title: Blood_Platelets_Vumc-LGG-VU634-TR2151

city: Amsterdam

first: Myron

last: Best

address: De Boelelaan 1117

department: Neurosurgery

country: Netherlands

institute: VU University Medical Center

description:
Vumc-LGG-VU634-TR2151
Vumc-LGG-VU634-TR2151_S38_L002

data_processing:
Single-end 100 bp reads were subjected to pre-aligment 5'-end quality trimming and sequence adapter clipping using Trimmomatic.
Cleaned-up reads were mapped to the hg19 reference genome using STAR (version 2.3.0), using splice aware alignments and allowing for 10 mismatches.
Intron-spanning read summarization was performed using a samtools-based filtering step and HTSeq (version 0.6.1) using union-mode, unstranded reads and minimal mapping quality of 35, all guided by the Ensembl gene annotation version 75.
Genome_build: hg19
Supplementary_files_format_and_content: Samples in the tab-delimited text file were processed according to the described protocol and data of all samples was merged in a comprehensive read count matrix.

extract_protocol:
Blood platelets were isolated from whole blood in purple-cap BD Vacutainers containing the EDTA anti-coagulant. The cells and aggregates were removed by centrifugation at room temperature for 20 minutes at 120g, resulting in platelet-rich plasma. The platelets were isolated from the platelet-rich plasma by centrifugation at room temperature for 20 minutes at 360g. The platelet pellet was collected in 30 μl RNAlater (Life Technologies), incubated overnight at 4°C and frozen at -80°C for further use. Frozen platelets were thawed on ice and total RNA was isolated using the mirVana RNA isolation kit (Life Technologies) according to the manufacturers’ protocol. Complementary purification of small RNAs was included in the isolation procedure by addition of miRNA homogenate (Life Technologies). Total RNA was dissolved in 30 μl Elution Buffer (Life Technologies) and RNA quality and quantity was measured using Bioanalyzer 2100 with RNA 6000 Picochip (Agilent).
100-500 pg of platelet total RNA diluted in nuclease free H2O was subjected to cDNA synthesis and amplification using the SMARTer Ultra Low RNA Kit for Illumina Sequencing v3 (Clontech, cat. nr. 634853) according to the manufacturers’ protocol. Conversion and efficient amplification of cDNA was quality-controlled using the Bioanalyzer 2100 with DNA High Sensitivity chip (Agilent). Samples with detectable fragments in the 300-7500 bp region were selected for further processing and Covaris shearing by sonication (Covaris Inc). Sample preparation for Illumina sequencing was performed using the Truseq DNA Sample Preparation Kit (Illumina, cat nr. FC-121-2001) or Truseq Nano DNA Sample Preparation Kit (Illumina, cat nr. FC-121-4001). Sample quality and quantity was measured using the DNA 7500 chip or DNA High Sensitivity chip (Agilent). High-quality samples with product sizes between 300-500 bp were pooled in equimolar concentrations (12-19 samples per Hiseq lane) and submitted for 100 bp Single Read sequencing on the Hiseq 2500 platform (Illumina).

tag: subject status

value: patient with low-grade glioma (LGG)

value: Blood platelets


title: Blood_Platelets_Vumc-LGG-VU653-TR2152

status: Public on Mar 20 2019

type: SRA

description:
Vumc-LGG-VU653-TR2152
Vumc-LGG-VU653-TR2152_S58_L004

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: linearEZH2

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

country: China

institute: Fudan University

description: linearEZH2 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.

data_processing:
Library strategy: SHAPE-MaP
Basecalling using Illumina bcl2fastq v2.17.1.14 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Mapped to  target RNA sequence by ShapeMapper software (v2.1.3) and circSHAPEmapper (--target RNA.fa --out folder --nproc 16 --verbose --serial --min-depth 50 –modified –untreated --denatured)
Reads from SHAPE-MaP libraries were processed with default settings in ShapeMapper software version v2.1.3. Pre-processed reads were then mapped to target sequences by Bowtie2 (v2.1.0) (-p 24 --local --sensitive-local --mp 3,1 --rdg 5,1 --rfg 5,1 --dpad 30 --maxins 800 --ignore-quals --no-unal). Mutation rates (MutR) were calculated at each position by summing the number of mismatches and indels (deletions and insertions) and dividing by the number of all mapped reads to the position. SHAPE reactivities were calculated by [(ModifiedMutR – UntreatedMutR)/DenaturedMutR] and further normalized by a model-free box-plot approach (Deigan et al., 2009).
Genome_build: hg19 for human samples (For circSHAPE-Map, circCAMSAP1, circCCNB1, circEPHB4, circEZH2, circFCHO2, circFGFR1_1, circPOLR2A, circPVT1, circRELL1, circSDHAF2, circTBCD, circUIMC1, circARID1B, circCNN2, circDHX34, circFKBP8, circKIAA0368, circMBOAT2, circPIP5K1C, circPPP1CB, circPROSC, circPTK2, circSLC22A23, circSNHG4, circTMEM181, circVAPB, circASAP1, circASXL1, circDYNC1H1, circFGFR1_2, circLDLRAD3, circPHF21A, circRTN4, circSMARCA5; For linearSHAPE-Map, linearCAMSAP1, linearCCNB1, linearEPHB4, linearEZH2, linearFCHO2, linearFGFR1_1, linearPOLR2A, linearPVT1, linearRELL1, linearSDHAF2, linearTBCD, linearUIMC1).
Supplementary_files_format_and_content: TXT files include the read depths, standard errors and SHAPE reactivity of each base. Column "Norm_profile" is the SHAPE reactivity.

source_name: PA1 cells

growth_protocol: PA-1 (human ovarian adenocarcinoma cell) were cultured with MEMα medium supplemented with 10% FBS.

extract_protocol:
For SHAPE-MaP, isolated RNAs were treated with DNase I (Ambion, DNA-freeTM kit) to remove possible DNA contamination. About 50-100 μg of RNAs were obtained under each treatment, and were then used for SHAPE-MaP reverse transcription by adding 1 μL (200 U/μL) of SuperScript II (Invitrogen), 6 mM Mn2+ and gene-specific primers for linear or circular RNAs (5S rRNA was used as a spike-in control). Mn2+ was removed using G-25 micro-spin columns (GE Healthcare) after SHAPE-MaP reverse transcription. Second-strand synthesis was performed with Q5 hot start high-fidelity DNA polymerase and nested PCR was performed to further improve DNA yield.
SHAPE-MaP libraries were prepared from 1 ng of DNAs for linear (linearSHAPE-MaP) or circular (circSHAPE-MaP) RNAs, and size-selected with AmpureXP beads (Agencourt) with a 1:1 (bead to sample) ratio to obtain library DNA products spanning 100-400 bp in length. Final libraries were quantified using Agilent Bioanalyzer 2100 and QuBit high-sensitivity dsDNA assay. Deep sequencing was performed by Illumina NextSeq 500 at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.

treatment_protocol: For SHAPE-MaP, PA1 cells were incubated with 900 uL of fresh cell culture medium and 100 μL of 10x SHAPE Chemical in DMSO with the final concentration of NAI at 100 mM for 10 minutes at 37°C.

tag: cell line

value: ovarian adenocarcinoma cell line PA1

tag: type

value: cDNA

tag: treatment

value: DC samples denatured by formamide at 95℃; DMSO samples only DMSO; NAI samples modified by NAI in DMSO.


title: linearCCNB1

description: linearCCNB1 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: Blood_Platelets_Vumc-LGG-VU658-TR2153

description:
Vumc-LGG-VU658-TR2153
Vumc-LGG-VU658-TR2153_S59_L004


title: linearCAMSAP1

description: linearCAMSAP1 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: HEK293_control2_ChIPseq

city: Sherbrooke

first: Karine

last: Choquet

state: Québec

address: 3201 rue Jean-Mignault

department: Biochemistry and Functional Genomics

country: Canada

institute: Université de Sherbrooke

description:
HEK293.ChIP.Pol3_known.normCounts.csv
HEK293.Pol3_known.scores.csv

library_source: genomic

data_processing:
Read trimming was performed with Trimmomatic v0.35
Alignment was performed with STAR v2.3.0e (RNA-seq and small RNA-seq) or bowtie2 v.2.2.9 (ChIP-seq)
Reads were counted with featureCounts v1.5.0
Normalization and differential expression analysis (RNAseq and small RNAseq) were performed with DESeq2
ChIP-seq read counts were normalized to the median of total read counts and Pol III occupancy scores were calculated as the log2(IPread_count/Inputread_count)
Genome_build: hg19
Supplementary_files_format_and_content: For each dataset, raw and normalized counts per sample are provided in one file (tsv, csv or txt)

molecule: genomic DNA

source_name: HEK293 cell line

growth_protocol: HEK293 and MO3.13 cells were grown in DMEM supplemented with 10% FBS and 1% pen-strep

extract_protocol: Illumina TruSeq

treatment_protocol: CRISPR-Cas9 editing was used to introduce POLR3A mutations or BC200 KO

tag: genotype/variation

value: control

tag: chip antibody


title: circSMARCA5

description: circSMARCA5 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: RNA_H04_D1

city: Boston

first: Joann

middle: Diray

last: Arce

state: MA

address: 300 Longwood Ave

department: Infectious Disease

country: USA

institute: Boston Childrens Hospital- Harvard Medical School

data_processing:
Base-calling and de-multiplexing were done using built-in software on the Illumina HiSeq 2500
fastq file quality control was performed using FastQC v.0.11.5 and MulitQC v.0.8.dev0
fastq files were aligned to the human genome using STAR v.2.5
read count tables were generated from bam fles using htseq-count v.0.6.1p1
globin transcripts were removed from libraries ("ENSG00000206172","ENSG00000188536", "ENSG00000244734","ENSG00000223609")
Genome_build: Ensembl GRCh38.86
Supplementary_files_format_and_content: tab delimited files containing uniquely mapped reads per gene for each sample

molecule: polyA RNA

source_name: whole blood

extract_protocol:
Blood was stored in RNAlater (Ambion), RNA was extracted using a RiboPure Blood kit (ThermoFisher) and polyA RNA was purified using a NEBNEXT Poly(A) mRNA magnetic isolation kit (NEB)
cDNA libraries were constructed for sequencing using a KAPA Stranded Total RNA Kit (Kapa Biosystems)

value: whole blood

tag: day of life

tag: Sex

value: M

tag: subject id


title: Blood_Platelets_Vumc-LGG-VU683-TR2156

description:
Vumc-LGG-VU683-TR2156
Vumc-LGG-VU683-TR2156_S24_L002


title: Blood_Platelets_Vumc-LGG-VU633-TR2150

description:
Vumc-LGG-VU633-TR2150
Vumc-LGG-VU633-TR2150_S19_L001


title: Blood_Platelets_Vumc-LGG-VU656-TR2154

description:
Vumc-LGG-VU656-TR2154
Vumc-LGG-VU656-TR2154_S60_L004


title: circPHF21A

description: circPHF21A of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: Blood_Platelets_Vumc-LGG-VU680-TR2155

description:
Vumc-LGG-VU680-TR2155
Vumc-LGG-VU680-TR2155_S61_L004


title: circLDLRAD3

description: circLDLRAD3 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: linearFGFR1

description: linearFGFR1 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: linearFCHO2

description: linearFCHO2 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: linearEPHB4

description: linearEPHB4 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circFGFR1_2

description: circFGFR1 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circDYNC1H1

description: circDYNC1H1 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circASXL1

description: circASXL1 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circASAP1

description: circASAP1 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circTMEM181

description: circTMEM181 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circRTN4

description: circRTN4 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circVAPB

description: circVAPB of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circSNHG4

description: circSNHG4 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circPTK2

description: circPTK2 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: Blood_Platelets_Vumc-LGG-VU526

description:
Vumc-LGG-VU526-TR1590
Vumc-LGG-VU526-TR1590_GTGAAA_L005


title: Blood_Platelets_Vumc-LGG-VU625

description:
Vumc-LGG-VU625-TR1723
Vumc-LGG-VU625-TR1723_ACTTGA_L008


title: Blood_Platelets_Vumc-LGG-VU532

description:
Vumc-LGG-VU532-TR1591
Vumc-LGG-VU532-TR1591_GTGAAA_L006


title: Blood_Platelets_Vumc-LGG-VU545-TR1902

description:
Vumc-LGG-VU545-TR1902
Vumc-LGG-VU545-TR1902_ACAGTG_L002


title: Blood_Platelets_Vumc-LGG-VU566

description:
Vumc-LGG-VU566-TR1608
Vumc-LGG-VU566-TR1608_CCGTCC_L006


title: Blood_Platelets_Vumc-LGG-VU612

description:
Vumc-LGG-VU612-TR1614
Vumc-LGG-VU612-TR1614_ACTGAT_L005


title: Blood_Platelets_Vumc-LGG-VU600

description:
Vumc-LGG-VU600-TR1665
Vumc-LGG-VU600-TR1665_ACAGTG_L007


title: Blood_Platelets_Vumc-LGG-VU603

description:
Vumc-LGG-VU603-TR1664
Vumc-LGG-VU603-TR1664_TGACCA_L005


title: circSLC22A23

description: circSLC22A23 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: Blood_Platelets_Vumc-LGG-VU619

