title: CD31-CD45-CD90+ cells [cd90 cell74]

description:
cd90 cell74
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell72]

status: Public on Feb 12 2018

type: SRA

city: London

first: Magnus

middle: David

last: Lynch

address: 28th Floor, Tower Wing, Guy's Campus

department: Centre for Stem Cells and Regenerative Medicine

country: United Kingdom

institute: King's College London

description:
cd90 cell72
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv

library_source: transcriptomic

data_processing:
Reads were mapped to hg19 reference genome with Tophat.
For single cell RNA sequencing, gene-specific expression was quantified using featureCounts.
For spatial RNA sequencing, maximal exonic read density was quantified for each gene.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.csv: Comma-separated text files include gene expression quantification.

molecule: total RNA

organism: Homo sapiens

source_name: Human Dermal Cells

extract_protocol:
Separated papillary and reticular dermis samples were transferred to lysis buffer containing 2-mercaptoethanol (PureLink RNA micro scale kit, Invitrogen) and homogenized for 2 minutes using a mechanical homogenizer (Polytron, Kinematica). Subsequent RNA extraction was performed using the PureLink micro kit according to the manufacturer’s instructions.
Library preparation was performed with SmartSeq2 followed by the Nextera XT protocol (Illumina). Sequencing was performed on the Illumina HiSeq 2000 or HiSeq 2500 with TruSeq SBS v3 chemistry.

treatment_protocol: Spatial RNA sequencing was performed using fresh human skin samples (from three separate individuals). Skin samples were incubated with Dispase II (Stemcell Technologies) for 1h at 37° C permitting separation of the epidermis. The dermis was separated into papillary (upper 100 μm) reticular (200-500 μm) dermis by microdissection under a dissecting microscope. For single cell RNA sequencing, single cells were isolated by flow cytometry and sorted into individual wells of a 96 well plate containing 2μl lysis buffer (0.2% (vol/vol) Triton X-100 and 2 U/ul recombinant RNase inhibitor (Clontech).

tag: cell type

value: Primary dermal fibroblasts

tag: cell subpopulation


title: CD31-CD45-CD90+ cells [cd90 cell70]

description:
cd90 cell70
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell71]

description:
cd90 cell71
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell64]

description:
cd90 cell64
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell90]

description:
cd90 cell90
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell59]

description:
cd90 cell59
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell58]

description:
cd90 cell58
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell57]

description:
cd90 cell57
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell66]

description:
cd90 cell66
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell67]

description:
cd90 cell67
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell61]

description:
cd90 cell61
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell62]

description:
cd90 cell62
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell85]

description:
cd90 cell85
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell68]

description:
cd90 cell68
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell55]

description:
cd90 cell55
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell63]

description:
cd90 cell63
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell52]

description:
cd90 cell52
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell65]

description:
cd90 cell65
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell51]

description:
cd90 cell51
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell53]

description:
cd90 cell53
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell54]

description:
cd90 cell54
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell48]

description:
cd90 cell48
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell47]

description:
cd90 cell47
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell46]

description:
cd90 cell46
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell45]

description:
cd90 cell45
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell49]

description:
cd90 cell49
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell50]

description:
cd90 cell50
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell44]

description:
cd90 cell44
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell69]

description:
cd90 cell69
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell60]

description:
cd90 cell60
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell43]

description:
cd90 cell43
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell56]

description:
cd90 cell56
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell41]

description:
cd90 cell41
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell40]

description:
cd90 cell40
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell38]

description:
cd90 cell38
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell37]

description:
cd90 cell37
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell36]

description:
cd90 cell36
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell35]

description:
cd90 cell35
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell34]

description:
cd90 cell34
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell42]

description:
cd90 cell42
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell33]

description:
cd90 cell33
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell26]

description:
cd90 cell26
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell24]

description:
cd90 cell24
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell30]

description:
cd90 cell30
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell29]

description:
cd90 cell29
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell32]

description:
cd90 cell32
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell22]

description:
cd90 cell22
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell31]

description:
cd90 cell31
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell28]

description:
cd90 cell28
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell23]

description:
cd90 cell23
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell27]

description:
cd90 cell27
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell18]

description:
cd90 cell18
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell20]

description:
cd90 cell20
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell16]

description:
cd90 cell16
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell17]

description:
cd90 cell17
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell14]

description:
cd90 cell14
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell13]

description:
cd90 cell13
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell15]

description:
cd90 cell15
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell12]

description:
cd90 cell12
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell39]

description:
cd90 cell39
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell19]

description:
cd90 cell19
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell25]

description:
cd90 cell25
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell11]

description:
cd90 cell11
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell9]

description:
cd90 cell9
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell21]

description:
cd90 cell21
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell10]

description:
cd90 cell10
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell5]

description:
cd90 cell5
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell6]

description:
cd90 cell6
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell2]

description:
cd90 cell2
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell4]

description:
cd90 cell4
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell1]

description:
cd90 cell1
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: L136-pre

city: Louisville

first: Theodore

middle: Samuel

last: Kalbfleisch

state: KY

address: 221F Baxter II, 580 S Preston St

department: Biochemistry and Molecular Genetics

country: USA

institute: University of Louisville

data_processing:
bcl2Fastq
TrimGalore
mirDeep2
Genome_build: GCA_000002305.1
Supplementary_files_format_and_content: miRDeep2 csv result output

organism: Equus caballus

source_name: Seminal exosomes

extract_protocol:
Exosomal RNA was extracted using the SeraMir Exosome RNA Isolation kit (System Biosciences, Palo Alto, CA)
cDNA libraries were prepared using TailorMix Micro RNA Sample Preparation version 2 (SeqMatic LLC, Fremont, CA) and perfomed by a commercial company (System Biosciences, Palo Alto, CA). cDNA libraries were size-selected on an 8% Tris-borate-EDTA (TBE) polyacrylamide gel
cDNA libraries were sequenced (1x75bp) in a Illumina NextSeq 500 platform.

treatment_protocol: Seminal exosomes were isolated using the ExoQuick Exosome Precipitation Solution (System Biosciences, Palo Alto, CA) from seminal plasma samples derived from the stallions at the specific time-points post-infection as described

tag: infection

value: Uninfected

tag: time

value: Pre-challenge


title: GRO-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4, 1hVeh)

city: Debrecen

first: Gergely

last: Nagy

address: Egyetem ter 1.

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen

data_processing:
Library strategy: GRO-Seq
alignment with bwa v0.7.10 using default parameters
bam generation with samtools v0.1.19 using default parameters
tag directory generation with homer v4.2 makeTagDirectory using -checkGC parameter
bedgraph generation with homer v4.2 makeUCSCfile using -fsize 1e50 -fragLength 120 -noadj -style chipseq parameters (srand-specifically using -strand '+' or '-' -neg parameters and than uniting and sorting by coordinates). Due to the stranded nature of the data there are overlapping coordinates in the bedGraph files. Files can be loaded into IGV genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

organism: Mus musculus

source_name: bone marrow-derived macrophage

extract_protocol:
Bone marrow-derived macrophages were differentiated in the presence of M-CSF for 6 days. Cells were treated with IL-4 (20ng/ul) for 24 hours followed by vehicle or ligand exposure for 1 hour (LG268 - 100nM, RSG - 1uM). Cells were lysed in the following lysis buffer: 10mM Tris-HCl pH7.4, 2mM MgCl2, 3mM CaCl2, 0.5% IGEPAL, 10% Glycerol, 1mM DTT.
After nuclei isolation run-on reactions were performed for 5 minutes at 30C. Run-on RNA were pulled down with Br-U antibody coated agarose beads and washed extensively. Libraries were prepared with NEBNext® Small RNA Library Prep Set for Illumina® according to the protocol provided by the manufacturer.

value: bone marrow-derived macrophage

tag: strain

tag: age

value: 3 months

tag: Sex

value: male


title: GRO-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hRSG)


title: L140-d86

value: Equiena arteritis virus

value: 86 days post-infection


title: L140-pre


title: L136-d726

value: Equiena arteritis virus (long-term, persistent infection)

value: 726 days post-infection


title: L140-d726


title: L136-d86


title: L139-pre


title: GRO-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (1hVeh)


title: GRO-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4, 1hRSG)


title: GRO-Seq analysis of Wt mouse BMDM cells differentiated in the presence of MCSF (24hIL4, 1hLG268)


title: CD31-CD45-CD90+ cells [cd90 cell8]

description:
cd90 cell8
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell7]

description:
cd90 cell7
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: CD31-CD45-CD90+ cells [cd90 cell3]

description:
cd90 cell3
Single cell RNA sequencing of primary dermal cells Lin-CD31-CD45-CD90+.
PolyA
processed data file: CD90.csv


title: L139-d86


title: Th2 + IL-33_4

type: RNA

city: Sydney

first: Cristan

last: Herbert

state: NSW

address: High Street

department: School of Medical Sciences/Pathology

country: Australia

institute: University of New South Wales

description:
Expt H4 - Th2+IL-33
microRNA expression
Replicate 4

hyb_protocol: Samples were hybridised to arrays for 20 hours at 55C rotating at 20 rpm.

scan_protocol: Slides were scanned using the AgilentG3_miRNA  scanner protocol for G3 format. Data were extracted using Feature Extraction Software – FE protocol miRNA_QCMT_Jan09.

data_processing: Data were imported into Partek Genomics Suite 6.6. Background noise correction was applied to raw probe-level data and quantile normalisation was performed as per RMA (robust mean average) procedure. Samples were labelled according to their position on the slides, and a one-way ANOVA was performed with the Partek Genomics Suite across all groups.

source_name: RAW cells, Th2 cytokines, IL-33

label_protocol: 100 ng RNA was labelled using the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb kit Protocol Version 3.0.

growth_protocol: RAW264.7 cells were grown in RPMI1640 (+L-glut) + 10% FCS (with Pen/Strep); For experiments, cells were cultured in 6-well plates @ 5x10(5) cells per well in complete medium, and allowed to adhere overnight.

extract_protocol: Media was removed and cells were lysed with 1 ml of TriReagent. Total RNA was extracted according to the TriReagent protocol.

treatment_protocol: Cells were cultured in complete medium with or without (+/-) 10ng/ml of Th2 cytokines (IL-4 and IL-13) for 48 hours. Cells were washed with PBS and relevant groups were then stimulated with 20 ng/ml of murine recombinant IL-33 and incubated for 4 hours.

