title: Tsp1KO_stretch_#3

city: Toyama

first: Jun-Dal

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

data_processing:
Reads were mapped on Rnor_6.0 rat reference genome and quantified using CLC Genomics Workbench version 12.0 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0 (Qiagen).
Filtering characteristics of fold-change and false discovery rate (FDR) were used to identify the DEGs.
Genome_build: Rnor_6.0

organism: Rattus norvegicus

source_name: Primary rat aortic SMCs

growth_protocol: Rat aortic smooth muscle cells (rAoSMCs) (Lonza, R-ASM-580) were grown in DMEM with 20% (v/v) fetal bovine serum and 1 x Antibiotic-Antimycotic (Thermo Fisher Scientific).

extract_protocol:
RNA was extracted from CTRL (n=3) and Thbs1KO (n=3) Rat SMCs in static and stretch condition. Total RNA was isolated using TRIZOL reagent (Thermo Fisher) and quality of RNA was examined using an RNA 6000 Pico kit (Agilent). An amount of 500 ng total RNA was used for RNA-seq library preparation with NEB NEBNext Poly(A) mRNA Magnetic Isolation Module and ENBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). Sequencing was performed with NextSeq500 (Illumina) with paired-end 36-base read option. Reads were mapped on rat genome (Rnor_6.0) and quantified annotated genes using CLC Genomics Workbench version 12.0 (QIAGEN). Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0. Filtering characteristics of fold-change -2 to 2 (false discovery rate (FDR) at p < 0.05) were used to identify the differentially expressed genes (DEGs).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Generation of Tsp1 knockout cell line: CRISPR-Cas9 plasmid, pSpCas9(BB)-2A-GFP (px458, #48138) was purchased from Addgene. The CRISPR design tool (http://crispr.mit.edu) was used to identify candidate sgRNA sequences of Thbs1 gene. sgRNA sequence was PCR amplified and ligated into BbsI site of px458. After transformation into E.Coli, the plasmid DNA was purified by using Midi prep kit (QIAGEN, Chatsworth, CA). Rat SMCs were plated in a 24-well plate and transfected with px458_sgRNA plasmid. Forty-eight h after transfection, FACS (BD FACSAriaTM II, BD) was performed to isolate GFP-positive cells. Following isolation, cells were plated in a 96-well plate by limiting dilution for a single-cell cloning. Gene mutations were confirmed using Sanger sequencing (3130xl Genetic Analyzer, Applied Biosystems). In vitro mechanical stretch: Cyclic stretch was performed using a uniaxial cell stretch system (Central Workshop Tsukuba University) following 24 h of serum starvation as described previously13. Rat vascular SMCs were plated on silicon elastomer bottomed culture plates (SC4Ha, Menicon Life Science) coated with cell attachment factor (Thermo Fisher Scientific) and subjected to cyclic stretch with a frequency of 1.0 Hz (60 cycles/min) and 20% strain for the indicated time.

value: Wistar Rat

value: Vascular smooth muscle cell

tag: passages

value: passages 5~8

value: Tsp1 Knockout_stretch


title: PulsedInduction_G3B2

status: Public on Mar 17 2020

type: SRA

city: Boston

first: Duluxan

last: Sritharan

state: MA

address: 240 Longwood Avenue, Bldg. C

country: USA

institute: Harvard University

library_source: genomic

data_processing:
Library strategy: DNA-seq
Cellranger v2.2.0 (with default parameters) was used to process single-cell RNA sequencing datasets prepared using CellRanger V2 Chemistry
Cellranger v3.0.2 (with default parameters) was used to process single-cell RNA sequencing datasets prepared using CellRanger V3 Chemistry
Genome_build: mm10
Supplementary_files_format_and_content: H5 - CellRanger single-cell count matrix

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse embryonic stem cells

growth_protocol: Cells were cultured on mouse embryonic fibroblast feeder layers in embryonic stem cell medium with LIF

extract_protocol:
Cells were trypsinized, pelleted and resuspended in DNA lysis buffer
Up to 250ng gDNA was input into an initial UMI tagging reaction using a primer specific to the CARLIN region. Following this the CARLIN array + UMI was amplified in a PCR reaction before indexing and sequencing via MiSeq

tag: cell type

value: Mouse embryonic stem cells

tag: treatment

value: Dox

tag: system

value: cCARLIN


title: PulsedInduction_G3B1


title: PulsedInduction_G3A1


title: Tsp1KO_stretch_#2

last: Kim

library_source: transcriptomic

molecule: total RNA

tag: strain

tag: genotype/variation


title: PulsedInduction_G3A2


title: Tsp1KO_stretch_#1


title: PulsedInduction_G2A


title: Tsp1KO_static_#3

value: Tsp1 Knockout_static


title: PulsedInduction_G2B


title: PulsedInduction_G1


title: PulsedInduction_G0


title: Patient 102

type: RNA

city: Munich

first: Oliver

last: Weigert

address: Max-Lebsche-Platz 30

country: Germany

institute: Experimental Leukemia and Lymphoma Research

hyb_protocol: See manufacturer's website http://www.nanostring.com

scan_protocol: maschine: NanoString nCounter MAX system; scan protocol: 555 fields of view (FOV)

data_processing: nSolver 4.0, standard settings

organism: Homo sapiens

source_name: lymph node_diagnostic_biopsy

label_protocol: NanoString nCounter technology

growth_protocol: formalin-fixed paraffin-embedded tissue

extract_protocol: AllPrep FFPE (Qiagen)

tag: age

tag: female

tag: ffs

tag: protein exchange

tag: watch and wait


title: Patient 100


title: Patient 103


title: Patient 101


title: ChronicInduction_NegDox_Trial2_96h

value: No dox


title: Tsp1KO_static_#1


title: Patient 99


title: ChronicInduction_NegDox_Trial2_72h


title: Patient 104


title: WT_stretch_#3

value: Wild type _stretch


title: ChronicInduction_NegDox_Trial2_24h


title: Patient 98


title: ChronicInduction_NegDox_Trial2_48h


title: ChronicInduction_NegDox_Trial2_0h


title: WT_stretch_#2


title: Patient 97


title: ChronicInduction_NegDox_Trial1_96h


title: Patient 96


title: WT_stretch_#1


title: ChronicInduction_NegDox_Trial1_72h


title: Tsp1KO_static_#2


title: ChronicInduction_NegDox_Trial1_48h


title: WT_static_#3

value: Wild type _static


title: ChronicInduction_NegDox_Trial1_24h


title: Patient 95


title: WT_static_#2


title: Wounded_2_scRNA-Seq

city: Irvine

first: Daniel

last: Haensel

state: California

address: Medical Sciences D288

institute: UC Irvine

data_processing:
Alignment of 3’ end counting libraries from droplet-enabled scRNAseq analyses was completed utilizing 10x Genomics Cell Ranger 1.3.1
Each library was aligned to an indexed mm10 genome using Cell Ranger Count. “Cell Ranger Aggr” function was used to normalize the number of confidently mapped reads per cells across the libraries from different samples.
Order of samples in aggregated file are: Un-Wounded_1_scRNA-Seq, Wounded_1_scRNA-Seq, Un-Wounded_2_scRNA-Seq, Wounded_2_scRNA-Seq, Wounded_3_scRNA-Seq
Genome_build: mm10
Supplementary_files_format_and_content: Processed files include the standard 'filtered gene bc matrices' found in the outs folder, which can be easily read into Seruat for analysis. Included is the (1) the files post "Cell Ranger Aggr" funtion containing all 5 samples and (2) individual samples files with no "Cell Ranger Aggr" processing. Both options make the datasets more useful to potential users.

molecule: polyA RNA

source_name: Skin

growth_protocol: Mice were housed in animal facility.

extract_protocol:
Normal un-wounded mouse skin and mouse wound were isolated, made into a single cell suspension, sorted for live cells, and then processed as per 10X Genomics 3' scRNA-Seq v1 protocol.
Sorted cells were washed in PBS with 0.04% BSA and reseupended at a concentration of approximately 1000 cells/µl. Library generation for 10x Genomics v1 chemistry was performed following the Chromium Single Cell 3’ Reagents Kits User Guide: CG00026 Rev B.
Quantification of cDNA libraries was performed using Qubit dsDNA HS Assay Kit (Life Technologies Q32851) and high-sensitivity DNA chips (Agilent. 5067-4626). Quantification of library construction was performed using KAPA qPCR (Kapa Biosystems KK4824)

treatment_protocol: For wounded samples, mice were wounded at 7 weeks of age with 6-mm punch biopsy. Samples were collected 4 days later with a 10-mm punch biobspy to isolate all cells in wound region.

tag: tissue

value: Skin

value: All cells from skin


title: Wounded_3_scRNA-Seq


title: Patient 94


title: ChronicInduction_NegDox_Trial1_0h


title: ChronicInduction_PosDox_Low_96h


title: Wounded_1_scRNA-Seq


title: WT_static_#1


title: Un-Wounded_2_scRNA-Seq


title: Patient 93


title: Patient 92


title: ChronicInduction_PosDox_Low_48h


title: ChronicInduction_PosDox_Low_72h


title: Patient 91


title: Patient 90


title: ChronicInduction_PosDox_Low_24h


title: Insc-Gal4>UAS- (hb, ase, Kr; wor, nub, SoxN); denoted UAS-Hexa#3

city: linkoping

first: shahrzad

last: Bahrampour

address: Campus HU: Lab 1, floor 13

department: IKE

country: Sweden

institute: Linkoping University

description: Experiment 3

data_processing: Expression profiling was conducted using DNAStar 14.1, SeqMan NextGen software, adjusted for reads per kilobase per million mapped sequence reads (RPKM), and we have showne the linear and log2 PRKM and raw reads for each sample also the fold change (Control VS Test).

organism: Drosophila melanogaster

source_name: Drosophila embryo

extract_protocol:
Drosophila embryos at stages 16-AFT have been collected in 3 biological replicates per genoptype (>200 embryo); sampel collections were used for RNA extraction, using RNeasy Mini Kit (Qiagen, Hilden, Germany).
RNA sequencing was performed by (GeneWiz, New Jersey, NJ), in 2x150 bp single-read sequencing configuration, which yielded 15-35 M reads/sample ( each set of experiment had been sequencing on 1 lane of Illumina HiSeq2500 platform in a 2X150bp single-read (SR) configuration. receive on average ~25M reads/sample with a total data output of ~150M reads/lane).

