title: FK.unlab

city: Worcester

first: Huan

middle: Raya

last: Shu

address: 373 Plantation St

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description:
Drosophila melanogaster, Saccharomyces cerevisiae
INSPEcTrates
LimmaDiff_Deg
LimmaDiff_Syn
LimmaDiff_Pro

data_processing:
reads were separated based on sample barcode sequences using in-house codes
known 3’ adapter sequences and low quality bases were removed with Cutadapt(Martin, 2011) using parameters -O 2 -q 15 -a “TGGAATTCTCGGGTGCCAAGGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG”
reads mapped to rRNA and tRNA genes were removed using Bowtie2(Langmead and Salzberg, 2012) with parameter -N 1
remaining reads were mapped to the mm10 + dm6 + sacCer3 combined genome using TopHat2(Kim et al., 2013)
PCR duplicates were removed based on Unique Molecular Identifier sequences using in-house codes
RPKM of mouse transcripts were calculated using the reads uniquely mapped to the mm10+dm6+sacCer3 genome. Filtering thresholds were identified for WT and FK at 0.95 and 1.05 RPKM, respectively. Genes were filtered for those that had RPKM higher than threshold in input (i.e., that are expressed) and lower than threshold in unlab libraries.
Uniquely mapped reads that are depleted of rRNA, tRNA sequences and PCR duplicates were again mapped to mm10 genome with hisat2. Intron and exon read quantification, and RNA metabolism rates (synthesis, processing and degradation) estimation was performed using INSPEcT(de Pretis et al., 2015) (v1.10.0), with the degDuringPulse parameter set to TRUE.
For the genes that survived filtering, raw RNA metabolism rates estimated by INSPEcT were normalized between libraries A and B for WT and FK neurons separately using the limma package(Ritchie et al., 2015) with the “cyclicloess” method.
After normalization, genes with different metabolism rates were tested using the limma package.
Genome_build: mm10, dm6, sacCer3
Supplementary_files_format_and_content: tab delimited values include raw RNA metabolism rates estimated by INSPEcT for WT and FK neurons respectively (INSPEcTrates) and differential analysis of RNA synthesis, processing and degradation rates between WT and FK by Limma after normalization (LimmaDiff_Syn, LimmaDiff_Pro, LimmaDiff_Deg)

source_name: mouse cortical neurons

growth_protocol: Cortical cell suspension were obtained by dissociating cerebral cortices from E18 embryos using the Papain Dissociation System (Worthington, cat. no. LK003150). One million live cells were plated in 5 ml complete Neurobasal culture medium (Neurobasal™ Medium (Gibco, cat. no. 21103049), 1x B-27 supplement (Gibco, cat. no. 17504044), 1x Antibiotic‐Antimycotic (Gibco, cat. no. 15240096), 1x GlutaMAX (Gibco, cat. no. 35050061)) per 60 mm poly-L-lysine treated cell culture dish. Neurons were fed by half-replacing the complete Neurobasal culture medium twice per week for 14 days.

extract_protocol:
Neuronal RNA was extracted by lysing using Trizol directly
Five-EU labeled RNA was enriched and RNA-seq library was prepared by adapting the Coller lab (Case Western Reserve University) protocol (personal communication). Specifically, mouse neuron RNA was spiked-in with 10% (w/w) 5-EU labeled fly RNA and 10% (w/w) yeast RNA. The mixed RNA was depleted of rRNA using the Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) and fragmented using NEBNext® Magnesium RNA Fragmentation Module (NEB, cat. no. E6150S) for 5 min. RNA samples for libraries unlab, A and B were biotinylated by Click-iT chemistry and pulled-down using the Click-iT™ Nascent RNA Capture Kit. The pulled-down samples, together with the input sample, were subjected to library construction the same as for ribosome profiling libraries(Heyer et al., 2015). Here, for the pulled-down samples, all reactions were performed directly on beads until after the reverse transcription step. Sequencing library fraction with insert size 50-200nt was collected and sequenced with Illumina NextSeq
RNA labeled with 5EU clicked to biotin, enriched, followed by RNA-seq

treatment_protocol: DIV14 neurons were incubated with 200 µM 5-EU (Click-iT™ Nascent RNA Capture Kit, Invitrogen, cat. no.  C10365) for 0 (input and “unlab”), 20 (“A”), and 60 (“B”) min before RNA was collected.

value: DIV 14

value: FVB.129P2-Pde6b+ Tyrc-ch/AntJ

tag: experiment

value: RNA-seq of enriched unlabeled mouse neuron RNA, with D melanogaster (5EU labeled) and S cerevisiae (unlabeled) as spike-in


title: FK.input.rep2

status: Public on Jun 01 2020

type: SRA

state: MA

country: USA

description: Drosophila melanogaster, Saccharomyces cerevisiae

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: developmental stage

tag: genotype

tag: strain

value: RNA-seq of unenriched mouse neuron RNA, with D melanogaster (5EU labeled) and S cerevisiae (unlabeled) as spike-in


title: 31-V4020-P2

city: Louisville

first: Dylan

middle: MacGregor

last: Johnson

state: KY

address: 505 S Hancock St., CTRB RM642B

department: Microbiology & Immunology

institute: University of Louisville, School of Medicine

description: rRNA depleted total RNA

data_processing:
Trimmomatic (Galaxy Version 0.36.6) Sliding window trimming across 4 average bases with 20 average quality required
Bowtie2 (Galaxy Version 2.3.4.2) Alignment to TC-83 or V4020 reference sequence with default settings, unaligned reads to new fastq file
Samtools mpileup (Galaxy Version 2.1.4) on Bowtie2 BAM files with TC-83 or V4020 reference sequence
Filter pileup (Galaxy Version 1.0.2)
HiSat2 (Galaxy Version 2.1.0) alginment of unalinged reads fastq from Bowtie2 to mm10 genome
htseq-count (Galaxy version 0.9.1) on HiSat2 alignment
DESeq2 (Galaxy Version 2.11.40.2) both by passage and with a virus x passage facor model
goseq (Galaxy Version 1.26.0)
Genome_build: L01443.1
Genome_build: mm10
Supplementary_files_format_and_content: Excel spreadsheet containing filtered pileup data from each virus alignment. Also includes analysis of mutation rate, read depth, and nucleotide variation.
Supplementary_files_format_and_content: Excel spreadsheet containing the output from DESeq2 showing differential expression from both a "virus x passage" model and each individual passage, along with normalized read counts.

source_name: brain

growth_protocol: BALB/c mice were inoculated via the intracranial route with 10^5 PFU of serial passaged VEEV strain V4020 or strain TC-83. Two days post inoculation, mice were sacrificed and brain tissue was collected in Trizol reagent for total RNA isolation.

extract_protocol:
Tissue was placed in 1 ml trizol (ThermoFisher #15596018) with glass beads,  homogenized on an omni bead-beater, and isolated with BCP according to the manufactuer's protocol.
RNA was DNAse I treated (Zymo Research, #E1010) and purified with an Rneasy mini kit (Quiagen, #74104) followed by rRNA depletion (NEB, #E6310), and Illumina library prep (NEB, #7775).

value: BALB/c

tag: veev strain

value: VEEV strain V4020

tag: tissue

value: Brain

tag: passage

value: Passage 2


title: 82-V4020-P4

description: rRNA depleted total RNA

value: Passage 4


title: Sample 1522_Single mESC cell

city: Stanford

first: Alina

last: Isakova

state: CA

address: 318 Campus drive

department: Bioengineering

institute: Stanford University

data_processing:
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.19.0.316. Reads were trimmed from polyA tails using cutadapt v 1.18 with the following parameters: -m 18 -j 4 -a AAAAAAAAAA -a TTTTTTTTTT. Reads were then aligned to the human (GRCh38) or mouse genome (GRCm38) using STAR v2.7.0d 37 with the following parameters --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 18 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0  --outMultimapperOrder Random. Reads mapping to multiple locations were assigned either to a location with the best mapping score or, in the case of equal multimapping score – to the genomic location randomly chosen as “primary”.
Genome_build: GRCm38, GRCh38
Supplementary_files_format_and_content: tab-delimited text files of count tables

source_name: Single mESC cell

growth_protocol: HEK293T cells were cultured in complete DMEM high glucose medium (Gibco, ThermoFisher 11965092) supplemented with 5% Fetal Bovine Serum (ThermoFisher 16000044), 1mM Sodium Pyruvate (ThermoFisher 11360070) and 100 μg/mL Pencillin/Streptomycin (ThermoFisher 15070063). They were collected 2h after passaging and sorted in either 96-well plates with 3uL lysis buffer or 384-well paltes with 0.3 uL of lysis buffer in each well.    Human primary dermal fibroblasts were obtained from ATCC (ATCC® PCS-201-012™). Cells were cultured and passaged four times in Fibroblast Basal Medium (ATCC® PCS-201-030™) supplemented with 5ng/mL rh FGF β, 7.5mM L-glutamine, 50 ug/mL Ascorbic acid, 5ug/mL rh Insulin, and 1% Fetal Bovine Serum (Fibroblast Growth kit- low serum, ATCC® PCS-201-041™).  MCF7 cells (ATCC® HTB¬22™) were cultured in complete DMEM high glucose medium (Gibco, ThermoFisher 11965092) supplemented with 10% Fetal Bovine Serum (ThermoFisher 16000044), 1mM Sodium Pyruvate (ThermoFisher 11360070) and 100 μg/mL Pencillin/Streptomycin (ThermoFisher 15070063).  mESCs were maintained and differentiated as described previously35,36. Briefly, mESCs were grown in serum-free 2i+LIF medium (complete medium: DMEM/F12 glutaMAX (Gibco, ThermoFisher  10565018) , 1% N2 supplement (Gemini Bio), 2% B27 supplement (Gemini Bio), 0.05% BSA fraction V (ThermoFisher, 15260037), 1% MEM-non-essential amino acids (c  11140050), and 110 μM 2-mercaptoethanol (Pierce); supplemeted with MEK inhibitor PD0325901 (0.8 μM), GSK3β inhibitor CHIR99021 (3.3 μM) and 10ng/mL mouse LIF (Gibco, PMC9484) in tissue culture (TC) dishes pretreated with 7.5 μg/ml polyL-ornithine (Sigma) and 5 μg/ml laminine (BD). To induce spontaneous embryoid body formation cells were washed with PBS, dissociated with StemPro Accutase (Gibco, ThermoFisher cat# A1110501), transferred to serum-rich medium (complete medium: DMEM/F12 glutaMAX (Gibco) , 1% N2 supplement (Gemini Bio), 2% B27 supplement (Gemini Bio), 0.05% BSA fraction V, 1% MEM-non-essential amino acids, and 110 μM 2-mercaptoethanol; supplemented with 10% FBS (ThermoFisher 10439001) and diluted to 10^6 cells/mL. Each 10 uL of cell suspension were plated as a hanging drop in 10 cm2 TC dishes (15-20 drops per dish). 10uL of fresh serum-rich media was added to each drop on day 4 of the culture. Primed mESCs were collected 6h after hanging drop culture. Embryoid bodies were collected and dissociated at days 4, 8 and 12 of culture.

extract_protocol:
Lysis plates were prepared by dispensing 0.3μL lysis buffer (4 U Recombinant RNase Inhibitor (RRI) (Takara Bio, 2313B), 0.12% TritonTM X-100 (Sigma, 93443-100ML), 1μM Smart-seq4 oligo-dT primer (5’-Biotin- /5BiosG/CATAGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGT30VN-3’;IDT) (see Supplementary Table 3 for a full list of oligos used in the present study) into 384-well hard-shell PCR plates (Bio-Rad HSP3901) using Mantis liquid handler (Formulatrix). 96-well lysis plates were prepared with 3 μl lysis buffer. All plates were sealed with AlumaSeal CS Films (Sigma-Aldrich Z722634), spun down and snap-frozen on dry ice.   Cells were stained with calcein-AM and ethidium homodimer-1 (LIVE/DEAD® Viability/Cytotoxicity Kit, ThermoFisher L3224) and individual live cells were sorted in 384 well lysis plates using SONY sorter (SH800S) with 100um nozzle chip. Plates were spun down and stored at -80 degrees immediately after sorting.
Smart-seq-total

tag: cell line

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: FK.5EU20min

value: RNA-seq of enriched 5EU labeled (20min) mouse neuron RNA, with D melanogaster (5EU labeled) and S cerevisiae (unlabeled) as spike-in


title: Lkyn_Uncut_3_2

city: Rehovot

first: Idan

last: Efroni

address: POB 12

department: Plant Sciences

country: Israel

institute: Hebrew University

data_processing:
Reads were aligned to the genome using Bowtie2, followed by readcount using htseq-count
Expression data were normalized using Deseq2
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: Normalized expression reads for all replicates

organism: Arabidopsis thaliana

source_name: Apical root meristem

growth_protocol: Seedslings were germinated on 1/2MS agar plates containing 0.5% sucrose. Following 2 days at 4c, plates were move to a 22c for 16h light/8h dark cycle for 7 days

extract_protocol:
Root tips were flash frozen, grinded and RNA extracted using RNeasy micro-kit (Qiagen) according to the manufacturer instructions
sequencing libraries prepared using Lexigen 3’ Quant-Seq kit, according to the manufacturer instructions.

