1342

description: Library name: sample4


title: O9-1 neural crest cells, d2.5 siY/T with FGF2, rep1

description: Library name: O9-1_d2.5_siY/T_with_FGF2_rep1


title: protein100

first: Stephen

last: Wong

address: 6565 Fannin St

institute: Houston Methodist

description:
Library name: DSP-1001660022162-A-H09
DSP-1001660022162-A-H09.dcc
DSP-1001660022162-A-H09.stats.txt

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

molecule: protein

source_name: Brain

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

value: Brain


title: RP13-349O20.2_D_LP6

description: Library name: RNA017630


title: IP XL1 (DDX3X)

value: No treatment

value: Day 0


title: O9-1 neural crest cells, d2.5 siCtrl with FGF2, rep3

description: Library name: O9-1_d2.5_siCtrl_with_FGF2_rep3

value: O9-1 cells


title: RP13-349O20.2_C_LP6

description: Library name: RNA017629


title: MEC1340

description: Library name: sample2


title: O9-1 neural crest cells, d2.5 siCtrl with FGF2, rep2

description: Library name: O9-1_d2.5_siCtrl_with_FGF2_rep2

value: Neural crest cells


title: MEC1341

description: Library name: sample3


title: RP13-349O20.2_B_LP6

description: Library name: RNA017628


title: IP IgG (DDX3X)


title: Input XL2 (DDX3X)


title: Input XL2 (DDX21)


title: O9-1 neural crest cells, d2.5 siCtrl with FGF2, rep1

description: Library name: O9-1_d2.5_siCtrl_with_FGF2_rep1

value: Wildtype


title: MEC1337

description: Library name: sample1


title: RP13-349O20.2_A_LP6

description: Library name: RNA017627


title: Input XL1 (DDX3X)


title: O9-1 neural crest cells, d2.5 siCtrl no FGF2, rep3

description: Library name: O9-1_d2.5_siCtrl_no_FGF2_rep3


title: Ocy454 cells, differentiation day 14, Rep 2

first: Courtney

last: Mazur

address: 50 Blossom Street

department: Endocrine Unit

institute: Massachusetts General Hospital

description: Library name: Ocy454 Day 14_2

data_processing:
For differentiation samples, STAR aligner was used to map sequencing reads to transcripts in reference genome. Read counts for individual transcripts were produced with HTSeq-count.
For FACS-sorted samples, transcript abundances were calculated using Salmon
Assembly: GRCm39
Supplementary files format and content: Tab-delimited file contains counts per million for all 8 differentiation samples.
Supplementary files format and content: Tab-delimited files contain Salmon-calculated transcript abundances for each FACS sample

growth_protocol: Ocy454 cells were grown on standard tissue culture plastic in MEM alpha supplemented with 10% FBS and 1% antibiotic/antimycotic. Cells are cultured at 33C until confluent, then cultured at 37C to induce differentiation.

extract_protocol:
Differentiated cells were lysed in RLT buffer. Lysates were passed through QIAshredder columns, then total RNA was isolated using the PureLink RNA Mini Kit with on-column DNase. FACS-sorted cells were pelleted and lysed in RLT buffer. Lysates were passed through QIAshredder columns, then total RNA was isolated using the Arcturus PicoPure RNA isolation kit with on-column DNase treatment.
mRNA molecules were purified from total RNA using oligo(dT)-magnetic beads. After fragmentation and reverse transcription, adapters were ligated and products amplified by PCR. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The ssCir DNA was formatted as the final library.

treatment_protocol: Differentiation samples were collected after the indicated days at 37C. CD61-sorted samples were prepared for flow cytometry after 17 days of differentiation by labeling with CD61-PE antibody and DAPI. The top 10% and bottom 10% of live cells were collected based on CD61-PE fluorescence intensity. Sorted cells were collected into PBS with 2% FBS and RNase inhibitor.


title: Input IgG (DDX3X)


title: MSTRG.84190_D_LP6

description: Library name: RNA017626


title: O9-1 neural crest cells, d2.5 siCtrl no FGF2, rep2

description: Library name: O9-1_d2.5_siCtrl_no_FGF2_rep2


title: Ocy454 cells, differentiation day 14, Rep 1

description: Library name: Ocy454 Day 14_1


title: IP XL2 (DDX6)


title: Ocy454 cells, differentiation day 10, Rep 2

description: Library name: Ocy454 Day 10_2


title: O9-1 neural crest cells, d2.5 siCtrl no FGF2, rep1

description: Library name: O9-1_d2.5_siCtrl_no_FGF2_rep1


title: IP XL1 (DDX6)


title: MSTRG.84190_C_LP6

description: Library name: RNA017625


title: Ocy454 cells, differentiation day 10, Rep 1

description: Library name: Ocy454 Day 10_1


title: O9-1 neural crest cells, siY/T without FGF2, Yap

description: Library name: O9-1_siY/T_no_FGF2_Yap

library_source: genomic

data_processing:
FASTQ format raw reads were aligned to mm10 by Bowtie2 with the setting of “--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700”, separately.  Only uniquely mapped reads with MAPQ>30 were retained.
The bigwig files were generated by bamCoverage of deepTools with the normalization of reads per genome coverage (RPGC).
The alignment files were used to call peaks by SEACR with the parameters of “norm stringent”.
Assembly: mm10
Supplementary files format and content: bigwig files for visualization
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
nuclei from O9-1 cells were incubated with concanavalin A (Con A)-coated magnetic beads (Bangs Laboratories, BP531) at room temperature for 10 min to immobilize the nuclei on the Con A-coated magnetic beads. The bead-bound nuclei were then incubated with antibodies overnight at 4 oC with rotation. Guinea pig anti-rabbit secondary antibody (Antibodies-Online, ABIN101961, 1:100) was added to the nuclei and incubated for 30 min at room temperature. The pA-Tn5 adapter complex was incubated with nuclei at room temperature for 1 h. Nuclei were then resuspended in tagmentation buffer at 37 oC for 1 h for DNA fragmentation. After 1 h, 0.5 M EDTA, 10% SDS, and 20 mg/mL proteinase K were added to terminate tagmentation and incubate for 10 min at 70 oC. DNA was then purified by using phenol-chloroform-isoamyl alcohol extraction and ethanol precipitation and dissolved in 21 μL 1 mM Tris-HCl (pH=8) and 0.1 mM EDTA.
CUT&Tag-seq libraries were prepared using the guidelines  CUT&Tag protocol. Add barcoded primers and NEBNext HiFi 2× PCR Master mix into 21uL of DNA solution. Libraries were amplified using 12 cycles on the thermocycler. Post amplification libraries were size selected at 175-1,000 bp in length using AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA kit.

