title: SARS-CoV-2 in vitro transcribed 85nt

first: Silvi

last: Rouskin

institute: Whitehead Institute for Biomedical Research

description: in vitro transcribed from DNA template

data_processing:
Reads were aligned to the genome of SARS-CoV-2 strain USA-WA1/2020 (GenBank: MN985325.1) using Bowtie2 v2.3.4.1 with the parameters --local --no-unal --no-discordant --no-mixed -L 12 -X 1000.
Mutations with respect to the reference genome were identified using DREEM software.
Average mutational frequencies ber base were computed and normalized (setting the median of the top 5% of frequences to 1, scaling linearly, and winsorizing all values >1 to 1) using DREEM software.
The structure of the entire genome was folded in ten segments using the Fold program from RNAstructure v6.0.1 with the normalized mutational frequencies as folding constraints.
Reads were filtered using DREEM if they had a pair of mutations closer than 4 bases, had a mutation next to a position with no information, or had a number of mutations greater than 3 standard deviations above the median among all reads.
Filtered reads were clustered and the mutation rate per position in each cluster was computed and normalized (setting the median of the top 5% of frequences to 1, scaling linearly, and winsorizing all values >1 to 1) with DREEM.
The structure of the frameshift element was folded using the ShapeKnots program from RNAstructure v6.0.1 with the normalized cluster mutation rates as constraints in folding.
Genome_build: USA-WA1/2020 (GenBank: MN985325.1)

organism: Severe acute respiratory syndrome coronavirus 2

source_name: gBlock (IDT)

extract_protocol:
The cells were centrifuged at 1,000g for 5 min at 4 °C. The cells were washed twice by resuspending the pellet with 15 ml PBS with 30% β-mercaptoethanol and centrifugation to pellet then just once with 15 ml PBS. After washes, the pellet was resuspended in 1 ml Trizol (ThermoFisher Scientific) and RNA was extracted following the manufacturer’s specifications. Total RNA was purified using RNA Clean and Concentrator -25 kit (Zymo).
rRNA was subtracted from the RNA extracted from Vero cells using rRNA subtraction mix and RNase H (Lucigen). RNA was fragmented at 70 °C for 2.5 min. The ends were dephosphorylated and repaired with Shrimp Alkaline Phosphatase at 37 °C for 1 h. Linker was added with T4 RNA ligase at 22 °C for 18 h. RNA was reverse-transcribed with TGIRT-III (Ingex) at 60 °C for 1.5 h. RT product was gel-purified and size-selected for ~250 nt, circularized with CircLigase (Lucigen), and PCR-amplified with Phusion High-Fidelity DNA Polymease (NEB) for up to 16 cycles. The product was run on a gel to select for fragments ~300 nt and sequenced on an iSeq100 (Illumina).

tag: sars-cov-2 strain

value: SARS-CoV-2 strain USA-WA1/2020 (Passage 6)

tag: dms treatment


title: Patient_27_AN_m0

status: Public on Sep 01 2020

type: SRA

city: Tampere

first: Lena

last: Möbus

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

library_source: transcriptomic

data_processing:
Illumina bcl2fastq v2.20.0.422 software used for basecalling.
Illumina standard primers were trimmed using cutadapt (version 1.15)
Reads were mapped to the human reference genome (GRCh38, Ensembl release 91) using Tophat2 (version 2.1.1) and Bowtie2 (version 2.3.2)
Mapped reads were cleaned and sorted using Samtools (version 1.5)
Number of reads for each gene was counted using HTSeq (version 0.10.0) and annotated according to the Gencode version 27 annotation gtf file
Genome_build: GRCh38, Ensembl release 91
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts as generated by HTSeq

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
RNAlater fixed skin tissue samples were disrupted using innuSPEED Lysis Tubes W (1.4 – 1.6 mm steel beads & 3.5 mm ceramic beads) (Analytik Jena, Jena, Germany) in a SpeedMill Plus (3x 1min intervals) (Analytik Jena) in Lysis/Binding Buffer (Lifetechnologies). Total RNA was isolated using the mirVanaTM miRNA Isolation Kit (Lifetechnologies, Carlsbad, CA) following the manufacturers specifications with an additional on-column DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq stranded mRNA)

tag: patient id

tag: disease state

value: atopic dermatitis

tag: timepoint

value: baseline (m0)

tag: tissue

value: skin


title: F01_1

city: Belfast

first: David

middle: Arthur

last: Simpson

state: N. Ireland

address: The Wellcome – Wolfson Institute for Experimental Medicine, 97 Lisburn Road

department: Wellcome-Wolfson Institite for Experimental Medicine

country: United Kingdom

institute: Queen's University Belfast

description:
Fluidigm_1_expression_matrix.csv
Cell 32

data_processing:
Base call files were generated on board the nextseq 500 sequencer using real time analysis (RTA) and then converted to fastq format post-run using bcl2fastq2 in BaseSpace which also removed illumina adapters
Sequencing QC was assessed using Fastqc (v0.11.3) to ensure good quality sequencing and that adapters were successfully removed
Sequenced reads (fastq format) were  aligned to bovine genome UMD3.1 (Bos Tau4) using STAR (v2.5.3a) with default settings
Alignment QC was assessed using multiQC
Gene counts calculated using HTseq (v0.6.1p1) with default settings
Created expression matrix from HTseq output
Genome_build: UMD 3.1 (bos Tau4)
Supplementary_files_format_and_content: csv files with expression matrices created from HTseq output with genes in rows and single cells in columns

molecule: total RNA

organism: Bos taurus

source_name: Retinal microvascular endothelial cells

extract_protocol:
RMECs were isolated from bovine retinas according to (Stitt, Chakravarthy, Archer, & Gardiner, 1995). RMECs were maintained in DMEM supplemented with 0.1mg/ml Primocin, 0.38μg/ml insulin, 1mg/ml heparin and 10% (v/v) porcine serum (PS). BRECs were passaged at approximately 80% confluency in a 1:3 ratio and grown until confluency at passage 3 for Fluidigm C1 runs . RMECs were dissociated form flask using TryPLE Express dissociation reagent and single cells were captured on Fluidigm C1 Microfluidics chip.
Clontech modified Illumina® Nextera® XT DNA sample preparation protocol was used for single-cell mRNA sequencing library preparation from cDNA acquired using the C1 system which was miniaturised using the Labcyte Access Robotic System in conjunction with Echo 525 Acoustic Dispenser

tag: passage


title: SARS-CoV-2 in vitro transcribed 283nt

city: Cambridge

state: MA

address: 455 Main Street

country: USA

description: in vitro transcribed from DNA template

growth_protocol: Vero cells (ATCC CCL-81) were cultured in DMEM (Gibco) supplemented with 10% FBS (Gibco) plated into 100 mm dishes and infected at a MOI of 0.01 with 2019-nCoV/USA-WA1/2020 (Passage 6). Infected cells  were incubated at 37 °C, 5% CO2 and harvested 2 days post infection. Infected cell pellets were centrifuged at 5000xg for 5 min at 4 °C and resuspended in Trizol (Ambion).

treatment_protocol: 200 μl DMS (or 2% v/v) was added dropwise to the plated Vero cells 48 h post SARSCoV-2 infection and incubated for 4 min at 37 °C. DMS was neutralized by adding 15 ml PBS (ThermoFisher Scientific) with 30% β-mercaptoethanol.

tag: cell type

tag: cell line


title: E12_1

description:
Fluidigm_1_expression_matrix.csv
Cell 31


title: Patient_26_AN_m0


title: E09_1

description:
Fluidigm_1_expression_matrix.csv
Cell 30


title: SARS-CoV-2 genomic RNA

description: RNA extracted from virions and refolded

source_name: Vero cells supernatant


title: Patient_26_AL_m0


title: "Hongyang" flesh core - rep 3

city: Jishou

first: Gui-Sheng

last: Li

address: 120 Renmin South Street

country: China

institute: Jishou University

data_processing:
Trimmomatic v0.36 to purify reads
HISAT2, v2.1.0 to align reads to genome sequences
Genome_build: http://bioinfo.bti.cornell.edu/kiwi
Supplementary_files_format_and_content: sequencing read counts

organism: Actinidia chinensis

source_name: ripened fruits

growth_protocol: ripened fruits just harvested from trees

extract_protocol:
Total RNA was isolated with CTAB method
purified mRNA by virtue of oligo (dT) was fragmented into 100 – 400 bp long with divalent cations. Random hexamer primers were used to synthesize the first-strand cDNA, and Illumina paired-end adapters were then ligated onto the both ends of the double-strand cDNA, which would produce 200 ± 25 bp molecules that immediately underwent gel purification. Sequencing was conducted on the Illumina HiSeq2000 or 4000 platform in Beijing Genomics Institute (BGI) - Shenzhen (Shenzhen, China, http://www,genomics.cn/index.php). Both forward and reverse strands were analyzed using a sequencing-by-synthesis method.

tag: cultivar

value: Hongyang

value: fruit flesh core


title: Patient_25_AL_m0


title: "Hongyang" flesh core - rep 2


title: day 0 lung, control, replicate 2

type: RNA

city: Austin

first: James

middle: C

last: Fleet

state: TX

address: 1400 Barbara Jordan Blvd

department: Nutritional Sciences

institute: University of Texas at Austin

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

hyb_protocol: Samples were hybridized with Clariom D Rat Arrays (also known as the GeneChip Rat Transcriptome Array 1.0, ThermoFisher) and scanned at the University of Colorado Anschutz Medical Campus Microarray and Genomics Core Facility. Samples were hybridized for 16 hours at 4°C.  cRNA was purified and 15 ug cRNA product was added to prepare 2nd-cycle single-stranded cDNA (ss-cDNA) synthesis by reverse transcription of cRNA.  RNase H was added to remove template RNA. 5ug purified ss-cDNA was obtained for fragmentation.  UDG and APE 1 were added to break the DNA strand.  The fragmented cDNA was labeled with TdT and biotinylated labeling reagents.  5.2 ug (in 60µl) of fragmented and biotinylated ss-cDNA was added to 160 µl hybridization master mix.  The hybridization cocktails were heated at 99° for 5 minutes and 45°C before injecting 200 µl into the Clariom D Rat array.  The arrays were incubated in the GeneChip Hybridization Oven 640 and rotated at 60 rpm for 16 hours at 45°C.  Immediately after the completion of hybridization, the arrays were stained and washed using GeneChip Hybridization, wash, and stain kit (Thermo Fisher Scientific REF 901240) and GeneChip Fluidics Station 450. Array was scanned using GeneChip Scanner 3000 7G.