treatment_protocol: For L-Kyn treatments, 7 days old seedlings were

tag: treatment

value: L-kyn 3h


title: WT.unlab

value: wild type


title: Lkyn_Uncut_3_1


title: FK.input.rep1


title: Mock_Uncut_2

value: mock


title: WT.5EU20min

description:
Mus musculus
INSPEcTrates
LimmaDiff_Deg
LimmaDiff_Syn
LimmaDiff_Pro


title: WT.input.rep1


title: FK.5EU1hr

value: RNA-seq of enriched 5EU labeled (1hr) mouse neuron RNA, with D melanogaster (5EU labeled) and S cerevisiae (unlabeled) as spike-in


title: WT.input.rep2


title: WT.5EU1hr


title: Sample 1519_Single mESC cell


title: Mock_Uncut_1


title: Sample 1518_Single mESC cell


title: rep2_RPF_CK

description:
processed data file:
RPFDEseq_2KxCK
RPFDEseq_CKxWT
RPFDEseq_FKxCK
ROXtail_2KxCK
ROXtail_CKxFK
ROXtail_CXxWT

data_processing:
library strategy: ribosom profiling
reads were separated based on sample barcode sequences using in-house codes
known 3’ adapter sequences and low quality bases were removed with Cutadapt(Martin, 2011) using parameters -O 2 -q 15 -a “TGGAATTCTCGGGTGCCAAGGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG”
reads mapped to rRNA and tRNA genes were removed using Bowtie2(Langmead and Salzberg, 2012) with parameter -N 1
remaining reads were mapped to the mm10 genome using TopHat2(Kim et al., 2013)
PCR duplicates were removed based on Unique Molecular Identifier sequences using in-house codes
Uniquely mapped reads were then used as input to RSEM(Li and Dewey, 2011) for quantification of gene expression and either mapped to RefSeq (v69) mouse coding sequences (RPF) or to whole-transcriptome (RNA-seq). Genes were filtered to have a minimum of 10 TPM (transcripts per million) in at least one sample.
We used log transformed TPM expression values to correct for batch effects using ComBat(Leek et al., 2012) (v3.18.0).
Corrected values were transformed back to read counts using the expected size of each transcript informed by RSEM.
Batch-corrected counts were used to identify differentially translated/expressed genes with DESeq2(Love et al., 2014, p. 2) (RPF and RNA) or Xtail10 (ribosome occupancy, RO).
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited values include RSEM quantification of all mm10 genes (*.genes.results.txt) and differential expression analysis generated by DEseq2 (RNADEseq_* and RPFDEseq_*) or Xtail (ROXtail_*)

source_name: Cpeb1 single KO_brain cortex

growth_protocol: All mice were maintained in a temperature- (25°C), humidity- (50–60%) and light-controlled (12 hr light-dark cycle) and pathogen-free environment

extract_protocol:
The brain was rapidly removed from P28–P35 mice, rinsed in ice-cold dissection buffer (1× HBSS + 10 mM HEPES-KOH), rapidly dissected in dissection buffer ice-liquid mixture to collect cerebral cortex as described previously(Stefani et al., 2004). Both cortex hemispheres were homogenized in 900µl of homogenization buffer(Stefani et al., 2004) (10 mm HEPES-KOH, pH 7.4, 150 mm KCl, 5 mm MgCl2, 0.5 mm DTT, 100 µg/ml cycloheximide and 2 µg/ml harringtonine), containing protease and phosphatase inhibitors (cOmplete, EDTA-free Protease Inhibitor Cocktail and PhosSTOP from Roche/Sigma, cat. no. 11836170001 and 4906837001), in a pre-chilled 2-mL glass Dounce homogenizer, 20 strokes loose, 20 strokes tight, and centrifuged at low speed (2000 rcf 10 min 4°C) to pellet insoluble material(Udagawa et al., 2013). Five hundred microliters of the resulted ~700µl supernatant (cytoplasmic lysate) were used for ribosome profiling, the rest for RNA-seq. For ribosome profiling, the lysate was digested by 60 U RNase T1 (Thermo Scientific, cat. no. EN0541) and 100ng RNase A (Ambion, cat. no. AM2270) per A260 unit(Cenik et al., 2015) for 30 min at 25°C with gentle mixing. Digestion was stopped by adding 30 µl SUPERase·In (Invitrogen, cat. no. AM2694). Digested lysate was separated by sedimentation through sucrose gradients. Monosome fractions were identified, pooled, and extracted with TRIzol LS (Invitrogen, cat. no. 10296028). For RNA-seq, cytoplasmic RNA was extracted from the lysate using TRIzol LS. Ten micrograms of RNA were depleted of rRNA using Ribo-Zero Gold rRNA Removal Kit, Human/Mouse/Rat (illumina, discontinued), and fragmented by incubating with PNK buffer (NEB, cat. no. M0201S) for 10 min at 94°C. Fragmented RNA as separated on 15% urea-polyacrylamide gel, and 50-60nt fraction was collected.
Ribosome profiling and RNA-seq libraries were prepared following published protocols(Heyer et al., 2015)

tag: strain background

value: FVB.129P2-/Pde6b^+ Tyr^c-ch //AntJ

tag: genotype/variation

value: Cpeb1 single KO

value: mouse brain cortex

value: ribosome profiling

tag: molecule subtype

value: ribosome protected RNA footprint


title: rep2_RPF_FK

description:
processed data file:
RPFDEseq_2KxFK
RPFDEseq_FKxCK
RPFDEseq_FKxWT
ROXtail_2KxFK
ROXtail_CKxFK
ROXtail_FXxWT

source_name: Fmr1 single KO_brain cortex

value: Fmr1 single KO


title: rep2_RPF_2K

description:
processed data file:
RPFDEseq_2KxCK
RPFDEseq_2KxFK
RPFDEseq_2KxWT
ROXtail_2KxCK
ROXtail_2KxFK
ROXtail_2XxWT

source_name: Fmr1/Cpeb1 double KO_brain cortex

value: Fmr1/Cpeb1 double KO


title: Sample 1521_Single mESC cell


title: Mock_Uncut_3


title: Sample 1520_Single mESC cell


title: Sample 1517_Single mESC cell


title: rep1_RPF_WT

description:
processed data file:
RPFDEseq_2KxWT
RPFDEseq_CKxWT
RPFDEseq_FKxWT
ROXtail_2XxWT
ROXtail_CXxWT
ROXtail_FXxWT

source_name: wild type_brain cortex


title: rep1_RPF_FK


title: normal control skin_Human_rep4

type: RNA

city: Jinan

first: Q

last: Sun

state: Shandong

address: Medical College of Shandong University 44 Wenhua West Road, Lixia District,

department: Dermatology

country: China

institute: Shandong University; Qilu hospital

description: Samples of normal skin tissue. Sample tissues were treated with formalin and embedded with paraffin.

hyb_protocol: After labeling was complete, the sample was hybridized to a miRCURYTM LNA Array (v.18.0) microarray (Exiqon), using 25 μL of the sample mixed with 25 μL of hybridization buffer, which was denatured for 2 min at 95 °C and then incubated on ice for 2 min. Hybridization was performed in a 12-Bay Hybridization System (Nimblegen Systems, Inc., Madison, WI, USA) for 16–20 h at 56 °C. After hybridization, the slides were washed several times using Wash buffer kit (Exiqon) and scanned using a GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA, USA).

scan_protocol: GenePix Pro 6.0 (Axon Instruments) was used to read the chip scan image and for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs with intensities ≥ 30 in all samples were chosen for calculating the normalization factor.

data_processing: Expressed data were normalized using median normalization. After normalization, significantly differentially expressed miRNAs between the two groups were identified through fold change and P-value, which was performed twice. Further, measures of fold change were used to screen for differential expression of miRNAs between two samples, and finally, hierarchical clustering was performed to identify distinguishable miRNA expression profiles among samples.

organism: Homo sapiens

source_name: skin,normal control

label_protocol: Total RNA was extracted from four patients with psoriasis and four normal controls, and miRNA was labeled using the miRCURYTM Array Power Labeling kit (Cat no. 208032-A, Exiqon, Vedbaek, Denmark), using 1 μg of labeled RNA with 2 μL of water and 1 μL each of CIP buffer and CIP enzyme. Reactions were mixed and incubated at 37 °C for 30 min followed by 95 °C for 5 min to terminate the reaction. Next, 3 μL of the labeling buffer, 1.5 μL of fluorescent label (Hy3™), 2 μL of DMSO, and 2 μL of labeling enzyme were added followed by an incubation at 16 °C for 1 h. The reaction was stopped by placing the sample at 65 °C for 15 min.

growth_protocol: Recruited patients did not have other types of skin diseases or other types of diseases, such as heart disease, liver, lung, kidney, blood, or other systemic diseases, or autoimmune disease. In addition, they had not received systematic treatment with glucocorticoid steroids, immunosuppressive agents, Vitamin A, or other drugs during the past 3 months and they did not receive phototherapy or psoriasis treatment using external preparations within the last month.

extract_protocol: RNA was extracted by TRIzol (Invitrogen Life Technologies, San Diego, CA, USA) and purified using the RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturers’ instructions. The concentration of purified RNA was measured using a ND-1000 Spectrophotometer (NanoDrop, Wilmington, DE, USA) and electrophoresis was performed to assess RNA integrity.

treatment_protocol: Eight samples from patients with psoriasis and  healthy volunteers were used.  Sample tissues were treated with formalin and embedded with paraffin

tag: gender

value: female

tag: age

value: adult


title: rep1_RPF_2K


title: rep1_RPF_CK


title: Sample 1515_Single mESC cell


title: Sample 1516_Single mESC cell


title: rep2_RNA_WT

description:
processed data file:
RNADEseq_WTx2K
RNADEseq_WTxCK
RNADEseq_WTxFK
RNADEseq_WT2KxFKCK
ROXtail_2XxWT
ROXtail_CXxWT
ROXtail_FXxWT

data_processing:
reads were separated based on sample barcode sequences using in-house codes
known 3’ adapter sequences and low quality bases were removed with Cutadapt(Martin, 2011) using parameters -O 2 -q 15 -a “TGGAATTCTCGGGTGCCAAGGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG”
reads mapped to rRNA and tRNA genes were removed using Bowtie2(Langmead and Salzberg, 2012) with parameter -N 1
remaining reads were mapped to the mm10 genome using TopHat2(Kim et al., 2013)
PCR duplicates were removed based on Unique Molecular Identifier sequences using in-house codes
Uniquely mapped reads were then used as input to RSEM(Li and Dewey, 2011) for quantification of gene expression and either mapped to RefSeq (v69) mouse coding sequences (RPF) or to whole-transcriptome (RNA-seq). Genes were filtered to have a minimum of 10 TPM (transcripts per million) in at least one sample.
We used log transformed TPM expression values to correct for batch effects using ComBat(Leek et al., 2012) (v3.18.0).
Corrected values were transformed back to read counts using the expected size of each transcript informed by RSEM.
Batch-corrected counts were used to identify differentially translated/expressed genes with DESeq2(Love et al., 2014, p. 2) (RPF and RNA) or Xtail10 (ribosome occupancy, RO).
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited values include RSEM quantification of all mm10 genes (*.genes.results.txt) and differential expression analysis generated by DEseq2 (RNADEseq_* and RPFDEseq_*) or Xtail (ROXtail_*)

value: cytoplasmic fraction RNA-seq

value: random fragmented RNA


title: DMSO treated 786-0 cells 2

type: genomic

city: NASHVILLE

first: Aguirre

middle: A

last: de Cubas

state: TN

address: 2220 Pierce Ave

department: Hematology and Oncology

institute: Vanderbilt University Medical Center

hyb_protocol: Hybridization was performed in accordance to the manufacture's recommendations.

scan_protocol: Raw IDAT files were processed with Illumina’s GenomeStudio software V2011.1 and background normalized using negative control probes to generate methylation β-values.

data_processing: The MethylationEPIC_v-1-0_B2 manifest was used for processing EPIC data.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: DNA (250–750 ng) was treated with sodium bisulphite using the EZ DNA methylation kit (Zymo Research, CA, USA). DNA methylation was quantified using the Illumina Infinium HumanMethylationEPIC (EPIC) BeadChip (Illumina, CA, USA) run on an Illumina iScan System (Illumina, CA, USA) using the manufacturer’s standard protocol.

extract_protocol: DNA was extracted from cell lines using the DNeasy Blood and Tissue Kit (Qiagen). DNA concentration was determined using a NanoDrop2000 Spectrometer (NanoDrop Technologies). Quality was assessed by agarose gel electrophoresis.

treatment_protocol: Cells were treated daily with decitabine (100nM and 300nM) or DMSO, for three consecutive days. After 72 hours, fresh media was added, cells were cultured for two additional days, and harvested at 120 hours (day 5).

