title: FKC3d_2

source_name: Spleen isolated from fish on 3d after intraperitoneally injected with FKC

value: Edwardsiella tarda formallin-killed cells (FKC)

value: 3 days


title: FKC3d_3

status: Public on Dec 31 2018

type: RNA

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

country: Japan

institute: Tokyo University of Marine Science and Technology

hyb_protocol: After hybridization cocktails preparation, the Agilent 8x15 k custom oligo DNA microarray was hybridized with the fragmented labelled cRNA for 15 h at 65 °C as described in the Agilent QuickAmp Labeling kit one-color protocol.

scan_protocol: The microarray was scanned with a Agilent G2565CA scanner. Scanner setting was a 5μm resolution using a PMT setting of 600 and a laser power of 100 percents.

data_processing: The scanned images were analyzed with Feature Extraction Software v9.5.3.1 (Agilent, USA) using default parameters (protocol GE1-v5_95 and Grid: 016320_D_F_20070321) to obtain background subtracted and spatially detrended Processed Signal intensities (raw values). Limma calculated normalized values that the log summarized values from the baseline transformed by control samples after corrected the average of a 50th percentile values of the arrays in the experiments.

molecule: total RNA

organism: Paralichthys olivaceus

label_protocol: The RNA was reverse-transcribed into cDNA with a T7-(dT) oligomer to prime the double-strand synthesis. double-strand cDNA was converted and labeled into cRNA with Cy3. Cy3-labeld cRNA was purified using the RNeasy mini kit. Following cleanup, fragmentation of the cRNA for target preparation was done according to the Agilent QuickAmp Labeling kit one-color protocol.

extract_protocol: Total RNA was extracted from fish spleen using the RNeasy Mini Kit.

treatment_protocol: Fish were treated with Edwardsiella tarda formallin-killed cells (FKC) or FKC with Freund's complete adjuvant

tag: treatment

tag: time

tag: tissue

value: spleen


title: IL17KO_Na_BAPN_2

city: Kurume

first: Hiroki

last: Aoki

state: Fukuoka

address: 67 Asahimachi

department: Cardiovascular Research Institute

institute: Kurume University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

organism: Mus musculus

source_name: IL-17 Knockout, NaCl + BAPN, repliate2

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Wild type C57BL/6 mice or IL-17-deicient mice were kept on normal chow throughout the experimental period.

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

treatment_protocol: Wild type C57BL/6 mice or IL-17-deicient mice were with or without high salt challenge by 1% NaCl as drinking water prior to and during 3 days of continuous infusion of BAPN and angiotensin II or vehicle.

tag: genotype/variation

value: IL-17 Knockout

tag: agent

value: NaCl + BAPN

tag: strain

tag: cell

value: aorta


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AAGAGGCA-ATTAGACG

type: SRA

city: Atlanta

first: Steven

last: Sloan

state: GA

address: 615 Michael Street, Whitehead Building Room 375

department: Human Genetics

country: USA

institute: Emory University

description: Single cell

library_source: transcriptomic

data_processing:
Read alignment: reads were aligned to the hg38 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ).
Per-gene read assignement: aligned reads were converted to counts for every gene using FeatureCounts (-p -t exon -g gene_id -a ).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample

molecule: polyA RNA

organism: Homo sapiens

source_name: human oligodendrocyte spheroids

growth_protocol: Human induced pluripotent stem cells (hiPSCs) grown in feeder free conditions were enzymatically dissociated and plated in microwells to form spheroids. The following day the spheroids were flushed from the microwellsand transferred into ultra-low attachment plastic dishes (Thermo Fisher Scientific) in EssentialTM 6 medium (Thermo Fisher Scientific) supplemented with two SMAD pathway inhibitors– dorsomorphin (DM, 2.5 μM, Sigma-Aldrich, P5499-CONF) and SB-431542 (10 μM, R&D systems, 1614) for five days. On day 6 in suspension the spheroids were transferred to differentiation and maintenance medium (DMM) containing DMEM/F12 (Thermo Fisher Scientific), B-27 Supplement without vitamin A (Thermo Fisher Scientific), N-2 Supplement (Thermo Fisher Scientific), MEM Non-Essential Amino Acids (1:100, Thermo Fisher Scientific), GlutaMax (1:100, Thermo Fisher Scientific), human insulin (25 μg/mL, Sigma-Aldrich), and penicillin-streptomycin (1:100, Thermo Fisher Scientific). The DMM medium was supplemented with 20 ng/ml EGF (R&D Systems) and 20 ng/ml bFGF (Peprotech) for 19 days. IWP-2 (5 μM, Selleckchem) was added from day 4 until day 24, and SAG (1 μM, Millipore Sigma) was added from day 12 to day 24. From day 25 to day 36, hOLS were cultured in DMM supplemented with T3 (60 ng/mL, Sigma Aldrich), biotin (100 ng/mL, Sigma Aldrich), NT-3 (20 ng/mL, Peprotech), BDNF (20 ng/mL, Peprotech), cAMP (1 μM, Sigma Aldrich), HGF (5 ng/mL, Peprotech), IGF-1 (10 ng/mL, VWR), and PDGFaa (10 ng/mL, R&D Systems). From day 37 onwards, hOLs were cultured in complete DMM (DMM supplemented with T3, biotin, cAMP, and ascorbic acid (AA, 20 μg/mL, Wako Pure Chemical).

extract_protocol:
Single cells were sorted into lysis buffer according to a published Smartseq2  protocol (Picelli, S. et al. 2014). ERCC RNA Spike-In Mix was added at 1: 2.4X10^7  dilution in the buffer.
Sorted cells in 96-well plates were used for library preparation following the  Smartseq2 protocol (Picelli, S. et al. 2014) with modifications. Briefly, plates were  incubated at 72˚C, 3 min for annealing with Oligo-dT 30 VN. Reverse transcription  mixture was added 6ul per well, and RT was performed at 42˚C for 90 min, followed  by 70˚C, 5 min. To amplify the whole transcriptome, 15ul of DNA amplification  mixture was added and cDNA was amplified for 21 cycles. Amplified cDNA was then  purified using PCRClean DX beads. cDNA quality and quantity were assessed using a  Fragment Analyzer (AATI, High Sensitivity NGS Fragment Analysis Kit:1 bp - 6000  bp), and samples with concentrations below 0.08ng/ul or abnormal peak patterns  were filtered out. A total of 295 cDNA samples (retaining 88.9% of initially sorted)  were diluted down to 0.15ng/ul (only if above it) and consolidated into a 384-well  plate using a Mosquito X1 (TTP Labtech). Library preparation was performed using  Nextera XT DNA Sample Prep Kit (Illumina, Cat: FC-131-1096) and Nextera XT 384  dual index primers, with the help of a Mosquito HTS machine for liquid transfer.  Tagmentation was performed in 1.2ul at 55˚C for 10 min and amplification was  performed in 4ul system, 10 cycles. In the end, all samples were pooled (0.5ul each)  together into a 1.5ml Eppendorf tube, and the mixed libraries were purified twice  with PCRClean DX beads. The final sample was reconstituted in 50ul EB buffer, and  the concentration and peaks were measured by Qubit and Bioanalyzer before  Illumina sequencing (Hiseq).
Single cell RNA-seq

tag: plate id

value: plate 2

tag: age

value: Day 133

tag: line


title: IL17KO_Na_BAPN_3

source_name: IL-17 Knockout, NaCl + BAPN, repliate3


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AAGAGGCA-CGGAGAGA

description: Single cell

value: Day 134


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AAGAGGCA-ATAGCCTT

description: Single cell

value: Day 132


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AAGAGGCA-ATAGAGAG

description: Single cell

value: Day 131


title: FKC3d_1


title: ADJ3d_1

source_name: Spleen isolated from fish on 3d after intraperitoneally injected with FKC + FCA

value: Edwardsiella tarda formallin-killed cells (FKC) with Freund's complete adjuvant


title: ADJ3d_2


title: ADJ3d_3


title: IL17KO_BAPN_3

source_name: IL-17 Knockout, BAPN, repliate3

value: BAPN


title: IL17KO_BAPN_2

source_name: IL-17 Knockout, BAPN, repliate2


title: CONT_3

source_name: Spleen isolated from fish before injection

value: control

value: 0 hour


title: CONT_4


title: IL17KO_Na_BAPN_1

source_name: IL-17 Knockout, NaCl + BAPN, repliate1


title: wt control wit auxin

city: Jerusalem

first: Avital

last: Klein Brill

address: Edmond J. Safra Campus

country: Israel

institute: The hebrew university

description: screen sample 30

library_source: genomic

data_processing:
mapped to the yeast (sacCer3) genomes using bowtie2 default parameters. Reads longer than 200 bp were filtered out.
For paired end data, we used read centers position. For single end data, we estimated read center as 75 bp downstream/upstream to the read position.
Mnase coverage was calculated using matlab “ksdensity” function with read centers count as weights and 30bp width.
Genome_build: sacCer3
Supplementary_files_format_and_content: Mnase coverage over the genome
count of read centers (measured / estimated) over the genome

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: wt control wit auxin

growth_protocol: yeast cells were grown in YPD at 24ºC with constant shaking to OD 0.3-0.6

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. The reaction was stopped by adding glycine to a final concentration of 125 mM, and cells were harvested by centrifugation and washed. Pellet were kept in -80oC. Yeast cells were resuspended in Zymolyase buffer and treated with zymolyase (6U/od) and incubated for 25 min at 30 °C to generate spheroplasts. cells were centrifuged, washed and resuspended NP buffer. Lysed Spheroplasts were treated with MNAse (Micrococcal nuclease, worthington). MNAse concentration was calibrated to generate 80% mono nucleosomes (1 unit for 2.5od, 37C, 20m). The reactions were stopped by adding 100 μl of 5% SDS and 50 mM EDTA.
MNase digested chromatin was reverse cross linked, and MNase sequencing libraries were prepared (Blecher-Gonen et al. 2013).

treatment_protocol: Auxin was added to mid-log culture. Cells were sampled after 1h.

tag: experiment type

value: screen

tag: genotype

value: wt


title: ADJ6h_2

source_name: Spleen isolated from fish at 6h after intraperitoneally injected with FKC + FCA

value: 6 hours


title: wt control without auxin

description: screen sample 29

source_name: wt control without auxin

treatment_protocol: Auxin was added to mid-log culture. Cells were sampled after 0h.


title: CONT_2


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AAGAGGCA-AGAGGATA

description: Single cell

value: Day 128


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AAGAGGCA-AGGCTTAG

description: Single cell

value: Day 130


title: CONT_1

value: spleen


title: WM2664-MEK162-3ha

city: Emeryville

first: Guoying

middle: Karen

last: Yu

state: CA

address: 4560 Horton St, MS 4.1

department: bioinformatics

institute: Novartis - NIBR

description: MEK162 treatment 3hr

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Bioconductor affy package (http://bioconductor.org) with RMA method and HGU133Plus2_Hs_ENTREZG custom CDF v16 for target gene definition (Dai et al., 2005)

label: biotin

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

growth_protocol: WM266-4 cells or WM266-6 carrying inducible shRNAs were seeded on 6-well plates at 300,000 cells per well, 24hr before treatment

extract_protocol: Total RNA was extracted with RNAeasy Plus kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: WM266-4 cells were treated with 0.05uM LGX818, 0.003uM trametinib, 0.3uM MEK162,  0.2uM ERK1/2 inhibitor or DMSO for 3hr or 24hr in triplicates. WM266-4 cells carrying inducible shRNAs were treated with 100ng/ml doxycycline for 3 or 7 days in triplicates.

