title: T55_3.94_S190

status: Public on Jul 25 2020

data_processing:
After trimming adapters with cutadapt [v2.3], 150 base-pair paired-end reads were aligned to mm10 GENCODE M10 using STAR [v2.5.1b].
Since the first 96 samples were sequenced at twice the depth, picard DownsampleSam [v1.130] was used to down-sample the reads.
Uniquely aligned reads mapped across the whole gene body were quantified by Homer [v4.8]. Only one read per position was kept to control for PCR duplicates.
Raw count table was further analyzed by Seurat [v2.3.4]
Genome_build: mm10 GENCODE M10
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each single-nuclei

source_name: mouse primary visual cortex V1 neurons

growth_protocol: All experimental procedures followed procedures approved by the Salk Institute Animal Care and Use Committee.  Animals were given water with ibuprofen (30 mg/kg) and housed for 3 weeks before tissue harvest.

extract_protocol:
The dissected samples in 1ml NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DL-Dithiothreitol solution (Sigma 646563), 10μl of Protease inhibitor (Sigma P8340), 1.5μl of RNasin Plus RNase inhibitor (Promega, N2611), 0.1% Triton X-100, 5μM Hoechst 33342) were homogenized gently using the ice-cold dounce and pestle. After centrifuge at 3000 rpm for 8 min at 4°C, the supernatant was aspirated and gently resuspended in 1ml NIM buffer. After one repeat, the pellet was resuspended in 450μl of nuclei storage buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DL-Dithiothreitol solution, 9ul of Protease inhibitor), and filtered through 40μM cell strainer on ice. The sample was incubated with 50μl of nuclease-free BSA for 1-2 hours at 4°C, then with GFP antibody conjugated with Alexa Fluor 488 (Invitrogen, A-21311) for 1 hour at 4°C. Fluorescence-activated nuclei sorting of single nuclei was performed using a BD Influx sorter with an 85μm nozzle at 22.5 PSI sheath pressure. Single cell (1 drop single) mode was used for the stringent sorting. GFP+ single nuclei were sorted into 96-well plates preloaded with 2μl of lysis buffer (Triton X-100 10%, 0.1μl RNasin Plus RNase inhibitor in H2O). After fast freeze on dry-ice, the plate was stored at -80°C before library preparation.
Using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech, 634894), cDNA was amplified with 21 PCR cycle following polyA reverse transcription. The quantity and quality of cDNA was validated using the Agilent 2100 Bioanalyzer. 0.2ng/nl of amplified cDNA was used as input to prepare sequencing libraries using the Nextera XT DNA Library Preparation Kit (Illumina). Multiplexed libraries after normalized concentration were sequenced on Illumina HiSeq 4000 to generate 150bp paired-end reads.

treatment_protocol: To label individual nuclei of V1 neurons projecting to AL or PM, 30 nl of AAVretro-Cre was injected to AL or PM after defining visual area borders using ISI. After animals were euthanized in a CO2 chamber and decapitated, the brains were dissected out from the skull and submerged in ice-cold PBS. Coronal brain slices (350μm thick) were cut using VF-300 CompresstomeTM (Precisionary Instruments, Greenville, NC) and submerged in ice-cold PBS. Subregion of V1 containing GFP+ nuclei in brain slices was micro-dissected out into upper and lower halves under the fluorescent dissection microscope (Olympus SZX16) and transferred to microcentrifuge tubes with ice-cold PBS for single-nuclei isolation. The remaining brain slices after dissection were collected, fixed with ice-cold 4% PFA for 2-4 hours, stained with GFP antibody conjugated to Alexa Fluor 488 (Invitrogen, A-21311), and scanned to validate the correct V1 dissection using Olympus BX63 Microscope.

tag: strain

value: C57BL/6 knock-in R26-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT)

tag: cell projection

value: L5 AL

tag: animal


title: T55_3.92_S188

type: SRA

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

country: USA

institute: Salk Institute for Biological Studies

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus


title: T55_3.9_S105


title: T55_3.91_S187


title: T55_3.93_S189


title: WT siGLO Rep 1

status: Public on Aug 10 2020

city: Chapel Hill

first: Jill

last: Dowen

state: NC

address: 250 Bell Tower Drive

institute: University of North Carolina at Chapel Hill

data_processing:
Reads Per Gene: Reads per gene were analyzed using STAR --runThreadN 24 -c SortedByCoordinate
Differentially expressed genes were identified using DESeq2 from Bioconductor (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: For each sample, a text file with reads per gene (gene count) is given.

source_name: mESC v6.5_WT siGLO

growth_protocol: Murine embryonic stem cells (v6.5, male) were grown on gelatinized tissue culture dishes under standard ESC conditions as previously described (Whyte et al., 2012).

extract_protocol:
Cells were resuspended in Trizol (Invitrogen, Carlsbad CA) and Chloroform (Sigma Aldrich, St. Louis, MO) was added for phase separation. After collection, RNA was purified using the Zymo RNA Clean and Concentrator Kit (Zymo, Irvine, CA).
Libraries were prepared by Novogene, with poly-A transcript enrichment and sequenced by Novogene (Beijing, China).

treatment_protocol: Cells were counted and 5 x 10^5 were plated per well in 6-well plates. Each well was treated with 50nM of siRNA or siGLO transfection control using DharmaFECT (Dharmacon, Lafayette, CO) transfection reagent following manufacturer’s instructions: siGLO (D-001630-01-0) and siStag1 (M-041989-01-0005). Cell were harvested after 48 hours for RNA collection.

tag: cell line

tag: cell type

value: Mouse embryonic stem cells

tag: genotype/variation

value: Wildtype

tag: sirna treatment

value: siGLO control


title: EVV18_L4_2

status: Public on Jul 30 2020

description: fpkm.txt

data_processing:
Sequenced reads were quality-tested using FASTQC and aligned to the hg19 human genome using the STAR version 2.5.3a.
Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read).
Gene expression counts were quantified with HOMER v4.10.4 analyzeRepeats.pl using the parameters -fpkm -count exons -condenseGenes -strand + -normMatrix 1000000
Genome_build: hg19 Illumina iGenomes
Supplementary_files_format_and_content: fpkm.txt contains FPKM quantification for all RNA-Seq samples.

molecule: total RNA

organism: Homo sapiens

source_name: naïve T cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated over Lymphoprep (STEMCELL Technologies) gradient . T cells were isolated from fresh PBMCs using EasySep Human T Cell Isolation Kit (STEMCELL Technologies, negative selection) and re-suspended in RPMI media supplemented with 10% FBS, L-glutamine (2 mM), penicillin (100 U/mL), and streptomycin (100 µg/mL) at 2 x 10^6 cells/mL.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) and RNAse free DNAse set (Qiagen) for on column DNA digestion.
RNA-Seq libraries were prepared using the TruSeq stranded mRNA Sample Preparation Kit v2 according to Illumina protocols.

treatment_protocol: The compounds were added to cells as 1000x DMSO stocks and mixed well by pipetting up and down after addition. The cells were kept at 37 °C in 5% CO2 containing incubators for 24 h, then pelleted by centrifugation (524 g, 5 min, 4 °C), washed with cold PBS (10 mL) and

tag: treatment

tag: concentration

value: 10 µM

value: T cells


title: T55_3.96_S192


title: EVV17_DMSO_2

description: fpkm.txt

value: DMSO


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title: EVV5_DMSO_2

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title: T50_3.52_S438


title: T50_3.29_S415


title: T50_3.31_S417


title: T50_3.28_S414


title: T50_3.2_S388


title: T50_3.34_S420


title: T50_3.21_S407


title: T50_3.22_S408


title: T50_3.24_S410


title: T50_3.25_S411


title: T50_3.30_S416


title: T50_3.23_S409


title: T50_3.32_S418


title: T50_3.20_S406


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title: T50_3.19_S405


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title: T50_3.42_S428


title: T50_3.13_S399


title: T50_3.10_S396


title: T50_1.9_S299

value: L23 AL


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title: T50_1.13_S303


title: T45_4.9_S9

value: L5 PM


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title: T45_1.54_S54


title: T45_1.51_S51


title: T45_1.50_S50


title: T45_1.49_S49


title: T45_1.4_S4


title: T45_1.46_S46


title: T45_1.45_S45


title: T45_1.44_S44


title: T45_1.52_S52


title: T45_1.41_S41


title: T45_1.39_S39


title: T45_1.42_S42


title: T45_1.40_S40


title: T45_1.3_S3


title: T45_1.38_S38


title: T45_1.48_S48


title: T45_1.35_S35


title: T45_1.30_S30


title: T45_1.33_S33


title: T45_1.36_S36


title: T45_1.29_S29


title: T45_1.2_S2


title: T45_1.28_S28


title: T45_1.27_S27


title: T45_1.26_S26


title: T45_1.21_S21


title: T45_1.47_S47


title: T45_1.22_S22


title: T45_1.24_S24


title: T45_1.20_S20


title: T45_1.1_S1


title: T45_1.18_S18


title: T45_1.37_S37


title: T45_1.34_S34


title: T45_1.19_S19


title: T45_1.15_S15


title: T45_1.16_S16


title: T45_1.14_S14


title: T44_3.9_S107


title: T45_1.10_S10


title: T44_3.95_S193


title: T44_3.92_S190


title: T45_1.12_S12


title: T44_3.8_S106


title: T44_3.88_S186


title: T44_3.84_S182


title: T44_3.89_S187


title: T44_3.7_S105


title: T44_3.86_S184


title: T44_3.77_S175


title: T44_3.90_S188


title: T44_3.78_S176


title: T44_3.76_S174


title: T44_3.79_S177


title: T45_1.17_S17


title: T44_3.75_S173


title: T44_3.74_S172


title: T44_3.6_S104


title: T44_3.73_S171


title: T45_1.13_S13


title: T44_3.72_S170


title: T44_3.70_S168


title: T45_1.11_S11


title: T44_3.66_S164


title: T44_3.91_S189


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title: T44_3.5_S103


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title: T44_3.58_S156


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title: T44_3.85_S183


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title: T44_3.42_S140


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title: T44_3.19_S117


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title: T44_3.11_S109


title: T44_2.8_S352


title: T44_3.13_S111


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title: T44_3.55_S153


title: T44_2.83_S427


title: T44_2.93_S437


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title: T44_2.7_S351


title: T44_2.92_S436


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title: T44_1.16_S264


title: T44_1.48_S296


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title: T41_T35.30_S224


title: T41_T35.2_S196


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title: T41_T35.22_S216


title: T41_T35.21_S215


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title: T41_T35.20_S214


title: T41_T35.19_S213


title: T41_T35.1_S195


title: T41_T35.15_S209


title: T31_3.8_S160


title: T41_T35.16_S210


title: T31_3.92_S244


title: T41_T35.11_S205


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title: T31_1.H1_S32


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title: T31_1.C5_S59


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title: U87 control IP RNA replicate 3

status: Public on Jul 22 2020

city: Bloomington

first: Heather

middle: Ann

last: Hundley

state: IN

address: 1001 E 3rd St

department: Biology

institute: Indiana University Bloomington

description: ribosomal depleted RNA

data_processing:
Reads were aligned to reference genome hg19 (gencode release 28) using STAR (v2.5.2b)
Mapped  reads were counted using Feature counts (v1.5.2)
Enrichment of transcripts in IP compared to input was analyzed using DESeq2 and EdgeR

