title: GM-CSF+ HMGB1+FPS-ZM1 treated mono, biological replicate 1

value: GM-CSF+ HMGB1+FPS-ZM1


title: GM-CSF+ HMGB1+FPS-ZM1 treated mono, biological replicate 2

status: Public on Jul 19 2024

type: RNA

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

description: Gene expression data from human monocytes treated with recombinant HSP90α (2µg/mL) in RPMI medium for 24h

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data was analyzed with R (version 4.3.2). Gene expression profiling was performed using arrays of Human Clariom S from Thermo Fischer Scientific. A Custom CDF Version 25 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Human monocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Human monocytes were isolated from peripheral blood mononuclear cells (PBMC) from buffy coats of healthy donors

extract_protocol: Total RNA from 24h treated monocytes was isolated using Rneasy Kit from Qiagen (Hilden, Germany) according to manufacturer`s instructions. RNA concentration was determined by the microplate reader Tecan Infinite M200 using a Nanoquant plate. The quality of total RNA was confirmed by gel analysis using the total RNA Nano chip assay on an Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Berlin, Germany). Quality and concentration of all samples were checked again on Nanodrop ND-1000, Agilent 2100 Bioanalyzer (Agilent Technologies GmbH, Germany). Microarray experiment were performed at Genomics and Proteomics Core Facility at the German Cancer Research Center (DKFZ) in Heidelberg, Germany.

treatment_protocol: HSP90a treated monocyte: Human monocytes were treated with recombinant HSP90α (2CD14 monocytes were pre-treated with inhibitors Resatorvid (5 μM) or FPS-ZM1 (30 nM) or DMSO (as control) for 1 hour. They were then stimulated with either rHMGB1 (5 μg/mL) or rS100A9 (10 μg/mL) in the presence of GM-CSF (40 ng/mL) for 72 hours. The control group consisted of monocytes stimulated only with GM-CSF (40 ng/mL).µg/mL) in RPMI 1640 medium supplemented with 10% FBS, and 1% penicillin/streptomycin for 24h. Control monocytes: Human monocytes were incubated in RPMI 1640 medium supplemented with 10% FBS, and 1% penicillin/streptomycin for 24h.

tag: tissue

value: Peripheral blood

tag: treatment


title: CGND-HRA-02283

type: SRA

city: New York

first: Oliver

middle: H

last: Tam

state: New York

address: 435 E 30th St

department: Institute for Systems Genetics

country: USA

institute: NYU Grossman School of Medicine

library_source: transcriptomic

data_processing:
Reads from samples with RIN > = 5.5 were aligned to the hg38 human genome using STAR v2.7.6, allowing for a 4% mismatch rate and up to 100 alignments per read to ensure capture of young transposon sequences. Abundance of gene and transposon sequences was calculated with TEtranscripts v2.2.3
Assembly: hg38
Supplementary files format and content: Text file of gene and transposable element counts

source_name: frontal cortex

extract_protocol:
RNA was extracted from flash-frozen patient samples homogenized in Trizol-Chloroform and purified using the QIAGEN RNeasy Mini kit. RNA was assessed using the Bioanalyzer.
RNA-seq libraries were prepared from 500 ng of total RNA using the KAPA Stranded RNA-seq kit with RiboErase for rRNA depletion and Illumina compatible indexes. Pooled libraries were sequenced on an Illumina HiSeq 2500 or NextSeq V1 using a paired end 125 nucleotide

value: frontal cortex

tag: disease state

value: ALS

tag: gender

value: Female

tag: subject id


title: GM-CSF+ HMGB1 treated mono, biological replicate 4

description: Gene expression data from human monocytes incubated in RPMI medium for 24h

value: GM-CSF+ HMGB1


title: GM-CSF+ S100A9 treated mono, biological replicate 1

value: GM-CSF+ S100A9


title: GM-CSF+ HMGB1+FPS-ZM1 treated mono, biological replicate 3


title: GM-CSF+ HMGB1+FPS-ZM1 treated mono, biological replicate 4


title: CGND-HRA-02275

source_name: motor cortex

value: motor cortex

value: Male


title: MNU_FFPE_2ng_OVA_NG_rep2 (Nanostring)

city: Paris

first: Jennifer

last: Wong

address: 12 rue lhomond

country: France

institute: Institue Curie

hyb_protocol: cDNA or RNA were hybridized overnight in a nCounter Prep Station according to NanoString recommendation

scan_protocol: nCounter Digital Analyzer were used for digital counting

data_processing: Data were normalized using the nSolver software provided by NanoString

label: Fluorescent tag barcode

organism: Mus musculus

source_name: mouse normal urothelium (MNU)

label_protocol: Gene of interest are targeted by a specific pair of probe: fluorescently-labeled specific Reporter Tags, and a biotinylated universal Capture Tag. Each report tag has a unique pattern of six spots of color, creating fluorescent barcodes that can be individually resolved and counted   during data collection.

growth_protocol: The mouse bladder cancer cells, BC57, have been culture in DMEM 10% fetal bobine serum. Nine mice were sacrificed and their normal urothelium were removed.

extract_protocol: Total RNA from FFPE were extracted by using Qiagen RNeasy FFPE. Ten slices of five microns of thickness of FFPE samples were dewaxed using Deparaffinization solution and were extracted according to manufacturer instructions (RNeasy FFPE tissue Handbook). Total RNA from FF samples were extracted with Qiagen RNeasy mini according to manufacturer instructions.

treatment_protocol: The normal urothelium of each mouse was divided in two parts, one part was frozen in liquid nitrogen and the other part was conserved in a solution of buffered formalin for 24 hours. Formalin Fixed Paraffin Embedded (FFPE) samples were embedded into wax blocks. The fresh frozen (FF) specimens were conserved in a freezer until the RNA extraction. The mouse bladder cancer cell line (BC57) harvested cell pellet was divided in two parts and underwent the same protocol as the mouse normal urothelium.

tag: cell type

value: normal urothelium

tag: nanostring amplification method

value: Ovation SoLo NuGEN RNA-seq System (OVA-NG)

tag: rna input quantity

tag: method of sample preservation

value: FFPE


title: MNU_FFPE_2ng_OVA_NG_rep3 (Nanostring)


title: BC57_FFPE_2ng_OVA_NG_rep3 (Nanostring)

source_name: mouse bladder cancer cell line (BC57)

value: bladder cancer cells


title: BC57_FFPE_2ng_OVA_NG_rep2 (Nanostring)


title: PAM010, CD4 T cells, sTCRseq

city: Groningen

first: Marco

last: de Bruyn

address: Hanzeplein 1

department: Obstetrics&Gynecology

country: Netherlands

institute: University Medical Center Groningen

description: 10x Genomics

library_source: other

data_processing:
Reads from single cells isolated using 10x chromium were demultiplexed and aligned to the GRCh38.p12 human reference genome (from 10x Genomics) using Cell Ranger (version 6.0.1; 10x Genomics)).
Assembly: GRCh38.p12
Supplementary files format and content: Tab-separated values files, matrix files and comma-separated values files
Library strategy: scTCR-Seq

molecule: other

source_name: Endometrial tumor tissue

extract_protocol:
Tumour digests were thawed in FCS and resuspended in RPMI + 10% FCS. After 1.5h incubation at 37°C/5% CO2, samples were stained and incubated with a CXCR5 PerCP-Cy5.5 antibody for an additional 0.5h at 37°C. After a total of 2h recovery at 37°C/5% CO2, samples were centrifuged and resuspended in 100 µl PBS + 2% FCS. Samples were incubated for 30-45 minutes on ice (in dark) with the following antibodies: CD45 BV605, CD8 APC Cy7, CD4 PE, CD19 BV421, PD1 APC, CD3 PE-Cy7 and the dump channel antibodies CD14 FITC, CD56 FITC and EpCAM FITC. 3 µl of each antibody was used per 1x10e6 cells. Samples were washed twice with PBS + 2% FCS and filtered using a 35 µm strainer (Falcon) before sorting on a Beckman Coulter MoFlo Astrios cytometer. UltraComp eBeads (Thermo Fisher Scientific) were used as compensation controls. Before sorting, Propidium Iodide was added to exclude dead cells. Sorting was done in 1.5 mL Low Bind DNA tubes (Eppendorf) in 150 µl PBS 0.04 % BSA. CD45+ CD3+ CD19- CD8+ and CD4+ cells were sorted. Sorted cells were centrifuged and resuspended at a concentration of 727 cells/µl (total 16.5 µl) for PAM-007 or 2121 cells/µl (total 16.5 µl) for PAM-010 and PAM-011, in PBS 0.04% BSA.
Library was performed according to manufacturer’s protocol (10x genomics): ‘chromium next GEM single cell 5’ reagents kit v2 (dual index)’. For the cDNA amplification step, 13 cycli were done. For each sample, both the V(D)J library as well as the gene expression (GEX) library was constructed. All cDNA quality control and quantification steps were done with the Qubit 4 Fluorometer (Thermo Fisher) and the Agilent 4200 Tapestation (with D5000 and high sensitivity D5000 screen tapes). For the sequencing, V(D)J and GEX libraries were pooled at a 1:4 molar ratio, with 2 GEX libraries and 2 V(D)J libraries in one pool. 1.5 pM of this superpool was sequenced on a NextSeq 500 (Illumina inc., San Diego, CA, USA) A 150 bp NextSeq high-output reagent kit was used for the sequencing (paired end).

treatment_protocol: Patients were treated with neoadjuvant pembrolizumab Q3W for 2 cycles.

value: Endometrial tumor tissue

value: CD4 T cell

tag: genotype

value: MMRd tumor, WT T cells

value: Pembrolizumab 200mg Q3W; 2 cycles


title: PAM011, CD3 T cells, scTCRseq

description: 10x Genomics

value: T cell


title: GM-CSF treated mono, biological replicate 4

value: Peripheral blood

value: GM-CSF


title: PAM010, CD8 T cells, scTCRseq

description: 10x Genomics

value: CD8 T cell


title: CGND-HRA-02269

value: ALS


title: CGND-HRA-02272

value: Female


title: GM-CSF+ HMGB1 treated mono, biological replicate 3

value: GM-CSF+ HMGB1


title: GM-CSF+ HMGB1 treated mono, biological replicate 2


title: CGND-HRA-02266

value: motor cortex


title: GM-CSF treated mono, biological replicate 2


title: GM-CSF+ HMGB1 treated mono, biological replicate 1


title: PAM011, CD3 T cells, scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Reads from single cells isolated using 10x chromium were demultiplexed and aligned to the GRCh38.p12 human reference genome (from 10x Genomics) using Cell Ranger (version 6.0.1; 10x Genomics)).
Assembly: GRCh38.p12
Supplementary files format and content: Tab-separated values files, matrix files and comma-separated values files


title: GM-CSF treated mono, biological replicate 3


title: BC57_FFPE_2ng_OVA_NG_rep1 (Nanostring)


title: GM-CSF treated mono, biological replicate 1


title: MNU_FFPE_50pg_OVA_NG_rep3 (Nanostring)


title: PAM007, CD4 T cells, scTCRseq

description: 10x Genomics


title: MNU_FFPE_50pg_OVA_NG_rep1 (Nanostring)


title: PAM007, CD8 T cells, scTCRseq

description: 10x Genomics


title: PAM010, CD8 T cells, scRNAseq

description: 10x Genomics


title: PAM007, CD8 T cells, scRNAseq

description: 10x Genomics


title: MNU_FFPE_50pg_OVA_NG_rep2 (Nanostring)


title: BC57_FFPE_50pg_OVA_NG_rep3 (Nanostring)


title: BC57_FFPE_50pg_OVA_NG_rep2 (Nanostring)


title: CUT&RUN MDA-MB231 IgG d7 sgMARK2+3, rep3

city: Cold Spring Harbor

first: Olaf

last: Klingbeil

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

library_source: genomic

data_processing:
fastq files were aligned using Bowtie 2 and duplicate reads were removed using Samtools.
Sam files were converted into bam files and index after sorting
Bam files were using to generate bw files normalized for spike-in control using DeepTools.
Normalization factors were calculated by using the number of reads aligned to the human genome vs E.coli. (E.coli DNA was used as spike-In DNA during library preparation)
Assembly: GRCh37(hg19) and E.coli (K-12)
Supplementary files format and content: bw files- read depth and spike-in control normalized read counts
Library strategy: CUT&RUN

molecule: genomic DNA

extract_protocol:
CUT&RUN DNA extraction was performed according tomanufacturer’s instructions (EpiCypher-CUTANA Kit)
Sequencing libraries were generated using  Ultra II DNA Library Prep Kit (NEBNext)

tag: cell line

tag: antibody

value: IgG

tag: time


title: PAM010, CD4 T cells, scRNAseq

description: 10x Genomics


title: CUT&RUN MDA-MB231 IgG d7 sgMARK2+3, rep2


title: MNU_FF_250pg_OVA_NG_rep1 (Nanostring)

value: normal urothelium

value: FF


title: MNU_FF_250pg_OVA_NG_rep3 (Nanostring)

value: Ovation SoLo NuGEN RNA-seq System (OVA-NG)


title: PAM007, CD4 T cells, scRNAseq

description: 10x Genomics


title: CGND-HRA-02245

source_name: medial motor cortex

value: medial motor cortex

value: Male


title: CGND-HRA-02255

value: frontal cortex


title: MNU_FF_250pg_OVA_NG_rep2 (Nanostring)


title: BC57_FFPE_50pg_OVA_NG_rep1 (Nanostring)

value: bladder cancer cells

value: FFPE


title: healthy2

first: Volker

last: Ast

department: NGS Core Facility

institute: University Hospital Mannheim

description: 10x genomics

data_processing:
Demultiplexing, barcode processing and gene counting were performed with CellRanger version 7.1.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated files for cell barcodes and features, count matrices in mtx format

source_name: Peripheral blood

extract_protocol:
CD14+ monocytes were isolated by MACS (Miltenyi Biotech) from the peripheral blood of melanoma patients and healthy individuals. Purity and viability of cells were checked and cells were resuspended in PBS.
Library was performed according to manufacturer's instructions (Chromium Next Gem Single Cell 3' reagent V3.1, dual index). Briefly, cells were loaded onto a Chromium Chip.Within each gel bead, mRNA molecules were captured and barcoded during reverse transcription using unique molecular identifiers (UMIs).cDNA was synthesized and amplified, incorporating cell-specific barcodes and UMIs. Amplified cDNA libraries were prepared by adding adapter sequences for downstream sequencing. Excess reagents were removed from the libraries.The quality and concentration of the prepared libraries were assessed using Bioanalyzer.


