title: adipocyte HFD PPARG ChIP

data_processing:
RNA-seq:
RNA-seq data were aligned to the mm10 mouse genome using HISAT2 (Kim et al., 2015).
Duplicates and low quality reads were removed by Picard (http://picard.sourceforge.net)
Reads were assigned to transcripts, normalized and quantified using featureCounts (Liao et al., 2014) and EdgeR (Robinson et al., 2010).
Low expressed genes (log2 CPM≥2) were filtered out, and differentially expressed genes were defined at log2 fold-change (FC) ≥0.5 and log2 false discovery rate (FDR)≤0.05
Gene ontology analysis was performed using Metascape. Morpheus (https://software. broadinstitute.org/morpheus/) was used to visualize heatmaps.
ChIP-seq:
ChIP-seq data were aligned to the mm10 mouse genome using Bowtie2 (Langmead and Salzberg, 2012).
Duplicates and low quality reads were removed by Picard (http://picard.sourceforge.net)
Reads were processed using samtools (Li et al., 2009)
Peaks were called by MACS2 (Zhang et al., 2008), and low peaks (4<fold higher coverage than whole cell extract (WCE)) were removed.
Reads were assigned to peaks, normalized and quantified using featureCounts and EdgeR. We used the cutoffs of log2CPM≥2, log2FC≥1, FDR≤0.05 for H3K27ac ChIP-seq and log2CPM≥6, log2FC≥1, FDR≤0.25 for PPARg ChIP-seq.
For ChIP-seq track visualization, reads were processed to the BigWig file format using bedtools (Quinlan and Hall, 2010) and bedGraphToBigWig (Kent et al., 2010).
Processed Bigwig files were viewed in WashU Epigenome Browser (Zhou and Wang, 2012).
ChIP-seq peak heatmaps and distribution plots were generated with the normalized BigWig files within 10kb genomic regions surrounding peaks by using deepTools2 (Ramirez et al., 2016).
Intersecting peaks were determined using bedtools, and peaks were assigned to genes using HOMER (Heinz et al., 2010), and GO analysis was performed by Metascape.
Motif enrichment analysis was conducted using FIMO from the MEME package (Grant et al., 2011) with the JASPAR database (Mathelier et al., 2014)
Genome_build: mm10
Supplementary_files_format_and_content: read counts with batch normalization; bigwig

source_name: adipocyte HFD PPARG ChIP

growth_protocol: Mice were maintained on a standard chow diet (8664 Harlan Teklad, 6.4% w/w fat) under a regular 12h light/12h dark cycle at constant temperature (23°C).

extract_protocol:
RNA-seq: TRAP was performed as previously described (Roh et al., Cell Rep 2017). Adipose tissues were homogenized and processed to immunoprecipitation using anti-GFP antibody. Immunoprecipitates were washed and subjected to RNA extraction using Qiagen Micro RNeasy kit according to the manufacturer’s instructions. Isolated RNA was quantified by Qubit, and RNA integrity was analyzed by Agilent Bioanalyzer.
ChIP-seq: Tissues were dounce homogenized, and cross-linked nuclei were isolated and sorted by BD FACS Aria II using mCherry fluorescence. Sorted nuclei were sheared by Covaris E220 and used for ChIP for overnight. Immunoprecipitates were washed and subjected to elution and reverse crosslinking. DNA was then extracted by AMPure XP beads according to the manufacturer’s manual.
RNA-seq: TRAP-isolated RNA (≤100ng) was treated with the Ribo-Zero rRNA removal kit (Epicentre) to deplete ribosomal RNA and converted into double stranded cDNA using NEBNext mRNA Second Strand Synthesis Module. cDNA was subsequently tagmented and amplified for 12 cycles by using Nextera XT DNA Library Preparation Kit. Sequencing libraries were analyzed Qubit and Agilent Bioanalyzer, pooled at a final concentration of 12pM, and sequenced on a HiSeq2500.
ChIP-seq: Sequencing libraries were constructed using the “on-bead” preparation method as previously described (Roh et al., Cell Rep, 2017). ChIP-isolated DNA was subjected to end repair/phosphorylation using the End-It DNA End-Repair Kit (Epicentre), A-tailing using the Klenow Fragment and index adaptor ligation using Quick Ligase (NEB). AMPure XP beads were left in all the reactions to allow isolation of DNA using PEG (Polyethylene Glycol 8000)/NaCl solution, thus minimizing loss between reactions. After ligation, DNA was eluted and amplified by PCR for 14-16 cycles using the PfuUltra II Hotstart PCR Master Mix. DNA sized between 250 and 600bp was selected by gel electrophoresis and extraction using E-Gel EX Agarose Gels (Invitrogen) and MinElute Gel Extraction kits (Qiagen). Libraries were analyzed using the Qubit and Agilent Bioanalyzer, pooled at a final concentration of 12pM and sequenced on a HiSeq2500 or NextSeq 500500 system.

tag: strain background

value: HFD for 10 weeks

value: epididymal WAT

tag: chip antibody

value: PPARG (Santa Cruz, sc-7196X)


title: Staphylococcus aureus-C12753_C12800-high

status: Public on Jul 05 2020

type: SRA

city: Oxford

first: Craig

last: MacLean

address: 11a Mansfield Road

country: United Kingdom

institute: University of Oxford

library_source: transcriptomic

data_processing:
Transcript quantification from the raw reads was performed using Salmon v0.11.3, mapping to BX571856.1, using the inbuilt fragment GC bias correction and automatic detection of library type.
The BX571856.1 reference transcriptome was indexed using Salmon, which removed sequence-identical duplicate transcripts and used a kmer length of 31bp.
The DESeq2 library in R was used to estimate gene counts and perform differential expression analysis in bioconductor, with the requirement of at least 1 read mapping to each gene for every strain.
Genome_build: BX571856.1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Staphylococcus aureus

source_name: Staphylcoccus aureus colony

growth_protocol: The strains were grown for 16 h overnight in MH2 broth at 37 °C at 225 rpm, diluted 1:20 in a fresh pre-warmed MH2 and incubated for an additional 1 h and 20 min until they reached a density of 0.160-0.170 OD595 (including blank). Ciprofloxacin was added to achieve a final concentration of 1 mg/l.

extract_protocol:
The cells in RNA-protect solution were thawed, centrifuged for 10 min at 5000 rpm and separated from the supernatant. Next, the cells were mixed with 100 µl of enzymatic digest buffer (30 mM Tris-HCl, 1 mM EDTA, 2 mg/ml protease K (Thermo Fisher), 3.25 mg/ml lysozyme (Sigma-Aldrich, 62970) and 0.15 mg/ml lysostaphin (Sigma-Aldrich, L7386)), re-suspended by pipetting and incubated for 10 min at room temperature with shaking. 350 µl of RTL buffer (containing 2-mercaptoethanol (Sigma-Aldrich, M3148)) was added and RNA extraction was performed using RNeasy Mini Kit (Qiagen), following the manufacturer’s protocol and including the optional step of DNase I on-column digestion. Elution was performed twice using the same volume of 50 µl of RNase-free water. RNA concentration was determined using the QuantiFluor RNA System (Promega).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 1.5 h exposure to ciprofloxacin, treatment was stopped by spinning cells for 10 min at 7000 rpm, decanting supernatant and re-suspending the cells in 200 µl of PBS. Finally, 500 µl of RNA-protect Bacteria Reagent (Qiagen) was added and the cells were equilibrated at room temperature for 5 min and then frozen at -80 °C.

tag: strain

tag: evolvability

value: high

tag: multilocus sequence type


title: Staphylococcus aureus-C13353_C03402-low

value: low

value: Missing


title: HsXIST-SDAUV

city: Ann Arbor

first: Chase

middle: Andrew

last: Weidmann

state: MI

address: 1150 W. Medical Center Drive

department: Biological Chemistry

country: USA

institute: University of Michigan

description:
HsXIST_ncRNA.fa
Hs-XIST-RNPMaP-shapemapper-output.txt
Hs-XIST-RNPMaP-ringmapper-output.txt

library_source: genomic

data_processing:
Library strategy: RNP-MaP
For XIST/Xist, nextera reads were trimmed (TrimGalore) an additional 14 nt on each side to accommodate RT primer.
Adduct locations identified by Shapemapper2 software
Correlated mutation events were identified using ringmapper software on shapemapper outputs (.mut files)
In-cell perturbations in SHAPE reactivity were calculated using deltaSHAPE software
RNA structure models were generated from SHAPE data using SuperFold software
RNP-MaP analysis was generated with in-house software from shapemapper outputs

molecule: other

organism: Homo sapiens

source_name: Human HEK293 cells

growth_protocol: Adherent mammalian cells used in chemical probing experiments, either SM33 or HEK293 cells, were grown to 80-90% confluency in either 6-well plates (for targeted priming) or 10-cm dishes (for RNA antisense pulldown). HEK293 cells were cultured in DMEM with 10% FBS. SM33 cells were cultured in embryonic stem cell media [DMEM high glucose with sodium pyruvate, 15 % FBS, 0.1 mM non-essential amino acids (Gibco), 2 mM L-glutamine, 0.1 mM β-mercaptoethanol,1000 U/mL leukemia inhibitory factor (ESGRO, Millipore Sigma)]. Cultures were grown with 100 U/mL penicillin and 100 µg/mL streptomycin. To induce expression of the Xist RNA, SM33 cells were supplemented with 2 µg/mL doxycycline 16 hours before treatment. For all experiments when performing biological replicates, chemical probing and sequencing library preparation were performed on distinct populations of cells on different days.

extract_protocol:
library prep: Nextera XT
nuclear fractionation, proteinase K lysis, PCA extraction

tag: treatment

value: 3JUV and 10mM SDA

tag: treatment type

value: In-Cell

tag: enrichment

value: RNA antisense pulldown

tag: target

value: XIST lncRNA

tag: rt priming

value: random (9-mer)


title: Staphylococcus aureus-C03167_C13176-low


title: Staphylococcus aureus-C03107_C03255-high


title: 91_Normal Risk

type: RNA

city: Bethesda

first: David

middle: N

last: Danforth

state: MD

address: 10 Center drive

department: NCI/CCR

institute: NIH

hyb_protocol: cDNA was hybridized to Affymetrix human U133 plus 2.0 GeneChip array

scan_protocol: GeneChip arrayrs were scanned on an Affymetrix GeneChip scanner 3000

data_processing:
Unsupervised hierarchcal clustering, differential expression of individual genes, and signature analysis of microaary data was conducted by bioinformatic analysis.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
affymetrix-array-type = HG-U133_Plus_2
affymetrix-progid = GeneChip.CallGEBaseCall.1
program-name = Expression Console
program-id = 1.3.1.187

label: biotin

source_name: Normal Risk

label_protocol: Total RNA was amplified and labeled with the Ovation Whole Blood Solution kit (Nugen, CA)

growth_protocol: Ductal cells were collected by ductal lavage from women at normal risk or high risk for breast cancer

extract_protocol: RNA was extracted from ductal cells with the RNeasy Micro Kit (Qiagen)

treatment_protocol: No treatment

tag: subject status

value: premenopausal women

tag: subject group

value: Normal Risk

tag: cell type

value: Breast ductal cells

tag: subject age


title: Hs-XIST-5NIA-CF-2

description:
HsXIST_ncRNA.fa
Hs-XIST-CellFree-SHAPE-MaP-Rep2.txt
Hs-XIST-CellFree-SHAPE-MaP-Rep2-SuperFold.ct

data_processing:
Library strategy: SHAPE-MaP
For XIST/Xist, nextera reads were trimmed (TrimGalore) an additional 14 nt on each side to accommodate RT primer.
Adduct locations identified by Shapemapper2 software
Correlated mutation events were identified using ringmapper software on shapemapper outputs (.mut files)
In-cell perturbations in SHAPE reactivity were calculated using deltaSHAPE software
RNA structure models were generated from SHAPE data using SuperFold software
RNP-MaP analysis was generated with in-house software from shapemapper outputs

extract_protocol:
library prep: Nextera XT
nuclear fractionation, proteinase K lysis, buffer exchange (treatment), PCA extraction

value: 25mM 5NIA

value: Extracted


title: 87_Normal Risk


title: Staphylococcus aureus-C13331_C13244-high


title: 81_Normal Risk


title: 78_Normal Risk Atypia

source_name: Normal Risk Atypia

value: Normal Risk Atypia


title: Staphylococcus aureus-C12753_C12800-low


title: adipocyte chow PPARG ChIP

city: Boston

first: NORC

last: Boston

state: MA

address: 3 Blackfan Circle, CLS0733

institute: Beth Israel Deaconess Medical Center

molecule: genomic DNA

organism: Mus musculus

source_name: adipocyte chow PPARG ChIP

treatment_protocol: Mice were fed chow or HFD for 10 weeks.