description:
Vumc-LGG-VU619-TR1615
Vumc-LGG-VU619-TR1615_CTTGTA_L005


title: Blood_Platelets_Vumc-LGG-VU599

description:
Vumc-LGG-VU599-TR1613
Vumc-LGG-VU599-TR1613_CGTACG_L005


title: Blood_Platelets_Vumc-LGG-VU572

description:
Vumc-LGG-VU572-TR1609
Vumc-LGG-VU572-TR1609_GATCAG_L005


title: circPPP1CB

description: circPPP1CB of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circPROSC

description: circPROSC of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circPIP5K1C

description: circPIP5K1C of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circMBOAT2

description: circMBOAT2 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: Blood_Platelets_Vumc-LGG-VU575

description:
Vumc-LGG-VU575-TR1610
Vumc-LGG-VU575-TR1610_GTCCGC_L003


title: Blood_Platelets_Vumc-LGG-VU588

description:
Vumc-LGG-VU588-TR1612
Vumc-LGG-VU588-TR1612_TAGCTT_L002


title: Blood_Platelets_Vumc-LGG-VU536

description:
Vumc-LGG-VU536-TR1592
Vumc-LGG-VU536-TR1592_GTGGCC_L001


title: Blood_Platelets_Vumc-LGG-VU621

description:
Vumc-LGG-VU621-TR1722
Vumc-LGG-VU621-TR1722_CAGATC_L003


title: circKIAA0368

description: circKIAA0368 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circFKBP8

description: circFKBP8 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: Blood_Platelets_Vumc-LGG-467

description:
Vumc-GBM-467-TR1453
Vumc-GBM-467-TR1453_GTTTCG_L005


title: Blood_Platelets_Vumc-LGG-VU576

description:
Vumc-LGG-VU576-TR1611
Vumc-LGG-VU576-TR1611_TAGCTT_L001


title: Blood_Platelets_Vumc-LGG-VU528

description:
Vumc-LGG-VU528-TR612
Vumc-LGG-VU528-TR612_AGTCAA_L002


title: circDHX34

description: circDHX34 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circARID1B

description: circARID1B of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: Blood_Platelets_Vumc-LGG-VU479-1

description:
Vumc-LGG-VU479-1-TR554
Vumc-LGG-VU479-1-TR554_ATCACG_L006


title: circPVT1

description: circPVT1 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: Blood_Platelets_Vumc-LGG-VU487-1

description:
Vumc-LGG-VU487-1-TR555
Vumc-LGG-VU487-1-TR555_CGATGT_L005


title: circRELL1

description: circRELL1 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: Blood_Platelets_Vumc-LGG-VU509-1

description:
Vumc-LGG-VU509-1-TR617
Vumc-LGG-VU509-1-TR617_GTGAAA_L001


title: circCNN2

description: circCNN2 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circSDHAF2

description: circSDHAF2 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circFCHO2

description: circFCHO2 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circTBCD

description: circTBCD of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circUIMC1

description: circUIMC1 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circPOLR2A

description: circPOLR2A of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: circEZH2

description: circEZH2 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: Blood_Platelets_Vumc-LGG-449-1

description:
Vumc-LGG-449-1-TR585
Vumc-LGG-449-1-TR585_GTGAAA_L004


title: Blood_Platelets_Vumc-LGG-VU525

description:
MGH-LGG-VU525-TR610
MGH-LGG-VU525-TR610_GGCTAC_L003


title: Blood_Platelets_Vumc-LGG-VU507

description:
Vumc-LGG-VU507-TR513
Vumc-LGG-VU507-TR513_CGATGT_L008


title: Blood_Platelets_Vumc-LGG-VU427-T03

description:
Vumc-LGG-VU427-T03-TR582
Vumc-LGG-VU427-T03-TR582_GGCTAC_L001


title: Blood_Platelets_Vumc-LGG-446-1

description:
Vumc-LGG-446-1-TR584
Vumc-LGG-446-1-TR584_ATGTCA_L002


title: Blood_Platelets_Vumc-LGG-503-1

description:
Vumc-LGG-503-1-TR557
Vumc-LGG-503-1-TR557_TGACCA_L003


title: Blood_Platelets_Vumc-LGG-VU441-1

description:
Vumc-LGG-VU441-1-TR583
Vumc-LGG-VU441-1-TR583_AGTCAA_L003


title: circEPHB4

description: circEPHB4 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: Blood_Platelets_Vumc-LGG-VU490

description:
Vumc-LGG-VU490-TR512
Vumc-LGG-VU490-TR512_ATTCCT_L007


title: Blood_Platelets_Vumc-LGG-VU473

description:
Vumc-LGG-VU473-TR510
Vumc-LGG-VU473-TR510_GAGTGG_L005


title: Blood_Platelets_Vumc-LGG-498-1

description:
Vumc-LGG-498-1-TR556
Vumc-LGG-498-1-TR556_TTAGGC_L004


title: circCCNB1

description: circCCNB1 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: Blood_Platelets_Vumc-LGG-VU464

description:
Vumc-LGG-VU464-TR509
Vumc-LGG-VU464-TR509_GTTTCG_L003


title: circCAMSAP1

description: circCAMSAP1 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: Blood_Platelets_Vumc-HD-239-TR1781_1

description:
Vumc-HD-239-TR1781
Vumc-HD-239-TR1781_GTTTCG_L004

value: healthy control (HC)


title: Blood_Platelets_Vumc-HD-10-2

description:
Vumc-HD-10-2-TR1642
Vumc-HD-10-2-TR1642_AGTCAA_L005


title: Blood_Platelets_Vumc-HD-247-TR1859_1

description:
Vumc-HD-247-TR1859
Vumc-HD-247-TR1859_CAGATC_L002


title: AZ9_Compound_H10_AZ63_16

city: St Lucia

first: James

middle: E.

last: Hudson

address: Level 3, Skerman Building (65)

department: School of Biomedical Sciences

country: Australia

institute: The University of Queensland

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq2-v2.17.
The quality of the reads was assessed thanks to FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
The reads were then processed and mapped to the human genome hg38 using the Bcbio-nextgen framework version 1.0.3 (https://github.com/chapmanb/bcbio-nextgen). The aligner used was HISAT2 2.0.5.
For sample quality assessment, raw counts were normalised with DESeq2 regularized logarithm function. A principal component analysis (PCA) was performed using Matlab R2013a (Mathworks) and lead to the detection of a batch effect was detected among samples which was corrected using the removeBatchEffect function from Limma v3.30.13.
The identification of the differentially expressed genes between treated and non-treated samples was performed using DESeq2 v1.14.141 in R v 3.3.142 using the design ~Batch+Compound to account for the batch effect directly.
Genome_build: hg38
Supplementary_files_format_and_content: Each processed data files is tab separated. It directly reports the output of DeSeq2 for the following comparisons: AZ3 versus DMSO, AZ65 versus DMSO and AZ63 versus DMSO.

source_name: human cardiac organoids

growth_protocol: Heart-dyno culture inserts were fabricated using standard SU-8 photolithography and PDMS molding practices1. CTRL medium: α-MEM GlutaMAX (ThermoFisher Scientific), 10% fetal bovine serum (FBS) (ThermoFisher Scientific), 200 μM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate (Sigma) and 1% Penicillin/Streptomycin (ThermoFisher Scientific). For each hCO, 5 x 104 cardiac cells in CTRL medium were mixed with collagen I to make a 3.5 μL final solution containing 2.6 mg/mL collagen I and 9% Matrigel. The bovine acid-solubilized collagen I (Devro) was first salt balanced and pH neutralized using 10X DMEM and 0.1 M NaOH, respectively, prior to mixing with Matrigel and cells. The mixture was prepared on ice and pipetted into the Heart-Dyno. The Heart-Dyno was then centrifuged at 100 x g for 10 s to ensure the hCO form halfway up the posts. The mixture was then gelled at 37°C for 30 min prior to the addition of CTRL medium to cover the tissues (150 μL/hCO). The Heart-Dyno design facilitates the self-formation of tissues around in-built PDMS exercise poles (designed to deform ~0.07 μm/μN). The medium was changed every 2-3 days (150 μL/hCO).    hCOs were cultured in CTRL medium for formation for 5 days and then either kept in CTRL medium culture or changed to maturation medium comprising DMEM without glucose, glutamine and phenol red (ThermoFisher Scientific) supplemented with 4% B27 (with or without insulin) (ThermoFisher Scientific), 1% GlutaMAX (ThermoFisher Scientific), 200 μM L-ascorbic acid 2-phosphate sesquimagnesium salt hydrate and 1% Penicillin/Streptomycin (ThermoFisher Scientific), 1 mM glucose and 100 μM palmitic acid (conjugated to bovine serum albumin within B27 by incubating for 2h at 37°C, Sigma) with changes every 2-3 days.

extract_protocol:
For each experiment 10-20 hCO were pooled, snap frozen and RNA extracted using Trizol (ThermoFisher Scientific), treated with DNAse (Qiagen) and purified using RNeasy Minielute Cleanup Kit (Qiagen). The quality of the RNA was assessed by Fragment Analyzer (Advances Analytical Technologies) and samples with RNA quality number ≥8.9 were used for library preparation.
RNA samples were processed with Illumina TruSeq Stranded mRNA Library prep kit selecting for poly(A) taled RNA following the manufacturer’s recommendations. Libraries were quantified with Qubit HS (ThermoFisher) and Fragment Analyzer (Advances Analytical Technologies) adjusted to the appropriate concentration for sequencing. Indexed libraries were pooled and sequenced at a final concentration of 1.8 pM on an Illumina NextSeq 500 high-output run using paired-end chemistry with 75 bp read length.

treatment_protocol: We screened for small molecule activators of cardiomyocyte proliferation that did not alter contractile force in hCOs. Initial screens were performed in a 2D high-content primary screen, measuring DNA synthesis in human pluripotent stem cell-derived cardiomyocytes (hPSC-CM) exposed to 5-ethynyl-2'-deoxyuridine (EdU) over 2 days and the hits were assayed in a counter-screen of cardiac fibroblasts to select compounds that preferentially induced proliferation in hPSC-CMs. Subsequently, we screened 105 potential hit compounds in immature hCOs where the proliferative response would be robust. Both negative vehicle (DMSO) and positive (CHIR99021) controls were included on each plate in each experiment.  hCO treated for 2 days. Compounds 3, 63 and 65 increased proliferation with no impact on contractile force.

tag: replicatebatch

value: AZ9 - experiment 4

tag: compound

value: AZ63 - compound 63

tag: compoundtarget


title: AZ9_Compound_H9_AZ3_15

value: AZ3 - compound 3


title: Blood_Platelets_Vumc-HD-37-2

description:
Vumc-HD-37-2-TR1580
Vumc-HD-37-2-TR1580_GGCTAC_L005


title: AZ9_Compound_DMSO_13

description:
AZ3vsDMSO_AllGenes.xls
AZ63vsDMSO_AllGenes.xls
AZ65vsDMSO_AllGenes.xls

value: DMSO


title: AZ7_Compound_H10_AZ63_12

value: AZ7 - experiment 3


title: Blood_Platelets_Vumc-HD-159

description:
Vumc-HD-159-TR1521
Vumc-HD-159-TR1521_GTTTCG_L001


title: AZ9_Compound_D5_AZ65_14

value: AZ65 - compound 65


title: AZ7_Compound_D5_AZ65_10


title: circFGFR1_1

description: circFGFR1 of denatured control (DC), DMSO, NAI replicate1 and NAI replicate2.