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

data_processing:
RMA Normalization was done using RMA express (http://rmaexpress.bmbolstad.com/).  The full list of 68,842 RMA normalized probesets is provided with this submission.   This list was reduced to 22,133 by removing probesets that had no annotation, were annotated to ESTs, or were annotatated to non coding RNAs.  Differential gene expression was determined using Significance Analysis of Microarrays in BRB Array Tools v 4.5.1. and the following settings: exclude genes with log-ratio variation < 50%; 500 permutations; FDR = 5%, and 90% false negative rate (type II error). 11066 probesets met the exclusion criteria.  Following statistical analysis, probesets that represented duplicate analysis of genes were removed to create the final results (this list is provided with the submission).
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = RTA-1_0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

organism: Rattus norvegicus

source_name: newborn pup from vitamin D adequate mother

label_protocol: Samples were prepared according to the standard GeneChip Whole Transcript Expression protocol.  In the reverse transcription procedure, high quality total RNA was primed with primers containing a T7 promoter sequence.  The reaction synthesized first-strand cDNA with T7 promoter sequence at the 5’ end. The second –strand cDNA was synthesized using DNA polymerase and RNAase H.  The second-strand cDNA was converted to double-stranded cDNA, which acted as a template for in vitro transcription.

growth_protocol: The whole lungs of offspring from vitamin D adequate or vitamin D deficent mothers were harvested on day of life 1.

extract_protocol: Lung tissue was homogenized in TRIzol reagent (Invitrogen) using a PowerGen 500 homogenizer (Fisher Scientific). Total RNA was extracted using the Qiagen miRNeasy Mini Kit as per the manufacturer’s instructions.

tag: maternal status

value: vitamin D adequate mother

tag: age

value: day 0 newborn

value: lung


title: E07_1

description:
Fluidigm_1_expression_matrix.csv
Cell 28


title: pcDNA cells, 16h, replicate 2

city: Gentofte

first: Flemming

last: Pociot

address: Niels Steensens Vej 2

department: T1D Biology

country: Denmark

institute: Steno Diabetes Center Copenhagen

hyb_protocol: A total of 7.5 µg of labeled cRNA was fragmented, and a hybridization cocktail was prepared, plated, and loaded into an Affymetrix GeneTitan system. Hybridization was performed for 16h on HT Rat230+PM microarrays. The GeneTitan system was used to perform the microarray hybridization, washing, and scanning.

scan_protocol: Image acquisition and quantification were performed using the Affymetrix GeneChip Operating Software (GCOS).

data_processing: Cel files were read into an AffyBatch object, quantile normalized and corrected for background using RMA background correction in the affy package in R statistical environment. Differential expression analysis was carried out on non-control probes with an empirical Bayes approach using LIMMA package in R. Principal Component Analysis (PCA) method was employed for the initial interpretation of the data. P-values were adjusted for multiple comparisons using the FDR correction. Differentially expressed genes were identified using the double-filtering criterion: FDR-adjusted p-value < 0.05 and an absolute log2 fold change > 1.2. For transcripts targeted by more than one probe only those probes that were changing in the same direction and the probes with highest fold change values were retained for further analysis.

source_name: INS1 cells, transfected with empty pcDNA vector, treated with IL-1β and IFNγ for 16 hours

label_protocol: Briefly, double-stranded cDNA was synthesized for each of the 21 samples from 100ng of total RNA, and biotin-labeled cRNA was transcribed using the IVT Express Kit (Affymetrix, Santa Clara, California).

growth_protocol: The generation of INS-1 cells stably transfected with a plasmid encoding CTSH (pCTSH) or an empty control vector (pcDNA) has been described previously (Floyel et al. PNAS 2014). Untransfected INS-1 cells, pcDNA cells, and two CTSH-overexpressing clones (pCTSH#1, pCTSH#2) were cultured as previously described (Floyel et al. PNAS 2014).

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. RNA quantity and purity was determined by UV absorbance using a NanoDrop 2000 (Thermo Scientific) and the RNA integrity was evaluated using the 2100 Bioanalyzer RNA 6000 Nanochips (Agilent Technologies, CA, USA). All samples had RNA Integrity Number (RIN) above 8.5.

treatment_protocol: Cells were seeded in 12-well culture plates (0.25x106 cells/well) and precultured for 3 days before exposure to 150 pg/ml recombinant mouse IL-1β (BD Pharmingen) and 5 ng/ml recombinant rat IFNγ (R&D Systems) for 0, 6, and 16 hours.

value: Rat insulin secreting INS1 cells

tag: treatment


title: E08_1

description:
Fluidigm_1_expression_matrix.csv
Cell 29


title: day 0 lung, control, replicate 3


title: Patient_25_AN_m0


title: pCTSH1 cells, 6h, replicate 2

source_name: INS1 cells, transfected with pCTSH vector, treated with IL-1β and IFNγ for 6 hours


title: day 0 lung, Vit D deficient mother replicate 1

source_name: newborn pup from vitamin D deficient mother

value: vitamin D deficient mother


title: E05_1

description:
Fluidigm_1_expression_matrix.csv
Cell 27


title: "Hongyang" flesh core - rep 1


title: pcDNA cells, 6h, replicate 2

source_name: INS1 cells, transfected with empty pcDNA vector, treated with IL-1β and IFNγ for 6 hours


title: pCTSH1 cells, 0h, replicate 2

source_name: INS1 cells, transfected with pCTSH vector, no treatment


title: pcDNA cells, 0h, replicate 2

source_name: INS1 cells, transfected with empty pcDNA vector, no treatment


title: Patient_24_AL_m0


title: day 0 lung, control, replicate 1


title: pCTSH1 cells, 16h, replicate 1

source_name: INS1 cells, transfected with pCTSH vector, treated with IL-1β and IFNγ for 16 hours


title: INS1 cells, 0h, replicate 2

source_name: INS1 cells, no treatment

value: no treatment


title: pcDNA cells, 16h, replicate 1

value: transfected with empty pcDNA vector, treated with IL-1β and IFNγ for 16 hours


title: E03_1

description:
Fluidigm_1_expression_matrix.csv
Cell 26


title: Patient_24_AN_m0


title: "Hongyang" whole fruit - rep 3

value: whole fruit


title: pcDNA cells, 6h, replicate 1

value: transfected with empty pcDNA vector, treated with IL-1β and IFNγ for 6 hours


title: "Hongyang" whole fruit - rep 2


title: Patient_23_AN_m0


title: "Hongyang" whole fruit - rep 1


title: Patient_23_AL_m0


title: Patient_22_AN_m0


title: "Jinyan" flesh core - rep 3

value: Jinyan


title: D11_1

description:
Fluidigm_1_expression_matrix.csv
Cell 23


title: E01_1

description:
Fluidigm_1_expression_matrix.csv
Cell 24


title: "Jinyan" flesh core - rep 2


title: Patient_22_AL_m0


title: D09_1

description:
Fluidigm_1_expression_matrix.csv
Cell 22


title: "Jinyan" flesh core - rep 1


title: D08_1

description:
Fluidigm_1_expression_matrix.csv
Cell 21


title: Patient_21_AL_m0


title: pcDNA cells, 0h, replicate 1

value: transfected with empty pcDNA vector, no treatment


title: pCTSH1 cells, 0h, replicate 1

value: transfected with pCTSH vector, no treatment


title: E02_1

description:
Fluidigm_1_expression_matrix.csv
Cell 25


title: D06_1

description:
Fluidigm_1_expression_matrix.csv
Cell 20


title: "Jinyan" whole fruit - rep 2


title: INS1 cells, 0h, replicate 1


title: Patient_21_AN_m0

value: atopic dermatitis


title: Patient_20_AL_m0

value: baseline (m0)


title: D04_1

description:
Fluidigm_1_expression_matrix.csv
Cell 19


title: "Jinyan" whole fruit - rep 3


title: "Jinyan" whole fruit - rep 1


title: D02_1

description:
Fluidigm_1_expression_matrix.csv
Cell 18


title: pCTSH1 cells, 6h, replicate 1

value: transfected with pCTSH vector, treated with IL-1β and IFNγ for 6 hours


title: A10_2

description:
Fluidigm_2_expression_matrix.csv
Cell 56


title: Soleus_WT_200 [24]

city: Paris

first: Nicolas

last: Vignier

address: 105 bld de l'Hopital

country: France

institute: INSERM

hyb_protocol: Samples were hybridized for 16 hours at 45°C (60rpm) on Affymetrix Mouse Gene 2.0 ST Arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: R – Bioconductor , Partek GS ®

organism: Mus musculus

source_name: Soleus skeletal muscle from wild type mouse at post symptomatic stage

label_protocol: GeneChip™ WT Pico Reagent Kit (Applied Biosystem)

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

tag: strain background

tag: genotype/variation

value: WT

tag: age (days)

value: Soleus skeletal muscle


title: Soleus_WT_200 [25]


title: Patient_20_AN_m0

value: skin


title: Faecalicatena contorta 588 Porphyran 2

city: Ann Arbor

first: Eric

last: Martens

state: MI

address: 1150 W. Medical Center Dr.

institute: University of Michigan

description:
Fcontorta588 DEseq
126123_GAATTCGT-ATAGAGGC_S16_L004_R1_001

data_processing:
Data was analyzed using Arraystar software (DNASTAR, Inc.)
DEseq2 normalization with default parameters
Gene expression in seaweed polysaccharides was compared to gene expression in galactose reference
Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >10-fold and with both biological replicates with a normalized expression level >1%
Genome_build: B. thetaiotaomicron 3731 is NZ_CVOY00000000.1 (B. xylanisolvens 18002P, F contorta 548 and 588 are de novo assemblies)
Supplementary_files_format_and_content: xslx files include DEseq2 values for each sample

organism: Faecalicatena contorta

source_name: Bacterial Total RNA

growth_protocol: Strains were grown to mid-log on 5 mg/ml seaweed polysaccharides (carrageenan, agarose and/or poprhyran respective to strain) or galactose as a sole carbon source in vitro.

extract_protocol:
Qiagen Rneasy kit and rRNA depleted with Microbe Express Kit (Thermo Fisher)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were centrifuged to remove negatively charged polysaccharides and cell pellets were treated with two volumes of RNA Protect (Qiagen) of the original culture volume then frozen at -80C until RNA was extracted

tag: strain

tag: carbon source

value: Porphyran


title: D01_1

description:
Fluidigm_1_expression_matrix.csv
Cell 17


title: Patient_19_AN_m0


title: C08_1

description:
Fluidigm_1_expression_matrix.csv
Cell 16


title: Soleus_WT_200 [50]


title: Faecalicatena contorta 588 Galactose 2

description:
Fcontorta588 DEseq
126121_ATTCAGAA-ATAGAGGC_S14_L004_R1_001

value: Galactose


title: Faecalicatena contorta 588 Porphyran 1

description:
Fcontorta588 DEseq
126122_GAATTCGT-TATAGCCT_S15_L004_R1_001


title: Faecalicatena contorta 588 Galactose 1

description:
Fcontorta588 DEseq
126120_ATTCAGAA-TATAGCCT_S13_L004_R1_001


title: C07_1

description:
Fluidigm_1_expression_matrix.csv
Cell 15


title: Patient_19_AL_m0


title: Soleus_WT_200 [108]


title: C05_1

description:
Fluidigm_1_expression_matrix.csv
Cell 14


title: Faecalicatena contorta 548 Porphyran 2

description:
Fcontorta548 DEseq
126119_GAGATTCC-GTACTGAC_S12_L004_R1_001


title: Soleus_WT_200 [107]


title: Soleus_HMZ_200 [6122]

source_name: Soleus skeletal muscle from Lmnap.H222P homozygous mouse at post symptomatic stage

value: p.H222P homozygote


title: Faecalicatena contorta 548 Porphyran 1

description:
Fcontorta548 DEseq
126118_GAGATTCC-CAGGACGT_S11_L004_R1_001


title: C02_1

description:
Fluidigm_1_expression_matrix.csv
Cell 13


title: Patient_18_AN_m0


title: Soleus_HMZ_200 [609]


title: Soleus_HMZ_200 [6121]


title: B12_1

description:
Fluidigm_1_expression_matrix.csv
Cell 12


title: Patient_17_AN_m0


title: Soleus_HMZ_200 [601]


title: Patient_17_AL_m0


title: B09_1

description:
Fluidigm_1_expression_matrix.csv
Cell 11


title: Patient_16_AN_m0


title: Faecalicatena contorta 548 Agarose 1

description:
Fcontorta548 DEseq
126116_CGCTCATT-CAGGACGT_S9_L004_R1_001

value: Low-melt agarose


title: Soleus_HMZ_200 [139]


title: Faecalicatena contorta 548 Agarose 2

description:
Fcontorta548 DEseq
126117_CGCTCATT-GTACTGAC_S10_L004_R1_001


title: Soleus_WT_80 [692]

source_name: Soleus skeletal muscle from wild type mouse at pre symptomatic stage


title: B08_1

description:
Fluidigm_1_expression_matrix.csv
Cell 10


title: Patient_18_AL_m0


title: Faecalicatena contorta 548 Galactose 2

description:
Fcontorta548 DEseq
126115_TCCGGAGA-TAATCTTA_S8_L004_R1_001


title: Soleus_WT_80 [691]


title: B07_1

description:
Fluidigm_1_expression_matrix.csv
Cell 9


title: Patient_15_AL_m0


title: Soleus_WT_80 [689]


title: B06_1

description:
Fluidigm_1_expression_matrix.csv
Cell 8


title: Faecalicatena contorta 548 Galactose 1

description:
Fcontorta548 DEseq
126114_TCCGGAGA-AGGCGAAG_S7_L004_R1_001


title: Patient_15_AN_m0


title: B04_1

description:
Fluidigm_1_expression_matrix.csv
Cell 7


title: Soleus_WT_80 [688]


title: Patient_14_AN_m0


title: myh7b_aso_3

city: Boulder

first: Lindsey

middle: Joe

last: Broadwell

state: CO

address: 3415 Colorado Avenue, Apt, Suite, Bldg. (optional)

department: Biochemistry

institute: University of Colorado Boulder

data_processing:
nf-core/rnaseq v1.4.2
DEseq2/R
Genome_build: v33/GRCh38.p13
Supplementary_files_format_and_content: comma separated values file summarizing TPM for each sample and gene
Supplementary_files_format_and_content: comma separated file summarizing differential expression for scrambled vs knockdown samples

source_name: hiPSC cardiomyocytes

growth_protocol: iPSCs were differentiated to cardiomyocytes using the small molecule protocol then matured for 35 days before treatment.

