title: 425675: WT_Striatum_male_rep2 [miRNA]

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

description:
Q175B1783_02_Left_Striatum
miRNA
425675_Q175B1783_02_Left_Striatum_L7.LB23
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling.
Genome mapped via Omicsoft OSA 4.0.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using fastq-mcf sequence quality filter, clipping and processor with following settings for Omicsoft: Trimming  /Mode=TrimByQuality /ReadTrimQuality=2; Options  /ParallelJobNumber=4 /PairedEnd=True /FileFormat=FASTQ /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /WriteReadsInSeparateFiles=True /GenerateSamFiles=False /ThreadNumber=6 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=False /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False;
Genome_build: Genome version Mouse.mm10, gene models version Ensembl.R78
Supplementary_files_format_and_content: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx: Excel file includes Count values for each Sample.
Supplementary_files_format_and_content: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx: Excel file includes FPKM values for each Sample.

source_name: Corpus striatum of left cerebral hemisphere

growth_protocol: Housed with Wild Type and Het z_Q175 KI mice.

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the miQiagen RNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: background

value: Wild Type

tag: Sex

value: male

value: 6 months

value: Striatum


title: CAL70_3

status: Public on Dec 19 2018

type: RNA

city: MADRID

first: ROBERTO

last: MARTIN-HERNANDEZ

address: CANTOBLANCO

department: BIOSTATISTICS AND BIOINFORMATICS UNIT

country: Spain

institute: IMDEA ALIMENTACION

hyb_protocol: 1.5 ug 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 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°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 (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Homo sapiens

source_name: MIA PaCa-2 after 48h marigold 70 µg/mL

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions

extract_protocol: Total RNA was isolated from each condition with RNeasy Mini Kit (Qiagen Iberica) following manufacturer´s instructions. RNA quality and quantity were checked by UV spectroscopy (Nanodrop 2000 Spectrophotometer, Thermo Scientific, Waltham).

tag: treatment

value: 48h marigold 70 µg/mL

tag: cell line

value: MIA PaCa-2

tag: cell type

value: Commercial cell line derived from pancreatic cancer patient.


title: 425664: WT_Striatum_female_rep2 [miRNA]

type: SRA

country: USA

description:
Q175B1782_02_Left_Striatum
miRNA
425664_Q175B1782_02_Left_Striatum_L7.LB12
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

library_source: transcriptomic

organism: Mus musculus

tag: strain

tag: genotype

value: female

tag: age

tag: tissue


title: 425671: WT_Striatum_male_rep1 [miRNA]

description:
Q175B1783_01_Left_Striatum
miRNA
425671_Q175B1783_01_Left_Striatum_L7.LB19
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425680: WT_Striatum_female_rep3 [miRNA]

description:
Q175B1782_03_Left_Striatum
miRNA
425680_Q175B1782_03_Left_Striatum_L7.LB28
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425687: WT_Striatum_male_rep3 [miRNA]

description:
Q175B1783_03_Left_Striatum
miRNA
425687_Q175B1783_03_Left_Striatum_L8.LB35
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: CONTROL1

source_name: MIA PaCa-2 after 48h control (DMSO)

value: 48h control (DMSO)


title: GO1_sc13

city: Beijing

first: Fan

last: Guo

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

library_source: genomic

data_processing:
Process of sciCOOL-seq data: Data quality was checked and reads were mapped according to our recent publication (Guo F, Yan L, Guo H et al. The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells. Cell 2015; 161:1437-1452). Briefly, raw reads were trimmed and QC filtered before aligned to mouse reference genome (mm9). Duplicated reads were removed and only those non-duplicated ones were retained for further analysis.
Process of single-cell RNA seq data:Raw reads were firstly classified by cell barcodes on read2, then read1 were trimmed and aligned to the mm9 mouse transcriptome. After de-duplicated by UMIs information, the transcript copy numbers of each gene were counted. Single cells with less than 3,000 detected genes and 20,000 transcripts were excluded. And the retained 275 single cells were used for downstream analysis. Genes with averaged counts above 0.1 among all the retained single cells were used.
Genome_build: mm9
Supplementary_files_format_and_content:
scRNA-seq: mOocy_rna_rawCounts.txt contains abundance measurements;mOocy_rna_barcodes.txt contains sequences of barcodes used to split RNA fastq files to single cells
sciCOOL-seq: bigWig; *.gch.bw are bigwig files which included the methylation level of covered GCH (GCA,GCC,GCT) sites to estimate chromatin accessibility; *.wcg.bw are bigwig files which included the methylation level of covered WCG (ACG, TCG) sites to estimate DNA methylation.

molecule: genomic DNA

source_name: Growing Oocyte

extract_protocol:
All the animal procedures were carried out according to the ethical guidelines of Laboratory Animal Center of the Sichuan University. None-growing oocytes (NGO) with diameters less than 20μm were collected from 3- to 4-day-old female ICR mice. Growing oocytes (GO) and fully-growing oocytes (FGO) were collected from 3- to 4-week-old female ICR mice, the diameters of oocytes for each stage were: GO1 (30μm< diameters <45μm), GO2 (50μm< diameters <55μm), GO3 (60μm< diameters <65μm), FGO (diameters >70μm). Excessive washes were performed to remove the contamination of somatic cells from oocytes. Individual oocyte was then picked for the downstream single-cell experiments.
Firstly, individual oocyte was in vitro methylated by GpC methylase (New England Biolabs), digested by protease and bisulfite converted26. Then, the single-cell genomic DNA was randomly primed and dC tailed. The oligos with anchor sequences were then introduced to fragmented genomic DNA and PCR amplified. Finally, libraries were checked, pooled together and sequenced with paired-end 150-bp reads on Illumina HiSeq 4000 platform (Novogene).

value: ICR

value: wild type

value: Ovary

value: oocyte

tag: oocyte size

value: 30-45 microns


title: CONTROL3


title: 425739: WT_Liver_male_rep4 [miRNA]

description:
Q175B1783_04_Left_Liver
miRNA
425739_Q175B1783_04_Left_Liver_L2.LB16
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

source_name: Left lobe of liver

value: Liver


title: 425681: WT_Striatum_male_rep4 [miRNA]

description:
Q175B1783_04_Left_Striatum
miRNA
425681_Q175B1783_04_Left_Striatum_L7.LB29
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: S15_13-C3_S14-COL_day200b

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

country: United Kingdom

institute: Newcastle University

data_processing:
Demulitplex
C1 mRNA Seq HT Demultiplex Script
The fludigm mRNASeqHT_demultiplex.pl was used to demulitplex the fastq files into single cells.
Trimming
Trimmomatic version 0.33
trailing = 20, minlength = 60 and end = “PE
Alignment
STAR 2.4.0
Default parameters
Quantification
HTSEQ 0.6.
-f bam, -r name, -a 4, -i gene_id, -m union
Genome_build: Human reference genome GRCh38.p7 version 25 from GenCode
Supplementary_files_format_and_content: rawCounts.csv

molecule: polyA RNA

source_name: human ESC

growth_protocol: human ESC line (CRX-GFP) was expanded in mTeSR™1 (StemCell Technologies) at 37°C and 5% CO2 on 6 well plates pre-coated with Low Growth Factor Matrigel (Corning) as described in our previous publication (Collin et al. 2015, , Collin et al.Stem Cells. 2016 Feb;34:311-21) ). Differentiation to retinal organoids was performed as described in Mellough et al. 2015 (Stem Cells. 2015 Aug;33(8):2416-30) with minor modifications which included addition of 10µM Y27632 dihydrochloride for the first 48 hours of differentiation and 10% foetal calf serum, T3 (40 ng/ml; Sigma-Aldrich), Taurine (0.1 mM; Sigma-Aldrich) & Retinoic Acid (0.5 µM; Sigma-Aldrich) from day 18 of differentiation.

extract_protocol: Full length cDNA libraries were prepared using the Illumina Nextera XT DNA library preparation kit (Illumina). Libraries were pooled and sequenced (2 x 75 bp) on the Ilumina NextSeq 500 using a Mid Output v2 kit.

treatment_protocol: Retinal organoids were dissociated to single cells using the Embryoid Body Dissociation Kit (Miltenyi Biotech) following the manufacturer’s instructions. Single cells were loaded onto the C1 Single-Cell mRNA-Seq HT IFC [10-17 µm] (Fluidigm). Array Control RNA Spikes (Thermo Fisher Scientific) were prepared and added to lysis mix as described in the Fluidigm protocol. Cell lysis, reverse transcription and cDNA amplification were performed using the SMART-Seq v4 Ultra Low Input RNA Kit for the Fluidigm C1 System (Clontech).

tag: time point

value: Day 200 of retinal organoid differentiation

value: human ESC (CRX-GFP line)


title: GO1_sc14


title: 425750: WT_Liver_male_rep3 [miRNA]

description:
Q175B1783_03_Left_Liver
miRNA
425750_Q175B1783_03_Left_Liver_L2.LB27
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: Wild Type


title: 425679: WT_Striatum_female_rep1 [miRNA]

description:
Q175B1782_01_Left_Striatum
miRNA
425679_Q175B1782_01_Left_Striatum_L7.LB27
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425665: WT_Striatum_female_rep4 [miRNA]

description:
Q175B1782_04_Left_Striatum
miRNA
425665_Q175B1782_04_Left_Striatum_L7.LB13
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: CAL30_2

source_name: MIA PaCa-2 after 48h marigold 30 µg/mL

value: 48h marigold 30 µg/mL


title: GO1_sc12


title: 425734: WT_Liver_male_rep2 [miRNA]

description:
Q175B1783_02_Left_Liver
miRNA
425734_Q175B1783_02_Left_Liver_L1.LB11
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: male

value: 6 months


title: S14_13_C3-COL13_day90

value: Day 90 of retinal organoid differentiation


title: CAL70_1

value: 48h marigold 70 µg/mL

value: MIA PaCa-2


title: 425757: WT_Liver_male_rep1 [miRNA]

description:
Q175B1783_01_Left_Liver
miRNA
425757_Q175B1783_01_Left_Liver_L3.LB34
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: S16_13-C3_S18-COL9_day200a


title: GO1_sc11


title: 425759: WT_Liver_female_rep3 [miRNA]

description:
Q175B1782_03_Left_Liver
miRNA
425759_Q175B1782_03_Left_Liver_L3.LB36
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: female


title: 425745: WT_Liver_female_rep2 [miRNA]

description:
Q175B1782_02_Left_Liver
miRNA
425745_Q175B1782_02_Left_Liver_L2.LB22
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425752: WT_Liver_female_rep1 [miRNA]

description:
Q175B1782_01_Left_Liver
miRNA
425752_Q175B1782_01_Left_Liver_L3.LB29
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: GO1_sc9


title: S11_12-C2_S1-COL_day200b


title: 425727: WT_Cortex_male_rep1 [miRNA]

description:
Q175B1783_01_Left_Cortex
miRNA
425727_Q175B1783_01_Left_Cortex_L2.LB4
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

source_name: Cortex of left cerebral hemisphere

value: Cortex


title: S12_12-C2_S5-COL9_day200a


title: 425717: WT_Cortex_male_rep3 [miRNA]

description:
Q175B1783_03_Left_Cortex
miRNA
425717_Q175B1783_03_Left_Cortex_L1.LB30
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425712: WT_Cortex_female_rep3 [miRNA]

description:
Q175B1782_03_Left_Cortex
miRNA
425712_Q175B1782_03_Left_Cortex_L1.LB25
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: CAL70_2

value: Commercial cell line derived from pancreatic cancer patient.