Genome_build: GRCh37-hg19 (gencode release 28)
Supplementary_files_format_and_content: tab-delimited text files include the counts for each gene in U87 cells carrying empty vector and U87 cells expressing 3X-FLAG ADAR3

source_name: U87 cells

growth_protocol: U87 cells were maintained in  Dulbecco’s modified Eagle’s medium (DMEM)  (Mediatech) supplemented with 10% fetal bovine  serum (FBS) (Sigma), 100ug/ml penicillin and 100  units/ml streptomycin (MediaTech).

extract_protocol:
RNA was isolated using Trizol (Invitrogen), purified by treatment with TURBO DNAase (Ambion) and isolated using the RNeasy Extraction Kit (Qiagen).
The RNA libraries were prepared using the Clontech pico v2 kit stranded-RNA library preparation kit according the manufacturer’s instructions. The samples were sequenced on a NextSeq500 as paired ends reads of 75 bp according to the manufacturer’s instructions.

treatment_protocol: Cells subjected to to 150mj/cm2 of UV radiation using  the Spectrolinker (Spectronic Corp) and sonciated.

value: U87 cells

tag: expression plasmid

value: empty vector (neomycin)

tag: rna source

value: Immunoprecipitated RNA


title: U87 ADAR3 IP RNA replicate 2

description: ribosomal depleted RNA

value: 3X-FLAG ADAR3 (neomycin)


title: U87 ADAR3 IP RNA replicate 3

description: ribosomal depleted RNA


title: T31_1.D12_S116


title: U87 control IP RNA replicate 2

description: ribosomal depleted RNA


title: U87 control IP RNA replicate 1

description: ribosomal depleted RNA


title: U87 control input RNA replicate 3

description: ribosomal depleted RNA

value: RNA from whole cell lysate


title: U87 ADAR3 input RNA replicate 3

description: ribosomal depleted RNA


title: U87 control input RNA replicate 1

description: ribosomal depleted RNA


title: U87 ADAR3 IP RNA replicate 1

description: ribosomal depleted RNA


title: U87 control input RNA replicate 2

description: ribosomal depleted RNA


title: U87 ADAR3 replicate 3

data_processing:
Reads were aligned to reference genome hg19 (gencode release 28) using STAR (v2.5.2b)

A-to-I editing sites were de novo identified using SAILOR program
Variant calling was performed using Samtools (v1.3.1) to quantify editing levels
Genome_build: GRCh37-hg19 (gencode release 28)

Supplementary_files_format_and_content: .csv files from the de novo identification of SAILOR output include all the predicted sites and the confidence score for each predicted site

growth_protocol: U87 cells were maintained in Dulbecco's modified Eagle's medium (DMEM) (Mediatech) supplemented with 10% fetal bovine serum (FBS) (Sigma), 200ug/ml G418, 100ug/ml penicillin and 100 units/ml streptomycin (MediaTech).

extract_protocol:
RNA was isolated using Trizol (Invitrogen), purified by treatment with TURBO DNAase (Ambion) and isolated using the RNeasy Extraction Kit (Qiagen).
Poly-A selected mRNA library preparation was done using KAPPA stranded library preparation kit

treatment_protocol: All cells were incubated at 37°C in 5% CO2 and grown to 80-90% under optimum conditions


title: U87 control replicate 3


title: U87 control replicate 2


title: U87 control replicate 1


title: lesion from epidemic KS patient c037

status: Public on Jun 26 2020

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
c037P
processed data file: KS_RNAseq.txt

data_processing:
The RNA-seq data was aligned against human (hg19 genome, Ensembl v75 transcriptome) or KSHV (NC_009333.1) genomes and transcriptomes using the bowtie2 algorithm, and RSEM v1.2.31 software was used to estimate read counts and FPKM values at the gene level.
DESeq2 was used for differential expression analysis.
Genome_build: Human: hg19 (GRCh37); KSHV: NC_009333.1
Supplementary_files_format_and_content: KS_RNAseq.txt: Processed data file contains the raw counts for each gene from human and KSHV transcriptome.

source_name: lesion from KS patient

growth_protocol: A 4 mm cylindrical single-use punch was used to collect biopsy samples from a representative KS lesion and a second identical punch biopsy was collected from an uninvolved ipsilateral /contralateral site on the same individual. The collected tissues were treated overnight in RNALater (Ambion) to facilitate subsequent DNA/RNA extraction. RNALater was removed prior to freezing at -80˚C.

extract_protocol:
Genomic RNA was extracted from the homogenized sample with miRNeasy mini kit with on-column DNase I treatment according to the manufacturer’s protocol (Qiagen, Hilden, Germany).
Library preparation was performed using the TruSeq™ RNA Library Prep Kit v2.

treatment_protocol: Fresh frozen biopsies from KS lesions and ipsilateral/contralateral normal sites were homogenized by cryo-cracking (pulverizing) in liquid nitrogen.

tag: diagnosis

value: Kaposi's Sarcoma

tag: origin

value: epidemic

tag: patient

tag: tissue

value: lesion

tag: gender

value: female

tag: hiv

value: yes

tag: batch


title: U87 ADAR3 replicate 2


title: U87 ADAR3 replicate 1


title: control skin from epidemic KS patient c032

description:
c032N
processed data file: KS_RNAseq.txt

source_name: control skin from KS patient

value: control skin


title: control skin from epidemic KS patient c037

description:
c037N
processed data file: KS_RNAseq.txt


title: lesion from epidemic KS patient 21221

description:
21221P
processed data file: KS_RNAseq.txt


title: control skin from epidemic KS patient 21221

description:
21221N
processed data file: KS_RNAseq.txt


title: lesion from epidemic KS patient 21214

description:
21214P
processed data file: KS_RNAseq.txt


title: lesion from epidemic KS patient 21196

description:
21196P
processed data file: KS_RNAseq.txt


title: control skin from epidemic KS patient 21196

description:
21196N
processed data file: KS_RNAseq.txt


title: lesion from epidemic KS patient c038

description:
c038P
processed data file: KS_RNAseq.txt


title: U87 ADAR3 input RNA replicate 2

description: ribosomal depleted RNA


title: lesion from epidemic KS patient c023

description:
c023P
processed data file: KS_RNAseq.txt


title: control skin from epidemic KS patient c038

description:
c038N
processed data file: KS_RNAseq.txt


title: U87 ADAR3 input RNA replicate 1

description: ribosomal depleted RNA


title: lesion from epidemic KS patient c025

description:
c025P
processed data file: KS_RNAseq.txt

value: male


title: control skin from epidemic KS patient c023

description:
c023N
processed data file: KS_RNAseq.txt


title: lesion from epidemic KS patient c035

description:
c035P
processed data file: KS_RNAseq.txt


title: control skin from epidemic KS patient c026

description:
c026N
processed data file: KS_RNAseq.txt


title: lesion from epidemic KS patient c034

description:
c034P
processed data file: KS_RNAseq.txt


title: control skin from epidemic KS patient c034

description:
c034N
processed data file: KS_RNAseq.txt


title: control skin from epidemic KS patient c035

description:
c035N
processed data file: KS_RNAseq.txt


title: lesion from epidemic KS patient c032

description:
c032P
processed data file: KS_RNAseq.txt


title: lesion from epidemic KS patient c3128

description:
c3128P
processed data file: KS_RNAseq.txt


title: lesion from epidemic KS patient c3122

description:
c3122P
processed data file: KS_RNAseq.txt


title: lesion from epidemic KS patient c3129

description:
c3129P
processed data file: KS_RNAseq.txt


title: control skin from epidemic KS patient c3122

description:
c3122N
processed data file: KS_RNAseq.txt


title: lesion from endemic KS patient c3140

description:
c3140P
processed data file: KS_RNAseq.txt

value: endemic

value: no

value: untreated


title: control skin from epidemic KS patient c3128

description:
c3128N
processed data file: KS_RNAseq.txt


title: control skin from epidemic KS patient c3129

description:
c3129N
processed data file: KS_RNAseq.txt


title: control skin from endemic KS patient c3140

description:
c3140N
processed data file: KS_RNAseq.txt


title: control skin from endemic KS patient c3139

description:
c3139N
processed data file: KS_RNAseq.txt


title: lesion from epidemic KS patient 21199

description:
21199P
processed data file: KS_RNAseq.txt


title: control skin from epidemic KS patient 21199

description:
21199N
processed data file: KS_RNAseq.txt


title: control skin from epidemic KS patient c025

description:
c025N
processed data file: KS_RNAseq.txt


title: lesion from endemic KS patient c3136

description:
c3136P
processed data file: KS_RNAseq.txt


title: lesion from endemic KS patient c3124

description:
c3124P
processed data file: KS_RNAseq.txt


title: control skin from endemic KS patient c3136

description:
c3136N
processed data file: KS_RNAseq.txt


title: control skin from endemic KS patient c3124

description:
c3124N
processed data file: KS_RNAseq.txt


title: lesion from endemic KS patient c3135

description:
c3135P
processed data file: KS_RNAseq.txt


title: control skin from endemic KS patient c3135

description:
c3135N
processed data file: KS_RNAseq.txt


title: lesion from endemic KS patient c3139

description:
c3139P
processed data file: KS_RNAseq.txt


title: normal skin from donor c3215

description:
c3215N
processed data file: KS_RNAseq.txt

source_name: normal skin

value: normal skin


title: lesion from endemic KS patient c3111

description:
c3111P
processed data file: KS_RNAseq.txt


title: normal skin from donor c3212

description:
c3212N
processed data file: KS_RNAseq.txt


title: normal skin from donor c3214

description:
c3214N
processed data file: KS_RNAseq.txt


title: 3h G1-EtOH-RNA-seq_r1

status: Public on Jun 11 2020

data_processing:
Raw read quality was checked using FastQC and contamination was checked with FastqScreen and BLAST.
Reads were mapped to an hg19(human) using the STAR aligner version 2.5.3b (Dobin et al., 2013).
FPKM (fragments per kilobase per million mapped reads) gene expression was quantified across the entire gene with HOMER analyzeRepeats. In addition, reads mapping to spikin sequences were used to calculate the normalization slope based on the expected concentrations of the spikeins as was done previously (Palazola et al., 2017).
Expression values were further log2 transformed, averaged across replicates, and NoEU control expression values were subtracted from EU values at each time point.
Next time point-specific genes were identified as genes whose expression exceeds  50% of the average expression across all times (excluding asynchronous) and continues to exceed 50% for the duration of the timecourse.  Asynchronous genes were defined as those that were not timepoint specific and whose values were at least twice as high in the asynchronous time point compared to any of the other time points.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated text file containing normalized expression and cluster id for expressed genes.

