title: RA patient, bio rep 2 [110-459.2]

city: Cambridge

first: Ty

last: Thomson

address: 1 Alewife Center

institute: Selventa

hyb_protocol: The fragemented and biotion labeled ss-DNA samples were hybridized in HTA.

scan_protocol: The standard Affymetrix protocol

data_processing: The data was processed using justRMA from Bioconductor with a custom cdf (brainarray) and is in terms of EGIDs.

source_name: rhuetmoid arthritis (RA) patient

label_protocol: The RNA samples were labeled with GeneChip WT Plus Reagent Kit.

extract_protocol: The RNA was isolated using Paxgene Blood mRNA kit from Qiagen and then used Agilent 2100 Bioanalyzer to evaluate the RNA integrity.

treatment_protocol: Whole blood samples were acuqired with constent through a commerical biobank (Biooptions).

tag: subject status

value: rhuetmoid arthritis (RA) patient

tag: gender

value: F

tag: age

value: whole blood


title: timeseries sample33

status: Public on May 01 2018

type: SRA

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

library_source: genomic

data_processing:
Library strategy: DNA-Seq
Mutation identification: In each sequence read, the distance between a fixed sequence at the start and at the end are determined and used to calculate a score, defined as the difference between the measured distance in the read and the expected distance in a wild-type sequence. Insertions and deletions have score >0 and <0, respectively. A point mutation has score=0, but some bases in the sgRNA target site differ from the wild-type sequence. The intact type specifies reads identical to wild-type sequences.   Per time point, the ratio of each type over the total of reads is calculated. We observed only 2 - 6.5% sequence reads in which we could not find a match with the constant parts and we discarded these reads in subsequent analyses. The called point mutations (score = 0) showed a very similar kinetic profile as the intact sequence (wild-type), indicating that they are mostly sequencing errors. We therefore assigned them as intact sequence in the analysis. Insertion and deletion levels at time point t = 0 h were considered as background and subtracted from all time points.  In the double-cut assays, paired end sequencing was performed. The forward and reverse read were matched by the unique sequence ID of a pair of reads. The deletion events were divided into two types: (i) perfectly excised DNA, and (ii) excised DNA with an indel when the deletion was larger than the expected excised product or up to 5 nucleotides smaller.
Supplementary_files_format_and_content: txt files with barcode, indel type, indel score, sequence; sum txt files with indel type, indel score of pool

molecule: genomic DNA

organism: Homo sapiens

source_name: K562 + DD-Cas9

growth_protocol: We established K562#17, which is a clonal cell line of the female K562 cells (American Type Culture Collection) stably expressing DD-Cas9. K562#17 cells were cultured in RPMI 1640 (Life Technologies) supplemented with 10% fetal bovine serum (FBS, HyClone®), 1% penicillin/streptomycin.

extract_protocol:
Cells were collected by centrifugation (300xg, 5 min) and the genomic DNA was isolated using the Isolate II Genomic DNA Kit (Bioline).
PCR was performed in two steps; PCR1 with ~100 ng genomic DNA and site specific barcoded primers. PCR2 used 2 µL of each PCR1 product with Illumina PCR Index Primers Sequences 1–12. Each sample was generated with a unique combination of a barcode and index. Both PCR reactions were carried out with 25 µL MyTaq Red mix (Bioline), 4 µM of each primer and 50 µL final volume in a 96 well plate. PCR conditions were 1 min at 95 ˚C, followed by 15 sec at 95 ˚C, 15 sec at 58 ˚C and 1 min at 72 ˚C (15x). 20 µL of 8 samples were pooled and 100 µL was loaded onto a 1% agarose gel. PCR product was cut from gel to remove the primer dimers and cleaned with PCR Isolate II PCR and Gel Kit (Bioline).

treatment_protocol: For transient transfection, 6x106 K562 cells were resuspended in self-made transfection buffer (100 mM KH2PO4, 15 mM NaHCO3, 12 mM MgCl2, 8 mM ATP, 2 mM glucose (pH 7.4)) (Hendel et al., 2014). After addition of 3.0 µg plasmid DNA, the cells were electroporated in an Amaxa 2D Nucleofector using program T-016. DD-Cas9 was induced with a final concentration of 500 nM Shield-1 (Aobious).  For kinetics experiments, 18x106 cells were transfected and divided over 12-well plates, one well for each time point and each well carrying 1x106 cells. Cas9 was activated 24h after nucleofection and cells were collected at the indicated time points after Cas9 induction. As controls, cells without Shield-1 were collected at various time points. DNA-PKcs inhibitor NU7441 (Cayman) (final concentration 1 µM) or DMSO (control) was added to K562#17 at the same time when the cells were supplemented with Shield-1 to induce DD-Cas9. 10 Gy of IR was administered by Cs source Gammacell®40 Exactor (Best Theratronics).

tag: cell type

tag: strain

value: K562#17 clone with DD-Cas9 stably integrated

tag: sgrna target site

value: sgRNA LBR2

tag: time point

tag: time series + conditions

tag: conditions

value: +shield +NU7441


title: timeseries sample30

value: +shield


title: timeseries sample31


title: RA patient, bio rep 2 [110-461.2]

type: RNA

state: MA

country: USA

label: biotin

molecule: total RNA


title: RA patient, bio rep 2 [110-464.2]


title: timeseries sample28


title: RA patient, bio rep 2 [110-458.2]

value: M


title: timeseries sample27


title: timeseries sample29


title: RA patient, bio rep 2 [110-457.2]


title: RA patient, bio rep 2 [110-455.2]


title: SCC9_cisplatin-resistant_rep3

city: Guangzhou

first: Bodu

last: Liu

state: State...

address: School of Life Sciences, Sun Yat-sen U East Camp, High. Edu. Meg. Cntr.

country: China

institute: Sun Yat-sen University

description: Non

hyb_protocol: Labeled cDNA was hybridized to Arraystar Human lncRNA array version 1 lncRNA expression microarray in NimbleGen Hybridization System.

scan_protocol: After hybridization and washing, the processed slides were scanned with the Axon GenePix 4000B microarray scanner.

data_processing: Raw data were extracted as paired files by NimbleScan software (version 2.5), which offers quantile normalization and background correction. Files of probe level (*_norm_RMA.pair) and gene summary (*_RMA.calls)  were produced

source_name: Cisplatin-resistant SCC9 cells

label_protocol: Double-stranded cDNA was Cy3 labeled.

growth_protocol: SCC9 and SCC9-res cells were cultured in DMEM-F12 (Gibco) supplemented with 10% foetal bovine serum and 400 ng/ml hydrocortisone (Sigma).

extract_protocol: RNA were extracted by Trizol Reagent (Life Technologies) according to manufacturer's instructions.

treatment_protocol: SCC9 cells were treated with cisplatin (Sigma, St Louis, MO, USA) with concentrations that gradually increased from 10^-7 M to 10^-5 M.

tag: cisplatin-resistance

value: Yes


title: timeseries sample26

value: -shield


title: Healthy [111-124]

source_name: healty control

value: healty control


title: SCC9_cisplatin-resistant_rep2

description: Non


title: Healthy [111-122]


title: SCC9_parental_rep3

description: Non

source_name: Parental SCC9 cells

value: No


title: Healthy [111-123]


title: timeseries sample24


title: RA patient [110-466]


title: RA patient, bio rep 1 [110-464.1]


title: timeseries sample25


title: timeseries sample23


title: timeseries sample22


title: SCC9_cisplatin-resistant_rep1

description: Non


title: Healthy [111-121]


title: Healthy [111-120]


title: timeseries sample21


title: RA patient [110-462]


title: Cdx1-/- SIEC 2

city: Freiburg

first: Ana

last: Izcue

address: Am Stübeweg 51

country: Germany

institute: Max Planck Institut of Immunobiology and Epigenetics

description:
Gene expression in mouse Cdx1-/- intestinal epithelial cells
SAMPLE 8

hyb_protocol: Performed by Milteny Biotech following standard procedures

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. Data show normalized signal intensity by dividing the intensity values by their median

organism: Mus musculus

source_name: Small intestine

extract_protocol: RNA extraction was performed by Miltenyi Biotech following standard procedures

tag: strain background

value: Mixed C57BL/6, 129

tag: tissue

value: Small intestine

value: small intestine epithelial cells

tag: genotype

tag: sorting gate

value: Epcam+ CD45- Fluorogold-


title: RA patient [110-463]


title: Cdx1-/- mTEC 1

description:
Gene expression in mouse Cdx1-/- thymic epithelial cells
SAMPLE 4

scan_protocol: Performed by Milteny Biotech following standard procedures

source_name: Thymus

value: Thymus

value: medullary thymic epithelial cells

value: Epcam+ UEA1+ CD45- Fluorogold- CD80hi MHCIIhi


title: Cdx1-/- mTEC 2

description:
Gene expression in mouse Cdx1-/- thymic epithelial cells
SAMPLE 5

label_protocol: Performed by Milteny Biotech following standard procedures


title: timeseries sample19


title: Cdx1+/+ SIEC 1

description:
Gene expression in mouse Cdx1+/+ intestinal epithelial cells
SAMPLE 7


title: SCC9_parental_rep1

description: Non


title: timeseries sample20


title: RA patient [110-460]

value: rhuetmoid arthritis (RA) patient

value: whole blood


title: RA patient, bio rep 1 [110-461.1]

value: F


title: Cdx1+/+ mTEC 3

description:
Gene expression in mouse Cdx1+/+ thymic epithelial cells
SAMPLE 3


title: SCC9_parental_rep2

description: Non


title: RA patient, bio rep 1 [110-459.1]


title: Cdx1-/- mTEC 3

description:
Gene expression in mouse Cdx1-/- thymic epithelial cells
SAMPLE 6


title: RA patient, bio rep 1 [110-458.1]


title: timeseries sample18

value: K562#17 clone with DD-Cas9 stably integrated

value: sgRNA LBR2

value: +shield +NU7441


title: Cdx1+/+ mTEC 2

description:
Gene expression in mouse Cdx1+/+ thymic epithelial cells
SAMPLE 2


title: RA patient, bio rep 1 [110-457.1]


title: Cdx1+/+ mTEC 1

description:
Gene expression in mouse Cdx1+/+ thymic epithelial cells
SAMPLE 1


title: RA patient, bio rep 1 [110-455.1]


title: Crc_Rif C

city: Boston

first: Simon

middle: L

last: Dove

address: 300 Longwood Ave

department: Division of Infectious Diseases

institute: Boston Children's Hospital and Harvard Medical School

description:
Immunoprecipitated DNA was not size-selected during library construction
Crc_Rif_AllPeaks.bed
R1  raw file checksum: ed030480c378b8729d305cac2fd66518
R2  raw file checksum: ffd7f70d8747f16c41f973ac89b00877

data_processing:
Paired ChIP-Seq reads corresponding to fragment sizes of either 200 or 400 bp (see SAMPLES section) were aligned to the PAO1 genome using bowtie2 (version 2.3.1) allowing 1 mismatch in a 28 bp seed region with no discordant or unpaired alignments.
The program samtools (version 1.3.1) was used to extract read 1 from each mapped read pair.
For Hfq experiments (samples 1-4): Peaks were identified using QuEST (version 2.4; Valouev et al., 2008) using control data from stationary-phase wild-type cells (sample 5) with the following settings: KDE = 50,  seeding fold enrichment = 1.25, extension fold enrichment = 1.5, ChIP to background fold enrichment = 2
For Crc experiments (samples 6 and 7): Peaks were identified using QuEST (version 2.4; Valouev et al., 2008) using control data from log-phase wild-type cells (sample 8) with the following settings: KDE = 30,  seeding fold enrichment = 1.25, extension fold enrichment = 1.5, ChIP to background fold enrichment = 2; only peaks with greater than 3x enrichment were considered.
Bed files for each experimental replicate were created by QuEST and the final processed bed files were generated by identifying the largest overlapping peak region which statisfy the following conditions: (1) peak regions must have a positive peak shift, (2) peak regions must have a positive strand correlation, (3) peak regions must have a q-value of less than 0.01, and (4) peak regions must be shared by two or more experimental replicates.
Genome_build: NC_002516.2
Supplementary_files_format_and_content: wig files were generated using QuEST; Scores represent normalized smoothed read density
Supplementary_files_format_and_content: bed intervals reflect regions with significant (as defined above) enrichment of reads in the experimental condition in comparision to the mock control condition.

