title: EpiLC, rep2

description: 3'-RNAseq amplified from 1ng RNA

source_name: Mouse EpiLC

value: Unsorted


title: EpiLC, rep1

status: Public on Feb 16 2021

type: SRA

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: 3'-RNAseq amplified from 1ng RNA

library_source: transcriptomic

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCC -g CTCGAGGGCGCGCCGGATCC -a AAAAAAAAAAAAAAAAAAAA -a TTTTTTTTTTTTTTTTTTTT". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the mouse genome mm10 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the “—compatible-hits-norm”,  “—max-mle-iterations 50000", “—no-length-correction” and “—library-type fr-secondstrand” options and macfas5.0 reference gene annotations with extended TTSs. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample

molecule: total RNA

organism: Mus musculus

growth_protocol:
ESCs were cultured and maintained in N2B27 medium with 2i (PD0325901,0.4 mM: Stemgent; CHIR99021, 3 mM: Stemgent) and LIF (1,000 U/ml; Merck Millipore) on a dish coated with poly-L-ornithine (0.01%; Sigma) and laminin (10 ng/ml; BD Biosciences)
Induction of EpiLCs and PGCLCs was performed as reported previously.  Briefly, the EpiLCs were induced by plating 1 × 105 ESCs on a well of a 12-well plate coated with human plasma fibronectin (16.7 mg/ml: Merck Millipore) in N2B27 medium containing activin A (20 ng/ml: Peprotech), FGF2 (12 ng/ml: Thermo Fisher Scientific), and KSR (1%: Thermo Fisher Scientific). The PGCLCs were induced from d2 EpiLCs under a floating condition in a well of a low-cell-binding U-bottom 96-well plate (Thermo Scientific) in serum-free medium [GK15; GMEM (Thermo Fisher Scientific) with 15% KSR, 0.1 mM NEAA, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin, and 2 mM L-glutamine] in the presence of the cytokines BMP4 (500 ng/ml; R&D Systems), LIF (1,000 U/ml; Merck Millipore), SCF (100 ng/ml; R&D Systems), and EGF (50 ng/ml; R&D Systems).
Fluorescence-activated cell sorting (FACS) was performed with a FACSAriaIII (BD) cell sorter for purifying BV-positive-d4 PGCLCs or EGFP-positive-E9.5 PGCs (B6D2F1×Stella–EGFP).  m220-5 cells were used as the feeder cells for PGCLCs or E9.5 PGCs as described previously.  Briefly, m220-5 cells were cultured for three passages with 10 µM of both forskolin and rolipram (FR10) to permit adaptation to these compounds prior to mitomycin C (MMC) treatment (1–2 µg/ml, 2 h).  Purified d4 PGCLCs or E9.5 PGCs were plated on m220-5 cells in GMEM containing 10% KSR, 0.1 mM NEAA, 1 mM sodium pyruvate, 0.1 mM 2-mercaptoethanol, 100 U/ml penicillin, 0.1 mg/ml streptomycin, 2 mM L-glutamine, 2.5% FCS, 100 ng/ml SCF, 10 µM forskolin, and 10 mM rolipram.  Half of the culture medium was changed every 2 days.  Following chemicals and cytokine were used in this study: cyclosporin A (Sigma), FK506 (Sigma), FGF2 (Thermo Fisher Scientific), FGF7 (R&D Systems), FGF10 (R&D Systems), and WNT5A (R&D Systems).

extract_protocol:
Total RNAs were purified from d4c7 PGCLCs and E9.5c5 PGCs cultured with each condition (two biological replicates for each) using an RNAeasy Micro Kit (Qiagen).
For SC3-seq analysis, cDNA synthesis / amplification from single cells and library construction from the cDNAs were performed as described previously [Nakamura et al. 2015, NAR, 43, e60].

tag: strain

tag: transgene

value: Blimp1-mVenus reporter; Stella-ECFP reporter (BVSC)

tag: cell sorting


title: HH-OX-44_6

city: Hamburg

first: Manuel

middle: A

last: Friese

address: Falkenried 94

department: Institut für Neuroimmunologie und Multiple Sklerose

country: Germany

institute: Universitätsklinikum Hamburg-Eppendorf

description:
RNA_counts.tar.gz
RNA_normalised.tar.gz
RNA_SCTnormalised.tar.gz
RNA_integrated.tar.gz
ADT_counts.tar.gz
ADT_integrated.tar.gz
saverx.tar.gz
saverx_integrated.tar.gz
metadata_per_cell.csv
metadata_per_sample.csv

data_processing:
library deconvolution with bcl2fastq (Illumina, v2.20.0.422)
single cell deconvolution and mapping using zUMIs (v2.5.6b) with STAR (v2.6.0c) for RNA and CITE-seq-Count (v. 1.4.2) for protein surface markers
cell hashing demultiplexing with Seurat (v3.1.1)
doublet removal with DoubletFinder (2.0.2)
Standard log normalisation of RNA using Seurat (v3.1.1)
Non-standard normalisation of RNA using sctransform (v0.2.0) as described in Hafemeister and Satija 2019 (Genome Biology)
Sample integration for RNA with Seurat (v3.1.1)
Marker imputation from RNA with SAVER-X (v1.0.0)
Integration of imputed RNA markers with Seurat (v3.1.1)
Normalisation (centered log transformation) and sample integration for surface protein markers with Seurat (v3.1.1)
Genome_build: GRCh38 without alternative contigs
Supplementary_files_format_and_content: All processed data files are provided as tar.gz archives, which contain a sparse matrix in the market matrix format (.mtx) specifying expression values and the cell barcodes and features as tab seperated value files (barcodes.tsv and genes.tsv), the matrices contain cells as columns and features (genes or antibody-derived tags = ADT) as rows; all metadata files are provided as comma separated text files (.csv)

molecule: polyA RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
10X chromium v2/v3 (see V_10X for each sample)
CITE-seq/Cell hashing as described in Stoeckius et al 2018 (Genome Biology)

tag: donor

tag: hash

tag: match

tag: group

tag: cohort

tag: Sex

value: female

tag: edss

value: no

tag: molecule

value: polyA RNA + protein surface markers


title: HH-OX-44_1


title: RA (replicate 2)

city: Kansas City

first: Sumedha

middle: S

last: Gunewardena

state: Kansas

address: 2146 West 39th Avenue

department: Dept. of Molecular and Integrative Physiology

country: USA

institute: University of kansas medical center

data_processing:
Illumina bcl2fastq2 conversion software used for basecalling.
reads were aligned using the STAR (2.6.1c) software.
raw read counts were obtained using featureCounts (1.6.4)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files of raw count values for each Sample (not normalized)

source_name: spermatogonia RA treatment

growth_protocol: Spermatogonia culture supplemented with  N2 and 10 ng/ml of both bFGF and GDNF.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA-seq (NuGENUPRNA); RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RA, NR and NRRA

tag: tissue

value: spermatogonia

tag: treatment

value: RA treatment


title: mESC, rep2

description: 3'-RNAseq amplified from 1ng RNA

source_name: Mouse ESC


title: RA (replicate 1)


title: HH-OX-44_2


title: GM12878_rep1_atac

city: Stanford

first: Kevin

middle: Eric

last: Wu

state: CA

address: 353 Jane Stanford Way

department: Computer Science

institute: Stanford University

description: Single cell multiome ATAC library

library_source: genomic

data_processing:
Processed with cellranger-arc pipeline, version 1.0.0
Genome_build: hg38

molecule: genomic DNA

source_name: GM12878 cells

extract_protocol: 10X Genomics Single Cell Multiome ATAC + Gene Expression Kit

tag: cell line


title: GM12878_rep2_atac

description: Single cell multiome ATAC library


title: GM12878_rep2_gex

description: Single cell multiome gene expression library


title: GM12878_rep1_gex


title: HH-OX-44_3


title: EBSS (replicate 2)

source_name: spermatogonia NR treatment

value: NR treatment


title: mESC, rep1

description: 3'-RNAseq amplified from 1ng RNA


title: EBSS (replicate 1)


title: WT time 24 hours rep 8

city: St Louis

first: Daniel

last: Paiva Agustinho

state: MO

address: 660 S Euclid Ave

department: Molecular Microbiology

institute: Washington University in St. Louis

data_processing:
The quality of the reads was evaluated by FastQC
Fastq files were aligned to the KN99 genome using NovoAlign
SAM files were converted to bam, reads were sorted and indexed, and read duplicates were removed from the final bam files using samtools
Samtools was also used to filter out reads with a mapping quality lesser than 20 phreds to guarantee single alignment of the reads. Read counts were assigned to specific genes with HTseq.
Differential expression was measured with DEseq2, p-values were adjusted using the IHW package.
Genome_build: Cryptococcus neoformans serotype A KN99  ASM221672v1

organism: Cryptococcus neoformans

source_name: Yeast

growth_protocol: Wild type and ∆Pdr802 strains were cultivated in DMEM for 24 hours at 37°C and 5% CO2.

extract_protocol:
RNA extraction was performed by Trizol method.
The samples were sonicated to obtain fragments of about 200bp. Libraries were prepared using NEBNext Ultra II  RNA Library Prep Kit for Illumina E7770L, following the manufactrer's instructions
RNAseq - Illumina NextSeq 1x75

treatment_protocol: The cells were lysed by mechanical bead-beating, and the cell debris removed by centrifugation.

tag: time point

value: 24 hours

tag: genotype

value: Wild-type

tag: replicate


title: HH-OX-44_4


title: WT time 24 hours rep 7


title: Set 2-15 [lymph2_se_Group_15]

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

data_processing:
RNAseq sequences were aligned to the International Human Genome Sequencing Consortium human reference sequence (hg19 refGene annotation from the University of California at Santa Cruz genome browser) using SOLiDLifescope v2.5.1 (Life Technologies)
Gene expression was measured in reads per kilobase per million (RPKM), as reported by the wtcounts module of Lifescope calculated based on reads that aligned to coding regions of genes annotated by RefSeq
Genome_build: hg19
Supplementary_files_format_and_content: square table with RPKM per gene per sample

extract_protocol:
Each blood sample consisted of:  a) 8 ml of peripheral blood drawn into a CPT® tube with sodium citrate anticoagulant (Becton & Dickenson, Franklin Lakes, NJ), and b) 2.5 ml of peripheral blood drawn into a PaxGene® tube (PreAnalytiX GmbH, Switzerland).  Samples in CPT tubes were processed immediately to isolate peripheral blood leukocytes and plasma, or, depending on the participating center, were shipped overnight at ambient temperature before processing.  Leukocytes were isolated from blood by standard protocols and stored at -80oC.  Frozen PaxGene tubes were processed to isolate total peripheral blood RNA according to the manufacturer's instructions (PreAnalytiX).
Total leukocyte RNA was extracted using Trizol reagent (Life Technologies, Grand Island, NY) according to the manufacturer's instructions.  RNA quality was verified on a 2100 Bioanalyzer (Agilent, Santa Clara, CA), with all samples showing an RNA integrity number >6.5.  NuGen Ovation RNASEQ System (San Carlos, CA) was used to generate cDNA libraries from 10 ng of total RNA per sample (NuGen Technologies, San Carlos, CA).  This kit employs poly-dT and random hexamer primers for cDNA synthesis, the latter designed to reduce cDNAs from rRNA by at least 90%.  This NuGen library preparation is able to capture RNA lacking polyA tails, including ncRNA RNAs, although in this study we focused sequence analysis on annotated coding genes1.  A linear amplification step enables RNAseq analysis of small amounts of RNA (we used 10-20 ng total RNA).  Samples were processed to produce 8-barcoded, paired-end libraries or 16-barcoded, single-end libraries. Samples were sequenced using the SOLiD 5500 Next-Generation Sequencing instrument (Life Technologies).