source_name: U2OS osteosarcoma cell line

extract_protocol: cDNA libraries were generated using the Ovation Human FFPE RNA-Seq Multiplex System.

tag: cell cycle phase

value: 3h G1


title: 3h G1-EtOH-RNA-seq_r2


title: 3h G1-A485-RNA-seq_r1


title: Cytokinesis-EtOH-RNA-seq_r2

value: Cytokinesis


title: Cytokinesis-A485-RNA-seq_r1


title: Cytokinesis-EtOH-RNA-seq_r1


title: Cytokinesis-A485-RNA-seq_r2


title: A485-24h release-RNA-seq_r2

value: 24h release (asynchronous)


title: A485-24h release-RNA-seq_r1


title: EtOH-24h release-RNA-seq_r2


title: A485-Cytokinesis-RNA-seq_r1


title: EtOH-Cytokinesis-RNA-seq_r2


title: A485-Cytokinesis-RNA-seq_r2


title: control skin from epidemic KS patient 21214

description:
21214N
processed data file: KS_RNAseq.txt


title: EtOH-Prometaphase-RNA-seq_r1

value: Prometaphase


title: EtOH-Cytokinesis-RNA-seq_r1


title: A485-Prometaphase-RNA-seq_r2


title: NoEU-noA485-RNA-seq_r2

value: Asynchrounous


title: control skin from endemic KS patient c3111

description:
c3111N
processed data file: KS_RNAseq.txt


title: EtOH-Prometaphase-RNA-seq_r2


title: 180 min-RNA-seq-r1

description: WaveExpressionClusters.txt

growth_protocol: U2OS osteosarcoma cells were cultured in DMEM (Gibco) and 10% FBS. To obtain mitotic cells, U2OS cells were treated with filter sterilized 2.5 mM thymidine for 30 h, washed and released into thymidine-free fresh medium. After 10 h release from S phase arrest, the cells were incubated with 20 ng/ml nocodazole for 4 h. To enrich for mitotic cells, rounded floating cells were collected with shake-off. To release the cells from arrest, mitotic cells were washed three with PBS to remove nocodazole and then incubated in fresh medium in suspension culture.

extract_protocol:
Total RNA was harvested using Trizol (Ambion) and purified using miRNeasy (Qiagen). Click reaction was performed to conjugate biotin to the EU-labelled RNA using Click-iT Nascent RNA Capture Kit (Invitrogen). Two biotinylated spike-in control RNAs were added to 1.5 ug of each biotinylated sample (0.36 ng of control #1 and 0.036 ng of control #2). Biotin-EU-RNAs including spike-in controls were pulled down with streptavidin-coated magnetic beads.
cDNA libraries were generated using the Ovation Human FFPE RNA-Seq Multiplex System.

treatment_protocol: U2OS cells were pulse labeled with 0.5 mM for 35 min at 37°C.

value: 180 min G1

tag: molecule

value: eu-labeled nascent RNA


title: 180 min-RNA-seq-r2

description: WaveExpressionClusters.txt

tag: cell line


title: NoEU-noA485-RNA-seq_r1


title: 120 min-RNA-seq-r2

description: WaveExpressionClusters.txt

value: 120 min G1


title: 120 min-RNA-seq-r1

description: WaveExpressionClusters.txt


title: 3h G1-A485-RNA-seq_r2


title: 90 min-RNA-seq-r2

description: WaveExpressionClusters.txt

value: 90 min G1


title: Asynch-RNA-seq-r1

description: WaveExpressionClusters.txt


title: 35 min-RNA-seq-r2

description: WaveExpressionClusters.txt

value: Anaphase/Telophase


title: 60 min-RNA-seq-r2

description: WaveExpressionClusters.txt


title: 0 min-RNA-seq-r1

description: WaveExpressionClusters.txt


title: Asynch-RNA-seq-r2

description: WaveExpressionClusters.txt


title: 90 min-RNA-seq-r1

description: WaveExpressionClusters.txt


title: 0 min-RNA-seq-r2

description: WaveExpressionClusters.txt


title: EtOH-24h release-RNA-seq_r1


title: NoEU-RNA-seq_r2

description: WaveExpressionClusters.txt

value: total RNA


title: 35 min-RNA-seq-r1

description: WaveExpressionClusters.txt


title: 60 min-RNA-seq-r1

description: WaveExpressionClusters.txt


title: NoEU-RNA-seq_r1

description: WaveExpressionClusters.txt


title: RPE1 Input-anaphase/telophase-ChIP-seq-r3

library_source: genomic

data_processing:
Raw read quality was checked using FastQC and contamination was checked with FastqScreen and BLAST.
Reads were mapped to an hg19(human) and dm6(fly spikein) combined genome using the STAR aligner version 2.5.3b (Dobin et al., 2013). Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read). The genome index was constructed using the gene annotation supplied with the hg19 and dm6 Illumina iGenomes[3] collection and sjdbOverhang value of 100.
After mapping, fly reads were quantified separately and used to determined spikein normalization factors for all samples assuming a constant amount of spikin added.
Peaks were identified using HOMER (Heinz et al., 2010), using default parameters and input condition as background reference. Normalized read counts for peaks were calculated using the fragments per kilobase per million mapped reads (FPKM) normalization multiplied by the spikein factors.
Low coverage peaks were filtered out (average log2 normalized read counts < 3 across all phases for H3K27ac, H3K4me3, and H3K4me1, and average log2 normalized read counts < 1 across all phases for CTCF, due to lower quality ChIP for CTCF). Then peaks were defined as present in a phase if the average normalized expression in that phase was at least the ¾ the maximum normalized read count across all 3 phases. Peak overlap across cell cycle phases was calculated using HOMER mergePeaks routines with a maximum distance for merging of 1000 bp.
Genome_build: hg19
Supplementary_files_format_and_content: HOMER peak files and bigWig tracks

molecule: genomic DNA

source_name: RPE1 retinal pigment epithelial cell line

growth_protocol: U2OS osteosarcoma cells were cultured in DMEM (Gibco) and 10% FBS. To obtain mitotic cells, U2OS cells were treated with filter sterilized 2.5 mM thymidine for 30 h, washed and released into thymidine-free fresh medium. After 10 h release from S phase arrest, the cells were incubated with 20 ng/ml nocodazole for 4 h. To enrich for mitotic cells, rounded floating cells were collected with shake-off. To release the cells from arrest, mitotic cells were washed three with PBS to remove nocodazole and then incubated in fresh medium in suspension culture. RPE1 hTERT immortalized cells were cultured in DMEM-F12 (Gibco) and 10% FBS. RPE1 cells were synchronized in S phase by double thymidine block with 2 mM thymidine for 14 h, release into fresh media for 10 h, and 2 mM thymidine for 14 h. After 6 h release from thymidine block, cells were synchronized in prometaphase using 20 ng/ml nocodazole for 4 h cells. The mitotic cells were then collected by mitotic shake-off. To release the cells from arrest, mitotic cells were washed three with PBS to remove nocodazole and then incubated in fresh medium in suspension culture.

extract_protocol:
Cells were cross-linked with 1% formaldehyde at room temperature for 10 min and neutralized with 0.125 M glycine for 5 min . After sonication, 25 ug of chromatin was incubated with 5 μg of anti-H3K4me3, anti-H3K4me1, anti-H3K27ac, or anti-CTCF antibodies at 4°C overnight. For spike-in normalization, 50 ng of Spike-in chromatin (53083, Active Motif) with 2 μg Spike-in antibody were added. Immunoprecipitated complexes were collected using Dynabeads M280 sheep-anti-rabbit IgG (Invitrogen). Subsequently, immuno-complexes were washed, decorsslinked and DNA was purified by QIAquick Spin columns (Qiagen). Cells (5 × 106) were cross-linked with 1% formaldehyde for 10 min, and ChIP-seq was performed as previously described (Toyama et al. 2018). Spike-in was carried out according to vendor protocols (Active Motif). Briefly,  DNA libraries were generated using the Kapa Hyper Prep Kit for Illumina Platforms (Kapa biosystems). Libraries were sequenced in a NextSeq 500 system (Illumina).
ChIP-seq libraries were generated using the Kapa Hyper Prep Kit for Illumina Platforms (Kapa biosystems).