extract_protocol:
Trizol
poly-A selection

treatment_protocol: Treated passively with either scrambled or targeted ASO at 2 uM for 96 hrs.

value: induced pluripotent stem cell cardiomyocyte

value: anti-MYH7b ASO


title: myh7b_aso_4


title: myh7b_aso_2


title: Patient_13_AN_m0


title: B02_1

description:
Fluidigm_1_expression_matrix.csv
Cell 5

source_name: Retinal microvascular endothelial cells


title: Patient_14_AL_m0


title: myh7b_aso_1


title: Patient_16_AL_m0


title: Patient_13_AL_m0


title: A08_1

description:
Fluidigm_1_expression_matrix.csv
Cell 4


title: Ctl_aso_3

value: scrambled ASO


title: A05_1

description:
Fluidigm_1_expression_matrix.csv
Cell 3


title: B03_1

description:
Fluidigm_1_expression_matrix.csv
Cell 6


title: Patient_12_AL_m0


title: siCNTRL_normoxia_patient_2_replicate_2

city: Stanford

first: Marlene

last: Rabinovitch

state: California

address: 269 Campus Drive CCSR Building, Room 1215A

institute: Stanford

data_processing:
Data was aligned to the human genome (GRCh37.p13) by STAR (STAR_2.5.4b) (https://github.com/alexdobin/STAR).
The aligned transcripts were quantitated based on features in the GENCODE annotation database (GRCh37, version 19) by RSEM (http://deweylab.biostat.wisc.edu/rsem/).
Differentially expressed genes were detected using DESeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) with a p-value cutoff of <0.01.
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: raw gene counts matrix of all samples combined

source_name: Pulmonary Artery

growth_protocol: PAEC were grown in complete EC media (EC basal medium, ECGS and 5% FBS; (ScienCell, Carlsbad, CA) supplemented with 5% FBS.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (#74136, Qiagen) from PAEC (2 biological, 2 technical replicates).
Libraries were prepared using QuantSeq 3′ mRNA-Seq Library Prep Kit REV for Illumina (#016.96, Lexogen).

treatment_protocol: Hypoxia treatment of cells was performed with a Ruskinn InVivo2 Hypoxia Work Station (0.5% O2).

value: Endothelial Cell

tag: treatment 1

value: siCNTRL

tag: treatment 2

value: Normoxia


title: A03_1

description:
Fluidigm_1_expression_matrix.csv
Cell 2


title: Ctl_aso_2


title: Soleus_HMZ_80 [94]

source_name: Soleus skeletal muscle from Lmnap.H222P homozygous mouse at pre symptomatic stage


title: Soleus_HMZ_80 [95]


title: Soleus_HMZ_80 [97]


title: Ctl_aso_1


title: Soleus_HMZ_80 [549]


title: Patient_12_AN_m0

tag: patient id

tag: disease state


title: Soleus_WT_80 [687]

tag: tissue


title: A02_1

description:
Fluidigm_1_expression_matrix.csv
Cell 1

tag: passage


title: Patient_11_AN_m0

tag: timepoint


title: siCNTRL_normoxia_patient_1_replicate_2

tag: cell type


title: PAIVS 2 - hCAS

city: Hong Kong

first: Yin Yu

last: Lam

address: 102 Pokfulam Road

department: Department of Paediatrics and Adolescent Medicine

institute: The University of Hong Kong

data_processing:
Raw sequencing reads filtered and aligned with Cell Ranger 2.0
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.mtx (RNA expression levels)
Supplementary_files_format_and_content: barcodes.tsv (Cell identification code)
Supplementary_files_format_and_content: features.tsv (List of genes)

source_name: Human induced pluripotent stem cell derived cardiomyocytes

extract_protocol:
hiPSC-CMs and hCAS were dissociated with 1X TrypLE and hCTS were dissociated with collagenase IV. Dissociated cells were resuspended in RPMI/B27 for cell encapsulation.
Constructed with Chromium Single Cell 3' Reagent Kit according to manufacturer's protocol
scRNA-seq

value: PAIVS


title: Soleus_HMZ_80 [96]


title: Patient_11_AL_m0

value: atopic dermatitis


title: Patient_10_AN_m0

value: baseline (m0)


title: Patient_9_AL_m0


title: siCNTRL_normoxia_patient_1_replicate_1


title: Control 2 - hCAS

value: Human induced pluripotent stem cell derived cardiomyocytes

value: Normal


title: Δcol-26_2%G_rep1

city: Tianjin

first: chaoguang

last: Tian

address: 32 Xi Qi Dao, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic (v0.36) with parameters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:50
Clear reads were mapped to Neurospora crassa OR74A genome (version 12) using HISAT2 (v2.1.0) with parameters --dta --phred64 unstranded --new-summary -x index -1 read_r1 -2 read_r2（PE）
The counts of reads uniquely mapped to only one gene for each gene were calculated by RSEM (v1.2.8) with default parameters.
The normalized expression values for each gene were calculated by the number of uniquely mapped fragments per kilobase of transcript per million mapped reads (FPKM) and differential gene expression was determined by DESeq package (v1.5.1).
Genome_build: Neurospora crassa OR74A
Supplementary_files_format_and_content: tab-delimited text files including FPKM values for each sample.

organism: Neurospora crassa

source_name: Mycelia

growth_protocol: Conidia  from 10-day-old agar culture were collected and counted by haemocytometer, then  inoculated into 100 mL liquid Vogel's minimal medium (VMM) supplemented with 2.0% sucrose and grown at 28˚C and 200 rpm in constant light for 16 h. The mycelial biomass was washed with sterilized water at least five times and then transferred to 100 mL VMM with different glucose concentration (0%, 0.05%, 0.5%, 2%) for 1 h before RNA extraction.

extract_protocol:
Mycelia were harvested by vacuum filtration with Whatman filter paper, frozen immediately in liquid nitrogen. Total RNA from frozen samples was isolated using TRIzol reagent and an additional clean-up was performed for DNA degradation using the RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mycelia

tag: glucose concentration

tag: genotype


title: PAIVS 2 - hiPSC-CM


title: Control 2 - hCTS


title: siCNTRL_6h_hypoxia_patient_2_replicate_2

value: 6h Hypoxia


title: Δcol-26_0.5%G_rep2


title: Δcol-26_0.5%G_rep1


title: Patient_10_AL_m0

value: skin


title: siCNTRL_6h_hypoxia_patient_2_replicate_1


title: Control 1 - hiPSC-CM


title: siCNTRL_normoxia_patient_2_replicate_1


title: Control 1 - hCTS


title: RIP_seq THP1 stimulated sample IgG-IP rep 1

city: Nashville

first: Manuel

last: Ascano

state: TN

address: 2215 Garland Avenue

institute: Vanderbilt University

description:
ribo-minus
RIPseq_countdata
2379-KR-10-CAACTCCA-GAATCCGT_S61
RIP_THP1_stimulated_IgG_rep1

data_processing:
RNA-seq and RIP-seq data were aligned to human genome (hg19) using STAR mapper and CPM values for each gene were calculated using DeSeq2
PAR-CLIP data was processed using PARa-lyzer
SLAM-seq data was processed using SLAM-DUNK
Genome_build: Encode hg19
Supplementary_files_format_and_content: counts for RNA-Seq and RIP-seq; PARalyzer output for clusters; SLAM-seq Tcounts outout

source_name: innate immune cell line

growth_protocol: Human THP-1s monocytes (male) were cultured in RPMI (Gibco) with 10% fetal bovin serum (FBS from Peal Serum), 100 μg/ml streptomycin (Gibco), 100 U/ml penicillin (Gibco), 25 μg/ml blasticidin and 100 μg/ml hygromycin (Invivogen).

extract_protocol:
RNA-Seq, RIP-Seq, and SLAM-Seq: total RNA was extracted using TriZol.
RNA-Seq and RIP-Seq: ribo-minus and standard Illumina protocol.
PAR-CLIP: small-RNA cloning and TruSeq Small RNA library prep kit
SLAM-Seq: Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina

treatment_protocol: Stimulated cells were treated with EC50 cGAMP for 16 hours to initiate an IRF3 innate immune response

tag: cell line

value: THP-1 monocytic-like cell line

value: treated for 16 hours with (70 nM cGAMP)

tag: antibody

value: anti-IgG antibody


title: Δcol-26_2%G_rep2


title: Δcol-26_NoC_rep1


title: Δcol-26_0.05%G_rep1


title: siCNTRL_6h_hypoxia_patient_1_replicate_1


title: Patient_8_AN_m0


title: siCNTRL_24h_hypoxia_patient_2_replicate_2

value: 24h Hypoxia


title: siCNTRL_6h_hypoxia_patient_1_replicate_2


title: Δcol-26_NoC_rep2


title: RIP_seq THP1 stimulated sample IgG-IP rep 2

description:
ribo-minus
RIPseq_countdata
2379-KR-11-GTCATCGT-CCGCTTAA_S62
RIP_THP1_stimulated_IgG_rep2

tag: treatment


title: Δrco-3_2%G_rep2


title: Δcol-26_0.05%G_rep2


title: RIP_seq THP1 naïve sample IgG-IP rep 2

description:
ribo-minus
RIPseq_countdata
2379-KR-8-TATGGCAC-TTGCGAGA_S59
RIP_THP1_naive_IgG_rep2


title: RIP_seq THP1 naïve sample IgG-IP rep 1

description:
ribo-minus
RIPseq_countdata
2379-KR-7-GTCGATTG-AAGACCGT_S58
RIP_THP1_naive_IgG_rep1


title: RIP_seq THP1 stimulated sample Flag-IP rep 2

description:
ribo-minus
RIPseq_countdata
2379-KR-5-CCGCTTAA-GTCATCGT_S56
RIP_THP1_stimulated_Flag_rep2

value: untreated

value: monoclonal anti-FLAG M2 antibody (sigma F1804-5MG)


title: Patient_8_AL_m0


title: siCNTRL_24h_hypoxia_patient_1_replicate_1

value: Endothelial Cell


title: Patient_7_AL_m0


title: siCNTRL_24h_hypoxia_patient_2_replicate_1

value: siCNTRL


title: Patient_9_AN_m0


title: Δrco-3_2%G_rep1


title: Patient_6_AL_m0


title: siBMPR2_normoxia_patient_2_replicate_2

value: Normoxia


title: Patient_7_AN_m0


title: Δrco-3_0.5%G_rep1


title: RIP_seq THP1 stimulated sample Flag-IP rep 1

description:
ribo-minus
RIPseq_countdata
2379-KR-4-GAATCCGT-CAACTCCA_S55
RIP_THP1_stimulated_Flag_rep1


title: Δrco-3_0.5%G_rep2


title: Patient_6_AN_m0


title: Patient_5_AN_m0


title: siBMPR2_normoxia_patient_2_replicate_1


title: siCNTRL_24h_hypoxia_patient_1_replicate_2


title: siBMPR2_normoxia_patient_1_replicate_2


title: siBMPR2_normoxia_patient_1_replicate_1


title: RIP_seq THP1 naive sample Flag-IP rep 2

description:
ribo-minus
RIPseq_countdata
2379-KR-2-TTGCGAGA-TATGGCAC_S53
RIP_THP1_naive_Flag_rep2


