title: WholeBlood_CRC305A7012105_Day28 [US22502595_254890810094_S01_GE1_1105_Oct12_2_2]

data_processing: The scanned microarray images were processed with the Image Analysis/Feature Extraction software G2567AA v. A.11.5.1.1 (Agilent Technologies) using default settings and the GE1_1105_Oct12 extraction protocol.

extract_protocol: mRNA was reverse transcribed and amplified using an oligo-dT-T7 promoter primer

tag: participant


title: ot7-2

status: Public on Jan 05 2019

type: SRA

city: Seoul

first: Chul-Yong

last: Park

address: Yonsei-ro 50-1

department: Physiology

country: South Korea

institute: Yonsei University

library_source: genomic

data_processing:
Illumina NextSeq 500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then merged by flash2 (version 1.2.11)
Merged sequences were mapped to hg19 by bowtie2 software(version 2.3.2).
CrispRVariants performed from the merged reads were to investigate CRISPR-Cas9 mutagenesis
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file includes counts of variants from CrispRVariants results

molecule: genomic DNA

organism: Homo sapiens

source_name: HEK293T_Cas9 Treated

extract_protocol:
Genomic DNA was isolated from the cells using the DNeasy Blood &     Tissue kit (Qiagen) according to the manufacturer's instructions.
The quantity and quality of the amplocon were evaluated using Agilent 2100 bioanalyzerRNA kit (Agilent). The amplicon was processed for preparing amplicon sequencing library using TruSeq DNA Nano Sample Preparation Kit(Illumina) according to the manufacturer's protocol

tag: cell line

tag: cell type

value: transient transfection

tag: treatment

value: Cas9 Treated

tag: molecule subtype

value: PCR amplicon


title: ot6-2


title: ot5-3


title: ot6-3


title: 6 month ENT1-null AF, 1

type: RNA

city: London

first: Matthew

middle: A

last: Veras

state: ON

address: 1151 Richmond St.

country: Canada

institute: Western University

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Command Console v3.2.4 using Affymetrix default analysis settings and RMA as normalization method.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Pool of 5-6 thoracic AF tissues from 6 month ENT1-null mouse

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were housed in standard cages and maintained on a 12 hr light/dark cycle, with rodent chow and water available ad libitum

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

treatment_protocol: ENT1-null mice were generated by deletion of exons 2-4 of the gene encoding ENT1 (Slc29a1)

tag: strain

value: Black 6

tag: tissue

value: thoracic annulus fibrosus

tag: genotype

tag: age

value: 6 months


title: WholeBlood_CRC305A7012105_Day21 [US22502595_254890810094_S01_GE1_1105_Oct12_2_1]

first: David

last: Lewis

address: Du Cane Road

department: ICRF

country: United Kingdom

institute: Imperial College London

description: Whole blood gene expression of participant on day

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented and hybridized to custom whole genome human 8 × 60K multipack microarrays (Agilent-048908) following the manufacturers instructions. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent) according the manufacturers protocol.

scan_protocol: Slides were scanned immediately after washing using a high resolution DNA Microarray Scanner (G2505B, Agilent Technologies) with 3 µm resoltion and 20 bit image depth

source_name: Peripheral Blood, PaxGene

label_protocol: Total RNA was amplified and labeled with the low input Quick-Amp Labelling Kit (Agilent Technologies) with cyanine 3-CTP followed by precipitation, purification, and quantification.

treatment_protocol: Microarray experiments were performed as single-color hybridization. Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

tag: gender

value: male

tag: race

value: white

tag: ethnicity

value: not hispanic or latino

tag: protocol

tag: day

value: whole blood


title: ot4-3


title: ot4-2


title: ot5-2


title: 6 month WT AF, 1

source_name: Pool of 5-6 thoracic AF tissues from 6 month WT mouse

value: WT


title: Breasttumour_PatientX350_Timepoint2

city: Edinburgh

first: Cigdem

last: Selli

address: Little France Crescent

department: Centre for Reproductive Health

institute: Queen's Medical Research Institute

hyb_protocol: Labeled cDNA was hybridized to bead arrays according to the standard protocol for NuGEN amplified samples.

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was log2 tranformed, normalised using quantile normalisation, and detectiona and probe quality filtered using lumi and illuminaHumanv4.db in R

source_name: breast tumour

label_protocol: RNA was then biotinylated using the Encore Biotin IL Module (NuGEN) and purified using minElute Reaction Cleanup Kit (Qiagen).

extract_protocol: RNA was extracted with Trizol reagent, followed by column-based purification (miRNeasy mini kit, Qiagen) in accordance with the protocol provided. Quality control was performed with Agilent Bioanalyser. RNA was then reverse transcribed and amplified using the Ovation FFPE WTA System (NuGEN), followed by purification using the Qiaquick PCR Purification Kit (Qiagen).

value: breast tumour


title: ot3-3


title: ot2-3


title: WholeBlood_CRC305A7012105_Day14 [US22502595_254890810094_S01_GE1_1105_Oct12_1_4]


title: Breasttumour_PatientX373R_Timepoint2


title: WholeBlood_CRC305A7012105_Day7 [US22502595_254890810094_S01_GE1_1105_Oct12_1_3]


title: Breasttumour_PatientX350_Timepoint1


title: WholeBlood_CRC305A7012105_Day4 [US22502595_254890810094_S01_GE1_1105_Oct12_1_1]


title: WholeBlood_CRC305A7012105_Day5 [US22502595_254890810094_S01_GE1_1105_Oct12_1_2]


title: ot2-2


title: ot1-3


title: Breasttumour_PatientX347_Timepoint1


title: Breasttumour_PatientX347_Timepoint4


title: WholeBlood_CRC305A7012105_Day2 [US22502595_254890810093_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7012105_Day3 [US22502595_254890810093_S01_GE1_1105_Oct12_2_4]


title: ot3-2


title: on-3


title: Breasttumour_PatientX341_Timepoint4


title: on-2


title: ot1-2


title: WholeBlood_CRC305A7012105_Day1 [US22502595_254890810093_S01_GE1_1105_Oct12_2_2]


title: Breasttumour_PatientX341_Timepoint2


title: Breasttumour_PatientX347_Timepoint2


title: con-ot8-3

source_name: HEK293T_Cas9 Non-treated

value: Cas9 Non-treated


title: con-ot8-2


title: Breasttumour_PatientX341_Timepoint1


title: con-ot7-3


title: WholeBlood_CRC305A7012105_Day-1 [US22502595_254890810093_S01_GE1_1105_Oct12_1_4]


title: con-ot6-3


title: con-ot6-2


title: WholeBlood_CRC305A7012105_Day0 [US22502595_254890810093_S01_GE1_1105_Oct12_2_1]


title: con-ot5-2


title: con-ot5-3


title: con-ot3-2


title: con-ot4-2


title: con-ot2-3


title: WholeBlood_CRC305A7009106_Day21 [US22502595_254890810093_S01_GE1_1105_Oct12_1_2]

value: female

value: hispanic or latino

value: VARILRIX


title: con-ot4-3


title: WholeBlood_CRC305A7009106_Day14 [US22502595_254890810093_S01_GE1_1105_Oct12_1_1]


title: Breasttumour_PatientX330_Timepoint4


title: con-ot2-2


title: WholeBlood_CRC305A7009106_Day28 [US22502595_254890810093_S01_GE1_1105_Oct12_1_3]


title: Breasttumour_PatientX330_Timepoint2


title: con-ot1-3


title: Breasttumour_PatientX333_Timepoint4


title: WholeBlood_CRC305A7009106_Day7 [US22502595_254890810092_S01_GE1_1105_Oct12_2_4]


title: Breasttumour_PatientX333_Timepoint2


title: Breasttumour_PatientX323_Timepoint4


title: WholeBlood_CRC305A7009106_Day4 [US22502595_254890810092_S01_GE1_1105_Oct12_2_2]


title: con-ot1-2


title: con-ot7-2


title: WholeBlood_CRC305A7009106_Day2 [US22502595_254890810092_S01_GE1_1105_Oct12_1_4]


title: con-on-3


title: WholeBlood_CRC305A7009106_Day3 [US22502595_254890810092_S01_GE1_1105_Oct12_2_1]


title: WT hippocampus MI, biological rep 4

city: Guelph

first: Dr. Tami

middle: A.

last: Martino

state: Ontario

address: 50 Stone Road E

department: Centre for Cardiovascular Investigations, Department of Biomedical Science

institute: University of Guelph

hyb_protocol: Following fragmentation, cRNA were hydridized on Affymetrix GeneChip Mouse Gene 2.0 ST arrays, according to manufacturer's instructions. GeneChips were washed and stained on the Gene Atlas platform.

scan_protocol: GeneChips were scanned on the GeneAtlas platform.

data_processing: The data were analyzed with GeneSpring GX software v. 14.9 using default Affymetrix settings.

source_name: WT MI hippocampus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng total RNA.

growth_protocol: The mice were collected at 8 weeks of age (baseline and 64h post-MI surgery) and at 16 weeks of age (8 weeks post-MI surgery) at 7 hours after lights off.

extract_protocol: Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: The brain regions (mPFC and hippocampus) were collected and snap frozen in liquid nitrogen and stored at -80C.

value: hippocampus

tag: Sex

tag: disease state

value: short-term post-MI


title: con-on-2

value: transient transfection


title: Breasttumour_PatientX323_Timepoint1


title: WholeBlood_CRC305A7009106_Day5 [US22502595_254890810092_S01_GE1_1105_Oct12_2_3]


title: ma10.k1e2.OT10

source_name: del K1e2 iPSCs_Cas9 Treated

value: del K1e2 iPSCs

value: corrected cell line

value: Cas9 Treated

value: PCR amplicon


title: Breasttumour_PatientX333_Timepoint1


title: WholeBlood_CRC305A7009106_Day1 [US22502595_254890810092_S01_GE1_1105_Oct12_1_3]


title: Breasttumour_PatientX330_Timepoint1


title: Breasttumour_PatientX302_Timepoint4


title: ma10.k1e2.OT8


title: Breasttumour_PatientX32_Timepoint4


title: ma10.k1e2.OT7


title: ma10.k1e2.OT4


title: WholeBlood_CRC305A7009106_Day0 [US22502595_254890810092_S01_GE1_1105_Oct12_1_2]


title: ma10.k1e2.OT6


title: ma10.k1e2.OT5


title: ma10.k1e2.OT9


title: Breasttumour_PatientX32_Timepoint1


title: ma10.k1e2.OT3


title: ma10.k1e2.OT1


title: ma10.k1e2.OT2


title: ma10.k1e1.OT10

source_name: del K1e1 iPSCs_Cas9 Treated

value: del K1e1 iPSCs


title: ma10.k1e1.OT9


title: ma10.k1e1.OT8


title: ma10.k1e1.OT7


title: Breasttumour_PatientX298_Timepoint1


title: ma10.k1e1.OT6


title: ma10.k1e1.OT5


title: WholeBlood_CRC305A7007104_Day21 [US22502595_254890810091_S01_GE1_1105_Oct12_2_1]

value: male

value: white


title: WholeBlood_CRC305A7007104_Day28 [US22502595_254890810091_S01_GE1_1105_Oct12_2_2]

value: not hispanic or latino

value: whole blood


title: Breasttumour_PatientX283L_Timepoint1

value: breast tumour


title: WholeBlood_CRC305A7007104_Day7 [US22502595_254890810091_S01_GE1_1105_Oct12_1_3]


title: WholeBlood_CRC305A7007104_Day5 [US22502595_254890810091_S01_GE1_1105_Oct12_1_2]


title: Breasttumour_PatientX302_Timepoint1


title: WholeBlood_CRC305A7009106_Day-1 [US22502595_254890810092_S01_GE1_1105_Oct12_1_1]


title: Breasttumour_PatientX298_Timepoint2


title: ma10.k1e1.OT4


title: Breasttumour_PatientX298_Timepoint4


title: ma10.k1e1.OT2


title: WholeBlood_CRC305A7007104_Day14 [US22502595_254890810091_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7007104_Day4 [US22502595_254890810091_S01_GE1_1105_Oct12_1_1]


title: ma10.k1e1.OT1


title: Breasttumour_PatientX283L_Timepoint4


title: Breasttumour_PatientX281_Timepoint1


title: Breasttumour_PatientX281_Timepoint4


title: del.ori.OT10

source_name: del iPSCs_Cas9 Non-treated

value: del iPSCs

value: original del patient cell line

value: Cas9 Non-treated


title: ma10.k1e1.OT3


title: del.ori.OT9


title: del.ori.OT5


title: del.ori.OT7


title: WholeBlood_CRC305A7007104_Day3 [US22502595_254890810090_S01_GE1_1105_Oct12_2_4]