tag: subject status

value: children with nephrotic syndrome

value: Pre-treatment

tag: response

value: Steroid Sensitive

tag: tissue/cell type

value: peripheral blood leukocytes


title: WT time 24 hours rep 6


title: HH-OX-43_6

tag: donor

value: PPMS


title: HH-OX-43_5

tag: hash


title: WT time 24 hours rep 5


title: Set 2-14 [lymph2_se_Group_14]

value: Post-treatment


title: Set 2-16 [lymph2_se_Group_16]


title: HH-OX-43_1

tag: match


title: WT time 24 hours rep 4


title: Set 2-13 [lymph2_se_Group_13]


title: WT time 24 hours rep 3


title: HH-OX-43_3

tag: group


title: WT time 24 hours rep 2


title: Set 2-11 [lymph2_se_Group_11]

value: Steroid Resistant


title: HH-OX-43_4

tag: cohort


title: WT time 24 hours rep 1


title: Set 2-9 [lymph2_se_Group_9]


title: HH-OX-42_2

description:
RNA_counts.tar.gz
RNA_normalised.tar.gz
RNA_SCTnormalised.tar.gz
RNA_integrated.tar.gz
metadata_per_cell.csv
metadata_per_sample.csv

tag: Sex

value: male

value: polyA RNA


title: Set 2-10 [lymph2_se_Group_10]


title: HH-OX-42_1

tag: edss


title: WT time 0 rep 39

value: 0 hours


title: WT time 0 rep 38


title: HH-OX-41A_1

value: Rebif, Interferon beta

value: no

tag: molecule


title: HH-OX-41B_1

value: yes


title: Set 2-8 [lymph2_se_Group_8]


title: WT time 0 rep 37


title: WT time 0 rep 36


title: HH-OX-41A_2


title: Set 2-5 [lymph2_se_Group_5]


title: HH-OX-43_2

value: female

value: polyA RNA + protein surface markers


title: WT time 0 rep 34


title: Set 2-12 [lymph2_se_Group_12]


title: HH-OX-40_1


title: Set 2-6 [lymph2_se_Group_6]


title: HH-OX-40_2


title: Set 2-3 [lymph2_se_Group_3]


title: WT time 0 rep 35


title: Set 2-4 [lymph2_se_Group_4]


title: HH-OX-41B_2


title: Set 2-7 [lymph2_se_Group_7]


title: WT time 0 rep 33


title: WT time 0 rep 32


title: Set 2-2 [lymph2_se_Group_2]


title: HH-OX-39A_1

value: Copaxone


title: WT time 0 rep 31

value: Wild-type


title: HH-OX-39B_1


title: WT time 0 rep 30


title: WT time 0 rep 29


title: HH-OX-39B_2


title: S19ID00880

city: Madrid

first: Nerea

last: Matamala

address: Calle de Pedro Rico, 6

country: Spain

institute: IDIPAZ

data_processing:
The resulting reads were aligned using HISAT2 and hg19 as a reference
Transcript assembly and quantification were achieved with StringTie.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with cpm log gene counts for every gene and every sample

source_name: Natural killer (NK) cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from buffy coats from healthy volunteers by using Ficoll–Paque gradient centrifugation. CD45RA+ fractions were obtained after magnetic enrichment using CD45RA microbeads and running “Pos-sel” program in the AutoMACS device (both from Miltenyi Biotec) following manufacturer instructions.

extract_protocol:
Total RNA was isolated using the RNeasy Mini kit (QIAGEN, Hilden, Germany) accord-ing to the manufacturer’s instructions. To remove residual genomic DNA, the RNA sam-ples were digested with DNAse I. The RNA concentration was assessed by fluorescence quantitation using Qubit 2.0 and the HS RNA assay kit (Thermo Fisher Scientific Inc., Waltham, MA, USA), the RNA purity by spectrophotometry using Nanodrop 2000 (Ther-mo Fisher Scientific Inc., Waltham, MA, USA) and the RNA integrity by electrophoresis using TapeStation 4200 RNA ScreenTape (Agilent Technologies, Santa Clara, CA, USA).
Library samples were prepared with the TruSeq Stranded mRNA Library Prep kit (Illu-mina, San Diego, California, USA) as recommended by the manufacturer. Paired-end se-quencing (2 × 100 pb) was performed with NovaSeq 6000 system (Illumina, San Diego, CA, USA), with a minimum of 25 million reads per sample and read quality of 90% > Q30.

treatment_protocol: PBMC or CD45RA+ cells were cocultured with irradiated K562mbIL15 or K562mbIL21 in a 1:1.5 ratio, using complete TexMACs.

tag: activation

tag: cell source


title: S19ID00882

value: pbmc


title: S19ID00881


title: WT time 0 rep 28


title: HH-OX-38_2


title: WT time 0 rep 27


title: HH-OX-38_1


title: S19ID00878


title: Set 1-6 [lymph1_pe_lymph6]

value: children with nephrotic syndrome

tag: treatment


title: HH-OX-37A_1


title: Set 1-5 [lymph1_pe_lymph5]

value: Pre-treatment

value: Steroid Sensitive


title: Set 1-3 [lymph1_pe_lymph3]

value: peripheral blood leukocytes


title: S19ID00876


title: S19ID00877


title: HH-OX-37B_1


title: S19ID00875


title: Set 1-4 [lymph1_pe_lymph4]

value: Post-treatment


title: WT time 0 rep 25

tag: time point


title: Set 2-1 [lymph2_se_Group_1]


title: Set 1-8 [lymph1_pe_lymph8]

value: Steroid Resistant


title: Set 1-2 [lymph1_pe_lymph2]


title: WT time 0 rep 24

tag: genotype


title: HH-OX-39A_2


title: S19ID00874


title: HH-OX-37A_2


title: WT time 0 rep 23

tag: replicate


title: S19ID00879


title: Set 1-7 [lymph1_pe_lypmh7]

tag: subject status


title: Set 1-1 [lymph1_pe_lymph1]

tag: response


title: HH-OX-37B_2


title: S19ID00873


title: Pulp5

city: Basel

first: Andreas

last: Moor

address: Mattenstrasse 26

department: Department of Biosystems Science and Engineering

country: Switzerland

institute: ETH

description: Age 18-35yo, healthy dental pulp

data_processing:
The quality and concentration of the single cell preparations were evaluated using an haemocytometer in a Leica DM IL LED microscope and adjusted to 1,000 cells/µl
10,000 cells per sample were loaded in to the 10X Chromium controller and library preparation was performed according to the manufacturer’s indications (single cell 3’ v2 or v3 protocol)
The resulting libraries were sequenced in an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=26, i7=8, R2=98) to a depth of around 50,000 reads per cell
Genome_build: Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_91-2018-02-26
Supplementary_files_format_and_content: cell ranger output

source_name: Human dental pulp

extract_protocol:
PULP: Teeth (third molars) were collected immediately after extraction and preserved in sterile NaCl 0.9%, on ice for the time needed to transfer them from the clinic to the processing laboratory (< 10 minutes).  Periodontium was carefully removed (see below). The cleansed tooth was then carefully wiped with 70% ethanol. The tooth was then cracked with a press, and carefully opened with forceps. The dental pulp was then removed from the tooth with a separate set of instruments, placed in a Petri dish filled with cold HBSS and minced into small pieces (< 2 mm diameter). Dental pulp pieces were transferred in falcon tubes filled with HBSS, centrifuged at 4°C, 300g, for 10 minutes. Tissues were digested in 10 mL Collagenase P 5 U/mL (11 213 873 001, Sigma Aldrich, Buchs, Switzerland) for 40 minutes at 37°C. After digestion, samples were disaggregated by pipetting, filtered through a 70 um cell strainer, and resuspended in HBSS + 0.002% Bovine Serum Albumin (BSA; 0163.2, Roth AG, Arlesheim, Switzerland).
library preparation was performed according to the manufacturer’s indications (single cell 3’ v2 or v3 protocol)

tag: cell types

value: Single cells, heterogeneous

tag: 10x kit


title: WT time 0 rep 26


title: Pulp4

description: Age 18-35yo, healthy dental pulp


title: WT time 0 rep 20


title: WT time 0 rep 21


title: HH-OX-35A_1

tag: donor

tag: hash

value: Avonex, Copaxone


title: HH-OX-36_2

tag: match

tag: group


title: WT time 0 rep 18

value: 0 hours


title: HH-OX-35A_2

tag: cohort

tag: Sex


title: WT time 0 rep 17


title: Pulp1

description: Age 18-35yo, healthy dental pulp


title: HH-OX-35B_2

tag: edss

tag: molecule


title: HH-OX-36_1

value: polyA RNA


title: Perio5 scRNA-seq

description: Age 18-35yo, healthy periodontium

data_processing:
The quality and concentration of the single cell preparations were evaluated using an haemocytometer in a Leica DM IL LED microscope and adjusted to 1,000 cells/µl
10,000 cells per sample were loaded in to the 10X Chromium controller and library preparation was performed according to the manufacturer’s indications (single cell 3’ v2 or v3 protocol)
The resulting libraries were sequenced in an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired-end reads, R1=26, i7=8, R2=98) to a depth of around 50,000 reads per cell
Genome_build: Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_91-2018-02-26

source_name: Single cells, heterogeneous

extract_protocol:
Teeth (third molars) were collected immediately after extraction and preserved in sterile NaCl 0.9%, on ice for the time needed to transfer them from the clinic to the processing laboratory (< 10 minutes). The periodontium was isolated by scratching the lower two-thirds of the root of the teeth with a surgical scalpel directly into a Petri dish filled with sterile, cold Hank’s Balanced Salt Solution (HBSS, Thermo Fisher Scientific, Reinach, Switzerland). The upper-third of the root was excluded to minimize contamination from the gingival epithelium. Periodontal tissues were transferred in falcon tubes filled with HBSS, centrifuged at 4°C, 300g, for 10 minutes. Tissues were digested in 10 mL Collagenase P 5 U/mL (11 213 873 001, Sigma Aldrich, Buchs, Switzerland) for 40 minutes at 37°C. After digestion, samples were disaggregated by pipetting, filtered through a 70 mm cell strainer, and resuspended in HBSS + 0.002% Bovine Serum Albumin (BSA; 0163.2, Roth AG, Arlesheim, Switzerland).
library preparation was performed according to the manufacturer’s indications (single cell 3’ v2)

