title: Neu_8d_injured_ipsi_female_1

city: London

first: Sara

middle: Elgaard

last: Jager

address: Hodgkin Building, Guy's Campus

country: United Kingdom

institute: King's College London

description:
Sequenced over 2 lanes
DESeq2_values_8d_neu.txt
FPKM_values_neurons.txt

data_processing:
FastQ files were aligned to the UCSC mm10 build of the mouse genome using STAR.
Aligned BAM files from separate lanes were combined using the Merge BAM tool from SamTools
Fragments per kilobase per million (FPKM) estimates were obtained using Cufflinks
DESeq2 was used to determine the foldchange in gene expression between the following samples: naive SGCs vs naive DRG; SGCs 3 days after injury vs SGCs 3 days after sham; SGCs 14 days after injury vs SGCs 14 days after sham; nociceptors 8 days after injury vs nociceptors 8 days after sham
Genome_build: mm10
Supplementary_files_format_and_content: FPKM estimates for all samples in .txt format and DESeq2 data also in .txt format

source_name: MACS sorted neurons (ipsi) 8 days after partial sciatic nerve ligation

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

value: 9-11 weeks

tag: extract protocol

value: L3-L5 DRGs were dissected, dissociated with enzymes, sorted with MACS Neuronal isolation kit (Miltenyi catalog no 130-115-389) and finally purified with Qiagen Rnease micro kit (catalog number 74004)


title: Neu_8d_sham_ipsi_female_1

status: Public on Jan 22 2020

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: MACS sorted neurons (ipsi) 8 days after sham operation

tag: strain

tag: age


title: Neu_8d_sham_ipsi_female_2


title: Neu_8d_sham_ipsi_female_3


title: MF.PC_3

status: Public on Jan 23 2020

type: RNA

city: New York

first: Brian

last: Brown

state: NY

address: 1470 Madison Avenue

department: Genetics and Genomic Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Critical threshold (Ct) values were obtained from qPCR profiling with an upper limit of 40. Across sample normalization was performed for each qPCR plate separately as follows: i) the arithmetic mean of all assays for each sample was calculated. ii) the median of sample means was divided by the arithmetic mean for each sample to create a scaling factor. iii) Ct values for each sample were multiplied by their scaling factor. Following normalization, individual assay outliers were identified either by visual inspection or based on a Z-score greater than 4, relative to all other samples. Next, normalization was redone with outlier assays set as missing. Missing values were then imputed using the mice package in R with default settings and 10 iterations.
Batch correction was performed only for a subset of miRNAs (223 total) that were assessed to have a significant association with batch, because batch correcting all miRNAs would have removed signal from cell type specific miRNAs that were only seen in a limited number of batches. Batch associated miRNAs were selected in 2 rounds. The first was a broad round of selection that included all cell types that had at least one replicate in 2 different batches. Variation due to cell type was removed using the removeBatchEffect function from the limma package, then an F-test in limma was performed with respect to batch for each miRNA on the resulting values. miRNAs were selected for batch correction if they had a Bonferroni adjusted p value <0.01 and a mean Ct value <35 across all samples involved. After miRNA selection, batch correction was performed using ComBat only for the selected miRNAs.
Following normalization and batch correction, Ct values were converted to arbitrary units (AU) for easier interpretation. We determined a limit of reliable detection at a Ct value of 28, which was assessed through the standard curves of 10 miRNAs and inter-replicate variability at different Ct thresholds. Our AU scale was designed so that a Ct value of 28 corresponded to a value of 1 AU. Ct values were converted to AU with the formula: 2^(28 - exp[i,j]), where exp is the Ct value matrix for all samples and miRNAs, i is a given miRNA, and j is a given cell type. A pseudocount of 0.1 was added to all assays following conversion.

label: SYBR

source_name: primary

growth_protocol: Primary cells harvested from 6-8 week old mice

extract_protocol: miRNeasy Micro Kit (Qiagen)

tag: organ

value: Peritoneal cavity

tag: cell type

value: Peritoneal macrophages

tag: cell markers

tag: isolation date

tag: lab

tag: cell count (thousands)

tag: rna concentration (ng/ul)

tag: processing batch

tag: gender

value: male


title: P7 unfractionated Rep2

city: La Jolla

first: Kun

last: Tan

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 4812

department: Department of Obstetrics, Gynecology, and Reproductive Sciences

institute: UCSD

description:
Whole cell
Cell ranger V3.0 based mapping and filtering

data_processing:
De-multiplexing and FastQ file generation
Cell ranger based mapping and filtering
Seurat R package for QC filtering and normalization
Seurat and monocle for clustering and trajectory
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of genes, counts and cell barcodes

source_name: perinatal testicular cells

extract_protocol:
Testis tissue was dissociated with two step enzymatic digestion with collagenase-IV and trypsin-EDTA. Single cell suspension were diluted for loading on Chromium chip for 10X Genomics library preparation and subsequent sequencing.
Chromium Single Cell Kit [v2 chemistry]
10x single cell RNA sequencing

value: Postnatal day 7

tag: tissue

value: Testes


title: Neu_8d_injured_ipsi_female_3


title: Neu_8d_injured_ipsi_female_2


title: MF.PC_2


title: Neu_8d_sham_ipsi_male_3


title: Neu_8d_injured_ipsi_male_3


title: Neu_8d_sham_ipsi_male_2


title: Patient 2_C2

city: Beijing

first: Yonggang

last: Wang

address: South 4th Ring West Road 119, Fengtai District

department: Neurosurgery

country: China

institute: Beijing Tiantan Hospital, Capital Medical University

description:
Among the probes, 28,264 probes correspond to the annotated genes in RefSeq v70 and Ensembl v80 database. Besides, 940 control probes are also included.
1h617080203_raw_Data.txt_C2

hyb_protocol: Fluorescent targets were hybridized to the Human Whole Genome OneArray® with Phalanx hybridization buffer using Phalanx Hybridization System. After 16 hrs hybridization, non-speciﬁc binding targets were washed away.

scan_protocol: The slides scanned using a DNA Microarray Scanner (Model G2505C, Agilent Technologies). The Cy5 ﬂuorescent intensities of each spot were analyzed by GenePix 4.1 software (Molecular Devices).

data_processing: Each single sample was at least performed twice in terms of technical or biological replicates under the reproducibility more than 0.975. The signal intensity was loaded into Rosetta Resolver System® (Rosetta Biosoftware, USA) to do data preprocessing and apply to 75 percentile centering normalization. The errors of the sample were estimated by using the error-weighted approach at the same time. Both of fold change and p-value for pair-wise sample comparison were calculated for evaluating differentially expressed genes.

organism: Homo sapiens

source_name: atypical meningioma

label_protocol: Fluorescent aRNA targets were prepared from 1 μg total RNA samples using OneArray® Amino Allyl aRNA Amplification Kit (Phalanx Biotech Group, Taiwan) and Cy5 dye (GE Healthcare).

extract_protocol: otal RNA was extracted using the TRIzol® Reagent (Invitrogen,Carlsbad, CA) according to the manufacturer's instructions. The concentration and purity of the RNA was measured by NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific). Purity was checked by the ratio of the OD260/OD280 and OD260/OD230. The quality of total RNA was accessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)

treatment_protocol: All patients underwent gross total surgery resection and adjuvant radiotherapy, the external-beam radiation was delivered by conventional fractionation up to a total dose of 50–60 Gy.

tag: recurrence status 3 years after operation

value: no

tag: histology

value: atypical

value: female


title: Patient 1_C1

description:
Among the probes, 28,264 probes correspond to the annotated genes in RefSeq v70 and Ensembl v80 database. Besides, 940 control probes are also included.
1h617080202_raw_Data.txt_C1


title: Neu_8d_sham_ipsi_male_1


title: Neu_8d_injured_ipsi_male_2


title: Blood_0 hr_SHAM_rep3

city: Guangzhou

first: Dan

last: Lu

state: Guangdong

address: No.601, West Huangpu Avenue

department: Neurology and Stroke center

institute: Jinan University

description:
[3](normalized)
circRNA expression in SHAM mouse blood

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing:
Two microarray platform definitions, GPL21826 and GPL7173, were used to uncover genes probed by the arrays. Regular probes that were not at least 10% brighter than the control probes in all twelve arrays were removed, resulting in 10324 high quality probes out of 15712 (66%). Bioconductor’s limma package (Ritchie et al., 2015) was used to identify differently expressed circRNAs at four different time points i.e. time 0, 5 minutes, 3 hours, and 24 hours, each with three replicates, resulting in twelve samples in total. Time 0 is the control group (SHAM), resulting in three comparisons: 5 min (MCAO 5m) versus 0 h (SHAM), 3 h (MCAO 3h) versus 0 h (SHAM), and 24 h (MCAO 24h) versus 0 h (SHAM). Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Briefly, the single-channel Agilent data collection model was used where only green signal was considered. Intra-array variation was normalized by adaptive background correction recommended by limma. Inter-array background signals were further corrected by quantile method.
Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering (absolute log fold-change 2, adjusted P value < 0.05). Differentially expressed circRNAs between two samples were identified through Fold-change filtering. Hierarchical Clustering was performed to show the distinguishable circRNA expression pattern among samples. Differentially expressed circRNAs were ranked by log fold-change, and were considered significant if the fold-change was 2.

source_name: Peripheral Blood_0hr_SHAM

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Prior to blood collection, the PAXgene RNA stabilizer solution was removed from the BD Vacutainer style PAXgene blood RNA tubes. Whole blood obtained from the cardiac puncture of mice under anesthesia was collected into heparinized tube (Wang et al., 2004, Krawiec et al., 2009). All tubes were gently inverted for 5 min directly after collection and incubated for 2 h at room temperature and then stored at -80 °C until processing for RNA extraction. Total RNA was extracted from blood samples using PAXgene Blood RNA kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: Focal ischemia was induced by intraluminal middle cerebral artery occlusion (MCAO) for 5 min, 3h and 24 h using a monofilament nylon string coated with silicon (MSMC23B104PK100, RWD Life Science, Shenzhan, China) in male Balb/c mice under isoflurane anesthesia as described earlier (Wang et al., 2004, Krawiec et al., 2009). Physiological parameters (PaO2, PaCO2, blood pressure) were monitored and rectal temperature was controlled at 37.0±0.5 °C. Cortical cerebral blood flow was monitored using a blood perfusion imager (PeriCam PSI System, Perimed AB, Stockholm, Sweden). None of the animals showed any adverse effects before euthanasia. Animal blood was extracted after different time points of surgery. Sham-operated mice underwent the same surgical procedure except MCAO was used for 0 min time point.

value: 8 weeks

tag: Sex

tag: treatment

value: sham-operated

tag: timepoint

value: whole blood

tag: molecule subtype

value: circRNA


title: Blood_0 hr_SHAM_rep2

description:
[2](normalized)
circRNA expression in SHAM mouse blood

tag: age


title: Neu_8d_injured_contra_3

source_name: MACS sorted neurons (contra) 8 days after partial sciatic nerve ligation

tag: strain

tag: extract protocol


title: Neu_8d_injured_contra_4


title: Neu_8d_injured_ipsi_2


title: Neu_8d_injured_ipsi_1


title: SGC_14d_sham_3

description:
Sequenced over 3 lanes
DESeq2_values_14d_14dS_SGCs.txt
FPKM_values_3d_14d_3dS_14dS_SGCs.txt

source_name: Sorted SGCs 14 days after sham operation

value: L3 and L4 DRGs were dissected, dissociated with enzymes, fixed with 4% PFA, stained with antibodies and hoechst, sorted with FACS and finally purified with Qiaqens RNeasy FFPE kit (catalog number 73504)


title: Blood_0 hr_SHAM_rep1

description:
[1](normalized)
circRNA expression in SHAM mouse blood


title: SGC_14d_sham_2


title: Neu_8d_injured_ipsi_male_1


title: SGC_3d_sham_2

description:
Sequenced over 3 lanes
DESeq2_values_3d_3dS_SGCs.txt
FPKM_values_3d_14d_3dS_14dS_SGCs.txt

source_name: Sorted SGCs 3 days after sham operation


title: SGC_14d_sham_1


title: SGC_3d_sham_3


title: SGC_3d_sham_4


title: SGC_14d_sham_4


title: SGC_3d_sham_1


title: SGC_14d_injured_4

source_name: Sorted SGCs 14 days after full sciatic nerve ligation


title: SGC_14d_injured_2


title: SGC_14d_injured_1


title: SGC_3d_injured_2

source_name: Sorted SGCs 3 days after full sciatic nerve ligation


title: SGC_14d_injured_3


title: SGC_3d_injured_4


title: E18.5 unfractionated Rep1

data_processing:
De-multiplexing and FastQ file generation
Cell ranger based mapping and filtering
Seurat R package for QC filtering and normalization
pagoda2 and monocle for clustering and trajectory
Genome_build: mm10
Supplementary_files_format_and_content: Matrix of genes, counts and cell barcodes Cell Ranger Version (V3.0) given in 'description' field.

