title: PATIENT 9 (4346): PTC-metastatic

city: Adana

first: Esra

last: Gov

state: Turkey

address: Gültepe Mahallesi, Çatalan Caddesi

department: Bioengineering

country: Turkey

institute: Adana Alparslan Türkeş Science and Technology University

description: gene expression profile from follicular variant of papillary thyroid carcinoma

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45 oC on GeneChip® Primeview Human Gene Expression Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450.

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

data_processing: CEL files were normalized with RMA using the affy Bioconductor package in R language.

source_name: PTC-metastatic

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip® 3' IVT PLUS Manual, 2013-2015, Affymetrix).

growth_protocol: The formalin-fixed paraffin embedded (FFPE) carcinoma tissues of PTC patients having (i) non-aggressive tumors, (ii) minimal invasion of extrathyroidal soft tissue, or (iii) distant organ metastasis were included in the study. Each FFPE tissue specimen was stained with hematoxylin and eosin (H&E) to ensure that characteristic features of the thyroid tumor were present. Areas with high density and purity (>80%) of tumor cells were chosen to minimize contamination from surrounding healthy thyroid tissue or infiltrating cells. Unstained histological sections of 10 µm thickness were manually sectioned from the FFPE tissues and used for RNA isolation.

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

tag: diagnosis

value: papillary thyroid cancer

value: Patient have papillary thyroid carcinoma of bone metastasis

tag: age


title: 9: Control

status: Public on Mar 23 2020

type: SRA

city: New York

first: Michael

middle: Seth

last: Garshick

state: NY

address: 435 East 30th Street

country: USA

institute: NYU Langone Health

description: Paxgene tubes

library_source: transcriptomic

data_processing:
Mapped to reference human genome GRCH37/hg19
Read counts with HTSeq V 0.60
Normalization with DSEeq v3.7
Supplementary_files_format_and_content: Tab-deliminated tet files lincluding FPKM values

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood RNA

extract_protocol:
Automatic QIAsymphony PAXgene Blood RNA Kit
Illumina TruSeq
200ng, 12 cyles of amplication 2 lanes of single read 50 on an Illumina HiSeq 4000 Sequencer

tag: disease state

value: Control

tag: tissue

value: Whole blood


title: 6: Control

description: Paxgene tubes


title: PCR-constant experiment replicate 1 1X Tn5

city: Ann Arbor

first: Stephen

last: Parker

state: MI

address: 100 Washtenaw Avenue

institute: University of Michigan

library_source: genomic

data_processing:
Basecalls performed using Illumina CASAVA bcl2fastq v2.17.1.14
Adapters were trimmed using cta (v. 0.1.2) with default settings
Reads were aligned to hg19 using bwa mem (v. 0.7.15-r1140; using the -M flag)
Read groups (corresponding to fastq files with '_1964'/'_1979') for PCR-constant samples were merged within each sample using samtools merge (v. 1.7)
Duplicates were marked using picard MarkDuplicates (v. 2.18.27) with VALIDATION_STRINGENCY=LENIENT
Reads were filtered to autosomal reads using samtools view with options -f 3 -F 4 -F 8 -F 256 -F 1024 -F 2048 -q 30
Peak calling was performed using MACS2 (v. 2.1.1.20160309; options: --nomodel --broad --shift -100 --extsize 200 --keep-dup all)
Peaks were filtered against the ENCODE hg19 blacklists (downloaded from  http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDacMapabilityConsensusExcludable.bed.gz and http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeMapability/wgEncodeDukeMapabilityRegionsExcludable.bed.gz)
To generate the list of "master peaks" (peaks that would be used for downstream analysis) for the PCR-variable and the PCR-constant experiments, we took all blacklist-filtered, FDR 1% peak calls from the 1X Tn5 libraries in that experiment, merged these peaks (bedtools merge; v. 2.27.1), and kept (as master peaks) those merged intervals that overlapped with the blacklist filtered, FDR 1% peak calls from at least two of the 1X Tn5 libraries in that experiment
Genome_build: hg19
Supplementary_files_format_and_content: broadPeak files contain the peak calls as output by MACS2. Each of the PCR-constant samples has only one set of peak calls, but the PCR-variable samples each have two sets of peak calls ('_low' and '_high'), since each of these samples was sequenced on a sequencing run with high cluster density as well as a sequencing run with low cluster density. The bedgraph files represent the 'treat_pileup' bedgraph files output by macs2 during peak calling. The 'counts' BED files represent read counts in master peaks, generated using bedtool's coverageBed (v. 2.27.1; with -counts flag) on each sample's filtered bam file.

molecule: genomic DNA

growth_protocol: We cultured GM12878 cells following the ENCODE GM12878 cell culture protocol (available at https://www.encodeproject.org/documents/1bb75b62-ac29-4368-9855-68d410e1963a/), except that we added plasmocin (Invivogen; 50 ug/mL) to the growth media to prevent mycoplasma contamination.

extract_protocol:
We isolated nuclei from three independent cultures for the PCR-variable experiment and six additional cultures for the PCR-constant experiment.
We conducted ATAC-seq as described in (Buenrostro et al. 2015) using a home-made Tn5 that we synthesized as described in (Picelli et al. 2014). For each replicate we incubated 50,000 nuclei with various concentrations of enzyme (1/5X, 1/2X, 2/3X, 1X, 1.5X, 2X, 5X; 1X corresponds to 2.5 uL of 1:1 Tn5-A/B mix) at 37 degrees C for 30 minutes in a 50 uL reaction. We column-purified the tagmented DNA using the Zymo DNA Clean & Concentrator-5 kit (Zymo Research, Irvine, CA). In the PCR-variable experiment, we PCR-amplified the entire eluate until amplification curve reached its mid-log phase (1/3 to 1/2 of max signal); whereas in the PCR-constant experiment, we amplified the entire eluate with a fixed number of PCR cycles (16) for all samples. We purified the products using SPRI beads prepared as in (Rohland and Reich, 2012) and eluted in 20 uL of TE buffer with Tween-20 (10 mM Tris-HCl, 0.1 mM EDTA, 0.05% Tween-20, pH 8)

tag: pcr cycles


title: PCR-constant experiment replicate 1 0.66X Tn5


title: 4: Psoriasis

description: Paxgene tubes

value: Psoriasis


title: PCR-constant experiment replicate 1 1.5X Tn5


title: PATIENT 8 (13739): PTC-metastatic

type: RNA

label: biotin

value: Patient have papillary thyroid carcinoma of lung and bone metastasis

tag: gender

value: female


title: Mononuclear_cells_patient_2_placebo

city: Kuopio

first: Jaana

last: Rysae

address: Yliopistonranta 1C

department: School of Pharmacy

country: Finland

institute: University of Eastern Finland

description:
Gene expression data from patient no:2 after administration of placebo for one week.
084-2K2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was log2-transformed, normalized with shift to 75 percentile and baseline transformed to median of all samples in GeneSpring 12.6 Software

label: Biotin

label_protocol: Biotinylated cRNA were prepared with the Illumina® Total PrepT RNA Ampification kit (Life Technologies) for Illumina arrays

extract_protocol: Blood samples were collected, and peripheral blood mononuclear cells were separated. part of the cell suspension was isolated and centrifuged at 800 x g for 8 min at 22°C to collect the mononuclear cell pellet. The harvested cells were then lysed by suspending in RLT-buffer (RNeasy® Mini Kit; Qiagen, Hilden, Germany) containing 1%-β-mercaptoethanol. For the homogenization of samples and elimination of unsolubilized cellular particles both the macrophage and mononuclear cell lysates were centrifuged at 16 000 x g for 2 min through QIAshredder (Qiagen) spin columns, and RNA was extracted with RNeasy® Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Healthy volunteers, aged 19-38 years, were administered 600 mg rifampicin (Rimapen; Orion Corporation, Espoo, Finland) or placebo daily for a week with at least a 4-week washout period before the next treatment arm. At the end of each arm, blood samples were collected on the morning of the eighth day.

value: blood

tag: individual

value: patient 2

value: male

tag: treatment

value: Placebo

tag: cell type

value: Peripheral blood mononuclear cells


title: PATIENT 7 (5254): PTC-metastatic

description: gene expression profile from classical variant of papillary thyroid carcinoma

value: Patient have papillary thyroid carcinoma of lung metastasis


title: PATIENT 5 (10424): PTC-invasive

source_name: PTC-invasive

value: Tumor with invasion of extrathyroidal soft tissue


title: PCR-constant experiment replicate 1 2X Tn5


title: PATIENT 6 (8339): PTC-invasive


title: PCR-constant experiment replicate 1 5X Tn5


title: Mononuclear_cells_patient_2_rifampicin

description:
Gene expression data from patient no:2 after administration of rifampicin for one week.
084-2K1

value: rifampicin


title: 1: Control

description: Paxgene tubes


title: PATIENT 3 (6769): PTC-non-aggressive

source_name: PTC-non-aggressive

value: İntrathyroidal tumor, with no lymphovascular invasion


title: PATIENT 4 (3221): PTC-invasive


title: CHON_H3K36me3_Rep2

city: NEWCASTLE UPON TYNE

first: David

last: Young

address: Centre For Life

country: United Kingdom

institute: Newcastle University

data_processing:
Quality control of sequencing reads was performed using FastQC (v.0.11.5).
Reads were aligned to the reference human genome hg38 using Bowtie2 (v.2.2.4)
MACS2 (v.2.1.0.2) was used to call broad peaks (parameters –broad and –no-model) using input samples as controls.
ChromHMM (v.1.12) was used to train a 16 state model
Genome_build: hg38

extract_protocol:
Chromatin from hMSCs and differentiated chondrocytes were extracted using the Diagenode iDeal histone ChIP-seq kit (Diagenode SA, Ougrée, Belgium). Extracted chromatin was sonicated using a Diagenode Bioruptor Standard or Bioruptor Pico to an average size of 200-500bp, using 15 sonication cycles (30s on/30s off).
Replicate 1: Diagenode MicroPLEX v2 kit, replicate 2: NEBNext Ultra II kit (New England Biolabs, Hitchin, UK)

tag: msc donor

value: differentiated chondrocytes

tag: chip antibody

value: ChIP-seq grade polyclonal rabbit H3K36me3 (Diagenode, cat. no. C15410192)

tag: differentiation time point


title: MAFB_KO_beta-like_stage

city: San Francisco

first: Simone

last: Giacometti

address: 513 Parnassus Avenue

institute: UCSF

data_processing:
Cells were prepared separately using a 10X Genomics Chromium Controller and deeply sequenced
genome build: hg19
Supplementary_files_format_and_content: MAFB_WT_PP_stage_matrix.mtx: a gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: MAFB_WT_PP_stage_genes.tsv: gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: MAFB_WT_PP_stage_barcodes.tsv: cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: MAFB_KO_PP_stage_matrix.mtx: a gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: MAFB_KO_PP_stage_genes.tsv: gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: MAFB_KO_PP_stage_barcodes.tsv: cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: MAFB_WT_beta-like_stage_matrix.mtx: a gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: MAFB_WT_beta-like_stage_genes.tsv: gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: MAFB_WT_beta-like_stage_barcodes.tsv: cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: MAFB_KO_beta-like_stage_matrix.mtx: a gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: MAFB_KO_beta-like_stage_genes.tsv: gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: MAFB_KO_beta-like_stage_barcodes.tsv: cell names (colname names of the sparse count matrix)

source_name: hESC-derived beta-like cells

growth_protocol: Differentiation of hESCs to PPs and beta-like cells was carried out according to a previously published protocol see: Nair et al., 2019.

