title: KO 1

city: Shanghai

first: Li

last: Li

address: 1954 Huashan Road

department: State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center

institute: Shanghai Jiao Tong University

description: replicate 1

scan_protocol: Standard Illumina scanning protocol

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

source_name: colon tissue

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

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

tag: background strain

value: colon

value: Setd2 KO

value: 6 week


title: Asp_leaf-mRNA

status: Public on Jul 07 2018

type: SRA

city: St. Louis

first: Blake

middle: C.

last: Meyers

state: MO

address: 975 N Warson Road

country: USA

institute: Donald Danforth Plant Science Center

description: Asparagus, cladophylls, BM14-72

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed to remove adapters and converted to flat file format using the pre-processing script described in Mathioni et al. (DOI: 10.1002/cppb.20043). Processed files for sRNA libraries were aligned to the Asparagus genome (v.1) using Bowtie (v0.12.8) with no allowed mismatches. Mapped sRNA reads were finally normalized to empirically derived, 30 s. Raw SMRT-sequencing data was pre-processed using the pbscript-tofu tool set (v2.3.0) from Pacific Biosciences using the default settings. The pre-processing included generation of subreads FASTA file using the RS_subreads protocol, followed by classification of reads to full-length and non-full-length categories, clustering of transcripts to consensus isoforms by ICE algorithm and final polishing by Quiver algorithm (min. accuracy = 0.99). For all downstream analysis, “high QV” transcript set generated from Quiver analyses was used. mRNA-seq assembly was performed using “Trinity RNA-Seq assembler”.For this, reads from paired-end libraries were first combined into two (FASTQ) files, one corresponding to left reads and other to right reads. Reads from the single-end libraries were then added to the combined left reads (FASTQ) file. These left and right reads files were used to generate a hybrid assembly with the default settings except for the minimum assembled contig length (set to 250 nt). ExN50 and the quality of assemblies was accessed as recommended in Trinity workflow. Transcripts from de novo assembly were annotated using Trinotate workflow with the default settings (https://trinotate.github.io/).
Supplementary_files_format_and_content: Flat file with tab separated reads and abundance counts for sRNAs, FASTA files for SMRT-seq and FASTA files for Illumina mRNA seq. Since the mRNAseq and SMRT-seq samples were used for transcriptome assembly, there are no quantitative data for these samples. The transcriptome assembly made from the mRNA-seq samples is available on the series record.

molecule: total RNA

organism: Asparagus officinalis

source_name: Asparagus, cladophylls, BM14-72

growth_protocol: Flowering Asparagus plants were harvested from T.S. Smith and Sons Farms (Bridgeville, Delaware)

extract_protocol:
Anthers were dissected using a 2 mm stage micrometer in a stereo microscope, and immediately frozen in liquid nitrogen until total RNA isolation was performed. Total RNA was isolated using the PureLink Plant RNA Reagent following the manufacturer’s instructions. Total RNA quality and quantity were assessed before proceeding to the next step.
Small RNAs (20 to 30 nt) were size selected in a 15% polyacrylamide/urea gel and libraries were constructed using the TruSeq Small RNA Prep Kit (Illumina, cat. # RS-200-0012). Small RNA libraries containing different index tags were pooled and sequenced on an Illumina HiSeq 2500 instrument at the Delaware Biotechnology Institute. The complete protocol for sRNA library preparation is described in Mathioni et al. (DOI: 10.1002/cppb.20043). RNA-seq libraries (for mRNA) were constructed using the TruSeq Stranded Total RNA Library Preparation Kit with Ribo-Zero Plant (Illumina, cat # RS-122-2401), and RNA was treated with DNase I (NEB, cat # M0303S) and then cleaned using the RNA Clean & Concentrator™-5 (Zymo Research, cat # R1015). Single Molecule Real Time (SMRT) sequencing libraries were prepared using protocol recommended by Pacific Biosciences for Isoform Sequencing using SageELF size selection system
Small RNA sequencing using Illumina single-end (1x50 bp) reads. Messenger RNA sequencing using Illumina single-end (2x150 bp) reads and Single Molecule Real Time (SMRT) sequencing of full length (cDNA) transcripts.

tag: tissue

value: leaf


title: Primary cardiomyocytes-No LeTx-24h-rep3

type: RNA

city: El Paso

first: Lihong

last: Wu

state: Texas

address: MSB1, Room 3105,5001 El Paso Drive

department: Department of Biomedical Sciences, Paul L. Foster School of Medicine

institute: Texas Tech University Health Sciences Center El Paso

description: P-cardio-No LeTx-3

hyb_protocol: Samples were hybridized with GeneChip Mouse Transcriptome Arrays (Affymetrix) and scanned at the UTSW Microarray Core Facility.

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

data_processing:
Raw data were processed with Affymetrix Expression console software for background correction and normalization.
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

organism: Mus musculus

source_name: PBS treated primary cardiomyocytes

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT plus reagent kit. (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was extracted according to the manufacturer's instructions of Qiagen Rneasy MiNi Kit.

treatment_protocol: Primary cardiomyocytes were exposed to 2 µg/ml LeTx for 24h, with PBS as a negative control.

value: Balb/c

tag: age

value: heart

tag: cell type

value: primary cardiomyocytes

tag: exposed to

value: PBS (negative control) for 24hrs


title: Primary cardiomyocytes-LeTx-24h-rep1

source_name: LeTx treated primary cardiomyocytes

value: 2 µg/ml Anthrax lethal toxin (LeTx) for 24hrs


title: Primary cardiomyocytes-LeTx-24h-rep4


title: breast cancer cell S16

city: Shantou

first: Jianzhen

last: Xu

address: No.22 Rd Xinling

country: China

institute: Shantou University Medical College

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65℃ in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 4 out of 11 tissue samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses.Differentially expressed circRNAs with statistical significance between two samples or two groups were identified using fold change cutoff or through Volcano Plot filtering respectively.

organism: Homo sapiens

source_name: breast cancer cell

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: Cells are cultured in EMEM containing 2 mM L-glutamine, 0.01 mg/mL bovine insulin (90%), fetal bovine serum (10%) and Earle’s BSS containing 1.5 g/L sodium bicarbonate, 0.1 mM non-essential amino acids and 1 mM sodium pyruvate.

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

treatment_protocol: Treated with Trizol for extraction

tag: cell line

value: breast cancer

tag: subtype

value: Primary cells isolated from breast ductal carcinoma


title: KO 2

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

tag: genotype


title: Primary cardiomyocytes-LeTx-24h-rep2


title: Asp_1_ant_budr-mRNA

description: Asparagus, 0.5 - 1.0 mm anthers (whole buds), BM14-182

value: floral bud


title: control 1

description: replicate 1

value: control


title: Asp_1_0_ant-sRNA

description: Asparagus, 0.5 - 1.0 mm anthers, BM14-184

value: anther


title: Asp_0_5_ant_budr-mRNA

description: Asparagus, <0.5 mm anthers (whole buds), BM14-181


title: Asp_1_5_ant-sRNA

description: Asparagus, 1.0 - 1.5 mm anthers, BM14-185


title: Asp_1_5_ant_bud-sRNA

description: Asparagus, 1.0 - 1.5 mm anthers (whole buds), BM14-183


title: Primary cardiomyocytes-LeTx-24h-rep3


title: KO 3

description: replicate 3


title: Primary cardiomyocytes-No LeTx-24h-rep1

description: P-cardio-No LeTx-1


title: Control-con_2

city: Wuhan

first: Huang

last: Fang

address: Jiefang  Avenue, qiaokou district, wuhan city, hubei province

institute: Tongji medical college huazhong university of science and technology

description: Ds-cDNA was synthesized from 2 μg total RNA using an Amino Allyl messageAmp II kit. The purified cDNA was quantified using NanoDrop ND-1000 spectrophotometer. After the microarray was washed and hybridized, scanning was processed using GenePix 4000B. Quantile normalization and subsequent data analysis were performed using Agilent 2200 Bio-analyzer.

hyb_protocol: pre-hybridization:  1)Assembled  CustomArray™ microarray with Hybridization Cap and Clips；  2)Fill the hybridization chambers with nuclease-free water.Avoid introducing air bubbles into the chambers. Cover the solution portals with adhesive tape to evaporation.  3)Incubate at 65°C for 10min.  4)Remove the microarray from the incubator and bring to room temperature.Remove the adhesive tape and aspirate the water out of the hybridization chambers.  5)Fill the hybridization chambers with Pre-hybridization Solution.Mix gently by pipetting.A small air bubble can be introduced to improve the mixing process if the arrays are rotated.Wipe the surface clean with a lint-free tissue and cover the solution portals with adhesive tape.  6)Load the microarry onto the rotisserie in the hybridization oven and incubate at 37°C for 60 min with gentle rotation.    Hybridization:  1)Prepare the hybridization solution with labeled mRNA target .  2)Denature the hybridization solution at 95°C for 3 minutes,and then cool for 20 seconds on ice.Remove the hybridization solution from ice and keep it at room temperature.  3)Spin down the hybridization solution in a microcentrifuge for 5 seconds at maximum speed.  4)Remove the adhesive tape and pipet the pre-hybridization solution out of the hybridization chambers.  5)Fill the hybridization chambers with the hybridization solution and mix gently with repeated pipetting.A small air bubble wil form,and it will improve the mixing process if the arrays are rotated in the hybridization rotisserie oven.  6)Carefully wipe excess solution from the surface of the hybridization cap with a lint-free tissue,and cover the solution portals with adhesive tape.  7)Load the microarry onto the rotisserie in the hybridization oven and incubate at 37°C for 16 hours with gentle rotation.    Hybridization washing:  1)Remove the microarray from the hybridization oven.Remove the adhesive tape and pipet the hybridization solution out of the chambers.  2)Using the Wash solution 1,rinse the hybridization chambers,fill the chambers,and incubate the array for 3 minutes at room temperatrue.Remove the Wash solution 1 from the hybridization chambers.  3)Using the Wash solution 2,rinse the hybridization chambers,fill the chambers,and incubate the array for 3 minutes at room temperatrue.Remove the Wash solution 2 from the hybridization chambers.  4)Using the Wash solution 3,rinse the hybridization chambers,fill the chambers,and incubate the array for 3 minutes at room temperatrue.Remove the Wash solution 3 from the hybridization chambers.  5)Repeat step one more time for a total of two washings with the Wash solution 3.

scan_protocol: Imaging is done by laser scanner GenePix4000B(Molecular Device). At first, remove the microarray from the clamp and place it horizontally. Then cover the semiconductor microarray surface with the imaging solution. Using a fresh lifterslip cover it,taking care not to introduce air bubbles. At last, load the microarray into the scanner to scan.

data_processing: Raw signals were normalized with subtract background correction and quantile normalization method, Normalized intensities were transformed to gene expression log2 value. Ratio and log2 ratio of normalized spot intensites between test sample and control sample were calculated. The p-values are calculated with ANOVA Method(O'Mahony, Michael (1986). Sensory Evaluation of Food: Statistical Methods and Procedures. CRC Press. pp. 487. ISBN 0-8247-7337-3). It means the probability of control sample and test sample are no differential expression. So, if p-value (Differentially expressed) is greater than thethreshold it means no differential expression was observed.

organism: Rattus norvegicus

source_name: cortical neurons

label_protocol: 1. Reverse Transcription to Synthesize First Strand cDNA is primed with the T7 Oligo(dT) Primer to synthesize cDNA containing a T7 promoter sequence.  2. Second Strand cDNA Synthesis converts the single-stranded cDNA into a double-stranded DNA (dsDNA) template for transcription. The reaction employs DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second-strand cDNA.  3. cDNA Purification removes RNA, primers, enzymes, and salts that would inhibit in vitro transcription.  4. In Vitro Transcription to Synthesize Amino Allyl-Modified aRNA with aaUTP generates multiple copies of amino allyl-modified aRNA from the double-stranded cDNA templates; this is the amplification step.  5. aRNA Purification removes unincorporated NTPs, salts, enzymes, and inorganic phosphate to improve the stability of the aRNA and to facilitate NHS ester coupling or subsequent enzymatic reactions.  6.aRNA:Dye Coupling Reaction takes place between the amino allyl-modified UTP residues on the aRNA and amine reactive Cy5 dyes.  7. Dye Labeled aRNA Purification removes free dye and exchanges the buffer with Nuclease-free Water.

growth_protocol: Primary cortical neurons were isolated from embryonic E18 Sprague-Dawley rats.Neurons were cultured with Neurobasal medium supplemented with 2% B27 (maintenance medium).

