title: CCR2+_monocytes_ICM_rep2

city: St Louis

first: Kory

middle: J

last: Lavine

address: 660 South Euclid, Campus Box 8086

institute: Washington University

hyb_protocol: Cy5 labeled cRNA was used for hybridization per recommended Agilent Protocol

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) to obtain background subtracted and Processed Signal intensities.

source_name: Heart

label_protocol: Cy5 labeled cRNA was produced

extract_protocol: RNA was extracted using Qiagen microRNAseasy kit

value: Heart

tag: disease

value: ischemic cardiomyopathy

value: CCR2+ monocytes


title: CCN4

status: Public on Apr 04 2018

type: SRA

city: Tsukuba

first: Keiko

last: Nohara

address: 16-2 Onogawa

department: Center for Health and Environmental Risk Research

country: Japan

institute: National Institute for Environmental Studies

library_source: genomic

data_processing:
Bisulfite-treated sequencing reads were aligned by a paired-end alignment method for a unique  best hit to the mouse reference genome (NCBI/mm10) using the Bismark program
adapter trimming and quality control was performed using Trim Galore  (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). The aligned data were used  for analyzing DNA methylation profiles using a methylKit package on R
The aligned data were used for analyzing DNA methylation profiles using a methylKit package on R
DMCs were extracted using methylKit for the cytosines in CpG sites with ≥10 reads in  coverage and ≥25% methylation differences between normal and tumor tissues using the logistic  regression method. DMRs were detected for regions containing ≥3 CpG sites and at least 1  DMC and with ≥30% absolute mean CpG methylation difference by using an eDMR package on  R
Promoter DMRs, which were defined as regions within ±2000 bp from TSSs for Refseq  transcripts, were extracted using bedtools 2.25.0 (bedtools.readthedocs.io).
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing the results of DMRs between 3 normal liver tissues and 3 liver tumor tissues, and the distance of DMRs from closest gene calculated by bedtools.

molecule: genomic DNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Tissues were lysed in lysis buffer, treated with RNase, and purified with a phenol-chloroform mixture
RRBS libraries were prepared from genomic DNA of 3 normal liver tissues and 3 tumor tissues  having a Ha-ras mutation according to the protocol reported by Boyle et al (Genome Biol. 2012, 13:R92. doi: 10.1186/gb-2012-13-10-r92). with some modifications. Briefly, 100 ng of genomic DNA was digested with MspI, subjected to gapfilling  and A-tailing, and ligated with TruSeq adaptors included in the TruSeq DNA Sample Prep  Kit (FC-121-1001, Illumina). After DNA size selection and ligation efficiency were checked,  adaptor-ligated DNA was subjected to bisulfite conversion and amplified by PCR. The PCR  products were cleaned-up using Agencourt AMPure XP beads

tag: strain

tag: tissue

value: liver

tag: age

value: 74 weeks

tag: normal or tumor

value: normal


title: CCR2+_monocytes_ICM_rep3

type: RNA

state: MO

country: USA

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: CCR2+_monocytes_ICM_rep1


title: CCR2-_macrophages_ICM_rep4

value: CCR2- macrophages


title: CCR2-_macrophages_ICM_rep5


title: CCR2+_macrophages_ICM_rep6

value: CCR2+ macrophages


title: CCR2+_macrophages_ICM_rep5


title: CCR2+_macrophages_ICM_rep4


title: CCR2-_macrophages_ICM_rep2


title: CCR2-_macrophages_ICM_rep3


title: CCR2+_macrophages_ICM_rep1


title: CCR2+_macrophages_ICM_rep3


title: CCR2-_macrophages_ICM_rep1


title: CCR2+_macrophages_ICM_rep2


title: CCR2+_monocytes_DCM_rep6

value: dilated cardiomyopathy


title: CCR2+_monocytes_DCM_rep7


title: CCR2-_macrophages_ICM_rep6


title: CCR2+_monocytes_DCM_rep4


title: microglia from Cx30KO EAE brain

city: Fukuoka

first: Ryo

last: Yamasaki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-Ku

department: Neurology

institute: Kyushu University

description:
SAMPLE 3
microglia from Cx30KO EAE brain

hyb_protocol: cRNA was hybridized to Affymetrix Mouse Transcriptome Array 1.0 array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The data were analyzed with median polish summarization and quantile normalization by Affymetrix® Expression Console™ 1.1 software, and obtained normalized intensity values.

label: biotin

source_name: Cx30 deficient mice with EAE

label_protocol: The cRNA was amplified, labeled using GeneChip WT Pico Reagent Kit according to the manufacturer's instructions.

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: strain background

tag: genotype/variation

value: Cx30 deficient

value: brain

tag: tissue subtype

value: microglia

tag: eae score


title: microglia from Cx30KO EAE Spinal cord

description:
SAMPLE 4
microglia from Cx30KO EAE Spinal cord

value: spinal cord


title: Cx30KO_naive_spinal

description:
SAMPLE 4
microglia from Cx30KO naive Spinal cord

source_name: Cx30 deficient naïve mice


title: wt_naive_spinal

description:
SAMPLE 2
microglia from WT naive Spinal cord

source_name: wild type naïve mice

value: wild type


title: microglia from WT EAE Spinal cord

description:
SAMPLE 2
microglia from WT EAE Spinal cord

source_name: wild type mice with EAE


title: CCR2+_monocytes_DCM_rep3


title: CCR2+_monocytes_DCM_rep5


title: microglia from WT EAE brain

description:
SAMPLE 1
microglia from WT EAE brain


title: CCR2+_monocytes_DCM_rep2


title: Cx30KO_naive_brain

description:
SAMPLE 3
microglia from Cx30KO naive brain


title: CCR2+_macrophages_DCM_rep8


title: CCR2+_macrophages_DCM_rep7


title: CCR2+_monocytes_DCM_rep1


title: wt_naive_brain

description:
SAMPLE 1
microglia from WT naive brain


title: AF_cultured_DNA

type: genomic

city: Istanbul

first: Esra

last: Yucel

state: Topkapı

address: Davutpasa Cd. No:4

department: Diagnosis Centre For Genetic Disorders

country: Turkey

institute: Koc University Hospital

description:
SAMPLE 1
3998972053_R02C01

hyb_protocol: PB1 was added to RA1 resuspended DNA and the mixture was loaded onto HumanCytoSNP-12 v2.1 BeadChip arrays. After overnight incubation at 48oC, single-base extension and staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a İscan (Illumina).

data_processing:
Genomic DNA extracted from AF culture cells was scanned according to the array barcodes and  Infinium HumanCytoSNP-12 v2.1 BeadChips datasheets (Illumina).  Data was analysed with GenomeStudio  Software (Illumina)
CNVs deletion - duplication

label: Cy3, Cy5

source_name: Amniotic fluid culture

label_protocol: 1000ng of genomic DNA was whole-genome amplified in an overnight reaction at 37oC using amplification master mix (MSM+MA1+MA2+0,1N NaOH+gDNA) . After incubation the amplified DNA was fragmented with fragmentation mix (FMS), precipitated with isopropanol and precipitation mix (PM1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from amniotic fluid culture cells was performed using proteinase K and salting out procedure

tag: gender

value: male

value: Tetra-Amelia Syndrome characterized by lung aplasia and a total absence of the four limbs

tag: tissue/cell type

value: Cultured cells from amniotic fluid


title: CCR2+_macrophages_DCM_rep5

value: Heart


title: CCR2+_macrophages_DCM_rep4


title: CCR2+_macrophages_DCM_rep6


title: CCR2+_macrophages_DCM_rep2


title: CCR2-_macrophages_DCM_rep8


title: CCR2+_macrophages_DCM_rep3


title: Tg-120d-3

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

library_source: transcriptomic

data_processing:
Read quality trimming (with Phred score > 20 at least in 80% in read) with Trimmomatic v 0.32
Aligning reads with STAR (2.5.2) at reference genome GRCm38(mm10)
Aligned read counting with HTSeq-count ver. 0.9.1
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Processed files are standard output of HTSeq-count read counting (text format, tab-delimeted). Gene name is provided as RefSeq ID. Also, some supplemental information in the end of file included

molecule: polyA RNA

source_name: Transgenic(120 days) - 3

extract_protocol:
For RNA extraction cervical sections of spinal cord were isolated from control group (30-60 days), presymptomatic (90 days) and symptomatic (120 days) heterozygous animals and age mice matched wild-type control animals. Each experimental group consisted five individuals with exception of presymptomatic group of DFUS(1-359) mice which consisted of four animals in total. Total RNA was extracted using Extract RNA reagent (Evrogen). Concentration of RNA was measured by Qubit Fluorometer (Invitrogen). The quality of RNA was determined by Agilent BioAnalyzer 2100 using RNA 600 nano kit. RNA Integrity Number (RIN) of all RNA samples was not less than 8
Libraries for RNA-seq were prepared using TruSeq RNA Library Preparation kit v2 (Illumina) according to the manufacturer’s guidelines.