tag: cell line

value: macrophage-like cell line

tag: growth condition

value: Th2 cytokines

tag: stimulation


title: Th2 + IL-33_2

description:
Expt E4 - Th2+IL-33
microRNA expression
Replicate 2


title: Th2 + IL-33_3

description:
Expt F4 - Th2+IL-33
microRNA expression
Replicate 3


title: Th2 + IL-33_1

description:
Expt D4 - Th2+IL-33
microRNA expression
Replicate 1


title: Media + IL-33_3

description:
Expt F3 - IL-33
microRNA expression
Replicate 3

source_name: RAW cells, media only, IL-33

value: Media only


title: 090216_HaCaT_shKMT2D

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: knockdown

data_processing:
Raw reads were mapped to the reference human genome assembly GRCh37 (hg19) using STAR.
Normalized gene counts and differential expression analysis result were produced by BaseSpace DESeq2 workflow.
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2_normalized_read_count

source_name: HaCaT keratinocytes

growth_protocol: Normal human epidermal keratinocytes (NHEKs) and HaCaT keratinocytes were grown in 10cm plates and harvested at 75% confluency

extract_protocol:
RNAeasy kit (Qiagen)
NEBNext poly(A) mRNA magnetic isolation followed by NEBNext Ultra Directional RNA library preparation kit for Illumina

treatment_protocol: Cells were treated with either shRNAs for a scrambled control (shSC) or KMT2D (shKMT2D)

tag: tissue

value: skin

tag: genotype/variation


title: 090216_HaCaT_shSC

description: control

value: shSC


title: Th2_3

description:
Expt F2 - Th2
microRNA expression
Replicate 3

source_name: RAW cells, Th2 cytokines, unstimulated


title: Media + IL-33_2

description:
Expt E3 - IL-33
microRNA expression
Replicate 2


title: Media + IL-33_4

description:
Expt H3 - IL-33
microRNA expression
Replicate 4


title: Th2_1

description:
Expt D2 - Th2
microRNA expression
Replicate 1


title: 082216_HaCaT_shSC

description: control


title: Th2_4

description:
Expt H2 - Th2
microRNA expression
Replicate 4


title: Media + IL-33_1

description:
Expt D3 - IL-33
microRNA expression
Replicate 1


title: 4415_NHEK_shKMT2D

description: knockdown

source_name: normal human epidermal keratinocytes


title: Ago2IP_3-miR146a

city: Lisbon

first: Francisco

middle: J.

last: Enguita

address: Av. Professor Egas Moniz

department: Instituto de Medicina Molecular

country: Portugal

institute: Faculdade de Medicina, Universidade de Lisboa

data_processing:
Alignment with Bowtie2
Differential expression with CuffDiff

source_name: pooled spleens of Ago-2 tagged (3xFLAG-6xHIS tag) mice and stimulated with plate-bound anti-CD3ε plus anti-CD28 mAb

growth_protocol: CD3+ T cells were FACS sorted from pooled spleens of Ago-2 tagged (3xFLAG-6xHIS tag) mice and stimulated with plate-bound anti-CD3ε (145.2C11) plus anti-CD28 mAb (37.51) (both 2,5 mg/ml) and transduced either with RV-miR-146a-vector or RV-control vector. 24h after transduction GFP+ live cells (using Live/dead stain kit (Life technologies) were FACS sorted.  Cells (7×105 to 2×106) were UV-crosslinked in Stratalinker 2400 (400mJ cm-2) and lysed. AGO-interacting RNA were immunoprecipitated using anti-Flag (M2) magnetic beads (Sigma). Following, Ago-2-bound RNA was partially digested using RNase IT (Agilent technologies) and in second step purified using the HIS-tag and Ni-NTA beads (Qiagen) under high stringent denaturing wash conditions.

extract_protocol:
Afte proteinase K treatment RNA was isolated using Phenol-chloroform isoamyl extraction
Libraries were prepared using Clonetch SMARTer Stranded RNA-Seq Kit, starting with 8μl of the IPed RNA. The manufacturer’s protocol was followed, using 4 minutes for RNA fragmentation, double SPRI bead clean-up after reverse transcription and 20 PCR cycles for amplification. The resulting libraries were sequenced using Illumina Hiseq2000 instrument with 50 base pair single read sequencing mode.

value: CD3+T lymphocytes

tag: transfection


title: 082216_HaCaT_shKMT2D

description: knockdown


title: 090816_HaCaT_shKMT2D

description: knockdown


title: Th2_2

description:
Expt E2 - Th2
microRNA expression
Replicate 2


title: Ago2IP_3-empty

value: RV-control vector


title: 090816_HaCaT_shSC

description: control


title: 4483_NHEK_shKMT2D

description: knockdown


title: Ago2IP_1-empty


title: 4534_NHEK_shKMT2D

description: knockdown


title: Ago2IP_1-miR146a


title: 4415_NHEK_shSC

description: control


title: Media_2

description:
Expt E1 - Media
microRNA expression
Replicate 2

source_name: RAW cells, media only, unstimulated


title: Media_1

description:
Expt D1 - Media
microRNA expression
Replicate 1


title: Media_4

description:
Expt H1 - Media
microRNA expression
Replicate 4


title: 4534_NHEK_shSC

description: control


title: Media_3

description:
Expt F1 - Media
microRNA expression
Replicate 3


title: 4483_NHEK_shSC

description: control


title: D4-IP-030917

description: control for shKMT2D R2 KMT2D

library_source: genomic

data_processing:
Raw reads were mapped to the reference human genome assembly GRCh37 (hg19) using Bowtie2 local alignment.
The alignment result was further processed by SAMtools to remove low-quality alignments (a minimum mapping quality of 10), duplicate reads, reads mapped to the mitochondria, unplaced (chrUn) and random (chr_random) contigs, and reads mapped to the ENCODE blacklisted genomic regions.
MACS2 was used to identify ChIP-seq enriched regions (or peaks), requiring peak calling FDR<0.01.
Distribution of resulting peaks in different genomic regions and motif analysis were conducted using the HOMER suite (“annotatePeaks -size given” and “findMotifsGenome”).
The gene target for each peak was identified as the gene with the transcription start site (TSS) nearest to the peak.
Genome-wide tag density was computed using BEDTools and UCSC command line utilities to generate tracks for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were converted from bedgraph files, which were generated using Bedtools. Scores were normalized to 1 million reads per sample.

molecule: genomic DNA

source_name: keratinocytes

growth_protocol: Keratinocytes cultured in 10-cm2 dishes were fixed in 1% formaldehyde for 5 min and quenched with the addition of glycine to 125 mM for an additional 5 min.

extract_protocol:
ChIP extracts were sonicated nine times for 5 min each round (30 sec of sonication with intermediate incubation of 30 sec per round) using a Bioruptor (Diagenode). All ChIPs were performed using 500 μg of extract and 2 μg of antibody per sample.
ChIP DNA was also used to make sequencing libraries using NEBNext Ultra DNA library preparation kit for Illumina (New England Biolabs).

treatment_protocol: Cells were harvested by scraping from plates and washed twice in 1× PBS before storage at −80°C.

value: keratinocytes

tag: chip antibody


title: SC-IP-030917

description: control for shSC R2 KMT2D


title: SC-P63-030917

value: anti-p63 (4A4) (Santa Cruz Biotechnology, sc-8431)


title: D4-Sham-H3

description: control for shKMT2D H3K27ac and shKMT2D H3K4me1

value: anti-Histone H3 (Abcam, ab1791)


title: D4-IP

description: control for shKMT2D R1 KMT2D


title: SC-KMT2D-030917

value: anti-KMT2D (HPA035977) (Sigma-Aldrich)


title: D4-KMT2D


title: SC-Sham-H3K4me1

value: anti-Histone H3 (monomethyl K4) (Abcam, ab8895)


title: D4-Sham-H3K4me1


title: SC-Sham-H3K27ac

value: anti-Histone H3 (acetyl K27) (Abcam, ab4729)


title: D4-Sham-H3K27ac


title: D4-KMT2D-030917


title: SC-Sham-H3

description: control for shSC H3K27ac and shSC H3K4me1


title: SC-KMT2D


title: SC-IP

description: control for shSC R1 KMT2D and shSC p63


title: Dlk1+Sca1-, biological rep3

city: San Francisco

first: Angela

last: Oliveira Pisco

state: CA

address: 499 Illinois St

department: Data Science

institute: Chan Zuckerberg Biohub

description: dermis of P2 mouse

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials, according to the manufacturer's protocol

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneSpring v13 software.
meta-probeset file: MoGene-2_0-st-v1.na35.mm10.transcript

label: biotin

source_name: wild-type dermal mouse fibroblasts

label_protocol: Samples were labelled using Affymetrix labelling kit materials, according to the manufacturer's protocol

growth_protocol: Mouse dermis dissected from P2 mouse

extract_protocol: Fibroblasts were isolated as previously described (Jensen et al., 2010). Briefly, back skin was isolated and incubated in dispase-trypsin solution at 37°C, 1h. Dermis was separated from the epidermis, transferred to 0.25% Collagenase in FAD medium, minced and incubated at 37°C, 1h. The digest was passed through a 70Î¼m filter before centrifugation. For cell sorting, cells were washed with PBS and sorted using a BD-FACS-Aria-Fusion. For FACS-analysis, fibroblasts were incubated 1h with antibodies CD26, Sca1 and Dlk1, washed with PBS and analysed with a FACS-Canto-TMII

value: dermis

tag: genotype

value: wild-type

tag: fac sorted cell


title: Dlk1+Sca1+, biological rep3

description: dermis of P2 mouse


title: Dlk1+Sca1+, biological rep2

description: dermis of P2 mouse


title: Donor 3 - Reticular Dermis

description:
Dermis Sample 6
RNA sequencing of spatially dissected primary human dermis.
PolyA
processed data file: dermis.csv

source_name: Human Dermis

value: Primary reticular dermis

tag: donor


title: Dlk1+Sca1-, biological rep2

description: dermis of P2 mouse


title: CD26+, biological rep3

description: dermis of P2 mouse


title: Dlk1-Sca1+, biological rep2

description: dermis of P2 mouse


title: Donor 3 - Papillary Dermis

description:
Dermis Sample 5
RNA sequencing of spatially dissected primary human dermis.
PolyA
processed data file: dermis.csv

value: Primary papillary dermis


title: Dlk1-Sca1+, biological rep3

description: dermis of P2 mouse


title: Dlk1-Sca1+, biological rep1

description: dermis of P2 mouse


title: CD26+, biological rep1

description: dermis of P2 mouse


title: Dlk1+Sca1+, biological rep1

description: dermis of P2 mouse


title: Dlk1+Sca1-, biological rep1

description: dermis of P2 mouse


title: BCR-ABL1 transduced Ppp2r1afl/fl mouse bone marrow pre-B cells transduced with Cre for PP2A deletion, repeat 3

first: Huimin

last: Geng

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

hyb_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

data_processing: The CEL files were processed with Affymetrix GeneExpression Console software (Version 1.1) using RMA normalization to the gene level expression

source_name: BCR-ABL1 transduced PP2Afl/fl mouse bone marrow pre-B cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Affymetrix GeneChip Expression Analysis Technical Manual)

extract_protocol: Extraction Method: Qiagen RNeasy Kit

tag: cell type

value: Cre-mediated PP2A deletion


title: Donor 2 - Reticular Dermis

description:
Dermis Sample 4
RNA sequencing of spatially dissected primary human dermis.
PolyA
processed data file: dermis.csv


title: CRC parental 1136

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

country: Spain

institute: Parc Taulí Research and Innovation Institute (I3PT)

