title: TM-4 EtOH1 03072011

description:
biological rep1
EtOH-treated  HTM TM-4 cells
isolated TM cells from 27 yr old donor eye
gene expression from isolated human trabecular meshwork cells


title: TM-4 EtOH3 03072011

status: Public on Dec 20 2018

type: RNA

city: MADISON

first: Donna

last: Peters

state: WI- WISCONSIN

address: 1300 UNIVERSITY AVE

department: Pathology & Laboratory Medicine

country: USA

institute: UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE

description:
biological rep2
EtOH-treated  HTM TM-4 cells
isolated TM cells from 27 yr old donor eye
gene expression from isolated human trabecular meshwork cells

hyb_protocol: Following fragmentation, 2.5ug ss cDNA was hybridized for 16 hr at 45C on GeneChip Human Array St 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were read using the GeneChip G7 Scanner

data_processing: Raw data was anlyzed using the open source software Bioconductor 2.9 in R. RMA was used for normalization of data using the AFFY package

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: 6-day EtOH treatment

label_protocol: Biotinylated cDNA was prepared the GeneChip WT terminal labeling kit

growth_protocol: human trabecular meshwork cells were cultured in low glucose DMEM, 15% fetal bovine serum (FBS), 1ng/ml FGF-2, 1% amphoteracin B, and 0.05% gentamicin until they reached conlfuency

extract_protocol: Total RNA was extracted using the QIAshredder and RNAeasy Plus mini kits (Qiagen, Inc) according to manufacturer's instructions. cDNA synthesis from 300ng of total RNA was done using the GeneChip WT cDNA synthesis kit

treatment_protocol: Confluent cultures were treated with  500nM dexamethasone dissolved in 0.1% EtOH or 0.1% EtOH for 6 days. Media used was DMEM containing10% FBS, 1% amphoteracin and 0.05% gentamicin. FGF-2 was not present

tag: tissue

value: trabecular meshwork cells

tag: isolate

tag: donor age


title: IFNmockCD103-2_S14

type: SRA

city: Parkville

first: Joel

middle: Zhi-Iong

last: Ma

state: Victoria

address: Grattan Street

country: Australia

institute: University of Melbourne

description:
Batch 2 - 150928_SN7001291_0299_AHYLW2ADXX
counts.tsv

library_source: transcriptomic

data_processing:
RNA-seq reads were aligned to the mouse genome mm10 using STAR (Dobin et al., 2013). Aligned fragments were summarised by gene (mm10 annotation from Ensembl) using featureCounts (Liao et al., 2014), ignoring those where both reads of the pair had mapping quality scores <10. Raw counts were transformed to log Counts Per Million (CPM) for visualisation. Normalisation and differential expression testing was conducted using edgeR (Robinson et al., 2010). The HTSFilter package (Rau et al., 2013) was used to remove genes with consistent low expression following normalisation and testing as suggested by the HTSFilter documentation.
For the IAV genome, RNAseq reads were aligned to a synthetic genome containing the 8 gene segments of the PR8 virus retrieved from NCBI using Tophat (Trapnell et al., 2009). Aligned reads were assigned to the appropriate viral segments using feature Counts function from Bioconductor Rsubread package (Liao et al., 2013). Differential expression analysis was performed on normalised counts in every viral segment by the total (virus and mouse) number of reads in each sample with limma package (Ritchie et al., 2015), treating every viral segment as a gene.
Genome_build: mouse genome mm10

organism: Mus musculus

source_name: IFNAR2-/- lung lobes, Allantoic fluid (Mock), 9h post intranasal

extract_protocol:
Lung lobes were processed as described in Ma et al. ~3000 cells were collected for each sample. Total RNA was extracted from sorted cells using the RNeasy Micro Kit (Qiagen).
First strand cDNA synthesis and tailing by reverse transcription was performed using Clontech’s proprietary SMART (Switching Mechanism at 5’ End of RNA Template) technology. Following first strand synthesis, cDNA was amplified 13 cycles by LD PCR using blocked PCR primers. Amplified cDNA was purified using AMPure XP prior to QC using the Bioanalyser 2100 HS DNA kit (Agilent Technologies). Library preparation of purified amplified cDNA was performed following Nextera XT library preparation (Illumina). Following QC, 150pg of cDNA was tagmented (simultaneously fragmented with adaptors inserted) using Nextera transposon. Molecular barcodes were incorporated during 12 cycles of amplification followed by purification using AMPure XP. The libraries passed a quality checkpoint (Qubit and Bioanalyser HS DNA) prior to normalisation and pooling before loading onto a HiSeq 2500 (Illumina) sequencer for paired-end sequencing. The libraries were each sequenced to 10-20 million reads.
RNA-seq and library construction were performed as 4 independent batches.

value: LUNG LOBES

tag: mouse strain

tag: infection


title: 35S:LBD16-GR_CHX_rep1

city: Kobe

first: Hidehiro

last: Fukaki

state: Hyogo

address: Rokko-dai 1-1

country: Japan

institute: Kobe University

description: Gene expression data from 5-day-old LBD16-GR roots CHX treatment (4h)

hyb_protocol: Hybridization, washing, staining procedures were run on Fluidics Station 450 (Affymetrix) with GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G.

data_processing: Data procession was performed with Expression Console Version 1.3 (Affymetrix).

organism: Arabidopsis thaliana

source_name: Arabidopsis 5-day-old root

label_protocol: Sense-strand DNA target preparation was performed in combination with Ambion WT Expression Kit (Affymetrix) and GeneChip WT Terminal Labeling Kit and Controls Kit (Affymetrix)

growth_protocol: Arabidopsis seedlings of 35S:LBD16:GR arf7 arf19 were grown for 5 days on 1x MS agar plate under continuous light condition.

extract_protocol: Total RNA was extracted with RNeasy Plant Mini Kit (QIAGEN).

treatment_protocol: 5-day-old seedlins of 35S:LBD16:GR arf7 arf19 were treated with/without 2 µM DEX and 10 µM CHX for 4 hours

tag: genotype

value: 5-day-old root

tag: treatment

value: 10 µM CHX treatment for 4 hours


title: TM-2 EtOH4_10182010

description:
technical rep6
EtOH-treated  HTM TM-2 cells
isolated TM cells from 27 yr old donor eye
gene expression from isolated human trabecular meshwork cells


title: IFNmockCD103_S14

description:
Batch 1 - 150922_SN7001291_0298_AHVL7LADXX
counts.tsv

value: Allantoic fluid (Mock), 9h post intranasal


title: IFNmockCC-4_S16

description:
Batch 4 - 151106_SN7001291_0311_BHYLF2ADXX
counts.tsv


title: puchi-2, TOLS2, biological rep3

address: 1-1 Rokkodai

department: Department of Biology

hyb_protocol: Hybridization, washing, and staining procedures were run on Fluidics Station 450 (Affymetrix) with GeneChip Hybridization, Wash, and Stain Kit (Affymetrix).

data_processing: The data were analyzed with RMA function of R's 'oligo' library.

source_name: puchi-2 root tip_TOLS2-treated

label_protocol: Sense-strand DNA target preparation was performed in combination with WT Expression Kit (Affymetrix) and GeneChip WT Terminal Labeling Kit and Controls Kit (Thermo Fisher Scientific) following the manufacturer's protocols.

growth_protocol: seeds inbibed in dark and 4 degree for 2 days are sowed on the NY-100 mesh on 1xMS 1% sucrose 0.5% gellan gum plate and grown on continuous light and 23 degree condition for 5 days.

extract_protocol: Collect root tips of approximately 1 cm and extract RNA by RNeasy Plant Mini Kit (Qiagen).

treatment_protocol: seedlings are transfered to medium with or without 1 µM TOLS2 peptide.

tag: genotype/variation

tag: treated with

value: 1 µM TOLS2 peptide

value: root tips


title: puchi-2, TOLS2, biological rep2


title: puchi-2, control, biological rep3

source_name: puchi-2 root tip_control

value: none (control)


title: IFNmockCC-3_S16

description:
Batch 3 - 151102_SN7001291_0303_BH5N3GADXX
counts.tsv


title: TM-2EtOH1_05252010

description:
technical rep5
EtOH-treated  HTM TM-2 cells
isolated TM cells from 27 yr old donor eye
gene expression from isolated human trabecular meshwork cells


title: puchi-2, control, biological rep2


title: rlk7-3, TOLS2, biological rep3

source_name: rlk7-3 root tip_TOLS2-treated


title: IFNmockCD103-3_S14


title: rlk7-3, TOLS2, biological rep2


title: puchi-2, TOLS2, biological rep1


title: rlk7-3, TOLS2, biological rep1


title: IFNmockCC-2_S16


title: rlk7-3, control, biological rep3

source_name: rlk7-3 root tip_control


title: puchi-2, control, biological rep1


title: IFNmockCC_S16


title: IFNmockAM-4_S13


title: IFNmockAM-3_S13


title: TM-2 EtOH1_06292010

description:
technical rep1
EtOH-treated  HTM TM-2 cells
isolated TM cells from 27 yr old donor eye
gene expression from isolated human trabecular meshwork cells


title: TM-4 DEX6 03072011

description:
biological rep3
Dex-treated  HTM TM-4 cells
isolated TM cells from 27 yr old donor eye
gene expression from isolated human trabecular meshwork cells

source_name: 6-day DEX treatment


title: TM-4 DEX4 03072011

description:
biological rep2
Dex-treated  HTM TM-4 cells
isolated TM cells from 27 yr old donor eye
gene expression from isolated human trabecular meshwork cells


title: TM-4 DEX2 03072011

description:
biological rep1
Dex-treated  HTM TM-4 cells
isolated TM cells from 27 yr old donor eye
gene expression from isolated human trabecular meshwork cells


title: rlk7-3, control, biological rep1


title: IFNmockAM-2_S13


title: wild-type, TOLS2, biological rep3

source_name: wild-type root tip_TOLS2-treated

value: wild type


title: TM-2 ETOH_0413201

description:
technical rep3
EtOH-treated  HTM TM-2 cells
isolated TM cells from 27 yr old donor eye
gene expression from isolated human trabecular meshwork cells


title: TM-2 DEX3_10182010

description:
technical rep6
Dex-treated  HTM TM-2 cells
isolated TM cells from 27 yr old donor eye
gene expression from isolated human trabecular meshwork cells


title: TM-2 DEX2_05252010

description:
technical rep5
Dex-treated  HTM TM-2 cells
isolated TM cells from 27 yr old donor eye
gene expression from isolated human trabecular meshwork cells


title: wild-type, TOLS2, biological rep1


title: wild-type, TOLS2, biological rep2


title: rlk7-3, control, biological rep2


title: IFNmockAM_S13


title: TM-2 EtOH9 0525201

description:
technical rep2
EtOH-treated  HTM TM-2 cells
isolated TM cells from 27 yr old donor eye
gene expression from isolated human trabecular meshwork cells


