title: CjCutting_Base_3wpi_rep3

description:
Gene expression at 3 weeks post insertion in base of C. japonica cutting
Base of Cutting, 3 weeks hour post insertion, replicate 3

value: 3 weeks post insertion


title: KTB21-hTERT3_S25

status: Public on Dec 25 2018

type: SRA

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St.,R3 C218C

country: USA

institute: IU School of Medicine

description: mRNA-seq

library_source: transcriptomic

data_processing:
Base calling and quality scoring were performed by Real-Time Analysis (RTA) v2 in Illumina HiSeq 4000.
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to hg19 refGene genes using featureCounts (from subread v1.5.1) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 3 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.12.1).
Genome_build: UCSC hg19 (GRCh37)
Supplementary_files_format_and_content: *_Aligned.sortedByCoord.out.bam.counts.txt: Tab-delimited text files include raw counts in the last column.

molecule: total RNA

organism: Homo sapiens

source_name: Immortalized normal breast epithelial cell line

growth_protocol: Cells were cultured in low glucose (1 gm/liter) DMEM and F12 medium (1:3), supplemented with 5% fetal bovine serum (FBS; Gibco, USA), 1% penicillin/streptomycin (Corning, USA), 5µg/ml insulin, 0.4µg/ml hydrocortisone, 24µg/ml adenine (Sigma, USA), 10ng/ml EGF (Millipore, USA) and 10mM ROCK inhibitor.

extract_protocol:
Total RNA extraction and purification were done with Qiagen RNeasy Plus Mini Kit.
Illumina TruSeq Stranded mRNA Lib Prep Kit.

tag: cell type


title: CjCutting_Base_6wpi_rep1

type: RNA

city: Hitachi

first: Yuki

last: Fukuda

state: Ibaraki

department: Breeding Department, Breeding Division

country: Japan

institute: Forestry and Forest Products Research Institute, Forest Tree Breeding Center

description:
Gene expression at 6 weeks post insertion in base of C. japonica cutting
Base of Cutting, 6 weeks post insertion, replicate 1

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to 8×60k microarrays for 17 hours at 65°C in a rotating microarray hybridization oven (Agilent Technologies). After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute at 37°C with GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarray Scanner (Agilent Technologies) using one color scan setting for 8x60k array slides (Scan Region full agilent slide, Scan resolution 3 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 11.5 (Agilent Technologies) using default parameters (protocol: GE1_1105_Oct12 and Grid: 069025_D_F_20140811) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Cryptomeria japonica

source_name: Base of Cutting, 6 weeks post insertion

label_protocol: Cyanine-3 (Cy3) labeled cRNA were synthesized from 200 ng of total RNA from each sample using Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop 2000C (Thermo Fisher Scientific).

growth_protocol: Stem cuttings were excised from 18-year-old donor trees of C. japonica in the field and inserted into soil in a greenhouse with an automatic irrigation and no regulation of environment condition.

extract_protocol: Total RNA from each sample was extracted using RNeasy Plant Mini kit (Qiagen, Hilden, Germany) with a DNase digestion on-column using RNase-Free DNase Set (Qiagen). RNA concentration was measured by NanoDrop 2000C (Thermo Fisher Scientific, Waltham, MA, USA) and RNA integrity was assessed by Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using Agilent RNA 6000 Nano Kit (Agilent Technologies).

tag: clone

value: Tsukuba 1

tag: cutting

value: base

tag: time

value: 6 weeks post insertion


title: CjCutting_Base_3wpi_rep2

description:
Gene expression at 3 weeks post insertion in base of C. japonica cutting
Base of Cutting, 3 weeks hour post insertion, replicate 2


title: L6_11.5

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: S092_TruSeq_mm10_UCSC_20140923_093440_TS14

data_processing:
Read quality filtering: Every read that was considered valid by the Illumina control software was processed and filtered as follows: a) any 3' bases with a quality score of 'B' were removed; b) if the read ended in a poly(A)-sequence leaving less than 25 transcript-derived bases, the read was discarded; c) if the remaining sequence consisted of less than six non-A bases, or a dinucleotide repeat with less than six other bases at either end, the read was discarded.
Alignment:the reads were aligned to the genome using the Bowtie aligner, allowing for up to three mismatches and up to 24 alternative mappings for each read. Any reads with no alignments were re-aligned against an artifical chromosome, containing all possible splice junctions arising from the exons defined by the known transcript variants. Reads mapping within these splice junctions were translated back to the corresponding actual genomic positions. The UCSC transcript models were used for the expression level calculation. If a locus had several transcript variants, the exons of these were merged to a combined model that represented all expression from the locus. To account for incomplete cap site knowledge, the 5' ends of all models were extended by 100 bases, but not beyond the 3' end of any upstream nearby exon of another gene of the same orientation.
Annotation and quantitation:  Reads that had one or more repeat mappings that was outside exons, was assigned randomly as one of these repeats and contributed to the summarized read count of that repeat class. Else, if it had one or more mappings to exons, it was assigned randomly to one of the exons, even if the sequence was repeat-like. If it had no exon mapping, it was assigned randomly at one of the mappings. The expression level of each transcript model was taken as the total number of reads at all its possible mapping positions, normalized as Reads Per Kilobase mRNA Per Million (RPKM).
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-separated file with RPKM.

organism: Mus musculus

source_name: alar plate

growth_protocol: Mouse embryos were obtained from  TH-GFP animals  (Matsushita et al, J Neurochem. 82: 295, 2002) that were mated overnight, and noon of the plug day was considered  E0.5.  Embryos were dissected out of the uterine horns at E11.5 - E14.5 and placed in ice cold sterile PBS where brain regions were dissected under a stereomicroscope with a UV attachment to detect GFP. VM samples corresponded to domains M3 to M7 of the floor and basal plate (Nakatani et al, Development 134: 2783, 2007). Tissue samples were collected in separate tubes and stored at  - 80 ̊C until RNA isolation.

extract_protocol:
Total RNA isolation was performed with the RNeasy kit  (Qiagen). The RNA  integrity and concentration was checked using Qubit and 2200 TapeStation (Agilent).
Illumina TruSeq libraries were prepared using the kit and standard protocol from Illumina.

tag: tissue

value: alar plate

tag: developmental stage

tag: genotype

value: TH-GFP


title: L2_11.5

description: S092_TruSeq_mm10_UCSC_20140923_093440_TS13


title: KTB21-hTERT2_S2

description: mRNA-seq

value: Immortalized normal breast epithelial cell line


title: KTB21-hTERT1_S1

description: mRNA-seq


title: DM4_13.5

description: S075_TruSeq_mm10_UCSC_20140930_162006_TS9

source_name: dorsal midbrain

value: dorsal midbrain


title: L4_13.5

description: S075_TruSeq_mm10_UCSC_20140930_162006_TS8


title: RM6_11.5

description: S092_TruSeq_mm10_UCSC_20140923_093440_TS12

source_name: ventral forebrain

value: ventral forebrain


title: HME-TERT-WT-horizon2_S22

description: mRNA-seq


title: HME-TERT-WT-horizon3_S35

description: mRNA-seq


title: RM4_13.5

description: S075_TruSeq_mm10_UCSC_20140930_162006_TS3


title: RM6_13.5

description: S075_TruSeq_mm10_UCSC_20140930_162006_TS27


title: HME-TERT-WT-horizon1_S21

description: mRNA-seq


title: 1505-10B-hTERT3_S34

description: mRNA-seq


title: CM6_13.5

description: S075_TruSeq_mm10_UCSC_20140930_162006_TS25

source_name: ventral hindbrain

value: ventral hindbrain


title: 1505-10B-hTERT2_S20

description: mRNA-seq


title: CjCutting_Base_3wpi_rep1

description:
Gene expression at 3 weeks post insertion in base of C. japonica cutting
Base of Cutting, 3 weeks hour post insertion, replicate 1


title: CjCutting_Base_1wpi_rep3

description:
Gene expression at 1 week post insertion in base of C. japonica cutting
Base of Cutting, 1 week post insertion, replicate 3

source_name: Base of Cutting, 1 week post insertion

value: 1 week post insertion


title: DM5_13.5

description: S075_TruSeq_mm10_UCSC_20140930_162006_TS22


title: CjCutting_Base_3dpi_rep3

description:
Gene expression at 3 days post insertion in base of C. japonica cutting
Base of Cutting, 3 days post insertion, replicate 3

source_name: Base of Cutting, 3 days post insertion

value: 3 days post insertion


title: CjCutting_Base_1wpi_rep2

description:
Gene expression at 1 week post insertion in base of C. japonica cutting
Base of Cutting, 1 week post insertion, replicate 2


title: CjCutting_Base_1wpi_rep1

description:
Gene expression at 1 week post insertion in base of C. japonica cutting
Base of Cutting, 1 week post insertion, replicate 1


title: CjCutting_Base_3dpi_rep1

description:
Gene expression at 3 days post insertion in base of C. japonica cutting
Base of Cutting, 3 days post insertion, replicate 1


title: 6-Shogaol

city: Gyeongsan-Si

first: Jintae

last: Lee

state: Gyeongsangbuk-Do

address: 214-1 Daedong

department: Chemical engineering

country: South Korea

institute: Yeungnam University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to Candida_albicans_SC5314 whole genome using Tophat
Read count extraction and nomalization were performed using edgeR.
Genome_build: Candida_albicans_SC5314 (NCBI)
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Candida albicans

source_name: Whole cell

growth_protocol: 25 ml of C. albicans DAY185 at an initial turbidity of 0.1 at OD600 was inoculated into PDB broth in 250 ml Erlenmeyer flasks and incubated for 4 h at 37ºC with agitation (250 rpm)

extract_protocol:
To prevent RNA degradation, RNase inhibitor (RNAlater, Ambion, TX, USA) was added to cells. Total RNA was isolated using a hot acidic phenol method, and RNA was purified using a Qiagen RNeasy mini Kit (Valencia, CA, USA). After that RNA was harvested using Trizol reagent (Invitrogen). 1.3ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Clontech SMARTer Stranded RNA-Seq Kit standard protocols.

treatment_protocol: Cells were incubated for 4 h at 37ºC with agitation (250 rpm) in the presence or absence of 6-gingerol (50 µg/ml) or 6-shogaol (10 µg/ml)

tag: strain

tag: treated with

value: 6-shogaol (10 µg/ml)


title: L5_13.5

description: S075_TruSeq_mm10_UCSC_20140930_162006_TS21


title: CjCutting_Base_3dpi_rep2

description:
Gene expression at 3 days post insertion in base of C. japonica cutting
Base of Cutting, 3 days post insertion, replicate 2


title: CjCutting_Base_1dpi_rep3

description:
Gene expression at 1 day post insertion in base of C. japonica cutting
Base of Cutting, 1 day post insertion, replicate 3

source_name: Base of Cutting, 1 day post insertion

value: 1 day post insertion


title: 6-Gingerol

value: 6-gingerol (50 µg/ml)


title: RM5_13.5

description: S075_TruSeq_mm10_UCSC_20140930_162006_TS20


title: VM6_13.5

description: S075_TruSeq_mm10_UCSC_20140930_162006_TS14

source_name: ventral midbrain

value: ventral midbrain


title: Control

value: none (control)


title: CjCutting_Base_3hpi_rep3

description:
Gene expression at 3 hours post insertion in base of C. japonica cutting
Base of Cutting, 3 hours post insertion, replicate 3

source_name: Base of Cutting, 3 hours post insertion

value: 3 hours post insertion


title: CjCutting_Base_1dpi_rep1

description:
Gene expression at 1 day post insertion in base of C. japonica cutting
Base of Cutting, 1 day post insertion, replicate 1

value: Tsukuba 1


title: CjCutting_Base_3hpi_rep2

description:
Gene expression at 3 hours post insertion in base of C. japonica cutting
Base of Cutting, 3 hours post insertion, replicate 2