extract_protocol: 1. For proper amount of cells or homogenized tissue, add 1mL of TRIzol reagent and mix by briefly vortex. Stand for 5 mins at room temperature. If a lot of insoluble material exists after homogenization and room-temperature incubation, remove by centrifugation at 12,000Xg for 10 mins at 4ºC. Transfer the supernatant to a fresh tube.  2. Add 200ul chloroform for 1ml mixture and vortex for 15 sec. Then stand for 5 mins at room temperature.  3. Centrifuge the mixture for 15 min at ≥12000xg at 4ºC.  4. Transfer the aqueous phase (the upper layer containing RNA) to a fresh tube.  5. Add equal volume of 100% Isopropanol to the aqueous phase, mix by inverting the tube several times.  6. Incubate at ‐20ºC for ≥30 min.  7. Centrifuge at 13000 rpm for 15 min at 4ºC.  8. Wash the pellet with 80% EtOH, invert the tube several times. Centrifuge at 7500 rpm for 5 min at -4ºC.  9. Carefully discard the supernatant without touching the pellet, dry the pellet at room temperature.  10. Dissolve the pellet with 20‐30ul DEPC-treated H2O, based on the size of the pellet. RNA solution should be stored at -80ºC.

treatment_protocol: Selective synaptic NMDAR stimulation was achieved by blocking GABAA receptor function with 50 μM bicucullin (Bic) in the presence of 2.5 mM 4-aminopyridine (4-AP), a weak potassium channel blocker. For extrasynaptic NMDAR stimulation, we first activated synaptic NMDAR with Bic/4AP treatment. After blocking activated synaptic NMDAR with 10 μM MK-801, 30 μM NMDA and 10 μM Glycine were applied to selectively activate extrasynaptic NMDAR

value: brain


title: Control-con_1


title: Control-con_3


title: NMDA-nmda_1


title: Primary cardiomyocytes-No LeTx-24h-rep2

description: P-cardio-No LeTx-2


title: NMDA-nmda_2


title: Asp_1_ant_bud-sRNA

source_name: Asparagus, 0.5 - 1.0 mm anthers (whole buds), BM14-182


title: NMDA-nmda_3


title: control 2

description: replicate 2


title: control 3

description: replicate 3


title: shoot_you_r1

description: Asparagus shoot, young plant, rep1, BM14-70

value: shoot (young)


title: Arsenite-transformed cells (HBE-T cells)

city: Chengdu

first: shiyan

middle: Shi

last: Gu

state: Sichuan

address: Number 17 on the 3rd The people of South Road

department: Department of Environmental and Occupational Health

institute: Sichuan University

description: The arsenite-induced malignant transformation HBE cells were established from the parental HBE cells by continuously maintaining in the medium containing 0 or 2.5 μM sodium arsenite (NaAsO2, Sigma, St. Louis, MO, purity: 99.0%) for 24 h per passage. This process was continued for 40 passages (about 13 weeks) and these NaAsO2 treatment cells were termed as HBE-T cells. The growth characteristics and malignant phenotypes of cells were observed under the microscope during the process of NaAsO2 exposure,

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.16.0) (Exiqon) according to array manual

scan_protocol: 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>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, differentially expressed miRNAs with statistical significance were identified through Volcano Plot filtering

source_name: HBE-T cells

label_protocol: The miRCURY™ Hy3™/Hy5™ Power labeling kit (Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling

growth_protocol: The cells were cultured in high glucose Dulbecco's modified Eagle's medium (DMEM, Life Technologies/Gibco, Grand Island, NY, USA) supplemented with 10% (v/v) fetal bovine serum, 100 units/mL penicillin and 100 μg/mL streptomycin. Cultures were maintained at 37°C in a humidified atmosphere containing 5% CO2 and 95% air.

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

treatment_protocol: The arsenite-induced malignant transformation HBE cells were established from the parental HBE cells as described previously with some modifications (7-8). Briefly, HBE cells were continuously maintained in the medium containing 0 or 2.5 μM sodium arsenite (NaAsO2, Sigma, St. Louis, MO, purity: 99.0%) for 24 h per passage. This process was continued for 40 passages (about 13 weeks) and these NaAsO2 treatment cells were termed as HBE-T cells. The growth characteristics and malignant phenotypes of cells were observed under the microscope during the process of NaAsO2 exposure,

value: malgnant transformed cells


title: Asp_0_5_ant_bud-sRNA

source_name: Asparagus, <0.5 mm anthers (whole buds), BM14-181


title: shoot_old_r1

description: Asparagus shoot, old spear, rep1, BM14-68

value: shoot (old)


title: HBE cells

description: Human bronchial epithelial (HBE) cell line is generously provided by Stem Cells and Tissue Engineering Laboratory, State Key Laboratory of Biotherapy, Sichuan University, China.

source_name: HBE cells

value: parent cells


title: C. jejuni PT14 filament stationary phase replicate 2

city: Loughborough

first: Ian

middle: Frank

last: Connerton

state: Leicestershire

address: College Road, Sutton Bonington

department: School of Biosciences

country: United Kingdom

institute: University of Nottingham

data_processing:
Illumina CASAVA v1.8.2
Illumina bcl2fastq v1.8.4
CLC Genomics Workbench 10.1 Trim and Quality Filter
CLC Genomics Workbench 10.1 RNAseq strand specific abundance and normalisation recorded as TPM (Transcripts Per Kilobase Million) and RPKM (Reads Per Kilobase Million)
Genome_build: C. jejuni PT14 NCBI accession CP003871.2
Supplementary_files_format_and_content: tab-delimited text files that include TPM and RPKM values for each gene location

organism: Campylobacter jejuni

source_name: Filamentous morphotype stationary phase

growth_protocol: Three independent biological replicates of C. jejuni PT14 were inoculated into 500 ml of sterile MEM (minimum essential medium without glutamine and phenol red; Catalogue number 51200-038; Life Technologies Ltd) with 10 mM sodium pyruvate, to a final density of approximately 10exp5 CFU/ml. The culture flasks were incubated in a shaking incubator at 100 rpm, at 37 °C under microaerobic conditions (approximately 7% O2, v/v) for 30 h.

extract_protocol:
Total RNA was isolated from the cell morphotypes using the Trizol Max Bacterial Isolation kit (Invitrogen) and purified using an RNeasy Mini kit (Qiagen) and the integrity was measured using a Bioanalyser 2100 (Agilent Technologies).
Ribosomal RNAs were depleted from the total RNAs using the Ribo-Zero™ Magnetic Kit for bacteria (Illumina) and used to prepare cDNA libraries using the NEBNext Ultra directional Prep Kit.

treatment_protocol: Short C. jejuni spiral cells were separated from filamentous cells using  a 0.8 µm sterile nitrocellulose membrane on a vacuum manifold.

tag: strain

tag: growth phase

value: Stationary

tag: cell morphology

value: Filamentous


title: pis_fe6_45mm_r1-sRNA

description: Asparagus pistil 4.5mm, female6, rep1, BM14-84

value: pistil


title: C. jejuni PT14 filament stationary phase replicate 1


title: C. jejuni PT14 spiral stationary phase replicate 3

source_name: Spiral morphotype stationary phase

value: Spiral


title: pis_fe5_42mm_r1-sRNA

description: Asparagus pistil 4.2mm, female5, rep1, BM14-82


title: Bicucullin-bic_2


title: pis_fe4_35mm_r1-sRNA

description: Asparagus pistil 3.5mm, female4, rep1, BM14-80


title: Bicucullin-bic_1


title: C. jejuni PT14 filament stationary phase replicate 3


title: C. jejuni PT14 spiral stationary phase replicate 2


title: Bicucullin-bic_3


title: TA_pair_4

city: Liverpool

first: Kim

last: Clarke

address: Crown Street

institute: University of Liverpool

hyb_protocol: 600 ng of labeled cRNA was hybridized to Agilent Sureprint G3 Mouse whole-genome microarrays according to manufacturers instructions

scan_protocol: Agilent SureScan microarray scanner

data_processing: Microarray data were log2 transformed and normalized using loess (normalizeWithinArrays function in R package marrray) without background subtraction

label_protocol: Cy3 and Cy5-labeled cRNA was generated using the Agilent Low-Input QuickAmp Kit following the manufacturer’s instructions.

growth_protocol: Mice were housed in standard housing units, fed ab libitum with rodent laboratory chow. Mice were sacrificed by cervical dislocation, and skeletal muscle was immediately removed, cleaned of any excess fat or connective tissue, and flash frozen in liquid nitrogen

extract_protocol: Frozen gastrocnemius, and tibialis anterior muscle was homogenized in RLT buffer (QIAGEN) with β-mercaptoethanol (1% v/v) using a Precellys-24 tissue homogenizer system (Precellys, UK). Each tissue lysate was centrifuged at 13,000 rpm for 10 min, and the supernatant was removed for RNA extraction. RNA was isolated using QIAGEN RNeasy columns following the manufacturer’s instructions. Sample purity was assessed by measuring absorbance at 260 and 280 nm using a NanoDrop spectrophotometer.

value: Het

value: WT


title: pis_fe2_20mm_r1-sRNA

description: Asparagus pistil 2.0mm, female2, rep1, BM14-76


title: C. jejuni PT14 spiral stationary phase replicate 1


title: TA_pair_3


title: TA_pair_2


title: TA_pair_1


title: Gastroc_pair_4

value: Gastrocnemius


title: Aurantimicrobium sp. strain MWH-Mo1, grown in constant dark. Replicate 2

city: Newark

first: Shawn

middle: William

last: Polson

state: DE

department: Center for Bioinformatics and Computational Biology

institute: University of Delaware

data_processing:
Quality filtering used Trim Galore v. 0.4.1, Cutadapt v. 1.12, and FASTQC with parameters trimming mode: single end, quality Phred score cutoff: 25, maximum trimming error rate: 0.1, minimum required adapter overlap: 1 bp, and minimum required sequence length before sequence gets removed: 35 bp to remove low-quality reads.
Alignment of reads to genomes used TopHat
Number of reads assigned to each gene calculated using Cufflinks
The number of reads assigned to genes in light and dark conditions were compared using Cuffmerge and the significance of this difference (H0 = there is no difference in the mean number of reads mapping to a particular gene) was tested using Cuffdiff.
Genome_build: GCF_003194085.1
Supplementary_files_format_and_content: cufflinks output - tracking_id,class_code,nearest_ref_id,gene_id,gene_short_name,tss_id,locus,length,coverage,FPKM,FPKM_conf_lo,FPKM_conf_hi,FPKM_status

organism: Aurantimicrobium photophilum

source_name: Bacterial culture

growth_protocol: Cultures (4 replicates, 50 mL each) of Rhl. lacicola and Aurantimicrobium sp. strain MWH-Mo1 were grown in 6 g L-1 NSY medium until late exponential phase in constant light (~30-40 µmol photons m-2 s-1 with a 13W compact fluorescent lamp) or darkness with gentle shaking.

extract_protocol:
Total RNA was extracted using protocols modified from the Qiagen RNAprotect Bacteria Reagent Handbook.
The ethanol-precipitated, rRNA-depleted RNA pellet was resuspended in 18 µL of the Fragment, Prime, Finish Mix from Illumina’s TruSeq Stranded mRNA LT product (RS-122-2101). RNA was fragmented for 1 min. at 94°C. Subsequently, cDNA copies of the RNA were synthesized using SuperScript II Reverse Trancriptase (Invitrogen 18064022) and double-stranded cDNA was purified with Agencourt AMPure XP beads (Beckman Coulter A63880) following Illumina’s TruSeq protocol (RS-122-9004DOC). The 3’ ends of the cDNA were adenylated, indexing adapters were ligated onto the ends, then the cDNA was amplified by PCR using primers that anneal to the ends of the adapters. The Pippin Blue DNA size selection system was used to select for fragments <500 bp.

treatment_protocol: Cells were harvested by centrifugation, resuspended in RNAlater (Invitrogen), and stored at -80°C until processing.