value: Spinal cord

tag: spinal cord region

value: cervical


title: Tg-120d-2

source_name: Transgenic(120 days) - 2


title: Tg-120d-1

source_name: Transgenic(120 days) - 1


title: Tg-120d-4

source_name: Transgenic(120 days) - 4


title: Tg-120d-5

source_name: Transgenic(120 days) - 5


title: CCR2+_macrophages_DCM_rep1


title: Tg-90d-4

source_name: Transgenic(90 days) - 4


title: CCR2-_macrophages_DCM_rep7


title: Tg-90d-3

source_name: Transgenic(90 days) - 3


title: Tg-90d-2

source_name: Transgenic(90 days) - 2


title: Tg-90d-1

source_name: Transgenic(90 days) - 1


title: CCR2-_macrophages_DCM_rep6


title: CCR2-_macrophages_DCM_rep5


title: CCR2-_macrophages_DCM_rep4


title: Tg-60d-4

source_name: Transgenic(60 days) - 4


title: CCR2-_macrophages_DCM_rep1

source_name: Heart


title: CCR2-_macrophages_DCM_rep3


title: CCR2-_macrophages_DCM_rep2


title: Tg-60d-2

source_name: Transgenic(60 days) - 2


title: Tg-60d-1

source_name: Transgenic(60 days) - 1


title: nTg-120d-4

source_name: Non-transgenic(120 days) - 4


title: nTg-120d-3

source_name: Non-transgenic(120 days) - 3


title: nTg-120d-2

source_name: Non-transgenic(120 days) - 2


title: nTg-120d-1

source_name: Non-transgenic(120 days) - 1


title: nTg-60d-4

source_name: Non-transgenic(60 days) - 4


title: nTg-60d-5

source_name: Non-transgenic(60 days) - 5


title: nTg-60d-3

source_name: Non-transgenic(60 days) - 3


title: nTg-60d-2

source_name: Non-transgenic(60 days) - 2


title: Tg-60d-5

source_name: Transgenic(60 days) - 5


title: nTg-60d-1

source_name: Non-transgenic(60 days) - 1


title: RIBOseq wildtype

city: ORSAY

first: Pierre

last: Bertin

address: Batiment 400, Université Paris Sud

country: France

institute: Institut de Biologie Intégrative de la Cellule

data_processing:
Library strategy: RIBO-seq
The RIBOseq was conducted to observe the ribosome occupancy on each protein coding gene after the stop codon of SACCER3 yeast genome assembly
Quality assessement with FastQC
Low quality reads (< 30) and read’s adapters were trimmed using Cutadapt version 1.9.1 (selected kmer sizes were between 24 and 35 nucleotides)
RNA filtering was conducted mapping all reads on SACCER3 rRNA genes. Unmapped reads with bowtie 1.1.2 were conserved.
Filtered reads were mapped using bowtie 1.1.2 on the SACCER3 genome allowing 2 mismatches. Only uniquely mapped reads are conserved.
We defined from the reference genome all the 3' extensions (between the stop of the CDS and the next in-frame stop codon) longer than 9 nucleotides. We counted the number of 28-mers reads that are in-frame with the official CDS in this extension. This value is normalised with the length of the 3'extension and the size of the dataset to obtain the density of 28mers reads within the extension. The p value was calculated using student test with  = 0.05.
Genome_build: SACCER3 (from SGD, last version)
Supplementary_files_format_and_content: Tabular file containing the readthrough values for each mRNA for the WildType and Mutant.

organism: Saccharomyces cerevisiae

source_name: Whole cell extract

growth_protocol: Cells were grown to an OD600 of 0.6 in 1 litre of liquid glucose-YNB supplemented with CSM and 2X adenine

extract_protocol:
Total RNA and polysomes were extracted
Illumina TrueSeq Small RNA RS-200-0012

treatment_protocol: Flash-Freeze

tag: delta


title: Tg-60d-3

source_name: Transgenic(60 days) - 3


title: RIBOseq mutant

value: UPF1, PUS7


title: nTg-120d-5

source_name: Non-transgenic(120 days) - 5


title: Ctrl3

city: Seoul

first: Joha

last: Park

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

description: normalised_expression_values_rescue_exps

data_processing:
Sequencing reads were preprocessed using cutadapt v.1.14; 3′ adapter sequences were trimmed and low quality reads (< 18 nt, < 20 Phred score for 5% of the read) were discarded.
High quality reads were then collapsed and mapped to the human genome (hg38) with Bowtie2 aligner with the options allowing multimapping
Reads that mapped to the miRNA loci were collected, and only the reads that have no mismatch in the region from the 5′-end to the -3 position were used for further analysis
The read counts of mature miRNAs were normalized to reads per million (rpm) and re-scaled to get relative abundance to the geometric mean of the non-canonical miRNAs (hsa-miR-320 family and hsa-miR-877) which bypass Microprocessor processing. For the rescue experiments, normalized expression values of the biological replicates were aggregated by taking the mean.
Genome_build: GRCh38

source_name: DGCR8ΔCTT HCT116 cells

extract_protocol:
Total RNAs were extracted with TRIzol reagent.
Total RNAs were size-fractionated by 15% urea-polyacrylamide gel running with the range of 17-30 nt to enrich small RNA species. Small RNA-seq libraries were generated with TruSeq Small RNA Sample Prep Kit (Illumina).

tag: disease state

value: colon carcinoma

tag: cell line

value: DGCR8[delta]CTT + Mock rescue

tag: replicate


title: ALA3

value: DGCR8[delta]CTT + P351A DGCR8 + ALA rescue


title: Ctrl1


title: Ctrl2


title: ALA1


title: Vehicle_WT

city: Kobe

first: Kazunori

last: YOSHIKIYO

state: Hyogo

address: 6-4-3, Minatojima-Minamimachi, Chuo-ku

institute: Asubio Pharma Co., LTD.

description:
Gene expression of hypertrophic zone purified from rat tibiae.
The growth plate from F344/Stm rat.

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Rat GE 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 028279_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities. Each chip was then normalized to the 75th percentile of the measurements taken from that chip. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Rattus norvegicus

source_name: Vehicle, WT

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 25 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy column purification (QIAGEN, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Tibiae from E18.5 embryonic rat were isolated and pre-cultured in BGJb media for 1 day, followed by culturing in the presence of vehicle or U0126 (0.02mM) for 1 day.

tag: strain/background

value: WT

tag: developmental stage

value: hypertrophic zone from tibiae

tag: treatment

value: Vehicle


title: PA-PTEN KD_2

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: After labeling, 2ug of each aRNA was mixed with 2 ug of reference RNA and purified with Qiagen MinElute PCR Purification kit according to manufacturer’s instructions. Eluted sample was mixed with 10× Blocking Solution and 2× HiRPM buffer (Agilent Technologies), incubated for 2 min at 95°C and hybridized on 8× 60K Whole Human Genome Oligo Microarray chip (Agilent Technologies) using SureHyb DNA Microarray Hybridization Chambers in DNA Microarray hybridization oven (Agilent Technologies) at 10 rpm, 65°C for 18 h.

scan_protocol: After hybridization, slides were washed in Gene Expression Wash Buffer 1 and 2 for 1 min. Microarrays were scanned with a dynamic autofocus microarray scanner (Agilent Microarray Scanner–G2565BA, Agilent Technologies) using Agilent-provided parameters (Red and Green photomultiplier tube (PMT) were each set at 100%, and scan resolution was set to 3 μm). The Feature Extraction Software v9.1.3.1 (Agilent Technologies) was used to extract and analyze the signals.

data_processing: Expression arrays were processed and loess-normalized using BioConductor.

source_name: PNT1A prostate cell line

label_protocol: The cDNA reverse transcription and fluorescent labeling reactions were carried out using Invitrogen SuperScript Plus Direct cDNA Labeling System with Alexa Fluor S’-Aminohexylacrylamido-dUTP.Briefly, 2ug of aRNA and Universal Human Reference RNA (Stratagene) were labeled in reverse transcription with Alexa647 and Alexa 555 aha-dUTPs respectively.

growth_protocol: The PNT1A cell line was originally established by SV40 T-Ag immortalization of benign prostate epithelial cells. PNT1A are immortal but do not form colonies in soft agar or tumors in immunocompromised mice. They do not express androgen receptor (AR), as is typical for benign prostate epithelial cells in culture.

extract_protocol: Total RNA samples were extracted with RNeasy Mini Kit (Qiagen) according to the manufacture’s recommendations. RNA quality was assessed with Nanodrop (Invitrogen). The cDNA reverse transcription and fluorescent labeling reactions were carried out using Invitrogen SuperScript Plus Direct cDNA Labeling System with Alexa Fluor S’-Aminohexylacrylamido-dUTP.

treatment_protocol: To determine if ERG expression and PTEN loss were sufficient to transform prostate epithelial cells we constructed cell lines with expression of the TMPRSS2/ERG fusion gene (TE), stable knockdown of PTEN with shRNA (PTEN KD) or both alterations (PTEN KD/TE) using the PNT1A cell line.

value: PTEN knockdown

source_name: reference RNA

tag: sample type

value: reference RNA


title: PA_1

value: control group


title: ALA2


title: PA-PTEN KD_1


title: P351A2

value: DGCR8[delta]CTT + P351A DGCR8 rescue


title: PA-TE_2

value: TMPRSS2/ERG fusion gene (TE)


title: PA-TE+PTEN KD_2

value: combined TMPRSS2/ERG fusion gene (TE) and PTEN knockdown


title: PA_2


title: Hepa1c1c7_Mst1r

description: Gene expression of Hepa1c1c7 transfected Mst1r vector

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE Ver 2.0 Microarrays (G4858A) for 17 hours at 65℃ in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37℃ GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um high sensitivity, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 074809_D_F_20150624) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the One-Color Low RNA Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

extract_protocol: RNA was prepared using the RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's recommendations.  The protocol include an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Hepa1c1c7 cells were transfected Mst1r or Slpi vector.  The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

tag: tissue

value: liver


title: C352A3

value: DGCR8[delta]CTT + C352A DGCR8 rescue


title: P351A1


title: U0126_WT

description:
Gene expression of hypertrophic zone purified from rat tibiae.
The U0126 treated growth plate from F344/Stm rat.


title: Pancreas 3 endo scar

city: Berlin

first: Bastiaan

last: Spanjaard

address: Robert-Rössle-Straße 10

country: Germany

institute: Max Delbrück Center

description:
PolyA RNA
Read type of raw data files: R1 is technical read, R2 is biological read.
Processed data file: A7_scars_compared.csv

data_processing:
Library strategy: Targeted amplification
Scar reads have the same structure as transcript reads: they consist of a barcode, a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped, had an incorrect barcode, or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences.
To correct for sequencing errors, we implemented several rounds of scar filtering (Supplementary Fig. 2 in publication). We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step, we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step, we aimed to remove easily recognizable sequencing errors. To this end, we consecutively considered scar sequences that have the same cellular barcode and UMI, UMIs that have the same cellular barcode and scar sequence, and cellular barcodes that have the same UMI and scar sequence. In each step, we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI, or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus, but information about scar expression levels was not required in our downstream analysis.
In the third filtering step, we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?, Do both scars occur in cells independently from each other?, Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true, the scars were kept and the sequences were placed on a list of validated scars that, if they occurred in the same cell in another library, did not have to be tested anymore. If one or zero criteria were true, the scar that had only one transcript, or the scar that did not occur independently, were filtered out.
Genome_build: N/A
Supplementary_files_format_and_content: List of scar transcripts with cell barcode, scar name, cell type, scar probability and number of organisms that have this cell.

