title: Osteroporosis 4

city: Nanjing

first: Wang

last: Bin

address: No.305Zhongshan East Rd

institute: Jinling hospital, Medical School of Nanjing University

data_processing:
For primary analysis, the length distribution of the clean sequences in the reference genome was determined. Non-coding RNAs were annotated as rRNAs, tRNAs, small nuclear RNAs (snRNAs), and so on.
Assembly: Rfam v.10.1
Supplementary files format and content: Excel file include TPM values for each Sample

source_name: serum

extract_protocol:
This study recruited a total of 10 postmenopausal patients. To control for confounding bias, patients with the following diseases will be excluded from the study: tumor; known chronic, systemic, metabolic, or endocrine diseases; inflammation, or acute trauma. The patients participating in the study were fasting before blood collection, with a time window of 8:00-11:00 in the morning. They gently dropped the whole blood into a clean EP tube (without adding anticoagulants). To reduce the deviation caused by hemolysis, the collected blood was kept in a refrigerator at 4 ℃ for 3-4 hours, and the serum (light yellow transparent liquid) was allowed to precipitate; Centrifuge at 5,000 rpm for 10 minutes at 4 ℃ to obtain pale yellow serum. After removing the supernatant, centrifuge again at 3,000 rpm for 10 minutes at 4 ℃ to ensure maximum serum quality. Total RNA was extracted using mirVana miRNA Isolation Kit (Ambion) according to the manufacturer’s protocol. Quantitation of total RNA was carried out using the Nanodrop 2000 (Thermo Fisher Scientific Inc., USA). RNA integrity was assessed by Agilent 2100 Bioanalyzer (Agilent Technology, USA).
RNA integrity was assessed by Agilent 2100 Bioanalyzer (Agilent Technology, USA). 1 μg total RNA of each sample was used for the small RNA library construction using TruSeq Small RNA Sample Prep Kits (Cat. No. RS-200-0012, Illumina, USA.) following the manufacturer’s recommendations. Briefly, total RNA were ligated to adapters at each end. Then the adapter-ligated RNA were reverse transcribed to cDNA and performed PCR amplification. The PCR products ranging from 140–160 bp were isolated and purified as small RNA libraries. Library quality was assessed on the Agilent Bioanalyzer 2100 system using DNA High Sensitivity Chips. The libraries were finally sequenced using the Illumina HiSeq X Ten platform. 150 bp single-end reads were generated.

tag: group

value: Osteroporosis

value: serum

value: Extract exosomes


title: COX1204A29_Hhepaticus_antiIL-10R_prdm1 fl/fl maf fl/fl

status: Public on Feb 18 2024

type: SRA

city: London

first: Anne

last: OGarra

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Insititue

description:
RNA_Hhepaticus_antiIL-10R_prdm1 fl/fl maf fl/fl
For infection, mice received 1x10^8 colony forming units (c.f.u.) of Helicobacter hepaticus by oral gavage using a 22G curved blunted needle on Day 0 and Day 1, together with 1mg of either anti-mouse IL-10R (CD210) [Clone 1B1.3A, Rat IgG1, kappa] blocking antibody, or Rat IgG1 [Clone GL113, Rat IgG1] isotype control on Day 0 and Day 7 by intraperitoneal injection. Uninfected mice were housed at the same animal facility and received antibody treatment alone.

library_source: transcriptomic

data_processing:
sequencing quality control done with Skewer 0.2.2
sequencing reads mapped to mm10 genome and the GENCODE reference transcriptome version M22 with STAR software
Raw gene counts were retrieved using QoRTs software
Normalised read counts were retrieved using DeSeq2
To retrieve bigwig files we used DeepTools 2.4.2, bamCoverage command to retrieve RPKM normalised coverage
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are provided  for RNA-seq data separated for both strands and normalised to RPKMs

molecule: total RNA

organism: Mus musculus

source_name: colon LPL from mice with the treatment: Hhepaticus_antiIL-10R

growth_protocol: Helicobacter hepaticus (NCl-Frederick isolate 1A, strain 51449) was grown under anaerobic gas conditions 10% CO2, 10% H2/N2 (BOC) on blood agar plates containing 7% laked horse blood (Thermo Scientific) and the campylobacter selective supplement (Skirrow) antibiotics trimethoprim, vancomycin and polymyxin B (all from Oxoid). Cultures were then transferred to and expanded, again under the anaerobic gas conditions above, for 3-4 days to OD 0.6 in tryptone soya broth (Oxoid) supplemented with 10% FCS (Gibco) and the antibiotics above.

extract_protocol:
On Day 14 following infection with Helicobacter hepaticus, colon lamina propria leukocytes were isolated from individual  infected and uninfected control mice. RNA was extracted using the QIAShredder and RNeasy Mini Kit with on-column DNase digestion, according to the manufacturer’s instructions (Qiagen).
RNA-seq libraries were made with total RNA using the KAPA RNA HyperPrep with RiboErase and unique multiplexing indexes, according to the manufacturer’s instructions (Roche).

treatment_protocol: Mice received 1x10^8 colony forming units (c.f.u.) of Helicobacter hepaticus by oral gavage using a 22G curved blunted needle on Day 0 and Day 1, together with 1mg of either anti-mouse IL-10R (CD210) [Clone 1B1.3A, Rat IgG1, kappa] blocking antibody, or Rat IgG1 [Clone GL113, Rat IgG1] isotype control on Day 0 and Day 7 by intraperitoneal injection. Uninfected mice were housed at the same animal facility and received antibody treatment alone.

tag: strain

value: prdm1 fl/fl maf fl/fl

tag: treatment

value: LPL from mice treated with Hhepaticus_antiIL-10R


title: Osteroporosis 3

state: Jiangsu

country: China

organism: Homo sapiens

tag: cell type


title: 51.4.2 vehicle

type: protein

city: Freiburg

first: Robert

last: Zeiser

address: Hugstetter Straße 53

department: Interdisziplinäres Tumorzentrum

country: Germany

institute: University Medical Center Freiburg

description:
180-205 30
Protein lysates with active kinases, phosphorylation of spotted peptides on chip detected with fluorescently labeled anti-phospho antibody

hyb_protocol: sample is pumped through porous membrane

scan_protocol: when the solution is underneath the array, images are taken at several exposure times

data_processing: images are used by the BioNavigator software to calculate signal values for each phosphosite.

label: fluorescently labelled anti phospho antibody

molecule: protein

source_name: BMDMs

label_protocol: maximum 15 µl was used as per proprietary protocol of PamGene

growth_protocol: Bone marrow was isolated from five wild-type C57BL/6 mice, erythrocytes were lyzed and residual cells were plated in RPMI+10%FCS+1%PenStrep+20ng/ml rmCSF at 3.5x10^6 cells per 10cm dish. Cells were cultivated until d7, when they were treated with LPS and IFNg. 16 hours after stimulation, cell pellets were harvested.

extract_protocol: Cell pellets were frozen, shipped, and lyzed in 25 µl buffer with protease and phosphatase inhibitors.

treatment_protocol: From start of differentiation, cells were kept with 150 ng/ml LCN2 or vehicle.

value: bone marrow derived macrophages

tag: genotype

value: C57BL/6 wildtype

tag: gender

value: female

tag: treament

value: vehicle


title: Osteroporosis 5


title: RLT-ACC_NCIH295R-IC50(4,5uM)

city: Ribeirão Preto

first: Carlos

middle: Alberto

last: Scrideli

state: São Paulo

address: Avenida Bandeirantes 3900

department: Pediatrics

country: Brazil

institute: Ribeirao Preto Medicine School - University of Sao Paulo

description: Famele

data_processing:
Sequencing and base calling: RNA-seq Clustering and sequencing were performed on the Illumina NovaSeq 6000 equipment by using the NovaSeq SP Kit (200 cycles) (Illumina Inc), to generate 800 million reads per sequencing (Illumina, San Diego, CA, USA)
The generated libraries were evaluated by using the Tapestation equipment (Agilent Technologies) and quantified on a Qubit fluorimeter with the Qubit dsDNA BR Assay kit (Life Technologies).  The data quality of the two samples (Rottlerin at IC50 and DMSO) was evaluated by using the FastQC (0.11.3) and MultiQC (v1.10) programs, which provide information about basic sequence statistics, quality, GC content, sequence size distribution, sequence duplication levels, and over-represented sequences.
Gene specific read counts: Gene specific read counts were determined with to FastQC tool (Andrews, 2010) and MultiQC (Ewels et al., 2016). From the count of reads in each sample, the R programming language (v4.1.2) was applied; more specifically, the DESeq2 package was employed, which enabled differential expression between the different conditions of the experiment to be analyzed
Assembly: RFor alignment, mapping, and counting of the sequences against the reference genome, the STAR aligner (v2.7.8a) was used.
Supplementary files format and content: Gene counts are in .txt format and contain the number of counts for every gene and every sample.

source_name: Cortex

extract_protocol:
Total RNA was extracted using AllPrep DNA/RNA/Protein Mini kit (QIAGEN, Hilden, Germany) and RNA integrity was evaluated by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA) following manufacturer’s specifications.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Cortex

tag: cell line

value: rottlerin


title: Osteroporosis 2


title: maternal LFD_female offspring, replicate2, snRNA-seq

city: Shenzhen

first: John

middle: R.

last: Speakman

state: Guangdong

address: 1068 Xueyuan Avenue, Shenzhen University Town

institute: Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences

description:
10x Genomics
m47f

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0
qc, normalization, dimentional reduction, integration and clustering were processed in Seurat
Assembly: mm10
Supplementary files format and content: processed (qc'ed, integrated and subsetted) rds file

source_name: hypothalamus

extract_protocol:
Male and female pup brains were rapidly dissected between 9 and 12 a.m., hypothalamus was spooned out immediately and cut into tiny pieces in HEB buffer (Hibernate A®, 2% B27®, 0.5mM GlutaMAXTM). Hypothalamus pieces were then incubated in 2 ml pre-chilled lysis buffter (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, and 0.1% NonidetTM P40 Substitute in Nuclease-Free Water, 0.1U/μl RNase Inhibitor) on ice for 15 min. Added 2ml HEB buffer to the lysed tissue and triturated the tissue with a fire polished silanized Pasteur pipette 10–15 times. After trituration, a 30 μm MACS® SmartStrainer was used to remove cell debris and large clumps. The single nucleus suspension was centrifuged at 400g for 5min at 4°C and washed in a wash and resuspension buffer (1X PBS with 1.0% BSA and 0.2U/μl RNase Inhibitor).
Library was constructed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
snRNA-seq

treatment_protocol: Female C57BL/6N mice at 11 weeks of age were fed with low fat diets (10% fat by energy) for 2 weeks of baseline. Mice were mated at 13 weeks old and remained on LFD until parturition. Mice were then randomly allocated to low fat diets and high fat diets (45% fat by energy) on lactation day 1 and kept feeding them those diets during the lactation.

value: neuronal, non-neuronal, and immune cells

value: hypothalamus

tag: age

value: postnatal day15

tag: Sex

tag: maternal diet

value: LFD


title: COX1204A20_Hhepaticus_Isotype_prdm1 fl/fl maf fl/fl CD4-Cre

description:
RNA_Hhepaticus_Isotype_prdm1 fl/fl maf fl/fl CD4-Cre
For infection, mice received 1x10^8 colony forming units (c.f.u.) of Helicobacter hepaticus by oral gavage using a 22G curved blunted needle on Day 0 and Day 1, together with 1mg of either anti-mouse IL-10R (CD210) [Clone 1B1.3A, Rat IgG1, kappa] blocking antibody, or Rat IgG1 [Clone GL113, Rat IgG1] isotype control on Day 0 and Day 7 by intraperitoneal injection. Uninfected mice were housed at the same animal facility and received antibody treatment alone.

