title: KO liver at 8W, biological rep1

city: New York

first: Miki

last: JIshage

address: 1230 York Avenue

institute: Rockefeller University

description:
Gdown1_KO1
Gene expression data from Gdown1 KO liver at 8W.

hyb_protocol: Hybridization was performed at 45 degrees Celsius for 17 hours. The arrays were washed and stained in the GeneChip Fluidic Station 450 (Affymetrix) by using Hybridization, Wash and Stain kit (Affymetrix).

scan_protocol: The arrays were scanned by the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data expressed as CEL files were normalized by the robust multiarray average (RMA) method with the Expression Console software (Affymetrix).

source_name: Mouse Gdown1 KO liver at 8W

label_protocol: Three hundred ng of total RNA was processed for cRNA synthesis with the Ambion WT Expression Kit (PN4411974). Fragmentation and terminal labeling were performed with the Affymetrix GeneChip WT Terminal Labeling Kit (PN 900671).

growth_protocol: Mice were maintained under controlled environmental conditions under a 12-h light /dark cycle and allowed ad libitum access to water and standard laboratory diet.

extract_protocol: Using the RNeasy kit from Qiagen according to manufacturer's protocol.

treatment_protocol: Untreated

tag: strain/background

value: Gdown1 KO

value: 8 weeks

value: Liver


title: V24Is

status: Public on Jan 06 2021

type: SRA

city: Columbia

first: Wipawee

last: Winuthayanon

state: Missouri

address: 1030 Hitt Street

department: OB/GYN & Women's Health

country: USA

institute: University of Missouri

description: 10x Chemistry: Single Cell 3’ v2

library_source: transcriptomic

data_processing:
Both mouse and human data, processing of the raw sequencing data (mkfastq files) was carried out using Cell Ranger v3.1.0 to generate fastq files with default settings.
Fastq files were then processed through Velocyto v0.1.24 to produce loom files with spliced and unspliced mRNA information. Velocyto was run using the command run10x with default setting and a repeat masker gtf file from UCSC Genome Browser for mouse with an assembly for GRCm38/mm10 to mask expressed repeated elements. Generated loom files were then read in scanpy v1.6.0 using JupyterLab for analyses and saved in an h5ad format. For subsequent data analysis and visualization, a virtual machine (Docker) was used to create the analysis environment. Analysis packages including scanpy v1.6.0, anndata v0.7.5, umap v0.4.6, numpy v1.19.4, scipy v1.5.3, pandas v1.1.4, scikit-learn v0.23.2, statsmodels v0.12.1, python-igraph v0.8.3, louvain v0.7.0, and leidenalg v0.8.2 were installed on the Docker.
Genome_build: Reference genomes, mm10-3.0.0 and GRCh38-3.0.0, were used for sequence alignment in mouse and human samples, respectively.
Supplementary_files_format_and_content: Cell Ranger output

molecule: total RNA

organism: Mus musculus

source_name: Mouse oviduct

extract_protocol:
For mouse samples, oviducts were collected 24 hrs after Veh or E2 treatment (n=5-6 mice/group) or at estrus (n=5 mice). Oviducts were pooled and collected in Leibovitz-15 media supplement with 1% fetal bovine serum (L15+1%FBS) and placed on ice. For Veh and E2-treated samples, the oviduct was dissected into distal (infundibulum with ampulla, referred to as InfAmp) or proximal (isthmus with UTJ, referred to as IsthUTJ) regions. To isolate oviductal cells, oviducts were quickly uncoiled by trimming the mesosalpinx in order to locate the ampulla-isthmus junction (AIJ). Then, the tissues were dissected at the AIJ region for subsequent InfAmp and IsthUTJ cell isolation. For estrus samples, the entire length of the oviduct was used. After dissection, 0.25% trypsin-EDTA was injected into the oviduct using a blunted 30-gauge needle until the trypsin was visibly flushed out from the other end of the oviduct. The tissues were then placed in a tube containing 500 µL of trypsin and incubated on ice for 30 min and at 37°C for another 30 min. After the incubation, 500 uL of FBS was added to stop the enzymatic activity of trypsin. Oviductal cells were then flushed out from oviductal tubes with 4°C L15+10%FBS. At this stage, the epithelial, stromal, and parts of muscle cell layers were visibly flushed out. Only translucent longitudinal muscle cells were left intact. Cell clumps and tissue debris were strained twice through 40-µm cell strainers. Cells were then spun down and resuspended in 0.04% bovine serum albumin in phosphate-buffered saline. The final cell concentration was targeted for 8,000 cells/run. For human sample, To obtain cell singlets, the Fallopian tubes were transected so that the luminal portion of the tube was exposed. The mucosal lining of the tubes was gently dissected with a scalpel and enzymatically digested in a solution of 0.05% Trypsin (Sigma, T1426) dissolved in HBSS (Gibco) for 30 minutes, followed by incubation in Collagenase (5 mg/ml, Sigma C5138) and DNAse I (200 µg/ml, Sigma DN25) solution for 20 minutes. The cells were filtered through a 40 µm filter, collected by centrifugation and resuspended in DMEM/F12 (Gibco, 11-330-057) supplemented with 10% FBS (Sigma, F2442) and antibiotics (Gibco, 15-240-096). Live cells were sorted on a BD FACS Aria II at the Cytometry and Cell Sorting Core Laboratory at Baylor College of Medicine (BCM) and submitted for single cell sequencing at the Single Cell Genomics Core Laboratory at BCM.
For mouse samples, scRNA-seq libraries were performed using manufacturer’s protocol (10X Genomics Inc, Pleasanton, CA). Single Cell 3’ v2 chemistry was used. Briefly, individual cells (~8,000 cells/run) were separated into droplets by Gel bead in EMulsion (GEM) technology using 10X Chromium Controller. Emulsion beads were broken and barcoded cDNAs were pooled for amplification. For human sample, scRNA-seq libraries were also performed using 10X Chromium Controller with Single Cell 3’ v3 chemistry.
For mouse samples, libraries generated were sequenced using an Illumina HiSeq4000, targeting 400M reads/run, paired-end, and 100bp read length. For human sample, libraries generated were sequenced using an Illumina NovaSeq 6000, targeting 300M reads/run, paired-end, 50bp read length.

treatment_protocol: Female mice were ovariectomized and left for 14 days to recover and eliminate endogenous steroid hormones. Sesame oil (100 µL) was used as a negative (Vehicle or Veh) control group. 17beta-estradiol (E2) at a dose of 0.25 µg was diluted in 100 µL of 10% ethanol and sesame oil. Ovariectomized females were subcutaneously injected with Veh or E2. Twenty-four hrs after injection, the oviduct was collected for scRNA-seq analysis. Vaginal washes were collected from adult female mice (between 8-12 weeks old) to determine the stage of estrous cycle21. At 11:00 h, oviducts from females in estrus were collected for subsequent scRNA-seq analysis. For human sample, the tissue was collected from an individual without underlying gynecological diseases who underwent post-partum bilateral salpingectomy for sterilization.

tag: tissue

value: oviduct

tag: region

value: isthmus, uterotubal junction

tag: treatment

value: Vehicle 24 hrs

tag: strain


title: KO_MTX_4

city: Valencia

first: Daniel

last: Perez-Cremades

state: Valencia

address: 15 Blasco Ibañez Avenue

department: Physiology Department

country: Spain

institute: University of Valencia

data_processing:
All samples were processed using an RNA-seq pipeline implemented by Genewiz (South Plainfield, NJ).
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
BAM files were generated as a result
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Genome_build: GRCm38

molecule: polyA RNA

source_name: white adipose tissue

extract_protocol: Trizol (Invitrogen) was used for RNA isolation from white adipose tissue.

treatment_protocol: miR-181a2b2-/- (KO) and miR-181a2b2flox/flox (flox) mice were placed on a 60% high fat diet for 12 weeks. Each group of mice was weekly i.p. injected with vehicle control or methotrexate (1 mg/kg).

value: methotrexate

value: white adipose


title: run2_CC5390_N_neg_rep1

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Libraries were sequenced by Illumina NextSeq500 and NovaSeq Sequencing System.
fastq files were generated using Cellranger mkfastq (version 3.0.2). The raw reads were mapped to the Chlamydomonas reference genome (Chlamydomonas reinhardtii v5.5) using cellranger count.
Multiple samples were aggregated by cellranger aggr.
Genome_build: Chlamydomonas reinhardtii v5.5
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

organism: Chlamydomonas reinhardtii

source_name: run2 no cell wall N– replicate 1

growth_protocol: We used the Chlamydomonas reinhardtii strains CC-5390 (cw15 arg7-8::ARG7 MT+) and CC-4532 (CW MT-), which we procured from laboratory stocks. We grew all pre-cultures in Tris Acetate Phosphate (TAP) medium supplemented with micronutrients  at 24 ºC in constant light (~50 µmol/m2/s) and under constant agitation (180 rpm) in an Innova-44R incubator.

extract_protocol: Single-cell RNAseq libraries were prepared by using the Chromium single cell 3′ library and gel bead kit v3 (10x Genomics).

value: Cultured Chlamydomonas cells


title: FF liver at 8W, biological rep2

type: RNA

state: NY

description:
Gdown1_FF2
Gene expression data from Gdown1 FF liver at 8W.

label: biotin

source_name: Mouse Gdown1 FF liver at 8W

tag: genotype/variation

value: Control

tag: age


title: FLOX_MTX_2

value: miR-181a2b2flox/flox (flox)


title: FLOX_MTX_1


title: S11 refeed

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

data_processing:
trimgalore with options '-p --illumina' to trim reads
HISAT2 align with options '-p --no-mixed --no-discordant' to align to GRCh38 + GRCm38 combined reference genome
Sambamba view to reformat aligned reads from .sam to .bam and sambamba sort to sort reads by coordinate
subread featureCounts with options '-p -P -s2' using Gencode H29 reference annotation to generate raw gene counts for aligned files
Genome_build: GRCh38 + GRCm38
Supplementary_files_format_and_content: tab delimited text file includes raw gene counts for each sample

organism:
Homo sapiens
Mus musculus

source_name: Liver

extract_protocol:
Whole livers were removed from the humanized mice either with ad libitum, a 24h fasting, or a 24h fasting followed by a 4h refeeding. The livers were flash frozen and powdered in liquid nitrogen, and the RNA was harvested using Trizol reagent.  Strand specific sequencing libraries were constructed using illumine TruSeq RNA sample Prep kit.
RNA libraries were prepared for sequencing using standard Illumina kit and protocols; strand-specific

treatment_protocol: TK-NOG mice, in which a herpes simplex virus type 1 thymidine kinase (TK) transgene under a mouse albumin promoter is expressed within the liver of highly immune-deficient NOG mice, were obtained from Taconic Biosciences. The TK converts an antiviral medication ganciclovir (GCV) into a toxic product that allows selective elimination of TK positive cells in vivo. The cryopreserved primary human hepatocytes were obtained from Thermo Fisher Scientific. The humanized TK-NOG mice were prepared as previously described (Hasegawa, M. et al.). Briefly, The TK-NOG mice at 8-9 weeks old received an i.p. injection of GCV at a dose of 25 mg/kg. One week later, 50ul volume of 1 106 human primary hepatocytes suspended in HBSS solution were transplanted via intra-splenic injection. 8-12 weeks after transplantation, the serum human albumin in the mice were measured as an index of the extent of human hepatocytes replacement. Humanized TK-NOG mice with serum human albumin levels above 0.5 mg/ml were used for experiments, in which human hepatic genes could be reliably detected by q-PCR. Reference paper PMID: 21238430.

tag: condition

value: fast 24h then refed for another 4h, from 9:00am to 13:00pm

value: Human Liver cells xenografted into TKNOG mice


title: KM-H2 cells with high Rhodamine 123 efflux capacity

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

country: Germany

description: KM-H2 cells with low Rhodamin 123 fluorescence (high efflux capacity)

hyb_protocol: Standard Affymetrix/Applied Biosystems protocol

data_processing: The data were analyzed using Transcriptome Analysis Console. Summarization method: Gene+ Exon-SST-RMA

organism: Homo sapiens

source_name: KM-H2 cells

growth_protocol: Cells were grown in RPMI medium supplemented with 10 % FCS under standard conditions

extract_protocol: RNA was isolated by using the High Pure RNA Isolation kit (Roche, Basel, Switzerland) according to manufacturer's instructions.

