title: R6/1 good rep4

description:
50
processed data file: Processed.txt

value: Good


title: Re-Sub hour 24 culutre, replicate 2, experiment set 3

status: Public on Dec 29 2019

type: SRA

city: Cleveland

first: Thaddeus

last: Stappnbeck

state: OH

address: 9500 Euclid Ave

department: Inflammation and Immunity

country: USA

institute: Cleveland Clinic, Lerner Research Institute

description:
Exp3_all.genes_counts_final.txt
ReSub_24h_2_exp3

library_source: transcriptomic

data_processing:
Sequence reads are aligned to the reference genome using STAR
gene counts are derived from uniquely aligned reads using Subread:featureCount
Supplementary_files_format_and_content: genes_counts

molecule: total RNA

organism: Mus musculus

source_name: colonic epithelial monolayer

growth_protocol: Colonic spheroids were passaged in L-WRN media for up to 30 generations. Spheroids were dissociated and plated onto Transwells pre-coated with 10% Matrigel to form an epithelial monolayer. In the first 7 days, L-WRN media was present in both the top and bottom compartment of Transwell. L-WRN media was then removed to create air-liquid interface (ALI). Monolayers were cultured under ALI conditions for up to 28 days. In some experimental settings, ALId21 monolayers were re-submerged with L-WRN media in the top compartment for various amount of time.

extract_protocol:
Rneasy micro kit (Qiagen) was used to extract total RNA from the monolayer cultures
rRNA was depleted using Ribo-Zero kit. RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: cell type

value: colonic spheroid-derived monolayer

tag: experiment

value: experimental set 3

tag: time point

value: 24 hours after re-submersion

tag: replication

value: replication 2


title: heat stress Hypothalamus biological replicate 3

city: Hangzhou

first: Jialiang

last: Han

address: yuhantang street 866

country: China

institute: zhejiang university

data_processing:
Clean reads were generated by removing reads containing adapter, reads containing ploy-N and low quality (Phred score Q ≤20) reads from raw data.
the clean reads were mapped to the latest mouse reference genome (ftp://ftp.ensembl.org/pub/release-91/fasta/mus_musculus/) using Hisat2 v2.0.5.
The expression values (FPKM) of each gene were calculated based on the length of the gene and the read count mapped to this gene by featureCounts v1.5.0-p3.
Differential expression analysis between two groups (three biological replicates per group) was performed using the DESeq2 R package (1.16.1).
Genome_build: mm9
Supplementary_files_format_and_content: FPKMs

source_name: hypothalamus

extract_protocol:
The hypothalamus, pituitary and left inguinal (#4) mammary gland of all dams were collected, cleaned in ice-cold phosphate-buffered saline (PBS), and snap frozen in liquid nitrogen before storage at –80 °C.RNA was harvested using Trizol reagent. A total amount of 3 μg RNA per sample was used as input material for the RNA sequencing library preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: animals：timed-pregnancy ICR mice, control group (25 °C, 55% ±5% RH) and heat stress group (36 °C, 55% ±5% RH). Temperature: controlled by an artificial climate incubator to expose the cages housing the mice to the experimental temperature (36 °C) and relative humidity (RH: 55% ±5%). Animals were sacrificed immediately after treatment on day 13 for the purpose to study the peak lactation responses to heat stress. The hypothalamus, pituitary and left inguinal (#4) mammary gland of all dams were collected.

value: ICR

tag: age

value: 10 weeks, lactating 13 days

tag: stress

value: heat stress

tag: tissue

value: hypothalamus


title: R6/1 good rep2

city: Alicante

first: Luis

middle: M

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

country: Spain

institute: ISABIAL

description:
25
processed data file: Processed.txt

data_processing:
Base calling using Illumina CASAVA software.
Filtering of ribosomal and mitochondrial sequences and 5’end trimming of 2 bases (bowtie in TopHat Alignment v1.0.1).
Assignment to genomic features (GenomicAlignment -R version 3.5.3).
Genome_build: UCSC mm20
Supplementary_files_format_and_content: Processed.txt: Tab-delimited text file with Ensembl ID and read counts for all the samples.

source_name: Striatum

growth_protocol: Standard animal housing conditions.

extract_protocol:
Freshly dissected striata were submerged in RNAlater until processing using TRIzol reagent and further clean-up with RNeasy Mini columns, following manufacturers’ recommendations.
Libraries were prepared using Illumina standard protocols (TruSeq Strander mRNA kit) from 150 ng of starting material.

treatment_protocol: No treatment.

tag: strain/background

tag: genotype/variation

value: 14 weeks

tag: gender

value: Male

value: Striatum

tag: performance


title: R6/1 good rep3

description:
48
processed data file: Processed.txt


title: heat stress Hypothalamus biological replicate 4


title: control Mammary gland biological replicate 6

source_name: mammary gland

value: control

value: mammary gland


title: heat stress Hypothalamus biological replicate 1


title: R6/1 good rep1

description:
17
processed data file: Processed.txt


title: heat stress Hypothalamus biological replicate 2


title: wt poor rep3

description:
59
processed data file: Processed.txt

value: WT

value: Poor


title: wt poor rep4

description:
66
processed data file: Processed.txt


title: Rseq_S3

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

description:
RNA-Seq library ~ 92 M reads per sample
Rseq_counts.txt, RseqSal_counts.txt

data_processing:
RNA-Seq and QuantSeq reads (fastq files) were mapped to the Ensembl Homo sapiens genome (GRCh38). Mapping was performed with Tophat2 (v 2.0.12)  (Langmead and Salzberg 2012) calling Bowtie2 (v 2.2.3) (Kim et al. 2013)
The featureCounts function of Subread (v 1.4.6-p5) (Liao et al. 2014) was used to generate counts of reads uniquely mapped to annotated genes using the GRCh38 gtf file.
The table of read counts was used as input to assess differential expression using the Bioconductor packages, edgeR and limma (voom).
The abundance quantification method Salmon (Patro et al. 2017) to calculate transcript abundance based on the transcript fasta files downloaded from ensemble-release87, (Homo_sapiens.GRCh38.cdna.all.fa and Homo_sapiens.GRCh38.ncrna.all.fa)
The Bioconductor package tximport (Soneson et al. 2015) was used to convert transcripts to gene counts which could be used in downstream differential expression analysis.
The table of read counts was used as input to assess differential expression using the Bioconductor packages, edgeR and limma (voom).
Genome_build: Ensembl Homo sapiens genome (GRCh38).
Supplementary_files_format_and_content: Tab-delimited text file with read count for each sample.

organism: Homo sapiens

extract_protocol:
total RNA was extracted using TRIzol (Invitrogen) followed by purification on an RNeasy column (Qiagen)
mRNA libraries were prepared at the Ramaciotti Centre for Genomics (UNSW University of New South Wales, Australia). The Illumina TruSeq Stranded mRNA Prep Kit was used  .The six RNA-Seq libraries  were sequenced using the Illumina NextSeq 500. R1.fastq and R2.fastq files were produced for each sample.
QuantSeq libraries were prepare using Lexogen’s QuantSeq 3’ mRNA-Seq Library Prep Kit for Illumina, according to the manufacturer’s instructions.
QuantSeq libraries were sequenced using the Illumina NextSeq 500 to produce 75 bp single-end reads for each sample

treatment_protocol: Cryobanked peripheral blood mononuclear cells (PBMC) were thawed and cultured in AIM-V medium (Gibco) with 50 μg/ml polyI:C extract (Invivogen), or medium alone (control) in triplicate. After 24 h, cells were harvested and total RNA was extracted.

tag: condition

value: Control


title: control Hypothalamus biological replicate 8


title: control Hypothalamus biological replicate 7


title: wt good rep4

description:
34
processed data file: Processed.txt

value: Good


title: control Hypothalamus biological replicate 6


title: control Hypothalamus biological replicate 5


title: wt poor rep1

description:
36
processed data file: Processed.txt


title: control Hypothalamus biological replicate 4


title: control Hypothalamus biological replicate 3


title: wt good rep3

description:
26
processed data file: Processed.txt


title: wt good rep2

description:
8b
processed data file: Processed.txt


title: control Hypothalamus biological replicate 2


title: control Hypothalamus biological replicate 1


title: wt good rep1

description:
8
processed data file: Processed.txt


title: heat stress Pituitary biological replicate 8

source_name: pituitary

value: pituitary


title: heat stress Pituitary biological replicate 7


title: heat stress Pituitary biological replicate 4


title: heat stress Pituitary biological replicate 5


title: heat stress Pituitary biological replicate 2


title: wt poor rep2

description:
40
processed data file: Processed.txt


title: control Pituitary biological replicate 8


title: heat stress Pituitary biological replicate 1


title: control Pituitary biological replicate 7


title: control Pituitary biological replicate 6


title: MAT-Ad-EX-LPS-1

type: RNA

city: Kingston

first: Xinzhi

last: Li

state: Ontario

address: 18 Stuart Street

department: Biomedical and Molecular Sciences

country: Canada

institute: Queen's University

hyb_protocol: Procedures were performed according to the manufacturer’s protocol (Nanostring Technologies, Seattle, WA, USA).

scan_protocol: Raw data were generated with the nCounter digital analyzer by counting individual barcodes.

data_processing: Collected data were imported into nSolver 3.0 software (Nanostring Technologies). Annotated groups （NCD or HFD) and treatments (LPS or PBS) were used to group the data. Grouped data then were normalized to the geometric means of spiked-in positive controls (controls for assay efficiency) and spiked-in negative controls (normalized for background). The miRNA expression data were further normalized to miR-186, 191, 26a, 320a, 361, 423-3p.

label: Fluorescent barcode and biotin moiety

source_name: MAT-adipocyte-derived exosome

growth_protocol: Mesenteric pre-adipocytes derived from stromal vascular cells were obtained by collagenase digestion and differentiated to primary adipocytes, designated MAT-Ad. Cells were challenged with PBS or lipopolysaccharide (LPS 1 µg/ml) for 24 h. The culture supernatants were used for exosome isolation and exosomal RNA purification (annotated as MAT-Ad-EX-LPS/PBS), and cells were pelleted for RNA isolation (annotated as MAT-Ad-LPS/PBS).

extract_protocol: Total Cellular RNAs were extracted from cells/tissues using the Direct-zol RNA MiniPrep kit (Zymo research). The exosome-containing RNAs were extracted by the miRCURY RNA isolation kit-Biofluids (EXIQON). RNA quality of the isolated RNA was then checked with Agilent RNA 6000 Nano Assay kit reagents using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The RNA samples were quantified using a standard Nanodrop ND-1000 spectrophotometer (Nanodrop, Wilmington, DE, USA). The RNA concentrations were then adjusted to 30-40 ng/µl.

treatment_protocol: C57BL6 mice were fed a normal chow diet (NCD) or a high fat diet (HFD, 60% fat) ad libitum from 4 weeks of age to 20 weeks of age. Mouse mesenteric adipose tissue (MAT, annotated as MAT-NCD or MAT-HFD) and abdominal aorta (AA, annotated as AA-NCD or AA-HFD) were snap-frozen by liquid nitrogen and saved for future RNA assays.

