title: OSCC_L6_FFPE_LN_NonRecur

city: Ansan

first: Yoon Chan

last: Rah

address: 123 Jeokgeum-ro, Danwon-gu

department: Otorhinolaryngology

institute: Korea University

hyb_protocol: 300 ng of Cy3-labelled 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 Whole Genome 8X60k Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. The hybridized slides were washed in 2 X SSC, 0.1 % SDS for 2 min, 1 X SSC for 3 min, and then 0.2 X SSC for 2 min at room temperature. The slides were centrifuged at 3000 rpm for 20 sec to dry.

scan_protocol: Slides were scanned using an Agilent 2505C scanner using one color scan setting.

data_processing: Gene expression levels were calculated with Feature Extraction v.10.7.3.1TM (Agilent technologies, CA, USA). The normalized and log2-transformed intensity values were then analyzed using GeneSpring GX 12.1 TM software (Agilent technologies, CA, USA). // Data flagging: We defined Not detected when the detected feature of a probe was not above the backgroud level or was not positive and significant. And those were removed from the signal value data.

source_name: lymph node in the non-recurrent patient

label_protocol: Each total RNA sample (300ng) was labelled with Cyanine-3 (Cy3) 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 from FFPE samples using an RNeasy Mini Kit with DNase treatment (Qiagen, Valencia, CA, USA) according to the manufacturer's protocol. RNA integrity and purity were checked by agarose gel electrophoresis and analyzed on an Agilent Bioanalyzer 2100TM.

tag: subject status

value: stage IV oral squamous cell carcinoma patient

tag: gender

value: female

tag: recurrence status

value: Non-recur

value: Lymph node

value: FFPE


title: OSCC_T6_FFPE_T_NonRecur

status: Public on Sep 30 2019

type: RNA

country: South Korea

molecule: total RNA

organism: Homo sapiens

source_name: tumor in the non-recurrent patient

tag: tissue

value: Primary tumor

tag: sample type


title: OSCC_L7_FFPE_LN_NonRecur

value: male


title: Col-0_NaCl_Rep2

type: SRA

city: Cuernavaca

first: Veronica

last: Jimenez-Jacinto

state: Morelos

address: Av. Universidad 2001. Col. chamilpa

department: Unidad Universitaria de Secuenciación Masiva y Bioinformática

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

description:
ColMSvsColNaCl.txt
ColNaClvsago43NaCl.txt
ColNaClvsago42NaCl.txt

library_source: transcriptomic

data_processing:
Sequencing control software: HCSv2.2
Alignment: smalt VN:0.7.6, with deafult parameters
converse sam to bam: samtools view  0.1.19-96b5f2294a
MarkDuplicates: VN:1.114 picard.sam.MarkDuplicates. Parameters: REMOVE_DUPLICATES=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25
calculation of coverages: bamtools coverge bed
Analisys Differential Expresion: DESeq package R, NOISeq package R, EdgeR package R
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited text files include: col1: gene_id, col2: logFC; col3: logCPM; col4: Pvalue; col5: FDR; col6,col7,col8,col9: rawcounts for each Sample with replica; col10,col11,col12,col13: normalizated counts for each Sample and Replica; col14: DiffExp=100-FDR; col15: Regulation;  For each paired comparation.

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Germinating seeds

growth_protocol: Seeds were sown in MS media and germinated under 16/8 light/dark photoperiod at 21ºC and 100uE of light intensity

extract_protocol: RNA was extracted using the mini hot phenol method for plant seeds

treatment_protocol: MS 1X was used as control medium while for salinity we added 100 mM of NaCl to MS

tag: ecotype

tag: condition

value: Salinity


title: OSCC_T8_FFPE_T_Recur

source_name: tumor in the patient with postoperative recurrrence

value: Recur


title: E4.5-5.5_new_Plate1_G07 (scRNA-Seq)

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina Nextseq 500 platform using the default RTA analysis software.
RNA-seq libraries were aligned to the GRCm38 mouse genome build using HiSat270 (v2.1.0) using options --dta --sp 1000,1000 --no-mixed --no-discordant, yielding a mean of 611,000 aligned reads per cell.
Subsequently, gene expression counts were quantified from the mapped reads using featureCounts with the Ensembl gene annotation (version 87). Only protein-coding genes matching canonical chromosomes were considered. The read counts were log-transformed and size-factor adjusted.
Genome_build: GRCm38
Supplementary_files_format_and_content: A table of genes (rows) x cells (columns). The first column is the ensembl gene ID.  RNAseq quantitation file.

organism: Mus musculus

source_name: Early embryo

extract_protocol: Single-cells were sorted either manually (E4.5, E5.5) or using flow cytometry (E6.5, E7.5) into 96 well PCR plates containing 2.5μl of methylase reaction buffer (1 × M.CviPI Reaction buffer (NEB), 2 U M.CviPI (NEB), 160 μM S-adenosylmethionine (NEB), 1 U μl−1 RNasein (Promega), 0.1% IGEPAL (Sigma)). Samples were incubated for 15 minutes at 37°C to methylate accessible chromatin before the reaction was stopped with the addition of RLT plus buffer (Qiagen) and samples frozen down and stored at -80°C prior to processing. Poly-A RNA was captured on oligo-dT conjugated to magnetic beads and amplified cDNA was prepared according to the G&T-seq and Smartseq2 protocols. The lysate containing gDNA was purified on AMPureXP beads before bisulfite-seq libraries were prepared according to the scBS-seq protocol.

tag: strain

tag: developmental stage

value: single cell


title: Col-0_Control_Rep2

description:
ColMSvsColNaCl.txt
ColMSvsago43MS.txt
ColMSvsago42MS.txt

value: control


title: OSCC_T5_FFPE_T_NonRecur


title: OSCC_T7_FFPE_T_NonRecur


title: OSCC_L5_FFPE_LN_NonRecur


title: OSCC_L8_FFPE_LN_Recur

source_name: lymph node in the patient with postoperative recurrrence


title: Col-0_Control_Rep1


title: E4.5-5.5_new_Plate1_G03 (scRNA-Seq)


title: E4.5-5.5_new_Plate1_F03 (scRNA-Seq)


title: OSCC_L4_FFPE_LN_NonRecur


title: E4.5-5.5_new_Plate2_D12 (scRNA-Seq)


title: OSCC_T3_FFPE_T_Recur


title: E4.5-5.5_new_Plate1_E11 (scRNA-Seq)


title: OSCC_T2_FFPE_T_Recur


title: OSCC_L2_FFPE_LN_Recur


title: OSCC_T4_FFPE_T_NonRecur


title: E4.5-5.5_new_Plate1_E08 (scRNA-Seq)


title: E4.5-5.5_new_Plate1_E09 (scRNA-Seq)


title: E4.5-5.5_new_Plate1_E03 (scRNA-Seq)


title: E4.5-5.5_new_Plate1_E02 (scRNA-Seq)


title: E4.5-5.5_new_Plate1_C11 (scRNA-Seq)


title: E4.5-5.5_new_Plate1_E05 (scRNA-Seq)


title: E4.5-5.5_new_Plate1_C08 (scRNA-Seq)


title: E4.5-5.5_new_Plate1_D03 (scRNA-Seq)


title: E4.5-5.5_new_Plate1_D05 (scRNA-Seq)


title: E4.5-5.5_new_Plate1_D11 (scRNA-Seq)


title: CD34+ selected HSPCs from MDS-MSC 627 UT co-culture

city: Singapore

first: Zhiyong

last: Poon

address: 20 College Road

country: Singapore

institute: Singapore General Hospital

description: HSPC (HR627 UT)

data_processing:
Paired end raw data fastq files were imported into Partek Flow 7.0. The sequences were aligned to hg19 using STAR version 2.5.3a default parameters. Transcript abundance was determined using Partek E/M algorithm based on Ensembl Transcripts release 751. Raw read count were generated and normalized for sequence depth –RPM, a small offset of 0.0001 were added to each value to deal with 0s. Low expression genes are indistinguishable from noise, so genes with total raw counts less than or equal 10 were removed during quantification. After normalization, another filter was performed so that only genes with geometric average greater than or equal to 1 are used for the downstream analysis. Partek GSA were used to detect differential expressed genes between treated vs not treatment groups. The default setting for GSA is LIMMA2. p < 0.05 were considered significant.
Genome_build: hg19

source_name: co-culture with untreated mesenchymal stromal cells from patients with myelodyplastic syndrome

growth_protocol: For MSCs, the culture reagents used were: Dulbecco’s Modified Eagle’s Medium (DMEM) - low glucose (Gibco) supplemented with 10% fetal bovine serum (FBS) (Hyclone) and 50 U/ml penicillin and streptomycin (Gibco), subsequently referred to as D10 media. To derive MSCs, 2.0 - 3.0 × 105 cells/cm2 of BM derived mononuclear cells were inoculated in D10 media that was changed completely after 3 days and subsequently replaced twice a week until confluence and cryopreserved for experiments at P1. MDS patient derived mononuclear cells (1.0 × 106 – 1.0 × 107 cells/ml) were also inoculated in D10 media in a T75 flask. Non-adherent cells were removed after 3 days with subsequent media change twice a week. MDS-MSCs were further expanded, frozen down and all experiments were carried out using MSCs derived from P1 - P2.

extract_protocol:
CD34+ HSPCs were isolated using the CD34+ MicroBead Kit and magnetic-activated cell sorting (MACS) (Miltenyi Biotec).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 5-azacitidine treated or untreated MDS-MSCs were plated at a near confluent density of 2.0 × 104 cells/cm2 in DMEM with 10% FBS. 24 h later, healthy CD34+ HSPCs were seeded in contact with the MSC feeder layer at a density of 2.0 × 103 cells/cm2 in hematopoietic media and cultured for 14-21 days with replacement of media after 7 days. On the last day, CD34+ HSPCs were flow sorted for RNA extraction and subsequent sequencing.

tag: mds-msc 5-aza treatment

value: No

tag: co-culture with mds derived mscs

value: Yes

tag: cell type

value: Healthy bone marrow CD34+ hematopoietic stem and progenitor cells


title: E4.5-5.5_new_Plate1_C09 (scRNA-Seq)


title: OSCC_T1_FFPE_T_Recur


title: OSCC_L3_FFPE_LN_Recur


title: E4.5-5.5_new_Plate1_C03 (scRNA-Seq)


title: E4.5-5.5_new_Plate1_C02 (scRNA-Seq)


title: OSCC_L1_FFPE_LN_Recur


title: E4.5-5.5_new_Plate1_B11 (scRNA-Seq)


title: E4.5-5.5_new_Plate1_B12 (scRNA-Seq)


title: E4.5-5.5_new_Plate1_B07 (scRNA-Seq)


title: E4.5-5.5_new_Plate1_C05 (scRNA-Seq)


title: liver_CL-166-12m

city: Toronto

first: Johane

middle: P.

last: Allard

state: Ontario

address: 585 University Ave, 9-NU-973

department: Medicine

country: Canada

institute: University Health Network

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was checked for overall quality using R (v2.15.1) with the lumi Bioconductor package. Two samples (1 baseline, 1 at 12 months) that fell below the threshold for one or more of the quality metrics  calculated with this package, were excluded from further analysis. The data were imported in GeneSpring v12.5 (Agilent) and normalized using a quantile normalization followed by a “per  probe” median centered normalization (for visualization).

source_name: liver

label_protocol: 200 ng of RNA were labelled and amplified following Illumina Whole Genome Expression - DASL assay kit for partially degraded and FFPE derived RNA.