title: Δrco-3_0.05%G_rep2


title: RIP_seq THP1 naive sample Flag-IP rep 1

description:
ribo-minus
RIPseq_countdata
2379-KR-1-AAGACCGT-GTCGATTG_S52
RIP_THP1_naive_Flag_rep1


title: siBMPR2_6h_hypoxia_patient_2_replicate_1


title: Patient_4_AN_m0


title: siBMPR2_6h_hypoxia_patient_2_replicate_2


title: Δrco-3_NoC_rep2


title: Patient_4_AL_m0


title: siBMPR2_6h_hypoxia_patient_1_replicate_2


title: RNA_seq THP1 stimulated rep 2

description:
ribo-minus
RNAseq_countdata
THP1_16H_2_1_sequence
RNAseq_THP1_stimulated_rep2


title: RNA_seq THP1 stimulated rep 3

description:
ribo-minus
RNAseq_countdata
THP1_16H_3_1_sequence
RNAseq_THP1_stimulated_rep3


title: Δrco-3_0.05%G_rep1


title: Δrco-3_NoC_rep1


title: siBMPR2_6h_hypoxia_patient_1_replicate_1


title: Patient_3_AL_m0


title: RNA_seq THP1 naïve rep 3

description:
ribo-minus
RNAseq_countdata
THP1_0H_3_1_sequence
RNAseq_THP1_naive_rep3


title: Patient_3_AN_m0


title: RNA_seq THP1 stimulated rep 1

description:
ribo-minus
RNAseq_countdata
THP1_16H_1_1_sequence
RNAseq_THP1_stimulated_rep1


title: RNA_seq THP1 naïve rep 2

description:
ribo-minus
RNAseq_countdata
THP1_0H_2_1_sequence
RNAseq_THP1_naive_rep2


title: siBMPR2_24h_hypoxia_patient_2_replicate_2


title: WT_2%G_rep2

value: WT


title: Patient_2_AN_m0

value: atopic dermatitis


title: WT_2%G_rep1


title: WT_0.5%G_rep1


title: Patient_5_AL_m0

value: baseline (m0)


title: siBMPR2_24h_hypoxia_patient_2_replicate_1


title: RNA_seq THP1 naïve rep 1

description:
ribo-minus
RNAseq_countdata
THP1_0H_1_1_sequence
RNAseq_THP1_naive_rep1


title: WT_0.05%G_rep2


title: siBMPR2_24h_hypoxia_patient_1_replicate_2


title: WT_0.05%G_rep1


title: Patient_2_AL_m0


title: TEAD4_2F4

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: ChIP-seq

library_source: genomic

data_processing:
Basecalls were performed using  bcl2fastq v2.17 for NextSeq output.
ChIP-seq reads were trimmed from the 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

molecule: genomic DNA

growth_protocol: HCT116 cells (ATCC CCL-247) were grown at 37 °C in DMEM supplemented with 10% FBS (Fisher Scientific, 35-015-CV).

extract_protocol:
1x10^8 cells were fixed in 1% formaldehyde (Sigma, 252549) in PBS for 15- 20 min at room temperature and quenched with 1/10th volume of 1.25 M glycine for 5 minutes at room temperature. Cells were collected at 1,000xg for 5 minutes, washed in PBS, pelleted at 1,000xg for 5 min and pellets were flash frozen in liquid nitrogen and stored at -80°C until use. Pellets were thawed on ice and resuspended in 10 ml lysis buffer 1 (50 mM HEPES, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630, 0.25% Triton X-100 with 5μl/ml Sigma 8340 protease inhibitor cocktail incubated on ice 10 minutes, pelleted 1,500xg and subsequently washed in lysis buffer 2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and 5ul/ml protease inhibitor) as with lysis buffer 1 before resuspending in 1 ml lysis buffer 3 (10 mM tris-HCl pH 8.0, 1 mM EDTA, 0.1% SDS and 5 ul/ml protease inhibitors) for sonication. Chromatin was sheared in a 1 ml milliTUBE with AFA fiber on a Covaris E220 using 10% duty factor for 2 min. The sheared chromatin concentration was estimated with Nanodrop at OD 260 and diluted to 1 mg/ml in ChIP Dilution Buffer (10% Triton X-100, 1M NaCl and 1% Sodium deoxycholate). 1 mg chromatin was combined with 4 μg hybridoma tissue culture supernatant and rotated overnight at 4°C. 40 μl protein A/G Dynabeads was added and incubated for 2-4 hr rotating at 4°C. Samples were washed 5 times with 1 ml RIPA buffer, 2 times with TE with 50 mM NaCl. Chromatin was eluted with 800 μl elution buffer (50 mM Tris pH 8.0, 1 mM EDTA, 0.1% SDS) for 30 min at 65°C shaking at 1,500 rpm in a ThermoMixer (Eppendorf). Supernatants were collected, digested with 20 μl of 20 mg/ml Proteinase K and incubated overnight at 65°C. DNA was purified with phenol chloroform extraction. 500 μl of the aqueous phase was precipitated with 20 μl 5M NaCl, 1.5 μg glycogen and 1 ml EtOH on ice for 1 hr or at -20°C overnight.
Sequencing libraries were prepared with the KAPA HTP library prep kit (Roche) using 1-10 ng DNA and libraries were size selected with AMPure XP beads (Beckman Coulter).

treatment_protocol:
Heat shock and non-heat shock HCT116 cells were washed with PBS before fixing with 1% formaldehyde (Sigma, 252549) in PBS for 15 minutes and processing for ChIP-seq.
For RNAi, Lentiviruses were mixed with an equal volume of fresh media supplemented with 10% FBS and polybrene was added at a final concentration of 5 µg/mL to increase infection efficiency. The medium was changed 6 hours after infection. Cells were selected with 2 µg/ml puromycin for three days before processing for ChIP-seq.

value: colorectal carcinoma

tag: associated input


title: Patient #5-scRNA

city: Shanghai

first: Jia

last: Wang

state: Shanghai China

address: Huashan Rd. 1940, build 3.  Shanghai,

institute: SJTU CHINA

data_processing:
CellRanger was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 16bp 10x barcode and the 10bp UMI (bases 17-26).Index contains the sample barcode. Read 2 contains the cDNA information
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized median scaling values for each cell

source_name: Castration resistant prostate cancer (CRPC) tissue

extract_protocol:
Tumor tissues were ressected by biopsy surgery and transported in DMEM/F12 medium on ice to the laboratory within an hour.
For scRNA-seq, the tissues were dissociated into single cells suspensions using digestion buffer (DMEM/F12 Medium+ 2 mg/ml of collagenase IV + 100 IU/ml DNase I), and single cell GEMs were generated by 10X genomics Chromium Controller. cDNA library was constructed following the manufacture’s protocol.

tag: Sex

value: Male

tag: age

tag: tumor stage

value: primary tumor


title: MB1_RNAseq

city: Heidelberg

first: Venu

last: Thatikonda

address: Technologiepark III, Im Neuenheimer Feld

country: Germany

institute: German Cancer Research Center

description: MYC amplified Group 3 Medulloblastoma

data_processing:
base calling performed using RTA 1.18.64
All RNA-seq data was processed with kallisto (v 0.43.0).
Normalized read clunts (TPM; Transcripts Per Million) were quantified with 'kallisto quant' function with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Text file with TPM counts

source_name: Cerebellum

extract_protocol:
RNA was extracted from fresh frozen tissue samples using the AllPrep DNA/RNA/Protein Mini kit (Qiagen) including DNase I treatment on column according to manufacturer's instructions.
RNA sequencing libraries were prepared from 10 μg of total RNA. Sequencing was carried out with 2×51 cycles on a HiSeq 2000 instrument (Illumina)

value: Cerebellum


title: MB2_RNAseq

description: MYC amplified Group 3 Medulloblastoma


title: WT_0.5%G_rep2

tag: strain

value: Mycelia


title: HDMB03_RNApolII_ChIPSeq_MS275

description: MYC amplified Group 3 Medulloblastoma

data_processing:
base calling performed using RTA 1.18.64
ChIP-seq reads were aligned to human genome reference build hg19 using bwa mem (0.7.15). PCR duplicates were removed using picard (2.16.0).
Peaks from ChIP-seq were identified using MACS2 (2.1.0) against a genomic background with FDR < 0.05 as significant enrichments over background.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files containing genomewide normalized read density scores (log2 ratio over background)

source_name: HDMB03 cells (cerebellum)

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA (in case of H3K27ac) and protein-DNA (in case of MYC, HDAC2 and RNApolII) complexes were isolated with antibody.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on the Illumina HiSeq 2000 platform using 2 × 101 cycles according to the manufacturer’s instructions.

value: HDMB03 cells (cerebellum)

tag: chip antibody

value: RNApolII, ActiveMotif #39097

value: 5uM entinostat (MS275) for 6 hours


title: WT_NoC_rep2


title: Retina, P30-2

city: wenzhou

first: xue

middle: jiao

last: chen

address: xueyuan road

institute: wenzhou medical university

data_processing:
use trimmomatic for filtering
use find_circ and CIRI for predicting
Genome_build: mm9
Supplementary_files_format_and_content: Excel file reports counts.

source_name: Retina

extract_protocol:
Retinas 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.  Ribosome-deleted RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: retina

value: post natal day 30


title: TEAD4_1G7

description: ChIP-seq


title: TEAD3_1A4

description: ChIP-seq


title: Retina, P14-1

value: post natal day 14


title: 41-OX shoot rep 4

city: Durham

first: Peter

last: Etchells

address: Durham University

department: Department of Biosciences

institute: Durham University

data_processing:
Creation of Fastq with Casava
QC and Trimming with SeqImp
Alignment to Arabidopsis genome witrh Tophat2
Gene Counting with HTSeq
Genome_build: TAIR 10
Supplementary_files_format_and_content: Matrix of HTSeq count outputs in tab delimited format

organism: Arabidopsis thaliana

source_name: 41-OX shoot

extract_protocol:
As described in Kumar et al., (2012). A high-throughput method for Illumina RNA-Seq library preparation. Front. Plant Sci., 28 August 2012 | https://doi.org/10.3389/fpls.2012.00202
As described in Kumar et al., (2012). A high-throughput method for Illumina RNA-Seq library preparation. Front. Plant Sci., 28 August 2012 | https://doi.org/10.3389/fpls.2012.00202

value: shoot

value: 7 days old

value: Constitutive CLE41


title: Retina, P14-3


title: BRPF1_2E11

description: ChIP-seq


title: HDMB03_H3K27ac_ChIPSeq_MS275

description: MYC amplified Group 3 Medulloblastoma

value: H3K27ac, ActiveMotif #39133


title: 41-OX shoot rep 3


title: Patient_1_AN_m0

city: Tampere

first: Lena

last: Möbus

address: Arvo Ylpön katu 34

institute: Tampere University

data_processing:
Illumina bcl2fastq v2.20.0.422 software used for basecalling.
Illumina standard primers were trimmed using cutadapt (version 1.15)
Reads were mapped to the human reference genome (GRCh38, Ensembl release 91) using Tophat2 (version 2.1.1) and Bowtie2 (version 2.3.2)
Mapped reads were cleaned and sorted using Samtools (version 1.5)
Number of reads for each gene was counted using HTSeq (version 0.10.0) and annotated according to the Gencode version 27 annotation gtf file
Genome_build: GRCh38, Ensembl release 91
Supplementary_files_format_and_content: Tab-delimited text file includes raw counts as generated by HTSeq

extract_protocol:
RNAlater fixed skin tissue samples were disrupted using innuSPEED Lysis Tubes W (1.4 – 1.6 mm steel beads & 3.5 mm ceramic beads) (Analytik Jena, Jena, Germany) in a SpeedMill Plus (3x 1min intervals) (Analytik Jena) in Lysis/Binding Buffer (Lifetechnologies). Total RNA was isolated using the mirVanaTM miRNA Isolation Kit (Lifetechnologies, Carlsbad, CA) following the manufacturers specifications with an additional on-column DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq stranded mRNA)