treatment_protocol: Cells were stained with 0.2 µg/mL Rhodamin 123 for 30 min. Cells were washed and incubated for 4 hrs. Cells with high and low Rhodamin 123 fluorescence were separated by flow cytometry and immediately used for RNA extraction.

tag: cell type

value: cell line from Hodgkin lymphoma

tag: sorted cells

value: low


title: S10 refeed


title: KO_3

value: vehicle


title: KO liver at 8W, biological rep2

description:
Gdown1_KO2
Gene expression data from Gdown1 KO liver at 8W.


title: FF liver at 8W, biological rep1

description:
Gdown1_FF1
Gene expression data from Gdown1 FF liver at 8W.


title: KO_2


title: S6 fast

value: fast 24h from 9:00am to 9:00am


title: S5 fast


title: S7 fast


title: KM-H2 cells with low Rhodamine 123 efflux capacity

description: KM-H2 cells with high Rhodamin 123 fluorescence low efflux capacity)

scan_protocol: Standard Affymetrix/Applied Biosystems protocol

value: high


title: S8 fast


title: FLOX_4


title: S4 fed

value: ad libitum harvest at 9:00am


title: S3 fed


title: KO_1


title: S9 fast


title: ΦKZ infected [ID-005733-Grad-14-Fraction-21P]

city: Würzburg

first: Jörg

last: Vogel

address: Josef-Schneider-Straße 2

department: Institute for Molecular Infection Biology

institute: Würzburg University

data_processing:
library strategy: Grad-seq
READemption analysis, for details see https://reademption.readthedocs.io/en/latest/example_analysis.html, after gene-quantification the reads were normalized to the ERCC spike-in
Supplementary_files_format_and_content: wig files were generated using READemption; Scores represent 'coverage-tnoar_min_normalized', tdf files were generated with igvtools

organism:
Phikzvirus phiKZ
Pseudomonas aeruginosa PAO1

source_name: infected bacterial culture

growth_protocol: Pseudomonas aeruginosa cells were grown in LB media to an OD600 of 0.3

extract_protocol:
500 µl gradient fractionation samples were deproteinized with 1% SDS and extracted with an equal volume acidic phenol:chloroform:isoamylalcohol (PCI), and precipitated with ethanol and 1:30 volume NaOAc pH 5.2 with 1 µl glycoblue
Samples were solubilized in 50 µl, 5 µl were diluted with 45 µl water, 10 µl were mixed with 10 µl 1:100 diluted ERCC RNA spike-in mix1. RNA samples were prepared as described in Hör et al. 2020 NAR.

treatment_protocol: Cells were optionally infected with an MOI of 15 with ΦKZ bacteriophage and incubated for 10 min

value: infection with ΦKZ bacteriophage for 10 min


title: ΦKZ infected [ID-005732-Grad-14-Fraction-20]


title: S1 fed


title: ΦKZ infected [ID-005731-Grad-14-Fraction-19]


title: WDR76-/- E14 total RNA seq replicate 1

city: Chicago

first: Alexander

last: Ruthenburg

state: IL

address: 920 E 58th St, CLSC 855

department: MGCB/BMB

institute: University of Chicago

description: Wdr76_knockout_differential_expression_refseq.txt

data_processing:
Reads were mapped to mm9 reference genome, using Bowtie2 (Langmead et al., 2009), with default parameters and SAM output
SAM files were filtered to reject unmapped reads, and converted to sorted and indexted bam files using SAMtools (Li et al., Bioinfomatics 2009)
Peaks were called relative to input using macs2 using "--broad" and "--extsize 284" parameters, and filtered for overlap with mm9-blacklist by Bedtools (https://sites.google.com/site/anshulkundaje/projects/blacklists)
align to mm9 genome with tophat2
prepare for DE analysis with cufflinks then cuffmerge
Differential Expression was performed in Cuffdiff with  rRNA, tRNA, 7SK, snoRNA, and mitochondrial RNA masked using per condition dispersion fitting, then filtered for blacklist and refseq overlap using bedtools.
Genome_build: mm9
Supplementary_files_format_and_content: bed file of called ChIP peaks with fourth column normalized ChIP signal (IP/input); txt file of differential expression

source_name: Embryonic stem cells

growth_protocol: Mouse Embryonic Stem Cells (mESC) E14 cell line (129/Ola background) (Hooper et al., 1987) were grown at 37°C, 5% CO2, 95% humidity in ES media high glucose DMEM (Invitrogen) supplemented with 15% (v/v) FBS (Gibco), 2mM L-glutamine (Gibco), 1% (v/v) non-essential amino acids (Gibco), 1X Penicillin/Streptomycin (Gibco), 0.1 mM  2-mercaptoethanol (Gibco), 1000U/mL LIF (ESG1107, Millipore), 3 µM CHIR99021 (04-0004, Stemgent), 1 µM PD0325901 (04-0006, Stemgent), sterile filtered 0.1 µm membrane, stored in 4°C for up to 1 week. E14 cells were cultured on dishes coated with 0.1% gelatin (Sigma) without feeder cells, and passaged daily in 1:3 ratio (media was changed 3 hours prior passage). Cells were harvested at 80-90% confluence, with media changed at least 3 hours prior.

extract_protocol:
RNA libraries were prepared from ribosome-depleted RNA using the Next Ultra Directional RNA Library Kit (NEB) and Next Multiplex index oligonucleotide primers (NEB) for use with Illumina sequencing platforms. The library was prepared according the manufacturer’s instructions and amplified using 15 cycles of PCR. Indices for each library sample were chosen to minimize the Hamming distance between index reads in order to ensure proper assignment of reads to samples during sequencing. The libraries were sequenced on an Illumina HighSeq4000 at the University of Chicago Functional Genomics Core Facility.
cDNA libraries were prepared from the total RNA isolated from triplicate independent cultures of wild type and Wdr76-/- (g1-3.1 clone) E14 cells grown in parallel. Briefly, cells were passaged side-by-side at similar confluence over the course of five days. Total RNA from 4 million cells of each genotype was isolated in triplicate by Trizol-chloroform extraction and purification using RNA Clean & Concentrator (Zymo). For each sample, 2 μg of total RNA was ribosome-depleted using Ribo Zero (Illumina).

value: E14 Wdr76-/- (CRISPR biallelic ablation of exon 11)


title: WDR76-/- E14 total RNA seq replicate 3


title: WDR76-/- E14 total RNA seq replicate 2


title: ΦKZ infected [ID-005730-Grad-14-Fraction-18]


title: FLOX_3


title: E14 total RNA seq replicate 3


title: SP-A2 (1A0)-M-O3-3-X48

city: hershey

first: Nithyananda

last: Thorenoor

state: PA

address: 500 University Drive

department: Pediatrics

institute: Penn State University College of Medicine

description: SAMPLE 45

data_processing:
De-multiplexed sequencing reads passed the default purify filtering of Illumina CASAVA pipeline (released version 1.8) and were quality trimmed/filtered using The FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit).  The filtered reads were further trimmed with both 5’ and 3’ adapter sequences and subjected to Chimira suite to align and count miRNA expression (Vitsios and Enright, 2015).  The differentially expressed miRNAs (DEG) between FA to O3, males and females were identified by using the edgeR (Robinson et al., 2010) and the TCC v1.14.0 R package (Sun et al., 2013) with false discovery rate (FDR) adjusted p value of 0.1 as a significance cutoff.
miRNAs with good correlation between mice (3 out of 4).  We used two different parameters (methods) to analyze the identified miRNA expression (fold change).  a) The expression levels (fold change) of miRNAs from co-ex (FA to O3 for males and females) SP-A2 (1A0) (FA to O3 for males and females) and KO (FA to O3 for males and females) were analyzed and differentially expressed miRNAs in co-ex, SP-A2 (1A0) and KO males and females were identified in response to FA or O3.
Supplementary_files_format_and_content: Matrix- excel sheet

source_name: Male mouse exposed to Ozone (O3)-Alveolar Macrophage (AM) cells

extract_protocol:
AM cells were isoalated from Broncho alveolar lavage, Total RNA extracted
Small RNA-seq libraries were generated by NEXTflex Small RNA Library Prep Kit v3 for Illumina (BioO Scientific, Austin, TX), followed by deep sequencing on an Illumina HiSeq 2500 as per the manufacturer’s instructions.  Briefly, 1-2 ng of total RNA was ligated with chemically modified 3’- and 5’- adapters that can specifically bind to mature micro RNAs, followed by reverse transcription and PCR amplification.  Unique index sequence tags were introduced during PCR to enable multiplexed sequencing.  Each library was assessed for the presence of desired micro RNA population and approximate library quantity by Bioanalyzer High Sensitivity DNA Kit (Agilent Technologies).  Pooled libraries were denatured and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.

treatment_protocol: The animals were exposed to FA or O3 in parallel as described previously (Haque et al., 2007).   A group of 4 animals/sex/condition (FA, O3, except for SP-A2 (1A0) and co-ex male, 3 animals/condition) and alveolar macrophages (AM) were isolated after 18 h of recovery

tag: agent

value: Ozone (O3)

value: Alveolar Macrophage (AM) cells

tag: exposure time

value: 3 hours

tag: Sex

value: Male


title: E14 total RNA seq replicate 2


title: E14 total RNA seq replicate 1


title: MCF-SM-31  NTSH-EV-NoF-3

city: Houston

first: Shaolin

state: Tx

address: 1881 East Road

institute: MD Anderson Cancer Center

description: MCF-SM-31_(Clariom_D_Human)_NTSH-EV-NoF-3.CEL(normalized)

hyb_protocol: Following fragmentation, 5 micrograms of biotin-labeled sense-strand cDNA fragments in 200 µL of hybridization mix was loaded onto a human Clariom D array and hybridized to probes on the array in a GeneChip Hybridization Oven 645 (Affymetrix) for 16 h at 45°C with 60 rpm rotation.

scan_protocol: GeneChips were scanned using GeneArray G7 scanner (Affymetrix) and quantified into .CEL files with image and signal intensities.

data_processing: Transcriptome Analysis Console software v4.0 (Affymetrix) was used for probe set summarization and robust multiarray average (SST+RMA) normalization procedures.

source_name: MCF-SM-31 NTSH-EV-NoF

label_protocol: The fragmented cDNA was labeled by terminal deoxynucleotidyl transferase using the Affymetrix proprietary DNA labeling reagent, which is covalently linked to biotin.

growth_protocol: NoF 151 fibroblasts were cultured in a 1:1 mixture of Medium 199 (Sigma-Aldrich, Cat. # M5017-10X1L) and medium MCDB 105 (Sigma-Aldrich, Cat. # M6395-10X1L) supplemented with 10% FBS, 1% penicillin-streptomycin, and 5 µg epidermal growth factor.

extract_protocol: The fibroblasts were then harvested and total RNA was isolated using a Direct-zol kit (Zymo Research, Cat. # R2062)

treatment_protocol: Fibroblasts were plated on a six-well plate and treated with 10 µg/mL small EVs harvested from HT29-ntsh or -shP53 cells for 48 hr.