title: 425701: WT_Cortex_female_rep4 [miRNA]

description:
Q175B1782_04_Left_Cortex
miRNA
425701_Q175B1782_04_Left_Cortex_L8.LB14
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: GO1_sc8

value: ICR

value: wild type


title: GO1_sc7

value: Ovary

value: oocyte


title: 425698: WT_Cortex_male_rep2 [miRNA]

description:
Q175B1783_02_Left_Cortex
miRNA
425698_Q175B1783_02_Left_Cortex_L8.LB10
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: S8_11-G2-6_S1-COL_day60

value: Day 60 of retinal organoid differentiation


title: S10_12_C2-COL12_day90


title: 425700: WT_Cortex_female_rep2 [miRNA]

description:
Q175B1782_02_Left_Cortex
miRNA
425700_Q175B1782_02_Left_Cortex_L8.LB13
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425676: WT_(neo-)_Striatum_male_rep3 [miRNA]

description:
Q175NM0011_03_Left_Striatum
miRNA
425676_Q175NM0011_03_Left_Striatum_L7.LB24
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

growth_protocol: Housed with Wild Type and Z_Q175 (neo-) KI mice.

value: Striatum


title: 425686: WT_(neo-)_Striatum_male_rep4 [miRNA]

description:
Q175NM0011_04_Left_Striatum
miRNA
425686_Q175NM0011_04_Left_Striatum_L8.LB34
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: S7_11-C1_S7-COL9_day200a

value: Day 200 of retinal organoid differentiation

value: human ESC (CRX-GFP line)


title: GO1_sc4

value: 30-45 microns


title: GO1_sc5


title: 425744: WT_Liver_female_rep4 [miRNA]

description:
Q175B1782_04_Left_Liver
miRNA
425744_Q175B1782_04_Left_Liver_L2.LB21
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: Wild Type

value: Liver


title: S13_13-B3-19_S19-COL_day60


title: 425690: WT_(neo-)_Striatum_male_rep2 [miRNA]

description:
Q175NM0011_02_Left_Striatum
miRNA
425690_Q175NM0011_02_Left_Striatum_L8.LB2
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: male

value: 6 months


title: 425719: WT_Cortex_male_rep4 [miRNA]

description:
Q175B1783_04_Left_Cortex
miRNA
425719_Q175B1783_04_Left_Cortex_L1.LB32
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425691: WT_(neo-)_Striatum_male_rep1 [miRNA]

description:
Q175NM0011_01_Left_Striatum
miRNA
425691_Q175NM0011_01_Left_Striatum_L8.LB3
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: S9_12-A3-20_S13-COL_day60


title: 425670: WT_(neo-)_Striatum_female_rep4 [miRNA]

description:
Q175NM0009_04_Left_Striatum
miRNA
425670_Q175NM0009_04_Left_Striatum_L7.LB18
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: GO1_sc3


title: GO1_sc6


title: S5_11_C1-COL11_day90

value: Day 90 of retinal organoid differentiation


title: GO1_sc1


title: GO1_sc2


title: S4_10-F2-7_S5-COL_day60


title: 425737: WT_(neo-)_Liver_male_rep3 [miRNA]

description:
Q175NM0011_03_Left_Liver
miRNA
425737_Q175NM0011_03_Left_Liver_L2.LB14
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: NGO_sc156

source_name: Non-Growing Oocyte

value: < 20 microns


title: 425674: WT_(neo-)_Striatum_female_rep2 [miRNA]

description:
Q175NM0009_02_Left_Striatum
miRNA
425674_Q175NM0009_02_Left_Striatum_L7.LB22
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: female


title: 425731: WT_(neo-)_Liver_male_rep4 [miRNA]

description:
Q175NM0011_04_Left_Liver
miRNA
425731_Q175NM0011_04_Left_Liver_L1.LB8
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: S2_10-D2_S11-COL9_day200a


title: S3_10-D2_S3-COL_day200b


title: 425699: WT_Cortex_female_rep1 [miRNA]

description:
Q175B1782_01_Left_Cortex
miRNA
425699_Q175B1782_01_Left_Cortex_L8.LB11
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: Cortex


title: 425743: WT_(neo-)_Liver_male_rep2 [miRNA]

description:
Q175NM0011_02_Left_Liver
miRNA
425743_Q175NM0011_02_Left_Liver_L2.LB20
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: NGO_sc155

value: ICR


title: GO1_sc10

value: wild type


title: 425758: WT_(neo-)_Liver_female_rep4 [miRNA]

description:
Q175NM0009_04_Left_Liver
miRNA
425758_Q175NM0009_04_Left_Liver_L3.LB35
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425732: WT_(neo-)_Liver_female_rep3 [miRNA]

description:
Q175NM0009_03_Left_Liver
miRNA
425732_Q175NM0009_03_Left_Liver_L1.LB9
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: NGO_sc154

value: Ovary


title: S1_10_D2-COL10_day90


title: S6_11-C1_S2-COL_day200b


title: 425746: WT_(neo-)_Liver_female_rep1 [miRNA]

description:
Q175NM0009_01_Left_Liver
miRNA
425746_Q175NM0009_01_Left_Liver_L2.LB23
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: EGF_rep3

city: Boston

first: Lorena

last: Pantano

state: MA

address: 655 Huntington Ave

department: Biostatistics

institute: Harvard Chan School of Public Health

data_processing:
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/)
Differential expression at the gene level were called with DESeq2 (Love, Huber, and Anders 2014), preferring to use counts per gene estimated from the Salmon quasialignments by tximport (Soneson, Love, and Robinson 2015). DEGreport was used for QC and clustering analysis (github.com/lpantano/DEGreport).
Genome_build: hg19
Supplementary_files_format_and_content: text file with TPM

source_name: Human proximal tubular epithelial cells

growth_protocol: HPTECs in passage 3 were seeded in collagen VI-coated 96 well plates in full medium. On day 1 full medium was replaced by EGF-free medium. On day 3 cells were either maintained in EGF-free medium (control) or submitted to hypoxia (1% of O2) for 24h.

extract_protocol:
Total RNA samples were isolated using RNeasy plus (Qiagen)
Libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer and the quality was assesed by Agilent TapeStation 2200. Uniquely indexed libraries were pooled in equimolar ratios and this pool was quantitated by qPCR then sequenced on two Illumina HiSeq High-Output run with single-end 75bp reads.

treatment_protocol: After 24 hours of hypoxia-induced damage 1uM of ID-8; or 1uM of Harmine; or EGF (10ng/mL) were added to fresh EGF-free medium for 48 hours. Non-treated cells and control cells were kept in fresh EGF-free medium.

value: kidney

tag: passage

value: proximal tubular epithelial cells

tag: biological group

value: Damaged cells treated with EGF


title: 425713: WT_(neo-)_Cortex_male_rep4 [miRNA]

description:
Q175NM0011_04_Left_Cortex
miRNA
425713_Q175NM0011_04_Left_Cortex_L1.LB26
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: NGO_sc153

value: oocyte


title: 425728: WT_(neo-)_Liver_female_rep2 [miRNA]

description:
Q175NM0009_02_Left_Liver
miRNA
425728_Q175NM0009_02_Left_Liver_L1.LB5
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425682: WT_(neo-)_Striatum_female_rep3 [miRNA]

description:
Q175NM0009_03_Left_Striatum
miRNA
425682_Q175NM0009_03_Left_Striatum_L8.LB30
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: Striatum


title: EGF_rep2


title: NGO_sc152


title: 425673: WT_(neo-)_Striatum_female_rep1 [miRNA]

description:
Q175NM0009_01_Left_Striatum
miRNA
425673_Q175NM0009_01_Left_Striatum_L7.LB21
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425696: WT_(neo-)_Cortex_male_rep3 [miRNA]

description:
Q175NM0011_03_Left_Cortex
miRNA
425696_Q175NM0011_03_Left_Cortex_L8.LB8
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425721: WT_(neo-)_Cortex_male_rep2 [miRNA]

description:
Q175NM0011_02_Left_Cortex
miRNA
425721_Q175NM0011_02_Left_Cortex_L1.LB34
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425751: WT_(neo-)_Liver_male_rep1 [miRNA]

description:
Q175NM0011_01_Left_Liver
miRNA
425751_Q175NM0011_01_Left_Liver_L2.LB28
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: EGF_rep1


title: 425708: WT_(neo-)_Cortex_male_rep1 [miRNA]

description:
Q175NM0011_01_Left_Cortex
miRNA
425708_Q175NM0011_01_Left_Cortex_L1.LB21
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425711: WT_(neo-)_Cortex_female_rep2 [miRNA]

description:
Q175NM0009_02_Left_Cortex
miRNA
425711_Q175NM0009_02_Left_Cortex_L1.LB24
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: NGO_sc150


title: 425705: WT_(neo-)_Cortex_female_rep1 [miRNA]

description:
Q175NM0009_01_Left_Cortex
miRNA
425705_Q175NM0009_01_Left_Cortex_L8.LB18
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: Harmine_rep3

value: Damaged cells treated with Harmine


title: 425685: Het_z_Q175_KI_Striatum_female_rep4 [miRNA]

description:
Q175B1785_04_Left_Striatum
miRNA
425685_Q175B1785_04_Left_Striatum_L8.LB33
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: Het z_Q175 KI