value: base


title: L6_13.5

description: S075_TruSeq_mm10_UCSC_20140930_162006_TS12


title: VM5_13.5

description: S075_TruSeq_mm10_UCSC_20140930_162006_TS23


title: DM6_13.5

description: S075_TruSeq_mm10_UCSC_20140930_162006_TS13


title: 1505-10B-hTERT1_S19

description: mRNA-seq


title: CM5_13.5

description: S075_TruSeq_mm10_UCSC_20140930_162006_TS11


title: CM4_13.5

description: S075_TruSeq_mm10_UCSC_20140930_162006_TS1


title: VM4_13.5

description: S075_TruSeq_mm10_UCSC_20140930_162006_TS10


title: CM1_12.5

description: E12dot5_TruSeq_mm10_UCSC_20140930_153655_TS9


title: L1_12.5

description: E12dot5_TruSeq_mm10_UCSC_20140930_153655_TS8


title: VM3_12.5

description: E12dot5_TruSeq_mm10_UCSC_20140930_153655_TS5


title: CjCutting_Needle_3hpi_rep1

description:
Gene expression at 3 hours post insertion in needle of C. japonica cutting
Needle, 3 hours post insertion, replicate 1

source_name: Needle, 3 hours post insertion

value: needle


title: CjCutting_Base_0hpi_rep2

description:
Gene expression at 0 hour post insertion in base of C. japonica cutting
Base of Cutting, 0 hour post insertion, replicate 2

source_name: Base of Cutting, 0 hour post insertion

value: 0 hour post insertion


title: CjCutting_Base_0hpe_rep3

description:
Gene expression at 0 hour post excision in base of C. japonica cutting
Base of Cutting, 0 hour post excision, replicate 3

source_name: Base of Cutting, 0 hour post excision

value: 0 hour post excision


title: CjCutting_Base_0hpi_rep3

description:
Gene expression at 0 hour post insertion in base of C. japonica cutting
Base of Cutting, 0 hour post insertion, replicate 3


title: CM3_12.5

description: E12dot5_TruSeq_mm10_UCSC_20140930_153655_TS4

value: TH-GFP


title: DM3_12.5

description: E12dot5_TruSeq_mm10_UCSC_20140930_153655_TS27

value: dorsal midbrain


title: CjCutting_Base_0hpe_rep1

description:
Gene expression at 0 hour post excision in base of C. japonica cutting
Base of Cutting, 0 hour post excision, replicate 1


title: RM3_12.5

description: E12dot5_TruSeq_mm10_UCSC_20140930_153655_TS25

value: ventral forebrain


title: CjCutting_Base_3hpi_rep1

description:
Gene expression at 3 hours post insertion in base of C. japonica cutting
Base of Cutting, 3 hours post insertion, replicate 1


title: CjCutting_Base_1dpi_rep2

description:
Gene expression at 1 day post insertion in base of C. japonica cutting
Base of Cutting, 1 day post insertion, replicate 2


title: DM1_12.5

description: E12dot5_TruSeq_mm10_UCSC_20140930_153655_TS3


title: CjCutting_Base_0hpe_rep2

description:
Gene expression at 0 hour post excision in base of C. japonica cutting
Base of Cutting, 0 hour post excision, replicate 2


title: CM2_12.5

description: E12dot5_TruSeq_mm10_UCSC_20140930_153655_TS22

value: ventral hindbrain


title: L2_12.5

description: E12dot5_TruSeq_mm10_UCSC_20140930_153655_TS21

value: alar plate


title: DM2_12.5

description: E12dot5_TruSeq_mm10_UCSC_20140930_153655_TS20


title: L3_12.5

description: E12dot5_TruSeq_mm10_UCSC_20140930_153655_TS2


title: striatum_Selected_2

city: Urbana

first: Sandra

last: Rodriguez Zas

state: IL - Illinois

address: 1207 W. Gregory Dr.

institute: University of Illinois at Urbana

description: Striatum was obtained and RNA extracted using standards protocols  (Gibbons et al. 2014, Behavioural brain research, 272: 131-40.)

data_processing:
Quality-scores line in fastq files processed with Casava1.8 use an ASCII offset of 33
Sequences were trimmed for adaptor seuqences and masked for low-complexity and low-quality
100 nt paired-end reads were mapped to the Mus musculus NCBI GRCm38 assembly
Reads were assembled into transcript isoforms using Tophat2
FPKM values were calculated with Cuffdiff/Cuffnorm v2.2.1.
Genome_build: NCBI GRCm38/mm10 genome assembly (UCSC)
Supplementary_files_format_and_content: csv file with FPKM values.

source_name: striatum

extract_protocol:
Brain was extracted from each mouse and the whole striatum and cerebellum were dissected, snap frozen on dry ice and stored in a centrifuge tube at -80°C following proven protocols (Gibbons et al. 2014). Tissue from each mouse was homogenized with an RNase-free disposable pellet pestle (Fisher) and RNA was extracted using the commercially available RNeasy® Lipid Tissue Mini Kit (Qiagen, Valencia, CA). Purification of the isolated RNA included treatment with DNase I (Qiagen, Valencia, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: Selected

tag: Sex

value: male

value: striatum

tag: age

value: 6 weeks


title: VM1_12.5

description: E12dot5_TruSeq_mm10_UCSC_20140930_153655_TS10

value: ventral midbrain


title: RM1_12.5

description: E12dot5_TruSeq_mm10_UCSC_20140930_153655_TS1


title: RM2_12.5

description: E12dot5_TruSeq_mm10_UCSC_20140930_153655_TS11


title: MTB__ESX1_2

city: Jeddah

first: Qingtian

last: Guan

address: Thuwal

country: Saudi Arabia

institute: King Abdallah University of Science and Technology

description: processed data file: MTB_MTB_ESX1.txt

data_processing:
bcl2fastq2 Conversion Software
Trimming of Illumina adaptor sequences and low quality reads were done using Trimmomatic (v 0.33)
For the wild type and ESX1 mutants comparision, the Illumina reads were mapped with SMALT (default parameters) against the M. tuberculosis H37Rv or M. marinum M reference. From the read count, which was obtained with bedtools, parameter multicov, with -D to include duplicates and -q 5 to exclude repetitive mapping reads, we performed a differential expression analysis with DESeq using default parameters. For the whib6 knockout and complementary comparision, we mapped the trimmed reads back to the same reference genome with bowtie2 and the differently expressed genes were called by cuffdiff2.
Normalization of raw read counts and differential expression analysis was performed using DeSeq or CuffDiff2
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Mycobacterium tuberculosis H37Rv

source_name: M. tuberculosis ESX1 mutant

extract_protocol:
M. marinum and M. tuberculosis cultures were pelleted and bead beated in 1 ml of TRIzol (Invitrogen) with 0.1-mm zirconia/silica beads (BioSpec Products). After centrifugation, supernatants were extracted with chloroform, and RNA was precipitated with isopropanol. RNA pellets were washed with 80% ethanol and dissolved in RNAse-free water. Contaminant DNA was removed by incubation with DNAse I (Fermentas).
Total RNA was extracted with TRIzol (Invitrogen) and then purified on RNeasy spin columns (Qiagen) according to the manufacturer’s instructions. RNA integrity (RNA integrity score ≥ 6.8) and quantity were determined on an Agilent 2100 Bioanalyzer (Agilent; Palo Alto, CA, USA). As ribosomal RNA constitutes a vast majority of the extracted RNA population, depletion of these molecules via RiboMinus-based rRNA depletion was conducted. For mRNA enrichment, Invitrogen’s RiboMinus Transcriptome Isolation Kit, bacteria was used according to manufacturer’s instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA-sequence-specific 5′-biotin-labelled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinus concentrate module according to the manufacturer’s protocol. The final RiboMinus RNA sample was subjected to thermal mRNA fragmentation using the Elute, Prime, Fragment Mix from the Illumina TruSeq RNA Sample Preparation Kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeq RNA Sample Preparation Kit (low-throughput protocol) according to the manufacturer’s protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III reverse transcriptase (Invitrogen) and the SRA RT primer (Illumina). The cDNA was further converted into double-stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer’s instructions. A small aliquot (1 µl) was analysed on an Invitrogen Qubit and an Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled at equal concentrations before sequencing on an Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with Illumina Pipeline software v1.82.

value: M. tuberculosis wild type 6030

tag: genotype/variation

value: ESX1 mutant


title: MTB__ESX1_3

description: processed data file: MTB_MTB_ESX1.txt


title: striatum_Selected_1


title: CjCutting_Base_0hpi_rep1

description:
Gene expression at 0 hour post insertion in base of C. japonica cutting
Base of Cutting, 0 hour post insertion, replicate 1

value: Tsukuba 1


title: VM2_12.5

description: E12dot5_TruSeq_mm10_UCSC_20140930_153655_TS23


title: striatum_Control_2

value: Control


title: striatum_Selected_0


title: striatum_Control_3


title: EMN21 cells_ALDH-low

city: Niigata

first: Tatsuya

last: Ishiguro

address: 1-757, Asahimachi-dori, Chuo-ku

institute: Niigata university

description:
gene expression of EMN21 ALDH-high cells
21L

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing Agilent fragmentation buffer and  Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and then dried immediately.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 072363_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: EMN21 ALDH-low endometrial cancer cells

label_protocol: Cy3-labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by the RNeasy mini kit (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Endometrial cancer spheroids were grown in serum-free STEMPRO hESC SFM (Gibco) supplemented with 8 ng/ml bFGF (Invitrogen) on ultra-low-attachment culture dishes (Corning).

extract_protocol: RNA was isolated from cells with an miRNeasy Micro kit (Qiagen).

treatment_protocol: Endometrial cancer spheroids were sorted into ALDH-high and ALDH-low cells using FACS Aria II (BD).

tag: disease state

value: endometrial cancer

tag: individual id

value: endometrial cancer-derived spheroids

tag: cancer type

value: poorly differentiated adenocarcinoma

tag: sorted cells

value: ALDH-low


title: EMN24 cells_ALDH-high

description:
gene expression of EMN24 ALDH-low cells
24H

source_name: EMN24 ALDH-high endometrial cancer cells

value: endometrioid cancer grade 3

value: ALDH-high


title: EMN24 cells_ALDH-low

description:
gene expression of EMN24 ALDH-high cells
24L

source_name: EMN24 ALDH-low endometrial cancer cells


title: striatum_Control_1


title: striatum_Control_0


title: EMN8 cells_ALDH-high

description:
gene expression of EMN8 ALDH-low cells
8H

source_name: EMN8 ALDH-high endometrial cancer cells

value: endometrioid cancer grade 2


title: EMN8 cells_ALDH-low

description:
gene expression of EMN8 ALDH-high cells
8L

source_name: EMN8 ALDH-low endometrial cancer cells


title: EMN21 cells_ALDH-high

description:
gene expression of EMN21 ALDH-low cells
21H

source_name: EMN21 ALDH-high endometrial cancer cells


title: MTB__ESX1_1

description: processed data file: MTB_MTB_ESX1.txt


title: MTB__WT_2

description: processed data file: MTB_MTB_ESX1.txt

source_name: M. tuberculosis wild type H37Rv

value: M. tuberculosis wild type 6020

value: wild type


title: cerebellum_Selected_3

description: Cerebellum was obtained and RNA extracted using standards protocols  (Gibbons et al. 2014, Behavioural brain research, 272: 131-40.)