extract_protocol:
Testis tissue was dissociated with two step enzymatic digestion with collagenase-IV and trypsin-EDTA. Single cell suspension were diluted for loading on Chromium chip for 10X Genomics library preparation and subsequent sequencing.
Chromium Single Cell Kit [v2 chemistry]; 10x single cell RNA sequencing

value: Embryonic day 18.5


title: E18.5 unfractionated Rep2


title: SGC_3d_injured_1


title: P2 unfractionated Rep2

value: Postnatal day 2


title: P2 unfractionated Rep1


title: D.DRG_3

description:
Sequenced over 3 lanes
WTCHG_*_222168

data_processing:
FastQ files were aligned to the UCSC mm10 build of the mouse genome using STAR.
Aligned BAM files from separate lanes were combined using the Merge BAM tool from SamTools
Fragments per kilobase per million (FPKM) estimates were obtained using Cufflinks
DESeq2 was used to determine the foldchange in gene expression between the D.DRG and sorted SGC samples
Genome_build: mm10
Supplementary_files_format_and_content: FPKM estimates for all samples in .txt format and DESeq2 data also in .txt format

extract_protocol:
L3 and L4 DRGs were dissected, dissociated with enzymes, fixed with 4% PFA and finally purified with Qiaqens RNeasy FFPE kit (catalog number 73504)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 9 weeks

tag: cell type

value: dorsal root ganglia (DRG)


title: SGC_4

description:
Sequenced over 3 lanes
WTCHG_*_223180

source_name: Sorted SGCs

extract_protocol:
L3 and L4 DRGs were dissected, dissociated with enzymes, fixed with 4% PFA, stained with antibodies and hoechst, sorted with FACS and finally purified with Qiaqens RNeasy FFPE kit (catalog number 73504)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Satellite glial cells (SGCs)


title: D.DRG_4

description:
Sequenced over 3 lanes
WTCHG_*_224192


title: D.DRG_2

description:
Sequenced over 3 lanes
WTCHG_*_220144


title: SGC_2

description:
Sequenced over 3 lanes
WTCHG_*_219132


title: SGC_1

description:
Sequenced over 3 lanes
WTCHG_*_217108


title: SGC_3

description:
Sequenced over 3 lanes
WTCHG_*_221156


title: HFHS_Calcitriol3

city: Brisbane

first: Muralidhara Rao

last: Maradana

state: Queensland

address: 37 Kent St, Woolloongabba

country: Australia

institute: The University of Queensland

data_processing:
Reads were aligned to the reference mouse genome GRCm38 with STAR (version 2.4.0d).
Gene read counts were quantified against the GENCODE gene model (version M6).
Analysis and differential expression testing was performed with the DESeq2 (version 1.8.1)
Bioconductor package. R package (version 3.2.1) was used to further analysis.
Genome_build: md5
Supplementary_files_format_and_content: Tab-delimited text files include log transformed values for each sample

source_name: Liver

extract_protocol:
RNA is extracted from flash frozen livers using RNeasy mini kit (Qiagen). Quality and quantity of RNA was estimated either using Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were fed with high fat high sugar diet for 14 weeks and groups of mice were treated with either curcumin liposomes or calcitriol liposomes at week 12 and week 13.

tag: model

value: Mice fed with high fat high sugar diet for 14 weeks

value: Liver


title: CNT2


title: CNT3


title: CNT1


title: SGC_3d_injured_3

value: 9-11 weeks


title: HFHS_Curcumin3


title: HFHS_Calcitriol1


title: HFHS_Calcitriol2


title: HFHS_Curcumin2


title: HFHS_Curcumin1


title: HFHS3


title: D.DRG_1

description:
Sequenced over 3 lanes
WTCHG_*_218120


title: HFHS2


title: HFHS1


title: CLNDC_3-2

source_name: Liver dendritic cells

extract_protocol:
RNA is extracted from FACS sorted cells using RNeasy micro kit (Qiagen). Quality and quantity of RNA was estimated either using Bioanalyzer (Agilent Technologies). RNA collected from cells was used to prepare and amplify cDNA for RNA sequencing using SMARTer Ultra Low Input RNA Kit for Sequencing - v3 (Clontech Laboratories).
RNA libraries were prepared for sequencing using Nextera XT DNA library prep kit.

treatment_protocol: Mice fed methioinine and choline deficient diet for 2 weeks were treated with either empty liposomes or curcumin liposomes.

value: Mice fed with MCD diet for 2 weeks


title: CLNDC_1-2


title: stool at D16, cow's milk, naïve,rep1

type: genomic

city: Tainan

first: Jiu Yao

address: No.138,Sheng Li Road,Tainan

country: Taiwan

institute: Nation Cheng Kung University

description: stool at D16, cow's milk, naïve (1/3)

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 95° for 10 minutes, then 48° for 3 minutes. • Transfer 105μl of hyb solution to each array. • Hybridize 23 hours 30 minutes at 48°

scan_protocol: Affymetrix Gene ChIP Scanner

data_processing: Data were processed using MiDAS software.

label: biotin

molecule: genomic DNA

source_name: wild-type

label_protocol: Samples were enzymatically fragmented and biotinylated using the reagent Kit (Affymetrix)

growth_protocol: Stool samples were obtained from groups of offspring after the weaning period and HDM allergen sensitization (day 0), and sacrificed after allergen intra-tracheal challenge for 2 days (Day 16).

extract_protocol: Stool samples were frozen then stored at -80 °C. QIAamp DNA Stool Mini Kit was used to purify DNA from frozen stool samples according to protocol. DNA quality was evaluated using MaestroNano spectrophotometry (Maestrogen, Las Vegas, NV, USA) in the absorbance ratio A260 nm / A280 nm.

tag: asthma

value: naïve


title: ELNDC_2-2


title: ELNDC_1-2


title: CLNDC_2-2


title: ELPDC_3-2


title: CLPDC_3-2


title: ELPDC_1-2


title: cr-microspore.sRNA.WT.replicate2

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description: Capsella rubella microspore of wt (Cr1GR1)

data_processing:
Bisulfite-seq: For each sample, the 125 bp reads from the Illumina BS sequence libraries from the two replicates were  trimmed to 100 bp by cutting 5 bp from the start and 20 bp from the end of each read. After this first trimming, each read was split in two 50 bp long reads in order to improve mapping efficiency.  Reads were mapped to the Capsella reference genome using the Bismark read mapper (Krueger and Andrews, 2011) using the single end mode. Duplicated reads (aligning to the same genomic position) were eliminated before reporting methylation levels.
small-RNA: Adapters were removed from the 50 bp long single sRNA reads in each library. The resulting18-30 bp long reads were mapped to the reference genomes. Mapped reads from both replicates were pooled together, sorted in two categories (21-22-nt and 24-nt long) and remapped to the same reference masked genome mentioned above using ShorStack (--mismatches 2 --mmap f) in order to improve the localization of sRNAs mapping to multiple genomic locations. We normalized the alignments by converting coverage values to reads per million mapped reads (RPM) values.
RNA-seq: For each replicate, reads were mapped to the respective eference genomes using TopHat v2.1.0 (Trapnell et al, 2009)in single end mode. Gene and TE expression was normalized to reads per kilobase per million mapped reads (RPKM) using GFOLD.
WGS and TE insertion analysis: For each accession the 150 bp long reads were mapped to the Capsella reference genome using TEPID (Stuart el al 2016) in paired-end mode with default parameters.
Genome_build: TAIR10, Caprub1_0
Supplementary_files_format_and_content: Bisulfite-seq: Three genome-wide cytosine methylation reports (for CG, CHG, CHH) per sample were created. These reports have the  following format:  <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context>
Supplementary_files_format_and_content: small-RNA: Unique small RNAs (between 18-30 nts)  that mapped to the reference genomes. Accumulation number (raw reads) are represented in a three column format file: <sequence_smallRNA> <number_of_reads><read_length_bp> for each sample.
Supplementary_files_format_and_content: RNA-seq: expression levels (RPKM) are shown for genes and transposable elements in both genomes for each condition and replicate.
Supplementary_files_format_and_content: WGS and TE insertion analysis: Identified new TE insertions are shown for the six samples. Rows indicate chromosome (scaffold) and insertion position and values indicate TE identity.

organism: Capsella rubella

source_name: CR microspore wt

growth_protocol: All seeds were surface sterilized (5% sodium hypochlorite and 0.01% Triton X-100), stratified for 2 days at 4°C and germinated on half-strength Murashige and Skoog medium (1% sucrose) in long-day conditions (16 h light/8 h darkness; 21°C). Plants were transferred to soil after 10 to 12 days and grown under long day conditions.

extract_protocol:
Capsella microspores were ground in a pre-cooled mortar with Lysis/Binding Solution of the mirVana™ miRNA isolation kit. Short RNAs (< 200 nt) were seperated and followed by size selection on a 15% TBE-Urea polyacrylamide gel.
sRNA seq libraries were generated with the NEBNext® Multiplex Small RNA kit (NEB #E7300S).

treatment_protocol: Material was generated by Percoll percoll gradient following previously published procedures (Duplakova et al., 2016)

value: microspore

tag: genotype

value: wt (Cr1GR1)


title: Patient 9_T4

description:
Among the probes, 28,264 probes correspond to the annotated genes in RefSeq v70 and Ensembl v80 database. Besides, 940 control probes are also included.
1h617080210_raw_Data.txt_T4

value: yes

value: atypical

value: female


title: CLPDC_2-2


title: CLNDC_2-1


title: ELNDC_3-1


title: CLNDC_1-1


title: CLPDC_1-2


title: ELPDC_2-2


title: CLNDC_3-1


title: CLPDC_2-1


title: ELPDC_1-1


title: ELNDC_2-1


title: ELNDC_1-1


title: CLPDC_3-1


title: CLPDC_1-1


title: ELNDC_3-2


title: ELPDC_3-1


title: ELPDC_2-1


title: HomoSap.2CellCycle.Replicate1

city: Aurora

first: Joshua

last: Black

state: CO

address: 12801 East 17th Ave

department: Pharmacology

institute: University of Colorado

description:
Human replication timing samples
HomoSap.2CellCycle.merged.bedgraph

library_source: genomic

data_processing:
Human fastq files were aligned to HG38 using bowtie2
The resulting sam files were turned into bams and duplicate reads were removed using samtools
Bam files were turned into bedgraphs using the bedtools2.29.2
If samples were sequenced for additional depth, the bam files were merged at this point
Bedgraphs were read count normalized using an RPM calculation
RPM normalized bedgraphs were then scaled to mitochondria read percentages
The fully normalized bedgraphs were binned to 1kb and smoothed using a 100kb sliding window
To make the final processed files, replicates were merged and averaged to make a single bedgraph
Genome_build: Hg38
Supplementary_files_format_and_content: Bedgraph normalized by RPM and mitochondria content, merged across replicates
Library strategy: Rerep-seq

source_name: in vitro cell culture

growth_protocol: MDA-MB-231 cells were maintained in DMEM with 10% fetal bovine serum, 1% penicillin/streptomycin, and L-glutamine at 37 degrees Celsius with 5% CO2. 7.5 x 105 cells were seeded on 10 cm plates in 10 ml complete DMEM and allowed to adhere and grow for 48 hours prior to treatment.