title: AZ7_Compound_DMSO_09


title: Blood_Platelets_Vumc-HD-9

description:
Vumc-HD-9-TR1152
Vumc-HD-9-TR1152_ACAGTG_L002


title: Blood_Platelets_Vumc-HD-95

description:
Vumc-HD-95-TR1087
Vumc-HD-95-TR1087_CGTACG_L007


title: Blood_Platelets_Vumc-HD-79

description:
Vumc-HD-79-TR1081
Vumc-HD-79-TR1081_ATGTCA_L005


title: Blood_Platelets_Vumc-HD-82

description:
Vumc-HD-82-TR1082
Vumc-HD-82-TR1082_CCGTCC_L005


title: AZ5_Compound_H9_AZ3_03

value: AZ5 - experiment 1


title: AZ6_Compound_H10_AZ63_08

value: AZ6 - experiment 2


title: AZ6_Compound_H9_AZ3_07


title: Blood_Platelets_Vumc-HD-51-1

description:
Vumc-HD-51-1-TR1170
Vumc-HD-51-1-TR1170_ATGTCA_L006


title: AZ5_Compound_D5_AZ65_02


title: AZ5_Compound_DMSO_01


title: Blood_Platelets_Vumc-HD-22-1

description:
Vumc-HD-22-1-TR1157
Vumc-HD-22-1-TR1157_TAGCTT_L007


title: Blood_Platelets_Vumc-HD-186-TR1759_1

description:
Vumc-HD-186-TR1759
Vumc-HD-186-TR1759_CGTACG_L002


title: AZ7_Compound_H9_AZ3_11


title: Blood_Platelets_Vumc-HD-140

description:
Vumc-HD-140-TR1129
Vumc-HD-140-TR1129_GTCCGC_L001


title: Blood_Platelets_Vumc-HD-126

description:
Vumc-HD-126-TR1118
Vumc-HD-126-TR1118_GCCAAT_L007


title: Ctrl_1

city: Daejeon

first: Yoonjung

last: Choi

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

data_processing:
Prepared libraries were sequenced on a HiSeq2500 with single-end method (100-bp reads).
The sequenced reads were aligned to the human genome (version: Hg19) using the STAR aligner (v.2.4.0)
The number of mapped reads was further analyzed using HOMER and DESeq
Genome_build: Hg19
Supplementary_files_format_and_content: RNA-seq : tab-delimited text files include RPKM values for each Sample

source_name: HUVEC

growth_protocol: Human umbilical vein endothelial cells (HUVECs, Cat#CC-2519, Lonza) were cultured in EBM-2 (Cat#CC-3156, Lonza) supplemented with EGM-2 (Cat#CC-3162, Lonza) and 100 µg/ml penicillin/streptomycin on gelatin (Cat#G1890, Sigma-Aldrich; 0.1% in DDW) pre-coated plates. The cells were grown at 37°C and 5% CO2.

extract_protocol:
mRNA-seq libraries were made using NEXTflexTM Rapid RNA-Seq kit (cat. 5138) from isolated mRNA.
mRNA-seq libraries were made using NEXTflexTM Rapid RNA-Seq kit (cat. 5138) from isolated mRNA.

treatment_protocol: HUVEC cells were treated with VEGF (2.5 nM) or ginsenosides (F1 and Rh1, 10 μM) for one hour. Otherwise, the cells were pre-treated with VEGF (2.5 nM) for an hour and sequentially treated with ginsenoisdes (F1 and Rh1, 10 μM) for another hour.

tag: cell type

value: Human Umbilical Vein Endothelial Cells


title: Blood_Platelets_Vumc-HD-132

description:
Vumc-HD-132-TR1122
Vumc-HD-132-TR1122_TAGCTT_L004

value: Blood platelets


title: Blood_Platelets_Vumc-HD-16-1

description:
Vumc-HD-16-1-TR1155
Vumc-HD-16-1-TR1155_ACTTGA_L006


title: Blood_Platelets_Vumc-HD-136

description:
Vumc-HD-136-TR1125
Vumc-HD-136-TR1125_AGTCAA_L007


title: Blood_Platelets_Vumc-HD-15-1

description:
Vumc-HD-15-1-TR1154
Vumc-HD-15-1-TR1154_CAGATC_L003


title: Blood_Platelets_Vumc-HD-124

description:
Vumc-HD-124-TR1116
Vumc-HD-124-TR1116_TGACCA_L007


title: Blood_Platelets_Vumc-HD-21-1

description:
Vumc-HD-21-1-TR1161
Vumc-HD-21-1-TR1161_AGTTCC_L001


title: Blood_Platelets_Vumc-HD-20-1

description:
Vumc-HD-20-1-TR1156
Vumc-HD-20-1-TR1156_GATCAG_L005


title: Blood_Platelets_Vumc-HD-123

description:
Vumc-HD-123-TR1115
Vumc-HD-123-TR1115_TTAGGC_L008


title: AZ5_Compound_H10_AZ63_04


title: Blood_Platelets_Vumc-HD-3-1

description:
Vumc-HD-3-1-TR1149
Vumc-HD-3-1-TR1149_CGATGT_L003


title: Blood_Platelets_Vumc-HD-105

description:
Vumc-HD-105-TR1098
Vumc-HD-105-TR1098_GATCAG_L001


title: Blood_Platelets_Vumc-HD-119

description:
Vumc-HD-119-TR1111
Vumc-HD-119-TR1111_GAGTGG_L005


title: Blood_Platelets_Vumc-HD-98

description:
Vumc-HD-98-TR921
Vumc-HD-98-TR921_GCCAAT_L005


title: Blood_Platelets_Vumc-HD-92

description:
Vumc-HD-92-TR920
Vumc-HD-92-TR920_CGTACG_L006


title: Blood_Platelets_Vumc-HD-86

description:
Vumc-HD-86-TR893
Vumc-HD-86-TR893_GTGGCC_L004


title: Blood_Platelets_Vumc-HD-89

description:
Vumc-HD-89-TR896
Vumc-HD-89-TR896_GAGTGG_L005


title: Blood_Platelets_Vumc-HD-141

description:
Vumc-HD-141-TR1130
Vumc-HD-141-TR1130_GTGAAA_L001


title: Blood_Platelets_Vumc-HD-84

description:
Vumc-HD-84-TR892
Vumc-HD-84-TR892_GTGAAA_L003


title: Blood_Platelets_Vumc-HD-83

description:
Vumc-HD-83-TR891
Vumc-HD-83-TR891_GTCCGC_L003


title: Blood_Platelets_Vumc-HD-81

description:
Vumc-HD-81-TR890
Vumc-HD-81-TR890_CCGTCC_L003


title: KPRbTR_207A

city: Philadelphia

first: David

middle: M

last: Walter

state: PA

address: 421 Curie Blvd, Rm 745

department: Cancer Biology

institute: University of Pennsylvania

data_processing:
bcl2fastq v2.20.0.422 was used to perform base calling and demultiplexing using default parameters to generate fastq files.
Fastq files were mapped to GRCm38 using STAR v2.5.2b
Hits to genes described in Gencode M11 were counted for each BAM file using featureCounts.
Genome_build: GRCm38.p4 and Gencode M11 gene models
Supplementary_files_format_and_content: comma separated value matrix table of raw counts per gene

organism: Mus musculus

source_name: Mouse lung adenocarcinoma cell line

growth_protocol: Cell lines were grown at 37 degrees C in high glucose-containing DMEM supplemented with 10% FBS and GlutaMAX.

extract_protocol:
RNA was isolated from cell lines using the RNeasy Mini Kit (Qiagen) per manufacturers instructions.
Sequencing libraries were prepared using the TruSeq Stranded mRNA Library Prep Ki (Illumina) per manufacturer's instructions.

tag: strain

value: mixed

value: lung adenocarcinoma

tag: genotype

value: KPRbTR


title: KPRbTR_202


title: Blood_Platelets_Vumc-HD-56

description:
Vumc-HD-56-TR884
Vumc-HD-56-TR884_TAGCTT_L008


title: Blood_Platelets_Vumc-HD-149

description:
Vumc-HD-149-TR932
Vumc-HD-149-TR932_GTCCGC_L001


title: KPRbTR_7


title: KP_2474-1

value: KP


title: Blood_Platelets_Vumc-HD-80

description:
Vumc-HD-80-TR889
Vumc-HD-80-TR889_ATGTCA_L002


title: Blood_Platelets_Vumc-HD-143

description:
Vumc-HD-143-TR928
Vumc-HD-143-TR928_AGTCAA_L007


title: KP_2474-4


title: Blood_Platelets_Vumc-HD-142

description:
Vumc-HD-142-TR927
Vumc-HD-142-TR927_CTTGTA_L007


title: KPRbTR_68


title: KP_62


title: KP_54


title: Blood_Platelets_Vumc-HD-130

description:
Vumc-HD-130-TR926
Vumc-HD-130-TR926_GGCTAC_L006


title: GATA1_wt_3_RNA

first: Vijay

last: Sankaran

address: 1 Blackfan Cr

institute: Boston Children's Hospital

data_processing:
RNA sequencing data was aligned to the mouse reference genome GRCm38.p4  using STAR using a basic two-pass alignment strategy. Aligned reads were filtered for those reads that were uniquely mapping using the --outFilterMultimapNmax 1 flag.
Gene quantifications for ensembl v84 were summarized using the --quantMode GeneCounts parameter in STAR.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: Gene expression counts for hg19 / ensembl v84 gene annotations

growth_protocol: G1E cells were grown in IMDM, supplemented with FCS, Pen/Strep, MTG, murine SCF and EPO

extract_protocol:
Qiagen RCL lysis buffer supplemented with beta-mercaptoethanol
Smart-seq2; Nextera-based indexing

treatment_protocol: Cells were spin-infected with virus produced in 293T cells transfected (fuGENE) with HMD vector empty, GATA1 WT, GATA1 Mutant

tag: transfected with

value: GATA1 wildtype


title: HMD_2_RNA

value: HMD empty vector


title: GATA1_wt_2_RNA


title: GATA1_wt_1_RNA


title: GATA1_mut_3_RNA

value: GATA1 mutant


title: GATA1_mut_2_RNA


title: HMD_1_RNA


title: GATA1_mut_1_RNA


title: HMD_3_RNA


title: Blood_Platelets_Vumc-HD-125

description:
Vumc-HD-125-TR1117
Vumc-HD-125-TR1117_ACAGTG_L007

tag: subject status

value: healthy control (HC)


title: WT3_mNK2

city: London

first: Victoria

last: Male

state: Not Applicable (Outside of US and Canada)

address: Metabolism, Digestion and Reproduction, Imperial College London, Chelsea and Westminster Hospital Campus, 369 Fulham Road

country: United Kingdom

institute: Imperial College London

data_processing:
BaseCalling was performed using Illumina RTA (v2.4.11)
Fastq was demultiplexed and built using Illumina bcl2fastq (v2.19)
Fastq was then adaptor and quality trimmed using Trimmomatic (v0.36.5)
Processed fastq was aligned to the genome (GTF guided mm10 from Illumina iGenomes) using RNA-STAR (v2.5.2b)
Counts were generated with FeatureCounts (v1.6.0.2)
Normalization of counts and differential expression analysis were carried out using SARtools (v.1.3.2.0)
Genome_build: UCSC mm10
Supplementary_files_format_and_content: BM_NK_WT_Tbx21_KO_alldata.txt is a matrix file containing reads and normalised reads for all alignments

source_name: Bone marrow leukocytes

extract_protocol:
Total RNA was extracted from sorted cells using an RNeasy Micro kit (Qiagen)
Libraries were prepared from 2 ng of total RNA using the Ovation Solo assay (NuGEN) with 15 cycles of amplification. Libraries were assessed for correct size distribution on the Agilent 2200 TapeStation and quantified by Qubit DNA High Sensitivity assay (Thermo) before being pooled at an equimolar concentration.

treatment_protocol: WT and Tbx21 KO mice were killed by direct cervical dislocation, with death confirmed by cessation of circulation. Bones were dissected out and bone marrow cells were removed by flushing. iNK (Lin- NK1.1+ CD11b- CD27+), mNK1 (Lin- NK1.1+ CD11b+ CD27+) and mNK2 (Lin- NK1.1+ CD11b+ CD27-) were sorted.

tag: tissue

value: Bone marrow leukocytes

value: WT


title: HCC1187 with shRNA-1 rep2

type: RNA

city: Ciudad de México

first: Alfredo

last: Hidalgo-Miranda

state: CDMX

address: Periferico Sur #4809

department: Cancer Genomic

country: Mexico

institute: INMEGEN

description: SST-RMA expression value derived from Expression Console software

hyb_protocol: Samples were hybridized with GeneChip Human Transcriptome Array 2.0 Arrays (Affymetrix)

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix). GeneChips were scanned using The Genechip Scanner 3000 7G (Affymetrix , Santa Clara, USA).

data_processing: Array signal intensitive were analyzed with the Affymetrix Expression Console using Signal Space Transformation-Robust Multichip Analysis (SST-RMA) for the background correction.

label: biotin

label_protocol: SensationPlus™ FFPE Amplification and WT Labeling Kit  were used to generate the biotinylated cRNA starting from 100ng of total RNA according to the manufacturer (Manual Target preparation for GeneChip Whole transcript (WT) expression arrays, Affymetrix).