source_name: cerebellum

value: Selected

value: male

value: cerebellum


title: cerebellum_Selected_2

value: 6 weeks


title: cerebellum_Selected_1


title: cerebellum_Selected_0


title: MTB__WT_3

description: processed data file: MTB_MTB_ESX1.txt


title: cerebellum_Control_3


title: cerebellum_Control_2


title: siFto4

city: Aurora

first: Jayne

middle: F

last: Martin Carli

state: CO

department: Pediatrics - Neonatology

institute: University of Colorado Anschutz Medical Center

data_processing:
Sample integrity for RNA utilized for RNA-Seq was assessed with an Agilent 2100 Bioanalyzer. All samples had RIN numbers greater than 8.0. mRNA was isolated using poly-A pulldown and reverse transcribed to generate cDNA.
cDNA was sequenced using single-ended sequencing on a HiSeq2000 according to manufacturer’s recommendations (Illumina)
The pass filter reads were mapped to mouse reference genome mm9 using TopHat (version 2.0.11).
For each read, up to 3 mismatches and 10 multiple hits were allowed during mapping.
FPKM values indicating relative abundance were estimated using Cufflinks software (version 2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: .txt, FPKM, FPKM_status

growth_protocol: 3T3-L1 preadipocytes were purchased from ATCC and maintained in sub-confluent cultures. Growth medium consisted of DMEM (with 25mM glucose, GlutaMAX, and sodium pyruvate) supplemented with 10% newborn calf serum (both Thermo Fisher).

extract_protocol:
Total RNA was isolated using the RNeasy Lipid Tissue Mini Kit and columns were treated with DNase (both Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 3T3-L1 cells were transfected prior to confluence by incubation for 24 hours with a mix of 3 Stealth siRNAs targeted against Fto or 3 nontargeted controls with Lipofectamine 2000 (40 nM siRNA; designed to span multiple exons; all Thermo Fisher)

tag: cell type

value: 2 day post-confluent preadipocyte


title: cerebellum_Control_0


title: ATDT5BC

city: Wuhan

first: Mingqiu

last: Dai

state: Hubei

address: No.1,Shizishan Street · Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

country: China

institute: Huazhong Agriculture University

description:
RNA digested by RNase R
Exp_AtCirc.txt

data_processing:
For circRNA-seq data, clean FASTQ reads were first mapped to the maize B73 reference genome from EnsemblePlants or Arabidopsis genome BWA-MEM with a CIRI2 suggested parameter: T, 19. SAM alignment files generated by BWA-MEM with GTF-formatted gene annotations (Zea_mays.AGPv3.31.gtf, Arabidopsis_thaliana.TAIR10.32.gtf) were then called by the CIRI2 algorithm with default parameters except thread number to detect and annotate circRNAs. All CIRI2 circRNA outputs were supported by more than two junction reads (reads spanning back-spliced sites).
CircRNAs with at least two junction reads that occurred in both replicates were selected as high-confidence predictions. They were then compared with circRNAs in PlantcircBase (http://ibi.zju.edu.cn/plantcircbase/) (Chu et al., 2017) to identify new circRNAs discovered in this study. circRNAs in each treatment and normalized the number by total clean reads (units in million), and grouped circRNAs based on genomic origin type
RPB datasets were used to call differentially-expressed circRNAs (DE circRNAs) from different treatments by the Bioconductor package ‘edgeR’. The edgeR programs were performed in the OmicShare tools, a free online platform for data analysis, with default parameters (www.omicshare.com/tools). The cutoff we used to pick significant DE circRNAs was FDR<0.05.
For RNA-seq data,transcript quantification values were then calculated by rsem-calculateexpression with the following parameters: num-threads, 8; calc-pme; calc-ci. The TPM (transcripts per million) values were selected to represent relative expression of a transcript.
Differential expression analyses were performed on TPM datasets by ‘edgeR' in the OmicShare tools to identify differentially-expressed linear RNAs.Transcripts with FDR<0.05 and |Fold Change|≥2 were considered to be significant DE mRNAs.
Genome_build: ftp://ftp.ensemblgenomes.org/pub/plants/release-32/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna_sm.toplevel.fa.gz
Genome_build: ftp://ftp.ensemblgenomes.org/pub/plants/release-31/fasta/zea_mays/dna/Zea_mays.AGPv3.dna_sm.toplevel.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample in Exp_AtLinear.txt and Exp_ZmLinear.txt, tab-delimited text files include RPB values for each Sample in Exp_AtCirc.txt and Exp_ZmCirc.txt

organism: Arabidopsis thaliana

source_name: leaves

growth_protocol: Maize (Zea mays L.) inbred line B73 and Arabidopsis ecotype Col-0 were used in this study. B73 seeds were directly sown in soil at 28°C in black pots (10cm x 10cm x 9cm) with 16 h light (~140 μmol m-2 s-1)/8h dark in a greenhouse. Seeds of Col-0 were stratified in a cold room for 2 d at 4 °C in the dark, germinated on culture medium for 7 days and then transferred to soil to grow at 22°C with 16h light (~85 μmol m-2 s-1)/8h dark in a growth chamber.

extract_protocol:
Total RNAs were isolated from the pooled samples using TRI pure reagent (Aidlab, Beijing, CN) according to the manufacturer’s protocol. Total RNA samples were treated with DNase I (Thermo Scientific) and purified by RNA Clean & Concentrator-25 spin columns (ZYMO Research)
RNA samples from maize and Arabidopsis treated with various levels of drought were digested with RNase R before library preparation and then subjected to deep sequencing using an Illumina HiSeq 3000 on a 150 bp paired-end run (Ribobio, Guangzhou, CN). The same RNA samples used in circRNA sequencing were used for library preparation and RNA sequencing. 150bp paired-end raw reads were generated using an Illumina HiSeq3000 (ANOROAD, Beijing, CN)

treatment_protocol: For drought experiments, gradient drought treatments were administered 16 days after planting maize and 21 days after planting Arabidopsis according to a previous report (Su et al., 2013). Briefly, the soil moisture of each treatment was monitored by measuring the relative soil water content, followed with rationing of water to maintain a designated soil moisture. The pots were weighed and watered twice daily. After the most serious stress reached the preset levels, the plants were maintained for one more day, then the whole plants were harvested for fresh weight measurement and leaves were harvested for RNA extraction. The third leaves of B73 at V4 stage from at least 2 plants and leaves of 4 Col-0 plants were harvested and pooled, respectively, for RNA extraction.For the experiments on maize inbred lines, two treatments [well-watered  (WW), 65%~60% soil moisture; drought-stressed (DT), 25%~20% soil moisture] were applied. Eight plants of each inbred line were grown in two pots (10cm x 10cm x 9cm), with 4 plants in each pot. All pots were randomly placed in the growth room at 28°C with 16 h light/8h dark. Soil moisture was controlled by measuring the relative water content of soil and rationing water (pots were weighed and watered once daily). Drought treatments started 16 days after planting, then after 4 days of drought treatment leaves were sampled.

tag: treatment

value: drought-stressed DT5

value: leaves

tag: Stage

value: rosette leaves

tag: rnaser treatment

value: RNase R+

tag: ecotype

value: Col


title: siFto3


title: ATDT5AC

description:
RNA digested by RNase R
Exp_AtCirc.txt

tag: tissue


title: ATDT4BC

description:
RNA digested by RNase R
Exp_AtCirc.txt

value: drought-stressed DT4


title: siFto2


title: rheumatoid_synovium_CD21L-/IL-17A-_Patient8

city: Dunedin

first: Paul

last: Hessian

address: 362 Leith St, North Dunedin

department: Medicine

country: New Zealand

institute: UniDunedin School of Medicine, Health Sciences, University of Otago

description: CD21L-/IL-17A- P8

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45oC on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Confocal GeneArray Scanner 7G Plus.

data_processing: The data were analyzed with Affymetrix Expression Console version 1.1 (MAS 5.0) using Affymetrix default analysis settings, and with Robust Multi-array Average (RMA) as the normalization method. Fold-changes were calculated as the mean value of the six CD21L-/IL-17A- synovia compared to the mean value of the six CD21L+/IL-17A+ synovia for each probe set. Significance was determined by generating a t-statistic and p-value for each probe set using Bioconducter software AffyGUI.

label: biotin

source_name: rheumatoid synovium, CD21L-/IL-17A-

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Synovia were obtained from patients during joint replacement surgery.

extract_protocol: Extraction of total RNA was performed using RNeasy Mini kits (Qiagen) according to the manufacturer's instructions.

value: rheumatoid arthritis

tag: disease duration

value: 21.00 years

value: inflamed rheumatoid synovia

tag: subtype

tag: patient identifier


title: rheumatoid_synovium_CD21L+/IL-17A+_Patient1, rep1

description: CD21L+/IL-17A+ P1-1

source_name: rheumatoid synovium, CD21L+/IL-17A+

value: 21.33 years


title: rheumatoid_synovium_CD21L-/IL-17A-_Patient10

description: CD21L-/IL-17A- P10

value: 13.25 years


title: cerebellum_Control_1

tag: strain

tag: condition

value: Control


title: rheumatoid_synovium_CD21L+/IL-17A+_Patient3

description: CD21L+/IL-17A+ P3

value: 4.58 years


title: CHP134-NC-sample2-rep1

city: Chiba

first: Jason

last: Lin

state: Chiba

address: 666-2 Nitona-cho, Chuo-ku

institute: Chiba Cancer Center Research Institute

description: technical array replicate 1 of CRISPR/Cas9 negative control sample 2 RNA

hyb_protocol: Sample preparations were performed on SurePrint G3 Human GE 8x60K V2 microarrays per Agilent Technologies’ recommendations.

scan_protocol: Data acquisition was performed on an Agilent SureScan microarray scanner.

data_processing: Differential expressions of microarray data were calculated by the LIMMA package in R. Replicates underwent background correction by the “normexp” method with an offset of 18, and scale-normalized for replicate spots between arrays. After a linear model fit for each gene was determined, statistical evaluations and differential expressions were compiled via the method of empirical Bayes, with fold changes calculated based on difference in responses between MYCNcra and NC treatments. Spots with matching RefSeq mRNA, ncRNA and Ensemble accessions were filtered and retained for subsequent analyses.

source_name: NC

label_protocol: RNA Spike-In Kit

growth_protocol: CHP-134 cells were maintained in RPMI1640 supplemented with 10% FBS (Thermo Fisher Scientific) and penicillin/streptomycin (Thermo Fisher Scientific) and cultured in a humidified atmosphere at 37°C with 5% carbon dioxide.

extract_protocol: RNA was extracted using the RNeasy Plus Mini Kit (Qiagen).

treatment_protocol: Samples were administered with prepared CRISPR/Cas9 construct per manufacturer's recommendations.

value: neuroblastoma

tag: cell line


title: rheumatoid_synovium_CD21L+/IL-17A+_Patient1, rep2

description: CD21L+/IL-17A+ P1-2

value: 22.00 years


title: rheumatoid_synovium_CD21L-/IL-17A-_Patient7

description: CD21L-/IL-17A- P7

value: 16.83 years


title: MDA-MB-231-Plac1

city: nanjing

first: li

last: yongfei

address: 140 hanzhong RD.

institute: nanjing medical unversity

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Agilent DNA Microarray Scanner（part number G2505C）

