title: SW620 spheroid culture rep2 [mRNA]

city: Belvaux

first: Elisabeth

last: Letellier

address: 6, Avenue du Swing

department: Life Sciences Research Unit

country: Luxembourg

institute: University of Luxembourg

description: gene expression data from SW620 sphere culture

hyb_protocol: 3.5 ug of labeled DNA + hybridization controls are injected into Affymetrix cartridge. Incubate with rotation at 60 rpm for 16 hr at 45°C then arrays are washed and scanned

scan_protocol: Arrays were scanned with the Affymetrix® GeneChip® Scanner 3000 following the protocol: GeneChip® Expression Wash, Stain and Scan For Cartridge Arrays P/N 702731 Rev. 4

data_processing: The data were imported, normalized and summarized to transcript cluster level using Partek GS software. We used GC RMA method with quantile normalization.

source_name: colorectal cancer SW620 sphere culture

label_protocol: In this procedure, the purified, sense-strand cDNA is fragmented by uracil-DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE 1) at the unnatural dUTP residues and breaks the DNA strand. The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 μg of singlestranded cDNA is required for fragmentation and labeling

growth_protocol: Sphere cultures were maintained in serum-free medium containing growth factors

extract_protocol: Total RNA was extracted with Qiazol, using the miRNeasy extraction kit (Qiagen), following the user manual

tag: cell line

value: colorectal cancer

tag: vector

value: lymph node metastasis


title: SW480 spheroid culture rep2 [mRNA]

status: Public on Apr 12 2018

type: RNA

description: gene expression data from SW480 sphere culture

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: colorectal cancer SW480 sphere culture

tag: tissue

value: primary tumor


title: Nicotiana clevelandii Post secretory replicate 1

type: SRA

city: Duluth

first: Marshall

last: Hampton

state: MN

address: 1117 University Drive

country: USA

institute: University of Minnesota Duluth

library_source: transcriptomic

data_processing:
Contigs assembled with Trinity v.2.3
Reads aligned to contigs using NCBI blastn
Contigs mapped to Nicotiana tabacum mRNA, and secondarily to Arabidopsis thaliana.  Read counts for mapped contigs were tested for differential expression between stages using DESeq in R.
Supplementary_files_format_and_content: Nicotiana_Means_SDs_DEb.xls: Mean contig read counts, differential expression test results, and associations by similarity to Arabidopsis thaliana genes

organism: Nicotiana clevelandii

source_name: Nectary tissue

extract_protocol:
Six species of tobacco (Nicotiana rustica  [PI-34752; Accession TR-16]; Nicotiana glauca [PI-282690; Accession TW-54]; Nicotiana benthamiana [PI-555684; Accession TW-17]; Nicotiana clevelandii [PI-555490; Accession TW-31]; Nicotiana plumbaginifolia [PI-302476; Accession TW-107]; Nicotiana bonariensis [PI-555489; Accession TW-28]) seeds were obtained from Tobacco Germplasm Collection North Carolina State University Oxford NC 27565 (https://npgsweb.ars-grin.gov/).  These seeds were initially sewn in a single 24-cm pot of Sungro professional growing mix at high density.  After approximately 20 days, the seedlings reached ~15 cm tall. Subsequently individual plants were transplanted to separate 30-cm pots of Sungro mix.  The plants were grown to maturity under 16 h day/ 8 h night conditions until flowering.  Flowers were staged as described in Koltunow, et al., [Plant Cell 2(12): 1201-1224(1990)].  RNA samples were isolated from floral nectaries at floral stages:  Stage 6 [immature; beginning of metabolic switch]; Stage 9 [immature; pre-secretory], Stage 12 [mature flowers at anthesis] and Stage PF [post-fertilization].  All nectary tissues were manually dissected by hand with the RNA being immediately extracted by mechanical disruption with a microcentrifuge pestle and using an RNAqueous® RNA isolation kit (Ambion, Austin, TX) with Plant RNA Isolation Aid (Ambion, Austin, TX). Agarose gel electrophoresis and UV spectrophotometry were used to assess RNA quality for all samples prior to submission to the University of Minnesota Genomics Center for mRNA isolation, barcoded library creation and Illumina HiSeq 2500 sequencing. Seventy-five TruSeq RNA v2 libraries were created (triplicate samples for nectaries at four timepoints each from six independent species, plus 3 control libraries from Nicotiana plumbaginifolia (leaves, ovaries, and stems) and sequenced via 50 bp, paired-end runs on the HiSeq 2500 using Rapid chemistry. All libraries were pooled and sequenced across two full lanes. This generated 200 M reads for each lane and the average quality scores were above Q30.
Illumina’s Truseq RNA Preparation v2 kit (RS-122-2001)

value: nectary

tag: developmental stage

value: Post secretory


title: SW620 spheroid culture rep3 [mRNA]


title: donor liver sample 2 post-reperfusion in conventional liver transplantation

city: Guangzhou

first: Xiaoshun

last: He

address: NO.58 Zhongshan Er Road

department: Organ Transplant Center

country: China

institute: The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Liver

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

tag: sample type


title: SW480 spheroid culture rep3 [mRNA]


title: Nicotiana clevelandii Stage 12 replicate 3

value: stage 12


title: Nicotiana clevelandii Stage 12 replicate 2


title: Nicotiana clevelandii Stage 9 replicate 3

value: stage 9


title: SW620 spheroid culture rep1 [mRNA]


title: H9 HD D2 bicarb

city: Taipa

first: Guokai

last: Chen

address: University of Macau E12-3060

department: Faculty of Health Sciences

country: Macau

institute: University of Macau

hyb_protocol: cRNA was hybridized onto HumanHT-12 v4 Expression BeadChip (Illumina) using standerd protocol.

scan_protocol: BeadChips were scanned with the iScanner (Illumina).

data_processing:
Data was normalized by quantile normalization.
www.arrayanalysis.org computed the normalized signal intensity.

source_name: Human embryonic stem cell H9

label_protocol: RNA was converted to cRNA using the TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip (Epibio).

growth_protocol: Human ESCs (H9) were maintained in E8 medium on matrigel-coated plates with daily medium change. Cell culture of <70% confluence is designated as low density, and >90% confluence as high density.

extract_protocol: Toatal RNA was isolated by Qiagen Rneasy kit.

treatment_protocol: Control (ctrl): normal E8 medium. Sodium bicarbonate (bicarb) treatment: E8 medium supplemented with 20mM additional soidum bicarbonate.


title: H9 HD D2 ctrl


title: H9 LD D2 ctrl


title: Patient with AF-VHD 2

city: Chengdu

first: nini

last: rao

state: Sichuan

address: No.4, Section 2, North Jianshe Road

institute: University of Electronic Science and Technology of China

description: lncRNA and mRNA expression in human with AF-VHD

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: atrial appendage tissues of patients with AF-VHD

label_protocol: each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Right atrial (RA) appendage was removed from patients undergoing mitral valve surgery (VHD patients). tissue removed at surgery was placed immediately in ice-cold saline. Surgically removed tissues were treated with RNAl- ater (Invitrogen) within 10 min of excision. RNA later was removed after overnight treatment, and the samples were stored at -80°C.

extract_protocol: mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

value: atrial appendage


title: Nicotiana clevelandii Stage 9 replicate 2


title: Patient with AF-VHD 5


title: Patient with AF-VHD 4


title: H9 LD D2 bicarb


title: (6-4)PP_XR-seq_20M_rep2

city: Athens

first: Wentao

last: Li

state: GA

address: 500 D. W Brooks Drive

department: Environmental Health Science

institute: University of Georgia

library_source: genomic

data_processing:
Library strategy: XR-Seq
adaptor trimming
filtering reads based on length
alignment
strand separation
gene coverage count
Genome_build: sacCer3

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Yeast cells were cultured in YPD (1% yeast extract, 2% peptone and 2% dextrose) medium at 30°C in a shaking incubator at 250 rpm.chamber.

extract_protocol:
To isolate the excised oligomers carrying UV photoproducts in vivo, we first tested 3 different strategies to disrupt yeast cell walls and lyse cell membranes: 1) Cells were pelleted and resuspended in 300 µL STES (500 mM NaCl, 200mM Tris-Cl, 10 mM EDTA and 0.1% SDS), 300 µL phenol:chloroform:isoamyl alcohol (25:24:1) and 600 µL acid washed glass beads. 2) The same as the aforementioned method except STET (500 mM NaCl, 200mM Tris-Cl, 10 mM EDTA and 1% Triton X-100) was used instead of STES. 3) Cells were pelleted and resuspended in 600 µL TEP (150 mM Tris-Cl, 30 mM EDTA and 10 µL Proteinase K) and 600 µL acid washed glass beads. All the resuspension were bead beat on a Mini-Beadbeater-16 (Bio Spec) for 2.5 min at 4°C. For samples containing STES or STET buffer, the cell lysates were then centrifuged, and the supernatants were sequentially treated with 5 µL RNase A at 37°C for 1 h and 5 µL Proteinase K at 55°C for 1 h. Samples were then extracted with phenol:chloroform:isoamyl alcohol (25:24:1) and precipitated with ethanol. The precipitated small DNA molecules were further purified by a G-50 filtration column (GE Healthcare) and subjected to immunoprecipitation with anti-(6-4)PP antibody as described previously. For samples containing TEP buffer, 66 µL 10% SDS was mixed with the disrupted cells, and 165 µL 5M NaCl was mixed in after incubation at room temperature for 10 min. Following overnight incubation at 4°C, the supernatant fraction was separated by centrifugation, incubated with 10 µl RNase A at 37°C for 1 h and then 5 µl proteinase K at 55°C for 30 min. The excised oligomers were then sequentially purified by phenol-chloroform extraction, ethanol precipitation, G-50 column filtration and DNA damage immunoprecipitation. This latter approach approximates the Hirt lysis method used previously. For direct excision assay, the excised oligomers isolated by any of the three different methods were 3’ end labeled with 32P-Cordycepin and resolved in 11% denaturing sequencing gel. The results indicate that the strategy of cell wall disruption followed by Hirt extraction efficiently isolates the excised oligomers.
Excised oligomers, purified by the G-50 column filtration followed by anti-CPD or anti-(6-4)PP antibody immunoprecipitation, were ligated to adaptors as described previously. The ligated products were then subjected to a second round of DNA damage-specific immunoprecipitation. The CPDs and (6-4)PPs were then repaired by photoreactivation using CPD photolyase or (6-4)PP photolyase as described. One percent of the unrepaired and repaired ligation products were used in sets of PCR amplification reactions to determine the minimum number of PCR cycles needed for the final XR-seq library preparation. The number of PCR cycles used for CPD XR-seq and (6-4)PP XR-seq in this study ranged from 12 to 14. Libraries were gel-purified, pooled and sequenced using the Illumina Hiseq 2500 platform.

treatment_protocol: Yeast cells were grown to late log phase (OD600 ~1.0), washed twice with ice-cold ddH2O, resuspended in 2% dextrose and irradiated in ice-cold 150mm tissue culture dishes with 120 J/m2 of UV (254 nm). Following irradiation, one-tenth volume of a stock solution (10% yeast extract, 20% peptone) was immediately added to the cells, which were then incubated at 30°C in the dark to allow excision repair. At different times of the repair incubation (5 min, 20 min and 1 h), 10 mL aliquots were rapidly cooled in ice water to stop repair and then processed for excision assay and XR-seq.