source_name: colon LPL from mice with the treatment: Hhepaticus_Isotype

value: prdm1 fl/fl maf fl/fl CD4-Cre

value: LPL from mice treated with Hhepaticus_Isotype


title: 51.4.2 LCN2

description:
180-205 36
Protein lysates with active kinases, phosphorylation of spotted peptides on chip detected with fluorescently labeled anti-phospho antibody


title: COX1204A21_Hhepaticus_Isotype_prdm1 fl/fl maf fl/fl CD4-Cre


title: maternal LFD_female offspring, replicate1, snRNA-seq

description:
10x Genomics
m39f


title: Osteroporosis 1

value: Osteroporosis


title: maternal LFD_male offspring, replicate2, snRNA-seq

description:
10x Genomics
m44m

value: male


title: COX1204A19_Hhepaticus_Isotype_prdm1 fl/fl maf fl/fl CD4-Cre


title: RTL-ACC_NCIH295R-DMSO

description: Famele

value: DMSO


title: COX1204A31_Hhepaticus_antiIL-10R_prdm1 fl/fl maf fl/fl

value: prdm1 fl/fl maf fl/fl


title: Health control 5

value: Healthy

value: serum

value: Extract exosomes


title: THP-1 cells, GFP-ORF6-2

city: Los Angeles

first: Tianhao

last: Duan

state: CA

address: 1450 Biggy ST

department: Department of Medicine

country: USA

institute: Keck school of medicine of University of Southern California

data_processing:
Partek FlowBuild version 11.0.23.1023 (Partek Inc.)
Raw sequencing reads with Phred scores below 20 had bases trimmed from both ends, and trimmed reads shorter than 25 nt were excluded from subsequent analyses. Pre- and post-alignment quality checks were performed using default settings in the Partek Flow workflow. The trimmed reads were aligned to the human genome hg38 using the STAR method, with guidance from hg38-GENCODE Genes-release 42 annotation, also within Partek Flow, using default settings. Gene read counts for the samples were normalized using counts per million (CPM) plus 1.0E-4.
Assembly: hg38 - GENCODE Genes - release 42
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Peripheral blood

growth_protocol: THP-1 cell lines were cultured in RPMI-1640 medium (Gibco) supplemented with 10% fetal bovine serum (Hyclone) and 1% L-glutamine (Corning) in an incubator (Invitrogen) at 37°C and 5% CO2

extract_protocol:
Total RNA was harvested using RNeasy mini Kits (Qiagen)
An RNA-seq library was prepared using Novogene’s protocol. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: THP-1 cell lines were treated with Pam3CSK4 (1ug/ml) for 4 hours

value: Peripheral blood

value: human monocyticcell

value: Pam3CSK4 stimulation 4 hours


title: maternal LFD_male offspring, replicate1, snRNA-seq

description:
10x Genomics
m36m


title: Health control 4


title: THP-1 cells, GFP-ORF6-1


title: COX1204A17_Hhepaticus_Isotype_prdm1 fl/fl maf fl/fl CD4-Cre


title: COX1204A30_Hhepaticus_antiIL-10R_prdm1 fl/fl maf fl/fl

value: LPL from mice treated with Hhepaticus_antiIL-10R


title: COX1204A18_Hhepaticus_Isotype_prdm1 fl/fl maf fl/fl CD4-Cre


title: BMP9, replicate 3, scRNAseq

city: Chongqing

first: Haobo

last: Bai

address: No.1 Friendship Road, Yuzhong District

department: Department of Laboratory Medicine

institute: The First Affiliated Hospital of Chongqing Medical University

description:
B3
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peritoneallavagefluids

extract_protocol:
Murine recombinant BMP9 (catalog 5566-BP, R&D Systems) was injected intraperitoneally at 25 μg/kg after CLP, and 4 mM HCl containing 0.1% bovine serum albumin as Vehicle was delivered in a similar fashion as control solutions. The peritoneallavagefluids were obtained  at 24h after CLP,then send to Single-cell RNA sequencing.
The 10x Genomics Chromium is based on GemCode technology and allows high-throughput single-cell 3' mRNA quantitative analysis based on GemCode™ technology in which describes intercellular heterogeneity. This protocol is developed for 10x Genomics high-throughput single-cell gene expression profiling library construction.

value: peritoneallavagefluids


title: Health control 3


title: THP-1 cells, GFP-EV-2

value: GFP-expressing


title: COX1204A28_Hhepaticus_Isotype_maf fl/fl CD4-Cre

description:
RNA_Hhepaticus_Isotype_maf fl/fl CD4-Cre
For infection, mice received 1x10^8 colony forming units (c.f.u.) of Helicobacter hepaticus by oral gavage using a 22G curved blunted needle on Day 0 and Day 1, together with 1mg of either anti-mouse IL-10R (CD210) [Clone 1B1.3A, Rat IgG1, kappa] blocking antibody, or Rat IgG1 [Clone GL113, Rat IgG1] isotype control on Day 0 and Day 7 by intraperitoneal injection. Uninfected mice were housed at the same animal facility and received antibody treatment alone.

value: maf fl/fl CD4-Cre


title: BMP9, replicate 1, scRNAseq

description:
B1
10x Genomics


title: Health control 2


title: BMP9, replicate 2, scRNAseq

description:
B2
10x Genomics


title: COX1204A27_Hhepaticus_Isotype_maf fl/fl CD4-Cre


title: THP-1 cells, GFP-EV-1


title: COX1204A26_Hhepaticus_Isotype_maf fl/fl CD4-Cre


title: Vehicle, replicate 3, scRNAseq

description:
duizhao3
10x Genomics

value: Vehicle


title: Health control 1


title: Vehicle, replicate 2, scRNAseq

description:
duizhao2
10x Genomics


title: IDHm BWH35 oligodendroglioma

city: Rehovot

first: Itay

last: Tirosh

address: 234 Herzl St.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: fresh frozen spatial transcriptomics (10X Visium)

data_processing:
FASTQs were generated by the SpaceRanger pipeline (version 1.0 and 1.1, 10X Genomics).
Alignment of FASTQs with human reference genome GRCh38, UMI counting, and spot barcode filtering were performed using SpaceRanger.
Assembly: human reference genome GRCh38
Supplementary files format and content: barcodes.tsv: list of spatial barcodes
Supplementary files format and content: features.tsv: list of gene IDs
Supplementary files format and content: matrix.mtx: gene expression count data
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene expression data, list of genes, and spatial barcodes in compressed HDF5 format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: tissue_lowres_image.png: low-res tissue image
Supplementary files format and content: tissue_positions_list.csv: spatial barcodes and their positional coordinates
Supplementary files format and content: metrics.csv: sample QC metrics
Library strategy: spatial transcriptomics

source_name: IDH mutant glioma

extract_protocol:
Fresh frozen tumor samples with RIN >7 were embedded in OCT and 10 micron sections were cut on cryostat and placed on Visium capture slides.
Spatial transcriptomics libraries were prepared with the 10x Visium Spatial Gene Expression slides and reagent kit according to the manufacturer's instructions.
10X Visium spatial transcriptomics

value: IDH mutant glioma

tag: tumor stage

tag: tumor region

value: unannotated

tag: mgmt status

value: methylated


title: IDHm BWH25 astrocytoma


title: COX1204A25_Hhepaticus_Isotype_prdm1 fl/fl CD4-Cre

description:
RNA_Hhepaticus_Isotype_prdm1 fl/fl CD4-Cre
For infection, mice received 1x10^8 colony forming units (c.f.u.) of Helicobacter hepaticus by oral gavage using a 22G curved blunted needle on Day 0 and Day 1, together with 1mg of either anti-mouse IL-10R (CD210) [Clone 1B1.3A, Rat IgG1, kappa] blocking antibody, or Rat IgG1 [Clone GL113, Rat IgG1] isotype control on Day 0 and Day 7 by intraperitoneal injection. Uninfected mice were housed at the same animal facility and received antibody treatment alone.

value: prdm1 fl/fl CD4-Cre

value: LPL from mice treated with Hhepaticus_Isotype


title: COX1204A24_Hhepaticus_Isotype_prdm1 fl/fl CD4-Cre


title: COX1204A23_Hhepaticus_Isotype_prdm1 fl/fl CD4-Cre


title: Nat10_gKO_3

city: Hangzhou

first: Heng-yu

last: Fan

state: Zhejiang

address: Yuhangtang Road

institute: Life Sciences  Institute

data_processing:
The raw reads were first cleaned with Trim Galore v0.6.7, and the cleaned reads were further mapped to mm10 genome by using STAR v2.7.10a. Uniquely mapped reads were applied for gene expression quantification by using FeatureCounts b2.0.2. The trimmed reads were also mapped to the ERCC genome for gaining the percentage of ERCC.
Assembly: mm10
Supplementary files format and content: The count list calibrated by ERCC.

molecule: polyA RNA

source_name: oocyte

extract_protocol:
The fully growing oocytes (FGO) were harvested from WT and Gdf9-cre Nat10 conditional knockout female mice 36-48h after PMSG injection, then after washing by PBS with 0.2% containing, the oocytes were lysed with lysis buffer containing 0.2% Triton X-100 and RRI.
The library construction were standard Smart-seq2 protocol. Briefly, polyA RNA in cell lysis were first hybrided with Oligo-dT primer, then reverse transcripted by the PrimeScript Ⅱ RTase and TSO primer. The producted cDNA were pre-amplified with KAPA HiFi HotStart Ready Mix (2×) & TSO-PCR primer. Purified intact cDNA were then fragmented and amplified with barcodes adding by using TruePrep DNA Lybrary Prep Kit V2 for Illumina (cat.#TD502, Vazyme).
Smart-seq2

value: oocyte

value: Gdf9-cre Nat10 cKO


title: Nat10_gKO_2


title: Nat10_gKO_1


title: WT_FGO_2

value: WT


title: COX1204A13_Hhepaticus_Isotype_prdm1 fl/fl maf fl/fl

description:
RNA_Hhepaticus_Isotype_prdm1 fl/fl maf fl/fl
For infection, mice received 1x10^8 colony forming units (c.f.u.) of Helicobacter hepaticus by oral gavage using a 22G curved blunted needle on Day 0 and Day 1, together with 1mg of either anti-mouse IL-10R (CD210) [Clone 1B1.3A, Rat IgG1, kappa] blocking antibody, or Rat IgG1 [Clone GL113, Rat IgG1] isotype control on Day 0 and Day 7 by intraperitoneal injection. Uninfected mice were housed at the same animal facility and received antibody treatment alone.

value: prdm1 fl/fl maf fl/fl


title: COX1204A16_Hhepaticus_Isotype_prdm1 fl/fl maf fl/fl


title: GBM ZH881_1A bulk

source_name: human glioblastoma

value: human glioblastoma

value: bulk

value: partially methylated


title: WT_FGO_3


title: IDHm MGH259 oligodendroglioma


title: WT_FGO_1


title: IDHm BWH23 oligodendroglioma

value: unmethylated


title: GBM ZH881_2 bulk


title: COX1204A14_Hhepaticus_Isotype_prdm1 fl/fl maf fl/fl


title: COX1204A15_Hhepaticus_Isotype_prdm1 fl/fl maf fl/fl


title: GBM ZH1019 T1 contrast-enhancing

value: T1 contrast-enhancing


title: GBM ZH881_1B bulk


title: COX1204A4_Uninfected_Isotype_prdm1 fl/fl maf fl/fl

description:
RNA_Uninfected_Isotype_prdm1 fl/fl maf fl/fl
For infection, mice received 1x10^8 colony forming units (c.f.u.) of Helicobacter hepaticus by oral gavage using a 22G curved blunted needle on Day 0 and Day 1, together with 1mg of either anti-mouse IL-10R (CD210) [Clone 1B1.3A, Rat IgG1, kappa] blocking antibody, or Rat IgG1 [Clone GL113, Rat IgG1] isotype control on Day 0 and Day 7 by intraperitoneal injection. Uninfected mice were housed at the same animal facility and received antibody treatment alone.