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, genes that at least 1 out of 2 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes with statistical significance between the two groups were identified through Volcano Plot filtering. Differentially expressed genes between the two samples were identified through Fold Change filtering. Hierarchical Clustering was performed using the R scripts. GO analysis and Pathway analysis were performed in the standard enrichment computation method
t-test

source_name: breast cancer cell

label_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology).total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: MDA-MB-231 were cultured in DMEM medium (Gibco);  supplemented with 10% (v/v) fetal bovine serum (Gibco), 100 U/ml penicillin (Gibco), and 100 U/ml streptomycin (Gibco) at 37°C in a humidified atmosphere containing 5% CO2

extract_protocol: Total RNA was isolated fromMDA-MB-231 using Trizol reagent (Ambion, Carlsbad, CA), and then assessed by an Agilent 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: MDA-MB-231 cells were infected with the lentivirals of Plac1 and negative control

value: Plac1 is overexpressed in MDA-MB-231-Plac1


title: CHP134-NC-sample1-rep2

description: technical array replicate 2 of CRISPR/Cas9 negative control sample 1 RNA


title: CHP134-MYCNcra-sample2-rep1

description: technical array replicate 1 of MYCNcr-a modified sample 2 RNA

source_name: MYCNcra


title: rheumatoid_synovium_CD21L+/IL-17A+_Patient5

description: CD21L+/IL-17A+ P5

value: 28.33 years


title: rheumatoid_synovium_CD21L-/IL-17A-_Patient6

description: CD21L-/IL-17A- P6

value: 30.00 years


title: ATDT4AC

description:
RNA digested by RNase R
Exp_AtCirc.txt

value: leaves

value: rosette leaves


title: rheumatoid_synovium_CD21L-/IL-17A-_Patient4

description: CD21L-/IL-17A- P4-2

value: 2.08 years


title: MDA-MB-231-NC

value: control


title: CHP134-NC-sample2-rep2

description: technical array replicate 2 of CRISPR/Cas9 negative control sample 2 RNA


title: rheumatoid_synovium_CD21L+/IL-17A+_Patient2

description: CD21L+/IL-17A+ P2

value: rheumatoid arthritis

value: 11.00 years


title: siCtr4

value: 2 day post-confluent preadipocyte


title: CHP134-MYCNcra-sample1-rep2

description: technical array replicate 2 of MYCNcr-a modified sample 1 RNA


title: rheumatoid_synovium_CD21L-/IL-17A-_Patient9

description: CD21L-/IL-17A- P9

value: unknown

value: inflamed rheumatoid synovia


title: CHP134-NC-sample1-rep1

description: technical array replicate 1 of CRISPR/Cas9 negative control sample 1 RNA


title: siFto1


title: siCtr2


title: ATDT3AC

description:
RNA digested by RNase R
Exp_AtCirc.txt

value: drought-stressed DT3

value: RNase R+

value: Col


title: ATDT2BC

description:
RNA digested by RNase R
Exp_AtCirc.txt

value: drought-stressed DT2


title: ATDT2AC

description:
RNA digested by RNase R
Exp_AtCirc.txt


title: siCtr1


title: ATWWBC

description:
RNA digested by RNase R
Exp_AtCirc.txt

value: well-watered


title: CHP134-MYCNcra-sample2-rep2

description: technical array replicate 2 of MYCNcr-a modified sample 2 RNA

value: neuroblastoma


title: ATDT3BC

description:
RNA digested by RNase R
Exp_AtCirc.txt


title: wild type_mPFC sample 3

city: Seoul

first: Kihoon

last: Han

address: 73, Inchon-ro, Seongbuk-gu

department: Neuroscience

institute: Korea University College of Medicine

data_processing:
Transcript abundance was estimated with Salmon(v0.9.1) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.0) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.19.11).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: wild type_brain

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq Stranded mRNA LT Sample Prep Kit  (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Sample Preparation Guide)

tag: strain background

tag: genotype/variation

value: WT

tag: age

value: 10 to 12 week

value: medial prefrontal cortex


title: wild type_mPFC sample 2


title: ATWWAC

description:
RNA digested by RNase R
Exp_AtCirc.txt

value: leaves

value: rosette leaves


title: wild type_mPFC sample 1


title: ATDT5AL

value: drought-stressed DT5

value: RNase R-


title: ATDT5BL


title: CHP134-MYCNcra-sample1-rep1

description: technical array replicate 1 of MYCNcr-a modified sample 1 RNA


title: CHP134-DMSO-sample1-rep1

description: technical array replicate 1 of DMSO-treated sample RNA

data_processing: Differential expressions of microarray data were calculated by the LIMMA package in R. Replicates underwent background correction by the “normexp” method with an offset of 18, and scale-normalized for replicate spots between arrays. After a linear model fit for each gene was determined, statistical evaluations and differential expressions were compiled via the method of empirical Bayes, with fold changes calculated based on difference in responses between DMSO and MYCNA3 treatments. Spots with matching RefSeq mRNA, ncRNA and Ensemble accessions were filtered and retained for subsequent analyses.

source_name: DMSO

treatment_protocol: Samples were administered 10 nM MYCN-A3 or 0.15% DMSO for 6 h prior to extraction.


title: siCtr3


title: CHP134-DMSO-sample1-rep2

description: technical array replicate 2 of DMSO-treated sample RNA


title: CHP134-MYCNA3-sample2-rep1

description: technical array replicate 1 of MYCNA3-treated sample 2 RNA


title: Shank3 transgenic_mPFC sample 2

source_name: Shank3 transgenic_brain

value: Shank3 transgenic (TG)


title: CHP134-MYCNA3-sample1-rep2

description: technical array replicate 2 of MYCNA3-treated sample 1 RNA


title: CHP134-MYCNA3-sample1-rep1

description: technical array replicate 1 of MYCNA3-treated sample 1 RNA


title: ATDT4BL

value: drought-stressed DT4


title: ATDT4AL


title: Shank3 transgenic_mPFC sample 1


title: ATDT3BL


title: N708-S508=64

city: Cincinnati

first: Vikram

last: Prasad

state: OH

address: 240, Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Hospital Medical Center

description:
Mutant Gata4 KO endothelial cells
run2110_lane12_read1_indexN708-S508=64
Experimental_S508_64

data_processing:
Sequence reads were aligned using Strand NGS Software (Ver. 2.6) against Mouse mm10 (UCSC) using Ensembl transcript annotations ((2013.04.03)
Quantification using known annotation with Normalization Type: RPKM; Threshold for normalization =1;
Fold Change Analysis was carried out using Strand NGS Software and identifies genes with ratio between experimental and control conditions, above an assigned threshold. Our analysis had two conditions; therefore, control cells were chosen as the reference condition against which the fold change for the KO cells (experimental condition) was computed. As per Strand NGS manual, the exact fold change is computed as follows:
1. For each gene and condition, the average of the normalized signal values (in log-scale) is calculated.
2. Log Fold Change (Log FC) for a given gene, between the two conditions, is then the difference between their respective averages.
3. Fold change (FC) is then computed as (sign of Log FC) x 2ǀlogFCǀ; absolute FC is ǀFCǀ.
Genome_build: Mouse mm10 (UCSC)
Supplementary_files_format_and_content: Excel

source_name: Mutant Gata4 KO endothelial cells

growth_protocol: Mouse lines utilized in this study  include: Lines containing a Tie2-CreERT2 transgene comprising a version of the Tie2 promoter with a β-globulin intron sequence as a fusion with CreERT2 cDNA and a polyadenylation signal (pA) signal and Tie2 enhancer sequence was used for C57BL/6 pronuclear micro-injection to generate transgenic mouse lines (1), the Rosa26 reporter mice (R26eGFP) purchased from Jackson laboratories (Stock# 012429),  and LoxP-targeted Gata4 (2) mice. Mice received continuous tamoxifen-citrate chow (40 mg/kg body weight, Envigo - TD.130860) starting at 4 weeks of age until the experiment was terminated at 8 weeks of age. Interstitial cells were isolated from cardiac ventricles, as described previously (3), 4 weeks after tamoxifen induction. Flow cytometry analysis was performed on these cells using a Becton Dickinson FACSCanto II running FACSDiva software. For analysis and sorting of endothelial cells from Tie2-CreERT2 transgene expressing lineages, we utilized endogenous eGFP fluorescence expressed by the recombined reporter allele in combination with an APC-conjugated FACS antibody for PECAM1 (CD31).   1. Hochstetler CL, Feng Y, Zheng Y.  An altered bone marrow vascular niche impacts normal hematopoiesis and tilts the balance between myelopoiesis and lymphopoiesis. Am Soc Hematology. 2016:174. Abstract. (Manuscript Submitted)  2. Watt AJ et al. GATA4 is essential for formation of the proepicardium and regulates cardiogenesis. Proc Natl Acad Sci U S A. 2004. 101(34):12573-8.  3. Kanisicak O, et al. Genetic lineage tracing defines myofibroblast origin and function in the injured heart. Nat Commun. 2016;7:12260.

extract_protocol:
eGFP+ CD31+ endothelial cells were flow-sorted directly into Qiazol for lysis and RNA isolation.
Total RNA was extracted from endothelial cells. RNA quality and yield were determined using Agilent Bioanalyzer and submitted for RNA-seq analysis.

treatment_protocol: Upon induction of Tie2-CreERT2 transgene expression, and tamoxifen administration, expression of Cre-recombinase is turned on, Cre/LoxP-dependent recombination of the Gata4 gene occurs, and the eGFP reporter allele is recombined.

value: Tie2-CreERT2 transgene; enhanced green fluorescent protein (eGFP) Cre-dependent reporter transgene in Rosa locus

value: cardiac endothelial cells

tag: cell population

value: CRE+, GFP+, and Gata4-deficient.


title: ATDT3AL

value: drought-stressed DT3


title: Shank3 transgenic_mPFC sample 3


title: N707-S507=60

description:
Mutant Gata4 KO endothelial cells
run2110_lane12_read1_indexN707-S507=60
Experimental_S507_60


title: N706-S506=Tie2_5

description:
Control cells for Gata4 deficient endothelial cells
run2110_lane12_read1_indexN706-S506=Tie2_5plus7
Control_S506 Tie2_5_plus_7

treatment_protocol: Upon induction of Tie2-CreERT2 transgene expression, and tamoxifen administration, expression of Cre-recombinase is turned on, and eGFP reporter allele is recombined.

value: CRE+ and GFP+


title: ATDT2BL

value: drought-stressed DT2

value: Col


title: ATDT2AL


title: ATWWAL

value: well-watered


title: CD4+ CC62L+CCR7+ blood Replicate 3

city: Utrecht

first: Mariona

last: Baliu-Piqué

state: Utrecht

address: Lundlaan 6

department: Laboratory for Translational Immunology

country: Netherlands

institute: University Medical Center Utrecht

description: Biological replicate 3 of 3.

hyb_protocol: Hybridization and washing were performed according to manufacturer’s instructions with an Agilent G2565CA scanner (Agilent Technologies).

scan_protocol: Scanned on an Agilent G2565CA scanner (Agilent Technologies)

data_processing: Raw data was read and normalized in R (Version 3.4.0) using the Limma package of Bioconductor. The Normexp method with offset=16, was used for background correction and the resulting data was Quantile Normalized. The quantile normalized values provided  did not  take in account  both dyes.   We used the following  green.only is set to TRUE meaning we used only one dye. The reason for this was, that even if the array contained 2 dyes, the second  dye did not contain information for the  normalization.

organism: Capra hircus

source_name: CD4+ CC62L+CCR7+ blood

label_protocol: Total RNA (50ng) combined with Spike A was used for amplification and labelling according to the Two-Color Microarray-Based Gene Expression Analysis guide using the Low Input Quick Amp Labeling Kit (Agilent Technologies). For the common reference an equimolar pool of all samples was made and amplified similarly as the test samples with the exception that Spike B was used. Synthesized aRNA was purified with the E.Z.N.A. MicroElute RNA Clean Up Kit (OMEGA bio-tek).

extract_protocol:
Cells isolated from different organs of healthy goats were sorter on a FACS ARIA II or FACS ARIA III
Sorted cells were spun down and stored at −80°C prior to RNA extraction. Before thawing, cells were immersed in QIAzol Lysis Reagent (Qiagen). RNA was isolated and purified using the RNeasy kit (Qiagen). The concentration was measured on a NanoDrop ND-2000 (Thermo Scientific) and RNA integrity was examined using the 2200 TapeStation System with Agilent RNA ScreenTapes (Agilent Technologies).