value: siY/T without FGF2

tag: chip antibody

value: Yap

value: osteoblast differenitation


title: MSTRG.84190_A_LP6

description: Library name: RNA017623

value: embryonic kidney cell


title: IP IgG (DDX6)


title: O9-1 neural crest cells, siCtrl with FGF2, Yap

description: Library name: O9-1_siCtrl_with_FGF2_Yap

value: siCtrl with FGF2


title: Ocy454 cells, differentiation day 7, Rep 2

description: Library name: Ocy454 Day 7_2


title: MSTRG.84190_B_LP6

description: Library name: RNA017624


title: RP11-96H19.1_D_LP6

description: Library name: RNA017622


title: Input XL2 (DDX6)


title: O9-1 neural crest cells, siCtrl without FGF2, Yap

description: Library name: O9-1_siCtrl _no_FGF2_Yap

value: siCtrl without FGF2


title: Ocy454 cells, differentiation day 7, Rep 1

description: Library name: Ocy454 Day 7_1


title: Input XL1 (DDX6)


title: RP11-96H19.1_C_LP6

description: Library name: RNA017621


title: O9-1 neural crest cells, siCtrl without FGF2, H3K4me3

description: Library name: O9-1_siCtrl_no_FGF2_H3K4me3


title: Ocy454 cells, differentiation day 1, Rep 2

description: Library name: Ocy454 Day 1_2


title: Input IgG (DDX6)


title: RP11-96H19.1_B_LP6

description: Library name: RNA017620


title: RP11-96H19.1_A_LP6

description: Library name: RNA017619


title: Ocy454 cells, differentiation day 1, Rep 1

description: Library name: Ocy454 Day 1_1


title: O9-1 neural crest cells, siCtrl without FGF2, IgG

description: Library name: O9-1_siCtrl_no_FGF2_IgG

value: IgG


title: shDHX9 #286

data_processing:
using STAR to get the alignment results of each sample
using featureCounts to get the read counts matrix of all samples.
using DEseq2 to get differential expression genes of paired samples
Assembly: hg19
Supplementary files format and content: raw count matrix of all samples.

extract_protocol:
Total RNA samples were extracted using Qiagen Rneasy Mini Kit according to manufacturer's protocol.
Strand-specific cDNA library according to Illumina's TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Human ESCC cells were treated with specific shRNAs for the respective RNA helicases.

value: DHX9 knockdown

value: Lentiviral transduction

value: Day 4


title: PTBP1 KO, TGFb, biol rep 3

city: Chapel Hill

first: Shea

middle: N

last: Ricketts

state: NC

address: 111 Mason Farm Road

department: Pathology and Laboratory Medicine

institute: UNC Chapel Hill

description: Library name: kotgfb3

data_processing:
Data was assessed for quality with FastQC and aligned to mouse genome using STAR
Transcript expression was inferred using featureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited text file includs TPM values for each sample

source_name: Heart

growth_protocol: Cardiac fibroblasts isolated from Ptbp1 floxed mice were maintained in DMEM supplemented with 20% fetal bovine serum, 1% nonessential amino acids and 1% penicillin-streptomycin in humidified atmosphere at 37 ºC under 5% CO2

extract_protocol:
RNA was harvested with QIA shredder homogenization (Qiagen #795654) and RNeasy Plus Mini Kit (Qiagen #74134pi). 1.3 ug of total RNA was used for sequencing libraries
Library preparation was performed by Novogene

treatment_protocol:
Cardiac fibroblasts were treated with Adenoviral-Cre-GFP to remove PTBP1 for PTBP1 knockout and treated with Adenoviral-GFP for Control. Adenoviral treatments were supplemented with 8ug/mL of polybrene.
PTBP1 knockout and Control cardiac fibroblasts were treated with serum free media (DMEM supplemented with 1% nonessential amino acids and 1% penicillin-streptomycin) with or without 10 ng/ul TGFb (R&D Systems) for 24 hours

value: Heart

value: Fibroblast

value: PBTP1 Knockout

value: Profibrotic stimulation by TGFb (10 ng/ul)


title: Gastrocnemius_AAV9_GNDM_Control_rep4

city: Waltham

first: Keith

last: Connolly

address: 43 Foundry Ave, Dock #3

institute: Modalis Therapeutics - Cambridge, MA

description: Library name: 569GC

data_processing:
Fastq files were aligned to human genome assembly GRCh38.p12, which contains the modification of GNDM sequence, using the STAR aligner. Differential analysis was conducted using DESeq2
Assembly: GRCh38.p12
Supplementary files format and content: comma-delimited text file includes DESeq2 counts for each Sample

source_name: Gastrocnemius

extract_protocol:
Gastrocnemius muscle tissues were isolated 11 weeks post administration and total RNA was isolated using RNeasy kit according to manufacturer's protocol
Libraries were generated using NEBNext Ultra RNA Library Prep Kit (NEB, Ipswich, MA, USA) according to the manufacturer’s protocol

treatment_protocol: 7-week-old wildtype C57BL6 mice were administered systemically via tail vein with AAV9s containing NTG or m31 gRNA at the indicated dose. 11 weeks post administration animals were sacrificed, tissues were collected for further analysis

value: Gastrocnemius

value: Muscle

value: AAV9_GNDM with LAMA1 control guide


title: TERC_D_LP6

description: Library name: RNA017618

value: TERC


title: shDHX9 #5

value: human esophageal squamous carcinoma cells


title: Gastrocnemius_AAV9_GNDM_Control_rep3

description: Library name: 568GC


title: TERC_C_LP6

description: Library name: RNA017617


title: shScr (DHX9)

value: WT


title: Gastrocnemius_AAV9_GNDM_Control_rep2

description: Library name: 567GC


title: TERC_B_LP6

description: Library name: RNA017616

value: embryonic kidney cell


title: shDDX21 #2

value: DDX21 knockdown


title: PTBP1 KO, untreated, biol rep 3

description: Library name: ko3

value: Serum


title: Gastrocnemius_AAV9_GNDM_Control_rep1

description: Library name: 566GC


title: TERC_A_LP6

description: Library name: RNA017615


title: shDDX21 #1


title: PTBP1 KO, untreated, biol rep 2

description: Library name: ko2


title: Gastrocnemius_AAV9_GNDM_m31_rep4

description: Library name: 565GC

value: AAV9_GNDM with LAMA1 targeting guide


title: RP11-95D17.1_D_LP6

description: Library name: RNA017614


title: shScr (DDX21)


title: PTBP1 KO, untreated, biol rep 1

description: Library name: ko1


title: Gastrocnemius_AAV9_GNDM_m31_rep3

description: Library name: 564GC


title: RP11-95D17.1_C_LP6

description: Library name: RNA017613


title: shDDX10 #5

value: DDX10 knockdown


title: Gastrocnemius_AAV9_GNDM_m31_rep2

description: Library name: 563GC


title: control, TGFb treated, biol rep 3

description: Library name: ctgfb3

value: Control/WT


title: shDDX10 #1

value: Lentiviral transduction

value: Day 4


title: RP11-95D17.1_B_LP6

description: Library name: RNA017612


title: RP11-95D17.1_A_LP6

description: Library name: RNA017611


title: Gastrocnemius_AAV9_GNDM_m31_rep1

description: Library name: 560GC


title: control, TGFb treated, biol rep 2

description: Library name: ctgfb2

value: Heart

value: Fibroblast


title: shScr (DDX10)


title: hippocampus, PBS, biol rep1

city: New York

first: Joseph

middle: Michael

last: Castellano

state: NY

address: 1425 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

description: Library name: TD006476-2

data_processing:
Reads were aligned to the mouse genome (mm10-2020-A) using Cell Ranger (7.1.0). To remove ambient RNA, SoupX (Young 2020, GigaScience) was performed using a manual cut off set on a sample-by-sample basis. After initial filtering, doublets were removed using DoubletFinder (McGinnis 2019, Cell Syst.). Samples were  filtered by removing genes expressed in fewer than 3 cells, cells with a UMI count under 500, and cells with only 500 genes per cell to ensure we analyzed high-quality cells. Cells with > 2% mitochondria, ribosomal large subunit (RPL) and ribosomal small subunit gene expression content were regressed out.  Integration was performed using STACAS, a semi-supervised data integration method (Andreatta & Carmona 2021, Bioinformatics). Seurat (v5.2.1) was in R programming language (version 4.4.2 or version 4.2.0) for analysis.
Assembly: mm10-2020-A
Supplementary files format and content: Hierarchical Data Format (H5 files). Each file contains per-molecule information for all nuclei with a valid barcode, a valid UMI, and library information.