tag: light/dark

value: dark


title: Aurantimicrobium sp. strain MWH-Mo1, grown in constant dark. Replicate 4


title: Aurantimicrobium sp. strain MWH-Mo1, grown in constant dark. Replicate 1


title: Aurantimicrobium sp. strain MWH-Mo1, grown in constant dark. Replicate 3


title: Aurantimicrobium sp. strain MWH-Mo1, grown in constant light. Replicate 4

value: light


title: C. jejuni PT14 spiral exponential phase replicate 3

source_name: Spiral morphotype exponential phase

value: Exponential


title: Aurantimicrobium sp. strain MWH-Mo1, grown in constant light. Replicate 3


title: pis_fe1_15mm_r1-sRNA

description: Asparagus pistil 1.5mm, female1, rep1, BM14-74


title: Aurantimicrobium sp. strain MWH-Mo1, grown in constant light. Replicate 1


title: C. jejuni PT14 spiral exponential phase replicate 2


title: pis_fe3_28mm_r1-sRNA

description: Asparagus pistil 2.8mm, female3, rep1, BM14-78


title: pis_ma5_18mm_r1-sRNA

description: Asparagus pistil 1.8mm, male5 rep1, BM14-66


title: Daylily_01-mRNA

description: Daylily, <1.0 mm anthers, BM14-177

data_processing:
Sequenced reads were trimmed to remove adapters and converted to flat file format using the pre-processing script described in Mathioni et al. (DOI: 10.1002/cppb.20043). sRNA reads were normalized to empirically derived, 30 million reads base depth. Raw SMRT-sequencing data was pre-processed using the pbscript-tofu tool set (v2.3.0) from Pacific Biosciences using the default settings. The pre-processing included generation of subreads FASTA file using the RS_subreads protocol, followed by classification of reads to full-length and non-full-length categories, clustering of transcripts to consensus isoforms by ICE algorithm and final polishing by Quiver algorithm (min. accuracy = 0.99). For all downstream analysis, “high QV” transcript set generated from Quiver analyses was used. mRNA-seq assembly was performed using “Trinity RNA-Seq assembler”.For this, reads from paired-end libraries were first combined into two (FASTQ) files, one corresponding to left reads and other to right reads. Reads from the single-end libraries were then added to the combined left reads (FASTQ) file. These left and right reads files were used to generate a hybrid assembly with the default settings except for the minimum assembled contig length (set to 250 nt). ExN50 and the quality of assemblies was accessed as recommended in Trinity workflow. Transcripts from de novo assembly were annotated using Trinotate workflow with the default settings (https://trinotate.github.io/).
Supplementary_files_format_and_content: Flat file with tab separated reads and abundance counts for sRNAs, FASTA files for SMRT-seq and FASTA files for Illumina mRNA seq. Since the mRNAseq and SMRT-seq samples were used for transcriptome assembly, there are no quantitative data for these samples. The transcriptome assembly made from the mRNA-seq samples is available on the series record.

organism: Hemerocallis lilioasphodelus

source_name: Daylily, <1.0 mm anthers, BM14-177

growth_protocol: Flowering Daylily plants were harvested from fields at University of Delaware.


title: C. jejuni PT14 spiral exponential phase replicate 1


title: Gastroc_pair_2


title: Daylily_02-mRNA

description: Daylily, 1.5-2.0 mm anthers, BM14-178

source_name: Daylily, 1.5-2.0 mm anthers, BM14-178


title: Daylily_03mmr-mRNA

description: Daylily, 2.5-3.0 mm anthers, BM14-179

source_name: Daylily, 2.5-3.0 mm anthers, BM14-179


title: pis_ma4_15mm_r1-sRNA

description: Asparagus pistil 1.5mm,  male4, rep1, BM14-64


title: Gastroc_pair_1


title: Daylily_03-mRNA

description: Daylily, 2.5-3.0 mm anthers, BM14-179


title: Aurantimicrobium sp. strain MWH-Mo1, grown in constant light. Replicate 2


title: Gastroc_pair_3


title: Daylily_02mmr-mRNA

description: Daylily, 1.5-2.0 mm anthers, BM14-178


title: Daylily_01mmr-mRNA

description: Daylily, <1.0 mm anthers, BM14-177


title: pis_ma3_11mm_r1-sRNA

description: Asparagus pistil 1.1mm, male3 rep1, BM14-62


title: Daylily_wbudr-mRNA

description: Daylily, whole bud, no sepals, with <1.0 mm anthers, BM14-180

value: floral bud


title: pis_ma2_07mm_r1-sRNA

description: Asparagus pistil 0.7mm, male2 rep1, BM14-60


title: Daylily_le-mRNA

description: Daylily leaf rep1, BM14-01

source_name: Daylily leaf rep1, BM14-01

value: leaf


title: Daylily_fem_3_r1-sRNA

description: Daylily pistil stage 3 rep1, BM14-18

source_name: Daylily pistil stage 3 rep1, BM14-18


title: Daylily_leafr-mRNA

description: Daylily leaf rep1, BM14-01


title: pis_ma1_05mm_r1-sRNA

description: Asparagus pistil 0.5mm, male1 rep1, BM14-58


title: Daylily_fem_4_r1-sRNA

description: Daylily pistil stage 4 rep1, BM14-22

source_name: Daylily pistil stage 4 rep1, BM14-22


title: Daylily_wb-mRNA

source_name: Daylily, whole bud, no sepals, with <1.0 mm anthers, BM14-180


title: ant4_18mm_r1-sRNA

description: Asparagus anther 1.8mm, male4, rep1, BM14-54

value: anther


title: Daylily_fem_2_r1-sRNA

description: Daylily pistil stage 2 rep1, BM14-14

source_name: Daylily pistil stage 2 rep1, BM14-14


title: HSV_H3K27AC

city: Beijing

first: lili

last: Cao

address: Xueyuan road, haidian district

institute: Peking university health science center

library_source: genomic

data_processing:
Reads from ChIP-seq experiments were aligned to the mm9 revision of the mouse reference genome using only annotated chromosomes 1-19, chrX, chrY, and chrM  Alignment was performed using bowtie (Langmead et al., 2009) with parameters –best –k 1 –m 1 –sam and –l set to read  length.
Regions with an exceptionally high coverage of ChIP-Seq reads (i.e., peaks) were identified using MACS with parameters –keepdup = auto –p1e-9 and with corresponding input control.
Profiles of ChIP-seq signal at individual regions of interest were created by quantifying the signal in reads per million  per base pair (rpm/bp) in bins that equally divide each region of interest using bamToGFF (https://github.com/BradnerLab/pipeline)  with parameters –m 200 –r –d. Reads used for quantification were removed of presumed PCR duplicate reads using samtools  v0.1.19-44428cd rmdup.
Genome_build: mm9
Supplementary_files_format_and_content: text files include ChIP-Seq reads for each Sample

molecule: genomic DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27AC antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (VAHTS UniversalDNA Library Prep Kit for Illumina). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: macrophages

tag: infection status

value: HSV-1 infection

tag: chip antibody


title: Daylily_fem_1_r1-sRNA

description: Daylily pistil stage 1 rep1, BM14-10

source_name: Daylily pistil stage 1 rep1, BM14-10


title: ant2_11mm_r1-sRNA

description: Asparagus anther 1.1mm, male2, rep1, BM14-50


title: VSV_H3K27AC

value: VSV infection


title: no_treatment_H3K27AC

value: no treatment


title: Input

value: no treatment (input)

value: none (input)


title: ant1_07mm_r1-sRNA

description: Asparagus anther 0.7mm, male1, rep1, BM14-48


title: ant3_15mm_r1-sRNA

description: Asparagus anther 1.5mm, male3, rep1, BM14-52


title: Daylily_fem_0_r1-sRNA

description: Daylily pistil stage 0 rep1, BM14-06

source_name: Daylily pistil stage 0 rep1, BM14-06

value: pistil


title: R. lacicola strain Ta8, grown in constant dark. Replicate 4

data_processing:
Quality filtering used Trim Galore v. 0.4.1, Cutadapt v. 1.12, and FASTQC with parameters trimming mode: single end, quality Phred score cutoff: 25, maximum trimming error rate: 0.1, minimum required adapter overlap: 1 bp, and minimum required sequence length before sequence gets removed: 35 bp to remove low-quality reads.
Alignment of reads to genomes used TopHat
Number of reads assigned to each gene calculated using Cufflinks
The number of reads assigned to genes in light and dark conditions were compared using Cuffmerge and the significance of this difference (H0 = there is no difference in the mean number of reads mapping to a particular gene) was tested using Cuffdiff.
Genome_build: GCF_000699505.1
Supplementary_files_format_and_content: cufflinks output - tracking_id,class_code,nearest_ref_id,gene_id,gene_short_name,tss_id,locus,length,coverage,FPKM,FPKM_conf_lo,FPKM_conf_hi,FPKM_status

organism: Rhodoluna lacicola


title: ant5_20mm_r1-sRNA

description: Asparagus anther 2.0mm, male5, rep1, BM14-56


title: leaf_r1-sRNA

description: Asparagus cladophylls, rep1, BM14-72

source_name: Asparagus cladophylls, rep1, BM14-72


title: Daylily_ant_1_r1-sRNA

description: Daylily 4.1mm anther stage 1 rep1, BM14-08


title: R. lacicola strain Ta8, grown in constant dark. Replicate 3


title: Daylily_ant_2_r1-sRNA

description: Daylily 5.8mm anther stage 2 rep1, BM14-12


title: K562-parent

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

country: Japan

institute: Kinjo Gakuin University

description: Gene expression in K562 cells

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2519F-026652) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37Â°C GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 026652_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: K562 cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: K562 were provided by the ATCC through the American Type Culture Collection , and were grown in RPMI containing 10% fetal bovine serum (FBS) at 37 °C in a 5% CO2 incubator.

extract_protocol: RNA was prepared using RNeasy Mini Kit (Qiagen) following the manufacturer's recommendations. RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: K562  and the established cell clones  were plated at 80% confluence and cultured for 24 hours

tag: genotype/variation

value: parental K562

value: Human bone marrow

tag: gender

value: female


title: K562-FLT3-ITD-WT#1

description: Gene expression in K562-FLT3-ITD/WT#1cell clone

source_name: K562-FLT3-ITD/WT#1cell clone


title: DayLily-C-2-3KB-mRNA

description:
Single Molecule Real Time (SMRT) sequencing of full length (cDNA) transcripts
Daylily, 0.5-1.0mm anther, >3 kb insert length (3 SMRT cells)

source_name: Daylily, 0.5-1.0mm anther, >3 kb insert length (3 SMRT cells )


title: Daylily_ant_0_r1-sRNA

description: Daylily 3.3mm anther stage 0 rep1, BM14-04


title: K562-FLT3-ITD-WT#2

description: Gene expression in K562-FLT3-ITD/WT#2cell clone

source_name: K562-FLT3-ITD/WT#2cell clone


title: DayLily-B-3KB-mRNA

description:
Single Molecule Real Time (SMRT) sequencing of full length (cDNA) transcripts
Daylily, 0.5-1.0mm anther, 2-3 kb insert length (3 SMRT cells)


title: DayLily-A-1KB-mRNA

description:
Single Molecule Real Time (SMRT) sequencing of full length (cDNA) transcripts
Daylily, 0.5-1.0mm anther, 12kb insert length (3 SMRT cells)

source_name: Daylily, 0.5-1.0mm anther, <2kb insert length (3 SMRT cells)


title: Daylily_03mm-sRNA

description: Daylily, 2.5-3.0 mm anthers, BM14-179


title: R. lacicola strain Ta8, grown in constant dark. Replicate 2

source_name: Bacterial culture


title: Daylily_02mm-sRNA

description: Daylily, 1.5-2.0 mm anthers, BM14-178


title: K562-FLT3-ITD-ITD#1

description: Gene expression in K562-FLT3-ITD/ITD#1cell clone

source_name: K562-FLT3-ITD/ITD#1cell clone


title: R. lacicola strain Ta8, grown in constant dark. Replicate 1


title: R. lacicola strain Ta8, grown in constant light. Replicate 4


title: R. lacicola strain Ta8, grown in constant light. Replicate 3


title: Daylily_01mm-sRNA

description: Daylily, <1.0 mm anthers, BM14-177

source_name: Daylily, <1.0 mm anthers, BM14-177


title: R. lacicola strain Ta8, grown in constant light. Replicate 2


title: Aspa-denovo-B-2kb-3kb--SMRT

description:
Single Molecule Real Time (SMRT) sequencing of full length (cDNA) transcripts
Asparagus, <=0.5 and 0.5-1.0mm anther, 2-3 kb insert length (3 SMRT cells)


title: Aspa-denovo-A-2kb-SMRT

description:
Single Molecule Real Time (SMRT) sequencing of full length (cDNA) transcripts
Asparagus, <=0.5 and 0.5-1.0mm anther, <2kb insert length (3 SMRT cells)


title: R. lacicola strain Ta8, grown in constant light. Replicate 1


title: Aspa-denovo-C-3kb--SMRT

description:
Single Molecule Real Time (SMRT) sequencing of full length (cDNA) transcripts
Asparagus, <=0.5 and 0.5-1.0mm anther, >3 kb insert length (3 SMRT cells )


title: Daylily_leaf_1-sRNA

description: Daylily leaf rep1, BM14-01


title: Cast/Ei_oocyte_RNAseq_rep1

status: Public on Jul 06 2018

city: Vancouver

first: Matthew

middle: C

last: Lorincz

state: British Columbia

address: 2350 Health Sciences Mall

department: Medical Genetics

country: Canada

institute: University of British Columbia

data_processing:
RNA-seq: Paired-end reads were trimmed using Trimmomatic v.0.32, and aligned to the mm10 (mouse), hg19 (human) and rn6 (rat) assemblies using STAR v.2.4.0.i. Library technical quality was assessed using Picard-tools (http://broadinstitute.github.io/picard) v.1.92 and Samtools (http://www.htslib.org/) v.1.1. PCR duplicates were filtered out. Sequence alignment maps were converted to bedGraph and wiggle formats using Bedtools v2.22.1 and UCSC binary bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: GVO

extract_protocol:
RNA-seq: total RNA was isolated from 100-200 mouse or rat oocytes using TriReagent, and ribosomal RNA was depleted using NEB Next rRNA Depletion kit according to manufacturer’s instruction. Double stranded cDNA was synthesized using NEB Next first strand and second strand synthesis modules.
Libraries were constructed using a custom protocol (Brind’Amour et al. 2015) and amplified for 10-12 PCR cycles (RNA) or 15 PCR cycles (ChIP). 75 bp or 100bp paired-end libraries were sequenced on the NextSeq 500 or HiSeq 2500 platform an according to manufacturer’s protocols.