extract_protocol: Total RNA was extracted from liver biopsies using the mirVana miRNA Isolation kit (Life Technologies Corp., Carlsbad, CA, USA). RNA concentration and purity were assessed with a Thermo Scientific's NanoDrop 1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and quality was assessed with an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA).

tag: array ^sample

tag: time point

value: 12 months

tag: diagnosis

value: NASH

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: body mass index (kg/m2)

tag: waist (cm)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c

tag: diabetes

tag: erythrocyte arachidonic acid (% of total lipids)

tag: erythrocyte  eicosapentaenoic acid (% of total lipids)

tag: erythrocyte docosahexaenoic acid (% of total lipids)

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)

tag: liver arachidonic acid (% of diacylglycerols)

tag: liver eicosapentaenoic acid (% of diacylglycerols)

tag: liver docosahexaenoic acid (% of diacylglycerols)

tag: liver arachidonic acid (% of phospholipids)

tag: liver eicosapentaenoic acid (% of phospholipids)

tag: liver docosahexaenoic acid (% of phospholipids)

tag: liver arachidonic acid (% of triacylglycerols)

tag: liver eicosapentaenoic acid (% of triacylglycerols)

tag: liver docosahexaenoic acid (% of triacylglycerols)


title: liver_CL-151-12m

tag: array ^sample

tag: time point

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: waist (cm)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c


title: E4.5-5.5_new_Plate1_B02 (scRNA-Seq)

tag: strain

tag: developmental stage

tag: sample type


title: E4.5-5.5_new_Plate1_B01 (scRNA-Seq)


title: liver_CL-154-12m

tag: array ^sample

tag: time point

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: gender

tag: diabetes

tag: erythrocyte arachidonic acid (% of total lipids)

tag: erythrocyte  eicosapentaenoic acid (% of total lipids)

tag: erythrocyte docosahexaenoic acid (% of total lipids)

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)

tag: liver arachidonic acid (% of diacylglycerols)

tag: liver eicosapentaenoic acid (% of diacylglycerols)

tag: liver docosahexaenoic acid (% of diacylglycerols)

tag: liver arachidonic acid (% of phospholipids)

tag: liver eicosapentaenoic acid (% of phospholipids)

tag: liver docosahexaenoic acid (% of phospholipids)

tag: liver arachidonic acid (% of triacylglycerols)

tag: liver eicosapentaenoic acid (% of triacylglycerols)

tag: liver docosahexaenoic acid (% of triacylglycerols)


title: liver_CL-146-12m

tag: array ^sample

tag: time point

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: waist (cm)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c


title: liver_CL-169-12m

tag: array ^sample

tag: time point

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: diabetes

tag: erythrocyte arachidonic acid (% of total lipids)

tag: erythrocyte  eicosapentaenoic acid (% of total lipids)

tag: erythrocyte docosahexaenoic acid (% of total lipids)

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)

tag: liver arachidonic acid (% of diacylglycerols)

tag: liver eicosapentaenoic acid (% of diacylglycerols)

tag: liver docosahexaenoic acid (% of diacylglycerols)

tag: liver arachidonic acid (% of phospholipids)

tag: liver eicosapentaenoic acid (% of phospholipids)

tag: liver docosahexaenoic acid (% of phospholipids)

tag: liver arachidonic acid (% of triacylglycerols)

tag: liver eicosapentaenoic acid (% of triacylglycerols)

tag: liver docosahexaenoic acid (% of triacylglycerols)


title: liver_CL-127-12m

tag: array ^sample

tag: time point

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: waist (cm)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c


title: liver_CL-125-12m

tag: array ^sample

tag: time point

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: diabetes

tag: erythrocyte arachidonic acid (% of total lipids)

tag: erythrocyte  eicosapentaenoic acid (% of total lipids)

tag: erythrocyte docosahexaenoic acid (% of total lipids)

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)

tag: liver arachidonic acid (% of diacylglycerols)

tag: liver eicosapentaenoic acid (% of diacylglycerols)

tag: liver docosahexaenoic acid (% of diacylglycerols)

tag: liver arachidonic acid (% of phospholipids)

tag: liver eicosapentaenoic acid (% of phospholipids)

tag: liver docosahexaenoic acid (% of phospholipids)

tag: liver arachidonic acid (% of triacylglycerols)

tag: liver eicosapentaenoic acid (% of triacylglycerols)

tag: liver docosahexaenoic acid (% of triacylglycerols)


title: liver_CL-122-12m

tag: array ^sample

tag: time point

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: waist (cm)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c


title: liver_CL-151-BL

tag: array ^sample

tag: time point

value: baseline

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: diabetes

tag: erythrocyte arachidonic acid (% of total lipids)

tag: erythrocyte  eicosapentaenoic acid (% of total lipids)

tag: erythrocyte docosahexaenoic acid (% of total lipids)

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)

tag: liver arachidonic acid (% of diacylglycerols)

tag: liver eicosapentaenoic acid (% of diacylglycerols)

tag: liver docosahexaenoic acid (% of diacylglycerols)

tag: liver arachidonic acid (% of phospholipids)

tag: liver eicosapentaenoic acid (% of phospholipids)

tag: liver docosahexaenoic acid (% of phospholipids)

tag: liver arachidonic acid (% of triacylglycerols)

tag: liver eicosapentaenoic acid (% of triacylglycerols)

tag: liver docosahexaenoic acid (% of triacylglycerols)


title: liver_CL-166-BL

tag: array ^sample

tag: time point

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: waist (cm)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c


title: liver_CL-141-12m

tag: array ^sample

tag: time point

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: diabetes

tag: erythrocyte arachidonic acid (% of total lipids)

tag: erythrocyte  eicosapentaenoic acid (% of total lipids)

tag: erythrocyte docosahexaenoic acid (% of total lipids)

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)

tag: liver arachidonic acid (% of diacylglycerols)

tag: liver eicosapentaenoic acid (% of diacylglycerols)

tag: liver docosahexaenoic acid (% of diacylglycerols)

tag: liver arachidonic acid (% of phospholipids)

tag: liver eicosapentaenoic acid (% of phospholipids)

tag: liver docosahexaenoic acid (% of phospholipids)

tag: liver arachidonic acid (% of triacylglycerols)

tag: liver eicosapentaenoic acid (% of triacylglycerols)

tag: liver docosahexaenoic acid (% of triacylglycerols)


title: E4.5-5.5_new_Plate1_B08 (scRNA-Seq)

tag: strain

tag: developmental stage

tag: sample type


title: liver_CL-141-BL

tag: array ^sample

tag: time point

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: waist (cm)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c

tag: diabetes

tag: erythrocyte arachidonic acid (% of total lipids)

tag: erythrocyte  eicosapentaenoic acid (% of total lipids)


title: E4.5-5.5_new_Plate1_A12 (scRNA-Seq)

tag: strain

tag: developmental stage

tag: sample type


title: liver_CL-154-BL

tag: array ^sample

tag: time point

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: waist (cm)

tag: aspartate transaminase (u/l)

tag: erythrocyte docosahexaenoic acid (% of total lipids)

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)

tag: liver arachidonic acid (% of diacylglycerols)

tag: liver eicosapentaenoic acid (% of diacylglycerols)

tag: liver docosahexaenoic acid (% of diacylglycerols)

tag: liver arachidonic acid (% of phospholipids)

tag: liver eicosapentaenoic acid (% of phospholipids)

tag: liver docosahexaenoic acid (% of phospholipids)

tag: liver arachidonic acid (% of triacylglycerols)

tag: liver eicosapentaenoic acid (% of triacylglycerols)

tag: liver docosahexaenoic acid (% of triacylglycerols)


title: E4.5-5.5_new_Plate1_A08 (scRNA-Seq)

tag: strain

tag: developmental stage

tag: sample type


title: E4.5-5.5_new_Plate1_A05 (scRNA-Seq)


title: liver_CL-169-BL

tag: array ^sample

tag: time point

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: waist (cm)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c

tag: diabetes

tag: erythrocyte arachidonic acid (% of total lipids)

tag: erythrocyte  eicosapentaenoic acid (% of total lipids)


title: E4.5-5.5_new_Plate1_A11 (scRNA-Seq)

tag: strain

tag: developmental stage

tag: sample type


title: E4.5-5.5_new_Plate1_A03 (scRNA-Seq)


title: liver_CL-122-BL

tag: array ^sample

tag: time point

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: waist (cm)

tag: aspartate transaminase (u/l)

tag: erythrocyte docosahexaenoic acid (% of total lipids)

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)

tag: liver arachidonic acid (% of diacylglycerols)

tag: liver eicosapentaenoic acid (% of diacylglycerols)

tag: liver docosahexaenoic acid (% of diacylglycerols)

tag: liver arachidonic acid (% of phospholipids)

tag: liver eicosapentaenoic acid (% of phospholipids)

tag: liver docosahexaenoic acid (% of phospholipids)

tag: liver arachidonic acid (% of triacylglycerols)

tag: liver eicosapentaenoic acid (% of triacylglycerols)

tag: liver docosahexaenoic acid (% of triacylglycerols)


title: liver_CL-125-BL

tag: array ^sample

tag: time point

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: gender

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c

tag: diabetes

tag: erythrocyte arachidonic acid (% of total lipids)

tag: erythrocyte  eicosapentaenoic acid (% of total lipids)


title: E4.5-5.5_new_Plate1_A04 (scRNA-Seq)

tag: strain

tag: developmental stage

tag: sample type


title: E4.5-5.5_new_Plate1_A02 (scRNA-Seq)


title: liver_CL-146-BL

tag: array ^sample

tag: time point

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: waist (cm)

tag: aspartate transaminase (u/l)

tag: erythrocyte docosahexaenoic acid (% of total lipids)

tag: liver arachidonic acid (% of total lipids)

tag: liver eicosapentaenoic acid (% of total lipids)

tag: liver docosahexaenoic acid (% of total lipids)

tag: liver arachidonic acid (% of diacylglycerols)

tag: liver eicosapentaenoic acid (% of diacylglycerols)

tag: liver docosahexaenoic acid (% of diacylglycerols)

tag: liver arachidonic acid (% of phospholipids)

tag: liver eicosapentaenoic acid (% of phospholipids)

tag: liver docosahexaenoic acid (% of phospholipids)

tag: liver arachidonic acid (% of triacylglycerols)

tag: liver eicosapentaenoic acid (% of triacylglycerols)

tag: liver docosahexaenoic acid (% of triacylglycerols)


title: E4.5-5.5_new_Plate1_A07 (scRNA-Seq)

tag: strain

tag: developmental stage

tag: sample type


title: liver_CL-127-BL

tag: array ^sample

tag: time point

tag: diagnosis

tag: steatosis (%)

tag: fibrosis (stage)

tag: lobular inflammation (severity)

tag: ballooning (intensity)

tag: nafld activity score

tag: age (y)

tag: gender

tag: body mass index (kg/m2)

tag: waist (cm)

tag: aspartate transaminase (u/l)

tag: alanine transaminase (u/l)

tag: alkaline phosphatase (u/l)

tag: triglycerides (mmol/l)

tag: total cholesterol (mmol/l)

tag: ldl cholesterol (mmol/l)

tag: hdl cholesterol (mmol/l)

tag: fasting glucose (mmol/l)

tag: fasting insulin (pmol/l)

tag: homa-insulin resistance

tag: hemoglobin a1c

tag: diabetes

tag: erythrocyte arachidonic acid (% of total lipids)

tag: erythrocyte  eicosapentaenoic acid (% of total lipids)


title: E4.5-5.5_new_Plate2_C01 (scRNA-Seq)

tag: strain

tag: developmental stage

tag: sample type


title: TBM.SP.Tconv_2

city: Boston

first: JAE WON

last: CHO

state: MA

address: 60 Fenwood Road

department: Neurology

country: USA

institute: Brigham and Women's Hospital

data_processing:
Read mapping: STAR-s.5.sa
Quantification: FeatureCounts
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include counts for each Sample

source_name: CD4+GFP- Tconv

extract_protocol:
Total RNA was extracted using a QIAGEN RNeasy Plus Micro Kit.
Libraries were prepared using an Illumina TruSeq Stranded mRNA Library Prep Kit and sequenced using an Illumina NextSeq500.

