title: abdominal aortic aneurysm sample#36

description: sample#36-abdominal_aortic_aneurysms-elective-large


title: abdominal aortic aneurysm sample#31

status: Public on Feb 27 2018

type: RNA

city: Munich

first: Bernd

middle: Henrik

last: Northoff

address: Marchioninistr. 15

department: Institute of Laboratory Medicine

country: Germany

institute: Ludwig-Maximilians-University Munich

description: sample#31-abdominal_aortic_aneurysms-ruptured

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation and background substraction and log2 transformed using limma package for R (Bioconductor).

molecule: total RNA

organism: Homo sapiens

source_name: Abdominal aortic aneurysm (human infrarenal aneurysmatic aortic wall)

label_protocol: cRNA was prepared  using the TargetAmp™- Nano Labeling Kit for Illumina Expression BeadChip (Epicentre Biotechnologies, Madison, WI, USA).

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

tag: tissue

value: infrarenal aortic wall

tag: group of aortic aneurysms

value: ruptured abdominal aortic aneurysms (rAAA)

tag: diameter of aortic aneurysms

value: unknown


title: Control_3

city: Stanford

first: Kent

last: Imaizumi

state: CA

address: 318 Campus Drive

country: USA

institute: Stanford University

hyb_protocol: Cy3-Labeled cDNA was hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) 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 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Then, expression was quantile normalized, and corrected for chip batch effect via ComBat.

source_name: Untreated neurosphere at day 18 derived from ES cells

label_protocol: 20 ng of total RNA was converted into amplified cDNA by using Ovation Pico WTA System V2 (NuGEN). cDNA was Cy3-labeled by using the SureTag Complete DNA Labeling Kit (Agilent).

extract_protocol: Total RNA from neurospheres on day 18 was extracted by RNeasy Micro Kit (QIAGEN).

treatment_protocol: Human ES cells were differentiated into neural progenitor cells by the neurosphere method. On day 12-18, FGF8 was treated at the concentration of 200 ng/mL.

value: neurospheres


title: d5il10_cebp

type: SRA

city: Los Angeles

first: Peter

last: Tontonoz

address: 675 Charles E Young

department: Pathology

institute: UCLA

library_source: genomic

data_processing:
Reads were aligned to the mouse genome (NCBI37/mm9) with Bowtie2. Uniquely mapped reads were used for peak calling and annotation using HOMER (Heinz et al., 2010). Peaks were called if they passed a false discovery rate of 0.01 and were enriched over input. Peaks were annotated to the nearest TSS.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files for each sample represent the read coverage at each genomic position

molecule: genomic DNA

organism: Mus musculus

source_name: iBAd Cell Line

extract_protocol:
Purified nuclei from iBAD cells were lysed and chromatin was sheared using a Bioruptor prior to immunoprecipitation with anti-CEBPB antibodies
Libraries were constructed using Kapa's LTP Library Preparation kit according to manufactuer's instruction.

tag: strain

tag: genotype

tag: stimulus

value: differentiated, treated with IL10

tag: chip antibody

value: anti-CEBPB


title: abdominal aortic aneurysm sample#33

description: sample#33-abdominal_aortic_aneurysms-elective-large

value: elective stable abdominal aortic aneurysms (eAAA)

value: large size abdominal aortic aneurysms


title: abdominal aortic aneurysm sample#34

description: sample#34-abdominal_aortic_aneurysms-elective-large


title: ESC_D0_rep1

city: Shanghai

first: Xudong

last: Guo

address: No.1239, Siping Road

country: China

institute: Tongji University

description:
ESC
Gene expression analysis for undifferentiated ESCs (Day0)

hyb_protocol: Cy5-labelled aRNA was hybrided according to OneArray Plus Hybridization Protocol. 5 ug of Cy5-labelled aRNA was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x fragmentation buffer and 2x blocking agent. On completion of the fragmentation reaction, 22.5ul of hybridization buffer was added to the fragmentation mixture and hybridized for 16 hours at 50°C in a rotating hybridization oven. After hybridization, microarrays were washed 5 minute at 42°C with Wash Buffer I, 5 minute with 42°C Wash buffer II,  and 5 minute with Wash buffer II at room temperature, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using the Agilent 0.1 XDR Protocol (PMT is set to 100% or 10%), then gain the  scanned images with GenePixTM 4.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were loaded into Rosetta Resovler®  Systerm (Rosetta Biosoftware) to process data analysis.

source_name: mouse embryonic stem cells, day0

label_protocol: 5 ug Cyanine-5 (Cy5) labeled aRNA was performed using an Eberwine-based amplification method with Amino Allyl Message Amp II αRNA Amplification kit (Ambion, AM1753) to generate amino-allyl antisense RNA (aa-aRNA). Labeled aRNA coupled with NHS-CyDye was prepared and purified by RNAeasy column purification (QIAGEN, Valencia, CA) prior to hybridization. Purified coupled aRNA was quantified using NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The mESC line 46C was cultured in 15% fetal bovine serum + LIF (1,000 U/ml, Millipore) on feeder cells. The mesoderm cells derived from mESC were cultured in serum-free medium with N2 and B27+Bmp4 (0.2 ng/ml, R&D)+Activin A (5 ng/ml, R&D)+VEGF (5 ng/ml, R&D). The cardiomyocytes derived from mESC were cultured in StemCell Pro-34 medium with bFGF(10 ng/ml, R&D), VEGF(5 ng/ml, R&D) and FGF10 (25 ng/ml, R&D).

extract_protocol: RNA was prepared using the RNAiso (Takara) following the manufacturer's recommendations.

treatment_protocol: The mESCs were harvested after removing the feeder and the differentiated cells were harvested in the indicated days (day4 and 10) of ESC differentiation.

tag: cell type

value: mouse embryonic stem cells (mESCs)

tag: genotype/variation

value: control

tag: time point


title: abdominal aortic aneurysm sample#30

description: sample#30-abdominal_aortic_aneurysms-ruptured


title: FGF8_2

source_name: FGF8-treated neurosphere at day 18 derived from ES cells


title: abdominal aortic aneurysm sample#29

description: sample#29-abdominal_aortic_aneurysms-ruptured


title: Control_2


title: d5_input

value: differentiated

value: none (input)


title: abdominal aortic aneurysm sample#27

description: sample#27-abdominal_aortic_aneurysms-ruptured


title: CM_1405KIpA_D10_rep1

description:
CM_1405KIpA
Gene expression analysis for cardiomyocytes derived from linc1405 knockdown ESCs (Day10)

source_name: cardiomyocytes, knockdown linc1405, day10

value: cardiomyocytes derived from mESCs

value: knockdown linc1405

value: day10 of ESC differentiation


title: Day14-Uninjured-H3mm7KO-rep2

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi, Higashi-ku, Fukuoka

department: Medical Institute of Bioregulation, Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

description:
processed data file:
countMatrix_CELSeq_MuscleInjury.txt.gz

library_source: transcriptomic

data_processing:
The raw sequence reads were aligned to mouse genome (GRCm38) using HISAT2 (version 2.0.4), and the uniquely mapped reads were retained for ChIP-seq/ATAC-seq analysis.
The matrices of read counts on gencode genes (release M9) were generated using featureCounts (version 1.5.0-p3). For ATAC-seq, the option of featureCounts: -B -C -P -d 20 -D 150, were used to extract subnucleosomal fraction.
The coverage tracks of ATAC-seq (bigWig) were generated using bamCoverage command of deepTools (version 2.4.2) with the option: --smoothLength 60 --binSize 1 --extendReads.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: *.txt files include tab-delimited read count matrices

source_name: Injured TA muscle from H3mm7-KO mouse

growth_protocol: in vitro fertilized zygotes (C57BL/6 x C57BL/6) were electroporated with 100 ng/ul Cas9 protein, 100 ng/ul crRNAs and 100 ng/ul tracrRNA. Muscle injury was induced by the intramuscular injection of 100 ul cardiotoxin.

extract_protocol: Libraries were prepared according to the protocol described in Hashimshony, T. et al. (Genome Biol. 2016).

treatment_protocol: At days 5 and 14 after cardiotoxin injection, cryosections of injured (left leg) and uninjured (right) tibialis anterior muscle were prepared from H3mm7+/+ and H3mm7-/- mice.

value: Injured TA muscle


title: d5_cebp


title: Day14-Uninjured-H3mm7KO-rep1


title: FGF8_3


title: abdominal aortic aneurysm sample#32

description: sample#32-abdominal_aortic_aneurysms-ruptured


title: FGF8_1


title: Control_1


title: CM_Control_D10_rep1

description:
CM_Ctrl
Gene expression analysis for cardiomyocytes derived from control ESCs (Day10)

source_name: cardiomyocytes, control, day10


title: Day14-Injured-WT-rep1

source_name: Injured TA muscle from wild-type mouse

growth_protocol: Muscle injury was induced by the intramuscular injection of 100 ul CTX.

value: wild-type


title: MES_1405KIpA_D4_rep1

description:
MES_1405KIpA
Gene expression analysis for mesoderm cells derived from linc1405 knockdown ESCs (Day4)

source_name: mesoderm cells, knockdown linc1405, day4

value: mesoderm cells derived from mESCs

value: day4 of ESC differentiation


title: Day14-Injured-H3mm7KO-rep2


title: MES_Control_D4_rep1

description:
MES_Ctrl
Gene expression analysis for mesoderm cells derived from control ESCs (Day4)

source_name: mesoderm cells, control, day4


title: abdominal aortic aneurysm sample#26

description: sample#26-abdominal_aortic_aneurysms-ruptured

value: infrarenal aortic wall

value: ruptured abdominal aortic aneurysms (rAAA)

value: unknown


title: abdominal aortic aneurysm sample#28

description: sample#28-abdominal_aortic_aneurysms-ruptured


title: Day14-Injured-WT-rep2


title: abdominal aortic aneurysm sample#24

description: sample#24-abdominal_aortic_aneurysms-elective


title: abdominal aortic aneurysm sample#23

description: sample#23-abdominal_aortic_aneurysms-elective


title: Snord116+/- ZT9_rep1

city: Davis

first: Rochelle

last: Coulson

address: One Shields Ave.

institute: University of California, Davis

data_processing:
Reads were filtered by Illumina flag
Reads with adapter contamination were trimmed
Reads were aligned to mm10 using BSSeeker2
Trimmed reads and reads with no adapter contamination were combined
SAM files were converted to percent methylation bed files
Percent methylation files from each chromosome were combined
Genome_build: mm10
Supplementary_files_format_and_content: Bed files containing percent methyation values per base

source_name: Cerebral cortex

growth_protocol: Mice were housed in 12 hour light, 12 hour dark conditions

extract_protocol:
Mice were sacrificed at ZT0, 3, 6, 9, 12, and 16.  Genomic DNA was isolated from 5-10mg cortex using the Gentra Puregene kit (Qiagen)
500ng DNA was bisulfite converted using the EZ DNA Methylation-Lightening kit (Zymo).  Libraries were prepared with 100ng bisulfite converted DNA using the TruSeq DNA Methylation kit (Illumina) and barcoded using TruSeq DNA Methylation Kit Index PCR Primers (Illumina).

value: Cerebral cortex

tag: developmental stage

tag: Sex

value: Male


title: Day05-Uninjured-WT-rep3


title: Snord116+/- ZT3_rep3


title: abdominal aortic aneurysm sample#25

description: sample#25-abdominal_aortic_aneurysms-ruptured


title: Day05-Uninjured-WT-rep2


title: Snord116+/- ZT9_rep2


title: abdominal aortic aneurysm sample#21

description: sample#21-abdominal_aortic_aneurysms-elective

value: elective stable abdominal aortic aneurysms (eAAA)


title: Day14-Injured-H3mm7KO-rep1


title: Snord116+/- ZT3_rep2


title: Snord116+/- ZT9_rep3


title: WT ZT9_rep3

value: WT


title: Day05-Uninjured-WT-rep1


title: Day05-Uninjured-H3mm7KO-rep3


title: WT ZT9_rep2


title: Day05-Uninjured-H3mm7KO-rep1


title: Day05-Uninjured-H3mm7KO-rep2


title: WT ZT9_rep1


title: abdominal aortic aneurysm sample#20

description: sample#20-abdominal_aortic_aneurysms-elective


title: abdominal aortic aneurysm sample#22

description: sample#22-abdominal_aortic_aneurysms-elective


title: Snord116+/- ZT3_rep1


title: abdominal aortic aneurysm sample#18

description: sample#18-abdominal_aortic_aneurysms-elective


title: WT ZT3_rep2


title: WT ZT3_rep3


title: Day05-Injured-WT-rep2


title: abdominal aortic aneurysm sample#16

description: sample#16-abdominal_aortic_aneurysms-elective


title: abdominal aortic aneurysm sample#19

description: sample#19-abdominal_aortic_aneurysms-elective


title: WT ZT3_rep1


title: Snord116+/- ZT16_rep3

extract_protocol:
Mice were sacrificed at ZT0, 6, 12, and 16.  Genomic DNA was isolated from 5-10mg cortex using the Gentra Puregene kit (Qiagen)
500ng DNA was bisulfite converted using the EZ DNA Methylation-Lightening kit (Zymo).  Libraries were prepared with 100ng bisulfite converted DNA using the TruSeq DNA Methylation kit (Illumina) and barcoded using TruSeq DNA Methylation Kit Index PCR Primers (Illumina).