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

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

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

source_name: CRC parental

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

growth_protocol: See MTO derivation and growth in the paper. MTO140 organoids grown for 3 days were harvested from their 3D growth matrix (basement membrane extract, BME), counted and injected as intact spheroids in 30% BME below the serosa of the caecum of an anaesthetized mouse. Parental MTOs 68, 93, 54 and 207 were first injected subcutaneously and 1 mm3 pieces of resulting tumours were tranplanted onto the tip of syngeneic mice; the caecum tip was then folded over to mitigate carcinomatosis.

extract_protocol: Whole tumour fragments were dissected and put in trizol. RNA was extracted using the Ambion PureLink RNA mini kit (Life Technologies)

treatment_protocol: Mice were treated with 10mg of galunisertib twice per day by gavage, starting at day 11 and lasting until sacrifice at 5 weeks.

value: CRC parental

tag: organoid

tag: type

value: parental

value: LAKP

tag: treatment

value: Con


title: CRC parental 1137

value: LY


title: BCR-ABL1 transduced Ppp2r1afl/fl mouse bone marrow pre-B cells transduced with an empty vector (EV), repeat 2

scan_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual)

value: wild type


title: BCR-ABL1 transduced Ppp2r1afl/fl mouse bone marrow pre-B cells transduced with an empty vector (EV), repeat 3


title: BCR-ABL1 transduced Ppp2r1afl/fl mouse bone marrow pre-B cells transduced with Cre for PP2A deletion, repeat 1


title: Donor 2 - Papillary Dermis

description:
Dermis Sample 3
RNA sequencing of spatially dissected primary human dermis.
PolyA
processed data file: dermis.csv


title: CD26+, biological rep2

description: dermis of P2 mouse


title: CRC parental 1140

value: LAKT


title: CRC parental 1138


title: CRC parental 1141


title: CRC parental 1135


title: CRC parental 1139


title: Donor 1 - Reticular Dermis

description:
Dermis Sample 2
RNA sequencing of spatially dissected primary human dermis.
PolyA
processed data file: dermis.csv


title: CRC LiM 1133

source_name: CRC LiM

value: CRC LiM

value: LiM

value: LAKTP


title: Donor 1 - Papillary Dermis

description:
Dermis Sample 1
RNA sequencing of spatially dissected primary human dermis.
PolyA
processed data file: dermis.csv


title: CRC LiM 1131


title: CRC parental 1129


title: bESC_B_P24

status: Public on Feb 11 2018

city: Davis

first: Pablo

last: Ross

address: 1 Shields Ave

institute: University of California, Davis

data_processing:
Libraries were sequenced on an Illumina HiSeq 2500 platform
Sequence reads were mapped to the bovine UMD3.1 genome assembly and Ensembl 78 genebuild annotation using CLC Genomics Workbench 7.0 (CLCbio, Aarhus, Denmark).
Reads per million mapped reads per kilobase of exon model (RPKM) values were calculated for each gene and the levels of expression compared among groups using EdgeR with FDR correction for multiple testing.
Genome_build: UMD 3.1
Supplementary_files_format_and_content: tab-delimited text file including RPKM values for each gene and sample.

organism: Bos taurus

source_name: bESC

growth_protocol: bESC were grown in CTFR medium [a custom basal medium similar to mTeSR medium (STEMCELL Technologies)] that is completely devoid of growth factors FGF2 and TGFb and contains low fatty acid BSA (MP Biomedicals NZ), similar to basal medium in the published recipe (Ludwig TE, et al. (2006) Feeder-independent culture of human embryonic stem cells. Nat Methods 3:637–646), and supplemented with 20 ng/mL human FGF2 and 2.5 μM IWR1, and were incubated at 37 °C and 5% CO2 (Wu J, et al. (2015) An alternative pluripotent state confers interspecies chimaeric competency. Nature 521:316–321) in wells containing MEFs and were passaged every 4–5 d at a 1:10 split ratio.

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Mini Kit and then was reverse-transcribed using iScript RT Supermix (Bio-Rad).
Libraries were constructed using the TruSeq RNA Sample Prep Kit (Illumina)

value: BL-derived ESC

tag: passage number


title: bESC_A_P35


title: bESC_B_P12


title: bESC_A_P23


title: bESC_A_P13


title: Fibroblast_B

source_name: Skin fibroblasts

value: Skin


title: CRC parental 1130


title: CRC parental 1127


title: CRC parental 1126


title: CRC parental 1142


title: CRC parental 1128


title: bESC_B_P35


title: CRC parental 1125


title: CRC parental 1123


title: BCR-ABL1 transduced Ppp2r1afl/fl mouse bone marrow pre-B cells transduced with an empty vector (EV), repeat 1


title: ADCC stim NK cells, biological rep6

city: Silver Spring

first: Michael

middle: A

last: Eller

state: MD

address: 503 Robert Grant Ave. 1N11

department: U.S. Military HIV Research Program

institute: Henry Jackson Foundation

description:
Gene expression data from ADCC stimuated NK cells from a healthy donor.
ADCC 6.3

hyb_protocol: 5.5μg of biotin labeled cDNA was hybridized on the GeneChip Human Transcriptome Array 2.0 for 16 hours at 45°C. Arrays were washed and stained using the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned on the Affymetrix GeneChip Scanner 7G Plus

data_processing: The data were analyzed with TAC 2.0 software using Affymetrix default analysis settings and global scaling as normalization method.

source_name: NK cells stimulated with CEM.NKR.CCR5 targets donor 6

label_protocol: cDNA was prepared from 20ng total RNA using the NuGEN Ovation Pico WTA System v2. cDNA was then fragmented and biotin labeled with the Encore Biotin Module (NuGEN Technologies, Inc).

growth_protocol: Stimulation cell lines, K562 and CEM.NKR.CCR5, were grown in RPMI+20%FBS supplemented with pen/strep, L-glutamine and HEPES buffer.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Micro Kit, according to manufacturers instructions. After extraction, the RNA quality and quantity was assessed using the Agilent RNA 6000 Pico Kit on the Agilent 2100 Bioanalyzer.

treatment_protocol: PBMCs were stimulated by various in vitro stimulation conditions including K562 cells, CEM.NKR.CCR5 cells coated with gp120 and IL-12/!L-18.

tag: individual

value: donor 6

value: NK cells

tag: phenotype

value: CD56dimCD16dim/neg NK cells

value: ADCC


title: Cytokine stim NK cells, biological rep5

description:
Gene expression data from cytokine stimuated NK cells from a healthy donor.
Cytokine 5.4

source_name: NK cells stimulated with IL-12 and IL-18 donor 5

value: donor 5

value: Cytokine


title: Cytokine stim NK cells, biological rep6

description:
Gene expression data from cytokine stimuated NK cells from a healthy donor.
Cytokine 6.4

source_name: NK cells stimulated with IL-12 and IL-18 donor 6


title: CRC LiM 1132


title: unstim NK cells, biological rep6

description:
Gene expression data from unstimuated NK cells from a healthy donor.
Unstim 6.1

source_name: unstimulated NK cells donor 6

value: Unstimulated


title: CRC parental 1124

value: CRC parental

value: parental


title: K562 stim NK cells, biological rep6

description:
Gene expression data from K562 stimuated NK cells from a healthy donor.
K562 6.2

source_name: NK cells stimulated with K562 targets donor 6


title: invivo_BL_B

source_name: Blastocyst

tag: developmental stage

value: Blastocyst stage embryo


title: ADCC stim NK cells, biological rep5

description:
Gene expression data from ADCC stimuated NK cells from a healthy donor.
ADCC 5.3

source_name: NK cells stimulated with CEM.NKR.CCR5 targets donor 5


title: Cytokine stim NK cells, biological rep4

description:
Gene expression data from cytokine stimuated NK cells from a healthy donor.
Cytokine 4.4

source_name: NK cells stimulated with IL-12 and IL-18 donor 4

value: donor 4


title: K562 stim NK cells, biological rep4

description:
Gene expression data from K562 stimuated NK cells from a healthy donor.
K562 4.2

source_name: NK cells stimulated with K562 targets donor 4


title: unstim NK cells, biological rep5

description:
Gene expression data from unstimuated NK cells from a healthy donor.
Unstim 5.1

source_name: unstimulated NK cells donor 5


title: K562 stim NK cells, biological rep5

description:
Gene expression data from K562 stimuated NK cells from a healthy donor.
K562 5.2

source_name: NK cells stimulated with K562 targets donor 5


title: MH2-8d vs. Kep1.11

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: * 60 ul labeled sample is combined with 60 ul 2x-hybmix, containing 50% formamide, 10xSSC, 0.2% SDS, 200 ug/ml herring sperm DNA  * Hybridizations of spotted oligo-arrays (Codelink glass) or Agilent microarrays are performed on a HS4800Pro Hybstation (Tecan) * Priming: 5xSSC, 0.1%SDS * Probe injection: pre-hyb, 5xSSC, 25% formamide, 0.1%SDS, 1%BSA, Volume 110ul * Hybridization: 45 min at 42C. * Wash 2x: milliQ * Wash: 5xSSC, 0.1%SDS * Probe injection: sample. Volume 110ul (Agilent 4packs: 55ul) * Hybridization: 16 hours at 42C. * Wash 2x: 1xSSC, 0.2%SDS at 23C * Wash 2x: 0.1xSSC, 0.2%SDS at 23C * Wash 2x: 0.1xSSC at 23C * Drying: blow with nitrogen for 3min at 30C

scan_protocol: Scanning of slides using the Agilent G2565BA scanner. Features were extracted using Imagene software from Biodiscovery.