extract_protocol:
DNA extraction: As RerepSeq selectively fragments rereplicated DNA and enriches those sequences by size selection, it is imperative that the genomic input DNA is of high molecular weight. For yeast samples: cells were pelleted by centrifugation at 3000 rpm for 3 minutes and resuspended in SCE (1M sorbitol, 100 mM sodium citrate, 10 mM EDTA pH 8.0); fresh 0.125% (v/v) β-mercaptoethanol and 10 U/mL zymolyase was added and incubated for 30-60 minutes at 37ºC to digest cell walls; human cells or yeast spheroplasts were pelleted by centrifugation at 3000 rpm for 3 minutes and resuspended in 500uL RIPA buffer (10 mM Tris-Cl pH 8.0, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 140 mM NaCl, 1 mM PMSF) with RNase A, 0.2 mg/mL and incubated at 37ºC for 1 hour. 25uL 20% SDS and 10µl of 20 mg/ml proteinase K was then added and allowed in incubate at 55ºC for 2 hours. DNA was extracted twice using Phenol:Chloroform:Isoamyl alcohol (25:24:1, v/v) and precipitated using isopropanol.  DNA was resuspended and stored in nuclease free water. RerepSeq Digestion: In an 8 strip 200 µl PCR tube 1 – 5 µg (depending on the experiment) high molecular weight genomic DNA was mixed with 2.5uL 10X Hoechst 33258 (0.1mg/ml) and 2.5uL 10X NEB Buffer 4 (50 mM Potassium Acetate, 20 mM Tris-acetate , 10 mM Magnesium Acetate, 1 mM DTT pH 7.9@25°C) to a final volume of 24uL; open tubes placed upright in PCR tube rack, covered with glass plate (3" x 3" glass plate from VWR Vertical Gel Electrophoresis Systems), exposed to 7.5 minutes of glass plate filtered (UVA only) from a Stratalinker.  Following UVA treatment,  samples were digested with 0.5uL UDG (5 units of Uracil-DNA Glycosylase), 0.5uL APE1 (10 units of human apurinic/apyrimidinic endonuclease 1) for 2 hours at 37C. Digested DNA was repaired with NEB’s FFPE DNA Repair Mix for 30 minutes then separated on 0.8% agarose gel for 15 minutes.  Fragmented DNA ranging from 0.1Kb to 3Kb was gel extracted with Wizard® SV Gel and PCR Clean-Up System (Promega) and the purified DNA was resuspended in 50uL of water for subsequent qPCR and sequencing analysis.
Illumina Nextera DNA Flex Library Prep Kit

treatment_protocol: For G2/M arrest, 2.0x10e6 cells per p15 tissue culture plate were grown for 48 hours, followed by treatment with 30uM BrdU for 4 hours prior to addition of nocodazole to 12.5ng/ml for an additional 12 hours. For release, non-adhering G2/M phase arrested cells were tapped and rinsed off the plate, washed twice with media via centrifugation at 1000 rpm for 3 minutes and resuspened in 10ml fresh complete DMEM, then plated on new 10cm plates in 10ml media containing 30uM BrdU. Samples were collected at 0, 10, 15 and 25 hours after release for DNA and flow cytometry analysis.

tag: cell line


title: HomoSap.RepTiming.25hr.Replicate1

description:
Human replication timing samples
HomoSap.RepTiming.25hr.merged.bedgraph


title: HomoSap.RepTiming.0hr.Replicate2

description:
Human replication timing samples
HomoSap.RepTiming.0hr.merged.bedgraph


title: HomoSap.RepTiming.25hr.Replicate3


title: HomoSap.RepTiming.15hr.Replicate3

description:
Human replication timing samples
HomoSap.RepTiming.15hr.merged.bedgraph


title: HomoSap.RepTiming.0hr.Replicate3


title: HomoSap.RepTiming.15hr.Replicate2


title: HomoSap.RepTiming.25hr.Replicate2


title: HomoSap.RepTiming.10hr.Replicate2

description:
Human replication timing samples
HomoSap.RepTiming.10hr.merged.bedgraph


title: HomoSap.2CellCycle.Replicate2


title: HomoSap.RepTiming.10hr.Replicate1


title: M2_Endo_16

city: San Francisco

first: Julia

last: Vallve Juanico

state: California

address: 513 Parnassus Ave HSE1619

department: Obstetrics and Gynecology Department

institute: University of California San Francisco

data_processing:
Illumina HiSeq 4000 reads were trimmed and clipped for quality control
The quality of the fastq files was tested using the FastQC (v0.11.5) and the Qualimap (rnaseq module – v2.2.1) software
Reads were aligned with the STAR mapper (v2.5.2a) to release 88 of the Homo sapiens ENSEMBL version of the genome (GRCh38/hg38 assembly)
A raw count of reads per gene was also obtained with STAR mapper (v2.5.2a)
In order to overcome the heterogeneity between samples, first, samples were removed from the analysis if they had <5 million uniquely mapped reads , and the remaining samples were down-sampled to 30 million mapped reads when needed.
Genome_build: 88 of the Homo sapiens ENSEMBL version of the genome (GRCh38/hg38 assembly)
Supplementary_files_format_and_content: raw counts from computed with the STAR mapper (option --quantMode GeneCounts)

source_name: Macrophage 2 endometriosis replicate 3

growth_protocol: Single cells from endometrial tissue were obtained by mechanical and enzymatic digestion

extract_protocol:
Total RNA was extracted by using RNeasy micro kit (Qiagen)
Libraries were constructed by using SMART-SeqTM v4 UltraTM low input RNA kit for sequencing (Clontech) following manufacyrer's instructions

treatment_protocol: Macrophages were isolated from eutopic endometrium by fluorescence activated cell sorting (FACS Aria) by using CD45, CD14, CD163 (M2) and CD80 (M1) conjugated antibodies

value: Endometrium

value: M2 macrophages

tag: disease state

value: endometriosis

tag: stage endometriosis

value: Stage II

tag: phase menstrual cycle

value: Late secretory


title: HomoSap.RepTiming.10hr.Replicate3


title: F05 2nd ZsGreen Negative

city: La jolla

first: Qiong

last: Zhang

address: 9500 Gilman Dr.

department: Pediatrics

data_processing:
Sequencing reads were de-multiplexed and adapters trimmed using cutadapt (http://code.google.com/p/cutadapt/) leaving only the 20bp sgRNA spacer sequences. The sgRNA spacer sequences were then mapped to the Brunello or GeCKO library using bowtie (Langmead and Salzberg, 2012) allowing a maximum of one mismatch and allowing only uniquely aligning reads. Only sgRNA spacers with multiple reads were analyzed (sgRNA spacer with only a single read were filtered out). Normalized read counts were obtained by normalizing to total read count per sample (normalized reads per sgRNA = reads per sgRNA/total reads for all sgRNAs in sample x 106+1). Normalized reads were used for input in STARS software
Supplementary_files_format_and_content: excel file include STARS values and p values for the 2nd sorting compared to the mock group

growth_protocol: TS576 were cultured in DMEM/F12 medium supplemented with 1:100 B27 without vitamin A, EGF (20ng/ml), FGF (10ng/ml) and penicillin-streptomycin (100IU/ml).

extract_protocol:
Genomic DNA was extracted from cells using the salt-precipitation.
The sgRNA library readout was performed following described protocols using a two-step nested PCR process in which PCR1 amplifies the lentiviral sequence containing the 20bp sgRNA cassette followed by PCR2 which attaches illumina sequencing adapters and barcodes. Primer sequences were obtained from the Zhang lab online resource (http://genome-engineering.org/gecko/) using v2Adaptor_F and v2Adapter_R for PCR1 and Primers F01-F06 and R01-R02 for PCR2.  All PCR was performed using Herculase II Fusion DNA Polymerase (Agilent). Enough PCR1 reactions were performed to maintain full library representation and PCR2 was performed with one reaction per 104 constructs (7 reactions per sample). 10ug of genomic DNA was used per PCR1 reaction. After pooling PCR1 product, 10uL of pooled PCR1 product was used for each PCR2 reaction. PCR products were purified and quantified with Qubit and/or bioanalyzer and diluted libraries were sequenced on Illumina NextSeq.

treatment_protocol: human glioblastoma stem cells (GSCs) were transduced with the lentiviral Brunello CRISPR library (400 million cells at MOI = 0.3), selected with puromycin for 7 days for stable viral integration and completion of genome editing. We challenged 75 million of the transduced and selected cells with ZIKV at a low MOI (MOI=0.01) for 7 days. The other 40 million cells were mock infected as a control . After 7 days of infection, ZsGreen negative cells were sorted out. Half of the cells were collected, and another half was retained for a second round of infection and sorting. A ZIKV NS5 inhibitor (NITD008) was used to reduce the cytopathic effect of ZIKV and allowed cells to expand for 2 weeks. The expanded cells were re-infected with ZIKV-ZsGreen (MOI = 0.01) for 7 days and sorted for ZsGreen negative cells.

value: glioblastoma stem cells (GSCs)

tag: passages


title: F01 1st ZsGreen Negative


title: M2_Endo_35

source_name: Macrophage 2 endometriosis replicate 6

tag: tissue

value: Stage IV

value: Mid secretory


title: M2_Endo_20

source_name: Macrophage 2 endometriosis replicate 5

value: Stage I


title: M2_Endo_18

source_name: Macrophage 2 endometriosis replicate 4

value: Early secretory


title: M2_Ctrl_8

source_name: Macrophage 2 control replicate 4

value: fibroids

value: no


title: M2_Endo_14

source_name: Macrophage 2 endometriosis replicate 2


title: M2_Ctrl_6

source_name: Macrophage 2 control replicate 3

value: fibroids and adenomyosis


title: M2_Ctrl_10

source_name: Macrophage 2 control replicate 5

value: healthy


title: M2_Ctrl_2

source_name: Macrophage 2 control replicate 1


title: M1_Endo_19

source_name: Macrophage 1 endometriosis replicate 5

value: M1 macrophages


title: M1_Endo_15

source_name: Macrophage 1 endometriosis replicate 3


title: HomoSap.RepTiming.15hr.Replicate1


title: F03 mock group


title: M1_Ctrl_5

source_name: Macrophage 1 control replicate 3


title: M1_Endo_13

source_name: Macrophage 1 endometriosis replicate 2


title: M1_Endo_11

source_name: Macrophage 1 endometriosis replicate 1


title: M1_Ctrl_9

source_name: Macrophage 1 control replicate 5


title: HomoSap.RepTiming.0hr.Replicate1


title: M2_Endo_12

source_name: Macrophage 2 endometriosis replicate 1


title: EXT1-/-  rep4

city: Cambridge

first: Sayaka

last: Masuko

state: MA

address: 77 Massachusetts Ave.

department: Chemistry

institute: Massachusetts Institute of Technology

data_processing:
The trimming software skewer (Jiang et al. 2014) was used to preprocess raw fastq files.
Samples were normalized by the method of trimmed mean of M-values (TMM).
Reads were aligned against the selected reference genome sequence using STAR (Spliced Transcripts Alignment to a Reference) (Dobin et al. 2013)
Mapped reads for both genes and transcripts (isoforms) are counted in each sample using RSEM (RNASeq by Expectation Maximization), described in Li and Dewey (2011)
Analysis of differentially expressed genes is performed with a glm using the edgeR package (Robinson, McCarthy, and Smyth 2010).
Genome_build: Human genes (GRCh38.p10)
Supplementary_files_format_and_content: Results from contrast at the gene level are written to a MS Excel spreadsheet. Information includes gene/transcript length, FDR, effective length, TPM, and FPKM.

source_name: Human embryonic stem cell

growth_protocol: H9 and EXT1-/- human embryonic stem cells were maintained in E8™ medium (Stem Cell Technologies) on VTN-XF™ (Stem Cell Technologies)-coated non-tissue culture plates. Cells were maintained at 37 °C in 5% CO2. Cells were passaged manually using EDTA (1 mM) every 4-5 days, with the addition of 5 µM Y-27632 dihydrochloride (Tocris) during the first day of passage.

extract_protocol:
Total RNA extraction was performed using TRIzol (Life Technologies) and Direct-zol RNA MiniPrep kit (Zymo Research) as per manufacturer instructions.
Libraries were prepared using TruSeq Stranded Total RNA kit (Illumina).

tag: status

value: Undifferentiated


title: EXT1-/-  rep1


title: EXT1-/-  rep3


title: WT rep4

value: WT


title: M1_Endo_17

source_name: Macrophage 1 endometriosis replicate 4

value: Endometrium


title: WT rep1


title: SAM10

city: South San Francisco

first: Luz

middle: D

last: Orozco

address: 1 DNA Way

department: Bioinformatics

institute: Genentech Inc.