value: 786-0 cells

value: DMSO


title: decitabine treated (100nM) 786-0 cells 2

source_name: 786-0 100nM decitabine 2

value: 100nM decitabine


title: Sample 1514_Single mESC cell

value: Differentiated mESC

value: day 0


title: rep1_RNA_WT

value: wild type


title: decitabine treated (300nM) 786-0 cells 2

source_name: 786-0 300nM decitabine 2

value: 300nM decitabine


title: decitabine treated (300nM) 786-0 cells 1

source_name: 786-0 300nM decitabine 1


title: rep2_RNA_CK

description:
processed data file:
RNADEseq_2KxCK
RNADEseq_FKxCK
RNADEseq_WTxCK
RNADEseq_WT2KxFKCK
ROXtail_2KxCK
ROXtail_CKxFK
ROXtail_CXxWT

value: FVB.129P2-/Pde6b^+ Tyr^c-ch //AntJ

value: Cpeb1 single KO


title: rep2_RNA_FK

description:
processed data file:
RNADEseq_2KxFK
RNADEseq_FKxCK
RNADEseq_WTxFK
RNADEseq_WT2KxFKCK
ROXtail_2KxFK
ROXtail_CKxFK
ROXtail_FXxWT

value: mouse brain cortex


title: normal control skin_Human_rep3


title: rep2_RNA_2K

description:
processed data file:
RNADEseq_2KxCK
RNADEseq_2KxFK
RNADEseq_WTx2K
RNADEseq_WT2KxFKCK
ROXtail_2KxCK
ROXtail_2KxFK
ROXtail_2XxWT


title: DMSO treated 786-0 cells 1


title: rep2_RPF_WT

value: ribosome profiling

value: ribosome protected RNA footprint


title: decitabine treated (100nM) 786-0 cells 1

source_name: 786-0 100nM decitabine 1


title: rep1_RNA_FK

value: Fmr1 single KO


title: Sample 1513_Single mESC cell


title: Sample 1512_Single mESC cell


title: normal control skin_Human_rep2

value: male


title: psoriasis lesional skin_Human_rep4

description: Patients were diagnosed with psoriasis according to the diagnostic criteria for psoriasis vulgaris and histopathological diagnosis at the Department of Dermatology at Qilu Hospital. Sample tissues were treated with formalin and embedded with paraffin

source_name: skin,psooriasis

value: female

value: adult


title: normal control skin_Human_rep1


title: rep1_RNA_CK

value: cytoplasmic fraction RNA-seq

value: random fragmented RNA


title: psoriasis lesional skin_Human_rep3


title: psoriasis lesional skin_Human_rep2


title: rep1_RNA_2K

value: Fmr1/Cpeb1 double KO


title: Sam68_WT_P30_RNASeq_3

city: TORONTO

first: Robert

last: Weatheritt

state: Ontario

address: 160 College Street, Room 1030

country: Canada

institute: University of Toronto

description:
name in processed data file:
Sette_3_P30wt

data_processing:
Fastqc
Trimmomatic
VAST-TOOLS
Genome_build: mm9
Supplementary_files_format_and_content: cRPKM-Mmu13.tab = Expression data; INCLUSION_LEVELS_FULL-Mmu13.tab = Splicing data

source_name: P30 wild type mouse cerebella

extract_protocol:
RNA isolation with qiagen Kit
Illumina TruSeq Stranded mRNA library preparation (modified)

value: cerebella

tag: background strain

value: wildtype


title: Sample 1511_Single mESC cell

value: Differentiated mESC

value: day 0


title: Sample 1510_Single mESC cell


title: Sam68_WT_P30_RNASeq_1

description:
name in processed data file:
Sette_1_P30wt


title: Sam68_WT_P30_RNASeq_2

description:
name in processed data file:
Sette_2_P30wt


title: Sam68_WT_P10_RNASeq_6

description:
name in processed data file:
Sette_6_P10wt

source_name: P10 wild type mouse cerebella


title: GFP-CENH3-anti-CENH3

city: Wuhan

first: Handong

last: Su

state: Hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

library_source: genomic

data_processing:
Basecalls performed using Illumina CASAVA.
ChIP-seq reads were mapped to maize B73 genome with BWA version 0.6.1 with the following configurations.
Only uniquely mapping reads were chosen for further analysis, and only a random one was picked for duplicates (reads mapped to the same location).
RPM values were calculated with 10 kb windows along the genome to make it comparable between different samples.
Genome_build: Maize B73 RefGen_v3
Supplementary_files_format_and_content: bedGraph files were generated using bedtools.

organism: Zea mays

source_name: young leaves

growth_protocol: Suitable materials were planted in the greenhouse for ChIP experiments and bisulfite treatment.

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).180-400 bp fragments (contained the joint) were selected by gel extraction.

value: young leaves

tag: chip antibody


title: Sample 1508_Single mESC cell


title: Sample 1507_Single mESC cell


title: Sam68_KO_P1_RNASeq_13

description:
name in processed data file:
Sette_13_P1ko

source_name: P1 Sam68 ko mouse cerebella

value: Sam68 ko


title: Sample 1509_Single mESC cell


title: Sam68_WT_P1_RNASeq_9

description:
name in processed data file:
Sette_9_P1wt

source_name: P1 wild type mouse cerebella


title: Sam68_WT_P1_RNASeq_8

description:
name in processed data file:
Sette_8_P1wt


title: Sample 1506_Single mESC cell

source_name: Single mESC cell


title: Sam68_KO_P1_RNASeq_15

description:
name in processed data file:
Sette_15_P1ko


title: Sam68_KO_P1_RNASeq_14

description:
name in processed data file:
Sette_14_P1ko


title: B73 ChIP-Seq


title: Hill ChIP-Seq

value: Hill


title: Sam68_KO_P10_RNASeq_12

description:
name in processed data file:
Sette_12_P10ko

source_name: P10 Sam68 ko mouse cerebella


title: psoriasis lesional skin_Human_rep1


title: Sam68_KO_P10_RNASeq_11

description:
name in processed data file:
Sette_11_P10ko


title: Sam68_KO_P10_RNASeq_10

description:
name in processed data file:
Sette_10_P10ko


title: Sample 1505_Single mESC cell


title: A188 ChIP-Seq


title: Sample 1504_Single mESC cell


title: LV_IR-Sesn2-KO3

city: Jackson

first: Ji

last: Li

state: MS

address: 2500 N. State st.

department: Physiology and Biophysics

institute: University of Mississippi Medical Center

data_processing:
FastQC was applied to inspect the reads quality of each RNA-Seq raw sequencing file by measuring the quality score distribution of nucleotides per read, the existence of adapters, the duplication level of specific reads. Bowtie2, TopHat2, Cufflinks2, and HTSeq-count of the pipeline were used to perform alignment, transcript assembly, and read-counting. In addition, Samtools was used for sorting the mapped reads and format conversion.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw reads counts for each gene.

growth_protocol: Young (3-4 months) C57BL/6J mice (young-WT) were purchased from The Jackson Laboratory (Bar Harbor, ME, USA). Aged (24-26 months) C57BL/6J mice (aged-WT) were supplied from Charles River Laboratories (Wilmington, MA, USA). Sesn2 knockout (Sesn2-KO) (3-4 months, C57BL/6J) were bred and supplied by our lab

extract_protocol:
The left ventricle of heart was homogenized with liquid nitrogen and the total RNA of the sample was isolated using RNeasy® mini kit (Qiagen) according to the manufacturer protocol.
Subsequently, 1 μg total RNA was enriched for mRNA using Illumina TruSeq stranded mRNA Library Prep kit (Illumina, 20020594) according to the manufacturer instruction. Next, the Bioanalyzer was used to detect size distribution of the transcriptome after fragmentation and adapter ligation, and a Qubit® Fluorometer (InvitrogenTM, Waltham, MA) was used to quantify the yield post-PCR amplification.
Finally, the pooled cDNA libraries from each sample were sequenced on Illumina NextSeq 500-mRNA-Seq platform in a 2x100 bp paired-end (PE) at Molecular and Genomics Core of University of Mississippi Medical center (Jackson, MS).

treatment_protocol: Mice randomly selected for IR treatment were anesthetized, intubated and ventilated. After a left lateral thoracotomy, the left anterior descending coronary artery (LAD) was occulated for 45 mins with an 8-0 nylon suture and polyethylene tubing to prevent arterial injury and subsequently reperfused for 24 hours. Mice randomly selected for sham groups treatment were anesthetized, intubated, ventilated and a left lateral thoracotomy but without LAD occulation. The heart from all groups was then removed and the left ventricle was isolated and freeze clamped in liquid nitrogen for future total RNA extraction.

value: 3-4 months

value: IR

value: left ventricle


title: LV_IR-Sesn2-KO2


title: Sam68_WT_P10_RNASeq_5

description:
name in processed data file:
Sette_5_P10wt


title: CENH3-YFP-anti-GFP

value: GFP


title: LV_IR-Sesn2-KO1


title: Sample 1503_Single mESC cell


title: LV_Sham-Sesn2-KO3

value: Sham


title: OC08_ADN0182

city: PARIS

first: OUMOU

last: GOUNDIAM

address: 26 RUE D'ULM

country: France

institute: INSTITUT CURIE

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

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

data_processing:
CytoScan HD SNP-arrays (Affymetrix, ThermoFisher Scientific) data were processed using the GAP methodology to obtain absolute copy number (CN) proﬁles (Popova et al, Genome Biol., 2009, doi:10.1186/gb-2009-10-11-r128), including DNA structural rearrangements and chromosome number. The DNA index was calculated as the averaged CN and tumor ploidy of tumors was set as near-diploid (DNA index <1.3) or near-tetraploid (DNA index >1.3). HRD was detected based on the number of Large-scale State Transitions (LSTs) as described previously 47. Brieﬂy, LST was deﬁned as a chromosomal breakpoint (change in CN or major allele counts) between adjacent regions of at least 10 Mb. The number of LSTs was calculated after smoothing and ﬁltering out CN variant regions < 3 Mb in size based on two ploidy-speciﬁc cut-offs (15 and 20 LSTs per genome in near-diploid and near-tetraploid tumors respectively). Tumors were classiﬁed as HRD (equal or above the cut-off) or HR Proficient (HRP) (below the cut-off)
The matrix table contains the log2 intensity data by probe

label: Biotin

source_name: tumor sample

label_protocol: as per manufacturer (Affymetrix)

growth_protocol: DNA extract from tumor biopsies

extract_protocol: DNA was extracted using Macherey-Nagel NucleoSpin® Tissue kit

value: ovarian cancer biopsy


title: Sample 1502_Single mESC cell


title: LV_Sham-Sesn2-KO2


title: CENH3-YFP-anti-CENH3


title: OC08_ADN0179


title: OC08_ADN0181


title: OC08_ADN0178


title: Sample 1501_Single mESC cell


title: OC08_ADN0176


title: LV_IR-Aged3

value: WT

value: 24-26 months


title: LV_Sham-Sesn2-KO1


title: OC08_ADN0175


title: LV_IR-Aged2


title: Sample 1499_Single mESC cell


title: LV_Sham-Aged2


title: LV_Sham-Aged1


title: LV_IR-Aged1


title: LV_IR-Young3


title: Sample 1498_Single mESC cell


title: LV_IR-Young2


title: OC08_ADN0174


title: Sample 1497_Single mESC cell


title: LV_IR-Young1


title: OC08_ADN0173


title: LV_Sham-Young1


title: OC08_ADN0172


title: LV_Sham-Young3


title: Sample 1496_Single mESC cell


title: LV_Sham-Aged3


title: Sample 1500_Single mESC cell


title: Il13-KO_Trained3

city: Boston

first: Nelson

middle: Howard

last: Knudsen

address: 655 Huntington Avenue

department: Genetics and Complex Diseases

institute: Harvard T. H. Chan School of Public Health

data_processing:
Trimming of Illumina adapters (CLC Genomics Workbench v.10 )
Quality control for individual samples (CLC Genomics Workbench v.10 )
Mapping against the reference genome (CLC Genomics Workbench v.10 )
Calculation of expression values using unique matches (CLC Genomics Workbench v.10)
Normalization by scaling 10.000.000 reads per sample per transcript (TPM),
Genome_build: Genome_build: mouse mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Gastrocnemius

growth_protocol: All animals were 20-week old male C57Bl6/J mice.

extract_protocol:
Gastrocnemius muscles were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using Illumina’s TruSeq Stranded mRNA Library Preparation Kit based on the Kit’s manual. 2 ug total RNA was used as input.

treatment_protocol: WT or Il13-/- mice were untrained (control) or endurance exercise trained for 5 weeks by daily treadmill running.

