title: Smchd1 fl/fll F #1 WCE [H3K27ac]

status: Public on Jun 30 2018

type: SRA

city: Parkville

first: Marnie

last: Blewitt

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute

library_source: genomic

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
Aligned to mm10 using Bowtie v 0.12.9
Peaks were called using macs2 2.1.0.20140616
Reads log(counts per million) transformed in Seqmonk_v1.38.2
Genome_build: mm10
Supplementary_files_format_and_content: Files containing coordinates of macs2 peaks called against whole cell extract

molecule: genomic DNA

organism: Mus musculus

source_name: Neural stem cells

growth_protocol: Neural stem cells were generated from Smchd1 del/fl E14.5 embryos, as previously described (Chen et al., 2015 PNAS). In addition to the Smchd1 alleles, the maternal X was of 129 origin carrying an Xist deltaA allele, the X chromosome from the father was derived from Castaneus. After these lines were established, they were split in two - half were transduced with a retrovirus carrying Cre recombinase and a puromycin selection cassette (MSCV-Cre-puro), half were retained untransduced as controls. 24h post transduction puromycin was added to select transduced cells, and 7 days following transduction cells were harvested for genomic analyses.

extract_protocol:
Nuclei were isolated from formaldehyde crosslinked NSCs and chromatin was fragmented by sonication. Chromatin immunoprecipitation was performed with corresponding antibodies. DNA was extracted from the immunoprecipitated fraction following reverse-crosslinking.
Libraries were prepared according to standard Illumina Tru-seq library protocols

tag: cell type

value: Neural stem cells

tag: strain

tag: Sex

value: Female

tag: genotype

value: Smchd1 del/del Xist 129-KO/Xist WT-Cast

tag: chip antibody


title: Smchd1 fl/fl F #1 H3K27ac

value: Smchd1 del/fl Xist 129-KO/Xist WT-Cast

value: Millipore anti-H3K27me3


title: Smchd1 del/fl 98.8

description: Bisulphite converted Genomic DNA

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
TrimGalore version 0.4.0 was used to trim sequencing adapters
Bismark v0.13.0 was used to map RRBS data to an n-masked mm10 and extract methylation information
SNPsplit v0.3.0 was used to assign mapped reads to either the C57BL/6 or Castaneus genome
Read counts, and percent methylation counts were generated in Seqmonk v1.38.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with columns representing genomic coordinates and% methylation at CpGs for each C57BL/6 Castaneus and combined genomes.

growth_protocol: Neural stem cells were generated from Smchd1 del/fl Xist 129-KO/Xist WT-Cast E14.5 embryos, as previously described (Chen et al., 2015 PNAS). After these lines were established, they were split in two - half were transduced with a retrovirus carrying Cre recombinase and a puromycin selection cassette (MSCV-Cre-puro), half were retained untransduced as controls. 24h post transduction puromycin was added to select transduced cells, and 7 days following transduction cells were harvested for genomic analyses.

extract_protocol:
Cells were split off the plate and RNA harvested using Qiagen Blood and Tissue DNeasy kit
Libraries were prepared according to standard NuGen RRBS protocols

value: C57BL/6; castaneus; 129


title: Smchd1 fl/fl M 7 [Hi-C]

description: in situ Hi-C library Smchd1 wild-type control male

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
hicup_v0.5.8 was used to align HiC reads to mm10 and to remove common experimental artifacts as in Wingett et al. F1000Res. (2015)
DiffHic (Lun & Smith BMC Bioinformatics 2015) with default parameters was used to count reads into 1 MB or 100 kb bins, filter out low abundance reads based on a negative binomial distribution and using inter-chromosomal counts to determine non-specific ligation events, perform TMM normalisation of libraries, fit libraries to a generalised linear model, and use edgeR statistics to perform differential analysis of HiC reads between test and control
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 (.h5) files for each sample containing HiC reads counted into 1Mb bins against genome digested with MboI

growth_protocol: Neural stem cells were generated from Smchd1fl/fl E14.5 embryos, as previously described (Chen et al., 2015 PNAS). After these lines were established, they were transduced with a retrovirus carrying Cre recombinase and a puromycin selection cassette (MSCV-Cre-puro). 24h post transduction puromycin was added to select transduced cells, and 7 days following transduction cells were harvested for genomic analyses.

extract_protocol:
Cells were split from the tissue culture plate, and put stright into HiC library construction protocol.
Libraries were prepared according to Rao et al. Cell (2014) using the 4bp cutter MboI

value: Male

value: Smchd1 fl/fl


title: Smchd1 +/del 98.6

description: Bisulphite converted Genomic DNA

value: Smchd1 +l/fl Xist 129-KO/Xist WT-Cast


title: Smchd1 del/del M 7 [Hi-C]

description: in situ Hi-C library Smchd1 deleted male

value: Smchd1 del/del


title: Smchd1 fl/fll M 5 [Hi-C]


title: Smchd1 del/del F #1 WCE [H3K27ac]


title: Smchd1 del/del 98.8

description: Bisulphite converted Genomic DNA


title: Smchd1 del/del M 5 [Hi-C]


title: Smchd1 +/fl 98.6

description: Bisulphite converted Genomic DNA

value: Smchd1 +/del Xist 129-KO/Xist WT-Cast


title: Smchd1 del/fl F 2 H3K27me3

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
Aligned to mm10 using Bowtie v 0.12.9
Reads were assigned to the Castaneous or 129 Genome using SNPsplit version 0.3.0
Peaks were called using macs2 2.1.0.20140616
Genome_build: mm10
Supplementary_files_format_and_content: File containing mm10 coordinates of macs2 called peaks against whole cell extract

value: C57BL/6 129/Castaneus mix


title: Smchd1 del/del F #1 WCE [H3K27me3]


title: Smchd1 del/fl F #1 WCE [H3K27me3]


title: Smchd1 del/del F 1 H3K27me3


title: Smchd1 del/fl F #2 WCE[H3K27me3]


title: Smchd1 del/del F #2 WCE [H3K27me3]


title: Smchd1 del/del F #1 H3K27ac


title: Smchd1 del/del F 2 H3K27me3


title: Smchd1 del/fl F 2.

library_source: transcriptomic

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
Alignment using TopHat v2.0.12 with default parameters
Reads were assigned to the Castaneous or 129 Genome using SNPsplit version 0.3.0
Data were analysed in Seqmonk version seqmonk_v1.38.2. Reads were counted under mRNA, and a differential analysis was performed using the inbuilt edgeR function in Seqmonk. Reads were then transformed into log2 reads per million.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file of read counts to reads mapping to genes for Smchd1 deleted and heterozygous samples at each time point.

molecule: total RNA

extract_protocol:
Cells were split off the plate and RNA harvested using Zymo
Libraries were prepared according to standard Illumina RNA-seq protocols

tag: tissue


title: Smchd1 del/del F 2.


title: Smchd1 del/fl F 1.


title: Smchd1 del/fl F 1 H3K27me3


title: Smchd1 MommeD1/MommeD1 PSM #3

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
Alignment to mm10 using TopHat v2.0.12 with default parameters
Data were analysed in Seqmonk version seqmonk_v1.38.2. Reads were counted under mRNA, and a differential analysis was performed using the inbuilt edgeR function in Seqmonk. Reads were transformed into log2 reads per million.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file of log transformed(counts per million) read counts to reads mapping to genes for Smchd1 null and WT samples at each time point.

source_name: Postsomitic mesoderm

extract_protocol:
E9.5 embryos were dissected and the posterior part of the embryo, approximately 1 somite length after the last visible somite, was dissected and snap frozen. RNA was extracted using Qiagen Micro Rneasy Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Postsomitic mesoderm

tag: developmental stage

value: FVB/N

value: female

value: Smchd1 MommeD1/MommeD1


title: Smchd1 del/del F 1.


title: Smchd1 MommeD1/MommeD1 PSM #5


title: Smchd1 MommeD1/MommeD1 PSM #4


title: RCC-28a-R

type: RNA

city: Shanghai

first: Linhui

last: Wang

address: 415 Fengyang Road, 200003, Shanghai China

department: Department of Urology

country: China

institute: Changzheng Hospital, Second Military Medical University

description: Gene expression data from tissue of sorafenib-resistant

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human EG 1.0 ST Array in GeneChip® Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: Expression data were generated by Affymetrix Expression Console software and normalized by the RMA (Robust Multi-chip Average ) method.

label: biotin

organism: Homo sapiens

source_name: RCC-sorafenib-resistant

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

growth_protocol: The tissue was washed with PBS and then put into liquid nitrogen as soon as possible after separtated from body.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.

treatment_protocol: The patients accepted the sorafenib treatment. They were evaluated regularly and the best response achieved were determined by RECIST 1.0. Finally five patients with progressive disease (PD) and five patients with partial response (PR) were enrolled in this microarray as sorafenib resistant and sensitive groups, respectively.

value: Renal Cell Carcinoma

tag: phenotype

value: sorafenib-resistant


title: Smchd1 MommeD1/MommeD1 PSM #1


title: Smchd1 wild-type PSM #3

value: Smchd1 +/+


title: RCC-76a-S

description: Gene expression data from tissue of sorafenib-sensitive

source_name: RCC-sorafenib-sensitive

value: sorafenib-sensitive


title: Smchd1 wild-type PSM #2


title: RCC-877a-R


title: K01

type: genomic

city: Taichung

first: Yng-Tay

last: Chen

address: No 2 Yude road

department: Department of medical research

country: Taiwan

institute: China Medical University Hospital

description: fraction: promoter

scan_protocol: Array was scanned on an Affymetrix GeneChip Scanner 3000.

data_processing:
Hybridization was performed with an Affymetrix GeneChip Promoter 1.0R array.
The resulting processed data are generated by the Affymetrix Tiling Analysis Software.

label_protocol: Then, 3.5 mg (7 mL) of MBD-Biotin Protein was added to 10 mL Dynabeads M-280 Streptavidin according to the manufacturer’s instructions.

growth_protocol: Peripheral blood leukocytes was collected from T2D mice and control mice.

extract_protocol: One microgram of genomic DNA was sonicated to produce fragments ranging from 100 to 500 bp.

treatment_protocol: Genomic DNA was extracted from peripheral blood leukocytes by using the Genomic DNA extraction kit (Qiagen, Valencia, CA, USA), according to the manufacturer’s instructions.

value: Blood

tag: disease

value: Normal


title: DM-2-1-2-2

description: fraction: promoter

hyb_protocol: Hybridization was performed with an Affymetrix GeneChip Promoter 1.0R array.


title: K02

description: fraction: promoter


title: Smchd1 wild-type PSM #1


title: RCC-711a-S


title: Smchd1 fl/fl day 8 #2

description:
Day 8 of differentiation of ES to NMP differentiation
D8-fl3_S10

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
Alignment using TopHat v2.0.12 with default parameters
Data were analysed in Seqmonk version seqmonk_v1.38.2. Reads were counted under mRNA, and a differential analysis was performed using the inbuilt edgeR function in Seqmonk. Reads were then transformed into log2 reads per million.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text file of log transformed(counts per million) read counts to reads mapping to genes for Smchd1 deleted and WT samples at each time point.

source_name: Day 8 ES to NMP

growth_protocol: ES cells were derived from individual E3.5 blastocysts, in 2i+LIF media. Outgrowths were picked after 7 days and passaged to create ES cell lines. Each line was split, one half kept untransduced, the other half transduced with MSCV-Cre-puro, to delete Smchd1. Transduced cells were selected with puromycin 24 hours after transduction. These cells and the controls were weaned in serum+LIF media, then differentiated to neuromesodermal by progenitors, by removal of LIF and addition of Fgf2, then after 2 days addition of Gsk3 inhibitor, then after another 4 days addition of Gdf11. Samples were taken at day 0, 5 and 8 of differentiation.