value: Cast/EiJ

value: oocyte

tag: developmental stage

value: GV


title: Cast/Ei_oocyte_RNAseq_rep2


title: Cast/Ei_oocyte_H3K36me3_rep1

data_processing:
ChIP-seq: Paired-end reads were trimmed using Trimmomatic v.0.32, and aligned to the mm10 (mouse), hg19 (human) and rn6 (rat) assemblies using Bowtie2 v.2.2.3 with soft-clipping enabled. Library technical quality was assessed using Picard-tools (http://broadinstitute.github.io/picard) v.1.92 and Samtools (http://www.htslib.org/) v.1.1. PCR duplicates and alignments with mapping quality less than 10 were filtered out. Sequence alignment maps were converted to bedGraph and wiggle formats using Bedtools v2.22.1 and UCSC binary bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol:
ChIP-seq: purified ChIP DNA was extracted with Phenol:chloroform followed by ethanol precipitation.
Libraries were constructed using a custom protocol (Brind’Amour et al. 2015) and amplified for 10-12 PCR cycles (RNA) or 15 PCR cycles (ChIP). 75 bp or 100bp paired-end libraries were sequenced on the NextSeq 500 or HiSeq 2500 platform an according to manufacturer’s protocols.

value: anti-H3K36me3 (Abcam ab9050)


title: C57BL/6_oocyte_RNAseq_rep2


title: C57BL/6_oocyte_RNAseq_rep1


title: C57BL/6_oocyte_H3K36me3_rep1


title: Arabidopsis Col-0 miR1510

data_processing:
The adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the Pigeon pea,  mung bean, and Arabidopsis genomes.
Genome_build: Pigeon pea Cc1.0; mung bean Vr1.0; Arabidopsis thaliana TAIR10.
Supplementary_files_format_and_content: Tag count file

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Arabidopsis and mung bean were grown in a growth chamber or greenhouse  with a light cycle of 16 h light / 8 h dark, at 22 to 23 °C. Pigeon pea plants were grown  in a greenhouse with a light cycle of 16 h light / 8 h dark, at 24 to 28 °C.

value: 2-week old

tag: ecotype


title: Daylily_wbud-sRNA

description: Daylily, whole bud, no sepals, with <1.0 mm anthers, BM14-180

tag: tissue

value: floral bud


title: IP-Control

city: Miami

first: Antonio

last: Barrientos

state: Florida

address: 1420NW 9th Street, NRB # 103

department: Neurology

institute: University of Miami Miller School of Medicine

data_processing:
Basecalls performed using Illumina RTA 1.18.64.
Samples demultiplexed using bcl2fastq 2.20.
Sequenced reads were trimmed for sequencing adapters and low quality extrimities using Trimmomatic  and mapped to the reference genome using Bowtie version 2.1.0.
Coverage was computed using Bedtools 2.26.0 and normalized according to the total number of mapped reads.
Genome_build: GRCh37
Supplementary_files_format_and_content: Bedgraph files containing the normalized coverage on the mitochondrial genome.

source_name: HEK293T cells

extract_protocol:
Cells stably expressing Flag-tagged MTG1 proteins were grown in medium supplemented with 100 uM 4–thiouridine (SU) for 14 hr, and subjected to UV-mediated protein-RNA crosslinking once with 150 mL/cm2 at 365 nm using a Stratalinker UV crosslinker (Stratagene) before disrupting them with 1% NP40 lysis buffer (PBS, 1% NP-40, 0.1% SDS, 0.5% sodium deoxycholate) supplemented with EDTA-free protease inhibitor cocktail (Roche), and ribonucleoside vanadyl complexes (NEB) for 10 min at 4˚C. 4SU-labeled non-irradiated cells were used as control. The lysate was spun at 30,000 rpm for 20 min at 4˚C in a TLA 100 rotor, and the eluted protein-RNA complexes were applied for immunoprecipitation with anti-FLAG M2 beads. Bound protein-RNA complexes were treated with DNase for 30 min at 37˚C, and RNA was extracted from the beads by proteinase K treatment and QIAzol extraction (Qiagen).
KAPA Stranded RNA-Seq Library Preparation Kit

tag: tagged gene

tag: ip

value: IgG


title: IP-MTG1-2

value: FLAG


title: Sample 113: T5-swab_S6

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

data_processing:
Binary base call (bcl) files were generated on the NextSeq500 instrument and coverted to fastq files using bcl2fastq software v1.8.4
Sequenced reads were trimmed for TruSeq Small RNA adaptor sequence
Alignment of mature miRNA reads was performed to the miRbase21 database using the Shrimp2 algorithm in Partek Flow software (Partek, Inc., St. Louis, MO)
Alignment of microbial transcripts was performed using K-Slam software, which references the NCBI Taxonomy database
Human miRNAs present at counts of 10 or and microbial taxon IDs present at counts of 5 or more in at least 20% and 10% of samples, respectively, were interrogated for oscillating expression
Genome_build: hg38
Supplementary_files_format_and_content: Separate tab-delimited text files include matrix of quantified read counts surpassing the filter cutoffs for mature human miRNAs and microbial taxon IDs

source_name: Saliva

extract_protocol:
Saliva was collected by an absorbent swab (Oragene RNA, DNA Genotek) and RNA was harvested using Qiazol reagent.
llumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

value: Saliva

tag: Sex

value: Male

tag: age (yrs)

tag: time of day

tag: collection day


title: IP-MTG1-1

tag: cell line


title: IP-MTG1-3


title: Sample 114: T6-swab_S12


title: Sample 116: T8-swab_S24


title: Sample 107: R11-swab_S17


title: Sample 119: T11-swab_S42


title: Sample 120: T12-swab_S48


title: Sample 117: T9-swab_S30


title: Sample 118: T10-swab_S36


title: Sample 111: T3-swab_S41


title: Sample 108: R12-swab_S23


title: Sample 112: T4-swab_S47


title: Sample 106: R10-swab_S11


title: Sample 109: T1-swab_S29


title: Sample 105: R9-swab_S5


title: Sample 104: R8-swab_S46


title: Sample 103: R7-swab_S40


title: Sample 101: R5-swab_S28


title: Sample 99: R3-swab_S16


title: Sample 98: R2-swab_S10


title: Sample 115: T7-swab_S18


title: Sample 24: M004-060516-pm_S48

value: Female


title: Sample 97: R1-swab_S4


title: Sample 110: T2-swab_S35


title: Sample 23: M004-060516-am_S42


title: Sample 20: M004-052616-pm_S46


title: Sample 22: M004-053116-pm_S36


title: Sample 17: M003-060516-am_S18


title: Sample 15: M003-053116-am_S6


title: Sample 18: M003-060516-pm_S24


title: Sample 8: M002-052616-pm_S22


title: Sample 12: M002-060516-pm_S47


title: Sample 10: M002-053116-pm_S35


title: Sample 100: R4-swab_S22


title: Sample 21: M004-053116-am_S30


title: Sample 16: M003-053116-pm_S12


title: Sample 4: M001-053116-pm_S11


title: Sample 13: M003-052616-am_S28


title: Sample 7: M002-052616-am_S16


title: Sample 6: M001-060516-pm_S23


title: Sample 1: M001-052616-am_S4


title: Sample 72: J703-16_S48


title: Sample 14: M003-052616-pm_S34


title: Sample 3: M001-053116-am_S5


title: Sample 11: M002-060516-am_S41


title: Sample 70: J703-14_S36


title: Sample 71: J703-15_S42


title: Sample 68: J703-12_S24


title: Sample 102: R6-swab_S34


title: Sample 69: J703-13_S30


title: Sample 9: M002-053116-am_S29


title: Sample 2: M001-052616-pm_S10


title: Sample 5: M001-060516-am_S17


title: Sample 67: J703-11_S18


title: Sample 64: J703-8_S47


title: Sample 63: J703-7_S41


title: Sample 65: J703-9_S6


title: Sample 59: J703-3_S17


title: Sample 66: J703-10_S12


title: Sample 57: J703-1_S5


title: Sample 19: M004-052616-am_S40


title: Sample 56: J702-16_S46


title: Sample 61: J703-5_S29


title: Sample 60: J703-4_S23


title: Sample 51: J702-11_S16


title: Sample 52: J702-12_S22


title: Sample 50: J702-10_S10


title: Sample 62: J703-6_S35


title: Sample 58: J703-2_S11


title: Sample 45: J702-5_S27


title: Sample 47: J702-7_S39


title: Sample 54: J702-14_S34


title: Sample 48: J702-8_S45


title: Sample 49: J702-9_S4


title: Sample 53: J702-13_S28


title: Sample 46: J702-6_S33


title: Sample 44: J702-4_S21


title: Sample 43: J702-3_S15


title: Sample 41: J702-1_S3


title: Sample 55: J702-15_S40


title: Sample 40: J701-16_S44


title: Sample 36: J701-12_S20


title: Sample 34: J701-10_S8


title: Sample 32: J701-8_S43


title: Sample 39: J701-15_S38


title: Sample 35: J701-11_S14


title: Sample 37: J701-13_S26


title: Sample 28: J701-4_S19


title: Sample 38: J701-14_S32


title: Sample 25: J701-1_S1


title: Sample 27: J701-3_S13


title: Sample 29: J701-5_S25


title: Sample 33: J701-9_S2


title: Sample 31: J701-7_S37


title: Sample 42: J702-2_S9


title: Sample 96: J12-swab_S45


title: Sample 26: J701-2_S7


title: 1.2B_Schz_ATACseq_replicate2

city: Granada

first: Jose

middle: Luis

last: Ruiz Rodriguez

state: Granada

address: Avda. del Conocimiento 17. P. T. Ciencias de la Salud

country: Spain

institute: IPBLN-CSIC

description:
1.2BT4SchzR2
10G and 1.2B are subclones derived from the 3D7 strain (Rovira-Graells et al. 2012. PMID 22415456).
processed data file: 1.2B_MACS2_peaks_merged_ATAC_rpkm_counts.txt

data_processing:
Paired reads were aligned to the P. falciparum reference genome Pf3D7-28 (PlasmoDB) with Bowtie2 (v.2.3.1), using parameters --no-unal --no-mixed -X 2000. Reads were trimmed 10 bases from each read 3' end (-3 10).
Alignment files were sorted and deduplicated using Samtools (v.1.4). Quality threshold of 10 in MAPQ score was applied.
To adjust for fragment size and make sure Tn5 cutting site was mapped, aligned reads were shifted +4bp for + strands and -5 bp for – strands.
Nucleosome-free fragments were extracted filtering mapped reads with a size threshold of 130 bp.
Peak calling on nucleosome-free reads was performed using MACS2 (v.2.1.1) using the module “callpeak” with the c- option where the input corresponds to the transposed genomic DNA (gDNA) that we use as a control. Parameters used were as default except for -g 2.41e7 --keep-dup all -q 0.01 --nomodel --shift -35 --extsize 75 and -B.
We performed independent peak calling for each biological replicate, on the pooled sample and on the pseudoreplicates, and keep only consensus THSSs regions if present in the three data sets (replicate, pooled and pseudoreplicate). THSSs regions located in mitochondrion and apicoplast chromosomes were removed.
THSSs regions were annotated to genomic features using HOMER and the ones corresponding to the same genomic region from different stages merged using bedtools merge.
Genome_build: Pf3D7-28 (PlasmoDB)
Supplementary_files_format_and_content: *_bdgcmp-ppois.bedgraph: Tracks of ATAC signal, normalized and input (gDNA) corrected, per stage of development. The bedGraphs were built with MACS2 “bdgcmp" module (-m ppois).
Supplementary_files_format_and_content: *_MACS2_peaks_merged_ATAC_rpkm_counts.txt: Counts of normalized (RPKM) and input corrected nucleosome-free reads per stage of development and subclone computed for MACS2 merged peaks (txt).
Supplementary_files_format_and_content: *_track.bed: Peaks

organism: Plasmodium falciparum

growth_protocol: Parasites were cultured in B+ erythrocytes (3% hematocrit) under standard conditions with media containing Albumax II and no human serum.