tag: repair incubation time

value: 20 minutes

tag: antibody

tag: cell type

value: wild type

tag: strain

value: MATalpha, ura3-52, his3-1, leu2-3, leu2-112, cir0


title: Nicotiana clevelandii Stage 9 replicate 1


title: Patient with VHD 3

description: lncRNA and mRNA expression in human with VHD

source_name: atrial appendage tissues of patients with SR-VHD


title: SW480 spheroid culture rep1 [mRNA]


title: Nicotiana clevelandii Stage 6 replicate 3

value: stage 6


title: Nicotiana clevelandii Stage 12 replicate 1


title: MouseCortex_Barcoded_CG & CH_K00145_Run2

city: Portland

first: Ryan

middle: M

last: Mulqueen

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Molecular and Medical Genetics

institute: Oregon Health and Science

description:
MouseCortex_Barcoded_CG.bed.gz
MouseCortex_Barcoded_CH.bed.gz
The index read is 31 bp long and contains the cell barcode sequence.

data_processing:
Reads were processed using bcl2fastq (Illumina Inc., v2.19.0) with the “--create-fastq-for-index-reads” and “--with-failed-reads” options to produce fastq files.
Fastq reads were then identified by indexes, requiring each index (the two 10-nt indexes introduced by PCR, and the 11-nt index introduced by tagmentation) to independently be within a Hamming distance of two from the expected reference sequences.  Reads with all three indexes assigned  had the respective reference index sequences concatenated to a barcode and appended to the  read name, which served as the cell identifier.
Reads were then trimmed using TrimGalore! (v0.4.0) with option “-a AGATCGGAAGAGC” to identify adapters.
Alignment to the human (GRCh37), or mouse (GRCm38) genome was performed with Bismark (v0.14.3) using “--bowtie2” and “--unmapped” options
Aligned reads were then de-duplicated based on barcode, chromosome, and starting position.
Methylation information was extracted using bismark_methylation_extractor command with "--merge_non_CpG" option from Bismark (v0.14.3)
Genome_build: For Homo sapiens organism experiment: GRCh37. For Mus musculus organism experiment: GRCm38
Supplementary_files_format_and_content: Tab-delimited bed files. For "HumanCellLineSplit_Barcoded_CG" fields are:<Chromosome><Start><End><Barcode><Percent Methylation><Count Methylated><Count Non-methylated> <Cell-Specific Barcode> <Library Preparation Condition> <Tn5 Tracked Condition>. For "MouseCortex_Barcoded" files: <Chromosome> <Start> <End> <Count Methylated> <Count Non-Methylated> <Cell-Specific Barcode> <Mouse Sampled>.
Supplementary_files_format_and_content: The tar archive contains supplemental files including code to split read by index, cell barcode information provided in the barcodes*txt files and a README file with further explanation.

organism: Mus musculus

source_name: Sixty-day old mouse cortices

growth_protocol: All animal studies were approved by the Oregon Health and Science University Institutional Animal Care and Use Committee. C57BL/6J mice were obtained from Jackson Laboratory (stock number 000664). Sixty-day-old C57BL/6J mice were deeply anesthetized using isoflurane. After decapitation the brain was removed and the entire cortex isolated and placed in ice cold PBS.

extract_protocol:
Sample preparation and nuclei isolation. For library preparation, cells were pelleted if cultured in suspension, or trypsinzed (Gibco, Cat. 25200056), if adherent. Cell were washed once with ice cold PBS and carried through cross-linking (for the xSDS method) or directly into nuclei preparation using nuclei isolation buffer (NIB, 10mM TrisHCl pH 7.4, 10 mM NaCl, 3mM MgCl2, 0.1% Igepal, 1X protease inhibitors (Roche, Cat. 1187358001)).  Cortical samples were cut with a sterile razor blade and resuspended in a chilled 5mL modified nuclei isolation buffer (NIB-HEPES, 20mM HEPES, 10mM NaCl, 3mM MgCl2, 0.1% Igepal, 1X protease inhibitors). Cells were given 5 minutes to equilibrate to the salt solution before 5 loose strokes in a dounce homogenize, another 5 minutes to equilibrate, another 5 loose strokes and 10 tight strokes. Nuclei were then spun in a pre-chilled 4C centrifuge for 5 minutes at 600xg.
Cross-linking and SDS nucleosome depletion (xSDS): Cells were cross-linked by incubation in 10 mL of media with 1.5% formaldehyde (final conc. by vol.) and incubated at room temperature for 10 minutes with gentle agitation. Cross-linking was quenched with 800 uL 2.5 M glycine and incubated on ice for 5 minutes. Cells were then spun down, washed with ice-cold PBS, and resuspended in ice cold NIB for a 20 minute incubation on ice with gentle agitation. Cells were then pelleted, washed with 900 uL of 1X NEBuffer 2.1m and resuspended in 800 uL 1X NEBuffer 2.1 with 0.3% SDS (Sigma, Cat. L3771) and incubated at 42 ˚C with vigorous shaking for 30 minutes in a thermomixer (Eppendorf). 200 uL of 10% Triton-X was added to quench, and the solution was incubated at for another 30 minutes at 42 ˚C with vigorous shaking. Nuclei were then taken into the combinatorial indexing protocol.
Combinatorial indexing via tagmentation: Nuclei were stained with 8uL of 5mg/mL DAPI (Thermo Fisher, Cat. D1306) and passed through a 35-um cell strainer. A 96-well plate was prepared with 10 uL of 1X TD buffer diluted with NIB in each well. Fluorescence-assisted nuclei sorting (FANS) was performed with a Sony SH800 flow sorter to sort 2,500 single nuclei into each well in fast sort mode (Supplementary Fig. 24). 4uL of 500 nM transposome, pre-loaded with cytosine-depleted, uniquely indexed, custom oligonucleotides were placed in each well (described in supplement, transposomes assembled as described in Amini et. al. 2014. Reactions were incubated at 55˚C for 20 minutes. All wells were then pooled and stained with DAPI as done for the first FANS sort. A second 96-well plate was prepared with each well containing digestion reagents as described by the manufacturer’s protocol for the EZ-96 DNA Methylation MagPrep Kit (Zymo, Cat. D5040) at one-fifth the volumes (for 5 uL per well). 22 post-tagmentation nuclei from the pool of all reactions were sorted into each well using the single-cell sorting setting. Some wells were selected to receive only 10 nuclei, to allow for unmethylated controls. The plate was then spun down at 600 x g for 5 minutes at 4˚C. Library preparation. Prior to bisulfite conversion, several wells, which only received 10 nuclei in the final sort, were spiked with ~35 pg of the prepared unmethylated control DNA, to keep DNA mass constant per well. Nuclei were then processed following manufacturer’s protocol for the EZ-96 DNA Methylation MagPrep Kit, with volumes reduced to one-fifth those described by the manufacturer to allow for single-well reaction processing, and other slight modifications. Following the final post-bisulfite library cleanup, each well was eluted in 25 uL of Zymo M-Elution Buffer and transferred to a well in a 96-well plate prepared with the following reaction mixture for linear amplification: 16 uL PCR-clean ddH2O, 5 uL 10X NEBuffer 2.1 (NEB, Cat. B7202), 2 uL 10 mM dNTP mix (NEB, Cat. N0447), and 2 uL of 10 uM random nonamer primer with a partial sequence of the Illumina Standard Read 2 sequencing primer (9NP, 3’-NNNNNNNNNAGATCGGAAGAGCACACGTCTG-5’). To render libraries single stranded prior to linear amplification, reactions were heat shocked at 95˚C for 45 seconds and then flash cooled on ice. Following cooling, 10 U Klenow (3’->5’ exo-) polymerase (Enzymatics, Cat. P7010-LC-L), was added to each reaction and followed by incubation at 4 ˚C for 5 minutes, then a slow ramp of +1 ˚C/15 seconds, and 37 ˚C for 90 minutes. This was repeated for 2-4 times dependent on library and in accordance with previously describe scWGBS protocols (Supplementary Fig. 1). For each repetition, 1 uL 10 uM 9NP, 1 uL 10 mM dNTP mix, 1.25 4X NEBuffer 2.1, and 10 U Klenow (3’ -> 5’ exo-) polymerase was added after the heat shock and cooling. Following completion of linear amplifications, wells were cleaned with 1.1X (by volume) of 18% PEG SPRI Bead mixture (Sera-Mag SpeedBeads (GE, Cat. 65152105050250) washed and resuspended in 18% PEG 8000 (by mass), 1M NaCl, 10mMTris-HCl, pH 8.0, 1mM EDTA, 0.05% Tween-20), with a 5 minute room temperature incubation, then placed on a magnetic rack until the supernatant was cleared. The supernatant was discarded, and beads were washed with 80% ethanol while held in place by the magnets. Beads were then dried and libraries were eluted in 21 uL 10 mM Tris-Cl (pH 8.5). The full 21 uL eluate was then placed into a 96-well plate prepared with a PCR reaction mixture containing 25 uL 2X KAPA HiFi HotStart ReadyMix (Kapa, Cat. KK2602), 2 uL of 10 uM forward and reverse uniquely indexed primers (each introducing a 10-nt indexing sequence), and 0.5 uL of 100X SYBR Green I (FMC BioProducts, Cat. FC-121-1031). Real time PCR was performed on a Bio-Rad CFX thermocycler with the following conditions: 95°C for 2 minutes, (94°C for 80 seconds, 65°C for 30 seconds, 72°C for 30 seconds [Image]) for 18-22 cycles. PCR was stopped once libraries reached the inflection point of measured SYBR green fluorescence. Following PCR, libraries were then pooled by column (10 uL/well) and with 0.8X (by volume) 18% PEG SPRI Bead Mixture as described previously. Libraries were eluted off the magnetic beads in 25 uL of 10 mM Tris-Cl (pH 8.5). A detailed step-by-step protocol can be found as a Supplementary Protocol document associated with this manuscript.

tag: experiment

value: Mouse Cortex

value: cortex

tag: barcoded cell count

tag: dinucleotide

value: CG & CH


title: Patient with VHD 1


title: MouseCortex_Barcoded_CG & CH_K00145_Run1


title: Patient with AF-VHD 3


title: (6-4)PP_XR-seq_20M_rep1


title: Patient with VHD 4


title: Nicotiana glauca Post secretory replicate 3

organism: Nicotiana glauca


title: Nicotiana clevelandii Stage 6 replicate 2


title: Nicotiana clevelandii Stage 6 replicate 1


title: (6-4)PP_XR-seq_5M_rep1

value: 5 minutes


title: Nicotiana glauca Post secretory replicate 1


title: Patient with VHD 5


title: Patient with AF-VHD 1


title: Nicotiana glauca Post secretory replicate 2


title: (6-4)PP_XR-seq_5M_rep2


title: Nicotiana plumbaginifolia Sepal replicate 2

organism: Nicotiana plumbaginifolia

source_name: Sepal tissue

value: sepal


title: Nicotiana plumbaginifolia Sepal replicate 3


title: Nicotiana glauca Stage 12 replicate 3


title: CPD_XR-seq_1H_rep2

value: 1 hour

value: anti-CPD


title: Patient with VHD 2


title: Nicotiana glauca Stage 12 replicate 2


title: SW620 spheroid culture rep3 [miRNA]

description: miRNA expression data from SW620 sphere culture

hyb_protocol: Labeling reaction was checked by an Elosa QC Assay before performing hybridization. GeneChip Eukaryotic Poly-A RNA Controls and Control Oligonucleotide B2 (Affymetrix, High Wycombe, United Kingdom) were added to the hybridization mix. 130µl of the hybridization cocktail were injected onto the arrays.