value: CD4+ CD62L+CCR7+ lymphocytes

tag: organ

value: Blood

tag: goat number

value: Crosbread female goat


title: ATWWBL

tag: treatment

value: leaves


title: Col_0_time0_rep2

city: Shanghai

first: Lin

last: XU

address: 300 Fenglin Road

department: Chinese Academy of Sciences

institute: Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences

data_processing:
Raw RNA-seq reads were trimmed by quality using Trimmomatic and paired reads mapped to the Arabidopsis thaliana genome (TAIR10) using STAR 2.5.4b with default settings.
The returned alignments were stringently filtered so as to remove ambiguously mapped reads and read pairs with conflicting alignments.
RSEM v1.2.31 is used to quantitate gene abundance and the expression of individual gene is shown as the average of transcripts per million (TPM) in two biological replicates, all genes were filtered by the average of TPM > 1 at eight timepoints to remove genes with low transcript levels.
Differentially expressed genes were detected by EBSeq based on the combined criteria: |log2(fold change)| > 1 and false discovery rates < 0.05.
Genome_build: TAIR10
Supplementary_files_format_and_content: expression for genes(TAIR10) was provided. The format is tab delimited file format. Each row contains seven columns: gene_id, transcript_id, length, effective_length, expected_count,TPM and FPKM.

molecule: polyA RNA

source_name: Col-0 detached first-pair rosette leaves before culture from 12-day-old seedlings

growth_protocol: Arabidopsis seeds were germinated on ½ MS medium at 22°C under a 16-h light/8-h dark photoperiod. Detached leaf explants from 12-day-old seedlings were cultured on B5 medium without sucrose at 22°C under 24-h light conditions.

extract_protocol:
RNA extraction using Trizol protocols.
Library construction and deep sequencing were performed by Genergy Biotechnology Co. Ltd. (Shanghai, China) using Illumina HiSeq 3000 following the manufacturer’s instructions (Illumina)

treatment_protocol: No treatment applied.

value: Columbia

value: wild type

tag: developmental stage

value: leaves of 12-day-old seedlings

tag: growth conditions

value: 16-h light/8-h dark


title: Col_0_time0_rep1

tag: ecotype


title: MZ-CRC-1 24h_20nM_2

city: Columbus

first: Matthew

last: Ringel

state: Oh

address: 565 McCampbell Hal

department: Division of Endocrinology, Diabetes, and Metabolism

institute: The Ohio State University Wexner Medical Center and Arthur G. James Comprehensive Cancer Center

description: FeatureCounts.txt

data_processing:
Illumina BaseCalling pipeline
RNA sequencing reads were first mapped to the human genome GRCh38 build using TopHat (Version 2.0.13). Raw read counts for each gene were quantified by using featureCounts (Version 1.4.6). Then NCBI RefSeq was used for gene annotation.
Genes with raw read counts below 5 for more than 50% of samples within each condition were first filtered out.
Count data were normalized using Trimmed Mean of M-values (TMM) method within controls or drug treatments due to global drug inhibition effect. To improve the estimate of gene variability and to identify genes differentially expressed between samples, R package limma with Voom transformation. was used for testing differential expression between conditions. The p-value cut-offs were determined by controlling the mean number of false positives.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text file includes raw read counts

source_name: MZ-CRC-1 medullary thyroid cancer cells

growth_protocol: TT and MZ-CRC-1 cells were seeded in 10cm plates and incubated for 24h, then washed with PBS and incubated in 2% FBS-RPMI medium for another 24h. After this time, the untreated cells were incubated with vehicle control at 37deg celcius for 12 or 24h.

extract_protocol:
At the desired exposure time, the supernatant and scraped cells were collected into 50mL tubes, centrifuged at 300xg for 5min, the supernatant aspirated, and the pellet washed with 1mL of PBS and transferred into 1.5mL tubes. After a centrifugation step at 500xg for 5min, the supernatant was aspirated and the pellet resuspended in 1mL of TRIzol reagent (Invitrogen) to isolate the total RNA present in the cells. The RNA isolation was performed following the protocol provided by Invitrogen for TRIzol reagent use.
TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold (RS-122-2301)

treatment_protocol: TT and MZ-CRC-1 cells were seeded in 10cm plates and incubated for 24h, then washed with PBS and incubated in 2% FBS-RPMI medium for another 24h. After this time, the cells were treated with Dinaciclib and incubated at 37deg celsius for 12 or 24 hours.

value: MZ-CRC-1 medullary thyroid cancer cells

tag: agent

value: Dinaciclib

tag: dose

tag: time


title: CD8+ CC62L-CCR7- bone marrow Replicate 3

description: Biological replicate 3 of 3.

source_name: CD8+ CC62L-CCR7- bone marrow

tag: cell type

value: CD8+ CD62L-CCR7- lymphocytes

value: Bone marrow


title: N705-S505=Tie2_1plus2

description:
Control cells for Gata4 deficient endothelial cells
run2110_lane12_read1_indexN705-S505=Tie2_1plus2
Control_S505 Tie2_1_plus_2

value: Tie2-CreERT2 transgene; enhanced green fluorescent protein (eGFP) Cre-dependent reporter transgene in Rosa locus

value: cardiac endothelial cells


title: Col_0_8h_rep2

source_name: Col-0 detached first-pair rosette leaves 8h after culture from 12-day-old seedlings

treatment_protocol: cultured 8h on B5 medium without sucrose.

tag: tissue


title: MZ-CRC-1 24h_20nM_1

description: FeatureCounts.txt


title: MTB__WT_1

description: processed data file: MTB_MTB_ESX1.txt

source_name: M. tuberculosis wild type H37Rv

value: M. tuberculosis wild type 6020


title: CD11b+CD14+ lung Replicate 3

description: Biological replicate 3 of 3.

source_name: CD11b+CD14+ lung

value: Lung

tag: strain


title: rheumatoid_synovium_CD21L+/IL-17A+_Patient4

description: CD21L+/IL-17A+ P4-1

tag: disease state

value: rheumatoid arthritis

tag: disease duration

value: 2.50 years

value: inflamed rheumatoid synovia

tag: subtype

tag: patient identifier


title: CD8+ CC62L-CCR7- blood Replicate 3

description: Biological replicate 3 of 3.

source_name: CD8+ CC62L-CCR7- blood

value: Blood

value: Crosbread female goat


title: Col_0_8h_rep1

value: Columbia

tag: genotype/variation


title: Monocytes blood Replicate 1

description: Biological replicate 1 of 1.

source_name: Monocytes blood

value: Monocyte

tag: organ


title: CD11b+ blood Replicate 3

description: Biological replicate 3 of 3.

source_name: CD11b blood

tag: goat number


title: CD8+ CC62L+CCR7+ blood Replicate 2

description: Biological replicate 2 of 3.

source_name: CD8+ CC62L+CCR7+ blood

value: CD8+ CD62L+CCR7+ lymphocytes


title: CD8+ CC62L-CCR7- blood Replicate 2

description: Biological replicate 2 of 3.


title: CD4+ CC62L-CCR7- blood Replicate 2

description: Biological replicate 2 of 3.

source_name: CD4+ CC62L-CCR7- blood

value: CD4+ CD62L-CCR7- lymphocytes


title: CD4+ CC62L-CCR7- blood Replicate 3

description: Biological replicate 3 of 3.


title: 48 hr hdv

city: Vermillion

first: Michael

middle: S

last: Chaussee

state: SD

address: 414 E Clark St

department: Basic Biomedical Sciences

institute: University of South Dakota

hyb_protocol: 10 micrograms of cRNA was mixed with fragmentation buffer and heated to 94C for 20 min.  The fragmented cRNA was mixed with CodeLink hybridization buffer, loaded on the microarray slides, and hybridized for 18 hours at 37C.  The slides were washed in 0.75x TNT (Tris-HCl, NaCl, Tween-20) at 46C for 1h then incubated with streptavidin-Alexa 647 fluorescent dye for 30 min at room temperature.  The Alexa fluor was prepared in TNB blocking buffer (0.1M Tris-HCl, 0.15M NaCL, 0.5% NEN Blocking Reagent-PerkinElmer)  The slides were then washed 4 times for 5 min each in 1x TNT and once in 0.05% Tween 20 for 5 sec each.  The slides were dried by centrifugation and scanned in an Axon GenePix 4000B scanner.

scan_protocol: The slides were scanned in an Axon GenePix 4000B scanner using GenePix Pro 4.1 to align and acquire the microarray image.  CodeLink Expression Analysis 4.1.0.4163 was used to apply the background correction.

data_processing: Data in the matrix table were prepared by global median normalization applied by CodeLink Expression Analysis 4.1.0.4163.

label: streptavidin Alexa Fluor 647

source_name: adenocarcinoma human alveolar basal epithelial cells (A549) cells

label_protocol: Labeled cRNA was prepared using the MessageAmp II-Biotin enhanced kit (Ambion).  1.0 microgram of total RNA was mixed with bacterial control RNA spikes and primed with T7 oligo(dT) primer for 10 min at 70C.  (The bacterial control spikes included araB, entF, fixB, gnd, hisB, and leuB.)  The first strand of cDNA was synthesized with first strand buffer, dNTP mix, RNase inhibitor, and reverse transcriptase for 2 h at 42C.  The second strand cDNA synthesis reaction was prepared using second strand buffer, dNTP mix, DNA polymerase mix, and RNase H; the reaction was carried out for 2h at 16C.  The double-stranded cDNA was purified on columns.  The double-stranded cDNA was mixed with T7 reaction buffer, T7 ATP, T7 GTP, T7 UTP, T7 CTP, biotin-11-UTP, and T7 enzyme mix for the synthesis of cRNA.  The cRNA synthesis reaction was terminated after 14h at 37C by purifying the cRNA.  The concentration of cRNA was determined by spectrophotometry. Streptavidin Alexa fluor 647 was incubated with the slides after hybridization to complete the labeling reaction.  One sample was hybridized with each slide so no dye swaps were necessary.

extract_protocol: Total RNA was extracted from the control and infected cells at 24 hours post-IAV infection using Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA) and RNA was purified with the RNeasy kit (Qiagen, Valencia, CA). RNA purity and quantity was evaluated with Agilent chips (Agilent RNA 600 Nano kit).The purity and quantity of RNA were evaluated by an Agilent Bioanalyzer using the RNA 6000 Nanoassay LabChip.

treatment_protocol: Monolayers of A549 cells (6 X 105 cells/ml) were infected with IAV at 5 X 102 TCID50, or 105 TCID50 IAV.  The inoculum was removed, after one hour and the cells were washed twice with PBS and incubated with media containing 1 µg/ml TPEC trypsin for 30 minutes, 24 hours, or 48 hours  at 37°C and 5% CO2.

tag: cell line

value: influenza A/Hong Kong/1/68-H3N2 (HK68)

tag: infection time point

value: 48 hour

tag: iav dose

value: 2 X 10^5 TCID50 IAV


title: 48 hr ldv

value: adenocarcinoma human alveolar basal epithelial cells

value: 5 X 10^2 TCID50 IAV


title: 24 hr hdv

value: 24 hour


title: 48 hr media


title: 24 hr ldv


title: CD8+ CC62L-CCR7- bone marrow Replicate 2

description: Biological replicate 2 of 3.

value: CD8+ CD62L-CCR7- lymphocytes

value: Bone marrow


title: Macrophage lung Replicate 1

description: Biological replicate 1 of 1.

source_name: Macrophage lung

value: Macrophage

value: Lung


title: CD8+ CC62L+CCR7+ blood Replicate 3

description: Biological replicate 3 of 3.


title: CD4+ CC62L+CCR7+ blood Replicate 2

description: Biological replicate 2 of 3.

value: CD4+ CD62L+CCR7+ lymphocytes


title: Col_0_4h_rep2

source_name: Col-0 detached first-pair rosette leaves 4h after culture from 12-day-old seedlings

treatment_protocol: cultured 4h on B5 medium without sucrose.

tag: ecotype

value: wild type

tag: developmental stage

value: leaves of 12-day-old seedlings

tag: growth conditions

value: 16-h light/8-h dark


title: MZ-CRC-1 24h_0nM_1

description: FeatureCounts.txt

value: MZ-CRC-1 medullary thyroid cancer cells

tag: agent

value: control

tag: dose

tag: time


title: MZ-CRC-1 12h_20nM_1

description: FeatureCounts.txt

value: Dinaciclib


title: MZ-CRC-1 12h_20nM_2

description: FeatureCounts.txt


title: Col_0_4h_rep1

value: Columbia

tag: tissue


title: MZ-CRC-1 24h_0nM_2

description: FeatureCounts.txt


title: Col_0_30min_rep2

source_name: Col-0 detached first-pair rosette leaves 30min after culture from 12-day-old seedlings

treatment_protocol: cultured 30min on B5 medium without sucrose.


