title: LGP2-/-, 6Gy IR, 48h, rep2

city: Chicago

first: Diana Rose

middle: E

last: Ranoa

state: IL

address: 900 E 57th St, KCBD, Rm 6160

department: Radiation and Cellular Oncology

institute: University of Chicago

description:
9482913021_F
irradiated, replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with Illumina  Beadstudio software

label: biotin UTP

source_name: mouse embryonic fibroblasts (MEFs)

label_protocol: Biotinylated cRNA were prepared with the Illumina™ TotalPrep™ RNA Amplification Kit, Catalog number:  AMIL1791

growth_protocol: WT, MAVS-/-, STING-/-, and LGP2-/- primary MEFs were seeded in 6-well plates at a density of 2x10^5 cells/well.

extract_protocol: Total RNA was isolated from MEFs at 48 hours post-irradiation using Trizol reagent following the manufacturer’s protocol. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Approximately 15 hours post-seeding, cells were either mock-irradiated (un-irradiated) or exposed to 6 Gy ionizing radiation.

tag: cell type

value: mouse embryonic fibroblasts (MEFs)

value: embryo at day 13.5 post-coitus


title: MAVS-/-, 6Gy IR, 48h, rep2

status: Public on May 08 2018

type: RNA

country: USA

description:
9482913034_D
irradiated, replicate 2

molecule: total RNA

organism: Mus musculus

tag: strain

tag: genotype

value: MAVS-/-

tag: tissue


title: mRNA_Tg_Wh_10mo_rep3

city: Obu

first: SAYURI

last: HIGAKI

state: Aichi

address: 7-430 Morioka-cho

department: Medical Genome Center

country: Japan

institute: National Center for Geriatrics and Gerotology

description:
Transgenic mouse, whole brain, 10-month, replicate3
Gene expression in the whole brain from 10-month-old Tg2576 mouse

hyb_protocol: Cy3-labelled cRNA was hybridized to a Mouse miRNA Release 16.0 8x60 K array (Agilent) or a SurePrint G3 Mouse GE 8x60 K array (Agilent), according to manufacturer’s protocol.

scan_protocol: Slides were scanned using one color scan setting for 8 x 60K array slides with a G2505C Agilent DNA microarray scanner.

data_processing: Images were extracted with Feature Extraction Software 10.7.3.1 (Agilent). For per-chip normalization, miRNA expression data and gene expression data were normalized to the 90th percentiles and median of all values on that chip using GeneSpring GX  (Agilent).

source_name: Transgenic mouse, whole brain, 10-month

label_protocol: For miRNA array, the total RNA was labeled using a miRNA Complete Labeling and Hyb kit. For gene expression array, total RNA was labeled by a Low Input Quick Amp Labeling Kit (Agilent). All procedures were performed according to the manufacturer’s instructions.

extract_protocol: Total RNA including both large and small RNA was extracted from mouse cortices or whole brains using the mirVana PARIS (Ambion, Austin, TX) according to the manufacturer’s instructions. The purity and the quality of RNA samples evaluated by using Nanodrop (Thermo scientific, Hudson, NH) and bioanalyzer (Agilent, Santa Clara, CA) were the required levels for microarray analysis.

value: Whole brain

tag: age

tag: Sex

value: male


title: LGP2-/-, no IR, 48h, rep1

description:
9482913021_C
non-irradiated, replicate 1


title: mRNA_Tg_Wh_10mo_rep1

description:
Transgenic mouse, whole brain, 10-month, replicate1
Gene expression in the whole brain from 10-month-old Tg2576 mouse


title: LGP2-/-, 6Gy IR, 48h, rep1

description:
9482913021_E
irradiated, replicate 1


title: mRNA_Wt_Wh_10mo_rep1

description:
Wild type mouse, whole brain, 10-month, replicate1
Gene expression in the whole brain from 10-month-old wild type mouse

source_name: Wild type mouse, whole brain, 10-month

value: Wild type


title: mRNA_Wt_Wh_17mo_rep3

description:
Wild type mouse, whole brain, 17-month, replicate3
Gene expression in the whole brain from 17-month-old wild type mouse

source_name: Wild type mouse, whole brain, 17-month


title: LGP2-/-, no IR, 48h, rep2

description:
9482913021_D
non-irradiated, replicate 2


title: MAVS-/-, no IR, 48h, rep2

description:
9482913034_B
non-irradiated, replicate 2


title: mRNA_Wt_Co_17mo_rep2

description:
Wild type mouse, cortex, 17-month, replicate2
Gene expression in the brain cortex from 17-month-old wild type mouse

source_name: Wild type mouse, cortex, 17-month

value: Brain cortex


title: STING-/-, 6Gy IR, 48h, rep2

description:
9482913039_B
irradiated, replicate 2

value: STING-/-


title: mRNA_Tg_Co_17mo_rep1

description:
Transgenic mouse, cortex, 17-month, replicate1
Gene expression in the brain cortex from 17-month-old Tg2576 mouse

source_name: Transgenic mouse, cortex, 17-month


title: mRNA_Wt_Co_17mo_rep3

description:
Wild type mouse, cortex, 17-month, replicate3
Gene expression in the brain cortex from 17-month-old wild type mouse


title: mRNA_Tg_Co_17mo_rep3

description:
Transgenic mouse, cortex, 17-month, replicate3
Gene expression in the brain cortex from 17-month-old Tg2576 mouse


title: L01

type: genomic

city: Lebanon

first: Lucas

middle: A.

last: Salas

state: NH

address: 1 Medical Center Dr, DHMC

department: Epidemiology

institute: Geisel School of Medicine at Dartmouth

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: whole blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from samples using Qiagen DNeasy Kit according to standard instructions

value: whole blood

tag: ChIP

value: Male

tag: time point (days)

tag: date of blood collection

tag: array

tag: slide

tag: included in the analysis

value: Yes

tag: lymphocytes proportion

tag: monocytes proportion

tag: granulocytes proportion

tag: cd4t proportion

tag: cd8t proportion

tag: nontcells (b +nk) proportion


title: MAVS-/-, 6Gy IR, 48h, rep1

description:
9482913034_C
irradiated, replicate 1

tag: strain

tag: cell type


title: mRNA_Tg_Co_17mo_rep2

description:
Transgenic mouse, cortex, 17-month, replicate2
Gene expression in the brain cortex from 17-month-old Tg2576 mouse

tag: genotype

tag: tissue


title: STING-/-, 6Gy IR, 48h, rep1

description:
9482913039_A
irradiated, replicate 1


title: mRNA_Wt_Wh_10mo_rep3

description:
Wild type mouse, whole brain, 10-month, replicate3
Gene expression in the whole brain from 10-month-old wild type mouse

tag: age

tag: Sex


title: MAVS-/-, no IR, 48h, rep1

description:
9482913034_A
non-irradiated, replicate 1


title: STING-/-, no IR, 48h, rep1

description:
9482913034_E
non-irradiated, replicate 1


title: STING-/-, no IR, 48h, rep2

description:
9482913034_F
non-irradiated, replicate 2


title: Wild-type, no IR, 48h, rep1

description:
9482913020_E
non-irradiated, replicate 1

value: Wild-type


title: Wild-type, 6Gy IR, 48h, rep2

description:
9482913021_B
irradiated, replicate 2


title: mRNA_Tg_Co_10mo_rep2

description:
Transgenic mouse, cortex, 10-month, replicate2
Gene expression in the brain cortex from 10-month-old Tg2576 mouse

source_name: Transgenic mouse, cortex, 10-month


title: Wild-type, no IR, 48h, rep2

description:
9482913020_F
non-irradiated, replicate 2


title: mRNA_Tg_Co_10mo_rep3

description:
Transgenic mouse, cortex, 10-month, replicate3
Gene expression in the brain cortex from 10-month-old Tg2576 mouse


title: Wild-type, 6Gy IR, 48h, rep1

description:
9482913021_A
irradiated, replicate 1


title: mRNA_Wt_Co_17mo_rep1

description:
Wild type mouse, cortex, 17-month, replicate1
Gene expression in the brain cortex from 17-month-old wild type mouse


title: mRNA_Wt_Co_10mo_rep3

description:
Wild type mouse, cortex, 10-month, replicate3
Gene expression in the brain cortex from 10-month-old wild type mouse

source_name: Wild type mouse, cortex, 10-month


title: mRNA_Wt_Co_10mo_rep2

description:
Wild type mouse, cortex, 10-month, replicate2
Gene expression in the brain cortex from 10-month-old wild type mouse


title: mRNA_Wt_Co_10mo_rep1

description:
Wild type mouse, cortex, 10-month, replicate1
Gene expression in the brain cortex from 10-month-old wild type mouse


title: mRNA_Tg_Co_10mo_rep1

description:
Transgenic mouse, cortex, 10-month, replicate1
Gene expression in the brain cortex from 10-month-old Tg2576 mouse


title: L05

tag: ChIP

tag: time point (days)


title: A_OA_H_4

type: SRA

city: beijing

first: li

last: Michael

address: beiqing road

country: China

institute: Basepedia

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using Hisat2 v2.0.4 with  default parameters
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Heart

extract_protocol:
Total RNA from the mouse ventricle of different treated groups was used to perform transcriptome sequencing in the Beijing Annoroad Genomics Co. Ltd , five biological replicates was performed in each group. Total RNA of all sample were isolated with Mini RNeasy Mini kit (QIAGEN). Agilent 2100 RNA Nano 6000 Assay Kit (Agilent Technologies, CA, USA) were used to detected the integrity of the RNA, and then mRNA were enriched with beads with Oligo (dT). Purified mRNA was degraded by Fragmentation Buffer to perform short mRNA fragment. Random primer and relevant buffer were used to synthesis cDNA, and then cDNA was purified with QIAQuick PCR kit and EB buffer. Purified cDNA was modified and amplified by PCR to construct cDNA libraries . Each cDNA library was sequenced on an Illumina HiSeq2000 instrument. Bioinformatically, reads with no more than 30nt length are considered from mature miRNAs, and were counted and mapped to the genome using Bowtie alignment tool.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 10 weeks old

value: Heart


title: A_OA_H_5


title: A_OA_H_3


title: ERFko-untreated-replicate1

city: Madrid

first: Oscar

last: Fernandez-Capetillo

address: MFA 3

department: Genomic Instability Group

country: Spain

institute: CNIO

description: mix of two clones

hyb_protocol: Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 1.65 µg. Volume: 100 uL. Temperature (ºC): 65. Duration: 17 hours. Further details in One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) kit manual, Agilent version 6.7.

scan_protocol: Scanned on a G2505C DNA microarray scanner (Agilent) with Protocol GE1_1105_Oct12 and Grid 028005_D_F_20140728.

data_processing: Images were analyzed by Feature Extraction Software (Agilent v11.5), which performed feature quantitation and background subtraction by spatial detrending algorithms. Subsequent processing was performed with GeneSpring 13 software (Agilent), 1) values below 1 were thresholded to 1, and on-chip probe replicates summarized by computing their geometric mean; 2) values were Logbase2 transformed; 3) a global normalization step adjusted then all the probe intensities within an array, by subtracting the 75th percentile of each array from the log transformed signal value of each entity; and 4) in order to visualize relative differences between samples, independently of the abundance level, a Per-gene Baseline Transformation was done by subtracting for each probe signal the median of its intensities among all samples.

label_protocol: MMLV-RT retrotranscription from a T7 promoter primer on 100ng of RNA samples is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of Cy3-CTP fluorophore (commercial One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) kit, Agilent version 6.7, by following manufacturer instructions). Labeled samples are purified with silica-based spin columns.

growth_protocol: ES cells were grown on gelatin at 37°C, 5% CO2, in high glucose DMEM (Invitrogen) supplemented with 15% fetal bovine serum (FBS), LIF (1000 U/ml), 0.1 mM non-essential aminoacids, 1% glutamax, 55 mM b-mercaptoethanol and 1% Penicillin/Streptomycin

extract_protocol: RNA was prepared using the Absolutely RNA Microprep Kit (Stratagene), following  the manufacturer's recommendations.

treatment_protocol: ERFwt-OHT and ERFko-OHT samples were treated with 4-hydroxy-tamoxifen for at least 2days, aiming to detect quick transcriptional changes upon K-Ras deletion.

value: mouse ES cells

value: ERF-KO

tag: agent


title: A_OA_H_2


title: ERFko-OHTtreated-replicate2

description: mix of two clones

value: OHT


title: ERFko-untreated-replicate2

description: mix of two clones


title: ERFko-OHTtreated-replicate1

description: mix of two clones


title: IkL/L MDP DMSO treated replicate 2

city: Illkirch

first: Peggy

last: Kirstetter

address: 1, rue Laurent Fries

department: Functional Genomic and Cancer

country: France

institute: Institut de Génétique et de Biologie Cellulaire et Moléculaire

description: Purified MDP from IkL/L BM (CD45.2+)  co-cultured 24h with total bone marrow cells (CD45.1+) in presence of vehicule DMSO

hyb_protocol: Following fragmentation and end-labelling, 2.07 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix) interrogating 28,853 genes represented by approximately 27 probes spread across the full length of the gene.