tag: cell line

value: fibroblasts

value: 10 µg/mL small EVs harvested from HT29-ntsh for 48 hr


title: MCF-SM-31 ShP53-EV-NoF-3

description: MCF-SM-31_(Clariom_D_Human)_ShP53-EV-NoF-3.CEL(normalized)

source_name: MCF-SM-31 ShP53-EV-NoF

value: 10 µg/mL small EVs harvested from HT29-shP53 cells for 48 hr


title: MCF-SM-31 ShP53-EV-NoF-2

description: MCF-SM-31_(Clariom_D_Human)_ShP53-EV-NoF-2.CEL(normalized)


title: MCF-SM-31  ShP53-EV-NoF-1

description: MCF-SM-31_(Clariom_D_Human)_ShP53-EV-NoF-1.CEL(normalized)


title: ΦKZ infected [ID-005729-Grad-14-Fraction-17]


title: MCF-SM-31 NTSH-EV-NoF-1

description: MCF-SM-31_(Clariom_D_Human)_NTSH-EV-NoF-1.CEL(normalized)


title: ΦKZ infected [ID-005728-Grad-14-Fraction-16]


title: SP-A2 (1A0)-M-O3-1-X46

description: SAMPLE 43


title: MCF-SM-31 NTSH-EV-NoF-2

description: MCF-SM-31_(Clariom_D_Human)_NTSH-EV-NoF-2.CEL(normalized)


title: FLOX_1

value: miR-181a2b2flox/flox (flox)

value: white adipose


title: SP-A2 (1A0)-M-FA-3-X44

description: SAMPLE 42

source_name: Male mouse exposed to Filtered air-Alveolar Macrophage (AM) cells

value: Filtered air


title: S2 fed

value: Human Liver cells xenografted into TKNOG mice


title: ΦKZ infected [ID-005725-Grad-14-Fraction-13]


title: SP-A2 (1A0)-M-FA-2-X42

description: SAMPLE 41


title: ΦKZ infected [ID-005726-Grad-14-Fraction-14]


title: WT_IP_sorted

description: WT_IPvinput_MACS_broad_blacklist_subtracted.bed

library_source: genomic

molecule: genomic DNA

extract_protocol:
Illumina sequencing libraries were made with NEBNext Ultra II DNA Library Prep for Illumina (NEB), according to the manufacturer protocol. Cluster generation and sequencing was performed using the standard Illumina protocols for Illumina HiSeq 4000 by the University of Chicago Functional Genomics Core facility. Each library was sequenced using single-end 50bp sequencing.
The ChIP workflow described by Lee and colleagues (Lee et al., Nat. Protocol, 2006) as used as a general guide. For each ChIP-seq experiment, 25,000,000 mouse embryonic stem cells of (E14 WT or WT hWDR76 FRT mESCs) were cultured, crosslinked, and harvested. These cells were grown in parallel at low to moderate colony density over several days prior to crosslinking. Freshly cracked 10% paraformaldehyde was used to crosslink the cells at a final concentration of 1% in 1x PBS supplemented with 1 mM MgCl2 wash buffer for fifteen minutes. Crosslinking was quenched with 1M Tris base (for a final concentration of 300 mM) for three minutes, followed by three washes in 1x PBS + 1mM MgCl2. Cells were collected via a plastic spatula and passed through a 28-gauge needle to afford a coarse homogenate, then pelleted by centrifugation at 700g for five minutes, flash frozen and stored at -80˚C until used for ChIP. Thawed cell pellets were resuspended in 10 mL of 50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, supplemented with 200x Protease Inhibitor Cocktail. This suspension was incubated with gentle rocking for ten minutes at 4˚C, followed by centrifugation at 1,350g for five minutes at 4˚C. This pellet was gently resuspended in 10 mL of 10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, supplemented to 1x Protease Inhibitor Cocktail to effect cell lysis. The released crude nuclei were then pelleted as before and then carefully resuspended in 6 mL of 10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA,
0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine, supplemented to 1x Protease Inhibitor Cocktail. This nuclei suspension was subjected to sonication to shear chromatin via Covaris S220 in TC12 glass vials (Covaris) with 600 μL of nuclei suspension and 100 mg of glass beads (0.5 mm diameter, Sigma). The Covaris S220 was used at water level 15 with 140W peak incident power (affording an actual average output of 25W) at 20% duty, for 200 cycles per burst. With these settings, the nuclear suspension was sonicated for 20s on, 10 off per cycle for 14 cycles. The batches of sheared chromatin were combined and clarified by addition of 1/10 volume of 10% Triton X-100 and centrifugation at 14,000g for 10 minutes. 100 μL of sheared clarified lysate was saved as input before proceeding to immunoprecipitation. The degree of shearing for 20 μL of clarified lysate assessed after quick decrosslinking by RNAse A digestion at 37˚C for 30 minutes and heat denaturation at 65˚C for 30 minutes. This material was then visualized on a 2% agarose gel to confirm uniform shearing between batches and samples with a fragment distribution between 200-700 bp and centered at 500 bp. Centrifuge clarified and sterile filtered media collected from 12CA5 hybridomas cultured in low IgG serum was immobilized on Protein G dynabeads (Life Technologies). Resin was washed in 1x PBS + 0.05% BSA prior to overnight incubation with 15 μL of 12CA5 solution per 50 μL of Protein G dynabeads with end-over-end rotation at 4˚C. The beads were then washed in 1 mL of 1x PBS + 0.05% BSA three times prior to use in ChIP. This preparation was validated to successfully IP HA-tagged proteins by western blot. IP incubations were set up with 1 mL of clarified nuclear lysate and 100 μL of prepared dynabeads. IP occurred overnight (14-16 hours) with gentle end-over-end rotation at 4˚C in low rentention 1.6 mL microcentrifuge tubes. The next day, beads were washed using a neodymium magnetic rack to collect beads and exchange buffers, followed by tube changes. Beads were washed twice in 1 mL of 50 mM HEPES-KOH, pKa 7.55, 500 mM LiCl, 1 mM EDTA, 1.0% NP-40, 0.7% Na-deoxycholate for three minutes of end-over-end rotation at 4˚C. This was followed by a final wash in 1 mL 1x TE + 50 mM NaCl. The IP-recovered material was eluted with 100 μL of 1x TE + 1% SDS heated at 65˚C for 20 minutes. This was repeated for a final elution volume of 200 μL. Crosslinks in the eluted material were then reversed by incubation at 65C for 8-12 hours, incubation with RNAse A (0.2 mg/mL final concentration) at 37C for 2 hours, and incubation with proteinase K (0.2 μg/mL final concentration) at 55C for 2 hours. The remaining DNA was purified by recovery on Sera-mag Speedbeads (GE Healthcare) and eluted in 1x TE.

value: E14 frt with FLAG-HA-WDR76 flp-in

tag: chip antibody

value: 12CA5 clone (antibody purified from hybridoma in house)


title: SP-A2 (1A0)-F-O3-4-X40

description: SAMPLE 39

source_name: Female mouse exposed to Ozone (O3)-Alveolar Macrophage (AM) cells

value: Female


title: ΦKZ infected [ID-005727-Grad-14-Fraction-15]


title: WT_input_sorted


title: MM20567

description: 10x Chemistry: Single Cell 3’ v3

source_name: Human Fallopian tube

value: fallopian tube

value: infundibulum, ampulla, isthmus


title: ERCC00048_polyI_ONT_2

city: Sherbrooke

first: Karine

last: Choquet

state: Québec

address: 3201 rue Jean-Mignault

department: Biochemistry and Functional Genomics

country: Canada

institute: Université de Sherbrooke

description: ERCC-00048 with poly(I) tail addition rep 2

data_processing:
Library strategy: nano-COP
Raw signal fast5 files were basecalled during sequencing with MINKNOW. RNA sequences that pass basecalling thresholds were converted into DNA by substituting U to T bases before sequence alignment. Sequences were aligned to the reference genomes using minimap2 (version 2.10-r764-dirty) with recommended parameters for Oxford Nanopore Technologies direct RNA sequencing (-ax splice -uf -k14) or cDNA sequencing (-ax splice). All analyses were performed using reads that pass the MINKNOW sequencing threshold (QC>7) and align uniquely to the genome.
The splice_df datasets were generated by first intersecting reads with constitutively spliced introns. Constitutively spliced introns with “medium stringency” included in this dataset have at least 20 reads total RNA-seq dataset that span either splice junction by at least 4 nt overlap and more than 80% of the spanning reads are spliced. For reads mapping to constitutive introns, the features of read cigar strings were extracted for the 50 nt around the intron 5’ and 3’ splice sites and the entirety of the intron. Reads were called as ‘not spliced’ if the alignment file shows no indication of splicing within the 50 nt around each splice site, mapped portions of the read (rather than deletions) represent greater than 50% of the 50 nt around each splice site, and at least 75% of the read within the intron is aligned to the reference. Reads were called as ‘spliced’ if the alignment file displays the start or end of a splicing event within the 50nt around both splice sites and the size of the aligned splicing event is within 90-110% and 100 nt of the intron size. If aligned reads that map to introns do not meet these qualifications, the splicing event is characterized as ‘undetermined’ and not used in subsequent analyses. Other information included in this file include the soft clipped length at the start of the read alignment, the distance between the read start (or aligned RNA end) and the 3’SS of the intron, and whether or not the read start (or aligned RNA end) is close to the poly(A) site of a gene (within 150 nt upstream or any distance downstream of the annotated poly(A) site of the gene)
The polyA_polyI_estimates datasets were obtained with nanopolish_polyI using default parameters
Genome_build: hg38

organism: synthetic construct

growth_protocol: K562 cells (ATCC, CCL-243) were maintained at 37°C and 5% CO2 in RPMI 1640 medium containing 10% FBS, 100 U/ml penicillin and 100 ug/ml streptomycin

extract_protocol: Oxford Nanopore Technologies direct RNA sequencing with SQK-RNA002 kit

value: synthetic construct

tag: rna preparation

value: in vitro transcription of ERCC-00048


title: SP-A2 (1A0)-M-O3-2-X47

description: SAMPLE 44

value: Ozone (O3)

value: Alveolar Macrophage (AM) cells


title: SP-A2 (1A0)-F-O3-3-X39

description: SAMPLE 38

value: 3 hours


title: SP-A2 (1A0)-M-FA-1-X41

description: SAMPLE 40

value: Male


title: ΦKZ infected [ID-005722-Grad-14-Fraction-10]

value: infection with ΦKZ bacteriophage for 10 min


title: ERCC00048_polyA_ONT_1

description: ERCC-00048 with poly(A) tail addition rep 1


title: ΦKZ infected [ID-005720-Grad-14-Fraction-08]


title: ΦKZ infected [ID-005723-Grad-14-Fraction-11]


title: ΦKZ infected [ID-005724-Grad-14-Fraction-12]


title: ERCC00048_polyI_ONT_1

description: ERCC-00048 with poly(A) tail addition rep 2


title: ERCC00048_polyA_polyI_ONT

description: ERCC-00048 with poly(A) and poly(I) tails addition


title: ΦKZ infected [ID-005719-Grad-14-Fraction-07]


title: SP-A2 (1A0)-F-O3-2-X38

description: SAMPLE 37


title: iPSC_input_rep2_re-used

city: Seoul

first: Young-Joon

last: Kim

address: Yonsei-ro 50

country: South Korea

institute: Yonsei university

data_processing:
Prior to mapping, quality control steps were executed. We assessed reads by ‘FastQC’ for read quality control and adapter removing process was done by ‘Cutadapt’ (cutadapt -a CTGTCTCTTATACACATCT -q 10 --minimum-length 36 -o sample_1_trimmed.fastq -p sample_2_trimmed.fastq sample_1.fastq sample_2.fastq). Processed reads were aligned by ‘Bowtie2’ (bowtie2 --very-sensitive -x <genomeIndexName> -X 2000 -1 sample_1_trimmed.fastq -2 sample_2_trimeed.fastq). We next removed duplicated reads using Picard MarkDuplicate (1.141) for elimination of technical bias. iPSC and NPC chromatin accessible peaks were determined by MACS2 with specific option (macs2 callpeak --verbose 3 --treatment sample.bam -g hs -B -q 0.05 --extsize 200 –nomodel --shift -100 --nolambda --keep-dup all -f BAMPE --outdir dir --call-summits). To identify the confident stage-specific ATAC peaks, we employed a strategy that confirming background signal of each iPSC and NPC ATAC peaks. We first listed stage-specific peaks based macs2 peak calling results by selecting peaks which was not defined in other cell types. To define cell type-specific accessible regions, we further manipulated macs2 peak calling results. For each stage-specific peak, we plotted normalized ATAC peak intensity (log2RPKM) distribution graph of corresponding cell types and another cell types simultaneously. We observed crossing point of two distribution plot and defined this point as background signal. Finally, we defined revised stage-specific ATAC peaks. For data visualization on genome browser, we used bamCoverage tool with following options; --normalizeUsing CPM --effectiveGenomeSize 2864785220.
We utilized H3K4me3 and H3K27me3 ChIP-seq data for iPSC and NPC in GEO (GSE156723). For read alignment, we used BWA (0.7.7) to map reads to the human genome sequence (hg19). We further removed duplicated reads using Picard MarkDuplicate (1.141). We further inspected the quality of the ChIP-seq experiment by measuring FRiP (fraction of reads in peaks) using ChIPQC (3.3). For peak calling, we used MACS2 (2.1.0) to call the significantly enriched ChIP region compare to the input IgG control “q -0.01 (FDR <0.01%)”. For the ATAC peak intensity comparison, we generated the normalized RPKM values by counting the number of reads for 50bp bins then dividing by the total sequencing depth.
Hi-C data processing is executed by described method in Yang et al. Raw reads were aligned to hg19 human reference genome. To focus on cis-chromosomal interactions, invalid Hi-C reads were removed by criteria which defined in previous studies; inter-chromosomal interactions, putative self-ligations, and non-restriction site specific ligations. Valid cis-interactions were collected to build raw interaction frequency matrix with 5 kb resolution. A negative binomial model-based normalization pipeline removed biases of the interaction frequency matrix. Finally, distance dependent background signal was used to normalization for emphasizing biologically significant long-range chromatin interactions.
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq: peak calling data
Supplementary_files_format_and_content: ChIP-seq: RPKM with 50bin; peak calling data
Supplementary_files_format_and_content: Hi-C: Interaction contact map

source_name: induced pluripotent stem cell

growth_protocol: Human iPS Cell line were kindly provided from Yonsei University College of Medicine. First, STO fibroblast (American Type Culture Collection (ATCC)) was cultured and inactivated by mitomycin C (10μg/ml, Sigma-Aldrich) for feeder cell preparation. iPSCs were cultured on feeder cell layers and maintained using hiPSC maintain medium consist of DMEM/F12 (Invitrogen, Carlsbad, CA, USA), 20% knockoutserum replacement (Invitrogen), 1% penicillin-streptomycin (Invitrogen), 1×non-essential amino acid (Invitrogen), 0.1mM β-mercaptoethanol (Sigma), and 10ng/ml basic fibroblast growth factor (bFGF) (Peprotech).