source_name: colon LPL from mice with the treatment: Uninfected_Isotype

value: LPL from mice treated with Uninfected_Isotype


title: IDHm BWH28 astrocytoma


title: COX1204A22_Hhepaticus_Isotype_prdm1 fl/fl CD4-Cre


title: GBM ZH1019 infiltrating

value: infiltrating


title: COX1204A3_Uninfected_Isotype_prdm1 fl/fl maf fl/fl


title: Vehicle, replicate 1, scRNAseq

description:
duizhao1
10x Genomics

value: peritoneallavagefluids

value: male

value: Vehicle


title: IDHm BWH24 astrocytoma

value: IDH mutant glioma

value: unannotated

value: methylated


title: GBM ZH916 infiltrating


title: GBM ZH1007 necrotic

value: necrotic


title: COX1204A2_Uninfected_Isotype_prdm1 fl/fl maf fl/fl


title: case #10 of PRNRP

type: RNA

city: San Sebastian

first: Stéphane

last: Nemours

state: Guipúzcoa

address: Paseo Dr. Begiristain, s/n

country: Spain

institute: Biogipuzcoa

hyb_protocol: none provided

scan_protocol: GeneChips were scanned using theAffymetrix gene chip scanner 3000, GCS3000 DX system .

data_processing: The raw intensity data (i.e., cel files) were imported and analysed within Transcriptome Analysis Console (TAC) software version 4.0.2 (Affymetrix, USA)

label: biotin

source_name: PRNRP case

label_protocol: We used 2 µg of total RNA for Affymetrix Genechip miRNA v.4.0 microarrays to measure ncRNA. RNA was labelled and hybridised to microarrays in accordance with the manufacturer’s instructions (Affymetrix, USA).

extract_protocol: Total RNA was extracted from formalin-fixed, paraffin-embedded (FFPE) biopsy material using the Recover All kit from Ambion (LifeTechnologies, UK) according to the manufacturer's instructions.

value: PRNRP


title: case #9 of PRNRP


title: GBM ZH1007 infiltrating


title: Primary peritoneal macrophages, Vehicle, replicate 3

data_processing:
The sequencing data was filtered with SOAPnuke by  Removing reads containing sequencing adapter
Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%;
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com)
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: peritoneal exudates

extract_protocol:
This procedure is suitable for Total RNA extraction of animal tissues, cells and other samples to provide high quality RNA for library preparation
After the reaction system and program are configured and set up, double-stranded cDNA fragments are subjected to end-repair, and then a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments. The reaction system and program for adaptor ligation are subsequently configured and set up to ligate adaptors with the cDNAs

value: peritoneal exudates

value: Primary peritoneal macrophages


title: GBM ZH881 T1 contrast-enhancing

value: human glioblastoma


title: COX1204A1_Uninfected_Isotype_prdm1 fl/fl maf fl/fl

value: prdm1 fl/fl maf fl/fl


title: GBM ZH916 T1 contrast-enhancing


title: Primary peritoneal macrophages, Vehicle, replicate 2


title: GBM MGH258


title: LCMV-Docile, D41, IFNAR1 block, replicate 2, ATAC-seq

status: Public on Feb 17 2024

city: Clayton

first: Kim

last: Good-Jacobson

state: Victoria

address: Gr Fl Reception (Bldg 77) 23 Innovation Walk

country: Australia

institute: Monash University

description:
ATAC
diff.glm.ATACseq.LCMV_IFN_MBC_ATAC.GEO.txt

library_source: genomic

data_processing:
Reads were aligned to the NCBI37/mm10 build of the Mus musculus genome using Bowtie2 and PCR duplicate reads were flagged using the Picard MarkDuplicates tool.
Enriched accessible regions were determined using MACS2 and reads overlapping peaks were annotated for each sample using GenomicRanges tool in R.
DARs were determined using DESeq2. PCA was performed using the vegan package in R.
Assembly: mm10
Supplementary files format and content: diff.glm.ATACseq.LCMV_IFN_MBC_ATAC.GEO.txt. peak information, normalized counts for all samples in each peak, and the annotation

molecule: genomic DNA

source_name: Spleen

extract_protocol:
C57Bl6 mice were infected with LCMV-WE or LCMV-Docile. Mice were treated with IFNγ- or IFNAR1-blocking antibody, or an isotype control, on days 2-14 post-infection (day 15 cohort) or days 28-40 post-infection (day 41 cohort). At day 15 or day 41 post-infection, spleens were surgically removed from culled mice and non-RBC splenocytes were isolated. LCMV-specific B cells were magnetically enriched using an LCMV-NP tetramer system. Enriched cells were then stained with viability dye (FVS) and relevant antibodies, and 15,000 LCMV-specific memory B cells per sample were sorted using the BD Influx (BD Biosciences) cell sorter.
Cells were washed with PBS. One-step permeabilization and tagmentation method was used by resuspending the cell pellets in Digitonin (EZSolution), Tween-20 (Sigma) buffer. High-molecular-weight tagmented DNA was then removed by incubating samples with a 0.7X ratio of Agencourt AMPureXP beads (Invitrogen). The same process was applied using a 1.2X ratio of beads to exclude low-molecular-weight DNA. Purified DNA was then pre-amplified with indexed primers and HiFi HotStart Polymerase Ready Mix (KAPA Biosystems). After estimation of additional PCR cycles required, the genomic library was fully amplified using the SYBR qPCR Master Mix with primers included in the Illumina Library Quantification kit for Bio-Rad iCycler (KAPA Biosystems). Libraries were sequenced on the Illumina NextSeq 2000 using 60-nt paired-end Illumina chemistry.

treatment_protocol: Infection with lymphocytic choriomeningitis virus (LCMV) (WE or Docile strain) for 15 days or 41 days. Mice were treated with IFNγ- or IFNAR1-blocking antibody, or an isotype control, on days 2-14 post-infection (day 15 cohort) or days 28-40 post-infection (day 41 cohort).

value: Spleen

tag: time

value: Day 41

value: LCMV-specific memory B cells

tag: disease state

value: Chronic infection

value: LCMV-Docile

value: IFNAR1 blocking antibody


title: GBM ZH916 bulk

value: bulk


title: case #3 of PRNRP


title: Primary peritoneal macrophages, Vehicle, replicate 1

value: Vehicle


title: Primary peritoneal macrophages, BMP9, replicate 3


title: Primary peritoneal macrophages, BMP9, replicate 1


title: case #7 of PRNRP


title: case #5 of PRNRP


title: Primary peritoneal macrophages, BMP9, replicate 2


title: case #1 of PRNRP


title: GBM ZH881 infiltrating

value: infiltrating

value: partially methylated


title: LCMV-Docile, D41, IFNAR1 block, replicate 1, ATAC-seq


title: LCMV-Docile, D41, IFNγ block, replicate 3, ATAC-seq

value: IFNγ blocking antibody


title: LCMV-Docile, D41, IFNγ block, replicate 2, ATAC-seq


title: case #4 of PRNRP


title: case #6 of PRNRP


title: LCMV-Docile, D41, IFNγ block, replicate 1, ATAC-seq


title: case #8 of PRNRP


title: LCMV-Docile, D41, Control, replicate 1, ATAC-seq

value: Isotype control


title: LCMV-Docile, D15, IFNAR1 block, replicate 2, ATAC-seq

value: Day 15


title: LCMV-Docile, D15, IFNAR1 block, replicate 1, ATAC-seq


title: LCMV-Docile, D15, Control, replicate 2, ATAC-seq


title: LCMV-WE, D15, Control, replicate 2, ATAC-seq

value: Acute infection

value: LCMV-WE


title: LCMV-Docile, D15, IFNAR1 block, replicate 3, ATAC-seq


title: LCMV-WE, D15, Control, replicate 1, ATAC-seq


title: case #2 of PRNRP

value: PRNRP


title: I0480

city: Cleveland

first: Kenneth

last: Matreyek

state: OH

address: 2103 Cornell Rd

department: Pathology

institute: Case Western Reserve University

data_processing:
The DNA was sequenced with a NextSeq 550 using a NextSeq 550 High output 75 cycle or Mid output 150 cycle kit (Illumina).
Following sequencing, the reads were converted to fastq format and de-multiplexed with bcl2fastq. To process the demultiplexed files, we created a custom Python script that extracted the first 10 nucleotides and quality scores from the read1 fastq file, the reverse complement of the first 10 nucleotides and quality scores from the read2 fastq file, and only retained reads that had sequences that matched the known sequences used in the barcoding procedure. Reads that passed this step were output into a single fastq file where the two sets of 10 nucleotides were concatenated as a 20-nucleotide barcode. Files i0192 through i0220, the sixth nucleotide of the read 1 sequences globally exhibited low quality, with many sequences returned with an ambiguous N nucleotide at that position, so the Python script and downstream analyses were modified to retrieve sample identities using a 9 nucleotide character string, and a 19-nucleotide barcode, for those samples.
All resulting fastq files were processed with Enrich2 [32], which was used to tally the counts of all barcodes where the minimum nucleotide quality score was 20 or higher. This process was repeated for every sample, and the resulting barcode counts were written as individual tab-separated value barcode count files for further analysis.
Sequence counts were imported into R, where they were converted into frequencies and plotted for the manuscript.
Assembly: Synthetic barcode sequences
Supplementary files format and content: "Processed_enrichment_scores.csv" is a comma separated value table containing the enrichment scores for all barcoded plasmid constructs across all replicate infection experiments.

growth_protocol: DMEM with 10% FBS, 1 % Penicillin / Streptomycin, and 2 ug/mL doxycycline.

extract_protocol:
The genomic DNA was extracted from thawed pellets using a DNeasy Blood & Tissue Kit (Qiagen, 69506) or JetFlex™ Genomic DNA Purification Kit (A30700, Thermo Scientific).
The extracted genomic DNA was used as the template material for PCR amplification of a 490 bp segment containing the plasmid barcode. To avoid sequencing any lingering unintegrated plasmid DNA, a forward primer directly 5-prime of the plasmid barcode was paired with a reverse primer hybridizing to the Bxb1 integrase coding region encoded in the landing pad, so that only integrated barcodes would be amplified. Each sample was amplified with a single 50 μL reaction containing 2 μg of genomic DNA (as assessed by spectrophotometry at A260), 0.25uM forward primer containing an i7 index and p7 cluster generator sequence, 0.25uM reverse primer containing i5 index barcode and p5 cluster generator sequence, and 25 μL of Phusion plus high-fidelity PCR mix (Thermo Scientific, F631S). The amplicons were created with an initial 95°C incubation for 3 mins, and 28 total cycles of 95°C for 15 secs, 60°C for 15 secs, 72°C for 30 secs, followed by a final extension step of 72°C for 1 min. The PCR reaction contents were mixed with 6x DNA loading dye (New England Biolabs, B7024S) and separated on 1% agarose gel prepared in Tris-acetate-EDTA buffer, and electrophoresed. Double stranded DNA bands migrating at 490 nt were observed with SYBR Safe DNA Gel Stain (Thermo Scientific, S33102) were excised and extracted with a Freeze and Squeeze kit (Bio-Rad, 7326166) and further purified using a silica column (Zymo Research, D4003). The concentrations of the final DNA were quantified with a Qubit dsDNA BR assay kit (Life technologies, Q32853). Amplicons from all the experimental conditions were pooled together in equimolar ratios, subject to a final quality control step for homogeneity with an Agilent Fragment Analyzer and cluster estimation with quantitative PCR.
Amplicon sequencing of DNA recombined within cells

value: HEK 293T

value: Cultured cells

value: Recombination into genomic landing pad


title: I0481


title: I0478


title: I0483


title: I0482


title: I0477


title: LCMV-Docile, D41, Control, replicate 2, ATAC-seq

value: Spleen

value: Day 41

value: LCMV-specific memory B cells


title: I0475


title: I0476


title: I0474


title: I0471


title: I0469


title: I0468


title: I0470


title: I0467


title: I0299


title: OV90_TPM1.9 OE_3 [19_1.9]

city: Rotterdam

first: Mathijs

last: Verhagen

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

data_processing:
Adapter trimming and quality filtering was performed using the SOAPnuke pipeline
Clean fastq files were aligned to the GRCh37 reference genome with RSEM (v1.3.3) using the STAR aligner (v2.7.9a)
Gene level data was imported with tximport (v1.24.0) and downstream analysis was performed using DESeq2 (v1.36.0)
Counts were normalized with a variance stabilizing transformation (VST)
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include Ensemble Gene Id  and read count, VST

source_name: ovarian cancer cell line

growth_protocol: OV90 ovarian cancer cell lines were grown in standard culture medium (1:1 mixture of MCDB105 and Medium 199).