title: CGND-HRA-02263-2


title: patient2

description: 10x genomics


title: CGND-HRA-02393

value: ALS+FTD


title: CUT&RUN MDA-MB231 IgG d5 sgCtrl

value: sgCtrl


title: CUT&RUN MDA-MB231 H3K27ac d7 sgMARK2+3, rep3

data_processing:
fastq files were aligned using Bowtie 2 and duplicate reads were removed using Samtools.
Sam files were converted into bam files and index after sorting
Bam files were using to generate bw files normalized for spike-in control using DeepTools.
Normalization factors were calculated by using the number of reads aligned to the human genome vs E.coli. (E.coli DNA was used as spike-In DNA during library preparation)
Assembly: GRCh37(hg19) and E.coli (K-12)
Supplementary files format and content: bw files- read depth and spike-in control normalized read counts
Supplementary files format and content: bed files
Library strategy: CUT&RUN


title: CGND-HRA-02252

source_name: lateral motor cortex

value: lateral motor cortex


title: CGND-HRA-02251


title: healthy1

description: 10x genomics

value: Peripheral blood


title: CGND-HRA-02246

value: ALS


title: CGND-HRA-02249


title: CGND-HRA-02243


title: CUT&RUN MDA-MB231 IgG d7 sgCtrl


title: CUT&RUN MDA-MB231 IgG d5 sgYAP/TAZ

value: sgYAP/TAZ


title: patient1

description: 10x genomics


title: CUT&RUN MDA-MB231 H3K27ac d7 sgMARK2+3, rep2


title: CGND-HRA-02260-2


title: BC57_FF_250pg_OVA_NG_rep2 (Nanostring)


title: CUT&RUN MDA-MB231 IgG d7 sgMARK2+3, rep1


title: CUT&RUN MDA-MB231 H3K27ac d7 sgMARK2+3, rep1


title: BC57_FF_250pg_OVA_NG_rep1 (Nanostring)


title: CGND-HRA-02240


title: BC57_FF_250pg_OVA_NG_rep3 (Nanostring)


title: QM9414 SESp-cbh1 wtXYR1, glucose feed day 4, rep4

city: Espoo

first: Emmi

last: Sveholm

address: Tekniikantie 21

country: Finland

institute: VTT Technical Research Centre of Finland

description: wtXYR1 glu feed d4 rep4

data_processing:
Reads were quality filtered and trimmed using FastP v0.20.0 and the quality of the raw sequence data was evaluated using FastQC v0.11.8. Reads were then aligned to T. reesei genome version 2.0 with GFF annotations using HISAT2 v2.1.0. Sam-files were sorted and compressed with SAMtools v1.9 and the alignments were assembled and quantified using StringTie v2.0.4. Downstream analyses were carried out in R v4.2.2. Differential gene expression analysis was carried out with R package DESeq2 v1.34.0.
Assembly: JGI Trichoderma reesei QM6a v2.0
Supplementary files format and content: tab-delimited text file includes DESeq2-normalized counts for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Trichoderma reesei

source_name: mycelia

growth_protocol: Trichoderma reesei trains were grown in 250 mL Ambr bioreactors (Sartorius), first with batch lactose as the carbon source, then with glucose feed.

extract_protocol:
Total RNA was extracted from mycelia using TRIzol (Thermo Fisher Scientific) according to manufacturer’s instructions with small modifications. Mycelium samples were ground using cooled mortars under liquid nitrogen into fine powder and about 50 µL of powder was transferred into a 2 mL tube, after which 1 mL of TRIzol was immediately added. Mixture was vortexed and incubated at room temperature for 5 minutes, after which it was centrifuged (12000 x g, 4 °C, 10 minutes) and the supernatant was transferred to a new tube. After this, the protocol was continued according to manufacturer’s instructions. RNA was then purified using RNeasy Mini kit (Qiagen) according to manufacturer’s instructions, except that 950 µl of 94 vol-% ethanol was added instead of 250 µl during the second step.
Extracted and purified RNA samples were sent for RNA-sequencing in Source BioScience (Cambridge, UK). rRNA depletion libraries were prepared using Next Ultra II Directional RNA Library Prep kit (New England Biolabs). Sequencing of the rRNA libraries was done using Illumina NovaSeq 6000.

tag: strain

value: mycelia

value: wild-type XYR1 under pdc1 promoter, SESp-cbh1

tag: condition

value: fed-batch:glucose feed

value: day 4


title: CUT&RUN MDA-MB231 H3K27ac d7 sgCtrl


title: CUT&RUN MDA-MB231 H3K27ac d5 sgYAP/TAZ


title: CGND-HRA-02234


title: QM9414 SESp-cbh1 wtXYR1, glucose feed day 4, rep2

description: wtXYR1 glu feed d4 rep2


title: CGND-HRA-02239


title: MNU_FF_2ng_OVA_NG_rep3 (Nanostring)

value: normal urothelium

value: FF


title: CGND-HRA-02233

value: medial motor cortex


title: QM9414 SESp-cbh1 mutXYR1, glucose feed day 4, rep2

description: mutXYR1 glu feed d4 rep2

value: mutated (V821F) XYR1 under pdc1 promoter, SESp-cbh1


title: BC57_FF_2ng_OVA_NG_rep3 (Nanostring)

value: Ovation SoLo NuGEN RNA-seq System (OVA-NG)


title: QM9414 SESp-cbh1 wtXYR1, glucose feed day 3, rep3

description: wtXYR1 glu feed d3 rep3

value: day 3


title: CGND-HRA-02237

value: frontal cortex

value: Male


title: QM9414 SESp-cbh1 wtXYR1, glucose feed day 3, rep4

description: wtXYR1 glu feed d3 rep4


title: QM9414 SESp-cbh1 wtXYR1, glucose feed day 4, rep3

description: wtXYR1 glu feed d4 rep3


title: QM9414 SESp-cbh1 wtXYR1, glucose feed day 3, rep2

description: wtXYR1 glu feed d3 rep2


title: QM9414 SESp-cbh1 wtXYR1, glucose feed day 4, rep1

description: wtXYR1 glu feed d4 rep1


title: QM9414 SESp-cbh1 mutXYR1, glucose feed day 4, rep4

description: mutXYR1 glu feed d4 rep4


title: QM9414 SESp-cbh1 wtXYR1, glucose feed day 3, rep1

description: wtXYR1 glu feed d3 rep1


title: QM9414 SESp-cbh1 mutXYR1, glucose feed day 4, rep3

description: mutXYR1 glu feed d4 rep3


title: MNU_FF_2ng_OVA_NG_rep2 (Nanostring)


title: CGND-HRA-02222


title: QM9414 SESp-cbh1 mutXYR1, glucose feed day 3, rep1

description: mutXYR1 glu feed d3 rep1


title: CGND-HRA-02221


title: MNU_FF_50pg_OVA_NG_rep1 (Nanostring)


title: MNU_FF_2ng_OVA_NG_rep1 (Nanostring)


title: CGND-HRA-02231


title: CGND-HRA-02219

value: ALS+FTD


title: QM9414 SESp-cbh1 mutXYR1, glucose feed day 4, rep1

description: mutXYR1 glu feed d4 rep1


title: CUT&RUN MDA-MB231 H3K27ac d5 sgCtrl

value: sgCtrl


title: CGND-HRA-02227


title: BC57_FF_2ng_OVA_NG_rep2 (Nanostring)

value: bladder cancer cells


title: CGND-HRA-02225

value: ALS


title: BC57_FF_2ng_OVA_NG_rep1 (Nanostring)


title: CGND-HRA-02216

value: lateral motor cortex


title: QM9414 SESp-cbh1 mutXYR1, glucose feed day 3, rep4

description: mutXYR1 glu feed d3 rep4

value: mycelia


title: BC57_FF_50pg_OVA_NG_rep1 (Nanostring)


title: QM9414 SESp-cbh1 mutXYR1, glucose feed day 3, rep3

description: mutXYR1 glu feed d3 rep3


title: QM9414 SESp-cbh1 mutXYR1, glucose feed day 3, rep2

description: mutXYR1 glu feed d3 rep2


title: MNU_FF_50pg_OVA_NG_rep3 (Nanostring)


title: QM9414 SESp-cbh1 wtXYR1, batch lactose day 2, rep4

description: wtXYR1 lac d2 rep4

value: wild-type XYR1 under pdc1 promoter, SESp-cbh1

value: fed-batch:batch lactose

value: day 2


title: L2D4_S_3

city: Zhanjiang

first: Mingming

last: Chen

address: Haida Street No.1

country: China

institute: Guangdong Ocean University

description: RNA sequencing

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Trimmomatic
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
Alignment with hisat2
Read quantitation using cufflinks
Supplementary_files_format_and_content: csv files contain nine information: 1. gene_id;2-7. readcounts for each sample;3. gene_symbol; 4.description; 5.GO_id; 6.GO_term; 7.pathway; 8.pathway_description

organism: Vigna radiata

source_name: leaf

growth_protocol: low temperature or room temperature

extract_protocol:
Trizol extraction
RNA extraction, poly-A pulling, reverse transcription, 3'end adenylation, linker ligation, and PCR amplification

treatment_protocol: Low temperature + water or low temperature + uniconazole

value: Low temperature + uniconazole S3307

tag: genetic background

value: WT

value: mungbean leaf


title: QM9414 SESp-cbh1 wtXYR1, batch lactose day 2, rep3

description: wtXYR1 lac d2 rep3


title: L2D4_S_2

description: RNA sequencing

value: Low temperature + uniconazole S3306


title: MNU_FF_50pg_OVA_NG_rep2 (Nanostring)

value: normal urothelium

value: Ovation SoLo NuGEN RNA-seq System (OVA-NG)

value: FF


title: BC57_FF_50pg_OVA_NG_rep2 (Nanostring)


title: QM9414 SESp-cbh1 wtXYR1, batch lactose day 2, rep2

description: wtXYR1 lac d2 rep2


title: MNU_FFPE_50ng_std_rep2 (Nanostring)

value: direct quantification (std)

value: FFPE


title: CGND-HRA-02176

value: medial motor cortex

value: CTL

value: Male


title: L2D4_3

description: RNA sequencing

value: Low temperature + water


title: L2D4_1

description: RNA sequencing


title: CGND-HRA-02174

value: frontal cortex

value: ALS

value: Female


title: QM9414 SESp-cbh1 wtXYR1, batch lactose day 2, rep1

description: wtXYR1 lac d2 rep1

value: mycelia

value: wild-type XYR1 under pdc1 promoter, SESp-cbh1

value: fed-batch:batch lactose

value: day 2


title: QM9414 SESp-cbh1 mutXYR1, batch lactose day 2, rep2

description: mutXYR1 lac d2 rep2

value: mutated (V821F) XYR1 under pdc1 promoter, SESp-cbh1


title: QM9414 SESp-cbh1 mutXYR1, batch lactose day 2, rep4

description: mutXYR1 lac d2 rep4


title: QM9414 SESp-cbh1 mutXYR1, batch lactose day 2, rep3

description: mutXYR1 lac d2 rep3


title: CGND-HRA-02215

value: ALS+FTD


title: CGND-HRA-02177

value: lateral motor cortex


title: BC57_FF_50pg_OVA_NG_rep3 (Nanostring)

value: bladder cancer cells

value: Ovation SoLo NuGEN RNA-seq System (OVA-NG)

value: FF


title: BC57_FFPE_50ng_std_rep3 (Nanostring)

value: direct quantification (std)

value: FFPE


title: L2CK_2

description: RNA sequencing

value: water

value: WT

value: mungbean leaf


title: MNU_FFPE_50ng_std_rep3 (Nanostring)

value: normal urothelium


title: L2D4_2

description: RNA sequencing

value: Low temperature + water


title: CGND-HRA-02180

value: frontal cortex

value: CTL

value: Male


title: L2D4_S_1

description: RNA sequencing

value: Low temperature + uniconazole S3305


title: JR65_control

data_processing:
Libraries were sequenced on an Illumina Nextseq2000, and quantified using analyzed using 10x Genomics Cell Ranger version 5.0.1, with a GRCh38 reference genome database built with GENCODE v35 gene annotation and TE annotation
Assembly: GRCh38
Supplementary files format and content: Filtered count matrix output from Cell Ranger software (compressed as a gzipped tar-ball)

molecule: nuclear RNA

source_name: Motor cortex

extract_protocol:
Single nuclei were extracted from archived human postmortem motor cortex tissue using a Dounce homogenizer After removing cell debris, the lysed, filtered homogenate was then promptly centrifuged and supernatant decanted without disrupting the nuclei pellet. Following wash processes, the nucleus suspension was purified via gradient centrifugation, and sorted by FACS.
Nuclei were loaded onto 10x Chromium chips, with library preparation performed using the Single Cell 3' Gene Expression kit v3.1 according to the manufacturer's instructions.
Single nuclei RNA-seq

value: Motor cortex

value: control

tag: site of_disease_onset

value: Not applicable

tag: Sex


title: MNU_FFPE_50ng_std_rep1 (Nanostring)