title: IFNmockAECII-4_S15


title: 150130_SND393_B_L003_HLD-10b

city: Villeurbanne

first: aurore

last: gallot

address: 43, Bd du 11 Novembre 1918

country: France

institute: universite Lyon 1

data_processing:
Low quality bases at the ends of reads were trimmed using Trimmomatic-0.36: adaptors-containing reads, low quality reads (scores phred < 30) and N containing reads were filtered out.
Curated reads were then processed through TopHat-Cufflinks pipeline: paired-reads of each sample were aligned to Venturia canescens genome with TopHat was used with each of the 18 library as input, with the following parameters: stranded library (first strand), 5 mismatches/indel allowed, and report the best alignment possible for each read.
After mapping, resulting alignment files were provided to Cufflinks that generated a transcriptome assembly for each sample, annotated into genes, transcripts and isoforms.
The 18 transcriptomes were merged into one master transcriptome with Cuffmerge. This final transcriptome assembly contains a total of 16,752 genes, and provides a uniform basis for calculating gene expression in each condition.
The gene model produced with Cuffmerge was combined to the 18 mapping files previously obtained with TopHat for each gene in each library. The final raw count table was obtained by using HTSeq.
Genome_build: v1.0 http://bipaa.genouest.org/sp/venturia_canescens/
Supplementary_files_format_and_content: tab-delimited text file include raw count values for each sample

organism: Venturia canescens

source_name: head

growth_protocol: Wild parasitic wasps were collected via a large field sampling during summer 2014 in orchards of southern France (Valence, N 44°58’21’’ E 4°55’39’’). Wasps were maintained on the host Ephestia kuehniella (Lepidoptera: Pyralidae) in climatic chamber (25°C, 60% humidity, DL 12:12) and fed with 50/50 honey/water solution.

extract_protocol:
A total of 10 individual’s heads were collected per experimental condition and pooled. Total ). RNA was extracted using Qiazol reagent and RNeasy MiniKit according to manufacturer protocol (Qiagen), with optional DNase treatment (Thermo Fisher Scientific).
Polyadenylated RNA were enriched from 1 mg of high-quality total RNA with oligo-dT magnetic beads, fragmented and converted to cDNA (Illumina TruSeq Stranded mRNA Library Prep kit). After adding an A in 3’ of cDNA, adapters were ligated, and fragments amplified with PCR to generate DNA colonies. Each library was labelled, multiplexed and pooled for sequencing on HiSeq 2500 Illumina sequencer (Fasteris, Switzerland), with paired-end protocol (2x125bp).

treatment_protocol: Virgin females newly emerged were individually placed in box and randomly submitted to one of the three following conditions: 1) with a compatible male (i.e. unrelated male), 2) with an incompatible male (i.e. a brother), 3) isolated (control); for a maximum duration of 10 minutes. This period coincides with an active male courtship behavior

tag: condition

value: courtship by compatible male (unrelated)

tag: biological replicate

tag: technical replicates

tag: gender

value: female

value: head


title: IFNmockAECII-3_S15


title: wild-type, control, biological rep3

source_name: wild-type root tip_control


title: IFNmockAECII-2_S15


title: 150130_SND393_B_L003_HLD-8b


title: IFNmockAECII_S15


title: 150130_SND393_B_L003_HLD-7b

value: courtship by incompatible male (brother)


title: C57PR8CD103-4_S2

source_name: C57/BL6 lung lobes, PR8 Influenza virus, 9h post intranasal

value: PR8, 9h post infection (intranasal)


title: TM-2 DEX1_10182010

description:
technical rep4
Dex-treated  HTM TM-2 cells
isolated TM cells from 27 yr old donor eye
gene expression from isolated human trabecular meshwork cells


title: 150130_SND393_B_L003_HLD-6b


title: TM-2 DEX10_05252010

description:
technical rep2
Dex-treated  HTM TM-2 cells
isolated TM cells from 27 yr old donor eye
gene expression from isolated human trabecular meshwork cells


title: wild-type, control, biological rep1


title: 150130_SND393_B_L003_HLD-5b


title: C57PR8CD103-2_S2

description:
Batch 2 - 150928_SN7001291_0299_AHYLW2ADXX
counts.tsv


title: TM-2 Dex1_06292010

description:
technical rep1
Dex-treated  HTM TM-2 cells
isolated TM cells from 27 yr old donor eye
gene expression from isolated human trabecular meshwork cells


title: TM-2 DEX_0413201

description:
technical rep3
Dex-treated  HTM TM-2 cells
isolated TM cells from 27 yr old donor eye
gene expression from isolated human trabecular meshwork cells


title: C57PR8CD103-3_S2


title: 150130_SND393_B_L003_HLD-4b

value: isolated (control)


title: wild-type, control, biological rep2


title: 150130_SND393_B_L003_HLD-9b


title: C57PR8CD103_S2

description:
Batch 1 - 150922_SN7001291_0298_AHVL7LADXX
counts.tsv


title: 150130_SND393_B_L003_HLD-3b


title: 150130_SND393_B_L003_HLD-2b


title: 141114_SND405_A_L008_HLD-10


title: LX-ZLQ-KI-1

city: Beijing

first: Liqing

last: Cheng

state: Beijing

address: Tsinghua University,Hai Dian, Beijing

department: school of medicine

country: China

institute: Tsinghua university

description: CD4+YFP+ Treg cells were sorted from Foxp3Cre-YFP /malt1fl/C472A  mice (6w old), which means Malt1 protease activity was specifically inhibited in Treg cells

data_processing:
Illumina Casava software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using hisat2 version 2.1.0 by Daehwan Kim with parameters -p 16 -5 9 --qc-filter --mm --dta
Fragments Per Kilobase of exon per million reads (FPKM) were calculated using Cufflinks v2.2.1.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: CD4+YFP+ Treg cells

extract_protocol:
Total RNA was extracted by using Trizol according to the manufactural protocol (Invitrogen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: CD4+YFP+ Treg cells

tag: strain

tag: age

value: 6 weeks

value: Foxp3Cre-YFP /malt1fl/C472A  mice (Malt1 inhibited in Treg cells)


title: C57PR8CC-3_S4

description:
Batch 3 - 151102_SN7001291_0303_BH5N3GADXX
counts.tsv

value: LUNG LOBES


title: C57PR8CC-2_S4


title: LX-ZLQ-KO

description: CD4+YFP+ Treg cells were sorted from Foxp3Cre-YFP /malt1fl/fl  mice (21d old), which means Malt1 was specifically deleted in Treg cells

value: Foxp3Cre-YFP /malt1fl/fl  mice (Malt1 deleted in Treg cells)


title: C57PR8CC_S4


title: 141114_SND405_A_L008_HLD-8


title: C57PR8AM-4_S1

description:
Batch 4 - 151106_SN7001291_0311_BHYLF2ADXX
counts.tsv


title: LX-ZLQ-WT-1

description: CD4+YFP+ Treg cells were sorted from Foxp3-Cre-YFP reporter wild type mice (21d old)

value: Foxp3-Cre-YFP reporter wild type mice


title: 141114_SND405_A_L008_HLD-9


title: LX-ZLQ-WT-2

description: CD4+YFP+ Treg cells were sorted from Foxp3-Cre-YFP reporter wild type mice (6weeks old)


title: 141114_SND405_A_L008_HLD-7


title: 141114_SND405_A_L008_HLD-6


title: C57PR8AM-2_S1


title: 141114_SND405_A_L008_HLD-5


title: C57PR8AM-3_S1


title: C57PR8AM_S1


title: LX-ZLQ-KI-2


title: C57PR8CC-4_S4


title: 141114_SND405_A_L008_HLD-4


title: C57PR8AECII-4_S3


title: C57PR8AECII-3_S3


title: 141114_SND405_A_L008_HLD-3


title: C57PR8AECII-2_S3


title: 141114_SND405_A_L008_HLD-2


title: C57PR8AECII_S3


title: C57mockCD103-4_S6

source_name: C57/BL6 lung lobes, Allantoic fluid (Mock), 9h post intranasal


title: FMDV_3

city: Wuhan

first: Jiadai

last: Li

state: Hubei

address: Luojiashan street  No.16

department: College of Life Science

institute: Wuhan University

data_processing:
The cDNA library was constructed following  the  standard  protocols provided  by  Illumina (NEBNextUltraTMRNA  library  Prep  kit,  Illumina,  USA).
The clean reads used for further analysis were acquired by filtering the raw data utilizing Cutadapt software.
The clean reads were aligned to the reference genome by HISAT software.
Genome_build: https://www.ncbi.nlm.nih.gov/genome/?term=txid10036[orgn]
Supplementary_files_format_and_content: tab-delimited text files including: Gene id, fpkm, chromosome, Strand, start, end and length for each Sample

organism: Mesocricetus auratus

source_name: Baby Syrian Hamster Kidney

growth_protocol: The BHK-21 cells were cultured in Minimum Essential Medium supplemented with 10% fetal bovine serum at 37℃ with 5% CO2.

extract_protocol:
Total RNA was extracted with RNAiso Plus (Takara, Japan) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BHK-21 was infected with FMDV at 10^(-3) TCID50/cell according to standard infection protocol.

value: fibroblast

value: kidney


title: C57mockCD103-3_S6

value: Allantoic fluid (Mock), 9h post intranasal


title: FMDV_1


title: BHK-21_3


title: Primary cutaneous mast cell tumour_non-metastasising_rep16 [W2]

city: Newmarket

first: Mike

last: Starkey

address: Lanwades Park

country: United Kingdom

institute: Animal Health Trust

hyb_protocol: 5µg of each labelled cDNA was included in a 125µl 'hybridisation cocktail' comprising 1 x Hyb Add 1, 30pM Control Oligo B2, 1 x Hybridisation Controls, 1 x WT Hyb Add 4 and 1 x WT Hyb Add 6. The cocktail was incubated at 99°C for 5 min and then at 48°C for 5 min, and centrifuged for 5s to remove insoluble material. Hybridisation was performed at 48°C for 20h in the GeneAtlas Hybridisation Station. Post-hybridisation washing and staining (SensationPlus.xml washing and staining protocol; IVT/WT Wash/Stain and Imaging Tray maps) was performed using the GeneAtlas System Fluidics Station.

scan_protocol: Arrays were scanned using the GeneAtlas System Imaging Station.

data_processing:
Gene-level probe set expression values were generated by quantile normalisation, log2 transformation and signal summarisation, performed using the Robust Multichip Analysis algorithm, implemented within ‘Affymetrix Expression Console Software 1.3’.
probe group file: CanGene-1_1-st-v1.na36.canfam2.probeset.csv
meta-probeset file: CanGene-1_1-st-v1.na36.canfam2.transcript.csv
Gene-level probe set expression values generated by quantile normalisation, log2 transformation and signal summarisation.