value: male

tag: treatment

value: NCD-fed

value: LPS

value: mesenteric adipose tissue (MAT)

tag: sample type

value: adipocyte-derived exosome

tag: rna fraction

value: exosomal RNA


title: MAT-Ad-EX-LPS-3


title: MAT-Ad-EX-LPS-2


title: control Pituitary biological replicate 4

value: ICR

value: 10 weeks, lactating 13 days


title: control Pituitary biological replicate 5


title: heat stress Hypothalamus biological replicate 6

value: heat stress

value: hypothalamus


title: control Pituitary biological replicate 3

value: control


title: control Pituitary biological replicate 2


title: control Pituitary biological replicate 1


title: MAT-Ad-LPS-4

source_name: MAT-adipocyte

value: adipocyte

value: total RNA


title: MAT-Ad-EX-PBS-2

value: PBS


title: MAT-Ad-EX-PBS-1


title: heat stress Pituitary biological replicate 3


title: BMDMs, IL-4,  replicate 3

city: Shanghai

first: Xiao

state: Select state...

address: 399 Wanyuan Rd, Minhang, Shanghai, China

institute: Children’s Hospital of Fudan University

description:
lncRNA expression after 24hr in IL-4-treated BMDM
3nd IL_4-007

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, GeneSpring Software GX 12.6.1 (Agilent technologies, Santa Clara, CA, US).

source_name: BMDMs, IL-4

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: Bone marrow was extracted from femurs and, after lysis of erythrocytes, plated in complete medium (CM), consisting of DMEM containing 10% FBS and 10 ng/mL macrophage colony-stimulating factor-1. Cells were allowed to differentiate for 7–8 days at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit（Cat#217004，QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: The BMDMs cultures were incubated for IL-4 24hours,  LPS 3 hours  or untreated, respectively, at 37 ºc in a humidified incubator with 5% CO2.

value: bone marrow derived macrophages (BMDMs)

tag: agent


title: BMDMs, Ctrl,  replicate 3

description:
lncRNA expression in untreated BMDM
3nd Ctrl-009

source_name: BMDMs, Ctrl

value: Ctrl


title: BMDMs, LPS,  replicate 3

description:
lncRNA expression after 3hr in LPS-treated BMDM
3nd LPS-008

source_name: BMDMs, LPS


title: BMDMs, LPS,  replicate 2

description:
lncRNA expression after 3hr in LPS-treated BMDM
2nd LPS-005


title: MAT-Ad-EX-PBS-3

tag: strain


title: BMDMs, IL-4,  replicate 2

description:
lncRNA expression after 24hr in IL-4-treated BMDM
2nd IL_4-004

tag: cell type


title: BMDMs, Ctrl,  replicate 1

description:
lncRNA expression in untreated BMDM
1st Ctrl-003


title: BMDMs, Ctrl,  replicate 2

description:
lncRNA expression in untreated BMDM
2nd Ctrl-006


title: Cg8-1_set4 (tech-replicate)

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

description: tech-replicate

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The first 6 nucleotides and the last nucleotides at the point where the Phred score of an examined base fell below 20 were trimmed using in-house scripts.  If, after trimming, the read was shorter than 45-bp, the whole read was discarded.
Trimmed reads were aligned to the C. globosum genome (assembly ASM14336v1) from the NCBI using its genome annotation with Tophat v2.1.1 using the very-sensitive preset, first strand library type, and providing the corresponding gene model annotation. Only the reads that mapped to a single unique location within the genome, with a maximum of two mismatches in the anchor region of the spliced alignment, were reported in these results. We used the default settings for all other Tophat options.
We tallied reads aligning to exons of genes with the program HTSeq v0.6.1p1. A tally of the number of the reads that overlapped the exons of a gene, was calculated using aligned reads and the gene structure annotation file for the reference genome.
Genome_build: ASM14336v1
Supplementary_files_format_and_content: excel file with relative gene abundance as outout by LOX software

organism: Chaetomium globosum CBS 148.51

source_name: perithecial stage 6

growth_protocol: In order to achieve enough materials for synchronic perithecial development, hyphae of C. globosum were inoculate in 500ml flasks of  200ml liquid CA, and the flask cultures were incubated at 27C on a shaker (100 rpm) under constant light. 10-day liquid cultures were filtered with a sterilized single-layer miracloth (Calbiochem™), and abundant hyphal elements were harvested from the filtrate (Fig. S1). 2 ml filtrate was plated out on cellophane membrane covering solid CA in petri dish (9cm in diameter) and incubated were incubated in a refrigerated incubator (VWR Signature™ Diurnal Growth Chamber), maintained at 27 C under constant white light. Light-colored protoperithecia were spotted in 5 day after inoculation and fully developed perithecia with ripen ascospores were abundant in 8 days after appearance of protoperithecia. A disturbance with spreader was applied to protoperithecia plates to set a synchrony start-time for further perithecial development.

extract_protocol:
Total RNA was extracted from homogenized tissue with TRI REAGENT (Molecular Research Center) as in Clark et al. (2008). Messenger RNA was purified using Dynabeads oligo(dT) magnetic separation (Invitrogen).
Preparation of cDNA for sequencing followed the Illumina mRNA Sequencing Sample Preparation Guide. Complementary DNA was prepared using N6 primers for samples of all time-points.
22 sequencing libraries were produced from purified total RNA samples by the Illumina TruSeq stranded protocol. The libraries underwent 76 bp paired-end sequencing using Illumina HiSeq 2500 according to Illumina protocols.

treatment_protocol: Cellophane membranes with fungal tissues were collected at protoperithecial stage (0 time point right before the disturbance), 2, 24, 48, 72, 96, 120, 144 and 168 hr after. Tissue samples were flash frozen in liquid nitrogen and stored at ﹣80 C. All tissues/perithecia that were collected from a single plate were counted as one biological replicate. At least three biological replicates were prepared for each sampled time-point and16  high quality samples were sequenced for transcriptomics.

tag: time points

tag: morphology

value: mature asci and ascospore


title: Cg7-1_set2 (tech-replicate)

description: tech-replicate

source_name: perithecial stage 5

value: dark ascospores


title: human_embryo_d12_rep1

city: Cambridge

last: Sun

state: MA

address: 455 Main St

department: EECS

institute: Whitehead Institute

data_processing:
The reads from single cell RNA-seq were aligned to the GRCh38 human reference genome using the Cell Range v.2.2.0 pipeline with default parameters (10x Genomes).
The generated cell-by-gene unique molecular identifier (UMI) count matrix was analyzed using the Seurat R package v.2.3.4.
We used Seurat(v3.0.0) package for further analysis and only kept the cells expressing at least 200 genes and genes with expression in at least 3 cells. The cells were also filtered by the maximum of 8000 expressed genes and of 20% mitochondrial genes.
The UMI counts were then normalized for each cell by the total expression, multiplied by 10000, and log-transformed.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files with raw read counts

molecule: polyA RNA

source_name: embryo

growth_protocol: hESCs were cultured on mitomycin C-inactivated mouse embryonic fibroblasts (MEFs) in hESC media, which is composed of 20% knockout serum replacement (KSR) (GIBCO, 10828-028), 100mM L-Glutamine (GIBCO, 25030-081), 1x MEM Non-Essential Amino Acids (NEAA) (GIBCO, 11140-050), 55mM 2-Mercaptoethanol (GIBCO, 21985-023), 10ng/mL recombinant human FGF basic (R&D systems, 233-FB), 1x Penicillin-Streptomycin (GIBCO, 15140-122), and 50ng/mL primocin (InvivoGen, ant-pm-2) in DMEM/F12 media (GIBCO, 11330-032). The hESCs were split every 7 days using Collagenase type IV (GIBCO, 17104-019). All hESC lines used in this study are registered with the National Institute of Health Human Embryonic Stem Cell Registry and are available for research use with NIH funds. Mycoplasma test (Lonza, LT07-418) was performed every month. All experiments were approved by the UCLA Embryonic Stem Cell Research Oversight Committee.

extract_protocol: Single cell suspension was made from hESCs, iMeLCs, day 1 to day 4 aggregates after trypsin treatment. Single cells were washed three to five times in PBS supplemented with 0.04% BSA. Single cell suspension was sequenced using 10X Genomics.

treatment_protocol: hESCs were dissociated into single cells with 0.05% Trypsin-EDTA (GIBCO, 25300-054) and plated onto Human Plasma Fibronectin (Invitrogen, 33016-015)-coated 12-well-plates at the density of 200,000 cells/well in 2mL/well of iMeLC media, which is composed of 15% KSR (GIBCO, 10828-028), 1x NEAA (GIBCO, 11140-050), 0.1mM 2-Mercaptoethanol (GIBCO, 21985-023), 1x Penicillin-Streptomycin-Glutamine (GIBCO, 10378-016), 1mM sodium pyruvate (GIBCO, 11360-070), 50ng/mL Activin A (Peprotech, AF-120-14E), 3mM CHIR99021 (Stemgent,04-0004), 10mM of ROCKi (Y27632, Stemgent, 04-0012-10), and 50ng/mL primocin in Glasgow’s MEM (GMEM) (GIBCO, 11710-035). After 24 hr, iMeLCs were dissociated into single cells with 0.05% Trypsin-EDTA and plated into ultra-low cell attachment U-bottom 96-well plates (Corning, 7007) at the density of 3,000 cells/well in 200ml/well of hPGCLC media, which is composed of 15% KSR (GIBCO, 10828-028), 1x NEAA (GIBCO, 11140-050), 0.1mM 2-Mercaptoethanol (GIBCO, 21985-023), 1x Penicillin-Streptomycin-Glutamine (GIBCO, 10378-016), 1mM sodium pyruvate (GIBCO, 11360-070), 10ng/mL human LIF (Millipore, LIF1005), 200ng/mL hu- man BMP4 (R&D systems, 314-BP), 50ng/mL human EGF (R&D systems, 236-EG), 10mM of ROCKi (Y27632, Stemgent, 04-0012-10), and 50ng/mL primocin in Glasgow’s MEM (GMEM) (GIBCO, 11710-035).

tag: genotype

value: wild type

value: embryo


title: ucla2.batch2.iMeLC

source_name: hESCs

value: hESCs


title: Cg5-1_set3 (tech-replicate)

description: tech-replicate

source_name: perithecial stage 3

value: young asci


title: ucla2.batch2.hESC


title: human_embryo_d12_rep2


title: MAT-Ad-LPS-1

value: male

value: NCD-fed

value: LPS

value: mesenteric adipose tissue (MAT)


title: ucla2.batch2.PGCLCd3


title: Cg5-1_set2 (tech-replicate)

description: tech-replicate


title: ucla2.batch2.PGCLCd2


title: ucla2.batch1.iMeLC


title: ucla2.batch2.PGCLCd1


title: MAT-Ad-LPS-3


title: Cg2-1_set2 (tech-replicate)

description: tech-replicate

source_name: disturbance

value: 2hr after disturbance

value: protoperithecia


title: Cg8-2_set4 (bio-replicate3)


title: BMDMs, LPS,  replicate 1

description:
lncRNA expression after 3hr in LPS-treated BMDM
1st LPS-002

tag: age


title: ucla2.batch1.PGCLCd3


title: BMDMs, IL-4,  replicate 1

description:
lncRNA expression after 24hr in IL-4-treated BMDM
1st IL_4-001


title: ucla2.batch2.PGCLCd4


title: MAT-Ad-PBS-3

tag: stress

value: adipocyte


title: MAT-Ad-PBS-2

tag: tissue

value: total RNA


title: MAT-Ad-LPS-2


title: ucla2.batch1.PGCLCd2


title: MAT-Ad-PBS-4

value: PBS


title: ucla2.batch1.hESC


title: Cg7-2_set2 (bio-replicate3)


title: ucla1t2c.iMeLC

value: TFAP2C mutant


title: ucla2.batch1.PGCLCd1


title: Cg2-2_set2 (bio-replicate3)