scan_protocol: Arrays were incubated at 48°C, 60 rpm for 16 hours. Then arrays were stained and washed with the GeneChip® Hybridization Wash and Stain kit (Affymetrix, High Wycombe, United Kingdom) using the Fluidic script FS450_0002. GeneChip® miRNA Array v4.0 st (Affymetrix, High Wycombe, United Kingdom) were performed according to manufacturer’s user guide FlashTag™ Biotin HSR RNA  Labeling Kit For Affymetrix® GeneChip® miRNA Arrays P/N 703095 Rev3

label_protocol: 300ng of total RNA were subjected to a Poly (A) tailing with a PAP Enzyme, a Biotin Labeling was performed with a T4 DNA Ligase using the FlashTagTM Biotin RNA Labeling kit (Affymetrix, High Wycombe, United Kingdom).

value: colorectal cancer

value: lymph node metastasis


title: CPD_XR-seq_20M_rep2


title: CPD_XR-seq_1H_rep1


title: Nicotiana plumbaginifolia Sepal  replicate 1


title: Nicotiana glauca Stage 12 replicate 1

value: nectary


title: Nicotiana plumbaginifolia Ovary replicate 3

source_name: Ovary tissue

value: ovary


title: SW620 spheroid culture rep2 [miRNA]


title: CPD_XR-seq_20M_rep1


title: CPD_XR-seq_5M_rep2


title: Nicotiana glauca Stage 9 replicate 3

value: stage 9


title: Nicotiana plumbaginifolia Ovary replicate 2


title: Nicotiana glauca Stage 9 replicate 1


title: Nicotiana plumbaginifolia Leaf replicate 3

source_name: Leaf tissue

value: leaf


title: Nicotiana glauca Stage 6 replicate 3


title: Nicotiana plumbaginifolia Ovary replicate 1


title: CPD_XR-seq_5M_rep1


title: Nicotiana glauca Stage 9 replicate 2


title: Nicotiana plumbaginifolia Leaf replicate 2


title: Nicotiana bonariensis Post secretory replicate 3

organism: Nicotiana bonariensis

value: Post secretory


title: Nicotiana bonariensis Post secretory replicate 2


title: Nicotiana bonariensis Post secretory replicate 1


title: Nicotiana glauca Stage 6 replicate 2


title: SW480 spheroid culture rep2 [miRNA]

description: miRNA expression data from SW480 sphere culture

value: primary tumor


title: Nicotiana plumbaginifolia Leaf replicate 1


title: SW620 spheroid culture rep1 [miRNA]


title: Nicotiana plumbaginifolia Post secretory replicate 3


title: Nicotiana rustica Post secretory replicate 3

organism: Nicotiana rustica


title: Nicotiana glauca Stage 6 replicate 1


title: Nicotiana bonariensis Stage 12 replicate 3

value: stage 12


title: SW480 spheroid culture rep1 [miRNA]


title: Nicotiana bonariensis Stage 12 replicate 2


title: SW480 spheroid culture rep3 [miRNA]


title: Nicotiana plumbaginifolia Post secretory replicate 2


title: Nicotiana rustica Post secretory replicate 2


title: Nicotiana bonariensis Stage 12 replicate 1


title: Nicotiana plumbaginifolia Post secretory replicate 1


title: Nicotiana rustica Post secretory replicate 1


title: Nicotiana bonariensis Stage 9 replicate 3


title: Nicotiana plumbaginifolia Stage 12 replicate 3


title: Nicotiana plumbaginifolia Stage 12 replicate 2


title: Nicotiana rustica Stage 12 replicate 3


title: Nicotiana rustica Stage 9 replicate 3


title: Nicotiana bonariensis Stage 6 replicate 2

value: stage 6


title: Nicotiana plumbaginifolia Stage 9 replicate 3


title: Nicotiana rustica Stage 12 replicate 1


title: Nicotiana bonariensis Stage 9 replicate 1


title: Nicotiana rustica Stage 12 replicate 2


title: Nicotiana plumbaginifolia Stage 12 replicate 1


title: Nicotiana rustica Stage 9 replicate 2


title: Nicotiana plumbaginifolia Stage 9 replicate 2


title: Nicotiana bonariensis Stage 6 replicate 1


title: Nicotiana plumbaginifolia Stage 6 replicate 3


title: Nicotiana rustica Stage 6 replicate 3


title: Nicotiana plumbaginifolia Stage 6 replicate 2


title: Nicotiana plumbaginifolia Stage 9 replicate 1


title: Nicotiana bonariensis Stage 9 replicate 2


title: Transcriptomes of Pleurotus ostreatus young fruit body

city: Wuhan

first: Danyun

last: Xu

address: No. 1, Shizishan Street

institute: Huazhong Agricultural University

description:
Yfb
processed data file: FPKM.txt

data_processing:
Raw Sequence Data: Image data output from sequencing machine is transformed by base calling into sequence data, which is called raw data or raw reads and stored in fastq format.
Clean reads: Dirty raw reads are discarded, including reads with adaptors, reads with unknown nucleotides larger than 5%, low quality reads (the rate of reads which quality value <= 10 is more than 20%), and then got the clean reads.
Assembly: Transcriptome de novo assembly was carried out with short reads assembling program - Trinity. The result sequences called Unigenes.
Then the Unigenes are taken into further process of sequence splicing and redundancy removing with sequence clustering software to acquire non-redundant Unigenes as long as possible.
In the final step, blastx alignment (evalue < 0.00001) between Unigenes and protein databases like NR, Swiss-Prot, KEGG and COG is performed, and the best aligning results are used to decide sequence direction of Unigenes. When a Unigene happens to be unaligned to the above databases, a software named ESTScan will be introduced to decide its sequence direction.
Genome_build: All-Unigene.fa (de novo)
Supplementary_files_format_and_content: FPKM.txt: Tab-delimited text file includes FPKM values for each Sample.

organism: Pleurotus ostreatus

source_name: young fruit body

extract_protocol:
Sample were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina HiSeq2000 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

tag: genotype/variation

value: wild type

value: young fruit body


title: Transcriptomes of Pleurotus ostreatus primordium

description:
Pri
processed data file: FPKM.txt

source_name: primordium

value: primordium


title: Nicotiana rustica Stage 6 replicate 1


title: Nicotiana rustica Stage 6 replicate 2


title: Nicotiana plumbaginifolia Stage 6 replicate 1


title: Nicotiana bonariensis Stage 6 replicate 3


title: Transcriptomes of Pleurotus ostreatus mature fruit body

description:
Mfb
processed data file: FPKM.txt

source_name: mature fruit body

value: mature fruit body


title: Transcriptomes of Pleurotus ostreatus mycelium

description:
Myc
processed data file: FPKM.txt

source_name: mycelium

value: mycelium


title: Nicotiana rustica Stage 9 replicate 1


title: Pf-3D7-t15, ATACseq, replicate2

status: Public on Apr 11 2018

city: Nijmegen

first: Christa

last: Toenhake

state: Netherlands

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

data_processing:
For dirRNAseq: libraries were sequenced on a NextSeq 500 system to obtain 75bp single-end reads (TruSeq SR Cluster Kit v2) according to standard protocols of the manufacturer (Illumina). Single-end reads were mapped against the annotated P. falciparum 3D7 transcriptome from PlasmoDB release 26 using BWA samse (version 0.7.12-r1039). Single-end reads were filtered to mapping quality >= 15 (samtools version 1.2) and only uniquely mapped reads (between 9.2 and 11.6 million per library) were used for further analysis. To visualize RNA-seq data in the UCSC Genome browser, 75bp reads were additionally mapped against the annotated P. falciparum 3D7 genome from PlasmoDB version 26, filtered for uniquely mapped reads and mapping quality >= 15. Reads were separated according to the strand they mapped to (sense strand FLAG16, antisense strand FLAG0) and normalized to the number of mapped reads per million (RPM). Bedgraph files were generated (bedtools v2.20.1) and visualized in the UCSC genome browser.
The ATAC-seq libraries were sequenced for 75 bp, paired-end on a NextSeq500 system (Illumina) using NextSeq500/550 HighOutput kit V2 (75 cycles) reagents (Illumina). Raw fastq reads were first evaluated using FastQC before continuing ((Andrew, 2010) and reads obtained from the two gDNA control libraries were combined after sequencing. Paired-end libraries were mapped with BWA-mem (version 0.7.10; (Li, 2013)) against the P. falciparum 3D7 reference genome (PlasmoDB release 26; (Aurrecoechea et al., 2009; Logan-Klumpler et al., 2012)) and filtered for mapping quality >= 30 ((samtools version 1.3.1; (Li et al., 2009)). Duplicate reads were removed using Picard tools (version 1.139; (BroadInstitute)) and reads mapping to the apicoplast and mitochondrial DNA were removed as well as supplementary alignments (FLAG 2048). Finally, an in silico size selection was performed to select for read pairs with insert sizes between 50 and 150 bp (or different when indicated) and these libraries were used for further analysis (between 5.9M-9.7M reads for replicate 1; between 3.6M-6.4M per library for replicate 2; and 36.9M for the merged gDNA control library). For visualization, these libraries were converted to bedgraph files using bedtools genomecov (version 2.20.1; (Quinlan and Hall, 2010)) with the option "-pc" for paired end data and scaled per million reads (RPM). Alternatively, for genomic DNA-corrected tracks, the coverage in each of the t05 to t40 libraries (with an offset of +0.1) was divided by the coverage in the merged gDNA library (with an offset of +0.1). Bedgraph files were visualized in the UCSC genome browser (Kent et al., 2002).
ATAC-seq mapping and generation of tracks *ATAC-seq_50-150_gDNAcorr.bedGraph.gz:(01) mapping with bwa mem agains PlasmoDB release 26 of Pfalciparum 3D7 genome (02) filter for mapq => 30 with samtools view (03) remove duplicates with "picard-tools-1.139/picard.jar MarkDuplicates" with settings REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=STRICT QUIET=true (04) remove supplementary alignments (-F 2048) and select reads mapping to chromosomes using samtools view (05) manually select reads between 150 and 50 bp using awk (06) generate bedgraph file scaled per million reads using bedtools genomeCoverage with options -bga -pc -scale xx (07) generate one file with per-million-reads-coverage of ATAC library and gDNA control library using "bedtools unionbedg" with options -g $genome_noMito_NoApi -filler (08) manually calculate ratio of ATAC library over gDNA control library coverage with offset of 0.1 using awk
For MACS2 peak calling on ATAC-seq data: Step (01) till (05) of generation of *ATAC-seq_50-150_gDNAcorr.bedGraph.gz tracks, followed by:(09) manually split bam file in increments of 5bp insertsizes from 5<=50 till 145<=150 using "awk" (10) shift reads with in-house script in each sub-bamfile with +4 bp for reads aligning to plus strand and -5bp for those aligning to the minus strand (11) for every sub-bamfile generate pileup file using "macs2-2.7 pileup" with options -f BAM and --extsize [half of the original mean insert size of sub file] (12) sum coverage in from all sub-bamfiles using "bedtools unionbedg" and "awk" (13) manually scale coverage to 1M reads using "awk" (14) add offset of 0.1 to every positiong in per-million-coverage using "awk" (15) use "bdgcmp" with pe-million-coverage in gDNA control track as control (-c) and -qpois (16) call peaks using "macs2 bdgpeakcall" on output from (15) with options -c 3.0 -g 150 -l 100
Genome_build: Plasmodium falciparum 3D7 PlasmoDB release 26
Supplementary_files_format_and_content: *ATACseq_50-150_gDNAcorr.bedGraph.gz: coverage of filtered, 50-150 bp insert size ATAC-seq libraries that were prepared as replicate 1, corrected for coverage in gDNA.
Supplementary_files_format_and_content: *ATACseq_rep2_50-150_gDNAcorr.bedGraph.gz: coverage of filtered, 50-150 bp insert size ATAC-seq libraries that were prepared as replicate 2, corrected for coverage in gDNA.
Supplementary_files_format_and_content: *[alltp|tp]*peaks.bed: genomic locations of peaks for specific time point or merged over time points ("alltps"), called using MACS2 subcommand on 50-150 bp insert size, shifted ATAC-seq libraries with gDNA as control.
Supplementary_files_format_and_content: *[alltp|tp]*summits.bed: genomic locations of peak summits for specific time point or the highest scoring peak summit for merged time points, called using MACS2 subcommand on 50-150 bp insert size, shifted ATAC-seq libraries with gDNA as control.
Supplementary_files_format_and_content: *.minus_strand_bedGraph.gz: RNA-seq coverage for minus strand normalized to complete (plus and minus) library after filtering.
Supplementary_files_format_and_content: *.plus_strand_bedGraph.gz: RNA-seq coverage for plus strand normalized to complete (plus and minus) library after filtering.