extract_protocol:
Cultures were tightly synchronized to a defined 5 h age window by purification of parasites at the schizont stage using Percoll gradients (63% Percoll) followed by sorbitol lysis 5 h later, which eliminates erythrocytes infected with late asexual stages (trophozoites and schizonts). Parasites were collected at the following times post invasion: 10-15 hpi (early ring stage), 20-25 hpi (late ring stage), 30-35 hpi (trophozoite stage) and 40-45 hpi (schizont stage). Genomic DNA was isolated by proteinase K treatment (0.2 mg/ml, 55°C for 3 hr and 95°C for 25 min), then RNase treatment (1.25 mg/ml, 37°C for 30 min). Genomic DNA was purified from schizonts by phenol/chloroform/isoamyl alcohol (25:24:1, pH 8.0) extraction, with an additional chloroform extraction, and precipitated with ethanol and NaOAc (3mM, pH 5.5), and resuspended in TE (10mM Tris-HCl pH7.5, 1mM EDTA). 10ng of gDNA used for a standard ATAC-seq protocol as described by the Nextera library preparation protocol by Illumina (5 min at 55º C).
ATAC-seq protocol was performed using 10 million cells for early ring, late ring and throphozoite cell stages and 1 million cells for schizonts that were obtained after saponin RBC lysis. Parasite cells were resuspended in lysis buffer in order to permeabilize membranes. The nuclei pellet were immediately resuspended in the transposition reaction mix (25 μl of 2x TD Buffer, 1.25 μl of Tn5 Transposase and 23.75 μl of nuclease-free water), and incubated for 30 min at 37ºC. The samples were purified using the Qiagen MiniElute Kit. Following purification, library amplification was carried out with 2X KAPA HiFi mix and 1.25 μM of Nextera primers. Optimal cycle number was determined using qPCR. ATAC-seq libraries were sequenced using an Illumina HiSeq2000 sequencer to obtain 20-40M of 2x50 bp paired-end sequencing reads.

tag: subclone

tag: cell type

value: culture of parasite cells

value: schizont (40-45h)

tag: replicate


title: 1.2B_Schz_ATACseq_replicate1

description:
1.2BT4SchzR1
10G and 1.2B are subclones derived from the 3D7 strain (Rovira-Graells et al. 2012. PMID 22415456).
processed data file: 1.2B_MACS2_peaks_merged_ATAC_rpkm_counts.txt


title: Sample 93: J9-swab_S27


title: 1.2B_Troph_ATACseq_replicate2

description:
1.2BT3TrophR2
10G and 1.2B are subclones derived from the 3D7 strain (Rovira-Graells et al. 2012. PMID 22415456).
processed data file: 1.2B_MACS2_peaks_merged_ATAC_rpkm_counts.txt

value: trophozoite (30-35h)


title: Sample 30: J701-6_S31


title: 1.2B_Troph_ATACseq_replicate1

description:
1.2BT3TrophR1
10G and 1.2B are subclones derived from the 3D7 strain (Rovira-Graells et al. 2012. PMID 22415456).
processed data file: 1.2B_MACS2_peaks_merged_ATAC_rpkm_counts.txt


title: 1.2B_LRing_ATACseq_replicate1

description:
1.2BT2LRingR1
10G and 1.2B are subclones derived from the 3D7 strain (Rovira-Graells et al. 2012. PMID 22415456).
processed data file: 1.2B_MACS2_peaks_merged_ATAC_rpkm_counts.txt

value: late ring (20-25h)


title: gDNA_ATACseq

description:
gDNA
10G and 1.2B are subclones derived from the 3D7 strain (Rovira-Graells et al. 2012. PMID 22415456).


title: Sample 92: J8-swab_S21


title: Sample 95: J11-swab_S39


title: 1.2B_ERing_ATACseq_replicate2

description:
1.2BT1ERingR2
10G and 1.2B are subclones derived from the 3D7 strain (Rovira-Graells et al. 2012. PMID 22415456).
processed data file: 1.2B_MACS2_peaks_merged_ATAC_rpkm_counts.txt

value: early ring (10-15h)


title: Sample 91: J7-swab_S15


title: Sample 90: J6-swab_S9


title: 10G_Schz_ATACseq_replicate2

description:
10GT4SchzR2
10G and 1.2B are subclones derived from the 3D7 strain (Rovira-Graells et al. 2012. PMID 22415456).
processed data file: 10G_MACS2_peaks_merged_ATAC_rpkm_counts.txt


title: Sample 89: J5-swab_S3


title: 1.2B_ERing_ATACseq_replicate1

description:
1.2BT1ERingR1
10G and 1.2B are subclones derived from the 3D7 strain (Rovira-Graells et al. 2012. PMID 22415456).
processed data file: 1.2B_MACS2_peaks_merged_ATAC_rpkm_counts.txt


title: Sample 88: J4-swab_S44


title: Sample 94: J10-swab_S33


title: 1.2B_LRing_ATACseq_replicate2

description:
1.2BT2LRingR2
10G and 1.2B are subclones derived from the 3D7 strain (Rovira-Graells et al. 2012. PMID 22415456).
processed data file: 1.2B_MACS2_peaks_merged_ATAC_rpkm_counts.txt


title: Sample 87: J3-swab_S38


title: Sample 84: D12-swab_S20


title: 10G_ERing_ATACseq_replicate2

description:
10GT1ERingR2
10G and 1.2B are subclones derived from the 3D7 strain (Rovira-Graells et al. 2012. PMID 22415456).
processed data file: 10G_MACS2_peaks_merged_ATAC_rpkm_counts.txt


title: Sample 85: J1-swab_S26


title: 10G_ERing_ATACseq_replicate1

description:
10GT1ERingR1
10G and 1.2B are subclones derived from the 3D7 strain (Rovira-Graells et al. 2012. PMID 22415456).
processed data file: 10G_MACS2_peaks_merged_ATAC_rpkm_counts.txt


title: Sample 83: D11-swab_S14


title: Sample 82: D10-swab_S8


title: 10G_LRing_ATACseq_replicate2

description:
10GT2LRingR2
10G and 1.2B are subclones derived from the 3D7 strain (Rovira-Graells et al. 2012. PMID 22415456).
processed data file: 10G_MACS2_peaks_merged_ATAC_rpkm_counts.txt


title: Sample 79: D7-swab_S37


title: 10G_LRing_ATACseq_replicate1

description:
10GT2LRingR1
10G and 1.2B are subclones derived from the 3D7 strain (Rovira-Graells et al. 2012. PMID 22415456).
processed data file: 10G_MACS2_peaks_merged_ATAC_rpkm_counts.txt


title: Sample 80: D8-swab_S43


title: Sample 78: D6-swab_S31


title: 10G_Troph_ATACseq_replicate2

description:
10GT3TrophR2
10G and 1.2B are subclones derived from the 3D7 strain (Rovira-Graells et al. 2012. PMID 22415456).
processed data file: 10G_MACS2_peaks_merged_ATAC_rpkm_counts.txt


title: Sample 86: J2-swab_S32


title: 10G_Schz_ATACseq_replicate1

description:
10GT4SchzR1
10G and 1.2B are subclones derived from the 3D7 strain (Rovira-Graells et al. 2012. PMID 22415456).
processed data file: 10G_MACS2_peaks_merged_ATAC_rpkm_counts.txt


title: Sample 77: D5-swab_S25


title: HC, amygdala_5

city: Atlanta

first: Adriana

last: Lori

state: GA

address: 101 Woodruff Circle

department: PsychDepartment of Psychiatry and Behavioral Sciences

institute: Emory University

description:
exp1_all_FPKM_exprs.txt
Sample_23_Homecage

data_processing:
Alignment to the mm10 UCSC Mouse Assembly was performed using STAR version 2.3 (Dobin et al, 2013).
Parameters were set using the annotation as a splice junction reference.
Sample reads were assembled into transcript models using cufflinks (v2.1.1).
Cuffdiff v2.1.1 (Trapnell et al, 2012)  was used to produce per sample FPKM expression levels and estimate differential expression between the sample groups.
Genome_build: Mus_musculus/UCSC/mm10/
Supplementary_files_format_and_content: .txt file includes FPKM values for each Sample

source_name: HC, amygdala

extract_protocol:
amygdala: miRNeasy Mini kit (Qiagen, CA); blood: PAXgene blood RNA kits (QIAGEN)
RNA libraries were prepared using the TruSeq protocol (Illumina)

tag: tag

value: brain-amygdala

tag: age

value: 2 - 3 months old

tag: treatment

value: Home Cage


title: HC, amygdala_2

description:
exp1_all_FPKM_exprs.txt
Sample_20_Homecage


title: HC, amygdala_4

description:
exp1_all_FPKM_exprs.txt
Sample_22_Homecage


title: HC, amygdala_6

description:
exp1_all_FPKM_exprs.txt
Sample_24_Homecage


title: FC, amygdala_6

description:
exp1_all_FPKM_exprs.txt
Sample_12_FC-Alone

source_name: FC, amygdala

value: Fear Conditioning


title: HC, amygdala_1

description:
exp1_all_FPKM_exprs.txt
Sample_19_Homecage


title: Sample 75: D3-swab_S13


title: Sample 76: D4-swab_S19


title: Sample 73: D1-swab_S1


title: Sample 74: D2-swab_S7


title: FC, amygdala_4

description:
exp1_all_FPKM_exprs.txt
Sample_10_FC-Alone


title: Sample 81: D9-swab_S2


title: FC, amygdala_3

description:
exp1_all_FPKM_exprs.txt
Sample_9_FC-Alone


title: FC, amygdala_2

description:
exp1_all_FPKM_exprs.txt
Sample_8_FC-Alone


title: FC, amygdala_1

description:
exp1_all_FPKM_exprs.txt
Sample_7_FC-Alone


title: Immo+FC, amygdala_4

description:
exp1_all_FPKM_exprs.txt
Sample_4_IMMO-FC

source_name: Immo+FC, amygdala

value: Immobilization + Fear Conditioning


title: E16.5_control_rep2

first: huanwei

last: huang

address: 7 Science Park Rd., ZGC life science park

institute: NIBS

data_processing:
Illumina Casava1.8 software used for basecalling.
For analysis, raw transcriptome sequence data were mapped to the mouse genome (GRCm38/mm9) using TopHat (v2.0.13) with default settings to produce a reference-guided transcript assembly.
Cufflinks (v2.2.1) was used to normalize expression levels for each sample to fragments per kilobase of transcript per million mapped reads (FPKM).
Genome_build: GRCm38/mm9
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

extract_protocol:
E16.5 lungs were lysed with Trizol (Life Techologies). Total RNA was extracted using a direct-Zol RNA mini prep kit (Zymo research).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: lung

value: Embryonic day 16.5

tag: genotype

value: Shh-Cre; Stk11F/+


title: E16.5_Shh-Stk11FF_rep2

value: Shh-Cre; Stk11F/F


title: Immo+FC, amygdala_3

description:
exp1_all_FPKM_exprs.txt
Sample_3_IMMO-FC


title: E16.5_control_rep1


title: Immo+FC, amygdala_2

description:
exp1_all_FPKM_exprs.txt
Sample_2_IMMO-FC


title: HC, blood_4

description:
exp1_all_FPKM_exprs.txt
Sample_14_24-bHomecage

source_name: HC, blood

value: blood


title: HC, blood_3

description:
exp1_all_FPKM_exprs.txt
Sample_13_23-bHomecage


title: Immo+FC, amygdala_1

description:
exp1_all_FPKM_exprs.txt
Sample_1_IMMO-FC


title: FC, amygdala_5

description:
exp1_all_FPKM_exprs.txt
Sample_11_FC-Alone


title: HC, blood_1

description:
exp1_all_FPKM_exprs.txt
Sample_11_19-bHomecage


title: HC, blood_2

description:
exp1_all_FPKM_exprs.txt
Sample_12_20-bHomecage


title: FC, blood_4

description:
exp1_all_FPKM_exprs.txt
Sample_9_10-bFC-Alone

source_name: FC, blood


title: E16.5_Shh-Stk11FF_rep1


title: FC, blood_3

description:
exp1_all_FPKM_exprs.txt
Sample_8_9-bFC-Alone


title: FC, blood_2

description:
exp1_all_FPKM_exprs.txt
Sample_7_8-bFC-Alone


title: FC, blood_1

description:
exp1_all_FPKM_exprs.txt
Sample_6_7-bFC-Alone


title: Immo+FC, blood_4

description:
exp1_all_FPKM_exprs.txt
Sample_4_4-bIMMO-FC

source_name: Immo+FC, blood


title: FC, blood_5

description:
exp1_all_FPKM_exprs.txt
Sample_10_12-bFC-Alone


title: Immo+FC, blood_3

description:
exp1_all_FPKM_exprs.txt
Sample_3_3-bIMMO-FC


title: Immo+FC, blood_2

description:
exp1_all_FPKM_exprs.txt
Sample_2_2-bIMMO-FC


title: rtTA + SOD2 shRNA 2-2

city: La Jolla

first: Gerald

last: Shadel

state: CA

address: 10010 N Torrey Pines Road MCBL-C

department: Biomedical Sciences

institute: Salk Institute for Biological Sciences

description: gene expression from adult mouse liver

hyb_protocol: Labeled cDNA was hybridized to whole transcriptome Mouse Gene 2.0 ST GeneChip microarrays at 45 degrees C for 16-18 hours. Hybridized microarrays were washed and stained on an Affymetrix GeneChip 450 fluidics station using the appropriate chip dependent fluidics script.