data_processing: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from the hybset itself, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009

label_protocol: All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman).   mRNA amplification protocol description: * all RNAs are diluted to 0.6 ug/ul and 5 ul is put in a 96-wells plate (Abgene). All subsequent steps are performed by the robot script. * mix1 containing 100 ng T7 Mlu VN primer (custom mix) and EC-control RNA per 5 ul is added and mixed in each well. * plate is incubated @ 70C for 10 mins, cooled to 48C. * mix2 containing 4ul 5x 1st strand buffer, 2 ul 0.1M DTT (Invitrogen), 1ul RNAse Inhibitor (Boehringer), 1ul 20mM dNTPs (GE Healthcare), 1ul linear acrylamide, and  1ul SuperScriptIII (Invitrogen) per sample is prewarmed to 48C; 10 ul per sample is added and mixed in each well. * plate is incubated @ 48C for 2 hours and cooled to room temperature. * 106 ul water and subsequently  mix3 containing 15ul second strand buffer, 3ul 20mM dNTPs (GE Healthcare), 1 ul T4 DNA ligase, 4 ul E.coli DNA polymerase I and 1 ul RNAseH  (Promega) is added and mixed in each well. * plate is incubated @ 16C for 2 hours, @65C for 10 mins. * ds cDNA product is purified and concentrated with RNAClean (Agencourt, GC biotech) according to manufacturers protocol, to an end volume of 25 ul . * 8 ul cDNA is put in a 96 wells plate and mixed with 12 ul IVT mix containing 2 ul 10x rxn-buffer, 2 ul each ATP, CTP, GTP, 0.6 ul UTP, 2 ul T7 enzyme mix (MegaScript kit, Ambion, Applied Biosystems), and 2.1 ul 50 mM 5-(3-aminoallyl)-UTP (Ambion, Applied Biosystems). * Plate is incubated @37C for 4 hours. * cRNA product is purified with RNAClean (Agencourt, Beckman) according to manufacturers protocol.  * Concentration  is measured (SpectraMax 190) and adjusted to 600 ng/ul by the robot. * Resulting cRNA plates are sampled for Bioanalyzer QC, snapfrozen and stored at -80C.  Labeling protocol description:  * NHS-ester Cy3 or Cy5 dye (Amersham PA 23001 and 25001): entire tube is resuspended in 100 ul DMSO (Merck 8.02912.10).   All subsequent steps are performed by the robot script : * 8 ul of each cRNA (0.6 ug/ul) is put in a 96-wells plate (Abgene), the accompanying reference sample is put in the next column (final step combines cy3 and cy5 labeled material ). * 3 ul 0.5 M NaBicarbonate buffer, pH 9 is added and mixed to all wells. * 3 ul cy-dye solution is added and mixed to the appropriate wells, plate is incubated at 18C for 1 hour. * 4.5 ul 5M hydroxylamine is added and mixed, incubated at 18o C for 15 minutes. * Labeled cRNA product is purified with RNA Clean (Agencourt, GC biotech) according to manufacturers protocol. * RNA concentration and labeling incorporation are measured (SpectraMax 190). * 2.5 ug of each labeled sample and reference cRNA are pooled and subjected to fragmentation according to protocol (Ambion, Applied Biosystems), 15 min 70C. * Samples are stored at -20C until hybridization.

extract_protocol: 1. Add 1 ml Trizol per 5x 106 cells in suspension (1 ml trizol per 10 cm culture disk) and mix by pipetting, transfer to 1.5 ml eppendorf tube.   2. Incubate 5 min at room temperature.  3. Add chloroform (200 Âµl per ml Trizol), mix for 15 seconds by shaking vigorously. Incubate 2-3 min at room temperature.  4. Centrifuge 20 min at 14000 rpm 4Â°C. After centrifugation, transfer the water-phase to a new 1.5-ml micro centrifuge tube.  5. add isopropanol to precipitate RNA. Use 0.5 ml per 1 ml trizol. Mix by shaking, leave samples at RT for 10 minutes. Centrifuge at 14000 rpm for 15 min.  6. wash pellet with 75% ethanol. Centrifuge at 14000 rpm for 15 min. Carefully pipet off all ethanol (respin briefly and use a P20 for the last microliters). Airdry pellets briefly before dissolving in MilliQ water. Depending on pellet-size, this may take a while. Continue with RNeasy columns (Qiagen) for clean-up of RNA (maximal 100 Âµg/column)  7. Adjust each sample to a volume of 300 Âµl with sterile MilliQ water. Add 160 Âµl buffer RLT to the samples, and mix (= lysis buffer).  8. Add 240 Âµl ethanol (100% stored at -20 Â°C) to the lysate, mix well by pipetting and immediately apply the sample to an RNeasy mini spin column sitting in a 2 ml collection tube (use a second P1000 pipet and work as quick as possible). Next lysate, and so on.  9. Centrifuge at 8000 rpm for 15 seconds in an Eppendorf centrifuge. Discard flowthrough, reuse collection tube. All centrifugation steps at roomtemperature! DNAse treatment: D1. Pipet 350 Âµl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm to wash. Discard the flow-through. Reuse the collection tube in step D3. D2. Prepare DNase I incubation mix (80 Âµl/reaction): add 10 Âµl DNase I stock solution to 70 Âµl Buffer RDD. Mix by gently inverting the tube. Buffer RDD is supplied with the RNase-Free DNase Set. Note: DNase I is especially sensitive to physical denaturation. Mixing should only be carried out by gently inverting the tube. Do not vortex. D3. Pipet the DNase I incubation mix (80 Âµl) directly onto the RNeasy silica-gel membrane, and place on the benchtop (20-30Â°C) for 15 min. Note: Make sure to pipet the DNase I incubation mix directly onto the RNeasy silica-gel membrane. DNase digestion will be incomplete if part of the mix sticks to the walls or the O-ring of the RNeasy column. D4. Pipet 350 Âµl Buffer RW1 into the RNeasy mini column, and centrifuge for 15 s at 8000 rpm. Discard the flow-through and collection tube.  10. Transfer the RNeasy column into a new 2 ml collection tube. Add 500 Âµl buffer RPE, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse the collection tube in next steps. 11. Pipet 500 Âµl buffer RPE onto the RNeasy column, wait 1 minute, and centrifuge at 8000 rpm for 15 seconds. Discard flow-through and reuse collection tube.  12. Centrifuge at 10,000 rpm for 2 minutes (to dry the RNeasy membrane).  13. Transfer the RNeasy column into a new 1.5 ml collection tube. Pipet 100 Âµl milliQ directly onto the RNeasy membrane and incubate for 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. Note: When small yields are expected, the elution volume can be lowered to a minimum of 35 Âµl milliQ.  14. Pipet the eluate of step 13 again onto the RNeasy membrane and incubate for another 4 minutes at room temperature. Centrifuge at 14,000 rpm for 1 minute to elute. After elution, put all RNA-samples on ice. 15. Determine RNA concentration by measuring A260, and RNA intactness by Bioanalyzer. Snap-freeze and store eluate at -80 Â°C.

tag: strain

value: cultured cells

value: common-REF


title: ADCC stim NK cells, biological rep4

description:
Gene expression data from ADCC stimuated NK cells from a healthy donor.
ADCC 4.3

source_name: NK cells stimulated with CEM.NKR.CCR5 targets donor 4


title: MH2-6d vs. Kep1.11


title: MH2-7d vs. Kep1.11


title: unstim NK cells, biological rep4

description:
Gene expression data from unstimuated NK cells from a healthy donor.
Unstim 4.1

source_name: unstimulated NK cells donor 4


title: MH2-4d vs. Kep1.11


title: MH2-5d vs. Kep1.11


title: ADCC stim NK cells, biological rep3

description:
Gene expression data from ADCC stimuated NK cells from a healthy donor.
ADCC 3.3

source_name: NK cells stimulated with CEM.NKR.CCR5 targets donor 3

value: donor 3


title: Fibroblast_A


title: MH2-5b vs. Kep1.11


title: K562 stim NK cells, biological rep3

description:
Gene expression data from K562 stimuated NK cells from a healthy donor.
K562 3.2

source_name: NK cells stimulated with K562 targets donor 3


title: BCR-ABL1 transduced Ppp2r1afl/fl mouse bone marrow pre-B cells transduced with Cre for PP2A deletion, repeat 2

source_name: BCR-ABL1 transduced PP2Afl/fl mouse bone marrow pre-B cells

value: Cre-mediated PP2A deletion


title: MH2-7b vs. Kep1.11


title: unstim NK cells, biological rep3

description:
Gene expression data from unstimuated NK cells from a healthy donor.
Unstim 3.1

source_name: unstimulated NK cells donor 3


title: MH2-6b vs. Kep1.11


title: MH2-8b vs. Kep1.11


title: MH2-4b vs. Kep1.11


title: Cytokine stim NK cells, biological rep3

description:
Gene expression data from cytokine stimuated NK cells from a healthy donor.
Cytokine 3.4

source_name: NK cells stimulated with IL-12 and IL-18 donor 3


title: MH2-3b vs. Kep1.11


title: MH2-3d vs. Kep1.11


title: MH2-1d vs. Kep1.11


title: MH2-2d vs. Kep1.11


title: Kep1.11 vs. MH2-5a


title: SEM_CX+DEC_48h

type: genomic

city: Rostock

first: Catrin

last: Roolf

address: Ernst-Heydemann-Str 6

country: Germany

institute: Rostock university medical center

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: The data were normalised for red and green channel separately using quantile normalisation with BeadStudio software v3.2.

label: Cy3, Cy5

source_name: SEM cell line, 48 h CX+DEC

label_protocol: Standard Illumina Protocol.

growth_protocol: Maintained at 37°C and 5% CO2; cultured in Iscoves Medium supplemented with 10% heat-inactivated FCS and 1% penicillin/streptomycin; split every 3-4 days and seeded in a density of 3x10E5 cells per mL.

extract_protocol: Macherey-Nagel Nucleo Spin Tissue DNA extraction kit; peqGOLD bisulfite conversion kit.

treatment_protocol: 5 µM CX-4945, 0.1 µM DEC, combination or 5 µM DMSO for 48 h.

tag: cell line

value: SEM

value: B-ALL cell line

value: CX-4945 + Decitabine


title: Kep1.11 vs. MH2-8a


title: Kep1.11 vs. MH2-7c


title: Cytokine stim NK cells, biological rep2

description:
Gene expression data from cytokine stimuated NK cells from a healthy donor.
Cytokine 2.4

source_name: NK cells stimulated with IL-12 and IL-18 donor 2

value: donor 2

value: NK cells


title: ADCC stim NK cells, biological rep2

description:
Gene expression data from ADCC stimuated NK cells from a healthy donor.
ADCC 2.3

source_name: NK cells stimulated with CEM.NKR.CCR5 targets donor 2

value: CD56dimCD16dim/neg NK cells

value: ADCC


title: Cytokine stim NK cells, biological rep1

description:
Gene expression data from cytokine stimuated NK cells from a healthy donor.
Cytokine 1.4

source_name: NK cells stimulated with IL-12 and IL-18 donor 1

value: donor 1

value: Cytokine


title: Kep1.11 vs. MH2-4a


title: Kep1.11 vs. MH2-4c


title: Kep1.11 vs. MH2-8c


title: K562 stim NK cells, biological rep1

description:
Gene expression data from K562 stimuated NK cells from a healthy donor.
K562 1.2

source_name: NK cells stimulated with K562 targets donor 1


title: MH2-1b vs. Kep1.11


title: MH2-2b vs. Kep1.11


title: ADCC stim NK cells, biological rep1

description:
Gene expression data from ADCC stimuated NK cells from a healthy donor.
ADCC 1.3