extract_protocol:
Cells were split off the tissue culture plate, then extracted using a Zymo Quick RNA kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Day 8 ES to NMP

value: male


title: CTL-1-4

description: fraction: promoter


title: RCC-47a-S


title: RCC-882a-S


title: RCC-545a-S


title: RCC-844a-R


title: 42W-2

description: fraction: promoter


title: DM-2-4-2-5

description: fraction: promoter


title: Smchd1 fl/fl day 5 #2

description:
Day 5 of differentiation of ES to NMP differentiation
D5-fl3_S6

source_name: Day 5 ES to NMP

value: Day 5 ES to NMP

value: Smchd1 fl/fl


title: RCC-587a-R


title: 42W-1

description: fraction: promoter


title: Smchd1 fl/fl day 5 #1

description:
Day 5 of differentiation of ES to NMP differentiation
D5-fl1_S5


title: 6W-2

description: fraction: promoter


title: CTL-1-5

description: fraction: promoter


title: RCC-800a-R


title: Smchd1 fl/fl day 1 #1

description:
ES cells, not differentiated
D1-fl1_S1

source_name: Day 1 ES to NMP

value: Day 1 ES to NMP


title: 42WKKA

description: fraction: promoter


title: 6W-1

description: fraction: promoter


title: Smchd1 del/del day 8 #2

description:
Day 8 of differentiation of ES to NMP differentiation
D8-del3_S12

value: Smchd1 del/del


title: Smchd1 fl/fl day 8 #1

description:
Day 8 of differentiation of ES to NMP differentiation
D8-fl1_S9


title: Smchd1 del/del day 5 #1

description:
Day 5 of differentiation of ES to NMP differentiation
D5-del1_S7


title: Smchd1 del/del day 8 #1

description:
Day 8 of differentiation of ES to NMP differentiation
D8-del1_S11


title: Smchd1 fl/fl M7

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
Alignment to mm10 using TopHat v2.0.12 with default parameters
Data were TMM normalized (Robinson and Oshlack, Genome Biology 2010) using the edgeR package (version 3.8.2, Robinson et al. Bioinformatics 2010) and transformed to log2 counts per million
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with columns representing Gene name, Entrez Gene ID, chromosome, start and end coordinates, and the log count per million transcformed value of reads mapping to that gene for all samples.

growth_protocol: Neural stem cells were generated from Smchd1 fl/fl E14.5 embryos, as previously described (Chen et al., 2015 PNAS). After these lines were established, they were split in two - half were transduced with a retrovirus carrying Cre recombinase and a puromycin selection cassette (MSCV-Cre-puro), half were retained untransduced as controls. 24h post transduction puromycin was added to select transduced cells, and 7 days following transduction cells were harvested for genomic analyses.

extract_protocol:
Cells were split off the plate and RNA harvested using Zymo Quick RNA kit
Libraries were prepared according to standard Illumina RNA-seq protocols

value: Neural stem cells

value: Male


title: Smchd1 del/del day 1 #1

description:
ES cells, not differentiated
D1-del1_S3


title: Smchd1 del/del day 1 #2

description:
ES cells, not differentiated
D1-del3_S4


title: Smchd1 del/del day 5 #2

description:
Day 5 of differentiation of ES to NMP differentiation
D5-del3_S8


title: Smchd1 fl/fl F 3

value: Female


title: Smchd1 del/del F 3


title: Whole cell extract female Mnase [ChIP-Seq]

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
Aligned to mm10 using Bowtie v 0.12.9
Reads log(counts per million) transformed and peaks called using MACS like function in Seqmonk_v1.38.2 using default parameters and p<0.00000001
Domains detected in Edd version 1.1.18 with default parameters and required_fraction_of_informative_bins = 0.98
Genome_build: mm10
Supplementary_files_format_and_content: Coordinates from MACS2 like function on Seqmonk to call peaks (GFP_ChIP_sonication_peaks.txt and GFP_ChIP_MNase_peaks.txt) and output from Edd domain calling (GFP_edd_results_peaks.bed)

growth_protocol: Neural stem cells were generated from E14.5 embryos from the Smchd1-GFP fusion protein knockin allele, or wild-type embryos, as previously described (Chen et al., 2015 PNAS). These were passaged every 2-3 days for up to 20 passages before being harvested for ChIP.

extract_protocol:
Nuclei were isolated from formaldehyde crosslinked NSCs and chromatin was fragmented by either 30 minutes sonication in non-ionic detergent to release the inactive X chromosome or MNase Digestion. Chromatin immunoprecipitation was performed with corresponding antibodies. DNA was extracted from the immunoprecipitated fraction following reverse-crosslinking.
ChIP-seq library construction using standard Illumina protocols


title: Smchd1 wild-type female Mnase [ChIP-Seq]

value: Wild-type

value: anti-GFP abcam catalog #


title: Smchd1 del/del F 1


title: Smchd1 del/del F 2


title: Smchd1 wild-type male Mnase [ChIP-Seq]


title: Smchd1 GFP/GFP female Mnase [ChIP-Seq]

value: Smchd1 GFP fusion knockin allele, Smchd1 GFP homozygous


title: Whole cell extract female sonication #1 [ChIP-Seq]


title: Smchd1 wild-type female #2 sonication [ChIP-Seq]


title: Whole cell extract female sonication #2 [ChIP-Seq]


title: Smchd1 fl/fl day 1 #2

description:
ES cells, not differentiated
D1-fl3_S2


title: Smchd1 GFP/GFP male Mnase [ChIP-Seq]


title: Smchd1 fl/fl M5


title: Smchd1 GFP/GFP female #1 sonication [ChIP-Seq]


title: Smchd1 fl/fl M 7 [ATAC-Seq]

description:
ATAC-seq library Smchd1 wild-type control female
ATACmax_fl_male_nodup_noMT_peaks.xls

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
Adapters were trimmed using Trim Galore version 0.4.0
Sequences were aligned to mm10 using Bowtie 2 version 2.2.5 using parameter -X 2000
Mitochondrial reads were removed using Samtools
Duplicates were removed with Picard
MACS2 peak calling was performed on a merged .bam file using the following parameters: --bdg --nomodel --shift -75 --extsize 150 --qvalue 0.05
ATAC-seq data were analysed using Seqmonk v1.36.1. Reads under MACS2 peaks were quantified, transformed and normalised for library size to log counts per million reads. Differential ATAC-seq peak analysis was performed using edgeR statistics in Seqmonk.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text files containing coordinates of MACS2 peaks for each genotype and sex

extract_protocol:
Cells were detached from plates, and immediately used in ATAC-seq library construction protocol
ATAC-seq libraries were as described in Buenrostro et al. Nat Methods (2013) followed by purification with 1.5X AMPure XP beads


title: Smchd1 del/del M 5


title: Smchd1 fl/fl F 2


title: Smchd1 wild-type female #1 sonication [ChIP-Seq]


title: Smchd1 GFP/GFP female #2 sonication [ChIP-Seq]


title: 42WKKB

description: fraction: promoter


title: Smchd1 del/del M 7 [ATAC-Seq]

description:
ATAC-seq library Smchd1 deleted female
ATACmax_del_male_nodup_noMT_peaks.txt


title: Smchd1 fl/fl F 3 [ATAC-Seq]

description:
ATAC-seq library Smchd1 wild-type control female
ATACmax_fl_female_nodup_noMT_peaks.txt


title: Smchd1 fl/fl F 2 [ATAC-Seq]


title: Smchd1 fl/fl F 1 [ATAC-Seq]


title: Smchd1 fl/fl F 1


title: Smchd1 fl/fl M5 [ATAC-Seq]


title: Smchd1 del/del F 2 [ATAC-Seq]

description:
ATAC-seq library Smchd1 deleted female
ATACmax_del_female_nodup_noMT_peaks.txt


title: Smchd1 del/del M 5 [ATAC-Seq]


title: Smchd1 del/del F 1 [ATAC-Seq]


title: Smchd1 fl/fl F 2 [Hi-C]

description: in situ Hi-C library Smchd1 wild-type control female

data_processing:
Base calling using Real-Time Analysis v2.4.6
Demultiplexing and fastq.gz file generation and de-multiplexing using bcl2fastq conversion software v2.15.0.4
hicup_v0.5.8 was used to align HiC reads to mm10 and to remove common experimental artifacts as in Wingett et al. F1000Res. (2015)
DiffHic (Lun & Smith BMC Bioinformatics 2015) with default parameters was used to count reads into 1 MB or 100 kb bins, filter out low abundance reads based on a negative binomial distribution and using inter-chromosomal counts to determine non-specific ligation events, perform TMM normalisation of libraries, fit libraries to a generalised linear model, and use edgeR statistics to perform differential analysis of HiC reads between test and control
Genome_build: mm10
Supplementary_files_format_and_content: HDF5 (.h5) files for each sample containing HiC reads counted into 100 kb bins against genome digested with MboI


title: Smchd1 fl/fl F 1 [Hi-C]


title: Smchd1 fl/fl F 3 [Hi-C]


title: Smchd1 del/del F 3 [Hi-C]

description: in situ Hi-C library Smchd1 deleted female


title: H-CSNP_72h_rep1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression in H-CSNP treated tomato leaf sample after 72h

hyb_protocol: 1600ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to a Genotypic designed Tomato_GXP_4x44K (AMADID:22270). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours.

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

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

organism: Solanum lycopersicum

source_name: Tomato leaf, H-CSNP, 72h, replicate 1

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

growth_protocol: Tomato (Lycopersicon esculentum cv. Arka vikas) plants were allowed to grow in soil in a growth chamber with a 16 h photoperiod at 350 lE/m2 light intensity at 24⁰C with constant humidity (70%).

extract_protocol: Total RNA was isolated from 100 mg of the leaf tissue using RNeasy Plant Minikit (Qiagen’s RNeasy Minikit) and eluted in RNAse-free water for microarray experiment. RNA quality and quantity were analyzed with a NanoDrop 2000/2000c spectrophotometer and an Agilent 2100 Bioanalyzer prior to GeneChip hybridization. RNA was considered to be of good quality when RNA integrity number (RIN) was ≥7.0.

treatment_protocol: All samples were collected in two independently repeated experiments at 24, 48 and 72 h post inoculation (hpi). For each sample, leaf material was harvested from three plants treated with harpin (100 µg ml-1), H-CSNPs and CSNPs and pooled separately.

value: Leaf

tag: agent

value: H-CSNP

tag: time point


title: OC216-2

city: fuzhou

first: xiaolin

last: zhu

address: chazhong road

institute: fujian medical university

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: osteoclast transdifferent from immature dendritics

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: Vγ9Vδ2 T cells cultured in vitro : Peripheral blood mononuclear cells (PBMNCs) were cultured with zoledronate (ZOL) and recombinant human interleukin-2 (rhIL-2) to amplify Vγ9Vδ2 T cells. ImDC cells cultured in vitro: Immunomagnetic bead sorting CD14+ cells were cultured with recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF) and recombinant human interleukin 4 (rhIL-4) to differentiate to imDCs.