organism: Plasmodium falciparum

source_name: red blood cell stage, 7-15 hours post invasion

growth_protocol: 3D7 Plasmodium falciparum blood-stage parasites obtained from the Swiss Tropical and Public Health Institute (Basel, Switzerland - a kind gift from Dr. T. Voss) were cultured RPMI medium supplemented with 10% human serum, 0.2% NaHCO3 and 2.5% human O+ red blood cells. Cultures were selected for var2csa expression (Fraschka et al., 2016) and expanded and synchronized with multiple rounds of sorbitol treatments. After a final Percoll gradient centrifugation human red blood cells,  pre-filtered twice over sterile PlasmoPure (EuroProxima) filters to remove human white blood cells, were added  1.5 h later  to prevent “premature” invasion and therefore ensure better synchronicity of the culture.  The time of adding blood was set as time point zero (0 hours post invasion (hpi)) and this procedure resulted in a synchronicity window of 7 h (i.e. 7h difference between the first and last invasion) for >90% of parasites. Medium was changed every ten hours but not less than ten hours before collection. Cultures were mixed with every medium change and after 20 hpi kept at 1.25% hmt.  Native nuclei (for ATAC-Seq) and RNA (for dirRNA-Seq) were collected every 5 hours.

extract_protocol:
Native nuclei and RNA were collected from the pooled culture flasks of the same batch of synchronized parasites for each time point to ensure complete matching between ATAC-seq and dirRNA-seq.
ATAC-seq: Native parasite nuclei were isolated as in (Bartfai et al., 2010). In short, after lysis of RBCs by 0.05% saponin treatment and separating nuclei from parasite debris using a cell lysis buffer (CLB: 10 mM Tris-HCL pH8.0, 10 mM NaCl, 3 mM MgCl2, 0.2% NP-40) with 0.25 M sucrose cushion. A 10 u sized nuclei pellet was resuspended with a cut-off pipet tip in 337.5 u CLB and for ATAC-seq replicate 1 69 u of nuclei was used for t05 to t20 and 23 u of nuclei was used for t25 to t40 (these volumes were based on previous tests using a dilution series of nuclei). For ATAC-seq replicate 2 we had to optimize the amount of nuclei again due to the use of a kit from a different lot and this led us to use 466 u of nuclei for t05 and t10 and 155 u for t15 and t20. Nuclei were brought to 10.5 u in CLB and used in a 25 u ATAC reaction based on (Lara-Astiaso et al., 2014) with 2 u Tn5 transposase and 12.5 u TD buffer (Nextera DNA Library Prep Kit, #FC-121-1030, Illumina, USA). Reactions were incubated for 1 h in a 37Ã¢â‚¬â€°°C heat block. Nuclei were kept in suspension by gently tapping the tube every 10 minutes. The reaction was stopped by addition of 5 u clean up buffer (900 mM NaCl, 300 mM EDTA), 2 u 5% SDS and 2 u proteinase K (Sigma-Aldrich #P6556) and incubated for 30 min at 40C. Tagmentated DNA fragments were isolated using 2.4 sample volume of Agencourt AMPure XP beads (Beckman Coulter, #A63882, Inc. USA).
RNA isolation: Parasite cultures were immediately placed on ice and washed once with ice-cold PBS. Pelleted cultures were resuspended in RLT buffer (Qiagen, #74106) supplemented with 1% ÃŽÂ²-mercaptoethanol and snap-frozen in liquid nitrogen. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, #74106; including RNA clean-up and two on-column DNase treatments) and PolyA-selected using the Oligotex mRNA Mini Kit (Qiagen, #70022) according to manufacturer' instructions. Subsequently, 2000ng of PolyA-selected total RNA equivalent were fragmented by alkaline hydrolysis (40mM Tris acetate pH 8.2, 100mM potassium acetate,30mM magnesium acetate) for 1min 45sec at 85°C in a 150Âµl volume and precipitated as previously described in (Hoeijmakers et al., 2013). Next, PolyA-selected RNA was cleaned from remaining genomic DNA (detected by qPCR) by two additional TURBO DNase treatments (Ambion, #AM2238).
ATAC-seq libraries: Half of the isolated DNA was used for library preparation (the other half was stored as back-up) starting with a size selection using 0.85x volumes of AMPure XP beads to enrich for fragments of 500 bp and smaller. Size-selected fragments were amplified using the KAPA HiFi HotStart ready-mix (KAPA Biosystems, #KK2602, US) and Nextera index primers (Nextera DNA Sample Preparation Index Kit, #FC-121-1012) under the following conditions: 98°C for 2 min; 16 cycles of 98°C for 20 sec, and 62°C for 3 min; 62°C for 5 min. Libraries were purified using 1x volumes Agencourt AMPure XP beads. The fragment size distribution of the libraries was evaluated in a High-Sensitivity Bioanalyzer run (Agilent, #5067-4626, US) and the size selection was repeated when there was a large proportion of fragments longer than 500 bp (t05_69.66u, t05_23.22u, t15_69.66u, t30_23.22u, t35_23.22u, t40_23.22u). To control for sequence bias, the same ATAC protocol was applied to genomic DNA from synchronous wild type 3D7 P. falciparum ring stage parasites using 547.0 ng or 60.8 ng of input DNA. All ATAC-seq libraries were KAPA quantified (KAPA Library Quantification Kit, #KR0405).
Strand-specific RNA-seq libraries: Strand-specific RNA-seq was performed as in (Kensche et al., 2015). Accordingly, first strand cDNA synthesis was performed with AT-corrected Random N9 primers (76% AT) in the presence of 0.2ug Actinomycin D (Thermo 446 Fisher Scientific). During second strand synthesis dTTPs were substituted with dUTPs to preserve strand-specific information. Next, 10 ng of each double stranded cDNA library was end repaired, extended with 3Ã¢â‚¬â„¢ A-overhangs, barcoded with NextFlex adapters (Bio Scientific, #514122) and treated with USER enzyme (NEB, #M5505L) to specifically degrade the dUTP-containing second strand. Libraries were amplified by PCR (98°C for 2min; 4 cycles of 98°C for 20sec, 62°C for 3min; 62°C for 5 min) using KAPA HiFi HotStart ready mix (KAPA Biosystems, #KM2602) and NEXTflex primer mix (Bio Scientific, #514122) and subsequently gel size-selected for 300 - 400 bp using 2% E-Gel Size Select agarose gels (Invitrogen, #G6610-02). After an additional eight cycles of amplification (see above), libraries were purified and adapter dimers depleted using 1x volume of Agencourt AMPure XP beads (Beckman Coulter, #A63880).

tag: selection

value: late ring stage


title: Pf-3D7-t30, ATACseq, replicate2

source_name: red blood cell stage, 22-30 hours post invasion

value: early schizont


title: Pf-3D7-t20, ATACseq, replicate2

source_name: red blood cell stage, 12-20 hours post invasion

value: early trophozoite


title: Pf-3D7-t40, ATACseq, replicate2

source_name: red blood cell stage, 32-40 hours post invasion

value: late schizont


title: Pf-3D7-t25, ATACseq, replicate2

source_name: red blood cell stage, 17-25 hours post invasion

value: late trophozoite


title: Pf-3D7-t35, ATACseq, replicate2

source_name: red blood cell stage, 27-35 hours post invasion

value: medium schizont


title: Pf-3D7-t10, ATACseq, replicate2

source_name: red blood cell stage, 2-10 hours post invasion

value: medium ring stage


title: E.coli_Na20_rep1

city: Tianjin

first: Zhe

last: Sun

address: 32 West 7th Ave

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

description:
NC_000913.2+NC_000913.3
This sample is E. coli CC72 grown in LB medium after 0.5 M NaCl shock for 20 min. It is the first of two biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Expression values were generated using quantile normalization (Bolstad et al., 2003, Bioinformatics, 19:185), and the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003, Nucleic Acids Res. 31: e15 and Irizarry et al., 2003, Biostatistics 4:249) based on the raw data (.pair file) and background correction as implemented in the NimbleScan software package (Roche NimbleGen, Inc.).