title: ucla1t2c.hESC


title: AA-HFD-3

source_name: abdominal aorta

value: HFD-fed

value: abdominal aorta


title: MAT-Ad-PBS-1


title: ucla1t2c.PGCLCd3


title: ucla1t2c.PGCLCd2


title: Cg8-0_set2 (bio-replicate2)

value: mature asci and ascospore


title: Cg9-0_set4 (bio-replicate2)

source_name: Ascospore release

value: ascospore release


title: ucla1t2c.PGCLCd1


title: ucla1t2c.PGCLCd4


title: ucla1.batch2.iMeLC

value: wild type


title: Cg4-0_set2 (bio-replicate2)

source_name: perithecial stage 2

value: ascogenous center development


title: Cg7-0_set2 (bio-replicate2)

value: dark ascospores


title: ucla1.batch2.hESC

value: hESCs


title: AA-NCD-3

value: male

value: NCD-fed


title: AA-HFD-2


title: ucla1.batch2.PGCLCd4


title: Cg2-0_set2 (bio-replicate2)


title: ucla1.batch2.PGCLCd3


title: Cg9-1_set1 (bio-replicate1)


title: MAT-HFD-5

source_name: mesenteric adipose tissue (MAT)

value: mesenteric adipose tissue (MAT)


title: AA-NCD-2


title: Cg8-1_set1 (bio-replicate1)


title: AA-HFD-1


title: ucla1.batch2.PGCLCd2


title: Cg7-1_set1 (bio-replicate1)


title: AA-NCD-1


title: MAT-HFD-3


title: ucla1.batch2.PGCLCd1


title: Cg6-1_set1 (bio-replicate1)

source_name: perithecial stage 4

value: young ascospores


title: MAT-HFD-2


title: MAT-HFD-1


title: MAT-HFD-4


title: Cg5-1_set1 (bio-replicate1)

value: young asci


title: ucla1.batch1.hESC


title: MAT-NCD-5


title: Cg4-1_set1 (bio-replicate1)


title: ucla1.batch1.iMeLC


title: Cg2-1_set1 (bio-replicate1)

value: 2hr after disturbance

value: protoperithecia


title: ucla1.batch1.PGCLCd3


title: MAT-NCD-4

value: total RNA


title: ucla1.batch1.PGCLCd4


title: ucla1.batch1.PGCLCd2


title: Cg1-1_set1 (bio-replicate1)

source_name: protoperithecia

value: 0hr (matured protoperithecia)


title: LE of non-infected dogs_rep4

city: Araçatuba

first: Larissa

middle: Martins

last: Melo

address: Clovis Pestana st, 793

country: Brazil

institute: UNESP

description: miRNA profile expression in LE of non-infected dogs

hyb_protocol: For hybridization of samples to the strips was carried on at 48ºC for 20h using the GeneAtlas® Hybridization,  Wash, and Stain Kit for miRNA Array Strips. Following this period, strips were processed and scanned using the GeneAtlas® System (Affymetrix).

scan_protocol: After the array strip are registered in the GeneAtlas Software and the target hybridization steps are  complete, scanning processing on the GeneAtlas System was made. Transfer of the strip assembly into the imaging station's drawer starts the imaging process.

data_processing: Raw intensity values were background corrected, log2 transformed and then quantile normalized by the software Expression Console (Affymetrix) using the Robust Multi-array Average (RMA) algorithm.

label: biotin

organism: Canis lupus familiaris

source_name: LE of healthy and non-infected dogs

label_protocol: MicroRNA profiles were obtained from 250 ng/sample of total RNA (RNA Integrity Number over than 7) using the FlashTag™ Biotin HSR RNA Labeling Kit, and the Affymetrix® miRNA 4.1 Array strip (Affymetrix, Santa Clara, Califórnia, EUA), according to the manufacturer’s instructions. A recommended ELOSA quality control assay was run for all samples.

extract_protocol: Splenic leukocytes isolated from maceration of the fragment of spleen and added buffers for sample purification. Total RNA was extracted from 5x106 cells with a miRVana™ miRNA Isolation Kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions.  RNA samples were immediately stored at -80ºC. Quantification was performed using NanoDrop (ND-2000 spectrophotometer, Thermo Scientific, Wilmington, DE, USA) and quality of samples was assessed using a Capillary electrophoresis (Bioanalyzer 2100 Agilent, Santa Clara, CA, USA).

value: splenic leukocytes

tag: cell line

value: canine LE


title: ucla1.batch1.PGCLCd1


title: Cg3-1_set1 (bio-replicate1)

source_name: initiation of perithecia

value: young perithecia


title: MAT-NCD-3


title: MAT-NCD-2


title: LE of non-infected dogs_rep2


title: LE of non-infected dogs_rep3


title: LE of non-infected dogs_rep5


title: LE of infected dogs_rep10

description: miRNA profile expression in LE of dogs naturally infected with L. infantum


title: LE of non-infected dogs_rep1


title: LE of infected dogs_rep6

source_name: LE of dogs naturally infected with L. infantum


title: MAT-NCD-1


title: LE of infected dogs_rep4


title: LE of infected dogs_rep1


title: LE of infected dogs_rep8


title: LE of infected dogs_rep3


title: LE of infected dogs_rep5


title: LE of infected dogs_rep9


title: Donor 4 UT

status: Public on Dec 28 2019

city: Columbus

first: Jonathan

middle: P

last: Butchar

address: 400 W. 12th Avenue

department: Internal Medicine

institute: The Ohio State University

hyb_protocol: Standard hybridization at core facility

scan_protocol: Standard scanning at core facility

data_processing: R and BioConductor, using GCRMA to calculate expression values and limma to identify differentially-expressed genes

label: Biotin

source_name: Human peripheral blood monocytes

label_protocol: Standard Affymetrix Biotin labeling at core facility

growth_protocol: Peripheral blood freshly drawn, then monocytes isolated using MACS negative selection

extract_protocol: Qiagen RNA columns

treatment_protocol: Untreated (control) or 25 ng/ml IFNg, for 24 hours

tag: disease state

value: Healthy Donor

value: untreated

value: peripheral blood monocytes


title: LE of infected dogs_rep2


title: Donor 2 IFNg

value: IFNg-treated


title: Donor 2 UT


title: Donor 4 IFNg


title: HBCx_81

city: Paris

first: Tatiana

last: Popova

state: Veuillez choisir

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: gene expression data HBCx-81

hyb_protocol: GeneChip Human 1.1 ST arrays were hybridized according to Affymetrix recommendations using WT Expression Kit protocol (Life Technologies, Carlsbad, CA) and Affymetrix labeling and hybridization kits.

scan_protocol: Standard Affymetrix protocol

data_processing: Affymetrix CEL files were imported into the Gene Expression Workflow in Partek® Genomics Suite version 7.0 (Partek Inc., St. Louis, MO, USA, www.partek.com).

source_name: human breast xenograft 81

label_protocol: Standard Affymetrix protocol

growth_protocol: human breast cancer growing in Swiss Nude mice

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

treatment_protocol: gene expression were generated from untreated samples

value: human breast cancer xenograft

value: triple-negative breast cancer

tag: response to irinotecan treatment

value: Response


title: Donor 1 UT


title: HBCx_33

description: gene expression data HBCx-33

source_name: human breast xenograft 33


title: Donor 1 IFNg


title: HBCx_66

description: gene expression data HBCx-66

source_name: human breast xenograft 66


title: HBCx_43

description: gene expression data HBCx-43

source_name: human breast xenograft 43


title: HBCx_145

description: gene expression data HBCx-145

source_name: human breast xenograft 145


title: HBCx_149

description: gene expression data HBCx-149

source_name: human breast xenograft 149


title: Donor 3 IFNg


title: HBCx_17

description: gene expression data HBCx-17

source_name: human breast xenograft 17


title: HBCx_9

description: gene expression data HBCx-9

source_name: human breast xenograft 9


title: HBCx_14

description: gene expression data HBCx-14

source_name: human breast xenograft 14


title: HBCx_8

description: gene expression data HBCx-8

source_name: human breast xenograft 8


title: HBCx_16

description: gene expression data HBCx-16

source_name: human breast xenograft 16

value: Progressive disease


title: HBCx_152

description: gene expression data HBCx-152

source_name: human breast xenograft 152


title: HBCx_148

description: gene expression data HBCx-148

source_name: human breast xenograft 148


title: HBCx_15

description: gene expression data HBCx-15

source_name: human breast xenograft 15


title: HBCx_108

description: gene expression data HBCx-108

source_name: human breast xenograft 108


title: HBCx_60

description: gene expression data HBCx-60

source_name: human breast xenograft 60


title: HBCx_157

description: gene expression data HBCx-157

source_name: human breast xenograft 157


title: HBCx_106

description: gene expression data HBCx-106

source_name: human breast xenograft 106


title: HBCx_95

description: gene expression data HBCx-95

source_name: human breast xenograft 95


title: HBCx_4B

description: gene expression data HBCx-4B

source_name: human breast xenograft 4B


title: HBCx_92

description: gene expression data HBCx-92

source_name: human breast xenograft 92


title: F8

city: Urbana

first: Karen

last: Chen

state: IL

address: 1201 W Gregory St

department: Division of Nutritional Sciences

institute: University of Illinois at Urbana-Champaign

data_processing:
Paired-end reads were generated with the Illumina® MiSeq platform for each sample, at a read length of 250 nucleotides. The reads were demultiplexed and quality-filtered using Trimmomatic (version 0.30) with a Phred score cut-off of 33. Data analysis was performed through the QIIME pipeline (version 1.9.0). Operational taxonomical unit (OTU)-picking was performed by searching the Greengenes 16S rRNA gene database
Genome_build: Greengenes 16S rRNA gene database
Supplementary_files_format_and_content: There microbiome processed files represents the abundance of bacterial genera in each sample by percentage. One file is averaged by the group and  the other has the results for every sample.

organism: mouse gut metagenome

source_name: Fecal bacteria

extract_protocol:
Fecal and cecal samples collected at the time of harvest contents using QIAmp DNA stool Mini Kit (Qiagen, CA) with bead-beating. DNA concentration and quality was measured using Cytation5 (Biotek)
The V3-V5 variable regions of the 16S rDNA were amplified using primers (forward F357: 5’-CCTACGGGAGGCAGCAG-3’ and reverse R926: 5’-CCGTCAATTCMTTTRAGT-3’)