organism: Pseudomonas aeruginosa PAO1

source_name: Bacterial cells grown to OD 0.5

growth_protocol: Bacterial cultures were started from single colonies, grown overnight, and back-diluted in LB media

extract_protocol:
DNA associated with proteins of interest were immunoprecipitated from lysates with anti-VSVG monocolonal antibody
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following manufacturer’s instructions, bead-based size selection of DNA fragments was used in a subset of samples, see SAMPLES section

tag: optical density

value: Crc-VSVG

tag: treatment protocol

value: sample taken 30 minutes after treatment with 150 ug/mL rifampicin

tag: chip antibody

value: Agarose-immobilized anti-VSVG antibody (Sigma-Aldrich, catalog number A1970, monoclonal antibody clone P5D4)


title: Crc_Rif A

description:
Immunoprecipitated DNA was not size-selected during library construction
Crc_Rif_AllPeaks.bed
R1  raw file checksum: 30543b9d6b81af2dfeff9f6ae3f747fd
R2  raw file checksum: c119b0033871bbb92ec436a5262afa1c


title: SHH-N O9-1 cranial neural crest cells, biological rep3

city: Madison

first: Joshua

last: Everson

state: WI

address: 2015 Linden Drive, Rm 3217

department: Comparative Biosciences

institute: UW-Madison

description: Gene expression data from mouse cranial neural crest cells (O9-1) PMID: 22889333 + SHH-N and collected 48 hrs post-treatment

hyb_protocol: The end-terminus biotin labeled cDNA is hybridized to an AFX Gene ST 2.0 GeneChip for 16 hours at 45C.  Following hybridization, the GeneChip is washed and stained with Streptavidin-Phycoerythrin (SAPE) on the AFX Fluidics450 Station.

scan_protocol: GeneChips were scanned at 570 nm on a GC3000 G7 scanner

data_processing: Fluorescent signals corresponding to hybridization intensities were analyzed with the Affymetrix GCOS software, and Affymetrix Transcriptome Analysis Console v.2.0 was used to analyze relative expression.

source_name: mouse immortalized cranial neural crest cells exposed to SHH-N

label_protocol: 100-500ng of total RNA was input into the first strand cDNA synthesis reaction that uses a reverse transcription priming method that specifically primes non-ribosomal RNA, including both poly(A) and non-poly(A) mRNA, which is then followed immediately by second strand cDNA synthesis.  The 2nd cDNA is purified with paramagnetic beads and used for input into an 8 hour IVT reaction creating aRNA.  The aRNA is then used for input into the 2nd cycle cDNA synthesis, the ds cDNA is purified by paramagnetic particles, and finally end-terminus labeled with biotin.

growth_protocol: Immortalized 09-1 cranial neural crest cells were cultured as described by Ishii and colleagues (PMID: 22889333) with the following modifications: 0.25% trypsin in 0.5 mM EDTA was used for passaging at a subculture ratio of 1:3 to 1:10

extract_protocol: 48 hrs after SHH treatment, cells were lysed and total RNA (DNase-treated) was collected per the GE Illustra RNAspin kits (GE Healthcare) general protocol for a cell monolayer.

treatment_protocol: Cells were allowed to attach for 24 hrs and media were replaced with DMEM containing 1% FBS ± SHH-N peptide (R&D Systems, Minneapolis, MN) at 0.4 μg/mL.

value: Mouse immortalized cranial neural crest cells (O9-1)

tag: treatment

value: SHH-N


title: SHH-N O9-1 cranial neural crest cells, biological rep4


title: Crc_Rif B

description:
Immunoprecipitated DNA was not size-selected during library construction
Crc_Rif_AllPeaks.bed
R1  raw file checksum: e00d6c0754aba38ff31f18a4f464400e
R2  raw file checksum: 0cc4acaadf303d9ba943bc7ef6be3123


title: Crc C

description:
Immunoprecipitated DNA was not size-selected during library construction
Crc_AllPeaks.bed
R1  raw file checksum: 7425f7dc87f695d69fc01a7aa9ade8d0
R2  raw file checksum: 66b82103553a46352dd6420fa05b46b1

value: sample taken prior to rifampicin treatment


title: timeseries sample12

value: +shield


title: Crc B

description:
Immunoprecipitated DNA was not size-selected during library construction
Crc_AllPeaks.bed
R1  raw file checksum: e4770984daced6f197df2f4f5e14264a
R2  raw file checksum: 4ce87d5457d074e08a8296c974aecf30


title: timeseries sample15


title: timeseries sample13


title: timeseries sample14

value: -shield


title: SHH-N O9-1 cranial neural crest cells, biological rep2


title: PAO1_stationary

description: Immunoprecipitated DNA was size-selected using AMPure beads during library construction

source_name: Bacterial cells grown to OD 2.0

value: wild-type

value: no rifampicin treatment


title: Crc A

description:
Immunoprecipitated DNA was not size-selected during library construction
Crc_AllPeaks.bed
R1  raw file checksum: 17ea9667aff3dfab5de588088e69ffcf
R2  raw file checksum: 7c6526a987e37560aae6bb5ad5900dc2


title: timeseries sample17


title: SHH-N O9-1 cranial neural crest cells, biological rep1


title: timeseries sample10


title: timeseries sample16


title: timeseries sample11


title: PAO1_midlog

description: Immunoprecipitated DNA was not size-selected during library construction


title: Hfq_stationary_Rif C

description:
Immunoprecipitated DNA was size-selected using AMPure beads during library construction
Hfq_stat_Rif_AllPeaks.bed
R1  raw file checksum: 2ece84e95c64940eaedffd25437c3ee2
R2  raw file checksum: 2aed6b5f4bd7e09a6114770eee035ffe

value: Hfq-VSVG FRT


title: Vehicle O9-1 cranial neural crest cells, biological rep3

description: Gene expression data from mouse cranial neural crest cells (O9-1) PMID: 22889333 + Vehicle and collected 48 hrs post-treatment

source_name: mouse immortalized cranial neural crest cells exposed to vehicle

value: control


title: timeseries sample9


title: Vehicle O9-1 cranial neural crest cells, biological rep4


title: Vehicle O9-1 cranial neural crest cells, biological rep1


title: Vehicle O9-1 cranial neural crest cells, biological rep2


title: Control Replicate 3

city: Downers Grove

first: Michael

last: Ebeid

state: IL

address: 555 31st St, Anatomy

department: Anatomy

institute: Midwestern University

description: RMA expression value derived from Expression Console software; gene-level analysis

hyb_protocol: Hybridization, washing and staining was performed at University of Nebraska Medical Center Sequencing core facility using suggested protocols and reagents recommended for GeneChip Mouse Gene 2.0 ST arrays (Affymetrix ) and the Affymetrix Gene Chip system. All the arrays passed the quality control metrics for hybridization kinetics, background and specificity as outlined by Affymetrix for the 2.0 ST arrays.

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

data_processing: Raw data were processed with Expression Console Software using RMA.

source_name: P16 cochlea

label_protocol: 200 ng of total RNA was reverse transcribed and processed per manufacturers recommendations using the WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA).

growth_protocol: The whole encapsulated cochlea was used and the two cochleae from the same animal were pooled as one biological replicate.

extract_protocol: Following rotor-stator homogenization of tissue, total RNA including microRNA was purified using the mirVana miRNA Isolation Kit as suggested by the manufacturer (Life Technologies).

tag: postnatal age

value: cochlea


title: Hfq_stationary_Rif B

description:
Immunoprecipitated DNA was size-selected using AMPure beads during library construction
Hfq_stat_Rif_AllPeaks.bed
R1  raw file checksum: 092904c9be1c04da415ce49b5a1460ab
R2  raw file checksum: 4e28f16e90f2f46bdf5093c617d6ad30


title: timeseries sample8


title: Control Replicate 4


title: SW480 2-D4

city: Bethesda

first: Darawalee

last: Wangsa

state: MD

address: 50 South Drive, Bldg 50, Rm 1408

institute: National Cancer Institute

hyb_protocol: Each barcode is mixed with the sample, forming a multiplexed CodeSet.

scan_protocol: Scan was run on the NanoString GEN2 nCounter Analysis System

data_processing: Data from all runs were imported into nSolver version 2.0 (NanoString Technologies), matched to corresponding Reporter Library File (RLF), and subjected to quality control using the software quality metrics with default cutoff criteria.

source_name: Epithelial adherent cell line from Dukes' type B, colorectal adenocarcinoma

label_protocol: 100ng of RNA was used for each sample

growth_protocol: SW480 cells and all subsequent clones were grown in RPMI-1640 media supplemented in 10% FBS, antibiotics and glutamine at 37°C in 5% CO2. HT-29 cells and all subsequent clones were grown in McCoy's media supplemented in 10% FBS, antibiotics and glutamine at 37°C in 5% CO2.

extract_protocol: RNA was extracted using the Rneasy mini kit (Qiagen, Hilden, Germany)

treatment_protocol: Single cells were generated using FACS into 96-well plates based on size differences (i.e.forward scatter)

tag: clone

value: Male epithelial cells, colorectal adenocarcinoma


title: SW480 2-A9

tag: cell type


title: SW480 2-D2


title: timeseries sample7

tag: strain

value: K562#17 clone with DD-Cas9 stably integrated


title: Hfq_stationary_Rif A

description:
Immunoprecipitated DNA was size-selected using AMPure beads during library construction
Hfq_stat_Rif_AllPeaks.bed
R1  raw file checksum: 9a44a73c0adb1ef52a6c220dee0b0ddb
R2  raw file checksum: 37e04d13b8c40ccde6b3f9ff9ec5f32e


title: SW480 2-C8


title: timeseries sample6

tag: sgrna target site

value: sgRNA LBR2


title: Hfq_stationary C

description:
Immunoprecipitated DNA was size-selected using AMPure beads during library construction
Hfq_stat_AllPeaks.bed
R1  raw file checksum: 063b109c7c444ccaedf4c97a75e08340
R2  raw file checksum: 96bdd41349ca7f5dcecc08c29ce1d8ba


title: Hfq_stationary B

description:
Immunoprecipitated DNA was size-selected using AMPure beads during library construction
Hfq_stat_AllPeaks.bed
R1  raw file checksum: 715e5e6d61836d6e357b178b07eeefbe
R2  raw file checksum: c97c909dd14eabbff48686196ff0c3ef


title: Hfq_stationary A

description:
Immunoprecipitated DNA was size-selected using AMPure beads during library construction
Hfq_stat_AllPeaks.bed
R1  raw file checksum: 4526357175efff424f7ce84988d670f5
R2  raw file checksum: e15e2129e42ad3ad7169458fc34de203


title: timeseries sample4

tag: time point


title: SW480 2-H7


title: SW480 2-G4


title: timeseries sample5

tag: time series + conditions


title: Hfq_midlog_Rif C

description:
Immunoprecipitated DNA was size-selected using AMPure beads during library construction
Hfq_midlog_Rif_AllPeaks.bed
R1  raw file checksum: f5efaed3f894f35c24a3a3b29f93962a
R2  raw file checksum: fb89c6d32e351d4df13660ff90633369


title: SW480 2-F11


title: Control Replicate 2


title: timeseries sample3

tag: conditions


title: miR-183/96 KO Replicate 4


title: miR-183/96 KO Replicate 1


title: Hfq_midlog_Rif B

description:
Immunoprecipitated DNA was size-selected using AMPure beads during library construction
Hfq_midlog_Rif_AllPeaks.bed
R1  raw file checksum: d44526816d51e38b78631003dd6994ca
R2  raw file checksum: e7c8e33eac83012afc7f947db26c36e6