title: Day05-Injured-WT-rep3


title: Snord116+/- ZT16_rep2


title: abdominal aortic aneurysm sample#14

description: sample#14-abdominal_aortic_aneurysms-elective-intermediate

value: intermediate size abdominal aortic aneurysms


title: abdominal aortic aneurysm sample#12

description: sample#12-abdominal_aortic_aneurysms-elective-intermediate


title: abdominal aortic aneurysm sample#15

description: sample#15-abdominal_aortic_aneurysms-elective-intermediate


title: Day05-Injured-WT-rep1

description:
processed data file:
countMatrix_CELSeq_MuscleInjury.txt.gz


title: abdominal aortic aneurysm sample#17

description: sample#17-abdominal_aortic_aneurysms-elective


title: abdominal aortic aneurysm sample#13

description: sample#13-abdominal_aortic_aneurysms-elective-intermediate


title: Snord116+/- ZT16_rep1


title: Snord116+/- ZT12_rep3


title: Day05-Injured-H3mm7KO-rep3


title: Day05-Injured-H3mm7KO-rep2


title: Snord116+/- ZT12_rep1


title: Snord116+/- ZT6_rep1


title: Day05-Injured-H3mm7KO-rep1


title: Snord116+/- ZT12_rep2


title: Snord116+/- ZT6_rep3


title: Snord116+/- ZT6_rep2


title: Snord116+/- ZT0_rep3


title: Snord116+/- ZT0_rep1


title: WT ZT16_rep1


title: WT ZT16_rep3


title: abdominal aortic aneurysm sample#08

description: sample#08-abdominal_aortic_aneurysms-elective-intermediate


title: abdominal aortic aneurysm sample#07

description: sample#07-abdominal_aortic_aneurysms-elective-intermediate


title: WT ZT12_rep3


title: abdominal aortic aneurysm sample#10

description: sample#10-abdominal_aortic_aneurysms-elective-intermediate


title: abdominal aortic aneurysm sample#06

description: sample#06-abdominal_aortic_aneurysms-elective-intermediate


title: abdominal aortic aneurysm sample#09

description: sample#09-abdominal_aortic_aneurysms-elective-intermediate


title: WT ZT12_rep2


title: K562 PR20 - 3

city: Boston

first: Nicholas

middle: J

last: Kramer

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: Ctrl_Untr_vs_Ctrl_PR20-ExpDiff (k562).csv

data_processing:
illumina basecalling
STAR alignment
RSEM counts
DESeq2 normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_RNAseq.sh
Genome_build: hg38 for human samples, mm10 for mouse samples
Supplementary_files_format_and_content: comma separated value text files with normalized abundance measurements (output from DESeq2)

source_name: K562 cells

extract_protocol:
RNA extracted using a PureLink RNA Mini Kit (Ambion)
polyA enriched mRNA libraries (SureSelect Automated Strand-Specific RNA Library Prep, mRNA Library Prep for Illumina Paired-End Multiplexed Sequencing)

tag: treatment

value: 10uM PR20 treatement, overnight

tag: experiment grouping

value: Experiment 1


title: abdominal aortic aneurysm sample#11

description: sample#11-abdominal_aortic_aneurysms-elective-intermediate


title: MVN_4D_SO_rep2

city: Seoul

first: Munyoung

last: Chang

address: 102 Heukseok-ro, Dongjak-gu

department: Otorhinolaryngology-Head and Neck Surgery

country: South Korea

institute: Chung-Ang University College of Medicine

description: miRNA expression after 4D in sham operated rat medial vestibular nucleus nucleus

hyb_protocol: Labeled samples were subsequently hybridized by loading onto a microarray slide using Hybridization Chamber Kit (Agilent Technologies, Santa Clara, CA, USA) and Hybridization Gasket Slide Kit (Agilent Technologies, Santa Clara, CA, USA). Hybridization was performed over 20 hr at 55 °C followed by washing the microarray slide as recommended by the manufacturer.

scan_protocol: Processed microarray slides were scanned with Agilent G2565CA Microarray Scanner System (Agilent Technologies).

data_processing: The data were processed based on quantile normalization method using the GeneSpring GX 13.1 (Agilent technologies, Santa Clara, CA, USA). This normalization method aims to make the distribution of intensities for each array in a set of arrays the same. The normalized intensity values were analyzed using GeneSpring GX 13.1 (Agilent technologies, Santa Clara, CA, USA).

organism: Rattus norvegicus

source_name: Medial vestibular nucleus, 4D, sham operation, replicate 2

label_protocol: In 500ng of total RNA, we added calf intestinal phosphatase to dephosporylate the 3’-end of miRNA and by using T4 RNA Ligase, Cyanine3-pCp was labeled at the 3’-end of miRNA.

extract_protocol: RNA was extracted from the sample using the TRI REAGENT (MRC, Cincinnati, OH, USA) according to the manufacturer’s instructions. Following homogenization, 1 ml of solution was transferred to a 1.5 ml Eppendorf tube and centrifuged at 12,000 g for 10 min at 4°C to remove insoluble material. The supernatant containing RNA was collected, mixed with 0.2 ml of chloroform, and centrifuged at 12,000 g for 15 min at 4°C. After RNA in the aqueous phase was transferred into a new tube, the RNA was precipitated by mixing 0.5 ml of isopropyl alcohol and recovered by centrifuging the tube at 12,000 g for 10 min at 4°C. The RNA pellet was washed briefly in 1 ml of 75% ethanol and centrifuged at 7,500 g for 5 min at 4°C. Finally, the total RNA pellet was dissolved in Nuclease-water, and its quality and quantity was assessed by Agilent bioanalyzer 2100 analysis.

treatment_protocol: Seven week-old-male Sprague–Dawley rats were used. In the unilateral vestibular deafferentiation (UVD) group, labyrinthectomy was performed at left side as following methods. After anesthesia, a retroauricular incision was made to expose the external auditory canal. Then the external auditory canal was opened exposing the tympanic membrane. The tympanic membrane and ossicles were removed except for stapes. To fenestrate the vestibule, the hole was made with a 0.5 mm drill bur superior to the stapes. Then 99 % ethanol was injected through this hole and aspirated several times. In the sham operation group, the same operative procedures with labyrinthectomy was performed except for fenestrating the vestibule and injecting ethanol.

value: Sprague–Dawley

value: medial vestibular nucleus of brain tissue

tag: gender

value: male

tag: age


title: WT ZT16_rep2


title: WT ZT12_rep1


title: Snord116+/- ZT0_rep2


title: WT ZT6_rep3


title: K562 PR20 - 2


title: WT ZT6_rep2


title: WT ZT6_rep1


title: K562 PR20 - 1


title: K562 Ctl - 3

value: Vehicle control


title: WT ZT0_rep3


title: K562 Ctl - 1


title: K562 Ctl - 2


title: abdominal aortic aneurysm sample#04

description: sample#04-abdominal_aortic_aneurysms-elective-intermediate


title: abdominal aortic aneurysm sample#02

description: sample#02-abdominal_aortic_aneurysms-elective-intermediate


title: WT ZT0_rep2


title: abdominal aortic aneurysm sample#05

description: sample#05-abdominal_aortic_aneurysms-elective-intermediate


title: abdominal aortic aneurysm sample#03

description: sample#03-abdominal_aortic_aneurysms-elective-intermediate


title: WT ZT0_rep1


title: abdominal aortic aneurysm sample#01

description: sample#01-abdominal_aortic_aneurysms-elective-intermediate


title: MVN_4hr_SO_rep1

description: miRNA expression after 4hr in sham operated rat medial vestibular nucleus nucleus

source_name: Medial vestibular nucleus, 4hr, sham operation, replicate 1


title: MVN_4D_UVD_rep2

description: miRNA expression after 4D in unilateral vestibular deafferentiated rat medial vestibular nucleus nucleus

source_name: Medial vestibular nucleus, 4D, unilateral vestibular deafferentiation, replicate 2


title: MVN_4D_SO_rep1


title: MVN_4hr_SO_rep2


title: MVN_4hr_UVD_rep2

description: miRNA expression after 4hr in unilateral vestibular deafferentiated rat medial vestibular nucleus nucleus

source_name: Medial vestibular nucleus, 4hr, unilateral vestibular deafferentiation, replicate 1


title: MVN_4hr_UVD_rep1


title: MVN_4D_UVD_rep1


title: CD27WT_4

status: Public on Feb 26 2018

city: Chicago

first: Barbara

middle: L

last: Kee

state: Illinois

address: 924 E57th st

institute: The University of Chicago

data_processing:
Quality control and DNA alignment: All raw sequence data were quality-trimmed to a minimum Phred score of 20 with Trimmomatic. Alignment to reference genome mm10 was done with Bowtie2. PCR duplicates were removed using Picard MarkDuplicates, and alignments with an edit distance from the reference of more than 2, or those that were mapped to the reference multiple times, were removed.
ATAC-Seq analysis: Read-alignment positions were adjusted according to their strand: +4 bp for + strand alignments, and −5 bp for – strand alignments. We called open chromatin regions using Macs2 with the “—nomodel” option set. For nucleosome positioning, we filtered properly paired alignments by their fragment size. Fragments less than 100 bp in size were considered nucleosome free and were replaced with a single BED region and used as a background. Those with sizes between 180 and 247 bp were considered mononucleosomes and were replaced with a single BED region; those with sizes between 315 and 473 bp were considered dinucleosomes and were replaced with two BED regions, each spanning half the overall fragment length; and those with sizes between 558 and 615 bp were considered trinucleosomes and were replaced with three BED regions, each spanning one-third of the overall fragment length. The mono-, di- and trinucleosome regions were concatenated and used as the nucleosome signal. The resulting BED regions were analyzed with DANPOS with the parameters –p 1 –a 1 –d 20 –clonalcut 0 to identify regions enriched or depleted for nucleosomes.
Genome_build: mm10
Supplementary_files_format_and_content: open chromatin peak calls (*open_hiqual.bed)
Supplementary_files_format_and_content: open chromatin enrichment track (*open.bw)
Supplementary_files_format_and_content: nucleosome differential enrichment track (*nucl.diff_norm.bw)

source_name: C57Bl/6 BM CD27+CD11b- NK cells

extract_protocol:
Qiagen MiniElute kit
IluminaNextera Index kit followed by PCR using using the NEBnext PCR master mix

value: bone marrow

tag: cell population

value: natural killer (NK) cells


title: CD27Mut_4

value: Id2 knock-out

tag: tissue


title: sham-injured vs cryoinjured

city: Giessen

first: Sven

last: Reischauer

state: Hessen

address: Auweg 129

department: Cardiology/Angiology

institute: Medical Clinic I - JLU

hyb_protocol: cRNA is hybridised on 8x60K microarrays at 65°C for 17 h

scan_protocol: Fluorescence signals on microarrays are detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron for SurePrint G3 Gene Expression Microarrays and 5 micron for HD Microarray formats

data_processing: Agilent's Feature Extraction software version 11 is used to read and process the TIFF files.

organism: Danio rerio

source_name: sham-injured zebrafish heart

label_protocol: For 1st strand synthesis, either oligo-dT primer or a random primer / oligo-dT primer mixture (WT primer) is used. After 2nd strand synthesis, an in vitro transcription for synthesis of cRNA labelled with cyanine 3-CTP is performed.

extract_protocol: trizol RNA extraction

value: adult hearts

source_name: 4days post-cryoinjured zebrafish heart


title: CD27WT_2


title: CD11b25k_2

source_name: C57Bl/6 BM CD27-CD11b+ NK cells


title: CD27Mut_2


title: CD11b25k_4


title: MCF10A RUNX3-replicate2 b

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: Gene expression data from MCF10A RUNX3, replicate 2

hyb_protocol: Following fragmentation, 2 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000.