extract_protocol: Total RNA of osteoclasts was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: Co-culture system established: ImDCs were transdifferentiated into OCs in the present of recombinant human macrophage colony-stimulating factor (rhM-CSF) and recombinant human receptor activator nuclear factor ĸB ligand (rhRANKL). ImDCs were cultured alone as control group. Using Transwell inserts with Vγ9Vδ2 T cells in the upper compartment and imDC in the lower compartment（as γδT group）

value: osteoclasts


title: OCT216-2

source_name: osteoclast transdifferent from immature dendritics co-cultured with gamma delta t cell


title: H-CSNP_24h_rep1

description: Gene expression in H-CSNP treated tomato leaf sample after 24h

source_name: Tomato leaf, H-CSNP, 24h, replicate 1


title: H-CSNP_48h_rep1

description: Gene expression in H-CSNP treated tomato leaf sample after 48h

source_name: Tomato leaf, H-CSNP, 48h, replicate 1


title: H-CSNP_48h_rep2

source_name: Tomato leaf, H-CSNP, 48h, replicate 2


title: H-CSNP_24h_rep2

source_name: Tomato leaf, H-CSNP, 24h, replicate 2


title: OCT116-2


title: CSNP_72h_rep1

description: Gene expression in CSNP treated tomato leaf sample after 72h

source_name: Tomato leaf, CSNP, 72h, replicate 1

value: CSNP


title: Smchd1 del/del F 3 [ATAC-Seq]


title: Smchd1 del/del F 1 [Hi-C]


title: CSNP_72h_rep2

source_name: Tomato leaf, CSNP, 72h, replicate 2


title: H-CSNP_72h_rep2

source_name: Tomato leaf, H-CSNP, 72h, replicate 2


title: OC116-2


title: Smchd1 del/del F 2 [Hi-C]

source_name: Neural stem cells


title: Harpin_24h_rep2

description: Gene expression in harpin treated tomato leaf sample after 24h

source_name: Tomato leaf, harpin, 24h, replicate 2

value: harpin


title: CSNP_24h_rep2

description: Gene expression in CSNP treated tomato leaf sample after 24h

source_name: Tomato leaf, CSNP, 24h, replicate 2


title: CSNP_48h_rep2

description: Gene expression in CSNP treated tomato leaf sample after 48h

source_name: Tomato leaf, CSNP, 48h, replicate 2


title: TF64

city: Bergen

first: Hans-Peter

last: Marti

address: Jonas Liesvei 65

department: Department of Clinical Medicine

country: Norway

institute: University of Bergen

description: microRNA sequencing

data_processing:
Illumina Casava1.8 software used for basecalling.
Assembly of reads and alignment to the GRCh38
logcpm (counts per million) were calculated using EdgeR (R bioconductor), Filtering: Genes with more than 3 counts per million in at least 8/12 samples was retained
Comparative analysis was done with voom/limma R-package (R-Bioconductor version 3.4)
Pathway analysis was done with Ingenuity Pathway Analysis (Illumina, ver.27216297)
Genome_build: GRCh38
Supplementary_files_format_and_content: Strauss_et_al_count_matrix.txt (count matrix after EdgeR)
Strauss_et_al_logcpm_matrix_filtered.txt (filtered logcpm values)

source_name: renal biopsy

extract_protocol:
RNA was extracted using a miRNeasy FFPE kit (Qiagen, Venlo, Netherlands).
The sequencing libraries were generated with a TruSeq small RNA library kit (Illumina, USA, Inc., San Diego) in accordance with the manufacturer’s protocol, using 1 µg total RNA as starting materials

tag: individual

value: ccRCC (clear cell renal cell carcinoma)

tag: storage

value: FFPE

tag: tumor stage

value: I

tag: egfr (ml/min/1.73m2)

tag: tnm stage

tag: tumor size (mm)

tag: fuhrmann degree

tag: leibovich score

tag: nephrectomy type

value: Full

tag: gender


title: NF65

description: microRNA sequencing

value: non-cancerous

value: II

value: male


title: CSNP_48h_rep1

source_name: Tomato leaf, CSNP, 48h, replicate 1


title: TF65

description: microRNA sequencing


title: Harpin_24h_rep1

source_name: Tomato leaf, harpin, 24h, replicate 1


title: CSNP_24h_rep1

source_name: Tomato leaf, CSNP, 24h, replicate 1


title: NF64

description: microRNA sequencing


title: TF63b

description: microRNA sequencing

value: Partial


title: Harpin_48h_rep2

description: Gene expression in harpin treated tomato leaf sample after 48h

source_name: Tomato leaf, harpin, 48h, replicate 2


title: TF63a

description: microRNA sequencing

value: female


title: TF55

description: microRNA sequencing

value: III


title: NF57

description: microRNA sequencing


title: NF55

description: microRNA sequencing


title: TF50

description: microRNA sequencing


title: NF59

description: microRNA sequencing


title: TF59

description: microRNA sequencing


title: TF53

description: microRNA sequencing


title: TF57

description: microRNA sequencing


title: Harpin_72h_rep1

description: Gene expression in harpin treated tomato leaf sample after 72h

source_name: Tomato leaf, harpin, 72h, replicate 1


title: TF39

description: microRNA sequencing


title: TF46

description: microRNA sequencing


title: NF44

description: microRNA sequencing


title: NF46

description: microRNA sequencing


title: TF44

description: microRNA sequencing


title: [C26DYS] Patient C26 dysplasia

city: Bethesda

first: Yue

last: Hu

state: MD

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

country: USA

institute: NCI

description: Sample name in processed data: C26DYS

hyb_protocol: ULS-labeled tumor and genomic reference DNA was hybridized on Agilent SurePrint G3 Human CGH Microarrays 4 X 180 K or 8 X 60 K (Agilent), according to the manufacturer's protocol version 3.1.

scan_protocol: Slides were scanned with microarray scanner G2565BA (Agilent).

data_processing:
Images were analyzed by Feature Extraction software version 10.7.1.1 (Agilent). The aCGH data were visualized and analyzed using Nexus Copy Number software version 8.0 (BioDiscovery, Inc., El Segundo, CA, USA).
value definition in data matrix: Log2(copy number of segment/2)

source_name: dysplasia

label_protocol: Isolated FFPE DNA was labeled using the Genomic DNA ULS Labeling Kit (Agilent) according to the manufacturer's protocol version 3.1. Sex-matched human genomic DNA (Promega) was used as reference. Tumor DNA was labeled with ULS-Cy3 and genomic reference DNA with ULS-Cy5, respectively.

extract_protocol: DNA was isolated from formalin-fixed paraffin-embedded tissue after histopathologic determination of tumor areas on H&E sections, avoiding foci of inflammation as well as foci of high mucin and low cellular content. Tissue was deparaffinized in 1 ml of Histochoice Clearing Agent (Amresco, Solon, OH) in a thermomixer at 65 °C and two rounds of agitations at 1,100 rpm for 20 min. The tissue pieces were then washed with 1 ml of 50% ethanol/TE buffer and air dried before incubation in 400 ul of 1 M sodium thiocyanate at 65 °C, followed by agitation at 450 rpm for 2 hr. After washing once in 400 ul of TE buffer, Proteinase K digestion, RNase A treatment, and subsequent spin column purification of the extracted DNA were done using DNeasy Blood and Tissue Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. DNA concentration was measured by fluorometric quantitation (Qubit 3.0 Fluorometer, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA) using the Qubit dsDNA HS (High Sensitivity) Assay Kit (Life Technologies). DNA integrity was evaluated based on Bioanalyzer traces (2100 Bioanalyzer Instrument, Agilent) using the High Sensitivity DNA kit (Agilent).

value: dysplasia

tag: sample preparation

tag: crc etiology

value: Crohn's disease

tag: age at crc diagnosis, years

tag: duration of cd at crc diagnosis, years

tag: Sex

tag: ajcc stage

value: IV

tag: carcioma associated to fistula

tag: special histology

tag: microsatellite/hypermutation status

value: microsatellite stable

source_name: normal reference DNA

tag: manufacturer

value: Promega


title: [C01NOR] Patient C01 histologically  normal mucosa

description: Sample name in processed data: C01NOR

source_name: histologically normal mucosa

tag: tissue

value: histologically normal mucosa


title: [C18NOR] Patient C18 histologically normal mucosa

description: Sample name in processed data: C18NOR


title: [C12NOR] Patient C12 histologically normal mucosa

description: Sample name in processed data: C12NOR


title: [C28CA] Patient C28 carcinoma

description: Sample name in processed data: C28CA

source_name: carcinoma

value: carcinoma

value: no

value: microsatellite instable high-level


title: Control_rep1

description: Gene expression in control tomato leaf sample

source_name: Tomato leaf, control, replicate 1

value: Leaf

tag: agent

value: control


title: NF39

description: microRNA sequencing

tag: individual

value: non-cancerous

tag: storage

value: FFPE

tag: tumor stage

tag: egfr (ml/min/1.73m2)

tag: tnm stage

tag: tumor size (mm)

value: Full


title: [C07NOR] Patient C07 histologically normal mucosa

description: Sample name in processed data: C07NOR

tag: sample preparation

tag: crc etiology

value: I


title: NF63b

description: microRNA sequencing

tag: fuhrmann degree

tag: leibovich score

tag: nephrectomy type

value: Partial

tag: gender

value: male


title: NF63a

description: microRNA sequencing

value: female


title: NF50

description: microRNA sequencing


title: NF53

description: microRNA sequencing

value: II


title: Harpin_72h_rep2

source_name: Tomato leaf, harpin, 72h, replicate 2

value: harpin

tag: time point


title: RNA-Seq visceral adipocytes Repl1

city: Marburg

first: Robert

last: Liefke

state: Hessen

address: Hans-Meerwein-Str. 2

department: Institute of Molecular Biology and Tumor Research (IMT)

country: Germany

institute: Philipps University of Marburg

data_processing:
RNA-Seq data were aligned to hg38 by RNA STAR using a gffread filtered gencode.v28.basic.annotation.gtf file as template
ReadCounts were obtained by htseq-count
Normalized ReadCounts were obtained by DESeq2
Genome_build: hg38

source_name: visceral adipocytes

growth_protocol: Human primary preadipocytes were obtained from Innoprot and cultured in complete preadipocyte Medium (Innoprot).

extract_protocol:
RNA were isolated using the RNeasy Plus Mini Kit (Qiagen)
The libraries for RNA-Seq were prepared using TruSeq RNA Library Preparation Kit v2 (Illumina).

treatment_protocol: For differentiation, the preadipocytes were seeded with preadipocyte medium into poly-L-lysine coated 15 cm petri dishes and grown until they were confluent. Then, cells were differentiated with complete preadipocyte differentation medium (Innoprot) for 12 days to mature adipocytes. Medium was changed every 2-3 days.

tag: cell type

value: adipocyte


title: RNA-Seq subcutaneous adipocytes Repl2

source_name: subcutaneous adipocytes


title: RNA-Seq subcutaneous adipocytes Repl1


title: HFGSC rep2

city: Anseong

first: Buom-Yong

last: Ryu

state: Gyeonggi-Do

address: Seodong-daero

department: Animal Science and Technology

country: South Korea

institute: Chung-Ang University

description: SAMPLE 4

hyb_protocol: cRNA samples were hybridized to each mouse WG6 expression v.4 bead array.

scan_protocol: Arrays were scanned with an Illumina bead array Reader confocal scanner.

data_processing:
Data were extracted using the software provided by the manufacturer (Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)). Gene-Enrichment and Functional Annotation analysis for significant probe list was performed using DAVID (http://david.abcc.ncifcrf.gov/home.jsp). All data analysis and visualization of differentially expressed genes was conducted using R 3.0.2 (www.r-project.org).
Array probes transformed by logarithm and normalized by quantile method.

source_name: Mouse hair follicle-derived germline stem cells

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis, OD 260/280 ratio, and analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

tag: strain

tag: age

value: adult (4 months)

value: Dorsal skin; hair follicle

value: hair follicle-derived germline stem cells (HFGSCs)


title: RNA-Seq visceral adipocytes Repl2


title: RNA-Seq visceral pre-adipocytes

source_name: visceral pre-adipocytes

value: pre-adipocyte


title: Harpin_48h_rep1

source_name: Tomato leaf, harpin, 48h, replicate 1

tag: tissue

tag: agent


title: RNA-Seq subcutaneous pre-adipocytes

source_name: subcutaneous pre-adipocytes


title: GSC rep2

description: SAMPLE 6

source_name: Mouse testis germ cell

value: adult (3 months)

value: Testis

value: germline stem cells (GSCs)


title: HF rep2

description: SAMPLE 2

source_name: Mouse hair follicle

value: adult (2 months)


title: GSC rep1

description: SAMPLE 5


title: Control_rep2

source_name: Tomato leaf, control, replicate 2

value: Leaf

value: control


title: HFGSC rep1

description: SAMPLE 3


title: root +N, biological rep 3

city: Taipei

first: Ming-Hsiun

last: Hsieh

address: 128 Academia Road, Section 2

department: Institute of Plant and Microbial Biology

institute: Academia Sinica

description: Gene expression data from rice roots with NH4NO3 treatment

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

scan_protocol: The arrays were scanned on the Affymetrix GeneChip Scanner 3000.