title: 425716: WT_(neo-)_Cortex_female_rep4 [miRNA]

description:
Q175NM0009_04_Left_Cortex
miRNA
425716_Q175NM0009_04_Left_Cortex_L1.LB29
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: Wild Type


title: 425702: WT_(neo-)_Cortex_female_rep3 [miRNA]

description:
Q175NM0009_03_Left_Cortex
miRNA
425702_Q175NM0009_03_Left_Cortex_L8.LB15
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: NGO_sc151


title: Harmine_rep2


title: ID-8_rep3

value: Damaged cells treated with ID-8


title: Harmine_rep1


title: 425666: Het_z_Q175_KI_Striatum_female_rep2 [miRNA]

description:
Q175B1785_02_Left_Striatum
miRNA
425666_Q175B1785_02_Left_Striatum_L7.LB14
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: 6 months


title: NGO_sc149


title: 425677: Het_z_Q175_KI_Striatum_female_rep1 [miRNA]

description:
Q175B1785_01_Left_Striatum
miRNA
425677_Q175B1785_01_Left_Striatum_L7.LB25
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425692: Het_z_Q175_KI_Striatum_female_rep3 [miRNA]

description:
Q175B1785_03_Left_Striatum
miRNA
425692_Q175B1785_03_Left_Striatum_L8.LB4
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425684: Het_z_Q175_KI_Striatum_male_rep2 [miRNA]

description:
Q175B1784_02_Left_Striatum
miRNA
425684_Q175B1784_02_Left_Striatum_L8.LB32
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: male


title: NGO_sc147

value: < 20 microns


title: NGO_sc146


title: 425683: Het_z_Q175_KI_Striatum_male_rep4 [miRNA]

description:
Q175B1784_04_Left_Striatum
miRNA
425683_Q175B1784_04_Left_Striatum_L8.LB31
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425669: Het_z_Q175_KI_Striatum_male_rep1 [miRNA]

description:
Q175B1784_01_Left_Striatum
miRNA
425669_Q175B1784_01_Left_Striatum_L7.LB17
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: ID-8_rep2


title: 425689: Het_z_Q175_KI_Striatum_male_rep3 [miRNA]

description:
Q175B1784_03_Left_Striatum
miRNA
425689_Q175B1784_03_Left_Striatum_L8.LB1
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: ID-8_rep1


title: 425738: Het_z_Q175_KI_Liver_female_rep1 [miRNA]

description:
Q175B1785_01_Left_Liver
miRNA
425738_Q175B1785_01_Left_Liver_L2.LB15
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: female

value: Liver


title: Hypoxia_rep2

value: Damaged non treated cells


title: NGO_sc145

value: ICR

value: wild type


title: 425749: Het_z_Q175_KI_Liver_male_rep4 [miRNA]

description:
Q175B1784_04_Left_Liver
miRNA
425749_Q175B1784_04_Left_Liver_L2.LB26
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425753: Het_z_Q175_KI_Liver_female_rep4 [miRNA]

description:
Q175B1785_04_Left_Liver
miRNA
425753_Q175B1785_04_Left_Liver_L3.LB30
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425754: Het_z_Q175_KI_Liver_female_rep3 [miRNA]

description:
Q175B1785_03_Left_Liver
miRNA
425754_Q175B1785_03_Left_Liver_L2.LB31
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: Hypoxia_rep3

value: kidney


title: NGO_sc148

value: Ovary


title: Hypoxia_rep1

value: proximal tubular epithelial cells


title: NGO_sc144

value: oocyte


title: NGO_sc143


title: EGF free_rep3

value: Undamaged cells


title: 425733: Het_z_Q175_KI_Liver_male_rep3 [miRNA]

description:
Q175B1784_03_Left_Liver
miRNA
425733_Q175B1784_03_Left_Liver_L1.LB10
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: NGO_sc141


title: NGO_sc142


title: EGF free_rep2


title: 425748: Het_z_Q175_KI_Liver_male_rep2 [miRNA]

description:
Q175B1784_02_Left_Liver
miRNA
425748_Q175B1784_02_Left_Liver_L2.LB25
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425756: Het_z_Q175_KI_Liver_male_rep1 [miRNA]

description:
Q175B1784_01_Left_Liver
miRNA
425756_Q175B1784_01_Left_Liver_L3.LB33
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425709: Het_z_Q175_KI_Cortex_female_rep4 [miRNA]

description:
Q175B1785_04_Left_Cortex
miRNA
425709_Q175B1785_04_Left_Cortex_L1.LB22
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: Cortex


title: 425755: Het_z_Q175_KI_Liver_female_rep2 [miRNA]

description:
Q175B1785_02_Left_Liver
miRNA
425755_Q175B1785_02_Left_Liver_L3.LB32
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: Het z_Q175 KI


title: 425724: Het_z_Q175_KI_Cortex_female_rep2 [miRNA]

description:
Q175B1785_02_Left_Cortex
miRNA
425724_Q175B1785_02_Left_Cortex_L1.LB1
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425715: Het_z_Q175_KI_Cortex_female_rep3 [miRNA]

description:
Q175B1785_03_Left_Cortex
miRNA
425715_Q175B1785_03_Left_Cortex_L1.LB28
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: EGF free_rep1


title: NGO_sc140


title: NGO_sc139


title: 425710: Het_z_Q175_KI_Cortex_male_rep4 [miRNA]

description:
Q175B1784_04_Left_Cortex
miRNA
425710_Q175B1784_04_Left_Cortex_L1.LB23
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425726: Het_z_Q175_KI_Cortex_female_rep1 [miRNA]

description:
Q175B1785_01_Left_Cortex
miRNA
425726_Q175B1785_01_Left_Cortex_L1.LB3
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: NGO_sc138


title: 425723: Het_z_Q175_KI_Cortex_male_rep2 [miRNA]

description:
Q175B1784_02_Left_Cortex
miRNA
425723_Q175B1784_02_Left_Cortex_L1.LB36
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: NGO_sc137


title: 425718: Het_z_Q175_KI_Cortex_male_rep3 [miRNA]

description:
Q175B1784_03_Left_Cortex
miRNA
425718_Q175B1784_03_Left_Cortex_L1.LB31
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425693: Het_Z_Q175_(neo-)_KI_Striatum_female_rep2 [miRNA]

description:
Q175NM0012_02_Left_Striatum
miRNA
425693_Q175NM0012_02_Left_Striatum_L8.LB5
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: Het Z_Q175 (neo-) KI

value: Striatum


title: 425720: Het_z_Q175_KI_Cortex_male_rep1 [miRNA]

description:
Q175B1784_01_Left_Cortex
miRNA
425720_Q175B1784_01_Left_Cortex_L1.LB33
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: 6 months


title: 425668: Het_Z_Q175_(neo-)_KI_Striatum_male_rep3 [miRNA]

description:
Q175NM0010_03_Left_Striatum
miRNA
425668_Q175NM0010_03_Left_Striatum_L7.LB16
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: male


title: NGO_sc135

value: < 20 microns


title: NGO_sc136


title: 425678: Het_Z_Q175_(neo-)_KI_Striatum_female_rep3 [miRNA]

description:
Q175NM0012_03_Left_Striatum
miRNA
425678_Q175NM0012_03_Left_Striatum_L7.LB26
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: female


title: 425694: Het_Z_Q175_(neo-)_KI_Striatum_male_rep4 [miRNA]

description:
Q175NM0010_04_Left_Striatum
miRNA
425694_Q175NM0010_04_Left_Striatum_L8.LB6
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425688: Het_Z_Q175_(neo-)_KI_Striatum_female_rep4 [miRNA]

description:
Q175NM0012_04_Left_Striatum
miRNA
425688_Q175NM0012_04_Left_Striatum_L8.LB36
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: NGO_sc132


title: 425736: Het_Z_Q175_(neo-)_KI_Liver_female_rep4 [miRNA]

description:
Q175NM0012_04_Left_Liver
miRNA
425736_Q175NM0012_04_Left_Liver_L2.LB13
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx

value: Liver


title: 425735: Het_Z_Q175_(neo-)_KI_Liver_female_rep3 [miRNA]

description:
Q175NM0012_03_Left_Liver
miRNA
425735_Q175NM0012_03_Left_Liver_L2.LB12
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425730: Het_Z_Q175_(neo-)_KI_Liver_female_rep2 [miRNA]

description:
Q175NM0012_02_Left_Liver
miRNA
425730_Q175NM0012_02_Left_Liver_L1.LB7
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425740: Het_Z_Q175_(neo-)_KI_Liver_male_rep4 [miRNA]

description:
Q175NM0010_04_Left_Liver
miRNA
425740_Q175NM0010_04_Left_Liver_L2.LB17
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: NGO_sc131


title: 425695: Het_Z_Q175_(neo-)_KI_Striatum_male_rep2 [miRNA]

description:
Q175NM0010_02_Left_Striatum
miRNA
425695_Q175NM0010_02_Left_Striatum_L8.LB7
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425741: Het_Z_Q175_(neo-)_KI_Liver_male_rep2 [miRNA]

description:
Q175NM0010_02_Left_Liver
miRNA
425741_Q175NM0010_02_Left_Liver_L2.LB18
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425707: Het_Z_Q175_(neo-)_KI_Cortex_female_rep3 [miRNA]

description:
Q175NM0012_03_Left_Cortex
miRNA
425707_Q175NM0012_03_Left_Cortex_L8.LB20
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425725: Het_Z_Q175_(neo-)_KI_Cortex_female_rep2 [miRNA]

description:
Q175NM0012_02_Left_Cortex
miRNA
425725_Q175NM0012_02_Left_Cortex_L1.LB2
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425704: Het_Z_Q175_(neo-)_KI_Cortex_female_rep4 [miRNA]

description:
Q175NM0012_04_Left_Cortex
miRNA
425704_Q175NM0012_04_Left_Cortex_L8.LB17
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: NGO_sc130


title: 425742: Het_Z_Q175_(neo-)_KI_Liver_male_rep3 [miRNA]

description:
Q175NM0010_03_Left_Liver
miRNA
425742_Q175NM0010_03_Left_Liver_L2.LB19
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: NGO_sc129


title: NGO_sc128


title: 425747: Het_Z_Q175_(neo-)_KI_Liver_male_rep1 [miRNA]

description:
Q175NM0010_01_Left_Liver
miRNA
425747_Q175NM0010_01_Left_Liver_L2.LB24
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425697: Het_Z_Q175_(neo-)_KI_Cortex_male_rep4 [miRNA]

