title: XBP-1_ChIPSeq_Ern1-LKO_rep1

city: Nanjing

first: Zhenji

last: Gan

address: 12 Xuefu Road

department: Model Animal Research Center of Nanjing University

institute: Nanjing University

description:
Liver DNA from Ern1 liver specific knockout mouse
Ern1-LKO rep1

data_processing:
Illumina RTA used for base calling and converting into raw FASTQ files with Bcl2Fastq conversion software.
quality control using fastQC version 0.11.3
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 version 2.2.5 with the default parameters.
peaks were called using macs2 version 2.2.1 with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph and excel files including tag density and peak information were generated using macs2.

source_name: Liver from Ern1-LKO mouse

extract_protocol:
Lysates were clarified from sonicated nuclei and XBP-1-DNA complexes were isolated with antibody.
NEBNext® UNEBNext DNA Library Prep Master Mix Set for Illumina (cat# E6040L) was used with ChIP-DNA for the construction of sequencing libraries. ChIP libraries were prepared for sequencing using standard Illumina protocols

value: Liver specific Ern1 knockout

value: Xbp-1s (Santa Cruz,sc7610x,lot#D2910)


title: XBP-1_ChIPSeq_WT_rep2

status: Public on Jun 03 2019

type: SRA

country: China

description:
Liver DNA from wild-type mouse - control mouse for liver specific knockout Ern1
WT rep2

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Liver from wild-type mouse (control mouse for liver specific knockout Ern1)

tag: strain

tag: genotype

value: Wild-type

tag: tissue

value: Liver

tag: chip antibody


title: XBP-1_ChIPSeq_Ern1-LKO_rep2

description:
Liver DNA from Ern1 liver specific knockout mouse
Ern1-LKO rep2


title: In vitro derived macrophages M0 8 5

type: RNA

city: Bellinzona

first: Andrea

last: Rinaldi

state: Ticino

address: via vela 6

country: Switzerland

institute: IOR - oncology institute of southern switzerland

description: In vitro derived macrophages

hyb_protocol: Whole Genome Gene Expression Direct Hybridization

scan_protocol: Illumina HiScan

data_processing:
The data were normalised using quantile method
Signal calculated by GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.5.4 (Illumina, Inc.)

label: biotin

molecule: total RNA

source_name: Bone marrow derived macrophages, untreated

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays

growth_protocol: Ex vivo macrophages or epithelial cells were isolated from the prostatic tissue of  mice and immediately processed; in vitro macrophages were obstained from bone marrow precursors upon differentiation for 7 days

extract_protocol: Total RNA was quantified by NanoDrop ND-1000 Spectro-photometer (NanoDrop Technologies, Wilming-ton, DE) and RNA quality was assessed using Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mice were treated with intraperitoneal injections of 100ml of the vehicle or 100ml aCXCR2 (AZD5069) from Astrazeneca, at a final concentration of 100mg/kg daily for a period of 3 weeks

value: Bone marrrow


title: In vitro derived macrophages M2

description: In vitro derived macrophages

source_name: Bone marrow derived macrophages, IL-4/IL-13 treated


title: XBP-1_ChIPSeq_Fed_rep2

description:
Liver DNA from wild-type fed mouse
Fed rep2

source_name: Liver from wild-type fed mouse

tag: treatment

value: fed


title: XBP-1_ChIPSeq_Fed_rep1

description:
Liver DNA from wild-type fed mouse
Fed rep1


title: XBP-1_ChIPSeq_Fasted_rep2

description:
Liver DNA from wild-type fasted mouse
Fasted rep2

source_name: Liver from wild-type fasted mouse

value: fasted


title: Sorted macrophages  M0 P53null 1

description: Sorted macrophages

source_name: Macrophages were isolated from the prostatic tissue of Pten KO; Trp53 KO mice and immediately processed

value: Prostate


title: MEF_SirT7-KO_H3K18Ac_ChIP-seq_rep2

city: Piscataway

first: Joshua

middle: K

last: Thackray

state: NEW JERSEY

address: 145 Bevier Road

department: Human Genetics Institute of New Jersey

country: USA

institute: Rutgers University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw read quality was first assessed with fastqc (version 0.11.3, Babraham Bioinformatics), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36). Reads were then aligned to the mouse (UCSC mm9) or human (UCSC hg19) reference genome with Bowtie  with options –n 2 –k 10 (version 1.1.1), and converted to BAM format with Samtools (version 0.1.19).
Peak calling was performed using MACS (version 1.4.2) with default parameters.
For H3K18Ac ChIP, RPKM-normalized signal files (bigWig) were generated from BAM data using DeepTools (version 2.4.2). For SIRT7 ChIP, signal files generated by MACS peakcalling step were converted to bigWig using the UCSC utility wigToBigWig.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: bed files contain called peaks from ChIP-seq Data. BigWig files contain ChIP-seq signal that was RPKM normailzed (H3K18Ac ChIP data) or non-normalized (SIRT7 ChIP data)

source_name: MEF

growth_protocol: Mouse embryonic fibroblasts (MEFs; 14.5 days) were isolated from WT and SirT7-/- 129 mice as previously described. K562 cells were obtained from ATCC (CCL-121).

extract_protocol:
Samples were crosslinked in 1% formaldehyde for 10 minutes at 37°C, washed twice with PBS, and then collected from dishes. For SIRT7, ChIP was carried out with nuclear extracts. First, cells were resuspended in Lysis Buffer 1 (5 mM HEPES, 85 mM KCl, 0.5% NP-40) and incubated for 5 minutes on ice to disrupt cellular membranes. After centrifugation, nuclei were resuspended in Lysis Buffer 2 (1% SDS, 10mM EDTA, 50mM Tris, and protease inhibitors) and incubated on ice for 40 minutes. For H3K18Ac ChIP, whole cell extracts were obtained by directly lysing cells in Lysis Buffer 2 for 40 min on ice. Chromatin was then sonicated to an average fragment size of 150-300bp as analyzed by agarose gel electrophoresis, and subjected to immunoprecipitation with anti-SIRT7 (Cell Signalling, 5360, Lot 1) or anti-H3K18Ac (Abcam, ab1191, Lot GR277130-1) antibodies. ChIPs were washed 5 times with ice cold RIPA buffer (1% NP-40, 0.7% Na deoxycholate, 50mM Tris, 1mM EDTA, 500mM LiCl2, pH 8.0) and crosslinks reversed (1% SDS, 0.1M NaHCO3; 6 hr at 65°C), DNA purified (minElute PCR Purification Kit, Qiagen), and finally the concentration of ChIP and INPUT DNA was measured using PicoGreen (Life Technologies).
ChIP libraries were prepared using a ThruPlex DNA-seq library preparation Kit (Rubicon Genomics) following the manufacturer’s protocol. ChIP libraries were then size selected with PippinPrep (Sage Science) for a final library fragment size of 350-400bp, and quantified with KAPPA qPCR.

tag: cell type

value: Mouse Embrionic Fibroblasts

tag: passages


title: MEF_INPUT

value: wild type


title: In vitro derived macrophages M0

description: In vitro derived macrophages


title: In vitro derived macrophages M0 1 5

description: In vitro derived macrophages


title: Sorted macrophages  M0 P53null 2

description: Sorted macrophages


title: MEF_WT_H3K18Ac_ChIP-seq_rep2


title: Sorted macrophages  M0 Pten null 2

description: Sorted macrophages

source_name: Macrophages were isolated from the prostatic tissue of Pten KO mice and immediately processed


title: MEF_WT_SIRT7_ChIP-seq_rep2

value: SIRT7 (Cell Signalling, 5360, Lot 1)


title: MEF_SirT7-KO_H3K18Ac_ChIP-seq_rep1


title: MEF_WT_H3K18Ac_ChIP-seq_rep1


title: Sorted macrophages  M0 Pten null 1

description: Sorted macrophages


title: Sorted CD45+ negative epithelial cells 45neg P53null 1

description: Sorted CD45+ negative epithelial cells

source_name: CD45 negative cells were isolated from the prostatic tissue of Pten KO; Trp53 KO mice and immediately processed


title: Sorted CD45+ negative epithelial cells 45neg Pten null 2

description: Sorted CD45+ negative epithelial cells

source_name: CD45 negative cells were isolated from the prostatic tissue of Pten KO mice and immediately processed


title: XBP-1_ChIPSeq_WT_rep1

description:
Liver DNA from wild-type mouse - control mouse for liver specific knockout Ern1
WT rep1


title: Sorted CD45+ negative epithelial cells 45neg P53null 2

description: Sorted CD45+ negative epithelial cells


title: Input-2

description:
Liver DNA input control
Input-2

data_processing:
Illumina RTA used for base calling and converting into raw FASTQ files with Bcl2Fastq conversion software.
quality control using fastQC version 0.11.3
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 version 2.2.5 with the default parameters.
peaks were called using macs2 version 2.2.1 with the default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: macs2-generated Bedgraph and peaks files

source_name: Liver


title: Sorted CD45+ negative epithelial cells 45neg Pten null 1

description: Sorted CD45+ negative epithelial cells

source_name: CD45 negative were isolated from the prostatic tissue of Pten KO mice and immediately processed


title: Sorted macrophages  M0 WT

description: Sorted macrophages

source_name: Macrophages were isolated from the prostatic tissue of C57BL6 WT mice and immediately processed


title: Sorted CD45+ negative epithelial cells 45neg WT 2

description: Sorted CD45+ negative epithelial cells

source_name: CD45 negative were isolated from the prostatic tissue of C57BL6 WT mice and immediately processed


title: MEF_WT_SIRT7_ChIP-seq_rep1


title: XBP-1_ChIPSeq_Fasted_rep1

description:
Liver DNA from wild-type fasted mouse
Fasted rep1


title: Input-1

description:
Liver DNA input control
Input-1


title: Sorted CD45+ negative epithelial cells 45neg WT 1

description: Sorted CD45+ negative epithelial cells

source_name: CD45 negative cells were isolated from the prostatic tissue of C57BL6 WT mice and immediately processed


title: Lean_Serum Subject 078-6

city: Washington

first: Matthew

middle: David

last: Barberio

state: District of Columbia

address: 111 Michigan Avenue

department: Exercise and Nutrition Sciences

institute: George Washington University

description: microRNA profiles of adipocyte-derived (FABP4+) exosomes isolated in subject serum

hyb_protocol: For hybridization, we followed Affymetrix Gene Chip miRNA Array Procedure for Affymetrix miRNA 4.0 arrays to hybridize biotin-labeled sample

scan_protocol: We scanned the Affymetrix miRNA 4.0 arrays following the Affymetrix Command Console User Manual Instructions.

data_processing: We analyzed the resulting data in Expression Console using RMA+DMBG (Affymetrix) and then exported it to Partek Genomics Suite for analyses

organism: Homo sapiens

source_name: Serum

label_protocol: We used Affymetrix FlashTag Biotin HSR RNA Labeling Kit to label 1000 ng of cRNA from each sample

extract_protocol: To isolate exosomes, we used the serum from lean and obese subejcts and used ExoQuick-TC precipitation solution, according to ExoQuick-TC protocol. Total RNA was isolated following mirVana's total RNA Isolation kit. We also used StemCell Technologies Magnetic Isolation Technique to isolate FABP4+ specific exosomes.

tag: gender

value: Female

tag: age

tag: bmi

tag: race

value: Black

tag: cholesterol efflux

tag: sample type

value: FABP4+ (adipocyte-derived) exosomes isolated from serum


title: Lean_Serum Subject 077-1


title: Lean_Serum Subject 041-7

value: White


title: Obese_Serum Subject 023-6


title: Obese_Serum Subject 021-1


title: Obese_Serum Subject 022-7


title: Obese_Serum Subject 018-9


title: Obese_Serum Subject 019-1


title: Obese_Serum Subject 011-9


title: 1444GM

city: Barcelona

first: Emilio

last: Marmol

state: Barcelona

address: CSIC IRTA UAB UB Edifici CRAG., Campus Universitat Autònoma de Barcelona (UAB), Bellaterra (Cerdanyola del Vallès)

department: Animal Genetics

country: Spain

institute: Center for Research in Agrigenomics (CRAG)

description: Gene expression data from Gluteus medius

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: The data were analyzed with Microarray  affy package in R using default analysis settings and RMA algorithm was used for pre-processing background correction and normalisation of expression values.