tag: mouse status

value: tumor-bearing

tag: tissue

value: spleen

tag: cell type

value: CD4+GFP- Tconv


title: NM.SP.Treg_2

source_name: CD4+GFP+ Treg

value: normal

value: CD4+GFP+ Treg


title: TBM.SP.Treg_2


title: NM.SP.Treg_1


title: NM.SP.Tconv_2


title: TBM.TM.Treg_2

value: tumor


title: TBM.TM.Tconv_2


title: TBM.TM.Tconv_1


title: TBM.SP.Tconv_1


title: NM.SP.Tconv_1


title: WT + M

city: Hong Kong

first: Lifeng

last: Xiong

address: Pok Fu Lam

country: China

institute: the University of Hong Kong

data_processing:
BGISEQ-500 platform
Clean-tags were mapped to the reference genome of HLHK9
Genome_build: NC_012559.1
Supplementary_files_format_and_content: Excel file with abundance data

organism: Laribacter hongkongensis

growth_protocol: Strains of L. hongkongensis were grown in modified minimal medium M63 supplemented with 19 mM potassium nitrate, 1 mM each of vitamin B1 and vitamin B12, with or without malate supplementation

extract_protocol:
Bacterial total RNA were extracted using the RNeasy Mini kit (Qiagen). Extracted RNA was then treated with RNase-free DNase I (Roche) at 37°C for 30 min to decontaminate genomic DNA.
The mRNA was isolated from total RNA samples, and disrupted into short fragments as templates for cDNA synthesis.

tag: genotype

value: wild type

tag: malate supplementation

value: with malate


title: ChinBody rep2

city: Davis

first: Joanna

middle: C.

last: Chiu

state: California

address: One shield Av

institute: University of California

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then were performed de novo assembly using de Bruijn graph-based assembler (Trinity v2.5.1, release 10/20/2017). Assembly was performed using high-quality, cleaned, and filtered paired-end sequences with a fixed k-mer size of 25; minimum k-mer coverage was 3 and minimum isoform ratio was 0.05.
All contig sequences assembled on Trinity were annotated using Blast2GO pipeline (v.5.1.13). A Blastx searches of transcripts was generated against a local protein database in the following order: Bombyx mori (Lepidoptera: Bombycidae) > Drosophila melanogaster (Diptera: Drosophilidae) > Helicoverpa armigera (Lepidoptera: Noctuidae) > Danaus plexippus (Lepidoptera: Nymphalidae). The parameters used were: word size of 3, 4 threads, HSP length cutoff of 33.
Additionally, assembled transcripts were scanned against the public EMBL-EBI InterPro web-service implemented in Blast2GO software (v.5.1.13).
Annotation of transcripts with Gene Ontology IDs (GO), which reveals the properties of biological process, molecular function, and cellular component, was accomplished using the following parameters: cutoff of 55 and blast filters with E-value-hit-filter of 1.0E-6.
RNA-seq reads of head and body transcriptomes were mapped to the built reference transcriptome using TopHat and expression values of transcripts in FPKM were estimated using the mapped reads of head and body tissues on Cufflinks.
Genome_build: Trinity.fasta
Supplementary_files_format_and_content: output files (.txt) from Cufflinks

organism: Chrysodeixis includens

source_name: Body

extract_protocol:
Larvae was dissected into head and body and total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Library Prep Kit v2 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ordered from Benzon Research laboratory and its colony are being reared over 100 generations in the lab. This colony was originally from University of Georgia

value: Laboratory

tag: age

value: third instar

value: body


title: TBM.TM.Treg_1


title: ChinHead rep1

source_name: Head

value: head


title: ChinHead rep2


title: WT no M

value: without malate


title: CRP KO + M

value: DCRP


title: ChinBody rep1


title: E4.5-5.5_new_Plate1_A09 (scRNA-Seq)

value: single cell


title: spt20-TID repl2

city: Montpellier

first: Dominique

last: Helmlinger

address: 1919 route de Mende

department: CRBM

country: France

institute: CNRS

description: Illumina TruSeq Stranded mRNA Library

data_processing:
Basecalling pipeline at Fasteris: HiSeq Control Software HD 3.4.0.38; RTA 2.7.7; bcl2fastq2.17 v2.17.1.14
Sequenced reads were trimmed for adaptor sequence using FastQ Groomer and mapped to Schizosaccharomyces_pombe_1.1 reference genome using HISAT2 v2.1.0 with strand-specific information (--rna-strandness R) and otherwise default options
Reads were then counted for gene and exon features using htseq-count v0.9.1 in union mode (--mode union), reverse stranded (--stranded Reverse), and a minimum alignment quality of 10 (--minaqual 10)
Variance-mean dependence was estimated from count tables and tested for differential expression based on a negative binomial distribution, using DESeq2 v1.18.1. Pairwise comparison or one-way analysis of variance were run with a parametric fit and genotype as the source of variation (factor: ‘mutant’ or ‘control’)
Genome_build: Schizosaccharomyces_pombe_1.1
Supplementary_files_format_and_content: Tab-delimited txt files wee merged into one Excel spreadsheet, in which each sheet includes Gene ID, Log2 fold-change and normalized P values (P-adj) for each DESeq2 analysis. Tab-delimited text file with raw count data for all samples.

organism: Schizosaccharomyces pombe

source_name: Liquid cultures

growth_protocol: Yeast grown to mid-logarithmic phase

extract_protocol:
RNA was extracted from 50 mL of exponentially growing cells RNA using TRIzol. DNA was removed by DNase I digestion, using the TURBO DNA-free™ kit. RNA was cleaned using the RNeasy Mini kit. Total RNA quality and concentration was determined using an Agilent Bioanalyzer. Transcripts were purified by polyA-tail selection.
RNA libraries were prepared for sequencing using Illumina TruSeq Stranded mRNA Library prep kit

tag: strain genotype

tag: growth conditions

value: YES

tag: strain number in table s2


title: spt20D repl2

description: Illumina TruSeq Stranded mRNA Library


title: tra1-scTra1 repl2

description: Illumina TruSeq Stranded mRNA Library


title: spt20D repl1

description: Illumina TruSeq Stranded mRNA Library


title: spt20-TID repl1

description: Illumina TruSeq Stranded mRNA Library


title: tra1-spTra2 repl3

description: Illumina TruSeq Stranded mRNA Library


title: tra1-spTra2 repl2

description: Illumina TruSeq Stranded mRNA Library


title: tra1-scTra1 repl1

description: Illumina TruSeq Stranded mRNA Library


title: spt20-TID repl3

description: Illumina TruSeq Stranded mRNA Library


title: TBM.SP.Treg_1

value: tumor-bearing


title: tra1-spTra2 repl1

description: Illumina TruSeq Stranded mRNA Library


title: Tendon injured extracted 28 days post-injury [D05 - 28DAYS-PÓST-INJURY]

city: Brasíia

first: Fabrício

middle: Reichert

last: Barin

address: Centro Metropolitano, Conjunto A, Lote 01

country: Brazil

institute: Universidade de Brasília

description: 28 days post-injury

data_processing:
For the normalization it was tests three housekeeping genes: RPLPO, GAPDH, ACTB, however, the housekkeping that demonstrated variation less than 5% was RPLPO, so, they was used for data normalization.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The Excell performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports injury's day/control (i.e., 3 days post-injury/control) ratios.

label: Taqman

organism: Rattus norvegicus

source_name: tendon

label_protocol: PCR assays were performed using calcaneus tendon of rats following the Manufacturer’s instructions (GoTaq® Probe qPCR Master Mix - Invitrogen). Reverse transcription was performed from 1000ng total RNA using the SuperScript® VILO™ MasterMix (Invitrogen). Quantitative real-time PCR were performed (QuantStudio, ApliedBiosystems) with 40 cycles at 95 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with Trizol Reagent according to manufacturer's instructions (Invitrogen) followed by DNase I treatment.

value: calcaneus tendon


title: Tendon injured extracted 28 days post-injury [D06 - 28DAYS-PÓST-INJURY]

description: 28 days post-injury


title: Tendon injured extracted 28 days post-injury [D04 - 28DAYS-PÓST-INJURY]

description: 28 days post-injury


title: Tendon injured extracted 28 days post-injury [D02 - 28DAYS-PÓST-INJURY]

description: 28 days post-injury


title: tra2 bE 21h repl3

description: Illumina TruSeq Stranded mRNA Library

value: cre-ER lox-tra2-lox

value: YES-b-Estradiol


title: Tendon injured extracted 28 days post-injury [D01 - 28DAYS-PÓST-INJURY]

description: 28 days post-injury


title: Tendon injured extracted 14 days post-injury [C06 - 14DAYS-PÓST-INJURY]

description: 14 days post-injury


title: tra2 bE 21h repl2

description: Illumina TruSeq Stranded mRNA Library


title: spt20D repl3

description: Illumina TruSeq Stranded mRNA Library


title: tra1-scTra1 repl3

description: Illumina TruSeq Stranded mRNA Library


title: Tendon injured extracted 14 days post-injury [C04 - 14DAYS-PÓST-INJURY]

description: 14 days post-injury


title: Tendon injured extracted 14 days post-injury [C03 - 14DAYS-PÓST-INJURY]

description: 14 days post-injury


title: Tendon injured extracted 14 days post-injury [C02 - 14DAYS-PÓST-INJURY]

description: 14 days post-injury


title: tra2 bE 21h repl1

description: Illumina TruSeq Stranded mRNA Library


title: Tendon injured extracted 3 days post-injury [B05 - 3DAYS-PÓST-INJURY]

description: 3 days post-injury


title: tra2 DMSO 21h repl3

description: Illumina TruSeq Stranded mRNA Library

value: YES-DMSO


title: tra2 DMSO 21h repl2

description: Illumina TruSeq Stranded mRNA Library


title: tti2 bE 18h repl2

description: Illumina TruSeq Stranded mRNA Library

value: cre-ER lox-tti2-lox


title: Tendon injured extracted 28 days post-injury [D03 - 28DAYS-PÓST-INJURY]

description: 28 days post-injury


title: tti2 bE 18h repl1

description: Illumina TruSeq Stranded mRNA Library


title: tti2 bE 18h repl3

description: Illumina TruSeq Stranded mRNA Library


title: Tendon without injury [A05-  CONTROL]

description: control


title: Tendon injured extracted 3 days post-injury [B03 - 3DAYS-PÓST-INJURY]

description: 3 days post-injury


title: Tendon without injury [A04 - CONTROL]

description: control


title: tti2 DMSO 18h repl3

description: Illumina TruSeq Stranded mRNA Library


title: tti2 DMSO 18h repl2

description: Illumina TruSeq Stranded mRNA Library


title: Tendon without injury [A03 - CONTROL]

description: control


title: tti2 DMSO 18h repl1

description: Illumina TruSeq Stranded mRNA Library


title: Tendon without injury [A02 - CONTROL]

description: control


title: Tendon injured extracted 14 days post-injury [C01 - 14DAYS-PÓST-INJURY]

description: 14 days post-injury


title: Cre bE 21h repl1

description: Illumina TruSeq Stranded mRNA Library

value: cre-ER


title: Tendon injured extracted 3 days post-injury [B02 - 3DAYS-PÓST-INJURY]

description: 3 days post-injury


title: Cre bE 21h repl2

description: Illumina TruSeq Stranded mRNA Library


title: Cre DMSO 21h repl3

description: Illumina TruSeq Stranded mRNA Library


title: T2_Mys7079_2wk_cross

city: Seaside

first: Andrew

middle: Jacob

last: Cline

state: CA

address: 100 Campus Center

department: School of Natural Sciences

institute: California State University, Monterey Bay

data_processing:
FastQC (v. 0.11.5) was performed on the raw read files to assess base-by-base quality.
Trimmomatic (v. 0.36) was used to trim low-quality bases and clip off Illumina single-end adapters (ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 MINLEN:25).
FastQC (v. 0.11.5) was performed on the trimmed read files to assess base-by-base quality.
Within the RSEM software (v. 1.3.0), reads were aligned using Bowtie and transcript abundances estimated using RSEM.
Genome_build: Blue rockfish de novo transcript assembly, created 12/20/17 and awaiting submission to TSA (PRJNA526549). Three of the single-end files in this GEO submission were used to construct the assembly in addition to eight paired-end files, so no SRA accessions for the single-end files have been generated as of this submission, which is the reason for the delay in submitting to TSA.
Supplementary_files_format_and_content: edgeR output matrices (TMM) organized by experimental time-point: 12 h, 24 h and two weeks.