description:
Q175NM0010_04_Left_Cortex
miRNA
425697_Q175NM0010_04_Left_Cortex_L8.LB9
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425703: Het_Z_Q175_(neo-)_KI_Cortex_female_rep1 [miRNA]

description:
Q175NM0012_01_Left_Cortex
miRNA
425703_Q175NM0012_01_Left_Cortex_L8.LB16
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: NGO_sc134


title: NGO_sc127


title: 425672: Het_Z_Q175_(neo-)_KI_Striatum_female_rep1 [miRNA]

description:
Q175NM0012_01_Left_Striatum
miRNA
425672_Q175NM0012_01_Left_Striatum_L7.LB20
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425714: Het_Z_Q175_(neo-)_KI_Cortex_male_rep2 [miRNA]

description:
Q175NM0010_02_Left_Cortex
miRNA
425714_Q175NM0010_02_Left_Cortex_L1.LB27
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: NGO_sc126


title: NGO_sc133


title: 425706: Het_Z_Q175_(neo-)_KI_Cortex_male_rep1 [miRNA]

description:
Q175NM0010_01_Left_Cortex
miRNA
425706_Q175NM0010_01_Left_Cortex_L8.LB19
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: 425729: Het_Z_Q175_(neo-)_KI_Liver_female_rep1 [miRNA]

description:
Q175NM0012_01_Left_Liver
miRNA
425729_Q175NM0012_01_Left_Liver_L1.LB6
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: NGO_sc125


title: WT_Striatum_male_rep3 [mRNA]

description:
Q175B1783_03_Left_Striatum
mRNA
404228_Q175B1783_03_Left_Striatum_L16
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling.
Genome mapped via Omicsoft OSA 4.0.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using fastq-mcf sequence quality filter, clipping and processor with following settings for Omicsoft: Trimming /Mode=TrimByQuality /ReadTrimQuality=2; Options /ParallelJobNumber=4 /PairedEnd=True /FileFormat=FASTQ /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /WriteReadsInSeparateFiles=True /GenerateSamFiles=False /ThreadNumber=6 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=False /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False;
Genome_build: Genome version Mouse.mm10, gene models version Ensembl.R78
Supplementary_files_format_and_content: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx: Excel file includes FPKM and Count values for each Sample.

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype/variation

value: Wild Type


title: WT_Striatum_male_rep1 [mRNA]

description:
Q175B1783_01_Left_Striatum
mRNA
404212_Q175B1783_01_Left_Striatum_L31
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT_Striatum_female_rep4 [mRNA]

description:
Q175B1782_04_Left_Striatum
mRNA
404206_Q175B1782_04_Left_Striatum_L33
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT_Striatum_male_rep4 [mRNA]

description:
Q175B1783_04_Left_Striatum
mRNA
404222_Q175B1783_04_Left_Striatum_L42
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc124

value: ICR


title: NGO_sc123

value: wild type


title: WT_Striatum_female_rep2 [mRNA]

description:
Q175B1782_02_Left_Striatum
mRNA
404205_Q175B1782_02_Left_Striatum_L22
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT_Striatum_female_rep3 [mRNA]

description:
Q175B1782_03_Left_Striatum
mRNA
404221_Q175B1782_03_Left_Striatum_L38
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc121


title: 425722: Het_Z_Q175_(neo-)_KI_Cortex_male_rep3 [miRNA]

description:
Q175NM0010_03_Left_Cortex
miRNA
425722_Q175NM0010_03_Left_Cortex_L1.LB35
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_Count.xlsx
processed data file: zQ175_neo-in_neo-out_miRNA_HDGSE63_FPKM.xlsx


title: WT_Liver_male_rep3 [mRNA]

description:
Q175B1783_03_Left_Liver
mRNA
404291_Q175B1783_03_Left_Liver_L29
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT_Liver_male_rep4 [mRNA]

description:
Q175B1783_04_Left_Liver
mRNA
404280_Q175B1783_04_Left_Liver_L64
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT_Liver_male_rep1 [mRNA]

description:
Q175B1783_01_Left_Liver
mRNA
404298_Q175B1783_01_Left_Liver_L13
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT_Liver_female_rep4 [mRNA]

description:
Q175B1782_04_Left_Liver
mRNA
404285_Q175B1782_04_Left_Liver_L15
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc122


title: WT_Striatum_female_rep1 [mRNA]

description:
Q175B1782_01_Left_Striatum
mRNA
404220_Q175B1782_01_Left_Striatum_L33
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc119


title: NGO_sc120


title: NGO_sc118


title: WT_Liver_female_rep3 [mRNA]

description:
Q175B1782_03_Left_Liver
mRNA
404300_Q175B1782_03_Left_Liver_L2
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT_Liver_female_rep2 [mRNA]

description:
Q175B1782_02_Left_Liver
mRNA
404286_Q175B1782_02_Left_Liver_L14
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT_Liver_female_rep1 [mRNA]

description:
Q175B1782_01_Left_Liver
mRNA
404293_Q175B1782_01_Left_Liver_L19
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT_Liver_male_rep2 [mRNA]

description:
Q175B1783_02_Left_Liver
mRNA
404275_Q175B1783_02_Left_Liver_L11
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc117


title: WT_Striatum_male_rep2 [mRNA]

description:
Q175B1783_02_Left_Striatum
mRNA
404216_Q175B1783_02_Left_Striatum_L37
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: ZyA + RGM-A + β2 ADR

type: protein

city: Tuebingen

first: Andreas

last: Körner

address: Hoppe-Seyler-Straße 3

department: Clinic of Anesthesiology and Intensive Care Medicine

country: Germany

institute: University of Tuebingen

description: Peritoneal monocytes/macrophages from C57BL/6 mice treated with Zymosan A and RGM-A + β2 ADR agonist were used following 12 h of ZyA-induced peritonitis. Protein and phosphorylation (Phospho Explorer Antibody Array, FullMoonBioscience, #PEX100) profiling of peritoneal monocytes (pooled lavages from 3-4 mice / condition) was carried out according to the manufacturer’s instructions.

hyb_protocol: 1. 6 ml Protein Coupling Solution and one tube of biotinylated sample was mixed (Protein Coupling Mix) 2. Slides were incubated in Protein Coupling Mix for 2 hours on an orbital shaker (35 rpm) 3. For Detection, 60 µl of Cy3-streptavidin (0.5 mg/ml) were added to 60 ml of Detection Buffer. 4. Slides were submerged in 30 ml of Cy3-streptavidin solution for 20 minutes on an orbital shaker (35 rpm) at room temperature in the dark.

scan_protocol: Scans were performed by Full Moon BioSystems

data_processing:
Ratio data file is available on the series record and includes the following columns:
AB: Antibody Name
ID: UniProt ID
PER1: Protein Expression Ratio (ZyA + RGM-A/ZyA)
PER2: Protein Expression Ratio (ZyA + RGM-A + β2 ADR/ZyA)
PER3: Protein Expression Ratio (ZyA + RGM-A + β2 ADR/ZyA + RGM-A)
PA: Phosphorylation Antibody
PS: Phosphorylation Site
PPER1: Phospho Protein Expression Ratio (ZyA + RGM-A/ZyA)
PPER2: Phospho Protein Expression Ratio (ZyA + RGM-A + β2 ADR/ZyA)
PPER3: Phospho Protein Expression Ratio (ZyA + RGM-A + β2 ADR/ZyA + RGM-A)

molecule: protein

source_name: Peritoneal monocytes/macrophages

label_protocol:
1. 100 µg of protein was used and Labeling Buffer was added to bring the volume to 75 µl.
2. 3 µl of Biotin/DMF solution was added and the mixture incubated at room temperature for 2 hours with vortexing every 10 minutes.
3. 35 µl of Stop Reagent was added and solution mixed by vortexing. Incubation for 30 minutes.

extract_protocol:
1. Cells were washed 5 times with ice cold PBS and remaining PBS removed
2. 100 µl of Full Moon Lysis Buffer was added and cells detached using a cell scraper and transferred to a microcentrifuge tube. One tube of Lysis Beads was added.
3. Mixture were vortexed for 60 seconds and incubated on ice for 10 minutes. Procedure was repeated 5 times.
4. Mixture was centrifuged at 10000 g for 5 minutes at 4°C.
5. Liquid was transferred to a fresh tube and centrifuged  at 18000 g for 20 minutes at 4°C.
6. Supernatant was transferred to a fresh tube.

value: peritoneal macrophages


title: ZyA + β2 ADR

description: Peritoneal monocytes/macrophages from C57BL/6 mice treated with Zymosan A and  β2 ADR agonist were used following 12 h of ZyA-induced peritonitis. Protein and phosphorylation (Phospho Explorer Antibody Array, FullMoonBioscience, #PEX100) profiling of peritoneal monocytes (pooled lavages from 3-4 mice / condition) was carried out according to the manufacturer’s instructions.


title: WT_Cortex_male_rep4 [mRNA]

description:
Q175B1783_04_Left_Cortex
mRNA
404260_Q175B1783_04_Left_Cortex_L68
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT_Cortex_male_rep1 [mRNA]

description:
Q175B1783_01_Left_Cortex
mRNA
404268_Q175B1783_01_Left_Cortex_L18
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: ZyA + RGM-A

description: Peritoneal monocytes/macrophages from C57BL/6 mice treated with Zymosan A and RGM-A was  used following 12 h of ZyA-induced peritonitis. Protein and phosphorylation (Phospho Explorer Antibody Array, FullMoonBioscience, #PEX100) profiling of peritoneal monocytes (pooled lavages from 3-4 mice / condition) was carried out according to the manufacturer’s instructions.


title: NGO_sc116

value: Ovary


title: NGO_sc115


title: WT_Cortex_female_rep4 [mRNA]

description:
Q175B1782_04_Left_Cortex
mRNA
404242_Q175B1782_04_Left_Cortex_L27
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT_Cortex_female_rep3 [mRNA]

description:
Q175B1782_03_Left_Cortex
mRNA
404253_Q175B1782_03_Left_Cortex_L18
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: ZyA

description: Peritoneal monocytes/macrophages from C57BL/6 mice treated with Zymosan A-induced peritonitis. Protein and phosphorylation (Phospho Explorer Antibody Array, FullMoonBioscience, #PEX100) profiling of peritoneal monocytes (pooled lavages from 3-4 mice / condition) was carried out according to the manufacturer’s instructions.