value: VARILRIX


title: del.ori.OT6


title: Breasttumour_PatientX279_Timepoint1


title: WholeBlood_CRC305A7007104_Day2 [US22502595_254890810090_S01_GE1_1105_Oct12_2_3]


title: del.ori.OT3


title: Breasttumour_PatientX279_Timepoint4


title: Breasttumour_PatientX276_Timepoint4


title: del.ori.OT1


title: del.ori.OT2


title: WholeBlood_CRC305A7007104_Day1 [US22502595_254890810090_S01_GE1_1105_Oct12_2_2]


title: del.ori.OT8


title: Breasttumour_PatientX276_Timepoint1


title: PB9.k1e2.OT10

source_name: inv K1e2 iPSCs_Cas9 Treated

value: inv K1e2 iPSCs


title: PB9.k1e2.OT8


title: PB9.k1e2.OT9


title: WholeBlood_CRC305A7007104_Day0 [US22502595_254890810090_S01_GE1_1105_Oct12_2_1]


title: del.ori.OT4


title: PB9.k1e2.OT7


title: PB9.k1e2.OT6


title: PB9.k1e2.OT5


title: WholeBlood_CRC305A7007104_Day-1 [US22502595_254890810090_S01_GE1_1105_Oct12_1_4]


title: PB9.k1e2.OT4


title: PB9.k1e2.OT3


title: Breasttumour_PatientX268_Timepoint1


title: WholeBlood_CRC305A7006103_Day21 [US22502595_254890810090_S01_GE1_1105_Oct12_1_2]

value: other

value: STAMARIL


title: WholeBlood_CRC305A7006103_Day7 [US22502595_254890810089_S01_GE1_1105_Oct12_2_4]


title: Breasttumour_PatientX251_Timepoint4


title: WholeBlood_CRC305A7006103_Day28 [US22502595_254890810090_S01_GE1_1105_Oct12_1_3]


title: Breasttumour_PatientX251_Timepoint1


title: WholeBlood_CRC305A7006103_Day14 [US22502595_254890810090_S01_GE1_1105_Oct12_1_1]


title: Breasttumour_PatientX268_Timepoint4


title: PB9.k1e2.OT1


title: Breasttumour_PatientX249_Timepoint4


title: PB9.k1e1.OT9

source_name: inv K1e1 iPSCs_Cas9 Treated

value: inv K1e1 iPSCs


title: Breasttumour_PatientX268_Timepoint2


title: Breasttumour_PatientX249_Timepoint2


title: WholeBlood_CRC305A7006103_Day4 [US22502595_254890810089_S01_GE1_1105_Oct12_2_2]


title: WholeBlood_CRC305A7006103_Day5 [US22502595_254890810089_S01_GE1_1105_Oct12_2_3]


title: WholeBlood_CRC305A7006103_Day2 [US22502595_254890810089_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7006103_Day3 [US22502595_254890810089_S01_GE1_1105_Oct12_2_1]


title: PB9.k1e1.OT10

value: corrected cell line


title: Breasttumour_PatientX249_Timepoint1


title: PB9.k1e2.OT2

value: Cas9 Treated


title: PB9.k1e1.OT7

value: PCR amplicon


title: PB9.k1e1.OT4


title: PB9.k1e1.OT6


title: PB9.k1e1.OT3


title: PB9.k1e1.OT8


title: PB9.k1e1.OT1


title: inv.ori.OT9

source_name: inv iPSCs_Cas9 Non-treated

value: inv iPSCs

value: original inv patient cell line


title: inv.ori.OT10


title: inv.ori.OT7


title: PB9.k1e1.OT5


title: Breasttumour_PatientX226_Timepoint1


title: WholeBlood_CRC305A7006103_Day1 [US22502595_254890810089_S01_GE1_1105_Oct12_1_3]

value: male


title: inv.ori.OT6


title: Breasttumour_PatientX226_Timepoint2


title: inv.ori.OT5


title: Breasttumour_PatientX225_Timepoint4


title: inv.ori.OT8


title: inv.ori.OT4


title: con-ot3-3

value: transient transfection


title: Breasttumour_PatientX226_Timepoint4


title: PB9.k1e1.OT2


title: inv.ori.OT3


title: Breasttumour_PatientX225_Timepoint1


title: WholeBlood_CRC305A7006103_Day0 [US22502595_254890810089_S01_GE1_1105_Oct12_1_2]

value: not hispanic or latino

value: whole blood


title: WholeBlood_CRC305A7006103_Day-1 [US22502595_254890810089_S01_GE1_1105_Oct12_1_1]


title: Breasttumour_PatientX225_Timepoint2

value: breast tumour


title: WholeBlood_CRC305A7003102_Day21 [US22502595_254890810088_S01_GE1_1105_Oct12_2_1]


title: WholeBlood_CRC305A7003102_Day28 [US22502595_254890810088_S01_GE1_1105_Oct12_2_2]


title: Ot8


title: inv.ori.OT2


title: inv.ori.OT1


title: Breasttumour_PatientX195_Timepoint4


title: WholeBlood_CRC305A7003102_Day14 [US22502595_254890810088_S01_GE1_1105_Oct12_1_4]


title: WholeBlood_CRC305A7003102_Day5 [US22502595_254890810088_S01_GE1_1105_Oct12_1_2]


title: Ot6


title: Ot3


title: Ot4


title: Ot5


title: Ot1


title: Ot2


title: On


title: Con-Ot8


title: Con-Ot7


title: Breasttumour_PatientX195_Timepoint1


title: Ot7


title: Con-Ot5


title: Con-Ot4


title: Con-Ot3


title: Breasttumour_PatientX188_Timepoint1


title: WholeBlood_CRC305A7003102_Day7 [US22502595_254890810088_S01_GE1_1105_Oct12_1_3]


title: Con-Ot2


title: Breasttumour_PatientX188_Timepoint4


title: WholeBlood_CRC305A7003102_Day4 [US22502595_254890810088_S01_GE1_1105_Oct12_1_1]


title: Breasttumour_PatientX147_Timepoint2


title: WholeBlood_CRC305A7003102_Day0 [US22502595_254890810087_S01_GE1_1105_Oct12_2_1]


title: Con-Ot6


title: WholeBlood_CRC305A7003102_Day2 [US22502595_254890810087_S01_GE1_1105_Oct12_2_3]


title: Con-Ot1


title: WholeBlood_CRC305A7003102_Day3 [US22502595_254890810087_S01_GE1_1105_Oct12_2_4]


title: WholeBlood_CRC305A7002101_Day28 [US22502595_254890810087_S01_GE1_1105_Oct12_1_3]

value: white


title: WholeBlood_CRC305A7003102_Day-1 [US22502595_254890810087_S01_GE1_1105_Oct12_1_4]


title: CVW-5000LUX#6

city: Guangzhou

first: Ma

last: Huan

state: Guangdong

address: 132 East Waihuan Rd, Rm 438 Higher Education Mega

country: China

institute: Sun Yat-Sen University

library_source: transcriptomic

data_processing:
Illumina CASAVA 1.8 software used for basecalling.
Qualified reads were obtained after removing raw reads with adapters or of low quality and then aligned to the Neurospora crassa genome by HISAT with default parameters.
RSeQC was used to measured gene expression abundance as reads per kilobase per million mapped reads (RPKM).
Differential expression analysis of two samples was performed using the previous statistics model. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate and adjusted P-value <0.05 were assigned as differentially expressed gene.
Genome_build: Neurospora crassa OR74A
Supplementary_files_format_and_content: text file with RPKM values

molecule: polyA RNA

organism: Neurospora crassa

source_name: △cry,△vvd,△wc-1 strain_5000lux_2

growth_protocol: Strains were grown in minimal slants for two weeks and cultivated in 2% glucose media under different light intensity for 45min.

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and treated with DNase I.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The △cry,△vvd,△wc-1 strain was cultured under dark, 1000lux and 5000lux light intensity.

value: hyphae

tag: light intensity


title: WholeBlood_CRC305A7002101_Day21 [US22502595_254890810087_S01_GE1_1105_Oct12_1_2]

tag: participant

value: VARILRIX


title: Breasttumour_PatientX139_Timepoint4


title: Breasttumour_PatientX181_Timepoint4


title: CVW-5000LUX#5

source_name: △cry,△vvd,△wc-1 strain_5000lux_1


title: WholeBlood_CRC305A7003102_Day1 [US22502595_254890810087_S01_GE1_1105_Oct12_2_2]


title: Con-On

tag: cell line

value: Cas9 Non-treated


title: CVW-1000LUX#12

source_name: △cry,△vvd,△wc-1 strain_1000lux_2


title: Breasttumour_PatientX181_Timepoint1


title: Breasttumour_PatientX120_Timepoint4


title: Breasttumour_PatientX147_Timepoint4


title: CVW-1000LUX#10

source_name: △cry,△vvd,△wc-1 strain_1000lux_1


title: CVW-DD#1

source_name: △cry,△vvd,△wc-1 strain_dark_1

value: dark


title: Breasttumour_PatientX120_Timepoint2


title: CVW-DD#2

source_name: △cry,△vvd,△wc-1 strain_dark_2


title: Breasttumour_PatientX139_Timepoint1


title: WholeBlood_CRC305A7002101_Day7 [US22502595_254890810086_S01_GE1_1105_Oct12_2_4]

source_name: Peripheral Blood, PaxGene


title: TI: △tnaA EHEC with 500µM indole

city: Dallas

first: Aman

last: Kumar

state: Texas

address: 5323 Harry Hines Blvd.

department: Microbiology

country: USA

institute: UT Southwestern Medical Center

data_processing:
Our 12 bacteria RNA libraries were prepared using Illumina’s ScriptSeq Complete Kit (Bacteria) catlog # BB1224.
Sequencing run: Our 12 RNA libraries were run on illumine HiSeq 2500 sequencer with SE-50.
Raw data was processed using DNAStar Lasergene software as per the instructions provided on the DNAStar website
Genome_build: sakai genome downloaded from ncbi was used as a reference genome (NC_002695.1)
Supplementary_files_format_and_content: tab delimited text file includes the RKPM values for all samples under the conditions tested above.
Supplementary_files_format_and_content: .astar files can be accessed using DNAStar Lasergene software

organism: Escherichia coli O157:H7

source_name: EHEC

growth_protocol: WT and △tnaA EHEC strains were grown in low gluocse DMEM  until late log phase with either methanol or 500µM indole in three biological replicates. Samples were checked for similar O.D and then samples were harvested by centrfugation. The RNA was extracted from the pellet fraction using Ribopure RNA extraction kit (Ambion).

extract_protocol:
RNA was extracted using Ribopure RNA extraction kit (Ambion)
12 bacteria RNA libraries were prepared using Illumina’s ScriptSeq Complete Kit (Bacteria) catlog # BB1224.

treatment_protocol: 500µM of indole or only methanol in a dilution ratio of 1:1000 was added to the low gluocse DMEM before starting the experiment

value: tnaA deletion muant

value: indole


title: WI: WT EHEC with 500µM indole

value: WT


title: WholeBlood_CRC305A7002101_Day14 [US22502595_254890810087_S01_GE1_1105_Oct12_1_1]


title: Breasttumour_PatientX120_Timepoint1

source_name: breast tumour


title: WholeBlood_CRC305A7002101_Day5 [US22502595_254890810086_S01_GE1_1105_Oct12_2_3]


title: WM: WT EHEC

value: methanol


title: TM: △tnaA EHEC


title: Breasttumour_PatientX109_Timepoint1


title: Maternal plasma

city: Wenzhou

first: Ziyang

last: Li

state: Zhejiang Province

address: University-town, Chashan

institute: Wenzhou Medical University

description: cell-free DNA

data_processing:
Library strategy: DNA-Seq
Basecalls performed using bcl2fastq software
Reads were aligned to the human reference genome GRCh37 using BWA version 0.7.10
The aligned paired-end data was stored in BAM format using the SAMtools
We selected non-duplicated mapped reads with 167 bp length from BAM files, separately extended with 100 bp upstream and downstream to the aligned region, and extracted the sequences of each extended region using bedtools v2.20.1. Both the number of A/T (including AA/AT/TA/TT) and C/G (including CC/CG/GC/GG) dinucleotides were counted in these regions and the fraction of A/T and C/G were calculated using a sliding 2 bp window and reference alleles at each position.
Fragment endpoint coordinates were extracted from BAM files and non-duplicated mapped reads within 120-180 bp were selected using bedtools v2.20.1. A fragment’s coverage is defined as all positions between the two ends. Reads spanning the window were defined as the reads covering the whole genomic window, while non-spanning reads with an endpoint within the window as the reads partially covering the genomic window.
The nucleosome protection peaks were identified based on genome-wide windowed protection score (WPS) distribution. Regions started from the position with above-zero WPS and allowing up to three consecutive positions with below-zero WPS were considered as candidates for nucleosome protection peaks. If the median WPS value of a candidate was equal to or larger than 1, it was regarded as a nucleosome protection peak, and its start, end and centre coordinates were reported.
Genome_build: human NCBI genome build 37
Supplementary_files_format_and_content: Tar archives include the following files:
WPS score of neighbouring bins overlalpping with TSS (*WPS_overlapped_TSS.tsv)
Nucleosome Protection length of all chromosome (*chrAll.NP.tsv)
WPS score of all chromosome bins (*hrAll.WPS.tsv)
Di-nucleotide frequency of all chromosome bins (*diNucleotideFreq.tsv)
Frequency table of fregment insert size (*fragLengthDist.tsv)
Median WPS score of each distance group relatitve to TSS (*median_WPS_of_TSS.tsv)

source_name: plasma

extract_protocol:
The cfDNA was purified from a DENQCMs sample and a clinical plasma sample respectively with the Cell-Free DNA Extraction Kit (Annoroad) as per the manufacturer’s protocol.
Libraries were prepared with Detection Kit for Noninvasive Fetal Trisomy (Annoroad) according to the manufacturer’s recommendations. Samples were individually indexed during library preparation. The pooled libraries were sequenced using a 150-bp paired-end (PE) run on the Illumina NovaSeq platform following the manufacturer's protocols.