organism: Sus scrofa

source_name: Gluteus medius

label_protocol: standard Affymetrix protocol

growth_protocol: Commercial fedding and fattening until slaughtering

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

value: Gluteus medius

value: 190 days


title: Obese_Serum_Subject 007-2


title: Obese_Serum_Subject 005-5


title: 1443GM


title: 1446GM


title: 1431GM


title: 1450GM


title: 1412GM


title: 1429GM


title: 1404GM


title: 1402GM


title: 8695F_(Porcine)

description: Gene expression data from Liver


title: 8697F_(Porcine)

description: Gene expression data from Liver


title: 1403GM


title: 8694F_(Porcine)

description: Gene expression data from Liver


title: 8700F_(Porcine)

description: Gene expression data from Liver


title: Non-treated cells-replicate 3

first: Carmen

last: Bedia

address: Jordi Girona 18-26

department: Environmental Chemistry

institute: Institute of Environmental Assessment and Water Research (IDAEA-CSIC)

hyb_protocol: WTA2 protocol on Human PrimeView Array Chip.

scan_protocol: GeneChip® Scanner 3000 7G (GCS 3000 7G).

data_processing: Command Console Affymetrix software. Raw data were normalized and summarized with RMA algorithm.

source_name: 85% confluence cells-non-treated-replicate 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA.

growth_protocol: DU145 prostate cancer cells were cultured in RPMI 1640 medium supplemented with 10% heat inactivated fetal bovine serum (FBS),100U/ml penicillin and 100 μg/ml streptomycin, at 37 °C in a humidified atmosphere containing 5% of CO2.

extract_protocol: Total RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel). RNA quality was checked in an Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: DU145 cells were seeded in a 6-well plate at density of 2x10e5 per well in the presence of 1uM of Aldrin to a final volume of 2ml of supplemented RPMI (final concentration of DMSO 0.01%). Cells were cultured in standard conditions and diluted every 3 days. Cultures were treated after every passage to complete the 50-day treatment.

tag: cell line

value: Prostate cancer cell line


title: 8693F_(Porcine)

description: Gene expression data from Liver


title: Cells treated with 1uM Aldrin-replicate 4

source_name: 85% confluence cells-treatment Aldrin-replicate 4

value: Aldrin


title: Non-treated cells-replicate 4

source_name: 85% confluence cells-non-treated-replicate 4


title: 8689F_(Porcine)

description: Gene expression data from Liver


title: 8692F_(Porcine)

description: Gene expression data from Liver


title: 2820F_(Porcine)

description: Gene expression data from Liver


title: Non-treated cells-replicate 2

source_name: 85% confluence cells-non-treated-replicate 2


title: Cells treated with 1uM Aldrin-replicate 2

source_name: 85% confluence cells-treatment Aldrin-replicate 2


title: Non-treated cells-replicate 1

source_name: 85% confluence cells-non-treated-replicate 1


title: 8688F_(Porcine)

description: Gene expression data from Liver


title: 2807F_(Porcine)

description: Gene expression data from Liver


title: 2817F_(Porcine)

description: Gene expression data from Liver


title: 2823F_(Porcine)

description: Gene expression data from Liver


title: Cells treated with 1uM Aldrin-replicate 3

source_name: 85% confluence cells-treatment Aldrin-replicate 3


title: ThawGradient-Mo-Core6-5cm

type: genomic

city: Norman

first: Jizhong

last: Zhou

state: OK

address: 101 David L Boren Blvd

department: Department of Microbiology and Plant Biology

institute: University of Oklahoma

hyb_protocol: The labeled DNA was resuspended in 10 µL hybridization solution containing 2.68 µL sample tracking control (Roche NimbleGen, Inc., Madison, WI, USA), 40% formamide, 25% SSC, 1% SDS, 1.6% Cy3 labeled alignment oligo, 1.6% Cy5-labeled alignment oligo and 2% Cy5-labeled common oligonucleotide reference standard target (NimbleGen). After denaturing at 95°C for 5 min, the mixtures were spun down and kept at 42°C to be deposited onto the glass microarray. GeoChip 4.2 slides were synthesized by NimbleGen in a 12-plex format (i.e., 12 arrays per glass slide). An HX12 mixer (NimbleGen) was affixed onto the array using a Precision Mixer Alignment Tool (NimbleGen). The array was preheated at 42°C in the 12-Bay MAUI Hybridization System (BioMicro Systems, Inc., Salt Lake City, UT, USA) for at least 5 min before the samples were loaded onto the array. Hybridizations were performed on the MAUI Hybridization System at 42°C in the presence of 40% formamide for about 16 hours with mixing. Then the mixers were removed from the slides while soaking in buffer I. The slides were manually washed in buffer I for 120 s, in buffer II for 60 s and in buffer III for 15 s and spun to dry in a NimbleGen slide spinner. All washing buffers were provided by NimbleGen.

scan_protocol: The dried microarray was scanned with a laser power of 100% and a photomultiplier (PMT) gain of 100% by a MS 200 Microarray Scanner (NimbleGen) at 532 nm and 635 nm. NimbleScan software version 2.5 (NimbleGen) was used to grid the images. After gridding, every spot (containing one unique probe) on the GeoChip array was fixed into a 7 × 7 pixel square and was adjacent to four blank equal-sized squares (void spaces). The probe signal was then calculated as the average intensity of the center 5 × 5 pixels for each spot, and the background noise signal was the average void intensity for each spot. The signal and background intensity report was generated also in NimbleScan software.

data_processing: Data normalization was completed on a web-based pipeline (http://ieg.ou.edu/microarray/) as follows. First, the raw probe signals, calculated based on the average pixel intensity of each probe, were adjusted based on control dye intensity and sample set total intensity. Second, signals were filtered by removing the spots with a signal to noise ratio less than 2, and the spots with signal intensity less than 2 times background. Third, probes that generated positive signals in less than 10 % of the samples from a given thaw site (all replicates from within each field site and along the depth profile) were considered low abundance genes and removed from that site for downstream analyses. We identified low abundance genes on a site basis instead of globally to retain functional gene probes unique to one site. Fourth, the probe signals were then normalized to represent relative abundance of genes in each sample. Unless otherwise specified, all gene abundance data reported in this manuscript represent relative abundance estimations based on the normalized signal intensities of probes targeting said gene.

organism:
Bacteria
Archaea
Eukaryota
Viruses

source_name: soil microbial metagenome in Mo site

label_protocol: For each sample, 1µg DNA was diluted to a volume of 25 μL and was mixed with 20 μL random primers (Invitrogen by Life Technologies, Grand Island, NY, USA), denatured at 99.9°C for 5 min and immediately chilled on ice. Then, 2.5 μL dNTP (5 mM dAGC-TP, 2.5 mM dTTP), 1 μL fluorescent dye Cy-3 dUTP (GE Healthcare UK Limited, Buckinghamshire, UK) and 80 U of the large Klenow fragment (Imer Inc., CA, USA) were added to the denatured DNA. The 50 μL mixture was incubated at 37°C for 6 hours, followed by heating at 95°C for 3 min. Labeled DNA was purified using the QIAquick PCR purification kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. Cy-3 dye concentration was measured on a NanoDrop ND-1000 spectrophotometer (NanoDrop Products). The labeled DNA was then dried in a Savant SPD1010 SpeedVac concentrator system (Thermo Fisher Scientific) at 45°C for 45 min.

growth_protocol: uncultured

extract_protocol: Soil DNA was extracted using a PowerMax Soil DNA Isolation Kit (MO BIO Laboratories, Inc., Carlsbad, CA, USA) according to the manufacturer’s protocol. DNA quality was assessed based on spectrometry absorbance at wavelengths of 230 nm, 260 nm and 280 nm detected by a NanoDrop ND1000 Spectrophotometer (NanoDrop Technologies Inc., now NanoDrop Products by Thermo Fisher Scientific). The 260/280 nm absorbance ratios were around 1.8, and 260/230 nm ratios were greater than 1.7. Finally, DNA was quantified with Pico Green using a FLUOstar OPTIMA fluorescence plate reader (BMG LabTech, Jena, Germany) and used for gene array labeling and sequencing library preparation.

treatment_protocol: untreated natural soil

tag: soil origin

value: Akaska acidic tundra

organism: synthetic construct

source_name: synthesized common oligonucleotide reference standard

tag: sequence

tag: molecule subtype

value: single stranded oligonucleotide


title: 2805F_(Porcine)

description: Gene expression data from Liver

value: Liver


title: 2809F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mo-Core6-69cm


title: ThawGradient-Mo-Core6-35cm


title: KO_3

city: Kyoto

first: Wataru

last: Aoi

address: 1-5 Hangicho Shimogamo, Sakyo-ku

country: Japan

institute: Kyoto Prefectural University

description: SAMPLE 6

hyb_protocol: 2.3ug of Fragmented and Labeled ss-cDNA were hybridized for 16 hr at 45C on GeneChip® Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were normalized using the robust multi-array average method (Expression Console 1.3.0.187,Affymetrix, Santa Clara, CA).

label_protocol: Biotinylated ss-cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (GeneChip® WT PLUS Reagent Kit User Manual, 2013,Affymetrix, Santa Clara, CA).

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's instructions.

tag: strain background

tag: genotype/variation

value: homogenous SPARC knockout

value: 12 weeks

value: male

value: gastrocnemius muscle


title: ThawGradient-Mo-Core5-85cm


title: ThawGradient-Mo-Core6-25cm


title: ThawGradient-Mo-Core6-45cm


title: 2801F_(Porcine)

description: Gene expression data from Liver

tag: tissue


title: ThawGradient-Mo-Core6-16cm


title: Cells treated with 1uM Aldrin-replicate 1

source_name: 85% confluence cells-treatment Aldrin-replicate 1


title: 2808F_(Porcine)

description: Gene expression data from Liver

source_name: Liver


title: 2737F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mo-Core6-59cm


title: 2734F_(Porcine)

description: Gene expression data from Liver


title: KO_2

description: SAMPLE 5


title: 2709F_(Porcine)

description: Gene expression data from Liver


title: RS_RNAseq

city: Cerdanyola del Vallès (Bellaterra)

first: Covadonga

last: Vara

address: Campus UAB

department: Biologia cel·lular, Fisiologia i Immunologia

institute: Universitat Autònoma de Barcelona

description: counts_table_raw.txt [P0000_N701-S503, P0000_N701-S507, P0000_N702-S503, P0000_N702-S507]

library_source: transcriptomic

data_processing:
Hi-C: Reads were quality-checked and filtered using BBDuk version10/2015 and then aligned using TADbit version 0.2.0.23. Data was binned and normalised using an in-house script taht read the map files generated after filtering, obtaining matrix that were stored into a file in NPZ format (raw).
ChIP-seq: Reads were quality-checked and mapped with BWA. Mapped reads were filtered with SAMtools. Coverage files were obtained from bam files using DeepTools:bamCoverage. All the mentioned tools were used through the Galaxy server (https://usegalaxy.org/).
RNA-seq: Reads were analysed using AIR (https://transcriptomics.cloud), were reads were filtered according to quality, mapped using STAR (Dobin et al 2013) and gene expression quantification was done using featureCounts (Liao et al 2014).
Genome_build: mm10

source_name: Round Spermatids

extract_protocol:
Enriched cell populations were processed following the Smart-Seq2 protocol described by Picelli et. al 2014.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Round Spermatids

tag: strain


title: ThawGradient-Mo-Core5-55cm


title: Sperm_RNAseq

description: counts_table_raw.txt [P0000_N701-S504, P0000_N701-S508, P0000_N702-S504, P0000_N702-S508]

source_name: Sperm

value: Sperm


title: 2731F_(Porcine)

description: Gene expression data from Liver


title: 2723F_(Porcine)

description: Gene expression data from Liver


title: WT_3

description: SAMPLE 3

value: wild type


title: WT_2

description: SAMPLE 2


title: 2561F_(Porcine)

description: Gene expression data from Liver


title: 2716F_(Porcine)

description: Gene expression data from Liver


title: 2704F_(Porcine)

description: Gene expression data from Liver


title: KO_1

description: SAMPLE 4


title: 2705F_(Porcine)

description: Gene expression data from Liver


title: 2551F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mo-Core5-5cm


title: ThawGradient-Mo-Core5-35cm


title: ThawGradient-Mo-Core5-25cm


title: 2556F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mo-Core5-45cm


title: ThawGradient-Mo-Core5-15cm


title: 2557F_(Porcine)

description: Gene expression data from Liver


title: 2552F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mo-Core4-56cm


title: WT_1

description: SAMPLE 1


title: 2549F_(Porcine)

description: Gene expression data from Liver


title: 2550F_(Porcine)

description: Gene expression data from Liver


title: 2701F_(Porcine)