value: chow for 10 weeks

tag: tissue


title: Staphylococcus aureus-C03184_C03224-high


title: Staphylococcus aureus-C03167_C13176-high


title: adipocyte HFD H3K27ac ChIP rep 1

source_name: adipocyte HFD H3K27ac ChIP

value: HFD for 10 weeks

value: epididymal WAT

value: H3K27ac (Active Motif, 39133)


title: Staphylococcus aureus-C03206_C01268-high

value: high


title: Staphylococcus aureus-C12830_C03177-low

value: low


title: 82_Normal Risk


title: Staphylococcus aureus-C03353_C03415-high


title: Staphylococcus aureus-C13353_C03402-high


title: Staphylococcus aureus-C03299_C12783-high


title: 129_High Risk Atypia

source_name: High Risk Atypia

value: High Risk Atypia


title: adipocyte chow H3K27ac ChIP rep 3

source_name: adipocyte chow H3K27ac ChIP


title: adipocyte chow H3K27ac ChIP rep 2


title: 64_High Risk

source_name: High Risk

value: High Risk


title: adipocyte HFD H3K27ac ChIP rep 2


title: Staphylococcus aureus-C03107_C03255-low


title: adipocyte chow H3K27ac ChIP rep 1


title: 90_Normal Risk Atypia


title: 58_High Risk Atypia


title: 56B_High Risk Atypia


title: Staphylococcus aureus-C12830_C03177-high


title: 89_Normal Risk


title: Staphylococcus aureus-C03270_C03285-high


title: Staphylococcus aureus-C03215_C13396-high


title: Mm-Xist-DMSO-IC-2

description:
MmXist_ncRNA.fa
Mm-Xist-InCell-SHAPE-MaP-Rep2.txt
Mm-Xist-InCell-SHAPE-MaP-Rep2-SuperFold.ct

source_name: Mouse SM33 embryonic stem cells

extract_protocol:
library prep: Nextera XT
Trizol

value: DMSO

value: In-Cell

value: RNA antisense pulldown

value: Xist lncRNA


title: Mm-Xist-DMSO-IC-1

description:
MmXist_ncRNA.fa
Mm-Xist-InCell-SHAPE-MaP-Rep1.txt
Mm-Xist-InCell-SHAPE-MaP-Rep1-SuperFold.ct

value: random (9-mer)


title: Staphylococcus aureus-C12782_C12807-high


title: Staphylococcus aureus-C01186_C13179-high


title: D_persimilis

city: Leuven

first: Stein

last: Aerts

address: Herestraat 49

department: Center for Human Genetics

country: Belgium

institute: KULeuven

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to their respective genomes using tophat2 v 2.0.3 (default parameters)
HT-Seq count (option -str=no) was used to count the number of reads falling within each species exonic regions.
RPKM values were calculated for each sample independetly .
Ensembl GeneTreess 2013 was used to obtain orthology relationships across Drosophila species
Normalization across one-to-one orthologous regions was performed using the upper-quantile methodology.
Genome_build: D.melanogaster 5.46; D.persimilis 1.3; D.pseudoobscura 2.30; D.simulans 1.4; D.yakuba 1.3
Supplementary_files_format_and_content: tab-delimited text files include htseq counts for each sample and normalized values for one-to-one orthologs across the Drosophila species under study.

organism: Drosophila persimilis

source_name: Johnston's Organ

growth_protocol: All flies were raised at 25˚C on standards fly food

extract_protocol:
RNA was extracted with the RNAqueous micro kit (Ambion)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Johnston's Organ

tag: age

value: Adult

tag: reference genome annotation

value: D.persimilis 1.3


title: Mm-Xist-DMSO-CF-1

description:
MmXist_ncRNA.fa
Mm-Xist-CellFree-SHAPE-MaP-Rep1.txt
Mm-Xist-CellFree-SHAPE-MaP-Rep1-SuperFold.ct

value: Extracted


title: Mm-Xist-DMSO-CF-2

description:
MmXist_ncRNA.fa
Mm-Xist-CellFree-SHAPE-MaP-Rep2.txt
Mm-Xist-CellFree-SHAPE-MaP-Rep2-SuperFold.ct


title: Staphylococcus aureus-C03270_C03285-low


title: 5G24

city: Greensboro

first: Ramji

middle: Kumar

last: Bhandari

state: NC

address: 321 McIver St

department: Biology

institute: University of North Carolina Greensboro

description: EE2 Rep3

data_processing: Sequencing reads from each sample were mapped to medaka reference transcripts (Ensembl version 95) using TopHat2 software with default parameters. Only uniquely mapped reads were used for subsequent analysis. Cufflinks software was used to conduct differentially expressed gene analysis on the raw count data. Technical replicates were merged together using the Samtools software.

organism: Oryzias latipes

source_name: RNA-seq-testis

growth_protocol: The medaka strain Hd-rR was used and maintained under standard conditions

extract_protocol:
Total RNA from each sample tissues were extracted using a commercial combo kit for RNA/DNA isolation (Qiagen, Carlsbad, CA) according to manufacturer’s instructions.
The quality control and RNA-seq library preparation was conducted by the DNA sequencing Core facility of the University of Missouri Columbia.

treatment_protocol: Fertilized eggs were collected and exposed to EE2 (10 ng/L) or BPA (10 µg/L) through the incubation water over a period of 12 dpf in 50 ml glass petri-dishes. Exposures were static with daily renewal of test chemicals from fertilization through day 12.

value: Hd-rR

value: testis


title: 5G14

description: EE2 Rep2


title: 5G23

description: EE2 Rep3


title: Mm-Xist-5NIA-IC-2

value: 25mM 5NIA


title: 5G25

description: EE2 Rep3


title: 5G13

description: EE2 Rep2


title: Mm-Xist-5NIA-IC-1


title: 94_Norma Risk Atypia

source_name: Norma Risk Atypia

value: premenopausal women

value: Norma Risk Atypia

value: Breast ductal cells


title: 5G5

description: EE2 Rep1


title: 5G3

description: EE2 Rep1


title: Mm-Xist-5NIA-CF-2


title: 5G12

description: EE2 Rep2


title: Mm-Xist-5NIA-CF-1


title: 127_Normal Risk Atypia

value: Normal Risk Atypia


title: 3G25

description: BPA Rep3

value: BPA


title: 3G24

description: BPA Rep3


title: 3G22

description: BPA Rep3


title: MmXist-UV

description:
MmXist_ncRNA.fa
Mm-Xist-RNPMaP-shapemapper-output.txt
Mm-Xist-RNPMaP-ringmapper-output.txt

value: 3JUV only


title: 3G15

description: BPA Rep 2


title: MmXist-SDAUV

value: 3JUV and 10mM SDA

value: In-Cell


title: 108_Normal Risk

value: Normal Risk


title: 3G13

description: BPA Rep2


title: 3G14

description: BPA Rep 2


title: 3G4

description: BPA Rep 1


title: 3G3

description: BPA Rep 1


title: 1G25

description: Control Rep3

value: Control


title: 1G23

description: Control Rep3


title: 1G21

description: Control Rep3


title: 135_High Risk

value: High Risk


title: 119B_High Risk Atypia

value: High Risk Atypia


title: 41B_High Risk


title: 1G14

description: Control Rep2


title: 33E_High Risk Atypia


title: 115_High Risk


title: 116_High Risk


title: 114_High Risk


title: 102_Normal Risk Atypia


title: 133_High Risk


title: 3G1

description: BPA Rep 1


title: 2G5

description: Control Rep1


title: ID8 stimulated with 200ng/mL CCL6, biological rep1

city: Stanford

first: Oliver

last: Dorigo

address: 300 Pasteur Dr

institute: Stanford University

hyb_protocol: WT Plus reagent kit was used for ssDNA amplification from total RNA. Cartridge Array Hybridization was performed on the GeneChip Instrument according to manufacturer's protocol

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and CEL. intensity files were generated by Affymetrix GeneChip Command Console Software (AGCC, Thermo Fisher).

data_processing: Gene-level differential expression was detected on the Affymetrix Clariom S microarray using RMA methodology

source_name: ID8 ovarian cancer cell line treated with 200ng/mL CCL6 for 6 hours cultured in vitro

label_protocol: Fragment and ssDNA labeling was carried out according to manufacturer's protocol

growth_protocol: ID8 cells were cultured in growth medium containing DMEM + 10% fetal bovine serum + 1% Penn-Strep. For stimulation with recombinant CCL6, 200ng/mL CCL6 was added to DMEM serum free media

extract_protocol: RNA from serum starved unstimulated ID8 cells and ID8 stimulated with 200ng/mL recombinant CCL6 protein for 6 hours was extracted with Qiagen RNeasy Micro kit according to the manufacturer’s instructions.

treatment_protocol: ID8 cells were cultured in 10cm2 petri dishes in vitro and serum starved for 24 hours. ID8 cells were stimulated with 200ng/mL CCL6 for 6 hours such that unstimulated ID8 cells (n=3) and ID8 stimulated with 200ng/mL CCL6 (n=3) had biological replicates. RNA isolated from these cells was further used for Affymetrix Clariom S mouse transcriptome microarray analysis.

tag: cell line

value: ovarian cancer cell line


title: ID8-unstimulated, biological rep3

source_name: ID8 ovarian cancer cell line cultured in vitro


title: 28_High Risk


title: ID8 stimulated with 200ng/mL CCL6, biological rep3


title: 2G4

description: Control Rep1


title: 128_Normal Risk Atypia


title: 63_Normal Risk Atypia


title: 2G1

description: Control Rep1


title: D_melanogaster

organism: Drosophila melanogaster

value: Johnston's Organ

value: Adult

value: D.melanogaster 5.46


title: 1G12

description: Control Rep2

value: Hd-rR

value: testis


title: 5G1

description: EE2 Rep1


title: Stimulated_DGAT1i_M1_18h_3

status: Public on Jul 04 2020

city: Baltimore

first: Immunometabolism

last: Department

state: Maryland

address: 1650 Orleans Street

department: Immunometabolism

institute: Johns Hopkins University

description: Macrophage stimulated with IFNy and LPS and treated with T863

data_processing:
Sequenced libraries were analyzed with SnakePipes 1.2.0
Raw mapped reads were processed in R (Lucent Technologies) with DESeq2 (Love et al., 2014), to determine differentially expressed genes and generate normalized read counts to visualize as heatmaps using Morpheus (Broad Institute).
Genome_build: GRCm38
Supplementary_files_format_and_content: raw read counts matrix containing count for every sample

growth_protocol: Bone marrow cells were grown in complete medium (RPMI-1640 medium containing 10 mM glucose, 2 mM L-glutamine, 100 U ml–1 penicillin-streptomycin and 10% FCS) with 20 ng ml–1 murine macrophage colony- stimulating factor 1 (CSF-1; Peprotech) for 7 days, and supplemented with CSF-1 on days 3 and 5.

extract_protocol:
Total RNA was isolated using the PureLink RNA Mini kit (Ambion) and quantified using Qubit 2.0.
Libraries were prepared using the NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (New England Biolabs) and sequenced using the HiSeq 3000 (Illumina).

treatment_protocol: Resting Macrophages  (M0), or Macrophages stimulated with with 50 ng ml–1 IFN-γ  and 20 ng ml-1 LPS (γ+LPS),  were treated with 50 μM T863 for DGAT1 inhibition

value: Bone Marrow derived Macrophages

value: Bone Marrow


title: D_simulans

organism: Drosophila simulans

value: D.simulans 1.4


title: 100_Normal Risk

value: premenopausal women

value: Breast ductal cells


title: Stimulated_DGAT1i_M1_18h_1

source_name: Macrophage stimulated with IFNy and LPS and treated with T863


title: Stimulated_DGAT1i_M1_18h_2


title: Resting_DGAT1i_18h_3

description: Resting Macrophages treated with T865

source_name: Resting Macrophages treated with T863


title: Resting_DGAT1i_18h_2

description: Resting Macrophages treated with T864


title: Stimulated_M1_18h_3

description: Macrophage stimulated with IFNy and LPS

source_name: Macrophage stimulated with IFNy and LPS


title: Stimulated_M1_18h_2

description: Macrophage stimulated with IFNy and LPS


title: Stimulated_M1_18h_1

description: Macrophage stimulated with IFNy and LPS


title: Resting_M0_2

description: Resting Macrophages

source_name: Resting Macrophages


title: Resting_M0_3

description: Resting Macrophages


title: 104_Normal Rsk

source_name: Normal Rsk

value: Normal Rsk


title: Resting_M0_1

description: Resting Macrophages


title: ID8-unstimulated, biological rep2


title: ID8 stimulated with 200ng/mL CCL6, biological rep2


title: 112_Normal Risk

source_name: Normal Risk


title: 1G11

description: Control Rep2


title: Resting_DGAT1i_18h_1

description: Resting Macrophages treated with T863


title: OC21T: Ovarian tumor tissue

city: tianjin

first: kexin

last: chen

address: huanhu road, tiyuanbei, hexi district

country: China

institute: Tianjin Medical University Cancer Institute and Hospital

description: Gene expression of ovarian cancer tumor tissue

hyb_protocol: 0.6ug of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K V2 Microarray (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried naturally.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using G3 one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol: GE1_107_Sep09 and Grid: 039494_D_F_20150609) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Ovarian tumor tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng total RNA using the One-Color Low Input Quick Amp labeling kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop-2000 spectrophotometer.