data_processing:
Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package.
Gene models were from our internal database and available in the manuscript supplementary material.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include preMRNA_umi raw count values for each Sample

source_name: eye

extract_protocol:
Donor eyes with no retinal disease diagnosis from the Lions Eye Institute (Tampa, FL) were enucleated and flash frozen in LN2 within 5 h postmortem or less, shipped on dry ice and stored at -80C. The eye globes were cryosectioned at 60 μm starting at the base of the optic nerve and at a plane perpendicular to the optic nerve. Posterior sections with visible RPE layers were collected in batches of 8 for NucSeq (see below). Additional sections of more anterior eye regions were used to assess overall RNA quality. 108955 (right eye) is from a 78 year old female donor, PMI = 3:40 hours, RNA integrity number (RIN) = 8.0; 120974 (left eye) is from a 79 year old male donor, PMI = 2:40 hours, RIN = 8.0; 109829 (left eye) is from a 77 year old female donor, PMI = 4:08 hours, RIN = 8.4; 109373 (right eye) is from a 70 year old male donor, PMI = 4:40 hours RIN = 8.6; 110814 (right eye) is from a 65 year old male donor, PMI = 4:25 hours, RIN = 8.5. For donor eye 108955, sections 1-8 (region 1, most poterior) and 9-18 (region 2) are separately subjected to nuclei extraction and library construction with the 10X Chromium single cell 3’ gene expression kit v2. For the remaining 4 donor eyes, only region 2 was used for NucSeq with the v3 kit.  Nuclei were isolated and processed based on methods in (Krishnaswami et al., 2016). Briefly, sections were thawed directly in ice cold homogenization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris buffer pH 8.0, 1 μM DTT, 1X cOmpleteTM protease inhibitors with EDTA (Roche), 0.1% v/v Triton X 100, 0.4U/μL recombinant RNAse Inhibitor (Ambion), 0.2U/μL SUPERas-In (Ambion), 0.2 μg/ml DAPI) and dounced 15X with a loose pestle in a glass tissue homogenizer (Wheaton). Nuclei released were washed once in homogenization buffer and sorted for 2N DNA content gated on DAPI (linear scale) on a FACS-ARIA II (BD) with cooled chamber. Sorted single nuclei were collected in 1% BSA/1X PBS with 0.2U/μL RNase Inhibitor, concentrated, resuspended in ~50 μL residual buffer, counted manually with a hemocytometer, and immediately processed with 10X Chromium single cell 3’ gene expression kit v2 or v3 (10X Genomics) at ~16000 nuclei per library and 2-3 libraries per region, following manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Right

tag: Sex

value: Male

tag: donor id


title: SAM11


title: WT rep3


title: SAM9


title: SAM8


title: SAM7


title: SAM6


title: SAM4

value: Left


title: SAM5


title: M1_Ctrl_1

source_name: Macrophage 1 control replicate 1


title: SAM2

value: Female


title: WT rep2


title: EXT1-/-  rep2


title: JHH4_KO

city: Bunkyo-ku

first: Shu

last: Shimada

state: Tokyo

address: 1-5-45 Yushima

department: Department of Molecular Oncology

country: Japan

institute: Tokyo Medical and Dental University

description: Gene expression profile of human normal liver #NL001

hyb_protocol: Hybridization and signal detection of HG-U133 Plus 2.0 arrays (Affymetrix) were performed following the manufacturer's instruction by using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip Scanner 3000.

data_processing: The microarray data of 152 tumorous and 91 adjacent liver tissues from HCC patients as well as 14 normal liver were normalized by robust multichip analysis (RMA) using affy package in R/Bioconductor.

source_name: ARID2 knockout human hepatocellular carcinoma cell line JHH4

label_protocol: Amplified RNA was prepared by using 3' IVT Express Kit (Affymetrix).

extract_protocol: Total RNA was extracted from tissue specimens by using RNeasy Protect Mini Kit (QIAGEN). Contaminating DNA was removed by digestion with RNase-Free DNase Set (QIAGEN). The RNA Integrity Number (RIN) of all the samples was confirmed to be greated than 7.0 by using 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Hepatocellular cellular carcinoma cell lines (JHH4 and JHH5) were purchased from Health Science Research Resources Bank (Osaka, Japan). They were maintained in Dulbecco's modified Eagle's medium (Invitrogen, Carlsbad, CA) supplemented with 10% fetal bovine serum (Sigma-Aldrich, St. Louis, MO), 100 U/ml penicillin, and 100 μg/ml streptomycin (Invitrogen). All cell lines were cultivated in a humidified incubator at 37 °C in 5% carbon dioxide and collected with 0.05% trypsin-0.02% EDTA solution (Invitrogen).  The CRISPR targeting sequences were designed on the basis of the Opimized CRISPR Design web tool (http://crispr.mit.edu/). Oligos targeting ARID2 (5'-CCATTTCCGTGAGCATGTATAGC-3') were cloned into the gRNA Cloning Vector (Addgene, plasmid #41824) following hCRISPR gRNA Synthesis Protocol, and transfected with the hCas9 (Addgene, plasmid #41815) by using Neon Transfection System (Invitrogen). Cells were selected in media containing 2 mg/ml G418 (Invitrogen) for three days, and then isolated by limiting dilution.

value: Hepatocellular carcinoma


title: SAM3


title: SAM1


title: NRVC mef2Cγ+23/24, biological rep3

city: Campinas

first: Marcelo

middle: Falsarella

last: Carazzolle

state: São Paulo

address: Rua Carl Von Linnaeus

country: Brazil

institute: Instituto de Biologia/Unicamp

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Gene Chip Rat Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Rattus norvegicus

source_name: NRVC mef2Cγ+23/24

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The cells were maintained in the plating medium containing 10% horse serum, 5% fetal bovine serum and 0.5% penicillin–streptomycin, and plated in type-I collagen in Petri plates (25 mm) and incubated for 44 h under 95% air–5% CO2. The medium was then replaced by serum-free DMEM and the cells were incubated for 24 h before use

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

value: Wistar

value: culture of neonatal rat ventricular cardiomyocyte

tag: genotype/variation

value: transduced with mef2C{gamma}+ 23/24


title: JHH5_WT

source_name: ARID2 wild-type human hepatocellular carcinoma cell line JHH5


title: NRVC mef2Cγ-, biological rep1

source_name: NRVC mef2Cγ-

value: transduced with mef2C{gamma}-


title: JHH5_KO

source_name: ARID2 knockout human hepatocellular carcinoma cell line JHH5


title: NRVC mef2Cγ-, biological rep3


title: NRVC mef2Cγ+23/24, biological rep2


title: NRVC mef2Cγ+, biological rep3

source_name: NRVC mef2Cγ+

value: transduced with mef2C{gamma}+


title: MM_exo_10

first: Zhiyao

address: No. 8 Gongti South Road, Beijing

institute: Beijing Chao-yang hospital

description: Gene expression data from newly diagnosed multiple myeloma serum exosomes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 48C on GeneChip . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: newly diagnosed multiple myeloma patients

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 130 ng total RNA (Affymetrix microRNA 4.0).

growth_protocol: Peripheral blood of healthy individuals and newly diagnosed myeloma patients were collected with non-anticoagulant tubes, placed at 4 ℃ for no more than 1 hour

extract_protocol: Kit extraction of total RNA was performed according to the manufacturer's instructions.(miRNeasy Micro Kit)

treatment_protocol: Serum was extracted and exosomes were extracted by kit(exoquick).

value: newly diagnosed multiple myeloma

value: Peripheral blood serum exosomes

tag: ethnicity

value: Asian


title: NRVC mef2Cγ+23/24, biological rep1

tag: strain


title: JHH4_WT

source_name: ARID2 wild-type human hepatocellular carcinoma cell line JHH4


title: NRVC mef2Cγ-, biological rep2


title: NRVC Control, biological rep3

source_name: NRVC Control

value: control


title: MM_exo_12


title: MM_exo_6


title: MM_exo_11


title: MM_exo_9


title: NRVC mef2Cγ+, biological rep2


title: MM_exo_8


title: MM_exo_4


title: MM_exo_1


title: MM_exo_5


title: MM_exo_7


title: MM_exo_3


title: NRVC Control, biological rep1


title: MM_exo_2


title: NRVC mef2Cγ+, biological rep1


title: con_exo_10

description: Gene expression data from healthy individuals serum  exosomes

source_name: healthy individuals

value: healthy


title: NRVC Control, biological rep2


title: con_exo_8


title: con_exo_7


title: con_exo_5


title: con_exo_2


title: con_exo_11


title: con_exo_12


title: con_exo_4


title: HEK293_tRNA_His_P15_rep1

city: Aveiro

first: Ana Sofia

last: Varanda

address: Campus Universitário Santiago

department: Health Sciences

country: Portugal

institute: University of Aveiro

description: HEK293 cells expressing the mutant serine tRNA for His codons, in P15, replicate 1

hyb_protocol: Hybridizations were performed according to the Agilent protocol for One-Color Microarray Based Gene Expression Analysis Low Input Quick Amp Labeling v6.9 instructions. 600ng of labeled cDNA were hybridized in Sure Print G3 Human Gene Expression 8x60k v2 microarrays (Agilent Technologies, Cat.G4851B). Hybridizations were carried out using Agilent gasket slides in a rotating oven for 17h at 65ºC. Slides were then washed following manufacturer’s instructions.

scan_protocol: Slides were scanned in an Agilent G2565AA microarrays scanner according to Agilent protocol for One-Color Microarray Based Gene Expression Analysis Low Input Quick Amp Labeling v6.9 instructions.

data_processing: Probes signal values were extracted using Agilent Feature Extraction Software. Data were normalized using median centering of signal distribution with Biometric Research Branch BRB-Array tools v3.4.o software. Microarrays statistical analysis was carried out using Mev software (TM4 Microarray Software Suite). T-test was performed to identify genes that showed differences in expression between control (Mock) and samples. Significant genes that present a fold change above 1.5 or bellow -1.5 were considered for downstream analysis.

source_name: HEK293 cells, in Passage 15, expressing the tRNASer(H) (serine tRNA with Histidine anticodon)

label_protocol: Gene expression microarrays profiling was performed using the Agilent protocol for One-Color Microarray Based Gene Expression Analysis Low Input Quick Amp Labeling v6.9 (Agilent Technologies). RNA quality determination was performed using 2100 Bioanalyser (Agilent Technologies) and the kit Agilent RNA 6000 Nano kit (Agilent Technologies, Cat.5067-1512). 100ng of total RNA were used to synthesize labeled cDNA (with Cyanine 3-CTP) using Agilent T7 Promoter Primer and T7 RNA polymerase Blend (Agilent Technologies, Cat.5190-2305). cDNA was purified with RNAeasy mini spin columns (Quiagen, Cat.74104). Dye incorporation was quantified using Nanodrop 1000 Spectophotometer.

growth_protocol: Human embryonic kidney 293 (HEK293) cells were purchased from American Type Culture Collection (ATCC®CRL-1573). Cells were grown in Minimum Essential Medium (Gibco, Cat.41090-028) supplemented with 10% fetal bovine serum (FBS) (Sigma, Cat.F1051), 1% of Pen/Strep (Gibco, Cat.15070-063) and 1% of non-essential amino acids (Gibco, Cat.11140-050) in a humidified atmosphere at 37ºC in the presence of 5% CO2.

extract_protocol: RNA was extracted using Trizol®Reagent (Thermo Fisher Scientific, Cat.15596026). The content of one well from a 6 well plate, with around 5x105 cells, was collected for each experimental condition. Purification of RNA was done using DNaseI, Amplification Grade kit (Invitrogen, Cat.18068015), following manufacturer’s instructions. RNA was then precipitated with a standard Phenol/Chlorophorm/Isoamylalchohol (25:24:1) (Acros Organics, Cat.327111000) extraction protocol and conserved at -80ºC. RNA concentration was determined using NanoDrop1000 (Thermo Scientific). RNA quality was verified using Agilent 2100 Bioanalyser

treatment_protocol: HEK293 cells with approximately 60% of confluency were transfected with 1µg of plasmid DNA using Lipofectamine2000 (Invitrogen, Cat.11668019), following manufacturer’s instructions. Cells were transfected with an empty vector (Mock), and with the plasmid carrying tRNAserAGA(S), tRNASerAGC(A), tRNASerAAG(L) or tRNASerGTG(H) genes. To establish stable cell lines, 72h after transfection, geneticin (Formedium, Cat.G4185) was added to the medium at a concentration of 800µg/ml and selection lasted for 1 month. Cells were kept in low concentration of geneticin (100µg/ml) after selection and during evolution in culture. After transfection with the plasmids and selection, cells were kept in culture dishes (60mm) and subcultured ever 3 days using the same dilution (1/6) until passage 30. Cell culture conditions were the same during evolution. In P1, P15 and P30 cells were plated in 100mm culture dishes, to have enough cells to extract RNA.