title: Col_0_30min_rep1


title: CD11b+CD14+ lung Replicate 2

description: Biological replicate 2 of 3.

tag: cell type

tag: strain

value: Crosbread female goat


title: MZ-CRC-1 12h_0nM_2

description: FeatureCounts.txt


title: MZ-CRC-1 12h_0nM_1

description: FeatureCounts.txt


title: 24 hr media


title: TT 24h_10nM_2

description: FeatureCounts.txt

source_name: TT medullary thyroid cancer cells

value: TT medullary thyroid cancer cells


title: 30 min hdv

value: adenocarcinoma human alveolar basal epithelial cells

value: influenza A/Hong Kong/1/68-H3N2 (HK68)

value: 30 minute

value: 2 X 10^5 TCID50 IAV


title: Col_0_2h_rep2

source_name: Col-0 detached first-pair rosette leaves 2h after culture from 12-day-old seedlings

treatment_protocol: cultured 2h on B5 medium without sucrose.


title: Col_0_2h_rep1


title: Col_0_1h_rep1

source_name: Col-0 detached first-pair rosette leaves 1h after culture from 12-day-old seedlings

treatment_protocol: cultured 1h on B5 medium without sucrose.


title: 30 min ldv

value: 5 X 10^2 TCID50 IAV


title: 30 min media


title: CD8+ CC62L-CCR7- blood Replicate 1

description: Biological replicate 1 of 3.

value: CD8+ CD62L-CCR7- lymphocytes

value: Blood


title: TT 24h_0nM_2

description: FeatureCounts.txt


title: Col_0_12h_rep2

source_name: Col-0 detached first-pair rosette leaves 12h after culture from 12-day-old seedlings

treatment_protocol: cultured 12h on B5 medium without sucrose.


title: 24 hr Virus

value: 24 hour


title: CD8+ CC62L+CCR7+ blood Replicate 1

description: Biological replicate 1 of 3.

value: CD8+ CD62L+CCR7+ lymphocytes


title: 24 hr Control


title: 30 min Control


title: 30 min Virus


title: CD11b+ blood Replicate 2

description: Biological replicate 2 of 3.


title: CD8+ CC62L-CCR7- bone marrow Replicate 1

description: Biological replicate 1 of 3.

source_name: CD8+ CC62L-CCR7- bone marrow

value: Bone marrow


title: CD11b+CD14+ lung Replicate 1

description: Biological replicate 1 of 3.

value: Lung


title: CD11b+ jejunum Replicate 1

description: Biological replicate 1 of 1.

source_name: CD11b+ jejunum

value: Jejunum


title: TT 24h_0nM_1

description: FeatureCounts.txt

value: control


title: Col_0_12h_rep1

value: wild type

value: leaves of 12-day-old seedlings

value: 16-h light/8-h dark


title: Col_0_10min_rep2

source_name: Col-0 detached first-pair rosette leaves 10min after culture from 12-day-old seedlings

treatment_protocol: cultured 10min on B5 medium without sucrose.

value: Columbia


title: TT 12h_10nM_2

description: FeatureCounts.txt

value: TT medullary thyroid cancer cells

value: Dinaciclib


title: TT 12h_10nM_1

description: FeatureCounts.txt


title: Col_0_10min_rep1


title: TT 12h_0nM_2

description: FeatureCounts.txt


title: TT 12h_0nM_1

description: FeatureCounts.txt


title: Sdg8_2_2h_rep1

source_name: sdg8-2 detached first-pair rosette leaves 2h after culture from 12-day-old seedlings


title: Sdg8_2_time0_rep1

source_name: sdg8-2 detached first-pair rosette leaves before culture from 12-day-old seedlings


title: Coi1_2_time0_rep2

source_name: coi1-2 detached first-pair rosette leaves before culture from 12-day-old seedlings


title: LY6E Rep 1

city: Dallas

first: John

last: Schoggins

state: Texas

address: 5323 Harry Hines Blvd

department: Department of Microbiology

institute: UT Southwester Medical Center

description: Cells expressing LY6E vector for 13 passages

data_processing:
Single-end 50 bp read length Fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806).
Trimmed fastq files were mapped to human genome using TopHat (v2.0.12)
Duplicates were marked using picard-tools (v1.127)
Read counts were generated using featureCounts (subread) for coding genes from gencode (v19)
Normalized read counts generated using edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited txt files that includes normalized read counts for each sample per gene

source_name: STAT1-/- fibroblasts

growth_protocol: STAT1-/- fibroblasts were grown in RPMI supplemented with 10% FBS, 1X non-essential amino acids, and 4 ug/mL puromycin.

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen #74106) following the manufacturer's instructions. Integrity was verified using the Agilent 2100 Bioanalyzer. All samples had a RIN score of 8 or higher.
Four micrograms of total DNAse-treated RNA were then prepared with the TruSeq Stranded Total RNA LT Sample Prep Kit from Illumina (Illumina  #RS-122). Poly-A RNA was purified and fragmented before strand specific cDNA synthesis.  cDNA were then A-tailed and indexed adapters were ligated. After adapter ligation, samples were PCR amplified and purified with AmpureXP beads, then validated again on the Agilent 2100 Bioanalyzer. Before being normalized and pooled, samples were quantified by Qubit then run on the Illumina Hiseq 2500 using SBS v3 reagents.

treatment_protocol: Naïve STAT1-/- fibroblasts were spinoculated with lentivirus containing CMV-driven LY6E or empty control vector. The plasmid backbone also contains TagRFP and a puromycin-resistance cassette. Two days after spinoculation, cells were split into media containing 4 ug/mL puromycin. Cells were passaged at a 1:4 split for the indicated number of passages, No additional manipulations occurred prior to processing cells for RNA extraction.

value: Skin

tag: genotype


title: Sdg8_2_2h_rep2


title: LY6E Rep 3

description: Cells expressing  LY6E vector for 16 passages


title: Sdg8_2_time0_rep2


title: Empty control (LY6E) Rep 3

description: Cells stably expressing empty control vector for 10 passages


title: CD4+ CC62L-CCR7- blood Replicate 1

description: Biological replicate 1 of 3.

value: CD4+ CD62L-CCR7- lymphocytes

value: Crosbread female goat


title: sph-600-3-Cy5 (from hybridization sph-600-3-Cy5 vs. testRNA-Cy3)

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

description: Raw data file: US22502614_251485043645_S01_GE2_107_Sep09_2_NO_SPIKEIN_1_2.txt

hyb_protocol: Equal amounts of differentially labeled specimens were put together, fragmented and hybridized to Agilent Whole Human Genome Microarray 4x44k glass slides (containing 41000 probes corresponding to 19596 Entrez Gene RNAs) (Agilent Technologies).  All steps were performed using the In Situ Hybridization kit-plus (Agilent Technologies) and following the 60-mer oligo microarray processing protocol (Agilent Technologies). Then, slides were washed following the Agilent wash procedure.

scan_protocol: After hybridization, slides were washed following the Agilent procedure and scanned using an Agilent C dual-laser microarray scanner (G2505C, Agilent Technologies).

data_processing: Raw data elaboration was carried out with Bioconductor (www.bioconductor.org), using R statistical language. Background correction was performed with the normexp method with an offset of 50, loess was used for the within-array normalization and A-quantile for the between-array normalization. Separate channel analysis was then performed in order to analyze two-color data in terms of the individual channel intensities. The LIMMA (LInear Models for Microarray Analysis) package was used to identify differentially expressed genes in sphere cells versus adherent cells. The empirical Bayes method was used to compute a moderated t-statistics . p-values were adjusted for multiple testing by using a false discovery rate (FDR) correction.

label_protocol: RNA was amplified by means of the Amino Allyl MessageAmp II aRNA Kit (Life Technologies) to obtain amino allyl antisense RNA (aaRNA) following the method developed by Eberwine and coworkers. Briefly: mRNA was reverse transcribed in cDNA single strand; after the second strand synthesis, cDNA was in vitro transcribed in aaRNA including amino allyl modified nucleotides (aaUTP). Both dsDNA and aaRNA underwent a purification step using columns provided with the kit. mRNA amplification was checked by means of Bioanalyzer (Agilent Technologies) and NanoDrop ND-1000 Spectrophotometer (Thermo Scientific). Labeling was performed using NHS ester Cyanine3 or Cyanine5 dyes able to react with the modified RNA. Labeling efficiency and labeled mRNA quantity were checked by means of NanoDrop ND-1000 Spectrophotometer (Thermo Scientific).

growth_protocol: Cells were propagated in adherent culture conditions in High Glucose Dulbecco’s Modified Eagle’s Medium (DMEM, Euroclone) supplemented with 10% Fetal Bovine Serum (FBS, Lonza), 2 mM L-Glutamine, and 1X Non-Essential Amino Acids (Euroclone), 100 U/ml penicillin, and 0.1 mg/ml streptomycin (Euroclone) at 37°C in a 5% CO2 humidified incubator.   To perform sphere formation assays, cells were plated in Petri dishes at a concentration of about 104 cells per ml of sphere-forming medium consisting in a 1:1 mixture of high glucose DMEM and Ham’s Nutrient Mixture F-12 (Euroclone) supplemented with 20 ng/ml recombinant human Epidermal Growth Factor (EGF, Life Technologies), 20 ng/ml recombinant human Fibroblast Growth Factor-basic (FGFb, Life Technologies), 1X Insulin-Transferrin-Selenium (Life Technologies), 4 mg/ml Bovine Serum Albumin (BSA, Sigma), 2 mM glutamine (Euroclone), 50 U/ml penicillin, and 0.05 mg/ml streptomycin (Euroclone). After 6-7 days of growth, spheres were counted. When required, spheres were collected, dissociated with trypsin-EDTA and cells were used either for RNA or protein extraction, or replated either in sphere forming medium or in medium supplemented with serum to allow them to differentiate. To test single cell sphere formation, cells were seeded in 96 well plates with a limiting dilution approach and wells containing a single cell were monitored for sphere formation.

extract_protocol: RNA was extracted from two independent samples of adherently growing cells and 6 day spheres.  RNA was extracted by Direct-zol RNA Mini-prep kit (Zymo Research).

value: sph

tag: population doublings (pds)

value: spheres from cen3tel 600


title: CD4+ CC62L+CCR7+ blood Replicate 1

description: Biological replicate 1 of 3.

source_name: CD4+ CC62L+CCR7+ blood

value: CD4+ CD62L+CCR7+ lymphocytes

value: Blood


title: Empty control (LY6E) Rep 2


title: adh-600-1-Cy3 (from hybridization sph-600-1-Cy5 vs. adh-600-1-Cy3)

description: Raw data file: US22502614_251485043644_S01_GE2_107_Sep09_2_NO_SPIKEIN_1_3.txt

value: adh

value: adherent cen3tel 600


title: adh-1000-1-Cy5 (from hybridization adh-1000-1-Cy5 vs. testRNA-Cy3)

description: Raw data file: US22502614_251485043644_S01_GE2_107_Sep09_2_NO_SPIKEIN_1_1.txt

value: adherent cen3tel 1000


title: CD11b+ blood Replicate 1

description: Biological replicate 1 of 3.