extract_protocol:
Single cell suspensions were prepared from the PP and beta-like cell stages using Accumax.
Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v2

tag: day of differentiation

value: Pancreas

tag: genotype

value: MAFB-/-


title: LR-5 Rep3 [LR-5-3]

city: WuHan

first: Guosong

last: Jiang

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

country: China

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

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 used Trinity (Grabherr et al, 2011) to assemble the reads into transcriptome within para:min_kmer_cov:2 ,after that, we mapped reads  to transcriptome using bowtie2 with default parameters.
Reads Count were stated for each sample, and Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced(FPKM) were calculated for each unigene .
Genome_build: Trinity.fasta
Supplementary_files_format_and_content: FPKM

organism: Lycium ruthenicum

source_name: L. ruthenicum_fruit develoment stage 5

extract_protocol:
Fruits were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) 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: wild type

value: fruit develoment stage 5

value: Fruit


title: Mononuclear_cells_patient_3_rifampicin

description:
Gene expression data from patient no:3 after administration of rifampicin for one week.
084-3K1

value: patient 3

value: female


title: MAFB_WT_beta-like_stage

value: MAFB+/+


title: LR-5 Rep2 [LR-5-2]


title: MAFB_KO_PP_stage

source_name: hESC-derived Pancreatic progenitor cells


title: Mononuclear_cells_patient_1_placebo

description:
Gene expression data from patient no:1 after administration of placebo for one week.
084-1K1

value: blood

value: patient 1

value: male


title: Mononuclear_cells_patient_1_rifampicin

description:
Gene expression data from patient no:1 after administration of rifampicin for one week.
084-1K2

value: Peripheral blood mononuclear cells


title: Mononuclear_cells_patient_6_rifampicin

description:
Gene expression data from patient no:6 after administration of rifampicin for one week.
084-6K1

value: patient 6


title: PATIENT 2 (7842): PTC-non-aggressive

value: papillary thyroid cancer


title: LR-5 Rep1 [LR-5-1]


title: MAFB_WT_PP_stage


title: CHON_H3K27ac_Rep2

value: ChIP-seq grade polyclonal rabbit H3K27ac (Diagenode, cat. no. C15410196)


title: PATIENT 1 (1606): PTC-non-aggressive

value: İntrathyroidal tumor, with no lymphovascular invasion


title: CHON_H3K4me1_Rep2

value: differentiated chondrocytes

value: ChIP-seq grade polyclonal rabbit H3K4me1 (Diagenode, cat. no. C15410194)


title: LR-4 Rep3 [LR-4-3]

source_name: L. ruthenicum_fruit develoment stage 4

value: fruit develoment stage 4


title: CHON_H3K4me3_Rep2

value: ChIP-seq grade polyclonal rabbit H3K4me3 (Diagenode, included in iDEAL Histone ChIP-seq kit cat. no. C01010050)


title: LR-4 Rep2 [LR-4-2]

value: wild type


title: CHON_input_Rep2


title: MSC_H3K36me3_Rep2

value: human mesenchymal stem cells

value: ChIP-seq grade polyclonal rabbit H3K36me3 (Diagenode, cat. no. C15410192)


title: LR-3 Rep3 [LR-3-3]

source_name: L. ruthenicum_fruit develoment stage 3

value: fruit develoment stage 3

value: Fruit


title: GLY3

city: Hangzhou

first: rong

middle: rong

last: zhai

address: 198, Shiqiao Road, Hangzhou, Zhejiang, 310021, China

institute: Zhejiang Academy of Agricultural Sciences

description: Small RNA

data_processing:
Raw data were processed to remove the adaptor sequences, and short sequences with base length less than 18 nt or more than 26 nt were eliminated.
The filtered reads were then processed with a proprietary pipeline script ACGT101-miR v4.2 (LC Sciences, Houston, Texas, USA) to flter out adapter sequences, low-quality and low copy reads, as well as common RNA families (rRNA, tRNA, snRNA, snoRNA).
The known miRNAs and novel miRNAs were identified by mapping the unique sequences to specific species precursors in miRBase 20.0 (http://www.mirbase.org/).
Supplementary_files_format_and_content: excel,expression profiles

organism: Oryza sativa

source_name: plants leaves

growth_protocol: The glyphosate-tolerant rice CA21 was developed by Institute of Crop and Nuclear Technology Utilization. They were planted in 60 × 30 cm bowls.Three replications were maintained for each group.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
The libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol.

treatment_protocol: Glyphosate (100% glyphosate powder, Zhejiang Xin ’an Chemical Group Co., Ltd.) with an effective spray dose of 2 mg·ml-1 to treat the rice seedlings at the third-leaf stage.

value: leaf

tag: strain

value: glyphosate-tolerant variety

value: Glyphosate


title: LR-4 Rep1 [LR-4-1]


title: GLY2

department: Institute of Crop and Nuclear Technology Utilization

description: Small RNA


title: CA21 degradome

description: Degradome sequencing

data_processing:
Library strategy: Degradome-Seq
Degradome-Seq: Raw sequencing reads were obtained using Illumina’s software to remove adaptors and low quality reads.
Degradome-Seq: The extracted sequencing reads were then used to identify potentially cleaved targets by the CleaveLand pipeline.
Degradome-Seq: The degradome reads were matched to transcriptome to generate the degradome density file. In addition, the targeted mRNA sequences of the miRNAs were predicted using TargetFinder software (http://targetfinder.org/). The overlapped mRNAs of the predicted target mRNAs and the mRNAs in degradome density file were considered as the target genes of the miRNAs.
Supplementary_files_format_and_content: excel,expression profiles

tag: phenotype

tag: cultivar


title: MSC_H3K27me3_Rep2

value: ChIP-seq grade polyclonal rabbit H3K27me3 (Diagenode, cat. no. C15410195)


title: LR-3 Rep2 [LR-3-2]


title: MSC_H3K27ac_Rep2


title: PATIENT 9 (4346): PTC-metastatic

hyb_protocol: Biotinylated RNA were hybridized for 16 hr at 48 oC on GeneChip® miRNA 4.0 Array (Affymetrix). GeneChips were washed and stained in the GeneChip® Fluidics Station 450.

label_protocol: Biotinylated RNA were prepared according to a standard protocol from 1000 ng total RNA (FlashTag™ Biotin HSR Labeling Kit Manual, 2017, Thermo Fisher Scientific).

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions (miRNeasy FFPE kit, Qiagen).

tag: diagnosis

value: Patient have papillary thyroid carcinoma of bone metastasis

value: female


title: HCT116_Ctrl: Mock-treated HCT116 cell line

city: Murcia

first: Antonio

last: Parrado

address: Ctra. Madrid-Cartagena, s/n

country: Spain

institute: Hospital Clinico Universitario Virgen de la Arrixaca

hyb_protocol: Agilent Gene Expression Hybridization kit protocol following the manufacturer's instructions

scan_protocol: Agilent G2565CA scanner, Agilent Scan Control software, scanning at 3µm

data_processing: Agilent Feature Extraction software version 11.0.1.1

source_name: Reference sample: Universal Human Reference RNA (Agilent Technologies)

label_protocol: Agilent Two Color Quick Amp Labeling and RNA Spike-In kits protocols following the manufacturer's instructions

growth_protocol: HCT 116 cancer colorectal cells (50,000 cells) were plated in low 35-mm-dishes with culture inserts (Ibidi, Martinsried, Germany) and cultured in high glucose Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with glutamine and containing 50 U/ml penicillin and 50 µg/ml streptomycin (Sigma Aldrich Chemical Co., Saint-Louis, USA) in an atmosphere of 5% CO2 and 95% humidified air at 37°C.

extract_protocol: RNAs were isolated using the miRNeasy mini kit (Qiagen) protocol following the manufacturer's instructions

treatment_protocol: After appropriate cell attachment and monolayer formation (around or 24 h), inserts were then removed with sterile forceps to create a wound field of approximately 500 µm, according to the manufacturer protocol. Detached cells were gently removed with Dulbecco's Phosphate-Buffered Saline (DPBS) before the addition of drugs. Confluent cells were incubated in one of the following treatments: 20 µM imipramine (purchased via Molport, Letonia), and control dishes that were incubated in the presence of 0.1% Dymethyl Sulfoxide (DMSO). Cells were then allowed to migrate in a cell culture incubator for 24h.

value: Pool of 10 human cell lines

source_name: Test sample: mock-treated HCT 116 cell line

value: Colorectal carcinoma HCT 116 cell line, treated with DMSO


title: HCT116_Imipramine: Imipramine-treated HCT116 cell line

source_name: Test sample: imipramine-treated HCT 116 cell line

value: Colorectal carcinoma HCT 116 cell line, treated with DMSO plus imipramine


title: PATIENT 7 (5254): PTC-metastatic

value: papillary thyroid cancer

value: Patient have papillary thyroid carcinoma of lung metastasis

tag: age

value: male


title: PATIENT 8 (13739): PTC-metastatic

value: Patient have papillary thyroid carcinoma of lung and bone metastasis


title: GLY1

description: Small RNA


title: LR-3 Rep1 [LR-3-1]

value: wild type


title: MSC_H3K4me1_Rep2

value: human mesenchymal stem cells

value: ChIP-seq grade polyclonal rabbit H3K4me1 (Diagenode, cat. no. C15410194)


title: CK3

description: Small RNA

value: control


title: LR-2 Rep3 [LR-2-3]

source_name: L. ruthenicum_fruit develoment stage 2

value: fruit develoment stage 2

value: Fruit


title: MSC_H3K4me3_Rep2

value: ChIP-seq grade polyclonal rabbit H3K4me3 (Diagenode, included in iDEAL Histone ChIP-seq kit cat. no. C01010050)


title: CK2

description: Small RNA

value: leaf

value: glyphosate-tolerant variety


title: MSC_input_Rep2


title: PATIENT 5 (10424): PTC-invasive

value: Tumor with invasion of extrathyroidal soft tissue

value: female


title: LR-2 Rep2 [LR-2-2]


title: LR-2 Rep1 [LR-2-1]


title: CK1

description: Small RNA


title: LR-1 Rep3 [LR-1-3]

source_name: L. ruthenicum_fruit develoment stage 1

value: fruit develoment stage 1


title: negCtrl-sgRNA_Dox-on_7d_rep1

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

data_processing:
Multiplexed samples were sequenced on an Illumina NextSeq 500 system. Base-calling was perform using the Real-Time Analysis (RTA) software version 2.4.11. Conversion of the raw bcl2 output files to gzipped FASTQ files was performed using the bcl2fastq2 script version 2.20.0 provided by Illumina.
Raw reads were processed with a pipeline building upon the implementation of the ENCODE "Long RNA-seq" pipeline: Reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (primary assembly, excluding alternate contigs) using the STAR (v2.5.2b) aligner allowing for soft clipping of adapter sequences. For quantification, transcript annotation files from Ensembl version 86 were used. Samples were quantified with the above annotations using RSEM (v1.3.0) and featureCount (v1.5.1). Quality controls were implemented using FastQC (v0.11.5), picardmetrics (v0.2.4), and dupRadar (v1.0.0) at the respective steps. Finally, differential expression analysis was performed on the mapped counts derived from featureCount using limma/voom.
Genome_build: GRCh38
Supplementary_files_format_and_content: sample-wise results procuded by RSEM and included expected counts, TMP, and FPKM values.

growth_protocol: The cell lines were cultured with the media suggested by ATCC with 20% tet-free FCS at 37 degree Celsius incubators with 5% CO2.

extract_protocol:
Cells were lysed in TRI lysis reagent (Qiagen, #79306) according to the manufacturer's instructions. Instead of chloroform, 10% volume 1-bromo-2-chloropropane (SigmaAldrich, # B9673) was added. Total RNA was isolated with RNAeasy Mini Kit (Qiagen, #73404).
RNA-seq sequencing libraries were prepared using the TruSeq RNA Library Preparation Kit v2 with PolyA selection.

treatment_protocol: For treatment of SU-DHL-4 cells to induce Cas9 expression, doxycycline (Sigma #D9891) was dissolved in sterile water and was added to the cell culture medium at a final concentration of 100 ng/ml for 2d and 7d.