tag: cells

tag: cells passage


title: HEK293_tRNA_His_P30_rep2

description: HEK293 cells expressing the mutant serine tRNA for His codons, in P30, replicate 2

source_name: HEK293 cells, in Passage 30, expressing the tRNASer(H) (serine tRNA with Histidine anticodon)


title: HEK293_tRNA_Leu_P30_rep3

description: HEK293 cells expressing the mutant serine tRNA for Leu codons, in P30, replicate 3

source_name: HEK293 cells, in Passage 30, expressing the tRNASer(L) (serine tRNA with Leucine anticodon)


title: HEK293_tRNA_Leu_P15_rep3

description: HEK293 cells expressing the mutant serine tRNA for Leu codons, in P15, replicate 3

source_name: HEK293 cells, in Passage 15, expressing the tRNASer(L) (serine tRNA with Leucine anticodon)


title: con_exo_3


title: HEK293_tRNA_His_P15_rep2

description: HEK293 cells expressing the mutant serine tRNA for His codons, in P15, replicate 2


title: con_exo_1


title: HEK293_tRNA_His_P30_rep3

description: HEK293 cells expressing the mutant serine tRNA for His codons, in P30, replicate 3


title: HEK293_tRNA_Leu_P15_rep2

description: HEK293 cells expressing the mutant serine tRNA for Leu codons, in P15, replicate 2


title: HEK293_tRNA_His_P15_rep3

description: HEK293 cells expressing the mutant serine tRNA for His codons, in P15, replicate 3


title: con_exo_6


title: HEK293_tRNA_His_P1_rep1

description: HEK293 cells expressing the mutant serine tRNA for His codons, in P1, replicate 1

source_name: HEK293 cells, in Passage 1, expressing the tRNASer(H) (serine tRNA with Histidine anticodon)


title: HEK293_tRNA_Leu_P15_rep1

description: HEK293 cells expressing the mutant serine tRNA for Leu codons, in P15, replicate 1


title: HEK293_tRNA_His_P1_rep3

description: HEK293 cells expressing the mutant serine tRNA for His codons, in P1, replicate 3


title: con_exo_9


title: HEK293_tRNA_Leu_P1_rep3

description: HEK293 cells expressing the mutant serine tRNA for Leu codons, in P1, replicate 3

source_name: HEK293 cells, in Passage 1, expressing the tRNASer(L) (serine tRNA with Leucine anticodon)


title: HEK293_tRNA_Leu_P30_rep1

description: HEK293 cells expressing the mutant serine tRNA for Leu codons, in P30, replicate 1


title: HEK293_tRNA_His_P1_rep2

description: HEK293 cells expressing the mutant serine tRNA for His codons, in P1, replicate 2


title: HEK293_tRNA_Leu_P30_rep2

description: HEK293 cells expressing the mutant serine tRNA for Leu codons, in P30, replicate 2


title: HEK293_tRNA_His_P30_rep1

description: HEK293 cells expressing the mutant serine tRNA for His codons, in P30, replicate 1


title: HEK293_tRNA_Ala_P30_rep3

description: HEK293 cells expressing the mutant serine tRNA for Ala codons, in P30, replicate 3

source_name: HEK293 cells, in Passage 30, expressing the tRNASer(A) (serine tRNA with Alanine anticodon)


title: s14852

city: Boston

first: Samuel

last: Ng

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Paired-end RNASeq samples were mapped to the human genome reference assembly (hg19) with STAR 2.4.2a
STAR-Fusion was used for gene fusion detection.
Genome_build: hg19

source_name: clinical samples

extract_protocol:
RNA was harvested from frozen lymph node samples using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Adult T-cell leukemia/lymphoma


title: s10658


title: s9137


title: HEK293_tRNA_Leu_P1_rep1

description: HEK293 cells expressing the mutant serine tRNA for Leu codons, in P1, replicate 1


title: HEK293_tRNA_Ala_P30_rep1

description: HEK293 cells expressing the mutant serine tRNA for Ala codons, in P30, replicate 1


title: HEK293_tRNA_Leu_P1_rep2

description: HEK293 cells expressing the mutant serine tRNA for Leu codons, in P1, replicate 2


title: HEK293_tRNA_Ala_P15_rep1

description: HEK293 cells expressing the mutant serine tRNA for Ala codons, in P15, replicate 1

source_name: HEK293 cells, in Passage 15, expressing the tRNASer(A) (serine tRNA with Alanine anticodon)


title: HEK293_tRNA_Ala_P15_rep3

description: HEK293 cells expressing the mutant serine tRNA for Ala codons, in P15, replicate 3


title: HEK293_tRNA_Ala_P1_rep3

description: HEK293 cells expressing the mutant serine tRNA for Ala codons, in P1, replicate 3

source_name: HEK293 cells, in Passage 1, expressing the tRNASer(A) (serine tRNA with Alanine anticodon)


title: HEK293_tRNA_Ser_P30_rep1

description: HEK293 cells expressing the normal serine tRNA, in P30, replicate 1

source_name: HEK293 cells, in Passage 30, expressing the tRNASer(S) (wild type serine tRNA)


title: HEK293_tRNA_Ser_P30_rep3

description: HEK293 cells expressing the normal serine tRNA, in P30, replicate 3


title: HEK293_tRNA_Ser_P15_rep1

description: HEK293 cells expressing the normal serine tRNA, in P15, replicate 1

source_name: HEK293 cells, in Passage 15, expressing the tRNASer(S) (wild type serine tRNA)


title: HEK293_tRNA_Ala_P30_rep2

description: HEK293 cells expressing the mutant serine tRNA for Ala codons, in P30, replicate 2


title: HEK293_tRNA_Ser_P1_rep2

description: HEK293 cells expressing the normal serine tRNA, in P1, replicate 2

source_name: HEK293 cells, in Passage 1, expressing the tRNASer(S) (wild type serine tRNA)


title: HEK293_tRNA_Ser_P1_rep3

description: HEK293 cells expressing the normal serine tRNA, in P1, replicate 3


title: HEK293_tRNA_Ala_P15_rep2

description: HEK293 cells expressing the mutant serine tRNA for Ala codons, in P15, replicate 2


title: HEK293_tRNA_Ser_P15_rep2

description: HEK293 cells expressing the normal serine tRNA, in P15, replicate 2


title: HEK293_tRNA_emptyplasmid_control_P15_rep1

description: HEK293 cells expressing the empty plasmid, control, in passage 15, replicate 1

source_name: HEK293 cells, in Passage 15, expressing the Mock (empty plasmid, our control)


title: HEK293_tRNA_Ala_P1_rep2

description: HEK293 cells expressing the mutant serine tRNA for Ala codons, in P1, replicate 2


title: s11954


title: HEK293_tRNA_emptyplasmid_control_P30_rep3

description: HEK293 cells expressing the empty plasmid, control, in passage 30, replicate 3

source_name: HEK293 cells, in Passage 30, expressing the Mock (empty plasmid, our control)


title: s9060


title: HEK293_tRNA_Ser_P30_rep2

description: HEK293 cells expressing the normal serine tRNA, in P30, replicate 2


title: HEK293_tRNA_Ser_P1_rep1

description: HEK293 cells expressing the normal serine tRNA, in P1, replicate 1


title: HEK293_tRNA_emptyplasmid_control_P30_rep2

description: HEK293 cells expressing the empty plasmid, control, in passage 30, replicate 2


title: s10976


title: HEK293_tRNA_emptyplasmid_control_P15_rep3

description: HEK293 cells expressing the empty plasmid, control, in passage 15, replicate 3


title: HEK293_tRNA_emptyplasmid_control_P1_rep3

description: HEK293 cells expressing the empty plasmid, control, in passage 1, replicate 3

source_name: HEK293 cells, in Passage 1, expressing the Mock (empty plasmid, our control)


title: s13609


title: s11406


title: s13665

city: Changsha

first: Wu

last: Hao

state: Hunan

address: 138 Tongzipo Road

department: Department of General Surgery

institute: The Third Xiangya Hospital of Central South University

data_processing:
The quality of RNA-Seq raw reads was evaluated using NGSQC Toolkit software with default parameters, and only high quality reads were retained.
We then used the featureCounts script from the Subread software package (http://subread.sourceforge.net/) to calculate count data for genes in human and marmoset using their reference annotations from Ensembl version 89.
Next, we calculated the FPKM value from the counts data by normalizing it to the length of the gene and by the total number of high quality RNA-Seq reads from the sample. Common genes (using the gene name) between humans and marmosets were extracted. If the FPKM of any gene from all the human samples was less than 1, the entry was discarded. Similarly, if the FPKM of any gene from all the marmoset samples was less than 1, it was discarded. In the end, we were left with 7174 common genes between the two species.
To find differentially expressed genes in humans, we calculated the ratio of sample “si-gl2_FPKM” and sample “si-hMRPS31P5_FPKM” and used a cutoff of >=2 to identify upregulated genes, and a cutoff of <=0.5 to identify downregulated genes. Similarly, differentially expressed genes were found in marmosets.
Genome_build: For human, GRCh38.  For marmoset C_jacchus3.2.1.
Supplementary_files_format_and_content: csv files include FPKM values for each Sample

organism: Callithrix jacchus

source_name: Fibroblast

growth_protocol: Human foreskin fibroblast (HFF)  cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) with 4.5 g/L glucose (Gibco), 10% Fetal Bovine Serum (FBS) (Invitrogen, Gaithersburg, MD) and 1% Pen/Strep solution (Hyclone). The marmoset fibroblasts CJ-157 cell line were cultured in fresh M10 medium [DMEM (Gibco), 10% FBS, 1% Pen/Strep solution (Hyclone), 0.25 μg/mL Amphotericin B (Sigma), 1% MEM Non-Essential Amino Acids Solution (Gibco), and 2 mM GlutaMAX (Gibco)]. Cells were cultivated at 37°C in 5% CO2 humidity.

extract_protocol:
HFF and CJ-157 cells transfected with si-hMRPS31P5, si-H-S, or si-gl2 (control) were harvested 72 hours after transfection. RNA was extracted and purified with QIAGEN RNeasy Mini Kit according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Custom siRNAs were ordered from Invitrogen, and transfection was performed using Lipofectamine® RNAiMAX Transfection Reagent (Thermo Fisher Scientific) according to the manufacturer’s instructions.

tag: cell type

value: Fibroblast

tag: treatment


title: s13666


title: HEK293_tRNA_emptyplasmid_control_P30_rep1

description: HEK293 cells expressing the empty plasmid, control, in passage 30, replicate 1


title: HEK293_tRNA_emptyplasmid_control_P15_rep2

description: HEK293 cells expressing the empty plasmid, control, in passage 15, replicate 2


title: HEK293_tRNA_Ala_P1_rep1

description: HEK293 cells expressing the mutant serine tRNA for Ala codons, in P1, replicate 1


title: HTA11-FLAG-elf3-ZT20_S5

first: Phillip

last: Wigge

address: Bateman Street

department: Sainsbury Laboratory

institute: University of Cambridge

description:
lane: 164C
ChIP-seq
HTA11-FLAG-elf3-ZT20_S5

data_processing:
The raw reads obtained from the sequencing facilities were analysed using a combination of publicly available software and in-house scripts.
We first assessed the quality of reads using FastQC:(www.bioinformatics.babraham.ac.uk/projects/fastqc/). Potential adaptor contamination and low quality trailing sequences were removed using Trimmomatic (Bolger et al., 2014).
The reads were then mapped to TAIR10 reference genome using Bowtie2 (Langmead et al., 2009).
Duplicates were removed with the Picard tools (https://github.com/broadinstitute/ picard).
The read counts was normalised by the sample’s genome-wide reads coverage to generate bigWig files.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig

organism: Arabidopsis thaliana

source_name: elf3-1 HTA11::HTA11:FLAG seedlings

growth_protocol: Seedlings were grown at 17c in long days for 12 days and collected at ZT 0, ZT4, ZT8, ZT12, ZT16 and ZT20

extract_protocol:
ChIP was performed as described (Gendrel et al., 2002) with minor modifications. Approximately 1 g of 9-day-old Arabidopsis seedlings was harvested at the time points indicated in figure legends. The harvested seedlings were ground in liquid nitrogen to fine powder. The tissue powder was fixed for 10 min with 1% formaldehyde (SIGMA, F8775) in Buffer 1 (0.4 M sucrose, 10 mM HEPES, 10 mM MgCl2, 5 mM ß-mercaptoethanol, 0.1 mM phenylmethylsulfonyl fluoride (PMSF) and 1 X protease inhibitor (Roche, 11836145001)). The reaction was quenched by adding glycine to a final concentration of 127 mM. The homogenate was filtered through Mira-cloth twice and centrifuged to collect the pellet. The pellet was washed in Buffer 2 (0.24 M sucrose, 10 mM Tris-HCl (pH 8.0), 10 mM MgCl2, 5 mM -mercaptoethanol, 0.1 mM PMSF and 1 X protease inhibitor, 1% Triton) and then spun down in Buffer 3 (1.7 M sucrose, 10 mM Tris-HCl (pH 8.0), 10 mM MgCl2, 5 mM -mercaptoethanol, 0.1 mM PMSF and 1 X protease inhibitor, 0.15% Triton). The nuclei pellet was then resuspended in Mnase Digestion Buffer (20 mM Tris-HCl (pH 8.0), 50 mM NaCl, 1 mM DTT, 0.5% NP-40, 1 mM CaCl2, 0.5 mM PMSF, 1 X protease inhibitor) and was flash frozen in liquid nitrogen twice to break the nuclei membrane. The chromatin was digested by adding Mnase (SIGMA, N3755) to a final concentration of 0.4 U/ml for 12.5 min. The reaction was terminated by adding EDTA to a final concentration of 5 mM. For ChIP-seq samples, H2A.Z in transgenic line pHTA11:HTA11-FLAG were immunoprecipitated by anti-FLAG M2 magnetic beads (SIGMA, M8823) and then eluted with 3XFLAG peptide (Bimake, B23112). After reverse crosslinking, the DNA was purified with SPRI beads.
The libraries were constructed using TruSeq ChIP Sample Preparation Kit (Illumina, IP-202-1024) according to manufacturer’s instructions. The libraries were sequenced on an Illumina Nextseq 500 platform.