tag: tissue

value: healthy periodontium

tag: age


title: HH-OX-34_1

value: male

value: no


title: WT time 0 rep 22

tag: time point


title: WT time 0 rep 15

tag: genotype


title: Perio4 scRNA-seq

description: Age 18-35yo, healthy periodontium


title: HH-OX-34_2


title: HH-OX-35B_1

value: female

value: yes

value: polyA RNA + protein surface markers


title: WT time 0 rep 19

value: Wild-type

tag: replicate


title: WT time 0 rep 14


title: HH-OX-33A_1

value: Rebif, Copaxone, Betaferon


title: Perio2 scRNA-seq

description: Age 18-35yo, healthy periodontium


title: WT time 0 rep 13


title: Perio3 scRNA-seq

description: Age 18-35yo, healthy periodontium


title: Perio1 scRNA-seq

description: Age 18-35yo, healthy periodontium


title: HH-OX-33B_1


title: WT time 0 rep 12


title: WT time 0 rep 16


title: HH-OX-33A_2


title: HH-OX-33B_2


title: WT time 0 rep 11


title: M0 Macropahges - H syndrome 2 (R1)

city: Birmingham

first: Samuel

middle: J

last: Lara Reyna

address: Edgbaston

country: United Kingdom

institute: University of Birmingham

data_processing:
An average of 55.0 million raw reads were generated per sample (effective rate average 97.6% and Q30 average of 94.5%).
RNA-seq raw reads were trimmed using TrimGalore to remove library adaptors sequences and low-quality reads (QV≥30). High-quality reads were mapped to the reference genome (GRCh38/hg38) using STAR, and then the Cufflinks-Cuffdiff (v2.2.1) pipeline was employed to perform transcriptome assembly, normalization and differential expression (DE) analyses.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: fpkm_tracking obtained from Cufflinks (file contains the estimated isoform-level expression values in the generic FPKM Tracking Format)

source_name: Peripheral Blood

growth_protocol: Isolated human monocytes were cultured in complete RPMI medium (10% FBS, 50 U/ml penicillin, 50 ug/ml streptomycin and 1% L-Glutamine) (Merck) supplemented with 20 ng/mL human GM-CSF (PeproTech) for macrophage differentiation and incubated for 6 days, adding fresh media on day 3. On day 6, M0 macrophages were activated with 100 ng/mL human IFN-g (PeproTech) and 50 ng/mL LPS, for M1 macrophage polarisation, or 20 ng/mL IL-13 (PeproTech) and IL-4 (PeproTech), for M2 macrophage polarisation, and incubated for 24 hours.

extract_protocol:
Total RNA was obtained by using TRIzol and Phasemaker Tubes (Thermo Fisher Scientific) according to the manufacturers' protocol. RNA quality and quantity were further determined by NanoDrop spectrophotometer and with the Agilent TapeStation (Agilent Technologies).
Library preparation and RNA sequencing (RNA-seq) were performed on an Illumina Novaseq and generating 150bp paired-ended reads (Novogene Bioinformatics Technology Co., LTD).

tag: cell type/tissue

value: MDMs

tag: activation

value: GM-CSF

value: Peripheral Blood


title: M1 Macropahges - H syndrome 2 (R1)

value: GM-CSF and IFNg/LPS


title: WT time 0 rep 10


title: HH-OX-32_1


title: WT time 0 rep 9


title: WT time 0 rep 8


title: CD14+ Monocytes - H syndrome 2 (R1)

value: CD14+ Monocytes

value: Untreated


title: HH-OX-31_1

value: Copaxone


title: WT time 0 rep 7

value: 0 hours


title: M1 Macropahges - HC3


title: HH-OX-32_2

value: polyA RNA


title: HH-OX-31_2


title: WT time 0 rep 6


title: HH-OX-30_1


title: M1 Macropahges - H syndrome 1 (R1)


title: WT time 0 rep 5


title: M0 Macropahges - HC3


title: HH-OX-30_2


title: CD14+ Monocytes - H syndrome 1 (R1)


title: HH-OX-29A_1

value: Mitoxantron (1x, discontinued due to cardiomyopathie), Rebif, Azathioprin


title: WT time 0 rep 4


title: CD14+ Monocytes - HC3


title: Myotube_T2D_8a_14

type: genomic

city: Malmö

first: Charlotte

last: Ling

address: Jan Waldenströms gata 35, CRC 91:12

department: Clinical Sciences

country: Sweden

institute: Lund University

hyb_protocol: According to the manufacturer’s recommendations. Myoblasts and myotubes from one subject were always analyzed on the same chip and the samples from controls and individuals with type 2 diabetes were evenly distributed on the chips to reduce batch effects.

data_processing: The raw methylation score for each probe represented as methylation β-values was calculated using GenomeStudio Methylation module software. All included samples showed a high quality bisulfite conversion efficiency (signal intensity > 4000) and also passed all GenomeStudio quality control steps based on built in control probes for staining, hybridization, extension and specificity. Before further analysis, the DNA methylation data was exported from GenomeStudio and subsequently analyzed using Bioconductor and the lumi package. β-values were converted to M-values. Next, data were background corrected by subtracting the median M-value of the 600 built in negative controls and was further normalized using quantile normalization. Data were further processed using BMIQ to correct for probe type. As a result, 5,365 probes with a mean detection p-value >0.01, 65 rs-probes, 86 Y-chromosome probes, 2,835 ch-probes targeting non-CpG sites, 13,731 probes based on at least 49 cross reactivity 5 and 5,020 probes with a MAF >0.1 were excluded.

label: Cy3, Cy5

source_name: Myotube, T2D

growth_protocol: Muscle stem cells were isolated from human vastus lateralis muscle biopsies (n=14 individuals with type 2 diabetes [T2D], and n=14 control individuals with normal glucose tolerance [NGT]). Isolated myoblasts were cultured in growth medium (HAM’s/F10 supplemented with 20% fetal bovine serum (FBS), 1% penicillin/streptomycin and 1% Amphotericin B) until 70% confluent. To induce differentiation, cells were incubated in differentiation medium 1 (DMEM with 1.0 g/l L glucose supplemented with 10% FBS and 1% penicillin/streptomycin) for 2 days, followed by differentiation medium 2 (DMEM with 4.5 g/l L glucose supplemented with 2% horse serum and 1% penicillin/streptomycin) until cells were fully differentiated, as determined by visual confirmation of myotube formation (>3 nuclei per myotube in approximately 70% of cells) on day 7. Cells were harvested both as proliferating myoblasts (<50% confluent) and as differentiated myotubes.

extract_protocol: DNA was extracted by using DNeasy Blood and Tissue kit (Qiagen #69504, Hilden, Germany). Quantity and purity of DNA were determined using a NanoDrop 1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).

tag: diabetes status

value: Type 2 diabetes (T2D)


title: HH-OX-29B_1

value: male


title: M1 Macropahges - HC2


title: CD14+ Monocytes - HC2


title: WT time 0 rep 2


title: WT time 0 rep 3


title: WT time 0 rep 1


title: M1 Macropahges - HC1


title: Myotube_T2D_7a_13

scan_protocol: According to the manufacturer’s recommendations.


title: Myotube_T2D_46a_12

label_protocol: According to the manufacturer’s recommendations.


title: HH-OX-29A_2

value: no


title: Myoblast_T2D_7a_13

source_name: Myoblast, T2D


title: HH-OX-29B_2

value: yes


title: Myoblast_T2D_46a_11


title: CD14+ Monocytes - HC1


title: Myoblast_T2D_8a_14


title: ∆Pdr802 time 24 hours rep 6

value: 24 hours


title: HH-OX-28_1


title: Myotube_T2D_45_10


title: HH-OX-28_2


title: ∆Pdr802 time 24 hours rep 5


title: Myotube_T2D_63a_13


title: Lymph node tissue Biopsie 6 - RDD

value: Lymph node tissue


title: Lymph node tissue Biopsie 5 - RDD


title: ∆Pdr802 time 24 hours rep 4


title: Myotube_T2D_17_7


title: Myoblast_T2D_63a_12


title: ∆Pdr802 time 24 hours rep 3


title: Myoblast_T2D_45_10


title: Myotube_T2D_129a_6


title: Lymph node tissue Biopsie 4 - RDD


title: Myoblast_T2D_17_7


title: HH-OX-27B_1


title: Myoblast_T2D_128a_5


title: Myotube_T2D_20a_8


title: Myoblast_T2D_29H_9


title: Lymph node tissue Biopsie 3 - RDD


title: ∆Pdr802 time 24 hours rep 2


title: HH-OX-27A_2


title: Myotube_T2D_128a_5


title: ∆Pdr802 time 24 hours rep 1


title: Lymph node tissue Biopsie 2 - RDD


title: Myotube_T2D_29H_9


title: Myoblast_T2D_129a_6


title: HH-OX-27B_2


title: Lymph node tissue Biopsie 1 - RDD


title: ∆Pdr802 time 0 rep 3


title: Myoblast_T2D_127a_4


title: Myoblast_T2D_20a_8


title: M2 Macropahges - TRAPS

value: GM-CSF and IL-4/IL-13


title: ∆Pdr802 time 0 rep 1


title: N-term-mCherry-Pdr802 input rep 3

data_processing:
The quality of the reads was evaluated by FastQC
Fastq files were aligned to the KN99 genome using NextGenMap 0.5.3
SAM files were converted to bam, reads were sorted and indexed, and read duplicates were removed from the final bam files using samtools
Samtools was also used to filter out reads with a mapping quality lesser than 20 phreds to guarantee single alignment of the reads. Peaks were called using MACS2 (2.1.1.20160309)
Peaks were filtered by size (maximum threshold 5 kb and no minimum), and annotated using Homer 4.8
Genome_build: Cryptococcus neoformans serotype A KN99  ASM221672v1

growth_protocol: Wild type and N-terminal-mCherry-Pdr802 strains were cultivated in DMEM for 24 hours at 37°C and 5% CO2.

extract_protocol:
The remaining material was incubated with rabbit IgG anti-mCherry antibody (Abcam, ab213511) tethered to protein A sepharose (‘IP’) or sepharose alone (‘Mock’) overnight at 4°C. The beads were then washed, incubated at 65°C to reverse DNA-DNA and DNA-protein crosslinks and the DNA recovered by phenol/chloroform/isoamyl alcohol (25:24:1) extraction, ethanol precipitation, and resuspension in nuclease-free water.
The samples were sonicated to obtain fragments of about 200bp. Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina E7645L, following the manufactrer's instructions

treatment_protocol: The cells were then fixed with formaldehyde, lysed by mechanical bead-beating, and the cell debris removed by centrifugation. The supernatant fraction was sheared by sonication, centrifuged, and an aliquot was reserved as ‘Input’

tag: treatment

value: Input

tag: antibody

tag: strain


title: M1 Macropahges - TRAPS

value: MDMs


title: ∆Pdr802 time 0 rep 2


title: HH-OX-26_2

tag: donor

tag: hash

tag: match

value: polyA RNA + protein surface markers


title: HH-OX-25A_1

tag: group

tag: cohort

tag: Sex


title: HH-OX-25B_1

tag: edss

tag: molecule


title: N-term-mCherry-Pdr802 input rep 2


title: HH-OX-25A_2


title: M1 Macropahges - uSAID

value: GM-CSF and IFNg/LPS

tag: tissue

value: Peripheral Blood


title: HH-OX-27A_1


title: HH-OX-26_1


title: N-term-mCherry-Pdr802 input rep 1


title: M0 Macropahges - TRAPS

value: GM-CSF


title: Myotube_T2D_117a_2


title: Myotube_T2D_119a_3


title: HH-OX-25B_2

value: Copaxone


title: Myotube_T2D_127a_4


title: M2 Macropahges - uSAID


title: HH-OX-24_1

value: female


title: HH-OX-24_2

value: polyA RNA


title: N-term-mCherry-Pdr802 mock rep 3

value: Mock


title: N-term-mCherry-Pdr802 mock rep 1


title: N-term-mCherry-Pdr802 mock rep 2


title: M2 Macropahges - HC5


title: M1 Macropahges - HC5


title: M0 Macropahges - uSAID


title: HH-OX-23A_1

value: Avonex, Rebif, Copaxone, Betaferon, Azathioprin


title: N-term-mCherry-Pdr802 IP rep 3

value: IP

value: mCherry antibody (Abcam, ab213511)