data_processing: Data were normalized by Robust Multichip Average (RMA) using Affymetrix Powertools

label: Biotin

source_name: MCF10A RUNX3

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 200ng total RNA

growth_protocol: Stable MCF10A cell lines were grown following the standard growth conditions (Debnath et al 2003).

extract_protocol: Total RNA was extracted by Qiagen RNEasy kit according to the manufacturer's instructions.

treatment_protocol: RNA was extracted from non-confluent cultures of MCF10A stable cell lines. No treatment was given to the cells.

tag: cell line


title: MCF10A RUNX3-replicate1 b

description: Gene expression data from MCF10A RUNX3, replicate 1


title: MCF10A YAP-2SA+RUNX1-replicate2

description: Gene expression data from MCF10A YAP-2SA+RUNX1, replicate 2

source_name: MCF10A YAP-2SA+RUNX1


title: MCF10A YAP-2SA/ww+RUNX1-replicate1

description: Gene expression data from MCF10A YAP-2SA/ww+RUNX1, replicate 1

source_name: MCF10A YAP-2SA/ww+RUNX1


title: MCF10A YAP-2SA/ww+RUNX3-replicate1

description: Gene expression data from MCF10A YAP-2SA/ww+RUNX3, replicate 1

source_name: MCF10A YAP-2SA/ww+RUNX3


title: MCF10A YAP-2SA+RUNX3-replicate1

description: Gene expression data from MCF10A YAP-2SA+RUNX3, replicate 1

source_name: MCF10A YAP-2SA+RUNX3


title: MCF10A YAP-2SA-replicate1

description: Gene expression data from MCF10A YAP-2SA, replicate 1

source_name: MCF10A YAP-2SA


title: MCF10A YAP-2SA/ww+RUNX1-replicate2

description: Gene expression data from MCF10A YAP-2SA/ww+RUNX1, replicate 2


title: MCF10A YAP-2SA/ww+RUNX3-replicate2

description: Gene expression data from MCF10A YAP-2SA/ww+RUNX3, replicate 2


title: MCF10A YAP-2SA+RUNX1-replicate1

description: Gene expression data from MCF10A YAP-2SA+RUNX1, replicate 1


title: MCF10A YAP-2SA/ww-replicate2

description: Gene expression data from MCF10A YAP-2SA/ww, replicate 2

source_name: MCF10A YAP-2SA/ww


title: MCF10A YAP-5SA+RUNX3-Y312A-replicate2

description: Gene expression data from MCF10A YAP-5SA+RUNX3-Y312A, replicate 2

source_name: MCF10A YAP-5SA+RUNX3-Y312A


title: MCF10A Vector Control MSCV-replicate1

description: Gene expression data from MCF10A Vector Control MSCV, replicate 1

source_name: MCF10A Vector Control MSCV


title: MCF10A RUNX1-replicate1

description: Gene expression data from MCF10A RUNX1, replicate 1

source_name: MCF10A RUNX1


title: MCF10A Vector Control MSCV-replicate2

description: Gene expression data from MCF10A Vector Control MSCV, replicate 2


title: MCF10A RUNX1-replicate2

description: Gene expression data from MCF10A RUNX1, replicate 2


title: MCF10A RUNX3-Y312A-replicate1

description: Gene expression data from MCF10A RUNX3-Y312A, replicate 1

source_name: MCF10A RUNX3-Y312A


title: MCF10A RUNX3-Y312A-replicate2

description: Gene expression data from MCF10A RUNX3-Y312A, replicate 2


title: MCF10A YAP-5SA+RUNX3-Y312A-replicate1

description: Gene expression data from MCF10A YAP-5SA+RUNX3-Y312A, replicate 1


title: MCF10A YAP-2SA/ww-replicate1

description: Gene expression data from MCF10A YAP-2SA/ww, replicate 1


title: MCF10A YAP-2SA-replicate2

description: Gene expression data from MCF10A YAP-2SA, replicate 2


title: MCF10A YAP-2SA+RUNX3-replicate2

description: Gene expression data from MCF10A YAP-2SA+RUNX3, replicate 2


title: MCF10A YAP-5SA+RUNX3-replicate2

description: Gene expression data from MCF10A YAP-5SA+RUNX3, replicate 2

source_name: MCF10A YAP-5SA+RUNX3


title: MCF10A RUNX3-replicate1

description: Gene expression data from MCF10A RUNX3, replicate 1


title: MCF10A YAP-5SA+RUNX3-replicate1

description: Gene expression data from MCF10A YAP-5SA+RUNX3, replicate 1


title: MCF10A RUNX3-replicate2

description: Gene expression data from MCF10A RUNX3, replicate 2


title: MCF10A YAP-5SA-replicate1

description: Gene expression from MCF10A YAP-5SA, replicate 1

source_name: MCF10A YAP-5SA


title: MCF10A YAP-5SA-replicate2

description: Gene expression from MCF10A YAP-5SA, replicate 2


title: MCF10A Vector Control pQCXI-replicate2

description: Gene expression from MCF10A Vector Control, replicate 2

source_name: MCF10A Vector Control pQCXI


title: RNA-seq EV ctrl rep 1

city: Santa Cruz

first: David

last: Haussler

state: California

address: 1156 High St

institute: UC Santa Cruz

description:
46C_EV_01
processed data file: Mouse_EV_N2NL_rawcounts.txt
processed data file: Mouse_EV_N2NL_DESeq2.txt

data_processing:
Trimmomatic 0.36 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
STAR 2.4.0 --outStd SAM --outReadsUnmapped Fastx --chimSegmentMin 18 --chimScoreMin 12
Bowtie2 2.3.3.1 --local --very-sensitive-local -q --mm
Htseq-count 0.6.1p1 -t exon -i exon_id -q
DESeq2 2.11.39 (Galaxy).
Genome_build: Human hg38 (GRCh38), Mouse mm10 (GRCm38)
Supplementary_files_format_and_content: *_rawcounts.txt: Tab-delimited text files contain raw read counts per gene.
Supplementary_files_format_and_content: _DESeq2.txt: Tab-delimited text files contain subsequent DESeq2 analysis containing normalized read counts and statistical analysis.

source_name: Day 6 cortical organoids

growth_protocol: Mitomycin-C treated mouse embryonic fibroblasts (MEFs, GlobalStem) were seeded on 0.1% gelatin-coated plates at a density of 35.000 cell/cm2. MEFs were cultured in DMEM, 4.5 g/l glucose + GlutaMax (Thermofisher), 10% heat-inactivated fetal bovine serum (HIFBS, Thermofisher), 1x Penicillin/Streptomycin (P/S, Thermofisher) and 1x sodium pyruvate (NaPyr, Thermofisher). H9 human embryonic stem cells (H9 hESCs, WiCell) were cultured in W0 medium: DMEM/F12 (Thermofisher) with 20% KnockOut serum replacement (KOSR, Thermofisher), 2 mM L-glutamine (Thermofisher), 1x non-essential amino acids (NEAA, Thermofisher), 100 uM 2-mercaptoethanol (Thermofisher) and 1x P/S (Thermofisher). W0 was freshly supplemented daily with 8 ng/ml FGF2 (Sigma). H9 hESCs (WA09, WiCell Research Institute) were grown on MEF feeder layers, and manually passaged every 5-6 days when colonies reached approximately 2 mm in diameter. Mouse 46C ESCs were grown according to the BayGenomics protocol, on 0.1% gelatin-coated plates, and cultured in GMEM (Thermofisher) with 10% HIFBS, 2 mM L-Glutamine, 1x NEAA, 1x NaPyr, 100 µM 2-mercaptoethanol and 1x P/S. ESGRO LIF (Millipore) was added fresh daily.

extract_protocol:
Human organoid samples: Pools of 5-10 organoids per replicate were harvested in TRIzol at day 28 for RNA extraction. Mouse organoid samples: Three pools of 16 organoids were isolated in TRIzol after 6 days of differentiation for EV and NOTCH2NL-Sh_T197I organoids. RNA was isolated using standard TRIzol protocol, followed by DNaseI treatment (Rochte) and column purification (Zymo RNA clean and concentrator 5).
mRNA was isolated from total RNA using polyA selection Dynabeads mRNA DIRECT Micro Purification Kit (Thermofisher). Library was prepared using strand-specific Ion Total RNA-seq Kit v2 (Thermofisher) and Ion Xpress RNA-seq Barcode 1-16 (Thermofisher) to label different samples.

treatment_protocol: For organoid differentiation, medium was replaced with W0 medium + 1x NaPyr without FGF2 (Differentiation medium). Colonies of 2-3 mm in diameter were manually lifted using a cell lifter, and transferred to an ultra-low attachment 60mm dish (Corning). After 24 hours (day 0) embryoid bodies had formed, and 50% of medium was replaced with Differentiation medium supplemented with small molecule inhibitors and recombinant proteins to the following final concentrations: µM SB431542 (Sigma), 1 µM Dorsomorphin (Sigma), 3 µM IWR-1-Endo (Sigma) and 1 µM Cyclopamine (Sigma). Medium was then replaced every other day until harvest. On day 4, 60 mm dishes with organoids were placed on a hi/lo rocker in the incubator. From day 18 on, medium is replaced with Neurobasal/N2 medium. From day 24 on, Cyclopamine was not added anymore. Mouse 46C ESC organoid differentiation was performed as described previously (Eiraku and Sasai, 2011).

value: 46C embryonic stem cells

value: EV ctrl stable cell line

tag: time of differentiation

value: Day 6

value: Cortical organoids


title: RNA-seq EV ctrl rep 3

description:
46C_EV_03
processed data file: Mouse_EV_N2NL_rawcounts.txt
processed data file: Mouse_EV_N2NL_DESeq2.txt


title: RNA-seq EV ctrl rep 2

description:
46C_EV_02
processed data file: Mouse_EV_N2NL_rawcounts.txt
processed data file: Mouse_EV_N2NL_DESeq2.txt


title: RNA-seq N2NL-Sh_T197I rep 1

description:
46C_N2NL_01
processed data file: Mouse_EV_N2NL_rawcounts.txt
processed data file: Mouse_EV_N2NL_DESeq2.txt

value: NOTCH2NL-Sh_T197I stable cell line


title: RNA-seq N2NL-Sh_T197I rep 2

description:
46C_N2NL_02
processed data file: Mouse_EV_N2NL_rawcounts.txt
processed data file: Mouse_EV_N2NL_DESeq2.txt


title: RNA-seq N2NL-Sh_T197I rep 3

description:
46C_N2NL_03
processed data file: Mouse_EV_N2NL_rawcounts.txt
processed data file: Mouse_EV_N2NL_DESeq2.txt


title: MCF10A Vector Control pQCXI-replicate1

description: Gene expression from MCF10A Vector Control, replicate 1


title: Ezh2 +/+ Tet ON PyVmT tumour, biological replicate 3

city: Montreal

first: William

last: Muller

state: Quebec

address: 1160 Avenue des Pins

country: Canada

institute: McGill University

hyb_protocol: After fragmentation and labeling, 3.5μg of labeled DNA was hybridized on GeneChip Mouse Gene 2.0 ST arrays (Affymetrix) and incubated at 45°C in the Genechip Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips Fluidics Station 450 (Affymetrix) using Hybridization Wash and Stain kit according to the manufacturer’s instructions (Affymetrix)

scan_protocol: Affymetrix Gene ChIP Scanner 3000

data_processing: Raw data were first processed to perform gene-level normalization and quality control using Affymetrix Expression Console software (Affymetrix). Processed data were next subjected to Gene Level Differential Expression Analysis using Affymetrix Transcriptome Analysis Console software.

label: biotin

source_name: mammary gland tumour

label_protocol: Sense-strand cDNA was synthesized from 100ng of total RNA and fragmentation and labelling were performed to produce ssDNA with the GeneChip WT Terminal Labeling Kit according to manufacturer’s instructions (Affymetrix)

growth_protocol: Whole endpoint tumours flash frozen in liquid nitrogen

extract_protocol: For each sample, tail DNA was extracted to determine the genotype of the sample. Samples were flash frozen and also examined by immunblot analysis to confirm EZH2 status.

value: endpoint

value: mammary gland

value: wild-type


title: C1C12_ShZc3h10_2

city: Milano

first: Stefano

last: de Pretis

address: Via Olgettina, 58

department: Center for Omics Sciences

country: Italy

institute: IRCCS San Raffaele Institute

hyb_protocol: An aliquot (100 ng) of RNA was used for the preparation of targets for Affymetrix® MoGene 2.0 ST arrays, according to the Ambion WT Expression kit manual. Affymetrix® MoGene 2.0 ST arrays (which contain 41073 genes), were purchased from Affymetrix (Affymetrix, USA). The staining, washing and scanning of the arrays were conducted using the Fluidics 450 station, Command Console Software and GeneChip® Scanner 3000 7G, generating .CEL files for each array (Affymetrix, USA).