extract_protocol:
RNA was harvested using Trizol reagent.
RNA-Seq was performed at BGI (Shenzhen, China) according to the PE150 DNA Nanoball sequencing (DNBseq) protocol till a depth of 25M reads per sample.

treatment_protocol: Cells were transfected with pcDNA-TPM1.6/7/8/9 plasmids, and selected by Geneticin

value: ovary

value: OV90_TPM1.9 OE

tag: rna isolation_date

value: june 2022


title: I0290


title: OV90_TPM1.9 OE_1 [9_1.9]


title: I0289


title: LCMV-WE, D15, IFNAR1 block, replicate 1, ATAC-seq

value: IFNAR1 blocking antibody


title: OV90_TPM1.9 OE_2 [10_1]


title: LCMV-WE, D15, IFNAR1 block, replicate 2, ATAC-seq


title: OV90_TPM1.8 OE_3 [17_1.8]

value: OV90_TPM1.8 OE


title: I0282


title: I0275


title: OV90_TPM1.8 OE_2 [8_1.8]


title: I0219


title: I0274


title: I0218


title: OV90_TPM1.8 OE_1 [7_1.8]


title: OV90_TPM1.7 OE_3 [15_1]

value: OV90_TPM1.7 OE


title: I0300


title: OV90_TPM1.6 OE_3 [13_1]

value: OV90_TPM1.6 OE


title: OV90_TPM1.7 OE_1 [5_1.7]


title: I0217


title: OV90_Parental_3 [11_par]


title: OV90_TPM1.6 OE_2 [4_1.6]


title: I0214


title: OV90_TPM1.6 OE_1 [3_1.6]


title: OV90_Parental_2 [2_par]


title: I0283


title: I0215


title: I0216


title: I0211


title: I0212


title: I0213


title: OV90_Parental_1 [1_par]


title: NPC_sh4-4

city: Changsha

first: Zongyao

last: Ren

address: No.88 Xiangya Road

institute: Central South University

data_processing:
Quality control with SOAPnuke v1.5.2 to check the quality:
1. Remove low-quality reads (defined as reads with a base quality value <15 and >20% of total bases with low quality).
2. Remove reads with an unknown base (N) content greater than 5%.
3. Remove reads containing adapter sequences (adapter contamination).
Alignment to a reference genome or transcriptome with STAR
Quantification of gene or transcript expression with featureCounts.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

growth_protocol:
H9 embryonic stem cells (ESCs) were utilized and cultured in a standard environment of 37°C with 5% CO2. The ESCs were cultured in a 12-well plate coated with Matrigel (Corning) and maintained with mTeSR-Plus medium (STEMCELL Technologies). Once the cells reached 80-90% confluence, they were dissociated using ReLeSR (STEMCELL Technologies) and passaged at a ratio of 1:20. The culture medium was replaced every other day.
The method used to induce cerebral organoids was a modified version of Lancaster's protocol.

extract_protocol:
The total RNA was processed using mRNA enrichment, which involved enriching for mRNA with polyA tails using magnetic beads with OligodT.
The obtained RNA was fragmented using a fragmentation buffer, and reverse transcription was performed with random N6 primers to synthesize cDNA double strands. The synthesized double-stranded DNA was end-repaired and 5'-phosphorylated, and the 3'-end was extended with an "A" tail to form a sticky end. A bubble-shaped adapter with a protruding "T" at the 3' end was then ligated to the DNA fragments, which were PCR amplified using specific primers. The PCR products were denatured to form single-stranded DNA, which was circularized using a bridge primer to obtain a single-stranded circular DNA library.

treatment_protocol: When the embryonic stem cells (ESCs) were suitable for passaging, accutase was added to digest the cells, and the cells were passaged at a ratio of 1:20. After overnight incubation, the lentivirus was added to infect the cells (MOI=20). The infected cells were screened with puromycin (1ug/ml) for 48 hours, and the screening was continued for 5-7 days.

value: Neural progenitor cells

value: KDM2A knockdown

value: Cells were treated with siRNA-4 to knockdown KDM2A


title: I0210


title: NPC_sh4-5


title: I0209


title: NPC_sh4-2


title: I0220


title: OV90_TPM1.7 OE_2 [6_1.7]


title: I0208


title: NPC_sh4-1


title: I0206


title: NPC_sh1-3

value: Cells were treated with siRNA-1 to knockdown KDM2A


title: NPC_sh1-4


title: NPC_sh1-5


title: I0205

value: HEK 293T


title: NPC_sh1-2


title: I0203

value: Cultured cells


title: NPC_NC-4

value: WT

value: Cells were treated with Scrambled shRNA


title: I0201

value: Recombination into genomic landing pad


title: NPC_sh1-1


title: I0200


title: NPC_NC-3


title: NPC_sh4-3


title: NPC_NC-2


title: I0202


title: I0199


title: NPC_NC-1


title: I0198


title: I0195


title: I0196


title: TngidA_M9_2

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

institute: Twincore

description: Cells were grown in LB to an OD600 =2 and incubated for 10 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.

data_processing:
Reads were trimmed for adaptor sequences and mapped to the PA14 whole genome using a Stampy pipeline with default parameters.
Genome_build: NC_008463.1 (PA14)
Supplementary_files_format_and_content: Processed data file is a data matrix that contains raw unique gene reads.

organism: Pseudomonas aeruginosa

source_name: TngidA

growth_protocol: cell were grown in LB to an OD600 =2

extract_protocol:
The RNeasy Mini Kit (Qiagen) in combination with Qiashredder columns (Qiagen) was used according to the manufacturer’s instruction
The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina).

treatment_protocol: directly after cultivation the cells were treated with one volume of RNAprotect (Qiagen), incubated for 10 minutes at room temperature, centrifuged at 10.000 rpm and cell pellets were frozen at -80°C

tag: mutant

value: tngidA

tag: replicate


title: TngidA_M9_3


title: I0207

tag: cell type

tag: treatment


title: TngidA_M9_1


title: I0204

tag: genotype


title: I0194


title: I0193


title: TnladS_M9_2

source_name: TnladS

value: tnladS


title: TnladS_M9_1


title: I0192


title: TnladS_M9_3


title: Bioreactor_replicate3

city: Madison

first: Sean

last: McIlwain

state: WI

address: 1111 Highland Avenue

institute: University of Wisconsin

data_processing:
Sequencing data is analyzed for quality and contamination (FastQC version 0.10.1). Raw reads are trimmed to remove adapters (cutadapt version 1.2.1), then trimmed and filtered based on quality scores (trimmomatic version 0.32). The preprocessed reads are then assessed for quality and plots are generated of per base quality before and after trimming.
Alignment (Bowtie version 0.12.9 Bowtie2 version 2.1.0)
Abundance levels for ncRNAs (miRNAs, tRNAs, rRNAs, lincRNAs, piRNAs, snoRNAs), antisense transcripts, coding genes and repeat elements (LTR, LINE, SINE, and tandem repeats) are determined (HTseq version 0.5.4p3)
Assembly: hg19
Supplementary files format and content: Raw counts for each sample is in one file, comma separated format

source_name: mesenchymal stromal cells

extract_protocol:
total RNA isolation was performed using the SeraMir Exosome RNA Purification Column kit (System Biosciences)
small RNA libraries were constructed with the CleanTag Small RNA Library Preparation Kit (TriLink,Biotechnologies, San Diego, CA, USA)

value: mesenchymal stromal cells

value: bioreactor


title: NPC_NC-5


title: Bioreactor_replicate2


title: Bioreactor_replicate1


title: I0197


title: Flask_replicate5

value: flask


title: Flask_replicate4


title: Flask_replicate2


title: Flask_replicate1


title: Flask_replicate3


title: Homo49_dTAGV1_1

city: Stanford

first: Tomasz

last: Swigut

address: 265 Campus Drive

department: Chemical and Systems Biology

institute: Stanford University

data_processing:
salmon quant
Assembly: gencode v29
Supplementary files format and content: CSV of salmon pseudocunt and tpm

source_name: cell culture

growth_protocol: MNT-1 cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated from melanocytes using an RNA isolation kit (Zymo Research) following manufacturer’s instructions
RNA libraries for RNA-seq were prepared by Novogene.

treatment_protocol: Cells were treated with 5mm nm dTAG-V1 or DMSO vehicle control for 24 hours

value: cell culture

value: melanoma


title: ccRCC with PC destruction 2

city: Kashihara

first: Takuto

last: Shimizu

state: Nara

address: 840 Shijo-cho

department: Department of Urology

country: Japan

institute: Nara Medical University

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: ACTB, B2M, HPRT1, LDHA, RPL1
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

organism: Rattus norvegicus

source_name: renal cell carcinoma

label_protocol: PCR assays were performed using RT2 Profiler PCR Array (QIAGEN,Venlo, Netherland) , Rat Tumor Metastasis <PARN-028-ZD> ,  following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (QIAGEN, Venlo, Netherland). Quantitative real-time PCR were performed (Light Cycler 480, Roche) 40 cycles of denaturation at 95˚C for 15 s; annealing and a final extension at 60˚C for 1 min.

extract_protocol: Total RNA was extracted with miRneasy FFPE (QIAGEN, Venlo, Netherland)Kit followed by DNase I treatment.

tag: sample type

value: i-Cap 2-3 (PC destruction)


title: ccRCC without PC destruction 1

description: Contorol

value: i-Cap 1 (contorol)


title: ccRCC without PC destruction 2

description: Contorol


title: ccRCC without PC destruction 3

description: Contorol


title: Homo25_dTAGV1_2

tag: tissue


title: Homo25_dTAGV1_1

tag: cell line


title: Het66_dTAGV1_1


title: Het50_dTAGV1_1


title: Het50_dTAGV1_2


title: Het66_dTAGV1_2


title: Flask_replicate6


title: ccRCC with PC destruction 3

description: Test


title: Homo49_DMSO_1

value: DMSO


title: Homo49_DMSO_2


title: ccRCC with PC destruction 1

description: Test


title: Homo49_dTAGV1_2


title: Het66_DMSO_1


title: Het66_DMSO_2


title: Het50_DMSO_1


title: M7

city: Shanghai

first: Run

last: Yang

address: No.83 Fenyang Rd

institute: Eye&ENT Hospital of Fudan University

description:
Gene expression of microtia
Elastic cartilage

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 15 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: Auricular Cartilage

label_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: The isolated cartilage tissues were rapidly immersed in TRIzol reagent (Invitrogen). RNA was extracted by adding chloroform and then precipitated with isopropyl alcohol. The RNA precipitates were washed twice with 70% ethanol, dried, and resolved in water without RNase. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis or Agilent 2100 Bioanalyzer.