extract_protocol: RNA was prepared using the Trizol reagent (Invitrogen) following the manufacturer's protocol. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: gender

value: Female

value: Ovarian tumor tissue


title: OC23T: Ovarian tumor tissue


title: OC23N: Adjacent normal tissue paired with OC23T

description: Gene expression of ovarian normal tissue

source_name: Ovarian normal tissue

value: Ovarian normal tissue


title: pLXSN (E6/E7) HPV115 duplicate2

city: LYON

first: Alexis

last: Robitaille

state: Rhône-Alpes

address: 150 Cours Albert Thomas

department: Section of Infections

country: France

institute: International Agency for Research on Cancer (IARC)

hyb_protocol: Subsequent steps included washing, streptavadin-Cy3 staining

scan_protocol: Scanning of the arrays done on an Illumina BeadArray Reader

data_processing: Differential expression analysis was performed using BRB-ArrayTools software v4.2 developed by Dr Richard Simon and BRB-ArrayTools Development Team. Project annotated by Bioconductor (www.bioconductor.org) annotation package lumiHumanAll.db(Version:1.14.0).

source_name: Human Foreskin Keratinocytes (HFK)

label_protocol: Biotin labeled single-stranded cRNAs

extract_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion®), 500 ng of extracted RNAs were converted to cDNAs

tag: hpv

value: Betapapillomavirus 3


title: OC22T: Ovarian tumor tissue


title: pLXSN (E6/E7) HPV76


title: OC21N: Adjacent normal tissue paired with OC21T


title: OC20T: Ovarian tumor tissue


title: OC20N: Adjacent normal tissue paired with OC20T


title: pLXSN (E6/E7) HPV115


title: pLXSN empty


title: pLXSN (E6/E7) HPV115 duplicate1


title: pLXSN empty duplicate2


title: pLXSN (E6/E7) HPV76 duplicate2


title: pLXSN empty duplicate1


title: pLXSN (E6/E7) HPV49


title: pLXSN (E6/E7) HPV75 duplicate2


title: pLXSN (E6/E7) HPV38

value: Betapapillomavirus 2


title: pLXSN (E6/E7) HPV16

value: Alphapapillomavirus 9


title: pLXSN (E6/E7) HPV76 duplicate1


title: pLXSN (E6/E7) HPV16 duplicate

description: Duplicate


title: pLXSN (E6/E7) HPV75


title: pLXSN (E6/E7) HPV38 duplicate

description: Duplicate


title: pLXSN (E6/E7) HPV49 duplicate

description: Duplicate


title: OC22N: Adjacent normal tissue paired with OC22T


title: OC19T: Ovarian tumor tissue


title: Empty HFK


title: Empty HFK duplicate

description: Duplicate


title: OC18T: Ovarian tumor tissue


title: OC17N: Adjacent normal tissue paired with OC17T


title: OC17T: Ovarian tumor tissue


title: OC19N: Adjacent normal tissue paired with OC19T


title: OC15T: Ovarian tumor tissue


title: OC15N: Adjacent normal tissue paired with OC15T


title: HC7

city: Vienna

first: Patrick

middle: M

last: Brunner

address: Waehringer Guertel 18-20

department: Dermatology

country: Austria

institute: Medical University of Vienna

data_processing:
Raw sequencing data were demultiplexed, aligned to a reference genome (GrCh38) and counted using Cell Ranger (version 3.0.2; 10x Genomics).
Genome_build: GrCh38
Supplementary_files_format_and_content: mtx (count matrix in sparse matrix format), barcodes.tsv (barcode ids),  features.tsv: (gene ids)

source_name: Skin Biopsy

extract_protocol:
Skin suction blisters were formed using a low pressure device from Electronic Diversities (Ridge Road, Finksburg, Md) by mounting 2 sterile 5-hole (5-mm diameter per hole) skin suction plates onto each antecubital fossa. Negative pressure (150-200 mm Hg) was applied over 1 to 2 hours, and blister fluid obtained was centrifuged to clear the fluid from cells and debris. The blister roof (constituting an epidermal sheet) was collected using standard surgical instruments and processed using 0.25% trypsin/EDTA (10 minutes at 37°C; Invitrogen, San Diego, Calif) to obtain a single-cell suspension. Cells from blister fluid and from the epidermis (blister roof) were enriched for CD45+ cells using fluorescence-activated cell sorting ([FACS]; FACSAria III, BD Biosciences, Franklin Lakes, NJ) and pooled within each donor sample. CD45− cells from the blister fluid and the epidermis were added to obtain a total number of 15,000 cells per scRNA-seq sample. For biopsies, tissue was minced, collagenase IV (Worthington Biochemical) treated and cell suspensions were prepared using a cell dissociation sieve (Sigma-Aldrich). CD45+ and CD45− cells were FACS-sorted at equal amounts for each sample. Immediately after sorting, cells were subjected to scRNA-seq processing (10x Genomics, Pleasanton, Calif).
Single-cell libraries were generated using the Chromium Controller and Single Cell 3− Library & Gel Bead Kit versions 2 and 3 (10x Genomics) according to the manufacturer’s protocol.

value: Skin Biopsy

tag: easi score

tag: diagnosis

value: Healthy Control

tag: chemistry

value: Single Cell 3' v3


title: HC6


title: OC18N: Adjacent normal tissue paired with OC18T


title: OC14N: Adjacent normal tissue paired with OC14T


title: HC5

source_name: Skin Suction blister

value: Skin Suction blister


title: OC13T: Ovarian tumor tissue


title: HC4

value: Single Cell 3' v2


title: HC2


title: HC1


title: OC13N: Adjacent normal tissue paired with OC13T


title: OC08N: Adjacent normal tissue paired with OC08T


title: OC04T: Ovarian tumor tissue


title: OC08T: Ovarian tumor tissue


title: AD8

value: Atopic Dermatitis


title: AD6


title: OC14T: Ovarian tumor tissue


title: Cut_and_Run_seq_Scid.ahd.2C2_anti-nIgG_rep2

city: Lund

first: Mikael

last: Sigvardsson

address: Sölvegatan 19

country: Sweden

institute: Lund University

data_processing:
Library strategy: Cut&Run
RNA-Sequencing and data analysis: Libraries  were single-end sequenced on a NexSeq500.  For analysis of RNA-Seq experiments the reads were aligned to mouse reference  genome (mm10 / GRCm38) using STAR (2.6.0b-1) (Dobin, A etal. 2012), with single read, standard settings. If not indicated, further  analyses were performed using the HOMER platform (v4.8, v4.10) (Heinz et al. 2010). For analysis of statistically significance among  differently expressed genes, the data was analyzed using analyzeRepeats.pl with the –  noadj option, followed by the getDiffExpression.pl  command using DESeq2.
ATAC-sequencing and data analysis: For ATAC-Seq samples, Libraries were single-end sequenced on a NexSeq500, reads were aligned to the mm10 genome using default single end parameters for Bowtie2 (2.3.4.2) (Langmead, B. etal. 209 and 2012).  Aligned read files from ATAC seq experiments were analyzed with HOMER (v4.8, v4.10) (Heinz et al. 2010). ATAC-signal from of the DN3 Arid1a Wt and KO cells was assayed on ATAC peak positions determined by reanalysis of ATAC-data from GSE100738 (duplicate samples). This data was paired-end processed with the ENCODE ATAC-Seq/DNase-Seq Pipeline (https://github.com/kundajelab/atac_dnase_pipelines) for ATAC-peak finding with the following settings: -species mm10 -enable_idr -no_xcor -auto_detect_adapter -mapq_thresh 10 -multimapping 4 -rm_chr_from_tag mito -nth 24.
Cut&Run: Reads were trimmed with Trim-galore in paired-end mode (Babraham Bioinformatics) and mapped to the mm10 genome (Gencode version GRCm38) with Bowtie2 (2.3.5) . Bam-files were generated using Samtools v.1.9 and PCR duplicates were removed with Picard MarkDuplicates (2.21.4) followed by a filtration of read för MAPQ-score  10 using Samtools. The filtered bam-file was subsequently converted back to the sam-format and larger than 120 bp were filtered out followed by conversion back to the bam-format using Samtools. Peaks were called from the filtered bam-file using MACS2 callpeak with default settings, using the Normal IgG as the control. Due to the sparsity of Cut&Run data, the duplicates were merged prior to peak calling. T-cell TF and co-factors overlapping peaks were derived using mergePeaks.pl from the HOMER package.
Genome_build: mm10
Supplementary_files_format_and_content: Homer processed raw read count txt file of RNA-seq expression and a HOMER processed annotation of Arid1a WT/KO ATAC signal on merged DN3 DN4 peak positions (peaks positions generated from data in GSE100738). For the Cut&Run data, MACS2 generated peak-files in the narrowPeak format are provided.

extract_protocol:
For RNA-seq: Total RNA was isolated by use of RNAeasy Micro Kit (Qiagen, Hilden, Germany) according to  manufacturer’s recommendations.
RNA-seq: Libraries were constructed using NuGEN’s Ovation Ultralow Library systems (NuGEN Technologies, San Calros, CA) and were subsequently subjected to 76 cycles of NextSeq500 sequencing (Illumina, San Diego,CA).
ATAC-seq: ATAC-seq library preparation was done as described in (Buenrostro et al. 2013) using Transposomes from Nextera DNA library preparation kit (Illumina, San Diego, CA) and custom primers Libraries were run single read on the Illumina NexSeq500. The following antibodies are used for Cut&Run experiment: : rabbit monoclonal aTCF1 (Cell Signaling, C63D9(2203S), Lot 8), rabbit monoclonal aARID1a (Cell Signaling, D2A8V (12354S), Lot 3) and polyclonal Normal Rabbit IgG (Millipore 12-370, Lot 3109265). Libraries for sequencing was essentially prepared as previously descried for ChIP-sequencing (Okuyama et al. PLoS Genet. 2019, PMID:31381561) with two modifications: 1) Prior to adapter ligation all purification steps were carried out using Zymo Research ChIP DNA Clean and Concentrator to not lose fragments smaller than 100 nt and 2) size-selection with Ampure XP beads was performed after adapter ligation with a targeted mean fragment size of 150-300 bp. Libraries were paired-end sequenced on an Illumina Nextseq 500 (read-length: 2 × 38 bp).

treatment_protocol: DN3 progenitor T-cells from Arid 1a Wt and KO mice thymuses were sorted on Fc blocked fresh thymus with the following markers  Lin- (GR1, Mac1, TER119, CD19, NK1.1, CD11c), CD45+CD3-CD4-CD8-CD44-CD25+). Scid.adh.2C2 cells were cultured in RPMI1640 with 10% fetal bovine serum, sodium pyruvate, non-essential amino acids, gentamicine and 50 μM β-mercaptoethanol.