tag: cell line

value: BRAF V600D

tag: time point


title: IL17KO_Na_3

source_name: IL-17 Knockout, NaCl, repliate3

value: IL-17 Knockout

value: NaCl

value: aorta


title: FKC6h_2

source_name: Spleen isolated from fish at 6h after intraperitoneally injected with FKC

value: Edwardsiella tarda formallin-killed cells (FKC)


title: ADJ6h_1


title: FKC6h_1


title: FKC6h_3


title: IL17KO_Na_2

source_name: IL-17 Knockout, NaCl, repliate2


title: IL17KO_Na_1

source_name: IL-17 Knockout, NaCl, repliate1


title: IL17KO_BAPN_1

source_name: IL-17 Knockout, BAPN, repliate1


title: Rebecca-Oligo_HMMKJ_L7_AAGAGGCA-ACTCTAGG

description: Single cell

value: plate 2

value: Day 127


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AAGAGGCA-AGCTAGAA

description: Single cell

value: Day 129


title: swr1 KO

description: screen sample 28

source_name: swr1 KO

treatment_protocol: Cells were grown to midlog and sampled.


title: WM2664-DMSO-24hb

description: DMSO treatment  24hr

value: DMSO


title: swr1 depletion, 3h

description: screen sample 27

source_name: swr1 depletion, 3h

treatment_protocol: Auxin was added to mid-log culture. Cells were sampled after 3h.


title: swr1 depletion, 1h

description: screen sample 26

source_name: swr1 depletion, 1h


title: IL17KO_Cont_3

source_name: IL-17 Knockout, Control, repliate3

value: vehicle


title: swr1 depletion, 0h

description: screen sample 25

source_name: swr1 depletion, 0h


title: Jej_7_EEC

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

description: Human Jejunum GLP1-/CHGA+/SCG2+ from participant 7

data_processing:
Sequenced reads were trimmed for adapter sequence and mapped to the human genome (GRCh37) using Tophat and raw counts generated with Htseq-count
Differential gene expression modelling and normalised counts per million were generated using DESEQ2.
Genome_build: GRCh37
Supplementary_files_format_and_content: all_raw_counts.txt is tab delimited file of number of counts for ensembl gene ids for each biological sample

source_name: Jejunum

extract_protocol:
Human jejunal mucosal samples were dissociated to single cells, fixed in paraformaldehyde (4%), permeabilised with Saponin, Antibody labelled against GLP-1, CHGA and SCG2 and FACS sorted into 3x populations (GLP1-/CHGA+/SCG2+ [Single positive]; GLP1+/CHGA+/SCG2+ [Double positive]; triple negative [Neg]). RNA was extracted using the Ambion Recoverall total Nucelic Acid isolation kit following the MARIS protocol and concentrated using a Qiagen RNeasy Minelute cleanup kit.
The library was constructed with 4ng of input RNA using the Clontech Smarter Stranded total RNA-seq - Pico Input mammalian kit v1

tag: facs population

tag: participant


title: Jej_7_L

description: Human Jejunum GLP1+/CHGA+/SCG2+ from participant 7


title: sth1 depletion, 3h

description: screen sample 24

source_name: sth1 depletion, 3h


title: sth1 depletion, 1h

description: screen sample 23

source_name: sth1 depletion, 1h


title: sth1 depletion, 0h

description: screen sample 22

source_name: sth1 depletion, 0h


title: Jej_11_Neg

description: Human Jejunum GLP1-/CHGA-/SCG2- from participant 11


title: Jej_11_EEC

description: Human Jejunum GLP1-/CHGA+/SCG2+ from participant 11


title: snf2 depletion, 1h

description: screen sample 20

source_name: snf2 depletion, 1h


title: IL17KO_Cont_2

source_name: IL-17 Knockout, Control, repliate2


title: Jej_11_L

description: Human Jejunum GLP1+/CHGA+/SCG2+ from participant 11


title: isw2 depletion, 3h

description: screen sample 17

source_name: isw2 depletion, 3h


title: isw2 KO

description: screen sample 18

source_name: isw2 KO


title: snf2 depletion, 0h

description: screen sample 19

source_name: snf2 depletion, 0h


title: isw2 depletion, 1h

description: screen sample 16

source_name: isw2 depletion, 1h


title: Jej_10_Neg

description: Human Jejunum GLP1-/CHGA-/SCG2- from participant 10


title: isw2 depletion, 0h

description: screen sample 15

source_name: isw2 depletion, 0h


title: Jej_10_EEC

description: Human Jejunum GLP1-/CHGA+/SCG2+ from participant 10


title: Jej_10_L

description: Human Jejunum GLP1+/CHGA+/SCG2+ from participant 10


title: isw1 depletion, 3h

description: screen sample 13

source_name: isw1 depletion, 3h


title: isw1 depletion, 0h

description: screen sample 11

source_name: isw1 depletion, 0h


title: snf2 depletion, 3h

description: screen sample 21

source_name: snf2 depletion, 3h


title: ino80 depletion, 3h

description: screen sample 10

source_name: ino80 depletion, 3h


title: ino80 depletion, 1h

description: screen sample 9

source_name: ino80 depletion, 1h


title: Jej_9_Neg

description: Human Jejunum GLP1-/CHGA-/SCG2- from participant 9


title: ino80 depletion, 0h

description: screen sample 8

source_name: ino80 depletion, 0h


title: fun30 depletion, 3h

description: screen sample 7

source_name: fun30 depletion, 3h


title: Jej_8_Neg

description: Human Jejunum GLP1-/CHGA-/SCG2- from participant 8

source_name: Jejunum


title: O58.TH

city: Barcelona

first: Ilario

last: De Toma

address: Carrer del Dr. Aiguader, 88

country: Spain

institute: Center for Genomic Regulation

description: Gene expression after 8-week free choice access to standard chow (SC) and chocolate-mixture (CM) diet, followed by a 11-day test battery

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).   The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Samples were imported into R using the limma function maimages, with specific parameter for agilent microarray, background corrected and normalized using the normexp limma normalization. Background has been computed from the 95% perfentile of the intensity of the negative control probes on each array, keeping probes that are at least 10% higher than the negative controls on at least four arrays (because there are four biological replicates)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA from tissue has been extracted with the RNeasy Mini Kit (Qiagen)

treatment_protocol: For 8 weeks, lean group mice had access to SC diet and obese group mice had a free choice access to SC and CM. Frontal cortex, striatum and hypothalamus were dissected upon  completion of an 11-day test battery.

tag: group

value: obese

tag: diet

value: thalamic region

tag: Sex

value: female

value: 5 weeks


title: fun30 depletion, 1h

description: screen sample 6

source_name: fun30 depletion, 1h

value: screen


title: isw1 KO

description: screen sample 14

source_name: isw1 KO


title: fun30 depletion, 0h

description: screen sample 5

source_name: fun30 depletion, 0h


title: O56.ST

value: free choice access to standard chow (SC) and chocolate-mixture (CM) diet

tag: tissue

value: striatum


title: O58.FC

value: frontal cortex


title: Jej_9_EEC

description: Human Jejunum GLP1-/CHGA+/SCG2+ from participant 9


title: chd1 KO

description: screen sample 4

source_name: chd1 KO


title: isw1 depletion, 1h

description: screen sample 12

source_name: isw1 depletion, 1h


title: O54.TH


title: O56.FC


title: O58.ST


title: O56.TH


title: O54.ST


title: Jej_8_EEC

description: Human Jejunum GLP1-/CHGA+/SCG2+ from participant 8


title: O54.FC


title: chd1 depletion, 3h

description: screen sample 3

source_name: chd1 depletion, 3h


title: IL17KO_Cont_1

source_name: IL-17 Knockout, Control, repliate1

tag: genotype/variation

value: IL-17 Knockout


title: Jej_9_L

description: Human Jejunum GLP1+/CHGA+/SCG2+ from participant 9


title: chd1 depletion, 1h

description: screen sample 2

source_name: chd1 depletion, 1h


title: chd1 depletion, 0h

description: screen sample 1

source_name: chd1 depletion, 0h


title: O52.TH


title: Jej_8_L

description: Human Jejunum GLP1+/CHGA+/SCG2+ from participant 8


title: Jej_4_Neg

description: Human Jejunum GLP1-/CHGA-/SCG2- from participant 4


title: Jej_7_Neg

description: Human Jejunum GLP1-/CHGA-/SCG2- from participant 7


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_AAGAGGCA-CTTAATAG

description: Single cell

source_name: human oligodendrocyte spheroids

value: Day 137


title: Jej_4_EEC

description: Human Jejunum GLP1-/CHGA+/SCG2+ from participant 4


title: Ileum_2_Neg

description: Human Ileum GLP1-/CHGA-/SCG2- from participant 2

source_name: Ileum


title: Jej_3_Neg

description: Human Jejunum GLP1-/CHGA-/SCG2- from participant 3


title: Jej_6_Neg

description: Human Jejunum GLP1-/CHGA-/SCG2- from participant 6


title: Ileum_2_L

description: Human Ileum GLP1+/CHGA+/SCG2+ from participant 2


title: Jej_4_L

description: Human Jejunum GLP1+/CHGA+/SCG2+ from participant 4


title: Jej_6_EEC

description: Human Jejunum GLP1-/CHGA+/SCG2+ from participant 6


title: Jej_3_L

description: Human Jejunum GLP1+/CHGA+/SCG2+ from participant 3


title: Ileum_1_Neg

description: Human Ileum GLP1-/CHGA-/SCG2- from participant 1


title: Ileum_2_EEC

description: Human Ileum GLP1-/CHGA+/SCG2+ from participant 2


title: Jej_6_L

description: Human Jejunum GLP1+/CHGA+/SCG2+ from participant 6


title: L54.TH

description: Gene expression after 8-week access to standard chow (SC) mouse diet, followed by a 11-day test battery

source_name: thalamic region_standard_chow

value: lean

value: standard chow


title: Jej_5_Neg

description: Human Jejunum GLP1-/CHGA-/SCG2- from participant 5


title: L56.ST


title: L58.ST


title: L54.ST


title: L52.ST


title: Jej_5_EEC

description: Human Jejunum GLP1-/CHGA+/SCG2+ from participant 5


title: Jej_3_EEC

description: Human Jejunum GLP1-/CHGA+/SCG2+ from participant 3


title: L56.FC

source_name: frontal cortex_standard_chow


title: L58.FC


title: L58.TH


title: O52.ST

description: Gene expression after 8-week free choice access to standard chow (SC) and chocolate-mixture (CM) diet, followed by a 11-day test battery


title: L52.FC


title: L54.FC


title: L52.TH


title: L56.TH


title: Jej_1_EEC

description: Human Jejunum GLP1-/CHGA+/SCG2+ from participant 1


title: Jej_2_Neg

description: Human Jejunum GLP1-/CHGA-/SCG2- from participant 2


title: Jej_5_L

description: Human Jejunum GLP1+/CHGA+/SCG2+ from participant 5


title: Jej_1_Neg

description: Human Jejunum GLP1-/CHGA-/SCG2- from participant 1


title: Ileum_1_L

description: Human Ileum GLP1+/CHGA+/SCG2+ from participant 1


title: TSA_(+)_rep2

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

country: South Korea

institute: POSTECH

hyb_protocol: Standard Agilent hybridization protocols

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: Control probes were excluded before data processing. Scanned signal intensity (gMedianSignal) was log2-transformed. The data processing including quantile normalization was done using MATLAB 7.13.0 (R2011b).

label: Cyanine 3-CTP

source_name: TSA(+) human keratinocytes

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: Normal human keratinocytes (Cascade Biologies, Portland, OR, USA) were maintained in keratinocytes growth (KGM) GOLD medium (Lonza, Based, Switzerland)

extract_protocol: Total RNA was isolated from tissues using Qiazol (QIAGEN) following the manufacturers’ protocols.