scan_protocol: Arrays were scanned and intensity data extracted using an GeneChip 3000 7G scanner.

data_processing: Three iSOD2 adapted liver samples from shRNA 1, and three samples from shRNA 2 were analyzed. Four total rtTA only littermate controls were analyzed, including 3 from the shRNA 2 cohort and 1 from the shRNA 1 cohort. Data were normalized with Genome Expression Console. PCA analysis was conducted in Genome Expression Console, and all data were exported into Affymetrix Transcriptome Software to obtain a list of differentially expressed genes. Differentially expressed genes (fold change greater than 1.01) from both SOD2 shRNA microarray lists were overlaid in Excel. Commonly differentially expressed genes were analyzed in Ingenuity Pathway Analysis Software (Figure 6.1) and Enrichr.

source_name: Four week old mouse liver

label_protocol: Samples were processed according to the Applied Biosystems WT Plus Reagent Kit protocol and the GeneChip WT Terminal Labeling and Hybridization kit protocol. Using the Applied Biosystems kit, 50ng-500ng of good quality, intact Total RNA was reverse transcribed using a proprietary mix of oligo-dT and random primers designed to prime both poly-A and non-poly-A transcripts, while reducing ribosomal representation. Single stranded cDNA was converted to ds-cDNA, and then amplified in a 16hr IVT reaction. Amplified RNA was then converted back to ss-cDNA. Using the GeneChip terminal labeling kit, ss-cDNA was fragmented and terminal labeled.

growth_protocol: SOD2 was knocked down during days 0-12.5e in utero by feeding pregnant dams doxycycline chow (625 mg/kg, Harlan Taklad). At four weeks of age, liver tissues were harvested and 25 mg of tissue was used to extract RNA.

extract_protocol: RNA was prepared from 25 mg of homogenized liver using the Qiagen RNeasy Kit Plus DNA exclusion columns.

treatment_protocol: Livers were rinsed with 1x PBS without calcium or magnesium before RNA purification.

value: liver

value: male

value: Rosa26-rtTA + SOD2 shRNA 2

value: 4 weeks


title: 10G_Troph_ATACseq_replicate1

description:
10GT3TrophR1
10G and 1.2B are subclones derived from the 3D7 strain (Rovira-Graells et al. 2012. PMID 22415456).
processed data file: 10G_MACS2_peaks_merged_ATAC_rpkm_counts.txt

value: culture of parasite cells

tag: developmental stage

value: trophozoite (30-35h)


title: rtTA 1

description: gene expression from adult mouse liver

tag: tissue


title: rtTA 3

description: gene expression from adult mouse liver


title: rtTA 2

description: gene expression from adult mouse liver


title: rtTA + SOD2 shRNA 2-1

description: gene expression from adult mouse liver


title: Immo+FC, blood_5

description:
exp1_all_FPKM_exprs.txt
Sample_5_6-bIMMO-FC


title: rtTA + SOD2 shRNA 2-3

description: gene expression from adult mouse liver


title: rtTA + SOD2 shRNA 1-1

description: gene expression from adult mouse liver

value: Rosa26-rtTA + SOD2 shRNA 1


title: UT-SCC-122

type: genomic

city: Helsinki

first: Outi

last: Monni

address: Haartmaninkatu 8

department: Research Programs Unit

country: Finland

institute: University of Helsinki

hyb_protocol: An arrayCGH was carried out using an Agilent Human Genome CGH 244A Oligo Microarray. The samples were preprocessed according to an Agilent protocol (version 6.0, November 2008; Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis).

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing:
Data were LOESS normalized, segmented with circular binary segmentation using an R package DNAcopy (1), and the regions with segment means more than two standard deviations from the mean (±0.67) of three self-versus-self control cell lines were called altered. The control cell lines are available under an ArrayExpress accession number E-MEXP-3415. The significance of frequent alterations was assessed with the GISTIC v.2.0.21 software (the parameters used were q < 0.25, tamp = 20.67, tdel = 2-0.67, cap = 2, join segment size = 20). Copy number polymorphic loci were excluded before data segmentation. The data were analyzed with the Anduril software framework (20). As due to the stringent criteria in arrayCGH analysis some previously reported alterations might be missed, the data were checked manually for consistency for selected regions with reported alterations.
The significance of frequent alterations was assessed with the GISTIC v.2.0.21 software (the parameters used were q < 0.25, tamp = 20.67, tdel = 2-0.67, cap = 2, join segment size = 20). Copy number polymorphic loci were excluded before data segmentation. The data were analyzed with the Anduril software framework (2).

source_name: head and neck cancer cell line

growth_protocol: The cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 2 mM L-glutamine, 10% fetal bovine serum, non-essential amino acids solution, penicillin (100 U/ml), and streptomycin (100 μg/ml) at 37°C in an atmosphere of 5% CO2 (all reagents were purchased from Lonza BioWhittaker, Allendale, NJ, USA)

extract_protocol: Genomic DNA was isolated from the cell lines using a DNeasy Blood and Tissue kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.

treatment_protocol: No treatment was carried out for the cells

tag: cancer type

value: Head and neck squamous cell carcinoma

tag: gender

tag: site-of-origin

value: buchal mucosa

source_name: control male DNA


title: γδ T-cell WT_rep3

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix Mouse Gene 2.0 ST GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using Partek Genomics Suite software v6.6

source_name: γδ T-cells from WT mouse

label_protocol: Twelve (12) nanograms of total RNA were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: WT and Rptor-/- cell populations were purified from mouse thymus by fluorescence activated cell sorting (FACS) based on the following cell surface markers: DN3a thymocytes (CD4-CD8-TCRγδ-TCRβ-CD25hiCd44-CD28-); ISP T-cells (CD4-CD8+TCRβ-); gd T-cells (CD4-CD8-TCRb-NK1-1-Gr1-).

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

value: γδ T-cells

value: WT


title: rtTA + SOD2 shRNA 1-3

description: gene expression from adult mouse liver

tag: Sex


title: rtTA 4

description: gene expression from adult mouse liver


title: γδ T-cell Raptorfl/fl_rep3

source_name: γδ T-cells from CD2-cre mouse crossed with Raptorfl/fl mouse

value: Rptor-/-


title: γδ T-cell WT_rep1


title: rtTA + SOD2 shRNA 1-2

description: gene expression from adult mouse liver


title: UT-SCC-126A

label_protocol: An arrayCGH was carried out using an Agilent Human Genome CGH 244A Oligo Microarray. The samples were preprocessed according to an Agilent protocol (version 6.0, November 2008; Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis).

value: female

value: lower lip

source_name: control female DNA


title: γδ T-cell Raptorfl/fl_rep2


title: γδ T-cell WT_rep2


title: γδ T-cell Raptorfl/fl_rep1


title: DN3a WT_rep2

source_name: DN3a thymocytes from WT mouse

value: DN3a thymocytes


title: DN3a WT_rep3


title: Immo+FC, blood_1

description:
exp1_all_FPKM_exprs.txt
Sample_1_1-bIMMO-FC

value: 2 - 3 months old

value: Immobilization + Fear Conditioning


title: UT-SCC-112

value: gingiva of mandib.


title: DN3a Raptorfl/fl_rep3

source_name: DN3a thymocytes from CD2-cre mouse crossed with Raptorfl/fl mouse


title: DN3a WT_rep1


title: UT-SCC-107

value: male

value: larynx


title: UT-SCC-110A

value: maxillary sinus


title: UT-SCC-114


title: UT-SCC-106A


title: UT-SCC-99

value: tongue


title: UT-SCC-95


title: UT-SCC-81


title: Mock inoculated leaves

city: Cuernavaca

first: Damien

last: Formey

state: Morelos

address: Avenida de la Universidad

department: Center for Genomic Science

country: Mexico

institute: UNAM

data_processing:
Contamination and adapter removal was carried out using in-house Perl scripts
Fastq sequences were filtered based on quality (FASTQ Quality Filter v0.0.6, Q 33
mapped on A. thaliana transcriptome (TAIR10) thanks to Bowtie2
Gene expression was calculated using RSEM v1.3
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: tab-delimited txt file of RSEM FPKM

source_name: Leaves

extract_protocol:
RNA was prepared using the Trizol reagent containing 38% saturated phenol, 0.8 M guanidine thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate and 5% glycerol as previously described (Blanc et al., 2018)
The RNA-seq libraries were prepared from total RNA using the Illumina TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) following the manufacturer’s instructions

tag: ecotype

value: Leaves


title: UT-SCC-74A


title: UT-SCC-73


title: UT-SCC-72

value: gingiva


title: UT-SCC-65

value: Head and neck squamous cell carcinoma

value: soft palate&tonsilla


title: HOFs-treated leaves


title: UT-SCC-60A

value: tonsil (left)


title: UT-SCC-87


title: UT-SCC-75


title: DN3a Raptorfl/fl_rep2


title: ISP WT_rep1

source_name: ISP T-cells from WT mouse

value: Immature Single Positive T-cells

value: WT


title: ISP WT_rep4


title: UT-SCC-76A


title: ISP WT_rep2


title: UT-SCC-47

value: floor of mouth


title: UT-SCC-53


title: DN3a Raptorfl/fl_rep1

value: Rptor-/-


title: Pooled RNA Ccnb3 mRNA 16-cell 2

city: Princeton

first: Nicholas

last: Treen

state: NJ

address: Carl Icahn Laboratory,, Princeton University, Washington Rd

institute: Princeton University

description:
whole 16-cell stage embryos
Full length cDNA from purified total RNA

data_processing:
Base calling software: HiSeq Control Software, Version: 2.2.58, defualt paramaters
Data filtering by Illumina default parameters
Data demultiplexed by unique barcodes and trimmed of illumina adaptors and polyA tails
Genome_build: Ciona intestinalis KH2012
Supplementary_files_format_and_content: Gene expression level determined by RPKM

organism: Ciona intestinalis

source_name: 16-cell embryos

growth_protocol: Dechorionated Ciona embryos were developed in artificial sea water

extract_protocol:
For single cells, cDNA was prepared directly from cell lysate. For pooled embryos total RNA was purified using Trizol.
cDNA was synthesized and amplified from the poly-A containing RNA transcripts in the single-cell lysate using the Smart-Seq2 method. cDNA from cells at 4-cell stage was amplified by 15 cycles of PCR, while 16 cycles of PCR was applied on the cDNA from cells of 8-cell and 16-cell stage embryos. The amplified cDNA samples were cleaned up with Ampure XP beads (Beckman Coulter, CA, USA), quantified by Qubit fluorometer (Invitrogen, CA, USA), and examined on Bioanalyzer with High Sensitivity DNA chips (Agilent, CA, USA) for size distribution. Nextera DNA library prep kit (Illumina, CA, USA) was used to convert the cDNA samples to Illumina sequencing libraries. For pooled embryo samples, cDNA synthesis and sequencing was performed as described for single-cells with the exception that 12 cycles of PCR were performed.

treatment_protocol: Single cells were hand dissected in calcium/magnesium free sea water following a brief protease treatment.

tag: genotype/variation

value: Ccnb3 over-expressed

tag: cell identity

value: 8 pooled embryos

value: 16-cell embryo


title: UT-SCC-54A

tag: cell line

value: female

value: buchal mucosa


title: Pooled RNA Ccnb3 mRNA 16-cell 3


title: ISP WT_rep3

tag: cell type


title: UT-SCC-44

value: gingiva of maxilla


title: ISP Raptorfl/fl_rep3

source_name: ISP T-cells from CD2-cre mouse crossed with Raptorfl/fl mouse


title: Pooled RNA Ccnb3 mRNA 16-cell 1


title: ISP Raptorfl/fl_rep1


title: Pooled RNA Ccnb3 MO 16-cell 3

value: Ccnb3 knockdown


title: ISP Raptorfl/fl_rep2


title: Pooled RNA Ccnb3 MO 16-cell 2


title: UT-SCC-42A

value: male

value: larynx


title: UT-SCC-43

value: gingiva of mandib.