extract_protocol:
For ATAC-seq, 50000 cells were washed with cold-PBS and resuspended by cell lysis buffer (10mM Tris-HCl (pH 7.4), 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and centrifuged (10min, 2000g at 4°C). For H3K27ac ChIP-seq, CCells were washed with DPBS and crosslinked by crosslinking buffer (100mM NaCl, 0.1mM EDTA, 5mM HEPES (pH8.0), 1% formaldehyde) for 10min at room temperature. The crosslinking process was halted with 125mM glycine in room temperature for 5 min with rotation and washed twice with cold DPBS. Crosslinked samples were resuspended in SDS lysis buffer (1%SDS, 50mM Tris-HCl (pH8.0), 10mM EDTA) with protease inhibitor. For Hi-C, about 1 million cells were used for crosslinking with 1% formaldehyde. Crosslinked cells were lysed (10nM Tris-HCl (pH8.0), 10mM NaCl, and 0.2% IGEPAL CA630) and digested with 100U MboI.
For ATAC-seq, the nuclei pellet were resuspended with Transposase mixture in Illumina Nextera Kit (FC-121-1031) and incubated for 30min at 37°C. Tagmented DNA fragments were puriﬁed using MinElute PCR purification kit following manufacturer’s protocol. For eluted DNA samples, we executed small scale qPCR to determine adequate PCR amplification cycles for library preparation. We checked Ct value for qPCR sample mix (5ul 2×KAPA HiFi HotStart Ready Mix, 0.1ul 100x SYBR green, 0.3ul Nextera Ad1.2 (25uM), 0.3ul Nextera Ad2.X (25uM), 2.3ul Nuclease-free water and 2ul eluted DNA) and determined PCR amplification cycles with value of Ct+1. We then executed large scale PCR (25ul 2×KAPA HiFi HotStart Ready Mix, 1.5ul Nextera Ad1.2 (25uM), 1.5ul Nextera Ad2.X (25uM), 2ul Nuclease-free water and 20ul eluted DNA). After PCR step, we cleaned library samples and performed size selection (200~400bp) by AMPure XP beads (Beckman Coulter, A63881) following manufacturer’s instruction. For H3K27ac ChIP-seq, sonicated chromatin samples were incubated with H3K27ac antibody and magnetic bead for 4 hours in 4°C with rotation. At the same time, input chromatin was stored from sonicated samples to be used as input control. After incubation, the bead complex was washed by RIPA-α (140mM NaCl, 1mM EDTA pH8, 0.5mM EGTA pH8, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 10mM Tris pH8) with 4 times. The chromatin immunoprecipitated complex was treated with RNaseA and executed overnight reverse-crosslinking at 68°C. The chromatin immunoprecipitated DNA was extracted using AMPure XP beads and libraries were prepared using NEB Next Ultra II DNA library Prep Kit. For Hi-C library, digested fragments were labelled with biotin-14-dCTP and proximally ligated with T4 DNA Ligase, followed by reverse-crosslinking. The fragments were then subjected to sonication and purified with AMPure XP beads. The final ligated DNA was pulled down with Dynabeads MyOne streptavidin T1 beads.

treatment_protocol: For neuronal differentiation, an embryoid body (EB) was generated by culturing human iPSCs for 5-6 days on non-adherent Petri dishes in hiPSC maintain medium absence of bFGF. To guide differentiation of EBs into neuroectodermal fate, additional supplement of 5μM dorsomorphin (DM) (Sigma-Aldrich) and 5μM SB431542 (Sigma-Aldrich) were added to the hiPSC medium during EB formation. EBs were then attached to the culture dish coated with Matrigel (BD Biosciences) and were cultured in neural induction medium consist of DMEM/F12 medium (Invitrogen), 1×N2 supplement (Invitrogen), 1×nonessential amino acids (Invitrogen) for 6 days10-12. When neural rosettes appear in the center of the EBs, then NPCs were collected through manipulated Pasteur pipet. Collected NPCs were re-plated on Matrigel coated plate for neuronal maturation and cultured for 14 days in Neurobasal medium (Invitrogen) containing 1X B27 supplement without vitamin A (Invitrogen), 1x Glutamax (Invitrogen) supplemented with 10 ng/ml brain-derived neurotrophic factor (BDNF, Peprotech), 10 ng/ml glial cell-derived neurotrophic factor (GDNF, Peprotech), 10 ng/ml neurotrophin-3 (NT3, Peprotech). Early neurons were collected by Accutase (Invitrogen) treatment.

value: Human induced pluripotent stem cell

tag: developmental stage

value: Stem cell


title: gDNALer353

city: Pozuelo de Alarcon

first: Miguel

middle: Angel

last: Moreno-Risueno

state: Madrid

department: Biotechnology

institute: Center for Plant Biotechnology and Genomics

data_processing:
The SNPtrack pipeline (Leshchiner et al., (2012) Genome Res, 22:1541) was used to identify single variant/nucleotide polymorphisms associated to Ler ecotype as well as all the heterozygous mutations present in the potent sample.
Homozygous Ler polymorphisms in the potent sample were used to define Col-0 DNA islands associated to the potent phenotype.
A heterozygous mutation present in the potent sample within the Col-0 DNA islands identified a dominant mutation in the DII domain of the IAA18 gene.
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Table_S1.xlsx: Position in each of the chromosomes of Arabidopsis thaliana of the homozygous polymorphisms found in the potent mutant sample.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis thaliana seeds were surface sterilized with gas chlorine (1% HCl) in a confined environment for 2 hours. After stratification for 1-2 days at 4ºC, plants were grown on 12x12 cm plates with Murashige and Skoog basal medium (2,2 g/l MS, 0.05% MES, 1% sucrose, 1% plant-agar) in a walk-in custom made chamber with 16/8-hour light/dark photoperiod at 21-23ºC.

extract_protocol:
Approximately 200 seeds generated in the fifth cross were sown and seedlings with and without potent phenotype collected and frozen at -80° C. Samples were ground with liquid nitrogen using mortar and pestle and incubated with extraction buffer (0.055M Cetyl Trimethyl Ammonium Bromid (CTAB), 1.4M NaCl, 0.02M EDTA 0.02M, 0.1M Tris-HCl pH 8.0) at 60ºC for 30 minutes. Samples were cleaned with equal volume of chloroform and the supernatant precipitated with isopropanol and washed with 70% EtOH before their re-suspension in DNase-free water.
Genomic DNA of each individual is extracted and then fragmented randomly. After electrophoresis, DNA fragments of desired length are gel purified. Adapter ligation and DNA cluster preparation are performed and subjected to Hiseq2000 sequencing.

treatment_protocol: Seeds from the triply marked line DR5::Luciferase pWOX5::ER-YFP pSCR::ER-GFP were mutagenized using ethyl methanesulfonate solution (EMS 50mM, 0.1M sodium phosphate buffer, pH 5.5) for 12 hours. About 50 seeds from 2,000 independent M2 lines (N= 100,000 seeds) were screened for impairment in lateral root formation using a fluorescent scope or in luciferase assays. potent was crossed six times with the parental reporter line in Col-0 ecotype and maintained in heterozygosity as it is a dominant mutation. To map the mutation, potent was then crossed five more times with Ler ecotype.

tag: ecotype

value: Ler

tag: phenotype

value: with potent phenotype

value: Seedlings


title: ERCC00048_polyA_ONT_2

description: ERCC-00048 with poly(I) tail addition rep 1


title: gDNALerWT

value: without potent phenotype

tag: tissue


title: SP-A2 (1A0)-F-FA-2-X34

description: SAMPLE 33

source_name: Female mouse exposed to Filtered air-Alveolar Macrophage (AM) cells

value: Filtered air


title: NPC_input_rep2_re-used

value: Human induced pluripotent stem cell derived

value: Neuronal progenitor cell


title: SP-A2 (1A0)-F-FA-3-X35

description: SAMPLE 34

value: Female


title: ΦKZ infected [ID-005717-Grad-14-Fraction-05]

tag: treatment


title: arf7 3

description:
processed data file: Table_S1.xlsx
processed data file: Table_S2.xlsx

data_processing:
The bowtie2-build indexer was used to build a Bowtie index from the set of the reference genome.
The tophat2 function from TopHat was used to align reads from the RNA-Seq experiment.
Cufflinks was used to perform transcript assembly of each sample with the .bam files generated by Tophat and the reference genome and annotation files.
Cuffmerge was used to assemble all samples transcripts with the reference genome annotation.
Cuffdiff program was used to calculate differential gene expression.
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Table_S1.xlsx: Differentially expressed genes between control and mutants arf7 and potent lines.
Supplementary_files_format_and_content: Table_S2.xlsx: FPKM values for each gene within clusters of replicates.

source_name: Oscillation zone from arf7 line

extract_protocol:
Samples were ground in the same tube with an adapted pestle in the presence of liquid nitrogen, next added 0.2 ml of RNAzol and incubated for 15 minutes at r.t. Following centrifugation (12,000 g for 15 min at 4 °C) 1.25μl of 4-bromoanisole (BAM) were added to the supernatant, incubated for 5 min at r.t and centrifuged (12,000 g for 10 min at 4ºC). 1μL of 15mg/ml of Glycoblue was then added to the supernatant, mix with 300 μL of isopropanol and precipitated over-night at 4 °C. Samples were centrifuged (12,000 g for 30 min at 4 °C), and the pellet rinsed was 70 % ethanol and air-dried. The pellet was resuspended in 8μL of RNA-free water.
Library was prepared following the protocol described by Picelli et al., (2013) in Nature Protocols 9: 171.

treatment_protocol: DR5::Luciferase expression was followed in using a Lumazone CA Automated Chemiluminescence System (Roper Bioscience). OZs were dissected at 7dpi using an ophthalmological blade under a dissecting scope and immediately frozen in ultrapure RNA-free water (Invitrogen) using liquid nitrogen.