tag: embryonic stage

value: whole embryo - St16-AFT

tag: strain/genotype

value: Drosophila melanogaster. Insc-Gal4 (Bl# ---)/ UAS-(hb, ase, Kr; woR, nub, SoxN)


title: Patient 89


title: PBMC_LongInsert

city: Raleigh

first: Xinxia

last: Peng

address: 1060 William Moore Drive

institute: North Carolina State University

data_processing:
Reads were basecalled using SCS version 2.9 software and processed using version CASAVA 1.8.2
Raw reads were cleaned (remove adaptors and low qualtiy reads) using Trimmomatic
Reads were mapped against rhesus transcritptome using STAR
Transcript abundance was estimated using Isolator
Genome_build: Rhesus macaque Ensembl release 75
Supplementary_files_format_and_content: tab-delimited text files of transcript abundance

organism: Macaca mulatta

source_name: blood

extract_protocol:
Qiagen miRNeasy Isolation Kit from Trizol homogenates Illumina TruSeq mRNA
The RNA library for NextSeq run was prepared for sequencing using standard Illumina protocols. For the MiSeq run, cDNA was synthesized using the SMRT cDNA synthesis kit. The cDNA was then used for a Nextera library reaction. The library was size selected by automated gel electrophoresis using the Blue Pippen.

value: peripheral blood mononuclear cell


title: ChronicInduction_PosDox_Low_12h


title: Insc-Gal4>UAS- (hb, ase, Kr; wor, nub, SoxN); denoted UAS-Hexa#2

description: Experiment 3


title: Patient 88


title: Foci Astro4

city: Tokyo

first: Nicolas

last: Leventoux

state: Tokyo

address: 35, Shinanomachi

department: Physiology

institute: Keio University

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were hybridized with GeneChip Human 2.1 ST Arrays (Affymetrix) and scanned at the IRMB Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Transcriptome Analysis Consol v4.0 software

label: biotin

source_name: Astrocytoma Female

label_protocol: Single-stranded cDNA was generated from the amplified cRNA using WT Pico Kit (Affymetrix).

growth_protocol: Drills of tumor blocks were performed using biopsy punches used for tissue microarray (TMA)

extract_protocol: Total RNA were isolated from foci and adjacent tissues using Qiagen RNeasy FFPE kit

value: FFPE sample

tag: Sex

value: Female


title: ChronicInduction_PosDox_Medium_96h


title: Patient 87


title: Insc-Gal4>UAS- (hb, ase, Kr; wor, nub, SoxN); denoted UAS-Hexa#1

description: Experiment 3


title: Insc-Gal4>UAS- (ase, Kr; wor, SoxN); denoted UAS-Quad#3

description: Experiment 2

value: Drosophila melanogaster. Insc-Gal4 (Bl# ---)/ UAS-(ase, Kr; woR, SoxN)


title: Un-Wounded_1_scRNA-Seq


title: DLGG Astro4


title: Insc-Gal4>UAS- (ase, Kr; wor, SoxN); denoted UAS-Quad#2

description: Experiment 2


title: ChronicInduction_PosDox_Medium_24h


title: ChronicInduction_PosDox_Medium_48h


title: DLGG Astro3

source_name: Astrocytoma Male

value: Male


title: Patient 86


title: Patient 84


title: Patient 85


title: Insc-Gal4>UAS- (ase, Kr; wor, SoxN); denoted UAS-Quad#1

description: Experiment 2


title: ChronicInduction_PosDox_Medium_12h


title: Foci Astro2


title: Patient 83


title: Insc-Gal4/+ (Ctrl)3

description: Experiment 1

value: Drosophila melanogaster. Insc-Gal4 (Bl# ---)/OregonR (BDSC# 2376)


title: DLGG Astro1


title: Patient 82


title: ChronicInduction_PosDox_High_96h

value: Mouse embryonic stem cells


title: DLGG Astro2


title: Insc-Gal4/+ (Ctrl)2

description: Experiment 1


title: Foci Astro3


title: Foci Oligo4

source_name: Oligodendroglioma Male


title: ChronicInduction_PosDox_Medium_72h

value: Dox


title: Foci Astro1


title: Patient 81


title: Foci Oligo3


title: ChronicInduction_PosDox_High_48h

value: cCARLIN


title: Insc-Gal4/+ (Ctrl)1

description: Experiment 1


title: ChronicInduction_PosDox_High_24h


title: SMMC7721-Hx-IP

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

description:
RNA IP against m6A
7721-Hx.bed

data_processing:
Library strategy: m6A-seq
For m6A-seq, reads were aligned to the reference genome (hg38) using Tophat (v2.0.14, ref) with parameter -g 1 --library-type=fr-firststrand. RefSeq Gene structure annotations were downloaded from UCSC Table Browser. The longest isoform was used if the gene has multiple isoforms. Aligned reads were extended to 150bp (average fragments size) and converted from genome-based coordinates to isoform-based coordinates, in order to eliminate the interference from intron in peak calling. The peak calling method was modified from Dan Dominissini nature 2012 work. To call m6A peaks, the longest isoform of each human gene was scanned using a 100 bp sliding window with 10 bp step. To reduce bias from potential inaccurate gene structure annotation and the arbitrary usage of the longest isoform, windows with reads counts less than 1/20 of the top window in both m6A-IP and input sample were excluded. For each gene, the reads count in each window was normalized by the median count of all windows of that gene. edgeR was used to identify the differential windows between IP and input samples. The window was called as positive if the fdr < 0.01 and log2(Enrichment Score) >= 1. Overlapping positive windows were merged. The following four numbers were calculated to obtain the enrichment score of each peak (or window): reads count of the IP sample in the current peak/window (a), median reads count of the IP sample in all 100 bp windows on the current mRNA (b), reads count of the input sample in the current peak/window (c) and median reads count of the input sample in all 100 bp windows on the current mRNA (d). The enrichment score of each window was calculated as (a×d)/(b×c).
Genome_build: hg38
Supplementary_files_format_and_content: bed

source_name: Hepatocellular carcinoma cell line

growth_protocol: SMMC7721 cells were grown in DMEM medium (Gibco) supplemented with 10% fetal bovine serum (FBS) (Gibco), and 1% penicillin–streptomycin (Gibco), incubated at 37 °C and 5% CO2.

extract_protocol:
Tissues were homogenized in Trizol reagent with a Tissure-Tearor. Total RNA were extracted using manufacturer’s instructions.Poly-adenylated RNA was enriched by using Oligotex® mRNA purification kit (Qiagen). RNA fragmentation, m6A-seq, and library preparation were performed as in Dominissini et al 2013 Nature Protocols. Cell line total RNA was isolated with TRIZOL reagent. Poly-adenylated RNA was enriched by using Oligotex® mRNA purification isolation kit (Qiagen). RNA fragmentation, m6A-seq, and library preparation were performed as in Dominissini et al 2013 Nature Protocols.
TruSeq Small RNA Sample Preparation Kit (Illumina)

treatment_protocol: To render culture hypoxic (Hx), SMMC7721 cells were incubated in an atmosphere of 1% O2, 5% CO2 and 94% N2 for 24 h. Nomoxic (Nx) culture was set up as a control.

tag: cell line

tag: technology

tag: antibody

value: m6A-antibody (202003; Synaptic Systems)


title: Patient 79


title: Patient 80


title: ChronicInduction_PosDox_High_12h

tag: cell type


title: SMMC7721-Hx-input

description:
no IP (input RNA)
7721-Hx.bed

value: no IP (input RNA)


title: DLGG Oligo3


title: SMMC7721-Nx-IP

description:
RNA IP against m6A
7721-Nx.bed


title: Patient 78


title: ChronicInduction_PosDox_0h

tag: treatment

value: No dox


title: ChronicInduction_PosDox_High_72h

tag: system


title: Foci Oligo2


title: brain, KO4

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample

source_name: Brain

extract_protocol:
Total RNA was harvested by Trizol reagent.2 ug of total RNA was used to construct sequencing libraries.
RNA libraries sequencing  was performed using standard Illumina protocols

tag: strain

tag: genotype

value: KO

value: brain


title: SMMC7721-Nx-input

description:
no IP (input RNA)
7721-Nx.bed


title: Patient 77

tag: age


title: brain, WT8

value: WT


title: ChIPSeq_IgG_PTH(1-34)C

city: Montreal

first: Hadla

last: Hariri

state: Quebec

address: 1003 Decarie Boulevard, Shriners Hospital For Children

department: Human Genetics

country: Canada

institute: Shriners Hospital for Children, Canada-Montreal, Department of Human Genetics, McGill University, Montreal,Quebec,Canada

data_processing:
Raw reads were adapter clipped, quality-trimmed (trailing end 30 phred score) and filtered for minimum length of 32 bp with Trimmomatic version 0.3.
Reads were  aligned to the mm10 reference genome using bwa-aln version 0.7.8.
Alignments were filtered for minimal mapping quality of 20 with samtools 0.1.19 and duplicates were marked with Picard 1.107
Peaks were called using MACS version 2.0.10.09132012.
Peaks were annotated and analyzed for motifs with HOMER 4.1
Genome_build: mm10
Supplementary_files_format_and_content: Bed files were generated for all samples.

source_name: MC3T3-E1 cells

growth_protocol: MC3T3-E1 cells (P5-P8) were cultured in minimum essential medium alpha (αMEM; Invitrogen) supplemented with 10% fetal bovine serum (FBS; Hyclone, Logan, UT). We used approximately 4 X 10^(6) cells for each immunoprecipitation for all samples.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with either anti-NACA or naïve IgG antibodies.
ChIP-Seq libraries from immunoprecipitated DNA were constructed using the TruSeq gDNA library kit from Illumina (San Diego, CA) following the manufacturer's instructions. Single reads of 50 base pairs were obtained using a HiSeq 2000 sequencing system (Illumina).