title: UT-SCC-40

value: Head and neck squamous cell carcinoma

value: tongue


title: Pooled RNA Ccnb3 MO 16-cell 1


title: UT-SCC-55

value: gingiva


title: UT-SCC-38


title: Pooled RNA control 16-cell 3

value: control


title: UT-SCC-49


title: UT-SCC-37


title: Pooled RNA control 16-cell 2


title: Pooled RNA control 16-cell 1


title: Pooled RNA Ccnb3 MO 8-cell 2

description:
whole 8-cell stage embryos
Full length cDNA from purified total RNA

source_name: 8-cell embryos

value: 8-cell embryo


title: Pooled RNA Ccnb3 MO 8-cell 1


title: UT-SCC-36

value: floor of mouth


title: UT-SCC-29


title: Pooled RNA Ccnb3 MO 8-cell 3


title: Pooled RNA control 8-cell 3


title: UT-SCC-30

value: oral tongue


title: Pooled RNA control 8-cell 1


title: UT-SCC-21


title: Pooled RNA control 8-cell 2


title: UT-SCC-27


title: UT-SCC-19A


title: Pooled RNA Ccnb3 MO 4-cell 3

description:
whole 4-cell stage embryos
Full length cDNA from purified total RNA

source_name: 4-cell embryos

value: 4-cell embryo


title: UT-SCC-16A


title: UT-SCC-24A


title: Pooled RNA control 4-cell 3

value: 8 pooled embryos


title: Pooled RNA Ccnb3 MO 4-cell 1


title: UT-SCC-14


title: UT-SCC-10


title: UT-SCC-11


title: UT-SCC-8


title: Pooled RNA Ccnb3 MO 4-cell 2


title: Pooled RNA control 4-cell 1


title: Pooled RNA control 4-cell 2


title: HC, amygdala_3

description:
exp1_all_FPKM_exprs.txt
Sample_21_Homecage

source_name: HC, amygdala

value: brain-amygdala

value: 2 - 3 months old

value: Home Cage


title: Single cell 84 16-cell embryo 3

description:
Single isolated cell
Full length cDNA from single-cell lysate

source_name: 16-cell embryo 3

value: b5.4 cell

value: 16-cell embryo


title: UT-SCC-28

value: female


title: UT-SCC-6A

value: larynx


title: Single cell 83 16-cell embryo 3

value: b5.3 cell


title: UT-SCC-2

value: Head and neck squamous cell carcinoma

value: male

value: baseos oris


title: Single cell 82 16-cell embryo 3

value: a5.4 cell


title: Single cell 81 16-cell embryo 3

value: a5.3 cell


title: MafiWAT

city: Freising

first: Tobias

last: Fromme

address: Gregor-Mendel-Str. 2

department: Molecular Nutritional Medicine

country: Germany

institute: Technical University of Munich

description: humanBATWAT.txt

data_processing:
Sequencing software: HiSeq Control Software 2.2.58 Image analysis and base calling: Real-Time Analysis (RTA) 1.18.64 fastq-file generation: CASAVA BCL2FASTQ Conversion Software 1.8.3
Sequenced reads with masked adaptor sequence were mapped to the human genome, NCBI build 37, by the Genomatix Mapper 3.7.6 (Genomatix Mining Station, settings: 'deep', min. quality 92%).
Unique hits were subjected to expression analysis for RNA-seq (Genomatix Genome Analyzer, ElDorado version 12-2013) and provided as reads per kilobase of exon per megabase of library size (RPKM) as well as total read number.
Genome_build: human NCBI genome build 37
Supplementary_files_format_and_content: tab-delimited text file providing RPKM values for each sample.

source_name: WAT

extract_protocol:
Paired biopsies of WAT and BAT were obtained from the supraclavicular region of healthy subjects. Total RNA was prepared from frozen tissue with Trisue (Bioline) and column-purified (SV Total RNA Isolation System, Promega).
Libraries were constructed from enriched coding RNA (TruSeq RNA Access Coding Transcriptome, RS-301-2001, Illumina).

tag: individual

value: Mafi

value: WAT

value: BAT positive


title: MafiBAT

description: humanBATWAT.txt

source_name: BAT

value: BAT


title: JuaaWAT

description: humanBATWAT.txt

value: Juaa


title: Single cell 80 16-cell embryo 3

value: B5.2 cell


title: MivaWAT

description: humanBATWAT.txt

value: Miva


title: Single cell 77 16-cell embryo 3

value: A5.1 cell


title: PaoiBAT

description: humanBATWAT.txt

value: Päoi


title: MivaBAT

description: humanBATWAT.txt


title: JuaaBAT

description: humanBATWAT.txt


title: PaoiWAT

description: humanBATWAT.txt


title: Single cell 74 16-cell embryo 3

value: A5.2 cell

value: 16-cell embryo


title: Single cell 76 16-cell embryo 3


title: JaheBAT

description: humanBATWAT.txt

value: Jahe


title: JaheWAT

description: humanBATWAT.txt


title: Single cell 73 16-cell embryo 3


title: Single cell 75 16-cell embryo 3

value: B5.1 cell


title: TenoWAT

description: humanBATWAT.txt

value: Teno


title: TenoBAT

description: humanBATWAT.txt


title: Single cell 70 16-cell embryo 3


title: SihyWAT

description: humanBATWAT.txt

value: Sihy


title: Single cell 71 16-cell embryo 3

value: b5.3 cell


title: Single cell 72 16-cell embryo 3

value: b5.4 cell


title: SihyBAT

description: humanBATWAT.txt


title: Single cell 69 16-cell embryo 3

value: a5.3 cell


title: Single cell 78 16-cell embryo 3


title: JojuBAT

description: humanBATWAT.txt

value: Joju


title: JojuWAT

description: humanBATWAT.txt

value: WAT

value: BAT positive


title: Single cell 68 16-cell embryo 2

source_name: 16-cell embryo 2


title: Single cell 79 16-cell embryo 3


title: Single cell 66 16-cell embryo 2

value: a5.4 cell


title: Single cell 67 16-cell embryo 2


title: LakoWAT

description: humanBATWAT.txt

value: Lako


title: Single cell 65 16-cell embryo 2


title: NisiWAT

description: humanBATWAT.txt

value: Nisi

value: BAT negative


title: Single cell 64 16-cell embryo 2

value: B5.2 cell


title: Single cell 63 16-cell embryo 2


title: NisiBAT

description: humanBATWAT.txt

value: BAT


title: Single cell 62 16-cell embryo 2

value: A5.2 cell

value: 16-cell embryo


title: Single cell 61 16-cell embryo 2

value: A5.1 cell


title: ElsiBAT

description: humanBATWAT.txt

value: Elsi


title: Single cell 60 16-cell embryo 2


title: Single cell 59 16-cell embryo 2

value: B5.1 cell


title: SavadeWAT

description: humanBATWAT.txt

value: Savade


title: ElsiWAT

description: humanBATWAT.txt


title: AnliWAT

description: humanBATWAT.txt

value: Anli


title: SavadeBAT

description: humanBATWAT.txt


title: Single cell 58 16-cell embryo 2


title: Single cell 57 16-cell embryo 2


title: KimaWAT

description: humanBATWAT.txt

value: Kima


title: LakoBAT

description: humanBATWAT.txt


title: Single cell 56 16-cell embryo 2

value: b5.4 cell


title: Single cell 55 16-cell embryo 2

value: b5.3 cell


title: KimaBAT

description: humanBATWAT.txt


title: ToniWAT

description: humanBATWAT.txt

value: Toni

value: WAT


title: Single cell 54 16-cell embryo 2

value: a5.4 cell


title: ToniBAT

description: humanBATWAT.txt


title: Single cell 53 16-cell embryo 2

value: a5.3 cell


title: AnliBAT

description: humanBATWAT.txt

value: BAT negative


title: Single cell 52 16-cell embryo 1

source_name: 16-cell embryo 1


title: Single cell 51 16-cell embryo 1


title: Single cell 49 16-cell embryo 1


title: Single cell 48 16-cell embryo 1

value: B5.2 cell


title: Single cell 47 16-cell embryo 1


title: Single cell 50 16-cell embryo 1


title: eWAT Abhd15 KO, replicate 3

city: Graz

first: Juliane

last: Bogner-Strauss

address: Petersgasse 10-12/II

country: Austria

institute: Institute of Biochemistry, Graz University of Technology

description:
eWAT_KO_3
eWAT Gene expression data from a Abhd15 KO mouse placed for up to 14 weeks on NC

hyb_protocol: Affymetrix GeneChip® Mouse Gene 2.1 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray Average) quantile normalization and signal extraction using R package oligo

label: Biotin

source_name: eWAT Abhd15 KO

label_protocol: 200ng of total RNA were amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Nr. 4211511, Affymetrix, Santa Clara, CA)  and GeneChip® WT Terminal Labeling  (Nr. 4214400, Affymetrix, Santa Clara, CA)

growth_protocol: WT and Abhd KO mice were placed for up to 14 weeks NC diet.

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

tag: strain background

value: Abhd15 KO

value: male

tag: diet

value: Normal chow (NC)

value: epididymal white adipose tissue (eWAT)


title: eWAT WT, replicate 3

description:
eWAT_WT_3
eWAT Gene expression data from a WT mouse placed for up to 14 weeks on NC

source_name: eWAT WT

value: Wild Type (WT)


title: SAMPLE 15: Otx2-/-_d6_EB_rep3

city: Jinan

first: Detian

last: Yuan

address: Wenhuaxi 44

institute: Shandong University

hyb_protocol: The hybridizations were carried out by the Eurofins Genomics AROS in Denmark. The samples were hybdized on Illumina MouseWG-6 v2 BeadChip, with 6 samples on each chip.

scan_protocol: The scanning of the hybridized chips were carried out by the Eurofins Genomics AROS in Denmark. The chips were scanned on Illumina iScan.

data_processing: Quantile-normalization was performed using the "limma" package with the default settings.

source_name: Otx2-/-, SSEA1+; CD61+ population from day6 aggregates without cytokines, rep3

label_protocol: RNAs contain polyA tails were labeled using Illumina® TotalPrep™ RNA Amplification Kit (Illumina, cat.# AMIL1791) following manufacturer's instructions. Briefly, 100ng total RNA were reverse transcribed using oligodT primers, followed by 2nd strand cDNA synthesis. The biotin labelled complementary RNA (cRNA) were yielded following IVT of the dsDNAs at 37℃ for 12hours. The cRNAs were collected and quality analysed using Agilent Bioanalyzer 2100.

growth_protocol: EpiLCs were differentiated by plating naive ESCs into N2B27 medium with Activin, FGF and 1% KSR for 2 days. PGCLC were aggregated from dissociated EpiLCs in GK15 medium (15% KSR/GMEM) with cytokine cocktails, including BMP4, LIF, BMP8a, SCF and EGF. EB are aggregates, similar to PGCLCs, but with basal medium GK15 medium only. PGCLCs and EBs samples were collected at day6.

extract_protocol: Total RNAs were extracted using RNeasy Plus Micro Kit (Qiagen, cat.#74034), following supplier's instructions.