value: Oscillation zone from roots


title: arf7 2


title: SP-A2 (1A0)-F-O3-1-X37

description: SAMPLE 36

tag: strain


title: SP-A2 (1A0)-F-FA-1-X33

description: SAMPLE 32


title: ΦKZ infected [ID-005716-Grad-14-Fraction-04]


title: NPC H3K27me3_rep2_re-used

description:
NPC_h3k27me3_merged_sorted_noDup.rpkm50.txt
GSM4743061


title: NPC_input_rep1_re-used


title: ΦKZ infected [ID-005718-Grad-14-Fraction-06]


title: ΦKZ infected [ID-005721-Grad-14-Fraction-09]


title: arf7 1

tag: genotype/variation


title: ΦKZ infected [ID-005715-Grad-14-Fraction-03]


title: SP-A2 (1A0)-F-FA-4-X36

description: SAMPLE 35


title: KO-M-O3-3-X31

description: SAMPLE 30


title: NPC H3K27me3_rep1_re-used


title: KO-M-O3-4-X32

description: SAMPLE 31


title: iPSC_input_rep1_re-used


title: iPSC H3K27me3_rep2_re-used

description:
iPSC_h3k27me3_merged_sorted_noDup.rpkm50.txt
GSM4743060


title: ΦKZ infected [ID-005713-Grad-14-Fraction-01]


title: potent 2

source_name: Oscillation zone from potent line

value: potent


title: ΦKZ infected [ID-005714-Grad-14-Fraction-02]


title: potent 1


title: ΦKZ infected [ID-005712-Grad-14-Fraction-00L]


title: KO-M-O3-1-X29

description: SAMPLE 28

value: Ozone (O3)


title: potent 3


title: Control OZ minimum 3

source_name: Oscillation zone from control line

value: WT


title: NPC H3K4me3_rep2_re-used

description:
NPC_h3k4me3_merged_sorted_noDup.rpkm50.txt
GSM4743059


title: KO-M-FA-4-X28

description: SAMPLE 27

value: Alveolar Macrophage (AM) cells

value: 3 hours


title: NPC H3K4me3_rep1_re-used


title: Control OZ minimum 2


title: Induced γδT17 cells from mouseB

city: Hangzhou

first: Lin

last: Xu

address: 261 Huansha Road

department: Department of Hematology

country: China

institute: Affliated Hangzhou First People's Hospital, Zhejiang University School of Medicine

data_processing:
Illumina CASAVA software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome. The reference genome index was built using hisat2-build, and paired-end clean reads were aligned to the reference genome using Hisat2(v2.0.5).
Cuffdiff (v1.3.0) was used to calculate FPKMs for coding genes in each sample.
Cuffdiff (v2.2.1) provides statistical routines for determining differential expression in digital transcript or gene expression datasets using a model based on a negative binomial distribution. Genes with corrected p value less than 0.05 and the absolute value of log2 (fold change) greater than or equal to 1 were assigned as significantly differentially expressed.
Genome_build: mm9
Supplementary_files_format_and_content: Csv files include FPKM value for each sample.

source_name: Induced γδT17 cells from TCRβ-/-  mouse

extract_protocol: Sequencing libraries were generated using the VAHTS mRNA-seq v2 Library Prep Kit (Vazyme, Nanjing, China). Clustering of the index-coded samples was performed on a cBot Cluster Generation System (Illumia, CA, USA) and then sequenced on Illumina Hiseq X Ten platform. Cuffdiff (v1.3.0) calculated fragments per kilobase million for coding genes in each sample and provided statistical routines.

treatment_protocol: Initial γδT17 cells were sorted from splenocytes of C57BL/6 TCRβ-/- mice as control. We generated γδT17 cells from splenocytes following the protocol based on IL-1β and IL-23. Cells were harvested at day 8. Purified γδT cells were sorted using Pan T Cell Isolation kit II (Miltenyi, BG, Germany) and more than 90% expressed IL-17A; therefore, we considered these cells as induced γδT17 cells.

tag: strain background

value: TCR{beta}-/-

value: spleen

value: [gamma][delta]T17 cells sorted from splenocytes

tag: treatment/timepoint

value: After culture


title: Induced γδT17 cells from mouseC

tag: cell type


title: iPSC H3K4me3_rep2_re-used

description:
iPSC_h3k4me3_merged_sorted_noDup.rpkm50.txt
GSM4743058

value: Human induced pluripotent stem cell

value: Stem cell


title: KO-M-FA-3-X27

description: SAMPLE 26

value: Male


title: hiPSC-derived_microglia_ATAC-seq_rep2

first: Alison

last: Goate

address: Icahn (East) Building Floor 10 Room 10-70C, 1425 Madison Ave

department: Department of Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
FASTQ files were aligned to hg19 human reference genome using Bowtie2 (v2.4.1).
Uniquely mapped reads were obtained using SAMtools(v1.9). Reads were filtered for MAPQ score of 5. Bam files were sorted and indexed.
Coverage tracks (at 1 bp resolution and normalized to RPKM) was generated from reads in BAM files using the bamCoverage utility of deepTools (v 3.3.2).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: microglia

growth_protocol: Isolated CD43+ iHPCs were washed using iMGL base differentiation medium and centrifuged at 300 x g for 5 min at room temperature. After centrifugation, supernatant was aspirated to waste and iHPCs were gently suspended in complete differentiation medium: M-CSF (25 ng/ml), IL-34 (100 ng/ml; PeproTech), and TGFb-1 (50 ng/ml; Militenyi) added fresh each time. Cell density was adjusted to seed at 2 x10^5 cells in 2mL of complete medium per well in growth factor-reduced Matrigel-coated 6-well plates. Every two days: Each well was supplemented with 1 mL per well of complete differentiation medium. Day (12; or day 22 from iPSC): Early iMGLs were collected (300x g for 5 min at room temperature) and a 50% media change was performed. After 25 days of microglial differentiation, iMGLs were cultured in complete differentiation media supple- mented with CD200 (100 ng/ml, Novoprotein) and CX3CL1 (100 ng/ml; PeproTech) for an additional three days.

extract_protocol:
ATAC-seq reactions were performed using an established protocol (Buenrostro et al PMID: 25559105)
hiPSC-derived microglia (50K cells) from each patient line were collected and processed as previously described (Abud et al. 2017). Samples were either processed at New York Genome Center or at UCI’s Genomics High-Throughput Facility and sequenced as 50 bp paired-end reads on a HiSeq 2500 and 100 bp paired-end reads on a HiSeq 4000, respectively.

value: hiPSC-derived microglia


title: Induced γδT17 cells from mouseA


title: iPSC H3K4me3_rep1_re-used


title: KO-M-O3-2-X30

description: SAMPLE 29


title: Control OZ minimum 1


title: KO-M-FA-2-X26

description: SAMPLE 25

value: Filtered air


title: hiPSC-derived_microglia_ATAC-seq_rep1


title: Initial γδT17 cells from mouseC

source_name: Initial γδT17 cells from TCRβ-/-  mouse

value: Before culture


title: iPSC H3K27me3_rep1_re-used


title: NPC H3K27ac_rep2

description: NPC_h3k27ac_merged_sorted_noDup_peaks.narrowPeak

value: Human induced pluripotent stem cell derived

value: Neuronal progenitor cell


title: NPC ATAC_rep2


title: KO-F-O3-4-X24

description: SAMPLE 23

value: Female


title: Initial γδT17 cells from mouseB


title: KO-F-O3-3-X23

description: SAMPLE 22

value: Ozone (O3)


title: iPSC H3K27ac_rep2

description: iPSC_h3k27ac_merged_sorted_noDup_peaks.narrowPeak


title: NPC H3K27ac_rep1


title: Initial γδT17 cells from mouseA


title: NPC ATAC_rep1


title: RNAseq_D4pDOXRep3

city: Madison

first: Igor

middle: I.

last: Slukvin

address: 1220 Capitol Court

institute: University of Wisconsin

data_processing:
ATAC-seq fragments were mapped to human genome by BWA with default settings.  Human genome were divided into 32 bp bins and the number of reads in each bin was counted.  In order to smooth the data, reads were extended to 200 bp.  To normalize signals across ATAC-seq datasets, the number of reads in each dataset was reduced by random sampling to the smallest number of reads present in the datasets.   ATAC-seq peaks were called by MACS2.
ChIP-seq fragments were aligned by BWA (version 0.7.15) with quality threshold at 5 for read trimming and all the other options in default settings.  Normalized SOX17 ChIP-seq signals were calculated by MACS2 by using all the tags at the same loci.
RNA-seq fragments were aligned by STAR (version 2.5.2b) to human genome with gene annotations from GENCODE (version 27).  Transcript expression levels were quantified by RSEM (version 1.3.0).
Genome_build: hg38
Supplementary_files_format_and_content: ATAC-seq BED files contain peaks called by MACS2
Supplementary_files_format_and_content: ATAC-seq bigWig files contain normalized ATAC-seq signals as described in ATAC-seq data processing step
Supplementary_files_format_and_content: ChIP-seq bigWig files contain normalized SOX17 fold enrichment over IgG control calculated by MACS2
Supplementary_files_format_and_content: RNA-seq TSV files contain gene expression levels quantified by RSEM

source_name: Primordial hemogenic endothelium from H9

growth_protocol: Inducible SOX17 H9 ESC s were differentiated in ColIV coating plate. Singular Cells were plated 5,000 cells/cm2 to 10cm plates coated with ColIV (Sigma-Aldrich). After 1 day, media was changed to IF9S media with 50 ng/ml FGF, 2 mM LiCl, 15 ng/ml Activin A, and 50 ng/ml BMP4. On day 2, media was changed to IF9S media with 50 ng/ml VEGF, 2.5 uM SB431542 and 50 ng/ml FGF and D4 PHE cells were collected (1 X 106 cells).

extract_protocol:
D4 PHE cell were CD31 MACs, and then cells were extracted total RNA using Rneasy micro kit of Qaigen.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Inducible SOX17 H9 ESC

value: DOX+

tag: replicate

tag: description

value: CD31 MACs cell at D4


title: iPSC ATAC_rep2


title: iPSC H3K27ac_rep1


title: RNAseq_D4pDOXRep2


title: KO-F-O3-1-X21

description: SAMPLE 20

tag: agent

value: Alveolar Macrophage (AM) cells

tag: exposure time

value: 3 hours


title: iPSC ATAC_rep1


title: RNAseq_D4pDOXRep1


title: KO-M-FA-1-X25

description: SAMPLE 24

tag: Sex


title: KO-F-FA-3-X19

description: SAMPLE 18


title: NPC mRNA-seq

data_processing:
We used trim-galore (v.0.4.0) to trim off the adapter sequences or low-quality reads. Trimmed sequences were then aligned to the human reference genome (hg19) using Bismark (0.14.4) with –bowtie2 option. Duplicated reads were removed using Picard markduplicate (1.141). Methylated value (Beta value, the ratio of intensities between methylated and un-methylated alleles) for all the covered CpG sites were calculated using bismark_methylation_extractor (0.14.4) “–no_overlap –comprehensive –bedgraph”.
Raw reads were aligned to the human reference (hg19) using STAR (v2.6.0a) with the support of transcriptome reference (GRCh37, UCSC). From the mapped reads, we further calculated the TPM (Transcripts per Million) using RSEM (v1.2.31) at the gene level. To reduce any technical bias among the samples, we further quantile normalized using R library, preprocesscore.
For read alignment, we used BWA (0.7.7) to map reads to the human genome sequence (hg19). We further removed duplicated reads using Picard MarkDuplicate (1.141). For peak calling, we used MACS2 (2.1.0) to call the significantly enriched ChIP region compare to the input IgG control “q -0.01 (FDR <0.01%)”
Genome_build: hg19
Supplementary_files_format_and_content: abundance measurements
Supplementary_files_format_and_content: peak calling data

extract_protocol:
Genomic DNA was extracted by PureLink™ Genomic DNA Kit according to manufacturer’s protocol. Total RNA of each cell type was extracted by TRIzol™ Reagent (Invitrogen) and RNA integrity (RIN) was assessed by Agilent Bioanalyzer (RIN>=8). 1 million cells were crosslinked in crosslinking buffer (100 mM NaCl, 0.1mM EDTA, 5mM Hepes, pH 8.0, 1% formaldehyde) for 10 min at 25°C. The crosslinking was quenched with 125 mM glycine in 25°C for 5 min with rotation and washed twice with ice-cold PBS. The cross-linked cells were re-suspended in SDS lysis buffer (1% SDS, 50 mM Tris-HCl, pH8.0, 10mM EDTA) with protease inhibitor (Roche). Mono- and di-nucleosome size chromatin was obtained through sonication (Covaris, S220)
Total 300ng of genomic DNA was used for bisulfite conversion (EZ DNA Methylation-Gold Kit, Zymo research) and library preparation (TruSeq DNA Methylation, Illumina). We sequenced the bisulfite converted genomic library (2x150bp) using HiseqX. 200ng of total RNA was used for library preparation with TruSeq rapid SBS kit or Truseq SBS Kit v4 according to the kit guidelines. We sequenced the paired-end RNA-sequencing library (2x101bp) using HiSeq 2500 system. The immunoprecipitated DNA was recovered using AMPure XP beads (Beckman Coulter) and ChIP-seq libraries were prepared using NEBNext Ultra II DNA library Prep Kit following the manufacturer’s instruction. The ChIP-seq libraries were sequenced in 150 bp paired-end mode using Illumina NovaSeq 6000 platform.