title: CGND-HRA-02164

tag: tissue

value: medial motor cortex

value: ALS


title: QM9414 SESp-cbh1 mutXYR1, batch lactose day 2, rep1

description: mutXYR1 lac d2 rep1

value: mycelia

value: mutated (V821F) XYR1 under pdc1 promoter, SESp-cbh1

value: fed-batch:batch lactose

value: day 2


title: L2CK_3

description: RNA sequencing

tag: treatment

value: water

value: WT


title: CGND-HRA-02171

value: lateral motor cortex

tag: disease state

tag: gender

value: Female


title: L2CK_1

description: RNA sequencing

value: mungbean leaf


title: CGND-HRA-02165

tag: subject id


title: JR67_control


title: CGND-HRA-02158

value: ALS+FTD


title: JR34_sALS

value: sporadic ALS

value: bulbar


title: RH30_YAP_5SA_rep2

data_processing:
fastq files were pseudo-aligned using Kallisto (paired-end mode) in bootstrap mode (100)
pseudo-alignment was performed using the NCBI_hg38_p12 transcriptome
resulting TPM per transcripts were collapsed into gene level TPM values
Assembly: NCBI_hg38_p12
Supplementary files format and content: text files containing transcriptome wide expression levels combined by cell line

molecule: polyA RNA

extract_protocol:
total RNA was extracted using Triazol and poly-A enrichment step (Illumina Tureseq Kit)
Library preparation was performed in accordance to manufacturer’s instructions (Illumina Truseq Kit)

value: Ctrl


title: BC57_FFPE_50ng_std_rep2 (Nanostring)

tag: cell type

value: bladder cancer cells

tag: nanostring amplification method

value: direct quantification (std)

value: FFPE


title: CGND-HRA-02170

value: medial motor cortex

value: ALS


title: JR47_sALS_FTD

value: Motor cortex

value: sporadic ALS with FTD


title: JR27_sALS

value: Male


title: MNU_FF_50ng_std_rep3 (Nanostring)

value: normal urothelium

tag: rna input quantity

tag: method of sample preservation

value: FF


title: MNU_FF_50ng_std_rep2 (Nanostring)


title: CGND-HRA-02150


title: RH30_YAP_wt_rep2

tag: cell line


title: MNU_FF_50ng_std_rep1 (Nanostring)


title: JR9_ALS


title: RH30_YAP_wt_rep1


title: BC57_FF_50ng_std_rep2 (Nanostring)


title: CGND-HRA-02154

value: frontal cortex


title: BC57_FFPE_50ng_std_rep1 (Nanostring)


title: RH30_YAP_5D_rep1


title: RH30_YAP_5SA_rep1


title: CGND-HRA-02147

value: Female


title: CGND-HRA-02151

value: lateral motor cortex


title: RNA-seqM13_sgY1T1_rep1

description:
M13_sgY1T1_rep1
MOLM13_TPM.txt


title: BC57_FF_50ng_std_rep3 (Nanostring)


title: BC57_FF_50ng_std_rep1 (Nanostring)


title: RH30_empty_rep1


title: CGND-HRA-02144

value: ALS+FTD


title: RNA-seqM13_sgM2_3_rep2

description:
M13_sgM2_3_rep2
MOLM13_TPM.txt


title: RNA-seqM13_sgM2_3_rep1

description:
M13_sgM2_3_rep1
MOLM13_TPM.txt


title: CGND-HRA-02143


title: RNA-seqM13_sgCtrl_rep1

description:
M13_sgCtrl_rep1
MOLM13_TPM.txt

value: sgCtrl


title: RH30_YAP_5D_rep2


title: RNA-seqCHL1_sgY1T1_rep2

description:
CHL1_sgY1T1_rep2
CHL1_TPM.txt


title: RNA-seqM13_sgCtrl_rep2

description:
M13_sgCtrl_rep2
MOLM13_TPM.txt


title: CGND-HRA-01977

value: CTL


title: RH30_empty_rep2

value: Ctrl


title: CGND-HRA-01930


title: RNA-seqCHL1_sgM2_3_rep2

description:
CHL1_sgM2_3_rep2
CHL1_TPM.txt


title: RNA-seqCHL1_sgY1T1_rep1

description:
CHL1_sgY1T1_rep1
CHL1_TPM.txt


title: BC57_FFPE_50ng_2 (microarray)

hyb_protocol: Affymetrix microarrays were hybridized with 10µg of biotinylated cRNA according the supplier recommendations. Microarrays were washed and stained using FS450 fluidics upon a protocol provided by Affymetrix

scan_protocol: Microarrays were scanned using a 7G, Affymetrix GCS3000 scanner, raw data were acquired with Affymetrix Genechip Command Console.

data_processing: Signal reconstruction was performed with the RMA algorithm as implemented in Bioconductor affy package on R statistical software using the Dai custom CDF package: mta10_Mm_ENSG Brainarray Custom CDF Ensembl version 20

label: biotin

source_name: mouse bladder cancer cell line, BC57

label_protocol: 500pg, 2ng, 50ng and 100ng of total RNA were amplified to produced biotinylated complementary RNAs, as as decribe below and recommended by Affymetrix.

value: bladder cancer cells

tag: amplification kit

value: SensationPlus


title: BC57_FFPE_50ng_1 (microarray)

value: FFPE


title: CGND-HRA-01927


title: RNA-seqCHL1_sgCtrl_rep2

description:
CHL1_sgCtrl_rep2
CHL1_TPM.txt


title: RNA-seqM13_sgY1T1_rep2

description:
M13_sgY1T1_rep2
MOLM13_TPM.txt


title: CGND-HRA-01617-2


title: RNA-seq YAPC_Y1-Ctrl1_rep2_S16

description:
YAPC_Y1-Ctrl1_rep2_S16
YAPC_TPM.txt

source_name: YAPC

value: YAPC


title: RNA-seq YAPC_Ctrl-Ctrl2_rep1_S6

description:
YAPC_Ctrl2-T1_rep1_S7
YAPC_TPM.txt


title: RNA-seqCHL1_sgCtrl_rep1

description:
CHL1_sgCtrl_rep1
CHL1_TPM.txt


title: RNA-seq YAPC_Ctrl2-T1_rep2_S15

description:
YAPC_Ctrl-M3-5_rep2_S18
YAPC_TPM.txt


title: RNA-seq YAPC_Y1-Ctrl1_rep1_S8

description:
YAPC_Y1-Ctrl1_rep1_S8
YAPC_TPM.txt


title: BC57_FFPE_2ng_3 (microarray)

value: GeneChip WT Pico


title: RNA-seq YAPC_Y1-T1_rep2_S13

description:
YAPC_Y1-T1_rep2_S13
YAPC_TPM.txt


title: CGND-HRA-01586-2

value: medial motor cortex

value: ALS


title: CGND-HRA-01645


title: BC57_FFPE_2ng_1 (microarray)


title: RNA-seqCHL1_sgM2_3_rep1

description:
CHL1_sgM2_3_rep1
CHL1_TPM.txt


title: BC57_FFPE_2ng_2 (microarray)


title: RNA-seq YAPC_Ctrl2-T1_rep1_S7

description:
YAPC_Ctrl-M3-5_rep1_S6
YAPC_TPM.txt


title: CGND-HRA-00871

value: NEURCTL

value: Unknown


title: RNA-seq YAPC_Ctrl-Ctrl2_rep2_S14

description:
YAPC_Ctrl2-T1_rep2_S15
YAPC_TPM.txt


title: CGND-HRA-01218

value: Male


title: RNA-seq YAPC_sgCtrl-Ctrl2_rep2_S22

description:
YAPC_Ctrl-M3-2_rep2_S17
YAPC_TPM.txt


title: BC57_FFPE_0.5ng_3 (microarray)


title: RNA-seq YAPC_sgCtrl-Ctrl2_rep1_S10

description:
YAPC_Ctrl-M3-2_rep1_S5
YAPC_TPM.txt


title: RNA-seq YAPC_Y1-T1_rep1_S5

description:
YAPC_Y1-T1_rep1_S5
YAPC_TPM.txt


title: CGND-HRA-00792

value: frontal cortex


title: BC57_FFPE_0.5ng_1 (microarray)


title: BC57_FFPE_0.5ng_2 (microarray)


title: RNA-seq YAPC_sgCtrl-M3-2_rep2_S17

description:
YAPC_Ctrl-Ctrl_rep2_S24
YAPC_TPM.txt


title: RNA-seq YAPC_sgCtrl-M3-5_rep2_S18

description:
YAPC_Ctrl-M3-1_rep2_S16
YAPC_TPM.txt


title: urothelium_FFPE_50ng_2 (microarray)

source_name: mouse normal urothelium

value: normal urothelium


title: RNA-seq YAPC_sgCtrl-M3-5_rep1_S6

description:
YAPC_Ctrl-M3-1_rep1_S4
YAPC_TPM.txt


title: RNA-seq YAPC_sgCtrl-M3-2_rep1_S5

description:
YAPC_Ctrl-Ctrl_rep1_S12
YAPC_TPM.txt


title: CGND-HRA-00654

value: FTD


title: RNA-seq YAPC_sgCtrl-M3-1_rep2_S16

description:
YAPC_Ctrl-Ctrl2_rep2_S22
YAPC_TPM.txt


title: CGND-HRA-00569

value: lateral motor cortex

value: Female


title: urothelium_FFPE_50ng_1 (microarray)


title: RNA-seq YAPC_sgCtrl-Ctrl_rep1_S12

description:
YAPC_Ctrl-Ctrl2_rep1_S10
YAPC_TPM.txt

value: sgCtrl-Ctrl


title: CGND-HRA-00529


title: CGND-HRA-00502

value: motor cortex


title: RNA-seq YAPC_sgM2-3-Ctrl_rep2_S15

description:
YAPC_M2-3-Ctrl_rep2_S15
YAPC_TPM.txt


title: RNA-seq YAPC_sgM2-3-Ctrl_rep1_S3

description:
YAPC_M2-3-Ctrl_rep1_S3
YAPC_TPM.txt


title: urothelium_FFPE_2ng_3 (microarray)


title: urothelium_FFPE_2ng_2 (microarray)


title: RNA-seq YAPC_sgM2-2-Ctrl_rep2_S14

description:
YAPC_M2-2-Ctrl_rep2_S14
YAPC_TPM.txt


title: RNA-seq YAPC_sgM2-3-M3-1_rep2_S21

description:
YAPC_M2-3-M3-1_rep2_S21
YAPC_TPM.txt


title: urothelium_FFPE_2ng_1 (microarray)


title: CGND-HRA-00501


title: RNA-seq YAPC_sgM2-3-M3-1_rep1_S9

description:
YAPC_M2-3-M3-1_rep1_S9
YAPC_TPM.txt


title: urothelium_FFPE_0.5ng_1 (microarray)


title: CGND-HRA-00496


title: RNA-seq YAPC_sgM2-2-Ctrl_rep1_S2

description:
YAPC_M2-2-Ctrl_rep1_S2
YAPC_TPM.txt


title: urothelium_FFPE_0.5ng_2 (microarray)


title: RNA-seq YAPC_sgCtrl-Ctrl_rep2_S24

description:
YAPC_Ctrl-Ctrl2_rep1_S6
YAPC_TPM.txt


title: CGND-HRA-00655


title: BC57_FF_2ng_3 (microarray)

value: bladder cancer cells

value: FF


title: RNA-seq YAPC_sgM2-2-M3-5_rep2_S20

description:
YAPC_M2-2-M3-5_rep2_S20
YAPC_TPM.txt


title: RNA-seq YAPC_sgM2-1-Ctrl_rep2_S13

description:
YAPC_M2-1-Ctrl_rep2_S13
YAPC_TPM.txt


title: CGND-HRA-00497


title: RNA-seq YAPC_sgM2-2-M3-5_rep1_S8

description:
YAPC_M2-2-M3-5_rep1_S8
YAPC_TPM.txt


title: RNA-seq YAPC_sgCtrl-M3-1_rep1_S4

description:
YAPC_Ctrl-Ctrl2_rep2_S14
YAPC_TPM.txt


title: BC57_FF_2ng_2 (microarray)


title: CGND-HRA-00493


title: RNA-seq YAPC_sgM2-1-Ctrl_rep1_S1

description:
YAPC_M2-1-Ctrl_rep1_S1
YAPC_TPM.txt


title: RNA-seq YAPC_sgM2-1-M3-2_rep2_S19

description:
YAPC_M2-1-M3-2_rep2_S19
YAPC_TPM.txt


title: RNA-seq YAPC_sgM2-1-M3-2_rep1_S7

description:
YAPC_M2-1-M3-2_rep1_S7
YAPC_TPM.txt


title: CGND-HRA-00415


title: RNA-seq MDAMB231_sgY1-T1_rep1_S4

description:
MDAMB231_sgY1-T1_rep1_S4
MDA_MB231_TPM.txt


title: RNA-seq MDAMB231_sgY1-T1_rep2_S12

description:
MDAMB231_sgY1-T1_rep2_S12
MDA_MB231_TPM.txt


title: RNA-seq MDAMB231_sgY1-Ctrl_rep2_S11

description:
MDAMB231_sgY1-Ctrl_rep2_S11
MDA_MB231_TPM.txt


title: CGND-HRA-00412


title: BC57_FF_100ng_2 (microarray)

value: GeneChip WT Plus


title: RNA-seq MDAMB231_sgY1-Ctrl_rep1_S3

description:
MDAMB231_sgY1-Ctrl_rep1_S3
MDA_MB231_TPM.txt


title: BC57_FF_2ng_1 (microarray)


title: CGND-HRA-00409


title: RNA-seq MDAMB231_sgCtrl-Ctrl2_rep2_S9

description:
MDAMB231_sgCtrl-Ctrl2_rep2_S9
MDA_MB231_TPM.txt


title: BC57_FF_100ng_1 (microarray)