title: M0 Macropahges - HC5


title: Myoblast_T2D_117a_2

value: Type 2 diabetes (T2D)


title: Myotube_T2D_109a_1


title: HH-OX-23B_1

value: yes


title: N-term-mCherry-Pdr802 IP rep 2


title: HH-OX-23A_2

value: no


title: CD14+ Monocytes - HC5

value: CD14+ Monocytes

value: Untreated


title: M1 Macropahges - H syndrome 1 (R2)

value: MDMs


title: M2 Macropahges - H syndrome 1 (R2)

value: GM-CSF and IL-4/IL-13


title: N-term-mCherry-Pdr802 IP rep 1


title: WT input

value: Input

value: Wild Type


title: HH-OX-23B_2


title: Myotube_NGT_92a_14

source_name: Myotube, NGT

value: Normal glucose tolerance (NGT)


title: Myoblast_T2D_109a_1


title: HH-OX-22_1


title: HH-OX-21_1

value: polyA RNA + protein surface markers


title: WT mock


title: M0 Macropahges - H syndrome 1 (R2)

value: GM-CSF

value: Peripheral Blood


title: CD14+ Monocytes - H syndrome 1 (R2)


title: WT mCherry IP


title: HH-OX-20_1

value: female


title: M2 Macropahges - HC4


title: HH-OX-20_2

value: polyA RNA


title: M1 Macropahges - HC4

value: GM-CSF and IFNg/LPS


title: Myoblast_NGT_55a_13

source_name: Myoblast, NGT


title: Myoblast_NGT_92a_14


title: Myotube_NGT_40a_12


title: M0 Macropahges - HC4


title: HH-OX-19_2


title: Myoblast_T2D_119a_3


title: 36D-2 Astrocytes_Media control_rep1

type: RNA

city: Lund

first: Laurent

last: Roybon

address: Solvegatan 19

department: Experimental Medical Science

hyb_protocol: Sample preparation for microarray hybridization was carried out as described in the Affymetrix GeneChip WT PLUS Reagent Kit User Manual (Affymetrix, Inc., Santa Clara, CA, USA).  In brief, 200 ng of total RNA was used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin. 3,8 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Clariom S human arrays for 16 h at 45 ° C in a GeneChip hybridization oven 640. Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by Affymetrix GeneChip Command Console v4.1.3 software.  Sample processing was performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de).

data_processing: Summarized probe set signals in log2 scale were calculated by using the GCCN-SST-RMA algorithm with the Affymetrix GeneChip Expression Console v1.4 Software. After exporting into Microsoft Excel, average signal values, comparison fold changes and significance P values were calculated. Probe sets with a fold change above 2.0 fold and a student’s t test P value lower than 0.05 were considered as significantly regulated.

label: biotin

source_name: Human iPSC-derived astrocytes treated with media (control) for 6 days

growth_protocol: On day one of differentiation, human iPSC colonies were harvested, dissociated, filtered (100 µm), and added to an ultra-low-adherent flask (Sigma-Aldrich) with 0.1 µM LDN (Stemgent), 10 µM SB (Selleckchem), 200 ng/ml SHH-C25II (Thermo Fisher Scientific), 0.8 µM CHIR (Stemgent), and 1 µM SAG (Millipore) for 0-4 days in neural induction medium [NIM; advanced DMEM-F12 with 1% L-Glu, 1% NEAA, 1% N2, and 1% P/S (100 U/mL)]. From day 6-8 NIM with 0.1 µM LDN, 0.8 µM CHIR (Stemgent), and 2 µM SAG (Millipore) was used. On day 10, NIM with 0.8 µM CHIR (Stemgent) and 2 µM SAG (Millipore) were used. From days 12-30, NIM with 100 ng/ml FGF8b (Thermo Fisher Scientific) and 2 µM SAG (Millipore) was used. On day 30 EBs were dissociated, filter strained (100 µm), and transferred to a new ultra-low-adherent flask containing neural expansion medium [(NEM; DMEM-F12 with 1% L-Glu, 1% NEAA, 2% B27 without vitamin A, 1% P/S, and 0.2 µg/ml heparin (Sigma-Aldrich)] with 20 ng/ml FGF2 (Thermo Fisher Scientific) and 20 ng/ml EGF (Peprotech) for 30 days. On day 60, EBs were washed and dissociated with 0.05% trypsin/1X-EDTA and seeded to adherent culture flasks coated with 20 µg/ml Poly-L-ornithine hydrobromide (P/O; Sigma-Aldrich) and mouse laminin (15 µg/ml for initial seeding, then 5 µg/ml for subsequently passages) containing NEM and 20 ng/ml CNTF (R&D Systems) for 60-80 days in NDM. Finally, from days 80-100, astrocytes were cultured in neural differentiation medium [NDM; (NB with 1% L-Glu, 1% NEAA, 1% N2, and 1% P/S] with and 20 ng/ml CNTF (R&D Systems). Cells were passaged at confluency. Media was changed every 2 days from day 0-30 and every 3-4 days from day 30-100.

extract_protocol: Astrocytes were then washed twice with PBS and frozen at -80oC before shipping to Kompetenzzentrum Fluoreszente Bioanalytik (Germany) for gene expression analysis using the Clariom S array (Affymetrix). Total RNA was extracted from dry cells according to the “Purification of total RNA from animal cells using spin technology” protocol of the RNeasy Micro Kit (QIAGEN, Hilden, Germany).  In brief, cells were grown in 6-well plates. After removing the cell-culture medium, the plates were frozen and shipped on dry ice. After thawing, 250 µl of lysis buffer RLT was added to each well and the cells were harvested with a cell scraper. The lysates were pipeted into QIAshredder spin columns and homogenized by centrifugation. Next 1 volume of 70% ethanol was added and the samples were applied to RNeasy MinElute spin columns followed by an on-column DNase digestion and several wash steps. Finally total RNA was eluted in 14 μl of nuclease free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip reagent set (Agilent, Palo Alto, CA, USA).

treatment_protocol: Day 97-105 astrocytes were seeded at 300,000 cells/well in a 6-well plate coated with 20 µg/ml P/O (Sigma-Aldrich) and 5 µg/ml mouse laminin for 2 days and treated with either PBS (referred to as non-treated in the study), 100 ng/ml TNFα, or 10 µM αSYN (monomers or fibrils) for 6 days.

tag: cell type

value: iPSC-derived astrocyte

value: control media


title: CD14+ Monocytes - HC4


title: HH-OX-18_1


title: HH-OX-19_1


title: Myotube_NGT_55a_13


title: Myotube_NGT_32a_10


title: Myoblast_NGT_35a_11


title: M1 Macropahges - H syndrome 2 (R2)


title: M2 Macropahges - H syndrome 2 (R2)


title: HH-OX-17_1


title: 37R-3 Astrocytes_Media control_rep1

scan_protocol: Sample preparation for microarray hybridization was carried out as described in the Affymetrix GeneChip WT PLUS Reagent Kit User Manual (Affymetrix, Inc., Santa Clara, CA, USA).  In brief, 200 ng of total RNA was used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin. 3,8 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Clariom S human arrays for 16 h at 45 ° C in a GeneChip hybridization oven 640. Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by Affymetrix GeneChip Command Console v4.1.3 software.  Sample processing was performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de).


title: HH-OX-16_1


title: Myotube_NGT_24a_9


title: 37R-4 Astrocytes_Media control_rep1

label_protocol: Sample preparation for microarray hybridization was carried out as described in the Affymetrix GeneChip WT PLUS Reagent Kit User Manual (Affymetrix, Inc., Santa Clara, CA, USA).  In brief, 200 ng of total RNA was used to generate double-stranded cDNA. 12 µg of subsequently synthesized cRNA was purified and reverse transcribed into sense-strand (ss) cDNA, whereat unnatural dUTP residues were incorporated. Purified ss cDNA was fragmented using a combination of uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) followed by a terminal labeling with biotin. 3,8 µg fragmented and labeled ss cDNA were hybridized to Affymetrix Clariom S human arrays for 16 h at 45 ° C in a GeneChip hybridization oven 640. Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450, and the fluorescent signals were measured with an Affymetrix GeneChip Scanner 3000 7G. Fluidics and scan functions were controlled by Affymetrix GeneChip Command Console v4.1.3 software.  Sample processing was performed at an Affymetrix Service Provider and Core Facility, “KFB - Center of Excellence for Fluorescent Bioanalytics” (Regensburg, Germany; www.kfb-regensburg.de).


title: 9A-4 Astrocytes_Media control_rep1


title: 36D-2 Astrocytes_aSYN F110 10uM_rep1

source_name: Human iPSC-derived astrocytes treated with aSYN F110 for 6 days

value: alpha-synuclein F110


title: Myoblast_NGT_24a_9


title: Myoblast_NGT_32a_10


title: HH-OX-16_2

value: no


title: CD14+ Monocytes - H syndrome 2 (R2)

value: CD14+ Monocytes


title: 37R-4 Astrocytes_aSYN F110 10uM_rep1


title: Myotube_NGT_35a_11


title: Myoblast_NGT_23a_8


title: HH-OX-15_1


title: 592T treated with Azathioprine_rep2

city: Daejeon

first: Hye Jin

last: Nam

email: nhj0120@gmail.com, hjnam@krict.re.kr

state: Not US or Canada

address: 141 Gajeongro, Yuseong

country: South Korea

institute: Korea Research Institute of Chemical Technology

data_processing:
We preprocessed the raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to the Homo sapiens (hg19) using HISAT v2.3.4.1
HISAT utilizes two types of indexes for alignment (a global, whole-genome index and tens of thousands of small local indexes).
These two types’ indexes are constructed using the same BWT (Burrows–Wheeler transform)/ a graph FM index (GFM) as Bowtie2.
Because of its use of these efficient data structures and algorithms, HISAT generates spliced alignments several times faster than Bowtie and BWA widely used.
Genome_build: Homo sapiens (hg19)
Supplementary_files_format_and_content: transcript assembly of known transcripts was processed by StringTie v1.3.4d. Base on the result of that, expression abundance of transcript and gene were calculated as read count or FPKM value (Fragments Per Kilobase of exon per Million fragments mapped) per sample.

source_name: primary glioblastoma cells

growth_protocol: 559T and 592T: Cells were maintained in spheroidal suspension in Neurobasal-A medium (Gibco, 10888-022) supplemented with 0.5X B-27 (Gibco, 17504-001), 0.5X N2 (Gibco, 17502-001), L-glutamine (2 mM, Gibco, 25030-081), EGF (100 ng/ml, R&D systems, 236-EG), FGF (100 ng/ml, R&D systems, 3718-FB) and ZellShield (Minerva Biolabs GmbH). NHA: NHA cells were purchased from Lonza (CC-2563) and cultured in ABM medium (Lonza, CC-3187) supplemented with AGM SingleQuots (CC-4123) and ZellShield (Minerva Biolabs GmbH).