value: male

value: 20-weeks old

value: 5 weeks endurance exercise

value: gastrocnemius muscle

tag: mouse id


title: LV_Sham-Young2


title: OC08_ADN0171


title: Sample 1494_Single mESC cell

value: Differentiated mESC


title: Il13-KO_Trained4


title: OC08_ADN0169


title: Sample 1493_Single mESC cell

value: day 0


title: Sample 1495_Single mESC cell


title: OC08_ADN0168


title: Il13-KO_Trained1


title: Il13-KO_Untrained3

value: Untrained


title: Il13-KO_Untrained2


title: Il13-KO_Untrained4


title: Il13-KO_Trained2


title: Sample 1492_Single mESC cell


title: Il13-KO_Untrained1


title: WT_Trained4

value: wild type


title: OC08_ADN0166


title: OC08_ADN0162


title: WT_Trained2


title: WT_Trained3


title: OC08_ADN0158


title: Sample 1490_Single mESC cell


title: WT_Untrained4


title: Sample 1489_Single mESC cell


title: WT_Trained1


title: WT_Untrained3


title: OC08_ADN0153


title: OC08_ADN0155


title: WT_Untrained2


title: Sample 1488_Single mESC cell


title: Sample 1487_Single mESC cell


title: OC08_ADN0152


title: WT_Untrained1


title: liver_3m_2_rna

city: Vienna

first: Aleksandra

middle: S

last: Anisimova

address: Dr. Bohr Gasse 9

country: Austria

institute: Max Perutz Labs, Vienna BioCenter, University of Vienna, Medical University of Vienna

description: Total RNA

data_processing:
For the Ribo-Seq data: adapter sequences were cut with cutadapt v1.14 (-a AGATCGGAAGAGCACACGTCT)
For the Ribo-Seq data: the remaining low-quality base calls at the read ends were additionally removed with sickle v1.33.
RNA-Seq data: no special trimming was applied
Read mapping and counting was performed with STAR v2.5.3.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text files containing read counts per gene as estimated by STAR.

source_name: Liver

extract_protocol:
N2l frozen and stored at -80°C liver and kidney samples of approximate weight of 55 mg and 75 mg respectively were taken for lysis.  Tissues were lysed with the same lysis protocol as described in Gerashchenko et al., 2018, bioRxiv. After homogenization and centrifugation 250 µl of lysate were supplied with 20 Units of SUPERase-In RNAse inhibitor and taken for RNA-Seq library preparation, the 500 µl of lysate were brought to 1 ml with lysis buffer and taken for ribosome profiling library preparation.
Ribosome profiling libraries were prepared as described in doi:10.1101/279257 with modification in RNase digestion indicated below. RNA digestion of lysates was performed for 1 hour with mixture of RNase T1 (2000 Units) and RNase S7 (300 Units). After 30 minutes of incubation 0.8 mg of heparin were added to inhibit all RNases except for RNase T1. After digestion lysates were supplied with 80 Units of SUPERase-In RNAse inhibitor. For RNA-Seq total RNA was isolated from 250 µl of lysate with 750 µl of TRIzol LS Reagent and treated with RQ1 RNase-Free DNase (1 Unit for 1 µg of total RNA) for 30 minutes at 37°C with subsequent water saturated acidic phenol extraction and precipitation by the ethanol method (with addition of 1/100 volume of glycogen RNA grade). 500 ng of DNase treated total RNA was depleted of ribosomal RNA with NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (#E6310) and used for transcriptome libraries preparation with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (#E7760).

value: 3 months

value: Liver


title: Sample 1486_Single mESC cell


title: liver_3m_3_rna

description: Total RNA


title: OC08_ADN0150


title: Sample 1491_Single mESC cell


title: Sample 1484_Single mESC cell


title: liver_3m_3_ribo

description: Ribosome-bound RNA

data_processing:
Library strategy: Ribosome profiling
For the Ribo-Seq data: adapter sequences were cut with cutadapt v1.14 (-a AGATCGGAAGAGCACACGTCT)
For the Ribo-Seq data: the remaining low-quality base calls at the read ends were additionally removed with sickle v1.33.
RNA-Seq data: no special trimming was applied
Read mapping and counting was performed with STAR v2.5.3.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text files containing read counts per gene as estimated by STAR.


title: Sample 1485_Single mESC cell


title: OC08_ADN0149


title: liver_3m_2_ribo

description: Ribosome-bound RNA


title: liver_32m_3_rna

description: Total RNA

value: 32 months


title: liver_3m_1_rna

description: Total RNA


title: liver_32m_3_ribo

description: Ribosome-bound RNA


title: liver_3m_1_ribo

description: Ribosome-bound RNA


title: liver_32m_2_rna

description: Total RNA


title: Sample 1483_Single mESC cell


title: liver_32m_1_rna

description: Total RNA


title: liver_32m_2_ribo

description: Ribosome-bound RNA


title: OC08_ADN0148


title: Sample 1482_Single mESC cell


title: OC08_ADN0147


title: Sample 1481_Single mESC cell


title: liver_32m_1_ribo

description: Ribosome-bound RNA


title: OC08_ADN0146


title: liver_26m_3_ribo

description: Ribosome-bound RNA

value: 26 months


title: liver_26m_3_rna

description: Total RNA


title: OC08_ADN0151


title: OC08_ADN0145


title: Sample 1480_Single mESC cell


title: liver_26m_2_rna

description: Total RNA


title: OC08_ADN0144


title: Sample 1479_Single mESC cell


title: liver_20m_3_rna

description: Total RNA

value: 20 months


title: liver_26m_1_ribo

description: Ribosome-bound RNA


title: OC08_ADN0143_s2


title: Sample 1478_Single mESC cell


title: liver_20m_3_ribo

description: Ribosome-bound RNA


title: OC08_ADN0139


title: liver_20m_2_rna

description: Total RNA


title: liver_20m_2_ribo

description: Ribosome-bound RNA


title: Sample 1477_Single mESC cell


title: liver_20m_1_rna

description: Total RNA


title: Sample 1476_Single mESC cell


title: liver_20m_1_ribo

description: Ribosome-bound RNA


title: OC08_ADN0138


title: Sample 1475_Single mESC cell


title: liver_1m_2_rna

description: Total RNA

value: 1 month


title: liver_1m_2_ribo

description: Ribosome-bound RNA


title: OC08_ADN0137

value: ovarian cancer biopsy


title: liver_26m_2_ribo

description: Ribosome-bound RNA


title: OC08_ADN0136


title: Sample 1474_Single mESC cell


title: liver_1m_3_ribo

description: Ribosome-bound RNA


title: liver_1m_3_rna

description: Total RNA


title: Sample 1473_Single mESC cell


title: liver_1m_1_rna

description: Total RNA


title: liver_1m_1_ribo

description: Ribosome-bound RNA


title: liver_10m_3_rna

description: Total RNA

value: 11 months


title: Sample 1472_Single mESC cell


title: liver_26m_1_rna

description: Total RNA


title: liver_10m_3_ribo

description: Ribosome-bound RNA


title: OC08_ADN0117


title: liver_10m_2_rna

description: Total RNA


title: OC08_ADN0116


title: liver_10m_2_ribo

description: Ribosome-bound RNA


title: OC08_ADN0115


title: liver_10m_1_rna

description: Total RNA


title: Sample 1470_Single mESC cell


title: OC08_ADN0114


title: Sample 1469_Single mESC cell


title: kidney_3m_3_rna

description: Total RNA

source_name: Kidney

value: Kidney


title: OC08_ADN0113


title: kidney_3m_3_ribo

description: Ribosome-bound RNA


title: OC08_ADN0111


title: Sample 1467_Single mESC cell


title: kidney_3m_4_ribo

description: Ribosome-bound RNA


title: kidney_3m_2_ribo

description: Ribosome-bound RNA


title: kidney_3m_1_rna

description: Total RNA


title: Sample 1466_Single mESC cell


title: kidney_3m_1_ribo

description: Ribosome-bound RNA


title: OC08_ADN0099


title: Sample 1465_Single mESC cell


title: Sample 1468_Single mESC cell


title: kidney_3m_2_rna

description: Total RNA


title: kidney_32m_3_ribo

description: Ribosome-bound RNA


title: kidney_32m_2_rna

description: Total RNA


title: Sample 1464_Single mESC cell


title: kidney_3m_4_rna

description: Total RNA


title: OC08_ADN0103


title: Sample 1463_Single mESC cell


title: liver_10m_1_ribo

description: Ribosome-bound RNA


title: Sample 1471_Single mESC cell


title: kidney_32m_1_rna

description: Total RNA


title: OC08_ADN0096


title: kidney_20m_3_rna

description: Total RNA


title: kidney_32m_1_ribo

description: Ribosome-bound RNA


title: Sample 1462_Single mESC cell


title: kidney_32m_3_rna

description: Total RNA


title: kidney_20m_3_ribo

description: Ribosome-bound RNA


title: OC08_ADN0091


title: kidney_20m_2_rna

description: Total RNA


title: OC08_ADN0090


title: OC08_ADN0098


title: Sample 1461_Single mESC cell


title: kidney_32m_2_ribo

description: Ribosome-bound RNA


title: kidney_20m_2_ribo

description: Ribosome-bound RNA


title: OC08_ADN0089


title: Sample 1459_Single mESC cell


title: Sample 1460_Single mESC cell


title: RNA-seq Jurkat H3B-8800 24hr 300bp replicate 2

city: Chicago

first: Yalu

last: Zhou

state: IL

address: 303 E. Superior St,

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Basecalls performed using bcl2fastq
RNA-seq reads were aligned to the hg19 genome assembly using Tophat
Reads were counted on the exons of hg19 genes using htseq
Differential gene expression analysis was performed using edgeR.
Diferential alternative splicing analysis was performed using rMATS.
Genome_build: hg 19
Supplementary_files_format_and_content: TAB-delimited text, edgeR output containing normalized expression values.

source_name: RNA-seq Jurkat H3B-8800 24hr 300bp

growth_protocol: cells in suspension, growing in RPMI

extract_protocol:
Aurum Total RNA Mini Kit (Bio-Rad)
Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina NextSeq 500 using 300bp paired-read method.

treatment_protocol: cells treated with the splicing inhibitor H3B-8800 with DMSO as the control.

value: Jurkat

tag: cell type

value: human T cell leukemia cells


title: RNA-seq Jurkat H3B-8800 24hr 300bp replicate 3


title: OC08_ADN0085


title: RNA-seq Jurkat H3B-8800 24hr 300bp replicate 1


title: OC08_ADN0083


title: RNA-seq Jurkat DMSO replicate 3

source_name: RNA-seq Jurkat DMSO

value: DMSO


title: RNA-seq Jurkat DMSO replicate 2


title: OC08_ADN0092


title: Thymus replicate 3

source_name: Thymus

growth_protocol: in vivo

extract_protocol:
Aurum Total RNA Mini Kit (Bio-Rad)
Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina NextSeq 500 using 150bp paired-read method.

value: Thymocytes


title: RNA-seq Jurkat DMSO replicate 1


title: OC08_ADN0082


title: Sample 1457_Single mESC cell

value: Differentiated mESC


title: Thymus replicate 2


title: Thymus replicate 1


title: kidney_20m_1_ribo

description: Ribosome-bound RNA


title: kidney_20m_1_rna

description: Total RNA


title: Sample 1455_Single mESC cell

value: day 0


title: OC08_ADN0081


title: OC08_ADN0062


title: Sample 1458_Single mESC cell


title: Sample 1454_Single mESC cell


title: OC08_ADN0054


title: Sample 1451_Single mESC cell


title: Sample 1456_Single mESC cell


title: OC08_ADN0040


title: Sample 1452_Single mESC cell


title: OC08_ADN0039


title: Molm13_EPZ5676_d9_rep3

city: Hannover

first: Florian

last: Perner

address: Carl-Neuberg-Str. 1

department: Hematology, Hemostasis, Oncology and Stem Cell Transplantation

country: Germany

institute: Hannover Medical School

data_processing:
Raw Illumina NextSeq BCL files converted to FASTQs using Illumina bcl2fastq v02.14.01.07 and reads trimmed using Trimmomatic v0.36 (phred quality threshold 33).
Reads aligned using STAR (v2.6.1b) and UCSC hg19 genome, gene and transcriptome references from Illumina iGenomes resource.
Aligned BAM files indexed with samtools v1.2; sorted, duplicate reads marked and removed (in cell line samples) using Broad picard tools v.2.9.4; and deduplicated BAMs indexed using samtools.
Read counts per gene calculated using HTSeq v0.11 htseq-count with hg19 gene reference from Illumina iGenomes and differential expression calculated using Bioconductor DESeq2 package.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: MOLM13_compound-10_EPZ5676_DEGs_d3_d6_d9_DESeq2_rmdup.txt: Summary of DESeq2 FC and padj values for EPZ5676 and compound10 treated samples vs. DMSO at days 3, 6 and 9 (.txt)
Supplementary_files_format_and_content: Molm13_compound-10_EPZ5676_raw counts_rmdup.txt: Raw counts per gene from all RNAseq samples in this series (.txt)

source_name: MOLM13 cultured cells

growth_protocol: MOLM13 cells  were cultured in PRMI1640 media supplemented with 10% Fetal bovine serum (v/v) (Gibco), 1x penicillin/streptomycin (Gibco), plasmocin (ThermoFisher) and treated with the prespective drugs dissolved in DMSO at a 1:1000 dilution.