source_name: NK cells stimulated with CEM.NKR.CCR5 targets donor 1


title: Kep1.11 vs. MH2-6c


title: Co1Na_TE_5

city: Leuven

first: Alvaro

last: Cortés Calabuig

address: Herestraat 49 PO box 602

country: Belgium

institute: Genomics Core Leuven

data_processing:
Adapter and pol-A  removal Bbduk, bbtools/36.84-Java1.8.0_77, pars: =$SAMPLE\".R1.fastq\" out=$SAMPLE\"_trimmed.R1.fastq\" $REF k=13 ktrim=r forcetrimleft=11 useshortkmers=t mink=3 qtrim=t trimq=10 minlength=20 -Xmx20g
QC FastQC – 0.11.5-Java-1.8.0_77
Mapping  STAR 2.5.2b, pars: --runMode alignReads --runThreadN \$THREADS --genomeDir $GENOME_DIR --outSamUnmapped --readFilesIn $SAMPLE.R1.fastq --outStd SAM --outSAMtype SAM --outFileNamePrefix $TMP_DIR/$SAMPLE/$SAMPLE | elprep /dev/stdin $SAMPLE\".bam\" --replace-read-group \"I  D:$SAMPLE LB:$SAMPLE PL:illumina SM:$SAMPLE CN:GenomicsCoreLeuven\" --sorting-order coordinate --nr-of-threads \$THREADS
Feature count htseq v0.6.1p1, pars: s yes -a 10 -i Name -t gene -m union
Genome_build: oreochromis_niloticus,  ASM185804, v2 https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Oreochromis_niloticus/102/
Supplementary_files_format_and_content: text file with raw count from HTSeq

organism: Ophthalmotilapia nasuta

source_name: telencephalon

extract_protocol: Lexogen QuantSeq library prep

tag: Sex

value: female

tag: tissue

value: brain

tag: brain region

value: telencephalon


title: K562 stim NK cells, biological rep2

description:
Gene expression data from K562 stimuated NK cells from a healthy donor.
K562 2.2

source_name: NK cells stimulated with K562 targets donor 2


title: SEM_DEC_48h

source_name: SEM cell line, 48 h DEC

value: Decitabine


title: Kep1.11 vs. MH2-7a

value: cultured cells


title: Kep1.11 vs. MH2-6a

value: common-REF


title: unstim NK cells, biological rep1

description:
Gene expression data from unstimuated NK cells from a healthy donor.
Unstim 1.1

source_name: unstimulated NK cells donor 1

value: Unstimulated


title: Co1Ve_TE_4

organism: Ophthalmotilapia ventralis


title: Kep1.11 vs. MH2-5c


title: unstim NK cells, biological rep2

description:
Gene expression data from unstimuated NK cells from a healthy donor.
Unstim 2.1

source_name: unstimulated NK cells donor 2


title: Co1Ve_TE_5


title: Co1Ve_TE_3


title: Kep1.11 vs. MH2-3c


title: Co1Na_TE_2


title: Co1Ve_TE_1


title: Co1Ve_TE_2


title: Co1Na_OT_5

source_name: optic tectum

value: optic tectum


title: Co1Na_TE_3


title: Co1Ve_OT_4


title: Co1Na_OT_4


title: Co1Ve_OT_5


title: SEM_DMSO_48h

source_name: SEM cell line, 48 h DMSO

value: SEM

value: DMSO (control)


title: Co1Na_OT_3


title: SEM_CX_48h

source_name: SEM cell line, 48 h CX-4945

value: B-ALL cell line


title: Co1Na_OT_1


title: Co1Ve_OT_2


title: Co1Ve_OT_3


title: Co1Ve_OT_1


title: Co1Ve_OB_5

source_name: olfactory bulb

value: olfactory bulb


title: Kep1.11 vs. MH2-3a


title: Kep1.11 vs. MH2-2c


title: Kep1.11 vs. MH2-1c


title: Kep1.11 vs. MH2-2a


title: Co1Na_OB_4


title: Co1Ve_OB_4


title: Kep1.11 vs. MH2-1a


title: Co1Na_TE_1


title: Wildtype 3

city: Montreal

first: Przemyslaw

last: Sapieha

state: Quebec

address: 5345 Assumption Blvd

country: Canada

institute: Maisonneuve-Rosemont Research Center

data_processing:
Analysis was performed using the Torrent Suite software v4.4 (Thermo Fisher) and the whole Transcriptome Analysis Plugin v 4.2-r7 (Thermo Fisher)
The whole Transcriptome Analysis Plugin aligns reads on mouse reference genome (mm10) using Tophat2 then unmapped reads are aligned using Bowtie2 and merged together.
FPKM are calculated using Cufflinks.
Genome_build:  mm10
Supplementary_files_format_and_content: Excel file includes FPKM values for each Sample

source_name: Peritoneal macrophage

growth_protocol: F12 DMEM growth medium supplemented with 10% FBS

extract_protocol:
Total RNA was isolated from macrophages using the RNeasy Mini Kit (QIAGEN). The mRNA was then purified from 1μg of total RNA using the Dynabeads® mRNA DIRECT™ Micro Kit (Thermo Fisher). Whole transcriptome libraries were prepared using the Ion Total RNA-seq Kit v2. The yield and size distribution of the amplified libraries were assessed with an Agilent Bioanalyzer using a DNA 1000 Kit. Sequencing was performed on an Ion Chef™ Instrument (Ion Torrent™, Thermo Fisher).
Analysis was performed using the Torrent Suite software v4.4 (Thermo Fisher) and the whole Transcriptome Analysis Plugin v 4.2-r7 (Thermo Fisher). The whole Transcriptome Analysis Plugin aligns reads on mouse reference genome (mm10) using Tophat2 then unmapped reads are aligned using Bowtie2 and merged together. FPKM are calculate using Cufflinks.

value: Wildtype

value: Peritoneal macrophage


title: Co1Ve_OB_1


title: Co1Na_OT_2


title: Co1Na_OB_3


title: Co1Na_DI_5

source_name: diencephalon

value: diencephalon


title: Co1Ve_OB_2


title: Co1Na_OB_2


title: Co1Na_DI_4


title: Co1Ve_OB_3


title: Co1Na_OB_1


title: CRC LiM 1134

source_name: CRC LiM

value: CRC LiM

value: LiM

value: LAKTP

value: LY


title: Co1Na_DI_3

value: female

value: brain


title: Co1Na_OB_5


title: Co1Ve_DI_4


title: Co1Ve_DI_3


title: Co1Na_DI_1


title: Co1Ve_DI_2


title: Co1Ve_DI_1


title: Co1Ve_DI_5


title: Co1Na_CE_5

source_name: cerebellum

value: cerebellum


title: Co1Ve_CE_5


title: Co1Na_CE_4


title: Co1Ve_CE_3


title: Co1Na_CE_3


title: Co1Ve_CE_4


title: Co1Ve_CE_2


title: Co1Na_CE_2


title: Co1Na_CE_1


title: bESC_B_H3K27me3

data_processing:
Libraries were sequenced at the Vincent J. Coates Genomics Sequencing Laboratory at the University of California, Berkeley in an Illumina HiSeq 4000 platform where sequencing was performed as 100-bp paired-end.
Sequenced reads were aligned to the annotated bovine genome (UMD3.1 assembly) using bwa.
Peak calling was done using MACS2 with narrow settings for H3K4me3 (-g 2.67e9 -q 0.01 -m 2 100 -B -SPMR) and broad settings for H3K27me3 (-g 2.67e9 -q 0.05 -m 2 100 -broad -B -SPMR -fix-bimodal -extsize 200).
Genome_build: UMD3.1
Supplementary_files_format_and_content: bed files containing peaks were generated using MACS2

source_name: bESC

extract_protocol:
Chromatin from bESCs was prepared following the protocol recommended by the True MicroChIP manual (C01010130; Diagenode). Sonication was performed using a Covaris S220 ultrasonicator (500217; Covaris) with the following settings: duty cycle 5%, intensity 3, cycle/burst 200, number of cycles: 12 (60 s).
Sequencing libraries were prepared following the manufacturer’s instructions using the ThruPLEX DNA-seq kit (R400406;Rubicon) with 16 cycles in the library-amplification step.

treatment_protocol: bESCs were separated from the MEFs using Feeder Removal MicroBeads (130-095-531; Miltenyi Biotech) following the manufacturer’s protocol.

value: BL-derived ESC

tag: chip antibody

value: anti-H3K27me3 (ABE 44; Millipore)


title: Co1Na_BS_5

source_name: brain stem

value: brain stem


title: bESC_B_H3K4me3

value: anti-H3K4me3 (provided in the True MicroChIP Kit, C01010130;Diagenode)


title: Co1Ve_CE_1


title: Co1Na_DI_2


title: Co1Na_BS_4


title: bESC_B_input


title: Co1Ve_BS_5


title: Co1Ve_BS_4


title: U87cells F, 72h, biological rep2

city: CDMX

first: Ignacio

last: Camacho-Arroyo

address: AV. UNIVERSIDAD Nº 3000, UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO, C.U., DISTRITO FEDERAL

department: Biology

country: Mexico

institute: Universidad Nacional Autónoma de México

hyb_protocol: Labeled nucleic acids were hybridized to the Affymetrix GeneChip Human Gene 1.0 ST Array in a hybridization cocktail, and GeneChip Fluidics Station 450 was used for washing and staining steps according to manufacturer’s recommendations.

scan_protocol: Scanning of microarray platforms was performed in the GeneChip Scanner 3000 7G.

data_processing: Raw intensity data were pre-processed and quantile normalized using the Expression Console Software 1.4. Expression values were used to analyze the differential expressions between different groups was computed in the Transcriptomic Analysis Console Software 3.0. The statistical analysis was an unpaired one-way ANOVA and a false discovery rate analysis.

source_name: U87 human glioblastoma cell line, 72 h of treatment with F 100 nM

label_protocol: Biotinylation of cRNA was performed according to the Affymetrix Whole-Transcript Sense Target Labeling Protocol.

growth_protocol: The U87 cell line was cultured in Dulbecco’s Modified Eagle’s medium (DMEM) supplemented with 10 % of fetal bovine serum (FBS), 1 mM pyruvate, 2 mM glutamine, and 0.1 mM non-essential amino acids, at 37 °C in a humidified 5% CO2 atmosphere.

extract_protocol: Total RNA was extracted by the phenol-guanidine isothiocyanate-chloroform method, using TRI Reagent (Molecular Research Center Inc., OH, USA), according to manufacturer’s instructions.

treatment_protocol: 24 h before the beginning of treatments, cells were cultured in phenol red-free DMEM supplemented with 10% of charcoal-stripped FBS. Then, different treatments with vehicle (DMSO 10 %), allopregnanolone (10 nM), progesterone (10 nM), or finasteride (100 nM) during 72 h were performed.

