title: HOXB4-3

city: Essen

first: Stefan

last: Heinrichs

address: Virchowstr. 179

department: Institute of Transfusion Medicine

institute: University Hospital Essen

description: gene expression of dissociated iRUNX EBs with HOXB4 expression

hyb_protocol: The hybridization was performed in a single cartridge format according to the standard Affymetrix protocol.

scan_protocol: The chips were scanned on a Affymetrix Gene Chip Scanner 3000 7G using AGCC (Affymetrix GeneChip Command Console).

data_processing: Raw data were processed in Expression Console (Affymetrix) using SST-RMA normalization.

source_name: iRunx EB with HOXB4 expression

label_protocol: The Affymetrix WT PLUS Reagent Kit was used to generate end-labelled biotinylated cDNA starting from 100ng RNA.

growth_protocol: ESCs and EBs were grown as described in the accopanying publication Teichweyde et al.(2017).

extract_protocol: Total RNA was extracted using Trizol followed by a column-based purification step.

treatment_protocol: iRunx EBs at day4 were dissociated and Flk1+PDFGRα- cells with or without retroviral expression of tdTomato/HOXB4 were sorted by FACS.

value: embryoid bodies

tag: timepoint

value: day 4 of EB differentiation

value: iRunx with HOXB4 expression


title: iCellAstro_Br3

status: Public on Feb 15 2018

type: SRA

city: Stockholm

first: Anders

last: Lundin

address: Retzius väg 8

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description: (total RNA >200nt)

library_source: transcriptomic

data_processing:
RNASeq data was processed using the bcbio pipeline version 0.9.7
Hisat2 version 2.0.2-beta aligner was used to align reads to the human genome version hg38
Gene-level counts were derived using featureCounts version 1.4.4
Genome_build: hg38

molecule: total RNA

organism: Homo sapiens

source_name: hiPSC derived Astrocyte (commercial line)

growth_protocol: ltNES cells grown according to Falk et al. 2012 using adherent culture of FGF2 and EGF supplmeneted media. NES-Astro grown adherently with FGF2, Heregulin1b, IGF1, and ActivinA supplemented media. Commertial lines grown according to manufacturer's instructions.

extract_protocol:
Cells detached using TryPLE and two rounds of washing step using PBS-/- followed by 300g centrifugation was peformed before RNA isolation using miRNeasy Kit
Libraries were prepared according to Illumina's instructions accompanying the Illumina TrueSeq Stranded mRNA LT Sample Prep Kit

tag: cell type

tag: donor gender

value: Unknown

tag: donor age


title: HOXB4-2

type: RNA

country: Germany

label: biotin

organism: Mus musculus

tag: tissue

tag: genotype/variation


title: iCellAstro_Br2

description: (total RNA >200nt)

value: hiPSC derived Astrocyte (commercial line)


title: iCellAstro_Br1

description: (total RNA >200nt)


title: C9_ltNES_d29_Br3

description: (total RNA >200nt)

source_name: hiPSC derived Astrocyte

value: hiPSC derived Astrocyte

value: Male

value: Teenager


title: C9_ltNES_d29_Br1

description: (total RNA >200nt)


title: E10.5_24R3_PLACENTA_108.2454.2.1

city: La Jolla

first: Mana

last: Parast

state: California

address: 9500 Gilman drive #0695

department: Pathology

country: USA

institute: University of California San Diego

description: SAMPLE 23

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were filtered for detection pValue > 0.01 and normalised using Robust Spline Normalisation with lumi in R

label: Biotin

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Total RNA was purified using the MirVana RNA extraction kit (Ambion). Total RNA was quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina HT12 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.

tag: origin

value: Placenta

tag: gestational age


title: E9.5_21L6_PLACENTA_108.2452.4.1

description: SAMPLE 17


title: E10.5_22L3_PLACENTA_108.2453.2.1

description: SAMPLE 20


title: C1_ltNES_d29_Br3

description: (total RNA >200nt)

value: Female

value: Old Age


title: E10.5_22L2_PLACENTA_108.2453.1.1

description: SAMPLE 19


title: E9.5_21R2_PLACENTA_108.2452.5.1

description: SAMPLE 18


title: C1_ltNES_d29_Br2

description: (total RNA >200nt)


title: HOXB4-1


title: C1_ltNES_d29_Br1

description: (total RNA >200nt)


title: ctrl-1

description: gene expression of dissociated iRUNX EBs

source_name: iRunx EB

value: iRunx


title: ctrl-2


title: E9.5_21L4_PLACENTA_108.2452.3.1

description: SAMPLE 16


title: E10.5_22L8_PLACENTA_108.2453.3.1

description: SAMPLE 21


title: B6liver8

type: genomic

city: Memphis

first: Khyobeni

last: Mozhui

state: TN

address: 66 N. Pauline Street, #631

department: Preventive Medicine

institute: University of Tennessee Health Science Center

description: Cross-species analysis of DNA methylation

hyb_protocol: Bisulphite converted DNA hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Illumina scaner

data_processing: Raw intensity data files (idat files) for both mouse and human samples were processed using the R package Minfi. The probe sequences were aligned to the mouse genome (mm10) using bowtie2 (version 2.2.6) with standard default parameters. 13,665 high quality probes that are conserved sequences and provide reliable methylation assays in mice were identified.

label: Cy3, Cy5

molecule: genomic DNA

source_name: Liver

label_protocol: Illumina

extract_protocol: DNA was purified using the Qiagen AllPrep kit (http://www.qiagen.com) on the QIAcube system.

tag: strain

tag: Sex

value: F

tag: age in days


title: E9.5_21L3_PLACENTA_108.2452.2.1

description: SAMPLE 15


title: AF22_NES-Astro_d29_Br3

description: (total RNA >200nt)

value: Middle Age


title: E10.5_24L5_PLACENTA_108.2454.1.1

description: SAMPLE 22


title: D2liver5

value: M


title: B6liver9


title: C9_ltNES_d29_Br2

description: (total RNA >200nt)


title: B6liver7


title: E8.5_18R1_PLACENTA_108.2450.3.1

description: SAMPLE 12

value: Extraembryonic tissue


title: D2liver6


title: E9.5_16L3_PLACENTA_108.2451.1.1

description: SAMPLE 13


title: B6liver10


title: E9.5_21L1_PLACENTA_108.2452.1.1

description: SAMPLE 14


title: B6liver11


title: ctrl-3


title: E8.5_18L3_PLACENTA_108.2450.2.1

description: SAMPLE 11


title: D2liver4


title: C9_ltNES_d0_Br3

description: (total RNA >200nt)

source_name: hiPSC derived Long-Term NeuroEpithelial Stem (ltNES) Cell


title: C9_ltNES_d0_Br2

description: (total RNA >200nt)

value: hiPSC derived Long-Term NeuroEpithelial Stem (ltNES) Cell


title: E8.5_17R3_PLACENTA_108.2449.3.1

description: SAMPLE 9


title: D2liver2


title: C9_ltNES_d0_Br1

description: (total RNA >200nt)


title: AF22_NES-Astro_d29_Br2

description: (total RNA >200nt)


title: D2liver3


title: E8.5_18L2_PLACENTA_108.2450.1.1

description: SAMPLE 10


title: C1_ltNES_d0_Br2

description: (total RNA >200nt)


title: C1_ltNES_d0_Br1

description: (total RNA >200nt)


title: AF22_NES-Astro_d29_Br1

description: (total RNA >200nt)


title: E8.5_17L2_PLACENTA_108.2449.1.1

description: SAMPLE 7


title: AF22_ltNES_d0_Br3

description: (total RNA >200nt)


title: AF22_ltNES_d0_Br2

description: (total RNA >200nt)


title: E8.5_17L4_PLACENTA_108.2449.2.1

description: SAMPLE 8


title: E7.5_11R1_PLACENTA_108.2448.4.1

description: SAMPLE 5


title: E7.5_11R2_PLACENTA_108.2448.5.1

description: SAMPLE 6


title: E7.5_11L2_PLACENTA_108.2448.2.1

description: SAMPLE 3


title: AF22_ltNES_d0_Br1

description: (total RNA >200nt)


title: C1_ltNES_d0_Br3

description: (total RNA >200nt)


title: E7.5_11L1_PLACENTA_108.2448.1.1

description: SAMPLE 2


title: Primary_CTB_wk39_581.1588.1.1

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were filtered for detection pValue > 0.01 and normalised using Robust Spline Normalisation with lumi in R.

source_name: purified primary cytotrophoblasts (CTB)