molecule: nuclear RNA

source_name: hippocampus

extract_protocol:
Single nuceli isolation adapted from Habib et al., 2020 Nature Neuroscience. Following isolation, two biological samples from the same treatment condition were pooled to load 20,000 nuclei total (10,000 nuclei each) for a total of N = 2 samples per treatment condition.
10x Genomics Single Cell 3' v3

value: hippocampus

tag: strain

tag: Sex

value: male

value: PBS


title: control, TGFb treated, biol rep 1

description: Library name: ctgfb1

value: Profibrotic stimulation by TGFb (10 ng/ul)


title: SNHG8_D_LP6

description: Library name: RNA017610


title: CD8 cells, Na Lactate and Oxyrase treatment, DNA replicate 3

city: Bar Harbor

first: Christopher

middle: Lee

last: Baker

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description: Library name: ATAC249

data_processing:
RNA-seq reads were filtered and trimmed for quality scores >30 using trimmomatic for nextera adapters. The filtered reads were aligned to Gencode (M25) reference transcripts using RSEM (v1.2.12) equipped with Bowtie2 (v2.2.0) (command: rsem-calculate-expression  --bowtie2 --paired-end). RSEM calculates expected counts and transcript per million (TPM). The expected counts from RSEM were used in the Bioconductor edgeR 3.20.9 package to determine differentially expressed genes.
ATAC-seq reads were trimmed with Trimmomatic to remove adapters and low-quality bases, then aligned to the mouse genome (mm10) using BWA. Duplicate reads were removed using picard tools, and reads adjusted for Tn5 insertion using custom script from Greenleaf lab. Peak calling was performed with MACS2, and regions present in at least three biological replicates were retained as high-confidence accessible sites. Read counts across regions were quantified using bedtools, filtered to exclude low-abundance regions, and normalized using the TMM method in edgeR.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read counts for each sample (ATAC-seq), and batch corrected counts for RNA-seq (tpm)
Supplementary files format and content: bigWig files for each ATAC-seq sample and replicate

source_name: CD8 T cells

growth_protocol: CD8 T cells were isolated from mouse spleens and lymph nodes using MACS microbeads. Purified cells were then activated on these plates in RPMI-1640 complete medium supplemented with 50 μmol/L β-mercaptoethanol, 1% L-glutamine, 0.5 μg/mL anti-CD28, and 100 U/mL IL-2, and cultured for 3 days.

extract_protocol:
Total RNA was isolated via PureLink RNA Mini Kit (Invitrogen).
RNA-seq libraries were generated from Poly(A) RNA capture using the Illumina TruSeq RNA Sample preparation kit v2. ATAC-seq libraries were prepared from approximately 100,000 T cells via Tn5 transposition with digitonin at 37 °C for 30 minutes, followed by DNA purification and 8–10 cycles of PCR amplification.

treatment_protocol: For treatment the CD8 T cells were supplemented with either lactate (20 mM), sodium pyruvate (20mM), or sodium chloride (20mM) from day 2 to day 3 post activation.

value: CD8 T cells

value: Na Lactate+Oxyrase treatment


title: GFP_Biological-replicate-1

description: Library name: GFP_Biological-replicate-1

value: 7th leaf

value: Plant


title: shDDX17 #2

value: human esophageal squamous carcinoma cells

value: DDX17 knockdown


title: control, untreated, biol rep 3

description: Library name: c3

value: Serum


title: PTBP1 KO, TGFb, biol rep 1

description: Library name: kotgfb1

value: PBTP1 Knockout


title: CD8 cells, Na Lactate and Oxyrase treatment, DNA replicate 2

description: Library name: ATAC245


title: shDDX17 #1


title: control, untreated, biol rep 2

description: Library name: c2

value: Control/WT


title: SNHG8_B_LP6

description: Library name: RNA017608

data_processing:
High performance computing 3'-RNAseq analysis pipeline (Quantseq)
QC via FASTQC 0.11.9
Quality related trimming via bbduk (BBMap v38.87, k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20)
read mapping via STAR 2.7.6a
bam file indexing via SAMtools 1.15
count tables generated via HTSeq 0.11.3
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw count tables

extract_protocol:
Cells were lysed directly in the culture plate using the SingleShot™ Cell Lysis Kit (Bio-Rad) according to the manufacturer’s instructions. Cell lysates were used directly for downstream RNA-seq library preparation.
Libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit (Lexogen) .

value: embryonic kidney cell


title: CD8 cells, Na Lactate and Oxyrase treatment, DNA replicate 1

description: Library name: ATAC241


title: control, untreated, biol rep 1

description: Library name: c1


title: CD8 cells, Na Lactate treatment, DNA replicate 3

description: Library name: ATAC248

value: Na Lactate treatment


title: shDHX30 #4

value: DHX30 knockdown

value: Lentiviral transduction

value: Day 4


title: SNHG8_A_LP6

description: Library name: RNA017607


title: SNHG8_C_LP6

description: Library name: RNA017609


title: CD8 cells, Na Lactate treatment, DNA replicate 2

description: Library name: ATAC244


title: RP11-834C11.4_D_LP6

description: Library name: RNA017606


title: BMDM, db/dbGLP1-Fc +MA-BA.1

city: Hong Kong

first: Ming

last: Yue

address: 21 Sassoon Road, Pokfulam

institute: The University of Hong Kong

description:
Library name: Sample5
Column name in raw counts: DB4-GLP, DB5-GLP.

data_processing:
Raw fastq data was quality-controlled using FastQC v0·11·7 and fastp.
The clean reads were aligned to the UCSC GRCm38 reference using Hisat2 v2.2.1
HTSeq v0.6.1 was used to generate raw read counts for each gene
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file inculdes raw counts for each sample

source_name: bone marrow

growth_protocol: Mice were euthanized by injection of pentobarbital Sodium. Bone marrows were washed out by 2 ml of PBS from the end of femur and tibia with a 23G needle after removal of epiphyses. Erythrocytes were removed by 1× lyse buffer on ice. Bone marrows were then washed by PBS and seeded in 12-well plates (3-5×105 cell/well) with DMEM medium (10% FBS, 1% penicillin/streptomycin and 1 ng/ml of M-CSF1). Half volume of medium were added to the cells on day 4. Bone marrow-derived macrophages were ready for use at day 7.