description: Gene expression data from Liver


title: Spermatogonia_RNAseq

description: counts_table_raw.txt [P0000_N701-S505, P0000_N701-S517, P0000_N702-S505, P0000_N702-S517]

source_name: Spermatogonia

value: Spermatogonia


title: ThawGradient-Mo-Core4-66cm


title: PD_RNAseq

description: counts_table_raw.txt [P0000_N701-S502, P0000_N701-S506, P0000_N702-S502, P0000_N702-S506]

source_name: Pachynema/Diplonema

value: Pachynema/Diplonema


title: Fibros_HiC

source_name: Fibroblasts

extract_protocol:
Enriched cell populations were processed following the in situ Hi-C protocol described by Rao et. al 2014.
Hi-C libraries were prepared for sequencing using standard Illumina protocols

value: Fibroblasts


title: Sperm_HiC


title: 2546F_(Porcine)

description: Gene expression data from Liver


title: 2542F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mo-Core4-46cm


title: 2545F_(Porcine)

description: Gene expression data from Liver


title: 2195F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mo-Core4-34cm


title: 2189F_(Porcine)

description: Gene expression data from Liver


title: 2179F_(Porcine)

description: Gene expression data from Liver


title: 2178F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mo-Core4-25cm


title: ThawGradient-Mo-Core4-17cm


title: 2187F_(Porcine)

description: Gene expression data from Liver


title: RS_HiC


title: LZ_HiC

source_name: Leptonema/Zygonema

value: Leptonema/Zygonema


title: Spermatogonia_HiC


title: PD_HiC


title: ThawGradient-Mo-Core3-25cm


title: 2176F_(Porcine)

description: Gene expression data from Liver

value: 190 days


title: 2172F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mo-Core3-45cm


title: 2168F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mo-Core3-35cm


title: 2164F_(Porcine)

description: Gene expression data from Liver


title: 2151F_(Porcine)

description: Gene expression data from Liver


title: 2174F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mo-Core3-16cm


title: ThawGradient-Mo-Core4-0cm


title: 2157F_(Porcine)

description: Gene expression data from Liver


title: 1919F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mo-Core3-0cm


title: ThawGradient-Mo-Core2-55cm


title: ThawGradient-Mo-Core2-45cm


title: 1918F_(Porcine)

description: Gene expression data from Liver


title: 2144F_(Porcine)

description: Gene expression data from Liver


title: 2149F_(Porcine)

description: Gene expression data from Liver


title: Tonsil HPV16 idat 5826629088 rep2

city: Cambridge

first: Anna

last: Salzberg

state: MA

address: 399 Binney St UNIT 300

institute: Rubius Therapeutics

description:
replicate 2
Sample 30

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with CLC Genomics Workbench v4.8

source_name: Human tonsil

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep Amplification kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: tonsil

tag: infection


title: 1911F_(Porcine)

description: Gene expression data from Liver


title: 1917F_(Porcine)

description: Gene expression data from Liver


title: 1910F_(Porcine)

description: Gene expression data from Liver


title: 2152F_(Porcine)

description: Gene expression data from Liver


title: Tonsil HPV16 idat 5885320010 rep1

description:
replicate 1
Sample 27


title: 1903F_(Porcine)

description: Gene expression data from Liver


title: Tonsil HPV16 idat 5885320010 rep2

description:
replicate 2
Sample 28


title: 2142F_(Porcine)

description: Gene expression data from Liver


title: Tonsil HPV16 idat 5826629064 rep2

description:
replicate 2
Sample 29


title: Tonsil HPV16 idat 5826629088 rep1

description:
replicate 1
Sample 26


title: 1906F_(Porcine)

description: Gene expression data from Liver


title: 1624F_(Porcine)

description: Gene expression data from Liver


title: 1901F_(Porcine)

description: Gene expression data from Liver


title: Tonsil Primary idat 5826629064 rep2

description:
replicate 2
Sample 24


title: ThawGradient-Mo-Core2-25cm


title: ThawGradient-Mo-Core2-15cm


title: 1619F_(Porcine)

description: Gene expression data from Liver


title: 1604F_(Porcine)

description: Gene expression data from Liver


title: Tonsil HPV16 idat 5826629064 rep1

description:
replicate 1
Sample 25


title: ThawGradient-Mo-Core2-35cm


title: Tonsil Primary idat 5826629088 rep2

description:
replicate 2
Sample 23


title: 1605F_(Porcine)

description: Gene expression data from Liver


title: Tonsil Primary idat 5885320008 rep2

description:
replicate 2
Sample 22


title: 1602F_(Porcine)

description: Gene expression data from Liver


title: Tonsil Primary idat 5885320008 rep1

description:
replicate 1
Sample 21


title: 1567F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mo-Core1-60cm


title: ThawGradient-Mo-Core2-0cm


title: 1586F_(Porcine)

description: Gene expression data from Liver


title: 1559F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mo-Core1-50cm


title: Tonsil Primary idat 5826629064 rep1

description:
replicate 1
Sample 20


title: 1553F_(Porcine)

description: Gene expression data from Liver


title: 1563F_(Porcine)

description: Gene expression data from Liver


title: 1592F_(Porcine)

description: Gene expression data from Liver


title: 1551F_(Porcine)

description: Gene expression data from Liver


title: 1550F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mo-Core1-0cm


title: Tonsil Primary idat 5826629088 rep1

description:
replicate 1
Sample 19


title: Foreskin HPV16 idat 5885320010 rep1

description:
replicate 1
Sample 18

source_name: Human foreskin

value: foreskin


title: Foreskin HPV16 idat 5826629088 rep1

description:
replicate 1
Sample 16


title: 1540F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mi-Core7-76cm

source_name: soil microbial metagenome in Mi site

value: Akaska acidic tundra


title: 1502F_(Porcine)

description: Gene expression data from Liver


title: 1538F_(Porcine)

description: Gene expression data from Liver


title: 1503F_(Porcine)

description: Gene expression data from Liver


title: 1545F_(Porcine)

description: Gene expression data from Liver


title: 1533F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mi-Core7-46cm

value: single stranded oligonucleotide


title: 1498F_(Porcine)

description: Gene expression data from Liver

value: Liver


title: 1539F_(Porcine)

description: Gene expression data from Liver


title: Peg033.v3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
PBMC cells from patient Peg 033, visit 3
5655639051_K

hyb_protocol: Hybridized on Illumina Human-HT12 v4 Expression BeadChip Kit using Illumina whole-Genome Gene Exprssion with Intellihyb Seal system which detect signal with streptavidin-Cy3

scan_protocol: Illumina Setting with PMTFactor=2

data_processing: Illumina GenomeStudio software was used to export expression levels and detection p-values for each probe of each sample. Signal intensity data was quantile normalized, log2-transformed and  genes that showed insignificant detection p-value (p>0.05) in all samples were removed from further analysis.

source_name: PBMC cells from patients_visit 3

label_protocol: amplified cRNA was generated from 100ng RNA using the TargetAmp Nano-g Biotin-aRNA Labeling Kit (Epicentre, Madison WI)

growth_protocol: PBMC from patients was isolated using standard Ficoll-hypaque density gradient centrifugation

extract_protocol: Isolation of total RNA from cryo-preserved PBMCs was performed using the Tri-reagent (Sigma Aldrich, St Louis, MO) according to the manufacturer’s instructions.

treatment_protocol: PBMC was cryo-preserved

tag: patient id

value: Peg 033

tag: patient status

value: chronic HIV-infected subject

tag: visit

tag: response

tag: cell type

value: peripheral blood mononuclear cell (PBMC)


title: Foreskin HPV16 idat 5885320008 rep1

description:
replicate 1
Sample 17


title: Foreskin Primary idat 5885320008 rep1

description:
replicate 1
Sample 14


title: 1528F_(Porcine)

description: Gene expression data from Liver

tag: age


title: ThawGradient-Mi-Core7-0cm


title: ThawGradient-Mi-Core6-60cm


title: Foreskin Primary idat 5885320010 rep1

description:
replicate 1
Sample 15


title: ThawGradient-Mi-Core7-25cm


title: ThawGradient-Mi-Core7-36cm


title: ThawGradient-Mi-Core7-15cm


title: 1497F_(Porcine)

description: Gene expression data from Liver


title: Foreskin Primary idat 5826629064 rep1

description:
replicate 1
Sample 13


title: 1487F_(Porcine)

description: Gene expression data from Liver


title: 1495F_(Porcine)

description: Gene expression data from Liver


title: 1496F_(Porcine)

description: Gene expression data from Liver


title: 1513F_(Porcine)

description: Gene expression data from Liver


title: Peg033.v5

description:
PBMC cells from patient Peg 033, visit 5
5655639051_L

source_name: PBMC cells from patients_visit 5


title: Peg032.v8

description:
PBMC cells from patient Peg 032, visit 8
5655639051_J

source_name: PBMC cells from patients_visit 8

value: Peg 032

value: RC


title: 1483F_(Porcine)

description: Gene expression data from Liver


title: 1469F_(Porcine)

description: Gene expression data from Liver


title: Peg032.v5

description:
PBMC cells from patient Peg 032, visit 5
5655639051_I


title: 1488F_(Porcine)

description: Gene expression data from Liver


title: 1444F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mi-Core6-50cm


title: ThawGradient-Mi-Core6-40cm


title: 1467F_(Porcine)

description: Gene expression data from Liver


title: 1452F_(Porcine)

description: Gene expression data from Liver


title: Peg032.v3

description:
PBMC cells from patient Peg 032, visit 3
5655639051_H


title: 1468F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mi-Core6-13cm


title: Peg031.v5

description:
PBMC cells from patient Peg 031, visit 5
5655639051_F

value: Peg 031


title: Peg031.v8

description:
PBMC cells from patient Peg 031, visit 8
5655639051_G


title: 1431F_(Porcine)

description: Gene expression data from Liver


title: 1412F_(Porcine)

description: Gene expression data from Liver


title: Peg031.v3

description:
PBMC cells from patient Peg 031, visit 3
5655639051_E


title: 1450F_(Porcine)

description: Gene expression data from Liver


title: 1456F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mi-Core6-30cm


title: ThawGradient-Mi-Core6-25cm


title: ThawGradient-Mi-Core6-0cm


title: 1443F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mi-Core5-39cm


title: Peg029.v5

description:
PBMC cells from patient Peg 029, visit 5
5655639050_K

value: Peg 029

value: NN


title: 1446F_(Porcine)

description: Gene expression data from Liver


title: 1404F_(Porcine)

description: Gene expression data from Liver


title: 1429F_(Porcine)

description: Gene expression data from Liver


title: 8692GM

source_name: Gluteus medius

value: Gluteus medius


title: 1403F_(Porcine)

description: Gene expression data from Liver


title: ThawGradient-Mi-Core4-41cm


title: 1402F_(Porcine)

description: Gene expression data from Liver


title: Peg029.v3

description:
PBMC cells from patient Peg 029, visit 3
5655639050_J


title: 8697GM


title: Peg025.v5

description:
PBMC cells from patient Peg 025, visit 5
5707478034_F

value: Peg 025


title: Peg025.v3

description:
PBMC cells from patient Peg 025, visit 3
5707478034_E


title: 8695GM

description: Gene expression data from Gluteus medius


title: ThawGradient-Mi-Core5-15cm


title: Peg027.v5

description:
PBMC cells from patient Peg 027, visit 5
5655639050_G

value: Peg 027

value: RN


title: ThawGradient-Mi-Core4-35cm


title: 8693GM

value: 190 days


title: 8689GM


title: Peg025.v8

description:
PBMC cells from patient Peg 025, visit 8
5707478034_G


title: 8694GM


title: ThawGradient-Mi-Core4-25cm


title: 8688GM


title: 2823GM


title: 8700GM


title: ThawGradient-Mi-Core4-18cm


title: 2820GM


title: ThawGradient-Mi-Core5-5cm


title: Peg027.v3

description:
PBMC cells from patient Peg 027, visit 3
5655639050_F


title: Peg024.v5

description:
PBMC cells from patient Peg 024, visit 5
5655639050_C

value: Peg 024


title: ThawGradient-Mo-Core1-40cm

source_name: soil microbial metagenome in Mo site

value: Akaska acidic tundra


title: 2809GM


title: 2817GM


title: ThawGradient-Mi-Core4-5cm

source_name: synthesized common oligonucleotide reference standard

value: single stranded oligonucleotide


title: Peg023.v8

description:
PBMC cells from patient Peg 023, visit 8
5701375042_I

value: Peg 023


title: Peg024.v3

description:
PBMC cells from patient Peg 024, visit 3
5655639050_B


title: 2807GM


title: Peg023.v5

description:
PBMC cells from patient Peg 023, visit 5
5701375042_H


title: 2808GM


title: ThawGradient-Mi-Core3-55cm


title: ThawGradient-Mi-Core3-35cm


title: 2801GM


title: Peg022.v5

description:
PBMC cells from patient Peg 022, visit 5
5655639049_K

value: Peg 022


title: 2723GM


title: Peg022.v3

description:
PBMC cells from patient Peg 022, visit 3
5655639049_J

value: chronic HIV-infected subject


title: ThawGradient-Mi-Core3-45cm


title: 2805GM


title: 2737GM


title: 2704GM


title: 2709GM


title: 2731GM


title: 2705GM


title: 2561GM


title: ThawGradient-Mi-Core3-75cm


title: Peg020.v5

description:
PBMC cells from patient Peg 020, visit 5
5655639049_G

value: Peg 020

value: peripheral blood mononuclear cell (PBMC)