value: Preosteoblast Calvarial cells, subclone 4

tag: chip antibody

value: Naïve Rabbit IgG (sc-2027)

value: PTH-treated (100nM) 30min prior to extraction


title: DLGG Oligo4

value: FFPE sample


title: DLGG Oligo2


title: #8 Paratumor-input

description:
no IP (input RNA)
0204.13P.bed

source_name: Hepatocellular carcinoma tissue samples

tag: disease

value: Hepatocellular carcinoma


title: DLGG Oligo1


title: ChIPSeq_IgG_PTH(1-34)B


title: ChIPSeq_IgG_PTH(1-34)


title: Patient 76

tag: female

tag: ffs

tag: protein exchange


title: Patient 75

tag: watch and wait


title: Foci Oligo1

tag: tissue


title: #8 Tumor-IP

description:
RNA IP against m6A
0204.13T.bed


title: #8 Paratumor-IP

description:
RNA IP against m6A
0204.13P.bed


title: Patient 74


title: brain, WT6


title: ChIPSeq_NACA_PTH(1-34)C

value: Rabbit Polyclonal anti-NACA


title: #8 Tumor-input

description:
no IP (input RNA)
0204.13T.bed


title: Patient 73


title: ChIPSeq_NACA_PTH(1-34)B


title: Patient 72


title: #7 Paratumor-IP

description:
RNA IP against m6A
0204.5P.bed


title: D4C

city: BOSTON

first: Michele

last: Jacob

state: Massachusetts

address: 136 Harrison Ave, Neuroscience Arnold 305A

department: Neuroscience

institute: Tufts University

data_processing:
Illumina bcl2fastq software for basecalling demultiplexing
The reads were align to mouse reference genome (UCSC mm10) using Tophat v2.0.10
Normalized count (FPKM) was generated with Cuffdiff (v2.1.1)
Differential expression were perform using Cuffdiff (v2.1.1) or Qlucore Omics Explorer (v3.4)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: prefrontal cortex

extract_protocol:
RNA from freshly dissected prefrontal cortex was extracted using Qiagen Rneasy extraction kit followed by quality analysis using an Agilent Bioanalyzer.
Library was prepared using Illumina TruSeq Stranded mRNA Sample Preparation Kit, per manufacturer instruction

value: prefrontal cortex

value: APC/Bcat cKO


title: D3C


title: ChIPSeq_NACA_PTH(1-34)


title: Patient 71


title: #7 Paratumor-input

description:
no IP (input RNA)
0204.5P.bed


title: brain, KO2


title: ChIPSeq_NACA_VehC

value: Vehicle-treated for 30min prior to extraction


title: #7 Tumor-IP

description:
RNA IP against m6A
0204.5T.bed


title: Patient 70


title: D1C


title: #7 Tumor-input

description:
no IP (input RNA)
0204.5T.bed


title: ChIPSeq_NACA_VehB


title: ChIPSeq_NACA_Veh


title: C4C

value: Control


title: Patient 69


title: #6 Paratumor-input

description:
no IP (input RNA)
0204.4P.bed


title: Patient 68


title: #6 Paratumor-IP

description:
RNA IP against m6A
0204.4P.bed


title: C2C


title: Patient 67


title: Patient 66


title: #6 Tumor-IP

description:
RNA IP against m6A
0204.4T.bed


title: Patient 65


title: #6 Tumor-input

description:
no IP (input RNA)
0204.4T.bed


title: #5 Paratumor-IP

description:
RNA IP against m6A
0204.2P.bed


title: B4C

value: Bcat cOE


title: #5 Paratumor-input

description:
no IP (input RNA)
0204.2P.bed


title: B3C


title: Patient 64


title: D2C


title: B2C


title: Patient 63


title: Patient 62


title: B1C


title: #5 Tumor-IP

description:
RNA IP against m6A
0204.2T.bed

value: m6A-antibody (202003; Synaptic Systems)


title: #5 Tumor-input

description:
no IP (input RNA)
0204.2T.bed

value: no IP (input RNA)


title: A5C

value: APC cKO


title: C3C


title: Patient 61


title: #4 Paratumor-IP

description:
RNA IP against m6A
patient.4P.bed


title: A2C


title: C1C


title: #4 Paratumor-input

description:
no IP (input RNA)
patient.4P.bed


title: A4C


title: Patient 60


title: A1C


title: Patient 58


title: Patient 56


title: Patient 59


title: #4 Tumor-input

description:
no IP (input RNA)
patient.4T.bed


title: #3 Paratumor-IP

description:
RNA IP against m6A
patient.3P.bed


title: Patient 57


title: #3 Paratumor-input

description:
no IP (input RNA)
patient.3P.bed


title: Maj2-4 [CTR2]

first: Maria

middle: Agustina

last: Battistone

department: Program in Membrane Biology, Center for Systems Biology and Nephrology Division, Department of Medicine

institute: Massachusetts General Hospital. Harvard Medical Scholl

data_processing:
RNA-seq libraries were prepared using the Clontech SMARTER Kit v4, followed by sequencing on an Illumina HiSeq2500 instrument.
Transcriptome mapping was performed with STAR (PMID:23104886) using the Ensembl annotation of mm9 reference genome. Read counts for individual genes were produced using HTSeq (PMID:25260700).
Genome_build: mm9
Supplementary_files_format_and_content: Read counts for individual genes were produced using HTSeq (PMID:25260700). Differential expression analysis was performed using the EdgeR package (PMID:19910308) after normalizing read counts and including only those genes with CPM > 1 for at least one out of all samples.

source_name: EGFP+ intercalated cells from sham animals

growth_protocol: EGFP+ intercalated cells were isolated by double cell sorting from the renal medullary region from B1 VATPase EGFP mice, 2 hours after renal ischemia reperfusion injury or sham surgery. Each sample was obtained using 4 kidneys fron 2 mice.

extract_protocol:
The RNA was isolated using PicoRNA KIT (Thermo Fisher Scientific)
RNA-seq libraries were prepared using the Clontech SMARTER Kit v4, followed by sequencing on an Illumina HiSeq2500 instrument.

treatment_protocol: no treatment

tag: genotype/variation

value: B1 VATPase EGFP transgenic expressing EGFP under the control of the CX3CR1 gene

value: 12 weeks

value: sham

value: epididymis

value: EGFP+ intercalated cells


title: Maj2-6 [IRI3]

source_name: EGFP+ intercalated cells from animals 2h after renal ischemia reperfusion injury

value: renal ischemia reperfusion injury


title: #3 Tumor-IP

description:
RNA IP against m6A
patient.3T.bed


title: Maj2-5 [CTR3]


title: Patient 55


title: Maj2-3 [IRI2]


title: Maj2-2 [IRI1]


title: #2 Paratumor-IP

description:
RNA IP against m6A
patient.2P.bed


title: Maj2-1 [CTR1]


title: #2 Paratumor-input

description:
no IP (input RNA)
patient.2P.bed


title: #4 Tumor-IP

description:
RNA IP against m6A
patient.4T.bed


title: OBs_d14_biological_rep3

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: Osteoblasts in Col2.3-ECFP mice from Day 16

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the mouse reference genome sequences (mm10) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: mm10

source_name: Sorted ECFP+ osteoblasts in Col2.3-ECFP mice from Day 14

extract_protocol:
RNA was purified using miRNeasy mini kit (Qiagen, CA, USA)
cDNA was generated using a Clontech SMART-Seq Ultra Low Input RNA Kit (Takara Clontech, Mountain View, CA, USA). Each cDNA sample was sheared (200 - 500 bp) using the Covaris S220 (Covaris, Woburn, MA, USA) and prepared using KAPA Library Preparation Kits (Kapa Biosystems, Wilmington, MA) for 75 bp single-end reads, according to the manufacturer’s instructions.

treatment_protocol: For the analysis and sorting of ECFP+ OBs, BMP-2-induced ectopic bone from Col2.3-ECFP mice was extracted and minced into ~1–2-mm2 pieces by using scissors. The bone pieces were digested once with 0.25% trypsin for 15 min at 37°C and then once (Day 10) or twice (Day 14) with 0.2% collagenase II (Worthington) for 40 min at 37°C. Cells were collected and resuspended in PBS containing 2% foetal bovine serum and then stained with allophycocyanin-conjugated anti-mouse CD45 antibody (BioLegend), phycoerythrin-conjugated anti-mouse CD45 antibody (eBioscience), and 7-aminoactinomycin D (7AAD) (eBioscience). Haematopoietic cells and dead cells were gated out based on anti-CD45 and 7AAD staining. Stained cells were sorted using a FACSAria II system (BD Biosciences).

value: Osteoblasts


title: Patient 52


title: #2 Tumor-IP

description:
RNA IP against m6A
patient.2T.bed

value: Hepatocellular carcinoma


title: OBs_d14_biological_rep2

description: Osteoblasts in Col2.3-ECFP mice from Day 15


title: #2 Tumor-input

description:
no IP (input RNA)
patient.2T.bed


title: Patient 49


title: Patient 48


title: #1 Paratumor-input

description:
no IP (input RNA)
patient.1P.bed


title: OBs_d10_biological_rep2

description: Osteoblasts in Col2.3-ECFP mice from Day 10

source_name: Sorted ECFP+ osteoblasts in Col2.3-ECFP mice from Day 10


title: OBs_d10_biological_rep3


title: Patient 54


title: #1 Tumor-IP

description:
RNA IP against m6A
patient.1T.bed


title: OBs_d10_biological_rep1


title: Patient 53


title: #1 Tumor-input

description:
no IP (input RNA)
patient.1T.bed


title: Patient 47


title: Patient 46


title: #3 Tumor-input

description:
no IP (input RNA)
patient.3T.bed


title: Patient 45


title: Patient 44


title: Het_LD2

city: Fukuoka

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

institute: Kyushu University

data_processing:
Illumina Casava1.4 software used for basecalling.
Targeted methylome sequencing reads were mapped to the mouse reference genome sequence (mm9) using Bmap (http://itolab.med.kyushu-u.ac.jp/BMap/index.html).
Methylation levels were calculated for individual CG sites.
Genome_build: mm9
Supplementary_files_format_and_content: files include chrmosome, position, strand, the number of mC reads and the number of total reads.

source_name: Spermatozoa

growth_protocol: Caudal epididymis and vas deferens were incubated in M2 medium for 1 hour at 37C to prepare total sperm fraction.

extract_protocol:
After treatment of sperm lysis buffer, genomic DNA was extracted from each sperm sample. DNA is purified by RNase and pronaseK treatment, and extracted by PCI separation and EtOH precipitation. DNA samples were prepared from 2 independent mice per each group.
Libraries for targeted methylome sequencing were prepared according to the post-bisulfite adaptor tagging (PBAT) protocol (Miura F et al., 2012; Miura F and Ito T, 2015) with slight modifications. Briefly, 300 ng of genomic DNA was fragmented to ~500 bp with Covaris S220 and used for target enrichment with SureSelectXT Mouse Methyl-Seq kit (Agilent). The enriched DNA was subjected to PBAT followed by 5 cycles of PCR enrichment with Kapa Library Amplification Kit. Single-read sequencing (100 cycles) was performed on Illumina HiSeq 2500 using HiSeq SR Rapid Cluster Kit v2 and HiSeq Rapid SBS Kit v2. Two indexed libraries were combined with a high concentration of spike-in PhiX control DNA (20%) and loaded on a single lane of the flow cell.
Target BS-seq

treatment_protocol: Wild-type (WT) and ATF7 heterozygous mutant (Het) mice were fed with control diet (CD) or low-protein diet (LD) in 3-12 weeks age.