tag: strain/background

value: NOD SCID

tag: cell line background

value: Pro-T tumor derived cell line from CB17-Prkdc<scid> mice

value: T-cell progenitor

tag: antibody


title: AD5


title: AD4


title: OC04N: Adjacent normal tissue paired with OC04T


title: OC03T: Ovarian tumor tissue


title: OC03N: Adjacent normal tissue paired with OC03T


title: Cut_and_Run_seq_Scid.ahd.2C2_anti-nIgG_rep1

value: polyclonal Normal Rabbit IgG (Millipore 12-370, Lot 3109265)


title: AD3


title: Cut_and_Run_seq_Scid.ahd.2C2_anti-TCF1_rep2

value: rabbit monoclonal aTCF1 (Cell Signaling, C63D9(2203S), Lot 8)


title: Cut_and_Run_seq_Scid.ahd.2C2_anti-TCF1_rep1


title: Cut_and_Run_seq_Scid.ahd.2C2_anti-ARID1a_rep1

value: rabbit monoclonal aARID1a (Cell Signaling, D2A8V (12354S), Lot 3)


title: HC3


title: OC09N: Adjacent normal tissue paired with OC09T

value: Female


title: OC09T: Ovarian tumor tissue

value: Ovarian tumor tissue


title: OC02T: Ovarian tumor tissue


title: RNA_seq_ARID_CRE_DN3_rep2

description: processed data file: AnalyzeRepeats_mm10_count-exons_condenseGenes_noadj_on-DN3-ARID-Control_n3-ARID-KO_n3.txt

data_processing:
ATAC-sequencing and data analysis: For ATAC-Seq samples, libraries were single-end sequenced on a NexSeq500, and reads were aligned to the mm10 genome using default single end parameters for Bowtie2 (2.3.4.2) (Langmead, B. et al. 209 and 2012). Aligned read files from ATAC seq experiments were analyzed with HOMER (v4.8, v4.10) (Heinz et al. 2010). ATAC-signal from the DN3 Arid1a Wt and KO cells was assayed on ATAC peak positions determined by reanalysis of ATAC-data from GSE100738 (duplicate samples). This data was paired-end processed with the ENCODE ATAC-Seq/DNase-Seq Pipeline (https://github.com/kundajelab/atac_dnase_pipelines) for ATAC-peak finding with the following settings: -species mm10 -enable_idr -no_xcor -auto_detect_adapter -mapq_thresh 10 -multimapping 4 -rm_chr_from_tag mito -nth 24.
RNA-Sequencing and data analysis: Libraries were single-end sequenced on a NexSeq500. For analysis of RNA-Seq experiments the reads were aligned to mouse reference genome (mm10 / GRCm38) using STAR (2.6.0b-1) (Dobin, A et al. 2012), with single read, standard settings. If not indicated, further analyses were performed using the HOMER platform (v4.8, v4.10) (Heinz et al. 2010). For analysis of statistically significance among differently expressed genes, the data was analyzed using analyzeRepeats.pl with the – noadj option, followed by the getDiffExpression.pl command using DESeq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Annotate_DN3_Arid_WT_KO_ATAC_on_merged_DN3_DN4_ATAC_peaks_mm10.txt: HOMER processed annotation of Arid1a WT/KO ATAC signal on merged DN3 DN4 peak positions (peaks positions generated from data in GSE100738).
Supplementary_files_format_and_content: AnalyzeRepeats_mm10_count-exons_condenseGenes_noadj_on-DN3-ARID-Control_n3-ARID-KO_n3.txt: Homer processed raw read count txt file of RNA-seq expression.

source_name: Thymus

extract_protocol:
ATAC-seq: ATAC-seq library preparation was done as described in (Buenrostro et al. 2013) using Transposomes from Nextera DNA library preparation kit (Illumina, San Diego, CA) and custom primers. Libraries were run single read on the Illumina NexSeq500.
RNA-seq: Total RNA was isolated by use of RNeasy Micro Kit (Qiagen, Hilden, Germany) according to manufacturer’s recommendations.
RNA-seq libraries were constructed using NuGEN’s Ovation Ultralow Library systems (NuGEN Technologies, San Carlos, CA) and were subsequently subjected to 76 cycles of NextSeq500 sequencing (Illumina, San Diego, CA).

treatment_protocol: DN3 progenitor T-cells from Arid1a Wt and KO mice thymuses were sorted on Fc blocked fresh thymus with the following markers Lin- (GR1, Mac1, TER119, CD19, NK1.1, CD11c), CD45+CD3-CD4-CD8-CD44-CD25+).

tag: genotype/variation

value: Thymic DN3 T-cell progenitor


title: AD7


title: Cut_and_Run_seq_Scid.ahd.2C2_anti-ARID1a_rep2


title: OC02N: Adjacent normal tissue paired with OC02T

value: Ovarian normal tissue


title: RNA_seq_ARID_CRE_DN3_rep1


title: Rep3_Vehicle

city: Cambridge

first: Sebastian

last: Lourido

address: 455 Main St.

institute: Whitehead Institute

data_processing:
sgRNAs were counted using a custom analysis script (see PMID  29323662).
Supplementary_files_format_and_content: The file allDHAcounts.csv contains the processed data for all the fastq files. Each column in allDHAcounts.csv was generated by counting the sgRNAs for each gene in a particular fastq file.

organism: Toxoplasma gondii

source_name: SgRNAs from a pool of T gondii mutated using CRISPR, then treated with vehicle control

extract_protocol:
DNA was extracted from parasites using a Dneasy DNA extraction kit from Qiagen and sgRNAs were amplified using custom primers (see PMID  29323662).
See PMID  29323662

treatment_protocol: Cas9-expressing parasites were transfected with sgRNA-expressing plasmids, cultured for approximately one week (until passage 3, or P3) then cultured with DHA or vehicle control for a approximately one additional week.

tag: replicate

tag: treatment

value: Vehicle control


title: RNA_seq_ARID_Control_rep3

value: Wt

tag: cell type


title: Rep3_P3

source_name: SgRNAs from a pool of T gondii mutants generated by CRISPR prior to DHA treatment


title: Rep3_DHA_0.05_uM

source_name: SgRNAs from a pool of T gondii mutants generated using CRISPR, then treated with 0.05 uM DHA

value: 0.05 uM DHA


title: RNA_seq_ARID_CRE_DN3_rep3


title: AD2


title: RNA_seq_ARID_Control_rep2


title: Rep3_DHA_0.5_uM

source_name: SgRNAs from a pool of T gondii mutants generated using CRISPR, then treated with 0.5 uM DHA

value: 0.5 uM DHA


title: RGC_P6_2

city: Hong Kong

first: Heather

middle: Kayew

last: Mak

address: 147K Argyle Street

department: Ophthalmology and Visual Sciences

institute: The Chinese University of Hong Kong

description: Endogenous microRNA expression

hyb_protocol: The hybridization used miRNA Complete Labeling and Hyb Kit  (5190-0456, Agilent), according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA, Agilent) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software (v9.5.3.1) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Data was further analyzed using GeneSpring GX Software (v11.5), and were log2 transformed and normalized by Percentile method.

organism: Rattus norvegicus

source_name: Retinal ganglion cell, post-natal day 6, biological replicate 2

label_protocol: An input of 100 ng of total RNA per sample was dephosphorylated and ligated with 3', 5'-cytidine bisphosphate (pCp-Cy3) using  Agilent’s miRNA Complete Labeling and Hyb Kit (5190-0456, Agilent).

extract_protocol: Total RNA was isolated with miRNeasy kit (Qiagen, Hombrechtikon, Switzerland). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: No treatment. Embryonic day 21 (E21), post-natal day 6 (P6), and post-natal day 30 (P30) Sprague Dawley rat retinal ganglion cells (RGCs) were freshly purified using Neural Tissue Dissociation Kit – Postnatal Neurons (130-094-802, Miltenyi Biotec) and rat Retinal Ganglion Cell Isolation Kit - Rat (130-096-209, Miltenyi Biotec), according to manufacturer's instructions. Total RNA was immediately extracted after RGC purification.

value: Retinal ganglion cell

tag: developmental stage

value: Post-natal day 6

tag: strain

value: Sprague Dawley


title: RGC_P6_3

description: Endogenous microRNA expression

source_name: Retinal ganglion cell, post-natal day 6, biological replicate 3

tag: tissue


title: RGC_P6_1

description: Endogenous microRNA expression

source_name: Retinal ganglion cell, post-natal day 6, biological replicate 1


title: RGC_P30_1

description: Endogenous microRNA expression

source_name: Retinal ganglion cell, post-natal day 30, biological replicate 1

value: Post-natal day 30


title: RGC_P30_2

description: Endogenous microRNA expression

source_name: Retinal ganglion cell, post-natal day 30, biological replicate 2


title: ATAC_ARID_Control_DN3

description: processed data file: Annotate_mm10_DN3_Arid_WT_and_KO_ATAC_on_merged_DN3_DN4_ATAC_peaks.txt


title: RGC_E21_3

description: Endogenous microRNA expression

source_name: Retinal ganglion cell, embryonic day 21, biological replicate 3

value: Embryonic day 21


title: RGC_E21_2

description: Endogenous microRNA expression

source_name: Retinal ganglion cell, embryonic day 21, biological replicate 2


title: Rep3_Lib

organism: synthetic construct

source_name: Pool of sgRNAs used to generate mutant T gondii using CRISPR


title: ATAC_ARID_CRE_DN3


title: Rep1_Vehicle

source_name: SgRNAs from a pool of T gondii mutants generated using CRISPR, then treated with vehicle control

value: vehicle control


title: AD1

value: Skin Suction blister

value: Atopic Dermatitis

value: Single Cell 3' v2


title: Rep2_P3


title: AD9554: SF5_6.mut

city: Barcelona

first: Gwenvael

last: Le Dréau

email: ledreau.g@gmail.com, gldbmc@ibmb.csic.es, gwenvael.le-dreau@inserm.fr, ledreaugwenvael@yahoo.fr

address: Parc Cientific de Barcelona, Helix building

department: Developmental Biology

country: Spain

institute: Instituto de Biologia Molecular de Barcelona - CSIC

data_processing:
The RNA-seq libraries were prepared following the manufacturer’s recommendations of KAPA Stranded mRNASeq Illumina® Platforms Kit (Roche-Kapa Biosystems).
The libraries were sequenced on HiSeq2500 (Illumina) in paired-end mode with a read length of 2×100 bp using TruSeq SBS Kit v4 (Illumina). Each sample was sequenced in a fraction of a sequencing v4 flow cell lane, following the manufacturer’s protocol.
Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.18.66.3) and followed by generation of FASTQ sequence files.
RNA-seq paired-end reads were mapping against Mus musculus reference genome (GRCm38) using STAR version 2.5.3a with ENCODE parameters for long RNA.
Isoforms were quantified using RSEM version 1.3.0 with default parameters for stranded sequencing and the gencode version M15.
Genome_build: mmusculus.10
Supplementary_files_format_and_content: Differential isoform analysis was performed using DESeq2 version 1.18 with default parameters. We considered differentially expressed transcripts to be those showing an adjusted P-value <0.05 or adjusted P-value <0.1 (extended list).

growth_protocol: Mouse embryos were recovered and sacrificed at embryonic day E12.5

extract_protocol:
Forebrains were dissected, cells mechanically dissociated, incubated for 30 min with an APC-conjugated anti-Prominin1 antibody, purified by FACS and diluted to a final concentration of 2-3×10^6 cells/ml. RNA was extracted using the miRNeasy Micro Kit (Qiagen). Quantification of total RNA was performed by Qubit® RNA BR Assay kit (Thermo Fisher Scientific) and RNA 6000 Nano Bioanalyzer 2100 Assay (Agilent) was used to estimate the total RNA integrity. The three pairs of samples of RNAs from SmadNes mutant and control RGCs presenting the best RNA integrity were used for sequencing.
RNA-seq libraries were prepared following the manufacturer’s recommendations of KAPA Stranded mRNASeq Illumina® Platforms Kit (Roche-Kapa Biosystems).
The libraries were sequenced on HiSeq2500 (Illumina) in paired-end mode with a read length of 2×100 bp using TruSeq SBS Kit v4 (Illumina). Each sample was sequenced in a fraction of a sequencing v4 flow cell lane, following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.18.66.3) and followed by generation of FASTQ sequence files. RNA-seq paired-end reads were mapping against Mus musculus reference genome (GRCm38) using STAR version 2.5.3a with ENCODE parameters for long RNA. Isoforms were quantified using RSEM version 1.3.0 with default parameters for stranded sequencing and the gencode version M15.