tag: cell line

value: B-cell lymphoma cell line

tag: genotype/variation

value: negCtrl-sgRNA

tag: internal id


title: LR-1 Rep2 [LR-1-2]

tag: tissue


title: AQ Cre+ 4C H3K27Ac Chip Seq rep2

city: Philadelphia

first: Anthony

last: Angueira

state: Pennsylvania

address: 3400 Civic Center Blvd

department: IDOM

institute: University of Pennsylvania

data_processing:
ChIP-seq sequencing reads were aligned to UCSC mm9 using STAR aligner.
Before downstream analysis, reads were downsampled to 33%. BigWig files were generated using Homer and bedGraphToBigWig from UCSC toolkit in 1bp resolution.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bigWig file

organism: Mus musculus

source_name: BAT

extract_protocol:
Frozen BAT was thawed and minced in 1% formaldehyde for 20 minutes at room temperature and quenched with the addition of 2.5M glycine. BAT was sonicated in (50 mM HEPES pH7.5, 155 mM NaCl, 1 mM EDTA, 1.1% Triton X-100, 0.11% Sodium-deoxycholate, 0.1% SDS) using probe sonication (30 sec on 30 sec off, 3 times at amplitude 10 then 30 sec on 30 sec off, 3 times at amplitude 15) at 4°C (Fischer Scientific, FB705 Sonic Dismembrator). Inputs were removed, and primary antibodies were added for overnight incubation at 4°C with rotation.
NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: Control and Adioq-Cre+; Ebf2 loxp/loxp mice were housed at RT or cold.

value: Adipoq-Cre+; Ebf2 fl/fl

value: 8-10 weeks

value: Brown adipose tissue (BAT)

tag: temperature

value: Rb anti-Histone H3 (acetyl K27) (RRID:AB_2118291)


title: WT 4C H3K27Ac Chip Seq rep2

value: Adipoq-Cre-; Ebf2 fl/fl


title: triptolide_3

city: Nanchang

first: Xiaoning

last: Zhang

address: 999 Xuefu R.D., Nanchang

institute: Nanchang University

data_processing:
The raw data produced by the Illumina HiSeq™ X Ten platform was subjected to quality control tests. The clean data were aligned to reference genome via software Hisat2 (v2.0.1).
HTSeq (v0.6.1) was used to estimate gene and isoform expression levels from the pair-end clean data. Differential expression analysis used the DESeq Bioconductor package, a model based on the negative binomial distribution.
LncRNA-targeted genes were predicted based on cis and trans regulatory principles. The cis regulation by lncRNAs can be predicted by software Bedtools (v2.17.0) and regulation in trans was analyzed via Blast (v 2.2.28+). CIRI（V2.0）software and CircBase were used to identify and screen the circRNA, and expression level of circRNA were calculated with SRPBM (spliced reads per billion mapping).
Genome_build: hg19
Supplementary_files_format_and_content: excel files include gene_id, transcript_id(s), length expected_count, FPKM values for each Sample

source_name: Testis

extract_protocol:
Total RNAs were extracted from the testes using TaKaRa MiniBEST Universal RNA Extraction Kit (TaKaRa, Dalian, China) according to the manufacturer’s protocol with some modifications. Briefly, on-column DNase I digestion was performed to eliminate trace amounts of DNA contamination for all samples. Finally, the concentration and purity of the total RNA samples were evaluated using a NanoPhotometer (IMPLEN, Munich, Germany) with optical density measurements at 1.8 < A260/A280 < 2.2. The integrity of RNA was always checked by electrophoresis in 1.5% agarose gels and the 2100 Bioanalyzer (Agilent Corporation, Palo Alto, CA, USA).
After the rRNA was depleted from total RNA using Ribo-Zero™ rRNA removal Kit (Illumina, San Diego, CA, USA), next generation sequencing library preparations were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina®). Sequencing was carried out using a 2 x 150 paired-end (PE) configuration. The sequences were processed and analyzed by GENEWIZ, Inc. (Suzhou, China).

treatment_protocol: Ten-week-old male C57BL/6J mice (body weight 25.0 ± 1.5 g) were purchased from Beijing Vital River Laboratory Animal Technology Co., Ltd., (Beijing, China). All mice were kept in a constant temperature (22 ± 2 °C) and relative humidity (40 - 60%) environment with a 12/12-h light/dark cycle and were allowed to acclimate for one week before experiments. The mice were divided randomly into two groups. The triptolide group (n = 6) were administered with intragastric administration (i.g.) of 50 μg/kg Body weight/day. The control group (n = 6) was fed with saline (0.9% NaCl). Water and food were provided ad libitum. Mice were euthanized by cervical dislocation at 35 days after treatment.

value: Testis

value: 10-week old

tag: treatment

value: triptolide


title: AQ Cre+ 4C H3K27Ac Chip Seq rep1


title: negCtrl-sgRNA_Dox-on_7d_rep3

tag: cell type


title: LR-1 Rep1 [LR-1-1]

value: wild type

value: Fruit


title: triptolide_2


title: negCtrl-sgRNA_Dox-on_2d_rep3


title: PATIENT 2 (7842): PTC-non-aggressive

value: papillary thyroid cancer

value: İntrathyroidal tumor, with no lymphovascular invasion

tag: gender


title: PATIENT 4 (3221): PTC-invasive

value: Tumor with invasion of extrathyroidal soft tissue


title: PATIENT 3 (6769): PTC-non-aggressive

value: female


title: PATIENT 6 (8339): PTC-invasive

value: male


title: WT 4C H3K27Ac Chip Seq rep1

tag: chip antibody


title: triptolide_1


title: SW620_Methylation_DMaKG_rep2

type: genomic

city: Duarte

first: Haiqing

last: Li

state: CA

address: 1500 East Duarte Road

department: Department of Computational & Quantitative Medicine

institute: Beckman Research Institute of City of Hope, Center for Informatics

description:
203282450101_R06C01_Grn.idat
203282450101_R06C01_Red.idat
invitro

hyb_protocol: Hybridized to Illumina EPIC BeadChip according to manufacturer's protocol

scan_protocol: Standard Illumina iScan scanning protocol

data_processing:
Partek GS (v.7.18.0723)
Normalized Average Beta using Bioconduct minfi package's Functioanl Normalization Method (exlucde chrX and chrY, and probe detection p-value >0.05)

label: cy3 and cy5

source_name: Sw620 cells, DM-aKG treatment

label_protocol: Illumina Protocal

growth_protocol: organoid medium

extract_protocol: DNA  extraction by Qiagen DNeasy kit

treatment_protocol: DM-aKG treatment

value: colon cancer

tag: sample type

value: cell line


title: blood_96

city: Kongens Lyngby

first: Haja

middle: N

last: Kadarmideen

address: Richard Petersens Plads, Building 324

department: Department of Applied Mathematics and Computer Science

country: Denmark

institute: Technical University of Denmark

hyb_protocol: Service provided by Geneseek, NE, http://www.neogen.com/GeneSeek/

data_processing: Genome studio, GenCall Version = 7.0.0. The Final Report from GenomeStudio was converted into PLINK files by the software SNPConvert (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003493/) and loaded into PLINK software (v. 1.90b6.9)

label: Cy3, Cy5

organism: Sus scrofa

source_name: blood

growth_protocol: Blood samples were collected at ~30kg weight

extract_protocol: Blood samples were collected in EDTA tubesm DNA was extracted by Geneseek, NE, http://www.neogen.com/GeneSeek/

treatment_protocol: Feed intake and growth was measured from ~28 to ~100kg, and Feed Conversion Ratio and Residual feed intake was calculated

tag: breed

tag: Sex

value: blood

tag: fcr

tag: rfi


title: negCtrl-sgRNA_Dox-on_7d_rep2

value: B-cell lymphoma cell line

value: negCtrl-sgRNA


title: blood_72

scan_protocol: Service provided by Geneseek, NE, http://www.neogen.com/GeneSeek/


title: negCtrl-sgRNA_Dox-on_2d_rep2


title: negCtrl-sgRNA_Dox-on_2d_rep1


title: SW620_Methylation_DMaKG_rep1

description:
203282450101_R05C01_Grn.idat
203282450101_R05C01_Red.idat
invitro


title: PATIENT 1 (1606): PTC-non-aggressive


title: blood_64

label_protocol: Service provided by Geneseek, NE, http://www.neogen.com/GeneSeek/


title: control_2

tag: strain

value: control


title: negCtrl-sgRNA_Dox-off_7d_rep3


title: negCtrl-sgRNA_Dox-off_7d_rep2


title: WT RT H3K27Ac Chip Seq rep2

value: Adipoq-Cre-; Ebf2 fl/fl

value: 8-10 weeks

value: Brown adipose tissue (BAT)

value: RT

value: Rb anti-Histone H3 (acetyl K27) (RRID:AB_2118291)


title: AQ Cre+ RT H3K27Ac Chip Seq rep1

value: Adipoq-Cre+; Ebf2 fl/fl


title: AQ Cre+ 4C RNA SEQ rep3

description:
B12
Raw.BAT_KO_Cold_r3
processed data file: featureCount.GEO.txt.gz

data_processing:
RNA-seq sequencing reads were aligned to UCSC mm9 genome using STAR aligner with an option, “--outSAMstrandField intronMotif --outFilterMultimapNmax 1”. Mitochondrial reads were filtered out to avoid sequencing depth bias due to mitochondrial abundance. Then, reads aligned to genes were counted using featureCounts.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: featureCount.GEO.txt: Raw tag count for each gene.

extract_protocol:
Total RNA was extracted from using TRIzol (Invitrogen) combined with Purelink RNA columns (Fisher) and quantified using a Nanodrop. Total RNA was sent to Novogene for library preparation and sequencing.
NEB Next Ultra RNA Library Prep Kit.


title: control_1

value: Testis

value: 10-week old


title: WT RT H3K27Ac Chip Seq rep1


title: AQ Cre+ 4C RNA SEQ rep2

description:
B11
Raw.BAT_KO_Cold_r2
processed data file: featureCount.GEO.txt.gz


title: AQ Cre+ RT H3K27Ac Chip Seq rep2


title: SW620_Methylation_Control_rep1

description:
203282450101_R01C01_Grn.idat
203282450101_R01C01_Red.idat
invitro

source_name: Sw620 cells, control treatment


title: negCtrl-sgRNA_Dox-off_7d_rep1


title: SW620_Methylation_Control_rep2

description:
203282450101_R02C01_Grn.idat
203282450101_R02C01_Red.idat
invitro


title: AQ Cre+ 4C RNA SEQ rep1

description:
B10
Raw.BAT_KO_Cold_r1
processed data file: featureCount.GEO.txt.gz


title: blood_28


title: negCtrl-sgRNA_Dox-off_2d_rep2


title: WT 4C RNA SEQ rep3

description:
B9
Raw.BAT_WT_Cold_r3
processed data file: featureCount.GEO.txt.gz


title: negCtrl-sgRNA_Dox-off_2d_rep1


title: blood_53


title: TAP_SCREEN, chromosome 11 screen, sample 13

city: Barcelona

first: Lars

last: Velten

address: C. Dr. Aiguader 88, P05

department: Bioinformatics and Genomics

institute: CRG

description: K562 cells expressing dCas9-KRAB were infected with a lentiviral gRNA library targeting all enhancers on a defined region of chromosome 11. Binary Perturbation status per cell is contained in the pertStatus.csv.gz file.

data_processing:
Homo Sapiens hg38
Conversion of paired end fastq files to unaligned bam; Picard Tools FastqToSam (v. 2.18.14)
Extraction of UMI observations using the Drop-seq tools workflow (v. 1.13; http://mccarrolllab.org/dropseq/) with STAR (v. 2.5.3a) for read alignment.
Filtering for chimeric reads and UMI count extraction using an approach adapted from Dixit et al. (python v. 3.6.6 ; https://www.biorxiv.org/content/10.1101/093237v1.full)
Extraction of perturbation status for each cell based on a cutoff on detected vector molecule counts (R v. 3.5.1).
Supplementary_files_format_and_content: Count tables (.counts.csv) and binary tables specifyng perturbation status (.pertStatus.csv)

molecule: polyA RNA

source_name: K562 dCas9-KRAB

growth_protocol: K562 cells (ATCC CCL-243) stably infected with dCas9-BFP-KRAB were routinely cultivated in RPMI + 10 % FCS + Pen/Strep and replated twice a week. Cells infected with lentivirus were selected using Puromycn and kept under Puromycin selection upon stable growth.

extract_protocol:
Cells were collected using centrifugation, FACS-sorted (high dCas9-BFP-KRAB expression,  viability with Draq7) and  subjectd to single-cell RNAseq using 10X Genomics or DropSeq technologies.
TAP-seq, 10x genomics based
Libraries were prepared according to DropSeq protocol (Macosko Cell 2015) or 10X Genomics single-cell RNAseq v2 (Chromium 3' Reagent Kits v2 User Guide Rev C "CG00052") for whole transcriptome or TAP-seq protocol for targeted transcriptome readouts.