value: ATF7 heterozygous

tag: diet

value: Low-protein diet

tag: dna selection

value: SureSelect (Agilent)


title: Het_CD2

value: Control diet


title: Het_LD1


title: PBMC_Regular

value: peripheral blood mononuclear cell


title: Patient 51

source_name: lymph node_diagnostic_biopsy


title: GCERB

city: Mumbai

first: Nafisa

last: Balasinor

state: Maharashtra

address: Jehangir Merwanji Street

department: Neuroendocrinology

country: India

institute: ICMR-National Institute for Research in Reproductive Health (NIRRH-ICMR)

data_processing:
Alignment was done using Bowtie version 1.2 to reference genome Rnor06
Peaking calling was done using MACS version 14
Peaks with the following threshold were considered: p Value <0.01; Fold enrichment >2
Genome_build: Rnor6
Supplementary_files_format_and_content: bed

source_name: Male germ cells

growth_protocol: The animals were sacrificed and testes were dissected out, detunicated and the tubules were teased apart. Interstitial cells were lysed by hypotonic treatment by suspending the tubules in distilled water twice for 1 min and decanting the supernatant. The tubules were then resuspended in DMEM F12 and treated with trypsin followed by DNase twice and incubated at 37ᵒC on the shaker (80rpm) for 8 mins and 5 mins respectively. The tubules were then allowed to settle down and the supernatant was passed through 70µm nylon mesh. The filtrate collected through the 70µm nylon mesh was filtered through 40µm nylon mesh to separate Sertoli cells. The filtrate thus obtained was centrifuged at 800rpm for 8 mins at 4ᵒC. The supernatant was discarded and the pellet was resuspended in Hank’s balanced salt solution (HBSS). A part of the pellet was separated for RNA extraction to check for purity of the germ cell enrichment and the remaining cells were crossed-linked using formaldehyde and stored at -80ᵒC for chromatin immunoprecipitation.

extract_protocol:
The enriched germ cells were subjected to sonication followed by immunoprecipitation using ERα and ERβ antibody.
The immuno-precipitated DNA was quantified by Qubit2.0 and for size distribution Agilent Bioanalyser was used as a QC step for chip sequencing library. Chip Sequencing libraries were generated using NEBNext® Ultra™ II DNA kit for Illumina as per the recommended protocol. Briefly, a total amount of 200-500pg input material is used for Chip sequencing. The fragmented DNA overhangs were converted into blunt ends via exonuclease/polymerase activities (END REPAIR). After adenylation of 3’ ends of DNA fragments, adapter oligonucleotides were ligated. DNA fragments with ligated adapter molecules on both ends were selectively enriched in final PCR reaction. Products were purified using AMPure XP system (Beckman Coulter, Beverly,USA) and quantified using the Agilent high sensitivity DNA assay on the Agilent Bioanalyzer 2100 system for size distribution. The final libraries are quantified using Kapa qPCR Kit for adapter ligated molecules and was sequenced on PE75 Illumina platform.

treatment_protocol: Not applicable

value: Holtzman strain

value: 75 - 90 days old

value: Anti-ERβ (Sigma, E1276-1ML, lot SLBF4802)


title: GCMock

value: Anti-Rabbit IgG


title: Het_CD1


title: Patient 42


title: Patient 43


title: #1 Paratumor-IP

description:
RNA IP against m6A
patient.1P.bed

tag: technology

tag: antibody

value: m6A-antibody (202003; Synaptic Systems)


title: OBs_d14_biological_rep1

description: Osteoblasts in Col2.3-ECFP mice from Day 14

tag: cell type


title: WT_LD2

value: Wild-type


title: Patient 50


title: WT_LD1


title: Patient 39


title: GCERA

value: Anti-ERα (Millipore, CS200620, lot DAM1794327)


title: Patient 38


title: Patient 41


title: htr10 H3K27me1_rep3

city: Tübingen

first: Michael

last: Borg

address: Max Planck Ring 5

department: Algal Development & Evolution

institute: Max Planck Insititue for Biology

description:
H3K27me1_rep3
anti-H3K27me1_rep1 IP from Input_rep3
htr10_H3K27me1.log2r.bw
narrow_htr10_H3K27me1_peaks.narrowPeak
broad_htr10_H3K27me1_peaks.broadPeak

data_processing:
Raw, unaligned BAM files were first sorted with samtools sort -n and then converted to fastq files with bedtools bamtofastq.
Adapter trimming was performed using TrimGalore version 0.4.1.
Reads were mapped to the Arabidopsis genome (TAIR10) using Bowtie2 version 2.1.0.
Reads were filtered for a MAPQ score > 10 using SAMtools version 1.3 and subsequently filtered for duplicate reads using Picard tools MarkDuplicates version 1.141.
Biological replicates were subsequently merged for downstream analysis after confirming high correlation among replicates.
For data visualization, log2 ratio bigwig coverage files relative to input were generated using the deepTools version 2.5.0.1 utility bamCoverage with a bin size of 10 bp.
Peaks were called using the MACS2 version 2.1.0 callpeak function using -f BAMPE --broad --broad-cutoff 0.1 -g 1.2e8
Genome_build: TAIR10 (Arabidopsis thaliana)
Supplementary_files_format_and_content: *.bw: Normalized log2 ratio coverage of histone marks relative to relevant input sample. Data is generated from merged replicates.
Supplementary_files_format_and_content: *.narrowPeak: MACS2 narrowPeaks generated from merged replicates.
Supplementary_files_format_and_content: *.broadPeak: MACS2 broadPeaks generated from merged replicates.

organism: Arabidopsis thaliana

source_name: Sperm nuclei

extract_protocol:
Sperm nuclei from htr10 mutant plants were  isolated by FACS using SYBR Green I stain and stored at -80°C in Cryopreservation Buffer (50 mM Tris-Cl pH 8.0, 40% glycerol, 5 mM MgCl2, 0.1 mM EDTA, 1 mM PMSF, 1x Roche protease inhibitor cocktail). Sperm mononucleosomes were generated by micrococcal nuclease (MNase, New England Biolabs) digestion. Aliquots of frozen sperm nuclei were thawed on ice and subsequently subjected to MNase digestion in MNase digestion buffer (1x NEB MNase reaction buffer, 1.5 mM DTT, 5% PEG 6000). EDTA was added to a final concentration of 10 mM to stop the MNase digestion. Nuclei were lysed by adding Triton X-100 and sodium deoxycholate to a final concentration of 0.1% each, incubated on ice for 15 minutes and then vortexed. Soluble material containing mononucleosomes were recovered after centrifugation and subjected to immunoprecipitation. Sequencing libraries were prepared using a NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) and sequenced on an Illumina Hiseq 2500 to generate 50 bp paired-end reads.
NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs)

tag: ecotype

tag: chip-antibody

value: anti-H3K27me1 (Millipore, 17-643)


title: htr10 H3K27me3_rep1

description:
H3K27me3_rep1
anti-H3K27me3_rep1 IP from Input_rep1
htr10_H3K27me3.log2r.bw
narrow_htr10_H3K27me3_peaks.narrowPeak
broad_htr10_H3K27me3_peaks.broadPeak

tag: genotype

value: anti-H3K27me3 (Millipore, 07-449)


title: htr10 H3K27me3_rep2

description:
H3K27me3_rep2
anti-H3K27me3_rep1 IP from Input_rep2
htr10_H3K27me3.log2r.bw
narrow_htr10_H3K27me3_peaks.narrowPeak
broad_htr10_H3K27me3_peaks.broadPeak


title: PPRV Infected Caecum_replicate1

city: Karnal

first: Ravi Kumar

last: Gandham

state: Haryana

address: Makrampur

institute: ICAR-NBAGR

description: lncRNAs and mRNAs expression in PPRV infected Caecum

data_processing: Fastq files containing sequencing reads, each of control and infected samples were processed to remove adaptors and low-quality reads. Thereafter, filtered reads were mapped to goat genome(assembly ARS1) by Tophat software and transcripts were assembled by Cufflinks. Cuffmerge was further used to merge the replicate assemblies and to categorized the novel transcripts. Long non-coding RNAs were filtered according to transcript length (≥ 200 nt), classcode- “I’, “j”, “o”, “u” and “x”, ORF length ≤ 300 nt and protein domains. Long non-coding RNA transcripts were evaluated using coding potential calculator (CPC). At last, cuffdiff was used to carry out differential expression analysis of long non-coding transcripts and mRNA transcripts between the infected and control samples.

organism: Capra hircus

source_name: Caecum sample at 9 day post infection from infected group

extract_protocol:
Total RNA from control and PPRV infected lung, spleen and caecum was isolated using the RNeasy Mini kit (Qiagen GmbH, Germany) according to the manufacturer’s protocol. The integrity and quantity of isolated RNA were assessed  based on a Bioanalyzer (Agilent Technologies, Inc). The RNA integrity number (RIN) value of all the samples was found greater than 8, which is considered suitable for further processing.
Library was prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NewEngland Biolabs Inc.) following the manufacturer’s protocol. Approximately, 100ng of RNA from each sample was used for RNA library preparation. The quality of the libraries was assessed on Bioanalyzer and further quantified using a Qubit 2.0 Fluorometer (Life technologies) and by qPCR. Libraries were sequenced on Illumina – NextSeq500  following manufacturer’s protocol.

treatment_protocol: Two groups including one control and one virus infected of tissues including lung, spleen and caecum were used in the study. For the control group, healthy tissues of goats were collected and screened for the absence of PPRV antigen, and for the infected group tissues were isloated from goat infected with Izatnagar 94 PPRV at 9 day post infection. The tissues of both groups were collected in RNase free 1.5 ml centrifuge tube in RNA later.