scan_protocol: The images were scanned by Affymetrix GeneChip Command Console (AGCC) and analyzed with the Affymetrix GeneChip Expression Console.

data_processing:
The quality control of the scanned data was first estimated by confirming the order of the signal intensities of the Poly-A and Hybridization controls using Expression Console Software (Affymetrix, USA). Raw expression values were imported as Affymetrix.CEL files into Partek Genomics Suite 6.6 (Partek Inc., St. Louis, MO, USA). Raw expression values from the Affymetrix MoGene 2.0 ST arrays were analyzed and normalized using Partek Genomics Suite 6.6, which includes the Preprocessing, Differentially Expressed Genes (DEGs) Finding and Clustering modules. A total of 10 .CEL files were uploaded and normalized in PM (perfect match)-only conditions as a PM intensity adjustment.
A Robust Multichip Analysis (RMA) quantification method was used as a probe set summarization algorithm for log transformation with base 2 (log2) and the Quantile normalization method was chosen to evaluate the preliminary data quality in the Preprocessing module, which functions as a data quality control through the Affymetrix Expression Console Software. The mean signal intensities of all genes were obtained using 2 array strips from each group.

source_name: mouse muscle

label_protocol: not provided

growth_protocol:
Cells were maintained in growth medium (high-glucose DMEM supplemented with 10% fetal bovine serum (FBS) (v/v) (Gibco), 2% glutamine (v/v) (Thermo Scientific), 2% pen/strep (v/v) (Thermo Scientific) and in 37°C, 5% CO2 and 90% humidified atmosphere.
genotype: Zc3h10 targeted silencing used a validated adenoviral construct contained specific short hairpin RNA sequence under a U6 promoter (shADV-276549), while control vector contained a scrambled sequence (Vector Biolabs, 1122). Both constructs were transduced using a MOI of 100 carried out by 48 hr exposure.

extract_protocol:
Cells were rinsed in 1 ml of ice-cold PBS. Total RNA was isolated using silica column approach (NucleoSpin® RNA extraction kit, Macherey-Nagel, 740955.250). Briefly, cells were washed in ice-cold PBS and lysed in 350 of lysis buffer supplemented with 1% β-mercaptoethanol. After adding 100µl of chloroform, mouse samples were centrifuged at 10,000g at 4°C for 15 min. Upper polar phases and cell samples were then transferred to silica columns and spun 11,000g for 30 seconds. Total RNA was then isolated by following manufacturer’s instructions and eluted from columns with 50µl of RNase free water.
3µg of RNA were used for the analyses. Total RNA concentration and purity was assessed by UV spectrophotometry (NanoDrop 1000 Spectrophotometer, Thermo Scientific). Total RNA integrity was assessed by Agilent Bioanalyzer and the RNA Integrity Number (RIN) was calculated before differential gene expression evaluation.

value: myotubes

value: Zc3h10 targeted short hairpin

tag: differentiation protocol

value: C2C12 myoblasts were differentiated to myotubes by growing cells to complete confluence and switching growth medium to differentiation medium (2% horse serum (v/v) (Euroclone), 2% glutamine (v/v), 2% pen/strep (v/v)). C2C12 myotubes were differentiated for 2 days.


title: Ezh2 +/+ Tet ON PyVmT tumour, biological replicate 4

tag: genotype


title: C1C12_Scr_4

value: Scrambled short hairpin


title: Ezh2 +/+ Tet ON PyVmT tumour, biological replicate 1


title: Ezh2 -/- Tet ON PyVmT tumour, biological replicate 2


title: Ezh2 -/- Tet ON PyVmT tumour, biological replicate 4


title: Ezh2 -/- Tet ON PyVmT tumour, biological replicate 3


title: Ezh2 -/- Tet ON PyVmT tumour, biological replicate 5


title: Ezh2 -/- Tet ON PyVmT tumour, biological replicate 1


title: C1C12_Scr_5


title: C1C12_ShZc3h10_3


title: C1C12_ShZc3h10_1


title: C1C12_Scr_2


title: Ezh2 +/+ Tet ON PyVmT tumour, biological replicate 5


title: C1C12_Scr_3


title: C1C12_ShZc3h10_4


title: Ezh2 +/+ Tet ON PyVmT tumour, biological replicate 2


title: pancreatic_islets_15w_WT_Rpb1_NTD

city: Freiburg

first: Steffen

last: Heyne

address: Stübeweg 51

department: Epigenetic Focus

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
BCL2Fastq pipeline version: 0.2.1 (bcl2fastq version: 2.17.1.1)
Reads for mouse bulk RNA-seq datasets were mapped with TopHat v2.0.13 against mouse genome version GRCm38. Reads were counted with featureCounts (subread-1.5.0-p1) against gene models from Gencode version M9.
All Chip-seq data was mapped with Bowtie2 (v2.2.8) and filtered for PCR duplicates. Bigwig tracks for visualization in IGV were created with DeepTools v2.4.1 and normalized to sequencing depth (Ramirez et al., 2016).
Genome_build: GRCm38 (Ensembl naming scheme)
Supplementary_files_format_and_content: RNA-Seq: tab-delimited text files with raw counts for each sample; ChIP-Seq: sequencing-depth normalized bigwig files with raw (but filtered) ChIP signal.

source_name: whole islet

extract_protocol:
NEXSON ChIP-seq workflow (Arrigoni et al., 2015) was applied to freshly isolated mouse islets
Primary islets were obtained by collagenase digestion with reference to (Li et al., 2009). In brief, adult pancreata were perfused through the common bile duct using a 27/30-gauge needle with Collegenase IV (Sigma) solution. Perfused pancreata were digested and purified by centrifugation in Histopaque gradient (Sigma). Isolated islets were hand picked and cultured in complete media (RMPI-1640 containing 11mM glucose, 10% FBS, 0.1% Penincillin/Streptomycin) and maintained at 37°C in 5% CO2 environment.

tag: strain

value: 15 weeks

value: wild type

value: Pol-II (Diagenode Cat #C15200004)


title: C1C12_Scr_1


title: C1C12_ShZc3h10_5


title: pancreatic_islets_15w_WT_Input

tag: chip antibody


title: WT_NK_14

description: Replicate 2

hyb_protocol: GeneChip Hybridization, Wash and Stain kit Affymetrix.

scan_protocol: GeneChip Scanner 3000 Affymetrix.

data_processing: CEL files were normalized using the rma function in the R Bioconductor package oligo.

source_name: C57Bl/6 mouse NK Cells

label_protocol: GeneChip 3' IVT Express kit Affymetrix.

extract_protocol: Qiagen RNeasy Micro kit.

tag: strain/background

value: Rag1-/- Id2f/f

tag: cell type

value: Natural killer (NK)


title: pancreatic_islets_15w_WT_H3K4me3

value: H3K4me3 (Diagenode Cat #pAb-003-050)


title: WT_NK_19

description: Replicate 3

tag: genotype/variation


title: WT_NK_11

description: Replicate 1


title: Id2KO_NK_12

description: Replicate 1

value: Rag1-/- GzmbCre Id2f/f


title: pancreatic_islets_15w_WT_H3K27ac

value: H3K27ac (Diagenode Cat# C15410196)


title: pancreatic_islets_15w_WT_H3K27me2

value: H3K27me2 (Diagenode Cat# C15410046)


title: pancreatic_islets_14w_EedKO_Input

value: 14 weeks

value: Eed -/-


title: pancreatic_islets_14w_EedKO_H3K27ac


title: pancreatic_islets_WT_Input_rep3

value: 8-16 weeks


title: Id2KO_NK_16

description: Replicate 3


title: pancreatic_islets_WT_H3K36me3_rep3

value: H3K36me3 (Diagenode)


title: pancreatic_islets_WT_H3K27ac_rep3


title: pancreatic_islets_WT_H3K9me3

value: 8-10 weeks

value: H3K9me3 (Diagenode Cat# C15410193)


title: RE_25wks_KO_02

extract_protocol:
Illumina TruSeq RNA Sample Prevp v2
Primary islets were obtained by collagenase digestion with reference to (Li et al., 2009). In brief, adult pancreata were perfused through the common bile duct using a 27/30-gauge needle with Collegenase IV (Sigma) solution. Perfused pancreata were digested and purified by centrifugation in Histopaque gradient (Sigma). Isolated islets were hand picked and cultured in complete media (RMPI-1640 containing 11mM glucose, 10% FBS, 0.1% Penincillin/Streptomycin) and maintained at 37°C in 5% CO2 environment.

value: 25 weeks


title: RE_25wks_KO_03


title: pancreatic_islets_WT_H2AK119Ub

value: H2AK119ub (Cell Signaling Cat# 8240)


title: pancreatic_islets_WT_H3K27me3

value: H3K27me3 (Diagenode Cat# C15410195)


title: RE_25wks_WT_03

value: wild type


title: pancreatic_islets_WT_H3K27ac


title: RE_25wks_WT_04


title: RE_25wks_WT_02


title: pancreatic_islets_WT_H3K27me1_rep3

value: H3K27me1 (Diagenode Cat# C15410045)


title: RE_8wks_WT_03

value: 8 weeks


title: RE_25wks_HET_02

value: heterzygous


title: RE_8wks_KO_01


title: RE_8wks_KO_05


title: RE_8wks_KO_04


title: RE_8wks_WT_01


title: Id2KO_NK_13

description: Replicate 2

value: Natural killer (NK)


title: RNA-seq NOTCH2NL KO rep 3

description:
H9_KO_E5del42_03
processed data file: Human_WT_KO_rawcounts.txt
processed data file: Human_WT_KO_DESeq2.txt

source_name: Week 4 cortical organoids

value: H9 (WiCell WA09) embryonic stem cells

value: KO NOTCH2NL

value: Week 4

value: Cortical organoids


title: RNA-seq NOTCH2NL WT rep 3

description:
H9_WT_E2del19_03
processed data file: Human_WT_KO_rawcounts.txt
processed data file: Human_WT_KO_DESeq2.txt

value: WT


title: RNA-seq NOTCH2NL KO rep 1

description:
H9_KO_E5del42_01
processed data file: Human_WT_KO_rawcounts.txt
processed data file: Human_WT_KO_DESeq2.txt


title: RNA-seq NOTCH2NL KO rep 2

description:
H9_KO_E5del42_02
processed data file: Human_WT_KO_rawcounts.txt
processed data file: Human_WT_KO_DESeq2.txt


title: pancreatic_islets_WT_Input


title: RE_8wks_HET_02


title: RNA-seq NOTCH2NL WT rep 1

description:
H9_WT_E2del19_01
processed data file: Human_WT_KO_rawcounts.txt
processed data file: Human_WT_KO_DESeq2.txt


title: Biotin_UDPGlcNAz_wtOGT_rep6_StainActivityMedianNorm

type: other

first: Suzanne

last: Walker

address: 4 Blackfan Circle

department: Microbiology and Immunobiology

description:
raw data file: Biotin_wt6.gpr
Array barcode 74583, batch HA20358
Biotin_wt6_MedNorm

hyb_protocol: Antibody detection: After enzyme incubation, the arrays were washed four times with TBST (5 mL × 5 min/wash) plus a middle wash with 0.5 % SDS in TBS. Microarrays were incubated with primary antibody (anti-O-GlcNAc, CTD110.6; 1:250 dilution in TBST) overnight in a moistened ziplock bag at 4 °C. To label modified proteins, an anti-mouse Alexa Fluor 647 conjugated secondary antibody (1:250 dilution in TBST) was incubated for 1 hour at room temperature. The arrays were washed again as above and dipped in water three times, spin-dried (200 ×g, 5 min), and scanned. Chemoenzymatic biotin tagging: the arrays were washed four times with TBST (5 mL × 5 min/wash) and incubated with 200 μL 270 µM iodoacetoamide and 1 µM 2,9-dimethyl-5,6,11,12-tetrahydro-dibenzocyclooctene in PBS buffer under a coverslip for 30 min. After the incubation, the arrays were washed again and incubated with 200 μL 1 µM ADIBO-biotin in PBS buffer under a coverslip for 30 min. The arrays were washed with TBS containing 0.5% SDS three times (5 mL × 5 min/wash) and twice with TBST (5 mL × 5 min/wash). The arrays were incubated with 200 μL 0.5 µg/mL streptavidin-Alexa Fluor 647 for 30 min at 4 °C. Finally, the arrays were washed again as above and dipped in water three times, spin-dried (200 ×g, 5 min), and scanned.