title: SW480 2-G6


title: Control Replicate 1


title: SW480 1-A5


title: timeseries sample2


title: timeseries sample1


title: SW480 2-B9


title: Hfq_midlog_Rif A

description:
Immunoprecipitated DNA was size-selected using AMPure beads during library construction
Hfq_midlog_Rif_AllPeaks.bed
R1  raw file checksum: e09a986c2e630130b1849d4bf9a94c06
R2  raw file checksum: 49a839711b85967a434a94f0a99ae2a6


title: Hfq_midlog B

description:
Immunoprecipitated DNA was size-selected using AMPure beads during library construction
Hfq_midlog_AllPeaks.bed
R1  raw file checksum: 68769ce71ff4387c9be7b01c1183a591
R2  raw file checksum: 1772db35bdf79d1eef8248016eb8d9cb


title: Hfq_midlog A

description:
Immunoprecipitated DNA was size-selected using AMPure beads during library construction
Hfq_midlog_AllPeaks.bed
R1  raw file checksum: 9fc736d9208d61e52393142fcd1dda62
R2  raw file checksum: e459c0f38b7d1d5c3a8729d2f155749c


title: Hfq_midlog C

description:
Immunoprecipitated DNA was size-selected using AMPure beads during library construction
Hfq_midlog_AllPeaks.bed
R1  raw file checksum: be29cec48dfe5526ff4b6946fd15374b
R2  raw file checksum: b62abf5fc9f35bb824684fa5b1159601


title: SW480 Parental

value: SW480 Parental


title: SW480 2-B4


title: HT29 Parental

source_name: Epithelial adherent cell line, colorectal adenocarcinoma

value: HT29 Parental

value: Female epithelial cells, colorectal adenocarcinoma


title: HT29 2-B1


title: miR-183/96 KO Replicate 3


title: ALK002

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: Gene expression primary mouse tumor

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Affymetrix Titan scanner

data_processing: RMA summarization via Partek Genomics 6.6 (St Louis, MO USA)

label: Biotin

source_name: ALK TH-MYCN NB tumor model

label_protocol: cDNA was prepared using standard Affymetrix kit

extract_protocol: Trizol was used to extract total RNA

tag: genotype/variation

value: Alk mutant; TH-MYCN; Stat6-/-

value: sternocleidomastoid muscle


title: HT29 2-G5


title: ALK001

description: Gene expression primary mouse tumor

tag: strain background


title: HT29 2-E4


title: HT29 2-E1


title: Islet_10_BL001_Rep2

city: Seville

first: Benoit

middle: Raymond

last: Gauthier

state: Seville

address: Americo Vespucio Avenue

department: Stem Cells

country: Spain

institute: Andalusian Center for Molecular Biology and Regenerative Medicine (CABIMER)

description: The mouse presented healthy appearance

hyb_protocol: Following fragmentation, 3.5 ug of single-stranded cDNA were hybridized for 16 hr at 45C on GeneChip® Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The .CEL files were generated using Affymetrix GCOS software and further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis were performed using the limma package from R/Bioconductor project.

source_name: Primary isolated islets treated with 10 uM BL001

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 500ng total RNA Labeling Protocol (GeneChip ® WT Pico Reagent Kit, Manual Target Preparation for GeneChip ® Whole Transcript (WT) Expression Arrays Rev.1, ( (c) 2015 Affymetrix Inc.)

growth_protocol: Standard feeding

extract_protocol: RNA from approximatelly 200 islets per replicate was isolated using the Single Cell Norgen kit according to the manufacturer´s protocol

treatment_protocol: Animals were maintained under standard conditions

tag: age

value: 2 month old

tag: tissue

value: Primary isolated islets


title: HT29 2-D8


title: ALK003

description: Gene expression primary mouse tumor


title: Islet_10_BL001_Rep3

description: The mouse presented healthy appearance


title: HT29 2-C6


title: HUVECs_24h_Normoxia_Series4

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

description: Gene expression data from untreated HUVECs

hyb_protocol: Affymetrix GeneChip® Human PrimeView arrays were washed, stained and scanned according to the protocol described in GeneChip® 3` IVT Express Labeling Assay User Manual (Fluidics Protocol FS450_0002)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

source_name: HUVECs, untreated, Normoxia

label_protocol: 250ng of total RNA were amplified and labeled using the Affymetrix 3` IVT Express Kit (Catalog Number 901229, Affymetrix, Santa Clara, CA)

growth_protocol: HUVECs were cultured on 1% gelatine coated cell culture dishes in endothelial cell growth medium-2. HUVECs of passage 3 to 5 were used for experiments.

extract_protocol: For the extraction of RNA, cells were incubated with RNAlater (Ambion) for 1 min, washed with DEPC-treated water and lysed with QIAzol (Qiagen). RNA was extracted using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: HUVECs were grown to density, starved overnight and treated with VEGF-A (30 ng/ml) or recombinant CYTL1 (20 ng/ml) for the indicated time points, for hypoxic conditions cells were preincubated for 4h at 2% O2 before treatment

value: Human Umbilical Vein Endothelial Cells


title: Islet_1_BL001_Rep1

description: The mouse presented healthy appearance

source_name: Primary isolated islets treated with 1 uM BL001


title: NB-39-nu_EZH2sh_10475_day11_rep3

city: Kitaadachi-gun

first: Hisanori

last: Takenobu

state: Saitama

address: 818, Komuro, Ina-machi

department: Research Institute for Clinical Oncology

country: Japan

institute: Saitama Cancer Center

hyb_protocol: One-color mixes of labelled cRNA pairs were hybridized to8x60K whole human genome oligonucleotide microarray (Agilent G4851B, grid ID 039494), at 65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit.

scan_protocol: Purified labeled total RNA was hybridized to the expression microarray. Hybridization, the scanning of microarrays (SureScan Microarray Scanner), and data extraction from scanned images were conducted according to Agilent protocol version 6.9.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters to obtain background-subtracted and spatially detrended processed signal intensities.

source_name: human neuroblastoma cell line NB-39-nu, infected EZH2 RNA (TRCN0000010475) bearing lentivirus, 11 days after infection

label_protocol: Two hundred nanograms of total RNA was labeled with Cyanine3 using a Low Input Quick-Amp Labeling Kit (one color, Agilent Technologies) according to the manufacturer’s instructions.

growth_protocol: Human NB cell line NB-39-nu were cultured in RPMI1640 (Wako) supplemented with 10% heat-inactivated fetal bovine serum (Invitrogen) and 50 μg/ml penicillin/streptomycin (Sigma–Aldrich) in an incubator with humidified air at 37 °C with 5% CO2

extract_protocol: Total cellular RNA for preparing RT–PCR templates was extracted using ISOGEN II (Nippon Gene KK). RNA was extracted at two time points, 8 and 11 days after shEZH2-expressing lentiviral infection.

treatment_protocol: pLKO.1 control, EZH2 sh (TRCN0000018365) or  EZH2 sh (TRCN0000010475) vectors shRNA plasmids, including TRCN0000018365 (shEZH2-1), TRCN0000010475 (shEZH2-2), and the pLKO.1-puro control vector (shCont), were purchased from the MISSION(TM) shRNA Library (Sigma-Aldrich). In the preparation of the shRNA/lentivirus, the packaging cell line HEK 293T (4 × 106) was plated on a 10-cm dish and co-transfected the next day with 1.5 μg of each of the shRNA plasmids and 2.0 μg of the packaging vectors (Sigma-Aldrich) using the Fugene 6 transfection reagent (Roche Applied Science) according to the manufacturer’s protocol. Medium was changed the next day and cells were cultured for another 24 h. Conditioned medium was collected and cleared of debris by filtering through a filter with 0.45-μm pores.  Thereafter, 1 × 105 NB cells were seeded on each well of a 6-well plate, and infected by lentiviral-conditioned media with 4 μg/mL polybrene.

tag: cell line

value: neuroblastoma

tag: infected with

tag: days after infection


title: NB-39-nu_EZH2sh_18365_day11_rep3

source_name: human neuroblastoma cell line NB-39-nu, infected EZH2 RNA (TRCN0000018365) bearing lentivirus, 11 days after infection


title: Islet_1_BL001_Rep2

description: The mouse presented healthy appearance


title: HUVECs_VEGF_1h_Normoxia_Series4

description: Gene expression data from VEGF-treated HUVECs

source_name: HUVECs, treated with VEGF for 1h, Normoxia


title: NB-39-nu_EZH2sh_18365_day11_rep1

value: infected EZH2 RNA (TRCN0000018365) bearing lentivirus


title: NB-39-nu_EZH2sh_10475_day11_rep1

value: infected EZH2 RNA (TRCN0000010475) bearing lentivirus


title: Islet_1_BL001_Rep3

description: The mouse presented healthy appearance


title: NB-39-nu_EZH2sh_10475_day11_rep2


title: Islet_01_BL001_Rep3

description: The mouse presented healthy appearance

source_name: Primary isolated islets treated with 0.1 uM BL001


title: HT29 2-E2


title: HUVECs_Cytl1_24h_Hypoxia_Series4

description: Gene expression data from Cytl1-treated HUVECs

source_name: HUVECs, treated with Cytl1 for 24h, Hypoxia


title: HUVECs_Cytl1_16h_Hypoxia_Series4

source_name: HUVECs, treated with Cytl1 for 16h, Normoxia


title: HUVECs_Cytl1_1h_Normoxia_Series4

source_name: HUVECs, treated with Cytl1 for 1h, Normoxia


title: NB-39-nu_pLKO.1_day11_rep3

source_name: human neuroblastoma cell line NB-39-nu, infected pLKO.1 bearing lentivirus, 11 days after infection

value: pLKO.1 bearing lentivirus


title: NB-39-nu_EZH2sh_18365_day11_rep2


title: Islet_01_BL001_Rep2

description: The mouse presented healthy appearance


title: Islet_01_BL001_Rep1

description: The mouse presented healthy appearance


title: HUVECs_24h_Hypoxia_Series4

source_name: HUVECs, untreated, Hypoxia


title: HT29 2-G1


title: HT29 2-C12


title: HUVECs_0h_Normoxia_Series4


title: miR-183/96 KO Replicate 2

tag: genotype


title: Islet_10_BL001_Rep1

description: The mouse presented healthy appearance


title: Islet_DMSO_Control_Rep3

description: The mouse presented healthy appearance

source_name: Primary isolated islets treated with DMSO/control


title: HT29 1-A4


title: NB-39-nu_pLKO.1_day11_rep2


title: HT29 2-D3


title: 6_3360Aarhus_A549-siNrf2-3

city: aarhus

first: Yonglun

last: Luo

address: Wilhelm Meyers Allé 4

country: Denmark

institute: Aarhus University

library_source: transcriptomic

data_processing:
RNA-sequencing performed by Active Motif generates 100-nt sequence reads using Illumina HiSeq 4000. The reads are mapped to the genome using the STAR algorithm with default settings. Alignment information for each read is stored in the BAM format.
Only read pairs that have both ends aligned were counted. Read pairs that have their two ends mapping to different chromosomes or mapping to same chromosome but on different strands were discarded. We also require that at least 25 bp overlapping bases in a fragment for read assignment.
The gene annotations we used were obtained from Subread package. These annotations were originally from NCBI RefSeq database and then adapted by merging overlapping exons from the same gene to form a set of disjoint exons for each gene. Genes with the same Entrez gene identifiers were also merged into one gene.
After obtaining the gene table containing the fragment counts of genes, we performed differential analysis to identify statistically significant differential genes using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: A tab-delimited text file include RPKM values for all six samples and DESeq2 comparison results are included. The condition.DESeq2_results_allgenes.csv file includes normalized fragment counts for each sample and normalized sum of fragment counts for each group of samples under comparison.

growth_protocol: Human lung adenocarcinoma epithelial A549 cells are cultured in DMEM (Lonza) supplemented with 10% heat inactivated fetal calf serum, 200 IU.mL-1 penicillin, 100 μg.mL-1 streptomycin and 600 μg.mL-1 glutamine .