extract_protocol:
TRIzol (Invitrogen)
Library preparation, sequencing, and basic analysis were conducted by MACROGEN Company (Republic of Korea). In order to construct cDNA libraries with the TruSeq Stranded mRNA LT Sample Prep Kit, total RNA was used. PolyA-selected RNA extraction, RNA fragmentation, random hexamer primed reverse transcription and 100 nt paired-end sequencing by Illumina NovaSeq 6000 were performed. The libraries were quantified using qPCR according to the qPCR Quantification Protocol Guide and qualified using an Agilent Technologies 2100 Bioanalyzer.

treatment_protocol: Azathioprine (10 uM) was treated for 48 hours

value: patient-derived rimary glioblastoma cells

value: treated with azathioprine

tag: tumor subtype

value: mesenchymal subtype


title: Myoblast_NGT_21a_7


title: Myotube_NGT_21a_7


title: HH-OX-15_2

source_name: blood


title: 592T treated with Azathioprine_rep1


title: 592T untreated_rep2

value: untreated


title: HH-OX-13_1


title: 592T untreated_rep1


title: 36D-4 Astrocytes_aSYN fibril 10uM_rep1

source_name: Human iPSC-derived astrocytes treated with aSYN fibril (10uM) for 6 days

value: alpha-synuclein fibril


title: 9A-4 Astrocytes_aSYN F110 10uM_rep1


title: Myoblast_NGT_18a_6

value: Normal glucose tolerance (NGT)


title: HH-OX-12_1

value: polyA RNA + protein surface markers


title: Myotube_NGT_23a_8


title: 37R-4 Astrocytes_aSYN fibril 10uM_rep1


title: 37R-3 Astrocytes_aSYN fibril 10uM_rep1


title: 559T treated with Azathioprine_rep2

value: proneural subtype


title: HH-OX-11_1


title: 559T treated with Azathioprine_rep1


title: HH-OX-10_1


title: 9A-4 Astrocytes_aSYN fibril 10uM_rep1


title: Myoblast_NGT_40a_12


title: Myotube_NGT_14a_5


title: Myotube_NGT_18a_6


title: 36D-4 Astrocytes_aSYN monomer 10uM_rep1

source_name: Human iPSC-derived astrocytes treated with aSYN monomer (10uM) for 6 days

value: alpha-synuclein monomer


title: M0 Macropahges - H syndrome 2 (R2)

tag: cell type/tissue

value: MDMs

value: GM-CSF

value: Peripheral Blood


title: HH-OX-09_1

value: female


title: 559T untreated_rep1


title: 559T untreated_rep2


title: HH-OX-08_1


title: HH-OX-07_1


title: 559T whole exome sequencing

data_processing:
Library strategy: WES
Paired-end sequences produced by HiSeq Instrument were firstly mapped to the human genome, where the reference sequence is UCSC assembly hg19 (original GRCh37 from NCBI, Feb. 2009), without unordered sequences and alternate haplotypes, using the mapping program ‘BWA’ (http://bio-bwa.sourceforge.net/bwa.shtml, version 0.7.12),
generate a mapping result file in BAM format using ‘BWA-MEM’
we applied programs packaged in Picard-tools (ver.1.130) in order to remove PCR duplicates reducing those reads identically match to a position at start into a single one, using MarkDuplicates.jar, which requires reads to be sorted.
The local realignment process was performed to consume BAM files and to locally realign reads such that the number of mismatching bases is minimized across all the read. Base quality score recalibration (BQSR) and local realignment around indels were performed using Genome Analysis Toolkit to locally realign reads such that the number of mismatching bases is minimized across all the read. Variant genotyping for each sample was performed with Haplotype Caller of GATK (https://www.broadinstitute.org/gatk/). Based on the BAM file previously generated, Variant genotyping for each sample was performed with Haplotype Caller of GATK. In this stage SNP and short indels candidates were detected at nucleotide resolution. Those variants were annotated by another program called SnpEff v4.1g (http://snpeff.sourceforge.net/SnpEff.html), to vcf file format, filtering with dbSNP for the version of 142, and SNPs from the 1000 genome project. Then, in-house program and SnpEff was applied to filter additional databases, including ESP6500, ClinVar, dbNSFP2.9. For advanced Analysis, we gathered all the per-sample GVCFs and passed them all together to the joint genotyping tool, GenotypeGVCFs. The enrichment test based on KEGG Pathway (Kyoto Encyclopedia of Genes and Genomes (Kanehisa et al., 2012) was conducted using the genes annotated from the variants in the VCF.
Genome_build: Homo sapiens (hg19)
Supplementary_files_format_and_content: Those variants were annotated by another program called SnpEff v4.1g (http://snpeff.sourceforge.net/SnpEff.html), to vcf file format, filtering with dbSNP for the version of 142, and SNPs from the 1000 genome project. Then, in-house program and SnpEff was applied to filter additional databases, including ESP6500, ClinVar, dbNSFP2.9. For advanced Analysis, we gathered all the per-sample GVCFs and passed them all together to the joint genotyping tool, GenotypeGVCFs.

extract_protocol:
RenillaPrep gDNA Tissue Miniprep System (Promega A2051)
Library preparation, sequencing, and basic analysis were conducted by MACROGEN Company (Republic of Korea). The samples were prepared according to an Agilent SureSelect Target Enrichment Kit preparation guide. The libraries were sequenced with Illumina platform sequencer.
Whole exome sequencing (Agilent SureSelect Target Enrichment Kit preparation guide)


title: 37R-3 Astrocytes_aSYN F110 10uM_rep1

value: iPSC-derived astrocyte


title: 592T whole exome sequencing


title: 37R-4 Astrocytes_aSYN monomer 10uM_rep1


title: 36D-4 Astrocytes_TNFa 100ng/ml_rep1

source_name: Human iPSC-derived astrocytes treated with TNFa (100ug/ml) for 6 days

value: tumor necrosis factor alpha


title: Myoblast_NGT_13a_4


title: Myotube_NGT_13a_4


title: 9A-4 Astrocytes_aSYN monomer 10uM_rep1


title: HH-OX-06_1

value: no


title: 37R-3 Astrocytes_aSYN monomer 10uM_rep1


title: 37R-4 Astrocytes_TNFa 100ng/ml_rep1


title: HH-OX-05_1


title: Myoblast_NGT_115a_3


title: Myotube_NGT_105_1


title: Myotube_NGT_112a_2


title: Myoblast_NGT_112a_2


title: 37R-3 Astrocytes_TNFa 100ng/ml_rep1


title: HH-OX-02_1


title: ITNET_1304

city: Brisbane

first: Katia

last: Nones

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer MEdical Research Institute

hyb_protocol: Illumina protocol

scan_protocol: Iscan Illumina

data_processing:
2015
Beta value (Raw IDAT files were imported, filtered and normalized using the ChAMP package implemented in R.  Probes were primarily filtered out if detection p-value >0.01 or there were fewer than 3 beads in at least 5% of samples. A beta-mixture quantile (BMIQ) normalisation was performed to account for probe type1 and type2 biases, followed by a quantile normalisation (QN). Further filtering was performed to remove probes in non-CpG sites, X or Y chromosome, SNP related polymorphisms and probes that map to multiple locations. After the filtering process, 411,159 probes were used for further analysis.

source_name: Normal Adjacent

label_protocol: Illumina protocol

growth_protocol: not applicable

extract_protocol: All prep DNA/RNA kit (qiagen)

treatment_protocol: no applicable

value: Normal adjacent Pancreata

tag: disease

value: pancreatic neuroendocrine tumor


title: PBMC_CHB_subject3

city: Hangzhou

first: Jian

last: Yao

state: Zhejiang

address: 79th Qingchun Rd

country: China

institute: Zhejiang University

hyb_protocol: 1 ?g of each labeled cRNA was fragmented by adding 5 ?l 10 × Blocking Agent and 1 ?l of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 ?l 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 ?l of hybridi

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 quanti

source_name: human, PBMC, CHB

label_protocol: Briefly, 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 utiliz

extract_protocol: About 5 ml blood samples were collected, and the PBMCs were isolated using standard density-gradient centrifugation on Ficoll-Paque (MultiSciences (Lianke) Biotech, China). Total RNA was isolated using RNAiso Plus (Takara Bio, Dalian, China) according to

tag: diagnosis

value: chronic HBV

value: peripheral blood mononuclear cells (PBMCs)

tag: gender

value: male

tag: age


title: 36D-4 Astrocytes_Media control_rep1

tag: treatment

value: control media


title: 37R-4 Astrocytes_Media control_rep1


title: 9A-4 Astrocytes_TNFa 100ng/ml_rep1


title: PBMC_ASC_subject3

source_name: human, PBMC, ASC

value: asymptomatic carriers


title: 37R-3 Astrocytes_Media control_rep1


title: HH-OX-01_1

tag: donor

value: polyA RNA + protein surface markers


title: PBMC_CHB_subject2


title: PBMC_CHB_subject1


title: ITNET_1257


title: PBMC_ASC_subject2


title: ITNET_1081


title: S30_12Sham_5

status: Public on Feb 15 2021

city: Williamsburg

first: Margaret

last: Saha

state: VA

address: 540 Landrum Drive

department: Biology

institute: College of William and Mary

data_processing:
Quality assessment of RNA-Seq reads was performed using FastQC
Paired-end mapping was performed using Hisat2 with Xenopus laevis v9.1 and v9.2 genome
Output sequence alignment map (SAM) files were converted to binary alignment map (BAM) format and sorted by name using samtools
Read quantification for transcripts was performed using HTSeq-Count and abundance measurements with Kallisto
Differential expression analysis done with DESeq2
Supplementary_files_format_and_content: raw counts

organism: Xenopus laevis

source_name: Embryo presumptive neural tissue

extract_protocol:
RNA was extracted by homogenizing all individual embryos in 600 ul TRI reagent (Ambion) then dividing the homogenate equally between two tubes. Partially separated mixture was spun down in a Phase Lock Gel Heavy tube (QuantaBio) and RNA was then purified using the MagMAX™- 96 for Microarrays. RNA quality and yield was assessed by spectrophotometry (NanoDrop®), agarose gel electrophoresis, and Agilent Bioanalyzer analysis. RNA was extracted from single embryos using the  MagMAX™-96 Total RNA Isolation Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Stage 30