label: Biotin

organism: Canis lupus familiaris

source_name: Primary cutaneous mast cell tumour, non-metastasising

label_protocol: Fragmented, biotinylated double-stranded cDNA was prepared from 50ng of each total RNA sample using the SensationPlus FFPE amplification and WT labelling Kit (ThermoFisher Scientific).

extract_protocol: Total RNA was isolated using the RecoverAll Total Nucleic Acid Isolation Kit. RNA was treated with Heparinase I (10U/µg RNA) in 5mM Tris-HCl (pH7.5), 1mM CaCl2, 4U/µl RNasin Plus RNase Inhibitor for 3h at 25°C, and subject to further DNase digestion (TURBO DNA-free kit).

tag: breed

value: Whippet

value: primary cutaneous mast cell tumour

tag: metastatic status

value: Non-metastasising


title: Primary cutaneous mast cell tumour_metastasising_rep17 [SBT1]

source_name: Primary cutaneous mast cell tumour, metastasising

value: Staffordshire Bull Terrier

tag: tissue

value: Metastasising


title: Primary cutaneous mast cell tumour_non-metastasising_rep15 [SBT2]


title: C57mockCD103-2_S6


title: Primary cutaneous mast cell tumour_metastasising_rep18 [W1]


title: Activated Ezh2-knockout CD8+ Tcells, mouse #4

city: Ann Arbor

first: Rork

last: Kuick

state: MI

address: University of Michigan, SPH II, 1415 Washington Heights, Room M2533

institute: University of Michigan

hyb_protocol: standard Affymetrix procedures, using Affymetrix HT Mouse 430 PM Array Plates

scan_protocol: standard Affymetrix procedures

data_processing: RMA was used to obtain (base 2 log-transformed) estimated expression values. Note there are no mismatch (MM) probes on this array.

source_name: Ezh2-knockout mouse #4 CD8+ T-cells

label_protocol: About 200 ng of total RNA was processed using the Nugen Ovation Pico WTA system V2 kit, to produce biotinylated cRNA targets.

extract_protocol: Total RNA was extracted from CD8+ T-cells using Trizol (Invitrogen) and cleanup performed with an RNeasy kit (Qiagen).

value: activated with anti-CD3 and anti-CD38 antibodies for 3 days

tag: background strain

value: C57BL/6 (B6) mice

value: Conditional knockout of both Ezh2 alleles

value: CD8+ T-cells

tag: Sex

value: male


title: BHK-21_2


title: C57mockCD103_S6

tag: mouse strain

tag: infection


title: Activated Ezh2-knockout CD8+ Tcells, mouse #6

source_name: Ezh2-knockout mouse #6 CD8+ T-cells

tag: treatment

tag: genotype


title: Naïve Ezh2-knockout CD8+ Tcells, mouse #6

value: without activation


title: Naïve Ezh2-knockout CD8+ Tcells, mouse #4


title: FMDV_2


title: Naïve Ezh2-knockout CD8+ Tcells, mouse #5

source_name: Ezh2-knockout mouse #5 CD8+ T-cells


title: Activated Ezh2-wildtype CD8+ Tcells, mouse #3

source_name: Ezh2-wildtype mouse #3 CD8+ T-cells

value: Wildtype at Ezh2


title: BHK-21_1


title: Activated Ezh2-wildtype CD8+ Tcells, mouse #2

source_name: Ezh2-wildtype mouse #2 CD8+ T-cells


title: Primary cutaneous mast cell tumour_metastasising_rep15 [LR9]

value: Labrador Retriever


title: C57mockCC-4_S8

value: LUNG LOBES


title: C57mockCC-3_S8


title: Naïve Ezh2-wildtype CD8+ Tcells, mouse #3


title: C57mockCC-2_S8


title: Primary cutaneous mast cell tumour_non-metastasising_rep13 [LR7]


title: Activated Ezh2-wildtype CD8+ Tcells, mouse #1

source_name: Ezh2-wildtype mouse #1 CD8+ T-cells


title: C57mockCC_S8


title: Activated Ezh2-knockout CD8+ Tcells, mouse #5


title: ALE_38.28_replicate1

city: San Diego

first: Amitesh

last: Anand

state: California

address: 9500 Gilman Drive

department: Bioengineering

institute: UCSD

description:
log_tpm_GEO.csv
QN28A

data_processing:
The base calling was done using Illumina’s Real-Time Analysis (RTA) v2.7.7; data was converted to fastq and demultiplexed using Illumina’s bcl2fastq2 Conversion Software v2.20;
Sequence reads generated from RNA-Seq were mapped onto the reference genome (NC_000913.2) using bowtie with default options to generate SAM output files
Transcript abundance was quantified using summarizeOverlaps from the R GenomicAlignments package with strand inversion for the dUTP protocol and strict intersection mode
Estimated the dispersion of each gene using DESeq2
Transcript per Million (TPM) were calculated by DESeq2
Genome_build: E.coli genome(NC_000913.3)
Supplementary_files_format_and_content: csv file includes TPM values for each Sample

organism: Escherichia coli K-12

source_name: bacteria

growth_protocol: Glycerol stocks of E. coli strains were inoculated into M9 minimal media with glucose as carbon source, supplemented with 1 ml trace element solution (100X). The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5).

extract_protocol: KAPA Stranded RNA-Seq Kit

tag: media

value: M9 minimal media w/ 4g/L glucose


title: ALE_37.25_replicate1

description:
log_tpm_GEO.csv
QN27A


title: ALE_37.25_replicate2

description:
log_tpm_GEO.csv
QN27B


title: C57mockAM-4_S5


title: ALE36.86_replicate2

description:
log_tpm_GEO.csv
QN26B


title: ALE_38.28_replicate2

description:
log_tpm_GEO.csv
QN28B


title: Primary cutaneous mast cell tumour_non-metastasising_rep14 [MS1]

value: Miniature Schnauzer


title: Naïve Ezh2-wildtype CD8+ Tcells, mouse #2


title: Primary cutaneous mast cell tumour_non-metastasising_rep12 [LR6]


title: Primary cutaneous mast cell tumour_metastasising_rep16 [LR10]


title: ALE36.86_replicate1

description:
log_tpm_GEO.csv
QN26A


title: C57mockAM-2_S5

value: Allantoic fluid (Mock), 9h post intranasal


title: Primary cutaneous mast cell tumour_non-metastasising_rep11 [LR4]


title: Primary cutaneous mast cell tumour_metastasising_rep14 [LR8]


title: ALE_30.83_replicate2

description:
log_tpm_GEO.csv
QN23B

value: Ferrous sulfate and sodium citrate


title: Primary cutaneous mast cell tumour_metastasising_rep13 [LR5]

value: primary cutaneous mast cell tumour


title: Primary cutaneous mast cell tumour_metastasising_rep11 [LR2]


title: Naïve Ezh2-wildtype CD8+ Tcells, mouse #1


title: Primary cutaneous mast cell tumour_metastasising_rep10 [LR1]


title: ALE_30.83_replicate1

description:
log_tpm_GEO.csv
QN23A


title: ALE_29.82_replicate2

description:
log_tpm_GEO.csv
QN22B


title: C57mockAM-3_S5


title: ALE_29.82_replicate1

description:
log_tpm_GEO.csv
QN22A


title: C57mockAECII-4_S7


title: C57mockAECII_S7


title: C57mockAECII-2_S7


title: ∆menF∆entC_replicate2

description:
log_tpm_GEO.csv
QN20B


title: Primary cutaneous mast cell tumour_metastasising_rep8 [GS1]

value: German Shepherd Dog


title: Primary cutaneous mast cell tumour_metastasising_rep12 [LR3]


title: ALE_39.91_replicate1

description:
log_tpm_GEO.csv
QN21A


title: ∆menF∆entC_replicate1

description:
log_tpm_GEO.csv
QN20A


title: C57mockAM_S5


title: Mutant78-M0ANT_Pooled

city: Gainesville

first: Robert

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

library_source: genomic

data_processing:
Demultiplexed subreads from sequencing were aligned to the A. thaliana ecotype Col-0 genome, using the coNvex Gap-cost alignMents for Long-Reads (NGMLR) software (ver. 0.2.7; Sedlazeck et al., 2018) using default parameters
Aligned subreads were submitted to the SV detection software Sniffles (ver. 1.0.8; Sedlazeck et al., 2018), with a required split-read support of 5, but otherwise using default parameters
Raw datasets were additionally curated to remove artefactual SVs caused by spurious alignments due to high coverage of organellar and some regions of the nuclear genome by aligned subreads. These appear in the variant call files as nuclear-organellar translocations, and regions highly-enriched in translocation breakpoints across all samples.
Genome_build: TAIR10
Supplementary_files_format_and_content: Sniffles output SV datasets are provided in the .bedpe format. Hand-curated .bedpe files are also provided, as these were primarily used for analysis in the study, and these are denoted by the FILT tag in their filenames

molecule: genomic DNA

source_name: Mutant Pools #7&8 from the M0 generation of ANT plants, comprised of: M0ANT_P19-1 H2, M0ANT_R2-1 E12, M0ANT_P19-1 H3, M0ANT_R2-2 F7, M0ANT_P19-1 G12, and M0ANT_C18-2 C10

growth_protocol: Wet-sterilized seeds were stored for 4-5 days at 4 °C to vernalize before being planted on Petri plates containing a Phytagel™-based nutrient media, supplemented with: 0.5x Murashige and Skoog (MS) salts [Caisson Laboratories], 0.5% (w/v) sucrose [Sigma], and 1x Gamborg’s Vitamin Mixture [Caisson Laboratories]. The plates were sealed with tape [Micropore™] and stored in a growth chamber at 19 ± 2 °C with 24-h lighting at approximately 80 µmol m-2 s-1 PAR. 14 days after planting, they were scored for mutation and germination rates. The plates remained in the growth chamber afterward, only being removed to track, transplant, and image mutants of interest.