value: K562 Cell line

tag: targeting panel

value: Chromosome 11 panel

tag: perturbations

value: Chromosome 11 enhancer perturbations


title: LSCC, tumor sample 14

city: Rio de Janeiro

first: Pedro

last: Nicolau Neto

state: RJ

address: 37 Andre Cavalcanti Street

department: PCM

country: Brazil

institute: INCA

hyb_protocol: AFFYMETRIX GENECHIP WT TERMINAL LABELING AND HYBRIDIZATION KIT

scan_protocol: Genechip Scanner 3000 7G

data_processing:
EXPRESSION CONSOLE AFFYMETRIX, RMA
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
RMA ESTIMATES FROM EXPRESSION CONSOLE SOFTWARE

source_name: LSCC patient 15

extract_protocol: RNEAsy MINI KIT QIAGEN

tag: disease state

value: LSCC

tag: individual

value: LSCC patient 15

value: laryngeal tumor


title: blood_15

value: male

value: blood


title: LSCC, nonmalignant sample 14

label_protocol: AFFYMETRIX GENECHIP WT TERMINAL LABELING AND HYBRIDIZATION KIT

value: nonmalignant surrounding mucosa


title: BCL6-sgRNA_Dox-on_7d_rep3

tag: cell line

value: B-cell lymphoma cell line

tag: genotype/variation

tag: internal id


title: LSCC, tumor sample 13

source_name: LSCC patient 14

value: LSCC patient 14

tag: tissue


title: blood_11


title: blood_46


title: WT 4C RNA SEQ rep2

description:
B8
Raw.BAT_WT_Cold_r2
processed data file: featureCount.GEO.txt.gz

value: Adipoq-Cre-; Ebf2 fl/fl

tag: age

value: 8-10 weeks

value: Brown adipose tissue (BAT)

tag: temperature


title: AQ Cre+ RT RNA SEQ rep3

description:
B6
Raw.BAT_KO_RT_r3
processed data file: featureCount.GEO.txt.gz

value: Adipoq-Cre+; Ebf2 fl/fl

value: RT


title: blood_7


title: AQ Cre+ RT RNA SEQ rep2

description:
B5
Raw.BAT_KO_RT_r2
processed data file: featureCount.GEO.txt.gz


title: BCL6-sgRNA_Dox-on_7d_rep1

tag: cell type

tag: treatment


title: BCL6-sgRNA_Dox-on_7d_rep2


title: blood_3

tag: breed


title: AQ Cre+ RT RNA SEQ rep1

description:
B4
Raw.BAT_KO_RT_r1
processed data file: featureCount.GEO.txt.gz


title: BCL6-sgRNA_Dox-on_2d_rep3


title: blood_25

tag: Sex


title: LSCC, tumor sample 12

source_name: LSCC patient 12

value: LSCC patient 12


title: negCtrl-sgRNA_Dox-off_2d_rep3

value: negCtrl-sgRNA


title: blood_2

tag: fcr


title: LSCC, nonmalignant sample 13


title: WT 4C RNA SEQ rep1

description:
B7
Raw.BAT_WT_Cold_r1
processed data file: featureCount.GEO.txt.gz


title: WT RT RNA SEQ rep3

description:
B3
Raw.BAT_WT_RT_r3
processed data file: featureCount.GEO.txt.gz


title: LSCC, tumor sample 11

source_name: LSCC patient 11

value: LSCC patient 11


title: LSCC, tumor sample 10

source_name: LSCC patient 10

value: LSCC patient 10


title: blood_113

tag: rfi


title: blood_112


title: WT RT RNA SEQ rep2

description:
B2
Raw.BAT_WT_RT_r2
processed data file: featureCount.GEO.txt.gz


title: BCL6-sgRNA_Dox-on_2d_rep1


title: BCL6-sgRNA_Dox-off_7d_rep3


title: WT RT RNA SEQ rep1

description:
B1
Raw.BAT_WT_RT_r1
processed data file: featureCount.GEO.txt.gz


title: blood_111


title: BCL6-sgRNA_Dox-off_7d_rep2


title: blood_110


title: LSCC, nonmalignant sample 12

value: LSCC


title: MS CP 6

city: Amsterdam

first: Helga

middle: E

last: de Vries

address: De Boelelaan 1108

department: MCBI

country: Netherlands

institute: Amsterdam UMC

data_processing:
Ilumina 1.9
FASTQ files were checked for quality control metrics using FastQC (version 0.11.5) and Qualimap (version 2.2.1)
Post-Quality control, raw reads were mapped to the reference genome using TopHat2 (version 2.1.1) proceeded by exon-counting using HTSeq-count (version 0.6.1)
Genome_build: Ensembl GRCh38, build 84
Supplementary_files_format_and_content: Tab-delimeted files containing the Ensembl gene id and the RLE normalized counts

source_name: Choroid Plexus

extract_protocol:
Up to 30 mg of tissue was disrupted from the whole lateral CP by cutting slices approximately 10 µm thick using a cryotome at -20oC. Tissue was homogenized with a POLYTRON PT 1200 (Kinematica). Total RNA from the CP was extracted with the RNeasy mini kit (Qiagen, 74104), following the manufacturer's instructions (using 600 µL of lysis buffer).
RNA libraries were prepared according to the manufacturer’s instructions using TruSeq stranded mRNA Library Prep Kit including an rRNA depletion step (RiboMinus, ThermoFisher).

treatment_protocol: Frozen postmortem tissue

tag: condition

value: Multiple Sclerosis

tag: gender

value: Female

tag: age (years)


title: BCL6-sgRNA_Dox-off_7d_rep1


title: MS CP 5

value: Male


title: LSCC, nonmalignant sample 10

tag: disease state


title: BCL6-sgRNA_Dox-off_2d_rep3


title: blood_108

value: male

value: blood


title: LSCC, tumor sample 9

source_name: LSCC patient 9

tag: individual

value: LSCC patient 9

value: laryngeal tumor


title: E12.5_Meis2_ChIP

city: New Orleans

first: Linyan

last: Wang

state: LA

address: 6400 freret street

institute: Tulane University

data_processing:
Paired end 2x 150bp reads were  gained using Illumina HiSeq 2500, and aligned to the mouse genome mm10 with Bowtie2
After filtration, the bigwig file of ChIP was performed using bamCompare through normalization to input.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file including peaks

extract_protocol:
The anterior palate mesenchyme from E12.5 Meis2HA mouse embryos was fixed in 1% formaldehyde for 10 min and quenched by glycine for 5 min at room temperature. After washing with ice-cold PBS containing cocktail protease inhibitor, tissues were dispersed into single cell suspension on ice.
ChIP-seq DNA Library Prep Kit for Illumina

tag: strain background

tag: development stage

tag: tissue/cell type

value: anterior palate mesenchyme

tag: chip antibody

value: Anti-HA tag antibody (Abcam, ab9110)


title: LSCC, nonmalignant sample 9

tag: tissue

value: nonmalignant surrounding mucosa


title: blood_107


title: MS CP 4


title: BCL6-sgRNA_Dox-off_2d_rep2

tag: cell line

value: B-cell lymphoma cell line

tag: genotype/variation

tag: internal id


title: MS CP 3


title: LSCC, nonmalignant sample 8

source_name: LSCC patient 8

value: LSCC patient 8


title: BCL6-sgRNA_Dox-off_2d_rep1

tag: cell type

tag: treatment


title: LSCC, tumor sample 7

source_name: LSCC patient 7

value: LSCC patient 7


title: blood_105

tag: breed

tag: Sex

tag: fcr


title: MS CP 2

tag: condition

tag: gender


title: MS CP 1

tag: age (years)


title: blood_104

tag: rfi


title: LSCC, nonmalignant sample 7

tag: disease state

tag: individual


title: blood_103


title: Control CP 6

value: Control


title: Control CP 5


title: blood_102


title: Control CP 4


title: blood_106


title: blood_100


title: Control CP 3


title: blood_99


title: Control CP 2


title: LSCC, nonmalignant sample 6

source_name: LSCC patient 6

value: LSCC patient 6


title: Control CP 1


title: LSCC, tumor sample 5

source_name: LSCC patient 5

value: LSCC patient 5


title: Giardia lamblia WB: 5'5npac control vs pPTop3b

city: Taipei

first: Chin-Hung

last: Sun

address: Department of Parasitology, College of Medicine, National Taiwan University

department: Department of Parasitology

country: Taiwan

description: stable cell lines

hyb_protocol: Correspondingly fragmented labeled cRNA was then pooled and hybridized to a G. lamblia oligonucleotide microarray (Agilent Technologies, USA) at 60°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5.

data_processing: Scanned images were analyzed by Feature Extraction version 9.1 software (Agilent Technologies, USA), and image analysis and normalization software was used to quantify signal and background intensity for each feature; data were substantially normalized by the rank consistency filtering LOWESS method.

organism: Giardia duodenalis

source_name: Giardia lamblia WB

label_protocol: 0.5 mg of total RNA was amplified by a Low RNA Input Fluor Linear Amp kit (Agilent Technologies) and labeled with Cy3 or Cy5 (CyDye, PerkinElmer Life Sciences) during the in vitro transcription process. 0.825 mg of Cy-labeled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60oC for 30 minutes.

growth_protocol: PCR amplification and standard cloning techniques were used to insert Top3b gene from genomic DNA and then cloned into the pPop2NHA vector, resulting in plasmid pPTop3bI.

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

treatment_protocol: Giardia cells were transfected with the pPTop3b or 5'5npac plasmid containing the pac gene were selected and maintained with 54 ug/ml puromycin.

tag: transfection

value: 5'5npac plasmid

value: pPTop3b plasmid


title: LSCC, tumor sample 4

source_name: LSCC patient 4

value: LSCC

value: LSCC patient 4


title: blood_101

value: male


title: LSCC, tumor sample 6


title: LSCC, nonmalignant sample 5


title: LSCC, tumor sample 3

source_name: LSCC patient 3

value: LSCC patient 3


title: LSCC, nonmalignant sample 3


title: blood_98

source_name: blood

value: blood


title: Δcph2-48h_green-light-rep1

city: Freiburg

first: Thomas

last: Wallner

address: Schaenzlestrasse 1

department: Institute of Biology III

country: Germany

institute: University of Freiburg

description: gene expression after light treatment for 48h

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the protocol GE1_107_Sep09  for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensity was quantile normalized.

organism: Synechocystis sp. PCC 6803

source_name: cells from liquid culture grown 48h under 5 µmols photons m-2 s-1 of green light

label_protocol: Aliquots of three micrograms of DNA-depleted total-RNA was labeled directly with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: Wild-type and Δcph2 strains were grown in BG11 medium (Rippka et al., 1979; J Gen Microbiol 111: 1–61) in Erlenmeyer flasks and supplemented with 10 mM N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid (TES)-KOH at pH 8.0 at 50 µmols photons m-2 s-1 of white light.

extract_protocol: Cells were lysed in 1.6 ml PGTX, with the following composition: 39.6% (w/v) phenol, 7% (v/v) glycerol, 7 mM 8-hydroxyquinoline, 20 mM EDTA, 97.5 mM sodium acetate, 0.8 M guanidine-thiocyanate, and 0.48 M guanidine hydrochloride (Pinto et al., 2009; BMC Mol Biol 10: 79). Phenol was extracted twice with 1-Bromo-3-chloropropane and RNA was precipitated with isopropanol at -20°C, followed by centrifugation at 4°C. The RNA pellet was washed with 70% ethanol and resuspended in RNase-free A. dest.

treatment_protocol: Cultures were diluted to the same optical density at 750nm with BG11 medium supplemented with 11 mM glucose and 10 mM N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid (TES)-KOH at pH 8.0 and grown further for 48h under 5 µmols photons m-2 s-1 of blue light (Lee filter #119, dark blue) or green light (Lee filter #089, moss green).