treatment_protocol: 3 pools of FACS-purified cortical radial glial cells were analyzed for each genotype

value: FACS-purified E12.5 cortical radial glial cells (RGCs)

value: mixed genetic backgrounds (CD1, 129/ola and C57BL6)

tag: genotype


title: Rep2_0.5_uM_DHA


title: Rep2_Vehicle


title: Rep2_Lib


title: RGC_E21_1

description: Endogenous microRNA expression

source_name: Retinal ganglion cell, embryonic day 21, biological replicate 1


title: Rep1_Lib


title: Rep1_P3


title: AD9552: SF4.mut


title: RNA_seq_ARID_Control_rep1

value: Thymic DN3 T-cell progenitor


title: K562_input_rep2

city: Bangkok

first: Waritta

last: Sawaengdee

address: 272 Rama VI Road

department: Department of Biochemistry, Faculty of Science

country: Thailand

institute: Mahidol University, Thailand

data_processing:
Basecalls performed using RTA v1.17.21.3
Demultiplexing and alignment using CASAVA package v1.8.2, which uses the aligner ELANDv2
Peak calling performed using MACS1.4, which generated bed files
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from genome-mapped BAM files using deepTools: bamCoverage, bin size=10
Supplementary_files_format_and_content: bed files report MACS peaks

source_name: K562 cell line

growth_protocol: K562 cell line (ATCC) was cultured in RPMI 1640 medium with GlutaMAX™ (Invitrogen) supplemented with 10% fetal bovine serum at 37°C with 5% CO2 and passaged every three days

extract_protocol:
Sheared chromatin was pulled down by customed oligo probes targeting either  lncRNA SRA or LacZ transcript.
Library was prepared using MicroPlex Library Preparation kit (Diagenode, C05010010).
ChIRP-Seq

tag: chirp oligonucletide


title: K562_input_rep3


title: K562_SRA_rep2

value: Customed oligo probes targeting lncRNA SRA


title: AD9549: SF3.WT


title: AD9550: SF3.mut


title: Rep1_10_uM_DHA

source_name: SgRNAs from a pool of T gondii mutants generated using CRISPR, then treated with 10 uM DHA

value: 10 uM DHA


title: K562_input_rep1


title: AD9553: SF5_6.WT


title: K562_SRA_rep1


title: Cobalt treatment_rep3

city: Yangzhou

first: Chengkun

last: Zheng

address: East wenhui road No.48

institute: Yangzhou University

description:
The transcriptome of Streptococcus suis following treatment with cobalt
Co3

data_processing:
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.
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3. (Langmead, B. and S. L. Salzberg, 2012).
HTSeq v0.6.1 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 (Trapnell, Cole, et al., 2010).
Genome_build: Streptococcus suis SC84, complete genome (NC_012924.1).
Supplementary_files_format_and_content: read counts for each gene and each sample.
Supplementary_files_format_and_content: fpkm values for each gene and each sample.

organism: Streptococcus suis

source_name: Co-treated Streptococcus suis

growth_protocol: Streptococcus suis was grown at 37 °C in Tryptic Soy Broth (TSB) supplemented with 10% (vol/vol) newborn bovine serum.  Overnight culture of the strain was diluted 1:100 in fresh medium, and grown to the mid-exponential phase (OD600 = 0.6).

extract_protocol:
RNA was extracted using an Eastep Super Total RNA Isolation Kit (Promega, Shanghai, China), according to the manufacturer’s instructions. RNA integrity and concentration were evaluated by gel electrophoresis and spectrophotometric analysis, respectively.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The culture was divided into 3 aliquots, which were supplemented with 2 mM FeSO4, 0.25 mM CoSO4, or H2O, respectively. Following 15 min treatment, bacterial cells were collected for RNA extration.

value: 0.25 mM cobalt, 15 min

tag: growth phase

value: mid-exponential phase


title: Cobalt treatment_rep2

description:
The transcriptome of Streptococcus suis following treatment with cobalt
Co2


title: K562_LacZ_rep3

value: Customed oligo probes targeting LacZ transcript


title: S2: U251, TMZ-sensitive cell line-2

city: Nanjing

first: Yali

last: Zhou

address: 22 Hankou Road

institute: Nanjing University

description: MiRNA expression profiles from TMZ-sensitive cell line

hyb_protocol: 0.1 µg Cy5-labeled aRNA of the respective sample was fragmented and hybridized onto HmiOA 7.1 using Phalanx OneArray hybridization kit (Phalanx Biotech Group). Hybridization was performed for 17h, rotating at a speed of 10rpm at 65℃ in an Agilent hybridization oven (G2545A). After hybridization, microarrays were washed 1 minute at room temperature with Wash Buffer 1 and 1 minute with 37℃ Wash buffer 2.

scan_protocol: HmiOA 7.1 arrays were scanned by Agilent Microarray Scanner (G2505C) HD_1X color protocol (Dye channel: R ; Scan resolution: 2 um; Tiff: 20-bit; Red PMT gain: 100%; XDR: No) and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by R language (v3.3.0). The probes will filter out control probes and normalized by median scaling method between all samples. Pair-wise comparisons between samples were calculated by Bioconductor limma package and presented by log2 fold change and p-value.

source_name: U251, TMZ-sensitive cell line

label_protocol: 0.5 µg of total RNA was reverse-transcribed and amplified using Onearray Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group). Indirect labeled the aa-UTP by NHS-Cy5 (AAT Bioquest ). Dye incorporation and aRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using Trizol Reagent (Thermo Fisher Scientific) following the manufacture’s instructions. RNA quality was assessed by spectrophotometry (NanoDrop, ND1000) and gel electrophoresis. To be considered as high-quality, the RNA had to have the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧5).

value: brain

tag: cell line

tag: phenotype

value: TMZ-sensitive


title: AD9551: SF4.WT


title: S3: U251, TMZ-sensitive cell line-3


title: K562_LacZ_rep2


title: Ferrous iron treatment_rep3

description:
The transcriptome of Streptococcus suis following treatment with ferrous iron
Fe3

source_name: Fe(II)-treated Streptococcus suis

value: 2 mM ferrous iron, 15 min


title: Cobalt treatment_rep1

description:
The transcriptome of Streptococcus suis following treatment with cobalt
Co1


title: Ferrous iron treatment_rep2

description:
The transcriptome of Streptococcus suis following treatment with ferrous iron
Fe2


title: K562_LacZ_rep1


title: R3: U251, TMZ-resistant cell line-3

description: MiRNA expression profiles from TMZ-resistant cell line

source_name: U251, TMZ-resistant cell line

value: TMZ-resistant


title: S1: U251, TMZ-sensitive cell line-1


title: Ferrous iron treatment_rep1

description:
The transcriptome of Streptococcus suis following treatment with ferrous iron
Fe1


title: K562_SRA_rep3


title: 190_min_Rif

city: Skolkovo

first: Matvei

last: Kolesnik

address: 3 Nobel str

department: Life Sciences

country: Russia

institute: Skoltech

description:
total RNA extracted at 190 min after infection from rifampicine-treated cells
raw_read_counts.tsv
feature_counts_RPKM_normalized.tsv
phage_genes_times_classes_and_relative_transcripts_abundances.tsv

data_processing:
FastQ quality trimming: (Trimmomatic 0.38)
Adaptor trimming (Trimmomatic 0.38)
Read mapping (bowtie2 2.3.4.3 with default parameters)
Gene quantification (featureCounts in Rsubread package 1.34.3). A custom genome annotation was used for the gene quantification.
RPKM values were calculated using edgeR package. The total number of mapped reads in each library were used during normalization.
Genome_build: NC_021806.1
Supplementary_files_format_and_content: Tab-separated files with raw read counts, RPKM normalized transcript abundances, relative transcript abundances (normalized to the max. abundance of each gene across all time points)

organism:
Cellulophaga baltica
Cellulophaga phage phi14:2

source_name: infected cells

growth_protocol: C. baltica culture was grown in liquid MLB medium (12 g sea salt (Sigma), 0.5 g yeast extract, 0.5 g Bacto Peptone, 0.5 g casamino acids, 3 mL glycerol per liter) to OD600 of 0.14 and infected with phi14:2 at a MOI of 10. Immediately after the infection, the culture was split into two flasks; one of the two cultures was supplemented with rifampicin (10 μg/mL). To synchronize the infection, 40 min after the infection, the two cultures were centrifuged (RT, 5000g, 15min) and the pellets were resuspended in the same amount of fresh MLB medium with and without rifampicin correspondingly. At various time points (40, 90, 140, 190 min post-infection), 20-ml aliquots of infected cultures were withdrawn, collected by centrifugation and kept at -20°C.

extract_protocol:
Total RNA was purified from the cell pellets using GeneJET RNA Purification Kit (Thermo Fisher Scientific) following the manufacturer’s instruction (Bacteria Total RNA Purification Protocol) with an additional step: after resuspension in the Lysis Buffer the cells were disrupted by sonication (two rounds of exposure for 10 sec with a 50 sec interval at an amplitude 20% (Q500 Sonicator by Qsonica)). RNA samples (5 μg of each) were treated with RNase-free DNase I (Thermo Fisher Scientific) in the presence of RiboLock (Thermo Fisher Scientific) for 1 h at 37°C and RNA was subsequently purified by GeneJET RNA Purification Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. RNA concentrations were determined with a NanoDrop spectrophotometer; the quality of RNA was ascertained by agarose gel electrophoresis. The overall levels of rRNA did not change throughout the infection, as determined by visual inspection of agarose gel lanes.
cDNA libraries were constructed by the Skoltech Genomics Core Facility as follows. Ribosomal RNA was depleted from the total-RNA samples using Ribo-Zero® rRNA Removal Kit (Illumina), according to the manufacturer's protocol. Subsequently, strand-specific cDNA libraries were generated by NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB) following the manufacturer’s instructions. Eight libraries were created (40 min, 90 min, 140 min, 190 min, 40 min Rif, 90 min Rif, 140 min Rif, 190 min Rif). The single-end strand-specific sequencing with 84 bp length of the reads was performed on an Illumina Nextseq500. In total, 13.1 million to 25.6 million sequence reads were obtained for each cDNA library.

value: Cellulophaga baltica culture infected with phage phi14:2

tag: time point


title: R1: U251, TMZ-resistant cell line-1


title: CD36+ shSRA-3

data_processing:
Sequenced reads were trimmed for adaptor sequence. Read quality was checked for each sample using FastQC.
Sequencing was annotated to the human reference genome GRch38 by Tophat2.
The raw read counts and FPKMs were acquired by HTseq and Cufflinks, respectively
TPMs were then calculated according to their FPKMs.
Differentially expressed genes with at least two fold-change were subsequently identified by using DEseq. Three individual shRNA knockdown samples, which contain different siRNA targets, were used as biological replicates for the analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Excel files include FPKM, TPM, and Raw read count values for each Sample …

source_name: CD36-positive erythroid progenitor cells

growth_protocol:
K562 cell line (ATCC) was cultured in RPMI 1640 medium with GlutaMAX™ (Invitrogen) supplemented with 10% fetal bovine serum at 37°C with 5% CO2 and passaged every three days
CD36-positive human proerythroblasts were derived from bone marrow CD34-positive cells, which were purchased from Stem Cell Technologies (70002.1) and cultured in erythroid differentiation condition as previous described (Wong et al., 2008).
Briefly, the CD34-positive cells at 104 cells/ml were grown in the serum-free erythroid expansion medium containing Alpha minimum essential medium (AMEM; Mediatech) and 20% BIT9500 (Stem Cell Technologies) to achieve bovine serum albumin, recombinant human insulin and iron-saturated human transferrin at 10 mg/ml, 10 µg/ml and 200 µg/ml, respectively. In addition, 900 ng/ml ferrous sulfate (Sigma), 90 ng/ml ferric nitrate (Sigma), 1 µM hydrocortisone (Sigma), 100 ng/ml of recombinant human stem cell factor (SCF; Stem Cell Technologies), 5 ng/ml of recombinant human interleukin-3 (IL-3; R&D Systems) and 3 IU/ml of recombinant human EPO were also included. Fresh medium was added into the culture to maintain cells at 2 X 106 cells/ml. The cells were cultured for 7 days to obtain CD36-positive cells.

extract_protocol:
Total RNA was extracted from the sorted cells and purified using QIAzol Lysis Reagent and miRNeasy Micro Kit (Qiagen).
The RNA samples for sequencing were prepared according to Smart-seq2 method (Picelli et al., 2014) with some modifications as previous described (Hu et al., 2018). The RNA-seq libraries were prepared with an End-It DNA End-repair Kit (Epicenter #ER81050) and a Multiplexing Sample Preparation Oligonucleotide Kit (Illumina) and submitted for single-end sequencing on illumina Hiseq2500 as previous described (Hu et al., 2013).

treatment_protocol: Lentiviral particles were produced by co-transfecting LentiX-293T cells (Clontech) with a packaging vector (psPAX2), an envelope vector (pLP/VSVG) and an shRNA plasmid (shLuc, shSRA-1, shSRA-2, or shSRA-3) using Lipofectamine 2000 (Invitrogen) as previous described (Kidder et al., 2017). Twenty four hour after the transfection, the medium was changed to the target cell medium. Then the medium containing lentiviral particles were collected and filtered through 0.22 µM filter at 48 hour post-transfection. Transduction was performed by adding the medium containing lentiviral particles with 10 µg/ml polybrene into either K562 or CD36-positive proerythroblasts. The cells were then centrifuged at 1,000 g at room temperature for 2 hours and incubated at 37°C with 5% CO2 overnight before changing medium. Expression of GFP was examined under fluorescent microscope to validate transduction efficiency at 48 hour post-transduction. The GFP-positive cells were then sorted by FACS at 96 hour post-transduction and maintained in the presence of 0.5 µg/ml puromycin for further analysis.