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays.

extract_protocol: Human CTB were isolated from first trimester placentae as follow: chorionic villi were minced and subjected to three sequential digestions. Collected cells were separated on a Percoll (Sigma-Aldrich, St. Louis, MO) gradient. Human cytotrophoblast cells were isolated from second trimester and term placentae, based on the protocol described in Li et al. (2013). CTB from gestational weeks 8, 10, 12, and 18 (two each), one 20 week, and two term placentae were isolated and subjected to microarray-based gene expression profiling as described below. Total RNA was purified using the MirVana RNA extraction kit (Ambion) on the isoalted CTB. Total RNA was quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina HT12 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.

value: purified primary cytotrophoblasts (CTB)


title: ChIP-chip of Swd1-HA from cells at 3 hr in meiosis

city: PARIS

first: Valerie

last: Borde

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: DNA was amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye coupling with Cy3 (Whole cell extract DNA) or Cy5 (immunoprecipitated DNA)

hyb_protocol: 16 hours at 65°C in the 1X hybridization buffer supplied by Agilent

scan_protocol: Axon 4000B scanner. GenePix6.0 software

data_processing: Ratios of background-corrected intensities were normalized such that the median of all ratios equals one. Then the ratios from replicate #1 and replicate #2 were averaged, and the resulting mean ratios were divided by the mean of the lowest 10% ratio probes of the array (decile normalization, as described in Panizza et al, Cell, 2011)

organism: Saccharomyces cerevisiae

source_name: ChIP of Swd1-HA

label_protocol: two-thirds of the immunoprecipitated DNA was amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye coupling

growth_protocol:
For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml (t=0 hr). Cells were processed after 3 hr in meiosis
For sporulation, cells were grown in rich medium (YPD) for 24h, then transferred into SPS pre-sporulation medium and grown overnight to ~4.107 cells/ml. Cells were then harvested by centrifugation, washed with one volume 1% potassium acetate and resuspended into sporulation medium (1% potassium acetate, 1/1000 polypropylene glycol 2000, 20µg/ml uracil) at a density of 2.107 cells/ml (t=0 hr).

extract_protocol: (2*108 (Spp1-Myc) or 2*108 (Swd1-HA) cells were crosslinked with 1% formaldehyde for 15 min at room temperature, then the reaction was stopped by the addition of 125mM glycin for 5 min. Cells were washed twice with cold PBS, and then chromatin immunoprecipitation was performed as described (Duroc et al, 2017), using either 0.8 µg of mouse monoclonal 9E10 anti-Myc (Santa Cruz) and 30 µl protein G magnetic beads suspension (New England Biolabs for Spp1-Myc, or 1 µg of mouse monoclonal 16B12 anti-HA (Covance) for HA-Set1

treatment_protocol: Cells were processed for chromatin immunoprecipitation after 3 or 4 hr in meiosis

tag: genotype

value: a/l leu2/ arg4/ SWD1-HA3/

tag: chip antibody

value: 1 ug of monoclonal 16B12 anti-HA antibody (Covance)

source_name: Whole cell extract

label_protocol: 1/70 of the DNA from the whole-cell extract was amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye coupling

tag: sample type

value: strain VBD1378 at 4 hr in meiosis


title: Primary_CTB_wk20_581.1583.1.1


title: Primary_CTB_wk18.1_581.1923.1.1


title: ChIP-chip of Spp1-Myc from mer2∆ cells at 3 hr in meiosis

source_name: ChIP of Spp1-Myc

value: a/l leu2/ arg4/ SPP1-Myc13::HphMX/ mer2-delta::URA3/

value: 0.8 ug of c-Myc monoclonal antibody (9E10, Santa Cruz)

value: strain VBD1220 at 3 hr in meiosis


title: ChIP-chip of Spp1-Myc from set1∆ cells at 3 hr in meiosis

value: a/l leu2/ arg4/ SPP1-Myc13::HphMX/ set1-delta::KanMX/

value: strain VBD1209 at 3 hr in meiosis


title: Primary_CTB_wk39_581.1587.1.1

value: Placenta


title: Primary_CTB_wk18_581.1922.1.1


title: E7.5_11L3_PLACENTA_108.2448.3.1

description: SAMPLE 4


title: E7.5_10R4_PLACENTA_108.2393.1.1

description: SAMPLE 1


title: Primary_CTB_wk10_581.1921.1.1


title: Primary_CTB_wk12_581.1584.1.1


title: Primary_CTB_wk12_581.1585.1.1


title: Primary_CTB_wk10_581.1586.1.1


title: VSMC clonal isolate PTEN knock down , biological rep2

city: Aurora

first: Mary

last: Weiser-Evans

state: Colorado

address: 12700 East 19th Ave

department: Department of Renal Medicine and Hypertension

institute: University of Colorado Denver

description: Gene expression data from VSMC clonal isolate PTEN knock down conditions for cell culture

hyb_protocol: Hybridization of the probes to the Affymetrix RAE-230 rat Genechip was preformed according to the manufacturer’s recommendations (Affymetrix, Santa Clara, CA) in the UCHSC Microarray Core Facility.

scan_protocol: DNA chips were scanned (6 μm resolution) with a HP Gene Array scanner.

data_processing: The results were analyzed with GeneChip Suite 4.0 analysis software from Affymetrix and Genespring software from Silicon Genetics.

organism: Rattus norvegicus

source_name: clonal isolate vascular smooth muscle cell PTEN knock down

label_protocol: To label the probes for microarray, cDNA was synthesized by using Superscript Choice System (Invitrogen), and purified by phenol-Chloroform extraction and ethanol precipitation.  In vitro transcription of labeled cRNA was performed from purified cDNA using Bioarray high yield RNA transcript labeling kit (Enzo Diagnostics, NY) in the presence of biotinylated UTP and CTP.  Labeled cRNA was purified and then fragmented using fragmentation buffer (40mM Tris Acetate, pH 8.1, 10mM KOAc, 30mM MgOAc).

growth_protocol: The isolated cells were plated at a density of 1x10^4 cells/ml culture medium (EMEM) containing 100 units/ml penicillin, 100 mg/ml streptomycin, and 10% FCS in 35-mm culture dishes. Cells were passed by trypsinization and used at passage 5. For all experiments, cells were growth arrested in EMEM with 0.1% calf serum the day after plating.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: A short hairpin RNA (shRNA) sequence based on the mouse PTEN gene (NCBI accession #NM008960) was designed and cloned into a retroviral expression vector driven by the U6 promoter (Open Biosystems, Huntsville, AL). To generate stable SMC clones, control or PTEN shRNA vectors were packaged into replication-defective retrovirus by transfecting HEK293 cells. SMC were incubated with secreted virus for 48 hrs and cells expressing control or PTEN shRNA were selected by culturing in medium containing puromycin. Individual clones were screened by immunoblotting with total PTEN.

value: vascular smooth muscle cell

tag: infection

value: shRNA specific to PTEN


title: Primary_CTB_wk8_581.1924.1.1


title: Primary_CTB_wk8.6_581.1925.1.1


title: VSMC clonal isolate wild type, biological rep2

description: Gene expression data from VSMC clonal isolate under control conditions for cell culture

source_name: clonal isolate vascular smooth muscle cell wild type control

value: non-targeting shRNA


title: VSMC clonal isolate PTEN knock down , biological rep1


title: PLACENTA_Wk39_Tr3___108.1594.1.1

description: SAMPLE 53

extract_protocol: Total RNA was purified using the MirVana RNA extraction kit (Ambion) on a representative samples of the villous portion of the placenta. Total RNA was quantified using the Ribogreen reagent (Lifetech, Inc.), and quality-controlled on a Bioanalyzer (Agilent). Two hundred nanograms of input total RNA was amplified and labeled using the TotalPrep kit (Ambion). The labeled product was then hybridized to Illumina HT12 arrays and scanned on a BeadArray Reader (Illumina, Inc.) according to the manufacturer’s instructions.

value: Term


title: PLACENTA_Wk39_Tr3___108.1368.1.1

description: SAMPLE 50


title: PLACENTA_Wk39_Tr3___108.1371.1.1

description: SAMPLE 51


title: RootHair_df1_rep2

city: Yokohama

first: Michitaro

last: Shibata

state: Kanagawa

address: 1-7-22 Suehirocho Tsurumi

department: CSRS

country: Japan

institute: RIKEN

description: Gene expression data from root hair cells isolated by FACS using pEXPA7:NLS-GFP

hyb_protocol: Standard Operating Procedure performed at the Duke Microarray Facility

data_processing: The gcRMA implementation in the Bioconductor and R software packages were used for background correction, quantile normalization and expression-estimate computation.