tag: infection status

value: PPRV-Infected

value: caecum


title: Patient 36

tag: age


title: Patient 37


title: htr10 H3K27me1_rep2

description:
H3K27me1_rep2
anti-H3K27me1_rep1 IP from Input_rep2
htr10_H3K27me1.log2r.bw
narrow_htr10_H3K27me1_peaks.narrowPeak
broad_htr10_H3K27me1_peaks.broadPeak


title: PPRV Infected Caecum_replicate2


title: Caecum Control_replicate1

description: lncRNAs and mRNAs expression in Caecum

source_name: Caecum sample at 9 day post infection from control group

value: Control


title: htr10 H3K27me1_rep1

description:
H3K27me1_rep1
anti-H3K27me1_rep1 IP from Input_rep1
htr10_H3K27me1.log2r.bw
narrow_htr10_H3K27me1_peaks.narrowPeak
broad_htr10_H3K27me1_peaks.broadPeak


title: Caecum Control_replicate2

description: lncRNAs and mRNAs expression in Caecum


title: Patient 35


title: PPRV Infected Spleen_replicate2

description: lncRNAs and mRNAs expression in PPRV infected Spleen

source_name: Spleen sample at 9 day post infection from infected group

value: spleen


title: htr10 Input_rep2

description:
Input_rep2
Mnase-digested chromatin input DNA
none
none
none


title: PPRV Infected Spleen_replicate1


title: Patient 33


title: Patient 34


title: htr10 Input_rep1

description:
Input_rep1
Mnase-digested chromatin input DNA
none
none
none


title: htr10 Input_rep3

description:
Input_rep3
Mnase-digested chromatin input DNA
none
none
none


title: Patient 32


title: Spleen Control_replicate1

description: lncRNAs and mRNAs expression in Spleen

source_name: Spleen sample at 9 day post infection from control group


title: htr10 H3K27me3_rep3

description:
H3K27me3_rep3
anti-H3K27me3_rep1 IP from Input_rep3
htr10_H3K27me3.log2r.bw
narrow_htr10_H3K27me3_peaks.narrowPeak
broad_htr10_H3K27me3_peaks.broadPeak


title: Spleen Control_replicate2

description: lncRNAs and mRNAs expression in Spleen


title: Patient 30


title: PPRV Infected Lung_replicate2

description: lncRNAs and mRNAs expression in PPRV infected Lungs

source_name: Lung sample at 9 day post infection from infected group

value: lung


title: PPRV Infected Lung_replicate1


title: Patient 40


title: SMMC7721-shYTHDF2

city: Shanghai

first: Zhenjun

last: Zhao

state: Shanghai

address: 1630 Dongfang Road, Puundong New District, Shanghai, China

institute: Renji Hospital, Shanghai Jiao Tong University, School of Medicine

data_processing:
Sequence reads were aligned to the human genome GRCh19 with TopHat2
the resulting alignment files were reconstructed with Cufflinks
An adjusted P value< 0.05 and fold change>2 was used as the cut-oﬀfor significantly differentially expressed genes using Cuffdiff
Genome_build: the human genome GRCh19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: Liver cancer cells

growth_protocol: SMMC7721-Ctrl and SMMC-shYTHDF2 cells were seeded at 1-5*10^5 in a 10cm dish and cultured in DMEM supplemented with 10% FBS and 1%P/S.

extract_protocol:
Cells were washed three times with PBS before RNA was harvested using Trizol reagent. ΒioTeke RNA extraction Kit  (Cat#RP4002) was used with 1 ug of total RNA for the construction of sequencing libraries.
For RNA-sequencing, ribosomal RNA was removed and strand-specifc sequencing libraries were generated using KAPA Riboerase-RNA Hyper Prep Kit following manufacture’s recommendations. After proper quality control steps, the libraries were sequenced on illumina HiSeq platform

value: Hepatocellular carcinoma

tag: passage

value: YTHDF2 knockdown


title: Patient 29

tag: female


title: Lung Control_replicate2

description: lncRNAs and mRNAs expression in Lungs

source_name: Lung sample at 9 day post infection from control group


title: SMMC7721-shCtrl

value: wild type


title: SMMC7721-OE+Nx

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to ensembl GRCh38 whole genome using TopHat(version:2.0.9).
HTSeq was used to count the number of fragments of each gene after TopHat alignment, and then normalized by TMM (M value trimmed mean) method, and finally the FPKM value of each gene was calculated.
Genome_build: ensembl GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: SMMC7721 and YTHDF2 overexpressing SMMC7721 cells were seeded at 1-5*10^5 in a 10cm dish and cultured in DMEM supplemented with 10% FBS and 1%P/S.

extract_protocol:
Cells were washed three times with PBS before RNA was harvested using Trizol reagent. ΒioTeke RNA extraction Kit  (Cat#RP4002) was used with 1 ug of total RNA for the construction of sequencing libraries.
According to the experimental instructions, the purified total RNA was subjected to mRNA isolation, fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, terminal repair, 3' end plus A, ligation linker, enrichment and other steps to complete the library construction of the samples.

treatment_protocol: Cells were cultured in normoxia or hypoxia (1% oxygen) for 12 hours

tag: cell line

value: YTHDF2 overexpression

tag: stress

value: Normoxia


title: ES1_3

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

description:
PolyA RNA
processed data file: read_count_all_final.txt

data_processing:
The quality of the reads was verified using FASTQC version 0.11.5 (HiSeq 2500 sequencing data) and FASTQC 0.11.8 (HiSeq 3000 sequencing data).
All reads were aligned to the T. urticae three pseudochromosome assembly (Wybouw et al. 2019, doi: 10.1534/genetics.118.301803) using STAR version 2.5.x (Dobin et al. 2013, doi: 10.1093/bioinformatics/bts635) with a 2-pass mode and a maximum intron size (--alignIntronMax) of 20 kb, without the use of the GFF annotation file, and with --sjdbOverhang 124 (for HiSeq 2500 sequencing data) or --sjdbOverhang 149 (for HiSeq 3000 sequencing data).
Next, read counts per gene were obtained using the htseq-count script included in the HTSeq package (Anders et al. 2015, doi: 10.1093/bioinformatics/btu638) with the following settings "-f bam -r pos -s reverse -i Parent" and a GFF3 annotation file ((Tetranychus_urticae_2016.transformed.GenomeTools.gff3), see genome build).
Genome_build: T. urticae three pseudochromosome assembly, included in GEO upload (Tetranychus_urticae_2016.transformed.GenomeTools.gff3.txt, Tetranychus_urticae_3Chr.fasta).
Supplementary_files_format_and_content: read_count_all_final.txt: Tab-delimited text file including raw read counts (HTSeq) per T. urticae gene ID for each sample.

organism: Tetranychus urticae

source_name: complete organism

growth_protocol: Mites were grown on bean (Phaseolus vulgaris) in controlled condition, 25 ± 1°C, 60 % RH and 16:8 h (L:D) photoperiod.

extract_protocol:
Total RNA was extracted from 100-120 adult female mites of each T. urticae population using the RNeasy Plus mini kit (Qiagen, Belgium) with four-fold biological replication for each population. The quality and quantity of the total RNA were analyzed by a DeNovix DS-11 spectrophotometer (DeNovix, USA) and by running an aliquot on a 1% agarose gel.
Illumina libraries were constructed with the TruSeq Stranded mRNA Library Preparation Kit with polyA selection (Illumina, USA).
For RO1, IT2, IT3 and ES1, RNAseq libraries were sequenced on an Illumina HiSeq 2500 to generate strand-specific paired reads of 2 x 125 bp (library construction and sequencing were performed at the Genomics Core Facility of the University of Utah, Utah, USA) while for UK6, RNAseq libraries were sequenced on an Illumina HiSeq 3000 to generate strand-specific paired reads of 2 x 150 bp (NXTGNT sequencing platform, Ghent University, Ghent, Belgium).

treatment_protocol: ES1, IT2 and UK6 were highly resistant/resistant against abamectin/milbemectin compared to the susceptible populations RO1 or IT3.

tag: population

value: whole body

tag: Sex

value: female

value: adult

tag: colour morph

value: red

tag: resistance status

value: resistant to abamectin/milbemectin


title: IT3_4

tag: tissue

value: susceptible to abamectin/milbemectin


title: Patient 31

first: Oliver

last: Weigert

institute: Experimental Leukemia and Lymphoma Research

data_processing: nSolver 4.0, standard settings

extract_protocol: AllPrep FFPE (Qiagen)

tag: ffs

tag: protein exchange

tag: watch and wait


title: RO1_1

value: green


title: ES1_4


title: ES1_1


title: IT3_2


title: Patient 24


title: Patient 27


title: Patient 26


title: IT3_3


title: Patient 28


title: Patient 22


title: Patient 23


title: Lung Control_replicate1

description: lncRNAs and mRNAs expression in Lungs


title: SMMC7721-EV+Nx


title: ES1_2


title: SMMC7721-OE+Hx(12h)

value: Hypoxia (1% oxygen)


title: Patient 21


title: Patient 25


title: Control chondrocytes

city: TOKYO

first: Taku

last: Saito

address: 7-3-1 Hongo, Bunkyo-ku

department: Orthopaedic Surgery, Faculty of Medicine

institute: The University of Tokyo

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

scan_protocol: Slides were scanned immediately after washing on the the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Hif1afl/fl primary chondrocytes transduced with adenovirus expressing GFP

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Primary chondrocytes were isolated from 6-day-old neonatal Hif1afl/fl mice, and cultured for 3 days in DMEM with 10% FBS.

extract_protocol: Total RNA was extracted from the chondrocytes using RNeasy mini kits (Qiagen) according to manufacturer’s protocol.

treatment_protocol: The chondrocytes were transduced with adenovirus expressing GFP or Cre at 100 MOI.

tag: cell type

value: chondrocytes

value: control


title: SMMC7721-EV+Hx(12h)


title: IT2_4


title: Patient 20

city: Munich

address: Max-Lebsche-Platz 30


title: Hif1a knockdown chondrocytes

source_name: Hif1afl/fl primary chondrocytes transduced with adenovirus expressing Cre

value: Hif1a KO


title: IT2_2


title: IT2_3


title: Input_S2 line_FLAG-EcR_20E-0h

city: Moscow

first: Nadezhda

middle: E

last: Vorobyeva

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

data_processing:
bcl2fastq v2.17.1.14 Conversion Software (Illumina)
ChIP-seq reads were aligned to the dm6 genome by bowtie2 v2.3.4.2 (using UseGalaxy.eu online tools)
Genome_build: dm6 (Drosophila melanogaster Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: BigWig files were generated using  bamCoverage 3.0.2. Scores represent number of reads normalized by the size of the library.

source_name: S2 Schneider cells

growth_protocol: Drosophila Schneider line 2 (S2) cells were maintained at 25°C in the Schneider’s insect medium (Sigma) containing 10% FBS (HyClone).

extract_protocol:
Crosslinking was performed with 1% formaldehyde for 10 min at RT and stopped by adding glycine. After washings, chromatin was lysed in SDS-containing buffer (50 mM HEPESKOH, pH 7.9; 140 mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS) with protease inhibitors cocktail (Roche) and sheared to 500-bp fragments by sonication. Sonicated chromatin was centrifuged twice at 16 000 g for 20 min, and used in immunoprecipitation experiments. For one experiment, about 5 ug of antibodies and 8 uL of MabSelect sepharose (GE healthcare) were taken; BSA were added to a final concentration of 1%. The precipitated chromatin was sequentially washed twice with SDS-containing buffer and with TE buffer (20mM Tris-HCl, pH 8.0; 1mM EDTA). Precipitated chromatin complexes were eluted by sequential incubation in two portions of elution buffer (50mM Tris-HCl, pH 8.0; 1mM EDTA, 1% SDS), 30 min each, at room temperature. The eluted chromatin solution was supplemented with 5 M NaCl (16 uL per 500 uL sample) and incubated at 65°C for 16 h on a thermoshaker for de-crosslinking. De-crosslinked chromatin was subjected to proteinase treatment (3 uL of proteinase K and 5 uL of 0.5M EDTA per 500 uL sample) and incubated at 55°C for 4 h on thermoshaker. DNA was extracted with a phenol/chloroform mixture and precipitated with isopropanol. The precipitate was dissolved in TE buffer and subjected to library preparation.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were co-transfected by expression contructs and pCoBlast plasmid gaving blasticidin resistance in 1 to 20 molar ratio using Effectene transfection reagent (Qiagen). Stable cell lines were selected and cultivated in blasticidin-containing S2 medium (20 ug/ml final concentration).