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Escherichia coli CC72 NaCl 20 min

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: E. coli CC72 was grown in water bath to early-exponential phase (OD600 0.2) at 37°C in LB medium, then samples were collected.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.

treatment_protocol: When the OD600 of the cell culture reached 0.2, solid NaCl was added and dissolved to a final concentration of 0.5 M to induce osmotic stress. After 0.5 M NaCl treatment for 10 min, 20 min and 45 min, samples were collected, respectively.

tag: substrain

tag: genotype

value: Fusion of venus to the 3' end of rpoC in E. coli wild-type MG1655


title: E.coli_Na20_rep2

description:
NC_000913.2+NC_000913.3
This sample is E. coli CC72 grown in LB medium after 0.5 M NaCl shock for 20 min. It is the second of two biological replicates used in this experiment, each from separate cultures.


title: E.coli_Na45_rep1

description:
NC_000913.2+NC_000913.3
This sample is E. coli CC72 grown in LB medium after 0.5 M NaCl shock for 45 min. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: Escherichia coli CC72 NaCl 45 min


title: ER-464195-01 6

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

data_processing:
Reads were mapped on mm10 mouse reference genome and quantified using CLC Genomics Workbench version 10.1.1 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 10.1.1.
Filtering characteristics of fold-change -2 to 2 (false discovery rate (FDR) at P < 0.05) were used to identify the DEGs.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

source_name: Intestine

extract_protocol:
Intestines were removed, flash frozen on dry ice, and total RNA was extracted from colon of mice using ISOGEN II Reagent (Life Technologies). 500 ng of total RNA were ribosomal RNA-depleted using NEBNext rRNA Depletion Kit (New England Biolabs), and converted to Illumina sequencing library using NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Balb/c

value: Intestine

tag: age

value: 7 weeks

tag: Sex

value: male

tag: treatment


title: ER-464195-01 4

tag: tissue


title: E.coli_LB_rep2

description:
NC_000913.2+NC_000913.3
This sample is E. coli CC72 grown in LB medium at eary-exponential phase. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: Escherichia coli CC72 LB


title: E.coli_Na45_rep2

description:
NC_000913.2+NC_000913.3
This sample is E. coli CC72 grown in LB medium after 0.5 M NaCl shock for 45 min. It is the second of two biological replicates used in this experiment, each from separate cultures.


title: E.coli_Na10_rep1

description:
NC_000913.2+NC_000913.3
This sample is E. coli CC72 grown in LB medium after 0.5 M NaCl shock for 10 min. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: Escherichia coli CC72 NaCl 10 min


title: ER-464195-01 2


title: ER-464195-01 3


title: E.coli_Na10_rep2

description:
NC_000913.2+NC_000913.3
This sample is E. coli CC72 grown in LB medium after 0.5 M NaCl shock for 10 min. It is the second of two biological replicates used in this experiment, each from separate cultures.


title: E.coli_Na45_rep3

type: genomic

description: This sample is E. coli CC72 grown in LB medium after 0.5 M NaCl shock for 45 min. It is the third of three biological replicates used in this experiment, each from separate cultures.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan ChIP data extraction..

source_name: RNAP beta subunit ChIP DNA from E. coli CC72 45 min after osmotic stress

growth_protocol: E. coli CC72 was grown in water bath to early-exponential phase (OD600 0.2) at 37°C in LB medium.

extract_protocol: The ChIP experiment was performed essentially as described previously (Herring, Raffaelle et al. 2005). Briefly, the cell cultures were fixed by a 1% formaldehyde and 10 mM sodium phosphate (pH 7.6) solution for 20 min at room temperature. After cell lysis, RNase A treatment and sonication, the chromosome was fragmented to 100-1200 bp. RNAP binding DNA (IP DNA) was immunoprecipitated with RNAP using an antibody against the RNAP β’ subunit and pan mouse magnetic beads. The same sample without the β’ antibody was used as mock immunoprecipitation DNA (mock IP DNA). After washing and de-crosslinking, DNA was purified using the PCR purification kit (Qiagen).

treatment_protocol: After 0.5 M NaCl treatment for 45 min of the early-exponential phase cells, samples were collected.

tag: chip antibody

tag: accession

value: RNAP beta subunit antibody


title: E.coli_Na45_rep2

description: This sample is E. coli CC72 grown in LB medium after 0.5 M NaCl shock for 45 min. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: E.coli_LB_rep1

description:
NC_000913.2+NC_000913.3
This sample is E. coli CC72 grown in LB medium at eary-exponential phase. It is the first of two biological replicates used in this experiment, each from separate cultures.


title: Normal water 6

value: normal water


title: E.coli_Na45_rep1

description: This sample is E. coli CC72 grown in LB medium after 0.5 M NaCl shock for 45 min. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Pf-3D7-t05, ATACseq, replicate2

source_name: red blood cell stage, 40-5 hours post invasion

tag: developmental stage

value: early ring stage


title: Normal water 5


title: Normal water 3


title: Normal water 4


title: ER-464195-01 5


title: E.coli_Na20_rep3

description: This sample is E. coli CC72 grown in LB medium after 0.5 M NaCl shock for 20 min. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: RNAP beta subunit ChIP DNA from E. coli CC72 20 min after osmotic stress

treatment_protocol: After 0.5 M NaCl treatment for 20 min of the early-exponential phase cells, samples were collected.


title: E.coli_Na20_rep2

description: This sample is E. coli CC72 grown in LB medium after 0.5 M NaCl shock for 20 min. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: E.coli_Na10_rep3

description: This sample is E. coli CC72 grown in LB medium after 0.5 M NaCl shock for 10 min. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: RNAP beta subunit ChIP DNA from E. coli CC72 10 min after osmotic stress

treatment_protocol: After 0.5 M NaCl treatment for 10 min of the early-exponential phase cells, samples were collected.


title: E.coli_Na20_rep1

description: This sample is E. coli CC72 grown in LB medium after 0.5 M NaCl shock for 20 min. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: E.coli_Na10_rep2

description: This sample is E. coli CC72 grown in LB medium after 0.5 M NaCl shock for 10 min. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: Control cells

city: Hangzhou

first: Chenfang

last: Dong

address: 866 Yuhangtang Rd

institute: Zhejiang University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Primeview. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: MDA-MB231 cells control

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: MDA-MB231 cells were grown in DMEM containing 5.6mmol/L glucose.

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

treatment_protocol: After 48h of cell passage, cells were harvested for RNA extraction.

tag: cell line

value: MDA-MB-231 breast cancer cell line

value: control


title: UGT8 knockdown cells

source_name: MDA-MB231 cells with UGT8 knockdown

value: UGT8 knockdown


title: E.coli_LB_rep3

description: This sample is E. coli CC72 grown in LB medium at eary-exponential phase. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: RNAP beta subunit ChIP DNA from E. coli CC72 at early-exponential phase

treatment_protocol: The early-exponential phase cells were collected without NaCl treatment.


title: E.coli_Na10_rep1

description: This sample is E. coli CC72 grown in LB medium after 0.5 M NaCl shock for 10 min. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Normal water 1

tag: strain


title: Normal water 2


title: E.coli_LB_rep2

description: This sample is E. coli CC72 grown in LB medium at eary-exponential phase. It is the first of two biological replicates used in this experiment, each from separate cultures.


title: ER-464195-01 1


title: PAO1_FBI (exposed to hexadecane-water interface for 1h)_1

city: Pittsburgh

first: Tagbo

last: Niepa

state: PA

address: 3700 OHara Street, 926 Benedum Hall

department: Chemical and Petroleum Engineering

institute: University of Pittsburgh

description:
PAO1_TranscriptRawReadCounts.txt
replicate 1

data_processing:
Illumina Casava-1.8.2 software was used for basecalling.
RNA-Seq - Low quality reads as well as ribosomal and other repeat sequences were filtered out before alignment. RUM software was used for aligning reads to Pseudomonas aeruginosa genomes PAO1 and PA14, the Refseq transcriptome, and for transcript quantitation. Differential expression analysis was carried out using a custom script implementing EdgeR software.
Genome_build: PAO1 - NCBI Build ASM676v1 (GCF_000006765.1), PA14 - NCBI Build Pseu_aeru_PA14_V1 (GCF_000404265.1)
Supplementary_files_format_and_content: transcript raw read counts of each sample

organism: Pseudomonas aeruginosa PAO1

source_name: Stationary phase microbial culture

extract_protocol:
To evaluate changes in the transcriptional profile of cells after interfacial confinement, PAO1 and PA14 cells were exposed to the hexadecane-water interface and the cells total RNA were isolated. First the cells were grown for 16 h in the LB medium, washed and resuspended in 154 mM NaCl solution as described above. To form the FBIs, 5 mL of suspensions and 5 mL of hexadecane were introduced in 25 mL glass vials. The vials were rotated at 60 rpm for 2 h using a Rugged Rotator (Glas-Col, Terre Haute, USA) for 1 h and the emulsions were collected in microcentrifuge tubes, then centrifuges at 15,000 g for 2.5 min at 4C to remove cells, which are not attached to the FBIs. The FBIs were collected from the hexadecane water interfaces, introduced in a vial and stored at 80C for RNA isolation. Similarly, the control cells, which were only suspended in 154 mM NaCl solution, were collected by centrifugation and stored at 80C for RNA extraction. Three independent samples were prepared for the control experiments. The RNeasy Mini Kit (Qiagen, CA, USA), which includes on-column DNase, was employed to extract the total RNA of cells following a protocol previously developed. The total RNA of PA14 and PAO1 FBIs as well as the untreated controls (PAO1 and PA14 in suspension) were isolated and bioanalyzed for their quality. The RNA samples were sent to the Penn Next-Generation Sequencing Core to acquire the transcriptional profile of the cells using RNA sequencing.
Illumina's TruSeq Stranded Total RNA Sample Preparation protocol with Ribo-Zero rRNA removal was used to construct libraries. All steps conformed to as listed in manufacturer's sample preparation guide.

tag: culture

value: 16h culture

tag: cell type

value: whole cell

tag: stress


title: PAO1_FBI (exposed to hexadecane-water interface for 1h)_2

description:
PAO1_TranscriptRawReadCounts.txt
replicate 2


title: PAO1_FBI (exposed to hexadecane-water interface for 1h)_3

description:
PAO1_TranscriptRawReadCounts.txt
replicate 3


title: PAO1 Control (exposed to NaCl solution for 1h)_2


title: PAO1 Control (exposed to NaCl solution for 1h)_1


title: PAO1 Control (exposed to NaCl solution for 1h)_3


title: corpuscallosum_remyel_2days_rep1

city: Budapest

first: Viktor

last: Molnár

address: Nagyvárad tér 4.

department: Department of Genetics, Cell- and Immunobiology

country: Hungary

institute: Semmelweis University

description: miRNA expression

hyb_protocol: The labeled samples were hybridized for 20 hours at 55°C to Agilent Mouse miRNA Microarrays (G4472A, 8x15k) in a rotating Agilent hybridization oven.

scan_protocol: The arrays were scanned with an Agilent DNA Microarray Scanner BA.

data_processing: Signal quantification was carried out by Feature Extraction (ver. 10.5.1.1) using default parameters (protocol: miRNA_105_Dec08 and Grid: 019119_D_F_20081129). Image Analysis Software and data were further analyzed by Genespring GX10.0.

source_name: Corpus callosum, remyelinating, 4 weeks feeding with cuprizone followed by 2 days regular diet, replicate 1

label_protocol: 100 ng of total RNA was first dephosphorylated by using calf intestine alkaline phosphatase and labeled by using miRNA labeling Reagent & Hybridization Kit according to the manufacturer’s protocol with no modification.