organism: Danio rerio

source_name: Primary pancreatic islet

extract_protocol:
Single cell dissociation.
10X Genomics Chromium

value: Zebrabow M

value: Primary pancreatic islet

value: Adult


title: C352A1

value: colon carcinoma


title: PA-TE_1


title: Hepa1c1c7_Empty

description: Gene expression of Hepa1c1c7 transfected empty vector


title: C352A2


title: Heart 3 scar

source_name: Heart and blood

value: Heart and blood


title: Pancreas 3 exo scar

source_name: Pancreas except primary islet, liver

value: Pancreas except primary islet, liver


title: Brain 3 scar

source_name: Brain

value: Brain


title: brass_med_post_2

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

institute: University of Minnesota Duluth

description: Medial nectary post-secretory replicate 2

data_processing:
Contigs assembled with Trinity v.2.3
Reads aligned to contigs using NCBI blastn
Contigs matched to closest Brassica rapa and Arabidopsis thaliana mRNA sequences
Genome_build: Brassica rapa from NCBI, downloaded 6/9/2016; Arabidopsis thaliana from Araport 11 build 201606
Supplementary_files_format_and_content: Brassica_juncea_to_Brassica_rapa.xls, a spreadsheet with mapped normalized counts

organism: Brassica juncea

source_name: Medial nectary post-secretory

extract_protocol: Illumina’s Truseq RNA Preparation v2 kit (RS-122-2001)

value: Nectary


title: WT3

value: DGCR8[delta]CTT + WT DGCR8 rescue


title: brass_med_post_3

description: Medial nectary post-secretory replicate 3


title: WT2


title: WT1


title: Pancreas 3 exo mRNA

description:
Single cell RNA-seq
PolyA RNA
Read type of raw data files: R1 is technical read, R2 is biological read.
Processed data file: genes.tsv

data_processing:
Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2.
Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 of publication.
Genome_build: GRCz10 - release 90
Supplementary_files_format_and_content: *_matrix.mtx: Single-cell transcript count table; *_barcodes.tsv: List of cell barcodes.


title: P351A3


title: brass_med_post_1

description: Medial nectary post-secretory replicate 1


title: Pancreas 3 endo mRNA


title: dCCT_HCT116

description: normalised_expression_values_WT_dCTT.csv

value: Functional KO of DGCR8 by deleting CTT domain using CRISPR-Cas9


title: WT_HCT116

source_name: Wild type, parental HCT116 cells

value: Wild type, parental HCT116 strain


title: Heart 3 mRNA


title: brass_med_sec_2

description: Medial nectary secretory replicate 2

source_name: Medial nectary secretory


title: PA-TE+PTEN KD_1

value: reference RNA


title: brass_med_sec_3

description: Medial nectary secretory replicate 3


title: brass_med_sec_1

description: Medial nectary secretory replicate 1


title: Brain 3 mRNA


title: Brain 1 mRNA

description:
Single cell RNA-seq
PolyA RNA
Processed data file: genes.tsv

data_processing:
Alignment and transcript counting of libraries were done using Cell Ranger 2.0.2.
Cell numbers to be extracted were set at a minimum of 6000 but were increased if there were substantially more cells with more than 500 unique transcripts. Exact numbers can be found in Supplementary Table 1 in publication.
Every sequencing read consists of a cellular barcode, a UMI, and a transcript sequence originating from an mRNA molecule. These transcript sequences were aligned using bwa aln3 with setting '-q 50' to a reference transcriptome constructed from Ensembl release 74 (www.ensembl.org) with extended 3' UTR regions. We filtered out all unmapped reads and all reads that were not uniquely mapped. After alignment, we determined which cellular barcodes corresponded to cells. We defined a cell to be a cellular barcode with at least five hundred uniquely mapped molecules.
For each cellular barcode, we counted the number of molecules mapped to each gene, using the UMI-correction method described by Grün et al. This method corrects for the possibility of the same UMI being used for two different transcripts in the same cell with the formula t = -K ln(1 – k_o/K), with t the final number of transcripts, k_o the observed UMIs, and K the total number of UMIs possible.
As protection against barcode sequencing errors, we counted the occurrence of each nucleotide for each barcode and filtered out barcodes in which one nucleotide occurred ten or more times. Furthermore, we filtered out barcodes that were one nucleotide substitution removed from a barcode with at least eight times as many transcripts.
Genome_build: GRCz10 - release 90
Supplementary_files_format_and_content: *_matrix.mtx: Single-cell transcript count table; *_barcodes.tsv: List of cell barcodes.


title: Heart 2 mRNA


title: Pancreas 2 mRNA

source_name: Pancreas and liver

value: Pancreas and liver


title: brass_med_pre_3

description: Medial nectary pre-secretory replicate 3

source_name: Medial nectary pre-secretory


title: brass_med_pre_2

description: Medial nectary pre-secretory replicate 2


title: Heart 1 mRNA


title: brass_med_pre_1

description: Medial nectary pre-secretory replicate 1


title: Pancreas 1 mRNA


title: Larva F1_2 scar

description:
PolyA RNA
Read type of raw data files: R1 is technical read, R2 is biological read.

data_processing:
Library strategy: Targeted amplification
Scar reads have the same structure as transcript reads: they consist of a barcode, a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped, had an incorrect barcode, or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences.
To correct for sequencing errors, we implemented several rounds of scar filtering (Supplementary Fig. 2 in publication). We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step, we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step, we aimed to remove easily recognizable sequencing errors. To this end, we consecutively considered scar sequences that have the same cellular barcode and UMI, UMIs that have the same cellular barcode and scar sequence, and cellular barcodes that have the same UMI and scar sequence. In each step, we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI, or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus, but information about scar expression levels was not required in our downstream analysis.
In the third filtering step, we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?, Do both scars occur in cells independently from each other?, Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true, the scars were kept and the sequences were placed on a list of validated scars that, if they occurred in the same cell in another library, did not have to be tested anymore. If one or zero criteria were true, the scar that had only one transcript, or the scar that did not occur independently, were filtered out.
Genome_build: N/A
Supplementary_files_format_and_content: List of scar transcripts with CIGAR, cell name, cell barcode and UMI sequence.

source_name: Full organism

value: Whole body

value: Larva


title: Larva F1_1 scar


title: Heart 2 scar

description:
Targeted amplification
PolyA RNA
Processed data file: A6_scars_compared.csv

data_processing:
Library strategy: Targeted amplification
Scar reads have the same structure as transcript reads: they consist of a barcode, a UMI and a scar. The scar sequences were aligned using bwa mem6 to a reference of RFP. We defined a cell as a barcode with at least 500 reads. We removed reads that were unmapped, had an incorrect barcode, or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and filtered out shorter sequences.
To correct for sequencing errors, we implemented several rounds of scar filtering (Supplementary Fig. 2 in publication). We started by counting the number of times each molecule was sequenced. Sequencing errors will typically have fewer reads than the actual scars they originate from. As a first filtering step, we therefore removed all molecules only seen once to reduce the complexity in the dataset for consecutive filtering steps. In the second filtering step, we aimed to remove easily recognizable sequencing errors. To this end, we consecutively considered scar sequences that have the same cellular barcode and UMI, UMIs that have the same cellular barcode and scar sequence, and cellular barcodes that have the same UMI and scar sequence. In each step, we kept only the molecule with the highest number of reads. The rationale behind this is that it is very improbable to have two valid scar sequences in the same cell with the same UMI, or to have a scar sequence with the same UMI appear in two different cells. The observation of two different UMIs for the same scar in the same cell is much more likely and corresponds to detection of multiple transcripts from the same locus, but information about scar expression levels was not required in our downstream analysis.
In the third filtering step, we specifically targeted sequencing errors within each cell. We compared the scar sequences found within a cell to each other. We filtered out sequences that had a Hamming distance of 2 or less to another scar sequence in the same cell that occurred in at least eight times as many reads. Scar sequences in the same cell that were one Hamming distance apart but had a read ratio less than eight were tested on three criteria if both of them occurred at least twice in the scar library: Do both scars have more than one transcript?, Do both scars occur in cells independently from each other?, Do the UMIs of both scars have Hamming distance of two or more? If two of these criteria were true, the scars were kept and the sequences were placed on a list of validated scars that, if they occurred in the same cell in another library, did not have to be tested anymore. If one or zero criteria were true, the scar that had only one transcript, or the scar that did not occur independently, were filtered out.
In the fourth filtering step, we determined the distribution of reads for the scars we had kept so far. Based on this distribution, we set a cut-off and filtered out the scars that did not have at least this number of reads. Finally, for each cell type, we determined the distribution of different scars seen per cell and set a maximum number of scars a cell of that type can have. We filtered out cells in which we observed more than this maximum number as possible doublets.
Genome_build: N/A
Supplementary_files_format_and_content: List of scar transcripts with cell barcode, scar name, cell type, scar probability and number of organisms that have this cell.


title: brass_lat_post_2

description: Lateral nectary post-secretory replicate 2

source_name: Lateral nectary post-secretory


title: ecoli_termseq_rep2

city: Rehovot

first: Daniel

last: Dar

address: 234 Herzl St

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
Library strategy: Term-seq
Illumina sequencing and standard base calling
Alignment to the E.coli genome with NovoAlign (Novocraft) V3.02.02 with default parameters, discarding reads that mapped to more than one genomic position
Genome_build: CP009273
Supplementary_files_format_and_content: Genomic position, strand, number of 3' ends in rep1, rep2, rep3 (There is a header line)

organism: Escherichia coli

source_name: Bacterial RNA

growth_protocol: Bacteria were cultured in LB media under aerobic conditions at 37°C until OD=0.5

extract_protocol:
Standard RNA isolation
RNA 3' end sequencing

tag: strain


title: ecoli_termseq_rep3


title: ecoli_termseq_rep1


title: Larva F1_2 mRNA


title: brass_lat_post_1

description: Lateral nectary post-secretory replicate 1


title: Pancreas 2 scar


title: Heart 1 scar

description:
Targeted amplification
PolyA RNA
Processed data file: A5_scars_compared.csv


title: 188725L: Human HCC noncancerous tissue3

city: Jingmen

first: Qian

last: Zhu

state: Hubei

address: 67 Xiangshan Avenue

department: Department of Hepatobiliary Surgery

country: China

institute: Jingmen First People's Hospital

description: gene expression in Human HCC noncancerous tissue3

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts.