title: ThawGradient-Mi-Core3-0cm


title: Peg023.v3

description:
PBMC cells from patient Peg 023, visit 3
5701375042_G

value: RC


title: ThawGradient-Mi-Core3-14cm


title: 2701GM


title: 2716GM


title: Peg020.v3

description:
PBMC cells from patient Peg 020, visit 3
5655639049_F


title: 2557GM


title: Peg019.v8

description:
PBMC cells from patient Peg 019, visit 8
5655639051_C

value: Peg 019


title: 2556GM


title: Peg019.v3

description:
PBMC cells from patient Peg 019, visit 3
5655639051_B


title: 2552GM


title: ThawGradient-Mi-Core2-35cm


title: ThawGradient-Mi-Core3-25cm


title: 2734GM


title: 2551GM


title: 2545GM


title: 2550GM


title: 2542GM


title: ThawGradient-Mi-Core2-25cm


title: 2546GM


title: ThawGradient-Ex-Core6-83cm

source_name: soil microbial metagenome in Ex site


title: Peg013.v5

description:
PBMC cells from patient Peg 013, visit 5
5655639049_C

value: Peg 013


title: ThawGradient-Mi-Core2-5cm


title: 2195GM


title: ThawGradient-Mi-Core2-18cm


title: Peg013.v3

description:
PBMC cells from patient Peg 013, visit 3
5655639049_B

value: NN


title: 2549GM

description: Gene expression data from Gluteus medius

value: Gluteus medius


title: Peg012.v8

description:
PBMC cells from patient Peg 012, visit 8
5701375042_D

value: Peg 012


title: 2189GM


title: ThawGradient-Ex-Core6-63cm


title: 2187GM


title: 2179GM


title: Peg012.v5

description:
PBMC cells from patient Peg 012, visit 5
5701375042_C


title: 2176GM


title: 2178GM


title: 2172GM


title: Peg012.v3

description:
PBMC cells from patient Peg 012, visit 3
5701375042_B


title: ThawGradient-Ex-Core6-43cm


title: Peg011.v8

description:
PBMC cells from patient Peg 011, visit 8
5707478034_B

value: Peg 011


title: Peg011.v5

description:
PBMC cells from patient Peg 011, visit 5
5707478034_A


title: 2152GM


title: 2164GM


title: 2168GM


title: ThawGradient-Ex-Core6-35cm


title: 2151GM


title: 2174GM


title: 2157GM


title: ThawGradient-Ex-Core6-25cm


title: ThawGradient-Ex-Core5-63cm


title: 2144GM


title: 1919GM


title: 2142GM


title: Peg011.v3

description:
PBMC cells from patient Peg 011, visit 3
5701375042_L


title: ThawGradient-Ex-Core5-53cm


title: ThawGradient-Ex-Core6-0cm


title: Peg010.v5

description:
PBMC cells from patient Peg 010, visit 5
5655639033_L

value: Peg 010


title: ThawGradient-Ex-Core6-54cm


title: Peg009.v5

description:
PBMC cells from patient Peg 009, visit 5
5655639033_I

value: Peg 009


title: 2149GM

value: 190 days


title: ThawGradient-Ex-Core5-39cm

value: Akaska acidic tundra


title: Peg010.v3

description:
PBMC cells from patient Peg 010, visit 3
5655639033_K


title: 1918GM


title: 1917GM


title: ThawGradient-Ex-Core5-35cm

value: single stranded oligonucleotide


title: 1911GM


title: Peg008.v3

description:
PBMC cells from patient Peg 008, visit 3
5655639033_D

value: Peg 008


title: 1906GM


title: Peg009.v3

description:
PBMC cells from patient Peg 009, visit 3
5655639033_H


title: 1903GM


title: ThawGradient-Ex-Core5-15cm


title: ThawGradient-Ex-Core5-25cm


title: 1910GM


title: ThawGradient-Ex-Core5-5cm


title: 1901GM


title: Peg007.v3

description:
PBMC cells from patient Peg 007, visit 3
5655639033_A

value: Peg 007

value: RN


title: Peg007.v5

description:
PBMC cells from patient Peg 007, visit 5
5655639033_B

value: chronic HIV-infected subject


title: Peg008.v5

description:
PBMC cells from patient Peg 008, visit 5
5655639033_E

value: peripheral blood mononuclear cell (PBMC)


title: 1619GM


title: ThawGradient-Ex-Core4-50cm


title: Peg006.v5

description:
PBMC cells from patient Peg 006, visit 5
5707478034_K

value: Peg 006


title: 1624GM


title: ThawGradient-Ex-Core4-34cm


title: ThawGradient-Ex-Core4-45cm


title: 1602GM


title: 1567GM


title: 1604GM


title: Peg006.v3

description:
PBMC cells from patient Peg 006, visit 3
5707478034_J


title: 1592GM

description: Gene expression data from Gluteus medius


title: ThawGradient-Ex-Core4-25cm


title: 1559GM


title: 1605GM


title: 1586GM


title: Peg005.v5

description:
PBMC cells from patient Peg 005, visit 5
5701375036_J

value: Peg 005

value: RC


title: Peg005.v3

description:
PBMC cells from patient Peg 005, visit 3
5701375036_I


title: 1553GM


title: 1540GM


title: 1563GM


title: ThawGradient-Ex-Core4-15cm


title: ThawGradient-Ex-Core3-63cm


title: Peg005.v8

description:
PBMC cells from patient Peg 005, visit 8
5701375036_K


title: ThawGradient-Ex-Core4-5cm


title: 1550GM


title: Peg002.v8

description:
PBMC cells from patient Peg 002, visit 8
5701375036_F

value: Peg 002


title: 1551GM

value: Gluteus medius


title: 1538GM


title: 1539GM


title: 1528GM


title: 1497GM


title: 1533GM


title: Peg002.v5

description:
PBMC cells from patient Peg 002, visit 5
5701375036_E


title: 1513GM


title: 1502GM


title: Peg002.v3

description:
PBMC cells from patient Peg 002, visit 3
5701375036_D


title: 1498GM


title: 1545GM


title: inflamed_R3

city: Oxford

first: Stephen

last: Sansom

state: Oxfordshire

address: Roosevelt Drive

department: NDORMS

country: United Kingdom

institute: Kennedy Institute of Rheumatology

description:
matrix.mtx
barcodes.tsv
genes.tsv

data_processing:
Read mapping, quantitation and aggregation of sample count matrices was performed with the "cellranger count" and "cellranger aggr" (--normalize=mapped) tools as provided by the 10x Genomics Cell Ranger pipeline (version 2.1.0) and the 10x Genomics mouse reference sequences (version 1.2.0).
Removal of cells with barcodes common to more than one sample. These samples were sequenced in a batch that also contained other 10x samples (unpublished data). All of the samples in the batch were used for the identification of common barcodes. Cells with common barcodes were removed from the analysis to avoid issues associated with index hopping.
The aggregated count matrix was randomly down-sampled in order to normalize the median number of umis per-cell between the replicate samples (with the "downsampleMatrix" function from the DropletUtils R package).
Genome_build: mm10
Supplementary_files_format_and_content: The "matrix.mtx" file contains the aggregated count matrix is provided as a MEX file (cells in columns, genes in rows). The "barcodes.tsv" TSV file contains the cell barcodes with replicate indicated in the cell barcode ("-R1", "-R2" or "-R3"). The "genes.tsv" file contains the Ensembl gene identifiers and names. These files can be read with the "Read10X" function from the Seurat R package.

source_name: Synovial joints

extract_protocol:
Digestion of hind limb joints, sort purification of CD45-ve live synovial cells.
Libraries were generated using 10x Genomics Single Cell 3’ Solution (version 2) kit and subjected to Illumina sequencing (HiSeq 4000).

treatment_protocol: Day 9 Serum transfer inflammatory arthritis model.

tag: disease state

value: serum transfer inflammatory arthritis model

value: CD45-ve synovial cells

tag: replicate


title: 1503GM


title: inflamed_R2

description:
matrix.mtx
barcodes.tsv
genes.tsv


title: 1496GM


title: 1495GM


title: 1488GM


title: inflamed_R1

description:
matrix.mtx
barcodes.tsv
genes.tsv


title: MN_inv(Nsi-Itga6)del(13HD) (ssRNA-seq)

city: Lausanne

first: Fabrice

last: Darbellay

address: Station 19

department: SV/ISREC

institute: EPFL

description: metanephros E13.5 polyA RNA homozygote HoxD inv(Nsi-Itga6)del(13HD)

data_processing:
adapters and bad quality bases were removed with cutadapt (Martin et al 2011, v.1.6, options -m 15 -q 30 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
reads were then mapped using STAR with the ENCODE settings (Dobin et al 2013, v.2.5.2b) on the relevant wild-type or customized mm10 mutant genome, with the corresponding gtf files (sequences and gtf annotations available on figshare DOI: 10.6084/m9.figshare.7752065)
FPKM values were determined by Cufflinks (Trapnell et al 2010, v.2.2.1) with the following options: -I 600000 -F 0.05 -j 0.05—compatible-hits-norm–multi-read-correct-library-type fr-firststrand -m 45 -s 20 --min-intron-length 40
reads were filtered for uniquely mapped read (NH:i:1) and strand specific coverage was computed using BEDTools (Quinlan et al. 2010, v.2.19.1)
Genome_build: mm10 for: AUT_bal, MN_bal1, MN_bal2, MN_1, MN_2, MN_inv(Nsi-Itga6)_1, MN_inv(Nsi-Itga6)_2, MN_inv(Nsi-Itga6)del(13HD), mutant genome versions of mm10: HoxD d13lacZ for MN_d13Z, HoxD inv(11-12)d13lacZ for MN_inv1112d13Z and MN_inv1112del11d13Z, HoxD del(CTCF:d12d13) for MN_del(CTCFd12d13)_1 and MN_del(CTCFd12d13)_2, HoxD inv(11) for AUT_inv(11) and MN_inv(11), HoxD inv(12) for AUT_inv(12) and MN_inv(12) (sequences and gtf annotations available on figshare DOI: 10.6084/m9.figshare.7752065)
Supplementary_files_format_and_content: bedgraph files contain the strand specific coverage, txt files contains FPKM values

molecule: polyA RNA

source_name: E13.5 metanephros

extract_protocol:
Whole RNA was extracted from micro-dissected tissues using RNeasy plus micro kit (Qiagen) following the manufacturer recommendations
At least 1.5ug of total RNA (RIN>9) was prepared for stranded RNA sequencing using TruSeq kits (Illumina). Samples were poly(A)-enriched.

tag: genotype

tag: embryonic age

value: metanephros


title: MN_inv1112del11d13Z (ssRNA-seq)

description: metanephros E13.5 polyA RNA homozygote HoxD inv(11-12)del(11)d13lacZ


title: ThawGradient-Ex-Core3-35cm

tag: soil origin

tag: sequence


title: 1487GM


title: ThawGradient-Ex-Core3-25cm

tag: molecule subtype


title: ThawGradient-Ex-Core2-91cm


title: ThawGradient-Ex-Core3-0cm


title: ThawGradient-Ex-Core2-81cm


title: ThawGradient-Ex-Core3-14cm


title: 1469GM


title: ThawGradient-Ex-Core2-41cm


title: 1483GM


title: ThawGradient-Ex-Core2-51cm


title: MN_inv1112d13Z (ssRNA-seq)

description: metanephros E13.5 polyA RNA homozygote HoxD inv(11-12)d13lacZ


title: aCGH_HIVneg_DLBCL_pt39

city: Scottsdale

first: Alanna

last: Maguire

state: Arizona

address: 13400 East Shea Blvd

department: Research

institute: Mayo Clinic

hyb_protocol: Labeled DNA was hybridized without ozone scavenger and chips washed according to manufacture's protocol for 40 hours in a rotating 65°C oven.