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0,7µm.

data_processing:
Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.1.2.
CEL files were further processed with Affymetrix Expression Console software version 1.4.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

label: biotin

source_name: IkL/L MDP DMSO treated

label_protocol: Biotinylated double strand cDNA targets were prepared from 0.69ng to 20ng of total RNA using the NuGEN Ovation Pico WTA System V2 Kit (Cat # 3302) followed by the NuGEN Encore Biotin Module Kit (Cat # 4200) according to manufacturer recommendations.

growth_protocol: MDPs or CDPs BM cells (CD45.2+) which were co-cultured with 1 million of unfractionated CD45.1+ BM cells and culture 24h in RPMI 1640 medium containing 20mM HEPES, 2mM L-glutamine, 2mM Sodium Pyruvate, 50uM beta-mercapto-ethanol, 1x Minimal Essential Medium (Life Technologies), 10% fetal calf serum (Sigma), 1% Pen/Strep and 50ug/ml gentamycin. Cultures were supplemented with 25 ul/ml of conditioned medium from a Flt3L-producing cell line (B16-Flt3L, Mach et al, 2000).

extract_protocol: After 24h of GSI or DMSO treatment, CD45.2+ cells were FACS purified. MDP and CDP CD45.2+ cells were snap frozen in liquid N2. The RNA was extracted with the Micro RNeasy Plus kit (Qiagen) and reverse transcribed using SuperscriptII (Invitrogen).

treatment_protocol: GSI (Compound E, Calbiochem) was used at 5 uM.

tag: cell

value: Monocyte dendritic progenitor

tag: treatment

value: DMSO

value: IkL/L


title: ERFwt-OHTtreated-replicate2

description: mix of two clones

value: ERF-WT


title: WT CDP DMSO treated replicate 2

description: Purified CDP from WT BM (CD45.2+)  co-cultured 24h with total bone marrow cells (CD45.1+) in presence of vehicule DMSO

source_name: WT CDP DMSO treated

value: Common dendritic progenitor

value: wild type


title: A_H_5

value: Wild type


title: IkL/L MDP DMSO treated replicate 1


title: IkL/L CDP GSI treated replicate 2

description: Purified CDP from IkL/L BM (CD45.2+)  co-cultured 24h with total bone marrow cells (CD45.1+) in presence of GSI

source_name: IkL/L CDP GSI treated

value: GSI


title: IkL/L MDP GSI treated replicate 2

description: Purified MDP from IkL/L BM (CD45.2+)  co-cultured 24h with total bone marrow cells (CD45.1+) in presence of GSI

source_name: IkL/L MDP GSI treated


title: ERFwt-OHTtreated-replicate1

description: mix of two clones


title: IkL/L CDP DMSO treated replicate 2

description: Purified CDP from IkL/L BM (CD45.2+)  co-cultured 24h with total bone marrow cells (CD45.1+) in presence of vehicule DMSO

source_name: IkL/L CDP DMSO treated


title: IkL/L CDP DMSO treated replicate 1


title: IkL/L CDP GSI treated replicate 1


title: A_H_4


title: IkL/L MDP GSI treated replicate 1


title: ERFwt-untreated-replicate2

description: mix of two clones


title: A_H_3


title: WT CDP GSI treated replicate 2

description: Purified CDP from WT BM (CD45.2+)  co-cultured 24h with total bone marrow cells (CD45.1+) in presence of GSI

source_name: WT CDP GSI treated


title: ERFwt-untreated-replicate1

description: mix of two clones


title: A_H_2


title: A_H_1


title: WT MDP GSI treated replicate 2

description: Purified MDP from WT BM (CD45.2+)  co-cultured 24h with total bone marrow cells (CD45.1+) in presence of GSI

source_name: WT MDP GSI treated


title: WT MDP GSI treated replicate 1


title: WT MDP DMSO treated replicate 2

description: Purified MDP from WT BM (CD45.2+)  co-cultured 24h with total bone marrow cells (CD45.1+) in presence of vehicule DMSO

source_name: WT MDP DMSO treated


title: WT MDP DMSO treated replicate 1


title: WT CDP GSI treated replicate 1


title: WT CDP DMSO treated replicate 1


title: Veh_H_3


title: Veh_H_4


title: Veh_H_2


title: Veh_H_5


title: Veh_H_1


title: CRC109

city: Sendai

first: Akira

last: Okita

state: Miyagi

address: 4-1, Seiryomachi, Aobaku

institute: Tohoku University Hospital

hyb_protocol: Labeled cDNA was hybridized to Whole Human Genome 4x44K Microarray (Agilent, Santa Clara, CA, USA).

scan_protocol: Scanning and image analysis were performed using DNA Microarray Scanner (Agilent, Santa Clara, CA, USA). Raw fluorescence intensities were quantified and normalized using Agilent Feature Extraction Software (Agilent, Santa Clara, CA, USA). Data analysis and visualization were performed with GeneSpring GX (Agilent, Santa Clara, CA, USA).

data_processing: Data was normalized by the percentile shift (all samples were normalized to the signal value of 75th percentile of all of probes on the microarray) and the scaling (all genes were normalized to the median of all samples).

source_name: formalin-fixed and paraffin embedded primary tumor samples

label_protocol: 300ng total RNA was amplified using TransPlex Complete Whole Transcriptome Amplification Kit (Sigma, St Louis, MO, USA). Amplified cDNA was purified using QIAquick PCR Purification Kit (Qiagen, Valencia, CA, USA). 1.5μg cDNA was labeled with Cy-3 dye using Genomic DNA ULS Labeling Kit (Agilent, Santa Clara, CA, USA). Labeled cDNA was assessed by the nanodrop (Thermo Fisher Scientific, Madison, WI, USA) and was confirmed that degree of labeling was 1.5-3.0%.

extract_protocol: FFPE samples were obtained from resected primary tumor. Two or four unstained thin slice slides (5-10μm thick) were made and tumor tissue was collected by the macrodissection under a Hematoxylin-Eosin stained tissue slide guide. Total RNA was extracted by Absolutely RNA FFPE Kit (Agilent, Santa Clara, CA, USA).

value: colorectal cancer

tag: gender

value: Female

tag: primary site

value: Transverse

tag: 1st-line chemotherapy regimens

value: IRIS

tag: best response of 1st-line chemotherapy

value: Stable disease


title: CRC106

value: FOLFIRI+Bev

value: Partial response


title: CRC104

value: Rectum

value: FOLFOX

value: Not evaluated


title: CRC105

value: Male

value: Descending


title: CRC110

value: Sigmoid


title: CRC108


title: CRC111

value: Ascending


title: CRC102

value: Others


title: CRC107

value: Progressive disease


title: siHic5 etoh replicate 2

city: Los Angeles

first: Brian

middle: Hae Kang

last: Lee

state: CA

address: 1441 Eastlake Avenue, NOR 6316

department: Biochemistry and Molecular Medicine

institute: University of Southern California

description:
ATAC_07
processed data file: siHic5etoh_ATAC.bw

library_source: genomic

data_processing:
NextSeq Control Software (NCS) v1.4 was used for base calling.
After trimming the raw reads for quality and adapter sequence, the samples were mapped using bowtie2 with default parameters against the GRCh38/hg38 human reference genome.
Duplicate reads and reads aligning to the mitochondrial DNA were discarded.
The remaining mapped reads were quantified and peaks were called using MACS2 with broad settings was used to determine open chromatin regions for each sample.
Overlapping peaks from the two replicates were identified as open chromatin regions for each condition.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *bw: bigWig files with peaks.

source_name: U2OS-GR⍺ cells

growth_protocol: Cells were grown in low glucose DMEM medium (ThermoFisher) supplemented with 5% (vol/vol) FBS.

extract_protocol:
U2OS-GRα cells grown on 6-well dishes were transfected with the appropriate siRNAs. After 48 h, the cells were treated with 100 nM dex or equivalent amounts of ethanol for 1 h before harvesting 50,000 cells and treating with transposase (FC-121-1030; Illumina). Transposition reaction was performed at 37 °C for 30 min, and the samples were purified using a Qiagen PCR MinElute kit (28006; Qiagen). Library fragments were amplified using Nextera PCR Primers (FC-121-1011; Illumina) and NEBnext PCR master mix (0541; New England Lab) for a total of 6–8 cycles. The libraries were then purified and size selected in the 100–450 bp range using Agencourt AMPure XP.
Quality of the size-selected libraries were assessed using Agilent Technologies 2100 Bioanalyzer.

treatment_protocol: siRNA transfection was performed using Lipofractamine RNAimax (Invitrogen) according to the manufacturer's protocol. 48 h after siRNA transfection, the cells were either treated for 1 hour with 100 nM dex (Sigma) or ethanol as control.

value: U2OS cell line stably transfected with GR-alpha

tag: sirna

value: etoh


title: CRC099

value: colorectal cancer

value: FOLFIRI


title: CRC103

value: Transverse


title: siHic5 dex replicate 2

description:
ATAC_08
processed data file: siHic5dex_ATAC.bw

value: dex


title: CRC094

value: FOLFOX+Bev


title: CRC082

value: Partial response


title: CRC089

value: Female

value: Rectum


title: CRC101


title: CRC100

value: Not evaluated


title: CRC087

value: Male


title: CRC085

value: FOLFOX


title: CRC098

value: IRIS+Bev

value: Stable disease


title: CRC080

value: Ascending


title: CRC079

value: Sigmoid


title: siNS dex replicate 2

description:
ATAC_06
processed data file: siNSdex_ATAC.bw

value: U2OS cell line stably transfected with GR-alpha

value: siNS


title: CRC084

value: colorectal cancer


title: siNS etoh replicate 2

description:
ATAC_05
processed data file: siNSetoh_ATAC.bw

value: etoh


title: CRC083


title: CRC093

value: Descending


title: CRC090


title: CRC097


title: siHic5 dex replicate 1

description:
ATAC_04
processed data file: siHic5dex_ATAC.bw

value: dex


title: CRC081


title: siHic5 etoh replicate 1

description:
ATAC_03
processed data file: siHic5etoh_ATAC.bw


title: siNS etoh replicate 1

description:
ATAC_01
processed data file: siNSetoh_ATAC.bw


title: siNS dex replicate 1

description:
ATAC_02
processed data file: siNSdex_ATAC.bw


title: siBRMsiHic5 dex input

data_processing:
NextSeq Control Software (NCS) v1.4 was used for base calling
After trimming the raw reads for quality and adapter sequence, the samples were mapped using BWA with default parameters against the GRCh38/hg38 human reference genome
Duplicate reads and reads aligning to the mitochondrial DNA were discarded
The remaining mapped reads were quantified and peaks were called using MACS2 and IDR framework was used to determine the GR peaks for each condition
MACS+IDR peaks were called using Model-based Analysis for ChIP-Seq version 2 (MACS2) (22) and the Irreproducibility Discovery Rate (IDR) framework
Differentially bound peaks were identified using MACS2 called peaks followed by DiffBind analysis
Genome_build: hg38
Supplementary_files_format_and_content: comma separated file (csv) containing CPM values with each gene represented in each row and the experimental conditions as columns

growth_protocol: Cells were grown in low glucose DMEM medium (ThermoFisher) supplemented with 5% (vol/vol) FBS

extract_protocol:
U2OS-GRα cells grown on 15-cm dishes were transfected with the appropriate siRNAs. After 48 h, the cells were treated with 100 nM dex for 1 h before crosslinking with 1% (v/v) formaldehyde for 10 mins at room temperature and extracting chromatin from the harvested cells. Chromatin was sonicated 20-30 min (30s on/off cycles) with the Biorupter (Diagenode) at 4ºC to produce DNA fragment size of 400-600 bp. Immunoprecipitation of the sonicated chromatin samples was conducted with a cocktail of GR antibodies: H300 (6 µg, Santa Cruz Biotechnology), PA1-511A (2 µg, Thermo Scientific), D6H2L (2 µg, Cell Signaling Technology) in a volume of 1 ml containing chromatin from 20 x 106 cells. Protein G Sepharose magnetic beads (GE Healthcare) were used to isolate the immune complexes with the crosslinked DNA.
Quality of the DNA was assessed using Agilent Technologies 2100 Bioanalyzer and RT-qPCR analysis was performed for selected GR binding sites as quality control. Standard illumina protocols were used to construct the library for sequencing.