tag: patient id

value: atopic dermatitis

value: skin


title: Retina, P7-2

value: post natal day 7


title: BRPF1_1E2

description: ChIP-seq

value: colorectal carcinoma


title: HDMB03_HDAC2_ChIPSeq_MS275

description: MYC amplified Group 3 Medulloblastoma

value: HDAC2, Abcam #ab12169


title: 41-OX shoot rep 2


title: Retina, P7-1


title: HDMB03_cMYC_ChIPSeq_MS275

description: MYC amplified Group 3 Medulloblastoma

value: cMYC, Santa Cruz #sc-764


title: Patient #6-scRNA

tag: disease state

value: Castration resistant prostate cancer (CRPC)

value: Male

value: primary tumor


title: siBMPR2_24h_hypoxia_patient_1_replicate_1

value: Endothelial Cell

tag: treatment 1

tag: treatment 2

value: 24h Hypoxia


title: Patient_1_AL_m0

tag: timepoint

value: baseline (m0)

tag: tissue


title: Retina, P30-3

value: retina

value: post natal day 30


title: WT_NoC_rep1

value: Mycelia

tag: glucose concentration

value: WT


title: BRPF1_1B2

description: ChIP-seq

tag: cell type


title: 41-OX shoot rep 1

value: shoot

value: 7 days old

tag: genotype

value: Constitutive CLE41


title: pxy shoot rep 4

source_name: pxy shoot


title: Retina, P1-1

value: post natal day 1


title: HDMB03_H3K27ac_ChIPSeq_DMSO

description: MYC amplified Group 3 Medulloblastoma

value: HDMB03 cells (cerebellum)

value: H3K27ac, ActiveMotif #39133

value: DMSO


title: HDMB03_RNApolII_ChIPSeq_DMSO

description: MYC amplified Group 3 Medulloblastoma

value: RNApolII, ActiveMotif #39097


title: Retina, P1-2


title: pxy shoot rep 3


title: HDMB03_HDAC2_ChIPSeq_DMSO

description: MYC amplified Group 3 Medulloblastoma

value: HDAC2, Abcam #ab12169


title: Retina, E18.5-1

value: embryonic 18.5


title: pxy shoot rep 2


title: Ratio40

city: Parkville

first: Kynan

middle: Thomas

last: Lawlor

state: VIC

address: Murdoch Children's Research Institute, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

data_processing:
10x library demultiplexing: CellRanger 3.1.0
HTO library demultiplexing: Cite-seq-count 1.4.3
Genome_build: GRCh38

source_name: Human iPSC kidney organoid

growth_protocol: Takasato et al, 2015 (PMID: 26444236) kidney organoid protocol, modified to use E6 base media as in Howden et al, 2019 (PMID: 30858339).

extract_protocol: 10x libraries were constructed using 10x Chromium Next GEM Single Cell 3' Reagent kit v3.1. HTO librares were constructed following "BioLegend TotalSeq™-A Antibodies and Cell Hashing with 10x Single Cell 3' Reagent Kit v3 3.1 Protocol". HTOs used were : Replicate 1 (GTCAACTCTTTAGCG), Replicate 2 (TGATGGCCTATTGGG), Replicate 3 (TTCCGCCTCTCTTTG), Replicate 4 (AGTAAGTTCAGCGTA).

treatment_protocol: Organoids were prepared in different conformations, either manually or with different bioprinting parameters

value: Kidney organoid

tag: sample type

value: bioprinting single cell


title: Ratio0

value: single cell deposition


title: BRD1_1B5

description: ChIP-seq

tag: cell line

value: colorectal carcinoma

tag: antibody


title: Bacteroides xylanisolvens 18002P Porphyran 2

description:
Bxylanisolvens18002P DEseq
104697_GGCTAC_S18_L004_R1_001

organism: Bacteroides xylanisolvens

source_name: Bacterial Total RNA

tag: carbon source

value: Porphyran


title: pxy shoot rep 1

tag: age


title: WT shoot rep 4

source_name: WT shoot

value: Col-0 wild type


title: Manual

value: manual


title: WT shoot rep 3

value: shoot


title: 15235X2 control without gRNA

city: Loma Linda

first: Hironori

last: Uehara

address: 11021 Campus st

department: Ophthalmology

institute: Loma Linda University

description: In vitro SpCas9 digested genomic DNA

data_processing:
The human GRCh38 FASTA file was downloaded from Ensembl and a reference database was created using bowtie2 version 2.3.4.
Adapters were trimmed out of reads using Cutadapt 1.16  and then aligned using Bowtie 2 in end-to-end mode (full options --end-to-end --sensitive --no-unal -k 20).
The aligned reads were loaded into R using the GenomicAlignments package and total coverage and read start coverage were calculated for the plus and minus strands.
Positions with 5 or more read starts were compared to the total coverage and read starts with less than 25% of total coverage were removed.
The filtered read starts on the positive and negative strands were joined to find predicted cut sites with either no overlap (blunt end), 1 base pair gap or 1 base pair overhang.
Genome_build: GRCh38
Supplementary_files_format_and_content: BigWig file from BamCoverage with binSize 1 and samFlagExclude 1792

extract_protocol:
Quick-DNA Plus Kit (ZymoResearch)
Illumina TruSeq Nano DNA Sample Prep kit
NovaSeq 2 x 150 bp Sequencing 30X Human Whole Genome

treatment_protocol: To produce the gRNA, in vitro transcription was performed with MEGAshortscript™ T7 Transcription Kit (Thermofisher). SpCas9 protein was obtained from NEB (M0386M). The reaction was performed in 8µg genomic DNA (AD-293), 120pmol (300nM) SpCas9, 120pmol (300nM) or 360pmol (900nM) gRNA with 1X NEBuffer™ 3.1 (total volume is 400µL) at 37℃ for 8 hours. We found that 360pmol gRNA (Cas9 : gRNA = 1 : 3) showed efficient digestion at the target site. Therefore, we proceeded with 360pmol gRNA treated gDNA for deep sequencing.

tag: group

value: SpCas9 without gRNA.


title: Bacteroides xylanisolvens 18002P Galactose 2

description:
Bxylanisolvens18002P DEseq
104695_ACTGAT_S16_L004_R1_001

tag: strain

value: Galactose


title: 15235X1 treatment with gRNA

description: In vitro SpCas9 digested genomic DNA

value: SpCas9 witht gRNA.


title: MB3_RNApolII_ChIPSeq

description: MYC amplified Group 3 Medulloblastoma

value: Cerebellum

tag: chip antibody


title: WT shoot rep 2

value: 7 days old


title: Bacteroides xylanisolvens 18002P Galactose 1

description:
Bxylanisolvens18002P DEseq
104694_GATCAG_S15_L004_R1_001


title: Retina, E18.5-2

value: retina


title: BRD1_2H2

description: ChIP-seq

tag: associated input


title: line-3-3

data_processing:
Fastq files were generated using the Illumina bcl to fastQ converter 2.20.0.422
The raw reads were quality and adapter trimmed using trimmomatic (v0.35)
The trimmed reads were mapped to the human genome (GRCh38) using the STAR aligner version 2.5.3a
The mapped reads were quantified at the gene level using the QuantMode feature in STAR aligner
Genome_build: GRCh38
Supplementary_files_format_and_content: Comma delimited text file of counts per gene with Ensembl Gene id in the first column, followed by 9 columns containing counts for each sample

source_name: human iPSCs

extract_protocol:
RNA were extracted using a Bioline Isolate II Mini kit
Illumina Truseq stranded total RNA; 150bp reads using an Illumina Novaseq 6000

value: ES-derived kidney organoid

tag: clone

tag: day of differentiation


title: HDMB03_cMYC_ChIPSeq_DMSO

description: MYC amplified Group 3 Medulloblastoma

value: HDMB03 cells (cerebellum)

value: cMYC, Santa Cruz #sc-764

tag: treatment

value: DMSO


title: line-3-2


title: WT shoot rep 1


title: 41-OX root rep 4

source_name: 41-OX root

value: root

value: Constitutive CLE41


title: LACZRNAi_GAFChIP_Rep2

city: Ithaca

first: Julius

last: Judd

state: NY

address: 417 Biotechnology Bldg; 215 Tower Road

department: Molecular Biology and Genetics

institute: Cornell University

data_processing:
Adapter sequences were trimmed using fastp v0.20.0
Reads were aligned to the dm6 genome assembly using bowtie2 v2.3.5.1
Signal tracks were generated using deepTools bamCoverage (--extendReads) v3.3.0
Genome_build: dm6
Supplementary_files_format_and_content: bigWig files of raw signal for each replicate, as well as merged normalized (reads per million) signal tracks in bigWig format

organism: Drosophila melanogaster

growth_protocol: Drosophila S2 cells were maintained in M3+BPYE medium supplemented with 10% FBS at 25 °C.

extract_protocol:
Cells were washed with ice cold PBS, then fixed in 1% Formaldehyde in PBS at 25 °C for 10 min. Formaldehyde was quenched with 0.125 M glycine. Anti-GAF (affinity purified, lab made) was coupled to Sheep-Anti-Rabbit M280 dynabeads (1:200 concentration). IPs were performed overnight at 4 °C, and after washing beads, crosslinks were reversed using SDS and Proteinase K overnight at 65 °C.
Libraries were constructed using the NEB Next Ultra II DNA library prep kit.

treatment_protocol: Growing S2 cells were diluted to 10^6 cells/mL in serum free media containing dsRNA complementary to the target transcript at final concentration 10 µg/mL. After 45 min at 25 °C, serum-containing media was added to a final serum concentration of 10%. After 2.5 days, cells were passaged 1:2 and more ds RNA was added to maintain the concentration. After a total of 5 days, flasks were harvested and pooled. Two independent knockdown replicates were performed for each target.

tag: genotype/variation

value: LACZRNAi

tag: chip anitbody

value: Anti-GAF (affinity purified, lab made)


title: LACZRNAi_GAFChIP_Rep1


title: Bacteroides xylanisolvens 18002P Porphyran 1

description:
Bxylanisolvens18002P DEseq
104696_ATTCCT_S17_L004_R1_001

data_processing:
Data was analyzed using Arraystar software (DNASTAR, Inc.)
DEseq2 normalization with default parameters
Gene expression in seaweed polysaccharides was compared to gene expression in galactose reference
Genes with significant up- or down-regulation were determined by the following criteria: genes with an average fold-change >10-fold and with both biological replicates with a normalized expression level >1%
Genome_build: B. thetaiotaomicron 3731 is NZ_CVOY00000000.1 (B. xylanisolvens 18002P, F contorta 548 and 588 are de novo assemblies)
Supplementary_files_format_and_content: xslx files include DEseq2 values for each sample

extract_protocol:
Qiagen Rneasy kit and rRNA depleted with Microbe Express Kit (Thermo Fisher)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Porphyran


title: line-3-1


title: GAFRNAi_GAFChIP_Rep1

value: GAFRNAi


title: GAFRNAi_GAFChIP_Rep2


title: MB2_HDAC2_ChIPSeq

description: MYC amplified Group 3 Medulloblastoma

tag: tissue

value: HDAC2, Abcam #ab12169


title: 41-OX root rep 3


title: 41-OX root rep 2


title: MB2_cMYC_ChIPSeq

description: MYC amplified Group 3 Medulloblastoma


title: MB3_cMYC_ChIPSeq

description: MYC amplified Group 3 Medulloblastoma


title: line-1-3

tag: cell type


title: MB3_HDAC2_ChIPSeq

description: MYC amplified Group 3 Medulloblastoma


title: MB2_RNApolII_ChIPSeq

description: MYC amplified Group 3 Medulloblastoma

value: RNApolII, ActiveMotif #39097


title: MB3_H3K27ac_ChIPSeq

description: MYC amplified Group 3 Medulloblastoma

value: H3K27ac, ActiveMotif #39133


title: line-1-2


title: 41-OX root rep 1

tag: genotype


title: MB1_RNApolII_ChIPSeq

description: MYC amplified Group 3 Medulloblastoma


title: BAPRNAi_GAFChIP_Rep2

value: BAPRNAi


title: line-1-1


title: pxy root rep 4

source_name: pxy root


title: dot-3


title: MB2_H3K27ac_ChIPSeq

description: MYC amplified Group 3 Medulloblastoma

value: Cerebellum


title: MB1_H3K27ac_ChIPSeq

description: MYC amplified Group 3 Medulloblastoma


title: BAPRNAi_GAFChIP_Rep1


title: pxy root rep 3

value: 7 days old


title: MB1_HDAC2_ChIPSeq

description: MYC amplified Group 3 Medulloblastoma


title: pxy root rep 2


title: dot-1


title: dot-2


title: MB1_cMYC_ChIPSeq

description: MYC amplified Group 3 Medulloblastoma


title: pxy root rep 1


title: SM1_MM400_OD600=1.1_Rep1

city: Taipei

first: James

middle: C.