title: CGND-HRA-00406


title: RNA-seq MDAMB231_sgCtrl-Ctrl2_rep2_S22

description:
MDAMB231_sgCtrl-Ctrl2_rep2_S22
MDA_MB231_TPM.txt


title: RNA-seq MDAMB231_sgCtrl-Ctrl2_rep1_S10

description:
MDAMB231_sgCtrl-Ctrl2_rep1_S10
MDA_MB231_TPM.txt


title: RNA-seq MDAMB231_sgCtrl-Ctrl2_rep1_S1

description:
MDAMB231_sgCtrl-Ctrl2_rep1_S1
MDA_MB231_TPM.txt


title: CGND-HRA-00405


title: RNA-seq MDAMB231_sgCtrl-T1_rep2_S10

description:
MDAMB231_sgCtrl-T1_rep2_S10
MDA_MB231_TPM.txt


title: RNA-seq MDAMB231_sgCtrl-T1_rep1_S2

description:
MDAMB231_sgCtrl-T1_rep1_S2
MDA_MB231_TPM.txt


title: urothelium_FFPE_0.5ng_3 (microarray)

value: FFPE


title: CGND-HRA-00400


title: RNA-seq MDAMB231_sgCtrl-M3-2_rep2_S17

description:
MDAMB231_sgCtrl-M3-2_rep2_S17
MDA_MB231_TPM.txt


title: RNA-seq MDAMB231_sgCtrl-M3-2_rep1_S5

description:
MDAMB231_sgCtrl-M3-2_rep1_S5
MDA_MB231_TPM.txt


title: BC57_FF_0.5ng_2 (microarray)

value: GeneChip WT Pico


title: RNA-seq MDAMB231_sgCtrl-M3-5_rep2_S18

description:
MDAMB231_sgCtrl-M3-5_rep2_S18
MDA_MB231_TPM.txt


title: BC57_FF_0.5ng_3 (microarray)


title: BC57_FF_0.5ng_1 (microarray)


title: RNA-seq MDAMB231_sgCtrl-M3-5_rep1_S6

description:
MDAMB231_sgCtrl-M3-5_rep1_S6
MDA_MB231_TPM.txt


title: urothelium_FF_2ng_2 (microarray)


title: urothelium_FF_2ng_3 (microarray)


title: RNA-seq MDAMB231_sgCtrl-M3-1_rep1_S4

description:
MDAMB231_sgCtrl-M3-1_rep1_S4
MDA_MB231_TPM.txt


title: CGND-HRA-00399

value: medial motor cortex


title: CGND-HRA-00297

value: CTL


title: RNA-seq MDAMB231_sgM2-3-Ctrl_rep2_S15

description:
MDAMB231_sgM2-3-Ctrl_rep2_S15
MDA_MB231_TPM.txt


title: CGND-HRA-00251


title: CGND-HRA-00242


title: urothelium_FF_2ng_1 (microarray)


title: CGND-HRA-00296


title: RNA-seq MDAMB231_sgM2-3-M3-1_rep1_S9

description:
MDAMB231_sgM2-3-M3-1_rep1_S9
MDA_MB231_TPM.txt


title: RNA-seq MDAMB231_sgM2-3-M3-1_rep2_S21

description:
MDAMB231_sgM2-3-M3-1_rep2_S21
MDA_MB231_TPM.txt


title: RNA-seq MDAMB231_sgCtrl-Ctrl_rep2_S24

description:
MDAMB231_sgCtrl-Ctrl_rep2_S24
MDA_MB231_TPM.txt


title: CGND-HRA-00067-2

value: ALS


title: RNA-seq MDAMB231_sgM2-2-Ctrl_rep2_S14

description:
MDAMB231_sgM2-2-Ctrl_rep2_S14
MDA_MB231_TPM.txt


title: RNA-seq MDAMB231_sgM2-3-Ctrl_rep1_S3

description:
MDAMB231_sgM2-3-Ctrl_rep1_S3
MDA_MB231_TPM.txt


title: urothelium_FF_100ng_2 (microarray)


title: urothelium_FF_100ng_1 (microarray)


title: RNA-seq MDAMB231_sgM2-2-Ctrl_rep1_S2

description:
MDAMB231_sgM2-2-Ctrl_rep1_S2
MDA_MB231_TPM.txt


title: Mnip3

city: Athens

first: Anumantha

middle: G

last: Kanthasamy

state: GA

address: B122 Life Sciences Bldg University of Georgia

institute: University of Georgia

data_processing:
AltAnalyze_v.2.1.4.3-Win64 was used to process the data by inputting the fastq files and generating the final expression files in TPM. Embedded Kallisto was used for alignment. https://www.altanalyze.org/
Assembly: EnsMart72(hg19)
Supplementary files format and content: Separate files include ensemble identifiers with counts, isocounts, expression, and summary alignment and also expression analysis file

extract_protocol:
Briefly, cells were lysed in 2 volumes of modified TNE buffer containing 1% NP-40, Halt protease and phosphatase inhibitors, 1 mM sodium orthovanadate, 1 mM phenylmethanesulfonyl fluoride, and SUPERase RNase inhibitor (Invitrogen, 1:100). Lysates were cleared twice through centrifugation, and 2.5% of the total cleared lysate was collected and mixed with 1 mL of TRIzol for the RNA input fraction. RNA input was poly (A) purified using the GenElute mRNA kit (Sigma, #MRN 70). The remaining cleared lysate was subjected to immunoprecipitation with 10 μg of YTHDF2 antibody under constant rotation at 4° C for 4 h. The Protein A/G Magnetic Beads from Thermo Scientific Pierce (#88803) were then added to incubate under constant rotation at 4° C for 1 h. Then the YTHDF2 mRNP complexes were magnetically isolated, washed with TNE buffer, and placed in 1 mL of TRIzol for RNA isolation for the immunoprecipitated fraction. Sequencing was performed using a 50 cycle (paired-end) with a HiSeq 3000 system (Illumina) with a total 100 ng of RNA from both input and immunoprecipitated fractions.
100 ng of Input and IP RNA were used to generate the library using Illumina TruSeq stranded mRNA sample preparation kit.

value: Astrocyte

value: 2% FBS MEM + Manganese 100 µM

tag: rip antibody


title: Mnip2


title: urothelium_FF_0.5ng_2 (microarray)


title: urothelium_FF_0.5ng_3 (microarray)


title: AL8, FdiA, scRNA-seq

city: San Antonio

first: Melanie

middle: Anita

last: Carless

state: Texas

address: One UTSA Circle

institute: The University of Texas at San Antonio

data_processing:
Data was processed using a cloud-based analysis platform, Trailmaker(TM) (https://app.trailmaker.parsebiosciences.com/). Standard QC thresholds were utilized, including ones based on: cellular distribution of unique molecular identifier (UMI) counts; mitochondrial content; linear relationship of the number of genes expressed and the number of UMIs per cell; and doublet identification.
Assembly: GRCh38
Supplementary files format and content: Matrix of normalized gene expression counts for fibroblasts and FdiAs at four timepoints: Day 0, Day 10, Day 30, and Day 50

source_name: Connective tissue

extract_protocol:
Total RNA was extracted from samples of fibroblasts (Day 0) and FdiAs (Day 10, 30, and 50) using the All-Prep DNA/RNA mini kit (Qiagen)
Carried out according to manufacturer’s instructions for the Evercode Whole Transcriptome v2 Mini kit (Parse Biosciences, Seattle, USA)

value: Connective tissue

value: Fibroblast-derived induced-astrocytes

tag: genotype

value: WT

value: Combination of small molecules to induce trans-differentiation of human adult fibroblasts to astrocytes


title: RNA-seq MDAMB231_sgM2-2-M3-5_rep1_S8

description:
MDAMB231_sgM2-2-M3-5_rep1_S8
MDA_MB231_TPM.txt


title: RNA-seq MDAMB231_sgM2-1-M3-2_rep1_S7

description:
MDAMB231_sgM2-1-M3-2_rep1_S7
MDA_MB231_TPM.txt


title: RNA-seq MDAMB231_sgM2-1-M3-2_rep2_S19

description:
MDAMB231_sgM2-1-M3-2_rep2_S19
MDA_MB231_TPM.txt


title: RNA-seq MDAMB231_sgCtrl-Ctrl_rep1_S12

description:
MDAMB231_sgCtrl-Ctrl_rep1_S12
MDA_MB231_TPM.txt


title: RNA-seq MDAMB231_sgM2-1-Ctrl_rep2_S13

description:
MDAMB231_sgM2-1-Ctrl_rep2_S13
MDA_MB231_TPM.txt


title: RNA-seq T3M4_sgY1T1_rep1

description:
T3M4_sgY1T1_rep1
T3M4_TPM.txt


title: I17932_3

city: Houston

first: Sara

middle: Chloe

last: Di Rienzi

state: TX

address: 1 Baylor Plaza Room 743E

department: Molecular Virology and Microbiology

institute: Baylor College of Medicine

description: enteroid batch 2; replicate 3

data_processing:
Basecalling was performed using CASAVA version 1.8. Reads were filtered as follows: reads containing adaptors were removed, reads with more than 10% N reads were removed,reads where > 50% of the bases have Qscore <= 5 were removed.
Reads were aligned to hg19 human genome using STAR v2.5, with mismatch=2
Reads were quantified using HTSeq v0.6.1, with -m union
Assembly: Homo_sapiens_hg19
Supplementary files format and content: One tab-delimited text file with the read counts for each Sample by each gene mapped

source_name: NGN3 J2 human enteroids

growth_protocol: NGN3 J2 enteroids were propagated in 3D CMGF+ media + 10 umol Y-27632 Rock inhibitor + 200 ug/ml geneticin. NGN3 J2 enteroids were then seeded onto 24-well transwells and differentiated in the presence of differentiation media with or without 1 ug/ml doxycycline.

extract_protocol:
Transwell inserts were excised and placed in Trizol. Following a chloroform extraction, the aqueous phase was extracted using the Qiagen Rneasy Isolation Kit.
Paired-end Illumina sequencing libraries were prepared by Novogene. Briefly, total RNA was enriched for Eukaryote mRNA. mRNA was fragmented and cDNA synthesis proceeded using the standard NEB library construction.

treatment_protocol: All treatments were performed in differentiation media. LDM4 media was lyophilized and resuspended in differentiation media for use on the enteroids. L. reuteri conditioned media were prepared as follows: A single colony was grown overnight in MRS. The overnight was diluted into LDM4 media and grown until reaching an OD of 0.5-0.6. Cells were pelleted and supernatants were removed. Supernatants were pH adjusted to 7.0 and lyophilized. Lyophilized material was resuspended in differentiation media for use on the enteroids. LDM4 media recipe is provided in PMID 19210794.

value: NGN3 J2 human enteroids

value: engineered jejunal enteroid line

value: induced

value: L. reuteri 17938 conditioned medium


title: RNA-seq MDAMB231_sgM2-1-Ctrl_rep1_S1

description:
MDAMB231_sgM2-1-Ctrl_rep1_S1
MDA_MB231_TPM.txt


title: Mnip1


title: I17932_2

description: enteroid batch 2; replicate 2


title: I17932_1

description: enteroid batch 2; replicate 1


title: RNA-seq T3M4_sgCtrl_rep2

description:
T3M4_sgCtrl_rep2
T3M4_TPM.txt

value: sgCtrl


title: Visceral Sensory Ganglion Organoid (VSGO) in chip, fresh, E3, spheroid, day38, snRNAseq

city: Seoul

first: Hwee-Seon

last: Park

address: 103, Daehak-ro, Jongno-gu, Seoul

department: Department of Biomedical Sciences

country: South Korea

institute: Seoul National University

description: 10x Genomics

data_processing:
10x Genomics Cell Ranger (version 8.0.0) with reference genome GRCh38-2024-A was used for generating feature-barcode matrices from FASTQs.  CellBender (version 0.2.0) was used to perform ambient RNA correction on the raw gene count matrices.
Assembly: GRCh38 (2024-A version)
Supplementary files format and content: Ambient RNA-corrected raw count h5 file.  The output of the filtered_bc_matrices includes tab-separated values files and matrix files, which are generated using the cellranger --count with default parameters.

extract_protocol:
Dissociated cells and extracted nuclei were respectively suspended in 0.04% bovine serum albumin (BSA) in PBS and 1% BSA in PBS containing 0.2U/µl SUPERase RNase Inhibitor.  Each sample was treated with either ReadyCount Green/Red Viability Stain (Invitrogen) for dissociated cells or YOYO-1 Iodide (ThermoFisher Scientific) for nuclei.  The number of cells/nuclei was measured, and cell viability was checked using the automated cell counter Countess 3 FL (ThermoFisher Scientific). The cell/nuclei suspension was centrifuged at 400 × g for 5 minutes at 4 °C and then resuspended in the BSA solution at an appropriate volume for microfluidic chip loading.  Each sample was loaded per lane of a 10x microfluidic chip device (Chromium Next GEM Chip G).  Generally, for each library, 16,000 cells or nuclei were loaded onto a 10× chromium controller to target the recovery of 10,000 cells or nuclei.
Library preparation was carried out using Chromium Single Cell 3′ Reagent Kits (v.3.1), following the manufacturer's instructions.  Libraries were sequenced on a Novaseq system (Illumina) with the aim of achieving a minimum of 30,000 paired-end reads per cell.