organism: Arabidopsis thaliana

source_name: Root hair cells

label_protocol: Affy two-cycle labeling (raw 21-26) and one-cycle (everything else) labeling protocol

growth_protocol: On MS media for 5 days

extract_protocol: Plotoplasts were isolated from root tissues and GFP-expressing cells were collected by FACS methods. Total RNA from plotoplasts was purified by Qiagen Rneasy kit.

treatment_protocol: Seedling roots, 5 days after germination

tag: gfp flourescent

value: FACS using pEXPA7:NLS-GFP


title: RootHair_gtl1df1_rep2

scan_protocol: Standard Operating Procedure performed at the Duke Microarray Facility


title: RootHair_gtl1df1_rep3


title: PLACENTA_Wk16_Tr2___108.1366.1.1

description: SAMPLE 49

value: Week 16


title: PLACENTA_Wk16_Tr2___108.1365.1.1

description: SAMPLE 48


title: RootHair_df1_rep3


title: RootHair_gtl1df1_rep1


title: PLACENTA_Wk39_Tr3___108.1595.1.1

description: SAMPLE 54


title: PLACENTA_Wk39_Tr3___108.1593.1.1

description: SAMPLE 52


title: VSMC clonal isolate wild type, biological rep1


title: RootHair_gtl1_rep1


title: PLACENTA_Wk14_Tr2___108.1363.1.1

description: SAMPLE 47

value: Week 14


title: RootHair_gtl1_rep2


title: RootHair_gtl1_rep3


title: LPKO 402

city: St. Louis

first: Jason

last: Ulrich

address: 425 S. Euclid

institute: Washington University

description: LPKO 402

data_processing:
BAM files imported into Partek Genomic Suite 6.16.0812 using mm10 build
gene level RPKM determined using Partek Genomic Suite 6.16.0812 genome build Refseq-81
Genome_build: mm 10, Refseq-81
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: cortex

extract_protocol:
cortex was removed, flash frozen on dry ice and RNA extracted using Trizol reagent per the manufacturer's instructions.
Clontech SMARTer

tag: age


title: RootHair_df1_rep1


title: LPKO 403

description: LPKO 403


title: LPKO 415

description: LPKO 415


title: LPKO 391

description: LPKO 391


title: PLACENTA_Wk14_Tr2___108.1342.1.1

description: SAMPLE 46


title: RootHair_DF1ox_rep3

description: Gene expression data from root hair cells isolated by FACS using pEXPA7:DF1-GFP

value: FACS using pEXPA7:DF1-GFP


title: LPKO 390

description: LPKO 390


title: LPKO 416

description: LPKO 416


title: LPKO 388

description: LPKO 388


title: PLACENTA_Wk14_Tr2___108.1329.1.1

description: SAMPLE 44


title: RootHair_DF1ox_rep2


title: PLACENTA_Wk14_Tr2___108.1336.1.1

description: SAMPLE 45


title: LP22


title: LP57


title: LP49


title: LP30


title: RootHair_DF1ox_rep1


title: PLACENTA_Wk14_Tr2___108.1322.1.1

description: SAMPLE 43


title: LP67


title: RootHair_GTL1ox_rep3

description: Gene expression data from root hair cells isolated by FACS using pEXPA7:GTL1-GFP

value: FACS using pEXPA7:GTL1-GFP


title: LP70


title: PLACENTA_Wk12_Tr1___108.1343.1.1

description: SAMPLE 40

value: Week 12


title: PLACENTA_Wk12_Tr1___108.1361.1.1

description: SAMPLE 42


title: PLACENTA_Wk12_Tr1___108.1339.1.1

description: SAMPLE 39


title: RootHair_WT_rep2

value: WT


title: Insm1-overexpressing neocortical cells 2

city: Dresden

first: Holger

last: Brandl

state: Choose One...

address: Pfotenhauerstrasse 108

department: Bioinformatics Service

institute: Max Planck Institute of Molecular Cell Biology and Genetics

description:
tavano_et_al_2018.counts.txt
tavano_et_al_2018.tpms.txt

data_processing:
Basecalls performed using bcl2fastq
Quality-trimmed reads were mapped using tophat v2.0.13 (-p6  -G $gtfFile -g1 -o $outputdir $bowtie_gindex $fastqFile)
Abundance estimation was performed using cuffiff v2.2.1
Genome_build: GRCm38, Ensembl v67
Supplementary_files_format_and_content: Raw counts and TPM normalized expression scores

source_name: E14.5 Insm1-overexpressing neocortical cells

growth_protocol: in utero eletroporation at E13.5 and dissection at E14.5

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit  (QIAGEN) according to the manufacturer's instructions.
Complete cDNA was synthesized from half of the isolated mRNA with SmartScribe reverse transcriptase (Clontech) using a universally tailed poly-dT primer and template switching oligos. This was followed by amplification of the purified cDNA with the Advantage 2 DNA Polymerase (12 cylces). After ultrasonic shearing of the amplified cDNA (Covaris S2), samples were subjected to standard Illumina fragment library preparation using the NEBnext chemistries (New England Biolabs), in brief: fragments were end repaired, A-tailed and ligated to indexed Illumina Truseq adapters. Subsequently, the NGS libraries were finalized by a universally primed PCR amplification (15 cycles). Libraries were purified using XP beads (Beckman Coulter), quantified by qPCR (KAPA Biosysytems) and subjected to Illumina 75-bp single end sequencing on the Illumina HiSeq 2000 platform providing on average 35 Mio reads per sample.

treatment_protocol: Control (in utero electroporation with plasmid encoding only mCherry) and Insm1-overexpression (in utero electroporation with plasmid encoding both Insm1 and mCherry)

tag: fluorescent protein

value: mCherry+

tag: plasmid


title: Insm1-overexpressing neocortical cells 1


title: Insm1-overexpressing neocortical cells 3


title: RootHair_GTL1ox_rep1


title: RootHair_GTL1ox_rep2


title: RootHair_WT_rep3


title: PLACENTA_Wk11_Tr1___108.1360.1.1

description: SAMPLE 37

value: Week 11


title: PLACENTA_Wk12_Tr1___108.1330.1.1

description: SAMPLE 38


title: RootHair_WT_rep1


title: Control neocortical cells 3

source_name: E14.5 neocortical cells control

value: control


title: PLACENTA_Wk12_Tr1___108.1346.1.1

description: SAMPLE 41


title: PLACENTA_Wk11_Tr1___108.1327.1.1

description: SAMPLE 35


title: PLACENTA_Wk11_Tr1___108.1320.1.1

description: SAMPLE 33


title: Control neocortical cells 2


title: PLACENTA_Wk11_Tr1___108.1326.1.1

description: SAMPLE 34


title: PLACENTA_Wk11_Tr1___108.1332.1.1

description: SAMPLE 36


title: PLACENTA_Wk10_Tr1___108.1367.1.1

description: SAMPLE 32

value: Week 10


title: D2liver1

value: F


title: Control neocortical cells 1


title: DF1_rep4

hyb_protocol: Hybridization was performed according to the Agilent ChIP-chip protocol

scan_protocol: Images were obtained using an Agilent microarray scanner (model G2565BA) at a resolution of 5 μm. Signal extraction and initial data processing were done using the Agilent feature extraction software

data_processing: Signal ratio (FC) was used to obtain a Z-Score of the foldchange that was then used to conduct the analysis

source_name: Roots from 5-day old seedlings

label_protocol: After labelling with Cy3 and Cy5, respectively, following an amino-allyl-dye coupling protocol (http://camd.bio.indiana.edu/files/amino-allyl-protocol.pdf), DNA was cleaned up using the PCR purification kit (Qiagen) and 3 μg from the ChIP and from the mock samples were taken and mixed for hybridization to a custom long oligonucleotide (~60 bases) Arabidopsis promoter microarray.

extract_protocol: Chip was performed like described in Busch W, Miotk A, Ariel FD, Zhao Z, Forner J, Daum G, Suzaki T, Schuster C, Schultheiss SJ, Leibfried A, Haubeiss S, Ha N, Chan RL, Lohmann JU. (2010) Transcriptional control of a plant stem cell niche. Dev. Cell 18:849-61. except that DNA-free protein A agarose beads (Invitrogen) were used. Immunoprecipitation was performed using a rabbit polyclonal antibody against GFP (ab290, Abcam). DNA from the ChIP and mock experiments was amplified using a random-primer-based genome amplification method described in http://cat.ucsf.edu/pdfs/22_Round_A_B_C_protocol.pdf, with minor modifications.