extract_protocol:
Cell Lines: The cells were collected and washed twice in ice-cold PBS followed by lysis and RNA extraction using RNEasy (Qiagen) kit.  Quality of RNA was tested using RNA TAPE and samples qith RIN >7 were used for library preparation.
10-100 ng of total RNA converted to illumina compatible sequencing libraries using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina

treatment_protocol: Molm13 cells were treated with EPZ5676 (1uM), compound 10 (100nM) or DMSO for a total of 9 days. Samples for RNA-isolation were taken at days 3, 6 and 9. On these days the medium was replaced and supplemented with fresh drug.

tag: timepoint

value: 9 days post treatment


title: Molm13_comp10_d6_rep2

value: 6 days post treatment

value: compound 10


title: Molm13_comp10_d6_rep3


title: Molm13_comp10_d3_rep1

value: 3 days post treatment


title: Molm13_comp10_d3_rep2


title: Molm13_comp10_d9_rep1


title: Molm13_comp10_d9_rep3


title: Molm13_comp10_d6_rep1


title: Sample 1450_Single mESC cell


title: Molm13_comp10_d9_rep2


title: Molm13_comp10_d3_rep3


title: Molm13_EPZ5676_d9_rep1


title: OC08_ADN0076


title: Sample 1449_Single mESC cell


title: Molm13_EPZ5676_d6_rep2


title: OC08_ADN0031


title: Molm13_EPZ5676_d6_rep3


title: Molm13_EPZ5676_d6_rep1


title: Sample 1453_Single mESC cell


title: OC08_ADN0029


title: Molm13_EPZ5676_d3_rep3


title: OC08_ADN0053


title: Sample 1447_Single mESC cell


title: Molm13_EPZ5676_d9_rep2


title: Molm13_EPZ5676_d3_rep2


title: Sample 1446_Single mESC cell


title: Molm13_EPZ5676_d3_rep1


title: OC08_ADN0028


title: Molm13_DMSO_d9_rep3


title: OC08_ADN0025


title: OC08_ADN0023


title: Molm13_DMSO_d6_rep2


title: Molm13_DMSO_d6_rep3


title: Molm13_DMSO_d3_rep3


title: Sample 1445_Single mESC cell


title: Sample 1444_Single mESC cell


title: Molm13_DMSO_d6_rep1


title: OC08_ADN0021


title: Molm13_DMSO_d9_rep2


title: Sample 1448_Single mESC cell


title: Sample 1443_Single mESC cell


title: Molm13_DMSO_d3_rep2


title: Molm13_DMSO_d3_rep1


title: OC08_ADN0020


title: RS4,11_ChIP-input

data_processing:
Raw Illumina NextSeq BCL files converted to FASTQs using Illumina bcl2fastq v02.14.01.07 and reads trimmed using Trimmomatic v0.36 (phred quality threshold 33).
Reads aligned to human GRCh37/hg19 or GRCh38/hg38 genome using bowtie2 v2.1 (params: -q -p 11 --phred33 -N 1 --very-sensitive ) or STAR 2.6.1b (181116 samples; params: --twopassMode Basic --outReadsUnmapped None --runThreadN 4 --limitBAMsortRAM 12000000000 --outSAMstrandField intronMotif --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat).
The H3K79me2 samples also contain Drosophila spike-in chromatin as described; these samples were additionally aligned to dm6 as above. Global differences in fly-human chromatin ratios were found, so H3K79me2 TSS signals were normalized accordingly.
Aligned BAM files sorted, duplicate reads marked and removed, and deduplicated BAMs indexed using Broad picard tools v2.9.4.
For Chip-seq, total signal was assessed around transcription start site (TSS) regions using the sitepro tool (version: 0.6.6) from the CEAS (Cis-regulatory Element Annotation System, version: 1.0.2) package (using 4kb windows off-centered around TSS regions [1kb upstream, 3kb into gene bodies] with 200bp tiling and signal summed across each TSS window), based on signal from WIG files generated using IGVtools (v2.3.98).
Genome_build: GRCh37/hg19 (H3K79me2 ChIPseq); GRCh38/hg38 (DOT1L & Menin ChIPseq)
Supplementary_files_format_and_content: Sample signal files for visualization in IGV (.tdf), MACS peak calling output (.xls) and summary SitePro TSS signal output + dm6 spike-in counts/ratios (.txt)

source_name: RS4,11 cultures cells

growth_protocol: MOLM13 or RS4;11 cells were cultured in PRMI1640 media supplemented with 10% Fetal bovine serum (v/v) (Gibco), 1x penicillin/streptomycin (Gibco), plasmocin (ThermoFisher). For the treatment the cells were plated at 2x10^5 cells/ml in T75 tissue culture treated flasks. DMSO, EPZ5676, VTP-50469, compound 10 or compound 11 were added at 1:1000 dilution

extract_protocol:
The cells were collected and washed twice in ice-cold PBS followed by crosslinking in 1% formaldehide (methanol free) for 5 minutes. Excess of formaldehyde was quenched by addition of Tris pH 8.0 to 100nM final and Glycine 125 mM final. Chromatin was cheared using Covaris E220 for 20 min with power 140; duty 5; bursts 200/sec. We then used 5ul aliquote of sherared chromatin to decrosslink in order to test completeness of shearing. Chromatin was considered passed QC if fragments 100-600bp were >90%. For immunoprecipitation we used aproximately chromatin from 1-10x10^6 cells, 5-10ug of specific antibody and 10-20ul of Protein-A/G magnetic beads (Dynal). In 16 hours the immune complexes were wased in Mixed Micelle Buffer, buffer 500, LiCl/detergent solution and TE buffers. DNA was eluted from the beads using 100mM NaHCO3 100mM NaCl 1% SDS and purified using AmpureXP beads.
1-10 ng of ChIP'ed DNA was used for Illumina compatibl library generation using ThruPlex DNA-seq kit with 10 to 14 cycles of amplification with single or paired end barcodes

treatment_protocol: DMSO or VTP-50469 (in DMSO) were added at 1:3000 dilution, for final concentration of DMSO 0.33% and VTP-50469 100 to 330nM

tag: chip target

tag: antibody


title: Sample 1441_Single mESC cell


title: OC08_ADN0019

tag: tissue


title: MOLM13_ChIP-input_2


title: RS4,11_H3K79me2-ChIP_comp10_9d

value: anti-H3K79me2 (Cell signaling # 5427S clone D15E8 lot 4)

value: compound 10 (100nM)


title: Sample 1440_Single mESC cell


title: OC08_ADN0027


title: OC08_ADN0016


title: Molm13_DMSO_d9_rep1


title: RS4,11_H3K79me2-ChIP_comp10_3d


title: RS4,11_H3K79me2-ChIP_EPZ5676_9d


title: RS4,11_H3K79me2-ChIP_EPZ5676_6d


title: Sample 1438_Single mESC cell


title: Sample 1439_Single mESC cell


title: RS4,11_H3K79me2-ChIP_EPZ5676_3d


title: Sample 1436_Single mESC cell


title: RS4,11_H3K79me2-ChIP_comp10_6d


title: Sample 1442_Single mESC cell


title: HEK293T_96well cell4

source_name: Single HEK293T cell

value: HEK293T Cell


title: OC08_ADN0010


title: HEK293T_96well cell3


title: OC08_ADN0006


title: Sample 1435_Single mESC cell


title: RS4,11_H3K79me2-ChIP_DMSO_6d


title: MOLM13_H3K79me2-ChIP_comp10_9d


title: RS4,11_H3K79me2-ChIP_DMSO_3d


title: Sample 1434_Single mESC cell


title: MOLM13_H3K79me2-ChIP_EPZ5676_9d


title: MOLM13_H3K79me2-ChIP_comp10_6d


title: MOLM13_H3K79me2-ChIP_comp10_3d


title: MOLM13_H3K79me2-ChIP_EPZ5676_6d


title: HEK293T_96well cell2


title: HEK293T_96well cell1


title: Sample 1433_Single mESC cell


title: MOLM13_H3K79me2-ChIP_EPZ5676_3d


title: MOLM13_H3K79me2-ChIP_DMSO_9d


title: MOLM13_H3K79me2-ChIP_DMSO_6d


title: Sample 1437_Single mESC cell


title: RS4,11_H3K79me2-ChIP_DMSO_9d


title: Sample 1432_Single mESC cell


title: Sample 1431_Single mESC cell


title: MOLM13_H3K79me2-ChIP_DMSO_3d


title: MOLM13_MEN1-ChIP_EPZ5676_4d

value: Menin

value: anti-Menin( Bethyl #A300-105A Lot:8)


title: MOLM13_MEN1-ChIP_comp10_4d


title: Sample 1430_Single mESC cell


title: MOLM13_MEN1-ChIP_comp11_4d

value: compound 11 (100nM)


title: MOLM13_MEN1-ChIP_VTP50469_4d


title: MOLM13_DOT1L-ChIP_comp11_4d

value: anti-DOT1L (Cell signaling # 77087S clon 1W4Z lot 0)


title: MOLM13_MEN1-ChIP_DMSO_4d


title: Sample 1428_Single mESC cell


title: Sample 1429_Single mESC cell


title: MOLM13_DOT1L-ChIP_comp10_4d


title: Sample 1427_Single mESC cell


title: AN1

city: Houston

first: Peng

last: Wei

state: TX

department: Biostatistics

institute: The University of Texas MD Anderson Cancer Center

description: male

hyb_protocol: After we prepared biotin-labeled cRNA fragments, samples were turned over immediately to our Microarray Core Facility which used Gene Chip Hybridization Oven 640, Affymetrix FS4000 Fluidics Station for staining with a streptavidin-fluorochrome probe and washing

scan_protocol: An Affymetrix High Resolution Scanner was used according to the manufacturer's standard manual

data_processing:
For raw microarray data, we used the RMA (robust multi-array average) method to summarize expression values from probe pair values; data were background-adjusted, quantile normalized (global scaling across multiple arrays).
Expression measures were summarized based on log transformed PM (perfect match) values using Median Polish algorithm. Then, we used locally weighted scatterplot smoothing (LOWESS) to do within-array normalization. RMA and LOWESS were performed in Genedata Expressionist Pro3.1® (Basel, Switzerland).

label: biotin

source_name: BOEC

label_protocol: We used the Invitrogen SuperScript Choice system to reverse transcribe and synthesize double-stranded cDNA. For in vitro transcription and biotin-labeling, we synthesized biotin-labeled cRNA using the Enzo Life Sciences BioArray High Yield RNA Transcript Labeling kit. Then fragmentation of cRNA was done by standard protocol, and fragmentation was verified by gel electrophoresis.

growth_protocol: From patients undergoing cardiac catherization stujdy at Mayo Clinic (Dr. Amir Lerman), peripheral venous blood was drawin into citrate anticoagulant, packed in Saf-T-Pak cartons pre-equilibrated to room termperature, and driven to University of Minnesota (to lab of Dr. Robert P Hebbel). Within 5 hours of venipuncture, cultures were set up using the method we originally developed (Lin et al, J Clin Invest.  2000;105(1):71-77) but using the extraordinary precautions we previously adopted and validated for BOEC gene expression study (Wei et al, BMC Med 2011;9:2. doi: 10.1186/1741-7015-9-2). Key elements of the BOEC culture method include: collection of blood mononuclear cells using Histopaque-1077; washing using the culture medium we previously developed for dermal microvsacular endothelial cells [per Gupta et al, Exptl Cell Research 1997;230(2):244-251], supension in EGM2 medium [from Clonetics}, plating onto collagen I, discard non-adherent cells on day 2, change culture medium daily.  Additional precautions are essential for reproduciblity and validity [Milbauer et al, Blood 2008;11(1):3872-3879, and Wei et al BMC Med 2001;9:2.doi 1186/1741-7015-9-2].

extract_protocol: We prepared BOEC lysates by adding 10 ml trizol (Gibco) to each T75 flask to solubilize the sample. As necessary, trizol lysates were stored in liquid nitrogen. We then isolated total RNA, and cleaned it using an RNeasy kit (Qiagen, CA).

treatment_protocol: BOEC were always harvested at passage 3, which comprised a nominal million-fold expansion since establishing culture and amounted to ~3x107 BOEC. They were always harvested 4 hours after the last change of culture medium, and always when they were at 85-90% confluent.