value: glioblastoma cell line

value: after 72 h of treatment with finasteride 100 nM


title: U87cells F, 72h, biological rep1


title: U87cells P4, 72h, biological rep1

source_name: U87 human glioblastoma cell line, 72 h of treatment with P4 10 nM

value: after 72 h of treatment with progesterone 10 nM


title: bESC_A_H3K27me3


title: U87cells P4, 72h, biological rep3


title: U87cells 3α-THP, 72h, biological rep2

source_name: U87 human glioblastoma cell line, 72 h of treatment with 3α-THP 10 nM

value: after 72 h of treatment with allopregnanolone 10 nM


title: Co1Na_BS_2


title: bESC_A_input


title: U87cells 3α-THP, 72h, biological rep1


title: U87cells F, 72h, biological rep3


title: U87cells 3α-THP, 72h, biological rep3


title: Co1Na_BS_1


title: U87cells V, 72h, biological rep 2

source_name: U87 human glioblastoma cell line, 72 h of treatment with vehicle

value: after 72 h of treatment with vehicle (DMSO 0.1 %)


title: bESC_A_H3K4me3


title: U87cells P4, 72h, biological rep2


title: U87cells V, 72h, biological rep 1


title: Co1Ve_BS_1


title: Co1Na_BS_3


title: U87cells V, 72h, biological rep3


title: Co1Ve_BS_3


title: Co1Ve_BS_2


title: WARM ISCHEMIA + 6h COLD STORAGE corticomedullary junction (N=4)

status: Public on Feb 10 2018

city: Poitiers

first: Sebastien

last: Giraud

address: CHU de Poitiers, 2 rue de la miletrie

country: France

institute: Inserm U1313 IRMETIST, Université de Poitiers, CHU de Poitiers-Service Biochimie

hyb_protocol: The slides (Agilent Porcine V2 ref 026440) were hybridized following the One-Color Microarray-Based Gene Expression Analysis Protocol (Agilent)

scan_protocol: The slides were scanned on a Tecan MS200 scanner.

data_processing: The median signal of each spot in the hybridized arrays was determined and quantified using Feature Extraction software v11.5.1.1. The data from all the microarrays were transformed in log2 intensity. Then they were normalized together using the “limma” package function “normalizeQuantiles” and the “quantile” method. Normalization of the data was performed using the Bioconductor packages (http://www.bioconductor.org) and R software v2.15.2.

organism: Sus scrofa

source_name: Warm Ischemic (60 min)+6h cold storage (ischemia 4°C UW) porcine kidney, corticomedullary junction biopsy

label_protocol: The labeling was done using the Low Input Quick Amp Labeling kit (Agilent)

growth_protocol: We used 3 months old Large White pigs

extract_protocol: Total RNA from renal cortex or corticomedullary junction were extracted using a commercial kit including a Dnase to remove genomic DNA (Rneasy plus mini, Qiagen, France), following the manufacturer's recommendations.

treatment_protocol: CONTROL samples: 5 independent porcine kidneys (from Large White pig) were removed and then immediately sampled and frozen. WARM ISCHEMIA samples: 5 independent porcine kidneys (from Large White pig) were clamped, removed and maintained clamped 60 min at 37°C, and then immediately sampled and frozen. WARM ISCHEMIA + 6h and 24h COLD STORAGE samples: 5 independent porcine kidneys (from Large White pig) were clamped, removed and maintained clamped 60 min at 37°C, and then flushed with cold (4°C) University of Wisconsin preservation solution (UW) and stored at 4°C, at 6h of cold storage kidneys were sampled and frozen and at 24h of cold storage these same kidneys were sampled and frozen.

tag: breed

value: Large White pig

tag: age

value: 3 months

tag: treatment group

value: kidney (corticomedullary junction)


title: WARM ISCHEMIA + 24h COLD STORAGE corticomedullary junction (N=4)

source_name: Warm Ischemic (60 min)+24h cold storage (ischemia 4°C UW) porcine kidney, corticomedullary junction biopsy


title: WARM ISCHEMIA corticomedullary junction (N=4)

source_name: Warm Ischemic (60 min) porcine kidney, corticomedullary junction biopsy

value: Warm Ischemic (60 min)


title: WARM ISCHEMIA + 24h COLD STORAGE corticomedullary junction (N=2)

value: Warm Ischemic (60 min)+24h cold storage (ischemia 4°C UW)


title: WARM ISCHEMIA corticomedullary junction (N=3)


title: WARM ISCHEMIA + 24h COLD STORAGE corticomedullary junction (N=1)


title: WARM ISCHEMIA + 24h COLD STORAGE corticomedullary junction (N=5)


title: WARM ISCHEMIA + 6h COLD STORAGE corticomedullary junction (N=2)

value: Warm Ischemic (60 min)+6h cold storage (ischemia 4°C UW)


title: WARM ISCHEMIA corticomedullary junction (N=5)


title: WARM ISCHEMIA + 6h COLD STORAGE corticomedullary junction (N=1)


title: WARM ISCHEMIA corticomedullary junction (N=2)


title: WARM ISCHEMIA + 6h COLD STORAGE corticomedullary junction (N=5)


title: WARM ISCHEMIA + 6h COLD STORAGE corticomedullary junction (N=3)


title: WARM ISCHEMIA corticomedullary junction (N=1)


title: WARM ISCHEMIA + 24h COLD STORAGE cortex (N=2)

source_name: Warm Ischemic (60 min)+24h cold storage (ischemia 4°C UW) porcine kidney, cortex biopsy

value: kidney (cortex)


title: CONTROL corticomedullary junction (N=5)

description: CONTROL corticomedullary junction (N=5)

source_name: Control porcine non treated kidney, corticomedullary junction biopsy

value: Control


title: WARM ISCHEMIA + 24h COLD STORAGE cortex (N=1)


title: WARM ISCHEMIA + 6h COLD STORAGE cortex (N=5)

source_name: Warm Ischemic (60 min)+6h cold storage (ischemia 4°C UW) porcine kidney, cortex biopsy


title: WARM ISCHEMIA + 24h COLD STORAGE cortex (N=3)


title: CONTROL corticomedullary junction (N=4)

description: CONTROL corticomedullary junction (N=4)


title: CONTROL corticomedullary junction (N=2)

description: CONTROL corticomedullary junction (N=2)


title: WARM ISCHEMIA + 6h COLD STORAGE cortex (N=3)


title: WARM ISCHEMIA + 24h COLD STORAGE cortex (N=5)


title: CONTROL corticomedullary junction (N=3)

description: CONTROL corticomedullary junction (N=3)


title: WARM ISCHEMIA + 24h COLD STORAGE cortex (N=4)


title: WARM ISCHEMIA + 6h COLD STORAGE cortex (N=4)


title: WARM ISCHEMIA + 24h COLD STORAGE corticomedullary junction (N=3)


title: WARM ISCHEMIA + 6h COLD STORAGE cortex (N=2)


title: WARM ISCHEMIA cortex (N=4)

description: WARM ISCHEMIA cortex (N=4)

source_name: Warm Ischemic (60 min) porcine kidney, cortex biopsy


title: WARM ISCHEMIA cortex (N=1)

description: WARM ISCHEMIA cortex (N=1)


title: CONTROL cortex (N=3)

description: CONTROL cortex (N=3)

source_name: Control porcine non treated kidney, cortex biopsy


title: WARM ISCHEMIA cortex (N=3)

description: WARM ISCHEMIA cortex (N=3)


title: WARM ISCHEMIA + 6h COLD STORAGE cortex (N=1)


title: CONTROL cortex (N=4)

description: CONTROL cortex (N=4)


title: CONTROL cortex (N=2)

description: CONTROL cortex (N=2)


title: WARM ISCHEMIA cortex (N=2)

description: WARM ISCHEMIA cortex (N=2)


title: WARM ISCHEMIA cortex (N=5)

description: WARM ISCHEMIA cortex (N=5)


title: CONTROL cortex (N=5)

description: CONTROL cortex (N=5)


title: GW23_PFC2_2

city: Beijing

first: Shu

last: Zhang

state: Beijing

address: Peking University, No.5 Yiheyuan Road Haidian District

country: China

institute: BIOPIC

description: polyA RNA

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
The first 8bp of read2 were used to split the mixed data into single cells according to the barcode sequences. The following 8bp were recorded and attached to the end of each read2 as unique molecular identifier (UMI). After that, reads1 were separated by the header of the corresponding read2 and then added UMI information. Hereafter, the split reads1 were trimmed off ploy(A) tail sequence and template switch oligo (TSO) sequence. Then we did quality control by removing out reads with adaptor contaminants (length < 37bp) and low-quality bases (N > 10%).
Subsequently, TopHat (version 2.0.12) was applied to align clean reads to the hg19 human transcriptome downloaded from UCSC.  Uniquely aligned reads were counted by the tool ‘htseq-count’ of HTSeq. According to the UMI information, transcripts with same UMI sequence of each gene were merged as one, thus the number of different UMIs for each gene was considered as the transcript counts of that gene without PCR bias for each sequenced cell.
The transcript counts of each cell were normalized to transcript per million (TPM), and the formula to calculate TPM is: the transcript counts of each gene divided by the sum of transcript counts of that cell, and multiplied by one million. TPM values were then normalized by log2(TPM/10 + 1) for the following analysis, since the sequencing depth of most single cell samples were less than 1,000,000 reads, we divided TPM values by 10.
Genome_build: hg19
Supplementary_files_format_and_content: xls files which include the TPM values of RefSeq genes.

source_name: Cells From Prefrontal Cortex

extract_protocol:
Single cells were directly picked into 2.5ul cell lysis buffer the same as Smartseq2 except that we used barcoded reverse transcription primers instead of oligdT30VN primer. Further cell lysis, reverse transcription and amplification was referred to Smartseq2 with little modification.
Each cell was amplified for 18 cycles in total. The PCR product for each barcode 1 to barcode 96 was pooled together for purification and library construction. The libraries were sequenced on illumina platform for 1.8M 150bp pair-end reads per cell.

treatment_protocol: To maintain the cell activity, we dissected all prefrontal cortex from nine fetal brain in ice cold artificial cerebrospinal fluid containing 125.0 mM NaCl, 26.0 mM NaHCO3, 2.5 mM KCl, 2.0mM CaCl2, 1.0 mM MgCl2, 1.25 mM NaH2PO4 at a pH of 7.4 when oxygenated (95% O2 and 5% CO2).The PFC tissue was first digested in brain tissue digestion medium 1 (BTDM1, 2mg/ml collagenase IV (Gibco, Cat.17104-019) and 10 U/μl DNase I (NEB, Cat.M0303L) in hybradate E medium). After brief pipet to roughly digest the tissue into small pieces, brain tissue digestion medium 2 (BTDM2, 1mg/ml papain (Sigma, Cat.P4762) and 10 U/μl DNase I in hybradate E medium).