tag: transcription factor

source_name: Root tip from 5-day old seedlings

tag: ecotype


title: PLACENTA_Wk10_Tr1___108.1354.1.1

description: SAMPLE 31

value: Placenta


title: DF1_rep3


title: PLACENTA_Wk10_Tr1___108.1351.1.1

description: SAMPLE 30


title: DF1_rep1


title: DF1_rep2


title: WT_Naive_rep3

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

description: 3'end DGE

data_processing:
Files obtained from sequencing center the were demultiplexed with fastq-multx tool. Fastq files for each sample were aligned to mm10 genome (Release M8 Gencode, GRCm38.p4) using STAR. Each sample was evaluated according to a variety of both pre- and post-alignment QC measures with Picard tools.  Aligned reads were quantified using quant3p script (github.com/ctlab/quant3p) to account for specifics of 3' sequencing: higher dependency on good 3' annotation and lower level of sequence specificity close to 3' end. Actual read countings were carried out by HTSeq with enriched genome annotation and alignment with fixed multimapper flags. DESeq2 was used for analysis of differential gene expression. Pre-ranked GSEA analysis was used to identify pathway enrichments in hallmark and canonical pathways.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited file that includes raw count data for each sample which includes the barcode information

molecule: polyA RNA

source_name: BMDM

extract_protocol: RNA was extracted from purified BMDM and neutrophils using TriZol reagent (Invitrogen). mRNA was extracted with oligo-dT beads (Invitrogen) and cDNA synthesized using custom oligo-dT primer with a barcode and adaptor-linker sequence (CCTACACGACGCTCTTCCGATCT-XXXXXXXX-T15). Samples were pooled based on Actb qPCR values, RNA-DNA hybrids degraded with acid-alkali treatment and a second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated with T4 ligase (NEB). After SPRI-bead clean-up (Agencourt AMPure XP, BeckmanCoulter) the mixture was PCR-enriched (12 cycles) and SPRI-purified yielding final strand-specific RNA-seq libraries.

tag: tissue

value: bone marrow

tag: cell type

value: macrophage

tag: strain background

value: wildtype

tag: hour post infection

tag: treatment


title: WT_Naive_rep2

description: 3'end DGE


title: GTL1_rep4


title: PLACENTA_Wk10_Tr1___108.1331.1.1

description: SAMPLE 29

tag: origin

tag: gestational age


title: WT_Naive_rep1

description: 3'end DGE

tag: genotype


title: PLACENTA_Wk10_Tr1___108.1324.1.1

description: SAMPLE 28


title: WT_4h_rep3

description: 3'end DGE

value: Mycobacterium tuberculosis


title: PLACENTA_Wk9_Tr1___108.1355.1.1

description: SAMPLE 27

value: Week 9


title: GTL1_rep3


title: GTL1_rep2


title: GTL1_rep1


title: WT_4h_rep2

description: 3'end DGE


title: WT_4h_rep1

description: 3'end DGE


title: Irg1KO_Naive_rep3

description: 3'end DGE


title: Irg1KO_Naive_rep2

description: 3'end DGE


title: PLACENTA_Wk9_Tr1___108.1341.1.1

description: SAMPLE 24


title: PLACENTA_Wk9_Tr1___108.1349.1.1

description: SAMPLE 25


title: Irg1KO_Naive_rep1

description: 3'end DGE


title: PLACENTA_Wk9_Tr1___108.1352.1.1

description: SAMPLE 26


title: PLACENTA_Wk8_Tr1___108.1328.1.1

description: SAMPLE 22

value: Week 8


title: Irg1KO_Ita_4h_rep3

description: 3'end DGE

value: 0.25 mM itaconic acid + Mycobacterium tuberculosis


title: PLACENTA_Wk9_Tr1___108.1340.1.1

description: SAMPLE 23


title: PLACENTA_Wk8_Tr1___108.1325.1.1

description: SAMPLE 21


title: PLACENTA_Wk8_Tr1___108.1323.1.1

description: SAMPLE 20


title: Irg1KO_Ita_4h_rep2

description: 3'end DGE


title: Irg1KO_Ita_4h_rep1

description: 3'end DGE


title: Irg1KO_4h_rep3

description: 3'end DGE


title: PLACENTA_Wk7_Tr1___108.1359.1.1

description: SAMPLE 18

value: Week 7


title: PLACENTA_Wk8_Tr1___108.1321.1.1

description: SAMPLE 19


title: Irg1KO_4h_rep2

description: 3'end DGE


title: Irg1KO_4h_rep1

description: 3'end DGE


title: PLACENTA_Wk7_Tr1___108.1347.1.1

description: SAMPLE 15


title: blood_Sham operated_1 (miRNA)

city: Bunkyo-ku

first: Ayako

last: Takuma

state: Tokyo

department: Graduate School of Agricultural and Life Sciences

institute: The University of Tokyo

hyb_protocol: Biotin-labeled RNA 21.5µL were hybridized for 16hr at 48C on GeneChip miRNA 4.0 Array. GeneChips were washed and stained with Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed using the Expression Console Software (Affymetrix), and the RMA+DABG method.

source_name: blood extracted from Sham treated rats

label_protocol: Biotin-labeled RNA was synthesized from 900ng total RNA according to the manufacture's protocol.

growth_protocol: The rats had free access to food and water, and were kept in a 12 hour light/dark cycle.

extract_protocol: Total RNA was extracted according to the manufacture's protocol.

treatment_protocol: The rats were subjected to operation, and blood was extracted from the heart 24hr after the reperfusion.  The blood was mixtured with TRIzol LS Reagent(Thermo Fisher Scientific) and Nuclease-free water, according to the manufacture's protocol.

tag: gender

value: male

value: 8 weeks old

tag: stress

value: Sham

value: blood


title: blood_Sham operated_3 (miRNA)


title: blood_Sham operated_2 (miRNA)


title: PLACENTA_Wk7_Tr1___108.1358.1.1

description: SAMPLE 17


title: PLACENTA_Wk7_Tr1___108.1353.1.1

description: SAMPLE 16


title: blood_MCAO operated_3 (miRNA)

source_name: blood extracted from MCAO treated rats

value: Middle Cerebral Artery Occlusion


title: KO4

city: hangzhou

first: Xiaoling

last: Li

state: Zhejiang

department: Life Sciences Institute

country: China

institute: Zhejiang University

data_processing:
Illumina bcl2fastq Conversion Software v1.8.4 used to convert BCL files to FASTQ file formats.
Sequenced reads were trimmed for adaptor sequence and filtered low quality sequence, then mapped to mm9 whole genome using tophat v2.0.11 with parameters --solexa-quals -p 10 --no-coverage-search. Gene and/or known transcripts annotations file was download from Refseq database and represented with gtf format.
Reads Per Kilobase of exon per Megabase of library size (RPKM) and different expression genes were calculated using software edgeR v3.18.1. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of sequencing library and the length of meta-transcript.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include genes name, reads count, RPKM and P-value.

source_name: Lis1 conditional knockout

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

tag: strain

value: 1 month old


title: PLACENTA_Wk7_Tr1___108.1344.1.1

description: SAMPLE 14


title: blood_MCAO operated_2 (miRNA)


title: PLACENTA_Wk6_Tr1___108.1334.1.1

description: SAMPLE 10

value: Week 6


title: DCIS_core_biopsy J

city: Lebanon

first: Youdinghuan

last: Chen

state: NH

address: Hinman Box 7650

department: Epidemiology

institute: Dartmouth College

hyb_protocol: Bisulfite-modified DNA were hybridized to the Illumina Infinium HumanMethylation450 BeadChip array.

scan_protocol: (standard procedure; see Illumina)

data_processing: Raw intensity data files (IDAT) were processed by minfi R/Bioconductor package version 1.2.0.

source_name: Breast DCIS

label_protocol: standard Affymetrix protocol

extract_protocol: DNA was extracted from guided 2mm cores of formalin fixed paraffin embedded (FFPE) specimens, bisulfite-modified, and measured on the Illumina HumanMethylation450 BeadChip.