scan_protocol: Arrays were scanned with an axon GenePix 4000B using GenePix 5.0

data_processing:
Unormalized data was read into R using limma with normal-exponential background correction. For the unnormalized data set, the mean value of each control protein on each array was calculated and this data is reported. For staining and activity normalized data, a robust linear fit was obtained of the control series of V5-biotin control proteins on each block of each array was obtained, and the fluorescent values of all protein spots on each block was divided by the slope of the linear fit on the corresponding control block. The OGT-treated arrays (both wild-type and 5N5A) were then normalized for activity measurement by comparing the median staining-normalized signal for the control Estrogen Receptor alpha spots on every block. All proteins that showed evidence of OGT activity on blocks were scaled based upon the difference in staining-normalized Estrogen Receptor alpha between a given array block and the median of control arrays. Detailed methods are available in the supplemental information of the associated publication. The mean for each protein from each array was calculated for the resulting staining-and-activity normalized data and reported as the "ActivityNorm" samples, with the control samples being only normalized for staining. For comparisons between control arrays and OGT-treated arrays directly, we further median-normalized the staining and activity normalized groups of OGT-treated arrays (wild-type treated or 5N5A treated), so that each group of arrays had the same log2-transformed median. Values reported in the MedNorm samples are these protein-level, median-normalized data, and are compared to the control ActivtyNorm arrays in the reported median normalized dataset.
Three types of data are provided in the supplemental files: unnormalized data reports the per protein mean signal as described above for one pair of antibody stained arrays and one pair of chemoenzymatically biotinylated arrays; ActivityNormalized data reports per protein mean signal of all the chemoenzymatically biotin-tagged arrays that has been normalized for staining and activity; and MedNorm data reports staining normalized control array data with OGT arrays that have been staining, activity, and median normalized relative to the control. Note that NA in the data table means the data point was not analyzed, either due to the protein not being shared between arrays, the accession code not corresponding to a protein, or the individual data point failed the normalization protocol due to being an outlier and was thus excluded.

label: Alex Fluor 647 conjugated streptavidin

molecule: other

source_name: OGT enzymatic reaction

label_protocol: Human ProtoArray microarrays were warmed from -20 °C to 4 °C for 20 min and washed twice (5 mL × 5 min/wash) with TBS containing 0.04% Tween 20 (TBST) in a four-well array incubation plate on a circular shaker at 50 rpm. Microarrays were then blocked for 1.5 hours at 4 °C with Microarray Blocking buffer (ArrayIt) and washed again with TBST buffer (5 mL × 5 min/wash) three time. UDP-GlcNAc sugar donor: Microarrays were then incubated with 200 μL 3 µM OGT and 40 µM UDP-GlcNAc in PBS buffer under a coverslip for 2 hours at room temperature. OGT was omitted in the control arrays in the incubation step. UDP-GlcNAz sugar donor: The microarrays were then incubated with 200 μL 3 µM OGT and 290 µM UDP-GlcNAz in PBS buffer under a coverslip for 2 hours at room temperature. Control arrays lacked OGT, while 5N5A arrays had the mutant enzyme at 3 µM instead of wild-type OGT.

growth_protocol: OGT was produced recombinantly from E. coli as described in the associated publication and purified by metal affinity and size exclusion chromatography. UDP-GlcNAc was purchased from Sigma Aldrich, and UDP-GlcNAz was synthesized as described by Vocadlo et al. Proc. Natl. Acad. Sci. USA 2003, 100, 9116–21.

extract_protocol: Not applicable- arrays were treated enzymatically with recombinant protein. "Label protocol" describes treatment of array with sugar donor. "hyb protocol" describes washing, which differs between CTD110.6 antibody detection and Chemoenzymatic Biotin Tagging.

tag: sugar donor

value: UDP-GlcNAz

tag: ogt variant

value: wild-type

tag: detection method

value: Chemoenzymatic Biotin Tagging

tag: normalization

value: Staining, Activity, and Median Normalized


title: Biotin_UDPGlcNAz_5N5AOGT_rep3_StainActivityMedianNorm

description:
raw data file: Biotin_5N5A3.gpr
Array barcode 91454, batch HA20358
Biotin_5N5A3_MedNorm

value: 5N5A mutant


title: Biotin_UDPGlcNAz_5N5AOGT_rep1_StainActivityMedianNorm

description:
raw data file: Biotin_5N5A1.gpr
Array barcode 74600, batch HA20358
Biotin_5N5A1_MedNorm


title: Biotin_UDPGlcNAz_5N5AOGT_rep2_StainActivityMedianNorm

description:
raw data file: Biotin_5N5A2.gpr
Array barcode 91384, batch HA20446
Biotin_5N5A2_MedNorm


title: Biotin_UDPGlcNAz_wtOGT_rep5_StainActivityMedianNorm

description:
raw data file: Biotin_wt5.gpr
Array barcode 74619, batch HA20358
Biotin_wt5_MedNorm


title: Biotin_UDPGlcNAz_wtOGT_rep8_StainActivityMedianNorm

description:
raw data file: Biotin_wt8.gpr
Array barcode 74578, batch HA20358
Biotin_wt8_MedNorm


title: Biotin_UDPGlcNAz_wtOGT_rep7_StainActivityMedianNorm

description:
raw data file: Biotin_wt7.gpr
Array barcode 74579, batch HA20358
Biotin_wt7_MedNorm


title: RE_25wks_HET_01

value: 25 weeks


title: RE_8wks_HET_03


title: Biotin_UDPGlcNAz_wtOGT_rep3_StainActivityMedianNorm

description:
raw data file: Biotin_wt3.gpr
Array barcode 74586, batch HA20358
Biotin_wt3_MedNorm


title: Biotin_UDPGlcNAz_wtOGT_rep4_StainActivityMedianNorm

description:
raw data file: Biotin_wt4.gpr
Array barcode 74617, batch HA20358
Biotin_wt4_MedNorm


title: Biotin_UDPGlcNAz_5N5AOGT_rep3_StainActivityNorm

description:
raw data file: Biotin_5N5A3.gpr
Array barcode 91454, batch HA20358
Biotin_5N5A3_ActivityNorm

value: Staining and Activity Normalized


title: Biotin_UDPGlcNAz_wtOGT_rep2_StainActivityMedianNorm

description:
raw data file: Biotin_wt2.gpr
Array barcode 74585, batch HA20358
Biotin_wt2_MedNorm


title: RNA-seq NOTCH2NL WT rep 2

description:
H9_WT_E2del19_02
processed data file: Human_WT_KO_rawcounts.txt
processed data file: Human_WT_KO_DESeq2.txt


title: RE_8wks_WT_04

value: wild type


title: Untreated, biological replicate 1 (SM)

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

description:
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0
Total RNA from wild-type cells biological replicate 1

data_processing:
Sequencing reads were align to the yeast genome (sacCer3) using TopHat2, using the default parameters.
Reads aligned to the forward and reverse strands were separated using samtools.
IGV tracks (tdf.files) were generated using R and igvtools.
Genome_build: sacCer3
Supplementary_files_format_and_content: tdf files containing the normalized occupancy profiles, for the IGV browser

organism: Saccharomyces cerevisiae

source_name: Untreated

growth_protocol: YDC111 was grown to log-phase (A600 ~0.70) at 30 °C in synthetic complete medium without histidine and 3-aminotriazole (3-AT) was added to 10 mM. Aliquots (6 ml) of cells were removed after 0, 1, 5, 20 or 40 min at 30 °C and rapidly cooled by immediate transfer to tubes containing ice. Cells were collected by centrifugation at 4 °C and stored at -80 °C. BY4741 strains was grown to mid-log phase (OD600 about 0.5 to 0.6) at 30 degC in synthetic complete medium lacking isoleucine and valine (SC-Ilv), sulfometuron (SM) was added at 1µg/ml for 25 min to induce Gcn4, or without adding SM (no SM).

extract_protocol:
RNA was extracted, using the YeaStart RNA kit (Zymo Research R1002) for Experiment 1, and the RNeasy Mini kit (Qiagen 74104) for Experiment 2.
Libraries were prepared and sequenced using an Illumina NextSeq 500 machine by ACGT Inc.

treatment_protocol: Cells were treated with 3-AT or SM as described in growth protocol

value: MATa his3delta1 leu2delta0 met15delta0 ura3delta0


title: Untreated, biological replicate 2 (SM)

description:
MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0
Total RNA from wild-type cells biological replicate 2


title: Biotin_UDPGlcNAz_wtOGT_rep1_StainActivityMedianNorm

description:
raw data file: Biotin_wt1.gpr
Array barcode 74576, batch HA20358
Biotin_wt1_MedNorm


title: SM-treated for 25 min, biological replicate 1

source_name: SM-treated for 25 min


title: RE_8wks_HET_01

value: 8 weeks


title: Biotin_UDPGlcNAz_noEnzyme_rep7_StainActivityNorm

description:
Array barcode 74582, batch HA20358
Biotin_cont7_ActivityNorm

source_name: No enzymatic reaction


title: 3AT-treated for 40 min, biological replicate 2

description:
MATa ade2–1 can1-100 leu2-3,112 trp1-1 ura3-1
Total RNA from wild-type cells biological replicate 2

source_name: 3AT-treated for 40 min


title: Biotin_UDPGlcNAz_5N5AOGT_rep1_StainActivityNorm

description:
raw data file: Biotin_5N5A1.gpr
Array barcode 74600, batch HA20358
Biotin_5N5A1_ActivityNorm


title: Biotin_UDPGlcNAz_noEnzyme_rep5_StainActivityNorm

description:
Array barcode 74616, batch HA20358
Biotin_cont5_ActivityNorm


title: SM-treated for 25 min, biological replicate 2


title: Biotin_UDPGlcNAz_noEnzyme_rep4_StainActivityNorm

description:
Array barcode 74618, batch HA20358
Biotin_cont4_ActivityNorm


title: 3AT-treated for 10 min, biological replicate 1

description:
MATa ade2–1 can1-100 leu2-3,112 trp1-1 ura3-1
Total RNA from wild-type cells biological replicate 1

source_name: 3AT-treated for 10 min


title: Biotin_UDPGlcNAz_5N5AOGT_rep2_StainActivityNorm

description:
raw data file: Biotin_5N5A2.gpr
Array barcode 91384, batch HA20446
Biotin_5N5A2_ActivityNorm


title: 3AT-treated for 1 min, biological replicate 1

source_name: 3AT-treated for 1 min


title: 3AT-treated for 40 min, biological replicate 1


title: Untreated, biological replicate 1 (3AT)


title: Untreated, biological replicate 2 (3AT)


title: 3AT-treated for 5 min, biological replicate 1

source_name: 3AT-treated for 5 min


title: Biotin_UDPGlcNAz_noEnzyme_rep3_StainActivityNorm

description:
Array barcode 91412, batch HA20446
Biotin_cont3_ActivityNorm


title: Biotin_UDPGlcNAz_noEnzyme_rep2_StainActivityNorm

description:
Array barcode 74584, batch HA20358
Biotin_cont2_ActivityNorm


title: Biotin_UDPGlcNAz_noEnzyme_rep1_StainActivityNorm

description:
Array barcode 74577, batch HA20358
Biotin_cont1_ActivityNorm


title: Biotin_UDPGlcNAz_wtOGT_rep5_StainActivityNorm

description:
raw data file: Biotin_wt5.gpr
Array barcode 74619, batch HA20358
Biotin_wt5_ActivityNorm


title: 3AT-treated for 20 min, biological replicate 1

source_name: 3AT-treated for 20 min


title: Biotin_UDPGlcNAz_wtOGT_rep8_StainActivityNorm

description:
raw data file: Biotin_wt8.gpr
Array barcode 74578, batch HA20358
Biotin_wt8_ActivityNorm


title: Biotin_UDPGlcNAz_wtOGT_rep7_StainActivityNorm

description:
raw data file: Biotin_wt7.gpr
Array barcode 74579, batch HA20358
Biotin_wt7_ActivityNorm


title: 24hr Control 3

city: Winston-Salem

first: Jeff

last: Chou

state: NC

address: Medical Center Blvd

institute: Atrium Health Wake Forest Baptist

hyb_protocol: 10 ug biotinylated cRNA was hybridized to the Affymetrix Gene Atlas U219 Human Genome array strips according to current Affymetrix protocols.

scan_protocol: The arrays were washed and scanned according to standard Affymetrix GeneAtlas instructions using the GeneAtlas scanner and software control(GeneAtlas Instrument Control (GAIC) v. 1.0.6.).