tag: strain

value: delta-cph2 lacking bacteriophytochrome Cph2


title: Δcph2-48h_green-light-rep2


title: blood_97

tag: tissue


title: WT-48h_green-light-rep1

value: WT


title: WT-48h_green-light-rep2


title: blood_94


title: L-F-O2

first: Chen

last: Biao

state: Jiang Xi

address: Zhimin main street 1101#

department: College of animal science and technology

institute: Jiangxi Agricultural University

description: L-F-O1 vs. L-F-O2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to gallus gallus whole genome using TopHat.
To estimate the expression of each gene, the total number of reads mapped to its unigenes were calculated and normalized with FPKM (fragments per kilobase of transcript per million mapped reads).
Genome_build: Gallus_gallus.Galgal4.73
Supplementary_files_format_and_content: abundance measurements

organism: Gallus gallus

source_name: ovary

growth_protocol: All broilers were reared in cages with a 24-h photoperiod for the first 2 d of age and then changed to a 16-h photoperiod. They were fed with free access to water and fedad libitum with 16.5% CP and 2, 800 kcal of ME/kg.

extract_protocol:
Total RNA from ovaries of different chickens were extracted using Trizol reagent (TaKaRa, Ostu, Japan) according to the manufacturer’s instructions. RNA degradation were evaluated by loading on 1% agarose gels. The concentration and quality of all RNA samples were examined with NanoDrop 2000 spectrophotometer (NanoDrop, Wilmington, DE). All samples were kept at -80 °C.
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: All chickens were sacrificed and ovaries were collected, quick-frozen by liquid nitrogen and stored at -80 °C until RNA extraction.

value: Ningdu Yellow

tag: phenotype

value: late sexual maturity chicken

tag: age

value: 153 days

tag: group

value: laying-hen


title: LSCC, tumor sample 1

source_name: LSCC patient 1

value: LSCC patient 1

value: laryngeal tumor


title: TR5: Prostate tumor

city: New York

first: Nicholas

middle: D

last: Socci

address: 1275 York Ave

department: Computational & Systems Biology Program

institute: Memorial Sloan Kettering Cancer Center

description: isolation protocol: Whole male genitourinary tracts were isolated and prostate lobes (anterior, dorsolateral, and ventral) were separated by microdissection from  27-week-old TRAMP+/- TCRbTg males. Prostate lobes were injected and digested with Liberase TL (10 mg/mL, Roche) and DNase (20 mg/mL, Roche) in RPMI for 30 min at 37 C. Digested tissue was mechanically disrupted with frosted microscope slides and viable lymphocytes were enriched using Histopaque 1119 (Sigma). CD8+ T cells were purified by FACs.

data_processing: See iRepertoire website (https://www.irepertoire.com/dataanalysisfaq)

source_name: Prostate tumor

extract_protocol:
RNA was harvested from FACs purified CD8+ T cells using Trizol reagent. RNA was submitted to iRepertoire for library preparation and sequencing.
From the iRepertoire wesite: "We have developed a multiplex PCR technology, called amplicon rescued multiplex PCR (or arm-PCR, patent pending), that uses hundreds of VDJ specific primers in one reaction, semi-quantitatively amplifying all the expressed VDJs in B and T cells from an RNA sample. In a parallel reaction, the genomic DNA from the MHC loci are also amplified with arm-PCR for sequencing. To conduct the study B and T cells as well as subsets of B and T cells (such as naive, mature and memory B and T cells, and Tc, Th, Tnk, Treg etc) are obtained by flow cytometry or magnetic-bead purification methods from peripheral blood, and RNA is extracted from each of the cell populations. The VDJs are amplified by reverse transcription PCR with our arm-PCR method. The amplicon mixture is then subjected to high-throughput sequencing with the next-generation Roche 454 sequencing platform."

tag: background

tag: genotype

value: TCRbtg TRAMP+/-

value: 27 weeks

tag: facs sort gating

value: CD8b+ CD4neg

value: Prostate tumor


title: MANCR KD RNA-seq Rep3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software was used for base calling.
The sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat version 2.0.13 in combination with Bowtie2 version 2.2.3 and SAMtools version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: txt and FPKM

source_name: MANCR KD RNA-seq

growth_protocol: PC3 cells were cultured in RPMI-1640 medium supplemented with 10%  FBS

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: MANCR siRNAs and negative control siRNA were transfected into PC3 cells using Lipofectamine RNAiMAX according to manufacturer’s instructions.  After 48 hours of transfection, cells were collected for further experiments.

tag: cell line

tag: cell type

value: Androgen receptor (AR)-negative castration-resistant prostate cancer (CRPC) cell line

tag: genotype/variation

value: MANCR knockdown


title: TR4: Prostate tumor


title: WT-48h_blue-light-rep2

source_name: cells from liquid culture grown 48h under 5 µmols photons m-2 s-1 of blue light


title: Δcph2-48h_blue-light-rep2


title: MANCR KD RNA-seq Rep2


title: L-F-O1

description: L-F-O1 vs. L-F-O2

tag: breed

value: 32 days

value: pre-laying-hen


title: blood_91

tag: Sex

value: male

value: blood

tag: fcr


title: P-F-O2

description: P-F-O1 vs. P-F-O2

value: early sexual maturity chicken

value: 103 days


title: LSCC, tumor sample 2

source_name: LSCC patient 2

tag: disease state

value: LSCC

value: LSCC patient 2


title: UVB non-irradiated HaCaT

city: Seoul

first: Donghwa

last: Kim

state: Seoul

address: Gwanakro-1, Gwanakgu

country: South Korea

institute: Seoul National University

hyb_protocol: RNA-array hybridization was performed with agitation at 60 rotations per minute for 16 hours at 48°C on an Affymetrix® 450 Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000 canner.

data_processing: Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC). The CEL files import, miRNA level RMA+DABG-All analysis and result export using Affymetrix® Expression Console™ Software.

source_name: HaCaT cells

label_protocol: 1000ng RNA samples were labeled with the FlashTag™ Biotin RNA Labeling Kit (Genisphere, Hatfield, PA, USA).

growth_protocol: HaCaT cells were cultured in DMEM (Gibco-Invitrogen) supplemented with 10% FBS, 100 units/mL penicillin, 100 μg/mL of streptomycin, and 250 ng/mL of amphotericin B at 37 °C in a humidified incubator under an atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted from cells with TRI reagent (Invitrogen Grand Island, NY, USA)

treatment_protocol: HaCaT cells were plated in 60 mm diameter dishes at a density of 22 × 104 cells/well. After an additional 48 h incubation, the cells were washed with Ca2+- and Mg2+-free phosphate-buffered saline (PBS) a total of 3 times. The cell media were replaced with UV media (Colorless DMEM, Hyclone-Invirogen) with or without sample. The cells were then irradiated with 15 mJ/cm2 UVB using BIO-SUN (Vilber Lourmat, Marne, France).

value: HaCaT

tag: treatment

value: without UVB irradiation


title: blood_90

tag: rfi


title: MANCR KD RNA-seq Rep1


title: TR3: Prostate tumor


title: Δcph2-48h_blue-light-rep1

tag: strain

value: delta-cph2 lacking bacteriophytochrome Cph2


title: LSCC, tumor sample 8

tag: individual

value: LSCC patient 8

tag: tissue

value: laryngeal tumor


title: P-F-O1

description: P-F-O1 vs. P-F-O2

value: Ningdu Yellow

tag: phenotype

tag: age


title: LSCC, nonmalignant sample 1

value: LSCC patient 1

value: nonmalignant surrounding mucosa


title: Control RNA-seq Rep 3

source_name: Control RNA-seq

value: Androgen receptor (AR)-negative castration-resistant prostate cancer (CRPC) cell line

value: Control


title: TR2: Prostate tumor

tag: background

value: TCRbtg TRAMP+/-

value: 27 weeks

value: CD8b+ CD4neg

value: Prostate tumor


title: blood_89

value: male

value: blood


title: UVB irradiated HaCaT

value: UVB irradiation


title: WT-48h_blue-light-rep1

value: WT


title: TR1: Prostate tumor

tag: genotype


title: blood_93


title: blood_54


title: MP 5: Pooled spleen and lymph nodes

description: isolation protocol: CD8+ T cells from pooled spleen and lymph nodes (axillary, brachial, cervical, inguinal, and periaortic) from 9-week old TCRbtg males were enriched for CD8+ T cells by MACs and CD8b+ CD44hiCD122+ cells were purified by FACs

source_name: Pooled spleen and lymph nodes

value: TCRbtg

value: 9 weeks

tag: facs sort gating

value: CD8b+ CD4neg CD44hi CD122+

value: Pooled spleen and lymph nodes


title: blood_87


title: MP 4: Pooled spleen and lymph nodes


title: Control RNA-seq Rep 1

tag: cell line


title: blood_86


title: Recurrence32

city: Badalona

first: Carolina

last: Armengol

state: Barcelona

address: Crta Can Ruti; cami de les escoles, S/N

institute: Germans Trias i Pujol Health Research Institute

description:
R32
processed data file: RNAseq_counts_32patients.txt

data_processing:
STAR alignment to hg38.
gatk to generate filtered vcf.
Filter SNPs.
Filter ALUs, seq biases.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RNAseq_counts_32patients.txt: Tab-delimited text file containing the table counts.

source_name: Tumor liver tissue

extract_protocol:
20mg of frozen tissue was homogenized with FASTprep. RNA was extracted using the MirVana kit (Thermofisher) and subsequently treated with DNase (kit DNA free kit, Thermofisher) following manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: disease diagnosis

value: Hepatoblastoma

value: Tumor liver tissue

tag: sample type

value: Recurrence

tag: gender

value: Male

tag: patient


title: Recurrence19

description:
R19
processed data file: RNAseq_counts_32patients.txt


title: Nontumor22

description:
NT22
processed data file: RNAseq_counts_32patients.txt

source_name: Normal liver tissue

value: Normal liver tissue

value: Nontumor

value: Female


title: blood_83

tag: breed

tag: Sex

tag: fcr


title: blood_84

tag: rfi


title: Nontumor20

description:
NT20
processed data file: RNAseq_counts_32patients.txt


title: blood_85


title: blood_81


title: MP 1: Pooled spleen and lymph nodes


title: Nontumor32

description:
NT32
processed data file: RNAseq_counts_32patients.txt


title: Control RNA-seq Rep 2

tag: cell type

value: Androgen receptor (AR)-negative castration-resistant prostate cancer (CRPC) cell line

tag: genotype/variation

value: Control


title: MP 2: Pooled spleen and lymph nodes

tag: tissue


title: blood_82

value: male


title: blood_80

value: blood


title: BCL6-sgRNA_Dox-on_2d_rep2

data_processing:
Multiplexed samples were sequenced on an Illumina NextSeq 500 system. Base-calling was perform using the Real-Time Analysis (RTA) software version 2.4.11. Conversion of the raw bcl2 output files to gzipped FASTQ files was performed using the bcl2fastq2 script version 2.20.0 provided by Illumina.
Raw reads were processed with a pipeline building upon the implementation of the ENCODE "Long RNA-seq" pipeline: Reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (primary assembly, excluding alternate contigs) using the STAR (v2.5.2b) aligner allowing for soft clipping of adapter sequences. For quantification, transcript annotation files from Ensembl version 86 were used. Samples were quantified with the above annotations using RSEM (v1.3.0) and featureCount (v1.5.1). Quality controls were implemented using FastQC (v0.11.5), picardmetrics (v0.2.4), and dupRadar (v1.0.0) at the respective steps. Finally, differential expression analysis was performed on the mapped counts derived from featureCount using limma/voom.
Genome_build: GRCh38
Supplementary_files_format_and_content: sample-wise results procuded by RSEM and included expected counts, TMP, and FPKM values.

extract_protocol:
Cells were lysed in TRI lysis reagent (Qiagen, #79306) according to the manufacturer's instructions. Instead of chloroform, 10% volume 1-bromo-2-chloropropane (SigmaAldrich, # B9673) was added. Total RNA was isolated with RNAeasy Mini Kit (Qiagen, #73404).
RNA-seq sequencing libraries were prepared using the TruSeq RNA Library Preparation Kit v2 with PolyA selection.