growth_protocol: The hcc1187 cell line was grown in RPMI + 10% fetal bovine serum prior to treatment with shRNAs

extract_protocol: Trizol method was used to extract the total RNA

treatment_protocol: HCC1187 cell line was transfected with 3 μg of plasmid (shRNA-1) to silence lnc-KLHDC7B. As negative control (NC) a shRNA directed to GFP was transfected.

value: RNA from HCC1187 transfected with shRNA-1 versus lnc-KLHDC7B


title: HCC1187 with shRNA-NC (negative control) rep1

source_name: Negative Control

value: RNA from HCC1187 transfected with shRNA negative control


title: HCC1187 with shRNA-NC (negative control) rep3


title: 17K48S50

city: Indianapolis

first: Brittney-Shea

last: Herbert

state: IN

address: 975 West Walnut St, IB 130

institute: IU School of Medicine

hyb_protocol: We analyzed the RNA on Affymetrix U133 Plus 2.0 expression arrays. Microarray processing was performed at Yale. The cDNA and cRNA preparation, cRNA labeling and hybridization to Affymetrix Human Genome U133 Plus 2.0 GeneChip® microarrays (Affymetrix, Santa Clara, CA) was performed as per standard protocols according to manufacturer’s instructions.

scan_protocol: The arrays were scanned using Hewlett-Packard GeneArray Scanner and the scanned output files were visually inspected for hybridization artifacts. The data quality was checked for the presence of spiked control cRNAs, background values caused by array autofluorescence and non-specific binding, and Q value.

source_name: Keratinocyte

growth_protocol: Four 5 mm punch biopsies were obtained from unaffected skin of the upper inner arm of each case and control. Keratinocyte and fibroblast cultures were established as previously described [Levanat S, Gorlin RJ, Fallet S, Johnson DR, Fantasia JE, Bale AE: A two-hit model for developmental defects in Gorlin syndrome. Nat Genet 1996, 12(1):85-87.]. Briefly, keratinocytes were harvested from epidermis by overnight exposure to Dispase at 4°C and seeded onto mitomycin C-treated feeders of 3T3 cells. Once colonies of keratinocytes were growing, they were expanded in low calcium MCDB medium. Fibroblasts were harvested from minced pieces of dermis obtained after dispase treatment of skin biopsies and expanded in DMEM plus 10% serum. Twenty-four vials of low-passage cells with approximately 5x10e5 cells/vial were frozen in liquid nitrogen from each subject.

extract_protocol: The RNA was extracted using our standard Guanidine Thiocyanate Procedure and cleaned using the Qiagen RNeasy Micro Kit (according to the manufacturer’s directions).

treatment_protocol: Low pass Fibroblast and Keratinocyte cell lines from study participants were treated with 0 ng/ml, 10 ng/ml, and 50 ng/ml of Sirolimus for 48 hours.

tag: disease status

value: Basal cell nevus syndrome

value: Keratinocyte

value: Sirolimus (50 ng/ml) for 48 hours

tag: participant


title: WT3_mNK1


title: HCC1187 with shRNA-NC (negative control) rep2

tag: treatment


title: HCC1187 with shRNA-1 rep3


title: WT2_mNK2


title: WT2_mNK1


title: HCC1187 with shRNA-1 rep1


title: 14K48S50

data_processing: The arrays were scanned using Hewlett-Packard GeneArray Scanner and the scanned output files were visually inspected for hybridization artifacts. The data quality was checked for the presence of spiked control cRNAs, background values caused by array autofluorescence and non-specific binding, and Q value.

label_protocol: We analyzed the RNA on Affymetrix U133 Plus 2.0 expression arrays. Microarray processing was performed at Yale. The cDNA and cRNA preparation, cRNA labeling and hybridization to Affymetrix Human Genome U133 Plus 2.0 GeneChip® microarrays (Affymetrix, Santa Clara, CA) was performed as per standard protocols according to manufacturer’s instructions.


title: WT1_mNK1


title: 04K48S50


title: 11K48S50


title: WT1_mNK2


title: WT2_iNK

value: iNK


title: 12K48S50


title: WT1_iNK


title: KO3_mNK1

value: Tbx21 KO


title: KO2_mNK1


title: 09K48S50

value: Normal


title: KO3_iNK


title: KO2_iNK


title: 18K48S50


title: WT3_iNK


title: 15K48S50


title: KO1_iNK


title: 07K48S50


title: Week25t_UVB_0 [Bisulfite-seq]

city: Piscataway

first: Renyi

last: Wu

state: NJ

address: 160 Frelinghuysen road

department: Pharmacy School

institute: Rutgers University

data_processing:
Illumina standard procedure for base calling. Adapter removed
Reads were aligned to mm10 using Bismark with default parameters
Duplicates removed by Picard
Methylation calls were extracted by DMRfinder
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited tables with raw counts.

source_name: skin tumor

growth_protocol: 12 hours light and dark cycles; Food and water were provided ad libitum;

extract_protocol:
Qiagen Allprep DNA/RNA extraction
Standard Illumina protocols

treatment_protocol: 60 mJ/cm2 UVB-irradiation twice per week.

value: skin

value: female

tag: duration of treatment

value: 25 weeks

tag: agent

value: 60 mJ/cm2 UVB-irradiation


title: Week25t_UVB_1 [Bisulfite-seq]


title: 03K48S50


title: 13K48S50


title: 22K48S50


title: 05K48S50


title: 07F48S50

source_name: Fibroblast

value: Fibroblast


title: 01K48S50


title: 14F48S50


title: 02K48S50


title: 22F48S50


title: 12F48S50


title: KO1_mNK1


title: Week25t_CON_0 [Bisulfite-seq]

source_name: whole skin


title: Week25t_CON_1 [Bisulfite-seq]


title: 17F48S50


title: Week25_UVB_1 [Bisulfite-seq]

source_name: epidermis


title: 18F48S50


title: 08K48S50


title: 16K48S50


title: 11F48S50


title: Blood_Platelets_Vumc-HD-73

description:
Vumc-HD-73-TR887
Vumc-HD-73-TR887_AGTCAA_L002

value: Blood platelets


title: Week25_UVB_0 [Bisulfite-seq]


title: 13F48S50


title: Week25_CON_1 [Bisulfite-seq]


title: Week25_CON_0 [Bisulfite-seq]


title: 04F48S50


title: Week15_UVB_1 [Bisulfite-seq]

value: 15 weeks


title: 09F48S50


title: 16F48S50


title: Week15_UVB_0 [Bisulfite-seq]


title: 15F48S50


title: Week15_CON_0 [Bisulfite-seq]


title: Week15_CON_1 [Bisulfite-seq]


title: 03F48S50


title: Week2_UVB_1 [Bisulfite-seq]

value: 2 weeks


title: 05F48S50


title: Week2_UVB_0 [Bisulfite-seq]


title: Week2_CON_0 [Bisulfite-seq]


title: Week25t_UVB_1

data_processing:
Illumina standard procedure for base calling. Adapter removed
Reads were aligned to mm10 using Hisat2 with default parameters
Duplicates removed by Picard
Reads overlapping gene features were counted by featureCounts.
Differential expression by DESeq2 in R
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited tables with raw counts.


title: Week2_CON_1 [Bisulfite-seq]


title: Week25t_UVB_0


title: Week25t_CON_0


title: 08F48S50


title: 02F48S50


title: Week25_UVB_1


title: 14K48S10

value: Sirolimus (10 ng/ml) for 48 hours


title: 17K48S10


title: Week15_UVB_1


title: 01F48S50


title: 11K48S10


title: 07K48S10


title: Week25_UVB_0


title: 16K48S10


title: Week25_CON_1


title: 22K48S10


title: 13K48S10


title: 12K48S10


title: Week25_CON_0


title: 15K48S10


title: Week2_UVB_1


title: Week15_UVB_0


title: Week2_UVB_0


title: Week25t_CON_1


title: 18K48S10


title: Week15_CON_1


title: 09K48S10


title: 05K48S10


title: Week2_CON_0


title: 04K48S10


title: Week15_CON_0


title: 03K48S10


title: 72hr treated timepoint #3

city: Edinburgh

first: Thomas

middle: Graham

last: Bird

state: Midlothian

address: Queens Medical Research Institute

institute: University of Edinburgh

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S23_L001
IC57-1171

data_processing:
Quality checks on the raw RNASeq data files were done using fastqc version 0.10.1 [http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc] and fastq_screen version 0.4.2 [http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/]. RNASeq reads were aligned to the GRCm38[Church et al 2011 PLoS Biol] version of the mouse genome using tophat2 version 2.1.0 [Kim et al  2013 Genome Biol] with Bowtie version 2.2.6.0[Langmead et al 2012 Nat Methods ]. Expression levels were determined and statistically analysed by a combination of HTSeq version 0.5.4p3 [http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html], the R version 3.4.2 environment, utilizing packages from the Bioconductor data analysis suite and differential gene expression analysis based on the negative binomial distribution using the DESeq2 [Love et al Genome Biology 2014]. The data were normalised for library size using the DESeq2 sizeFactors function.
Genome_build: GRCm38
Supplementary_files_format_and_content: [results_20180108_paracetamol_time_series.xlsx]  Normalised counts in worksheet "combined", columns AG-BD.

source_name: Murine liver - whole tissue extract

extract_protocol:
Following cardiac puncture and exsanguination, liver (caudate lobe) was harvested and immediately frozen on dry ice. Samples were stored for <6months at  -80. Total RNA was extracted from 30-50mg tissue samples using a combination of TRIzol reagent (Invitrogen) and Qiagen RNeasy Mini system (Qiagen, UK) according to both manufacturers’ instructions. Purified RNA was tested on an Agilent 2200 Tapestation using RNA screentape.
Libraries for cluster generation and DNA sequencing were prepared following an adapted method from  Fisher et al.PLOS Biology 9;e1001091(2011), using Illumina TruSeq Stranded mRNA LT Kit, Quality and quantity of the DNA libraries was assessed on a Agilent 2200 Tapestation (D1000 screentape) and Qubit (Thermo Fisher Scientific) respectively.
The libraries were run on the Illumina Next Seq 500 using the High Output 75 cycles kit (2x36cycles, paired end reads, single index). Quality checks on the raw RNASeq data files were done using fastqc version 0.10.1 and fastq_screen version 0.4.2.

treatment_protocol: Male 9-10 week animals were fasted for 10hrs prior to administration of 350mgkg-1 acetaminophen (PBS vehicle) by intraperitoneal injection (20µl/g body weight) to generate clinically relevant hepatic injury in vivo.  Animals were sacrificed and samples prepared at defined timepoints post treatment and compared to untreated control samples.

value: acetaminophen

tag: time

value: liver


title: Week2_CON_1

tag: Sex


title: 72hr treated timepoint #4

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S24_L001
IC57-1172


title: 17F48S10

value: Basal cell nevus syndrome


title: 72hr treated timepoint #2

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S22_L001
IC57-1170


title: 72hr treated timepoint #1

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S21_L001
IC57-1169


title: 08K48S10

value: Keratinocyte


title: 48hr treated timepoint #3

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S19_L001
IC57-1166


title: 48hr treated timepoint #4

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S20_L001
IC57-1167


title: 01K48S10


title: 36hr treated timepoint #4

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S16_L001
IC57-9


title: 48hr treated timepoint #2

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S18_L001
IC57-1165


title: 02K48S10


title: 14F48S10


title: 07F48S10


title: 13F48S10


title: 36hr treated timepoint #2

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S14_L001
IC57-7


title: 36hr treated timepoint #3

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S15_L001
IC57-8


title: 36hr treated timepoint #1

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S13_L001
IC57-6


title: 24hr treated timepoint #4

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S12_L001
IC57-1162


title: 04F48S10


title: 12F48S10


title: 22F48S10


title: 24hr treated timepoint #2

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S10_L001
IC57-1160


title: 11F48S10


title: 18F48S10


title: 15F48S10


title: 24hr treated timepoint #1

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S09_L001
IC57-1159


title: 02F48S10


title: 03F48S10


title: 05F48S10


title: 09F48S10


title: 01F48S10


title: 17KER

value: Untreated


title: 08F48S10


title: 12hr treated timepoint #1

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S05_L001
IC57-1


title: 16F48S10


title: 12hr treated timepoint #2

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S06_L001
IC57-2


title: 0hr untreated control #4

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S04_L001
IC57-1152

value: control


title: 0hr untreated control #2

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S02_L001
IC57-1150


title: 0hr untreated control #3

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S03_L001
IC57-1151


title: 0hr untreated control #1

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S01_L001
IC57-1149


title: 12hr treated timepoint #3

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S07_L001
IC57-3


title: 14KER


title: 04KER


title: 13KER


title: 07KER


title: 22KER


title: 11KER


title: 18KER


title: Second Aerated Bio Rep4

city: Ames

first: Andrew

middle: J

last: Severin

email: severin@iastate.edu, csiva@iastate.edu

state: IA

address: 2200 Osborn Drive

department: Office of Biotechnology

institute: Iowa State University

description:
12-AER
mRNA
processed file: Results_second_dataset.csv

data_processing:
Reads to aligned to Arabidopsis genome (TAIR10) using HISAT2, version 2.0.4 (Kim et al., 2015).
Read counts were calculated using featureCounts ver 1.5.2 (Liao et al., 2014).
The counts were then normalized and differential expression analysis was carried out using DESeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: Results_second_dataset.csv: csv; normalized counts for gene expression, log2fold change and adjusted pvalue.