value: SRA knockdown

value: CD36-positive proerythroblasts


title: CD36+ shSRA-2


title: SpLG: late gastrula

city: Providence

first: Gary

last: Wessel

state: RI

address: 185 Meeting St

department: Molecular Biology, Cell Biology & Biochemistry

institute: Brown University

data_processing:
The Cell Ranger Single Cell Software Suite 3.0.2 was used to perform single cells demultiplexing and UMI counting.The custom transcriptome reference was generated from assembly Spur_4.2 using CellRanger. Cells that have at least 400 or at most 7,000 genes detected were included in the downstream analysis using Seurat 3.1.4. The union of the top 2,000 highest dispersion genes from the compared datasets were selected for the alignment. T‐SNE projection and clustering analysis (dims = 1:20 and resolution = 0.5) were performed using Seurat. Markers were found using FindConservedMarkers and FindMarkers functions.
Aggregate technical replicates of hatched blastula (HB), mesenchyme blastula (MB), early gastrula (EG) and late gastrula (LG) using cellanger aggr.
Genome_build: Spur_4.2
Supplementary_files_format_and_content: tab-delimited text files include matrices that contain UMI-corrected counts for each cell and integrated seurat object

organism: Strongylocentrotus purpuratus

source_name: single cell mRNA

extract_protocol: The single‐cell RNA‐seq protocol was performed using the ChromiumTM Single Cell 3′ reagent kit v3 chemistry and cells were loaded on a 10x Chromium Controller (10× Genomics, Pleasanton, CA). Libraries were sequenced on Illumina HiSeq with the  configuration of 2x150 bp paired-end runs.

value: late gastrula


title: SpMB: mesenchyme blastula stage

value: mesenchyme blastula stage


title: SpEG: early gastrula

value: early gastrula


title: 90_min_Rif

description:
total RNA extracted at 90 min after infection from rifampicine-treated cells
raw_read_counts.tsv
feature_counts_RPKM_normalized.tsv
phage_genes_times_classes_and_relative_transcripts_abundances.tsv


title: ID8-unstimulated, biological rep1

source_name: ID8 ovarian cancer cell line cultured in vitro

value: ovarian cancer cell line


title: CD36+ shSRA-1


title: CD36+ shLuc

value: wild-type


title: 40_min_Rif

description:
total RNA extracted at 40 min after infection from rifampicine-treated cells
raw_read_counts.tsv
feature_counts_RPKM_normalized.tsv
phage_genes_times_classes_and_relative_transcripts_abundances.tsv


title: R2: U251, TMZ-resistant cell line-2


title: 140_min

description:
total RNA extracted at 140 min after infection
raw_read_counts.tsv
feature_counts_RPKM_normalized.tsv
phage_genes_times_classes_and_relative_transcripts_abundances.tsv

value: 140 min after infection


title: K562 shSRA-2


title: K562 shSRA-3


title: Sp3: morula stage

value: morula stage


title: 140_min_Rif

description:
total RNA extracted at 140 min after infection from rifampicine-treated cells
raw_read_counts.tsv
feature_counts_RPKM_normalized.tsv
phage_genes_times_classes_and_relative_transcripts_abundances.tsv


title: 90_min

description:
total RNA extracted at 90 min after infection
raw_read_counts.tsv
feature_counts_RPKM_normalized.tsv
phage_genes_times_classes_and_relative_transcripts_abundances.tsv

value: 90 min after infection


title: Sp2: 64-cell stage

value: 64-cell stage


title: SpEB: early blastula stage

value: early blastula stage


title: K562 shSRA-1


title: K562 shLuc


title: 40_min

description:
total RNA extracted at 40 min after infection
raw_read_counts.tsv
feature_counts_RPKM_normalized.tsv
phage_genes_times_classes_and_relative_transcripts_abundances.tsv

value: 40 min after infection


title: Sp1: 8-cell stage

value: 8-cell stage


title: SpHB: hatched blastula stage

value: hatched blastula stage


title: 190_min

description:
total RNA extracted at 190 min after infection
raw_read_counts.tsv
feature_counts_RPKM_normalized.tsv
phage_genes_times_classes_and_relative_transcripts_abundances.tsv

value: 190 min after infection


title: pLXSN (E6/E7) HPV75 duplicate1

source_name: Human Foreskin Keratinocytes (HFK)

tag: hpv

value: Betapapillomavirus 3


title: TuraR-I3220_RTS-ON_e

status: Public on Jul 03 2020

city: Marseille

first: Karel

last: Naiman

address: BD Lei Roure

institute: CRCM

data_processing:
The reads were mapped using bowtie2.
Polymerase usage was determined by the tools published and described in detail in Daigaku et al. 2015 and Keszthelyi et al. 2015.
Genome_build: Schizosaccharomyces pombe reference sequence (http://www.pombase.org/downloads/genome-datasets) with inserted replication fork barrier RTS1, 10xrDNA barrier as written in the paper.
Supplementary_files_format_and_content: CSV files contain read counts corresponding to incorporated rNTPs sorted into 300bp bins on each chromosome. They are in two files for forward and reverse strands separately.

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe

growth_protocol: Cells were grown at 30C in YE media to log phase. For ‘wt’ datasets two strains were used, both strains containing rnh201 deletion (or rnh201-RED mutant deficient in rNTP recognition) together with either polymerase δ (cdc6-L591G or cdc6-L591M) or polymerase ε (cdc20-M630F) mutations. These strains incorporate more rNTPs on the strands synthetized by the mutant polymerase. These sites can be mapped by Pu-seq.

extract_protocol:
DNA was prepared using the QIAGEN 100/G Genomic-tip. The isolated DNA was then subjected to alkali treatment (0.3 M NaOH, 2h 55°C) which digested the DNA at the positions of rNTP incorporation and also separated the double strands. The resulting ssDNA fragments were size selected on agarose gel (fragments between 300-500bp were isolated).
Polymerase usage sequence (Pu-seq) technique was performed as previously described (Daigaku et al. 2015 and Keszthelyi et al. 2015) with minor modifications: size selection was performed using Blue Pippin (Sage Science). In some instances we used rnh201-RED instead of rnh201::kan (see results).


title: 10xrDNA_e

value: cdc20-M630F ChI-3220:10xrDNA rnh201:kan rtf1::nat ade6-704 leu1-32 ura4-D18


title: TuraR-II8535_RTS-ON_d

value: h- ChII-8535:TuraR rnh201::kan cdc6-L591G ade6-704 leu1-32 ura4-d18


title: 10xrDNA_d


title: TuraR-I5234_RTS-ON_d

value: h- ChI-5234:TuraR rnh201::kan cdc6-L591G ade6-704 leu1-32 ura4-d18


title: TuraR-II8535_RTS-ON_e

value: h- ChII-8535:TuraR rnh201::kan cdc20-M630F ade6-704 leu1-32 ura4-d18


title: TuraR-I5234_RTS-ON_e


title: TuraR-I3220_RTS-ON_d


title: TuraR-47401_RTS-ON_e

value: h- rtf1::nat ChI-4740:TuraR rnh201::kan cdc20-M630F ade6-704 leu1-32 ura4-d18


title: cartilage endplate_normal_3

city: Nanchang

first: Jinghong

last: Yuan

state: Jiangxi

address: No.1 Minde Road

institute: The Secondly Affiliated Hospital of Nanchang University

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

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

data_processing: Data were extracted with Feature Extraction software 12.0 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: cartilage endplate_normal_3

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free Dnase.

treatment_protocol: All specimens were obtained from patients who received anterior cervical discectomy and fusion. Cartilage endplate in cervical disc were collected , about 1×1×0.2cm3 size, and preserved in 600μl RNA Stabilization Solution (Cat#AM7020, Ambion, Austin, TX, US)under -80℃.

value: cartilage endplate in cervical disc

tag: gender

value: female

tag: diagnosis

value: healthy

tag: age


title: TuraR-47401_RTS-ON_d

value: h- rtf1::nat ChI-4740:TuraR rnh201::kan cdc6-L591G ade6-704 leu1-32 ura4-d18


title: cartilage endplate_degenerate_3

source_name: cartilage endplate_degenerate_3

value: male

value: cervical spondylosis myelopathy


title: tandem_RTS_ON_e

value: h- cdc20-M630F ChII-8535:tandemRTS1-ura4-10xrDNA rnh201::kan RTS1natural::Phleo smt0 ade6-704 leu1-32 ura4-D18


title: rnh_RTS-ON_a

value: h- ChII-8535:Rura-10xrDNA pol1-L850F rnh201::kan RTS1natural::Phleo ade6-704 leu1-32 ura4-D18


title: cartilage endplate_normal_1

source_name: cartilage endplate_normal_1


title: cartilage endplate_normal_2

source_name: cartilage endplate_normal_2


title: rnh_RTF_OFF_e

value: h- cdc20-M630F Rura::ChII-853542 RTS1natural::Phleo rnh201::kan rtf1::nat ade6-704 leu1-32 ura4-D18


title: rnh_RTF_ON_d

value: h- cdc6-L591G ChII-8535:Rura-10xrDNA RTS1natural::Phleo, rnh201::kan, ade6-704 leu1-32 ura4-D18


title: cartilage endplate_degenerate_2

source_name: cartilage endplate_degenerate_2


title: rnh_RTF_OFF_d

value: h- cdc6-L591G Rura::ChII-853542 RTS1natural::Phleo rnh201::kan rtf1::nat ade6-704 leu1-32 ura4-D18


title: rnh_RTS-OFF_a

value: h- ChII-8535:Rura-10xrDNA pol1-L850F rnh201::kan rtf1::nat RTS1natural::Phleo ade6-704 leu1-32 ura4-D18


title: rnh_ku70_RTS_OFF_e

value: h- cdc20-M630F Ku70:leu2 ChII-8535:Rura-10xrDNA RTS1natural::Phleo smt0x rnh201::kan rtf1::nat ade6-704 leu1-32 ura4d18


title: cartilage endplate_degenerate_1

source_name: cartilage endplate_degenerate_1


title: adhRtf-e

value: h- ChII-8535:Rura-10xrDNA, cdc20-M630F, RTS1natural::Phleo, rnh201:kan, NAT:adh1-rtf1, ade6-704, leu1-32, ura4-D18


title: rnh_ku70_RTS_ON_e

value: h- cdc20-M630F Ku70:leu2 ChII-8535:Rura-10xrDNA RTS1natural::Phleo smt0x rnh201::kan ade6-704 leu1-32 ura4d18


title: rnh_RTF_ON_e

value: h- cdc20-M630F ChII-8535:Rura-10xrDNA RTS1natural::Phleo rnh201::kan ade6-704 leu1-32 ura4-D18


title: rnh_ku70_RTS_ON_d

value: h- cdc6-L591G Ku70:leu2 ChII-8535:Rura-10xrDNA RTS1natural::Phleo smt0x rnh201::kan ade6-704 leu1-32 ura4d18


title: adhRtf-d

value: h- ChII-8535:Rura-10xrDNA, cdc6-L591G, RTS1natural::Phleo, rnh201:kan, NAT:adh1-rtf1, ade6-704, leu1-32, ura4-D18


title: RED-RTS-OFF-e

value: h- cdc20-M630F ChII-8535:Rura-10xrDNA rnh201-RED:kan RTS1natural::Phleo, rtf1:nat smt0 ade6-704 leu1-32 ura4-D18


title: RED-RTS-ON-e

value: h- cdc20-M630F ChII-8535:Rura-10xrDNA rnh201-RED:kan RTS1natural::Phleo smt0 ade6-704 leu1-32 ura4-D18


title: RED-RTS-ON-d

value: h- cdc6-L591G ChII-8535:Rura-10xrDNA rnh201-RED:kan RTS1natural::Phleo, smt0 ade6-704 leu1-32 ura4-D18


title: rnh_ku70_RTS_OFF_d

value: h- cdc6-L591G Ku70:leu2 ChII-8535:Rura-10xrDNA RTS1natural::Phleo smt0x rnh201::kan rtf1::nat ade6-704 leu1-32 ura4d18


title: RED-RTS-OFF-a

value: h- ChII-8535:Rura-10xrDNA pol1-L850F rnh201-RED:kan rtf1::nat RTS1natural::Phleo ade6-704 leu1-32 ura4-D18


title: RED-RTS_ON-a

value: h- ChII-8535:Rura-10xrDNA pol1-L850F rnh201-RED:kan RTS1natural::Phleo, ade6-704 leu1-32 ura4-D18


title: RED-Ku-RTS_ON-e

value: h- cdc20-M630F ChII-8535:Rura-10xrDNA rnh201-RED:kan Ku70::hyg RTS1natural::Phleo smt0 ade6-704 leu1-32 ura4-D18


title: RED-Ku-RTS_OFF-e

value: h- cdc20-M630F ChII-8535:Rura-10xrDNA rnh201-RED:kan Ku70::hyg RTS1natural::Phleo smt0 rtf1::nat ade6-704 leu1-32 ura4-D18


title: RED-Ku-RTS_ON-d

value: h- cdc6-L591G ChII-8535:Rura-10xrDNA rnh201-RED:kan Ku70::hyg RTS1natural::Phleo smt0 ade6-704 leu1-32 ura4-D18


title: T_3

city: beijing

first: yuyuan

last: li

address: 1 Beichen West Road, Chaoyang District

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw datas of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas were obtained. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Subsequently, a clean read number with a sequence length greater than 18 nt was calculated and a unique reading was obtained by deleting the exact same sequence in each sample (OmicShare tools) (www.omicshare.com/tools). MiRdeep2 mapped the selected clean reads to the gallus reference genome (ftp://ftp.ensembl.org/pub/release-81/fasta/gallus_gallus/dna/) in order to avoid errors, such as substitutions, insertions, deletions, etc. Being generated during the sequencing process, the mature miRNA and miRNA precursor sequences of gallus in miRbase (http://www.mirbase.org/) were then mapped to obtain small RNA annotations. The special hairpin structure of the miRNA precursor was used to predict novel miRNAs using the mireap software (https://sourceforge.net/projects/mireap/). The reads of each known and novel miRNAs were normalized using transcripts per kilobase million (TPM). Normalized expression = (mapped readcount × 1,000,000)/libsize (libsize: total miRNA readcounts), and the significance was determined by normalizing the raw reads and calculating the p-value while using DESeq (http://bioconductor.org/packages/release/bioc/html/DESeq.html), miRNA with |fold change| > 1 and p-value < 0.05 were identified as DEmiRNAs.