value: B-cell lymphoma cell line

tag: treatment

tag: internal id


title: Nontumor31

description:
NT31
processed data file: RNAseq_counts_32patients.txt


title: Naïve 5: Pooled spleen and lymph nodes

description: isolation protocol: CD8+ T cells from pooled spleen and lymph nodes (axillary, brachial, cervical, inguinal, and periaortic) from 9-week old TCRbtg males were enriched for CD8+ T cells by MACs (Miltenyi) and CD8b+ CD44loCD122neg cells were purified by FACs

tag: background

tag: age

value: CD8b+ CD4neg CD44lo CD122neg


title: CHON_H3K27me3_Rep2

city: NEWCASTLE UPON TYNE

first: David

last: Young

address: Centre For Life

institute: Newcastle University

data_processing:
Quality control of sequencing reads was performed using FastQC (v.0.11.5).
Reads were aligned to the reference human genome hg38 using Bowtie2 (v.2.2.4)
MACS2 (v.2.1.0.2) was used to call broad peaks (parameters –broad and –no-model) using input samples as controls.
ChromHMM (v.1.12) was used to train a 16 state model
Genome_build: hg38

extract_protocol:
Chromatin from hMSCs and differentiated chondrocytes were extracted using the Diagenode iDeal histone ChIP-seq kit (Diagenode SA, Ougrée, Belgium). Extracted chromatin was sonicated using a Diagenode Bioruptor Standard or Bioruptor Pico to an average size of 200-500bp, using 15 sonication cycles (30s on/30s off).
Replicate 1: Diagenode MicroPLEX v2 kit, replicate 2: NEBNext Ultra II kit (New England Biolabs, Hitchin, UK)

tag: msc donor

value: differentiated chondrocytes

tag: chip antibody

value: ChIP-seq grade polyclonal rabbit H3K27me3 (Diagenode, cat. no. C15410195)

tag: differentiation time point


title: Naïve 3: Pooled spleen and lymph nodes

tag: genotype

value: TCRbtg

value: 9 weeks

tag: facs sort gating


title: Naïve 4: Pooled spleen and lymph nodes

value: Pooled spleen and lymph nodes


title: blood_88


title: Nontumor29

description:
NT29
processed data file: RNAseq_counts_32patients.txt

tag: disease diagnosis

value: Hepatoblastoma

tag: sample type

tag: gender

tag: patient


title: Naïve 2: Pooled spleen and lymph nodes


title: Naïve 1: Pooled spleen and lymph nodes


title: Nontumor27

description:
NT27
processed data file: RNAseq_counts_32patients.txt


title: Nontumor21

description:
NT21
processed data file: RNAseq_counts_32patients.txt


title: Nontumor25

description:
NT25
processed data file: RNAseq_counts_32patients.txt


title: Nontumor24

description:
NT24
processed data file: RNAseq_counts_32patients.txt


title: blood_76

tag: breed

tag: Sex

tag: fcr

tag: rfi


title: Nontumor3

description:
NT3
processed data file: RNAseq_counts_32patients.txt

tag: tissue


title: blood_75


title: Nontumor23

description:
NT23
processed data file: RNAseq_counts_32patients.txt


title: blood_73


title: Nontumor33

description:
NT33
processed data file: RNAseq_counts_32patients.txt


title: blood_79


title: Nontumor28

description:
NT28
processed data file: RNAseq_counts_32patients.txt


title: blood_70


title: blood_69


title: blood_78


title: Nontumor19

description:
NT19
processed data file: RNAseq_counts_32patients.txt


title: Nontumor6

description:
NT6
processed data file: RNAseq_counts_32patients.txt


title: sputum sample, patient #9

city: Singapore

first: Philip

middle: Kam Weng

last: Kwan

address: 21 Lower Kent Ridge Rd

country: Singapore

institute: National University of Singapore

description: Gene expression data from sputum sample from TB patient within 1-2 weeks standard therapy

hyb_protocol: Following fragmentation, 11 ug of ds-cDNA were hybridized for 16 hr at 50 ℃ on Custom GeneChip Mycobacterium tuberculosis MtubEX1. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000.

data_processing: Microarray signals were generated using a custom Affymetrix Mtb chip (MTubEX1; Thermofisher scientific, Massachusetts, USA) that was designed with signal processing algorithms specific for Mtb H37rv genes. Signal processing and normalization was done by Robust Multiarray Analysis (RMA), performed using R software package Affy and Affycoretools.

organism: Mycobacterium tuberculosis

label_protocol: Biotinylated ds-cDNA were prepared according to the standard Affymetrix protocol from 10ng total RNA (GeneChip™ 3’ IVT Pico Reagent Kit, 2015-2016)

growth_protocol: log-phase Mtb cultures: Mtb H37Rv lab strain was grown in 7H9 medium containing 0.2% glycerol, 0.05% tween 80 and ADC supplement (sodium chloride, Bovine Serum Albumin Fraction V, anhydrous Dextrose and Catalase) to mid-log phase, and aliquots were taken and frozen in glycerol at −80°C. Volumes of this stock were then serially diluted and each inoculated into a Mycobacteria Growth Indicator Tube (MGIT) tubes to determine the relationship between inoculum volume and time-to-positivity (TTP). The specific volume of stock that gave a TTP of 5.5 days was identified (containing ~105 CFU/ml) and this was used as the standard inoculum in all experiments.

extract_protocol: RNA was extracted from 15ml whole blood cultures by adding Guanidium Thiocyanate solution for host cell lysis, followed by resuspension of cells in 1ml TRIzol Reagent (Thermo Fisher Scientific, Massachusetts, USA) for Mtb inactivation, Mtb cells were mechanically lyzed using the FastPrep 24 Tissue Homogenizer (MP Biomedicals, California, USA) at 4x30s, 6.0 m/s followed by phenol-chloroform steps outlined in the TRIzol user manual. Samples were treated with DNAse-I using TURBO DNA-free kit (Thermo Fisher Scientific, Massachusetts, and USA).

treatment_protocol: Whole-blood cultures were prepared by mixing 300ul heparinized blood with one of the study drugs and made up to a total volume of 600ul by adding RPMI 1640 culture medium with 25 mmol/L N-2-hydroxyethylpiperazine-N′-2 ethane sulfonic acid). These were incubated for 30 minutes at room temperature. Study drug was then added in the amount required to achieve a final concentration based on the published values of Cmax in pharmacokinetic studies performed with standard clinical doses: rifampicin 10 µg/ml;isoniazid 5 µg/ml; , pyrazinamide 25µg/ml;,ethambutol 5 µg/ml; moxifloxacin 4 µg/ml;  and faropenem sodium (Farobact, Cipla, Mumbai), amoxicillin and clavulanic acid (5, 10, and 3 µg/ml respectively). Eight separate cultures were set-up with individual rifampicin, isoniazid, pyrazinamide, ethambutol and moxifloxacin; faropenem (with amoxicillin and clavulanic acid); the combination of rifampicin, isoniazid, pyrazinamide and ethambutol; and a drug-free control culture with 0.9% dimethyl sulfoxide added (DMSO; control for the purpose of comparing the bactericidal curves). The standard volume of Mtb stock (identified as above), was added to all cultures and incubated at 37°C with slow constant mixing. From each of the three 50ml blood samples, 154 cultures were set-up (9 incubation times for each of 8 drug conditions in duplicates).

value: sputum


title: sputum sample, patient #72

source_name: sputum sample from TB patient within 1-2 weeks standard therapy


title: sputum sample, patient #96


title: blood_71


title: sputum sample, patient #66


title: blood_77


title: blood_68


title: Nontumor30

description:
NT30
processed data file: RNAseq_counts_32patients.txt


title: blood_67


title: blood_74


title: sputum sample, patient #30


title: sputum sample, patient #60


title: sputum sample, patient #48


title: sputum sample, patient #18


title: sputum sample, patient #107


title: Nontumor26

description:
NT26
processed data file: RNAseq_counts_32patients.txt

value: Male


title: Nontumor5

description:
NT5
processed data file: RNAseq_counts_32patients.txt

value: Normal liver tissue


title: blood_65


title: Nontumor18

description:
NT18
processed data file: RNAseq_counts_32patients.txt

value: Nontumor


title: MP 3: Pooled spleen and lymph nodes

description: isolation protocol: CD8+ T cells from pooled spleen and lymph nodes (axillary, brachial, cervical, inguinal, and periaortic) from 9-week old TCRbtg males were enriched for CD8+ T cells by MACs and CD8b+ CD44hiCD122+ cells were purified by FACs

value: CD8b+ CD4neg CD44hi CD122+


title: blood_63


title: Nontumor17

description:
NT17
processed data file: RNAseq_counts_32patients.txt


title: Nontumor16

description:
NT16
processed data file: RNAseq_counts_32patients.txt


title: blood_66


title: blood_61


title: Nontumor15

description:
NT15
processed data file: RNAseq_counts_32patients.txt

value: Female


title: blood_60


title: Nontumor14

description:
NT14
processed data file: RNAseq_counts_32patients.txt


title: broth culture, biological rep2,technical rep1

description: Gene expression data from log-phase Mycobacterium tuberculosis broth culture

value: broth culture


title: blood_59

value: male


title: blood_62

value: blood


title: Nontumor4

description:
NT4
processed data file: RNAseq_counts_32patients.txt


title: Nontumor13

description:
NT13
processed data file: RNAseq_counts_32patients.txt


title: broth culture, biological rep1,technical rep2

source_name: log-phase Mycobacterium tuberculosis broth culture


title: blood_58


title: broth culture, biological rep1,technical rep3


title: blood_57


title: Nontumor1

description:
NT1
processed data file: RNAseq_counts_32patients.txt


title: Nontumor2

description:
NT2
processed data file: RNAseq_counts_32patients.txt


title: whole blood from volunteer 4, moxifloaxacin added

description: Gene expression data from Mycobacterium tuberculosis in whole blood culture containing moxifloxacin

value: whole blood culture


title: broth culture, biological rep1,technical rep1


title: blood_56


title: Nontumor12

description:
NT12
processed data file: RNAseq_counts_32patients.txt


title: blood_55


title: broth culture, biological rep2,technical rep2


title: RNAseq-4T1-TVI-Met-3

city: Bethesda

first: Jae Young

last: So

state: MD

address: 37 Convent Drive, Rm 3134

department: LCBG

institute: NCI/NIH

data_processing:
Basecalling: RTA 1.18.64
Demultiplexing: Bcl2fastq 1.8.4
Alignment: TopHat v2.08
RNA statistics: Picard 1.84
Read count normalization: DESeq2 v 3.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files for counts, differentially expressed genes

source_name: 4T1 mammary tumor cell

extract_protocol:
ZR-Duet DNA/RNA miniprep
Ultra Low Input RNA - v3
Illumina TruSeq V4.0

tag: cell line

value: 4T1 mammary tumor cell

tag: tissue source

value: Lung metastases

tag: strain

value: BALB/c


title: blood_52

data_processing: Genome studio, GenCall Version = 7.0.0. The Final Report from GenomeStudio was converted into PLINK files by the software SNPConvert (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5003493/) and loaded into PLINK software (v. 1.90b6.9)

extract_protocol: Blood samples were collected in EDTA tubesm DNA was extracted by Geneseek, NE, http://www.neogen.com/GeneSeek/


title: whole blood from volunteer 4, isoniazid added

description: Gene expression data from Mycobacterium tuberculosis in whole blood culture containing isoniazid


title: whole blood from volunteer 4, isoniazid, pyrazinamide, rifampicin, ethambutol added

description: Gene expression data from Mycobacterium tuberculosis in whole blood culture containing isoniazid,pyrazinamide,rifampicin,ethambutol


title: RNAseq-4T1-TVI-Met-2


title: whole blood from volunteer 4, rifampicin added

description: Gene expression data from Mycobacterium tuberculosis in whole blood culture containing rifampicin


title: blood_51


title: whole blood from volunteer 4, pyrazinamide added

description: Gene expression data from Mycobacterium tuberculosis in whole blood culture containing pyrazinamide


title: RNAseq-4T1-TVI-Met-1


title: whole blood from volunteer 4, faropenem added

description: Gene expression data from Mycobacterium tuberculosis in whole blood culture containing faropenam


title: Nontumor10

description:
NT10
processed data file: RNAseq_counts_32patients.txt


title: Nontumor11

description:
NT11
processed data file: RNAseq_counts_32patients.txt


title: whole blood from volunteer 4, ethambutol added

description: Gene expression data from Mycobacterium tuberculosis in whole blood culture containing ethambutol