treatment_protocol: siRNA transfection was performed using Lipofractamine RNAimax (invitrogen) according to the manufacturer's protocol. 48 h after siRNA transfection the cells were treated for 1 hour with 100 nM dex (Sigma).

tag: cell line

value: U2OS cell line stably transfected with GRalpha


title: siBRMsiNS dex input


title: siCHD9siHic5 dex input


title: siHic5siNS dex input


title: siBRMsiNS dex replicate 2


title: siBRMsiHic5 dex replicate 2


title: siNSsiNS dex input


title: siCHD9siHic5 dex replicate 2


title: siCHD9siNS dex replicate 2


title: CRC076

value: IRIS

value: Partial response


title: siCHD9siNS dex input


title: CRC077

value: Rectum

value: Others


title: CRC073

value: Male


title: CRC078

value: Transverse

value: FOLFOX+Bev


title: CRC074


title: siHic5siNS dex replicate 2


title: CRC075


title: siNSsiNS dex replicate 2


title: CRC070


title: CRC071

value: Complete response


title: CRC067

value: FOLFOX


title: CRC061

value: Not evaluated


title: CRC059

value: Female


title: siBRMsiNS dex replicate 1


title: CRC057

value: Ascending

value: FOLFIRI+Bev


title: CRC058

value: colorectal cancer


title: CRC062

value: Descending

value: FOLFIRI


title: CRC072

value: Sigmoid


title: CRC063


title: CRC068

value: Progressive disease


title: CRC066

value: Partial response


title: CRC064


title: CRC060


title: CRC053

value: Rectum

value: Stable disease


title: siBRMsiHic5 dex replicate 1

value: U2OS cell line stably transfected with GRalpha


title: siCHD9siNS dex replicate 1


title: siCHD9siHic5 dex replicate 1


title: CRC054

value: Male


title: CRC052

value: FOLFOX+Bev


title: siHic5siNS dex replicate 1


title: CRC056

value: Cecum

value: IRIS

value: Complete response


title: CRC051

value: Female


title: CRC049

value: FOLFOX


title: A_OA_H_1

tag: strain

value: 10 weeks old

value: Wild type

value: Heart


title: siNSsiNS dex replicate 1


title: CRC050

value: colorectal cancer


title: CRC044


title: CRC047

value: FOLFIRI+Bev


title: CRC042

value: Sigmoid

value: FOLFIRI


title: CRC045

value: Rectum


title: CRC041

value: Stable disease


title: CRC034

value: Partial response


title: CRC043

value: Male

value: Transverse


title: CRC032

value: IRIS+Bev

value: Not evaluated


title: CRC035

value: Cecum

value: Complete response


title: CRC040

value: XELOX


title: CRC033

value: Female

value: Descending


title: CRC025


title: CRC030

value: FOLFOX+Bev


title: CRC029

value: colorectal cancer

value: FOLFOX


title: CRC037

value: Ascending

value: FOLFIRI+Bev


title: CRC027

value: Sigmoid


title: CRC019

value: Stable disease


title: CRC022

value: Partial response


title: CRC026

value: Male


title: CRC038

value: Rectum


title: CRC036


title: CRC023

value: FOLFIRI


title: CRC028


title: CRC021


title: CRC039

value: IRIS+Bev


title: CRC020


title: CRC024

value: Others


title: CRC017


title: CRC031


title: Heart_BMAL1_Input_replicate3

city: College Station

first: Jerome

last: Menet

state: Texas

address: Texas A&M University Biology Department 3258 TAMU College Station, TX 77843

department: Biology

institute: Texas A&M University

data_processing:
Fastq files were aligned to the genome mm10 with bowtie2 with the following settings --end-to-end -x.
Unique reads were retreaved from the sam files using a custom perl script.
Bam files were generated with samtools with the following command -bS -h.
Bam files were sorted using samtools sort.
Biological replicates were then merged and downsampling was performed for replicates with higher read counts. No downsampling was done for the liver. Both replicate 1 samples for the heart were merged and downsampled to 36% of reads randomly using samtools. Kidney replicate 1 was downsampled to 33% of total reads randomly using samtools.
PCR duplicates over 3 were removed with a custom made perl script.
BigWig files were generated with a custom made perl script.
Peak calling was done with HOMER with the following settings -style factor -i (input)
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files (visualization files); bed files (BMAL1 DNA binding sites peak location)

source_name: kidney BMAL1 input

growth_protocol: C57BL/6 mice (3-6 month-old) were entrained to a 12 hours light 12 hours dark cycle with food and water provided ad libitum

extract_protocol:
Mouse liver, kidneys, and heart were extracted were collected at ZT06 (middle of the light phase), rinsed in ice-cold 1X PBS, homogenized and crosslinked with 1% formaldehyde in 1X PBS at room temperature. Nuclei were then purified, sonicated and immunoprecipitated with BMAL1 antibody.
BMAL1 and input ChIP-Seq libraries were generated from liver, kidney, and heart samples originating from the same animals (n = 3 mice per tissue) using NEBNext® ChIP-Seq Library Prep Master Mix Set (# E6240, NEB) as per the manufacturer’s instructions. DNA from ChIP and input were quantified using a Quantus Fluorometer (# E6150, Promega), and 10 ng was used to generate the libraries. DNA end repair was performed with NEBNext End Repair Reaction Buffer and Enzyme Mix for 30 minutes at 20°C. dA-Tailing of end-repaired DNA was performed with NEBNext dA-Tailing Reaction Buffer and Klenow Fragment (3’-5’ exo) for 30 minutes at 37°C. Adapter ligation of dA-tailed DNA was performed with Quick Ligation Reaction Buffer, NEBNext Adaptor (1.5 μM), and Quick T4 DNA Ligase. Libraries were generated by PCR amplification of adaptor ligated DNA using with NEBNext Multiplex oligonucleotides and Phusion Taq (M0530S). Libraries were amplified for 16 cycles. Libraries were quantified with qPCR with TRUseq library standards, and with a Quantus Fluorometer. DNA cleanup between each reaction was performed using Solid Phase Reversible Immobilization (SPRI) beads generated in the lab from Sera-mag SpeedBeads (# catalog number 09-981-123, Thermo-Fisher). BMAL1 ChIP-seq libraries were sequenced with an Illumina NextSeq with a sequence length of 75bp.

tag: strain background

tag: genotype/variation

value: wild type

value: 3-6 months

value: Heart

tag: molecule subtype

value: input DNA


title: Heart_BMAL1_ChIP_replicate2

description: Chromatin_Immunoprecipitation_DNA_Fragment

source_name: heart BMAL1 ChIP-seq

tag: age

tag: tissue

tag: chip antibody

value: affinity purified chicken anti-BMAL1 (serum generated by Cocaligo Biologicals against mouse BMAL1 N-term domain)

tag: chip antibody ref.

value: ChIP DNA


title: Heart_BMAL1_ChIP_replicate3


title: Heart_BMAL1_Input_replicate1


title: Heart_BMAL1_Input_replicate2


title: CRC018

value: colorectal cancer

value: Female

value: FOLFOX


title: Heart_BMAL1_ChIP_replicate1


title: Kidney_BMAL1_Input_replicate3

value: Kidney


title: Kidney_BMAL1_ChIP_replicate3

source_name: kidney BMAL1 ChIP-seq


title: CRC012

value: Sigmoid


title: Kidney_BMAL1_Input_replicate2


title: CRC016

value: Partial response


title: CRC015

value: Male


title: CRC014

value: Rectum

value: FOLFIRI+Bev


title: CRC009

value: Stable disease


title: CRC013


title: CRC010

value: FOLFIRI


title: CRC007

value: Transverse

value: Not evaluated


title: CRC004

value: Cecum

value: FOLFOX+Bev

value: Progressive disease


title: Kidney_BMAL1_ChIP_replicate2

value: wild type

value: 3-6 months

value: affinity purified chicken anti-BMAL1 (serum generated by Cocaligo Biologicals against mouse BMAL1 N-term domain)

value: ChIP DNA


title: CRC006

value: colorectal cancer

value: Female


title: CRC002

value: FOLFOX


title: CRC001

value: Male

value: IRIS+Bev


title: CRC008

value: Partial response


title: Macrophage GM-CSF + siPPARg replicate 1

first: Amaya

last: Puig

state: Madrid

address: Dr. Esquerdo 46

department: Immunology

institute: Hospital Gregorio Marañón

description: M1 r1 +siPPARg

hyb_protocol: After fragmentation, 600 ng of labeled cRNA from each sample was hybridized in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at room temperature in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wahs buffer 2 (Agilent).

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Scanned images and raw data were pre-processed with GeneSpring GX (Agilent).

source_name: Macrophage GM-CSF + siPPARg

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit – 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.

growth_protocol: Freshly isolated CD14+ monocytes were cultured for 7 days in RPMI 10% FCS containing GM-CSF and, after 7 days were transfected with siRNA for PPARG (siPPARG) or siRNA with a scramble sequence (siControl) from Ambion and using Hiperfect transfection reagent, for 48 hours.

extract_protocol: Total RNA from each condition was extracted and purified using the RNA isolation kit (Macheray-Nagel).Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.

treatment_protocol: Cells were were treated with GM-CSF (1000 U/ml) every 48 hours

tag: donor

tag: cell type

value: GM-CSF Macrophage

value: PPARG knockdown


title: CRC005

value: Rectum

value: FOLFIRI+Bev


title: NCC555

value: Stable disease


title: CRC011

value: Transverse

value: IRIS


title: Kidney_BMAL1_Input_replicate1

value: wild type

value: Kidney

value: input DNA


title: Macrophage GM-CSF + siPPARg replicate 2

description: M1 r2 +siPPARg


title: NCC538

value: Ascending

value: FOLFIRI+Pmab


title: Kidney_BMAL1_ChIP_replicate1

value: 3-6 months

value: affinity purified chicken anti-BMAL1 (serum generated by Cocaligo Biologicals against mouse BMAL1 N-term domain)

value: ChIP DNA


title: Macrophage GM-CSF + siPPARg replicate 3

description: M1 r3 +siPPARg


title: Liver_BMAL1_Input_replicate3

source_name: liver BMAL1 input

value: Liver


title: Macrophage GM-CSF + siControl replicate 2

description: M1 r2 +siC

source_name: Macrophage GM-CSF + siControl

value: control


title: NCC542

value: colorectal cancer

value: Male

value: Others


title: CRC003

value: Female

value: Rectum

value: FOLFOX

value: Partial response


title: Liver_BMAL1_ChIP_replicate3

source_name: liver BMAL1 ChIP-seq

value: wild type


title: Liver_BMAL1_Input_replicate2


title: Macrophage GM-CSF + siControl replicate 3

description: M1 r3 +siC

value: GM-CSF Macrophage


title: 12-070115 O replicate 2

city: Rochester

first: Steven

middle: R.