tag: host biomaterial_provider

value: Jackson Laboratory

tag: host sex

value: Female

tag: host tissue

value: Fecal

tag: host strain


title: HBCx_63

description: gene expression data HBCx-63

source_name: human breast xenograft 63


title: HBCx_30

description: gene expression data HBCx-30

source_name: human breast xenograft 30


title: F6


title: HBCx_31

description: gene expression data HBCx-31

source_name: human breast xenograft 31


title: HBCx_12B

description: gene expression data HBCx-12B

source_name: human breast xenograft 12B


title: HBCx_39

description: gene expression data HBCx-39

source_name: human breast xenograft 39


title: Donor 3 UT

source_name: Human peripheral blood monocytes

tag: treatment


title: HBCx_24

description: gene expression data HBCx-24

source_name: human breast xenograft 24


title: HBCx_48

description: gene expression data HBCx-48

source_name: human breast xenograft 48


title: HBCx_161

description: gene expression data HBCx-161

source_name: human breast xenograft 161


title: ucla2.batch1.PGCLCd4

source_name: hESCs

value: wild type

value: hESCs


title: F5


title: F9


title: F4


title: F33


title: F34


title: F7


title: F18


title: F16


title: F2


title: F15


title: F10


title: F12


title: F1


title: F11


title: F13


title: F14


title: C9

source_name: Cecal bacteria

value: Cecum


title: C8


title: F31


title: F30


title: F3


title: F29


title: F27


title: F28


title: C7


title: F19


title: F24


title: F23


title: F26


title: F22


title: C5


title: C4


title: F21


title: F20


title: C3


title: C31


title: C30


title: C32


title: C33


title: C28


title: C29


title: CD4+ Naive rep 3

first: Jesper

last: Kers

address: 400 Technology Square

institute: Ragon Institute of MGH, MIT & Harvard

data_processing:
RNA-seq reads were processed with the zUMIs 2.2 pipeline (STAR 2.5.4a, SAMtools 1.9, R 3.5.1, pigz 2.3.4) with the following obligatory setting in the yaml file: BC (read 1): 1-8, UMI (read 1): 9-18, cDNA (read 2): 1-50, STAR_index: GRCh38.p12, GTF_file: gencode.v29.annotation.gtf, num_threads: 16, mem_limit: 40, num_bases (BC_filter): 1, phred (BC_filter): 20, num_bases (UMI_filter): 1, phred (UMI_filter): 20, BarcodeBinning: 0, nReadsperCell: 96.
As a result of the zUMIs version 2.2 pipeline, an .rds data tables with counts per gene per barcode is generated. Exon counts are used for downstream applications
Count tables were normalized with the median of ratios method (Anders et al. 2010 Genome Biology), which is built in the DESeq() algorithm of DESeq2 version 1.22.1 (fitType = "local", sfType = "poscounts", goodness-of-fit was validated by dispersion plots).
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: tsv-files with normalized abundance measurements per gene

source_name: PBMC

extract_protocol:
Frozen PBMCs were thawed, sorted into effector CD4+CTLs (CD3+ CD4+ CD8- CCR7- CD45RA- SLAMF7+ CD28lo) and naive CD4+ Th cells (CD3+ CD4+ CD8- CCR7+ CD45RA+). Cells were lysed in lysis buffer and total RNA was extracted with the RNeasy Plus Micro Kit (Qiagen).
Libraries were prepared according to the mcSCRB-seq V2 protocol adjusted for bulk RNA sequencing. https://www.protocols.io/view/mcscrb-seq-protocol-p9kdr4w

tag: sample barcode

value: TTGGACGC

tag: patient

value: Patient 3

tag: disease

value: SSc

value: PBMC


title: CD4+ CTL CD28lo CD57hi rep 3

value: TTGTTGAG


title: C34


title: CD4+ Naive rep 2

value: GCACAGCT

value: Patient 2


title: C27


title: CD4+ CTL CD28lo CD57hi rep 1

value: CTGAATCT

value: Patient 1


title: F25


title: C26


title: CD4+ CTL CD28lo CD57hi rep 2

value: ATGTGCAC


title: CD4+ Naive rep 1

value: AAGGACTT


title: Ccrescentus_total_RNA

city: Boston

first: Peter

last: Culviner

address: 677 Huntington Ave

department: IID

institute: Harvard School of Public Health

description: total RNA

data_processing:
Single-end reads mapped to respective genomes using bowtie2.
For the majority of analyses (all processed csv files except those ending in "density"), a single count was added for each read at the middle of the aligned region (strand, genomic_position). These counts could then be summed for genes (i.e. coding regions, rRNA) to assess rRNA depletion and quantify gene expression.
For processed csv files ending in "density", a single count was added at each aligned position in a read (e.g. a read of length 75 adds 75 total counts, 1 at each aligned position). These density maps could then be used to assess depletion across the rRNA genes.
Genome_build: NC_000913.2 (E. coli), NC_000964.3 (B. subtilis), NC_011916.1 (C. crescentus)
Supplementary_files_format_and_content: csv files record counts (see data processing) at each position in the genome. Each row corresponds to a single nt position, the two columns correspond to the positive and negative strand, respectively.

organism: Caulobacter vibrioides

source_name: Bacterial liquid culture

growth_protocol: Cells were harvested at mid-log phase after outgrowth from a back-diluted overnight culture. E. coli and B. subtilis were grown at 37°C; C. crescentus was grown at 30°C.

extract_protocol:
RNA was extracted using Trizol (Invitrogen) and Direct-zol RNA MiniPrep kit (Zymo).
See publication for complete protocol. Briefly, samples with rRNA subtraction with treated with either a custom ribosome depletion technique or the Ribo-Zero kit (Illumina). Next, RNA was fragmented with RNA fragmentation reagents (Ambion). First strand cDNA synthesis was conducted using random primers and Superscript III (Invitrogen). To enable strand specificity, second strand synthesis was conducted using dUTP instead of dTTP with RNase H, E. coli DNA ligase, and E. coli DNA polymerase. Ends were repaired with T4 DNA polymerase, Klenow DNA polymerase, and T4 PNK. 3’ ends were adenylated with the Klenow fragment (3’>5’ exo-). Y-shaped adapters were ligated and 9-12 cycles of PCR were conducted with standard Illumina primers with multiplexing indexes. Amplified libraries were cleaned up with AMPure XP beads and submitted for sequencing at the MIT BioMicro Center using standard Illumina protocols.

tag: strain

tag: media

value: PYE

tag: rrna depletion

value: none (total RNA)

tag: perturbation

value: none, mid-log


title: Ccrescentus_diy_depletion

description: rRNA subtracted total RNA

value: custom biotinylated oligos


title: C23

value: Jackson Laboratory

value: Female


title: C22

value: Cecum


title: Ago.CLIP_BAT_9t

city: New York

first: Sean

last: O'Connor

state: NY

address: 1230 York Ave

department: Laboratory of Molecular Metabolism

institute: Rockefeller University

data_processing:
Library strategy: CLIP-seq
collapsing of exact sequences
stripping of degenerate linker (5nt; ends with a G)
removal of 3'adaptor (GTGTCAGTCACTTCCAGCGG)
alignment with novoalign (unambiguous mapping on mm10)
collapsing of PCR duplicates (unique CLIP tags)
clustering of unique reads
Genome_build: Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files generated from Ago-CLIP unique tags for genome browser

source_name: interscapular brown adipose tissue

extract_protocol:
Tissues were UV-irradiated and subjected to Ago-CLIP with mouse anti-Ago (citation), clone INSERT (detailed desription in accompanying paper).
partial RNAse digestion, RNA linker ligation and PCR amplificiation. Ago-bound fragments were ligated to a degenerate 3'linker.

value: interscapular brown adipose tissue

tag: pooling

value: 2 mice per replicate

tag: age

value: 15 week


title: Ago.CLIP_BAT_10t

tag: tissue


title: C21


title: Ago.CLIP_BAT_7t


title: C20


title: KO CD11b+Ly6G+ cells S2

city: Bethesda

first: Hiroki

last: Ishii

state: Maryland

address: Building 37, Room 3134, 37 Convent Dr.

institute: National Cancer Institute

data_processing:
For RNA-sequencing, the sequencing quality of the 51-77 million reads per sample was assessed using FastQC (version 0.11.5), Preseq (version 2.0.3), Picard tools (version 1.119), and RSeQC (version 2.6.4). Reads were then trimmed using Cutadapt (version 1.14) to remove sequencing adapters, prior to mapping to the mm10 mouse genome using STAR (version 2.5.2b) in two-pass mode. Overall expression levels were quantified using RSEM version 1.3.0 with GENCODE annotation M12. DESeq2 (version 1.20.0) was used for differential expression analysis. For differential gene expression, q ≤ 0.05 and absolute fold-change ≥ 1.5 were used to define significant changes.
Genome_build: mm10
Supplementary_files_format_and_content: text file

source_name: myeloid cells

extract_protocol:
Myeloid cell subsets were sorted from spleens, and RNA was harvested using RNeasy Mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 6-8 week old

value: spleen

tag: cell type

value: myeloid cells

tag: cell markers

tag: genotype

value: Lmna KO


title: C6

tag: host biomaterial_provider

tag: host sex


title: C25

tag: host tissue

tag: host strain


title: KO CD11b+Ly6G+ cells S1


title: F17

value: Fecal


title: C24


title: C2


title: HBCx_12A

description: gene expression data HBCx-12A

source_name: human breast xenograft 12A

value: human breast cancer xenograft

tag: disease state

value: triple-negative breast cancer

tag: response to irinotecan treatment

value: Progressive disease


title: TNF+/+ biological rep4

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

description: Adult male brain lysate

hyb_protocol: Arrays were hybridized and washed according to the manufacturer's specifications (Affymetrix Inc., Santa Clara, CA, USA)

scan_protocol: Arrays were scanned in a GeneChip® Scanner 3000 (Affymetrix Inc., Santa Clara, CA, USA)

data_processing: Image analysis was performed using GeneChip® Operating Software (GCOS, Affymetrix). Expression data was normalized, background corrected and summarized using the GC-RMA algorithm implemented in the Partek Genomic Suite software.

source_name: wild type, brain

label_protocol: GeneChip® WT Terminal Labeling Kit (Affymetrix Inc, Santa Clara, CA, USA)

growth_protocol: Adult male TNF+/+ and TNF-/- brain lysates

extract_protocol: Total RNA was extracted from frozen braines using Trizol reagent  (Invitrogen, Carlsbad, CA, USA) according to the manufacturers' instructions.

treatment_protocol: not applicable

tag: gender

value: male

value: 2-4 months-old

value: brain


title: TNF-/- biological rep3

description: Adult male brain lysate

source_name: TNF-/-, brain

value: TNF-/-


title: TNF-/- biological rep1

description: Adult male brain lysate


title: Ago.CLIP_WAT_5t

source_name: epididymal white adipose tissue

tag: strain

value: epididymal white adipose tissue


title: TNF-/- biological rep2

description: Adult male brain lysate


title: TNF+/+ biological rep3

description: Adult male brain lysate


title: C19

value: Jackson Laboratory

value: Female

value: Cecum


title: TNF+/+ biological rep1

description: Adult male brain lysate


title: Ago.CLIP_BAT_8t

value: interscapular brown adipose tissue

value: 2 mice per replicate

value: 15 week


title: TNF+/+ biological rep2

description: Adult male brain lysate


title: Ago.CLIP_BAT_4t


title: C18


title: WT CD11b+Ly6C+ cells S2

value: 6-8 week old

value: spleen

value: myeloid cells

value: WT


title: Ago.CLIP_WAT_3t


title: WT CD11b+Ly6C+ cells S1


title: Ago.CLIP_BAT_6t


title: KO CD11b+Ly6C+ cells S2

value: Lmna KO


title: C17


title: TNF-/- biological rep4

description: Adult male brain lysate


title: KO CD11b+Ly6C+ cells S1


title: Ago.CLIP_WAT_1t


title: C16


title: WT CD11b+Ly6G+ cells S2


title: shoot apical, JXe rep 4

city: Chongqing

first: quan

last: sun

address: Chongwen road 2#

department: College of Bioinformation

institute: Chongqing University of Posts and Telecommunications

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to cotton genome no more than 5 mismatches using the SOAP aligner/SOAP2 software after low-quality reads (reads with unknown sequences ‘N’), adaptor sequence fragments, and empty reads were removed
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: NCBI WGS Project: LBLM01 (Gossypium hirsutum)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Gossypium hirsutum

source_name: stem tip

extract_protocol:
RNA was harvested using Plant RNA EASYspin Plus Kit(Aidlab, Peking, China).
RNA  libraries were prepared for sequencing using standard Illumina protocols

value: Jinxian-short branch

value: shoot apical

tag: developmental stage

value: seedling stage

value: silenced GhBRC1 by VIGS

tag: phenotype

value: short fruit branch


title: C15


title: shoot apical, JXe rep3


title: WT CD11b+Ly6G+ cells S1


title: F32

source_name: Fecal bacteria

value: Fecal


title: C13

value: Jackson Laboratory


title: C12

value: Female


title: BU.MPT H/R+B12-2

city: Chapel Hill

first: Feng

middle: of

state: NC

address: 101 Meical Drive

department: Pathology

institute: UNC-CH

description: Gene expression data from cells with H/R+B13

hyb_protocol: 5.5µg of the labled cDNA was hybridized to Mouse Clariom S array following manufacturer's instruction (Thermo Fisher).