source_name: HCC noncancerous tissue3

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. 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 utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

extract_protocol: Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C.

treatment_protocol: RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis or Agilent 2100 Bioanalyzer

value: Liver

value: male

tag: age

tag: tissue type

value: resection


title: 189554T: Human HCC tissue4

description: gene expression in Human HCC tissue4

source_name: HCC tissue4


title: Larva F1_1 mRNA

value: Zebrabow M


title: 189618T: Human HCC tissue5

description: gene expression in Human HCC tissue5

source_name: HCC tissue5

value: female


title: brass_lat_post_3

description: Lateral nectary post-secretory replicate 3


title: 187694N: Human HCC noncancerous tissue2

description: gene expression in Human HCC noncancerous tissue2

source_name: HCC noncancerous tissue2


title: 188725T: Human HCC tissue3

description: gene expression in Human HCC tissue3

source_name: HCC tissue3


title: brass_lat_sec_3

description: Lateral nectary secretory replicate 3

source_name: Lateral nectary secretory


title: 189554L: Human HCC noncancerous tissue4

description: gene expression in Human HCC noncancerous tissue4

source_name: HCC noncancerous tissue4


title: 189618L: Human HCC noncancerous tissue5

description: gene expression in Human HCC noncancerous tissue5

source_name: HCC noncancerous tissue5


title: 187444T: Human HCC tissue1

description: gene expression in Human HCC tissue1

source_name: HCC tissue1


title: 187694T: Human HCC tissue2

description: gene expression in Human HCC tissue2

source_name: HCC tissue2


title: Larva 5 scar


title: Brain 1 scar

source_name: Brain

value: Adult


title: Pancreas 1 scar


title: 187444N: Human HCC noncancerous tissue1

description: gene expression in Human HCC noncancerous tissue1

source_name: HCC noncancerous tissue1


title: CNP53_KO

description:
Gene expression of hypertrophic zone purified from rat tibiae.
The CNP53-treated growth plate from C-type natriuretic peptide knocked out rat (F344/Stm).

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Rat GE 8x60K Ver. 2 Microarray (G4858A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 074036_D_F_20150914) to obtain background subtracted and spatially detrended Processed Signal intensities. Each chip was then normalized to the 75th percentile of the measurements taken from that chip. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CNP53, KO

treatment_protocol: Tibiae from E18.5 embryonic rat were isolated and pre-cultured in BGJb media for 1 day, followed by culturing in the presence of vehicle or CNP53 (100 ng/mL) for 1 day.

tag: genotype/variation

value: C-type natriuretic peptide knockout

value: hypertrophic zone from tibiae


title: brass_lat_pre_3

description: Lateral nectary pre-secretory replicate 3

source_name: Lateral nectary pre-secretory


title: Larva 4 scar

source_name: Full organism


title: Bulk scar probabilities

description: Targeted amplification

data_processing:
Library strategy: Targeted amplification
We aligned DNA-amplified reads of thirty-two embryos to a reference of RFP. We filtered out unmapped reads and reads that did not start with the exact PCR primer, and truncated all reads to one hundred nucleotides, removing shorter ones. To determine the creation probabilities of the different scars, we removed all unscarred RFP reads from each embryo. We normalized the scar content of each embryo to one and calculated scar probabilities as the average ratio with which each scar was observed.
To account for the slightly different sequencing read structure of single cell and bulk scar detection (see above), we considered only the nucleotides that are shared between the two approaches, and we assigned the bulk scar probabilities to single cell scars accordingly. Since scars with a high creation probability contain little lineage information, we conservatively removed all scars for which we cannot determine the probability in bulk. We filtered out all single cell scars that were not detected in bulk experiments and that were partially soft-clipping, meaning they contained nucleotides that cannot be aligned to RFP or identified as insertions or single nucleotide polymorphisms. Single cell scars that were not detected in bulk but that did not have any soft-clipping nucleotides are indeed detectable, so we set their probability to the lowest probability value detected in bulk.
Genome_build: N/A
Supplementary_files_format_and_content: List of scar sequences with probabilities.

extract_protocol:
Trizol extraction of DNA.
CEL-seq

value: Embryo


title: brass_lat_sec_1

description: Lateral nectary secretory replicate 1

value: Nectary


title: Larva 5 mRNA

description:
Single cell RNA-seq
PolyA RNA
Read type of raw data files: R1 is technical read, R2 is biological read.
Processed data file: genes.tsv


title: Time-course 10h24h mRNA

description:
Targeted amplification
PolyA RNA

data_processing:
Library strategy: Targeted amplification
Embryos were injected with Cas9 and sgRNA at the 1-cell stage. After 1, 2, 3, 4, 6, 8, 10, and 24 hours, 2-3 embryos were collected and RNA and/or DNA were extracted using TRIzol Reagent according to the manufacturer’s protocols. Bulk scar libraries were produced similarly to the bulk libraries for the scar probabilities. For each sample, we calculated the percentage of unscarred RFP. We fit a negative exponential to this data, assuming that the fraction of unscarred RFP at t=0 was one.
Genome_build: N/A
Supplementary_files_format_and_content: List of scar sequences with CIGAR and cell barcode.

extract_protocol:
Trizol extraction of RNA.
CEL-seq

tag: time point


title: Larva 4 mRNA


title: Time-course 3h6h8h mRNA

description:
Targeted amplification
PolyA RNA


title: brass_lat_pre_2

description: Lateral nectary pre-secretory replicate 2


title: brass_lat_sec_2

description: Lateral nectary secretory replicate 2


title: Larva 3 mRNA

description:
Single cell RNA-seq
PolyA RNA
Read type of raw data files: R1 is biological read, R2 and R3 are technical reads.
Processed data file: genes.tsv


title: Vehicle_KO

description:
Gene expression of hypertrophic zone purified from rat tibiae.
The growth plate from C-type natriuretic peptide knocked out rat (F344/Stm).

source_name: Vehicle, KO

value: Vehicle


title: brass_lat_pre_1

description: Lateral nectary pre-secretory replicate 1


title: Hepa1c1c7_Slpi

description: Gene expression of Hepa1c1c7 transfected Slpi vector

value: liver


title: brass_leaf_3

description: Leaf replicate 3

source_name: Leaf

value: Leaf


title: Time-course 8h10h24h DNA

description: Targeted amplification


title: Larva 2 mRNA

description:
Single cell RNA-seq
PolyA RNA
Processed data file: genes.tsv


title: Time-course 3h4h6h DNA

description: Targeted amplification


title: placenta-small fetus-normal MCDA

city: Hangzhou

first: Jun

last: Lin

address: No. 1 Xueshi Road, Uptown District

institute: Department of Obstetrics, The Women’s Hospital, School of Medicine, Zhejiang University

description:
Gene expression in nor MCDA small fetus C2placenta
C2

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human miRNA (8*60K，Design ID: 046064)for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: placenta, normal MCDA small fetus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Fresh placenta tissuse get from Siugr fetus and normal MCDA fetus by Cesarean-section, we collected the cord insert regions of the placenta in the marternal side, sample size was 2*2*1cm,then put in samples tubes into nitrogen canister immediaterly

value: placenta, cord insert region, maternal side

tag: tissue status

value: normal MCDA

tag: fetus gender

tag: fetus weight

tag: gestation weeks


title: brass_leaf_2

description: Leaf replicate 2


title: placenta-big fetus-normal MCDA

description:
Gene expression in nor MCDA big fetus C1 placenta
C1

source_name: placenta, normal MCDA big fetus


title: Larva 1 mRNA

value: Whole body


title: placenta-small fetus-sIUGR2

description:
Gene expression in sIUGR small fetus B2 placenta
B2

source_name: placenta, sIUGR2 small fetus


title: Larva 1 scar

description:
Targeted amplification
PolyA RNA

value: Larva


title: placenta-big fetus-sIUGR2

description:
Gene expression in sIUGR big fetus B1 placenta
B1

source_name: placenta, sIUGR2 big fetus


title: Time-course 1h2h DNA

description: Targeted amplification


title: brass_leaf_1

description: Leaf replicate 1


title: placenta-big fetus-sIUGR1

description:
Gene expression in sIUGR big fetusA1 placenta
A1

source_name: placenta, sIUGR1 big fetus


title: placenta-small fetus-sIUGR1

description:
Gene expression in sIUGR small fetusA2 placenta
A2

source_name: placenta, sIUGR1 small fetus


title: MS-PCX066AB-CD4

status: Public on Apr 03 2018

city: NY

first: Achillefs

last: Ntranos

state: New York

address: 5 E 98th St, CGD MS Center, 1st floor

institute: Icahn School of Medicine at Mount Sinai

description: CD4 T cells

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina InfiniumEPIC Human Methylation Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner setting

data_processing: R studio. methylated and unmethylated signal intensities with detection p-values are included in the file GEOrawintensities.csv on the series record.  The file GEOmatrixprocessed.csv contains Average Beta values and detection p-values.