organism: Gallus gallus

source_name: spinal cord

extract_protocol:
Spinal cords were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Beijing white

value: Adult laying hens

value: 10 month

tag: disease state

value: OPIDN

value: spinal cord


title: far_RTS_d

value: h- cdc20-M630F ChII-8535:Rura second RTS barrier RTS1natural::Phleo rnh201-RED:kanR nat:adh1-rtf1 ade6-704 leu1-32 ura4-D18


title: T_2


title: T_1


title: C_3

value: healthy control


title: C_2


title: C_1


title: far_RTS_e

value: h- cdc6-L591M ChII-8535:Rura second RTS barrier RTS1natural::Phleo rnh201-RED:kanR nat:adh1-rtf1 ade6-704 leu1-32 ura4-D18


title: Chip-seq Jurkat/LEDGINS H3K36me3 rep1

first: Guillaume

last: Filion

address: Dr. Aiguader 88

department: GRSCC

institute: CRG

description:
jurlf_h3k36me3.01
GC091294

data_processing:
Map samples to hg38 using bwa-mem with default parameters
Discretize chip-seq signal with zerone (github.com/nanakiksc/zerone) setting the enrichment probability threshold at 0.99
Genome_build: hg38
Supplementary_files_format_and_content: BED format: Last column indicates the enrichment probability

source_name: Jurkat cell line: Human T lymphocyte

growth_protocol: Jurkat and SupT1 human T cells line were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum and 0,1% Gentamicin (1000x) at 37℃ under a 95% air/5% CO2 atmosphere. Jurkat and SupT1 cells were passaged twice a week with 1 to 6 dilution.

extract_protocol: Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (Merck Millipore).

treatment_protocol: Cells were treated in the presence of varying concentrations of LEDGIN CX014442: None or 31.25 µM.

value: Jurkat

value: T lymphocyte

tag: pre-treatment

tag: antibody

value: H3K36me3 (ab9050, Abcam)


title: Chip-seq Jurkat/LEDGINS H3K36me3 rep2

description:
jurlf_h3k36me3.01
GC091295

tag: cell type


title: Chip-seq Jurkat/WT input


title: Chip-seq Jurkat/WT H3K36me3 rep2

description:
jurkat_h3k36me3.01
GC091290


title: Chip-seq Jurkat/LEDGINS H3K27Ac rep1

description:
jurlf_h3k27ac.01
GC091296

value: H3K27ac (ab4729, Abcam).


title: Chip-seq Jurkat/WT H3K27Ac rep1

description:
jurkat_h3k27ac.01
GC091291


title: Chip-seq Jurkat/LEDGINS H3K27Ac rep2

description:
jurlf_h3k27ac.01
GC091297


title: Chip-seq SupT1/WT H3K27Ac rep2

description:
supt1_h3k27ac.01
GC091287

source_name: SupT1 cell line: Human T cell lymphoblastic Lymphoma

value: T lymphoblast


title: RED-RTS-OFF-d

tag: strain

value: h- cdc6-L591G ChII-8535:Rura-10xrDNA rnh201-RED:kan RTS1natural::Phleo, rtf1::nat smt0 ade6-704 leu1-32 ura4-D18


title: Chip-seq SupT1/WT H3K27Ac rep1

description:
supt1_h3k27ac.01
GC091286


title: Chip-seq SupT1/WT H3K36me3 rep2

description:
supt1_h3k36me3.01
GC091285


title: Chip-seq SupT1/WT H3K36me3 rep1

description:
supt1_h3k36me3.01
GC091284


title: RED-Ku-RTS_OFF-d

value: h- cdc6-L591G ChII-8535:Rura-10xrDNA rnh201-RED:kan Ku70::hyg RTS1natural::Phleo smt0 rtf1::nat ade6-704 leu1-32 ura4-D18


title: Chip-seq Jurkat/LEDGINS input


title: RNAseq SupT1 LEDGINS 31.25uM rep3

data_processing:
Map RNAseq reads to human cDNA GRCh37.75 using kallisto in quant mode with options –bias and mean 300, standard deviation 100.
Extracted TPM values from results
Genome_build: Human cDNA GRCh37.75
Supplementary_files_format_and_content: rnaseq*.tpm files contain Gene ID, expression in TPM, gene type, gene name, position in reference genome

extract_protocol: RNA extraction: Aurum Total RNA Mini kit #732-6820;RNA library: Lexogen Quant Seq 3' mRNA-Seq library prep kit (catalog no. #O15)


title: RNAseq SupT1 LEDGINS 31.25uM rep2


title: RNAseq SupT1 LEDGINS 31.25uM rep1


title: Chip-seq Jurkat/WT H3K27Ac rep2

description:
jurkat_h3k27ac.01
GC091292


title: RNAseq SupT1 LEDGINS 31.25uM rep4


title: RNAseq SupT1 WT rep3


title: RNAseq SupT1 WT rep4


title: Chip-seq Jurkat/WT H3K36me3 rep1

description:
jurkat_h3k36me3.01
GC091289


title: RNAseq Jurkat WT rep1


title: RNAseq Jurkat WT rep4


title: RNAseq SupT1 WT rep1


title: RNAseq Jurkat WT rep3


title: B-HIVE_3 iPCR Jurkat WT 31.25uM

description:
genomic DNA
S311
ledgins3_integration_features.txt
ledgins3_expression.txt

data_processing:
Sequencing lane demultiplexing: Sequences were demultiplexed using bcl2fastq. In case the index was inside the sequenced amplicon, demultiplexing was carried out with custom scripts using the provided PCR indices.
Barcode extraction: Barcodes were extracted from the forward reads. The barcode sequences in the construct are flanked by the Illumina adaptor and the T7 promoter sequence (TATAGTGAGTCGTATTAAAA). The promoter sequence was identified using Seeq (github.com/ezorita/seeq) allowing up to 2 mismatches.
Barcode clustering: Barcodes were clustered by sequence similarity using starcode and allowing up to 1 mismatch (github.com/gui11aume/starcode).
Alignment: Reverse reads were aligned on GRCh37/h19 using BWA-mem with default parameters.
Filtering on alignment quality: Only SAM mapping qualities greater or equal than 20 were used in the analysis.
Filtering of recombinant molecules: A barcode was associated to a mapped locus based on their co-ocurrence in paired-end reads. Associations between a barcode and a mapped locus reported by less than 10 paired-end reads were discarded. The remaining associations were considered reliable if both the barcode and the mapped locus were found together at least 90% of the time.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: ledgins1_integration_features.txt: B-HIVE1 Integration sites
Supplementary_files_format_and_content: ledgins2_integration_expression.txt: B-HIVE2 Integration sites and expression levels
Supplementary_files_format_and_content: ledgins3_expression.txt: B-HIVE3 Expression levels
Supplementary_files_format_and_content: ledgins3_integration_features.txt: B-HIVE3 integration sites

extract_protocol:
Genomic DNA and total RNA from the same infected cell pool were extracted by the AllPrep DNA/RNA Mini Kit. Total RNA was further proceeded to purify mRNA by Oligotex mRNA Mini Kit.
Libraries used for mapping HIV integrations were prepared by inverse PCR. Briefly, 3 µg DNA were harvested and digested by the restriction enzyme BplI. Fragments were blunt-end self-ligated in the total volume 1 mL at 16℃ overnight. The pellet was dissolved in 84 µL distilled water for plasmid-safe DNase treatment. DNase-treated samples were cleaned up by the QIAquick PCR purification kit. Samples were eluted in 20 µL EB buffer. 8 µL eluted product were used for two rounds of nested PCR. PCR products with different indexes were pooled together in the final concentration of 4 nM for sequencing 50 bp paired end on a Illumina NextSeq sequencer. RNA and DNA libraries were prepared by RT-PCR and regular PCR, respectively, with the same primers. RNA and DNA libraries were sequenced 50 bp single read by on a Illumina NextSeq sequencer.

treatment_protocol: Cells were transduced with barcoded HIV in the presence of varying concentrations of LEDGIN CX014442: 6.25, 15.62 or 31.25 µM.

tag: start number of the cells

value: 10 Million

tag: facs sorting


title: RNAseq Jurkat WT rep2


title: RNAseq Jurkat LEDGINS 31.25uM rep1


title: RNAseq Jurkat LEDGINS 31.25uM rep3


title: RNAseq Jurkat LEDGINS 31.25uM rep4


title: RNAseq SupT1 WT rep2


title: B-HIVE_3 iPCR Jurkat WT 15.62uM

description:
genomic DNA
S309
ledgins3_integration_features.txt
ledgins3_expression.txt


title: B-HIVE_2 iPCR Jurkat WT 31.25uM

description:
genomic DNA
S303
ledgins2_integration_expression.txt


title: B-HIVE_3 iPCR Jurkat WT 0uM

description:
genomic DNA
S305
ledgins3_integration_features.txt
ledgins3_expression.txt


title: B-HIVE_3 iPCR Jurkat WT 6.25uM

description:
genomic DNA
S307
ledgins3_integration_features.txt
ledgins3_expression.txt

value: 6.25 uM LEDGIN CX014442


title: B-HIVE_2 iPCR SupT1 WT 15.62uM

description:
genomic DNA
S298
ledgins2_integration_expression.txt


title: B-HIVE_2 iPCR Jurkat WT 15.62uM

description:
genomic DNA
S302
ledgins2_integration_expression.txt


title: B-HIVE_2 iPCR Jurkat WT 6.25uM

description:
genomic DNA
S301
ledgins2_integration_expression.txt


title: B-HIVE_2 iPCR Jurkat WT 0uM

description:
genomic DNA
S300
ledgins2_integration_expression.txt


title: B-HIVE_2 iPCR SupT1 WT 0uM

description:
genomic DNA
S296
ledgins2_integration_expression.txt


title: B-HIVE_1 iPCR SupT1 LEDGF/p75 KD 0uM

description:
genomic DNA
S181
ledgins1_integration_features.txt


title: B-HIVE_2 iPCR SupT1 WT 6.25uM

description:
genomic DNA
S297
ledgins2_integration_expression.txt


title: B-HIVE_1 iPCR SupT1 WT 31.25uM

description:
genomic DNA
S180
ledgins1_integration_features.txt


title: B-HIVE_1 iPCR SupT1 WT 6.25uM

description:
genomic DNA
S179
ledgins1_integration_features.txt


title: B-HIVE_1 iPCR SupT1 WT 0uM

description:
genomic DNA
S178
ledgins1_integration_features.txt


title: B-HIVE_1 iPCR SupT1 WT 31.25uM GFP-

description:
genomic DNA
S173
ledgins1_integration_features.txt

value: GFP-


title: B-HIVE_1 iPCR SupT1 WT 31.25uM GFP+

description:
genomic DNA
S172
ledgins1_integration_features.txt

value: GFP+


title: B-HIVE_1 iPCR SupT1 WT 6.25uM GFP-

description:
genomic DNA
S171
ledgins1_integration_features.txt


title: B-HIVE_1 iPCR SupT1 WT 0uM GFP+

description:
genomic DNA
S168
ledgins1_integration_features.txt


title: B-HIVE_1 iPCR SupT1 WT 6.25uM GFP+

description:
genomic DNA
S170
ledgins1_integration_features.txt


title: B-HIVE_1 iPCR SupT1 WT 0uM GFP-

description:
genomic DNA
S169
ledgins1_integration_features.txt


title: H_MO-MG8_R3-1202940

city: St Louis

first: Winnie

middle: W

last: Pong

state: MO

address: 660 S. Euclid Avenue

department: Department of Neurology

institute: Washington University School of Medicine

description: JPA R3 biological replicate 2

data_processing:
Basecalls performed using Illumina Real-Time Analysis (RTA) version 1.13.48.0 (1.13.56.0 for MiSeq, 1.15.19.5 for flow cell D1CGMACXX) followed by demultiplexing of the index sequence using CASAVA 1.8.2.
SPIA adapter sequence aligned and trimmed from raw sequence reads using FAR 2.17 with command line parameters : --adapter CTTTGTGTTTGA --trim-end left --adaptive-overlap yes --format fastq --write-lengthdist yes --nr-threads 4 --min-overlap 7 --max-uncalled 150 --min-readlength 25
Aligned with TopHat 2.0.4, Bowtie 2.0.0-beta7 and Ensembl 67 annotation (-G param)
FPKM calculated per sample with Cufflinks 2.0.2  and Ensembl 67 annotation with -G param
Genome_build: hg19
Supplementary_files_format_and_content: JPA_gene_fpkm.tsv a tab delimited file with columns for gene ID and the normalized expression values per sample name