last: Gill

state: NY

address: 601 Elmwood Avenue

department: Microbiology & Immunology

institute: University of Rochester

data_processing:
Sequences were cleaned using Trimmomatic-0.32  "SLIDINGWINDOW:4:20 TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 MINLEN:15"
Sequences were mapped using STAR_2.4.2a "--runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
Differential expression using cufflinks-2.0.2 (cuffdiff) - " --FDR 0.05 -u -b GENOME"
Genome_build: All sequences were aligned to MRSA252 (GenBank ID = NC_002952.2).
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample in "Lacey_GEO_040718_frm_genes.fpkm_tracking.txt " AND Tab-delimited text files include raw read counts for each sample in "Lacey_GEO_040718_frm_genes.count_tracking.txt"

organism: Staphylococcus aureus

source_name: nos KO_2 mM DEA NONOate

growth_protocol: S.aureus strains were cultured overnight, then diluted and grown to an OD600 of 0.5 whence they were shifted to either anaerobic conditions or NO stress (DEA NONOate)

extract_protocol:
aliquots from each culture were transferred to RNAProtect and then RNA extracted by TRIzol/mechanical lysis.
Illumina TruSeq library preparation from RiboZero depleted total RNA

treatment_protocol: anaerobic growth or NO stress using 2mM DEA NONOate

value: nos KO

tag: growth condition

value: 2 mM DEA NONOate


title: 10-070115 M replicate 2

source_name: nor KO_2 mM DEA NONOate

value: nor KO


title: 9-070115 L replicate 2

source_name: nor KO_0 mM DEA NONOate

value: 0 mM DEA NONOate


title: 8-070115 O replicate 1


title: 11-070115 N replicate 2

source_name: nos KO_0 mM DEA NONOate


title: Macrophage GM-CSF + siControl replicate 1

description: M1 r1 +siC


title: Liver_BMAL1_ChIP_replicate2

value: 3-6 months

value: affinity purified chicken anti-BMAL1 (serum generated by Cocaligo Biologicals against mouse BMAL1 N-term domain)


title: 7-070115 N replicate 1


title: NCC508

tag: gender

value: FOLFOX+Bev


title: NCC445

tag: primary site

value: FOLFIRI+Pmab

value: Stable disease


title: NCC469

value: colorectal cancer

value: Male

value: Transverse

tag: 1st-line chemotherapy regimens

value: SOX+Bev


title: NCC490

value: Rectum

tag: best response of 1st-line chemotherapy


title: NCC454

value: Partial response


title: NCC488

value: FOLFOX

value: Progressive disease


title: NCC440

value: Descending


title: NCC444

value: XELOX+Bev


title: NCC437

value: Ascending


title: NCC419

value: Female


title: NCC424

value: Sigmoid


title: Liver_BMAL1_Input_replicate1

value: wild type

value: 3-6 months

value: Liver

value: input DNA


title: Liver_BMAL1_ChIP_replicate1

value: affinity purified chicken anti-BMAL1 (serum generated by Cocaligo Biologicals against mouse BMAL1 N-term domain)

value: ChIP DNA


title: 5-070115 L replicate 1

value: nor KO

value: 0 mM DEA NONOate


title: 3-070115 J replicate 2

source_name: wt _0 mM DEA NONOate

value: wt


title: NCC510

value: colorectal cancer

value: Male

value: FOLFOX+Bev

value: Partial response


title: 6-070115 M replicate 1

value: 2 mM DEA NONOate


title: 2-070115 K replicate 1

source_name: wt_2 mM DEA NONOate


title: 1-070115 J replicate 1


title: 18-050615A I replicate 2

source_name: nos KO_240 min anaerobic

value: nos KO

value: 240 minutes anaerobic


title: NCC399

value: Female

value: Sigmoid

value: Progressive disease


title: NCC395

value: Ascending

value: SOX+Bev


title: 17-050615A H replicate 2

source_name: nos KO_120 min anaerobic

value: 120 minutes anaerobic


title: 4-070115 K replicate 2


title: NCC383

source_name: formalin-fixed and paraffin embedded primary tumor samples


title: NCC373

value: XELOX+Bev


title: 16-050615A G replicate 2

source_name: nos KO_0 min anaerobic

value: 0 minutes anaerobic


title: NCC369


title: NCC317

value: Stable disease


title: 15-050615A F replicate 2

source_name: nor KO_240 min anaerobic

value: nor KO


title: NCC354

value: colorectal cancer

value: IRIS+Bev


title: NCC410

value: Male

value: Rectum

value: XELOX


title: 14-050615A E replicate 2

source_name: nor KO_120 min anaerobic


title: NCC350

value: FOLFOX+Bev


title: NCC299

value: Partial response


title: NCC286


title: NCC358


title: NCC288

value: Cecum


title: NCC323

value: FOLFOX


title: NCC261

value: Female

value: Sigmoid

value: Progressive disease


title: NCC256


title: NCC293

value: Ascending


title: NCC289


title: 13-050615A D replicate 2

source_name: nor KO_0 min anaerobic


title: NCC263

value: XELOX+Bev


title: 11-050615A B replicate 2

source_name: wt_120 min anaerobic

value: wt

value: 120 minutes anaerobic


title: NCC257


title: NCC315

value: Stable disease


title: NCC311

value: colorectal cancer

value: SOX+Bev


title: 10-050615A A replicate 2

source_name: wt_0 min anaerobic

value: 0 minutes anaerobic


title: NCC250

value: Male

value: Rectum

value: Complete response


title: 12-050615A C replicate 2

source_name: wt_240 min anaerobic

value: 240 minutes anaerobic


title: 9-050615A I replicate 1

value: nos KO


title: 8-050615A H replicate 1


title: NCC225

value: FOLFOX+Bev

value: Partial response


title: NCC241


title: NCC228

value: Female


title: NCC255

value: Sigmoid


title: NCC245

value: FOLFOX


title: 5-050615A E replicate 1

value: nor KO


title: NCC216


title: NCC222

value: Transverse

value: FOLFIRI+Bev


title: 7-050615A G replicate 1


title: 6-050615A F replicate 1


title: NCC217


title: NCC214

value: Progressive disease


title: NCC211

value: colorectal cancer

value: Ascending


title: NCC202


title: NCC215

value: Cecum


title: NCC204

value: Male

value: IRIS


title: 2-050615A B replicate 1

value: wt

value: 120 minutes anaerobic


title: 4-050615A D replicate 1

value: 0 minutes anaerobic


title: 3-050615A C replicate 1

value: 240 minutes anaerobic


title: NCC199

value: Rectum

value: FOLFOX+Bev

value: Partial response


title: NCC164

value: FOLFOX


title: NCC184

value: FOLFIRI


title: NCC187

value: Sigmoid

value: Stable disease


title: 1-050615A A replicate1

source_name: wt _0 min anaerobic


title: NCC172

value: Female


title: NCC149

value: colorectal cancer


title: NCC195

value: Transverse

value: FOLFIRI+Bev


title: NCC160

value: Male


title: NCC139

value: Others


title: NCC128


title: P3

city: Bethesda

first: Sijung

last: Yun

state: Maryland

address: 8908 Ewing Drive

institute: NIH/JHU

data_processing:
We aligned to hg38 reference genome using HISAT2, version 2.0.5.
FPKM values were obtained using Cufflinks, patched version of 2.2.1.
Genome_build: hg38
Supplementary_files_format_and_content: .fpkm_tracking

source_name: BEAS-2B cell line

growth_protocol: Grown in 6 well plate for 48 hours with Lonza bronchial epithelial cell growth media (no gentamicin) according to ATCC protocol

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen).
To obtain the final sequencing library, 14 cycles of PCR were performed using Phusion Hot Start High-Fidelity DNA Polymerase (Finnzymes, Espoo, Finland). Three biological replicates were used and for each sample replicate we obtained ~50 million paired 50-mer reads (using Illumina HiSeq 2500 platform).

value: Bronchial epithelial cell line

tag: genotype

value: Wild type, constitutive expression


title: P2

tag: cell line


title: NCC123

value: Ascending


title: P1


title: NCC117


title: NCC120

value: IRIS+Bev


title: NCC090


title: NCC106

value: Rectum

value: IRIS

value: Complete response


title: NCC110

value: FOLFOX


title: NCC088

value: Partial response


title: NCC081


title: NCC069


title: BEAS-2B_3


title: NCC085


title: NCC055


title: NCC087


title: NCC052

value: Sigmoid


title: NCC061

value: Stable disease


title: NCC043

value: Female


title: NCC077

value: colorectal cancer


title: BEAS-2B_2


title: PTO 19T trametinib 100 nM R2

city: Heidelberg

first: Tianzuo

last: Zhan

address: Im Neuenheimer Feld 580

country: Germany

institute: German Cancer Research Center

description: Replicate 2

hyb_protocol: 11 ug of fragmented and labeled cRNA were hybridized for 17 hr at 45°C on Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays according to user manual GeneChip® 3' IVT PLUS Reagent Kit, P/N 703210.

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays (P/N 702731).

data_processing: Data were normalized using the 'affy' R/Bioconductor package. Normalization steps include background correction using the 'rma' method and quantile normalization.

source_name: patient-derived colorectal cancer organoid

label_protocol: The Affymetrix GeneChip 3´IVT PLUS Reagent Kit is used to generate labeled single-stranded cRNA from input amounts of 100ng total RNA, Label: Biotin.

growth_protocol: Organoids were cultured in ENA media.

extract_protocol: Qiagen RNeasy Extraction Kit.

treatment_protocol: Treatment with indicated drugs for 72 h.

tag: treatment

value: Trametinib


title: PTO 19T trametinib 100 nM R1

description: Replicate 1

value: patient-derived colorectal cancer organoid


title: NCC041

value: Male


title: PTO 19T DMSO R1

description: Replicate 1

value: DMSO


title: PTO 19T DMSO R2

description: Replicate 2


title: NCC045


title: NCC056


title: A549_3

source_name: A549 cell line

growth_protocol: Grown in 6 well plate for 48 hours with Hams F12K with 10% FBS and 5mM L-glutamine according to ATCC protocol

value: Alveolar epithelial cell


title: A549_1

value: Wild type, constitutive expression


title: NCC039


title: A549_2


title: SUDHL4_day6_200nM_GSK595

city: Collegeville

first: Shawn

middle: W

last: Foley

state: PA

address: 1250 S. Collegeville Rd

department: Oncology

institute: GlaxoSmithKline

description:
PRMT5_80_SUDHL4_day_6_200nm_595_n2_TAATGCGC_L004
PRMT5_79_SUDHL4_day_6_200nm_595_n1_CTGAAGCT_L004

data_processing:
fastq files were aligned to humanhg38 with the gencode GRCh38.v23 annotation using a 2-pass STAR-2.5.2b
ribosomal and mitochondrial alignments were removed
Differential gene expression was calculated using Cufflinks2 suite considering genes with a q-value >0.05, and a minimum expression >1 FPKM, and a minimum 2-fold change in expression as significant.
Alternative splicing analysiss was perfomed using rMATS-3.2.5 and run using default parameters with the –novelSS flag to identify novel splicing events. Events were considered significant with FDR<0.01, SD<0.2, junctioncoverage >10 for both the spliced in and excluded junctions, and -0.2< IncLevelDifference >0.2 for alternative splicing events from “Junction_Count_Only” outputfiles.
Genome_build: hg38
Supplementary_files_format_and_content: Complete text tab delimited output files from CuffDiff of differential gene expression testing (*gene_exp.diff) . Only significant alternatively spliced events from rMATS are reported in excel workbook format (*novel_filtered_rMATS.xlsx)

source_name: CellLine: SU-DHL-4

growth_protocol: Cell lines were obtained from ATCC or DSMZ and were grown in recommended medium, which was most frequently RPMI-1640 containing 10% FBS.