organism: Arabidopsis thaliana

source_name: Pooled shoots of 10 plants (one plate)

growth_protocol: Seeds were sterilized with 70% ethanol for 1 min and then with imers in 1:4 Sodium hypochlorite v/v for 5 min. and washed 4 times with sterile dH2O. Plants were plated on square 10x10cm sterile Petri dish (FisherBrand USA) with 1/2x MS medium with 1% of sucrose and 0.8% of agar. Seeds on plates were vernalized in 4oC for 4 days and later moved to growth chamber (T=22oC, Light=140 mmol/s/m2).

extract_protocol:
Plant were harvested 15 days after vernalization, freeze in liquid nitrogen, grind in (LN2) cold mortar and total RNA was isolated using plant RNA-easy kit (IBI Scientific, USA). Total RNA was checked for quality using Bioanalyzer (Bio-Rad).
RNA sequencing libraries were prepared using standard unstranded RNA Sample Prep Kits (Illumina Inc., San Diego, CA) and samples sequenced single end 100 bps sequencing on an Illumina HiSeq 3000 instrument at the Iowa State DNA facility.

treatment_protocol: One day after vernalization (5th day after sawing) half (4) plates covers were change for covers with mounted syringe filters 0.22 mm (inlet and outlet) and air flow was initiated (0.15-0.25 L/min.) - aerated treatment. Rest of plates (4) were just opened and closed briefly on day 5 after sawing - non-aerated treatment.

value: shoots

value: aerated


title: Second Non-Aerated Bio Rep4

description:
8-NAP
mRNA
processed file: Results_second_dataset.csv

value: non-aerated


title: 12KER


title: 13 FIB


title: 11 FIB


title: 14 FIB


title: 22 FIB


title: 02KER

value: Normal


title: 48hr treated timepoint #1

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S17_L001
IC57-1164


title: 03KER


title: 07 FIB


title: 01KER


title: 18 FIB


title: 08KER


title: mDE6, 5 mM CHIR99021 treated, 6hr

city: Fukuoka

first: Shinsuke

last: Fujii

state: Fukuoka

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

department: Faculty of Dental Science

country: Japan

institute: Kyushu University

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

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

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

source_name: mDE6, 5 mM CHIR99021 treated, 6hr

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

tag: cell line

value: mouse odontogenic epithelial cells


title: Second Non-Aerated Bio Rep3

description:
7-NAP
mRNA
processed file: Results_second_dataset.csv


title: Second Aerated Bio Rep3

description:
11-AER
mRNA
processed file: Results_second_dataset.csv


title: Second Aerated Bio Rep2

description:
10-AER
mRNA
processed file: Results_second_dataset.csv


title: Second Aerated Bio Rep1

description:
9-AER
mRNA
processed file: Results_second_dataset.csv


title: 09 FIB


title: Second Micropore Bio Rep2

description:
2-NAM
mRNA
processed file: Results_second_dataset.csv

value: micropore filter


title: Second Micropore Bio Rep4

description:
4-NAM
mRNA
processed file: Results_second_dataset.csv


title: 15KER


title: 12 FIB

value: Fibroblast


title: 15 FIB


title: Second Micropore Bio Rep1

description:
1-NAM
mRNA
processed file: Results_second_dataset.csv


title: 16 FIB


title: 09KER


title: Second Non-Aerated Bio Rep1

description:
5-NAP
mRNA
processed file: Results_second_dataset.csv


title: Second Micropore Bio Rep3

description:
3-NAM
mRNA
processed file: Results_second_dataset.csv


title: 02 FIB


title: Non Aerated Bio Rep4

data_processing:
Reads to aligned to Arabidopsis genome (TAIR10) using HISAT2, version 2.0.4 (Kim et al., 2015).
Read counts were calculated using featureCounts ver 1.5.2 (Liao et al., 2014).
The counts were then normalized and differential expression analysis was carried out using DESeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html)
Genome_build: Arabidopis thaliana TAIR10
Supplementary_files_format_and_content: csv; normalized counts for gene expresion, log2fold change and adjusted pvalue

extract_protocol:
Plant were harvested 15 days after vernalization, freeze in liquid nitrogen, grind in (LN2) cold mortar and total RNA was isolated using plant RNA-easy kit (IBI Scientific, USA). Total RNA was checked for quality using Bioanalyzer (Bio-Rad)
RNA sequencing libraries were prepared using standard unstranded RNA Sample Prep Kits (Illumina Inc., San Diego, CA) and samples sequenced single end 100 bps sequencing on an Illumina HiSeq 3000 instrument at the Iowa State DNA facility


title: Second Non-Aerated Bio Rep2

description:
6-NAP
mRNA
processed file: Results_second_dataset.csv


title: Aerated Bio Rep4


title: Non Aerated Bio Rep3


title: Non Aerated Bio Rep2


title: 24hr treated timepoint #3

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S11_L001
IC57-1161


title: 08 FIB


title: 05 FIB


title: 01 FIB


title: Ovarian normal tissue [ZON18]

city: hunan

first: Ding

last: qi

state: changsha

address: tong zi po

institute: huan cancer  hospital

description:
ZON18
Normal

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized in an Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and GeneSpring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: Normal ovary

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: Ovarian normal tissue


title: Ovarian normal tissue [ZON4]

description:
ZON4
Normal


title: Ovarian normal tissue [ZON11]

description:
ZON11
Normal


title: Aerated Bio Rep3


title: Non Aerated Bio Rep1


title: MDA_MB_231 IgG Rep3

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

description:
MDA_MB_231_3_IGG
processed data file: MDA_MB_231_IGG_peaks.narrowPeak.gz

data_processing:
Reads were mapped to hg38 genome using bwa version 0.7.12.
Aligned reads with the mapping quality less than 15 were filtered out.
The Bioconductor package GreyListChIP version 1.8.0 and the blacklist file for hg38 was downloaded from http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz was used to identify regions for filtering.
For each antibody/input and cell type combination the 3 replicate filtered bams were merged after having reads marked as duplicates removed.
Peak calling was carried out using MACS2 version 2.1.1.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_peaks.narrowPeak: bed/text

growth_protocol: MCF7 cells were grown in DMEM supplemented with 10% FBS, 2mM L-glutamine, 50 U/ml penicillin, 50 ug/ml streptomycin. MDA-MB-231 cells were grown in RPMI supplemented with 10% FBS, 2mM L-glutamine and 50 U/ml penicillin and 50 ug/ml streptomycin.

extract_protocol:
Cells were crosslinked in 1% formaldehyde for 10 min and then quenched in 100mM glycine. Nuclear enrichment was performed followed by sonication (Bioruptor plus, Diagenode). Chromatin was immunoprecipitated over night using specific antibodies. Beads were washed six times in RIPA buffer and eluted from beads using SDS buffer. After RNase and proteinase K treatment, DNA was purified by phenol/chloroform extraction.
Libraries were prepared using the Thruplex kit (Illumina) according to the manufacturer's instructions.

value: Breast cancer cell line

tag: passages

tag: chip antibody

value: IgG (Abcam, ab171870)


title: MDA_MB_231 ERa Abcam Rep3

description:
MDA_MB_231_3_ER_ABCam
processed data file: MDA_MB_231_ER_ABCam_peaks.narrowPeak.gz

value: anti-ERalpha (Abcam, ab3575)


title: MDA_MB_231 Input Rep3


title: MDA_MB_231 Input Rep2


title: MDA_MB_231 ERa Santacruz Rep3

description:
MDA_MB_231_3_ER_Santa
processed data file: MDA_MB_231_ER_Santa_peaks.narrowPeak.gz

value: anti-ERalpha (Santa Cruz, sc-543)


title: MDA_MB_231 ERa Millipore Rep3

description:
MDA_MB_231_3_ER_Milli
processed data file: MDA_MB_231_ER_Milli_peaks.narrowPeak.gz

value: anti-ERalpha (Millipore, 06-935)


title: MDA_MB_231 ERa Millipore Rep2

description:
MDA_MB_231_2_ER_Milli
processed data file: MDA_MB_231_ER_Milli_peaks.narrowPeak.gz


title: Ovarian malignant tissue [ZOC19]

description:
ZOC19
Cancer

source_name: Ovarian cancer

value: Ovarian malignant tissue


title: 12hr treated timepoint #4

description:
results_20180108_paracetamol_time_series.xlsx
MMR9180108_S08_L001
IC57-4

value: acetaminophen

value: liver


title: Ovarian malignant tissue [ZOC8]

description:
ZOC8
Cancer


title: 03 FIB

value: Untreated


title: MDA_MB_231 ERa Santacruz Rep2

description:
MDA_MB_231_2_ER_Santa
processed data file: MDA_MB_231_ER_Santa_peaks.narrowPeak.gz


title: Ovarian malignant tissue [ZOC13]

description:
ZOC13
Cancer


title: Ovarian malignant tissue [ZOC7]

description:
ZOC7
Cancer


title: MDA_MB_231 ERa Millipore Rep1

description:
MDA_MB_231_1_ER_Milli
processed data file: MDA_MB_231_ER_Milli_peaks.narrowPeak.gz


title: MDA_MB_231 IgG Rep1

description:
MDA_MB_231_1_IGG
processed data file: MDA_MB_231_IGG_peaks.narrowPeak.gz


title: MDA_MB_231 IgG Rep2

description:
MDA_MB_231_2_IGG
processed data file: MDA_MB_231_IGG_peaks.narrowPeak.gz


title: Ovarian malignant tissue [ZOC2]

description:
ZOC2
Cancer


title: Aerated Bio Rep2


title: MDA_MB_231 Input Rep1


title: MDA_MB_231 ERa Santacruz Rep1

description:
MDA_MB_231_1_ER_Santa
processed data file: MDA_MB_231_ER_Santa_peaks.narrowPeak.gz


title: MDA_MB_231 ERa Abcam Rep1

description:
MDA_MB_231_1_ER_ABCam
processed data file: MDA_MB_231_ER_ABCam_peaks.narrowPeak.gz


title: Ovarian normal tissue [ZON18]

description:
ZON18
Normal

hyb_protocol: Hybridization of samples to the strips was carried out at 48 °C for 20 h. Strips were then washed, stained and scanned using the GeneAtlas®System (Affymetrix).

scan_protocol: Affymetrix® GeneChip® Command Console® Software.

data_processing: Expression Console software was used to analyze the raw data, which are normalized by RMA normalization.

label_protocol: The biotin-labeled signal molecule is linked to it by RNA ligase, and the product and the chip are ligated for hybridization reaction.


title: 16KER

value: Keratinocyte


title: MCF7 ERa Millipore Rep2

description:
MCF7_2_ER_Milli
processed data file: MCF7_ER_Milli_peaks.narrowPeak.gz


title: MCF7 Input Rep2


title: Ovarian malignant tissue [ZOC8]

description:
ZOC8
Cancer


title: Ovarian malignant tissue [ZOC7]

description:
ZOC7
Cancer


title: Ovarian malignant tissue [ZOC21]

description:
ZOC21
Cancer


title: Ovarian normal tissue [ZON11]

description:
ZON11
Normal


title: Ovarian normal tissue [ZON4]

description:
ZON4
Normal


title: Ovarian malignant tissue [ZOC19]

description:
ZOC19
Cancer


title: Ovarian malignant tissue [ZOC13]

description:
ZOC13
Cancer


title: MCF7 IgG Rep2

description:
MCF7_2_IGG
processed data file: MCF7_IGG_peaks.narrowPeak.gz


title: Ovarian malignant tissue [ZOC2]

description:
ZOC2
Cancer


title: Day11_H1_1000_cells

city: Singapore

first: Aida

last: Moreno-Moral

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

description: Cells maintained on LN-521 for four days and then seven days on LN-521+LN-221

data_processing:
The reads were mapped to the human genome (Ensembl version 90) and quantified using Cell Ranger 2.1.1 (10x Genomics).
Cell Ranger was run with the expect number of cells parameter (expect-cells) set to 1,000, which resulted in 713, 841, 591 and 636 cells for the day9_HS1001, day9_H1, day11_HS1001 and day11_H1 samples respectively.
Reads were quantified using RSEM 1.2.31. Cell Ranger output matrices (i.e. genes.tsv and barcodes.tsv) were then input into R, the four 10x data runs were merged and genes with zero counts in all cells were discarded.
Genome_build: Human genome (Ensembl version 90). We provided to Cell Ranger a custom-built reference transcriptome generated by filtering the Ensembl transcriptome for the gene biotypes: protein coding, lincRNA and antisense.
Supplementary_files_format_and_content: CVPs_single_cell_sequencing_gene_raw_counts.txt: tab separated file with raw gene expression counts for each gene and cell sequenced

source_name: H1 from WiCell International

growth_protocol: Cells were cultured in wells coated with LN-521 and LN-221. Cells at day 0 were cultured with Nutristem medium. Cells at Day 5 and 7 were cultured in RMPI 1640 with B27 without insulin supplement and CHIR99021. Cells at day 9 were cultured in RMPI 1640 with B27 without insulin supplement and IWP2. Cells at day 11 were cultured in RMPI 1640 with B27 without insulin supplement.