tag: condition

value: abnormal coronary endothelial function


title: AN4

description: female


title: MOLM13_DOT1L-ChIP_VTP50469_4d

tag: cell line


title: MOLM13_DOT1L-ChIP_EPZ5676_4d


title: MOLM13_DOT1L-ChIP_DMSO_4d


title: MOLM13_ChIP-input_1


title: Sample 1426_Single mESC cell

data_processing:
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.19.0.316. Reads were trimmed from polyA tails using cutadapt v 1.18 with the following parameters: -m 18 -j 4 -a AAAAAAAAAA -a TTTTTTTTTT. Reads were then aligned to the human (GRCh38) or mouse genome (GRCm38) using STAR v2.7.0d 37 with the following parameters --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 18 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0  --outMultimapperOrder Random. Reads mapping to multiple locations were assigned either to a location with the best mapping score or, in the case of equal multimapping score – to the genomic location randomly chosen as “primary”.
Genome_build: GRCm38, GRCh38
Supplementary_files_format_and_content: tab-delimited text files of count tables

tag: day of differentiation


title: RNA-seq Jurkat shSRSF6 replicate 2

source_name: Jurkat

extract_protocol:
Aurum Total RNA Mini Kit (Bio-Rad)
Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina NextSeq 500 using 50bp single-read method.

treatment_protocol: cells treated with short hairpin against SRSF6.

value: human T cell leukemia cells

value: Jurkat


title: Sample 1425_Single mESC cell

extract_protocol:
Lysis plates were prepared by dispensing 0.3μL lysis buffer (4 U Recombinant RNase Inhibitor (RRI) (Takara Bio, 2313B), 0.12% TritonTM X-100 (Sigma, 93443-100ML), 1μM Smart-seq4 oligo-dT primer (5’-Biotin- /5BiosG/CATAGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGT30VN-3’;IDT) (see Supplementary Table 3 for a full list of oligos used in the present study) into 384-well hard-shell PCR plates (Bio-Rad HSP3901) using Mantis liquid handler (Formulatrix). 96-well lysis plates were prepared with 3 μl lysis buffer. All plates were sealed with AlumaSeal CS Films (Sigma-Aldrich Z722634), spun down and snap-frozen on dry ice.   Cells were stained with calcein-AM and ethidium homodimer-1 (LIVE/DEAD® Viability/Cytotoxicity Kit, ThermoFisher L3224) and individual live cells were sorted in 384 well lysis plates using SONY sorter (SH800S) with 100um nozzle chip. Plates were spun down and stored at -80 degrees immediately after sorting.
Smart-seq-total


title: RNA-seq Jurkat shSRSF6 replicate 3


title: RNA-seq Jurkat shSRSF6 replicate 1


title: AN7

description: male


title: AN5

description: female


title: RNA-seq Jurkat shCtrl replicate 2


title: AN6

description: male


title: AN8

description: male


title: Sample 1424_Single mESC cell


title: RNA-seq Jurkat shCtrl replicate 1


title: AN9

description: male


title: Sample 1423_Single mESC cell


title: Sample 1422_Single mESC cell


title: RNA-seq CUTLL1 P5091 24hr replicate 1

treatment_protocol: cells treated with the USP7 inhibitor P5091 with DMSO as the control.


title: AN11

description: female


title: RNA-seq CUTLL1 P5091 24hr replicate 2


title: RNA-seq CUTLL1 DMSO control for P5091  replicate 3


title: Sample 1421_Single mESC cell


title: AN10

description: male


title: Sample 1420_Single mESC cell


title: RNA-seq CUTLL1 DMSO control for P5091 replicate 1


title: RNA-seq CUTLL1 DMSO control for P5091 replicate 2


title: RNA-seq Jurkat P5091 24hr replicate 2


title: RNA-seq Jurkat P5091 24hr replicate 3


title: Sample 1419_Single mESC cell


title: AN14

description: female


title: RNA-seq Jurkat shCtrl replicate 3


title: RNA-seq Jurkat P5091 24hr replicate 1


title: AN15

description: female


title: RNA-seq Jurkat DMSO control for P5091 replicate 3


title: RNA-seq Jurkat DMSO control for P5091 replicate 1


title: Sample 1417_Single mESC cell


title: RNA-seq Jurkat DMSO control for P5091 replicate 2


title: AN17

description: male


title: RNA-seq CUTLL1 P5091 24hr replicate 3


title: RNA-seq Jurkat H3B-8800 24hr replicate 3


title: N1

description: female

value: normal coronary endothelial function


title: RNA-seq Jurkat H3B-8800 24hr replicate 2


title: Sample 1416_Single mESC cell

value: Differentiated mESC


title: RNA-seq Jurkat H3B-8800 24hr replicate 1


title: RNA-seq Jurkat DMSO control for H3B-8800 24h replicate 3


title: Sample 1415_Single mESC cell

value: day 0


title: RNA-seq Jurkat DMSO control for H3B-8800 24h replicate 2


title: N2

description: female


title: AN13

description: female


title: Sample 1414_Single mESC cell


title: RNA-seq Jurkat DMSO control for H3B-8800 24h replicate 1


title: N4

description: female


title: N6

description: male


title: Sample 1418_Single mESC cell


title: RNA-seq Jurkat H3B-8800 6hr replicate 3


title: RNA-seq Jurkat H3B-8800 6hr replicate 2


title: Sample 1412_Single mESC cell


title: RNA-seq Jurkat DMSO control for H3B-8800 6h replicate 3


title: RNA-seq Jurkat DMSO control for H3B-8800 6h replicate 1


title: N10

description: female


title: Sample 1411_Single mESC cell


title: N8

description: male


title: RNA-seq Jurkat DMSO control for H3B-8800 6h replicate 2


title: RNA-seq CUTLL1 H3B-8800 6hr replicate 3

data_processing:
Basecalls performed using bcl2fastq
RNA-seq reads were aligned to the hg19 genome assembly using Tophat
Reads were counted on the exons of hg19 genes using htseq
Differential gene expression analysis was performed using edgeR.
Diferential alternative splicing analysis was performed using rMATS.
Genome_build: hg 19
Supplementary_files_format_and_content: rMATS output. SAMPLE_1=CUTLL1_DMSO, SAMPLE_2=CUTLL1_H3B-8800.


title: RNA-seq Jurkat H3B-8800 6hr replicate 1


title: RNA-seq CUTLL1 H3B-8800 6hr replicate 2


title: Sample 1410_Single mESC cell


title: RNA-seq CUTLL1 DMSO replicate 3


title: RNA-seq CUTLL1 DMSO replicate 1


title: Sample 1408_Single mESC cell


title: AGS_CLDN6_KD_2

city: Tokushima

first: Kohmoto

last: Tomohiro

address: Kuramoto-cho 3-18-15

country: Japan

institute: Tokushima University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >20.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE Oligo Microarrays (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.6 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit, One-Color (Agilent, 5190-2305) according to the manufacturer's instructions. Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Mini Kit (Qiagen, Valencia, CA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (G2938C, Agilent Technologies, Santa Clara, CA).

value: AGS

value: gastric adenocarcinoma cell


title: T-ALL patient No.3 replicate 2

source_name: patient-derived T-cell acute lymphoblastic leukemia cells


title: AGS_CLDN6_KD_1


title: Sample 1409_Single mESC cell


title: T-ALL patient No.3 replicate 1

value: T-cell acute lymphoblastic leukemia cells


title: 4H_Z1363: Htt+/+ Hdac2D/D rep7

first: Serkan

last: Erdin

address: 185 Cambridge Street

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

data_processing:
Read quality was assessed using fastQC.
Sequence reads were aligned using GSNAP version 2015-06-23 with parameters -a off -N 1 -pairexpect=450 -B 3 -query-unk-mismatch=1.
Gene level counts were tabulated using BedTools's multibamcov algorithm on unique alignments for each library.
Quality checking of alignments were assessed by custom scripts utilizing PicardTools, RNASeQC, RSeQC and SamTools. This data processing step identified 2A_5794 as an outlier, which was excluded from further analyses.
The threshold for detection (≥ 6) was determined using ERCC spike-ins, as described in Blumenthal et al AJHG 2014. Genes for which the threshold was met in all retained libraries in at least one genotype group within a given comparison were kept. Genes with less than 250 nt in length, as well as genes assigned a "tRNA" or "rRNA" biotype in the gtf file, were filtered out.
Differential expression analysis was carried out on the following comparisons:  groups 1 vs 2; 3 vs 4, 3 vs 1 and 4 vs 2  using EdgeR + SVA pipeline.
Genome_build: GRCm38 (Ensembl bult version 75)
Supplementary_files_format_and_content: Comma separated text file of expression of mouse genes as counts

source_name: Mouse striatal tissue

growth_protocol: HttQ111/+ (C57B6/J) Huntington's disease knock-in mice (Lee JM, Pinto RM, Gillis T, St Claire JC, Wheeler VC. PLoS One. 2011;6(8):e23647) were crossed with D9-Cre transgenic mice (C57B6/J) containing a genomic fragment of the mouse Ppp1r1b gene encoding DARPP-32, driving the expression of Cre recombinase in MSNs after 5-6 weeks of age (Bogush AI, McCarthy LE, Tian C, Olm V, Gieringer T, Ivkovic S, et al. Genesis. 2005;42(1):37-46) and with mice harboring a conditional “floxed” Hdac2 allele (Montgomery RL, Davis CA, Potthoff MJ, Haberland M, Fielitz J, Qi X, et al. Genes Dev. 2007;21(14):1790-802). The Hdac2 floxed line was originally on a mixed C57BL/6/129SeEv background and subsequently maintained by crossing to C57BL/6J. Resulting mice for RNA-seq were either wild type (Htt+/+) or heterozyogus (HttQ111/+) for the HttQ111 allele, and either wild-type for the Hdac2 allele (Hdac+/+) or homozygous for the Hdac2 floxed allele and also expressing the D9-Cre transgene, resulting in MSN-specific Hdac2 deletion (Hdac2D/D).

extract_protocol:
Total RNA was isolated using Trizol/chloroform extraction. Briefly, pelleted cells were resuspended in Trizol reagent and then extracted with chloroform, followed by isoproponal precipitation of RNA from the aqueous phase and three 70% ethanol washes. RNA pellets were solubilized in 30-50 micro liter of RNase-free water. RNA quality was assessed using the Agilent Bioanalyzer TapeStation 2200 .
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Sample PrepKit. Each library also included 1 ul of a 1:10 dilution of ERCC RNA Control Spike-Ins (Ambion) that were added from one of two mixes, each containing the same 92 synthetic RNA standards of known concentration and sequence.

treatment_protocol: Genetic manipulations only as above

value: Mouse striatal tissue

tag: genotype

value: Htt+/+ Hdac2-/-

tag: groups

value: group 4

tag: Sex

value: F

tag: age (week)

tag: cre

value: Cre+

tag: extraction date

tag: cag length


title: AGS_control_1

tag: genotype/variation

value: control


title: 5C_Z1372: Htt+/+ Hdac2D/D rep9


title: AGS_control_2


title: 5B_Z1367: Htt+/+ Hdac2D/D rep8

value: M


title: RNA-seq CUTLL1 H3B-8800 6hr replicate 1


title: Sample 1407_Single mESC cell


title: T-ALL patient No.2 replicate 2


title: Sample 1413_Single mESC cell


title: T-ALL patient No.2 replicate 1


title: 4G_Z1361: Htt+/+ Hdac2D/D rep6


title: T-ALL patient No.1 replicate 1


title: Sample 1405_Single mESC cell


title: RNA-seq CD4 T-cells replicate 2

source_name: CD4 T-cells

value: Human CD4 positive T cells


title: RNA-seq CD3 T-cells replicate 3

source_name: CD3 T-cells

value: Human CD3 positive T cells


title: Sample 1406_Single mESC cell

source_name: Single mESC cell


title: 3G_V1977: Htt+/+ Hdac2D/D rep4


title: 4B_Z1355: Htt+/+ Hdac2D/D rep5


title: RNA-seq CD4 T-cells replicate 1


title: RNA-seq CUTLL1 DMSO replicate 2

value: human T cell leukemia cells


title: RNA-seq CD3 T-cells replicate 2


title: 3F_V1976: Htt+/+ Hdac2D/D rep3


title: Sample 1404_Single mESC cell


title: RNA-seq CD3 T-cells replicate 1


title: Sample 1403_Single mESC cell


title: Sample 1402_Single mESC cell


title: X3.022_SLAMhi

city: New York City

first: Ramin

last: Herati

state: NY

address: 429 E. 29th Street, room 308

institute: NYU School of Medicine

description: Human splenic nonnaive SLAMhiCXCR5++PD1++ CD4 T cells

data_processing:
FASTQ files were trimmed using Trimmomatic 0.32.
Trimmed FASTQ files were aligned using STAR 2.5.2a against the HG38 reference genome.
The aligned files were processed using PORT 0.8.5 gene-based normalization (https://github.com/itmat/Normalization).
Variance-stabilizing transformation and differential expression analysis were performed using DESeq2 1.20.0.
Genome_build: HG38
Supplementary_files_format_and_content: Counts data

source_name: SLAMhi GC-Tfh

extract_protocol:
Human splenic lymphocytes were isolated by mechanical dissociation followed by density gradient centrifugation using Ficoll to eliminate red blood cells. Splenic mononuclear cells were sorted on a BD Aria II sorter. Sorted cells were lysed and RNA isolated using the Rneasy Plus Micro kit (Qiagen catalog #74034 ) using the standard protocol.
cDNA libraries were prepared using the Clontech SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian kit, according to manufacturer instructions.