last: Liao

address: 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan

country: Taiwan

institute: Academia Sinica

data_processing:
bcl2fastq 2.1.8 for base-calling
CLC Genomics Workbench 20.0
Genome_build: CP009273.1
Supplementary_files_format_and_content: Raw and normalized reads

organism: Escherichia coli

source_name: Synthetic methylotrophic E. coli

growth_protocol: SM1 strain was cultured in 400 mM methanol MOPS medium at 37°C 250 rpm in a New Brunswick Scientific Innova 44

extract_protocol:
SM1 total RNA was prepared using RNeasy mini kit (Qiagen)
RNA libraries were constructed using  Illumina TureSeq Standard mRNA with Ribo-Zero rRNA Removal kit

tag: culture medium

value: 400 mM methanol MOPS medium

tag: harvest od600


title: SM1_MM400_OD600=1.1_Rep2


title: WT root rep 4

source_name: WT root

value: Col-0 wild type


title: Patient #3-scRNA

tag: disease state

value: Castration resistant prostate cancer (CRPC)

tag: Sex

value: Male

tag: tumor stage

value: primary tumor


title: WT root rep 3

value: root

tag: age


title: SM1_MM400_OD600=0.7_Rep2

tag: strain


title: Patient #2-scRNA


title: WT root rep 2


title: SM1_MM400_OD600=0.7_Rep1


title: SM1_MM400_OD600=1.1_Rep3


title: Patient #1-scRNA


title: Patient #4-scRNA


title: WT root rep 1


title: Medullary thymic epitethial cell, VEGF-Trap #4

status: Public on Aug 31 2020

city: Los Angeles

first: Gay

middle: Miriam

last: Crooks

address: 610 Charles E. Young Drive, East

department: Pathology & Laboratory Med

institute: University of California Los Angeles

data_processing:
Data quality check was done on an Illumina SAV. Demultiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program.
The STAR ultrafast universal RNA-seq aligner (v2.5.2b) was used to generate the genome index and perform paired-end alignments. Reads were aligned to a genome index that includes both the genome sequence (GRCm38 primary assembly) and the exon/intron structure of known gene models (Gencode M18 genome annotation). Alignment files were used to generate gene-level count summaries with STAR's built-in gene counter. Differential expression analysis was performed with DESeq2.
Counts were normalized per-sample in units of FPKMs after correcting for gene mappable length and sample total counts.
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tab delimited, per-sample, gene expression estimates in units of FPKMs

source_name: Thymus

growth_protocol: Primary cells obtained from neonatal mice (postnatal day 3)

extract_protocol:
Cells were lyzed in QIAzol lysis agent (Qiagen cat# 79306) and RNA was extracted using the miRNeasy microkit (Qiagen cat# 217084 Hilgen, Germany) as per the manufacturer’s instructions. Total RNA was quantified using the Agilent 6000 pico kit (cat#5067-1513) in the Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA sequencing and library preparation was performed by the UCLA Technology Center for Genomics and Bioinformatics. cDNA generation and amplification was made using the Ovation RNA-Seq System V2 (cat# 7102-32, NuGEN Technologies, San Carlos, CA). Library preparation was done using the KAPA LTP kit (# KK8232, Kapa Biosystems/Roche, Wilmington, MA), according to the manufacturer’s instructions. The work flow consisted of mRNA enrichment, cDNA generation, end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on the HiSeq3000 System for a paired-ended 150bp run (Illumina).

treatment_protocol: Aflibercept (VEGF-Trap) or hFC antibodies (control)

tag: gender

value: mixed

tag: phenotype

value: 3 days


title: Medullary thymic epitethial cell, Control #2


title: Medullary thymic epitethial cell, VEGF-Trap #2


title: Medullary thymic epitethial cell, VEGF-Trap #1


title: Medullary thymic epitethial cell, VEGF-Trap #3


title: Medullary thymic epitethial cell, Control #1


title: SM1_MM400_OD600=0.7_Rep3


title: Endothelial cell, Control #1


title: Endothelial cell, VEGF-Trap #3


title: Endothelial cell, VEGF-Trap #1


title: Endothelial cell, Control #2


title: Cortical thymic epitethial cell, VEGF-Trap #4


title: Endothelial cell, VEGF-Trap #2


title: Cortical thymic epitethial cell, Control #1


title: Cortical thymic epitethial cell, Control #2


title: Cortical thymic epitethial cell, VEGF-Trap #2


title: Cortical thymic epitethial cell, VEGF-Trap #1


title: Cortical thymic epitethial cell, VEGF-Trap #3


title: CD146 mesenchymal cell, VEGF-Trap #4


title: CD146 mesenchymal cell, VEGF-Trap #2


title: CD146 mesenchymal cell, VEGF-Trap #1


title: CD146 mesenchymal cell, Control #2


title: CD146 mesenchymal cell, Control #1


title: CD146 mesenchymal cell, VEGF-Trap #3


title: CD140a+ mesenchymal cell, VEGF-Trap #4


title: CD140a+ mesenchymal cell, VEGF-Trap #3


title: Endothelial cell, VEGF-Trap #4


title: CD140a+ mesenchymal cell, Control #1


title: CD140a+ mesenchymal cell, VEGF-Trap #2


title: CD140a+ mesenchymal cell, Control #2


title: CD140a+ mesenchymal cell, VEGF-Trap #1


title: B cell+T cell+Nef WT_t=4h_rep2

first: Sheetal

last: Kaw

address: Im Neuenheimer Feld 344

department: CIID

institute: University of Heidelberg

description: Gene expression in murine B cells

hyb_protocol: The fragmented, Biotin-labeled cRNA is then added to the array  Anywhere on the array where a RNA fragment and a probe are complimentary, the RNA hybridizes to the probes in the feature.  The array is then washed to remove any RNA that is not stuck to an array (i.e., no match was made) and then stained with the fluorescent molecule that sticks to Biotin (Cy5 conjugated to streptavidin)

scan_protocol: The entire array is scanned with a laser and the information is kept in a computer for quantitative analysis of what genes were expressed and at what approximate level. GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A

data_processing: CHP files were generated using Transcriptome Analysis Console (Affymetrix).  Abs values were extracted for all samples for all genes. The values in the samples were normalized with respect to the value obtained in t=0 sample (to quantify gene modulation wrt naive B cells)

source_name: Peripheral B cells from SW-HEL mice

label_protocol: The RNA is turned into a double stranded cDNA. This is done through reverse transcription. This is done because RNA itself is not a very stable molecule and the cDNA is a way to store the RNA for a much longer period of time. When it comes time to run the array, the cDNA is allowed to go through in vitro transcription back to RNA (now known as cRNA), but this RNA is labeled with Biotin. This is done by having all the uracil bases tagged with the Biotin. This labeled cRNA is then randomly fragmented in to pieces anywhere from 30 to 400 base pairs in length

growth_protocol: Mice were kept in SPF environment, B cells were harvested from spleen and pLN and cocultured with T cells

extract_protocol: For RNA extraction: "Macherey-Nagel NucleoSpin RNA"kit was used. Total RNA was extracted.

treatment_protocol: After harvesting from mice, B cells were cocultured with T cells for indicated time

value: SW-HEL transgenic mice

value: Peripheral B cells


title: B cell+T cell+Nef WT_t=24h_rep3

description: Gene expression in murine B cells


title: B cell+T cell_t=4h_rep2

description: Gene expression in murine B cells


title: B cell+T cell+Nef WT_t=24h_rep2

description: Gene expression in murine B cells


title: B cell+T cell+Nef mut_t=24h_rep2

description: Gene expression in murine B cells


title: B cell+T cell_t=24h_rep2

description: Gene expression in murine B cells


title: B cell_t=0_rep3

description: Gene expression in murine B cells


title: B cell_t=0_rep2

description: Gene expression in murine B cells


title: B cell+T cell_t=24h_rep1

description: Gene expression in murine B cells


title: B cell+T cell+Nef WT_t=24h_rep1

description: Gene expression in murine B cells


title: B cell+T cell+Nef mut_t=24h_rep1

description: Gene expression in murine B cells


title: B cell+T cell_t=24h_rep3

description: Gene expression in murine B cells


title: B cell+T cell_t=4h_rep1

description: Gene expression in murine B cells


title: B cell+T cell+Nef WT_t=4h_rep1

description: Gene expression in murine B cells


title: B cell_t=0_rep1

description: Gene expression in murine B cells


title: Ctrl_LA4_MHS_48_rep4

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from LA-4 and MH-S coculture, control at 48h, biological replicate 4

hyb_protocol: According to the Thermo Fisher Scientific expression protocol (HWS kit)

scan_protocol: According to the Thermo Fisher Scientific expression protocol, Scanner 3000 7G

data_processing: SST-RMA gene-level probeset summary with standard settings of the Transcriptome Analysis Console (TAC; version 4.0.1.36; Thermo Fisher Scientific) . The provided SST-RMA data was obtained by including samples from an additional dataset (GEO....submitted together)

label_protocol: Total RNA (150 ng) was amplified using the WT PLUS Reagent Kit (Thermo Fisher Scientific Inc., Waltham, USA).

growth_protocol: As described in the paper. Briefly, LA-4 and MH-S cells were seeded in Ibidi 1.5H dishes of various surface area, depending on the experiment. For co-cultures, LA-4 and MH-S were grown in separate dishes up to desired confluency (lower than for monocultures) and then mixed together by adding MH-S in the LA-4 dish (1 : 40).

extract_protocol: Total RNA was isolated with the RNeasy Plus Mini Kit (Qiagen)

treatment_protocol: As described in the paper. Briefly, 24 h after seeding NM (c=1mg/mL) was added in a 10:1 (NMsurface : Cellsurface) ratios. Before exposure, NM suspension was sonicated for 10s in an ultrasonic bath (Bransonic ultrasonic cleaner, Branson 2510EMT). Cells were then incubated at 37°C and 5% CO2 atmosphere with the NM. 24 after seeding cells were exposed to NM as described above and incubated for additional desired amount of time. Growth medium for co-cultures was mixture of equal volumes of F12K and RPMI 1.