title: p790_S6

city: Buffalo

first: Rose-Anne

last: Romano

address: 3435 Main Street

department: Oral Biology

institute: State University of New York at Buffalo

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ncbi-GRCh38 whole genome using hisat2-2.1.0 with parameters --fr
Reads aligning to the ncbi-GRCh38 build were quantified with featureCounts (v1.5.1) , which disregarded any read/read pair that aligned to more than one location, or more than one gene at a single location.
Counts Normalisation was done to generate Transript per Million reads (TPM) according to the method of Wagner et al., Theory in Bioscience, 2012
Genome_build: ncbi-GRCH38
Supplementary_files_format_and_content: Matrix table with TPM values for all samples

source_name: Salivary Gland

extract_protocol:
Biopsies of minor salivary glands obtained from Sjogren's syndrome patient during routine checkup were embedded in Optimal Cutting Temperature (OCT) media and later process for RNA extraction using Direct-Zol RNA mini-prep kit
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: analysis group

value: Control

tag: disease state

value: Normal

value: Salivary Gland


title: iPSC mRNA-seq

value: Human induced pluripotent stem cell

tag: developmental stage

value: Stem cell


title: KO-F-FA-4-X20

description: SAMPLE 19


title: KO-F-O3-2-X22

description: SAMPLE 21


title: RNAseq_D4mDOXRep1

value: DOX-


title: p749_S5


title: RNAseq_D4mDOXRep2


title: A549/cDDP_L2cis2

city: Gothenburg

first: Subazini

last: TK

address: Medicineragatan 9A

country: Sweden

institute: Gothenburg university

description:
A549 cells
Unsynchronized heterogenous population

data_processing:
The samples from ILLUMINA  system were aligned using Tophat2
All alignments were made using hg38.82 as reference genome assembly
The reads are quantified using HTSeq v0.6.1
Genome_build: hg38.82
Supplementary_files_format_and_content: Tab dellimited files containing FPKM values

source_name: cisplatin resistant line (A549/cDDP)

growth_protocol: A549 cells were routinely cultured using DMEM medium supplemented with 10% FBS and 200mM L-glutamin. A549/cDDP cells were maintained using DMEM medium supplemented with 10% FBS and 200mM L-glutamin, and 15 mM cisplatin. All cells were maintained in humified incubator with continuous 5% CO2 flow.

extract_protocol:
Cells were collected 48 hours post-transfection (24h post-cisplatin treatment) and RNA extraction was carried out using ReliaPrep RNA Cell Miniprep System
The mRNA is enriched using oligo(dT) beads and fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase. After first-strand synthesis, a custom second-strand synthesis buffer (Illumina) is added with dNTPs, RNase H and Escherichia coli polymerase I to generate the second strand by nick-translation. The final cDNA library is ready after a round of purification, terminal repair, A-tailing, ligation of sequencing adapters, size selection and PCR enrichment.

treatment_protocol:
Transient knockdown experiments were performed using 12pmole of LNA-GapmeRs targeting the specific transcript. For each knockdown experiment, 35000 cells were seeded in 24 well plate and transfected with lipofectamin RNAi-MAX overnight; cells were then treated with 15 mM cisplatin for 24h
Transient knockdown experiments were performed using 12 picomoles of LNA-GapmeRs targeting the specific transcript. For each knockdown experiment, 35000 cells were seeded and transfected with lipofectamin RNAi-MAX. Cells were collected 48h post-transfection. For cisplatin treated cells, 24 h post-transfection cells were treated with 15mM cisplatin or drug solvent and collected after 24 h (total tie post-transfection 48h).

tag: cell line

value: cisplatin resistant line (A549/cDDP)

value: cisplatin

tag: time

value: Collected 48h post-transfection-24h post-cisplatin treatment

tag: sirna

value: LNA-GapmeR Sequence


title: KO-F-FA-1-X17

description: SAMPLE 16

value: Filtered air

value: Female


title: co-ex-M-O3-3-X16

description: SAMPLE 15

source_name: Male mouse exposed to Ozone (O3)-Alveolar Macrophage (AM) cells

value: Ozone (O3)

value: Male


title: ChIPseq_SOX17pDOX

extract_protocol:
Sample followed the Millipore EZ-Magna CHIP A/G protocol. Eluted CHIP DNA IN 50 uL of elution buffer from kit. Lysates were clarified from sonicated nuclei and SOX17-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing using standard Illumina protocols

value: Inducible SOX17 H9 ESC

tag: antibody

value: anti SOX17

tag: treatment

value: DOX+

value: Total cell at D4


title: co-ex-M-O3-2-X15

description: SAMPLE 14

value: Alveolar Macrophage (AM) cells

value: 3 hours

tag: strain


title: A549/cDDP_L2cis1


title: KO-F-FA-2-X18

description: SAMPLE 17


title: ChIPseq_IgGpDOX

value: control


title: p570_S4

value: Control

value: Normal

tag: tissue

value: Salivary Gland


title: A549/cDDP_L2nt2

treatment_protocol:
Transient knockdown experiments were performed using 12 pmole of LNA-GapmeRs targeting the specific transcript. For each knockdown experiment, 35000 cells were seeded in 24 well plate and transfected with lipofectamin RNAi-MAX overnight; cells were then treated with cisplatin solvent for 24h
Transient knockdown experiments were performed using 12 picomoles of LNA-GapmeRs targeting the specific transcript. For each knockdown experiment, 35000 cells were seeded and transfected with lipofectamin RNAi-MAX. Cells were collected 48h post-transfection. For cisplatin treated cells, 24 h post-transfection cells were treated with 15mM cisplatin or drug solvent and collected after 24 h (total tie post-transfection 48h).

value: cisplatin resistant line (A549/cDDP)

value: cisplatin solvent

value: Collected 48h post-transfection-24h post-cisplatin solvent treatment


title: A549/cDDP_L2nt1

value: LNA-GapmeR Sequence


title: WT-mitoRNA [wt3]

first: Mehdi

last: Pirooznia

address: 12 SOUTH DR

institute: National Institutes of Health

data_processing:
Raw data files in FASTQ format were generated from the Illumina sequencer.
After Illumina quality control, the sequencing reads were 5’, 3’-adaptor trimmed and filtered reads (length < 10nt or length > 40nt) with cutadapt
and aligned to the mitochondrial mature-tRNA sequences from mitotRNAdb using BWA
The tRNAs expression levels were measured by tag count. For each tRNA sequence-based profile, the mapped reads number used to estimate the expression level of each tRNA. The tRNAs expression profiling was calculated based on uniquely mapped reads and including mapped reads, respectively.
Differentially expressed tRNA analyses was performed with R package edgeR
Genome_build: Drosophila melanogster (DM6)
Supplementary_files_format_and_content: Expression_Count (Excel file contains ucount (uniquely mapped) and mrcount (multi map counts))

organism: Drosophila melanogaster

source_name: Wild type mitochondria

extract_protocol:
Whole adult fly mitochondria were extracted and mitochondrial RNA was harvested using Trizol reagent. tRNAs were purified from total mitochondrial RNA and m1A&m3C demethylated, then partially  hydrolyzed according to Hydro-tRNAseq method.
Fragments of ~19-35 nt for partially hydrolyzed and re-phosphorylated tRNAs  were converted to small RNA sequencing libraries using NEBNext® Multiplex  Small RNA Library Prep Set for Illumina® kit.

tag: genotype

value: Wild type RNA polymerase overexpression

tag: age

value: Two weeks old

tag: molecule subtype

value: mitochondrial tRNA


title: co-ex-M-O3-1-X13

description: SAMPLE 13

value: Ozone (O3)

tag: cell type

value: Male


title: A549/cDDP_CTRci2

value: cisplatin

value: Collected 48h post-transfection-24h post-cisplatin treatment


title: RNAseq_D4mDOXRep3

value: Inducible SOX17 H9 ESC

value: DOX-

tag: replicate

tag: description

value: CD31 MACs cell at D4


title: WT-mitoRNA [wt2]


title: p567_S3

value: Control


title: coex-M-FA-3-X11

description: SAMPLE 11

source_name: Male mouse exposed to Filtered air-Alveolar Macrophage (AM) cells

tag: agent

value: Filtered air

value: Alveolar Macrophage (AM) cells

tag: exposure time

value: 3 hours

tag: Sex


title: A549/cDDP_CTRci1

value: cisplatin resistant line (A549/cDDP)

value: control


title: WT-mitoRNA [wt1]


title: coex-M-FA-4-X12

description: SAMPLE 12


title: A549/cDDP_CTRnt2

value: cisplatin solvent

value: Collected 48h post-transfection-24h post-cisplatin solvent treatment


title: coex-M-FA-2-X10

description: SAMPLE 10


title: E423P-mitoRNA [mu3]

source_name: E423P mitochondria

value: E423P RNA polymerase overexpression

value: Two weeks old


title: A549/cDDP_CTRnt1


title: A549/cDDP_cis2

treatment_protocol:
35000 cells/well in a 24 well plate were seeded overnight and treated with 15 mM cisplatin for 24h
Transient knockdown experiments were performed using 12 picomoles of LNA-GapmeRs targeting the specific transcript. For each knockdown experiment, 35000 cells were seeded and transfected with lipofectamin RNAi-MAX. Cells were collected 48h post-transfection. For cisplatin treated cells, 24 h post-transfection cells were treated with 15mM cisplatin or drug solvent and collected after 24 h (total tie post-transfection 48h).

value: Collected after 24h cisplatin treatment

value: Not applicable


title: co-ex-F-O3-4-X8

description: SAMPLE 8

source_name: Female mouse exposed to Ozone (O3)-Alveolar Macrophage (AM) cells

value: Ozone (O3)

value: Female


title: coex-M-FA-1-X9

description: SAMPLE 9

value: Male


title: A549/cDDP_cis1

value: cisplatin


title: p491_S2

tag: analysis group

tag: disease state

value: Normal

value: Salivary Gland


title: E423P-mitoRNA [mu2]

value: mitochondrial tRNA


title: WT_ESCs

city: Tianjin

first: Ling

last: Shuai

address: 38 Tong Yan Road, Jinnan district

department: State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy

institute: Nankai University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
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 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: embryonic stem cells

extract_protocol:
ESCs, EpiSCs or EpiLCs were collected and RNA was harvested using Trizol reagent. NEB Next® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM 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 m in followed by 5 min at 95 °Cbefore 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: embryonic stem cells

value: wild type diploid


title: WT_haEpiLCs

source_name: Epiblast stem cell like cells

value: Epiblast stem cell like cells

value: wild type haploid


title: E423P-mitoRNA [mu1]


title: p335_S8

value: Control


title: co-ex-F-O3-1-X5

description: SAMPLE 5

value: Alveolar Macrophage (AM) cells

value: 3 hours


title: A549/cDDP_NT2

treatment_protocol:
35000 cells/well in a 24 well plate were seeded overnight and treated with cisplatin solvent for 24h
Transient knockdown experiments were performed using 12 picomoles of LNA-GapmeRs targeting the specific transcript. For each knockdown experiment, 35000 cells were seeded and transfected with lipofectamin RNAi-MAX. Cells were collected 48h post-transfection. For cisplatin treated cells, 24 h post-transfection cells were treated with 15mM cisplatin or drug solvent and collected after 24 h (total tie post-transfection 48h).