tag: protocol

value: Sham


title: S30_12Sham_3


title: S30_12Sham_4


title: 9A-4 Astrocytes_Media control_rep1


title: S30_12Sham_2


title: ITNET_1286


title: ITNET_1270


title: S30_12Rotated_3

value: Rotated


title: S30_12Rotated_4


title: S30_12Transplant_5

value: Transplant


title: ITNET_1053


title: PBMC_ASC_subject1


title: S30_12Rotated_1


title: HH-OX-14_1

data_processing:
library deconvolution with bcl2fastq (Illumina, v2.20.0.422)
single cell deconvolution and mapping using zUMIs (v2.5.6b) with STAR (v2.6.0c) for RNA and CITE-seq-Count (v. 1.4.2) for protein surface markers
cell hashing demultiplexing with Seurat (v3.1.1)
doublet removal with DoubletFinder (2.0.2)
Standard log normalisation of RNA using Seurat (v3.1.1)
Non-standard normalisation of RNA using sctransform (v0.2.0) as described in Hafemeister and Satija 2019 (Genome Biology)
Sample integration for RNA with Seurat (v3.1.1)
Marker imputation from RNA with SAVER-X (v1.0.0)
Integration of imputed RNA markers with Seurat (v3.1.1)
Normalisation (centered log transformation) and sample integration for surface protein markers with Seurat (v3.1.1)
Genome_build: GRCh38 without alternative contigs
Supplementary_files_format_and_content: All processed data files are provided as tar.gz archives, which contain a sparse matrix in the market matrix format (.mtx) specifying expression values and the cell barcodes and features as tab seperated value files (barcodes.tsv and genes.tsv), the matrices contain cells as columns and features (genes or antibody-derived tags = ADT) as rows; all metadata files are provided as comma separated text files (.csv)

extract_protocol:
10X chromium v2/v3 (see V_10X for each sample)
CITE-seq/Cell hashing as described in Stoeckius et al 2018 (Genome Biology)

tag: hash

tag: match

tag: group

value: polyA RNA


title: S30_12Transplant_4


title: S30_12Rotated_5


title: ITNET_0850


title: ITNET_0993


title: Myotube_NGT_115a_3

tag: diabetes status

value: Normal glucose tolerance (NGT)


title: HH-OX-03_1

tag: cohort

tag: Sex

value: female

tag: edss

tag: molecule


title: ITNET_0107

tag: tissue


title: S30_11Sham_2


title: S30_11Sham_3


title: S30_12Transplant_2


title: Myoblast_NGT_105_1


title: S30_11Sham_5


title: Myoblast_NGT_14a_5


title: S30_11Sham_1


title: S30_12Transplant_1


title: S30_11Rotated_5


title: S30_12Rotated_2


title: S30_12Transplant_3


title: S30_11Rotated_3


title: S30_11Sham_4


title: S30_11Transplant_3


title: S30_11Transplant_5


title: S30_11Rotated_2


title: S30_11Transplant_4


title: ITNET_0026

tag: disease


title: S30_11Transplant_2


title: S30_11Transplant_1


title: ICGC_0428


title: S30_11Rotated_1


title: S18_12Sham_5

value: Stage 18


title: S30_Control_2

value: Control


title: S30_SelfieControl_2

value: SelfieControl


title: S18_12Sham_4


title: S30_Control_5


title: S18_12Sham_2


title: S30_SelfieControl_1


title: S18_12Sham_3


title: S30_Control_1


title: S30_11Rotated_4


title: S30_Control_3


title: S18_12Sham_1


title: HH-OX-04_1

value: no


title: S18_12Rotated_4


title: S18_12Rotated_5


title: S18_12Rotated_3


title: S18_12Transplant_2


title: S18_12Transplant_4


title: S18_12Rotated_1


title: S18_12Transplant_5


title: S18_12Rotated_2


title: S18_12Transplant_1


title: S18_11Sham_4


title: S18_11Sham_1


title: S18_12Transplant_3


title: S30_Control_4


title: S18_11Sham_3


title: S18_11Sham_2


title: S18_11Sham_5


title: S18_11Rotated_3


title: S18_11Transplant_5


title: S18_11Rotated_4


title: S18_11Transplant_2


title: S18_11Rotated_2


title: S18_11Rotated_1


title: S18_11Transplant_4


title: S18_Control_5


title: S18_11Transplant_1


title: S18_SelfieControl_2


title: S18_11Transplant_3


title: S18_SelfieControl_1


title: S18_Control_4


title: S18_Control_3


title: S18_Control_2


title: P15-1

city: Cinicnnati

first: Katherine

middle: E

last: Yutzey

state: OH

address: 240 Albert Sabin Way

department: Divison of Molecular Cardiovascular Biology

institute: Cinicnnati Children's Hospital Medical Center

description: No treatment

data_processing:
Fastq files were trimmed to remove adapter and loq quality sequences using Trimmomatic V 0.33
Trimmed reads were mapped to the reference (Sscrofa11) using hisat2 V 2.0.5
After trimming the reads were quantified using Kallisto V 0.43.1, this gives us TPM
Genome_build: Sscrofa11
Supplementary_files_format_and_content: Tab-delimited text files include TPM for all samples

organism: Sus scrofa

source_name: Pig left ventricles

extract_protocol:
Pig left ventricular tissues were excised, flash frozen in liquid nitrogen, and RNA was isolated using NucleoSpin RNA kit (740955, Macherey-Nagel).
RNA libraries were prepared for sequencing using Illumina Truseq stranded mRNA protocol

value: Myocardium

value: Postnatal Day 15

tag: genotype

value: Wild Type


title: S18_Control_1


title: P15-6

description: No treatment


title: P15-2

description: No treatment


title: P7-5

description: No treatment

value: Postnatal Day 7


title: P7-2

description: No treatment


title: P7-6

description: No treatment


title: P0-6

description: No treatment

value: Postnatal Day 0


title: P0-4

description: No treatment


title: S18_11Rotated_5


title: P0-5

description: No treatment


title: RNA-MCER136

city: Boston

first: Assunta

last: De Rienzo

state: MA

address: 75 Francis Street

institute: Brigham and Women's Hospital

hyb_protocol: The cRNA was hybridized to Affymetrix® Human Gene 1.1 ST Array (ThermoFisher Scientific, Carlsbad, CA)

scan_protocol: Scanning performed with a GeneAtlas Workstation (ThermoFisher Scientific) as recommended by the manufacturer.

data_processing: Array intensities were normalized by RMA using Bioconductor.

source_name: Pleural Mesothelioma Tumor

label_protocol: cRNA was labeled with GeneChip WT Terminal Labeling Kit (ThermoFisher Scientific)

growth_protocol: All tumor specimens were collected at surgery as discarded specimens from patients who provided informed consent, fresh frozen, stored, and annotated by the institutional tumor bank with the Institutional Review Board approval

extract_protocol: RNA was extracted from tumor enriched (>80%) samples using the Trizol (ThermoFisher Scientific, Carlsbad, CA) method in combination with RNeasy kit (Qiagen, Valencia, CA). DNase (Qiagen) treatment was conducted per the manufacturer’s instructions. The RNA was quantified using an ND-1000 spectrophotometer (ThermoFisher Scientific), and its integrity (RIN≥7) was determined using the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).

treatment_protocol: Two additional samples (MAQCa and MAQCb) were added in the analysis for quality control across platforms.  In addition, two replicate samples were included to determine the variability of the expression values across the entire experiment.

tag: organ

value: Tumor

tag: compartment

value: Tissue

value: M


title: RNA-MCER152


title: RNA-MCER137


title: RNA-MCER146


title: RNA-MCER149


title: RNA-MCER142


title: RNA-MCER139


title: RNA-MCER133


title: RNA-MCER147


title: RNA-MCER138


title: RNA-MCER154


title: S30_12Sham_1

value: Stage 30

value: Sham


title: RNA-MCER141


title: RNA-MCER144


title: RNA-MCER134


title: RNA-MCER140


title: RNA-MCER143


title: RNA-MCER125

value: F


title: RNA-MCER131


title: RNA-MCER124


title: RNA-MCER148


title: RNA-MCER153


title: RNA-MCER132


title: RNA-MCER145


title: RNA-MCER150


title: RNA-MCER126


title: RNA-MCER129


title: RNA-MCER135


title: RNA-MCER130


title: RNA-MCER128


title: RNA-MCER118


title: RNA-MCER119


title: RNA-MCER120


title: RNA-MCER115


title: RNA-MCER111


title: RNA-MCER107


title: RNA-MCER121


title: RNA-MCER110


title: RNA-MCER109


title: RNA-MCER113


title: RNA-MCER123


title: RNA-MCER106


title: RNA-MCER99


title: RNA-MCER92


title: RNA-MCER93


title: RNA-MCER88


title: RNA-MCER101


title: RNA-MCER114


title: RNA-MCER108


title: RNA-MCER91


title: RNA-MCER103


title: RNA-MCER85


title: RNA-MCER105


title: RNA-MCER87


title: RNA-MCER86


title: RNA-MCER98


title: RNA-MCER84


title: RNA-MCER94


title: RNA-MCER83


title: RNA-MCER81 Rep1


title: RNA-MCER74


title: RNA-MCER73


title: RNA-MCER66


title: RNA-MCER81 Rep 2


title: RNA-MCER82


title: RNA-MCER75


title: RNA-MCER69


title: RNA-MCER70


title: RNA-MCER77


title: RNA-MCER79


title: RNA-MCER97


title: RNA-MCER63


title: RNA-MCER71


title: RNA-MCER56


title: RNA-MCER53


title: RNA-MCER64


title: RNA-MCER51


title: RNA-MCER65


title: RNA-MCER61


title: RNA-MCER57


title: RNA-MCER52


title: RNA-MCER62


title: RNA-MCER80


title: RNA-MCER67


title: RNA-MCER68


title: RNA-MCER54


title: RNA-MCER60


title: RNA-MCER50


title: RNA-MCER59


title: RNA-MCER49


title: RNA-MCER47


title: RNA-MCER45


title: RNA-MCER41 Rep2


title: RNA-MCER46


title: RNA-MCER48


title: RNA-MCER43


title: RNA-MCER39


title: RNA-MCER35


title: RNA-MCER34


title: RNA-MCER40


title: RNA-MCER37


title: RNA-MCER42


title: RNA-MCER33


title: RNA-MCER32


title: RNA-MCER23


title: RNA-MCER21


title: RNA-MCER41 Rep1


title: RNA-MCER29


title: RNA-MCER28


title: RNA-MCER20


title: RNA-MCER18


title: RNA-MCER25


title: RNA-MCER31


title: RNA-MCER16


title: RNA-MCER26


title: RNA-MCER19


title: RNA-MCER15


title: RNA-MCER30


title: RNA-MCER14


title: RNA-MCER11


title: RNA-MCER8


title: RNA-MCER5


title: RNA-MCER7


title: RNA-MCER13


title: RNA-MCER1


title: RNA-MCER2


title: RNA-MCER4


title: RNA-MCER9


title: RNA-MCER3


title: A364a_rad53K227A_Exp1

city: Syracuse

first: Wenyi

last: Feng

state: NY

address: 750 East Adams Street

department: Biochemistry and Molecular Biology

institute: SUNY Upstate Medical University

hyb_protocol: Scanned on an Agilent G2565B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 9.5.1) was used for background subtraction and LOWESS normalization.  Chromosome coordinates (kb) for each probe were extracted.

organism: Saccharomyces cerevisiae

label_protocol: In each experiment a G1 control sample and an S phase sample (released into S phase at 37C for 10, 15, 20 and 25 min) were paired and the DNA cohybridized to Agilent G4493A Yeast Whole Genome ChIP-on-Chip 4x44k microarrays.

growth_protocol: Yeast cells were grown to approx. 5x10E6 cells/ml before alpha factor treatment in YEAST MINIMAL COMPLETE (YCOMP) medium.

extract_protocol: Agarose plugs containing yeast cells for spheroplasting were prepared as described (Van Brabant et al., 2001 Mol Cell 7, 705-713).