value: plasma


title: DENQCMs

description: cell-free DNA

source_name: human cell lines

value: B-Lymphocyte cell line


title: Breasttumour_PatientX109_Timepoint4


title: Breasttumour_PatientX109_Timepoint2


title: WholeBlood_CRC305A7002101_Day4 [US22502595_254890810086_S01_GE1_1105_Oct12_2_2]


title: striatum Helios -/- 9

status: Public on Jan 04 2019

city: Barcelona

first: Albert

last: Giralt

state: Barcelona

address: C/ Casanova 143

country: Spain

institute: Universitat de Barcelona

data_processing:
Library preparation was done using the TruSeq mRNA Stranded library prep kit from Illumina following the manufacturer's instructions. Libraries were quality tested using the Bioanalyzer system from Agilent and semi-quantitative PCR. Sequencing was done using the NextSeq500 from Illumina, generating 75 bp single reads (NextSeq 500 High Output Kit 75 cycles).
The data were demultiplexed using the distribution of CASAVA software (CASAVA-1.8.2 bcl2fastq2 v2.15.0). The quality of the data was checked with the software FastQC 0.11. Illumina adapters was removed using Cutadapt-1.3, keeping only reads with a minimal length of 10 nucleotides.
After Cutadapt step, the data were mapped using bwa-0.7.4 on reference genome mouse mm10. The bam output files were sorted with samtools. The counting of number reads in each exon has been done with HTSeq-count and DESeq2 for the differential analysis.
FINALLY, raw data file was obtained by using the package RSubread by summaryzing reads number  with the function: featureCounts

source_name: brain

value: striatum

value: Helios -/-


title: striatum Helios -/- 10

extract_protocol: Library preparation was done using the TruSeq mRNA Stranded library prep kit from Illumina following the manufacturer's instructions. Libraries were quality tested using the Bioanalyzer system from Agilent and semi-quantitative PCR. Sequencing was done using the NextSeq500 from Illumina, generating 75 bp single reads (NextSeq 500 High Output Kit 75 cycles).


title: striatum wild type 3

value: wild type


title: hippocampus Helios -/- 10


title: striatum Helios -/- 7


title: striatum wild type 5


title: striatum wild type 4


title: striatum Helios -/- 6


title: striatum Helios -/- 8


title: striatum wild type 1


title: hippocampus Helios -/- 5

value: hippocampus


title: hippocampus Helios -/- 8


title: hippocampus Helios -/- 7


title: hippocampus Helios -/- 9


title: hippocampus wild type 6


title: WholeBlood_CRC305A7002101_Day-1 [US22502595_254890810086_S01_GE1_1105_Oct12_1_1]

value: male

value: not hispanic or latino

value: whole blood


title: WholeBlood_CRC305A7002101_Day1 [US22502595_254890810086_S01_GE1_1105_Oct12_1_3]

value: white


title: hippocampus wild type 4


title: hippocampus wild type 3


title: hippocampus wild type 1


title: hippocampus wild type 2


title: WholeBlood_CRC305A7002101_Day0 [US22502595_254890810086_S01_GE1_1105_Oct12_1_2]

value: VARILRIX


title: WholeBlood_CRC305A7002101_Day3 [US22502595_254890810086_S01_GE1_1105_Oct12_2_1]


title: Bisulfite sequencing of whole suvh1/3/7/8 genome

city: Shanghai

first: Mingguang

last: Lei

address: No. 3888, Chenhua Road

institute: Shanghai Center for Plant Stress Biology

data_processing:
Basecalls performed using CASAVA version 1.4.
Low quality sequences were trimmed using trim in BRAT-BW.
Reads were mapped to the TAIR10 genome using BRAT-BW and allowing two mismatches.
Genome_build: TAIR10
Supplementary_files_format_and_content: bedGraph files with data values.

organism: Arabidopsis thaliana

growth_protocol: Growth at 22 °C with 100 μmol·m-2·s-1 for 12 days.

extract_protocol:
Genomic DNA extraction kit.
The libraries were prepared for sequencing using standard protocols.

treatment_protocol: 1/2 MS with 1% sucrose and 1% agar.

tag: ecotype/background

tag: genotype/variation

value: 12 days

value: seedling


title: Bisulfite sequencing of whole ros1-4 genome


title: Bisulfite sequencing of whole Col-0 genome


title: H1_THZ531_1

city: Houston

first: Charles

middle: Yang

last: Lin

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

description:
genes.fpkm_table
H1_531_0

data_processing:
Fastq files were aligned to the HG19 genome using HiSat2 (version 2.0.4) with default parameters.
Transcripts were quantified and FPKM values were generated using cuffquant and cuffnorm from the cufflinks suite (version 2.2.1) (http://cole-trapnell-lab.github.io/cufflinks/) on the HG19 RefSeq transcriptome.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text file of raw fpkm expression values

source_name: Chronic Myelogenous Leukemia

growth_protocol:
All Hap1 cell lines were cultured in IMDM media containing 10% fetal bovine serum (FBS, GIBCO, Life technologies, Carlsbad, CA, United States), 100 U/mL penicillin, and 100 mg/mL streptomycin (GIBCO, Life technologies, Carlsbad, CA, United States).
Hap1 cell lines were cultured in IMDM media containing 10% fetal bovine serum (FBS, GIBCO, Life technologies, Carlsbad, CA, United States), 100 U/mL penicillin, and 100 mg/mL streptomycin (GIBCO, Life technologies, Carlsbad, CA, United States).

extract_protocol:
Cells were harvested by resuspension in RLT buffer with beta-mercaptoethanol and RNA was harvested using Rneasy Plus mini kit (Qiagen, Strausse 1, 40742 Hilden, Germany) and eluted in 30uL of water.
Total RNA was subject to polyA selection and adapter ligation in preparation for next-generation sequencing (Illumina stranded mRNA library prep)

treatment_protocol: Cells were treated for 24 hours before sample collection. See above for individual sample treatments

value: Chronic Myelogenous Leukemia

value: HAP1 CDK7 C312S

tag: treatment

tag: time

value: 24 hours


title: H1_YKL_500_1

description:
genes.fpkm_table
H1_5-124_500_0


title: H1_THZ1_2

description:
genes.fpkm_table
H1_THZ1_1


title: A2_YKL_500_2

description:
genes.fpkm_table
A2_5-124_500_1

value: HAP1 WT


title: H1_Combo_2_2

description:
genes.fpkm_table
H1_531_5-124_2_1


title: H1_YKL_2_2

description:
genes.fpkm_table
H1_5-124_2_1


title: H1_Combo_2_3

description:
genes.fpkm_table
H1_531_5-124_2_2


title: H1_DMSO_3

description:
genes.fpkm_table
H1_DMSO_2

value: DMSO


title: H1_DMSO_2

description:
genes.fpkm_table
H1_DMSO_1


title: H1_YKL_500_3

description:
genes.fpkm_table
H1_5-124_500_2


title: H1_YKL_2_1

description:
genes.fpkm_table
H1_5-124_2_0


title: H1_THZ1_3

description:
genes.fpkm_table
H1_THZ1_2


title: H1_Combo_500_1

description:
genes.fpkm_table
H1_531_5-124_500_0


title: H1_YKL_2_3

description:
genes.fpkm_table
H1_5-124_2_2


title: H1_THZ1_1

description:
genes.fpkm_table
H1_THZ1_0


title: H1_Combo_500_2

description:
genes.fpkm_table
H1_531_5-124_500_1


title: H1_Combo_500_3

description:
genes.fpkm_table
H1_531_5-124_500_2


title: H1_DMSO_1

description:
genes.fpkm_table
H1_DMSO_0


title: H1_YKL_500_2

description:
genes.fpkm_table
H1_5-124_500_1


title: H1_Combo_2_1

description:
genes.fpkm_table
H1_531_5-124_2_0


title: A2_YKL_500_3

description:
genes.fpkm_table
A2_5-124_500_2


title: H1_THZ531_2

description:
genes.fpkm_table
H1_531_1


title: A2_YKL_500_1

description:
genes.fpkm_table
A2_5-124_500_0


title: A2_YKL_2_2

description:
genes.fpkm_table
A2_5-124_2_1


title: H1_THZ531_3

description:
genes.fpkm_table
H1_531_2


title: A2_YKL_2_1

description:
genes.fpkm_table
A2_5-124_2_0


title: A2_THZ1_1

description:
genes.fpkm_table
A2_THZ1_0


title: A2_DMSO_3

description:
genes.fpkm_table
A2_DMSO_2


title: A2_Combo_500_3

description:
genes.fpkm_table
A2_531_5-124_500_2


title: A2_THZ1_2

description:
genes.fpkm_table
A2_THZ1_1


title: A2_THZ1_3

description:
genes.fpkm_table
A2_THZ1_2


title: A2_DMSO_2

description:
genes.fpkm_table
A2_DMSO_1


title: A2_DMSO_1

description:
genes.fpkm_table
A2_DMSO_0


title: A2_THZ531_3

description:
genes.fpkm_table
A2_531_2


title: A2_Combo_500_2

description:
genes.fpkm_table
A2_531_5-124_500_1


title: A2_Combo_2_3

description:
genes.fpkm_table
A2_531_5-124_2_2


title: A2_Combo_2_1

description:
genes.fpkm_table
A2_531_5-124_2_0


title: A2_THZ531_1

description:
genes.fpkm_table
A2_531_0


title: A2_YKL_2_3

description:
genes.fpkm_table
A2_5-124_2_2


title: A2_THZ531_2

description:
genes.fpkm_table
A2_531_1


title: A2_Combo_2_2

description:
genes.fpkm_table
A2_531_5-124_2_1


title: A2_Combo_500_1

description:
genes.fpkm_table
A2_531_5-124_500_0


title: Whole PBMC, Control 3

city: Budapest

first: Nikolett

last: Lupsa

state: Pest

address: Nagyvárad tér 4

department: Genetics, Cell-and Immunbiology

country: Hungary

institute: Semmelweis University

hyb_protocol: Amplified samples were hybridized to 4x44k mouse whole genome microarrays using the Gene Expression Hybridization Kit (Agilent)

scan_protocol: Samples were scanned on an Agilent Microarray Scanner using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent). Raw data were quantile normalized and further analyzed by Partek GS (Partek). To identify T-cell transcripts, whole organs were also processed in parallel, and used to identify mRNAs enriched in respective T cell samples (ANOVA with FDR Correction, p<0.005, >2 fold change). To assess organ-specific differences in T cell gene expression profiles, these 6411 transcripts were subjected to multidimensional scaling (MDS), ANOVA or t-tests, as appropriate (with FDR Correction, p<0.05), to identify differentially expressed genes (DEGs).