tag: cell type

value: keratinocytes

value: WT


title: TSA_(-)_rep1

source_name: TSA(-) human keratinocytes


title: Ileum_1_EEC

description: Human Ileum GLP1-/CHGA+/SCG2+ from participant 1


title: FOC4(nox1OEvsFOC4)_BC3

city: Nanjing

first: Youzhi

last: Miao

address: WeiGang NO.1

country: China

institute: Nanjing Agricultural University

data_processing:
quality control(adaptor trimming, masking of low-complexity or low-quality sequence)
reads alignment and sample comparisons using TopHat 2.0
RPKM is used for normalization
Genome_build: NJAU4742 and FOC4
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each gene in each sample

organism: Fusarium oxysporum

source_name: hypha

growth_protocol: Different mutants or wide type of NJAU4742 were seprately incubated together with FOC4 on the confrontation 9 mm plates with GSM medium in darkness at 28℃.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the samples of Before contact were scraped from the plates in the time when the distance between two different stains was equal to 1 cm; the samples of After contact were scrapted from the plates in 30 h later after contact of two different strains, and the sampling regions should contain both hypha.

tag: strain

value: wild type

tag: condition

value: Before contact in condition of nox1OE vs FOC4


title: FOC4(nox1OEvsFOC4)_BC1


title: FOC4(nox1OEvsFOC4)_BC2


title: Jej_2_EEC

description: Human Jejunum GLP1-/CHGA+/SCG2+ from participant 2

source_name: Jejunum


title: Jej_1_L

description: Human Jejunum GLP1+/CHGA+/SCG2+ from participant 1


title: Jej_2_L

description: Human Jejunum GLP1+/CHGA+/SCG2+ from participant 2


title: FOC4(∆nox1vsFOC4)_BC2

value: Before contact in condition of <delta>nox1 vs FOC4


title: FOC4(WTvsFOC4)_BC1

value: Before contact in condition of NJAU4742 vs FOC4


title: FOC4(WTvsFOC4)_BC2


title: FOC4(WTvsFOC4)_BC3


title: ume6 large intestine 1

city: San Francisco

first: Suzanne

middle: M

last: Noble

address: 513 Parnassus Ave., Box 0414

institute: UCSF

description: animals sacrificed, dissected and large intestine contents extracted

data_processing:
Real time base calling on Illumina HiSeq 4000
kallisto to align reads to genome with parameters: --plaintext --bias --single --rf-stranded -l $AvgLibSize -s $SD (AvgLibSize and SD pulled from BioAnalyzer traces)
extract estimated counts and tpms from abundances.tsv files
tpms and estimated counts = 0 replaced with 1, transcripts filtered to included only those with values greater than 10 in at least one sample
limma/voom with genotype.environment as factor to produce log base 2 fold changes and adj. p values from estimated counts
tpms were used for heat map generation
Genome_build: C. albicans SC5314 Assembly 21
Supplementary_files_format_and_content: excel files containing 1. fold changes and adjusted p-values and 2. tpms

organism:
Candida albicans
Mus musculus

source_name: Murine large intestine colonization

extract_protocol:
Acid phenol chloroform extraction 4 times, phenol chloroform isoamyl extraction 4 times, additional cleanup using RNA SPRI bead mix
NEB Ultra Directional mRNA-seq

tag: strain (c. albicans/mus musculus)

tag: growth condition

value: large intestine

value: 10 days


title: ume6 large intestine 5


title: ume6 large intestine 2


title: ume6 large intestine 4


title: ume6 large intestine 3


title: spt7-1180_rep2

city: VALENCIA

first: VARINIA

last: GARCIA-MOLINERO

address: EDUARDO PRIMO YÚFERA, 3

institute: CENTRO DE INVESTIGACIÓN PRÍNCIPE FELIPE

hyb_protocol: standard protocol for the Ambion® WT Expression kit of Affymetrix

scan_protocol: The tiling arrays were scanned using an Affymetrix Scanner according to manufacturer's instruction.

data_processing:
Microarray data of the raw .CEL images were analyzed using Tiling Analysis Software (TAS, Affymetrix) with the signal detection parameters set by default. The data For each strain, microarray analysis was conducted in triplicate; the values presented are the average of these three determinations. The signal of each mutant was normalized to the signal obtained for the WT using the “Two sample comparison analysis” option in TAS.
For the comparison of each mutant respect to the WT strain, two results files are obtained: the "mutant vs WT_R_signal" which corresponds to the signal for the Crick strand; and the "mutant vs WT_F_signal" which corresponds to the signal for the Watson strand of the DNA.

source_name: spt7-1180_YPD o/n 25 ºC

extract_protocol: Total RNA was harvested from yeast exponential-phase cultures grown in YPD at 25 ºC by phenol:chloroform extraction. For reverse transcription (RT) 2 µg of total RNA were treated with DNase-I (Roche) and purified by phenol:chloroform extraction. RT was performed following standard procedures with random hexamers and M-MLV reverse transcriptase (Invitrogen).


title: spt8dspt7-1180_rep2

source_name: spt8Δspt7-1180_YPD o/n 25 ºC

label_protocol: standard protocol for the Ambion® WT Expression kit of Affymetrix

growth_protocol: yeast exponential-phase cultures grown in YPD at 25 ºC


title: spt7-1180_rep3


title: spt8dspt7-1180_rep3


title: spt7-1180_rep1


title: spt8dspt7-1180_rep1


title: TSA_(-)_rep2


title: spt8d_rep2

source_name: spt8Δ_YPD o/n 25 ºC


title: spt8d_rep3


title: SB3: si_TR_bexa

city: New York

first: Maria

middle: Victoria

last: Revuelta

state: New York

address: 1300 York Avenue

department: Medicine

institute: Weill Cornell Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads aligned with STAR 2.4
Raw counts were obtained with htseq-count function in HTSeq package with the following parameters (--type exon  -m union)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: HuT78 cell line

growth_protocol: RPMI 1640 medium, supplemented with 10% fetal bovine serum, 2 mM glutamine, antibiotics and levothyroxine (T4) and triiodothyronine (T3)

extract_protocol:
RNA was isolated from the samples. Genomic DNA was eliminated and RNA concentration and purity were determined by the Nanodrop (Thermo Scientific). RNA integrity was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA integrity number values were greater than 8 for all samples.
Sequencing libraries were generated with polyA+ RNA using the TruSeq RNA sample prep kit (Illumina). Sequencing was performed at the Epigenomics Core Facility of Weill Cornell Medicine.

treatment_protocol: HuT 78 cells were transfected with siRNA for integrins (si-ITGAV/B3); TRA (si-TR) or non-target sequences (si-CT) followed by treatment with bexarotene in the presence of physiological concentrations of TH, for 6 hours using TRI-REAGENT (Genbiotech).

value: cutaneous T-cell lymphoma (CTCL)

value: siTR

value: bexarotene


title: FOC4(∆nox1vsFOC4)_BC3


title: TSA_(+)_rep1


title: SB1: si_TR_bexa


title: SA3: si_veh_ct

value: vehicle

value: control


title: FOC4(∆nox1vsFOC4)_BC1


title: SA2: si_veh_ct


title: spt8d_rep1


title: nox1OE(nox1OEvsFOC4)_BC3

organism: Trichoderma guizhouense


title: WT_rep3

source_name: WT_YPD o/n 25 ºC


title: nox1OE(nox1OEvsFOC4)_BC2


title: SA1: si_veh_ct


title: WT_rep2


title: nox1OE(nox1OEvsFOC4)_BC1


title: ∆nox1(∆nox1vsFOC4)_BC3


title: SB2: si_TR_bexa


title: S16: si_INT_bexa

value: siINT


title: WT(WTvsFOC4)_BC3


title: ∆nox1(∆nox1vsFOC4)_BC2


title: WT(WTvsFOC4)_BC1


title: Screen 3 day 10 mouse 2 feces

description:
growth in murine GI tract 10 days followed by plating to Sabouraud dextrose agar 2 days 30C
GI_Screen_3.xlsx

data_processing:
Base calls performed by Illumina HiSeq 2500 platfom
Reads aligned to Candida genome using bowtie with default parameters
Maximum read count within 200 bp of start or end of each ORF reported
Gene lists filtered to only the genes included in the knockout collections screened
Each column divided by the total number of reads for that column to generate fractional abundance
Genes in knockout collection with less than 100 reads present in screen inoculum were removed from further analysis as they were assumed to be absent from the inoculum pool
Fractional abundance values for each knockout in each mouse sample was divided by the fractional abundance of the assciated screen inoculum
All ratios were log base 2 transformed
Genome_build: Candida albicans SC5314 Assembly 21
Supplementary_files_format_and_content: GI_Screen_1-3 contain log base 2 fold changes of each mutant abundance recovered from the mouse compared to the inoculum

organism: Candida albicans

source_name: Yeast cells grown on Sabouraud plates

extract_protocol:
Phenol chloroform DNA extraction protocol
Fully described in STAR methods of Witchley, Penumetcha et al. 2018
LAM-PCR mediated deep-sequencing

tag: background strain

tag: selection

value: mouse GI tract


title: WT(WTvsFOC4)_BC2

tag: genotype


title: S15: si_INT_ct

tag: cell line


title: S14: si_veh_bexa


title: Screen 3 day 3 mouse 2 feces

description:
growth in murine GI tract 3 days followed by plating to Sabouraud dextrose agar 2 days 30C
GI_Screen_3.xlsx


title: S17: si_TR_ct


title: S11: si_TR_ct


title: Screen 3 day 10 mouse 1 feces


title: QM.RNASeq Rep 3

city: Nottingham

first: Richard

middle: D

last: Emes

state: Nottinghamshire

department: School of Veterinary Medicine and Sciences.

institute: University of Nottingham

data_processing:
Genome_build: AquaS1.4
Genome index was built using hisat2-build (version 2.1.0)
Reads trimmed using scythe and Tru-seq adapters (version 0.981)
Alignment of reads using hisat2 (version 2.1.0)
Assemble GTF using stringtie (version 1.2.3)
Generate normalized transcript abundances using stringtie (version 1.2.3)
Genome_build: www.vectorbase.org
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Anopheles quadriannulatus

source_name: Male Acessory Glands (MAGs)

growth_protocol: All the mosquito stocks were obtained from the Malaria Research and Reference Reagent Resource Center (MR4) in Atlanta (https://www.beiresources.org/Catalog/BEIVectors/MRA-762.aspx).

extract_protocol: Preparation of Illumina libraries  The total RNA libraries were prepared in accordance with the Illumina TruSeq RNA sample preparation  v2 guide (Part # 15026495, rev.D, September 2012) for Illumina Paired-End Indexed Sequencing.  Step 1: RNA purification and fragmentation  According to the Illumina mRNA libraries preparation protocol, poly-A mRNA in the tRNA samples  were first purified using Illumina poly-T oligo-attached magnetic beads and two rounds of purification.  During the second elution of the poly-A-RNA, the mRNA was also fragmented and primed with random  hexamers for cDNA synthesis.  Step2: Generation of double-stranded cDNA  Cleaved mRNAs were reverse transcribed into first strand cDNA using reverse transcriptase and  random primers. The RNA template was then removed and a replacement strand synthesized to  generate double-stranded cDNA.  Step 3: Preparation of ds cDNA samples for Indexed paired-end sequencing  Following the standard protocol, after the first and second strand cDNA synthesis, ends were repaired,  dA base added, and Illumina indexing adapters were ligated. Finally, cDNA fragments that have  adapter molecules on both ends underwent 15 cylcles of PCR to amplify the amount of prepared  material.