extract_protocol:
A previously-developed DNA extraction protocol (LeFrois et al., 2016) was further modified to optimize yields from small samples and provide DNA suitable for PacBio sequencing. Samples were ground in 500 mL lysis buffer (100 mM EDTA, 50 mM EGTA, 50 mM Tris-Cl ph 7.5), 1 µL RNase A (100 mg/mL), and 55.6 µL 10% SDS. Samples were then incubated overnight at 55 °C with 44.4  µL Proteinase K (25 mg/mL). The following day, 1/3 volume of 5M Potassium Acetate (KOAc) was added, and the samples were placed on ice for 30-60 minutes, before being spun down at 4 °C for 5 minutes. The supernatant was then transfered to a new tube, spun an additional time, and transferred once more to a new tube. Isopropanol (0.7 vol) was added, and the solution set at room temperature for 30 minutes. Then, after a 10 minute centrifugation, the supernatant was decanted. The pellet was dried, and resuspended in 50 µL TE. 20 µL 7.5 M Ammonium Acetate (AmOAc) and 150 µL 95% EtOH were added, and the tube was mixed by inversion. The samples were set at -20 °C for 2 hours, and centrifuged at 4 °C for 10 minutes. The supernatant was decanted, and the pellet washed three times with 70% EtOH. After drying, the pellet was resuspended in 25-50 µL TE and stored at -20 °C
Barcoded, large-insert (10 kb) libraries were constructed, using 600 ng of pure, high MW DNA (>40 kb) from the five different Arabidopsis samples (Mutant1-M0ANT W3-2 D7, Mutant2- M0ANT H16-2 , Mutant4-M1BNL H13-1 H10, Mutant5-M1BNL P18-3 F3, and Mutant7-M0ANT-Pooled-Mutants). The integrity of the samples was evaluated on the Agilent TapeStation using a genomic tape. A slightly modified protocol from the one recommended by PacBio for multiplex SMRT sequencing of bacterial genomes (manual PN 101-069-200-02) was used, in conjunction with barcodes from the Barcoded Adaptor kit 8B (PN101-475-100). Briefly, DNA (in 150 ul) was sheared down to 10 kb using Covaris g-TUBES (Covaris Inc. Cat # 520079), using two passes at 7,000 rpm. The resulting size of the fragments was verified on the Agilent TapeStation (genomic tape). The library construction reactions for individual samples consisted of the following sequential steps: ExoVII treatment, DNA Damage Repair, End Repair, and Blunt-end ligation of barcoded SMRT bell adaptors. After ligation, all samples were pooled, AMPure-cleaned, and submitted to an ExoIII/ExoVII treatment for elimination of excess adaptors and of any damaged DNA. This procedure resulted in 350 ng of adaptor-ligated SMRT bell library. The final library was further size-selected in the SageELF™ instrument (Cat# ELD 7510), using 0.75% agarose gel cassettes and the 1-18 kb v2 cassette definition program. Fractions in wells 5-9 contained library fragments in the 5-20 kb range with ~10 kb average (TapeStation). The desired SageELF fractions were cleaned using AMPure magnetic beads (0.6:1.0 beads to sample ratio) and eluted in 15 ul of 10 nM Tris HCl, pH 8.0.
Pacific Biosciences SEQUEL, Long-Read Whole-Genome Sequencing:   Sequencing was performed at the UF Interdisciplinary Center for Biotechnology Research (ICBR). Sequencing was done using the Chemistry Bundle 5.0.1 that includes Sequencing and Binding kits 2.1 in combination with the SMRTLink 5.1 software. The pooled library at 8 pM, with each sample being uniquely barcoded within it, was applied to the PacBio SEQUEL sample plate by diffusion-loading for sequencing on a single LR-SMRT cell with 20-hr data collection. All other steps for sequencing were done according the protocol recommended by the PacBio sequencing calculator.

treatment_protocol: No additional treatments were applied to the mutant seedlings before extract preparation.

tag: ecotype

tag: radiation environment

value: Cosmic Radiation

tag: material type

value: Whole-Plants

tag: state at extraction

value: Frozen Prior

tag: biomass for extract

value: 15 mg

value: 17 days old (C18-2 C10), 21 days old (all others), 24hr light grown

tag: growth protocol

value: solid 0.5x MS media plates; grown at 19 ± 2 °C, with 24-h light at approximately 80 µmol m-2 s-1


title: Primary cutaneous mast cell tumour_metastasising_rep9 [HV1]

value: Hungarian Vizsla

value: Metastasising


title: ∆menF∆entC (citrate supp)_replicate2

description:
log_tpm_GEO.csv
QN2B

tag: strain


title: Mutant5-M1BNL_P18-3 F3

source_name: Mutant #5, from the M1 generation of BNL plants, from Plate 3 of bin P18, on grid F3

value: Simulated Cosmic Radiation

value: Single Leaf

value: Fresh

value: 20 mg

tag: age

value: 45 days old, 24hr light grown

value: solid 0.5x MS media plates; grown at 19 ± 2 °C, with 24-h light at approximately 80 µmol m-2 s-1; Transferred to soil at 14 days in similar conditions


title: C57mockAECII-3_S7

value: LUNG LOBES

value: Allantoic fluid (Mock), 9h post intranasal


title: ∆menF∆entC (citrate supp)_replicate1

description:
log_tpm_GEO.csv
QN2A

value: M9 minimal media w/ 4g/L glucose

value: Ferrous sulfate and sodium citrate


title: ALE_39.91_replicate2

description:
log_tpm_GEO.csv
QN21B


title: Mutant4-M1BNL_H13-1 H10

source_name: Mutant #4, from the M1 generation of BNL plants, from Plate 1 of bin H13, on grid H10

value: 10 mg


title: Primary cutaneous mast cell tumour_non-metastasising_rep10 [GR4]

tag: breed

value: Golden Retriever

value: primary cutaneous mast cell tumour

tag: metastatic status

value: Non-metastasising


title: Primary cutaneous mast cell tumour_metastasising_rep6 [D1]

value: Dogue de Bordeaux

tag: tissue


title: Primary cutaneous mast cell tumour_non-metastasising_rep7 [ETT1]

value: English Toy Terrier


title: Primary cutaneous mast cell tumour_metastasising_rep7 [GR1]

value: Metastasising


title: Primary cutaneous mast cell tumour_non-metastasising_rep8 [GR2]


title: Mutant1-M0ANT_W3-2 D7

source_name: Mutant #1, from the M0 generation of ANT plants, from Plate 2 of bin W3, in grid D7

value: Cosmic Radiation

value: Whole-Plant

value: Frozen Prior

value: 44 days old, 24hr light grown

value: solid 0.5x MS media plates; grown at 19 ± 2 °C, with 24-h light at approximately 80 µmol m-2 s-1


title: TM-2 EtOH2_10182010

description:
technical rep4
EtOH-treated  HTM TM-2 cells
isolated TM cells from 27 yr old donor eye
gene expression from isolated human trabecular meshwork cells

source_name: 6-day EtOH treatment

value: trabecular meshwork cells

tag: isolate

tag: donor age


title: Primary cutaneous mast cell tumour_non-metastasising_rep9 [GR3]


title: Primary cutaneous mast cell tumour_metastasising_rep5 [CCR1]

value: Curly Coated Retriever


title: Mutant2-M0ANT_H16-2 K9

source_name: Mutant #2, from the M0 generation of ANT plants, from Plate 2 of bin H16, in grid K9

value: 45 days old, 24hr light grown


title: Primary cutaneous mast cell tumour_non-metastasising_rep6 [CB5]

value: Cross-breed


title: Primary cutaneous mast cell tumour_non-metastasising_rep4 [CB2]


title: Primary cutaneous mast cell tumour_metastasising_rep4 [CB6]


title: ZIKV-infected A549 cells rep1

city: Guangzhou

first: Wang

last: Yi

address: Room1426, Yixue Keji Lou,74 Zhongshan 2nd Road

department: Department of Immunology

institute: Zhongshan School of Medicine, Sun Yat-sen University

description: Gene expression after 24 hours of ZIKV infection

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

data_processing: The data processing were performed with the GeneSpring GX version 12.1 software package (Agilent Technologies). Selecting differentially expressed genes according to the P-value and fold change. P-value <0.05 and fold change >2 for mRNA or lncRNA, were considered as significant difference.

source_name: ZIKV-infected A549 cells

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Human lung carcinoma epithelial cells (A549, ATCC CCL-185) were maintained in Dulbecco Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) (Gibco) at 37 C with 5% CO2. The media were added with 100 units/ml of streptomycin and penicillin (Invitrogen).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Human lung carcinoma epithelial cells (A549) were seeded into 12-well plates. Cells were infected with ZIKV at an multiplicity of infection (MOI) of 8. Then the samples were harvested for further treatment.

tag: cell line

value: human lung carcinoma epithelial cells (A549)

tag: infection

value: ZIKV infection


title: Cd Treated_rep2

city: Allahabad

first: Ashutosh

last: Mani

address: Teliarganj

country: India

institute: MNNIT, Allahabad

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to a Genotypic designed Chickpea GXP_8X60K (AMADID: 037094). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65°C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327) and scanned using the Agilent Microarray Scanner (AgilentTechnologies, Part Number G2600D).

scan_protocol: Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the quantile normalization method .Gene based analysis was performed.

organism: Cicer arietinum

source_name: Cd Treated_rep2

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

extract_protocol: RNA extraction was perforemd by using Qiagen Rneasy mini kit following the manufacturer's recommendations.

tag: agent

value: Cd

tag: leaves

value: 15 days leaves


title: As Treated_rep1

source_name: As Treated_rep1

value: As


title: Cr Treated_rep1

source_name: Cr Treated_rep1

value: Cr


title: Primary cutaneous mast cell tumour_metastasising_rep3 [CB4]

source_name: Primary cutaneous mast cell tumour, metastasising

value: primary cutaneous mast cell tumour


title: Primary cutaneous mast cell tumour_metastasising_rep2 [CB1]

value: Metastasising


title: Primary cutaneous mast cell tumour_non-metastasising_rep5 [CB3]

source_name: Primary cutaneous mast cell tumour, non-metastasising

value: Non-metastasising


title: ZIKV-infected A549 cells rep3


title: Cd Treated_rep1

source_name: Cd Treated_rep1


title: Cr Treated_rep2

source_name: Cr Treated_rep2


title: As Treated_rep2

source_name: As Treated_rep2


title: Control A549 cells rep3

description: Gene expression after 24 hours of mock infection

source_name: Control A549 cells

value: mock infection


title: ZIKV-infected A549 cells rep2


title: Control_rep2

value: Control


title: Primary cutaneous mast cell tumour_non-metastasising_rep3 [B4]

value: Boxer


title: Control_rep1


title: Control A549 cells rep2


title: Primary cutaneous mast cell tumour_non-metastasising_rep1 [B2]


title: Primary cutaneous mast cell tumour_non-metastasising_rep2 [B3]


title: Kwon201408_XenopusHybrid_LELS1

status: Public on Dec 19 2018

city: Ulsan

first: Taejoon

last: Kwon

address: 50 Unist-gil

department: Department of Biomedical Engineering

country: South Korea

institute: Ulsan National Institute of Science and Technology

description:
Xenopus laevis
LELS1

data_processing:
Mapped paired-reads to primary transcripts with bwa mem (0.7.10)
Filtered out reads mapped on multiple targets (i.e. reads mapped on both species)
Genome_build: Xenopus transcripts UTA2014 version (uploaded to GEO)
Supplementary_files_format_and_content: indiv_tpm.txt.gz - TPM for each samples
Supplementary_files_format_and_content: fa.gz - transcripts FASTA file

molecule: polyA RNA

organism: Xenopus laevis

source_name: 9 hpf whole embryo

growth_protocol: Embryos at 9 hpf were collected

extract_protocol:
To isolate RNA, embryos at stage 9 were homogenized mechanically in TRIzol® (Thermo Fisher Scientific, Waltham, MA) using up to a 30-gauge needle and processed according to manufacturer instructions. After resuspension in nuclease-free H2O, RNAs were cleaned using a RNeasy kit (Qiagen Inc.) according to manufacturer instructions.
Libraries were prepared using manufacturer’s non-standard specific RNA-seq library protocol with poly-A capturing mRNA enrichment method (Illumina, CA, USA)