treatment_protocol: Alpha factor was used at 3 micromolar and hydroxyurea was used at 200 mM.  At the time of sampling, cells were treated with 0.1% sodium azide.

tag: strain

tag: time point

value: G1 control

tag: molecule subtype

value: labeled ssDNA

value: 1 h after release from G1 to 200 mM HU


title: RNA-T502

description: microarray expression data from human malignant pleural mesothelioma

hyb_protocol: After labelling, samples were hybridized using the CodeLink Expression Assay Reagent Kit (GE-Amersham Biosciences) per manufacturer’s instructions.

scan_protocol: Chips were scanned using the GenePix 4000B instrument (Axon instruments).

data_processing: Array intensities were median-normalized using Codelink Expression Analysis v4.1 software to produce normalized intensity values for each gene probe in each microarray.

label_protocol: Tumor mRNA was labelled using the CodeLink Expression Assay Reagent Kit (GE-Amersham Biosciences) per manufacturer’s instructions.

tag: tissue type


title: W303_rad53K227A_Exp1


title: RNA-T445


title: RNA-MCER10


title: RNA-MCER6


title: RNA-T447


title: W303_RAD53_Exp2

value: WT


title: RNA-T459


title: RNA-T444


title: RNA-T451


title: RNA-T485


title: A364a_RAD53_Exp2


title: A364a_RAD53_Exp1


title: W303_rad53K227A_Exp2


title: W303_RAD53_Exp1


title: RNA-T478


title: A364a_rad53K227A_Exp2


title: RNA-T452


title: RNA-T437


title: RNA-T448


title: RNA-T455


title: RNA-T467


title: RNA-T441


title: RNA-T464


title: RNA-T644


title: RNA-T497


title: RNA-T463


title: RNA-T481


title: RNA-T450


title: RNA-T454


title: RNA-T479


title: RNA-T496


title: RNA-T458


title: RNA-T504


title: RNA-T443


title: RNA-T500


title: RNA-T499


title: RNA-T439


title: RNA-T495


title: RNA-T446


title: RNA-T505


title: RNA-T461


title: RNA-T457


title: RNA-T465


title: RNA-T468


title: RNA-T498


title: RNA-T501


title: RNA-T456


title: RNA-T438


title: RNA-T460


title: MUM04 cells vehicle treated

city: Saint Louis

first: Michael

middle: D

last: Onken

address: 660 S. Euclid Ave

department: Biochemistry & Molecular Biophysics

institute: Washington University School of Medicine

data_processing:
FastQ files aligned with STAR.
Biologic replicates analyzed by edgeR and Sailfish for gene-level features.
Normalized abundance measurements generated from edgeR.
Genome_build: ENSEMBL_R76
Supplementary_files_format_and_content: *.txt: Tab-delimited text files of gene-level moderated log2 CPM.

source_name: biopsy sample from metastatic liver tumor

growth_protocol: 5% CO2, 37˚C, RPMI 1640 with 10% FBS for cell lines; 5% CO2, 37˚C, MDMF for human samples.

extract_protocol:
Qiagen RNeasy mini kit.
RNA-polyA

treatment_protocol: 100 nM FR900359 in DMSO added to medium at start.

tag: treatment

value: DMSO

tag: molecular class


title: MUM04 cells FR treated

value: biopsy sample from metastatic liver tumor


title: UM033 cells FR treated

source_name: biopsy sample from primary eye tumor

value: biopsy sample from primary eye tumor

value: class 1


title: RNA-T442


title: RNA-T480


title: UM033 cells vehicle treated


title: UM031 cells FR treated

value: class 2


title: UM032 cells vehicle treated


title: UM030 cells vehicle treated


title: UM030 cells FR treated


title: MP46 cells FR exp2

source_name: MP46 uveal melanoma cell line

tag: cell line

tag: cell type

value: uveal melanoma cell line


title: RNA-T483


title: MP46 cells FR exp1


title: MP46 cells DMSO exp2


title: MP41 cells FR exp2

source_name: MP41 uveal melanoma cell line


title: MP46 cells DMSO exp1


title: MP41 cells DMSO exp2


title: MP41 cells DMSO exp1


title: UM031 cells vehicle treated


title: RNA-MCER22


title: RNA-T466


title: RNA-T440


title: UM032 cells FR treated


title: 100_percent_d40_rep3_Hsap_Mmul_Chimera

first: Jared

last: Brown

address: Mailtop CLS11007, 450 Brookline Ave

department: Data Science

institute: Dana Farber Cancer Institute

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d40_rep3

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequences were filtered and trimmed to remove low quality reads, adapters, and other sequencing artifacts.
Sequencing reads were mapped to chimera transcriptome using bowtie 1.2.3
Gene expected counts were calculated using RSEM 1.2.31
Genome_build: A joint hg19/mm10 transcriptome reference was built by appending hg19 or mm10 respectively to the chromosome sequences and gene symbols. Tagging the gene symbols with the ID of the reference genome ensured easy decomposition of the resulting expression estimates into mouse and human subsets.
Supplementary_files_format_and_content: collated rsem output into tab files, expected counts (ec), transcripts per million (tpm's), and fragments per kilobase million (fpkm)

source_name: Co-cultured human and mouse pluripotent stem cell-derived neural cells

growth_protocol: All cells were differentiated in vitro in DF3S (DMEM/F12, 64 mg/L L-ascorbic acid phosphate Mg salt, 0.014 mg/L sodium selenite, 1,743 mg/L sodium bicarbonate; Thermo Fisher Scientific, USA) + N2 and B27 Supplements (Thermo Fisher Scientific, USA) + 100ng/mL Noggin (R&D Systems, USA) on matrigel-coated multiwell culture plates.

extract_protocol:
Total RNA was then purified from 350 µL RLT-Plus Buffer using RNeasy Plus 96 and Micro Kits (Qiagen, Netherlands) and quantitated with the Quant-iT RNA Assay Kit (Thermo Fisher Scientific, USA).  RNA was diluted to one hundred nanograms for input.
The Ligation-Mediated Sequencing (LM-Seq) protocol was used to prepare and index all cDNA libraries (Hou et al 2015). Final cDNA libraries were quantitated with the Quant-iT PicoGreen Assay Kit (Thermofisher, Waltham, Massachusetts).
Twenty-five to forty-eight uniquely indexed samples were pooled per lane on an Illumina HiSeq 2500 with a single 51 base pair read and a 10 base pair index read.

treatment_protocol: For RNA sample collection, samples were washed with 1XPBS (Thermo Fisher Scientific, USA) and lysed in 700 µL RLT-PLUS buffer (Qiagen, USA), and stored at -80C until further processing.

tag: tissue composition

value: Homo sapiens cells only

tag: growth time (days)

tag: mixing day

tag: mixing percent human

tag: biological replicate number

value: Neural induction medium (see protocols section below)


title: 100_percent_d40_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d40_rep3.1

value: pluripotent stem cell-derived neural cells


title: 100_percent_d42_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d42_rep3.3


title: 100_percent_d38_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d38_rep3.1


title: 100_percent_d42_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d42_rep3


title: 100_percent_d40_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d40_rep3.3


title: 100_percent_d38_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d38_rep3.3


title: 100_percent_d38_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d38_rep3.2


title: 100_percent_d42_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d42_rep3.2


title: 100_percent_d38_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d38_rep3


title: 100_percent_d42_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d42_rep3.1


title: MP41 cells FR exp1


title: 100_percent_d36_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d36_rep3.3


title: 100_percent_d36_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d36_rep3


title: 100_percent_d34_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d34_rep3.2


title: 100_percent_d34_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d34_rep3.3


title: 100_percent_d36_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d36_rep3.1


title: 100_percent_d30_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d30_rep3.2


title: 100_percent_d36_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d36_rep3.2


title: 100_percent_d30_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d30_rep3.3


title: 100_percent_d34_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d34_rep3.1


title: 100_percent_d28_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d28_rep3.3


title: 100_percent_d30_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d30_rep3


title: 100_percent_d34_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d34_rep3


title: 100_percent_d30_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d30_rep3.1


title: 100_percent_d28_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d28_rep3.2


title: 100_percent_d28_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d28_rep3


title: 100_percent_d28_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d28_rep3.1


title: 100_percent_d40_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d40_rep3.2


title: 100_percent_d26_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d26_rep3.3


title: 100_percent_d26_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d26_rep3.2


title: 100_percent_d24_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d24_rep3.3


title: 100_percent_d26_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d26_rep3.1


title: 100_percent_d24_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d24_rep3.2


title: 100_percent_d22_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d22_rep3


title: 100_percent_d22_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d22_rep3.1


title: 100_percent_d20_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d20_rep3.3


title: 100_percent_d20_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d20_rep3.2


title: 100_percent_d20_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d20_rep3.1


title: 100_percent_d20_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d20_rep3


title: 100_percent_d16_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d16_rep3.1


title: 100_percent_d16_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d16_rep3.2


title: 100_percent_d18_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d18_rep3


title: 100_percent_d18_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d18_rep3.2


title: 100_percent_d18_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d18_rep3.3


title: 100_percent_d16_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d16_rep3


title: 100_percent_d16_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d16_rep3.3


title: 100_percent_d18_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d18_rep3.1


title: 100_percent_d14_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d14_rep3.2


title: 100_percent_d14_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d14_rep3.1


title: 100_percent_d14_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d14_rep3.3


title: 100_percent_d12_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d12_rep3.2


title: 100_percent_d12_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d12_rep3.3


title: 100_percent_d24_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d24_rep3


title: 100_percent_d26_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d26_rep3


title: 100_percent_d12_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d12_rep3.1


title: 100_percent_d24_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d24_rep3.1


title: 100_percent_d22_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d22_rep3.2


title: 100_percent_d22_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d22_rep3.3


title: 100_percent_d10_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d10_rep3.2


title: 100_percent_d12_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d12_rep3


title: 100_percent_d10_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d10_rep3.3


title: 100_percent_d10_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d10_rep3.1


title: 100_percent_d10_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d10_rep3


title: 100_percent_d8_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d8_rep3.2


title: 100_percent_d8_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d8_rep3.1


title: 100_percent_d8_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d8_rep3.3


title: 100_percent_d8_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d8_rep3


title: 100_percent_d7_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d7_rep3.1


title: 100_percent_d14_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d14_rep3


title: 100_percent_d6_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d6_rep3.3


title: 100_percent_d7_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d7_rep3.3


title: 100_percent_d6_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d6_rep3.1


title: 100_percent_d6_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d6_rep3.2


title: 100_percent_d5_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d5_rep3.2


title: 100_percent_d6_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d6_rep3


title: 100_percent_d5_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d5_rep3.3


title: 100_percent_d5_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d5_rep3.1


title: 100_percent_d7_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d7_rep3


title: 100_percent_d4_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d4_rep3.2


title: 100_percent_d4_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d4_rep3.3


title: 100_percent_d5_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d5_rep3


title: 100_percent_d4_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d4_rep3.1


title: 100_percent_d3_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d3_rep3.2


title: 100_percent_d3_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d3_rep3.3


title: 100_percent_d4_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d4_rep3


title: 100_percent_d3_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d3_rep3.1


title: 100_percent_d3_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d3_rep3


title: 100_percent_d2_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d2_rep3.3


title: 100_percent_d2_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d2_rep3.1