extract_protocol:
RNA was extracted using the High Pure RNA Isolation kit (Roche) and RNA quality was  assessed by Nanodrop spectrometry (Thermo Fisher).
library preparation, RNAseq and bioinformatics analysis was performed at Active Motif  (Carlsbad, California, USA).

treatment_protocol: One million of A549 cells silenced or not for Nrf2 using siRNA were snap-frozen on dry ice. RNA  extraction, library preparation, RNAseq and bioinformatics analysis was performed at Active Motif  (Carlsbad, California, USA).

value: lung adenocarcinoma


title: 4_3360Aarhus_A549-siNrf2-1

source_name: Human lung adenocarcinoma epithelial A549 cells


title: ALK004

description: Gene expression primary mouse tumor


title: 3_3360Aarhus_A549-siCTRL-3

value: siControl


title: Islet_DMSO_Control_Rep1

description: The mouse presented healthy appearance


title: HUVECs_Cytl1_8h_Hypoxia_Series4

source_name: HUVECs, treated with Cytl1 for 8h, Hypoxia


title: NB-39-nu_pLKO.1_day11_rep1


title: Islet_DMSO_Control_Rep2

description: The mouse presented healthy appearance


title: HUVECs_VEGF_8h_Hypoxia_Series4

source_name: HUVECs, treated with VEGF for 8h, Hypoxia


title: NB-39-nu_EZH2sh_18365_day8_rep3

source_name: human neuroblastoma cell line NB-39-nu, infected EZH2 RNA (TRCN0000018365) bearing lentivirus, 8 days after infection


title: 5_3360Aarhus_A549-siNrf2-2


title: HUVECs_Cytl1_2h_Hypoxia_Series4

source_name: HUVECs, treated with Cytl1 for 2h, Hypoxia


title: Iah1-KO_Kidney

city: Nagoya

first: Misato

last: Kobayashi

state: Aichi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

description: High-fat diet for 12 weeks

hyb_protocol: Following fragmentation, biotinylated cRNA were hybridized for 17 hr at 45C on GeneChip Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G System.

data_processing: The data were analyzed with RMA-Sketch (RMA-Gene-Default) using Affymetrix Expression Console Software ver.1.3.0.

source_name: Kidney

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Affymetrix Gene Chip WT PLUS Reagent Kit, Affymetrix).

growth_protocol: Until 6 weeks of age, all male mice were fed a standard laboratory chow (CE2, Nihon CLEA). From 6 weeks of age, mice were fed a high-fat diet (pellet, 07053003 from Research Diet). Mice were kept at one animal per cage.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. After that, RNA was performed a cleanup using the QIAGEN Rneasy Mini kit.

treatment_protocol: Mice were fed a high fat diet for 12 weeks. Mice were killed by decapitation, and tissues were collected at 13:00-14:00 hours after 4-hour diet deprivation.

value: Kidney


title: Iah1-KO_Liver

description: High-fat diet for 12 weeks

source_name: Liver

value: Liver


title: HUVECs_VEGF_4h_Hypoxia_Series4

source_name: HUVECs, treated with VEGF for 4h, Hypoxia


title: 2_3360Aarhus_A549-siCTRL-2


title: HUVECs_Cytl1_4h_Hypoxia_Series4

source_name: HUVECs, treated with Cytl1 for 4h, Hypoxia


title: NB-39-nu_EZH2sh_10475_day8_rep2

source_name: human neuroblastoma cell line NB-39-nu, infected EZH2 RNA (TRCN0000010475) bearing lentivirus, 8 days after infection


title: Iah1-WT_Kidney

description: High-fat diet for 12 weeks


title: NB-39-nu_EZH2sh_18365_day8_rep2


title: 1_3360Aarhus_A549-siCTRL-1


title: NB-39-nu_EZH2sh_18365_day8_rep1


title: NB-39-nu_EZH2sh_10475_day8_rep1


title: HUVECs_VEGF_2h_Hypoxia_Series4

source_name: HUVECs, treated with VEGF for 2h, Hypoxia


title: Iah1-WT_Liver

description: High-fat diet for 12 weeks


title: OPLL_RNA

city: Kurume

first: Michiyo

last: Tsuru

state: Fukuoka

address: 67 Asahimachi

department: Orthopardic Surgery

institute: Kurume Universuty

hyb_protocol: Labeled miRNA was hybridized to a 60K oligomicroarray (Human miRNA Microarray Kit Release 16.0, 8x60K; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: OPLL RNA OPLL miRNA 76F

label_protocol: miRNA was labelled using a miRNA Complete Labeling Reagent and Hyb Kit (Agilent Technologies).

extract_protocol: Total RNA was prepared from cells using an AllPrep DNA/RNA Mini Kit (Qiagen), according to the manufacturer’s instructions.

value: cells

tag: status

value: OPLL


title: NB-39-nu_pLKO.1_day8_rep2

source_name: human neuroblastoma cell line NB-39-nu, infected pLKO.1 bearing lentivirus, 8 days after infection


title: Myoblast-like cell line

first: Ori

last: Bar-Nur

address: 185 Cambridge st.

department: Center of Regenerative medicine

institute: Harvard University

hyb_protocol: Hybridization was done by the Partners Center for Personalized Genetic Medicine.

scan_protocol: Scanning was done by the Partners Center for Personalized Genetic Medicine.

data_processing: Data was processed using Expression Console software, the processing algorithm was RMA

label_protocol: Labeling was done by the Partners Center for Personalized Genetic Medicine.

growth_protocol: Cells were grown in iMPCs as described in the Online methods section

extract_protocol: RNA (Dnase treated) was islolated and extracted using the Rneasy Mini Kit (Qiagen).

value: myoblasts


title: HUVECs_VEGF_1h_Hypoxia_Series4

source_name: HUVECs, treated with VEGF for 1h, Hypoxia


title: HUVECs_Cytl1_18h_Normoxia_Series1

source_name: HUVECs, treated with Cytl1 for 18h, Normoxia


title: Breast tumor T0249_A

type: genomic

city: Paris

first: Elodie

last: Girard

address: 11-13 rue Pierre et Marie Curie

country: France

institute: Institut Curie

hyb_protocol: Probes annealing and ligation on tumor DNA, amplification by PCR, probes digestion and DNA hybridization on each array were performed according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using fluidics wash, and scanned using the Gene Chip Scanner 3000.

data_processing: Each sample has two CEL files (= array fluorescence intensity files generated per sample by the Affymetrix GeneChip® Command Console (version 4.0, 2013)) , as it was hybridized with two arrays: the A/T array and with the G/C array to obtain the genotype for each SNP present on the OncoScan.  Therefore sample name descriptors _A and _C correspond to the CEL file for the A/T array and for the G/C array, respectively. Copy number values for individual SNPs were extracted and converted from CEL file and processed using the Genome Alteration Print (GAP) method (Popoval et al., Genome Biol, 2009) to determine the ploidy of each tumour and CNV.

source_name: Breast tumor DNA T0249

label_protocol: Performed according to manufacturer's protocols.

growth_protocol: All samples were formamid-fixed paraffin-embedded tumors.

extract_protocol: Tumor tissues were microdissected from four 10μm section and tumor DNA was extracted from the Macherey-Nagel Nucleospin Tissue protocol according to the manufacturer's instruction. DNA quality and quantity was assessed using Qubit andq-PCR.

treatment_protocol: No treatment was performed

tag: Sex

value: Female

tag: atm status

value: Homozygote

tag: variant type

value: truncating variant

tag: molecular suptype

value: Luminal B

value: breast tumor


title: HUVECs_VEGF_18h_Normoxia_Series1

source_name: HUVECs, treated with VEGF for 18h, Normoxia

tag: cell type

value: Human Umbilical Vein Endothelial Cells


title: NB-39-nu_EZH2sh_10475_day8_rep3

value: neuroblastoma


title: NB-39-nu_pLKO.1_day8_rep3


title: Mouse embryonic fibroblasts (sorted for Thy1) induced to express MyoD in the presence of small moleculesfor 14 days,

description: Mice were Black6-129X1/SvJ; age-2-3 month, both genders

source_name: MEFs+MyoD+chemicals (FR)

value: Fibroblasts / myocytes / muscle progenitor

value: 2-3 months

tag: strain


title: Breast tumor T0249_C


title: HUVECs_Cytl1_8h_Normoxia_Series1

source_name: HUVECs, treated with Cytl1 for 8h, Normoxia


title: OPLL_Blood

source_name: OPLL Blood miRNA

value: blood


title: Control_Blood

source_name: Blood miRNA

value: healthy


title: HUVECs_VEGF_8h_Normoxia_Series1

source_name: HUVECs, treated with VEGF for 8h, Normoxia


title: HUVECs_0h_Hypoxia_Series4

source_name: HUVECs, untreated, Hypoxia


title: Mouse embryonic fibroblasts

source_name: MEFs

value: Fibroblasts


title: NB-39-nu_pLKO.1_day8_rep1

value: pLKO.1 bearing lentivirus


title: Mouse embryonic fibroblasts (sorted for Thy1) induced to express MyoD for 14 days, sorted for the MEF marker Thy1

source_name: MEFs+MyoD

value: Fibroblasts / / myocytes


title: an established iMPC line at passage 6

value: muscle progenitors


title: Breast tumor T0248_C

source_name: Breast tumor DNA T0248

value: Heterozygote

value: Missense variant

value: Luminal A


title: HUVECs_Cytl1_4h_Normoxia_Series1

source_name: HUVECs, treated with Cytl1 for 4h, Normoxia


title: Breast Cancer 136

city: Heidelberg

first: Sven

last: Diederichs

address: Im Neuenheimer Feld 280

department: RNA Biology & Cancer

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Agilent gene expression hybridization kit

scan_protocol: Agilent scanner

data_processing: Agilent Feature Extraction Software (FE) 10.7.3.1.

source_name: Breast Tumor

label_protocol: Invitrogen SuperScript Indirect cDNA labeling system

extract_protocol: TRIzol from fresh frozen tissue samples cut into cryosections

value: Tumor ER/PR+


title: Breast tumor T0248_A

value: Female


title: Breast Cancer 135


title: Breast tumor T0180_C

source_name: Breast tumor DNA T0180

value: truncating variant

value: Luminal B


title: Breast Cancer 133


title: HUVECs_VEGF_4h_Normoxia_Series1

source_name: HUVECs, treated with VEGF for 4h, Normoxia

value: Human Umbilical Vein Endothelial Cells


title: Breast Cancer 134


title: Breast tumor T0180_A

value: breast tumor


title: Breast tumor T0179_C

source_name: Breast tumor DNA T0179

value: Unknown


title: Breast tumor T0179_A


title: Breast Cancer 110


title: Breast Cancer 106


title: HUVECs_Cytl1_2h_Normoxia_Series1

source_name: HUVECs, treated with Cytl1 for 2h, Normoxia


title: TR-A

first: SHUYI

last: CHEN

state: Guangdong

address: 54 S. Xianlie Rd

department: State Key Laboratory of Ophthalmology

institute: Zhongshan Ophthalmic Center, SYSU

description: center temporal optic cup

hyb_protocol: standard Affymetrix proctocol

scan_protocol: standard Affymetrix proctocol

data_processing: none provided by submitter

source_name: temporal optic cup, sample A

label_protocol: standard Affymetrix proctocol

extract_protocol: none provided by submitter


title: Breast tumor T0078_C

source_name: Breast tumor DNA T0078

value: Luminal B/HER2


title: TR-B

source_name: temporal optic cup, sample B


title: HUVECs_VEGF_2h_Normoxia_Series1

source_name: HUVECs, treated with VEGF for 2h, Normoxia


title: Breast Cancer 101


title: TR-C

source_name: temporal optic cup, sample C


title: HUVECs_Cytl1_1h_Normoxia_Series1

source_name: HUVECs, treated with Cytl1 for 1h, Normoxia


title: Breast Cancer 096


title: Breast tumor T0078_A


title: NR-C

source_name: nasal optic cup, sample C


title: NR-B

source_name: nasal optic cup, sample B


title: Breast tumor T0077-R_C

source_name: Breast tumor DNA T0077-R


title: Breast Cancer 094


title: HUVECs_VEGF_30min_Normoxia_Series1

source_name: HUVECs, treated with VEGF for 30 min, Normoxia


title: HUVECs_VEGF_1h_Normoxia_Series1

source_name: HUVECs, treated with VEGF for 1h, Normoxia


title: Breast Cancer 095


title: Breast tumor T0077-R_A


title: OF-C

source_name: optic fissue, sample C


title: NR-A

description: center nasal optic cup

source_name: nasal optic cup, sample A


title: Breast tumor T0077-L_C

source_name: Breast tumor DNA T0077-L


title: HUVECs_VEGF_24h_Hypoxia_Series4

source_name: HUVECs, treated with VEGF for 24h, Hypoxia


title: WT.1

city: Salamanca

first: Isidro

last: Sánchez García

address: Campus Miguel de Unamuno

department: Centro de inv. del Cáncer (CIC).