extract_protocol:
Total RNA of BMDMs were extracted by RNeasy Mini Kit (QIAGEN) according to the instructions.
KAPA mRNA HyperPrep Kit Technical Data Sheet(KR1352)

treatment_protocol: BMDMs were infected with MA-BA.1 (MOI:1) for 24 hours in the presence or absence of GLP1-Fc treatment (50 ng/ml).

value: bone marrow

value: bone marrow-derived macrophages

value: GLP1-Fc +MA-BA.1


title: shDHX30 #2


title: BMDM, db/dbctrl-Fc+MA-BA.1

description:
Library name: Sample4
Column name in raw counts: DB4-Omi, DB5-Omi.


title: shScr (DDX17)

value: WT


title: CD8 cells, Na Lactate treatment, DNA replicate 1

description: Library name: ATAC240

value: CD8 T cells


title: shScr (DHX30)


title: RP11-834C11.4_C_LP6

description: Library name: RNA017605


title: BMDM, db/dbMock

description:
Library name: Sample3
Column name in raw counts: DB4-Mock, DB5-Mock.


title: RP11-834C11.4_B_LP6

description: Library name: RNA017604


title: CD8 cells, Na Pyruvate treatment, DNA replicate 3

description: Library name: ATAC247

value: Na Pyruvate treatment


title: shDDX3X #2

value: DDX3X knockdown


title: BMDM, db/+MA-BA.1

description:
Library name: Sample2
Column name in raw counts: WT-Omi, WT2-Omi, WT3-Omi.


title: RP11-834C11.4_A_LP6

description: Library name: RNA017603


title: CD8 cells, Na Pyruvate treatment, DNA replicate 2

description: Library name: ATAC243


title: shDDX3X #1

value: human esophageal squamous carcinoma cells


title: NT_B_LP5

description: Library name: RNA017602

value: NT


title: CD8 cells, Na Pyruvate treatment, DNA replicate 1

description: Library name: ATAC239


title: shScr (DDX3X)


title: CD8 cells, NaCl treatment, DNA replicate 3

description: Library name: ATAC246

value: NaCl treatment


title: NT_A_LP5

description: Library name: RNA017601


title: Atrial tissue WT8

first: Xander

middle: H T

last: Wehrens

address: 1 Baylor Plz

institute: Baylor College of Medicine

description:
Library name: T15
Batch 2

data_processing:
RNA-seq read quality from the whole-atrium total RNA samples were verified with FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/, Simon Andrews, Babraham Institute, Babraham, Cambridgeshire, UK) and MultiQC. All samples had mean quality scores > 35 and > 90% of reads with quality score > 30. Quality and adapter trimming of the read ends was performed using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/, Felix Krueger, Babraham Institute). Reads were mapped to the GRCm39 mouse reference genome using the STAR package, and transcripts were quantified as Ensembl gene IDs using the RSEM package. BAM files of the aligned reads were sorted and indexed using SAMtools, and the indexed reads were viewed in Integrative Genomics Viewer to determine the relative frequencies of WT and c.2966A>G Mrc2 transcripts.
Differential expression analyses on the whole-atrium samples were performed in R using the EDASeq, limma, and edgeR packages. whole-atrial tissue data were filtered for genes with at least 1 count per million (CPM) in at least 5 samples with the sum of CPM for all 10 samples being at least 5. Sex and age of the mice from which the atria were harvested were accounted for as explanatory variables in the linear model. The data were normalized for sample library size using the weighted trimmed mean of M-values method and corrected for changes in variance across different mean CPMs using the voom method. For each of the E990G-het vs. WT contrasts, the t-statistic and p-value for each gene was determined with H0: |log2(fold change)| < log2(1.2) and Ha: |log2(fold change)| > log2(1.2).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw count, transcripts per million, and fragments per kilobase million of each gene for each sample
Supplementary files format and content: tab-delimited text file includes raw count, transcripts per million, fragments per kilobase million, and relative counts per million of each transcript variant for each gene for each sample

source_name: Cardiac atria

extract_protocol:
The atria were lysed with 250 μL TRI reagent (T9424, Sigma-Aldrich, Inc., St. Louis, MO) per atrial pair. The lysates were partially homogenized by brief mechanical homogenization at 4 °C and incubated for 5 minutes at room temperature. Total RNA was then isolated from the supernatant using the Direct-zol RNA Miniprep Kit (R2050, Zymo Research, Irvine, CA) according to the manufacturer’s protocol. 200 μL fresh TRI reagent was added to each leftover unhomogenized tissue sample, and the samples were completely homogenized by additional mechanical homogenization at 4 °C. Total RNA was extracted from these homogenates upon addition of chloroform according to the manufacturer’s protocol. The Direct-zol kit-extracted and Tri Reagent/chloroform-extracted RNA fractions from each sample were combined for RNA-seq. Total RNA sample quantity, purity, and integrity were determined by spectrophotometric absorbance at 260 nm, the 260/280 nm absorbance ratio, and gel electrophoresis, respectively.
The total-RNA samples were shipped to GENEWIZ (Azenta, South Plainfield, NJ) on dry ice for standard RNA-seq at a targeted depth of 30 million reads per sample. The yield for 9 of the 10 whole-atrium samples exceeded 30 million reads per sample; one of the atrium samples had a yield of 24.3 million reads. At Azenta, RNA sample quantity was confirmed using the Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA), and RNA integrity was confirmed using the Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA). Library preparation with stranded polyA selection was then performed.
The libraries were sequenced using a 2x150bp Paired End (PE) configuration on the Illumina® NovaSeq™ 6000 platform. Raw sequence data (.bcl files) generated from Illumina platform were converted into .fastq files, de-multiplexed using Illumina's bcl2fastq 2.17 software, and delivered by File Transfer Protocol (FTP).

value: Cardiac atria

value: Wild-type


title: BMDM, db/+Mock

description:
Library name: Sample1
Column name in raw counts: WT-Mock, WT2-Mock, WT3-Mock.


title: shDDX6 #9

value: DDX6 knockdown


title: Atrial tissue WT7

description:
Library name: T14
Batch 2


title: Mock_B_LP5

first: Xin

address: Corneel Heymanslaan 10, B

institute: University Gent

description: Library name: RNA017600

value: embryonic kidney cell

value: Mock


title: CD8 cells, NaCl treatment, DNA replicate 2

description: Library name: ATAC242


title: shDDX6 #6

value: Lentiviral transduction


title: Atrial tissue Het7

description:
Library name: T13
Batch 2

value: MRC2 E990G-het


title: CD8 cells, NaCl treatment, DNA replicate 1

description: Library name: ATAC238


title: shScr (DDX6)

value: Day 4


title: Atrial tissue Het6

description:
Library name: T12
Batch 2


title: Mock_A_LP5

description: Library name: RNA017599


title: WT (XEFW1.2f), VPA/CHIR99021, repA

city: Oxford, Oxfordshire

last: Lu

address: Roosevelt Drive

country: United Kingdom

institute: Ludwig Institute for Cancer Research, University of Oxford

description:
XEFW1.2f_WT_VC.5d_repA
archive.QIN_E0001.illumina_wtss.star_aligned.QIN_S0006.bam

data_processing:
Reads were aligned to the mouse genome (GRCm38/Ensembl 85) using STAR
featureCounts v1.5.0-p3 was used to generate a read counts table
Counts were converted to CPMs prior to downstream MDS analysis.
Assembly: mm10 (GRCm38, Ensembl 85)
Supplementary files format and content: featureCounts Output Table

source_name: small intestinal organoids

growth_protocol: WT and Trp53 knock-out small intestinal organoids were cultured in standard ENR organoid culture medium at 5% CO2, 37 ℃

extract_protocol:
Intestinal organoids were retrieved from Matrigel using ice-cold PBS, washed 2 to 3 times to remove dead cells, and collected using a benchtop centrifuge. Total RNA was extracted with the RNeasy Plus Micro Kit (Qiagen Cat# 74034).
1.4 ug of total RNA was used for the construction of sequencing libraries. First-strand cDNA was generated following a poly(A) enrichment protocol, and the resulting cDNA libraries were sequenced as 100 bp paired-end reads on the HiSeq 2500 System (Illumina). Library preparation and sequencing were performed by the Oxford Genomics Centre.