scan_protocol: All microarray slides were scanned using an Agilent 2565C DNA scanner and the images were analyzed with Agilent Feature Extraction version 11.0 using default settings.

data_processing: Data was extracted from the TIFF files using Agilent FE 10.  The aCGH data was assessed with a series of QC metrics then analyzed using an aberration detection algorithm (ADM2) [PMID16597236]. The latter identifies all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score derived from the average normalized log ratios of all probes in the genomic interval multiplied by the square root of the number of these probes. This score represents the deviation of the average of the normalized log ratios from its expected value of zero and is proportional to the height h (absolute average log ratio) of the genomic interval, and to the square root of the number of probes in the interval.

source_name: DLBCL

label_protocol: Extracted DNA was treated with DNAse 1 prior to Klenow-based labeling. High molecular weight templates were digested for 30 minutes while the smaller fragmented FFPE-derived DNA samples were digested for only 1 minute. In each case 1 ul of 10x DNase 1 reaction buffer and 2 μl of DNase 1 dilution buffer were added to 7 μl of DNA sample and incubated at room temperature then transferred to 70°C for 30 minutes to deactivate DNase 1. Sample and reference templates were then labeled with Cy-3 dUTP and Cy-5 dUTP respectively using a BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to our published protocols [PMID 26317899]. All labeling reactions were assessed using a Nanodrop assay (Nanodrop, Wilmington, DE) prior to mixing and hybridization to CGH arrays (Agilent Technologies, Santa Clara, CA).

extract_protocol: Qiagen Allprep DNA/RNA FFPE kit (cat#80204) was used to extract total mRNA and DNA from FFPE sections as per manufacturer guidelines found here. No more than two 10mm sections were applied to a single spin column.

treatment_protocol: One 5mm and two 10mm sections were cut from each FFPE tissue block. H&E staining was performed on the 5mm section. H&E stained sections were reviewed by a hematopathologist to confirm diagnosis and assess tumor content (tumors with <70% were macrodissected)

tag: subject id

tag: tissue preparation

value: FFPE

tag: specimen site

value: Brain

tag: hiv status

value: HIV negative

tag: Sex

value: Female

source_name: Reference pooled 46XX

tag: sample type

value: Normal female genome


title: 1468GM

tag: tissue

value: 190 days


title: aCGH_HIVneg_DLBCL_pt38

value: Small bowel

value: Male


title: ThawGradient-Ex-Core2-25cm

value: Akaska acidic tundra

value: single stranded oligonucleotide


title: ThawGradient-Ex-Core2-13cm


title: 1467GM


title: MN_del(CTCFd12d13)_2 (ssRNA-seq)

description: metanephros E13.5 polyA RNA trans-heterozygote HoxD del(CTCFd12d13)/del(8-13)

value: HoxD del(CTCFd12d13)/del(8-13)

tag: strain


title: MN_del(CTCFd12d13)_1 (ssRNA-seq)


title: MN_inv(12) (ssRNA-seq)

description: metanephros E13.5 polyA RNA trans-heterozygote HoxD inv(12)/del(8-13)


title: RNA-seq_HEK293-GR_siNON_dex_rep3

city: Kuopio

first: Einari

middle: A

last: Niskanen

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

description:
RNA-seq sample
RNA-seq_HEK293-GR_siNON-vs-siIRF2BP2_EtOH-vs-dex.txt.gz

data_processing:
The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artifacts, trimming reads, quality filtering and collapsing identical reads).
For RNA-seq, raw reads were trimmed using trimmomatic (v. 0.33; parameters LEADING:5 TRAILING:5 MINLEN:36) and poly-A tails were removed using HOMER (homerTools trim -3 AAAAAAAA -mis 1 -min 36). Contaminants reported in iGENOME hg19 were removed using bowtie2 and remaining reads were mapped to human hg19 transcriptome and genome with tophat2. Differential expression of genes was analyzed using edgeR and expression values (FPKM) from combined replicates using HOMER.
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-seq, tables with results from the differential gene expression analysis (siNON vs siIRF2BP2, EtOH vs dex vs TNF vs DT) and expression (FPKM) are given as tab delimited text files.

growth_protocol: Isogenic HEK293 cells (Flp-In 293, ThermoFisher Scientific) that constitutively express GR (HEK293-GR) were maintained in Dulbecco’s modified Eagle’s medium (Gibco® Invitrogen) supplemented with 10% (v/v) fetal bovine serum (FBS), 25 U/ml penicillin, 25 µg/ml streptomycin and 100 µg/ml hygromycin-B. Adenocarcinoma human alveolar basal epithelial cells (A549, ATCC) were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Gibco® Invitrogen) supplemented with 10% (v/v) fetal bovine serum (FBS), 25 U/ml penicillin and 25 µg/ml streptomycin.

extract_protocol:
For RNA-seq, RNA was extracted using RNease Plus Mini kit (Qiagen) and mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
Library preparation was done using NEBNext Ultra II kit (New England Biolabs) and sequenced using Illumina Hiseq2000 at EMBL GeneCore (Heidelberg, Germany).

treatment_protocol: For siRNA transfection, medium was changed to steroid-depleted medium (DMEM containing 2.5% (v/v) charcoal-stripped FBS). Cells were transfected with 20 nM siRNAs (Dharmacon, ON-TARGETplus SMARTpool) against IRF2BP2 (L-007177-02-0005), or non-targeting control siRNA (Dharmacon, non-targeting pool) for two (ChIP-seq) or three (RNA-seq) days using Lipofectamine RNAiMAX transfection reagent (Invitrogen). For ChIP-seq, HEK293-GR cells were treated with 100 nM dexamethasone (dex) or vehicle (EtOH, equal amount of ethanol) for 1h before fixing with formaldehyde. For RNA-seq, cells were treated for six hours with vehicle (EtOH, ethanol), 100 nM dexamethasone (dex), 10 ng/ml tumor necrosis factor alpha (TNF), or co-treated with both dex and TNF (DT), before extracting the RNA.

tag: cell line

tag: treatment 1

value: siNON transfection in steroid-depleted medium, 72h

tag: treatment 2

value: dexamethasone, 100 nM, 6h


title: RNA-seq_HEK293-GR_siNON_dex_rep4


title: ThawGradient-Ex-Core2-35cm


title: RNA-seq_HEK293-GR_siNON_dex_rep2


title: MN_inv(11) (ssRNA-seq)

description: metanephros E13.5 polyA RNA trans-heterozygote HoxD inv(11)/del(8-13)

data_processing:
samples MN_inv(Nsi-Itga6)_1 and MN_inv(Nsi-Itga6)_2 were decontaminated from 4C-seq viewpoints reads using barcode_splitter (http://hannonlab.cshl.edu/fastx_toolkit/galaxy.html, v1.2, options –mismatches 3 –partial 0 –bol) and the barcode file decontamination_4C_inv(Nsi-Itga6).txt provided
adapters and bad quality bases were removed with cutadapt (Martin et al 2011, v.1.6, options -m 15 -q 30 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
reads were then mapped using STAR with the ENCODE settings (Dobin et al 2013, v.2.5.2b) on the relevant wild-type or customized mm10 mutant genome, with the corresponding gtf files (sequences and gtf annotations available on figshare DOI: 10.6084/m9.figshare.7752065)
FPKM values were determined by Cufflinks (Trapnell et al 2010, v.2.2.1) with the following options: -I 600000 -F 0.05 -j 0.05—compatible-hits-norm–multi-read-correct-library-type fr-firststrand -m 45 -s 20 --min-intron-length 40
reads were filtered for uniquely mapped read (NH:i:1) and strand specific coverage was computed using BEDTools (Quinlan et al. 2010, v.2.19.1)
Genome_build: mm10 for: AUT_bal, MN_bal1, MN_bal2, MN_1, MN_2, MN_inv(Nsi-Itga6)_1, MN_inv(Nsi-Itga6)_2, MN_inv(Nsi-Itga6)del(13HD), mutant genome versions of mm10: HoxD d13lacZ for MN_d13Z, HoxD inv(11-12)d13lacZ for MN_inv1112d13Z and MN_inv1112del11d13Z, HoxD del(CTCF:d12d13) for MN_del(CTCFd12d13)_1 and MN_del(CTCFd12d13)_2, HoxD inv(11) for AUT_inv(11) and MN_inv(11), HoxD inv(12) for AUT_inv(12) and MN_inv(12) (sequences and gtf annotations available on figshare DOI: 10.6084/m9.figshare.7752065)
Supplementary_files_format_and_content: bedgraph files contain the strand specific coverage, txt files contains FPKM values and the supplementary text file decontamination_4C_inv(Nsi-Itga6).txt contains the sequences of the 4C-seq viewpoints used to treat samples MN_inv(Nsi-Itag6)_1 and MN_inv(Nsi-Itga6)_2


title: MN_d13Z (ssRNA-seq)

description: metanephros E13.5 polyA RNA homozygote HoxD d13lacZ

value: HoxD d13lacZ/d13lacZ


title: 1456GM

value: Gluteus medius

tag: age


title: 1452GM


title: aCGH_HIVneg_DLBCL_pt37

value: Tongue


title: ThawGradient-Ex-Core1-83cm


title: aCGH_HIVneg_DLBCL_pt34

value: Liver


title: MN_bal_2 (ssRNA-seq)

description: metanephros E13.5 polyA RNA heterozygote HoxD +/del(8-13)

data_processing:
adapters and bad quality bases were removed with cutadapt (Martin et al 2011, v.1.6, options -m 15 -q 30 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
reads were then mapped using STAR with the ENCODE settings (Dobin et al 2013, v.2.5.2b) on the relevant wild-type or customized mm10 mutant genome, with the corresponding gtf files (sequences and gtf annotations available on figshare DOI: 10.6084/m9.figshare.7752065)
FPKM values were determined by Cufflinks (Trapnell et al 2010, v.2.2.1) with the following options: -I 600000 -F 0.05 -j 0.05—compatible-hits-norm–multi-read-correct-library-type fr-firststrand -m 45 -s 20 --min-intron-length 40
reads were filtered for uniquely mapped read (NH:i:1) and strand specific coverage was computed using BEDTools (Quinlan et al. 2010, v.2.19.1)
Genome_build: mm10 for: AUT_bal, MN_bal1, MN_bal2, MN_1, MN_2, MN_inv(Nsi-Itga6)_1, MN_inv(Nsi-Itga6)_2, MN_inv(Nsi-Itga6)del(13HD), mutant genome versions of mm10: HoxD d13lacZ for MN_d13Z, HoxD inv(11-12)d13lacZ for MN_inv1112d13Z and MN_inv1112del11d13Z, HoxD del(CTCF:d12d13) for MN_del(CTCFd12d13)_1 and MN_del(CTCFd12d13)_2, HoxD inv(11) for AUT_inv(11) and MN_inv(11), HoxD inv(12) for AUT_inv(12) and MN_inv(12) (sequences and gtf annotations available on figshare DOI: 10.6084/m9.figshare.7752065)
Supplementary_files_format_and_content: bedgraph files contain the strand specific coverage, txt files contains FPKM

tag: genotype

value: metanephros


title: ThawGradient-Ex-Core2-0cm


title: ThawGradient-Ex-Core1-53cm


title: ThawGradient-Ex-Core1-73cm


title: RNA-seq_HEK293-GR_siNON_dex_rep1


title: ThawGradient-Ex-Core1-43cm


title: MN_bal_1 (ssRNA-seq)

tag: embryonic age


title: aCGH_HIVneg_DLBCL_pt33

value: FFPE

value: Lt anterior cervical LN


title: RNA-seq_HEK293-GR_siNON_EtOH_rep4

value: ethanol, 6h


title: aCGH_HIVneg_DLBCL_pt35

value: Lt Femoral LN

value: HIV negative

value: Normal female genome


title: aCGH_HIVneg_DLBCL_pt36

value: Lt axillary mass

value: Male


title: RNA-seq_HEK293-GR_siNON_EtOH_rep3


title: RNA-seq_HEK293-GR_siNON_EtOH_rep2


title: AUT_inv(11) (ssRNA-seq)

description: distal forelimbs E12.5 polyA RNA trans-heterozygote HoxD inv(11)/del(8-13)

source_name: E12.5 distal forelimbs

value: distal forelimbs


title: AUT_inv(12) (ssRNA-seq)

description: distal forelimbs E12.5 polyA RNA trans-heterozygote HoxD inv(12)/del(8-13)


title: aCGH_HIVneg_DLBCL_pt32

value: Lt supraclavicular LN


title: gene_expression_HIVpos_DLBCL_pt39

description:
The commerical PanCancer Pathways panel was customised with the addition of 9 genes. This necessitated two RLF files, which were merged prior to running samples on the nCounter system. PanCancer rlf file = NS_CANCERPATH_C2535. BCL2 spike-in rlf file = PLS_SCHATZ_C5316
RLF File version: 1.7

hyb_protocol: The now hybridized RNA/capture/reporter complexes are loaded onto the automated nCounter Prep Station where it is bound to the stredavidin coated glass cartridge via the biotin labeled capture probe.