scan_protocol: The arrays were scanned by the Affrymetrix Gene Chip Scanner 3000 7G and CEL. Intensity files were generated by Affymetric GeneChip Command Consol Software (Thermo Fisher).

data_processing:
The microarry results were analyzed by Affymetric Expression Console with the SST-RMA. The differential expression was analyzed by the Affymetrix Transcriptome Analysis Console.
The significant genes were ranked by fold-cahnge with a cutoff of 2 and the ANOVA p-value less than 0.05.

source_name: BU.MPT H/R+B12

label_protocol: Microarray was performed in the Core facility in UNC-CH. 700pg of RNA was used to generate dobule-strand cDNA, which was fragmented and biotin labled following manufacturer's instruction (Thermo Fisher)

growth_protocol: Cells were grown to ≥90% confluence at 39 ºC, in the absence of IFN-γ

extract_protocol: Total RNA from cells was extracted using Trizol following the manufacturer's instruction. RNA was purified using RNeasy Mini Kit (QIAGEN)

treatment_protocol: Cells were randomly divided into 4 groups: (1) normal culture conditions (21% oxygen, 10% FBS, and 4.5 g/L glucose in medium); (2) normal culture condition with 0.3 µM cyanocobalamin (B12); (3) hypoxia/reperfusion (H/R); (4) H/R with 0.3 µM B12.  Hypoxia was induced by placing cells in an anaerobic chamber equilibrated to approximately 1% O2, 5%CO2, and 94% N2 using culture medium lacking glucose and FBS with or without B12.  After 3 hr of hypoxia, cells were returned to normoxic culture conditions with addition of glucose (4.5 g/L) and FBS (10%) for a period of 1hr, which was regarded as reperfusion

value: mouse proximal tubular cell line


title: shoot apical, JXc rep 4

value: control


title: BU.MPT H/R+B12-1

description: Gene expression data from cells with H/R+B12


title: shoot apical, JXc rep3


title: BU.MPT H/R-2

description: Gene expression data from cells with H/R

source_name: BU.MPT H/R


title: BU.MPT H/R-1


title: BU.MPT contr+B12-4

description: Gene expression data from control cells with B15

source_name: BU.MPT contr+B12


title: C10

value: Cecum


title: BU.MPT contr+B12-3

description: Gene expression data from control cells with B14


title: BU.MPT contr+B12-2

description: Gene expression data from control cells with B13


title: BU.MPT H/R-4


title: BU.MPT control-3

description: Gene expression data from control cells

source_name: BU.MPT control


title: BU.MPT H/R+B12-4

description: Gene expression data from cells with H/R+B15


title: C14


title: shoot apical, JXc rep1


title: shoot apical, JXc rep2


title: shoot apical, JXe rep2


title: shoot apical, JXe rep1


title: C11


title: C1


title: BU.MPT control-1

description: Gene expression data from control cells


title: BU.MPT control-2

description: Gene expression data from control cells


title: BU.MPT contr+B12-1

description: Gene expression data from control cells with B12


title: serologically cured patients_D4

city: Guangzhou

first: li

middle: xue

last: fei

state: Guangdong

address: Wushang Road  No.483

institute: SMUDH

hyb_protocol: The pre-hybridization of HmiOA v7.1 arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled small RNA was hybridize on HmiOAv7.1 in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 520-550 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing:
Among the probe triplicates, the median value were selected into signal normalization processed by R program (2.12.1).  We ﬁltered out probes that ﬂag <0 in all samples. Porbes that passed the criteria were normalized by 75% media scaling normalization method.
The Matrix value is normalized intensities. Based on the normalized intensities, we calculate average ratios and find significant values for each gene by pairwise comparision (Ranking and hypothesis testing).

source_name: Homo sapiens

label_protocol: Small RNA population were enriched by (Nanosep100k, Pall Corp.) from 2.5 µg of total RNA. NHS-CyDye (Cy5, Amershan) were direct labeled to Guanine (G) by chemical labeling method using ULS™ microRNA Labeling Kit (EA-038, Kreatech).

extract_protocol: RNA extraction by RNeasy Protect Animal Blood Kit (QIAGEN Cat. no. 73224). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧ 1.8, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧8).

tag: condition

value: serologically cured patients


title: serologically cured patients_D6


title: BU.MPT H/R+B12-3

description: Gene expression data from cells with H/R+B14


title: BU.MPT H/R-3


title: shoot apical, 3798e rep 4

value: nulliplex-branch


title: serologically cured patients_D5


title: BU.MPT control-4

description: Gene expression data from control cells


title: DNA-GN03-B

city: Seoul

first: Jongil

last: Kim

address: Daehak-ro 103

country: South Korea

institute: Seoul National University

library_source: genomic

data_processing:
Library strategy: whole exome sequencing
rsem-calculate-expression (RSEM-1.3.1); expected counts was calculated with rsem
STAR 2.6.0a; rsem use STAR aligner to align the read to the GRCh37
Genome_build: GRCh37

molecule: genomic DNA

source_name: WBC

extract_protocol:
DNA was extracted from the frozen tumor tissue and WBC samples with Qiagen QIAamp DNA mini kit (Qiagen, Valencia, CA) and RNA was extracted from the frozen tumor tissue with RNeasy Lipid Tissue Mini Kit (Qiagen, Valencia, CA)
Library preparation was done using SureSelectXT library prep kit for whole exome sequencing and TruSeq standard mRNA LT sample prep kit for RNA sequencing.

value: WBC

tag: type

value: Normal

tag: grade


title: DNA-GN03-T

source_name: Brain neoplasm

tag: tissue

value: Brain neoplasm

value: Glioneuronal tumor

value: I


title: serologically cured patients_D3


title: shoot apical, 3798e rep3

value: shoot apical


title: serologically cured patients_D1


title: serologically cured patients_D2


title: syphilitic patients_C6

value: syphilitic patients


title: RNA-GN03-T

data_processing:
rsem-calculate-expression (RSEM-1.3.1); expected counts was calculated with rsem
STAR 2.6.0a; rsem use STAR aligner to align the read to the GRCh37
Genome_build: GRCh37


title: shoot apical, 3798e rep2

value: seedling stage

value: silenced GhBRC1 by VIGS


title: syphilitic patients_C4


title: shoot apical, 3798c rep 4


title: shoot apical, 3798e rep1


title: syphilitic patients_C3


title: shoot apical, 3798c rep3


title: serofast state_B5

value: serofast state


title: serofast state_B6


title: syphilitic patients_C1


title: syphilitic patients_C2


title: shoot apical, 3798c rep2


title: SAMPLE 6_HCT116 p21-/-

city: Erlangen

first: Pablo

last: Lindner

state: Bavaria

address: Universitaetsstr. 22

country: Germany

institute: Universityclinic Erlangen

description: Test Sample 1

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php. The three different cell lines were analyzed in three biological triplicates. The mean expression Ct values of the target genes were normalized against the mean Ct value for GAPDH to calculate the Fold Change values.
Fold Change worksheet reports mean Ct values of normalized test samples / mean Ct values of normalized control (i.e., HCT p21-/-/HCT WT) ratios.

label: SYBR Green

label_protocol: RT-qPCR analysis was performed following the manufacturer's instructions using the Epigenetic Chromatin Modification Enzymes   RT² Profiler PCR Array from Qiagen. The CFX96TM Real-Time System and the C1000TM Thermal Cycler from Bio-Rad were used   to perform the RT-PCR runs.

growth_protocol: HCT116 cell lines were cultured at 37°C in a humidified atmosphere with 5% CO2. Cells were harvested at a confluency of ~60-80%.

extract_protocol: mRNA was extracted using the QIAzol Kit from Qiagen. mRNA was purified using the Rneasy Mini Kit from Qiagen.   cDNA was produced equal amounts of RNA using the RT² First Strand Kit from Qiagen.

treatment_protocol: No treatment was performed

tag: cell line (background)

value: Colorectal cancer

tag: cell type

value: Human colorectal carcinoma cell line

tag: genotype/variation

value: Depletion of the p21 gene


title: SAMPLE 9_HCT116 p53-/-

description: Test Sample 2

value: Depletion of the p53 gene


title: SAMPLE 7_HCT116 p53-/-

description: Test Sample 2


title: shoot apical, 3798c rep1

tag: genotype

value: control


title: SAMPLE 8_HCT116 p53-/-

description: Test Sample 2


title: serofast state_B4


title: syphilitic patients_C5


title: serofast state_B2


title: serofast state_B3


title: SAMPLE 5_HCT116 p21-/-

description: Test Sample 1


title: serofast state_B1


title: Ecoli_chloramphenicol_diy_depletion

description: rRNA subtracted total RNA

organism: Escherichia coli

tag: media

value: M9 media supplemented with 0.1% casamino acids, 0.4% glycerol, 0.4% glucose, 2 mM MgSO4, and 0.1 mM CaCl2

tag: rrna depletion

value: custom biotinylated oligos

tag: perturbation

value: Chloramphenicol (50 µg/mL), 5 minutes


title: Ecoli_total_RNA

description: total RNA

value: LB

value: none (total RNA)

value: none, mid-log


title: Ecoli_rifampicin_diy_depletion

description: rRNA subtracted total RNA

value: Rifampicin (25 µg/mL), 5 minutes


title: Ecoli_diy_depletion

description: rRNA subtracted total RNA


title: healthy controls_A6

value: healthy controls


title: healthy controls_A5


title: SAMPLE 4_HCT116 p21-/-

description: Test Sample 1


title: SAMPLE 3_HCT116 WT

description: Control

source_name: HCT116 WT

value: Parental human colorectal carcinoma cell line


title: GRL18076-FAMAB3

city: Roanoke

first: Yuchin

middle: Albert

last: Pan

state: VA

address: 2 Riverside Circle

institute: Virginia Tech

data_processing:
Following sequencing, data was trimmed for both adaptor and quality using a combination of ea-utils and Btrim.
Sequencing reads were then aligned to the genome (Ensembl Danio_rerio.GRCz11.92 with and without unplaced contigs) using Tophat2/HiSat2 and counted via HTSeq.
Read counts for genes annotated on the unplaced contigs were added to the chromosome only count summary.  QC summary statistics were examined to identify any problematic samples (e.g. total read counts, quality and base composition profiles (+/- trimming)), raw fastq formatted data files, aligned files (bam and text file containing sample alignment statistics), and count files (HTSeq text files).
Genome_build: Ensembl Danio_rerio.GRCz11.92
Supplementary_files_format_and_content: counts

organism: Danio rerio

source_name: Whole-larvae total RNA from 10 animals

growth_protocol: Zebrafish larvae were grown under standard rearing conditions (28.5 degrees, 14:10 light:dark cycle)

extract_protocol:
Tissue was dissociated with gentle pipetting and total RNA was prepared using the Zymo RNA miniprep kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No treatments were applied.