value: Male Acessory Glands (MAGs)


title: Screen 3 day 3 mouse 1 feces


title: QM.RNASeq Rep 2

address: School of Veterinary Medicine and Science

data_processing:
Genome_build:AquaS1.4
Genome index was built using hisat2-build (version 2.1.0)
Reads trimmed using scythe and Tru-seq adapters (version 0.981)
Alignment of reads using hisat2 (version 2.1.0)
Assemble GTF using stringtie (version 1.2.3)
Generate normalized transcript abundances using stringtie (version 1.2.3)
Genome_build: www.vectorbase.org
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample


title: QT.RNASeq Rep 1

source_name: Testes

value: Testes


title: S10: si_INT_bexa


title: Screen 3 inoculum

description:
in vitro, 4 hour growth at 30C of individual strains in 1ml of YPD in 96 well plate followed by pooling of all strains, Sabouraud dextrose agar 2 days 30C
GI_Screen_3.xlsx

value: no selection


title: MET.RNASeq Rep 3

data_processing:
Genome_build:AmerM2.2
Genome index was built using hisat2-build (version 2.1.0)
Reads trimmed using scythe and Tru-seq adapters (version 0.981)
Alignment of reads using hisat2 (version 2.1.0)
Assemble GTF using stringtie (version 1.2.3)
Generate normalized transcript abundances using stringtie (version 1.2.3)
Genome_build: www.vectorbase.org
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Anopheles merus


title: QM.RNASeq Rep 1


title: QT.RNASeq Rep 3


title: S9: si_INT_ct


title: MET.RNASeq Rep 2


title: QT.RNASeq Rep 2


title: MET.RNASeq Rep 1


title: WT_rep1


title: MEM.RNASeq Rep 3


title: ∆nox1(∆nox1vsFOC4)_BC1


title: S4: si_INT_bexa


title: MEM.RNASeq Rep 2


title: MEM.RNASeq Rep 1


title: S2: si_veh_bexa


title: Screen 2 day 5 mouse 3 feces

description:
growth in murine GI tract 5 days followed by plating to Sabouraud dextrose agar 2 days 30C
GI_Screen_2.xlsx


title: Screen 2 day 5 mouse 1 feces


title: Screen 2 day 10 mouse 3 feces

description:
growth in murine GI tract 10 days followed by plating to Sabouraud dextrose agar 2 days 30C
GI_Screen_2.xlsx


title: Screen 2 inoculum

description:
in vitro, 4 hour growth at 30C of individual strains in 1ml of YPD in 96 well plate followed by pooling of all strains, Sabouraud dextrose agar 2 days 30C
GI_Screen_2.xlsx


title: Screen 1 day 10 mouse 3 feces

description:
growth in murine GI tract 10 days followed by plating to Sabouraud dextrose agar 2 days 30C
GI_Screen_1.xlsx


title: Screen 1 day 10 mouse 2 feces


title: Screen 1 day 10 mouse 1 feces


title: Screen 2 day 10 mouse 2 feces


title: Screen 2 day 10 mouse 1 feces


title: S3: si_INT_ct


title: Screen 1 day 3 mouse 2 feces

description:
growth in murine GI tract 3 days followed by plating to Sabouraud dextrose agar 2 days 30C
GI_Screen_1.xlsx


title: Screen 2 day 5 mouse 2 feces


title: Screen 1 day 3 mouse 1 feces


title: Pre-operation plasma sample of subject X222956

city: Shenzhen

first: Rihong

last: Zhai

state: Guangdong

address: 1066 Xueyuan Ave.

institute: Shenzhen University School of Medicine

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

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

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  using the GeneSpring GX v12.1 software package. After quantile normalization of the raw data, LncRNAs and mRNAs that at least 6 out of 12 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

source_name: Collection before operation

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: age

value: Plasma

tag: disease state

value: non-small cell lung cancer


title: Pre-operation plasma sample of subject Y446053


title: Pre-operation plasma sample of subject T433711


title: Screen 1 inoculum

description:
in vitro, 4 hour growth at 30C of individual strains in 1ml of YPD in 96 well plate followed by pooling of all strains, Sabouraud dextrose agar 2 days 30C
GI_Screen_1.xlsx


title: Post-operation plasma sample of subject Z433442

source_name: Collection after operation


title: Post-operation plasma sample of subject Ni


title: Post-operation plasma sample of subject Zhang


title: Pre-operation plasma sample of subject C434091


title: Post-operation plasma sample of subject X222956


title: Pre-operation plasma sample of subject Z433442


title: Post-operation plasma sample of subject T433711


title: Pre-operation plasma sample of subject Zhang


title: Post-operation plasma sample of subject C434091


title: Post-operation plasma sample of subject Y446053


title: mock 12 h rep2

first: Yukiko

last: Yasui

address: Hongo 7-3-1, Bunkyo-ku

department: Department of Biological Sciences

institute: The University of Tokyo

description: mock 12 h

hyb_protocol: Hybridization, washing, and staining procedures were run on Fluidics Station 450 (Thermo Fisher Scientific) with GeneChip Hybridization, Wash, and Stain Kit (Thermo Fisher Scientific).

scan_protocol: GeneChips were scanned with GeneChip Scanner 3000 7G (Thermo Fisher Scientific).

data_processing: Normalization was performed by using the standard settings for GeneChip Gene 1.0 ST arrays on Expression Console Version 1.3 (Thermo Fisher Scientific).

organism: Oryza sativa

source_name: pACT1-GVG>OsWOX4:RNAi, 5-day-old seedling, SAM and leaf primordia

label_protocol: The sense-strand DNA target was prepared by using a WT Expression Kit (Thermo Fisher Scientific) and a GeneChip WT Terminal Labeling and Controls Kit (Thermo Fisher Scientific) in accordance with the manufacturers’ instructions.

growth_protocol: Sterilized seeds were germinated and grown on the filter papers immersed with MS-medium in a petri dishe for 5 days at 28ºC.

extract_protocol: Total RNA was extracted with TRIsure (BIOLINE) and purified with column of NucleoSpin RNA Plant Kit (Macherey-Nagel).

treatment_protocol: Seedlings were cultured in liquid MS medium with or without DEX (10 uM) in Erlenmeyer flask with shaking for 3 or 12 h.

tag: time point

value: induction after 12 h

tag: treatment

value: mock


title: Post-operation plasma sample of subject Z433583


title: DEX 12 h rep2

description: DEX 12 h

value: DEX


title: Pre-operation plasma sample of subject Z433583


title: mock 12 h rep3

description: mock 12 h


title: Pre-operation plasma sample of subject Ni


title: C6G3_MnOx_rep2

city: MARSEILLE CEDEX 09

first: Aurelie

last: Bergon

address: parc scientifique de Luminy, case 928

country: France

institute: TAGC INSERM U1090

data_processing:
Alignement were processed using PGM aligner using the Shewanella undefined undefined RAST v.22.6 genome.
Genome coverage were calculated using genomeCoverage (bedtools) and normalize at 100000 reads.
Genome_build: ASM95636v1
Supplementary_files_format_and_content: bedgraph files were generated using genomeCoverage (bedtools).

organism: Shewanella algae

source_name: Shewanella algae C6G3_MnOx, bacteria

growth_protocol: Shewanella algae C6G3 was grown anaerobically at 28 °C on artificial sea water (Baumann et al., 1971) with DL-lactate (25 mM), K 2 HPO 4 (0.43 mM), FeSO 4 (13,2 μM), ammonium (20mM) and trace mineral element solution and vitamin (Balch et al., 1979). Nitrate (3 mM) or manganese oxides (1 mM) were added as sole source of electron acceptor. Manganese oxide was synthesized following the protocol of Laha (Laha & Luthy, 1990).

extract_protocol:
Cells from three quarters of the exponential phase of growth were pelleted and washed twice with RNAprotect® Bacteria Reagent (Qiagen): Tris-NaCl buffer (0.05M Tris; 0.15 M NaCl; pH  7.8) 2:1and rinsed with Tris-NaCl buffer After lyses in RLT buffer of RNeasy® kit (Qiagen) total RNA were extracted with phenol: chloroform: isoamyl alcohol 125:24:1 pH 4.5 gently mixed and centrifuged 15 min at 12.000 g at 4 °C and then with chloroform: isoamyl alcohol 24:1 gently mixed and centrifuged 15 min at 12.000 g at 4 °C. Total RNA were purified using RNeasy® Mini QIAcube Kit (Qiagen) and DNA contamination was removed using the TURBO DNA-free TM kit (Ambion® by Life Technologies TM ) according to the manufacturer's instructions.
After reception of total RNA and second quality control (NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and Agilent 2100 Bioanalyzer with RNA 6000 Nano chip Kit) which showed the need to carry an ethanol precipitation, the ribo-depletion was performed on 3 µg of total RNA using Ribo-Zero™ Magnetic Kit for Gram-Negative Bacteria (Epicentre®). The RNA integrity and the resulting concentration were also determined using respectively Bioanalyser (RNA 6000 Pico chip Kit) and NanoDrop; 8-22% of the input RNA was recovered after purification. The preparation of libraries was performed using the kit SOLIDTM Whole Transcriptome (Life Technology) according to manufacturer's instructions with the steps of fragmentation (with approximately 0.07 µg of ribo-depleted RNA), hybridization/ligation, reverse transcription and amplification (allowing the addition of ion Torrent adapter), followed by quality control (Bioanalyzer, RNA 6000 Pico chip Kit). Sample enrichment was performed using Ion PI™ Template OneTouch2 Kit (Life Technology) with 400 pb amplification product.
Templates sequencing was performed with semiconductor sequencing chips 318 on the Ion Torrent PGM (Life Technology)

treatment_protocol: Cells were grown under strict anaerobic conditions with a 100% N 2 gas head space.

value: MnOx


title: C6G3_NO3_rep1

source_name: Shewanella algae C6G3_NO3, bacteria


title: C6G3_NO3_rep2


title: C6G3_MnOx_rep1


title: DEX 12 h rep3

description: DEX 12 h


title: DEX 12 h rep1

description: DEX 12 h


title: 7D3_SH

city: Warsaw

first: Bartosz

last: Wojtas

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

data_processing:
Basecalling with HCS 2.2.68
Bcl2Fastq processing of bcl files to fastq
Fastq trimming for adapter contamination and low quality reads and aligned with tophat2 to rn5.fa reference
FPKM calculation with RSEM software using Ensembl transcriptome annotations for rn5.fa genome version
Genome_build: rn5

organism: Rattus norvegicus

source_name: sorted microglia from brain after sham operation

extract_protocol:
After the behavioural assessment of ischemic stroke, the rats (n=4-6) were transcardially perfused with 250 ml of cold PBS to remove blood from the brain. The brain was isolated and transported in HBSS. The ipsilateral side of the brain was dissected and subjected to mechanical and enzymatic dissociation using neural tissue dissociation kit (Milteny Biotech) according to the manufacterer’s instruction. Myelin was removed using Percoll density gradient centrifugation. Briefly, single suspension of cells was mixed with the Percoll solution and centrifuged for 20 min., 950 rcf at 4°C. Cell pellet was resuspended in DPBS containing 2% BSA and counted. For staining, the cells were suspended (1 x 10^6 cells per each) and incubated with the respective antibodies at 4ºC: FITC Mouse Anti-Rat CD11b, FITC Mouse IgA Kappa Isotype control, PE-Cy 5 Mouse Anti-Rat CD45, PE-Cy 5 Mouse IgG1 Kappa Isotype control to determinate the percentages of microglia and macrophages subpopulations and analyzed using CellQuest software. Immune subpopulations were determined by flow cytometry. Quadrant gates were drawn on two cell subpopulations with differences in the surface expression of CD11b and CD45 antigen: microglia (CD11b+CD45low), blood–derived macrophages (CD11b+CD45high). All antibodies used were purchased from BD biosciences.
In total, 21 strand-specific RNA libraries for high-throughput sequencing were prepared (three biological replicates for each treatment) using the KAPA Stranded mRNA Sample Preparation Kit according to the manufacturer’s protocol. Briefly, the poly-A containing mRNA molecules were purified from 500ng of total RNA (extracted FACS sorted cells from the brain samples of sham operated and MCAo animals) using poly-T oligo-attached magnetic beads (Kapa Biosystems, MA, USA ) The mRNA was then fragmented and the first-strand cDNA was synthesized using reverse transcriptase and random hexamers. Second cDNA synthesis was performed by removing the RNA template and synthesizing a replacement strand, incorporating dUTP in place of dTTP, to generate double-stranded (ds) cDNA. dsDNA was then subjected to the addition of “A” bases to the 3′ ends and ligation of adapters from NEB followed by uracil digestion in a loop structure of adapter by USER enzyme from NEB (Ipswich, MA, USA). Amplification of fragments with adapters ligated on both ends was performed by PCR using primers containing Truseq barcodes from NEB (Ipswich MA, USA).