tag: replicate

tag: antibody


title: RPE1 Input-prometaphase-ChIP-seq-r3


title: A485-Prometaphase-RNA-seq_r1


title: RPE1 Input-prometaphase-ChIP-seq-r2


title: RPE1 Input-anaphase/telophase-ChIP-seq-r2


title: RPE1 Input-interphase-ChIP-seq-r3

value: Interphase


title: RPE1 Input-prometaphase-ChIP-seq-r1


title: RPE1 Input-anaphase/telophase-ChIP-seq-r1


title: RPE1 Input-interphase-ChIP-seq-r1


title: RPE1 H3K4me1-anaphase/telophase-ChIP-seq-r1


title: RPE1 H3K4me1-anaphase/telopphase-ChIP-seq-r2


title: RPE1 H3K4me1-interphase-ChIP-seq-r2


title: RPE1 H3K4me1-prometaphase-ChIP-seq-r2


title: RPE1 H3K27ac-anaphase/telopphase-ChIP-seq-r2


title: RPE1 Input-interphase-ChIP-seq-r2


title: RPE1 H3K4me1-interphase-ChIP-seq-r1


title: RPE1 H3K4me1-prometaphase-ChIP-seq-r1


title: RPE1 H3K27ac-anaphase/telophase-ChIP-seq-r1


title: RPE1 H3K4me3-prometaphase-ChIP-seq-r2


title: RPE1 H3K4me3-prometaphase-ChIP-seq-r1


title: RPE1 H3K27ac-interphase-ChIP-seq-r1


title: RPE1 H3K27ac-interphase-ChIP-seq-r2


title: RPE1 H3K27ac-prometaphase-ChIP-seq-r1


title: RPE1 H3K27ac-prometaphase-ChIP-seq-r2


title: RPE1 H3K4me3-anaphase/telopphase-ChIP-seq-r2


title: U2OS Input-anaphase/telophase-ChIP-seq-r3


title: RPE1 H3K4me3-interphase-ChIP-seq-r1


title: U2OS Input-prometaphase-ChIP-seq-r3


title: U2OS Input-anaphase/telophase-ChIP-seq-r2


title: U2OS Input-interphase-ChIP-seq-r3


title: RPE1 H3K4me3-interphase-ChIP-seq-r2


title: lesion from epidemic KS patient c026

description:
c026P
processed data file: KS_RNAseq.txt

value: Kaposi's Sarcoma

value: epidemic

value: lesion

value: male

value: yes


title: U2OS Input-interphase-ChIP-seq-r2


title: U2OS Input-prometaphase-ChIP-seq-r2


title: U2OS Input-interphase-ChIP-seq-r1


title: U2OS Input-anaphase/telophase-ChIP-seq-r1


title: U2OS CTCF-anaphase/telopphase-ChIP-seq-r2

value: CTCF


title: U2OS CTCF-interphase-ChIP-seq-r2


title: U2OS Input-prometaphase-ChIP-seq-r1


title: U2OS CTCF-anaphase/telophase-ChIP-seq-r1


title: U2OS CTCF-prometaphase-ChIP-seq-r2


title: U2OS CTCF-prometaphase-ChIP-seq-r1


title: U2OS H3K4me1-prometaphase-ChIP-seq-r1


title: U2OS CTCF-interphase-ChIP-seq-r1


title: U2OS H3K27ac-interphase-ChIP-seq-r1


title: U2OS H3K27ac-prometaphase-ChIP-seq-r1


title: U2OS H3K4me1-anaphase/telophase-ChIP-seq-r1


title: RPE1 H3K4me3-anaphase/telophase-ChIP-seq-r1


title: U2OS H3K4me3-prometaphase-ChIP-seq-r2


title: U2OS H3K4me1-prometaphase-ChIP-seq-r2


title: U2OS H3K4me1-interphase-ChIP-seq-r1


title: U2OS H3K27ac-anaphase/telopphase-ChIP-seq-r2


title: U2OS H3K27ac-interphase-ChIP-seq-r2


title: U2OS H3K27ac-prometaphase-ChIP-seq-r2


title: U2OS H3K4me1-interphase-ChIP-seq-r2


title: U2OS H3K27ac-anaphase/telophase-ChIP-seq-r1


title: U2OS H3K4me3-anaphase/telophase-ChIP-seq-r1


title: U2OS H3K4me3-interphase-ChIP-seq-r2


title: 360 min-Hi-C-r1

data_processing:
Sequencing reads generated from samples of eight time points with two replicates were subjected to standard alignment using bwa-mem
Contact matrices were constructed using alignment bam files and normalized by matrix balancing as previously discribed (Dixon et al., 2012).
.hic files were generated by hiccups using contact matrix files (Durand et al., 2016)
Genome_build: hg38
Supplementary_files_format_and_content: binary contact matrix files

extract_protocol:
Hi-C was performed as previously described (Lieberman-Aiden et al. 2009). Briefly, U2OS cells (2 x 10^6) were cross-linked with formaldehyde. Chromatin was digested with a restriction enzyme Mbol (NEB), biotinylated with biotin-ATP (Life Technologies), and then ligated with T4 DNA ligase (NEB). DNA was purified and sheared with Covaris LE220 instrument (Covaris).
Biotinylated DNA interactions were pulled down with Dynabeads MyOne Streptavin T1 Beads (Life Technologies) and ligated with indexed Illumina Truseq adapters. Amplified libraries were sequenced with Illumina Novoseq platform using the S4 flow cell.

value: 360 min G1


title: U2OS H3K4me1-anaphase/telopphase-ChIP-seq-r2


title: U2OS H3K4me3-prometaphase-ChIP-seq-r1


title: 180 min-Hi-C-r2


title: 360 min-Hi-C-r2


title: 240 min-Hi-C-r1

value: 240 min G1


title: 180 min-Hi-C-r1


title: 240 min-Hi-C-r2


title: 90 min-Hi-C-r2


title: U2OS H3K4me3-interphase-ChIP-seq-r1


title: 120 min-Hi-C-r1


title: 120 min-Hi-C-r2


title: 90 min-Hi-C-r1


title: 60 min-Hi-C-r2

value: Cytokinesis


title: U2OS H3K4me3-anaphase/telopphase-ChIP-seq-r2


title: 0 min-Hi-C-r2

value: Prometaphase


title: 35 min-Hi-C-r2


title: 35 min-Hi-C-r1


title: 0 min-Hi-C-r1


title: 60 min-Hi-C-r1


title: mRNA_ColorectalCancer_rep90

status: Public on Mar 12 2020

type: RNA

city: Tokyo

first: Norio

last: Tanaka

address: Ariake 3-8-31, Koto

country: Japan

institute: Japanese Foundation Cancer Research

hyb_protocol: After fragmentation, cRNA was hybridized with Affymetrix Hybridization,Wash, and Stain Kit on Affymetrix Human Genome GeneChip U133 Plus 2.0 array following manufactuer's instruction.

scan_protocol: GeneChip was scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data was processed with RMA using Affymetrix Expression Console software.

label: biotin

source_name: mRNA from fresh frozen colorectal tumor tissue

label_protocol: Biotinylated cRNA was prepared with Affymetrix GeneChip 3'IVT Plus kit  according to the manufactuer's instruction.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy mini kit following manufacturer's instruction.

value: colorectal tumor

tag: age

value: female

tag: sample id


title: mRNA_ColorectalCancer_rep87


title: mRNA_ColorectalCancer_rep88


title: mRNA_ColorectalCancer_rep80


title: mRNA_ColorectalCancer_rep82


title: mRNA_ColorectalCancer_rep86


title: mRNA_ColorectalCancer_rep76


title: mRNA_ColorectalCancer_rep77


title: mRNA_ColorectalCancer_rep74


title: mRNA_ColorectalCancer_rep72


title: mRNA_ColorectalCancer_rep85


title: mRNA_ColorectalCancer_rep79


title: mRNA_ColorectalCancer_rep75


title: mRNA_ColorectalCancer_rep73


title: mRNA_ColorectalCancer_rep63


title: mRNA_ColorectalCancer_rep84


title: mRNA_ColorectalCancer_rep78


title: mRNA_ColorectalCancer_rep81


title: mRNA_ColorectalCancer_rep83


title: mRNA_ColorectalCancer_rep70


title: mRNA_ColorectalCancer_rep71


title: mRNA_ColorectalCancer_rep69


title: mRNA_ColorectalCancer_rep64


title: mRNA_ColorectalCancer_rep68


title: mRNA_ColorectalCancer_rep67


title: mRNA_ColorectalCancer_rep89


title: mRNA_ColorectalCancer_rep62


title: mRNA_ColorectalCancer_rep65


title: mRNA_ColorectalCancer_rep61


title: mRNA_ColorectalCancer_rep66


title: ECA2

status: Public on Mar 10 2020

city: Helsinki

first: Zhilin

last: Li

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description: Endothelial cell-specific Ang2-overexpressing mice were induced with EAE.

data_processing:
The Cell Ranger v 2.1.1 mkfastq and count pipelines (10x Genomics, Pleasanton, CA) were used to demultiplex and convert Chromium single-cell 3’ RNA-sequencing barcodes and read data to FASTQ files and to generate aligned reads and gene-cell matrices.
Reads were aligned to mouse reference genome mm10.
We used the Seurat R package (v2.3.4) for QC, filtering and analysis of the aggregated data (Butler et al. Nature Biotechnology 2018)
Cells were filtered based on the number of genes and the percentage of mitochondrial genes.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: Spinal cord immune cells and endothelial cells

extract_protocol:
Single cells from spinal cords were isolated for single-cell RNA-sequencing as described previously (Vanlandewijck et al. Nature 2018). Mice were perfused with ice-cold PBS and spinal cords were dissected. Briefly, after enzymatic digestion, mechanical dissociation and myelin debris removal, eluted cells were incubated with mouse Fc Blocker (clone 2.4G2, BD Pharmingen) stained with CD45-FITC (clone 30-F11, BioLegend), CD31-APC (clone MEC13.3, BD Pharmingen), and DAPI. Equal numbers of viable DAPI-CD45+ leukocytes and DAPI-CD31+ ECs were sorted with BD Influx Cell Sorter (BD Biosciences) into PBS supplemented with 0.04% BSA.
Subsequent cDNA purification, amplification (12 cycles) and library construction (sample index PCR 14 cycles) was performed as instructed.
Sample libraries were sequenced on the Illumina NovaSeq 6000 system using S1 flow cell (Illumina)

treatment_protocol: For sample 1 and 2, wild-type mice were induced with EAE by immunization with MOG35-55 emulsified in CFA and treated with antibodies prophylacticly starting at the time of EAE induction for two weeks. For Sample 3 and 4, mice were induced with EAE by immunization with MOG35-55 emulsified in CFA.

tag: strain

tag: protocol

value: 12-14 weeks

value: Spinal cord


title: A2

description: EAE mice were treated with A2 antibody.

value: A2 antibody

value: 15 weeks


title: C3H10T1/2 cells, shMLL1, Day0

status: Public on Feb 26 2020

city: Incheon

first: Hansol

last: Lee

address: 100, Inha-ro, Michuhol-gu

department: Biological science

country: South Korea

institute: Inha University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Mesenchymal cells

growth_protocol: C3H 10T1/2 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

tag: cell type

value: mesenchymal stem cells

tag: genotype

value: MLL1 knockdown

tag: treatment

value: adipogenic differentiation

tag: time

value: Day 0


title: C3H10T1/2 cells, shNFIB, Day5

value: NFIB knockdown

value: Day 5


title: IgG

description: EAE mice were treated with mIgG1 antibody.

value: mIgG1 antibody

tag: tissue


title: C3H10T1/2 cells, shKDM4D, Day5

value: KDM4D knockdown


title: C3H10T1/2 cells, shMLL1, Day5


title: C3H10T1/2 cells, shKDM4D, Day0


title: C3H10T1/2 cells, shControl, Day5

value: WT


title: ATAC-seq_SiHa

status: Public on Feb 14 2020

city: Toronto

first: Michael

middle: M.

last: Hoffman

state: ON

address: 101 College St PMCRT 11-311

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

description: 100–600 bp fragments

data_processing:
RNA-seq: trim galore version 1.1.0, alignment with STAR version 2.6.0c, TPMs called with Stringtie RefSeq GTF annotation of GRCh38 from Illumina iGenomes
CTCF ChIP-seq: trim galore version 1.1.0, bowtie2 version 2.2.6, peak calling with MACS2 version 2.1.2
ATAC-seq: trim galore version 1.1.0, bowtie2 version 2.2.6, peak calling with MACS2 version 2.1.2
Genome_build: GRCh38 from illumina iGenomes merged with HPV16 K02718.1
Supplementary_files_format_and_content: Gzipped narrowPeak and expression matrix

source_name: SiHa

growth_protocol: HMS-001, 93-VU147T, SCC-090 were cultured in DMEM/F12 (Gibco), Caski were cultured in RPMI (Gibco) and SiHa were cultured in DMEM (Gibco). All supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were routinely grown in 150 mm culture dishes and incubated in humidified atmosphere containing 5% CO2 at 37°C.

extract_protocol: ATAC-seq: We assessed open chromatin using OMNI-ATAC49 followed by size selection to 100 bp–600 bp using a Pippin HT 2% Agarose Casette (Sage Science, Beverly, Massachusetts) and paired-end 125 bp sequencing on an Illumina HiSeq 2500 to a depth of 60 million reads per sample at the Princess Margaret Genomics Core, Toronto, Ontario.