data_processing: Raw data (CEL files) were generated using Affymetrix AGCC software and quantile normalized by the RMA method. Log intensity distributions, pair-wise correlations and internal Affymetrix controls were examined to evaluate hybridization quality using Partek Genomics Suite software (Partek Inc.).

source_name: SOX7-No induction for 24 h repeat 3

label_protocol: 250 ng total RNA was amplified and labeled according to the Affymetrix 3’-IVT labeling protocol.

extract_protocol: Total RNA was isolated from peripheral blood mononuclear cells using the RiboPure-Blood Kit (Life Technologies (AM1928)).

value: Triple negative breast cancer cells

tag: gender

value: F


title: Biotin_UDPGlcNAz_wtOGT_rep4_StainActivityNorm

description:
raw data file: Biotin_wt4.gpr
Array barcode 74617, batch HA20358
Biotin_wt4_ActivityNorm


title: Biotin_UDPGlcNAz_wtOGT_rep3_StainActivityNorm

description:
raw data file: Biotin_wt3.gpr
Array barcode 74586, batch HA20358
Biotin_wt3_ActivityNorm


title: 24hr+Dox 3

source_name: SOX7-induction for 24 h repeat 3


title: Biotin_UDPGlcNAz_wtOGT_rep6_StainActivityNorm

description:
raw data file: Biotin_wt6.gpr
Array barcode 74583, batch HA20358
Biotin_wt6_ActivityNorm


title: Biotin_UDPGlcNAz_noEnzyme_rep6_StainActivityNorm

description:
Array barcode 74581, batch HA20358
Biotin_cont6_ActivityNorm


title: 24hr Control 2

source_name: SOX7-No induction for 24 h repeat 2


title: 24hr Control 1

source_name: SOX7-No induction for 24 h repeat 1


title: 12hr+Dox 3

source_name: SOX7-induction for 12 h repeat 3


title: 24hr+Dox 1

source_name: SOX7-induction for 24 h repeat 1


title: CTD_UDPGlcNAc_NoEnzyme

description:
Array barcode 52641, batch HA20301
CTDcont1

label: Alexa Fluor 647 conjugated anti-mouse secondary antibody

value: UDP-GlcNAc

value: CTD110.6 antibody

value: None (pre-ratio)


title: 12hr+Dox 2

source_name: SOX7-induction for 12 h repeat 2


title: Biotin_UDPGlcNAz_wtOGT_rep2_StainActivityNorm

description:
raw data file: Biotin_wt2.gpr
Array barcode 74585, batch HA20358
Biotin_wt2_ActivityNorm


title: Biotin_UDPGlcNAz_noEnzyme_rep1_UnNorm

description:
raw data file: Biotin_cont1.gpr
Array barcode 74577, batch HA20358
Biotin_cont1_unNorm


title: Biotin_UDPGlcNAz_wtOGT_rep1_StainActivityNorm

description:
raw data file: Biotin_wt1.gpr
Array barcode 74576, batch HA20358
Biotin_wt1_ActivityNorm


title: 24hr+Dox 2

source_name: SOX7-induction for 24 h repeat 2


title: 6hr+Dox 3

source_name: SOX7-induction for 6 h repeat 3


title: 6hr+Dox 2

source_name: SOX7-induction for 6 h repeat 2


title: 12hr+Dox 1

source_name: SOX7-induction for 12 h repeat 1


title: CTD_UDPGlcNAc_wtOGT

description:
Array barcode 52630, batch HA20301
CTDwt1

source_name: OGT enzymatic reaction


title: Biotin_UDPGlcNAz_wtOGT_rep1_UnNorm

description:
raw data file: Biotin_wt1.gpr
Array barcode 74576, batch HA20358
Biotin_wt1_unNorm


title: 6hr+Dox 1

source_name: SOX7-induction for 6 h repeat 1


title: HUVEC_HbLPHp22_10hrs_k

status: Public on Feb 25 2018

city: Zurich

first: Christian

middle: Andreas

last: Schaer

address: Raemistrasse 100

country: Switzerland

institute: University Hospital Zurich

description: Human umbilical vein endothelial cells (HUVEC), incubated with oxyhemoglobin, reconstituted lipoprotein (composed of apoA-I lipoprotein) and haptoglobin.

hyb_protocol: After purification of amplified cRNA according to the QIAgen RNeasy purification protocol (QIAGEN), 825 ng of Cy3- and Cy5-labeled cRNA were competitively hybridized to Agilent-026652 Whole Human Genome Microarrays for 17 hours at 65° C in a hybridization oven (Agilent G2545A) set to 10 rpm in GEx Hybridization buffer HI-RPM according to the manufacturer's protocol (Agilent’s Two-Color Microarray-Based Gene Expression Analysis). Washing was performed according to the recommended protocol including the Stabilization and Drying Solution step.

scan_protocol: Array slides were XDR scanned at 5 mcm resolution on an Agilent Microarray High-Resolution C Scanner (G2505C) with 100% PMT and 10% for lower intensity.

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software Version 10.5.1.1. Spot values were normalized using the default linear-lowess normalization. To identify differentially expressed features, calculated log10 ratio values (Cy5/Cy3) were imported into JMP Genomics 5.1 without further normalization and the built-in Basic Expression Workflow (ANOVA, LSMeans Differences) was performed.

source_name: HUVEC, no treatment, 0h

label_protocol: Fluorescently labeled cRNA was generated from 500 ng total RNA with the Quick Amp Labeling Kit (Agilent) according to Agilent’s Two-Color Microarray-Based Gene Expression Analysis Protocol Version 5.7, March 2008 (Agilent publication number G4140-90050). In short, total RNA was reverse transcripted to cDNA using T7 Promotor Primer and MMLV-RT. Then cDNA was converted to cRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP.

extract_protocol: After washing and lysing the cells with Buffer RLT, total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Basel, Switzerland) according to the manufacturer’s instructions, including an on-column DNA digestion step (RNase-Free DNase Set; QIAGEN). To ensure that only high quality RNA (RIN >7.0) was used for gene expression analysis, each RNA sample was checked on a RNA Nanochip with a Bioanalyzer 2100 (Agilent Technologies, Basel, Switzerland). RNA was quantified spectrophotometrically with a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: HUVECs were untreated, or incubated with LP 0.5g/L, oxyHb 10mcM, oxyHb 10mcM + LP 0.5g/L, oxyHb 10mcM + LP 0.5g/L + Hp00 15mcM, oxyHb 10mcM + LP 0.5g/L + Hp11 15mcM, oxyHb 10mcM + LP 0.5g/L + Hp22 15mcM, or oxyHb 10mcM + LP 0.5g/L + Hpx 15mcM for 10h.

value: HUVEC

value: human umbilical vein endothelial cell line

tag: treatment

tag: incubation time

source_name: HUVEC, oxyHb  + LP + Hp22, 10h

value: oxyHb 10mcM + LP 0.5g/L + Hp22 15mcM


title: HUVEC_HbLPHp22_10hrs_l


title: HUVEC_HbLPHpx_10hrs_b

description: Human umbilical vein endothelial cells (HUVEC), incubated with oxyhemoglobin, reconstituted lipoprotein (composed of apoA-I lipoprotein) and hemopexin.

source_name: HUVEC, oxyHb  + LP + Hpx, 10h

value: oxyHb 10mcM + LP 0.5g/L + Hpx 15mcM


title: HUVEC_HbLPHp22_10hrs_h


title: HUVEC_HbLPHp11_10hrs_g

source_name: HUVEC, oxyHb  + LP + Hp11, 10h

value: oxyHb 10mcM + LP 0.5g/L + Hp11 15mcM


title: HUVEC_HbLPHpx_10hrs_c


title: HUVEC_HbLPHpx_10hrs_d


title: HUVEC_HbLPHp11_10hrs_e


title: HUVEC_HbLPHp11_10hrs_d


title: HUVEC_HbLPHpx_10hrs_a


title: HUVEC_HbLPHp11_10hrs_c


title: HUVEC_HbLPHp11_10hrs_f


title: HUVEC_HbLPHp22_10hrs_m


title: HUVEC_HbLPHp22_10hrs_i


title: HUVEC_HbLP_10hrs_h

description: Human umbilical vein endothelial cells (HUVEC), incubated with oxyhemoglobin and reconstituted lipoprotein (composed of apoA-I lipoprotein).

source_name: HUVEC, oxyHb  + LP, 10h

value: oxyHb 10mcM + LP 0.5g/L


title: HUVEC_HbLP_10hrs_c


title: HUVEC_HbLPHp00_10hrs_b

source_name: HUVEC, oxyHb  + LP + Hp00, 10h

value: oxyHb 10mcM + LP 0.5g/L + Hp00 15mcM


title: HUVEC_HbLP_10hrs_f


title: HUVEC_HbLP_10hrs_d


title: HUVEC_HbLP_10hrs_e


title: HUVEC_HbLP_10hrs_b


title: HUVEC_Hb_10hrs_h

description: Human umbilical vein endothelial cells (HUVEC), incubated with oxyhemoglobin.

source_name: HUVEC, oxyHb, 10h

value: oxyHb 10mcM


title: HUVEC_HbLPHp00_10hrs_a


title: HUVEC_Hb_10hrs_a


title: HUVEC_Hb_10hrs_c


title: HUVEC_HbLP_10hrs_g


title: HUVEC_Hb_10hrs_g


title: HUVEC_Hb_10hrs_e


title: HUVEC_HbLP_10hrs_a


title: HUVEC_Hb_10hrs_f


title: HUVEC_Hb_10hrs_d


title: HUVEC_LP_10hrs_a

description: Human umbilical vein endothelial cells (HUVEC), incubated with reconstituted lipoprotein (composed of apoA-I lipoprotein).

source_name: HUVEC, LP, 10h

value: LP 0.5g/L


title: HUVEC_LP_10hrs_b


title: HUVEC_LP_10hrs_d


title: HUVEC_LP_10hrs_c


title: CF966 IgG

city: Baltimore

first: Peter

middle: M

last: Abadir

address: 5501 Hopkins Bayview Circle. Rm 1a62

department: Geriatrics

institute: Johns Hopkins University

description: Test

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control ratios.

label: SYBR Green

source_name: Peripheral blood mononuclear cells

label_protocol: PCR assays were performed using the Dendritic Cell - Antigen Presenting Cell and the Toll-like Receptor Pathway PCR assay panel (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from 500 ng total RNA using the RT2 First Strand Kit (SA Biosciences). Quantitative real-time PCR were performed (Light Cycler 480, Roche) with 45 cycles at 94 oC for 15 seconds and 60 oC for 60 seconds.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

value: Peripheral blood mononuclear cells

tag: activation agent

tag: time


title: CF966 Control

description: Control

value: control


title: CF970 Control

description: Control


title: CF972 IgG

description: Test


title: CF968 Control

description: Control


title: HUVEC_Hb_10hrs_b

tag: cell line


title: CF972 Control

description: Control


title: CF968 IgG

description: Test


title: CF974 IgG

description: Test


title: CF974 Control

description: Control


title: CF949 IgG

description: Test


title: HUVEC_LP_10hrs_e


title: CF970 Control

description: Control

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control  ratios.