tag: developmental stage

value: 9 hpf


title: Kwon201408_XenopusHybrid_LELS3

description:
Xenopus laevis
LELS3


title: ChIP-seq_LTR5HS_Sp_KRAB_Cas9

city: Stanford

first: Daniel

middle: R

last: Fuentes

state: CA

address: 265 Campus Drive, G3065

department: Chemical and Systems Biology

institute: Stanford University

data_processing:
Base calling was performed using CASAVA 1.8
Reads were aligned to hg38 genome using bowtie2 2.2.9: “bowtie2 -p $threads --end-to-end --no-mixed --no-discordant --minins 100 --maxins 1000 -x hg38 -1 $read1 -2 read2 > aligned.sam”
Duplicate reads were removed using MarkDuplicates function of Picard tools 1.95: "picard-tools MarkDuplicates REMOVE_DUPLICATES=true I=$bam O=$unique.bam M=$metrics.txt"
Bigwig plots were generated using Deeptools 2.5.4: "bamCoverage --bam $.bam -o $.bw --binSize 10 --normalizeTo1x 2451960000 --extendReads --numberOfProcessors $threads"
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files (scores represent enrichment normalized to 1x genome coverage)

source_name: NCCIT cell line (human embryonic carcinoma)

growth_protocol: NCCIT cells were obtained from ATCC. NCCIT cells were grown in RPMI-1640 (Thermo Fisher Scientific, Waltham, MA, USA), supplemented with 10% FBS (Omega Scientific, Tarzana, CA, USA), 1x Glutamax (Thermo Fisher Scientific), 1x non-essential amino acids (Thermo Fisher Scientific), and 1x antibiotic/antimycotic (Thermo Fisher Scientific).

extract_protocol:
ChIP assays were performed as described previously (Rada-Iglesias et al., 2011). Briefly, approximately 10&7 NCCIT cells were fixed in 1% formaldehyde for 10 minutes at room temperature in PBS, then quenched with glycine to a final concentration of 0.125 M for 10 minutes. Chromatin was sonicated to 0.5-2.0 kb using Bioruptor (Diagenode, Liège, Belgium), cleared by centrifugation, divided into separate aliquots for each antibody, and incubated with 5 mg of antibody overnight at 4° C. Subsequently, 100 mL of Dynabeads protein G (Thermo Fisher Scientific) were added to the ChIP reactions and incubated for 4-6 hours at 4° C. Magnetic beads were washed and chromatin was eluted, followed by reversal of crosslinks overnight at 65° C, proteinase K and RNase A treatment, and DNA purification by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation. ChIP DNA was resuspended in water.
Libraries were prepared using Ovation Ultralow System V2 UDI (NuGEN Technologies, San Carlos, CA, USA) according to manufacturer’s instructions, starting with 10 ng of ChIP DNA. Library DNA was analyzed on Bioanalyzer DNA HS (Agilent, Santa Clara, CA, USA), then pooled and sequenced on a HiSeq 4000 (Illumina, San Diego, CA, USA) at the Stanford Genome Sequencing Service Center, using 2x150 sequencing with dual index read.

treatment_protocol: NCCIT cells were treated with doxycycline for four days before extraction to induce dCas9 expression

value: NCCIT

tag: cell type

value: Human embryonal carcinoma

tag: chip antibody

value: Cas9 (Active Motif 61757)

tag: grna target

tag: grna scaffold species

value: S. pyogenes

tag: dcas9 fusion expressed


title: ChIP-seq_LTR5HS_Sp_KRAB_Input


title: Control A549 cells rep1

value: human lung carcinoma epithelial cells (A549)


title: ChIP-seq_LTR5HS_Sp_KRAB_H3K9me3

value: H3K9me3 (Abcam ab8898)


title: ChIP-seq_LTR5HS_Sp_KRAB_H3K27ac

value: H3K27ac (Active Motif 39133)


title: Primary cutaneous mast cell tumour_metastasising_rep1 [B1]


title: ChIP-seq_LTR5HS_Sp_KRAB_H3K4me3

value: H3K4me3 (Active Motif 39159)


title: C-2W-B

city: Chicago

last: Cavanaugh

state: IL

address: 1050 W Sheridan Rd., Life Sciences Building Room 215

department: Biology

institute: Loyola University Chicago

data_processing:
Novogene filtered raw reads to remove reads containing adapters, reads containing N > 10% (N represents the bases that cannot be determined), and reads containing Phred quality score ≥5 over more than 50% of the read. Following filtering, >94.78% of reads remained for each sample.
Reads were mapped to Dmel Reference Genome (dm6) with RNA Star in Galaxy (using the public Galaxy server at usegalaxy.org). Drosophila_melanogaster.BDGP6.87.gtf was used for the annotation file and filtered to remove all non-coding genes because we were interested in identifying differentially expressed genes that encode for proteins.
The aligned BAM files were processed with MMquant to quantify the number of reads that mapped to each gene.
Genome_build: dm6
Supplementary_files_format_and_content: Tab-delimited text files contain number of mapped reads per gene as quantified by MMquant.

organism: Drosophila melanogaster

source_name: 24-hour schedule (LD 12:12; control group)

extract_protocol:
Total RNA was extracted at ZT0-3 with TRIreagent (Molecular Research Center, Inc., Cincinnati, OH) according to the manufacturer’s recommendations. Following phase separation, samples were additionally subjected to DNAse treatment and purification with the Zymo Direct-zol RNA kit (Zymo Research, Irvine, CA).
Library preparation was performed by Novogene with the NEB Next Ultra II kit

tag: strain

value: whole fly

tag: treatment

value: exposed to 2 weeks of 12hr light:12 hr dark


title: J-3W-B

source_name: LD 14:14; chronic circadian misalignment (CCM) group

value: exposed to 3 weeks of 14hr light:14 hr dark


title: J-2W-B

value: exposed to 2 weeks of 14hr light:14 hr dark


title: J-3W-A


title: C-2W-C


title: C-3W-C

value: exposed to 3 weeks of 12hr light:12 hr dark


title: J-2W-C


title: J-3W-C


title: J-2W-A


title: C-3W-A


title: ChIP-seq_LTR5HS_Sp_VPR_Input


title: ChIP-seq_LTR5HS_Sp_VPR_Cas9


title: C-2W-A


title: C-3W-B


title: ChIP-seq_LTR5HS_Sp_VPR_H3K4me3


title: ChIP-seq_LTR5HS_Sp_VPR_H3K9me3


title: ChIP-seq_LTR5HS_Sp_VPR_H3K27ac


title: ChIP-seq_WT_H3K4me3


title: ChIP-seq_WT_H3K9me3


title: ChIP-seq_WT_Cas9


title: ChIP-seq_WT_H3K27ac


title: LS_EVL37

city: Houston

first: Eduardo

last: Vilar

state: TX

address: 1515 Holcombe Blvd., Unit 1360

department: Clinical Cancer Prevention

institute: The University of Texas MD Anderson Cancer Center

description: colonic tubular adenoma from patient with Lynch Syndrome (LS)

data_processing:
mRNA sequences were aligned with Bowtie 1.1.2 on hg19 and quantified with RSEM 1.2.21 using default settings. RSEM expected counts were used for analysis
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited RSEM output with expected counts, TPM, FPKM values

source_name: tubular adenoma

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) and the RNeasy kit (Qiagen). RNA was quantified using Qubit (Life Technologies) and RNA quality was assessed with the Agilent 2100 Bioanalyzer to select samples with RNA integrity numbers (RIN) ≥8 for analysis.
Sample preparation, library construction, and sequencing was performed at the DNA Analysis Facility Core at MD Anderson

value: tubular adenoma

tag: disease state

value: Lynch Syndrome


title: LS_EVL38


title: LS_EVL29


title: LS_EVL40


title: ChIP-seq_WT_Input


title: FGO_sc142

first: Fan

last: Guo

address: 1 Beichen West Road, Chaoyang District

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

institute: Institute of Zoology, Chinese Academy of Sciences

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: 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.

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

tag: genotype

value: wild type

value: Ovary

value: oocyte


title: LS_EVL28

tag: tissue


title: FGO_sc141


title: FGO_sc138


title: FGO_sc137


title: GO3_sc118


title: GO3_sc125


title: GO3_sc122


title: GO3_sc116


title: GO2_sc139


title: FGO_sc140


title: GO2_sc137


title: GO2_sc138


title: FGO_sc135


title: GO3_sc121


title: GO3_sc123


title: GO3_sc120


title: GO2_sc136


title: FGO_sc139


title: GO3_sc124


title: GO2_sc134


title: GO2_sc135


title: FGO_sc136


title: GO2_sc132


title: GO2_sc131


title: GO2_sc130


title: GO3_sc117


title: GO1_sc148


title: GO2_sc129


title: GO1_sc147


title: GO1_sc146


title: GO1_sc144


title: GO1_sc142


title: GO1_sc140


title: GO1_sc137


title: GO1_sc133


title: GO1_sc145


title: GO1_sc141


title: GO1_sc136


title: GO1_sc131


title: GO1_sc143


title: GO1_sc139


title: GO1_sc132


title: GO1_sc138


title: GO1_sc134


title: GO1_sc135


title: GO2_sc133


title: ES_sc36

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: 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.