value: female

tag: matched surgical specimen accession (gse66313)


title: DCIS_core_biopsy I


title: DCIS_core_biopsy G


title: DCIS_core_biopsy K


title: DCIS_core_biopsy M


title: KO2

tag: age


title: KO3


title: PLACENTA_Wk6_Tr1___108.1333.1.1

description: SAMPLE 9

value: Placenta


title: PLACENTA_Wk6_Tr1___108.1337.1.1

description: SAMPLE 12


title: PLACENTA_Wk6_Tr1___108.1357.1.1

description: SAMPLE 13


title: PLACENTA_Wk5_Tr1___108.1364.1.1

description: SAMPLE 8

value: Week 5


title: CT3

source_name: control


title: GAT24_no Wnt_no Rspondin_P12 MOI 100 3d

city: Berlin

first: Thomas

middle: F

last: Meyer

address: Chariteplatz 1

department: Molecular Biology

institute: Max Planck Institute for Infection Biology

hyb_protocol: After precipitation, purification and quantification, 0.75µg labeled samples were hybridized according to the supplier's protocol (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 3µm resolution using a G2565CA high resolution laser microarray scanner (Agilent Technologies).

data_processing: Microarray image data were extracted and analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.10.10.1, Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol. The extracted single-color raw data txt files were further analyzed using R and the associated BioConductor package limma. Background was removed using method normexp with offset 15, followed by quantile normalization.

source_name: GAT24_no Wnt_no Rspondin_P12 MOI 100 3d

label_protocol: RNA was labeled with the single-color Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to manufacturer’s instructions.

growth_protocol: Gastric primary cells were grown in corresponding media as described in the accompanying publication (materials and methods).

extract_protocol: Total RNA was isolated by the TRIzol Reagent RNA preparation method (Invitrogen, Karlsruhe, Germany) using Glycogen as carrier.

treatment_protocol: Cells were cultured in an air-liquid interface and infected with H.pylori as described in the accompanying publication.

tag: patient

tag: wnt

value: no Wnt

tag: rspondin

value: no Rspondin

tag: infection


title: DCIS_core_biopsy L


title: DCIS_core_biopsy A


title: PLACENTA_Wk5_Tr1___108.1362.1.1

description: SAMPLE 7


title: DCIS_core_biopsy B


title: CT1

tag: tissue


title: CT4


title: GAT24_Wnt_Rspondin1_NI

value: Wnt

value: NI


title: DCIS_core_biopsy H


title: blood_MCAO operated_1 (miRNA)


title: PLACENTA_Wk6_Tr1___108.1335.1.1

description: SAMPLE 11


title: PLACENTA_Wk5_Tr1___108.1356.1.1

description: SAMPLE 6


title: DCIS_core_biopsy E


title: KO1


title: PLACENTA_Wk5_Tr1___108.1348.1.1

description: SAMPLE 5


title: DCIS_core_biopsy F


title: PLACENTA_Wk5_Tr1___108.1345.1.1

description: SAMPLE 4


title: GAT24_no Wnt_no Rspondin_NI

source_name: GAT24_no Wnt_no Rspondin_NI


title: DCIS_core_biopsy C


title: DCIS_core_biopsy D


title: PLACENTA_Wk4_Tr1___108.1592.1.1.

description: SAMPLE 3

value: Week 4


title: TN_P63 replicat1

city: Brussels

first: Cédric

last: Blanpain

address: Route de Lennik 808

country: Belgium

institute: ULB

description: so-mm_PS2-SCC10-TN-P15_AACTCGGA-TCTTTCCC

data_processing:
Approximately 12 millions of paired-end reads of 125bp per sample for each subpopulation samples were mapped against the mouse reference genome (Grcm38/mm10) using STAR software to generate read alignments for each sample.
Annotations Grcm38.87 was obtained from ftp.Ensembl.org.
After transcripts assembling, gene level counts were obtained using HTseq and normalized to 20 millions of aligned reads.
Average expression for each gene for the different tumour cell subpopulations was computed based on 3 biological replicates and fold  changes were calculated between the subpopulations.
Genes for which all the mean expressions across the subpopulations was lower than 1 read per million of mapped reads are considered not expressed and removed for further analysis.
Genes having a fold change of expression greater or equal than 2 are considered as up-regulated and those having a fold change of expression lower or equal to 0.5 are considered down-regulated.
Genome_build: Grcm38.87
Supplementary_files_format_and_content: count files in csv contening the counts normalized per 20 millions of mapped reads for each subpopulation across all the genes

growth_protocol: Rosa26-YFP38, Lgr5CreER39, KRasLSL-G12D40and p53fl/fl41mice have been imported from the NCI mouse repository and the Jackson Laboratories.K8CreERT2 were described previously.42Pik3caH1047Rknock-in mice, in which wild-type exon 20 is replaced by H1047 mutant exon 20 upon Cre recombination, were described previously (ref. 14).Wim Declercq (Ghent University, Belgium) generated the Lgr5CreER/KrasLSL-G12D/p53fl/fl/Rosa26-DNp63-IRES-GFP mice. MMTV-PyMT female mice were kind gift of Geert Berx from Ghent University and Massimiliano Mazzone from VIB, University of Leuven. NOD/SCID/Il2Rγ null mice were purchased from Charles River.All mice used in this study were composed of males and females withmixed genetic background. No randomization and no blinding were performed in this study.Mouse colonies were maintained in a certified animal facility in accordance with the European guidelines and with approved ethical protocols (#483N, #633N)

extract_protocol:
RNA extraction from FACS isolated cells was performed using RNeasy micro kit (QIAGEN) according to the manufacturer ́s recommendations.
Prior to sequencing the quality of RNA was evaluated by Bioanalyzer 2100 (Agilent). Indexed cDNA libraries were obtained using the Ovation Solo RNA-seq Systems (NuGen) following manufacturer’srecommendations. The multiplexed libraries (11pM / 18pM) were loaded on flow cells and sequences were produced using a HiSeq PE Cluster Kit v4 and TruSeq SBS Kit v3-HS (250 cycles) on a HiSeq 1500 (Illumina).

treatment_protocol: KRasLSL-G12D p53fl/fl induced skin tumours. Tamoxifen was diluted at 25 mg/ml in sunflower seed oil (Sigma). Four daily intraperitoneal injection (IP) doses of 2,5 mg of TAM were administered at P28 as previously described43 to Lgr5CreER/KrasLSL-G12D/p53fl/fl/Rosa26-YFP+/+ and Lgr5CreER/KrasLSL-G12D/p53fl/fl/Rosa26-DNp63-IRES-GFP.

value: mixed

tag: cell type

value: skin squamous cell carcinoma YFP positive

tag: surface marker


title: TN_P63 replicat2

tag: strain background


title: GAT24_Wnt_Rspondin1_P12 MOI 100 3d

source_name: GAT24_Wnt_Rspondin1_P12 MOI 100 3d


title: PLACENTA_Wk4_Tr1___108.1589.1.1.

description: SAMPLE 1


title: GAT23_Wnt_Rspondin1_P12 MOI 100 3d

source_name: GAT23_Wnt_Rspondin1_P12 MOI 100 3d


title: Epplus_P63 replicat2

value: epcam+


title: Organoid_4

city: Rochester

first: Hu

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

description: Gene expression data obtained from Organoid H202 cells

hyb_protocol: cDNA was fragmented and 10ug hybridized to an Affymetrix Human Exon 1.0 ST Array for 16 hours. Arrays were washed and stained using the Affy 450 Fluidics Station according to the manufacturer's protocol

scan_protocol: Arrays were scanned using a GeneChip 3000 scanner according to the manufacturers recommendation

data_processing: RMA

source_name: Organoid cells

label_protocol: Preparation of biotinylated cDNA was performed according to the standard Nugen amplification sample preparation protocol, starting with 100ng of total RNA

growth_protocol: Organoids were grown in expansion medium (EM) consisting of Advanced DMEM F12 supplemented with L-WRN conditioned medium glutamax, HEPES, murine epidermal growth factor (50 ng ml-1), N2 supplement, B27 supplement, 10 nM human [Leu15]-gastrin I, 1 mM n-acetyl cysteine, 10 mM nicotinamide, 10 μM SB202190, 500 nM A83-01. Intestine Chips were fabricated from PDMS and assembled, or they were obtained from Emulate Inc. (Boston, MA). Total RNA was collected for microarray.

extract_protocol: Epithelial RNA recovered from the Intestine Chip was extracted using RNeasy Mini Kit  followed by cDNA synthesis with SuperScript VILO cDNA Synthesis Kit (Thermo Fisher  Scientific).