treatment_protocol: No treatment

value: SiHa

tag: chip antibody

tag: sequencing type

value: Paired


title: ATAC-seq_Caski

description: 100–600 bp fragments

source_name: Caski

value: Caski


title: ATAC-seq_SCC-090

description: 100–600 bp fragments


title: ATAC-seq_HMS-001

description: 100–600 bp fragments


title: RNA-seq_SiHa

extract_protocol: RNA-seq: We prepared samples for RNA-seq using TruSeq Stranded Total RNA Sample Preparation kit with RiboZero Gold (Illumina, San Diego, California). We performed RNA sequencing for each sample to ∼80 million paired-end 150 bp reads on an Illumina NextSeq 500 at the Princess Margaret Genomics Centre, Toronto, Ontario. We collected input RNA using an AllPrep mini kit (Qiagen, Hilden, Germany).


title: C3H10T1/2 cells, shControl, Day0


title: ATAC-seq_93-VU147T

description: 100–600 bp fragments


title: RNA-seq_HMS-001


title: CTCF ChIP-seq_HMS-001_R3

description: CTCF ChIP-seq

extract_protocol: CTCF ChIP-seq:  We prepared 10 µl of both protein A and protein G beads through three washes of 5mg/mL Dulbecco’s phosphate-buffered saline (dPBS) + bovine serum albumin (BSA). We added 10 µl of CTCF antibody (Cell Signalling Technology, Danvers, Massachusetts, Cat No. 2899, Lot 002) to the beads in 300 µl dPBS + BSA and left it to bind for > 6 hours of rotation at 4°C. After incubation, we washed the beads three more times with dPBS + BSA and resuspended in 100 µl of modified Radioimmunoprecipitation assay buffer (RIPA) (10 mmol/l Tris-HCl, pH 8.0; 1 mmol/l EDTA; 140 mmol/l NaCl; 1% Triton X-100; 0.1% SDS; 0.1% sodium deoxycholate) + protease inhibitor (PI). We collected 1 million cells by trypsinization and then fixed for 10 min at room temperature in 300 µl of dPBS + 1% formaldehyde. We added 15 µl of 2.5M glycine after fixing then washed the cells once in PBS + PI before resuspending them in 300 µl of modified RIPA + PI. We sonicated the samples for 32 cycles of 30 sec at full intensity using a Bioruptor Pico (Diagenode, Seraing, Belgium) and pelleted cell debris by spinning at 21130 xG for 15 min. We set aside 15 µl of the supernatant as an input control, and diluted the remaining supernatant with 1700 µl of modified RIPA + PI and 100 µl of washed beads. We incubated the samples at 4°C overnight with rotation. We washed the beads with the following cold buffers in order: modified RIPA, modified RIPA + 500 µmol l−1 NaCl, LiCl buffer (10 mmol l−1 Tris-HCl, pH 8.0; 1 mM EDTA; 250 mmol l−1 LiCl; 0.5% NP-40; 0.5% sodium deoxycholate), and finally twice with TE buffer (pH 8). We resuspended the samples and inputs in 100 µl of de-crosslinking buffer (1% SDS, 0.1000 mol l−1 NaHCO3) and incubated at 65°C for 6 h. We cleaned the samples and inputs using the Monarch PCR & DNA clean-up kit (New England BioLabs, Ipswich, Massachusetts), prepared libraries using the ThruPLEX DNA-seq Kit (Rubicon Genomics, Ann Arbor, Michigan), and size selected to 240 bp–360 bp using a PippinHT 2% Agarose Casette (Sage Science, Beverly, Massachusetts). We sequenced the samples to ∼25 million single-end 50 bp reads each at the Princess Margaret Genomics Core, Toronto, Ontario.

value: CTCF

value: Unpaired


title: RNA-seq_93-VU147T


title: CTCF ChIP-seq_SCC-090_R3

description: CTCF ChIP-seq


title: RNA-seq_Caski


title: CTCF ChIP-seq_SiHa_R3

description: CTCF ChIP-seq


title: CTCF ChIP-seq_93-VU147T_R3

description: CTCF ChIP-seq


title: CTCF ChIP-seq_Caski_R3

description: CTCF ChIP-seq


title: CTCF ChIP-seq_SiHa_R2

description: CTCF ChIP-seq


title: Input ChIP-seq_SiHa

description: Input ChIP-seq

value: none (input)


title: CTCF ChIP-seq_SCC-090_R2

description: CTCF ChIP-seq


title: C3H10T1/2 cells, shNFIB, Day0


title: CTCF ChIP-seq_HMS-001_R2

description: CTCF ChIP-seq


title: Input ChIP-seq_SCC-090

description: Input ChIP-seq


title: Input ChIP-seq_Caski

description: Input ChIP-seq


title: CTCF ChIP-seq_93-VU147T_R2

description: CTCF ChIP-seq


title: Input ChIP-seq_93-VU147T

description: Input ChIP-seq


title: CTCF ChIP-seq_HMS-001_R1

description: CTCF ChIP-seq


title: Input ChIP-seq_HMS-001

description: Input ChIP-seq


title: KT_2

status: Public on Jan 22 2020

description:
OA_GEO.fpkm.xlsx
OA_GEO_Deresult.xlsx

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Alignment to the rn6 genome (from illumina iGenome) was performed using the STAR aligner version 2.5.3a using the --outFilterIntronMotifs RemoveNoncanonical parameter
Gene expression was quantified using the HOMER analysis suite version 4.9.1, makeTagDirectory, analyzeRepeats.pl, and getDiffExpression.pl. The differential gene expression analysis was carried out using the DESeq2 package v1.18.1 with cutoff of FDR < 0.05 and log2 fold change greater than 0.5
Genome_build: rn6 (illumina iGenome)
Supplementary_files_format_and_content: OA_GEO.fpkm.txt (FPKM normalized gene expression in Excel spreadsheet)
Supplementary_files_format_and_content: OA_GEO_DEresult.txt (Differential gene expression results in Excel spreadsheet)

organism: Rattus norvegicus

source_name: KT, knee cartilage

growth_protocol: All animal procedures were performed according with protocols approved by the IACUC and Animal Resources Department of the Salk Institute for Biological Studies.

extract_protocol:
The cartilage surface was rinsed with saline and then dissected from the joint surfaces with a blade
mRNA-Seq libraries were prepared using the TruSeq RNA Library Preparation Kit according to the manufacturer’s instructions (Illumina).
stranded paired-end mRNA-seq

treatment_protocol: HC samples: non treated; OAC samples: 4 weeks after Papain/L-cysteine injection; SHAM: 10 weeks after Papain/L-cysteine injection, AAV-DJ-GFP injection 4 weeks after the papain injection; KT samples: 10 weeks after Papain/L-cysteine injection, AAV-DJ-Klotho+ AAV-DJ-TGFBR2 injection 4 weeks after the papain injection

tag: disease state

value: Osteoarthritis (OA)

value: αKlotho and sTGFBR2

value: 5 months

value: knee cartilage


title: SHAM_2

description:
OA_GEO.fpkm.xlsx
OA_GEO_Deresult.xlsx

source_name: SHAM, knee cartilage

value: none (SHAM)


title: RNA-seq_SCC-090


title: CTCF ChIP-seq_SCC-090_R1

description: CTCF ChIP-seq


title: OAC_2

description:
OA_GEO.fpkm.xlsx
OA_GEO_Deresult.xlsx

source_name: OAC, knee cartilage

value: none (OAC)


title: SHAM_1

description:
OA_GEO.fpkm.xlsx
OA_GEO_Deresult.xlsx


title: CTCF ChIP-seq_Caski_R1

description: CTCF ChIP-seq


title: SB_MDActrl_Nup93_3_S53_R1_001

status: Public on Jan 18 2020

description:
Cut and Run for Nup93
GEOsubmission_Cut_and_Run_totalPeaks_raw.txt
SB_MDActrl_Nup93_3_S53_R1_001

data_processing:
Library strategy: Cut and Run
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Reads were mapped to the hg19 genome (from illumina iGenome) for RNA-Seq and both hg19 genome and yeast sacCer3 genome for Cut and Run. Alignment was performed using the STAR aligner version 2.5.3a using default parameters for RNA-Seq and "--alignIntronMax 1 --alignEndsType EndToEnd" for Cut and Run to disable splicing.
Gene expression was quantified using the HOMER analysis suite version 4.9.1, makeTagDirectory, analyzeRepeats.pl across exons of RefSeq genes. Peak calling was performed using HOMER findPeaks on pooled biological replicates and then merged using mergePeaks.
The differential gene expression (DE) analysis was carried out using DESeq2 package v1.18.1 with batch effect correction to correct for the introduction of vectors in cell lines when comparing Nup93 KD vs control samples (WT + Luciferase). The DE cutoff applied was FDR < 0.05 and absolute log2 fold change greater than 1. Spike-in ratios were included in size estimates for Cut and Run data to account for global shift in peak density between conditions.
Genome_build: hg19, sacCer3 (illumina iGenomes)
Supplementary_files_format_and_content: GEOsubmission_RNA_raw.txt (raw count and DE statistics for RNA-Seq)
Supplementary_files_format_and_content: GEOsubmission_Cut_and_Run_totalPeaks_raw.txt (peaks identified in both conditions with raw count quantification within each peak and DE statistics)

source_name: human MDA231 cell line

growth_protocol: Cell lines were cultured in DMEM supplemented with 10% FBS and 1% P/S

extract_protocol:
For RNA-Seq, RNA was extracted following standard procedures based on Trizol and chloroform. The RNeasy Mini kit was used to purify RNA (Qiagen). Samples were incubated with DNAse I for 30 min to degrade genomic DNA. RNA was resuspended in RNAse-free water. The amount of RNA was quantified with Nanodrop. For Cut and Run, libraries were prepared according to published protocols [Skene and Henikoff_eLife_2017]. Briefly, cells were bound to concanavalin-A coated magnetic beads and incubated with the desired primary antibody after membrane permeabilization with digitonin. After washing, cells were incubated with protein A and Micrococcal Nuclease (pA-MN) on ice and Ca++ was added to start the reaction. DNA fragments were released by nuclease cleavage and finally extracted from the supernatant. Spike-in control of yeast DNA was added to each sample for normalization.
mRNA-Seq libraries were prepared using the TruSeq RNA Library Preparation Kit according to the manufacturer’s instructions (Illumina).
stranded single-end mRNA-seq for RNA-Seq; regular library prep for Cut and Run

treatment_protocol: For NUP93 silencing, cells were seeded in 6-wells plates at 70% confluency and then treated with siRNA (Ibarra et al., Genes and Development, 2016) dissolved in Opti-MEM. siLentFect (Bio-Rad) was used for siRNA delivery. The ratio between siLentFect and siRNA was kept constant and equal to 1.25.