data_processing: The Affymetrix CEL data were generated from GCOS and normalized using RMA algorithm in Genespring 11.5 software. Baselines were transformed to median of control samples. Expression value of probeset that >100 was defined as present. Unpaired t-test was performed to examine the reproducibility of the data sets. Probesets with P-value <0.05 and at least two-fold change between control and treatment groups were selected into the final list.

organism: Oryza sativa Japonica Group

source_name: rice roots with NH4NO3 treatment for 0.5 hour

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Rice (Oryza sativa L. ssp. Japonica cv. TNG67) seeds were germinated in continuous dark at 30°C for 3 days and then transferred to hydroponic solution (Yoshida et al., 1976) (+N) and grown under controlled conditions (30°C, 12-h photoperiod, 200 µmol photons m-2 s-1, 70% relative humidity) for 1 week.

extract_protocol: Total RNA from +N and -N-treated roots was extracted using a phenol extraction protocol.

treatment_protocol: 10-day-old rice seedlings grown in hydroponic solution (+N) were transferred to +N or -N solution for 1 hour.

tag: variety

value: root

tag: growth stage

value: seedling


title: Knockdown of STMN1 by shRNA vs. Non-targeting shRNA in LnCap

city: Birmingham

first: Sooryanarayana

last: Varambally

state: Alabama

address: 1824 6th Avenue S

department: Pathology

institute: University of Alabama

description: LnCap_STMN1 shRNA Vs Non-T shRNA

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software.

data_processing: Data from the two channel experiment arrays were lowess normalized usinf 'agilp' bioconductor package. Then, differential expression is measured by log2(test/reference).

source_name: STMN1 shRNA  LnCap cells

label_protocol: 1 µg of total RNA were primed with 2 µl of 100 µM T7-oligo-dT DNA primer at 65°C for 10 min, then reversed transcribed at 40°C for 2 h in the presence of 400 U MMLV RTase (Agilent), and labeled with T7 polymerase with 100 µM each of dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy5-label or Cy3-label.

growth_protocol: Prostate cancer cell lines PC3 and LnCaP were grown in RPMI-1640 (Life Technologies, Carlsbad, CA, USA) with penicillin–streptomycin (100 U/ml) and 10% fetal bovine serum (Invitrogen, Carlsbad, CA, USA) in 5% CO2 cell culture incubator.

extract_protocol: Total RNA was isolated from prostate cancer cell lines using the RNeasy Mini Kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Prostate cancer cells were infected with lentiviruses expressing STMN1 shRNAs or Non-T shRNA controls and stable cell lines were generated by selection with 1 μg/ml puromycin (Life Technologies).

tag: cell line

value: LnCap

value: prostate cancer cell line

tag: shRNA

source_name: Non-targeting shRNA

value: Non-targeting


title: root -N, biological rep 3

description: Gene expression data from rice roots treated with N starvation for 1 hour

source_name: rice roots without N for 1 hour


title: root -N, biological rep 2 reanalysis


title: root +N, biological rep 2

source_name: rice roots with NH4NO3 treatment


title: HF rep1

description: SAMPLE 1


title: Knockdown of STMN1 by shRNA vs. Non-targeting shRNA in PC3

description: PC3_STMN1 shRNA Vs Non-T shRNA

source_name: STMN1 shRNA  PC3 cells


title: root -N, biological rep 1 reanalysis


title: P. aeruginosa PAO1_wildtype_Cy3_PA1226 mutant_Cy5 Rep3

city: Honolulu

first: Tung

last: Hoang

state: HI

address: 1800 East-West Road

department: Microbiology

institute: University of Hawaii at Manoa

description: Replicate 3 of 3

hyb_protocol: cDNA from PAO1 and PA1226 mutant strains were mixed and hybridized to microarray slides for 20 h at 42oC.

scan_protocol: Scanned on a GenePix 4000 microarray scanner.

data_processing: Individual TIFF images from each channel were processed with Spotfinder software 3.2.1 to generate mev data. Microarray data were then normalized by low intensity filtering (Genes not detected in one or both channels were filtered out), LOWESS normalization, standard deviation regularization, and in-slide replicate analysis using MIDAS software 2.21.  Finally, the mev files from MIDAS were used to generate the data table in MEV software 4.5.1. The fold-change data for all detected genes were then obtained by combining the triplicate samples.

organism: Pseudomonas aeruginosa

label_protocol: Extracted RNA was verified on an agarose gel and 10 ug used in subsequent reverse transcription reactions, cDNA was purified and labeled with amino-allyl-dUTP. PAO1 cDNA was labeled with Cy3 and PA1226 with Cy5.

growth_protocol: P. aeruginosa wildtype strain PAO1 and PA1226 mutant strain were grown overnight in LB medium. Bacteria were harvested from overnight cultures, washed twice with LB, and and diluted 200 times in fresh LB medium. Subcultured PAO1 and PA1226 muatnt strains were grown at 37°C for 24 h without shaking.

extract_protocol: Total RNA was extracted using Qiagen RNeasy columns, including the additional on-column DNaseI digestion.

tag: genotype

value: wild type

tag: phase

value: Log phase

source_name: PA1226 mutant

value: PA1226 mutant


title: P. aeruginosa PAO1_wildtype_Cy3_PA1226 mutant_Cy5 Rep2

description: Replicate 2 of 3


title: P. aeruginosa PAO1_wildtype_Cy3_PA1226 mutant_Cy5 Rep1

description: Replicate 1 of 3


title: root +N, biological rep 1


title: Fibroblasts Crtl rep2

city: LYON

first: Jerome

last: Lamartine

address: 7 passage du Vercors

country: France

institute: Université Lyon I

description: SAMPLE 2

hyb_protocol: Hybridization was performed with 750 ng biotin-labeled cRNA on each BeadChip

scan_protocol: The standard Illumina scanning protocol was used to scan the arrays with the iScan System

data_processing: Data were normalized by quantile normalization on GenomeStudio software 2010 (Illumina). Data were analyzed with tools in the Partek Genomic Suite 6.6 (Partek Inc., St. Louis, Missouri, USA). One-way ANOVA was performed to compare the illuminated samples against controls.

source_name: Human skin fibroblasts Sham illuminated

label_protocol: Total RNA (500 ng) was amplified and biotin-labeled with the Illumina TotalPrep™ RNA Amplification Kit

growth_protocol: Cells were obtained from abdomen biopsies of Caucasian female donors and cultured in Dulbecco’s modified Eagle’s medium (DMEM), supplemented with 10% fetal bovine serum (FBS) and 100 µg/ml Normocin  at 37°C and 5% CO2. The culture medium was changed three times a week. Cells between passages 5-7 were used in this study.

extract_protocol: RNA extraction from NHF was performed using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: NHF were exposed with our equipment emitting the artificial visible light (99 J/cm2) in Minimum Essential Media (MEM)  without phenol supplemented with 1% FBS under regular culture conditions.

value: Human skin fibroblasts

tag: treatment

value: Sham illuminated


title: Fibroblasts Treated rep4

description: SAMPLE 8

source_name: Human skin fibroblasts illuminated at 99 J/cm2

value: illuminated at 99 J/cm2


title: Fibroblasts Treated rep1

description: SAMPLE 5


title: Fibroblasts Crtl rep4

description: SAMPLE 4


title: Fibroblasts Treated rep3

description: SAMPLE 7


title: Pre-therapy 5

city: Woolloongabba

first: Gayathri

last: Thillaiyampalam

state: QLD

address: 37 Kent Street

department: UQDI

institute: University of Queensland

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with bioconductor package limma in R

source_name: Monocytes isolated from PBMC

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

extract_protocol: Qiagen RNEasy RNA isolation kit according to manufacturer's instructions

tag: disease state

tag: tumor stage

value: IV


title: Post-therapy 1

value: II


title: Pre-therapy 2

value: III


title: Fibroblasts Crtl rep1

description: SAMPLE 1


title: Pre-therapy 4


title: Fibroblasts Treated rep2

description: SAMPLE 6


title: Post-therapy 6


title: Pre-therapy 6


title: Fibroblasts Crtl rep3

description: SAMPLE 3


title: 4C embryos LINE1 ASO rep3

city: London

first: Michelle

last: Percharde

address: Du Cane Road

department: Imperial College London

country: United Kingdom

institute: MRC Laboratory of Medical Sciences

data_processing:
Reads were quality and adaptor trimmed using trim_galore v0.4.0, and standard parameters
Trimmed reads were aligned to mm9 (Thermo Fisher Scientific) using tophat2 v2.0.9, using standard parameters
Bam files were used to generate count data using Rsubread package feature-counts v1.22.3, parameters: -t exon -T 4 -s 2 -g gene_id
Count data was analyzed in R v3.3.0, using Bioconductor v3.3, Deseq2 v.1.12.3
Genome_build: mm9
Supplementary_files_format_and_content: Unfiltered raw reads, generated from Feature-counts as above

source_name: Mouse embryos

growth_protocol: Animal experiments were performed with 5-8-week-old female and 2-6-month-old male C57BL/6J mice. Females were superovulated by administration of 7.5 I.U. of pregnant mare serum gonadotropin (PMSG; National Hormone Pituitary Program (NHPP), Harbor-UCLA Medical Center, CA, USA or Intervet UK) and 48 hours later with 7.5 I.U. of human chorionic gonadotropin (hCG; Sigma-Aldrich or Intervet UK). Embryos were cultured in KSOM-AA medium (Millipore) at 37°C in 5% CO2.

extract_protocol:
RNA isolation was performed using the PicoPure RNA Extraction Kit (Arcturus)
Libraries were generated using the SMARTer Stranded total RNA-seq kit v2 pico input mammalian, with 500pg RNA used per sample, and run across 2xlanes SE50 of HiSeq4000

treatment_protocol: Zygotes were microinjected with 0.5x ASO(0.75mM)  and cultured in KSOM medium. Early 2 cells were collected on approximately 33 h post hCG (~9 h post-microinjection). 4 cells were collected after two days of in vitro culture

tag: embryo stage


title: Pre-therapy 3


title: Post-therapy 2


title: Healthy 5

value: healthy


title: Post-therapy 5


title: Pre-therapy 1


title: 4C embryos LINE1 ASO rep2


title: Post-therapy 3


title: Healthy 6


title: 4C embryos LINE1 ASO rep1


title: Post-therapy 4


title: Healthy 4


title: 4C embryos RC ASO rep3


title: 4C embryos RC ASO rep2


title: early2C embryos LINE1 ASO rep3

value: early 2C


title: Healthy 3


title: 4C embryos RC ASO rep1


title: early2C embryos LINE1 ASO rep2


title: early2C embryos LINE1 ASO rep1


title: Healthy 2


title: early2C embryos RC ASO rep3


title: M4-shGal4, replicate 2

first: Chin-Hsien

last: Tsai

state: Others

address: Nan-Kang

department: ABRC

description: SAMPLE 17

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

extract_protocol: RNA was extracted with ZYMO research mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: Prostate cancer (PCa) cell line

tag: genotype/variation

value: galectin-4 knocked down


title: M4-shCtrl, replicate 3

description: SAMPLE 15

value: scramble knocked down


title: M4-shGal4, replicate 3

description: SAMPLE 18


title: early2C embryos RC ASO rep2


title: M4-shCtrl, replicate 1

description: SAMPLE 13


title: LNCaP-tetO-Gal4 + Dox, replicate 2

description: SAMPLE 11

source_name: LNCaP-tetO-Gal4 + Dox

value: LNCaP

value: expressing galectin-4


title: LNCaP-tetO-Gal4, replicate 3

description: SAMPLE 9

value: control cells


title: LNCaP-tetO-Gal4, replicate 1

description: SAMPLE 7


title: early2C embryos RC ASO rep1


title: M4-shGal4, replicate 1

description: SAMPLE 16


title: LNCaP-tetO-Gal4 + Dox, replicate 1

description: SAMPLE 10


title: LNCaP-tetO-Gal4, replicate 2

description: SAMPLE 8


title: study day 2, 10 mg, subject 05-9009

city: Hampton

first: Venky

last: Ramakrishna

state: NJ

address: 53 Frontage Rd, Suite 220

department: R&D Human Immunology

institute: Celldex Therapeutics

description:
S001BBF
SD2, 10 mg, subject 05-9009

data_processing: Arrays were assessed for quality using the arrayQualityMetrics R package from Bioconductor using 3 metrics: maplot, boxplot, and heatmap.  One sample, S001BBD, was identifed as an outlier by at least 2 of the 3 metrics and was removed from subsequent analysis.  After QC, probes were filter to retain only probes that were detected at least once across all arrays.  After filtering, only 23,035 features remained. The filtered raw data were then transformed using a variance stabilizing transformation (VST) method prior to normalisation across all arrays using the robust spline normalisation (RSN) method.