value: Auricular Cartilage

tag: gender

value: Female

tag: age

tag: diagnosis

value: Microtia


title: M9

value: Male


title: M10


title: M8


title: M5


title: Normal endometrial stroma with the treatment of SMAD1/5 siRNA and EPC, replicate 5

city: Houston

first: Peixin

last: Jiang

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Raw sequencing reads were preprocessed using fastp for low-quality reads filtering and adapter-trimming.
Reads were aligned to reference genome using STAR Aligner.
The gene count table was generated using htseq-count.
The raw counts were filtered, normalized, and analyzed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized gene counts for each Sample

source_name: Endometrium

extract_protocol:
RNA was extracted using QIAGEN RNeasy Micro Kit.
Illumina library was prepared using Illumina TruSeq RNA Library Prep Kit and sequenced with Illumina Novaseq.

value: Endometrium

value: Stromal cells

value: SMAD1/5 siRNAs, EPC


title: M3


title: Normal endometrial stroma with the treatment of SMAD1/5 siRNA and vehicle, replicate 5

value: SMAD1/5 siRNAs, Vehicle


title: M4


title: Normal endometrial stroma with the treatment of scrambled siRNA and EPC, replicate 5

value: Scrambled siRNA, EPC


title: Normal endometrial stroma with the treatment of scrambled siRNA and vehicle, replicate 5

value: Scrambled siRNA, Vehicle


title: 5751 NB

city: Liège

first: Joris

last: Thomas

address: Quartier Hôpital avenue de l'Hôpital 11

country: Belgium

institute: Universite de Liege

description:
Sheep_NB_MUT_vs_Sheep_NB_healthy_table.csv
Sheep_NB_WT_vs_Sheep_NB_healthy_table.csv
5751_NB

data_processing:
Reads were aligned on the ovine reference genome using HISAT2 (version 2.2.1)
The number of sequences that mapped to known genes were quantified with the featureCounts method from subread package (version= 2.0.3)
Differentially expressed genes were identified using DESEq2 (version 1.32.0).
Assembly: Oar_rambouillet_v1.0
Supplementary files format and content: comma-delimited text files including raw counts, ID.1,basemean,log2FC,stderr,waldstat,pval,padj,chr,start,stop,strand,fun,gene for each DEG analysis

organism: Ovis aries

source_name: All PBMCs excepts B cells

growth_protocol: Sheep were kept under L2-restricted conditions (registration number LA1900600), according to the ethical protocols n°1515/2067, at the Centre d’Etude en Production Animales (CEPA) facility located in Gembloux (Belgium).

extract_protocol:
Whole blood was collected by jugular venipuncture using 2% EDTA (v/v) as anticlotting agent. After collecting the plasma, PBMCs were separated by Percoll (Merck) gradient centrifugation.
poly-A libraries were generated with the Illumina TruSeq stranded mRNA kit (Illumina)

treatment_protocol: Plasmids pBLV344 or pBLV344-A1 (20 µg) were transfected into HEK293FT cells (9x106 cells in a 15 cm diameter culture plate), using 60 µL of polyethyleneimine (1 µg/µL, 25 kD, Polysciences) in 1 mL of OPTI-MEM (Gibco). After overnight culture, cells were washed with PBS and cultured in fresh medium for 24 hours. Transfected HEK293FT cells were detached with trypsin-EDTA (Biowest), pelleted by centrifugation and resuspended in 1 mL PBS. After a freeze-thaw cycle at -80°C, the cell lysate was inoculated intravenously and subcutaneously into sheep.

value: All PBMCs excepts B cells


title: M6


title: Normal endometrial stroma with the treatment of SMAD1/5 siRNA and vehicle, replicate 4


title: Normal endometrial stroma with the treatment of SMAD1/5 siRNA and EPC, replicate 4


title: 5751 B

description:
Sheep_B_MUT_vs_Sheep_B_healthy_table.csv
Sheep_B_WT_vs_Sheep_B_healthy_table.csv
5751_B

source_name: B cells

value: B cells


title: Het50_DMSO_2

value: cell culture


title: M1


title: C5

description:
Gene expression of control
Elastic cartilage

value: Tympanitis


title: Normal endometrial stroma with the treatment of scrambled siRNA and EPC, replicate 4


title: M2


title: LCMV-WE, replicate 2 + LCMV-Docile, replicate 2, VDJ

description:
VDJ
BCR

library_source: other

data_processing:
library strategy: CITE-seq
Cellranger (v5.0.1) multi was used to process the gene expression, cite-seq and VDJ libraries simultaneously. The following details were provided for the feature reference file: C0301,C0301_TotalSeqC,R2,5PNNNNNNNNNN(BC),ACCCACCAGTAAGAC,Antibody Capture, C0302,C0302_TotalSeqC,R2,5PNNNNNNNNNN(BC),GGTCGAGAGCATTCA,Antibody Capture.
C0301 corresponds to hashtag antibody 1(used on acute samples) and C0302 corresponds to hashtag antibody 2 (used on chronic samples)
Further processing was done with Seurat v3.0.0 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis). Seurat's HTO Demux function was used to demultiplex the samples and then Seurat was used for quality control, filtering, dimensionality reduction and clustering of the gene expression data.
The Immcantation suite (v 4.1.0) was used for VDJ analysis.
Assembly: mm10

extract_protocol:
C57Bl6 mice were infected with LCMV-WE or LCMV-Docile. 28 days after infection, spleens were surgically removed from culled mice and non-RBC splenocytes were isolated. LCMV-specific B cells were magnetically enriched using an LCMV-NP tetramer system. Enriched cells were then stained with viability dye (FVS) and relevant antibodies, and 100,000 LCMV-specific B cells per sample were sorted using the BD Influx (BD Biosciences) cell sorter. After FACS, cells were spun down and resuspended in washing buffer (PBS 0.04% BSA) (50μl per ~1-2 million cells) and incubated with mouse Fc blockers (FcX, Biolegend) for 10 minutes at 4°C to block non-specific antibody binding. Following Fc blocking, each sample was incubated with either TotalSeq anti-mouse Hashtag Antibody 1 (Biolegend #155861) or 2 (Biolegend #155863) for 20 minutes at 4°C. Acute samples were tagged with Hashtag Antibody 1 and chronic samples were tagged with Hashtag Antibody 2. Following incubation, cells were washed 3x with 1ml of washing buffer to remove unbound antibodies. LCMV-WE and LCMV-Docile samples were then pooled at equal ratios in (PBS 0.04% BSA 0.2 U/ml RNAse inhibitor) at 1200 cells/ul. Cell viability >95% was confirmed via Trypan Blue staining.
Reverse transcription, cDNA amplification and library preparation for single cell gene expression and V(D)J clonotypes were performed based on the manufacturers protocol using the Chromium Single Cell 5′ Library & Gel Bead Kit v3 (10X Genomics).
Libraries were pooled at equimolar ratios and gene expression libraries were sequenced on the Illumina NovaSeq 6000 System, while HTO (hashtag oligo) and V(D)J (BCR) libraries were sequenced on Illumina NextSeq 500.

treatment_protocol: Infection with lymphocytic choriomeningitis virus (LCMV) (WE or Docile strain) for 28 days

value: Spleen

value: 28 days post-infection

value: LCMV-specific B cells

value: Acute + Chronic infection

value: LCMV-WE + LCMV-Docile


title: C4

value: Auricular Cartilage


title: Normal endometrial stroma with the treatment of scrambled siRNA and vehicle, replicate 4


title: LCMV-WE, replicate 2 + LCMV-Docile, replicate 2, HTO

description:
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

tag: antibodies/tags

value: C0301 TotalSeq C anti-mouse Hashtag Antibody 1 (Biolegend #155861)


title: LCMV-Docile, D15, Control, replicate 1, ATAC-seq

value: Day 15

value: LCMV-specific memory B cells

value: Chronic infection

value: LCMV-Docile

value: Isotype control


title: C2

value: Male

value: Cholesteatoma of middle ear


title: Normal endometrial stroma with the treatment of SMAD1/5 siRNA and vehicle, replicate 1

value: Endometrium

value: Stromal cells

value: SMAD1/5 siRNAs, Vehicle


title: C3

value: Female


title: C1

value: Acquired external auditory canal stenosis


title: Normal endometrial stroma with the treatment of SMAD1/5 siRNA and EPC, replicate 1

value: SMAD1/5 siRNAs, EPC


title: 4235 B

description:
Sheep_B_MUT_vs_Sheep_B_healthy_table.csv
Sheep_B_WT_vs_Sheep_B_healthy_table.csv
4235_B

value: B cells


title: LCMV-WE, replicate 1 + LCMV-Docile, replicate 1, VDJ

description:
VDJ
BCR

value: Spleen

value: 28 days post-infection

value: LCMV-specific B cells

value: Acute + Chronic infection

value: LCMV-WE + LCMV-Docile


title: Normal endometrial stroma with the treatment of scrambled siRNA and EPC, replicate 1

value: Scrambled siRNA, EPC


title: Normal endometrial stroma with the treatment of scrambled siRNA and vehicle, replicate 1

value: Scrambled siRNA, Vehicle


title: 8619 NB

description:
Sheep_NB_MUT_vs_Sheep_NB_healthy_table.csv
Sheep_NB_WT_vs_Sheep_NB_healthy_table.csv
8619_NB

value: All PBMCs excepts B cells


title: LCMV-WE, replicate 1 + LCMV-Docile, replicate 1, HTO

value: C0301 TotalSeq C anti-mouse Hashtag Antibody 1 (Biolegend #155861)


title: Endometriosis stroma, Replicate 13, Day8

data_processing:
Raw sequencing reads were preprocessed using fastp for low-quality reads filtering and adapter-trimming.
Reads were aligned to reference genome using STAR Aligner.
The gene count table was generated using featureCounts.
The raw counts were filtered, normalized, and analyzed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include normalized gene counts for each Sample

extract_protocol:
RNA was extracted using QIAGEN RNeasy Micro Kit.
Library was prepared using Illumina TruSeq RNA Library Prep Kit and sequenced with Illumina Novaseq.

value: EPC

value: Day 8


title: 8619 B

description:
Sheep_B_MUT_vs_Sheep_B_healthy_table.csv
Sheep_B_WT_vs_Sheep_B_healthy_table.csv
8619_B


title: 4235 NB

description:
Sheep_NB_MUT_vs_Sheep_NB_healthy_table.csv
Sheep_NB_WT_vs_Sheep_NB_healthy_table.csv
4235_NB


title: NFATc2M rep2

city: Beijing

first: Jing

last: Huang

address: No. 10, Xitoutiao, Youanmenwai

institute: capital medical university

data_processing:
Raw reads were obtained in FASTQ format from Illumina Hiseq X Ten sequencing platform.
The clean reads in compressed FASTQ format were aligned using HISAT2 to the reference of human genome (Homo_sapiens.GRCh38.dna.primary_assembly.fa).
The resulted BAM files were sorted with SAMtools (version 1.18).The depth counts were called with HTSeq (version 0.11.2. Linux_x86_64, Simon Anders (sanders@fs.tum.de)) with the reference of human genome (Homo_sapiens.GRCh38.94.gtf), European Molecular Biology Laboratory (EMBL)) used to calculate the Fold change (FC) of FPKM and p value among sample groups according to an over-dispersed Poisson model.
Genome_build: Ensembl hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: A549 cell line

growth_protocol: Cells were maintained at 37°C in a 5% CO2 incubator in Ham’s F12 Nutrient Medium (Ham’s F12) with 10% fetal bovine serum (FBS)  and 1% penicillin-streptomycin.