institute: Inst. de Inv. Biomédica de Salamanca (IBSAL). H. U. de Salamanca. Inst. de Biología Molecular y Celular del Cáncer (IBMCC).

description: rawCounts.xls

data_processing:
Illumina RTA and bcl2fastq software
The RNA-seq data was aligned against the mouse reference genome (mm10/GRCm38.83) with TopHat 2.1.0, and FPKM values per gene were calculated with the R/Bioconductor package bamsignals.
Genes with FPKM values > 1 in less than three samples were excluded from the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file, including raw counts (produced by bamsignals) of sequencing reads for each gene

source_name: Thymus

extract_protocol:
Thymus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols; Non-stranded-RNA Seq

value: Thymus

value: 4 months-old

value: Wild type control


title: WT.3

description: rawCounts.xls


title: WT.4

description: rawCounts.xls


title: WT.2

description: rawCounts.xls


title: OF-B

source_name: optic fissue, sample B


title: Breast tumor T0077-L_A


title: HUVECs_Cytl1_30min_Normoxia_Series1

source_name: HUVECs, treated with Cytl1 for 30 min, Normoxia


title: Sca1.Lmo2.4

description: rawCounts.xls

value: 8 months-old


title: OF-A

description: OC cells within 5-cell diameter from the edge of the optic fissue was included as optic fissure region

source_name: optic fissue, sample A


title: Breast Cancer 098

source_name: Breast Tumor


title: Breast Cancer 083


title: Breast tumor T0076_C

source_name: Breast tumor DNA T0076


title: HUVECs_0h _Normoxia_Series1

source_name: HUVECs, untreated, Normoxia


title: Sca1.Lmo2.3

description: rawCounts.xls


title: Breast Cancer 092


title: Breast tumor T0076_A


title: Sca1.Lmo2.2

description: rawCounts.xls

data_processing:
Illumina RTA and bcl2fastq software
The RNA-seq data was aligned against the mouse referbamence genome (mm10/GRCm38.83) with TopHat 2.1.0, and FPKM values per gene were calculated with the R/Bioconductor package bamsignals.
Genes with FPKM values > 1 in less than three samples were excluded from the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file, including raw counts (produced by bamsignals) of sequencing reads for each gene

value: 7 months-old


title: Breast Cancer 084


title: Breast Cancer 081


title: Breast Cancer 089


title: Breast tumor T0016-L_C

source_name: Breast tumor DNA T0016-L


title: E14_shCtrl

city: Shanghai

first: Qianshu

last: Zhu

state: Shanghai

address: Siping Road

department: School of Life Science and Technology

institute: Tongji University

description: Gene expression data from ESCs infected with shCtrl virus as control

hyb_protocol: Array hybridization and wash was performed using GeneChip Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US) in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instruction.

scan_protocol: Slides were scanned by GeneChip Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 4.0 (Affymetrix, Santa Clara, CA, US) with default settings. Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing:
Expression microarray of Affmetrix TVT analyses were performed using affy of Bioconductor, applying the MAS5 method for normalization.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id = 1.4.1.46

source_name: embryonic stem cells

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacter’s instructions to obtain biotin labeled cRNA.

growth_protocol: Low passage (p9) E14 cells were maintained on plates coated with 0.1% gelatin in high glucose Dulbecco’s modified Eagle’s medium (DMEM; Gibco) containing 15% fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco), 2 mM L-glutamine (Thermo), 100 mM nonessential amino acids (NEAA; Thermo), 100 μM β-mercaptoethanol (Gibco), and leukemia inhibitory factor (1000 U/ml LIF; Millipore).

extract_protocol: Total RNA was isolated from the cells using TRIzol reagent (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: E14 cells were infected with lentivirus expressing non-targeting shRNA (shCtrl) or shSin3a-1. After puromycin selection, E14 cells were collected and placed on ice in the Trizol solution (Invitrogen).

value: embryonic stem cells (ESCs)

tag: shRNA

value: shCtrl


title: Sca1.Lmo2.1

description: rawCounts.xls


title: Rosa26.Lmo2.3

description: rawCounts.xls

value: 9 months-old


title: E14_shSin3a-1

description: Gene expression data from ESCs infected with shSin3a-1 virus to knockdown Sin3a


title: DLN B cell

first: Liu

last: Yanfang

address: 800 Xiangyin Road

department: Immunology

institute: Second Military Medical University

description: Gene expression for B cells from tumor draining lymph node

hyb_protocol: The fragmented cRNA was hybridized to Mouse Genome 430 2.0 Arrary. Hybridization was performed at 45oC with rotation for 16 h (AffymetrixGeneChip Hybridization Oven 640). The GeneChip arrays were washed and then stained (streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450.

scan_protocol: The GeneChip arrays were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and RMA as normalization method.

source_name: B cells from tumor draining lymph node

label_protocol: An aliquot of 100ng of total RNA was used to synthesize double-stranded cDNA, and then produce biotin-tagged cRNA using the MessageAmpTM II aRNA Amplification Kit. The resulting bio-tagged cRNA were fragmented to strands of 35-200 bases in length according to the protocols from Affymetrix.

extract_protocol: Total RNA of parietal cortex of the patient was extracted with RNeasy Mini Kit (Qiagen), according to the manufacturer’s instruction.

treatment_protocol: We subcutaneously inoculated Balb/c mice with breast cancer cell line 4T1. DLN was harvest two weeks later. To purify B cells, single-cell suspensions from DLN and NLN were stained with antibodies, and CD3- CD19+ cells were sorted using a MoFlo XDP flow cytometer (Beckman-Coulter) with purities of >95%.

value: B cell

value: Balb/c


title: Breast Cancer 077

value: Tumor ER/PR+


title: HUVECs_Cytl1_1h_Hypoxia_Series4

source_name: HUVECs, treated with Cytl1 for 1h, Hypoxia


title: NLN B cell

description: Gene expression for B cells from normal lymph node

source_name: B cells from normal lymph node


title: Breast tumor T0015_C

source_name: Breast tumor DNA T0015

value: Female

value: Heterozygote

value: truncating variant


title: Rosa26.Lmo2.2

description: rawCounts.xls


title: Breast Cancer 075


title: HBL1 shTLR9 (D7) DOX Treated - 2 days - mAdbID:125686

first: Louis

middle: M.

last: Staudt

address: 9000 Rockville Pike, Bldg 10, Rm 4N114

department: Lymphoid Malignancies Branch

description: mAdb experiment ID: 125686

hyb_protocol: Agilent Hybridization Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Scan_MicronsPerPixelX: 5 Scan_MicronsPerPixelY: 5 Scan_ScannerName: Agilent Technologies Scanner G2505C US45102888 Agilent Scanning Protocol Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505C, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing:
Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. Spot values were normalized using the default linear-lowess normalization.
FeatureExtractor_Version: 10.1.1.1
Protocol_Name: GE2-v5_10_Apr08 (Read Only)

source_name: HBL1 shSC4 DOX Treated, control - 2 days

label_protocol:
Agilent Labeling-Cy3
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol:
RNEasy Mini Kit
Other: Total RNA was purified using RNeasy Mini Kits (Qiagen).

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 200 ng/mL
Treatment time: 2 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shSC4. shRNA expression was induced with 200 ng/mL doxycycline for 2 days.

value: ABC DLBCL cells

tag: disease state

value: activated B cell-like (ABC) subtype of diffuse large B cell lymphoma (DLBCL)

source_name: HBL1 shTLR9 (D7) DOX Treated - 2 days

label_protocol:
Agilent Labeling-Cy5
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 200 ng/mL
Treatment time: 2 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shTLR9 (D7). shRNA expression was induced with 200 ng/mL doxycycline for 2 days.


title: Breast tumor T0016-L_A

value: Luminal A

value: breast tumor


title: Mb1.Cre.2

description: rawCounts.xls

value: Thymus

value: 20 months-old


title: HBL1 shTLR9 (D7) DOX Treated - 1 day - mAdbID:125685

description: mAdb experiment ID: 125685

source_name: HBL1 shSC4 DOX Treated, control - 1 day

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 200 ng/mL
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shSC4. shRNA expression was induced with 200 ng/mL doxycycline for 1 day.

source_name: HBL1 shTLR9 (D7) DOX Treated - 1 day

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 200 ng/mL
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shTLR9 (D7). shRNA expression was induced with 200 ng/mL doxycycline for 1 day.


title: Breast tumor T0009_C

source_name: Breast tumor DNA T0009

value: Luminal B


title: Breast Cancer 068


title: Breast Cancer 070


title: HBL1 shTLR9 (C4) DOX Treated - 2 days - mAdbID:125684

description: mAdb experiment ID: 125684

source_name: HBL1 shTLR9 (C4) DOX Treated - 2 days

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 200 ng/mL
Treatment time: 2 days
In-vitro treatment: Cells were transduced with retroviral vectors expressing shTLR9 (C4). shRNA expression was induced with 200 ng/mL doxycycline for 2 days.


title: Breast tumor T0015_A


title: Breast Cancer 065


title: Rosa26.Lmo2.1

description: rawCounts.xls

source_name: Thymus


title: Breast tumor T0009_A


title: Mb1.Cre.1

description: rawCounts.xls


title: Aid.Cre

description: rawCounts.xls

value: 22 months-old


title: TMD8 shTLR9 (D7) DOX Treated - 2 days - mAdbID:125682

description: mAdb experiment ID: 125682

source_name: TMD8 shSC4 DOX Treated, control - 2 days

source_name: TMD8 shTLR9 (D7) DOX Treated - 2 days


title: HBL1 shTLR9 (C4) DOX Treated - 1 day - mAdbID:125683

description: mAdb experiment ID: 125683

source_name: HBL1 shTLR9 (C4) DOX Treated - 1 day

treatment_protocol:
Treatment type: shRNA transduction
Treatment dose: 200 ng/mL
Treatment time: 1 day
In-vitro treatment: Cells were transduced with retroviral vectors expressing shTLR9 (C4). shRNA expression was induced with 200 ng/mL doxycycline for 1 day.


title: Breast Cancer 064

source_name: Breast Tumor


title: Breast Cancer 063


title: Breast Cancer 060


title: Breast Cancer 057


title: TMD8 shTLR9 (D7) DOX Treated - 1 day - mAdbID:125681

description: mAdb experiment ID: 125681

source_name: TMD8 shSC4 DOX Treated, control - 1 day

source_name: TMD8 shTLR9 (D7) DOX Treated - 1 day


title: TMD8 shTLR9 (C4) DOX Treated - 2 day - mAdbID:125680

description: mAdb experiment ID: 125680

source_name: TMD8 shTLR9 (C4) DOX Treated - 2 days


title: Breast tumor T0005_A

source_name: Breast tumor DNA T0005


title: Breast tumor T0005_C


title: TMD8 shTLR9 (C4) DOX Treated - 1 day - mAdbID:125679

description: mAdb experiment ID: 125679

source_name: TMD8 shTLR9 (C4) DOX Treated - 1 day


title: Breast Cancer 055


title: Breast Cancer 053


title: TIGR4 Δhk08 mutant strain_replicate 3

city: Greifswald

last: Hammerschmidt

state: MV

address: Felix-Hausdorff-Str. 8

department: Molecular Genetics and Infection Biology

institute: University of Greifswald

hyb_protocol: 100 ng of Cy3-labeled cDNA were hybridized to the microarray followed by hybridization, washing and scanning protocol as provided by Agilent Technologies (One Color Microarray-based Gene Expression Analysis, version 6.9).