label: cy3 and cy5

source_name: CD4 T cells

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted with QIAamp DNA Blood Mini Kit (Qiagen)

tag: cell type

value: CD4 T cells

tag: diagnosis

value: Multiple sclerosis (MS)

tag: age (years)

tag: gender

value: M

tag: race

value: Caucasian

tag: therapy

value: FAE

tag: disease duration (months)

tag: cd4 percentage

tag: ccr6-ccr4+ percentage

tag: ccr6+ccr4+ percentage

tag: ccr6+ccr4- percentage


title: MS-PCX068AB-CD4

description: CD4 T cells

value: Black


title: MS-PCX071AB-CD4

description: CD4 T cells

value: F


title: MS-PCX074AB-CD4

description: CD4 T cells


title: MS-PCX073AB-CD4

description: CD4 T cells


title: MS-PCX061AB-CD4

description: CD4 T cells


title: MS-PCX072AB-CD4

description: CD4 T cells

value: Hispanic


title: MS-PCX067AB-CD4

description: CD4 T cells


title: MS-PCX065AB-CD4

description: CD4 T cells

value: GA


title: MS-PCX064AB-CD4

description: CD4 T cells


title: MS-PCX059AB-CD4

description: CD4 T cells


title: MS-PCX056AB-CD4

description: CD4 T cells


title: MS-PCX057AB-CD4

description: CD4 T cells


title: MS-PCX063AB-CD4

description: CD4 T cells


title: MS-PCX058AB-CD4

description: CD4 T cells


title: MS-PCX055AB-CD4

description: CD4 T cells


title: MS-PCX050AB-CD4

description: CD4 T cells


title: MS-PCX048AB-CD4

description: CD4 T cells


title: MS-PCX054AB-CD4

description: CD4 T cells


title: MS-PCX069AB-CD4

description: CD4 T cells


title: MS-PCX070AB-CD4

description: CD4 T cells


title: MS-PCX047AB-CD4

description: CD4 T cells


title: MS-PCX042AB-CD4

description: CD4 T cells


title: MS-PCX040AB-CD4

description: CD4 T cells


title: MS-PCX039AB-CD4

description: CD4 T cells


title: MS-PCX035AB-CD4

description: CD4 T cells

value: Asian


title: MS-PCX062AB-CD4

description: CD4 T cells


title: MS-PCX036AB-CD4

description: CD4 T cells


title: MS-PCX030AB-CD4

description: CD4 T cells


title: MS-PCX033AB-CD4

description: CD4 T cells


title: MS-PCX029AB-CD4

description: CD4 T cells


title: MS-PCX024AB-CD4

description: CD4 T cells


title: MS-PCX023AB-CD4

description: CD4 T cells


title: MS-PCX028AB-CD4

description: CD4 T cells


title: MS-PCX019AB-CD4

description: CD4 T cells


title: MS-PCX015AB-CD4

description: CD4 T cells


title: MS-PCX016AB-CD4

description: CD4 T cells


title: MS-PCX010AB-CD4

description: CD4 T cells


title: MS-PCX011AB-CD4

description: CD4 T cells


title: MS-PCX013AB-CD4

description: CD4 T cells


title: MS-PCX009AB-CD4

description: CD4 T cells


title: MS-PCX005AB-CD4

description: CD4 T cells


title: MS-PCX051AB-CD4

description: CD4 T cells


title: MS-PCX004AB-CD4

description: CD4 T cells


title: MS-PCX037AB-CD4

description: CD4 T cells


title: MS-PCX001AB-CD4

description: CD4 T cells


title: MS-PCN7055AB-CD4

description: CD4 T cells

value: Naive


title: MS-PCN7054AB-CD4

description: CD4 T cells


title: MS-PCX002AB-CD4

description: CD4 T cells


title: MS-PCN7057AB-CD4

description: CD4 T cells


title: MS-PCN7053AB-CD4

description: CD4 T cells


title: MS-PCN7056AB-CD4

description: CD4 T cells


title: MS-PCN7051AB-CD4

description: CD4 T cells


title: MS-PCN7052AB-CD4

description: CD4 T cells


title: MS-PCX034AB-CD4

description: CD4 T cells


title: MS-PCX014AB-CD4

description: CD4 T cells


title: MS-PCN7049AB-CD4

description: CD4 T cells


title: MS-PCN7046AB-CD4

description: CD4 T cells


title: MS-PCN7050AB-CD4

description: CD4 T cells


title: MS-PCN7048AB-CD4

description: CD4 T cells


title: MS-PCN7045AB-CD4

description: CD4 T cells


title: MS-PCX008AB-CD4

description: CD4 T cells


title: MS-PCN7043AB-CD4

description: CD4 T cells


title: MS-PCN7042AB-CD4

description: CD4 T cells


title: MS-PCN7040AB-CD4

description: CD4 T cells


title: MS-PCN7036AB-CD4

description: CD4 T cells


title: MS-PCN7041AB-CD4

description: CD4 T cells


title: MS-PCN7037AB-CD4

description: CD4 T cells


title: MS-PCN7037CB-CD4

description: CD4 T cells


title: MS-PCN7038AB-CD4

description: CD4 T cells


title: MS-PCN7035AB-CD4

description: CD4 T cells


title: MS-PCN7033AB-CD4

description: CD4 T cells


title: MS-PCN7034AB-CD4

description: CD4 T cells


title: MS-PCN7029AB-CD4

description: CD4 T cells


title: MS-PCN7030AB-CD4

description: CD4 T cells


title: MS-PCN7031AB-CD4

description: CD4 T cells


title: MS-PCN7032AB-CD4

description: CD4 T cells


title: MS-PCN7028AB-CD4

description: CD4 T cells


title: MS-PCN7027AB-CD4

description: CD4 T cells


title: MS-PCN7026AB-CD4

description: CD4 T cells


title: MS-PCN7047AB-CD4

description: CD4 T cells


title: MS-PCN7025AB-CD4

description: CD4 T cells


title: MS-PCN7024AB-CD4

description: CD4 T cells


title: MS-PCN7023AB-CD4

description: CD4 T cells


title: MS-PCN7044AB-CD4

description: CD4 T cells


title: MS-PCN7021AB-CD4

description: CD4 T cells


title: MS-PCN7039AB-CD4

description: CD4 T cells


title: MS-PCN7020AB-CD4

description: CD4 T cells


title: MS-PCN7023DB-CD4

description: CD4 T cells


title: MS-PCN7019AB-CD4

description: CD4 T cells


title: MS-PCN7018DB-CD4

description: CD4 T cells


title: MS-PCN7017AB-CD4

description: CD4 T cells


title: MS-PCN7013AB-CD4

description: CD4 T cells


title: MS-PCN7013CB-CD4

description: CD4 T cells


title: MS-PCN7011DB-CD4

description: CD4 T cells


title: MS-PCN7012AB-CD4

description: CD4 T cells


title: MS-PCN7027CB-CD4

description: CD4 T cells


title: MS-PCN7009DB-CD4

description: CD4 T cells


title: MS-PCN7011AB-CD4

description: CD4 T cells


title: MS-PCN7009AB-CD4

description: CD4 T cells


title: MS-PCN7007AB-CD4

description: CD4 T cells


title: MS-PCN7010AB-CD4

description: CD4 T cells


title: MS-PCN7006AB-CD4

description: CD4 T cells


title: MS-PCN7008AB-CD4

description: CD4 T cells


title: MS-PCN7003AB-CD4

description: CD4 T cells


title: MS-PCN7005AB-CD4

description: CD4 T cells


title: MS-PCN7022AB-CD4

description: CD4 T cells


title: MS-PCN7002AB-CD4

description: CD4 T cells


title: MS-PCN7001AB-CD4

description: CD4 T cells


title: MS-PCN7016AB-CD4

description: CD4 T cells


title: Pre-enriched-2

city: Philadelphia

first: Erica

last: Carpenter

state: PA

address: #8-104, 3400 Civic Center Blvd

department: Hematology and Oncology

institute: University of Pennsylvania

description: PD798_enrich_workflow_WTA_processed_data.txt

data_processing:
Base-calling from integrated Illumina's NextSeq software; trimming and FASTQ generation from default lllumina's BaseSpace workflow (Workflow and Analysis Software Version 2.6.17.15)
Multilane FASTQ files for a sample were merged into single R1 and R2 FASTQ files using a custom script.
Reads were aligned with 2-pass alignment using STAR version 2.52 and default settings; counts were generated with the software featureCounts.
Features were filtered such that at least two samples had counts of 5 or greater; each sample was upper-quartile normalized using the R package EDASeq 2.10.0.
Counts were converted to TPM.  Briefly, RPK was calculated by dividing gene counts by gene length.  To derive scaling factors for each sample, RPK were summed for all genes.  Each sample was then divided by the scaling factor and multiplied by 1e6 to generate Transcripts Per Million.
Genome_build: mm10
Supplementary_files_format_and_content: Gene IDs and filtered, unlogged, TPM for each sample

source_name: Cell line

growth_protocol: PD798 cells were cultured in DMEM + 10% FBS for 48-72h prior to dissociation and cell sorting

extract_protocol:
Bulk RNA was extracted using the Qiagen RNeasy Mini Extraction kit as per manufacturer's protocol.
Libraries were prepared from cell lysate or bulk RNA according to manufacturers' instructions.  cDNA was synthesized and amplified using Takara Clontech SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (PN 634891).  Takara Clontech Low Input Library Prep Kit HT was used to dual index samples and amplify libraries for sequencing (PN 634900).

treatment_protocol: Cells were spiked into normal mouse blood and sorted for single cell analysis.

tag: cell line

value: Pancreatic ductal adenocarcinoma

tag: cell number input

value: Bulk

tag: flow treatment

value: Pre-enrichment -> BD Influx


title: E2F1 at 200 nM concentration

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to 200 or 100 nM in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Alexa-488-conjugated rabbit polyclonal antibody to GST (Invitrogen) was diluted to 50 μg/ml in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-488-conjugated antibody (488 nm ex, 522 nm em) using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices), bad spots were manually flagged and removed, and data from multiple Alexa 488 scans of the same slide were combined using masliner (MicroArray LINEar Regression) software.

data_processing: To correct for any possible non-uniformities in protein binding, we adjusted the Alexa488 (or Alexa647) signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber. For each unique sequence represented on the array, we then calculated the median over replicate spots, applying a natural logarithm transformation, and then normalized the signal to the [0,1] range.