treatment_protocol: WT and Trp53 knock-out small intestinal organoids were cultured in standard ENR organoid culture medium supplemented with VPA (1 mM) and CHIR99021 (3 µM) at 5% CO2, 37 ℃

tag: individual

value: small intestinal organoids

value: Day 5

tag: replicate

value: repA


title: Atrial tissue Het5

description:
Library name: T11
Batch 2


title: PoolCTL_B_LP5

last: Wang

description: Library name: RNA017598

tag: cell line

value: PoolCTL


title: PoolCTL_A_LP5

description: Library name: RNA017597

tag: cell type


title: LPS.RHEB.WT4

city: 深圳

first: Yingjie

state: Guangdong

address: No. 1088 Xueyuan Avenue, Nanshan District

institute: Southern university of science and technology

data_processing:
Sequencing quality was assessed with FastQC(v0.11.9). Adapter sequences were removed using Cutadapt(v4.4). The reads aligned to the hg38 reference genome with STAR(2.7.10b). Uniquely mapped reads were quantified using featureCounts(v2.0.1) against genome annotations (Ensembl 99) .
Assembly: hg38 reference genome
Supplementary files format and content: TPM for each samples

source_name: microglia

extract_protocol:
TRIZOL extraction method
VAHRS universal V8 RNA-seq Library Prep Kit for Illumina NR605

value: microglia

tag: genotype

value: Rheb F/F

value: LPS


title: WT (XEFW1.2f), Untreated control, repB

description:
XEFW1.2f_WT_CNT_repB
archive.QIN_E0001.illumina_wtss.star_aligned.QIN_S0025.bam

value: WT

tag: treatment

value: Untreated control

tag: time

value: repB


title: PTBP1 KO, TGFb, biol rep 2

description: Library name: kotgfb2

tag: tissue

value: Heart

value: Fibroblast

value: PBTP1 Knockout

value: Profibrotic stimulation by TGFb (10 ng/ul)


title: TET2-knockdown Human Keratinocyte Cells 2

type: RNA

city: Nantong

address: Affiliated Hospital of Nantong University, Medical School of Nantong University, 20 Xisi Road, Nantong 226001,P.R. China

description: Ten-eleven translocation-2 transfected HaCat cells2, harvested after several passages.

hyb_protocol: One ug of each labeled cRNA was fragmented by adding 11 ul 10 x Blocking Agent and 2.2 ul of 25x Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 ul2 x GE Hybridization buffer was added to dilute the labeled cRNA.

scan_protocol: Scanned on an Agilent G2505C

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. The GeneSpring GX v12.1 software program was employed to do quantile normalization. The R scripts were utilized in order to achieve hierarchical clustering.

source_name: TET2-transfected HaCaT cells

growth_protocol: HaCaT cells were cultivated in Dulbecco's Modified Eagle's Medium medium with 10 percent of overall fetal bovine serum, with one percent of penicillin-streptomycin and incubated in 5% CO2 at a constant temperature in 37 ̊C for further experiments, usually the 3 to 4 generations of keratinocytes were employed.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: HaCaT (C6282)

value: day 4


title: WT (XEFW1.2f), Untreated control, repA

description:
XEFW1.2f_WT_CNT_repA
archive.QIN_E0001.illumina_wtss.star_aligned.QIN_S0005.bam


title: GAL4_B_LP5

city: Ghent

description: Library name: RNA017596

value: embryonic kidney cell

tag: batch


title: TET2-knockdown Human Keratinocyte Cells 1

institute: Affiliated  Hospital  of Nantong  University

description: Ten-eleven translocation-2 transfected HaCat cells1, harvested after several passages.

label_protocol: One ug of each labeled cRNA was fragmented by adding 11 ul 10 x Blocking Agent and 2.2 ul of 25x Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 ul2 x GE Hybridization buffer was added to dilute the labeled cRNA.


title: LPS.RHEB.WT3


title: GAL4_A_LP5

description: Library name: RNA017595


title: LPS.RHEB.WT2


title: WT (XEFW1.2b), VPA/CHIR99021, repA

description:
XEFW1.2b_WT_VC.5d_repA
archive.QIN_E0001.illumina_wtss.star_aligned.QIN_S0004.bam

value: small intestinal organoids


title: WT (XEFW1.2b), Untreated control, repB

description:
XEFW1.2b_WT_CNT_repB
archive.QIN_E0001.illumina_wtss.star_aligned.QIN_S0021.bam


title: NEAT1_B_LP5

description: Library name: RNA017594


title: Pancreas from lean donor D382

city: NYC

first: Alexey

last: Koshkin

state: New York

department: Department of Pathology and Cell Biology

institute: Columbia University Medical center, department of Pathology and Cell Biology

description:
Library name: DS023_library
Bulk RNA-seq from pancreas of lean donor D382 in batch B

data_processing:
Data Preprocessing Whole-Transcriptome Profiling by RNA-Seq D8+ TRM (DAPI- CD45+ CD3+ CD8+ CD45RA- CCR7- CD69+ 70 cells) from pancreas, small  intestine, lymph node and spleen were individually sorted. Analysis was restricted to CD8 TRM  because they are the predominant TRM lineage in pancreas. RNA was isolated from cell pellets  using the RNeasy Mini Kit (QIAGEN) and quantitated using an Agilent 2100 Bioanalyzer (Agilent  Technologies), and library preparation and RNA-seq was performed by the Columbia Genome Center as previously described4. To analyze the effect of obesity on TRM gene expression, RNA-Seq reads from sorted CD8+ 259 TRM were mapped, filtered and read counts computed as we previously described7 260 . Data from samples that were included in our previous study7 261 (GEO: GSE135582) were merged with 24 additional samples and batch correction was performed using ComBat-seq21  4. Kumar, B.V., et al. Human Tissue-Resident Memory T Cells Are Defined by Core  Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites. Cell Rep 20, 2921-  2934 (2017) 7. Weisberg, S.P., et al. Tissue-Resident Memory T Cells Mediate Immune Homeostasis in the  Human Pancreas through the PD-1/PD-L1 Pathway. Cell Rep 29, 3916-3932 e3915 (2019) . 21. Zhang, Y., Parmigiani, G. & Johnson, W.E. ComBat-seq: batch eject adjustment for RNA-seq  count data. NAR Genom Bioinform 2, lqaa078 (2020).
Assembly: Homo sapiens
Supplementary files format and content: Counts_Table_bulkRNAseq_GEO.txt