extract_protocol: The affected areas of corpus callosum was punched out and RNA was extracted by the miRNeasy micro Kit (Qiagen, Valencia, CA). The quantity and quality of total RNA was assessed by NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA), respectively. Only those samples that gave >8.0 for RNA integrity number, showed a clear gel image and no DNA contamination was observed on the histogram were used for microarray experiments.

treatment_protocol: To induce demyelination, cuprizone (CPZ) was administrated for four weeks orally. The powdered standard chow was mixed with 0.2-0.4% CPZ. After 4 weeks, treatment with cuprizone diet was stopped. Remyelination was examined at two time points: acute remyelination induced by four weeks feeding with CPZ followed by two days of regular diet and full remyelination induced by four weeks CPZ feeding followed by two weeks of regular diet. Control mice were kept on a normal diet.

value: corpus callosum

tag: gender

value: normal diet for 2 days after completion  cuprizone treatment for 4 weeks


title: corpuscallosum_demyel_4weeks_rep4

description: miRNA expression

source_name: Corpus callosum, demyelinated, after 4 weeks treatment by cuprizone, replicate 4

value: cuprizone treatment for 4 weeks


title: corpuscallosum_remyel_2days_rep2

description: miRNA expression

source_name: Corpus callosum, remyelinating, 4 weeks feeding with cuprizone followed by 2 days regular diet, replicate 2


title: HFD+binge-3

city: Rockville

first: Ming-Jiang

state: MD

address: 5625 Fishers LN, 2S12

department: NIAAA

institute: NIH

description: High-fat diet 3 months plus binge 3

hyb_protocol: Blocking buffer 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 sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: mages were quantified using Agilent Feature Extraction Software. Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: Mouse liver with High-fat diet for 3 months plus EtOH binge (5 g/kg)

label_protocol: cDNA was generated with SuperScript® Indirect cDNA Labeling Core kit (Invitrogen) and labeled with Cy3/Cy5-mono reactive dye pack (GE healthcare), and the labeled cDNA was purified with Qiagen kit (#28004)

extract_protocol: Total RNA extracted using Trizol from liver and purified with QIAGEN kit (#74104) following manufacturer's instructions.

treatment_protocol: Collected tissues from fresh liver

value: Male

value: Liver

source_name: Ambion Mouse Assorted Total RNA

value: liver


title: HFD+maltose-4

description: High-fat diet 3 months plus maltose gavage 4

source_name: Mouse liver with High-fat diet for 3 months plus maltose gavage


title: corpuscallosum_remyel_2weeks_rep1

description: miRNA expression

source_name: Corpus callosum, remyelinating, 4 weeks feeding with cuprizone followed by 2 weeks regular diet, replicate 5

value: normal diet for 2 weeks after completion  cuprizone treatment for 4 weeks


title: corpuscallosum_remyel_2days_rep4

description: miRNA expression

source_name: Corpus callosum, remyelinating, 4 weeks feeding with cuprizone followed by 2 days regular diet, replicate 4


title: corpuscallosum_remyel_2days_rep3

description: miRNA expression

source_name: Corpus callosum, remyelinating, 4 weeks feeding with cuprizone followed by 2 days regular diet, replicate 3


title: HFD+maltose-1

description: High-fat diet 3 months plus maltose gavage 1


title: HFD+binge-1

description: High-fat diet 3 months plus binge 1


title: corpuscallosum_demyel_4weeks_rep3

description: miRNA expression

source_name: Corpus callosum, demyelinated, after 4 weeks treatment by cuprizone, replicate 3


title: corpuscallosum_untreated_rep3

description: miRNA expression

source_name: Corpus callosum, untreated controls, replicate 3

value: untreated


title: corpuscallosum_remyel_2weeks_rep2

description: miRNA expression

source_name: Corpus callosum, remyelinating, 4 weeks feeding with cuprizone followed by 2 weeks regular diet, replicate 6

value: male


title: HFD+maltose-3

description: High-fat diet 3 months plus maltose gavage 3


title: HFD+binge-4

description: High-fat diet 3 months plus binge 4


title: HFD+binge-5

description: High-fat diet 3 months plus binge 5


title: HFD+maltose-2

description: High-fat diet 3 months plus maltose gavage 2


title: Chow+binge-4

description: Chow diet 3 months plus binge 4

source_name: Mouse liver with Chow diet for 3 months plus EtOH binge (5 g/kg)


title: Chow+binge-3

description: Chow diet 3 months plus binge 3


title: Chow+maltose-1

description: Chow diet 3 months plus maltose gavage 1

source_name: Mouse liver with Chow diet for 3 months plus maltose gavage


title: Chow+binge-1

description: Chow diet 3 months plus binge 1


title: Chow+maltose-4

description: Chow diet 3 months plus maltose gavage 4


title: Chow+maltose-2

description: Chow diet 3 months plus maltose gavage 2


title: HFD+binge-2

description: High-fat diet 3 months plus binge 2


title: Chow+binge-2

description: Chow diet 3 months plus binge 2


title: Chow+maltose-3

description: Chow diet 3 months plus maltose gavage 3


title: corpuscallosum_untreated_rep4

description: miRNA expression

source_name: Corpus callosum, untreated controls, replicate 4


title: GI-142

city: Jinan

first: Yujie

last: Dang

address: 157 Jingliu Road

institute: Center for Reproductive Medicine, Shandong University.

description: MiRNA expression of granulosa cells from bPOI patients

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual. The total 25 μL mixture from Hy3TM-labeled samples with 25 μL hybridization buffer were first denatured for 2 min at 95°C, incubated on ice for 2 min and then hybridized to the microarray for 16–20 h at 56°C in a 12-Bay Hybridization Systems (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA), which provides an active mixing action and constant incubation temperature to improve hybridization uniformity and enhance signal. Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm.

scan_protocol: Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).

source_name: granulosa cells

label_protocol: After RNA isolation from the samples, the miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling. One microgram of each sample was 3'-end-labeled with Hy3TM fluorescent label, using T4 RNA ligase by the following procedure: RNA in 2.0 μL of water was combined with 1.0 μL of CIP buffer and CIP (Exiqon). The mixture was incubated for 30 min at 37°C, and was terminated by incubation for 5 min at 95°C. Then 3.0 μL of labeling buffer, 1.5 μL of fluorescent label (Hy3TM), 2.0 μL of DMSO, 2.0 μL of labeling enzyme were added into the mixture. The labeling reaction was incubated for 1 h at 16°C, and terminated by incubation for 15 min at 65°C.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions, which efficiently recovered all RNA species, including miRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

tag: disease state

value: bPOI

value: granulosa cells

value: Female


title: corpuscallosum_demyel_4weeks_rep1

description: miRNA expression

source_name: Corpus callosum, demyelinated, after 4 weeks treatment by cuprizone, replicate 1


title: PA14_FBI (exposed to hexadecane-water interface for 1h)_3

description:
PA14_TranscriptRawReadCounts.txt
replicate 3

organism: Pseudomonas aeruginosa PA14

source_name: Stationary phase microbial culture


title: GI-135


title: GI-121


title: GI-100


title: GI-113


title: GI-103


title: PA14_FBI (exposed to hexadecane-water interface for 1h)_2

description:
PA14_TranscriptRawReadCounts.txt
replicate 2


title: PA14_FBI (exposed to hexadecane-water interface for 1h)_1

description:
PA14_TranscriptRawReadCounts.txt
replicate 1


title: GI-95


title: GI-94


title: 2BCBpos_4_S14

city: Melbourne

first: Tesha

last: Tsai

state: Vic

address: 27-31 Wright Street, Clayton

country: Australia

institute: Hudson Institute of Medical Research

description: processed data file: gene_counts1.txt

data_processing:
Data QC using fastqc and trimgalore.
Alignment of the reads with pig genome using tophat2 v2.0.14.
Differential expression analysis was done using RUVseq (RUVr) and edgeR.
Genome_build: GCF_000003025.5_Sscrofa10.2
Supplementary_files_format_and_content: gene_counts1.txt: Tab-delimited text table of geneX raw counts in single cell samples.
Supplementary_files_format_and_content: gene_counts2.txt: Tab-delimited text table of geneX raw counts in pooled samples.

organism: Sus scrofa

source_name: metaphase II oocyte

extract_protocol:
RNA samples which are labelled with the word "SPIA" were extracted using Arcturus Picopure RNA extraction kit; RNA samples from single cells were prepared from in-tube extraction.
SPIA libraries were prepared using Nugen Ovation RNA-seq system V2 and Ovation Ultralow system V2; SoLo libraries were prepared using Nugen SoLo kit with Sus scrofa InDA-C primer mix.
RNA sequencing 100 bp paired end reads on Illumina HiSeq 3000.

tag: breed

value: commercial hybrid (Large White, Duroc and Berkshire)

value: metaphase II oocyte

value: mature oocyte

tag: mtdna state

value: normal

tag: sample type

value: single cell


title: 2BCBpos_3_S13

description: processed data file: gene_counts1.txt


title: PA14 Control (exposed to NaCl solution for 1h)_2

value: 16h culture

value: whole cell

value: control


title: 2BCBpos_2_S12

description: processed data file: gene_counts1.txt


title: 2BCBpos_1_S11

description: processed data file: gene_counts1.txt


title: PA14 Control (exposed to NaCl solution for 1h)_1


title: 4BCBpos_5_S5

description: processed data file: gene_counts1.txt


title: 4BCBpos_3_S10

description: processed data file: gene_counts1.txt


title: 4BCBpos_1_S8

description: processed data file: gene_counts1.txt


title: PA14 Control (exposed to NaCl solution for 1h)_3


title: GC-94

description: MiRNA expression of granulosa cells from age and BMI matched normal control women


title: 3BCBpos_1_S6

description: processed data file: gene_counts1.txt


title: 4BCBpos_2_S2

description: processed data file: gene_counts1.txt


title: 4BCBpos_3_S3

description: processed data file: gene_counts1.txt


title: 3BCBpos_2_S30

description: processed data file: gene_counts1.txt


title: 4BCBpos_4_S4

description: processed data file: gene_counts1.txt


title: GC-92


title: 4BCBpos_1_S1

description: processed data file: gene_counts1.txt


title: 3BCBpos_2_S7

description: processed data file: gene_counts1.txt


title: GC-121


title: GC-133


title: GC-95


title: GC-136


title: GC-138


title: GC-117


title: GC-109


title: GI-78


title: GI-91


title: GC-131


title: siTet1/Tet2 3

city: Beijing

first: Ruili

last: Yang

address: 22# South Zhongguancun  Ave

institute: Peking University

data_processing:
The resulting base calling (.bcl) files were converted to FASTQ files using Illunina’s bcl  cl2fastq v1.8.4 software (Illumina,San Diego, CA).
Mapping RNA-seq reads on the mouse genome  after trimming the adaptors, transcript assembly, and abundance estimation were performed using DNASTAR Lasergene v15.0 (DNASTAR, Madison, WI)
For each sample (Control1: C1; Control2: C2; Control3:C3; si(Tet1/Tet2) 1: s1; si(Tet1/Tet2) 2: s2; si(Tet1/Tet2) 3: s3), the individual gene expression was reported using linear total RPKMs. The difference of each gene bewteen control and si(Tet1/Tet2) 2 was analyzed by two  tailed Student’s t-tests and showed as P value.
Genome_build: Mus musculus GRCm38
Supplementary_files_format_and_content: RPKMs

source_name: siTet1/Tet2, BMMSCs

growth_protocol: Bone marrow cells were flushed out from femurs and tibias with 2% heat-inactivated fetal bovine serum (FBS; Equitech-Bio, Kerrville, NY, USA) in PBS. All nuclear cells (ANC) were seeded (15 × 10^6 cells per dish) in 100 mm culture dishes (Corning, Tewsburg, MA, USA) and incubated at 37°C under 5% CO2 conditions. Non-adherent cells were removed after 48 h and adherent cells were cultured for an additional 14 days in alpha minimum essential medium (α-MEM, Invitrogen, Grand Island, NY, USA) supplemented with 20% FBS, 2 mM L-glutamine (Invitrogen), 55 μM 2-mercaptoethanol (Invitrogen), 100 U/ml penicillin, and 100 μg/ml streptomycin (Invitrogen).