value: iPSC derived visceral sensory ganglion oraganoids (VSGO)

value: APOE E3/E3


title: induced Human Colon Organoid (HCO) in chip co-cultured for 7days, fresh, E4, organoid, scRNAseq

description: 10x Genomics

value: iPSC derived human colon organoids (HCO)

value: APOE E4/E4


title: Ctrl2ip

value: 2% FBS MEM


title: RNA-seq T3M4_sgM2_3_rep2

description:
T3M4_sgM2_3_rep2
T3M4_TPM.txt


title: urothelium_FF_0.5ng_1 (microarray)

value: normal urothelium

value: GeneChip WT Pico

value: FF


title: RNA-seq MDAMB231_sgCtrl-M3-1_rep2_S16

description:
MDAMB231_sgCtrl-M3-1_rep2_S16
MDA_MB231_TPM.txt


title: Ctrl1ip

value: Astrocyte


title: RNA-seq SUIT2_sgY1T1_rep2

description:
SUIT2_sgY1T1_rep2
SUIT2_TPM.txt


title: Ctrl3ip


title: RNA-seq SUIT2_sgY1T1_rep1

description:
SUIT2_sgY1T1_rep1
SUIT2_TPM.txt


title: RNA-seq T3M4_sgM2_3_rep1

description:
T3M4_sgM2_3_rep1
T3M4_TPM.txt


title: RNA-seq T3M4_sgY1T1_rep2

description:
T3M4_sgY1T1_rep2
T3M4_TPM.txt


title: RNA-seq MDAMB231_sgM2-2-M3-5_rep2_S20

description:
MDAMB231_sgM2-2-M3-5_rep2_S20
MDA_MB231_TPM.txt


title: Mn2

value: 2% FBS MEM + Manganese 100 µM


title: I64752_3

description: enteroid batch 2; replicate 3

value: L. reuteri 6475 conditioned medium


title: Mn3


title: Ctrl3


title: I17931_3

description: enteroid batch 1; replicate 3


title: RNA-seq SUIT2_sgCtrl_rep1

description:
SUIT2_sgCtrl_rep1
SUIT2_TPM.txt


title: I17931_2

description: enteroid batch 1; replicate 2


title: Mn1


title: Ctrl2


title: RNA-seq SUIT2_sgM2_3_rep1

description:
SUIT2_sgM2_3_rep1
SUIT2_TPM.txt


title: I17931_1

description: enteroid batch 1; replicate 1


title: RNA-seq SUIT2_sgCtrl_rep2

description:
SUIT2_sgCtrl_rep2
SUIT2_TPM.txt


title: RNA-seq RH30_sgY1T1_rep2

description:
RH30_sgY1T1_rep2
RH30_TPM.txt


title: RNA-seq RH30_sgCtrl_rep2

description:
RH30_sgCtrl_rep2
RH30_TPM.txt


title: RNA-seq RH30_sgM2_3_rep2

description:
RH30_sgM2_3_rep2
RH30_TPM.txt


title: RNA-seq RH30_sgCtrl_rep1

description:
RH30_sgCtrl_rep1
RH30_TPM.txt


title: I64752_2

description: enteroid batch 2; replicate 2


title: RNA-seq RD_sgY1T1_rep2

description:
RD_sgY1T1_rep2
RD_TPM.txt

source_name: RD

value: RD


title: Ctrl1


title: RNA-seq RD_sgY1T1_rep1

description:
RD_sgY1T1_rep1
RD_TPM.txt


title: I64751_2

description: enteroid batch 1; replicate 2

value: NGN3 J2 human enteroids


title: I64752_1

description: enteroid batch 2; replicate 1

value: engineered jejunal enteroid line


title: RNA-seq T3M4_sgCtrl_rep1

description:
T3M4_sgCtrl_rep1
T3M4_TPM.txt


title: RNA-seq RH30_sgM2_3_rep1

description:
RH30_sgM2_3_rep1
RH30_TPM.txt


title: RNA-seq RD_sgM2_3_rep2

description:
RD_sgM2_3_rep2
RD_TPM.txt


title: RNA-seq SUIT2_sgM2_3_rep2

description:
SUIT2_sgM2_3_rep2
SUIT2_TPM.txt


title: I64751_3

description: enteroid batch 1; replicate 3

value: induced


title: U64752_3

description: enteroid batch 2; replicate 3

value: uninduced


title: RNA-seq RH30_sgY1T1_rep1

description:
RH30_sgY1T1_rep1
RH30_TPM.txt


title: RNA-seq PATU8988T_sgY1T1_rep1

description:
PATU8988T_sgY1T1_rep1
PATU8988T_TPM.txt


title: RNA-seq RD_sgCtrl_rep1

description:
RD_sgCtrl_rep1
RD_TPM.txt

value: sgCtrl


title: RNA-seq PATU8988T_sgM2_3_rep2

description:
PATU8988T_sgM2_3_rep2
PATU8988T_TPM.txt


title: RNA-seq RD_sgCtrl_rep2

description:
RD_sgCtrl_rep2
RD_TPM.txt


title: U64752_2

description: enteroid batch 2; replicate 2


title: RNA-seq RD_sgM2_3_rep1

description:
RD_sgM2_3_rep1
RD_TPM.txt


title: I64751_1

description: enteroid batch 1; replicate 1


title: RNA-seq PATU8988T_sgM2_3_rep1

description:
PATU8988T_sgM2_3_rep1
PATU8988T_TPM.txt


title: RNA-seq PATU8988T_sgCtrl_rep1

description:
PATU8988T_sgCtrl_rep1
PATU8988T_TPM.txt


title: RNA-seq PATU8902_sgY1T1_rep2

description:
PATU8902_sgY1T1_rep2
PATU8902_TPM.txt


title: RNA-seq PATU8902_sgM2_3_rep2

description:
PATU8902_sgM2_3_rep2
PATU8902_TPM.txt


title: U64751_2

description: enteroid batch 1; replicate 2


title: RNA-seq PATU8902_sgM2_3_rep1

description:
PATU8902_sgM2_3_rep1
PATU8902_TPM.txt


title: RNA-seq PATU8988T_sgY1T1_rep2

description:
PATU8988T_sgY1T1_rep2
PATU8988T_TPM.txt


title: U64752_1

description: enteroid batch 2; replicate 1


title: RNA-seq PATU8902_sgCtrl_rep2

description:
PATU8902_sgCtrl_rep2
PATU8902_TPM.txt


title: heart biopsy_pABMR_TH136

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

source_name: heart biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol:
All human heart biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.
Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

value: heart biopsy

tag: mmdx (abmr, tcmr, mixed, pabmr, nr)

value: pABMR


title: heart biopsy_pABMR_TH137


title: RNA-seq PATU8902_sgCtrl_rep1

description:
PATU8902_sgCtrl_rep1
PATU8902_TPM.txt


title: RNA-seq PANC1_sgY1T1_rep2

description:
PANC1_sgY1T1_rep2
PANC1_TPM.txt


title: heart biopsy_NR_TH133

value: NR


title: heart biopsy_NR_TH134


title: heart biopsy_NR_TH132


title: RNA-seq PATU8988T_sgCtrl_rep2

description:
PATU8988T_sgCtrl_rep2
PATU8988T_TPM.txt


title: heart biopsy_NR_TH131


title: heart biopsy_NR_TH130


title: heart biopsy_ABMR_TH135

value: ABMR


title: U64751_3

description: enteroid batch 1; replicate 3


title: heart biopsy_NR_TH129


title: induced Visceral Sensory Neurons(i-VSN), fresh, E3, monolayer, day42, scRNAseq

description: 10x Genomics

value: iPSC derived sensory neurons(iVSN)

value: APOE E3/E3


title: RNA-seq PANC1_sgM2_3_rep1

description:
PANC1_sgM2_3_rep1
PANC1_TPM.txt


title: RNA-seq PANC1_sgY1T1_rep1

description:
PANC1_sgY1T1_rep1
PANC1_TPM.txt


title: RNA-seq PANC1_sgM2_3_rep2

description:
PANC1_sgM2_3_rep2
PANC1_TPM.txt


title: RNA-seq PATU8902_sgY1T1_rep1

description:
PATU8902_sgY1T1_rep1
PATU8902_TPM.txt


title: RNA-seq PANC1_sgCtrl_rep1

description:
PANC1_sgCtrl_rep1
PANC1_TPM.txt


title: induced Visceral Sensory Neurons(i-VSN), fresh, E3, monolayer, day24, scRNAseq

description: 10x Genomics


title: RNA-seq MIAPACA2_sgY1T1_rep2

description:
MIAPACA2_sgY1T1_rep2
MIAPACA2_TPM.txt


title: U64751_1

description: enteroid batch 1; replicate 1


title: RNA-seq PANC1_sgCtrl_rep2

description:
PANC1_sgCtrl_rep2
PANC1_TPM.txt


title: heart biopsy_NR_TH128


title: induced Visceral Sensory Neurons(i-VSN), fresh, E3, monolayer, day19, scRNAseq

description: 10x Genomics


title: heart biopsy_NR_TH127


title: heart biopsy_NR_TH126


title: induced Visceral Sensory Neurons(i-VSN), fresh, E3, monolayer, day32, scRNAseq

description: 10x Genomics


title: RNA-seq MIAPACA2_sgM2_3_rep2

description:
MIAPACA2_sgM2_3_rep2
MIAPACA2_TPM.txt


title: induced Visceral Sensory Neurons(i-VSN), frozen, E4, monolayer, day40, snRNAseq

description: 10x Genomics

value: APOE E4/E4


title: RNA-seq MDAMB231_MKI-wt_rep2_24h

description:
MDAMB231_MKI-wt_rep2_24h
MDA_MB231_MKI_TPM.txt

value: MKI-wt


title: RNA-seq MIAPACA2_sgCtrl_rep1

description:
MIAPACA2_sgCtrl_rep1
MIAPACA2_TPM.txt


title: RNA-seq MIAPACA2_sgCtrl_rep2

description:
MIAPACA2_sgCtrl_rep2
MIAPACA2_TPM.txt


title: heart biopsy_NR_TH125


title: heart biopsy_pABMR_TH124


title: Visceral Sensory Ganglion Organoid(VSGO), fresh, E4, spheroid, day32, snRANseq

description: 10x Genomics

value: iPSC derived visceral sensory ganglion oraganoids(VSGO)


title: RNA-seq MDAMB231_MKI-mut2_rep2_24h

description:
MDAMB231_MKI-mut2_rep2_24h
MDA_MB231_MKI_TPM.txt


title: heart biopsy_NR_TH123


title: induced Visceral Sensory Neurons(i-VSN), frozen, E3, monolayer, day40, snRNAseq

description: 10x Genomics


title: Visceral Sensory Ganglion Organoid(VSGO), frozen, E3, spheroid, day33, snRNAseq

description: 10x Genomics


title: RNA-seq KP2_sgY1T1_rep2

description:
KP2_sgY1T1_rep2
KP2_TPM.txt


title: RNA-seq MDAMB231_MKI-wt_rep1_24h

description:
MDAMB231_MKI-wt_rep1_24h
MDA_MB231_MKI_TPM.txt


title: heart biopsy_NR_TH122


title: heart biopsy_NR_TH121


title: RNA-seq MIAPACA2_sgY1T1_rep1

description:
MIAPACA2_sgY1T1_rep1
MIAPACA2_TPM.txt


title: heart biopsy_NR_TH120


title: RNA-seq KP2_sgM2_3_rep2

description:
KP2_sgM2_3_rep2
KP2_TPM.txt


title: RNA-seq KP2_sgM2_3_rep1

description:
KP2_sgM2_3_rep1
KP2_TPM.txt


title: RNA-seq KP2_sgCtrl_rep2

description:
KP2_sgCtrl_rep2
KP2_TPM.txt


title: RNA-seq MIAPACA2_sgM2_3_rep1

description:
MIAPACA2_sgM2_3_rep1
MIAPACA2_TPM.txt


title: Embryoid body, fresh, E3, day15, scRNAseq

description: 10x Genomics

value: iPSC derived embryoid body


title: Visceral Sensory Ganglion Organoid(VSGO), frozen, E4, spheroid, day33, snRNAseq

description: 10x Genomics


title: RNA-seq KP2_sgY1T1_rep1

description:
KP2_sgY1T1_rep1
KP2_TPM.txt


title: Embryoid body, fresh, E3, day8, scRNAseq

description: 10x Genomics


title: RNA-seq KLM1_sgY1T1_rep2

description:
KLM1_sgY1T1_rep2
KLM1_TPM.txt


title: 24h-Auxin_DCW448_rep4

city: Mainz

first: Jan

last: Padeken

address: Ackermannweg 4

institute: Institute of Molecular Biology

data_processing:
Basecalling was performed using RTA v. 1.13.48.
Reads were aligned to the ce10 (WS220) genome assembly using the qAlign function from the QuasR R package (v. 3.2) with the parameter "splicedAlignment = TRUE", which calls the SpliceMap aligner with default parameters.
Gene expression was quantified using WS220 annotations downloaded from UCSC. The qCount function in the QuasR package was used to count reads overlapping all annotated exons for each gene.
Assembly: Genome_build: ce10 (WS220)
Supplementary files format and content: Supplementary_files_format_and_content: Tab-delimited file. First column contains gene names (Wormbase identifiers) and width of genes, following columns contain raw counts of reads overlapping each gene for each sample.

organism: Caenorhabditis elegans

source_name: intestine

growth_protocol: RNA was isolated from dissected intesties from synchronized L1  larvae grown at 20°C for the indicated amount of time on Auxin containing plates in 4 independent biological replicates.

extract_protocol:
Extraction of RNA was performed according to the WormBook protocol (Stiernagle, 2006). For isolated tissues, RNA was purified from lysed muscle or seam cells following the instructions of the Norgen Single Cell RNA Purification Kit (51800, Norgen Biotek).
Libraries were produced using the Smart-Seq2 mRNA sequencing kit (Illumina).

treatment_protocol: For dissected tissues, RNA was purified from lysed intestinal cells cells following the instructions of the Norgen Single Cell RNA Purification Kit (51800, Norgen Biotek). Libraries were produced using the Smart-Seq2 mRNA sequencing kit (Illumina).

value: intestine

tag: strain

value: ieSi57 [eft-3p::TIR1::mRuby::unc-54 3'UTR + Cbr-unc-119(+)] II ; unc-119(ed3) III.