organism: Sebastes mystinus

source_name: Blue rockfish (Sebastes mystinus) white muscle

growth_protocol: 10 juvenile blue rockfish were held in each of eight black 55-gallon aquaria supplied with flow-through seawater at the NOAA Southwest Fisheries Science Center in Santa Cruz, CA. Seawater pH and oxygen content were artificially decreased in the experimental treatments via carbon dioxide and nitrogen bubbling, respectively. Seawater temperature was maintained between 11.4-12.3° C for the two-week duration of the experiment.

extract_protocol:
For all listed samples, we isolated total RNA using a Qiagen Rneasy Plus Mini™ Kit (Qiagen®, Valencia, CA; cat. no. 74134).
We constructed cDNA libraries using two Illumina® TruSeq™ Stranded mRNA Library Preparation Kits (Illumina®, cat. no. RS-122-2101 and RS-122-2102, Adaptor Sets A and B) (Figure 1 ). Libraries were prepared in two sets of 24 and randomized to account for batch effects. Briefly, we removed ribosomal and other non‑coding RNAs to purify messenger RNA (mRNA) and fragmented the isolated mRNA. We synthesized first strand cDNA using SuperScript III Reverse Transcriptase (Invitrogen™, cat. no. 18080-044), and second strand cDNA using the 2'-deoxyuridine 5'-triphosphate (dUTP) nucleotide method for strand specificity. We then ligated a unique adapter index to each cDNA library and amplified the libraries through 15 cycles of polymerase chain reaction (PCR). cDNA purification steps were completed with PCRClean™ DX paramagnetic beads (Aline Biosciences®, cat. no. C-1003-5) and Agencourt AMPure™ XP beads (Beckman-Coulter®, cat. no. A63881). We quantified cDNA using a Qubit® 2.0 fluorometer and Qubit® dsDNA High Sensitivity Assay kit (Invitrogen™, cat. no. Q32851) and verified that fragments were distributed in the 260-320 bp range using an Advanced Analytical® Fragment Analyzer™ (High Sensitivity Large Fragment Analysis Kit, Advanced Analytical®, cat. no. DNF‑493‑0500). Adapter dimers were removed with a 1.2X bead:sample volume clean‑up step. Two libraries were not constructed due to poor RNA quality and two libraries were lost during construction due to ethanol carryover for a total of 44 libraries.

treatment_protocol: White muscle tissue was dissected at 12 h, 24 h and two weeks of exposure and immediately frash-frozen in liquid nitrogen. Frozen samples were transported on dry ice to long-term storage at -80° C.

value: juvenile


title: T2_Mys7077_2wk_cross


title: T2_Mys7078_2wk_cross


title: Cre DMSO 21h repl2

description: Illumina TruSeq Stranded mRNA Library


title: Cre DMSO 21h repl1

description: Illumina TruSeq Stranded mRNA Library


title: T2_Mys7070_24h_cross


title: Tendon injured extracted 14 days post-injury [C05 - 14DAYS-PÓST-INJURY]

description: 14 days post-injury


title: Porphyromonas gingivalis 381 replicate 2 [SC5]

city: Seattle

first: Jeffrey

middle: S

last: McLean

state: WA

address: 1959 NE Pacific St, Box 357444

department: Periodontics

institute: University of Washington

data_processing:
Basecalls performed by CASAVA version 1.4
Barcodes were trimmed, low quality and short sequences (<100bp) were filtered using BBDuk (https://sourceforge.net/projects/bbmap) implemented in Geneious version 11 (https://www.geneious.com).
Expression values for each mRNA sample were generated by mapping of paired reads onto the annotated reference genome of P. gingivalis ATCC 33277.
Expression level counts and differential expression calculations in triplicate between conditions were performed using Geneious version 11 (https://www.geneious.com) using DESeq2 normalization. DESeq2 uses a model based on the negative binomial distribution with variance and mean linked by local regression (36).
Genome_build: Porphyromonas gingivalis ATCC 33277
Supplementary_files_format_and_content: Pg_Coats_RNAseq_processeddata.xlsx: Excel file containing the output prior to statistical analysis from all of the samples for each gene in the genome

organism: Porphyromonas gingivalis 381

source_name: Porphyromonas gingivalis 381

growth_protocol: Bacterial cutlures were grown in anaerobic conditions to mid-logarithmic phase in trypticase soy media supplemented with yeast extract, vitamin K, and hemin.

extract_protocol:
RNA extraction was performed using Trizol/chloroform extraction, followed by treatment with RQ1 Dnase, and cleanup with Zymo RNA Clean & Concentrator column kit.
cDNA libraries from rRNA-depleted RNA were generated using random-primed cDNA synthesis methods according to the ScriptSeq v2 RNASeq Library preparation protocol (Epicentre, Madison, WI).  Prior to second strand cDNA synthesis, the di-tagged cDNA was purified using the Agencourt AMPure XP system (Beckman Coulter, Brea, CA).  ScriptSeq index primers were added to the libraries which were then PCR amplified for 15 cycles.


title: Porphyromonas gingivalis 381 replicate 3 [SC6]


title: T2_Mys7068_24h_cross


title: Porphyromonas gingivalis 381 replicate 1 [SC4]


title: T2_Mys7069_24h_cross


title: ΔcadA/Mutant Rep3

city: Starkville

first: Bindu

last: Nanduri

state: MS

address: P.O. Box 6100, 240 Wise Center Drive

department: Basic Science

institute: Mississippi State University

data_processing:
Licensed CLC Genomic Workbench 11 software (https://www.qiagenbioinformatics.com/) was used for data analysis:
Sequenced reads were trimmed for low-quality sequence, then mapped to Streptococcus pneumoniae TIGR4 whole genome using CLC genomic workbench 11 proprietary algorithms
The mapped reads were assigned to transcripts using EM estimation algorithm.
Differentially expressed genes were identified based on the fold change generated by the edgeR algorithm
Fold change with cutoff ±1.3 and false discovery rate (FDR) p-value ≤ 0.05 was accepted to be significant.
Genome_build: GCF_000006885.1
Supplementary_files_format_and_content: csv file include Locus_Tag, Fold change and FDR p-value

organism: Streptococcus pneumoniae TIGR4

source_name: Cell

growth_protocol: Streptococcus pneumoniae serotype 4 strain TIGR4 and ∆cadA were cultured in Todd-Hewitt broth supplemented with 0.5% yeast extract (THY) or on 5% sheep blood agar plates (BAP) in 5% CO₂. Both strains were grown to mid-log phase (O.D600 nm 0.4) and cells were pelleted, for extraction of total RNA. Colony forming units were enumerated to ensure comparable number of working cells.

extract_protocol:
Total RNA was isolated and purified from mid-log phase cultures of TIGR4 and ΔcadA grown in THY (n = 3) using the RNeasy Midi Kit and QIAcube (Qiagen, Valencia, CA). The quality was analyzed by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)
Libraries for RNA-Seq were prepared with the KAPA RNA Hyper Kit with RiboErase (KAPA Biosystem, Wilmington, MA) using 5 µg RNA as input. The workflow consists of rRNA removal, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one sequencing run. Library concentrations and quality were measured using Qubit ds DNA HS Assay Kit (Life Technologies, Carlsbad, CA) and Agilent Tapestation (Agilent Technologies, Santa Clara, CA). Sequencing was performed on an Illumina Hiseq 3000 for a single read 50 run. Data quality check was done on Illumina SAV. De-multiplexing was performed with Illumina Bcl2fastq2 v 2.17.

value: delta cadA


title: ΔcadA/Mutant Rep2


title: Cre bE 21h repl3

description: Illumina TruSeq Stranded mRNA Library


title: T2_Mys7064_12h_cross


title: T2_Mys7065_12h_cross


title: ΔcadA/Mutant Rep1


title: Tendon without injury [A01 - CONTROL]

description: control


title: TIGR4/Wild-type Rep3

value: wildtype


title: TIGR4/Wild-type Rep2


title: T2_Mys7076_2wk_cross


title: T2_Mys60_2wk_DO


title: T2_Mys59_2wk_DO


title: T2_Mys58_2wk_DO


title: TIGR4/Wild-type Rep1


title: T2_Mys7071_24h_cross


title: Porphyromonas gingivalis ATCC 33277 replicate 3 [SC3]

organism: Porphyromonas gingivalis ATCC 33277

source_name: Porphyromonas gingivalis ATCC 33277


title: Porphyromonas gingivalis ATCC 33277 replicate 2 [SC2]


title: T2_Mys57_2wk_DO


title: T2_Mys54_2wk_pH


title: Porphyromonas gingivalis ATCC 33277 replicate 1 [SC1]


title: T2_Mys53_2wk_pH


title: T2_Mys51_2wk_control


title: T2_Mys50_2wk_control


title: T2_Mys7066_12h_cross


title: T2_Mys49_2wk_control


title: T2_Mys7067_12h_cross


title: T2_Mys36_24h_DO


title: T2_Mys52_2wk_control


title: T2_Mys35_24h_DO


title: T2_Mys32_24h_pH


title: T2_Mys31_24h_pH


title: T2_Mys34_24h_DO


title: T2_Mys30_24h_pH


title: tra2 DMSO 21h repl1

description: Illumina TruSeq Stranded mRNA Library


title: emu_FL_Splancnopleure_6

first: John

last: Young

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
RNA-seq reads were mapped using STAR to reference genomes (galGal4 or droNov1)
Quantification via FeatureCounts
Differential gene expression was determined using DESeq.
Genome_build: galGal4 for chick or droNov1 for emu
Supplementary_files_format_and_content: Tab delimited .txt files with transcript counts generated from featureCounts

organism: Dromaius novaehollandiae

source_name: Embryonic tissue

extract_protocol:
RNA was harvested using PicoPure columns
libraries were synthesized from 50ng of total RNA by automation using Kappa reagents followed by 15 cycles of replication.