source_name: CD11b blood


title: adh-1000-2-Cy5 (from hybridization adh-1000-2-Cy5 vs. testRNA-Cy3)

description: Raw data file: US22502614_251485043644_S01_GE2_107_Sep09_2_NO_SPIKEIN_1_2.txt


title: LY6E Rep 2

description: Cells expressing LY6E vector for 16 passages


title: adh-600-2-Cy5 (from hybridization adh-600-2-Cy5 vs. testRNA-Cy3)

description: Raw data file: US22502614_251485043645_S01_GE2_107_Sep09_2_NO_SPIKEIN_1_4.txt


title: adh-600-2-Cy3 (from hybridization sph-600-2-Cy5 vs. adh-600-2-Cy3)

description: Raw data file: US22502614_251485043644_S01_GE2_107_Sep09_2_NO_SPIKEIN_1_4.txt


title: sph-600-2-Cy5 (from hybridization sph-600-2-Cy5 vs. adh-600-2-Cy3)


title: sph-600-1-Cy3 (from hybridization testRNA-Cy5 vs. sph-600-1-Cy3)

description: Raw data file: US22502614_251485043645_S01_GE2_107_Sep09_2_NO_SPIKEIN_1_1.txt


title: sph-600-1-Cy5 (from hybridization sph-600-1-Cy5 vs. adh-600-1-Cy3)


title: adh-600-1-Cy5 (from hybridization adh-600-1-Cy5 vs. testRNA-Cy3)

description: Raw data file: US22502614_251485043645_S01_GE2_107_Sep09_2_NO_SPIKEIN_1_3.txt


title: Coi1_2_2h_rep1

source_name: coi1-2 detached first-pair rosette leaves 2h after culture from 12-day-old seedlings

tag: genotype/variation


title: sph-1000-1-Cy3 (from hybridization testRNA-Cy5 vs. sph-1000-1-Cy3)

description: Raw data file: US22502614_251485043643_S01_GE2_107_Sep09_2_NO_SPIKEIN_1_3.txt

value: spheres from cen3tel 1000


title: Golden Delicious ALT1-2

city: Beijing

first: Tianzhong

last: Li

address: Yuanmingyuan Street No.2

department: Horticulture

institute: China Agricultural University

data_processing:
Next Generation Sequencing of small RNAs
Sequenced raw reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Clean reads were mapped to reference genome allowing no mismatches by bowtie.
Genome_build: GDDH13 Version 1.1
Supplementary_files_format_and_content: Processed files include: 'miRNA name' is the name of microRNA from miRBase database; 'miRNA sequence' is the sequence of nature microRNA which is known in miRBase database; 'GDWT(mean)' is the mean of norm value in twice biological repeats of ‘GDWT’; 'GDALT1(mean)' is the mean of norm value in twice biological repeats of ‘GDALT1’; 'fold_change(JGALT(mean)/JGWT(mean))' the value is the fold change between JGALT(mean) and JGWT(mean) and P value(t_test).

organism: Malus domestica

source_name: Golden Delicious_ALT1

growth_protocol: Four-week-old apple (Malus domestica cv. ‘Golden Delicious’) plants were grown by tissue culture on Murashige and Skoog (MS) medium containing 0.6 mg/ L 6-benzylaminopurine (6-BA) and 0.15 mg/L 1-naphthylacetic acid (NAA) in a climate-controlled culture room at 25±1°C with a 16/8-h light/dark photoperiod.

extract_protocol:
Leaf samples were harvested from control and ALT1-infected plants at 24 hpi, frozen in liquid nitrogen, and stored at -80°C until required. RNA was extracted from 100 mg of leaf tissue using the cetyltrimethylammonium bromide (CTAB) method and construction of  sequencing libraries by Illumina TruSeq small RNA Sample Prep Kit.
Small RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The fungus was grown on Potato Dextrose Agar (PDA) medium at 25°C for 6 days. Inoculum spores were suspended in deionized water at 2×10^5 c.f.u./mL, and yields were assessed by microscopy (Olympus, CX31RTSF, Japan). 'Mock-inoculated' is treated the leaves with deionized water; and 'Inoculated with ALT1' is treated the leaves with inoculum spores were suspended in deionized water at 2×105 c.f.u./mL.

tag: cultivar

value: cv. Golden Delicious

tag: age

value: Four-week-old

value: leaves

tag: treated with

value: A. alternata f. sp. mali (ALT1)

tag: time point

value: 24 hours post inoculation

tag: molecule subtype

value: small RNAs


title: sph-1000-2-Cy3 (from hybridization testRNA-Cy5 vs. sph-1000-2-Cy3)

description: Raw data file: US22502614_251485043643_S01_GE2_107_Sep09_2_NO_SPIKEIN_1_4.txt


title: Coi1_2_2h_rep2

tag: ecotype

value: Columbia

value: leaves of 12-day-old seedlings

value: 16-h light/8-h dark


title: ZMDT4BC

description:
RNA digested by RNase R
Exp_ZmCirc.txt

organism: Zea mays

source_name: leaves

treatment_protocol: For drought experiments, gradient drought treatments were administered 16 days after planting maize and 21 days after planting Arabidopsis according to a previous report (Su et al., 2013). Briefly, the soil moisture of each treatment was monitored by measuring the relative soil water content, followed with rationing of water to maintain a designated soil moisture. The pots were weighed and watered twice daily. After the most serious stress reached the preset levels, the plants were maintained for one more day, then the whole plants were harvested for fresh weight measurement and leaves were harvested for RNA extraction. The third leaves of B73 at V4 stage from at least 2 plants and leaves of 4 Col-0 plants were harvested and pooled, respectively, for RNA extraction.For the experiments on maize inbred lines, two treatments [well-watered  (WW), 65%~60% soil moisture; drought-stressed (DT), 25%~20% soil moisture] were applied. Eight plants of each inbred line were grown in two pots (10cm x 10cm x 9cm), with 4 plants in each pot. All pots were randomly placed in the growth room at 28°C with 16 h light/8h dark. Soil moisture was controlled by measuring the relative water content of soil and rationing water (pots were weighed and watered once daily). Drought treatments started 16 days after planting, then after 4 days of drought treatment leaves were sampled.

tag: treatment

value: drought-stressed DT4

tag: Stage

value: leaves at V4 stage

tag: rnaser treatment

value: RNase R+


title: Golden Delicious CK-2

source_name: Golden Delicious_mock inoculated

value: deionized water


title: Golden Delicious ALT1-1


title: ZMDT4AC

description:
RNA digested by RNase R
Exp_ZmCirc.txt


title: Golden Delicious CK-1


title: Empty control (LY6E) Rep 1

description: Cells stably expressing empty control vector for 7 passages

value: Skin


title: ZMDT3BC

description:
RNA digested by RNase R
Exp_ZmCirc.txt

value: drought-stressed DT3


title: PMEN3_uninduced_T6h_reanalyzed

city: Oxford

first: Angela

middle: B

last: Brueggemann

address: Peter Medawar Building for Pathogen Research

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

description:
broth culture
GSM2360606

data_processing:
RNA-seq data for PMEN3 grown individually was retrieved from GEO (accession number GSE89200) and combined in silico with the sequenced reads for PMEN6 grown individually (generated as part of this study).  These samples are included in this series for access of the complete data set from a single SRP.
Data from all time points were combined in silico and mapped to the pseudo-reference genome using Bowtie2 with the highest sensitivity option.
Differential expression analyses were performed using the DESeq method by comparing reads generated when strains were competing in broth culture to those from when strains were grown individually
Genome_build: A pseudo-reference genome was constructed using PMEN3 and PMEN6 reference genomes by sorting genes into three categories: those unique to PMEN3, those unique to PMEN6, and those shared between the two.
Supplementary_files_format_and_content: Excel (.xlsx) file include normalised TPM values, the ratio of the normalized values between the in vitro competition experiment and the control (Log 2 of Differential Expression Ratio) for genes unique to PMEN3, unique to PMEN6 and shared between the two, and a p-value indicating the confidence that each gene is differentially expressed (Differential Expression p-value). Nucleotide sequence for each gene is also provided.

organism: Streptococcus pneumoniae

source_name: PMEN3 grown individually

extract_protocol:
RNA was immediately extracted from the samples using the Promega Maxwell® 16 Instrument and LEV simplyRNA Cells purification kit, following the manufacturer’s protocol.
RNA extracts were sent to the Oxford Genomics Centre where library preps were made using RNA-Seq Ribozero kits (Illumina, Inc)

tag: timepoint

value: 6 hour

tag: condition

value: Grown at 37C


title: shRNA_UBC9_3

city: Nanning

first: Xiaoliang

last: Huang

address: 22 Shuangyong road

institute: Guangxi Medical University

description: Treatment with a UBC9 shRNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human genome (hg38) using the CLC Biomedical Genomics Workbench 4 (QIAGEN Bioinformatics).
The read numbers mapped of each gene was counted and Reads Per Kilobase of exon model per Million mapped reads,(RPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene by using the CLC Biomedical Genomics Workbench 4 (QIAGEN Bioinformatics).
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample.

source_name: shRNA_UBC9, T24 cell line

extract_protocol:
Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions.
The construction of RNA-seq library was based on the protocol of the IlluminaTruSeq RNA Sample Preparation Kit (illumina)

value: bladder cancer cell

tag: cell line

value: shRNA UBC9

value: UBC9 knockdown


title: shRNA_UBC9_1

description: Treatment with a UBC9 shRNA

tag: cell type


title: adh-1000-2-Cy3 (from hybridization sph-1000-2-Cy5 vs. adh-1000-2-Cy3)

description: Raw data file: US22502614_251485043643_S01_GE2_107_Sep09_2_NO_SPIKEIN_1_2.txt

value: adh

value: adherent cen3tel 1000


title: PMEN3_uninduced_T4h_reanalyzed

description:
broth culture
GSM2360602

value: 4 hour

tag: strain


title: shRNA_UBC9_2

description: Treatment with a UBC9 shRNA

tag: genotype


title: adh-1000-1-Cy3 (from hybridization sph-1000-1-Cy5 vs. adh-1000-1-Cy3)

description: Raw data file: US22502614_251485043643_S01_GE2_107_Sep09_2_NO_SPIKEIN_1_1.txt

tag: population doublings (pds)


title: ZMDT2AC

description:
RNA digested by RNase R
Exp_ZmCirc.txt

value: drought-stressed DT2

tag: tissue

value: leaves


title: ZMDT2BC

description:
RNA digested by RNase R
Exp_ZmCirc.txt


title: PMEN3_uninduced_T3h_reanalyzed

description:
broth culture
GSM2360600

value: 3 hour


title: sph-1000-1-Cy5 (from hybridization sph-1000-1-Cy5 vs. adh-1000-1-Cy3)

value: sph

value: spheres from cen3tel 1000


title: shRNA_NC_3

description: Treatment with a control shRNA

source_name: shRNA_NC, T24 cell line

value: shRNA control

value: control


title: shRNA_NC_2

description: Treatment with a control shRNA


title: ZMWWBC

description:
RNA digested by RNase R
Exp_ZmCirc.txt

value: well-watered

value: leaves at V4 stage

value: RNase R+


title: PMEN3_PMEN6_together_T6h

description: broth culture

source_name: PMEN3 and PMEN6 grown together

value: 6 hour

value: PMEN3 and PMEN6

value: Grown at 37C


title: ZMWWAC

description:
RNA digested by RNase R
Exp_ZmCirc.txt


title: s54-WT_3

city: Frederick

first: Jack

last: Chen

state: MD

address: SAIC-Frederick Miller Dr

institute: NIH

data_processing:
Illumina HiSeq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to E.coli K-12 genome using bowtie2 with default parameters.
Reads were counted by featurecount and then Reads per Megabase of library size (CPM) were generated and normalized by the limmaVoom pipeline.
Genome_build: E. coli K-12
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

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

source_name: ATCC

growth_protocol: MG1655 E. coli were grown in Gutnick minimal media to induce nitrogen starvation.

extract_protocol:
RNA was stabilized after 80 minutes after treatment using the RNAprotect Bacteria Reagent (Qiagen), and purified using the RNeasy Mini Kit and RNase-free DNase (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At OD600 0.5, cells were treated with 10 µM stapled peptide.