value: seedlings

tag: genotype

value: elf3-1 HTA11::HTA11:FLAG

tag: time

tag: temperature

tag: replicate

tag: fragmentation method (mnase digestion or sonication)

value: sonication

tag: chip antibody

value: Anti-FLAG® M2 Magnetic Beads (M8823 SIGMA)


title: MB05 AH

city: Saint Louis

first: Bo

state: MO

address: 660 S. Euclid Avenue

department: Developmental Biology

institute: Washington University School of Medicine

description: mb05 ah

data_processing:
mRNA-seq reads were aligned to the human genome hg38 with STAR version 2.5.4b. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:feature, version 1.4.6, with gene-body annotation of human GENCODE V27. [30].
Genome_build: hg38
Supplementary_files_format_and_content: gene level reads count table

source_name: Abductor Hallucis Muscle

extract_protocol:
RNA was isolated from muscle samples by homogenization in Trizol reagent (Invitrogen) followed by chloroform extraction and purification by RNEasy columns (Qiagen).
Library preparation and sequencing was performed by the Genome Technology Access Center of Washington University.  Briefly, libraries were prepared using 500 ng – 1 μg total RNA validated for size and puirity.  mRNA was fragmented and  reverse transcribed using SuperScript III RT enzyme (Life Technologies), with a second strand reaction to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were sequenced on an Illumina HiSeq-3000, using single reads extending 50

tag: diagnosis

value: MNC

tag: group designation

value: MNC AH

tag: tissue

value: Abductor Hallucis Muscle


title: MB05 MG

description: mb05 mg

source_name: Medial Gastrconemius Muscle

value: MNC MG

value: Medial Gastrconemius Muscle


title: HTA11-FLAG-elf3-ZT16_S4

description:
lane: 164C
ChIP-seq
HTA11-FLAG-elf3-ZT16_S4


title: A2780 Wild-type / Myc-MAGE-A11 + HA-FLAG-PCF11 I689A 1

city: Irvine

first: Lei

last: Li

address: University of California, Irvine

institute: University of California, Irvine

data_processing:
RNA-seq reads were mapping to human hg19 genome using STAR (version:2.4.1) with default parameters
The sorted BAM files were then converted to wig format using samtools (version: 0.1.19)
The wig files were further converted to bigwig format using wigtobigwig
Genome_build: hg19
Supplementary_files_format_and_content: bigwig format

source_name: A2780 (Xenograft tumor)

extract_protocol:
Total RNA was extracted from cultured cells or xenograft tumors using RNeasy kit (Qiagen) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols for Illumina TruSeq mRNA.

tag: cell line


title: A2780 Wild-type / Myc-MAGE-A11 + HA-FLAG-Vector 2


title: HEK293_tRNA_emptyplasmid_control_P1_rep1

description: HEK293 cells expressing the empty plasmid, control, in passage 1, replicate 1


title: A2780 Wild-type / Myc-MAGE-A11 + HA-FLAG-Vector 1


title: A2780 PCF11 I689A Knock-In Clone #1/Myc-MAGE-A11 C3


title: A2780 PCF11 I689A Knock-In Clone #1/Myc-MAGE-A11 C2


title: HTA11-FLAG-elf3-ZT8_S3

description:
lane: 164C
ChIP-seq
HTA11-FLAG-elf3-ZT8_S3


title: HEK293_tRNA_emptyplasmid_control_P1_rep2

description: HEK293 cells expressing the empty plasmid, control, in passage 1, replicate 2


title: A2780 Wild-type / Myc-MAGE-A11 + HA-FLAG-PCF11 I689A 2


title: MB09 MG

description: mb09 mg


title: A2780 PCF11 I689A Knock-In Clone #1 C3


title: A2780 PCF11 I689A Knock-In Clone #1/Myc-MAGE-A11 C1


title: MB09 AH

description: mb09 ah


title: HTA11-FLAG-elf3-ZT0_S1

description:
lane: 164C
ChIP-seq
HTA11-FLAG-elf3-ZT0_S1


title: MB10 MG

description: mb10 mg

value: DPN

value: DPN MG


title: A2780 PCF11 I689A Knock-In Clone #1 C1


title: MB02 MG

description: mb02 mg


title: MB12 AH

description: mb12 ah

value: DPN (sev)

value: DPN (sev) AH


title: HTA11-FLAG-Col-ZT20_S11

description:
lane: 164C
ChIP-seq
HTA11-FLAG-Col-ZT20_S11

source_name: Col-0 HTA11::HTA11:FLAG seedlings

value: Col-0 HTA11::HTA11:FLAG


title: MB07 MG

description: mb07 mg2


title: HTA11-FLAG-elf3-IN_S6

description:
lane: 164C
Input for ChIP-seq
HTA11-FLAG-elf3-IN_S6


title: HTA11-FLAG-elf3-ZT4_S2

description:
lane: 164C
ChIP-seq
HTA11-FLAG-elf3-ZT4_S2


title: MB11 AH

description: mb11 ah

value: DPN AH


title: MB14 MG

description: mb14 mg


title: HTA11-FLAG-Col-ZT16_S10

description:
lane: 164C
ChIP-seq
HTA11-FLAG-Col-ZT16_S10


title: MB01 AH

description: mb01 ah


title: MB02 AH

description: mb02 ah


title: OV56 vector control C1

source_name: OV56 (Xenograft tumor)


title: HTA11-FLAG-Col-ZT0_S7

description:
lane: 164C
ChIP-seq
HTA11-FLAG-Col-ZT0_S7


title: HTA11-FLAG-Col-ZT4_S8

description:
lane: 164C
ChIP-seq
HTA11-FLAG-Col-ZT4_S8


title: MB01 MG

description: mb01 mg2


title: A2780 PCF11 I689A Knock-In Clone #1 C2


title: A2780 MAGE-A11 overexpression C2


title: HTA11-FLAG-Col-ZT8_S9

description:
lane: 164C
ChIP-seq
HTA11-FLAG-Col-ZT8_S9


title: OV56 vector control C2


title: MB12 MG

description: mb12 mg


title: A2780 vector control C2


title: A2780 MAGE-A11 overexpression C1


title: HOXC6_Input

city: Los Angeles

first: Zhifei

last: Luo

address: 1450 Biggy Street, NRT 6514

institute: University of Southern California

data_processing:
For RNA_seq, quality control of the sequenced datasets was performed using FastQC and reads were trimmed using Trimmomatic (Bolger, Lohse et al. 2014) ; reads were mapped to the human genome GRCh38 reference using Gencode V29 annotation and STAR (Dobin, Davis et al. 2013) . Differentially expressed genes were determined using DESeq2 (Liao, Smyth et al. 2014) . Transcripts per million (TPM) for each gene were calculated with R script. Genes with an average TPM less than 1 in both control and deletion groups were excluded from downstream analysis.
All ChIP_seq data were quality checked using FASTQC and MultiQC (Ewels,Magnusson et al. 2016) and mapped to GRCh38 using BWA. Low quality, duplicated, not primary aligned, and not properly paired reads were filtered out using SAMtools, Sambamb and Samblaster (Li, Handsaker et al. 2009, Faust and Hall 2014, Tarasov, Vilella et al. 2015) . Peaks were called using MACS2 (Zhang, Liu et al. 2008) on each ChIP_seq replicate and common peaks were identified using IDR (for transcription factors) or the overlap method (for histones).
Genome_build: GRCh38

source_name: Human prostate cell line 22Rv1

growth_protocol: The human prostate cell line 22Rv1 was grown in RPMI 1640 medium (Corning Cellgro) with 10% fetal bovine serum (Gibco Life Technologies) without antibiotics. Cells were grown at 37 °C with 5% CO2 for under 20 passages. The cell line identity was confirmed using the STR cell line authentication method at the Norris Comprehensive Cancer Center Media Core and was shown to be free of mycoplasma using the universal mycoplasma detection kit (ATCC 30_1012K).

extract_protocol:
RNA was extracted using the DirectZol RNA kit (Zymo, R2062).
The RNA_seq libraries were made using Kapa mRNA HyperPrep Kit (KAPA, KKK8581) according to manufacturer’s instructions. ChIP_seq libraries were prepared using the Kapa Hyper prep kit (Kapa, KK8503) according to the manufacturer’s protocol.

treatment_protocol: 22RV1 cells were transfected with DharmaFECT1 reagent (Dharmacon, #T_2001_01) plus siRNAs against human HOXC4 (ON_TARGETplus Human HOXC4 (3221) siRNA_SMARTpool, L_013462_00_0005), human HOXC6 (ON_TARGETplus Human HOXC6 (3223)siRNA_SMARTpool, L_011871_00_0005), or a non_targeting control (ON_TARGETplus Non_targeting Pool). The final concentration of siRNAs in the cell culture media was 50nmol. Cell were incubated for 24 hours and then transfected again using same amount of the same siRNAs and incubated for another 24 hours.

value: human prostate cancer

value: HOXC6 expression

value: wild type


title: elf3-1-ZT12-2_S18

description:
lane: 140C
Mnase-seq
elf3-1-ZT12-2_S18

source_name: elf3-1 seedlings

value: seedlings

value: MNase (mononucleosome)


title: HTA11-FLAG-Col-IN_S12

description:
lane: 164C
Input for ChIP-seq
HTA11-FLAG-Col-IN_S12

value: sonication


title: A2780 vector control C1


title: HOXC6_rep2


title: HOXC6_rep1


title: elf3-1-ZT12-1_S17

description:
lane: 140C
Mnase-seq
elf3-1-ZT12-1_S17


title: DAOY(3B6) MAGE-A11 Knockout C2

source_name: DAOY

value: DAOY


title: elf3-1-ZT8-2_S16

description:
lane: 140C
Mnase-seq
elf3-1-ZT8-2_S16


title: siHOXC4_siHOXC6_rep5

value: HOXC4 and HOXC6 knockdown


title: DAOY(3F5) MAGE-A11 Knockout C1


title: OV56 MAGE-A11 overexpression C2


title: OV56 MAGE-A11 overexpression C1


title: siHOXC4_siHOXC6_rep4


title: MB10 AH

description: mb10 ah

value: Abductor Hallucis Muscle


title: DAOY Wild type C2


title: elf3-1-ZT0-2_S14

description:
lane: 140C
Mnase-seq
elf3-1-ZT0-2_S14


title: DAOY Wild type C1


title: siHOXC4_siHOXC6_rep3


title: elf3-1-ZT0-1_S13

description:
lane: 140C
Mnase-seq
elf3-1-ZT0-1_S13


title: siHOXC4_siHOXC6_rep1


title: Col-0-ZT12-2_S6

description:
lane: 140C
Mnase-seq
Col-0-ZT12-2_S6

source_name: Col-0 seedlings


title: Col-0-ZT12-1_S5

description:
lane: 140C
Mnase-seq
Col-0-ZT12-1_S5


title: HEK293FT MAGE-A11 overexpression C2


title: Col-0-ZT8-2_S4

description:
lane: 140C
Mnase-seq
Col-0-ZT8-2_S4


title: HEK293FT MAGE-A11 overexpression C1


title: siHOXC6_rep5

value: HOXC6 knockdown


title: siHOXC4_siHOXC6_rep2


title: siHOXC6_rep4


title: HEK293FT vector control C2


title: HEK293FT vector control C1


title: elf3-1-ZT8-1_S15

description:
lane: 140C
Mnase-seq
elf3-1-ZT8-1_S15


title: Col-0-ZT8-1_S3

description:
lane: 140C
Mnase-seq
Col-0-ZT8-1_S3


title: s13152

source_name: Foreskin fibroblast

value: Fibroblast


title: siHOXC6_rep3


title: HEK293_tRNA_Ser_P15_rep3

description: HEK293 cells expressing the normal serine tRNA, in P15, replicate 3

source_name: HEK293 cells, in Passage 15, expressing the tRNASer(S) (wild type serine tRNA)


title: Col-0-ZT0-2_S2

description:
lane: 140C
Mnase-seq
Col-0-ZT0-2_S2


title: siHOXC6_rep1


title: siHOXC6_rep2


title: s13151


title: Col-0-ZT0-1_S1

description:
lane: 140C
Mnase-seq
Col-0-ZT0-1_S1


title: siHOXC4_rep5

value: HOXC4 knockdown


title: siHOXC4_rep4


title: siHOXC4_rep1


title: siHOXC4_rep2


title: siControl_rep3

value: siControl


title: siControl_rep4


title: siControl_rep5


title: siControl_rep2


title: standard dilution 5

type: protein

city: Urbana

first: Aidan

last: Gilchrist

state: IL

address: 1206 W Gregory Dr., suite 2200

institute: University of Illinois at Urbana-Champaign

description:
raw data files in .xlsx and .jpg format:
CYT4-1
CYT5-1
CYT6-1
CYT7-1
CYT8-1
standard 6

hyb_protocol: not provided

scan_protocol: The microarrays were sent to Raybiotech for imaging. URL=Http://www.perkinelmer.com/microarray .  Wavelength = 532. Velocity=35 l/s. laserPower=5.0. PMTGain=1.7976931348623157E308.