extract_protocol:
Cells were scraped off from the surface in trypsin-versene solution and collected by 500 g centrifugation. The pellet was washed with PBS to remove residual media. Total RNA extractions were performed with the RNA-Quick Purification Kit following the manufacturer's protocol. The RNA concentrations were determined using a Nanodrop ND1000 spectrophotometer .
The mRNA sequencing libraries were performed with the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (NR604-01, Vazyme Biotech, Nanjing, China), VAHTS RNA Multiplex Oligos Set1- Set2 for Illumina (N323, Vazyme Biotech, Nanjing, China), VAHTS DNA Clean Beads (N311-01, Vazyme Biotech, Nanjing, China), VAHTS mRNA Capture Beads (N401-01, Vazyme Biotech, Nanjing, China). The quality assessments were performed in the laboratory of GENEWIZ, lnc (Suzhou, China).

treatment_protocol: Cells cultured in 6-well plate were transfected with pENTER-NFATc2 or pENTER-NFATc2M. The conditioned medium containing secretory OPNc were collected and added to fresh medium for conditioned culture.

value: NFATc2M oe

value: OPNc-CM


title: Endometriosis stroma, Replicate 13, Day6

value: Endometrium

value: Stromal cells

value: Day 6


title: 5667 NB

description:
Sheep_NB_MUT_vs_Sheep_NB_WT_table.csv
Sheep_NB_WT_vs_Sheep_NB_healthy_table.csv
5667_NB

value: BLV WT


title: Endometriosis stroma, Replicate 13, Day4

value: Day 4


title: Endometriosis stroma, Replicate 13, Day2

value: Day 2


title: 5667 B

description:
Sheep_B_MUT_vs_Sheep_B_WT_table.csv
Sheep_B_WT_vs_Sheep_B_healthy_table.csv
5667_B

value: B cells


title: Endometriosis stroma, Replicate 13, Day0

value: Day 0


title: Endometriosis stroma, Replicate 12, Day6


title: NFATc2M rep1


title: NFATc2 rep2

value: NFATc2 oe


title: Endometriosis stroma, Replicate 12, Day8


title: 2777 NB

description:
Sheep_NB_MUT_vs_Sheep_NB_WT_table.csv
Sheep_NB_WT_vs_Sheep_NB_healthy_table.csv
2777_NB


title: Endometriosis stroma, Replicate 12, Day4


title: Endometriosis stroma, Replicate 12, Day2


title: 2777 B

description:
Sheep_B_MUT_vs_Sheep_B_WT_table.csv
Sheep_B_WT_vs_Sheep_B_healthy_table.csv
2777_B


title: NFATc2 rep1


title: Endometriosis stroma, Replicate 10, Day8


title: Endometriosis stroma, Replicate 12, Day0


title: 2130 NB

description:
Sheep_NB_MUT_vs_Sheep_NB_WT_table.csv
Sheep_NB_WT_vs_Sheep_NB_healthy_table.csv
2130_NB


title: Endometriosis stroma, Replicate 10, Day4


title: Endometriosis endometrium stroma, EPC, IgG, replicate 2

data_processing:
Basecalls were performed using bcl2fastq v2.20 for NextSeq500 output.
Raw sequencing reads were aligned to the hg19 reference genome using bowtie2/2.2.7 in paired-end mode with parameters --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
Raw sequencing reads for Spike-in were aligned to the  E. coli genome U00096.3 using bowtie2/2.2.7 in paired-end mode with parameters --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
Spike-in normalization was achieved through multiply primary genome coverage by scale factor (100000 / fragments mapped to E. coli genome).Then normalized alignments were converted into fragments using bedtools bamtobed (v2.29.2)
bigWig files were generated using the bedGraphToBigWig tool. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: GRCh37
Supplementary files format and content: bigWig, representing the normalized coverage of DNA fragments at a given genomic coordinate.
Library strategy: CUT&Run

extract_protocol:
Human endometrial stromal cells were digested with 0.25% Trypsin for 5 min at 37 ℃ to get single cell suspension, then washed and incubated with activated concanavalin A beads for 10 min at room temperature. Cells were then resuspended in antibody buffer containing 0.01% digitonin, 1ul of each antibody was added to individual cell aliquots, and tubes were rotated at 4°C overnight. The following day, targeted chromatin digestion and release were performed with 2.5 ul of Cutana pA/G-MNase and 1 ul of 100 mM CaCl2. Genomic DNA with 0.05ng of Spike-in DNA together was purified with phenol-chloroform and ethanol precipitated.
Sequencing libraries were prepared using NEBNext Ultra II DNA Library Prep Kit following manufacture's protocol.

value: IgG


title: Endometriosis stroma, Replicate 10, Day6


title: Endometriosis stroma, Replicate 10, Day0


title: Endometriosis endometrium stroma, EPC, H3K27ac, replicate 2


title: Endometriosis endometrium stroma, EPC, IgG, replicate 1


title: 2492 NB

description:
Sheep_NB_MUT_vs_Sheep_NB_healthy_table.csv
Sheep_NB_MUT_vs_Sheep_NB_WT_table.csv
2492_NB

value: BLV A1


title: Endometriosis stroma, Replicate 10, Day2


title: Endometriosis stroma, Replicate 1, Day8


title: Endometriosis stroma, Replicate 1, Day6


title: Endometriosis stroma, Replicate 1, Day4


title: 2130 B

description:
Sheep_B_MUT_vs_Sheep_B_WT_table.csv
Sheep_B_WT_vs_Sheep_B_healthy_table.csv
2130_B


title: 2492 B

description:
Sheep_B_MUT_vs_Sheep_B_healthy_table.csv
Sheep_B_MUT_vs_Sheep_B_WT_table.csv
2492_B


title: Endometriosis endometrium stroma, EPC, H3K27ac, replicate 1


title: Endometriosis endometrium stroma, EPC, SMAD4, replicate 2


title: 0523 NB

description:
Sheep_NB_MUT_vs_Sheep_NB_healthy_table.csv
Sheep_NB_MUT_vs_Sheep_NB_WT_table.csv
0523_NB

value: All PBMCs excepts B cells


title: Endometriosis stroma, Replicate 1, Day2


title: Endometriosis stroma, Replicate 1, Day0


title: Normal endometrial stroma, Replicate 7, Day6


title: Normal endometrial stroma, Replicate 7, Day8


title: Endometriosis endometrium stroma, EPC, SMAD4, replicate 1


title: Normal endometrium stroma, EPC, IgG, replicate 2


title: 0523 B

description:
Sheep_B_MUT_vs_Sheep_B_healthy_table.csv
Sheep_B_MUT_vs_Sheep_B_WT_table.csv
0523_B


title: Normal endometrial stroma, Replicate 7, Day2


title: Normal endometrial stroma, Replicate 7, Day4


title: Normal endometrial stroma, Replicate 7, Day0


title: 0522 B

description:
Sheep_B_MUT_vs_Sheep_B_healthy_table.csv
Sheep_B_MUT_vs_Sheep_B_WT_table.csv
0522_B


title: Normal endometrial stroma, Replicate 6, Day8


title: Normal endometrial stroma, Replicate 6, Day6


title: Normal endometrium stroma, EPC, H3K27ac, replicate 1


title: Normal endometrial stroma, Replicate 6, Day2


title: Normal endometrial stroma, Replicate 6, Day4


title: Normal endometrium stroma, EPC, H3K27ac, replicate 2


title: Normal endometrium stroma, EPC, IgG, replicate 1


title: Normal endometrial stroma, Replicate 6, Day0


title: TDP43-ALS iPSC-derived miRNA MN_2

city: Rostock

first: Andreas

last: Hermann

state: Mecklenburg-Western Pomerania

address: Gehlsheimer Str.20

department: Neurology

institute: University Medical Center Rostock

description: TDP43 G294V_BRC2TDP4312

data_processing:
Partek Flow Lab Edition 11.0.24.0204 (Partek Inc., St. Louis, MO, USA)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using the Partek Flow software, the minimum read length after trimming was set to 15
Trimmed sequence reads were aligned to miRBase mature miRNAs version 22 of the latest human genome assembly, hg38 (GRCh38) using the Bowtie 2 aligner. Read counts were then quantified to the transcriptome using Partek Flow software Quantify to annotaion model (Expectation Maximization (EM) algorithm) and normalization was performed using DESeq2
Differential expression levels of miRNAs in each sample and the corresponding fold changes were estimated by DESeq2 (Partek Flow)
Assembly: miRBase v22 human miRNAs
Supplementary files format and content: tab-delimited text file includes log2 normalized values per miRNA for each Sample

source_name: iPSC-derived spinal motor neurons

growth_protocol: Neurons were cultured in N2B27 medium with 10 ng/µl BDNF, 500 µM dbcAMP and 10 ng/µl GDNF

extract_protocol:
Total RNA was isolated using miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol for small amounts of RNA for the neuronal fraction including a column DNase digest for all samples.
1 ug of total RNA was used to construct sequencing libraries using the TruSeq Small RNA Library Prep Kit (HiSeq 2500, Illumina) following manufacturer's protocols.

treatment_protocol: Not applicable

tag: disease status

value: Familial ALS (fALS)

tag: cell line_(ipsc_source)

value: Fibroblast

value: iPSC-derived spinal motor neurons

tag: genotype (donor)

value: fALS patient1 carrying TDP43 mutation

value: not applicable


title: TDP43-ALS iPSC-derived miRNA MN_1

description: TDP43 G294V_BRC15TDP4311


title: Normal endometrial stroma, Replicate 4, Day8

value: Endometrium

value: EPC

tag: time

value: Day 8


title: SOD1-ALS iPSC-derived miRNA MN_2

description: SOD1 D90A_MM41

value: fALS patient2 carrying SOD1 mutation


title: TDP43-ALS iPSC-derived miRNA MN_3

description: TDP43 S393L_MCC25TDP4321

value: fALS patient2 carrying TDP43 mutation


title: Normal endometrium stroma, EPC, SMAD4, replicate 1

value: Stromal cells


title: Normal endometrial stroma, Replicate 4, Day6

value: Day 6


title: 0522 NB

description:
Sheep_NB_MUT_vs_Sheep_NB_healthy_table.csv
Sheep_NB_MUT_vs_Sheep_NB_WT_table.csv
0522_NB


title: Normal endometrial stroma, Replicate 4, Day4

value: Day 4


title: Healthy control iPSC-derived miRNA MN_3

value: Healthy

value: Healthy donor 3-clone 1


title: Total-Vehicle-M3

city: Toronto

first: Pamela

last: Ohashi

state: ON

address: 610 University Ave

department: Tumor Immunotherapy Program

country: Canada

institute: University Health Network

data_processing:
For the riboseq sequencing reads, both RPF and total fractions were processed similarly. First, adapter sequences were trimmed off using cutadapt version 1.18 and removed if shorter than 15 bp (special parameters -m 15 -q 25).
Then, all remaining reads were aligned against a non-coding RNA database in order to remove any remaining reads that cannot be uniquely assigned to ribosome-translated genes. To this end, we downloaded ncRNA sequences (tRNAs, rRNAs and others) from Ensembl version 85, and aligned all reads against this ncRNA database with bowtie2 version 2.3.4.1 (parameters: -L 18; 49).
All unaligned reads were extracted (--un parameter) and aligned against the mouse reference genome GRCm38/mm10 using STAR version 2.5.0c (parameters --outFilterMultimapNmax 1; --outFilterMismatchNoverLmax 0.05; 50), with the STAR-integrated read-counting method (--quantMode GeneCounts) using gene annotations downloaded from Ensembl Version 85.
In order to assess the quality of the Riboseq libraries, we checked for intra-gene read distribution as well as read-length of reads uniquely aligned to the reference genome after filtering.
Assembly: GRCm38/mm10
Supplementary files format and content: Processed expression data files are tab-delimited text files (.txt), containing 2 columns: the 1st containing Ensembl Ids for the quantified gene, and the second containing FPKM expression values for the gene in a given sample.