source_name: Embryonic stem cell

value: Embryonic stem cell


title: ES_sc38


title: ES_sc35


title: ES_sc37


title: ES_sc33


title: ES_sc39


title: ES_sc34


title: ES_sc32


title: ES_sc30


title: ES_sc31


title: ES_sc28


title: ES_sc27


title: ES_sc40


title: ES_sc23


title: ES_sc25


title: ES_sc22


title: ES_sc21


title: ES_sc20


title: ES_sc17


title: ES_sc14


title: ES_sc15


title: ES_sc18


title: ES_sc19


title: ES_sc12


title: ES_sc13


title: ES_sc29


title: ES_sc11


title: ES_sc10


title: ES_sc9


title: ES_sc7


title: GO3_sc119


title: ES_sc5


title: ES_sc8


title: ES_sc3


title: ES_sc4


title: ES_sc2


title: ES_sc24


title: ES_sc26


title: ES_sc1


title: M2_sc20

source_name: MⅡ Oocyte

value: MII oocyte


title: ES_sc16


title: M2_sc19


title: M2_sc18


title: M2_sc17


title: M2_sc16


title: M2_sc15


title: M2_sc13


title: M2_sc11


title: M2_sc12


title: M2_sc10


title: M2_sc8


title: M2_sc9


title: ES_sc6


title: M2_sc5


title: M2_sc6


title: M2_sc3


title: M2_sc1


title: M2_sc4


title: spleen_mutpbs_bs025

city: Santa Cruz

first: Susan

last: Carpenter

address: 1156 High Street

department: Molecular Cell and Developmental Biology

institute: University of California Santa Cruz

data_processing:
RNAseq 1: the 150x150bp pairedEnd reads were trimmed by 50bp at the 3prime end to 100x100bp
RNAseq 2: reads mapping (by bowtie2) to mouse repeatMasker elements were discarded
RNAseq 3: reads were mapped to mm10 by STAR (2.5.3a), aided by a gtf file based on Gencode VM9basic with 100bp overlap
RNAseq 4: duplicate read mappings of the same start and end position were discarded using samtools rmdup.
RNAseq 5: bam files were converted to mm10 genomic coverage using bedtools genomeCoverageBed
RNAseq 6: the dup-removed coverage was used to extract coverage of all exonic positions for each gene in UCSC KnownGenes for mm10.
RNAseq 7: the exonic coverage (from paired-end 100x100bp reads) for each gene was divided by 200 to get read counts per gene for input to DESeq2
RNAseq 8: DESeq2 was run using the read counts for UCSC KnownGenes.
RNAseq 9: DESeq2 pairwise comparisons were separately performed for lung tissue samples and spleen tissue samples.
RNAseq 10: Within each tissue, wild-type samples were compared to mutant and knockout samples. Mutant and knockout samples were compared to each other.
Genome_build: mm10
Supplementary_files_format_and_content: There are two text files containing all differentially expressed genes following LPS stimulation in the lung and spleen as measured using DESeq2 analysis. There is one Excel file with a separate worksheet for each DESeq2 pairwise comparison for some subset of genes that displayed a log2fold change of 1.2 with a P value of less than 0.05

source_name: lincRNA-Cox2 Mutant Spleen PBS

extract_protocol:
Following in vivo LPS challenge in which mice were injected by the intraperitoneal route with 20mg/kg LPS intraperitoneal lungs and spleens were extracted and placed in Trizol. RNA was extracted and 3ug was used to prepare libraries using illumna mRNA isolation kits
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Spleen

value: lincRNA-Cox2 Mutant

value: PBS


title: spleen_koxlps_bs027

source_name: lincRNA-Cox2 knockout Spleen LPS 6hr

value: lincRNA-Cox2 knockout

value: LPS


title: spleen_koxlps_bs028


title: spleen_koxpbs_bs030

source_name: lincRNA-Cox2 knockout Spleen PBS


title: spleen_koxlps_bs026


title: spleen_mutlps_bs022

source_name: lincRNA-Cox2 Mutant Spleen LPS 6hr


title: spleen_mutlps_bs021


title: spleen_mutlps_bs023


title: spleen_mutpbs_bs024


title: M2_sc14


title: spleen_wtxpbs_bs019

source_name: C56/Bl6 Wild Type Spleen PBS

value: Wild Type


title: M2_sc7


title: spleen_wtxlps_bs018

source_name: C56/Bl6 Wild Type Spleen LPS 6hr


title: spleen_wtxpbs_bs020


title: lungxx_koxpbs_bs014

source_name: lincRNA-Cox2 knockout lung PBS

value: Lung


title: spleen_wtxlps_bs016


title: lungxx_koxlps_bs012

source_name: lincRNA-Cox2 knockout lung LPS 6hr


title: lungxx_mutpbs_bs010

source_name: lincRNA-Cox2 Mutant Lung PBS


title: lungxx_mutpbs_bs009


title: lungxx_koxpbs_bs015


title: spleen_wtxlps_bs017


title: M2_sc2


title: lungxx_koxlps_bs013


title: lungxx_koxlps_bs011


title: lungxx_mutlps_bs006

source_name: lincRNA-Cox2 Mutant Lung LPS 6hr


title: lungxx_mutlps_bs008


title: spleen_koxpbs_bs029


title: lungxx_mutlps_bs007


title: lungxx_wtxpbs_bs005

source_name: C56/Bl6 Wild Type Lung PBS


title: lungxx_wtxpbs_bs004


title: lungxx_wtxlps_bs002

source_name: C56/Bl6 Wild Type Lung LPS 6hr


title: lungxx_wtxlps_bs003


title: lungxx_wtxlps_bs001


title: FGO_sc134

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: bw


title: FGO_sc133


title: FGO_sc128


title: FGO_sc129


title: FGO_sc131


title: FGO_sc132


title: FGO_sc130


title: FGO_sc127


title: FGO_sc126


title: FGO_sc123


title: FGO_sc120


title: FGO_sc125


title: FGO_sc121


title: FGO_sc122


title: FGO_sc119


title: FGO_sc118


title: FGO_sc115


title: FGO_sc124


title: FGO_sc116


title: FGO_sc114


title: FGO_sc113


title: FGO_sc112


title: FGO_sc108


title: FGO_sc110


title: FGO_sc111


title: FGO_sc107


title: FGO_sc109


title: FGO_sc106


title: FGO_sc105


title: FGO_sc103


title: GO3_sc115


title: GO3_sc111


title: GO3_sc112


title: GO3_sc110


title: GO3_sc113


title: FGO_sc117


title: GO3_sc109


title: GO3_sc105


title: GO3_sc107


title: GO3_sc108


title: GO3_sc106


title: GO3_sc103


title: GO3_sc100


title: GO3_sc101


title: GO3_sc98


title: GO3_sc99


title: GO3_sc96


title: FGO_sc104


title: GO3_sc95


title: GO3_sc93


title: GO3_sc94


title: GO3_sc92


title: GO3_sc91


title: GO3_sc89


title: GO3_sc90


title: GO3_sc87


title: GO3_sc104


title: GO3_sc102


title: GO3_sc84


title: GO3_sc81


title: GO3_sc83


title: GO3_sc86


title: GO3_sc82


title: GO3_sc79


title: GO3_sc97


title: GO3_sc75


title: GO3_sc77


title: GO3_sc74


title: GO3_sc114


title: GO3_sc78


title: GO3_sc76


title: GO3_sc73


title: GO3_sc80


title: GO3_sc68


title: GO3_sc88


title: GO3_sc70


title: GO3_sc67


title: GO3_sc66


title: GO3_sc65


title: GO3_sc72


title: GO3_sc64


title: GO3_sc71


title: GO3_sc85


title: GO3_sc63


title: GO3_sc62


title: GO3_sc61


title: GO2_sc126


title: GO2_sc127


title: GO3_sc58


title: GO3_sc60


title: GO2_sc123


title: GO3_sc69


title: GO2_sc124


title: GO2_sc120


title: GO2_sc121


title: GO2_sc128


title: GO2_sc117


title: GO2_sc116


title: GO2_sc113


title: GO2_sc115


title: GO2_sc110


title: GO2_sc118


title: GO2_sc114


title: GO2_sc111


title: GO2_sc109


title: GO2_sc108


title: GO2_sc106


title: GO2_sc105


title: GO2_sc112


title: GO3_sc59


title: GO2_sc107


title: GO2_sc103


title: GO2_sc119


title: GO2_sc104


title: GO2_sc102


title: GO2_sc101


title: GO2_sc122


title: GO2_sc100


title: GO2_sc99


title: GO2_sc98


title: GO2_sc95


title: GO2_sc96


title: GO2_sc97


title: GO2_sc92


title: GO2_sc93


title: GO2_sc89


title: GO2_sc90


title: GO2_sc87


title: GO2_sc84


title: GO2_sc86


title: GO2_sc82


title: GO2_sc80


title: GO2_sc83


title: GO2_sc85


title: GO2_sc88


title: GO2_sc81


title: GO2_sc79


title: GO1_sc129


title: GO2_sc77


title: GO1_sc130


title: GO1_sc126


title: GO2_sc94


title: GO1_sc127


title: GO1_sc125


title: GO2_sc76


title: GO2_sc91


title: GO1_sc122


title: GO1_sc121


title: GO1_sc120


title: GO1_sc123


title: GO1_sc124


title: GO1_sc119


title: GO1_sc117


title: GO2_sc78


title: GO1_sc115


title: GO1_sc114


title: GO1_sc118


title: GO1_sc109


title: GO1_sc116


title: GO1_sc110


title: GO1_sc108


title: GO1_sc112


title: GO1_sc128


title: GO1_sc113


title: GO1_sc107


title: GO1_sc105


title: GO1_sc104


title: GO1_sc103


title: GO1_sc106


title: GO1_sc100


title: GO1_sc99


title: GO1_sc102


title: GO1_sc101


title: GO1_sc97


title: GO1_sc98


title: GO1_sc95


title: GO1_sc94


title: GO1_sc96


title: GO1_sc111


title: GO1_sc91


title: GO1_sc92


title: GO1_sc93


title: GO1_sc90


title: GO1_sc88


title: GO1_sc86


title: GO1_sc89


title: GO1_sc85


title: GO1_sc87


title: GO1_sc80


title: GO1_sc83


title: GO1_sc81


title: GO1_sc82


title: GO1_sc78


title: GO1_sc79


title: GO1_sc77


title: GO1_sc76


title: GO1_sc75


title: GO1_sc74


title: GO1_sc73


title: GO1_sc72


title: NGO_sc159


title: GO1_sc71


title: NGO_sc160


title: NGO_sc157


title: GO1_sc84


title: FGO_sc102

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.

tag: oocyte size

value: >70 microns


title: FGO_sc101


title: FGO_sc100


title: FGO_sc99


title: FGO_sc97


title: FGO_sc98


title: FGO_sc96


title: FGO_sc94


title: FGO_sc93


title: FGO_sc95


title: FGO_sc91


title: FGO_sc90


title: FGO_sc89


title: FGO_sc88


title: FGO_sc87


title: FGO_sc86


title: FGO_sc83


title: FGO_sc82


title: FGO_sc84


title: NGO_sc158


title: FGO_sc85


title: FGO_sc81


title: FGO_sc80


title: FGO_sc92


title: FGO_sc76


title: FGO_sc79


title: FGO_sc77


title: FGO_sc78


title: FGO_sc75


title: FGO_sc74


title: FGO_sc73


title: FGO_sc72


title: FGO_sc71


title: FGO_sc67


title: FGO_sc70


title: FGO_sc68


title: FGO_sc66


title: FGO_sc64


title: FGO_sc62


title: FGO_sc57


title: FGO_sc60


title: FGO_sc59


title: FGO_sc55


title: FGO_sc56


title: FGO_sc58


title: FGO_sc54


title: FGO_sc53


title: FGO_sc52


title: FGO_sc50


title: FGO_sc48


title: FGO_sc49


title: FGO_sc69


title: FGO_sc51


title: FGO_sc46


title: FGO_sc44


title: FGO_sc65


title: FGO_sc47


title: FGO_sc45


title: FGO_sc43


title: FGO_sc63


title: FGO_sc40


title: FGO_sc41


title: FGO_sc61


title: FGO_sc37


title: FGO_sc39


title: FGO_sc36


title: FGO_sc33


title: FGO_sc35


title: FGO_sc34


title: FGO_sc30


title: FGO_sc32


title: FGO_sc27


title: FGO_sc28


title: FGO_sc24


title: FGO_sc25


title: FGO_sc23


title: FGO_sc42


title: FGO_sc22


title: FGO_sc38


title: FGO_sc20


title: FGO_sc19


title: FGO_sc16


title: FGO_sc18


title: FGO_sc15


title: FGO_sc21


title: FGO_sc14


title: FGO_sc17


title: FGO_sc11


title: FGO_sc9


title: FGO_sc31


title: FGO_sc29


title: FGO_sc10


title: FGO_sc12


title: FGO_sc8


title: FGO_sc6


title: FGO_sc26


title: FGO_sc7


title: FGO_sc2


title: FGO_sc4


title: FGO_sc3


title: FGO_sc5


title: GO3_sc57

value: 60-65 microns


title: FGO_sc1


title: GO3_sc55


title: GO3_sc56


title: FGO_sc13


title: GO3_sc50


title: GO3_sc52


title: GO3_sc51


title: GO3_sc53


title: GO3_sc48


title: GO3_sc49


title: GO3_sc47


title: GO3_sc46


title: GO3_sc45


title: GO3_sc44


title: GO3_sc43


title: GO3_sc42


title: GO3_sc41


title: GO3_sc40


title: X105

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

data_processing:
torrent mapper, version 5.0.13
htseq-count, version 0.9.1, default parameters
DESeq2, version 1.16.1, normalization
removal of bottom 20% of features according to sum of normalized counts across all samples
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 normalized count matrix