label: Alexa 647

molecule: protein

source_name: Human E2f1

label_protocol: Proteins were tagged with GST by cloning. Protein-bound arrays were incubated with Alexa-488-conjugated rabbit polyclonal antibody to GST (Life Technologies, A11001). For the E2f1_200nM experiment, an anti-E2f1 antibody was used (Santa Cruz Biotechnologies, SC-193), followed by a seconday, Alexa647-conjugated antibody (Life Technologies, A21244).

growth_protocol: The Life Technologies Gateway cloning system was used to insert full length human E2f1, E2f3, and E2f4 genes into the pET-60 destination vector with a C-terminal GST tag. Cells were grown in LB culture to an OD600 of 0.4, then protein expression was induced with 1mM IPTG at 30°C for 2hrs (E2f1), or 20°C overnight (E2f4). Pelleted cells were frozen, then thawed cells were lysed in PBS lysis buffer for two hours at 4°C while gently rocking. The lysate was centrifuged, and the protein was recovered from the soluble lysate using a GE GSTrap FF GST tag affinity column according to manufacturer’s instructions.       This vector enables the production of N-terminally GST-tagged proteins. Cells were grown in LB broth to an OD600 of 0.4 to 0.6 and then expression was induced with IPTG at 30° to 37° C. Pelleted cells were frozen, stored at -20 C, and thawed cells were lysed with lysozyme.

extract_protocol: GST-tagged protein was purified from the soluble portion of the lysate using a GE GSTrap FF GST tag affinity column according to manufacturer’s instructions.

tag: transcription factor

tag: protein concentration

value: Protein concentration:200nM


title: E2F1 at 250 nM concentration

label: Alexa 488

value: Protein concentration:250nM


title: Pre-FACS-3

value: Pre-experiment, no treatment


title: Pre-enriched-3


title: E2F4 at 500 nM concentration

source_name: Human E2f4

value: Protein concentration:500nM


title: E2F3 at 250 nM concentration

source_name: Human E2f3


title: Pre-enriched-1


title: Pre-FACS-1


title: FACS-only-3

value: BD Influx


title: MS-PCN7018AB-CD4

description: CD4 T cells

value: CD4 T cells

value: Multiple sclerosis (MS)

value: M


title: Pre-FACS-2


title: FACS-only-2


title: Mock-1

value: None, benchtop


title: Mock-3


title: 100-6

description: PD798_single_cell_WTA_processed_data.txt


title: Mock-2


title: 100-5


title: RNA-1


title: MS-PCX025AB-CD4

description: CD4 T cells

value: F

value: Caucasian


title: 100-4


title: 100-2


title: E2F4 at 800 nM concentration

value: Protein concentration:800nM


title: 100-1


title: 10-4


title: 100-3


title: 10-2


title: 10-8


title: 10-6


title: 10-7


title: 10-11


title: RNA-2


title: 10-9


title: 10-10


title: 10-3


title: SC-11


title: SC-9


title: SC-6


title: 10-1


title: 10-12


title: SC-10


title: SC-1


title: SC-7


title: FACS-only-1


title: SC-5


title: SC-4


title: SC-3


title: combo

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

data_processing:
Use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC: RNA concentration, RIN value,28S/18S and the fragment length distribution
Use internal software SOAPnuke to filter reads
Use hisat2 to map to mm10 genome
Map clean reads to reference using Bowtie2, and then calculate gene expression level with RSEM
Detect DEGs with PossionDis
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including RPKM/FPKM values for each Sample

source_name: TIL

growth_protocol: 1 million E.G7 were inoculated subcutaneously into 6-8 wk female mice on Day 0

extract_protocol:
On Day 21, OVA-specific CD8+ TILs from E.G7-bearing WT and B7S1 KO mice (6 mice per group), or PD-1+Tim-3-B7S1R+(B7S1R_SP), PD-1+Tim-3+B7S1R-(TIM-3_SP), PD-1+Tim-3-B7S1R-(DN) CD8+ TILs from E.G7-bearing WT or B7S1 KO mice were sorted into lysis buffer using BD FACSAria Cell Sorter.
cDNA was made and library was constructed using SMARTer Ultra Low Input RNA for Illumina Sequencing-HV kit and Creator SMART cDNA Library Construction Kit (Clontech) according to manufacturer’s instructions.

tag: strain

tag: tissue

value: tumor

tag: age

tag: genotype

value: wild type


title: anti_PD1


title: G9a_KO_rep2_me3

city: Saint Louis

first: Takeshi

last: Egawa

address: 660 South Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

data_processing:
Fastq file was groomed.
Sequence tags were mapped onto the NCBI37 mm9 genome with bowtie.
Homer Peak calling was used to determine peaks.
Homer Annotatepeaks.pl was used to annotate peaks.
Peaks were visualized using Cluster3 and treeviewer.
Genome_build: mm9
Supplementary_files_format_and_content: Peak files

source_name: CD8+ T cells

extract_protocol:
Native ChIP was performed. Nuclei  from cultured CD8 T cells was extracted with 50mM Tris, 1mM CaCl2, 0.2% Triton, and proteinase inhibitors. Then nuclei were subjected to micrococcal nuclease digestion for 5min. Soluble chromatin was used for input and immunoprecipitation with anti-H3K9me3 (ab8898).
DNA was prepped by Genome Technology Access Center using standard ChIP library prep for Illumina.

value: spleen

tag: cell type

value: T cell

tag: antibody


title: G9a_KO_rep2_input


title: G9a_KO_rep1_me3


title: anti_B7S1


title: G9a_KO_rep1_input


title: 10-5

value: Pancreatic ductal adenocarcinoma

value: Pre-enrichment -> BD Influx


title: SC-8


title: WT_rep2_me3


title: SC-2


title: DN_KO

value: B7S3 KO


title: WT_rep1_input


title: Control


title: WT_rep1_me3


title: KO

value: B7S1 KO


title: B7S1R_SP_KO


title: TIM-3_SP_KO

value: B7S2 KO


title: B7S1R_SP_WT_2


title: WT


title: DN_WT_2


title: TIM-3_SP_WT_2


title: DN_WT_1


title: TIM-3_SP_WT_1


title: B7S1R_SP_WT_1


title: IL4pos_nonTFH_rep_2

city: Cambridge

first: Vinay

middle: S

last: Mahajan

state: MA

address: 65 Landsdowne Street

institute: Brigham and Women's Hospital

data_processing:
FASTQ files were obtained using the Illumina demultiplexing pipeline.
RSEM (1.2.29) was used to align to the hg38 reference and to calculate the expected counts for genes.
Transcripts per million (TPM) values were then median normalized and differential expression analysis was performed using EBSeq.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files with expected counts, TPM and FPKM

source_name: Tonsil

extract_protocol:
RNA extract protocol not provided.
Whole transcriptome amplification and tagmentation-based library preparation were performed using the SMART-seq2 approach (Trombetta JJ et al. Curr Protoc Mol Biol. 2014) followed by sequencing on an Illumina NextSeq-500 instrument.

value: IL4-positive non-TFH

tag: cell markers

value: CD4+ C45RA- CXCR5- IL4+

value: Tonsil


title: IL4pos_nonTFH_rep_1


title: IL4neg_TFH_rep_2

value: IL4-negative TFH

value: CD4+ C45RA- CXCR5+ PD1+ IL4-


title: IL4pos_TFH_rep_2

value: IL4-positive TFH

value: CD4+ C45RA- CXCR5+ IL4+


title: IL4pos_TFH_rep_1


title: Naive_CD4_rep_2

value: CD45RA+ Naive

value: CD4+ CD45RA+


title: M1382 - inguinal white adipose tissue (ingWAT) - LoxP

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneAtlas Fluidics Station (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneAtlas Imaging station scanner (Affymetrix, Santa Clara, CA)

data_processing: RMA normalization method as implemented in affy Bioconductor R package

source_name: ingWAT - LoxP

label_protocol: 8 µg of cDNA was subsequently fragmented and labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: The TP53INP2 KOUbc mouse line was generated by crossing homozygous TP53INP2loxP/loxP mice with a mouse strain expressing Cre recombinase (Ubc CRE-ERT2). To generate the experimental groups, 2-month-old mice, both those expressing UbcCre-ERT2 TP53INP2loxP/loxP and their non-expressing UbcCre-ERT2 TP53INP2loxP/loxP littermates, were fed a tamoxifen diet.  Four-month-old male mice were used in this experiment. Mice had a C57BL/6J pure genetic background.

extract_protocol: RNA was isolated using Trizol / RNeasy method (Qiagen RNeasy mini kit (#74104)). Library preparation and amplification were performed using Ovation RNA Amp System V (Nugen;3100-60)

treatment_protocol: Inguinal white adipose tissue from mice were used in this experiment.

tag: strain background

tag: genotype/variation

value: LoxP; control

tag: gender

value: male

value: 4 months

tag: litter

value: inguinal white adipose tissue (ingWAT)

tag: biological replicate


title: IL4neg_TFH_rep_1


title: M1379 - inguinal white adipose tissue (ingWAT) - KO

source_name: ingWAT - KO

value: KO; TP53INP2-deficient


title: M1369 - inguinal white adipose tissue (ingWAT) - LoxP


title: M1381 - inguinal white adipose tissue (ingWAT) - KO


title: M1371 - inguinal white adipose tissue (ingWAT) - KO


title: Naive_CD4_rep_1


title: M1382 - perigonadal white adipose tissue (pgWAT) - LoxP

description: Sample 8

treatment_protocol: Perigonadal white adipose tissue from mice were used in this experiment.