value: 1 mM Auxin

tag: time


title: P175_P187|024|FABP4+

city: london

first: Paula

last: Longhi

address: charterhouse sq

country: United Kingdom

institute: Queen Mary University of London

description: All Data WTA_1_7_22.xlsx

data_processing:
Count data were processed and normalized usingGeoMx® DSP Analysis Suite
AOIs with fewer than 1000 raw reads  were filtered out of the analysis. A second step assesses the percentage aligned reads; alignment here matches the sequenced barcode to GeoMx library of barcodes. The sequenced barcodes should match the known GeoMx library of barcodes hence a high percentage alignment should be expected (an alignment threshold value <80% is typically used to flag segments). Sequencing saturation was then assessed to ascertain whether sufficient sequencing depth was attained calculated as 1- (aligned reads/de-duplicated reads). A value<50% sequencing saturation was used to flag segments.
A background quality control step was additionally performed based on negative probes included in the sequencing run which do not bind any specific sequences but should be detected due to non-specific binding to tissue and indicates the limits of detection in the tissue. A no template control was also included in the first well of each collection plate with the negative control in PCR reading very low counts.
The Grubbs outlier test is performed to exclude a probe from all segments if the probe is higher or lower in >20% segments. A limit of quantitation value is also defined where a target is considered to be detected with high confidence, the default setting here being 2 standard deviations above the geometric mean of the negative probes. Filtering was performed to further refine the dataset followed by Q3 normalisation.
Assembly: GeoMx RNA detection probes.
Supplementary files format and content: normalised data in Excel spreadsheet

source_name: Epicardial AT

extract_protocol:
DSP aspirate was dried and resuspended in 10 µL DEPC-treated water, and 4 µL was used in a PCR reaction. NanoString SeqCode primers were used to amplify the tags and add Illumina adaptor sequences and sample demultiplexing barcodes. PCR products were pooled and purified with two rounds of AMPure XP beads (Beckman Coulter). Libraries were sequenced on an Illumina NextSeq 550, NextSeq 2000, or NovaSeq 6000 according to the manufacturer’s instructions, with at least 27 × 27 paired end reads.
FASTQ files were processed using the NanoString GeoMx NGS Pipeline  v2.2. Briefly, reads were trimmed to remove low quality bases and adapter sequences. Paired end reads were stitched and aligned, and the barcode and UMI sequences were extracted. Barcodes were matched to known probe barcodes with maximum one mismatch allowed. Reads matching the same barcode were deduplicated by UMI.

treatment_protocol: AA tissue with surrounding EAT samples were selected from 4 patients of which 2 were from AF patients and 2 from SR patients. Freshly cut paraffin-embedded sample slides were sent to NanoString Technologies. Sample slides were deparaffinised and stained with fluorescent antibody markers to distinguish between the adipose tissue (FABP4) and cardiac tissue (troponin). Specific regions of interest (ROIs) were then pre-selected either side of the border zones of the AA/EAT and deep in the AA and deep in the EAT. Thus 4 ROIs were selected per slide. Following dewaxing of the FFPE slides, they were treated with a Tris-EDTA buffer to expose the RNA targets and a proteinase K digestion was performed to remove any protein bound to RNA. The tissue was then incubated overnight at 37°C with the GeoMx RNA detection probes (consisting of oligonucleotide probes with an antisense target-binding region and an indexing oligonucleotide sequence linked by a photocleavable linker). Slides were imaged in four fluorescence channels (FITC/525 nm, Cy3/568 nm, Texas Red/615 nm, Cy5/666 nm) to visualize morphology markers, and regions of interest were selected for collection. AOIs were illuminated and released tags were collected into 96-well plates as previously described.

value: Epicardial AT

tag: slide id

tag: roi number

tag: area

value: border


title: RNA-seq KLM1_sgY1T1_rep1

description:
KLM1_sgY1T1_rep1
KLM1_TPM.txt

tag: treatment


title: heart biopsy_NR_TH119

tag: tissue


title: 12h-Auxin_DCW447_rep4

value: qzIs15[rpoa-2p::degron1(TIR1)::GFP::rpoa-2] I; ieSi57 [eft-3p::TIR1::mRuby::unc-54 3'UTR+Cbr-unc-119(+)] II


title: RNA-seq KLM1_sgM2_3_rep2

description:
KLM1_sgM2_3_rep2
KLM1_TPM.txt


title: P175_P187|022|FABP4+

description: All Data WTA_1_7_22.xlsx


title: heart biopsy_NR_TH118


title: 12h-Auxin_DCW448_rep4


title: heart biopsy_NR_TH117


title: heart biopsy_NR_TH116


title: heart biopsy_NR_TH115


title: RNA-seq KLM1_sgM2_3_rep1

description:
KLM1_sgM2_3_rep1
KLM1_TPM.txt


title: heart biopsy_TCMR_TH114

value: TCMR


title: pre-Auxin_DCW447_rep4

value: 0 mM Auxin


title: Visceral Sensory Ganglion Organoid(VSGO), fresh, E3, spheroid, day32, snRANseq

description: 10x Genomics


title: P175_P187|021|FABP4+

description: All Data WTA_1_7_22.xlsx

value: distal


title: 24h-Auxin_DCW447_rep4


title: RNA-seq KP2_sgCtrl_rep1

description:
KP2_sgCtrl_rep1
KP2_TPM.txt

value: sgCtrl


title: pre-Auxin_DCW448_rep4


title: RNA-seq KLM1_sgCtrl_rep2

description:
KLM1_sgCtrl_rep2
KLM1_TPM.txt


title: 24h-Auxin_DCW447_rep3


title: P175_P187|020|FABP4+

description: All Data WTA_1_7_22.xlsx


title: RNA-seq KLM1_sgCtrl_rep1

description:
KLM1_sgCtrl_rep1
KLM1_TPM.txt


title: P175_P187|019|FABP4+

description: All Data WTA_1_7_22.xlsx


title: heart biopsy_NR_TH113

value: heart biopsy

value: NR


title: RNA-seq HPAFII_sgY1T1_rep2

description:
HPAFII_sgY1T1_rep2
HPAFII_TPM.txt

source_name: HPAFII

value: HPAFII


title: P175_P187|018|DNA

description: All Data WTA_1_7_22.xlsx

source_name: Atrial appendage

value: Atrial appendage


title: P175_P187|023|FABP4+

description: All Data WTA_1_7_22.xlsx


title: 12h-Auxin_DCW447_rep3


title: 24h-Auxin_DCW448_rep3


title: RNA-seq HPAFII_sgY1T1_rep1

description:
HPAFII_sgY1T1_rep1
HPAFII_TPM.txt


title: P175_P187|016|DNA

description: All Data WTA_1_7_22.xlsx


title: heart biopsy_NR_TH111


title: P175_P187|017|DNA

description: All Data WTA_1_7_22.xlsx


title: heart biopsy_NR_TH112


title: P175_P187|014|DNA

description: All Data WTA_1_7_22.xlsx


title: RNA-seq HPAFII_sgM2_3_rep2

description:
HPAFII_sgM2_3_rep2
HPAFII_TPM.txt


title: 12h-Auxin_DCW448_rep3


title: RNA-seq HPAFII_sgM2_3_rep1

description:
HPAFII_sgM2_3_rep1
HPAFII_TPM.txt


title: P175_P187|015|DNA

description: All Data WTA_1_7_22.xlsx


title: P175_P187|013|DNA

description: All Data WTA_1_7_22.xlsx


title: pre-Auxin_DCW447_rep3


title: heart biopsy_NR_TH109


title: heart biopsy_pABMR_TH110

value: pABMR


title: 24h-Auxin_DCW448_rep2


title: heart biopsy_NR_TH107


title: RNA-seq HPAFII_sgCtrl_rep2

description:
HPAFII_sgCtrl_rep2
HPAFII_TPM.txt


title: 24h-Auxin_DCW447_rep2


title: RNA-seq HPAFII_sgCtrl_rep1

description:
HPAFII_sgCtrl_rep1
HPAFII_TPM.txt


title: heart biopsy_NR_TH105


title: RNA-seq H23_sgY1T1_rep2

description:
H23_sgY1T1_rep2
H23_TPM.txt


title: RNA-seq H23_sgY1T1_rep1

description:
H23_sgY1T1_rep1
H23_TPM.txt


title: 12h-Auxin_DCW447_rep2


title: pre-Auxin_DCW448_rep3


title: P175_P187|011|FABP4+

description: All Data WTA_1_7_22.xlsx


title: RNA-seq H23_sgM2_3_rep2

description:
H23_sgM2_3_rep2
H23_TPM.txt


title: 12h-Auxin_DCW448_rep2


title: P175_P187|010|FABP4+

description: All Data WTA_1_7_22.xlsx


title: P175_P187|009|FABP4+

description: All Data WTA_1_7_22.xlsx


title: heart biopsy_NR_TH108


title: P175_P187|012|FABP4+

description: All Data WTA_1_7_22.xlsx


title: RNA-seq H23_sgM2_3_rep1

description:
H23_sgM2_3_rep1
H23_TPM.txt


title: pre-Auxin_DCW447_rep2


title: heart biopsy_NR_TH104


title: RNA-seq H23_sgCtrl_rep2

description:
H23_sgCtrl_rep2
H23_TPM.txt


title: P175_P187|008|FABP4+

description: All Data WTA_1_7_22.xlsx


title: pre-Auxin_DCW448_rep2


title: RNA-seq H23_sgCtrl_rep1

description:
H23_sgCtrl_rep1
H23_TPM.txt


title: 24h-Auxin_DCW180_rep1


title: P175_P187|007|FABP4+

description: All Data WTA_1_7_22.xlsx


title: RNA-seq H1299_sgY1T1_rep2

description:
H1299_sgY1T1_rep2
H1299_TPM.txt


title: 24h-Auxin_DCW143_rep1


title: P175_P187|006|DNA

description: All Data WTA_1_7_22.xlsx


title: RNA-seq H1299_sgY1T1_rep1

description:
H1299_sgY1T1_rep1
H1299_TPM.txt


title: P175_P187|005|DNA

description: All Data WTA_1_7_22.xlsx


title: 12h-Auxin_DCW180_rep1


title: P175_P187|004|DNA

description: All Data WTA_1_7_22.xlsx


title: RNA-seq H1299_sgM2_3_rep2

description:
H1299_sgM2_3_rep2
H1299_TPM.txt


title: 12h-Auxin_DCW143_rep1


title: heart biopsy_NR_TH103


title: heart biopsy_NR_TH101


title: RNA-seq H1299_sgM2_3_rep1

description:
H1299_sgM2_3_rep1
H1299_TPM.txt


title: P175_P187|003|DNA

description: All Data WTA_1_7_22.xlsx


title: pre-Auxin_DCW180_rep1


title: RNA-seq H1299_sgCtrl_rep2

description:
H1299_sgCtrl_rep2
H1299_TPM.txt


title: P175_P187|002|DNA

description: All Data WTA_1_7_22.xlsx


title: RNA-seq H1299_sgCtrl_rep1

description:
H1299_sgCtrl_rep1
H1299_TPM.txt


title: P175_P187|001|DNA

description: All Data WTA_1_7_22.xlsx


title: heart biopsy_NR_TH106


title: starved_rep4

value: wild-type

value: starved


title: RNA-seq H1048_sgY1T1_rep2

description:
H1048_sgY1T1_rep2
H1048_TPM.txt


title: heart biopsy_NR_TH97


title: heart biopsy_NR_TH102


title: heart biopsy_NR_TH100


title: P161_P167|024|FABP4+

description: All Data WTA_1_7_22.xlsx


title: heart biopsy_NR_TH96


title: heart biopsy_NR_TH98


title: heart biopsy_NR_TH95


title: heart biopsy_NR_TH99


title: non-starved_rep4

value: intestine

value: non-starved


title: P161_P167|023|FABP4+

description: All Data WTA_1_7_22.xlsx


title: RNA-seq H1048_sgY1T1_rep1

description:
H1048_sgY1T1_rep1
H1048_TPM.txt


title: pre-Auxin_DCW143_rep1

value: ieSi57 [eft-3p::TIR1::mRuby::unc-54 3'UTR + Cbr-unc-119(+)] II ; unc-119(ed3) III.


title: starved_rep3


title: non-starved_rep3


title: RNA-seq H1048_sgM2_3_rep2

description:
H1048_sgM2_3_rep2
H1048_TPM.txt


title: P161_P167|022|FABP4+

description: All Data WTA_1_7_22.xlsx

value: Epicardial AT


title: RNA-seq H1048_sgM2_3_rep1

description:
H1048_sgM2_3_rep1
H1048_TPM.txt


title: P161_P167|021|FABP4+

description: All Data WTA_1_7_22.xlsx

value: border


title: heart biopsy_NR_TH92


title: heart biopsy_NR_TH93


title: starved_rep2


title: RNA-seq H1048_sgCtrl_rep2

description:
H1048_sgCtrl_rep2
H1048_TPM.txt


title: non-starved_rep2


title: RNA-seq H1048_sgCtrl_rep1

description:
H1048_sgCtrl_rep1
H1048_TPM.txt


title: heart biopsy_NR_TH90


title: starved_rep1


title: P161_P167|018|DNA+

description: All Data WTA_1_7_22.xlsx


title: non-starved_rep1


title: heart biopsy_ABMR_TH89

value: ABMR


title: P161_P167|019|FABP4+

description: All Data WTA_1_7_22.xlsx


title: RNA-seq ASPC1_sgY1T1_rep2

description:
ASPC1_sgY1T1_rep2
ASPC1_TPM.txt


title: RNA-seq ASPC1_sgY1T1_rep1

description:
ASPC1_sgY1T1_rep1
ASPC1_TPM.txt


title: P161_P167|017|DNA+

description: All Data WTA_1_7_22.xlsx


title: RNA-seq MDAMB231_MKI-mut2_rep1_24h

description:
MDAMB231_MKI-mut2_rep1_24h
MDA_MB231_MKI_TPM.txt


title: P161_P167|016|DNA+

description: All Data WTA_1_7_22.xlsx


title: HeLa-siRAD52-rep3

first: Simon

last: Powell

state: NY

address: 1250 1st Ave

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-Seq reads were aligned to GRCh37 human genome using STAR RNA-Seq aligner, and then reads from transcripts were counted using GenomicAlignments package in Bioconductor. The raw counts were tranformed to RPKM values in R.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: HeLa

extract_protocol:
48 hours post transfection, samples were sent to Zymo Research for Total RNA-Seq Service. Total RNA-Seq libraries were constructed from 500 ng of total RNA.
Libraries were prepared using the Zymo-Seq RiboFree Total RNA Library Prep Kit (Zymo Research Corp., #R3000) according to the manufacturer’s instructions. Briefly, RNA was reverse transcribed into cDNA, which was followed by ribosomal RNA depletion. After that partial P7 adapter sequence was ligated at 3’ end of cDNAs, followed by second strand synthesis and partial P5 adapter ligation to 5’ end of the double stranded DNAs. Lastly, libraries were amplified to incorporate full length adapters under the following conditions: initial denaturation at 95°C for 10 min; 10 - 16 cycles of denaturation at 95°C for 30 sec, annealing at 60°C for 30 sec, and extension at 72°C for 60 sec; and final extension at 72°C for 7 min. Successful library construction was confirmed with Agilent’s D1000 ScreenTape Assay on TapeStation.