extract_protocol:
A chromium instrument (10x Genomics) was used to partition viable cell suspensions into single cell droplets using Single Cell 3’ library and gel bead kit version 2 (10x Genomics, Cat.#120237) as per manufacturer’ protocol. Illumina Hi-Seq3000 sequencing platform in a single sequencing lane.
The samples were loaded into single cell chip (10x Genomics, Cat.No.120236) to capture 1000 cells in each of the four sets of cells

treatment_protocol: At day 4, medium was supplemented with 10 mg of CHIR99021 and at day 7, medium was supplemented with 5 mg IWP2

tag: cellline

tag: biological replicate

value: day 11


title: MCF7 ERa Santacruz Rep2

description:
MCF7_2_ER_Santa
processed data file: MCF7_ER_Santa_peaks.narrowPeak.gz

tag: cell type


title: Day9_1001_1000_cells

description: Cells maintained on LN-521 for four days and then five days on LN-521+LN-221

source_name: HS1001 from Dr. Hovatta’s laboratory (Rodin et al., 2014)

value: day 9


title: MCF7 ERa Abcam Rep2

description:
MCF7_2_ER_ABCam
processed data file: MCF7_ER_ABCam_peaks.narrowPeak.gz


title: MCF7 Input Rep1


title: MCF7 ERa Santacruz Rep1

description:
MCF7_1_ER_Santa
processed data file: MCF7_ER_Santa_peaks.narrowPeak.gz


title: MCF7 IgG Rep1

description:
MCF7_1_IGG
processed data file: MCF7_IGG_peaks.narrowPeak.gz


title: Day11_1001_1000_cells


title: gly24h-3

city: Zhejiang

first: Anqi

last: Li

state: Hangzhou

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
For the data analysis, basecalls were performed using CASAVA.
Reads were aligned to the genome using the split read aligner TopHat (v2.0.7) and Bowtie2, using default parameters.
HTSeq was used for estimating their abun-dances.
Differential expression analysis of two condi-tions/groups (two biological replicates per condition) was performed using the DESeq R package (1.18.0).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implement-ed by the GOseq R package, in which gene length bias was corrected.GO terms with corrected P value less than 0.05 were considered significantly enriched by dif-ferential expressed genes.
Genome_build: 9606(Homo sapiens)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: MCF-7 cell line

growth_protocol: MCF-7 cells were cultured at 37 °C in 5 % CO2 in EMEM (Genom, Hangzhou, China), supplemented with 10% fetal bovine serum (Gibco), 100 IU/ml penicillin and 100 μg/ml streptomycin (Sigma-Aldrich)

extract_protocol:
Total RNA from MCF-7 with or without GlyH-101 treatment was isolated using TRIzol reagent and treated with RNase-free DNase I (New England Biolabs, MA, USA) to remove any contaminating genomic.  DNA.
mRNA-seq library was prepared for sequencing using standard Illumina protocols

treatment_protocol: cells were treated with 10uM GlyH-101 for 1h and 24h.


title: MCF7 ERa Millipore Rep1

description:
MCF7_1_ER_Milli
processed data file: MCF7_ER_Milli_peaks.narrowPeak.gz


title: MCF7 ERa Abcam Rep1

description:
MCF7_1_ER_ABCam
processed data file: MCF7_ER_ABCam_peaks.narrowPeak.gz


title: Blood_Patient5_wt_48hours

city: Lund

first: Ines

last: Ambite

address: Klinikgatan 28

department: Laboratory Medicine

country: Sweden

institute: Lund University

hyb_protocol: Following fragmentation, 6ug (GeneChip) or 7.5ug (Array strip) of cRNA were hybridized for 16 hr at 45°C on Human Genome U219 Arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: RNA hybridisation and microarray analysis was conducted by AROS Applied Biotechnology AS (Aarhus, Denmark) using Affymetrix Human Genome U219 GeneChip (Affymetrix) or in-house using the GeneAtlas system and Affymetrix Human Genome U219 array strip.

data_processing:
Transcriptomic data was normalized using Robust Multi Average (RMA) implemented in the free software packages R and Bioconductor and Partek Express software. Fold change was calculated by comparing each sample to the pre-inoculation samples in each individual. Genes with absolute fold change >2.0 were considered differentially expressed. Heat-maps were constructed using the Gitools software. Differentially expressed genes and regulated pathways were analyzed using the Gene Set Enrichment Analysis (GSEA, Broad Institute) and the Ingenuity Pathway Analysis (IPA, Qiagen Bioinformatics) softwares.
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.1.2800.28061

source_name: Peripheral blood lymphocytes from patient 5, 48 hours after inoculation with E. coli 83972

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix's GeneChip 3´IVT Express Kit protocol from 150ng (GeneChip) or 100ng (Array strip) total RNA.

growth_protocol: E. coli 83972 wild type, the P or type 1- fimbriated derivatives were cultured overnight (16 h) in lysogeny broth, cells were harvested by centrifugation and re-suspended in PBS to a concentration of 10^5 cfu/ml.

extract_protocol: RNA was extracted from 1 ml of heparinized peripheral whole blood using the QIAamp RNA Blood Mini Kit (Qiagen), according to the manufacturer's instructions. Blood samples were collected prior to inoculation, 3, 24 and 48 hours and at 1 and 2 weeks after inoculation.

treatment_protocol: Prior to inoculation, patients were treated with appropriate antibiotics to sterilize their urine, followed by an antibiotic free interval. Patients were then were catheterized.  After emptying the bladder, 30 ml of the solution was inoculated  hrough the catheter, which was then removed.

tag: subject id

value: patient 5

tag: gender

value: female

tag: batch

value: in-house

tag: time point

value: peripheral blood lymphocytes


title: gly24h-1


title: Blood_Patient5_wt_1week

source_name: Peripheral blood lymphocytes from patient 5, 1 week after inoculation with E. coli 83972

tag: tissue


title: KO9_4

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

data_processing:
Fastq files were mapped to the human transcriptome using Bowtie2, relative gene expression was determined using RSEM.
Genome_build: hg38
Supplementary_files_format_and_content: Gene level RSEM output files.

source_name: Del SE 3-9

growth_protocol: Cells grown under standard tissue culture conditions in RPMI + 10% FBS.

extract_protocol:
RNA was extracted from 80% confluent cells using the RNeasy Mini Kit (Qiagen 74104) following the manufacturer’s recommendations. RNA quality was assessed with the RNA Nano 6000 kit (Agilent 5067-1511) and Agilent Bionalyzer 2100 instrument.
RNA-Seq libraries were prepared using the SENSE mRNA-Seq Library Prep Kit V2 (Lexogen) following the manufacturer’s recommendations with 1μg of total RNA as the starting material. The size and quality of the final library products were assessed using the Agilent High Sensitivity DNA Kit (Agilent 5067-4626). Library concentration was determined using the KAPA Library Quantification Kit (KR0405). Libraries were pooled in equimolar concentrations and subjected to Illumina sequencing.

value: renal cancer cell line

value: no 113kb SE deletion


title: Blood_Patient4_wt_2weeks

source_name: Peripheral blood lymphocytes from patient 4, 2 weeks after inoculation with E. coli 83972

value: patient 4

value: male


title: Blood_Patient5_wt_24hours

source_name: Peripheral blood lymphocytes from patient 5, 24 hours after inoculation with E. coli 83972


title: Blood_Patient5_wt_sterile

source_name: Peripheral blood lymphocytes from patient 5, before inoculation with E. coli 83972

value: before inoculation with E. coli 83972


title: Blood_Patient4_wt_48hours

source_name: Peripheral blood lymphocytes from patient 4, 48 hours after inoculation with E. coli 83972

value: AROS


title: Blood_Patient4_wt_1week

source_name: Peripheral blood lymphocytes from patient 4, 1 week after inoculation with E. coli 83972


title: Blood_Patient5_wt_3hours

source_name: Peripheral blood lymphocytes from patient 5, 3 hours after inoculation with E. coli 83972


title: Blood_Patient4_wt_24hours

source_name: Peripheral blood lymphocytes from patient 4, 24 hours after inoculation with E. coli 83972


title: Blood_Patient4_wt_3hours

source_name: Peripheral blood lymphocytes from patient 4, 3 hours after inoculation with E. coli 83972


title: gly24h-2


title: Blood_Patient4_wt_sterile

source_name: Peripheral blood lymphocytes from patient 4, before inoculation with E. coli 83972


title: KO9_3


title: gly1h-3


title: KO9_2


title: KO9_1


title: KO19_4

source_name: Del SE 3-19

value: 113kb SE deletion


title: gly0h-3


title: Blood_Patient3_wt_2weeks

source_name: Peripheral blood lymphocytes from patient 3, 2 weeks after inoculation with E. coli 83972

value: patient 3


title: Blood_Patient3_wt_1week

source_name: Peripheral blood lymphocytes from patient 3, 1 week after inoculation with E. coli 83972


title: Blood_Patient3_wt_24hours

source_name: Peripheral blood lymphocytes from patient 3, 24 hours after inoculation with E. coli 83972


title: gly0h-2

source_name: MCF-7 cell line


title: 17 FIB

source_name: Fibroblast

tag: disease status

value: Basal cell nevus syndrome

value: Fibroblast

tag: participant


title: Blood_Patient3_wt_3hours

source_name: Peripheral blood lymphocytes from patient 3, 3 hours after inoculation with E. coli 83972


title: 05KER

source_name: Keratinocyte

value: Normal

value: Keratinocyte

tag: treatment

value: Untreated


title: Blood_Patient3_wt_48hours

source_name: Peripheral blood lymphocytes from patient 3, 48 hours after inoculation with E. coli 83972


title: Blood_Patient3_wt_sterile

source_name: Peripheral blood lymphocytes from patient 3, before inoculation with E. coli 83972


title: gly1h-2


title: gly0h-1


title: mDE6, 0/1%DMSO treated, 6hr

source_name: mDE6, 0/1%DMSO treated, 6hr

value: mouse odontogenic epithelial cells


title: KO19_2


title: gly1h-1


title: Blood_Patient2_wt_24hours

source_name: Peripheral blood lymphocytes from patient 2, 24 hours after inoculation with E. coli 83972

value: patient 2


title: Blood_Patient2_wt_1week

source_name: Peripheral blood lymphocytes from patient 2, 1 week after inoculation with E. coli 83972


title: ChIP-seq_786-M1A_FLAG-KLF6_hg38

data_processing:
Fastq files were aligned to hg38 using Bowtie2.
Genomewide coverage was determined in 10bp windows and normalized to counts/million uniquely mapped reads.
Genomewide coverage data was converted to BigWig format.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files display counts/million uniquely mapped reads in 10bp windows.

source_name: 786-M1A cell line

growth_protocol: Cells grown under standard tissue culture conditions in RPMI + 10% FBS.Cells grown under standard tissue culture conditions in RPMI + 10% FBS.