title: WT_Cortex_female_rep2 [mRNA]

description:
Q175B1782_02_Left_Cortex
mRNA
404241_Q175B1782_02_Left_Cortex_L36
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc114


title: WT_Cortex_female_rep1 [mRNA]

description:
Q175B1782_01_Left_Cortex
mRNA
404240_Q175B1782_01_Left_Cortex_L17
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: KO Th17 48h [218_6]

city: La Jolla

first: Alain

last: Domissy

state: CA

address: 10550 North Torrey Pines Road

department: Immunology

institute: The Scripps Research Institute

description:
218_6_1_Total.fastq.gz
processed data file: processed_218.xlsx

data_processing:
BCL files from Illumina sequencing were demultiplexed and fastq data files were obtained using Illumina's bcl2fastq conversion software version 2.19. Raw data were aligned to the mouse genome (M.musculus-UCSC-mm10 ) using the STAR aligner v(2.5.2a).
Gene abundance was estimated with python version 2.7.11, and htseq version 0.9.1.
Raw counts were transformed into "Relative Log Expression” normalization (RLE) implemented in the DESeq2 package that was used to assess differential expression and perform gene set testing.
Genome_build: M.musculus UCSC mm10 build
Supplementary_files_format_and_content: Excel files (HT-seq Count raw counts)

source_name: KO Th17 48h

extract_protocol:
Total RNA was extracted using Qiagen RNeasy kits on Day 2 (WT vs KO) or Day 3 (MIGR1 transduced) of in vitro differentiated Th17 cells.  rRNA-depleted RNA was processd using the TruSeq Stranded Total RNA sample prep kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain background

value: REV-ERBa-/- (KO)

value: Th17 cells

tag: molecule subtype

value: ribo-depleted RNA


title: WT_(neo-)_Striatum_male_rep2 [mRNA]

description:
Q175NM0011_02_Left_Striatum
mRNA
404231_Q175NM0011_02_Left_Striatum_L63
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT_(neo-)_Striatum_male_rep3 [mRNA]

description:
Q175NM0011_03_Left_Striatum
mRNA
404217_Q175NM0011_03_Left_Striatum_L41
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT_Cortex_male_rep3 [mRNA]

description:
Q175B1783_03_Left_Cortex
mRNA
404258_Q175B1783_03_Left_Cortex_L67
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: Cortex


title: WT_(neo-)_Striatum_female_rep4 [mRNA]

description:
Q175NM0009_04_Left_Striatum
mRNA
404211_Q175NM0009_04_Left_Striatum_L38
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT TH17_48h [218_2]

description:
218_2_1_Total.fastq.gz
processed data file: processed_218.xlsx

source_name: WT TH17_48h

value: REV-ERBa+/+ (WT)


title: WT_Cortex_male_rep2 [mRNA]

description:
Q175B1783_02_Left_Cortex
mRNA
404239_Q175B1783_02_Left_Cortex_L20
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT_(neo-)_Striatum_male_rep1 [mRNA]

description:
Q175NM0011_01_Left_Striatum
mRNA
404232_Q175NM0011_01_Left_Striatum_L77
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc112

value: oocyte


title: KO Th17 48h [218_5]

description:
218_5_1_Total.fastq.gz
processed data file: processed_218.xlsx


title: NGO_sc111


title: RevB_2 [193_8]

description:
193_8_Total
processed data file: processed_193.xlsx

source_name: REVERBb overexpressing Th17 cells

value: WT; overexpressing REVERBb


title: NGO_sc110


title: WT_(neo-)_Striatum_female_rep3 [mRNA]

description:
Q175NM0009_03_Left_Striatum
mRNA
404223_Q175NM0009_03_Left_Striatum_L16
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: 6 months

value: Striatum


title: WT_(neo-)_Striatum_female_rep2 [mRNA]

description:
Q175NM0009_02_Left_Striatum
mRNA
404215_Q175NM0009_02_Left_Striatum_L35
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT TH17_48h [218_1]

description:
218_1_1_Total.fastq.gz
processed data file: processed_218.xlsx


title: WT_(neo-)_Liver_male_rep4 [mRNA]

description:
Q175NM0011_04_Left_Liver
mRNA
404272_Q175NM0011_04_Left_Liver_L25
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: male


title: WT_(neo-)_Liver_male_rep3 [mRNA]

description:
Q175NM0011_03_Left_Liver
mRNA
404278_Q175NM0011_03_Left_Liver_L1.D704_507
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: RevB_1 [193_7]

description:
193_7_Total
processed data file: processed_193.xlsx


title: WT_(neo-)_Liver_male_rep2 [mRNA]

description:
Q175NM0011_02_Left_Liver
mRNA
404284_Q175NM0011_02_Left_Liver_L30
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc109

value: < 20 microns


title: WT_(neo-)_Liver_male_rep1 [mRNA]

description:
Q175NM0011_01_Left_Liver
mRNA
404292_Q175NM0011_01_Left_Liver_L9
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: Liver


title: RevA_3 [193_6]

description:
193_6_Total
processed data file: processed_193.xlsx

source_name: REVERBa overexpressing Th17 cells

value: WT; overexpressing REVERBa


title: NGO_sc108

value: ICR


title: WT_(neo-)_Liver_female_rep4 [mRNA]

description:
Q175NM0009_04_Left_Liver
mRNA
404299_Q175NM0009_04_Left_Liver_L8.D710
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: Wild Type

value: female


title: WT_(neo-)_Striatum_male_rep4 [mRNA]

description:
Q175NM0011_04_Left_Striatum
mRNA
404227_Q175NM0011_04_Left_Striatum_L7
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc113

value: wild type

value: Ovary


title: WT_(neo-)_Liver_female_rep3 [mRNA]

description:
Q175NM0009_03_Left_Liver
mRNA
404273_Q175NM0009_03_Left_Liver_L32
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: RevA_1 [193_4]

description:
193_4_Total
processed data file: processed_193.xlsx

value: Th17 cells


title: WT_(neo-)_Liver_female_rep2 [mRNA]

description:
Q175NM0009_02_Left_Liver
mRNA
404269_Q175NM0009_02_Left_Liver_L5
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT_(neo-)_Striatum_female_rep1 [mRNA]

description:
Q175NM0009_01_Left_Striatum
mRNA
404214_Q175NM0009_01_Left_Striatum_L39
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT_(neo-)_Liver_female_rep1 [mRNA]

description:
Q175NM0009_01_Left_Liver
mRNA
404287_Q175NM0009_01_Left_Liver_L10
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: MIG_2 [193_2]

description:
193_2_Total
processed data file: processed_193.xlsx

source_name: MIGR1 transduced Th17 cells

value: WT; MIGR1 transduced

value: ribo-depleted RNA


title: NGO_sc106


title: NGO_sc105


title: WT_(neo-)_Cortex_male_rep2 [mRNA]

description:
Q175NM0011_02_Left_Cortex
mRNA
404262_Q175NM0011_02_Left_Cortex_L5
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: Cortex


title: WT_(neo-)_Cortex_male_rep3 [mRNA]

description:
Q175NM0011_03_Left_Cortex
mRNA
404237_Q175NM0011_03_Left_Cortex_L73
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT_(neo-)_Cortex_male_rep4 [mRNA]

description:
Q175NM0011_04_Left_Cortex
mRNA
404254_Q175NM0011_04_Left_Cortex_L11
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: MIG_1 [193_1]

description:
193_1_Total
processed data file: processed_193.xlsx


title: WT_(neo-)_Cortex_male_rep1 [mRNA]

description:
Q175NM0011_01_Left_Cortex
mRNA
404249_Q175NM0011_01_Left_Cortex_L8
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc104

value: oocyte


title: WT_(neo-)_Cortex_female_rep4 [mRNA]

description:
Q175NM0009_04_Left_Cortex
mRNA
404257_Q175NM0009_04_Left_Cortex_L6
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: WT_(neo-)_Cortex_female_rep2 [mRNA]

description:
Q175NM0009_02_Left_Cortex
mRNA
404252_Q175NM0009_02_Left_Cortex_L31
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc103


title: WT_(neo-)_Cortex_female_rep3 [mRNA]

description:
Q175NM0009_03_Left_Cortex
mRNA
404243_Q175NM0009_03_Left_Cortex_L65
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: E18_green

city: Vancouver

first: Francis

middle: C

last: Lynn

state: BC

address: 950 28th Ave W

department: Surgery

country: Canada

institute: University of British Columbia

data_processing:
Alignment to reference genome and generation of UMI counts performed with cellranger counts, with parameter "--cells=5000".
Samples can be merged using cellranger aggr, with parameter "--normalize=mapped"
10x output files are read into Scater R package for quality control steps.
1. Load 10x raw matrix output folder into a SingleCellExperiment object using read10xResults.
2. Filter out cells that have less than 1000 transcripts. The output matrix includes all the barcodes used, including barcodes associated to empty GEMs, which are background noise. Here, we are assuming a cell-containing GEM should have more than 1000 RNA transcripts.
3. Gene symbols are used as row names from now on, duplicated gene names, which are genes corresponding to multiple ensemble id, will have an additional number suffix attached to the gene name. (e.g. gene_1)
4. (Optional: if dealing with aggregated dataset) Uses the suffix attached to each barcode to obtain library origin information and add this information to colData to the object. (E.g., the attachment of “-1” means coming from red population while “-2” means from green. The order depends on the aggregation csv file.
Scater R script
5. Filter out genes that are not expressed by any cells; the output matrix includes all genes in the reference transcriptome even some of them are not expressed at all, so this step is removing those unexpressed genes.
6. Select out the mitochondrial DNAs by using searching for gene names starting with “mt-” (“MT-” for human) and set them as Spike-in using isSpike function.
7. Calculate QC Metrics using Scater’s calculateQCMetrics with use_spikes parameter set to true and filter out genes base on total counts, total features and percentage of cells transcribing the mitochondrial DNAs, using isOutlier function. Cells are discarded if a cell has one of them above feature greater than three median absolute deviation away from the mean.
(total_counts: filter on both ends, log10 scale; total_features: filter on the lower end, non-logged; pct_counts_MT: filter on the higher end, non-logged.
8. Another automatic filtering algorithm, runPCA is used to filter out genes and cells base on PCA.
9. After removing out invalid genes and cells, genes are selected for one last time to keep only genes that are expressed by more than three cells.
Post filtered Scater object is loaded into Seurat R package for downstream biological analysis.
1. Seurat object is then created using the post-scater-filtering raw counts, with an additional minimal threshold of genes being expressed in three cells and cells having 500 genes.
2. Seurat object is then undergone log-normalization using Seurat’s NormalizeData with default size factor of 10000.
3. Data is then scaled while regressing out the effect of cell cycle phases.
4. Variable genes are then found using mean expression and LogVMR dispersion function.
5. The variable genes are inputted for PCA.
6. Cluster division is then performed using the first 15 principle components, which utilizes a “shared nearest neighbor (SNN) modularity optimization-based clustering algorithm” (not K-means clustering), with resoultion of 0.6.
7.  TSNE embedding is then performed, which allows the visualization of data in reduced dimensions.
8. Markers that are dimensionally expressed in each cluster comparing to all other cells in the dataset are used for cell type identification.
Genome_build: Customized reference transcriptomes were made by adding tdTomato and eGFP gene sequences to mm10 v1.3.1 mouse transcriptome and adding eGFP to GRCh38 v2.0.0 human transcriptome. These two customized transcriptomes are uploaded as supplementary files of this submission.
Supplementary_files_format_and_content: Three files, barcodes.csv, genes.tsv and matrix.mtx, outputted from cellranger counts pipeline, form the raw UMI counts matrix. Seurat normalized counts matrix is also included. Cells and genes in this matrix have undergone the whole quality control and filtering process as described and they are natural log-transformed, with a scale factor of 10000, using Seurat's NormalizeData function, with default parameter. For each normalized counts matrix, each row represents a cell and each column is a gene. Cell metadata is also stored in columns: column 1 is cell barcode; column 2 is cell type assignment, column 3 is cell phase assignment.  For aggregated libraries: E15_aggr -E18_aggr, E18_endocrine_aggr -the raw UMI counts matrix are treated as raw data because do not have corresponding bam file. Therefore, only the normalized counts matrix is included here as processed data.