value: pheta1/2 maternal zygotic double mutant

tag: age

value: 5 days-post fertizliation

tag: background

value: TL-AB mixed


title: healthy controls_A4


title: Ecoli_control_diy_depletion

description: rRNA subtracted total RNA

source_name: Bacterial liquid culture

value: Negative control, 5 minutes


title: SAMPLE 2_HCT116 WT

description: Control

value: Colorectal cancer


title: GRL18075-FAMAB2


title: Ecoli_chloramphenicol_Ribozero

description: rRNA subtracted total RNA

value: Ribo-Zero


title: healthy controls_A3


title: GRL18074-FAMAB1


title: SAMPLE 1_HCT116 WT

description: Control


title: Ecoli_rifampicin_RiboZero

description: rRNA subtracted total RNA


title: Ecoli_control_RiboZero

description: rRNA subtracted total RNA


title: healthy controls_A2


title: GRL18072-FAMA2

value: pheta1 maternal zygotic mutant


title: Bsubtilis_total_RNA

description: total RNA

organism: Bacillus subtilis


title: bzip76-2-1

city: Yangzhou

first: Chen

state: Jiangsu

address: 12 E. Wenhui Rd.

department: Agricultural College

institute: Yangzhou University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The clean reads were imported into CLC Genomics Workbench 12.0 and mapped to reference genome (IRGSP-1.0) using global alignment mode with the default mapping parameters.
The RPKM (reads per kilobase per million mapped reads) values were calculated.
The statistical differential expression test for two groups (mutants vs. WT) was then performed.
Supplementary_files_format_and_content: WT and osbzip76 RPKM.txt

organism: Oryza sativa

source_name: caryopsis

growth_protocol: The rice plants were grown in paddy fields at Yangzhou, Jiangsu Province, China with regular management in summer.

extract_protocol:
Total RNA from the endospwem was isolated using the Plant RNA Kit (OMEGA) following the manufacturer’s protocol. The total RNA was treated with an RNA-free DNase set (OMEGA) to remove contaminating DNA per the manufacturer’s protocol.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: caryopsis

tag: developmental

value: 2 days after fertilization


title: bzip76-2-2


title: bzip76-1-2


title: T32_miRNA seq

city: Zhengzhou

first: Jing

last: Wang

address: Huayuan Road No.116

institute: Institute of Animal Husbandry and Veterinary Science

data_processing:
The preliminary quality control analyses of raw data in FASTQ format were firstly processed using FASTQC software (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Clean data were obtained by removing reads containing poly-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing poly A or T or G or C and low quality reads.
The small RNA tags were mapped to a reference sequence (Pelodiscus sinensis genome) using the Bowtie sequence aligner (Johns Hopkins University, Baltimore, MD, USA) without mismatch to analyze their expression and distribution on the reference. MiRBase20.0 was used as a reference, and the modified software miRDeep2 was used to obtain the potential known miRNAs.
The available software miREvo and miRDeep2 were integrated to predict novel miRNA by exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the small RNA tags unannotated in the former steps.
The miRNA expression levels were estimated by TPM (transcript per million) through the following criteria : Normalization formula: Normalized expression = mapped readcount/total reads*1000000.
Genome_build: PelSin_1.0
Supplementary_files_format_and_content: Readcount and TPM

organism: Mauremys reevesii

source_name: gonad

growth_protocol: Four hundred and fifty freshly laid Chinese pond turtle eggs were obtained from LVCA Company (Guangzhou Guangdong, China).

extract_protocol:
Eggs were incubated until they reached Greenbaum’s embryonic stage 16, at which point the embryonic gonads become responsive to ambient temperature. The AKG complexes, with three replicates at each incubation temperature, were collected using a stereoscopic microscope, and stored in liquid nitrogen for subsequent RNA extraction
Total RNA was isolated from the frozen AKG complexes samples using Trizol reagent (TaKaRa, Dalian, China). The quantity and quality of the RNA were determined using a NanoPhotometer spectrometer (Implen Inc., Westlake Village, CA, USA). Then the RNAs of the three biological samples from the same incubation temperature were pooled together prior to constructing Illumina-indexed small RNA libraries.

treatment_protocol: The eggs were randomly allocated into plastic containers filled with moist vermiculite. Then the containers were put into one of three incubators, in which the temperatures were set at 26, 29 and 32°C, respectively.

tag: temperature

value: Incubation at 32 oC

value: adrenal-kidney-gonad (AKG) complex


title: SAMPLE 6_HCT116 p21-/-_EMT

description: Test Sample 1

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php. The two different cell lines were analyzed in three biological triplicates. The mean expression Ct values of the target genes were normalized against the mean Ct value for B2M to calculate the Fold Change values.
Fold Change worksheet reports mean Ct values of normalized test samples / mean Ct values of normalized control (i.e., HCT p21-/-/HCT WT) ratios.

label_protocol: RT-qPCR analysis was performed following the manufacturer's instructions using the Epithelial to Mesenchymal Transition RT² Profiler PCR Array from Qiagen.   The CFX96TM Real-Time System and the C1000TM Thermal Cycler from Bio-Rad were used to perform the RT-PCR runs.

value: Human colorectal carcinoma cell line

value: Depletion of the p21 gene


title: Kitaake-2

value: WT


title: healthy controls_A1


title: Kitaake-3


title: GRL18069-WT2

value: Wild type


title: SAMPLE 4_HCT116 p21-/-_EMT

description: Test Sample 1


title: bzip76-1-1


title: T29_miRNA seq

value: Incubation at 29 oC


title: SAMPLE 5_HCT116 p21-/-_EMT

description: Test Sample 1


title: GRL18073-FAMA3


title: SAMPLE 3_HCT116 WT_EMT

description: Control

value: Parental human colorectal carcinoma cell line

value: wild type


title: Kitaake-1


title: SAMPLE 2_HCT116 WT_EMT

description: Control


title: GRL18068-WT1

value: 5 days-post fertizliation


title: SAMPLE 1_HCT116 WT_EMT

description: Control


title: Bsubtilis_diy_depletion

description: rRNA subtracted total RNA

tag: strain

value: LB

value: custom biotinylated oligos

value: none, mid-log


title: specimen 11-064 [X11064R2]

status: Public on Dec 27 2019

type: genomic

city: Tallahassee

first: David

last: Gilbert

state: FL

address: 319 Stadium Drive

department: Biology

institute: Florida State University

hyb_protocol: Standard NimbleGen protocol. Briefly, Cy3 and Cy5 labeled DNA samples (31 ug each) were co-hybridized to Nimblegen CGH arrays containing oligonucleotide probes across the entire human genome.

scan_protocol: GenePix 4000B scanner (Molecular Devices) and GenePix software were used per NimbleGen's standard protocol (www.nimblegen.com/products/lit/index.html).

data_processing: Genome-wide RT profiles were constructed by Repli-chip, Repli-seq, Capture Repli-seq and deep whole genome sequencing (WGS). Replication timing profiles were scaled and pooled for analysis as previously described (Ryba et al., 2011; Marchal et al., 2018). Briefly, Log2 transformed early/late replication timing ratios were quantile normalized and loess smoothed in R

source_name: Early S Fraction

label_protocol: Standard NimbleGen protocol (www.nimblegen.com/products/lit/index.html). Briefly, randomly-amplified BrdU-immunoprecipitated DNA samples (1 ug each) were Cy3- or Cy5-labeled by Klenow reaction using end-labeled Cy3- or Cy5-random 9-mers.

extract_protocol: Replication timing data were obtained by hybridizing early and late replication intermediates to NimbleGen oligonucleotide arrays, as previously described (Ryba, T. et al., 2011. Nat Protoc 6: 870–895). Briefly, replication intermediates were prepared from cells pulse-labeled with BrdU and then sorted into early (1st half of S) and late (2nd half of S) stages of S-phase by flow cytometry, followed by anti-BrdU immunoprecipitation of the BrdU-substituted (nascent) replication intermediates that were synthesized either early or late during S-phase. Samples were labeled after unbiased amplification of recovered DNA by whole-genome amplification (WGA; Sigma, GenomePlex). Further details can be found in Hiratani et al [PLoS Biology (2008) 6: e245] and Ryba, T. et al [Nat Protoc (2011) 6: 870–895].

treatment_protocol: BrdU labeled

tag: gender

value: Female

tag: method

value: E/L

tag: replicate

source_name: Late S Fraction


title: GRL18070-WT3

value: TL-AB mixed


title: specimen 11-128 [X11128R2]

value: Male


title: NC_3

city: Changzhou

first: Yimeng

address: No.185, Juqian Street

institute: The Third Affiliated Hospital of Soochow University

data_processing:
Basecalls performed using CASAVA version 1.8
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). First, clean reads of all libraries were aligned to the reference genome (HG19) by Hisat2 software (v2.0.4). Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps. These peaks identified by both softwares overlapping with exons of mRNA were figured out and chosen by home-made scripts.
Genome_build: hg19
Supplementary_files_format_and_content: bed
Supplementary_files_format_and_content: peak files

source_name: normal tissue

extract_protocol:
RNA extraction protocol
m6A RNA immunoprecipitation was performed with the GenSeq™ m6A-MeRIP Kit (GenSeq Inc., China) by following the manufacturer's instructions. Both the input samples without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.

tag: tumor stage

value: normal


title: specimen 11-015 [X11015R3]


title: specimen PARTEA [PARTEA]

source_name: S Fraction

source_name: G1 Fraction


title: specimen 11-129 [X11129R2]


title: GRL18071-FAMA1

value: pheta1 maternal zygotic mutant


title: NC_1


title: NC_2


title: specimen PARTSP [PARTSP]


title: Cancer_3

source_name: ccRCC tissue

value: Ⅳ


title: Cancer_1

value: Ⅲ


title: Cancer_2


title: RPP631 cells, YKL rep1

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

data_processing:
Paired-end reads were aligned to mm10 genome using STAR (v2.5.2b) (Dobin et al., 2013) with the options --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 -- alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterType BySJo.
Reads with good mapping quality (MAPQ > 30) that aligned to genomic exons were counted using featureCounts (mm10 Ensembl 93)
Differential gene expression analysis was performed using the R package DESeq2 using the lfcShrink function.
Genome_build: mm10
Supplementary_files_format_and_content: YKL_vs_DMSO_counts.txt count data; genes_metadata.tsv provides gene id mapping; YKL_vs_DMSO_DEG.txt shows differential expression

source_name: SCLC

growth_protocol: mouse lung cancer cells were cultured in standard medium as described in method section

extract_protocol:
Qiagen RNA exctration kit to acquire total RNA
NYU genome core standard protocol, see https://med.nyu.edu/research/scientific-cores-shared-resources/genome-technology-center/fees-sample-submission-guidelines

treatment_protocol: cells were treated with either DMSO or YKL for 48 hours

tag: disease state

value: SCLC

tag: cell line

value: lung cancer cells

tag: treatment

value: 100nM YKL for 48h


title: CDK7 inhibitor YKL treated tumor experiment 2

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
Genome_build: hg19
Supplementary_files_format_and_content: Indexed BAM files containing position-sorted reads aligned to the genome and gene-barcode matrices.

source_name: CDK7 inhibitor YKL treated tumor

growth_protocol: Tumor cells were injected orthotopically to the lung and umor-bearing mice were monitored by MRI scan.