value: Splanchnopleure at the forelimb level

tag: Stage


title: emu_FL_Somatopleure_5

value: Somatorpleure at the forelimb leve


title: emu_FL_Somatopleure_53


title: T2_Mys27_24h_control


title: T2_Mys26_24h_control


title: emu_FL_Somatopleure_13


title: T2_Mys28_24h_control


title: T2_Mys25_24h_control


title: emu_FL_LPM_8

value: Undifferentiated lateral plate mesoderm at the forelimb level


title: T2_Mys24_12h_DO


title: Tendon injured extracted 3 days post-injury [B01 - 3DAYS-PÓST-INJURY]

description: 3 days post-injury


title: emu_FL_LPM_23


title: emu_FL_LPM_1


title: T2_Mys22_12h_DO


title: T2_Mys23_12h_DO


title: 595K

extract_protocol:
RNA was harvested via lysis in Trizol followed by isolation using RNeasy micro columns.
Libraries were synthesized from 200ng total RNA using the stranded TruSeq kit (Illumina) followed by 15 cycles of amplification.

value: Flank somatopleure


title: emu_FL_Splancnopleure_pool


title: T2_Mys21_12h_DO


title: T2_Mys20_12h_pH


title: WL3

city: Oslo

first: Nur

last: Duale

address: Lovisenbergg. 8, P.O.Box 4404 Nydalen,

department: Division of Climate and Environment Health

country: Norway

institute: Norwegian Institute of Public Health

description:
samples from mice on HFD, expode whole life (23 weeks)
SAMPLE 12

data_processing: The real-time qPCR analysis were carried out as previously described 17,18 in 384-well plates on a CFX384 Touch Real-Time PCR Detection System (Bio-Rad, Norway). In the miRNA expression profiling, cDNA (1:100 dilution) from each treatment group (N=12 mice) was divided into three groups and each group consisted of pooled cDNA from four mice (i.e., resulting in three pooled independent biological replicates per treatment group. All 12 pooled samples were measured in 384-well plate qPCR layout. The expression profile of 505 miRNA assays were performed using this qPCR layout. The raw data Cq-values from 505 miRNAs were pre-processed and miRNAs with inadequate measurements, with multiple Tm peaks and Cq-values >35 were removed from downstream analyses. The Cq-values were normalized with mean expression value for individual samples. The normalized ∆Cq-values were transformed to linear scale (normalized relative expression [NRQ = 2-∆Cq(sample); where ∆Cq(sample) = Cq (miRNA) – Cq (mean Cq-values of all expressed miRNAs)]. The fold change (FD) between HFD and CD samples were then calculated by dividing the NRQ of the HFD samples by the NRQ of the CD samples [FD = NRQ (HFD)/NRQ (CD)]. All miRNA expression data are reported as fold differences between the CD and the HFD samples.

source_name: epididymal fat pads

extract_protocol: Total RNA was isolated from fat pads (~22 mg tissue) using miRNeasy kit (QIAGEN, Norway) according to the manufacturer's instructions. The quantity and quality of isolated RNA was determined using a NanoDrop Spectrophotometer (Thermo Scientific, Norway) and Agilent 2100 Bioanalyzer (Agilent Technologies, Norway). RNA purity was estimated by examining the OD 260/280 and the OD 260/230 ratios. RNA integrity numbers (RIN) from 1 to 10 (low to high RNA quality) were calculated using the 2100 Expert software (Agilent Technologies, Norway).

treatment_protocol: The experimental litters were given diets of purified ingredients from Research Diets Inc. (New Brunswick, NJ, USA) in various life periods. The D12451 diet, containing 20%, 35%, and 45% of kcal from protein, carbohydrates, and fat, respectively, was used as a HFD. The D12450H diet, containing 20%, 70%, and 10% of kcal from protein, carbohydrates, and fat, respectively, was used as a matching control diet (CD). Mice were randomly assigned to the experimental groups and exposed to the CD (22 mice/17 litters) or the HFD during combinations of three periods of life; in utero, from mating via the dams (UT; 27mice/17litters); from mating to weaning (UL; 25 mice/19 litters); and from mating to termination at 23 weeks (WL; 23 mice/21 litters).

tag: treatment

value: HFD, expode whole life (23 weeks)


title: 707HL

value: Hindlimb somatopleure


title: T2_Mys19_12h_pH


title: WL1

description:
samples from mice on HFD, expode whole life (23 weeks)
SAMPLE 10


title: WL2

description:
samples from mice on HFD, expode whole life (23 weeks)
SAMPLE 11


title: 710HL


title: T2_Mys18_12h_pH


title: 595HL


title: T2_Mys16_12h_control


title: T2_Mys17_12h_pH


title: UL3

description:
samples from mice on HFD, expode in utero and lactation
SAMPLE 9

value: HFD, expode in utero and lactation


title: T2_Mys15_12h_control


title: 583HL


title: UL1

description:
samples from mice on HFD, expode in utero and lactation
SAMPLE 7


title: UL2

description:
samples from mice on HFD, expode in utero and lactation
SAMPLE 8


title: 710FL

value: Forelimb somatopleure


title: UT3

description:
samples from mice on HFD, expode in utero
SAMPLE 6

value: HFD, expode in utero


title: UT2

description:
samples from mice on HFD, expode in utero
SAMPLE 5


title: 707K


title: UT1

description:
samples from mice on HFD, expode in utero
SAMPLE 4


title: T2_Mys13_12h_control


title: 707FL


title: 583K


title: 583FL


title: CD3

description:
samples from mice on matching control diet (CD)
SAMPLE 3

value: matching control diet (CD)


title: 595FL


title: CD2

description:
samples from mice on matching control diet (CD)
SAMPLE 2


title: Tendon injured extracted 3 days post-injury [B04 - 3DAYS-PÓST-INJURY]

description: 3 days post-injury

value: calcaneus tendon


title: T2_Mys14_12h_control


title: CD1

description:
samples from mice on matching control diet (CD)
SAMPLE 1


title: Yang-DC10

status: Public on Sep 29 2019

city: Beijing

first: dan

last: liu

address: NO.1 Beichen West Road, Chaoyang District, Beijing

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

description: Gene expression data from Sample Yang-DC10

hyb_protocol: Samples were prepared according to the standard Affymetrix protocol

scan_protocol: Using GeneChip® Scanner 3000 from Affymetrix

data_processing: Using Robust Multichip Analysis（RMA）to normalized data.

label: biotin

source_name: PBMC

label_protocol: These RNA samples were then prepared for hybridizing to the Affymetrix HG-U133Plus2.0 array

extract_protocol: Between 8 and 9 am, samples of venous blood (8 mL) were collected. The serum was separated by centrifuging centrifugation at 3000 rgf for 5 min, and the peripheral blood mononuclear cells (PBMCs) were isolated by gradient centrifugation for 2 hours. Then, the total ribonucleic acid (RNA) of white blood cells was extracted with TRIzol and preserved in a freezer at -80°C

value: Venous blood

tag: ethnic group

value: Chines Han

tag: phenotype

value: Yang deficiency


title: Yang-DC4

description: Gene expression data from Sample Yang-DC4


title: Yang-DC6

description: Gene expression data from Sample Yang-DC6


title: Yang-DC7

description: Gene expression data from Sample Yang-DC7


title: Yang-DC3

description: Gene expression data from Sample Yang-DC3


title: Yang-DC9

description: Gene expression data from Sample Yang-DC9


title: Yang-DC12

description: Gene expression data from Sample Yang-DC12


title: Yang-DC11

description: Gene expression data from Sample Yang-DC11


title: Yang-DC5

description: Gene expression data from Sample Yang-DC5


title: Yin-DC10

description: Gene expression data from Sample Yin-DC10

value: Yin deficiency


title: Yang-DC1

description: Gene expression data from Sample Yang-DC1


title: Yin-DC9

description: Gene expression data from Sample Yin-DC9


title: Yin-DC12

description: Gene expression data from Sample Yin-DC12


title: Yin-DC7

description: Gene expression data from Sample Yin-DC7


title: Yin-DC8

description: Gene expression data from Sample Yin-DC8


title: Yang-DC2

description: Gene expression data from Sample Yang-DC2


title: Yin-DC6

description: Gene expression data from Sample Yin-DC6


title: Yin-DC3

description: Gene expression data from Sample Yin-DC3


title: Yin-DC11

description: Gene expression data from Sample Yin-DC11


title: Yin-DC2

description: Gene expression data from Sample Yin-DC2


title: BLC5

description: Gene expression data from Sample BLC5

value: balanced constitution


title: BLC6

description: Gene expression data from Sample BLC6


title: BLC8

description: Gene expression data from Sample BLC8


title: Yin-DC1

description: Gene expression data from Sample Yin-DC1


title: BLC7

description: Gene expression data from Sample BLC7


title: BLC3

description: Gene expression data from Sample BLC3


title: Yang-DC8

description: Gene expression data from Sample Yang-DC8


title: GS0278_CD4_Sri Lanka 1°

first: Yuan

last: Tian

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

description: Microscaled (SmartSeq2) cDNA amplification - RNA seq

data_processing:
The single-end reads that passed Illumina filters were filtered for reads aligning to tRNA, rRNA, adapter sequences, and spike-in controls. The reads were then aligned to UCSC hg19 reference genome using TopHat (v 1.4.1) (Trapnell et al., 2009). DUST scores were calculated with PRINSEQ Lite (v 0.20.3) (Schmieder et al., 2011) and low-complexity reads (DUST > 4) were removed from the BAM files.  The alignment results were parsed via the SAMtools (Li et al., 2009) to generate SAM files. Read counts to each genomic feature were obtained with the htseq-count program (v 0.6.0) (Anders et al., 2014) using the “union” option.
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements as a matrix table

source_name: Cryopreserved PBMC

growth_protocol: Cells were directly isolated post thawing of cryopreserved PBMC samples and lysed, no culture were involved.

extract_protocol:
Cryopreserved PBMC were thawed, stained with antibodies, and 100,000 memory CD4 or memory CD8 T cells sorted using BD Aria 3 or BD Aria Fusion cell sorter direclty in Trizol. Memory cells were defined as the combination of CCR7-CD45RA-, CCR7-CD45RA+ and CCR7+CD45RA- populations. Total RNA was purified using a miRNAeasy micro kit (Qiagen, USA) and quantified by qPCR as described previously (Seumois et al., 2012).
Purified total RNA (1 to 5 ng) was amplified following the smart-seq2 protocol (16 cycles of cDNA amplification) (Picelli et al., 2014). cDNA was purified using AMPure XP beads (Beckman Coulter). From this step, 1 ng of cDNA was used to prepare a standard Nextera XT sequencing library (Nextera XT DNA sample preparation kit and index kit, Illumina).