title: 100_percent_d2_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d2_rep3.2


title: 100_percent_d2_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d2_rep3


title: 100_percent_d7_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d7_rep3.2


title: 100_percent_d1_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d1_rep3.3


title: 100_percent_d1_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d1_rep3.2


title: 100_percent_d0_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d0_rep3.3


title: 100_percent_d1_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d1_rep3


title: 100_percent_d1_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d1_rep3.1


title: 100_percent_d0_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d0_rep3.1


title: 100_percent_d0_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d0_rep3


title: 100_percent_d0_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
100_percent_d0_rep3.2


title: 0_percent_d40_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d40_rep3

value: Mus musculus cells only


title: 0_percent_d40_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d40_rep3.2


title: 0_percent_d42_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d42_rep3.1


title: 0_percent_d42_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d42_rep3


title: 0_percent_d40_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d40_rep3.1


title: 0_percent_d42_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d42_rep3.3


title: 0_percent_d38_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d38_rep3.2


title: 0_percent_d38_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d38_rep3.3


title: 0_percent_d38_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d38_rep3.1


title: 0_percent_d38_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d38_rep3


title: 0_percent_d36_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d36_rep3.3


title: 0_percent_d42_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d42_rep3.2


title: 0_percent_d36_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d36_rep3.2


title: 0_percent_d40_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d40_rep3.3


title: 0_percent_d36_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d36_rep3


title: 0_percent_d34_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d34_rep3.3


title: 0_percent_d34_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d34_rep3.2


title: 0_percent_d34_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d34_rep3.1


title: 0_percent_d36_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d36_rep3.1


title: 0_percent_d34_rep3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d34_rep3


title: 0_percent_d32_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d32_rep3.3


title: MC3T3_LFF_direct

city: Hamburg

first: Thorsten

last: Schinke

address: Martinistr. 52

department: Department of Osteology and Biomechanics

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 h at 45 °C on mouse Clariom D Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC 4.0) using  default analysis settings (version 1) and Gene + Exon - SST-RMA as summarization and normalization method.

source_name: MC3T3-E1, 1 h LFF, directly after treatment

label_protocol: Proprietary labeled 2nd-cycle ss-cDNA was prepared from 100 ng total RNA using the mouse Clariom D kit according to the GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript (WT) Expression Arrays user guide (version 23 January 2017) from ThermoFisher Scientific

growth_protocol: MC3T3-E1 cells were plated at a density of 10000 cells/cm² on collagen-coated glass slides. Cells were cultured in alpha-MEM with 10% FCS at 37 °C, 5 % CO2, 95 % rH for 4 days.

extract_protocol: RNA was extraced directly or 4 h after treatment using theRNeasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Cells were submitted or not (static control) to mechanical loading by laminar fluid flow (LFF) with a shear stress of 10 dynes/cm2 for 1 h using the FlexCell Streamer System.

value: 1 h LFF

tag: timepoint

value: directly after treatment

value: osteoblastic cell line MC3T3-E1


title: MC3T3_noLFF_4h

source_name: MC3T3-E1, static control, 4 h after treatment

value: static

value: 4 h after treatment


title: Non-cancerous Renal Tissue 184

city: Vilnius

first: Raimonda

last: Kubiliūtė

state: Saulėtekis

address: Sauletekio al., 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

description: DNA methylation profile in non-cancerous renal tissue adjacent primary renal tumor from patient R184

hyb_protocol: 40 µl of each (Cy5 or Cy3) labeled DNA (80 µl in total) was prepared for hybridization using Oligo aCGH/ChIP-Chip Hybridization Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized onto Human DNA Methylation 1×244K Microarrays (Agilent Technologies) for 40 hours at 65°C in a rotating hybridization oven (Agilent Technologies).

scan_protocol: Microarrays were scanned immediately after washing using SureScan microarray scanner (Agilent Technologies).

data_processing: Scanned images were analyzed with Feature Extraction software v10.7.3.1 (Agilent Technologies) using default parameters (protocol ChIP_107_Sep09 (Read Only), grid 023795_D_F_20140814). Background subtracted and spatially detrended signals were obtained.

source_name: Non-cancerous renal tissue, donor R184

label_protocol: Cyanine-5 and Cyanine-3 labeled DNA was prepared from 26 µl of Anti-5-mC monoclonal antibody 33D3 immunoprecipitated DNA and total DNA respectively using SureTag DNA Labeling Kit acording to manufacturer's protocol (Agilent Technologies) followed by purification using Purification Column provided with the SureTag DNA Labeling Kit. Dye incorporation and DNA yield was measured with NanoDrop 2000.

extract_protocol: Renal tissue samples were homogenized using liquid nitrogen and cryoPREP™ CP02 Impactor with tissue TUBE TT1 (Covaris, Woburg, MA, USA). Homogenized tissue powder were treated for up to 18 h at 55 °C with 10-25 μl of proteinase K and 500 μl of lysis buffer, consisting of 50 mM Tris-HCl pH 8.5, 1 mM EDTA, 0.5% Tween-20. DNA was extracted following the standard phenol-chloroform purification and ethanol precipitation protocol.

treatment_protocol: Tissue samples were obtained from partial or radical nephrectomy material of patients diagnosed with clear cell renal cell carcinoma. None of the patients had preoperatively received radiotherapy, chemotherapy, or hormone therapy.

tag: subject id

value: donor R184

tag: gender

value: Female

tag: age

value: Non-cancerous renal tissue

tag: donor id


title: Non-cancerous Renal Tissue 255

description: DNA methylation profile in non-cancerous renal tissue adjacent primary renal tumor from patient R255

source_name: Non-cancerous renal tissue, donor R255

value: donor R255

value: Anti-5-mC monoclonal antibody 33D3 immunoprecipitated DNA


title: Non-cancerous Renal Tissue 171

description: DNA methylation profile in non-cancerous renal tissue adjacent primary renal tumor from patient R171

source_name: Non-cancerous renal tissue, donor R171

value: donor R171

value: Male


title: cObl d2_Piezo1ff Cre+_DMSO_rep3

source_name: Calvarial osteoblasts, day 2 of differentiation, 6 h treatment

growth_protocol: calvarial osteoblasts were isolated by collagenase/dispase digestions from the calvaria of 4 day old mice. These cells were cultured in alpha-MEM with 10% FCS at 37 °C, 5 % CO2, 95 % rH until 80 % confluency was reached. Then osteogenic differentiation was intiated by the addition of 50 µg/ml ascorbic acid and 10 mM beta-glycerophosphate.

extract_protocol: RNA was extraced using the Macherey-Nagel NucleoSpin RNA kit according to the manufacturer's instructions.

treatment_protocol: After one day of osteogenic differentiation the cells were serum-starved over night and treated at day 2 after the induction of the osteogenic differentation with 5 µmol Yoda 1 or the equivalent volume of DMSO for 6 h.

tag: genotype

value: Piezo1 fl/fl; Runx2-Cre+

value: DMSO

value: Calvarial osteoblasts


title: MC3T3_noLFF_direct

source_name: MC3T3-E1, static control, directly after treatment


title: 0_percent_d32_rep3.1_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d32_rep3.1

value: pluripotent stem cell-derived neural cells

value: Neural induction medium (see protocols section below)


title: 0_percent_d32_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d32_rep3.2

value: Mus musculus cells only


title: cObl d2_Piezo1ff Cre+_DMSO_rep2


title: cObl d2_Piezo1ff Cre-_Yoda1_rep3

value: Piezo1 fl/fl; Runx2-Cre-

value: Yoda 1


title: Non-cancerous Renal Tissue 019

description: DNA methylation profile in non-cancerous renal tissue adjacent primary renal tumor from patient R019

source_name: Non-cancerous renal tissue, donor R019

value: donor R019

tag: molecule subtype


title: Cancerous Renal Tissue 184

description: DNA methylation profile in primary renal tumor from patient R184

source_name: Cancerous renal tissue, donor R184

tag: tissue type

value: Cancerous renal tissue

tag: histological subtype

value: Clear cell renal cell carcinoma

tag: pathological tumor stage

tag: tumor size, mm


title: 0_percent_d30_rep3.3_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d30_rep3.3

tag: cell type

tag: treatment


title: Cancerous Renal Tissue 102

description: DNA methylation profile in primary renal tumor from patient R102

source_name: Cancerous renal tissue, donor R102

value: donor R102

value: Female


title: Cancerous Renal Tissue 134

description: DNA methylation profile in primary renal tumor from patient R134

source_name: Cancerous renal tissue, donor R134

value: donor R134


title: cObl d2_Piezo1ff Cre+_DMSO_rep1


title: cObl d2_Piezo1ff Cre-_Yoda1_rep1


title: cObl d2_Piezo1ff Cre-_DMSO_rep3


title: Cancerous Renal Tissue 050

description: DNA methylation profile in primary renal tumor from patient R050

source_name: Cancerous renal tissue, donor R050

value: donor R050

value: Anti-5-mC monoclonal antibody 33D3 immunoprecipitated DNA


title: Cancerous Renal Tissue 052

description: DNA methylation profile in primary renal tumor from patient R052

source_name: Cancerous renal tissue, donor R052

value: donor R052

value: Male


title: Non-cancerous Renal Tissue 050

description: DNA methylation profile in non-cancerous renal tissue adjacent primary renal tumor from patient R050

source_name: Non-cancerous renal tissue, donor R050

value: Non-cancerous renal tissue


title: 0_percent_d30_rep3.2_Hsap_Mmul_Chimera

description:
processed data files:
genes_464.ec.tab
genes_464.tpm.tab
0_percent_d30_rep3.2

tag: tissue composition

tag: growth time (days)


title: Non-cancerous Renal Tissue 027

description: DNA methylation profile in non-cancerous renal tissue adjacent primary renal tumor from patient R027

source_name: Non-cancerous renal tissue, donor R027

value: donor R027


title: Non-cancerous Renal Tissue 052

description: DNA methylation profile in non-cancerous renal tissue adjacent primary renal tumor from patient R052

source_name: Non-cancerous renal tissue, donor R052


title: Cancerous Renal Tissue 171

description: DNA methylation profile in primary renal tumor from patient R171

source_name: Cancerous renal tissue, donor R171

value: donor R171


title: Non-cancerous Renal Tissue 134

description: DNA methylation profile in non-cancerous renal tissue adjacent primary renal tumor from patient R134

source_name: Non-cancerous renal tissue, donor R134


title: cObl d2_Piezo1ff Cre-_DMSO_rep1

value: DMSO

value: Calvarial osteoblasts


title: Cancerous Renal Tissue 034

description: DNA methylation profile in primary renal tumor from patient R034

source_name: Cancerous renal tissue, donor R034

value: donor R034


title: cObl d2_Piezo1ff Cre-_DMSO_rep2

value: Piezo1 fl/fl; Runx2-Cre-


title: cObl d2_Piezo1ff Cre-_Yoda1_rep2

value: Yoda 1


title: Cancerous Renal Tissue 255

description: DNA methylation profile in primary renal tumor from patient R255

source_name: Cancerous renal tissue, donor R255

value: donor R255

value: Cancerous renal tissue


title: Non-cancerous Renal Tissue 102

description: DNA methylation profile in non-cancerous renal tissue adjacent primary renal tumor from patient R102

source_name: Non-cancerous renal tissue, donor R102

value: donor R102