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNaseI treatment with QIAGEN Rneasy mini kit in accordance with the prescribed protocol provided with the kit. QC was performed with Agilent Bioanalyser.
Preparation of sequencing libraries using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold Library Prep, Protocol E

treatment_protocol: Cells were treated with either 200nM GSK3326595 or DMSO and collected at 3 and 6 days post-treament.

tag: tumor type

value: Diffuse Large B-cell Lymphoma

tag: treated with

tag: time point

value: Day 6


title: NCC014

value: Rectum


title: SUDHL4_day6_vehicle

description:
PRMT5_78_SUDHL4_day_6_vehicle_n2_GAATTCGT_L003
PRMT5_77_SUDHL4_day_6_vehicle_n1_ATTCAGAA_L003

value: Vehicle


title: NCC024


title: BEAS-2B_1

value: Bronchial epithelial cell line


title: NCC020

value: Others


title: SUDHL4_day3_200nM_GSK595

description:
PRMT5_76_SUDHL4_day_3_200nm_595_n2_GAGATTCC_L002
PRMT5_75_SUDHL4_day_3_200nm_595_n1_CGCTCATT_L002

value: Day 3


title: NCC009

value: Transverse

value: XELOX+Bev

value: Partial response


title: SUDHL4_day3_vehicle

description:
PRMT5_74_SUDHL4_day_3_vehicle_n2_TCCGGAGA_L001
PRMT5_73_SUDHL4_day_3_vehicle_n1_ATTACTCG_L001


title: SUDHL5_day6_200nM_GSK595

description:
PRMT5_72_SUDHL5_day_6_200nm_595_n2_AGCGATAG_L008
PRMT5_71_SUDHL5_day_6_200nm_595_n1_TCTCGCGC_L008

source_name: CellLine: SU-DHL-5


title: NCC chi3

value: colorectal cancer

value: Descending

value: SOX

value: Stable disease


title: NCC001

value: Male

value: FOLFOX


title: NCC028


title: NCC chi2

value: FOLFOX+Bev


title: NCC016

value: Sigmoid


title: SUDHL5_day6_vehicle

description:
PRMT5_70_SUDHL5_day_6_vehicle_n2_TCCGCGAA_L008
PRMT5_69_SUDHL5_day_6_vehicle_n1_CGGCTATG_L007

value: Diffuse Large B-cell Lymphoma

value: Day 6


title: NCC023

value: Female

value: Rectum

value: Progressive disease


title: SUDHL5_day3_200nM_GSK595

description:
PRMT5_68_SUDHL5_day_3_200nm_595_n2_TAATGCGC_L007
PRMT5_67_SUDHL5_day_3_200nm_595_n1_CTGAAGCT_L007

value: Day 3


title: Liver, high-wakame diet administrated for 28d, biological rep2

city: Aomori

first: Yuji

last: Nakai

state: Aomori

address: 2-1-1, Yanagawa

department: Institute of Regional Innovation

institute: Hirosaki University

description: No additional information

hyb_protocol: Following fragmentation, 12.5 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were quantified with the Factor Analysis for Robust Microarray Summarization (FARMS) method, using the statistical language R (R-2.7.2) and Bioconductor 2.2.

organism: Rattus norvegicus

source_name: Liver, fed 1% wakame powder containing diet for 28d

label_protocol: biotinylated cRNA was obtained from 100 ng of purified total RNA using a GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using ISOGEN reagent (Nippon Gene Co., Toyama, Japan), then purified with an RNeasy mini kit (Qiagen K.K., Tokyo, Japan).

treatment_protocol: Excised liver sample was immediately immersed in RNAlater and treated according to the manufacturer's protocol.

tag: strain

value: Sprague Dawley (SD)

value: Liver

tag: age

value: 9 weeks


title: Liver, high-wakame diet administrated for 28d, biological rep1

description: No additional information

tag: tissue


title: NCC chi1

value: colorectal cancer

value: Cecum

value: Partial response


title: SUDHL5_day3_vehicle

description:
PRMT5_66_SUDHL5_day_3_vehicle_n2_GAATTCGT_L006
PRMT5_65_SUDHL5_day_3_vehicle_n1_ATTCAGAA_L006

value: Vehicle


title: Liver, low-wakame diet administrated for 28d, biological rep3

description: No additional information

source_name: Liver, fed 0.1% wakame powder containing diet for 28d

value: Male


title: Liver, high-wakame diet administrated for 28d, biological rep3

description: No additional information


title: NCC013

value: FOLFOX


title: input DNA_1

city: Fukuoka

first: SHINYA

last: TANAKA

address: 3-1-1, maidashi, Higashi-ku

institute: Kyushu University

data_processing:
Quality check and adaprtor triming were performed using TrimGalore version 0.3.7 with the following setting: -q 30 --length 35
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie (version 1.2.1.1) with the following setting: -n 3 -m 1 -a --best --strata
peaks were called using MACS2 (version 2.1.1.20160309) with the following setting: q-value cutoff of 0.01 for narrow peaks
Genome_build: mm10
Supplementary_files_format_and_content: BED file with called peaks

source_name: Th17 cells

growth_protocol: Primary Th17 cells were routinely generated by Th17 skewing culture (typically Naive CD4+ T cells into anti-CD3 and CD28-coated plate in 10 % FCS complete RPMI medium supplemented with IL-6, TGF-b, anti-IL-4 Ab and anti-IFN-g Abs)

extract_protocol:
Lysates were clarified from sonicated nuclei and Trim33 complexes were isolated with antibody.
Libraries were prepared according to KAPA's instructions accompanying the KAPA hyper prep kit. Briefly, DNA was subjected to end-repaire and  A-tailing to produce 5'-phosphorylated, 3'-dA-tailed dsDNA fragment. Illumina's adapters with 3'-dTMP overhangs are ligated to 3'-dA-tailed molecules. After adapter ligation, DNA was PCR amplified with Illumina primers and library fragments of 50~400 bp (insert plus adaptor and PCR primer sequences) were isolated with AMpure XP beads (Beckman Coulter). The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina Hiseq 2000 following the manufacturer's protocols.

tag: differentiated cell type

value: Primary Th17 cells

tag: extracted cell type

value: naive CD4+T cells

value: spleen and lymph nodes

tag: differentiation status

value: In vitro differentiated

tag: chip antibody


title: input DNA_2


title: Liver, high-wakame diet administrated for 28d, biological rep4

description: No additional information

tag: gender


title: Liver, low-wakame diet administrated for 28d, biological rep4

description: No additional information


title: Trim33_ChIPSeq_2

value: Trim33 (Bethyl, A301-060A)


title: Liver, low-wakame diet administrated for 28d, biological rep1

description: No additional information


title: Liver, low-wakame diet administrated for 28d, biological rep2

description: No additional information


title: Trim33_ChIPSeq_1


title: Liver, control diet administrated for 28d, biological rep3

description: No additional information

source_name: Liver, fed control AIN-93G diet for 28d


title: Liver, control diet administrated for 28d, biological rep4

description: No additional information


title: Liver, control diet administrated for 28d, biological rep1

description: No additional information


title: JM12_ChIA-PET-3_ZT18

data_processing:
Reads from the orginal fastq files were processed to extract the tag 1 and 2 (i.e., read 1 and 2) along with their accompanying half-linker code and generate two fastq files (R1 and R2 file) containing the sequence identifier, the raw sequence, and the sequence quality values for each tag.
The R1 and R2 fastq files were aligned to the mouse genome (mm10 version) as paired-end reads using bowtie2 and the options -X 5 and --fast
Paired-end tags with both reads mapping uniquely to the mouse genome were filtered in and all other paired tags removed from the analysis.
Paired-end tags (PETs) were parsed based on the half-linker barcodes into non-chimeric PETs (specific products) or chimeric PETs (non-specific products).
Duplicated PETs were removed for both chimeric and non-chimeric products.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimitated text file containing all paired-end tags for the 3 biological replicates with the following data columns;
Supplementary_files_format_and_content: Experiment   Read1   Tag1   chr   start   Read2   Tag2   chr   start   Distance_Read1_Read2

extract_protocol:
Mouse liver were collected at ZT06 (middle of the day) or ZT18 (middle of the night), rinsed in ice-cold 1X PBS and flash-frozen. Frozen livers were crushed to a fine powder in liquid nitrogen using a mortar, and crosslinked with 1% formaldehyde (JM11) or with 1. 5mM EGS and 1% formaldehyde (JM08 and JM12). Nuclei were purified, sonciated, and sonicated. Sonicated chromatin was then used to isolate Pol II -DNA complexes with an antibody.
Nuclei were sonicated in 10 mM Tris pH 7.5, 150 mM NaCl, 2 mM EDTA, 0.5% SDS, 0.2% Triton, 1X protease inhibitor cocktail. Chromatin samples from 3-7 livers were pulled together, diluted 5-fold to obtain a final concentration of ChIP buffer of 10mM Tris-Cl pH 7.5, 150mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 1X protease inhibitor cocktail. Pol II ChIP were performed in 50 ml canonical tube with 65 µg of anti-RNA Polymerase II 8WG16 monoclonal antibody (# MMS-126R, Covance). Immunoprecipitated chromatin was washed once with TSE I buffer (10mM Tris pH 7.5, 0.1%SDS, 1% Triton X-100, 2mM EDTA, 150mM NaCl, 1mM DTT, 1 mM PMSF), once with TSE II buffer (10mM Tris pH 7.5, 0.1%SDS, 1% Triton X-100, 2mM EDTA, 500mM NaCl, 1mM DTT, 1mM PMSF), once with LiCl Buffer III (10mM Tris pH 7.5, 0.25M LiCl, 1% NP-40, 1% Na Deoxycholate, 1mM EDTA, 1mM DTT, 1mM PMSF), and once with TET buffer (10mM Tris pH 7.5, 1mM EDTA, 0.1% Triton). Beads were finally resuspended in 2 ml of 1X TE buffer supplemented with 1X TE. Immunoprecipitated chromatin was end-repaired, processed for ligation with biotinylated half-linkers, and 5’ phosphorylated while still complexed with Pol II antibodies on magnetic beads following published protocols. Chromatin was then eluted, diluted to a final volume of 10 ml, and used for the proximity ligation step (performed for a minimum of 16 hours at 4ºC under extremely diluted conditions, i.e., < 0.2 ng DNA/μL, to favor ligation events within individual crosslinked chromatin complexes). Following the proximity ligation step, chromatin was treated with proteinase K, reverse crosslinked, and the DNA purified. ChIA-PET DNA was then digested with MmeI, immobilized on streptavidin beads, and ligated to the ChIA-PET adapters. The DNA samples were finally proceeded through nick translation and a PCR amplification step to generate the library. Libraries were ran on an agarose gel, and fragment of ~229 bp were gel-extracted, purified, and quantified.

tag: strain background

tag: genotype/variation

value: wild type

value: 3-6 months

value: ZT18 (middle of the night)

value: RNA Polymerase II, clone 8WG16  (Covance, MMS-126R)


title: JM08_ChIA-PET-1_ZT18_rep1

value: Liver


title: JM12_ChIA-PET-3_ZT06

value: ZT06 (middle of the day)


title: SUDHL6_day6_200nM_GSK595

description:
PRMT5_64_SUDHL6_day_6_200nm_595_n2_GAGATTCC_L006
PRMT5_63_SUDHL6_day_6_200nm_595_n1_CGCTCATT_L005

source_name: CellLine: SU-DHL-6

value: Diffuse Large B-cell Lymphoma

value: Day 6


title: JM08_ChIA-PET-1_ZT18_rep2


title: Liver, control diet administrated for 28d, biological rep2

description: No additional information

value: Sprague Dawley (SD)

value: 9 weeks


title: SUDHL6_day6_vehicle

description:
PRMT5_62_SUDHL6_day_6_vehicle_n2_TCCGGAGA_L005
PRMT5_61_SUDHL6_day_6_vehicle_n1_ATTACTCG_L005

value: Vehicle


title: SUDHL6_day3_200nM_GSK595

description:
PRMT5_60_SUDHL6_day_3_200nm_595_n2_AGCGATAG_L004
PRMT5_59_SUDHL6_day_3_200nm_595_n1_TCTCGCGC_L004

value: Day 3


title: JM08_ChIA-PET-1_ZT06_rep2


title: JM08_ChIA-PET-1_ZT06_rep1


title: SUDHL6_day3_vehicle

description:
PRMT5_58_SUDHL6_day_3_vehicle_n2_TCCGCGAA_L004
PRMT5_57_SUDHL6_day_3_vehicle_n1_CGGCTATG_L003


title: JVM2_day6_200nM_GSK595

description:
PRMT5_40_JVM2_day_6_200nm_595_n2_GAGATTCC_L006
PRMT5_39_JVM2_day_6_200nm_595_n1_CGCTCATT_L005

source_name: CellLine: JVM-2

value: Mantle Cell Lymphoma


title: JVM2_day6_vehicle

description:
PRMT5_38_JVM2_day_6_vehicle_n2_TCCGGAGA_L005
PRMT5_37_JVM2_day_6_vehicle_n1_ATTACTCG_L005


title: JVM2_day3_200nM_GSK595

description:
PRMT5_36_JVM2_day_3_200nm_595_n2_AGCGATAG_L004
PRMT5_35_JVM2_day_3_200nm_595_n1_TCTCGCGC_L004


title: JVM2_day3_vehicle

description:
PRMT5_34_JVM2_day_3_vehicle_n2_TCCGCGAA_L004
PRMT5_33_JVM2_day_3_vehicle_n1_CGGCTATG_L003


title: MAVER1_day6_200nM_GSK595

description:
PRMT5_32_MAVER1_day_6_200nm_595_n2_TAATGCGC_L003
PRMT5_31_MAVER1_day_6_200nm_595_n1_CTGAAGCT_L003

source_name: CellLine: MAVER-1


title: MAVER1_day6_vehicle

description:
PRMT5_30_MAVER1_day_6_vehicle_n2_GAATTCGT_L002
PRMT5_29_MAVER1_day_6_vehicle_n1_ATTCAGAA_L002


title: MAVER1_day3_200nM_GSK595

description:
PRMT5_28_MAVER1_day_3_200nm_595_n2_GAGATTCC_L002
PRMT5_27_MAVER1_day_3_200nm_595_n1_CGCTCATT_L001


title: Clr4D_18C_NETSEQ

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

description: NET sequencing in Clr4 deleted cells at 18C

data_processing:
Alignment was done using Tophat.
FPKM values were calculated using cufflinks
Genome_build: asm294v2.28
Supplementary_files_format_and_content: Tab delimited text files, from cufflinks

organism: Schizosaccharomyces pombe

source_name: log growing cells

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). Cultures were first grown at 30°C to OD600~0.1-0.2 and then shifted to 18˚C for 3 days.