extract_protocol:
Mice were humanely euthanized, and mouse lungs were perfused using sterile PBS through heart perfusion from the left ventricle. The whole lung was cut and minced into small pieces followed by digestion in collagenase D (Sigma) and DNase I (Sigma) in Hank’s Balanced Salt Solution (HBSS) at 37°C for 30 minutes. After incubation, the digested tissue was subjected to a 70-μm cell strainer (ThermoFisher Scientific) to obtain single-cell suspensions. Live cell swere then sorted using DAPI  staining. Cells were then resuspended into single cells at a concentration of 1 x 106 per ml in 1X PBS with 0.4% BSA for 10x genomics processing.
Single Cell 3’ Reagent Kits v2: Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, PN-120237; Single Cell 3’ Chip Kit v2 PN-120236 and i7 Multiplex Kit PN-120262" (10x Genomics)
scRNA-seq

treatment_protocol: Mice were treated with either vehicle and isotype IgG (control), anti-PD-1 200 µg/mouse (PD-1, clone 29F.1A12), YKL-5-124 10 mg/kg and combined anti-PD-1 and YKL (Combo). YKL-5-124 was administered daily from Monday to Friday, and PD-1 antibody was administered three times a week (Monday, Wednesday, and Friday).

tag: cell type

value: mouse SCLC


title: Combination treated tumor experiment 2

source_name: Combination treated tumor


title: RPP631 cells, YKL rep2


title: control treated tumor experiment 2

source_name: control treated tumor


title: RPP631 cells, DMSO rep2

value: DMSO 48h


title: Combination treated tumor experiment 1


title: CDK7 inhibitor YKL treated tumor experiment 1


title: control treated tumor experiment 1


title: anti-PD-1 treated tumor experiment 2

source_name: anti-PD-1 treated tumor


title: RPP631 cells, DMSO rep1


title: A549-ONECUT2(∆DBD)_EZH2_ChIP-seq

city: Shanghai

first: Qingyang

last: Ma

state: Xuhui

address: Yue Yang Road 320#

institute: Shanghai Institutes for Biological Sciences

data_processing:
RNA-seq fastq files were trimmed to remove adapter sequences and low-quality bases with Trimmomatic (v.0.33) and then mapped to the hg19 genome and transcriptome with Tophat2 (v.2.1.0) or Hisat2 (v.2.0.1) using default parameters. Raw count tables were generated using featureCounts (v.1.4.6).
ChIP-seq fastq files were trimmed to remove adapter sequences and low-quality bases with Trimmomatic (v.0.33) and then mapped to the hg19 genome with Bowtie2 (v.2.2.4) or Hisat2 (v.2.0.1) using default parameters. Peak calling was performed and bigwig coverage files were generated with MACS2 callpeak and bdgcmp (v.2.1.1), respectively.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated using MACS2 bdgcmp (v.2.1.1); Scores represent fold enrichment versus input. Peak files were generated using MACS2 callpeak (v.2.1.1). The RNA-seq raw count table (RNA-seq_raw_counts_table.xls) was generated using featureCounts (v.1.4.6).

source_name: A549 lung cancer cell line

growth_protocol: All cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Invitrogen) containing 10% fetal bovine serum (FBS, Gibco) supplemented with penicillin (100 U/ml) and streptomycin (100 mg/ml) (Invitrogen).

extract_protocol:
Chromatin immunoprecipitation and DNA extraction were performed using SimpleChIP Enzymatic Chromatin IP Kit (9003, Cell Signaling) following manufacturer’s instructions.
ChIP-seq libraries were prepared with TruSeq DNA sample prep kit using standard protocols.

value: A549 lung cancer cell line

tag: chip antibody

value: EZH2 (Cell Signaling Technology,#5346)


title: A549-ONECUT2(∆DBD)_RNA-seq_rep

extract_protocol:
RNA was extracted from cells by using RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA-seq libraries were prepared with Illumina’s TruSeq RNA sample Prep Kit using standard protocols.


title: A549-ONECUT2_RNA-seq_rep


title: 40BInp: SJSA-1_Input_C

first: Jiajun

last: Zhang

address: #58，Zhongshan 2nd Road

institute: the First Affiliated Hospital of Sun Yat-Sen University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Raw reads were treated with Trimmomatic tools(V0.36) to remove adapters. Following reads quality control:Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15, drop reads which are less than 35% of initiation read length. Then reads quality was inspected using the FastQC software then output statistical result.
The reads that passed the prefiltering step were aligned with the Bowtie2 v2.2.5 software to the human genome (hg19). Peak calling was performed with MACS2. Homer software was used to annotate ChIP-seq peaks, and to find differential peaks between treated and control samples.
Genome_build: hg19

source_name: Osteosarcoma cells

growth_protocol: U2-OS and SJSA-1 were maintained in Dulbecco’s modified Eagle medium. All media were supplemented with 10% fetal bovine serum, penicillin (100 U/mL) and streptomycin (100 mg/mL). Cells were incubated at 37℃ with 5% CO2.

extract_protocol:
U2-OS and SJSA-1 cells were cultured at 37 °C in 5% CO2, and were cross-linked with 1% formaldehyde at room temperature for 10 min followed by neutralization with glycine. Cells were resuspended, lysed in lysis buffer, and sonicated on ice to shear most DNA to 200-750 bp.
Libraries were generated for ChIP samples following the NEBNext® Ultra™DNA Library Prep Kit for Illumina protocol.

tag: tissue

value: bone

tag: disease

value: osteosarcoma


title: A549-ONECUT2_EZH2_ChIP-seq


title: anti-PD-1 treated tumor experiment 1


title: 40AInp: SJSA-1_Input_B


title: 40B: SJSA-1_H3K29Ac_C

value: anti-H3K27ac (#ab4729, Abcam)


title: 20Inp: SJSA-1_Input_A


title: 20: SJSA-1_H3K27Ac_A


title: 40A: SJSA-1_H3K28Ac_B


title: U2-OS_Input_C


title: Spheroid A549 48hr_rep2

city: Bangkok

first: Piyapat

last: Pin-on

address: ChalongKrung

country: Thailand

institute: KMITL

description: Gene expression after 48hr in PNA A15 transfectted spheroid A549 cell line

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Human GE 8X60K, V2 Microarrays (Agilent®). . The slides were incubated for 17 h at 65°C in an Agilent hybridization oven. then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc.)

data_processing: All microarray experiment were classified as down-regulated (Dn), neutral (Nu), or up-regulated (Up) genes using our software, namely CU-DREAM.

source_name: Spheroid cell, A549, 48hr, replicate 2

label_protocol: RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000 (NanoDrop, Wilmington, USA).

growth_protocol: H292 cells were cultivated in Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% fetal bovine serum (FBS), 2 mM L-glutamine and 100 U/mL penicillin and 100 µg/mL streptomycin. A459 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, 2 mM L-glutamine and 100 U/mL of penicillin and 100 µg/mL streptomycin. Cells were incubated in a 37°C humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA). Purity and integrity were evaluated by the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA), Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: PNA-A(15) was synthesised from PANAGENE (PANAGENE, Deajeon, Korea. 7.5x104 cells in 24 well-plate were treated with either 5 μM of PNA-A(15) or scramble (control) for 48 h. The culturing medium was replaced by medium containing PNA-A(15) or scramble every day.

value: Spheroid lung cancer cell line

value: male


title: Spheroid H292 48hr_rep2

description: Gene expression after 48hr in PNA A15 transfectted spheroid H292 cell line

source_name: Spheroid cell, H292, 48hr, replicate 2

value: female


title: Spheroid A549 with PNA A15 48hr_rep1

source_name: Spheroid cell, A549, PNA A15, 48hr, replicate 1


title: Spheroid A549 with PNA A15 48hr_rep2

source_name: Spheroid cell, A549, PNA A15, 48hr, replicate 2


title: A549 48hr_rep2

description: Gene expression after 48hr in scramble transfectted spheroid A549 cell line

source_name: Lung cancer cell, A549, 48hr, replicate 2

value: Lung cancer cell line


title: H292 48hr_rep2

description: Gene expression after 48hr in scramble transfectted spheroid H292 cell line

source_name: Lung cancer cell, H292, 48hr, replicate 2


title: Spheroid H292 with scramble 48hr_rep2

source_name: Spheroid cell, H292, scramble, 48hr, replicate 2


title: Spheroid H292 with PNA A15 48hr_rep1

source_name: Spheroid cell, H292, PNA A15, 48hr, replicate 1


title: Spheroid H292 48hr_rep1

source_name: Spheroid cell, H292, 48hr, replicate 1


title: H292 48hr_rep1

source_name: Lung cancer cell, H292, 48hr, replicate 1


title: U2-OS_Input_B


title: Spheroid A549 with scramble 48hr_rep1

source_name: Spheroid cell, A549, scramble, 48hr, replicate 1


title: Spheroid A549 48hr_rep1

source_name: Spheroid cell, A549, 48hr, replicate 1


title: Spheroid A549 with scramble 48hr_rep2

source_name: Spheroid cell, A549, scramble, 48hr, replicate 2


title: Spheroid H292 with scramble 48hr_rep1

source_name: Spheroid cell, H292, scramble, 48hr, replicate 1


title: Spheroid H292 with PNA A15 48hr_rep2

source_name: Spheroid cell, H292, PNA A15, 48hr, replicate 2


title: A549 48hr_rep1

source_name: Lung cancer cell, A549, 48hr, replicate 1


title: U2-OS_H3K29Ac_C

source_name: Osteosarcoma cells


title: X697R5-Late S Fraction

data_processing:
Genome-wide RT profiles were constructed by Repli-chip, Repli-seq, Capture Repli-seq and deep whole genome sequencing (WGS). Replication timing profiles were scaled and pooled for analysis as previously described (Ryba et al., 2011; Marchal et al., 2018). Briefly, Log2 transformed early/late replication timing ratios were quantile normalized and loess smoothed in R
Genome_build: HG38
Supplementary_files_format_and_content: processed data are 50kb windows in HG38 genome.

source_name: cell line 697

growth_protocol: Cell lines were cultured in RPMI1640+10-20% FBS

extract_protocol:
Genome-wide replication timing profiles were constructed as previously described (Hiratani et al. 2008; Ryba et al. 2011; Marchal et al., 2017). Briefly, cells were pulse labeled with BrdU and separated into early and late S-phase fractions by flow cytometry and processed  by either microaray or NGS.
Sequencing libraries of BrdU-substituted DNA from early and late fractions were prepared by NEBNext Ultra DNA Library Prep Kit for Illumina (E7370).

treatment_protocol: Asynchronous cells were labeled with 100 micromolar BrdU for 2 hours at 37˚C  in RPMI 1640+ 10% FBS

tag: s phase fraction

value: Late S fraction

value: Male


title: X697R5-Early S Fraction

value: Early S fraction


title: X697R4-Late S Fraction


title: X697R3-Early S Fraction


title: X697R4-Early S Fraction


title: X697R3-Late S Fraction


title: U2-OS_H3K28Ac_B


title: X697R2-Late S Fraction


title: U2-OS_Input_A


title: X697R2-Early S Fraction


title: X697R1-Late S Fraction


title: X697R1-Early S Fraction


title: PANBUL-G1 Fraction

source_name: specimen PANBUL

value: G1 fraction

value: not collected


title: U2-OS_H3K27Ac_A


title: KasumiR2-Late S Fraction

source_name: cell line Kasumi2


title: KasumiR2-Early S Fraction


title: PALTWS-S Fraction

source_name: specimen PALTWS

value: S fraction


title: KasumiR1-Late S Fraction


title: PALTWS-G1 Fraction


title: CD34posCD38negCB14-Early S Fraction

source_name: cord blood pool 14 CD34+CD38- fraction

value: not applicable


title: CD34posCD38negCB14-Late S Fraction


title: CD34posCD38negCB96-Late S Fraction

source_name: cord blood pool 96 CD34+CD38- fraction


title: CD34posCD38negCB96-Early S Fraction


title: CD34posCD19posROR1posCB96DAPI-Late S Fraction

source_name: cord blood pool 96 CD34+CD19+ROR1+ fraction


title: CD34posCD19posROR1posCB96DAPI-Early S Fraction


title: CD34posCD19posROR1negCB96DAPI-Early S Fraction

source_name: cord blood pool 96 CD34+CD19+ROR1- fraction


title: CD34posCD19posROR1negCB96DAPI-Late S Fraction


title: CD34posCD19posCB96-Late S Fraction

source_name: cord blood pool 96 CD34+CD19+ fraction


title: CD34posCD19posCB96-Early S Fraction


title: PANBUL-S Fraction


title: KasumiR1-Early S Fraction


title: CD34posCD19posCB14DAPI-Late S Fraction

source_name: cord blood pool 14 CD34+CD19+ fraction


title: CD34posCD19posCB14DAPI-Early S Fraction


title: CD34posCD19posCB14-Late S Fraction


title: Spleen_Stinggt/gt_CFA+CII_rep6

city: Ratchathewi

first: Mookmanee

last: Tansakul

state: Bangkok

institute: Mahidol university

description: Gene expression after injection with CFA and CII for two weeks

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Mouse GE 8X60K, V2 Microarrays (Agilent®). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven. then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc.)