extract_protocol:
Total RNA from BMMSCs were extracted using Qiagen RNeasy mini kit.
The NEBNext Ultra RNA library Pre Kit was used to prepare a sequencing library from 1μg of total RNA, and 2×100 paired-end sequencing in fat run mode was performed using the HiSeq 2500 and Illumina TruSeq SBS-Kit v2 (200 Cycles).

treatment_protocol: 0.2×10^6 BMMSCs were seeded on a 6-well culture plate. Tet1 and Tet2 siRNAs (Santa Cruz Biotechnology) were used to treat the BMMSCs according to the manufacturer’s instructions. Non-targeting control siRNAs (Santa Cruz Biotechnology) were used as negative controls.

value: Bone marrow mesenchymal stem cells (BMMSCs)

tag: passage


title: 4BCBneg_1_S17

description: processed data file: gene_counts1.txt

value: deficient


title: 4BCBneg_3_S19

description: processed data file: gene_counts1.txt


title: siTet1/Tet2 2


title: 3BCBneg_2_S32

description: processed data file: gene_counts1.txt


title: siTet1/Tet2 1


title: Control 3

source_name: Control, BMMSCs

value: Control


title: corpuscallosum_untreated_rep1

description: miRNA expression

source_name: Corpus callosum, untreated controls, replicate 1

value: corpus callosum


title: corpuscallosum_untreated_rep2

description: miRNA expression

source_name: Corpus callosum, untreated controls, replicate 2

value: untreated


title: corpuscallosum_demyel_4weeks_rep2

description: miRNA expression

source_name: Corpus callosum, demyelinated, after 4 weeks treatment by cuprizone, replicate 2

value: male

value: cuprizone treatment for 4 weeks


title: 3BCBneg_1_S31

description: processed data file: gene_counts1.txt


title: 4BCBneg_5_S26

description: processed data file: gene_counts1.txt


title: 2BCBneg_2_S28

description: processed data file: gene_counts1.txt


title: 4BCBneg_4_S20

description: processed data file: gene_counts1.txt


title: 4BCBneg_4_S25

description: processed data file: gene_counts1.txt


title: 4BCBneg_1_S22

description: processed data file: gene_counts1.txt


title: 4BCBneg_2_S23

description: processed data file: gene_counts1.txt


title: 3BCBneg_1_S21

description: processed data file: gene_counts1.txt


title: 3BCBpos_1_S29

description: processed data file: gene_counts1.txt


title: 2BCBneg_1_S27

description: processed data file: gene_counts1.txt


title: Control 1


title: Control 2


title: 1BCBneg_1_S15

description: processed data file: gene_counts1.txt


title: B2_pos_SPIA

description: processed data file: gene_counts2.txt

source_name: metaphase II oocytes

value: metaphase II oocytes

value: pooled


title: 1BCBneg_2_S16

description: processed data file: gene_counts1.txt

value: commercial hybrid (Large White, Duroc and Berkshire)


title: B1_pos_SPIA

description: processed data file: gene_counts2.txt


title: A4_pos_SPIA

description: processed data file: gene_counts2.txt


title: A3_pos_SPIA

description: processed data file: gene_counts2.txt


title: Orientin+Irradiated (ORI+IR-10)

city: Columbus

first: NADUPARAMBIL

middle: Korah

last: JACOB

state: Ohio

address: 410 W 12th Ave

department: Radiation Oncology

institute: The Ohio State University

description: 8-10 weeks old C57BL/6 mouse was pre treated with Orientin (5mg/kg) followed by 6Gy irradiation. RNA extracted from whole bone marrow bulk cells at indicated time. Total RNA was extracted and measured via nanoString.

hyb_protocol: Hyb protocol was performed following manufacturer's standard protocol

scan_protocol: Scan protocol was performed following manufacturer's standard protocol

data_processing: Normalized data came from the NanoString nCounter system.

label: nanoString Dye

source_name: Orientin+Irradiated

label_protocol: Label protocol was performed following manufacturer's standard protocol

extract_protocol: RNA was extracted from whole bone marrow bulk cells using miRVANA kit.

value: Bone marrow bulk cells

value: Orientin+Radiation

tag: dose

tag: day

tag: conc

tag: Sex

value: Male


title: A2_pos_SPIA

description: processed data file: gene_counts2.txt

value: mature oocyte

value: normal


title: Orientin+Irradiated (ORI+IR-12)

tag: treatment


title: R6/2_mouse_10w_striatum

city: Kodaira

first: Hirohiko

last: Hohjoh

state: Tokyo

address: 4-1-1 Ogawahigashi

institute: National Institute of Neuroscience, NCNP

description: small RNA

hyb_protocol: Hybridized for 16 h at 37 C with rotary shaking (250 rpm). Hybridization and washing were followed by the protocols supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: Signal intensities of each spot were normalized by substitution with a mean intensity of the background signals determined by all the blank spots’ signal intensities of 95% confidence intervals.

source_name: R6/2 mouse striatum

label_protocol: Extracted total RNAs were labeled with Hy5 using a miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

extract_protocol: Total RNAs were extracted from striatum using a TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.

tag: age

tag: tissue

value: striatum


title: Irradiated (IR-09)

description: 8-10 weeks old C57BL/6 mouse was irradiated with 6Gy. RNA extracted from whole bone marrow bulk cells at indicated time. Total RNA was extracted and measured via nanoString.

source_name: Irradiated

tag: strain

value: Radiation


title: Wt_mouse_10w_striatum

description: small RNA

source_name: Wt mouse striatum


title: Irradiated (IR-08)


title: B4_pos_SPIA

description: processed data file: gene_counts2.txt

tag: developmental stage


title: Orientin+Irradiated (ORI+IR-11)

tag: cell type


title: A1_neg_SPIA

description: processed data file: gene_counts2.txt


title: A3_neg_SPIA

description: processed data file: gene_counts2.txt


title: B2_neg_SPIA

description: processed data file: gene_counts2.txt


title: A2_neg_SPIA

description: processed data file: gene_counts2.txt


title: B4_neg_SPIA

description: processed data file: gene_counts2.txt


title: Orientin Treated (ORI-06)

description: 8-10 weeks old C57BL/6 mouse was treated with Orientin (5mg/kg). RNA extracted from whole bone marrow bulk cells at indicated time. Total RNA was extracted and measured via nanoString.

source_name: Orientin Treated

value: Orientin Treated


title: Irradiated (IR-07)


title: Unirradiated Controls (CT-03)

description: 8-10 weeks old C57BL/6 mouse was used as a unirradiated control. RNA extracted from whole bone marrow bulk cells at indicated time. Total RNA was extracted and measured via nanoString.

source_name: Unirradiated Controls

value: Unirradiated Controls


title: Orientin Treated (ORI-05)


title: Unirradiated Controls (CT-02)


title: Unirradiated Controls (CT-01)


title: 287: 4X choline female rep 3 (smallRNA)

status: Public on Apr 10 2018

city: Ithaca

first: Jennifer

middle: K

last: Grenier

state: NY

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.8 (-m 10 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
miRDeep2: mapper.pl was used to collapse non-redunadant trimmed reads to fasta format
miRDeep2: quantifier.pl was used to match reads to mouse mature miRNAs (miRBase) and generate normalized counts
Genome_build: mature mouse miRNAs in miRBase
Supplementary_files_format_and_content: Tab delimited miRDeep2 output files contain raw and normalized read counts for mature mouse miRNAs (miRBase).

source_name: Mouse placenta

growth_protocol: Prior to euthanization and tissue harvesting, the mice in this study had ad libitum access to the diet and water, and were housed in microisolator cages in an environmentally-controlled room (22-25°C, 70% humidity) with a 12-hour light-dark cycle.

extract_protocol:
Placenta tissues were removed from the mice after they were sacrificed at gestational day 15.5 and were immediately flash frozen in liquid nitrogen. RNA were extracted from the tissues using Trizol following the manufacturer's protocol.
RNA-seq libraries were prepared from 1 ug total RNA using the NEBNext Small RNA Library Prep Kit  for Illumina (New England Biolabs), with size selection for 18-30nt inserts.

treatment_protocol: Prior to euthanization and tissue harvesting, the mice in this study were fed the AIN-93G diet, with either 1X choline concentration (1.4g choline chloride/kg diet; Dyets Cat #103345) or 4X choline concentration (5.6g choline chloride/kg diet; Dyets Cat #103347).

value: non-Swiss Albino (NSA)

value: Placenta

value: Gestational day 15.5

tag: fetal sex

value: Female

tag: diet treatment

value: 4X choline


title: 225: 4X choline female rep 2 (smallRNA)


title: Orientin Treated (ORI-04)


title: 198: 4X choline female rep 1 (smallRNA)


title: 71: 1X choline female rep 2 (smallRNA)

value: 1X choline


title: 252: 1X choline female rep 3 (smallRNA)


title: 241: 4X choline male rep 2 (smallRNA)


title: 269: 4X choline male rep 3 (smallRNA)


title: 273: 1X choline male rep 3 (smallRNA)


title: 222: 1X choline male rep 1 (smallRNA)


title: 234: 1X choline male rep 2 (smallRNA)


title: RAD21_IP_2

city: Dallas

first: Hongtao

last: Yu

state: TX

address: 6001 Forest Park Rd

department: Pharmacology

institute: University of Texas Southwestern Medical Center

data_processing:
Basecalling was done using bcl2fastq/2.17
Fastq files were trimmed for quality and adapters using fastq-mcf (ea-utils/1.1.2-806)
Fastq files were mapped to hg19 (UCSC) using bowtie/2.2.3
Reads with mapping quality less than 10 were removed using samtools/1.2-2-gf8a6274
Duplicates were removed using picard-tools/1.127
Normalized bigwig files were made using homer/v4.8.3
Peak calling was done using MACS/2.0.10
For MCM2 sample, peak calling was also done using SICER (epic/v0.2.2)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files contain normalized read coverage, Reads per 10 million
Supplementary_files_format_and_content: broadPeak files contain tab delimited bed files in broadPeak format
Supplementary_files_format_and_content: bed file format for SICER

source_name: HeLa Tet-On cells

growth_protocol: HeLa Tet-On cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS) and 2 mM L-glutamine

extract_protocol:
HeLa Tet-On cells were lysed, sonicated. The resulting whole cell extract was centrifuged. The supernatant was incubated with RAD21 or NIPBL antibody. RAD21 or NIPBL bound DNA was isolated and purified.
Next-generation sequencing library preparation using KAPA Hyper Prep kit (KAPA Biosystems) using TruSeq adapters (Integrated DNA Technologies). A quality check of the purified libraries was carried out using the Tapestation 4200 (Agilent).

treatment_protocol: HeLa Tet-On cells were synchronized with 2 mM thymidine for 16-18 h

tag: chip antibody

value: anti-RAD21 ChIP-grade (Abcam, ab992)

tag: cell line

value: HeLa Tet-On cells


title: INPUT_2


title: RAD21_IP_1


title: NIPBL_IP_2

value: anti-NIPBL (Bethyl Laboratories, A301-779A)


title: NIPBL_IP_1


title: 223: 4X choline male rep 1 (smallRNA)


title: MCM2_IP

value: anti-MCM2 (Bethyl Laboratories, A300-191A)


title: INPUT_1


title: breast-benign-1133358

city: Wenzhou

first: jiang

last: yang

address: The First Affiliated Hospital of Wenzhou Medical University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 1.5 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 2x GEx hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-045997 Arraystar human lncRNA microarray V3(GPL16956) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Gene Expression Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Region 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% to Lo 10%).