title: blood_50


title: RNAseq-4T1-MFP-Met-3


title: Nontumor7

description:
NT7
processed data file: RNAseq_counts_32patients.txt


title: Nontumor9

description:
NT9
processed data file: RNAseq_counts_32patients.txt


title: whole blood from volunteer 4, drug-free

description: Gene expression data from Mycobacterium tuberculosis in whole blood culture


title: blood_49


title: RNAseq-4T1-MFP-Met-2


title: whole blood from volunteer 3, pyrazinamide added

source_name: Mycobacterium tuberculosis in whole blood culture containing pyrazinamide


title: whole blood from volunteer 3, rifampicin added

source_name: Mycobacterium tuberculosis in whole blood culture containing rifampicin


title: blood_48

source_name: blood


title: Tumor7

description:
T7
processed data file: RNAseq_counts_32patients.txt

value: Tumor liver tissue

value: Tumor


title: RNAseq-4T1-MFP-Met-1


title: whole blood from volunteer 3, moxifloaxacin added

source_name: Mycobacterium tuberculosis in whole blood culture containing moxifloxacin


title: blood_47


title: RNAseq-4T1-Tumor-2

value: Primary tumor


title: blood_45


title: Tumor18

description:
T18
processed data file: RNAseq_counts_32patients.txt

value: Hepatoblastoma


title: Tumor1

description:
T1
processed data file: RNAseq_counts_32patients.txt


title: whole blood from volunteer 3, isoniazid added

source_name: Mycobacterium tuberculosis in whole blood culture containing isoniazid


title: RNAseq-4T1-Tumor-1


title: blood_44


title: blood_43


title: Methyl-seq-Lung_Met_3_TVI

data_processing:
Adaptor trimming: Trimmomatic software
Bisulfite analysis: Bismark package
Genome_build: mm10
Supplementary_files_format_and_content: beta values

extract_protocol: ZR-Duet DNA/RNA miniprep

treatment_protocol: Bisulfite_conversion: EZ-DNA Methylation Gold kit


title: Tumor15

description:
T15
processed data file: RNAseq_counts_32patients.txt


title: Tumor16

description:
T16
processed data file: RNAseq_counts_32patients.txt


title: Methyl-seq-Lung_Met_2_TVI


title: blood_42


title: whole blood from volunteer 3, isoniazid, pyrazinamide, rifampicin, ethambutol added

source_name: Mycobacterium tuberculosis in whole blood culture containing isoniazid,pyrazinamide,rifampicin,ethambutol


title: whole blood from volunteer 3, faropenem added

source_name: Mycobacterium tuberculosis in whole blood culture containing faropenam


title: Tumor4

description:
T4
processed data file: RNAseq_counts_32patients.txt


title: Tumor2

description:
T2
processed data file: RNAseq_counts_32patients.txt


title: whole blood from volunteer 3, drug-free

source_name: Mycobacterium tuberculosis in whole blood culture


title: blood_41


title: Methyl-seq-Lung_Met_1_TVI


title: whole blood from volunteer 3, ethambutol added

source_name: Mycobacterium tuberculosis in whole blood culture containing ethambutol


title: Methyl-seq-Lung_Met_3_MFP


title: blood_40


title: whole blood from volunteer 2, rifampicin added


title: whole blood from volunteer 2, pyrazinamide added


title: Tumor9

description:
T9
processed data file: RNAseq_counts_32patients.txt


title: Methyl-seq-Lung_Met_2_MFP


title: Tumor19

description:
T19
processed data file: RNAseq_counts_32patients.txt


title: blood_38


title: Tumor6

description:
T6
processed data file: RNAseq_counts_32patients.txt


title: blood_39


title: Methyl-seq-Tumor_2_MFP

value: Mammary tumor


title: Methyl-seq-Lung_Met_1_MFP


title: Recurrence27

description:
R27
processed data file: RNAseq_counts_32patients.txt

value: Recurrence


title: whole blood from volunteer 2, moxifloaxacin added

description: Gene expression data from Mycobacterium tuberculosis in whole blood culture containing moxifloxacin


title: MIN_Low_Gln_rep3

data_processing:
Basecalls performed using CASAVA version 1.8
The RNA-seq sequence reads were mapped to mouse genome assembly mm10 using open source RNA-seq alignment tool HISAT2 (ver 2.0.4)
The alignment results were converted to RNA-seq gene expression measurement as RPKM (reads/kilo base of total exon length/million mapped) using Partek Genome Suite (version 6.6) with NCBI RefSeq database.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for all Samples

source_name: Apc Min cells, Low Glutamine medium

extract_protocol:
RNA extraction by Qiagen RNA kit
RNA libraries were prepared with TruSeq SR Cluster V3 kits (Illumina).

treatment_protocol: Low glutamine medium

value: intestinal organoids

value: Apc Min

value: primary cell

tag: description

value: invitro


title: Tumor24

description:
T24
processed data file: RNAseq_counts_32patients.txt

value: Female


title: whole blood from volunteer 2, isoniazid added

description: Gene expression data from Mycobacterium tuberculosis in whole blood culture containing isoniazid


title: whole blood from volunteer 2, isoniazid, pyrazinamide, rifampicin, ethambutol added

description: Gene expression data from Mycobacterium tuberculosis in whole blood culture containing isoniazid,pyrazinamide,rifampicin,ethambutol


title: Tumor3

description:
T3
processed data file: RNAseq_counts_32patients.txt

value: Male


title: blood_35

value: male

value: blood


title: blood_33


title: MIN_Low_Gln_rep2


title: whole blood from volunteer 2, faropenem added

description: Gene expression data from Mycobacterium tuberculosis in whole blood culture containing faropenam

value: whole blood culture


title: whole blood from volunteer 2, ethambutol added

description: Gene expression data from Mycobacterium tuberculosis in whole blood culture containing ethambutol


title: Tumor23

description:
T23
processed data file: RNAseq_counts_32patients.txt


title: MIN_Low_Gln_rep1


title: blood_32


title: MIN_Control_for_Low_Gln_rep3

source_name: Apc Min cells, control medium


title: whole blood from volunteer 2, drug-free

description: Gene expression data from Mycobacterium tuberculosis in whole blood culture


title: blood_37


title: blood_31


title: blood_36


title: whole blood from volunteer 1, rifampicin added

description: Gene expression data from Mycobacterium tuberculosis in whole blood culture containing rifampicin


title: MIN_Control_for_Low_Gln_rep2


title: Tumor29

description:
T29
processed data file: RNAseq_counts_32patients.txt


title: MIN_Control_for_Low_Gln_rep1


title: Tumor22

description:
T22
processed data file: RNAseq_counts_32patients.txt


title: whole blood from volunteer 1, pyrazinamide added

description: Gene expression data from Mycobacterium tuberculosis in whole blood culture containing pyrazinamide


title: Methyl-seq-Tumor_1_MFP

value: 4T1 mammary tumor cell


title: whole blood from volunteer 1, moxifloaxacin added


title: blood_30


title: Tumor21

description:
T21
processed data file: RNAseq_counts_32patients.txt


title: blood_29


title: Tumor33

description:
T33
processed data file: RNAseq_counts_32patients.txt


title: MIN_DMaKG_rep3

description: invitro

source_name: Apc Min cells, DM-aKG treatment


title: blood_27


title: whole blood from volunteer 1, isoniazid, pyrazinamide, rifampicin, ethambutol added


title: MIN_DMaKG_rep2

description: invitro


title: blood_26


title: Tumor31

description:
T31
processed data file: RNAseq_counts_32patients.txt

source_name: Tumor liver tissue


title: whole blood from volunteer 1, faropenem added


title: MIN_DMaKG_rep1

description: invitro


title: Tumor30

description:
T30
processed data file: RNAseq_counts_32patients.txt


title: blood_24


title: whole blood from volunteer 1, ethambutol added


title: MIN_Control_rep3

description: invitro

source_name: Apc Min cells, control treatment


title: Tumor26

description:
T26
processed data file: RNAseq_counts_32patients.txt


title: blood_23


title: MIN_Control_rep2

description: invitro


title: Tumor25

description:
T25
processed data file: RNAseq_counts_32patients.txt


title: whole blood from volunteer 1, isoniazid added

description: Gene expression data from Mycobacterium tuberculosis in whole blood culture containing isoniazid


title: blood_21


title: Tumor13

description:
T13
processed data file: RNAseq_counts_32patients.txt


title: WT_tissue_rep7

description: invitro

source_name: WT mouse, no treatment

value: WT


title: MIN_Control_rep1

description: invitro


title: GLY2

city: Hangzhou

first: li

last: lei

address: xiashas street num 6

data_processing:
Transcripts that overlapped with known mRNAs and transcripts shorter than 200 bp were discarded. Then we utilized CPC  and CNCI to predict transcripts with coding potential. All transcripts with CPC score <-1 and CNCI score <0 were removed. The remaining transcripts were considered as lncRNAs
StringTie  was used to perform expression level for mRNAs and lncRNAs by calculating FPKM . The differentially expressed mRNAs and lncRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package – Ballgown .
genome build: https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Osativa  Version  JGI 323 v7.0
Supplementary_files_format_and_content: FPKM

source_name: plants leaves

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was used to deplete ribosomal RNA according to the manuscript of the Epicentre Ribo-Zero Gold Kit (Illumina, San Diego, USA).
Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (LC Bio, China) following the vendor's recommended protocol

value: leaf

tag: cultivar

value: glyphosate-tolerant CA21

tag: agent

value: glyphosate


title: Tumor12

description:
T12
processed data file: RNAseq_counts_32patients.txt

value: Hepatoblastoma

value: Tumor liver tissue

value: Tumor


title: blood_20


title: GLY3


title: GLY1


title: Tumor32

description:
T32
processed data file: RNAseq_counts_32patients.txt


title: CK3

value: no spray


title: WT_tissue_rep6

first: Haiqing

last: Li

address: 1500 East Duarte Road

description: invitro

value: intestinal organoids

tag: genotype


title: CK2


title: blood_19

first: Haja

last: Kadarmideen

address: Richard Petersens Plads, Building 324


title: Tumor11

description:
T11
processed data file: RNAseq_counts_32patients.txt


title: CK1


title: WT_tissue_rep4

description: invitro

value: primary cell


title: Tumor20

description:
T20
processed data file: RNAseq_counts_32patients.txt


title: Tumor5

description:
T5
processed data file: RNAseq_counts_32patients.txt


title: whole blood from volunteer 1, drug-free

description: Gene expression data from Mycobacterium tuberculosis in whole blood culture


title: blood_17


title: WT_tissue_rep3

description: invitro


title: blood_16


title: blood_14


title: Tumor10

description:
T10
processed data file: RNAseq_counts_32patients.txt


title: WT_tissue_rep2

description: invitro


title: A318 bud  Pre-bloom  rep4

city: Knoxville

first: Margaret

last: Staton

email: mestato@gmail.com, mstaton1@utk.edu

state: Tennessee

address: 2505 EJ Chapman Blvd, 370 PBB

institute: University of Tennessee

data_processing:
Adaptors and low-quality reads were trimmed by skewer for each library
Trimmed reads were aligned to Prunus persica v1 and Prunus persica v2 by STAR-2.5.3a
Gene counts were quantified by HTSeq-count
Gene counts of Prupe.1G531100 to Prupe.1G531700 (Pp01:43417246...43480648) in the Purnus persica v2 were replaced by ppa018667m, ppb017585m, ppa010758m, ppa011123m, ppa010822m, and ppa010714m in Prunus persica v1
Genome_build: Prunus persica v2 and Prunus persica v1
Supplementary_files_format_and_content: comma-delimited files with gene counts for apricot and peach

organism: Prunus persica

source_name: floral bud

growth_protocol: Apricot trees were grown in France. Peach trees were grown in South Carolina, USA

extract_protocol:
Total RNA from apricot bud tissue were extracted using NuceloSpin RNA XS Isolation kit (Macherey-Nagel, France). Total RNA from peach tissue were extracted using ??? Kit
Library construction was followed the illumina TruSeq RNA Library Prep Kit