scan_protocol: The microarray slides were scanned immediately using the Agilent microarray scanner G2505C (Agilent Technologies).

data_processing: Data were extracted using the Agilent Feature Extraction software (version 11.5, Agilent Technologies).

organism: Streptococcus pneumoniae TIGR4

source_name: Δhk08 mutant grown in CDM early-log phase (OD 0,35)

label_protocol: 5 ug of total RNA was used for conversion into cDNA labeled with Cy3-dCTP using Agilent One Color RNA Spike-In Kit and the supertranscriptase II. The resulting product was cleaned using RNAse H and CyScribe GFX Purification Kit. The quality and concentration of cDNA was checked using a Nanodrop ND-1000 (PeqLab)

growth_protocol: Each bacterial strain was cultured in a blood agar plate for 6 hours at 37ºC and 5% CO2. The bacteria were then inoculated into liquid CDM at a starting OD600nm of 0,1 and grown in a water bath at 37ºC until a final OD600nm of 0,35.

extract_protocol: The pellets were processed for total RNA extraction using acid phenol-chloroform and DNase treatment to remove genomic DNA. The products were purified using the RNA Clean-Up and Concentration kit (NORGEN BIOTEK CORP), the quality of the RNA was determined by agarose gel electrophoresis and the amount was quantified using a Nanodrop ND-1000 (PeqLab)

treatment_protocol: 24 ml of the bacterial culture was added into a vial containing frozen killing buffer. Tubes were inmediately centrifuged for 5 min at 10000g and 4ºC, the supernatant was removed and the vials with the pellet were flash frozen in liquid nitrogen and stored at -80ºC

tag: genotype/variation

value: deltahk08 mutant


title: KidneyEC_rep2

city: Freiburg

first: Ana

last: Izcue

address: Am Stübeweg 51

institute: Max Planck Institut of Immunobiology and Epigenetics

description: SAMPLE 14

hyb_protocol: Performed by Milteny Biotech following standard procedures

data_processing: The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For the normalised data, the signal intensities from the single-experiment raw data lists are normalized by dividing the intensity values by their median.

source_name: KidneyEC

extract_protocol: RNA was extracted with Trizol (thymus, Thyroid) or performed by Miltenyi Biotech following standard procedure

tag: strain background

value: Kidney

value: kidney epithelial cells

tag: sorting gate

value: Epcam+ CD45- Fluorogold-


title: TIGR4 Δhk08 mutant strain_replicate 2


title: KidneyEC_rep3

description: SAMPLE 15

scan_protocol: Performed by Milteny Biotech following standard procedures

tag: tissue


title: KidneyEC_rep1

description: SAMPLE 13

label_protocol: Performed by Milteny Biotech following standard procedures


title: TIGR4 Δtcs08 mutant strain_replicate 3

source_name: Δrr08 mutant grown in CDM early-log phase (OD 0,35)

value: deltatcs08 mutant


title: Breast Cancer 035

value: Tumor ER/PR+


title: IntestineEC_MHCIIlo_rep3

description: SAMPLE 12

value: Small intestine MHCII int

value: MHCIIint intestinal epithelial cells

value: Epcamint MHCint CD45- Fluorogold-


title: IntestineEC_MHCIIlo_rep1

description: SAMPLE 10


title: IntestineEC_MHCIIlo_rep2

description: SAMPLE 11


title: TIGR4 Δrr08 mutant strain_replicate 3

source_name: wild-type grown in CDM early-log phase (OD 0,35)

value: deltarr08 mutant


title: TIGR4 wild-type strain_replicate 3

source_name: Δtcs08 mutant grown in CDM early-log phase (OD 0,35)

value: wild-type


title: TIGR4 Δrr08 mutant strain_replicate 2


title: TIGR4 Δtcs08 mutant strain_replicate 2


title: IntestineEC_MHCIIhi_rep3

description: SAMPLE 9

value: Small intestine MHCII+

value: MHCIIhi intestinal epithelial cells

value: Epcamhi MHChi CD45- Fluorogold-


title: Breast Cancer 043


title: TIGR4 Δhk08 mutant strain_replicate 1


title: Breast Cancer 036


title: Breast Cancer 046


title: IntestineEC_MHCIIhi_rep1

description: SAMPLE 7


title: ThyroidEC_rep3

description: SAMPLE 6

source_name: ThyroidEC

value: Thyroid

value: thyroid epithelial cells


title: Breast Cancer 028


title: TIGR4 wild-type strain_replicate 2


title: IntestineEC_MHCIIhi_rep2

description: SAMPLE 8


title: Breast Cancer 031


title: Breast Cancer 048


title: Breast Cancer 027


title: Breast Cancer 025


title: TIGR4 Δrr08 mutant strain_replicate 1


title: ThyroidEC_rep2

description: SAMPLE 5


title: ThyroidEC_rep1

description: SAMPLE 4


title: TIGR4 wild-type strain_replicate 1


title: Breast Cancer 021


title: ThymusEC_rep3

description: SAMPLE 3

source_name: ThymusEC

value: Thymic medulla

value: thymic epithelial cells

value: Epcam+ UEA1+ CD45- Fluorogold-


title: ThymusEC_rep2

description: SAMPLE 2


title: Breast Cancer 019


title: transgenic control,line60,biological rep4

city: Ardmore

first: Kiran

last: Mysore

state: Oklahoma

address: 2510 Sam Noble Parkway

institute: Noble Research Institute

description: Gene expression data from leaf4 at E4 stage,before lesion initiation (At E4 stage, lesion was fully expanded in leaf2, half expanded in leaf3, and could not be observed in leaf4)

hyb_protocol: hybridized to Affymetrix switchgrass cDNA chip containing over 100 000 switchgrass probe sets.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G System

data_processing: Data normalization was conducted by using the robust multi-array average (RMA). Data analysis of differentially expressed probe sets on the chip was performed by associative analysis as described by Dozmorov and Centola (2003).

organism: Panicum virgatum

source_name: switchgrass leaf4 at E4 stage

label_protocol: Purified RNA (500 ng) was amplified and labelled using the GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA)

growth_protocol: Plants were grown in the greenhouse with 16-h light photoperiod (390 μEm-2S-1) and 26℃.

extract_protocol: High-quality total RNA from duplicate biological replicates of the transgenic lines MT/CO-37 and MT/CO-47 (severe phenotype group), MT/CO-38 and MT/CO-67 (moderate phenotype group) was isolated from young leaves (Leaf 4) at E4 stage using Spectrum157™ Plant Total RNA Kit (Sigma-Aldrich).

treatment_protocol: No treatment

tag: background

tag: Stage

value: E4 stage

tag: phenotype

value: transgenic control


title: Breast Cancer 010


title: Breast Cancer 007


title: Normal Breast 141

source_name: Normal Breast

value: Normal


title: Breast Cancer 005

value: Tumor ER/PR+


title: TIGR4 Δtcs08 mutant strain_replicate 1

value: deltatcs08 mutant


title: Normal Breast 140


title: wild type,biological rep1

value: wild type


title: Normal Breast 144


title: Breast Cancer 003


title: Breast Cancer 013


title: Normal Breast 138


title: Breast Cancer 001


title: Normal Breast 142


title: ThymusEC_rep1

description: SAMPLE 1


title: moderate lesion phenotype,line67,biological rep1

value: moderate lesion


title: moderate lesion phenotype,line67,biological rep2


title: transgenic control,line60,biological rep1


title: moderate lesion phenotype,line38,biological rep2


title: Normal Breast 139


title: moderate lesion phenotype,line38,biological rep1


title: stronge lesion phenotype,line47,biological rep2

value: stronge lesion


title: stronge lesion phenotype,line47,biological rep1


title: transgenic control,line60,biological rep2


title: stronge lesion phenotype,line37,biological rep2


title: transgenic control,line60,biological rep3


title: stronge lesion phenotype,line37,biological rep1


title: Normal Breast 130


title: Normal Breast 137


title: Normal Breast 115


title: 16eCeN10

city: Beijing

first: Qun

last: Gao

state: Beijing

address: Shuang Qing Road

department: Environmental sicence and engineering

institute: Tsinghua University

description: GeoChip data for soil sample collected at elevated CO2, elevated N

hyb_protocol: Then DNA was dried in a SpeedVac (ThermoSavant, Milford, MA, USA) at 45°C for 45 minutes. The hybridization was carried out at 42°C for 16 hours on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA).

scan_protocol: After purification, GeoChip microarrays were scanned by a NimbleGen MS200 scanner (Roche, Madison, WI, USA) at 633 nm using a laser power and photomultiplier tube (PMT) gain of 100% and 75%, respectively.

data_processing: Signal intensities were quantified and processed using the data analysis pipeline as previously described (He et al 2010). Then processed GeoChip data were analyzed using the following steps: (i) remove the poor quality spots, which were flagged as 1 or 3 by ImaGene or with a signal to noise ratio (SNR) of less than 2.0; (ii) normalize the signal intensity of each spot by dividing the signal intensity by the total intensity of the microarray followed by multiplying by a constant; (iii) transform the data to the natural logarithmic form; and (iv) remove genes detected in only one out of three samples from the same elevation.

organism: soil metagenome

source_name: Soil microbes in BioCON plots

label_protocol: As previously described (Yang et al 2013), DNA samples were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA).

growth_protocol: In August 2009, soil samples were collected from all of the plots. Soil cores at a depth of 0-20 cm and diameter of 1.5 cm were randomly taken from each plot and mixed thoroughly to generate a soil sample representing the plot. Soil samples were kept on ice when transporting to laboratory, and sieved with 2 mm mesh to remove roots and stones. Soil samples were preserved at -80°C before DNA extraction.

extract_protocol: Soil genomic DNA was extracted using a FastDNA spin kit for soil (MP Biomedical, Carlsbad, CA, USA) following the manufacturer’s instructions. To purify it, DNA extract was mixed with 2.5 volume of 100% ice cold ethanol and 0.1 volume of 3 M NaOAc (pH 5.2) prior to overnight incubation at -20°C. DNA was precipitated by centrifugation for 30 minutes at 13,000 x g. Then supernatant was decanted and washed with 1 ml of 70% ethanol. DNA was air-dried and dissolved in 50 µl of nuclease-free water. DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen (Ahn et al 1996) using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

tag: different carbon and nitrogen levels

value: elevated CO2, elevated N


title: Normal Breast 116


title: 16eCeN7

treatment_protocol: In August 2009, soil samples were collected from all of the plots. Soil cores at a depth of 0-20 cm and diameter of 1.5 cm were randomly taken from each plot and mixed thoroughly to generate a soil sample representing the plot. Soil samples were kept on ice when transporting to laboratory, and sieved with 2 mm mesh to remove roots and stones. Soil samples were preserved at -80°C before DNA extraction.


title: 16eCeN11


title: OSC19_4

city: Chiyoda-ku

first: Shogo

last: Okazaki

state: Tokyo

address: 1-8-13 Kanda-Surugadai

department: School of Dentistry

institute: Nihon University

description: Gene expression data from parental OSC19 cell

hyb_protocol: The Agilent array were hybridized and washed using the manufacturer's protocol.

scan_protocol: Agilent arrays were scanned using the Agilent Technologies Scanner G2505C.

data_processing: The data were normalized with 75 Percentile method

label_protocol: Cy3 labeled cRNA were prepared according to the standard Agilent protocol.

growth_protocol: OSC19 and sulfasalazine resistant OSC19 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% FBS in 5% CO2.