treatment_protocol: No specific treatment involved

tag: disease group

value: Sri Lanka 1degree

tag: cell subset

value: Memory CD3+CD4+ T cells


title: GS0278_CD8_Sri Lanka 1°

value: Memory CD3+CD8+ T cells


title: GS0253_CD8_Sri Lanka 1°


title: GS0263_CD4_Sri Lanka 1°


title: GS0263_CD8_Sri Lanka 1°


title: GS0259_CD4_Sri Lanka 2°

value: Sri Lanka 2degree


title: GS0253_CD4_Sri Lanka 1°


title: GS0259_CD8_Sri Lanka 2°


title: Yin-DC4

description: Gene expression data from Sample Yin-DC4


title: Yin-DC5

description: Gene expression data from Sample Yin-DC5


title: BLC2

description: Gene expression data from Sample BLC2


title: GS0239_CD4_Sri Lanka 1°


title: GS0239_CD8_Sri Lanka 1°


title: GS0241_CD4_Sri Lanka 1°


title: GS0229_CD8_Sri Lanka 1°


title: GS0229_CD4_Sri Lanka 1°


title: GS0227_CD8_Sri Lanka 1°


title: GS0227_CD4_Sri Lanka 1°


title: GS0222_CD8_Sri Lanka_negative

value: Sri Lanka negative


title: GS0222_CD4_Sri Lanka_negative


title: GS0216_CD8_Sri Lanka_negative


title: GS0213_CD4_Sri Lanka_negative


title: GS0200_CD8_Sri Lanka 1°


title: BLC4

description: Gene expression data from Sample BLC4


title: GS0241_CD8_Sri Lanka 1°


title: GS0210_CD8_Sri Lanka 2°


title: GS0193_CD8_Sri Lanka 2°


title: GS0193_CD4_Sri Lanka 2°


title: GS0174_CD8_Sri Lanka_negative


title: GS0164_CD8_Sri Lanka_negative


title: GS0181_CD4_Sri Lanka_negative


title: GS0182_CD4_Sri Lanka 1°


title: BLC1

description: Gene expression data from Sample BLC1


title: GS0164_CD4_Sri Lanka_negative


title: GS0159_CD8_Sri Lanka 1


title: GS0159_CD4_Sri Lanka 1°


title: GS0143_CD8_Sri Lanka 2°


title: GS0133_CD8_Sri Lanka 2°


title: GS0136_CD8_Sri Lanka_negative


title: GS0133_CD4_Sri Lanka 2°


title: GS0128_CD4_Sri Lanka 2°


title: GS0128_CD8_Sri Lanka 2°


title: GS0132_CD4_Sri Lanka 2°


title: GS0119_CD8_Sri Lanka_negative


title: GS0127_CD8_Sri Lanka_negative


title: GS0174_CD4_Sri Lanka_negative


title: GS0127_CD4_Sri Lanka_negative


title: GS0119_CD4_Sri Lanka_negative


title: GS0118_CD4_Sri Lanka_negative


title: GS0118_CD8_Sri Lanka_negative


title: GS0117_CD8_Sri Lanka 2°


title: GS0162_CD8_Sri Lanka 1°


title: GS0109_CD4_Sri Lanka 1°


title: GS0099_CD8_Sri Lanka 2°


title: GS0108_CD4_Sri Lanka 2°


title: GS0117_CD4_Sri Lanka 2°


title: GS0143_CD4_Sri Lanka 2°


title: GS0099_CD4_Sri Lanka 2°


title: GS0136_CD4_Sri Lanka_negative


title: GS0098_CD8_Sri Lanka 2°


title: Nkx2-1;Sftpc P8 AT2 Mutant_A

city: Memphis

first: Danielle

middle: R.

last: Little

state: Tennessee

address: 262 Danny Thomas Pl Rm D2031

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

data_processing:
The libraries were bar-coded (New England BioLabs, E7335S) and sequenced on a NextSeq 500 at the UT MD Anderson Sequencing and Microarray Facility to obtain 18−30 million 76 nucleotide pair-end reads for each sample.
Alignment to the mm10 genome using a tophat2 v2.0.14 /bowtie2 v2.2.3 pipeline followed by normalization with cufflinks v2.2.1 pipeline
Pairwise comparisons made using paired T-test on Cuffnorm ouptut
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet with all control and mutant samples, their FPKM, fold change and p value.

source_name: Lung alveolar type 2 epithelial cells

extract_protocol:
QIAgen RNeasy Mini  100~200 ng total RNA was used to prepare an RNAseq library using an mRNA isolation kit (New England BioLabs, E7490) and a NEBNext Ultra RNA library prep kit (New England BioLabs, E7530S) with a final double (0.65 x -1 x bead volume) size selection step using a SPRIselect reagent kit (Beckman Coulter, B23318).
Seventy-six nucleotide pair-end reads were generated for each sample and aligned to the UCSC mm10 reference genome using tophat2 and bowtie2 in R

value: alveolar type 2 epithelial cells

value: Postnatal day 8

value: mutant


title: Nkx2-1;Sftpc P9 AT2 Mutant_C

value: Postnatal day 9


title: Nkx2-1;Sftpc P8 AT2 Mutant_B


title: Nkx2-1;Sftpc P9 AT2 Control_C

value: control


title: Nkx2-1;Sftpc P8 AT2 Control_B


title: GS0094_CD8_Sri Lanka_negative


title: GS0132_CD8_Sri Lanka 2°


title: GS0098_CD4_Sri Lanka 2°


title: GS0094_CD4_Sri Lanka_negative


title: Nkx2-1;Sftpc P8 AT2 Control_A


title: GS0089_CD8_Sri Lanka 2°


title: P10_Input_ChIP-seq

library_source: genomic

data_processing:
Fastqc was run on the raw Fastq files to determine initial quality of reads.
Trimmomatic was performed to remove barcodes and poor quality bases.
Fastqc was run for quality control.
Bowtie alignment to the mm10 genomic with -m1 -k1 -v1 parameters and filtered for unmapped reads with sam file output
Convert sam to bam using samtools.
Bam files were checked using SPP analysis then run through MACS2 for peak calling with the --scaleup option for input due to low read depth in the input. Output of MACS2 are in excel format for called peaks.
Bam files were combind in equal proportions then normalized to input using the SES method through the BamCompare function of DeepTools to make a bigwig for profile ploting specific idenfied peaks.
Genome_build: mm10
Supplementary_files_format_and_content: Peak txt files have locations of called peaks from each antibody against the scaled up input, while the bigwig file is useful for making profile plots and heatmaps of identified regions of interest.

molecule: genomic DNA

source_name: Lung tissue

extract_protocol:
Lungs from Avertin anesthetized mice were harvested after perfusion with cold PBS through the right ventricle. Extra-pulmonary tissues were then removed and lungs were minced using forceps and crosslinked with 1:4 dilution of 10% buffered formalin (ThermoFisher Scientific, 23-245-685) in PBS on a rocker at room temperature for 10 minutes. Samples were then quenched by adding 1M glycine (pH5) to a final concentration of 125mM and incubated on a rocker for 10 minutes at room temperature. Samples were washed two times with 2mL of PBS and resuspended with 1mL of isolation of nuclei tagged in specific cell types (INTACT) (20mM Hepes pH7.4, 25mM KCl, 0.5mM MgCl2, 0.25M sucrose, 1mM DTT, 0.4% NP-40, 0.5 mM Spermine, 0.5mM Spermidine) with protease inhibitor cocktail (cOmplete ULTRA Tablets, Mini, EDTA-free, EASY pack, Roche) (Mo et al., 2015, Deal and Henikoff, 2010). Resuspended samples were then homogenized using an electric homogenizer with three pulses lasting five seconds each. The resulting solution was then filtered through a 70µm cell strainer and centrifuged in a 2mL tube at 384 rcf for 5 minutes. The pellet was resuspended in a PBS with protease inhibitor cocktail (cOmplete ULTRA Tablets, Mini, EDTA-free, EASY pack, Roche, 05 892 791 001). Nuclei were counted and 1 million nuclei aliquots were added to six 1.7mL tubes (Olympus plastics, 24-282). These subdivided samples were then centrifuged down at 384 rcf for 5 minutes. The pellet was resuspended in 100µL ChIP nuclei lysis buffer (50mM Tris-HCl pH 8.1, 10mM EDTA, 1% SDS with 1x protease inhibitor cocktail). After incubation on ice for fifteen minutes, samples were then sonicated using a Bioruptor Twin (Diagenode, UCD-400-TO) in a 4°C cold room on the high setting for 37 cycles of 30 seconds on 30 seconds off to achieve DNA fragment size of 200-500bp. The samples were then centrifuged at 12,052 rcf for 15 minutes at 4°C. The supernatant from each tube was pooled to a total volume of 600µL. From this pooled chromatin, 20µL of the sample was taken as an input control, diluted with Tris-EDTA (TE) buffer (1mM EDTA, 10mM Tris-HCl pH 8.1), and stored at -80°C. The remaining 580µL of chromatin was diluted to 1mL with ChIP dilution buffer (16.7mM Tris-HCl pH 8.1, 1.2 mM EDTA, 1.1% Triton X-100, 0.01% SDS with 1x protease inhibitor cocktail) and precleared with 40µL Protein G Dynabeads (ThermoFisher Scientific, 10004D) in a 2mL tube for 1 hr on a rotator at 4°C. Precleared chromatin divided into four tubes (250µL/tube) and diluted to 1mL with ChIP dilution buffer such that roughly 1 million nuclei were incubated with 1 µg of each Nkx2-1 antibody overnight at 4°C on a rotator. Concurrently, 30µL protein G Dynabeads for each antibody were blocked overnight at 4°C on a rotator in 500µL ChIP dilution buffer with the addition of 200µL 25mg/mL Bovine Serum Albumin (Jackson ImmunoResearch, 001-000-161), and 4µL 10mg/mL Salmon DNA Sperm (Invitrogen, 15632-011). The next morning, the blocked beads were washed with ChIP dilution buffer twice and transferred to new 2mL tubes. The antibody-chromatin solution was added and incubated for 3 hr at 4°C while rotating. The dynabeads were then isolated using a magnetic adaptor and washed with 1 mL of each of the following buffers for five minutes each on a rotator: low salt buffer (150mM NaCl, 2mM EDTA, 1% Triton X-100, 20mM Tris-HCl pH 8.1, 0.1% SDS), high salt buffer (500mM NaCl, 2mM EDTA, 1% Triton X-100, 20mM Tris-HCl pH 8.1, 0.1% SDS), lithium chloride buffer (250mM LiCl, 1mM EDTA, 1% NP-40, 10mM Tris-HCl pH 8.1, 0.1% sodium deoxycholate) twice and TE buffer twice. The resuspended sample after the second TE wash was transferred to fresh 2mL tubes and a magnetic adaptor was used to collect the dynabeads and 300µL fresh TE was added. The samples and the frozen input chromatin were then incubated at 37°C with 1.5µL of 10mg/mL RNase A (Qiagen, 1007885) for 1 hr, followed by a 4 hr incubation at 55°C after adding 3.5µL of 20mg/mL Proteinase K (ThermoFisher Scientific, EO0491) and 15µL of 10% SDS. The incubation continued overnight at 65°C to reverse the crosslinking. DNA extraction was then performed by adding 1 volume of phenol–chloroform-isoamyl solution (Sigma, P2069-400ML) followed by centrifugation at 12,052 rcf for 15 minutes. DNA in the upper phase were precipitated by adding 2 volumes of 100% ethanol, 1/10 volume of 3M NaCl and 3µL of 20 µg/µL glycogen (Invitrogen, 10814-010). The solution was then vortexed briefly and centrifuged for 30 minutes at 12,052 rcf in a 4°C cold room. The pellet was washed with 70% ethanol without resuspension. The sample was then centrifuged for 5 minutes at 9,200 rcf at room temperature. The pellet was air dried for 10 minutes and dissolved in 10µL nuclease free ddH2O.
ChIP DNA quantity was measured using the Qubit dsDNA HS Assay Kit (Invitrogen, Q32851). 2-5ng of sample DNA was used to generate sequencing libraries using the NEB Next Ultra II DNA Library Prep Kit for Illumina (NEB, E7645). Step 3.1 in the NEB protocol was skipped to improve sample retention per manufacturer’s recommendation. Samples were PCR amplified for 12 cycles and barcoded using indexing primers (New England BioLabs, E7335s or E7500S) followed by a final (.65 x -1 x bead volume) size selection and purification step using a SPRIselect reagent (Beckman Coulter, B23318). Samples were then verified for library size by gel electrophoresis and concentration measured using the Qubit HS dsDNA assay. Samples were then sequenced on the Illumina NextSeq500.