tag: cell line


title: Ctrl_MHS_48_rep2

description: Gene expression data from MH-S cells, control at 48h, biological replicate 2

value: MH-S


title: Ctrl_LA4_MHS_48_rep2

description: Gene expression data from LA-4 and MH-S coculture, control at 48h, biological replicate 2


title: Ctrl_MHS_48_rep3

description: Gene expression data from MH-S cells, control at 48h, biological replicate 3


title: Ctrl_LA4_MHS_48_rep3

description: Gene expression data from LA-4 and MH-S coculture, control at 48h, biological replicate 3


title: Ctrl_MHS_0_rep1

description: Gene expression data from MH-S cells, control at 0h, biological replicate 1


title: Ctrl_MHS_0_rep3

description: Gene expression data from MH-S cells, control at 0h, biological replicate 3


title: Ctrl_MHS_48_rep1

description: Gene expression data from MH-S cells, control at 48h, biological replicate 1


title: Ctrl_MHS_48_rep4

description: Gene expression data from MH-S cells, control at 48h, biological replicate 4


title: Ctrl_MHS_0_rep4

description: Gene expression data from MH-S cells, control at 0h, biological replicate 4


title: Ctrl_MHS_0_rep2

description: Gene expression data from MH-S cells, control at 0h, biological replicate 2


title: Ctrl_LA4_MHS_48_rep1

description: Gene expression data from LA-4 and MH-S coculture, control at 48h, biological replicate 1


title: Ctrl_LA4_MHS_0_rep4

description: Gene expression data from LA-4 and MH-S coculture, control at 0h, biological replicate 4


title: Ctrl_LA4_MHS_0_rep3

description: Gene expression data from LA-4 and MH-S coculture, control at 0h, biological replicate 3


title: Ctrl_LA4_0_rep3

description: Gene expression data from LA-4 cells, control at 0h, biological replicate 3


title: TiO2_MHS_48_rep4

description: Gene expression data from MH-S cells, treated with TiO2 nanotubes for 48h, biological replicate 4


title: Ctrl_LA4_48_rep3

description: Gene expression data from LA-4 cells, control at 48h, biological replicate 3


title: Ctrl_LA4_0_rep4

description: Gene expression data from LA-4 cells, control at 0h, biological replicate 4


title: Ctrl_LA4_48_rep4

description: Gene expression data from LA-4 cells, control at 48h, biological replicate 4


title: Ctrl_LA4_MHS_0_rep2

description: Gene expression data from LA-4 and MH-S coculture, control at 0h, biological replicate 2


title: Ctrl_LA4_MHS_0_rep1

description: Gene expression data from LA-4 and MH-S coculture, control at 0h, biological replicate 1


title: TiO2_MHS_48_rep1

description: Gene expression data from MH-S cells, treated with TiO2 nanotubes for 48h, biological replicate 1


title: TiO2_MHS_48_rep3

description: Gene expression data from MH-S cells, treated with TiO2 nanotubes for 48h, biological replicate 3


title: Ctrl_LA4_0_rep2

description: Gene expression data from LA-4 cells, control at 0h, biological replicate 2


title: TiO2_MHS_48_rep2

description: Gene expression data from MH-S cells, treated with TiO2 nanotubes for 48h, biological replicate 2


title: TiO2_MHS_4_rep4

description: Gene expression data from MH-S cells, treated with TiO2 nanotubes for 4h, biological replicate 4


title: Ctrl_LA4_48_rep2

description: Gene expression data from LA-4 cells, control at 48h, biological replicate 2


title: TiO2_LA4_MHS_48_rep3

description: Gene expression data from LA-4 and MH-S coculture, treated with TiO2 nanotubes for 48h, biological replicate 3


title: TiO2_MHS_4_rep2

description: Gene expression data from MH-S cells, treated with TiO2 nanotubes for 4h, biological replicate 2


title: TiO2_LA4_MHS_48_rep4

description: Gene expression data from LA-4 and MH-S coculture, treated with TiO2 nanotubes for 48h, biological replicate 4


title: TiO2_LA4_MHS_4_rep2

description: Gene expression data from LA-4 and MH-S coculture, treated with TiO2 nanotubes for 4h, biological replicate 2


title: H3K27Ac_4h

city: Boston

first: Li

last: Pan

address: 77 Ave Louis Pasteur

department: Pathology

institute: Brigham and Women's Hospital

data_processing:
Reads were trimmed with Trim Galore (v.0.3.7 using cutadapt v.1.8), assessed for quality with FastQC (v.0.11.3), and aligned to GRCh38/hg38 with bowtie (v.2.0.0).
Peaks were identified using MACS2 (v.2.1.1) and annotated using Homer (v3.12, 6-8-2012).
Genome_build: hg38
Supplementary_files_format_and_content: bw files

source_name: Squamous cell carcinoma (SCC) cells

growth_protocol: Cells were grown in keratinocyte medium with 1 μM GSI (compound E).

extract_protocol:
ChIP assay kit protocol (millipore)
Illumina ChIP DNA library preparation kit

treatment_protocol: GSI washout was performed for 1, 2 and 4 hours.

value: SCC IC8 cells

tag: chip antibody

value: H2K27ac (ab4729, Abcam)

value: GSI washout for 4h


title: H3K27Ac_0h

tag: treatment

value: GSI (Compound E 1 microM)


title: H3K27Ac_2h

value: GSI washout for 2h


title: TiO2_LA4_MHS_48_rep2

description: Gene expression data from LA-4 and MH-S coculture, treated with TiO2 nanotubes for 48h, biological replicate 2


title: TiO2_LA4_MHS_4_rep3

description: Gene expression data from LA-4 and MH-S coculture, treated with TiO2 nanotubes for 4h, biological replicate 3


title: TiO2_MHS_4_rep1

description: Gene expression data from MH-S cells, treated with TiO2 nanotubes for 4h, biological replicate 1


title: GRO-seq, TFF1p-KO MCF7_clone25_E2

city: Houston

first: Jiaofang

last: Shao

state: Texas

address: 6431 Fannin St

department: Department of Biochemistry and Molecular Biology

institute: McGovern Medical School, University of Texas Health Science Center

description: GRO-seq, TFF1p-KO MCF7_clone25_E2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to h19 whole genome using bowtie2 v2.2.6
The aligned reads were filtered to remove reads with MAPQ<10 by samtools, and converted to bam files. The bam files were then processed by HOMER v4.8.2 to generate bedgraph file.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files

source_name: MCF7 breast cancer cell

growth_protocol: We originally purchased MCF-7 from ATCC, which were maintained in DMEM (Gibco® #10566) media supplemented with 10% FBS (Omega Scientific, CA) in a 5% CO2 humidified incubator at 37°C (MCF-7 without stripping).

extract_protocol: Methods: The transfected MCF7 cells were subjected to GRO-seq experiments. GRO-Seq experiments were performed as previously reported (Li et al., 2013, Nature). Briefly, ~10-20 millions of MCF-7 cells were washed 3 times with cold PBS and then sequentially swelled in swelling buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2) for 5 min on ice, harvested, and lysed in lysis buffer (swelling buffer plus 0.5% NP-40 and 10% glycerol). The resultant nuclei were washed one more time with 10mL lysis buffer and finally re-suspended in 100uL of freezing buffer (50mM Tris-Cl pH8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA). For the run-on assay, re-suspended nuclei were mixed with an equal volume of reaction buffer (10mM Tris-Cl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of SUPERase-IN, 1% sarkosyl, 500uM ATP, GTP, and Br-UTP, 2uM CTP) and incubated for 5 min at 30°C . The resultant nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol LS reagent (Life Technologies) following manufacturer’s instructions. NRO-RNA was fragmented to ~300-500nt by alkaline base hydrolysis on ice and followed by treatment with DNase I and Antarctic phosphatase. These fragmented Br-UTP labeled nascent RNA was then immunoprecipitated with an anti-BrdU argarose beads (Sc32323ac, Santa Cruz Biotechnology) in binding buffer (0.5XSSPE, 1mM EDTA, 0.05% tween) for 3 hrs at 4°C with rotation. Subsequently, T4 PNK was used to repair the end of the immunoprecipitated BrU-NRO-RNA, at 37°C for 1hr. The RNA was extracted and precipitated using acidic phenol-chloroform.    cDNA synthesis was performed as per a published method (54) with few modifications. The RNA fragments were subjected to poly-A tailing reaction by poly-A polymerase (NEB) for 30 min at 37°C. Subsequently, reverse transcription was performed using oNTI223 primer and superscript III RT kit (Life Technologies). The cDNA products were separated on a 10% polyacrylamide TBE-urea gel and only those migrated between ~100-500bp were excised and recovered by gel extraction. After that, the first-strand cDNA was circularized by CircLigase (Epicentre) and re-linearized by APE1 (NEB). Re-linearized single strand cDNA (sscDNA) was separated by a 10% polyacrylamide TBE gel as described above and the product of needed size was excised (~170-400bp) for gel extraction. Finally, sscDNA template was amplified by PCR (usually between 10-14 PCR cycles) using the Phusion High-Fidelity enzyme (NEB) according to the manufacturer’s instructions. The resulted library was subjected to deep sequencing.

treatment_protocol: To induce the estrogen gene transcriptional responses, MCF-7 cells at 60-80% confluency were first hormone-stripped for 3 days in phenol-free DMEM media plus 5% charcoal dextran treated FBS (Omega Scientific, CA), and they were then treated with 100nM 17β-estradiol (E2) (Sigma) for indicated time points (usually for 1 hour). Transfection of small interfering RNAs (siRNAs) into MCF-7 cells was performed using Lipofectamine 2000 (Life technologies) following manufacturer's instructions. For all experiments, two rounds of siRNA transfection (40nM each time) were performed to achieve higher efficiency. The siRNAs used in this study include: Qiagen Negative Control siRNA (Qiagen Cat# 1027310) and/or Sigma Mission siRNA universal control #2 (SIC002); siRAD21 (Sigma SASI_Hs02_00341219 and SASI_Hs01_00195799).

value: MCF7 breast cancer cell

value: brU sc-32323 AC, Santa Cruz


title: GRO-seq, TFF1p-KO MCF7_clone28_E2

description: GRO-seq, TFF1p-KO MCF7_clone28_E2


title: TiO2_LA4_MHS_4_rep4

description: Gene expression data from LA-4 and MH-S coculture, treated with TiO2 nanotubes for 4h, biological replicate 4


title: GRO-seq, TFF1p-KO MCF7_clone28_EtOH

description: GRO-seq, TFF1p-KO MCF7_clone28_EtOH


title: TiO2_LA4_MHS_48_rep1

description: Gene expression data from LA-4 and MH-S coculture, treated with TiO2 nanotubes for 48h, biological replicate 1


title: GRO-seq, Wildtype MCF7_E2

description: GRO-seq, Wildtype MCF7_E2


title: TiO2_MHS_4_rep3

description: Gene expression data from MH-S cells, treated with TiO2 nanotubes for 4h, biological replicate 3


title: TiO2_LA4_MHS_4_rep1

description: Gene expression data from LA-4 and MH-S coculture, treated with TiO2 nanotubes for 4h, biological replicate 1


title: H3K27Ac_1h

value: GSI washout for 1h


title: TiO2_LA4_48_rep2

description: Gene expression data from LA-4 cells, treated with TiO2 nanotubes for 48h, biological replicate 2


title: TiO2_LA4_48_rep3

description: Gene expression data from LA-4 cells, treated with TiO2 nanotubes for 48h, biological replicate 3


title: GRO-seq, Wildtype MCF7_EtOH

description: GRO-seq, Wildtype MCF7_EtOH


title: TiO2_LA4_4_rep4

description: Gene expression data from LA-4 cells, treated with TiO2 nanotubes for 4h, biological replicate 4


title: GRO-seq, siRAD21_EtOH (repeat2) MCF7

description: GRO-seq, siRAD21_EtOH (repeat2) MCF7


title: TiO2_LA4_4_rep1

description: Gene expression data from LA-4 cells, treated with TiO2 nanotubes for 4h, biological replicate 1


title: TiO2_LA4_4_rep2

description: Gene expression data from LA-4 cells, treated with TiO2 nanotubes for 4h, biological replicate 2


title: TiO2_LA4_4_rep3

description: Gene expression data from LA-4 cells, treated with TiO2 nanotubes for 4h, biological replicate 3


title: GRO-seq, siRAD21_E2 (repeat2) MCF7

description: GRO-seq, siRAD21_E2 (repeat2) MCF7


title: GRO-seq, TFF1p-KO MCF7_clone25_EtOH

description: GRO-seq, TFF1p-KO MCF7_clone25_EtOH


title: USP39-depleted H358 cells

city: Oviedo

first: Jose

last: Freije

state: Asturias

address: C/ Fernando Bongera s/n

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universidad de Oviedo

description:
Gene expression data from USP39-depleted H358 cells.
4.Hs_HuEx-1_0-st-v2.27n.rma-exon-full-dabg-Signal

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Human Exon 1.0 ST Array according to the protocols recommended by the manufacturer (Affymetrix, Santa Clara, CA, USA).

scan_protocol: Washing and scanning were performed using Fluidics Station 400 and GeneChip Scanner (Affymetrix Inc.).

data_processing:
After scanning, raw data (Affymetrix CEL files) were processed with Affymetrix Expression Console v1.1, using default settings.
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.full.mps

source_name: USP39-depleted H358 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Control and USP39-silenced lung cancer cell lines were grown at 37 ºC, 5% CO2, under standard conditions for each cell type.