source_name: Whole PBMC_Control

label_protocol: Three hundred pg of total RNA, with an RNA integrity number >8.0 per sample was reverse transcribed, amplified in two rounds, and Cy3 labeled by the Arcturus RiboAmp HS PLUS, Cy3 Kit (Life Technologies) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from MACS-separated T cells using the RNeasy Plus Micro Kit (Qiagen) following the manufacturer's recommendations. RNA yield was measured and integrity checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Healthy wild type C57BL/6 female mice were sacrificed to obtain the small intestine, lungs, liver and peripheral blood (as reference). Organs were disintegrated on a Gentle MACS Octo Dissociator using the Mouse Lamina Propria Dissociation, Mouse Lung Dissociation, and Mouse Tumor Dissociation kits, respectively (all from Miltenyi Biotec), according to the manufacturer’s instructions. Crude lysates were subjected to 40%/80% Percoll gradient centrifugation (Sigma Aldrich). Then, CD8b+ CD103+ Trm cells were isolated using Miltenyi’s AutoMACS Pro magnetic sorter and Multisort MACS kits, performing two subsequent rounds of positive selection. First, cells were labeled with anti-CD8b-biotin (eBioscience) and anti-CD103-PE (BD Biosciences) antibodies. Next, CD8b+ T cells were positively selected with Anti-Biotin Multisort Microbeads (Miltenyi Biotec). Microbeads were released, the cells incubated with Anti-PE Microbeads (Miltenyi Biotec), and subjected to a second round of positive selection to retrieve the CD103+ subset. As a reference, peripheral blood-derived, non-naïve CD8b+ CD62L- T cells were also isolated from the same animals by CD8b+ T cell separation and subsequent depletion of CD62L+ cells with anti-mouse CD62L microbeads (Miltenyi Biotec). As an additional control, whole organ samples were used (n=3), which were not isolated after organ disintegration.

tag: strain  background

value: female

value: 8-16 weeks

tag: tissue

value: peripheral blood


title: Whole Sm. Intestine, Control 1

source_name: Whole Sm. Intestine_Control

value: wild type

tag: age

value: small intestine


title: Whole Sm. Intestine, Control 3

tag: gender


title: Whole liver, Control 3

source_name: Whole liver_Control

value: Liver


title: Whole Sm. Intestine, Control 2


title: Whole PBMC, Control 1


title: Whole lung, Control 2

source_name: Whole lung_Control

value: Lung


title: CD8+ Trm, sm. intestine 1

source_name: CD8+ Trm_sm. intestine

tag: cell type

value: CD8+ T resident memory (Trm) cells


title: Whole liver, Control 1


title: WholeBlood_CRC305A7002101_Day2 [US22502595_254890810086_S01_GE1_1105_Oct12_1_4]

value: male

tag: race

value: white

tag: ethnicity

value: not hispanic or latino

value: whole blood


title: CD8+ Tem, p. blood 6

source_name: CD8+ Tem_p. blood

value: CD8+ T effector memory (Tem) cell


title: CD8+ Trm, lung 6

source_name: CD8+ Trm_lung


title: CD8+ Tem, p. blood 5


title: CD8+ Trm, sm. intestine 3


title: Whole lung, Control 1


title: CD8+ Trm, sm. intestine 6


title: CD8+ Trm, lung 5


title: CD8+ Trm, sm. intestine 5


title: CD8+ Tem, p. blood 1


title: CD8+ Tem, p. blood 4


title: CD8+ Tem, p. blood 2


title: Whole PBMC, Control 2


title: CD8+ Trm, sm. intestine 4


title: Whole lung, Control 3


title: CD8+ Trm, lung 4


title: Whole liver, Control 2


title: CD8+ Tem, p. blood 3


title: CD8+ Trm, sm. intestine 2


title: striatum wild type 2

tag: strain

value: striatum

tag: genotype


title: CD8+ Trm, lung 3


title: CD8+ Trm, lung 2


title: CD8+ Trm, liver 3

source_name: CD8+ Trm_liver


title: CD8+ Trm, lung 1


title: CD8+ Trm, liver 6


title: CD8+ Trm, liver 1


title: CD8+ T eff, Lung 2

scan_protocol: Samples were scanned on an Agilent Microarray Scanner using one color scan setting for 4x44k array slides

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent). Raw data were quantile normalized and further analyzed by Partek GS (Partek).

source_name: CD8+ Teff_Lung

label_protocol: Two rounds of linear RNA amplificaton were performed by the Arcturus RiboAmp HS PLUS, Cy3 Kit (Life Technologies) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: On the BMT+4 day transplanted recipients were sacrificed to obtain the small intestine, lungs, liver and peripheral blood. Grafted CD8+ T cells were labeled with anti-CD45.1 antibodies (Miltenyi Biotec), anti-Biotin Microbeads were added, and grafted CD45.1 CD8+ OT-I T cells were retrieved by positive selection using the AutoMACS Pro system (Miltenyi Biotec). Total RNA was extracted from MACS-separated T cells using the RNeasy Plus Micro Kit (Qiagen) following the manufacturer's recommendations. RNA yield was measured and integrity checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Lethal acute graft versus host disease (aGVHD) was induced in healthy m-act OVA C57Bl/6 female mice by allogeneic bone marrow transplantation (BMT). On the day of BMT (BMT 0) recipient m-act OVA mice (C57Bl/6-Tg(CAG-OVA)-916Jen/J) received 11Gy total body irradiation (TBI) in two split doses (5,5 Gy each), 3 hours apart, using a linear accelerator (1,07Gy/min). Irradiated animals were transplanted with 3x10^6 bone allogeneic marrow cells and 1.5x10^7 splenocytes via retroorbital injection, under ketamine-xylazine anesthesia from donor OT-I mice (C57BL/6-Tg(TcraTcrb) 1100Mjb/J). Graft OT-I CD8+ T cells were obtained from CD45.1 animals, while all other graft cells and recipients carried the CD45.2 allele. Four days after BMT (BMT+4) recipients were euthanized for sample retrieval.

tag: strain background

value: C57Bl/6 m-act OVA

value: CD8+ T effector (Teff) cells


title: CD8+ T eff, Sm. Intestine 4

source_name: CD8+ Teff_Sm. Intestine


title: CD8+ T eff, Lung 5


title: CD8+ T eff, Sm. Intestine 5


title: CD8+ Trm, liver 2


title: CD8+ T eff, Sm. Intestine 3


title: CD8+ T eff, P. blood 3

source_name: CD8+ Teff_P. blood


title: CD8+ T eff, Lung 1


title: CD8+ T eff, Sm. Intestine 1


title: CD8+ T eff, Liver 3

source_name: CD8+ Teff_Liver


title: CD8+ T eff, Lung 4


title: CD8+ T eff, Lung 3


title: Bisulfite sequencing of whole suvh1/3 genome

value: 12 days

value: seedling


title: CD8+ T eff, P. blood 4

value: female

value: 8-16 weeks


title: CD8+ T eff, Liver 2


title: CD8+ T eff, Sm. Intestine 2


title: CD8+ T eff, P. blood 1

value: peripheral blood


title: CD8+ T eff, Liver 4


title: CD8+ T eff, P. blood 5


title: CD8+ T eff, Liver 5


title: CD8+ T eff, P. blood 2


title: CD8+ Trm, liver 5

value: wild type


title: lamb heart Septum cortisol telemetry newborn replicate 5

city: Gainesville

first: Elaine

middle: Mary

last: Richards

state: FL

department: Pharmacodynamics

institute: University of Florida

description: Gene expression at birth in septum of heart of newborn lamb

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.6 pmol Cy3/µg cRNA) was fragmented and hybridized to Agilent Sheep Oligo Microarrays (G4813A) by the ICBR facility at the University of Florida according to Agilent's methodology.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2505B) using one color (green) scan setting for 8x15k array slides, by the ICBR facility at University of Florida.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.1.1.1 (Agilent) using default parameters (protocol GE1-v5_10 and Grid: 019921_D_F_20100112), and were background detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers and probes with low expression (less than 10% brighter than negative control probes) were excluded. Data were normalized using the quantile method and log transformed.These files are uploaded as the Telemetry LV matrix and the Telemetry Septum Matrix. The remaining probes were analyzed using a moderated t test that employs an empirical Bayes method for small sample size (P < 0.05). This was all performed using the Limma package in R software.

organism: Ovis aries

source_name: newborn heart

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

growth_protocol: Continuous infusions of 1mg/kg/day cortisol or vehicle to the ewe were begun at approximately day 115 of gestation and continued until birth

extract_protocol: RNA was extracted with Trizol (Life Technologies, Carlsbad, CA), and purified through Qiagen Rneasy+ kits with on-column DNase digestion (QIAGEN, Valencia, CA) according to manufacturers' protocols. Total RNA concentration was measured by Nanodrop ND-1000 and RNA quality was monitored by Agilent Bioanalyzer

treatment_protocol: Ewes were infused with 1mg/kg/day cortisol or vehicle from approximately day 115 of pregnancy (n=5/group) until birth. Lamb heart (septum and left ventricle) samples were collected at or just after birth.

tag: organ

value: newborn heart

value: Septum

value: cortisol


title: lamb heart Septum cortisol telemetry newborn replicate 4


title: CD8+ T eff, Liver 1

value: Liver


title: lamb heart Septum control telemetry newborn replicate 4

value: control


title: lamb heart Septum cortisol telemetry newborn replicate 3


title: lamb heart Septum control telemetry newborn replicate 5


title: lamb heart Septum cortisol telemetry newborn replicate 2


title: lamb heart Septum cortisol telemetry newborn replicate 1


title: lamb heart Left ventricle cortisol telemetry newborn replicate 3

description: Gene expression at birth in left ventricle of heart of newborn lamb

value: Left ventricle


title: lamb heart Left ventricle control telemetry newborn replicate 3


title: lamb heart Septum control telemetry newborn replicate 3


title: lamb heart Left ventricle cortisol telemetry newborn replicate 2


title: lamb heart Left ventricle cortisol telemetry newborn replicate 4


title: lamb heart Left ventricle control telemetry newborn replicate 4


title: lamb heart Septum control telemetry newborn replicate 1


title: lamb heart Left ventricle cortisol telemetry newborn replicate 1


title: lamb heart Septum control telemetry newborn replicate 2


title: lamb heart Left ventricle cortisol telemetry newborn replicate 5


title: lamb heart Left ventricle control telemetry newborn replicate 2


title: lamb heart Left ventricle control telemetry newborn replicate 5


title: lamb heart Left ventricle control telemetry newborn replicate 1


title: PBYAF2

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
PBYAF12_252828211750_4
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with autistic behavior_postnatally treated with ACTH P15_Replicate 2

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples from two rats were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) rat (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 10.7.3.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.
Normalized log2 ratio of the background subtracted signal of that feature and the median of the background subtracted signals of all valid features in the green or red channel of the array. A NULL indicates that the feature was not considered because is a control fetarure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal

organism: Rattus norvegicus

source_name: prenatally exposed to betamethasone_with autistic behavior_postnatally treated with ACTH P15_Replicate 2

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: Time-pregnant Sprague-Dawley rats were purchased from approved source (Taconic Farms, Germantown, NY). The rats were housed individually during the remainder of their pregnancy in the animal facility with free access to standard rat chow and water on the regular 12 hour light-dark cycle with the lights on at 07:00 am.