title: CF968 IgG

description: Test


title: CF970 IgG

description: Test


title: CF966 Control

description: Control


title: CF972 IgG

description: Test


title: CF974 IgG

description: Test


title: CF598B IgG

description: Test


title: CF972 Control

description: Control


title: iKO1

city: Hong Kong

first: Han

last: ZHU

address: Room 6312, Academic Building, HKUST

department: Department of Life Science

institute: HKUST

data_processing:
Illumina Casava1.8 software used for basecalling
Low quality reads and adaptor sequences were trimmed from the raw reads file using Trim Galore
Trimmed sequencing reads were mapped to the mouse mm10 genome assembly using the STAR RNA-seq aligner with the --twopassMode.
Annotated and novel transcripts were assembled with Cufflinks software
Differential expression analysis was done by Cuffdiff
Genome_build: mm10 (mus musculus)
Supplementary_files_format_and_content: gene_exp.diff file was provided as an output of cuffdiff. In this file, offical gene symbols were used as identifier, gene loci, averaged FPKM value, log2 of FPKM value and test statistics were listed

extract_protocol:
RNA was extracted from each sample with NucleoSpin® RNA XS kit from Macherey-Nagel
For each sample, cDNA reverse transcripition was performed with the SMART-Seq™ Ultra™ Low Input RNA Kit for Sequencing form Clontech, followed by sonicaiton based cDNA fragmentation. The NuGEN ovation ultral low system was used for adaptor ligation and amplification of sequencing library.
Whole transcriptome shotgun sequencing (Illumina HiSeq2500, high output, PE125)

treatment_protocol: Muscle stem cells were harvested from adult mouse with a fluorescent activated cell sorting protocol described previously

value: MuSC-specific p110alpha-null (iKO, p110alpha-f/f:R26-YFP/YFP:Pax7-CreER/CreER)

tag: age

value: 2 month-old

value: Adult muscle stem cells (MuSC)


title: CF974 Control

description: Control


title: iKO3


title: iKO2


title: Ctrl4


title: Ctrl3


title: CF949 Control

description: Control


title: CF968 Control

description: Control


title: CF949 Control

description: Control


title: Ctrl1


title: Ctrl2


title: CF970 IgG

description: Test


title: CF949 IgG

description: Test


title: iKO4


title: Human 4 - CD4+ T-cells PMA+Ionomycin

city: Ithaca

first: Charles

middle: G

last: Danko

state: NY

address: Hungerford Hill Rd

department: Baker Institute

institute: Cornell University

description:
library strategy: PRO-seq
nascent RNA

data_processing:
We trimmed adapter sequences and mapped PRO-seq data using BWA.
Data was converted into bigWig format and converted to reads per kilobase per million mapped (RPKM).
dREG (v. 1.0) was used to identify TREs using the indicated dataset (*TSS.bw).
Genome_build: hg19
Genome_build: panTro4
Genome_build: rheMac3
Genome_build: mm10
Genome_build: rn6
Supplementary_files_format_and_content: Raw dREG scores, peak calls, and PRO-seq or GRO-seq data are provided in standard bigWig or BED file formats.

source_name: Primary Pan-CD4+ cells isolated by positive selection of the CD4 antigen

growth_protocol: CD4+ T-cells isolated from peripheral blood using positive selection for the CD4 antigen.

extract_protocol:
Nuclei were isolated using the protocol in Danko et. al. (2013) Nature Methods.
We prepared PRO-seq libraries as described in Kwak et. al. (2013) Science.

treatment_protocol: Cells were treated for 30 minutes with ethanol+DMSO or PMA+Ionomycin.

tag: tissue

value: CD4+ T-cells

tag: species

value: Human

tag: individual

value: PMA+Ionomycin


title: Human 4 - CD4+ T-cells Untreated

description:
library strategy: PRO-seq
nascent RNA

value: Untreated


title: 30 umol/kg bw CDDO-Im treated, Nrf2-null mouse liver, biological rep 4

city: Memphis

first: Thomas

middle: R

last: Sutter

state: Tennessee

address: 3700 Walker Avenue Ellington Hall RM 239

department: Biological Sciences

institute: University of Memphis

hyb_protocol: Following fragmentation, aRNA was hybridized for 16 hr at 45C on Mouse Genome 430 2.0 Array. Arrays were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Gene chips were scanned using an Affymetrix GeneChip Scanner 3000 7G

data_processing: The .CEL files from the microarray chips were preprocessed by GCRMA.  The normalized data was filtered using mas5 calls where probe sets that had at least 3 present calls in any treatment group and filtered using a 1.5-fold-change threshold.  Multiple hypothesis testing was corrected for by a false discovery rate of 0.05.  The Kruskal-Wallis nonparametric analysis of variance, permuted one million times to compute exact P-values, was used to identify differentially expressed genes by treatment.

source_name: 30 umol/kg bw treated, Nrf2-null mouse liver

label_protocol: Biotinylating aRNA were prepared according to the standard Affymetrix protocol (Gene Chip 3' IVT Express Kit).

growth_protocol: Provided food and water ad libitum.  Fed AIN-76A purified diet without ethoxyquin.

extract_protocol: Animals were euthanized, liver tissue was extracted and snap frozen in liquid nitrogen.

treatment_protocol: 12 week old male mice were treated by gavage every other day for 5 days, resulting in 3 total treatments.  Treatments included vehicle (10% Cremophor-EL, 10% DMSO, and PBS), 300 umol/kg bw D3T, or 3, 10, 30 umol/kg bw CDDO-Im.  Animals were euthanized 24 hours following the final treatment.

tag: strain

tag: genotype

tag: Sex

value: Male

value: 12 weeks

tag: agent

value: CDDO-Im

tag: dose

value: 30 umol/kg bw

value: Liver

tag: number of treatments

value: treated 3 times


title: 30 umol/kg bw CDDO-Im treated, Nrf2-null mouse liver, biological rep 1


title: 10 umol/kg bw CDDO-Im treated, Nrf2-null mouse liver, biological rep 2

source_name: 10 umol/kg bw treated, Nrf2-null mouse liver

value: 10 umol/kg bw


title: 30 umol/kg bw CDDO-Im treated, Nrf2-null mouse liver, biological rep 2


title: 10 umol/kg bw CDDO-Im treated, Nrf2-null mouse liver, biological rep 3


title: 30 umol/kg bw CDDO-Im treated, Nrf2-null mouse liver, biological rep 3


title: 10 umol/kg bw CDDO-Im treated, Nrf2-null mouse liver, biological rep 4


title: 3 umol/kg bw CDDO-Im treated, Nrf2-null mouse liver, biological rep 3

source_name: 3 umol/kg bw treated, Nrf2-null mouse liver

value: 3 umol/kg bw


title: Agt_blocked

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

data_processing:
the original fastq files were converted to fasta format and reads without Ns were kept for further analysis
the 3' adapter and HD signatures [Sorefan et al 2012] were trimmed and the files were converted from redundant to non-redundant format
the reads were mapped to the reference genome, allowing 0, 1 or 2 mis-matches and 0 gaps using PatMaN [Pruffer et al 2008]
the reads were mapped to mature miRNAs and miRNA hairpins, retrieved from miRbase, release 21
the abundances of the reads were normalized using the RPM method [Mortazavi et al 2008]
the differential expression was called on offset fold change on confidence intervals built on replicates, offset = 20
Genome_build: D. melanogaster v6.11
Supplementary_files_format_and_content: csv files, sRNA expression levels

organism: Drosophila melanogaster

source_name: accessory glands and testes

growth_protocol: Wildtype males (derived from 1970s Dahomey lAgt population) were reared at 25°C, 50% humidity, 12:12 light:dark cycle on sugar, yeast, agar food.

extract_protocol:
RNA enriched for fragments <200nt was extracted from 50 pooled male accessory glands and testes, using the miRvana miRNA kit (Ambion). The RNA sample was split and subjected to two different library construction protocols - one using a blocking oligo complentary to a contaminating 30mer rRNA sequence, and one without the blocking oligo.
HD sRNA-seq libraries, created using HiSeq2500 IL adapter
library sequenced by BaseClear provider

value: male

value: accessory glands and testes

value: wildtype (derived from 1970s Dahomey lAgt population)

tag: library

value: blocked


title: 3 umol/kg bw CDDO-Im treated, Nrf2-null mouse liver, biological rep 4


title: 3 umol/kg bw CDDO-Im treated, Nrf2-null mouse liver, biological rep 2


title: 10 umol/kg bw CDDO-Im treated, Nrf2-null mouse liver, biological rep 1


title: 3 umol/kg bw CDDO-Im treated, Nrf2-null mouse liver, biological rep 1


title: Agt_unblocked

tag: gender

value: not blocked


title: USP2 shRNA LPS_rep2

city: Ebetsu

first: Hiroshi

last: Kitamura

address: 582 Midorimachi, Bunkyodai

department: School of Veterinary Medicine

institute: Rakuno Gakuen University

description: Expression profiles of USP2shRNA expressing HL60 cells (PMA 1day, LPS 4hr)

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneChip Human Genome U133 Plus 2.0 Array as a standard Affymetrix protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000.

data_processing: CHP and CEL files were obtained using an Affymetrix GCOS software packaging.

source_name: Total RNA from HL60-derivatives expressing USP2shRNA (PMA 1day, LPS 4hr)

label_protocol: Biotinylated cRNA were prepared using GeneChip 3'IVT Express kits according to the standard Affymetrix protocol from 100 ng of polyA RNA.

growth_protocol: RPMI1640 supplemented with 10%FCS, 37C, 5%CO2 Passage: three times/week

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

treatment_protocol: HL60 derivatives expressing shRNAs were cultured in the presence of PMA (30nM) for 1 day, and subsequently stimulated with LPS (10ug/mL) for 4 hr.

tag: transduction

value: USP2 shRNA

value: phorbol 12-myristate 13-acetate

value: 1 day

value: LPS


title: Control-shRNA exprssing HL60, LPS, rep3

description: Expression profiles of negative control shRNA expressing HL60 cells (PMA 3days, LPS 4hr)

source_name: Total RNA from HL60-derivatives expressing control shRNA (PMA 3days, LPS 4hr)

label_protocol: Biotinylated cRNA were prepared using GeneChip 3'IVT Express kits according to the standard Affymetrix protocol from 100 ng of total RNA.

treatment_protocol: HL60 derivatives expressing shRNAs were cultured in the presence of PMA (30nM) for 3 days, and subsequently stimulated with LPS (10ug/mL) for 4 hr.

value: control shRNA


title: Negative control shRNA LPS_1

description: Expression profiles of negative control shRNA expressing HL60 cells (PMA 1day, LPS 4hr)

source_name: Total RNA from HL60-derivatives expressing control shRNA (PMA 1day, LPS 4hr)


title: Control-shRNA exprssing HL60, LPS, rep1


title: USP2-shRNA exprssing HL60, LPS, rep3

description: Expression profiles of USP2shRNA expressing HL60 cells (PMA 3days, LPS 4hr)

source_name: Total RNA from HL60-derivatives expressing USP2shRNA (PMA 3days, LPS 4hr)


title: 300 umol/kg bw D3T treated, Nrf2-null mouse liver, biological rep 3

source_name: 300 umol/kg bw treated, Nrf2-null mouse liver

value: Male

value: 12 weeks

value: 300 umol/kg bw


title: Negative control shRNA LPS_3


title: 300 umol/kg bw D3T treated, Nrf2-null mouse liver, biological rep 1

value: Liver


title: USP2 shRNA LPS_rep3


title: Negative control shRNA LPS_2


title: Veh treated, Nrf2-null mouse Liver, biological rep 3

source_name: Veh treated, Nrf2-null mouse Liver

value: vehicle

value: control

value: treated 3 times


title: USP2-shRNA exprssing HL60, LPS, rep1


title: 300 umol/kg bw D3T treated, Nrf2-null mouse liver, biological rep 4


title: 300 umol/kg bw D3T treated, Nrf2-null mouse liver, biological rep 2


title: USP2 shRNA LPS_rep1


title: Control-shRNA exprssing HL60, LPS, rep2


title: USP2-shRNA exprssing HL60, LPS, rep2


title: Veh treated, Nrf2-null mouse Liver, biological rep 4


title: Veh treated, Nrf2-null mouse Liver, biological rep 2


title: 30 umol/kg bw CDDO-Im treated, Wt mouse liver, biological rep 4

source_name: 30 umol/kg bw treated, Wt mouse liver

value: Wild-type

value: CDDO-Im

value: 30 umol/kg bw


title: 10 umol/kg bw CDDO-Im treated, Wt mouse liver, biological rep 4

source_name: 10 umol/kg bw treated, Wt mouse liver

value: 10 umol/kg bw


title: 30 umol/kg bw CDDO-Im treated, Wt mouse liver, biological rep 3


title: Veh treated, Nrf2-null mouse Liver, biological rep 1


title: Rhesus Macaque 4 - CD4+ T-cells PMA+Ionomycin

description:
library strategy: PRO-seq
nascent RNA

organism: Macaca mulatta

value: CD4+ T-cells

value: R. Macaque

tag: treatment

value: PMA+Ionomycin


title: Rhesus Macaque 4 - CD4+ T-cells Untreated

description:
library strategy: PRO-seq
nascent RNA

value: Untreated


title: LPS_PLX_4

status: Public on Feb 24 2018

city: Shanghai

first: Bo

last: Peng

address: 138 Yixueyuan Road

department: Institute for Translational Brain Research

institute: Fudan University

data_processing:
Quality control: 1) remove reads with adaptors; 2)remove reads in which unkown bases are more than 10%; 3)remove low qulity reads(the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more than 5)
Hisat2 was used to align clean reads to the mouse genome
Htseq was used to estimate raw counts for each gene
FPKM was calculated using Stringtie
Edgr was use to detect differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: HT-seq counts and FPKM are provided in Excel files. Column headers are found in the 'description' field.