value: 10 mM s54-WT

tag: nitrogen condition

value: nitrogen-starved


title: ZMDT4BL

data_processing:
For circRNA-seq data, clean FASTQ reads were first mapped to the maize B73 reference genome from EnsemblePlants or Arabidopsis genome BWA-MEM with a CIRI2 suggested parameter: T, 19. SAM alignment files generated by BWA-MEM with GTF-formatted gene annotations (Zea_mays.AGPv3.31.gtf, Arabidopsis_thaliana.TAIR10.32.gtf) were then called by the CIRI2 algorithm with default parameters except thread number to detect and annotate circRNAs. All CIRI2 circRNA outputs were supported by more than two junction reads (reads spanning back-spliced sites).
CircRNAs with at least two junction reads that occurred in both replicates were selected as high-confidence predictions. They were then compared with circRNAs in PlantcircBase (http://ibi.zju.edu.cn/plantcircbase/) (Chu et al., 2017) to identify new circRNAs discovered in this study. circRNAs in each treatment and normalized the number by total clean reads (units in million), and grouped circRNAs based on genomic origin type
RPB datasets were used to call differentially-expressed circRNAs (DE circRNAs) from different treatments by the Bioconductor package ‘edgeR’. The edgeR programs were performed in the OmicShare tools, a free online platform for data analysis, with default parameters (www.omicshare.com/tools). The cutoff we used to pick significant DE circRNAs was FDR<0.05.
For RNA-seq data,transcript quantification values were then calculated by rsem-calculateexpression with the following parameters: num-threads, 8; calc-pme; calc-ci. The TPM (transcripts per million) values were selected to represent relative expression of a transcript.
Differential expression analyses were performed on TPM datasets by ‘edgeR' in the OmicShare tools to identify differentially-expressed linear RNAs.Transcripts with FDR<0.05 and |Fold Change|≥2 were considered to be significant DE mRNAs.
Genome_build: ftp://ftp.ensemblgenomes.org/pub/plants/release-32/fasta/arabidopsis_thaliana/dna/Arabidopsis_thaliana.TAIR10.dna_sm.toplevel.fa.gz
Genome_build: ftp://ftp.ensemblgenomes.org/pub/plants/release-31/fasta/zea_mays/dna/Zea_mays.AGPv3.dna_sm.toplevel.fa.gz
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample in Exp_AtLinear.txt and Exp_ZmLinear.txt, tab-delimited text files include RPB values for each Sample in Exp_AtCirc.txt and Exp_ZmCirc.txt

value: drought-stressed DT4

value: RNase R-


title: ZMDT4AL


title: PMEN3_PMEN6_together_T4h

description: broth culture

value: 4 hour


title: sph-1000-2-Cy5 (from hybridization sph-1000-2-Cy5 vs. adh-1000-2-Cy3)


title: PMEN3_PMEN6_together_T5h

description: broth culture

value: 5 hour


title: ZMDT3AC

description:
RNA digested by RNase R
Exp_ZmCirc.txt

value: drought-stressed DT3

value: leaves


title: s54-WT_2


title: PMEN3_uninduced_T5h_reanalyzed

description:
broth culture
GSM2360604


title: PMEN3_PMEN6_together_T3h

description: broth culture

value: 3 hour


title: PMEN3_uninduced_T2h_reanalyzed

description:
broth culture
GSM2360598

value: 2 hour


title: s54-WT_1


title: PMEN6_T6h

description: broth culture

source_name: PMEN6 grown individually


title: ZMDT3AL


title: PMEN6_T5h

description: broth culture


title: Ss54-4_3


title: PMEN3_PMEN6_together_T2h

description: broth culture


title: Ss54-4_2


title: ZMDT2AL

value: drought-stressed DT2


title: ZMDT2BL


title: shRNA_NC_1

description: Treatment with a control shRNA

value: bladder cancer cell

value: shRNA control

value: control


title: Ss54-3_2


title: ZMWWBL

value: well-watered

value: leaves at V4 stage


title: PMEN6_T4h

description: broth culture

value: Grown at 37C


title: MVU_KOWhiB6_2

city: Jeddah

first: Qingtian

last: Guan

address: Thuwal

institute: King Abdallah University of Science and Technology

description: processed data file: VU_EmptyVector_KnockOut.txt

data_processing:
bcl2fastq2 Conversion Software
Trimming of Illumina adaptor sequences and low quality reads were done using Trimmomatic (v 0.33)
For the wild type and ESX1 mutants comparision, the Illumina reads were mapped with SMALT (default parameters) against the M. tuberculosis H37Rv or M. marinum M reference. From the read count, which was obtained with bedtools, parameter multicov, with -D to include duplicates and -q 5 to exclude repetitive mapping reads, we performed a differential expression analysis with DESeq using default parameters. For the whib6 knockout and complementary comparision, we mapped the trimmed reads back to the same reference genome with bowtie2 and the differently expressed genes were called by cuffdiff2.
Normalization of raw read counts and differential expression analysis was performed using DeSeq or CuffDiff2
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Mycobacterium marinum M

source_name: M. marinum MVU WhiB6 mutant

extract_protocol:
M. marinum and M. tuberculosis cultures were pelleted and bead beated in 1 ml of TRIzol (Invitrogen) with 0.1-mm zirconia/silica beads (BioSpec Products). After centrifugation, supernatants were extracted with chloroform, and RNA was precipitated with isopropanol. RNA pellets were washed with 80% ethanol and dissolved in RNAse-free water. Contaminant DNA was removed by incubation with DNAse I (Fermentas).
Total RNA was extracted with TRIzol (Invitrogen) and then purified on RNeasy spin columns (Qiagen) according to the manufacturer’s instructions. RNA integrity (RNA integrity score ≥ 6.8) and quantity were determined on an Agilent 2100 Bioanalyzer (Agilent; Palo Alto, CA, USA). As ribosomal RNA constitutes a vast majority of the extracted RNA population, depletion of these molecules via RiboMinus-based rRNA depletion was conducted. For mRNA enrichment, Invitrogen’s RiboMinus Transcriptome Isolation Kit, bacteria was used according to manufacturer’s instructions. Briefly, 2 µg of total RNA samples was hybridized with prokaryotic rRNA-sequence-specific 5′-biotin-labelled oligonucleotide probes to selectively deplete large rRNA molecules from total RNA. Then, these rRNA-hybridized, biotinylated probes were removed from the sample with streptavidin-coated magnetic beads. The resulting RNA sample was concentrated using the RiboMinus concentrate module according to the manufacturer’s protocol. The final RiboMinus RNA sample was subjected to thermal mRNA fragmentation using the Elute, Prime, Fragment Mix from the Illumina TruSeq RNA Sample Preparation Kit v2 (Low-Throughput protocol). The fragmented mRNA samples were subjected to cDNA synthesis using the Illumina TruSeq RNA Sample Preparation Kit (low-throughput protocol) according to the manufacturer’s protocol. Briefly, cDNA was synthesized from enriched and fragmented RNA using SuperScript III reverse transcriptase (Invitrogen) and the SRA RT primer (Illumina). The cDNA was further converted into double-stranded DNA using the reagents supplied in the kit, and the resulting dsDNA was used for library preparation. To this end, cDNA fragments were end-repaired and phosphorylated, followed by adenylation of 3′ ends and adapter ligation. Twelve cycles of PCR amplification were then performed, and the library was finally purified with AMPure beads (Beckman Coulter) as per the manufacturer’s instructions. A small aliquot (1 µl) was analysed on an Invitrogen Qubit and an Agilent Bioanalyzer. The bar-coded cDNA libraries were pooled at equal concentrations before sequencing on an Illumina HiSeq2000 using the TruSeq SR Cluster Generation Kit v3 and TruSeq SBS Kit v3. Data were processed with Illumina Pipeline software v1.82.

value: M. marinum MVU WhiB6 mutant

tag: genotype/variation

value: WhiB6 mutant


title: PMEN6_T3h

description: broth culture


title: Ss54-3_1

value: nitrogen-starved


title: ZMWWAL

city: Wuhan

first: Mingqiu

last: Dai

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agriculture University

extract_protocol:
Total RNAs were isolated from the pooled samples using TRI pure reagent (Aidlab, Beijing, CN) according to the manufacturer’s protocol. Total RNA samples were treated with DNase I (Thermo Scientific) and purified by RNA Clean & Concentrator-25 spin columns (ZYMO Research)
RNA samples from maize and Arabidopsis treated with various levels of drought were digested with RNase R before library preparation and then subjected to deep sequencing using an Illumina HiSeq 3000 on a 150 bp paired-end run (Ribobio, Guangzhou, CN). The same RNA samples used in circRNA sequencing were used for library preparation and RNA sequencing. 150bp paired-end raw reads were generated using an Illumina HiSeq3000 (ANOROAD, Beijing, CN)

value: RNase R-


title: ZMDT3BL


title: Ss54-2_3


title: MVU_CompWhiB6_1

description: processed data file: VU_EmptyVector_Complementary.txt

source_name: M. marinum MVU complemented with WhiB6

value: M. marinum MVU complemented with WhiB6

value: complemented with WhiB6


title: PMEN6_T2h

description: broth culture


title: E11_ESX1_INT

description: processed data file: Mmar_Mmar_ESX1_INT.txt

organism: Mycobacterium marinum E11

source_name: M. marinum ESX-1 mutant during THP-1 infection

value: ESX1 mutant


title: Ss54-2_1


title: RESTV 3dpi [RNA-482]

city: Atlanta

first: César

last: Albariño

state: GA

address: 1600 Clifton Rd, MS G14

institute: Centers for Disease Control and Prevention

data_processing:
RNA-Seq Analysis performed using default parameters on CLC Genomics Workbench 11.0
reference sequences were used for EBOV, SUDV, BDBV, and RESTV
Genome_build: EBOZ-2014-IC (KT589389); SUDV Gulu-2000 (NC_006432); BDBV 2007 (NC_014373); RESTV_ITA_1992_(KY798007)
Supplementary_files_format_and_content: each table file (.xlxs format) contains measurments of mRNA abundance for each virus from 1-3 dpi (3 sheets per table)

organism: Reston ebolavirus

source_name: Huh7 cells_RESTV

growth_protocol: cell monolayers were infected with low moi, and harvested at 1-3 dpi

extract_protocol:
total RNA was harvested, and mRNA was purified
RNA libraries were prepared for sequencing using standard Illumina protocols

value: human liver cells

tag: infected with

value: RESTV

value: 3 dpi


title: MVU_EmptyVector_2

source_name: M. marinum MVU with empty vector

value: M. marinum MVU with empty vector

value: empty vector


title: Ss54-1_2


title: E11_WT_INT

source_name: M. marinum wild type E11 during THP-1 infection

value: wild type


title: RESTV 1dpi [RNA-480]

tag: time point

value: 1 dpi


title: MVU_EmptyVector_1


title: Ss54-1_1


title: MUSA_KOWhiB6_2

description: processed data file: USA_EmptyVector_KnockOut.txt

source_name: M. marinum MUSA WhiB6 mutant

value: M. marinum MUSA WhiB6 mutant


title: MVU_KOWhiB6_1


title: Nplus_3

value: no treatment

value: nitrogen-rich


title: EBOV 3dpi [RNA-478]

organism: Ebola virus

source_name: Huh7 cells_EBOV

value: EBOV


title: E11_ESX1_2

description: processed data file: Mmar_Mmar_ESX1.txt

source_name: M. marinum E11 ESX1 mutant

value: M. marinum E11 ESX1 mutant


title: EBOV 2dpi [RNA-477]

value: 2 dpi


title: MUSA_KOWhiB6_1

value: WhiB6 mutant


title: MVU_CompWhiB6_2

value: M. marinum MVU complemented with WhiB6


title: Nplus_2


title: MUSA_CompWhiB6_2

description: processed data file: USA_EmptyVector_Complementary.txt

source_name: M. marinum MUSA complemented with WhiB6

value: M. marinum MUSA complemented with WhiB6

value: complemented with WhiB6


title: MUSA_CompWhiB6_1