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE).

treatment_protocol: On G15, some pregnant rats received 2 injections of betamethasone (Sigma-Aldrich, St. Louis, MO) at 0.4 mg/kg each at 08:30 and 18:30. Delivery was consistent on G23, considered as postnatal day (P) 0 for the offspring. On P1, the offspring were identified and marked, and litters were culled down to four males and four females. The rats prenatally exposed (G15) to betamethasone had repeated adiministration of N-Methyl-D-Aspartic acid on postnatal days 12, 13 and 15 which triggered infantile spasms and autistic behavior. Pups were treated with ATCH on days 13, 14 and 15 prior to NMDA administration to determine what effects the treatment had on transcriptome recovery.

tag: Sex

value: Sprague-Dawley

value: hypothalamic arcuate nucleus

tag: developmental stage

tag: prenatal exposure

value: betamethasone

tag: condition

value: autistic behavior

tag: postnatal treatment

value: ACTH


title: PBYAM3

description:
PBYAM34_252828211747_3
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with autistic behavior_postnatally treated with ACTH P15_Replicate 3

source_name: prenatally exposed to betamethasone_with autistic behavior_postnatally treated with ACTH P15_Replicate 3

value: male


title: PBNSF2

description:
PBNSF12_252828211749_4
Gene expression in hypothalamic paraventricular nucleus of prenatally expossed to betamethasone_no infantile spasms_postnatally treated with saline P15_Replicate 2

source_name: prenatally exposed to betamethasone_no infantile spasms_postnatally treated with saline P15_Replicate 2

treatment_protocol: On G15, pregnant rats received 2 injections of betamethasone (Sigma-Aldrich, St. Louis, MO) at 0.4 mg/kg each at 08:30 and 18:30. Delivery was consistent on G23, considered as postnatal day (P) 0 for the offspring. On P1, the offspring were identified and marked, and litters were culled down to four males and four females. The rats prenatally exposed (G15) to betamethasone were treated with saline on days 13, 14 and 15 to determine what effects the prenatal bethamethasone had on the neurotransmission.

value: hypothalamic paraventricular nucleus

value: no spasms

value: saline


title: PBYAF3

description:
PSNSM1-PBYAF3_252828211742_4
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with autistic behavior_postnatally treated with ACTH P15_Replicate 3

value: female


title: PBYAF1

description:
PBYAF12_252828211750_4
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with autistic behavior_postnatally treated with ACTH P15_Replicate 1

source_name: prenatally exposed to betamethasone_with autistic behavior_postnatally treated with ACTH P15_Replicate 1


title: PBNSM3

description:
PBNSM34_252828211745_3
Gene expression in hypothalamic paraventricular nucleus of prenatally expossed to betamethasone_no infantile spasms_postnatally treated with saline P15_Replicate 3

source_name: prenatally exposed to betamethasone_no infantile spasms_postnatally treated with saline P15_Replicate 3


title: Oplr16 RAT-seq in iPSC

city: Palo Alto

first: Jifan

last: Hu

state: CA

address: 3801 Miranda Ave, Bldg 100, Room E4-200

department: Palo Alto Veterans Institute for Research

institute: Stanford University Medical School

description:
LncRNA Oplr16 genome-wide target sequencing data by RAT-Seq in iPSCs.
PSC Oplr16 RAT
NEBNext Index 18

data_processing:
Library strategy: RAT-Seq
The low quality reads were filtered using Fastx (version:0.0.13). Clean reads were mapped to the mouse genome (genome version: mm10) using the Bowtie (version:0.12.8) software with default parameters.
Enriched regions of the genome were identified by comparing the RAT-Seq peaks to input samples using MACS2 (version:2.1.1) and q-value of 0.05 was used as the initial cutoff threshold.
Differential binding analysis was performed with the DiffBind package using parameters of fold change difference ≥2 and p-value < 0.05, with false discovery rate (FDR) <0.1.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

source_name: iPS cells

growth_protocol: Fibroblasts were reprogrammed by Oct4-Sox2-Klf4-c-Myc defined factors. Fibroblasts and iPS cells were collected for the study.

extract_protocol:
iPS cells were treated with formaldehyde to fix the lncRNA-chromatin structure. RNAs were reverse transcribed in situ using lncRNA-specific complementary primers or random oligo primers containing biotin-dCTP. The lncRNA-interacting chromatin complex was pulled down with streptavidin beads and the target gene DNAs were eluted for library sequencing.
RAT-DNA libraries were prepared using Illumina's Kit (Part# 0801-0303).

value: Induced pluripotent stem cells

tag: project

value: Reprogramming


title: Oeblr20 RAT-seq in iPSC

description:
LncRNA Oeblr20 genome-wide target sequencing data by RAT-Seq in iPSCs.
PSC Oeblr20 RAT
NEBNext Index 4


title: PBNSM2

description:
PBNSM12_252828211745_4
Gene expression in hypothalamic paraventricular nucleus of prenatally expossed to betamethasone_no infantile spasms_postnatally treated with saline P15_Replicate 2


title: PBYAM1

description:
PBYAM12_252828211747_4
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with autistic behavior_postnatally treated with ACTH P15_Replicate 1


title: PBNSF3

description:
PBNSF34_252828211749_3
Gene expression in hypothalamic paraventricular nucleus of prenatally expossed to betamethasone_no infantile spasms_postnatally treated with saline P15_Replicate 3


title: PBYAM2

description:
PBYAM12_252828211747_4
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with autistic behavior_postnatally treated with ACTH P15_Replicate 2


title: PBYAF4

description:
PSNSM2-PBYAF4_252828211750_3
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with autistic behavior_postnatally treated with ACTH P15_Replicate 4

source_name: prenatally exposed to betamethasone_with autistic behavior_postnatally treated with ACTH P15_Replicate 4


title: PBNSF4

description:
PBNSF34_252828211749_3
Gene expression in hypothalamic paraventricular nucleus of prenatally expossed to betamethasone_no infantile spasms_postnatally treated with saline P15_Replicate 4

source_name: prenatally exposed to betamethasone_no infantile spasms_postnatally treated with saline P15_Replicate 4


title: PBNSM4

description:
PBNSM34_252828211745_3
Gene expression in hypothalamic paraventricular nucleus of prenatally expossed to betamethasone_no infantile spasms_postnatally treated with saline P15_Replicate 4


title: PBNSM1

description:
PBNSM12_252828211745_4
Gene expression in hypothalamic paraventricular nucleus of prenatally expossed to betamethasone_no infantile spasms_postnatally treated with saline P15_Replicate 1

source_name: prenatally exposed to betamethasone_no infantile spasms_postnatally treated with saline P15_Replicate 1


title: PBYAM4

description:
PBYAM34_252828211747_3
Gene expression in hypothalamic arcuate nucleus of prenatally expossed to betamethasone_with autistic behavior_postnatally treated with ACTH P15_Replicate 4


title: Peln1 RAT-seq in FIB

description:
LncRNA Peln1 genome-wide target sequencing data by RAT-Seq in fibroblasts.
FIB Peln1 RAT
NEBNext Index 11

source_name: Fibroblasts

value: Fibroblasts


title: PBNSF1

description:
PBNSF12_252828211749_4
Gene expression in hypothalamic paraventricular nucleus of prenatally expossed to betamethasone_no infantile spasms_postnatally treated with saline P15_Replicate 1


title: GL cells_RML_vs_PBS_dpi EP_rep2 NML_251486812100_RML_2_555_PBS_2_647_dpi_EP_GL_1_4

city: WInnipeg

first: Sarah

last: Medina

state: Manitoba

address: 1015 Arlington Street

department: One Health

institute: Public Health Agency of Canada

description: Biological replicate 2/2

hyb_protocol: Hybridization and washing was performed according to the Two-Color Microarray-Based Gene Expression Analysis protocol for a 4x44K microarray format (Agilent technologies) following manufacturer's instructions.

scan_protocol: Slides were scanned using the Agilent Microarray Scanner system with surescan technology (v.6.3) following the scan settings for a 4x44K microarray format according to manufacturer's instructions.

data_processing: The .TIFF images were uploaded into Feature Extraction (Agilent technologies, G2567AA FE software, v.10.5), the spots were identified, and the grids constructed using the GE2-v5_95_Feb07 and GE2_105_Dec08 protocol and the 014868_D_20060807 grid file for the whole mouse genome 4x44K expression arrays which were downloaded from the Agilent technologies website. Background calculations were performed by the feature extraction software using spatial and multiplicative detrending and normalization was performed using linear and lowess. The p-value to determine differential expression was 0.01 and the resulting log10 ratios from the feature extraction software were provided as the red (AlexaFlour 647)/green (AlexaFlour 555) channel.

label: AlexaFluor 555

source_name: GL cells RML

label_protocol: Production of aRNA from total RNA was accomplished using the MessageAmpII kit (Fisher Scientific) following manufacturer's instructions. Upon 2 rounds of amplification, each aRNA was split into two samples (for dye-swapping) and labeled each with AlexaFluor 555 carboxylic acid, succinimidyl ester dye (Invitrogen) or AlexaFluor 647 (Invitrogen).

growth_protocol: RML scrapie infection of CD1 mice was performed as described and mice were sacrificed at five time-points spanning very early to terminal disease [70, 90, 110, 130 and terminal 153-161 days post infection (DPI) (Majer et al., 2012).

extract_protocol: Total RNA extracted using the RNAqueous® Micro kit (Fisher Scientific) following manufacturer's instructions.

treatment_protocol: Similarly, IP BSE infection was performed in c57/BL6 mice between 4 and 6 weeks of age using 200 µl of a 1% brain homogenate prepared from a passage 1 of a Classical BSE case in c57/Bl/6 mice and an equal number of control animals. Animals were sacrificed in groups of 6 at intervals following inoculation [60, 140, 200, 300 days] and at a terminal time point delineated by the progress of clinical signs including, weight loss of 20% or more, kyphosis and ataxia, which occurred between 282-327 DPI.

value: GL

tag: dpi

value: EP

label: AlexaFluor 647

source_name: GL cells PBS


title: GL cells_RML_vs_PBS_dpi 130_rep1 NML_251486812101_RML_1_555_PBS_1_647_dpi_130_GL_1_2

description: Biological replicate 1/2


title: GL cells_RML_vs_PBS_dpi 110_rep1 NML_251486811933_PBS_1_555_RML_1_647_dpi_110_GL_1_1

description: Biological replicate 1/2


title: GL cells_RML_vs_PBS_dpi 110_rep2 NML_251486811933_RML_2_555_PBS_2_647_dpi_110_GL_1_4

description: Biological replicate 2/2


title: GL cells_RML_vs_PBS_dpi 110_rep2 NML_251486811933_PBS_2_555_RML_2_647_dpi_110_GL_1_3

description: Biological replicate 2/2


title: GL cells_RML_vs_PBS_dpi 90_rep2 NML_251486811932_RML_2_555_PBS_2_647_dpi_90_GL_1_4

description: Biological replicate 2/2


title: GL cells_RML_vs_PBS_dpi 110_rep1 NML_251486811933_RML_1_555_PBS_1_647_dpi_110_GL_1_2

description: Biological replicate 1/2


title: GL cells_RML_vs_PBS_dpi EP_rep1 NML_251486812100_PBS_1_555_RML_1_647_dpi_EP_GL_1_1

description: Biological replicate 1/2


title: GL cells_RML_vs_PBS_dpi 130_rep1 NML_251486812101_PBS_1_555_RML_1_647_dpi_130_GL_1_1

description: Biological replicate 1/2


title: GL cells_RML_vs_PBS_dpi EP_rep1 NML_251486812100_RML_1_555_PBS_1_647_dpi_EP_GL_1_2

description: Biological replicate 1/2


title: GL_cells_BSE_vs_PBS_dpi_EP_rep1 NML_251486817756_BSE_1_555_PBS_1_647_dpi_EP_GL_1_2

description: Biological replicate 1/2

source_name: GL cells BSE


title: GL_cells_BSE_vs_PBS_dpi_300_rep2 NML_251486817755_PBS_2_555_BSE_2_647_dpi_300_GL_1_3

description: Biological replicate 2/2


title: GL_cells_BSE_vs_PBS_dpi_EP_rep2 NML_251486817756_BSE_2_555_PBS_2_647_dpi_EP_GL_1_4

description: Biological replicate 2/2


title: GL_cells_BSE_vs_PBS_dpi_EP_rep2 NML_251486817756_PBS_2_555_BSE_2_647_dpi_EP_GL_1_3

description: Biological replicate 2/2


title: GL_cells_BSE_vs_PBS_dpi_EP_rep1 NML_251486817756_PBS_1_555_BSE_1_647_dpi_EP_GL_1_1

description: Biological replicate 1/2


title: GL cells_RML_vs_PBS_dpi 90_rep1 NML_251486811932_PBS_1_555_RML_1_647_dpi_90_GL_1_1

description: Biological replicate 1/2


title: GL cells_RML_vs_PBS_dpi EP_rep2 NML_251486812100_PBS_2_555_RML_2_647_dpi_EP_GL_1_3

description: Biological replicate 2/2


title: GL cells_RML_vs_PBS_dpi 70_rep2 NML_251486811764_RML_2_555_PBS_2_647_dpi_70_GL_1_4

description: Biological replicate 2/2


title: GL cells_RML_vs_PBS_dpi 90_rep2 NML_251486811932_PBS_2_555_RML_2_647_dpi_90_GL_1_3

description: Biological replicate 2/2


title: GL cells_RML_vs_PBS_dpi 70_rep1 NML_251486811764_PBS_1_555_RML_1_647_dpi_70_GL_1_1

description: Biological replicate 1/2


title: GL_cells_BSE_vs_PBS_dpi_300_rep1 NML_251486817755_PBS_1_555_BSE_1_647_dpi_300_GL_1_1

description: Biological replicate 1/2


title: GL_cells_BSE_vs_PBS_dpi_200_rep2 NML_251486817759_BSE_2_555_PBS_2_647_dpi_200_GL_1_4

description: Biological replicate 2/2


title: GL_cells_BSE_vs_PBS_dpi_300_rep2 NML_251486817755_BSE_2_555_PBS_2_647_dpi_300_GL_1_4

description: Biological replicate 2/2


title: GL_cells_BSE_vs_PBS_dpi_300_rep1 NML_251486817755_BSE_1_555_PBS_1_647_dpi_300_GL_1_2

description: Biological replicate 1/2


title: GL cells_RML_vs_PBS_dpi 90_rep1 NML_251486811932_RML_1_555_PBS_1_647_dpi_90_GL_1_2