value: Spleen


title: X3.022_nonGCTfh

description: Human splenic nonnaive CXCR5+PD1+ CD4 T cells

source_name: non-GC Tfh

value: splenic nonnaive CXCR5+PD1+ CD4 T cells


title: 3D_V1974: Htt+/+ Hdac2D/D rep2


title: X3.019_SLAMlo

description: Human splenic nonnaive SLAMloCXCR5++PD1++ CD4 T cells

source_name: SLAMlo GC-Tfh


title: 4F_Z1360: HttQ111/+ Hdac2D/D  rep11

value: group 3


title: X3.022_Naive

description: Human splenic naïve CD4 T cells

source_name: Naïve CD4

value: splenic naive CD4 T cells


title: X3.019_SLAMhi

value: splenic nonnaive SLAMhiCXCR5++PD1++ CD4 T cells


title: X3.018_SLAMlo

value: splenic nonnaive SLAMloCXCR5++PD1++ CD4 T cells


title: Sample 1400_Single mESC cell

value: Differentiated mESC

value: day 0


title: Sample 1401_Single mESC cell


title: 1H_A5788: Htt+/+ Hdac2D/D rep1

value: Mouse striatal tissue

value: Htt+/+ Hdac2-/-


title: X3.018_SLAMhi


title: Sample 1399_Single mESC cell


title: 4E_Z1359: HttQ111/+ Hdac2D/D  rep10


title: 4D_Z1358: HttQ111/+ Hdac2D/D  rep9


title: X3.007_SLAMlo


title: Sample 1398_Single mESC cell


title: X2.034_SLAMlo


title: 4A_V1980: HttQ111/+ Hdac2D/D  rep8


title: X2.034_SLAMhi


title: X3.007_SLAMhi


title: Sample 1397_Single mESC cell


title: X2.034_nonGCTfh


title: 3E_V1975: HttQ111/+ Hdac2D/D  rep7


title: X2.034_Naive

description: Human splenic naïve CD4 T cells


title: X3.022_SLAMlo


title: Sample 1396_Single mESC cell


title: X2.033_SLAMlo


title: X2.033_nonGCTfh


title: 2G_v1802: HttQ111/+ Hdac2D/D  rep5


title: X2.022_SLAMlo


title: 3A_v1804: HttQ111/+ Hdac2D/D  rep6


title: X2.033_SLAMhi


title: Sample 1395_Single mESC cell


title: 1E_A5779: HttQ111/+ Hdac2D/D  rep3


title: X2.033_Naive

description: Human splenic naïve CD4 T cells


title: Sample 1394_Single mESC cell


title: 2D_V1346: HttQ111/+ Hdac2D/D  rep4


title: Sample 1393_Single mESC cell


title: X2.020_SLAMhi


title: X2.019_SLAMlo


title: X2.022_SLAMhi


title: X1.027_SLAMlo


title: Sample 1391_Single mESC cell


title: 1A_A5312: HttQ111/+ Hdac2D/D  rep2

value: F


title: Sample 1390_Single mESC cell


title: X1.027_SLAMhi


title: 1B_A5313: HttQ111/+ Hdac2D/D  rep1

value: Cre+


title: 5A_Z1365: Htt+/+ Hdac2+/+  rep9

value: Htt+/+ Hdac2+/+

value: group 2

value: Cre-


title: X1.025_SLAMhi


title: Sample 1389_Single mESC cell


title: X1.022_SLAMlo


title: 3H_V1979: Htt+/+ Hdac2+/+  rep8

value: M


title: X1.022_SLAMhi


title: X2.020_SLAMlo


title: X1.017_SLAMhi


title: 3C_V1973: Htt+/+ Hdac2+/+  rep7


title: X1.017_nonGCTfh


title: 2H_v1803: Htt+/+ Hdac2+/+  rep6


title: Sample 1392_Single mESC cell


title: X1.017_Naive

description: Human splenic naïve CD4 T cells


title: X2.019_SLAMhi


title: Sample 1386_Single mESC cell


title: 2C_V1345: Htt+/+ Hdac2+/+  rep5


title: X1.014_Naive

description: Human splenic naïve CD4 T cells


title: 2B_V1344: Htt+/+ Hdac2+/+  rep4


title: X1.014_SLAMhi


title: X1.014_SLAMlo


title: Sample 1385_Single mESC cell


title: 1G_A5786: Htt+/+ Hdac2+/+  rep2


title: X1.014_nonGCTfh


title: Sample 1383_Single mESC cell


title: 1D_A5446: Htt+/+ Hdac2+/+  rep1


title: Sample 1382_Single mESC cell


title: Patient 4 Plate 8 (P4_P8)

city: MILAN

first: BIANCA

last: CIONI

state: MI

address: Via Amadeo 41

department: Molecular Oncology

country: Italy

institute: Istituto Nazionale Tumori

description: single cell RNA sequencing

data_processing:
Single-cell transcriptomics analysis was performed using the RaceID3 algorithm, following an adapted version of the RaceID manual.
Cells were clustered with RaceID, after removing cells with less than 2000 UMIs and genes expressed in less than 3 cells with at least 4 UMIs.
For follow up clustering, cells belonging to samples that yielded very few cells were removed, as well as contaminant NK cells.
Cells with high levels of technical artefact genes like KCNQ1OT1 were removed.
The resulting cells were clustered again with RaceID, with the same filter cutoff

source_name: CD14+CD11b+ cells isolated from Pca biopsies

growth_protocol: Single-cell suspension was prepared from fresh PCa biopsies by mechanical  dissociation within two hours after surgery. Biopsies were transported from the  operation room on ice and minced with a scalpel in cold PBS + 0.5% BSA. Tissue  was then mechanically dissociated with the gentleMACS TM Dissociator (MACS  Milteny Biotec) using C-tubes for 2 minutes. Subsequently, the sample was filtered through a 70 μm strainer (BD  Falcon) and spun down for 5 min at 300 g at 4°C. Cells were re-filtered through a 40-  μm strainer, spun down for 5 min at 300 g at 4°C and re-suspended in  cold PBS + 0.5% BSA.

extract_protocol:
Cells were heat-lysed at 65° C followed by cDNA synthesis using the CEL-Seq2 protocol using robotic liquid handling  platforms Nanodrop II (GC Biotech) and Mosquito (TTP Labtech). After second strand cDNA synthesis, the barcoded material was pooled into libraries of 384 cells  and amplified using in vitro transcription (IVT).
Following amplification, the rest of the CEL-seq2 protocol was followed for preparation of the amplified cDNA library, using  TruSeq small RNA primers (Illumina). The DNA library was paired-end sequenced  on an Illumina Nextseq™500, high output, 1x75 bp.
After Illumina sequencing, Read 1 was assigned 26 base pairs and was used  for identification of the illumina library barcode and cell barcode. Unique molecular  identifiers (UMI) tags were added to each read. These are molecular tags used in  order to detect and quantify unique mRNA transcripts. More specifically, mRNA  libraries were generated by fragmentation and reverse transcribed to cDNA with tag-  specific primers. R2 was assigned 60 base pairs and used to map to the reference  transcriptome of Hg19.

treatment_protocol: Cells of the dissociated biopsies were incubated with APC-CD45, PE-CD14, PE-CD11b and FITC-CD3 for 20 minutes and washed before sorting using a Moflo Astrios or FACSAria IIu.

tag: gleason score

tag: pt

tag: tumorous vs non-tumorous side

value: non-tumorous


title: Sample 1388_Single mESC cell

first: Alina

last: Isakova

institute: Stanford University


title: Patient 3 Plate 4 (P3_P4)

description: single cell RNA sequencing

tag: cell type

value: CD14+CD11b+ cells isolated from Pca biopsies

value: Tumorous


title: Patient 2 Plate 3 (P2_P3)

description: single cell RNA sequencing


title: Patient 4 Plate 7 (P4_P7)

description: single cell RNA sequencing


title: Sample 1387_Single mESC cell


title: X1.017_SLAMlo

value: Spleen


title: 5D_Z1392: HttQ111/+ Hdac2+/+  rep7

value: group 1


title: Sample 1381_Single mESC cell


title: Patient 1 Plate 1 (P1_P1)

description: single cell RNA sequencing

value: Tumorous and non-tumorous


title: 3B_V1972: HttQ111/+ Hdac2+/+  rep5


title: X1.025_SLAMlo

value: splenic nonnaive SLAMloCXCR5++PD1++ CD4 T cells


title: Sample 1384_Single mESC cell

value: Differentiated mESC


title: Sample 1379_Single mESC cell

value: day 0


title: 2F_v1801: HttQ111/+ Hdac2+/+  rep4

value: Mouse striatal tissue


title: Patient 3 Plate 5 (P3_P5)

description: single cell RNA sequencing


title: 10ATGFbD6_1

city: TALLAHASSEE

first: LAUREN

last: COLE

state: Florida

address: 319 STADIUM DR

institute: FLORIDA STATE UNIVERSITY

description: MCF10A TGF-beta treated day 6 rep1

data_processing:
base calling was performed using the bcl2fq script
transcript abundance estimation was performed using kallisto (0.43.0)
transcript abundances were further analysed and normalised using sleuth
gene-level abundance estimates were generated by summing transcript abundances per gene
Genome_build: UCSC hg19
Supplementary_files_format_and_content: TSV format; target ID, target length, target effective length, estimated counts, transcripts per million (TPM)

molecule: polyA RNA

source_name: Human breast epithelial cells, immortalized

growth_protocol: MCF-10A and MCF-10Ca1a cell lines were grown in DMEM/Nutrient F12 (DMEM/F12) media supplemented with 5% Horse Serum, 14 mM NaHCO3, 10 µg/mL insulin, 2 mM L-glutamine, 20 ng/mL human EGF, 500 ng/mL Hydrocortisone and 100 ng/mL Cholera Toxin.

extract_protocol:
RNA was purified using the RNeasy Mini Kit (Qiagen) and cDNA synthesized using the QuantiTect Reverse Transcription Kit (Qiagen). The knockdown of H2A.Z expression was analysed by qPCR on the 7900HT Fast Real-Time PCR system using SYBR Green I master mix (applied biosystems) and 0.15mM primers as previously described (Domaschenz, 2017). Relative expression values were normalized to pooled housekeeping genes Glyceraldehyde 3-phosphate dehydrogenase (GAPDH), Beta-actin (B- actin), Ribsomal Protein S23 (RPS23) and Splicing Factor 3a Subunit 1 (SF3A1) (Maltseva et al., 2013).
Libraries were constructed according to the Illumina TruSeq stranded mRNA protocol with poly-A enrichment.

treatment_protocol: For EMT induction, MCF-10A cells were treated with 5 ng/ml TGF-β1 (Redsystems) for 8 days. MCF-10A cells were transduced with the lentviral vector pLVTHM shH2A.Z as previously described (Domaschenz, 2017). GFP-positive cells were sorted 2 days post-transduction and further cultured for 8 days before being processed.

value: Human breast epithelial cells

tag: treatment

value: TGF-beta-1 added to growth medium

tag: days post treatment


title: 10ATGFbD6_3

description: MCF10A TGF-beta treated day 6 rep3

tag: tissue


title: 10ATGFbD6_2

description: MCF10A TGF-beta treated day 6 rep2


title: 10AshZD8_2

description: MCF10A H2A.Z sh KD day 8 rep2

value: shRNA targeting H2A.Z, retroviral transduction


title: Sample 1378_Single mESC cell

city: Stanford

address: 318 Campus drive

tag: cell line


title: 10AD8_3_S18

description: MCF10A WT day 8 rep3


title: 2E_V1347: HttQ111/+ Hdac2+/+  rep3


title: Sample 1377_Single mESC cell

tag: day of differentiation


title: 10AshZD8_1

description: MCF10A H2A.Z sh KD day 8 rep1


title: 1F_A5783: HttQ111/+ Hdac2+/+  rep2

tag: genotype

value: F


title: 10AD8_2_S17

description: MCF10A WT day 8 rep2


title: Sample 1376_Single mESC cell


title: 1C_A5445: HttQ111/+ Hdac2+/+  rep1

tag: groups


title: 4C_Z1356: HttQ111/+ Hdac2+/+  rep6

tag: Sex


title: Patient 1 Plate 2 (P1_P2)