tag: cell line/tissue

value: S2 Schneider cells

tag: expression of nuclear receptor

value: 3xFLAG-EcR expression under Act5C promoter

tag: isoform of nuclear receptor

value: D. melanogaster EcR-A isoform full length (1-849 aa)

tag: treatment

value: sham-treated (DMSO) for 1 hour

tag: chip antibody

value: input chromatin (before precipitation)


title: Patient 18

tag: age

tag: female


title: Patient 17


title: Input_white-prepupa_Oregon

source_name: White prepupa (Oregon-Modencode)

value: White prepupa (Oregon-Modencode)


title: ChIP-CP190_white-prepupa_Oregon

value: anti-CP190 antibodies obtained by A. Golovnin (Golovnin et al (2012) J. Cell Sci. 125, 2064–2074)


title: Patient 19


title: Input_S2 line_FLAG-Usp_20E-1h

value: 3xFLAG-Usp expression under Act5C promoter

value: D. melanogaster Usp full length (1-508 aa)

value: 0.3 uM 20-hydroxyecdysone (20E) for 1 hour


title: Input_S2 line_FLAG-EcR_20E-1h


title: RO1_4

value: whole body

value: female

value: adult


title: IT3_1

value: red

value: susceptible to abamectin/milbemectin


title: Patient 15


title: M2-BAPN (rep 2)

city: Haifa

first: Peleg

last: Hasson

address: 1 Efron Street

department: Department of Genetics and Developmental Biology

country: Israel

institute: Technion

data_processing:
Reads were trimmed using cutadapt [1] (DOI: 10.14806/ej.17.1.200) and mapped to mouse genome, GRCm38 using STAR [2] (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (default parameters). Counting proceeded over genes annotated in Ensembl release 88, using htseq-count [3] (DOI: 10.1093/bioinformatics/btu638) (intersection-strict mode).
Differential expression analysis was performed using DESeq2 [5] (DOI: 10.1186/s13059-014-0550-8) with the betaPrior, cooksCutoff and independentFiltering parameters set to False. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg. Pipeline was constructed using Snakemake (DOI: 10.1093/bioinformatics/bts480)
Genome_build: mm10
Supplementary_files_format_and_content: counts matrix, DESeq2 output

source_name: satellite cells from gastrocnemius_BAPN

growth_protocol: Muscle tissue (Gastrocnemius) was extracted from 6 weeks old mice and digested into single cells using trypsin B solution in 37C. Following digestion, fibroblasts were sorted out by three sequential seeding the cell culture on plates with proliferation medium (BIO-AMF™- 2; Biological Industries). As fibroblast adhere to the plates faster than the myogenic progenitor cells, the medium is transferred every 15 minutes to a new plate allowing for the enrichment of the progenitors. The isolated cells were cultured on 4% matrigel with proliferation or differentiation medium [DMEM (containing 1% L-glutamine and 1% penicillin and streptomycin [PS] + 10% fetal calf serum)] depending on the specific assay.

extract_protocol:
Total RNA was extracted from tissue after homogenization using the Qiacube (Qiagen) with the RNeasy kit (cat no. 74106). Fresh tissues were disrupted in 3ml Buffer RLT and homogenized by Kinematica AG homogenizer. 1ml of lysate was centrifuged for 5min at 5000 x g., then 600ul of lysate was loaded on the Qiacube for automated extraction. Ethanol precipitation was preformed to all RNA samples to ascent quality of samples. Quality measurements for total RNA were performed using TapeStation (Agilent). The RINe value of most of the samples was above 8.1, except two samples which showed poor quality (RIN value <7.5).
Libraries were prepared from the RNA using in-house (Weizmann Institute) protocol. Samples were sequenced on one lane of Illumina HiSeq machine, using the Single-Read 60 protocol. The output was ~24 million reads per sample

treatment_protocol: For Lox-enzymatic inhibition, corresponding media containing a final concentration of 0.25% βAPN (Sigma A3134) was used.

tag: strain

value: 8 weeks

value: satellite cells from gastrocnemius

value: cultured for 24 hrs with 0.25% BAPN


title: M1-d (rep 1)

source_name: satellite cells from gastrocnemius


title: M3-d (rep 3)


title: M2-d (rep 2)


title: M3-BAPN (rep 3)


title: RO1_3

tag: population

value: green


title: ChIP-CP190_S2 line_FLAG-EcR_20E-1h

value: S2 Schneider cells

value: 3xFLAG-EcR expression under Act5C promoter

value: D. melanogaster EcR-A isoform full length (1-849 aa)


title: ChIP-CP190_S2 line_FLAG-EcR_20E-0h

value: sham-treated (DMSO) for 1 hour


title: M1-BAPN (rep 1)


title: ChIP-Rpb3_S2 line_FLAG-EcR_20E-1h

value: anti-Rpb3 antibodies (Mazina et al (2018) Biochim. Biophys. Acta BBA - Gene Regul. Mech. 1861, 178–189. )


title: UK6_4

tag: Sex

value: resistant to abamectin/milbemectin


title: Patient 13

source_name: lymph node_diagnostic_biopsy


title: IT2_1

tag: colour morph


title: ChIP-Rpb3_S2 line_FLAG-EcR_20E-0h


title: AD-input: Patient with aortic dissection for input RNA

city: guangzhou

first: xianwu

last: zhou

address: No. 106, Zhongshan Second Road, Yuexiu District, Guangzhou

institute: Guangdong Provincial People's Hospital

data_processing:
Library strategy: m6A-seq
150 bp paired-end reads were mapped to the reference human genome build GRCh38/hg38 by using Bowtie2.
Only unique mapping paired reads were sorted using SAMtools and kept for subsequent analysis.
Peaks of each samples and differential methylation peak were called  using the exomePeak R-package.
Genome_build: GRCh38/hg38

source_name: aorta

extract_protocol:
RNA fragments were incubated with anti-N6-methyladenosine (m6A) antibodies (Sigma-Aldrich, Burlington, USA) inimmunoprecipitation (IP) buffer for 2 h at 4℃. The samples were then washed with low-salt precipitation buffer and high-salt buffer thrice continuously. RNA was extracted using a phenol-chloroform lysate to obtain a purified product.
The purified RNA was collected for the generation of an RNA-seq library with NEBNext R Ultra™ RNA Library Prep Kit (New England Biolabs, MA, USA). The quality of the library was done using Bioptic Qsep100 analyzer and sequencing was done using NovaSeq's high-throughput sequencing platform

value: aorta

tag: disease state

value: acute aortic dissection


title: NOR-input: Healthy Donor for input RNA

tag: tissue

value: healthy donor


title: ChIP-FLAG_S2 line_FLAG-APEX2_20E-1h

value: 3xFLAG-APEX2 expression under Act5C promoter

value: 0.3 uM 20-hydroxyecdysone (20E) for 1 hour

value: Monoclonal ANTI-FLAG® M2 antibody produced in mouse F1804 (Sigma-Aldrich)


title: UK6_3

value: whole body

value: female

value: adult

tag: resistance status


title: Patient 12

tag: ffs

tag: protein exchange


title: Patient 14

tag: watch and wait


title: NOR: Healthy Donor for m6a-seq


title: ChIP-FLAG_S2 line_FLAG-BioID2_20E-1h

tag: cell line/tissue

value: 3xFLAG-BioID2 expression under Act5C promoter


title: UK6_2

value: green


title: Patient 16


title: UK6_1


title: Patient 11


title: A00720: patient with aortic dissection4

data_processing:
150 bp paired-end reads were mapped to the reference human genome build GRCh38/hg38 by using hisat2.
The reads mapped the genome were calculated using HT-seq.
Differential gene expression analysis was performed using the DESeq2 R-package.
Genome_build: hg38

extract_protocol:
Total RNA from the tissue was extracted using TRIzol reagent (Invitrogen Corporation, CA, USA) in accordance with the manufacturer’s instructions. The RNA was then fragmented chemically into about 100 nucleotides in length using fragmentation buffer (Illumina, Inc.). The RNA was precipitated using the aqueous phase by mixing with isopropyl alcohol. The samples were incubated at 15ºC to 30℃ for 10 minutes and centrifuged at 12,000 x g for 10 minutes at 4℃.
The ribosomal RNA-depleted RNAs were then used to construct RNA libraries with TruSeq Stranded Total RNA Library Prep kit (Illumina, CA, USA). The strand-specific library construction uses dUTP instead of dTTP to label the second-strand cDNA during synthesis. Uracil-DNA glycosylase (UDG) was used to hydrolyze the strand before polymerase chain reaction (PCR) enrichment to ensure that the final sequencing data was from the first cDNA strand.


title: Patient 10


title: A00717: patient with aortic dissection3


title: RO1_2

value: susceptible to abamectin/milbemectin


title: ChIP-FLAG_S2 line_FLAG-BioID2-Usp_20E-1h

value: S2 Schneider cells

tag: expression of nuclear receptor

value: 3xFLAG-BioID2-Usp expression under Act5C promoter

value: D. melanogaster Usp full length (1-508 aa) fused with BioID2 through a 25nm GS linker


title: Patient 8


title: ChIP-FLAG_S2 line_FLAG-Usp_20E-1h

value: 3xFLAG-Usp expression under Act5C promoter

tag: isoform of nuclear receptor

value: D. melanogaster Usp full length (1-508 aa)


title: A00711: patient with aortic dissection2

value: aorta


title: Patient 7


title: Patient 9


title: ChIP-FLAG_S2 line_FLAG-APEX2-EcR_20E-1h

value: 3xFLAG-APEX2-EcR expression under Act5C promoter

value: D. melanogaster EcR-A isoform full length (1-849 aa) fused with APEX2 through a 25nm GS linker

tag: treatment


title: ChIP-FLAG_S2 line_FLAG-BioID2-EcR_20E-1h

value: 3xFLAG-BioID2-EcR expression under Act5C promoter

value: D. melanogaster EcR-A isoform full length (1-849 aa) fused with BioID2 through a 25nm GS linker

tag: chip antibody


title: AD: Patient with aortic dissection for m6a-seq

value: acute aortic dissection


title: A00710: patient with aortic dissection1


title: Patient 6

tag: age


title: Patient 5

tag: female


title: X262982: Donor4

value: healthy donor


title: Normol3: Donor2


title: Patient 4


title: GA1: Donor1


title: X262708: Donor3


title: ChIP-FLAG_S2 line_FLAG-EcR_20E-1h

value: 3xFLAG-EcR expression under Act5C promoter

value: D. melanogaster EcR-A isoform full length (1-849 aa)