value: Organoid cells


title: GAT23_no Wnt_no Rspondin_P12 MOI 100 3d

source_name: GAT23_no Wnt_no Rspondin_P12 MOI 100 3d


title: 5161 replicat 3 [RNA-seq]

data_processing:
Approximately 8 millions of paired-end reads of 75bp per sample for each subpopulation samples were mapped against the mouse reference genome (Grcm38/mm10) using STAR software to generate read alignments for each sample.
Annotations Grcm38.87 was obtained from ftp.Ensembl.org.
After transcripts assembling, gene level counts were obtained using HTseq and normalized to 20 millions of aligned reads.
Average expression for each gene for the different tumour cell subpopulations was computed based on 3 biological replicates and fold  changes were calculated between the subpopulations.
Genes for which all the mean expressions across the subpopulations was lower than 1 read per million of mapped reads are considered not expressed and removed for further analysis.
Genes having a fold change of expression greater or equal than 2 are considered as up-regulated and those having a fold change of expression lower or equal to 0.5 are considered down-regulated.
Genome_build: Grcm38.87
Supplementary_files_format_and_content: count files in csv contening the counts normalized per 20 millions of mapped reads for each subpopulation across all the genes

extract_protocol:
RNA extraction from FACS isolated cells was performed using RNeasy micro kit (QIAGEN) according to the manufacturer ́s recommendations.
Prior to sequencing the quality of RNA was evaluated by Bioanalyzer 2100 (Agilent). Indexed cDNA libraries were obtained using the Ovation Solo RNA-seq Systems (NuGen) following manufacturer’srecommendations. The multiplexed libraries (11pM / 18pM) were loaded on flow cells and sequences were produced using a HiSeq PE Cluster Kit v4 and TruSeq SBS Kit v3-HS (250 cycles) on a HiSeq 1500 (Illumina). A


title: PLACENTA_Wk4_Tr1___108.1590.1.1.

description: SAMPLE 2

data_processing: The data were filtered for detection pValue > 0.01 and normalised using Robust Spline Normalisation with lumi in R


title: 1065161 replicat 3 [RNA-seq]


title: Organoid_1

description: Gene expression data obtained from Organoid H195 cells


title: 10651 replicat 3 [RNA-seq]


title: GAT23_Wnt_Rspondin1_NI


title: Organoid_2


title: GAT16_no Wnt_no Rspondin_NI

source_name: GAT16_no Wnt_no Rspondin_NI


title: GAT23_no Wnt_no Rspondin_NI

source_name: GAT23_no Wnt_no Rspondin_NI


title: GAT16_Wnt_Rspondin1_NI


title: Organoid_3


title: 51 replicat 3 [RNA-seq]


title: CT2


title: Intestine_Chip_1

description: Gene expression data obtained from Intestine On Chip H195 cells

source_name: Intestine On Chip cells

value: Intestine On Chip cells


title: Intestine_Chip_2


title: GAT16_Wnt_Rspondin1_P12 MOI 100 3d

source_name: GAT16_Wnt_Rspondin1_P12 MOI 100 3d


title: Epplus_P63 replicat1

description: so-mm_PS1-SCC10-EP-P22_CGTCTAAC-TCTTTCCC


title: Intestine_Chip_3

description: Gene expression data obtained from Intestine On Chip H202 cells


title: 106 replicat 3 [RNA-seq]


title: Caco2_Transwell_2

description: Gene expression data obtained from Caco2 transwell cells

source_name: Caco2 transwell cells

value: Caco2 transwell cells


title: TN replicat 3 [RNA-seq]

source_name: TN


title: Epplus replicat 3 [RNA-seq]

source_name: Epplus


title: Serum_RNA_lcSSc_8

city: Utrecht

first: Eleni

last: Chouri

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht, Utrecht University

description: patients

data_processing:
miRNA profiling data was analyzed using the ExpressionSuite Software (Life Technologies) using the relative threshold cycle (Crt) and the comparative threshold cycle method. Briefly, miRNA relative expression was calculated after normalization by exogenous ath-miR-159a spike-in (ΔCrt = Crt target – Crt miR-159a). The relative fold change (FC) of each sample was determined by setting the FC of a randomly selected Healthy Control sample at 1, and the FC was calculated compared to this reference (FC=2–ΔΔCrt , where –ΔΔCrt = ΔCrt reference – ΔCrt sample). Low expressed miRNAs, i.e. having Crt higher than 27 or undetermined, were set at 27.
Non-normalized data report CRT value, i.e. the Raw Ct value; normalized data report the deltaCRT mean, after normalization of Raw Ct vs the spike-in; Fold Change data reports the relative expression of each patients versus a randomly selected healthy control sample (sample 30)

label: TaqMan

source_name: Serum

label_protocol: Samples were prepared according to the protocol of Taqman OpenArray Human microRNA Panel  version miRBase 20.1 (Life Technologies catalog number 4470187) according to manufacturer's instructions

extract_protocol: Serum RNA was extracted using the miRcury RNA Isolation kit for Biofluids (Exiqon) after addition of 300pg spike-in ath-miR-159a

treatment_protocol: Blood was collected in a Vacutainer® SST II tube (BD Vacutainer) and serum was isolated after centrifugation at 1500g for 10 min at room temperature and stored at -80C prior to use

value: serum

tag: diagnosis

value: limited cutaneous systemic sclerosis

value: male


title: Serum_RNA_lcSSc_9

description: patients

value: female


title: Serum_RNA_lcSSc_6

description: patients


title: Serum_RNA_lcSSc_5

description: patients


title: 5161 replicat 2 [RNA-seq]


title: Caco2_Transwell_1


title: Serum_RNA_lcSSc_4

description: patients


title: 10651 replicat 2 [RNA-seq]


title: Intestine_Chip_4


title: Caco2_Gut_Chip_2

description: Gene expression data obtained from Caco2 Gut on Chip cells

source_name: Caco2 Gut on Chip cells

value: Caco2 Gut on Chip cells


title: 106 replicat 2 [RNA-seq]


title: Serum_RNA_lcSSc_2

description: patients


title: 51 replicat 2 [RNA-seq]


title: TN replicat 2 [RNA-seq]


title: Caco2_Gut_Chip_1


title: GAT16_no Wnt_no Rspondin_P12 MOI 100 3d

source_name: GAT16_no Wnt_no Rspondin_P12 MOI 100 3d


title: 1065161 replicat 1 [RNA-seq]


title: Serum_RNA_lcSSc_1

description: patients


title: 5161 replicat 1 [RNA-seq]


title: Serum_RNA_dcSSc_8

description: patients

value: diffuse cutaneous systemic sclerosis


title: Serum_RNA_dcSSc_9

description: patients


title: Serum_RNA_dcSSc_7

description: patients


title: 1065161 replicat 2 [RNA-seq]


title: Serum_RNA_dcSSc_6

description: patients


title: 51 replicat 1 [RNA-seq]


title: 10651 replicat 1 [RNA-seq]


title: Serum_RNA_lcSSc_3

description: patients


title: Serum_RNA_lcSSc_7

description: patients


title: Epplus replicat 2 [RNA-seq]


title: 106 replicat 1 [RNA-seq]


title: Epplus replicat 1 CD106 positive [RNA-seq]

value: epcam+, CD106+


title: Epplus replicat 1 CD106 negative [RNA-seq]

value: epcam+, cd106-


title: Serum_RNA_dcSSc_4

description: patients


title: TN replicat 1 [RNA-seq]


title: Serum_RNA_ncSSc_7

description: patients

value: non-cutaneous systemic sclerosis


title: Serum_RNA_dcSSc_3

description: patients


title: 10651

library_source: genomic

data_processing:
Adaptors sequences were removed with TrimmomaticPE using options “ILLUMINACLIP:adaptor.file:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”.
ATAC-seq paired-end reads were then aligned to mouse genome Grcm38 using Bowtie2 (version 2.2.6) using options “-X 2000 --fr --very-sensitive --no-discordant --no-unal --no-mixed –non-deterministic”.
Mitochondrial reads, reads from unmapped or random contigs and reads with a mapping quality less than 20 were removed using samtools.
Duplicate reads were removed by Picard tools  (http://broadinstitute.github.io/picard/).
Peak calling was performed on each individual sample by macs2 (version 2.1.0.20151222)  using options “-f BAMPE -g mm -q 0.05 --nomodel --call-summits -B –SPMR”. TDF files were generated with IGVtools from the treat_pileup.bdg files generated by MACS2.
Peaks from the different subpopulations were merged for downstream analysis.
Reads counts of each merged peaks for each individual sample were calculated by HTSeq-count using options “-s no -m intersection-nonempty”. These counts were normalized for one million of mapped reads in merged peaks and fold of change were calculated between the subpopulations.
Peaks were associated to genes with GREAT software with the following association rules : “basal plus extension” with parameters : 5.0kb in proximal upstream, 1.0kb in proximal downstream and 100.0kb in distal.
Genome_build: Grcm38
Supplementary_files_format_and_content: peaks; tdf; counts