value: Wildtype


title: GS0089_CD4_Sri Lanka 2°


title: GS0108_CD8_Sri Lanka 2°


title: P10_Abcam133638-NKX2-1_ChIP-seq

tag: chip antibody


title: GS0088_CD8_Sri Lanka_negative


title: GS0088_CD4_Sri Lanka_negative


title: P10_Abcam76013-NKX2-1_ChIP-seq


title: GS0076_CD8_Sri Lanka 2°


title: GS0079_CD4_Sri Lanka 2°


title: Mutant scRNAseq Nkx2-1;Aqp5

data_processing:
Chromium single-cell RNA-seq output was processed with Cell Ranger using “cellranger count” and “cellranger aggr”.
Further analysis was carried out using Loupe Cell Browser (10x Genomics) or an R package Seurat
Genome_build: mm10
Supplementary_files_format_and_content: tsv and mtx files can be opened with Seurat (R package) and analyzed. Cloupe file can be opened with Loupe cell browser to visualize the data.

source_name: Lung epithelial, immune, endothelial, and mesenchymal cells

extract_protocol:
FACS-purified lung epithelial, immune, endothelial, and mesenchymal cells were processed through the Chromium Single Cell Gene Expression Solution Platform (10X Genomics) using the Chromium Single Cell 3' Library and Gel Bead Kit in accordance with the manufacturer’s user guide (v2, rev D).
The libraries were sequenced on an Illumina NextSeq500 using a 26X124 sequencing run format with 8 bp index (Read1).

tag: "cell type"

tag: "age"

value: Postnatal day 10

tag: "genotype"


title: P10_Abcam133737-NKX2-1_ChIP-seq


title: P10_Millipore07-601-NKX2-1_ChIP-seq


title: GS0075_CD8_Sri Lanka_negative


title: GS0213_CD8_Sri Lanka_negative


title: Control scRNAseq Nkx2-1

value: epithelial, immune, endothelial, and mesenchymal cells


title: GS0075_CD4_Sri Lanka_negative


title: Nkx2-1;Aqp5 P14 lung Mutant_A

data_processing:
The libraries were bar-coded (New England BioLabs, E7335S) and sequenced on a NextSeq 500 at the UT MD Anderson Sequencing and Microarray Facility to obtain 18−30 million 76 nucleotide pair-end reads for each sample.
Alignment to the mm10 genome using a tophat2 v2.0.14 /bowtie2 v2.2.3 pipeline followed by normalization with cufflinks v2.2.1 pipeline
Pairwise comparisons made using cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet with all control and mutant samples, their FPKM, fold change and p value.

source_name: Lung cells

value: lung cells

value: Postnatal day 14


title: GS0073_CD8_Sri Lanka_negative


title: Nkx2-1;Aqp5 P5 AT1 Mutant_C

source_name: Lung alveolar type 1 epithelial cells

value: alveolar type 1 epithelial cells

value: Postnatal day 5


title: GS0058_CD8_Sri Lanka 1

value: Sri Lanka 1degree


title: Nkx2-1;Aqp5 P5 AT1 Mutant_A


title: Nkx2-1;Aqp5 P5 AT1 Mutant_B


title: GS0073_CD4_Sri Lanka_negative

value: Memory CD3+CD4+ T cells


title: GS0058_CD4_Sri Lanka 1°


title: GS0053_CD4_Sri Lanka_negative


title: GS0079_CD8_Sri Lanka 2°

value: Memory CD3+CD8+ T cells


title: Nkx2-1;Aqp5 P5 AT1 Control_A


title: GS0053_CD8_Sri Lanka_negative


title: Nkx2-1;Aqp5 P5 AT1 Control_B


title: Nkx2-1;Aqp5 P5 AT1 Control_C


title: GS0011_CD8_Sri Lanka 1°


title: GN0114CD8_Nicaragua 2

value: Nicaragua 2degree


title: GS0011_CD4_Sri Lanka 1°


title: GN0109 CD8_Nicaragua 2


title: GN0114_CD4_Nicaragua 2°


title: Nkx2-1;Aqp5 P14 lung Control_A


title: GN0109_CD4_Nicaragua 2°


title: GN0108CD8_Nicaragua 2


title: GN0108_CD4_Nicaragua 2°


title: LN_H3K4me2_ctrl_rep1

first: Changmeng

last: Cai

state: Massachusetts

address: 100 William T. Morrissey Blvd.

institute: University of Massachusetts Boston

data_processing:
Raw reads were aligned to hg19 using bwa (version 0.7.2-r351)
sam files are converted to bam with samtools (version 0.1.18 (r982:295))
MACS2 (version 2.0.10.20131216) was used to call peak on the bam files
bedGraph files containing signal per million reads produced from MACS2 was converted to bigwig files with ucsctool kit (315)
Genome_build: GRCh37
Supplementary_files_format_and_content: bigWig and narrowPeak files containing normalized signal and peak intervals

growth_protocol: The LNCaP cells were cultured in RPMI-1640 with 10% FBS (fetal bovine serum), and were recently authenticated using short tandem repeat (STR) profiling by DDC Medical (Fairfield, OH, USA).

extract_protocol: Libraries construction was performed using ThruPLEX DNA-seq 48D Kit (Rubicon Genomics)

treatment_protocol: LNCaP were grown in5% CSS for 3 days，then treated with GSK2879552 for 4 or 24 hrs

tag: cell line

value: LNCaP

tag: cell type

value: prostate cancer cell line

value: vehicle without GSK


title: LN_H3K4me2_GSK4_rep2

value: DHT with GSK2879552 for 4hrs


title: LN_H3K4me2_ctrl_rep2


title: LN_H3K4me2_GSK4_rep1


title: LN_H3K4me2_GSK24_rep1

value: DHT with GSK2879552 for 24 hrs


title: LN_H3K4me2_GSK24_rep2


title: GSK2wVEH_L002

description:
technical replicate for GSK2wVEH treatment
rnaseq_gsk48h2w_normalized_count_lfc.csv

data_processing:
Raw reads were aligned to hg19 (genecode v24lift37) using STAR (v2.4.2a)
Gene level read counts was produced by setting the parameter 'quantMode' as 'GeneCounts' in STAR
Counts were normalized to the same depth as GSK48hDHT condition and the log2FC was calculated using the normalized counts with a pseudo count of 1
Genome_build: GRCh37
Supplementary_files_format_and_content: csv files for gene level normalized count and log2FC

source_name: LNCaP

extract_protocol:
RNA was extracted with Rneasy Mini Kit (QIAGEN) following manufacturer’s protocol
TruSeq® Strnd Total RNA LT (Illumina) was used for library construction

treatment_protocol: LNCaP cells were treated with vehicle or DHT and together with or without GSK2879552 for 24, 48 hrs or 2 weeks.


title: GSK2wDHT_L002

description:
technical replicate for GSK2wDHT treatment
rnaseq_gsk48h2w_normalized_count_lfc.csv


title: GN0107_CD4_Nicaragua 2°


title: GN0107CD8_Nicaragua 2


title: GSK2wDHT_L001


title: GN0106CD8_Nicaragua 2


title: GSK48hVEH_L002

description:
technical replicate for GSK48hVEH treatment
rnaseq_gsk48h2w_normalized_count_lfc.csv


title: GN0106_CD4_Nicaragua 2°


title: GSK48hDHT_L002

description:
technical replicate for GSK48hDHT treatment
rnaseq_gsk48h2w_normalized_count_lfc.csv


title: GSK48hVEH_L001


title: GN0105_CD4_Nicaragua 2°


title: GN0105CD8_Nicaragua 2


title: GSK48hDHT_L001


title: GN0104_CD4_Nicaragua 2°


title: GSK24hDHT_L002

description:
technical replicate for GSK24hDHT treatment
rnaseq_gsk24h_normalized_count_lfc.csv


title: GSK24hDHT_L001


title: GN0104 CD8_Nicaragua 2


title: GN0103CD8_Nicaragua 2


title: GSK2wVEH_L001


title: GN0103_CD4_Nicaragua 2°


title: GSK24hVEH_L001

description:
technical replicate for GSK24hVEH treatment
rnaseq_gsk24h_normalized_count_lfc.csv


title: GN0102_CD4_Nicaragua 2°


title: DHT_L001

description:
technical replicate for DHT treatment
rnaseq_gsk48h2w_normalized_count_lfc.csv


title: DHT_L002


title: GN0102 CD8_Nicaragua 2


title: GN0073_CD4_Nicaragua 2°


title: GN0072_CD4_Nicaragua 2°


title: LN_VEH_K27AC_L002

growth_protocol: The LNCaP cells were cultured in RPMI-1640 with 10% FBS (fetal bovine serum), and were recently authenticated using short tandem repeat (STR) profiling by DDC Medical (Fairfield, OH, USA)

extract_protocol:
Cells were crosslinked with formaldehyde and then sonicated. DNA were immunoprecipitatted with ARC19 antibody and protein A/G beads. After reverse crosslinking, DNA were purifed with Qiagen PCR purification kit.
Libraries construction was performed using ThruPLEX DNA-seq 48D Kit (Rubicon Genomics)

treatment_protocol: LNCaP cells treated with vehicle, DHT (10nM at 4h), DHT (4h) with pretreated GSK2879552 (50µM for 4h), or DHT (4h) with pretreated GSK2879552 (48h)


title: VEH_L002

description:
technical replicate for VEH treatment
rnaseq_gsk24h_normalized_count_lfc.csv


title: GN0077CD8_Nicaragua 2


title: GS0182_CD8_Sri Lanka 1°


title: GN0072 CD8_Nicaragua 2


title: LN_VEH_K27AC_L001


title: LN_GSK4H_K27AC_L001


title: LN_GSK4H_K27AC_L002


title: GN0068_CD4_Nicaragua 2°


title: LN_GSK2D_K27AC_L001


title: GN0066 CD8_Nicaragua 2


title: GSK24hVEH_L002


title: GN0068 CD8_Nicaragua 2


title: LN_GSK2D_K27AC_L002


title: LN_VEH_FOXA1_L002


title: LN_VEH_FOXA1_L001


title: GN0064_CD4_Nicaragua 2°


title: LN_S2101_4H_FOXA1_L002


title: GN0073CD8_Nicaragua 2


title: LN_S2101_4H_FOXA1_L001


title: VEH_L001


title: LN_S2101_48H_FOXA1_L002


title: LN_S2101_48H_FOXA1_L001


title: LN_GSK_4H_FOXA1_L002


title: LN_GSK_4H_FOXA1_L001


title: Tbr1 homo sample 3

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

institute: IBS/KAIST

data_processing:
Transcript abundance was estimated with Salmon(v0.11.2) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.5.3) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.22.2).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Brain