source_name: brain

extract_protocol:
Total RNA was extracted from brain homogenate using the TriPure Isolation Reagent (Roche) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard BGISEQ-500 protocols. The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification.  We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.

treatment_protocol: Mice were treated by either PLX5622, control diet (CD), PLX5622 + CD (RP = PLX5622 treated for 14 days, followed by CD (control diet) treatment for several days), LPS or vehicle

value: brain

value: adult

value: 4 days


title: 3 umol/kg bw CDDO-Im treated, Wt mouse liver, biological rep 3

source_name: 3 umol/kg bw treated, Wt mouse liver

value: Male

value: 12 weeks

value: 3 umol/kg bw


title: LPS_PLX_3


title: 3 umol/kg bw CDDO-Im treated, Wt mouse liver, biological rep 2

value: Liver


title: 30 umol/kg bw CDDO-Im treated, Wt mouse liver, biological rep 1


title: 30 umol/kg bw CDDO-Im treated, Wt mouse liver, biological rep 2


title: LPS_CD_2


title: LPS_CD_3


title: LPS_PLX_2


title: 10 umol/kg bw CDDO-Im treated, Wt mouse liver, biological rep 3


title: RP2M_2

value: RP

value: 60 days


title: RP2M_3


title: 300 umol/kg bw D3T treated, Wt mouse liver, biological rep 4

source_name: 300 umol/kg bw treated, Wt mouse liver

value: Wild-type

value: 300 umol/kg bw

value: treated 3 times


title: 300 umol/kg bw D3T treated, Wt mouse liver, biological rep 3


title: 3 umol/kg bw CDDO-Im treated, Wt mouse liver, biological rep 4

value: CDDO-Im


title: 3 umol/kg bw CDDO-Im treated, Wt mouse liver, biological rep 1


title: Veh treated, Wt mouse Liver, biological rep 3

source_name: Veh treated, Wt mouse Liver

value: vehicle

value: control


title: Mtb_mBMG290_rep1

city: Saranac Lake

first: Brian

last: Weinrick

address: 154 Algonquin Avenue

institute: Trudeau Institute

description: Biological replicate 1 of 3

hyb_protocol: Slide was hybridized for 16 hours at 42 in water bath with volume of 60 uL in solution of standard gene expression hybridization solution, and blocked in standard prehybridization solution. After hybridization, the slide was washed with standard wash protocol.

scan_protocol: scanned with PMT voltage adjusted for maximum dynamic range on Axon Genepix 4000B scanner

data_processing: Spots were gridded and quantitated in TIGR Spotfinder, data were processed in TIGR MIDAS with lowess normalization, standard deviation regularization, in-slide replicate analysis, one bad channel policy set to generous, all flags on

organism: Mycobacterium tuberculosis

source_name: untreated Mtb

label_protocol: 2 ug total RNA was used as template for reverse transcription with random hexamer primers and aminoallyl-dUTP in a 2:3 ratio to dTTP in the nucleotide mix. After overnight incubation at 42°C, the reaction was stopped, RNA was hydrolyzed, and unincorporated nucleotides and free amines were removed with the Qiagen MinElute kit as per protocol, with amine-free phosphate wash and elution buffers. cDNA concentration and purity were measured by Nanodrop. Cy3 and Cy5 dyes were coupled to the aminoallyl-cDNA, which was then purified using a MinElute kit. Probe concentration, purity, and dye incorporation were measured by Nanodrop.

growth_protocol: Cultures were prepared by diluting an exponentially growing culture of M. tuberculosis H37Rv to an OD600nm of 0.2 in a 10 mL volume of 7H9 OADC 0.2% glycerol 0.05% tyloxapol broth in a 30 mL ink-well bottle which was incubated shaking at 37°C.

extract_protocol: Cultures were harvested by centrifugation then resuspended in 1mL Qiagen RNA protect and stored at 4°C. Cells were later pelleted and resuspended in 1ml Trizol and transferred to a Fast-Prep lysing matrix B tube. Tubes are processed in Fast-Prep apparatus for 45 seconds at 6.5 M per second then cooled on ice for 1 minute before debris is pelleted by centrifugation. RNA is then purified and sample is DNase-treated following Direct-zol kit manufacturer instructions.

treatment_protocol: Cultures were treated with 4μM mBMG290 for 4 hours.

tag: treated with

value: none (untreated control)

source_name: mBMG290-treated Mtb

value: 4μM mBMG290 for 4 hrs


title: LPS_PLX_1

value: brain

tag: time


title: Mtb_mBMG290_rep3

description: Biological replicate 3 of 3


title: Mtb_mBMG290_rep2

description: Biological replicate 2 of 3


title: 300 umol/kg bw D3T treated, Wt mouse liver, biological rep 2


title: 10 umol/kg bw CDDO-Im treated, Wt mouse liver, biological rep 1

value: 10 umol/kg bw


title: LPS_CD_1

value: adult

value: 4 days


title: RP2M_4


title: Veh treated, Wt mouse Liver, biological rep 1

value: Male

value: 12 weeks


title: Veh treated, Wt mouse Liver, biological rep 2

value: Liver


title: RP21_2

value: RP

value: 21 days


title: Veh treated, Wt mouse Liver, biological rep 4

value: Wild-type


title: 300 umol/kg bw D3T treated, Wt mouse liver, biological rep 1

value: 300 umol/kg bw


title: RP10_4

value: 10 days


title: RP14_3

value: 14 days


title: RP21_4


title: RP14_4


title: RP21_3


title: RP2M_1

value: 60 days


title: RP21_1


title: RP14_1


title: RP10_2


title: RP14_2


title: RP10_1


title: RP7_3

value: 7 days


title: RP7_5


title: RP10_3


title: RP5_1

value: 5 days


title: 10 umol/kg bw CDDO-Im treated, Wt mouse liver, biological rep 2

value: CDDO-Im

value: treated 3 times


title: RP3_3

value: brain

value: 3 days


title: RP3_1

value: adult


title: RP7_4


title: PLX21_1


title: PLX21_2


title: RP5_3


title: RP7_2


title: RP5_4


title: RP5_2


title: PLX14_4


title: RP3_4


title: RP3_2


title: PLX21_4


title: PLX21_3


title: PLX14_3


title: PLX14_2


title: PLX7_3


title: PLX7_2


title: PLX7_1


title: PLX7_4


title: PLX10_4


title: PLX14_1


title: PLX5_3


title: PLX2_4

value: 2 days


title: PLX2_3


title: PLX2_2


title: Patient 4

city: Hiroshima

first: Tetsumi

last: Yoshida

address: Kasumi 1-2-3 Minami-ku

institute: Hiroshima University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 039494_D_F_20120628) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Lymph node, exercised, frozen, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent 5190-2305) 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-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations. The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion. Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: male

tag: serum lactate dehydrogenase levels (unv - upper normal value)

value: >=UNV

tag: serum soluble interleukin-2 receptor levels

tag: international prognostic index

tag: clinical stage based on cotswold staging classification

value: >=III

tag: the eastern cooperative oncology group performance status

tag: number of extranodal sites

tag: gcb/ non-gcb

value: non-GCB

tag: igh-r(+) in all fr1-3/ igh(-) in entire dh1-7

value: Yes


title: Patient 11

value: female

tag: age

value: <UNV

value: <III

value: No


title: Patient 12

value: GCB


title: Patient 10


title: Patient 2


title: PLX10_2

tag: strain

tag: tissue

value: 10 days


title: PLX10_3


title: CD_2

value: CD


title: RP7_1

value: RP

value: 7 days


title: PLX10_1

value: brain


title: PLX5_2

value: adult

value: 5 days


title: PLX5_4


title: PLX5_1


title: Patient 1

value: male


title: Nrd1-AA dSet2 BrdU-seq +Rap rep2

city: Geneva

first: Julien

last: Soudet

address: 30 quai Ansermet

department: BICEL

institute: Université de Genève

description: BrdUseq_Nrd1dSet2_PlusRap_merged_final.bigWig

data_processing:
Library strategy: BrdU-Seq
fastq files were processed through the mapping function of HTS EPFL station.PCR duplicates were discarded from the analysis.
bigwig were generated using HTS EPFL station. Strands were merged by 125bp for BrdU-seq.
Genome_build: saccer3
Supplementary_files_format_and_content: bigwig

source_name: Nrd1-AA dSet2 BrdU-seq +Rap

growth_protocol: Cells grown at 30°C to an OD600= 0.4 were synchronized in G1-phase with α-factor (20 ng/ml, Sigma) for 3h in total. After two washes with distilled water, cells were released into S-phase at 18°C. Depending on the experiment, cells were released or not in YEPD medium containing BrdU (100 μg/ml, Sigma) and treated or not with rapamycin. Cells were then collected at t=70min 18°C after G1-release and treated with 0.1% Sodium Azide (Sigma).

extract_protocol:
BrdU immunoprecipitation was mainly performed as described in (Soudet et al., 2014) with the following modifications. Genomic DNA was sonicated into 300-400 bp fragments and denatured. 5 μg  BrdU antibody (BD PharMingen, 555627) coupled to 75μl of Dynabeads Protein G (Invitrogen) were added to 5μg of denatured BrdU-containing genomic DNA in BrdU IP buffer (PBS + 0.0625% Triton X-100). After 1 hour incubation at room temperature on a wheel, beads were washed twice with BrdU IP buffer and eluted in Tris-HCl 10mM (pH 8.0), EDTA 1mM, 1% SDS. Eluates were cleared of SDS using the NucleoSpin Gel and PCR Clean-up (Macherey-Nagel).
iDeal library preparation kit was used for library construction.

value: Nrd1-AA dSet2

value: +Rap

tag: chip antibody

value: BrdU antibody (BD PharMingen, 555627)


title: PLX2_1

value: 2 days


title: Repop D5

description: SRA accessions include 3 reads per sample: barcode, Forward and Reverse.

data_processing:
Fastq files were generated using CellRanger v2.1.0 using the Illumina BCL files as input
Read alignment and count summarization were performed using CellRanger v2.1.0  CellRanger count
Counts from different samples were aggregated using CellRanger aggr in CellRanger software
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx files contain genewise read counts for all cells in a space-efficient matrix market format; genes.tsv files contain Ensembl IDs and gene symbols as tab-delimited text; barcode.tsv files contain the 10X barcodes used to identify cells. Aggregated processed data files are available on the series record.

source_name: brain microglia

extract_protocol: C57BL/6J mouse was perfused by 20 mL L15 culture medium. Brain was quickly minced on ice. Then the tissue was dissociated with papain (Sigma) for 20 min at 37℃, followed by the termination of ovomucoid containing L15 culture medium (2 mg/mL). Next, myelin was removed from the single cell suspension by Percoll density gradient centrifugation (25% v/v, SolarBio). Then the cells were reacted with 1:250 PE rat anti-mouse CD11b (BD Pharmingen, 553311) and 1:250 APC anti-mouse CD45 (BD Pharmingen, 561018) on ice for 1 h. After FACS buffer rinse for 3 times, the cells were reacted with 7-AAD (1:80, BD Pharmingen, 559925) on ice for 10 min to exclude the dead cells. Microglia were sorted as CD11b+/CD45+ cells30 by BD FACS Aria III (BD Biosciences). Then the harvested cells were sent to prepare library through 10X genomics, followed by the pair-end 100 sequencing via Illumina HiSeq 4000. 609 cells from 4 CD-treated mice were sequenced at 0.544 M mean reads of sequencing depth per cell, while 585 cells from 6 mice of repopulation day 5 were sequenced at 0.564 M raw reads of sequencing depth per cell.

treatment_protocol: CD mice were treated by control diet (CD) for 19 days. Repopulation mice were treated with PLX5622 for 14 days, followed by CD treated for 5 days

tag: cell type

value: CD11b+/CD45+ microglia

value: Repop D5


title: Nrd1-AA dSet2 BrdU-seq -Rap rep2

description: BrdUseq_Nrd1dSet2_MinusRap_merged_final.bigWig

source_name: Nrd1-AA dSet2 BrdU-seq -Rap

value: -Rap


title: CD_2M


title: Nrd1-AA dSet2 BrdU-seq -Rap rep1


title: CD_3


title: CD_1


title: Ysh1-AA BrdU-seq +Rap rep2

source_name: Ysh1-AA BrdU-seq +Rap


title: Ysh1-AA BrdU-seq -Rap rep2

source_name: Ysh1-AA BrdU-seq -Rap


title: Ysh1-AA BrdU-seq +Rap rep1


title: Nrd1-AA BrdU-seq +Rap rep1

source_name: Nrd1-AA BrdU-seq +Rap


title: Ysh1-AA BrdU-seq -Rap rep1