source_name: FACS population R3

growth_protocol: not applicable

extract_protocol:
Total RNA was isolated from snap-frozen flow sorted cell pellets using TRIzol-chloroform extraction. RNA was resuspended in 10µl Ambion Nuclease-free water (Life Technologies) and DNAse treated (Ambion TURBO DNA-free Kit)
For cDNA synthesis, we added 5µl of isolated RNA into the Ovation® RNA-Seq method.  500ng cDNA was fragmented using covaris shearing and processed for Illumina library construction with the Illumina paired-end LT indexing protocol as previously published (Mardis et al., 2009; Govindan et al., 2012). Each library was sequenced on the Illumina HiSeq, generating between 15-22Mbp per lane.
RNA-Seq (300-500bp size fractionation): cDNA samples were constructed into Illumina libraries according to the manufacturer’s protocol (Illumina Inc, San Diego, CA) with the following modifications:  1) DNA was fragmented using Covaris S2 DNA Sonicitor using the following condtions: Duty Cycle: 5, Intensity: 4, Cycles/Burst: 200, Time: 90sec (Covaris, Inc. Woburn, MA).  Fragment sizes ranged between 100 and 500bp.  2) Illumina adapter-ligated DNA was amplified in a single 50ml PCR for five cycles.  3) Solid Phase Reversible Immobilization (SPRI) bead cleanup was used to purify the PCR and select for 300-500bp fragments.   We added 0.8 volumes of the AmpureXP solution (preformulated with polyethylene glycol and sodium chloride) to size select DNA molecules greater than 300 bp.  The size-fractioned cDNA was washed three times with 750 µl of 70% ethanol, the beads were dried, and the cDNA library was eluted off the beads by adding 20µl 10 mM Tris-HCl (pH 8.0).  The size-fractioned libraries were assayed using the Agilent BioAnalyzer High Sensitivity DNA chips.

treatment_protocol: Tissue was dissociated and cells were flow sorted.

tag: tissue

value: tumor


title: H_MO-MG8_R4-1202941

description: JPA R4 biological replicate 2

source_name: FACS population R4


title: H_MO-MG6_R4-1202939

description: JPA R4 biological replicate 1


title: H_MO-MG6_R3-1202938

description: JPA R3 biological replicate 1


title: Chip-seq SupT1/WT input


title: tandem_RTS_ON_d

tag: genotype

value: h- cdc6-L591G ChII-8535:tandemRTS1-ura4-10xrDNA rnh201:kan RTS1natural::Phleo smt0 ade6-704 leu1-32 ura4-D18


title: PD-TALL26_XENO26

city: Padua

first: Erich

last: Piovan

address: via Gattamelata 64

department: Dep. Surgery, Oncology and Gastroenterology

institute: University of Padua

hyb_protocol: 600ng cy3-labeled, linearly amplified cRNA (specific activity > 6 pmol cy3 per Âµg cRNA) was hybridised with the Gene Expression Hybridization Kit (Cat nr. 5188-5242, Agilent Technologies) to the SurePrint G3 Human Gene Expression Microarray G4851A (design ID 028004). After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with GE Wash Buffer 2 (Agilent) at room temperature and 1 minute with GE Wash Buffer 3 (Agilent) at 37Â°C.

scan_protocol: Slides were scanned on the Agilent G2564CA Microarray Scanner. Data was extracted using Agilent Feature Extraction Software.

data_processing: The data were normalized using R software [www.r-ptoject.org] with BioConductor package [www.bioconductor.org] using limma. normalizeVSN function was used to normalize samples from GPL13607 Platform and removed duplicated probes by limma function avereps.

source_name: T-ALL xenografts in NOD/SCID mouse

label_protocol: RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit, One Color (5190-2305; Agilent Technologies, Santa Clara, CA, USA)

growth_protocol: Frozen Leukemia cells (from xenografted mice) were injected into NOD/SCID mice. When mice became sick, cells from the spleens were harvested and processed for RNA extraction.

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

treatment_protocol: No treatment was performed on cells which were subjected to RNA extraction.

tag: subject status

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_26

value: Spleen

tag: gant-61 sensitivity


title: PD-TALL9_XENO9

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_9


title: PD-TALL20_XENO20

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_20


title: PD-TALL18_XENO18

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_18


title: PD-TALL36_XENO36

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_36


title: PD-TALL22_XENO22

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_22


title: SS2_17_154_O20_R1

city: Uppsala

first: Åsa

last: Wallén-Mackenzie

address: Norbyvägen 18A

institute: Uppsala University

data_processing:
All reads were aligned to the mouse (mm10) genome using STAR (Dobin et al., 29, 2013)
Non-uniquely mapped reads were removed
The expression values of merged RefSeq and Ensemble gene annotations were computed as described in Rämsköld et al. (PLoS Comput. Biol., 5,2013) , using uniquely aligned reads and correcting for the uniquely alignable positions using MULTo (Storvall et al. PLoS One, 8, 2013)
Genome_build: mm10
Supplementary_files_format_and_content: gene expression values (tab-delimited text)

molecule: polyA RNA

source_name: cDNA - brain / subthalamic nucleus

extract_protocol:
Snap frozen tissue was dissociated with lysis buffer+0.32Msucrose in 1ml dounce homogenizers. Homogenate was added over a 1.8Msucrose layer and centrifuged 2 h 20 min at 30,000 × g (Beckman J-25 centrifuge with a J13.1 rotor).  cDNA was generated from FACS sorted single nuclei using Smart-seq2 protocol (Picelli et al. Nature Methods 2013).  ERCC spike-in RNA was added to the lysis buffer
Nextera XT DNA sample preparation index kit, 384 indices (Illumina)

tag: mouse strain

value: postnatal day 28

tag: spike-in

value: ERCC


title: SS2_17_154_O1_R1


title: SS2_17_154_O21_R1


title: SS2_17_154_O23_R1


title: SS2_17_154_O2_R1


title: PD-TALL10_XENO10

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_10


title: PD-TALL16_XENO16

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_16


title: PD-TALL28_XENO28

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_28


title: PD-TALL30_XENO30

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_30


title: PD-TALL21_XENO21

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_21


title: B-HIVE_2 iPCR SupT1 WT 31.25uM

description:
genomic DNA
S299
ledgins2_integration_expression.txt

tag: cell line

value: T lymphoblast

value: 10 Million


title: PD-TALL31_XENO31

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_31


title: PD-TALL12_XENO12

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_12


title: PD-TALL40_XENO40

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_40

value: Spleen


title: SS2_17_154_O19_R1


title: PD-TALL27_XENO27

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_27


title: SS2_17_154_O24_R1


title: PD-TALL11_XENO11

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_11


title: SS2_17_154_O22_R1


title: PD-TALL13_XENO13

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_13


title: SS2_17_154_O18_R1


title: PD-TALL7_XENO7

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_7


title: SS2_17_154_O17_R1

value: postnatal day 28


title: SS2_17_154_O15_R1

value: ERCC


title: SS2_17_154_O13_R1


title: SS2_17_154_O14_R1


title: SS2_17_154_O16_R1


title: PD-TALL25_XENO25

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_25


title: SS2_17_154_N8_R1


title: SS2_17_154_N2_R1


title: SS2_17_154_N4_R1


title: SS2_17_154_O11_R1


title: SS2_17_154_N7_R1


title: SS2_17_154_N3_R1


title: SS2_17_154_O10_R1


title: SS2_17_154_N9_R1


title: SS2_17_154_N5_R1


title: SS2_17_154_N19_R1


title: SS2_17_154_N21_R1


title: SS2_17_154_N23_R1


title: SS2_17_154_N24_R1


title: SS2_17_154_N17_R1


title: SS2_17_154_N18_R1


title: SS2_17_154_N6_R1


title: SS2_17_154_N22_R1


title: SS2_17_154_N14_R1


title: SS2_17_154_N15_R1


title: SS2_17_154_N10_R1


title: SS2_17_154_N11_R1


title: SS2_17_154_N12_R1


title: SS2_17_154_M9_R1


title: SS2_17_154_M7_R1


title: SS2_17_154_M4_R1


title: SS2_17_154_M6_R1


title: SS2_17_154_M24_R1


title: SS2_17_154_M3_R1


title: SS2_17_154_N20_R1


title: SS2_17_154_N1_R1


title: SS2_17_154_M5_R1


title: SS2_17_154_M23_R1


title: PD-TALL43_XENO43

value: pediatric T-cell Acute Lymphoblastic Leukemia (T-ALL) patient_43


title: SS2_17_154_N13_R1


title: SS2_17_154_M16_R1


title: SS2_17_154_M14_R1


title: SS2_17_154_M20_R1


title: SS2_17_154_M17_R1


title: SS2_17_154_M18_R1


title: SS2_17_154_M19_R1


title: SS2_17_154_M21_R1


title: SS2_17_154_M15_R1


title: SS2_17_154_M1_R1


title: SS2_17_154_M12_R1


title: SS2_17_154_M11_R1


title: SS2_17_154_M22_R1


title: SS2_17_154_M13_R1


title: SS2_17_154_M8_R1


title: SS2_17_154_M2_R1


title: SS2_17_154_L9_R1


title: SS2_17_154_L8_R1


title: SS2_17_154_L7_R1


title: SS2_17_154_M10_R1


title: SS2_17_154_L4_R1


title: SS2_17_154_L6_R1


title: SS2_17_154_L24_R1


title: SS2_17_154_L3_R1


title: SS2_17_154_L23_R1


title: SS2_17_154_L22_R1


title: SS2_17_154_L5_R1


title: RNAseq Jurkat LEDGINS 31.25uM rep2

value: Jurkat

value: T lymphocyte


title: SS2_17_154_L16_R1


title: SS2_17_154_L1_R1


title: SS2_17_154_L17_R1


title: SS2_17_154_L19_R1


title: SS2_17_154_L14_R1


title: SS2_17_154_L18_R1


title: SS2_17_154_L10_R1


title: SS2_17_154_K9_R1


title: SS2_17_154_L11_R1


title: SS2_17_154_L2_R1


title: SS2_17_154_K8_R1


title: SS2_17_154_K7_R1


title: SS2_17_154_L21_R1


title: SS2_17_154_K5_R1


title: SS2_17_154_K6_R1


title: SS2_17_154_K2_R1


title: SS2_17_154_K24_R1


title: SS2_17_154_K3_R1


title: SS2_17_154_L15_R1


title: SS2_17_154_K1_R1


title: SS2_17_154_K20_R1


title: SS2_17_154_L13_R1


title: SS2_17_154_L12_R1


title: SS2_17_154_K21_R1


title: SS2_17_154_K22_R1


title: SS2_17_154_K14_R1


title: SS2_17_154_K15_R1


title: SS2_17_154_K17_R1


title: SS2_17_154_K19_R1


title: SS2_17_154_K13_R1


title: SS2_17_154_K11_R1


title: SS2_17_154_K12_R1


title: SS2_17_154_K10_R1


title: SS2_17_154_L20_R1


title: SS2_17_154_K4_R1


title: SS2_17_154_J9_R1


title: SS2_17_154_J8_R1


title: SS2_17_154_J7_R1


title: SS2_17_154_J6_R1


title: SS2_17_154_K16_R1


title: SS2_17_154_J24_R1


title: SS2_17_154_J3_R1


title: SS2_17_154_J4_R1


title: SS2_17_154_J22_R1


title: SS2_17_154_O12_R1


title: SS2_17_154_J21_R1


title: SS2_17_154_J20_R1


title: SS2_17_154_J1_R1