description: Biological replicate 1/2


title: GL_cells_BSE_vs_PBS_dpi_60_rep2 NML_251486817758_BSE_2_555_PBS_2_647_dpi_60_GL_1_4

description: Biological replicate 2/2


title: CA1_cells_RML_vs_PBS_dpi_EP_rep2 NML_251486812086_RML_2_555_PBS_2_647_dpi_EP_ca1_1_4

description: Biological replicate 2/2

source_name: CA1 cells RML

source_name: CA1 cells PBS


title: GL_cells_BSE_vs_PBS_dpi_60_rep2 NML_251486817758_PBS_2_555_BSE_2_647_dpi_60_GL_1_3

description: Biological replicate 2/2


title: KO_Treg2

city: Frankfurt am Main

first: Nikita

middle: Aaron

last: Verheyden

state: Hessen

address: Sandhofstr. 2-4

country: Germany

institute: Institute for Molecular Medicine

description:
Sample8
18116XR-01-08V_S8_L001

data_processing:
For fwd reads: Adapters were removed using Flexbar with the following configurations : flexbar -r sample_fwd_in.fastq.gz -n 4 -t sample_fwd_out  -a adapter_sequences.fasta --min-read-length 15 --adapter-trim-end RIGHT -ao 5 –pre-trim-left 3  --zip-output GZ
For rev reads: Adapters were removed using Flexbar with the following configurations : flexbar -r sample_rev_in.fastq.gz -n 4 -t sample_rev_out  -a adapter_sequences.fasta --min-read-length 15 --adapter-trim-end LEFT -ao 5 –pre-trim-right 3  –zip-output GZ
bowtie2 rRNA reference genome was created as follows: bowtie2-build rRNA.fasta rRNA
rRNA was filtered out using Bowtie 2 with the following configurations: bowtie2 --very-sensitive -x rRNA -1 sample_fwd_in.fastq.gz -2 sample_rev_in.fastq.gz --un-conc-gz sample_out.fastq.gz --met-file sample_stats > /dev/null
STAR reference genome was created as follows: STAR --runMode genomeGenerate --genomeDir reference_genome_dir --genomeFastaFiles reference_genome.fa --runThreadN 4 --sjdbGTFfile Annotation.gtf --sjdbOverhang 100
Remaining fwd sequences were aligned to the gencode M19 reference genome with the following configurations: STAR   --runThreadN 4   --genomeDir reference_genome_dir   --readFilesIn sample_fwd_in.fastq.gz      --readFilesCommand zcat      --outFileNamePrefix Sample_out   --outFilterMultimapNmax 5   --alignEndsType EndToEnd
Files were transformed into .bam format: samtools view -bS sample_in.sam > sample_out.bam
.bam files were sorted: samtools sort -o sample_out.bam sample_in.bam
Reads were counted using HTSeq with the following specifications: htseq-count --format=bam --stranded=yes sample_in Annotation.gtf > sample_out.txt
DE analysis was performed in R using DESeq2
Genome_build: GENCODE Release M19 (GRCm38.p6)
Supplementary_files_format_and_content: Counts: Read counts of aligned sequences
Supplementary_files_format_and_content: diffexpr-resultsTREG-miRNAonly-beforeDESeq.csv: Results of DE-analysis using only micro RNA counts

growth_protocol: Mice were harvested at the age of 7 weeks

extract_protocol:
Thymi were extracted from mice, thymocytes isolated by size and sorted for Treg through FACS sorting
SMARTer smRNA-Seq Kit for Illumina

tag: genotype/variation

tag: tissue

value: Thymus

value: Treg cells


title: KO_Treg3

description:
Sample12
18116XR-01-12V_S12_L001


title: KO_Treg1

description:
Sample4
18116XR-01-04V_S4_L001


title: GL_cells_BSE_vs_PBS_dpi_60_rep1 NML_251486817758_PBS_1_555_BSE_1_647_dpi_60_GL_1_1

description: Biological replicate 1/2


title: GL cells_RML_vs_PBS_dpi 70_rep1 NML_251486811764_RML_1_555_PBS_1_647_dpi_70_GL_1_2

description: Biological replicate 1/2


title: CA1_cells_RML_vs_PBS_dpi_EP_rep1 NML_251486812086_PBS_1_555_RML_1_647_dpi_EP_ca1_1_1

description: Biological replicate 1/2


title: CA1_cells_RML_vs_PBS_dpi_EP_rep1 NML_251486812086_RML_1_555_PBS_1_647_dpi_EP_ca1_1_2

description: Biological replicate 1/2


title: CA1_cells_RML_vs_PBS_dpi_130_rep1 NML_251486812083_RML_1_555_PBS_1_647_dpi_130_ca1_1_2

description: Biological replicate 1/2


title: GL_cells_BSE_vs_PBS_dpi_60_rep1 NML_251486817758_BSE_1_555_PBS_1_647_dpi_60_GL_1_2

description: Biological replicate 1/2


title: CA1_cells_RML_vs_PBS_dpi_EP_rep2 NML_251486812086_PBS_2_555_RML_2_647_dpi_EP_ca1_1_3

description: Biological replicate 2/2


title: CA1_cells_RML_vs_PBS_dpi_130_rep2 NML_251486812083_RML_2_555_PBS_2_647_dpi_130_ca1_1_4

description: Biological replicate 2/2


title: CA1_cells_RML_vs_PBS_dpi_130_rep2 NML_251486812083_PBS_2_555_RML_2_647_dpi_130_ca1_1_3

description: Biological replicate 2/2


title: CA1_cells_RML_vs_PBS_dpi_130_rep1 NML_251486812083_PBS_1_555_RML_1_647_dpi_130_ca1_1_1

description: Biological replicate 1/2


title: GL_cells_BSE_vs_PBS_dpi_140_rep2 NML_251486817532_PBS_2_555_BSE_2_647_dpi_140_GL_1_3

description: Biological replicate 2/2


title: CA1_cells_RML_vs_PBS_dpi_110_rep1 NML_251486812143_RML_1_555_PBS_1_647_dpi_110_ca1_1_2

description: Biological replicate 1/2


title: CA1_cells_RML_vs_PBS_dpi_90_rep2 NML_251486812085_RML_2_555_PBS_2_647_dpi_90_ca1_1_4

description: Biological replicate 2/2


title: CA1_cells_RML_vs_PBS_dpi_90_rep1 NML_251486812085_PBS_1_555_RML_1_647_dpi_90_ca1_1_1

description: Biological replicate 1/2


title: CA1_cells_RML_vs_PBS_dpi_90_rep1 NML_251486812085_RML_1_555_PBS_1_647_dpi_90_ca1_1_2

description: Biological replicate 1/2


title: CA1_cells_RML_vs_PBS_dpi_90_rep2 NML_251486812085_PBS_2_555_RML_2_647_dpi_90_ca1_1_3

description: Biological replicate 2/2


title: CA1_cells_RML_vs_PBS_dpi_110_rep1 NML_251486812143_PBS_1_555_RML_1_647_dpi_110_ca1_1_1

description: Biological replicate 1/2


title: CA1_cells_RML_vs_PBS_dpi_110_rep2 NML_251486812143_PBS_2_555_RML_2_647_dpi_110_ca1_1_3

description: Biological replicate 2/2


title: GL_cells_BSE_vs_PBS_dpi_140_rep2 NML_251486817532_BSE_2_555_PBS_2_647_dpi_140_GL_1_4

description: Biological replicate 2/2


title: WT_Treg2

description:
Sample7
18116XR-01-07V_S7_L001

value: wild type


title: WT_Treg3

description:
Sample11
18116XR-01-11V_S11_L001


title: E14.5 GFP+ Lin-Ckit+Sca1+Cd150 fetal liver cells_ Rep 4

city: Santa Cruz

first: Camilla

last: Forsberg

state: California

address: 1156 High Street

department: Biomolecular engineering

institute: University of California, Santa Cruz

data_processing:
Paired-end Illumina reads were trimmed from the 3’ end of read1 and read2 to 75x75bp.
Bowtie2 v2.2.1 was used with the “--very-sensitive” parameter to filter reads against the repeatMasker library for the mouse genome.
Tophat v2.0.11 was used to map RNA-seq reads to mm9.
Tophat  alignments were converted to genomic position coverage with the bedtools command genomeCoverageBed -split.
Total gene coverage for a gene was converted to read counts by dividing the coverage by 150 since each paired-end 75x75 mapped read induces a total coverage of 150 across its genomic positions.
DESeq  was used to perform differential expression analysis
Genome_build: mm9
Supplementary_files_format_and_content: DESeq results for genes analyzed comparing the hsct replicates to the hscg replicates; normalized counts for both conditions.

source_name: e14.5 fetal liver, embryo, mTmG strain crossed to Flt3-Cre

growth_protocol: Flt3-cre mice were crossed to mTmG mice and embryos were isolated at E14.5

extract_protocol:
Total RNA was isolated from sorted  using trizol and following manufacturers instructions
RNA-seq libraries  were prepared using NEBNext® Ultra kit (New England Biolabs) following manufacturer instructions

treatment_protocol: FL cells were stained with fluorescent antibodies, and Tom+ or GFP+ fractions of lineage-cKit+ Sca1+ CD150+ fetal livers were isolated by flow cytometry

value: fetal liver

tag: age

value: hematopoietic progenitor

tag: fraction


title: CA1_cells_RML_vs_PBS_dpi_70_rep1 NML_251486812084_RML_1_555_PBS_1_647_dpi_70_ca1_1_2

description: Biological replicate 1/2

tag: cell type


title: CA1_cells_RML_vs_PBS_dpi_70_rep2 NML_251486812084_PBS_2_555_RML_2_647_dpi_70_ca1_1_3

description: Biological replicate 2/2


title: CA1_cells_RML_vs_PBS_dpi_70_rep1 NML_251486812084_PBS_1_555_RML_1_647_dpi_70_ca1_1_1

description: Biological replicate 1/2


title: E14.5 GFP+ Lin-Ckit+Sca1+Cd150 fetal liver cells_ Rep 2


title: E14.5 GFP+ Lin-Ckit+Sca1+Cd150 fetal liver cells_ Rep 3


title: E14.5 GFP+ Lin-Ckit+Sca1+Cd150 fetal liver cells_ Rep 1


title: E14.5 Tomato+ Lin-Ckit+Sca1+Cd150 fetal liver cells_ Rep 4


title: E14.5 Tomato+ Lin-Ckit+Sca1+Cd150 fetal liver cells_ Rep 3


title: WT_Treg1

description:
Sample3
18116XR-01-03V_S3_L001


title: E14.5 Tomato+ Lin-Ckit+Sca1+Cd150 fetal liver cells_ Rep 2


title: E14.5 Tomato+ Lin-Ckit+Sca1+Cd150 fetal liver cells_ Rep 1


title: CA1_cells_RML_vs_PBS_dpi_110_rep2 NML_251486812143_RML_2_555_PBS_2_647_dpi_110_ca1_1_4

description: Biological replicate 2/2


title: CA1_cells_BSE_vs_PBS_dpi_EP_rep2 NML_251486811759_PBS_2_555_BSE_2_647_dpi_EP_ca1_1_3

description: Biological replicate 2/2

source_name: CA1 cells BSE


title: CA1_cells_RML_vs_PBS_dpi_70_rep2 NML_251486812084_RML_2_555_PBS_2_647_dpi_70_ca1_1_4

description: Biological replicate 2/2


title: H16-107-PIM1

city: San Diego

first: Oscar

middle: E

last: Echeagaray

address: 5500 Campanile Drive

department: Biology

institute: San Diego State University

data_processing:
The raw data was processed with the HISAT2, Stringtie pipeline (10X Genomics; version 2.0). Reads were aligned to the Human reference genome GRCh38.24
Low abundance genes were filtered out (Transcripts with detected expression less than 1 FPKM). Altogether, expression of 9079 genes in 6 samples were kept for downstream analysis using Ballgown R Package (v2.12.0).
Sequenced reads were aligned to the Human reference genome GRCh38.24
GRCh38.24
Supplementary_files_format_and_content: comma separated values of digital expression matrix; rows are genes; columns are samples

source_name: human derived cardiac interstitial cells

extract_protocol:
Cell lines for individual isolates from three patients undergoing surgical implantation of a left ventricular assist device (LVAD) were used for characterizations. Cells were isolated and expanded as previously described (Monsanto, M. M. et al. Concurrent Isolation of 3 Distinct Cardiac Stem Cell Populations From a Single Human Heart Biopsy. Circ Res 121, 113-124, doi:10.1161/CIRCRESAHA.116.310494 (2017)) and each was subjected to lentiviral modification to express Pim-1 GFP in a bicistronic construct or GFP alone as a control cell line.
cDNA Libraries were prepared for mRNA-enriched sequencing using TruSeq Stranded mRNA kit (Illumina).