extract_protocol:
RNAPII was immunopurified using anti-FLAG M2 affinity gel (Sigma) and nascent RNA was isolated using Qiagen miRNeasy Mini Kit.
Custom oligos were used in library construction for sequencing on the Illumina platform.
Libraries were analyzed using the Agilent D1000 TapeStation (Agilent) and sequenced on the Illumina MiSeq platform.

treatment_protocol: Genomic tagging of RPB3. Genomic deletion of CLR4. Growth treatment at 18°C.

value: Clr4 mutant


title: WT_18C_NETSEQ

description: NET sequencing in WT cells at 18C


title: MINO_day6_200nM_GSK595

description:
PRMT5_24_MINO_day_6_200nm_595_n2_AGCGATAG_L008
PRMT5_23_MINO_day_6_200nm_595_n1_TCTCGCGC_L008

source_name: CellLine: MINO

value: MINO


title: Gro_Input

first: Jemma

middle: L.

last: Webber

address: 929 E 57th Street

department: Ben May Department for Cancer Research

institute: University of Chicago

data_processing:
ChIP seq reads were aligned to the Drosophila April 2006 genome using BWA
SPP was used to generate Wig files with scale.by.dataset.size=T
Genome_build: dm3
Supplementary_files_format_and_content: Wig files were generated using SPP with scale.to.dataset.size=T option

organism: Drosophila melanogaster

source_name: Stage 11 embryos

extract_protocol:
Hand-selected embryos were fixed with 1.8% formaldehyde. Lysates were clarified from sonicated nuclei andTF-DNA complexes isolated with an antibody.
Libraries were prepared for sequencing using standard Illumina protocols.

tag: Stage

value: stage 11 embryo


title: MAVER1_day3_vehicle

description:
PRMT5_26_MAVER1_day_3_vehicle_n2_TCCGGAGA_L001
PRMT5_25_MAVER1_day_3_vehicle_n1_ATTACTCG_L001


title: ccr4D_Fep1D_Dip_treated_18C

description: RNA sequencing in CCR4 and FEP1 deleted cells treated with Dip iron chealator at 18C

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). For sequencing librarys from strains grown at 30°C, cultures were grown at 30˚C to OD600~0.5.  For sequencing libraries from strains grown at 18°C, cultures were first grown at 30°C to OD600~0.1-0.2 and then shifted to 18˚C for 3 days.

extract_protocol:
RNA was extracted using the MasterPure™ Yeast RNA Purification Kit (Epicentre)
ScriptSeq v2 RNA-Seq Library Preparation Kit was used according to manufacturer's recommendation.
Libraries were analyzed using the Agilent D1000 TapeStation (Agilent) and sequenced on the Illumina MiSeq platform.

treatment_protocol: Genomic deletion of AGO1, RED1, RRP6, CLR4, CCR4, and genetic mutations in CLR6 and FEP1.  Growth treatment at 30°C or 18°C.

tag: genotype

value: CCR4 and FEP1 deleted


title: Gro_ChIP

description: Gro ChIP from WT stage 11 embryos

value: anti-Groucho antibody (1:200), Negre et al. (2011) Nature, 471:527-531


title: Yan_ChIP

description: Yan ChIP from WT stage 11 embryos

value: Guinea pig anti-Yan antibody (1:500), Webber et al. (2013) Genetics, 193:633-649


title: Yan_Input


title: MINO_day6_vehicle

description:
PRMT5_22_MINO_day_6_vehicle_n2_TCCGCGAA_L008
PRMT5_21_MINO_day_6_vehicle_n1_CGGCTATG_L007

tag: cell line


title: MYC ChIP for Ssn6 in Fep1D

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (ChIP_1200_Jun14 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

source_name: MYC immunoprecipitated DNA

label_protocol: ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). In ChIP experiments performed at 30°C, cultures were grown at 30˚C to OD600~0.5.  In ChIP experiments performed at 18°C, cultures were first grown at 30°C to OD600~0.1-0.2 and then shifted to 18˚C for 3 days.

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 500-1000bp fragments and immunoprecipitated with H3K9dime antibody (Abcam, ab115159), or with GFP antibody (Abcam, ab290). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at room temperature. For Fep-GFP ChIP, cells were further crosslinked with DMA for 45 min at room temperature.

value: log growing cells

source_name: Whole-cell extract DNA


title: GFP ChIP for Feb1

source_name: log. growing cells

value: wildtype

tag: fraction

value: GFP immunoprecipitated DNA

value: Whole-cell extract DNA


title: CCR4 deletion H3K9 dimethyl ChIP 18c

value: CCR4 deletion

value: H3K9me2 immunoprecipitated DNA


title: MINO_day3_200nM_GSK595

description:
PRMT5_20_MINO_day_3_200nm_595_n2_TAATGCGC_L007
PRMT5_19_MINO_day_3_200nm_595_n1_CTGAAGCT_L007

tag: tumor type


title: CCR4 deletion and feb1 mutant H3K9 dimethyl ChIP grown a18C

value: CCR4 deletion and feb1 mutant


title: Wildtype H3K9 dimethyl ChIP grown at 30C

value: Wildtype


title: RNA sequencing followed by 2,2′-Bipyridyl at 18C

tag: growth temperature


title: Wildtype H3K9 dimethyl ChIP grown at 18C


title: MYC ChIP for Ssn6


title: RNA sequencing in clr4 deleted cells at 18C


title: DIP treatment H3K9 dimethyl ChIP grown a18C


title: RNA sequencing in rrp6 deleted cells at 18C


title: REC1_day6_200nM_GSK595

description:
PRMT5_16_REC1_day_6_200nm_595_n2_GAGATTCC_L006
PRMT5_15_REC1_day_6_200nm_595_n1_CGCTCATT_L005

source_name: CellLine: REC-1

tag: treated with

tag: time point

value: Day 6


title: RNA sequencing in clr4 deleted cells at 30C

tag: strain


title: PTO 19T Trametinib 100 nM R2

description:
SAMPLE 22
Patient-derived colorectal cancer organoid line treated with Trametinib.

hyb_protocol: Standard Illumina Hybridisation Protocol Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide). 750 ng of cRNA were hybridized for 17 hr at 58°C on Illumina Human HT-12 V4.0 Microarray.

scan_protocol: Gene Expression Microarrays were scanned using the Illumina iScan-Scanner according to Standard Illumina Scanning Protocol  Part # 11322355 (Whole-Genome Gene Expression Direct Hybridization Assay Guide).

data_processing:
Non-normalized data were generated by the Illumina GenomeStudio software version V2011.1 Raw expression values were processed using the R/Bioconductor package 'lumi' (version 2.30.0). Normalization steps include background correction using the 'rma' method, variance stabilization and quantile normalization.
Non-normalized.txt: Signal values and detection P-values are as provided by the Illumina Genome Studio software.

label: Biotin, Cy3-Streptavidin

source_name: patient-derived colorectal cancer organoid

label_protocol: The Illumina TotalPrep RNA Amplification Kit (Life Technologies) is used to generate single-stranded cRNA from input amounts of 200ng total RNA, Label: Biotin, Cy3-Streptavidin.

growth_protocol: Organoids were cultured in ENAS media.

tag: tissue

tag: treatment

value: Trametinib


title: PTO 19T Trametinib 100 nM + PRI-724 10 μM R1

description:
SAMPLE 23
Patient-derived colorectal cancer organoid line treated with Trametinib and PRI-724.

value: patient-derived colorectal cancer organoid

value: Trametinib and PRI-724


title: AGO1 deletion H3K9 dimethyl ChIP 18c

value: AGO1 deletion


title: RNA sequencing in clr6 deleted cells at 18C


title: REC1_day6_vehicle

description:
PRMT5_14_REC1_day_6_vehicle_n2_TCCGGAGA_L005
PRMT5_13_REC1_day_6_vehicle_n1_ATTACTCG_L005

value: Mantle Cell Lymphoma

value: Vehicle


title: RNA sequencing in cells containing ccr4 deletion and feb1 mutation at 18C


title: PTO 19T Trametinib 100 nM + PRI-724 10 μM R2

description:
SAMPLE 24
Patient-derived colorectal cancer organoid line treated with Trametinib and PRI-724.


title: PTO 19T Trametinib 100 nM R1

description:
SAMPLE 21
Patient-derived colorectal cancer organoid line treated with Trametinib.


title: PTO 19T DMSO R1

description:
SAMPLE 19
Patient-derived colorectal cancer organoid line treated with DMSO.

value: DMSO


title: REC1_day3_200nM_GSK595

description:
PRMT5_12_REC1_day_3_200nm_595_n2_AGCGATAG_L004
PRMT5_11_REC1_day_3_200nm_595_n1_TCTCGCGC_L004

value: Day 3


title: PTO 4T Trametinib 100 nM R3

description:
SAMPLE 18
Patient-derived colorectal cancer organoid line treated with Trametinib.


title: PTO 19T DMSO R2

description:
SAMPLE 20
Patient-derived colorectal cancer organoid line treated with DMSO.


title: RNA sequencing in ago1 deleted cells at 18C


title: Z138_day6_vehicle

description:
PRMT5_6_Z138_day_6_vehicle_n1_GAATTCGT_L002
PRMT5_5_Z138_day_6_vehicle_n2_ATTCAGAA_L002

source_name: CellLine: Z-140


title: MINO_day3_vehicle

description:
PRMT5_18_MINO_day_3_vehicle_n2_GAATTCGT_L006
PRMT5_17_MINO_day_3_vehicle_n1_ATTCAGAA_L006

value: MINO


title: RNA sequencing in WT cells grown at 18C rep1

value: wildtype


title: Z138_day6_200nM_GSK595

description:
PRMT5_8_Z138_day_6_200nm_595_n2_TAATGCGC_L003
PRMT5_7_Z138_day_6_200nm_595_n1_CTGAAGCT_L003

source_name: CellLine: Z-141


title: Z138_day3_200nM_GSK595

description:
PRMT5_4_Z138_day_3_200nm_595_n1_GAGATTCC_L002
PRMT5_3_Z138_day_3_200nm_595_n2_CGCTCATT_L001

source_name: CellLine: Z-139


title: Z138_day3_vehicle

description:
PRMT5_2_Z138_day_3_vehicle_n1_TCCGGAGA_L001
PRMT5_1_Z138_day_3_vehicle_n2_ATTACTCG_L001

source_name: CellLine: Z-138


title: RNA sequencing in WT cells grown at 18C rep2


title: RNA sequencing in CCR4 deleted cells at 18C


title: REC1_day3_vehicle

description:
PRMT5_10_REC1_day_3_vehicle_n2_TCCGCGAA_L004
PRMT5_9_REC1_day_3_vehicle_n1_CGGCTATG_L003


title: PTO 4T Trametinib 100 nM R1

description:
SAMPLE 16
Patient-derived colorectal cancer organoid line treated with Trametinib.


title: PTO 4T DMSO R2

description:
SAMPLE 14
Patient-derived colorectal cancer organoid line treated with DMSO.


title: PTO 4T DMSO R1

description:
SAMPLE 13
Patient-derived colorectal cancer organoid line treated with DMSO.


title: PTO 4T Trametinib 100 nM R2

description:
SAMPLE 17
Patient-derived colorectal cancer organoid line treated with Trametinib.