source_name: whole-blood, study day 2, 10 mg Varilumab

label_protocol: Biotinylated cRNA was prepared using the Ambion MessageAmp kit for Illumina arrays following the manufacturer's protocol

extract_protocol: Total RNA was isolated from PaxGene whold-blood samples using the QIAGEN PaxGene Blood RNA Kit following the manufacturer's protocol.

value: whole blood

tag: study day

tag: dose

value: 10 mg

tag: subject

tag: date collected

value: No


title: 22Rv1-tetO-Gal4, replicate 3

description: SAMPLE 3

tag: tissue


title: M4-shCtrl, replicate 2

description: SAMPLE 14


title: 22Rv1-tetO-Gal4 + Dox, replicate 2

description: SAMPLE 5

source_name: 22Rv1-tetO-Gal4 + Dox


title: study day 1, 10 mg, subject 06-9001

description:
S002061
SD1, 10 mg, subject 06-9001

source_name: whole-blood, study day 1

value: Yes


title: 22Rv1-tetO-Gal4 + Dox, replicate 1

description: SAMPLE 4


title: study day 29, 10 mg, subject 05-9009

description:
S001BC0
SD29, 10 mg, subject 05-9009

source_name: whole-blood, study day 29, 10 mg Varilumab


title: 22Rv1-tetO-Gal4 + Dox, replicate 3

description: SAMPLE 6


title: study day 1, 3 mg, subject 02-9011

description:
S001C0B
SD1, 3 mg, subject 02-9011

value: 3 mg


title: study day 2, 10 mg, subject 06-9001

description:
S002062
SD2, 10 mg, subject 06-9001


title: study day 8, 3 mg, subject 02-9011

description:
S001C0D
SD8, 3 mg, subject 02-9011

source_name: whole-blood, study day 8, 3 mg Varilumab


title: 22Rv1-tetO-Gal4, replicate 1

description: SAMPLE 1


title: 22Rv1-tetO-Gal4, replicate 2

description: SAMPLE 2


title: study day 29, 3 mg, subject 05-9008

description:
S001BBC
SD29, 3 mg, subject 05-9008

source_name: whole-blood, study day 29, 3 mg Varilumab


title: study day 8, 3 mg, subject 05-9008

description:
S001BBA
SD8, 3 mg, subject 05-9008


title: study day 29, 3 mg, subject 02-9013

description:
S001C12
SD29, 3 mg, subject 02-9013


title: Healthy 1


title: study day 8, 3 mg, subject 02-9013

description:
S001C11
SD8, 3 mg, subject 02-9013


title: study day 2, 1 mg, subject 05-9007

description:
S0016B0
SD2, 1 mg, subject 05-9007

source_name: whole-blood, study day 2, 1 mg Varilumab

value: 1 mg


title: study day 2, 1 mg, subject 05-9006

description:
S000FF6
SD2, 1 mg, subject 05-9006


title: study day 2, 0.3 mg, subject 02-9004

description:
S000C2E
SD2, 0.3 mg, subject 02-9004

source_name: whole-blood, study day 2, 0.3 mg Varilumab


title: study day 1, 1 mg, subject 02-9008

description:
S0016A8
SD1, 1 mg, subject 02-9008


title: study day 29, 0.1 mg, subject 05-9003

description:
S001BC8
SD29, 0.1 mg, subject 05-9003

source_name: whole-blood, study day 29, 0.1 mg Varilumab


title: study day 1, 3 mg, subject 05-9008

description:
S001BBD
Failed QC, not used in final analysis


title: study day 1, 0.3 mg, subject 02-9004

description:
S000C2D
SD1, 0.3 mg, subject 02-9004


title: study day 8, 1 mg, subject 02-9008

description:
S0016AA
SD8, 1 mg, subject 02-9008

source_name: whole-blood, study day 8, 1 mg Varilumab


title: study day 29, 1 mg, subject 05-9007

description:
S0016B2
SD29, 1 mg, subject 05-9007

source_name: whole-blood, study day 29, 1 mg Varilumab


title: study day 1, 1 mg, subject 05-9006

description:
S000FF5
SD1, 1 mg, subject 05-9006


title: study day 8, 0.3 mg, subject 05-9005

description:
S001034
SD8, 0.3 mg, subject 05-9005

source_name: whole-blood, study day 8, 0.3 mg Varilumab


title: study day 1, 0.3 mg, subject 05-9005

description:
S001032
SD1, 0.3 mg, subject 05-9005


title: 786O-Z2sh45-1

city: Chapel Hill

first: Qing

last: Zhang

state: NC

address: 450 West Dr.

institute: Lineberger Cancer Center

hyb_protocol: Hyb protocol were followed by standard affymetrix protocol

scan_protocol: Data Chip was scanned by using a Genearray scanner

data_processing: RMA

source_name: human cancer cell line

label_protocol: cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: 786-O cells were cultured in RPMI with 10%FBS supplemented with 1% Pen-Strep

extract_protocol: Total RNA was extracted by Qiagen RNAeasy plus kit

treatment_protocol: 786-O cells were infected with lentivirus followed by puromycin selection at (2 ug/ml)

tag: kidney tumor cell line

value: kidney cancer


title: study day 29, 10 mg, subject 06-9001

description:
S002064
SD29, 10 mg, subject 06-9001


title: study day 8, 0.1 mg, subject 05-9003

description:
S001BC7
SD8, 0.1 mg, subject 05-9003

source_name: whole-blood, study day 8, 0.1 mg Varilumab


title: study day 2, 3 mg, subject 02-9011

description:
S001C0C
SD2, 3 mg, subject 02-9011

source_name: whole-blood, study day 2, 3 mg Varilumab


title: study day 8, 10 mg, subject 05-9009

description:
S001A72
SD8, 10 mg, subject 05-9009

source_name: whole-blood, study day 8, 10 mg Varilumab


title: study day 2, 0.1 mg, subject 05-9002

description:
S000B49
SD2, 0.1 mg, subject 05-9002

source_name: whole-blood, study day 2, 0.1 mg Varilumab


title: 786O-Z2sh44-1


title: 786O-Scr-2


title: study day 29, 0.1 mg, subject 05-9002

description:
S000B4C
SD29, 0.1 mg, subject 05-9002


title: study day 1, 10 mg, subject 05-9009

description:
S001BBE
SD1, 10 mg, subject 05-9009


title: study day 29, 3 mg, subject 02-9011

description:
S001C0E
SD29, 3 mg, subject 02-9011


title: 786O-Z2sh44-2


title: 786O-Z2sh45-2


title: study day 2, 3 mg, subject 02-9013

description:
S001C10
SD2, 3 mg, subject 02-9013


title: study day 8, 10 mg, subject 06-9001

description:
S002063
SD8, 10 mg, subject 06-9001


title: study day 2, 3 mg, subject 05-9008

description:
S001BBB
SD2, 3 mg, subject 05-9008


title: study day 8, 1 mg, subject 05-9007

description:
S0016B1
SD8, 1 mg, subject 05-9007


title: 786O-Scr-1


title: study day 1, 3 mg, subject 02-9013

description:
S001C0F
SD1, 3 mg, subject 02-9013


title: study day 1, 1 mg, subject 05-9007

description:
S0016AF
SD1, 1 mg, subject 05-9007


title: study day 2, 1 mg, subject 02-9008

description:
S0016A9
SD2, 1 mg, subject 02-9008


title: siRNA KDM5A biological rep1 in p53-/- HCT116

city: Memphis

first: JUN

last: YANG

state: TN

address: 262 Danny Thomas Place

department: Surgery

institute: St Jude Children's Research Hospital

hyb_protocol: The WT Plus assay from Affymetrix fragments and labels 5.5 ug of ss-cDNA of which 2.3 ug is hybridized on the HuGene_2.0_st chip  with a constant temperature of 45° C for 16 hours while rotating at 60 rpm.

scan_protocol: The samples were the stained and washed using the Affymetrix Fluidics 450 stations and  recommended protocol. Then the HuGene_2.0_st chip arrays were then scanned by the Affymetrix GeneChip Scanner 3000 7G

data_processing: Data were background adjusted, normalized and summarized by the RMA method.

source_name: Cells treated with siRNA for 72h_KDM5A

label_protocol: The protocol used for the samples run on the HuGene_2.0_st chip  was the Whole Transcript Plus assay from Affymetrix.  The initial input of RNA was 100 ng

growth_protocol: Cells were cultured in DMEM medium (10%FBS, 1% glutamine, 1% penicillin/streptomycin).

extract_protocol: Qiagen RNeasy mini kit

treatment_protocol: Cells were  treated with siRNA for 72 hours.