description: single cell RNA sequencing


title: Sample 1380_Single mESC cell


title: Sample 1375_Single mESC cell


title: 10AD6_1_S10

description: MCF10A WT day 6 rep1


title: 10AD8_1_S16

description: MCF10A WT day 8 rep1


title: 10AD6_2_S11

description: MCF10A WT day 6 rep2


title: 10AD6_3_S12

description: MCF10A WT day 6 rep3


title: Sample 1374_Single mESC cell


title: T_2_RNA-seq

city: Sacramento

middle: J

last: Canter

address: 4645 2nd Ave, Research III, Room 2200D

department: Surgery

institute: University of California, Davis

data_processing:
The quality of raw reads were assessed using fastqc
Ribosomal RNA content was determined by aligning the reads against a set of Mouse rRNA sequences using bowtie2 v.2.3.4.1.
Raw reads were processed and trimmed to remove phiX and adapter sequences, and to remove the first 20 bases from each read.
Processed reads were aligned to GRCm38.p6 primary genome assembly using GENCODE v21 annotation, with STAR v.2.7.0f to generate counts per gene.
Tables of raw counts and counts-per-million (CPM) normalized counts were generated. Prior to analysis, genes with low expression (defined here as a those with mean CPM less than 2.5) were filtered, leaving 10,279 genes.  Differential expression analyses were conducted using the limma-voom Bioconductor pipeline
Genome_build: GRCm38.p6 primary genome assembly using GENCODE v21 annotation
Supplementary_files_format_and_content: Normalized expression values in excel format

source_name: Intra-tumoral T cells

growth_protocol: CT26 tumors cells were cultured in RPMI with 10% Nu-Serum for three passages prior to use

extract_protocol:
Subcutaneous tumors were extracted from euthenized mice and mechanically dissociated, washed with PBS then strained through a 70 um filter. Immune cells were enriched using Percoll gradient centrifugation. Cells were stained and isolated using a FACS Aria machine. Cells were then processed for RNA isolation using the Norgen BioTek Total RNA Purification Plus Micro Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CT26 tumors were injected into the subcutaneous space of syngeneic BALB/C mice in 200 uL PBS containing 500,000 live cells

tag: strain

value: BALB/C

value: T cells


title: 10AshZD8_3

description: MCF10A H2A.Z sh KD day 8 rep3


title: T_1_RNA-seq


title: MCF10Ca1a_wt_rep1

description: MCF10ACa1A rep1

source_name: Human breast epithelial cells, virally transformed


title: MCF10A_wt_rep2

description: MCF10A WT rep2


title: MCF10A_wt_rep1

description: MCF10A WT rep1


title: Sample 1373_Single mESC cell

growth_protocol: HEK293T cells were cultured in complete DMEM high glucose medium (Gibco, ThermoFisher 11965092) supplemented with 5% Fetal Bovine Serum (ThermoFisher 16000044), 1mM Sodium Pyruvate (ThermoFisher 11360070) and 100 μg/mL Pencillin/Streptomycin (ThermoFisher 15070063). They were collected 2h after passaging and sorted in either 96-well plates with 3uL lysis buffer or 384-well paltes with 0.3 uL of lysis buffer in each well.    Human primary dermal fibroblasts were obtained from ATCC (ATCC® PCS-201-012™). Cells were cultured and passaged four times in Fibroblast Basal Medium (ATCC® PCS-201-030™) supplemented with 5ng/mL rh FGF β, 7.5mM L-glutamine, 50 ug/mL Ascorbic acid, 5ug/mL rh Insulin, and 1% Fetal Bovine Serum (Fibroblast Growth kit- low serum, ATCC® PCS-201-041™).  MCF7 cells (ATCC® HTB¬22™) were cultured in complete DMEM high glucose medium (Gibco, ThermoFisher 11965092) supplemented with 10% Fetal Bovine Serum (ThermoFisher 16000044), 1mM Sodium Pyruvate (ThermoFisher 11360070) and 100 μg/mL Pencillin/Streptomycin (ThermoFisher 15070063).  mESCs were maintained and differentiated as described previously35,36. Briefly, mESCs were grown in serum-free 2i+LIF medium (complete medium: DMEM/F12 glutaMAX (Gibco, ThermoFisher  10565018) , 1% N2 supplement (Gemini Bio), 2% B27 supplement (Gemini Bio), 0.05% BSA fraction V (ThermoFisher, 15260037), 1% MEM-non-essential amino acids (c  11140050), and 110 μM 2-mercaptoethanol (Pierce); supplemeted with MEK inhibitor PD0325901 (0.8 μM), GSK3β inhibitor CHIR99021 (3.3 μM) and 10ng/mL mouse LIF (Gibco, PMC9484) in tissue culture (TC) dishes pretreated with 7.5 μg/ml polyL-ornithine (Sigma) and 5 μg/ml laminine (BD). To induce spontaneous embryoid body formation cells were washed with PBS, dissociated with StemPro Accutase (Gibco, ThermoFisher cat# A1110501), transferred to serum-rich medium (complete medium: DMEM/F12 glutaMAX (Gibco) , 1% N2 supplement (Gemini Bio), 2% B27 supplement (Gemini Bio), 0.05% BSA fraction V, 1% MEM-non-essential amino acids, and 110 μM 2-mercaptoethanol; supplemented with 10% FBS (ThermoFisher 10439001) and diluted to 10^6 cells/mL. Each 10 uL of cell suspension were plated as a hanging drop in 10 cm2 TC dishes (15-20 drops per dish). 10uL of fresh serum-rich media was added to each drop on day 4 of the culture. Primed mESCs were collected 6h after hanging drop culture. Embryoid bodies were collected and dissociated at days 4, 8 and 12 of culture.


title: Sample 1372_Single mESC cell


title: NK_2_RNA-seq

source_name: Intra-tumoral NK cells

value: NK cell


title: T1D subject ID:eb23

city: Paris

first: Felipe

middle: Leal

last: Valentim

state: Île-de-France

address: Bâtiment Cervi, 4ème étage, pièce 052

institute: INSERM/UPMC

description: Whole blood RNA-seq, sample from T1D subject

data_processing:
Nextera adaptor removal:Trimmomatic (Bolger et al., 2014)
Reads alignment:  hisat2 (Kim et al., 2015)
Read counts: featureCounts (Liao et al., 2014)
Read counts normalization: DESeq2 (Anders and Huber, 2010)
SAM to BAM conversion: samtools (Li et al., 2009)
Genome_build: The GRCh37 assembly in Ensembl (Yates et al., 2016)
Supplementary_files_format_and_content: reads_count.gene_level.txt: Raw read counts as outputed by featureCounts for all samples.

source_name: Whole blood

extract_protocol:
Total RNA from whole blood has been extracted following a two-step procedure. First, RNA from blood collected on PAX-Gene tubes has been extracted using Maxwell 16 LEV simplyRNA blood kit (Promega) following manufacturer recommendations and second b-globin, dominant RNA from red blood cells, has been removed using the GLOBINclear kit (Ambion) on extracted RNA.
RNA sequencing has been performed from using the TruSeq Stranded mRNA preparation kit (Illumina) on 500 ng b-globin depleted RNA with a RNA Integrity Number > 8 (measured on Bioanalyzer following manufacturer recommendations). Libraries were sequenced following a pair-end 2x75 bp protocol on NextSeq 500 or HiSeq 4000 (Illumina) at LIGAN Equipex (Lille, France).

tag: patient diagnosis

value: type 1 diabetes

value: Whole blood

tag: age

tag: batch


title: NK_1_RNA-seq


title: Sample 1371_Single mESC cell


title: T1D subject ID:dc2c


title: T1D subject ID:db6e

value: M


title: Sample_13015GP28

city: Philadelphia

first: Gregory

middle: Robert

last: Grant

state: PA

address: 3400 Civic Center Blvd.

department: Genetics

institute: University of Pennsylvania

data_processing:
CASAVA was used to demultiplex pooled samples and convert BCL to FASTQ.
RNA-seq data were aligned to the mouse genome build mm9 by STAR-2.4.1d.
Data were normalized using a resampling strategy, the code is available at https://github.com/itmat/Normalization . We performed gene-level normalization using default parameters for the mm9 genome.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file from gene-level normalization contains counts from unique reads that only map to one gene.

source_name: liver

growth_protocol: All mice were housed under 12h:12h LD conditions with free access to food and water unless specified. All procedures were approved by the University of Pennsylvania Institutional Animal Care and Use Committee. Bmal1f/f mice (PMID: 25512522) were obtained from C. Bradfield (University of Wisconsin, Madison, WI, USA). The floxed mice were crossed with an aP2 driven Cre (aP2-Cre) mice (Jackson Laboratories, Bar Harbor, ME) to yield Bmal1f/f-aP2-Cre mice.

extract_protocol:
Liver samples were quickly excised every four hour for 20 hours and snap-frozen in liquid nitrogen. Mouse liver (50 - 100 mg) was homogenized using magnetic beads and a TissueLyzer. Total RNA was isolated using Qiagen RNeasy Kit and the RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer.
Illumina TruSeq RNA Sample Prep v2 was used for library construction, according to manufacturer's instructions. Briefly, poly-A containing mRNA was isolated using poly-T oligo-attached magnetic beads and fragmented during elution. First strand cDNA was reverse transcribed from cleaved RNA fragments primed with random hexamers. Second strand cDNA was synthesized and isolated using Ampure XP beads. Blunt ends were created using 3' to 5' exonuclease activity and polymerase activity. A single "A" nucleotide was added to the 3' end and adapters were subsequently ligated onto the ends of the ds cDNA. Indices for multiplexing were attached during this ligation step. 13 cycles of PCR selectively amplified cDNA with adapter molecules on both ends. Using the molarity from Bioanalyzer (DNA 1000), libraries were diluted to 10nM. Libraries at 10nM were run on Bioanalyzer again (HighSensitivity DNA) and taking the lowest molarity, two samples with distinct barcodes were pooled. Clusters were generated using cBOT, and sequenced in one flow cell lane.

treatment_protocol: Mice were kept under constant darkness for 36 h and then sacrificed. Four aP2-Cre Bmal1 fx/fx mice and four littermate controls were sacrificed in darkness every 4h for 20h (6 time points)

value: WT

tag: sample collection time

tag: replicate

value: Liver

value: Adipocyte


title: Sample 1370_Single mESC cell


title: MCF10Ca1a_wt_rep2

description: MCF10ACa1A rep2


title: T1D subject ID:d76a


title: Sample 1369_Single mESC cell


title: Sample_13015GP23


title: Sample_13015GP17


title: Sample 1368_Single mESC cell


title: T1D subject ID:d119


title: Sample_13015GP13


title: T1D subject ID:a15a


title: T1D subject ID:bc66


title: T1D subject ID:c173


title: Sample 1366_Single mESC cell


title: T1D subject ID:b73e


title: Sample_13015GP39


title: T1D subject ID:903a


title: T1D subject ID:9c1a


title: T1D subject ID:e2da


title: T1D subject ID:8185


title: T1D subject ID:82a5


title: T1D subject ID:b302


title: Sample_13015GP11


title: Sample 1364_Single mESC cell


title: T1D subject ID:db19


title: T1D subject ID:71b1


title: T1D subject ID:7d99


title: Sample 1367_Single mESC cell


title: Sample 1365_Single mESC cell


title: T1D subject ID:6733


title: Sample 1363_Single mESC cell


title: Sample 1362_Single mESC cell


title: Sample 1361_Single mESC cell


title: Sample_13015GP25


title: Sample_13015GP04


title: T1D subject ID:64a0


title: T1D subject ID:38b0


title: T1D subject ID:2b2b


title: T1D subject ID:5ed7


title: Sample_13015GP40


title: T1D subject ID:14df


title: Sample_13015GP20


title: T1D subject ID:726e


title: Sample 1359_Single mESC cell


title: Sample 1360_Single mESC cell


title: T1D subject ID:1a72


title: T1D subject ID:1250


title: Sample_13015GP05


title: Sample_13015GP14


title: Sample_13015GP30


title: T1D subject ID:09cf


title: Sample 1358_Single mESC cell


title: T1D subject ID:04b0


title: Sample_13015GP43


title: Sample_13015GP16


title: T1D subject ID:0089


title: Sample 1356_Single mESC cell


title: Sample_13015GP44


title: healthy subject ID:fe48

description: Whole blood RNA-seq, sample from healthy subject

value: healthy


title: Sample 1355_Single mESC cell

value: Differentiated mESC


title: T1D subject ID:0d40


title: Sample_13015GP06


title: healthy subject ID:fbf7


title: healthy subject ID:f27d


title: healthy subject ID:e5ac


title: Sample 1357_Single mESC cell

value: day 0


title: Sample 1353_Single mESC cell


title: Sample 1354_Single mESC cell


title: Sample 1352_Single mESC cell


title: T1D subject ID:54c3


title: T1D subject ID:0935


title: Sample_13015GP22


title: Sample_13015GP41


title: healthy subject ID:ad10


title: healthy subject ID:bb58


title: healthy subject ID:c8a9


title: healthy subject ID:98a3


title: healthy subject ID:8cd0


title: Sample 1351_Single mESC cell


title: healthy subject ID:7f1a


title: healthy subject ID:4d4e


title: healthy subject ID:50e8


title: Sample 1350_Single mESC cell


title: healthy subject ID:471e


title: Sample_13015GP36


title: Sample 1349_Single mESC cell


title: Sample_13015GP02


title: healthy subject ID:1790


title: Sample 1348_Single mESC cell


title: Sample 1347_Single mESC cell


title: Sample_13015GP10


title: Sample_13015GP07