scan_protocol: Once the RNA/capture/reporter complex is bound to the glass cartridge, the cartridge is transferred to the nCounter Digital Analyzer. An E-field orientates RNA complexes for imaging. Up to 555 fields of view (FOV) are imaged and the flourescent barcodes are enumerated.

data_processing:
Expression data was extracted and QC'd using nSolver 3.0. Using the internal NanoString negative controls, the 99% CI threshold was determined and the data normalized as described and demonstrated in this webinar.
The sample table data is the QC'd and normalised data used to perform differential expression analysis using the statistical method NanoStringDiff described here.

label: Biotin capture probe, fluorescent barcoded reporter probe

label_protocol: 300 ng of total RNA was hybridized for 12-20 hours at 65°C with the NanoString biotin labeled capture and flourescent barcoded reporter codesets as described here.

value: Diffuse Large B-Cell Lymphoma (DLBCL)

value: Superior cervical LN

value: HIV positive

tag: age (yrs)

tag: coo

value: GCB

tag: fov

tag: binding density


title: gene_expression_HIVpos_DLBCL_pt40

tag: subject id

tag: tissue preparation

value: Lt neck mass


title: ThawGradient-Ex-Core1-15cm

tag: soil origin

value: Akaska acidic tundra

tag: sequence

tag: molecule subtype

value: single stranded oligonucleotide


title: AUT_bal (ssRNA-seq)

description: distal forelimbs E12.5 polyA RNA heterozygote HoxD +/del(8-13)

tag: tissue


title: RNA-seq_HEK293-GR_siNON_EtOH_rep1

value: siNON transfection in steroid-depleted medium, 72h


title: gene_expression_HIVpos_DLBCL_pt38

value: FFPE

tag: specimen site

value: Thoracic epidural mass

tag: hiv status

tag: Sex


title: Ern1-LKO biological rep2

description: Liver total RNA from Ern1 liver specific knockout mouse

data_processing:
Illimina RTA used for base calling and converting into raw FASTQ files with Bcl2Fastq conversion software.
quality control using fastQC version 0.11.3
mRNA-seq reads were aligned to the mm10 genome assembly using TopHat2 version 2.0.14 with the default parameters.
FPKM (fragments per kilobase of exon per million fragments mapped)  were calculated using Cufflinks version 2.2.1 .
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each Sample and gene expression ratio.

source_name: Liver from Ern1-LKO mouse

extract_protocol:
Liver were harvested and flash frozen in liquid nitrogen, and total RNA was isolated using RNAiso reagent.
NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used with 1.5 μg of total RNA for librariesgeneration. RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Liver

value: 8 weeks of age

value: Liver specific Ern1 knockout mouse


title: gene_expression_HIVpos_DLBCL_pt37

value: Iliac crest, bilateral


title: RNA-seq_HEK293-GR_siIRF2BP2_dex_rep4

tag: cell line

tag: treatment 1

value: siIRF2BP2 transfection in steroid-depleted medium, 72h

tag: treatment 2

value: dexamethasone, 100 nM, 6h


title: ThawGradient-Ex-Core1-5cm


title: aCGH_HIVneg_DLBCL_pt30

value: Soft tissue chest wall

value: HIV negative

value: Female

tag: age

tag: sample type

value: Normal female genome


title: aCGH_HIVneg_DLBCL_pt29

value: Lt groin LN

value: Male


title: RNA-seq_HEK293-GR_siIRF2BP2_dex_rep3


title: aCGH_HIVneg_DLBCL_pt31

value: Rt lobe of thyroid


title: Ern1-LKO biological rep1

tag: genotype


title: wildtype biological rep2

description: Liver total RNA from wild-type mouse - control mouse for liver specific Ern1 knockout

source_name: Liver from wild-type mouse

value: Wild-type mouse - control mouse for liver specific knockout Ern1


title: gene_expression_HIVpos_DLBCL_pt35

value: Diffuse Large B-Cell Lymphoma (DLBCL)

value: Lt neck LN

value: HIV positive

tag: age (yrs)

tag: coo

value: GCB

tag: fov

tag: binding density


title: gene_expression_HIVpos_DLBCL_pt36

tag: subject id

tag: tissue preparation

value: FFPE

value: Rt thyroid


title: gene_expression_HIVpos_DLBCL_pt34

tag: tissue

value: Rt atrium


title: RNA-seq_HEK293-GR_siIRF2BP2_dex_rep2

value: siIRF2BP2 transfection in steroid-depleted medium, 72h


title: aCGH_HIVneg_DLBCL_pt27

tag: specimen site

value: Lt supraclavicular LN


title: aCGH_HIVneg_DLBCL_pt28

value: Rt cervical LN

tag: hiv status


title: aCGH_HIVneg_DLBCL_pt26

value: Rt axillary LN bx

value: HIV negative

tag: Sex


title: RNA-seq_HEK293-GR_siIRF2BP2_EtOH_rep4

value: ethanol, 6h


title: K562_WT_H3K18Ac_ChIP_rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw read quality was first assessed with fastqc (version 0.11.3, Babraham Bioinformatics), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36). Reads were then aligned to the mouse (UCSC mm9) or human (UCSC hg19) reference genome with Bowtie  with options –n 2 –k 10 (version 1.1.1), and converted to BAM format with Samtools (version 0.1.19).
Peak calling was performed using MACS (version 1.4.2) with default parameters.
For H3K18Ac ChIP, RPKM-normalized signal files (bigWig) were generated from BAM data using DeepTools (version 2.4.2). For SIRT7 ChIP, signal files generated by MACS peakcalling step were converted to bigWig using the UCSC utility wigToBigWig.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: bed files contain called peaks from ChIP-seq Data. BigWig files contain ChIP-seq signal that was RPKM normailzed (H3K18Ac ChIP data) or non-normalized (SIRT7 ChIP data)

value: wild type

tag: chip antibody


title: wildtype biological rep1

tag: strain

value: Liver

value: 8 weeks of age


title: gene_expression_HIVpos_DLBCL_pt32

value: Rt breast chest wall lesion

value: Female


title: K562_WT_SIRT7_ChIP_rep2

tag: cell line

value: SIRT7 (Cell Signalling, 5360, Lot 1)


title: RNA-seq_HEK293-GR_siIRF2BP2_EtOH_rep3

tag: treatment 1

tag: treatment 2


title: RNA-seq_HEK293-GR_siIRF2BP2_EtOH_rep2


title: aCGH_HIVneg_DLBCL_pt23

value: Ovary/sm bowel LN

tag: age

tag: sample type

value: Normal female genome


title: RNA-seq_HEK293-GR_siIRF2BP2_dex_rep1

value: dexamethasone, 100 nM, 6h


title: gene_expression_HIVpos_DLBCL_pt33

value: Diffuse Large B-Cell Lymphoma (DLBCL)

value: FFPE

value: Pancreas

value: HIV positive

value: Male

tag: age (yrs)

value: GCB


title: K562_WT_H3K18Ac_ChIP_rep1

tag: genotype


title: aCGH_HIVneg_DLBCL_pt25

value: Sm bowel, mid jejunum

value: HIV negative


title: K562_INPUT

value: wild type


title: gene_expression_HIVpos_DLBCL_pt31

value: Rt mandibular mass

tag: coo

tag: fov


title: gene_expression_HIVpos_DLBCL_pt30

tag: subject id

value: Rt neck mass

tag: binding density


title: aCGH_HIVneg_DLBCL_pt24

tag: tissue preparation

value: Rt axillary LN


title: gene_expression_HIVpos_DLBCL_pt29

tag: tissue

tag: specimen site

value: Lt axillary mass


title: polysome-seq rep1

city: Beijing

first: shaofang

last: Li

state: Beijing

address: No 50, ZhanghuaLu, HAIDIAN

department: Beijing Vegetable Research Center

institute: Beijing Academy of Agriculture and Forestry Science

description:
RNA-seq
rRNA-depleted Total RNA

data_processing:
All sequenced reads were collapsed to non-redudant reads and mapped back to Araport 11 genome using STAR with maximum 8 mismatches.
Genome_build: Araport 11
Supplementary_files_format_and_content: Wiggle format files with normalized read densities for each nucleotide. The normalized reads were calculated as RPM(reads per million)

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis thaliana Col-0 seeds were stratified at 4°C for 3 days in the dark. Sterilized seeds were dispersed onto plates containing 1/2 Murashige and Skoog (MS) medium, 1% (w/v) sucrose and 0.7% (w/v) agar, and grown for 12 days in growth rooms with 16h light/8h dark cycles at 22°C. 12-day-old seedlings and unopen flower buds were collected for this study.

extract_protocol:
Total RNAs were extracted from 12-day-old seedlings and inflorescences by the Trizol reagent, and then treated with DNase I (Roche; 1U /μgRNA at 37 °C for 60 min).
NEBNext® Ultra™ Directional RNA Library Prep Kit was used for subsequent RNA library preparation. The First Strand Synthesis Reaction Buffer (containing zinc ions to fragment RNA) was mixed with the random primers to make the reverse transcription mixture (RT mixture). The beads with bound NAD+-capped RNAs were suspended with the RT mixture and incubated at 94°C for 6 min to 1) elute the RNAs from beads, 2) fragment the RNAs, and 3) denature the RNAs. Then RNase Inhibitor and reverse transcriptase were added to initiate first strand cDNA synthesis. The remaining steps were performed according to manufacturer’s instructions
NAD+- capture RNA seq

treatment_protocol: Isolation of NAD+-capped RNA was according to the original capture protocol (6, 13) with minor modifications as follows. 100 μg total or polysomal RNAs were incubated in 100μl reactions containing 0.85 μM ADPRC (or left out as a control), 10%(vol/vol) of 4-pentyn-1-ol (Sigma), 50 mM Hepes, and 5 mM MgCl2 (pH 7) at 37 °C for 30 min. The reactions were stopped by low PH phenol/chloroform extraction. The RNAs were precipitated and then treated with 250 μM biotin-PEG3-azide, 1 mM fresh CuSO4, 0.5 mM Tris (3-hydroxypropyltriazolylmethyl) amine (THPTA, Sigma), 2 mM sodium ascorbate, 50 mM Hepes, and 5 mM MgCl2 (pH 7) at 25°C for 30 min. After acid phenol/chloroform extraction and precipitation, the RNAs were incubated with 25μl MyOne Streptavidin C1 beads (pre-blocked with BSA and E. coli tRNA for 20 min) for 1 hr in 100μl immobilization buffer (1M NaCl, 10mM Hepes pH7 and 5mM EDTA).