tag: cell line

value: cisplatin resistant line (A549/cDDP)

value: cisplatin solvent

tag: time

value: Collected after 24h cisplatin solvent treatment


title: co-ex-F-O3-2-X6

description: SAMPLE 6

value: Ozone (O3)


title: p307_S7


title: A549/cDDP_NT1

tag: sirna

value: Not applicable


title: p53KO2nEpiSCs

source_name: Epiblast stem cells

value: Epiblast stem cells

value: P53 - diploid


title: MEF

source_name: mouse embryo fibroblasts

value: mouse embryo fibroblasts


title: co-ex-F-FA-3-X3

description: SAMPLE 3

source_name: Female mouse exposed to Filtered air-Alveolar Macrophage (AM) cells

value: Filtered air

value: Female


title: p179_S1

value: Normal

value: Salivary Gland


title: A549 wt_NT2

source_name: A549 cells

value: A549 cells

tag: treatment


title: A549 wt_cis2

value: cisplatin

value: Collected after 24h cisplatin treatment


title: A549 wt_cis1


title: co-ex-F-FA-2-X2

description: SAMPLE 2

value: Alveolar Macrophage (AM) cells

tag: strain


title: co-ex-F-FA-4-X4

description: SAMPLE 4

value: 3 hours


title: iPSC_input_rep2

source_name: induced pluripotent stem cell

value: Human induced pluripotent stem cell

tag: developmental stage

value: Stem cell


title: haESCs

value: embryonic stem cells

tag: genotype

value: wild type haploid


title: iPSC_input_rep1


title: co-ex-F-O3-3-X7

description: SAMPLE 7

value: Ozone (O3)


title: co-ex-F-FA-1-X1

description: SAMPLE 1


title: Epi_male

value: Epiblast stem cells

value: wild type diploid


title: A549 wt_NT1

value: cisplatin solvent

value: Collected after 24h cisplatin solvent treatment

value: Not applicable


title: syd-5_RNA rep3

city: London

first: YUHAI

last: CUI

state: ON

address: 1391 Sandford Street

department: London Research and Development Centre

institute: Agriculture and Agri-Food Canada

data_processing:
ChIP-seq reads were aligned to the TAIR10 genome assembly using Bowtie2
Mapped reads were filted by removing PCR duplications and unmapped reads
unique mapped reads were converted to bed file by bedtools2
Reads were mapped to genome using TopHat v2.0.4 with default settings, except that a minimum intron length of 20 bp and a maximum intron length of 4000 bp were used. Calculations to identify differentially expressed genes were carried out as described (Trapnell et al., 2012)
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for WT and syd-5

source_name: seedlings

growth_protocol: Arabidopsis seedlings were growth on 1/2 MS plates for 14 days under 16h light/ 8h dark condition.

extract_protocol:
Lysates were clarified from sonicated nuclei and the associated complexes were isolated with antibodies.
14-day-old seedlings were  frozen with liquid nitrogen. Total RNA was isolated from   ̴50 mg of in vitro-grown seedlings using the RNeasy Plant Mini kit (Qiagen) according to supplier’s instructions. Total RNA was treated with RNase-free DNaseI kit (Life Techologies).
5 ng of ChIP DNAs were used for library construction per sample.
Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol.

tag: tissue

value: seedlings

tag: developmental

value: 14 days

tag: antibody

tag: ecotype and genotype

value: Col-0 (syd-5)


title: NPC_input_rep2

tag: cell type

value: Human induced pluripotent stem cell derived

value: Neuronal progenitor cell


title: BMDMs, Lyz2Cre:KLF6 Fl/Fl-HKCA-3

city: Cleveland

first: Ernest

middle: R

last: Chan

state: OH

address: 10900 Euclid Ave, Robbins E211

department: PQHS

institute: CWRU

data_processing:
Illumina reads were mapped to mouse genome release mm10 using STAR Aligner program.
The expression levels of genes were determined using Cufflinks and presented as FPKM
Differential expression analysis was done using Cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: TSV text file containing FPKM for all samples and genes

source_name: BMDMs

extract_protocol:
Total RNA was isolated from indicated samples using the High Pure RNA Isolation Kit.
Illumina TruSeq Stranded Total RNA kit

value: BMDMs

tag: age

value: Postnatal week 10

value: Lyz2Cre:KLF6 Fl/Fl

value: HKCA


title: p53KOhaEpiLCs

value: Epiblast stem cell like cells

value: P53 - haploid


title: Epi_fema


title: syd-5_RNA rep2


title: NPC_input_rep1


title: syd-5_RNA rep1


title: WT_RNA rep3

value: Col-0 (wild type)


title: iPSC H3K27me3

value: Human induced pluripotent stem cell

value: Stem cell


title: NPC H3K27me3


title: BMDMs, Lyz2Cre-HKCA-2


title: WT_RNA rep1


title: haEpi1_1

value: Epiblast stem cells


title: BMDMs, Lyz2Cre:KLF6 Fl/Fl-HKCA-1


title: WT_RNA rep2


title: iPSC H3K4me3


title: NPC H3K4me3


title: BMDMs, Lyz2Cre-HKCA-3


title: BMDMs, Lyz2Cre:KLF6 Fl/Fl-Scleroglucan-3

value: Scleroglucan


title: BMDMs, Lyz2Cre:KLF6 Fl/Fl-HKCA-2


title: BMDMs, Lyz2Cre-HKCA-1


title: haEpi5_1


title: BMDMs, Lyz2Cre-Scleroglucan-2


title: BMDMs, Lyz2Cre-Scleroglucan-3


title: Col-0-rep2

city: Beijing

first: Xin-Jian

last: He

address: No. 7, zhongguancun life science park road, changping district

institute: National Institute of Biological Sciences

data_processing:
Zebracall software used for basecalling.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using HISAT2 version 2.2.0 with the default parameters.
The differentially expressed genes and transposable elements were identified with |log2FC| >1 and FDR < 0.05 using edgeR.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited text file include normalized reads for each sample.

source_name: Arabidopsis seedlings_WT

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates in a long-day photoperiod (22℃, 16 h light/8 h dark).

extract_protocol:
Total RNA was isolated from 10-day-old seedlings in long-day conditions using Trizol reagent.
Sequencing libraries were built for RNA-seq (the paired-end 150bp strategy).

tag: ecotype background

tag: genotype/variation

value: wild type

tag: growth conditions

value: long day (16 h light/8 h dark)

value: 10-day-old seedlings


title: Col-0-rep1


title: BMDMs, Lyz2Cre:KLF6 Fl/Fl-Scleroglucan-1


title: BMDMs, Lyz2Cre:KLF6 Fl/Fl-Scleroglucan-2


title: BMDMs, Lyz2Cre-Scleroglucan-1


title: ELOX34-09L1

city: Delft

first: Raúl

middle: Antonio

last: Ortiz-Merino

address: van der Maasweg 9

country: Netherlands

institute: Delft University of Technology

data_processing:
RNAseq reads were mapped to the genome using bowtie v1.2.1.1 with parameters  -v 0 -k 10 --best -M 1
Alignments were filtered and sorted using samtools (v1.3.1)
Read counts were obtained with featureCounts (v1.6.0) using parameters -B -C t
Differential gene expression analysis was performed using edgeR (v3.28.1). Genes with 0 read counts in all conditions were filtered out from the analysis, same as genes with less than 10 counts per million
Counts were normalized using the TMM method, and dispersion was estimated using generalized linear models
Differentially expressed genes were then calculated using a log ratio test adjusted with the Benjamini-Hochberg method. Absolute log2 fold-change values > 2, false discovery rate < 0.5, and P value < 0.05 were used as significance cutoffs.
Genome_build: GCA_002571405.2 (scer)
Genome_build: (kmar)
Supplementary_files_format_and_content: raw gene counts in text format
Supplementary_files_format_and_content: differential gene expression data in text format

organism: Kluyveromyces marxianus

source_name: Bioreactor cell culture sample

extract_protocol:
Cells were flash frozen on liquid nitrogen, and RNA was harvested using acidic phenol chloroform extraction. Illumina TruSeq stranded mRNA LT protocol (#15031047) with polyA enrichment was used with approximately 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild-type

value: Chemostat aerobic, 7.5 g/L glucose, SM urea medium, D = 0.1 h-1, aerobic, pH=6, antifoam pluronic acid, 0 mg/L Tween 80, 10 mg/L ergosterol


title: ELOX36-08R1

value: Chemostat O-limited, 20 g/L glucose, SM urea medium, D = 0.1 h-1, micro-aerobic, pH=6, antifoam pluronic acid, 420 mg/L Tween 80, 10 mg/L ergosterol


title: BMDMs, Lyz2Cre:KLF6 Fl/Fl-Control-3

value: BMDMs

value: Control


title: 09-19-12_JCipollo10_SG_Celegans_10_bus17_D1

city: Bethesda

first: WeiPing

last: Chen

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were nomanized by RMA with Parteck Genomic Suit 6.6

organism: Caenorhabditis elegans

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: mRNA is  converted to cDNA and amplified using NuGEN pico amplification kit

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

treatment_protocol: L2-L3 stage


title: 09-19-12_JCipollo12_SG_Celegans_12_bus17_D3


title: 09-19-12_JCipollo14_SG_Celegans_14_srf5_D2


title: 09-19-12_JCipollo13_SG_Celegans_13_srf5_D1


title: 09-19-12_JCipollo11_SG_Celegans_11_bus17_D2


title: 09-19-12_JCipollo15_SG_Celegans_15_srf5_D3


title: bdt1-rep1

source_name: Arabidopsis seedlings_btl1-/-


title: NCI-H460 cells grown under normoxia [H460_O-2]

city: Yongin

first: Young-Chul

last: Choi

state: Gyeonggi-do

address: 1 Seocheon-dong Giheung-gu

institute: Kyung Hee University

description: total RNA isolated from NCI-H460 cells grown under normoxia

hyb_protocol: Hybridization was performed in Agilent SureHyb Hybridization Chambers.

scan_protocol: After washing, the slides were scanned with Agilent DNA Microarray Scanner.

data_processing: Data were extracted using Agilent Feature Extraction software. Normalization was performed using Agilent GeneSpring GX Software v12.1. Further data analysis was performed using Agilent GeneSpring GX Software v12.1.

source_name: NCI-H460 cells grown under normoxia

label_protocol: Arraystar Flash RNA Labeling Kit was used for sample labeling.

growth_protocol: A549 and NCI-H460 cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum under hypoxia and normoxia

extract_protocol: Total RNA was purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturer's protocol.

treatment_protocol: A549 and NCI-H460 cells were cultured under normoxia and hypoxia and after 24 hr, total RNA was prepared

value: lung cancer cells

tag: culture condition

value: normoxia


title: ELOX36-08L1


title: NCI-H460 cells grown under hypoxia [H460_H-1]

description: total RNA isolated from NCI-H460 cells grown under hypoxia

source_name: NCI-H460 cells grown under hypoxia

tag: cell line

value: hypoxia


title: 09-19-12_JCipollo9_SG_Celegans_9_bus4_D3


title: NCI-H460 cells grown under hypoxia [H460_H-3]


title: A549 cells grown under normoxia [A549_O-3]

description: total RNA isolated from A549 cells grown under normoxia

source_name: A549 cells grown under normoxia


title: 09-19-12_JCipollo7_SG_Celegans_7_bus4_D1


title: bdt1-rep2


title: BMDMs, Lyz2Cre:KLF6 Fl/Fl-Control-2

value: Postnatal week 10

value: Lyz2Cre:KLF6 Fl/Fl


title: ELOX34-08L1


title: ELOX19-09L3

value: Chemostat anaerobic, 20 g/L glucose, SM urea medium, D = 0.1 h-1, anaerobic, pH=6, antifoam pluronic acid, 420 mg/L Tween 80, 0 mg/L ergosterol


title: 09-19-12_JCipollo8_SG_Celegans_8_bus4_D2


title: 09-19-12_JCipollo6_SG_Celegans_6_bus2_D3


title: NCI-H460 cells grown under normoxia [H460_O-3]


title: NCI-H460 cells grown under hypoxia [H460_H-2]


title: BMDMs, Lyz2Cre-Control-2


title: BMDMs, Lyz2Cre-Control-3


title: 09-19-12_JCipollo5_SG_Celegans_5_bus2_D2


title: ELOX19-08R3


title: ELOX19-08R2

value: Chemostat anaerobic, 20 g/L glucose, SM urea medium, D = 0.1 h-1, anaerobic, pH=6, antifoam pluronic acid, 420 mg/L Tween 80, 10 mg/L ergosterol


title: BMDMs, Lyz2Cre-Control-1


title: ELOX19-09L2


title: A549 cells grown under normoxia [A549_O-1]


title: A549 cells grown under hypoxia [A549_H-2]

description: total RNA isolated from A549 cells grown under hypoxia

source_name: A549 cells grown under hypoxia


title: 09-19-12_JCipollo1_SG_Celegans_1_N2D1


title: A549 cells grown under hypoxia [A549_H-3]


title: 09-19-12_JCipollo3_SG_Celegans_3_N2D3


title: 09-19-12_JCipollo2_SG_Celegans_2_N2D2


title: A549 cells grown under hypoxia [A549_H-1]


title: 09-19-12_JCipollo4_SG_Celegans_4_bus2_D1


title: NCI-H460 cells grown under normoxia [H460_O-1]


title: QDCS-057: Peripheral Blood_Colorectal cancer

status: Public on Jan 05 2021

city: Shanghai

first: changming

last: cheng

address: No. 151, Libing Road

institute: National Engineering Center for Biochip at Shanghai China

description: Gene expression data from colorectal cancer patient before surgical or drug treatment

hyb_protocol: Following fragmentation, 15 μg cRNA were hybridized for 16 hr at 45℃ on GeneChip 3’IVT Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip® System 3000Dx (GCS 3000Dx).