value: Control

value: Mammary gland/breast. Derived from metastatic site:pleural effusion


title: CTCF ChIP-seq_Caski_R2

description: CTCF ChIP-seq


title: CTCF ChIP-seq_93-VU147T_R1

description: CTCF ChIP-seq


title: SB_MDActrl_H3K27ac_1

description: Cut and Run

data_processing:
Library strategy: Cut and Run
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Reads were mapped to the hg19 genome (from illumina iGenome) for RNA-Seq and both hg19 genome and yeast sacCer3 genome for Cut and Run. Alignment was performed using the STAR aligner version 2.5.3a using default parameters for RNA-Seq and "--alignIntronMax 1 --alignEndsType EndToEnd" for Cut and Run to disable splicing.
Gene expression was quantified using the HOMER analysis suite version 4.9.1, makeTagDirectory, analyzeRepeats.pl across exons of RefSeq genes. Peak calling was performed using HOMER findPeaks on pooled biological replicates and then merged using mergePeaks.
Super enhancers were identified by HOMER findPeaks with parameter -style super for each of the replicates and then merged using "mergePeaks" to identify the common super enhancers shared by both replicates.
Genome_build: hg19, sacCer3 (illumina iGenomes)
Supplementary_files_format_and_content: peak file


title: SHAM_3

description:
OA_GEO.fpkm.xlsx
OA_GEO_Deresult.xlsx


title: HC_2

description:
OA_GEO.fpkm.xlsx
OA_GEO_Deresult.xlsx

source_name: HC, knee cartilage

value: control (WT)

value: untreated


title: CTCF ChIP-seq_SiHa_R1

description: CTCF ChIP-seq


title: SB_MDActrl_H3K27ac_2

description: Cut and Run


title: HC_1

description:
OA_GEO.fpkm.xlsx
OA_GEO_Deresult.xlsx


title: SB_MDA93KD_Nup93_3_S51_R1_001

description:
Cut and Run for Nup93
GEOsubmission_Cut_and_Run_totalPeaks_raw.txt
SB_MDA93KD_Nup93_3_S51_R1_001


title: SB_MDActrl_Nup93_1_S46_R1_001

description:
Cut and Run for Nup93
GEOsubmission_Cut_and_Run_totalPeaks_raw.txt
SB_MDActrl_Nup93_1_S46_R1_001

value: Luciferase control


title: SB_MDActrl_Nup93_2_S52_R1_001

description:
Cut and Run for Nup93
GEOsubmission_Cut_and_Run_totalPeaks_raw.txt
SB_MDActrl_Nup93_2_S52_R1_001


title: OAC_1

description:
OA_GEO.fpkm.xlsx
OA_GEO_Deresult.xlsx


title: SB_12bis_H1299_93_02_S36_R1_001

description:
GEOsubmission_RNA_raw.txt
SB_12bis_H1299_93_02_S36_R1_001

data_processing:
Sequenced reads were quality tested using FASTQC v0.11.2 using the default parameters.
Reads were mapped to the hg19 genome (from illumina iGenome) for RNA-Seq and both hg19 genome and yeast sacCer3 genome for Cut and Run. Alignment was performed using the STAR aligner version 2.5.3a using default parameters for RNA-Seq and "--alignIntronMax 1 --alignEndsType EndToEnd" for Cut and Run to disable splicing.
Gene expression was quantified using the HOMER analysis suite version 4.9.1, makeTagDirectory, analyzeRepeats.pl across exons of RefSeq genes. Peak calling was performed using HOMER findPeaks on pooled biological replicates and then merged using mergePeaks.
The differential gene expression (DE) analysis was carried out using DESeq2 package v1.18.1 with batch effect correction to correct for the introduction of vectors in cell lines when comparing Nup93 KD vs control samples (WT + Luciferase). The DE cutoff applied was FDR < 0.05 and absolute log2 fold change greater than 1. Spike-in ratios were included in size estimates for Cut and Run data to account for global shift in peak density between conditions.
Genome_build: hg19, sacCer3 (illumina iGenomes)
Supplementary_files_format_and_content: GEOsubmission_RNA_raw.txt (raw count and DE statistics for RNA-Seq)
Supplementary_files_format_and_content: GEOsubmission_Cut_and_Run_totalPeaks_raw.txt (peaks identified in both conditions with raw count quantification within each peak and DE statistics)

source_name: human H1299 cell line

value: Lung. Derived from metastatic site:lymph node


title: SB_11bis_H1299_93_01_S35_R1_001

description:
GEOsubmission_RNA_raw.txt
SB_11bis_H1299_93_01_S35_R1_001


title: SB_MDA93KD_Nup93_2_S50_R1_001

description:
Cut and Run for Nup93
GEOsubmission_Cut_and_Run_totalPeaks_raw.txt
SB_MDA93KD_Nup93_2_S50_R1_001


title: SB_MDA93KD_Nup93_1_S49_R1_001

description:
Cut and Run for Nup93
GEOsubmission_Cut_and_Run_totalPeaks_raw.txt
SB_MDA93KD_Nup93_1_S49_R1_001


title: OAC_3

description:
OA_GEO.fpkm.xlsx
OA_GEO_Deresult.xlsx


title: SB_10_H1299_Luci_02_S34_R1_001

description:
GEOsubmission_RNA_raw.txt
SB_10_H1299_Luci_02_S34_R1_001


title: SB_09_H1299_Luci_01_S33_R1_001

description:
GEOsubmission_RNA_raw.txt
SB_09_H1299_Luci_01_S33_R1_001


title: SB_08_H1299_Ctrl_02_S32_R1_001

description:
GEOsubmission_RNA_raw.txt
SB_08_H1299_Ctrl_02_S32_R1_001


title: KT_1

description:
OA_GEO.fpkm.xlsx
OA_GEO_Deresult.xlsx


title: SB_04_MDA_Luci_02_S28_R1_001

description:
GEOsubmission_RNA_raw.txt
SB_04_MDA_Luci_02_S28_R1_001


title: SB_05_MDA_93_01_S29_R1_001

description:
GEOsubmission_RNA_raw.txt
SB_05_MDA_93_01_S29_R1_001


title: SB_03_MDA_Luci_01_S27_R1_001

description:
GEOsubmission_RNA_raw.txt
SB_03_MDA_Luci_01_S27_R1_001


title: SB_01_MDA_Ctrl_01_S25_R1_001

description:
GEOsubmission_RNA_raw.txt
SB_01_MDA_Ctrl_01_S25_R1_001


title: SB_06_MDA_93_02_S30_R1_001

description:
GEOsubmission_RNA_raw.txt
SB_06_MDA_93_02_S30_R1_001


title: SB_07_H1299_Ctrl_01_S31_R1_001

description:
GEOsubmission_RNA_raw.txt
SB_07_H1299_Ctrl_01_S31_R1_001


title: SB_02_MDA_Ctrl_02_S26_R1_001

description:
GEOsubmission_RNA_raw.txt
SB_02_MDA_Ctrl_02_S26_R1_001


title: B2_TI_MCD_285

status: Public on Jan 01 2020

city: Ann Arbor

first: Sean

last: Eddy

state: MI

address: 1150 West Medical Center Drive

institute: University of Michigan

description: Gene Expression data from the tubulointerstitial compartment of human Minimal Change Disease

hyb_protocol: not provided

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing:
The data were analyzed using RMA method and Human Entrez Gene custom CDF annotation version 19 (Brainarray) on two individual batches. Each of the hybridizations was normalized seperately and expression matrix contains the batch corrected data using Combat.
ID_REF denotes Entrez Gene IDs, data are presented as normalized log base 2 expression values

source_name: Kidney Biopsy from Human Minimal Change Disease

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

extract_protocol: Total RNA was isolated using Rneasy kit (Qiagen) following manufacturer's protocol

value: Tubulointerstitium from kidney biopsy

value: Minimal Change Disease


title: B2_TI_MCD_171


title: B2_TI_FSGS_21

description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis

source_name: Kidney Biopsy from Human Focal and Segmental Glomerulosclerosis

value: Focal and Segmental Glomerulosclerosis


title: B2_TI_FSGS_60


title: B2_TI_MN_295

description: Gene Expression data from the tubulointerstitial compartment of human Membranous Nephropathy

source_name: Kidney Biopsy from Human Membranous Nephropathy

value: Membranous Nephropathy


title: B2_TI_Other_194

description: Gene Expression data from the tubulointerstitial compartment of human Glomerular Disease (Other)

source_name: Kidney Biopsy from Human Glomerular Disease (Other)

value: Glomerular Disease (Other)


title: B2_TI_FSGS_96


title: B2_TI_Other_207


title: B2_TI_Other_214


title: B2_TI_Other_279


title: B2_TI_Other_181


title: B2_TI_Other_238


title: B2_TI_MCD_234


title: B2_TI_Other_220


title: B2_TI_MN_38


title: B2_TI_Other_212


title: B2_TI_Other_290


title: B2_TI_MCD_263


title: B2_TI_Other_192


title: B2_TI_MCD_149


title: B2_TI_Other_287


title: B2_TI_MCD_126


title: B2_TI_MCD_106


title: B2_TI_FSGS_20


title: Ctrl

description: Control mice were induced with EAE.

value: Control mice were induced with EAE.

value: 12-14 weeks

value: Spinal cord


title: B2_TI_FSGS_74


title: B2_TI_MN_135


title: B2_TI_FSGS_63


title: B2_TI_Other_249


title: B2_TI_MCD_246


title: B2_TI_FSGS_31


title: B2_TI_FSGS_80


title: B2_TI_Other_276


title: B2_TI_Other_289


title: B2_TI_MCD_269


title: B2_TI_MCD_184


title: B2_TI_MN_288


title: B2_TI_Other_278


title: B2_TI_MCD_261


title: B2_TI_FSGS_67


title: B2_TI_Other_166


title: B2_TI_MCD_140


title: B2_TI_FSGS_272


title: B2_TI_FSGS_30


title: B2_TI_Other_216


title: B2_TI_MCD_221


title: B2_TI_MCD_143


title: B2_TI_MCD_266


title: B2_TI_Other_291


title: B2_TI_FSGS_202


title: B2_TI_MCD_228


title: B2_TI_Other_230


title: B2_TI_MN_134


title: B2_TI_FSGS_61


title: B2_TI_FSGS_28


title: B2_TI_MCD_160


title: B2_TI_FSGS_29


title: B2_TI_Other_281


title: B2_TI_FSGS_142


title: B2_TI_FSGS_89


title: B2_TI_Other_236


title: B2_TI_MN_110


title: B2_TI_Other_257


title: B2_TI_FSGS_65


title: B2_TI_MCD_208


title: B2_TI_Other_240


title: B2_TI_MCD_177


title: B2_TI_FSGS_27


title: B2_TI_Other_223


title: B2_TI_MN_40


title: B2_TI_MCD_258


title: B2_TI_FSGS_85


title: B2_TI_MCD_235


title: B2_TI_MN_146


title: B2_TI_FSGS_86


title: B2_TI_Other_283


title: B2_TI_MCD_117


title: B2_TI_FSGS_26


title: B2_TI_MN_222


title: B2_TI_MCD_233


title: B2_TI_FSGS_25


title: B2_TI_MN_37


title: B2_TI_MCD_157


title: B2_TI_FSGS_227


title: B2_TI_FSGS_66


title: B2_TI_MCD_55


title: B2_TI_FSGS_24


title: B2_TI_Other_172


title: B2_TI_MCD_130


title: B2_TI_MN_36


title: B2_TI_FSGS_62


title: B2_TI_MCD_253


title: B2_TI_Other_165


title: B2_TI_FSGS_69


title: B2_TI_FSGS_197


title: B2_TI_FSGS_59


title: B2_TI_MCD_251


title: B2_TI_MCD_167


title: B2_TI_FSGS_53


title: B2_TI_MN_39


title: B2_TI_FSGS_112


title: B2_TI_MCD_150


title: B2_TI_FSGS_58


title: B2_TI_MN_152


title: B2_TI_MN_129


title: B2_TI_MCD_224


title: B2_TI_MN_109


title: B2_TI_Other_286


title: B2_TI_Other_200


title: B2_TI_FSGS_70


title: B2_TI_MN_148


title: B2_TI_FSGS_41


title: B2_TI_FSGS_72


title: B2_TI_MCD_176


title: B2_TI_Other_173


title: B2_TI_MCD_144


title: B1_TI_LD_1

description: Gene Expression data from the tubulointerstitial compartment of human Healthy Living Donor