title: PTO 15T Trametinib 100 nM R3

description:
SAMPLE 12
Patient-derived colorectal cancer organoid line treated with Trametinib.


title: PTO 4T DMSO R3

description:
SAMPLE 15
Patient-derived colorectal cancer organoid line treated with DMSO.


title: PTO 15T DMSO R3

description:
SAMPLE 11
Patient-derived colorectal cancer organoid line treated with DMSO.


title: miRNA_Tg_Wh_17mo_rep3

first: SAYURI

last: HIGAKI

address: 7-430 Morioka-cho

institute: National Center for Geriatrics and Gerotology

description:
Transgenic mouse, whole brain, 17-month, replicate3
MiRNA expression in the whole brain from 17-month-old Tg2576 mouse

data_processing: Images were extracted with Feature Extraction Software 10.7.3.1 (Agilent). For per-chip normalization, miRNA expression data and gene expression data were normalized to the 90th percentiles and median of all values on that chip using GeneSpring GX  (Agilent).

source_name: Transgenic mouse, whole brain, 17-month

extract_protocol: Total RNA including both large and small RNA was extracted from mouse cortices or whole brains using the mirVana PARIS (Ambion, Austin, TX) according to the manufacturer’s instructions. The purity and the quality of RNA samples evaluated by using Nanodrop (Thermo scientific, Hudson, NH) and bioanalyzer (Agilent, Santa Clara, CA) were the required levels for microarray analysis.

value: Whole brain

tag: age

tag: Sex

value: male


title: miRNA_Tg_Wh_17mo_rep2

description:
Transgenic mouse, whole brain, 17-month, replicate2
MiRNA expression in the whole brain from 17-month-old Tg2576 mouse


title: PTO 15T Trametinib 100 nM R1

description:
SAMPLE 8
Patient-derived colorectal cancer organoid line treated with Trametinib.


title: Control-2: miR-NC-2

city: Beijing

first: Heyu

last: Zhang

address: 22 South Zhongguancun Avenue, Haidian District

institute: Peking university school of stomatology

description: SCC-9 cells transfected with miR-NC

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hours at 45℃ on GeneChip Human Gene 1.0.GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: Normalized probeset data were generated with Robust Multi-array Averaging (RMA) method.

source_name: SCC-9 cells transfected with miR-NC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetix protocol from 2 ug total RNA.

growth_protocol: 3*10^5 of SCC-9 cells were seeded in 6-well plate and transfected with mimics (30nM) 24 hours later.

extract_protocol: RNA was extracted by Qiangen RNA Isolation Kit according to the manufacturer' instructions

treatment_protocol: 36 hours after transfection,cells were collected for further total RNA extracion.

value: Tongue squamous cell carcinoma cell line


title: venous anastomosis_day 14_rep4

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

hyb_protocol: Microarrays were hybridized using the Agilent Two-color Gene Expression Hyb/Wash Protocol

scan_protocol: Microarrays were scanned on an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.

data_processing:
Control features and featues labeled non-uniform or population outliers were removed.
Remaining features for each probe were averaged, log2 transformed.
Array data set was median centered to normalize between arrrays, then batch-adjusted using ComBat.

organism: Sus scrofa

source_name: venous anastomosis, day 14

label_protocol: Samples were labeled using the Agilent Two-Color Quick Amp Labeling Protocol

extract_protocol: Total RNA was extracted using the Qiagen RNEasy Micro kit

value: venous anastomosis

tag: biological replicate

tag: time

value: day 14


title: vein segment downstream of anastomosis_day 5_rep4

source_name: vein segment downstream of anastomosis, day 5

value: vein segment downstream of anastomosis

value: day 5


title: venous anastomosis_day 5_rep4

source_name: venous anastomosis, day 5


title: external jugular vein control_day 5_rep4

source_name: external jugular vein control, day 5

value: external jugular vein control


title: PTO 15T DMSO R2

description:
SAMPLE 9
Patient-derived colorectal cancer organoid line treated with DMSO.

value: patient-derived colorectal cancer organoid


title: vein segment downstream of anastomosis_day 5_rep3


title: Mimics-2: miR-585-5p-2

description: SCC-9 cells transfected with miR-585-5p mimics


title: Control-1: miR-NC-1

description: SCC-9 cells transfected with miR-NC


title: PTO 7T DMSO R2

description:
SAMPLE 3
Patient-derived colorectal cancer organoid line treated with DMSO.


title: Mimics-1: miR-585-5p-1

source_name: SCC-9 cells transfected with miR-585-5p mimics


title: external jugular vein control_day 14_rep4

source_name: external jugular vein control, day 14


title: PTO 15T DMSO R1

description:
SAMPLE 7
Patient-derived colorectal cancer organoid line treated with DMSO.


title: vein segment downstream of anastomosis_day 14_rep4

source_name: vein segment downstream of anastomosis, day 14


title: 9_ACSH_AGACO

city: Madison

first: Robert

last: Landick

state: WI

address: 1550 Linden Dr

institute: University of Wisconsin

data_processing:
Transcriptome alignment was performed using Bowtie version 0.12.7 followed by probabilistic counting with RSEM version 1.2.4. Strand specificity of the libraries (generated with dUTP protocol) was accounted for as "--forward-prob 0" RSEM parameter.
RSEM-derived RPKM values were then imported into JMP Genomics (https://www.jmp.com/en_us/home.html) and log2-transformed before for data normalization and testing for differential expression. Pearson correlation between vectors of counts that belong to biological replicates was employed to detect outlier libraries. All the retained libraries show the inter-replicate Pearson correlation of at least 0.95.
Features representing rRNA and tRNA were removed from the matrix before the normalization. The matrix of counts for the entire set of libraries was pre-normalized as a pool using linear scaling to equilibrate the median values across the libraries followed by quantile-normalization via Bioconductor “affy” package.
Genome_build: Reads were mapped to genome sequences assembled as part of this study. For samples collected from strain 2032, sequences are available from GenBank under the following acession numbers: CP023677, CP023678, CP023679, CP023680, CP023681. For samples collected from strain ZM4, sequences are available from GenBank under the following acession numbers: CP023715, CP023716, CP023717, CP023718, CP023719
Supplementary_files_format_and_content: Tab-delimited text file providing normalized plasmid gene FPKM values.

organism: Zymomonas mobilis subsp. mobilis

source_name: bacterial cell culture

extract_protocol:
Cells for RNA isolation were collected using ice-cold ethanol/phenol stop solution and RNA was extracted using hot phenol method. RNA was then DNase treated.  rRNA subtraction was performed using either Ribo-Zero rRNA Removal Kits from Epicentreby using a customized rRNA depletion kit developed together with Life Technologies using species-specific rDNA probes.
Illumina TruSeq Paired-end RNA-seq kit

tag: molecule

value: rRNA-depleted RNA


title: PTO 7T Trametinib 100 nM R3

description:
SAMPLE 6
Patient-derived colorectal cancer organoid line treated with Trametinib.

value: Trametinib


title: venous anastomosis_day 5_rep3


title: miRNA_Tg_Wh_17mo_rep1

city: Obu

description:
Transgenic mouse, whole brain, 17-month, replicate1
MiRNA expression in the whole brain from 17-month-old Tg2576 mouse


title: miRNA_Wt_Wh_17mo_rep3

description:
Wild type mouse, whole brain, 17-month, replicate3
MiRNA expression in the whole brain from 17-month-old wild type mouse

source_name: Wild type mouse, whole brain, 17-month

value: Wild type


title: vein segment downstream of anastomosis_day 14_rep3


title: PTO 7T Trametinib 100 nM R1

description:
SAMPLE 2
Patient-derived colorectal cancer organoid line treated with Trametinib.


title: PTO 7T Trametinib 100 nM R2

description:
SAMPLE 4
Patient-derived colorectal cancer organoid line treated with Trametinib.


title: venous anastomosis_day 14_rep3


title: PTO 7T DMSO R1

description:
SAMPLE 1
Patient-derived colorectal cancer organoid line treated with DMSO.


title: PTO 7T DMSO R3

description:
SAMPLE 5
Patient-derived colorectal cancer organoid line treated with DMSO.


title: PTO 15T Trametinib 100 nM R2

description:
SAMPLE 10
Patient-derived colorectal cancer organoid line treated with Trametinib.


title: 9_ACSH_AGACH


title: 9_ACSH_AGACC


title: miRNA_Wt_Wh_17mo_rep2

description:
Wild type mouse, whole brain, 17-month, replicate2
MiRNA expression in the whole brain from 17-month-old wild type mouse


title: 9_ACSH_AGABW


title: 9_ACSH_AGABT


title: 9_ACSH_AGACN


title: 9_ACSH_AGACG


title: miRNA_Wt_Wh_10mo_rep2

description:
Wild type mouse, whole brain, 10-month, replicate2
MiRNA expression in the whole brain from 10-month-old wild type mouse

source_name: Wild type mouse, whole brain, 10-month


title: 6_ACSH_AGACA


title: miRNA_Tg_Wh_10mo_rep3

description:
Transgenic mouse, whole brain, 10-month, replicate3
MiRNA expression in the whole brain from 10-month-old Tg2576 mouse

source_name: Transgenic mouse, whole brain, 10-month


title: miRNA_Tg_Wh_10mo_rep2

description:
Transgenic mouse, whole brain, 10-month, replicate2
MiRNA expression in the whole brain from 10-month-old Tg2576 mouse


title: miRNA_Wt_Wh_17mo_rep1

description:
Wild type mouse, whole brain, 17-month, replicate1
MiRNA expression in the whole brain from 17-month-old wild type mouse


title: miRNA_Tg_Wh_10mo_rep1

description:
Transgenic mouse, whole brain, 10-month, replicate1
MiRNA expression in the whole brain from 10-month-old Tg2576 mouse


title: 6_ACSH_AGABY


title: 9_ACSH_AGABU


title: miRNA_Wt_Wh_10mo_rep3

description:
Wild type mouse, whole brain, 10-month, replicate3
MiRNA expression in the whole brain from 10-month-old wild type mouse


title: external jugular vein control_day 5_rep3


title: miRNA_Wt_Wh_10mo_rep1

description:
Wild type mouse, whole brain, 10-month, replicate1
MiRNA expression in the whole brain from 10-month-old wild type mouse


title: 6_ACSH_AGABO


title: vein segment downstream of anastomosis_day 14_rep2


title: external jugular vein control_day 14_rep2


title: venous anastomosis_day 5_rep2


title: venous anastomosis_day 14_rep2


title: 6_ACSH_AGABC


title: miRNA_Tg_Co_17mo_rep3

description:
Transgenic mouse, cortex, 17-month, replicate3
MiRNA expression in the brain cortex from 17-month-old Tg2576 mouse

source_name: Transgenic mouse, cortex, 17-month

value: Brain cortex


title: external jugular vein control_day 5_rep2


title: vein segment downstream of anastomosis_day 5_rep2


title: miRNA_Tg_Co_17mo_rep2

description:
Transgenic mouse, cortex, 17-month, replicate2
MiRNA expression in the brain cortex from 17-month-old Tg2576 mouse


title: miRNA_Tg_Co_17mo_rep1

description:
Transgenic mouse, cortex, 17-month, replicate1
MiRNA expression in the brain cortex from 17-month-old Tg2576 mouse


title: external jugular vein control_day 14_rep3


title: 6_ACSH_AGABX


title: venous anastomosis_day 5_rep1


title: 6_ACSH_AGABZ


title: vein segment downstream of anastomosis_day 14_rep1


title: vein segment downstream of anastomosis_day 5_rep1


title: 6_ACSH_AGABN


title: miRNA_Wt_Co_17mo_rep3

description:
Wild type mouse, cortex, 17-month, replicate3
MiRNA expression in the brain cortex from 17-month-old wild type mouse

source_name: Wild type mouse, cortex, 17-month


title: miRNA_Wt_Co_17mo_rep2

description:
Wild type mouse, cortex, 17-month, replicate2
MiRNA expression in the brain cortex from 17-month-old wild type mouse


title: Pnt-GFP_ChIP_yanmutant

city: Chicago

description: GFP ChIP from Pnt-GFP yan mutant stage 11 embryos

source_name: Stage 11 embryos

tag: chip antibody

value: rabbit anti-GFP antibody (1:100), Invitrogen A6455, Lot# 1603336

value: stage 11 embryo


title: miRNA_Wt_Co_17mo_rep1

description:
Wild type mouse, cortex, 17-month, replicate1
MiRNA expression in the brain cortex from 17-month-old wild type mouse