source_name: skin tumor

extract_protocol:
For ATAC sequencing 100000 sorted cells from different tumoursubpopulations were collected in 1mL of PBS supplemented with 3% FBS at 4ºC.
Cells were centrifuged and cell pallets were resuspended in 100ul of lysis buffer (TrisHCl 10mM, NaCl 10mM, MgCl2 3mM, Igepal 0.1%) and centrifuged at 500g for 25 minutes at 4ºC. Supernatant was carefully discarded and nuclei were resuspended in 50ul of reaction buffer (Tn5 transposase 2.5ul, TD buffer 22.5ul, from Nextera DNA sample preparation kit, Illumina, and 25ul H20). The reaction was performed at 37ºC for 30min and was stopped by addition of 5ul of clean up buffer (NaCl 900mM, EDTA 300mM). DNA was purified using the MiniElute purification kit (QIAGEN) following manufacturer protocol. DNA libraries were PCR amplified (Nextera DNA Sample Preparation Kit, Illumina), and size selected from200 to 800bp (BluePippin, Sage Sciences), following manufacturer ́s recommendations.


title: TN


title: 1065161


title: Serum_RNA_dcSSc_1

description: patients


title: 106


title: Epplus


title: Serum_RNA_ncSSc_6

description: patients


title: Serum_RNA_ncSSc_5

description: patients


title: Serum_RNA_ncSSc_3

description: patients


title: Serum_RNA_dcSSc_5

description: patients


title: Serum_RNA_ncSSc_2

description: patients


title: Serum_RNA_ncSSc_1

description: patients


title: Serum_RNA_HC_9

description: healthy controls

value: healthy control


title: 15#08387 Eedwt/wt (WT)

city: Clayton

first: Patrick

middle: S

last: Western

state: VIC

address: 27-31 Wright Street

department: Centre for Reproductive Health

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
Raw reads from the 8 ChIPseq libraries were trimmed using the trimmomatic tool (Lohse et al. 2012) in order to keep only high quality sequences before the mapping step.
Remaining good quality sequences were then mapped to the mouse genome (mm10) using the bowtie2 tool as recommended for this type of data. A good alignment rate was obtained across all libraries with over 97% mapped reads.
PCR duplicates (if any) were then marked in the mapping files (BAM format) for filtering in further steps.
Peak identification was done using the HOMER tool (http://homer.salk.edu/homer/), a suite of tools for next-generation sequencing data analysis and in particular ChIPseq data analysis. A total of 55453 and 60933 peaks (or regions) were identified for the WT group and HYPO groups, respectively.
Peak annotation iwas performed in HOMER based on alignments of RefSeq transcripts to the UCSC Mm10 genome.
Genome_build: Mm10

source_name: E15.5 fetal male germ cells

growth_protocol: Mice were maintained under a light dark cycle in a temperature and humidity controlled Specifically Pathogen Free (SPF) facility with access to food and water ad libitum. Natural timed mates were used to generate E15.5 fetuses.

extract_protocol:
Cells were collected via FACS using Oct4GFP expression to identify germ cells. Approximately 10,000 germ cells were FACS purified from individual Eedwt/wt (n=4) and Eedhypo/hypo (n=4) embryos and ChIP performed as described [81, 82] with minor alterations. Briefly, cells were cross-linked in 1% Formaldehyde/PBS for 5 min before adding Glycine/PBS at a final concentration of 125mM. Cells were pelleted and washed in PBS and stored -80°C.
Libraries were prepared from using the Ovation Ultralow System V2 using Nugen protocol M01379v1. Each library was quantitated using a Qubit instrument and the DNA size profile determined using an Agilent Bioanalyzer. Libraries were finally quantitated by qPCR, pooled in an equimolar ratio and all eight libraries run on one lane of a HiSeq1500 sequencer to obtain 50bp single end reads.

value: fetal germ cells

tag: developmental stage

value: embryonic day 15.5

value: Embryonic Ectoderm Development (Eed) wild type

tag: antibody


title: 15#08385 Eedhypo/hypo (HOM)

tag: genotype

value: Embryonic Ectoderm Development (Eed) carrying 1989 hypomorphic mutation


title: 15#08386 Eedwt/wt (WT)

tag: gender


title: 15#08388 Eedwt/wt (WT)


title: Serum_RNA_dcSSc_2

description: patients


title: 15#08384 Eedhypo/hypo (HOM)


title: Serum_RNA_HC_8

description: healthy controls


title: lec1-4 rep3

city: guangzhou

first: yilong

last: hu

state: guangdong

address: No.723, xingke road, tianhe district

institute: south china botanical gardern, chinese academy of science

data_processing:
Illumina Casava1.8 software used for basecalling.
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using Bowtie v2.2.3 and  paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM  of each gene was calculated based on the length of the gene and reads count mapped to this  gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq  R package (1.18.0). The resulting P-values were adjusted using the Benjamini and Hochberg’s  approach for controlling the false discovery rate . Genes with an adjusted P-value <0.05  found by DESeq were assigned as differentially expressed.
GO analysis was performed by the GO Annotation of TAIR.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Developing seeds

growth_protocol: Arabidopsi grown in full-spectrum white fluorescent light at 22°C under long day conditions (16 h light/8 h dark).

extract_protocol:
Developing seeds at 9 DAP were dissected from siliques by needle, and total RNA was extracted by Plant RNA Kit (R6827, Omega).
A total amount of 3 µg RNA per sample was used as input material for the RNA sample  preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library  Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index  codes were added to attribute sequences to each sample. Briefly, mRNA was purified from  total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out  using divalent cations under elevated temperature in NEBNext First Strand Synthesis  Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer  and M-MuLV Reverse Transcriptase（RNase H-） . Second strand cDNA synthesis was  subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs  were converted into blunt ends via exonuclease/polymerase activities. After adenylation of  3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to  prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp  in length, the library fragments were purified with AMPure XP system (Beckman Coulter,  Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected,  adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then  PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers  and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and  library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Developing seeds

tag: development stage

value: embryo development


title: lec1-4 rep2


title: lec1-4 rep1


title: 15#08389 Eedwt/wt (WT)

tag: strain


title: Serum_RNA_ncSSc_8

description: patients


title: Col-0-2 rep3

value: wild type


title: 15#08383 Eedhypo/hypo (HOM)


title: Serum_RNA_HC_7

description: healthy controls

value: serum


title: 15#08382 Eedhypo/hypo (HOM)


title: dellaq rep3

value: dellaq


title: Col-0-2 rep1


title: Serum_RNA_HC_5

description: healthy controls


title: TT-5-1

city: Wuhan

first: Lianrong

last: Wang

address: Bayi Road

institute: Wuhan University

data_processing:
basecalling by Illumina Casava1.7
Adaptor sequences were removed from sequenced reads and reads with Ns and low-quality sequencing scores were removed. Reads were then mapped to the reference genome sequence CP000094 using bwa 0.7.10-r789 with parameters aln -o 1 -e 63 -i 90 -L -k 2 -l 31 -t 4 -q 10.
Reads Per Kilobase of gene per Megabase of library size (RPKM) were calculated ( Chepelev et al., Nucleic Acids Research, 2009) . In brief, the number of reads mapped to a gene were counted and normalized by the size of the library.
Gene expression levels (RPKM) were tested for differences between the two samples using Poisson distribution. The p values and FDR values were calculated. Genes with p value <= 0.05, FDR <= 0.001, and folder change >=2 were filtered out as differentially expressed genes.
Genome_build: Pseudomonas fluorescens Pf0-1 (CP000094)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all and differentially expressed genes in each sample

organism: Pseudomonas fluorescens

source_name: Bacteria cells

growth_protocol: 1 mL over-night culture of pf0-1 and TT-5 was added into 50 mL Luria-Bertani (LB) respectively to extend culture. The OD of each culture reached 1.0 after shaking at 28℃ for 4 hours,then 10 ml culture of each was used for next analysis.