title: K562_WT_SIRT7_ChIP_rep1

value: SIRT7 (Cell Signalling, 5360, Lot 1)


title: RNA-seq_A549_siNON_dex_rep1

description:
RNA-seq sample
RNA-seq_A549_siNON-vs-siIRF2BP2_EtOH-vs-dex-vs-TNF-vs-DT.txt.gz

source_name: A549 cells

value: siNON transfection in steroid-depleted medium, 72h


title: polysome-seq rep2

description:
RNA-seq
rRNA-depleted Total RNA


title: RNA-seq_HEK293-GR_siIRF2BP2_EtOH_rep1

value: siIRF2BP2 transfection in steroid-depleted medium, 72h

value: ethanol, 6h


title: RNA-seq_A549_siNON_dex_rep3

value: dexamethasone, 100 nM, 6h


title: RNA-seq_A549_siNON_dex_rep2


title: total mRNA-seq rep2

description:
RNA-seq
rRNA-depleted Total RNA


title: gene_expression_HIVpos_DLBCL_pt28

value: Diffuse Large B-Cell Lymphoma (DLBCL)

value: FFPE

value: Lt axilla

tag: hiv status

tag: Sex


title: gene_expression_HIVpos_DLBCL_pt27

value: Scalp

value: HIV positive

value: Male


title: RNA-seq_A549_siNON_TNF_rep3

value: TNF, 10 ng/ml, 6h


title: gene_expression_HIVpos_DLBCL_pt26

value: Rt axillary mass

value: GCB


title: RNA-seq_A549_siNON_TNF_rep2


title: aCGH_HIVneg_DLBCL_pt21

value: LN, site not specified

value: HIV negative

value: Female

value: Normal female genome


title: aCGH_HIVneg_DLBCL_pt20

value: Rt inguinal LN


title: total_mRNA-seq rep1

description: RNA-seq

tag: strain


title: aCGH_HIVpos_DLBCL_pt18

value: Lt groin mass


title: RNA-seq_A549_siNON_EtOH_rep2

tag: cell line

value: siNON transfection in steroid-depleted medium, 72h

value: ethanol, 6h


title: gene_expression_HIVpos_DLBCL_pt25

value: Diffuse Large B-Cell Lymphoma (DLBCL)

value: Rt axillary LN, Dermis


title: aCGH_HIVpos_DLBCL_pt14

value: FFPE

value: Rt axilliary mass


title: polysome NAD_N rep2

description:
NAD captureSeq
rRNA-depleted Total RNA


title: gene_expression_HIVpos_DLBCL_pt24

value: RT testes

value: HIV positive


title: gene_expression_HIVpos_DLBCL_pt22

value: Male


title: aCGH_HIVpos_DLBCL_pt16

value: Lt axilla LN


title: aCGH_HIVpos_DLBCL_pt19

value: Lt neck mass


title: polysome NAD_N rep1

description:
NAD captureSeq
rRNA-depleted Total RNA


title: gene_expression_HIVpos_DLBCL_pt23

value: Lt axillary LN

value: GCB


title: gene_expression_HIVneg_DLBCL_pt21

value: Brain

value: HIV negative

value: Female


title: polysome NAD_P rep2

description:
NAD captureSeq
rRNA-depleted Total RNA


title: RNA-seq_A549_siNON_EtOH_rep3

tag: treatment 1


title: aCGH_HIVpos_DLBCL_pt15

value: Thoracic epidural mass

value: Normal female genome


title: aCGH_HIVneg_DLBCL_pt22

value: Lt cervical LN


title: polysome NAD_P rep1

description:
NAD captureSeq
rRNA-depleted Total RNA


title: total NAD_N rep2

description:
NAD captureSeq
rRNA-depleted Total RNA


title: RNA-seq_A549_siNON_EtOH_rep1

value: siNON transfection in steroid-depleted medium, 72h

tag: treatment 2

value: ethanol, 6h


title: aCGH_HIVpos_DLBCL_pt10

value: FFPE

value: Rt atrium

tag: age


title: total NAD_N rep1

description:
NAD captureSeq
rRNA-depleted Total RNA


title: aCGH_HIVpos_DLBCL_pt11

value: Lt neck LN

tag: sample type


title: aCGH_HIVpos_DLBCL_pt17

value: Superior cervical LN

value: HIV positive


title: gene_expression_HIVneg_DLBCL_pt20

value: Diffuse Large B-Cell Lymphoma (DLBCL)

value: Small bowel

value: Male

tag: age (yrs)


title: RNA-seq_A549_siNON_DT_rep3

value: dexamethasone (100 nM) and TNF (10 ng/ml), 6h


title: RNA-seq_A549_siNON_DT_rep1


title: total NAD_P rep2

description:
NAD captureSeq
rRNA-depleted Total RNA


title: RNA-seq_A549_siNON_DT_rep2


title: aCGH_HIVpos_DLBCL_pt09

value: Terminal ileum, rt colon


title: aCGH_HIVpos_DLBCL_pt13

value: Rt thyroid


title: gene_expression_HIVneg_DLBCL_pt19

value: Tongue

value: HIV negative

value: GCB


title: gene_expression_HIVneg_DLBCL_pt18

value: Abdominal wall mass

value: Female


title: total NAD_P rep1

description:
NAD captureSeq
rRNA-depleted Total RNA


title: mRNAseq rep2

description: RNA-seq


title: RNA-seq_A549_siIRF2BP2_dex_rep2

value: siIRF2BP2 transfection in steroid-depleted medium, 72h

value: dexamethasone, 100 nM, 6h


title: RNA-seq_A549_siIRF2BP2_dex_rep3


title: gene_expression_HIVneg_DLBCL_pt17

value: FFPE

value: Lt axillary mass


title: mRNAseq rep1

description: RNA-seq


title: gene_expression_HIVneg_DLBCL_pt16

value: Lt Femoral LN


title: gene_expression_HIVneg_DLBCL_pt15

value: Liver


title: RNA-seq_A549_siIRF2BP2_dex_rep1


title: RNA-seq_A549_siIRF2BP2_TNF_rep3

value: TNF, 10 ng/ml, 6h


title: aCGH_HIVpos_DLBCL_pt08

value: Pancreas

value: HIV positive

value: Normal female genome


title: MDA-MB-231_4hr_+Glucose_rep3

city: Houston

first: Liuqing

last: Yang

state: Texas

address: 1515 Holcombe Blvd.

department: Molecular and Cellular Oncology

institute: The University of Texas MD Anderson Cancer Center

description: LncRNA expression after 4hr in 25mM glucose-stimulated human breast cancer cells

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs that at least 2 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs were identified through Fold Change filtering between two samples. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 12.1). GO analysis and Pathway analysis were performed in the standard enrichment computation method.

source_name: Breast cancer cell line, 4hr, 25mM glucose,replicate 3

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: MDA-MB-231 cells were maintained in Dulbecco modified essential medium (DMEM) supplemented with 10% fetal bovine serum (FBS) at 37 °C in 5% CO2 (v/v).

extract_protocol: Total RNAs were  isolated from glucose-starved and - stimulated cells using RNeasy Plus RNA Purification Kit (Qiagen, Valencia CA) following the manufacturer's recommendations. RNA quantity and quality were measured by NanoDrop ND-2000 and RNA integrity was assessed by Bioanalyzer.

treatment_protocol: MDA-MB-231 cells were subjected to glucose starvation overnight in glucose-free DMEM supplemented with 10% fetal bovine serum (FBS). The next morning, glucose-starved cells were either continuously maintained in glucose-free DMEM or stimulated with DMEM containg 25 mM glucose for 4 hr.

value: breast; derived from metastatic site:pleural effusion

tag: gender


title: mRNA NAD_N rep2

description:
NAD captureSeq
rRNA-depleted Total RNA


title: MDA-MB-231_4hr_+Glucose_rep1

source_name: Breast cancer cell line, 4hr, 25mM glucose,replicate 1


title: mRNA NAD_N rep1

description:
NAD captureSeq
rRNA-depleted Total RNA


title: mRNA NAD_P rep2

description:
NAD captureSeq
rRNA-depleted Chromatin RNA


title: RNA-seq_A549_siIRF2BP2_TNF_rep2


title: RNA-seq_A549_siIRF2BP2_TNF_rep1


title: mRNA NAD_P rep1


title: RNA-seq_A549_siIRF2BP2_EtOH_rep3

value: ethanol, 6h


title: gene_expression_HIVneg_DLBCL_pt13

value: Diffuse Large B-Cell Lymphoma (DLBCL)

value: Lt supraclavicular LN

value: Male

tag: coo


title: gene_expression_HIVneg_DLBCL_pt12

value: Rt lobe of thyroid

value: HIV negative

value: GCB

tag: fov


title: gene_expression_HIVneg_DLBCL_pt11

tag: subject id

value: Soft tissue chest wall

value: Female


title: aCGH_HIVpos_DLBCL_pt12

value: FFPE

value: Sm bowel mesentery


title: MDA-MB-231_4hr_-Glucose_rep3

description: LncRNA expression after 4hr in glucose-starved human breast cancer cells

source_name: Breast cancer cell line, 4hr, glucose starvation,replicate 3


title: MDA-MB-231_4hr_+Glucose_rep2

source_name: Breast cancer cell line, 4hr, 25mM glucose,replicate 2


title: MDA-MB-231_4hr_-Glucose_rep1

source_name: Breast cancer cell line, 4hr, glucose starvation,replicate 1


title: tandem5splicesites_library_protein

city: Haifa

first: Martin

last: Mikl

address: Abba Khoushy 199

department: Department of Human Biology

country: Israel

institute: University of Haifa

description:
amplicon sequencing
fivedf.csv

data_processing:
base-calling (Illumina)
mapping to the designed sequence libraries with custom Python scripts (will be provided as part of the published manuscript)
computing RNA-based splicing ratios or protein-based splicing values using custom Python scripts (will be provided as part of the published manuscript)
Supplementary_files_format_and_content: csv, contains the sequences of the library and the computed splicing ratios/splicing values

organism:
Homo sapiens
synthetic construct

source_name: K562 cells with integrated reporter construct

growth_protocol: 37deg Celsius, 5% CO2

extract_protocol:
NucleoSpin RNA II kit (MACHEREY-NAGEL), SuperScript® III First-Strand Synthesis System (Thermo Fisher Scientific) for RNA samples, DNeasy Blood & Tissue Kit (Qiagen) for genomic DNA samples
PCR to amplify the reporter library, library preparation following Illumina protocols for Truseq. End repair, poly A addition, adaptor ligation, enrichment.
Sequencing of PCR amplicons (from cDNA or genomic DNA)

value: splicing library integrated in the AAVS1 locus (single copy per cell)

tag: genotype

value: 6 AAVS1 site mutated


title: MDA-MB-231_4hr_-Glucose_rep2

source_name: Breast cancer cell line, 4hr, glucose starvation,replicate 2


title: gene_expression_HIVneg_DLBCL_pt14

tag: tissue preparation

value: Lt anterior cervical LN

tag: binding density


title: inflorenscence NAD_N rep2

source_name: inflorenscence


title: aCGH_HIVpos_DLBCL_pt03

tag: specimen site

value: Scalp

value: HIV positive


title: retained_introns_library_protein

description:
amplicon sequencing
irdf.csv

value: 5 AAVS1 site mutated


title: RNA-seq_A549_siIRF2BP2_EtOH_rep2

value: siIRF2BP2 transfection in steroid-depleted medium, 72h

value: ethanol, 6h


title: inflorenscence NAD_N rep1


title: gene_expression_HIVneg_DLBCL_pt10

tag: tissue

value: Diffuse Large B-Cell Lymphoma (DLBCL)

value: Lt groin LN

tag: hiv status


title: aCGH_HIVpos_DLBCL_pt06

value: Rt neck mass

tag: Sex

value: Male

value: Normal female genome


title: RNA-seq_A549_siIRF2BP2_EtOH_rep1

tag: cell line


title: aCGH_HIVpos_DLBCL_pt04

value: Lt axilla


title: aCGH_HIVpos_DLBCL_pt05

value: Lt axillary mass


title: aCGH_HIVpos_DLBCL_pt02

value: FFPE

value: Rt axillary LN, Dermis


title: tandem3splicesites_library_RNA

description:
amplicon sequencing
threedf.csv

value: splicing library integrated in the AAVS1 locus (single copy per cell)

value: 4 AAVS1 site mutated


title: tandem5splicesites_library_RNA

description:
amplicon sequencing
fivedf.csv

value: 3 AAVS1 site mutated


title: RNA-seq_A549_siIRF2BP2_DT_rep3

tag: treatment 1

value: dexamethasone (100 nM) and TNF (10 ng/ml), 6h


title: inflorenscence NAD_P rep2

tag: strain


title: inflorenscence NAD_P rep1


title: cassette_exons_library_RNA

description:
amplicon sequencing
casdf.csv

value: 2 AAVS1 site mutated


title: seelding NAD_N rep3

description:
NAD captureSeq
rRNA-depleted Total RNA


title: gene_expression_HIVneg_DLBCL_pt08

value: Soft palate mass

value: HIV negative

value: GCB


title: seelding NAD_N rep2

description:
NAD captureSeq
rRNA-depleted Total RNA


title: retained_introns_library_RNA

description:
amplicon sequencing
irdf.csv

value: 1 AAVS1 site mutated


title: ChIP-seq_HEK293-GR_IRF2BP2_dex_rep2

description:
ChIP-seq sample
ChIP-seq_HEK293-GR_IRF2BP2_dex.bed

data_processing:
The quality of raw reads was analyzed by FastQC and FASTX-toolkit was used for preprocessing raw reads (removal of artifacts, trimming reads, quality filtering and collapsing identical reads).
For ChIP-seq, reads were aligned against human genome hg19 with Bowtie software (version 0.12.9) with the command line: -v 1 -k 1 -m 1 -f -S --best hg19. Peak calling was done in HOMER (version 4.10.3) using findPeaks command (-F 3, -tagTreshold 20, -minDist 35) and approppriate input as a control. Two replicates were compared with each other using bedTools (intersectBed) and only those binding sites found in both replicates were used for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: For ChIP-seq, the genomic intervals of IRF2BP2 binding sites that were common to two replicates are given in bed format.