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

value: lung cancer cell line

tag: shRNA


title: GRO-seq, siCTL_E2 (repeat2) MCF7

description: GRO-seq, siCTL_E2 (repeat2) MCF7


title: GRO-seq, siCTL_EtOH (repeat2) MCF7

description: GRO-seq, siCTL_EtOH (repeat2) MCF7


title: GRO-seq, siRAD21_E2 (repeat1) MCF7

description: GRO-seq, siRAD21_E2 (repeat1) MCF7


title: TiO2_LA4_48_rep4

description: Gene expression data from LA-4 cells, treated with TiO2 nanotubes for 48h, biological replicate 4


title: Control A549 cells

description:
Gene expression data from control A549 cells.
1.Ap_HuEx-1_0-st-v2.27n.rma-exon-full-dabg-Signal

source_name: Control A549 cells

value: control


title: GRO-seq, siRAD21_EtOH (repeat1) MCF7

description: GRO-seq, siRAD21_EtOH (repeat1) MCF7


title: GRO-seq, siCTL_EtOH (repeat1) MCF7

description: GRO-seq, siCTL_EtOH (repeat1) MCF7


title: ChIP-seq of H3K4me3_TFF1pKO_E2_MCF7

extract_protocol:
Cells were cross-linked with 1% formaldehyde at room temperature for 10 min. Or for some cases, cells were double cross-linked with 1mM DSG (ProteoChem) for 1 hr first and then for 10minutes by 1% formaldehyde. In both situations, the crosslinking was quenched by addition of 0.125M glycine for 10 minutes. ChIP chromatin was fragmented using (Diagenode) Bioruptor®300 (20-40 cycles, 30sec on, 30sec off, 4°C). Subsequently, the soluble chromatin was harvested by 16,100g centrifugation, pre-cleared with 10-20ul Dynabeads G (Life Technologies), and was then incubated with 1-5 μg of antibodies at 4°C overnight. The next morning, immuno-precipitated complexes were collected using 30ul Dynabeads protein G (Invitrogen) per reaction. The immune-complexes were subjected to washes with wash buffer I for once, with wash buffer II for twice, and with Tris-EDTA (TE) + 0.1% triton x-100 for once, with TE for once, the beads were incubated at 55°C for 2hrs with proteinase K and de-crosslinked at 65°C for overnight. The final ChIP DNA was extracted and purified using QIAquick spin columns (Qiagen).
The library was processed that the extracted DNA was ligated to specific adaptors for Illumina’s HiSeq system using KAPA Hyper Prep Kit (Kapa Biosystems)

treatment_protocol: To induce the estrogen gene transcriptional responses, MCF-7 cells at 60-80% confluency were first hormone-stripped for 3 days in phenol-free DMEM media plus 5% charcoal dextran treated FBS (Omega Scientific, CA), and they were then treated with 100nM 17β-estradiol (E2) (Sigma) for indicated time points (usually for 1 hour).

tag: passages

value: H3K4me3 (abcam, ab8580)


title: USP39-depleted A549 cells

description:
Gene expression data from USP39-depleted A549 cells.
2.As_HuEx-1_0-st-v2.27n.rma-exon-full-dabg-Signal

source_name: USP39-depleted A549 cells


title: GRO-seq, siCTL_E2 (repeat1) MCF7

description: GRO-seq, siCTL_E2 (repeat1) MCF7

tag: tissue


title: ChIP-seq of  H3K4me1_siCTL_E2_MCF7

tag: cell type

value: H3K4me1 (abcam, ab8895)


title: ChIP-seq of  H3K4me3_siCTL_E2_MCF7


title: ChIP-seq of  H3K4me3_siRAD21_E2_MCF7


title: Control H358 cells

description:
Gene expression data from control H358 cells.
3.Hp_HuEx-1_0-st-v2.27n.rma-exon-full-dabg-Signal

source_name: Control H358 cells


title: ChIP-seq of SMC1a_E2_MCF7

value: SMC1a (bethyl, A300-055A)


title: ChIP-seq of SMC1a_EtOH_MCF7


title: MDA-MB-453 Abemaciclib replicate 2

city: Melbourne

first: Shom

last: Goel

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

source_name: Breast carcinoma cell line

growth_protocol: Cells were cultured in sterile dishes in media as described. Cells were plated at densities such that final density at time of ChIP-seq was between 60-70%.

extract_protocol:
Cells were washed in phosphate-buffered saline (PBS), cross-linked with 1% formaldehyde (methanol-free) for 10 minutes at room temperature, quenched with 0.125 M glycine for 5 min at room temperature and washed with PBS complete. Cells were resuspended in lysis buffer (1%SDS, 50 mM Tris-HCl pH8, 10 mM EDTA) containing protease and deacetylase inhibitors, and incubated on ice for 15 min. Lysed cells were sonicated for 5 minutes with a Covaris E220 sonicator (PIP140, DF5%, 200cpb), in 1ml AFA Fiber milliTUBEs. 5 µg of soluble chromatin were immunoprecipitated overnight with 10 μg of H3K9me3 antibody (Abcam ab8898, polyclonal, Lot #GR3244172-1) on protein A and G magnetic beads, then washed, eluted and DNA purified.
ChIP-seq libraries were constructed using Accel-NGS 2S DNA library kit from Swift Biosciences.

treatment_protocol: Abemaciclib concentration 500 nM or equal volume of DMSO (control) for 7 days for all cell lines.

value: MDA-MB-453 breast carcinoma cell line

value: abemaciclib

tag: treatment length

value: 7 days

value: H3K9me3 (Abcam ab8898, polyclonal, Lot #GR3244172-1)


title: MDA-MB-453 DMSO replicate 2

value: DMSO


title: ChIP-seq of H3K4me3_WT_E2_MCF7


title: MDA-MB-453 DMSO replicate 1


title: MDA-MB-453 Abemaciclib replicate 1


title: MCF7 Abemaciclib replicate 2

value: MCF7 breast carcinoma cell line


title: MCF7 Abemaciclib replicate 1


title: MCF7 DMSO replicate 2


title: MCF7 DMSO replicate 1


title: MDA-MB-453 Abemaciclib 12 hours (replicate 2)

growth_protocol: Cells were cultured in sterile dishes in media as described. Cells were plated at densities such that final density at time of ATAC-seq was between 60-70%.

extract_protocol:
Nuclei were isolated following Omni-ATAC-seq protocol (Corces  et al , Nat. Methods, 2017) and ATAC-seq was performed as previously described (Buenrostro  et al.,Curr Protoc Mol Biol ,2015). 50,000 cells / sample were resuspended in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at max speed for 5 min in a pre-chilled (4 C) fixed-angle centrifuge. After centrifugation supernatant was carefully aspirated.  Cell pellets were then resuspended in 50 μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 5 min at max speed in a pre-chilled (4 C) fixed-angle centrifuge. Supernatant was removed and nuclei were resuspended in 50 μl of transposition mix (Corces et al., 2017): 2.5 μl transposase (100 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) by pipetting up and down six times. Transposition reactions were incubated at 37 C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Qiagen columns.
ATAC-seq libraries were amplified as described previously (Buenrostro et al., 2015).

treatment_protocol: Abemaciclib concentration 500 nM or equal volume of DMSO (control) for the indicated times for all cell lines.

value: MDA-MB-468 breast carcinoma cell line

value: 12 hours


title: MDA-MB-361 DMSO 7 days  (replicate 2)

value: MDA-MB-361 breast carcinoma cell line


title: MCF7 shRB DMSO 7 days (replicate 2)


title: MDA-MB-361 DMSO 7 days (replicate 1)


title: MDA-MB-453 Abemaciclib 12 hours (replicate 1)


title: MCF7 shRB Abemaciclib 7 days (replicate 2)


title: MCF7 shRB Abemaciclib 7 days  (replicate 1)


title: MDA-MB-361 Abemaciclib 7 days (replicate 1)


title: MCF7 shRB DMSO 7 days (replicate 1)


title: transgenic kidney cortex-DOCA/NaCl-rep2

city: La Laguna

first: Diego

last: Alvarez de la Rosa

state: Tenerife

address: Campus de Ciencias de la Salud

department: Basic Medical Sciences

institute: Universidad de La Laguna

description: uninephrectomized and treated with DOCA/NaCl for 6 weeks

hyb_protocol: Hybridized to Mouse Gene 2.0 ST Array (Affymetrix) following manufacturer's instructions. Performed by the Genomics Facility, Cancer Research Institute of Salamanca CSIC-USAL University, Spain.

scan_protocol: Washing and scanning were performed using GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G. Performed by the Genomics Facility, Cancer Research Institute of Salamanca CSIC-USAL University, Spain.

data_processing:
Raw cel files were normalized using rma from oligo package in R
MoGene-2_0-st.pgf
MoGene-2_0-st.mps

source_name: Tg.sgk1 kidney cortex

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Kidney cortex samples dissected from 12 weeks-old animals

extract_protocol: Animals were euthanized with carbox dioxide inhalation. Kidney cortices were rapidly dissected and inmediately processed for total RNA extraction using a commercially available kit (REAL Total RNA spin plus) that includes in-column DNA digestion. Quality control and quantitation of RNA samples was performed using the Agilent 2100 Bioanalyzer Platform.

treatment_protocol: Uninephrectomy at 4 weeks of age, followed by 2 weeks recovery and 6 weeks of deoxycorticosterone acetate (DOCA) / NaCl treatment. Treatment consisted on 75 mg/kg of DOCA suspended in sunflower seed oil and administered subcutaneously three times per week and 1% NaCl in driking water.

value: male

tag: genotype

value: 12 weeks

value: kidney cortex


title: transgenic kidney cortex-DOCA/NaCl-rep4


title: control kidney cortex-DOCA/NaCl-rep1

source_name: wild type kidney cortex

value: wild type


title: MDA-MB-361 Abemaciclib 7 days (replicate 2)


title: transgenic kidney cortex-DOCA/NaCl-rep1


title: control kidney cortex-DOCA/NaCl-rep4


title: control kidney cortex-DOCA/NaCl-rep3


title: control kidney cortex-DOCA/NaCl-rep2


title: transgenic kidney cortex-DOCA/NaCl-rep3


title: MCF7 Abemaciclib 24 hours (replicate 2)

value: 24 hours


title: MCF7 Abemaciclib 7 days (replicate 1)


title: MDA-MB-453 Abemaciclib 24 hours (replicate 2)


title: MDA-MB-453 Abemaciclib 24 hours (replicate 1)


title: MCF7 Abemaciclib 12 hours (replicate 2)


title: MCF7 Abemaciclib 24 hours (replicate 1)


title: MCF7 DMSO 7 days (replicate 2)


title: MCF7 Abemaciclib 12 hours (replicate 1)


title: MCF7 DMSO 7 days (replicate 1)


title: MDA-MB-468 Abemaciclib 7 days (replicate 2)


title: MDA-MB-468 Abemaciclib 7 days (replicate 1)


title: MDA-MB-468 Abemaciclib 24 hours (replicate 2)


title: MDA-MB-453 DMSO 7 days (replicate 1)


title: MCF7 Abemaciclib 7 days (replicate 2)


title: MDA-MB-453 DMSO 7days  (replicate 2)


title: MDA-MB-468 Abemaciclib 12 hours (replicate 2)


title: MDA-MB-468 DMSO 7 days (replicate 2)


title: MDA-MB-453 Abemaciclib 7 days (replicate 2)


title: MDA-MB-468 Abemaciclib 24 hours (replicate 1)


title: MDA-MB-468 DMSO 7 days (replicate 1)


title: MDA-MB-468 Abemaciclib 12 hours (replicate 1)