treatment_protocol: Focal cerebral ischemia was induced by transient occlusion of middle cerebral artery (MCA) as previously reported (Szydlowska, Zawadzka, & Kaminska, 2006; Zawadzka et al., 2012). Briefly, the rats were anesthetized using 1.5% isoflurane in oxygen and ischemia was produced by advancing the tip of a rounded 0.4 mm nylon suture (Doccol Co.) into the right internal carotid artery entering through the right external carotid artery. After 90 min of occlusion, the nylon filament was withdrawn to allow reperfusion. Throughout the surgery the animal’s core body temperature was maintained at 37±0.5°C with a thermostatically controlled heating pad. For the Sham operated animals the right common carotid artery was isolated and the external carotid artery was permanently ligated.

value: adult

value: Winstar

value: 24h PBS injection

tag: cell fraction


title: 7D2_SH


title: mock 12 h rep1

description: mock 12 h


title: DEX 3 h rep1

description: DEX 3 h

value: induction after 3 h


title: DEX 3 h rep2

description: DEX 3 h


title: MGAS27961-ES-3

city: Houston

first: Priyanka

last: Kachroo

address: 6670 Bertner Avenue

institute: Houston Methodist Research Institute

description: Parental strain (9T)

data_processing:
Multiplexed single-end (SE) libraries were sequenced on an Illumina NextSeq 500 instrument, basecalling and demultiplexing was done on the instrument, and the RNA-Seq data was output as fastq files
RNA-seq reads from all strains were mapped to reference strain MGAS6180 (GenBank accession number CP000056), using Edge-pro v1.3.1 (Estimated Degree of Gene Expression for Prokaryotes).
Low-expressed genes and genes encoding ribosomal RNAs and tRNAs were filtered out prior to running differential expression analyses
Differential expression analysis was perfomed using DESeq2 v1.6.3 running in R version 3.4.3. Raw reads were used as the input and normalized expression generated using DESeq2's default normalization method Relative log expression (RLE) approach was used to generate fold change values for each gene. Multiple testing correction was performed using Bonferroni method.
Genome_build: reference strain MGAS6180 (GenBank accession number CP000056)
Supplementary_files_format_and_content: normalized counts

organism: Streptococcus pyogenes

source_name: MGAS27961-ES_cell pellet

growth_protocol: Cells were grown in Todd-Hewitt broth supplemented with yeast extract (THY media) at 37 C in atmosphere supplemented with 5% CO2

extract_protocol:
Pelleted cells were mechanically disrupted using silica beads, RNA was isolated using RNeasy kit, contaminating DNA was degraded using Turbo DNA-free (Ambion), and rRNA was depleted using Ribo-Zero (Illumina)
Resultant RNA was reverse transcribed to cDNA and sequencing libraries were generated using ScriptSeq RNA-seq preparation kit (Illumina)

treatment_protocol: At the desired growth stage, mid-exponential (OD 600nm=0.5) and early-stationary (OD 600nm=1.65), the culture was treated with RNAprotect Bacteria Reagent and cells were harvested by centrifugation

tag: subclade

value: Subclade2A (SC2A)

tag: site of isolation

value: invasive infection isolate

value: MGAS27961_9T parental

tag: growth phase

value: Early-stationay (ES, OD600nm=1.65)


title: MGAS27961_10T-ES-3

description: Isogenic strain (10T)

source_name: MGAS27961_10T-ES_cell pellet

value: MGAS27961_10T isogenic mutant


title: MGAS27961-ES-2

description: Parental strain (9T)


title: MGAS27961-ES-1

description: Parental strain (9T)


title: DEX 3 h rep3

city: Tokyo

description: DEX 3 h


title: mock 3 h rep2

description: mock 3 h


title: mock 3 h rep1

description: mock 3 h


title: mock 3 h rep3

description: mock 3 h


title: MGAS27961_10T-ES-2

description: Isogenic strain (10T)


title: MGAS27961-ME-3

description: Parental strain (9T)

source_name: MGAS27961-ME_cell pellet

value: Mid-exponential (ME, OD600nm=0.5)


title: 7D1_SH


title: 7D4_MO

source_name: sorted microglia from brain after MCAO

value: 24h MCAO


title: MGAS27961_10T-ME-3

description: Isogenic strain (10T)

source_name: MGAS27961_10T-ME_cell pellet


title: MGAS27961-ME-1

description: Parental strain (9T)


title: MGAS27961-ME-2

description: Parental strain (9T)


title: MGAS27961_10T-ME-2

description: Isogenic strain (10T)


title: 7D4_SH


title: MGAS27961_10T-ME-1

description: Isogenic strain (10T)


title: 29216-2-ES

data_processing:
Multiplexed single-end (SE) libraries were sequenced on an Illumina NextSeq 500 instrument, basecalling and demultiplexing was done on the instrument, and the RNA-Seq data was output as fastq files
RNA-seq reads from all strains were mapped to reference strain MGAS6180 (GenBank accession number CP000056), using Edge-pro v1.3.1 (Estimated Degree of Gene Expression for Prokaryotes).
Low-expressed genes and genes encoding ribosomal RNAs and tRNAs were filtered out prior to running differential expression analyses
Differential expression analysis was perfomed using DESeq2 v1.6.3 running in R version 3.3.2. Raw reads were used as the input and normalized expression generated using DESeq2's default normalization method Relative log expression (RLE) approach was used to generate fold change values for each gene. Multiple testing correction was performed using Bonferroni method.
Genome_build: reference strain MGAS6180 (GenBank accession number CP000056)
Supplementary_files_format_and_content: normalized counts

source_name: 29216_ES_cell pellet

treatment_protocol: At the desired growth stage, mid-exponential (OD 600nm=0.5) or early-stationary (OD 600nm=1.65), the culture was treated with RNAprotect Bacteria Reagent and cells were harvested by centrifugation


title: 7D3_MO


title: 7D2_MO


title: 29216-3-ES


title: 7D1_MO


title: MGAS27961_10T-ES-1

description: Isogenic strain (10T)


title: 28836-1-ES

source_name: 28836_ES_cell pellet


title: 7D4_Mg


title: 28798-3-ES

source_name: 28798_ES_cell pellet


title: 29216-1-ES


title: 7D3_Mg


title: 7D2_Mg


title: 28798-1-ES


title: 28699-1-ES

source_name: 28699_ES_cell pellet


title: 28686-3-ES

source_name: 28686_ES_cell pellet


title: SH3


title: 28699-3-ES


title: 7D1_Mg


title: 28686-1-ES


title: 28669-3-ES

source_name: 28669_ES_cell pellet


title: SH2


title: 28669-2-ES


title: 28597-3-ES

source_name: 28597_ES_cell pellet


title: 28669-1-ES


title: 28597-2-ES


title: 28597-1-ES


title: MO3

source_name: sorted macrophages from brain after MCAO


title: SH1


title: MO2


title: 28836-3-ES


title: 28533-3-ES

source_name: 28533_ES_cell pellet


title: 28836-2-ES


title: 28798-2-ES


title: 28533-2-ES


title: 28533-1-ES


title: MO1


title: 28392-3-ES

source_name: 28392_ES_cell pellet


title: Mg3


title: Mg2


title: 28386-2-ES

source_name: 28386_ES_cell pellet


title: Mg1


title: 28386-3-ES


title: 28392-2-ES


title: 28686-2-ES


title: 28392-1-ES


title: 28386-1-ES


title: 28271-2-ES

source_name: 28271_ES_cell pellet


title: 28271-3-ES


title: 28271-1-ES


title: 28191-3-ES

source_name: 28191_ES_cell pellet


title: H3K9me2 IP ChIP-Seq biological replicate 2

city: London

first: Jessica

last: Greenwood

address: 1 Midland Rd

institute: The Francis Crick Institute

description: ChIP-Seq

data_processing:
Raw reads from each sample were adapter-trimmed with cutadapt (version 1.9.1) (Martin M, 2011), and subsequently filtered for the telomeric repeat motif “GTTACAGG” (Duffy & Chambers, 1996).
De novo assembly was performed independently for each sample on the motif filtered paired-end reads with both SPAdes (version 3.9.0; kmer=97) (Bankevich et al., 2012) and ABySS (version 1.9.0; kmer=95)  (Simpson et al., 2009). Upon manual inspection, we were able to identify 10 candidate telomeric contigs across the replicate groups that were assembled independently within both the input and IP samples and/or by both SPAdes and ABySS.
The S. pombe genome was reconstructed to include the assembled contigs, 3 nuclear chromosomes, mitochondrial chromosome, mating type region, gap filling sequence between SPBPB21E7.09 and SPBPB10D8.01 in chromosome 2 (contig AB325691) (Sasaki et al., 2008), and a set of small insert clones generated from a telomere plasmid library. Sequence files were downloaded from Pombase (Wood et al., 2012).
BWA (version 0.5.9-r16) (Li and Durbin, 2009) with default parameters was used to perform genome-wide mapping of the adapter-trimmed reads. Discordant, multi-mapped and soft-clipped read pairs were removed, leaving only those that mapped to the same contig in the correct orientation, had zero mismatches in both reads, and a maximum insert size of 1kb.
bedGraph files were generated from filtered BAM files using the genomeCoverageBed command from BEDTools (Quinlan & Hall, 2010) with parameters "-bg -pc -scale <NORM_FACTOR>". Normalisation factors were calculated by scaling the number of mapped paired-end reads to 1 million. bedGraph files were converted to bigWig using the wigToBigWig binary available from the UCSC with the "-clip" parameter (Kent et al., 2010).
Genome_build: Schizosaccharomyces pombe
Supplementary_files_format_and_content: Genome-wide bigWig files representing normalised coverage. These files will have to be visualised with respect to the contigs in the genome fasta file included in this submission. See data processing step for more details.
Supplementary_files_format_and_content: Whole genome fasta file including assembled contigs.

organism: Schizosaccharomyces pombe

source_name: Fission yeast culture

growth_protocol: Cells were grown in yeast extract medium (YE4S) in conical flasks at 32 °C, shaking at 200 RPM.

extract_protocol:
Cells lysed in ChIP buffer (50mM Hepes 140mM NaCl 1mM EDTA 1% IGEPAL 0.1%Sodium deoxycholate Pi, PMSF), Chromatin sonicated with bioruptor.
Input and IP DNA purified with Qiagen PCR purification kit.  Library constructed using TruSeq ChIP library preparation kit.

treatment_protocol: Cells were grown to OD600 ~.06, fixed with 1% formaldehyde for 15min, quenched in 0.125M glycine 10 min, washed in PBS and snap frozen.