treatment_protocol: Lentiviral preparations were created as previously described (Mohsin, S. et al. Human cardiac progenitor cells engineered with Pim-I kinase enhance myocardial repair. J Am Coll Cardiol 60, 1278-1287, doi:10.1016/j.jacc.2012.04.047 (2012); Fischer, K. M. et al. Pim-1 kinase inhibits pathological injury by promoting cardioprotective signaling. J Mol Cell Cardiol 51, 554-558, doi:10.1016/j.yjmcc.2011.01.004 (2011)) with modifications as detailed in Supplemental Methods section. Early passage (4-5) ckitCIC were plated over night at density of 50,000 cells/well on a 6-well plate. The following day cells were washed with 1xPBS prior to adding 1mL of ckitCIC medium (Table1). Lentivirus infection was performed at a multiplicity of infection ratio of 3 particles per cell, with virus added per well (PIM1 L1701 titer 2.6 x 108 TU/mL ; GFP L1702 titer 1.8 x 108 TU/mL ) in 1mL of warm cell culture medium. The plate was intermediately shaken throughout the day. At the end of the day, another mL of warm cell culture medium was added. The next morning the virus removed, cells were washed with PBS and replenished with cell culture medium. 2 days after infection cells were divided into two T25 flasks. 2 days after the division, one of the flasks was continued for expansion and the other one was used for FACS and protein quantification.

value: cardiac interstitial cells

tag: enhancement

tag: patient


title: H16-107-GFP

value: GFP


title: CA1_cells_BSE_vs_PBS_dpi_EP_rep2 NML_251486811759_BSE_2_555_PBS_2_647_dpi_EP_ca1_1_4

description: Biological replicate 2/2


title: H15-096-PIM1


title: CA1_cells_BSE_vs_PBS_dpi_300_rep2 NML_251486811758_BSE_2_555_PBS_2_647_dpi_300_ca1_1_4

description: Biological replicate 2/2


title: H15-096-GFP


title: GL cells_RML_vs_PBS_dpi 70_rep2 NML_251486811764_PBS_2_555_RML_2_647_dpi_70_GL_1_3

description: Biological replicate 2/2


title: CA1_cells_BSE_vs_PBS_dpi_EP_rep1 NML_251486811759_PBS_1_555_BSE_1_647_dpi_EP_ca1_1_1

description: Biological replicate 1/2


title: CA1_cells_BSE_vs_PBS_dpi_EP_rep1 NML_251486811759_BSE_1_555_PBS_1_647_dpi_EP_ca1_1_2

description: Biological replicate 1/2


title: CA1_cells_BSE_vs_PBS_dpi_300_rep1 NML_251486811758_BSE_1_555_PBS_1_647_dpi_300_ca1_1_2

description: Biological replicate 1/2


title: CA1_cells_BSE_vs_PBS_dpi_300_rep1 NML_251486811758_PBS_1_555_BSE_1_647_dpi_300_ca1_1_1

description: Biological replicate 1/2


title: HTR-8/SVneo EGF 24 h - miRNAseq

city: New Delhi

first: Satish

middle: Kumar

last: Gupta

address: Aruna Asaf Ali Marg

country: India

institute: NAtional Institute of Immunology

data_processing:
CLC Genomics Workbench 6.5.1. software used for basecalling.
Sequenced reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequences, then mapped to Human mature miRNA (miRBase release 21) accounting for a maximum of two gaps or mismatches in each sequence.
Unpaired group comparisons, based on Transcript Per Million (TPM), were chosen as expression values for comparison.
Kal’s Z test statistical analyses, based on p value < 0.05, fold change ± 1.5 and read count > 10 were used to filter the differentially expressed miRNA.
Genome_build: Human mature miRNA (miRBase release 21)
Supplementary_files_format_and_content: tab-delimited text files which include read count, normalized count and p-value for each Sample.

source_name: HTR-8/SVneo cells

growth_protocol: HTR-8/SVneo cells were grown in 1:1 DMEM + HAM's supplemented with 10 % FBS.

extract_protocol:
total RNA was isolated using standard Trizol reagent. TruSeq Small RNA sample prep kit was used with 1µg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Preparation protocol

treatment_protocol: HTR-8/SVneo cells were starved for 4h in 1:1 DMEM + HAM's F12 plain medium and treated with 10 ng/ml EGF for 24 h. Control HTR-8/SVneo cells were kept in 1:1 DMEM + HAM's F12 plain medium for 24 h.

value: HTR-8/SVneo trophoblast cell line (SV40 T antigen immortalized)

value: trophoblast


title: HTR-8/SVneo untreated - miRNAseq


title: H13-067-PIM1


title: H13-067-GFP


title: CA1_cells_BSE_vs_PBS_dpi_200_rep2 NML_251486811757_BSE_2_555_PBS_2_647_dpi_200_ca1_1_4

description: Biological replicate 2/2


title: CA1_cells_BSE_vs_PBS_dpi_300_rep2 NML_251486811758_PBS_2_555_BSE_2_647_dpi_300_ca1_1_3

description: Biological replicate 2/2


title: CA1_cells_BSE_vs_PBS_dpi_200_rep1 NML_251486811757_BSE_1_555_PBS_1_647_dpi_200_ca1_1_2

description: Biological replicate 1/2


title: 95D-2

city: xian

first: yingxuan

last: tian

state: Xi'an, Shaanxi

address: Xiwu road No.36

institute: the Second Affiliated Hospital

description: LncRNA expression data from 95D cell lines

hyb_protocol: The two groups total RNA were analyzed using LincRNA microarray of the GeneSpring GX v12.0 chip (Human LncRNA Array v3.0, Arraystar).

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

data_processing:
1. Raw LncRNA data normalization and low intensity filtering: Raw signal intensities were normalized in quantile method by GeneSpring GX v12.0, and low intensity LncRNAs were filtered (LncRNAs that at least 3 out of 6 samples have flags in Present or Marginal were chosen for further analysis, these LncRNAs can be found from the LncRNA Expression Profiling Data.xls file).
2. Quality assessment of LncRNA data after filtering: Contains Box Plot and Scatter Plot for LncRNAs after filtering (This data can be found from the LncRNA Expression Profiling Data.xls file).

source_name: 95D cell line

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

growth_protocol: RPMI-1640 medium containing 10% fetal bovine serum (FBS) and 1% dual antibody (chloramphenicol and streptomycin) was used for cell culture at 37˚C and 5% CO2 in a saturated humidity incubator.

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

tag: cell line

value: lung cancer cell line

tag: metastasis

value: high


title: CA1_cells_BSE_vs_PBS_dpi_200_rep2 NML_251486811757_PBS_2_555_BSE_2_647_dpi_200_ca1_1_3

description: Biological replicate 2/2


title: CA1_cells_BSE_vs_PBS_dpi_200_rep1 NML_251486811757_PBS_1_555_BSE_1_647_dpi_200_ca1_1_1

description: Biological replicate 1/2


title: 95C-2

description: LncRNA expression data from 95C cell lines

source_name: 95C cell line

value: low


title: 95D-1


title: CA1_cells_BSE_vs_PBS_dpi_140_rep2 NML_251486811756_PBS_2_555_BSE_2_647_dpi_140_ca1_1_3

description: Biological replicate 2/2


title: CA1_cells_BSE_vs_PBS_dpi_140_rep1 NML_251486811756_PBS_1_555_BSE_1_647_dpi_140_ca1_1_1

description: Biological replicate 1/2


title: GL_cells_BSE_vs_PBS_dpi_200_rep2 NML_251486817759_PBS_2_555_BSE_2_647_dpi_200_GL_1_3

description: Biological replicate 2/2


title: CA1_cells_BSE_vs_PBS_dpi_60_rep2 NML_251486811755_BSE_2_555_PBS_2_647_dpi_60_ca1_1_4

description: Biological replicate 2/2


title: 95C-1


title: CA1_cells_BSE_vs_PBS_dpi_60_rep2 NML_251486811755_PBS_2_555_BSE_2_647_dpi_60_ca1_1_3

description: Biological replicate 2/2


title: CA1_cells_BSE_vs_PBS_dpi_140_rep2 NML_251486811756_BSE_2_555_PBS_2_647_dpi_140_ca1_1_4

description: Biological replicate 2/2


title: GL_cells_BSE_vs_PBS_dpi_200_rep1 NML_251486817759_BSE_1_555_PBS_1_647_dpi_200_GL_1_2

description: Biological replicate 1/2


title: CA1_cells_BSE_vs_PBS_dpi_140_rep1 NML_251486811756_BSE_1_555_PBS_1_647_dpi_140_ca1_1_2

description: Biological replicate 1/2


title: 480: RPTEC_Cana2

city: Innsbruck

first: Johannes

last: Leierer

address: Anichstr. 35

department: Internal Medicine IV - Nephrology

country: Austria

institute: Medical University Innsbruck

description: gene expression

hyb_protocol: Hybridization to oligonucleotide microarrays (Human GE 4x44K v2, G4845A) according to the manufacturer`s protocol

scan_protocol: Arrays were scanned at 5 µm using an Axon Gene Pix 4000B scanner (Molecular Devices, Sunnyvale, CA) and signal intensity data extracted using Agilent Feature Extraction software (v.9.5.3.1).

data_processing: Data preprocessing consisted of (i) excluding low abundance features (intensity values < 1.5 above background signals), (ii) quantil-quantil data normalization, and (iii) summarization of identical sequence spots.

source_name: RPTEC mRNA

label_protocol: Cyanine 3 (Cy3) labelled cRNA was generated with the LowInput QuickAmp Labeling Kit (5190-2305) for hybridization to oligonucleotide microarrays (Human GE 4x44K v2, G4845A).

growth_protocol: Human renal proximal tubular cells (HK2 and RPTEC/TERT1) were cultured in the respective medium. All cells were grown at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol: Total RNA was isolated with RNeasy Mini Kit (Qiagen, Valencia, CA, USA) according to the manufacturer`s protocol

treatment_protocol: After growth to confluency, cells were serum- and supplement starved for 24 hours. Thereafter, cells were treated with either Empagliflozine (500nM), Canagliflozine (500nM) or TGF-beta1 (10ng/ml) for 24 hours in the absence of serum and any other growth supplements. Unstimulated control cells were grown in serum- and supplement-free medium.

value: RPTEC

value: Human renal proximal tubule cell line


title: CA1_cells_BSE_vs_PBS_dpi_60_rep1 NML_251486811755_BSE_1_555_PBS_1_647_dpi_60_ca1_1_2

description: Biological replicate 1/2


title: synovial tissues_TP_rep3

city: Hangzhou

first: Weifeng

address: NO.318, chaowang road

institute: The second affiliated hospital of Zhejiang Chinese medical university

description: Gene expression in synovial tissues from an adjuvant arthritis (AA) rat model with and without triptolide treatment

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: synovial tissue,TP treatment,replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen; Thermo Fisher Scientific, Inc., Carlsbad, CA, USA); 50-100 mg tissue/ml TRIzol was used in the present study, and all procedures were performed according to the manufacturer's protocol. Quality control of the RNA samples was performed by a Nanodrop ND-1000 spectrophotometer measuring the absorbance of each sample at 260 nm.

treatment_protocol: AA model was established by injecting 0.1 ml Freund's complete adjuvant (i.p.) daily for 18 days and scored by arthritis index assessment. Triptolide (0.4 mg/kg) or an equivalent amount of saline was administered daily for 14 days.

value: synovial tissue

tag: gender

value: male

value: 8 weeks


title: H_20_261

city: New York

first: Zeguo

last: Sun

address: 1468 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

data_processing:
Illumina bcl2fastq version 2.19 were used for basecalling
Reads was aligned to hg38 by star 2.5.3a with default parameters
Read count was summarized with HTSeq 0.8.0
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

source_name: lung squamous cell carcinoma tumor samples

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels.  RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA).
RNA libraries were prepared according to instructions ofNEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA).