source_name: Pancreatic progenitor cells

growth_protocol: Neurog3-Cre; Rosa26mT/mG embryos were dissected at E15.5 or E18.5, dissociated using Trypsin, and sorted for mTomato+ and mGreen+ cells. NEUROG3-eGFP hESCs were differentiated using Rezania et al. protocol and sorted for GFP+ cells.

extract_protocol:
The 10x Genomics ChromiumTM controller and Single Cell 3’ Reagent Kits v2 (Pleasanton, CA, USA) were used to generate single cell libraries. Briefly, cells were counted following FACS and cell suspensions were loaded for a targeted cell recovery of 3000 cells per channel.The microfluidics platform was used to barcode single cells using Gel Bead-In-Emulsions (GEMs). RT is performed within GEMs, resulting in barcoded cDNA from single cells.
The full length, barcoded cDNA is PCR amplified followed by enzymatic fragmentation and SPRI double sided size selection for optimal cDNA size. End repair, A-tailing, Adaptor Ligation, and PCR are performed to generate the final libraries that have P5 and P7 primers compatible with Illumina sequencing. The libraries were pooled and sequenced using an Illumina NextSeq500 platform with a 150 cycle High Output v2 kit in paired-end format with 26 bp Read 1, 8 bp I5 Index, and 85 bp Read 2.

value: Neurog3-Cre; Rosa26mTmG

value: FACS sorted mGreen+ E18.5 pancreatic cells


title: NGO_sc102


title: Th1 rep cells

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

institute: Deutsches Rheuma-Forschungszentrum

description: Th1 rep cells

data_processing:
Sequence reads were mapped to mouse GRCm38/mm10 genome with TopHat2 in very-sensitive settings for Bowtie2 and EnsEMBL annotation release 67.
Sequence coverage at each position was computed using IGVtools counts and wigToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: UCSC Genome Browser bigWig format with sequence coverage for each genomic position

source_name: spleen

growth_protocol: CD4+CD62Lhi (naϊve) from spleens and lymph nodes of 6- to 10-weeks old OTII mice were isolated and labeled with αCD4-FITC (GK1.5, DRFZ) followed by Magnetic Cell Sorting (MACS) with αFITC microbeads (Miltenyi Biotec). Subsequent purification of CD4+CD62Lhi cells was achieved using αCD62L microbeads (Miltenyi Biotec). Cells were cultured (1:5) with irradiated (30 Gy), CD90.2 depleted APCs in the presence of OVA323-339 (0.5 mM) in RPMI supplemented with 10% fetal calf serum (FCS), 100 units/ml penicillin, 0.1 mg/ml streptomycin and 10 μM β-mercaptoethanol, IL-12 (5 ng/ml, R&D Systems) and αIL-4 (10 µg/ml, 11B11). Viable cells were separated by density gradient centrifugation using Histopaque 1083 (Sigma Aldrich) and reactivated  with freshly isolated APCs every six days for three times consecutively. IL-2 (10 ng/ml, R&D Systems) was added  from the second stimulation on.

extract_protocol:
Unless stated otherwise, all kits were used according to the manufacturer’s recommendations. Total RNA was isolated using ZR RNA MiniPrepTM kit  according to the manufacturers instruction. Total RNA concentration and quality of each sample were determined with the NanoDrop ND-Lite (peqlab, Erlangen, Germany) and Qubit fluorometer (ThermoFisher Scientific, Darmstadt, Germany).
The “TruSeq Stranded Total RNA library PrepKit with Ribo-Zero” kit (Illumina, San Diego, CA, USA) was used to prepare cDNA libraries for total RNA sequencing from a minimum of 100ng of total RNA isolated from the Th1 rep cells. RNA quality was assessed on a bioanalyzer using the RNA 6000 Pico Kit (Agilent Technologies, Waldbronn, Germany) and the RNA had a  RIN >8 and was considered for further processing.  After quality control (High sensitivity DNA Kit, Agilent Technologies, Waldbronn, Germany). The final cDNA libraries were quality checked (High sensitivity DNA Kit, Agilent Technologies, Waldbronn, Germany), quantified (Qubit dsDNA HS Assay Kit, Invitrogen, Darmstadt, Germany) and were paired-end (75 bp) sequenced on a NextSeq500 Illumina Next Generation Sequencing Device (Illumina, San Diego, CA, USA).

tag: cells

value: T cells

tag: organ

value: spleen

tag: background strain


title: NGO_sc101

value: < 20 microns


title: Het_z_Q175_KI_Striatum_female_rep4 [mRNA]

description:
Q175B1785_04_Left_Striatum
mRNA
404226_Q175B1785_04_Left_Striatum_L9
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

source_name: Corpus striatum of left cerebral hemisphere

tag: background

value: Het z_Q175 KI

tag: Sex

value: 6 months

value: Striatum


title: NGO_sc107

value: ICR

tag: cell type


title: Het_z_Q175_KI_Striatum_female_rep2 [mRNA]

description:
Q175B1785_02_Left_Striatum
mRNA
404207_Q175B1785_02_Left_Striatum_L71
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

tag: strain

value: female


title: NGO_sc100

tag: genotype

value: wild type


title: Het_z_Q175_KI_Striatum_female_rep3 [mRNA]

description:
Q175B1785_03_Left_Striatum
mRNA
404233_Q175B1785_03_Left_Striatum_L35
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

tag: age


title: Het_z_Q175_KI_Striatum_female_rep1 [mRNA]

description:
Q175B1785_01_Left_Striatum
mRNA
404218_Q175B1785_01_Left_Striatum_L40
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

tag: tissue


title: E18_red

value: FACS sorted mTomato+ E18.5 pancreatic cells


title: E15_yellow_green

value: FACS sorted mTomato+mGreen+ and mGreen+ E15.5 pancreatic cells


title: Het_z_Q175_KI_Striatum_male_rep4 [mRNA]

description:
Q175B1784_04_Left_Striatum
mRNA
404224_Q175B1784_04_Left_Striatum_L78
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: male


title: NGO_sc99

value: Ovary

tag: oocyte size


title: Het_z_Q175_KI_Striatum_male_rep2 [mRNA]

description:
Q175B1784_02_Left_Striatum
mRNA
404225_Q175B1784_02_Left_Striatum_L24
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: Het_z_Q175_KI_Striatum_male_rep3 [mRNA]

description:
Q175B1784_03_Left_Striatum
mRNA
404230_Q175B1784_03_Left_Striatum_L70
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc98


title: NGO_sc97


title: Het_z_Q175_KI_Striatum_male_rep1 [mRNA]

description:
Q175B1784_01_Left_Striatum
mRNA
404210_Q175B1784_01_Left_Striatum_L61
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: Het_z_Q175_KI_Liver_female_rep4 [mRNA]

description:
Q175B1785_04_Left_Liver
mRNA
404294_Q175B1785_04_Left_Liver_L6
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: Liver


title: WT_(neo-)_Cortex_female_rep1 [mRNA]

description:
Q175NM0009_01_Left_Cortex
mRNA
404246_Q175NM0009_01_Left_Cortex_L3
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: Wild Type

value: Cortex


title: E18_yellow

value: Neurog3-Cre; Rosa26mTmG

value: FACS sorted mTomato+mGreen+ E18.5 pancreatic cells


title: NGO_sc96

value: oocyte


title: NGO_sc95

value: < 20 microns


title: Het_z_Q175_KI_Liver_female_rep1 [mRNA]

description:
Q175B1785_01_Left_Liver
mRNA
404279_Q175B1785_01_Left_Liver_L10
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: Het z_Q175 KI


title: Het_z_Q175_KI_Liver_female_rep2 [mRNA]

description:
Q175B1785_02_Left_Liver
mRNA
404296_Q175B1785_02_Left_Liver_L8.D707
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: 6 months


title: Het_z_Q175_KI_Liver_female_rep3 [mRNA]

description:
Q175B1785_03_Left_Liver
mRNA
404295_Q175B1785_03_Left_Liver_L1
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc93


title: NGO_sc94


title: NGO_sc92


title: E15_red

value: FACS sorted mTomato+ E15.5 pancreatic cells


title: Het_z_Q175_KI_Liver_male_rep4 [mRNA]

description:
Q175B1784_04_Left_Liver
mRNA
404290_Q175B1784_04_Left_Liver_L60
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: Het_z_Q175_KI_Liver_male_rep3 [mRNA]

description:
Q175B1784_03_Left_Liver
mRNA
404274_Q175B1784_03_Left_Liver_L72
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc91

value: ICR


title: Het_z_Q175_KI_Liver_male_rep2 [mRNA]

description:
Q175B1784_02_Left_Liver
mRNA
404289_Q175B1784_02_Left_Liver_L20
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc90


title: Het_z_Q175_KI_Liver_male_rep1 [mRNA]

description:
Q175B1784_01_Left_Liver
mRNA
404297_Q175B1784_01_Left_Liver_L8.D708
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: Th1 Antagomir-SCR 48h-2

description: T cells

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 3000, using the GCOS software version 1.4 from Affymetrix.