data_processing:
Fluorescence signal with background subtraction were translated to qualitative cytokoine concentrations via standard curve. Standard curves were generated by using the standard curve dilution with known concentrations. Outliers within the standard curve were deleted to improve R value.  Standard 3 was included on each slide to act as a normalization factor. Quantitative concentration results were extracted from the raw data using Q-analyzer software (Analysis Tool for QAM-CAA-4000, RayBiotech) with concentration values set within limits of detection.
Valeus are the concentration of the cytokine in pg/mL. These are extracted from the raw data using Q-analyzer software (Analysis Tool for QAM-CAA-4000, RayBiotech) with concentration values set within limits of detection.

label: Cy-3 equivalent dye-conjugated streptavidin

molecule: protein

organism: synthetic construct

source_name: cytokine standard mix

label_protocol: In brief, each well of the microarray was blocked and washed prior to incubation with 100 µL of sample overnight. The wells were then washed, incubated with a biotinylated antibody cocktail, and then incubated with a Cy3 equivalent dye-streptavidin. Each microarray also included a standard curve dilution for later quantitative analysis.

growth_protocol: HSPCs and MSPCs were cultured at increasing ratios of 1:0, 1:1, 1:10, 0:1, 0:10 (HSPCs:MSPCs) in 4, 5, 7.5 wt% methacrylamide-functionalized gelatin (GelMA) (49, 50) at constant crosslinking conditions (85% functionalization, 0.1% lithium acylphosphinate photoinitiator (PI), and 7.14 mW/cm2 UV light for 30 seconds). HSPC seeding density was kept constant at 1x105 HSPCs/mL, and cells were encapsulated in 5mm diameter hydrogels (20 µL) and cultured for 7 days in 300 µL SFEM media (#09650 Stemcell Technologies) supplemented with 100 ng/mL SCF (#250-03, Peprotech) and 0.1% PenStrep, changed every 2-days.

extract_protocol: Media was collected from each sample at day 2, 4, and 6 and store at -80°C for future use.

tag: day media collected

tag: block number in micrarray


title: standard dilution 4

description:
raw data files in .xlsx and .jpg format:
CYT4-1
CYT5-1
CYT6-1
CYT7-1
CYT8-1
standard 5


title: standard dilution 6

description:
raw data files in .xlsx and .jpg format:
CYT4-1
CYT5-1
CYT6-1
CYT7-1
CYT8-1
standard 7


title: siControl_rep1


title: 10882-44_21.100.4

city: Aberdeen

first: Claus

last: Mayer

address: Greenburn Road

institute: Biomathematics & Statistics Scotland

hyb_protocol: labelling and hybridisation of the RNA and the scanning was carried out by Service SX using the Affymetrix Rat230_2 GeneChip according to the manufacturer’s specifications.

scan_protocol: labelling and hybridisation of the RNA and the scanning was carried out by Service SX using the Affymetrix Rat230_2 GeneChip; the arrays are scanned following the GeneChip’s specifications using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The data were normalized using Bioconductor and a GCRMA method, a Robust Multiarray Analysis with correction for the G:C content of the oligos, and then statistically analysed using the Limma package, which allowed identification of the most differentially expressed genes between different conditions using a nominal p-value <0.05 to represent statistical significance.

label_protocol: labelling and hybridisation of the RNA and the scanning was carried out by Service SX using the Affymetrix Rat230_2 GeneChip and the GeneChip® 3' IVT Express labelling kit (cat. # 901229)

growth_protocol: A7r5 rattus norvegicus vascular smooth muscle cells were grown in cell culture medium containing 100ng/ml or 10ng/ml or 2.5ng/ml of folic acid for 7 days, 14 days or 21 days

extract_protocol: RNA was extracted with Trizol (Sigma) according to the manufacturer's instructions. The RNA was then treated with RNAse-free DNAse1 for 30min. at 37 C and then extracted with phenol/chloroform and precipitated with ethanol

treatment_protocol: the treatments with custom made DMEM medium reflect states of folate excess (100ng/ml), folate sufficiency (10ng/ml) or folate deficiency (2.5ng/ml)

value: vascular smooth muscle


title: standard dilution 3

description:
raw data files in .xlsx and .jpg format:
CYT4-1
CYT5-1
CYT6-1
CYT7-1
CYT8-1
standard 4


title: siHOXC4_rep3


title: standard dilution 2

description:
raw data files in .xlsx and .jpg format:
CYT4-1
CYT5-1
CYT6-1
CYT7-1
CYT8-1
standard 3


title: 10882-56_21.100.5


title: 10882-41_21.100.1


title: standard dilution 1

description:
raw data files in .xlsx and .jpg format:
CYT4-1
CYT5-1
CYT6-1
CYT7-1
CYT8-1
standard 2


title: standard

description:
raw data files in .xlsx and .jpg format:
CYT4-1
CYT5-1
CYT6-1
CYT7-1
CYT8-1
standard 1


title: 10882-52_21.10.2


title: 10882-35_21-2.5-6


title: 10882-42_21.100.2


title: 10882-29_14.100.4


title: 10882-33_21-2.5-4


title: 10882-34_21-2.5-5


title: 10882-30_14.100.5


title: 10882-55_21.100.3


title: 10882-38_21.10.4


title: 10882-37_21.10.3


title: 10882-32_21-2.5-3


title: 10882-31_21-2.5-2


title: 10882-50_14.100.6


title: 10882-54_14.100.3


title: HSC:MSC 1:1 high day 6

description:
raw data files in .xlsx and .jpg format:
CYT4-4
CYT5-4
CYT6-4
CYT7-4
CYT8-4
6.3

source_name: co-cuture HSC:MSC,1:1, high hydrogel day 6

value: day 6

tag: gelma wt%

tag: hsc

value: MSC seeding ratio (HSC=1x10^5 cells/mL):1:1


title: HSC:MSC 1:1 high day 2

description:
raw data files in .xlsx and .jpg format:
CYT4-4
CYT5-4
CYT6-4
CYT7-4
CYT8-4
6.1

source_name: co-cuture HSC:MSC,1:1, high hydrogel day 2

value: day 2


title: HSC:MSC 0:10 high 3

description:
raw data files in .xlsx and .jpg format:
CYT4-4
CYT5-4
CYT6-4
CYT7-4
CYT8-4
5.9

source_name: co-cuture HSC:MSC,0:10, high hydrogel

value: MSC seeding ratio (HSC=1x10^5 cells/mL):0:10


title: ZR-75-1 DEX 3

city: ADELAIDE UNIVERSITY

first: Geraldine

last: Laven-Law

state: South Australia

address: Adelaide Health & Med Sci Bldg, Corner George St & North Terrace

institute: The University of Adelaide

description: gene expression data from treated ZR-75-1 cells

hyb_protocol: Samples were hybridised to Affymetrix Human Gene 2.0 ST Arrays for 17 hours at 45 degrees Celsius prior to washing, staining and scanning.

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000 Targeted Genotyping System according the manufacturer's protocol.

data_processing: Data was analysed using Partek Genomics Suite. Briefly, .cel files were imported using RMA background correction, Partek’s own GC content correction, and mean probe summarization. Differential gene expression was assessed by ANOVA with the p value adjusted using step-up [Benjamini Y, Hochberg Y.  J R Statist Soc B. 1995;57:289–300] multiple test correction to control the false discovery  rate.  Adjusted p values < 0.05  were considered to be significant.

source_name: breast cancer cell line

label_protocol: 300ng of total RNA was linearly amplified and converted to cDNA using the Ambion WT Expression Kit and then fragmented and labelled using the Affymetrix WT Terminal Labelling and Controls Kit, both as per manufacturer's instructions.

growth_protocol: ZR-75-1 cells were grown in regular growth media (RPMI-1640 + 10% FBS).

extract_protocol: TRIzol reagent was used to extract RNA, which was then purified with the RNeasy Mini Kit and its integrity confirmed using the Experion Automated Electrophoresis System.

treatment_protocol: ZR-75-1 cells were treated for 6h with either vehicle (0.1% ethanol) or 10nM MPA, PROG, DHT or DEX.

value: 10 nM DEX


title: 10882-50_21.10.6


title: 10882-36_21.10.1


title: 10882-53_14.100.1


title: HSC:MSC 0:10 high 2

description:
raw data files in .xlsx and .jpg format:
CYT4-4
CYT5-4
CYT6-4
CYT7-4
CYT8-4
5.8


title: HSC:MSC 1:1 high day 4

description:
raw data files in .xlsx and .jpg format:
CYT4-4
CYT5-4
CYT6-4
CYT7-4
CYT8-4
6.2

source_name: co-cuture HSC:MSC,1:1, high hydrogel day 4

value: day 4


title: HSC:MSC 0:10 med 3

description:
raw data files in .xlsx and .jpg format:
CYT4-4
CYT5-4
CYT6-4
CYT7-4
CYT8-4
5.6

source_name: co-cuture HSC:MSC,0:10, med hydrogel


title: HSC:MSC 0:10 high 1

description:
raw data files in .xlsx and .jpg format:
CYT4-4
CYT5-4
CYT6-4
CYT7-4
CYT8-4
5.7


title: ZR-75-1 DEX 1


title: HSC:MSC 0:10 med 1

description:
raw data files in .xlsx and .jpg format:
CYT4-4
CYT5-4
CYT6-4
CYT7-4
CYT8-4
5.4


title: HSC:MSC 0:10 med 2

description:
raw data files in .xlsx and .jpg format:
CYT4-4
CYT5-4
CYT6-4
CYT7-4
CYT8-4
5.5


title: ZR-75-1 DHT 2

value: 10 nM DHT


title: 10882-22_14.10.5


title: HSC:MSC 0:10 low 3

description:
raw data files in .xlsx and .jpg format:
CYT4-4
CYT5-4
CYT6-4
CYT7-4
CYT8-4
5.3

source_name: co-cuture HSC:MSC,0:10, low hydrogel


title: ZR-75-1 DEX 2


title: 10882-49_14.10.4R


title: ZR-75-1 DHT 1


title: ZR-75-1 PROG 3

value: 10 nM PROG


title: 10882-22_14.10.2


title: ZR-75-1 PROG 2


title: ZR-75-1 DHT 3


title: 10882-48_14-2.5.5


title: HSC:MSC 0:10 low 1

description:
raw data files in .xlsx and .jpg format:
CYT4-4
CYT5-4
CYT6-4
CYT7-4
CYT8-4
5.1


title: ZR-75-1 PROG 1


title: HSC:MSC 0:10 low 2

description:
raw data files in .xlsx and .jpg format:
CYT4-4
CYT5-4
CYT6-4
CYT7-4
CYT8-4
5.2


title: ZR-75-1 MPA 2

value: 10 nM MPA


title: 10882-21_14.10.1


title: ZR-75-1 MPA 3


title: 10882-22_14.10.3


title: 10882-17_14-2.5-2


title: HSC:MSC 0:1 high 3

description:
raw data files in .xlsx and .jpg format:
CYT4-4
CYT5-4
CYT6-4
CYT7-4
CYT8-4
4.9

source_name: co-cuture HSC:MSC,0:1, high hydrogel

value: MSC seeding ratio (HSC=1x10^5 cells/mL):0:1


title: 10882-20_14-2.5-6


title: 10882-16_14-2.5-1


title: 10882-18_14-2.5-3


title: ZR-75-1 vehicle 3 (untreated)

description: gene expression data from untreated ZR-75-1 cells

value: vehicle (untreated)


title: ZR-75-1 MPA 1


title: Embyonic Mouse Cardiomyocytes_16% stretch sample C

city: Seattle

first: Vishal

last: Nigam

state: WA

address: 1900 9th Ave

institute: Seattle Childrens Research Institute

data_processing:
RNA sequences of 18-30 nt were mapped to the mouse transcriptome using the Bowtie2 aligner.
Gene counts were normalized using DESeq
Parametric p-values were adjusted for multiple testing using R package qvalue
Supplementary_files_format_and_content: logConc Log2(16/ST)

source_name: E16.5 mouse cardiomyocytes_cyclic stretch

growth_protocol: E16.5 mouse cardiomyocytes were cultured on collagen 1 coated Bioflex plates.