value: Prefrontal Cortex

value: week gestation

tag: gender

value: female


title: CONTROL cortex (N=1)

description: CONTROL cortex (N=1)


title: GW23_PFC2_1

description: polyA RNA


title: shEZH2 day 8 rep3

city: Providence

first: Nicola

last: Neretti

state: RI

address: 70 Ship St

department: Department of Molecular Biology, Cell Biology & Biochemistry

institute: Brown University

data_processing:
Paired-end reads were quality trimmed using Trim galore v0.4.0.
Reads were aligned to the human reference genome, hg19, using HISAT2 v2.1.0.
Reads mapping to annotated genes were quantified using featureCounts
Differential gene expression was determined using DESeq2 v1.12.4
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

molecule: polyA RNA

growth_protocol: Cells were infected with a lentivirus vector expressing shRNA against EZH2 and harvested at 4 and 8 days after infection.

extract_protocol:
Total RNA was harvested from cells using Trizol reagent (Invitrogen) and further purified using the Purelink RNA Mini kit (Invitrogen) with DNase I digestion
RNA libraries with polyA selection were prepared for sequencing using standard Illumina protocols

tag: shRNA

tag: time point

value: day 8


title: GW23_PFC2_3

description: polyA RNA


title: shEZH2 day 8 rep1


title: shEZH2 day 8 rep2


title: GW23_PFC2_4

description: polyA RNA


title: CTCF-F1-F11.unbound

city: Palo Alto

first: Zheng

last: Zuo

address: Stanford

department: Genetics

institute: Stanford university

data_processing:
Library strategy: Spec-seq
For each particular sample, there are two raw data files, i.e., bound reads and unbound reads with different Illumina Index. The processed data file was based on analysis of Bound and Unbound data together.
Variant reads counting and sorting: For each randomized binding site, its number in Bound and Unbound portions were counted separately. The Bound/Unbound ratio was supposedly porportional to its relative binding affinity, and the negative logarithm of this ratio indicates the relative binding energy in kT unit.
Data regression and energy logo visualization: Based on the binding energy for particular reference and all its single variants, an energy logo can be generated to indicate the specificity of particular protein-DNA interactions.
Supplementary_files_format_and_content: All processed data were saved in .excel files, including bound reads, unbound reads, Bound/Unbound ratio, relative binding energy for each variant.

organism: synthetic construct

source_name: mouse CTCF-F1-F11

extract_protocol:
All single stranded DNA library template were mixed in equal molar ratio, annealled by iPE2.0-reversed primer and further extended by Taq Polymerase at 95C 15s, 52C 10mins.
After EMSA, DNA fragments were cut and extracted by gel extraction buffer at 50C for 30mins.
For each portion of DNA fragment, PE1 and PE2 PCR primers were used to PCR amplify extracted DNA for 13 cycles (95C 15s, 52C 15s, 72C 45s)

treatment_protocol: All EMSA reactions were done in 9% Tris-glycine gel, 200V, 30mins

tag: dna library composition

value: CTCF-R1,R2,R2L, and R3

tag: recombinant protein used

value: mouse CTCF DNA binding domain (F1-F11)


title: CTCF-F1-F11.bound


title: CTCF-F1-F9.unbound

source_name: mouse CTCF-F1-F9

value: mouse CTCF DNA binding domain (F1-F9)


title: CTCF-F1-F9.bound


title: shEZH2 day 4 rep2

value: day 4


title: shEZH2 day 4 rep1


title: Co1Na_TE_4

source_name: telencephalon

value: brain

value: telencephalon


title: GW23_PFC2_5

description: polyA RNA


title: Control rep3


title: shEZH2 day 4 rep3


title: Control rep1

description: Control


title: Control rep2


title: UTX conditional knockout

city: Beijng

first: Xuepei

last: Lei

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

description: processed data file: Female_UTX_cKO_case_vs_Female_Ctrl_ctrl.all.anno.xls

data_processing:
Basecalling were performed with Illumina Casava1.7 software.
The original image data obtained after sequencing is converted into the sequence data stored in FASTQ file format by base calling.
Raw sequencing data is filtered through a series of data processing raw reads to get clean reads.
In order to control the quality of the data, the composition and mass distribution of the bases of the clean reads are plotted.
After the data quality evaluation passed, clean reads were aligned to the selected reference sequence (genome of C57BL/6 mouse) for evaluation. We aligned the clean reads to the reference genome using Tophat v2.0.12 software and Bowtie v1.0.1 aligned the clean reads to the reference genes.
Genome_build: Reference sequences were downloaded from: https://www.ncbi.nlm.nih.gov/genome/genomes/52 (GCA_000001635.8 GRCm38.p6 scaffolds:336 contig: 885 N50:32,273,079 L50:26)
Supplementary_files_format_and_content: Female_UTX_cKO_case_vs_Female_Ctrl_ctrl.all.anno.xls: Excel file includes RPKM values for each sample.

source_name: cortex

growth_protocol: Embryo 14.5.

extract_protocol:
Cortices were harvested at embryonic day 14.5, and immediately frozen at -80 ℃. After genotyping, RNA was isolated with Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols. After digesting the total RNA of the sample and digesting the DNA with DNaseI, the mRNA in total RNA is purified with Oligo d (T) magnetic beads, and the resulting mRNA is fragmented by adding an appropriate amount of an interrupting reagent under high temperature conditions. As a template, cDNA was synthesized, purified by magnetic beads, the end of the repair, 3' end plus base A, plus sequencing linker, PCR amplification, thus completing the entire library preparation.

treatment_protocol: WT or Utx cKO.

tag: strain/background

tag: genotype/variation

value: UTX fl/fl;Nesin-Cre

value: cerebral cortex

value: embryonic day 14.5


title: FOXP1 knockdown rep3

city: Shanghai

first: Yi

last: Xu

state: Shanghai

address: No. 221, West Yanan Road

department: Department of Respiration

institute: The Affiliated HuaDong hospital of Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase Million) (FPKM) were calculated using  TopHat v2, FPKM tracking files use a generic format to output estimated expression values.
Genome_build: hm19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: FOXP1 knockdown A549 cell lines

growth_protocol: PC9 and A549 cells were cultured in RPMI and MEM, both of which were supplemented with 10% fetal bovine serum (FBS), 2 mmol/ l glutamine, 100 units/mL penicillin and 100 μg/mL streptomycin.

extract_protocol:
The total RNA from PC9 or A549 cells was prepared using the Trizol reagent (Invitrogen, Carlsbad, CA). 1 ug of total RNA was treated with DNase I (Invitrogen) and the cDNA was synthesized in vitro from the mRNA template using SuperScript® III First-Strand Synthesis Kit (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells less than 30 passages were cultured in a humidified atmosphere of 95% air and 5% CO2 at 37°C. For transfection of siFOXP1, Lipofectamine® RNAiMAX Reagent (Invitrogen) was mixed with the siFOXP1 construct according to the manufacturer’s instructions.

value: lung adenocarcinoma

tag: genotype

value: FOXP1 knockdown


title: FOXP1 knockdown rep2

source_name: FOXP1 knockdown A549 cell linesl


title: WT rep2

source_name: A549 cell lines；control

value: wild type


title: WT rep3


title: WT rep1


title: FOXP1 knockdown rep1


title: WT

value: WT


title: HCT-116-P3 rep 2

city: Lyon

first: abdelakamel

last: chettab

address: 8 avenue Rockeffeler

department: centre de recherche en cancérologie de lyon

institute: université claude bernard lyon1

description: replicat 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GeneSpring Version 1.9.0

source_name: colorectal cancer cells

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification Kit

growth_protocol: Hercc1 cells (Stable HCT-116 cells transfected with ERCC1-coding plasmid) from tumors grown in scid mice  as xenografts

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN Qiamp RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with 2100 Bioanalyzer.

treatment_protocol: Scid mice treated or not with oxaliplatin (2 mg/kg) two hours before the recovery of tumors

tag: transfection

value: ERCC1-coding plasmid

tag: treatment

value: no


title: Inguinal WAT, thermoneutrality, wild type mouse, replicate 3

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 2.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.42.0).

source_name: Inguinal white adipose tissue from a wild type mouse housed at thermoneutrality (28 °C) for 10 days

label_protocol: Purified total RNA (100ng per sample) was labeled with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).

growth_protocol: Three to four months old male wildtype and PPARα−/− mice that had been backcrossed on a pure C57Bl/6J background for more than 10 generations were acquired from Jackson Laboratories (no. 000664 and 008154, respectively). The mice were further bred at the animal facility of Wageningen University under specific pathogen free conditions to generate the number of mice necessary for the experiments.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Forty 3-4-month-old male wildtype and PPARα−/− mice were placed at thermo-neutral temperature (28 °C) for 5 weeks. Thereafter, 20 wildtype and 20 PPARα−/− mice were randomly distributed across 2 groups: half of the mice of each genotype were kept at thermo-neutral temperature and half of the mice of each genotype was placed at 21 °C for one week followed by a period of 10 days at in the cold (5 °C) (n = 10 per group). For cold exposure, mouse cages were placed in a cold cabinet that was kept at 5 °C (ELDG800, VDW Coolsystems, Geldermalsen). Mice had ad libitum access to chow feed and water.

tag: background strain

tag: jackson laboratories mouse strain id

tag: housing temperature

value: thermoneutrality (28 C) for 10 days

tag: Sex

value: male


title: Children with Systemic Lupus Erythematosus rep4

city: beijng

first: shipeng

last: Li

address: Nan Li Shi Road No. 56,Beijing

institute: Beijing children's hospital

description: Gene expression data from Children with Systemic Lupus Erythematosus