extract_protocol:
Cells were crosslinked in 1% formaldehyde for 10min at room temperature, followed by 5 min quenching with 0.125M glycine. Cells were washed twice with PBS, the supernatant was aspirated and cell pellets were frozen in liquid nitrogen and stored at -80°C. 100µl of Protein A/G magnetic beads (Thermo 26162) were blocked with 0.5% BSA in PBS, followed by incubation with the antibody. Cross-linked cells were resuspendend and sonicated in lysis buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 0.1% SDS, and 1% Triton X-100). Sonication was performed using Bioruptor (Diagenode) for 14 cycles (30’’ on/ 30’’ off) at max output to obtain fragments of 100-500bp. Sonicated lysates were cleared and incubated overnight at 4°C with antibody-bound magnetic beads. Beads were sequentially washed three times with low salt buffer (50mM HEPES pH7.5, 140mM NaCl, 1% Triton) and once with high salt buffer (50mM HEPES pH7.5, 500mM NaCl, 1% Triton). DNA was eluted in elution buffer (50mM NaHCO3, 1%SDS) and cross-links were reversed for 3h (65°C, 1000rpm shaking). DNA was purified using the QuickClean II PCR Extraction Kit (Genescript L00419-100) according to the manufacturer’s recommendations and eluted with 100µl H2O.
Purified ChIP DNA was used to prepare Illumina multiplexed sequencing libraries with the KAPA Hyper Prep Kit (KR0961) Illumina platforms sample preparation protocol (v1.14). Briefly, DNA was end-repaired and A-tailed to produce end-repaired, 5’-phosphorylated, 3’-dA-tailed, dsDNA fragments. These 3’-dA-tailed library fragments were then ligated with dsDNA adapters with 3’dTMP overhangs. After adapter ligation, libraries were size selected to 150-350bp using AMPure XP reagent (Agencourt A63880) according to the protocol recommendations. Size selected libraries were amplified for 15 cycles using the KAPA HiFi HotStart ReadyMix. PCR libraries were pooled in equimolar concentrations and sequenced.

tag: cell line type

tag: target molecule

tag: antibody

value: F1804 Monoclonal Anti-Flag M2 Ab (Sigma)


title: Blood_Patient2_wt_48hours

source_name: Peripheral blood lymphocytes from patient 2, 48 hours after inoculation with E. coli 83972

value: peripheral blood lymphocytes


title: Blood_Patient2_wt_sterile

source_name: Peripheral blood lymphocytes from patient 2, before inoculation with E. coli 83972


title: Blood_Patient2_wt_2weeks

source_name: Peripheral blood lymphocytes from patient 2, 2 weeks after inoculation with E. coli 83972

value: in-house


title: MO3.13_BC200-KO-1_RNAseq

city: Sherbrooke

first: Karine

last: Choquet

address: 3201 rue Jean-Mignault

institute: Université de Sherbrooke

description:
MO313.Ensembl.ensGene.exon.s2.raw.tsv.gz
MO313.Ensembl.ensGene.exon.s2.norm.tsv.gz

data_processing:
Read trimming was performed with Trimmomatic v0.35
Alignment was performed with STAR v2.3.0e (RNA-seq and small RNA-seq) or bowtie2 v.2.2.9 (ChIP-seq)
Reads were counted with featureCounts v1.5.0
Normalization and differential expression analysis (RNAseq and small RNAseq) were performed with DESeq2
ChIP-seq read counts were normalized to the median of total read counts and Pol III occupancy scores were calculated as the log2(IPread_count/Inputread_count)
Genome_build: hg19
Supplementary_files_format_and_content: For each dataset, raw and normalized counts per sample are provided in one file (tsv, csv or txt)

source_name: MO3.13 cell line

extract_protocol:
Total RNA extracted with Qiagen miRNeasy
NEBNext rRNA-depleted stranded library preparation

tag: cell line

tag: genotype/variation

value: KO


title: MO3.13_POLR3A-M852V-2_RNAseq

tag: chip antibody


title: Astrocytes_ctr_02

city: Freiburg

first: Dieter

middle: Henrik

last: Heiland

address: Breisacherstr. 64

department: Department of Neurosurgery

country: Germany

institute: Medical Center Freiburg

data_processing:
Basecalling by Albacore 2.0.1, Quality Control, Identification of Barcoded Samples by PoreChop
Alignment by MiniMap2
Nanopore Pipeline (www.github.com/heilandd/)
Postprocessing by DESeq2 and AutoPipe (Cran)
Genome_build: GRch38
Supplementary_files_format_and_content: tab-delimited text files of counts per barcode

source_name: Astrocytes Cell line

extract_protocol:
Astrocytes were extracted by HepaCAM-Immunopanning
Library was constructed by Nanopore cDNA sequencing Kit, SQK-PCS109

value: Astrocytic Cell Line

tag: barcode


title: Bottom_T-_M+_A+_02


title: Bottom_T-_M+_A+_01


title: Astrocytes_ctr_01


title: Bottom_T+_M+_A+_02


title: Blood_Patient1_wt_1week

source_name: Peripheral blood lymphocytes from patient 1, 1 week after inoculation with E. coli 83972

value: patient 1

value: male


title: Bottom_T+_M+_A+_01


title: Blood_Patient1_wt_48hours

source_name: Peripheral blood lymphocytes from patient 1, 48 hours after inoculation with E. coli 83972

value: AROS


title: Blood_Patient1_wt_24hours

source_name: Peripheral blood lymphocytes from patient 1, 24 hours after inoculation with E. coli 83972


title: MO3.13_POLR3A-M852V-1_RNAseq


title: KO19_1

source_name: Del SE 3-19

value: renal cancer cell line

value: 113kb SE deletion


title: Blood_Patient1_wt_sterile

source_name: Peripheral blood lymphocytes from patient 1, before inoculation with E. coli 83972

value: before inoculation with E. coli 83972


title: Blood_Patient1_wt_3hours

source_name: Peripheral blood lymphocytes from patient 1, 3 hours after inoculation with E. coli 83972


title: MO3.13_WT-2_RNAseq

value: wild type


title: Bottom_T- M- A+_02


title: Bottom_T-_M-_A+_01


title: Bottom_T+_M-_ A+_02


title: MO3.13_WT-1_RNAseq


title: Bottom_T+_M-_A+_01


title: 786_M1A_NTC18-REP_3

value: 786-M1A renal cancer cell line

value: non-targeting CRISPRi

tag: genotype

value: control


title: 786_M1A_NTC18-REP_4


title: 786_M1A_NTC18-REP_2


title: 786_M1A_NTC18-REP_1


title: S_Tm_Mp_Microg_2

source_name: Microglia Slices

value: Microglia


title: 786_M1A_KLF6i_3-REP_4

value: CRISPRi – iKLF6-3

value: KLF6 knockdown


title: Aerated Bio Rep1

source_name: Pooled shoots of 10 plants (one plate)

value: aerated


title: S_Tp_Mp_Microg_2


title: S_Tp_Mp_Microg_3


title: S_Tm_Mp_Microg_1


title: S_Tp_Mp_Microg_1


title: 786_M1A_KLF6i_3-REP_2


title: 786_M1A_KLF6i_3-REP_1


title: S_Tm_Mm_A_3

source_name: Astrocytes Slices

value: Astrocytes


title: 04 FIB

data_processing: The arrays were scanned using Hewlett-Packard GeneArray Scanner and the scanned output files were visually inspected for hybridization artifacts. The data quality was checked for the presence of spiked control cRNAs, background values caused by array autofluorescence and non-specific binding, and Q value.

source_name: Fibroblast

value: Basal cell nevus syndrome

tag: cell type

value: Fibroblast

value: Untreated


title: 786_M1A_KLF6i_2-REP_4

value: CRISPRi – iKLF6-2


title: S_Tm_Mp_Microg_3


title: S_Tm_Mm_A_2


title: 786_M1A_KLF6i_2-REP_3


title: S_Tm_Mm_A_1


title: 786_M1A_KLF6i_2-REP_2


title: S_Tm_Mp_A_3


title: 786_M1A_KLF6i_3-REP_3


title: 786_M1A_KLF6i_2-REP_1


title: S_Tp_Mm_A_3


title: S_Tm_Mp_A_2


title: spermL07

city: Beltsville

first: Lingzhao

last: Fang

state: MD

address: 10300 Baltimore Avenue

department: ARS

institute: USDA

description:
low_GL;
different lane for spermL07 whole genome bisufite sequencing

data_processing:
Programs FastQC (0.11.2) and Trim Galore (0.4.0) were used to generate sequence quality reports and to trim/filter the sequences, respectively.
The cleaned data for each sample were merged and aligned to the reference genome (Bos taurus UMD3.1) using bowtie2 under the Bismark software (0.14.5)
The methylcytosine information was extracted using the bismark_methylation_extractor after deduplicating the duplication reads.
Genome_build: UMD3.1
Supplementary_files_format_and_content: The data files contain the methylatin information for the CG detected. The column names are: chrmosome, position, position (same as the second column), total coverage, methylation level (%) for cytosine, unmethylated cytosine (%)

organism: Bos taurus

source_name: sperm

extract_protocol:
Genomic DNA was isolated according to the QIAamp DNA Mini Kit protocol (QIAGEN, Valencia, CA, USA).
The qualified genomic DNA from sperm were used to construct libraries. Briefly, 3 μg of genomic DNA spiked with unmethylated lambda DNA were fragmented into 200-300 bp using a Covaris S220 (Covaris, Inc., Woburn, MA, USA), followed by teriminal repairing and A-ligation. Different cytosine methylated barcodes were ligated to sonicated DNA for different samples. The DNA bisufite conversion was performed using the EZ DNA Methylation Gold Kit (Zymo Research, Irvine, CA, USA). Then single-stranded DNA fragments were amplified using the KAPA HiFi HotStart Uracil + ReadyMix (2 X) (Kapa Biosystems, Wilmington, MA, USA). The library concentration was quantified using a Qubit 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA) and qPCR (iCycler, BioRad Laboratories, Hercules, CA, USA), and the insert size was checked using the Agilent 2100.

value: sperm

tag: breed

value: Holstein

tag: developmental stage

value: adult

tag: gestation length (gl)

value: low


title: spermL08

description:
high_BDE;low_CCR
different lane for spermL08 whole genome bisufite sequencing

tag: cow conception rate (ccr)

tag: body depth (bde)

value: high


title: Pax5-overexpressing A549 cells Replicate 2

city: Tianjin

first: Zhe

last: Liu

address: Heping District Qixiangtai Road No. 22

institute: Tianjin Medical University

description: Biological replicate 2 of 3. Gene expression changes in Pax5-overexpressing A549 cells versus control vector-expressing A549 cells

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential.

scan_protocol: Slides were scanned with an Agilent scanner Type C.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 11).

source_name: control vector-expressing A549 cells

label_protocol: 100ng of total RNA was used to produce polyadenylated RNA with polyA polymerase (Ambion, Austin, TX, USA).The products were transcribed to single-stranded DNA with oligo-dT primers. RNA was selectively degraded by RNase H, leaving RNA oligomers as primers for a DNA polymerase to synthesize double-stranded DNA (dsDNA). The dsDNA was purified and served as a template to generate antisense cDNA by cRNA reverse transcription.The fluorescence labeling reactions contained 5× Klenow buffer, dNTP (120 mM dATP, 120 mM dGTP, 120 mM dTTP, and 60 mM dCTP), 40 mM Cy5-dCTP or Cy3-dCTP (GE Healthcare) and Klenow enzyme (TaKaRa, Dalian, China). The reaction was carried out at 37°C for 90 min and stopped by addition of 25 mM EDTA and 0.25% sodium dodecyl sulfate (SDS).

growth_protocol: A549 cells were grown in RPMI1640 medium with 10% FBS, transfected with control vector or SpiB expression vector.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: Human lung adenocarcinoma epithelial cells

source_name: Pax5-overexpressing A549 cells


title: Pax5-overexpressing A549 cells Replicate 1

description: Biological replicate 1 of 3. Gene expression changes in Pax5-overexpressing A549 cells versus control vector-expressing A549 cells


title: S_Tm_Mp_A_1

tag: tissue


title: Pax5-overexpressing A549 cells Replicate 3

description: Biological replicate 3 of 3. Gene expression changes in Pax5-overexpressing A549 cells versus control vector-expressing A549 cells


title: Ovarian malignant tissue [ZOC21]

description:
ZOC21
Cancer

source_name: Ovarian cancer

value: Ovarian malignant tissue


title: ChIP-seq_iSE-Ctrl_hg38_H3K27ac

source_name: 786-M1A cell line

value: renal cancer cell line

value: non-targeting CRISPRi

tag: antibody catalog

value: ab4729 (Abcam)


title: ChIP-seq_iSE-5_hg38_H3K27ac

tag: treatment

value: CRISPRi - iSE-5


title: spermL06

description:
high_CCR
different lane for spermL06 whole genome bisufite sequencing


title: ChIP-seq_iSE-4_hg38_H3K27ac

tag: cell line type

value: CRISPRi - iSE-4


title: spermL09

description:
low_SCE;low_CCR
different lane for spermL09 whole genome bisufite sequencing

tag: sire calving ease (sce)


title: S_Tp_Mp_A_3

value: Astrocytes


title: Day9_H1_1000_cells

source_name: H1 from WiCell International

tag: cellline

tag: biological replicate

tag: time

value: day 9


title: S_Tp_Mm_A_2


title: ChIP-seq_iSE-3_hg38_H3K27ac

tag: cell line

value: CRISPRi - iSE-3

tag: antibody


title: spermL05

description:
high_GL
different lane for spermL05 whole genome bisufite sequencing


title: S_Tp_Mm_A_1

tag: barcode


title: spermL04

description: different lane for spermL04 whole genome bisufite sequencing


title: spermL03

description:
low_SCR;high_GL;high_BDE
different lane for spermL03 whole genome bisufite sequencing

tag: sire conception rate (scr)


title: ChIP-seq_iSE-2_hg38_H3K27ac

value: CRISPRi - iSE-2


title: S_Tp_Mp_A_2


title: Pet111_PAR-CLIP

city: Goettingen

first: Katharina

middle: Bettina

last: Hofmann

address: Am Fassberg 11

department: Molecular Biology

institute: Max Planck Institute for Biophysical Chemistry

description: RNA bound by Pet111p.