tag: p53 genotype

tag: si knockdown


title: study day 2, 0.3 mg, subject 05-9005

description:
S001033
SD2, 0.3 mg, subject 05-9005


title: LNCaP-tetO-Gal4 + Dox, replicate 3

description: SAMPLE 12

source_name: LNCaP-tetO-Gal4 + Dox

tag: cell line


title: study day 8, 1 mg, subject 05-9006

description:
S000FF7
SD8, 1 mg, subject 05-9006


title: study day 29, 0.3 mg, subject 02-9004

description:
S000C30
SD29, 0.3 mg, subject 02-9004

source_name: whole-blood, study day 29, 0.3 mg Varilumab


title: study day 29, 0.3 mg, subject 05-9005

description:
S001035
SD29, 0.3 mg, subject 05-9005


title: study day 29, 1 mg, subject 02-9008

description:
S0016AB
SD29, 1 mg, subject 02-9008


title: siRNA KDM5A biological rep2 in p53+/+ HCT116


title: siRNA KDM5A biological rep2 in p53-/- HCT116


title: siRNA control biological rep1 in p53-/- HCT116

source_name: Cells treated with siRNA for 72h_control

value: control


title: [M24CA] Patient M24 carcinoma

description: Sample name in processed data: M24CA

source_name: carcinoma

value: carcinoma

tag: sample preparation

value: FFPE

tag: crc etiology

value: sporadic

tag: age at crc diagnosis, years

tag: duration of cd at crc diagnosis, years

tag: Sex

value: male

tag: ajcc stage

value: III

tag: carcioma associated to fistula

value: no

tag: special histology

value: mucinous

tag: microsatellite/hypermutation status

value: microsatellite stable

source_name: normal reference DNA

tag: manufacturer

value: Promega


title: [M23CA] Patient M23 carcinoma

description: Sample name in processed data: M23CA

value: IV

value: mucinous, signet ring


title: study day 8, 0.3 mg, subject 02-9004

description:
S000C2F
SD8, 0.3 mg, subject 02-9004

value: whole blood

tag: study day

tag: dose

tag: subject

value: No


title: study day 1, 0.1 mg, subject 05-9002

description:
S000B4B
SD1, 0.1 mg, subject 05-9002

source_name: whole-blood, study day 1

tag: tissue

tag: date collected

value: Yes


title: siRNA KDM5A biological rep1 in p53+/+ HCT116

tag: p53 genotype

tag: si knockdown


title: siRNA control biological rep2 in p53+/+ HCT116

tag: cell line


title: study day 1, 0.1 mg, subject 05-9003

description:
S001BC5
SD1, 0.1 mg, subject 05-9003


title: study day 29, 1 mg, subject 05-9006

description:
S000FF8
SD29, 1 mg, subject 05-9006

value: 1 mg


title: study day 8, 0.1 mg, subject 05-9002

description:
S000BB5
SD8, 0.1 mg, subject 05-9002


title: siRNA control biological rep1 in p53+/+ HCT116


title: [M22CA] Patient M22 carcinoma

description: Sample name in processed data: M22CA

tag: sample preparation

tag: crc etiology


title: RpoN-1

city: Hong Kong

first: Xin

last: Deng

address: To Yuen Building

department: Biomedical Sciences

country: Hong Kong

institute: City University of Hong Kong

data_processing:
Bacterial RNA-seq reads were mapped to the P. auruginosa genome by using TopHat (version 2.0.0), with two mismatches allowed
Only the uniquely mapped reads were kept for the subsequent analyses.
The gene differential expression analysis was performed using Cuffdiff software (version 2.0.0)
Genome_build: ASM676v1 (NC_002516.2)
Supplementary_files_format_and_content: .txt file containing rawcounts and comparisons between RpoN mutant and wild-type

organism: Pseudomonas aeruginosa PAO1

source_name: liquid culture in LB (Luria-Bertani)  medium

growth_protocol: LB

extract_protocol:
To examine the effect of RpoN on the transcriptome, 2 ml of mid-log-phase (OD600= 0.6) bacterial cultures (PAO1 and ∆rpoN strains) were collected by centrifugation (12,000 rpm, 4℃). An RNeasy minikit (Qiagen) was used for subsequent RNA purification with DNaseI (NEB) treatment. After removing rRNA by using the MICROBExpress kit (Ambion), mRNA was used to generate the cDNA library according to the TruSeq RNA sample prep kit protocol (Illumina), which was then sequenced using the HiSeq 2000 system (Illumina). Bacterial RNA-seq reads were mapped to the P. auruginosa genome by using TopHat (version 2.0.0), with two mismatches allowed. Only the uniquely mapped reads were kept for the subsequent analyses. The gene differential expression analysis was performed using Cuffdiff software (version 2.0.0). GO enrich-ment analyses were conducted on all differentially transcribed genes using DAVID before data sets were imported into Cytoscape with an Enrichment Map plugin. The each sample in RNA-seq assay was repeated twice.
TruSeq RNA sample prep kit protocol (Illumina)

treatment_protocol: grow until mid-log phase in LB

tag: genotype

value: rpoN mutant


title: [M21CA] Patient M21 carcinoma

description: Sample name in processed data: M21CA

tag: age at crc diagnosis, years

tag: duration of cd at crc diagnosis, years

tag: Sex

value: female


title: study day 2, 0.1 mg, subject 05-9003

description:
S001BC6
SD2, 0.1 mg, subject 05-9003


title: [M18CA] Patient M18 carcinoma

description: Sample name in processed data: M18CA

value: carcinoma

tag: ajcc stage

tag: carcioma associated to fistula

tag: special histology


title: 6h_R-_2

city: Glasgow

first: Katarzyna

middle: Kinga

last: Modrzynska

state: Glasgow (City of)

address: B627 Sir Graeme Davies Building, 120 University Place

institute: Wellcome Trust Centre for Molecular Parasitology

data_processing:
base calling, quality checking, index sorting and generation of initial *cram files performed using the automatic pipelines of the sequencing service of the Wellcome Trust Sanger Institute. All details of the processing are included in the *cram file header.
concatenation of the *cram files from the two lanes of HiSeq2500 run using samtools (v.1.3.1)
generation of *fastq file from *cram files using Picard-tools SamToFastq (v.2.3)
re-alignment of the reads with from *fastq files against the reference genome in a splice-aware manner using hisat2-2.0.0-beta software and generation of *sam files
sorting and indexing of the resulting *sam files using samtools (v.1.3.1)
counting of the reads aligned to each of the Plasmodium genes using htseq-count command from  HTSeq Python library (v. 0.6.1) with  option '-s reverse'  and gff file matching the reference genome, http://plasmodb.org/common/downloads/release-30/PbergheiANKA/gff/data/
Genome_build: http://plasmodb.org/common/downloads/release-30/PbergheiANKA/fasta/data/
Supplementary_files_format_and_content: *.htseq_count files containing the raw read counts for all the genes in Plasmodium berghei genome

organism: Plasmodium berghei

source_name: inducible AP2-G overexpression line

growth_protocol: Female, outbred Theiler’s Original (TO) mice, 8-12 weeks old were injected with PBGAMi parasites synchronized to late schizont stage. The gametocyte conversion was induced in half of the animals by intraperitoneal injection of 4 mg/kg of rapamycin. Blood containing the developing parasites was harvested at different time point post induction  (0h, 6h, 12h, 18h, 24h and 30h) via cardiac puncture. Leucocyte depletion was achieved by filtration of the blood through two sequential Plasmodipur ® filters (Europroxima) according to the manufacturer’s instructions. Remaining red blood cells were resuspended in 10 volumes of pre-chilled erythrocyte lysis buffer (150mM NH4Cl; 10mM KHCO3; 1mM EDTA) and incubated on ice for 15min. After lysis parasites were pelleted by centrifugation for 8 minutes at 450g and washed with 1x phosphate buffered saline until complete removal of the coloration of the supernatant. Parasite pallet was resuspended in 1ml of Trizol reagent (Ambion) lysed for 10 min at room temperature and stored at -80°C for later RNA extraction. For each time point at least two independent biological replicates of treated parasites and matched untreated controls were generated.

extract_protocol:
Complete RNA was isolated from the samples using Trizol/chloroform extraction followed by isopropanol precipitation and its concentration and integrity was verified using Agilent Bioanalyzer (RNA 6000 Nano kit) and NanoDrop 1000 spectrophotometer.
1-2 µg of total RNA from each sample (all complete sample if the yield was lower) was used for mRNA isolation (Magnetic mRNA Isolation Kit, NEB). First strand cDNA synthesis was performed using the SuperScript III First-Strand Synthesis System and a 1:1 mix of Oligo(dT) and random primers (Invitrogen). The DNA/RNA hybrids were purified using Agencourt RNACleanXP beads (Beckman Coulter) and the second cDNA strand was synthesized using a 10 mM dUTP nucleotide mix, DNA Polymerase I (Invitrogen) and RNAseH (NEB) for 2.5 h at 16°C. The long cDNA fragments were purified and fragmented using a Covaris S220 system (duty cycles= 20, intensity = 5,cycles/burst =200,time= 30s). The ~200 bp long fragments were end-repaired, dA-tailed and ligated to “PCR-free” adapters (Kozarewa et al., 2009) with index tags using NEBNext kits according to the manufacturer’s instructions. Excess adapters were removed by two rounds of clean-up with 1xvolume of Agencourt AMPure XP beads. Final libraries were eluted in 30μl water, quality-controlled using Agilent Bioanalyzer (High Sensitivity DNA chip) digested with USER enzyme (NEB) and quantified by qPCR. For some libraries, additional 5 cycles of PCR amplification were performed, using KAPA HiFi HotStart PCR mix and tag-specific primers to obtain enough material for sequencing. Pools of indexed libraries were sequenced using an Illumina HiSeq2500 system (100 bp paired-end reads) according to manufacturer’s manual.

value: Plasmodium berghei cells

tag: host

value: Female, outbred Theiler's Original (TO) mice

tag: rapamycin treated?

value: NO

tag: time (hours post induction)

tag: plasmodium strain

value: inducible AP2-G overexpression line


title: 24h_R-_4

tag: tissue


title: Esc-TBHP B

city: Lyon

first: Anne

last: Wierinckx

state: select a state

address: 8, av Rockefeller

institute: University Lyon1

data_processing: The data were normalised using quantile normalisation with GenomeStudio from Illumina

source_name: Cells emerging from HCEC-hTERT cells committed into a senescence program in response to a chemical peroxide (experiment B)

growth_protocol: Human primary epithelial colonic cells (HCEC, abm) were immortalized through transduction of hTERT (HCEC-hTERT). Chronic inflammation was induced by submitting cells to supernatants of activated macrophages. These supernatants were obtained through sequential differentiation and activation of THP-1 monocytic cells with TPA and LPS. Supernatants were diluted one half in Prigrow III growth medium (abm) and renewed every two days. Transduction of Zeb1 or Zeb2 was achieved through retroviral infection. Cells were cultured in Prigrow III medium (abm) supplemented with 5% FBS and 100 U/ml PS on collagen-coated dishes (BD BioCoat Collagen type I, Dutscher).

extract_protocol: Total RNAs were extract with the Qiagen RNeasy minikit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: cell type


title: Esc-TBHP A

source_name: Cells emerging from HCEC-hTERT cells committed into a senescence program in response to a chemical peroxide (experiment A)


title: HCEC-Zeb2

source_name: HCEC-hTERT cells transduced with the murine Zeb2


title: Esc-Inf B

source_name: Cells emerging from HCEC-hTERT cells committed into a senescence program in response to a chronic inflammation (experiment B)


title: Esc-Inf A

source_name: Cells emerging from HCEC-hTERT cells committed into a senescence program in response to a chronic inflammation (experiment A)


title: [M17CA] Patient M17 carcinoma

description: Sample name in processed data: M17CA

value: FFPE

value: sporadic

value: male

value: III

value: no

tag: microsatellite/hypermutation status

tag: manufacturer


title: HCEC-hTERT

source_name: Human colonic epithelial cells (abm, T4056) immortalized by hTERT


title: siRNA control biological rep2 in p53-/- HCT116

tag: cell line

tag: p53 genotype

tag: si knockdown

value: control


title: 24h_R+_3

value: YES


title: HCEC-Zeb1

source_name: HCEC-hTERT cells transduced with the murine Zeb1


title: 0h_R+_4


title: [M20CA] Patient M20 carcinoma

description: Sample name in processed data: M20CA

tag: sample preparation

tag: crc etiology

tag: age at crc diagnosis, years

value: I

value: mucinous

value: microsatellite stable

value: Promega


title: 6h_R-_3


title: 6h_R+_2


title: 18h_R-_2


title: 0h_R-_3


title: 18h_R+_2


title: [M19CA] Patient M19 carcinoma

description: Sample name in processed data: M19CA

tag: duration of cd at crc diagnosis, years

tag: Sex

value: female

tag: ajcc stage


title: [M14CA] Patient M14 carcinoma

description: Sample name in processed data: M14CA

value: carcinoma

tag: carcioma associated to fistula

tag: special histology

value: mucinous, signet ring


title: [M16CA] Patient M16 carcinoma

description: Sample name in processed data: M16CA

value: IV


title: 6h_R+_3

value: Plasmodium berghei cells

tag: host

value: Female, outbred Theiler's Original (TO) mice

tag: rapamycin treated?