tag: antibody

value: wildtype


title: 28191-2-ES

tag: strain


title: Input ChIP-Seq biological replicate 1

description: ChIP-Seq

value: none, Input


title: H3K9me2 IP ChIP-Seq biological replicate 1

description: ChIP-Seq


title: 28078-2-ES

source_name: 28078_ES_cell pellet


title: 28191-1-ES


title: 28078-3-ES


title: 28078-1-ES


title: 27961-3-ES

source_name: 27961_ES_cell pellet


title: 27961-2-ES


title: 27961-1-ES


title: 29573-1-ES

source_name: 29573_ES_cell pellet

value: Subclade1B (SC1B)


title: 29573-3-ES


title: 29553-2-ES

source_name: 29553_ES_cell pellet


title: 29553-3-ES


title: 29502-3-ES

source_name: 29502_ES_cell pellet


title: 29553-1-ES


title: 29502-2-ES


title: 29502-1-ES


title: 29379-3-ES

source_name: 29379_ES_cell pellet


title: 29409-1-ES

source_name: 29409_ES_cell pellet


title: 29409-2-ES


title: 29379-2-ES


title: 29379-1-ES


title: Input ChIP-Seq biological replicate 2

description: ChIP-Seq


title: 29326-3-ES

source_name: 29326_ES_cell pellet


title: 29284-3-ES

source_name: 29284_ES_cell pellet


title: 29326-2-ES


title: 29284-2-ES


title: 29326-1-ES


title: 29284-1-ES


title: 29198-2-ES

source_name: 29198_ES_cell pellet


title: 29198-1-ES


title: 29184-3-ES

source_name: 29184_ES_cell pellet


title: 29573-2-ES


title: 29184-2-ES


title: 29184-1-ES


title: 29159-3-ES

source_name: 29159_ES_cell pellet


title: 29159-2-ES


title: 29409-3-ES


title: 29093-3-ES

source_name: 29093_ES_cell pellet


title: 29159-1-ES


title: 29093-1-ES


title: 29093-2-ES


title: 29064-3-ES

source_name: 29064_ES_cell pellet


title: 29064-1-ES


title: hsromega[66] rep 2

city: varanasi

first: subhas chandra

last: lakhotia

state: uttar pradesh

address: cytogenetics lab, department of Zoology BHU

department: Department of Zoology

country: India

institute: Brown University

data_processing:
The resulting sequencing FastQ files were mapped to the Drosophila genome (dm6) using Tophat with Bowtie.
The aligned SAM/BAM file for each was processed for guided transcript assembly using Cufflink 2.1.1 and gene counts were determined.
Mapped reads were assembled using Cufflinks. Transcripts from all samples were subjected to Cuffmerge to get final transcriptome assembly across samples.
In order to ascertain differential expression of gene transcripts between different samples, Cuffdiff 2.1.1 was used (Trapnell et al., 2012). A P-value <0.05 with correction for q values was taken to indicate significantly differentially expressing genes between different groups compared.
Genome_build: dm6
Supplementary_files_format_and_content: Cuffdiff 2.1.1 result showing differential gene expression between different samples in excel sheet

organism: Drosophila melanogaster

source_name: whole larvae

extract_protocol:
RNA was isolated from 5 wandering third instar larvae of the given genotype in PBS using Trizol (Invitrogen, USA) reagent as per manufacture’s protocol. 1µg of the isolated RNA was subjected to DNAase treatment using 2U of TurboTM DNase (Ambion, Applied Biosystem) enzyme for 30 min at 37°C. The reaction was stopped using 15mM EDTA followed by incubation at 65°C for 5-7 min and purification on RNAeasy column (Qiagen). The purified RNA samples were processed for preparations of cDNA libraries using the TruSeq Stranded Total RNA Ribo-Zero H/M/R (Illumina) and sequenced on HiSeq-2500 platform (Illumina) using 100bp pair-end reads.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: whole larvae

value: wandering third instar


title: hsromega[66] rep 1


title: control rep 1

value: Oregon R+


title: 29064-2-ES


title: 28932-2-ES

source_name: 28932_ES_cell pellet


title: Hsp90GFPhsromega66 rep2

description: w1118; Sp/CyO';hsp90GFPhsrω66

data_processing:
The resulting sequencing FastQ files were mapped to the Drosophila genome (dm6) using Tophat with Bowtie.
The aligned SAM/BAM file for each was processed for guided transcript assembly using Cufflink 2.1.1 and gene counts were determined.
Mapped reads were assembled using Cufflinks. Transcripts from all samples were subjected to Cuffmerge to get final transcriptome assembly across samples.
In order to ascertain differential expression of gene transcripts between different samples, Cuffdiff 2.1.1 was used (Trapnell et al., 2012). A P-value <0.05 was taken to indicate significantly differentially expressing genes between different groups compared.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: gene_expression_level.xlsx: Excel file includes Cuffdiff 2.1.1 results showing differential gene expression between different samples.

source_name: Whole Larvae

extract_protocol:
RNA was isolated from 5 whole wandering third instar larvae using Trizol (Invitrogen, USA) reagent as per manufacturer’s protocol. 1µg of the isolated RNA was subjected to DNase treatment using 2U of TurboTM DNase (Ambion, Applied Biosystem) enzyme for 30 min at 37°C. The reaction was stopped using 15mM EDTA followed by incubation at 65°C for 5-7 min and purification on RNeasy column (Qiagen). The purified RNA samples were processed for preparations of cDNA libraries using the TruSeq Stranded Total RNA Ribo-Zero H/M/R (Illumina) and sequenced on HiSeq-2500 platform (Illumina) using 50bp pair-end reads, 8 samples per lane and each sample run across 2 lanes.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: whole body

tag: developmental stage

value: wandering late third instar larvae

tag: genotype/variation

value: w1118; Sp/CyO';hsp90GFPhsromega66


title: Hsp90GFP rep2

description: processed data file: gene_expression_level.xlsx

value: w1118; Sp/CyO';hsp90GFP


title: 29198-3-ES


title: 28869-3-ES

source_name: 28869_ES_cell pellet


title: 28932-1-ES


title: hsromega66 rep2

description: w1118; Sp/CyO';hsrω66

value: w1118; Sp/CyO';hsromega66


title: 28869-2-ES

value: invasive infection isolate


title: 28869-1-ES


title: WT con rep2


title: Hsp90GFP rep1


title: control rep 2


title: Hsp90GFPhsromega66 rep1

description: w1118; Sp/CyO';hsp90GFPhsrω66


title: 28746-2-ES

source_name: 28746_ES_cell pellet


title: 28746-1-ES


title: 28746-3-ES


title: 28650-1-ES

source_name: 28650_ES_cell pellet


title: 28650-2-ES


title: 28650-3-ES


title: hsromega66 rep1

description: w1118; Sp/CyO';hsrω66


title: WT con rep1


title: 28932-3-ES


title: 28582-1-ES

source_name: 28582_ES_cell pellet


title: 28582-2-ES


title: 28278-2-ES

source_name: 28278_ES_cell pellet


title: 28278-1-ES


title: 28278-3-ES


title: 27784-3-ES

source_name: 27784_ES_cell pellet


title: 27784-2-ES


title: 27784-1-ES


title: RNAi hsromega rep2

description:
w1118; sev-GAL4/UAS-GFP';hsrωRNAi
processed data file: gene_expression_level.xlsx

source_name: eye disc

extract_protocol:
RNA was isolated from 30 pairs of eye discs dissected out from wandering third instar larvae in PBS using Trizol (Invitrogen, USA) reagent as per manufacturer’s protocol. 1µg of the isolated RNA was subjected to DNase treatment using 2U of TurboTM DNase (Ambion, Applied Biosystem) enzyme for 30 min at 37°C. The reaction was stopped using 15mM EDTA followed by incubation at 65°C for 5-7 min and purification on RNeasy column (Qiagen). The purified RNA samples were processed for preparations of cDNA libraries using the TruSeq Stranded Total RNA Ribo-Zero H/M/R (Illumina) and sequenced on HiSeq-2500 platform (Illumina) using 50bp pair-end reads, 6 samples per lane and each sample run across 2 lanes.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: eye disc

value: w1118; sev-GAL4/UAS-GFP';hsromegaRNAi


title: over expression of hsromega rep 1

value: w1118; sev-GAL4/UAS-GFP; EP3037


title: control rep2

value: w1118; sev-GAL4/UAS-GFP


title: over expression of hsromega rep 2


title: 11115-1-ES

source_name: 11115_ES_cell pellet

value: Early-stationay (ES, OD600nm=1.65)


title: 11108-3-ES

source_name: 11108_ES_cell pellet


title: 11108-2-ES


title: control rep1


title: 11108-1-ES


title: 11107-1-ES

source_name: 11107_ES_cell pellet


title: 11107-2-ES


title: 28582-3-ES


title: 11107-3-ES


title: 11052-2-ES

source_name: 11052_ES_cell pellet


title: 11052-1-ES


title: 28426-1-ES

source_name: 28426_ES_cell pellet

value: Subclade1A (SC1A)


title: 28360-3-ES

source_name: 28360_ES_cell pellet


title: 28360-2-ES


title: 28426-2-ES


title: 11052-3-ES


title: 28360-1-ES


title: 28330-2-ES

source_name: 28330_ES_cell pellet


title: 28330-3-ES


title: 11115-3-ES


title: 28330-1-ES


title: 11115-2-ES


title: 28426-3-ES


title: RNAi hsromega rep1


title: 28323-3-ES

source_name: 28323_ES_cell pellet


title: 28323-2-ES


title: 28323-1-ES


title: 28309-2-ES

source_name: 28309_ES_cell pellet


title: 28309-3-ES


title: 10826-3-ES

source_name: 10826_ES_cell pellet


title: 10826-2-ES


title: 28309-1-ES


title: 10812-3-ES

source_name: 10812_ES_cell pellet


title: 10826-1-ES


title: 10812-2-ES


title: 10812-1-ES


title: 10786-2-ES

source_name: 10786_ES_cell pellet


title: 10786-3-ES


title: PHH_WO_MD_exp1 [miRNA]

city: Maastricht

first: Linda

last: Rieswijk

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

description: Agilent Sureprint G3 Unrestricted Human miRNA V19 8 × 60 K microarrays

hyb_protocol: The hybridization was performed following standard protocols, after which the microarray slides were washed and scanned using a DNA microarray scanner (Agilent Technologies).

scan_protocol: The scanned images were converted into TXT files using the Feature Extraction Software v10.7.3.1 from Agilent Technologies.

data_processing: The scanned images were converted into TXT files using the Feature Extraction Software v10.7.3.1 from Agilent Technologies, which were imported in R 2.15.3 (http://www.r-project.org) for quality control with an in-house developed pipeline. Filtering and normalization was performed using AgiMicroRna (32). Total gene signals were log2-transformed and quantile-normalized. The selection criteria for determining differentially expressed microRNAs (DE-miRs) were identical to those for DEGs.

label_protocol: Samples were labeled according to the manufacturers protocol.

growth_protocol: Cryopreserved primary human hepatocytes (PHH) were purchased from Life Technologies. Cells were cultured in pre-coated 24-well and 6-well plates (700,000 cells/ml) in a 2-layer collagen sandwich (A11428-02, Gibco), according to the supplier’s protocol (Invitrogen, 2012). The following culture media were used: Hepatocyte Thawing Medium (HTM) for thawing (CM7500, Gibco), Williams’ Medium E (1x, no phenol red) (A1217601, Gibco) + Cell Maintenance supplement B kit (CM4000, Gibco) for plating and incubation.