source_name: Kidney Biopsy from Human Healthy Living Donor

value: Healthy Living Donor


title: B2_TI_Other_190


title: B2_TI_MCD_280


title: B2_TI_FSGS_22


title: B1_TI_LD_7


title: B2_TI_MCD_273


title: B1_TI_LD_3


title: B1_TI_MN_229


title: B2_TI_MCD_33


title: B1_TI_LD_6


title: B1_TI_LD_2


title: B2_TI_MN_123


title: B2_TI_MN_118


title: B1_TI_FSGS_132


title: B2_TI_MN_99


title: B1_TI_MCD_174


title: B1_TI_FSGS_51


title: B1_TI_Other_215


title: B1_TI_MCD_260


title: B1_TI_Other_179


title: B1_TI_MCD_241


title: B1_TI_MN_154


title: B1_TI_MCD_6


title: B1_TI_MN_11


title: B1_TI_FSGS_1


title: B1_TI_MCD_248


title: B1_TI_MN_127


title: B1_TI_MCD_277


title: B2_TI_FSGS_19


title: B1_TI_Other_217


title: B1_TI_FSGS_71


title: B1_TI_MCD_108


title: B1_TI_MN_103


title: B1_TI_MN_101


title: B1_TI_MN_107


title: B1_TI_FSGS_5


title: B1_TI_FSGS_78


title: B1_TI_Other_275


title: B1_TI_MCD_187


title: B1_TI_Other_189


title: B1_TI_MN_105


title: B1_TI_Other_196


title: B1_TI_FSGS_92


title: B1_TI_FSGS_87


title: B1_TI_Other_237


title: B1_TI_MN_147


title: B1_TI_Other_57


title: B1_TI_MCD_95


title: B1_TI_MN_124


title: B1_TI_FSGS_121


title: B1_TI_Other_170


title: B1_TI_MCD_158


title: B1_TI_Other_185


title: B1_TI_Other_262


title: B1_TI_Other_294


title: B1_TI_FSGS_47


title: B1_TI_MN_274


title: B1_TI_Other_252


title: B1_TI_FSGS_4


title: B1_TI_Other_244


title: B1_TI_FSGS_54


title: B1_TI_Other_225


title: B1_TI_FSGS_122


title: B1_TI_MN_131


title: B1_TI_FSGS_114


title: B1_TI_MN_91


title: B1_TI_MN_100


title: B1_TI_MCD_186


title: B1_TI_Other_293


title: B1_TI_MN_119


title: B1_TI_MN_14


title: B1_TI_Other_292


title: B1_TI_FSGS_104


title: B1_TI_Other_183


title: B1_TI_Other_245


title: B1_TI_MN_13


title: B1_TI_Other_256


title: B1_TI_FSGS_153


title: B1_TI_Other_265


title: B1_TI_MCD_128


title: B1_TI_Other_213


title: B1_TI_Other_247


title: B1_TI_Other_232


title: B1_TI_Other_180


title: B1_TI_MN_156


title: B1_TI_FSGS_116


title: B1_TI_MCD_145


title: B1_TI_Other_199


title: B1_TI_MN_138


title: B1_TI_FSGS_50


title: B1_TI_Other_226


title: B1_TI_MCD_169


title: B1_TI_MN_136


title: B1_TI_Other_255


title: B1_TI_FSGS_2


title: B1_TI_MN_125


title: B1_TI_Other_209


title: B1_TI_Other_264


title: B1_TI_Other_259


title: B1_TI_MN_159


title: B1_TI_MCD_205


title: B1_TI_MCD_219


title: B1_TI_FSGS_88


title: B1_TI_MN_97


title: B1_TI_FSGS_68


title: B1_TI_FSGS_79


title: B1_TI_MN_113


title: B1_TI_FSGS_120


title: B1_TI_FSGS_77


title: B1_TI_Other_56


title: B1_TI_MN_155


title: B1_TI_Other_168


title: B1_TI_FSGS_151


title: B1_TI_FSGS_82


title: B1_TI_FSGS_75


title: B1_TI_Other_211


title: B1_TI_Other_282


title: B1_TI_FSGS_48


title: B1_TI_MCD_9


title: B1_TI_MCD_271


title: B1_TI_MN_111


title: B1_TI_FSGS_49


title: B1_TI_FSGS_83


title: B1_TI_Other_296


title: B1_TI_MN_102


title: B1_TI_MN_133


title: 24-3 24h

status: Public on Dec 17 2019

data_processing:
Library strategy: RNA primer extension
Reads were trimmed using cutadapt(1) v2.4 with parameters --trimmed-only -e 0.25 --pair-filter both -n 2 -j 2 -a CTGTAGGCACCATCAATCTGTCTCTTATACACATCTCCGAGCCC -G ATTGATGGTGCCTACAG -A CTGTCTCTTATACACATCTGACGCTGCCGACGA.
The sequences without barcodes were filtered out with cutadapt -g CTACAGGGCACTCCACAC --action none -discard-untrimmed -e 0.05 --pair-filter both -n 1 -j 2.
Next, paired reads were combined into transFrags using FLASH(2) v1.2.11 with parameters -t 1 -m 4 -M 48 -x 0.3.
Tranfrags were filtered for quality using fastq_quality_filter from FASTX Toolkit(3) v0.0.13. With -Q33 -q 30 -p 100 to ensure only high quality reads were kept.
Then, bowtie2(4) was used to align the transFrags to the template sequence (containing both constant regions) using parameters --end-to-end -L 5 --reorder. Resulting sam files were converted to sorted indexed bam files using samtools(5) v1.9.
Afterward, breseq(6) bamtoaln (v 0.27.0) was used to produce a gapped alignment of the reads to the template sequence with format txt and -n 2000000 (to ensure all reads were aligned).
Finally, a custom java script (Supplemental File X) was used to calculate the number of matches, mismatches, deletions, and insertions as a function of template position and read length class. The script was compiled after extracting the java files using javac v1.7 (Oracle Inc.), and run with java using the output tables from breseq bamtoaln and a template length of 83.
Resulting tables were manually processed to produce position-specific and length-specific plots and analyses.
Genome_build: Synthetic construct
Supplementary_files_format_and_content: Excel Spreadsheet with statistics and plots

organism: synthetic construct

source_name: synthetic construct

extract_protocol:
Hammerhead ribozyme RNA was synthesized from a corresponding template RNA, a biotinylated RNA primer and the 24-3 or 38-6 RNA polymerase ribozymes at concentrations of 100 nM, 80 nM, and 100 nM, respectively, in a reaction mixture containing 4 mM each NTP, 200 mM MgCl2, 25 mM Tris-HCl (pH 8.3), and 0.05% Tween-20, which was incubated at 17 °C for 24 h for 24-3 and 1 h for 38-6. Extended RNA primers were captured on MyOne Streptavidin C1 dynabeads, washed to remove RNA template and polymerase ribozyme, and recovered by heating in 95% formamide and 10 mM EDTA at 95 °C for 10 min, then ethanol precipitated.
The purified RNAs were ligated to the NEB Universal miRNA cloning linker using K227Q T4 RNA ligase 2 according to the manufacturer protocols, reverse transcribed using Superscript IV (ThermoFisher), and the cDNA poly(C)-tailed using Terminal Transferase and a standard protocol (New England Biolabs). All enzymes were heat inactivated at 80 °C for 20 min, prior to library construction from cDNA by nested PCR using the Q5 Hot-Start High Fidelity DNA Polymerase (New England Biolabs), first using primers complementary to the constant flanking regions of the cDNA to append Illumina adapter sequences, then using Illumina Nextera primers to add index sequences (503 for both, 701 and 702 for 24-3 and 38-6 samples, respectively). 150-250nt PCR products were isolated by agarose gel and purified by the PureLink Gel Purification Kit (ThermoFisher) prior to sequencing.
Library was composed of two constant regions flanking the variable length and sequence products from the RNA polymerization reactions: 5'-CTACAGGGCACTCCACAC - X - CTGTAGGCACCATCAAT-3', where X is variable, but would be 5' - GACGTACTGATGAGGCCGAAAGGCCGAAAAGCGTTTTTTGTCATTGTC - 3' if the RNA template was copied accurately and completely. Adapter and index sequences were appended to the 5'- and 3'- ends as described in the library construction protocol.

tag: sample type

value: RNA polymerase ribozyme products


title: SAMP8_oldJ147_rep5

status: Public on Nov 26 2019

data_processing:
FastQC v0.11.5 with default parameter was used for quality test.
Reads were mapped to mm10/rn6 reference genome by STAR v2.5.1 with default parameters. Only uniquely mapped reads were considered for downstream analysis.
RNA-Seq gene expression was quantified by HOMER analyzeRepeats command, summing reads mapped across all gene exons of RefSeq genes.
RNA-Seq differential expression was carried out using edgeR v3.16.1 on the raw counts of replicates. FDR < 0.05 and logFC +/- 1.2 was used as cutoff to identify the DE genes.
Genome_build: mm10; rn6
Supplementary_files_format_and_content: tab delimited text file for RNA-Seq FPKM values.

growth_protocol: All experiments with the SAMP8 animals were performed in accordance with the US Public Health Service Guide for Care and Use of Laboratory Animals and protocols approved by the IACUC at the Salk Institute. Primary cortical neurons were prepared from day seventeen rat embryos and grown in culture as described in Soucek, T. Neuron. 2003 Jul 3;39(1):43-56.