source_name: CD8+ T cells

growth_protocol: Activated CD8+ T cells were IL-2 expanded in complete IMDM for 96 hours with Halo (50 ng/mL) being added for the last 48 hours of culture. Ribosomal profiling was conducted according to the TruSeq Ribo Profile kits manual. Cultured cells were incubated in 50 mg/ml cycloheximide (CHX) for 10 min and then washed in PBS containing CHX.

extract_protocol:
The samples were lysed in cytoplasmic lysis buffer and clarified by centrifugation at 12,000 g for 10 min, Aliquots (100 and 200 μL) from each supernatant were generated. 100-µL aliquot of supernatant was used to extract total RNA for constructing RNA-seq libraries and 200-µL aliquot of supernatant was treated with nuclease provided by the TruSeq Ribo Profile Kit (illumina). Nuclease digestion was stopped by adding 15 µL of SUPERase-in (Thermo Fisher Scientific; AM2696). Size exclusion columns (illustra MicroSpin S-400 HR Columns) Size exclusion columns (illustra MicroSpin S-400 HR Columns; GE Healthcare; catalog no. 27-5140-01) were equilibrated with 3 mL of polysome buffer by gravity flow and spun at 600 × g for 4 min. Ribosomes were isolated by applying digested lysate immediately onto the prepared size exclusion columns above (100 µL of lysate per column) and spinning them at 600 × g for 2 min. Next, 10 μL 10% (wt/vol) SDS was added to the elution, and RNA with a size greater than 17 nt was isolated according to the Zymo RNA clean and concentrator kit (Zymo Research; R1017). After checking digestion quality, RNA with a size less than 200 nt was isolated according to the Zymo RNA clean and concentrator kit (Zymo Research; R1015). rRNA was depleted using the Ribo-Zero Human/Mouse/Rat kit (illumine; RS-122-2201, RS-122-2202, and RS-122-2203). After rRNA depletion, purified RNA was separated by 15% (wt/vol) TBE-urea PAGE (Thermo Fisher Scientific; EC68852BOX), and gel slices from 28 to 30 nt were excised. Ribosome footprints were recovered from the excised gel slices following the overnight elution method specified in the kit manual. After obtaining ribosome footprints above, Ribo-seq libraries were constructed according to TruSeq Ribo Profile kit manual and amplified by 13 cycles of PCR with a barcode incorporated in the primer. The PCR products were gel purified using the overnight method described by protocol.
For RNA-seq, a 100-µL aliquot of supernatant as described above was used to extract total RNA by adding 5 µL of 10% (wt/vol) SDS followed by purification using the Zymo RNA clean and concentrator kit (Zymo Research; R1017). Then, 5 μg of total RNA were subjected to rRNA depletion using Ribo-Zero Human/Mouse/Rat kit (illumine; RS-122-2201, RS-122-2202, and RS-122-2203). The rRNA-depleted RNA was used to construct sequencing libraries using the TruSeq Ribo Profile kit (illumina). The circularized cDNA was amplified by 11 cycles of PCR and gel purified using the same procedure for the Ribo-seq libraries described above. Libraries were barcoded, pooled, and sequenced in a HiSeq 2500 machine (single-end 50 bp).

value: CD8+ T cells

value: Vehicle Control


title: Total-Vehicle-M2


title: Healthy control iPSC-derived miRNA MN_2

value: Healthy donor2-clone 1


title: Normal endometrial stroma, Replicate 4, Day0

value: Day 0


title: Total-Halo-M3

value: Halofuginone (Halo)


title: Normal endometrium stroma, EPC, SMAD4, replicate 2


title: Healthy control iPSC-derived miRNA MN_1

value: Fibroblast

value: iPSC-derived spinal motor neurons

value: Healthy donor1-clone 1


title: Total-Halo-M1


title: Normal endometrial stroma, Replicate 2, Day8

value: Endometrium

value: EPC


title: Normal endometrial stroma, Replicate 2, Day4


title: Normal endometrial stroma, Replicate 2, Day6


title: ccRCC without PC destruction 2

description: Contorol

label_protocol: PCR assays were performed using RT2 Profiler PCR Array (QIAGEN,Venlo, Netherland) , Rat Fibrosis <PARN-120-ZD> ,  following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (QIAGEN, Venlo, Netherland). Quantitative real-time PCR were performed (Light Cycler 480, Roche) 40 cycles of denaturation at 95˚C for 15 s; annealing and a final extension at 60˚C for 1 min.

value: i-Cap 1 (contorol)


title: ccRCC without PC destruction 3

description: Contorol


title: RPF-Vehicle-M3

data_processing:
*library strategy: RIBO-seq
For the riboseq sequencing reads, both RPF and total fractions were processed similarly. First, adapter sequences were trimmed off using cutadapt version 1.18 and removed if shorter than 15 bp (special parameters -m 15 -q 25).
Then, all remaining reads were aligned against a non-coding RNA database in order to remove any remaining reads that cannot be uniquely assigned to ribosome-translated genes. To this end, we downloaded ncRNA sequences (tRNAs, rRNAs and others) from Ensembl version 85, and aligned all reads against this ncRNA database with bowtie2 version 2.3.4.1 (parameters: -L 18; 49).
All unaligned reads were extracted (--un parameter) and aligned against the mouse reference genome GRCm38/mm10 using STAR version 2.5.0c (parameters --outFilterMultimapNmax 1; --outFilterMismatchNoverLmax 0.05; 50), with the STAR-integrated read-counting method (--quantMode GeneCounts) using gene annotations downloaded from Ensembl Version 85.
In order to assess the quality of the Riboseq libraries, we checked for intra-gene read distribution as well as read-length of reads uniquely aligned to the reference genome after filtering.
Assembly: GRCm38/mm10
Supplementary files format and content: Processed expression data files are tab-delimited text files (.txt), containing 2 columns: the 1st containing Ensembl Ids for the quantified gene, and the second containing FPKM expression values for the gene in a given sample.

tag: molecule subtype

value: ribosome-protected RNA Fragments (RPF)


title: si_control_rep1

city: Taiyuan

first: Liu

last: Hongliang

state: Shanxi

address: No. 56, South Xinjian Road

institute: Shanxi Medical University

description: TU-177 cells, si-control, replicate 1

hyb_protocol: Cyanine-3 (Cy3) labeled cRNA was hybridized and washed according to the manufacturer’s protocols(Agilent Human lncRNA Microarray 2018 Version, 4×180k, Design ID: 085630).

scan_protocol: The arrays were scanned using the Agilent Scanner G2505C (Agilent Technologies)

data_processing: Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to analyze array images to get raw data. Genespring (version 13.1, Agilent Technologies) were employed to finish the basic analysis with the raw data. To begin with, the raw data was normalized with the quantile algorithm. The probes that at least 1 conditions out of 2 conditions have flags in “P” were chosen for further data analysis.

source_name: Gene expression in control TU-177 cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared based on the manufacturer’s standard protocols(Agilent Human lncRNA Microarray 2018 Version, 4×180k, Design ID: 085630).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human LSCC cell line TU-177 were cultured in DMEM supplemented with 10% fetal bovine serum. The cultures were maintained at 37°C in 5% CO2.

extract_protocol: Total RNA was extracted from cells using TRIzol reagent (Thermo Fisher Scientific, Carlsbad, CA) and then quantified using the NanoDrop ND-2000 (Thermo Fisher Scientific). The integrity of RNA was assessed with Agilent Bioanalyzer 2200 (Agilent Technologies).

treatment_protocol: For siRNA transfection, TU-177 cells (2.0 × 10^5 cells per well) were seeded in 6-well plates. FSCN1 siRNA and control siRNA were transfected using Lipofectamine 3000. Cells were harvested after 48 h transfection.

tag: disease

value: Laryngeal squamous cell carcinoma

value: control


title: ccRCC without PC destruction 1

description: Contorol


title: si_control_rep3

description: TU-177 cells, si-control, replicate 3


title: RPF-Vehicle-M2


title: SOD1-ALS iPSC-derived miRNA MN_1

description: SOD1 R115G_D8.9

value: Familial ALS (fALS)

value: fALS patient1 carrying SOD1 mutation

value: not applicable


title: Normal endometrial stroma, Replicate 4, Day2

value: Stromal cells

value: Day 2


title: si_control_rep2

description: TU-177 cells, si-control, replicate 2


title: si_FSCN1_rep3

description: TU-177 cells, si-FSCN1, replicate 3

source_name: Gene expression in FSCN1 knockdown TU-177 cells

value: FSCN1 knockdown


title: RPF-Vehicle-M1

value: CD8+ T cells

value: Vehicle Control


title: Normal endometrial stroma, Replicate 2, Day0

value: Day 0


title: Total-Vehicle-M1


title: si_FSCN1_rep2

description: TU-177 cells, si-FSCN1, replicate 2


title: ccRCC with PC destruction 3

description: Test

value: i-Cap 2-3 (PC destruction)


title: si_FSCN1_rep1

description: TU-177 cells, si-FSCN1, replicate 1


title: Total-Halo-M2

value: Halofuginone (Halo)


title: RPF-Halo-M3


title: Normal endometrial stroma, Replicate 2, Day2

value: Endometrium


title: Blister-adjacent RDEB skin

city: Boston

first: Natasha

last: Frank

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine

institute: Brigham and Women's Hospital

data_processing:
Quality control was performed using FASTQC
Adaptor trimming was performed using cutadapt
Reads were aligned using the STAR aligner
Quantitation was performed using Salmon
DESeq2 in the R environment was used to generate normalized counts
Assembly: hg19
Supplementary files format and content: CSV includes DESeq2 normalized counts for each sample

source_name: RDEB skin

extract_protocol:
QIAGEN RNeasy Mini Kit (Cat. No. 74104, Germantown, MD, USA)
Roche Kapa mRNA Hyper prep reagents from 200ng of total RNA

value: RDEB skin

value: Skin

value: RDEB


title: RDEB SCC tumor tissue

source_name: RDEB SCC

value: RDEB SCC

value: Tumor


title: KDM2A_NC_Input

data_processing:
Fastp (version 0.23.0, Shifu Chen 2018) software was used for data quality control.The data was processed by removing adapter contamination, filtering out short reads (<15bp), low-quality reads (<Q15 with >40% of bases with low quality), and reads with >5 N bases.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Intranscription factorChIP-seq analysis with both Input and IP samples, we used Input as the background and called peaks on the IP sample using Macs2 in narrow peak mode. Macs2 is important for peak calling because it models the length of theprotein bindingsequence and determines therelative abundanceof peaks based on the length of that sequence and the number of pair-end reads mapped to it. In chromatin ChIP-seq analysis with both Input and IP samples, we also used Input as the background and called peaks on the IP sample using Epic2.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: excel, Fold_enrichment, Pvalue and FDR (except for Input sample)

growth_protocol: H9 embryonic stem cells (ESCs) were utilized and cultured in a standard environment of 37°C with 5% CO2. The ESCs were cultured in a 12-well plate coated with Matrigel (Corning) and maintained with mTeSR-Plus medium (STEMCELL Technologies). Once the cells reached 80-90% confluence, they were dissociated using ReLeSR (STEMCELL Technologies) and passaged at a ratio of 1:20. The culture medium was replaced every other day.