extract_protocol: Cells were cultured in triplicate in 24 wells (RNA) or 6 wells (DNA) in a collagen sandwich layer. Following 5 days of repetitive daily exposure, cells lysates were harvested for DNA and total RNA isolation. At the end of treatment, medium was removed and PHH were harvested in Qiazol (Qiagen). Total RNA was isolated using a miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and followed by DNase I (Qiagen) treatment. Upon purification, RNA concentrations were measured by means of a NanoDrop® ND-1000 spectrophotometer (Thermo Scientific) at 260 and 280 nm. RNA quality and integrity were assessed by using automated gel electrophoresis on an Agilent 2100 Bioanalyzer system (Agilent Technologies). Only RNA samples which showed clear 18S and 28S peaks and with an RNA integrity number (RIN) higher than 8, were used. Samples were stored at -80ºC until RNA hybridization.

treatment_protocol: After quick thawing in a water bath at 37°C, viability of the cells was checked by a Trypan blue (CAS no. 72-57-1, Sigma–Aldrich) exclusion test as instructed in the supplier’s protocol (Invitrogen, 2012). All viability scores after thawing were in agreement with those listed by the supplier. Before AFB1 treatment, cells were allowed to acclimatize for 48 hours. This is needed for the hepatocytes to restore an in vivo like cellular configuration and enzyme expression levels as optimally as possible.AFB1 doses causing moderate (IC40) cytotoxicity after 5 days of repetitive daily exposure were established by means of the MTT assay (23). Furthermore, crucial liver function enzymes such as lactate dehydrogenase (LDH) and alanine transaminase (ALT) were measured. LDH and ALT were spectrophotometrically determined on a Cobas 8000 Modular Analyser (Roche Diagnostics, Basel, Switzerland). Based on this data, 1 µM of AFB1, was selected for the main experiment.

tag: cell type

value: primary human hepatocytes

tag: main source

value: liver

tag: study type

value: Wash out effect

tag: assay type

value: ex vivo

tag: agent

value: aflatoxin B1

tag: dose

tag: dose unit

value: uM

tag: dose duration

tag: duration unit

value: days

tag: dose frequency

value: daily

tag: vehicle

value: DMSO

tag: route

value: medium


title: PHH_WO_MD_exp3 [miRNA]


title: PHH_WO_MD_exp2 [miRNA]


title: PHH_WO_MD_control_exp3 [miRNA]


title: PHH_WO_MD_control_exp2 [miRNA]


title: 10786-1-ES

tag: subclade

tag: site of isolation

value: invasive infection isolate

tag: growth phase


title: 8347-3-ES

source_name: 8347_ES_cell pellet

tag: strain


title: PHH_WO_MD_control_exp1 [miRNA]


title: 8347-2-ES


title: Cells at d5

city: Hamburg

first: Thorsten

last: Schinke

address: Martinistr. 52

department: Department of Osteology and Biomechanics

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description:
3_OCL diff d5
Gene expression data from bone marrow cells subjected to 4 days of osteoclastogenic differentiation with vitamin-D3, MCSF and RANKL

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software GCOS 1.4 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 300.

source_name: Bone marrow of C57Bl/6J mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Trizol extraction followed by Rneasy purification

tag: gender

value: female

value: primary osteoclast

tag: differentiation protocol

tag: time of differentiation

value: 4 days


title: 8347-1-ES


title: AK58_S_2hr_rep2

city: Xinxiang

first: Haiyan

last: Hu

state: Henan

address: East Hualan Road

department: School of Life Science and Technology

institute: Henan Institue of Science and Technology

description: Gene expression after 2hr under pH 4.0 stress  in wheat seedling roots

hyb_protocol: Each Slide was hybridized with 1.65ug Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green, Scan resolution=5μm, PMT 100%,10% ，16bit.

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Triticum aestivum

source_name: Variety AK58, 2hr under pH4.0, replicate 2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (QIAGEN, GmBH, Germany).

growth_protocol: Wheat seedlings were grown in a growth chamber at 22°C/12-h-light and 12°C/12-h-dark conditions, with a photosynthetic photon flux density of 100 μmol·m−2·s−1, and 65% relative humidity.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Life technologies, Carlsbad, CA, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy mini kit (QIAGEN, GmBH, Germany) and RNase-Free DNase Set (QIAGEN, GmBH, Germany).

treatment_protocol: At the one-leaf stage wheat seedlings were treated with pH 4.0 and 10.0 deionized water, repectively.

tag: tissue

value: roots

value: seedling

tag: age

value: one-leaf stage


title: C24 Pst infection 48h

city: Beer-Sheva

first: Isabel

last: Orf

department: Life Sciences

institute: Ben-Gurion University of the Negev

hyb_protocol: Hybridization and detection was performed by ATLAS Biolabs (Berlin, Germany)

data_processing: Raw microarray data were normalized using the RMA algorithm (Irizarry et al., 2003a,b)

organism: Arabidopsis thaliana

source_name: Leaves of Arabidobsis thaliana ecotype C24 sprayed with 5*10^8 cfu/ml Pst in 10mM MgCl2 solution, 48h after treatment

growth_protocol: Arabidopsis thaliana plants of two accessions, Col-0 and C24, were grown in soil (potting compost) in individual pots under a 16/8-h light/dark regime at 16 °C. Two days prior to bacterial inoculation plants were transferred to a different chamber and were grown under a 14/10-h light/dark regime at 23 °C until harvesting. Light intensity in all chambers was 150 µE m−2 s−1.

extract_protocol: RNA was extracted from frozen plant material using the RNeasy kit (Qiagen, Hilden, Germany)

treatment_protocol: Psuedomonas syringae pv tomato strain DC3000 bacteria were grown on modified King's B medium (King et al., 1954; 10 mg/ml peptone, 1.5 mg/ml K2HPO4, 15 mg/ml glycerol, 0.6 % (v/v) 1 M MgSO4 · 7H2O) plates at 28 °C for two days, then trasferred to liquid King's B medium for one night. All media were supplemented with 100 µg/ml rifamycin. Overnight cultures were washed with 10 mM MgCl2 then serially diluted in this buffer. For spray inoculation bacteria were diluted in 10 mM MgCl2 to 5 × 108 cfu ml−, then supplemented with 0.02 % (v/v) Silwet and sprayed evenly to saturation upon the plants. Mock solution was identical, save for bacteria.

tag: ecotype

tag: agent

value: Pst

tag: time point


title: AK58_J_2hr_rep2

description: Gene expression after 2hr under pH 10.0 stress  in wheat seedling roots

source_name: Variety AK58, 2hr under pH10.0, replicate 2


title: AK58_S_2hr_rep3

source_name: Variety AK58, 2hr under pH4.0, replicate 3


title: Cells at d7

description:
4_OCL diff d7
Gene expression data from bone marrow cells subjected to 6 days of osteoclastogenic differentiation with vitamin-D3, MCSF and RANKL

organism: Mus musculus

tag: cell type

value: 6 days


title: B-KO-OE#21

city: Yokohama

first: Junji

last: Hirota

state: Kanagawa

address: 4259-B63, Nagatsuta-cho

department: Center for Biological Resources and Informatics

institute: Tokyo Institute of Technology

description: MOE Bcl11b KO rep4

hyb_protocol: Target RNA was hybridized with probes at 45 °C for 16 hrs, washed at 50 °C, and stained with streptavidin-phycoerythrin followed by anti-streptavidin antibody and biotinylated anti-goat IgG and streptavidin-phycoerythrin

scan_protocol: Intensity of phycoerythrin fluorescence was scanned by GeneChip Scanner 3000 controlled by GCOS

data_processing:
Signal calculated by GCOS1.1 software
Specific intensity value of each probe was obtained by subtracting the intensity of mismatch probe from that of perfect match probe by GCOS

source_name: MOE Bcl11b KO

label_protocol: Biotinylated target RNA was synthesized using GeneChip Two-Cycle Target Labeling and Control Reagents

growth_protocol: All mice were housed in standard conditions in accordance with institutional and governmental guidelines.

extract_protocol: Total RNA was isolated using an RNeasy Micro Kit (Qiagen) with the manufacturer's instructions.

treatment_protocol: Whole MOE tissues from wild-type and Bcl11b KO mcie were freshly dissected, and stored in RNA later stabilization solution (Ambion) at -20℃

value: BALB/c

tag: genotype/variation

value: Bcl11b KO

value: male

value: MOE

value: postnatal day 0


title: C24 Pst infection 8h

scan_protocol: Hybridization and detection was performed by ATLAS Biolabs (Berlin, Germany)

source_name: Leaves of Arabidobsis thaliana ecotype C24 sprayed with 5*10^8 cfu/ml Pst in 10mM MgCl2 solution, 8h after treatment


title: AK58_J_2hr_rep3

source_name: Variety AK58, 2hr under pH10.0, replicate 3


title: Cells at d1

description:
1_OCL d1
Gene expression data from bone marrow cells at the day of extraction

value: at the day of extraction

value: 0 days


title: B-KO-OE#23

description: MOE Bcl11b KO rep6


title: AK58_S_2hr_rep1

source_name: Variety AK58, 2hr under pH4.0, replicate 1


title: C24 Pst infection 24h

source_name: Leaves of Arabidobsis thaliana ecotype C24 sprayed with 5*10^8 cfu/ml Pst in 10mM MgCl2 solution, 24h after treatment

label_protocol: Hybridization and detection was performed by ATLAS Biolabs (Berlin, Germany)


title: C24 Pst infection 4h

source_name: Leaves of Arabidobsis thaliana ecotype C24 sprayed with 5*10^8 cfu/ml Pst in 10mM MgCl2 solution, 4h after treatment


title: AK58_J_2hr_rep1

source_name: Variety AK58, 2hr under pH10.0, replicate 1


title: Cells at d4

description:
2_OCL diff d4
Gene expression data from bone marrow cells subjected to 3 days of osteoclastogenic differentiation with vitamin-D3

value: 3 days


title: C24 Pst infection 16h

source_name: Leaves of Arabidobsis thaliana ecotype C24 sprayed with 5*10^8 cfu/ml Pst in 10mM MgCl2 solution, 16h after treatment


title: B-KO-OE#22

description: MOE Bcl11b KO rep5


title: 7941-3-ES

source_name: 7941_ES_cell pellet

value: Subclade1A (SC1A)

value: invasive infection isolate

value: Early-stationay (ES, OD600nm=1.65)


title: 7941-2-ES


title: AK58_J_24hr_rep3

description: Gene expression after 24hr under pH 10.0 stress  in wheat seedling roots

source_name: Variety AK58, 24hr under pH10.0, replicate 3


title: AK58_J_24hr_rep2

source_name: Variety AK58, 24hr under pH10.0, replicate 2


title: 7941-1-ES


title: B-KO-OE#19

description: MOE Bcl11b KO rep3

value: female


title: 7914-3-ES

source_name: 7914_ES_cell pellet


title: 7914-2-ES


title: AK58_J_24hr_rep1

source_name: Variety AK58, 24hr under pH10.0, replicate 1

value: roots


title: C24 mock treatment 48h

source_name: Leaves of Arabidobsis thaliana ecotype C24 sprayed with 10mM MgCl2 solution, 48h after treatment

value: mock


title: C24 Pst infection 2h

source_name: Leaves of Arabidobsis thaliana ecotype C24 sprayed with 5*10^8 cfu/ml Pst in 10mM MgCl2 solution, 2h after treatment


title: 7914-1-ES


title: B-KO-OE#5

description: MOE Bcl11b KO rep1


title: AK58_0hr_rep3

description: Gene expression after 0hr under different pH stresses  in wheat seedling roots

source_name: Variety AK58, control, replicate 3

value: seedling

value: one-leaf stage


title: B-KO-OE#8

description: MOE Bcl11b KO rep2


title: WT-OE#16

description: MOE WT rep5

source_name: MOE WT

value: WT


title: 7888-3-ES

source_name: 7888_ES_cell pellet


title: C24 mock treatment 16h

source_name: Leaves of Arabidobsis thaliana ecotype C24 sprayed with 10mM MgCl2 solution, 16h after treatment


title: WT-OE#15

description: MOE WT rep4

value: BALB/c


title: C24 mock treatment 24h

source_name: Leaves of Arabidobsis thaliana ecotype C24 sprayed with 10mM MgCl2 solution, 24h after treatment


title: 7888-2-ES


title: 7888-1-ES


title: WT-OE#14

description: MOE WT rep3


title: WT-OE#12

description: MOE WT rep2


title: AK58_0hr_rep1

source_name: Variety AK58, control, replicate 1


title: C24 mock treatment 8h

source_name: Leaves of Arabidobsis thaliana ecotype C24 sprayed with 10mM MgCl2 solution, 8h after treatment


title: C24 mock treatment 2h

source_name: Leaves of Arabidobsis thaliana ecotype C24 sprayed with 10mM MgCl2 solution, 2h after treatment


title: AK58_0hr_rep2

source_name: Variety AK58, control, replicate 2


title: 20180124_102307_009: T2D

city: Jaipur

first: Dr. Sandeep

middle: Kumar

last: Mathur

state: Rajasthan

address: Tonk Road

department: Department of Endocrinology

institute: SMS Medical College and Hospital

hyb_protocol: Incubate 173.3 μL Hybridization Master Mix with 26.7 μL (10 μg) Fragmented and Labeled cRNA at 990 C for 5 minutes and then at 450 C for 5 Minutes in a thermal cycler using the“Hybridization Cocktail” program then rotate at 60 rpm for 16 hr at 45ºC

scan_protocol: GeneChip Scanner 3000 Dx V.2 was used for scanning arrays as per protocol supplied by Affymetrix inc.