value: HeLa

value: epithelial cell


title: RNA-seq ASPC1_sgM2_3_rep2

description:
ASPC1_sgM2_3_rep2
ASPC1_TPM.txt


title: HeLa-siRAD52-rep2


title: RNA-seq ASPC1_sgM2_3_rep1

description:
ASPC1_sgM2_3_rep1
ASPC1_TPM.txt


title: heart biopsy_NR_TH91


title: P161_P167|020|FABP4+

description: All Data WTA_1_7_22.xlsx


title: HeLa-siRAD52-rep1


title: heart biopsy_ABMR_TH88


title: heart biopsy_NR_TH86


title: heart biopsy_NR_TH85


title: P161_P167|015|DNA+

description: All Data WTA_1_7_22.xlsx

value: distal


title: heart biopsy_NR_TH87


title: RNA-seq ASPC1_sgCtrl_rep2

description:
ASPC1_sgCtrl_rep2
ASPC1_TPM.txt

value: sgCtrl


title: P161_P167|014|DNA+

description: All Data WTA_1_7_22.xlsx


title: heart biopsy_NR_TH83

value: heart biopsy


title: heart biopsy_NR_TH84

value: NR


title: HeLa-siNT-rep3

value: siNT


title: RNA-seq ASPC1_sgCtrl_rep1

description:
ASPC1_sgCtrl_rep1
ASPC1_TPM.txt


title: P161_P167|012|FABP4+

description: All Data WTA_1_7_22.xlsx


title: heart biopsy_NR_TH82


title: P161_P167|013|DNA+

description: All Data WTA_1_7_22.xlsx

value: Atrial appendage


title: RNA-seq A549_sgY1T1_rep2

description:
A549_sgY1T1_rep2
A549_TPM.txt


title: HeLa-siNT-rep2


title: heart biopsy_NR_TH81


title: HeLa-siNT-rep1


title: P161_P167|011|DNA+

description: All Data WTA_1_7_22.xlsx


title: RNA-seq A549_sgY1T1_rep1

description:
A549_sgY1T1_rep1
A549_TPM.txt


title: P161_P167|010|DNA+

description: All Data WTA_1_7_22.xlsx


title: HepG2 cells, shControl_rep

city: HEFEI

first: Yang

last: Yang

state: ANHUI

address: NO. 96, JinZhai Road

institute: University of Science and Technology of China

data_processing:
Basecalling were performed using Illumina Casava1.7 software.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie2 (v2.3.1) Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Peak visualizations were prepared using Deeptools. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Sonicator (Diagenode).
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 16 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Human Liver

tag: chip antibody

value: H3K9ac (Abclonal, A7255)


title: RNA-seq A549_sgM2_3_rep2

description:
A549_sgM2_3_rep2
A549_TPM.txt


title: heart biopsy_TCMR_TH80

value: TCMR


title: HepG2 cells, shcircEPB41(2)_rep

tag: cell type


title: P161_P167|009|FABP4+

description: All Data WTA_1_7_22.xlsx


title: nc,rep3

city: Wuhan

first: sheng

last: tian

address: 169 Donghu Road, Wuchang District, Wuhan City, Hubei Province.

institute: zhongnan hospital

data_processing:
HISAT2 for mapping, featureCounts for count the reads.
Assembly: hg18
Supplementary files format and content: tab-delimited text file includes raw counts data for each sample

source_name: gastric cancer

extract_protocol:
Total RNA from PDX after 3 weeks of CUMS on nude mouse was extracted using TRIzol. The RNA samples underwent stringent quality control through measure the purity and concentration, include agarose gel electrophoresis, NanoPhotometer spectrophotometer, Qubit2.0 Fluorometer, and Agilent 2100 bioanalyzer
Libraries were constructed according to the NEB normal method.

value: gastric cancer

value: nc


title: P161_P167|008|DNA+

description: All Data WTA_1_7_22.xlsx


title: RNA-seq A549_sgCtrl_rep2

description:
A549_sgCtrl_rep2
A549_TPM.txt


title: nc,rep2


title: RNA-seq A549_sgCtrl_rep1

description:
A549_sgCtrl_rep1
A549_TPM.txt


title: heart biopsy_ABMR_TH79


title: heart biopsy_NR_TH78


title: heart biopsy_ABMR_TH77


title: heart biopsy_pABMR_TH76

value: pABMR


title: nc,rep1


title: RNA-seq A549_sgM2_3_rep1

description:
A549_sgM2_3_rep1
A549_TPM.txt


title: P161_P167|006|DNA+

description: All Data WTA_1_7_22.xlsx


title: P161_P167|005|DNA+

description: All Data WTA_1_7_22.xlsx


title: cums,rep2

value: Chronic unpredictable mild stress


title: cums,rep3


title: P161_P167|007|DNA+

description: All Data WTA_1_7_22.xlsx

value: border


title: cums,rep1


title: P161_P167|004|DNA+

description: All Data WTA_1_7_22.xlsx


title: P161_P167|003|FABP4+

description: All Data WTA_1_7_22.xlsx

value: Epicardial AT


title: s_H18_Mix_062217

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

description: c-Jun KO HEI-286-Mix_rep3

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s reverse -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, which is used to both normalize the full dataset and analyze differential expression between sample groups.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited file containing normalized counts

source_name: c-Jun KO HEI-286-Mix_rep3

growth_protocol: HEI-286 Schwann cells were grown in 5% CO2 at 37°C in Dulbecco’s modified Eagle’s medium (DMEM, Cellgro, Herndon, VA) containing 10% fetal bovine serum (Gemini, Woodland, CA).

extract_protocol:
RNA was extracted from cells by using RNeasy mini kit (QIAGEN, cat #74104) as per the manufacturer’s instructions.
TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102; sequenced on a HiSeq 2500

treatment_protocol: Four million GFP-expressing HEI-286 cells were grown alone or mixed with RFP-expressing MiaPaCa-2 for four days (1:1). Cells were trypsinized, pelleted, re-suspended in PBS and passed through a 35um cell strainer to yield single cells. Live (DAPI negative) GFP cells were sorted on a BD SORP FACSAriaTM IIu equipped with a 488 nm laser and a 525/50 nm bandpass filter to excite, detect and select GFPHHEI-286 Schwann cells.

value: Human Schwann cell line

value: c-Jun KO


title: s_H18_Mix_061617

description: c-Jun KO HEI-286-Mix_rep2

source_name: c-Jun KO HEI-286-Mix_rep2


title: P161_P167|002|FABP4+

description: All Data WTA_1_7_22.xlsx

value: distal


title: P161_P167|001|DNA+

description: All Data WTA_1_7_22.xlsx


title: s_H18_Mix_060817

description: c-Jun KO HEI-286-Mix_rep1

source_name: c-Jun KO HEI-286-Mix_rep1


title: control

description: All Data WTA_1_7_22.xlsx

source_name: no templete

value: no templete

value: control


title: CD8_TRM_4

data_processing:
Raw FASTQ files were first trimmed using trim-galore (version 0.6.7) and inspected for quality control using fastqc (version 0.11.9) and multiqc (version 1.12). Transcript and genome files were downloaded from GENCODE, release 43 (GRCh38.p13) to generate a decoy index files with Salmon (version 1.10.1). Next, Salmon was used to perform transcript quantification with the additional parameter: --gcbias. Salmon transcript quantifications were imported into R (version 4.1.0) to aggregate transcripts to genes using the package tximport (version 1.22.0). Genes with a read count of less than 5 were excluded from further analysis: rowSums(counts()) >=5. Differential gene analysis was performed using DESeq2 (version 1.34.0). GSEA (version 4.3.2) was performed using normalized gene counts generated by DESeq2.
Assembly: GRCh38.p13
Supplementary files format and content: Comma delimited text file with normalised counts

source_name: iPSC-atrial cardiomyocyte

growth_protocol: Plates were coated with a vitronectin coating (ThermoFisher Scientific) to provide an appropiate adhesive surface for culturing iPSCs. Rho kinase (ROCK) inhibitor RevitaCell™ (Thermo Fisher Scientific) was added to TeSR™-E8 medium to achieve a final concentration of 10 μM (1:1000 dilution from the stock solution). Cells were plated in 2 ml TeSR™-E8- RevitaCell™ media/well in a 6 MW plate. iPSC media was replaced daily with fresh TeSR™-E8.  Cells were typically split at a ratio of 1:4 every 6-7 days following HipSci guidance. iPSC-cardiomyocyte derivation was carried out as per a recently published comprehensive and reproducible protocol based on Cygnaek et al 36. The base cardiomyocyte differentiation medium (CDM) used was RPMI 1640 with HEPES and Glutamax (ThermoFisher Scientific) supplemented with 0.2 mg/ml ascorbic acid and 0.5 mg/ml albumin. Cells were sequentially treated with 4μM CHIR99021 (Sigma-Aldrich) for 48 hrs followed by 5 μM IWP2 (Sigma-Aldrich) for 48 hrs to induce a cardiac cell lineage. To drive differentiation towards an atrial cell phenotype, the cells were administered 1 μM retinoic acid (RA) at days 3-6. At day 6, simple CDM was added.  Monolayers of beating iPSC-cardiomyocytes were typically observed at day 7-8 onwards. From this point onwards, the cells were maintained in RPMI 1640 + HEPES + Glutamax with the addition of 2% B27 supplement (Thermo Fisher Scientific).

extract_protocol:
1 ml of QIAzol (QIAGEN) was added to the wells. RNA was purified following manufacturer's instructions. RNA was then cleaned using RNA cleanup columns (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The atrial cardiomyocytes were differentiated on a 48-well plate set-up (Corning). Only wells where there was spontaneous and consistent beating of the cardiomyocytes across the well were imaged to ensure reliable and reproducible recordings. T cells were added to the cultures for 18 hours.

value: iPSC-atrial cardiomyocyte

value: culture with CD8 TRM


title: s_H18_061617

description: c-Jun KO HEI-286_rep2

source_name: c-Jun KO HEI-286_rep2


title: s_H18_062217

description: c-Jun KO HEI-286_rep3

source_name: c-Jun KO HEI-286_rep3


title: CD8_TRM_3


title: heart biopsy_NR_TH75

value: heart biopsy

value: NR


title: s_H18_060817

description: c-Jun KO HEI-286_rep1

source_name: c-Jun KO HEI-286_rep1


title: heart biopsy_NR_TH72


title: heart biopsy_NR_TH71


title: heart biopsy_NR_TH74


title: heart biopsy_ABMR_TH68

value: ABMR


title: heart biopsy_NR_TH73


title: heart biopsy_NR_TH69


title: heart biopsy_NR_TH70


title: s_HEI_Mix_062217


title: CD8_TRM_1


title: ds1, 4w, snRNAseq

city: Buenos Aires

first: Ariel

last: Chernomoretz

address: Av Patricias Argentinas 435

country: Argentina

institute: Fundacion Instituto Leloir

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the STARsolo software v2.7.4a (https://github.com/alexdobin/STAR). For QC, filtering, normalization, and doublet exclusion the scran R package v.1.24.0, scDblFinder v1.10.0 were used. Scripts for preprocessing and analyzing data with detailed descriptions are available here: https://github.com/chernolabs/NeuronalSwitch.
Assembly: mm10
Supplementary files format and content: Count matrix in market matrix format, nuclei barcodes as tab-delimited text file and feature names as tab-delimited text file
Supplementary files format and content: tab file with 14367 nuclei metadata ("nuclei_id", "sample_id", "cluster", "ptime"), all cohorts included, and log-normalized expression values for 13353 genes