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

source_name: benign tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy Mini Kit (Qiagen p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNasey Mini Kit(Qiagen p/n 74104) following the manufacturer's instruction. Quantification and quality of RNA was tested by NanoDrop ND-1000 spectrophotometer. RNA Integrity and gDNA contamination was tested by Denaturing Agarose Gel Electrophoresis.

treatment_protocol: Tissues from breast cancer patients were kept in liquid nitrogen. Homogenization of tissues was performed using the Mini-Bead-Beater-16 after adding TRIzol.

tag: subject id

tag: subject status

value: breast cancer patients

tag: gender

value: female

tag: tissue type

value: benign tissue


title: breast-tumor-1130727

institute: The First Affiliated Hospital of Wenzhou Medical University

source_name: ductal carcinoma in situ

value: ductal carcinoma in situ


title: breast-benign-1130727


title: GenD Replicate 3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression after 4hr in mouse uterus

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

source_name: Uterus with genistein and dexamethasone treatment

label_protocol: Starting with 400ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: RNA samples were isolated from the entire uterus using the Rneasy Mini Kit (Qiagen) with on-column DNAse digest.

treatment_protocol: 4hr treatment with 100ul saline vehicle or 1 mg/kg dexamethasone injected intraperiotoneally.

value: Uterus

tag: post-natal treatment

value: Genistein

tag: adult treatment

value: Dexamethasone


title: breast-tumor-1133358


title: GenD Replicate 4


title: breast-tumor-863374


title: breast-benign-863374


title: GenV Replicate 4

source_name: Uterus with genistein treatment

value: Vehicle


title: GenV Replicate 1


title: SalD Replicate 4

source_name: Uterus with saline and dexamethasone treatment

value: Saline


title: MRC5_si-Ctrl_rep1

city: Wuhan

first: Zongyuan

state: Hubei

address: Jiefang avenue 1095, Hankou,

department: Gyneconogical cancer

institute: cancer biology center

description: Gene expression data from MRC5-CAFs transfected with si-Ctrl .

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Transcriptome Array 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: PICR scanner 3000

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

source_name: MRC5-CAFs transfected with si-Ctrl for 72 hr replicate 1

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit. WT Expression Kit

extract_protocol: QIAGEN All prep DNA/RNA/protein mini kit extracted total RNA according to the manufacturer's instructions

value: CAFs


title: SalD Replicate 2


title: GenD Replicate 2


title: GenD Replicate 1


title: MRC5_si-Dicer1_rep2

description: Gene expression data from MRC5-CAFs transfected with si-Dicer1

source_name: MRC5-CAFs transfected with si-Dicer1 for 72 hr replicate 2


title: MRC5_si-Ctrl_rep2

source_name: MRC5-CAFs transfected with si-Ctrl for 72 hr replicate 2


title: MRC5_si-Dicer1_rep1

source_name: MRC5-CAFs transfected with si-Dicer1 for 72 hr replicate 1


title: GenV Replicate 2


title: MRC5_si-Dicer1_rep3

source_name: MRC5-CAFs transfected with si-Dicer1 for 72 hr replicate 3


title: GenV Replicate 3


title: SalD Replicate 3


title: SalV Replicate 4

source_name: Uterus with saline treatment


title: MRC5_si-Ctrl_rep3

source_name: MRC5-CAFs transfected with si-Ctrl for 72 hr replicate 3


title: SalD Replicate 1


title: SalV Replicate 1


city: Charleston

first: Michael

middle: C

last: Ostrowski

state: SC

address: 86 Jonathan Lucas street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

description:
Gene expression data from myeloid precursors treated with CSF-1 and RANKL for 96 h.
SS-MmuCR96h

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned in a GeneChip Scanner 3000 (Affymetrix Inc., USA)

data_processing: Gene expression levels were estimated from Expression console software from affymetrix.

label: Biotin

source_name: Murine myeloid precursors treated with CSF-1 alone according to Lonza OCP protocol (33 ng/ml CSF1 and 66ng/ml RANKL) for 96h

growth_protocol: For all mouse experiments bone marrow cells were flushed, grown on plastic plates with 100 ng/ml CSF-1 in DMEM supplemented with 10% FBS,

treatment_protocol: Enriched myeloid precursors from mouse as well as Lonza Poietics human osteoclast precurosrs were seeded at 100,000 cells/ml in OCP-BlueKit (PT-8001, Lonza) according to manufacturer's protocol for indicated time.

value: Murine enriched myeloid precurosrs

tag: treated with


title: SalV Replicate 2


description:
Gene expression data from myeloid precursors treated with CSF-1 and RANKL for 36 h.
SS-MmuCR36h

source_name: Murine myeloid precursors treated with CSF-1 alone according to Lonza OCP protocol (33 ng/ml CSF1 and 66ng/ml RANKL) for 36h


description:
Gene expression data from myeloid precursors treated with CSF-1 and RANKL for 72 h.
SS-MmuCR72h

source_name: Murine myeloid precursors treated with CSF-1 alone according to Lonza OCP protocol (33 ng/ml CSF1 and 66ng/ml RANKL) for 72h


title: HO8910_KO1#_rep1

city: Guangzhou

first: Xiaolin

last: Luo

state: Guangdong

address: 651 Dongfeng East Road

department: Gynecology Oncology

institute: Sun Yat'sen University Cancer Center

description: Gene expression data from WT and MED12 KO ovarian cancer cells

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 GeneChip® Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

source_name: HO8910 KO1# cells

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

growth_protocol: The cells were maintained in Dulbecco’s Modified Eagle’s Medium (Invitrogen, Carlsbad, CA) with 10% fetal bovine serum (Invitrogen, Carlsbad, CA) at 37 °C and 5% CO2.

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

treatment_protocol: Cells were rinsed with PBS and placed on ice in the Trizol solution.

value: Ovarian cancer cells

tag: genotype

value: MED12 KO


title: Seraphina_p53KO_shTRRAP_d6

city: Heidelberg

first: Alexander

last: Jethwa

address: Im Neuenheimer Feld 460

department: Translational Oncology

country: Germany

institute: German Cancer Research Center (DKFZ) / National Center for Tumor Diseases (NCT)

description:
Sample 11
SerKO_TRRAP_6

hyb_protocol: Standard Illumina Hybridisation Protocol Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide). 750 ng of cRNA were hybridized for 17 h at 58°C on an HumanHT-12 v4 Expression BeadChip.

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide).

data_processing: Data were normalized using quantile normalization with the Bioconductor package preprocessCore for R.

source_name: Seraphina, p53KO, shTRRAP, d6

label_protocol: The Illumina TotalPrep RNA Amplification Kit (Life Technologies) was used to generate single-stranded cRNA from input amounts of 200 ng total RNA.

growth_protocol: Cells were cultured in RPMI 1640 supplemented with 10% heat-inactivated FBS, 2 mM L-glutamine, 100 U/mL penicillin, and 100 µg/mL streptomycin at 37°C in a humidified, 5% CO2 atmosphere.

extract_protocol: Total DNase-digested RNA was extracted using the QIAGEN RNeasy Mini Kit according to the manufacturer's protocol. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Cells were transduced with a shRNA against TRRAP or a non-targeting control (NT), selected with 1 µg/mL puromycin for 48 h, and harvested at the indicated time points.

value: Seraphina p53 knock-out

tag: entity

value: Burkitt's lymphoma

tag: genotype/variation

value: p53 knock-out

tag: shRNA

value: shTRRAP

tag: time point

value: 6 d post-transduction


title: SalV Replicate 3

tag: tissue


title: Seraphina_p53KO_shTRRAP_d8

description:
Sample 12
SerKO_TRRAP_8

source_name: Seraphina, p53KO, shTRRAP, d8

value: 8 d post-transduction


title: Seraphina_p53KO_shNT_d6

description:
Sample 9
SerKO_NT_6

source_name: Seraphina, p53KO, shNT, d6

value: shNT


title: SKOV3 KO1#_MED12_rep1

description: Gene expression data from SKOV3 KO1#_MED12 cells

source_name: SKOV3 KO1#_MED12 cells

tag: cell type

value: MED12 KO + MED12 (rescue)


title: SKOV3_WT_rep1

source_name: SKOV3 WT cells

value: WT


title: SKOV3_KO2#_rep1

source_name: SKOV3 KO2# cells


title: Seraphina_shTRRAP_d8

description:
Sample 8
Ser_TRRAP_8

source_name: Seraphina, shTRRAP, d8

value: Seraphina

value: wild-type p53


title: HO8910_KO2#_rep1

source_name: HO8910 KO2# cells


title: Seraphina_shTRRAP_d6

description:
Sample 7
Ser_TRRAP_6

source_name: Seraphina, shTRRAP, d6


description:
Gene expression data from myeloid precursors treated with CSF-1 alone.
SS-MmuCSF-1

source_name: Murine myeloid precursors treated with CSF-1 alone according to Lonza OCP protocol (33 ng/ml CSF1)

tag: strain


title: SKOV3 KO1#_Vector_rep1

description: Gene expression data from SKOV3 KO1#_Vector cells

source_name: SKOV3 KO1#_Vector cells


title: HO8910_WT_rep1

source_name: HO8910 WT cells


title: Seraphina_shNT_d6

description:
Sample 5
Ser_NT_6

source_name: Seraphina, shNT, d6


title: Seraphina_shNT_d8

description:
Sample 6
Ser_NT_8

source_name: Seraphina, shNT, d8


title: Namalwa_shTRRAP_d8

description:
Sample 4
Nam_TRRAP_8

source_name: Namalwa, shTRRAP, d8

value: Namalwa

value: mutant p53 (R248Q)


title: Seraphina_p53KO_shNT_d8

description:
Sample 10
SerKO_NT_8

source_name: Seraphina, p53KO, shNT, d8