data_processing: Bioconductor package affy, method rma

organism: Homo sapiens

source_name: Visceral

label_protocol: 3’ IVT Biotin Labelling of aRNA

extract_protocol: RNA is isolated using Qiagen RNeasy® Mini Kit

value: M

tag: diagnosis

value: Type-2 Diabetes

value: Visceral


title: WT-OE#11

description: MOE WT rep1

value: male

value: MOE

value: postnatal day 0


title: SW480 cells (control)

city: Nanjing

first: Ying

last: Cao

address: 12 Xuefu Rd., Pukou High-Tech Zone

institute: Nanjing University

description: Gene expression data from SW480 cells (control)

hyb_protocol: Following fragmentation, 10 mg of cRNA were hybridized for 16 hr at 45°C on GeneChip® PrimeView™ Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® Scanner 3000.

data_processing: Normalized probeset data were generated with Robust Multi-array Averaging (RMA) method.

source_name: SW480 cells infected with lentivirus carrying empty shRNA knockdown vector pLKO.1, and cultured for 6 days

label_protocol: Biotin-labeled cRNA were prepared using MessageAmp™ Premier RNA Amplification Kit (Ambion) and the protocol of the kit manufacturer from 100 ng total RNA.

growth_protocol: SW480 cells were cultured in Leibovitz's L-15 medium (L-15. Thermo Fisher Scientific) supplemented with 5% bovine fetal serum (Hyclone). Cells were grown at 37°C with 5% CO2.

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

treatment_protocol: SW480 cells were infected with lentivirus carrying shRNA against EZH2 for 6 days after puromycin selection. In parallel, cells were infected with lentivirus carrying empty vector as a control. Afterwards, cells were trypsinized and washed twice with PBS, and subjected to total RNA extraction.

tag: cell line

value: SW480 colorectal carcinoma cell line

tag: genotype

value: control

value: 50 year old Caucasian male


title: Col-0 Pst infection 48h

source_name: Leaves of Arabidobsis thaliana ecotype Col-0 sprayed with 5*10^8 cfu/ml Pst in 10mM MgCl2 solution, 48h after treatment

value: Pst


title: 29216-3-ME

source_name: 29216_ME_cell pellet

tag: subclade

value: Subclade2A (SC2A)

value: invasive infection isolate

value: Mid-exponential (ME, OD600nm=0.5)


title: C24 mock treatment 4h

source_name: Leaves of Arabidobsis thaliana ecotype C24 sprayed with 10mM MgCl2 solution, 4h after treatment

value: mock


title: Col-0 Pst infection 24h

source_name: Leaves of Arabidobsis thaliana ecotype Col-0 sprayed with 5*10^8 cfu/ml Pst in 10mM MgCl2 solution, 24h after treatment


title: 20180124_102305_005: T2D


title: 20180124_102306_007: T2D


title: 29216-2-ME

tag: site of isolation


title: SW480 cells with EZH2 knockdown

description: Gene expression data from SW480 cells with knockdown of EZH2

source_name: SW480 cells infected with lentivirus carrying shRNA against EZH2 (shEZH2), and cultured for 6 days

value: EZH2 knockdown


title: 29216-1-ME

tag: growth phase


title: CSMN-L P7 sample2

city: Cambridge

first: Vibhu

last: Sahni

address: 7 Divinity Avenue

institute: Harvard University

description: Gene expression data from purified corticospinal motor neurons in caudo-medial  sensorimotor cortex at postnatal day 7

hyb_protocol: RNA samples were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Array chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000 7G

data_processing: Data fies were uploaded with Rosetta Resolver software. Robust Multiarray Average (RMA) was used for normalization

source_name: FACS purified corticospinal motor neurons in caudo-medial sensorimotor cortex from wild type mice at P7

label_protocol: RNA was amplified in two rounds of amplification using the MessageAmpII aRNA Amplification kit and THE MessageAmp-II-biotin enhanced kits (Ambion) for the first and second rounds of amplification, respectively.

extract_protocol: RNA was extracted using Absolutely RNA Micro Prep Kits (Stratagene) according to the manufacturer's instructions.

treatment_protocol: CSMN in C57BL/6 mice were retrogradely labeled with green fluorescent microspheres (Lumafluor Corp., FL) injected into either the cerebral peduncles of P0 mice or the cervical spinal cord of P3, and P5 mice. The rostrol-lateral and caudomedial cortex was microdissected from these labeled brains at P1, P4, and P7. The cortices were collected and dissociated; CSMN from these micro-dissected cortices were purified by FACS as described in (Catapano et al., 2001, and Arlotta et al., 2005)

tag: gentotype

tag: Stage

value: postnatal day 7

value: corticospinal motor neuron


title: CSMN-L P7 sample1


title: CSMN-C P7 sample2

description: Gene expression data from purified corticospinal motor neurons in rostro-lateral  sensorimotor cortex at postnatal day 7

source_name: FACS purified corticospinal motor neurons in rostro-lateral  sensorimotor cortex from wild type mice at P7


title: 28836-3-ME

source_name: 28836_ME_cell pellet

tag: strain


title: Col-0 Pst infection 8h

source_name: Leaves of Arabidobsis thaliana ecotype Col-0 sprayed with 5*10^8 cfu/ml Pst in 10mM MgCl2 solution, 8h after treatment


title: 28836-2-ME


title: 28836-1-ME


title: 28798-3-ME

source_name: 28798_ME_cell pellet


title: Col-0 Pst infection 16h

source_name: Leaves of Arabidobsis thaliana ecotype Col-0 sprayed with 5*10^8 cfu/ml Pst in 10mM MgCl2 solution, 16h after treatment


title: 20180124_102300_001: Normal

tag: gender

value: M

value: Normal


title: 20180124_102304_003: T2D

value: Type-2 Diabetes

tag: tissue

value: Visceral


title: CSMN-C P7 sample1


title: Col-0 Pst infection 2h

source_name: Leaves of Arabidobsis thaliana ecotype Col-0 sprayed with 5*10^8 cfu/ml Pst in 10mM MgCl2 solution, 2h after treatment


title: Col-0 mock treatment 48h

source_name: Leaves of Arabidobsis thaliana ecotype Col-0 sprayed with 10mM MgCl2 solution, 48h after treatment


title: Col-0 Pst infection 4h

source_name: Leaves of Arabidobsis thaliana ecotype Col-0 sprayed with 5*10^8 cfu/ml Pst in 10mM MgCl2 solution, 4h after treatment


title: Col-0 mock treatment 24h

source_name: Leaves of Arabidobsis thaliana ecotype Col-0 sprayed with 10mM MgCl2 solution, 24h after treatment


title: CSMN-C P4 sample1

description: Gene expression data from purified corticospinal motor neurons in rostro-lateral  sensorimotor cortex at postnatal day 4

source_name: FACS purified corticospinal motor neurons in rostro-lateral  sensorimotor cortex from wild type mice at P4

value: postnatal day 4


title: CSMN-L P4 sample2

description: Gene expression data from purified corticospinal motor neurons in caudo-medial  sensorimotor cortex at postnatal day 4

source_name: FACS purified corticospinal motor neurons in caudo-medial sensorimotor cortex from wild type mice at P4


title: 20180124_102306_008: T2D

source_name: Subcutaneous

value: Subcutaneous


title: 20180124_102307_010: T2D


title: CSMN-C P4 sample2


title: 28798-2-ME


title: 20180124_102304_002: Normal


title: CSMN-L P1 sample3

description: Gene expression data from purified corticospinal motor neurons in caudo-medial  sensorimotor cortex at postnatal day 1

source_name: FACS purified corticospinal motor neurons in caudo-medial sensorimotor cortex from wild type mice at P1

value: postnatal day 1


title: CSMN-L P1 sample2


title: EPC_HDAC7_KD_rep2

city: Wuhan

first: Ye

last: Wei

state: Hubei

address: Tongji Medical College, Huazhong University of Science and Technology

institute: Cancer Center, Union Hospital

description: Gene expression data from HDAC7 KD EPCs.

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

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

source_name: EPCs infected with lentivirus carrying HDAC7 shRNA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Isolated mononuclear cells were collected and plated on human plasma fibronectin-coated culture dishe for 3 days, nonadherent cells were discarded and fresh endothelial basal medium 2 supplemented with EGM-2 MV Single-Quots was added. Typical EPC colonies appeared after 2-3 weeks, and these cells were collected and incubated at 37C in a humidified 5% CO2 atmosphere.

treatment_protocol: EPCs and infected by lentivirus (NC/KD) at MOI 20 according to the manufacture’s instructions.

value: umbilical cord blood

tag: infection

value: lentivirus carrying HDAC7 shRNA


title: 20180124_102305_004: T2D


title: CSMN-L P4 sample1


title: 20180124_102305_006: T2D


title: 28699-3-ME

source_name: 28699_ME_cell pellet


title: 28699-2-ME


title: 28798-1-ME


title: Col-0 mock treatment 16h

source_name: Leaves of Arabidobsis thaliana ecotype Col-0 sprayed with 10mM MgCl2 solution, 16h after treatment

tag: ecotype


title: 28686-3-ME

source_name: 28686_ME_cell pellet


title: 28686-2-ME


title: Col-0 mock treatment 8h

source_name: Leaves of Arabidobsis thaliana ecotype Col-0 sprayed with 10mM MgCl2 solution, 8h after treatment

tag: agent


title: 28699-1-ME


title: Col-0 mock treatment 2h

source_name: Leaves of Arabidobsis thaliana ecotype Col-0 sprayed with 10mM MgCl2 solution, 2h after treatment

tag: time point


title: Col-0 mock treatment 4h

source_name: Leaves of Arabidobsis thaliana ecotype Col-0 sprayed with 10mM MgCl2 solution, 4h after treatment


title: CSMN-C P1 sample3

description: Gene expression data from purified corticospinal motor neurons in rostro-lateral  sensorimotor cortex at postnatal day 1

source_name: FACS purified corticospinal motor neurons in rostro-lateral sensorimotor cortex from wild type mice at P1

tag: cell type


title: CSMN-C P1 sample1

source_name: FACS purified orticospinal motor neurons in rostro-lateral  sensorimotor cortex from wild type mice at P1


title: CSMN-L P1 sample1