value: floral bud

tag: Stage

value: Pre-bloom

tag: cultivar number


title: A318 bud  Pre-bloom  rep2


title: WT_tissue_rep1

city: Duarte

description: invitro

tag: sample type


title: Tumor28

description:
T28
processed data file: RNAseq_counts_32patients.txt

tag: disease diagnosis

tag: gender

value: Male


title: A323 bud  100 chill hours rep3


title: A318 bud  Pre-bloom  rep3


title: Tumor14

description:
T14
processed data file: RNAseq_counts_32patients.txt

value: Female

tag: patient


title: MIN_tissue_DMaKG_rep6

description: invitro

source_name: Apc Min mouse, DM-aKG treatment

value: Apc Min


title: A318 bud  Pre-bloom  rep1


title: blood_13

city: Kongens Lyngby

tag: breed

tag: Sex

value: male

value: blood


title: MIN_tissue_DMaKG_rep5

description: invitro


title: WT_tissue_rep5

description: invitro

value: WT


title: CHON_H3K36me3_Rep1

tag: msc donor

tag: cell type

value: differentiated chondrocytes

tag: chip antibody

value: ChIP-seq grade polyclonal rabbit H3K36me3 (Diagenode, cat. no. C15410192)

tag: differentiation time point


title: blood_10

tag: tissue

tag: fcr

tag: rfi


title: blood_18


title: A323 bud  Pre-bloom  rep3


title: CHON_H3K27me3_Rep1

value: ChIP-seq grade polyclonal rabbit H3K27me3 (Diagenode, cat. no. C15410195)


title: blood_9


title: MIN_tissue_DMaKG_rep3

description: invitro


title: Tumor17

description:
T17
processed data file: RNAseq_counts_32patients.txt

value: Hepatoblastoma


title: blood_22


title: A323 bud  Pre-bloom rep2


title: blood_8


title: blood_6


title: MIN_tissue_DMaKG_rep2

description: invitro


title: blood_12


title: blood_5


title: A323 bud  Pre-bloom  rep1


title: MIN_tissue_Control_rep7

description: invitro

source_name: Apc Min mouse, control treatment


title: CHON_H3K27ac_Rep1

value: ChIP-seq grade polyclonal rabbit H3K27ac (Diagenode, cat. no. C15410196)


title: A323 bud  Pre-bloom  rep4


title: CHON_H3K4me3_Rep1

value: ChIP-seq grade polyclonal rabbit H3K4me3 (Diagenode, included in iDEAL Histone ChIP-seq kit cat. no. C01010050)


title: CHON_H3K4me1_Rep1

value: ChIP-seq grade polyclonal rabbit H3K4me1 (Diagenode, cat. no. C15410194)


title: A340 bud  Pre-bloom rep4


title: MIN_tissue_DMaKG_rep1

description: invitro

value: intestinal organoids


title: CHON_input_Rep1


title: A340 bud  Pre-bloom  rep3


title: A340 bud  Pre-bloom  rep1


title: A340 bud  Pre-bloom  rep2


title: MSC_H3K36me3_Rep1

value: human mesenchymal stem cells


title: blood_1

source_name: blood


title: MIN_tissue_Control_rep5

description: invitro

value: primary cell


title: blood_4


title: MIN_tissue_Control_rep4

description: invitro


title: Badami bud 800 rep3

organism: Prunus armeniaca

value: floral bud

tag: cultivar name

value: Badami


title: A323 bud  1000 chill hours rep4


title: MSC_H3K27ac_Rep1


title: A323 bud  1000 chill hours rep3


title: MSC_H3K4me1_Rep1


title: MIN_tissue_Control_rep6

description: invitro

tag: genotype


title: MIN_tissue_Control_rep2

description: invitro


title: Badami bud 100 rep3

tag: Stage


title: Badami bud 800 rep2

tag: cultivar number


title: MSC_H3K4me3_Rep1


title: A323 bud  1000 chill hours rep2


title: A323 bud  1000 chill hours rep1


title: Badami bud 400 rep2


title: MIN_tissue_Control_rep1

description: invitro

tag: sample type


title: A318 bud  1000 chill hours rep4


title: MSC_H3K27me3_Rep1


title: Badami bud 100 rep2


title: MIN_Methylation_DMaKG_rep2

description: invitro

data_processing:
Basecalls performed using CASAVA version 1.8
RRBS-seq sequences were aligned to mouse genome using novocraft’s Novoalign (V3.08.02). The bisulphite reference sequence was generated based on mm10 genome sequence using Novocraft’s novoindex with bisulphite mode.
The alignment results were used to detect CpG Methylation site using Novocraft’s novomyethyl tool.
Genome_build: mm10

extract_protocol:
DNA extraction from Qiagen DNeasy kit
Illumina HiSeq 2500 with HiSeq SBS V4 Kits


title: A318 bud  1000 chill hours rep3


title: Badami bud 0 rep2

value: 0 CH


title: A318 bud  1000 chill hours rep2


title: HSVEC_3

city: Edinburgh

first: Julie

last: Rodor

address: 47 Little France Crescent

department: Centre for Cardiovascular Science

institute: UNIVERSITY OF EDINBURGH

data_processing:
Fastq files obtained from Beckman Coulter Genomics
Mapping was performed by Beckman Coulter Genomics on the human genome reference sequence GRCh38, using Tophat version 2.0.10 in conjunction with Bowtie version 1.0.0. Tophat was provided with a transcriptome reference generated from the Ensembl annotation of GRCh38. HTSeq was used to obtain a read count for all genes of the GRCh38 ENSEMBL annotation.
The average gene expression value in each population, given as Fragments Per Kilobase of transcript per Million map read (FPKM), was obtained using Cufflinks.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt file with FPKM

source_name: Human saphenous vein endothelial cells

growth_protocol: A previously published protocol method was employed to generate endothelial cells from H9 human embryonic stem cells (Boulberdaa et al, 2016 Mol Ther). Briefly, hESCs, were dissociated into single cells using Tryple Select (Life Technologies). 1 × 10^4 cells were seeded into a 5% Pluronic F-127 (Sigma-Aldrich) coated 96- well round bottom microplates to generate embryoid bodies (EBs). The plates were centrifuged at 300 g for 3 minutes. Cells were cultured in Stemline II Hematopoietic expansion medium with the addition of 5 ng/mL Activin A (Peprotech), 10 µmol/L Y-27632 (Millipore), 10 ng/mL vascular endothelial growth factor (VEGF) (Peprotech), and 10 ng/mL bone morphogenetic protein 4 (BMP4) R and D Systems, Minneapolis. After 2 days, the EBs were supplemented Stemline II Hematopoietic expansion medium containing 10 ng/mL VEGF, 70 ng/mL Wnt3A, 140 ng/mL BMP4 and 35 ng/mL Activin A. On day 3, EBs were transferred to 0.1% gelatine-coated 6 well culture dishes (Sigma-Aldrich) and resuspended in endothelial growth medium-2 (EGM-2) (Lonza). The media was supplemented with 50 ng/ml of VEGF and the accompanying bullet kit, minus the VEGF and FBS supplement.  Cells were maintained until day 7, when they were harvested.

extract_protocol:
Total RNA was isolated using the miRNeasy kit (Qiagen)
Ribosomal-depleted stranded libraries were prepared by Beckman Coulter Genomics and sequenced with an Illumina HiSeq (paired end 2 x 100bp).

treatment_protocol: Cell populations were dissociated by enzymatic digestion. Harvested cells were washed in PBS and incubated with specific antibodies (BD Bioscience). FACS sorting was performed using anti-human CD326, anti human-CD56, anti human-CD31, and anti human-CD144 by  FACSAria I or Aria III cell sorter (BD Biosciences). Sorted cell populations were taken forward for RNA extraction.

value: Human saphenous vein endothelial cells

tag: replicate

value: replicate 3


title: MIN_Methylation_DMaKG_rep1

institute: Beckman Research Institute of City of Hope, Center for Informatics

description: invitro

value: Apc Min


title: HSVEC_4

value: replicate 4


title: Badami bud 400 rep3


title: MIN_tissue_Control_rep3

description: invitro


title: MIN_Methylation_Control_rep3

description: invitro


title: Badami bud 800 rep1


title: A318 bud  1000 chill hours rep1


title: HSVEC_1

value: replicate 1


title: Badami bud 400 rep1


title: MSC_input_Rep1


title: MIN_Methylation_DMaKG_rep3

description: invitro


title: MIN_Methylation_Control_rep2

description: invitro


title: MIN_Methylation_Control_rep1

description: invitro


title: Badami petal visible rep3

value: petal visible


title: A209 bud  Pre-bloom  rep3

value: Pre-bloom


title: MIN_exomeseq_Low_Gln

description: invitro

data_processing:
Library strategy: exome-seq
Basecalls performed using CASAVA version 1.8
The Exome-seq sequence reads were mapped to mouse genome assembly mm9 using open source alignment tool BWA (0.7.5a) and duplicate alignment was removed using picard (picard-tools-1.129)
The alignment results were converted to pileup file using samtool (v0.1.19) for genomic variants  detection using VarScan2 (v2.3.7)
Genome_build: mm9

extract_protocol:
DNA  extraction by Qiagen DNeasy kit
Agilent SureSelect Mouse All Exon V1


title: Badami bud 100 rep1


title: A209 bud  Pre-bloom  rep4


title: Badami sepal visble rep3

value: sepal visible


title: MIN_exomeseq_Control

description: invitro


title: non-EC_1

source_name: Endothelial cell (EC) differentiation from human embryonic stem cells (hESC)

value: the day 7 remaining population


title: EC_2

value: day 7 selected endothelial cells (CD144+CD31+)

value: replicate 2


title: HSVEC_2


title: Badami petal visible rep2


title: EC_1


title: A209 bud  Pre-bloom  rep2


title: Knock out animals, sequencing technical rep 2

city: Minneapolis

first: emilyn

middle: U

last: alejandro

state: MN

department: Integrative Biology and Physiology

institute: University of Minnesota

description: ko.count.txt

data_processing:
Cellranger (v 2.0.0) was used to generate the filtered UMI counts per gene with the following parameters: --id=Control --transcriptome=refdata-cellranger-mm10-1.2.0  --fastq=raw_data  --sample=Control  --expect-cells=1000 --nosecondary  --localcores=24 --localmem=62. Control samples and KO samples were processed separately.
Zifa (e40fdbf6c41cd7e564ab03d242fc071f5ac543b7) was first used to check cell grouping between control and knock out samples.  DBSCAN (SKLEARN) was used to group cells with parameter: eps=0.3, min_samples=10
After removing outliers identified in previous step, the remaining cells were imported into Seurat (v 2.0) for cell type classification.
3 methods were used to identify differentially expressed genes between KO and Control cells: impirical testing (Coin v 1.2-2), BPSC (v 0.99.1) and DESeq2 (v 1.14.1).
Impirical method ran 1000 simulations of background UMI count distribution in combined control and ko cells.
DESeq2 was used on pseudo bulk simulations, which grouped KO or control cells into 3 random groups, then summed up the UMI count per gene per group. So DESeq2 could be run on 3 KO samples vs 3 control samples.
Genome_build: mm10
Supplementary_files_format_and_content: ctrl.count.txt and ko.count.txt are the text files that record the raw UMI count per gene per cell per control (ctrl) or ko condition.

extract_protocol:
FACS for GFP
10x Genomic

value: OGT KO

value: Embryonic pancreas

value: Pancreatic epithelial cells

tag: developmental stage


title: A340 bud  600 chill hours rep4

value: floral bud


title: MIN_tissue_DMaKG_rep4

description: invitro

value: intestinal organoids

value: primary cell


title: Knock out animals, sequencing technical rep 1

description: ko.count.txt


title: non-MP_4

value: day 3 remaining cell population


title: non-MP_3

value: replicate 3


title: Badami sepal visble rep2

value: Badami


title: A340 bud  600 chill hours rep3


title: Control animals, sequencing technical rep 2

description: ctrl.count.txt

value: WT


title: Badami petal visible rep1


title: A340 bud  600 chill hours rep2


title: non-MP_2


title: Control animals, sequencing technical rep 1

description: ctrl.count.txt


title: non-MP_1

value: replicate 1


title: Badami sepal visble rep1


title: A340 bud  600 chill hours rep1


title: Bergeron sepal visble rep3

value: Bergeron


title: A209 bud  Pre-bloom  rep1

value: Pre-bloom