source_name: pancreas

extract_protocol:
Human Tissue Samples Human samples Tissues were obtained from deceased organ donors as part of organ acquisition for clinical transplantation through an approved protocol and material transfer agreement with LiveOnNY as described previously (Carpenter et al., 2018, Gordon et al., 2017, Granot et al., 2017, Kumar et al., 2017, Miron et al., 2018, Senda et al., 2019). Donors were free of cancer, chronic diseases, seronegative for hepatitis B, C, and HIV, and represented diverse ages. Use of organ donor tissues does not qualify as “human subjects” research, as confirmed by the Columbia University IRB as tissue samples were obtained from brain-dead (deceased) individuals.
library preparation and RNA-seq was performed by the Columbia Genome Center as previously described

value: pancreas

tag: sample group

value: lean

value: B


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 042 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 042 | Full ROI
FFPE

value: tuberculosis-infected human lung tissue

value: TLS


title: Spleen/PLN from obese donor D443

description:
Library name: DS018_library
Bulk RNA-seq from spleen/PLN of obese donor D443 in batch B

source_name: spleen/PLN

value: spleen/PLN

value: obese


title: LPS.RHEB.WT1

value: microglia

value: Rheb F/F

value: LPS


title: Human Keratinocyte Cells 2

description: Control HaCat cells2, untreated, harvested after several passages.

source_name: HaCaT cells

tag: age


title: WT (XEFW1.2b), Untreated control, repA

description:
XEFW1.2b_WT_CNT_repA
archive.QIN_E0001.illumina_wtss.star_aligned.QIN_S0003.bam

value: WT

value: Untreated control

value: repA


title: Human Keratinocyte Cells 1

description: Control HaCat cells1, untreated, harvested after several passages.

value: HaCaT (C6282)


title: NEAT1_A_LP5

description: Library name: RNA017593


title: p17_e6_TB_Granulomas_GeoMx_LSP16102_B5_scan1 | 045 | Full ROI

description:
Library name: LSP16102_B5_scan1 | 045 | Full ROI
FFPE


title: WT (XAYW20.4h), VPA/CHIR99021, repA

description:
XAYW20.4h_WT_VC.5d_repA
archive.QIN_E0001.illumina_wtss.star_aligned.QIN_S0016.bam

value: Day 5


title: LPS.RHEB.KO4

value: Rheb F/F; Tmem119-cre ER


title: WT (XAYW20.4h), Untreated control, repA

description:
XAYW20.4h_WT_CNT_repA
archive.QIN_E0001.illumina_wtss.star_aligned.QIN_S0045.bam

value: small intestinal organoids


title: DPH1_A_LP5

description: Library name: RNA017591

value: embryonic kidney cell


title: UPN827 cells, TN1434 TrailNet 3or6 month T1D plasma

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression data from UPN827 cells stimulated with T1D plasma

hyb_protocol: The Affymetrix GeneChip Human Genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

label: biotin

source_name: UPN827 cells stimulated with TN1434 TrailNet 3or6 month T1D plasma

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN827 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of participant plasma  that was sampled at baseline or the 3-6 months post-baseline from six TrailNet new-onset T1D intervention trails, or from our local Recent onset T1DM cohort. Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cells

value: UPN827 cells

tag: sample timepoint

value: TrailNet 3 or 6 month


title: UPN827 cells, TN1431 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1431 TrailNet 3or6 month T1D plasma


title: LPS.RHEB.KO2


title: WT (XAYW20.4a), VPA/CHIR99021, repA

description:
XAYW20.4a_WT_VC.5d_repA
archive.QIN_E0001.illumina_wtss.star_aligned.QIN_S0010.bam


title: RP11-626G11.4_D_LP5

description: Library name: RNA017590


title: WT (XAYW20.4a), Untreated control, repB

description:
XAYW20.4a_WT_CNT_repB
archive.QIN_E0001.illumina_wtss.star_aligned.QIN_S0033.bam

value: repB


title: RP11-626G11.4_C_LP5

description: Library name: RNA017589


title: Ctrl.RHEB.KO915

value: PBS


title: RP11-626G11.4_B_LP5

description: Library name: RNA017588


title: UPN827 cells, TN1419 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1419 TrailNet 3or6 month T1D plasma


title: Ctrl.RHEB.WT914


title: WT (XAYW20.4a), Untreated control, repA

description:
XAYW20.4a_WT_CNT_repA
archive.QIN_E0001.illumina_wtss.star_aligned.QIN_S0009.bam


title: Trp53-/- (XEFW1.2g), VPA/CHIR99021, repA

description:
XEFW1.2g_p53Null_VC.5d_repA
archive.QIN_E0001.illumina_wtss.star_aligned.QIN_S0008.bam


title: UPN827 cells, TN1418 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1418 TrailNet 3or6 month T1D plasma


title: RP11-626G11.4_A_LP5

description: Library name: RNA017587


title: UPN827 cells, TN1416 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1416 TrailNet 3or6 month T1D plasma


title: Ctrl.RHEB.WT913


title: Trp53-/- (XEFW1.2g), Untreated control, repB

description:
XEFW1.2g_p53Null_CNT_repB
archive.QIN_E0001.illumina_wtss.star_aligned.QIN_S0029.bam


title: RP11-430H10.1_D_LP5

description: Library name: RNA017586


title: Ctrl.RHEB.KO912


title: UPN827 cells, TN1407 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1407 TrailNet 3or6 month T1D plasma


title: RP11-430H10.1_C_LP5

description: Library name: RNA017585


title: Ctrl.RHEB.KO911


title: UPN827 cells, TN1406 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1406 TrailNet 3or6 month T1D plasma


title: RP11-430H10.1_B_LP5

description: Library name: RNA017584


title: Ctrl.RHEB.WT904


title: Trp53-/- (XEFW1.2a), Untreated control, repB

description:
XEFW1.2a_p53Null_CNT_repB
archive.QIN_E0001.illumina_wtss.star_aligned.QIN_S0017.bam


title: UPN827 cells, TN1402 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1402 TrailNet 3or6 month T1D plasma


title: RP11-430H10.1_A_LP5

description: Library name: RNA017583


title: UPN827 cells, TN1398 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1398 TrailNet 3or6 month T1D plasma


title: CD8 T cell, core-enriched, KO (F86)

city: Leuven

first: Lisa

middle: M

last: Becker

address: Herestraat 49

institute: VIB KU Leuven Center for Cancer Biology

data_processing:
Quality trimming: We trimmed low quality ends (< Q20) with FastX 0.0.14. Reads that are shorter than 35bp after trimming are removed.
Adapter trimming: The adapters are trimmed only at the end (at least 10bp overlap and 90% match) with cutadapt 3.2. Reads that are shorter than 35bp after adapter trimming are removed.
Quality filtering: Using FastX 0.0.14 and ShortRead 1.52.0, we remove polyA-reads (more than 90% of the bases equal A), ambiguous reads (containing N), low quality reads (more than 50% of the bases < Q25) and artifact reads (all but 3 bases in the read equal one base type).
Removal of contaminants: Using bowtie 2.4.5, we identify reads that align to phix illumina and remove them
Assembly: GRCm3882
Supplementary files format and content: Counts.csv coma separated file containing raw counts. Fastq files were aligned with HISAT2 vesrsion 2.1.0 for the M.musculus reference GRCm38 downloaded from HISAT2 website, Counting was done with subread-2.0.0 FeatureCounts for the reference mm10.ncbiRefSeq.gtf