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: Spleen

label_protocol: RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000(NanoDrop, Wilmington, USA).

extract_protocol: RNA was isolated with Trizol reagent (Invitrogen, CA, USA) and followed by the RNeasy mini kit from Qiagen, MD, USA.

value: Spleen

tag: age

value: 10-14 weeks


title: CD34negCD19posROR1posCB96DAPI-Late S Fraction

source_name: cord blood pool 96 CD34-CD19+ROR1+ fraction


title: Spleen_Stinggt/gt_CFA+CII_rep2


title: CD34posCD19posCB14-Early S Fraction


title: CD34negCD19posROR1posCB96DAPI-Early S Fraction


title: Spleen_Stinggt/gt_CFA+CII_rep7


title: Spleen_Stinggt/gt_CFA+CII_rep4


title: Spleen_Stinggt/gt_CFA+CII_rep1


title: Spleen_WT_CFA+CII_rep7


title: Spleen_Stinggt/gt_CFA+CII_rep3


title: Spleen_WT_CFA+CII_rep5


title: Spleen_WT_CFA+CII_rep6


title: CD34negCD19posROR1posCB96-Late S Fraction


title: Spleen_WT_CFA+CII_rep2


title: A549-ONECUT2_HA_ChIP-seq_rep

source_name: A549 lung cancer cell line

value: A549 lung cancer cell line

value: HA (Abcam,ab9110)


title: A549-ONECUT2_input_rep

value: input


title: CD34negCD19posROR1negCB96DAPI-Late S Fraction

source_name: cord blood pool 96 CD34-CD19+ROR1- fraction


title: CD34negCD19posROR1negCB96DAPI-Early S Fraction


title: Spleen_Stinggt/gt_CFA+CII_rep5


title: CD34negCD19posROR1posCB96-Early S Fraction


title: CD34negCD19posROR1negCB96-Late S Fraction


title: A549-ONECUT2(∆DBD)_input

data_processing:
ChIP-seq fastq files were trimmed to remove adapter sequences and low-quality bases with Trimmomatic (v.0.33) and then mapped to the hg19 genome with Bowtie2 (v.2.2.4) or Hisat2 (v.2.0.1) using default parameters. Peak calling was performed and bigwig coverage files were generated with MACS2 callpeak and bdgcmp (v.2.1.1), respectively.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated using MACS2 bdgcmp (v.2.1.1); Scores represent fold enrichment versus input. The peak file (A549-ONECUT2_HA_ChIP-seq_peaks.xls) was generated using MACS2 callpeak (v.2.1.1). The RNA-seq raw count table (RNA-seq_raw_counts_table.xls) was generated using featureCounts (v.1.4.6).

value: none (input)


title: CD34negCD19posROR1negCB96-Early S Fraction


title: A549-ONECUT2(∆DBD)_H3K4me3_ChIP-seq

value: H3K4me3 (Cell Signaling Technology,#9751)


title: Spleen_WT_CFA+CII_rep1


title: CD34negCD19posCB14DAPI-Early S Fraction

source_name: cord blood pool 14 CD34-CD19+ fraction


title: CD34negCD19posCB14DAPI-Late S Fraction


title: A549-ONECUT2_HA_ChIP-seq


title: A549-ONECUT2_input


title: CD34negCD19posCB14-Late S Fraction


title: A549-ONECUT2_H3K4me3_ChIP-seq


title: A549-ONECUT2_RNA-seq

data_processing:
RNA-seq fastq files were trimmed to remove adapter sequences and low-quality bases with Trimmomatic (v.0.33) and then mapped to the hg19 genome and transcriptome with Tophat2 (v.2.1.0) or Hisat2 (v.2.0.1) using default parameters. Raw count tables were generated using featureCounts (v.1.4.6).
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated using MACS2 bdgcmp (v.2.1.1); Scores represent fold enrichment versus input. The peak file (A549-ONECUT2_HA_ChIP-seq_peaks.xls) was generated using MACS2 callpeak (v.2.1.1). The RNA-seq raw count table (RNA-seq_raw_counts_table.xls) was generated using featureCounts (v.1.4.6).


title: CD34negCD19posCB14-Early S Fraction


title: AML5_5K_AML-Late S Fraction

source_name: cell line AML5


title: A549-ONECUT2(∆DBD)_RNA-seq


title: Spleen_WT_CFA+CII_rep4


title: Spleen_WT_CFA+CII_rep3


title: FLANC shRNA #1-1, biological rep1 vs empty vector control

city: Houston

first: George

last: Calin

state: TX

address: 1881 East Road

department: Experimental Therapeutics

institute: MD Anderson Cancer Center

description: FLANC shRNA #1-1 vector versus control shRNA, replicate 2

hyb_protocol: Hybridization done according to Agilent Gene expression hybridization kit. http://www.genomics.agilent.com/en/Gene-Expression-Hybridization-Wash-Reagents/Gene-Expression-Hybridization-Kits/?cid=AG-PT-133&tabId=AG-PR-1054

scan_protocol: Scanned on an Agilent G2505B scanner. Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: HCT116 cell line FLANC shRNA

label_protocol: Labeling was done according to Agilent Gene Expression Hybridization Kit. http://www.genomics.agilent.com/en/Gene-Expression-Hybridization-Wash-Reagents/Gene-Expression-Hybridization-Kits/?cid=AG-PT-133&tabId=AG-PR-1054

growth_protocol: The human colon cancer cell line HCT116 was obtained from the American Type Culture Collection (Manassas, VA, USA) and grown according to ATCC recommendations. Cells were cultured at 37°C in 5% CO2.

extract_protocol: Cell were transduce with lentivirus containing the specific vectors. Total RNA was extracted using Trizol following manufacturer's instructions

value: colon

source_name: HCT116 cell line control shRNA


title: FLANC shRNA #1-1, biological rep2 vs empty vector control


title: AML5_10K_AML-Late S Fraction


title: A549_GSK126_RNA-seq

treatment_protocol: Cells were exposed to 5 µM of GSK126 for 10 days.


title: T26_miRNA seq

source_name: gonad

value: Incubation at 26 oC

value: adrenal-kidney-gonad (AKG) complex


title: AML5_10K_AML-Early S Fraction


title: AML5_5K_AML-Early S Fraction


title: A549-ONECUT2(∆DBD)_H3K27me3_ChIP-seq

value: H3K27me3 (Cell Signaling Technology,#9733)


title: A549_DMSO_RNA-seq

treatment_protocol: Cells were exposed to 0.1% DMSO for 10 days.


title: H3K27m3_CD33_N1

city: tyuo-ku

first: noriko

last: nishi

state: Tokyo

address: 5-11 hakozaki 5F Yunibasaru Bldg

country: Japan

institute: Axiohelix Co. Ltd.

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 1.0.1 with default.
peaks were called using MACS version 2.0.9 with default.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using https://github.com/daler/rdbio-scripts/blob/master/sequenceFiles/bed2wig.py;

source_name: CD33+ LPMC

extract_protocol:
Isolated cells were immediately cross-linked with 1% formaldehyde/PBS for 10 minutes at room temperature. After washing, the cell pellet was lysed in the lysis buffer having the following final concentration: 50 mM Tris-HCl (pH 8.0), 10 mM EDTA, 1% sodium dodecyl sulfate (SDS), 1 mM phenylmethylsulfonyl fluoride (PMSF), 1x proteinase inhibitor complete cocktail (Roche). The lysed solution was subjected to chromatin shearing by using Covaris S2 System (Covaris, Woburn, MA) to shear the chromatin into 100300 bp fragments.
ChIP-seq libraries were prepared for sequencing using the SOLiD Fragment Library Construction Kit and multiplexed by using SOLiD™ Fragment Library Barcoding Kit Module 1-16 according to the manufacturer’s instructions.

value: CD33+ LPMC

value: Non-IBD

value: H3K27m3 (Millipore, clone 07-449)


title: H3K9m3_CD33_U1

value: UC

value: H3K9m3 (Abcam, clone ab8898)


title: H3K27m3_CD33_U1


title: HS01_CD3_U1

description: library strategy: SAGE-Seq

data_processing:
Sequenced reads were mapped to hg19 whole genome using LifeScope version 2.5.1 with set parameters analysis.filter.reference non coding RNA sequence.
Fragments Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a using a pipeline of Perl scripts.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files were generated using bedtools version 2.13.2; tab-delimited text files include RPKM values, count of tags, and total exon length for each gene;

source_name: CD3+ LPMC

extract_protocol:
Total RNA was prepared from sorted cells by using an AllPrep DNA/RNA Micro Kit (Qiagen), and then treated with DNase I and then bound to Dynabeads Oligo(dT) EcoP magnetic beads. The double-stranded cDNA synthesized on the beads was digested with Nla III and ligated to the adaptor containing an EcoP15I restriction enzyme recognition site. The adapter-ligated cDNA was digested with EcoP15I to release the tag containing the adaptor sequence and 27 bp of unique sequence from a single transcript.
SAGE-seq libraries were prepared for sequencing using SOLiD SAGE Kit with Barcoding Adaptor Module and multiplexed by using SOLiD RNA Barcoding Kit Module 1-16 according to the manufacturer’s instructions.

value: CD3+ LPMC


title: MS9_CD3_N2

description: library strategy: SAGE-Seq


title: H3K4m3_CD3_U1

value: H3K4m3 (Millipore, clone 07-473)


title: H3K4m3_CD33_N1


title: H3K4m3_CD3_N1


title: HS02_CD33_U1

description: library strategy: SAGE-Seq


title: H3K9m3_CD3_N1


title: H3K4m3_CD33_U1


title: MS10_CD33_N2

description: library strategy: SAGE-Seq


title: H3K9m3_CD33_N1


title: H3K9m3_CD3_U1


title: A549-ONECUT2_H3K27me3_ChIP-seq


title: FLANC overexpressing vector #1-1, biological rep2 vs empty vector

description: FLANC overexpressing vector versus Empty vector, replicate 2

source_name: HCT116 cell line FLANC overexpressing vector

source_name: HCT116 cell line empty vector


title: H3K27m3_CD3_N1


title: H3K27m3_CD3_U1


title: input_CD33_N1


title: input_CD33_U1