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: brain

tag: Sex

value: female

tag: genotype

value: Tbr1 homo


title: Tbr1 homo sample 4

tag: age

value: male


title: LN_GSK_48H_FOXA1_L002


title: GS0266_CD8_Sri Lanka 1°


title: Tbr1 hetero sample 5

value: Tbr1 hetero


title: ChIP-seq of SIN-3 in wild-type, replicate 1_1

first: Julie

last: Ahringer

address: Tennis Court Road

department: The Gurdon Institute

institute: University of Cambridge

data_processing:
SIN-3 ChIP-seq reads were aligned to the ce11/WBcel235 assembly of the C. elegans genome using BWA (Li and Durbin, 2010) with default settings.
HDA-1 ChIP-seq reads were aligned to a concatenated reference genome sequence containing C. elegans ce11 and C. briggsae cb3 assemblies using BWA (Li and Durbin, 2010) with default settings.
SIN-3 and HDA-1 ChIP-seq that mapped uniquely to ce11 (mapq>=10) were normalized using BEADS algorithm (Cheung et al, 2011).
Sequencing reads from H3K4me3 ChIP and corresponding input samples were mapped to a concatenated reference genome sequence containing C. elegans ce11 and C. briggsae cb3 and were then separated by species. Only reads that mapped uniquely (mapq>=10) to non-blacklisted regions were kept. The spike-in ratios of C. briggsae to C. elegans chromatin present in the combined extract were calculated from the input sequence as C. briggsae read count divided by C. elegans read count. C briggsae H3K4me3 peaks were called from ChIP data using macs2 (Zhang et al. 2008) with default parameters. Scaling factors for each ChIP samples were calculated as corresponding spike-in ratio divided by C. briggsae H3K4me3 ChIP read count in peak regions in millions. These scaling factors were applied to C .elegans H3K4me3 ChIP raw coverage track. As a last step, ChIP background was removed from the scale coverage tracks by subtracting the mode and setting negative values to zero.
ChIP-seq signals were exported to bigWig tracks.
Genome_build: ce11/WBcel235
Genome_build: Concatenated reference genome sequence containing C. elegans ce11/WBcel235 and C. briggsae cb3 assemblies
Genome_build: ftp://hgdownload.cse.ucsc.edu/goldenPath/ce11/bigZips/ce11.2bit
Genome_build: ftp://hgdownload.cse.ucsc.edu/goldenPath/cb3/bigZips/cb3.2bit
Supplementary_files_format_and_content: "linear" scores in bigWig tracks represent BEADS values; files were generated using BEADS normalization pipeline in R
Supplementary_files_format_and_content: "zscore" scores in bigWig tracks represent standardized BEADS values; files were generated using BEADS normalization pipeline in R
Supplementary_files_format_and_content: "spknorm" scores in bigWig tracks represent spike-in normalised values in linear scale

organism: Caenorhabditis elegans

source_name: Mixed Embryos

growth_protocol: Wild-type, cfp-1(tm6369), and set-2(bn129) mixed embryos were obtained by growing strains at 20°C in liquid culture using standard S-basal medium with HB101 bacteria.  Strains were grown to the adult stage then bleached to obtain embryos, which were washed in M9, then frozen into "popcorn" by dripping embryo slurry into liquid nitrogen. The age distributions of mixed embryo collections were in the following proportions (<300 cell/over300cell, average of the two replicates):  H3K4me3 ChIPs: WT N2, 51/49; cfp-1, 59/51, set-2, 54/46.  SIN-3 and HDA-1 ChIPs: WT N2, 48/52; cfp-1, 49/51.

extract_protocol: Chromatin immunoprecipitations and library preparations were conducted as in (McMurchy et al., 2017), using formaldehyde as a fixitive for the H3K4me3 ChIPs (30ug DNA, 2.5ug antibody) and formaldehyde and EGS as fixatives for the SIN-3 (15ug DNA, 2.5ug antibody) and HDA-1 (30ug DNA, 2.5ug antibody) ChIPs. Approximately 10% C. briggsae chromatin extract was spiked into the C. elegans extract for the H3K4me3 ChIPs and 5% into the HDA-1 ChIPs. The HDA-1 antibody did not detect C. briggsae HDA-1 and so was not used for normalization.

value: whole larvae

tag: Stage

value: MxE

tag: chip antibody supplier

value: Novus Biologicals

tag: chip antibody catalog#


title: ChIP-seq of SIN-3 in wild-type, replicate 2_1


title: ChIP-seq of HDA-1 in cfp-1, replicate 2

description: 5% C. briggsae spike-in


title: LN_GSK_48H_FOXA1_L001


title: GN0066_CD4_Nicaragua 2°


title: ChIP-seq of HDA-1 in cfp-1, replicate 1

description: 5% C. briggsae spike-in


title: LN_DHT_AR_L002


title: Tbr1 hetero sample 4


title: ChIP-seq of HDA-1 in wild-type, replicate 2

description: 5% C. briggsae spike-in


title: Tbr1 homo sample 5


title: Tbr1 hetero sample 3


title: LN_DHT_GSK2D_AR_L001


title: Tbr1 hetero sample 2


title: Tbr1 hetero sample 1


title: ChIP-seq of SIN-3 in wild-type, replicate 2


title: ChIP-seq of SIN-3 in cfp-1, replicate 2


title: ChIP-seq of SIN-3 in cfp-1, replicate 1


title: ChIP-seq of SIN-3 in wild-type, replicate 1


title: Tbr1 homo sample 1


title: ChIP-seq of HDA-1 in wild-type, replicate 1

description: 5% C. briggsae spike-in


title: Tbr1 homo sample 2


title: ChIP-seq of H3K4me3 in set-2, replicate 2

description: 10% C. briggsae spike-in

value: Abcam


title: wild type sample 5

value: WT


title: ChIP-seq of H3K4me3 in set-2, replicate 1

description: 10% C. briggsae spike-in


title: LN_VEH_AR_L002


title: ChIP-seq of H3K4me3 in cfp-1, replicate 2

description: 10% C. briggsae spike-in


title: wild type sample 4


title: LN_VEH_AR_L001


title: ChIP-seq of H3K4me3 in cfp-1, replicate 1

description: 10% C. briggsae spike-in


title: ChIP-seq of H3K4me3 in wild-type, replicate 2

description: 10% C. briggsae spike-in


title: LN_DHT_GSK4H_AR_L001


title: ChIP-seq of H3K4me3 in wild-type, replicate 1

description: 10% C. briggsae spike-in


title: wild type sample 3


title: wild type sample 2


title: LN_DHT_AR_L001


title: LN_DHT_GSK4H_AR_L002


title: wild type sample 1


title: degS mutant 1

city: 遵义市

first: 健

last: 黄

state: 贵州省

address: 汇川区大连路149号遵义医学院附属医院

institute: 遵义医学院附属医院

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.1.8 mapping to reference genome
count counting using HTSeq
Genome_build: hg19_GRCh37
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Vibrio cholerae

source_name: Vibrio cholerae

extract_protocol:
For in vitro RNA preparations, the wild type strain and degS deletion mutant strains were grown to mid-exponential phase (OD600 of ~0.6) in LB liquid medium. Total RNA was extracted from the wild type and degS deletion mutant using TRIzol Reagent (TaKaRa, Japan). After ensuring quality control, the cDNA libraries were prepared, and sequencing was performed by NovelBio Bio-Pharm Technology Co. Ltd. (Shanghai, China).
Ion  Proton Sequencing Protocol
RNA-Seq useing Ion Torrent Proton,Torrent Suite Software and Torrent Server for  base calling

treatment_protocol: The degS in-frame deletion mutants were generated by a suicide vector pWM91 as described previously (Metcalf et al., 1996).

value: degS deletion

value: HN375 strain


title: WT2

address: 汇川区大连路149号遵义医学院附属医院

growth_protocol: For in vitro RNA preparations, the wild type strain and degS deletion mutant strains were grown to mid-exponential phase (OD600 of ~0.6) in LB liquid medium.

value: wild type


title: WT1

address: 汇川区大连路149号遵义医学院附属医院


title: LN_DHT_GSK2D_AR_L002

value: prostate cancer cell line


title: degS mutant 2

address: 汇川区大连路149号遵义医学院附属医院


title: Col-0_15days_after_pollination_total_rep1

status: Public on Sep 28 2019

city: Wageningen

first: Leónie

last: Bentsink

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

hyb_protocol: GeneChip® 3' IVT Express kit (cat. # 901229) was used for hybridisation, washing and staining of the cartridges.

scan_protocol: Scanning of the arrays was performed using the Affimetrix 3000G scanner.

data_processing: The GeneChip data were analyzed using the R statistical programming environment and Bioconductor packages. The data were normalized using the RMA algorithm. The P values were adjusted for multiple testing with the Benjamini and Hochberg method to control for false positives.

source_name: Col-0 seeds

label_protocol: RNA was processed and cRNA synthesized according to the 3’ GeneChips OneCycle kit.

growth_protocol: For the transcriptome and  transcriptome analyses Col-0 were grown in a randomized complete block design with three replicates. Each replicate consisted of a bulk of eight plants. The precise growth conditions used were described by (El-Lithy et al., Genetics, 2006). Plant were harvested at specified developmental stages.

extract_protocol: The total RNA and polysomal RNA were purified with TriPure Isolation Reagent (Roche, Basel, Switzerland), further purified using RNeasy Mini spin columns (Qiagen, Hilden, Germany) and dissolved in RNase-free H2O for further analyses.

treatment_protocol: RNA was extracted from seeds developed at each stages with three biological replicates for each time point.

tag: developmental stage

value: 15 DAP

value: seeds

tag: ecotype

tag: rna type

value: Total RNA


title: Col-0_12days_after_pollination_total_rep1

value: 12 DAP


title: Col-0_18days_after_pollination_total_rep1

value: 18 DAP


title: Col-0_20days_after_pollination_total_rep1

value: 20 DAP


title: Col-0_18days_after_pollination_total_rep3


title: Col-0_20days_after_pollination_polysome_rep1

value: Polysomal RNA


title: Col-0_18days_after_pollination_polysome_rep3


title: Col-0_15days_after_pollination_total_rep2


title: Col-0_15days_after_pollination_total_rep3


title: Col-0_20days_after_pollination_polysome_rep3


title: Col-0_20days_after_pollination_total_rep3


title: Col-0_12days_after_pollination_polysome_rep3


title: Col-0_15days_after_pollination_polysome_rep3


title: Col-0_18days_after_pollination_polysome_rep2


title: Col-0_12days_after_pollination_total_rep2


title: Col-0_15days_after_pollination_polysome_rep1


title: Col-0_20days_after_pollination_total_rep2


title: Col-0_12days_after_pollination_polysome_rep2


title: normal gastric epithelium from Pdx1-1-Cre-negative mice 1

city: Seoul

first: Jun Won

last: Park

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Veterinary Pathology

institute: Seoul National University

hyb_protocol: According to the standard Affymetrix protocol

scan_protocol: Affymetrix GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Expression Console™ Software 1.3.1 using Affymetrix default analysis settings and global scaling as normalization method.

growth_protocol: monitoring mice

extract_protocol: Trizol reagent according to the manufacturer's instructions.

treatment_protocol: No treatment

value: normal gastric epithelium

tag: strain/genotype

value: Pdx1-1-Cre-negative mice

tag: histology

value: normal


title: gastric cancer tissues from Pdx-1-Cre;Cdh1F/+;Trp53F/F;Smad4F/F mice 1

label_protocol: According to the standard Affymetrix protocol

value: gastric cancer tissues

value: diffuse-type gastric cancer


title: Col-0_12days_after_pollination_polysome_rep1


title: Col-0_20days_after_pollination_polysome_rep2


title: normal gastric epithelium from Pdx1-1-Cre-negative mice 2


title: Col-0_15days_after_pollination_polysome_rep2


title: Col-0_12days_after_pollination_total_rep3


title: Col-0_18days_after_pollination_polysome_rep1