extract_protocol:
RNA from both primary neurons and adult brain hippocampus was isolated using the RNeasy Plus Universal mini kit (Qiagen).
RNA-seq libraries were performed using stranded mRNA kit from Illumina and sequenced in an Illumina HiSeq 2500 device.

treatment_protocol: Mice were fed control diet and diet containing CAD031, CMS 121 and J147 for four months. Primary neurons were treated with 1μM of each compound for 24h.

value: SAMP8 mice brain hippocampal tissue

value: 13 months


title: B1_TI_FSGS_81


title: SAMP8_oldJ147_rep2


title: SAMP8_oldJ147_rep3


title: SAMP8_oldJ147_rep4


title: SAMP8_old121_rep5


title: 38-6 1h


title: SAMP8_oldJ147_rep6


title: SAMP8_old121_rep6


title: SAMP8_oldJ147_rep1


title: B1_TI_Other_210


title: B1_TI_MN_94


title: SAMP8_old121_rep4


title: SAMP8_old121_rep2


title: SAMP8_old121_rep3


title: SAMP8_old_rep3

value: control


title: SAMP8_old_rep6


title: SAMP8_old_rep5


title: SAMP8_old121_rep1


title: SAMP8_old_rep4


title: SAMP8_old_rep2


title: SAMP8_young_rep5

value: 9 months


title: SAMP8_old_rep1


title: SAMP8_young_rep4


title: SAMP8_young_rep1


title: SAMP8_young_rep3


title: SAMP8_young_rep2


title: PrimaryNeuron_treatmentJ147_rep1

value: rat primary neuron

value: embryo


title: PrimaryNeuron_treatment121_rep1


title: PrimaryNeuron_treatment121_rep3


title: PrimaryNeuron_control_rep2


title: PrimaryNeuron_treatment121_rep2


title: PrimaryNeuron_control_rep1


title: N2_PA14_4

status: Public on Oct 15 2019

city: Spokane

first: Yiyong

last: Liu

state: WA

address: 412 E Spokane Falls Blvd

institute: Washington State University

data_processing:
HiSeq Control Software (HCS v2.2.68) was used for base-calling.
bcl2fastq2 Conversion Software v2.17.1 was used to convert base-calling files to fastq files and to trim adaptors.
Bowtie2 v2.3.4 was used for alignment
htseq-count from HTSeq v0.10.0 was used to quantify genes and transcripts.
DESeq2 v1.22.1 was used for differential gene expression analysis.
Genome_build: UCSC ce10
Supplementary_files_format_and_content: comma-delimited text files including read counts in genes and differential gene expression

organism: Caenorhabditis elegans

source_name: wild-type N2, 24-hrs exposure to P. aeruginosa

growth_protocol: C. elegans was cultured under standard conditions and fed E. coli strain OP50.

extract_protocol:
Total RNA was extracted using QIAzol lysis reagent (QIAGEN) and purified with Rneasy Plus Universal Kit (QIAGEN).
Library was prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: Synchronized L1 larvae were grown on E. coli OP50 at 20⁰C until they reached young adult stage.  The worms were transferred to NGM plates seeded with P. aeruginosa PA14 for 24 hrs at 25⁰C.  The worms were then collected and washed with M9 buffer.  Total RNA was extracted.

value: wild-type N2

value: 1-day old young adult

tag: infection

value: 24-hrs exposure to P. aeruginosa

value: whole animal


title: N2_PA14_3


title: N2_PA14_5


title: N2_PA14_1


title: N2_PA14_2


title: N2_OP50_5

source_name: wild-type N2, uninfected

value: uninfected


title: empty_vector_control_rep3

status: Public on Aug 01 2019

city: Poznan

first: Jadwiga

last: Jaruzelska

address: Strzeszynska 32

country: Poland

institute: Institute of Human Genetics, Polish Academy of Sciences

data_processing:
The pair-end sequence reads obtained from HiSeq4000 platform were trimmed and quality filtered using TRIMMOMATIC V0.36.3 with the following parameters: ILLUMINACLIP:TruSeq2:PE MINLEN:50, SLIDINGWINDOW:5:20
Sequence reads that passed quality filters were mapped to the human reference genome hg38 using Bowtie 2 v2.3.4.1 with default parameters
Mapped reads were counted using featureCounts v1.6.0.3 with default parameters
Differential Gene Expression analysis was performed with DESeq2 v2.11.40.1
Genome_build: hg38
Supplementary_files_format_and_content: Tabular text file with differentially expressed genes after NANOS1 overexpression in comparison to cells with empty pCMV6-Entry vector

source_name: TCam-2 cells

growth_protocol: TCam-2 cells were grown in 37oC and 5% CO2 in Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% FBS (HyClone) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
RNA was extracted using RNeasy Plus Micro Kit (Qiagen) according to manufacturer protocol
The cDNA libraries were prepared using Illumina Truseq RNA Sample Prep V2 with standard protocol

treatment_protocol: TCam-2 cells were transfected with pCMV6-Entry plasmid containing NANOS1 or NANOS3  ORF or empty plasmid, using NEON transfection/electroporation system (Thermo Fisher Scientific). Transfections were performed in Buffer R using 10µl NEON tips. Subsequently after transfection cells were cultured in antibiotic-free RPMI 1640 (Gibco) supplemented with 10% FBS (HyClone), at 37 oC and 5 % CO2, for 24 hours.

tag: passages

tag: genotype/variation

value: empty vector

value: TCam-2 cells


title: N2_OP50_4


title: empty_vector_control_rep2


title: N2_OP50_1


title: PrimaryNeuron_treatmentJ147_rep3


title: NANOS1_overexpression_rep1


title: N2_OP50_2


title: NANOS1_overexpression_rep2


title: empty_vector_control_rep1


title: NANOS1_overexpression_rep3


title: PrimaryNeuron_control_rep3


title: PrimaryNeuron_treatmentJ147_rep2


title: N2_OP50_3


title: B2_Glom_Other_249

status: Public on Jun 25 2019

data_processing: The data were analyzed using RMA method and Human Entrez Gene custom CDF annotation version 19 (Brainarray). Each of the hybridizations was normalized seperately, the expression matrix contains the batch corrected data using Combat.

tag: diagnosis

value: Glomerular Disease (Other)-IgAN

value: Glomeruli from kidney biopsy


title: B2_Glom_Other_281


title: U2OS_siCtl_B_total

status: Public on Jun 12 2019

data_processing:
Sequenced reads were quality-tested using FASTQC.
Excess 3´ adaptor sequences were trimmed using the FASTX-toolkit
Reads were aligned to the hg19 human genome using the STAR aligner version STAR v2.5.2b. Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read). The genome index was constructed using the gene annotation supplied with the hg19 Illumina iGenomes collection and sjdbOverhang value of 100.
Metagene analysis to assess overall Ribo-Seq resolution was performed using RibORF.
HTSeq-count in intersection-strict mode was used to calculate total RNA read counts for hg19 refGene annotations
RPF read counts for the same annotations were calculated using the custom python script in Xiao et al 2016
Xtail calulation of the log2 fold-changes in translation efficiency (TE) between siCDK12 and siControl treated cells from the read count tables
DESeq2 was also run in parallel with Xtail to calculate differential mRNA expression for hg19 refGene annotations.
Genome_build: hg19

source_name: U2OS cells

growth_protocol: DMEM supplemeted with 10% (v/v) Fetal Bovine Serum, Glutamine, 5% CO2

extract_protocol:
100 µg/mL cycloheximide treatment
Ribo-Zero Mammalian Kit (Illumina)
single-end RIP-Seq

treatment_protocol: siRNA transfection for 48 hr

tag: knockdown

tag: library

value: total RNA control

tag: replicate

value: B


title: U2OS_siCtl_B_RPF

value: ribosome footprinting


title: B2_Glom_Other_240


title: B2_Glom_Other_425


title: B1_Glom_Other_294


title: U2OS_siCtl_A_RPF

value: A


title: U2OS_siCDK12_A_total


title: B1_Glom_Other_215


title: B1_Glom_Other_180


title: B1_Glom_Other_17


title: B1_Glom_Other_210


title: B1_Glom_Other_452


title: B2_Glom_Other_290


title: B1_Glom_Other_185


title: B1_Glom_Other_293


title: B1_Glom_Other_189


title: B1_Glom_Other_16


title: B1_Glom_Other_209


title: B1_Glom_Other_245


title: B1_Glom_Other_1030


title: B1_Glom_Other_719


title: U2OS_siCDK12_A_RPF


title: U2OS_siCDK12_B_total


title: U2OS_siCtl_A_total

value: control


title: U2OS_siCDK12_B_RPF


title: B2_Glom_Other_276


title: B1_Glom_Other_244


title: B1_Glom_Other_262


title: RNA-Seq for eIF4G-IP RNA from U2OS treated with control siRNA+Rapamycin _150520_r2

description: FPKM RIP-Seq_eIF4G_IP.xlsx

data_processing:
Sequenced reads were quality-tested using FASTQC.
Reads were aligned to the hg19 human genome using the STAR aligner version 2.4.0k. Mapping was carried out using default parameters (up to 10 mismatches per read, and up to 9 multi-mapping locations per read). The genome index was constructed using the gene annotation supplied with the hg19 Illumina iGenomes collection and sjdbOverhang value of 100.
Raw gene expression was quantified across all gene exons (RNA-Seq) or across gene bodies (RIP-Seq), using the top-expressed isoform as proxy for gene expression and fragments per kilobase per million mapped reads (FPKM) values were calculated.
We then added a pseudocount of 1 and averaged the log2-transformed FPKM values to obtain average log-transformed expression values for Control, siCDK12, and Rapamycin treated conditions in both the RIP and Total RNA contexts.
We defined the relative change with siCDK12 and Rapamycin by subtracting the average log2 transformed values for those conditions from the control condition for the total RNA samples, and the relative RIP signal by subtracting the average log2-transformed RIP value for the corresponding average log2-transformed total RNA value for each gene.
We then filtered for genes for which the RIP signal was at least 0.5 lower in the siCDK12 vs control (CDK12-dependent), or for genes for which the RIP signal was at least 0.5 lower with Rapamycin treatment vs control (mTORc-dependent), or for genes for which both was true (CDK12- and mTORc-dependent), while simultaneously imposing that relative total RNA log2fold changes remain below 0.5 (not differentially expressed). This resulted in a list of 137 genes whose pulldown was sensitive to CDK12 depletion, 1992 genes whose pulldown was sensitive to mTORc inhibition and 181 genes whose pulldown was sensitive to both mTORc inhibition and CDK12 depletion, while maintaining approximately similar levels of overall abundance.
Genome_build: hg19
Supplementary_files_format_and_content: Excel table containing the FPKM expression values for all samples and the processing step results.

extract_protocol:
Trizol extraction
Ribo-Zero Mammalian Kit (Illumina)
single-end RIP-Seq

treatment_protocol: Rapamycin 50 ng/ml for 24 hr, siRNA transfection for 48 hr

tag: cell line

value: U2OS cells