tag: treatment

value: D6, without cytokines


title: SAMPLE 16: Otx2-/-; Blimp1-/-_EpiLCs_rep1

source_name: Otx2-/-; Blimp1-/-, EpiLCs day2, rep1

value: 2 days, with cytokines FGF2 and ActivinA


title: SAMPLE 8: Otx2-/-_EpiLCs_rep2

source_name: Otx2-/-, EpiLCs day2, rep2


title: eWAT Abhd15 KO, replicate 5

description:
eWAT_KO_5
eWAT Gene expression data from a Abhd15 KO mouse placed for up to 14 weeks on NC


title: eWAT Abhd15 KO, replicate 4

description:
eWAT_KO_4
eWAT Gene expression data from a Abhd15 KO mouse placed for up to 14 weeks on NC


title: SAMPLE 17: Otx2-/-; Blimp1-/-_EpiLCs_rep2

source_name: Otx2-/-; Blimp1-/-, EpiLCs day2, rep2


title: SAMPLE 12: Otx2-/-_d6_PGCLC_rep3

source_name: Otx2-/-, SSEA1+; CD61+ population from PGCLC day6, rep3

value: D6, with PGCLC induction cytokines


title: SAMPLE 18: Otx2-/-; Blimp1-/-_EpiLCs_rep3

source_name: Otx2-/-; Blimp1-/-, EpiLCs day2, rep3


title: SAMPLE 7: Otx2-/-_EpiLCs_rep1

source_name: Otx2-/-, EpiLCs day2, rep1


title: SAMPLE 11: Otx2-/-_d6_PGCLC_rep2

source_name: Otx2-/-, SSEA1+; CD61+ population from PGCLC day6, rep2

value: D6, with PGCLC inductioncytokines


title: SAMPLE 6: E14Tg2a_d6_PGCLC_rep3

source_name: wildtype E14Tg2a, SSEA1+; CD61+ population from PGCLC day6, rep3

value: wildtype E14Tg2a


title: eWAT Abhd15 KO, replicate 2

description:
eWAT_KO_2
eWAT Gene expression data from a Abhd15 KO mouse placed for up to 14 weeks on NC


title: SAMPLE 13: Otx2-/-_d6_EB_rep1

source_name: Otx2-/-, SSEA1+; CD61+ population from day6 aggregates without cytokines, rep1


title: SAMPLE 10: Otx2-/-_d6_PGCLC_rep1

source_name: Otx2-/-, SSEA1+; CD61+ population from PGCLC day6, rep1


title: SAMPLE 4: E14Tg2a_d6_PGCLC_rep1

source_name: wildtype E14Tg2a, SSEA1+; CD61+ population from PGCLC day6, rep1


title: eWAT Abhd15 KO, replicate 1

description:
eWAT_KO_1
eWAT Gene expression data from a Abhd15 KO mouse placed for up to 14 weeks on NC


title: SAMPLE 3: E14Tg2a_EpiLCs_rep3

source_name: wildtype E14Tg2a, EpiLCs day2, rep3


title: eWAT WT, replicate 2

description:
eWAT_WT_2
eWAT Gene expression data from a WT mouse placed for up to 14 weeks on NC


title: SAMPLE 20: Otx2-/-; Blimp1-/-_d6PGCLC_rep2

source_name: Otx2-/-; Blimp1-/-, SSEA1+; CD61+ population from PGCLC day6, rep2


title: SAMPLE 19: Otx2-/-; Blimp1-/-_d6PGCLC_rep1

source_name: Otx2-/-; Blimp1-/-, SSEA1+; CD61+ population from PGCLC day6, rep1


title: Single cell 46 16-cell embryo 1

source_name: 16-cell embryo 1

value: A5.2 cell

value: 16-cell embryo


title: UT-SCC-67

source_name: head and neck cancer cell line

value: Head and neck squamous cell carcinoma

value: female

value: tongue

source_name: control female DNA


title: SAMPLE 21: Otx2-/-; Blimp1-/-_d6PGCLC_rep3

source_name: Otx2-/-; Blimp1-/-, SSEA1+; CD61+ population from PGCLC day6, rep3


title: Single cell 44 16-cell embryo 1


title: SAMPLE 9: Otx2-/-_EpiLCs_rep3

source_name: Otx2-/-, EpiLCs day2, rep3


title: SAMPLE 14: Otx2-/-_d6_EB_rep2

source_name: Otx2-/-, SSEA1+; CD61+ population from day6 aggregates without cytokines, rep2


title: CA95_GNF_2 (rna-seq)

city: Darlinghurst

first: Drew

last: Neavin

state: New South Wales

address: 384 Victoria St

department: Cellular Science

country: Australia

institute: Garvan Institute of Medical Research

description: counts.txt

data_processing:
Sequences were aligned to hg38 genome with Tophat (2.0.14)
Raw counts were calculated with subread (1.4.6)
Genome_build: hg38
Supplementary_files_format_and_content: tab separated file with raw counts for each sample in the columns

source_name: lymphoblastoid cell line

growth_protocol: Gown in RPMI 1640 + 15% FBS +1% P/S; passaged by spinning down at 120g for 5 minutes and resuspended in growth media; cultured in 37C with 5% CO2

extract_protocol:
Cells were pelleted at 300g for 5 minutes at 4C, resuspended in ice cold phosphate buffered saline and pelleted again.  RNA was extracted using the miRNeasy RNA extraction kit.
TruSeq RNA Library Prep Kit v2

treatment_protocol: Cells treated with 1uM 3-MC, 1uM GNF-351 or 0.1% DMSO in fresh media for 24 hours


title: Single cell 42 16-cell embryo 1


title: CA95_GNF_1 (rna-seq)

description: counts.txt


title: CA95_DMSO_1 (rna-seq)

description: counts.txt

value: DMSO


title: Single cell 43 16-cell embryo 1

value: B5.1 cell


title: CA95_DMSO_2 (rna-seq)

description: counts.txt


title: CA95_3MC_2 (rna-seq)

description: counts.txt


title: Single cell 41 16-cell embryo 1

value: A5.1 cell


title: SAMPLE 5: E14Tg2a_d6_PGCLC_rep2

source_name: wildtype E14Tg2a, SSEA1+; CD61+ population from PGCLC day6, rep2


title: Single cell 40 16-cell embryo 1

value: b5.4 cell


title: CA95_3MC_1 (rna-seq)

description: counts.txt


title: eWAT WT, replicate 1

description:
eWAT_WT_1
eWAT Gene expression data from a WT mouse placed for up to 14 weeks on NC

source_name: eWAT WT

value: male

value: Normal chow (NC)


title: Single cell 39 16-cell embryo 1

value: b5.3 cell


title: CA81_GNF_2 (rna-seq)

description: counts.txt


title: SAMPLE 2: E14Tg2a_EpiLCs_rep2

source_name: wildtype E14Tg2a, EpiLCs day2, rep2


title: UT-SCC-122 [HumanHT-12 V4.0]

description:
9234921044F
HNSCC.UT-SCC-122

data_processing: The gene expression data were quantile normalized using the lumi R package

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina total prep RNA Amplification kit

extract_protocol: Total RNA was isolated using a Macherey-Nagel (Düren, Germany) Nucleospin RNA II kit. The quality of total RNA was assessed with a 2100 Agilent Bioanalyzer

value: Head and neck squamous cell carcinoma cell line

value: buchal mucosa


title: UT-SCC-126A [HumanHT-12 V4.0]

description:
9234921015H
HNSCC.UT-SCC-126A

value: lower lip


title: Single cell 38 16-cell embryo 1

value: a5.4 cell


title: SAMPLE 1: E14Tg2a_EpiLCs_rep1

source_name: wildtype E14Tg2a, EpiLCs day2, rep1

value: wildtype E14Tg2a

value: 2 days, with cytokines FGF2 and ActivinA


title: CA81_GNF_1 (rna-seq)

description: counts.txt


title: UT-SCC-114 [HumanHT-12 V4.0]

description:
9234921044K
HNSCC.UT-SCC-114


title: UT-SCC-112 [HumanHT-12 V4.0]

description:
9234921044E
HNSCC.UT-SCC-112

value: gingiva of mandib.


title: CA81_DMSO_2 (rna-seq)

description: counts.txt


title: UT-SCC-106A [HumanHT-12 V4.0]

description:
9234921015D
HNSCC.UT-SCC-106A

value: larynx


title: Single cell 36 8-cell embryo 3

source_name: 8-cell embryo 3

value: B4.1 cell

value: 8-cell embryo


title: UT-SCC-107 [HumanHT-12 V4.0]

description:
9234921015E
HNSCC.UT-SCC-107


title: UT-SCC-99 [HumanHT-12 V4.0]

description:
9234921026F
HNSCC.UT-SCC-99

value: tongue


title: UT-SCC-87 [HumanHT-12 V4.0]

description:
9234921015B
HNSCC.UT-SCC-87


title: Single cell 35 8-cell embryo 3

value: A4.1 cell


title: CA81_DMSO_1 (rna-seq)

description: counts.txt

value: DMSO


title: UT-SCC-76A [HumanHT-12 V4.0]

description:
9234921015A
HNSCC.UT-SCC-76A


title: UT-SCC-81 [HumanHT-12 V4.0]

description:
9234921016K
HNSCC.UT-SCC-81


title: UT-SCC-95 [HumanHT-12 V4.0]

description:
9234921015C
HNSCC.UT-SCC-95


title: CA81_3MC_2 (rna-seq)

description: counts.txt


title: UT-SCC-74A [HumanHT-12 V4.0]

description:
9234921016H
HNSCC.UT-SCC-74A


title: UT-SCC-110A [HumanHT-12 V4.0]

description:
9234921015F
HNSCC.UT-SCC-110A

value: maxillary sinus


title: Single cell 34 8-cell embryo 3

value: b4.2 cell


title: CA81_3MC_1 (rna-seq)

description: counts.txt


title: Single cell 33 8-cell embryo 3

value: a4.2 cell


title: UT-SCC-75 [HumanHT-12 V4.0]

description:
9234921016J
HNSCC.UT-SCC-75


title: UT-SCC-73 [HumanHT-12 V4.0]

description:
9234921016G
HNSCC.UT-SCC-73


title: UT-SCC-67 [HumanHT-12 V4.0]

description:
9234921016F
HNSCC.UT-SCC-67


title: UT-SCC-54A [HumanHT-12 V4.0]

description:
9234921016B
HNSCC.UT-SCC-54A


title: CA76_GNF_2 (rna-seq)

description: counts.txt


title: UT-SCC-60A [HumanHT-12 V4.0]

description:
9234921016D
HNSCC.UT-SCC-60A

value: tonsil (left)


title: UT-SCC-72 [HumanHT-12 V4.0]

description:
9234921044D
HNSCC.UT-SCC-72

value: Head and neck squamous cell carcinoma cell line

value: gingiva


title: Single cell 37 16-cell embryo 1

value: a5.3 cell

value: 16-cell embryo


title: UT-SCC-55 [HumanHT-12 V4.0]

description:
9234921044C
HNSCC.UT-SCC-55


title: UT-SCC-65 [HumanHT-12 V4.0]

description:
9234921026G
HNSCC.UT-SCC-65

value: soft palate&tonsilla


title: Single cell 32 8-cell embryo 3


title: CA76_GNF_1 (rna-seq)

description: counts.txt


title: Single cell 31 8-cell embryo 3


title: CA76_DMSO_2 (rna-seq)

description: counts.txt


title: Single cell 30 8-cell embryo 3


title: CA76_DMSO_1 (rna-seq)

description: counts.txt


title: Single cell 29 8-cell embryo 3


title: CA76_3MC_2 (rna-seq)

description: counts.txt


title: UT-SCC-44 [HumanHT-12 V4.0]

description:
9234921015L
HNSCC.UT-SCC-44

value: gingiva of maxilla


title: Single cell 27 8-cell embryo 2

source_name: 8-cell embryo 2


title: CA64_GNF_2 (rna-seq)

description: counts.txt


title: Single cell 26 8-cell embryo 2


title: UT-SCC-47 [HumanHT-12 V4.0]

description:
9234921044J
HNSCC.UT-SCC-47

value: floor of mouth


title: CA64_GNF_1 (rna-seq)

description: counts.txt


title: UT-SCC-49 [HumanHT-12 V4.0]

description:
9234921016A
HNSCC.UT-SCC-49

value: larynx


title: UT-SCC-53 [HumanHT-12 V4.0]

description:
9234921044B
HNSCC.UT-SCC-53


title: UT-SCC-42A [HumanHT-12 V4.0]

description:
9234921014K
HNSCC.UT-SCC-42A


title: UT-SCC-36 [HumanHT-12 V4.0]

description:
9234921015J
HNSCC.UT-SCC-36


title: UT-SCC-38 [HumanHT-12 V4.0]

description:
9234921014D
HNSCC.UT-SCC-38


title: Single cell 25 8-cell embryo 2


title: UT-SCC-30 [HumanHT-12 V4.0]

description:
9234921014J
HNSCC.UT-SCC-30

value: oral tongue


title: UT-SCC-28 [HumanHT-12 V4.0]

description:
9234921015I
HNSCC.UT-SCC-28


title: UT-SCC-19A [HumanHT-12 V4.0]

description:
9234921014C
HNSCC.UT-SCC-19A


title: UT-SCC-27 [HumanHT-12 V4.0]

description:
9234921026D
HNSCC.UT-SCC-27


title: CA64_DMSO_2 (rna-seq)

description: counts.txt


title: UT-SCC-21 [HumanHT-12 V4.0]

description:
9234921014F
HNSCC.UT-SCC-21


title: UT-SCC-29 [HumanHT-12 V4.0]

description:
9234921014I
HNSCC.UT-SCC-29


title: Single cell 28 8-cell embryo 2

value: B4.1 cell

value: 8-cell embryo


title: UT-SCC-40 [HumanHT-12 V4.0]

description:
9234921044L
HNSCC.UT-SCC-40

value: tongue


title: UT-SCC-37 [HumanHT-12 V4.0]

description:
9234921015K
HNSCC.UT-SCC-37

value: gingiva of mandib.


title: CA76_3MC_1 (rna-seq)

description: counts.txt


title: Single cell 24 8-cell embryo 2


title: Single cell 23 8-cell embryo 2

value: A4.1 cell


title: UT-SCC-14 [HumanHT-12 V4.0]

description:
9234921044I
HNSCC.UT-SCC-14


title: UT-SCC-10 [HumanHT-12 V4.0]

description:
9234921044H
HNSCC.UT-SCC-10


title: CA64_3MC_2 (rna-seq)

description: counts.txt


title: Single cell 22 8-cell embryo 2

value: b4.2 cell