data_processing: The data were analyzed with Affymetrix Expression Console (ver.1.3.1) using Affymetrix default analysis settings and MAS5 global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: Peripheral Blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Technical Manual for GeneChip 3’IVT Expression Kit,2013, Affymetrix).

growth_protocol: Elbow vein blood sampling and the blood was stored at -20℃ before RNA extraction.

extract_protocol: Peripheral blood of total RNA was performed according to the manufacturer's instructions (PAXgene Blood RNA kit).

treatment_protocol: Blood sample was treated according to the manusfacturer's instructions (PAXgene Blood RNA Tube)

tag: gender

value: Female

tag: disease status

value: colorectal cancer

value: Peripheral Blood


title: QDCS-053: Peripheral Blood_Colorectal cancer

value: Male


title: QDCS-055: Peripheral Blood_Colorectal cancer


title: QDCS-061: Peripheral Blood_Colorectal cancer


title: QDCS-058: Peripheral Blood_Colorectal cancer


title: QDCS-051: Peripheral Blood_Colorectal cancer


title: QDCS-056: Peripheral Blood_Colorectal cancer


title: QDCS-062: Peripheral Blood_Colorectal cancer


title: QDCS-045: Peripheral Blood_Colorectal cancer


title: QDCS-059: Peripheral Blood_Colorectal cancer


title: QDCS-054: Peripheral Blood_Colorectal cancer


title: QDCS-043: Peripheral Blood_Colorectal cancer


title: QDCS-044: Peripheral Blood_Colorectal cancer


title: QDCS-048: Peripheral Blood_Colorectal cancer


title: QDCS-042: Peripheral Blood_Colorectal cancer


title: QDCS-034: Peripheral Blood_Colorectal cancer


title: QDCS-036: Peripheral Blood_Colorectal cancer


title: QDCS-035: Peripheral Blood_Colorectal cancer


title: QDCS-037: Peripheral Blood_Colorectal cancer


title: QDCS-060: Peripheral Blood_Colorectal cancer


title: QDCS-038: Peripheral Blood_Colorectal cancer


title: QDCS-033: Peripheral Blood_Colorectal cancer


title: QDCS-031: Peripheral Blood_Colorectal cancer


title: QDCS-039: Peripheral Blood_Colorectal cancer


title: QDCS-041: Peripheral Blood_Colorectal cancer


title: QDCS-052: Peripheral Blood_Colorectal cancer


title: QDCS-046: Peripheral Blood_Colorectal cancer


title: QDCS-028: Peripheral Blood_Colorectal cancer


title: QDCS-050: Peripheral Blood_Colorectal cancer


title: QDCS-029: Peripheral Blood_Colorectal cancer


title: QDCS-024: Peripheral Blood_Colorectal cancer


title: QDCS-032: Peripheral Blood_Colorectal cancer


title: QDCS-040: Peripheral Blood_Colorectal cancer


title: QDCS-030: Peripheral Blood_Colorectal cancer


title: QDCS-027: Peripheral Blood_Colorectal cancer


title: QDCS-025: Peripheral Blood_Colorectal cancer


title: QDCS-018: Peripheral Blood_Colorectal cancer


title: QDCS-026: Peripheral Blood_Colorectal cancer


title: QDCS-015: Peripheral Blood_Colorectal cancer


title: QDCS-011: Peripheral Blood_Colorectal cancer


title: QDCS-017: Peripheral Blood_Colorectal cancer


title: QDCS-012: Peripheral Blood_Colorectal cancer


title: QDCS-020: Peripheral Blood_Colorectal cancer


title: QDCS-022: Peripheral Blood_Colorectal cancer


title: QDCS-019: Peripheral Blood_Colorectal cancer


title: QDCS-013: Peripheral Blood_Colorectal cancer


title: QDCS-006: Peripheral Blood_Colorectal cancer


title: QDCS-008: Peripheral Blood_Colorectal cancer


title: QDCS-003: Peripheral Blood_Colorectal cancer


title: QDCS-021: Peripheral Blood_Colorectal cancer


title: QDCS-007: Peripheral Blood_Colorectal cancer


title: QDCS-023: Peripheral Blood_Colorectal cancer


title: QDCS-005: Peripheral Blood_Colorectal cancer


title: HSBJ-051: Peripheral Blood_Healthy control

description: Gene expression data from healthy person with normal colonscopy

value: normal


title: QDCS-001: Peripheral Blood_Colorectal cancer


title: QDCS-014: Peripheral Blood_Colorectal cancer


title: QDCS-004: Peripheral Blood_Colorectal cancer


title: QDCS-047: Peripheral Blood_Colorectal cancer


title: BMDMs, Lyz2Cre:KLF6 Fl/Fl-Control-1

tag: treatment


title: QDCS-009: Peripheral Blood_Colorectal cancer


title: QDCS-010: Peripheral Blood_Colorectal cancer


title: HSNJ-021: Peripheral Blood_Healthy control


title: HSNJ-019: Peripheral Blood_Healthy control


title: A549 cells grown under normoxia [A549_O-2]


title: HSNJ-014: Peripheral Blood_Healthy control


title: HSNJ-017: Peripheral Blood_Healthy control


title: HSBJ-048: Peripheral Blood_Healthy control


title: HSNJ-008: Peripheral Blood_Healthy control


title: HSNJ-010: Peripheral Blood_Healthy control


title: HSNJ-011: Peripheral Blood_Healthy control


title: HSNJ-016: Peripheral Blood_Healthy control


title: HSNJ-009: Peripheral Blood_Healthy control


title: HSNJ-006: Peripheral Blood_Healthy control


title: HSNJ-018: Peripheral Blood_Healthy control


title: HSNJ-005: Peripheral Blood_Healthy control


title: HSNJ-012: Peripheral Blood_Healthy control


title: HSNJ-015: Peripheral Blood_Healthy control


title: HSNJ-004: Peripheral Blood_Healthy control


title: HSNJ-007: Peripheral Blood_Healthy control


title: HSNJ-013: Peripheral Blood_Healthy control


title: HSNJ-020: Peripheral Blood_Healthy control


title: HSNJ-001: Peripheral Blood_Healthy control


title: HSBJ-039: Peripheral Blood_Healthy control


title: HSBJ-040: Peripheral Blood_Healthy control


title: HSBJ-050: Peripheral Blood_Healthy control


title: HSBJ-043: Peripheral Blood_Healthy control


title: HSBJ-038: Peripheral Blood_Healthy control


title: HSBJ-035: Peripheral Blood_Healthy control


title: HSNJ-003: Peripheral Blood_Healthy control


title: HSBJ-034: Peripheral Blood_Healthy control


title: HSBJ-045: Peripheral Blood_Healthy control


title: HSBJ-028: Peripheral Blood_Healthy control


title: HSBJ-032: Peripheral Blood_Healthy control


title: HSBJ-030: Peripheral Blood_Healthy control


title: HSBJ-031: Peripheral Blood_Healthy control


title: HSBJ-033: Peripheral Blood_Healthy control


title: HSBJ-025: Peripheral Blood_Healthy control


title: HSBJ-020: Peripheral Blood_Healthy control


title: HSBJ-018: Peripheral Blood_Healthy control


title: HSBJ-021: Peripheral Blood_Healthy control


title: HSBJ-019: Peripheral Blood_Healthy control


title: HSBJ-026: Peripheral Blood_Healthy control


title: HSBJ-017: Peripheral Blood_Healthy control


title: HSBJ-023: Peripheral Blood_Healthy control


title: HSBJ-007: Peripheral Blood_Healthy control


title: JB283_ATAC

first: Tao

last: Liu

address: Elm and Carlton St

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Institute

data_processing:
ATAC-seq reads aligned to hg19 genome with bowtie2, using paired-end options (-1 and -2)
All aligned files were converted into BAM files with samtools
ATAC-seq peaks were called using HMMRATAC, using aligned BAM files and settings of -u 20 and -l 10. Top 100k peaks were kept for each sample
Merged ATAC-seq peak file made with bedtools merge
ATAC-seq count table made with HT-seq, using merged peak file and BAM files for each sample
Genome_build: hg19

source_name: CD4+ T cell

growth_protocol: Human CD4+ T cells were purified from whole blood by positive selection using the StemSep™ Human CD4+ T Cell Enrichment Kit.

extract_protocol: ATAC-seq was carried out according to Buenrostro’s protocol (doi:10.1002/0471142727.mb2129s109).  DNA-sequencing was conducted using the Illumina HiSeq 2500  platform. The sequencing libraries were generated on the streptavidin beads using the Nextera DNA Library Prep Kit.

value: Blood

value: White blood cell

value: CD4+ T cell

tag: disease state

value: Clinical Remission on medication


title: JB285_ATAC


title: HSBJ-011: Peripheral Blood_Healthy control


title: 006-ctr070: Peripheral Blood_Healthy control


title: JB261_ATAC


title: HSBJ-013: Peripheral Blood_Healthy control


title: HSBJ-003: Peripheral Blood_Healthy control


title: HSBJ-027: Peripheral Blood_Healthy control


title: HSBJ-002: Peripheral Blood_Healthy control


title: 006-ctr065: Peripheral Blood_Healthy control


title: 006-ctr069: Peripheral Blood_Healthy control


title: HSBJ-004: Peripheral Blood_Healthy control


title: HSBJ-024: Peripheral Blood_Healthy control


title: JB257_ATAC


title: 006-ctr030: Peripheral Blood_Healthy control


title: HSBJ-014: Peripheral Blood_Healthy control


title: HSBJ-009: Peripheral Blood_Healthy control


title: HSBJ-005: Peripheral Blood_Healthy control


title: JB230_ATAC


title: JB233_ATAC

value: Active Juvenile Idiopathic Arthritis on Treatment


title: JB211_ATAC


title: 006-ctr057: Peripheral Blood_Healthy control


title: JB205_ATAC


title: JB196_ATAC


title: JB245_ATAC


title: JB198_ATAC

value: Healthy Controls


title: JB195_ATAC


title: JB134_ATAC


title: JB283_RNA

data_processing:
RNA-seq  reads aligned to hg19 genome with bowtie2, using paired-end options (-1 and -2)
All aligned files were converted into BAM files with samtools
RNA-seq count table made with HT-seq, using gencode v19 gene annotations and aligned BAM files
Genome_build: hg19

extract_protocol:
Total RNA was extracted using TRIzol™ reagent and was further purified using RNeasy MiniElute Cleanup kit, including a DNase digest.
cDNA libraries were prepared for each sample using the Illumina TruSeq RNA Sample Preparation Kit following the manufacture’s recommended procedures. Libraries were sequenced using 100 base pair (bp) paired-end reads on the Illumina HiSeq 2500 platform.  Then DNA-sequencing was conducted using the Illumina HiSeq 2500  platform. The sequencing libraries were generated on the streptavidin beads using the Nextera DNA Library Prep Kit.


title: JB131_ATAC


title: JB290_RNA


title: JB133_ATAC


title: JB245_RNA


title: JB132_ATAC


title: JB230_RNA


title: JB233_RNA


title: JB285_RNA


title: JB226_RNA


title: 006-ctr016: Peripheral Blood_Healthy control


title: 006-ctr021: Peripheral Blood_Healthy control


title: JB218_RNA


title: JB205_RNA


title: JB261_RNA


title: JB214_RNA


title: JB199_RNA


title: JB211_RNA


title: JB197_RNA


title: JB198_RNA


title: JB196_RNA


title: JB182_RNA


title: JB173_RNA


title: JB195_RNA


title: JB145_RNA