source_name: Dentate Gyrus

extract_protocol:
Mice were deeply anesthetized (ketamine/xylazine, as described above), brains were carefully removed and placed into ice cold Earl’s balanced salt solution (EBSS, in mM: 117 NaCl, 5.4 KCl, 1 NaH2PO4, 26 NaHCO3, 5.6 glucose, 1.8 CaCl2 .2H2O and 0.8 MgSO4) with trehalose 5% v/v and kynurenic acid 0.8 mM. Dissection solution was equilibrated in 95% O2/5% CO2 before use. The brain was cut along the longitudinal fissure and the regions posterior to lambda were cut off. Under a dissection microscope and upon removal of the diencephalon, the medial side of the hippocampus was exposed. The dentate gyrus was isolated by inserting a sharp-needle tip and sliding it superficially along the septotemporal axis of the hippocampus. The dissected tissue was placed in a 0.5 ml microcentrifuge tube with a minimal amount of media, flash-freezed on dry ice and stored at -80ºC until use. Nuclei were isolated as previously described with several modifications. Dounce tissue grinder and pestles were sequentially washed with 100% EtOH, RNAse Zap (Sigma, Cat # R2020), 2-3 rounds with RNAse-free water, and finally rinsed with EZ Lysis Buffer (Sigma, Cat # NUC-101). All material and buffers were chilled on ice. The tissue was transferred to a chilled dounce prefilled with 2 ml ice-cold EZ Lysis Buffer and homogenized slowly with 20-25 strokes of pestle A, followed by 20 strokes with pestle B. Suspension was transferred to a chilled tube and incubated on ice 5 min. Then the suspension was centrifuged at 500 × g for 5 min at 4°C and the supernatant was removed. The pellet was resuspended in 4 ml ice-cold EZ Lysis Buffer and after a second round of ice incubation and centrifugation, the isolated nuclei were resuspended in 4 ml ice-cold Nuclei Suspension Buffer (NSB) (1x RNase-free molecular-biology grade PBS, 0.1% molecular-biology grade BSA 100 μg/ml and 0.2U/μl RNase inhibitor). Finally, nuclei were centrifuged at 500 × g for 5 min at 4°C and after removing the supernatant were resuspended in 1ml NSB-Ruby (final Ruby concentration 1:500) and filtered twice through a 35-μm cell strainer to remove as many debris as possible. Nuclei were kept on ice until sorting (Harvard University, Bauer Core Facility, BD FACSAria II) into 96 well plates, pre-coated with BSA to reduce adherence and improve recovery, containing with ~10-20 μl of rich-NSB (with final 2U/μl of RNase inhibitor and 1% BSA). The final nuclei concentration was determined using a C-chip Neubauer counting chamber and Trypan Blue (1:2 final dilution). Nuclei were immediately loaded for single-cell GEM formation (10x Genomics, single cell RNA sequencing 3ʹ, Chromium v3.1)
Dataset sampling for snRNA-seq experiments was carried out within a minimal time interval, processing two time points in a single experiment each day to minimize batch effects. For each time point, four dentate gyri (left hemispheres) from male and female mice were pooled. For snRNA-seq, nuclei were loaded in the 10x Genomics chips aiming to recover 2,000–10,000 nuclei. cDNA amplification and library construction were done following 10x Genomics protocols. Libraries were generated using Chromium v3.1, quantified in BioAnalyzer and sequenced on an Illumina HiSeq 2500. Samples were sequenced to a depth of 40–70,000 reads per cell.
snRNA-Seq

value: Dentate Gyrus

value: adult born Granule Cells

tag: cohort

tag: hemisphere

value: L


title: heart biopsy_NR_TH66


title: ds1, 8w, snRNAseq


title: s_HEI_Mix_061617


title: CD8_TRM_2


title: CD8_nonTRM_3

value: culture with CD8 memory T cells


title: s_HEI_Mix_060817


title: ds1, 2w, snRNAseq


title: CD8_nonTRM_2


title: heart biopsy_TCMR_TH65

value: TCMR


title: heart biopsy_NR_TH94


title: CD8_nonTRM_1


title: s_HEI_3_062217


title: heart biopsy_pABMR_TH67

value: pABMR


title: s_HEI_2_061617


title: ds2, 8w, right, snRNAseq

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the STARsolo software v2.7.4a (https://github.com/alexdobin/STAR). For QC, filtering, normalization, and doublet exclusion the scran R package v.1.24.0, scDblFinder v1.10.0 were used. Scripts for preprocessing and analyzing data with detailed descriptions are available here: https://github.com/chernolabs/NeuronalSwitch.
Assembly: mm10
Supplementary files format and content: Count matrix in market matrix format, nuclei barcodes as tab-delimited text file and feature names as tab-delimited text file.
Supplementary files format and content: tab file with 26716 nuclei metadata ("nuclei_id": unique identifier for single nuclei, "sample_id", "seuratLT": partition estimated by seurat label transfer function, "seuratLT_refined": refined partition based on seuratLT labeling, "ptime"), all cohorts included, and log-normalized expression values for 14220 genes

extract_protocol:
Mice were deeply anesthetized (ketamine/xylazine, as described above), brains were carefully removed and placed into ice cold Earl’s balanced salt solution (EBSS, in mM: 117 NaCl, 5.4 KCl, 1 NaH2PO4, 26 NaHCO3, 5.6 glucose, 1.8 CaCl2 .2H2O and 0.8 MgSO4) with trehalose 5% v/v and kynurenic acid 0.8 mM. Dissection solution was equilibrated in 95% O2/5% CO2 before use. The brain was cut along the longitudinal fissure and the regions posterior to lambda were cut off. Under a dissection microscope and upon removal of the diencephalon, the medial side of the hippocampus was exposed. The dentate gyrus was isolated by inserting a sharp-needle tip and sliding it superficially along the septotemporal axis of the hippocampus. The dissected tissue was placed in a 0.5 ml microcentrifuge tube with a minimal amount of media, flash-freezed on dry ice and stored at -80ºC until use. Nuclei were isolated as previously described with several modifications. Dounce tissue grinder and pestles were sequentially washed with 100% EtOH, RNAse Zap (Sigma, Cat # R2020), 2-3 rounds with RNAse-free water, and finally rinsed with EZ Lysis Buffer (Sigma, Cat # NUC-101). All material and buffers were chilled on ice. The tissue was transferred to a chilled dounce prefilled with 2 ml ice-cold EZ Lysis Buffer and homogenized slowly with 20-25 strokes of pestle A, followed by 20 strokes with pestle B. Suspension was transferred to a chilled tube and incubated on ice 5 min. Then the suspension was centrifuged at 500 × g for 5 min at 4°C and the supernatant was removed. The pellet was resuspended in 4 ml ice-cold EZ Lysis Buffer and after a second round of ice incubation and centrifugation, the isolated nuclei were resuspended in 4 ml ice-cold Nuclei Suspension Buffer (NSB) (1x RNase-free molecular-biology grade PBS, 0.1% molecular-biology grade BSA 100 μg/ml and 0.2U/μl RNase inhibitor). Finally, nuclei were centrifuged at 500 × g for 5 min at 4°C and after removing the supernatant were resuspended in 1ml NSB-Ruby (final Ruby concentration 1:500) and filtered twice through a 35-μm cell strainer to remove as many debris as possible. Nuclei were kept on ice until sorting (Harvard University, Bauer Core Facility, BD FACSAria II) into 96 well plates, pre-coated with BSA to reduce adherence and improve recovery, containing with ~10-20 μl of rich-NSB (with final 2U/μl of RNase inhibitor and 1% BSA). The final nuclei concentration was determined using a C-chip Neubauer counting chamber and Trypan Blue (1:2 final dilution). Nuclei were immediately loaded for single-cell GEM formation (10x Genomics, single cell RNA sequencing 3ʹ, Chromium v3.1)
Dataset sampling for snRNA-seq experiments was carried out within a minimal time interval, processing two time points in a single experiment each day to minimize batch effects. For each time point, four dentate gyri (left or right hemispheres) from male and female mice were pooled. For snRNA-seq, nuclei were loaded in the 10x Genomics chips aiming to recover 2,000–10,000 nuclei. cDNA amplification and library construction were done following 10x Genomics protocols. Libraries were generated using Chromium v3.1, quantified in BioAnalyzer and sequenced on an Illumina HiSeq 2500. Samples were sequenced to a depth of 40–70,000 reads per cell.
snRNA-Seq

value: R


title: heart biopsy_NR_TH63


title: CD4_TRM_4

value: culture with CD4 TRM


title: s_HEI_1_060817

value: Human Schwann cell line


title: CD4_TRM_5


title: ds2, 8w, left, snRNAseq


title: heart biopsy_NR_TH62


title: ds2, 5w, right, snRNAseq


title: heart biopsy_NR_TH61


title: heart biopsy_NR_TH60


title: OE-circSHPRH-3

city: Beijing

first: yaqiong

last: Jin

address: No.56 Nanlishi road

institute: Beijing Children’s Hospital, Capital Medical University

data_processing:
CLC Genomics Workbench v11.0.1
Sequence reads were trimmed for adaptor sequence\low-quality sequence using CLC genomic benchwork(parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GRCh37 using CLC genomic benchwork(parameters-mismath cost:2 insertion cost:3 deletion cost:3 length fraction:0.8 similarity fraction:0.8 )
Read count extration and nomalization were performed using CLC genomic benchwork
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include RPPKM values for each Sample

extract_protocol:
Total RNA was extracted from NB cells by TRIzol reagent (Invitrogen, USA).
RNA libraniesfor RNA-seq were prepared using SMARTER mRNA-Seq Libray Pre Kit following manufacturer's protocolss

value: cancer cell


title: CD4_TRM_3


title: OE-circSHPRH-2


title: heart biopsy_NR_TH59


title: OE-circSHPRH-1


title: ds2, 4w, right, snRNAseq


title: ds1, 1w, snRNAseq


title: ds2, 5w, left, snRNAseq


title: heart biopsy_TCMR_TH64


title: CD4_TRM_2


title: OE-NC-3


title: CD4_TRM_1


title: ds2, 4w, left, snRNAseq


title: heart biopsy_NR_TH57


title: ds2, 3w, right, snRNAseq


title: heart biopsy_NR_TH56


title: OE-NC-2


title: CD4_nonTRM_4

value: culture with CD4 memory T cells


title: ds2, 3w, left, snRNAseq


title: OE-NC-1


title: heart biopsy_NR_TH55


title: CD4_nonTRM_2


title: CD4_nonTRM_1


title: CD4_nonTRM_3


title: 2-hour refed, beta-cells, control mouse_22

city: Geneva

first: Marta

last: Perez Frances

state: Geneva

address: 1, rue Michel-Servet

country: Switzerland

institute: University of Geneva

data_processing:
All sequencing data were uploaded to and aligned on the Galaxy project against Ensembl reference genome GRCm38.p6 (release 100) using STAR version 2.7.2b (PMID: 23104886) n 2-pass mapping mode.
Aligned data were counted using HTSeq version 0.9.1  in union mode.
Analyses were performed in a pair-wise manner between the four conditions analyzed using DESeq2 version 1.28.1
For each pairwise comparison, genes were discarded if they had fewer than 5 counts per sample on average. After calculating differential expression between groups, log2 fold changes were shrunken using the normal estimator
Genes were considered to be differentially expressed if the absolute shrunken log2 fold changes were equal to or above 1, and adjusted p-values were equal to or below 0.05.
Assembly: GRCm38.p6
Supplementary files format and content: Tab-separated values files (.tsv) containing gene and sample names

source_name: pancreatic beta-cells

extract_protocol:
RNA extraction from pancreatic beta-cells was performed using the Qiagen RNeasy Micro Kit. . RNA was extracted as described above and assessed for quality by Agilent bioanalyzer prior to library generation and sequencing.
Reverse transcription and cDNA amplification were performed using the SMARTer Ultra Low RNA kit (Clontech). cDNA libraries were prepared using Nextera XT DNA Sample Preparation kit (Illumina) and sequenced on an Illumina HiSeq4000 platform with single-end 100-bp.

treatment_protocol: β-cells were FAC-sorted from one-month post-ablation and control mice, either under fasting or fasting plus 2-hour refed condition.

value: pancreatic beta-cells

tag: Sex

value: Male

value: GluDTR+, SstDTR htz, PpyDTR htz

value: Mix background

tag: age

value: 3 months old

tag: treatment 1

value: Control

tag: time after_treatment_1

value: One month post ablation

tag: treatment 2

value: 8h-fasting + 2h refed


title: ds2, 2w, right, snRNAseq

value: Dentate Gyrus

value: adult born Granule Cells


title: 2-hour refed, beta-cells, control mouse_21

tag: genotype


title: 2-hour refed, beta-cells, DT-treated mouse_20

tag: strain

value: Diphtheria toxin (DT)


title: telencephalon, abca7 k/o - Ab42 injected

city: New York

first: Caghan

last: Kizil

department: Neurology & TAUB Institute

institute: Columbia University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/metrics)
The fastq files were aligned to zebrafish genome (GRCz11) and (ensemble transcripts from Ensembl Release 105) by using STAR. The BAM files were as input for Cell Ranger (10X genomics) to generate processed data files that include gene names (row names) and cell names (column names) and counts. Further analysis done by using Seurat package in R.
Assembly: GRCz11
Supplementary files format and content: filtered_bc_matrix outputs from Cell Ranger

organism: Danio rerio

source_name: telencephalon

growth_protocol: Zebrafish were kept in the re-circulating system on a 14/10-h light/dark cycle, pH7.5, at 28°C (±1°C) in groups of 20 animals per 2.8L.

extract_protocol:
Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue (Invitrogen, Cat No. S34857) and Dycle Ruby (Invitrogen, Cat. No. V10309) were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol.
10X genomics

treatment_protocol: WT-AB and abca7 +/- knock-out lines were injected with Amyloid-beta 42 peptide, and PBS as control as descibed (Bhatatrai et al. 2016).

value: telencephalon

value: abca7 +/-


title: 2-hour refed, beta-cells, control mouse_19


title: 2-hour refed, beta-cells, control mouse_18


title: heart biopsy_NR_TH58

source_name: heart biopsy

value: heart biopsy

tag: mmdx (abmr, tcmr, mixed, pabmr, nr)

value: NR


title: telencephalon, abca7 k/o - PBS injected

description: 10x Genomics

value: PBS


title: heart biopsy_pABMR_TH52

value: pABMR


title: heart biopsy_NR_TH50


title: heart biopsy_NR_TH51


title: 2-hour refed, beta-cells, DT-treated mouse_16

value: pancreatic beta-cells


title: heart biopsy_NR_TH53


title: heart biopsy_NR_TH54