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Transcriptome Array 2.0 were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100

label: total RNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

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

tag: disease

value: Systemic Lupus Erythematosus

tag: tissue

value: Peripheral blood


title: Inguinal WAT, thermoneutrality, PPARα knockout mouse, replicate 6

source_name: Inguinal white adipose tissue from a PPARα knockout mouse housed at thermoneutrality (28 °C) for 10 days

value: PPARalpha-null


title: Inguinal WAT, thermoneutrality, wild type mouse, replicate 4


title: Health Children  rep2

description: Gene expression data from Health Children

source_name: Health Children

value: healthy


title: HCT-116-P3 rep 3

description: replicat 3

tag: cell line


title: HCT-116-P3 + oxalipt rep 3

description: replicat 3

value: oxaliplatin (2 mg/kg) two hours


title: HCT-116-P0 + oxalipt rep 3

description: replicat 3

value: control plasmid


title: Inguinal WAT, thermoneutrality, PPARα knockout mouse, replicate 5


title: HCT-116-P0 + oxalipt rep 1

description: replicat 1


title: HCT-116-P3 + oxalipt rep 1

description: replicat 1


title: Inguinal WAT, thermoneutrality, wild type mouse, replicate 1


title: HCT-116-P0 + oxalipt rep 2

description: replicat 2


title: HCT-116-P3 rep 1

description: replicat 1


title: Children with Systemic Lupus Erythematosus rep3


title: Health Children  rep3


title: Health Children  rep1


title: Children with Systemic Lupus Erythematosus rep2


title: Children with Systemic Lupus Erythematosus rep1


title: Inguinal WAT, thermoneutrality, wild type mouse, replicate 2


title: Inguinal WAT, thermoneutrality, PPARα knockout mouse, replicate 2


title: HCT-116-P0 rep 3

description: replicat 3


title: Inguinal WAT, thermoneutrality, wild type mouse, replicate 6


title: HCT-116-P3 + oxalipt rep 2

description: replicat 2


title: Inguinal WAT, thermoneutrality, wild type mouse, replicate 5


title: Inguinal WAT, thermoneutrality, PPARα knockout mouse, replicate 4


title: Health Children  rep4


title: Inguinal WAT, thermoneutrality, PPARα knockout mouse, replicate 3


title: CONTROL corticomedullary junction (N=1)

description: CONTROL corticomedullary junction (N=1)

tag: breed

value: Large White pig

tag: age

value: 3 months

tag: treatment group

value: Control

value: kidney (corticomedullary junction)


title: HCT-116-P0 rep 1

description: replicat 1


title: HCT-116-P0 rep 2

description: replicat 2


title: overexpression_CK

first: Bin

last: Yin

address: Tsinghua East Road

institute: Beijing Forestry University

description:
II_F vs WT_F
II_F

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based onthe clean data with high quality.
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. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
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. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Trapnell, Cole, et al., 2010).
Genome_build: Poptr2_0, https://www.ncbi.nlm.nih.gov/assembly/GCF_000002775.3
Supplementary_files_format_and_content: Tab-delimited xls file includes FPKMs (log2-transformed with an offset value of 1.0) for each sample

organism: Populus tomentosa

source_name: suspension cells

growth_protocol: All cell lines grew in bed temperature incubator at 25 ℃ (140 rpm, 24 h dark).

extract_protocol:
Total RNA was isolated from the main stem of different developmental stage of Arabidopsis plant, using EASYspin Plant RNA kit RN09 (Aidlab, China) according to the manufacturer's instructions.
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.

treatment_protocol: H2O2 treatment (10 mM, 3 h dark, 25 ℃， 140 rpm); ASA treatment (1 mM, 3 h dark, 25℃, 140 rpm)

value: normal condition

tag: Stage

value: 5 days after subculturing


title: anti sense_CK

description:
m811_F vs WT_F
m811_F


title: overexpression_H2O2

description:
II_H vs WT_H
II_H

value: H2O2 treatment (10 mM, 3 h)


title: anti sense_ASA

description:
m811_A vs WT_A
m811_A

value: ASA treatment (1 mM, 3 h)


title: overexpression_ASA

description:
II_A vs WT_A
II_A


title: anti sense_H2O2

description:
m811_H vs WT_H
m811_H


title: Inguinal WAT, cold exposure, wild type mouse, replicate 3

source_name: Inguinal white adipose tissue from a wild type mouse housed at cold (5 °C) for 10 days

value: wild type

value: cold (5 C) for 10 days


title: wild type_ASA

description:
m811_A vs WT_A; II_A vs WT_A
WT_A


title: Inguinal WAT, cold exposure, wild type mouse, replicate 2

value: male


title: Mouse nicotine-10 µg/ml-drinking water JMY117-100 µg/kg rep2

city: Hsinchu

first: Jinn-Moon

last: Yang

address: 75 Po-Ai Street

country: Taiwan

institute: National Chiao Tung University

description: Treatment of 100 µg/kg JMY117 with nicotine exposure for nine weeks

hyb_protocol: Fluorescent targets were hybridized to the Human Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization, non-speciﬁc binding targets were washed away.

scan_protocol: The slides scanned using a DNA Microarray Scanner (Model G2505C, Agilent Technologies). The Cy5 ﬂuorescent intensities of each spot were analyzed by GenePix 4.1 software (Molecular Devices).

data_processing: Raw data were normalized using the normalizeQuantiles function from 'limma' package (v. 3.30.7).

source_name: Nicotine (10 µg/ml, drinking water) and JMY117 (100 µg/kg)l

label_protocol: Fluorescent aRNA targets were prepared from 1 μg total RNA samples using OneArray® Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dye (GE Healthcare).

growth_protocol: The xenograft tumor from SCID was inoculated with MDA-MB-231 (5x106) cells subcutaneously and growth for nine month.

extract_protocol: Total RNA was extracted from the xenograft tumors using TRIzol Reagent through chloroform/isopropanol purification. RNA quantity and purity was assessed using NanoDrop ND-1000. Pass criteria for absorbance ratios are established as A260/A280 ≥ 1.8 and A260/A230 ≥ 1.5 indicating acceptable RNA purity. RIN values are ascertained using Agilent RNA 6000 Nano assay to determine RNA integrity. Pass criteria for RIN value is established at > 6 indicating acceptable RNA integrity.

treatment_protocol: The xenograft bearing mice were grouped with or without nicotine (10 μg/ml) treatments via the drinking water, and each group of mice were i.p. injected with saline, 100 or 200 µg/kg JMY117 three-time per week. After experiment, the mice were sacrificed and xenografts were snap-frozen in dry ice and stored at −80˚C.

tag: treatment of nicotine

value: Yes

tag: treatment of jmy117

value: Yes (100 µg/kg)


title: Mouse nicotine-10 µg/ml-drinking water JMY117-100 µg/kg rep1

source_name: Nicotine (10 µg/ml, drinking water) and JMY117 (100 µg/kg)


title: Inguinal WAT, cold exposure, wild type mouse, replicate 4


title: Inguinal WAT, thermoneutrality, PPARα knockout mouse, replicate 1

value: PPARalpha-null

value: thermoneutrality (28 C) for 10 days


title: wild type_H2O2

description:
m811_H vs WT_H; II_H vs WT_H
WT_H


title: Mouse nicotine-10 µg/ml-drinking water JMY117-200 µg/kg rep1

description: Treatment of 200 µg/kg JMY117 with nicotine exposure for nine weeks

source_name: Nicotine (10 µg/ml, drinking water) and JMY117 (200 µg/kg)

value: Yes (200 µg/kg)


title: Mouse nicotine-10 µg/ml-drinking water rep1

description: Nicotine exposure for nine weeks

source_name: Nicotine (10 µg/ml, drinking water)

value: No


title: Inguinal WAT, cold exposure, PPARα knockout mouse, replicate 4

source_name: Inguinal white adipose tissue from a PPARα knockout mouse housed at cold (5 °C) for 10 days


title: Inguinal WAT, cold exposure, PPARα knockout mouse, replicate 5


title: Mouse JMY117-200 µg/kg rep1

description: Treatment of 200 µg/kg JMY117 three times per week

treatment_protocol: The xenograft bearing mice were grouped with or without nicotine (1 μg/mL) treatments via the drinking water, and each group of mice were i.p. injected with saline, 100 or 200 µg/kg JMY117 three-time per week. After experiment, the mice were sacrificed and xenografts were snap-frozen in dry ice and stored at −80˚C.


title: Mouse JMY117-200 µg/kg rep2


title: wild type_CK

description:
m811_F vs WT_F; II_F vs WT_F
WT_F


title: Mouse nicotine-10 µg/ml-drinking water rep2

description: Nicotine exposure for nine weeks


title: Inguinal WAT, cold exposure, PPARα knockout mouse, replicate 3


title: Mouse JMY117-100 µg/kg rep1

description: Treatment of 100 µg/kg JMY117 three times per week


title: Mouse nicotine-10 µg/ml-drinking water JMY117-200 µg/kg rep2


title: Inguinal WAT, cold exposure, wild type mouse, replicate 1


title: Mouse JMY117-100 µg/kg rep2


title: Control rep2

description: Control

source_name: Control


title: Inguinal WAT, cold exposure, PPARα knockout mouse, replicate 2


title: Control rep1

description: Control


title: Inguinal WAT, cold exposure, PPARα knockout mouse, replicate 1


title: HET embryo_HET father_rep2

status: Public on Feb 09 2018

city: Clayton

first: Sam

last: Forster

state: Victoria

address: 27 - 31 Wright Street

department: Monash Institute

institute: Monash University

description: Gene expressin in stage matched heterozygous E8.5 embryo sired by heterozygous Eedl7Rn5-1989SB males

hyb_protocol: 600ng of Cy3 labeled cRNA (specific activity > 6 pmol Cy3/ug cRNA) was  fragmented at 60oC for 30 minutes in a reaction volume of 25ul containing 1x  Agilent fragmentation buffer and 2x Agilent blocking agent following the  manufacturer’s instructions. On completion 25ul of 2x Agilent gene expression  hybridisation buffer was added and 40ul of sample hybridised for 17 hours at  65oC in a rotating Agilent hybridisation oven. After hybridisation, microarrays  were washed 1 minute at room temperature with GE wash buffer 1(Agilent) and 1  minute with 37oC GE wash buffer 2(Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent C, DNA microarray  scanner using one color scan settings for 8x60k array slides; scan area  61x21.6mm, scan resolution 3um, dye channel is set to Green and 20 bit Tiff.

data_processing: The scanned images were analysed with Feature Extraction Software 11.0.1.1  (Agilent) using default parameters (protocol GE1-1100_Jul11 and  Grid:028005_D_F_20120201) to obtain background subtracted and spatially  detrended Processed Signal intensities.

source_name: 184-8_E8.5 embryo_HET father

label_protocol: Cyanine-3 (Cy3) labelled cRNA was prepared from 0.2ug total RNA using the  One-Color Low input Quick Amp labelling Kit (Agilent, v6.6 September 2012)  according to the manufacturer’s instructions, followed by RNeasy column  purification (Qiagen). Dye incorporation and cRNA yield were checked with the  NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted using the Genelute Mammalian total RNA miniprep kit (Sigma, RTN70-1KT), DNAse treated using TURBO DNA-free™ Kit (Ambion, AM1907) and purified from the DNAse reaction using Agencourt RNAClean XP (Beckman coulter, A63987).

treatment_protocol: Homozygous (HOM) and heterozygous (HET) Eedl7Rn5-1989SB C57bl6/129 male mice were time mated with C57bl6/129 wild-type mice. Embryos were collected 8.5 days after the female was plugged. Samples were stored at -80 °C until RNA extraction. RNA was extracted from accurately match samples of the same developmental time points.

tag: father's genotype

value: HET

tag: mothers's genotype

value: WT

tag: mouse strain and backgroud

tag: embryo's sex

value: M

value: embryo


title: HET embryo_HET father_rep3

source_name: 246-7_E8.5 embryo_HET father

value: F


title: HET embryo_HOM father_rep4

description: Gene expressin in stage matched heterozygous E8.5 embryo sired by homozygous Eedl7Rn5-1989SB males

source_name: 188-7_E8.5 embryo_HOM father

value: HOM


title: HET embryo_HOM father_rep3

source_name: 188-2_E8.5 embryo_HOM father


title: HET embryo_HOM father_rep1

source_name: 183-7_E8.5 embryo_HOM father


title: HET embryo_HOM father_rep2

source_name: 185-4_E8.5 embryo_HOM father