tag: time (hours post induction)


title: 0h_R-_2

tag: tissue

value: NO

tag: plasmodium strain

value: inducible AP2-G overexpression line


title: 6h_R-_1


title: [M15CA] Patient M15 carcinoma

description: Sample name in processed data: M15CA

value: FFPE

value: sporadic

value: male

tag: microsatellite/hypermutation status

tag: manufacturer


title: [M13CA] Patient M13 carcinoma

description: Sample name in processed data: M13CA

value: no


title: 18h_R+_1

value: YES


title: 30h_R+_2


title: [M11CA] Patient M11 carcinoma

description: Sample name in processed data: M11CA

value: III


title: [M10CA] Patient M10 carcinoma

description: Sample name in processed data: M10CA

value: I

value: mucinous


title: 12h_R+_2


title: [M12CA] Patient M12 carcinoma

description: Sample name in processed data: M12CA

value: microsatellite stable

value: Promega


title: 0h_R+_3


title: 30h_R-_2


title: 24h_R-_3


title: 12h_R-_2


title: [M08CA] Patient M08 carcinoma

description: Sample name in processed data: M08CA

value: carcinoma


title: [M09CA] Patient M09 carcinoma

description: Sample name in processed data: M09CA

value: II


title: [M07CA] Patient M07 carcinoma

description: Sample name in processed data: M07CA


title: 0h_R+_2


title: 30h_R+_1


title: 24h_R-_2


title: 24h_R+_1


title: [M06CA] Patient M06 carcinoma

description: Sample name in processed data: M06CA


title: 12h_R+_1


title: 24h_R-_1


title: 30h_R-_1


title: 24h_R+_2


title: 12h_R-_1


title: 0h_R+_1


title: 6h_R+_1


title: [M02CA] Patient M02 carcinoma

description: Sample name in processed data: M02CA


title: [M03CA] Patient M03 carcinoma

description: Sample name in processed data: M03CA

value: female


title: 0h_R-_1

value: Plasmodium berghei cells


title: [M01CA] Patient M01 carcinoma

description: Sample name in processed data: M01CA

value: mucinous, signet ring


title: [C27CA] Patient C27 carcinoma

description: Sample name in processed data: C27CA

value: Crohn's disease

value: yes


title: [M05CA] Patient M05 carcinoma

description: Sample name in processed data: M05CA

value: FFPE


title: [C26CA] Patient C26 carcinoma

description: Sample name in processed data: C26CA

value: IV


title: [C24CA] Patient C24 carcinoma

description: Sample name in processed data: C24CA


title: [M04CA] Patient M04 carcinoma

description: Sample name in processed data: M04CA

value: sporadic


title: [C25CA] Patient C25 carcinoma

description: Sample name in processed data: C25CA


title: [C23CA] Patient C23 carcinoma

description: Sample name in processed data: C23CA

value: no


title: [C22CA] Patient C22 carcinoma

description: Sample name in processed data: C22CA

value: male


title: 786-O Ctrl #1

source_name: human cancer cell line

tag: kidney tumor cell line

value: kidney cancer


title: 786-O Ctrl #2


title: [C20CA] Patient C20 carcinoma

description: Sample name in processed data: C20CA

value: microsatellite instable high-level


title: 786-O p65 sh #2


title: 786-O p65 sh #1


title: pancreatic cancer cell, 10Gy-irradiated, 24h, biological rep 2

city: Shanghai

first: Ling

last: Tian

state: Shanghai

address: No. 650, New Songjiang Road

department: Institute of Translational Medicine

institute: Shanghai General Hospital

description: whole transcript data from PANC-1 cells with 10Gy irradiation

hyb_protocol: Following labelling, ~20 ug of cDNA were hybridized at 45C hybridization oven, at 60 rpm for 16 hr on Array. GeneChips were washed and stained with Affymetrix® Hybridization, Wash and Stain Kit using the FS450_0001 fluidics protocol

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix Expression Console™ Software Version 1.0. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: pancreatic cancer cell line, 10Gy-irradiated

label_protocol: Biotinylated ds cDNA were prepared according to the standard Affymetrix protocol from 6.25 ug fragmented ds Cdna

growth_protocol: Pancreatic cancer cells were seeded into culture plate overnight with 2% FBS in culture medium

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

treatment_protocol: Pancreatic cancer cells were irradiated with 10Gy/0Gy using an Oncor linear accelerator, and collected at 24h after radiation for RNA extraction and hybridization on Affymetrix microarray.

value: pancreatic cancer

tag: cell line

tag: treatment


title: pancreatic cancer cell, 10Gy-irradiated, 24h, biological rep 3


title: pancreatic cancer cell, non-irradiated, biological rep 3

description: whole transcript data from PANC-1 cells without irradiation

source_name: pancreatic cancer cell line, non-irradiated

value: non-irradiated


title: [C21CA2] Patient C21 carcinoma 2

first: Yue

last: Hu

address: 50 South Drive, Bldg. 50, Rm. 1408

description: Sample name in processed data: C21CA2

data_processing:
Images were analyzed by Feature Extraction software version 10.7.1.1 (Agilent). The aCGH data were visualized and analyzed using Nexus Copy Number software version 8.0 (BioDiscovery, Inc., El Segundo, CA, USA).
value definition in data matrix: Log2(copy number of segment/2)

extract_protocol: DNA was isolated from formalin-fixed paraffin-embedded tissue after histopathologic determination of tumor areas on H&E sections, avoiding foci of inflammation as well as foci of high mucin and low cellular content. Tissue was deparaffinized in 1 ml of Histochoice Clearing Agent (Amresco, Solon, OH) in a thermomixer at 65 °C and two rounds of agitations at 1,100 rpm for 20 min. The tissue pieces were then washed with 1 ml of 50% ethanol/TE buffer and air dried before incubation in 400 ul of 1 M sodium thiocyanate at 65 °C, followed by agitation at 450 rpm for 2 hr. After washing once in 400 ul of TE buffer, Proteinase K digestion, RNase A treatment, and subsequent spin column purification of the extracted DNA were done using DNeasy Blood and Tissue Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. DNA concentration was measured by fluorometric quantitation (Qubit 3.0 Fluorometer, Life Technologies, Thermo Fisher Scientific, Waltham, MA, USA) using the Qubit dsDNA HS (High Sensitivity) Assay Kit (Life Technologies). DNA integrity was evaluated based on Bioanalyzer traces (2100 Bioanalyzer Instrument, Agilent) using the High Sensitivity DNA kit (Agilent).

tag: sample preparation

tag: crc etiology

value: I

value: microsatellite stable, hypermutated

value: Promega


title: pancreatic cancer cell, non-irradiated, biological rep 1


title: [C21CA1] Patient C21 carcinoma 1

description: Sample name in processed data: C21CA1

value: carcinoma

tag: age at crc diagnosis, years

tag: duration of cd at crc diagnosis, years

value: microsatellite stable


title: pancreatic cancer cell, 10Gy-irradiated, 24h, biological rep 1


title: [C19CA] Patient C19 carcinoma

description: Sample name in processed data: C19CA

tag: Sex

tag: ajcc stage

value: mucinous, signet ring


title: pancreatic cancer cell, non-irradiated, biological rep 2


title: 24hr_uninfected_batch1

city: Baltimore

middle: E.

last: Jedlicka

address: 615 N. Wolfe street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins University, School of Public Health

description: Gene Expression Data

hyb_protocol: 600ng of Cy3-labelled cRNA was purified, fragmented and hybridized to Agilent SurePrint G3 Mouse v2 8x60K Gene Expression Arrays, according to the Agilient Low Input QuickAmp Labeling Kit protocol.   Post-hybridization washing of arrays was also performed according to these protocols.

scan_protocol: The arrays were scanned in an Agilent G2600D SureScan Microarray Scanner using scan protocol AgilentG3_GX_1color. Agilent’s Feature Extraction Software was used to assign grids, provide raw image files per array, and generate QC metric reports from the microarray scan data. The QC metric reports were used for quality assessment of all hybridizations and scans.

data_processing: Txt files from Features Extraction Software were imported into Partek Genomics Suite v6.6 (Partek) for detailed analyses of gene expression. Within Partek, the gene expression workflow was followed for Agilent Feature Extraction files, including import of gProcessedSignal, quantile normalization, and Log Transformation base 2.0. The batch effect removal tool (ANOVA) was used to correct for effects of culture batch and array (slide). For genes for which multiple probes were present, a summarization of probes was performed (merge probes by gene symbol with mean of intensity values).

source_name: Uninfected (Control) BMDM, 24 hours, culture batch 1

label_protocol: One hundred nanograms of total RNA was processed for hybridization to Agilent SurePrint G3 Mouse v2 8x60K Gene Expression Arrays according Agilent’s One Color Microarray-Based Analysis (Low Input QuickAmp Labeling) protocol, including cDNA synthesis, cRNA synthesis with Cy3 labeling and purification, fragmentation, hybridization, and post-hyb washing. Spike-In controls were utilized and processed according to Agilent’s One Color RNA Spike-In kit protocol.

extract_protocol: Total RNA was extracted using the PureLink RNA Mini kit (Ambion/Life Technologies) according to the manufacturer’s protocol, including on-column DNAse treatment. Following elution of purified RNA from the PureLink columns with Nuclease-free water, quantitation was performed using a NanoDrop spectrophotometer and quality assessment determined by RNA LabChip analysis on an Agilent BioAnalyzer 2100 or RNA Screen tape on an Agilent TapeStation 2200.

treatment_protocol: Primary macrophages were harvested from bone marrow of C57B/6J mice and grown in DMEM Feeding media (20% L929 cell supernatant, 10% FBS, 0.1% β-mercaptoethanol, 1% Pen/Strep, 1% MEM-NEA Non-essential Amino Acids, 1% Glutamax, 1% HEPES Buffer). BMDM were activated for 16 hours with IFNy and LPS and then infected with either C. gattii or C. neoformans. Cells were harvested at 2 and 24 hours post-infection. Uninfected controls were also collected at these timepoints. Cultured BMDM were washed with 1x PBS, removed with a cell scraper, and pelleted. The cell pellet was resuspended in Trizol reagent.