source_name: colon tumor

growth_protocol: To establish PDXs, pieces of ~3mm3 of fresh colorectal carcinoma specimens, obtained after surgical resection, were implanted subcutaneously into the inter-scapular fat pad of NU/J mice (passage 0, P0). Growth of tumor was surveyed until it reached a volume of about 1 cm3, then tumor was excised and dissociated, and pieces of ~3mm3 were implanted into a new set of mice. The procedure was repeated.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit according to the manufacturer’s protocol
Library was prepared with the Ion AmpliSeq Transcriptome Human Gene Expression Panel (Thermo)

tag: pdx development

value: PDX

tag: type

value: p0 primary colon tumor

tag: batch


title: X105P2

value: p2 xenograft


title: GO3_sc38

value: ICR

value: wild type


title: GO3_sc39

value: Ovary

value: oocyte


title: GO3_sc37


title: X95P2


title: GO3_sc36


title: X95


title: GO3_sc35


title: GO3_sc54


title: X97


title: X87P2


title: GO3_sc34


title: GO3_sc33


title: GO3_sc31


title: GO3_sc32


title: X2G0


title: x64

value: noPDX


title: X52


title: GO3_sc30


title: X17G0


title: X37G0


title: GO3_sc26


title: GO3_sc29


title: GO3_sc28


title: GO2_sc125


title: X12P2


title: GO3_sc27


title: GO3_sc25


title: X97P2


title: X41G0


title: GO3_sc24


title: X12G0


title: X35P2


title: GO3_sc22


title: X17P2_2


title: X2P2


title: GO3_sc21


title: GO3_sc19


title: x123


title: X39P2


title: GO3_sc18


title: GO3_sc20


title: x118


title: X39G0


title: GO3_sc17


title: X29G0


title: X58P2


title: GO3_sc16


title: GO3_sc14


title: GO3_sc13


title: X35G0


title: GO3_sc15


title: GO3_sc12


title: X34G0


title: x99


title: GO3_sc23


title: X19G0


title: X49G0


title: GO3_sc10


title: GO3_sc11


title: X20G0


title: x94


title: GO3_sc8


title: GO3_sc9


title: GO3_sc7


title: X87


title: x89


title: GO3_sc6


title: GO3_sc5


title: x91


title: X20P2_2


title: x112


title: GO3_sc4


title: GO3_sc3


title: x69


title: GO3_sc2


title: X29P2


title: GO2_sc74

value: 50-55 microns


title: GO3_sc1


title: GO2_sc73


title: X19P2_1


title: x15


title: GO2_sc75


title: GO2_sc70


title: x13


title: GO2_sc69


title: x11


title: x115


title: GO2_sc72


title: x131


title: GO2_sc68


title: x5


title: GO2_sc67


title: X58


title: X53


title: x111


title: GO2_sc65


title: GO2_sc66


title: X53P2


title: GO2_sc64


title: X49P2


title: X52P2


title: GO2_sc63


title: GO2_sc62


title: GO2_sc71


title: X28G0


title: X41P2


title: X37P2


title: GO2_sc61


title: X34P2


title: GO2_sc60


title: X28P2


title: GO2_sc58


title: GO2_sc59


title: GO2_sc56


title: SO_2

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL - Illinois

address: 1207 W. Gregory Dr.

institute: University of Illinois at Urbana

description: Striatum was obtained and RNA extracted using standards protocols  (Gibbons et al. 2014, Behavioural brain research, 272: 131-40.)

data_processing:
Quality-scores line in fastq files processed with Casava1.8 use an ASCII offset of 33
Sequences were trimmed for adaptor seuqences and masked for low-complexity and low-quality
100 nt paired-end reads were mapped to the mm10 genome assembly
Reads were assembled into transcript isoforms using
Genome_build: Genome Reference Consortium GRCm38
Supplementary_files_format_and_content: gene abundance measurements (read counts)

extract_protocol:
Brain was extracted from each mouse and the whole striatum  were dissected, snap frozen on dry ice and stored in a centrifuge tube at -80°C following proven protocols (Gibbons et al. 2014). The RNase-free disposable pellet pestle (Fisher Scientific, Pittsburgh, PA, USA) was used for tissue homogenization and RNeasy1 Lipid Tissue Mini Kit (Qiagen, Valencia, CA, USA) was used for RNA extraction.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: line

value: Collaborative Cross

tag: gender

value: Male

tag: phenotype

value: Overactive

value: Saline

value: Striatum

tag: age

value: ~6 months


title: SO_4


title: SO_3


title: GO2_sc55

tag: cell type


title: SO_1


title: GO2_sc54


title: GO2_sc53


title: AO_4

value: Amphetamine


title: GO2_sc52


title: GO2_sc51


title: GO2_sc50


title: AO_3


title: GO2_sc49


title: AO_2


title: GO2_sc48


title: GO2_sc47


title: SO_5


title: GO2_sc57


title: GO2_sc45


title: SC_5

value: Control


title: SC_4


title: SC_2


title: SC_1


title: SC_3


title: GO2_sc44


title: AO_5


title: AC_5


title: AC_3


title: AC_4


title: GO2_sc41


title: GO2_sc42


title: AC_1


title: AO_1


title: GO2_sc43


title: GO2_sc38


title: GO2_sc37


title: AC_2


title: GO2_sc40


title: GO2_sc36


title: GO2_sc35


title: GO2_sc34


title: GO2_sc33


title: GO2_sc32


title: GO2_sc46


title: GO2_sc30


title: GO2_sc31


title: GO2_sc29


title: GO2_sc28


title: GO2_sc39


title: GO2_sc27


title: GO2_sc26


title: GO2_sc25


title: GO2_sc24


title: GO2_sc23


title: GO2_sc22


title: GO2_sc21


title: GO2_sc20


title: GO2_sc19


title: GO2_sc18


title: GO2_sc17


title: GO2_sc16


title: GO2_sc15


title: GO2_sc14


title: 1_CB

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

country: Germany

institute: RWTH Aachen University

description: gene expression analysis from in vitro activated  M(IL10) macrophages derived from cord blood

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials according to the manufacturers instructions: hybridization 45°C for 16 hours at 60 rpm; Fluidics Station Program FS_450_0001

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Raw image data were analysed with Affymetrix® Expression Console™ Software (Affymetrix, USA), and gene expression intensities were normalized and summarized with SST robust multiarray average algorithm - unpaired (Affymetrix): SST-RMA. Further analyses was performed using the Transcriptome Analysis Console (TAC) Software of Affymetrix.

source_name: cord blood

label_protocol: Fragmented, biotinylated cDNAs were prepared from 300 ng total RNA using  the Affymetrix WT plus reagent kit according to the manufacturers instructions.

growth_protocol: Leukocytes were prepared by density gradient centrifugation of whole blood from healthy adult donors and cord blood from term neonates. Polarization was induced with 100 ng/ml M-CSF for 72h in RPMI

extract_protocol: Total RNA was isolated using RNeasy miRNA Kit

treatment_protocol: Further polarization was achieved by addition of 50 ng/ml IFN-ɤ ( M(IFN-γ), 10ng IL-10 (M(IL-10) for additional 48h

value: cord blood

value: macrophages

tag: agent


title: 1_adult

description: gene expression analysis from in vitro activated  M(IL10) macrophages

source_name: adult peripheral blood

value: adult peripheral blood


title: 3_CB


title: 3_CBM

description: gene expression analysis from in vitro activated  M(IFN-γ) macrophages derived from cord blood

value: IFN-γ


title: 2_CB


title: GO2_sc12

source_name: Growing Oocyte

value: ICR

value: wild type


title: GO2_sc11

value: Ovary

value: oocyte


title: GO2_sc10

value: 50-55 microns


title: 3_adult


title: 2_CBM


title: GO2_sc13


title: 2_PBM

description: gene expression analysis from in vitro activated  M(IFN-γ) macrophages


title: GO2_sc9


title: 3_PBM


title: 1_PBM


title: GO2_sc8


title: GO2_sc7


title: M(IFN-γ) + Rapamycin, 1

description: gene expression analysis from in vitro activated  M(IFN-γ) macrophages in the presence of Rapamycin

data_processing: Raw image data were analysed with Affymetrix® Expression Console™ Software (Affymetrix, USA), and gene expression intensities were normalized and summarized with SST robust multiarray average algorithm - paired groups a, b and c - see sample name (Affymetrix): SST-RMA. Further analyses was performed using the Transcriptome Analysis Console (TAC) Software of Affymetrix.