title: M1368 - inguinal white adipose tissue (ingWAT) - KO


title: M1381 - perigonadal white adipose tissue (pgWAT) - KO

description: Sample 7


title: SPAR-Seq of multi-exon regions of 50 genes in CGR8, Phf13 knockdown (T1247), replicate 2

city: Toronto

first: Ulrich

last: Braunschweig

state: Ontario

address: 160 College Street

department: Donnelly Centre

country: Canada

institute: University of Toronto

description:
Forward (i5) barcode: AGATCGTC, reverse (i7) barcode: GAGTCTGT
KnockdownAnnotation.tab
ScreenJuncUp.20-77.fa
ScreenJuncDn.20-77.fa
ScreenEvents_junctions.tab
PSI.SSMD.CGR8.tab
Reads_perEvent_CGR8.tab
Expression.CGR8.treatments.tab

data_processing:
CASAVA 1.8 was used for base calling.
Fastq files contain demultiplexed reads which were assigned to the appropriate treatment by matching to expected forward and reverse barcodes (sequenced in dedicated reads; not supplied).
Forward and reverse event reads were mapped to custom junction libraries representing all expected splice variants (supplied as processed files), using bowtie with settings --best -v 3 -k 1 --trim3 26 --trim5 20. Trimming was done to remove lower-quality, uninformative ends and because forward reads had a missing base call at position 11 due to a power outage. Junction libraries were first constructed from NCBIm37/mm9 gene annotations, and then refined based on the results of de novo mapping of the reads from one full Illumina lane from each cell line using tophat (default settings with -i 40 and providing Ensembl transcript annotations for NCBIm37), after quality trimming (minimum MAPQ of 33) from the 3'-end with the fastx toolkit. Mapped reads were counted per junction.
Alternative splicing analysis: Percent-spliced-in (PSI) values were calculated for each alternative exon, or part thereof in the case of alternative 5'-/3'-splice sites ('event'), from read tallies as follows: PSI was calculated independently from forward and reverse reads as the percentage of reads supporting inclusion divided by the total number of reads for the event. For alternative 5'/3'-ss events that were part of an alternative exon (Foxm1.A2, Mta1.A1, Uspl1.A3), the PSI was instead calculated with reference to the total reads supporting inclusion of that exon in order to assess independent regulation of alternative splice site usage. Only the read direction in which all reads unambiguously supported either inclusion or exclusion of an event was used, and the average if that applied for both. Exploratory analysis revealed that PSI values showed low-level batch effects per 96-well plate which we moderated by subtracting a weighted plate median in which negative controls (siNT and mock treatment) were given 20x more weight than other samples. To derive variances, and because PSI values are not nearly normally distributed but roughly follow a beta distribution, we elected to fit a beta distribution to each pair of replicate treatments, as well as to all negative controls from both replicates, using maximum-likelihood fitting as implemented in the fitdistr() function from the R package MASS {Venables & Ripley, Modern Applied Statistics with S (2002)}. Iterative optimization of shape parameters was initiated with settings x=PSI, shape1=1, shape2=1, method=”L-BFGS-B”, lower=0.01, and upper=mean number of reads supporting each PSI value. A modified Strictly Standardized Mean Difference (SSMD {Zhang, Genomics (2007)}) was then calculated based on the formula: SSMD = (μt – μc)/SQRT(vart + varc) where μt and μc are the means (corresponding to the PSI), and vart and varc the variances of the beta distributions fitted to the treatment replicates and negative controls, respectively. Events for which not all reads from at least one direction were informative (Mff.A2, Tead1.A2) were excluded from further analysis, as were events in individual treatments with less than 20 reads in one or both replicates (~9% of all event x treatment combinations). Additionally, the following events were removed from further splicing analysis: expression only events or constitutive exons, Fgf4, Gapdh, Srpk2, Srrm4; events with consistently low read counts: Atg13.A1, H2afy.A2, Tcf7l1 (N2A only), Dnmt3b (N2A only); or because measured inclusion was biased by differential length of isoforms:, Fgfr1, Sall4.
Expression analysis: Read counts from all splice variants of each gene were used to estimate relative mRNA expression levels, reads per million reads (RPMs). Differential expression analysis based on raw read counts was performed using the generalized linear models workflow from the R package edgeR. Plate, position (edge/interior) and treatment were used as design factors (where all treatments of each type of control were treated as replicates.) Models fitted using estimateDisp() to estimate the common, trended, and tag-wise dispersion for the CGR8 and N2A data separately. Subsequently, differences attributable to treatment, plate, or position contrasts were extracted with glmLRT() and represented as log2-fold changes with associated FDR. Fold-changes for treatments are relative to the siNT and mock-treatment controls.
Genome_build: NCBIm37/mm9
Supplementary_files_format_and_content: Processed files are either tab-delimited  tables (.tab) or FASTA files (.fa). KnockdownAnnotation.tab contains treatment annotations and well/plate positions. ScreenJuncUp.20-77.tab and ScreenJuncDn.20-77.tab contain the custom junction upstream and downstram junction libraries, respectively, and ScreenEvent_junctions.tab contains the information which junctions were used to calculate PSI for each event. PSI.SSMD.CGR8.tab and PSI.SSMD.N2A.tab contain raw PSI of each replicate and final SSMD. Reads_perEvent_CGR8.tab and Reads_perEvent_N2A.tab contain raw read counts on which expression analyis was based, and Expression.CGR8.treatments.tab and Expression.N2A.treatments.tab contain modeled relative abundance and fold-change with associated FDR for each treatment type.

source_name: Embryonic stem cells

growth_protocol: CGR8 mouse embryonic stem cells (ESCs) were cultured as described previously on gelatin-coated plates (Gabut et al., Cell (2011), Han  et al., Nature (2013)). Mouse neuroblastoma (N2A) cells were grown in DMEM supplemented with 10% FBS, sodium pyruvate, MEM non-essential amino acids, and penicillin/streptomycin. All cell lines were maintained at 37°C with 5% CO2.

extract_protocol:
Forty-eight hours post-transfection, total RNA were purified from cultured cells using RNeasy Plus 96 Kit (Qiagen), as per the manufacturer’s instructions.
For each sample, a multiplex RT-PCR assay was first applied to simultaneously amplify 50 AS and/or expression events in a single reaction. The multiplex RT-PCR reaction was carried out in 96-well plates using the OneStep RT-PCR kit (Qiagen) as recommended by the manufacturer, with the following changes: reactions were performed in a volume of 20 uL with 2 uL of the purified total RNA as input, and a mixture of 50 pairs of primers was added to each reaction with a final concentration of 0.25 uM for each individual forward and reverse primer. Four identical Veriti 96-well Thermal Cyclers (Applied Biosystems) were used with the following conditions: 50°C for 30 minutes, 95°C for 15 minute, 30 cycles of 94°C for 40 seconds, 58°C for 1 minute (slow ramp rate), 72°C for 3 minutes, and a final extension step at 72°C for 10 minutes. Two sets of barcodes were incorporated into forward and reverse primers, respectively, after the universal adaptors and added to the amplicons in the second PCR reaction to allow demultiplexing all reads that were derived from a particular treatment. Primers sequences were: forward primer, AATGATACGGCGACCACCGAGATCTACACNNNNNNNNACACTCTTTCCCTACACGACGCTCTTCCGATCT (N denotes i5 barcode); reverse primer, CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT (N denotes i7 primer). The second PCR was performed using Phusion High-Fidelity DNA Polymerase (Thermo Scientific), as per the manufacturer’s instructions. For each 20 uL of reaction, 1 uL of the multiplex RT-PCR reaction products was used as templates. The thermal cycling conditions were as follows: 98°C for 30 seconds, 15 cycles of 98°C for 10 seconds, 65°C for 30 seconds, 72°C for 30 seconds, and a final extension step at 72°C for 5 minutes. The resulting libraries were pooled and sequenced.

treatment_protocol: Twenty-four hours prior to transfection, CGR8 and N2A cells were seeded in 96-well plates, 3000 and 5000 cells per well, respectively. Cells were transfected with the SMARTpool siRNAs at 50 nM final concentration using DharmaFECT1 reagent (Dharmacon), as recommended by the manufacturer.

tag: cell line


title: M1368 - perigonadal white adipose tissue (pgWAT) - KO

description: Sample 3


title: M1371 - perigonadal white adipose tissue (pgWAT) - KO

description: Sample 5


title: M1379 - perigonadal white adipose tissue (pgWAT) - KO

description: Sample 6


title: M1369 - perigonadal white adipose tissue (pgWAT) - LoxP

description: Sample 4


title: M1360 - perigonadal white adipose tissue (pgWAT) - LoxP

description: Sample 2


title: M1360 - inguinal white adipose tissue (ingWAT) - LoxP


title: Equine satellite cells pre-incubated with HMB vs equine satellite cells without HMB_2

city: Warsaw

first: Tomasz

last: Sadkowski

address: Nowoursynowska 159

department: Department of Physiological Sciences

country: Poland

institute: Warsaw University of Life Sciences - SGGW

description: Biological replicate 2 of 4. HMB pre-incubated and hydrogen peroxide-treated equine satellite cells_Cy5 vs. Equine satellite cells without HMB treatment_Cy3_rep1

hyb_protocol: On each two-colour microarray 825 ng of cRNA from HMB pre-incubated and hydrogen peroxide exposed cells (Cy5) and 825 ng of cRNA from control cells-exposed to hydrogen peroxide without HMB pre-incubation (Cy3) were hybridized using Gene Expression Hybridization Kit (Agilent Technologies, USA) according to the manufacturers protocol. RNA Spike In Kit (Agilent Technologies, USA) was used as an internal control.

scan_protocol: Acquisition and analysis of hybridization intensities were performed using the Agilent DNA microarray scanner and Agilent Feature Extraction software 10.7.3.1. according to the standard manufacturer’s procedures and Linar & LOWESS normalization.

data_processing: The statistical analysis was performed using Gene Spring 13 software default protocol (Agilent Technologies, USA). The statistical significance of the differences was evaluated using student test (p<0.05) and fold change FC>1.3. A multiple testing correction was performed using Benjamini and Hochberg False Discovery Rate (FDR) ≤0.05.

organism: Equus caballus

source_name: HMB and H2O2-treated equine satellite cells_Cy5

label_protocol: Low Input Quick Amp Labeling Kit (Agilent Technologies, USA) was used to amplify and label target RNA to generate complementary RNA (cRNA).

growth_protocol: Equine satellite cells were cultured in Primaria culture flask (BD, USA). The growth medium (10%FBS/10%HS/DMEM/AB) was changed every two days. On the 10th day of proliferation cells were transferred to Collagen I Cellware 6-well plate. After obtaining 80% of confluency proliferation medium was replaced by differentiation medium (2%HS/DMEM/AB). FBS - fetal bovine serum, HS - horse serum, DMEM - Dulbecco's Modified Eagle Medium, AB - antibiotics: 1% Penicillin-Streptomycin, 0.5% Amphotericin B.