data_processing: For quality control data were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Quality checks were performed according to the manufacturer's recommendations. Gene expression was quantified by RMA using affy R package for each time after the treatment.

label: Biotin

source_name: Th1 rep cells

label_protocol: Labeling and hybridization of total RNA to MG 430 2 GeneChips was performed using the whole-transcriptome pico KIT from Affymetrix according tot he manufactures instruction. Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 400 (both Affymetrix).

treatment_protocol: After the fourth round of stimulation, viable repeatedly activated Th1 cells were separated by density gradient centrifugation using Histopaque 1083 (Sigma Aldrich) and treated (5 x 10^6 cells/ml) in serum-free siRNA delivery medium (ACCELL, Dharmacon) containing antagomir-31 or antagomir-SCR (1 µM) for 1.5h at 37°C and 5% CO2. Cell suspension was diluted (1:5) with RPMI supplemented with 10% fetal calf serum (FCS), 100 units/ml penicillin, 0.1 mg/ml streptomycin and 10 μM β-mercaptoethanol, IL-12 (5 ng/ml, R&D Systems), αIL-4 (10 µg/ml, 11B11) and IL-2 (10 ng/ml, R&D Systems) and reactivated with plate-bound αCD3 and αCD28 (3 µg/ml, BD). 36h, 48h, and 72h after the treatment, cells were harvested and total RNA was isolated using ZR RNA MiniPrepTM kit (Zymo Research) according to the manufacturer’s recommendations.

value: T-cells

tag: mouse origin

value: OT-II

value: spleen

tag: treatment

value: Antagomir-SCR

tag: time point


title: Th1 Antagomir-SCR 48h-1

description: T cells

extract_protocol: 36h, 48h, and 72h after the treatment, cells were harvested and total RNA was isolated using ZR RNA MiniPrepTM kit (Zymo Research) according to the manufacturer’s recommendations.


title: Het_z_Q175_KI_Cortex_female_rep4 [mRNA]

description:
Q175B1785_04_Left_Cortex
mRNA
404250_Q175B1785_04_Left_Cortex_L15
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

tag: genotype/variation

value: female


title: Th1 antagomir-SCR 36h-2

description: T cells


title: Th1 Antagomir-31 48h-2

description: T cells


title: Th1 antagomir-SCR 36h-1

description: T cells


title: Th1 Antagomir-31 48h-1

description: T cells


title: Th1 Antagomir-31 36h-1

description: T cells


title: Th1 Antagomir-31 36h-2

description: T cells


title: NGO_sc88

value: wild type

value: Ovary


title: Het_z_Q175_KI_Cortex_female_rep3 [mRNA]

description:
Q175B1785_03_Left_Cortex
mRNA
404256_Q175B1785_03_Left_Cortex_L19
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: Th1 Antagomir-31 72h-4

description: T cells


title: NGO_sc89


title: Het_z_Q175_KI_Cortex_female_rep2 [mRNA]

description:
Q175B1785_02_Left_Cortex
mRNA
404265_Q175B1785_02_Left_Cortex_L76
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc85


title: NGO_sc86


title: NGO_sc87


title: Het_z_Q175_KI_Cortex_female_rep1 [mRNA]

description:
Q175B1785_01_Left_Cortex
mRNA
404267_Q175B1785_01_Left_Cortex_L7
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: Het_z_Q175_KI_Cortex_male_rep4 [mRNA]

description:
Q175B1784_04_Left_Cortex
mRNA
404251_Q175B1784_04_Left_Cortex_L13
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: male


title: NGO_sc84


title: NGO_sc83


title: NGO_sc82


title: Th1 Antagomir-SCR 72h-3

description: T cells


title: Het_z_Q175_KI_Cortex_male_rep2 [mRNA]

description:
Q175B1784_02_Left_Cortex
mRNA
404264_Q175B1784_02_Left_Cortex_L3
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: Cortex


title: Het_z_Q175_KI_Cortex_male_rep1 [mRNA]

description:
Q175B1784_01_Left_Cortex
mRNA
404261_Q175B1784_01_Left_Cortex_L8
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: Th1 Antagomir-31 72h-3

description: T cells


title: genomic DNA from neuroblastoma 217

type: genomic

city: Heidelberg

first: Kai-Oliver

last: Henrich

address: INF 280

institute: German Cancer Research Center DKFZ

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to llumina HumanMethylation450 BeadChips using the standard Illumina protocol.

scan_protocol: Illumina iScan System according to the manufacturer's protocol.

data_processing: Raw data files generated from the array usage were preprocessed using the minfi Bioconductor package (preprocessIllumina function).

label: Cy5 and Cy3

source_name: neuroblastoma 217

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from snap-frozen neuroblastoma tissue using standard procedures.

tag: tert status

value: TERT non-rearranged

tag: alt status

value: ALT negative

tag: mycn status

value: MYCN-non-amplified

tag: atrx status

value: ATRX non-mutated

value: TERT expression low

value: neuroblastoma


title: Th1 Antagomir-31 72h-2

description: T cells

tag: cells

tag: organ


title: Th1 Antagomir-SCR 72h-4

description: T cells


title: genomic DNA from neuroblastoma 21

source_name: neuroblastoma 21

value: MYCN-amplified

value: TERT expression high


title: Th1 Antagomir-SCR 72h-2

description: T cells

value: T-cells


title: Het_Z_Q175_(neo-)_KI_Striatum_female_rep4 [mRNA]

description:
Q175NM0012_04_Left_Striatum
mRNA
404229_Q175NM0012_04_Left_Striatum_L32
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

tag: background

value: Het Z_Q175 (neo-) KI

tag: Sex

value: 6 months

value: Striatum


title: genomic DNA from neuroblastoma 200

source_name: neuroblastoma 200


title: NGO_sc80

tag: strain

value: ICR

tag: cell type

value: oocyte

value: < 20 microns


title: Het_Z_Q175_(neo-)_KI_Striatum_female_rep3 [mRNA]

description:
Q175NM0012_03_Left_Striatum
mRNA
404219_Q175NM0012_03_Left_Striatum_L39
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: female

tag: age


title: genomic DNA from neuroblastoma 266

source_name: neuroblastoma 266

value: TERT rearranged

tag: tissue


title: Sorted GFRα1+ cells from Fgf5–/– testes_2

city: Okazaki

first: Yu

last: Kitadate

address: 5-1 Higashiyama, Myodaiji

country: Japan

institute: National Institute for Basic Biology

hyb_protocol: 600 ng of Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray (G4852A) 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.

scan_protocol: Slides were scanned using an Agilent Technologies Scanner (G2505C and G2565CA) with the default settings for 8 × 60k-format one-color arrays. Images were analyzed using Feature Extraction ver.10.7.3.1 (Agilent Technologies).

data_processing: Images were analyzed using Feature Extraction ver.10.7.3.1 (Agilent Technologies) using default parameters. I performed a 75% percentile shift as a normalize (I did not use any control genes), and it carried out using gene spring GX11-13 for my microarray data.

source_name: Sorted GFRα1+ cells from Fgf5–/–, sample2

label_protocol: cRNA synthesis from 25 ng total RNA and Cyanine 3 (Cy3)-CTP labeling was carried out using Low Input Quick Amp Labeling Kit (Agilent) according to manufacture’s protocol. Purification of labeled cRNA was performed using RNeasy Mini Kit (Qiagen). The concentration was determined using the NanoDrop.

extract_protocol: An extraction of total RNA was curried out by using RNeasy Micro Kit (Qiagen), with DNase digestion performed on a column. Recovered RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: isolated cells by FACS from testes

tag: genotype


title: genomic DNA from neuroblastoma 191

source_name: neuroblastoma 191

value: TERT non-rearranged

value: ALT negative


title: Het_Z_Q175_(neo-)_KI_Striatum_female_rep2 [mRNA]

description:
Q175NM0012_02_Left_Striatum
mRNA
404234_Q175NM0012_02_Left_Striatum_L2
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: genomic DNA from neuroblastoma 245

source_name: neuroblastoma 245

value: MYCN-non-amplified

value: ATRX non-mutated


title: Sorted GFRα1+ cells from Fgf5–/– testes_1

source_name: Sorted GFRα1+ cells from Fgf5–/–, sample1


title: NGO_sc81

source_name: Non-Growing Oocyte

value: wild type

value: Ovary

tag: oocyte size


title: genomic DNA from neuroblastoma 274

source_name: neuroblastoma 274

value: MYCN-amplified

value: TERT expression high

value: neuroblastoma


title: genomic DNA from neuroblastoma 130

source_name: neuroblastoma 130

value: TERT expression low


title: Sorted GFRα1+ cells from WT testes_3

source_name: Sorted GFRα1+ cells from WT, sample3

value: wildtype


title: NGO_sc79

value: ICR


title: genomic DNA from neuroblastoma 144

source_name: neuroblastoma 144


title: Sorted GFRα1+ cells from Fgf5–/– testes_3

source_name: Sorted GFRα1+ cells from Fgf5–/–, sample3


title: Sorted GFRα1+ cells from WT testes_2

source_name: Sorted GFRα1+ cells from WT, sample2


title: Het_Z_Q175_(neo-)_KI_Striatum_female_rep1 [mRNA]

description:
Q175NM0012_01_Left_Striatum
mRNA
404213_Q175NM0012_01_Left_Striatum_L36
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

source_name: Corpus striatum of left cerebral hemisphere

value: Het Z_Q175 (neo-) KI

value: 6 months

value: Striatum


title: Het_Z_Q175_(neo-)_KI_Striatum_male_rep4 [mRNA]

description:
Q175NM0010_04_Left_Striatum
mRNA
404235_Q175NM0010_04_Left_Striatum_L74
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: male


title: NGO_sc77

value: oocyte

value: < 20 microns


title: NGO_sc76


title: Het_Z_Q175_(neo-)_KI_Striatum_male_rep3 [mRNA]