source_name: lung tumor (core-enriched)

extract_protocol:
RNA was harvested using the Qiagen RNeasy Micro Kit
Libraries were prepared with the TruSeq RNA Library Prep Kit (Illumina) following manufacturer's protocols

value: lung tumor (core-enriched)

value: CD8 T cells

value: KO


title: UPN827 cells, TN1391RH TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1391RH TrailNet 3or6 month T1D plasma


title: RP11-620J15.3_D_LP5

description: Library name: RNA017582


title: Trp53-/- (XEFW1.2a), Untreated control, repA

description:
XEFW1.2a_p53Null_CNT_repA
archive.QIN_E0001.illumina_wtss.star_aligned.QIN_S0001.bam

source_name: small intestinal organoids


title: CD8 T cell, rim-enriched, KO (F15)

source_name: lung tumor (rim-enriched)

value: lung tumor (rim-enriched)


title: T cells, proliferative state, person 48

first: Zachary

middle: D

last: Nagel

address: 655 Huntington Avenue

department: Environmental Health

institute: Harvard University

description: Library name: TS_48

data_processing:
RNA-seq data were processed using the bcbio-nextgen pipeline with the hg38 genome build. The FASTQ files underwent pre-processing, where UMIs were incorporated into R2, and R1 was discarded, resulting in single FASTQ files per library. Reads were quality trimmed with Trim Galore and aligned to hg38 using TopHat2. Transcript quantification was performed with DEXSeq to produce a count matrix.
Assembly: hg38
Supplementary files format and content: csv file in .gz containing raw read counts for each sample

source_name: Blood

growth_protocol: RPMI 1640 medium supplemented with 20% FBS at 37C/5%CO2

extract_protocol:
RNA isolation was performed using PureLinkTM RNA Mini Kit protocol (Invitrogen, Cat no. 12183018A). 25 ng of isolated total RNA was used for constructing sequencing libraries
RNA samples were quantified and assessed using the Advanced Analytical Fragment Analyzer. Libraries were prepared using the 3’ Digital Gene Expression (DGE) sequencing protocol, following established methods. Custom 3’ DGE primers with barcodes and Unique Molecular Identifiers (UMIs) were incorporated to tag transcripts uniquely. After reverse transcription and template switching, cDNA was pooled, cleaned, amplified, and tagmented using Nextera tagmentation. Libraries were sequenced on an Illumina NextSeq500 platform. For more details on library construction, refer to the published protocol in the reference (doi: https://doi.org/10.1101/003236)

treatment_protocol: PBMCs and T cells were stimulated by 10ng/ml of Phytohemagglutinin-L and B cells were stimulated by human B cell Expansion kit for 3 days

value: Blood

value: Primary T cells

value: T cells

value: Phytohemagglutinin-L + 20%FBS


title: UPN827 cells, TN1388 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1388 TrailNet 3or6 month T1D plasma


title: RP11-620J15.3_C_LP5

description: Library name: RNA017581


title: T cells, resting state, person 48

description: Library name: T_48


title: RP11-620J15.3_B_LP5

description: Library name: RNA017580


title: CD8 T cell, core-enriched, KO (O)


title: CD8 T cell, rim-enriched, KO (O)


title: Bulk PBMCs, proliferative state, person 48

description: Library name: PS_48

value: Primary PBMCs

value: Peripheral blood mononuclear cells


title: CD8 T cell, core-enriched, WT (F164)

value: WT


title: LPS.RHEB.KO3

source_name: microglia

value: microglia

value: Rheb F/F; Tmem119-cre ER

value: LPS


title: UPN827 cells, TN1381 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1381 TrailNet 3or6 month T1D plasma

value: UPN827 cells

value: TrailNet 3 or 6 month


title: Bulk PBMCs, resting state, person 48

description: Library name: P_48


title: RP11-395G23.3_D_LP5

description: Library name: RNA017578

value: embryonic kidney cell


title: CD8 T cell, core-enriched, WT (pool)

value: lung tumor (core-enriched)


title: NK cells, resting state, person 48

description: Library name: NK_48

value: Primary NK cells

value: Natural killer cells


title: Trp53-/- (XEFW1.2g), Untreated control, repA

description:
XEFW1.2g_p53Null_CNT_repA
archive.QIN_E0001.illumina_wtss.star_aligned.QIN_S0007.bam

value: small intestinal organoids

value: Untreated control

value: repA


title: UPN827 cells, TN1380 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1380 TrailNet 3or6 month T1D plasma


title: RP11-395G23.3_C_LP5

description: Library name: RNA017577


title: UPN827 cells, TN1379 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1379 TrailNet 3or6 month T1D plasma


title: CD8 T cell, core-enriched, KO (F322)

value: CD8 T cells

value: KO


title: RP11-395G23.3_B_LP5

description: Library name: RNA017576


title: B cells, proliferative state, person 48

description: Library name: BS_48

value: Blood

value: Primary B Cells

value: B cells

value: Human B cell Expansion kit in 20%FBS


title: UPN827 cells, TN1376 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1376 TrailNet 3or6 month T1D plasma


title: RP11-395G23.3_A_LP5

description: Library name: RNA017575


title: UPN827 cells, TN1374 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1374 TrailNet 3or6 month T1D plasma


title: CD8 T cell, core-enriched, KO (F319)


title: B cells, resting state, person 48

description: Library name: B_48


title: CK2

city: Guangzhou, Guangdong

first: Siqi

last: Jiang

address: No.56 Lingyuanxi Road

institute: Sun Yat-sen University

description: Library name: CK2

data_processing:
After the completion of the library construction, the quality of the library was tested, and on-machine sequencing could be carried out only after the test results met the requirements. The detection methods were as follows :(1) The Qubit dye method was used for preliminary quantification, the fragment analyzer was used to detect the insert size of the library, and the next experiment could be carried out only after the insert size met the expectations; (2) The effective concentration of the library was accurately quantified by Q-PCR method (the effective concentration of the library was >2nM), and the library examination was completed. After the library test is qualified, different libraries are pooled according to the target data volume and sequenced by Illumina platform. Filter the offline Data to get Clean Data, sequence match with the specified reference genome, and carry out variable splicing analysis on the Mapped Data obtained; According to the expression levels of genes in different samples or different sample groups, differential expression analysis, functional annotation and functional enrichment of differential expression genes were performed.
Assembly: Homo_sapiens.GRCh38.109
Supplementary files format and content: Portable Document Format and Microsoft Office Excel

extract_protocol:
CKs were negative controls, GSK591s were treated with GSK591, and collect total RNA for RNA-seq.
mRNA with polyA tail was enriched by Oligo(dT) magnetic beads. Then the RNA was broken into short fragments by fragmentation buffer, and the first cDNA was synthesized with six-base random hexamers based on the fragment RNA template. Buffer solution, dNTPs(dTTP, dATP, dGTP and dCTP) and DNA polymerase were then added to synthesize the double-stranded cDNA, which was then purified by DNA purification magnetic beads. The purified double-stranded cDNA was then end-repaired, A tail was added and a sequencing joint was connected. Then the fragment size was selected by DNA purification magnetic beads, and the final cDNA library was obtained by PCR enrichment.