data_processing:
Library strategy: PAR-Clip
Sequencing reads were quality trimmed and mapped to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner STAR version 2.5.2b.
Coverage plots were generated using GenomicAlignments.
Genome_build: sacCer3, version 64.2.1
Supplementary_files_format_and_content: Pet111-160912-2-B6-KH.bw: bigWig file

organism: Saccharomyces cerevisiae

source_name: Yeast cells

extract_protocol:
The cells were lysed by bead beating and IP was performed with rabbit IgG-conjugated protein G magnetic Dynabeads (Invitrogen). The cross-linked RNA was partially digested with RNase T1 (Thermo Scientific) and the IP was controlled by performing a Western blot analysis of a part of the sample using the Peroxidase Anti-Peroxidase (PAP; Sigma) antibody. Protein-RNA crosslinking was controlled using radioactive labeling of the 5'-RNA end by 𝛾-[32P]-ATP (3000 Ci/mmol, Perkin Elmer) and T4 PNK (New England Biolabs). The protein-RNA complexes were separated by SDS-PAGE and visualized by a Typhoon FLA 9500 instrument (GE Healthcare). Following adapter ligation, RNA was recovered by digestion with proteinase K (New England Biolabs) and a subsequent acidic phenol/chloroform extraction.
Reverse transcription was performed with SuperScript III RTase (Invitrogen) and was followed by PCR amplification using the NEXTflex barcode primer kit (Bio Scientific). The generated cDNA was purified, size selected, and quantified using TapeStation (Agilent Technologies). The resulting samples were then PCR-amplified and sequenced on an Illumina HiSeq 2500 system.

treatment_protocol: 4tU-labeled yeast cells (BY4741) expressing C-terminally TAP-tagged Pet111p were UV-irradiated with an energy dose of 12 J/cm2 at 365 nm.

tag: strain/background

tag: expression

value: C-terminally TAP-tagged Pet111p


title: Blood_Patient5_wt_2weeks

source_name: Peripheral blood lymphocytes from patient 5, 2 weeks after inoculation with E. coli 83972

tag: subject id

value: patient 5

tag: gender

value: female

tag: batch

value: in-house

tag: time point

value: peripheral blood lymphocytes


title: ChIP-seq_iSE-1_hg38_H3K27ac

value: CRISPRi - iSE-1

tag: antibody catalog


title: ChIP-seq_del_SE_3-19_hg38_H3K27ac

tag: treatment


title: ChIP-seq_del_SE_3-9_hg38_H3K27ac

tag: cell line type


title: C17

type: genomic

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

description:
sample name:
201533610029_R04C01

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized according to Illumina's standard protocol

scan_protocol: Arrays were imaged using iSCAN BeadArray reader

data_processing: Raw data files generated by the iScan array scanner were read and preprocessed using minfi Bioconductor package (Aryee et al., 2014). With the minfi package the same preprocessing steps as in Illumina's Genomestudio software were performed. In addition, the following filtering criteria were applied: Removal of probes targeting the X and Y chromosomes, removal of probes containing-nucleotide polymorphism (dbSNP132 Common) within five base pairs of and including the targeted CpG-site, and probes not mapping uniquely to the human reference genome (hg19) allowing for one mismatch. In total 394,848 common probes of Illumina 450K and EPIC arrays were kept for clustering analysis.

label: Cy5, Cy3

source_name: astroblastomas

label_protocol: Standard Illumina protocol

extract_protocol: DNA isolation using DNA QIAamp FFPE Tissue Kit

tag: tissue

value: astroblastomas


title: Tumor_7

source_name: Astrocytes Tissue


title: Rdh1KO re-fed_1C

city: Berkeley

first: Joseph

last: Napoli

state: CA

address: 119 Morgan Hall

department: NST

institute: UC Berkeley

description: Sample 1C

data_processing:
Fastq sequencing files were filtered for common contaminants and mapped to the mm10 mouse reference genome using Tophat (v2.0.6). Cufflinks (2.0.2) was used to process the resulting BAM read alignments.
Cufflinks (2.0.2) was used to process the resulting BAM read alignments.
We determined differentially expressed genes using Cuffmerge and Cuffdiff with a false discovery rate cutoff of 0.05. All splice variants were sequenced and included in the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: output from Cufflinks

source_name: 16h fast followed by 6h feeding

extract_protocol:
Mice were either fasted for 16h, or fasted for 16h and then re-fed for 6h. Mice were euthanized by CO2 inhalation, followed by cervical dislocation.Brown adipose tissue was removed, flash frozen in liquid N2 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.
Pooled RNA libraries were generated using the Illumina TruSeq RNA sample preparation kit (RS-122-2001)

tag: strain

value: brown adipose tissue

tag: age

value: 4 weeks old

tag: genotype


title: C31

description:
sample name:
201516300040_R07C01


title: spermH09

description:
high_GL;low_BDE;high_CCR
different lane for spermH09 whole genome bisufite sequencing

value: sperm

tag: breed

value: Holstein

tag: developmental stage

value: adult

tag: gestation length (gl)

value: high

tag: cow conception rate (ccr)

tag: body depth (bde)

value: low


title: Cortex_4

value: Astrocytes

tag: barcode


title: spermH08

description:
high_CCR
different lane for spermH08 whole genome bisufite sequencing


title: Rdh1 WT fasted_1B

description: Sample 1B

source_name: 16h fast

value: wildtype


title: spermL01

description:
low_SCR;low_GL
different lane for spermL01 whole genome bisufite sequencing

tag: sire conception rate (scr)


title: ChIP-seq_M1A_xenograft_2_hg38_H3K27ac

value: renal cancer cell line

tag: cell line

value: xenograft

tag: antibody

value: ab4729 (Abcam)


title: ChIP-seq_OS-LM1_EV_hg38_H3K27ac

source_name: OS-LM1 cell line

value: empty vector


title: spermL02

description:
low_SCR;high_SCE;;low_BDE
different lane for spermL02 whole genome bisufite sequencing

tag: sire calving ease (sce)


title: ChIP-seq_OS-LM1_HA-VHL_hg38_H3K27ac

value: HA-VHL

tag: antibody catalog


title: Rdh1KO fasted_1A

description: Sample 1A


title: Rdh1WT re-fed_1D

description: Sample 1D


title: S_Tp_Mp_A_1


title: Cortex_5


title: ChIP-seq_del_SE_3-15_hg38_H3K27ac

tag: treatment


title: NIH3t3 Tg7hr

city: Haifa

first: Reut

last: Shalgi

address: 1 Efron st.

department: Faculty of Medicine

country: Israel

institute: Technion

description: 3t3s_rsem.genes.expected_count.txt; 3t3s_rsem.genes.tpm.txt

data_processing:
Ribosome footprint profiling data was mapped to mm10 version of the genome using RefSeq CDSs. Transcripts shorter that 100 nucleotides were filtered-out and 30 nucleotides were clipped form the start and end of each CDS, similarly to Ingolia (21). Ribosome footprint sequences were trimmed to maximal size of 34 and polyA sequences from the polyA tailing step were removes, such that footprints of lengths 22-34 were considered. FASTQ files were then filtered for rRNAs and tRNAs using STAR(22). Expression levels were quantified using RSEM (23) after mapping to clipped CDSs using Bowtie2(24) to produce transcript and gene level quantification TPM (Transcript Per Million) values.
Lowly expressed genes with an average TPM <2 across all samples were filtered out and  expression of all other genes was thresholded to a TPM of 4.
Genome_build: mm10
Supplementary_files_format_and_content: Samples' read counts and TPM values

source_name: NIH 3T3

growth_protocol: Ribosome footprint profiling was performed as in Shalgi et al.  Molecular Cell, 2013 with the following modification: cells were grown and treated with Tg for the indicated times, then trypsinized, pelleted by 5 minutes at 1000RPM centrifugation, and flash frozen in LN2, without prior Cycloheximide treatment. Cycloheximide was also omitted from the buffers.

extract_protocol: RNAseq- RNAeasy for RNA extraction and standard illumina PE including size selection. Riboseq - RNA extraction and library prepration as described in Ingolia et al. Science, 2009

treatment_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: NIH 3T3

value: WT


title: Tumor_5


title: spermH06

description:
low_SCE;low_CCR
different lane for spermH06 whole genome bisufite sequencing


title: ChIP-seq_M1A_xenograft_1_hg38_H3K27ac

tag: cell line type


title: spermH05

description:
low_GL;low_BDE
different lane for spermH05 whole genome bisufite sequencing

tag: tissue


title: spermH07

description:
high_SCE;
different lane for spermH07 whole genome bisufite sequencing


title: Cortex_3


title: Tumor_4


title: ChIP-seq_786-M1A_HA-VHL_hg38_H3K27ac


title: Tumor_3


title: PERK -/- Tg8hr MEF

description: MEFs_rsem.genes.expected_count.txt; MEFs_rsem.genes.tpm.txt

source_name: MEF

value: MEF

value: PERK -/-


title: spermH04

description: different lane for spermH04 whole genome bisufite sequencing


title: spermH03

description:
high_SCR;high_GL;high_SCE;
different lane for spermH03 whole genome bisufite sequencing


title: NIH3t3 Tg2hr


title: Tumor_2


title: PERK -/- Tg1hr MEF


title: ChIP-seq_786-M1A_EV_hg38_H3K27ac


title: spermH02

description:
high_SCR;low_GL;high_BDE
different lane for spermH02 whole genome bisufite sequencing


title: Tumor_1


title: BMP7-24h-2-Cy5

city: Moraga

first: Vidya

last: Chandrasekaran

address: 1928 Saint Mary's Road

department: Biology

institute: Saint Mary's College of California

description: Cultured neurons treated with BMP-7 at 50 ng/mL for 24 hours.

hyb_protocol: Not provided

scan_protocol: The chips were scanned using the Axon GenePix 4000B microarray scanner.

data_processing: The hybridization target signal was subtracted from the background signal and the data was normalized using the LOWESS (local weighted scatterplot smoothing method) on the background subtracted data. Each RNA sample was spiked with a known ratio of spike-in positive control 20-mer RNA as an external normalization control. Two-way ANOVA as performed to detect differences in miRNA expression between control and BMP-7 treated cells and the differences in gene expression over time. The p-value and power were calculated using a sample size of N=2 for the two biological replicates.

organism: Rattus norvegicus

source_name: E21 cultured rat SCG neurons under control conditions

label_protocol: The RNA sample was labeled with Cy5 - Single sample chips were labeled with Cy5.

growth_protocol: Sympathetic neurons from the superior cervical ganglia of E21 rat pups were dissociated and grown on poly-D-lysine coated plates in a defined media with 1:1 mixture of DMEM and F12 containing insulin, selenium, transferrin and Nerve growth factor.

extract_protocol: The total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA) per the manufacturer’s instructions.

treatment_protocol: On day 2 in culture, the neurons were treated with 2 microM Ara-C to eliminate non-neuronal cells. Following this, neurons were maintained in control media for 24 hours. Then culture wells were maintained in control media for 24 hours, BMP-7 at 50ng/mL for 6 hours or 24 hours, following which the cells were lysed to extract total RNA.

tag: strain/background

value: Sprague-Dawley

tag: cell type

value: Cultured sympathetic neurons

value: BMP-7 50 ng/mL

tag: time


title: PERK -/- Tg2hr MEF

tag: genotype


title: PERK -/- Tg5hr MEF


title: BMP7-24h-1-Cy5

tag: developmental stage


title: BMP7-6h-2-Cy5

description: Cultured neurons treated with BMP-7 at 50 ng/mL for 6 hours.


title: Tumor_6