extract_protocol:
The 10 ml culture was mixed with 20 ml RNAprotect Bacteria Reagent (Qiagen) and incubated for 20 min at room temperature to stabilize the mRNA. Next, the cell suspensions were centrifuged at 8,000 × g for 5 min to pellet the cells, and the supernatant was decanted. Total RNA was purified using RNeasy Mini Kit (Qiagen) according to the manufacturer's recommended protocol
After the total RNA extraction and DNase I treatment, mRNA was isolated by removing rRNAs from the total RNA. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After  that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000 or other sequencer when necessary.

value: early log-phase

value: DndBCDE-


title: Serum_RNA_ncSSc_4

description: patients

value: female


title: Serum_RNA_HC_6

description: healthy controls

value: male


title: WT-1


title: GAF Replicate 2

type: protein

city: Boston

first: Michael

last: Tolstorukov

state: MA

address: 185 Cambridge Street

institute: Massachusetts General Hospital

hyb_protocol: Protein samples were incubated with microarray for 1 hour @ 200 nM protein concention in binding buffer ( 10 mM Tris-HCl, pH 7.4; 0.2 ug/ul bovine serum albumin (BSA) (New England Biolabs #B9001S); 0.3 ng/ul Salmont testes DNA (Sigma #D7656), 2% non-fat dry milk; 1 mM dithiothreitol (DTT); 1 mM ehtylenediaminetetraacetic acid (EDTA); 50 uM zinc acetate dehydrate; 80 mM NaCl).

scan_protocol: Microarray scanning performed using GenePix 4400 A (Moleclar Devices)

data_processing: Image analysis and data normalization performed using Gene Pix Pro ver 6 and masliner (MicroArray LINear Regression) software. Median fluorescence intensities were calculated over replicate probes for each unique DNA sequence

molecule: protein

organism: Drosophila melanogaster

source_name: N-terminal GST-tagged GAF protein sample

label_protocol: Microarray-bound protein was labelled by incubation for 20 min with 0.05 mg/ml Alexa488-conjugated anti-GST antibody (Invitrogen, #A11131).

extract_protocol: The PureExpress in vitro transcription and translation kit (New England Biolabs) was used to express GST-GAF-DBD. The manufacturer’s protocol was altered by adding 1.25 μL 1mM zinc acetate to 25 μL IVT reactions prior to expression for 2 hours at 37˚C. Proteins were quantified by Western blotting and comparing to a dilution series of GST standard.

treatment_protocol: Microarray was incubated with GST-tagged GAF

value: N-terminal GST-tagged GAF protein


title: Serum_RNA_HC_4

description: healthy controls


title: Col-0-2 rep2


title: Serum_RNA_HC_3

description: healthy controls


title: GAF Replicate 1


title: PAF_KO_1_RNA-seq

city: Houston

first: Bo

last: Xia

state: TX

address: 6670 Bertner Ave, R10-414D

institute: Houston Methodist

description: Intestinal adenoma

data_processing:
Sequenced reads were mapped to mm9 whole genome using tophat2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated by Cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: text file includes RPKM values for each Sample.

source_name: PAF knock out  APC Min adenoma

extract_protocol:
RNA extract from mouse intestinal adenomas using Qaigen RNeasy mini kit
RNA libraries were prepared for sequencing using standard BGI and Illumina protocols

value: PAF KO; APC Min/+

value: small intestine

tag: disease state

value: adenoma


title: Col-0-1 rep2


title: WT_2_RNA-seq

description: Intestinal adenoma

source_name: wild type APC Min adenoma

value: APC Min/+


title: Col-0-1 rep1


title: WT_1_RNA-seq

description: Intestinal adenoma


title: Col-0-1 rep3


title: dellaq rep2


title: SpColCtrl_206

status: Public on Feb 14 2018

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
fastq quality read filtering (>80% with Sanger Q>20)
cell barcode demultiplexing (custom script)
mapping with tophat2 on the mm10 transcriptome
filtering out low alignment score reads and multiple mapping reads (samtools)
duplication filtering using unique molecular identifiers (custom scripts). UMI sequence is at the 4rth position in the read ID (separation by ":")
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: spleen

growth_protocol: Live cells were sorted by flow cytometry from the spleen and colon lamina propria of mice (carrying a Foxp3 reporter gene).

extract_protocol:
Spleen were mechanically dissociated and colon were digested with collagenase/dispase to single cell suspensions. Tregs were sorted by flow cytometry as DAPI- TCRb+ CD4+ GFP+ cells. Single cells were then encapsulated in nanodroplets according to the InDrops protocol.
mRNA was reverse transcribed using adapters containing oligo dT in each droplet. The emulsion was then broken and linear amplification was performed by in vitro transcription. Illumina adapters were added by reverse transcription and PCR. Library were sequenced using a NextSeq500.

value: spleen

tag: library name

tag: sample type

value: B6 Foxp3-Ires-Gfp

tag: Sex

tag: age (months)

tag: total number of reads

tag: number of mapped reads

tag: number of unique reads (umi)


title: SpColCtrl_204

tag: tissue


title: SpColCtrl_197


title: SpColCtrl_191


title: SpColCtrl_200


title: SpColCtrl_201


title: SpColCtrl_202


title: SpColCtrl_205


title: SpColCtrl_195


title: SpColCtrl_194


title: SpColCtrl_203


title: SpColCtrl_196


title: SpColCtrl_188


title: Serum_RNA_HC_2

description: healthy controls

value: healthy control


title: dellaq rep1

value: Developing seeds


title: SpColCtrl_186


title: SpColCtrl_184


title: SpColCtrl_198


title: SpColCtrl_187


title: SpColCtrl_182


title: SpColCtrl_183


title: SpColCtrl_181


title: Serum_RNA_HC_1

description: healthy controls


title: SpColCtrl_156


title: SpColCtrl_170


title: SpColCtrl_158


title: SpColCtrl_165


title: SpColCtrl_175


title: SpColCtrl_167


title: SpColCtrl_172


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title: SpColCtrl_173


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title: SpColCtrl_163


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title: SpColCtrl_134


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title: SpColCtrl_7


title: SpColCtrl_8


title: SpColCtrl_6


title: SpColCtrl_5


title: SpColCtrl_4


title: SpColCtrl_24


title: ColonTR_rep2_2143


title: ColonTR_rep2_2147


title: ColonTR_rep2_2146


title: SpColCtrl_2


title: ColonTR_rep2_2144


title: ColonTR_rep2_2142


title: ColonTR_rep2_2140


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title: SpColCtrl_73


title: ColonTR_rep2_2133


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title: ColonTR_rep2_2086


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title: ColonTR_rep2_2028


title: ColonTR_rep2_2027


title: ColonTR_rep2_2021


title: ColonTR_rep2_2018


title: ColonTR_rep2_2019


title: ColonTR_rep2_2043


title: ColonTR_rep2_2026


title: ColonTR_rep2_2012


title: ColonTR_rep2_2020


title: ColonTR_rep2_2016


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title: ColonTR_rep2_2014


title: ColonTR_rep2_2007


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title: ColonTR_rep2_2025


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title: ColonTR_rep2_2002


title: ColonTR_rep2_2023


title: ColonTR_rep2_2015


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title: ColonTR_rep2_1998


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title: ColonTR_rep2_1986


title: ColonTR_rep2_1982


title: ColonTR_rep2_1990


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title: ColonTR_rep2_1969


title: ColonTR_rep2_1997


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title: ColonTR_rep2_1966


title: ColonTR_rep2_1975


title: ColonTR_rep2_1963


title: ColonTR_rep2_1962


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title: ColonTR_rep2_1958


title: ColonTR_rep2_1957


title: ColonTR_rep2_1952


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title: ColonTR_rep2_1937


title: ColonTR_rep2_1976


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title: ColonTR_rep2_1930


title: ColonTR_rep2_1935


title: ColonTR_rep2_1928


title: ColonTR_rep2_1932


title: ColonTR_rep2_1961


title: ColonTR_rep2_1955


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title: ColonTR_rep2_1917


title: ColonTR_rep2_1915


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title: ColonTR_rep2_1822


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title: ColonTR_rep2_1818


title: ColonTR_rep2_1815


title: ColonTR_rep2_1836


title: ColonTR_rep2_1813


title: ColonTR_rep2_1825


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title: ColonTR_rep2_1823


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title: ColonTR_rep2_1797


title: ColonTR_rep2_1799


title: ColonTR_rep2_1796


title: ColonTR_rep2_1795


title: ColonTR_rep2_1798


title: ColonTR_rep2_1805


title: ColonTR_rep2_1793


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title: ColonTR_rep2_1775


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title: ColonTR_rep2_1728


title: ColonTR_rep2_1733


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title: ColonTR_rep2_1727


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