value: 0.3 uM 20-hydroxyecdysone (20E) for 1 hour

value: Monoclonal ANTI-FLAG® M2 antibody produced in mouse F1804 (Sigma-Aldrich)


title: Latent_GROseq

city: Los Angeles

first: Angela

last: Park

state: CA

address: 1501 San Pablo St, ZNI 521

department: Molecular Microbiology and Immunology

institute: University of Southern California

data_processing:
Library strategy: GRO-seq
Reads were trimmed based on quality score from both ends using Partek Flow and aligned  to hg19 genome using bowtie 2. Peak calling and annotation done using HOMER (-style groseq)
Reads were trimmed based on quality score from both ends using Partek Flow
Reads were aligned to hg19 genome using bowtie 2
(ChIP-Seq) Peak calling was done using HOMER (H3K27ac peaks used -size 1000)
(ChIP-Seq) Peak annotation was done using HOMER; TSS peaks were removed
(ChIP-Seq) Motif analysis was done using HOMER
(ChIP-Seq) Heatmaps and profiles were generated using NGSPlot (-SC global, -G hg19, -L 10000)
(ChIP-Seq) Potential superenhancers were identified using HOMER (-sytle super)
(4C-Seq) Genomic interactions were identified using 4cseqpipe (hg19 genome used; -stat_type linear_mean -trend_resolution 1000)
(GROSeq) Peak calling and annotation done using HOMER (-style groseq)
(GROSeq) NGSPlot used to generate heatmaps and profiles  (-SC global, -G hg19, -L 10000)
Genome_build: hg19
Supplementary_files_format_and_content: peaks

growth_protocol: RPMI1640 + 10% FBS + 1% Pen/Strep + 20ug/ml Hygromycin

extract_protocol: We followed a previous published protocol (Li et al., 2015 Mol Cell)

tag: cell line

tag: infection

value: KSHV

tag: replication

value: Latent


title: Mϕ THP-1_nuclear_RNA-seq

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

country: Australia

institute: Centenary Institute

data_processing:
The base-calling algorithm Albacore 2.3.1 (Oxford Nanopore Technologies) was used to process the raw FAST5 files. About half a million reads that passed the default quality threshold were mapped to the human genome (hg38 assembly) using Minimap2 (36) with -ax splice and -k14 options.
Alignments with MAPQ < 20 were skipped. SAM files were converted to the BAM format using samtools 1.9 and visualised in the UCSC genome browser (33). Further data processing and analysis was conducted using the R software (version 3.4.3).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: THP-1 macrophage

growth_protocol: Human THP-1 monocytic cells were maintained in RPMI medium supplemented with 2 mM L-glutamine, 25 mM HEPES, 10% (v/v) FBS, 1 mM sodium pyruvate, 1% (v/v) non-essential amino acids, and 0.1 mg/mL penicillin/streptomycin at 37°C in the presence of 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol. Genomic DNA was extracted using standard phenol-chloroform method.
Nanopore direct cDNA sequencing (SQK-DCS109) was performed using the flow cell R9.4 on the MinION machine (Oxford Nanopore Technologies) following the manufacturers’ instructions with minor modifications.
Briefly, first strand cDNA was made from 100 ng of poly-A-enriched RNA using the VN primer and SuperScript II (Invitrogen) at 42°C for 50 min.
After removal of RNA by RNase Cocktail Enzyme Mix (Thermo Fisher), second strand cDNA was made using random hexamers (Invitrogen) and LongAmp Taq Master Mix (New England Biolabs), which was followed by the End-prep and Adapter ligation before subjecting the library to the flow cell.

treatment_protocol: 1.5 × 10^7 cells per 75 cm2 culture flask of THP-1 cells were differentiated using phorbol-12-myristate 13-acetate (PMA) into macrophages. Resting macrophages are further polarised into pro-inflammatory macrophages using lipopolysaccharide (LPS) and interferon gamma (IFN-γ). To inhibit nuclear degradation by the RNA exosome, THP-1 macrophages were transfected with 300 nM EXOSC10 siRNA (sense: 5′ – GAAGGCAGCUGAGCAAACAdTdT – 3′, antisense: 5′ – UGUUUGCUCAGCUGCCUUCdTdT). ON-TARGETplus non-targeting siRNA (GE Dharmacon) was used as a negative control.

tag: cell type

value: THP-1-derived macrophage

tag: fraction

value: Nuclear M0 mRNA


title: DBr fraction of patient P40489 (GE)

status: Public on Mar 16 2020

city: Bronx

first: Boris

last: Bartholdy

state: NY

address: 1300 Morris Park Ave

department: Cell Biology

institute: Albert Einstein College of Medicine

description:
P40489-DBr
We only used (and normalized together these 103 samples that came from the same patients from whom we also had DNA methylation data, therefore there are no normalized data available for these.
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.

hyb_protocol: RNA samples were hybridized to the Illumina HumanHT-12 v4 Expression BeadChip following Illumina standard protocols.

scan_protocol: Standard Illumina scanning protocol

data_processing: GenomeStudio (Illumina) was used to generate files subsequently imported into R using the ‘beadarray’ package and processed using custom scripts. Raw values were processed using necq from ‘limma’ package to calibrate the background level, normalize and transform the probe intensities. Probes with a detection p < 0.05 in all samples, or annotated as having “Bad” quality or “No match” by the ‘illuminaHumanv4.db’ package were removed.

label: biotin, Cy3

source_name: sorted CLL PBMCs

label_protocol: Biotinylated cRNA was prepared following standard Illumina labeling protocol.

extract_protocol: Total RNA was extracted from sorted cells using the RNeasy mini kit (Qiagen) following manufacturer’s recommendations, and RNA quality was assessed with a Bioanalyzer (Agilent) using Agilent RNA 6000 Kit.

treatment_protocol: Peripheral blood mononuclear cells (PBMCs) were separated by Ficoll-Paque density gradient centrifugation from heparinized venous blood obtained 3 months before, during or 3 months after the 6 week 2H2O labeling period, and cryopreserved. Before sorting, CLL PBMCs were thawed and incubated with murine anti-human monoclonal antibodies CD5-PECy7, CXCR4-PE, and CD19-Pacific Blue (BD Biosciences). After gating on CD19+CD5+ cells, equal numbers of viable cells falling into proliferative (“Dim”; CXCR4DimCD5Bright), intermediate (“Int”, CXCR4IntCD5Int, IF), resting (“Br”; CXCR4BrightCD5Dim), or Dbr (CXCR4BrightCD5Bright) based on reciprocal densities of CXCR4 and CD5 (~5% of the clone for each fraction) were sorted with a BD FACSAria. After sorting, cells were washed, pelleted, and stored at -80º until RNA extraction was performed.

tag: patient

value: DBr

tag: ighv

value: M

tag: Sex

tag: birthrate (% cells/day)

value: sorted CLL PBMCs


title: Patient 3

tag: ffs

tag: protein exchange

tag: watch and wait


title: Patient 1


title: Mo THP-1_whole lysate_RNA-seq

source_name: THP-1 monocytic cells

value: Monocytic cell

value: Whole lysate ND mRNA


title: Mϕ THP-1_whole lysate_RNA-seq

value: Whole lysate M0 mRNA


title: Patient 2


title: Lytic_GROseq

treatment_protocol: 1ug/ml doxycycline for 24 h

value: Lytic


title: Dim-1 fraction of patient P40489 (GE)

description:
P40489-Dim.1
We only used (and normalized together these 103 samples that came from the same patients from whom we also had DNA methylation data, therefore there are no normalized data available for these.
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.

value: Dim


title: DBr fraction of patient P40323 (GE)

description:
P40323-DBr
We only used (and normalized together these 103 samples that came from the same patients from whom we also had DNA methylation data, therefore there are no normalized data available for these.
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.

value: F


title: ChIP-FLAG_S2 line_FLAG-APEX2-Usp_20E-1h

tag: cell line/tissue

value: S2 Schneider cells

tag: expression of nuclear receptor

value: 3xFLAG-APEX2-Usp expression under Act5C promoter

tag: isoform of nuclear receptor

value: D. melanogaster Usp full length (1-508 aa) fused with APEX2 through a 25nm GS linker


title: DBr fraction of patient P39242 (GE)

description:
P39242-DBr
We only used (and normalized together these 103 samples that came from the same patients from whom we also had DNA methylation data, therefore there are no normalized data available for these.
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient P39242 (GE)

description:
P39242-Br
We only used (and normalized together these 103 samples that came from the same patients from whom we also had DNA methylation data, therefore there are no normalized data available for these.
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.

value: Br


title: Tot fraction of patient CLL855 (GE)

description:
CLL855-Tot
We only used (and normalized together these 103 samples that came from the same patients from whom we also had DNA methylation data, therefore there are no normalized data available for these.
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.

value: Tot


title: Br fraction of patient CLL855 (GE)

description:
CLL855-Br
We only used (and normalized together these 103 samples that came from the same patients from whom we also had DNA methylation data, therefore there are no normalized data available for these.
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient CLL855 (GE)

description:
CLL855-Int
We only used (and normalized together these 103 samples that came from the same patients from whom we also had DNA methylation data, therefore there are no normalized data available for these.
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.

value: Int


title: Dim fraction of patient CLL855 (GE)

description:
CLL855-Dim
We only used (and normalized together these 103 samples that came from the same patients from whom we also had DNA methylation data, therefore there are no normalized data available for these.
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: DBr fraction of patient CLL855 (GE)

description:
CLL855-DBr
We only used (and normalized together these 103 samples that came from the same patients from whom we also had DNA methylation data, therefore there are no normalized data available for these.
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient P40489 (GE)

description:
P40489-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient P40489 (GE)

description:
P40489-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient P40489 (GE)

description:
P40489-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient P40323 (GE)

description:
P40323-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL931 (GE)

description:
CLL931-Tot
We only used (and normalized together these 103 samples that came from the same patients from whom we also had DNA methylation data, therefore there are no normalized data available for these.
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: DBr fraction of patient P40344 (GE)

description:
P40344-DBr
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient P40344 (GE)

description:
P40344-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient P40344 (GE)

description:
P40344-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient P40489 (GE)

description:
P40489-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient P40323 (GE)

description:
P40323-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient P40344 (GE)

description:
P40344-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient P40344 (GE)

description:
P40344-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient P39242 (GE)

description:
P39242-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient P40323 (GE)

description:
P40323-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient P40323 (GE)

description:
P40323-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient P39242 (GE)

description:
P39242-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient CLL934 (GE)

description:
CLL934-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.