source_name: Peripheral blood

growth_protocol: Leukocytes were prepared by density gradient centrifugation of whole blood from healthy adult donors. Polarization was induced with 100 ng/ml M-CSF for 72h in RPMI

treatment_protocol: Further polarization was achieved by addition of 50 ng/ml IFN-ɤ ( M(IFN-γ), 10ng IL-10 (M(IL-10) for additional 48h, Rapamycin was added to yield a final concentration of 1µM

value: M(IFN-gamma) + Rapamycin


title: M(IFN-γ), 3

value: M(IFN-gamma)


title: 2_adult


title: M(IFN-γ) + Rapamycin, 2


title: M (IL-10) + Rapamycin, 1

description: gene expression analysis from in vitro activated  M(IL10) macrophages in the presence of Rapamycin

value: M (IL-10) + Rapamycin


title: M (IL-10), 2


title: GO2_sc6


title: GO2_sc5


title: M (IL-10), 3


title: M (IL-10), 1


title: M (IL-10) + Rapamycin, 3


title: M(IFN-γ), 1


title: S76_9-COL9_day90

city: Newcastle Upon Tyne

first: Majlinda

last: Lako

address: International Centre for Life, Central Parkway

department: Institute of Genetic Medicine and Institute for Ageing

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

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 90 of retinal organoid differentiation

tag: cell line

value: human ESC (CRX-GFP line)


title: S77_9-D1_S3-COL9_day200a

value: Day 200 of retinal organoid differentiation


title: S79_9-E2-8_S4-COL_day60

value: Day 60 of retinal organoid differentiation


title: M(IFN-γ), 2


title: GO2_sc4

city: Beijing

tag: strain


title: S6D1_GFP

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: CyT49 parental hESC line

value: Human embryonic stem cell (hESC)-derived NEUROG3-eGFP+ cells


title: 1_CBM

value: cord blood

value: macrophages


title: GO2_sc2


title: M (IL-10) + Rapamycin, 2


title: GO2_sc3


title: M(IFN-γ) + Rapamycin, 3


title: GO2_sc1


title: S73_8_E2-COL8_day90


title: S74_8-E2_S1-COL9_day200a


title: GO1_sc70

value: 30-45 microns


title: S78_9-D1_S4-COL_day200b


title: x38

value: noPDX

value: p0 primary colon tumor


title: S69_7_F2-COL7_day90


title: S72_8-D2-10_S6-COL_day60


title: S71_7-F2_S9-COL_day200b


title: GO1_sc69

value: ICR

value: wild type

value: Ovary


title: S70_7-F2_S12-COL9_day200a


title: GO1_sc68

value: oocyte


title: GO1_sc66


title: S68_7-C2-12_S11-COL_day60


title: S67_6-G2_S9-COL9_day200a


title: S66_6-G2_S5-COL_day200b


title: S65_6_G2-COL6_day90


title: GO1_sc63


title: GO1_sc65


title: GO1_sc64


title: GO1_sc62


title: S64_6-B2-3_S2-COL_day60


title: GO1_sc60


title: S61_5_H2-COL5_day90


title: GO1_sc61


title: S63_5-H2_S8-COL9_day200a


title: S62_5-H2_S6-COL_day200b


title: GO1_sc59


title: GO1_sc57


title: S60_5-A2-1_S7-COL_day60


title: GO1_sc56


title: GO1_sc67


title: S58_4-B1_S7-COL_day200b


title: S59_4-D1-9_S8-COL_day60


title: S56_4_B1-COL4_day90


title: GO1_sc54


title: GO1_sc53


title: S54_3-B2_S2-COL9_day200a


title: S55_3-C1-11_S10-COL_day60


title: GO1_sc58


title: GO1_sc52


title: GO1_sc51


title: S53_3-B2_S10-COL_day200b


title: GO1_sc50


title: GO1_sc47


title: GO1_sc45


title: S49_2-A1_S10-COL9_day200a


title: S48_2_A1-COL2_day90


title: GO1_sc49


title: S52_3_B2-COL3_day90


title: GO1_sc48


title: S47_20-A3_S17-COL9_day200a


title: S50_2-A1_S11-COL_day200b


title: S51_2-B1-4_S3-COL_day60


title: GO1_sc44


title: GO1_sc43


title: S45_20_A3-COL20_day90


title: S44_1-A2_S6-COL9_day200a


title: GO1_sc46


title: S57_4-B1_S4-COL9_day200a


title: GO1_sc42


title: GO1_sc55


title: S43_1-A2_S12-COL_day200b


title: GO1_sc41


title: GO1_sc40


title: S42_1_A2-COL1_day90


title: S41_1-A1-2_S9-COL_day60


title: GO1_sc39


title: S40_19-H3-18_S16-COL_day60


title: GO1_sc38


title: S46_20-A3_S15-COL_day200b


title: GO1_sc37


title: GO1_sc36


title: GO1_sc35


title: S35_18-H3_S13-COL9_day200a


title: GO1_sc34


title: S37_19_B3-COL19_day90


title: GO1_sc33


title: S36_18-H3_S16-COL_day200b


title: GO1_sc31


title: S34_18_H3-COL18_day90


title: GO1_sc32


title: S33_18-G3-17_S17-COL_day60


title: S32_17-G3_S19-COL9_day200a


title: SL1

city: Kanchipuram

first: Subramaniam

last: Sivakumar

state: TamilNadu

address: Enathur

department: Biochemistry

institute: Sri Sankara Arts and Science College

data_processing:
BCL to Fastq conversion by bcl2fastq 2.19.0.316
Adapter sequences and low quality bases removal and filtering reads shorther than 17 and longer than 36 bp long using Trimgalore 0.4.3
removal of rRNA, tRNA, ncRNA, ncoRNA by mapping to Rfam v12.0 using Bowtie2
miRNA prediction using miRdeep 2 by mapping to huam genome build GRCh38.p7
Filter predicted miRNAs with miRDeep score less 1
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: Relative Log Expression normalized (DESeq2) miRNA expression values

source_name: Leukocytes

extract_protocol:
Leukocytes were isolated, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Standard Illumina RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Blood

tag: difference

value: Sample


title: GO1_sc30


title: GO1_sc29


title: S39_19-B3_S17-COL_day200b


title: S31_17-G3_S18-COL_day200b


title: S38_19-B3_S16-COL9_day200a


title: GO1_sc28


title: S30_17_G3-COL17_day90

value: Day 90 of retinal organoid differentiation


title: CL1

value: Control


title: GO1_sc27


title: S28_16-F3_S20-COL9_day200a

value: Day 200 of retinal organoid differentiation

value: human ESC (CRX-GFP line)


title: liver-Smurf2 KO, biological rep2

city: Bethesda

first: Ying

middle: E

last: Zhang

state: Maryland

address: 37 Convent Dr., Bldg.37, Rm.2056

department: LCMB/CCR

institute: National Cancer Institute, NIH

hyb_protocol: Samples were hybridized with GeneChip® Mouse Gene 1.0 ST Array (Affymetrix) and scanned at the Frederick National Laboratory for Cancer Research Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data were preprocessed using Bioconductor packages such as oligo, pd.mogene.1.0.st.v1, mogene10sttranscriptcluster.db. Gene level expression were summarized after quantile normalization

source_name: Liver of Smurf2 KO mice from mixed Black Swiss/129SvEv background

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Mice were housed in the animal facility until 11 month old

extract_protocol: RNA was isolated from frozen liver tissues with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

treatment_protocol: Liver tissue were dissected and snap frozed.

tag: strain background

value: mixed Black Swiss/129SvEv

tag: genotype/variation

value: Smurf2 KO

value: 11 month old

value: liver


title: liver-Smurf2 KO, biological rep1

tag: tissue


title: liver-WT, biological rep1

source_name: Liver of Wild type mice from mixed Black Swiss/129SvEv background

value: Wild type


title: GO1_sc26

tag: genotype

tag: oocyte size

value: 30-45 microns


title: GO1_sc25


title: liver-Smurf1 KO, biological rep2

source_name: Liver of Smurf1 KO mice from mixed Black Swiss/129SvEv background

value: Smurf1 KO


title: liver-WT, biological rep2


title: liver-Smurf1 KO, biological rep1


title: S27_16-F3_S13-COL_day200b


title: Unc45A SiRNA 2

city: Augusta

first: Ahmed

last: Chadli

state: GA

address: 1410 Laney Walker BLVD

department: Cancer Center

institute: Augusta University

description: Gene expression data from Hs578T cells transfected with Unc45A siRNA

hyb_protocol: Following labeling, cDNAs were hybridized for 16 hr at 45C on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were processed by Partek Genomic Suite (v6.6) using Robust Multi-array Avarage (RMA) that includes a background correction, quantile normalization, adjustment for GC content, and median polish as summarization.  Differential expressions were calculated using ANOVA of Partek package.

label_protocol: Biotinylated cDNAs were prepared according to the standard Ambion and Affymetrix protocol from 250 ng total RNA (The Ambion WT Expression Kit and GeneChip Terminal Labeling Kit, Affymetrix).

growth_protocol: Hs578T (ATCC® HTB-126™) human breast cancer cells were grown to 10-20% confluency on 96-well tissue culture plates (Corning #3599) following ATCC growth instructions before transient transfection.

extract_protocol: Cells were transfected with 100 nanomolar concentration of siRNA against Unc45A. Non-targeting siRNA #1 (Dharmacon/GE) was used as a negative control. Cells were harvested 96h after transient transfection. Cells were harvested and total RNA was was extracted using QIAzol lysis reagent (QIAGEN). The RNA extracts were analyzed by a Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA). RNA quality was determined. We used RNA with a standard RIN (RNA Integrity Number) of 8 for the mRNA library construction according to the Illumina protocol.

value: Female

value: breast cancer cell line Hs578T

value: Unc45A silencing


title: Unc45A SiRNA 1

source_name: Hs578T cells transfected with Unc45A siRNA


title: Control cells 1

description: Gene expression data from Hs578T cells transfected with control siRNA

value: control


title: S26_16_F3-COL16_day90


title: GO1_sc24

value: ICR

value: wild type

value: Ovary

value: oocyte


title: Control cells 2

source_name: Hs578T cells transfected with control siRNA


title: S29_17-F3-16_S14-COL_day60

value: Day 60 of retinal organoid differentiation


title: GO1_sc23


title: S25_16-E3-15_S18-COL_day60

value: human ESC (CRX-GFP line)


title: GO1_sc22


title: S24_15-E3_S19-COL_day200b

value: Day 200 of retinal organoid differentiation


title: CONTROL 3

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.

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

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 control (DMSO)

value: MIA PaCa-2

value: Commercial cell line derived from pancreatic cancer patient.


title: S23_15-E3_S14-COL9_day200a


title: MIL70_1

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

value: 48h yarrow 70 µg/mL


title: S22_15_E3-COL15_day90

value: Day 90 of retinal organoid differentiation


title: MIL70_3


title: MIL70_2


title: GO1_sc21

value: 30-45 microns


title: MIL30_2

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

value: 48h yarrow 30 µg/mL


title: CONTROL 4


title: CONTROL 1


title: CONTROL 2


title: MIL30_1


title: GO1_sc20


title: GO1_sc19


title: S75_8-E2_S8-COL_day200b


title: GO1_sc18


title: MIL30_3


title: S20_14-D3_S20-COL_day200b


title: S21_15-D3-14_S15-COL_day60


title: CONTROL4


title: CAL30_3

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

value: 48h marigold 30 µg/mL


title: S19_14-D3_S15-COL9_day200a


title: GO1_sc17


title: GO1_sc15


title: CAL30_1


title: S17_14-C3-13_S12-COL_day60


title: S18_14_D3-COL14__day90


title: GO1_sc16


title: CONTROL2