title: 6_ACSH_AGABB


title: miRNA_Tg_Co_10mo_rep3

description:
Transgenic mouse, cortex, 10-month, replicate3
MiRNA expression in the brain cortex from 10-month-old Tg2576 mouse

source_name: Transgenic mouse, cortex, 10-month


title: 6_ACSH_AGAAY


title: Pnt-GFP_ChIP

description: GFP ChIP from Pnt-GFP "WT" stage 11 embryos

tag: Stage


title: Pnt-GFP_Input_yanmutant

tag: genotype


title: miRNA_Tg_Co_10mo_rep2

description:
Transgenic mouse, cortex, 10-month, replicate2
MiRNA expression in the brain cortex from 10-month-old Tg2576 mouse


title: Gro_ChIP_pntmutant

description: Gro ChIP from pnt mutant stage 11 embryos

value: anti-Groucho antibody (1:200), Negre et al. (2011) Nature, 471:527-531

value: pnt -/- (pnt AF397)


title: miRNA_Tg_Co_10mo_rep1

description:
Transgenic mouse, cortex, 10-month, replicate1
MiRNA expression in the brain cortex from 10-month-old Tg2576 mouse


title: Pnt-GFP_Input


title: Gro_Input_pntmutant


title: miRNA_Wt_Co_10mo_rep3

description:
Wild type mouse, cortex, 10-month, replicate3
MiRNA expression in the brain cortex from 10-month-old wild type mouse

source_name: Wild type mouse, cortex, 10-month


title: miRNA_Wt_Co_10mo_rep2

description:
Wild type mouse, cortex, 10-month, replicate2
MiRNA expression in the brain cortex from 10-month-old wild type mouse


title: miRNA_Wt_Co_10mo_rep1

description:
Wild type mouse, cortex, 10-month, replicate1
MiRNA expression in the brain cortex from 10-month-old wild type mouse


title: RNA sequencing in red1 deleted cells at 18C

source_name: log. growing cells

tag: genotype/variation


title: yanE833 rep1

description: Gene expression from yan mutant embryos

hyb_protocol: Agilent Protocol

scan_protocol: GenePix400B was used to scan array slides to generate raw image files at 570PMT, 100% Power, Scan resolution 5µm

data_processing: Scanned images were analysed using the feature extraction software from Agilent using default parameter settings. Processed signals for the probes were used for downstream analysis.

source_name: yanE833 rep1

label_protocol: Total RNA was labeled and hybridized to the microarray using the Quick Amp One-Color labeling kit (Agilent) as described by the manufacturer.

extract_protocol: Total RNA was extracted from stage 11 Drosophila embryos with TRIzol following manufacturer's protocol and cleaned up using the Rneasy Mini Kit.


title: yanE833 rep2

description: Gene expression from yan mutant embryos

source_name: yanE833 rep2


title: w1118 rep3

description: Gene expression from WT embryos


title: venous anastomosis_day 14_rep1

source_name: venous anastomosis, day 14


title: yanE833 rep3

description: Gene expression from yan mutant embryos

source_name: yanE833 rep3


title: w1118 rep2

description: Gene expression from WT embryos


title: external jugular vein control_day 5_rep1

source_name: external jugular vein control, day 5


title: pntAF397 rep1

description: Gene expression from pnt mutant embryos

source_name: pntAF397 rep1


title: Yan_ChIP_pntmutant

description: Yan ChIP from pnt mutant stage 11 embryos

value: Guinea pig anti-Yan antibody (1:500), Webber et al. (2013) Genetics, 193:633-649

value: pnt -/- (pnt Delta88)


title: Yan_Input_pntmutant


title: external jugular vein control_day 14_rep1

source_name: external jugular vein control, day 14


title: pntAF397 rep2

description: Gene expression from pnt mutant embryos

source_name: pntAF397 rep2


title: pntAF397 rep3

description: Gene expression from pnt mutant embryos

source_name: pntAF397 rep3


title: Kidney_12w_S_rep3

first: Hao

last: Tang

address: Capital Medical University Beijing Chaoyang Hospital

department: Department of Urology

institute: Institute of Urology, Capital Medical University.

description: Gene expression after treatment with saline in rat kidney allograft 12 weeks after transplantation

hyb_protocol: 0.6 μg of Cy3-labeled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was gragmented at 60℃ for 30 minutes in a reaction volume of 22.5 μl containing 1× Agilent fragmentation buffer and 2× Agilent blocking agent following the manufacturer's instruction. On completion of the fragmentation reaction, 22.5 μl of 2× Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent LncRNA+mRNA Rat Gene Expression Microarray V1.0 (8x60K) for 17 hours at 65℃ in a rotating Agilent hybridization oven. After hybidization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37℃ GE Wash Buffer 2 (Agilent), then dried immediately by brif centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one colour scan setting for 4×180k array slides (Scan Area 61×21.6 mm ,Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with genespring 13.0 (Agilent). Probe that at least 1 out of 2 samples flagge as Detected were maintained.

source_name: Kidney graft, 12w, Saline, replicate 3

label_protocol: Cyanine-3(Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instrutions, 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 extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556) following the manufacturer's instructions.

treatment_protocol: CAN rat models were established using male Fisher 344 to Lewis rats. Rats in the experimental group(n=3) were treated with AMD3100 (1 mg/kg/day subcutaneously, 0–12 weeks), rats in the control group(n=3) were treated with saline. The kidney grafts were harvested 12 weeks after modeling for microarray analysis.

tag: model

value: chronic allograft nephropathy

tag: backgroud strain

value: Fisher 344 to Lewis

value: kidney graft

tag: gender

value: male


title: Kidney_12w_S_rep2

source_name: Kidney graft, 12w, Saline, replicate 2


title: Kidney_12w_AMD_rep2

description: Gene expression after treatment with AMD3100 in rat kidney allograft 12 weeks after transplantation

source_name: Kidney graft, 12w, AMD3100, replicate 2


title: ChagoK1+MAGOHV5/ ishMAGOHB+Dox_rep1

status: Public on May 07 2018

city: Boston

first: Srinivas

middle: Raghavan

last: Viswanathan

state: Massachusetts

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

description: sleuth.de.results.wald.oe

data_processing:
bcl2fastq v2.18
Transcript levels were quantified with kallisto and differential expression analysis was performed with sleuth
Genome_build: GRCh38 transcriptome (ENSEMBL cDNA, release 87)
Supplementary_files_format_and_content: tab-delimited text files show differential expression ("beta") between knockdown and control conditions in ChagoK1 cells or ChagoK1-MAGOHV5 cells

source_name: ChagoK1 cells

growth_protocol: Cells were cultured in 10% RPMI

extract_protocol:
Total RNA was extracted with RNAEasy kit (Qiagen)
TruSeq Stranded mRNA LT Sample Prep Kit Catalog Numbers: RS-122-2101, RS-122-2102

treatment_protocol: shRNA induction was performed with 100 ng/mL Doxycycline for 5 days.

tag: cell type

value: bronchogenic carcinoma

tag: agent

value: Doxycycline

value: ectopic re-expression of MAGOH-V5


title: ChagoK1+MAGOHV5/ ishMAGOHB+Dox_rep2

description: sleuth.de.results.wald.oe


title: ChagoK1+MAGOHV5/ ishMAGOHB+Dox_rep3

description: sleuth.de.results.wald.oe


title: Kidney_12w_S_rep1

source_name: Kidney graft, 12w, Saline, replicate 1


title: ChagoK1+MAGOHV5/ ishMAGOHB-Dox_rep3

description: sleuth.de.results.wald.oe


title: ChagoK1+MAGOHV5/ ishMAGOHB-Dox_rep2

description: sleuth.de.results.wald.oe


title: Single-cell mRNA sequencing of blastoid cells BLAS2

city: Utrecht

first: Jean-Charles

last: Boisset

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to a sample specific barcode. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases).
Genome_build: mm10
Supplementary_files_format_and_content: *.gene.coutt.csv or *.gene.coutc.csv: Tab separated data file for each sequencing library, listing all genes (rows) and the number of sequenced transcripts for all samples. Column name indicate the cell number of the experiment, separated by a space. The first column lists the official gene symbol followed by the chromosome name, separated by a double underscore.

source_name: Blastoids

extract_protocol:
Cells were sorted directly into 384-well plates containing 0.02 μL of 1:50,000 ERCC Spike-in RNA (Ambion), 0.015 µL of 1% IGEPAL (Sigma), 0.035 µL of RNAse inhibitor (Clonetech), and 0.020 µL of 10 mM dNTPs and water to a total volume of 100 nL, covered with 5µL of mineral oil
RNA was processed using the previously described CEL-seq2 technique (with modifications as described in Muraro et al., Cell Systems, 2016). Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

value: blastoid cells


title: Single-cell mRNA sequencing of trophectoderm stem cells in 3D culture 3DGFP

source_name: Trophectoderm stem cells

value: trophectoderm stem cells in 3D culture


title: Single-cell mRNA sequencing of trophectoderm stem cells in 2D culture TSC2D

value: trophectoderm stem cells in 2D culture


title: Single-cell mRNA sequencing of embryonic stem cells in 3D culture RFP3D

source_name: Embryonic stem cells

value: embryonic stem cells in 3D culture


title: Single-cell mRNA sequencing of blastoid cells BLAS1


title: Single-cell mRNA sequencing of embryonic stem cells in 2D culture ESC2D

value: embryonic stem cells in 2D culture


title: ChagoK1+MAGOHV5/ ishMAGOHB-Dox_rep1

description: sleuth.de.results.wald.oe


title: Kidney_12w_AMD_rep3

source_name: Kidney graft, 12w, AMD3100, replicate 3


title: w1118 rep1

description: Gene expression from WT embryos

value: stage 11 embryo


title: ChagoK1/ ishMAGOHB+Dox_rep3

description: sleuth.de.results.wald.ctl

value: knocking down MAGOHB


title: ChagoK1/ ishMAGOHB+Dox_rep1

description: sleuth.de.results.wald.ctl


title: ChagoK1/ ishMAGOHB-Dox_rep3

description: sleuth.de.results.wald.ctl


title: ChagoK1/ ishMAGOHB+Dox_rep2

description: sleuth.de.results.wald.ctl


title: ChagoK1/ ishMAGOHB-Dox_rep2

description: sleuth.de.results.wald.ctl


title: Smad4_ChIPSeq

city: New York

first: Chengguo

last: Wei

address: 1428 Madison Ave1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The read sequences and quality scores were generated by Illumina data analysis pipeline. Only the reads with at least 90% of cycles having ≥ quality score of 20 were included for data analysis.
The reads were mapped to the genome (UCSC mm9) using BWA alignment method and the differentially-enriched peaks between smad4-/-treated and un-treated samples were called on the alignment files by differential peak calling module in SICER algorithm with the following parameters: window size (bp) 200, gap size (bp) 200 and with FDR of 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: Peaks were generated with MACS14

source_name: forelimb

growth_protocol: Mouse forelimbs at E12.5 and E13.5 were collected in ice-cold PBS and crosslinked immediately in 1% formaldehyde PBS at room temperature for 15 minutes.

extract_protocol:
Lysates were clarified from sonicated nuclei and Smad4-DNA complexes were isolated with antibody.
DNA sample was purified by Qiagen MinElute PCR Purification Kit, and was amplified with an Illumina ChIP-seq DNA Sample Prep Kit (IP-102-1001). DNA libraries were sent for sequencing with an Illumina HiSeq 2500 sequencer.

treatment_protocol: The forelimbs were washed twice with PBS, and then crushed in Lysis Buffer (50 mM HEPES pH8.0, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL-CA630, 0.25% Triton X-100) with 1 mM PMSF and protease inhibitor cocktail (Roche) on a Benchmark BeadBug Homogenizer.

value: forelimb

value: Embryonic day 12.5&13.5

tag: strain

value: Smad4 antibody (04-1033, Millipore)


title: ChagoK1/ ishMAGOHB-Dox_rep1

description: sleuth.de.results.wald.ctl


title: Kidney_12w_AMD_rep1

source_name: Kidney graft, 12w, AMD3100, replicate 1

value: chronic allograft nephropathy

tag: tissue


title: input DNA