value: U


title: Int fraction of patient CLL753 (GE)

description:
CLL753-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: DBr fraction of patient CLL934 (GE)

description:
CLL934-DBr
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient P39242 (GE)

description:
P39242-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL934 (GE)

description:
CLL934-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL753 (GE)

description:
CLL753-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL934 (GE)

description:
CLL934-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL934 (GE)

description:
CLL934-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL753 (GE)

description:
CLL753-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: DBr fraction of patient CLL650 (GE)

description:
CLL650-DBr
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL650 (GE)

description:
CLL650-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL650 (GE)

description:
CLL650-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient CLL650 (GE)

description:
CLL650-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient CLL609 (GE)

description:
CLL609-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL625 (GE)

description:
CLL625-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL609 (GE)

description:
CLL609-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: DBr fraction of patient CLL606 (GE)

description:
CLL606-DBr
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL650 (GE)

description:
CLL650-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL638 (GE)

description:
CLL638-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL609 (GE)

description:
CLL609-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL638 (GE)

description:
CLL638-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL625 (GE)

description:
CLL625-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient CLL625 (GE)

description:
CLL625-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL638 (GE)

description:
CLL638-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL625 (GE)

description:
CLL625-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: DBr fraction of patient CLL609 (GE)

description:
CLL609-DBr
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient CLL606 (GE)

description:
CLL606-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: DBr fraction of patient CLL638 (GE)

description:
CLL638-DBr
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: DBr fraction of patient CLL493 (GE)

description:
CLL493-DBr
We only used (and normalized together these 103 samples that came from the same patients from whom we also had DNA methylation data, therefore there are no normalized data available for these.
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient CLL638 (GE)

description:
CLL638-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL609 (GE)

description:
CLL609-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: DBr fraction of patient CLL584 (GE)

description:
CLL584-DBr
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL753 (GE)

description:
CLL753-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL606 (GE)

description:
CLL606-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL584 (GE)

description:
CLL584-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL584 (GE)

description:
CLL584-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL584 (GE)

description:
CLL584-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL569 (GE)

description:
CLL569-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL606 (GE)

description:
CLL606-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL606 (GE)

description:
CLL606-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient CLL584 (GE)

description:
CLL584-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: DBr fraction of patient CLL569 (GE)

description:
CLL569-DBr
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL569 (GE)

description:
CLL569-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient CLL569 (GE)

description:
CLL569-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient CLL499 (GE)

description:
CLL499-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL499 (GE)

description:
CLL499-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL499 (GE)

description:
CLL499-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL499 (GE)

description:
CLL499-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL493 (GE)

description:
CLL493-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL569 (GE)

description:
CLL569-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL493 (GE)

description:
CLL493-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL493 (GE)

description:
CLL493-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient CLL493 (GE)

description:
CLL493-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL452 (GE)

description:
CLL452-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: DBr fraction of patient CLL452 (GE)

description:
CLL452-DBr
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient CLL452 (GE)

description:
CLL452-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: DBr fraction of patient CLL1078 (GE)

description:
CLL1078-DBr
We only used (and normalized together these 103 samples that came from the same patients from whom we also had DNA methylation data, therefore there are no normalized data available for these.
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL331 (GE)

description:
CLL331-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL452 (GE)

description:
CLL452-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL373 (GE)

description:
CLL373-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient CLL373 (GE)

description:
CLL373-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: DBr fraction of patient CLL331 (GE)

description:
CLL331-DBr
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL373 (GE)

description:
CLL373-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL276 (GE)

description:
CLL276-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL331 (GE)

description:
CLL331-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL1078 (GE)

description:
CLL1078-Dim
We only used (and normalized together these 103 samples that came from the same patients from whom we also had DNA methylation data, therefore there are no normalized data available for these.
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: DBr fraction of patient CLL1127 (GE)

description:
CLL1127-DBr
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL331 (GE)

description:
CLL331-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL373 (GE)

description:
CLL373-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL1127 (GE)

description:
CLL1127-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL1078 (GE)

description:
CLL1078-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL276 (GE)

description:
CLL276-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL276 (GE)

description:
CLL276-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient CLL331 (GE)

description:
CLL331-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL1078 (GE)

description:
CLL1078-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL1127 (GE)

description:
CLL1127-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: DBr fraction of patient CLL1039 (GE)

description:
CLL1039-DBr
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient CLL1127 (GE)

description:
CLL1127-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient CLL276 (GE)

description:
CLL276-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL1039 (GE)

description:
CLL1039-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL1127 (GE)

description:
CLL1127-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient CLL1039 (GE)

description:
CLL1039-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL1039 (GE)

description:
CLL1039-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: DBr fraction of patient CLL373 (GE)

description:
CLL373-DBr
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Tot fraction of patient CLL1026 (GE)

description:
CLL1026-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL1039 (GE)

description:
CLL1039-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Dim fraction of patient CLL1026 (GE)

description:
CLL1026-Dim
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: DBr fraction of patient CLL1026 (GE)

description:
CLL1026-DBr
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Int fraction of patient CLL1026 (GE)

description:
CLL1026-Int
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: Br fraction of patient CLL1026 (GE)

description:
CLL1026-Br
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.


title: 6432

city: Oklahoma City

first: Judith

middle: A.

last: James

state: Oklahoma

address: 825 NE 13th Street

department: Arthritis and Clinical Immunology

institute: Oklahoma Medical Research Foundation

hyb_protocol: Standard Illumina hybridization protocol

data_processing:
The data were normalized in R using bgAdjust background correction, vst variance stabilizing transformation, and rank invariant normalization.
6 samples were determined to be outliers and were dropped prior to normalization: 200319680117_E 200308380073_J 200308380073_K 200308380073_L 200308380104_E 200667730029_E

source_name: Whole Blood

label_protocol: RNA was amplified, in vitro transcribed, and labeled using the Illumina Bead-Expression Kit for Illumina Human HT-12 v4·0 whole genome expression chip.

extract_protocol: Total cellular RNA was isolated and purified from PAXgene tubes (PAXgene Blood RNA kit, Qiagen Inc, Valencia, CA). RNA quality and quantity were determined using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Globin mRNA and ribosomal RNAs (Globin-Zero Gold kit, Illumina, San Diego, CA, USA) were depleted.

tag: subject id

tag: case/control

value: SLE Case

tag: study group

value: High Only

tag: sledai group

value: High


title: 6612

value: High/Low


title: 6218

value: Low


title: 6903

value: Low Only


title: 3774


title: 5145


title: 6488


title: 7005


title: 4335


title: 6403


title: 3959

value: no val

value: Control


title: 3925


title: 6369


title: 7087


title: 6284


title: 3781


title: 532018


title: 3744


title: 6242


title: 6756


title: 6904


title: 6940


title: 6819


title: 590098


title: 6279


title: 6632


title: Tot fraction of patient CLL452 (GE)

description:
CLL452-Tot
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.

value: M

value: sorted CLL PBMCs


title: 6416


title: 4965


title: 5736


title: 6088


title: 5928


title: 3771


title: 3529


title: 3782


title: 4421


title: 6451


title: 3598


title: 6033


title: 6912


title: 3514


title: 4264


title: 3972


title: 3848


title: 6280


title: 3524


title: 6211


title: 4136


title: 7064


title: 4363


title: 4067


title: 6995


title: 3689


title: 3653


title: 500017


title: 7042


title: 5946


title: 5301


title: 5920


title: 6267


title: 3746


title: 5449


title: 5180


title: 533070


title: 3832


title: 6116


title: 6823


title: 6231


title: 4287


title: 6028


title: 7171


title: 6355


title: 5115


title: 6335


title: 4359


title: 6468


title: 4238


title: 6198


title: 6496


title: 5004


title: Int fraction of patient CLL1078 (GE)

description:
CLL1078-Int
We only used (and normalized together these 103 samples that came from the same patients from whom we also had DNA methylation data, therefore there are no normalized data available for these.
Illumina HumanHT-12 V4.0 expression BeadChip using standard Illumina protocol.

value: F


title: 4357


title: 590015


title: 5940


title: 3370


title: 4126


title: 6775


title: 3664


title: 5012


title: 5269


title: 4642


title: 3995


title: 3687


title: 3858


title: 6133


title: 6314


title: 4707


title: 6422


title: 4323


title: 5752


title: 500133


title: 6048


title: 4690


title: 7701


title: 4472


title: 7057


title: 5212


title: 4741


title: 4615


title: 3820


title: 4157


title: 4109


title: 5625


title: 4277


title: 5307


title: 6559


title: 6941


title: 4425


title: 6680


title: 3965


title: 5039


title: M4 Rep3

city: Beijing

first: Jiayang

last: Li

address: Beichen West Road

institute: Institute of Genetics and Developmental Biology, CAS

data_processing:
The paired end clean reads of RNA-seq were aligned using STAR with default parameter.
Then fragment quantifications were computed with featureCounts in the paired-end mode, whose features are exons with default parameters.
Expression differentiation analyses were conducted by R package DESeq with three biological replicates, and genes with P-value less than 0.05 were selected for further analysis.
Genome_build: Arabidopsis reference genome TAIR10
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each sample.

source_name: whole seedlings

growth_protocol: Arabidopsis seeds were surface sterilized, vernalized at 4 ºC for 2-4 days, germinated and grown on the 0.5× Murashige and Skoog (MS) medium containing 1.0% sucrose and 0.7% agar under a long day photoperiod (16-h light, 8-h dark cycle) with a light intensity of 60-80 μE m−2 sec−1 at 21 ºC

extract_protocol:
Seedlings were frozen and ground into powder in liquid nitrogen, and RNA was harvested using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Whole seedlings grown for 10 days on MS plates were collected and balanced in 0.5× MS liquid medium for 2h, then treated with 5 μM GR244DO in the greenhouse for 2h or 4 h.

tag: ecotype

value: Col

tag: genotype

value: wild-type

tag: tissue

value: seedling

tag: developmental stage

tag: treatment

value: solvent

tag: time

value: 4 hours


title: M4 Rep2


title: M4 Rep1


title: 4928


title: 6743


title: 500075


title: M2 Rep3

value: 2 hours


title: 5021

value: SLE Case


title: 4849


title: 6275


title: 3988

value: High Only


title: 6459

value: High


title: 500126


title: M2 Rep1


title: 4914


title: 6160

value: High/Low


title: 6365

value: Low


title: 5952


title: 5234


title: 4775

value: Low Only


title: 6322


title: 5339


title: M2 Rep2


title: 5483


title: 4339


title: 3914


title: 7320


title: 6585


title: 5935


title: M0 Rep1

value: 0 hours (start point)


title: 6379


title: 5299


title: 5713


title: G4 Rep3


title: 5083

value: no val

value: Control


title: M0 Rep3


title: G4 Rep2


title: G2 Rep3


title: M0 Rep2


title: G2 Rep1


title: G2 Rep2


title: 5990


title: 4106


title: 6326


title: 6568