value: squamous cell carcinoma

value: negetive control(replication2)


title: RP11-575F12.2_D_LP5

description: Library name: RNA017574


title: T cells, proliferative state, person 47

description: Library name: TS_47

value: Primary T cells

value: T cells

value: Phytohemagglutinin-L + 20%FBS


title: CD8 T cell, core-enriched, KO (F318)

value: lung tumor (core-enriched)


title: UPN827 cells, TN1362 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1362 TrailNet 3or6 month T1D plasma

value: UPN827 cells

value: TrailNet 3 or 6 month


title: UPN827 cells, TN1372 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1372 TrailNet 3or6 month T1D plasma


title: CD8 T cell, core-enriched, KO (F219)


title: DPH1_B_LP5

description: Library name: RNA017592

value: embryonic kidney cell


title: T cells, resting state, person 47

description: Library name: T_47


title: UPN827 cells, TN1432 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1432 TrailNet 3or6 month T1D plasma


title: UPN827 cells, TN1361 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1361 TrailNet 3or6 month T1D plasma


title: RP11-575F12.2_B_LP5

description: Library name: RNA017572


title: LPS.RHEB.KO1

value: microglia

value: Rheb F/F; Tmem119-cre ER

value: LPS


title: RP11-575F12.2_A_LP5

description: Library name: RNA017571


title: UPN827 cells, TN1421 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1421 TrailNet 3or6 month T1D plasma


title: RP11-357H14.17_D_LP5

description: Library name: RNA017570


title: UPN827 cells, TN1359 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1359 TrailNet 3or6 month T1D plasma


title: CD8 T cell, rim-enriched, WT (H874)

value: lung tumor (rim-enriched)

value: CD8 T cells

value: WT


title: Bulk PBMCs, resting state, person 47

description: Library name: P_47

value: Blood

value: Primary PBMCs

value: Peripheral blood mononuclear cells


title: NK cells, resting state, person 47

description: Library name: NK_47

value: Primary NK cells

value: Natural killer cells


title: RP11-357H14.17_C_LP5

description: Library name: RNA017569


title: UPN827 cells, TN1357 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1357 TrailNet 3or6 month T1D plasma


title: Monocytes, resting state, person 47

description: Library name: M_47

value: Primary Monocytes

value: Monocytes


title: CD8 T cell, rim-enriched, KO (F86)

value: KO


title: CD8 T cell, core-enriched, WT (H719)

source_name: lung tumor (core-enriched)

value: lung tumor (core-enriched)


title: UPN827 cells, TN1352 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1352 TrailNet 3or6 month T1D plasma

value: UPN827 cells

value: TrailNet 3 or 6 month


title: B cells, proliferative state, person 47

description: Library name: BS_47

source_name: Blood

value: Primary B Cells

value: B cells

value: Human B cell Expansion kit in 20%FBS


title: Trp53-/- (XEFW1.2a), VPA/CHIR99021, repA

description:
XEFW1.2a_p53Null_VC.5d_repA
archive.QIN_E0001.illumina_wtss.star_aligned.QIN_S0002.bam

source_name: small intestinal organoids

value: small intestinal organoids

value: Day 5

value: repA


title: RP11-357H14.17_A_LP5

description: Library name: RNA017567

value: embryonic kidney cell


title: RP11-357H14.17_B_LP5

description: Library name: RNA017568


title: UPN827 cells, TN1349 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1349 TrailNet 3or6 month T1D plasma


title: CD8 T cell, core-enriched, WT (H873)

value: CD8 T cells

value: WT


title: B cells, resting state, person 47

description: Library name: B_47

value: Blood


title: UPN827 cells, TN1348 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1348 TrailNet 3or6 month T1D plasma


title: RP11-539L10.3_D_LP5

description: Library name: RNA017566


title: Embryo, LibB_WT

city: Cambridge

first: Bertie

last: Gottgens

email: bg200@cam.ac.uk, nkw22@cam.ac.uk

address: Jeffrey Cheah Biomedical Centre

institute: University of Cambridge

description: 10x genomics scRNA-seq

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were carried out using the Cell Ranger software (version cellranger-7.0.1).
All downstream analysis is described in the methods section as well as in the associated code
Assembly: mm10 (refdata-cellranger-mm10-1.2.0)
Supplementary files format and content: Seurat object containing metadata, raw counts, processes counts, and more

source_name: Whole mouse embryo

extract_protocol:
(15) E6.5 control and (10) E6.5 Axin1DEpi;Axin2-/-  double mutant embryos were single cell dissociated to generate the sc-RNA libraries. Control and mutant embryos were dissected at the same time. Control embryos were obtained by crossing FVB females (Jackson) to the same males used to obtain the Axin1DEpi;Axin2-/-  double mutant embryos (Sox2-Cre+; Axin1DEpi/+;Axin2+/- ). Mutant embryos were identified by distinctive morphology (see Supplementary Figure) and dissected in DMEM-F12 + 5% Newborn Calf Serum (NCS) (Gibco). Individual embryos were washed three times in 40µl drops of DMEM-F12 media. Thereafter, batches of 4 embryos were digested in 40µl of a solution of 2:1 0.25% Trypsin (Gibco): Accutase (StemCell Technologies) at 37C for 15 minutes. After partial digestion, 40µl of (DMEM-F12 + 20% NCS + 4mM EDTA) solution was added to each batch of embryos which were mechanically dissociated by hand pipetting, followed by mouth pipetting with pulled glass capillaries of different diameters to obtain a single cell suspension. The cell suspension was collected in DMEM-F12 + 10% NCS and filtered through a FlowMi cell strainer (4mM Millipore, Sigma). Cells were centrifugated at 2,200 rpm for 4 minutes and washed twice with DMEM-F12 + 10% NCS. Cells were counted and diluted in DMEM-F12 + 10% NCS.
Cells were loaded on a Chromium Controller microfluidic chip for encapsulation with a target number of 10,000 cells for the generation of generate single cell 3’ RNA-seq libraries. Libraries were generated following the manufacturer’s instructions (10x Genomics Chromium Single Cell 3’ Reagent Kit User Guide v2 Chemistry), as previously (Nowotschin et al., 2019).

value: Whole mouse embryo


title: RP11-539L10.3_C_LP5

description: Library name: RNA017565


title: RP11-539L10.3_B_LP5

description: Library name: RNA017564


title: T cells, resting state, person 46

description: Library name: T_46

value: Primary T cells

value: T cells


title: UPN827 cells, TN1383 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1383 TrailNet 3or6 month T1D plasma


title: UPN827 cells, TN1340 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1340 TrailNet 3or6 month T1D plasma


title: RP11-539L10.3_A_LP5

description: Library name: RNA017563


title: Bulk PBMCs, proliferative state, person 46

description: Library name: PS_46

value: Primary PBMCs

value: Peripheral blood mononuclear cells

value: Phytohemagglutinin-L + 20%FBS