extract_protocol:
For ChIP-seq, the HEK293-GR cells were grown on 10-cm dishes in charcoal-stripped medium for 2 days, treated with vehicle or dex (100 nM, 1 h), and fixed with 1% (v/v) formaldehyde 10 min at room temperature. Chromatin was fragmented to ∼200–400 bp using sonication (Bioruptor UCD-300, Diagenode). Anti-IRF2BP2 antibody (A303190A, Bethyl laboratories) was coupled to protein-A- beads (Millipore), fragmented chromatin was incubated with antibody-coupled beads overnight, washed, eluted and de-crosslinked in the presence of proteinase K (Fermentas). Chromatin fragments were purified using MinElute columns (Qiagen). Fragmented de-crosslinked chromatin was used as an input control.
Library preparation was done using NEBNext Ultra II kit (New England Biolabs) and sequenced using Illumina Hiseq2000 at EMBL GeneCore (Heidelberg, Germany).

value: steroid-depleted medium, 48h

tag: treatment 2

value: dexamethasone, 100 nM, 1h

tag: chip antibody


title: RNA-seq_A549_siIRF2BP2_DT_rep1

value: siIRF2BP2 transfection in steroid-depleted medium, 72h


title: gene_expression_HIVneg_DLBCL_pt09

value: Diffuse Large B-Cell Lymphoma (DLBCL)

value: Rt cervical LN

value: Female

tag: age (yrs)


title: gene_expression_HIVneg_DLBCL_pt07

value: FFPE

value: Nasopharyngeal LN


title: gene_expression_HIVneg_DLBCL_pt06

value: Lt supraclavicular LN

value: Male


title: gene_expression_HIVneg_DLBCL_pt05

value: Sm bowel, mid jejunum


title: aCGH_HIVpos_DLBCL_pt01

value: Rt inguinal LN

value: HIV positive

tag: age

tag: sample type

value: Normal female genome


title: HCT_5-aza-CdR_4d_rep2_RNA

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

data_processing:
For mRRBS, basecalling was performed using Illumina RTA2 software. For RNA-seq basecalls were performed using bcl2fastq v2.17.1.14
For mRRBS and RNA-seq, indexed samples were demultiplexed to fastq files with bcl2fastq v2.17.1.14.
For mRRBS, reads were  trimmed of 10 base pairs from the 5’ end with TrimGalore! v0.4.3 to remove primer and adapter sequences. RNA-seq reads were trimmed from the 3′ end until the final base had a quality score > 30, using Trimmomatic version 0.33 (Bolger et al., 2014).
For mRRBS, Sequence alignment to the GRCh37/hg19 reference genome and methylation extraction ignoring 1 base at the 3’ end (after reviewing the M-bias plots) were performed with Bismark v0.16.3. For RNA-seq, reads were aligned to hg19 with Tophat version 2.1.0 with the following options -no-novel-juncs --read-mismatches 2 --read-edit-dist 2 --num-threads 10 --max-multihits 20 then post filtering for uniquely mapped reads using the NH flag.
Genome_build: hg19
Supplementary_files_format_and_content: Bismark tab-delimited "coverage" files for cytosines in CpG context with the following columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>
Supplementary_files_format_and_content: bigwig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA at a given genomic coordinate. RNA-seq bigwigs are split by strand.

growth_protocol: Cells were grown at 37 °C in DMEM, 1x glutamine, 10% serum, 1% penicillin/streptomycin, 5% CO2

extract_protocol:
Genomic DNA was obtained using the Dneasy blood/tissue Kit (Qiagen). RNA was exctracted using Rneasy plus mini Kit (Qiagen)
Genomic DNA was quantified with a Qubit 3.0 instrument. ~50-200 ng of genomic DNA was then digested with the restriction endonuclease MspI (New England BioLabs). Resulting fragments underwent size selection for fragments ~100-250-bp in length using SPRI beads (MagBio Genomics) and subsequent bisulfite conversion using the EZ DNA Methylation-Lightning Kit (Zymo Research) per the manufacturer’s protocol. Bisulfite conversion efficiency averaged 99.4% as estimated by the measured percent of unmethylated CpGs in λ-bacteriophage DNA (New England BioLabs N3013S) added at a 1:200 ratio to each sample. Libraries for Illumina-based sequencing were prepared with the Pico Methyl-Seq Library Prep Kit (Zymo Research) using Illumina TruSeq DNA methylation barcodes. Libraries were run on a High Sensitivity chip using an Agilent TapeStation 4200 to assess size distribution and overall quality of the amplified library. Fluorometric quantitation and TapeStation size distribution estimates permitted equimolar pooling, and six pooled libraries per run were sequenced on an Illumina NextSeq 500 instrument using the NextSeq 500/550 V2 High Output reagent kit (1 x 75 cycles). Total RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. polyA RNA was isolated with oligo d(T)25 Magnetic Beads from NEB. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit. RNA-sequencing was performed on the NextSeq 500 or Novaseq 6000 with 50 bp reads.

treatment_protocol: HEK-293T cells were treated once with [10µM] 5-azacytidine  for 24h,48h,72h,6 days,2 weeks. HCT-116 cells for bisulfite sequencing were treated once with [10µM] 5-azacytidine  for 24h,48h,72h. HCT-116 cells for RNA-seq were treated 4 times with [10µM] 5-aza-2-deoxyazacytidine for 4 days. U2OS cells were treated with  [5µM] EPZ-6438 for 7 days, treatment every other day.

tag: exposure


title: RNA-seq_A549_siIRF2BP2_DT_rep2

value: dexamethasone (100 nM) and TNF (10 ng/ml), 6h


title: seelding NAD_N rep1

description:
NAD captureSeq
rRNA-depleted Total RNA


title: ChIP-seq_HEK293-GR_IRF2BP2_dex_rep1

value: Anti-IRF2BP2 antibody (A303190A, Bethyl laboratories)


title: gene_expression_HIVneg_DLBCL_pt04

tag: subject id

value: Rt axillary LN

value: HIV negative

tag: coo

value: GCB

tag: fov


title: seelding NAD_P rep3


title: ChIP-seq_HEK293-GR_IRF2BP2_EtOH_rep1

description:
ChIP-seq sample
ChIP-seq_HEK293-GR_IRF2BP2_EtOH.bed

value: steroid-depleted medium, 48h

value: ethanol, 1h


title: seelding NAD_P rep1


title: seelding NAD_P rep2


title: gene_expression_HIVneg_DLBCL_pt03

value: Diffuse Large B-Cell Lymphoma (DLBCL)

tag: tissue preparation

value: Ovary/sm bowel LN

tag: binding density


title: gene_expression_HIVneg_DLBCL_pt02

tag: tissue

value: FFPE

tag: specimen site

value: Lt cervical LN

value: Female


title: ChIP-seq_HEK293-GR_IRF2BP2_EtOH_rep2


title: HCT_DMSO_rep2_RNA

value: DMSO


title: shPD-L1-2 repeat1

status: Public on Jun 02 2019

city: Rochester

first: Zhenkun

last: Lou

state: MN

address: 200 1st St SW

description: processed RNA-Seq data.xlsx

data_processing:
RNA seq was performed using an Illumina HiSeq 2000 sequencer at the Genomic Core facility of the Mayo Clinic, Rochester, MN. Paired-end sequencing libraries were prepared using the TruSeq Stranded Total Sample Preparation kit (Illumina) by the Mayo Clinic sequencing core facilities followed by quality control, cluster generation and sequencing on the Illumina HiSeq 2000 platform. RNA-Seq results were delivered as BAM files which were converted to FASTQ format using Picard. FASTQ files were aligned to the hg19 human reference genome using Tophat 2.0.14(Kim et al., 2013). Expression values were calculated with featureCounts v1.4.6-p2(Liao et al., 2014), and differential expression analysis was determined by DESeq2(Love et al., 2014). The downregulated genes for RNA seq were then defined by counts>100, folds>1.5 and p<0.02.
Supplementary_files_format_and_content: processed RNA-Seq data.xlsx

extract_protocol:
RNA extraction was performed using quick-RNA™ miniPrep kit (zymo) according to the manufacturer’s instructions.
Paired-end sequencing libraries were prepared using the TruSeq Stranded Total Sample Preparation kit (Illumina) by the Mayo Clinic sequencing core facilities

tag: genotype/variation

value: PD-L1 knockdown shRNA-2


title: shPD-L1-1 repeat1

description: processed RNA-Seq data.xlsx

tag: cell line

value: PD-L1 knockdown shRNA-1


title: HCT_DMSO_rep1_RNA


title: shPD-L1-1 repeat2

description: processed RNA-Seq data.xlsx


title: gene_expression_HIVneg_DLBCL_pt01

value: LN, site not specified

tag: hiv status

tag: Sex


title: control repeat1

description: processed RNA-Seq data.xlsx

value: control


title: shPD-L1-2 repeat2

description: processed RNA-Seq data.xlsx


title: control repeat2

description: processed RNA-Seq data.xlsx


title: WD liver 1

city: Cologne

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

country: Germany

institute: University of Cologne

description:
annotation_liver.csv
Liver_WDWT16_1.txt

data_processing:
All samples were sequenced on a NextSeq 500 sequencing system with the following run parameters:
26 cycles for read 1, 98 cycles for read 2, 8 cycles for index 1. Binary sequencing data were converted to the fastq format
Then the CellRanger analysis pipeline (v2.0.0) from 10x Genomics was used with standard parameters in order to
(1) align the reads and count them for each gene and each cell with cellranger count
(2) merge all liver samples with cellranger merge
(3) merge all bone marrow samples with cellranger merge
Seurat package (v 2.3.0) was used to generate a gene expression matrix for each of the merged samples (genes row wise and cell column wise)
Only Cell containing at least 50 genes and gene expressing in at least three cells were kept all others were filtered out.
Cell names ending with 1 to 4 in the liver expression matrix corresponds to sample 1 to sample 4 respectively
Cell names ending with 1 to 4 in the bone marrow expression matrix corresponds to sample 5 to sample 8 respectively
Cells were clustered and undergone cell type identification using the Seurat Package (v 2.3.0) which resulted with the annotation of each cell with a cell type.
Genome_build: mm10 (preprocessed release 84 downloaded from the website of 10x Genomics)
Supplementary_files_format_and_content: Two expression matrices in txt format containing genes row wise and cells column wise.
Supplementary_files_format_and_content: Two cell to cell type annotation files. One is for liver samples (1-4) and the other one for bone marrow samples (5-8)

source_name: CD45+ Ly6G- non-lymphoid

growth_protocol: mice received standard chow (normald diet) or Western diet (high-fat, high-sugar, high-cholesterol) for 24 weeks from 8 weeks of age

extract_protocol:
cells were isolated by collagenase digestion and FACS purified for CD45+ LY6G- CD3- CD4- CD19- NK11-, 50.000 cells were then resuspended in cold PBS + 0.1 % BSA and subjected to 10x single cell library generation according to manufacturers protocol
cDNA

tag: strain

value: 24 weeks

tag: diet

value: Western diet (WD) for 16 weeks


title: WD liver 2

description:
annotation_liver.csv
Liver_WDWT16_2.txt


title: aCGH_HIVpos_DLBCL_pt07

value: Rt breast chest wall lesion

value: HIV positive

value: Normal female genome


title: ND bonemarrow 1

description:
annotation_bonemarrow.csv
BM_CDWT16_1.txt

value: Normald diet (ND) for 16 weeks


title: WD bonemarrow 2

description:
annotation_bonemarrow.csv
BM_WDWT16_2.txt


title: WD bonemarrow 1

description:
annotation_bonemarrow.csv
BM_WDWT16_1.txt


title: ND liver 1

description:
annotation_liver.csv
Liver_CDWT16_1.txt


title: ND bonemarrow 2

description:
annotation_bonemarrow.csv
BM_CDWT16_2.txt


title: HCT_5-aza-CdR_4d_rep1_RNA