extract_protocol: Total RNA was isolated according to the protocol supplied with the miRNeasy Mini Kit (Qiagen, USA). RNA quantity was measured spectrophotometrically using NanoDrop (NanoDrop Technologies, USA). The analysis of final RNA quality and integrity was performed with BioAnalyzer 2100 (Agilent Technologies, USA). To ensure optimal data quality only RNA samples with RIN number ≥ 9.2 were included into the analysis.

treatment_protocol: After the 2nd day of differentiation equine satellite cells were pre-incubated with HMB (50 µM) for 24h and exposed to hydrogen peroxide (3mM, last hour during 24h pre-incubation with HMB).

tag: differentiation day

value: 3rd day of differentiation

tag: satellite cell origin

value: m. semitendinosus

source_name: Equine satellite cells exposed to H2O2 without HMB treatment_Cy3


title: Adipocyte  - 3T3-L1 cell line (VFI722)

hyb_protocol: Labeled DNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays were scanned with GeneChip scanner GSC3000 (Affymetrix, Santa Clara, CA)

source_name: Adipocyte  - 3T3-L1 cell line

label_protocol: Fragmentation and labelling were performed using Encode Biotin Module (Nugen; 4200-60)

growth_protocol: Preadipocytes were maintained in Proliferation medium.Two day post-confluent (T=0) cell were induced to diferentiate with Differentiation medium until T=7.

treatment_protocol: Preadipocytes were transduced with lentiviruses encoding scrambled or TP53INP2 siRNA sequences.

value: Adipose tissue

value: KD TP53INP2

tag: time

value: day 7 of differentiation

value: adipocyte

tag: replicate


title: M1359 - inguinal white adipose tissue (ingWAT) - LoxP


title: Equine satellite cells pre-incubated with HMB vs equine satellite cells without HMB_1

description: Biological replicate 1 of 4. HMB pre-incubated and hydrogen peroxide-treated equine satellite cells_Cy5 vs. Equine satellite cells without HMB treatment_Cy3_rep1


title: PLACEBO-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep6

description: Biological replicate 6 of 8. PLACEBO-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep1

hyb_protocol: For hybridization, Microarray Hybridization Chamber (Agilent, USA) and Hyb-Buffer (Agilent, USA) were used according to manufacturer protocol.

scan_protocol: Microarray Scanner (model G2565CA) with SureScan High-Resolution Technology (Agilent, USA). Microarray data were extracted, the background subtracted and LOWESS normalisation performed using the standard procedures contained in the Agilent Feature Extraction (FE) Software Version 10.7.3.1.

label_protocol: MiRNA Complete Labeling and Hyb Kit (Version 2.3, December 2010) (Agilent) was used for labeling, according to manufacturer protocol.

growth_protocol: Equine satellite cells were cultured in Primaria culture flask (BD, USA). The growth medium (10%FBS/10%HS/DMEM/AB) was changed every two days. On the 10th day of proliferation cells were transferred to Collagen I Cellware 6-well plate. After obtaining 80% of confluence proliferation medium was replaced by differentiation medium (2%HS/DMEM/AB). FBS - fetal bovine serum, HS - horse serum, DMEM - Dulbecco's Modified Eagle Medium, AB - antibiotics: 1% Penicillin-Streptomycin, 0.5% Amphotericin B.

extract_protocol: Total RNA was isolated according to the protocol supplied with the miRNeasy Mini Kit (Qiagen, USA). RNA quantity was measured spectrophotometrically using NanoDrop (NanoDrop Technologies, USA). The analysis of final RNA quality and integrity was performed with BioAnalyzer 2100 (Agilent Technologies, USA). To ensure optimal data quality only RNA samples with RIN number ≥ 9,2 were included into the analysis.

treatment_protocol: After the 2nd day of differentiation equine satellite cells were pre-incubated with HMB for 24h (50 µM) and exposed to hydrogen peroxide (3mM, last 1h during 24h pre-incubation with HMB).

tag: Stage


title: Equine satellite cells pre-incubated with HMB vs equine satellite cells without HMB_4

description: Biological replicate 4 of 4. HMB pre-incubated and hydrogen peroxide-treated equine satellite cells_Cy5 vs. Equine satellite cells without HMB treatment_Cy3_rep1


title: PLACEBO-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep3

description: Biological replicate 3 of 8. PLACEBO-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep1

tag: tissue


title: Equine satellite cells pre-incubated with HMB vs equine satellite cells without HMB_3

description: Biological replicate 3 of 4. HMB-preincubated and hydrogen peroxide-treated equine satellite cells_Cy5 vs. Equine satellite cells without HMB treatment_Cy3_rep1


title: Adipocyte  - 3T3-L1 cell line (VFI723)


title: PLACEBO-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep5

description: Biological replicate 5 of 8. PLACEBO-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep1


title: PLACEBO-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep4

description: Biological replicate 4 of 8. PLACEBO-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep1


title: PLACEBO-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep8

description: Biological replicate 8 of 8. PLACEBO-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep1


title: Adipocyte  - 3T3-L1 cell line (VFI724)


title: M1359 - perigonadal white adipose tissue (pgWAT) - LoxP

description: Sample 1

tag: age


title: PLACEBO-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep7

description: Biological replicate 7 of 8. PLACEBO-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep1


title: Adipocyte  - 3T3-L1 cell line (VFI721)


title: Adipocyte  - 3T3-L1 cell line (VF724)

value: Control


title: Adipocyte  - 3T3-L1 cell line (VF722)


title: WT_rep2_input

tag: strain

value: spleen

value: T cell


title: PLACEBO-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep2

description: Biological replicate 2 of 8. PLACEBO-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep1


title: HMB-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep8

description: Biological replicate 8 of 8. HMB-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep1


title: HMB-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep5

description: Biological replicate 5 of 8. HMB-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep1


title: HMB-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep6

description: Biological replicate 6 of 8. HMB-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep1


title: combo [ATAC-Seq]

data_processing:
Paired-end reads were mapped to the mm10 reference genome using Bowtie2. Only concordantly mapped pairs were kept for further analysis.
Peak calling was performed using MACS2 to identify areas of sequence tag enrichment.
BedTools was used to find common intersection between identified peaks (1bp minimum overlap) and to create a merged peak list.
ATAC-seq tag enrichment and DNA motif analysis across the merged peak list  were computed using HOMER (homer.salk.edu)
Genome_build: mm10
Supplementary_files_format_and_content: peak files with quantitative data for each Sample

extract_protocol:
On Day 21, OVA-specific CD8+ TILs were sorted using BD FACSAria Cell Sorter.
ATAC-seq DNA library was constructed using TruePrep DNA Library Prep Kit V2 for Illumina and TruePrep Index Kit V2 for Illumina.

treatment_protocol: control antibodies, 100μg anti-B7S1, 75μg anti-PD-1 (J43, Bioxcell) or 100μg anti-B7S1+ 75μg anti-PD-1 were injected i.p. every 3 days starting from Day 9.

value: tumor

tag: genotype

value: wild type


title: Preadipocyte  - 3T3-L1 cell line (VFI02)

source_name: Preadipocyte  - 3T3-L1 cell line

value: day 0 of differentiation

tag: cell type

value: preadipocyte


title: Preadipocyte  - 3T3-L1 cell line (VFI03)


title: Adipocyte  - 3T3-L1 cell line (VF723)


title: HMB-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep7

description: Biological replicate 7 of 8. HMB-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep1


description: Biological replicate 1 of 8. PLACEBO-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep1

source_name: PLACEBO-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep8


title: Preadipocyte  - 3T3-L1 cell line (VFCO3)


title: Adipocyte  - 3T3-L1 cell line (VF721)


title: anti_PD1 [ATAC-Seq]


title: Preadipocyte  - 3T3-L1 cell line (VFI01)


title: CCBS miRNA-Seq

city: Guangzhou

first: Ruixue

last: Chen

state: Guangdong

address: Huangpu Avenue West 601

department: School of Chinese Medicine

institute: Jinan University

data_processing:
Original images were transformed into raw reads by Base Calling.
Quality control of the reads was conducted.
The sequences of the same reads were combined to obtain the unique sequence.
The annotation of measured small RNAs was mapped to Rfam database.
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: TMM (trimmed means of M-values method) to standardize read count data obtained in the analysis of miRNA expression level, then applied DEGseq to do the difference analysis using a Benjamini q-value of 0.001 as the cut-off (corrected p-value < 0.001), combined with fold change (FC) > 2 (value indicated the normalized count of samples)

source_name: human umbilical vein endothelial cells

growth_protocol: CRL-1730 HUVECs (ATCC, USA) were cultured in culture flasks (1 × 105/ml, 25 ml) in Dulbecco's modified Eagle's medium (DMEM) (Gibco, USA) containing 10% fetal bovine serum (FBS) (Gibco, USA) for 24 hours at 37 °C plus 5% CO2.

extract_protocol:
The cells were digested in the culture flasks for 3 minutes with 1 ml TRIzol and the cells observed under an inverted microscope.
The small RNA library (140~160 bp) was constructed by Illumina Truseq Small RNA. The human small RNA sequence analysis was performed by the Hiseq2000 platform with 1 * 51 bp.

treatment_protocol: Then a 10% serum of QDBS, QSBS, CCBS, HABS, NBS and NC was added to 6 culture flasks for 24 hours. Finally, the cell models of QDBS, QSBS, CCBS, HABS, NBS and NC were established.

value: CRL-1730 human umbilical vein endothelial cells


title: NC miRNA-Seq


title: HABS miRNA-Seq


title: NBS miRNA-Seq


title: anti_B7S1 [ATAC-Seq]


title: HMB-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep2

description: Biological replicate 2 of 8. HMB-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep1


title: HMB-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep4

description: Biological replicate 4 of 8. HMB-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep1


title: HMB-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep3

description: Biological replicate 3 of 8. HMB-treated (24h) differentiated equine satellite cells_exposed to H2O2 (1h)_rep1