description:
Q175NM0010_03_Left_Striatum
mRNA
404209_Q175NM0010_03_Left_Striatum_L4
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: Het_Z_Q175_(neo-)_KI_Striatum_male_rep2 [mRNA]

description:
Q175NM0010_02_Left_Striatum
mRNA
404236_Q175NM0010_02_Left_Striatum_L4
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: Sorted GFRα1+ cells from WT testes_1

source_name: Sorted GFRα1+ cells from WT, sample1

value: isolated cells by FACS from testes


title: genomic DNA from neuroblastoma 71

source_name: neuroblastoma 71

value: TERT non-rearranged

value: ALT negative


title: NGO_sc73

value: wild type


title: NGO_sc75

value: Ovary


title: Het_z_Q175_KI_Cortex_male_rep3 [mRNA]

description:
Q175B1784_03_Left_Cortex
mRNA
404259_Q175B1784_03_Left_Cortex_L34
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

source_name: Cortex of left cerebral hemisphere

value: Het z_Q175 KI

value: Cortex


title: genomic DNA from neuroblastoma 140

source_name: neuroblastoma 140

value: MYCN-amplified

value: ATRX non-mutated

value: TERT expression high

value: neuroblastoma


title: Het_Z_Q175_(neo-)_KI_Liver_female_rep4 [mRNA]

description:
Q175NM0012_04_Left_Liver
mRNA
404277_Q175NM0012_04_Left_Liver_L22
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

source_name: Left lobe of liver

value: Het Z_Q175 (neo-) KI

value: female

value: Liver


title: genomic DNA from neuroblastoma 12

source_name: neuroblastoma 12

value: MYCN-non-amplified

value: TERT expression low


title: NGO_sc74

value: ICR

value: oocyte

value: < 20 microns


title: genomic DNA from neuroblastoma 150

source_name: neuroblastoma 150

value: TERT non-rearranged

value: ALT negative


title: genomic DNA from neuroblastoma 167

source_name: neuroblastoma 167


title: Cultured spermatogonia without FGF5_2

source_name: Cultured spermatogonia without FGF5, sample2

value: cultured spermatogonia

value: wildtype


title: genomic DNA from neuroblastoma 147

source_name: neuroblastoma 147


title: Cultured spermatogonia without FGF5_1

source_name: Cultured spermatogonia without FGF5, sample1


title: Cultured spermatogonia with FGF5_2

source_name: Cultured spermatogonia with FGF5, sample2


title: Het_Z_Q175_(neo-)_KI_Liver_female_rep3 [mRNA]

description:
Q175NM0012_03_Left_Liver
mRNA
404276_Q175NM0012_03_Left_Liver_L12
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: 6 months


title: Cultured spermatogonia with FGF5_1

source_name: Cultured spermatogonia with FGF5, sample1


title: NGO_sc72

source_name: Non-Growing Oocyte

value: wild type

value: Ovary


title: genomic DNA from neuroblastoma 159

source_name: neuroblastoma 159

value: MYCN-amplified

value: ATRX non-mutated

value: TERT expression high


title: C. parvum infection [B3]

city: Omaha

first: Xianming

last: Chen

state: NE

address: 2500 california plaza

institute: creighton university

description: Gene expression in infected cells

hyb_protocol: The labeled cRNAs were hybridized onto the microarray. The Agilent SurePrint G3 Mouse Gene Expression Microarray (G4852A) was used for the analysis, which provides full coverage of genes and transcripts with the most up-to-date content, including mRNAs and lincRNAs (http://www.chem.agilent.com/store/en_US/Prod-G4852A/G4852A

scan_protocol: A total of 2 µg RNA from each sample was then labeled with the Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242). After hybridization, the slides were scanned with the Agilent Microarray Scanner (Agilent p/n G2505C),

data_processing: Quantified signals were extracted and analyzed by using the Agilent Feature Extraction Software, in accordance with MIAME guidelines

source_name: IEC4.1 cells

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols. Briefly, total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

growth_protocol: Mouse intestinal epithelial cells (IEC4.1 cells) cultured in DMEM/F12 Medium 1:1 supplemented with 10 ng/ml epidermal growth factor (EGF), 5% fetal bovine serum and antibiotics (100 IU/ml of penicillin,100 µg/ml of streptomycin and 10ug/ml Gentamicin). Atmosphere: air, 95%; carbon dioxide (CO2), 5% ; Temperature: 37°C

treatment_protocol: The IEC4.1 cells  were grown to 80% confluence for two groups:  control (Group A, A1-A3) and C. parvum infection (Group B, B1-B3; cells exposed to C. parvum infection for 24h). Total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.

value: intestinal epithelial cells

tag: agent

value: Cryptosporidium parvum

tag: cell line


title: Het_Z_Q175_(neo-)_KI_Liver_female_rep1 [mRNA]

description:
Q175NM0012_01_Left_Liver
mRNA
404270_Q175NM0012_01_Left_Liver_L28
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

tag: genotype/variation

value: Het Z_Q175 (neo-) KI

value: female

value: Liver


title: genomic DNA from neuroblastoma 42

source_name: neuroblastoma 42

tag: tert status

value: MYCN-non-amplified

value: neuroblastoma


title: NGO_sc78

value: ICR

value: oocyte

value: < 20 microns


title: NGO_sc71


title: Het_Z_Q175_(neo-)_KI_Liver_female_rep2 [mRNA]

description:
Q175NM0012_02_Left_Liver
mRNA
404271_Q175NM0012_02_Left_Liver_L75
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc70


title: Het_Z_Q175_(neo-)_KI_Liver_male_rep4 [mRNA]

description:
Q175NM0010_04_Left_Liver
mRNA
404281_Q175NM0010_04_Left_Liver_L23
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: male


title: NGO_sc67


title: CD31+CD43+ HPCs

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC

data_processing:
Illumina GA Pipeline v1.5 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence,then use BWA (Li, H. and Durbin, R., 2009) to map clean reads to genome reference and use Bowtie (Langmead B, et al., 2009) to gene reference
We provide genome alignment data in BAM format and recommend using IGV(Ietegrative Genomics Viewer) tool to visualize BAM file in different scales.
Genes expression level are quantified by a software package: RSEM(RNASeq by Expectation Maximization). RSEM (Li B and Dewey C N., 2011)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: CD31+CD43+ HPCs samples collected from day 7 after hematopoietic differentiation through FACS.

growth_protocol: H1 were induced for stepwise hematopoietic differentiation. First, cells were cultured in Custom mTeSR1 medium supplemented with 40 ng/ml activinA (Peprotech) and 50 ng/ml BMP4 (Peprotech) for 2 days. Second, cells were incubated with Custom mTeSR1 medium supplemented with 40 ng/ml VEGF (Peprotech) and 50 ng/ml bFGF (Peprotech) for 2 days. Finally, cells were feeded with Custom mTeSR1 medium supplemented with  40 ng/ml VEGF (Peprotech) and 50 ng/ml bFGF (Peprotech) and SB-431542 (Sellleck) for 3 days.

extract_protocol:
H1 drived cells was collected and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CD31+CD43+ HPCs


title: CD31+CD34+ HEPs

source_name: CD31+CD34+ HEPs samples collected from day 4 after hematopoietic differentiation through FACS.

value: CD31+CD34+ HEPs


title: Het_Z_Q175_(neo-)_KI_Liver_male_rep3 [mRNA]

description:
Q175NM0010_03_Left_Liver
mRNA
404283_Q175NM0010_03_Left_Liver_L14
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: 6 months


title: Het_Z_Q175_(neo-)_KI_Liver_male_rep2 [mRNA]

description:
Q175NM0010_02_Left_Liver
mRNA
404282_Q175NM0010_02_Left_Liver_L12
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc68

value: wild type

value: Ovary


title: NGO_sc66


title: genomic DNA from neuroblastoma 40

source_name: neuroblastoma 40

value: TERT non-rearranged

tag: alt status

value: ALT negative

value: ATRX non-mutated

value: TERT expression high


title: Het_Z_Q175_(neo-)_KI_Liver_male_rep1 [mRNA]

description:
Q175NM0010_01_Left_Liver
mRNA
404288_Q175NM0010_01_Left_Liver_L26
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: Het Z_Q175 (neo-) KI


title: Het_Z_Q175_(neo-)_KI_Cortex_female_rep4 [mRNA]

description:
Q175NM0012_04_Left_Cortex
mRNA
404245_Q175NM0012_04_Left_Cortex_L62
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

source_name: Cortex of left cerebral hemisphere

value: female

value: Cortex


title: undifferentiated hESCs

source_name: Undifferentiated H1 cells

value: undifferentiated hESCs


title: Het_Z_Q175_(neo-)_KI_Cortex_female_rep3 [mRNA]

description:
Q175NM0012_03_Left_Cortex
mRNA
404248_Q175NM0012_03_Left_Cortex_L30
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx


title: NGO_sc65

value: ICR


title: NGO_sc64

value: oocyte


title: genomic DNA from neuroblastoma 41

source_name: neuroblastoma 41

value: ALT positive

tag: mycn status

value: MYCN-non-amplified

value: TERT expression low

value: neuroblastoma


title: genomic DNA from neuroblastoma 8

source_name: neuroblastoma 8

tag: atrx status


title: genomic DNA from neuroblastoma 169

source_name: neuroblastoma 169


title: NGO_sc69

value: < 20 microns


title: Ctrl [A2]

description: Gene expression in non-infected cells

extract_protocol: Total RNAs were prepared with the RNeasy Mini kit (Qiagen) according to the manufacturer’s instruction.

value: intestinal epithelial cells

value: Ctrl


title: NGO_sc63

value: wild type

value: Ovary


title: Het_Z_Q175_(neo-)_KI_Cortex_female_rep2 [mRNA]

description:
Q175NM0012_02_Left_Cortex
mRNA
404266_Q175NM0012_02_Left_Cortex_L66
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: 6 months


title: genomic DNA from neuroblastoma 368

source_name: neuroblastoma 368

value: TERT non-rearranged

value: ATRX mutated


title: Het_Z_Q175_(neo-)_KI_Cortex_female_rep1 [mRNA]

description:
Q175NM0012_01_Left_Cortex
mRNA
404244_Q175NM0012_01_Left_Cortex_L34
processed data file: Counts and FPKM from Q175 neo-in vs neo-out study.xlsx

value: Het Z_Q175 (neo-) KI

value: female


title: NGO_sc62


title: Ctrl [A1]

description: Gene expression in non-infected cells