extract_protocol:
Tissue or cells are cross-linked with formaldehyde to form covalent bonds between proteins and DNA. The cells are then lysed to releasecytoplasmic contentsand collect the nuclei. DNA-protein complexesare extracted from the lysate, and the DNA is fragmented into 200-1000bp pieces. The target protein-DNA complex is immunoprecipitated and washed. The complex is then eluted, and the DNA-protein cross-links are reversed, and DNA is extracted. The quality of theprecipitated DNAis checked, and the protein is detected using Western blotting. Finally, theimmunoprecipitated DNAis used to construct a library.
DNA from the IP was end-repaired and had an A-tail added. Sequencing adapters were then added to the repaired DNA. Target-sized fragments were recovered using magnetic beads and PCR amplified to obtain a library for sequencing. The library was quality checked using gel electrophoresis and quantified using Qubit 2.0 to ensure proper concentration for sequencing. Once the library passed quality control, it was sequenced on an Illumina sequencer, with different libraries sequenced based on their effective concentration and desired data output.

value: Neural progenitor cells

tag: chip antibody

value: none (input)


title: RPF-Halo-M2

tag: cell type

value: ribosome-protected RNA Fragments (RPF)


title: ccRCC with PC destruction 1

description: Test


title: ccRCC with PC destruction 2

description: Test


title: 15M HCC

city: New Haven

first: Jonathan

last: Sun

state: CT

address: 10 Amistad St

institute: Yale University

description: 10x Genomics

data_processing:
Reads were aligned against mouse genome mm9 using the CellRanger software (10x Genomics).
Gene-barcode matrices were analyzed in R (version 3.0) using Seurat v3. Cells were filtered for more than 500 genes detected in each cell, 20,000 or less total number of molecules detected within a cell and 5% or less mitochondrial gene content.
Significant principal components of variation (PCs) were calculated using JackStraw test, and clusters were calculated with 30 PCs
Differential expression analysis was done using wilcox
Assembly: mmp10
Supplementary files format and content: Cell-gene-barcode matrices

source_name: Single cell suspension from the HCC region

extract_protocol:
The liver of diet-fed mice were perfused with collagenase and dissociated to separate out parenchymal (hepatocytes, cholangiocytes) and non-parenchymal (endothelial cells, immune cells etc..) fractions. Parenchymal fractions were purified using a 30% percoll gradient. Non-parenchymal fraction were enriched for live cells by flourescent activated cell sorting. Purified parenchymal and non-parenchymal cells were combined at a 1:1 ratio before submission for sequencing.
Single cells were encapsulated into droplets and processed following standard manufacturer’s specification, using 10X Genomics GemCode technology. Cells were loaded on a 10x Genomics Chromium controller instrument to generate single-cell Gel Beads in emulsion (GEMS) at the Yale Center for Genome Analysis. Lysis and barcoded reverse transcription of polyadenylated mRNA from single cells were performed inside each GEM followed by complementary DNA (cDNA) generation using the single-Cell 3’ Regent Kits version 2 (10X Genomics). Libraries were sequenced on an Illumina HiSeq 4000 as 2x 100 paired-end reads.

value: Liver cells

tag: strain

value: 17M old


title: RPF-Halo-M1

tag: genotype

tag: treatment


title: 15M Control Diet (High AFP)

description: 10x Genomics

source_name: Parenchymal and Non-parenchymal fraction of the liver

tag: tissue


title: ccRCC without PC destruction 3

description: Contorol

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: ACTB, B2M, HPRT1, LDHA, RPL1
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test group average/control group average(i.e., i-Cap2-3/i-Cap1) ratios.

label_protocol: PCR assays were performed using RT2 Profiler PCR Array (QIAGEN,Venlo, Netherland) , Rat Extracellular Matrix & Adhesion Molecules <PARN-013-ZD> ,  following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (QIAGEN, Venlo, Netherland). Quantitative real-time PCR were performed (Light Cycler 480, Roche) 40 cycles of denaturation at 95˚C for 15 s; annealing and a final extension at 60˚C for 1 min.

tag: sample type

value: i-Cap 1 (contorol)


title: ccRCC without PC destruction 2

description: Contorol


title: P2_RET-EGFP_F_DRG_A

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

data_processing:
Assembly: GRCm38.p2
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Text file with raw gene and cpm counts, and rpkm values

source_name: P2 female Ret-EGFP mouse FACSd T11-S1 DRG sample A

extract_protocol:
1) Dissect the appropriate level DRGs from the mice carrying a fluorescence reporter of interest, dissociate according to the age appropriate DRG dissociation procedures described on the GUDMAP website under the Jain Group protocols.
2) Add 7-AAD at 1ug/ml concentration, if needed, 10min before sorting to estimate viability and estimating gating parameters (also use fluorescence negative set to establish compensation controls and settings to recover populations of interest).  We have had good success using MoFlo, Sony or AriaII, at 100um nozzle size, and 30psi.
3) Collect directly in 750ul TRIzol-LS (Life Technologies, cat# 10296-010). Can store at -80°C or continue with RNA isolation. The RNA was extracted according to M Southard-Smith's RNA isolation procedure from flow sorted cells found on the GUDMAP website (Southard-Smith Group protocols). After Trizol extraction the RNA was purified with Qiagen RNeasy micro kit and then stored at -80°C until further processing for QC and library preparation for RNA sequencing.
4) Following QC/QA on the Nanodrop and Bioanalyzer 'pico' chip the RNA concentration was adjusted to use a total of 10ng in 9ul unless indicated otherwise for library preparation and RNA sequencing.
1) 10ng total RNA (in 9Âµl) was reverse transcribed and amplified using the SMARTerÂ® Ultraâ„¢ Low Input RNA for IlluminaÂ® Sequencing - HV (Clontech, cat# 634828) according to the manufacturerâ€™s instructions. 2) The cDNA was sheared for 3 minutes with the Covaris ultra-sonicator. 3) The libraries were prepared using VeraSeqâ„¢ ULtra DNA Polymerase (Enzymatics, cat# P7520L) for 12 cycles. PCR conditions were 98Â°C for 30s; 12 cycles of 98Â°C for 10s, 64Â°C for 30s, 72Â°C for 30s; 72Â°C for 5 minutes and then hold at 4Â°C. The forward primer used was: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT. The reverse primer contains the unique reverse complement of the respective index nucleotides. The sequence of the reverse primer where "N" denotes the reverse complement of 7 nucleotides of the index is CAAGCAGAAGACGGCATACGAGATNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGA.  Refer to the details of the BAM file for the sequence of the index used.

treatment_protocol: Total RNA was extracted from 40 pooled DRGs dissected from a Ret-EGFP P2 mouse at spinal segment levels T11-S1. Following DRG dissection, cells were FACS sorted (E18.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Tg(Ret-EGFP)SJ/

value: peripheral nervous system,dorsal root ganglion

tag: developmental stage

tag: Sex

value: female

tag: pooled sample

value: yes

tag: pool size

value: Pooled sample of 40 FACSd DRGs from 1 female P2 mouse


title: KDM2A_NC_IP

tag: cell line

value: KDM2A (Abcam, #ab191387)


title: H3K36me2_sh4_IP

value: H3K36me2 (GeneTex, #GTX54108)


title: P2_RET-EGFP_M_DRG_A

source_name: P2 male Ret-EGFP mouse FACSd T11-S1 DRG sample A

treatment_protocol: Total RNA was extracted from 20 pooled DRGs dissected from a Ret-EGFP P2 mouse at spinal segment levels T11-S1. Following DRG dissection, cells were FACS sorted (E18.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: dorsal root ganglion,peripheral nervous system

value: male

value: Pooled sample of 20 FACSd DRGs from 1 male P2 mouse


title: H3K36me2_sh4_Input


title: Inhibitor

description: 10x Genomics

source_name: Single cell suspension from HCC

extract_protocol:
The HCC region of the liver was resected and digested in collagenase for 1 hour. After which an Annexin V enrichment kit was used to select for live cells for sequencing.
Single cells were encapsulated into droplets and processed following standard manufacturer’s specification, using 10X Genomics GemCode technology. Cells were loaded on a 10x Genomics Chromium controller instrument to generate single-cell Gel Beads in emulsion (GEMS) at the Yale Center for Genome Analysis. Lysis and barcoded reverse transcription of polyadenylated mRNA from single cells were performed inside each GEM followed by complementary DNA (cDNA) generation using the single-Cell 3’ Regent Kits version 2 (10X Genomics). Libraries were sequenced on an Illumina HiSeq 4000 as 2x 100 paired-end reads.

treatment_protocol: C57BL/6 mice fed a CD-HFD for 15 months. Starting from the 13M, mice were treated with FABP5 inhibitor to ameliorate HCC.

value: Single cell suspension from HCC

tag: age

value: FABP5 inhibitor


title: H3K36me2_sh1_Input

value: Neural progenitor cells

value: none (input)


title: 15M CD-HFD (Low AFP)

description: 10x Genomics

value: Liver cells

value: Parenchymal and Non-parenchymal fraction of the liver


title: ccRCC with PC destruction 3

description: Test

source_name: renal cell carcinoma

value: i-Cap 2-3 (PC destruction)


title: ccRCC without PC destruction 1

description: Contorol

value: i-Cap 1 (contorol)


title: P2_RET-EGFP_M_DRG_C

data_processing:
Genome build: GRCm38.p2
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Supplementary file format and content: Text file with raw gene and cpm counts, and rpkm values

source_name: P2 male Ret-EGFP mouse FACSd T11-S1 DRG sample C

treatment_protocol: Total RNA was extracted from 20 pooled DRGs dissected from a Ret-EGFP embryo at spinal segment levels T11-S1. Following DRG dissection, cells were FACS sorted (E18.5 mouse DRG dissociation for FACS under the Jain Group protocols on the GUDMAP website) and RNA was extracted from the FACS sorted cells (RNA isolation procedure from flow sorted cells found on the GUDMAP website under the Southard-Smith Group protocols).

value: Tg(Ret-EGFP)SJ/

value: Pooled sample of 20 FACSd DRGs from 1 male embryo


title: Huh7 cells, SBFI103, 48 hrs, replicate 3

data_processing:
Using the PartekFlow® software, version 8.0.19.0405 (Partek, Inc., St. Louis, MO) the reads were aligned with the STAR algorithm to the mouse genome mmu10.
To estimate the transcript expression abundance we used Quantify to annotation model (Partek E/M) algorithm.
Assembly: hg19
Supplementary files format and content: counts

growth_protocol: Huh7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were with performed TrueSeq Small RNA Library preparation (Illumina).RNA libraries were sequenced for 45 cycles on Illumina HiSeq 2000 platform (1 x 75bp read length)

treatment_protocol: Treatment with siRNA (10nM Ctrl or FABP5 siRNA) or inhibitor (5uM SBFI-103) in culture media for 48 hours

value: Hepatoma cells

value: FABP5 inhibition

value: 48 hrs


title: Control

description: 10x Genomics

value: 17M old

value: control


title: LCMV-WE, replicate 2 + LCMV-Docile, replicate 2, mRNA derived cDNA

city: Clayton

first: Kim

last: Good-Jacobson

address: Gr Fl Reception (Bldg 77) 23 Innovation Walk

institute: Monash University

description:
5' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

source_name: Spleen

value: Spleen

value: 28 days post-infection

value: LCMV-specific B cells

tag: disease state

value: Acute + Chronic nfection

value: LCMV-WE + LCMV-Docile