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen) according to the manufacturer’s instructions.

value: oral squamous carcinoma cell line

tag: cell line

value: OSC19 (parental)


title: 22.4 mM glucose treated INS-1 cells rep1

city: Miki-cho

first: Yasunori

last: Sugiyama

state: kagawa

address: ikenobe 2393

department: Department of Life Science

institute: Kagawa University

description: Gene expression data from INS-1 cells treated with 22.4 mM glucose

hyb_protocol: Following fragmentaion, single-stranded cDNA were hybridized for 20 hours at 48 ℃ with RaGene2.1ST Array Strip (Affymetrix)  and GeneChip Expression 3'-Amplification Reagents Hybridization Control kit (Affymetrix).

scan_protocol: The array was scanned using Imaging Station (Affymetrix) according to the manufacture's instructions.

data_processing: Arrays were summarized and normalized using GeneSpring GX software version 12.6.

organism: Rattus norvegicus

source_name: 22.4 mM glucose treated INS-1 cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT Amplification Kit Module 1(Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

extract_protocol: Total RNA was isolated from INS-1 cells using RNeasy kit (QIAGEN).

treatment_protocol: INS-1 cells were treated with 11.2 or 22.4 mM glucose for 7 days

tag: treatment

value: 22.4 mM glucose


title: Normal Breast 111


title: 16eCeN12


title: 16eCeN3


title: 16eCeN5


title: 11.2 mM glucose treated INS-1 cells rep2

description: Gene expression data from INS-1 cells treated with 11.2 mM glucose

source_name: 11.2 mM glucose treated INS-1 cells

value: 11.2 mM glucose


title: OSC19-SSZR_4

description: Gene expression data from parental sulfasalazine resistant OSC19 cell

source_name: Sulfasalazine resistant_4

value: OSC19 (Sulfasalazine resistant)


title: 22.4 mM glucose treated INS-1 cells rep2


title: Normal Breast 113


title: OSC19-SSZR_3

source_name: Sulfasalazine resistant_3


title: Normal Breast 128


title: 16eCeN8


title: OSC19_3


title: 16eCeN4


title: H3K4me1_Chipseq_WIS_female_2

city: Edinburgh

first: John

middle: Paterson

last: Thomson

address: Crewe Road

department: MRC Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh

description: mapped reads (RN6) were binned across 150bp windows.

data_processing:
Reads mapped to RN6 rat genome build using BWA (v0.7.12; default settings).
Data binned into 150bp windows across the genome
data normalised by read count
antibody enriched datasets normalised to matched input dataset to generate enrichment over background dataset
Genome_build: Rn6

source_name: Wistar Rat liver

extract_protocol:
Sheared chromatin was enriched using antibodies of choice. prior to enrichment through magnetic IgG beads . Following a series of buffer washes the DNA is then released through proteinase K digestion of the antibody and the DNA is subsequently cleaned up using Qiagen QIAquick PCR purification kits (Qiagen) and eluting in 20ul purified water. Enriched DNA was then subjectedto 18 cycles of whole genome amplification using using an enhanced amplification kit optimised for next generational sequencing (Sigma-Aldrich SeqPlex DNA Amplification Kit).
Individual libraries were generated from 100ng each of 5mc enriched and input DNA for each sample, using the Ion XpressPlus Fragment Library Kit (life Technologies™). The DNA was end repaired, purified and then ligated to Ion-compatible barcoded adapters (Ion Xpress™ Barcode Adapters 1–96: Life Technologies™), followed by nick-repair to complete the linkage between adapters and DNA inserts. The adapter-ligated library was then amplified (10 cycles) and finally size-selected using two rounds of AMPure XP bead capture to size‐select fragments approximately 100–250 bp in length. An equimolar pool of barcoded libraries was prepared at 100pM; each pool contained an meDIP enriched and corresponding input sample. 8pM of the pooled library was added into an emulsion PCR based template reaction; in this reaction the fragments generated during the library prep were attached to Ion sphere particles (ISPs) and clonally amplified. This process was carried out using the Ion One Touch 2 system and the Ion P1 Template OT2 200 Kit.

tag: gender

value: female

tag: strain/cell type

value: Wistar

tag: antibody

value: Anti H3K4me1 abcam cat # ab8895


title: H3K4me1_Chipseq_WIS_female_3


title: 16eCeN1


title: OSC19-SSZR_2

source_name: Sulfasalazine resistant_2

tag: cell type


title: 16eCeN6


title: 11.2 mM glucose treated INS-1 cells rep1


title: 16eCeN2


title: OSC19-SSZR_1

source_name: Sulfasalazine resistant_1


title: 16eCeN9


title: OSC19_2


title: H3K4me1_Chipseq_WIS_female_1


title: H3K27ac_Chipseq_WIS_female_2

value: Anti H3K27ac Millipore, cat # 07-362


title: Input_chip_WIS_female_pooled_2

value: None (input)


title: Input_chip_WIS_female_pooled_1


title: H3K27ac_Chipseq_WIS_female_1


title: H3K4me1_Chipseq_WIS_male_2

value: male


title: H3K4me1_Chipseq_WIS_male_3


title: 9eCeN15


title: H3K27ac_Chipseq_WIS_female_3


title: H3K4me1_Chipseq_WIS_male_1


title: H3K27ac_Chipseq_WIS_male_3


title: 9eCeN12


title: 9eCeN14


title: 9eCeN11


title: 9eCeN10


title: 9eCeN13


title: 9eCeN8


title: 9eCeN9


title: 9eCeN6


title: OSC19_1


title: 9eCeN7


title: H3K27ac_Chipseq_WIS_male_2


title: Ad-TFEB treated-rep1

city: Ann Arbor

first: Haocheng

last: Lu

state: Michigan

address: 2800 plymouth road

department: Internal Medicine

institute: University of Michigan

hyb_protocol: Following labeling procedure, 12.5 ug of aRNA were hybridized at 45C on Human U133 Plus 2.0 GeneChips.  GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.

data_processing: Log2 expression values were caluclated using RMA from the affy bioconductor package in R version 2.15.1.

source_name: HUVEC

label_protocol: Biotinylated aRNA were prepared according to the Affymetrix GeneChip 3’ IVT Express kit protocol from 400 ng total RNA (Affymetrix GeneChip 3’ IVT Express kit Instruction Manual, P/N 702646 Rev. 8)

growth_protocol: HUVECs were cultured in M199 supplemented with 16% fetal bovine serum, 1 ng/mL of recombinant human fibroblast growth factor, 20 mmol/L HEPES (pH 7.4) and 90 µg/mL of heparin and antibiotics.

extract_protocol: Total RNA was extracted with RNeasy mini kit according to the manufacturer's instructions (Qiagen).

treatment_protocol: When HUVEC reached approximately 90% confluence, they were infected with control adenovirus GFP (Ad-GFP) or adenovirus overexpressing (Ad-TFEB)  at multiplicities of infection of 10. Twenty four hours later, cells were collected for RNA extraction.

value: Human umbilical vein endothelial cells (HUVEC) overexpressing TFEB


title: Input_chip_WIS_male_pooled_2


title: Ad-TFEB treated-rep2


title: H3K27ac_Chipseq_WIS_male_1


title: 9eCeN5


title: Ad-GFP treated-rep2

value: Human umbilical vein endothelial cells (HUVEC) overexpressing control GFP


title: Input_chip_WIS_male_pooled_1


title: L363_Rapa-10nM__MS275-0.5uM_rep2

city: Bethesda

first: Aleksandra

middle: M

last: Michalowski

state: Maryland

address: 37 Convent Drive

institute: National Cancer Institute

description: Combination treatment

hyb_protocol: Prepared aRNA was hybridized to Affymetrix (Santa Clara, CA, USA) HG-U133 Plus 2 array chips and processed on Affymetrix Fluidics Workstation 450

scan_protocol: GenChips were analyzed with Gene Chip Operating Software (Affymetrix).

data_processing: CEL files were imported to the R Bioconductor affy package and processed with the default RMA algorithm

source_name: L363 cell line, 10nM Rapamycin and 0.5uM MS-275, 48hrs

label_protocol: Labeled aRNA was prepared from 1 μg RNA (MessageAmpII aRNA Amplification kit; Ambion).

extract_protocol: Total RNA was extracted with TRIzol® (Invitrogen)  according to the manufacturer's instructions.

tag: cancer type

value: Multiple Myeloma


title: L363_Rapa-10nM_rep3

description: Single treatment, mTOR inhibitor

source_name: L363 cell line, 10nM Rapamycin, 48hrs


title: 9eCeN4


title: L363_Rapa-10nM__MS275-0.5uM_rep1

description: Combination treatment


title: L363_Rapa-10nM_rep1

description: Single treatment, mTOR inhibitor


title: Ad-GFP treated-rep1


title: 9eCeN3


title: 9eCeN2


title: L363_Rapa-1nM__MS275-0.5uM_rep1

description: Combination treatment

source_name: L363 cell line, 1nM Rapamycin and 0.5uM MS-275, 48hrs


title: L363_Rapa-1nM__MS275-0.5uM_rep2

description: Combination treatment


title: L363_Rapa-10nM_rep2

description: Single treatment, mTOR inhibitor


title: CaCiPS1t

city: Tianjin

first: Haifeng

last: Fu

address: Weijin Road Num. 74

institute: Nankai University

data_processing:
FPKM
Supplementary_files_format_and_content: raw counts and FPKM

source_name: CiPS cell line derived from CA method

extract_protocol:
Total RNA was purified using a RNA mini kit (Qiagen)
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: In experiments by treatment with crotonic acid during induction, 6-8 mM crotonic acid (pH=7) was added into induction medium from day 16 to day 28 continuously.

tag: strain

value: CiPS cell line derived from CA method


title: CiPS1b

source_name: CiPS cell line derived from BrdU method

value: CiPS cell line derived from BrdU method


title: CaCiPS4t


title: CiPS2t

source_name: CiPS cell line derived from three-step method


title: OG4

source_name: ES cell line from the same starin

value: ES cell line from the same starin


title: D28+CA-rep

source_name: day 28 reprogramming cells with CA

value: day 28 reprogramming cells with CA


title: 9eCeN1

source_name: Soil microbes in BioCON plots

value: elevated CO2, elevated N


title: L363_Rapa-1nM_rep2

description: Single treatment, mTOR inhibitor

source_name: L363 cell line, 1nM Rapamycin, 48hrs


title: D24+CA

source_name: day 24 reprogramming cells with CA

value: day 24 reprogramming cells with CA


title: D24+CA-rep


title: L363_Rapa-1nM_rep1

description: Single treatment, mTOR inhibitor


title: L363_Rapa-1nM__MS275-0.5uM_rep3

description: Combination treatment


title: D20+CA-rep

source_name: day 20 reprogramming cells with CA

value: day 20 reprogramming cells with CA


title: L363_Rapa-1nM_rep3

description: Single treatment, mTOR inhibitor


title: L363_MS275-0.5uM_rep1

description: Single treatment, HDAC inhibitor

source_name: L363 cell line, 0.5uM MS-275, 48hrs


title: 4eCeN15


title: L363_MS275-0.5uM_rep3

description: Single treatment, HDAC inhibitor


title: 4eCeN14


title: 4eCeN13


title: L363_Control_rep3

description: Control, no treatment

source_name: L363 cell line, no-treatmant control, 48hrs


title: 4eCeN9


title: L363_Control_rep1

description: Control, no treatment


title: 4eCeN8


title: 4eCeN10


title: L363_MS275-0.5uM_rep2

description: Single treatment, HDAC inhibitor


title: 4eCeN7


title: D28+CA


title: D28-rep

source_name: day 28 reprogramming cells

value: day 28 reprogramming cells


title: ChIPmock: da-Gal4/+ ChIP-seq

first: Frédérique

last: Peronnet

address: 9, quai saint-Bernard

department: UMR7622-Developmental biology

institute: CNRS-SU

data_processing:
Quality checking with fastqc
Filtering with fastq_quality_filter (fastx-Toolkit suite). Parameters: p 90, q 20
Alignment with Bowtie2 (v2.1.0). Default parameters
Peak calling with MACS2 (v2.1.0). Fragment sized fixed at 110 bp
Peak reproducibility analysis by the IDR method with the "batch-consistency-analysis" function of the IDR package (v2.0.0)
Reproducible peaks merging with the "merge" function of the BEDtools suite
Generation of bedgraph files from bowtie2 alignement files with the genomeCoverageBed command from the BEDtools suite
Generation of bigWig files from the bedgraph with the bedGraphtoBigWig program from the UCSC binary utilities directory
Genome_build: dm6, r6.07
Supplementary_files_format_and_content: bigWig files contain tag density information for individual ChIP and Input experiments.