value: Macrophages, bone marrow-derived

value: female

tag: strain

value: C57B/6 from Jackson Labs

tag: slide id (array batch)

tag: culture batch

tag: time

value: uninfected (control)


title: [C18CA] Patient C18 carcinoma

city: Bethesda

institute: NCI

description: Sample name in processed data: C18CA

tag: tissue

value: FFPE

value: Crohn's disease

value: II

tag: carcioma associated to fistula

tag: special histology

value: mucinous


title: 2hr_R265 infected_batch1

description: Gene Expression Data

source_name: C. gattii R265 infected BMDM, 2 hours, culture batch 1

value: C. gattii R265 infected


title: 2hr_R265 infected_batch2

description: Gene Expression Data

source_name: C. gattii R265 infected BMDM, 2 hours, culture batch 2


title: [C16LR] Patient C16 local recurrence

description: Sample name in processed data: C16LR

source_name: local recurrence

value: local recurrence

value: no

tag: microsatellite/hypermutation status

source_name: normal reference DNA

tag: manufacturer


title: RpoN-2

source_name: liquid culture in LB (Luria-Bertani)  medium

tag: genotype

value: rpoN mutant


title: 24hr_H99 infected_batch1

description: Gene Expression Data

source_name: C. neoformans H99 infected BMDM, 24 hours, culture batch 1

value: I

tag: treatment

value: C. neoformans H99 infected


title: 2hr_H99 infected_batch1

description: Gene Expression Data

source_name: C. neoformans H99 infected BMDM, 2 hours, culture batch 1


title: [C16CA] Patient C16 carcinoma

description: Sample name in processed data: C16CA

source_name: carcinoma

value: carcinoma

tag: sample preparation

value: Promega


title: 24hr_R265 infected_batch1

description: Gene Expression Data

source_name: C. gattii R265 infected BMDM, 24 hours, culture batch 1


title: 24hr_R265 infected_batch2

description: Gene Expression Data

source_name: C. gattii R265 infected BMDM, 24 hours, culture batch 2


title: 2hr_uninfected_batch1

description: Gene Expression Data

source_name: Uninfected (Control) BMDM, 2 hours, culture batch 1


title: 24hr_R265 infected_batch3

description: Gene Expression Data

source_name: C. gattii R265 infected BMDM, 24 hours, culture batch 3

value: III


title: 24hr_uninfected_batch3

description: Gene Expression Data

source_name: Uninfected (Control) BMDM, 24 hours, culture batch 3

value: Macrophages, bone marrow-derived


title: 2hr_R265 infected_batch3

description: Gene Expression Data

source_name: C. gattii R265 infected BMDM, 2 hours, culture batch 3

value: female


title: 24hr_H99 infected_batch3

description: Gene Expression Data

source_name: C. neoformans H99 infected BMDM, 24 hours, culture batch 3

value: C57B/6 from Jackson Labs


title: 24hr_uninfected_batch2

description: Gene Expression Data

source_name: Uninfected (Control) BMDM, 24 hours, culture batch 2

value: uninfected (control)


title: 24hr_H99 infected_batch2

description: Gene Expression Data

source_name: C. neoformans H99 infected BMDM, 24 hours, culture batch 2


title: [C14CA] Patient C14 carcinoma

description: Sample name in processed data: C14CA

value: FFPE

tag: crc etiology

value: male

value: mucinous, signet ring

value: microsatellite stable


title: 2hr_uninfected_batch3

description: Gene Expression Data

source_name: Uninfected (Control) BMDM, 2 hours, culture batch 3


title: [C13CA] Patient C13 carcinoma

description: Sample name in processed data: C13CA

value: Crohn's disease

tag: age at crc diagnosis, years

value: yes


title: [C15CA] Patient C15 carcinoma

description: Sample name in processed data: C15CA

tag: duration of cd at crc diagnosis, years

value: II


title: [C12CA] Patient C12 carcinoma

description: Sample name in processed data: C12CA

tag: Sex

value: no


title: 2hr_H99 infected_batch2

description: Gene Expression Data

source_name: C. neoformans H99 infected BMDM, 2 hours, culture batch 2


title: 2hr_H99 infected_batch3

description: Gene Expression Data

source_name: C. neoformans H99 infected BMDM, 2 hours, culture batch 3


title: 14_Treg

city: 89 Beaumont ave

first: Dimitry

last: Krementsov

state: VT

address: 312C Rowell bldg, 106 Carrigan drive

department: BHSC

institute: University of Vermont

hyb_protocol: Affymetrix® GeneChip® Hybridization Oven 645 at 45° C and 60 RPM for 16.5 hours overnight. Arrays were stained using the Affymetrix® GeneChip® Fluidics Station 450.

scan_protocol: Scanned with the 7G Affymetrix® GeneChip® Scanner 3000.

data_processing:
Raw intensity CEL files were imported into Expression Console software (Affymetrix, USA), and CHP files were generated for gene-level analysis. CHP files were imported into Transcriptome Analysis Console software (Affymetrix, USA).
CHP files include log2 GC-RMA signals.

label: Biotin

source_name: spleen

label_protocol: Samples were then labeled with biotin using TdT (30U/µL), provided in the GeneChip® WT PLUS Reagent Kit.

growth_protocol: VitD high and low diet.

extract_protocol: RNeasy Qiagen mini kit.

treatment_protocol: Spleen cell isolation and sorting.

tag: cell type

value: CD4 Treg

tag: strain/background

value: PWD

value: Male

tag: diet

value: VitD low


title: 27_Treg


title: [C11INF] Patient C11 inflamed mucosa

description: Sample name in processed data: C11INF

source_name: inflamed mucosa

value: inflamed mucosa

tag: ajcc stage

value: III

source_name: normal reference DNA

value: Promega


title: 2hr_uninfected_batch2

description: Gene Expression Data

source_name: Uninfected (Control) BMDM, 2 hours, culture batch 2

value: Macrophages, bone marrow-derived

value: female

tag: strain

value: C57B/6 from Jackson Labs

tag: slide id (array batch)

tag: culture batch

tag: time


title: 29_Treg


title: [C12DYS] Patient C12 dysplasia

description: Sample name in processed data: C12DYS

source_name: dysplasia

tag: tissue

value: dysplasia

value: FFPE

tag: carcioma associated to fistula

tag: special histology

tag: microsatellite/hypermutation status


title: Class IV miRNA rep-3

city: Washington,DC

first: Nino

last: Gustavo

state: Washington,DC,

address: Sheikh Zayed Campus,111 Michigan Avenue,

department: Center for Precision Medicine and Genomics Research

institute: Childrens National Hospital

description:
raw files: 0_ are Hy3; 1_ are Hy5
The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile. 1000 ng total RNA from sample and control was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer. The Hy3™-labeled samples and a Hy5™-labeled control RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA Array version 11 Other Species (Exiqon, Denmark), which contains capture probes targeting all miRNAs for various species registered in the miRBASE version 16.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria). After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA). The probes were annotated according to miRBase 16. The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

hyb_protocol: The Hy3-labeled samples and a Hy5-labeled control RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA Array version 11 Other Species (Exiqon, Denmark), which contains capture probes targeting all miRNAs for various species registered in the miRBASE version 16.0 at the Sanger Institute.

organism: Drosophila melanogaster

source_name: Class IV Peripheral nervous system (PNS)

label_protocol: 1000 ng total RNA from sample(Class I, Class III and Class IV RNA) and control was labelled with Hy3 and Hy5 fluorescent label,respectively,using the miRCURY™ LNA Array power labelling kit (Exiqon, Denmark) following the procedure described by the manufacturer.

extract_protocol: The isolation and purification of Class I, Class III and Class IV da neurons was performed as previously described (Iyer et al., 2009). Briefly, 40-50 age-matched third instar larvae expressing mCD8::GFP under the control of the GAL80ppk.1.9; GAL4221 (CI), GAL80ppk.1.9, GAL4ppk,(CIII) or GAL4ppk.1.9 (CIV)  drivers were collected and washed several times in ddH20. The larvae were then rinsed in RNAse away, ddH20 and finally dissected. The tissue was then dissociated using a combination of enzymatic and mechanical perturbations to yield single cell suspensions which were filtered using a 30µm membrane. The filtrate is then incubated with superparamagnetic beads (Dynabeads MyOne Streptavidin T1, Invitrogen) coupled with biotinylated mouse anti-CD8a antibody (eBioscience) for 60 minutes. Finally the da neurons attached to the magnetic beads were then separated using a powerful magnetic field. The isolated neurons were washed at least five times with PBS to remove any potential non-specific cells and the quality and purity of isolated neurons was assessed under a stereo-fluorescent microscope equipped with phase contrast for examining the number of fluorescent vs. non-fluorescent cells. Only if the isolated cells were free of cellular debris and non-specific (i.e. non-fluorescing) contaminants were they retained. The purified CI and C-IV neuron populations were then lysed in miRCURY™ (Exiqon) RNA lysis buffer followed by storage at -80˚C.

treatment_protocol: Age-matched third larvae were used without any treatment.

tag: developemental stage

value: Third Instar Larvae

tag: strain background

value: Oregon-R

tag: genotype/variation

tag: tissue type

value: Dendritic arborization neuron of PNS

source_name: Whole Larvae


title: [C11CA] Patient C11 carcinoma

description: Sample name in processed data: C11CA

source_name: carcinoma

value: carcinoma

tag: sample preparation

tag: crc etiology

value: Crohn's disease

tag: age at crc diagnosis, years

tag: duration of cd at crc diagnosis, years

tag: Sex

value: mucinous, signet ring

value: microsatellite stable

tag: manufacturer


title: 48_Treg

tag: cell type

value: CD4 Treg

tag: strain/background

value: PWD

value: Male

tag: diet

value: VitD high


title: Class IV miRNA rep-2

scan_protocol: The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA).

data_processing: The probes were annotated according to miRBase 16. The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.


title: 28_Treg

value: VitD low


title: [C10CA] Patient C10 carcinoma

description: Sample name in processed data: C10CA

tag: tissue

tag: ajcc stage

value: II

value: yes

value: Promega


title: [C09CA] Patient C09 carcinoma

description: Sample name in processed data: C09CA

value: female

value: I

tag: carcioma associated to fistula

value: no

tag: special histology


title: 35_Treg


title: 31_Treg


title: [C08CA] Patient C08 carcinoma

description: Sample name in processed data: C08CA

value: FFPE

value: mucinous

tag: microsatellite/hypermutation status


title: 47_Treg


title: 18h_R-_1

source_name: inducible AP2-G overexpression line

value: Plasmodium berghei cells

tag: host

value: Female, outbred Theiler's Original (TO) mice

tag: rapamycin treated?

value: NO

tag: time (hours post induction)

tag: plasmodium strain

value: inducible AP2-G overexpression line


title: Class III miRNA rep-3

source_name: Class III Peripheral nervous system (PNS)

tag: developemental stage

value: Third Instar Larvae

tag: strain background

value: Oregon-R

tag: genotype/variation

value: GAL80ppk.1.9, GAL4ppk,UAS-mCD8::GFP

tag: tissue type

value: Dendritic arborization neuron of PNS


title: Class III miRNA rep-1


title: H1_EDECs

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol for PrimeView Human Gene Expression Array

data_processing: The data were normalized using RMA normalization from R/Bioconductor

source_name: endoderm derived epithelial cells (EDECs)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: H1 ESC were differentiated intohepatocyte like cells (HLCs) as described previously (Graffmann et al. 2016). To induce endoderm derived epithelial cells (EDEC) differentiation, hepatic endoderm cells were split and plated at a low density 25,000/cm² onto matrigel coated plates on day 9 of the differentiation.

extract_protocol: The RNA was extracted using TRIzol reagent (Thermo Fisher Scientific) and the manufactural protocol. The quality of the RNA was checked with a NanodropTM spectrophotometer (Thermo Scientific).

treatment_protocol: In order to dissect the role of Notch signalling for EDEC development, cells were treated with 100 nM y-secretase inhibitor 1 after splitting into low density

value: EDECs


title: Class I miRNA rep-3

source_name: Class I Peripheral nervous system (PNS)

value: GAL80ppk.1.9; GAL4221 ,UAS-mCD8::GFP


title: [C07CA] Patient C07 carcinoma

description: Sample name in processed data: C07CA

value: carcinoma

tag: sample preparation

tag: crc etiology

value: Crohn's disease

tag: age at crc diagnosis, years

tag: duration of cd at crc diagnosis, years

tag: Sex

value: microsatellite stable

tag: manufacturer


title: Class IV miRNA rep-1


title: H1_ESCs

source_name: human embryonic stem cells

tag: cell type

value: ESCs


title: 39_Treg

value: CD4 Treg

tag: strain/background

value: PWD

value: Female

tag: diet

value: VitD low


title: [C06LN] Patient C06 lymph node metastasis

description: Sample name in processed data: C06LN

source_name: lymph node metastasis

tag: tissue

value: lymph node metastasis

value: FFPE

value: male

tag: ajcc stage

value: IV

tag: carcioma associated to fistula

tag: special histology

tag: microsatellite/hypermutation status

value: Promega


title: Class I miRNA rep-2

tag: developemental stage

value: Third Instar Larvae

tag: strain background

value: Oregon-R


title: Class I miRNA rep-1

tag: genotype/variation

tag: tissue type

value: Dendritic arborization neuron of PNS


title: [C06CA] Patient C06 carcinoma

description: Sample name in processed data: C06CA

tag: sample preparation

tag: crc etiology

value: no

value: mucinous, signet ring