value: lung squamous cell carcinoma

tag: subgroup


title: synovial tissues_TP_rep2

source_name: synovial tissue,TP treatment,replicate 2


title: CA1_cells_BSE_vs_PBS_dpi_60_rep1 NML_251486811755_PBS_1_555_BSE_1_647_dpi_60_ca1_1_1

description: Biological replicate 1/2


title: H_19_277


title: GL_cells_BSE_vs_PBS_dpi_200_rep1 NML_251486817759_PBS_1_555_BSE_1_647_dpi_200_GL_1_1

description: Biological replicate 1/2

value: GL


title: H_18_198


title: 478: RPTEC_TGFB2

description: gene expression


title: H_17_56


title: 475: HK2_Empa2

description: gene expression

source_name: HK-2 mRNA


title: H_15_26


title: synovial tissues_AA_rep3

source_name: synovial tissue,AA model,replicate 3


title: synovial tissues_AA_rep2

source_name: synovial tissue,AA model,replicate 2


title: 477: RPTEC_ctrl2

description: gene expression


title: 479: RPTEC_Empa2

description: gene expression


title: H_14_203


title: H_13_39


title: 476: HK2_Cana2

description: gene expression


title: synovial tissues_AA_rep1

source_name: synovial tissue,AA model,replicate 1


title: H_16_67


title: H_12_152


title: synovial tissues_TP_rep1

source_name: synovial tissue,TP treatment,replicate 1


title: 474: HK2_TGFB2

description: gene expression


title: H_8_57


title: 473: HK2_ctrl2

description: gene expression


title: H_10_158


title: 472: RPTEC_Cana

description: gene expression


title: H_7_135


title: 471: RPTEC_Emp

description: gene expression


title: H_6_133


title: 470: RPTEC_TGFB

description: gene expression


title: H_5_238


title: H_4_280


title: 469: RPTEC_ctrl

description: gene expression


title: 468: HK2_Cana

description: gene expression


title: Pulmonary enteric adenocarcinoma biopsy 9

type: genomic

city: München

first: Philipp

last: Jurmeister

address: Thalkirchner Straße 36

department: Institute of Pathology

institute: Ludwig Maximilians University Hospital Munich

description: PEAD 9

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system with default settings

data_processing: Statistical analysis was performed using the minfi package running on RStudio version 1.1.444 based on the statistical language R version 3.4.2.

label: Cy5 and Cy3

source_name: Lung biopsy

label_protocol: Standard Illumina protocol

extract_protocol: Semi-automated DNA extraction from FFPE samples was performed according the manufacturer’s instructions (Maxwell RSC FFPE Plus DNA Purification Kit, Custom, AX4920, Promega, Madison, USA).

tag: primary site

value: Right upper lobe

tag: metastatic site


title: H_2_255


title: 465: HK2_ctrl

description: gene expression


title: 467: HK2_Empa

description: gene expression


title: 466: HK2_TGFB

description: gene expression


title: H_1_136


title: Pulmonary enteric adenocarcinoma biopsy 11

description: PEAD 11

value: Right middle lobe

value: Bone, Brain


title: H_3_188


title: Pulmonary enteric adenocarcinoma biopsy 7

description:
201876940067_R08C01
PEAD_7

value: Indeterminable

value: Bone, bilateral pulmonary


title: Pulmonary enteric adenocarcinoma biopsy 8

description:
202060330063_R07C01
PEAD_8

value: female

value: Left upper lobe

value: Contralateral lung, adrenal gland, left mandible


title: Pulmonary enteric adenocarcinoma biopsy 10

description: PEAD 10

value: Left lower lobe

value: Adrenal gland


title: Metastatic colorectal cancer resection 4

description:
202060330099_R01C01
MCC_4

source_name: Lung metastasis resection

value: Sigmoid


title: Metastatic colorectal cancer resection 3

description:
201465930047_R01C01
MCC_3

value: Rectum


title: NaCl stress vs. control Replicate 1

city: Gifu

first: Kazutaka

last: Kusunoki

state: Gifu

address: 1-1 Yanagido

department: Faculty of Applied Biological Sciences

country: Japan

institute: Gifu University

description: Biological replicate 1 of 3. 10 day-old seedlings of Col-4 were treated with hydroponic culture with or without NaCl at pH4.5 for 24 h, and the roots were harvested.

hyb_protocol: 0.825 micro g of Cy3- and Cy5-labelled cRNA (specific activity >10.0 pmol Cy3 or Cy5 per micro g cRNA) were fragmented with Gene Expression Hybridization Kit (5188-5242, Agilent) following the manufacturer's instructions. On completion of the fragmentation reaction, 55 micro litter of 2x GE hybridization buffer HI-PRM was added to the fragmentation mixture and hybridized to Agilent Arabidopsis 3 Oligo Microarray (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Scanned on the Agilent G2508B scanner

data_processing: Agilent Feature Extraction Software (v 9.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Col-4, NaCl 24 h

label_protocol: Cyanine-3 (Cy3) and Cyanine-5 (Cy5) labeled cRNA were prepared from 1 micro g of total RNA using the Two-Color Quick Amp Labeling kit (5190-0444, Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).

growth_protocol: Col-4 of Arabidopsis were grown hydroponically in the 2% modified MGRL solution  (0 µM AlCl3, pH 5.5, 2% MGRL containing 200 µM CaCl2)  for 10 days. All seedlings were kept under 12 h illuminations per day (30 µmol m–2 s–1) at 25°C .

extract_protocol: Total RNA was isolated by the method of Suzuki et al. (2004).

treatment_protocol: Root of the seedlings were exposed to toxic solutions containing 6 µM Al (pH5.0), 3 µM Cd, 1.3 µM Cu or 10 mM NaCl at pH 5.0 for 24 hrs at growth conditions.

tag: background

value: root

source_name: Col-4, control 24 h


title: NaCl stress vs. control Replicate 3

description: Biological replicate 3 of 3. 10 day-old seedlings of Col-4 were treated with hydroponic culture with or without NaCl at pH4.5 for 24 h, and the roots were harvested.


title: Pulmonary enteric adenocarcinoma resection 12

description: PEAD 12

source_name: Lung resection

value: male

value: Right lower lobe


title: Pulmonary enteric adenocarcinoma biopsy 6

description:
201869690097_R06C01
PEAD_6


title: HTR-8/SVneo EGF 24 h - mRNAseq

data_processing:
Basecalls performed using CASAVA version 1.4
RNA-seq reads were aligned to the hg38 genome assembly using Tophat 2.1.1
Tuxedo pipeline was used for transcripts identification and differential analysis
Genome_build: hg38

source_name: HTR-8/SVneo cells

growth_protocol: HTR-8/SVneo cells were grown in 1:1 DMEM + HAM's F12 supplemented with 10% FBS.

extract_protocol:
total RNA was isolated using standard Trizol reagent. TruSeq RNAsample prep kit was used with 1µg of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation v2 Guide, Part # 15026495 Rev. F

treatment_protocol: HTR-8/SVneo cells were serum starved for 4h in 1:1 DMEM + HAM's F12 plain medium and treated with 10 ng/ml EGF for 24 h. Control HTR-8/SVneo cells were kept in 1:1 DMEM + HAM's F12 plain medium for 24 h.

value: HTR-8/SVneo trophoblast cell line (SV40 T antigen immortalized)

value: trophoblast


title: Pulmonary enteric adenocarcinoma biopsy 13

description: PEAD 13

value: Right upper lobe

value: Brain


title: Taiyan8_24 h

city: Changsha

first: Xianwen

last: Zhang

state: Hunan

address: 1 Nongda Road Furong district

institute: Hunan Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.4
Filtering of adaptors and low-quality sequence with fastx_toolkit-0.0.13.2
Alignment with miRBase, ncRNA, piRNA and Rfam databases using CLC genomics_workbench 6.1
Prediction of novel miRNAs with sRNA Toolkit
Expression analysis with DEGseq R combined with perl
Supplementary_files_format_and_content: annonated and normalized abundance file

organism: Nicotiana tabacum

source_name: Leaf

growth_protocol: Both NC567 and Taiyan8 were cultured in plastic pots in a ventilated greenhouse. The seedlings with 6-8 leaves were moved into a growth chamber (Binder, Tuttlingen, Germany) and cultured at about 6  ℃ with humidity of 80% (16/8 h, light/dark).

extract_protocol:
The third leaf from the top from three plants were collected at 0 h (as control) and 24 h after cold treatment, washed carefully, and separately frozen in liquid nitrogen and stored at  80  ℃ prior to RNA extraction.
Approximately 5 µg of small RNA of each group was used for library preparation and sequencing. Small RNA sized at 18–30 nt was gel-purified. 59 and 39 Illumina RNA adapters were ligated to the small RNA molecules. The adapter-ligated small RNAs were then reversely transcribed and amplified for 15 cycles with PCR. Then 4 small RNA libraries were constructed and sequenced according to the Illumina HiSeq 2500 platform sequencing protocols.

tag: developmental stage

value: 5-6-leaf stage

value: the third leaf from the top

tag: time point

tag: stress

value: cold


title: Cu stress vs. control Replicate 2

description: Biological replicate 2 of 3. 10 day-old seedlings of Col-4 were treated with hydroponic culture with or without Cu at pH4.5 for 24 h, and the roots were harvested.

source_name: Col-4, Cu 24 h


title: Pulmonary enteric adenocarcinoma biopsy 14

description: PEAD 14

value: female


title: Metastatic colorectal cancer resection 1

description:
201465940044_R06C01
MCC_1


title: Cu stress vs. control Replicate 1

description: Biological replicate 1 of 3. 10 day-old seedlings of Col-4 were treated with hydroponic culture with or without Cu at pH4.5 for 24 h, and the roots were harvested.


title: Cd stress vs. control Replicate 2

description: Biological replicate 2 of 3. 10 day-old seedlings of Col-4 were treated with hydroponic culture with or without Cd at pH4.5 for 24 h, and the roots were harvested.

source_name: Col-4, Cd 24 h


title: NaCl stress vs. control Replicate 2

description: Biological replicate 2 of 3. 10 day-old seedlings of Col-4 were treated with hydroponic culture with or without NaCl at pH4.5 for 24 h, and the roots were harvested.


title: Cd stress vs. control Replicate 1

description: Biological replicate 1 of 3. 10 day-old seedlings of Col-4 were treated with hydroponic culture with or without Cd at pH4.5 for 24 h, and the roots were harvested.


title: MCF-7_DOX_60h_rep1

city: Quezon City

first: Jortan

middle: Oste

last: Tun

state: National Capital Region

address: Velasquez Street

department: Marine Science Institute

country: Philippines

institute: University of the Philippines

description: DOX 1

hyb_protocol: The aRNA was then fragmented and hybridized to Affymetrix PrimeView Human Expression Arrays for 16 hours at 45°C with rotation at 60 rpm. All the samples were processed using the same reagent kit.

scan_protocol: Arrays were then washed and stained using the FS450_0001 fluidics protocol and scanned using an Affymetrix 3000 7G scanner (S/N: 54716600).

data_processing:
The scanned images were inspected for hybridization efficiency. CEL files generated from AGCC (GeneChip Command Console Software) were also imported into Transcriptome Analysis Console (TAC 4.0) software for Data QC. RMA normalization were performed on the samples to generate the quality control (QC) metrics.
Q_probeset_summarize-Version = V916
affymetrix-algorithm-name =
rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0
affymetrix-array-type = PrimeView
program_name = q_probeset_summarize.exe

label_protocol: The RNA samples were processed according to the Affymetrix 3’ IVT PLUS protocol and Origen Lab’s SOP for 3’ IVT PLUS analysis. Briefly, 100 ng of total RNA was reverse transcribed to produce cDNA, which was subsequently used as a template to create biotin-labeled aRNA (amplified RNA).

growth_protocol: MCF-7 cells were maintained at 37°C, 5% CO2 in 10% MEM supplemented with 2 mM L-glutamine, 1X non-essential amino acids, 1 mM sodium pyruvate, 1.5 g/L sodium bicarbonate (Sigma-Aldrich®), 100 units of penicillin, and 100 μg/mL streptomycin, and 0.01 mg/mL recombinant human insulin (Sigma-Aldrich®). Culture media were renewed every 2-3 days, and cells were subcultured when 80-90% confluent. Only cells that have > 90% viability, passage number < 8, and in the log phase of growth were used for assays.

extract_protocol: MCF-7 cells were lysed using QIAshredder, followed by RNA extraction using QIAgen RNeasy mini kit and sent to Origen Labs Inc. (Singapore) within 24 h for microarray hybridization using Affymetrix PrimeView Human Expression Arrays.

treatment_protocol: MCF-7 cells were treated with near IC50 concentrations of RM (6.25 nM), DOX (313 nM) and its combination for 60 h. Individual drug treatments and vehicle control were prepared in duplicates, while the combination treatment was prepared in triplicates.

tag: treatment

value: IC50 concentrations of DOX (313 nM) for 60h


title: MCF-7_RM+DOX_60h_rep2

description: RM+DOX 2

value: IC50 concentrations of RM+DOX combination for 60h


title: Taiyan8_CK

treatment_protocol: 6  ℃ with humidity of 80% (16/8 h, light/dark).

tag: tissue

value: 0 h

value: control


title: HTR-8/SVneo untreated - mRNAseq