organism: Drosophila melanogaster

source_name: Third instar female larvae wing imaginal disc

growth_protocol: Flies were raised on standard yeast-cornmeal medium at 25°C.

extract_protocol:
600 wing imaginal discs were dissected (taking one disc per larva) in Schneider medium and aliquoted per 50 in 1.5 mL microtubes on ice. Discs were fixed at 22°C. 12 sonication cycles were performed (Diagenode Bioruptor sonifier; cycles of 30'' ON, 30'' OFF, high power). After centrifugation, the 12 supernatants were pooled, homogenized, and 2% were removed (Input). The remaining fragmented chromatin was redistributed into 12 tubes and each tube was adjusted to 1 mL with 140 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% BSA, Roche complete EDTA-free protease inhibitor cocktail). For immunoprecipitation, 3 µg of anti-Myc antibody (Abcam 9132) were added per tube. The  of water. Two biological replicates were performed.
Library preparation and Illumina sequencing were performed at the Ecole normale superieure Genomic Platform (Paris, France). Libraries were prepared using NEXTflex ChIP-Seq Kit (Bioo Scientific), using 5 ng of IP or Input DNA.
Libraries were multiplexed by 10 on one flowcell run. A 50 bp single read sequencing was performed on a NextSeq 500 device (Illumina).

treatment_protocol: No treatment.

value: Wing imaginal disc

tag: genotype

tag: age

value: Third instar larvae


title: Inputmock: Input DNA for mock


title: D24-rep

source_name: day 24 reprogramming cells

value: day 24 reprogramming cells


title: 4eCeN11


title: 4eCeN12


title: 4eCeN5


title: D20+CA


title: L363_Control_rep2

description: Control, no treatment


title: D24


title: D28


title: D20

source_name: day 20 reprogramming cells

value: day 20 reprogramming cells


title: D20-rep


title: D16-rep

source_name: day 16 reprogramming cells

value: day 16 reprogramming cells


title: D16


title: Pygo2 ChIPseq_2

city: St. John's

first: Phillip

last: Andrews

state: NL

address: HSC3307, 300 Prince Philip Dr.

department: Biomedical Sciences

country: Canada

institute: Memorial University

data_processing:
Unfiltered ChIP-seq reads were aligned to the human genome hg_19 using bwa_mem
Peaks were normalized to the inputs and called using MACS with a p-value cutoff of less than 1e-5
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: Hela S3

growth_protocol: Hela S3 cells grown on 150mm plates in DMEM supplemented with 10% fetal bovine serum

extract_protocol:
Lysates in RIPA buffer were clarified from sonicated nuclei and Pygo2-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina Truseq ChIP library preparation kit

treatment_protocol: No treatments

tag: chip antibody

value: Pygo2 (S3I4; Tzenov et al., J Clin Path.69, pp. 518-26, 2015 )


title: MEF

source_name: mouse embryonic fibroblasts

value: mouse embryonic fibroblasts


title: 4eCeN4


title: CD anti-TNF non-responder 1

city: Erlangen

first: Heike

last: Schmitt

address: Ulmenweg 18

department: First Department of Medicine

institute: University of Erlangen-Nuremberg

description: Gene expression of CD anti-TNF non-responder

hyb_protocol: Following fragmentation, 1.65 µg of Cy3-labeled cRNA were hybridisied for 17h at 65°C on 4x44K Agilent 026652 arrays. Arrays were washed according to the protocol (One-Color Microarray-based gene expression analysis v.5.5)

scan_protocol: Microarrays were scanned using Agilent G2505C Microarray Scanner. Data were extracted using Feature Extraction Version: FE Version 11.5.1. (Agilent Technologies Germany). Data extraction using protocol GE1_1105_0ct12

data_processing: txt. Files derived from feature extraction were imported into Genespring GX 12.6 (Silicon Genetics). Data were log2 transformed followed by normalization to the 75th percentile and adjusted to the median of all samples. Subsequently entities present in both replicates in at least one conditions were selected by filtering  on data present. Entitie lists were further filtered by selection of genes which do not change their expression in all conditions. This list was subtracted from the entities present in at least one conditions  by means of VENN diagramms. Entities differentially expressed  in anti-TNF non responders compared to anti-TNF responders  were obtained by Volcano plot analysis (fold change >=2, p-value <=0.05, Benjamini Hochberg fals discovery fals positive correction).

source_name: CD anti-TNF non-responder, replicate 1

label_protocol: Cy3-labeled cRNA were prepared according to the agilent protocol from 100ng total RNA (One-Color Microarray-based gene expression analysis v.5.5)

growth_protocol: Intestinal biopsies or gut resections from Crohn’s disease patients were used for microarray.

extract_protocol: RNA was isolated from intestinal biopsies using the Nucleo Spin II kit (Macherey-Nagel, Düren, Germany).

treatment_protocol: CD patients were classified as responders to anti-TNF therapy, if they had ongoing anti-TNF therapy (infliximab or adalimumab) for over 3 months and a Simple Endoscopic Score for Crohn's Disease (SES-CD)27,28 <5 during the endoscopic examination where the biopsy was taken. Non-response was defined by a SES-CD ≥5 to ongoing anti-TNF therapy (over 3 months), or if the surgical intestinal specimen used, had a segmental SES-CD ≥5. If clinical response to anti-TNF therapy was additionally defined as an evaluation criterion, the respective condition is stated in the text. Concomitant medication of the patients included salicylates, corticosteroids or azathioprine.

tag: patient

value: CD anti-TNF non- responder

value: Intestine


title: Pygo2 ChIPseq_1


title: CD anti-TNF non-responder 3

source_name: CD anti-TNF non-responder, replicate 3

tag: tissue


title: 1eCeN32


title: 4eCeN6


title: MEF-1

city: Boston

first: Ori

last: Bar-Nur

state: MA

address: 185 Cambridge st.

institute: Harvard University

description: Mouse embryonic fibroblasts#1

data_processing:
PICARD, Version: 1.100
STAR, version 2.3.0
HTSeq, version 0.6.0 (unstranded) using Ensembl release 67 transcript annotations
EdgeR
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files with whole-genome RNA-seq coverage; spreadsheets of gene expression values for each sample

source_name: Mouse embryonic fibroblasts#1

growth_protocol: Reprogramming of MEFs and TTFs into iMPCs was performed using “iMPC medium” containing KnockOut-DMEM (ThermoFisher Scientific, catalog number 10829-018) supplemented with 10% FBS (HyClone catalog number SH30396.03), 10% KnockOut Serum Replacement (ThermoFisher Scientific, Catalog number 10828028), 1% GlutaMAX (Catalog number 35050061), 1% non-essential amino acids (ThermoFisher Scientific, Catalog number 11140050), 1% penicillin-streptomycin (ThermoFisher Scientific, catalog number 15140122), 0.1% β-mercaptoethanol (ThermoFisher Scientific, catalog number 21985-023) and 10ng/ml basic FGF (R&D 233-FB). Forskolin (Sigma-Aldrich F6886) and RepSox (Sigma-Aldrich, R0158) were added at a concentration of 5μM each. For some experiments, 3μM of the GSK3β inhibitor CHIR99021 (Tocris) was used. Doxycycline (Sigma-Aldrich, D9891) was added at a final concentration of 2μg/ml. For all reprogramming experiments, cells were reprogrammed in “iMPC medium” with and without Forskolin, RepSox and GSK3βi. Expanded bulk cultures as well as iMPC clones were cultured in iMPC medium without dox and supplemented with Forskolin (5μM), RepSox (5μM), and GSK3 inhibitor (3μM).

extract_protocol:
DNase I-treated total RNA was extracted using RNeasy Mini or Micro Kit (74004) according to the manufacturer’s instructions (Qiagen).
PolyA selection followed by library construction using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs)

value: Mouse embryonic fibroblasts


title: Input_2

value: input


title: iMPC-Pax7-nGFP-minus

description: Pax7-nGFP- iMPCs (sorted)

source_name: Sorted for Pax7-nGFP- cells

value: Induced myogenic progenitors cells


title: Input_1


title: 4eCeN3

source_name: Soil microbes in BioCON plots


title: 4eCeN1


title: 4eCeN2


title: iMPC-Pax7-nGFP-plus

description: Pax7-nGFP+ iMPCs (sorted)

source_name: Sorted for Pax7-nGFP+ cells


title: ASCmyo-Pax7-plus-p1

description: Activated satellite cells

source_name: Activated satellite cells

value: Activated satellite cells


title: 1eCeN29

value: elevated CO2, elevated N


title: CD anti-TNF responder 1

description: Gene expression of CD anti-TNF responder

source_name: CD anti-TNF responder, replicate 1

value: CD anti-TNF responder


title: 1eCeN31


title: 1eCeN30


title: CD anti-TNF responder 2

source_name: CD anti-TNF responder, replicate 2


title: CD anti-TNF responder 3

source_name: CD anti-TNF responder, replicate 3


title: QSC-3

description: Quiescent satellite cells mouse#3

source_name: Quiescent satellite cells mouse#3

value: Quiescent satellite cells


title: TP53null-2

city: BOSTON

first: Teresa

last: Davoli

address: 12 Aberdeen Street, 2

institute: BRIGHAM AND WOMEN S Hospital

data_processing:
HISAT2 (Kim et al., Nat Method, 2015)
Aligned reads were annotated using a matched build of all known gene transcripts and spliceforms.
Sorted bam files from this alignment were then assessed for transcript frequency using the featureCounts application of the Subread suite, defining features at the exon-level (Liao et al. Bioinformatics, 2014)
We filtered raw counts to remove transcripts that had less than 20 reads across all samples.
Counts were then normalized with Limma’s voom function and differential expression was determined with Limma’s general linear model.
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: txt files that include counts normalized with Limma’s voom function.

molecule: polyA RNA

source_name: hTERT human mammary epithelial cells (hMEC)

growth_protocol: HMECs (Lonza cat # CC-2551) were immortalized with hTERT, and were maintained in MEGM (Lonza cat # CC-3150).

extract_protocol:
Cells were lysed and RNA extracted using the Qiagen RNeasy kit per manufacturer’s instructions. Poly-A tailed mRNAs were enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module per manufacturer’s instructions.
Poly-A tailed mRNAs were then prepped into RNA-Seq libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina. RNA-Seq libraries were amplified and indexed using NEBNext® Multiplex Oligos for Illumina® per manufacturer’s instructions.
Libraries were sequenced on an Illumina HiSeq 2500.

treatment_protocol: Cells plated at equal density, treated with 100 ng/ml dox for 96 hours.

value: cells TP53 knock-out

tag: sample type

value: CRISPR TP53 KO


title: QSC-1

description: Quiescent satellite cells mouse#1

source_name: Quiescent satellite cells mouse#1


title: EV-2

value: cells expressing Empty Vector

value: pInducer-rtTA-Neo


title: EV-1


title: TP53null-1


title: 1eCeN28


title: 1eCeN27


title: KAP106-2

value: cells overexpressing KRTAP10-6


title: 1eCeN24


title: SRC-2

value: cells overexpressing SRC

value: pInducer-rtTA-Neo and pHAGE-TRE-BC-SRC


title: KAP106-1


title: 1eCeN26


title: 1eCeN25


title: SRC-1