extract_protocol:
RNAeasy columns were used to isolate the RNA
TruSeq Small RNA protocol was used for library prep. Only RNA samples with RNA integity number >8 were used.
miRNA-Seq was performed using a Illumina HiSeq2500

treatment_protocol: Cells were exposed to cyclic stretch of 16% at 1Hz for 24 h or static conditions

tag: strain background

value: Swiss Webster

tag: genotype/variation

value: wild type

tag: developmental stage

value: cardiomyocytes

value: exposed to cyclic stretch of 16% at 1Hz for 24h


title: 10882-13_7.100.3

tag: cell type


title: HSC:MSC 0:1 high 1

description:
raw data files in .xlsx and .jpg format:
CYT4-3
CYT5-3
CYT6-3
CYT7-3
CYT8-3
4.7


title: 10882-14_7.100.4


title: Embyonic Mouse Cardiomyocytes_16% stretch sample B

tag: treatment


title: ZR-75-1 vehicle 2 (untreated)


title: HSC:MSC 0:1 med 3

description:
raw data files in .xlsx and .jpg format:
CYT4-3
CYT5-3
CYT6-3
CYT7-3
CYT8-3
4.6

source_name: co-cuture HSC:MSC,0:1, med hydrogel


title: 10882-47_7.100.6


title: ZR-75-1 vehicle 1 (untreated)


title: Embyonic Mouse Cardiomyocytes_Static control C

source_name: E16.5 mouse cardiomyocytes_static condition

value: cultured under static conditions for 24h


title: Embyonic Mouse Cardiomyocytes_16% stretch sample A


title: HSC:MSC 0:1 med 1

description:
raw data files in .xlsx and .jpg format:
CYT4-3
CYT5-3
CYT6-3
CYT7-3
CYT8-3
4.4


title: HSC:MSC 0:1 low 3

description:
raw data files in .xlsx and .jpg format:
CYT4-3
CYT5-3
CYT6-3
CYT7-3
CYT8-3
4.3

source_name: co-cuture HSC:MSC,0:1, low hydrogel


title: 10882-11_7.100.1

value: vascular smooth muscle


title: HSC:MSC 0:1 med 2

description:
raw data files in .xlsx and .jpg format:
CYT4-3
CYT5-3
CYT6-3
CYT7-3
CYT8-3
4.5


title: HSC:MSC 0:1 high 2

description:
raw data files in .xlsx and .jpg format:
CYT4-3
CYT5-3
CYT6-3
CYT7-3
CYT8-3
4.8


title: Embyonic Mouse Cardiomyocytes_Static control B


title: Embyonic Mouse Cardiomyocytes_Static control A


title: HSC:MSC 0:1 low 2

description:
raw data files in .xlsx and .jpg format:
CYT4-3
CYT5-3
CYT6-3
CYT7-3
CYT8-3
4.2


title: KO-1

city: Seoul

first: Young-Gyu

last: Ko

address: 145, Anam-ro, Seongbuk-gu

department: Division of Life Sciences

country: South Korea

institute: Korea University

data_processing:
Illumina NextSeq 500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to mm10 whole genome using STAR (version 2.5.0) with parameters -outFilterIntronMotifs RemoveNoncanonicalUnannotated.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by Cufflinks packages (version 2.2.1).
Differentially expressed genes were detected using Cuffdiff (version 2.2.1) against Ensemble genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Primary hepatocyte

growth_protocol: Primary hepatocytes were isolated from the liver and grown in 199 medium containing 10% FBS, 23 mM HEPES and 10 nM dexamethasone for 4 hours before removing serum.

extract_protocol:
Total RNA extraction was performed using TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions.
The quantity and quality of the total RNA were evaluated using Agilent 2100 bioanalyzerRNA kit (Agilent). The isolated total RNA was processed for preparing mRNA sequencing library using the Illumina TruSeqStranded mRNA Sample Preparation kit (Illumina), according to the manufacturer's protocol.

treatment_protocol: Primary hepatocytes were incubated in serum-free growth medium for overnight.

tag: strain

value: Liver

tag: age

value: 8 weeks

tag: genotype


title: KO-2


title: 10882-09_7.10.4


title: WT-2


title: HSC:MSC 1:10 high 3

description:
raw data files in .xlsx and .jpg format:
CYT4-3
CYT5-3
CYT6-3
CYT7-3
CYT8-3
3.9

source_name: co-cuture HSC:MSC,1:10, high hydrogel

value: MSC seeding ratio (HSC=1x10^5 cells/mL):1:10


title: HSC:MSC 1:10 high 1

description:
raw data files in .xlsx and .jpg format:
CYT4-3
CYT5-3
CYT6-3
CYT7-3
CYT8-3
3.7


title: HSC:MSC 1:10 high 2

description:
raw data files in .xlsx and .jpg format:
CYT4-3
CYT5-3
CYT6-3
CYT7-3
CYT8-3
3.8


title: HSC:MSC 0:1 low 1

description:
raw data files in .xlsx and .jpg format:
CYT4-3
CYT5-3
CYT6-3
CYT7-3
CYT8-3
4.1


title: WT-1


title: 10882-07_7.10.2


title: cDNA6421_7187_DETC

city: Dallas

first: Uthra

last: Balaji

state: Texas

address: 3434 Live Oak St

department: Biostatistics Core

institute: Baylor Scott & White Research Institute

data_processing:
RNAseq reads trimmed and aligned to mouse genome
Normalization and differential gene  expression (DGE) analysis was performed using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: csv file includes normalized counts

molecule: polyA RNA

source_name: epidermis

extract_protocol:
Total RNA was isolated from cell lysates using the RNeasy Micro Kit (Qiagen) including on column DNase digestion. Total RNA was analyzed for quantity and quality using the RNA 6000 Pico Kit (Agilent).
Poly-A enriched NGS library construction was performed using the KAPA mRNA Hyper Prep Kit (KAPA Biosystems) using 50ng of input total RNA according to manufacturer’s protocol using 16 amplification cycles. Quality of the individual libraries was assessed using the High Sensitivity DNA Kit (Agilent). Individual libraries were quantitated via qPCR using the KAPA Library Quantification Kit, Universal (KAPA Biosystems) and equimolar pooled. Final pooled libraries were sequenced on an Illumina NextSeq 500 with paired-end 75 base read lengths

tag: condition

value: DTA

value: DETC

tag: gender

value: female


title: 10882-10_7.10.5


title: pMEF_Pol_II_ChIPseq

city: Taipei

first: Wei-Yi

last: Chen

address: No. 155, Sec 2, Linong St.

department: Institute of Biochemistry and Molecular Biology

institute: National Yang Ming Chiao Tung University

description: ChIPed genomic DNA

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the mm9 murine genome assembly using bowtie version 1.12 with with parameters "-n 2 -m 1 -l 36 --best".
Potential PCR duplicates in ChIP-seq reads were removed using samtools rmdup command.
Tiled data files (TDF) were generated by igvtools with parameters "-z 5 -w 10 -e 200" for ChIP-seq.
peak calling performed using MACS (RNA Pol II) or HOMER package (POLR3C, POLR3G, and POLR3GL)
Genome_build: mm9
Supplementary_files_format_and_content: Tiled data files (TDF) for input and ChIP samples.

source_name: primary MEF

growth_protocol: ES-E14TG2a cells were cultured on 0.1% gelatinized tissue-culture plates in complete ESC growth medium (Gibco) supplemented with LIF and 10% ES-certificated fetal bovine serum at 37 °C. Primary MEFs were derived from E12.5 embryos, maintined in ESC growth medium supplemented with 10% FBS (without LIF), and passaged 3 to 5 times prior to ChIP-seq analyses.

extract_protocol:
Chromatin lysates were prepared by sonication and protein-DNA complexes were isolated with ~10 ug of indicated antibodies and 100 μL Dynal protein G matrix. ChIPed DNA fragments were recovered using a PCR purification kit from Qiagen and ~10 ng DNA were submitted to the Epigenomic Core Facility at Weill Cornell Medical Colleage for library construction and high throughput sequencing.
Multiplexing libraries were prepared for sequencing using Illumina TruSeq Rapid SR Cluster Kit according to the standard protocol.

treatment_protocol: Cells were fixed and harvested at 80% confluency. For each ChIP-seq assay, 30-50 million E14tg2A or primary MEFs were used. Chromatin was prepared from isolated nuclei and sonicated to an average size of 200 ~700 bp in FA lysis buffer (50 mM Hepes, pH 7.5, 150 mM NaCl, 1 mM EDTA, 0.1 % SDS, 0.1 % Na-deoxycholate, and 1X Complete protease inhibitor [Roche])

value: primary Mouse Embryonic Fibroblast

tag: biomaterial provider

value: in-house isolated

tag: chip antibody

value: anti-RNA Pol II (N-20), sc-889, Santa Cruz Biotech


title: pMEF_input

description: genomic DNA


title: cDNA6419_7185_DETC

value: WT


title: 10882-46_7.10.6

tag: tissue


title: 10882-06_7.10.1


title: 10882-05_7-2.5-6


title: pMEF_POLR3GL_ChIPseq

description: ChIPed genomic DNA

value: anti-POLR3GL, in-house antibody, Roeder Lab


title: 10882-04_7-2.5-5


title: 10882-02_7-2.5-2


title: HSC:MSC 1:10 med 2

description:
raw data files in .xlsx and .jpg format:
CYT4-3
CYT5-3
CYT6-3
CYT7-3
CYT8-3
3.5

source_name: co-cuture HSC:MSC,1:10, med hydrogel

tag: day media collected


title: cDNA6418_7184_DETC


title: HSC:MSC 1:10 low 3

description:
raw data files in .xlsx and .jpg format:
CYT4-2
CYT5-2
CYT6-2
CYT7-2
CYT8-2
3.3

source_name: co-cuture HSC:MSC,1:10, low hydrogel

tag: block number in micrarray


title: cDNA6416_7182_DETC


title: pMEF_POLR3C_ChIPseq

description: ChIPed genomic DNA

value: anti-POLR3C, in-house antibody, Roeder Lab


title: HSC:MSC 1:10 med 3

description:
raw data files in .xlsx and .jpg format:
CYT4-3
CYT5-3
CYT6-3
CYT7-3
CYT8-3
3.6

tag: gelma wt%


title: cDNA6415_7187_KC

value: KC


title: 10882-01_7-2.5-1


title: HSC:MSC 1:10 low 1

description:
raw data files in .xlsx and .jpg format:
CYT4-2
CYT5-2
CYT6-2
CYT7-2
CYT8-2
3.1

tag: hsc


title: ES_input

description: genomic DNA

value: Embryonic Stem Cell

value: ATCC CRL-1821


title: cDNA6413_7185_KC


title: cDNA6420_7186_DETC


title: ES_Pol_II_ChIPseq

description: ChIPed genomic DNA


title: HSC:MSC 1:10 med 1

description:
raw data files in .xlsx and .jpg format:
CYT4-3
CYT5-3
CYT6-3
CYT7-3
CYT8-3
3.4


title: HSC:MSC 1:1 high 3

description:
raw data files in .xlsx and .jpg format:
CYT4-2
CYT5-2
CYT6-2
CYT7-2
CYT8-2
2.9

source_name: co-cuture HSC:MSC,1:1, high hydrogel

value: MSC seeding ratio (HSC=1x10^5 cells/mL):1:1


title: cDNA6412_7184_KC


title: ES_POLR3C_ChIPseq

description: ChIPed genomic DNA


title: pMEF_POLR3G_ChIPseq

description: ChIPed genomic DNA

value: anti-POLR3G, in-house antibody, Roeder Lab


title: HSC:MSC 1:1 high 1

description:
raw data files in .xlsx and .jpg format:
CYT4-2
CYT5-2
CYT6-2
CYT7-2
CYT8-2
2.7


title: Input_Rep3

city: La Jolla

first: Tomas

last: Duffy

address: 10550 N Torrey Pines Rd

institute: TSRI

data_processing:
ChIP-seq tags of FoxO1 were aligned against the reference human genome hg19 using Bowtie2
peaks were called using PePr
Genome_build: hg19

source_name: Input

growth_protocol: 10^6 freshly isolated chondrocytes were plated on a 15 cm dish and cross-linked when 90% confluent.

extract_protocol:
FoxO1-DNA complexes were isolated with antibody.
For library preparation, 10 ng of each sample was prepared using the NEB Ultra DNA Library Prep Kit for Illumina following manufacturer’s instructions.

tag: donor status

value: total knee replacement surgery patient

value: primary chondrocytes